Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A08
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: 119882356
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2655529 characters in sequence are not A, C, G, or T
File 10 of 362
Found at i:3358905 original size:22 final size:22
Alignment explanation
Indices: 3358847--3358905 Score: 82
Period size: 22 Copynumber: 2.7 Consensus size: 22
3358837 CAGTCAGACA
*
3358847 TCGGTGTCGGGACACCTAAGCT
1 TCGGTGTCGCGACACCTAAGCT
*
3358869 TCGGTGTCGTGACACCTAAGCT
1 TCGGTGTCGCGACACCTAAGCT
* *
3358891 TTGGTGTCGCAACAC
1 TCGGTGTCGCGACAC
3358906 TCTCGTCAGT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.19, C:0.27, G:0.29, T:0.25
Consensus pattern (22 bp):
TCGGTGTCGCGACACCTAAGCT
Found at i:3363173 original size:17 final size:17
Alignment explanation
Indices: 3363151--3363184 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3363141 ATCTTGGAAA
* *
3363151 CTAAAATTACCTTAAAC
1 CTAAAACTAACTTAAAC
3363168 CTAAAACTAACTTAAAC
1 CTAAAACTAACTTAAAC
3363185 AATTTAAAAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (17 bp):
CTAAAACTAACTTAAAC
Found at i:3372163 original size:26 final size:24
Alignment explanation
Indices: 3372120--3372177 Score: 73
Period size: 26 Copynumber: 2.4 Consensus size: 24
3372110 TTATTTCATT
* *
3372120 AAATAAA-AAATTTTAAAATATAA
1 AAATAAATACATTTAAAAATATAA
3372143 TAAATCAAATACATTTAAAAATATAA
1 -AAAT-AAATACATTTAAAAATATAA
3372169 AAATAAATA
1 AAATAAATA
3372178 TTAAAACAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 9 0.30
25 7 0.23
26 14 0.47
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.29
Consensus pattern (24 bp):
AAATAAATACATTTAAAAATATAA
Found at i:3372188 original size:23 final size:24
Alignment explanation
Indices: 3372120--3372198 Score: 65
Period size: 26 Copynumber: 3.3 Consensus size: 24
3372110 TTATTTCATT
* ** *
3372120 AAATAAAAAATTTTAAAATATAAT
1 AAATAAATAATTAAAAAATATAAC
*
3372144 AAATCAAATACATTTAAAAATATAA-
1 AAAT-AAATA-ATTAAAAAATATAAC
3372169 AAATAAAT-ATTAAAACAATA-AAC
1 AAATAAATAATTAAAA-AATATAAC
3372192 AAATAAA
1 AAATAAA
3372199 AAATGAGACT
Statistics
Matches: 48, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
22 8 0.17
23 11 0.23
24 8 0.17
25 8 0.17
26 13 0.27
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (24 bp):
AAATAAATAATTAAAAAATATAAC
Found at i:3375613 original size:16 final size:16
Alignment explanation
Indices: 3375533--3375614 Score: 53
Period size: 16 Copynumber: 5.1 Consensus size: 16
3375523 TTTAATGTTT
3375533 ATATATATAAATTT-AA
1 ATAT-TATAAATTTAAA
* *
3375549 ATTTTATGAATTATAAA
1 ATATTATAAATT-TAAA
* *
3375566 TTA-TATAATATATAAA
1 ATATTATAA-ATTTAAA
* *
3375582 A-ATAATATAATATAAA
1 ATATTATA-AATTTAAA
3375598 ATATTATAAATTTAAA
1 ATATTATAAATTTAAA
3375614 A
1 A
3375615 AAAATGAAAT
Statistics
Matches: 50, Mismatches: 10, Indels: 12
0.69 0.14 0.17
Matches are distributed among these distances:
15 8 0.16
16 31 0.62
17 11 0.22
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.41
Consensus pattern (16 bp):
ATATTATAAATTTAAA
Found at i:3376710 original size:60 final size:59
Alignment explanation
Indices: 3376609--3376761 Score: 191
Period size: 60 Copynumber: 2.6 Consensus size: 59
3376599 TACACTACTC
* * * * *
3376609 GTCACCCAACTATTAGTAAATTTCTCTTTTAGTCATATAACTGTGAAAAGTTACAAAAT
1 GTCACCTAACTATTAGTAAATTTCTTTTTTGGTCACATAACTATGAAAAGTTACAAAAT
* * * * *
3376668 AGTCACCTAATTATTTGTAAATTTGTTTTTTGGTCACCTAACTATGAAAAGTTATAAAAT
1 -GTCACCTAACTATTAGTAAATTTCTTTTTTGGTCACATAACTATGAAAAGTTACAAAAT
3376728 GATCACCTAACTATTAGTAAA-TTCTTTTTTGGTC
1 G-TCACCTAACTATTAGTAAATTTCTTTTTTGGTC
3376762 GCCCAACTAT
Statistics
Matches: 79, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
59 13 0.16
60 66 0.84
ACGTcount: A:0.34, C:0.15, G:0.11, T:0.40
Consensus pattern (59 bp):
GTCACCTAACTATTAGTAAATTTCTTTTTTGGTCACATAACTATGAAAAGTTACAAAAT
Found at i:3379289 original size:29 final size:29
Alignment explanation
Indices: 3379233--3379290 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
3379223 AAAATGTAAA
* **
3379233 AAAAAAATTACGTGAGTAGATCGTTTTTT
1 AAAAAAATTACGAGAGTAGATCAATTTTT
* *
3379262 AAAAAAATTATGAGATTAGATCAATTTTT
1 AAAAAAATTACGAGAGTAGATCAATTTTT
3379291 GAATGGAAGT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.43, C:0.05, G:0.14, T:0.38
Consensus pattern (29 bp):
AAAAAAATTACGAGAGTAGATCAATTTTT
Found at i:3379623 original size:43 final size:43
Alignment explanation
Indices: 3379562--3379646 Score: 170
Period size: 43 Copynumber: 2.0 Consensus size: 43
3379552 GTCCAGTAAG
3379562 TTGTGAGTTTAGTCTTTGTTCTCCAATTTGATTATTTTTAATT
1 TTGTGAGTTTAGTCTTTGTTCTCCAATTTGATTATTTTTAATT
3379605 TTGTGAGTTTAGTCTTTGTTCTCCAATTTGATTATTTTTAAT
1 TTGTGAGTTTAGTCTTTGTTCTCCAATTTGATTATTTTTAAT
3379647 CATACTGCTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.19, C:0.09, G:0.14, T:0.58
Consensus pattern (43 bp):
TTGTGAGTTTAGTCTTTGTTCTCCAATTTGATTATTTTTAATT
Found at i:3382631 original size:30 final size:31
Alignment explanation
Indices: 3382572--3382634 Score: 78
Period size: 30 Copynumber: 2.1 Consensus size: 31
3382562 GTTAATAATT
*
3382572 TACAAGAATTGTATCAAATCAAATTTTCATG
1 TACAAGAATTGTATCAAATCAAATGTTCATG
3382603 TACAA-AATTGTA-CAAAATTCAAA-GTTCATG
1 TACAAGAATTGTATC-AAA-TCAAATGTTCATG
3382633 TA
1 TA
3382635 TACGAATGCA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
29 1 0.03
30 18 0.62
31 10 0.34
ACGTcount: A:0.44, C:0.13, G:0.10, T:0.33
Consensus pattern (31 bp):
TACAAGAATTGTATCAAATCAAATGTTCATG
Found at i:3383874 original size:24 final size:24
Alignment explanation
Indices: 3383833--3383880 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
3383823 AAAATTAGAA
*
3383833 ATATTTTTAATACTAAATACATAAT
1 ATATTTTTAATAC-AAATAAATAAT
3383858 ATATTTTTAATGA-AAATAAATAA
1 ATATTTTTAAT-ACAAATAAATAA
3383881 ATTTAACCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 9 0.43
25 11 0.52
26 1 0.05
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.42
Consensus pattern (24 bp):
ATATTTTTAATACAAATAAATAAT
Found at i:3388038 original size:13 final size:13
Alignment explanation
Indices: 3388020--3388047 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
3388010 AATATGAATC
3388020 TTATATCAAACCA
1 TTATATCAAACCA
3388033 TTATATCAAACCA
1 TTATATCAAACCA
3388046 TT
1 TT
3388048 GAACCAGATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.43, C:0.21, G:0.00, T:0.36
Consensus pattern (13 bp):
TTATATCAAACCA
Found at i:3389215 original size:9 final size:9
Alignment explanation
Indices: 3389201--3389225 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
3389191 TAAGTTTAAC
3389201 TGTTAATAT
1 TGTTAATAT
3389210 TGTTAATAT
1 TGTTAATAT
3389219 TGTTAAT
1 TGTTAAT
3389226 GTGAATATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.12, T:0.56
Consensus pattern (9 bp):
TGTTAATAT
Found at i:3390798 original size:42 final size:42
Alignment explanation
Indices: 3390711--3390799 Score: 106
Period size: 42 Copynumber: 2.1 Consensus size: 42
3390701 GCCCTTAGCT
* * * *
3390711 CGTGTGCAACACTGACTTTAAAACACGGCCATGACGCATGCC
1 CGTGTACAACACTAACTTTAAAACACGGCCATGACACACGCC
* * * *
3390753 CGTGTACAATACTAACTTTAATACACGGCCATGGCACACGTC
1 CGTGTACAACACTAACTTTAAAACACGGCCATGACACACGCC
3390795 CGTGT
1 CGTGT
3390800 GGCCTGCCCG
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.28, C:0.29, G:0.20, T:0.22
Consensus pattern (42 bp):
CGTGTACAACACTAACTTTAAAACACGGCCATGACACACGCC
Found at i:3393000 original size:26 final size:26
Alignment explanation
Indices: 3392971--3393023 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
3392961 ATTATGCTAG
3392971 TACACTAAAATATAAATAAAATAATT
1 TACACTAAAATATAAATAAAATAATT
3392997 TACACTAAAATATAAATAAAATAATT
1 TACACTAAAATATAAATAAAATAATT
3393023 T
1 T
3393024 TCTTAGCCTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (26 bp):
TACACTAAAATATAAATAAAATAATT
Found at i:3393955 original size:24 final size:24
Alignment explanation
Indices: 3393926--3393973 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
3393916 AAAAACATAG
3393926 TGTTTGAAATCTCCTATAGTCACA
1 TGTTTGAAATCTCCTATAGTCACA
3393950 TGTTTGAAATCTCCTATAGTCACA
1 TGTTTGAAATCTCCTATAGTCACA
3393974 GGTCATTGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.38
Consensus pattern (24 bp):
TGTTTGAAATCTCCTATAGTCACA
Found at i:3398627 original size:16 final size:16
Alignment explanation
Indices: 3398606--3398639 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
3398596 GTATGCTTCC
*
3398606 CATAGCTCAGCTTCAA
1 CATAGCTAAGCTTCAA
3398622 CATAGCTAAGCTTCAA
1 CATAGCTAAGCTTCAA
3398638 CA
1 CA
3398640 GTTGAACAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.35, C:0.29, G:0.12, T:0.24
Consensus pattern (16 bp):
CATAGCTAAGCTTCAA
Found at i:3410850 original size:43 final size:44
Alignment explanation
Indices: 3410757--3410844 Score: 158
Period size: 44 Copynumber: 2.0 Consensus size: 44
3410747 GATATTCCTG
*
3410757 AAATTTTTAAAAAGCATTGTAAGTAAATATTTTATATGACTCCA
1 AAATTTTAAAAAAGCATTGTAAGTAAATATTTTATATGACTCCA
*
3410801 AAATTTTAAAAAAGCATTGTAAGTAAATCTTTTATATGACTCCA
1 AAATTTTAAAAAAGCATTGTAAGTAAATATTTTATATGACTCCA
3410845 TATTTTCATT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.43, C:0.10, G:0.09, T:0.38
Consensus pattern (44 bp):
AAATTTTAAAAAAGCATTGTAAGTAAATATTTTATATGACTCCA
Found at i:3411098 original size:22 final size:23
Alignment explanation
Indices: 3411073--3411118 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
3411063 CAACCAAACC
3411073 AATTCA-ACATATTT-TCAAGATA
1 AATTCATACATATTTAT-AAGATA
*
3411095 AATTCATGCATATTTATAAGATA
1 AATTCATACATATTTATAAGATA
3411118 A
1 A
3411119 CGTCATCATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 14 0.67
24 1 0.05
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.37
Consensus pattern (23 bp):
AATTCATACATATTTATAAGATA
Found at i:3411124 original size:23 final size:22
Alignment explanation
Indices: 3411080--3411129 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 22
3411070 ACCAATTCAA
*
3411080 CATATTTTCAAGATAAATTCAT
1 CATATTTTCAAGATAAAGTCAT
*
3411102 GCATATTTAT-AAGATAACGTCAT
1 -CATATTT-TCAAGATAAAGTCAT
3411125 CATAT
1 CATAT
3411130 ACTCAAAATC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 5 0.21
23 18 0.75
24 1 0.04
ACGTcount: A:0.40, C:0.14, G:0.08, T:0.38
Consensus pattern (22 bp):
CATATTTTCAAGATAAAGTCAT
Found at i:3412970 original size:22 final size:23
Alignment explanation
Indices: 3412945--3412990 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
3412935 CAACCAAACC
3412945 AATTCA-ACATATTT-TCAAGATA
1 AATTCATACATATTTAT-AAGATA
*
3412967 AATTCATGCATATTTATAAGATA
1 AATTCATACATATTTATAAGATA
3412990 A
1 A
3412991 CGTCATCATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 14 0.67
24 1 0.05
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.37
Consensus pattern (23 bp):
AATTCATACATATTTATAAGATA
Found at i:3412996 original size:23 final size:22
Alignment explanation
Indices: 3412952--3413001 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 22
3412942 ACCAATTCAA
*
3412952 CATATTTTCAAGATAAATTCAT
1 CATATTTTCAAGATAAAGTCAT
*
3412974 GCATATTTAT-AAGATAACGTCAT
1 -CATATTT-TCAAGATAAAGTCAT
3412997 CATAT
1 CATAT
3413002 ACTCAAAATC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 5 0.21
23 18 0.75
24 1 0.04
ACGTcount: A:0.40, C:0.14, G:0.08, T:0.38
Consensus pattern (22 bp):
CATATTTTCAAGATAAAGTCAT
Found at i:3424291 original size:19 final size:20
Alignment explanation
Indices: 3424267--3424311 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
3424257 AAAAATATAA
*
3424267 ATTTTAAAATTTTATAAA-T
1 ATTTTAAAATTTTAAAAAGT
*
3424286 ATTTT-ATATTTTAAAAAGT
1 ATTTTAAAATTTTAAAAAGT
3424305 ATTTTAA
1 ATTTTAA
3424312 TTTTTTGTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 10 0.45
19 11 0.50
20 1 0.05
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (20 bp):
ATTTTAAAATTTTAAAAAGT
Found at i:3424316 original size:19 final size:18
Alignment explanation
Indices: 3424275--3424315 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
3424265 AAATTTTAAA
*
3424275 ATTTTATAAATATTTTAT
1 ATTTTAAAAATATTTTAT
3424293 ATTTTAAAAAGTATTTTA-
1 ATTTTAAAAA-TATTTTAT
3424311 ATTTT
1 ATTTT
3424316 TTGTTGAGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 14 0.67
19 7 0.33
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (18 bp):
ATTTTAAAAATATTTTAT
Found at i:3425962 original size:16 final size:16
Alignment explanation
Indices: 3425943--3425991 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
3425933 TTAATTTTTT
3425943 ATATAAAAAATTAAAA
1 ATATAAAAAATTAAAA
* * *
3425959 ATATAATACATCAAAA
1 ATATAAAAAATTAAAA
3425975 ATACTAAAAACATTAAA
1 ATA-TAAAAA-ATTAAA
3425992 TTTAATACTT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
16 16 0.64
17 4 0.16
18 5 0.20
ACGTcount: A:0.67, C:0.08, G:0.00, T:0.24
Consensus pattern (16 bp):
ATATAAAAAATTAAAA
Found at i:3429781 original size:11 final size:11
Alignment explanation
Indices: 3429742--3429782 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
3429732 CTGCTCTCTC
3429742 TTTTTCTTTTAT
1 TTTTTCTTTT-T
3429754 TTTTTCTTTTT
1 TTTTTCTTTTT
**
3429765 AATTTCTTTTT
1 TTTTTCTTTTT
3429776 TTTTTCT
1 TTTTTCT
3429783 CGGGATATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
11 15 0.60
12 10 0.40
ACGTcount: A:0.07, C:0.10, G:0.00, T:0.83
Consensus pattern (11 bp):
TTTTTCTTTTT
Found at i:3432315 original size:27 final size:27
Alignment explanation
Indices: 3432285--3432337 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
3432275 AAAATGTCAA
* *
3432285 AAATGACTAAATTGAAGGGAATTATCT
1 AAATGAATAAATTGAAGGAAATTATCT
* *
3432312 AAATTAATAAATTGAATGAAATTATC
1 AAATGAATAAATTGAAGGAAATTATC
3432338 AATTTAAGAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.49, C:0.06, G:0.13, T:0.32
Consensus pattern (27 bp):
AAATGAATAAATTGAAGGAAATTATCT
Found at i:3433422 original size:31 final size:31
Alignment explanation
Indices: 3433381--3433464 Score: 134
Period size: 31 Copynumber: 2.7 Consensus size: 31
3433371 AATAACCCAC
*
3433381 TAAA-AAAAACTTTTGAATAGTTGAGTAATT
1 TAAATAAAAACTTTTGAATAGTTGAATAATT
*
3433411 TAAATAAAAACTTTTGAATAGTTTAATAATT
1 TAAATAAAAACTTTTGAATAGTTGAATAATT
*
3433442 TAAATAAAAACTTTCGAATAGTT
1 TAAATAAAAACTTTTGAATAGTT
3433465 CTTTAATTAT
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
30 4 0.08
31 46 0.92
ACGTcount: A:0.48, C:0.05, G:0.10, T:0.38
Consensus pattern (31 bp):
TAAATAAAAACTTTTGAATAGTTGAATAATT
Found at i:3434289 original size:17 final size:17
Alignment explanation
Indices: 3434269--3434307 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
3434259 ATTAAAATAT
3434269 TTAAAATATATATTATA
1 TTAAAATATATATTATA
* *
3434286 TTAATATTTATATTATA
1 TTAAAATATATATTATA
3434303 TTAAA
1 TTAAA
3434308 TAAAAATAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TTAAAATATATATTATA
Found at i:3434299 original size:38 final size:36
Alignment explanation
Indices: 3434255--3434329 Score: 96
Period size: 38 Copynumber: 2.0 Consensus size: 36
3434245 ATTTAAAAAA
**
3434255 TTATATTAAAATATTTAAAATATATATTATATTAATAT
1 TTATATTAAAATAAATAAAA-ATA-ATTATATTAATAT
* *
3434293 TTATATTATATTAAATAAAAATAATTATATTAATAT
1 TTATATTAAAATAAATAAAAATAATTATATTAATAT
3434329 T
1 T
3434330 AAAAATATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 14 0.42
37 3 0.09
38 16 0.48
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (36 bp):
TTATATTAAAATAAATAAAAATAATTATATTAATAT
Found at i:3434334 original size:21 final size:21
Alignment explanation
Indices: 3434234--3434336 Score: 76
Period size: 21 Copynumber: 5.0 Consensus size: 21
3434224 AGTCATAATT
* *
3434234 TTATATTACTAATTTAAAA-AA
1 TTATATTAAT-ATTAAAAATAA
3434255 TTATATTAAAATATTTAAAATATATA
1 TTATATT--AATA-TTAAAA-ATA-A
*
3434281 TTATATTAATATT---TAT-A
1 TTATATTAATATTAAAAATAA
3434298 TTATATTAA-A-TAAAAATAA
1 TTATATTAATATTAAAAATAA
3434317 TTATATTAATATTAAAAATA
1 TTATATTAATATTAAAAATA
3434337 TATATATCCT
Statistics
Matches: 66, Mismatches: 4, Indels: 24
0.70 0.04 0.26
Matches are distributed among these distances:
15 1 0.02
16 1 0.02
17 10 0.15
18 2 0.03
19 12 0.18
20 1 0.02
21 15 0.23
22 1 0.02
23 9 0.14
24 5 0.08
25 1 0.02
26 8 0.12
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (21 bp):
TTATATTAATATTAAAAATAA
Found at i:3434875 original size:6 final size:6
Alignment explanation
Indices: 3434864--3434888 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
3434854 AATATCATAT
3434864 TTTAAA TTTAAA TTTAAA TTTAAA T
1 TTTAAA TTTAAA TTTAAA TTTAAA T
3434889 CTTTTCTTTA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TTTAAA
Found at i:3435132 original size:16 final size:16
Alignment explanation
Indices: 3435111--3435144 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
3435101 TTCATGCTAG
*
3435111 ATGTTTAAAGTGGAAA
1 ATGTTTAAAGTGAAAA
3435127 ATGTTTAAAGTGAAAA
1 ATGTTTAAAGTGAAAA
3435143 AT
1 AT
3435145 ATTTTATGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.21, T:0.32
Consensus pattern (16 bp):
ATGTTTAAAGTGAAAA
Found at i:3436575 original size:13 final size:13
Alignment explanation
Indices: 3436557--3436584 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
3436547 AATTTTTCAT
3436557 GATTTTGTTAATA
1 GATTTTGTTAATA
3436570 GATTTTGTTAATA
1 GATTTTGTTAATA
3436583 GA
1 GA
3436585 ATATATTTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.00, G:0.18, T:0.50
Consensus pattern (13 bp):
GATTTTGTTAATA
Found at i:3438080 original size:42 final size:42
Alignment explanation
Indices: 3438032--3438117 Score: 172
Period size: 42 Copynumber: 2.0 Consensus size: 42
3438022 TTAAATATTT
3438032 ATCCTTTCTCAAATACTACAATTTTAGGGTATTACAACTTAG
1 ATCCTTTCTCAAATACTACAATTTTAGGGTATTACAACTTAG
3438074 ATCCTTTCTCAAATACTACAATTTTAGGGTATTACAACTTAG
1 ATCCTTTCTCAAATACTACAATTTTAGGGTATTACAACTTAG
3438116 AT
1 AT
3438118 TTGAACATTC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.34, C:0.19, G:0.09, T:0.38
Consensus pattern (42 bp):
ATCCTTTCTCAAATACTACAATTTTAGGGTATTACAACTTAG
Found at i:3438245 original size:24 final size:26
Alignment explanation
Indices: 3438204--3438253 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 26
3438194 ATATACCTAT
3438204 ATATAAATTTTTAATAAA-TGAAAAAA
1 ATATAAA-TTTTAATAAATTGAAAAAA
*
3438230 ATATAAA-TTTATTAAATTGAAAAA
1 ATATAAATTTTAATAAATTGAAAAA
3438254 TGAAAATAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 8 0.36
25 7 0.32
26 7 0.32
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (26 bp):
ATATAAATTTTAATAAATTGAAAAAA
Found at i:3441274 original size:43 final size:44
Alignment explanation
Indices: 3441211--3441294 Score: 134
Period size: 43 Copynumber: 1.9 Consensus size: 44
3441201 ATCGAAATAT
*
3441211 GATATTCGGGCTTCGGGCCTAGCAGGCTATAATGCCAGTGAGAC
1 GATATTCGGGCTTCGAGCCTAGCAGGCTATAATGCCAGTGAGAC
* *
3441255 GATA-TCGGGCTTTGAGCCTAGCAGGCTATAATGCCGGTGA
1 GATATTCGGGCTTCGAGCCTAGCAGGCTATAATGCCAGTGA
3441295 AATGAAATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
43 33 0.89
44 4 0.11
ACGTcount: A:0.23, C:0.21, G:0.32, T:0.24
Consensus pattern (44 bp):
GATATTCGGGCTTCGAGCCTAGCAGGCTATAATGCCAGTGAGAC
Found at i:3441704 original size:78 final size:78
Alignment explanation
Indices: 3441575--3441791 Score: 357
Period size: 78 Copynumber: 2.8 Consensus size: 78
3441565 ATTTGATGTG
3441575 TATCCGGGCTTAAAGACCCGCAGGCTTCGTGCTGGTAATATATCCGGGTTAAATCCCGCAGGCTT
1 TATCCGGGCTTAAAGACCCGCAGGCTTCGTGCTGGTAATATATCCGGGTTAAATCCCGCAGGCTT
3441640 CGTGCTGGTAATA
66 CGTGCTGGTAATA
* * * *
3441653 TATCCGGGCTTAAAGGCCCGCAAGCTTTGTGCTGGTATTATATCCGGGTTAAATCCCGCAGGCTT
1 TATCCGGGCTTAAAGACCCGCAGGCTTCGTGCTGGTAATATATCCGGGTTAAATCCCGCAGGCTT
3441718 CGTGCTGGTAATA
66 CGTGCTGGTAATA
* * *
3441731 TATCCCGG-TTAAA-TCCCGCAGGCTTCGTGCTGGTAATATATCTGGGTTAAATCCCGCAGGC
1 TATCCGGGCTTAAAGACCCGCAGGCTTCGTGCTGGTAATATATCCGGGTTAAATCCCGCAGGC
3441792 CTAATACTGG
Statistics
Matches: 129, Mismatches: 10, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
76 43 0.33
77 5 0.04
78 81 0.63
ACGTcount: A:0.21, C:0.24, G:0.26, T:0.28
Consensus pattern (78 bp):
TATCCGGGCTTAAAGACCCGCAGGCTTCGTGCTGGTAATATATCCGGGTTAAATCCCGCAGGCTT
CGTGCTGGTAATA
Found at i:3441809 original size:38 final size:38
Alignment explanation
Indices: 3441575--3441791 Score: 335
Period size: 38 Copynumber: 5.6 Consensus size: 38
3441565 ATTTGATGTG
*
3441575 TATCCGGGCTTAAAGACCCGCAGGCTTCGTGCTGGTAATA
1 TATCCGGG-TTAAA-TCCCGCAGGCTTCGTGCTGGTAATA
3441615 TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAATA
1 TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAATA
* * * *
3441653 TATCCGGGCTTAAAGGCCCGCAAGCTTTGTGCTGGTATTA
1 TATCCGGG-TTAAA-TCCCGCAGGCTTCGTGCTGGTAATA
3441693 TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAATA
1 TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAATA
*
3441731 TATCCCGGTTAAATCCCGCAGGCTTCGTGCTGGTAATA
1 TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAATA
*
3441769 TATCTGGGTTAAATCCCGCAGGC
1 TATCCGGGTTAAATCCCGCAGGC
3441792 CTAATACTGG
Statistics
Matches: 163, Mismatches: 12, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
38 111 0.68
39 15 0.09
40 37 0.23
ACGTcount: A:0.21, C:0.24, G:0.26, T:0.28
Consensus pattern (38 bp):
TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAATA
Found at i:3441917 original size:43 final size:45
Alignment explanation
Indices: 3441814--3441937 Score: 141
Period size: 45 Copynumber: 2.8 Consensus size: 45
3441804 TTATATTCAG
* * * * *
3441814 GCCTTTGAGCCTAGCAAGCTATTATGTCGGTGAGAT-ACTATTCGG
1 GCCTTTGAGCCTAGTAGGCTATAATGCCGGTGA-ATGACTATTCGA
3441859 GCCTTTGAGCCTAGTAGGCTATAATGCCGGTGATATGA-TA-TCGA
1 GCCTTTGAGCCTAGTAGGCTATAATGCCGGTGA-ATGACTATTCGA
*
3441903 GCC-TTGAGCCTAGTAGGCGA-AATGCCGGTGAATGA
1 GCCTTTGAGCCTAGTAGGCTATAATGCCGGTGAATGA
3441938 ATAAAAGTCT
Statistics
Matches: 71, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
41 4 0.06
42 11 0.15
43 16 0.23
44 6 0.08
45 33 0.46
46 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.29, T:0.27
Consensus pattern (45 bp):
GCCTTTGAGCCTAGTAGGCTATAATGCCGGTGAATGACTATTCGA
Found at i:3446277 original size:31 final size:29
Alignment explanation
Indices: 3446242--3446299 Score: 71
Period size: 31 Copynumber: 1.9 Consensus size: 29
3446232 TAAATATAAG
* *
3446242 ATTATTAAAATGATAAAATTATATTTTTACT
1 ATTATAAAAAT-ATAAAATT-TAATTTTACT
*
3446273 ATTATAAAAATATATAATTTAATTTTA
1 ATTATAAAAATATAAAATTTAATTTTA
3446300 ATTTCTTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 7 0.29
30 7 0.29
31 10 0.42
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (29 bp):
ATTATAAAAATATAAAATTTAATTTTACT
Found at i:3473060 original size:19 final size:19
Alignment explanation
Indices: 3473034--3473080 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
3473024 ACCGGTCAAG
*
3473034 TTAAAAAATTATTAA-AAA
1 TTAAAAAATTAATAATAAA
*
3473052 TTCAAAAAAATAATAATAAA
1 TT-AAAAAATTAATAATAAA
3473072 TTAAAAAAT
1 TTAAAAAAT
3473081 CCAGTTCAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
18 2 0.08
19 17 0.71
20 5 0.21
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (19 bp):
TTAAAAAATTAATAATAAA
Found at i:3477750 original size:37 final size:36
Alignment explanation
Indices: 3477651--3477753 Score: 151
Period size: 32 Copynumber: 2.9 Consensus size: 36
3477641 AGAAAGAAAG
3477651 AATAACAATCCATTAGATTAAATTCATT-AAAAAAT
1 AATAACAATCCATTAGATTAAATTCATTAAAAAAAT
3477686 AAT---AATCCATTAGATTAAATTCATTAAAAAAAT
1 AATAACAATCCATTAGATTAAATTCATTAAAAAAAT
* *
3477719 AATAACAATCCATAAAGATTAAATTCGTTAAAAAA
1 AATAACAATCCAT-TAGATTAAATTCATTAAAAAA
3477754 TCGCAAAGAA
Statistics
Matches: 61, Mismatches: 2, Indels: 8
0.86 0.03 0.11
Matches are distributed among these distances:
32 22 0.36
33 10 0.16
35 3 0.05
36 7 0.11
37 19 0.31
ACGTcount: A:0.55, C:0.11, G:0.04, T:0.30
Consensus pattern (36 bp):
AATAACAATCCATTAGATTAAATTCATTAAAAAAAT
Found at i:3504396 original size:30 final size:29
Alignment explanation
Indices: 3504357--3504446 Score: 117
Period size: 30 Copynumber: 3.0 Consensus size: 29
3504347 ATAAGTTTGT
*
3504357 TTCTAATAATATTGCTTGTGATGAAAGAAA
1 TTCTGATAATATTGCTT-TGATGAAAGAAA
* * *
3504387 TTTTGATAATATTGCTTTTGGTGAACGAAA
1 TTCTGATAATATTGC-TTTGATGAAAGAAA
*
3504417 TTCTGATAATATTACTTTGATGAAAGAAA
1 TTCTGATAATATTGCTTTGATGAAAGAAA
3504446 T
1 T
3504447 GAGAAACAAA
Statistics
Matches: 51, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
29 13 0.25
30 36 0.71
31 2 0.04
ACGTcount: A:0.37, C:0.07, G:0.17, T:0.40
Consensus pattern (29 bp):
TTCTGATAATATTGCTTTGATGAAAGAAA
Found at i:3508083 original size:19 final size:17
Alignment explanation
Indices: 3508059--3508095 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
3508049 TAGTTAAATG
3508059 ATAAAATAATACAAAGAAA
1 ATAAAAT-ATA-AAAGAAA
3508078 ATAAAATATAAAAGAAA
1 ATAAAATATAAAAGAAA
3508095 A
1 A
3508096 ACAAAGAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 8 0.44
18 3 0.17
19 7 0.39
ACGTcount: A:0.76, C:0.03, G:0.05, T:0.16
Consensus pattern (17 bp):
ATAAAATATAAAAGAAA
Found at i:3508168 original size:9 final size:9
Alignment explanation
Indices: 3508145--3508178 Score: 61
Period size: 9 Copynumber: 3.9 Consensus size: 9
3508135 CAGGGGAAGA
3508145 AAAAGAAAG
1 AAAAGAAAG
3508154 -AAAGAAAG
1 AAAAGAAAG
3508162 AAAAGAAAG
1 AAAAGAAAG
3508171 AAAAGAAA
1 AAAAGAAA
3508179 AAGGAAAACT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 8 0.33
9 16 0.67
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (9 bp):
AAAAGAAAG
Found at i:3508168 original size:13 final size:13
Alignment explanation
Indices: 3508145--3508178 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
3508135 CAGGGGAAGA
3508145 AAAAGAAAGAAAG
1 AAAAGAAAGAAAG
3508158 -AAAGAAAAGAAAG
1 AAAAG-AAAGAAAG
3508171 AAAAGAAA
1 AAAAGAAA
3508179 AAGGAAAACT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
12 4 0.21
13 11 0.58
14 4 0.21
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (13 bp):
AAAAGAAAGAAAG
Found at i:3508812 original size:45 final size:45
Alignment explanation
Indices: 3508741--3508838 Score: 117
Period size: 45 Copynumber: 2.2 Consensus size: 45
3508731 CGACTACTGT
* * * * *
3508741 TACTGTTACCGTTATTGTTACCGATTC-GACAGTTTGTGTGTCGAA
1 TACTGTTACCGTTACTATTACAGATTCAG-CACTTTGTGTGTCAAA
* *
3508786 TACTGTTACCGTTACTATTATAGATTCAGCACTTTGTGTGTTAAA
1 TACTGTTACCGTTACTATTACAGATTCAGCACTTTGTGTGTCAAA
3508831 TACTGTTA
1 TACTGTTA
3508839 TAGTTACTGT
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
45 44 0.98
46 1 0.02
ACGTcount: A:0.23, C:0.16, G:0.18, T:0.42
Consensus pattern (45 bp):
TACTGTTACCGTTACTATTACAGATTCAGCACTTTGTGTGTCAAA
Found at i:3508854 original size:18 final size:18
Alignment explanation
Indices: 3508831--3508884 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
3508821 GTGTGTTAAA
3508831 TACTGTTATAGTTACTGT
1 TACTGTTATAGTTACTGT
** *
3508849 TACTGTTACCGTTTCTGAT
1 TACTGTTATAGTTACTG-T
*
3508868 TACTGTT-TAGGTACTGT
1 TACTGTTATAGTTACTGT
3508885 GTACCGTTAA
Statistics
Matches: 28, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
17 1 0.04
18 19 0.68
19 8 0.29
ACGTcount: A:0.19, C:0.15, G:0.19, T:0.48
Consensus pattern (18 bp):
TACTGTTATAGTTACTGT
Found at i:3510488 original size:93 final size:93
Alignment explanation
Indices: 3510375--3510639 Score: 494
Period size: 93 Copynumber: 2.8 Consensus size: 93
3510365 CGCCCATAAG
* * *
3510375 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
3510440 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
3510468 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
3510533 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
3510561 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
3510626 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
3510640 TCAACCATCC
Statistics
Matches: 167, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
93 167 1.00
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:3510636 original size:46 final size:46
Alignment explanation
Indices: 3510368--3510636 Score: 293
Period size: 46 Copynumber: 5.8 Consensus size: 46
3510358 TGTAACCCGC
* * *
3510368 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
3510414 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
3510464 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* * *
3510507 CCATAAGTGAACTCAGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
3510557 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
3510600 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
3510637 TGCTCAACCA
Statistics
Matches: 187, Mismatches: 18, Indels: 36
0.78 0.07 0.15
Matches are distributed among these distances:
42 4 0.02
43 8 0.04
44 4 0.02
45 4 0.02
46 91 0.49
47 57 0.30
48 4 0.02
49 4 0.02
50 7 0.04
51 4 0.02
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.21
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:3512167 original size:20 final size:20
Alignment explanation
Indices: 3512142--3512195 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
3512132 CTTCAGTAAA
3512142 CTTTTGGTGATGTGTATTTT
1 CTTTTGGTGATGTGTATTTT
*
3512162 CTTTTGGTGATGTATATTTT
1 CTTTTGGTGATGTGTATTTT
*
3512182 -TGTTTGGTAATGTG
1 CT-TTTGGTGATGTG
3512196 GCATGTACAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
19 1 0.03
20 29 0.97
ACGTcount: A:0.13, C:0.04, G:0.26, T:0.57
Consensus pattern (20 bp):
CTTTTGGTGATGTGTATTTT
Found at i:3517888 original size:117 final size:117
Alignment explanation
Indices: 3517682--3517893 Score: 307
Period size: 117 Copynumber: 1.8 Consensus size: 117
3517672 GATTTGGTGG
* * * *
3517682 ATAAGACCATAACTGGGTTATGGCACTATGAACATAAAACCATAGTTGGACCATGGCAGTATTTA
1 ATAAGACCATAACTCGGTTATGACACTATGAACATAAAACCATAGTTGAACCATGACAGTATTTA
*
3517747 TATGTAAGACCATAGATGGGCTATGGCATTAATGTAAATAATGAATTGATGA
66 TATGTAAGACCATAGATAGGCTATGGCATTAATGTAAATAATGAATTGATGA
* * * * * * *
3517799 ATAAGACCGTAACTCGGTTATGACACTATGAACGTAAGACCATGGTTGAACTATGATAGTGTTTA
1 ATAAGACCATAACTCGGTTATGACACTATGAACATAAAACCATAGTTGAACCATGACAGTATTTA
*
3517864 TATGTAAGACCATAGCTAGGCTATGGCATT
66 TATGTAAGACCATAGATAGGCTATGGCATT
3517894 CTGGTGATAA
Statistics
Matches: 82, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
117 82 1.00
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (117 bp):
ATAAGACCATAACTCGGTTATGACACTATGAACATAAAACCATAGTTGAACCATGACAGTATTTA
TATGTAAGACCATAGATAGGCTATGGCATTAATGTAAATAATGAATTGATGA
Found at i:3520865 original size:85 final size:85
Alignment explanation
Indices: 3520750--3520951 Score: 230
Period size: 85 Copynumber: 2.4 Consensus size: 85
3520740 TCTAGGGTTG
* * ** * **
3520750 TAATATTTTTTTC-AGAATAATTAAAATAATTTTTATTTAATTT-ATTTCATT-TTTGGGATATT
1 TAATATTTTTTTCGA-AATAATTATAATAATTTATATTT-ATTTCATTTCATTATTAAGG-CACC
* * * * **
3520812 TGGGTTTGAGTCTGGTGTTGTAA
63 TAGGCTTGAGCCTGGTGGTACAA
3520835 TAATATTTTTTTCGAAATAATTATAATAATTTATATTTATTTCATTTCATTATTAAGGCACCTAG
1 TAATATTTTTTTCGAAATAATTATAATAATTTATATTTATTTCATTTCATTATTAAGGCACCTAG
3520900 GCTTGAGCCTGGTGGTACAA
66 GCTTGAGCCTGGTGGTACAA
3520920 TAATATTTTTTTTCGAAATAATTATAATAATT
1 TAATA-TTTTTTTCGAAATAATTATAATAATT
3520952 GCAATTGTTT
Statistics
Matches: 100, Mismatches: 13, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
84 4 0.04
85 65 0.65
86 31 0.31
ACGTcount: A:0.32, C:0.07, G:0.12, T:0.49
Consensus pattern (85 bp):
TAATATTTTTTTCGAAATAATTATAATAATTTATATTTATTTCATTTCATTATTAAGGCACCTAG
GCTTGAGCCTGGTGGTACAA
Found at i:3521470 original size:175 final size:177
Alignment explanation
Indices: 3521113--3521517 Score: 417
Period size: 175 Copynumber: 2.3 Consensus size: 177
3521103 CAATATATTT
** * * ** *
3521113 TTTATTTTCCAAAATAACTACAATAATTGCTATTTGCTTCATTTCATTCCTGAGACACTTAGGTT
1 TTTATTTTCTGAAATAATTAAAATAATTGCTATTTATTTCATTTCATTTCTGAGACACTTAGGTT
* * *
3521178 TGAGGCTGGTGCTACAATAATATATTTTTTTATTTTCTAGAATAATTATAATAATTTTTATTTAT
66 TGAGGCTGGTGCTACAATAATATATTTTTTTATTTTCTAGAATAACTACAATAATTGTTATTTAT
* ***
3521243 TTCACTTCATTTATGGGCACTTGGACTTGAGCTTGGAGCTGCAGTAA
131 TTCACTTCATTCATGGGCACTTGGACTTGAGAAAGGAGCTGCAGTAA
* * * *
3521290 -TT-TTTTCTGAAATAATTAAAATAATTGTTATTTATTTCATTTCATTTTTGAGGCATTTAGGTT
1 TTTATTTTCTGAAATAATTAAAATAATTGCTATTTATTTCATTTCATTTCTGAGACACTTAGGTT
* ** * * *
3521353 TGAGTCTGGTGCTGTAATAATA-A-TTTTTTA-TTTCTCGGATAACTACAATACTTGTTATTTAT
66 TGAGGCTGGTGCTACAATAATATATTTTTTTATTTTCTAGAATAACTACAATAATTGTTATTTAT
* * * * *
3521415 TTCATTTTATTCATGGGGCACTTGGGCTTGAGAAAGGTGTTGC-GATAATA
131 TTCACTTCATTCAT-GGGCACTTGGACTTGAGAAAGGAGCTGCAG-T-A-A
* * *
3521465 TTTTTTATTTTTTGAAATAATTATAATAATTACTATTTATTTCATTTCATTTC
1 ---TTTATTTTCTGAAATAATTAAAATAATTGCTATTTATTTCATTTCATTTC
3521518 GATGCACTTG
Statistics
Matches: 185, Mismatches: 34, Indels: 15
0.79 0.15 0.06
Matches are distributed among these distances:
172 38 0.21
173 30 0.16
174 2 0.01
175 70 0.38
176 2 0.01
179 2 0.01
180 41 0.22
ACGTcount: A:0.28, C:0.11, G:0.14, T:0.47
Consensus pattern (177 bp):
TTTATTTTCTGAAATAATTAAAATAATTGCTATTTATTTCATTTCATTTCTGAGACACTTAGGTT
TGAGGCTGGTGCTACAATAATATATTTTTTTATTTTCTAGAATAACTACAATAATTGTTATTTAT
TTCACTTCATTCATGGGCACTTGGACTTGAGAAAGGAGCTGCAGTAA
Found at i:3522121 original size:177 final size:180
Alignment explanation
Indices: 3521891--3522229 Score: 438
Period size: 178 Copynumber: 1.9 Consensus size: 180
3521881 ACTTGGGCTT
* * * * **
3521891 GAGTCTATTGCTGCAAGAATATTTTGTTATTTTTTGGAATAACTATAATAATTGTAATTCA-TTC
1 GAGTCTATTACTACAAGAATATTTTCTTATTTTCTAAAATAACTATAATAATTGTAATTCATTTC
* * * * *
3521955 ATTTCA-TTTCAGGGGCACTTGGGCTTGAGTCTTGTGCTACAATAAAGTAATTTAA-TTTTTGAA
66 ATTTCATTTTCA-GGACACTTAGGCTTGAGTATGGTGCTACAATAAA-TAATTTAACTTTTAGAA
3522018 TTAATTATAATAATTGCTA-TTAATTTT-TTCATTCTCGGGAAAGTTGGTCTG
129 -TAATTATAATAATTGCTATTTAATTTTCTTCATTCTCGGGAAAGTTGGTCTG
* * * *
3522069 GAGTCTATTACTACAATAATA-TTTCTTATTTTCTAAAATAATTATAATAATTGTTATTTATTTC
1 GAGTCTATTACTACAAGAATATTTTCTTATTTTCTAAAATAACTATAATAATTGTAATTCATTTC
* * **
3522133 ATTTCATTTTCAGGACACTTAGGTTTGAGTATGGTGCTGCAATAAATTTTTTAACTTTTAGAATA
66 ATTTCATTTTCAGGACACTTAGGCTTGAGTATGGTGCTACAATAAATAATTTAACTTTTAGAATA
3522198 ATTATAATAATTGCTATTTAATTTTCTTCATT
131 ATTATAATAATTGCTATTTAATTTTCTTCATT
3522230 TTCGAGGTAC
Statistics
Matches: 137, Mismatches: 19, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
177 56 0.41
178 70 0.51
179 11 0.08
ACGTcount: A:0.30, C:0.10, G:0.13, T:0.46
Consensus pattern (180 bp):
GAGTCTATTACTACAAGAATATTTTCTTATTTTCTAAAATAACTATAATAATTGTAATTCATTTC
ATTTCATTTTCAGGACACTTAGGCTTGAGTATGGTGCTACAATAAATAATTTAACTTTTAGAATA
ATTATAATAATTGCTATTTAATTTTCTTCATTCTCGGGAAAGTTGGTCTG
Found at i:3522208 original size:89 final size:87
Alignment explanation
Indices: 3520758--3522251 Score: 610
Period size: 90 Copynumber: 16.7 Consensus size: 87
3520748 TGTAATATTT
* * ** * * *
3520758 TTTTCAGAATAATTAAAATAATTTTTATTTAATTT-ATTTCATTTTTGGGATATTTGGGTTTGAG
1 TTTT-AGAATAATTATAATAATTGTTATTT-ATTTCATTTCATTTTCAGGACACTTGGGCTTGAG
* * *
3520822 TCTGGTGTTGTAAT-AA-TATTT-
64 TCTGGTGCTGCAATAAATTTTTTA
* * * *
3520843 TTTTCGAAATAATTATAATAATT-TATATTTATTTCATTTCATTATTAAGG-CACCTAGGCTTGA
1 TTTTAG-AATAATTATAATAATTGT-TATTTATTTCATTTCATT-TTCAGGACACTTGGGCTTGA
* * * *
3520906 GCCTGGTGGTACAAT-AATATTTT-
63 GTCTGGTGCTGCAATAAATTTTTTA
* ** * *
3520929 TTTTCGAAATAATTATAATAATTGCAATTGTTTTTCATTTCATTCTCGAGAGTTGGGACACTTGG
1 TTTTAG-AATAATTATAATAATTGTTATT-TATTTCATTTCATTTTC---A----GGACACTTGG
*
3520994 GCTTGAGTTTGGTGCTGCAATAATATTTTTTTTGA
57 GCTTGAGTCTGGTGCTGCAATAA-A--TTTTTT-A
* * * * * * * **
3521029 TTTTCAAAATACTTATACT-ATATATTATTTATTTCATTTCATTATCGGGGCACTTAAGCTTGAG
1 TTTT-AGAATAATTATAATAAT-TGTTATTTATTTCATTTCATTTTCAGGACACTTGGGCTTGAG
* * * *
3521093 ACTTGTGCTACAATATATTTTTTA
64 TCTGGTGCTGCAATAAATTTTTTA
* * * * ** * * * *
3521117 TTTTCCAAAATAACTACAATAATTGCTATTTGCTTCATTTCA-TTCCTGAGACACTTAGGTTTGA
1 TTTT--AGAATAATTATAATAATTGTTATTTATTTCATTTCATTTTCAG-GACACTTGGGCTTGA
* *
3521181 GGCTGGTGCTACAATAATATATTTTTTTA
63 GTCTGGTGCTGCAAT-A-A-A-TTTTTTA
* * * *
3521210 TTTTCTAGAATAATTATAATAATTTTTATTTATTTCACTTCA-TTT-ATGGGCACTTGGACTTGA
1 -TTT-TAGAATAATTATAATAATTGTTATTTATTTCATTTCATTTTCA-GGACACTTGGGCTTGA
* *
3521273 G-CTTGGAGCTGCAGT-AA-TTTTT-
63 GTC-TGGTGCTGCAATAAATTTTTTA
* * * * * * *
3521295 TCTGA-AATAATTAAAATAATTGTTATTTATTTCATTTCATTTTTGAGG-CATTTAGGTTTGAGT
1 TTTTAGAATAATTATAATAATTGTTATTTATTTCATTTCA-TTTTCAGGACACTTGGGCTTGAGT
*
3521358 CTGGTGCTGTAATAATAATTTTTTA
65 CTGGTGCTGCAAT-A-AATTTTTTA
* * * * * * *
3521383 TTTCTCGGATAACTACAATACTTGTTATTTATTTCATTT--TATTCATGGGGCACTTGGGCTTGA
1 TTT-TAGAATAATTATAATAATTGTTATTTATTTCATTTCATTTTCA--GGACACTTGGGCTTGA
*** * *
3521446 GAAAGGTGTTGCGATAATATTTTTTA
63 GTCTGGTGCTGCAATAA-ATTTTTTA
* ** * *
3521472 TTTTTTGAAATAATTATAATAATTACTATTTATTTCATTTCA-TTTCGATG-CACTTGAGCTTGA
1 -TTTTAG-AATAATTATAATAATTGTTATTTATTTCATTTCATTTTC-AGGACACTTGGGCTTGA
** * **
3521535 GT-TTATGCTACAATAGTTTTTTTTTTCTAA
63 GTCTGGTGCTGCAATA----AATTTTT-T-A
* * * * *
3521565 TTTTTAGAATAATTAGAATAATT-TCTATTTATTTCATTTTA-TTTCAAGG-CATTTGAGATTGA
1 -TTTTAGAATAATTATAATAATTGT-TATTTATTTCATTTCATTTTC-AGGACACTTGGGCTTGA
* * * *
3521627 GTTTGGTGTTGCGACAATATATTTTTA
63 GTCTGGTGCTGCAATAA-AT-TTTTTA
* *
3521654 TTTTTAAGAATAATTATAATAATTATAATTTATTTCATTTCA--TTCAAGGAGCACTTGGGCTTG
1 -TTTT-AGAATAATTATAATAATTGTTATTTATTTCATTTCATTTTC-AGGA-CACTTGGGCTTG
*
3521717 AGT-TGGTGCTGCAAT-ATTTTTTTA
62 AGTCTGGTGCTGCAATAAATTTTTTA
* * * * * *
3521741 CTTTCCAAAATAATAATAATAATAATTGCTATATATTTCATTTAATTCCTT-GGGTACA--TGGG
1 -TTT-TAGAATAAT--T-ATAATAATTGTTATTTATTTCATTTCATT--TTCAGG-ACACTTGGG
* * ** * *
3521803 ATTGAGTCTAGTGCAACAAT--TTTTTTTC
58 CTTGAGTCTGGTGCTGCAATAAATTTTTTA
* * * * * * *
3521831 TTTCCAAAATAATTATAATATTTGCTATATATTTCATTTAATTCTC--GAGCACTTGGGCTTGAG
1 TTT-TAGAATAATTATAATAATTGTTATTTATTTCATTTCATTTTCAGGA-CACTTGGGCTTGAG
** *
3521894 TCTATTGCTGCAAGAATATTTTGTTA
64 TCTGGTGCTGCAATAA-ATTTT-TTA
* * * * *
3521920 TTTTTTGGAATAACTATAATAATTGTAATTCA-TTCATTTCA-TTTCAGGGGCACTTGGGCTTGA
1 --TTTTAGAATAATTATAATAATTGTTATTTATTTCATTTCATTTTCA-GGACACTTGGGCTTGA
* * * *
3521983 GTCTTGTGCTACAATAAAGTAATTTAA
63 GTCTGGTGCTGCAATAAA-T-TTTTTA
* * * * * * * * *
3522010 TTTTTGAATTAATTATAATAATTGCTATTAATTT--TTTCATTCTCGGGAAAGTTGGTCTGGAGT
1 TTTTAGAA-TAATTATAATAATTGTTATTTATTTCATTTCATTTTCAGGACACTTGGGCTTGAGT
** * * *
3522073 CTATTACTACAATAATATTTCTTA
65 CTGGTGCTGCAATAA-ATTTTTTA
* * *
3522097 TTTTCTAAAATAATTATAATAATTGTTATTTATTTCATTTCATTTTCAGGACACTTAGGTTTGAG
1 -TTT-TAGAATAATTATAATAATTGTTATTTATTTCATTTCATTTTCAGGACACTTGGGCTTGAG
*
3522162 TATGGTGCTGCAATAAATTTTTTAA
64 TCTGGTGCTGCAATAAATTTTTT-A
* *
3522187 CTTTTAGAATAATTATAATAATTGCTATTTAATTT--TCTTCATTTTCGAGG-TACTTGGGCTTG
1 -TTTTAGAATAATTATAATAATTGTTATTT-ATTTCAT-TTCATTTTC-AGGACACTTGGGCTTG
3522249 AGT
62 AGT
3522252 TTAGTGCACT
Statistics
Matches: 1067, Mismatches: 237, Indels: 206
0.71 0.16 0.14
Matches are distributed among these distances:
82 32 0.03
83 23 0.02
84 15 0.01
85 73 0.07
86 69 0.06
87 42 0.04
88 92 0.09
89 200 0.19
90 252 0.24
91 42 0.04
92 102 0.10
93 55 0.05
94 27 0.03
95 2 0.00
96 1 0.00
98 5 0.00
99 17 0.02
100 18 0.02
ACGTcount: A:0.29, C:0.11, G:0.14, T:0.46
Consensus pattern (87 bp):
TTTTAGAATAATTATAATAATTGTTATTTATTTCATTTCATTTTCAGGACACTTGGGCTTGAGTC
TGGTGCTGCAATAAATTTTTTA
Found at i:3523082 original size:88 final size:88
Alignment explanation
Indices: 3522929--3523103 Score: 305
Period size: 88 Copynumber: 2.0 Consensus size: 88
3522919 TTTGCACCAA
*
3522929 ATCCGGAAGATTCAAATACGAAGATAGATCGAGGAAAGGAAAAAGTTCGGGATTAGTAGAATTTT
1 ATCCGAAAGATTCAAATACGAAGATAGATCGAGGAAAGGAAAAAGTTCGGGATTAGTAGAATTTT
*
3522994 ATTGTTTACAAACAAGTATCAAG
66 ATTCTTTACAAACAAGTATCAAG
* * *
3523017 ATCCGAAAGATTCAAATACGAAGCTAGATTGAGGAAAGGAAAAAGTTCGGGATTAGTAGATTTTT
1 ATCCGAAAGATTCAAATACGAAGATAGATCGAGGAAAGGAAAAAGTTCGGGATTAGTAGAATTTT
3523082 ATTCTTTACAAACAAGTATCAA
66 ATTCTTTACAAACAAGTATCAA
3523104 TGTAAGTTCG
Statistics
Matches: 82, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
88 82 1.00
ACGTcount: A:0.42, C:0.11, G:0.21, T:0.26
Consensus pattern (88 bp):
ATCCGAAAGATTCAAATACGAAGATAGATCGAGGAAAGGAAAAAGTTCGGGATTAGTAGAATTTT
ATTCTTTACAAACAAGTATCAAG
Found at i:3524858 original size:90 final size:91
Alignment explanation
Indices: 3524719--3524984 Score: 241
Period size: 90 Copynumber: 2.9 Consensus size: 91
3524709 TATGATGTTG
* ** * * *
3524719 TAATAATATTTGATTTTATTTTAGGAATAATTATAATAATTGATATTTATTTCTTTTCATTTTCA
1 TAATAATATTT-TTTTTATTTT-TTAATAATTATAATAACTGATATTTATTTCATTTCATTCTCA
** *
3524784 AGACAATTGGGTTTGAGTCGGGTGC-AC
64 AGACAATTGGCCTTGAGTCGAGTGCTAC
* *
3524811 TAATAATATTTTTTTTATTTTTTAATAATTATAATGACTGATATTTATTTCATTTCATTCTCGAG
1 TAATAATATTTTTTTTATTTTTTAATAATTATAATAACTGATATTTATTTCATTTCATTCTCAAG
* * *
3524876 GCACTTGGCCTTGAGTCTAGTGCTAC
66 ACAATTGGCCTTGAGTCGAGTGCTAC
* * * * * * *
3524902 -AATAAT-TTTTGTTTTATTTTTTTGGAATAGTTATAATAAGTGCTATTCATTTTATTTTATTTT
1 TAATAATATTTT-TTTTA-TTTTTT--AATAATTATAATAACTGATATTTATTTCATTTCATTCT
* * *
3524965 CAAGATATTTGGGCTTGAGT
62 CAAGACAATTGGCCTTGAGT
3524985 TTGGCGTTGC
Statistics
Matches: 142, Mismatches: 27, Indels: 9
0.80 0.15 0.05
Matches are distributed among these distances:
89 4 0.03
90 65 0.46
91 17 0.12
92 11 0.08
93 45 0.32
ACGTcount: A:0.28, C:0.09, G:0.14, T:0.50
Consensus pattern (91 bp):
TAATAATATTTTTTTTATTTTTTAATAATTATAATAACTGATATTTATTTCATTTCATTCTCAAG
ACAATTGGCCTTGAGTCGAGTGCTAC
Found at i:3526483 original size:21 final size:21
Alignment explanation
Indices: 3526443--3526507 Score: 98
Period size: 21 Copynumber: 3.2 Consensus size: 21
3526433 CGAATACTCC
3526443 AACAGAAGCTCG-AA-AGCTG
1 AACAGAAGCTCGTAAGAGCTG
*
3526462 AATAGAAGCTCGTAAGAGCTG
1 AACAGAAGCTCGTAAGAGCTG
*
3526483 AACAGAAGCTCGTAGGAGCTG
1 AACAGAAGCTCGTAAGAGCTG
3526504 AACA
1 AACA
3526508 AAAACTCATT
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
19 11 0.27
20 2 0.05
21 28 0.68
ACGTcount: A:0.40, C:0.18, G:0.28, T:0.14
Consensus pattern (21 bp):
AACAGAAGCTCGTAAGAGCTG
Found at i:3528334 original size:86 final size:85
Alignment explanation
Indices: 3528188--3528353 Score: 205
Period size: 86 Copynumber: 1.9 Consensus size: 85
3528178 AGAAAGCTCG
* * *
3528188 TACAATGCCGACGTTCCAGACATGGTCTTACATGTAATCAAATATCGATGCCACTGTCCCAGACA
1 TACAATGCCAACGTTCCAGACATGGTCTTACACGTAATCAAATATCGATGCCAATGTCCCAGAC-
*
3528253 G-GGTCTTACACGAAATCAAA
65 GTGATCTTACACGAAATCAAA
**
3528273 TACAATGCCAACG-TCCTAGATGTGGTCTTACACGTAAATCATAAGT-T-GATGCCAATGTCCCA
1 TACAATGCCAACGTTCC-AGACATGGTCTTACACGT-AATCA-AA-TATCGATGCCAATGTCCCA
3528335 GACGTGATCTTACACGAAA
62 GACGTGATCTTACACGAAA
3528354 ACACATATCG
Statistics
Matches: 70, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
84 3 0.04
85 28 0.40
86 35 0.50
87 3 0.04
88 1 0.01
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.25
Consensus pattern (85 bp):
TACAATGCCAACGTTCCAGACATGGTCTTACACGTAATCAAATATCGATGCCAATGTCCCAGACG
TGATCTTACACGAAATCAAA
Found at i:3528346 original size:44 final size:42
Alignment explanation
Indices: 3528203--3528353 Score: 153
Period size: 43 Copynumber: 3.5 Consensus size: 42
3528193 TGCCGACGTT
* * * *
3528203 CCAGACATGGTCTTACATGTAATCAAATATCGATGCCACTGTC
1 CCAGACGTGGTCTTACACGAAATCAAATA-CGATGCCAATGTC
* *
3528246 CCAGACAG-GGTCTTACACGAAATCAAATACAATGCCAACGTC
1 CCAGAC-GTGGTCTTACACGAAATCAAATACGATGCCAATGTC
* * *
3528288 CTAGATGTGGTCTTACACGTAAATCATAAGT-TGATGCCAATGTC
1 CCAGACGTGGTCTTACACG-AAATCA-AA-TACGATGCCAATGTC
*
3528332 CCAGACGTGATCTTACACGAAA
1 CCAGACGTGGTCTTACACGAAA
3528354 ACACATATCG
Statistics
Matches: 89, Mismatches: 14, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
41 1 0.01
42 25 0.28
43 34 0.38
44 28 0.31
45 1 0.01
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.25
Consensus pattern (42 bp):
CCAGACGTGGTCTTACACGAAATCAAATACGATGCCAATGTC
Found at i:3529207 original size:163 final size:163
Alignment explanation
Indices: 3528937--3529263 Score: 636
Period size: 163 Copynumber: 2.0 Consensus size: 163
3528927 ATTGCTAAGC
3528937 AACGATTACAAAAACATAGAAATTATCAAAAACCGATCAAAACACATACCTTAATCCACAATCAC
1 AACGATTACAAAAACATAGAAATTATCAAAAACCGATCAAAACACATACCTTAATCCACAATCAC
3529002 AAGTGTCGAAACCCTAAAAGCTTTTATTCTTTCTTTTGTTCTTCAAATTTCGAAAAAATGAGCAT
66 AAGTGTCGAAACCCTAAAAGCTTTTATTCTTTCTTTTGTTCTTCAAATTTCGAAAAAATGAGCAT
3529067 ATAATGAACATTTTCATGTTTTGTTTAATTAAT
131 ATAATGAACATTTTCATGTTTTGTTTAATTAAT
3529100 AACGATTACAAAAACATAGAAATTATCAAAAACCGATCAAAACACATACCTTAATCCACAATCAC
1 AACGATTACAAAAACATAGAAATTATCAAAAACCGATCAAAACACATACCTTAATCCACAATCAC
*
3529165 AAGTGTCGAAACCCTAAGAGCTTTTATTCTTTCTTTTGTTCTTCAAATTTCGAAAAAATGAGCAT
66 AAGTGTCGAAACCCTAAAAGCTTTTATTCTTTCTTTTGTTCTTCAAATTTCGAAAAAATGAGCAT
*
3529230 ATAATGAACATTTTTATGTTTTGTTTAATTAAT
131 ATAATGAACATTTTCATGTTTTGTTTAATTAAT
3529263 A
1 A
3529264 TTAACATAAT
Statistics
Matches: 162, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
163 162 1.00
ACGTcount: A:0.40, C:0.17, G:0.09, T:0.33
Consensus pattern (163 bp):
AACGATTACAAAAACATAGAAATTATCAAAAACCGATCAAAACACATACCTTAATCCACAATCAC
AAGTGTCGAAACCCTAAAAGCTTTTATTCTTTCTTTTGTTCTTCAAATTTCGAAAAAATGAGCAT
ATAATGAACATTTTCATGTTTTGTTTAATTAAT
Found at i:3531486 original size:84 final size:83
Alignment explanation
Indices: 3531131--3531487 Score: 215
Period size: 84 Copynumber: 4.1 Consensus size: 83
3531121 TACAATAATT
* ** *
3531131 TATTTTTATTTTCTAAAATAATTATAATAATAGCTATTTATTTCATTTCA-TTATGAGGCATTTG
1 TATTTTT-TTTTC-AGAATAATTATAATAATTTCTATTTATTTCATTTCATTTCTG-GGCATTTG
* *
3531195 AGTTTGAGTCTGGTATTGCAATAAA
63 AGCTTGAGTCTGGTGTT---AT-AA
* ** * * *
3531220 TTTTTTTATTTTTTGGAATAATTATAATAATTGATTTATTTCATTCCATTTCATTTTTGGGCATT
1 -TATTTT-TTTTTCAGAATAATTATAATAATT--TCTATTT-ATTTCATTTCATTTCTGGGCATT
* *
3531285 T-AGGCTT--GTTTGGTATTGTAATAA
61 TGA-GCTTGAGTCTGG---TGTTATAA
** * * * * *
3531309 TATTTTTTATTTTTTGAAATAATTATAATATTTTTTATTTATTTTATTTCATTTCTAAGGTA-TT
1 TA-TTTTT-TTTTCAG-AATAATTATAATAATTTCTATTTATTTCATTTCATTTCT-GGGCATTT
* *
3531373 GAG-TGTGAG-CTGGTGTTGTGA
62 GAGCT-TGAGTCTGGTGTTATAA
*
3531394 TGATTTTTTTTTTCAGAATAATTATAATAATTTCTATTTATTTTATTTCATTTCTGGGCCATTTG
1 T-A-TTTTTTTTTCAGAATAATTATAATAATTTCTATTTATTTCATTTCATTTCTGGG-CATTTG
* *
3531459 GGCTTGAGTTTGGTGTTATAA
63 AGCTTGAGTCTGGTGTTATAA
3531480 TATTTTTT
1 TATTTTTT
3531488 ATATTTTTTT
Statistics
Matches: 210, Mismatches: 35, Indels: 50
0.71 0.12 0.17
Matches are distributed among these distances:
83 2 0.01
84 44 0.21
85 20 0.10
86 19 0.09
87 17 0.08
88 16 0.08
89 28 0.13
90 31 0.15
91 7 0.03
92 20 0.10
93 6 0.03
ACGTcount: A:0.26, C:0.06, G:0.14, T:0.54
Consensus pattern (83 bp):
TATTTTTTTTTCAGAATAATTATAATAATTTCTATTTATTTCATTTCATTTCTGGGCATTTGAGC
TTGAGTCTGGTGTTATAA
Found at i:3531524 original size:90 final size:88
Alignment explanation
Indices: 3531019--3531536 Score: 374
Period size: 90 Copynumber: 5.8 Consensus size: 88
3531009 TCATACCCAG
* * * * *
3531019 TTGAGTCTGGTGTTGTAATAATATTTTTTATTTTATGGAATAATCATAATAATTGTTATTAATTT
1 TTGAGTCTGGTGTTATAATAAT-TTTTTTATTTTTTGGAATAATTATAATAATTGCTATTTATTT
* *** * *
3531084 TATTTCATTATC-CAACACTTGGAC
65 CATTTCATT-TCTGGGCATTTGGGC
* * * * ** *
3531108 TTGAGTTTGGTGCTACAATAATTTATTTTTATTTTCTAAAATAATTATAATAATAGCTATTTATT
1 TTGAGTCTGGTGTTATAATAA-TT-TTTTTATTTTTTGGAATAATTATAATAATTGCTATTTATT
* * *
3531173 TCATTTCA-TTATGAGGCATTTGAGT
64 TCATTTCATTTCTG-GGCATTTGGGC
* ** *
3531198 TTGAGTCTGGTATTGCAATAAATTTTTTTATTTTTTGGAATAATTATAATAATTGATTTATTTCA
1 TTGAGTCTGGTGTTATAAT-AATTTTTTTATTTTTTGGAATAATTATAATAATTG--CTATTT-A
* * *
3531263 TTCCATTTCATTTTTGGGCATTTAGGC
62 TTTCATTTCATTTCTGGGCATTTGGGC
* * * * * **
3531290 TT--GTTTGGTATTGTAATAATATTTTTTATTTTTTGAAATAATTATAATATTTTTTATTTATTT
1 TTGAGTCTGGTGTTATAATAAT-TTTTTTATTTTTTGGAATAATTATAATAATTGCTATTTATTT
* * * *
3531353 TATTTCATTTCTAAGGTA-TTGAG-
65 CATTTCATTTCT-GGGCATTTGGGC
* * * ** *
3531376 TGTGAG-CTGGTGTTGTGATGA--TTTTT-TTTTTCAGAATAATTATAATAATTTCTATTTATTT
1 T-TGAGTCTGGTGTTATAATAATTTTTTTATTTTTTGGAATAATTATAATAATTGCTATTTATTT
*
3531437 TATTTCATTTCTGGGCCATTTGGGC
65 CATTTCATTTCTGGG-CATTTGGGC
* * *
3531462 TTGAGTTTGGTGTTATAAT-ATTTTTTATATTTTTTTGGAATACTTATAATAGTTGCTATTTATT
1 TTGAGTCTGGTGTTATAATAATTTTTT-TA-TTTTTTGGAATAATTATAATAATTGCTATTTATT
*
3531526 TCATTTTATTT
64 TCATTTCATTT
3531537 TCAAAGCATT
Statistics
Matches: 338, Mismatches: 68, Indels: 45
0.75 0.15 0.10
Matches are distributed among these distances:
83 2 0.01
84 43 0.13
85 14 0.04
86 12 0.04
87 21 0.06
88 22 0.07
89 50 0.15
90 143 0.42
91 7 0.02
92 20 0.06
93 4 0.01
ACGTcount: A:0.27, C:0.07, G:0.13, T:0.53
Consensus pattern (88 bp):
TTGAGTCTGGTGTTATAATAATTTTTTTATTTTTTGGAATAATTATAATAATTGCTATTTATTTC
ATTTCATTTCTGGGCATTTGGGC
Found at i:3538379 original size:44 final size:44
Alignment explanation
Indices: 3538309--3538437 Score: 201
Period size: 44 Copynumber: 3.0 Consensus size: 44
3538299 AATCCCTGTG
* *
3538309 ACTAGAACTCATAG-TTGTATGGAGGGTGAACACCCTTGGCCAA
1 ACTAGAACTCACAGATTGTATGTAGGGTGAACACCCTTGGCCAA
*
3538352 ACTAGAACTCAGAGATTGTATGTAGGGTGAACACCCTTGGCCAA
1 ACTAGAACTCACAGATTGTATGTAGGGTGAACACCCTTGGCCAA
*
3538396 ACTAGAACTCACAGATTGTATGTAAGGTGAAC-CCC-TGGCCAA
1 ACTAGAACTCACAGATTGTATGTAGGGTGAACACCCTTGGCCAA
3538438 TGAGTCAACA
Statistics
Matches: 81, Mismatches: 4, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
42 7 0.09
43 16 0.20
44 58 0.72
ACGTcount: A:0.32, C:0.22, G:0.24, T:0.22
Consensus pattern (44 bp):
ACTAGAACTCACAGATTGTATGTAGGGTGAACACCCTTGGCCAA
Found at i:3551725 original size:17 final size:17
Alignment explanation
Indices: 3551705--3551738 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
3551695 TAAGACTCGG
3551705 GAAAGAA-AAAGAAATAA
1 GAAAGAACAAA-AAATAA
3551722 GAAAGAACAAAAAATAA
1 GAAAGAACAAAAAATAA
3551739 ATCTTATGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.81
18 3 0.19
ACGTcount: A:0.76, C:0.03, G:0.15, T:0.06
Consensus pattern (17 bp):
GAAAGAACAAAAAATAA
Found at i:3555416 original size:113 final size:113
Alignment explanation
Indices: 3555218--3555438 Score: 424
Period size: 113 Copynumber: 2.0 Consensus size: 113
3555208 TGGTTATAGA
3555218 AGTTAAGAACGTCCTAACCACCAATTCTTCCTTTAGCAGCTGGTTCCGGTACGACCTGCAAACCA
1 AGTTAAGAACGTCCTAACCACCAATTCTTCCTTTAGCAGCTGGTTCCGGTACGACCTGCAAACCA
3555283 ACATTTACCGATTATCTAACCGAGATAAACGTATTCCCGATTCGTATC
66 ACATTTACCGATTATCTAACCGAGATAAACGTATTCCCGATTCGTATC
*
3555331 AGTTAAGAACGTCCTAACCACCAATTCTTCCTTTAGCAGCTGGTTCCGGTACGACCTGTAAACCA
1 AGTTAAGAACGTCCTAACCACCAATTCTTCCTTTAGCAGCTGGTTCCGGTACGACCTGCAAACCA
*
3555396 ACCTTTACCGATTATCTAACCGAGATAAACGTATTCCCGATTC
66 ACATTTACCGATTATCTAACCGAGATAAACGTATTCCCGATTC
3555439 AAGTTCCCGG
Statistics
Matches: 106, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
113 106 1.00
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.28
Consensus pattern (113 bp):
AGTTAAGAACGTCCTAACCACCAATTCTTCCTTTAGCAGCTGGTTCCGGTACGACCTGCAAACCA
ACATTTACCGATTATCTAACCGAGATAAACGTATTCCCGATTCGTATC
Found at i:3556095 original size:5 final size:5
Alignment explanation
Indices: 3556085--3556109 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
3556075 AACCTAAATT
3556085 AATAA AATAA AATAA AATAA AATAA
1 AATAA AATAA AATAA AATAA AATAA
3556110 TAAAACAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AATAA
Found at i:3556124 original size:23 final size:23
Alignment explanation
Indices: 3556079--3556127 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
3556069 TAGCTTAACC
* * *
3556079 TAAATTAATAAAATAAAATAAAA
1 TAAAATAATAAAACAAAACAAAA
*
3556102 TAAAATAATAAAACAAGACAAAA
1 TAAAATAATAAAACAAAACAAAA
3556125 TAA
1 TAA
3556128 TATATTCCTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.73, C:0.04, G:0.02, T:0.20
Consensus pattern (23 bp):
TAAAATAATAAAACAAAACAAAA
Found at i:3556741 original size:12 final size:12
Alignment explanation
Indices: 3556724--3556749 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3556714 TATTTATTTA
3556724 TTCTCTTTTTTT
1 TTCTCTTTTTTT
3556736 TTCTCTTTTTTT
1 TTCTCTTTTTTT
3556748 TT
1 TT
3556750 GTGTAAAGGC
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:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (12 bp):
TTCTCTTTTTTT
Found at i:3562335 original size:23 final size:25
Alignment explanation
Indices: 3562302--3562347 Score: 69
Period size: 23 Copynumber: 1.9 Consensus size: 25
3562292 CTAATCACTA
*
3562302 TTATTATATAT-TA-ATGTATATTT
1 TTATTACATATATATATGTATATTT
3562325 TTATTACATATATATATGTATAT
1 TTATTACATATATATATGTATAT
3562348 GTATATGTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 10 0.50
24 2 0.10
25 8 0.40
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (25 bp):
TTATTACATATATATATGTATATTT
Found at i:3562352 original size:12 final size:12
Alignment explanation
Indices: 3562332--3562363 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
3562322 TTTTTATTAC
3562332 ATATATATATGT
1 ATATATATATGT
*
3562344 ATATGTATATGT
1 ATATATATATGT
3562356 ATATATAT
1 ATATATAT
3562364 TTATACATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (12 bp):
ATATATATATGT
Found at i:3562446 original size:147 final size:145
Alignment explanation
Indices: 3562289--3562573 Score: 371
Period size: 145 Copynumber: 2.0 Consensus size: 145
3562279 TAATATTATT
* *
3562289 AATCTAATCACTATTATTATATATTAATGTATATTTTTA-T-TACA-TATATATATGTATATGTA
1 AATCTAATCACTATTATTAT-TATT-AT-TATA-TATTAGTGTACATTATATAT-TATATATGTA
* * ** **
3562351 TATGTATATATATTTATACATAAGTATTCTTTTTTAATTACTTTATTTTAGTATTTTTATTATA-
61 TATGTATATATATTTATACAT-AGTAGTATTTTTTAATTACTTTATTTTAACATCATTATTATAT
3562415 TATATTAGCTTTTTGTATTTC
125 TATATTAGCTTTTTGTATTTC
* * * *
3562436 AATCTAATCACTATTATTATTATTATTATATATTAGTGTATATTTTTTATTATATATGTATGTGT
1 AATCTAATCACTATTATTATTATTATTATATATTAGTGTACATTATATATTATATATGTATATGT
3562501 ATATATATTTATACATAGTAGTATTTTTTAATTACTTTATTTTAACATCATTATTATATTATATT
66 ATATATATTTATACATAGTAGTATTTTTTAATTACTTTATTTTAACATCATTATTATATTATATT
*
3562566 TGCTTTTT
131 AGCTTTTT
3562574 TTTTTGTATT
Statistics
Matches: 121, Mismatches: 13, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
143 4 0.03
144 41 0.34
145 47 0.39
146 9 0.07
147 20 0.17
ACGTcount: A:0.32, C:0.06, G:0.06, T:0.56
Consensus pattern (145 bp):
AATCTAATCACTATTATTATTATTATTATATATTAGTGTACATTATATATTATATATGTATATGT
ATATATATTTATACATAGTAGTATTTTTTAATTACTTTATTTTAACATCATTATTATATTATATT
AGCTTTTTGTATTTC
Found at i:3562479 original size:26 final size:27
Alignment explanation
Indices: 3562450--3562510 Score: 83
Period size: 26 Copynumber: 2.3 Consensus size: 27
3562440 TAATCACTAT
3562450 TATTATTATTATTATATAT-TA-GTGTA
1 TATTATT-TTATTATATATGTATGTGTA
3562476 TATT-TTTTATTATATATGTATGTGTA
1 TATTATTTTATTATATATGTATGTGTA
3562502 TATATATTT
1 TAT-TATTT
3562511 ATACATAGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.35
25 4 0.13
26 12 0.39
27 1 0.03
28 3 0.10
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.61
Consensus pattern (27 bp):
TATTATTTTATTATATATGTATGTGTA
Found at i:3573921 original size:46 final size:45
Alignment explanation
Indices: 3573861--3574035 Score: 221
Period size: 46 Copynumber: 3.9 Consensus size: 45
3573851 ATATTATGCC
* * *
3573861 TAAAAAAAAA-GAATCAAGATGAAAACCAGAAAATGGTGTCTTGA
1 TAAAAAAAAAGGAATCAAGATGAAAACCCGAAAAGGGCGTCTTGA
3573905 TTAAAAAAAAAGGAATCAAGATGAAAACCCGAAAAGGGCGTCTTGA
1 -TAAAAAAAAAGGAATCAAGATGAAAACCCGAAAAGGGCGTCTTGA
* *
3573951 TAAACAAAAAAGGAATCAAGATGAAAACCCGAAAAAGACGTCTTGA
1 TAAA-AAAAAAGGAATCAAGATGAAAACCCGAAAAGGGCGTCTTGA
* * * * *
3573997 T-AAACAAAAGG-GTTAGGATGCAAACCCGAAAAGGGCGTC
1 TAAAAAAAAAGGAATCAAGATGAAAACCCGAAAAGGGCGTC
3574036 CCAATGAAGT
Statistics
Matches: 116, Mismatches: 12, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
43 22 0.19
44 7 0.06
45 16 0.14
46 71 0.61
ACGTcount: A:0.50, C:0.14, G:0.21, T:0.15
Consensus pattern (45 bp):
TAAAAAAAAAGGAATCAAGATGAAAACCCGAAAAGGGCGTCTTGA
Found at i:3575055 original size:78 final size:76
Alignment explanation
Indices: 3574783--3575179 Score: 435
Period size: 77 Copynumber: 5.2 Consensus size: 76
3574773 GATATCCTGA
* * *
3574783 TATTTTT-ATTTATGTTTTTC--AAAAATCAACTCATGTTGCGAGAGGTGAGTTGAGCCCCGGGT
1 TATTTTTAATTT-TTTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGT
*
3574845 CACACG-TCGAGA
65 CACACGCT-GAGG
* *** ***
3574857 TATTTTCAATTTCTTTTTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAAT
1 TATTTTTAATTT-TTTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGT
* *
3574922 CACGCACTGAGG
65 CACACGCTGAGG
* * * *
3574934 TATTTTCAA-TTTATGTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCGGGT
1 TATTTTTAATTTTTTTTTTC-AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGT
3574998 CACACGCTGAGG
65 CACACGCTGAGG
* * * *
3575010 TATTTTTAGTCTCTGTTTTTTCAAAAAAATCAACTCATATAGCGAGAAGTGAGTTGAGCCTCGGG
1 TATTTTTAAT-T-TTTTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG
*
3575075 TCACACGCTAAGG
64 TCACACGCTGAGG
* * ** * *
3575088 CATTTTTAGTTTTTATTTTTCAAATCAATCAATTCATATTGCGAGAGGTGAGTTGAGCCTCAGGT
1 TATTTTTAATTTTT-TTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGT
*
3575153 CACACACTGAGG
65 CACACGCTGAGG
3575165 TATTTTTAATTTTTT
1 TATTTTTAATTTTTT
3575180 AATTTTTTTA
Statistics
Matches: 270, Mismatches: 44, Indels: 16
0.82 0.13 0.05
Matches are distributed among these distances:
74 6 0.02
75 15 0.06
76 60 0.22
77 120 0.44
78 63 0.23
79 6 0.02
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.36
Consensus pattern (76 bp):
TATTTTTAATTTTTTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC
ACACGCTGAGG
Found at i:3575406 original size:19 final size:19
Alignment explanation
Indices: 3575357--3575406 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
3575347 CTTATCTCCA
*
3575357 TGAAGTTGTAGCAGAACCC
1 TGAAGTTGTAGTAGAACCC
*
3575376 TGAAGTTGTAGTAGAACCT
1 TGAAGTTGTAGTAGAACCC
3575395 TGAAGTTGTAGT
1 TGAAGTTGTAGT
3575407 GGAGCGGACC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.30, C:0.12, G:0.28, T:0.30
Consensus pattern (19 bp):
TGAAGTTGTAGTAGAACCC
Found at i:3576944 original size:23 final size:25
Alignment explanation
Indices: 3576913--3576981 Score: 72
Period size: 23 Copynumber: 2.8 Consensus size: 25
3576903 TAATCACTAT
*
3576913 TATTATTATTATATAT-TAT-TGTA
1 TATTATTATTACATATGTATATGTA
*
3576936 TATTTTTATTACATATGTATATGTA
1 TATTATTATTACATATGTATATGTA
*
3576961 TATATATT-TATACATAAGTAT
1 TAT-TATTAT-TACATATGTAT
3576982 TATTTTTTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
23 14 0.37
24 3 0.08
25 8 0.21
26 13 0.34
ACGTcount: A:0.36, C:0.03, G:0.06, T:0.55
Consensus pattern (25 bp):
TATTATTATTACATATGTATATGTA
Found at i:3577282 original size:16 final size:16
Alignment explanation
Indices: 3577261--3577312 Score: 77
Period size: 16 Copynumber: 3.2 Consensus size: 16
3577251 TTTGGTTCGC
3577261 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
3577277 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
* * *
3577293 TGTAATGGAATAGAAG
1 TGTATTGGATTAGAGG
3577309 TGTA
1 TGTA
3577313 ATATCAAATC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.31, C:0.00, G:0.35, T:0.35
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:3577359 original size:45 final size:44
Alignment explanation
Indices: 3577293--3577387 Score: 120
Period size: 45 Copynumber: 2.1 Consensus size: 44
3577283 GGATTAGAGG
* *
3577293 TGTAATGGAATAGAAGTGTAATA-TCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAAGCGTAATAGT-AAAAC-ACTGTTTGGTTGAA
* **
3577338 TGTAATGGAATAGAGGCGTAATAGTAAAACTGTGTTTGGTTGAA
1 TGTAATGGAATAGAAGCGTAATAGTAAAACACTGTTTGGTTGAA
3577382 TGTAAT
1 TGTAAT
3577388 AGAGGTGTAA
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
44 18 0.41
45 25 0.57
46 1 0.02
ACGTcount: A:0.36, C:0.05, G:0.25, T:0.34
Consensus pattern (44 bp):
TGTAATGGAATAGAAGCGTAATAGTAAAACACTGTTTGGTTGAA
Found at i:3577557 original size:25 final size:25
Alignment explanation
Indices: 3577525--3577579 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
3577515 TAATTTAATC
*
3577525 ATAT-TTAAACATAATTATTATT-AA
1 ATATATTAAACAT-ATTATAATTAAA
*
3577549 ATATATTAAATATATTATAATTAAA
1 ATATATTAAACATATTATAATTAAA
3577574 ATATAT
1 ATATAT
3577580 AATTTAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 12 0.44
25 15 0.56
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (25 bp):
ATATATTAAACATATTATAATTAAA
Found at i:3577761 original size:47 final size:46
Alignment explanation
Indices: 3577710--3577858 Score: 132
Period size: 47 Copynumber: 3.3 Consensus size: 46
3577700 GATTTAATAA
3577710 AATTTAAAATAATTATAACTAATAAATTATCTTATATGAATTTGTAT
1 AATTTAAAATAATTATAA-TAATAAATTATCTTATATGAATTTGTAT
* * * * *
3577757 AATTTAAAATAATTATTATTACATATAAT-TTA-AT-AA---GATAT
1 AATTTAAAATAATTATAATAATAAATTATCTTATATGAATTTG-TAT
* * * *
3577798 AATTTCATAA-AATTATTGATAATAAATTTTCTTATATGAATTTATAT
1 AATTT-AAAATAATTA-TAATAATAAATTATCTTATATGAATTTGTAT
3577845 AATTTAAAATAATT
1 AATTTAAAATAATT
3577859 TAGGAAATGG
Statistics
Matches: 78, Mismatches: 14, Indels: 20
0.70 0.12 0.18
Matches are distributed among these distances:
40 1 0.01
41 13 0.17
42 11 0.14
43 5 0.06
44 4 0.05
45 5 0.06
46 10 0.13
47 29 0.37
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.46
Consensus pattern (46 bp):
AATTTAAAATAATTATAATAATAAATTATCTTATATGAATTTGTAT
Found at i:3582177 original size:21 final size:20
Alignment explanation
Indices: 3582148--3582187 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
3582138 TTTCCTTTAA
*
3582148 ACATATTCTTATATTATATT
1 ACATATTCTTATAATATATT
3582168 ACATAATTCTTATAATATAT
1 ACAT-ATTCTTATAATATAT
3582188 CTTTTAAATC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (20 bp):
ACATATTCTTATAATATATT
Found at i:3582869 original size:15 final size:15
Alignment explanation
Indices: 3582849--3582879 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3582839 TACTTGATTA
3582849 TTAGTCCATCATTTT
1 TTAGTCCATCATTTT
*
3582864 TTAGTCCATTATTTT
1 TTAGTCCATCATTTT
3582879 T
1 T
3582880 GTATCTTGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.19, C:0.16, G:0.06, T:0.58
Consensus pattern (15 bp):
TTAGTCCATCATTTT
Found at i:3592573 original size:4 final size:4
Alignment explanation
Indices: 3592564--3592592 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
3592554 TAAATTTAAA
3592564 AATT AATT AATT AATT AATT AATT AATT A
1 AATT AATT AATT AATT AATT AATT AATT A
3592593 GACCCAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
AATT
Found at i:3594667 original size:26 final size:26
Alignment explanation
Indices: 3594638--3594745 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
3594628 TGGTACAAAT
3594638 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
3594664 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
3594690 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
3594716 TGATAATGGTTTAGGTAAATGTTCTA
1 TGATAATGGGTTAGGTAAATGTTCCA
3594742 TGAT
1 TGAT
3594746 GGGCATTTCA
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 76 1.00
ACGTcount: A:0.32, C:0.06, G:0.24, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:3596391 original size:27 final size:27
Alignment explanation
Indices: 3596352--3596437 Score: 113
Period size: 27 Copynumber: 3.2 Consensus size: 27
3596342 GGAAGCGTCT
*
3596352 TGGTGGCTATGCCACAATTATTTGATC
1 TGGTGGCTCTGCCACAATTATTTGATC
* *
3596379 TGGTGGCTCTGCCAC-ATATATCTGTTC
1 TGGTGGCTCTGCCACAAT-TATTTGATC
3596406 TGGTGGCTCTGCCACAA-TATTTGTATC
1 TGGTGGCTCTGCCACAATTATTTG-ATC
3596433 TGGTG
1 TGGTG
3596438 ATTTCGTCAC
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
26 7 0.14
27 43 0.84
28 1 0.02
ACGTcount: A:0.17, C:0.21, G:0.24, T:0.37
Consensus pattern (27 bp):
TGGTGGCTCTGCCACAATTATTTGATC
Found at i:3598110 original size:32 final size:29
Alignment explanation
Indices: 3598040--3598097 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
3598030 ATTACTTAAA
3598040 AAAATTTATTGGTTGTGTAGTTTTTTTTT
1 AAAATTTATTGGTTGTGTAGTTTTTTTTT
3598069 AAAATTTATTGGTTGTGTAGTTTTTTTTT
1 AAAATTTATTGGTTGTGTAGTTTTTTTTT
3598098 TACTTTCATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.21, C:0.00, G:0.17, T:0.62
Consensus pattern (29 bp):
AAAATTTATTGGTTGTGTAGTTTTTTTTT
Found at i:3601599 original size:15 final size:13
Alignment explanation
Indices: 3601567--3601598 Score: 55
Period size: 13 Copynumber: 2.4 Consensus size: 13
3601557 TCAATCTTTT
3601567 TTTTTCAAATTTA
1 TTTTTCAAATTTA
3601580 TTTTTCAAATTTA
1 TTTTTCAAATTTA
3601593 TATTTT
1 T-TTTT
3601599 TGTCCAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 14 0.78
14 4 0.22
ACGTcount: A:0.28, C:0.06, G:0.00, T:0.66
Consensus pattern (13 bp):
TTTTTCAAATTTA
Found at i:3601618 original size:20 final size:20
Alignment explanation
Indices: 3601593--3601639 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
3601583 TTCAAATTTA
3601593 TATTTTTGTCCAAATTTTCT
1 TATTTTTGTCCAAATTTTCT
*
3601613 TATTTTTGTCTAAATTTTCT
1 TATTTTTGTCCAAATTTTCT
3601633 TATTTTT
1 TATTTTT
3601640 TGAGCAGACC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.19, C:0.11, G:0.04, T:0.66
Consensus pattern (20 bp):
TATTTTTGTCCAAATTTTCT
Found at i:3612095 original size:48 final size:48
Alignment explanation
Indices: 3612036--3612131 Score: 183
Period size: 48 Copynumber: 2.0 Consensus size: 48
3612026 CCATTGTGTC
3612036 GTCATCCCTCTCCCTTGCCATTAGATTTTCTATTTCCTTTGTAAGCTT
1 GTCATCCCTCTCCCTTGCCATTAGATTTTCTATTTCCTTTGTAAGCTT
*
3612084 GTCATCCCTCTCCCTTGCCATTAGATTTTTTATTTCCTTTGTAAGCTT
1 GTCATCCCTCTCCCTTGCCATTAGATTTTCTATTTCCTTTGTAAGCTT
3612132 ACTCTTTAAA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.15, C:0.28, G:0.10, T:0.47
Consensus pattern (48 bp):
GTCATCCCTCTCCCTTGCCATTAGATTTTCTATTTCCTTTGTAAGCTT
Found at i:3616459 original size:2 final size:2
Alignment explanation
Indices: 3616452--3616478 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3616442 CTGATGTAAC
3616452 CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT C
3616479 AGACACACAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:3618786 original size:13 final size:13
Alignment explanation
Indices: 3618768--3618799 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
3618758 AAGTTTAGTT
3618768 TTAATTAATGATG
1 TTAATTAATGATG
*
3618781 TTAATTGATGATG
1 TTAATTAATGATG
3618794 TTAATT
1 TTAATT
3618800 TGTCAGGTTC
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:0.34, C:0.00, G:0.16, T:0.50
Consensus pattern (13 bp):
TTAATTAATGATG
Found at i:3621659 original size:14 final size:16
Alignment explanation
Indices: 3621632--3621673 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
3621622 ATATTGTTTT
*
3621632 TTTTTGAATTTTTTATA
1 TTTTTGAATTTTATA-A
3621649 TTTTT-AATTTTATAA
1 TTTTTGAATTTTATAA
3621664 TTTTTGAATT
1 TTTTTGAATT
3621674 ATTTGTTGAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 6 0.26
16 12 0.52
17 5 0.22
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (16 bp):
TTTTTGAATTTTATAA
Found at i:3629704 original size:93 final size:93
Alignment explanation
Indices: 3629589--3629759 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
3629579 GCCCATAAGT
* *
3629589 GAACTCGGACTCAACTCAACGAGATCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGATCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
3629654 CGAGCTCGGATGCCTAGTTACATCTCTC
66 CGAGCTCGGATGCCTAGTTACATCTCTC
* *
3629682 GAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGATCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
3629747 CGAGTTCGGATGC
66 CGAGCTCGGATGC
3629760 TCAACCATCC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGATCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCTC
Found at i:3629756 original size:46 final size:46
Alignment explanation
Indices: 3629581--3629756 Score: 207
Period size: 46 Copynumber: 3.8 Consensus size: 46
3629571 TGTAACCCGC
* * * *
3629581 CCATAAGTGAACTCGGACTCAACTCAACGAGATCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
* * *
3629627 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-ATTTGCAT
*
3629677 CTC-T---CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
1 C-CATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
3629720 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
3629757 TGCTCAACCA
Statistics
Matches: 110, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
42 1 0.01
43 8 0.07
44 1 0.01
46 64 0.58
47 28 0.25
49 1 0.01
50 6 0.05
51 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
Found at i:3631479 original size:46 final size:46
Alignment explanation
Indices: 3631345--3631564 Score: 155
Period size: 46 Copynumber: 4.7 Consensus size: 46
3631335 GCATATCTGT
* * *
3631345 GCCGATGCCATGTCCCAGACATGGTCTTACACT-G-ACACATCTC-ATA
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTAGCACTCGTCTCGA-G
** *
3631391 GCTAATGCATGTCCCAGACATGTCTTACACTGGCTTA-T-GTCTCGAG
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGC--ACTCGTCTCGAG
* * *
3631437 GCCGATGCATGTCCTAGACATGTCTTACACTAGCACTCGTCTCAAT
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGCACTCGTCTCGAG
* * * * * * * *
3631483 GCCGATGTCATGTCTCAGGCACGGTCTTACACTGGCTCTCATAAT-GTG
1 GCCGATG-CATGTCCCAGACA-TGTCTTACACTAGCACTCGT-CTCGAG
* *
3631531 GCTGATGCATGTCCCAGTCATGTCTTACACTAGC
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGC
3631565 TCACACAAGT
Statistics
Matches: 137, Mismatches: 27, Indels: 20
0.74 0.15 0.11
Matches are distributed among these distances:
44 11 0.08
45 16 0.12
46 64 0.47
47 22 0.16
48 23 0.17
49 1 0.01
ACGTcount: A:0.22, C:0.29, G:0.20, T:0.28
Consensus pattern (46 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTAGCACTCGTCTCGAG
Found at i:3631511 original size:94 final size:92
Alignment explanation
Indices: 3631345--3631569 Score: 226
Period size: 94 Copynumber: 2.4 Consensus size: 92
3631335 GCATATCTGT
*
3631345 GCCGATGCCATGTCCCAGACATGGTCTTACACT-G-ACACATCTCATAGCTAATGCATGTCCCAG
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTAGCACACATCTCATAGCCAATGCATGTCCCAG
* **
3631408 ACATGTCTTACACTGGCT-T-ATGTCTCGAG
64 ACAGGTCTTACACTGGCTCTCAT-AAT-GAG
* * * * *
3631437 GCCGATGCATGTCCTAGACATGTCTTACACTAGCACTCGTCTCA-ATGCCGATGTCATGTCTCAG
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGCACACATCTCATA-GCCAATG-CATGTCCCAG
* *
3631501 GCACGGTCTTACACTGGCTCTCATAATGTG
64 ACA-GGTCTTACACTGGCTCTCATAATGAG
* * *
3631531 GCTGATGCATGTCCCAGTCATGTCTTACACTAGCTCACA
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGCACACA
3631570 CAAGTGACCC
Statistics
Matches: 109, Mismatches: 17, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
90 10 0.09
91 15 0.14
92 20 0.18
93 11 0.10
94 49 0.45
95 2 0.02
96 2 0.02
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.28
Consensus pattern (92 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTAGCACACATCTCATAGCCAATGCATGTCCCAGAC
AGGTCTTACACTGGCTCTCATAATGAG
Found at i:3634314 original size:67 final size:67
Alignment explanation
Indices: 3634197--3634380 Score: 226
Period size: 67 Copynumber: 2.7 Consensus size: 67
3634187 GTGGGCTGTA
* *
3634197 ATAGGGTATAATGTGTAAGACCATAGCTCGATTATGACAACACAGAGAGTTTGCCAAGACT-TTA
1 ATAGGGTATAATGTGTAAGACCATAGCTCGATTATGACAACATAGAGAGTTCGCCAAGA-TGTTA
3634261 AAC
65 AAC
* * * * **
3634264 ATGGGGTATAATGTGTAAGACCATAGGTCGATTATGACAACATAGGGAGTTCGTCTGGATGTTAA
1 ATAGGGTATAATGTGTAAGACCATAGCTCGATTATGACAACATAGAGAGTTCGCCAAGATGTTAA
*
3634329 AT
66 AC
* * * * *
3634331 ATAAGGTATAACGTGTAAGACCATAGCTCGACTATGACAGCATATAGAGT
1 ATAGGGTATAATGTGTAAGACCATAGCTCGATTATGACAACATAGAGAGT
3634381 CCACAAAGAC
Statistics
Matches: 99, Mismatches: 17, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
66 1 0.01
67 98 0.99
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (67 bp):
ATAGGGTATAATGTGTAAGACCATAGCTCGATTATGACAACATAGAGAGTTCGCCAAGATGTTAA
AC
Found at i:3637559 original size:23 final size:23
Alignment explanation
Indices: 3637515--3637573 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
3637505 TACAGAACGT
*
3637515 GCCACAAAGGCATCACGAAATAC
1 GCCACAAAGGCATCAAGAAATAC
* *
3637538 GCCACAAAGGCATTATAG-AATAT
1 GCCACAAAGGCATCA-AGAAATAC
*
3637561 GCCATAAAGGCAT
1 GCCACAAAGGCAT
3637574 AAAAAAGTTG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
23 30 0.97
24 1 0.03
ACGTcount: A:0.42, C:0.24, G:0.19, T:0.15
Consensus pattern (23 bp):
GCCACAAAGGCATCAAGAAATAC
Found at i:3641333 original size:15 final size:16
Alignment explanation
Indices: 3641313--3641352 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
3641303 GTCTTAAGAA
3641313 AAAAATAAATA-AAAT
1 AAAAATAAATAGAAAT
*
3641328 AAAAATAAAAAGAAAT
1 AAAAATAAATAGAAAT
3641344 -AAAATAAAT
1 AAAAATAAAT
3641353 GGACTCAGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 18 0.82
16 4 0.18
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (16 bp):
AAAAATAAATAGAAAT
Found at i:3643060 original size:18 final size:18
Alignment explanation
Indices: 3643037--3643071 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3643027 TAATGAAGAA
*
3643037 AAATAATTAAAAATAAAT
1 AAATAAATAAAAATAAAT
*
3643055 AAATAAATAAATATAAA
1 AAATAAATAAAAATAAA
3643072 GGGTAAAAGG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (18 bp):
AAATAAATAAAAATAAAT
Found at i:3650523 original size:35 final size:36
Alignment explanation
Indices: 3650473--3650567 Score: 115
Period size: 35 Copynumber: 2.7 Consensus size: 36
3650463 ATTTGTTAAT
*
3650473 ATTCTGATTCGCATGTTAATCATGCT-ATTATTCTG
1 ATTCTGATTTGCATGTTAATCATGCTCATTATTCTG
* * *
3650508 ATTTTGATTTGCATGTTAATCATG-TCGTTATTTTG
1 ATTCTGATTTGCATGTTAATCATGCTCATTATTCTG
*
3650543 ATTCTGATTCT-CATGTTAAGCATGC
1 ATTCTGATT-TGCATGTTAATCATGC
3650568 CACTGTATTA
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
34 1 0.02
35 49 0.96
36 1 0.02
ACGTcount: A:0.22, C:0.15, G:0.16, T:0.47
Consensus pattern (36 bp):
ATTCTGATTTGCATGTTAATCATGCTCATTATTCTG
Found at i:3664740 original size:12 final size:11
Alignment explanation
Indices: 3664702--3664750 Score: 66
Period size: 11 Copynumber: 4.5 Consensus size: 11
3664692 TATATATAAA
3664702 TTTTATTATA-
1 TTTTATTATAT
*
3664712 TGTTA-TATAT
1 TTTTATTATAT
3664722 TTTTATTATAT
1 TTTTATTATAT
3664733 TATTTATTATAT
1 T-TTTATTATAT
3664745 TTTTAT
1 TTTTAT
3664751 ATGTAAAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
9 4 0.12
10 8 0.24
11 11 0.32
12 11 0.32
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (11 bp):
TTTTATTATAT
Found at i:3664740 original size:18 final size:19
Alignment explanation
Indices: 3664702--3664740 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
3664692 TATATATAAA
3664702 TTTTATTATATGTTATATAT
1 TTTTATTATA-GTTATATAT
*
3664722 TTTTATTATA-TTATTTAT
1 TTTTATTATAGTTATATAT
3664740 T
1 T
3664741 ATATTTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 8 0.44
20 10 0.56
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (19 bp):
TTTTATTATAGTTATATAT
Found at i:3664762 original size:40 final size:42
Alignment explanation
Indices: 3664707--3664786 Score: 103
Period size: 40 Copynumber: 1.9 Consensus size: 42
3664697 ATAAATTTTA
* *
3664707 TTATATGTTATATATTT-TT-ATTA-TATTATTTATTATATTT
1 TTATATGTAAAATATTTGTTAATTATTATTA-TTATTATATTT
3664747 TTATATGTAAAATATTTGTTACATTATTATTATTATTATA
1 TTATATGTAAAATATTTGTTA-ATTATTATTATTATTATA
3664787 CTACATATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
40 15 0.44
41 2 0.06
43 12 0.35
44 5 0.15
ACGTcount: A:0.34, C:0.01, G:0.04, T:0.61
Consensus pattern (42 bp):
TTATATGTAAAATATTTGTTAATTATTATTATTATTATATTT
Found at i:3668787 original size:105 final size:105
Alignment explanation
Indices: 3668605--3668873 Score: 466
Period size: 105 Copynumber: 2.6 Consensus size: 105
3668595 TAACCGTTAT
* * **
3668605 TGGTGGATCTCGCACTTAGCACCACCGCTGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 TGGTGGATCACGCACATAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
3668670 AATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATA
66 AATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATA
*
3668710 TGGTGGATCACGCACATAGCACCACTAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 TGGTGGATCACGCACATAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
*
3668775 AATCAGCACATAGCAACCCCCTTTTTACATTTCAAAGATA
66 AATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATA
**
3668815 TGGTGGATCACGCACATAGCACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCT
1 TGGTGGATCACGCACATAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCT
3668874 TTATATACAA
Statistics
Matches: 155, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
105 155 1.00
ACGTcount: A:0.30, C:0.30, G:0.21, T:0.19
Consensus pattern (105 bp):
TGGTGGATCACGCACATAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
AATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATA
Found at i:3669234 original size:29 final size:29
Alignment explanation
Indices: 3669201--3669264 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
3669191 TAATCCACCA
3669201 CCCAACTTTTTG-AAAATTACAATTTTGCC
1 CCCAAC-TTTTGCAAAATTACAATTTTGCC
* * *
3669230 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGCAAAATTACAATTTTGCC
3669260 CCCAA
1 CCCAA
3669265 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (29 bp):
CCCAACTTTTGCAAAATTACAATTTTGCC
Found at i:3669238 original size:30 final size:30
Alignment explanation
Indices: 3669208--3669264 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
3669198 CCACCCAACT
3669208 TTTTG-AAAATTACAATTTTGCCCCCAAAC
1 TTTTGCAAAATTACAATTTTGCCCCCAAAC
* * *
3669237 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGCAAAATTACAATTTTGCCCCCAA
3669265 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTGCCCCCAAAC
Found at i:3671304 original size:12 final size:12
Alignment explanation
Indices: 3671287--3671312 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3671277 ATTAGGGCGA
3671287 AAGCGTATTTGT
1 AAGCGTATTTGT
3671299 AAGCGTATTTGT
1 AAGCGTATTTGT
3671311 AA
1 AA
3671313 TCCTCTTATA
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:0.31, C:0.08, G:0.23, T:0.38
Consensus pattern (12 bp):
AAGCGTATTTGT
Found at i:3671419 original size:16 final size:14
Alignment explanation
Indices: 3671390--3671439 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 14
3671380 TTTCCTTTTG
3671390 GCATTCATGCATTT
1 GCATTCATGCATTT
3671404 GCATTACATAGCATTT
1 GCATT-CAT-GCATTT
*
3671420 -CATCGCAT-CATTT
1 GCAT-TCATGCATTT
3671433 GCATTCA
1 GCATTCA
3671440 AAGTTATAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
13 7 0.23
14 8 0.27
15 9 0.30
16 6 0.20
ACGTcount: A:0.26, C:0.24, G:0.12, T:0.38
Consensus pattern (14 bp):
GCATTCATGCATTT
Found at i:3679686 original size:88 final size:85
Alignment explanation
Indices: 3679577--3680065 Score: 272
Period size: 88 Copynumber: 5.6 Consensus size: 85
3679567 CAAATCGAAG
* * *
3679577 ACATAGCAGATCTAACTTTCAGATGTTT-TCACATCAAAGCAGATCCAAGATAACAAATCTGCCA
1 ACATAGCAGATCTAACCTTCAGATGTTTAT-AC-T-AAAGCAGATCCAAGATAACAGATCTGGCA
3679641 TCTCCATTTCGACGGAGAGCAGGT
63 TCTCCATTTC-ACGGAGAGCAGGT
* * * *
3679665 ACATAGTAGGTCTAACCTTCAGGTGTTTATACTAAAGCAGATCCAAGAT----GATTTGGGCATT
1 ACATAGCAGATCTAACCTTCAGATGTTTATACTAAAGCAGATCCAAGATAACAGATCT-GGCA-T
*** *
3679726 CTTGTGTTTACAAGGA-A-CAAATTGAAG-
64 C-TCCATTT-CACGGAGAGC--A--G--GT
* *
3679753 ACATAGCAGATCTGACTTTCAGATGTTT-TCACATCAAAGCAGATCCAAGATAACAGATCTGGCA
1 ACATAGCAGATCTAACCTTCAGATGTTTAT-AC-T-AAAGCAGATCCAAGATAACAGATCTGGCA
3679817 TCTCCATTTCAACGGAGAGCAGGT
63 TCTCCATTTC-ACGGAGAGCAGGT
* * * *
3679841 ACATAGCAGGTCTAACCTTCAGGTGTTTATACTGAAGCAGATCCAAGAT----GATTTGGGCATT
1 ACATAGCAGATCTAACCTTCAGATGTTTATACTAAAGCAGATCCAAGATAACAGATCT-GGCA-T
*** * * * *
3679902 CTTGTGTTTACAAGGAACAAATCGAAG-
64 C-TCCATTT-CACGG---AGAGC-AGGT
* * * * *
3679929 ACATAGCAGATTTCACTTTC-GAATGTTCTCACACCAAAGCAGATCCAAGATAACAGATCTGGCA
1 ACATAGCAGATCTAACCTTCAG-ATGTT-T-ATACTAAAGCAGATCCAAGATAACAGATCTGGCA
* * **
3679993 TCTTCATTTCGACAGAGAGCATAT
63 TCTCCATTTC-ACGGAGAGCAGGT
* *
3680017 ACATAGCAGATCTAACCTTCAGATAATTTA-ACTGAAGCAGATCCAAGAT
1 ACATAGCAGATCTAACCTTCAGAT-GTTTATACTAAAGCAGATCCAAGAT
3680066 GATTTGACAT
Statistics
Matches: 301, Mismatches: 58, Indels: 86
0.68 0.13 0.19
Matches are distributed among these distances:
82 7 0.02
83 8 0.03
84 5 0.02
85 16 0.05
86 50 0.17
87 8 0.03
88 123 0.41
89 11 0.04
90 36 0.12
91 15 0.05
92 5 0.02
93 9 0.03
94 8 0.03
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.27
Consensus pattern (85 bp):
ACATAGCAGATCTAACCTTCAGATGTTTATACTAAAGCAGATCCAAGATAACAGATCTGGCATCT
CCATTTCACGGAGAGCAGGT
Found at i:3679805 original size:176 final size:176
Alignment explanation
Indices: 3679567--3680152 Score: 864
Period size: 176 Copynumber: 3.3 Consensus size: 176
3679557 CGACGAGAAG
*
3679567 CAAATCGAAGACATAGCAGATCTAACTTTCAGATGTTTTCACATCAAAGCAGATCCAAGATAACA
1 CAAATCGAAGACATAGCAGATCTGACTTTCAGATGTTTTCACATCAAAGCAGATCCAAGATAACA
* * *
3679632 AATCTGCCATCTCCATTTCGACGGAGAGCAGGTACATAGTAGGTCTAACCTTCAGGTGTTTATAC
66 GATCTGGCATCTCCATTTCGACGGAGAGCAGGTACATAGCAGGTCTAACCTTCAGGTGTTTATAC
*
3679697 TAAAGCAGATCCAAGATGATTTGGGCATTCTTGTGTTTACAAGGAA
131 TGAAGCAGATCCAAGATGATTTGGGCATTCTTGTGTTTACAAGGAA
*
3679743 CAAATTGAAGACATAGCAGATCTGACTTTCAGATGTTTTCACATCAAAGCAGATCCAAGATAACA
1 CAAATCGAAGACATAGCAGATCTGACTTTCAGATGTTTTCACATCAAAGCAGATCCAAGATAACA
*
3679808 GATCTGGCATCTCCATTTCAACGGAGAGCAGGTACATAGCAGGTCTAACCTTCAGGTGTTTATAC
66 GATCTGGCATCTCCATTTCGACGGAGAGCAGGTACATAGCAGGTCTAACCTTCAGGTGTTTATAC
3679873 TGAAGCAGATCCAAGATGATTTGGGCATTCTTGTGTTTACAAGGAA
131 TGAAGCAGATCCAAGATGATTTGGGCATTCTTGTGTTTACAAGGAA
* * * *
3679919 CAAATCGAAGACATAGCAGATTTCACTTTC-GAATGTTCTCACACCAAAGCAGATCCAAGATAAC
1 CAAATCGAAGACATAGCAGATCTGACTTTCAG-ATGTTTTCACATCAAAGCAGATCCAAGATAAC
* * ** * * *
3679983 AGATCTGGCATCTTCATTTCGACAGAGAGCATATACATAGCAGATCTAACCTTCAGATAATTTA-
65 AGATCTGGCATCTCCATTTCGACGGAGAGCAGGTACATAGCAGGTCTAACCTTCAGGT-GTTTAT
* *
3680047 ACTGAAGCAGATCCAAGATGATTT-GACATCCTTGTGTTTACAA-GAA
129 ACTGAAGCAGATCCAAGATGATTTGGGCATTCTTGTGTTTACAAGGAA
* * *
3680093 GCAAATCAAAGACATAGCAGGTCTGACCTTT-AGATGTTTAT-AC-T-GAAGCAGATCCAAGAT
1 -CAAATCGAAGACATAGCAGATCTGA-CTTTCAGATGTTT-TCACATCAAAGCAGATCCAAGAT
3680153 GATTTGGCAT
Statistics
Matches: 375, Mismatches: 29, Indels: 15
0.89 0.07 0.04
Matches are distributed among these distances:
173 15 0.04
174 3 0.01
175 46 0.12
176 307 0.82
177 4 0.01
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.27
Consensus pattern (176 bp):
CAAATCGAAGACATAGCAGATCTGACTTTCAGATGTTTTCACATCAAAGCAGATCCAAGATAACA
GATCTGGCATCTCCATTTCGACGGAGAGCAGGTACATAGCAGGTCTAACCTTCAGGTGTTTATAC
TGAAGCAGATCCAAGATGATTTGGGCATTCTTGTGTTTACAAGGAA
Found at i:3680138 original size:87 final size:88
Alignment explanation
Indices: 3679665--3680250 Score: 383
Period size: 87 Copynumber: 6.7 Consensus size: 88
3679655 GAGAGCAGGT
* * * * * *
3679665 ACATAGTAGGTCTAACCTTCAGGTGTTTATACTAAAGCAGATCCAAGATGATTTGGGCATTCTTG
1 ACATAGCAGATCTAACCTTTAGATGTTTATACTGAAGCAGATCCAAGATGATTT-GGCATCCTTG
**
3679730 TGTTTACAAGGAA-CAAATTGAAG
65 TGTTTACAAGGAAGCAAATCAAAG
* * *
3679753 ACATAGCAGATCTGA-CTTTCAGATGTTT-TCACATCAAAGCAGATCCAAGATAACAGATCTGGC
1 ACATAGCAGATCTAACCTTT-AGATGTTTAT-AC-T-GAAGCAGATCCAAGAT----GATTTGGC
*** * *
3679816 AT-C-TCCATTT-CAACGG-AG---AGC-AGG
58 ATCCTTGTGTTTACAA-GGAAGCAAATCAAAG
* * * *
3679840 TACATAGCAGGTCTAACCTTCAGGTGTTTATACTGAAGCAGATCCAAGATGATTTGGGCATTCTT
1 -ACATAGCAGATCTAACCTTTAGATGTTTATACTGAAGCAGATCCAAGATGATTT-GGCATCCTT
*
3679905 GTGTTTACAAGGAA-CAAATCGAAG
64 GTGTTTACAAGGAAGCAAATCAAAG
* * * * ** *
3679929 ACATAGCAGATTTCA-CTTTCGAATGTTCTCACACCAAAGCAGATCCAAGATAACAGATCTGGCA
1 ACATAGCAGATCTAACCTTTAG-ATGTT-T-ATACTGAAGCAGATCCAAGAT----GATTTGGCA
** * * * *
3679993 T-CTT-CATTT-C---GACAG-AGAGCATAT
59 TCCTTGTGTTTACAAGGA-AGCAAATCAAAG
* * *
3680017 ACATAGCAGATCTAACCTTCAGATAATTTA-ACTGAAGCAGATCCAAGATGATTTGACATCCTTG
1 ACATAGCAGATCTAACCTTTAGAT-GTTTATACTGAAGCAGATCCAAGATGATTTGGCATCCTTG
3680081 TGTTTACAA-GAAGCAAATCAAAG
65 TGTTTACAAGGAAGCAAATCAAAG
* *
3680104 ACATAGCAGGTCTGACCTTTAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGCATCCTTGT
1 ACATAGCAGATCTAACCTTTAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGCATCCTTGT
3680169 GTTTACAAGG-AGCAAATCAAAG
66 GTTTACAAGGAAGCAAATCAAAG
*** * ** * *
3680191 ACATAGCAGAT-TTGGCTTTCAGGTGTTTACGCTGAAGCAAATCTAAGATGATTTGGCATC
1 ACATAGCAGATCTAACCTTT-AGATGTTTATACTGAAGCAGATCCAAGATGATTTGGCATC
3680251 TCTGTATTGT
Statistics
Matches: 387, Mismatches: 69, Indels: 85
0.72 0.13 0.16
Matches are distributed among these distances:
82 12 0.03
83 8 0.02
84 4 0.01
85 7 0.02
86 47 0.12
87 141 0.36
88 84 0.22
89 14 0.04
90 39 0.10
91 9 0.02
92 4 0.01
93 10 0.03
94 8 0.02
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (88 bp):
ACATAGCAGATCTAACCTTTAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGCATCCTTGT
GTTTACAAGGAAGCAAATCAAAG
Found at i:3681802 original size:12 final size:11
Alignment explanation
Indices: 3681779--3681812 Score: 59
Period size: 11 Copynumber: 3.0 Consensus size: 11
3681769 TTATATGTTA
3681779 TATATTTTTAT
1 TATATTTTTAT
3681790 TATATTATTTAT
1 TATATT-TTTAT
3681802 TATATTTTTAT
1 TATATTTTTAT
3681813 ATGTAAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 11 0.50
12 11 0.50
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
TATATTTTTAT
Found at i:3682681 original size:35 final size:35
Alignment explanation
Indices: 3682635--3682706 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
3682625 TCATTTTGAG
*
3682635 ATAGGGATTTTCAAAAAGGGCTAGCTTAGCTTCGA
1 ATAGGGATTTTCAAAAAGGGCTAGCTTAGCATCGA
3682670 ATAGGGATTTTCAAAAAGGGCTAGCTTAGCATCGA
1 ATAGGGATTTTCAAAAAGGGCTAGCTTAGCATCGA
3682705 AT
1 AT
3682707 GTCTTAAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.33, C:0.14, G:0.25, T:0.28
Consensus pattern (35 bp):
ATAGGGATTTTCAAAAAGGGCTAGCTTAGCATCGA
Found at i:3686604 original size:15 final size:17
Alignment explanation
Indices: 3686571--3686607 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
3686561 GGGTCAAGAT
*
3686571 AAAAATATCAAAAGTCA
1 AAAAATATCAAAAGACA
3686588 AAAAATAT-AAAA-ACA
1 AAAAATATCAAAAGACA
3686603 AAAAA
1 AAAAA
3686608 ATGACTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 7 0.37
16 4 0.21
17 8 0.42
ACGTcount: A:0.76, C:0.08, G:0.03, T:0.14
Consensus pattern (17 bp):
AAAAATATCAAAAGACA
Found at i:3687809 original size:41 final size:41
Alignment explanation
Indices: 3687705--3687823 Score: 175
Period size: 42 Copynumber: 2.9 Consensus size: 41
3687695 ATTTTTTAGA
* * * *
3687705 AAAAAACGCCGCTAAAGACCACGATCTTTAGCGGCGTTTTT
1 AAAAAACGCCGCTAAAGACCAGGACCTTTAGCGGCGCTCTT
**
3687746 ATAAACGCGCCGCTAAAGACCAGGACCTTTAGCGGCGCTCTT
1 A-AAAAACGCCGCTAAAGACCAGGACCTTTAGCGGCGCTCTT
3687788 AAAAAACGCCGCTAAAGACCAGGACCTTTAGCGGCG
1 AAAAAACGCCGCTAAAGACCAGGACCTTTAGCGGCG
3687824 TTTTTTATAA
Statistics
Matches: 69, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
41 34 0.49
42 35 0.51
ACGTcount: A:0.31, C:0.28, G:0.23, T:0.18
Consensus pattern (41 bp):
AAAAAACGCCGCTAAAGACCAGGACCTTTAGCGGCGCTCTT
Found at i:3687863 original size:43 final size:43
Alignment explanation
Indices: 3687816--3687937 Score: 154
Period size: 43 Copynumber: 2.7 Consensus size: 43
3687806 CCAGGACCTT
* *
3687816 TAGCGGCGTTTTTTATAAAAGCGCCGCTAATGTTCTTGGTGTA
1 TAGCGGCGTTTTTTATAAAAGCGCCGCTAATATTCTTGGTCTA
* *
3687859 TAGCGGCATTTTTTATAAATGCGCCGCTAATATTCTTGGTCTA
1 TAGCGGCGTTTTTTATAAAAGCGCCGCTAATATTCTTGGTCTA
3687902 TAGCGGCGTCGGCGTTTTTTATAAAAGCGCCGCTAA
1 TA-----G-CGGCGTTTTTTATAAAAGCGCCGCTAA
3687938 AGACCAGGAC
Statistics
Matches: 67, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
43 41 0.61
48 1 0.01
49 25 0.37
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.35
Consensus pattern (43 bp):
TAGCGGCGTTTTTTATAAAAGCGCCGCTAATATTCTTGGTCTA
Found at i:3687972 original size:43 final size:43
Alignment explanation
Indices: 3687918--3688154 Score: 221
Period size: 43 Copynumber: 5.5 Consensus size: 43
3687908 CGTCGGCGTT
* * *
3687918 TTTTAT-AAAAGCGCCGCTAAAGACCAGGACCTTTAGCGGCGC
1 TTTTATAAAAAACGCCGCTAAAGACCAAGAACTTTAGCGGCGC
* * *
3687960 TTTTATAAAAAGCGCCGCTATACACCAAGAACTTTAGCGGCGC
1 TTTTATAAAAAACGCCGCTAAAGACCAAGAACTTTAGCGGCGC
* * * * ** *
3688003 TTTTATAAAAAAAGCCGCTACAGGTCC-TGGTCTTTGGCGGCG-
1 TTTTATAAAAAACGCCGCTA-AAGACCAAGAACTTTAGCGGCGC
* * *
3688045 TTTTGTACAAAAGCGCCGCTATAGACCAAGAACTTTAGC-GCGC
1 TTTTATA-AAAAACGCCGCTAAAGACCAAGAACTTTAGCGGCGC
* * *
3688088 TTTAATAAAAAAAACGCCGCTATAGACCAAGAACATTAGCGGCGC
1 TTT--TATAAAAAACGCCGCTAAAGACCAAGAACTTTAGCGGCGC
*
3688133 TTTTTTAAAAAAACGCCGCTAA
1 TTTTAT-AAAAAACGCCGCTAA
3688155 TTTGCCTAGT
Statistics
Matches: 155, Mismatches: 31, Indels: 16
0.77 0.15 0.08
Matches are distributed among these distances:
42 18 0.12
43 83 0.54
44 45 0.29
45 9 0.06
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (43 bp):
TTTTATAAAAAACGCCGCTAAAGACCAAGAACTTTAGCGGCGC
Done.