Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A11
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: 114316535
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4920000 characters in sequence are not A, C, G, or T
File 162 of 356
Found at i:52441075 original size:40 final size:40
Alignment explanation
Indices: 52440932--52441115 Score: 205
Period size: 40 Copynumber: 4.6 Consensus size: 40
52440922 TAACTCATAC
* *
52440932 AATGCCTTCGGGACTTAACCCGGATTTTAA-AACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACA
* *
52440972 AATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
*
52441012 AAGGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
** * * *
52441052 AATGCCTTC-GGATCTTAGTCCGG-ATATAGTCACTTAGCACA
1 AATGCCTTCGGGA-CTTAACCCGGAAT-TAATAAC-TCGCACA
*
52441093 AA-GCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
52441116 CAGCATTCAA
Statistics
Matches: 124, Mismatches: 14, Indels: 11
0.83 0.09 0.07
Matches are distributed among these distances:
39 8 0.06
40 105 0.85
41 11 0.09
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
Found at i:52448861 original size:39 final size:39
Alignment explanation
Indices: 52448808--52448985 Score: 130
Period size: 40 Copynumber: 4.5 Consensus size: 39
52448798 GATATAGCTC
* * * *
52448808 CTCATTCAAGTGCCTTCGGGACATAGCCCGG-TTATAGTAA
1 CTCATACAA-TGCCTTCGGGACTTAACCCGGATTATA-AAA
*
52448848 CTCATACAATGCCTTCGGGACTTAACCCGGATTTTAAAA
1 CTCATACAATGCCTTCGGGACTTAACCCGGATTATAAAA
** *
52448887 CTCGCACGAATGCCTTCGGGACTTAACCCGGAATTAGT--AT
1 CTCATAC-AATGCCTTCGGGACTTAACCCGG-ATTA-TAAAA
** * *
52448927 CTCGCACAAAGGCCTTCGGGACTTAACCCGGAATTA-ATAA
1 CTCATAC-AATGCCTTCGGGACTTAACCCGG-ATTATAAAA
**
52448967 CTCGCACAAATGCCTTCGG
1 CTCATAC-AATGCCTTCGG
52448986 ATCTTAGTCC
Statistics
Matches: 119, Mismatches: 13, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
39 26 0.22
40 89 0.75
41 3 0.03
42 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.25
Consensus pattern (39 bp):
CTCATACAATGCCTTCGGGACTTAACCCGGATTATAAAA
Found at i:52448969 original size:80 final size:80
Alignment explanation
Indices: 52448853--52449038 Score: 229
Period size: 80 Copynumber: 2.3 Consensus size: 80
52448843 AGTAACTCAT
* * *
52448853 ACAATGCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACGAATGCCTTCGGGA-CTTAACCCG
1 ACAAAGCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATGCCTTC-GGATCTTAACCCG
*
52448917 GA-ATTAGT-A-TCTCGC
65 GATA-TAGTCACT-TAGC
**
52448932 ACAAAGGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACAAATGCCTTCGGATCTTAGTCC
1 ACAAA-GCCTTCGGGACTTAACCCGGATATTAA-AACTCGCACAAATGCCTTCGGATCTTAACCC
52448996 GGATATAGTCACTTAGC
64 GGATATAGTCACTTAGC
*
52449013 ACAAAGCCTTCGGGACTTAGCCCGGA
1 ACAAAGCCTTCGGGACTTAACCCGGA
52449039 CAGCATTCAA
Statistics
Matches: 94, Mismatches: 7, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
79 11 0.12
80 72 0.77
81 10 0.11
82 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (80 bp):
ACAAAGCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATGCCTTCGGATCTTAACCCGG
ATATAGTCACTTAGC
Found at i:52448998 original size:40 final size:40
Alignment explanation
Indices: 52448855--52449038 Score: 205
Period size: 40 Copynumber: 4.6 Consensus size: 40
52448845 TAACTCATAC
* *
52448855 AATGCCTTCGGGACTTAACCCGGATTTTAA-AACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACA
* *
52448895 AATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
*
52448935 AAGGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
** * * *
52448975 AATGCCTTC-GGATCTTAGTCCGG-ATATAGTCACTTAGCACA
1 AATGCCTTCGGGA-CTTAACCCGGAAT-TAATAAC-TCGCACA
*
52449016 AA-GCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
52449039 CAGCATTCAA
Statistics
Matches: 124, Mismatches: 14, Indels: 11
0.83 0.09 0.07
Matches are distributed among these distances:
39 8 0.06
40 105 0.85
41 11 0.09
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
Found at i:52453402 original size:35 final size:35
Alignment explanation
Indices: 52453356--52453428 Score: 128
Period size: 35 Copynumber: 2.1 Consensus size: 35
52453346 TTTCCGAAGA
*
52453356 TTATTCATGCTTTAAGCATTCGCACACTTAGTACT
1 TTATTCATGCTTTAAGCATCCGCACACTTAGTACT
*
52453391 TTATTCATGCTTTAAGCATCCGCACGCTTAGTACT
1 TTATTCATGCTTTAAGCATCCGCACACTTAGTACT
52453426 TTA
1 TTA
52453429 AGGCTTAGCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.25, C:0.23, G:0.12, T:0.40
Consensus pattern (35 bp):
TTATTCATGCTTTAAGCATCCGCACACTTAGTACT
Found at i:52460328 original size:9 final size:9
Alignment explanation
Indices: 52460314--52460340 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
52460304 GCTATTCATG
52460314 AATACATCA
1 AATACATCA
52460323 AATACATCA
1 AATACATCA
52460332 AATACATCA
1 AATACATCA
52460341 TCTTGGATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.56, C:0.22, G:0.00, T:0.22
Consensus pattern (9 bp):
AATACATCA
Found at i:52462223 original size:24 final size:24
Alignment explanation
Indices: 52462196--52462265 Score: 64
Period size: 24 Copynumber: 3.2 Consensus size: 24
52462186 TTTTTATCAT
52462196 CTTTTAATTAATTAAATATTTTCA
1 CTTTTAATTAATTAAATATTTTCA
* *
52462220 CTTTTCA-T--TT---T-TTATCAA
1 CTTTTAATTAATTAAATATTTTC-A
52462238 CTTTTAATTAATTAAATATTTTCA
1 CTTTTAATTAATTAAATATTTTCA
52462262 CTTT
1 CTTT
52462266 CCAATTTAGT
Statistics
Matches: 34, Mismatches: 4, Indels: 16
0.63 0.07 0.30
Matches are distributed among these distances:
17 4 0.12
18 8 0.24
19 1 0.03
21 4 0.12
23 1 0.03
24 12 0.35
25 4 0.12
ACGTcount: A:0.31, C:0.11, G:0.00, T:0.57
Consensus pattern (24 bp):
CTTTTAATTAATTAAATATTTTCA
Found at i:52462242 original size:42 final size:42
Alignment explanation
Indices: 52462180--52462265 Score: 163
Period size: 42 Copynumber: 2.0 Consensus size: 42
52462170 GAAAATGATA
*
52462180 TTTCATTTTTTATCATCTTTTAATTAATTAAATATTTTCACT
1 TTTCATTTTTTATCAACTTTTAATTAATTAAATATTTTCACT
52462222 TTTCATTTTTTATCAACTTTTAATTAATTAAATATTTTCACT
1 TTTCATTTTTTATCAACTTTTAATTAATTAAATATTTTCACT
52462264 TT
1 TT
52462266 CCAATTTAGT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.29, C:0.12, G:0.00, T:0.59
Consensus pattern (42 bp):
TTTCATTTTTTATCAACTTTTAATTAATTAAATATTTTCACT
Found at i:52469457 original size:27 final size:27
Alignment explanation
Indices: 52469416--52469469 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
52469406 TGTCATGTGA
* *
52469416 AATTGAATGGCAAATTATTGTTACATG
1 AATTGAATGGCAAATTACTATTACATG
**
52469443 AATTGAATGTTAAATTACTATTACATG
1 AATTGAATGGCAAATTACTATTACATG
52469470 GGTTGTACCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.39, C:0.07, G:0.15, T:0.39
Consensus pattern (27 bp):
AATTGAATGGCAAATTACTATTACATG
Found at i:52469791 original size:49 final size:49
Alignment explanation
Indices: 52469702--52469940 Score: 232
Period size: 49 Copynumber: 4.8 Consensus size: 49
52469692 GTGAGGTCAC
* * *
52469702 GTGTGTAGTACTAAGTGCAGGCTGCTACGTGTACCGGATAATTGGTTGCA
1 GTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAATTGGTT-CA
* * * * * *
52469752 -TGTGTAGTACGAAGTGCAGGCTACTATGCGCACCCGATAACTTCGATCA
1 GTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAA-TTGGTTCA
* * * **
52469801 CGTGTGTAGTACTAAGTCCAGGCTACTACGTGTATCAGATGGTTAGG-TCAA
1 -GTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAATT-GGTTC-A
* * * *
52469852 GCGTGTAGTACTAAGTGTAGGCTACTATGTGTACCGGATAATTGGTCGCA
1 GTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAATTGGT-TCA
*
52469902 -TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATA
1 GTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATA
52469941 GCCTTGTCTG
Statistics
Matches: 151, Mismatches: 31, Indels: 15
0.77 0.16 0.08
Matches are distributed among these distances:
49 73 0.48
50 44 0.29
51 34 0.23
ACGTcount: A:0.25, C:0.18, G:0.28, T:0.28
Consensus pattern (49 bp):
GTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAATTGGTTCA
Found at i:52473182 original size:31 final size:31
Alignment explanation
Indices: 52473144--52473203 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
52473134 CCTTTTCATA
52473144 TTTCATATTTCATAACACTGGGCCGAAGCTT
1 TTTCATATTTCATAACACTGGGCCGAAGCTT
**
52473175 TTTCATATTTCATATTACTGGGCCGAAGC
1 TTTCATATTTCATAACACTGGGCCGAAGC
52473204 CTTTACTGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.25, C:0.22, G:0.17, T:0.37
Consensus pattern (31 bp):
TTTCATATTTCATAACACTGGGCCGAAGCTT
Found at i:52473468 original size:23 final size:24
Alignment explanation
Indices: 52473401--52473494 Score: 122
Period size: 23 Copynumber: 4.0 Consensus size: 24
52473391 GCTTTATCAT
*
52473401 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
* *
52473426 ATAACTGGGGCAAAATCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
52473450 ATAACT-GGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
52473472 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
52473495 TCACTTCCTC
Statistics
Matches: 61, Mismatches: 5, Indels: 7
0.84 0.07 0.10
Matches are distributed among these distances:
22 10 0.16
23 22 0.36
24 18 0.30
25 11 0.18
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:52473569 original size:20 final size:20
Alignment explanation
Indices: 52473544--52473610 Score: 107
Period size: 20 Copynumber: 3.4 Consensus size: 20
52473534 TTATGAATAC
52473544 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
52473564 ATCATGTGCATAGCATACAT
1 ATCATGTGCATATCATACAT
*
52473584 GTCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
52473604 ACCATGT
1 ATCATGT
52473611 TTACTAAAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.33, C:0.21, G:0.13, T:0.33
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:52478340 original size:27 final size:27
Alignment explanation
Indices: 52478298--52478352 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
52478288 GTGTCATGTG
* *
52478298 AAATTGAATGGCAAATTATTGTTACAT
1 AAATTGAATGGCAAATTACTATTACAT
**
52478325 AAATTGAATGTTAAATTACTATTACAT
1 AAATTGAATGGCAAATTACTATTACAT
52478352 A
1 A
52478353 GTTTGTATCT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.44, C:0.07, G:0.11, T:0.38
Consensus pattern (27 bp):
AAATTGAATGGCAAATTACTATTACAT
Found at i:52483514 original size:40 final size:40
Alignment explanation
Indices: 52483459--52483676 Score: 289
Period size: 40 Copynumber: 5.5 Consensus size: 40
52483449 TGGATGATAA
* * *
52483459 CCGGGCTAAGTCCCGAAGGCATTTGCGCTAGTGACTAGT-T
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TAT
52483499 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
52483539 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * *
52483579 CCGAGCTAAGTCCTGAAGGCATTGGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * *
52483619 CCGGGCTATGTCCCGAAGGCATTCGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* * *
52483659 TC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
52483677 TACTTGGCTT
Statistics
Matches: 161, Mismatches: 15, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
39 16 0.10
40 145 0.90
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:52487273 original size:21 final size:18
Alignment explanation
Indices: 52487224--52487270 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 18
52487214 TAAAATTTTT
52487224 TTTTTTATAATTAATATAA
1 TTTTTTA-AATTAATATAA
*
52487243 TTTTTT-AATTAATTTTAA
1 TTTTTTAAATTAA-TATAA
52487261 TATTTTTAAA
1 T-TTTTTAAA
52487271 ATTTTAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
17 6 0.25
18 5 0.21
19 11 0.46
20 2 0.08
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTTTTAAATTAATATAA
Found at i:52495096 original size:13 final size:13
Alignment explanation
Indices: 52495078--52495102 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
52495068 TTAATACTTT
52495078 ATTAATTTAAAAA
1 ATTAATTTAAAAA
52495091 ATTAATTTAAAA
1 ATTAATTTAAAA
52495103 TCAAATTGTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
ATTAATTTAAAAA
Found at i:52495260 original size:16 final size:17
Alignment explanation
Indices: 52495237--52495281 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 17
52495227 CTAAATTTTT
52495237 TAAAAATA-AAAAA-TA
1 TAAAAATACAAAAATTA
52495252 TACAAAATACAAAAATTA
1 TA-AAAATACAAAAATTA
52495270 TAAAAATTACAA
1 TAAAAA-TACAA
52495282 GAAAACTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
15 2 0.08
16 6 0.23
17 9 0.35
18 9 0.35
ACGTcount: A:0.71, C:0.07, G:0.00, T:0.22
Consensus pattern (17 bp):
TAAAAATACAAAAATTA
Found at i:52495265 original size:18 final size:18
Alignment explanation
Indices: 52495244--52495295 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
52495234 TTTTAAAAAT
52495244 AAAAAATATACAAAA-TAC
1 AAAAAATATA-AAAATTAC
*
52495262 AAAAATTATAAAAATTAC
1 AAAAAATATAAAAATTAC
*
52495280 AAGAAAA-CTAAAAATT
1 AA-AAAATATAAAAATT
52495296 GTTTAAAAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 4 0.14
18 22 0.76
19 3 0.10
ACGTcount: A:0.69, C:0.08, G:0.02, T:0.21
Consensus pattern (18 bp):
AAAAAATATAAAAATTAC
Found at i:52497977 original size:47 final size:47
Alignment explanation
Indices: 52497914--52498592 Score: 1070
Period size: 47 Copynumber: 14.4 Consensus size: 47
52497904 CCCTTCGGGA
* *
52497914 CTTATCACATTTATACACTTTCACATCCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* * * * *
52497961 CTTATCACATATATACACCTTCACATCCATCACATCGGCCATTAGGT
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* * *
52498008 CTTATCTCATATATACACTTTCACATTCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
*
52498055 CTTATCACATATATACACTTTCACATTCATCACATTGACCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
** *
52498102 CTTATCACATATATACACTTTCACATTCATCACATCAGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
52498149 CTTATCACATATACACACGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
*
52498196 CTTATCACATATGTACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
52498243 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
52498290 CTTATCACATATACACACTTTCACATTCATCACATCGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
*
52498337 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGCC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
52498384 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
*
52498431 CTTATCACATATACACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* * * * *
52498478 CTTATCACATATATACACCTTCACATCCATCACATCGGCCATTAGGT
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
52498525 CTTATCTCACATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
52498572 CTTATCACATATATACACTTT
1 CTTATCACATATATACACTTT
52498593 GTACACCAAT
Statistics
Matches: 574, Mismatches: 58, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 574 1.00
ACGTcount: A:0.28, C:0.31, G:0.08, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
Found at i:52498086 original size:25 final size:25
Alignment explanation
Indices: 52498058--52498136 Score: 85
Period size: 25 Copynumber: 3.3 Consensus size: 25
52498048 ACTCGGCCTT
52498058 ATCACATATATACACTTTCACATTC
1 ATCACATATATACACTTTCACATTC
* * * *
52498083 ATCACAT-T-GAC-CATTCGGCCTT-
1 ATCACATATATACACTTTC-ACATTC
52498105 ATCACATATATACACTTTCACATTC
1 ATCACATATATACACTTTCACATTC
52498130 ATCACAT
1 ATCACAT
52498137 CAGCCATTAG
Statistics
Matches: 41, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
22 11 0.27
23 6 0.15
24 6 0.15
25 18 0.44
ACGTcount: A:0.33, C:0.29, G:0.04, T:0.34
Consensus pattern (25 bp):
ATCACATATATACACTTTCACATTC
Found at i:52498205 original size:22 final size:22
Alignment explanation
Indices: 52498177--52498252 Score: 73
Period size: 22 Copynumber: 3.3 Consensus size: 22
52498167 GTTCACATTC
52498177 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
* * * *
52498199 ATCACATATGTACACTTTC-ACATT
1 ATCACAT-TG-GC-CATTCGGCCTT
52498223 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
52498246 ATCACAT
1 ATCACAT
52498253 ATATACACTT
Statistics
Matches: 41, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
22 18 0.44
23 6 0.15
24 6 0.15
25 11 0.27
ACGTcount: A:0.25, C:0.30, G:0.12, T:0.33
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:52501342 original size:18 final size:18
Alignment explanation
Indices: 52501302--52501345 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
52501292 CTATACATGT
* *
52501302 GAGCATATTAATTTATGT
1 GAGCCTATTAATTTATGC
*
52501320 GAGCCTATTCATTTATGC
1 GAGCCTATTAATTTATGC
52501338 GAGCCTAT
1 GAGCCTAT
52501346 GCATGTAAGC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.16, G:0.18, T:0.39
Consensus pattern (18 bp):
GAGCCTATTAATTTATGC
Found at i:52503626 original size:48 final size:47
Alignment explanation
Indices: 52503570--52503856 Score: 279
Period size: 48 Copynumber: 6.0 Consensus size: 47
52503560 GAGGGTGAAT
*
52503570 TGCCGATGCCATGTTCCTAACATGGTCTTACACTAGCTCACATATCGA
1 TGCCGATGCCATG-TCCTAACATGGTCTTACACTAGCTCACATATCAA
* * * * *
52503618 GGCCGATGCCATGTCCTAAACATTGTCTTACACTAGCTCTCGTTTCAA
1 TGCCGATGCCATGTCCT-AACATGGTCTTACACTAGCTCACATATCAA
* * * * * *
52503666 TGCAGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAAC-G
1 TGCCGATGCCATGTCCTA-ACATGGTCTTACACTAGCTCACATATCAA
* * *
52503713 TCGCCGATGTCATGTCCTAGACATGGTTTTACACTAGGTCACATATCAA
1 T-GCCGATGCCATGTCCTA-ACATGGTCTTACACTAGCTCACATATCAA
* * * * * * * *
52503762 TACCGATGCCATGTCTCAAATATGGTCTTACACTGGCTCTCACAACAT
1 TGCCGATGCCATGTC-CTAACATGGTCTTACACTAGCTCACATATCAA
* *
52503810 TGCCGATGCCATGTTCCAAACATGGTCTTACACTAGCACACATATCA
1 TGCCGATGCCATG-TCCTAACATGGTCTTACACTAGCTCACATATCA
52503857 CCCAAATGTC
Statistics
Matches: 191, Mismatches: 42, Indels: 12
0.78 0.17 0.05
Matches are distributed among these distances:
47 6 0.03
48 180 0.94
49 5 0.03
ACGTcount: A:0.26, C:0.29, G:0.17, T:0.29
Consensus pattern (47 bp):
TGCCGATGCCATGTCCTAACATGGTCTTACACTAGCTCACATATCAA
Found at i:52503745 original size:96 final size:95
Alignment explanation
Indices: 52503574--52503856 Score: 325
Period size: 96 Copynumber: 2.9 Consensus size: 95
52503564 GTGAATTGCC
* * * * **
52503574 GATGCCATGTTCCTAACATGGTCTTACACTAGCTCACATATCGAGGCCGATGCCATGTCCTAAAC
1 GATGCCATG-TCCCAACATGGTCTTACACTGGCTCTCATAACGTCGCCGATGCCATGTCCTAAAC
* * * * *
52503639 ATTGTCTTACACTAGCTCTCGTTTCAATGCA
65 ATGGTCTTACACTAGCTCACATATCAATACA
* *
52503670 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAACGTCGCCGATGTCATGTCCTAGAC
1 GATGCCATGTCCCA-ACATGGTCTTACACTGGCTCTCATAACGTCGCCGATGCCATGTCCTAAAC
* * *
52503735 ATGGTTTTACACTAGGTCACATATCAATACC
65 ATGGTCTTACACTAGCTCACATATCAATACA
* * * * *
52503766 GATGCCATGTCTCAAATATGGTCTTACACTGGCTCTCACAACATTGCCGATGCCATGTTCC-AAA
1 GATGCCATGTC-CCAACATGGTCTTACACTGGCTCTCATAACGTCGCCGATGCCATG-TCCTAAA
*
52503830 CATGGTCTTACACTAGCACACATATCA
64 CATGGTCTTACACTAGCTCACATATCA
52503857 CCCAAATGTC
Statistics
Matches: 158, Mismatches: 26, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
95 4 0.03
96 149 0.94
97 5 0.03
ACGTcount: A:0.26, C:0.28, G:0.17, T:0.29
Consensus pattern (95 bp):
GATGCCATGTCCCAACATGGTCTTACACTGGCTCTCATAACGTCGCCGATGCCATGTCCTAAACA
TGGTCTTACACTAGCTCACATATCAATACA
Found at i:52503833 original size:144 final size:144
Alignment explanation
Indices: 52503571--52503843 Score: 361
Period size: 144 Copynumber: 1.9 Consensus size: 144
52503561 AGGGTGAATT
* *
52503571 GCCGATGCCATGTTCCTAACATGGTCTTACACTAGCTCACATATCGAGGCCGATGCCATGTCCTA
1 GCCGATGCCATGTTCCTAACATGGTCTTACACTAGCTCACATATCAAGACCGATGCCATGTCCTA
* **** *
52503636 AACATTGTCTTACACTAGCTCTCGTTTCAATGCAGATGCCATGTCCCAGACATGGTCTTACACTG
66 AACATGGTCTTACACTAGCTCTCACAACAATGCAGATGCCATGTCCCAAACATGGTCTTACACTG
52503701 GCTCTCATAACGTC
131 GCTCTCATAACGTC
* * * *
52503715 GCCGATGTCATG-TCCTAGACATGGTTTTACACTAGGTCACATATCAATACCGATGCCATGT-CT
1 GCCGATGCCATGTTCCTA-ACATGGTCTTACACTAGCTCACATATCAAGACCGATGCCATGTCCT
* * * * *
52503778 CAAATATGGTCTTACACTGGCTCTCACAACATTGCCGATGCCATGTTCCAAACATGGTCTTACAC
65 -AAACATGGTCTTACACTAGCTCTCACAACAATGCAGATGCCATGTCCCAAACATGGTCTTACAC
52503843 T
129 T
52503844 AGCACACATA
Statistics
Matches: 110, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
143 7 0.06
144 103 0.94
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.29
Consensus pattern (144 bp):
GCCGATGCCATGTTCCTAACATGGTCTTACACTAGCTCACATATCAAGACCGATGCCATGTCCTA
AACATGGTCTTACACTAGCTCTCACAACAATGCAGATGCCATGTCCCAAACATGGTCTTACACTG
GCTCTCATAACGTC
Found at i:52518885 original size:5 final size:5
Alignment explanation
Indices: 52518877--52518908 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
52518867 AGAAAGAAAG
*
52518877 AAATA AAATA AAATA AAATA AAATA AAGTA AA
1 AAATA AAATA AAATA AAATA AAATA AAATA AA
52518909 TGAGATAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (5 bp):
AAATA
Found at i:52542300 original size:11 final size:11
Alignment explanation
Indices: 52542284--52542324 Score: 82
Period size: 11 Copynumber: 3.7 Consensus size: 11
52542274 ATAGTAGGTG
52542284 TCGATACTAAA
1 TCGATACTAAA
52542295 TCGATACTAAA
1 TCGATACTAAA
52542306 TCGATACTAAA
1 TCGATACTAAA
52542317 TCGATACT
1 TCGATACT
52542325 TTTTTTGAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 30 1.00
ACGTcount: A:0.41, C:0.20, G:0.10, T:0.29
Consensus pattern (11 bp):
TCGATACTAAA
Found at i:52559813 original size:42 final size:42
Alignment explanation
Indices: 52559751--52559880 Score: 143
Period size: 42 Copynumber: 3.0 Consensus size: 42
52559741 GAAATGTGAT
* *
52559751 ATTCGGGCTTCGGGCCTAGTAGGCTATAATGCCGGTGAAATG
1 ATTCGGGCTTTGAGCCTAGTAGGCTATAATGCCGGTGAAATG
* * * *
52559793 ATTCGGGCTTTGAGCTTAGTAGGCTATGATGCAGGTGAAATATT
1 ATTCGGGCTTTGAGCCTAGTAGGCTATAATGCCGGTG-AA-ATG
** * *
52559837 ATTCGACCCTTTGACCCTAGCAGGCTATAATGCCGGTGAAATG
1 ATTCG-GGCTTTGAGCCTAGTAGGCTATAATGCCGGTGAAATG
52559880 A
1 A
52559881 AATGTTATGT
Statistics
Matches: 71, Mismatches: 14, Indels: 5
0.79 0.16 0.06
Matches are distributed among these distances:
42 32 0.45
43 5 0.07
44 9 0.13
45 25 0.35
ACGTcount: A:0.25, C:0.18, G:0.28, T:0.28
Consensus pattern (42 bp):
ATTCGGGCTTTGAGCCTAGTAGGCTATAATGCCGGTGAAATG
Found at i:52560193 original size:38 final size:38
Alignment explanation
Indices: 52560150--52560423 Score: 372
Period size: 38 Copynumber: 7.2 Consensus size: 38
52560140 ATGATATTTG
* ** *
52560150 TATCCGGCTTAAAGACCGCAGGCTAT-ATGCTGG-AATTA
1 TATCCGGGTTAAATCCCGCAGGCT-TCGTGCTGGTAA-TA
52560188 TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAATA
1 TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAATA
52560226 TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAATA
1 TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAATA
* * *
52560264 TATCCGGGTTAATTCCTGCAGGCTTCGTGCTGGTATTA
1 TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAATA
52560302 TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAATA
1 TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAATA
* * * *
52560340 TATCCGGGTTAATTCCCGTAGGCTTCGTGCTAGTATTA
1 TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAATA
* * * *
52560378 TATCCGGGTTAAATCCCGCAGGCCTAGTGCTTGTATTA
1 TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAATA
*
52560416 TATTCGGG
1 TATCCGGG
52560424 CCTTTGAGCC
Statistics
Matches: 214, Mismatches: 20, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
37 1 0.00
38 211 0.99
39 2 0.01
ACGTcount: A:0.21, C:0.22, G:0.26, T:0.31
Consensus pattern (38 bp):
TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAATA
Found at i:52560480 original size:45 final size:45
Alignment explanation
Indices: 52560416--52560545 Score: 181
Period size: 45 Copynumber: 2.9 Consensus size: 45
52560406 GCTTGTATTA
* * *
52560416 TATTCGGGCCTTTGAGCCTAGTAGGCTATTATGTCGATGAGACAC
1 TATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGATGAGACAC
* * *
52560461 TATTCGGGCCTTTGGGCCTAGCAGGCTATAATGCCGGTGAGATAC
1 TATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGATGAGACAC
*
52560506 TATTTGGG-CTTTCGAGCCTAGCAGGCTATAATGCCGATGA
1 TATTCGGGCCTTT-GAGCCTAGCAGGCTATAATGCCGATGA
52560546 AATGATAATC
Statistics
Matches: 75, Mismatches: 9, Indels: 2
0.87 0.10 0.02
Matches are distributed among these distances:
44 4 0.05
45 71 0.95
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (45 bp):
TATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGATGAGACAC
Found at i:52572257 original size:43 final size:42
Alignment explanation
Indices: 52572174--52572343 Score: 146
Period size: 43 Copynumber: 4.0 Consensus size: 42
52572164 AGCTCGTACA
* * * * * *
52572174 ATGCCAATGTCCCAAACATGGACTTACATGTAATCCAATATCG
1 ATGCCAATGTCCCAGACAAGGTCTTACACGAAATCAAATAT-G
*
52572217 ATGCCACTGTCCCAGACAAGGTCTTACACGAAATCAAATATG
1 ATGCCAATGTCCCAGACAAGGTCTTACACGAAATCAAATATG
* ** * * *
52572259 ATACTGATGTCCTAGACATA-GTATTATACGTAAATTTCAAAT-TG
1 ATGCCAATGTCCCAGACA-AGGTCTTACACG-AAA--TCAAATATG
**
52572303 ATGCCAATGTCCCAGACGTGGTCTTACACGAAATCAAATAT
1 ATGCCAATGTCCCAGACAAGGTCTTACACGAAATCAAATAT
52572344 CAAAATCCTA
Statistics
Matches: 99, Mismatches: 22, Indels: 13
0.74 0.16 0.10
Matches are distributed among these distances:
41 6 0.06
42 23 0.23
43 41 0.41
44 23 0.23
45 6 0.06
ACGTcount: A:0.35, C:0.22, G:0.15, T:0.27
Consensus pattern (42 bp):
ATGCCAATGTCCCAGACAAGGTCTTACACGAAATCAAATATG
Found at i:52579823 original size:43 final size:43
Alignment explanation
Indices: 52579775--52579920 Score: 163
Period size: 43 Copynumber: 3.4 Consensus size: 43
52579765 AGCTCGTACA
* *
52579775 ATGCCAACGTCCCAGACATGGTCTTACATGTAATCCAATATTG
1 ATGCCAACGTCCCAGACATGGTCTTACACGTAATCCAATATCG
* * * *
52579818 ATGCC-ACTGTCCCAGATAGGGTCTTACACGAAATCAAATA-CG
1 ATGCCAAC-GTCCCAGACATGGTCTTACACGTAATCCAATATCG
* *
52579860 ATGCCGATGTCCCAGACATGGTCTTACACGTAAATCTCAA-ATCG
1 ATGCCAACGTCCCAGACATGGTCTTACACGT-AATC-CAATATCG
*
52579904 ATGCCAATGTCCCAGAC
1 ATGCCAACGTCCCAGAC
52579921 CTAGTATTCC
Statistics
Matches: 86, Mismatches: 12, Indels: 9
0.80 0.11 0.08
Matches are distributed among these distances:
42 28 0.33
43 38 0.44
44 20 0.23
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.24
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACATGGTCTTACACGTAATCCAATATCG
Found at i:52579883 original size:42 final size:41
Alignment explanation
Indices: 52579783--52579941 Score: 153
Period size: 43 Copynumber: 3.8 Consensus size: 41
52579773 CAATGCCAAC
* * * *
52579783 GTCCCAGACATGGTCTTACATGTAATCCAATATTGATGCCACT
1 GTCCCAGACATGGTCTTACACGAAATCAAATA-CGATGCCA-T
* *
52579826 GTCCCAGATAGGGTCTTACACGAAATCAAATACGATGCCGAT
1 GTCCCAGACATGGTCTTACACGAAATCAAATACGATGCC-AT
52579868 GTCCCAGACATGGTCTTACACGTAAATCTCAAAT-CGATGCCAAT
1 GTCCCAGACATGGTCTTACACG-AAA--TCAAATACGATGCC-AT
* * *
52579912 GTCCCAGACCTAGTATT-C-CGAAATCAAATA
1 GTCCCAGACATGGTCTTACACGAAATCAAATA
52579942 TCGGAATCCT
Statistics
Matches: 99, Mismatches: 12, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
39 6 0.06
41 3 0.03
42 29 0.29
43 32 0.32
44 23 0.23
45 6 0.06
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.25
Consensus pattern (41 bp):
GTCCCAGACATGGTCTTACACGAAATCAAATACGATGCCAT
Found at i:52579956 original size:86 final size:84
Alignment explanation
Indices: 52579783--52579941 Score: 209
Period size: 86 Copynumber: 1.9 Consensus size: 84
52579773 CAATGCCAAC
* * * *
52579783 GTCCCAGACATGGTCTTACATGTAATCCAATATTGATGCCACTGTCCCAGATAGGGTCTTACACG
1 GTCCCAGACATGGTCTTACACGTAATCCAATATCGATGCCAATGTCCCAGATA-GGTATTACACG
52579848 AAATCAAATACGATGCCGAT
65 AAATCAAATACGATGCCGAT
52579868 GTCCCAGACATGGTCTTACACGTAAATCTCAA-ATCGATGCCAATGTCCCAGACCTA-GTATT-C
1 GTCCCAGACATGGTCTTACACGT-AATC-CAATATCGATGCCAATGTCCCAGA--TAGGTATTAC
52579930 -CGAAATCAAATA
62 ACGAAATCAAATA
52579942 TCGGAATCCT
Statistics
Matches: 66, Mismatches: 4, Indels: 9
0.84 0.05 0.11
Matches are distributed among these distances:
84 12 0.18
85 23 0.35
86 26 0.39
87 3 0.05
88 2 0.03
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.25
Consensus pattern (84 bp):
GTCCCAGACATGGTCTTACACGTAATCCAATATCGATGCCAATGTCCCAGATAGGTATTACACGA
AATCAAATACGATGCCGAT
Found at i:52584531 original size:20 final size:20
Alignment explanation
Indices: 52584507--52584557 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
52584497 TATTTTTATT
52584507 ATTTTATTTCTTTT-TCAAA
1 ATTTTATTTCTTTTCTCAAA
*
52584526 ATTTT-TCTCTCTTTTCTCCAA
1 ATTTTAT-T-TCTTTTCTCAAA
52584547 ATTTTATTTCT
1 ATTTTATTTCT
52584558 CAGTTTTGCT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
18 1 0.04
19 6 0.22
20 9 0.33
21 10 0.37
22 1 0.04
ACGTcount: A:0.20, C:0.18, G:0.00, T:0.63
Consensus pattern (20 bp):
ATTTTATTTCTTTTCTCAAA
Found at i:52600164 original size:17 final size:18
Alignment explanation
Indices: 52600139--52600172 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
52600129 AAATAAAAAA
52600139 CCCTATTTT-TTTATTTT
1 CCCTATTTTATTTATTTT
*
52600156 CCCTTTTTTATTTATTT
1 CCCTATTTTATTTATTT
52600173 ATGTTCCTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.12, C:0.18, G:0.00, T:0.71
Consensus pattern (18 bp):
CCCTATTTTATTTATTTT
Found at i:52605940 original size:42 final size:42
Alignment explanation
Indices: 52605881--52605965 Score: 161
Period size: 42 Copynumber: 2.0 Consensus size: 42
52605871 GCTCAAAAGG
*
52605881 AAGGAATTGACTACAATAAAGTATTTTCCTCTGTTGTGAACC
1 AAGGAATTGACTACAATAAAGTATTTTCCTCTATTGTGAACC
52605923 AAGGAATTGACTACAATAAAGTATTTTCCTCTATTGTGAACC
1 AAGGAATTGACTACAATAAAGTATTTTCCTCTATTGTGAACC
52605965 A
1 A
52605966 TTCCTCCATT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.33
Consensus pattern (42 bp):
AAGGAATTGACTACAATAAAGTATTTTCCTCTATTGTGAACC
Found at i:52608354 original size:16 final size:19
Alignment explanation
Indices: 52608330--52608365 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
52608320 ATACTTTAAC
52608330 AATTCACATA-T-AACACA
1 AATTCACATACTCAACACA
52608347 AATT-ACATACTCAACACA
1 AATTCACATACTCAACACA
52608365 A
1 A
52608366 TGATATATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
16 5 0.29
17 5 0.29
18 7 0.41
ACGTcount: A:0.53, C:0.25, G:0.00, T:0.22
Consensus pattern (19 bp):
AATTCACATACTCAACACA
Found at i:52609236 original size:32 final size:30
Alignment explanation
Indices: 52609200--52609274 Score: 91
Period size: 32 Copynumber: 2.5 Consensus size: 30
52609190 CACCCACCTA
*
52609200 TATATATGTATATATATACAACCCCACTCTTT
1 TATATATGTATATATA-ACAACCCCA-TCATT
* *
52609232 TATATATGTATAT-TACCAACTCCATCATT
1 TATATATGTATATATAACAACCCCATCATT
52609261 TATATAT-TATATAT
1 TATATATGTATATAT
52609275 GTAACACCCA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
28 5 0.13
29 12 0.31
30 7 0.18
31 2 0.05
32 13 0.33
ACGTcount: A:0.36, C:0.17, G:0.03, T:0.44
Consensus pattern (30 bp):
TATATATGTATATATAACAACCCCATCATT
Found at i:52609293 original size:26 final size:25
Alignment explanation
Indices: 52609257--52609306 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
52609247 CCAACTCCAT
*
52609257 CATTTATATATTATATATGTA-ACACC
1 CATTAATATATT-TAT-TGTATACACC
52609283 CATTAATATATTTATTGTATACAC
1 CATTAATATATTTATTGTATACAC
52609307 AATAAAGCCC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 4 0.18
25 7 0.32
26 11 0.50
ACGTcount: A:0.38, C:0.14, G:0.04, T:0.44
Consensus pattern (25 bp):
CATTAATATATTTATTGTATACACC
Found at i:52611990 original size:16 final size:16
Alignment explanation
Indices: 52611966--52612007 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
52611956 AATACATCTC
52611966 TTTTTTTTTTCTT-TT
1 TTTTTTTTTTCTTCTT
52611981 TTTTTGTTTTTCTTCTT
1 TTTTT-TTTTTCTTCTT
*
52611998 TCTTTTTTTT
1 TTTTTTTTTT
52612008 ATATTTTTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 5 0.21
16 13 0.54
17 6 0.25
ACGTcount: A:0.00, C:0.10, G:0.02, T:0.88
Consensus pattern (16 bp):
TTTTTTTTTTCTTCTT
Found at i:52612014 original size:24 final size:22
Alignment explanation
Indices: 52611966--52612018 Score: 72
Period size: 23 Copynumber: 2.4 Consensus size: 22
52611956 AATACATCTC
*
52611966 TTTTT-TTTTTCTTTTTTTTTG
1 TTTTTCTTTTTCTTTTTTTTTA
52611987 TTTTTCTTCTTTCTTTTTTTTATA
1 TTTTTCTT-TTTCTTTTTTTT-TA
52612011 TTTTTCTT
1 TTTTTCTT
52612019 AAGAACATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 5 0.18
22 2 0.07
23 12 0.43
24 9 0.32
ACGTcount: A:0.04, C:0.09, G:0.02, T:0.85
Consensus pattern (22 bp):
TTTTTCTTTTTCTTTTTTTTTA
Found at i:52613189 original size:8 final size:8
Alignment explanation
Indices: 52613174--52613235 Score: 63
Period size: 8 Copynumber: 7.6 Consensus size: 8
52613164 TCCAAAAAAT
52613174 AATAATAA
1 AATAATAA
*
52613182 AGTAAT-A
1 AATAATAA
*
52613189 ATTAATAA
1 AATAATAA
52613197 AATAAAATAA
1 AAT--AATAA
*
52613207 AGTAATAA
1 AATAATAA
52613215 AATAATAA
1 AATAATAA
*
52613223 AACAATAA
1 AATAATAA
52613231 AATAA
1 AATAA
52613236 AAATTGGGTT
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
7 6 0.14
8 31 0.70
10 7 0.16
ACGTcount: A:0.71, C:0.02, G:0.03, T:0.24
Consensus pattern (8 bp):
AATAATAA
Found at i:52613210 original size:25 final size:27
Alignment explanation
Indices: 52613169--52613230 Score: 92
Period size: 26 Copynumber: 2.4 Consensus size: 27
52613159 TACTATCCAA
*
52613169 AAAATAATAATAAAGTAAT-AATTAAT
1 AAAATAATAATAAAGTAATAAAATAAT
52613195 AAAATAA-AATAAAGTAATAAAATAAT
1 AAAATAATAATAAAGTAATAAAATAAT
*
52613221 AAAACAATAA
1 AAAATAATAA
52613231 AATAAAAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
25 11 0.34
26 19 0.59
27 2 0.06
ACGTcount: A:0.71, C:0.02, G:0.03, T:0.24
Consensus pattern (27 bp):
AAAATAATAATAAAGTAATAAAATAAT
Found at i:52614663 original size:33 final size:33
Alignment explanation
Indices: 52614621--52614698 Score: 95
Period size: 33 Copynumber: 2.4 Consensus size: 33
52614611 TTGTTTCCTT
* * *
52614621 TTGGAAATCAAGAGTTTGCTA-TAGTATTTACTA
1 TTGGAAATCAAGAGTTTACCATTA-TATCTACTA
* *
52614654 TTGGAAATCAACAGTTTACCATTATATCTACTG
1 TTGGAAATCAAGAGTTTACCATTATATCTACTA
52614687 TTGGAAATCAAG
1 TTGGAAATCAAG
52614699 CACATTAGCT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
33 36 0.95
34 2 0.05
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.36
Consensus pattern (33 bp):
TTGGAAATCAAGAGTTTACCATTATATCTACTA
Found at i:52636021 original size:15 final size:15
Alignment explanation
Indices: 52636000--52636037 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
52635990 CTACTTTGCT
52636000 TTGTTCTGCTATAT-
1 TTGTTCTGCTATATC
*
52636014 TATGTTCTGCTCTATC
1 T-TGTTCTGCTATATC
52636030 TTGTTCTG
1 TTGTTCTG
52636038 GTTGGGTTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 1 0.05
15 19 0.90
16 1 0.05
ACGTcount: A:0.11, C:0.18, G:0.16, T:0.55
Consensus pattern (15 bp):
TTGTTCTGCTATATC
Found at i:52648985 original size:31 final size:31
Alignment explanation
Indices: 52648948--52649063 Score: 153
Period size: 31 Copynumber: 3.7 Consensus size: 31
52648938 AGTGTACAAT
* *
52648948 GTGAAAAGTGGTAGCTTCGGCTACCTGATCA
1 GTGAAAAGTAGTAGCTTCAGCTACCTGATCA
*
52648979 GTGAAAAGTAGTAGCTTCAGCTACCTGATTA
1 GTGAAAAGTAGTAGCTTCAGCTACCTGATCA
* *
52649010 GTGAAAAGTGGTAGCTCCAGCTACCTGATCA
1 GTGAAAAGTAGTAGCTTCAGCTACCTGATCA
* *
52649041 GT-AAATAGTAATAGCTTCGGCTA
1 GTGAAA-AGTAGTAGCTTCAGCTA
52649064 TTGAATGTGA
Statistics
Matches: 74, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
30 3 0.04
31 71 0.96
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27
Consensus pattern (31 bp):
GTGAAAAGTAGTAGCTTCAGCTACCTGATCA
Found at i:52649022 original size:62 final size:60
Alignment explanation
Indices: 52648945--52649092 Score: 183
Period size: 62 Copynumber: 2.4 Consensus size: 60
52648935 TTGAGTGTAC
*
52648945 AATGTGAAAAGTGGTAGCTTCGGCTACCTGATCAGTGAAA-AGTAGTAGCTTCAGCTACCTG
1 AATGTGAAAAGTGGTAGCTTCGGCTACCTGATCAGT-AAATAGTAATAGCTTCAGCTA-CTG
* * * * *
52649006 ATTAGTGAAAAGTGGTAGCTCCAGCTACCTGATCAGTAAATAGTAATAGCTTCGGCTATTG
1 AAT-GTGAAAAGTGGTAGCTTCGGCTACCTGATCAGTAAATAGTAATAGCTTCAGCTACTG
*
52649067 AATGTGAAAAG-GGATAGCTTTGGCTA
1 AATGTGAAAAGTGG-TAGCTTCGGCTA
52649093 TCGAATGTGA
Statistics
Matches: 74, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
59 2 0.03
60 17 0.23
61 9 0.12
62 46 0.62
ACGTcount: A:0.31, C:0.16, G:0.26, T:0.28
Consensus pattern (60 bp):
AATGTGAAAAGTGGTAGCTTCGGCTACCTGATCAGTAAATAGTAATAGCTTCAGCTACTG
Found at i:52649136 original size:29 final size:29
Alignment explanation
Indices: 52649051--52649123 Score: 128
Period size: 29 Copynumber: 2.5 Consensus size: 29
52649041 GTAAATAGTA
*
52649051 ATAGCTTCGGCTATTGAATGTGAAAAGGG
1 ATAGCTTCGGCTATCGAATGTGAAAAGGG
*
52649080 ATAGCTTTGGCTATCGAATGTGAAAAGGG
1 ATAGCTTCGGCTATCGAATGTGAAAAGGG
52649109 ATAGCTTCGGCTATC
1 ATAGCTTCGGCTATC
52649124 AAATTTGGAA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.29, C:0.14, G:0.29, T:0.29
Consensus pattern (29 bp):
ATAGCTTCGGCTATCGAATGTGAAAAGGG
Found at i:52649163 original size:33 final size:33
Alignment explanation
Indices: 52649126--52649324 Score: 254
Period size: 33 Copynumber: 6.0 Consensus size: 33
52649116 CGGCTATCAA
* *
52649126 ATTTGGAAAGGAAAGGTATACTTTGTGTATACT
1 ATTTGAAAAGGAAAGGTATACTTTGTGTATACC
* **
52649159 ATTTGAAAATGTTAGGTATACTTTGTGTATACC
1 ATTTGAAAAGGAAAGGTATACTTTGTGTATACC
52649192 ATTTGAAAAGGAAAGGTATACTTTGTGTATACC
1 ATTTGAAAAGGAAAGGTATACTTTGTGTATACC
** *
52649225 ATTTGAAAAGGTTAGGTATACTTTGCGTATACC
1 ATTTGAAAAGGAAAGGTATACTTTGTGTATACC
* * * * *
52649258 ATATGAAAAGGGAAGGTATATTTTTTGTATATC
1 ATTTGAAAAGGAAAGGTATACTTTGTGTATACC
* * *
52649291 ATATCAAAAGGAAAGGTATACTTTGTGTGTACC
1 ATTTGAAAAGGAAAGGTATACTTTGTGTATACC
52649324 A
1 A
52649325 CTCGGAAAGA
Statistics
Matches: 142, Mismatches: 24, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 142 1.00
ACGTcount: A:0.34, C:0.09, G:0.21, T:0.36
Consensus pattern (33 bp):
ATTTGAAAAGGAAAGGTATACTTTGTGTATACC
Found at i:52651525 original size:28 final size:27
Alignment explanation
Indices: 52651468--52651619 Score: 232
Period size: 27 Copynumber: 5.6 Consensus size: 27
52651458 TAAATTGTGC
* *
52651468 AGCACTAAGTGTGCGAATTGAATATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
52651495 AGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAG-TTGACTATGT
52651523 AGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
*
52651550 AGCACTAAGTGTGCGAGTATGATTATGT
1 AGCACTAAGTGTGCGAGT-TGACTATGT
* *
52651578 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGTTGACTATGT
*
52651605 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
52651620 GACTTAATAA
Statistics
Matches: 118, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
27 66 0.56
28 52 0.44
ACGTcount: A:0.28, C:0.13, G:0.29, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGTTGACTATGT
Found at i:52651533 original size:55 final size:55
Alignment explanation
Indices: 52651468--52651619 Score: 241
Period size: 55 Copynumber: 2.8 Consensus size: 55
52651458 TAAATTGTGC
* *
52651468 AGCACTAAGTGTGCGAATTGAATATGTAGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGAATATGTAGCACTAAGTGTGCGAGTATGACTATGT
* *
52651523 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTATGATTATGT
1 AGCACTAAGTGTGCGAGTTGAATATGTAGCACTAAGTGTGCGAGTATGACTATGT
* * *
52651578 AGCACTAAGTGTGCGAGTTGATTATATAGCACTGAGTGTGCG
1 AGCACTAAGTGTGCGAGTTGAATATGTAGCACTAAGTGTGCG
52651620 GACTTAATAA
Statistics
Matches: 90, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
55 90 1.00
ACGTcount: A:0.28, C:0.13, G:0.29, T:0.30
Consensus pattern (55 bp):
AGCACTAAGTGTGCGAGTTGAATATGTAGCACTAAGTGTGCGAGTATGACTATGT
Found at i:52659123 original size:12 final size:12
Alignment explanation
Indices: 52659106--52659131 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
52659096 CATTCCGAAG
52659106 TATATATATACA
1 TATATATATACA
52659118 TATATATATACA
1 TATATATATACA
52659130 TA
1 TA
52659132 AGTATGCCAT
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:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (12 bp):
TATATATATACA
Found at i:52659667 original size:28 final size:28
Alignment explanation
Indices: 52659585--52659706 Score: 149
Period size: 27 Copynumber: 4.4 Consensus size: 28
52659575 GAGATTGGTG
* * * *
52659585 CTAAGTGTGCGGGTTTAAATTGTGCAGCA
1 CTAAGTGTGCGAGTTT-GATTATGTAGCA
* *
52659614 CTAAGTGTGCGA-ATTGACTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATGTAGCA
52659641 CTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATGTAGCA
*
52659669 CTAAGTGTGCGAG-TTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATGTAGCA
*
52659696 CTGAGTGTGCG
1 CTAAGTGTGCG
52659707 GACTTAATAT
Statistics
Matches: 82, Mismatches: 10, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
27 43 0.52
28 28 0.34
29 11 0.13
ACGTcount: A:0.25, C:0.13, G:0.30, T:0.32
Consensus pattern (28 bp):
CTAAGTGTGCGAGTTTGATTATGTAGCA
Found at i:52659675 original size:55 final size:56
Alignment explanation
Indices: 52659585--52659706 Score: 165
Period size: 55 Copynumber: 2.2 Consensus size: 56
52659575 GAGATTGGTG
* * *
52659585 CTAAGTGTGCGGGTTTAAATTGTGCAGCACTAAGTGTGCGAATTGACTATGTAGCA
1 CTAAGTGTGCGAGTTTAAATTATGCAGCACTAAGTGTGCGAATTGACTATATAGCA
* * * *
52659641 CTAAGTGTGCGAGTTT-GATTATGTAGCACTAAGTGTGCGAGTTGATTATATAGCA
1 CTAAGTGTGCGAGTTTAAATTATGCAGCACTAAGTGTGCGAATTGACTATATAGCA
*
52659696 CTGAGTGTGCG
1 CTAAGTGTGCG
52659707 GACTTAATAT
Statistics
Matches: 58, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
55 43 0.74
56 15 0.26
ACGTcount: A:0.25, C:0.13, G:0.30, T:0.32
Consensus pattern (56 bp):
CTAAGTGTGCGAGTTTAAATTATGCAGCACTAAGTGTGCGAATTGACTATATAGCA
Found at i:52659717 original size:27 final size:27
Alignment explanation
Indices: 52659610--52659719 Score: 114
Period size: 27 Copynumber: 4.0 Consensus size: 27
52659600 TAAATTGTGC
* * *
52659610 AGCACTAAGTGTGCGAATTGACTATGT
1 AGCACTAAGTGTGCGACTTGAATATAT
* * *
52659637 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
52659665 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTGAATATAT
*
52659692 AGCACTGAGTGTGCGGACTT-AATATAT
1 AGCACTAAGTGTGC-GACTTGAATATAT
52659719 A
1 A
52659720 TTCTTGAATT
Statistics
Matches: 74, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
27 45 0.61
28 29 0.39
ACGTcount: A:0.29, C:0.13, G:0.26, T:0.32
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTGAATATAT
Found at i:52682626 original size:13 final size:13
Alignment explanation
Indices: 52682608--52682632 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
52682598 AAGTAATCGC
52682608 ACACGGGCATGTT
1 ACACGGGCATGTT
52682621 ACACGGGCATGT
1 ACACGGGCATGT
52682633 CCCTGCCGAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.24, G:0.32, T:0.20
Consensus pattern (13 bp):
ACACGGGCATGTT
Found at i:52697109 original size:18 final size:18
Alignment explanation
Indices: 52697086--52697122 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
52697076 AACATCAGAT
52697086 AAGGTTAATCATGTAACC
1 AAGGTTAATCATGTAACC
52697104 AAGGTTAATCATGTAACC
1 AAGGTTAATCATGTAACC
52697122 A
1 A
52697123 GCACTCAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.27
Consensus pattern (18 bp):
AAGGTTAATCATGTAACC
Found at i:52706647 original size:28 final size:28
Alignment explanation
Indices: 52706589--52706704 Score: 137
Period size: 28 Copynumber: 4.2 Consensus size: 28
52706579 AGCATGGCTG
* *
52706589 CCAG-AACAGATA-TTGTGACAGAGTCA
1 CCAGAAACAGATATTTGTGGCAGAGCCA
* * * *
52706615 CCAGATACAGATAATCGTGGCAGGGCCA
1 CCAGAAACAGATATTTGTGGCAGAGCCA
* **
52706643 CCAGAAACTGATATTTGTGATAGAGCCA
1 CCAGAAACAGATATTTGTGGCAGAGCCA
52706671 CCAGAAACAGATATTTGTGGCAGAGCCA
1 CCAGAAACAGATATTTGTGGCAGAGCCA
52706699 CCAGAA
1 CCAGAA
52706705 CACTTCCTCC
Statistics
Matches: 73, Mismatches: 15, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
26 4 0.05
27 7 0.10
28 62 0.85
ACGTcount: A:0.36, C:0.22, G:0.24, T:0.18
Consensus pattern (28 bp):
CCAGAAACAGATATTTGTGGCAGAGCCA
Found at i:52706673 original size:56 final size:55
Alignment explanation
Indices: 52706589--52706704 Score: 153
Period size: 56 Copynumber: 2.1 Consensus size: 55
52706579 AGCATGGCTG
* * *
52706589 CCAG-AACAGATATTGTGACAGAGTCACCAGATACAGATAATCGTGGCAGGGCCA
1 CCAGAAACAGATATTGTGACAGAGCCACCAGAAACAGATAATCGTGGCAGAGCCA
* * * *
52706643 CCAGAAACTGATATTTGTGATAGAGCCACCAGAAACAGATATTTGTGGCAGAGCCA
1 CCAGAAACAGATA-TTGTGACAGAGCCACCAGAAACAGATAATCGTGGCAGAGCCA
52706699 CCAGAA
1 CCAGAA
52706705 CACTTCCTCC
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
54 4 0.08
55 7 0.13
56 42 0.79
ACGTcount: A:0.36, C:0.22, G:0.24, T:0.18
Consensus pattern (55 bp):
CCAGAAACAGATATTGTGACAGAGCCACCAGAAACAGATAATCGTGGCAGAGCCA
Found at i:52707980 original size:18 final size:18
Alignment explanation
Indices: 52707933--52707983 Score: 68
Period size: 18 Copynumber: 2.8 Consensus size: 18
52707923 TGCTGTAGAG
52707933 GAAAAGAAGAAGA-AGAA
1 GAAAAGAAGAAGAGAGAA
* *
52707950 GAAATAGATGAAGAGAGGA
1 GAAA-AGAAGAAGAGAGAA
52707969 GAAAAGAAGAAGAGA
1 GAAAAGAAGAAGAGA
52707984 AAATAATTGT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
17 4 0.14
18 18 0.62
19 7 0.24
ACGTcount: A:0.63, C:0.00, G:0.33, T:0.04
Consensus pattern (18 bp):
GAAAAGAAGAAGAGAGAA
Found at i:52712677 original size:50 final size:50
Alignment explanation
Indices: 52712558--52712853 Score: 229
Period size: 50 Copynumber: 5.9 Consensus size: 50
52712548 ATTGTGAGAA
* *** *
52712558 CACATGTGTAGTACTATGTGCAGGCTACTATGTGTTTAAGATGGTTTTAGGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAG--TTAGGT
* * * *
52712610 CACGTGGGTAGTACTAAGTGCAGACTACTACGTGTACCAGATAGTTAGGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAGTTAGGT
* * * * * *
52712660 CGCATGTGTAGTACTAAGTGCAAGCTACTATGCGTACCTGAAAACTTCA-GT
1 CACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAG-ATAGTT-AGGT
** * ** ** *
52712711 CATGTGTGTAGTACTAAGTGTAGGCTACTACATGTATTAGATGGTTAGGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAGTTAGGT
*** * * *
52712761 CATGCGTGTAGTACTAAGTGGAGGCTACTATGTGTA-CTGAATTGTT-GGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAG-ATAGTTAGGT
* * * *
52712810 CGCATGTGTAGTATTAAGTGCAGGCTACTATGCGTACTAGATAG
1 CACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAG
52712854 CTTCGGTTAC
Statistics
Matches: 189, Mismatches: 50, Indels: 13
0.75 0.20 0.05
Matches are distributed among these distances:
49 37 0.20
50 81 0.43
51 35 0.19
52 36 0.19
ACGTcount: A:0.26, C:0.15, G:0.27, T:0.32
Consensus pattern (50 bp):
CACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAGTTAGGT
Found at i:52712761 original size:101 final size:99
Alignment explanation
Indices: 52712608--52712801 Score: 246
Period size: 101 Copynumber: 1.9 Consensus size: 99
52712598 ATGGTTTTAG
*
52712608 GTCACGTGGGTAGTACTAAGTGCAGACTACTACGTGTACCAGATAGTTAGGTCGCAT-GTGTAGT
1 GTCACGTGGGTAGTACTAAGTGCAGACTACTACATGTACCAGATAGTTAGGT--CATCGTGTAGT
52712672 ACTAAGTGCAAGCTACTATGCGTACCTGAAAACTTCA
64 ACTAAGTGCAAGCTACTATGCGTA-CTGAAAACTTCA
* * * * ** *
52712709 GTCATGTGTGTAGTACTAAGTGTAGGCTACTACATGTATTAGATGGTTAGGTCATGCGTGTAGTA
1 GTCACGTGGGTAGTACTAAGTGCAGACTACTACATGTACCAGATAGTTAGGTCAT-CGTGTAGTA
* * *
52712774 CTAAGTGGAGGCTACTATGTGTACTGAA
65 CTAAGTGCAAGCTACTATGCGTACTGAA
52712802 TTGTTGGTCG
Statistics
Matches: 80, Mismatches: 11, Indels: 5
0.83 0.11 0.05
Matches are distributed among these distances:
99 3 0.04
100 5 0.06
101 72 0.90
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (99 bp):
GTCACGTGGGTAGTACTAAGTGCAGACTACTACATGTACCAGATAGTTAGGTCATCGTGTAGTAC
TAAGTGCAAGCTACTATGCGTACTGAAAACTTCA
Found at i:52712816 original size:101 final size:98
Alignment explanation
Indices: 52712617--52712839 Score: 236
Period size: 101 Copynumber: 2.2 Consensus size: 98
52712607 GGTCACGTGG
* *
52712617 GTAGTACTAAGTGCAGACTACTACGTGTACCAGATAGTTAGGTCGCATGTGTAGTACTAAGTGCA
1 GTAGTACTAAGTGCAGGCTACTACATGTACCAGATAGTTAGGTCGCA-GTGTAGTACTAAGTGCA
52712682 AGCTACTATGCGTACCTGAAAACTTCAGTCATGTGT
65 AGCTACTATGCGTACCTGAAAACTTCAGTCA--TGT
* ** * *
52712718 GTAGTACTAAGTGTAGGCTACTACATGTATTAGATGGTTAGGTCATGC-GTGTAGTACTAAGTGG
1 GTAGTACTAAGTGCAGGCTACTACATGTACCAGATAGTTAGGTC--GCAGTGTAGTACTAAGTGC
* * *** *
52712782 AGGCTACTATGTGTA-CTGAATTGTT-GGTCGCATGT
64 AAGCTACTATGCGTACCTGAAAACTTCAGT--CATGT
*
52712817 GTAGTATTAAGTGCAGGCTACTA
1 GTAGTACTAAGTGCAGGCTACTA
52712840 TGCGTACTAG
Statistics
Matches: 103, Mismatches: 15, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
99 26 0.25
100 7 0.07
101 68 0.66
103 2 0.02
ACGTcount: A:0.27, C:0.15, G:0.26, T:0.31
Consensus pattern (98 bp):
GTAGTACTAAGTGCAGGCTACTACATGTACCAGATAGTTAGGTCGCAGTGTAGTACTAAGTGCAA
GCTACTATGCGTACCTGAAAACTTCAGTCATGT
Found at i:52723240 original size:46 final size:45
Alignment explanation
Indices: 52723070--52723245 Score: 174
Period size: 46 Copynumber: 3.8 Consensus size: 45
52723060 TGTAACCCGC
* * ** *
52723070 CCATAAGCGAACTCGAACTCAACTCAACGAGCCCGGGCGTTCGAAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGTTCG-AT
** * * * *
52723116 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCAAATGCCTAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACG-TTCGAT
* *
52723162 ACATTTCA-TGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCAT
1 CCA--TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGTTCG-AT
*
52723209 CCATAAGTAAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
52723246 TGCCAAAATA
Statistics
Matches: 103, Mismatches: 22, Indels: 10
0.76 0.16 0.07
Matches are distributed among these distances:
45 2 0.02
46 65 0.63
47 34 0.33
48 2 0.02
ACGTcount: A:0.31, C:0.28, G:0.19, T:0.21
Consensus pattern (45 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGAT
Found at i:52729233 original size:40 final size:40
Alignment explanation
Indices: 52729135--52729557 Score: 627
Period size: 40 Copynumber: 10.6 Consensus size: 40
52729125 TCCTCGTTCA
* * * * *
52729135 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
52729174 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
52729214 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
52729254 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
52729294 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
52729334 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
52729374 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
52729414 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
52729454 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * * *
52729494 AAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
52729534 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
52729558 CAGCATTCAA
Statistics
Matches: 358, Mismatches: 22, Indels: 7
0.93 0.06 0.02
Matches are distributed among these distances:
39 37 0.10
40 313 0.87
41 8 0.02
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:52737292 original size:37 final size:37
Alignment explanation
Indices: 52737207--52737314 Score: 114
Period size: 39 Copynumber: 2.9 Consensus size: 37
52737197 TCCTCGTTCA
* *
52737207 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC
1 AATGCCTTCGGGACATA-CCCGGATTTA-CAACTCACAC
* *
52737246 AATGCCTTCGGGACATAACCGGATTTACAACTCGCAC
1 AATGCCTTCGGGACATACCCGGATTTACAACTCACAC
*
52737283 GAATG-CTTC-GGA-TTACCCGGATTTAACAACTC
1 -AATGCCTTCGGGACATACCCGGATTT-ACAACTC
52737315 CGGATTACAT
Statistics
Matches: 61, Mismatches: 6, Indels: 7
0.82 0.08 0.09
Matches are distributed among these distances:
35 10 0.16
36 10 0.16
37 12 0.20
38 12 0.20
39 17 0.28
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.25
Consensus pattern (37 bp):
AATGCCTTCGGGACATACCCGGATTTACAACTCACAC
Found at i:52737446 original size:40 final size:39
Alignment explanation
Indices: 52737326--52737578 Score: 231
Period size: 40 Copynumber: 6.9 Consensus size: 39
52737316 GGATTACATA
52737326 AACTCGCA-GAATGCCTTC-GGACTTAACCCGGATTT-T
1 AACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTAT
52737362 AACTCGCACG-ATG-CTTCGGGACTT-ACCCGGA-TT-T
1 AACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTAT
52737396 AACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTAAT
1 AACTCGCACGAATGCCTTCGGGACTTAACCCGGATTT-AT
*
52737436 AACTCGCACG-ATGCCTT---GAC-T-A-CCGGATTAAT
1 AACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTAT
52737468 AA-TCGCACG-ATG-CTTCGGGACTTAACCCGGATTTAGT
1 AACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTA-T
* * * * *
52737505 ATCTCGCACAAAGGCCTTC-GGATCTTAATCCGGATATATT
1 AACTCGCACGAATGCCTTCGGGA-CTTAACCCGGATTTA-T
* * * *
52737545 CACTTAGCAC-AAAGCCTTCGGGACTTAGCCCGGA
1 AAC-TCGCACGAATGCCTTCGGGACTTAACCCGGA
52737579 CAGCATTCAA
Statistics
Matches: 182, Mismatches: 14, Indels: 38
0.78 0.06 0.16
Matches are distributed among these distances:
30 3 0.02
31 10 0.05
32 4 0.02
33 10 0.05
34 15 0.08
35 16 0.09
36 39 0.21
37 10 0.05
38 8 0.04
39 12 0.07
40 47 0.26
41 8 0.04
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.26
Consensus pattern (39 bp):
AACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTAT
Found at i:52737496 original size:69 final size:73
Alignment explanation
Indices: 52737314--52737513 Score: 251
Period size: 69 Copynumber: 2.8 Consensus size: 73
52737304 TTTAACAACT
52737314 CCGGATTACATAAACTCGCA-GAATGCCTTC-GGACTTAACCCGGATTT-TAACTCGCACGATGC
1 CCGGATTA-AT-AACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTATAACTCGCACGATGC
52737376 TTCGGGACTTAC
64 TT--GGACTTAC
52737388 CCGGATT--TAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGATGCC
1 CCGGATTAATAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTT-ATAACTCGCACGATG-C
52737451 TT-GAC-TA-
64 TTGGACTTAC
*
52737458 CCGGATTAATAA-TCGCACG-ATG-CTTCGGGACTTAACCCGGATTTAGTATCTCGCAC
1 CCGGATTAATAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTA-TAACTCGCAC
52737514 AAAGGCCTTC
Statistics
Matches: 117, Mismatches: 1, Indels: 21
0.84 0.01 0.15
Matches are distributed among these distances:
68 1 0.01
69 31 0.26
70 18 0.15
71 20 0.17
72 23 0.20
74 21 0.18
75 3 0.03
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.26
Consensus pattern (73 bp):
CCGGATTAATAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTATAACTCGCACGATGCTT
GGACTTAC
Found at i:52749481 original size:18 final size:17
Alignment explanation
Indices: 52749446--52749478 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
52749436 CTTTTTATTC
52749446 TTTTATTATTTCATTTA
1 TTTTATTATTTCATTTA
52749463 TTTTACTTATTT-ATTT
1 TTTTA-TTATTTCATTT
52749479 TATCATTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTTATTATTTCATTTA
Found at i:52751049 original size:27 final size:27
Alignment explanation
Indices: 52751019--52751195 Score: 176
Period size: 27 Copynumber: 6.5 Consensus size: 27
52751009 AAATTGTACA
* *
52751019 GCACTAAGGGTGCGATTTGACTATGTT
1 GCACTAAGTGTGCGATTTGACTATGTG
** *
52751046 GCACTAAGTGTGCGAAATGAATATGAT-
1 GCACTAAGTGTGCGATTTGACTATG-TG
* * *
52751073 GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCGATTTGACTATGTG
* *
52751100 GCACTAAGTGTGCGAGTCTGACTATGTA
1 GCACTAAGTGTGCGA-TTTGACTATGTG
* *
52751128 GCACTAAGTGTGCGATTTGATTACGTG
1 GCACTAAGTGTGCGATTTGACTATGTG
* * * *
52751155 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGATTTGACTATGTG
*
52751182 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
52751196 GGCTCAATAT
Statistics
Matches: 125, Mismatches: 22, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
27 102 0.82
28 23 0.18
ACGTcount: A:0.26, C:0.16, G:0.29, T:0.29
Consensus pattern (27 bp):
GCACTAAGTGTGCGATTTGACTATGTG
Found at i:52751132 original size:82 final size:81
Alignment explanation
Indices: 52751019--52751174 Score: 215
Period size: 82 Copynumber: 1.9 Consensus size: 81
52751009 AAATTGTACA
* * *
52751019 GCACTAAGGGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGAT-GCACTAAGTG
1 GCACTAAGGGTGCGATCTGACTATGTAGCACTAAGTGTGCGAAATGAATACG-TGGCACTAAGTG
52751083 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
* ** *
52751100 GCACTAAGTGTGCGAGTCTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTGGCACTAAGTG
1 GCACTAAGGGTGCGA-TCTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTG
*
52751165 TGCGAGTTGA
65 TGCGAATTGA
52751175 TTATATAGCA
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
81 15 0.23
82 50 0.77
ACGTcount: A:0.26, C:0.16, G:0.29, T:0.28
Consensus pattern (81 bp):
GCACTAAGGGTGCGATCTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:52751186 original size:82 final size:81
Alignment explanation
Indices: 52751015--52751195 Score: 211
Period size: 82 Copynumber: 2.2 Consensus size: 81
52751005 GATTAAATTG
* * * *
52751015 TACAGCACTAAGGGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATCTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
52751080 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
52751096 TGCGGCACTAAGTGTGCGAGTCTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TGGCACT
1 TACAGCACTAAGTGTGCGA-TCTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
52751160 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
52751178 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
52751196 GGCTCAATAT
Statistics
Matches: 82, Mismatches: 16, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
81 17 0.21
82 65 0.79
ACGTcount: A:0.27, C:0.16, G:0.29, T:0.29
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATCTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:52758641 original size:27 final size:27
Alignment explanation
Indices: 52758611--52758787 Score: 176
Period size: 27 Copynumber: 6.5 Consensus size: 27
52758601 AAATTGTACA
* *
52758611 GCACTAAGGGTGCGATTTGACTATGTT
1 GCACTAAGTGTGCGATTTGACTATGTG
** *
52758638 GCACTAAGTGTGCGAAATGAATATGAT-
1 GCACTAAGTGTGCGATTTGACTATG-TG
* * *
52758665 GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCGATTTGACTATGTG
* *
52758692 GCACTAAGTGTGCGAGTCTGACTATGTA
1 GCACTAAGTGTGCGA-TTTGACTATGTG
* *
52758720 GCACTAAGTGTGCGATTTGATTACGTG
1 GCACTAAGTGTGCGATTTGACTATGTG
* * * *
52758747 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGATTTGACTATGTG
*
52758774 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
52758788 GGCTCAATAT
Statistics
Matches: 125, Mismatches: 22, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
27 102 0.82
28 23 0.18
ACGTcount: A:0.26, C:0.16, G:0.29, T:0.29
Consensus pattern (27 bp):
GCACTAAGTGTGCGATTTGACTATGTG
Found at i:52758724 original size:82 final size:81
Alignment explanation
Indices: 52758611--52758766 Score: 215
Period size: 82 Copynumber: 1.9 Consensus size: 81
52758601 AAATTGTACA
* * *
52758611 GCACTAAGGGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGAT-GCACTAAGTG
1 GCACTAAGGGTGCGATCTGACTATGTAGCACTAAGTGTGCGAAATGAATACG-TGGCACTAAGTG
52758675 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
* ** *
52758692 GCACTAAGTGTGCGAGTCTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTGGCACTAAGTG
1 GCACTAAGGGTGCGA-TCTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTG
*
52758757 TGCGAGTTGA
65 TGCGAATTGA
52758767 TTATATAGCA
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
81 15 0.23
82 50 0.77
ACGTcount: A:0.26, C:0.16, G:0.29, T:0.28
Consensus pattern (81 bp):
GCACTAAGGGTGCGATCTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:52758778 original size:82 final size:81
Alignment explanation
Indices: 52758607--52758787 Score: 211
Period size: 82 Copynumber: 2.2 Consensus size: 81
52758597 GATTAAATTG
* * * *
52758607 TACAGCACTAAGGGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATCTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
52758672 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
52758688 TGCGGCACTAAGTGTGCGAGTCTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TGGCACT
1 TACAGCACTAAGTGTGCGA-TCTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
52758752 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
52758770 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
52758788 GGCTCAATAT
Statistics
Matches: 82, Mismatches: 16, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
81 17 0.21
82 65 0.79
ACGTcount: A:0.27, C:0.16, G:0.29, T:0.29
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATCTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:52764061 original size:30 final size:30
Alignment explanation
Indices: 52764027--52764089 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
52764017 ACTTATTTTA
*
52764027 TTGTTAATTTTGTTATTATTTTAAAGACAT
1 TTGTTAATTTTATTATTATTTTAAAGACAT
*
52764057 TTGTTAATTTTATTATTATTTTAGAGACAT
1 TTGTTAATTTTATTATTATTTTAAAGACAT
52764087 TTG
1 TTG
52764090 CTATTTAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.29, C:0.03, G:0.11, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTATTATTATTTTAAAGACAT
Found at i:52764192 original size:18 final size:18
Alignment explanation
Indices: 52764171--52764210 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
52764161 GAAATATTTA
*
52764171 TTTTGATGT-TTTTAGTAT
1 TTTTGATGTATTATA-TAT
52764189 TTTTGATGTATTATATAT
1 TTTTGATGTATTATATAT
52764207 TTTT
1 TTTT
52764211 AAAATTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.20, C:0.00, G:0.12, T:0.68
Consensus pattern (18 bp):
TTTTGATGTATTATATAT
Found at i:52764232 original size:12 final size:12
Alignment explanation
Indices: 52764211--52764244 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
52764201 ATATATTTTT
*
52764211 AAAATTATATAA
1 AAAATAATATAA
52764223 AAAATAATATAA
1 AAAATAATATAA
*
52764235 AAATTAATAT
1 AAAATAATAT
52764245 GGGTGGGCCG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AAAATAATATAA
Found at i:52764682 original size:20 final size:21
Alignment explanation
Indices: 52764644--52764685 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
52764634 TTAAAATTCA
* *
52764644 TTAAAATTATTTTTTAAAAAT
1 TTAAAAATATTTTTAAAAAAT
52764665 TTAAAAATA-TTTTAAAAAAT
1 TTAAAAATATTTTTAAAAAAT
52764685 T
1 T
52764686 AATTAAATGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
TTAAAAATATTTTTAAAAAAT
Found at i:52767432 original size:16 final size:16
Alignment explanation
Indices: 52767401--52767430 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
52767391 TTGTCATGTG
52767401 TTTTTTTAAATATTTA
1 TTTTTTTAAATATTTA
52767417 TTTTTTT-AATATTT
1 TTTTTTTAAATATTT
52767431 TACTATTTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTTTTTAAATATTTA
Found at i:52773941 original size:39 final size:40
Alignment explanation
Indices: 52773897--52774120 Score: 240
Period size: 40 Copynumber: 5.6 Consensus size: 40
52773887 CTCCTCGTTT
* * * *
52773897 AAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC
1 AAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
*
52773937 -AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
1 AAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* *
52773976 GAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCAC
1 AAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* * *
52774016 AAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCAC
1 AAATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCAC
** * * * *
52774056 AAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC
1 AAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCAC
*
52774097 AAA-GCCTTCGGGACTTAGCCCGGA
1 AAATGCCTTCGGGACTTAACCCGGA
52774121 CAGCATTCAA
Statistics
Matches: 158, Mismatches: 20, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
39 39 0.25
40 104 0.66
41 15 0.09
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.26
Consensus pattern (40 bp):
AAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
Found at i:52774129 original size:41 final size:41
Alignment explanation
Indices: 52774052--52774129 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
52774042 TTTGTATCTC
* * *
52774052 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
52774093 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
52774130 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:52776947 original size:26 final size:26
Alignment explanation
Indices: 52776918--52776998 Score: 71
Period size: 26 Copynumber: 3.2 Consensus size: 26
52776908 AGCTATCTGG
52776918 TACACATAGCAGCCTGCACTTAGTAC
1 TACACATAGCAGCCTGCACTTAGTAC
* * * *
52776944 TACACAT-GC-GAC--CAATTATCTAG
1 TACACATAGCAGCCTGCACTTA-GTAC
* *
52776967 TACACGTAGTAGCCTGCACTTAGTAC
1 TACACATAGCAGCCTGCACTTAGTAC
52776993 TACACA
1 TACACA
52776999 CGTGACCTAA
Statistics
Matches: 39, Mismatches: 11, Indels: 10
0.65 0.18 0.17
Matches are distributed among these distances:
22 5 0.13
23 8 0.21
24 3 0.08
25 4 0.10
26 14 0.36
27 5 0.13
ACGTcount: A:0.32, C:0.28, G:0.15, T:0.25
Consensus pattern (26 bp):
TACACATAGCAGCCTGCACTTAGTAC
Found at i:52776970 original size:49 final size:49
Alignment explanation
Indices: 52776911--52777155 Score: 301
Period size: 49 Copynumber: 4.9 Consensus size: 49
52776901 TAGCCAAAGC
* *
52776911 TATCTGGTACACATAGCAGCCTGCACTTAGTACTACACATGCGACCAAT
1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCAAT
* * * *
52776960 TATCTAGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAAC
1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACC-AAT
* ** * * *
52777010 CATCTAATACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGT
1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGA-CCAA-T
* * *
52777061 TATCGGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAAT
1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCAAT
* * *
52777110 AATCCGGTACACATAGTAGCCTGCATTTAGTACTACACATGTGACC
1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACC
52777156 TCATAATAGA
Statistics
Matches: 169, Mismatches: 24, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
49 83 0.49
50 49 0.29
51 37 0.22
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (49 bp):
TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCAAT
Found at i:52782235 original size:39 final size:39
Alignment explanation
Indices: 52782189--52782289 Score: 175
Period size: 39 Copynumber: 2.6 Consensus size: 39
52782179 GCTCTGGTGA
*
52782189 GCTTCAGTTAGCCTTCGGGCTTCCGTTTATCACTTATGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
52782228 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
* *
52782267 GCTTTAGTTAGACTTCGGGCTTC
1 GCTTCAGTTAGCCTTCGGGCTTC
52782290 AGATCACGAT
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 59 1.00
ACGTcount: A:0.13, C:0.25, G:0.23, T:0.40
Consensus pattern (39 bp):
GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
Found at i:52788538 original size:36 final size:35
Alignment explanation
Indices: 52788498--52788615 Score: 128
Period size: 36 Copynumber: 3.3 Consensus size: 35
52788488 TAAATAAAAG
* ** *
52788498 TACTGAATGACTGGCTGTTACTGAATAATTGATCGT
1 TACTAAATGACTGATTGCTACTGAATAATTGAT-GT
* * *
52788534 TACTGAATGACTGATTGCTACTGAACAAATGATTGT
1 TACTAAATGACTGATTGCTACTGAATAATTGA-TGT
* *
52788570 TACTAAATAACTAATTGCTACTGAATAATTGAATGT
1 TACTAAATGACTGATTGCTACTGAATAATTG-ATGT
52788606 TACTAAATGA
1 TACTAAATGA
52788616 AACTGATAAA
Statistics
Matches: 69, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
36 67 0.97
37 2 0.03
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.35
Consensus pattern (35 bp):
TACTAAATGACTGATTGCTACTGAATAATTGATGT
Found at i:52788596 original size:18 final size:18
Alignment explanation
Indices: 52788516--52788597 Score: 83
Period size: 18 Copynumber: 4.6 Consensus size: 18
52788506 GACTGGCTGT
* * *
52788516 TACTGAATAATTGATCGT
1 TACTGAATAACTGATTGC
*
52788534 TACTGAATGACTGATTGC
1 TACTGAATAACTGATTGC
* * *
52788552 TACTGAACAAATGATTGT
1 TACTGAATAACTGATTGC
* *
52788570 TACTAAATAACTAATTGC
1 TACTGAATAACTGATTGC
52788588 TACTGAATAA
1 TACTGAATAA
52788598 TTGAATGTTA
Statistics
Matches: 50, Mismatches: 14, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 50 1.00
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.34
Consensus pattern (18 bp):
TACTGAATAACTGATTGC
Found at i:52788609 original size:18 final size:18
Alignment explanation
Indices: 52788498--52788609 Score: 75
Period size: 18 Copynumber: 6.2 Consensus size: 18
52788488 TAAATAAAAG
* **
52788498 TACTGAATGACTGGCTGT
1 TACTGAATAACTGAATGT
*
52788516 TACTGAATAATTG-ATCGT
1 TACTGAATAACTGAAT-GT
* * *
52788534 TACTGAATGACTGATTGC
1 TACTGAATAACTGAATGT
* * *
52788552 TACTGAACAAATGATTGT
1 TACTGAATAACTGAATGT
* *
52788570 TACTAAATAACT-AATTGC
1 TACTGAATAACTGAA-TGT
*
52788588 TACTGAATAATTGAATGT
1 TACTGAATAACTGAATGT
52788606 TACT
1 TACT
52788610 AAATGAAACT
Statistics
Matches: 71, Mismatches: 19, Indels: 8
0.72 0.19 0.08
Matches are distributed among these distances:
17 2 0.03
18 66 0.93
19 3 0.04
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.36
Consensus pattern (18 bp):
TACTGAATAACTGAATGT
Found at i:52790755 original size:12 final size:12
Alignment explanation
Indices: 52790738--52790762 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
52790728 TCGTGTGGCC
52790738 AACACTTAGACT
1 AACACTTAGACT
52790750 AACACTTAGACT
1 AACACTTAGACT
52790762 A
1 A
52790763 TTTTCCAAGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.24, G:0.08, T:0.24
Consensus pattern (12 bp):
AACACTTAGACT
Found at i:52806337 original size:27 final size:27
Alignment explanation
Indices: 52806306--52806480 Score: 181
Period size: 27 Copynumber: 6.4 Consensus size: 27
52806296 TAAATTGTAC
*
52806306 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGAATTGACTATGT
* * *
52806333 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGAATTGACTATGT
* *
52806359 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGAATTGACTATGT
* *
52806387 GGCACTAAGTGTGCGAGATGGACTATGT
1 AGCACTAAGTGTGCGA-ATTGACTATGT
* * * *
52806415 GGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGAATTGACTATGT
* * *
52806442 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAATTGACTATGT
*
52806469 AGCACTGAGTGT
1 AGCACTAAGTGT
52806481 ACGGGCTCAA
Statistics
Matches: 124, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
27 100 0.81
28 24 0.19
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.29
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAATTGACTATGT
Found at i:52806367 original size:54 final size:55
Alignment explanation
Indices: 52806307--52806457 Score: 198
Period size: 55 Copynumber: 2.8 Consensus size: 55
52806297 AAATTGTACA
*
52806307 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAAT-GAATATGAT-
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGGAATATG-TG
* * ** * *
52806361 GCACTAAGTGTGCGAATTGACCATGCGGCACTAAGTGTGCGAGATGGACTATGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGGAATATGTG
* *
52806416 GCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTGTGCGA
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGA
52806458 GTTGATTATA
Statistics
Matches: 83, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
54 41 0.49
55 42 0.51
ACGTcount: A:0.27, C:0.16, G:0.29, T:0.28
Consensus pattern (55 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGGAATATGTG
Found at i:52806422 original size:82 final size:81
Alignment explanation
Indices: 52806307--52806462 Score: 215
Period size: 82 Copynumber: 1.9 Consensus size: 81
52806297 AAATTGTACA
* * * *
52806307 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGAATGGACTATGTGGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
52806371 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
52806388 GCACTAAGTGTGCGAGATGGACTATGTGGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-ATGGACTATGTGGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
52806453 TGCGAGTTGA
65 TGCGAATTGA
52806463 TTATATAGCA
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
81 15 0.23
82 49 0.75
83 1 0.02
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.28
Consensus pattern (81 bp):
GCACTAAGTGTGCGAATGGACTATGTGGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:52806474 original size:82 final size:81
Alignment explanation
Indices: 52806303--52806480 Score: 205
Period size: 82 Copynumber: 2.2 Consensus size: 81
52806293 GATTAAATTG
* * * *
52806303 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGAATGGACTATGTGGCACTAAGTGTGCGAAATGAATACGATGCACTAA
52806368 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
52806384 TGCGGCACTAAGTGTGCGAGATGGACTATGTGGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-ATGGACTATGTGGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
52806448 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
52806466 TATAGCACTGAGTGT
1 TACAGCACTAAGTGT
52806481 ACGGGCTCAA
Statistics
Matches: 79, Mismatches: 16, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
81 18 0.23
82 61 0.77
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGAATGGACTATGTGGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:52814899 original size:19 final size:20
Alignment explanation
Indices: 52814875--52814912 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
52814865 GGTACCACCA
52814875 AAACAT-ATATCA-CATCTTT
1 AAACATCAT-TCATCATCTTT
52814894 AAACATCATTCATCATCTT
1 AAACATCATTCATCATCTT
52814913 ACCACCTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (20 bp):
AAACATCATTCATCATCTTT
Found at i:52815253 original size:93 final size:93
Alignment explanation
Indices: 52815141--52815311 Score: 281
Period size: 93 Copynumber: 1.8 Consensus size: 93
52815131 GCCCATAAGT
*
52815141 GAACTCGGACTCAACTCAACGAGCTCCGG-CGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 GAACTCGGACTCAACTCAACGAG-TCCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
52815205 ACGAGTTCAGATGCCTAGTTACATTTCAC
65 ACGAGTTCAGATGCCTAGTTACATTTCAC
** *
52815234 GAACTCGGACTCAACTCAACGAGTTTGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCCA
1 GAACTCGGACTCAACTCAACGAGTCCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
52815299 CGAGTTCGGATGC
66 CGAGTTCAGATGC
52815312 TCAACCATCC
Statistics
Matches: 72, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
92 3 0.04
93 69 0.96
ACGTcount: A:0.28, C:0.29, G:0.20, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGTCCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCAGATGCCTAGTTACATTTCAC
Found at i:52815304 original size:46 final size:45
Alignment explanation
Indices: 52815133--52815304 Score: 163
Period size: 46 Copynumber: 3.7 Consensus size: 45
52815123 TGTAACCCGC
** *
52815133 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCCGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAG-TTAGGCATTCGCAT
*
52815179 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCAGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTT-AG--G-C-A-TTCGCAT
* * * *
52815229 --TTCA-CGAACTCGGACTCAACTCAACGAGTTTGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTAGG-CATTCGCAT
*
52815272 CCATAAGTGAACTCGGACTCAACTCCACGAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTT
52815305 CGGATGCTCA
Statistics
Matches: 102, Mismatches: 14, Indels: 20
0.75 0.10 0.15
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 3 0.03
46 57 0.56
47 25 0.25
48 3 0.03
49 1 0.01
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.23
Consensus pattern (45 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTAGGCATTCGCAT
Found at i:52832311 original size:45 final size:46
Alignment explanation
Indices: 52832259--52832364 Score: 178
Period size: 45 Copynumber: 2.3 Consensus size: 46
52832249 GATTAACACA
* *
52832259 AGTAAGACCATAGCTGGAAGACGCTATGGCAACATG-ATTAAAATG
1 AGTAAGACCATAGCTGAAAGACACTATGGCAACATGAATTAAAATG
*
52832304 AGTAAGACCATAGTTGAAAGACACTATGGCAACATGAATTAAAATG
1 AGTAAGACCATAGCTGAAAGACACTATGGCAACATGAATTAAAATG
52832350 AGTAAGACCATAGCT
1 AGTAAGACCATAGCT
52832365 AAGATATGTT
Statistics
Matches: 56, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
45 33 0.59
46 23 0.41
ACGTcount: A:0.42, C:0.15, G:0.22, T:0.21
Consensus pattern (46 bp):
AGTAAGACCATAGCTGAAAGACACTATGGCAACATGAATTAAAATG
Found at i:52840782 original size:46 final size:45
Alignment explanation
Indices: 52840628--52840890 Score: 201
Period size: 47 Copynumber: 5.6 Consensus size: 45
52840618 GTAAGGTGAT
* * * *
52840628 GATGTCATGTCCTAGACATGGTCTTACACTGGCTCAT-ATCTCAAGTC
1 GATG-CATGTCCCAGACAT-GTCTTACACTGGCTC-TCGTCTCGAGCC
* * * * * *
52840675 AATGCCATGTCCTAGACATGTTCTTACATTGACTATCATCAT-GTAGCC
1 GATG-CATGTCCCAGACATG-TCTTACACTGGCTCTCGTC-TCG-AGCC
*
52840723 GACGCATGTCCCAGACATGTCTTACACTGGCT-TACGTCTCGAGCCC
1 GATGCATGTCCCAGACATGTCTTACACTGGCTCT-CGTCTCGAG-CC
* * * *
52840769 GATGCATGCCCCAGACATGTCTTATACTAGCTCTCGTCTCAATGCC
1 GATGCATGTCCCAGACATGTCTTACACTGGCTCTCGTCTCGA-GCC
* * * *
52840815 GATGCCATGTCCCAGACATGGCCTTACACTGGCTCTCATAAT-GTGGCC
1 GATG-CATGTCCCAGACAT-GTCTTACACTGGCTCTCGT-CTCG-AGCC
52840863 GATGCATGTCCCAGACATGTCTTACACT
1 GATGCATGTCCCAGACATGTCTTACACT
52840891 AGCCAACAAT
Statistics
Matches: 176, Mismatches: 27, Indels: 27
0.77 0.12 0.12
Matches are distributed among these distances:
45 4 0.02
46 69 0.39
47 74 0.42
48 28 0.16
49 1 0.01
ACGTcount: A:0.23, C:0.30, G:0.19, T:0.29
Consensus pattern (45 bp):
GATGCATGTCCCAGACATGTCTTACACTGGCTCTCGTCTCGAGCC
Found at i:52861894 original size:40 final size:40
Alignment explanation
Indices: 52861846--52862152 Score: 560
Period size: 40 Copynumber: 7.7 Consensus size: 40
52861836 GCAAACACAT
* *
52861846 TTGCCTTCGGGTCTTAACCCGGACATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
52861886 TTGCCTTCGGGTCTTAGCCCGGATATATCATCTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
** *
52861926 TTGCCTTCGGGTCACAGCCCGGATATATCAACTCGCATAG
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
52861966 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
52862006 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
52862046 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
52862086 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
52862126 TTGCCTTCGGGTCTTAGCCCGGATATA
1 TTGCCTTCGGGTCTTAGCCCGGATATA
52862153 ATCCAATGCT
Statistics
Matches: 257, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 257 1.00
ACGTcount: A:0.22, C:0.28, G:0.21, T:0.30
Consensus pattern (40 bp):
TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
Found at i:52869793 original size:19 final size:19
Alignment explanation
Indices: 52869769--52869806 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
52869759 TTCCGCACAC
52869769 TTAGTGCCATCTCAACTAG
1 TTAGTGCCATCTCAACTAG
52869788 TTAGTGCCATCTCAACTAG
1 TTAGTGCCATCTCAACTAG
52869807 CCGAAACTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.32
Consensus pattern (19 bp):
TTAGTGCCATCTCAACTAG
Found at i:52869870 original size:40 final size:40
Alignment explanation
Indices: 52869823--52869916 Score: 188
Period size: 40 Copynumber: 2.4 Consensus size: 40
52869813 CTAAGTCAGT
52869823 ATCGCACACTTAGTGCCTTTAATAGCCGAAGCTAGCTTAG
1 ATCGCACACTTAGTGCCTTTAATAGCCGAAGCTAGCTTAG
52869863 ATCGCACACTTAGTGCCTTTAATAGCCGAAGCTAGCTTAG
1 ATCGCACACTTAGTGCCTTTAATAGCCGAAGCTAGCTTAG
52869903 ATCGCACACTTAGT
1 ATCGCACACTTAGT
52869917 TCCAATGCTT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 54 1.00
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.28
Consensus pattern (40 bp):
ATCGCACACTTAGTGCCTTTAATAGCCGAAGCTAGCTTAG
Found at i:52876885 original size:27 final size:27
Alignment explanation
Indices: 52876862--52877229 Score: 504
Period size: 27 Copynumber: 13.6 Consensus size: 27
52876852 TTAGTTTACC
52876862 AAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
* * *
52876889 AAATTACTAAAATA-CCATCGGTTTATA
1 AAATTACCAAAATACCCCT-GGTTTGTA
*
52876916 AAATCACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
* **
52876943 AAATTACCAAAATACCCTTGGTTTACA
1 AAATTACCAAAATACCCCTGGTTTGTA
52876970 AAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
* * * *
52876997 AAATTACTAAAATACCCTTTGTTTATA
1 AAATTACCAAAATACCCCTGGTTTGTA
52877024 AAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
52877051 AAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
* ** * *
52877078 AAATTACTAAAATACCTTTTGTTTATA
1 AAATTACCAAAATACCCCTGGTTTGTA
52877105 AAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
52877132 AAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
* *
52877159 AAATTATCAAAATACCCCTCGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
* ** *
52877186 AAATTACCAAAATATCCCTAATTTGTG
1 AAATTACCAAAATACCCCTGGTTTGTA
**
52877213 AAATTACTGAAATACCC
1 AAATTACCAAAATACCC
52877230 TCGACCTGTA
Statistics
Matches: 297, Mismatches: 42, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
26 3 0.01
27 291 0.98
28 3 0.01
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.32
Consensus pattern (27 bp):
AAATTACCAAAATACCCCTGGTTTGTA
Found at i:52877240 original size:81 final size:80
Alignment explanation
Indices: 52876862--52877283 Score: 499
Period size: 81 Copynumber: 5.2 Consensus size: 80
52876852 TTAGTTTACC
* * * *
52876862 AAATTACCAAAATACCCCTGGTTTGTAAAATTACTAAAATA-CCATCGGTTTATAAAATCACCAA
1 AAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCCT-GGTTTGTAAAATTA-CAA
*
52876926 AATACCCCTGGTTTGTA
64 AATACCCCTCGTTTGTA
* **
52876943 AAATTACCAAAATACCCTTGGTTTACAAAATTACCAAAATACCCCTGGTTTGTAAAATTACTAAA
1 AAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCCTGGTTTGTAAAATTAC-AAA
* * *
52877008 ATACCCTTTGTTTATA
65 ATACCCCTCGTTTGTA
52877024 AAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCCTGGTTTGTAAAATTACTAAA
1 AAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCCTGGTTTGTAAAATTAC-AAA
** * *
52877089 ATACCTTTTGTTTATA
65 ATACCCCTCGTTTGTA
52877105 AAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCCTGGTTTGTAAAATTATCAAA
1 AAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCCTGGTTTGTAAAATTA-CAAA
52877170 ATACCCCTCGTTTGTA
65 ATACCCCTCGTTTGTA
* ** * ** *** **
52877186 AAATTACCAAAATATCCCTAATTTGTGAAATTACTGAAATA-CCCTCGACCTGTAAAATTATTGA
1 AAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCCT-GGTTTGTAAAATTA-CAA
*
52877250 AATA-CCCTCGACTTGTA
64 AATACCCCTCG-TTTGTA
*
52877267 AAATTACCAAAGTACCC
1 AAATTACCAAAATACCC
52877284 TTGATTTACA
Statistics
Matches: 304, Mismatches: 32, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
80 11 0.04
81 289 0.95
82 4 0.01
ACGTcount: A:0.39, C:0.21, G:0.09, T:0.31
Consensus pattern (80 bp):
AAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCCTGGTTTGTAAAATTACAAAA
TACCCCTCGTTTGTA
Found at i:52877282 original size:27 final size:27
Alignment explanation
Indices: 52876862--52877338 Score: 423
Period size: 27 Copynumber: 17.7 Consensus size: 27
52876852 TTAGTTTACC
52876862 AAATTACCAAAATACCC-CTGGTTTGTA
1 AAATTACCAAAATACCCTC-GGTTTGTA
* * *
52876889 AAATTACTAAAATACCATCGGTTTATA
1 AAATTACCAAAATACCCTCGGTTTGTA
*
52876916 AAATCACCAAAATACCC-CTGGTTTGTA
1 AAATTACCAAAATACCCTC-GGTTTGTA
* **
52876943 AAATTACCAAAATACCCTTGGTTTACA
1 AAATTACCAAAATACCCTCGGTTTGTA
52876970 AAATTACCAAAATACCC-CTGGTTTGTA
1 AAATTACCAAAATACCCTC-GGTTTGTA
* ** *
52876997 AAATTACTAAAATACCCTTTGTTTATA
1 AAATTACCAAAATACCCTCGGTTTGTA
52877024 AAATTACCAAAATACCC-CTGGTTTGTA
1 AAATTACCAAAATACCCTC-GGTTTGTA
52877051 AAATTACCAAAATACCC-CTGGTTTGTA
1 AAATTACCAAAATACCCTC-GGTTTGTA
* * ** *
52877078 AAATTACTAAAATACCTTTTGTTTATA
1 AAATTACCAAAATACCCTCGGTTTGTA
52877105 AAATTACCAAAATACCC-CTGGTTTGTA
1 AAATTACCAAAATACCCTC-GGTTTGTA
52877132 AAATTACCAAAATACCC-CTGGTTTGTA
1 AAATTACCAAAATACCCTC-GGTTTGTA
*
52877159 AAATTATCAAAATACCCCTC-GTTTGTA
1 AAATTACCAAAATA-CCCTCGGTTTGTA
** *
52877186 AAATTACCAAAATATCCCT-AATTTGTG
1 AAATTACCAAAATA-CCCTCGGTTTGTA
** ***
52877213 AAATTACTGAAATACCCTCGACCTGTA
1 AAATTACCAAAATACCCTCGGTTTGTA
*** **
52877240 AAATTATTGAAATACCCTCGACTTGTA
1 AAATTACCAAAATACCCTCGGTTTGTA
* * * **
52877267 AAATTACCAAAGTACCCTTGATTTACA
1 AAATTACCAAAATACCCTCGGTTTGTA
* *** * **
52877294 GAATTACCATTTTACCCTCGATTTACA
1 AAATTACCAAAATACCCTCGGTTTGTA
*
52877321 AAATTACTAAAATACCCT
1 AAATTACCAAAATACCCT
52877339 TGTAGGGTAG
Statistics
Matches: 375, Mismatches: 63, Indels: 24
0.81 0.14 0.05
Matches are distributed among these distances:
26 5 0.01
27 365 0.97
28 4 0.01
29 1 0.00
ACGTcount: A:0.39, C:0.21, G:0.09, T:0.32
Consensus pattern (27 bp):
AAATTACCAAAATACCCTCGGTTTGTA
Found at i:52877360 original size:27 final size:28
Alignment explanation
Indices: 52877330--52877471 Score: 143
Period size: 27 Copynumber: 5.2 Consensus size: 28
52877320 AAAATTACTA
* *
52877330 AAATACCCTTGTAGGGTAGAAAT-CTCG
1 AAATACCCCTATAGGGTAGAAATACTCG
*
52877357 AAATACCCCTATAGGGTAGAATTACT-G
1 AAATACCCCTATAGGGTAGAAATACTCG
*
52877384 AAATACCCCTATAGGGTAGAATTAC-C-
1 AAATACCCCTATAGGGTAGAAATACTCG
* *
52877410 AGAATACCCCTTTAGGGTAGAATTAC-CG
1 A-AATACCCCTATAGGGTAGAAATACTCG
* * *
52877438 AAATACCCCTGTAGGGTGGAATTAC-CG
1 AAATACCCCTATAGGGTAGAAATACTCG
*
52877465 AGATACC
1 AAATACC
52877472 TTGTGGAGTA
Statistics
Matches: 104, Mismatches: 7, Indels: 8
0.87 0.06 0.07
Matches are distributed among these distances:
26 1 0.01
27 100 0.96
28 3 0.03
ACGTcount: A:0.35, C:0.21, G:0.20, T:0.24
Consensus pattern (28 bp):
AAATACCCCTATAGGGTAGAAATACTCG
Found at i:52877380 original size:54 final size:54
Alignment explanation
Indices: 52877322--52877471 Score: 189
Period size: 54 Copynumber: 2.8 Consensus size: 54
52877312 CGATTTACAA
* * *
52877322 AATTACTAAAATACCCTTGTAGGGTAGAAAT-CTC-GAAATACCCCTATAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAGAATTAC-CAG-AATACCCCTATAGGGTAG
* *
52877376 AATTACTGAAATACCCCTATAGGGTAGAATTACCAGAATACCCCTTTAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAGAATTACCAGAATACCCCTATAGGGTAG
* *
52877430 AATTACCGAAATACCCCTGTAGGGTGGAATTACC-GAGATACC
1 AATTACTGAAATACCCCTGTAGGGTAGAATTACCAGA-ATACC
52877472 TTGTGGAGTA
Statistics
Matches: 85, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
53 2 0.02
54 81 0.95
55 2 0.02
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.25
Consensus pattern (54 bp):
AATTACTGAAATACCCCTGTAGGGTAGAATTACCAGAATACCCCTATAGGGTAG
Found at i:52877407 original size:81 final size:81
Alignment explanation
Indices: 52877322--52877471 Score: 205
Period size: 81 Copynumber: 1.9 Consensus size: 81
52877312 CGATTTACAA
* *
52877322 AATTACTAAAATA-CCCTTGTAGGGTAGAAAT-CTCGAAATACCCCTATAGGGTAGAATTACTGA
1 AATTACCAAAATACCCCTT-TAGGGTAGAAATAC-CGAAATACCCCTATAGGGTAGAATTACCGA
52877385 AATACCCCTATAGGGTAG
64 AATACCCCTATAGGGTAG
* * * * *
52877403 AATTACCAGAATACCCCTTTAGGGTAGAATTACCGAAATACCCCTGTAGGGTGGAATTACCGAGA
1 AATTACCAAAATACCCCTTTAGGGTAGAAATACCGAAATACCCCTATAGGGTAGAATTACCGAAA
52877468 TACC
66 TACC
52877472 TTGTGGAGTA
Statistics
Matches: 60, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
81 54 0.90
82 6 0.10
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.25
Consensus pattern (81 bp):
AATTACCAAAATACCCCTTTAGGGTAGAAATACCGAAATACCCCTATAGGGTAGAATTACCGAAA
TACCCCTATAGGGTAG
Found at i:52877968 original size:22 final size:22
Alignment explanation
Indices: 52877917--52877980 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 22
52877907 TAAAGCCTTT
* *
52877917 TGATTATGGCTTTGTGTCAACC
1 TGATTATGGCTCTGTGCCAACC
* *
52877939 T-ACATATGACTCTGTGCCAACC
1 TGA-TTATGGCTCTGTGCCAACC
*
52877961 TGATTATGGCTGTGTGCCAA
1 TGATTATGGCTCTGTGCCAA
52877981 ACGTATTTGC
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
21 1 0.03
22 31 0.94
23 1 0.03
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.34
Consensus pattern (22 bp):
TGATTATGGCTCTGTGCCAACC
Found at i:52878169 original size:27 final size:27
Alignment explanation
Indices: 52878139--52878240 Score: 125
Period size: 27 Copynumber: 3.8 Consensus size: 27
52878129 ATTCTGTTAA
* *
52878139 GTGGCTTTGCCACATTATCTGTTTCTG
1 GTGGCTCTGCCACAATATCTGTTTCTG
*
52878166 GTGGCTATGCCACAAATATCTG-TTCTG
1 GTGGCTCTGCCAC-AATATCTGTTTCTG
* *
52878193 GTGGCTCTGCCACAATATCTATATCTG
1 GTGGCTCTGCCACAATATCTGTTTCTG
* *
52878220 GTGACTCTGTCACAATATCTG
1 GTGGCTCTGCCACAATATCTG
52878241 ATAACTAAGC
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
26 7 0.11
27 51 0.78
28 7 0.11
ACGTcount: A:0.20, C:0.24, G:0.21, T:0.36
Consensus pattern (27 bp):
GTGGCTCTGCCACAATATCTGTTTCTG
Found at i:52878415 original size:6 final size:6
Alignment explanation
Indices: 52878400--52878496 Score: 74
Period size: 6 Copynumber: 15.8 Consensus size: 6
52878390 ATTCTATTAC
* * *
52878400 CTGATA CTGATT CTGATT TTGATT CTG-TT ACCTGATA CTGATT CTGATT
1 CTGATT CTGATT CTGATT CTGATT CTGATT --CTGATT CTGATT CTGATT
* * *
52878449 CTGATT CTG-TCAC CTAATT CTGATT CTGATT TTGATT CT-AGTT CTGAT
1 CTGATT CTGAT--T CTGATT CTGATT CTGATT CTGATT CTGA-TT CTGAT
52878497 AATGTTTCTT
Statistics
Matches: 72, Mismatches: 11, Indels: 16
0.73 0.11 0.16
Matches are distributed among these distances:
5 4 0.06
6 60 0.83
7 6 0.08
8 2 0.03
ACGTcount: A:0.20, C:0.18, G:0.15, T:0.47
Consensus pattern (6 bp):
CTGATT
Found at i:52878431 original size:31 final size:31
Alignment explanation
Indices: 52878377--52878487 Score: 159
Period size: 31 Copynumber: 3.5 Consensus size: 31
52878367 TTGCATTTAC
* *
52878377 ATTCTGATTTTTTATTCTATTACCTGATACTG
1 ATTCTGA-TTTTGATTCTGTTACCTGATACTG
52878409 ATTCTGATTTTGATTCTGTTACCTGATACTG
1 ATTCTGATTTTGATTCTGTTACCTGATACTG
* * * *
52878440 ATTCTGATTCTGATTCTGTCACCTAATTCTG
1 ATTCTGATTTTGATTCTGTTACCTGATACTG
52878471 ATTCTGATTTTGATTCT
1 ATTCTGATTTTGATTCT
52878488 AGTTCTGATA
Statistics
Matches: 72, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
31 65 0.90
32 7 0.10
ACGTcount: A:0.20, C:0.17, G:0.13, T:0.50
Consensus pattern (31 bp):
ATTCTGATTTTGATTCTGTTACCTGATACTG
Found at i:52878472 original size:37 final size:31
Alignment explanation
Indices: 52878390--52878512 Score: 142
Period size: 31 Copynumber: 4.0 Consensus size: 31
52878380 CTGATTTTTT
* *
52878390 ATTCTATTACCTGATACTGATTCTGATTTTG
1 ATTCTGTTACCTGATACTGATTCTGATTCTG
52878421 ATTCTGTTACCTGATACTGATTCTGATTCTG
1 ATTCTGTTACCTGATACTGATTCTGATTCTG
* * * *
52878452 ATTCTGTCACCTAATTCTGATTCTGATTTTG
1 ATTCTGTTACCTGATACTGATTCTGATTCTG
* * *
52878483 ATTCTAGTT--CTGATAATGTTTCTTATTCTG
1 ATTCT-GTTACCTGATACTGATTCTGATTCTG
52878513 TAATGGGTTA
Statistics
Matches: 78, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
30 15 0.19
31 61 0.78
32 2 0.03
ACGTcount: A:0.20, C:0.17, G:0.14, T:0.49
Consensus pattern (31 bp):
ATTCTGTTACCTGATACTGATTCTGATTCTG
Found at i:52885998 original size:19 final size:18
Alignment explanation
Indices: 52885962--52886006 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
52885952 TTTTAATGTA
52885962 TTAAATATAAATCATTAC
1 TTAAATATAAATCATTAC
*
52885980 TGTAAAGTATAATTC-TTAC
1 T-TAAA-TATAAATCATTAC
52885999 TTAAATAT
1 TTAAATAT
52886007 CAACTCTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
17 3 0.12
18 5 0.21
19 9 0.38
20 7 0.29
ACGTcount: A:0.44, C:0.09, G:0.04, T:0.42
Consensus pattern (18 bp):
TTAAATATAAATCATTAC
Found at i:52886468 original size:10 final size:11
Alignment explanation
Indices: 52886447--52886479 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
52886437 CTATAGTAAT
52886447 TTTATATTTTA
1 TTTATATTTTA
52886458 TTTAT-TTTTA
1 TTTATATTTTA
*
52886468 TTTTTATTTTA
1 TTTATATTTTA
52886479 T
1 T
52886480 AAAATATCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTATATTTTA
Found at i:52886623 original size:13 final size:13
Alignment explanation
Indices: 52886605--52886638 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
52886595 ATTAAAATTT
52886605 ATATATATTAGAA
1 ATATATATTAGAA
*
52886618 ATATATATTATAA
1 ATATATATTAGAA
*
52886631 AAATATAT
1 ATATATAT
52886639 GTTAGAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (13 bp):
ATATATATTAGAA
Found at i:52886647 original size:15 final size:15
Alignment explanation
Indices: 52886605--52886654 Score: 59
Period size: 15 Copynumber: 3.5 Consensus size: 15
52886595 ATTAAAATTT
52886605 ATATATATTAG--AA
1 ATATATATTAGAAAA
*
52886618 ATATATATTATAAAA
1 ATATATATTAGAAAA
*
52886633 ATATATGTTAGAAAA
1 ATATATATTAGAAAA
*
52886648 ATTTATA
1 ATATATA
52886655 AATATAAACT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
13 10 0.33
15 20 0.67
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.40
Consensus pattern (15 bp):
ATATATATTAGAAAA
Found at i:52888125 original size:14 final size:15
Alignment explanation
Indices: 52888106--52888134 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
52888096 AGAAACCATG
52888106 ATTTGGA-TAAAAAT
1 ATTTGGATTAAAAAT
52888120 ATTTGGATTAAAAAT
1 ATTTGGATTAAAAAT
52888135 CCAAATTCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.48, C:0.00, G:0.14, T:0.38
Consensus pattern (15 bp):
ATTTGGATTAAAAAT
Found at i:52888440 original size:18 final size:19
Alignment explanation
Indices: 52888410--52888454 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
52888400 TCGGTTCGAC
52888410 TAAATAAATTA-TTAAAAA
1 TAAATAAATTATTTAAAAA
*
52888428 TAAA-AAATATATTTTAAAA
1 TAAATAAAT-TATTTAAAAA
52888447 TAAATAAA
1 TAAATAAA
52888455 AATTGATTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 4 0.17
18 6 0.26
19 10 0.43
20 3 0.13
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
TAAATAAATTATTTAAAAA
Done.