Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006985.1 Hibiscus syriacus cultivar Beakdansim tig00017996_pilon, whole genome shotgun sequence
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: 663392
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
File 3 of 5
Found at i:289054 original size:26 final size:25
Alignment explanation
Indices: 289025--289133 Score: 64
Period size: 26 Copynumber: 4.3 Consensus size: 25
289015 ACAATTCTAA
289025 CAGTGAAACTTAACATTGACTTACAC
1 CAGTGAAACTTAACA-TGACTTACAC
* ** * *
289051 CAGTGAAA-TGATTATGTAATT-CTAG
1 CAGTGAAACTTAACATG-ACTTAC-AC
* * *
289076 CACT-AAACTTATGACATGA-TTTCAG
1 CAGTGAAACTTA--ACATGACTTACAC
289101 CAGTGAAACTTAACATTGACTTACAC
1 CAGTGAAACTTAACA-TGACTTACAC
289127 CAGTGAA
1 CAGTGAA
289134 TTGAATATAT
Statistics
Matches: 62, Mismatches: 12, Indels: 18
0.67 0.13 0.20
Matches are distributed among these distances:
24 9 0.15
25 22 0.35
26 28 0.45
27 3 0.05
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.29
Consensus pattern (25 bp):
CAGTGAAACTTAACATGACTTACAC
Found at i:289118 original size:76 final size:76
Alignment explanation
Indices: 288985--289432 Score: 540
Period size: 76 Copynumber: 5.9 Consensus size: 76
288975 CAACATTAAC
* * * *
288985 ATGTAATTCCAGCACTAAA-TTAAACACATCACAATTCTAACAGTGAAACTTAACATTGACTTAC
1 ATGTAATTCCAACACTAAACTT-ATCACAT---AATTCCAGCAGTGAAACTTAACATTGACTTAC
*
289049 ACCAGTGAAATGATT
62 ACCAGTGAAATGAAT
* * * * *
289064 ATGTAATTCTAGCACTAAACTTATGACATGATTTCAGCAGTGAAACTTAACATTGACTTACACCA
1 ATGTAATTCCAACACTAAACTTATCACATAATTCCAGCAGTGAAACTTAACATTGACTTACACCA
*
289129 GTGAATTGAAT
66 GTGAAATGAAT
* * * * * * * *
289140 ATATAATT-CAAGCACCAAACTTATCTCATCATTTCAGCAATGAAATTTAACATTGACTTGCACC
1 ATGTAATTCCAA-CACTAAACTTATCACATAATTCCAGCAGTGAAACTTAACATTGACTTACACC
*
289204 AGTAAAATGAAT
65 AGTGAAATGAAT
** * *
289216 ACATAATTCCAACACTAAACTTATCACATAATTCCAGTAGTGAAACTTAACATTAACTTACACCA
1 ATGTAATTCCAACACTAAACTTATCACATAATTCCAGCAGTGAAACTTAACATTGACTTACACCA
**
289281 ACGAAATGAAT
66 GTGAAATGAAT
* *
289292 ATGTAATTCCAACACTAAACTTATCACATAATTCCAACAGTGAAACTTAAAATTGACTTACACCA
1 ATGTAATTCCAACACTAAACTTATCACATAATTCCAGCAGTGAAACTTAACATTGACTTACACCA
289357 GTGAAATGAAT
66 GTGAAATGAAT
* * * * *
289368 ACGTAATTCCAACACTAAACTTATCACCTAATTCCAACAATGAAATTTAACATTGACTTACACCA
1 ATGTAATTCCAACACTAAACTTATCACATAATTCCAGCAGTGAAACTTAACATTGACTTACACCA
289433 ATTCAAACTT
Statistics
Matches: 319, Mismatches: 47, Indels: 9
0.85 0.13 0.02
Matches are distributed among these distances:
75 1 0.00
76 290 0.91
77 3 0.01
79 23 0.07
80 2 0.01
ACGTcount: A:0.42, C:0.21, G:0.09, T:0.29
Consensus pattern (76 bp):
ATGTAATTCCAACACTAAACTTATCACATAATTCCAGCAGTGAAACTTAACATTGACTTACACCA
GTGAAATGAAT
Found at i:290122 original size:69 final size:69
Alignment explanation
Indices: 290012--290178 Score: 223
Period size: 69 Copynumber: 2.4 Consensus size: 69
290002 TACGATAATA
* * *
290012 TGCTCCCTTGTGAGTCACTCTAATCCTTAGGAGCTTCCGTGCGAGTCAACC-GAAATAATTACGA
1 TGCTCCCTTGTGAGTCACTCTAATCCTTCGGAGCTTCCGTGCGAGTCACCCAG-AATAATCACGA
290076 TTAGG
65 TTAGG
* * *
290081 TGCT-CCTGTGTGAGTCATTCTATTCCTTCGTG-GCTTTCGTGCGAGTCACCCAGAATAATCACG
1 TGCTCCCT-TGTGAGTCACTCTAATCCTTCG-GAGCTTCCGTGCGAGTCACCCAGAATAATCACG
290144 ATTAGG
64 ATTAGG
*
290150 TGCTCCCTTGCGAGTCACTCTAATCCTTC
1 TGCTCCCTTGTGAGTCACTCTAATCCTTC
290179 AAGGCTCATG
Statistics
Matches: 85, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
68 3 0.04
69 77 0.91
70 5 0.06
ACGTcount: A:0.20, C:0.27, G:0.21, T:0.32
Consensus pattern (69 bp):
TGCTCCCTTGTGAGTCACTCTAATCCTTCGGAGCTTCCGTGCGAGTCACCCAGAATAATCACGAT
TAGG
Found at i:290196 original size:69 final size:67
Alignment explanation
Indices: 290012--290206 Score: 205
Period size: 69 Copynumber: 2.8 Consensus size: 67
290002 TACGATAATA
* * *
290012 TGCTCCCTTGTGAGTCACTCTAATCCTT-AGGAGCTTCCGTGCGAGTCAACCGAAATAATTACGA
1 TGCTCCCTTGTGAGTCACTCTAATCCTTCAAG-GC-TCTGTGCGAGTCAACCG-AATAATCACGA
290076 TTAGG
63 TTAGG
* * ** * *
290081 TGCT-CCTGTGTGAGTCATTCTATTCCTTCGTGGCTTTCGTGCGAGTCACCCAGAATAATCACGA
1 TGCTCCCT-TGTGAGTCACTCTAATCCTTCAAGGCTCT-GTGCGAGTCAACC-GAATAATCACGA
290145 TTAGG
63 TTAGG
* *
290150 TGCTCCCTTGCGAGTCACTCTAATCCTTCAAGGCTCATGTGTGAGTCAACCGGAATA
1 TGCTCCCTTGTGAGTCACTCTAATCCTTCAAGGCTC-TGTGCGAGTCAACC-GAATA
290207 CTCATTATTA
Statistics
Matches: 103, Mismatches: 17, Indels: 12
0.78 0.13 0.09
Matches are distributed among these distances:
68 4 0.04
69 93 0.90
70 6 0.06
ACGTcount: A:0.22, C:0.26, G:0.22, T:0.30
Consensus pattern (67 bp):
TGCTCCCTTGTGAGTCACTCTAATCCTTCAAGGCTCTGTGCGAGTCAACCGAATAATCACGATTA
GG
Found at i:290404 original size:26 final size:25
Alignment explanation
Indices: 290375--290483 Score: 82
Period size: 26 Copynumber: 4.3 Consensus size: 25
290365 GCAATTCTAA
290375 CAGTGAAACTTAACATTGACTTACAC
1 CAGTGAAACTTAACA-TGACTTACAC
* * *
290401 CAGTGAAA-TGAATATGTACTT-CTAG
1 CAGTGAAACTTAACATG-ACTTAC-AC
* * *
290426 CACT-AAACTTATGACATGA-TTTCAA
1 CAGTGAAACTTA--ACATGACTTACAC
290451 CAGTGAAACTTAACATTGACTTACAC
1 CAGTGAAACTTAACA-TGACTTACAC
290477 CAGTGAA
1 CAGTGAA
290484 TTGAATATGT
Statistics
Matches: 64, Mismatches: 10, Indels: 18
0.70 0.11 0.20
Matches are distributed among these distances:
24 9 0.14
25 23 0.36
26 28 0.44
27 4 0.06
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28
Consensus pattern (25 bp):
CAGTGAAACTTAACATGACTTACAC
Found at i:290460 original size:76 final size:76
Alignment explanation
Indices: 290367--290784 Score: 550
Period size: 76 Copynumber: 5.5 Consensus size: 76
290357 AACACATCGC
* * * * * *
290367 AATTCTAACAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATATGTACTTCTAGCACTAA
1 AATTCCAACAGTGAAACTTAACATTGACTTACACCAATGAAATGAATACGTAATTCCAACACTAA
*
290432 ACTTATGACAT
66 ACTTATCACAT
* * * * * *
290443 GATTTCAACAGTGAAACTTAACATTGACTTACACCAGTGAATTGAATATGTAATT-CAAGCACCA
1 AATTCCAACAGTGAAACTTAACATTGACTTACACCAATGAAATGAATACGTAATTCCAA-CACTA
290507 AACTTATCACAT
65 AACTTATCACAT
* * * * * *
290519 CATTTCAGCAATGAAATTTAACATTGACTTACACCAATAAAATGAATACGTAATTCCAACACTAA
1 AATTCCAACAGTGAAACTTAACATTGACTTACACCAATGAAATGAATACGTAATTCCAACACTAA
290584 ACTTATCACAT
66 ACTTATCACAT
** * *
290595 AATTCCAGTAGTGAAACTTAACATTAACTTACACCAACGAAATGAATACGTAATTCCAACACTAA
1 AATTCCAACAGTGAAACTTAACATTGACTTACACCAATGAAATGAATACGTAATTCCAACACTAA
290660 ACTTATCACAT
66 ACTTATCACAT
* *
290671 AATTCCAACAGTGAAACTTAAAATTGACTTACACCATTGAAATGAATACGTAATTCCAACACTAA
1 AATTCCAACAGTGAAACTTAACATTGACTTACACCAATGAAATGAATACGTAATTCCAACACTAA
*
290736 ACTTATCACCT
66 ACTTATCACAT
* * * *
290747 AATTCCATCAATGAAATTTATCATTGACTTACACCAAT
1 AATTCCAACAGTGAAACTTAACATTGACTTACACCAAT
290785 TCAAACTTGA
Statistics
Matches: 301, Mismatches: 39, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
75 1 0.00
76 297 0.99
77 3 0.01
ACGTcount: A:0.41, C:0.21, G:0.09, T:0.29
Consensus pattern (76 bp):
AATTCCAACAGTGAAACTTAACATTGACTTACACCAATGAAATGAATACGTAATTCCAACACTAA
ACTTATCACAT
Found at i:290597 original size:25 final size:24
Alignment explanation
Indices: 290564--290690 Score: 78
Period size: 25 Copynumber: 5.0 Consensus size: 24
290554 AATAAAATGA
*
290564 ATACGTAATTCCAACACTAAACTT
1 ATACATAATTCCAACACTAAACTT
** *
290588 ATCACATAATTCCAGTAGTGAAACTT
1 AT-ACATAATTCCAACACT-AAACTT
* * * *
290614 A-ACATTAACTTACACCAACGAAA-TGA
1 ATACA-TAA-TTCCAAC-ACTAAACT-T
*
290640 ATACGTAATTCCAACACTAAACTT
1 ATACATAATTCCAACACTAAACTT
*
290664 ATCACATAATTCCAACAGTGAAACTT
1 AT-ACATAATTCCAACACT-AAACTT
290690 A
1 A
290691 AAATTGACTT
Statistics
Matches: 76, Mismatches: 17, Indels: 18
0.68 0.15 0.16
Matches are distributed among these distances:
24 12 0.16
25 36 0.47
26 25 0.33
27 3 0.04
ACGTcount: A:0.43, C:0.23, G:0.07, T:0.27
Consensus pattern (24 bp):
ATACATAATTCCAACACTAAACTT
Found at i:291490 original size:69 final size:69
Alignment explanation
Indices: 291371--291501 Score: 167
Period size: 69 Copynumber: 1.9 Consensus size: 69
291361 TATGCTCCCT
* *
291371 TGTGAGTCACTCTAATCCTTAGGAGCTTCCGTGCGAGTCAACCGAAATAATTACGATTAGGTACT
1 TGTGAGTCACTCTAATCCTTAGGAGCTTCCGTGCGAGTCAACCGAAATAATCACGAATAGGTACT
291436 GCTG
66 GCTG
* * * * *
291440 TGTGAGTCACTCTATTCCTTCGG-GACTTTCGTGCGAGTC-ACCCAGCATAATCACGAATAGGT
1 TGTGAGTCACTCTAATCCTTAGGAG-CTTCCGTGCGAGTCAACCGA-AATAATCACGAATAGGT
291502 GCTCCCTTCC
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
68 5 0.09
69 48 0.91
ACGTcount: A:0.24, C:0.24, G:0.23, T:0.29
Consensus pattern (69 bp):
TGTGAGTCACTCTAATCCTTAGGAGCTTCCGTGCGAGTCAACCGAAATAATCACGAATAGGTACT
GCTG
Found at i:291819 original size:76 final size:76
Alignment explanation
Indices: 291687--292132 Score: 499
Period size: 76 Copynumber: 5.8 Consensus size: 76
291677 ACATTAACAT
* *
291687 GTAATTCCAGCACTAAA-TTAAACACATCACAATTCTAAG-AGTGAAACTTAACATTGACTTACA
1 GTAATTCCAGCACTAAACTT-ATCACAT---AATTC-CAGCAGTGAAACTTAACATTGACTTACA
* *
291750 CCAGTGAAATGATTAT
61 CCAGTGAAATGAATAC
* * * *
291766 GTAATTCTAGCACTAAACTTATGACATGATTTCAGCAGTGAAACTTAACATTGACTTACACCAGT
1 GTAATTCCAGCACTAAACTTATCACATAATTCCAGCAGTGAAACTTAACATTGACTTACACCAGT
291831 GAAATGAATAC
66 GAAATGAATAC
* * * *
291842 GTAATT-CATGCACCAAACTTATCAGATCATTTCATG-AGTGAAA-TTGAACATTGACTTACACC
1 GTAATTCCA-GCACTAAACTTATCACATAATTCCA-GCAGTGAAACTT-AACATTGACTTACACC
291904 AGT-AAAGTGAATAC
63 AGTGAAA-TGAATAC
*** * * * * **
291918 GTAATTCCAATGCTAAACTTATCACTTAATTCCAGTAGTGAAATTTAACATTAACTTACACCAAC
1 GTAATTCCAGCACTAAACTTATCACATAATTCCAGCAGTGAAACTTAACATTGACTTACACCAGT
291983 GAAATGAATAC
66 GAAATGAATAC
* * * * *
291994 GTAATTCCAACACTAAACTTATCACATTATTCCAACAGTGAAACTTAAAATTGATTTACACCAGT
1 GTAATTCCAGCACTAAACTTATCACATAATTCCAGCAGTGAAACTTAACATTGACTTACACCAGT
*
292059 GAAATGAATAT
66 GAAATGAATAC
* * *
292070 GTAATTCCAGCACTAAACTTATCACCTAATTCCAGCAATGAAATTTAACATTGACTTACACCA
1 GTAATTCCAGCACTAAACTTATCACATAATTCCAGCAGTGAAACTTAACATTGACTTACACCA
292133 ATTCAAACTC
Statistics
Matches: 312, Mismatches: 45, Indels: 23
0.82 0.12 0.06
Matches are distributed among these distances:
75 9 0.03
76 272 0.87
77 8 0.03
79 21 0.07
80 2 0.01
ACGTcount: A:0.40, C:0.20, G:0.11, T:0.29
Consensus pattern (76 bp):
GTAATTCCAGCACTAAACTTATCACATAATTCCAGCAGTGAAACTTAACATTGACTTACACCAGT
GAAATGAATAC
Found at i:298862 original size:76 final size:73
Alignment explanation
Indices: 298723--298985 Score: 237
Period size: 76 Copynumber: 3.5 Consensus size: 73
298713 TTTAATACAG
* * *
298723 AAGA-TTCATCTCGCTTGAGATAGTTTCCACTCAAAACAAGACATTTCATTTCACTACAGATTGT
1 AAGACTTCATCTCGCTTGAGATTGTTT-CACTCGAAATAAGACATTTCATTTCACTACAGATTG-
298787 TTTTCTTAAAAC
64 -TTT-TTAAAAC
* * *
298799 -AGACTTCGTCTCGCTTGAGACTTTTTTTACTCGAAATAAGACATTTCATTTCACT-CAGTATTG
1 AAGACTTCATCTCGCTTGAGA-TTGTTTCACTCGAAATAAGACATTTCATTTCACTACAG-ATTG
298862 TTTTTAAAAC
64 TTTTTAAAAC
* * * * * **
298872 AAGATTTTATCTCGCTTGAGATTGTTTCACTCGAAAT-AGAAGATTTTATCTCACTTGAGATTGT
1 AAGACTTCATCTCGCTTGAGATTGTTTCACTCGAAATAAG-ACATTTCATTTCACTACAGATTGT
* *
298936 TTCACTCGAAACAG
65 TT---T-TAAA-AC
* *
298950 AAGATTTTATCTCGCTTGAGATTGTTTCACTCGAAA
1 AAGACTTCATCTCGCTTGAGATTGTTTCACTCGAAA
298986 CAGAAGATTT
Statistics
Matches: 159, Mismatches: 17, Indels: 20
0.81 0.09 0.10
Matches are distributed among these distances:
72 2 0.01
73 40 0.25
74 22 0.14
75 6 0.04
76 45 0.28
77 7 0.04
78 37 0.23
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.38
Consensus pattern (73 bp):
AAGACTTCATCTCGCTTGAGATTGTTTCACTCGAAATAAGACATTTCATTTCACTACAGATTGTT
TTTAAAAC
Found at i:298929 original size:39 final size:39
Alignment explanation
Indices: 298872--299075 Score: 381
Period size: 39 Copynumber: 5.2 Consensus size: 39
298862 TTTTTAAAAC
*
298872 AAGATTTTATCTCGCTTGAGATTGTTTCACTCGAAATAG
1 AAGATTTTATCTCGCTTGAGATTGTTTCACTCGAAACAG
*
298911 AAGATTTTATCTCACTTGAGATTGTTTCACTCGAAACAG
1 AAGATTTTATCTCGCTTGAGATTGTTTCACTCGAAACAG
298950 AAGATTTTATCTCGCTTGAGATTGTTTCACTCGAAACAG
1 AAGATTTTATCTCGCTTGAGATTGTTTCACTCGAAACAG
298989 AAGATTTTATCTCGCTTGAGATTGTTTCACTCGAAACAG
1 AAGATTTTATCTCGCTTGAGATTGTTTCACTCGAAACAG
*
299028 AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAG
1 AAGATTTTATCTCGCTTGAGATTGTTTCACTCGAAACAG
299067 AAGATTTTA
1 AAGATTTTA
299076 AGAAACAAAG
Statistics
Matches: 161, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 161 1.00
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36
Consensus pattern (39 bp):
AAGATTTTATCTCGCTTGAGATTGTTTCACTCGAAACAG
Found at i:299219 original size:41 final size:41
Alignment explanation
Indices: 299107--299235 Score: 141
Period size: 42 Copynumber: 3.1 Consensus size: 41
299097 AGGGTTTCTT
* *
299107 GATGAGTAAGTCCTTCGGGCCATCAATAAGTCTTTCAAGCAT
1 GATGA-TAAGTCCTTCGGGCCATCAATAAGTCTTTCGAGCAA
* * * * *
299149 GATGTTTAAATCCTTTGGGTCATCTATAAGTCTTTCGAGCAA
1 GATG-ATAAGTCCTTCGGGCCATCAATAAGTCTTTCGAGCAA
* * * *
299191 GATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGCAA
1 GATGATAAGTCCTTCGGGCCATCAATAAGTCTTTCGAGCAA
299232 GATG
1 GATG
299236 TTTTCAACAT
Statistics
Matches: 71, Mismatches: 15, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
41 33 0.46
42 38 0.54
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.29
Consensus pattern (41 bp):
GATGATAAGTCCTTCGGGCCATCAATAAGTCTTTCGAGCAA
Found at i:299563 original size:13 final size:13
Alignment explanation
Indices: 299488--299561 Score: 121
Period size: 13 Copynumber: 5.7 Consensus size: 13
299478 TGCGTCATAA
299488 ATTTATGACGCGC
1 ATTTATGACGCGC
*
299501 ATTTATGACACGC
1 ATTTATGACGCGC
299514 ATTTATGACGCGC
1 ATTTATGACGCGC
299527 ATTTATGACGCGC
1 ATTTATGACGCGC
**
299540 ATTTATGACTTGC
1 ATTTATGACGCGC
299553 ATTTATGAC
1 ATTTATGAC
299562 TTACATTGCG
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 57 1.00
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.35
Consensus pattern (13 bp):
ATTTATGACGCGC
Found at i:299568 original size:13 final size:13
Alignment explanation
Indices: 299539--299568 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
299529 TTATGACGCG
*
299539 CATTTATGACTTG
1 CATTTATGACTTA
299552 CATTTATGACTTA
1 CATTTATGACTTA
299565 CATT
1 CATT
299569 GCGCGTCATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.27, C:0.17, G:0.10, T:0.47
Consensus pattern (13 bp):
CATTTATGACTTA
Found at i:299683 original size:85 final size:85
Alignment explanation
Indices: 299540--299705 Score: 269
Period size: 85 Copynumber: 2.0 Consensus size: 85
299530 TATGACGCGC
** *
299540 ATTTATGACTTGCATTTATGACTTACATTGCGCGTCATTGAAGCCCCCGTCATAAATGAAGATGA
1 ATTTATGACACGCATTTATGACTTACATTGCGCGTCATTGAAGCCCCCGTCATAAATGAAAATGA
* *
299605 CACATATTTGTGTGTCATAA
66 CACACATTCGTGTGTCATAA
* *
299625 ATTTATGACACGCATTTATGACTTACATTGTGTGTCATTGAAGCCCCCGTCATAAATGAAAATGA
1 ATTTATGACACGCATTTATGACTTACATTGCGCGTCATTGAAGCCCCCGTCATAAATGAAAATGA
299690 CACACATTCGTGTGTC
66 CACACATTCGTGTGTC
299706 GTGATTGTAT
Statistics
Matches: 74, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
85 74 1.00
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (85 bp):
ATTTATGACACGCATTTATGACTTACATTGCGCGTCATTGAAGCCCCCGTCATAAATGAAAATGA
CACACATTCGTGTGTCATAA
Found at i:299732 original size:2 final size:2
Alignment explanation
Indices: 299725--299777 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
299715 TTTCGTGAAT
299725 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
299767 TA TA TA TA TA T
1 TA TA TA TA TA T
299778 TGTAGATTGA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:303902 original size:40 final size:40
Alignment explanation
Indices: 303736--303972 Score: 243
Period size: 39 Copynumber: 6.0 Consensus size: 40
303726 TATTTTCTTG
* * *
303736 TAGTGTTCACTCGAAACAGAAGA-CTTTATCTTGCTTAAGA
1 TAGT-TTCACTCGAAACAGAAGATTTTTATCTCGCTTGAGA
* ** **
303776 TACTTTCACTCGAAATGGAAGA-TTACATCTCGCTTGAGA
1 TAGTTTCACTCGAAACAGAAGATTTTTATCTCGCTTGAGA
** * *
303815 TAGTTTCACTCGAAACAGAAGA-TTACATTTCACTTGAGA
1 TAGTTTCACTCGAAACAGAAGATTTTTATCTCGCTTGAGA
* * *
303854 TAGTTTCACTCAAAACAGAAGATTTTTGTCTTGCTTGAGA
1 TAGTTTCACTCGAAACAGAAGATTTTTATCTCGCTTGAGA
*
303894 TAGTTTCACTCGAAACA-ACAGATTTTTATCTCGCTTGTGA
1 TAGTTTCACTCGAAACAGA-AGATTTTTATCTCGCTTGAGA
* * *
303934 TAGTTTCACTCGAAAAAGATGA--TTTATCTCACTTGAGA
1 TAGTTTCACTCGAAACAGAAGATTTTTATCTCGCTTGAGA
303972 T
1 T
303973 TGATTTTCTT
Statistics
Matches: 166, Mismatches: 28, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
38 15 0.09
39 84 0.51
40 66 0.40
41 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (40 bp):
TAGTTTCACTCGAAACAGAAGATTTTTATCTCGCTTGAGA
Found at i:303988 original size:118 final size:117
Alignment explanation
Indices: 303736--303972 Score: 298
Period size: 118 Copynumber: 2.0 Consensus size: 117
303726 TATTTTCTTG
* **
303736 TAGTGTTCACTCGAAACAGAAGACTTTATCTTGCTTAAGATACTTTCACTCGAAATGGAAGATTA
1 TAGT-TTCACTCAAAACAGAAGACTTTATCTTGCTTAAGATACTTTCACTCGAAATCAAAGATTA
* *
303801 CATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTACATTTCACTTGAGA
65 CATCTCGCTTGAGATAGTTTCACTCGAAAAAGAAGATTACATCTCACTTGAGA
* * * *
303854 TAGTTTCACTCAAAACAGAAGATTTTTGTCTTGCTTGAGATAGTTTCACTCGAAA-CAACAGATT
1 TAGTTTCACTCAAAACAGAAGA-CTTTATCTTGCTTAAGATACTTTCACTCGAAATCAA-AGA-T
** * * *
303918 TTTATCTCGCTTGTGATAGTTTCACTCGAAAAAGATGATT-TATCTCACTTGAGA
63 TACATCTCGCTTGAGATAGTTTCACTCGAAAAAGAAGATTACATCTCACTTGAGA
303972 T
1 T
303973 TGATTTTCTT
Statistics
Matches: 102, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
117 18 0.18
118 48 0.47
119 36 0.35
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (117 bp):
TAGTTTCACTCAAAACAGAAGACTTTATCTTGCTTAAGATACTTTCACTCGAAATCAAAGATTAC
ATCTCGCTTGAGATAGTTTCACTCGAAAAAGAAGATTACATCTCACTTGAGA
Found at i:305603 original size:22 final size:22
Alignment explanation
Indices: 305573--305623 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
305563 TTTTGTCTTA
305573 TTTTAATTTAG-TCACTGTTAGC
1 TTTTAATTTAGCT-ACTGTTAGC
*
305595 TTTTGATTTAGCTACTGTTA--
1 TTTTAATTTAGCTACTGTTAGC
305615 TTTTAATTT
1 TTTTAATTT
305624 TTGCATTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 8 0.31
22 17 0.65
23 1 0.04
ACGTcount: A:0.22, C:0.10, G:0.12, T:0.57
Consensus pattern (22 bp):
TTTTAATTTAGCTACTGTTAGC
Found at i:307335 original size:76 final size:76
Alignment explanation
Indices: 307242--307651 Score: 545
Period size: 76 Copynumber: 5.4 Consensus size: 76
307232 TTACAATTCT
*
307242 AGCAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCTAGCACTAAACTTAT
1 AGCAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAGCACTAAACTTAT
* *
307307 GACATGATTTC
66 CACATAATTTC
* * *
307318 AGCAGTGAAACTTAACATTGACTTACACCAGTGAGATGAATACGTAATTCAAGCACCAAACTTAT
1 AGCAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAGCACTAAACTTAT
*
307383 CACATCATTTC
66 CACATAATTTC
* * * * * *
307394 AGCAGTGAAATTTAACATTGACTTACACCAGTAAAATGAATATGTAATTCCAACGCTAAATTTAT
1 AGCAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAGCACTAAACTTAT
*
307459 CACATAATTCC
66 CACATAATTTC
* * * *
307470 AGTAGTGAAACTTAACATTAACTTACACCAAAT-AAATGAATACGTAATTCCAACACTAAACTTA
1 AGCAGTGAAACTTAACATTGACTTACACC-AGTGAAATGAATACGTAATTCCAGCACTAAACTTA
*
307534 TCACATAATTCC
65 TCACATAATTTC
* * * *
307546 AACAATGAAACTTAACATTGTCTTACACCAGTGAAATAAATACGTAATTCCAGCACTAAACTTAT
1 AGCAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAGCACTAAACTTAT
*
307611 CACCT-ATTTC
66 CACATAATTTC
* * *
307621 TAGCAATGAAATTTAACATTAACTTACACCA
1 -AGCAGTGAAACTTAACATTGACTTACACCA
307652 ATTCAAGCTC
Statistics
Matches: 294, Mismatches: 37, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
75 6 0.02
76 286 0.97
77 2 0.01
ACGTcount: A:0.41, C:0.20, G:0.10, T:0.29
Consensus pattern (76 bp):
AGCAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAGCACTAAACTTAT
CACATAATTTC
Found at i:307648 original size:228 final size:228
Alignment explanation
Indices: 307236--307651 Score: 629
Period size: 228 Copynumber: 1.8 Consensus size: 228
307226 AACATATTAC
* * * * *
307236 AATTCTAGCAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCTAGCACTAA
1 AATTCCAGCAGTGAAACTTAACATTAACTTACACCAATGAAATGAATACGTAATTCCAACACTAA
* * * * * * *
307301 ACTTATGACATGATTTCAGCAGTGAAACTTAACATTGACTTACACCAGTGAGATGAATACGTAAT
66 ACTTATCACATAATTCCAACAATGAAACTTAACATTGACTTACACCAGTGAAATAAATACGTAAT
* *
307366 TCAAGCACCAAACTTATCACATCATTTCAGCAGTGAAATTTAACATTGACTTACACCAGTAAAAT
131 TCAAGCACCAAACTTATCACATCATTTCAGCAATGAAATTTAACATTAACTTACACCAGTAAAAT
307431 GAATATGTAATTCCAACGCTAAATTTATCACAT
196 GAATATGTAATTCCAACGCTAAATTTATCACAT
*
307464 AATTCCAGTAGTGAAACTTAACATTAACTTACACCAAAT-AAATGAATACGTAATTCCAACACTA
1 AATTCCAGCAGTGAAACTTAACATTAACTTACACC-AATGAAATGAATACGTAATTCCAACACTA
*
307528 AACTTATCACATAATTCCAACAATGAAACTTAACATTGTCTTACACCAGTGAAATAAATACGTAA
65 AACTTATCACATAATTCCAACAATGAAACTTAACATTGACTTACACCAGTGAAATAAATACGTAA
* * *
307593 TTCCAGCACTAAACTTATCACCT-ATTTCTAGCAATGAAATTTAACATTAACTTACACCA
130 TTCAAGCACCAAACTTATCACATCATTTC-AGCAATGAAATTTAACATTAACTTACACCA
307652 ATTCAAGCTC
Statistics
Matches: 167, Mismatches: 19, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
227 5 0.03
228 160 0.96
229 2 0.01
ACGTcount: A:0.41, C:0.20, G:0.10, T:0.29
Consensus pattern (228 bp):
AATTCCAGCAGTGAAACTTAACATTAACTTACACCAATGAAATGAATACGTAATTCCAACACTAA
ACTTATCACATAATTCCAACAATGAAACTTAACATTGACTTACACCAGTGAAATAAATACGTAAT
TCAAGCACCAAACTTATCACATCATTTCAGCAATGAAATTTAACATTAACTTACACCAGTAAAAT
GAATATGTAATTCCAACGCTAAATTTATCACAT
Found at i:308412 original size:69 final size:69
Alignment explanation
Indices: 308232--308418 Score: 193
Period size: 69 Copynumber: 2.7 Consensus size: 69
308222 TACGATCATA
* * * * *
308232 TGCTCCCTTGTGAGTCACTTTAA-CCCTTCAGAGCTCTCGTGCGAGTCAACCGAAATAATTACGA
1 TGCTCCCTTGTGAGTCACTCTAATCCTTTAAG-GCTCTCGTGCGAGTCACCCGAAATAATAACGA
308296 TTAGG
65 TTAGG
* * * * * * *
308301 TGCT-CCTGTATAAGTCACTCTATTTCTTCAGGGCTTTCGTGCGAGTCACCC-AGAATAATAACG
1 TGCTCCCT-TGTGAGTCACTCTAATCCTTTAAGGCTCTCGTGCGAGTCACCCGA-AATAATAACG
308364 ATTAGG
64 ATTAGG
*
308370 TGCTCCCTTGCGAGTCACTCTAATCCTTTAAGGCTCAT-GTGCGAGTCAC
1 TGCTCCCTTGTGAGTCACTCTAATCCTTTAAGGCTC-TCGTGCGAGTCAC
308419 TCGGAATACT
Statistics
Matches: 93, Mismatches: 20, Indels: 10
0.76 0.16 0.08
Matches are distributed among these distances:
68 4 0.04
69 82 0.88
70 7 0.08
ACGTcount: A:0.23, C:0.26, G:0.20, T:0.30
Consensus pattern (69 bp):
TGCTCCCTTGTGAGTCACTCTAATCCTTTAAGGCTCTCGTGCGAGTCACCCGAAATAATAACGAT
TAGG
Found at i:308690 original size:76 final size:76
Alignment explanation
Indices: 308593--309002 Score: 556
Period size: 76 Copynumber: 5.4 Consensus size: 76
308583 TCAAAATTAT
* *
308593 AGCAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATATGTAATTCTAGCACTAAACTTAT
1 AGCAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAGCACTAAACTTAT
* *
308658 GACATGATTTC
66 CACATAATTTC
* * * *
308669 AGCACTGAAACTTAACATTGACATACACCAGTGAATTGAATACGTAATTCTAGCACTAAACTTAT
1 AGCAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAGCACTAAACTTAT
* *
308734 GACATGATTTC
66 CACATAATTTC
* * * *
308745 AGCAGTGAAATTTAACATTGACTTACACTAGTAAAATGAATACGTAATTCCAACGA-TAAACTTA
1 AGCAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAGC-ACTAAACTTA
*
308809 TCACATAATTCC
65 TCACATAATTTC
* * *
308821 AGTAGTGAAACTTAACATTAACTTACACCAAG-GAAATGAATACGTAATTCCAACACTAAACTTA
1 AGCAGTGAAACTTAACATTGACTTACACC-AGTGAAATGAATACGTAATTCCAGCACTAAACTTA
*
308885 TCACATAATTCC
65 TCACATAATTTC
*
308897 AACAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAGCACTAAACTTAT
1 AGCAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAGCACTAAACTTAT
*
308962 CACCTAA-TTC
66 CACATAATTTC
* * *
308972 TAGCAATGAAATTTAACATTAACTTACACCA
1 -AGCAGTGAAACTTAACATTGACTTACACCA
309003 ATTCAAGCTC
Statistics
Matches: 299, Mismatches: 30, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
75 5 0.02
76 291 0.97
77 3 0.01
ACGTcount: A:0.41, C:0.20, G:0.11, T:0.28
Consensus pattern (76 bp):
AGCAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAGCACTAAACTTAT
CACATAATTTC
Found at i:309764 original size:69 final size:69
Alignment explanation
Indices: 309584--309770 Score: 193
Period size: 69 Copynumber: 2.7 Consensus size: 69
309574 TACGATCATA
* * * * *
309584 TGCTCCCTTGTGAGTCACTTTAA-CCCTTCAGAGCTCTCGTGCGAGTCAACCGAAATAATTACGA
1 TGCTCCCTTGTGAGTCACTATAATCCTTTAAG-GCTCTCGTGCGAGTCACCCGAAATAATCACGA
309648 TTAGG
65 TTAGG
* * * * * *
309653 TGCT-CCTGTATGAGTCACTATATTTCTTCAGGGCTTTCGTGCGAGTCACCC-AGAATAATCACG
1 TGCTCCCT-TGTGAGTCACTATAATCCTTTAAGGCTCTCGTGCGAGTCACCCGA-AATAATCACG
309716 ATTAGG
64 ATTAGG
* *
309722 TGCTCCCTTGCGAGTCACTCTAATCCTTTAAGGCTC-CTGTGCGAGTCAC
1 TGCTCCCTTGTGAGTCACTATAATCCTTTAAGGCTCTC-GTGCGAGTCAC
309771 TCGGAATACT
Statistics
Matches: 94, Mismatches: 19, Indels: 10
0.76 0.15 0.08
Matches are distributed among these distances:
68 5 0.05
69 83 0.88
70 6 0.06
ACGTcount: A:0.22, C:0.27, G:0.21, T:0.30
Consensus pattern (69 bp):
TGCTCCCTTGTGAGTCACTATAATCCTTTAAGGCTCTCGTGCGAGTCACCCGAAATAATCACGAT
TAGG
Found at i:310040 original size:76 final size:76
Alignment explanation
Indices: 309939--310430 Score: 723
Period size: 76 Copynumber: 6.5 Consensus size: 76
309929 AACACATCAA
* * * * * *
309939 AATTCTAGAAGTGAAACTTAACATTGACCTACACCAGTGAAATGAATATGTAATTCTAGCACTAA
1 AATTCCAGCAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAACACTAA
*
310004 ACTTATGACAT
66 ACTTATCACAT
* * * ** *
310015 GATTTCAGCAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCGAGTACCAA
1 AATTCCAGCAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAACACTAA
310080 ACTTATCACAT
66 ACTTATCACAT
* * * * *
310091 CATTTCAGCAGTGAAATTTAACATTGACTTACACCAGTAAAATGAATACGTAATTCCAACGCTAA
1 AATTCCAGCAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAACACTAA
* *
310156 ACTTTTCACAA
66 ACTTATCACAT
* * **
310167 AATTCCAGTAGTGAAACTTAACATTAACTTACACCAAAGAAATGAATACGTAATTCCAACACTAA
1 AATTCCAGCAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAACACTAA
310232 ACTTATCACAT
66 ACTTATCACAT
*
310243 AATTCCAACAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAACACTAA
1 AATTCCAGCAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAACACTAA
310308 ACTTATCACAT
66 ACTTATCACAT
*
310319 AATTCCAACAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAACACTAA
1 AATTCCAGCAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAACACTAA
*
310384 ACTTATCACCT
66 ACTTATCACAT
* *
310395 AATTCCAGCAATGAAATTTAACATTGACTTACACCA
1 AATTCCAGCAGTGAAACTTAACATTGACTTACACCA
310431 ATTCAAGCTC
Statistics
Matches: 376, Mismatches: 40, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
76 376 1.00
ACGTcount: A:0.41, C:0.21, G:0.11, T:0.27
Consensus pattern (76 bp):
AATTCCAGCAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAACACTAA
ACTTATCACAT
Found at i:310052 original size:26 final size:25
Alignment explanation
Indices: 309948--310056 Score: 64
Period size: 26 Copynumber: 4.3 Consensus size: 25
309938 AAATTCTAGA
*
309948 AGTGAAACTTAACATTGACCTACACC
1 AGTGAAACTTAACA-TGACTTACACC
* * * *
309974 AGTGAAA-TGAATATGTAATT-CTAGC
1 AGTGAAACTTAACATG-ACTTAC-ACC
* * *
309999 ACT-AAACTTATGACATGA-TTTCAGC
1 AGTGAAACTTA--ACATGACTTACACC
310024 AGTGAAACTTAACATTGACTTACACC
1 AGTGAAACTTAACA-TGACTTACACC
310050 AGTGAAA
1 AGTGAAA
310057 TGAATACGTA
Statistics
Matches: 63, Mismatches: 11, Indels: 18
0.68 0.12 0.20
Matches are distributed among these distances:
24 9 0.14
25 22 0.35
26 28 0.44
27 4 0.06
ACGTcount: A:0.39, C:0.18, G:0.15, T:0.28
Consensus pattern (25 bp):
AGTGAAACTTAACATGACTTACACC
Found at i:310245 original size:25 final size:25
Alignment explanation
Indices: 310212--310418 Score: 115
Period size: 25 Copynumber: 8.2 Consensus size: 25
310202 AAAGAAATGA
* *
310212 ATACGTAATTCCAACACT-AAACTT
1 ATACATAATTCCAACAGTGAAACTT
310236 ATCACATAATTCCAACAGTGAAACTT
1 AT-ACATAATTCCAACAGTGAAACTT
* * * *
310262 A-ACATTGACTTACACCAGTGAAA-TGA
1 ATACA-T-AATTCCAACAGTGAAACT-T
* *
310288 ATACGTAATTCCAACACT-AAACTT
1 ATACATAATTCCAACAGTGAAACTT
310312 ATCACATAATTCCAACAGTGAAACTT
1 AT-ACATAATTCCAACAGTGAAACTT
* * * *
310338 A-ACATTGACTTACACCAGTGAAA-TGA
1 ATACA-T-AATTCCAACAGTGAAACT-T
* *
310364 ATACGTAATTCCAACACT-AAACTT
1 ATACATAATTCCAACAGTGAAACTT
* * * *
310388 ATCACCTAATTCCAGCAATGAAATTT
1 AT-ACATAATTCCAACAGTGAAACTT
310414 A-ACAT
1 ATACAT
310419 TGACTTACAC
Statistics
Matches: 138, Mismatches: 29, Indels: 32
0.69 0.15 0.16
Matches are distributed among these distances:
24 21 0.15
25 63 0.46
26 50 0.36
27 4 0.03
ACGTcount: A:0.42, C:0.23, G:0.08, T:0.27
Consensus pattern (25 bp):
ATACATAATTCCAACAGTGAAACTT
Found at i:311369 original size:26 final size:24
Alignment explanation
Indices: 311340--311449 Score: 64
Period size: 26 Copynumber: 4.3 Consensus size: 24
311330 AAAATTCTAG
311340 CAGTGAAACTTAACATTGAGTTACAC
1 CAGTGAAACTTAACA-TGA-TTACAC
* * *
311366 CAGTGAAA-TGAATATGTAATT-CTAG
1 CAGTGAAACTTAACATG--ATTAC-AC
* * *
311391 CACT-AAACTTATGACATGATTTCAG
1 CAGTGAAACTTA--ACATGATTACAC
311416 CAGTGAAACTTAACATTGACTTACAC
1 CAGTGAAACTTAACA-TGA-TTACAC
311442 CAGTGAAA
1 CAGTGAAA
311450 TGAATATGTA
Statistics
Matches: 65, Mismatches: 9, Indels: 20
0.69 0.10 0.21
Matches are distributed among these distances:
24 9 0.14
25 23 0.35
26 29 0.45
27 4 0.06
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.28
Consensus pattern (24 bp):
CAGTGAAACTTAACATGATTACAC
Found at i:311430 original size:76 final size:76
Alignment explanation
Indices: 311332--311747 Score: 564
Period size: 76 Copynumber: 5.5 Consensus size: 76
311322 AACACATCAA
* * * *
311332 AATTCTAGCAGTGAAACTTAACATTGAGTTACACCAGTGAAATGAATATGTAATTCTAGCACTAA
1 AATTCCAGCAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATATGTAATTCCAACACTAA
*
311397 ACTTATGACAT
66 ACTTATCACAT
* * * *
311408 GATTTCAGCAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATATGTAATT-CAAGTACCA
1 AATTCCAGCAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATATGTAATTCCAA-CACTA
311472 AACTTATCACAT
65 AACTTATCACAT
* * * * * * * *
311484 CATTTCAGCAGTGAAATTTAACATTGACTAACACCAGTAAAAGGAATACGTAATTCCAACGCTAA
1 AATTCCAGCAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATATGTAATTCCAACACTAA
*
311549 ACTTTTCACAT
66 ACTTATCACAT
* * **
311560 AATTCCAGTAGTGAAACTTAACATTAACTTACACCAACGAAATGAATATGTAATTCCAACACTAA
1 AATTCCAGCAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATATGTAATTCCAACACTAA
311625 ACTTATCACAT
66 ACTTATCACAT
* * *
311636 AATTCCAACAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCGAACACTAA
1 AATTCCAGCAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATATGTAATTCCAACACTAA
*
311701 ACTTATCACCT
66 ACTTATCACAT
* *
311712 AATTCCAGCAATGAAATTTAACATTGACTTACACCA
1 AATTCCAGCAGTGAAACTTAACATTGACTTACACCA
311748 ATTGAAACTC
Statistics
Matches: 295, Mismatches: 43, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
75 1 0.00
76 291 0.99
77 3 0.01
ACGTcount: A:0.41, C:0.20, G:0.11, T:0.28
Consensus pattern (76 bp):
AATTCCAGCAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATATGTAATTCCAACACTAA
ACTTATCACAT
Found at i:311738 original size:228 final size:228
Alignment explanation
Indices: 311332--311747 Score: 636
Period size: 228 Copynumber: 1.8 Consensus size: 228
311322 AACACATCAA
* * * ** * *
311332 AATTCTAGCAGTGAAACTTAACATTGAGTTACACCAGTGAAATGAATATGTAATTCTAGCACTAA
1 AATTCCAGCAGTGAAACTTAACATTAACTTACACCAACGAAATGAATATGTAATTCCAACACTAA
* * * * *
311397 ACTTATGACATGATTTCAGCAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATATGTAAT
66 ACTTATCACATAATTCCAACAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAAT
* * * *
311462 TCAAGTACCAAACTTATCACATCATTTCAGCAGTGAAATTTAACATTGACTAACACCAGTAAAAG
131 TCAAGCACCAAACTTATCACATAATTCCAGCAATGAAATTTAACATTGACTAACACCAGTAAAAG
311527 GAATACGTAATTCCAACGCTAAACTTTTCACAT
196 GAATACGTAATTCCAACGCTAAACTTTTCACAT
*
311560 AATTCCAGTAGTGAAACTTAACATTAACTTACACCAACGAAATGAATATGTAATTCCAACACTAA
1 AATTCCAGCAGTGAAACTTAACATTAACTTACACCAACGAAATGAATATGTAATTCCAACACTAA
311625 ACTTATCACATAATTCCAACAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAAT
66 ACTTATCACATAATTCCAACAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAAT
* * *
311690 TCGAA-CACTAAACTTATCACCTAATTCCAGCAATGAAATTTAACATTGACTTACACCA
131 TC-AAGCACCAAACTTATCACATAATTCCAGCAATGAAATTTAACATTGACTAACACCA
311748 ATTGAAACTC
Statistics
Matches: 167, Mismatches: 20, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
228 165 0.99
229 2 0.01
ACGTcount: A:0.41, C:0.20, G:0.11, T:0.28
Consensus pattern (228 bp):
AATTCCAGCAGTGAAACTTAACATTAACTTACACCAACGAAATGAATATGTAATTCCAACACTAA
ACTTATCACATAATTCCAACAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAAT
TCAAGCACCAAACTTATCACATAATTCCAGCAATGAAATTTAACATTGACTAACACCAGTAAAAG
GAATACGTAATTCCAACGCTAAACTTTTCACAT
Found at i:312860 original size:22 final size:20
Alignment explanation
Indices: 312828--312881 Score: 63
Period size: 22 Copynumber: 2.6 Consensus size: 20
312818 ACCGTAAGGG
* *
312828 GTATCGGTACCGTAGTATAGTA
1 GTATCGATACCATAGTA-AG-A
*
312850 GTATCGATACCATGGTAAGA
1 GTATCGATACCATAGTAAGA
312870 GTATCGATACCA
1 GTATCGATACCA
312882 GGCAACATCG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 13 0.45
21 2 0.07
22 14 0.48
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.28
Consensus pattern (20 bp):
GTATCGATACCATAGTAAGA
Found at i:312921 original size:94 final size:95
Alignment explanation
Indices: 312755--312974 Score: 284
Period size: 94 Copynumber: 2.3 Consensus size: 95
312745 TCATTCAATC
* * *
312755 AGTATCGATACCATGGTAAGGGTATCGATACCAAGCAACATCGAATCAAAAATCGGTATCGATAC
1 AGTATCGATACCATGGTAAGAGTATCGATACCAAGCAACATCGAACCAAAAATCAGTATCGATAC
* * * *
312820 CGTAA-GGGGTATCGGTACCGTAGTATAGT
66 CGAAAGGGGGTATCGATACCATAGTATAGA
*
312849 AGTATCGATACCATGGTAAGAGTATCGATACCAGGCAACATCGAACCTAAAAA-CAGTATCGATA
1 AGTATCGATACCATGGTAAGAGTATCGATACCAAGCAACATCGAACC-AAAAATCAGTATCGATA
*
312913 CTGAAAGGGGGTATCGATACCATAGTATAGA
65 CCGAAAGGGGGTATCGATACCATAGTATAGA
* * * *
312944 AATATCGGTACTAGGGT-AGTAGTATCGATAC
1 AGTATCGATACCATGGTAAG-AGTATCGATAC
312975 TATGGAGCCA
Statistics
Matches: 110, Mismatches: 13, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
94 60 0.55
95 50 0.45
ACGTcount: A:0.36, C:0.17, G:0.24, T:0.23
Consensus pattern (95 bp):
AGTATCGATACCATGGTAAGAGTATCGATACCAAGCAACATCGAACCAAAAATCAGTATCGATAC
CGAAAGGGGGTATCGATACCATAGTATAGA
Found at i:313435 original size:47 final size:47
Alignment explanation
Indices: 313381--314645 Score: 1908
Period size: 47 Copynumber: 27.2 Consensus size: 47
313371 TGAATACATT
** * *
313381 ACTAAAAATGCATGAGCGAATGCATTAAGGCATGAAAGGATTCCATA
1 ACTAAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATA
*
313428 ACTAAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATGCCATA
1 ACTAAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATA
* *
313475 ACTAAAAATGCATGAAAGGATGCATCAATGCATGAAAGGATGCCATA
1 ACTAAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATA
*
313522 ACTAAAAATGCATGAAAGGATGCATGAAGGCATGAAAGGATGCCATA
1 ACTAAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATA
* * *
313569 ACTAAAAATGCATGAACGGATGCATTAAGGGATGAAAGGACGCCATA
1 ACTAAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATA
*
313616 ACTAAAAATGCATGAAAGGATGCATTAAGGAATGAAAGGATGCCATA
1 ACTAAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATA
*
313663 ACTAAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGTCATA
1 ACTAAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATA
*
313710 ACTAAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATGCCATA
1 ACTAAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATA
* *
313757 ACTAAAAATGCAT-AAAGGATGCATTAAGGCATGAAATGATGACATA
1 ACTAAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATA
* * *
313803 ACTAAAAATGCATGAATGGATGCATGAAGGCATGAAAGGATACCATA
1 ACTAAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATA
* * *
313850 ACTAAAAATGCATGAACGGATGCATTAAGCCATGAAATGATGCCATA
1 ACTAAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATA
* * * *
313897 ACTAAAAATGCATGAACGGATGCATGAAGGTATGAAAGGATGTCATA
1 ACTAAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATA
* *
313944 ACTAAAAATGCATGAAAGGATTCATGAAGGCATGAAAGGATGCCATA
1 ACTAAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATA
*
313991 ACTAAAAATGCATGAAAGGATGCATGAAGGCATGAAAGGATGCCATA
1 ACTAAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATA
* *
314038 ACTAAAAATGCATGAACGGATGCATTAAGGGATGAAAGGATGCCATA
1 ACTAAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATA
*
314085 ACTAAAAATGCATGAAAGGATGCATTAAGGAATGAAAGGATGCCATA
1 ACTAAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATA
* * * * *
314132 ACTAAAAATACATGAAAGGATGCATGAAGGAATGAAAGGATTCAATA
1 ACTAAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATA
*
314179 ACTAAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATGCCATA
1 ACTAAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATA
*
314226 ACTAAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGACATA
1 ACTAAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATA
* * *
314273 ACTAAAAATGCATGAACGGATGCATGAAGGCATGAAAGGATACCATA
1 ACTAAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATA
* *
314320 ACTAAAAATGCATGAACGGATGCATTAAGCCATGAAAGGATGCCATA
1 ACTAAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATA
* * *
314367 ACTAAAAATGCATGAAAGGATGCATGAATGCATGAAAGGATACCATA
1 ACTAAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATA
** * *
314414 ACTAAAAATGCATGAAAGGATTAATGAATGCATGAAAGGATGCCATA
1 ACTAAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATA
* *
314461 ACTAAAAATGCATGAAAGGATGCATGAAGGCATGAAAGGATGTCATA
1 ACTAAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATA
* * * *
314508 ACTAAAAATGCATGAACGGATTCATTAAGGCATGAAAGAATGTCATA
1 ACTAAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATA
314555 ACTAAAAATGC--------ATG----AAGGCATGAAAGGATGCCATA
1 ACTAAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATA
* *
314590 ACTAAAAATGCATGAAATGATGCATGAAGGCATGAAAGGATGCCATA
1 ACTAAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATA
314637 ACTAAAAAT
1 ACTAAAAAT
314646 ACAAAATAGT
Statistics
Matches: 1118, Mismatches: 87, Indels: 26
0.91 0.07 0.02
Matches are distributed among these distances:
35 30 0.03
39 2 0.00
43 3 0.00
46 43 0.04
47 1040 0.93
ACGTcount: A:0.45, C:0.13, G:0.23, T:0.20
Consensus pattern (47 bp):
ACTAAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATA
Found at i:314580 original size:35 final size:35
Alignment explanation
Indices: 314534--314605 Score: 126
Period size: 35 Copynumber: 2.1 Consensus size: 35
314524 CGGATTCATT
*
314534 AAGGCATGAAAGAATGTCATAACTAAAAATGCATG
1 AAGGCATGAAAGAATGCCATAACTAAAAATGCATG
*
314569 AAGGCATGAAAGGATGCCATAACTAAAAATGCATG
1 AAGGCATGAAAGAATGCCATAACTAAAAATGCATG
314604 AA
1 AA
314606 ATGATGCATG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.49, C:0.12, G:0.21, T:0.18
Consensus pattern (35 bp):
AAGGCATGAAAGAATGCCATAACTAAAAATGCATG
Found at i:314590 original size:82 final size:82
Alignment explanation
Indices: 314480--314645 Score: 269
Period size: 82 Copynumber: 2.0 Consensus size: 82
314470 GCATGAAAGG
* * * *
314480 ATGCATGAAGGCATGAAAGGATGTCATAACTAAAAATGCATGAACGGATTCATTAAGGCATGAAA
1 ATGCATGAAGGCATGAAAGGATGCCATAACTAAAAATGCATGAAAGGATGCATGAAGGCATGAAA
*
314545 GAATGTCATAACTAAAA
66 GAATGCCATAACTAAAA
*
314562 ATGCATGAAGGCATGAAAGGATGCCATAACTAAAAATGCATGAAATGATGCATGAAGGCATGAAA
1 ATGCATGAAGGCATGAAAGGATGCCATAACTAAAAATGCATGAAAGGATGCATGAAGGCATGAAA
*
314627 GGATGCCATAACTAAAA
66 GAATGCCATAACTAAAA
314644 AT
1 AT
314646 ACAAAATAGT
Statistics
Matches: 77, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
82 77 1.00
ACGTcount: A:0.45, C:0.13, G:0.22, T:0.20
Consensus pattern (82 bp):
ATGCATGAAGGCATGAAAGGATGCCATAACTAAAAATGCATGAAAGGATGCATGAAGGCATGAAA
GAATGCCATAACTAAAA
Found at i:315842 original size:69 final size:69
Alignment explanation
Indices: 315689--315883 Score: 212
Period size: 69 Copynumber: 2.8 Consensus size: 69
315679 TACAATAATA
* ** * ** * *
315689 TGCTCCCTTGTGAGTCACTCTAATCCTTCGGAGCTCCCGTGGGAGTCAATCGAAATAATTACGAT
1 TGCTCCCTTGTGAGTCACTCTAATCCTTCGGGGCTCTTGTGCGAGTCACCCAAAATAATCACGAT
315754 TAGG
66 TAGG
** * * *
315758 TGCT-TTTGTGTGAGTCACTCTATTCTTTCGGGGCTTTTGTGCGAGTCACCCAAAATAATCACGA
1 TGCTCCCT-TGTGAGTCACTCTAATCCTTCGGGGCTCTTGTGCGAGTCACCCAAAATAATCACGA
315822 TTAGG
65 TTAGG
* * ** *
315827 TGCTCCCTTGCGAGTCATTCTAATCCTTCAAGGCTCTTGTGCGAGTCACCCAGAATA
1 TGCTCCCTTGTGAGTCACTCTAATCCTTCGGGGCTCTTGTGCGAGTCACCCAAAATA
315884 CTCAATATTA
Statistics
Matches: 101, Mismatches: 23, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
68 1 0.01
69 99 0.98
70 1 0.01
ACGTcount: A:0.22, C:0.25, G:0.22, T:0.32
Consensus pattern (69 bp):
TGCTCCCTTGTGAGTCACTCTAATCCTTCGGGGCTCTTGTGCGAGTCACCCAAAATAATCACGAT
TAGG
Found at i:316141 original size:76 final size:76
Alignment explanation
Indices: 316012--316459 Score: 506
Period size: 76 Copynumber: 5.9 Consensus size: 76
316002 GAACATTAAC
* * *
316012 ACGTAATTCCAACACTAAA-TTAAACACATCACAATTCTAGCAGTGAAACTTAACATTGACTTAC
1 ACGTAATTCCAGCACTAAACTT-ATCACAT---AATTCCAGCAGTGAAACTTAACATTGACTTAC
316076 ACCAGTGAAATGAAT
62 ACCAGTGAAATGAAT
* * *
316091 ACGTAATTCTAGCACTAAACTTATGACATGATAT-CAGCAGTGAAACTTAACATTGACTTACACC
1 ACGTAATTCCAGCACTAAACTTATCACATAAT-TCCAGCAGTGAAACTTAACATTGACTTACACC
316155 AGTGAAATGAAT
65 AGTGAAATGAAT
* * * * * *
316167 ACGTAATTCAAGCACCAAACTTATCACATCATTTCAGTAGTGAAATTTAACATTGACTTACACCA
1 ACGTAATTCCAGCACTAAACTTATCACATAATTCCAGCAGTGAAACTTAACATTGACTTACACCA
*
316232 GTAAAATGAAT
66 GTGAAATGAAT
* * * * * * *
316243 ACGAAATTCCAACGCTAAACTTATCACATAATTCCAGTAGTGAAACTTAACATTAACATACACTA
1 ACGTAATTCCAGCACTAAACTTATCACATAATTCCAGCAGTGAAACTTAACATTGACTTACACCA
** *
316308 ACGAAAGGAAT
66 GTGAAATGAAT
* * * * *
316319 ACATAACTCCAACACTAAACTTATCACATAATTCCAACAGTGAAACTTAACATTGACTTATACCA
1 ACGTAATTCCAGCACTAAACTTATCACATAATTCCAGCAGTGAAACTTAACATTGACTTACACCA
316384 GTGAAATGAAT
66 GTGAAATGAAT
* * * ** * *
316395 ATGTAATTCCAGCACTAAACTTATCACCTAACTT-CACCAACGAAATTTAACATTAACTTACACC
1 ACGTAATTCCAGCACTAAACTTATCACATAA-TTCCAGCAGTGAAACTTAACATTGACTTACACC
316459 A
65 A
316460 ATTCAAACTC
Statistics
Matches: 313, Mismatches: 52, Indels: 11
0.83 0.14 0.03
Matches are distributed among these distances:
75 1 0.00
76 285 0.91
77 3 0.01
79 22 0.07
80 2 0.01
ACGTcount: A:0.42, C:0.22, G:0.10, T:0.27
Consensus pattern (76 bp):
ACGTAATTCCAGCACTAAACTTATCACATAATTCCAGCAGTGAAACTTAACATTGACTTACACCA
GTGAAATGAAT
Found at i:316354 original size:25 final size:26
Alignment explanation
Indices: 316319--316367 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
316309 CGAAAGGAAT
316319 ACATAACTCCAACACT-AAACTTATC
1 ACATAACTCCAACACTGAAACTTATC
* *
316344 ACATAATTCCAACAGTGAAACTTA
1 ACATAACTCCAACACTGAAACTTA
316368 ACATTGACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 14 0.67
26 7 0.33
ACGTcount: A:0.45, C:0.27, G:0.04, T:0.24
Consensus pattern (26 bp):
ACATAACTCCAACACTGAAACTTATC
Found at i:316456 original size:228 final size:228
Alignment explanation
Indices: 316044--316459 Score: 573
Period size: 228 Copynumber: 1.8 Consensus size: 228
316034 AACACATCAC
* * * ** * * * * *
316044 AATTCTAGCAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCTAGCACTAA
1 AATTCCAGCAGTGAAACTTAACATTAACATACACCAACGAAAGGAATACATAACTCCAACACTAA
* * *
316109 ACTTATGACATGATATCAGCAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAAT
66 ACTTATCACATAATATCAACAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAAT
* * ** ** *
316174 TCAAGCACCAAACTTATCACATCATTTCAGTAGTGAAATTTAACATTGACTTACACCAGTAAAAT
131 TCAAGCACCAAACTTATCACATAACTTCACCAACGAAATTTAACATTAACTTACACCAGTAAAAT
316239 GAATACGAAATTCCAACGCTAAACTTATCACAT
196 GAATACGAAATTCCAACGCTAAACTTATCACAT
* *
316272 AATTCCAGTAGTGAAACTTAACATTAACATACACTAACGAAAGGAATACATAACTCCAACACTAA
1 AATTCCAGCAGTGAAACTTAACATTAACATACACCAACGAAAGGAATACATAACTCCAACACTAA
* *
316337 ACTTATCACATAAT-TCCAACAGTGAAACTTAACATTGACTTATACCAGTGAAATGAATATGTAA
66 ACTTATCACATAATAT-CAACAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAA
* * *
316401 TTCCAGCACTAAACTTATCACCTAACTTCACCAACGAAATTTAACATTAACTTACACCA
130 TTCAAGCACCAAACTTATCACATAACTTCACCAACGAAATTTAACATTAACTTACACCA
316460 ATTCAAACTC
Statistics
Matches: 160, Mismatches: 27, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
227 1 0.01
228 159 0.99
ACGTcount: A:0.42, C:0.21, G:0.10, T:0.27
Consensus pattern (228 bp):
AATTCCAGCAGTGAAACTTAACATTAACATACACCAACGAAAGGAATACATAACTCCAACACTAA
ACTTATCACATAATATCAACAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAAT
TCAAGCACCAAACTTATCACATAACTTCACCAACGAAATTTAACATTAACTTACACCAGTAAAAT
GAATACGAAATTCCAACGCTAAACTTATCACAT
Found at i:317105 original size:69 final size:70
Alignment explanation
Indices: 317042--317236 Score: 209
Period size: 69 Copynumber: 2.8 Consensus size: 70
317032 TACGATAATA
**
317042 TGCTCCCTTGTGAGTCACTCTATTCCTTCAGGGCTCCCGTGCGAGTCAACTGA-AATAATTACGA
1 TGCTCCCTTGTGAGTCACTCTATTCCTTCAGGGCTCCCGTGCGAGTCAACCCAGAATAATTACGA
317106 TTAGG
66 TTAGG
* * * ** * * *
317111 TGCT-CCTGTATGAGTCACTCTATTCCTTCGGGGATTTCGTGGGAGTC-ACCCAGAATAATCATG
1 TGCTCCCT-TGTGAGTCACTCTATTCCTTCAGGGCTCCCGTGCGAGTCAACCCAGAATAATTACG
317174 ATTAGG
65 ATTAGG
* * * * * *
317180 TGCTCCCTTGCGAGTCACTCTAATCCTTTAAGGCTCCTGTGCGAGTC-ACCCGGAATA
1 TGCTCCCTTGTGAGTCACTCTATTCCTTCAGGGCTCCCGTGCGAGTCAACCCAGAATA
317237 CTCATTATTA
Statistics
Matches: 101, Mismatches: 22, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
68 6 0.06
69 92 0.91
70 3 0.03
ACGTcount: A:0.21, C:0.26, G:0.23, T:0.30
Consensus pattern (70 bp):
TGCTCCCTTGTGAGTCACTCTATTCCTTCAGGGCTCCCGTGCGAGTCAACCCAGAATAATTACGA
TTAGG
Found at i:317434 original size:26 final size:25
Alignment explanation
Indices: 317405--317514 Score: 66
Period size: 26 Copynumber: 4.3 Consensus size: 25
317395 ACAATTCTAG
317405 CAGTGAAACTTAACATTGACTTACAC
1 CAGTGAAACTTAACA-TGACTTACAC
* * * * *
317431 CAGTGAAA-TGAATACGTAATT-CTAG
1 CAGTGAAACTTAACATG-ACTTAC-AC
* * *
317456 CACT-AAACTTATGACATGA-TTTCAG
1 CAGTGAAACTTA--ACATGACTTACAC
317481 CAGTGAAACTTAACATTGACTTACAC
1 CAGTGAAACTTAACA-TGACTTACAC
317507 CAGTGAAA
1 CAGTGAAA
317515 TGAATACGGA
Statistics
Matches: 63, Mismatches: 12, Indels: 18
0.68 0.13 0.19
Matches are distributed among these distances:
24 8 0.13
25 23 0.37
26 29 0.46
27 3 0.05
ACGTcount: A:0.39, C:0.19, G:0.15, T:0.27
Consensus pattern (25 bp):
CAGTGAAACTTAACATGACTTACAC
Found at i:317496 original size:76 final size:76
Alignment explanation
Indices: 317365--317812 Score: 558
Period size: 76 Copynumber: 5.9 Consensus size: 76
317355 GAACATTTAC
* * *
317365 ACGTAATTCCAGCACTAAA-TTAAACACATCACAATTCTAGCAGTGAAACTTAACATTGACTTAC
1 ACGTAATTCCAACACTAAACTT-ATCACAT---AATTCCAGCAGTGAAACTTAACATTGACTTAC
317429 ACCAGTGAAATGAAT
62 ACCAGTGAAATGAAT
* * * * *
317444 ACGTAATTCTAGCACTAAACTTATGACATGATTTCAGCAGTGAAACTTAACATTGACTTACACCA
1 ACGTAATTCCAACACTAAACTTATCACATAATTCCAGCAGTGAAACTTAACATTGACTTACACCA
317509 GTGAAATGAAT
66 GTGAAATGAAT
* * * * *
317520 ACGGAATT-CAAGCACCAAACTTATCACATCATTTCAGCAGTGAAATTTAACATTGACTTACACC
1 ACGTAATTCCAA-CACTAAACTTATCACATAATTCCAGCAGTGAAACTTAACATTGACTTACACC
*
317584 AGTAAAATGAAT
65 AGTGAAATGAAT
* * * *
317596 ACGTAATTCCAACGCTAAACTTTTCACATAATTCCAGTAGTGAAACTTAACATTAACTTACACCA
1 ACGTAATTCCAACACTAAACTTATCACATAATTCCAGCAGTGAAACTTAACATTGACTTACACCA
**
317661 ACGAAATGAAT
66 GTGAAATGAAT
** ** * *
317672 ACGTAAAACCAACACTAAACTTATCACATAATTAAAACAATGAAACTTAACATTGACTTACACCA
1 ACGTAATTCCAACACTAAACTTATCACATAATTCCAGCAGTGAAACTTAACATTGACTTACACCA
317737 GTGAAATGAAT
66 GTGAAATGAAT
* * * * *
317748 ACGTAATTCGAACACTAAACTTATCACGTAATTCCAGCAATGAAATTTAACATTGACTTAAACCA
1 ACGTAATTCCAACACTAAACTTATCACATAATTCCAGCAGTGAAACTTAACATTGACTTACACCA
317813 ATTCAAACTC
Statistics
Matches: 319, Mismatches: 47, Indels: 9
0.85 0.13 0.02
Matches are distributed among these distances:
75 1 0.00
76 290 0.91
77 3 0.01
79 23 0.07
80 2 0.01
ACGTcount: A:0.42, C:0.21, G:0.11, T:0.27
Consensus pattern (76 bp):
ACGTAATTCCAACACTAAACTTATCACATAATTCCAGCAGTGAAACTTAACATTGACTTACACCA
GTGAAATGAAT
Found at i:317803 original size:228 final size:228
Alignment explanation
Indices: 317397--317812 Score: 618
Period size: 228 Copynumber: 1.8 Consensus size: 228
317387 AACACATCAC
* * ** ** * *
317397 AATTCTAGCAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCTAGCACTAA
1 AATTCCAGCAGTGAAACTTAACATTAACTTACACCAACGAAATGAATACGTAAAACCAACACTAA
* * ** * *
317462 ACTTATGACATGATTTCAGCAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATACGGAAT
66 ACTTATCACATAATTAAAACAATGAAACTTAACATTGACTTACACCAGTGAAATGAATACGGAAT
* * * *
317527 TCAAGCACCAAACTTATCACATCATTTCAGCAGTGAAATTTAACATTGACTTACACCAGTAAAAT
131 TCAAGCACCAAACTTATCACATAATTCCAGCAATGAAATTTAACATTGACTTAAACCAGTAAAAT
317592 GAATACGTAATTCCAACGCTAAACTTTTCACAT
196 GAATACGTAATTCCAACGCTAAACTTTTCACAT
*
317625 AATTCCAGTAGTGAAACTTAACATTAACTTACACCAACGAAATGAATACGTAAAACCAACACTAA
1 AATTCCAGCAGTGAAACTTAACATTAACTTACACCAACGAAATGAATACGTAAAACCAACACTAA
*
317690 ACTTATCACATAATTAAAACAATGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAAT
66 ACTTATCACATAATTAAAACAATGAAACTTAACATTGACTTACACCAGTGAAATGAATACGGAAT
* *
317755 TCGAA-CACTAAACTTATCACGTAATTCCAGCAATGAAATTTAACATTGACTTAAACCA
131 TC-AAGCACCAAACTTATCACATAATTCCAGCAATGAAATTTAACATTGACTTAAACCA
317813 ATTCAAACTC
Statistics
Matches: 165, Mismatches: 22, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
228 163 0.99
229 2 0.01
ACGTcount: A:0.42, C:0.20, G:0.11, T:0.27
Consensus pattern (228 bp):
AATTCCAGCAGTGAAACTTAACATTAACTTACACCAACGAAATGAATACGTAAAACCAACACTAA
ACTTATCACATAATTAAAACAATGAAACTTAACATTGACTTACACCAGTGAAATGAATACGGAAT
TCAAGCACCAAACTTATCACATAATTCCAGCAATGAAATTTAACATTGACTTAAACCAGTAAAAT
GAATACGTAATTCCAACGCTAAACTTTTCACAT
Found at i:318573 original size:69 final size:68
Alignment explanation
Indices: 318393--318574 Score: 167
Period size: 69 Copynumber: 2.6 Consensus size: 68
318383 AACGATAATA
* * * *
318393 TGCTCCCTTGTGAGTCACTATAATCCTTCGGAGCTCCCGTGCGAGCCAACCGAAATAATTACGAT
1 TGCTCCCTTGCGAGTCACTCTAATCCTTCGG-GCTCCTGTGCGAGCCAACCGAAATAATCACGAT
318458 TAGG
65 TAGG
* * * * *
318462 TGCT-CC-TGCGTGAGTCACTCTATTCCTTTGGGGAT-TTGGTGCGA-CTC-ACCCAGAATAATC
1 TGCTCCCTTGC--GAGTCACTCTAATCC-TTCGGGCTCCT-GTGCGAGC-CAACCGA-AATAATC
318522 ACGATTAGG
60 ACGATTAGG
*
318531 TGCTCCCTTGCGAGTCACTCTAATCCTTCAAGGCTCCTGTGCGA
1 TGCTCCCTTGCGAGTCACTCTAATCCTTC-GGGCTCCTGTGCGA
318575 ATGACCCGAA
Statistics
Matches: 89, Mismatches: 14, Indels: 20
0.72 0.11 0.16
Matches are distributed among these distances:
67 2 0.02
68 9 0.10
69 68 0.76
70 7 0.08
71 3 0.03
ACGTcount: A:0.21, C:0.28, G:0.23, T:0.29
Consensus pattern (68 bp):
TGCTCCCTTGCGAGTCACTCTAATCCTTCGGGCTCCTGTGCGAGCCAACCGAAATAATCACGATT
AGG
Found at i:322822 original size:130 final size:130
Alignment explanation
Indices: 322674--323079 Score: 461
Period size: 130 Copynumber: 3.1 Consensus size: 130
322664 TTTTTCAAGT
322674 TAACTACTAACTTTTATTTTATTGCACTTTAACCATTGTTATTTATTTATTTATTGTTTCTAATA
1 TAACTACTAACTTTTATTTTATTGCACTTTAACCATTGTTATTTATTTATTTATTGTTTCTAATA
* * *
322739 TTCGATTGGACCTTGTGGTGACCATATCCGGGGTATGATCCACATTATTATGGTTTGGACTCTAC
66 TTCGATTCGACCTTGTGGTGACCATATCCGGGGTATGATCCACATTATTATGGTTCGGACTCTGC
* *
322804 TAACTACTGACTTTTATTTTATTGCACTCTAACCATTGATTATTTATTTATTTATTGTTTCTAAT
1 TAACTACTAACTTTTATTTTATTGCACTTTAACCATTG-TTATTTATTTATTTATTGTTTCTAAT
* * * * * * *
322869 ATTTGAATCGACCTTGTGGTGATC-TGATCAGGGGTATGATTCATATTATTATGGTTCAGACTCT
65 ATTCGATTCGACCTTGTGGTGACCAT-ATCCGGGGTATGATCCACATTATTATGGTTCGGACTCT
322933 GC
129 GC
* *
322935 TAACCACTAACTTTT-TTTTATAT--A-TTTATTA-TATT-TTATTTTATTT-TGTTAATTTGTT
1 TAACTACTAACTTTTATTTTAT-TGCACTTTA--ACCATTGTTA-TTTATTTAT-TT-A-TTGTT
* * ** * *
322993 T-GAATTATTCGATTCAACCTTGTGACGACCAGATCCGGGGTATGATCAACATTATTATGGTTCG
59 TCTAA-TATTCGATTCGACCTTGTGGTGACCATATCCGGGGTATGATCCACATTATTATGGTTCG
323057 GACTCTGC
123 GACTCTGC
**
323065 TAACCGCTAACTTTT
1 TAACTACTAACTTTT
323080 CTAACATCTA
Statistics
Matches: 235, Mismatches: 30, Indels: 22
0.82 0.10 0.08
Matches are distributed among these distances:
127 4 0.02
128 12 0.05
129 7 0.03
130 118 0.50
131 94 0.40
ACGTcount: A:0.25, C:0.16, G:0.14, T:0.46
Consensus pattern (130 bp):
TAACTACTAACTTTTATTTTATTGCACTTTAACCATTGTTATTTATTTATTTATTGTTTCTAATA
TTCGATTCGACCTTGTGGTGACCATATCCGGGGTATGATCCACATTATTATGGTTCGGACTCTGC
Found at i:323106 original size:16 final size:16
Alignment explanation
Indices: 323064--323106 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
323054 TCGGACTCTG
*
323064 CTAACCGCTAACTTTT
1 CTAACCGCTAACCTTT
**
323080 CTAACATCTAACCTTT
1 CTAACCGCTAACCTTT
323096 CTAACCGCTAA
1 CTAACCGCTAA
323107 TTACTAACTA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.30, C:0.33, G:0.05, T:0.33
Consensus pattern (16 bp):
CTAACCGCTAACCTTT
Found at i:323292 original size:13 final size:13
Alignment explanation
Indices: 323264--323306 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
323254 TTTTATGTAC
*
323264 TTTAATTTCATTTG
1 TTTAATTAC-TTTG
323278 TTTAATTACTTTG
1 TTTAATTACTTTG
*
323291 TTTTATTA-TTTG
1 TTTAATTACTTTG
323303 TTTA
1 TTTA
323307 TTTTACTTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
12 7 0.27
13 11 0.42
14 8 0.31
ACGTcount: A:0.21, C:0.05, G:0.07, T:0.67
Consensus pattern (13 bp):
TTTAATTACTTTG
Found at i:330956 original size:27 final size:27
Alignment explanation
Indices: 330926--330977 Score: 88
Period size: 27 Copynumber: 1.9 Consensus size: 27
330916 TATTTCTGCA
330926 CCTCAAAATAA-AAATATAGATATTTTC
1 CCTCAAAA-AATAAATATAGATATTTTC
330953 CCTCAAAAAATAAATATAGATATTT
1 CCTCAAAAAATAAATATAGATATTT
330978 GAAATAACAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
26 2 0.08
27 22 0.92
ACGTcount: A:0.50, C:0.13, G:0.04, T:0.33
Consensus pattern (27 bp):
CCTCAAAAAATAAATATAGATATTTTC
Found at i:331500 original size:17 final size:17
Alignment explanation
Indices: 331462--331499 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
331452 TATCTTAACA
331462 ATTTTAAATTTTTATAT
1 ATTTTAAATTTTTATAT
331479 ATTTTAAATTTTTATAT
1 ATTTTAAATTTTTATAT
331496 -TTTT
1 ATTTT
331500 TTAAAAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 4 0.19
17 17 0.81
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
ATTTTAAATTTTTATAT
Found at i:331586 original size:53 final size:53
Alignment explanation
Indices: 331484--331591 Score: 177
Period size: 52 Copynumber: 2.1 Consensus size: 53
331474 TATATATTTT
*
331484 AAATTTTTATATTTTTTTAAAAATAATTTATATTCTATCTTAAAATTTATATC
1 AAATTTTTATATTATTTTAAAAATAATTTATATTCTATCTTAAAATTTATATC
*
331537 AAATTTTTATA-TATTTTAAAAGTAATTTATATTCTATCTTAAAATTT-TAT-
1 AAATTTTTATATTATTTTAAAAATAATTTATATTCTATCTTAAAATTTATATC
331587 AAATT
1 AAATT
331592 CCTTATACCT
Statistics
Matches: 53, Mismatches: 2, Indels: 3
0.91 0.03 0.05
Matches are distributed among these distances:
50 5 0.09
51 3 0.06
52 34 0.64
53 11 0.21
ACGTcount: A:0.41, C:0.05, G:0.01, T:0.54
Consensus pattern (53 bp):
AAATTTTTATATTATTTTAAAAATAATTTATATTCTATCTTAAAATTTATATC
Found at i:342024 original size:37 final size:38
Alignment explanation
Indices: 341925--342077 Score: 163
Period size: 37 Copynumber: 4.1 Consensus size: 38
341915 TTTGAGATTG
* *
341925 TTTCTCTCAAAACAAAGTGTCGTCTCGCTAGAGACAGGT
1 TTTCTCTCAAAACAAATTGTCGTCTCGCTTGAGACA-GT
* * ** * *
341964 TTTCTTTAAAAATGAATT-TTGTCTCGTTTGAGACAGT
1 TTTCTCTCAAAACAAATTGTCGTCTCGCTTGAGACAGT
*
342001 TTTCTCT-AAAAGCAAATTGT-GTCTCGCTTGAGACAAT
1 TTTCTCTCAAAA-CAAATTGTCGTCTCGCTTGAGACAGT
*
342038 TTT-TCTCAAAACAAATT-TCGTCTCGCTTGAGACATT
1 TTTCTCTCAAAACAAATTGTCGTCTCGCTTGAGACAGT
342074 TTTC
1 TTTC
342078 CTTTGATATG
Statistics
Matches: 95, Mismatches: 14, Indels: 12
0.79 0.12 0.10
Matches are distributed among these distances:
35 1 0.01
36 32 0.34
37 34 0.36
38 15 0.16
39 13 0.14
ACGTcount: A:0.27, C:0.19, G:0.16, T:0.38
Consensus pattern (38 bp):
TTTCTCTCAAAACAAATTGTCGTCTCGCTTGAGACAGT
Found at i:342447 original size:36 final size:35
Alignment explanation
Indices: 342407--342525 Score: 115
Period size: 36 Copynumber: 3.5 Consensus size: 35
342397 CCTTTGAGAT
342407 TGTTTCTCTTGAAACAAATTTAGTCTCCCTTGATAC
1 TGTTTCTCTTGAAACAAATTTAGTCTCCCTTGA-AC
* *
342443 TGTTTCTCTTGAAACACAA---AATAT---TTGAATC
1 TGTTTCTCTTGAAACA-AATTTAGTCTCCCTTGAA-C
* *
342474 TGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGAC
1 TGTTTCTCTTGAAACAAATTTAGTCTCCCTTGA-AC
*
342510 AGTTTCTCTTGAAACA
1 TGTTTCTCTTGAAACA
342526 CAAATCTTTG
Statistics
Matches: 66, Mismatches: 8, Indels: 18
0.72 0.09 0.20
Matches are distributed among these distances:
30 3 0.05
31 20 0.30
33 2 0.03
34 3 0.05
36 35 0.53
37 3 0.05
ACGTcount: A:0.28, C:0.21, G:0.12, T:0.39
Consensus pattern (35 bp):
TGTTTCTCTTGAAACAAATTTAGTCTCCCTTGAAC
Found at i:342565 original size:66 final size:66
Alignment explanation
Indices: 342398--342788 Score: 518
Period size: 66 Copynumber: 5.9 Consensus size: 66
342388 ATTGATAAAC
* * * * *
342398 CTTTGAGATTGTTTCTCTTGAAACAAATTTAGTCTCCCTTGATACTGTTTCTCTTGAAACACAAA
1 CTTTGAGATCGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAC-AA
342463 AT
65 AT
*
342465 ATTTGA-ATCTGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAA
1 CTTTGAGATC-GTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAA
342529 AT
65 AT
* * * *
342531 CTTTGAGATCGTTTCCCTTGAAACAAATTTTGTCTCTCTTGATACAGTTTCCCTTGAAACACCAA
1 CTTTGAGATCGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAA
342596 T
66 T
*
342597 CTTTGA-ATCTGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAATTTCTCTTGAAACACAA
1 CTTTGAGATC-GTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAA
342661 AT
65 AT
* * * *
342663 CTTTGAGATTGTTTCCCTTGAAA-AGAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACACCA
1 CTTTGAGATCGTTTCCCTTGAAACA-AATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAA
*
342727 AC
65 AT
* * ** * **
342729 CTTTGAGATTGATTCCCTTGAAACATGTTTTGTCTCTCTTGAGATGGTTTCTCTTGAAAC
1 CTTTGAGATCGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAAC
342789 CATCATATCC
Statistics
Matches: 290, Mismatches: 28, Indels: 13
0.88 0.08 0.04
Matches are distributed among these distances:
65 4 0.01
66 227 0.78
67 59 0.20
ACGTcount: A:0.26, C:0.21, G:0.13, T:0.39
Consensus pattern (66 bp):
CTTTGAGATCGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAA
T
Found at i:342654 original size:132 final size:132
Alignment explanation
Indices: 342398--342788 Score: 588
Period size: 132 Copynumber: 3.0 Consensus size: 132
342388 ATTGATAAAC
* * * * * *
342398 CTTTGAGATTGTTTCTCTTGAAACAAATTTAGTCTCCCTTGATACTGTTTCTCTTGAAACACAAA
1 CTTTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCTCTTGATACAGTTTCCCTTGAAACAC-CA
*
342463 ATATTTGAATCTGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACA
65 ATCTTTGAATCTGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACA
342528 AAT
130 AAT
*
342531 CTTTGAGATCGTTTCCCTTGAAACAAATTTTGTCTCTCTTGATACAGTTTCCCTTGAAACACCAA
1 CTTTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCTCTTGATACAGTTTCCCTTGAAACACCAA
*
342596 TCTTTGAATCTGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAATTTCTCTTGAAACACAA
66 TCTTTGAATCTGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAA
342661 AT
131 AT
*
342663 CTTTGAGATTGTTTCCCTTGAAA-AGAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACACCA
1 CTTTGAGATTGTTTCCCTTGAAACA-AATTTTGTCTCTCTTGATACAGTTTCCCTTGAAACACCA
* * ** * **
342727 ACCTTTGAGAT-TGATTCCCTTGAAACATGTTTTGTCTCTCTTGAGATGGTTTCTCTTGAAAC
65 ATCTTTGA-ATCTGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAAC
342789 CATCATATCC
Statistics
Matches: 237, Mismatches: 19, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
131 1 0.00
132 178 0.75
133 58 0.24
ACGTcount: A:0.26, C:0.21, G:0.13, T:0.39
Consensus pattern (132 bp):
CTTTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCTCTTGATACAGTTTCCCTTGAAACACCAA
TCTTTGAATCTGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAA
AT
Found at i:344512 original size:4 final size:4
Alignment explanation
Indices: 344503--344532 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
344493 CTAACCATTG
344503 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
344533 GTTTCTAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:344659 original size:124 final size:120
Alignment explanation
Indices: 344503--344746 Score: 339
Period size: 124 Copynumber: 2.0 Consensus size: 120
344493 CTAACCATTG
* * *
344503 TTTATTTATTTATTTATTTATTTATTTATTGTTTCTAA-TATTTGAATCGACCTTGTGGTGATCC
1 TTTATATATTTATTTATTTATTTATTTATTGTTT-GAATTATTTGAATCAACCTTGTGGTGA-CC
344567 -GATCCGGGGTATGATCCACATTATTATGGTTTGGACTCTGCTAACAACTAACTTTT
64 AGATCCGGGGTATGATCCACATTATTATGGTTTGGACTCTGCTAACAACTAACTTTT
* *
344623 TTTATATATTTATTATATTTTATTTTTTTAATTTGTTTGAATTATTTGATTCAACCTTGTGGTGA
1 TTTATATATTTATT-TA-TTTATTTATTT-A-TTGTTTGAATTATTTGAATCAACCTTGTGGTGA
* * **
344688 CCAGATCTGGGGTATGATGCACATTATTATGGTTTGGACTCTGCTAACCGCTAACTTTT
62 CCAGATCCGGGGTATGATCCACATTATTATGGTTTGGACTCTGCTAACAACTAACTTTT
344747 CTAACATCTA
Statistics
Matches: 109, Mismatches: 9, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
120 13 0.12
121 2 0.02
122 10 0.09
123 5 0.05
124 79 0.72
ACGTcount: A:0.23, C:0.13, G:0.16, T:0.48
Consensus pattern (120 bp):
TTTATATATTTATTTATTTATTTATTTATTGTTTGAATTATTTGAATCAACCTTGTGGTGACCAG
ATCCGGGGTATGATCCACATTATTATGGTTTGGACTCTGCTAACAACTAACTTTT
Found at i:344773 original size:16 final size:16
Alignment explanation
Indices: 344731--344773 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
344721 TTGGACTCTG
*
344731 CTAACCGCTAACTTTT
1 CTAACCGCTAACCTTT
**
344747 CTAACATCTAACCTTT
1 CTAACCGCTAACCTTT
344763 CTAACCGCTAA
1 CTAACCGCTAA
344774 TTACTAACTA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.30, C:0.33, G:0.05, T:0.33
Consensus pattern (16 bp):
CTAACCGCTAACCTTT
Found at i:347917 original size:28 final size:28
Alignment explanation
Indices: 347877--347939 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
347867 AGTTTACAGA
*
347877 ATTTGAAGTTTATGATATAATTCATAGG
1 ATTTGGAGTTTATGATATAATTCATAGG
* *
347905 ATTTGGAGTTTATGATGTAATTTATAGG
1 ATTTGGAGTTTATGATATAATTCATAGG
*
347933 GTTTGGA
1 ATTTGGA
347940 TTAAATTTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.30, C:0.02, G:0.24, T:0.44
Consensus pattern (28 bp):
ATTTGGAGTTTATGATATAATTCATAGG
Found at i:349951 original size:69 final size:69
Alignment explanation
Indices: 349696--349951 Score: 291
Period size: 69 Copynumber: 3.7 Consensus size: 69
349686 TACGATAATA
* * * * * *
349696 TGCTCCCTTGTGATTCACTCTAATCCTTTGGAGCTCCCGTGCGAGTCAACCTA-AATAATTACGA
1 TGCTCCCGTGCGAGTCACTCTAATCCTTCGGGGCTCCCGTGCGAGTC-ACCCAGAATAATTACGA
349760 TTAGG
65 TTAGG
* * *
349765 TGCTCTCGTGCAAGTCACTCTAATCCTTCGGGGCTCCCGTGCAAGTCACCC-GAAATAATTACGA
1 TGCTCCCGTGCGAGTCACTCTAATCCTTCGGGGCTCCCGTGCGAGTCACCCAG-AATAATTACGA
349829 TTAGG
65 TTAGG
* * * *** * *
349834 TGCTCCCGTGTGAGTCACTCTATTCATTCGGGGCTTTTGTGCGAGTCACCCAGAATAATCACAAT
1 TGCTCCCGTGCGAGTCACTCTAATCCTTCGGGGCTCCCGTGCGAGTCACCCAGAATAATTACGAT
349899 TAGG
66 TAGG
* ** *
349903 TGCTCCCTTGCGAGTCACTCTAATCCTTCAAGGCTCCTGTGCGAGTCAC
1 TGCTCCCGTGCGAGTCACTCTAATCCTTCGGGGCTCCCGTGCGAGTCAC
349952 TAAGAATACA
Statistics
Matches: 156, Mismatches: 28, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
68 3 0.02
69 152 0.97
70 1 0.01
ACGTcount: A:0.21, C:0.28, G:0.21, T:0.29
Consensus pattern (69 bp):
TGCTCCCGTGCGAGTCACTCTAATCCTTCGGGGCTCCCGTGCGAGTCACCCAGAATAATTACGAT
TAGG
Found at i:350210 original size:76 final size:76
Alignment explanation
Indices: 350090--350494 Score: 449
Period size: 76 Copynumber: 5.3 Consensus size: 76
350080 ACATTAACAT
* * * * *
350090 GTAATTCCAGCACTAAA-TTAAACACATCACAATTCTAGCAGTGAAATTTAACAATGACTTAGAC
1 GTAATTCAAGCACTAAACTT-ATCACAT-A-ATTTC-AGCAGTGAAATTTAACATTGACTTACAC
* *
350154 CAGTGAAAT-CATGTC
62 CAGTGAAATGAAT-AC
* ** * *
350169 ATAATTTTAGCACTAAACTTATGACATGATTTCAGCAGTGAAATTTAACATTGACTTACACCAGT
1 GTAATTCAAGCACTAAACTTATCACATAATTTCAGCAGTGAAATTTAACATTGACTTACACCAGT
350234 GAAATGAATAC
66 GAAATGAATAC
* * * *
350245 GTAATTCAAGCACCAAATTTATCACATCATTTCAGCAGTGAAATTTAACATTGACTTACACCAAT
1 GTAATTCAAGCACTAAACTTATCACATAATTTCAGCAGTGAAATTTAACATTGACTTACACCAGT
*
350310 AAAATGAATAC
66 GAAATGAATAC
* * * * * *
350321 GTAATTCCAGCGCTAAACTTATCACATAATTCCAGTAGTGAAACTTAACATTGACTTAAACCAGT
1 GTAATTCAAGCACTAAACTTATCACATAATTTCAGCAGTGAAATTTAACATTGACTTACACCAGT
*
350386 GAAATGAATAT
66 GAAATGAATAC
* * * * * *
350397 GTAATTCCAGCACTAAACTTTTCACATAA-GTCAAGGAGTGAAATTAAACATTGACTTACACTAG
1 GTAATTCAAGCACTAAACTTATCACATAATTTC-AGCAGTGAAATTTAACATTGACTTACACCAG
350461 TGAAATGAATAC
65 TGAAATGAATAC
350473 GTAATTCCAA-CACTAAACTTAT
1 GTAATT-CAAGCACTAAACTTAT
350495 GATTTCACAT
Statistics
Matches: 278, Mismatches: 44, Indels: 11
0.83 0.13 0.03
Matches are distributed among these distances:
75 1 0.00
76 248 0.89
77 8 0.03
79 19 0.07
80 2 0.01
ACGTcount: A:0.40, C:0.19, G:0.12, T:0.29
Consensus pattern (76 bp):
GTAATTCAAGCACTAAACTTATCACATAATTTCAGCAGTGAAATTTAACATTGACTTACACCAGT
GAAATGAATAC
Found at i:356146 original size:29 final size:29
Alignment explanation
Indices: 356113--356174 Score: 124
Period size: 29 Copynumber: 2.1 Consensus size: 29
356103 CGCTGACCTA
356113 ACCCGCTTACCCGTGTCTGACTCGATCTG
1 ACCCGCTTACCCGTGTCTGACTCGATCTG
356142 ACCCGCTTACCCGTGTCTGACTCGATCTG
1 ACCCGCTTACCCGTGTCTGACTCGATCTG
356171 ACCC
1 ACCC
356175 AACCCAGTCC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.15, C:0.40, G:0.19, T:0.26
Consensus pattern (29 bp):
ACCCGCTTACCCGTGTCTGACTCGATCTG
Found at i:356212 original size:18 final size:18
Alignment explanation
Indices: 356189--356223 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
356179 CAGTCCGATC
*
356189 GTTGACCATTGATCGACT
1 GTTGACCATTCATCGACT
*
356207 GTTGACCGTTCATCGAC
1 GTTGACCATTCATCGAC
356224 CGTTAACTGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.20, C:0.26, G:0.23, T:0.31
Consensus pattern (18 bp):
GTTGACCATTCATCGACT
Found at i:356248 original size:14 final size:14
Alignment explanation
Indices: 356229--356273 Score: 63
Period size: 14 Copynumber: 3.2 Consensus size: 14
356219 TCGACCGTTA
356229 ACTGTTGGCTGTTG
1 ACTGTTGGCTGTTG
356243 ACTGTTGGCTGTTG
1 ACTGTTGGCTGTTG
* * *
356257 ACCGTTGACCGTTG
1 ACTGTTGGCTGTTG
356271 ACT
1 ACT
356274 TTGACCCAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.11, C:0.20, G:0.31, T:0.38
Consensus pattern (14 bp):
ACTGTTGGCTGTTG
Found at i:356256 original size:21 final size:21
Alignment explanation
Indices: 356221--356279 Score: 57
Period size: 21 Copynumber: 2.9 Consensus size: 21
356211 ACCGTTCATC
** * *
356221 GACCGTTAACTGTTGGCTGTT
1 GACCGTTGGCTGTTGACCGTT
*
356242 GACTGTTGGCTGTTGACCGTT
1 GACCGTTGGCTGTTGACCGTT
*
356263 GACCGTTGACT-TTGACC
1 GACCGTTGGCTGTTGACC
356280 CAAAAAGTCA
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
20 6 0.19
21 25 0.81
ACGTcount: A:0.14, C:0.22, G:0.29, T:0.36
Consensus pattern (21 bp):
GACCGTTGGCTGTTGACCGTT
Found at i:357111 original size:39 final size:39
Alignment explanation
Indices: 357052--357211 Score: 169
Period size: 39 Copynumber: 4.1 Consensus size: 39
357042 CGCTTTCTGT
* * * *
357052 AGGCTCCTCGGCTTTATGCTCAGGGTAAGTCCTTACAGC
1 AGGCTCCTCGGCTTTGTGCACAGGATAAGACCTTACAGC
* * *
357091 AGGCTCCTCGGCTTTGTGCTCAGGGTAAGTCCTTACTA-C
1 AGGCTCCTCGGCTTTGTGCACAGGATAAGACCTTAC-AGC
* * * *
357130 AGGCTCATCTGCTTTGTGCACAGGATAAGACCTTACTGT
1 AGGCTCCTCGGCTTTGTGCACAGGATAAGACCTTACAGC
* ** *
357169 AGGCTCTTATGCTTTGTGCACAGGATAAGACCTTACTGC
1 AGGCTCCTCGGCTTTGTGCACAGGATAAGACCTTACAGC
357208 AGGC
1 AGGC
357212 GTCTCTACTT
Statistics
Matches: 108, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
39 107 0.99
40 1 0.01
ACGTcount: A:0.20, C:0.26, G:0.25, T:0.29
Consensus pattern (39 bp):
AGGCTCCTCGGCTTTGTGCACAGGATAAGACCTTACAGC
Found at i:357183 original size:78 final size:78
Alignment explanation
Indices: 357101--357245 Score: 193
Period size: 78 Copynumber: 1.9 Consensus size: 78
357091 AGGCTCCTCG
* * * * * *
357101 GCTTTGTGCTCAGGGTAAGTCCTTACTACAGGC-TCATCTGCTTTGTGCACAGGATAAGACCTTA
1 GCTTTGTGCACAGGATAAGACCTTACTACAGGCGTC-TCTACTTTATACACAGGATAAGACCTTA
357165 CTGTAGGCTCTTAT
65 CTGTAGGCTCTTAT
* * *
357179 GCTTTGTGCACAGGATAAGACCTTACTGCAGGCGTCTCTACTTTATACACAGGGTAAGCCCTTAC
1 GCTTTGTGCACAGGATAAGACCTTACTACAGGCGTCTCTACTTTATACACAGGATAAGACCTTAC
357244 TG
66 TG
357246 GGTGTATAGG
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
78 55 0.96
79 2 0.04
ACGTcount: A:0.22, C:0.24, G:0.23, T:0.31
Consensus pattern (78 bp):
GCTTTGTGCACAGGATAAGACCTTACTACAGGCGTCTCTACTTTATACACAGGATAAGACCTTAC
TGTAGGCTCTTAT
Found at i:357230 original size:39 final size:38
Alignment explanation
Indices: 357063--357245 Score: 161
Period size: 39 Copynumber: 4.7 Consensus size: 38
357053 GGCTCCTCGG
* * * * * **
357063 CTTTATGCTCAGGGTAAGTCCTTACAGCAGGCTCCTCGG
1 CTTTGTGCACAGGATAAGACCTTACTGCAGGCT-CTCTA
* * * * *
357102 CTTTGTGCTCAGGGTAAGTCCTTACTACAGGCTCATCTG
1 CTTTGTGCACAGGATAAGACCTTACTGCAGGCTC-TCTA
*
357141 CTTTGTGCACAGGATAAGACCTTACTGTAGGCTCT-TA
1 CTTTGTGCACAGGATAAGACCTTACTGCAGGCTCTCTA
357178 TGCTTTGTGCACAGGATAAGACCTTACTGCAGGCGTCTCTA
1 --CTTTGTGCACAGGATAAGACCTTACTGCAGGC-TCTCTA
* * * *
357219 CTTTATACACAGGGTAAGCCCTTACTG
1 CTTTGTGCACAGGATAAGACCTTACTG
357246 GGTGTATAGG
Statistics
Matches: 124, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
37 1 0.01
38 2 0.02
39 116 0.94
40 3 0.02
41 2 0.02
ACGTcount: A:0.21, C:0.25, G:0.23, T:0.31
Consensus pattern (38 bp):
CTTTGTGCACAGGATAAGACCTTACTGCAGGCTCTCTA
Found at i:363365 original size:39 final size:39
Alignment explanation
Indices: 363297--363401 Score: 131
Period size: 39 Copynumber: 2.7 Consensus size: 39
363287 CTTTCCGCAT
* *
363297 GCTCATCGGTTTTATGCTCAGGGTAAGTCCTTAC-AGCAG
1 GCTCATCGGCTTTGTGCTCAGGGTAAGTCCTTACTA-CAG
*
363336 GCTCCTCGGCTTTGTGCTCAGGGTAAGTCCTTACTACAG
1 GCTCATCGGCTTTGTGCTCAGGGTAAGTCCTTACTACAG
* ** *
363375 GCGCATTTGCTTTGTGCACAGGGTAAG
1 GCTCATCGGCTTTGTGCTCAGGGTAAG
363402 CTTTTATTGG
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
39 56 0.98
40 1 0.02
ACGTcount: A:0.18, C:0.24, G:0.28, T:0.30
Consensus pattern (39 bp):
GCTCATCGGCTTTGTGCTCAGGGTAAGTCCTTACTACAG
Found at i:371938 original size:32 final size:31
Alignment explanation
Indices: 371900--371976 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 31
371890 CGAGGCCATG
* *
371900 GGGCCTACCTAAGAACACATCTTAGGGCCGTA
1 GGGCCTACCTAAGAAC-CATCTCAGGGCCGCA
** *
371932 GGGCCTACCCGAGAACGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAACCATCTCAGGGCCGCA
**
371963 AAGCCTACCTAAGA
1 GGGCCTACCTAAGA
371977 GTCACATTAG
Statistics
Matches: 36, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
31 22 0.61
32 14 0.39
ACGTcount: A:0.29, C:0.31, G:0.26, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAACCATCTCAGGGCCGCA
Found at i:373439 original size:18 final size:18
Alignment explanation
Indices: 373407--373445 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
373397 AATCATTTCC
** *
373407 TTTCATCCAGTCTTATTA
1 TTTCATCCAAACTTATCA
373425 TTTCATCCAAACTTATCA
1 TTTCATCCAAACTTATCA
373443 TTT
1 TTT
373446 ACTTTAGTCC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.26, C:0.23, G:0.03, T:0.49
Consensus pattern (18 bp):
TTTCATCCAAACTTATCA
Found at i:377121 original size:69 final size:69
Alignment explanation
Indices: 377047--377310 Score: 275
Period size: 69 Copynumber: 3.8 Consensus size: 69
377037 TACGATAATA
* *
377047 TGCTCCCTTGTGAGTCACTCTAATCCTTCGAAGCTCCCGTACGAGTCAACCGAAATAATTACGAT
1 TGCTCCCTTGTGAGTCACTCTAATCCTTCGAGGCTCCCGTGCGAGTCAACCGAAATAATTACGAT
377112 TAGG
66 TAGG
* * *
377116 TGCTCCCGTGTAAGTCACTCTAATCCTTCGAGGCTCCCGTGC-ATGTCACCCGAAATAATTACGA
1 TGCTCCCTTGTGAGTCACTCTAATCCTTCGAGGCTCCCGTGCGA-GTCAACCGAAATAATTACGA
*
377180 TTAGA
65 TTAGG
* * * * ** * *
377185 TGCT-TCTGTGTGAGTCACTCTATTCCTTTGGGGCTTTCGTGCGAGTC-ACCCAGAATAATCACG
1 TGCTCCCT-TGTGAGTCACTCTAATCCTTCGAGGCTCCCGTGCGAGTCAACCGA-AATAATTACG
377248 ATTAGG
64 ATTAGG
* * * * * * *
377254 TGCTCCCTTGCGAATCACTCTAAT-CGTCCATGGCTCCTGTGCGAGTCACCCGTAATA
1 TGCTCCCTTGTGAGTCACTCTAATCCTTCGA-GGCTCCCGTGCGAGTCAACCGAAATA
377311 CTCATTATTA
Statistics
Matches: 156, Mismatches: 32, Indels: 14
0.77 0.16 0.07
Matches are distributed among these distances:
68 7 0.04
69 144 0.92
70 5 0.03
ACGTcount: A:0.22, C:0.28, G:0.20, T:0.29
Consensus pattern (69 bp):
TGCTCCCTTGTGAGTCACTCTAATCCTTCGAGGCTCCCGTGCGAGTCAACCGAAATAATTACGAT
TAGG
Found at i:377289 original size:138 final size:138
Alignment explanation
Indices: 377055--377310 Score: 313
Period size: 138 Copynumber: 1.9 Consensus size: 138
377045 TATGCTCCCT
*
377055 TGTGAGTCACTCTAATCCTTCGAAGCTCCCGTACGAGTCAACCGAAATAATTACGATTAGGTGCT
1 TGTGAGTCACTCTAATCCTTCGAAGCTCCCGTACGAGTCAACCGAAATAATCACGATTAGGTGCT
* * *
377120 CCCGTGTAAGTCACTCTAATCCTTCGAGGCTCCCGTGC-ATGTCACCCGAAATAATTACGATTAG
66 CCCGTGGAAGTCACTCTAATCCGTCCAGGCTCCCGTGCGA-GTCACCCGAAATAATTACGATTAG
377184 ATGCTTCTG
130 ATGCTTCTG
* * ** ** * *
377193 TGTGAGTCACTCTATTCCTTTGGGGCTTTCGTGCGAGTC-ACCCAGAATAATCACGATTAGGTGC
1 TGTGAGTCACTCTAATCCTTCGAAGCTCCCGTACGAGTCAACCGA-AATAATCACGATTAGGTGC
* * *
377257 TCCCTTGCGAA-TCACTCTAAT-CGTCCATGGCTCCTGTGCGAGTCACCCGTAATA
65 TCCCGTG-GAAGTCACTCTAATCCGTCCA-GGCTCCCGTGCGAGTCACCCGAAATA
377311 CTCATTATTA
Statistics
Matches: 99, Mismatches: 15, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
137 8 0.08
138 88 0.89
139 3 0.03
ACGTcount: A:0.23, C:0.27, G:0.21, T:0.29
Consensus pattern (138 bp):
TGTGAGTCACTCTAATCCTTCGAAGCTCCCGTACGAGTCAACCGAAATAATCACGATTAGGTGCT
CCCGTGGAAGTCACTCTAATCCGTCCAGGCTCCCGTGCGAGTCACCCGAAATAATTACGATTAGA
TGCTTCTG
Found at i:377579 original size:76 final size:76
Alignment explanation
Indices: 377471--377993 Score: 686
Period size: 76 Copynumber: 6.9 Consensus size: 76
377461 AACACATTAC
* *
377471 AATTCTAGCAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCTAGCACTAA
1 AATTCCAGCAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAGCACTAA
* *
377536 ATTTATGACAT
66 ACTTATCACAT
* * * * * * *
377547 GATTTCAGCAGTGAAACTTAGCATTAATTTACACCAGTGAAATGAATACGTAATTCAAGCACCAA
1 AATTCCAGCAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAGCACTAA
*
377612 ATTTATCACAT
66 ACTTATCACAT
* * ** * * * **
377623 CATTTCAATAGTGAAATTTAACATTGACTTACACCAGTAAAATGAATACGTAATTTCAGCGTTAA
1 AATTCCAGCAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAGCACTAA
377688 ACTTATCACAT
66 ACTTATCACAT
* * ** * * *
377699 AATTCCAGTAGTGAAACTTAACATTAACTTACACCAACGAAATGAATATGTGATTCCAACACTAA
1 AATTCCAGCAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAGCACTAA
377764 ACTTATCACAT
66 ACTTATCACAT
* *
377775 AATTCTAACAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAGCACTAA
1 AATTCCAGCAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAGCACTAA
*
377840 ACTTATCACCT
66 ACTTATCACAT
* * * * *
377851 AATTCCAGCAATGAAATTTAACATTGACTTACACCAGTAAAATGAATAAGTAATTCCAACACTAA
1 AATTCCAGCAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAGCACTAA
377916 ACTTATCACAT
66 ACTTATCACAT
* * * *
377927 AATTCCAGCAGCGAAACTTAACATTGACTTACATCAGTGAAATGAATATGTAACTCCAGCACTAA
1 AATTCCAGCAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAGCACTAA
377992 AC
66 AC
377994 GTTGAAGCTT
Statistics
Matches: 384, Mismatches: 63, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
76 384 1.00
ACGTcount: A:0.41, C:0.20, G:0.11, T:0.28
Consensus pattern (76 bp):
AATTCCAGCAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAGCACTAA
ACTTATCACAT
Found at i:377877 original size:228 final size:227
Alignment explanation
Indices: 377471--378359 Score: 959
Period size: 228 Copynumber: 4.0 Consensus size: 227
377461 AACACATTAC
* * * * *
377471 AATTCTAGCAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCTAGCACTAA
1 AATTCCAGCAGTGAAACTTAACATTAACTTACACCAGCGAAATGAATACGTAATTCCAACACTAA
* * * * * * *
377536 ATTTATGACATGATTTCAGCAGTGAAACTTAGCATTAATTTACACCAGTGAAATGAATACGTAAT
66 ACTTATCACATAATTT-AACAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAAT
* * * * * **
377601 TCAAGCACCAAATTTATCACATCATTTCAATAGTGAAATTTAACATTGACTTACACCAGTAAAAT
130 TCCAGCACTAAACTTATCACATAATTCCAGCAGTGAAATTTAACATTGACTTACACCAGTAAAAT
**
377666 GAATACGTAATTTCAGCGTTAAACTTATCACAT
195 GAATACGTAATTTCAGCACTAAACTTATCACAT
* * * *
377699 AATTCCAGTAGTGAAACTTAACATTAACTTACACCAACGAAATGAATATGTGATTCCAACACTAA
1 AATTCCAGCAGTGAAACTTAACATTAACTTACACCAGCGAAATGAATACGTAATTCCAACACTAA
377764 ACTTATCACATAATTCTAACAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAAT
66 ACTTATCACATAATT-TAACAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAAT
* *
377829 TCCAGCACTAAACTTATCACCTAATTCCAGCAATGAAATTTAACATTGACTTACACCAGTAAAAT
130 TCCAGCACTAAACTTATCACATAATTCCAGCAGTGAAATTTAACATTGACTTACACCAGTAAAAT
* * *
377894 GAATAAGTAATTCCAACACTAAACTTATCACAT
195 GAATACGTAATTTCAGCACTAAACTTATCACAT
* * * * * * *
377927 AATTCCAGCAGCGAAACTTAACATTGACTTACATCAGTGAAATGAATATGTAACTCCAGCACT--
1 AATTCCAGCAGTGAAACTTAACATTAACTTACACCAGCGAAATGAATACGTAATTCCAACACTAA
* * * * *
377990 A---A--AC-----GT-----TGAAGCTTAACATTGACTTACATCATTGAAATGAATATGTAATT
66 ACTTATCACATAATTTAACAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATT
* * * * *
378040 CTACCACTAAACTTGTCACATAATTCCCGCAGTGAAATTTAACATTGACTTACACCAGTGAAATG
131 CCAGCACTAAACTTATCACATAATTCCAGCAGTGAAATTTAACATTGACTTACACCAGTAAAATG
378105 AATACGTAA-TTCTAGCACTAAACTTATCACAT
196 AATACGTAATTTC-AGCACTAAACTTATCACAT
* * * * * *
378137 AATTCCTGCAGTGAAACTTAACATTAACTTACACTAGCGAAATGAATACATAATTACATCATTAA
1 AATTCCAGCAGTGAAACTTAACATTAACTTACACCAGCGAAATGAATACGTAATTCCAACACTAA
* * * ** * * *
378202 ATTTATCACCTAATTCCAGTAGTGAAACTTAACATTGACTTAAACCAGTGAAGTGAATACGTCAT
66 ACTTATCACATAATT-TAACAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAAT
* * * * ** * * * *
378267 TCCAACACTAAACTTTTCACATAAGTCAAGGGGTGAAACTGAACATTGACTTACACTAGTGAAAT
130 TCCAGCACTAAACTTATCACATAATTCCAGCAGTGAAATTTAACATTGACTTACACCAGTAAAAT
* *
378332 GAATACGTAATTCCAACACTAAACTTAT
195 GAATACGTAATTTCAGCACTAAACTTAT
378360 GATTTCACAT
Statistics
Matches: 552, Mismatches: 88, Indels: 42
0.81 0.13 0.06
Matches are distributed among these distances:
209 2 0.00
210 175 0.32
212 1 0.00
215 2 0.00
217 2 0.00
221 2 0.00
223 1 0.00
226 1 0.00
228 363 0.66
229 3 0.01
ACGTcount: A:0.40, C:0.20, G:0.11, T:0.29
Consensus pattern (227 bp):
AATTCCAGCAGTGAAACTTAACATTAACTTACACCAGCGAAATGAATACGTAATTCCAACACTAA
ACTTATCACATAATTTAACAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATT
CCAGCACTAAACTTATCACATAATTCCAGCAGTGAAATTTAACATTGACTTACACCAGTAAAATG
AATACGTAATTTCAGCACTAAACTTATCACAT
Found at i:378108 original size:134 final size:134
Alignment explanation
Indices: 377868--378127 Score: 394
Period size: 134 Copynumber: 1.9 Consensus size: 134
377858 GCAATGAAAT
377868 TTAACATTGACTTACACCAGTAAAATGAATAAGTAATTCCAACACTAAACTTATCACATAATTCC
1 TTAACATTGACTTACACCAGTAAAATGAATAAGTAATTCCAACACTAAACTTATCACATAATTCC
* *
377933 AGCAGCGAAACTTAACATTGACTTACATCAGTGAAATGAATATGTAACTCCAGCACTAAACGTTG
66 AGCAGCGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAACTCCAGCACTAAACGTTG
377998 AAGC
131 AAGC
* * * * * * *
378002 TTAACATTGACTTACATCATTGAAATGAATATGTAATTCTACCACTAAACTTGTCACATAATTCC
1 TTAACATTGACTTACACCAGTAAAATGAATAAGTAATTCCAACACTAAACTTATCACATAATTCC
* * * * *
378067 CGCAGTGAAATTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCTAGCACTAAAC
66 AGCAGCGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAACTCCAGCACTAAAC
378128 TTATCACATA
Statistics
Matches: 112, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
134 112 1.00
ACGTcount: A:0.40, C:0.20, G:0.12, T:0.28
Consensus pattern (134 bp):
TTAACATTGACTTACACCAGTAAAATGAATAAGTAATTCCAACACTAAACTTATCACATAATTCC
AGCAGCGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAACTCCAGCACTAAACGTTG
AAGC
Found at i:378128 original size:76 final size:76
Alignment explanation
Indices: 377996--378359 Score: 440
Period size: 76 Copynumber: 4.8 Consensus size: 76
377986 CACTAAACGT
* * * * * * *
377996 TGAAGCTTAACATTGACTTACATCATTGAAATGAATATGTAATTCTACCACTAAACTTGTCACAT
1 TGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAACACTAAACTTATCACAT
*
378061 AATTCCCGCAG
66 AATTCCAGCAG
* * *
378072 TGAAATTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCTAGCACTAAACTTATCACAT
1 TGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAACACTAAACTTATCACAT
*
378137 AATTCCTGCAG
66 AATTCCAGCAG
* * * * * * * * *
378148 TGAAACTTAACATTAACTTACACTAGCGAAATGAATACATAATTACATCATTAAATTTATCACCT
1 TGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAACACTAAACTTATCACAT
*
378213 AATTCCAGTAG
66 AATTCCAGCAG
* * * *
378224 TGAAACTTAACATTGACTTAAACCAGTGAAGTGAATACGTCATTCCAACACTAAACTTTTCACAT
1 TGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAACACTAAACTTATCACAT
* * **
378289 AAGTCAAGGGG
66 AATTCCAGCAG
* *
378300 TGAAACTGAACATTGACTTACACTAGTGAAATGAATACGTAATTCCAACACTAAACTTAT
1 TGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAACACTAAACTTAT
378360 GATTTCACAT
Statistics
Matches: 244, Mismatches: 44, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
76 244 1.00
ACGTcount: A:0.39, C:0.20, G:0.12, T:0.30
Consensus pattern (76 bp):
TGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAACACTAAACTTATCACAT
AATTCCAGCAG
Found at i:378155 original size:210 final size:210
Alignment explanation
Indices: 377786--378359 Score: 628
Period size: 210 Copynumber: 2.6 Consensus size: 210
377776 ATTCTAACAG
* *
377786 TGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAGCACTAAACTTATCACCT
1 TGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCACCACTAAACTTATCACAT
377851 AATTCCAGCAATGAAATTTAACATTGACTTACACCAGTAAAATGAATAAGTAATTCCAACACTAA
66 AATTCCAGCAATGAAATTTAACATTGACTTACACCAGTAAAATGAATAAGTAATTCCAACACTAA
* *
377916 ACTTATCACATAATTCCAGCAGCGAAACTTAACATTGACTTACA-TCAGTGAAATGAATATGTAA
131 ACTTATCACATAATTCCAGCAGCGAAACTTAACATTAACTTACACT-AGCGAAATGAATATGTAA
377980 CTCCAGCACTAAACGT
195 CTCCAGCACTAAACGT
* * * * * *
377996 TGAAGCTTAACATTGACTTACATCATTGAAATGAATATGTAATTCTACCACTAAACTTGTCACAT
1 TGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCACCACTAAACTTATCACAT
* * * * * *
378061 AATTCCCGCAGTGAAATTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCTAGCACTAA
66 AATTCCAGCAATGAAATTTAACATTGACTTACACCAGTAAAATGAATAAGTAATTCCAACACTAA
* * *
378126 ACTTATCACATAATTCCTGCAGTGAAACTTAACATTAACTTACACTAGCGAAATGAATACATAAT
131 ACTTATCACATAATTCCAGCAGCGAAACTTAACATTAACTTACACTAGCGAAATGAAT--AT--G
** * *
378191 TACATCATTAAATTTATCACCTAATTCCAGT
192 TA-A-C------TCCAGCA-CTAA--AC-GT
* * * * *
378222 AGTGAAACTTAACATTGACTTAAACCAGTGAAGTGAATACGTCATTCCAACACTAAACTTTTCAC
1 --TGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCACCACTAAACTTATCAC
* * *** * * * * *
378287 ATAAGTCAAGGGGTGAAACTGAACATTGACTTACACTAGTGAAATGAATACGTAATTCCAACACT
64 ATAATTCCAGCAATGAAATTTAACATTGACTTACACCAGTAAAATGAATAAGTAATTCCAACACT
378352 AAACTTAT
129 AAACTTAT
378360 GATTTCACAT
Statistics
Matches: 302, Mismatches: 43, Indels: 20
0.83 0.12 0.05
Matches are distributed among these distances:
210 168 0.56
211 1 0.00
212 2 0.01
214 2 0.01
215 1 0.00
216 1 0.00
222 4 0.01
223 4 0.01
225 1 0.00
226 2 0.01
228 116 0.38
ACGTcount: A:0.40, C:0.20, G:0.11, T:0.29
Consensus pattern (210 bp):
TGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCACCACTAAACTTATCACAT
AATTCCAGCAATGAAATTTAACATTGACTTACACCAGTAAAATGAATAAGTAATTCCAACACTAA
ACTTATCACATAATTCCAGCAGCGAAACTTAACATTAACTTACACTAGCGAAATGAATATGTAAC
TCCAGCACTAAACGT
Found at i:378314 original size:362 final size:362
Alignment explanation
Indices: 377640--378355 Score: 979
Period size: 362 Copynumber: 2.0 Consensus size: 362
377630 ATAGTGAAAT
* **
377640 TTAACATTGACTTACACCAGTAAAATGAATACGTAATTTCAGCGTTAAACTTATCACATAATTCC
1 TTAACATTGACTTACACCAGTAAAATGAATACGTAATTTCACCACTAAACTTATCACATAATTCC
* * *
377705 AGTAGTGAAACTTAACATTAACTTACACCAACGAAATGAATATGTGATTCCAACACTAAACTTAT
66 AGCAGTGAAACTTAACATTAACTTACACCAACGAAATGAATACGTAATTCCAACACTAAACTTAT
* * * *
377770 CACATAATTCTAACAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAGC
131 CACATAATTCTAACAGTGAAACTTAACATTAACTTACACCAGCGAAATGAATACATAATTACAGC
* *
377835 ACTAAACTTATCACCTAATTCCAGCAATGAAATTTAACATTGACTTACACCAGTAAAATGAATAA
196 ACTAAACTTATCACCTAATTCCAGCAATGAAACTTAACATTGACTTAAACCAGTAAAATGAATAA
* * *
377900 GTAATTCCAACACTAAACTTATCACATAATTCCAGCAGCGAAACTTAACATTGACTTACA-TCAG
261 GTAATTCCAACACTAAACTTATCACATAAGTCAAGCAGCGAAACTGAACATTGACTTACACT-AG
* *
377964 TGAAATGAATATGTAACTCCAGCACTAAACGTTGAAGC
325 TGAAATGAATACGTAACTCCAACACTAAACGTTGAAGC
* * * * *
378002 TTAACATTGACTTACATCATTGAAATGAATATGTAA-TTCTACCACTAAACTTGTCACATAATTC
1 TTAACATTGACTTACACCAGTAAAATGAATACGTAATTTC-ACCACTAAACTTATCACATAATTC
* * * ** * *
378066 CCGCAGTGAAATTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCTAGCACTAAACTTA
65 CAGCAGTGAAACTTAACATTAACTTACACCAACGAAATGAATACGTAATTCCAACACTAAACTTA
* *
378131 TCACATAATTCCT-GCAGTGAAACTTAACATTAACTTACACTAGCGAAATGAATACATAATTACA
130 TCACATAATT-CTAACAGTGAAACTTAACATTAACTTACACCAGCGAAATGAATACATAATTACA
* * * * * * *
378195 TCATTAAATTTATCACCTAATTCCAGTAGTGAAACTTAACATTGACTTAAACCAGTGAAGTGAAT
194 GCACTAAACTTATCACCTAATTCCAGCAATGAAACTTAACATTGACTTAAACCAGTAAAATGAAT
* * * ** *
378260 ACGTCATTCCAACACTAAACTTTTCACATAAGTCAAGGGGTGAAACTGAACATTGACTTACACTA
259 AAGTAATTCCAACACTAAACTTATCACATAAGTCAAGCAGCGAAACTGAACATTGACTTACACTA
*
378325 GTGAAATGAATACGTAATTCCAACACTAAAC
324 GTGAAATGAATACGTAACTCCAACACTAAAC
378356 TTATGATTTC
Statistics
Matches: 306, Mismatches: 45, Indels: 6
0.86 0.13 0.02
Matches are distributed among these distances:
361 3 0.01
362 300 0.98
363 3 0.01
ACGTcount: A:0.40, C:0.20, G:0.11, T:0.28
Consensus pattern (362 bp):
TTAACATTGACTTACACCAGTAAAATGAATACGTAATTTCACCACTAAACTTATCACATAATTCC
AGCAGTGAAACTTAACATTAACTTACACCAACGAAATGAATACGTAATTCCAACACTAAACTTAT
CACATAATTCTAACAGTGAAACTTAACATTAACTTACACCAGCGAAATGAATACATAATTACAGC
ACTAAACTTATCACCTAATTCCAGCAATGAAACTTAACATTGACTTAAACCAGTAAAATGAATAA
GTAATTCCAACACTAAACTTATCACATAAGTCAAGCAGCGAAACTGAACATTGACTTACACTAGT
GAAATGAATACGTAACTCCAACACTAAACGTTGAAGC
Found at i:384891 original size:20 final size:19
Alignment explanation
Indices: 384859--384897 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
384849 CAGGAGTTGA
* *
384859 TTATTTCCTACATATCATG
1 TTATTTCCGACATAACATG
384878 TTATCTTCCGACATAACATG
1 TTAT-TTCCGACATAACATG
384898 GTAATGTGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.28, C:0.23, G:0.08, T:0.41
Consensus pattern (19 bp):
TTATTTCCGACATAACATG
Found at i:389108 original size:9 final size:9
Alignment explanation
Indices: 389094--389118 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
389084 AAACAAAGAC
389094 AAATTAATT
1 AAATTAATT
389103 AAATTAATT
1 AAATTAATT
389112 AAATTAA
1 AAATTAA
389119 AAATAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (9 bp):
AAATTAATT
Found at i:389127 original size:7 final size:6
Alignment explanation
Indices: 389116--389182 Score: 75
Period size: 6 Copynumber: 11.2 Consensus size: 6
389106 TTAATTAAAT
* * *
389116 TAAAAA TAAAAA TAAAAA TAAAAGA -AATAA TAAAAA TGAAAA TAAAAT
1 TAAAAA TAAAAA TAAAAA TAAAA-A TAAAAA TAAAAA TAAAAA TAAAAA
389164 TAAAAA -AACAAA TAAAAA T
1 TAAAAA TAA-AAA TAAAAA T
389183 GTCGGGAAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
5 3 0.06
6 45 0.88
7 3 0.06
ACGTcount: A:0.78, C:0.01, G:0.03, T:0.18
Consensus pattern (6 bp):
TAAAAA
Found at i:389183 original size:30 final size:30
Alignment explanation
Indices: 389116--389183 Score: 93
Period size: 30 Copynumber: 2.3 Consensus size: 30
389106 TTAATTAAAT
* *
389116 TAAAAATAAAAATAAAAATAAAAGAAATAA
1 TAAAAATGAAAATAAAAATAAAAGAAAAAA
*
389146 TAAAAATGAAAATAAAATTAAAA-AAACAAA
1 TAAAAATGAAAATAAAAATAAAAGAAA-AAA
389176 TAAAAATG
1 TAAAAATG
389184 TCGGGAAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 3 0.09
30 31 0.91
ACGTcount: A:0.76, C:0.01, G:0.04, T:0.18
Consensus pattern (30 bp):
TAAAAATGAAAATAAAAATAAAAGAAAAAA
Found at i:390474 original size:16 final size:15
Alignment explanation
Indices: 390453--390497 Score: 56
Period size: 14 Copynumber: 3.0 Consensus size: 15
390443 ACACAAAAAG
390453 AAAGAAAATAAATAAA
1 AAAGAAAAT-AATAAA
390469 AAAGAAAATAATAAA
1 AAAGAAAATAATAAA
* *
390484 TAA-TAAATAATAAA
1 AAAGAAAATAATAAA
390498 CCATAATAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
14 10 0.37
15 8 0.30
16 9 0.33
ACGTcount: A:0.78, C:0.00, G:0.04, T:0.18
Consensus pattern (15 bp):
AAAGAAAATAATAAA
Found at i:390481 original size:19 final size:20
Alignment explanation
Indices: 390447--390486 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
390437 CAAATAACAC
390447 AAAAAGAAAGAAAATAAATA
1 AAAAAGAAAGAAAATAAATA
*
390467 AAAAAGAAA-ATAATAAATA
1 AAAAAGAAAGAAAATAAATA
390486 A
1 A
390487 TAAATAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.80, C:0.00, G:0.07, T:0.12
Consensus pattern (20 bp):
AAAAAGAAAGAAAATAAATA
Found at i:390484 original size:7 final size:7
Alignment explanation
Indices: 390474--390555 Score: 83
Period size: 7 Copynumber: 10.4 Consensus size: 7
390464 ATAAAAAAGA
390474 AAATAAT
1 AAATAAT
390481 AAATAAT
1 AAATAAT
390488 AAATAAT
1 AAATAAT
390495 AAACCATAAT
1 -AA--ATAAT
390505 AATATAAT
1 AA-ATAAT
390513 AAATAAT
1 AAATAAT
390520 AAATAAT
1 AAATAAT
390527 ATAATAAT
1 A-AATAAT
390535 AATATACTAT
1 AA-ATA--AT
390545 AATATAAT
1 AA-ATAAT
390553 AAA
1 AAA
390556 AAACTATACT
Statistics
Matches: 67, Mismatches: 1, Indels: 14
0.82 0.01 0.17
Matches are distributed among these distances:
7 29 0.43
8 23 0.34
9 2 0.03
10 13 0.19
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (7 bp):
AAATAAT
Found at i:390488 original size:3 final size:3
Alignment explanation
Indices: 390475--390554 Score: 55
Period size: 3 Copynumber: 26.7 Consensus size: 3
390465 TAAAAAAGAA
390475 AAT AAT AAAT AAT AAAT AAT AA- ACCAT AAT AAT -AT AAT AAAT AAT
1 AAT AAT -AAT AAT -AAT AAT AAT A--AT AAT AAT AAT AAT -AAT AAT
*
390520 AAAT AAT -AT AAT AAT AAT -AT ACT -AT AAT -AT AAT AA
1 -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
390555 AAAACTATAC
Statistics
Matches: 63, Mismatches: 2, Indels: 24
0.71 0.02 0.27
Matches are distributed among these distances:
2 10 0.16
3 39 0.62
4 13 0.21
5 1 0.02
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:390506 original size:43 final size:42
Alignment explanation
Indices: 390459--390558 Score: 112
Period size: 43 Copynumber: 2.3 Consensus size: 42
390449 AAAGAAAGAA
390459 AATAAATAAAAAAGAAAATAATAA-ATAATAAATAATAAACCAT
1 AATAAATAAAAAAGAAAA-AATAATATAAT-AATAATAAACCAT
* * * * *
390502 AATAATATAATAAATAATAAATAATATAATAATAATATACTAT
1 AATAA-ATAAAAAAGAAAAAATAATATAATAATAATAAACCAT
390545 AATATAATAAAAAA
1 AATA-AATAAAAAA
390559 CTATACTATA
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
43 32 0.67
44 16 0.33
ACGTcount: A:0.69, C:0.03, G:0.01, T:0.27
Consensus pattern (42 bp):
AATAAATAAAAAAGAAAAAATAATATAATAATAATAAACCAT
Found at i:390513 original size:5 final size:5
Alignment explanation
Indices: 390503--390608 Score: 78
Period size: 5 Copynumber: 20.8 Consensus size: 5
390493 ATAAACCATA
*
390503 ATAAT ATAAT A-AAT AATAA- ATAAT ATAAT AATAAT ATACT ATAAT ATAAT
1 ATAAT ATAAT ATAAT -ATAAT ATAAT ATAAT -ATAAT ATAAT ATAAT ATAAT
* * *
390553 A-AA- A-AACT ATACT ATAAT ATAAT ATATGT ACAAT ATAATAT ATAAT
1 ATAAT ATAA-T ATAAT ATAAT ATAAT ATA-AT ATAAT AT-A-AT ATAAT
390599 ATACAT ATAA
1 ATA-AT ATAA
390609 ATATTTTCAA
Statistics
Matches: 82, Mismatches: 8, Indels: 22
0.73 0.07 0.20
Matches are distributed among these distances:
3 3 0.04
4 9 0.11
5 48 0.59
6 18 0.22
7 4 0.05
ACGTcount: A:0.59, C:0.05, G:0.01, T:0.35
Consensus pattern (5 bp):
ATAAT
Found at i:390561 original size:18 final size:19
Alignment explanation
Indices: 390503--390571 Score: 79
Period size: 19 Copynumber: 3.6 Consensus size: 19
390493 ATAAACCATA
*
390503 ATAATATAATAAATAATA-A
1 ATAATATAATAAA-AATACT
390522 ATAATATAATAATAATATACT
1 ATAATATAATAA-AA-ATACT
390543 ATAATATAATAAAAA-ACT
1 ATAATATAATAAAAATACT
*
390561 ATACTATAATA
1 ATAATATAATA
390572 TAATATATGT
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
18 13 0.29
19 14 0.31
20 6 0.13
21 12 0.27
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.33
Consensus pattern (19 bp):
ATAATATAATAAAAATACT
Found at i:390606 original size:18 final size:18
Alignment explanation
Indices: 390503--390612 Score: 67
Period size: 23 Copynumber: 6.1 Consensus size: 18
390493 ATAAACCATA
390503 ATAATATA-ATA-AATA-
1 ATAATATACATATAATAT
390518 ATAA-ATA-ATATAATA-
1 ATAATATACATATAATAT
390533 ATAATATAC-TATAATAT
1 ATAATATACATATAATAT
390550 AATAAAAAACTATAC-TATAATAT
1 -AT----AA-TATACATATAATAT
*
390573 AATATATGTACAATATAATAT
1 -ATA-ATATAC-ATATAATAT
390594 ATAATATACATATAA-AT
1 ATAATATACATATAATAT
390611 AT
1 AT
390613 TTTCAAAAAC
Statistics
Matches: 80, Mismatches: 2, Indels: 24
0.75 0.02 0.23
Matches are distributed among these distances:
14 6 0.08
15 12 0.15
16 10 0.12
17 4 0.05
18 8 0.10
19 10 0.12
20 4 0.05
21 8 0.10
22 2 0.03
23 16 0.20
ACGTcount: A:0.59, C:0.05, G:0.01, T:0.35
Consensus pattern (18 bp):
ATAATATACATATAATAT
Found at i:390611 original size:12 final size:12
Alignment explanation
Indices: 390503--390612 Score: 70
Period size: 12 Copynumber: 9.2 Consensus size: 12
390493 ATAAACCATA
390503 ATAATATAATAA-
1 ATAATAT-ATAAT
*
390515 ATAATAAATAAT
1 ATAATATATAAT
390527 ATAATA-ATAAT
1 ATAATATATAAT
*
390538 AT-A-CTATAAT
1 ATAATATATAAT
* *
390548 ATAATAAAAAACT
1 ATAATATATAA-T
390561 ATACTATAATATAAT
1 ATA--AT-ATATAAT
* *
390576 AT-ATGTACAAT
1 ATAATATATAAT
390587 ATAATATATAAT
1 ATAATATATAAT
390599 ATACATATA-AAT
1 ATA-ATATATAAT
390611 AT
1 AT
390613 TTTCAAAAAC
Statistics
Matches: 77, Mismatches: 11, Indels: 20
0.71 0.10 0.19
Matches are distributed among these distances:
10 8 0.10
11 19 0.25
12 32 0.42
13 9 0.12
15 5 0.06
16 4 0.05
ACGTcount: A:0.59, C:0.05, G:0.01, T:0.35
Consensus pattern (12 bp):
ATAATATATAAT
Found at i:390628 original size:39 final size:37
Alignment explanation
Indices: 390585--391127 Score: 504
Period size: 39 Copynumber: 14.4 Consensus size: 37
390575 TATATGTACA
* * *
390585 ATATAATATATAATATACATATAAATATTTTCAAAAACT
1 ATATATTATAT-ATAT-CTTATAAATGTTTTCAAAAACT
* *
390624 ATATAATATATATAT-TTTTAAAATGTTTTCAAAAACT
1 ATATATTATATATATCTTAT-AAATGTTTTCAAAAACT
* * *
390661 ATATATTATACATATGTTTTCAAAATGTTTTCAAAAACT
1 ATATATTATATATATCTTAT--AAATGTTTTCAAAAACT
* * *
390700 ATATATTATATATATTTTTTCAAAAAGTTTTCAAAAACT
1 ATATATTATATATATCTTAT--AAATGTTTTCAAAAACT
* *
390739 ACATATTATATATATTTTCA-AAATGTTTTCAAAAACT
1 ATATATTATATATATCTT-ATAAATGTTTTCAAAAACT
*
390776 ATATATTATATATAT-ATATTCAAAATGTTTTCAAAAACT
1 ATATATTATATATATCTTA-T--AAATGTTTTCAAAAACT
* *
390815 ATATATTATATATATATTTTCAAAATGTTTTCAAAAACT
1 ATATATTATATATATCTTAT--AAATGTTTTCAAAAACT
* *
390854 ATATATTATATATATGTTTTCAAAATGTTTTCAAAAACT
1 ATATATTATATATATCTTAT--AAATGTTTTCAAAAACT
*
390893 ATATATTATATATATTCTCA-AAATGTTTTCAAAAACT
1 ATATATTATATATA-TCTTATAAATGTTTTCAAAAACT
* *
390930 ATATATTATATATATATTCTCAAAATGTTTTCAAAAACT
1 ATATATTATATATATCTTAT--AAATGTTTTCAAAAACT
* * *
390969 ATTTATTATATATATGTTCTCAAAATGTTTTCAAAAAC-
1 ATATATTATATATATCTTAT--AAATGTTTTCAAAAACT
391007 -TATA-TAT-TATA---TAT--ATGTTTTCAAAAACT
1 ATATATTATATATATCTTATAAATGTTTTCAAAAACT
* *
391036 ATATATTATATAT-TTTTTTCAAAATGTTTTCAAAAACTAT
1 ATATATTATATATATCTTAT--AAATGTTTTCAAAAAC--T
* *
391076 ATATATTATACATATTTTCA-AAATGTTTTCAAAAACT
1 ATATATTATATATATCTT-ATAAATGTTTTCAAAAACT
391113 ATATATTATATATAT
1 ATATATTATATATAT
391128 ATTTTCAAAA
Statistics
Matches: 446, Mismatches: 30, Indels: 58
0.84 0.06 0.11
Matches are distributed among these distances:
28 14 0.03
30 4 0.01
31 3 0.01
32 5 0.01
34 2 0.00
35 5 0.01
36 8 0.02
37 108 0.24
38 22 0.05
39 255 0.57
40 16 0.04
41 4 0.01
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.45
Consensus pattern (37 bp):
ATATATTATATATATCTTATAAATGTTTTCAAAAACT
Found at i:390731 original size:115 final size:114
Alignment explanation
Indices: 390607--391137 Score: 780
Period size: 115 Copynumber: 4.7 Consensus size: 114
390597 ATATACATAT
* * *
390607 AAATATTTTCAAAAACTATATAATATATATATTTTTAAAATGTTTTCAAAAACTATATATTATAC
1 AAATGTTTTCAAAAACTATATATTATATATATTTTCAAAATGTTTTCAAAAACTATATATTATA-
* *
390672 ATATGTTTTCAAAATGTTTTCAAAAACTATATATTATATATATTTTTTCA
65 ATATATTTTCAAAATGTTTTCAAAAACTATATATTATATATATATTTTCA
* *
390722 AAAAGTTTTCAAAAACTACATATTATATATATTTTCAAAATGTTTTCAAAAACTATATATTATAT
1 AAATGTTTTCAAAAACTATATATTATATATATTTTCAAAATGTTTTCAAAAACTATATATTATA-
*
390787 ATATATATTCAAAATGTTTTCAAAAACTATATATTATATATATATTTTCA
65 ATATATTTTCAAAATGTTTTCAAAAACTATATATTATATATATATTTTCA
390837 AAATGTTTTCAAAAACTATATATTATATATATGTTTTCAAAATGTTTTCAAAAACTATATATTAT
1 AAATGTTTTCAAAAACTATATATTATATATA--TTTTCAAAATGTTTTCAAAAACTATATATTAT
* *
390902 -ATATATTCTCAAAATGTTTTCAAAAACTATATATTATATATATATTCTCA
64 AATATATTTTCAAAATGTTTTCAAAAACTATATATTATATATATATTTTCA
*
390952 AAATGTTTTCAAAAACTATTTATTATATATATGTTCTCAAAATGTTTTCAAAAACTATATA-T-T
1 AAATGTTTTCAAAAACTATATATTATATATAT-TT-TCAAAATGTTTTCAAAAACTATATATTAT
*
391015 -ATATA---T----ATGTTTTCAAAAACTATATATTATATAT-TTTTTTCA
64 AATATATTTTCAAAATGTTTTCAAAAACTATATATTATATATATATTTTCA
*
391057 AAATGTTTTCAAAAACTATATATATTATACATATTTTCAAAATGTTTTCAAAAACTATATATTAT
1 AAATGTTTTCAAAAAC--TATATATTATATATATTTTCAAAATGTTTTCAAAAACTATATATTAT
391122 ATATATATTTTCAAAA
64 A-ATATATTTTCAAAA
391138 AAATTATGTA
Statistics
Matches: 380, Mismatches: 19, Indels: 33
0.88 0.04 0.08
Matches are distributed among these distances:
105 47 0.12
106 31 0.08
107 15 0.04
109 5 0.01
110 1 0.00
112 1 0.00
113 7 0.02
114 3 0.01
115 237 0.62
116 1 0.00
117 32 0.08
ACGTcount: A:0.43, C:0.09, G:0.03, T:0.45
Consensus pattern (114 bp):
AAATGTTTTCAAAAACTATATATTATATATATTTTCAAAATGTTTTCAAAAACTATATATTATAA
TATATTTTCAAAATGTTTTCAAAAACTATATATTATATATATATTTTCA
Found at i:390835 original size:154 final size:151
Alignment explanation
Indices: 390607--391137 Score: 803
Period size: 154 Copynumber: 3.5 Consensus size: 151
390597 ATATACATAT
* *
390607 AAATATTTTCAAAAACTATATA-ATATATATATTTTTAAAATGTTTTCAAAAACTATATATTATA
1 AAATGTTTTCAAAAACTATATATATATATATATTTTCAAAATGTTTTCAAAAACTATATATTATA
* *
390671 CATATGTTTTCAAAATGTTTTCAAAAACTATATATTATATATATTTTTTCAAAAAGTTTTCAAAA
66 TATATATTTTCAAAATGTTTTCAAAAACTATATATTATATATA-TTTTTC-AAAAGTTTTCAAAA
*
390736 ACTACATATTATATATATTTTCA
129 ACTATATATTATATATATTTTCA
*
390759 AAATGTTTTCAAAAACTATATATTATATATATATATTCAAAATGTTTTCAAAAACTATATATTAT
1 AAATGTTTTCAAAAACTATATA-TATATATATATTTTCAAAATGTTTTCAAAAACTATATATTAT
390824 ATATATATTTTCAAAATGTTTTCAAAAACTATATATTATATATATGTTTTCAAAATGTTTTCAAA
65 ATATATATTTTCAAAATGTTTTCAAAAACTATATATTATATATAT-TTTTCAAAA-GTTTTCAAA
*
390889 AACTATATATTATATATATTCTCA
128 AACTATATATTATATATATTTTCA
* *
390913 AAATGTTTTCAAAAACTATATATTATATATATATTCTCAAAATGTTTTCAAAAACTATTTATTAT
1 AAATGTTTTCAAAAACTATATA-TATATATATATTTTCAAAATGTTTTCAAAAACTATATATTAT
* *
390978 ATATATGTTCTCAAAATGTTTTCAAAAACTATATATTATATATA----T-----GTTTTCAAAAA
65 ATATATATTTTCAAAATGTTTTCAAAAACTATATATTATATATATTTTTCAAAAGTTTTCAAAAA
*
391034 CTATATATTATATATTTTTTTCA
130 CTATATATTATATA-TATTTTCA
*
391057 AAATGTTTTCAAAAACTATATATATTATACATATTTTCAAAATGTTTTCAAAAACTATATATTAT
1 AAATGTTTTCAAAAACTATATATA-TATATATATTTTCAAAATGTTTTCAAAAACTATATATTAT
391122 ATATATATTTTCAAAA
65 ATATATATTTTCAAAA
391138 AAATTATGTA
Statistics
Matches: 354, Mismatches: 19, Indels: 20
0.90 0.05 0.05
Matches are distributed among these distances:
143 27 0.08
144 79 0.22
149 1 0.00
152 21 0.06
153 5 0.01
154 221 0.62
ACGTcount: A:0.43, C:0.09, G:0.03, T:0.45
Consensus pattern (151 bp):
AAATGTTTTCAAAAACTATATATATATATATATTTTCAAAATGTTTTCAAAAACTATATATTATA
TATATATTTTCAAAATGTTTTCAAAAACTATATATTATATATATTTTTCAAAAGTTTTCAAAAAC
TATATATTATATATATTTTCA
Found at i:391048 original size:28 final size:28
Alignment explanation
Indices: 390993--391059 Score: 118
Period size: 28 Copynumber: 2.4 Consensus size: 28
390983 TGTTCTCAAA
390993 ATGTTTTCAAAAACTATATATTATATAT
1 ATGTTTTCAAAAACTATATATTATATAT
391021 ATGTTTTCAAAAACTATATATTATATAT
1 ATGTTTTCAAAAACTATATATTATATAT
*
391049 -TTTTTTCAAAA
1 ATGTTTTCAAAA
391060 TGTTTTCAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
27 10 0.26
28 28 0.74
ACGTcount: A:0.42, C:0.07, G:0.03, T:0.48
Consensus pattern (28 bp):
ATGTTTTCAAAAACTATATATTATATAT
Found at i:391105 original size:144 final size:143
Alignment explanation
Indices: 390878--391137 Score: 432
Period size: 144 Copynumber: 1.8 Consensus size: 143
390868 TGTTTTCAAA
*
390878 ATGTTTTCAAAAACTATATATTATATATATTCTCAAAATGTTTTCAAAAACTATATATTATATAT
1 ATGTTTTCAAAAACTATATATTATATATATTCTCAAAATGTTTTCAAAAACTATATATTATATAC
* *
390943 ATATTCTCAAAATGTTTTCAAAAACTATTTATTATATATATGTTCTCAAAATGTTTTCAAAAACT
66 ATATTCTCAAAATGTTTTCAAAAACTATATATTATATATATATTCTCAAAATGTTTTCAAAAACT
391008 ATATATTATATAT
131 ATATATTATATAT
* *
391021 ATGTTTTCAAAAACTATATATTATATATTTTTTTCAAAATGTTTTCAAAAACTATATA-TATTAT
1 ATGTTTTCAAAAACTATATATTATATA-TATTCTCAAAATGTTTTCAAAAACTATATATTA-TAT
* *
391085 ACATATTTTCAAAATGTTTTCAAAAACTATATATTATATATATATTTTCAAAA
64 ACATATTCTCAAAATGTTTTCAAAAACTATATATTATATATATATTCTCAAAA
391138 AAATTATGTA
Statistics
Matches: 108, Mismatches: 7, Indels: 3
0.92 0.06 0.03
Matches are distributed among these distances:
143 29 0.27
144 79 0.73
ACGTcount: A:0.42, C:0.09, G:0.03, T:0.45
Consensus pattern (143 bp):
ATGTTTTCAAAAACTATATATTATATATATTCTCAAAATGTTTTCAAAAACTATATATTATATAC
ATATTCTCAAAATGTTTTCAAAAACTATATATTATATATATATTCTCAAAATGTTTTCAAAAACT
ATATATTATATAT
Found at i:391106 original size:105 final size:106
Alignment explanation
Indices: 390915--391138 Score: 373
Period size: 105 Copynumber: 2.1 Consensus size: 106
390905 TATTCTCAAA
*
390915 ATGTTTTCAAAAACTATATATTATATATATATTCTCAAAATGTTTTCAAAAACTATTTATTATAT
1 ATGTTTTCAAAAACTATATATTATATATATATTCTCAAAATGTTTTCAAAAACTATTTATTATAC
390980 ATATGTTCTCAAAATGTTTTCAAAAACTATATATTATATAT
66 ATATGTTCTCAAAATGTTTTCAAAAACTATATATTATATAT
* *
391021 ATGTTTTCAAAAACTATATATTATATAT-TTTTTTCAAAATGTTTTCAAAAACTATATATATTAT
1 ATGTTTTCAAAAACTATATATTATATATATATTCTCAAAATGTTTTCAAAAACTAT-T-TATTAT
391085 ACATAT-TT-TCAAAATGTTTTCAAAAACTATATATTATATAT
64 ACATATGTTCTCAAAATGTTTTCAAAAACTATATATTATATAT
*
391126 ATATTTTCAAAAA
1 ATGTTTTCAAAAA
391139 AATTATGTAT
Statistics
Matches: 112, Mismatches: 4, Indels: 5
0.93 0.03 0.04
Matches are distributed among these distances:
105 70 0.62
106 31 0.28
107 11 0.10
ACGTcount: A:0.42, C:0.09, G:0.03, T:0.46
Consensus pattern (106 bp):
ATGTTTTCAAAAACTATATATTATATATATATTCTCAAAATGTTTTCAAAAACTATTTATTATAC
ATATGTTCTCAAAATGTTTTCAAAAACTATATATTATATAT
Found at i:391154 original size:28 final size:28
Alignment explanation
Indices: 391101--391157 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 28
391091 TTTCAAAATG
*
391101 TTTTCAAAAACTATATATTATATATATA
1 TTTTCAAAAACAATATATTATATATATA
391129 TTTTCAAAAA-AAT-TATGTATATTATATA
1 TTTTCAAAAACAATATAT-TATA-TATATA
391157 T
1 T
391158 ATTAAATAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
26 3 0.12
27 6 0.23
28 17 0.65
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.47
Consensus pattern (28 bp):
TTTTCAAAAACAATATATTATATATATA
Found at i:393772 original size:3 final size:3
Alignment explanation
Indices: 393764--393796 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
393754 ATACCTAACA
393764 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
393797 TGAGAAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:395289 original size:80 final size:77
Alignment explanation
Indices: 395156--395318 Score: 245
Period size: 80 Copynumber: 2.1 Consensus size: 77
395146 AAAGAAGAGT
* *
395156 TTTATGATGGTTTAAGCCTCAAGGCTAGGCTAGAAGAGATTTGGAGCATACTATTATTATTTTTA
1 TTTATGATGGTTTAAACCTCAAGGCTAGACTAGAAGAGATTTGGAGCATAC---TATTATTTTTA
395221 AATTCATCCTTAGCA
63 AATTCATCCTTAGCA
* * *
395236 TTTATGATGGTTTAAACCTCGAGGCTAGACTAGGAGAGATTTGGAGCATACTATTATTTTTATAT
1 TTTATGATGGTTTAAACCTCAAGGCTAGACTAGAAGAGATTTGGAGCATACTATTATTTTTAAAT
395301 TCATCCTTAGCA
66 TCATCCTTAGCA
*
395313 CTTATG
1 TTTATG
395319 TTATCATTTT
Statistics
Matches: 77, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
77 30 0.39
80 47 0.61
ACGTcount: A:0.29, C:0.14, G:0.19, T:0.38
Consensus pattern (77 bp):
TTTATGATGGTTTAAACCTCAAGGCTAGACTAGAAGAGATTTGGAGCATACTATTATTTTTAAAT
TCATCCTTAGCA
Found at i:401992 original size:10 final size:10
Alignment explanation
Indices: 401979--402040 Score: 58
Period size: 10 Copynumber: 6.3 Consensus size: 10
401969 GAAAAAATAT
401979 AAAAAGAGAA
1 AAAAAGAGAA
*
401989 AAAATGA-AA
1 AAAAAGAGAA
401998 AATAATA-AGAA
1 AA-AA-AGAGAA
**
402009 AAAATTAGAA
1 AAAAAGAGAA
402019 AAAAA-AGAA
1 AAAAAGAGAA
402028 AAAAAGAGAA
1 AAAAAGAGAA
402038 AAA
1 AAA
402041 TGAAAAGAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
9 13 0.30
10 26 0.60
11 4 0.09
ACGTcount: A:0.79, C:0.00, G:0.13, T:0.08
Consensus pattern (10 bp):
AAAAAGAGAA
Found at i:402002 original size:22 final size:22
Alignment explanation
Indices: 401972--402048 Score: 63
Period size: 20 Copynumber: 3.6 Consensus size: 22
401962 AAATAAAGAA
401972 AAAATATAAAAAGAGAAAAAATG
1 AAAA-ATAAAAAGAGAAAAAATG
* *
401995 AAAAAT-AATA-AGAAAAAATT
1 AAAAATAAAAAGAGAAAAAATG
* *
402015 AGAAA-AAAAAGA-AAAAAAGAG
1 AAAAATAAAAAGAGAAAAAA-TG
*
402036 AAAAATGAAAAGA
1 AAAAATAAAAAGA
402049 AAGAAAGAAT
Statistics
Matches: 42, Mismatches: 8, Indels: 9
0.71 0.14 0.15
Matches are distributed among these distances:
20 22 0.52
21 8 0.19
22 8 0.19
23 4 0.10
ACGTcount: A:0.77, C:0.00, G:0.13, T:0.10
Consensus pattern (22 bp):
AAAAATAAAAAGAGAAAAAATG
Found at i:402010 original size:20 final size:19
Alignment explanation
Indices: 401966--402040 Score: 75
Period size: 19 Copynumber: 4.0 Consensus size: 19
401956 GAAAAGAAAT
*
401966 AAAGAAAAAAT-A-TAAAA
1 AAAGAAAAAATGAGAAAAA
*
401983 AGAGAAAAAATGA-AAAATA
1 AAAGAAAAAATGAGAAAA-A
*
402002 ATAAGAAAAAATTAGAAAAA
1 A-AAGAAAAAATGAGAAAAA
*
402022 AAAGAAAAAAAGAGAAAAA
1 AAAGAAAAAATGAGAAAAA
402041 TGAAAAGAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
17 10 0.21
18 4 0.08
19 18 0.38
20 12 0.25
21 4 0.08
ACGTcount: A:0.79, C:0.00, G:0.12, T:0.09
Consensus pattern (19 bp):
AAAGAAAAAATGAGAAAAA
Found at i:402049 original size:22 final size:21
Alignment explanation
Indices: 401995--402056 Score: 56
Period size: 22 Copynumber: 2.9 Consensus size: 21
401985 AGAAAAAATG
**
401995 AAAAATAATAAGAAAAAATTAG-
1 AAAA-TAA-AAGAAAAAAAGAGA
402017 AAAA-AAAAGAAAAAAAGAGA
1 AAAATAAAAGAAAAAAAGAGA
*
402037 AAAATGAAAAGAAAGAAAGA
1 AAAAT-AAAAGAAAAAAAGA
402057 ATAAAGAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
19 11 0.32
20 6 0.18
22 17 0.50
ACGTcount: A:0.77, C:0.00, G:0.15, T:0.08
Consensus pattern (21 bp):
AAAATAAAAGAAAAAAAGAGA
Found at i:402054 original size:9 final size:8
Alignment explanation
Indices: 401957--402054 Score: 61
Period size: 8 Copynumber: 11.0 Consensus size: 8
401947 AAAATGGTAG
401957 AAAAGAAA
1 AAAAGAAA
*
401965 TAAAGAAA
1 AAAAGAAA
*
401973 AAATATAAA
1 AAA-AGAAA
*
401982 AAGAGAAA
1 AAAAGAAA
*
401990 AAATGAAAAA
1 AAA--AGAAA
402000 TAATAAGAAA
1 -AA-AAGAAA
402010 AAATTAGAAAA
1 AAA--AG-AAA
402021 AAAAGAAA
1 AAAAGAAA
402029 AAAAGAGAA
1 AAAAGA-AA
*
402038 AAATGAAA
1 AAAAGAAA
402046 AGAAAGAAA
1 A-AAAGAAA
402055 GAATAAAGAA
Statistics
Matches: 70, Mismatches: 10, Indels: 19
0.71 0.10 0.19
Matches are distributed among these distances:
8 28 0.40
9 23 0.33
10 10 0.14
11 8 0.11
12 1 0.01
ACGTcount: A:0.78, C:0.00, G:0.13, T:0.09
Consensus pattern (8 bp):
AAAAGAAA
Found at i:402749 original size:28 final size:28
Alignment explanation
Indices: 402687--402750 Score: 83
Period size: 28 Copynumber: 2.3 Consensus size: 28
402677 CGCAAGAAGC
* *
402687 CAACCTGAAACACATTACCTCCCCAATT
1 CAACCTAAAACACATTACCTCCCCAAGT
* *
402715 TAACCTAAAACACATTACCTTCCCAAGT
1 CAACCTAAAACACATTACCTCCCCAAGT
*
402743 CAGCCTAA
1 CAACCTAA
402751 GCCTTTTATC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.38, C:0.36, G:0.05, T:0.22
Consensus pattern (28 bp):
CAACCTAAAACACATTACCTCCCCAAGT
Found at i:404260 original size:42 final size:40
Alignment explanation
Indices: 404214--404327 Score: 122
Period size: 42 Copynumber: 2.8 Consensus size: 40
404204 AAGGGTTTCT
*
404214 TGATGAGTAAGTCCTTCGGGCCATC-AGTAAGTCTTTTGAGC
1 TGATGA-TAAGTCCTTCGGGCCATCTA-TAAGTCTTTCGAGC
* * *
404255 ATGATGTTTAAATCCTTCGGGTCATCTATAAGTCTTTCGAGC
1 -TGATG-ATAAGTCCTTCGGGCCATCTATAAGTCTTTCGAGC
* *
404297 TAGATGATAAGTCCTTCGGACCATCCATAAG
1 T-GATGATAAGTCCTTCGGGCCATCTATAAG
404328 ACCTTCGGGC
Statistics
Matches: 60, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
41 21 0.35
42 38 0.63
43 1 0.02
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.32
Consensus pattern (40 bp):
TGATGATAAGTCCTTCGGGCCATCTATAAGTCTTTCGAGC
Found at i:404601 original size:275 final size:275
Alignment explanation
Indices: 404063--404726 Score: 1091
Period size: 275 Copynumber: 2.4 Consensus size: 275
404053 AGGGTTTCTT
* * * * *
404063 GATGTTCTCAAATGAGTTTTTAGAAATTAAGCC-AACTTTCAGGGGTTTCTTGATGATTATTTTC
1 GATGTTTTCAAATGAGTTTTTAGAAACTAAGCCTAATTTTCAGGGGTTTCTTGATGATTATCTCC
404127 AAAGAATTTTTAAAAGGAAGCTAAGACTAATTTTTAGGGGTTCCTTGATGACAACTAAGAAACTA
66 AAAGAATTTTTAAAAGGAAGCTAAGACTAATTTTTAGGGGTTCC-T--TGACAACTAAGAAACTA
*
404192 AGCTTGATTTTCAAGGGTTTCTTGATGAGTAAGTCCTTCGGGCCATCAGTAAGTCTTTTGAGCAT
128 AGCTTGATTTTCAAGGGTTTCTTGATGAGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCAT
* *
404257 GATGTTTAAATCCTTCGGGTCATCTATAAGTCTTTCGAGCTAGATGATAAGTCCTTCGGACCATC
193 GATGCTTAAATCCTTCGGGTCATCTATAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGACCATC
*
404322 CATAAGACCTTCGGGCAG
258 CATAAGACCTTCGGGCAA
*
404340 GATGTTTTCAAATGAGTTTTTAGAAACTAAGCCTGATTTTCAGGGGTTTCTTGATGATTATCTCC
1 GATGTTTTCAAATGAGTTTTTAGAAACTAAGCCTAATTTTCAGGGGTTTCTTGATGATTATCTCC
* * *
404405 AAAGAGTTTTTAAAAGGAAGCTAAGCCTAATTTTTAGTGGTTCCTTGACAACTAAGAAACTAAGC
66 AAAGAATTTTTAAAAGGAAGCTAAGACTAATTTTTAGGGGTTCCTTGACAACTAAGAAACTAAGC
* *
404470 TTGATTTTCAAGGGTTTCTTGATGAGTAAGTCCTTCGGGTCATCAGTAAGTCTTTCGAGCGTGAT
131 TTGATTTTCAAGGGTTTCTTGATGAGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGAT
* *
404535 GCTTAAATCCTTCGGGTCATCTATAAGTCTTTCGAGCAAGATGATACA-TCCTTCGGTCCCTCCA
196 GCTTAAATCCTTCGGGTCATCTATAAGTCTTTCGAGCAAGATGATA-AGTCCTTCGGACCATCCA
404599 TAAGACCTTCGGGCAA
260 TAAGACCTTCGGGCAA
*
404615 GATGTTTTCAAATGTGTTTTTAGAAACTAAGCCTAATTTTCAGGGGTTTCTTGATGATTATCTCC
1 GATGTTTTCAAATGAGTTTTTAGAAACTAAGCCTAATTTTCAGGGGTTTCTTGATGATTATCTCC
* *
404680 AAAGAATTTTT-AAAGGAAGTTAAGACTAATTTTTAGGGGGTCCTTGA
66 AAAGAATTTTTAAAAGGAAGCTAAGACTAATTTTTAGGGGTTCCTTGA
404727 TGACAACTGA
Statistics
Matches: 361, Mismatches: 24, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
274 32 0.09
275 228 0.63
276 1 0.00
277 32 0.09
278 68 0.19
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.35
Consensus pattern (275 bp):
GATGTTTTCAAATGAGTTTTTAGAAACTAAGCCTAATTTTCAGGGGTTTCTTGATGATTATCTCC
AAAGAATTTTTAAAAGGAAGCTAAGACTAATTTTTAGGGGTTCCTTGACAACTAAGAAACTAAGC
TTGATTTTCAAGGGTTTCTTGATGAGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGAT
GCTTAAATCCTTCGGGTCATCTATAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGACCATCCAT
AAGACCTTCGGGCAA
Found at i:404602 original size:41 final size:42
Alignment explanation
Indices: 404500--404618 Score: 118
Period size: 42 Copynumber: 2.9 Consensus size: 42
404490 GATGAGTAAG
** *
404500 TCCTTCGGGTCAT-CAGTAAGTCTTTCGAGCGTGATGCTTAAA
1 TCCTTCGGGTCATCCA-TAAGTCTTTCGAGCAAGATGCATAAA
* *
404542 TCCTTCGGGTCATCTATAAGTCTTTCGAGCAAGATG-ATACA
1 TCCTTCGGGTCATCCATAAGTCTTTCGAGCAAGATGCATAAA
* * * *
404583 TCCTTC-GGTCCCTCCATAAGACCTTCGGGCAAGATG
1 TCCTTCGGGT-CATCCATAAGTCTTTCGAGCAAGATG
404619 TTTTCAAATG
Statistics
Matches: 65, Mismatches: 10, Indels: 5
0.81 0.12 0.06
Matches are distributed among these distances:
40 3 0.05
41 30 0.46
42 31 0.48
43 1 0.02
ACGTcount: A:0.23, C:0.25, G:0.22, T:0.30
Consensus pattern (42 bp):
TCCTTCGGGTCATCCATAAGTCTTTCGAGCAAGATGCATAAA
Found at i:405773 original size:117 final size:117
Alignment explanation
Indices: 405561--405885 Score: 524
Period size: 117 Copynumber: 2.8 Consensus size: 117
405551 AAGATAAACT
405561 GATCAACATTTCAAGTGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTC
1 GATCAACATTTCAAGTGGAGAGTTCATAATGAGAAGAACTCATCCGAC-GAGGGAGAAGAAGTTC
* *
405626 ATAATGAGAAGAACTTGTTCAACCTTGGTTCAATTCCATCACAGAATGAGGTG
65 ATAATGAGAAGAACTTGTTCAACCTCGGTTCAATTCCATCACAGAAAGAGGTG
* * * *
405679 GATCAACGTTTCCAGTGGAGGGTTCATAACGAGAAGAACTCATCCGACGAGGGAGAAGAAGTTCA
1 GATCAACATTTCAAGTGGAGAGTTCATAATGAGAAGAACTCATCCGACGAGGGAGAAGAAGTTCA
*
405744 TAATGAGAAGAACTTGTTCAACCTCGGTTCGATTCCATCACAGAAAGAGGTG
66 TAATGAGAAGAACTTGTTCAACCTCGGTTCAATTCCATCACAGAAAGAGGTG
* * *
405796 GATCAACATTTCAAATGGAGAGTTCATAATGAGAAGAACTCATCTGAAAGAGGGAGAAGAAGTTC
1 GATCAACATTTCAAGTGGAGAGTTCATAATGAGAAGAACTCATCCG-ACGAGGGAGAAGAAGTTC
* *
405861 ATAATGAGAAGAGCTTGTTCGACCT
65 ATAATGAGAAGAACTTGTTCAACCT
405886 ATCACTTGAT
Statistics
Matches: 190, Mismatches: 16, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
117 106 0.56
118 84 0.44
ACGTcount: A:0.36, C:0.16, G:0.25, T:0.23
Consensus pattern (117 bp):
GATCAACATTTCAAGTGGAGAGTTCATAATGAGAAGAACTCATCCGACGAGGGAGAAGAAGTTCA
TAATGAGAAGAACTTGTTCAACCTCGGTTCAATTCCATCACAGAAAGAGGTG
Found at i:406109 original size:139 final size:139
Alignment explanation
Indices: 405952--406437 Score: 758
Period size: 139 Copynumber: 3.5 Consensus size: 139
405942 TCAAATGTAG
* *
405952 AGTTCATAATGAGAAGAACTCGTCCGATGAGGGAGAATAAGTTCATAATGAGAAGAACTTGTTCA
1 AGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
*
406017 ACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGCAACACCTCACTCGAGGGATCAACATTT
66 ACCTTAGCTCGATTCATCACATATAGAGTTGAATCAGCAACACCTCACTCGAGGGATCAACATTT
***
406082 CCAGCAAAA
131 CCAGTGGAA
*
406091 AGTTCATAATGAGAAGAACTCGTCCGATGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
1 AGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
* * ** *
406156 ACCTTAGCTCAATTTATCACATATAGAGTTGAATCAATAACACCTCACTTGAGGGATCAACATTT
66 ACCTTAGCTCGATTCATCACATATAGAGTTGAATCAGCAACACCTCACTCGAGGGATCAACATTT
*
406221 CCAGTGGAC
131 CCAGTGGAA
*
406230 ATTTCATAATGAGAAGAACTCATCCGATGAGGGAGAA-AATGTTCATAATGAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAA-GTTCATAATGAGAAGAACTTGTTC
* * * *
406294 AACCTTAGCTCGATTCATCACATATTGAGTTGGATCAGCAACACATTACTCGAGGGATCAACATT
65 AACCTTAGCTCGATTCATCACATATAGAGTTGAATCAGCAACACCTCACTCGAGGGATCAACATT
* **
406359 TCTAGTGGTG
130 TCCAGTGGAA
*
406369 AGTTCATAATGAGAAGAACTCATCCGATGAGAGAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
1 AGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
406434 ACCT
66 ACCT
406438 CAACAGTTGC
Statistics
Matches: 318, Mismatches: 27, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
138 2 0.01
139 314 0.99
140 2 0.01
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.26
Consensus pattern (139 bp):
AGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
ACCTTAGCTCGATTCATCACATATAGAGTTGAATCAGCAACACCTCACTCGAGGGATCAACATTT
CCAGTGGAA
Found at i:406154 original size:20 final size:19
Alignment explanation
Indices: 406092--406155 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 19
406082 CCAGCAAAAA
406092 GTTCATAATGAGAAGAACT
1 GTTCATAATGAGAAGAACT
* **
406111 CGTCCGATGAGGGAGAAGAA--
1 -GTTC-AT-AATGAGAAGAACT
406131 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAAC-T
406151 GTTCA
1 GTTCA
406156 ACCTTAGCTC
Statistics
Matches: 33, Mismatches: 6, Indels: 10
0.67 0.12 0.20
Matches are distributed among these distances:
17 9 0.27
18 2 0.06
19 3 0.09
20 8 0.24
21 2 0.06
22 9 0.27
ACGTcount: A:0.38, C:0.12, G:0.27, T:0.23
Consensus pattern (19 bp):
GTTCATAATGAGAAGAACT
Found at i:406289 original size:278 final size:275
Alignment explanation
Indices: 405816--406437 Score: 849
Period size: 278 Copynumber: 2.3 Consensus size: 275
405806 TCAAATGGAG
* * *
405816 AGTTCATAATGAGAAGAACTCATCTGAAAGAGGGAGAAGAAGTTCATAATGAGAAGAGCTTGTTC
1 AGTTCATAATGAGAAGAACTCATCCG-ATGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTC
* * * * * * * * *
405881 GACC-TATCACTTGATTCACGACCTTTCGAATCAGTGACGCCTCGCTTGATGGATTAACATTTCA
65 AACCTTATCAATTGATTCACGACATTTCGAATCAATAACACCTCACTTGAGGGATCAACATTTCA
* * *
405945 AATGTAGAGTTCATAATGAGAAGAACTCGTCCGATGAGGGAGAATAAGTTCATAATGAGAAGAAC
130 AATGGACAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAATAAGTTCATAATGAGAAGAAC
*
406010 TTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGCAACACCTCACTCGAGGGATC
195 TTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGCAACACATCACTCGAGGGATC
406075 AACATTTCCAGCAAAA
260 AACATTTCCAGCAAAA
*
406091 AGTTCATAATGAGAAGAACTCGTCCGATGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
1 AGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
* *
406156 ACCTTAGCTCAATTTA-TCAC-ATATAGAGTT-GAATCAATAACACCTCACTTGAGGGATCAACA
66 ACCTTA--TCAATTGATTCACGACAT----TTCGAATCAATAACACCTCACTTGAGGGATCAACA
* * *
406218 TTTCCAGTGGACATTTCATAATGAGAAGAACTCATCCGATGAGGGAGAA-AATGTTCATAATGAG
125 TTTCAAATGGACAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAATAA-GTTCATAATGAG
* * *
406282 AAGAACTTGTTCAACCTTAGCTCGATTCATCACATATTGAGTTGGATCAGCAACACATTACTCGA
189 AAGAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGCAACACATCACTCGA
* *****
406347 GGGATCAACATTTCTAGTGGTG
254 GGGATCAACATTTCCAGCAAAA
*
406369 AGTTCATAATGAGAAGAACTCATCCGATGAGAGAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
1 AGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
406434 ACCT
66 ACCT
406438 CAACAGTTGC
Statistics
Matches: 306, Mismatches: 33, Indels: 13
0.87 0.09 0.04
Matches are distributed among these distances:
274 39 0.13
275 28 0.09
276 4 0.01
277 8 0.03
278 225 0.74
279 2 0.01
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (275 bp):
AGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
ACCTTATCAATTGATTCACGACATTTCGAATCAATAACACCTCACTTGAGGGATCAACATTTCAA
ATGGACAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAATAAGTTCATAATGAGAAGAACT
TGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGCAACACATCACTCGAGGGATCA
ACATTTCCAGCAAAA
Found at i:417717 original size:21 final size:21
Alignment explanation
Indices: 417691--417730 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
417681 AAGACTTTAT
417691 TTTCAAAA-TACAAAAATGATG
1 TTTCAAAATTA-AAAAATGATG
417712 TTTCAAAATTAAAAAATGA
1 TTTCAAAATTAAAAAATGA
417731 AAATAATCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.55, C:0.07, G:0.07, T:0.30
Consensus pattern (21 bp):
TTTCAAAATTAAAAAATGATG
Found at i:421567 original size:20 final size:20
Alignment explanation
Indices: 421542--421596 Score: 67
Period size: 22 Copynumber: 2.6 Consensus size: 20
421532 TTGTGCTTCA
421542 TGCATCGATACACTT-AATAG
1 TGCATCGATACACTTGAAT-G
*
421562 TGCATCGATGCATCCTTGAATG
1 TGCATCGATACA--CTTGAATG
421584 TGCATCGATACAC
1 TGCATCGATACAC
421597 CATGAAGGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
20 12 0.40
22 15 0.50
23 3 0.10
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (20 bp):
TGCATCGATACACTTGAATG
Found at i:424299 original size:20 final size:20
Alignment explanation
Indices: 424270--424307 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
424260 TTTCAAAGTG
424270 ATGCACCGATGCACCAATCC
1 ATGCACCGATGCACCAATCC
*
424290 ATGCATCGATGCACCAAT
1 ATGCACCGATGCACCAAT
424308 TATTTTTTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.34, G:0.16, T:0.18
Consensus pattern (20 bp):
ATGCACCGATGCACCAATCC
Found at i:427983 original size:23 final size:23
Alignment explanation
Indices: 427957--428030 Score: 76
Period size: 23 Copynumber: 3.0 Consensus size: 23
427947 ATATAACACC
427957 ATTATATAAATAAATATTTATAT
1 ATTATATAAATAAATATTTATAT
* *
427980 ATTATATACATAACTATTTATATTT
1 ATTATATAAATAAATATTTATA--T
*
428005 ATTAGTATGTAAATAAATAATTATAT
1 ATTA-TA--TAAATAAATATTTATAT
428031 TTACTTTTAT
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
23 20 0.49
25 5 0.12
26 3 0.07
28 13 0.32
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (23 bp):
ATTATATAAATAAATATTTATAT
Found at i:428028 original size:28 final size:29
Alignment explanation
Indices: 427962--428033 Score: 78
Period size: 28 Copynumber: 2.6 Consensus size: 29
427952 ACACCATTAT
* *
427962 ATAAATAA--ATATTTATATATTATATAC
1 ATAAATAATTATATTTATATAGTATATAA
* * *
427989 ATAACTATTTATATTTAT-TAGTATGTAA
1 ATAAATAATTATATTTATATAGTATATAA
428017 ATAAATAATTATATTTA
1 ATAAATAATTATATTTA
428034 CTTTTATATA
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
27 6 0.17
28 22 0.61
29 8 0.22
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (29 bp):
ATAAATAATTATATTTATATAGTATATAA
Found at i:428134 original size:31 final size:29
Alignment explanation
Indices: 428096--428157 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 29
428086 TAATTTTTAC
*
428096 ATATAATTA-AATTAAAATTAAAATATTGTGT
1 ATATAATTACAA-T-AAATTAAAAT-TTATGT
428127 ATATAATTACAATAAATTAAAATTTATGT
1 ATATAATTACAATAAATTAAAATTTATGT
428156 AT
1 AT
428158 TACACCAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
29 7 0.24
30 10 0.34
31 10 0.34
32 2 0.07
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.42
Consensus pattern (29 bp):
ATATAATTACAATAAATTAAAATTTATGT
Found at i:433124 original size:2 final size:2
Alignment explanation
Indices: 433114--433416 Score: 100
Period size: 2 Copynumber: 152.0 Consensus size: 2
433104 AATTGAAAAA
* *
433114 AT AT A- AT AT AT AT AT AT AT AT -T AT AT TT AT AT -T AT AA ACT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T
* * *
433154 AT AT A- AT -T AT -T AT AA ACT AT AT AT AT AA AT -T AT AT TT AT
1 AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT
* * * * *
433193 GT GA- ACT AT AT AT AT AT AA ACT AT GT AT AT AA ACT AT AT AT GT
1 AT -AT A-T AT AT AT AT AT AT A-T AT AT AT AT AT A-T AT AT AT AT
* * * * * *
433236 AT AA ACT AT AA AA AGT AT AT AA ACT AT AT AT AT AGT TT AT AT TT
1 AT AT A-T AT AT AT A-T AT AT AT A-T AT AT AT AT A-T AT AT AT AT
* * * *
433280 AT AT A- AC AT AT AT AT AT AA ACT AT AT AT AT AA ACT AT AT AA AT
1 AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT A-T AT AT AT AT
* * *
433323 AT AGT TT AT AT GT -T AT A- AT TT AT AT -T A- AT AT AGT AT AT AT
1 AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
* * * *
433363 GT AT GT AA ACT A- AT AT A- AGT A- AT AT AT AG A- AT AT AT AT AT
1 AT AT AT AT A-T AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT
433403 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
433417 TAAAGAAACA
Statistics
Matches: 219, Mismatches: 49, Indels: 66
0.66 0.15 0.20
Matches are distributed among these distances:
1 17 0.08
2 186 0.85
3 16 0.07
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44
Consensus pattern (2 bp):
AT
Done.