Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr6
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: 47432654
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2298022 characters in sequence are not A, C, G, or T
File 20 of 136
Found at i:6354261 original size:133 final size:133
Alignment explanation
Indices: 6354024--6354314 Score: 308
Period size: 133 Copynumber: 2.2 Consensus size: 133
6354014 GCTTCAAATT
* * * *
6354024 TTATCTCTCTGAATTTGCAGTGGAGCAAATTAAAGCCATAAACCTTATCTCTCTGAAGTTGCAGT
1 TTATCTCTCTGAAGTTGCAGTGGAGCAAACTAAAGACATAAACCTTATCTCCCTGAAGTTGCAGT
* * * * *
6354089 AGAGCAGATTAAAATAATAAACTTTATCCCTCTGAAGTTGCAGTGGGGTAGGTTGAAGA-TAC-A
66 AGAGCAGATTAAAATAACAAACTTTATCCCTCTAAAGTTGCAGTGGAGCAGATTGAA-ACTACTA
6354152 AGT-C
130 A-TCC
* * * *
6354156 TTATCTCTCTGAAGTTGCAGTGGAGCAGACTGAAGATATCAAACCTTATTTCCCTGAAGTTGCAG
1 TTATCTCTCTGAAGTTGCAGTGGAGCAAACTAAAGACAT-AAACCTTATCTCCCTGAAGTTGCAG
* * * * * *
6354221 TGGAGCAGGTTAACGATACCAATC-TTATCTCC-CTAAAGTTGTAGTGGAGCAGATTGAAACTAC
65 TAGAGCAGATTAA-AATAACAAACTTTATC-CCTCTAAAGTTGCAGTGGAGCAGATTGAAACTAC
6354284 TAATCC
128 TAATCC
6354290 TATATC-CT-TGAAGTTGCAGTGGAGC
1 T-TATCTCTCTGAAGTTGCAGTGGAGC
6354315 GGATTAAAAT
Statistics
Matches: 133, Mismatches: 19, Indels: 13
0.81 0.12 0.08
Matches are distributed among these distances:
132 34 0.26
133 81 0.61
134 14 0.11
135 4 0.03
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.30
Consensus pattern (133 bp):
TTATCTCTCTGAAGTTGCAGTGGAGCAAACTAAAGACATAAACCTTATCTCCCTGAAGTTGCAGT
AGAGCAGATTAAAATAACAAACTTTATCCCTCTAAAGTTGCAGTGGAGCAGATTGAAACTACTAA
TCC
Found at i:6354345 original size:88 final size:89
Alignment explanation
Indices: 6354067--6354353 Score: 245
Period size: 88 Copynumber: 3.2 Consensus size: 89
6354057 AGCCATAAAC
* * * *
6354067 CTTATCTCTCTGAAGTTGCAGTAGAGCAGA-TTAAAATAAT-AAA-CTT-TATCCCTCTGAAGTT
1 CTTATCTCTCTAAAGTTGCAGTGGAGCAGACTGAAGAT-ATCAAACCTTATAT-CC-CTGAAGTT
* * *
6354128 GCAGTGGGGTAGGTTGAA-GATA-CAAGT
63 GCAGTGGAGCAGGTT-AACAATACCAA-T
* *
6354155 CTTATCTCTCTGAAGTTGCAGTGGAGCAGACTGAAGATATCAAACCTTATTTCCCTGAAGTTGCA
1 CTTATCTCTCTAAAGTTGCAGTGGAGCAGACTGAAGATATCAAACCTTATATCCCTGAAGTTGCA
*
6354220 GTGGAGCAGGTTAACGATACCAAT
66 GTGGAGCAGGTTAACAATACCAAT
* * * * *
6354244 CTTATCTCCCTAAAGTTGTAGTGGAGCAGATTGAA-ACTA-CTAATCC-TATATCCTTGAAGTTG
1 CTTATCTCTCTAAAGTTGCAGTGGAGCAGACTGAAGA-TATC-AAACCTTATATCCCTGAAGTTG
**
6354306 CAGTGGAGC-GGATTAA-AATGATGAAT
64 CAGTGGAGCAGG-TTAACAAT-ACCAAT
* *
6354332 TTTATCTATCTAAAGTTGCAGT
1 CTTATCTCTCTAAAGTTGCAGT
6354354 AAAGCAGATC
Statistics
Matches: 169, Mismatches: 20, Indels: 20
0.81 0.10 0.10
Matches are distributed among these distances:
87 4 0.02
88 84 0.50
89 71 0.42
90 8 0.05
91 2 0.01
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.31
Consensus pattern (89 bp):
CTTATCTCTCTAAAGTTGCAGTGGAGCAGACTGAAGATATCAAACCTTATATCCCTGAAGTTGCA
GTGGAGCAGGTTAACAATACCAAT
Found at i:6356015 original size:29 final size:29
Alignment explanation
Indices: 6355966--6356025 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
6355956 ATTAACTATT
*
6355966 TTAATCTTATTACTACTATTATTATA-TCA
1 TTAATATTATTACTACTATTATT-TACTCA
*
6355995 TTAATATTATTATTA-TCATTATTTACTCA
1 TTAATATTATTACTACT-ATTATTTACTCA
6356024 TT
1 TT
6356026 TATGTCTTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 3 0.11
29 24 0.89
ACGTcount: A:0.33, C:0.12, G:0.00, T:0.55
Consensus pattern (29 bp):
TTAATATTATTACTACTATTATTTACTCA
Found at i:6356710 original size:70 final size:72
Alignment explanation
Indices: 6356611--6356753 Score: 236
Period size: 70 Copynumber: 2.0 Consensus size: 72
6356601 TCTTTTCAAA
* * *
6356611 CTCAAGTTTTAAATGATCTCGGGAATTAAGAAGAGATCGTGTCCTAACTTACTGGGCATGAT-CC
1 CTCAAGTTTTAAATAATCTCGAGAATTAAGAAAAGATCGTGTCCTAACTTACTGGGCATGATCCC
6356675 TTTTTTT
66 TTTTTTT
6356682 CTCAAG-TTTAAATAATCTCGAGAATTAAGAAAAGATCGTGTCCTAACTTACTGGGCATGATCCC
1 CTCAAGTTTTAAATAATCTCGAGAATTAAGAAAAGATCGTGTCCTAACTTACTGGGCATGAT-CC
6356746 CTTTTTTT
65 CTTTTTTT
6356754 TTTAATCCGA
Statistics
Matches: 67, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
70 52 0.78
71 6 0.09
72 9 0.13
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.36
Consensus pattern (72 bp):
CTCAAGTTTTAAATAATCTCGAGAATTAAGAAAAGATCGTGTCCTAACTTACTGGGCATGATCCC
TTTTTTT
Found at i:6358100 original size:23 final size:24
Alignment explanation
Indices: 6358072--6358117 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
6358062 ATATTATTTA
6358072 AATAAAAA-ACCCTAAAATTTAAC
1 AATAAAAATACCCTAAAATTTAAC
* *
6358095 AATAAAAATACTCTAACATTTAA
1 AATAAAAATACCCTAAAATTTAA
6358118 AATTTTATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.59, C:0.15, G:0.00, T:0.26
Consensus pattern (24 bp):
AATAAAAATACCCTAAAATTTAAC
Found at i:6358862 original size:9 final size:9
Alignment explanation
Indices: 6358848--6358942 Score: 59
Period size: 9 Copynumber: 10.2 Consensus size: 9
6358838 AAACCAATAG
6358848 AAATTATAA
1 AAATTATAA
*
6358857 AAATTAT-T
1 AAATTATAA
*
6358865 AAATTTTAA
1 AAATTATAA
*
6358874 TAAA-AATAA
1 -AAATTATAA
*
6358883 AAATGTTTAA
1 AAAT-TATAA
* *
6358893 AATTTATTA
1 AAATTATAA
6358902 AAATTATAA
1 AAATTATAA
*
6358911 AATTTTATAA
1 AA-ATTATAA
*
6358921 AAATCATAAAA
1 AAAT--TATAA
6358932 AAATTATAA
1 AAATTATAA
6358941 AA
1 AA
6358943 TACATTAAAA
Statistics
Matches: 63, Mismatches: 16, Indels: 14
0.68 0.17 0.15
Matches are distributed among these distances:
8 9 0.14
9 29 0.46
10 17 0.27
11 8 0.13
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.37
Consensus pattern (9 bp):
AAATTATAA
Found at i:6358882 original size:26 final size:25
Alignment explanation
Indices: 6358853--6358917 Score: 76
Period size: 26 Copynumber: 2.5 Consensus size: 25
6358843 AATAGAAATT
*
6358853 ATAAAAATTATTAAATTTTAATAAAA
1 ATAAAAATT-TTAAAATTTAATAAAA
*
6358879 ATAAAAATGTTTAAAATTTATTAAAA
1 ATAAAAAT-TTTAAAATTTAATAAAA
*
6358905 TTATAAAATTTTA
1 ATA-AAAATTTTA
6358918 TAAAAATCAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
26 28 0.82
27 6 0.18
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.42
Consensus pattern (25 bp):
ATAAAAATTTTAAAATTTAATAAAA
Found at i:6358917 original size:19 final size:18
Alignment explanation
Indices: 6358890--6358931 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
6358880 TAAAAATGTT
* *
6358890 TAAAATTTATTAAAATTA
1 TAAAATTTATAAAAATCA
6358908 TAAAATTTTATAAAAATCA
1 TAAAA-TTTATAAAAATCA
6358927 TAAAA
1 TAAAA
6358932 AAATTATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (18 bp):
TAAAATTTATAAAAATCA
Found at i:6359419 original size:19 final size:19
Alignment explanation
Indices: 6359384--6359450 Score: 71
Period size: 19 Copynumber: 3.5 Consensus size: 19
6359374 CTTCTATATT
** *
6359384 TTTTTATAAAAAATTACAG
1 TTTTTATAAAATTTTACAA
6359403 TTTTTATAAAATTTTACAA
1 TTTTTATAAAATTTTACAA
* **
6359422 TTTTTTTATAAATTTTATGA
1 TTTTTATA-AAATTTTACAA
6359442 TTTTTATAA
1 TTTTTATAA
6359451 TTTTTTTCTA
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
19 24 0.60
20 16 0.40
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (19 bp):
TTTTTATAAAATTTTACAA
Found at i:6359473 original size:29 final size:29
Alignment explanation
Indices: 6359414--6359538 Score: 95
Period size: 29 Copynumber: 4.5 Consensus size: 29
6359404 TTTTATAAAA
*
6359414 TTTTACAATTTTTTTATAAATTTTATGAT
1 TTTTATAATTTTTTTATAAATTTTATGAT
*
6359443 TTTTATAATTTTTTTCT-AATTTTAAAT-AT
1 TTTTATAATTTTTTTATAAATTTT--ATGAT
* * *
6359472 TTTTAT-ATTTTTATTA-AAACTTAATAAT
1 TTTTATAATTTTT-TTATAAATTTTATGAT
* *
6359500 TTTTATAA--CTTTTATTAATTTT-T-AT
1 TTTTATAATTTTTTTATAAATTTTATGAT
*
6359525 TTTTATCATTTTTT
1 TTTTATAATTTTTT
6359539 GTCACATATC
Statistics
Matches: 76, Mismatches: 11, Indels: 20
0.71 0.10 0.19
Matches are distributed among these distances:
25 9 0.12
26 4 0.05
27 11 0.14
28 20 0.26
29 30 0.39
30 2 0.03
ACGTcount: A:0.30, C:0.04, G:0.01, T:0.65
Consensus pattern (29 bp):
TTTTATAATTTTTTTATAAATTTTATGAT
Found at i:6359483 original size:18 final size:19
Alignment explanation
Indices: 6359424--6359485 Score: 67
Period size: 18 Copynumber: 3.4 Consensus size: 19
6359414 TTTTACAATT
6359424 TTTTTATAA-A-TTTTATGA
1 TTTTTATAATATTTTTAT-A
* *
6359442 TTTTTATAATTTTTTTCTA
1 TTTTTATAATATTTTTATA
*
6359461 ATTTTA-AATATTTTTATA
1 TTTTTATAATATTTTTATA
6359479 TTTTTAT
1 TTTTTAT
6359486 TAAAACTTAA
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
18 24 0.69
19 6 0.17
20 5 0.14
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.68
Consensus pattern (19 bp):
TTTTTATAATATTTTTATA
Found at i:6360120 original size:13 final size:13
Alignment explanation
Indices: 6360102--6360131 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
6360092 TATATTAAAA
6360102 AAATTAATTCAAT
1 AAATTAATTCAAT
*
6360115 AAATTAATTCATT
1 AAATTAATTCAAT
6360128 AAAT
1 AAAT
6360132 ATTAAGCTAT
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:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (13 bp):
AAATTAATTCAAT
Found at i:6369675 original size:3 final size:3
Alignment explanation
Indices: 6369661--6369702 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
6369651 GGTTTGTTTC
*
6369661 TCT TCC TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
6369703 ACCAGGGTTC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
TCT
Found at i:6376644 original size:6 final size:6
Alignment explanation
Indices: 6376633--6376659 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
6376623 CTCTCAATGA
6376633 AAGCTG AAGCTG AAGCTG AAGCTG AAG
1 AAGCTG AAGCTG AAGCTG AAGCTG AAG
6376660 GGATTAAATC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.37, C:0.15, G:0.33, T:0.15
Consensus pattern (6 bp):
AAGCTG
Found at i:6383903 original size:29 final size:29
Alignment explanation
Indices: 6383862--6383923 Score: 117
Period size: 29 Copynumber: 2.2 Consensus size: 29
6383852 TGGTATTCCC
6383862 TAAG-GGTGGGAGTAAGAGAAATAAGAGT
1 TAAGTGGTGGGAGTAAGAGAAATAAGAGT
6383890 TAAGTGGTGGGAGTAAGAGAAATAAGAGT
1 TAAGTGGTGGGAGTAAGAGAAATAAGAGT
6383919 TAAGT
1 TAAGT
6383924 TATTTGACTT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 4 0.12
29 29 0.88
ACGTcount: A:0.42, C:0.00, G:0.37, T:0.21
Consensus pattern (29 bp):
TAAGTGGTGGGAGTAAGAGAAATAAGAGT
Found at i:6384036 original size:22 final size:22
Alignment explanation
Indices: 6384005--6384052 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
6383995 CAAGTTATTT
* * *
6384005 GACTTGATGGCATTTCTTGAAA
1 GACTTAATGGCATCTCTTAAAA
*
6384027 GACTTAATGGTATCTCTTAAAA
1 GACTTAATGGCATCTCTTAAAA
6384049 GACT
1 GACT
6384053 AAACTTTACC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.35
Consensus pattern (22 bp):
GACTTAATGGCATCTCTTAAAA
Found at i:6399710 original size:3 final size:3
Alignment explanation
Indices: 6399702--6399746 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
6399692 TGGGGGTCTC
6399702 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
6399747 GTTGTAGTTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:6400474 original size:16 final size:16
Alignment explanation
Indices: 6400453--6400488 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
6400443 TTTGGTTCGC
6400453 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
6400469 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
6400485 TGTA
1 TGTA
6400489 ATAGCTAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.25, C:0.00, G:0.36, T:0.39
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:6400553 original size:44 final size:45
Alignment explanation
Indices: 6400469--6400559 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
6400459 GGATTAGAGG
* * *
6400469 TGTATTGGATTAGAGGTGTAATAGCTAATCCACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
***
6400514 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
6400558 TG
1 TG
6400560 GAATAGAGGT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.27, C:0.07, G:0.29, T:0.37
Consensus pattern (45 bp):
TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
Found at i:6400745 original size:18 final size:17
Alignment explanation
Indices: 6400724--6400758 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
6400714 TTATTATTAA
*
6400724 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
6400742 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
6400759 TCTTATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:6409436 original size:26 final size:26
Alignment explanation
Indices: 6409398--6409450 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
6409388 TTGATAATAA
* *
6409398 TATCAATACCAACTAAATTAAGACTT
1 TATCAATAACAACCAAATTAAGACTT
*
6409424 TATCTATAACAACCAAATTAAGACTT
1 TATCAATAACAACCAAATTAAGACTT
6409450 T
1 T
6409451 TAAAAAATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.45, C:0.19, G:0.04, T:0.32
Consensus pattern (26 bp):
TATCAATAACAACCAAATTAAGACTT
Found at i:6413382 original size:42 final size:42
Alignment explanation
Indices: 6413323--6413491 Score: 338
Period size: 42 Copynumber: 4.0 Consensus size: 42
6413313 AAGAGGGGGA
6413323 CGGAAGTGCTGAACATCAGAACTTGCACCAGCATGAACCATC
1 CGGAAGTGCTGAACATCAGAACTTGCACCAGCATGAACCATC
6413365 CGGAAGTGCTGAACATCAGAACTTGCACCAGCATGAACCATC
1 CGGAAGTGCTGAACATCAGAACTTGCACCAGCATGAACCATC
6413407 CGGAAGTGCTGAACATCAGAACTTGCACCAGCATGAACCATC
1 CGGAAGTGCTGAACATCAGAACTTGCACCAGCATGAACCATC
6413449 CGGAAGTGCTGAACATCAGAACTTGCACCAGCATGAACCATC
1 CGGAAGTGCTGAACATCAGAACTTGCACCAGCATGAACCATC
6413491 C
1 C
6413492 TTTTCAGATA
Statistics
Matches: 127, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 127 1.00
ACGTcount: A:0.33, C:0.29, G:0.21, T:0.17
Consensus pattern (42 bp):
CGGAAGTGCTGAACATCAGAACTTGCACCAGCATGAACCATC
Found at i:6425248 original size:25 final size:25
Alignment explanation
Indices: 6425220--6425331 Score: 81
Period size: 25 Copynumber: 4.5 Consensus size: 25
6425210 ATGAACTCCC
*
6425220 CGATATATGGCTCTTCAGAGCTTTT
1 CGATATATGGCTCTTCAGAGCTTCT
* * *
6425245 CGATAAATGGCTCTT-ATGATCTTCC
1 CGATATATGGCTCTTCA-GAGCTTCT
* *
6425270 CGAT-TAATGGCCCTCCAGAGCTTCT
1 CGATAT-ATGGCTCTTCAGAGCTTCT
* *
6425295 CGATAT-TGGCTCGCTTGA-ACCTTCT
1 CGATATATGGCT--CTTCAGAGCTTCT
6425320 CGATAT-TGGCTC
1 CGATATATGGCTC
6425332 GTATGAGTTT
Statistics
Matches: 68, Mismatches: 13, Indels: 14
0.72 0.14 0.15
Matches are distributed among these distances:
23 1 0.01
24 5 0.07
25 57 0.84
26 5 0.07
ACGTcount: A:0.20, C:0.26, G:0.20, T:0.35
Consensus pattern (25 bp):
CGATATATGGCTCTTCAGAGCTTCT
Found at i:6425280 original size:50 final size:50
Alignment explanation
Indices: 6425204--6425299 Score: 131
Period size: 50 Copynumber: 1.9 Consensus size: 50
6425194 ACACATCGTA
* * *
6425204 GCTCTTATGAACTCCCCGATATATGGCTCTTCAGAGCTTTTCGATAAATG
1 GCTCTTATGAACTCCCCGATATATGGCCCTCCAGAGCTTCTCGATAAATG
* *
6425254 GCTCTTATGATCTTCCCGAT-TAATGGCCCTCCAGAGCTTCTCGATA
1 GCTCTTATGAACTCCCCGATAT-ATGGCCCTCCAGAGCTTCTCGATA
6425300 TTGGCTCGCT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
49 1 0.03
50 39 0.98
ACGTcount: A:0.22, C:0.27, G:0.18, T:0.33
Consensus pattern (50 bp):
GCTCTTATGAACTCCCCGATATATGGCCCTCCAGAGCTTCTCGATAAATG
Found at i:6425414 original size:25 final size:25
Alignment explanation
Indices: 6425334--6425422 Score: 76
Period size: 25 Copynumber: 3.5 Consensus size: 25
6425324 ATTGGCTCGT
* * *
6425334 ATGAGTTTCCGATTACATGT-CTCA
1 ATGAGCTTCCCATTATATGTGCTCA
*
6425358 CATGAGCTTCCCGTTATATG-GCTCGA
1 -ATGAGCTTCCCATTATATGTGCTC-A
*
6425384 AAGAGCTTCCCATT-TATGTGCTCA
1 ATGAGCTTCCCATTATATGTGCTCA
6425408 TATGAGCATTCCCAT
1 -ATGAGC-TTCCCAT
6425423 ATACGAATTG
Statistics
Matches: 52, Mismatches: 7, Indels: 9
0.76 0.10 0.13
Matches are distributed among these distances:
24 5 0.10
25 39 0.75
26 8 0.15
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.34
Consensus pattern (25 bp):
ATGAGCTTCCCATTATATGTGCTCA
Found at i:6425795 original size:25 final size:25
Alignment explanation
Indices: 6425761--6425813 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
6425751 ATATATGGTA
6425761 AGTTAATTTCCCGTCATACAAAAGC
1 AGTTAATTTCCCGTCATACAAAAGC
6425786 AGTTAATTTCCCGTCATACAAAAGC
1 AGTTAATTTCCCGTCATACAAAAGC
6425811 AGT
1 AGT
6425814 AAATGCTTAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.36, C:0.23, G:0.13, T:0.28
Consensus pattern (25 bp):
AGTTAATTTCCCGTCATACAAAAGC
Found at i:6439309 original size:20 final size:20
Alignment explanation
Indices: 6439284--6439323 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
6439274 CGTAAATTGA
*
6439284 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
6439304 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
6439324 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:6439313 original size:34 final size:34
Alignment explanation
Indices: 6439270--6439335 Score: 98
Period size: 35 Copynumber: 1.9 Consensus size: 34
6439260 AGTAAAATAT
* *
6439270 TTTTCGTAAATTGATTT-CTGGAAAATGTTTTAC
1 TTTTCGTAAAATGATTTACTGGAAAATATTTTAC
6439303 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTC-GTAAAATGATTTACTGGAAAATATTTT
6439336 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 5 0.17
34 11 0.38
35 13 0.45
ACGTcount: A:0.30, C:0.08, G:0.14, T:0.48
Consensus pattern (34 bp):
TTTTCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:6448452 original size:50 final size:50
Alignment explanation
Indices: 6448337--6448585 Score: 320
Period size: 50 Copynumber: 4.8 Consensus size: 50
6448327 GATAATAACA
* * **
6448337 TGCCAAAGCCCTGTCCCAGACATGGTCTTACATGGGATGTTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* * * * *
6448388 GGCCCATGCCATGTCCCAGACATGATCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
6448438 TGCCAACT-CCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAA-TGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
6448488 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATGATCTCAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC---ATCTC--GG
*
6448543 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
6448586 TTACCCAAAT
Statistics
Matches: 173, Mismatches: 17, Indels: 11
0.86 0.08 0.05
Matches are distributed among these distances:
50 95 0.55
51 31 0.18
53 5 0.03
55 2 0.01
56 40 0.23
ACGTcount: A:0.21, C:0.31, G:0.22, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:6451073 original size:22 final size:23
Alignment explanation
Indices: 6451048--6451091 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
6451038 TTGGTGAGAA
6451048 AGTCT-TTTTATAGTATGCAACG
1 AGTCTATTTTATAGTATGCAACG
6451070 AGTCTAGTTTTATAGTATGCAA
1 AGTCTA-TTTTATAGTATGCAA
6451092 TATTGTCATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 5 0.25
24 15 0.75
ACGTcount: A:0.30, C:0.11, G:0.18, T:0.41
Consensus pattern (23 bp):
AGTCTATTTTATAGTATGCAACG
Found at i:6466246 original size:9 final size:9
Alignment explanation
Indices: 6466232--6466262 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
6466222 GTTAAACGAA
6466232 TCGAGTTAT
1 TCGAGTTAT
*
6466241 TCGAGTTAA
1 TCGAGTTAT
6466250 TCGAGTTAT
1 TCGAGTTAT
6466259 TCGA
1 TCGA
6466263 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:6471885 original size:13 final size:14
Alignment explanation
Indices: 6471867--6471908 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
6471857 TCTCAATTTT
6471867 ATTTTAATAAT-TA
1 ATTTTAATAATATA
*
6471880 ATTTTAAAAATAATA
1 ATTTTAATAAT-ATA
6471895 ATTTTAAATAATAT
1 ATTTT-AATAATAT
6471909 TCTCCATACA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 10 0.42
15 9 0.38
16 5 0.21
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
ATTTTAATAATATA
Found at i:6471898 original size:15 final size:17
Alignment explanation
Indices: 6471871--6471907 Score: 60
Period size: 15 Copynumber: 2.3 Consensus size: 17
6471861 AATTTTATTT
6471871 TAATAATTAATTTTAAA
1 TAATAATTAATTTTAAA
6471888 -AATAA-TAATTTTAAA
1 TAATAATTAATTTTAAA
6471903 TAATA
1 TAATA
6471908 TTCTCCATAC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 10 0.53
16 9 0.47
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TAATAATTAATTTTAAA
Found at i:6473888 original size:114 final size:114
Alignment explanation
Indices: 6473688--6473908 Score: 352
Period size: 114 Copynumber: 1.9 Consensus size: 114
6473678 AAAATAAATG
* * * *
6473688 AAGGTGATTTGACCGTAGTTGCTTCGGCAACGAATGTACCACCTTTTAACTTGGACCCAACGATC
1 AAGGTGATTTGACCGTAGTTACTTCGGCAACAAATGTACCACCTTGTAACTCGGACCCAACGATC
6473753 AGGTTGGGTAACAAGGTGTTACAATATTAATATTTATTGAATCGGTAAC
66 AGGTTGGGTAACAAGGTGTTACAATATTAATATTTATTGAATCGGTAAC
* * * * * *
6473802 AAGGTTATTTGTCTGTAGTTACTTCGGCAACAAATGTGCTACCTTGTAACTCGGACCCAGCGATC
1 AAGGTGATTTGACCGTAGTTACTTCGGCAACAAATGTACCACCTTGTAACTCGGACCCAACGATC
6473867 AGGTTGGGTAACAAGGTGTTACAATATTAATATTTATTGAAT
66 AGGTTGGGTAACAAGGTGTTACAATATTAATATTTATTGAAT
6473909 GGTTCAAATT
Statistics
Matches: 97, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
114 97 1.00
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.32
Consensus pattern (114 bp):
AAGGTGATTTGACCGTAGTTACTTCGGCAACAAATGTACCACCTTGTAACTCGGACCCAACGATC
AGGTTGGGTAACAAGGTGTTACAATATTAATATTTATTGAATCGGTAAC
Found at i:6474460 original size:31 final size:29
Alignment explanation
Indices: 6474390--6474463 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 29
6474380 GGCTCAGGTT
* *
6474390 ACATTTTAGTCACTTATGTTTGAAATGTT
1 ACATTTTAGTCACTTATGTTTCAAATGTA
* **
6474419 ACGTTTTAGTCACTTATGTTATCACGTTGTA
1 ACATTTTAGTCACTTATGTT-TCA-AATGTA
6474450 ACATTTTAGTCACT
1 ACATTTTAGTCACT
6474464 GAGCCGTTAG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
29 19 0.51
30 2 0.05
31 16 0.43
ACGTcount: A:0.26, C:0.15, G:0.14, T:0.46
Consensus pattern (29 bp):
ACATTTTAGTCACTTATGTTTCAAATGTA
Found at i:6475080 original size:31 final size:29
Alignment explanation
Indices: 6475016--6475084 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
6475006 ACGATAATGT
* *
6475016 AAGTGACTAAAACGTAACATTTCAAACAT
1 AAGTGACTAAAACGTAACATGTCAAACAA
* *
6475045 AAGTGACTAAAATGTAACCTGAGTCAAACAA
1 AAGTGACTAAAACGTAACAT--GTCAAACAA
6475076 AAGTGACTA
1 AAGTGACTA
6475085 TTTTGGTAGT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 18 0.53
31 16 0.47
ACGTcount: A:0.48, C:0.16, G:0.14, T:0.22
Consensus pattern (29 bp):
AAGTGACTAAAACGTAACATGTCAAACAA
Found at i:6475187 original size:38 final size:38
Alignment explanation
Indices: 6475101--6475187 Score: 90
Period size: 38 Copynumber: 2.3 Consensus size: 38
6475091 TAGTTTACCC
* * *
6475101 TATAATTTATTACTTAATTTTAATTATTAATCAGTTAA
1 TATAATTTATTAATTAAATTTAAATATTAATCAGTTAA
*
6475139 TGTAGA-TTATTAATTAAATTTAAATATTATGATCA-TTAA
1 TATA-ATTTATTAATTAAATTTAAATATTA--ATCAGTTAA
6475178 -ATAATTTATT
1 TATAATTTATT
6475188 CTTACCTTAT
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
37 1 0.03
38 30 0.75
39 5 0.12
40 4 0.10
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (38 bp):
TATAATTTATTAATTAAATTTAAATATTAATCAGTTAA
Found at i:6485275 original size:16 final size:16
Alignment explanation
Indices: 6485256--6485290 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
6485246 GTTGTATGTC
6485256 TCTATCTTT-GTAGATA
1 TCTAT-TTTAGTAGATA
6485272 TCTATTTTAGTAGATA
1 TCTATTTTAGTAGATA
6485288 TCT
1 TCT
6485291 TTGTAGATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 3 0.17
16 15 0.83
ACGTcount: A:0.26, C:0.11, G:0.11, T:0.51
Consensus pattern (16 bp):
TCTATTTTAGTAGATA
Found at i:6485298 original size:12 final size:12
Alignment explanation
Indices: 6485258--6485302 Score: 54
Period size: 12 Copynumber: 3.4 Consensus size: 12
6485248 TGTATGTCTC
6485258 TATCTTTGTAGA
1 TATCTTTGTAGA
6485270 TATCTATTTTAGTAGA
1 TATC---TTT-GTAGA
6485286 TATCTTTGTAGA
1 TATCTTTGTAGA
6485298 TATCT
1 TATCT
6485303 GACAAACTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
12 14 0.48
13 3 0.10
15 3 0.10
16 9 0.31
ACGTcount: A:0.27, C:0.09, G:0.13, T:0.51
Consensus pattern (12 bp):
TATCTTTGTAGA
Found at i:6488374 original size:2 final size:2
Alignment explanation
Indices: 6488367--6488672 Score: 612
Period size: 2 Copynumber: 153.0 Consensus size: 2
6488357 AGCTTAAGCA
6488367 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6488409 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6488451 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6488493 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6488535 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6488577 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6488619 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6488661 AT AT AT AT AT AT
1 AT AT AT AT AT AT
6488673 CCTTATTCAG
Statistics
Matches: 304, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 304 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6489840 original size:41 final size:40
Alignment explanation
Indices: 6489753--6489846 Score: 102
Period size: 41 Copynumber: 2.3 Consensus size: 40
6489743 TACGAAACGT
* * * *
6489753 TTCTAGTTGGAAGCGTTTTCAATTGATTTGCAGAAAAGCG
1 TTCTAGCTAGAAGCGTTTTCAAATGATTTGCAGAAAAGCC
6489793 TGTCTAGCTAGAAGCGTTTTCAACAT-ATTTGCAGGAAAA-CAC
1 T-TCTAGCTAGAAGCGTTTTCAA-ATGATTTGCA-GAAAAGC-C
6489835 TTCTAGCTAGAA
1 TTCTAGCTAGAA
6489847 ACACTTTCTG
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
40 1 0.02
41 38 0.83
42 7 0.15
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.32
Consensus pattern (40 bp):
TTCTAGCTAGAAGCGTTTTCAAATGATTTGCAGAAAAGCC
Found at i:6490020 original size:23 final size:22
Alignment explanation
Indices: 6489960--6490022 Score: 58
Period size: 22 Copynumber: 2.8 Consensus size: 22
6489950 GGGTTTTGTA
6489960 ATTTTTTTATA-TTTTTTAAAT
1 ATTTTTTTATATTTTTTTAAAT
* *
6489981 -TTAAATTTTATGGTTTTTTTAAAT
1 ATT--TTTTTAT-ATTTTTTTAAAT
*
6490005 ATTTTTTTATAATTTTTT
1 ATTTTTTTATATTTTTTT
6490023 GAGATGTAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 9
0.70 0.11 0.20
Matches are distributed among these distances:
20 2 0.06
22 12 0.38
23 6 0.19
24 10 0.31
25 2 0.06
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (22 bp):
ATTTTTTTATATTTTTTTAAAT
Found at i:6493570 original size:56 final size:57
Alignment explanation
Indices: 6493465--6493688 Score: 292
Period size: 57 Copynumber: 4.0 Consensus size: 57
6493455 TATTGTTACT
* * * *
6493465 ATTTGCATGCTGTCATAAATTGAATTAAAGTTGTTGTTTGAGTGTTTCAAATTGAGC
1 ATTTTCATGCTGTCTTAAATTGAATTAAAGTTGCTGTTTTAGTGTTTCAAATTGAGC
* * * * *
6493522 ATTTTCATACTATCTTAAATTGAA-TCAAGATGCTGTTTTAGTGATTCAAATTGAGC
1 ATTTTCATGCTGTCTTAAATTGAATTAAAGTTGCTGTTTTAGTGTTTCAAATTGAGC
* * *
6493578 ATTTTCATGCTGTCATAAATTGAATTAAAGTTGGTGTTTTAGTGTATCAAATTGAGC
1 ATTTTCATGCTGTCTTAAATTGAATTAAAGTTGCTGTTTTAGTGTTTCAAATTGAGC
* * *
6493635 ATTTTCATGCTGTCTTAAATTAAATT-AAGTTGCT-ATTTAATGTTTCAAATTGAG
1 ATTTTCATGCTGTCTTAAATTGAATTAAAGTTGCTGTTTTAGTGTTTCAAATTGAG
6493689 TATTATTATG
Statistics
Matches: 143, Mismatches: 23, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
55 17 0.12
56 55 0.38
57 71 0.50
ACGTcount: A:0.30, C:0.10, G:0.17, T:0.43
Consensus pattern (57 bp):
ATTTTCATGCTGTCTTAAATTGAATTAAAGTTGCTGTTTTAGTGTTTCAAATTGAGC
Found at i:6493641 original size:57 final size:57
Alignment explanation
Indices: 6493465--6493718 Score: 277
Period size: 57 Copynumber: 4.5 Consensus size: 57
6493455 TATTGTTACT
* * * *
6493465 ATTTGCATGCTGTCATAAATTGAATTAAAGTTGTTGTTTGAGTGTTTCAAATTGAGC
1 ATTTTCATGCTGTCATAAATTGAATTAAAGTTGCTGTTTTAGTGTATCAAATTGAGC
* * * * *
6493522 ATTTTCATACTATCTTAAATTGAA-TCAAGATGCTGTTTTAGTG-ATTCAAATTGAGC
1 ATTTTCATGCTGTCATAAATTGAATTAAAGTTGCTGTTTTAGTGTA-TCAAATTGAGC
*
6493578 ATTTTCATGCTGTCATAAATTGAATTAAAGTTGGTGTTTTAGTGTATCAAATTGAGC
1 ATTTTCATGCTGTCATAAATTGAATTAAAGTTGCTGTTTTAGTGTATCAAATTGAGC
* * * * * *
6493635 ATTTTCATGCTGTCTTAAATTAAATT-AAGTTGCT-ATTTAATGTTTCAAATTGAGT
1 ATTTTCATGCTGTCATAAATTGAATTAAAGTTGCTGTTTTAGTGTATCAAATTGAGC
* *
6493690 ATTATT-ATGTTGTCCA-AAATTAAATTAAA
1 ATT-TTCATGCTGT-CATAAATTGAATTAAA
6493719 ATGTTGCTTC
Statistics
Matches: 167, Mismatches: 24, Indels: 13
0.82 0.12 0.06
Matches are distributed among these distances:
55 36 0.22
56 59 0.35
57 71 0.43
58 1 0.01
ACGTcount: A:0.32, C:0.09, G:0.16, T:0.43
Consensus pattern (57 bp):
ATTTTCATGCTGTCATAAATTGAATTAAAGTTGCTGTTTTAGTGTATCAAATTGAGC
Found at i:6496511 original size:25 final size:27
Alignment explanation
Indices: 6496483--6496537 Score: 64
Period size: 26 Copynumber: 2.1 Consensus size: 27
6496473 CATTTCAATT
6496483 ATGTGTTAAT-TTC-AAGACTTATGTA
1 ATGTGTTAATATTCAAAGACTTATGTA
*
6496508 A--TGTTAGTGATTCAAAGACTTATGTA
1 ATGTGTTAAT-ATTCAAAGACTTATGTA
6496534 ATGT
1 ATGT
6496538 TTTTAATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 7
0.75 0.03 0.22
Matches are distributed among these distances:
23 6 0.25
25 4 0.17
26 13 0.54
28 1 0.04
ACGTcount: A:0.33, C:0.07, G:0.18, T:0.42
Consensus pattern (27 bp):
ATGTGTTAATATTCAAAGACTTATGTA
Found at i:6496578 original size:9 final size:9
Alignment explanation
Indices: 6496566--6496615 Score: 82
Period size: 9 Copynumber: 5.6 Consensus size: 9
6496556 TCAATTTGGG
6496566 TAATTCGGT
1 TAATTCGGT
*
6496575 TAATTCGGG
1 TAATTCGGT
6496584 TAATTCGGT
1 TAATTCGGT
*
6496593 TAATGCGGT
1 TAATTCGGT
6496602 TAATTCGGT
1 TAATTCGGT
6496611 TAATT
1 TAATT
6496616 TTTAACCAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 37 1.00
ACGTcount: A:0.24, C:0.10, G:0.24, T:0.42
Consensus pattern (9 bp):
TAATTCGGT
Found at i:6496584 original size:18 final size:18
Alignment explanation
Indices: 6496558--6496615 Score: 89
Period size: 18 Copynumber: 3.2 Consensus size: 18
6496548 GTAGTGATTC
*
6496558 AATTTGGGTAATTCGGTT
1 AATTCGGGTAATTCGGTT
6496576 AATTCGGGTAATTCGGTT
1 AATTCGGGTAATTCGGTT
* *
6496594 AATGCGGTTAATTCGGTT
1 AATTCGGGTAATTCGGTT
6496612 AATT
1 AATT
6496616 TTTAACCAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.24, C:0.09, G:0.26, T:0.41
Consensus pattern (18 bp):
AATTCGGGTAATTCGGTT
Found at i:6498031 original size:42 final size:42
Alignment explanation
Indices: 6497949--6498054 Score: 149
Period size: 43 Copynumber: 2.5 Consensus size: 42
6497939 GGGTATATCT
* *
6497949 AACAACCGAAGTTTATCTTCTCATTTTTTAAATTCTTTTTTC
1 AACAACCCAAGATTATCTTCTCATTTTTTAAATTCTTTTTTC
* * *
6497991 AATAACCCAATATTATCTTCTCCTCTTTTTAAATTCTTTTTTC
1 AACAACCCAAGATTATCTTCTCAT-TTTTTAAATTCTTTTTTC
*
6498034 AACAACCCAAGATTATTTTCT
1 AACAACCCAAGATTATCTTCT
6498055 TTTAAAATTT
Statistics
Matches: 55, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
42 19 0.35
43 36 0.65
ACGTcount: A:0.28, C:0.22, G:0.03, T:0.47
Consensus pattern (42 bp):
AACAACCCAAGATTATCTTCTCATTTTTTAAATTCTTTTTTC
Found at i:6504453 original size:41 final size:40
Alignment explanation
Indices: 6504396--6504605 Score: 197
Period size: 41 Copynumber: 5.1 Consensus size: 40
6504386 TTCAGCAGCA
* *
6504396 TTTTTATCTAAGCGCCGCTAATGCTCGGATCTTTAGCGGTG
1 TTTTTATCTAAGCGCCGCTAATGCTCGG-CCTTTAGCGGCG
* *
6504437 TTTTTATCTGAGCGCCGCTAACT-CTCTGGCCTTTGGCGGCG
1 TTTTTATCTAAGCGCCGCTAA-TGCTC-GGCCTTTAGCGGCG
* **
6504478 TTTTTATCTAAGCACCGCTAATGCTCAGATCTTTAGCGGCG
1 TTTTTATCTAAGCGCCGCTAATGCTC-GGCCTTTAGCGGCG
* * * * *
6504519 TTTTTATTTGAGCGCCACTAATTCTATGGCCTTTAGCGGCG
1 TTTTTATCTAAGCGCCGCTAATGCT-CGGCCTTTAGCGGCG
* * * ***
6504560 TTTGTGTCTAAGCGCCGCTAATGTATTTACCTTTAGCGGCG
1 TTTTTATCTAAGCGCCGCTAATG-CTCGGCCTTTAGCGGCG
6504601 TTTTT
1 TTTTT
6504606 GCCGAAACGC
Statistics
Matches: 136, Mismatches: 28, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
40 1 0.01
41 131 0.96
42 4 0.03
ACGTcount: A:0.16, C:0.23, G:0.23, T:0.38
Consensus pattern (40 bp):
TTTTTATCTAAGCGCCGCTAATGCTCGGCCTTTAGCGGCG
Found at i:6504522 original size:82 final size:82
Alignment explanation
Indices: 6504396--6504582 Score: 284
Period size: 82 Copynumber: 2.3 Consensus size: 82
6504386 TTCAGCAGCA
* * *
6504396 TTTTTATCTAAGCGCCGCTAATGCTCGGATCTTTAGCGGTGTTTTTATCTGAGCGCCGCTAACTC
1 TTTTTATCTAAGCGCCGCTAATGCTCAGATCTTTAGCGGCGTTTTTATCTGAGCGCCACTAACTC
* *
6504461 TCTGGCCTTTGGCGGCG
66 TATGGCCTTTAGCGGCG
* * *
6504478 TTTTTATCTAAGCACCGCTAATGCTCAGATCTTTAGCGGCGTTTTTATTTGAGCGCCACTAATTC
1 TTTTTATCTAAGCGCCGCTAATGCTCAGATCTTTAGCGGCGTTTTTATCTGAGCGCCACTAACTC
6504543 TATGGCCTTTAGCGGCG
66 TATGGCCTTTAGCGGCG
* *
6504560 TTTGTGTCTAAGCGCCGCTAATG
1 TTTTTATCTAAGCGCCGCTAATG
6504583 TATTTACCTT
Statistics
Matches: 94, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
82 94 1.00
ACGTcount: A:0.17, C:0.24, G:0.24, T:0.36
Consensus pattern (82 bp):
TTTTTATCTAAGCGCCGCTAATGCTCAGATCTTTAGCGGCGTTTTTATCTGAGCGCCACTAACTC
TATGGCCTTTAGCGGCG
Found at i:6504594 original size:82 final size:82
Alignment explanation
Indices: 6504400--6504605 Score: 254
Period size: 82 Copynumber: 2.5 Consensus size: 82
6504390 GCAGCATTTT
* * * * * *
6504400 TATCTAAGCGCCGCTAATGCTCGGATCTTTAGCGGTGTTTTTATCTGAGCGCCGCTAACTCTCTG
1 TATCTAAGCACCGCTAATGCTCAGACCTTTAGCGGCGTTTTTATCTGAGCGCCACTAACTCTATG
* *
6504465 GCCTTTGGCGGCGTTTT
66 GCCTTTAGCGGCGTTTG
* * *
6504482 TATCTAAGCACCGCTAATGCTCAGATCTTTAGCGGCGTTTTTATTTGAGCGCCACTAATTCTATG
1 TATCTAAGCACCGCTAATGCTCAGACCTTTAGCGGCGTTTTTATCTGAGCGCCACTAACTCTATG
6504547 GCCTTTAGCGGCGTTTG
66 GCCTTTAGCGGCGTTTG
* * *
6504564 TGTCTAAGCGCCGCTAATG-T-ATTTACCTTTAGCGGCGTTTTT
1 TATCTAAGCACCGCTAATGCTCA--GACCTTTAGCGGCGTTTTT
6504606 GCCGAAACGC
Statistics
Matches: 109, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
80 1 0.01
81 1 0.01
82 107 0.98
ACGTcount: A:0.17, C:0.24, G:0.23, T:0.36
Consensus pattern (82 bp):
TATCTAAGCACCGCTAATGCTCAGACCTTTAGCGGCGTTTTTATCTGAGCGCCACTAACTCTATG
GCCTTTAGCGGCGTTTG
Found at i:6505158 original size:15 final size:15
Alignment explanation
Indices: 6505137--6505174 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
6505127 TTTAAGGTTA
6505137 ATTTAGGGGTTAGAG
1 ATTTAGGGGTTAGAG
* *
6505152 GTTTAGGGGTTTGAG
1 ATTTAGGGGTTAGAG
6505167 ATTTAGGG
1 ATTTAGGG
6505175 TTTCAACGGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.21, C:0.00, G:0.42, T:0.37
Consensus pattern (15 bp):
ATTTAGGGGTTAGAG
Found at i:6505177 original size:14 final size:14
Alignment explanation
Indices: 6505110--6505177 Score: 52
Period size: 15 Copynumber: 4.9 Consensus size: 14
6505100 TACGGGGTAT
*
6505110 AGATTTAAGGTTTG
1 AGATTTAGGGTTTG
* *
6505124 GGATTTAAGG-TT-
1 AGATTTAGGGTTTG
*
6505136 A-ATTTAGGGGTTAG
1 AGATTTA-GGGTTTG
*
6505150 AGGTTTAGGGGTTTG
1 AGATTTA-GGGTTTG
6505165 AGATTTAGGGTTT
1 AGATTTAGGGTTT
6505178 CAACGGTCAT
Statistics
Matches: 43, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
11 5 0.12
12 2 0.05
13 3 0.07
14 16 0.37
15 17 0.40
ACGTcount: A:0.24, C:0.00, G:0.35, T:0.41
Consensus pattern (14 bp):
AGATTTAGGGTTTG
Found at i:6507251 original size:10 final size:10
Alignment explanation
Indices: 6507236--6507262 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
6507226 CTAATTTTTT
6507236 GATATATATG
1 GATATATATG
6507246 GATATATATG
1 GATATATATG
6507256 GATATAT
1 GATATAT
6507263 TATATATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.19, T:0.41
Consensus pattern (10 bp):
GATATATATG
Found at i:6513575 original size:43 final size:43
Alignment explanation
Indices: 6513516--6513897 Score: 150
Period size: 43 Copynumber: 8.9 Consensus size: 43
6513506 GGCGTTTTTT
* * ** *
6513516 AAAAAGCGCCGCTAAAGGCCCTGTCCTTTAGCGGCGTTTGTAA
1 AAAAAGCACCGCTAAAGACAATGACCTTTAGCGGCGTTTGTAA
* * *
6513559 AAAAAGCACCGTTAAAGACAATGACTTTTAGCGGCGTTTGTGA
1 AAAAAGCACCGCTAAAGACAATGACCTTTAGCGGCGTTTGTAA
* * * ** * **
6513602 AAAAAGCGCCACTAAAG-CTCATGGTCTTTAGCGGCGTTTATGG
1 AAAAAGCACCGCTAAAGAC-AATGACCTTTAGCGGCGTTTGTAA
* * * *** * **
6513645 GAAAAGCGCCGCTAAAG-CTCATGGTTTTTAGCGGCGTTTATGG
1 AAAAAGCACCGCTAAAGAC-AATGACCTTTAGCGGCGTTTGTAA
* * * ** * **
6513688 GAAAAGCGCCACTAAAGATC-ATGGTCTTTAGCAGCGTTTGTGG
1 AAAAAGCACCGCTAAAGA-CAATGACCTTTAGCGGCGTTTGTAA
* * ** *
6513731 AAAAAGCGCCGCTAAAGGAC-ATGATCTTTAGCGGCGATTCCTAC
1 AAAAAGCACCGCTAAA-GACAATGACCTTTAGCGGCG-TTTGTAA
** * * * * * *
6513775 ACCAA-CGCCGCTAAAGACCATTATCTTTAGCGGCGCTTG-GA
1 AAAAAGCACCGCTAAAGACAATGACCTTTAGCGGCGTTTGTAA
* * * ** *
6513816 GAAAATCGCCGCTAAAGGAC-ATGGTCTTTAGCGGCGTTTGTAG
1 AAAAAGCACCGCTAAA-GACAATGACCTTTAGCGGCGTTTGTAA
* * *
6513859 AAAAAGCGCCGCTAAAGGAC-ATGATCTTTAGCGGTGTTT
1 AAAAAGCACCGCTAAA-GACAATGACCTTTAGCGGCGTTT
6513898 TTTTCATAAA
Statistics
Matches: 278, Mismatches: 52, Indels: 18
0.80 0.15 0.05
Matches are distributed among these distances:
41 2 0.01
42 32 0.12
43 235 0.85
44 8 0.03
45 1 0.00
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.25
Consensus pattern (43 bp):
AAAAAGCACCGCTAAAGACAATGACCTTTAGCGGCGTTTGTAA
Found at i:6513631 original size:86 final size:84
Alignment explanation
Indices: 6513516--6513897 Score: 294
Period size: 86 Copynumber: 4.5 Consensus size: 84
6513506 GGCGTTTTTT
* * ** * *
6513516 AAAAAGCGCCGCTAAAGGC-CCT-GTCCTTTAGCGGCGTTTGTAAAAAAAGCACCGTTAAAGACA
1 AAAAAGCGCCACTAAA-GCTCATGGT-CTTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGAC-
*
6513579 ATGACTTTTAGCGGCGTTTGTGA
63 ATGA-TTTTAGCGGCGTTTATGA
* * *
6513602 AAAAAGCGCCACTAAAGCTCATGGTCTTTAGCGGCGTTTATGGGAAAAGCGCCGCTAAAGCTCAT
1 AAAAAGCGCCACTAAAGCTCATGGTCTTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAG-ACAT
* *
6513667 GGTTTTTAGCGGCGTTTATGG
65 -GATTTTAGCGGCGTTTATGA
* * *
6513688 GAAAAGCGCCACTAAAGATCATGGTCTTTAGCAGCGTTTGTGGAAAAAGCGCCGCTAAAGGACAT
1 AAAAAGCGCCACTAAAGCTCATGGTCTTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAA-GACAT
**
6513753 GATCTTTAGCGGCGATTCCT-A
65 GAT-TTTAGCGGCG-TTTATGA
** * ** * *
6513774 CACCAA-CGCCGCTAAAGAC-CATTATCTTTAGCGGCG-CT-TGGAGAAAATCGCCGCTAAAGGA
1 -AAAAAGCGCCACTAAAG-CTCATGGTCTTTAGCGGCGTTTGTGGA-AAAAGCGCCGCTAAA-GA
* *
6513835 CATGGTCTTTAGCGGCGTTTGT-A
62 CATGAT-TTTAGCGGCGTTTATGA
* ** * *
6513858 GAAAAAGCGCCGCTAAAGGACATGATCTTTAGCGGTGTTT
1 -AAAAAGCGCCACTAAAGCTCATGGTCTTTAGCGGCGTTT
6513898 TTTTCATAAA
Statistics
Matches: 241, Mismatches: 42, Indels: 26
0.78 0.14 0.08
Matches are distributed among these distances:
84 11 0.05
85 64 0.27
86 156 0.65
87 10 0.04
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.25
Consensus pattern (84 bp):
AAAAAGCGCCACTAAAGCTCATGGTCTTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGACATG
ATTTTAGCGGCGTTTATGA
Found at i:6513747 original size:129 final size:127
Alignment explanation
Indices: 6513585--6513897 Score: 364
Period size: 129 Copynumber: 2.4 Consensus size: 127
6513575 GACAATGACT
* * ** * **
6513585 TTTAGCGGCGTTTGTGAAAAAAGCGCCACTAAAGCTCATGGTCTTTAGCGGCGTTTATGGGA-AA
1 TTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGACATGATCTTTAGCGGCGTTTAT-ACACAA
* * *
6513649 AGCGCCGCTAAAG-CTCATGGTTTTTAGCGGCGTTTATGG-GAAAAGCGCCACTAAA-GATCATG
65 A-CGCCGCTAAAGAC-CATGATCTTTAGCGGCG-CT-TGGAGAAAAGCGCCACTAAAGGA-CATG
6513711 GTC
125 GTC
* ** *
6513714 TTTAGCAGCGTTTGTGGAAAAAGCGCCGCTAAAGGACATGATCTTTAGCGGCGATTCCTACACCA
1 TTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGACATGATCTTTAGCGGCG-TTTATACACAA
* * *
6513779 ACGCCGCTAAAGACCATTATCTTTAGCGGCGCTTGGAGAAAATCGCCGCTAAAGGACATGGTC
65 ACGCCGCTAAAGACCATGATCTTTAGCGGCGCTTGGAGAAAAGCGCCACTAAAGGACATGGTC
* *
6513842 TTTAGCGGCGTTTGTAGAAAAAGCGCCGCTAAAGGACATGATCTTTAGCGGTGTTT
1 TTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGACATGATCTTTAGCGGCGTTT
6513898 TTTTCATAAA
Statistics
Matches: 158, Mismatches: 21, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
127 5 0.03
128 72 0.46
129 75 0.47
130 6 0.04
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.26
Consensus pattern (127 bp):
TTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGACATGATCTTTAGCGGCGTTTATACACAAA
CGCCGCTAAAGACCATGATCTTTAGCGGCGCTTGGAGAAAAGCGCCACTAAAGGACATGGTC
Found at i:6515968 original size:40 final size:40
Alignment explanation
Indices: 6515881--6515986 Score: 115
Period size: 40 Copynumber: 2.6 Consensus size: 40
6515871 TATTACTGTT
* * *
6515881 AGTAAAAAACTAGTATTATTATTATAGTTAGTTATTATTTTT
1 AGTAAAAAACTAATATTATT-TT-TAGTTAGCTATTATTTTG
* **
6515923 CGTAAAACCCTAATATTATTGTTTAGTTA-CTATTATTTTG
1 AGTAAAAAACTAATATTATT-TTTAGTTAGCTATTATTTTG
*
6515963 AGTAAAAAACTATTATTATTTTTA
1 AGTAAAAAACTAATATTATTTTTA
6515987 TTGTGTTAGT
Statistics
Matches: 53, Mismatches: 11, Indels: 3
0.79 0.16 0.04
Matches are distributed among these distances:
39 4 0.08
40 25 0.47
41 6 0.11
42 18 0.34
ACGTcount: A:0.37, C:0.07, G:0.08, T:0.48
Consensus pattern (40 bp):
AGTAAAAAACTAATATTATTTTTAGTTAGCTATTATTTTG
Found at i:6521665 original size:163 final size:162
Alignment explanation
Indices: 6521486--6522335 Score: 617
Period size: 163 Copynumber: 5.3 Consensus size: 162
6521476 TTATTTTCGT
* * *
6521486 ATTTTATTATTTTATATTATTTCAGTACATTTTGCTAGAAATATTTGTATTAATTATTTCTAAAT
1 ATTTTATAATTTTATATTATTTCAGTACATTATGTTAGAAATATTTGTATTAATTATTTCTAAAT
* *
6521551 TTTTAAAAAAGTTAGTAAGCGTTCACTCTTTACTTCGGCCATTTGTTCGTATTTTTTTCTCGGCA
66 TTTTAAAAAAGTTAGTAA-CGTACACTCTTTACTTCGGCCATTTGTTCGTATTTTTTTCTCCGCA
6521616 TTTTATTACTTTAAAAAAATATCATAATTTTTA
130 TTTTATTACTTTAAAAAAATATCATAATTTTTA
** ** * * * * *
6521649 ATTTTATAATTTTATATTATTTCAGCGCATTATGTT--ATTTCTTTATTAATTTAGTGTGTTTTT
1 ATTTTATAATTTTATATTATTTCAGTACATTATGTTAGAAATATTT-GT-A-TTAAT-TATTTCT
* * * * * * *
6521712 AAATTAATTTAGTGTAAAAA---A-AAACCTAAAC-C-TTA-TTCCTGCCCTTTGCTCGTATTAT
62 AAATT--TTTA----AAAAAGTTAGTAACGTACACTCTTTACTT-CGGCCATTTGTTCGTATTTT
* * * *
6521770 TTTC-CCGAATTTGATTACTTCCAAAAAAATAT-ATTATTTTCGT-
120 TTTCTCCGCATTTTATTACTT-TAAAAAAATATCATAATTTT--TA
* * * * * * * **
6521813 ATTATATTATTTTATATTATTTTAGTACATTCTGTTTAAAAAT-TTTCTATTAATTTTTTCCGAA
1 ATTTTATAATTTTATATTATTTCAGTACATTATG-TTAGAAATATTTGTATTAATTATTTCTAAA
* * *
6521877 TTTTTAAAAAAGTTAGTAAGTGTTCACTCTTTACTTCGGCCATTTGTTCGTATTTTTTTCTCGGC
65 TTTTTAAAAAAGTTAGTAA-CGTACACTCTTTACTTCGGCCATTTGTTCGTATTTTTTTCTCCGC
* *
6521942 ATTTTATTACTTTTAAAAAATATCATAATTTCTA
129 ATTTTATTACTTTAAAAAAATATCATAATTTTTA
* * * * *
6521976 ATTTTATAATTTTACATTATTTCAGTGCATTATGTTTG-AA-A-TT-TATTAATTTAATGTGT--
1 ATTTTATAATTTTATATTATTTCAGTACATTATGTTAGAAATATTTGTATTAA-TT-ATTTCTAA
* * *** * * * * *
6522035 -TTTTTAAATTAATTTAGTGTAAAAAAAAC-CTTTATTTCTG-CACTTTGCTCGTATTATTTTC-
64 ATTTTTAAA-AAAGTTA--GTAACGTACACTCTTTACTTCGGCCA-TTTGTTCGTATTTTTTTCT
* * * *
6522096 CCGAATTTTATTACTTCCAATAAAACTAT-ATTATTTTCGT-
125 CCGCATTTTATTACTT-TAA-AAAAATATCATAATTTT--TA
* * *
6522136 ATTTTATTATTTTATATTATTTCAGTACATTTTGTTAGAAATATTTGTATTAATTATTTCTGAAT
1 ATTTTATAATTTTATATTATTTCAGTACATTATGTTAGAAATATTTGTATTAATTATTTCTAAAT
* *
6522201 TTTTAAAAAAGTTAGTAA--AACATTC-TTACTTCGGCCATTTGTTCGT-TTTTTTTCCTCCGCA
66 TTTTAAAAAAGTTAGTAACGTACACTCTTTACTTCGGCCATTTGTTCGTATTTTTTT-CTCCGCA
* *
6522262 TTTTATTACTTT-AAAAGATATCATAATTTCTA
130 TTTTATTACTTTAAAAAAATATCATAATTTTTA
* * * *
6522294 ATTTTATAATTTTACATTATTTCAATGCATTATGTTTGAAAT
1 ATTTTATAATTTTATATTATTTCAGTACATTATGTTAGAAAT
6522336 TTATTAAATA
Statistics
Matches: 523, Mismatches: 112, Indels: 109
0.70 0.15 0.15
Matches are distributed among these distances:
156 5 0.01
157 1 0.00
158 66 0.13
159 57 0.11
160 71 0.14
161 37 0.07
162 22 0.04
163 122 0.23
164 98 0.19
165 23 0.04
166 7 0.01
167 8 0.02
168 1 0.00
171 5 0.01
ACGTcount: A:0.30, C:0.12, G:0.08, T:0.50
Consensus pattern (162 bp):
ATTTTATAATTTTATATTATTTCAGTACATTATGTTAGAAATATTTGTATTAATTATTTCTAAAT
TTTTAAAAAAGTTAGTAACGTACACTCTTTACTTCGGCCATTTGTTCGTATTTTTTTCTCCGCAT
TTTATTACTTTAAAAAAATATCATAATTTTTA
Found at i:6521932 original size:327 final size:321
Alignment explanation
Indices: 6521473--6522342 Score: 1333
Period size: 327 Copynumber: 2.7 Consensus size: 321
6521463 NNNNNNNNNN
*
6521473 ATATTATTTTCGTATTTTATTATTTTATATTATTTCAGTACATTTTGCTAGAAATATTTGTATTA
1 ATATTATTTTCGTATTTTATTATTTTATATTATTTCAGTACATTTTGTTAGAAATATTTGTATTA
*
6521538 ATTATTTCTAAATTTTTAAAAAAGTTAGTAAGCGTTCACTCTTTACTTCGGCCATTTGTTCGTAT
66 ATTATTTCTGAATTTTTAAAAAAGTTAGTAAG-GTTCACTCTTTACTTCGGCCATTTGTTCGTAT
* *
6521603 TTTTTTCTCGGCATTTTATTACTTTAAAAAAATATCATAATTTTTAATTTTATAATTTTATATTA
130 TTTTTTCTCGGCATTTTATTACTTT-AAAAAATATCATAATTTCTAATTTTATAATTTTACATTA
* *** *
6521668 TTTCAGCGCATTATGTTAT-TTCTTTATTAATTTAGTGTG-TTTTTAAATTAATTTAGTGTAAAA
194 TTTCAGTGCATTATGTT-TGAAATTTATTAATTTAATGTGTTTTTTAAATTAATTTAGTGT-AAA
*
6521731 AAAAACCTAAACCTTATTCCTGCCCTTTGCTCGTATTATTTTCCCGAATTTGATTACTTCCAA-A
257 AAAAACCT-----TTATTCCTGCACTTTGCTCGTATTATTTTCCCGAATTTGATTACTTCCAATA
6521795 AAAAT
317 AAAAT
* * * * *
6521800 ATATTATTTTCGTATTATATTATTTTATATTATTTTAGTACATTCTGTTTAAAAAT-TTTCTATT
1 ATATTATTTTCGTATTTTATTATTTTATATTATTTCAGTACATTTTG-TTAGAAATATTTGTATT
* *
6521864 AATTTTTTCCGAATTTTTAAAAAAGTTAGTAAGTGTTCACTCTTTACTTCGGCCATTTGTTCGTA
65 AATTATTTCTGAATTTTTAAAAAAGTTAGTAAG-GTTCACTCTTTACTTCGGCCATTTGTTCGTA
6521929 TTTTTTTCTCGGCATTTTATTACTTTTAAAAAATATCATAATTTCTAATTTTATAATTTTACATT
129 TTTTTTTCTCGGCATTTTATTAC-TTTAAAAAATATCATAATTTCTAATTTTATAATTTTACATT
6521994 ATTTCAGTGCATTATGTTTGAAATTTATTAATTTAATGTGTTTTTTAAATTAATTTAGTGTAAAA
193 ATTTCAGTGCATTATGTTTGAAATTTATTAATTTAATGTGTTTTTTAAATTAATTTAGTGTAAAA
* * *
6522059 AAAACCTTTATTTCTGCACTTTGCTCGTATTATTTTCCCGAATTTTATTACTTCCAATAAAACT
258 AAAACCTTTATTCCTGCACTTTGCTCGTATTATTTTCCCGAATTTGATTACTTCCAATAAAAAT
6522123 ATATTATTTTCGTATTTTATTATTTTATATTATTTCAGTACATTTTGTTAGAAATATTTGTATTA
1 ATATTATTTTCGTATTTTATTATTTTATATTATTTCAGTACATTTTGTTAGAAATATTTGTATTA
** *
6522188 ATTATTTCTGAATTTTTAAAAAAGTTAGTAA--AACATTC-TTACTTCGGCCATTTGTTCGT-TT
66 ATTATTTCTGAATTTTTAAAAAAGTTAGTAAGGTTCACTCTTTACTTCGGCCATTTGTTCGTATT
* *
6522249 TTTTTCCTCCGCATTTTATTACTTTAAAAGATATCATAATTTCTAATTTTATAATTTTACATTAT
131 TTTTT-CTCGGCATTTTATTACTTTAAAAAATATCATAATTTCTAATTTTATAATTTTACATTAT
*
6522314 TTCAATGCATTATGTTTGAAATTTATTAA
195 TTCAGTGCATTATGTTTGAAATTTATTAA
6522343 ATATACCATT
Statistics
Matches: 502, Mismatches: 34, Indels: 23
0.90 0.06 0.04
Matches are distributed among these distances:
318 77 0.15
319 36 0.07
320 4 0.01
322 54 0.11
323 86 0.17
326 1 0.00
327 215 0.43
328 29 0.06
ACGTcount: A:0.30, C:0.11, G:0.08, T:0.50
Consensus pattern (321 bp):
ATATTATTTTCGTATTTTATTATTTTATATTATTTCAGTACATTTTGTTAGAAATATTTGTATTA
ATTATTTCTGAATTTTTAAAAAAGTTAGTAAGGTTCACTCTTTACTTCGGCCATTTGTTCGTATT
TTTTTCTCGGCATTTTATTACTTTAAAAAATATCATAATTTCTAATTTTATAATTTTACATTATT
TCAGTGCATTATGTTTGAAATTTATTAATTTAATGTGTTTTTTAAATTAATTTAGTGTAAAAAAA
ACCTTTATTCCTGCACTTTGCTCGTATTATTTTCCCGAATTTGATTACTTCCAATAAAAAT
Found at i:6522674 original size:41 final size:40
Alignment explanation
Indices: 6522629--6522756 Score: 116
Period size: 40 Copynumber: 3.2 Consensus size: 40
6522619 AAACAGGCTT
6522629 TTAGCGGCGCTTGGACAAAAAACGCCACTAAAAATCAAGCA
1 TTAGCGGCGCTTGGA-AAAAAACGCCACTAAAAATCAAGCA
** * * ** *
6522670 TTAGCGGCGCTTTTATAAAAACGCCGCTAAAGGTCGAGCA
1 TTAGCGGCGCTTGGAAAAAAACGCCACTAAAAATCAAGCA
***** *
6522710 TTAGCGGCGCTT-TTTGGAAACGCCGCTAAAAAT-AAGCA
1 TTAGCGGCGCTTGGAAAAAAACGCCACTAAAAATCAAGCA
6522748 TTAGCGGCG
1 TTAGCGGCG
6522757 TTTTTTGAAA
Statistics
Matches: 74, Mismatches: 13, Indels: 3
0.82 0.14 0.03
Matches are distributed among these distances:
38 13 0.18
39 16 0.22
40 32 0.43
41 13 0.18
ACGTcount: A:0.33, C:0.23, G:0.24, T:0.20
Consensus pattern (40 bp):
TTAGCGGCGCTTGGAAAAAAACGCCACTAAAAATCAAGCA
Found at i:6522710 original size:40 final size:39
Alignment explanation
Indices: 6522646--6522779 Score: 164
Period size: 40 Copynumber: 3.4 Consensus size: 39
6522636 CGCTTGGACA
*
6522646 AAAAACGCCACTAAAAATCAAGCATTAGCGGCGCTTTTAT
1 AAAAACGCCGCTAAAAATCAAGCATTAGCGGCGCTTTT-T
** *
6522686 AAAAACGCCGCTAAAGGTCGAGCATTAGCGGCGCTTTTT
1 AAAAACGCCGCTAAAAATCAAGCATTAGCGGCGCTTTTT
** *
6522725 GGAAACGCCGCTAAAAAT-AAGCATTAGCGGCGTTTTTT
1 AAAAACGCCGCTAAAAATCAAGCATTAGCGGCGCTTTTT
*
6522763 GAAAAGCGCCGC-AAAAA
1 -AAAAACGCCGCTAAAAA
6522780 GCCTAAGCCA
Statistics
Matches: 80, Mismatches: 13, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
38 23 0.29
39 23 0.29
40 34 0.43
ACGTcount: A:0.36, C:0.22, G:0.22, T:0.21
Consensus pattern (39 bp):
AAAAACGCCGCTAAAAATCAAGCATTAGCGGCGCTTTTT
Found at i:6522881 original size:41 final size:41
Alignment explanation
Indices: 6522815--6523055 Score: 360
Period size: 41 Copynumber: 5.9 Consensus size: 41
6522805 TGAGTTTTTA
*
6522815 GGGCATTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
* ** *
6522856 GGGCCTTTAGCTGCGTTTTCAAAAAAGCGCCACTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
6522897 GGGCCTTTAGCGGCGTTTTTGAGAAAA-CGCCGCTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTGA-AAAAGCGCCGCTAATGCTC
* *
6522938 TGGCCTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
* *
6522979 TGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCACTAATGC-C
1 GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
* *
6523019 CGACCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAAT
1 GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAAT
6523056 AATAATAAAA
Statistics
Matches: 182, Mismatches: 16, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
40 38 0.21
41 140 0.77
42 4 0.02
ACGTcount: A:0.22, C:0.24, G:0.27, T:0.27
Consensus pattern (41 bp):
GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
Found at i:6524244 original size:33 final size:32
Alignment explanation
Indices: 6524207--6524273 Score: 107
Period size: 33 Copynumber: 2.1 Consensus size: 32
6524197 TATTTAGGGG
* *
6524207 TTAGGGATTTAGGGTCTGGTTAGGGTTTAAGGA
1 TTAGGGATTCAGGGTCGGGTTAGGGTTT-AGGA
6524240 TTAGGGATTCAGGGTCGGGTTAGGGTTTAGGA
1 TTAGGGATTCAGGGTCGGGTTAGGGTTTAGGA
6524272 TT
1 TT
6524274 TAGATTAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 6 0.19
33 26 0.81
ACGTcount: A:0.19, C:0.04, G:0.40, T:0.36
Consensus pattern (32 bp):
TTAGGGATTCAGGGTCGGGTTAGGGTTTAGGA
Found at i:6525572 original size:43 final size:43
Alignment explanation
Indices: 6525465--6525734 Score: 344
Period size: 43 Copynumber: 6.3 Consensus size: 43
6525455 AGGTTATGTT
* * * * *
6525465 TTTAGCGGTGTTTTTGCGAGAAGCGCCGCTAAAGGT-TTGTTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
** * *
6525507 TTTAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGGTCATGATC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
* * *
6525550 TATAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCGTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
* * * **
6525593 TATAGCGGCGTTTGCGGGAAAAGCGCCGCTAAAGGTCATGACC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
* *
6525636 TTTAACGGAGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
*
6525679 TTTAGCAGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
*
6525722 TTTATCGGCGTTT
1 TTTAGCGGCGTTT
6525735 TTTCTGGCGC
Statistics
Matches: 199, Mismatches: 28, Indels: 1
0.87 0.12 0.00
Matches are distributed among these distances:
42 31 0.16
43 168 0.84
ACGTcount: A:0.22, C:0.19, G:0.31, T:0.28
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
Found at i:6525893 original size:26 final size:25
Alignment explanation
Indices: 6525851--6525976 Score: 76
Period size: 27 Copynumber: 4.8 Consensus size: 25
6525841 AAAAATTACC
6525851 TTTTTTTCTTTCCCTCTTCTCCTTCTT
1 TTTTTTTCTTT-CCTCTTCT-CTTCTT
6525878 TTTTTTTCTCTT-CTCTTCTCTTCTCCT
1 TTTTTTTCT-TTCCTCTTCTCTTCT--T
* *
6525905 TTCCTTTTCTTTCCTTCTTTTCCTTTCTT
1 TT-TTTTTCTTTCC-TCTTCT-C-TTCTT
** * * *
6525934 TCCTCTCCTTTCCTTTTCT-TTCTT
1 TTTTTTTCTTTCCTCTTCTCTTCTT
* *
6525958 TTTCTTTCTTTCTTCTTCT
1 TTTTTTTCTTTCCTCTTCT
6525977 TTCCCTCTCC
Statistics
Matches: 77, Mismatches: 14, Indels: 19
0.70 0.13 0.17
Matches are distributed among these distances:
24 17 0.22
25 5 0.06
26 7 0.09
27 18 0.23
28 18 0.23
29 7 0.09
30 1 0.01
31 4 0.05
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (25 bp):
TTTTTTTCTTTCCTCTTCTCTTCTT
Found at i:6525902 original size:31 final size:31
Alignment explanation
Indices: 6525864--6525994 Score: 92
Period size: 28 Copynumber: 4.2 Consensus size: 31
6525854 TTTTCTTTCC
* *
6525864 CTCTTCTCC-TTCTTTTTTTTTCTCTTCTCTT
1 CTCTTCTCCTTTCCTTTTCTTTC-CTTCTCTT
*
6525895 CTCTTCTCCTTTCCTTTTCTTTCCTTCTTTT
1 CTCTTCTCCTTTCCTTTTCTTTCCTTCTCTT
* * *
6525926 C-CTT-T-CTTTCCTCTCCTTTCCTTTTCTT
1 CTCTTCTCCTTTCCTTTTCTTTCCTTCTCTT
* * *
6525954 -TCTTTTTCTTTCTTTCTTCTTCTTTCCCTCTCCTT
1 CTCTTCTCCTTTC---CTT-TTCTTTCCTTCT-CTT
6525989 CTCTTC
1 CTCTTC
6525995 CCCCCACCCA
Statistics
Matches: 78, Mismatches: 12, Indels: 15
0.74 0.11 0.14
Matches are distributed among these distances:
28 22 0.28
29 2 0.03
30 8 0.10
31 17 0.22
32 11 0.14
33 2 0.03
34 9 0.12
35 3 0.04
36 4 0.05
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (31 bp):
CTCTTCTCCTTTCCTTTTCTTTCCTTCTCTT
Found at i:6525909 original size:5 final size:5
Alignment explanation
Indices: 6525901--6525969 Score: 63
Period size: 5 Copynumber: 14.4 Consensus size: 5
6525891 TCTTCTCTTC
* * *
6525901 TCCTT TCCTT TTCTT TCC-T TCTTT TCCTT T-CTT TCCTC TCCTT TCCTT
1 TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT
* * *
6525949 TTCTT TCTTT TTCTT T-CTT TC
1 TCCTT TCCTT TCCTT TCCTT TC
6525970 TTCTTCTTTC
Statistics
Matches: 50, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
4 11 0.22
5 39 0.78
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (5 bp):
TCCTT
Found at i:6525916 original size:10 final size:10
Alignment explanation
Indices: 6525903--6525965 Score: 76
Period size: 10 Copynumber: 6.5 Consensus size: 10
6525893 TTCTCTTCTC
6525903 CTTTCCTTTT
1 CTTTCCTTTT
*
6525913 CTTTCCTTCT
1 CTTTCCTTTT
6525923 -TTTCC-TTT
1 CTTTCCTTTT
* *
6525931 CTTTCCTCTC
1 CTTTCCTTTT
6525941 CTTTCCTTTT
1 CTTTCCTTTT
*
6525951 CTTTCTTTTT
1 CTTTCCTTTT
6525961 CTTTC
1 CTTTC
6525966 TTTCTTCTTC
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
8 2 0.05
9 10 0.23
10 32 0.73
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (10 bp):
CTTTCCTTTT
Found at i:6525934 original size:28 final size:27
Alignment explanation
Indices: 6525854--6525948 Score: 84
Period size: 28 Copynumber: 3.4 Consensus size: 27
6525844 AATTACCTTT
* * **
6525854 TTTTCTTTCCCTCTTCTCCTTCTTTTT
1 TTTTCTTTCCTTCTTTTCCTTCTTTCC
* *
6525881 TTTTCTCTTCTCTTCTCTT-CTCCTTTCC
1 TTTTCT-TTC-CTTCTTTTCCTTCTTTCC
6525909 TTTTCTTTCCTTCTTTTCCTTTCTTTCC
1 TTTTCTTTCCTTCTTTTCC-TTCTTTCC
* *
6525937 TCTCCTTTCCTT
1 TTTTCTTTCCTT
6525949 TTCTTTCTTT
Statistics
Matches: 54, Mismatches: 10, Indels: 7
0.76 0.14 0.10
Matches are distributed among these distances:
26 7 0.13
27 10 0.19
28 32 0.59
29 5 0.09
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (27 bp):
TTTTCTTTCCTTCTTTTCCTTCTTTCC
Found at i:6525958 original size:14 final size:14
Alignment explanation
Indices: 6525903--6525980 Score: 52
Period size: 14 Copynumber: 5.4 Consensus size: 14
6525893 TTCTCTTCTC
6525903 CTTTCCTTTTCTTT
1 CTTTCCTTTTCTTT
*
6525917 CCTT-CTTTTCCTTT
1 CTTTCCTTTT-CTTT
* *
6525931 CTTTCCTCTCCTTT
1 CTTTCCTTTTCTTT
* *
6525945 CCTTTTCTTTCTTTTT
1 -CTTTCCTTT-TCTTT
*
6525961 CTTTCTTTCTTC-TT
1 CTTTCCTT-TTCTTT
6525975 CTTTCC
1 CTTTCC
6525981 CTCTCCTTCT
Statistics
Matches: 47, Mismatches: 12, Indels: 10
0.68 0.17 0.14
Matches are distributed among these distances:
13 5 0.11
14 21 0.45
15 17 0.36
16 4 0.09
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (14 bp):
CTTTCCTTTTCTTT
Found at i:6525965 original size:34 final size:34
Alignment explanation
Indices: 6525851--6525980 Score: 117
Period size: 34 Copynumber: 3.7 Consensus size: 34
6525841 AAAAATTACC
6525851 TTTT-TTTCTTTCC-CT-CTTCTCCTTCTT-TTT-T
1 TTTTCTTTCTTTCCTCTCCTT-TCCTT-TTCTTTCT
*
6525882 TTTCTCTTCTCTTCTCTTCTCCTTTCCTTTTCTTTCCTT
1 TTT-TCTT-TCTT-TCCTCTCCTTTCCTTTTCTTT-C-T
6525921 CTTTTCCTTTCTTTCCTCTCCTTTCCTTTTCTTTCT
1 -TTTT-CTTTCTTTCCTCTCCTTTCCTTTTCTTTCT
* *
6525957 TTTTCTTTCTTTCTTCTTCTTTCC
1 TTTTCTTTCTTTCCTCTCCTTTCC
6525981 CTCTCCTTCT
Statistics
Matches: 83, Mismatches: 4, Indels: 21
0.77 0.04 0.19
Matches are distributed among these distances:
31 3 0.04
32 1 0.01
33 2 0.02
34 22 0.27
35 8 0.10
36 11 0.13
37 4 0.05
38 20 0.24
39 6 0.07
40 6 0.07
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (34 bp):
TTTTCTTTCTTTCCTCTCCTTTCCTTTTCTTTCT
Found at i:6525966 original size:10 final size:10
Alignment explanation
Indices: 6525873--6525978 Score: 56
Period size: 10 Copynumber: 10.6 Consensus size: 10
6525863 CCTCTTCTCC
*
6525873 TTCTTTTTTT
1 TTCTTTTTCT
*
6525883 TTCTCTTCTCT
1 TTCT-TTTTCT
* *
6525894 TCTCTTCTCCT
1 T-TCTTTTTCT
*
6525905 TTCCTTTTCT
1 TTCTTTTTCT
* *
6525915 TTCCTTCT-T
1 TTCTTTTTCT
*
6525924 TTC-CTTTCT
1 TTCTTTTTCT
* * *
6525933 TTCCTCTCCT
1 TTCTTTTTCT
*
6525943 TTCCTTTTCT
1 TTCTTTTTCT
6525953 TTCTTTTTCT
1 TTCTTTTTCT
6525963 TTCTTTCTTC-
1 TTCTTT-TTCT
6525973 TTCTTT
1 TTCTTT
6525979 CCCTCTCCTT
Statistics
Matches: 74, Mismatches: 17, Indels: 10
0.73 0.17 0.10
Matches are distributed among these distances:
8 2 0.03
9 8 0.11
10 49 0.66
11 12 0.16
12 3 0.04
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (10 bp):
TTCTTTTTCT
Found at i:6526068 original size:27 final size:27
Alignment explanation
Indices: 6526037--6526095 Score: 100
Period size: 27 Copynumber: 2.2 Consensus size: 27
6526027 ATGGGCAGTA
6526037 CCGCCCATGGGAATGGCACCATCGGTG
1 CCGCCCATGGGAATGGCACCATCGGTG
* *
6526064 CCGCCCATGGGAATGGCACCTTTGGTG
1 CCGCCCATGGGAATGGCACCATCGGTG
6526091 CCGCC
1 CCGCC
6526096 ATCAGTGGCC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.15, C:0.36, G:0.32, T:0.17
Consensus pattern (27 bp):
CCGCCCATGGGAATGGCACCATCGGTG
Found at i:6534043 original size:2 final size:2
Alignment explanation
Indices: 6534036--6534065 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
6534026 ATAAAAGGCG
6534036 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6534066 CAATTACACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6535321 original size:63 final size:63
Alignment explanation
Indices: 6535253--6535509 Score: 514
Period size: 63 Copynumber: 4.1 Consensus size: 63
6535243 ATTTAATAAT
6535253 ATTATTAATATTTGTATGTAAATTATTAAATTAATTTGTTATATTAAAATATAAGCCCCGCAC
1 ATTATTAATATTTGTATGTAAATTATTAAATTAATTTGTTATATTAAAATATAAGCCCCGCAC
6535316 ATTATTAATATTTGTATGTAAATTATTAAATTAATTTGTTATATTAAAATATAAGCCCCGCAC
1 ATTATTAATATTTGTATGTAAATTATTAAATTAATTTGTTATATTAAAATATAAGCCCCGCAC
6535379 ATTATTAATATTTGTATGTAAATTATTAAATTAATTTGTTATATTAAAATATAAGCCCCGCAC
1 ATTATTAATATTTGTATGTAAATTATTAAATTAATTTGTTATATTAAAATATAAGCCCCGCAC
6535442 ATTATTAATATTTGTATGTAAATTATTAAATTAATTTGTTATATTAAAATATAAGCCCCGCAC
1 ATTATTAATATTTGTATGTAAATTATTAAATTAATTTGTTATATTAAAATATAAGCCCCGCAC
6535505 ATTAT
1 ATTAT
6535510 ATTGAAACGA
Statistics
Matches: 194, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 194 1.00
ACGTcount: A:0.40, C:0.09, G:0.08, T:0.43
Consensus pattern (63 bp):
ATTATTAATATTTGTATGTAAATTATTAAATTAATTTGTTATATTAAAATATAAGCCCCGCAC
Found at i:6536332 original size:6 final size:6
Alignment explanation
Indices: 6536323--6536350 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
6536313 TTCAATATTG
6536323 GAAAAA GAAAAA GAAAAA GAAAAA GAAA
1 GAAAAA GAAAAA GAAAAA GAAAAA GAAA
6536351 CTGAGTGACC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (6 bp):
GAAAAA
Found at i:6541141 original size:20 final size:19
Alignment explanation
Indices: 6541108--6541152 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
6541098 TTAAGTTTTT
6541108 AAAATTTTTGAAAAAGAATA
1 AAAATTTTTGAAAAA-AATA
*
6541128 AAAATATTTT-AAAAAATTA
1 AAAAT-TTTTGAAAAAAATA
6541147 AAAATT
1 AAAATT
6541153 AAAATTTATC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 1 0.04
19 8 0.35
20 10 0.43
21 4 0.17
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.33
Consensus pattern (19 bp):
AAAATTTTTGAAAAAAATA
Found at i:6542343 original size:6 final size:6
Alignment explanation
Indices: 6542332--6542357 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
6542322 TATATCATGT
6542332 TGATTA TGATTA TGATTA TGATTA TG
1 TGATTA TGATTA TGATTA TGATTA TG
6542358 GATAAAATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.19, T:0.50
Consensus pattern (6 bp):
TGATTA
Found at i:6543671 original size:11 final size:12
Alignment explanation
Indices: 6543645--6543698 Score: 60
Period size: 11 Copynumber: 4.8 Consensus size: 12
6543635 AACTAATCCT
6543645 CTCTCAAATTTC
1 CTCTCAAATTTC
*
6543657 CTCTC-AATTTG
1 CTCTCAAATTTC
*
6543668 CTCTTAAATTTC
1 CTCTCAAATTTC
*
6543680 TTC-CAAATTT-
1 CTCTCAAATTTC
6543690 CTCTCAAAT
1 CTCTCAAAT
6543699 CCATATTTAA
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
10 2 0.06
11 20 0.59
12 12 0.35
ACGTcount: A:0.26, C:0.28, G:0.02, T:0.44
Consensus pattern (12 bp):
CTCTCAAATTTC
Found at i:6543671 original size:23 final size:22
Alignment explanation
Indices: 6543644--6543698 Score: 67
Period size: 23 Copynumber: 2.5 Consensus size: 22
6543634 AAACTAATCC
6543644 TCTCTCAAATTTCCTCTC-AATT
1 TCTCTCAAATTTCCTC-CAAATT
* *
6543666 TGCTCTTAAATTTCTTCCAAATT
1 T-CTCTCAAATTTCCTCCAAATT
6543689 TCTCTCAAAT
1 TCTCTCAAAT
6543699 CCATATTTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
22 10 0.36
23 18 0.64
ACGTcount: A:0.25, C:0.27, G:0.02, T:0.45
Consensus pattern (22 bp):
TCTCTCAAATTTCCTCCAAATT
Found at i:6543739 original size:51 final size:51
Alignment explanation
Indices: 6543658--6543757 Score: 130
Period size: 51 Copynumber: 2.0 Consensus size: 51
6543648 TCAAATTTCC
* *
6543658 TCTCAATTTGCTCTTAAATTTCTTCCAAATTTCTCTCAAATCCATATTTAA
1 TCTCAATTTACTCTTAAATTTCCTCCAAATTTCTCTCAAATCCATATTTAA
* * * *
6543709 TCTCAATTTACTC-TCAATTTCCTCTTAAATTTCTCTTAAATCCCTATTT
1 TCTCAATTTACTCTTAAATTTCCTC-CAAATTTCTCTCAAATCCATATTT
6543758 TTAAATAATT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
50 9 0.21
51 33 0.79
ACGTcount: A:0.27, C:0.25, G:0.01, T:0.47
Consensus pattern (51 bp):
TCTCAATTTACTCTTAAATTTCCTCCAAATTTCTCTCAAATCCATATTTAA
Found at i:6544918 original size:7 final size:7
Alignment explanation
Indices: 6544906--6544931 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
6544896 TAGTCGATTG
6544906 GTATTTA
1 GTATTTA
6544913 GTATTTA
1 GTATTTA
6544920 GTATTTA
1 GTATTTA
6544927 GTATT
1 GTATT
6544932 ATGTATATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (7 bp):
GTATTTA
Found at i:6545607 original size:18 final size:18
Alignment explanation
Indices: 6545580--6545619 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
6545570 CAGGTGCGTT
* *
6545580 TCCTAGCCCTTTTATGTA
1 TCCTAACCCTTGTATGTA
*
6545598 TCCTAACCCTTGTATGTT
1 TCCTAACCCTTGTATGTA
6545616 TCCT
1 TCCT
6545620 TTTTCGAGTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.15, C:0.30, G:0.10, T:0.45
Consensus pattern (18 bp):
TCCTAACCCTTGTATGTA
Found at i:6546577 original size:13 final size:13
Alignment explanation
Indices: 6546559--6546610 Score: 61
Period size: 13 Copynumber: 4.0 Consensus size: 13
6546549 AGTTTAGCAA
6546559 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
*
6546572 TGCTTTTAAAAAG
1 TGCTTTTGAAAAG
*
6546585 TGC-TGTGAAAAAG
1 TGCTTTTG-AAAAG
*
6546598 TACTTTTGAAAAG
1 TGCTTTTGAAAAG
6546611 CTTGGTTTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
12 2 0.06
13 27 0.84
14 3 0.09
ACGTcount: A:0.37, C:0.08, G:0.21, T:0.35
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:6560619 original size:88 final size:89
Alignment explanation
Indices: 6560478--6560656 Score: 351
Period size: 88 Copynumber: 2.0 Consensus size: 89
6560468 GTTTTTTCAA
6560478 CTTATAGATGTGGAAATTGGTTTTTTTTTTTTGTGAAATTTCAAACTAAGGATGACTATAAGAAA
1 CTTATAGATGTGGAAATTGGTTTTTTTTTTTTGTGAAATTTCAAACTAAGGATGACTATAAGAAA
6560543 GTGTCACGGGGCTA-AGTTTTCGT
66 GTGTCACGGGGCTAGAGTTTTCGT
6560566 CTTATAGATGTGGAAATTGGTTTTTTTTTTTTGTGAAATTTCAAACTAAGGATGACTATAAGAAA
1 CTTATAGATGTGGAAATTGGTTTTTTTTTTTTGTGAAATTTCAAACTAAGGATGACTATAAGAAA
6560631 GTGTCACGGGGCTAGAGTTTTCGT
66 GTGTCACGGGGCTAGAGTTTTCGT
6560655 CT
1 CT
6560657 CTCGAGCCGT
Statistics
Matches: 90, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
88 79 0.88
89 11 0.12
ACGTcount: A:0.28, C:0.09, G:0.23, T:0.40
Consensus pattern (89 bp):
CTTATAGATGTGGAAATTGGTTTTTTTTTTTTGTGAAATTTCAAACTAAGGATGACTATAAGAAA
GTGTCACGGGGCTAGAGTTTTCGT
Found at i:6562244 original size:21 final size:20
Alignment explanation
Indices: 6562196--6562244 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
6562186 TTAGTTTTAA
*
6562196 ATGTTTTAGCCTTTAAAACC
1 ATGTTTTAGCCATTAAAACC
* *
6562216 AAGTTTTTAGCCATTAAATCGC
1 ATG-TTTTAGCCATTAAAAC-C
6562238 ATGTTTT
1 ATGTTTT
6562245 GAATAAAAGC
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 2 0.09
21 18 0.78
22 3 0.13
ACGTcount: A:0.29, C:0.16, G:0.12, T:0.43
Consensus pattern (20 bp):
ATGTTTTAGCCATTAAAACC
Found at i:6563412 original size:23 final size:23
Alignment explanation
Indices: 6563386--6563431 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
6563376 TGTTTCATAG
6563386 CTCAAGTGTCAAATTATCTTAAA
1 CTCAAGTGTCAAATTATCTTAAA
6563409 CTCAAGTGTCAAATTATCTTAAA
1 CTCAAGTGTCAAATTATCTTAAA
6563432 GTGTATTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.39, C:0.17, G:0.09, T:0.35
Consensus pattern (23 bp):
CTCAAGTGTCAAATTATCTTAAA
Found at i:6570191 original size:145 final size:146
Alignment explanation
Indices: 6569928--6570233 Score: 580
Period size: 145 Copynumber: 2.1 Consensus size: 146
6569918 TCTTATTCGA
6569928 TCAATCTCATTTATATCAATTTGGTATAGGATGTTGATATTTTAAATTAACTTTTTATTTTTATT
1 TCAATCTCATTTATATCAATTTGGTATAGGATGTTGATATTTTAAATTAACTTTTTATTTTTATT
6569993 TTAATAATTTTTTATAATTACATTTATTATTAAAATACAGTTATTAAATAAAGTTATCAAACTTA
66 TTAATAATTTTTTATAATTACATTTATTATTAAAATACAGTTATTAAATAAAGTTATCAAACTTA
6570058 ATT-AAATTTTAAATT
131 ATTAAAATTTTAAATT
6570073 TCAATCTCATTTATATCAATTTGGTATAGGATGTTGATATTTTAAATTAACTTTTTATTTTTATT
1 TCAATCTCATTTATATCAATTTGGTATAGGATGTTGATATTTTAAATTAACTTTTTATTTTTATT
6570138 TTAATAATTTTTTATAATTACATTTATTATTAAAATACAGTTATTAAATAAAGTTATCAAACTTA
66 TTAATAATTTTTTATAATTACATTTATTATTAAAATACAGTTATTAAATAAAGTTATCAAACTTA
6570203 ATTAAAATTTTAAATT
131 ATTAAAATTTTAAATT
* *
6570219 TTAATAT-ATTTATAT
1 TCAATCTCATTTATAT
6570234 GTATGTAATT
Statistics
Matches: 158, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
145 141 0.89
146 17 0.11
ACGTcount: A:0.38, C:0.06, G:0.05, T:0.51
Consensus pattern (146 bp):
TCAATCTCATTTATATCAATTTGGTATAGGATGTTGATATTTTAAATTAACTTTTTATTTTTATT
TTAATAATTTTTTATAATTACATTTATTATTAAAATACAGTTATTAAATAAAGTTATCAAACTTA
ATTAAAATTTTAAATT
Found at i:6581528 original size:12 final size:14
Alignment explanation
Indices: 6581489--6581524 Score: 63
Period size: 15 Copynumber: 2.5 Consensus size: 14
6581479 GACTCTATTT
6581489 TAATTATATTAAGA
1 TAATTATATTAAGA
6581503 TAATTAATATTAAGA
1 TAATT-ATATTAAGA
6581518 TAATTAT
1 TAATTAT
6581525 TAAGGATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 7 0.33
15 14 0.67
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (14 bp):
TAATTATATTAAGA
Found at i:6585824 original size:43 final size:43
Alignment explanation
Indices: 6585770--6586016 Score: 271
Period size: 43 Copynumber: 5.7 Consensus size: 43
6585760 TTCTAAAAAT
* * *
6585770 GCCGTTAAAGGTCATGGTCTTTAGCAGCGCTTACCACACAAAC
1 GCCGCTAAAGGTCATGGTCTTTAGCGGCGCTTACCAAACAAAC
*
6585813 GCCGCTAAAGGTCATGGTCTTTAGCGGCGCTTACCACACAAAC
1 GCCGCTAAAGGTCATGGTCTTTAGCGGCGCTTACCAAACAAAC
* * *
6585856 ACCGCTAAAGGTCATGGTCTTTAGCGGAGCTTACAAAACAAAC
1 GCCGCTAAAGGTCATGGTCTTTAGCGGCGCTTACCAAACAAAC
* * * *
6585899 TCCGCTGAAGGTCATGGACTTTAGCGGCGCTTACCAAACAAAT
1 GCCGCTAAAGGTCATGGTCTTTAGCGGCGCTTACCAAACAAAC
* * ** * **
6585942 GCCGCTAAA-GACAACGACCTTTAGCGGCGCTTCCCTTACAAAC
1 GCCGCTAAAGGTC-ATGGTCTTTAGCGGCGCTTACCAAACAAAC
*** * *
6585985 GCCGCTAAATACCCTGATCTTTAGCGGCGCTT
1 GCCGCTAAAGGTCATGGTCTTTAGCGGCGCTT
6586017 CTCTATAAAA
Statistics
Matches: 175, Mismatches: 27, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
42 2 0.01
43 172 0.98
44 1 0.01
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (43 bp):
GCCGCTAAAGGTCATGGTCTTTAGCGGCGCTTACCAAACAAAC
Found at i:6586007 original size:129 final size:129
Alignment explanation
Indices: 6585777--6586016 Score: 302
Period size: 129 Copynumber: 1.9 Consensus size: 129
6585767 AATGCCGTTA
* * * * **
6585777 AAGGTCATGGTCTTTAGCAGCGCTTACCACACAAACGCCGCTAAAGGTCATGGTCTTTAGCGGCG
1 AAGGTCATGGACTTTAGCAGCGCTTACCAAACAAACGCCGCTAAAGGACACGACCTTTAGCGGCG
** *
6585842 CTTACCACACAAACACCGCTAAAGGTCATGGTCTTTAGCGGAGCTTACAAAACAAACTCCGCTG
66 CTTACCACACAAACACCGCTAAAGACCATGATCTTTAGCGGAGCTTACAAAACAAACTCCGCTG
* *
6585906 AAGGTCATGGACTTTAGCGGCGCTTACCAAACAAATGCCGCTAAA-GACAACGACCTTTAGCGGC
1 AAGGTCATGGACTTTAGCAGCGCTTACCAAACAAACGCCGCTAAAGGAC-ACGACCTTTAGCGGC
* ** * * * *
6585970 GCTTCCCTTACAAACGCCGCTAAATACCCTGATCTTTAGCGGCGCTT
65 GCTTACCACACAAACACCGCTAAAGACCATGATCTTTAGCGGAGCTT
6586017 CTCTATAAAA
Statistics
Matches: 92, Mismatches: 18, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
128 2 0.02
129 90 0.98
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (129 bp):
AAGGTCATGGACTTTAGCAGCGCTTACCAAACAAACGCCGCTAAAGGACACGACCTTTAGCGGCG
CTTACCACACAAACACCGCTAAAGACCATGATCTTTAGCGGAGCTTACAAAACAAACTCCGCTG
Found at i:6586033 original size:129 final size:127
Alignment explanation
Indices: 6585759--6586037 Score: 292
Period size: 129 Copynumber: 2.2 Consensus size: 127
6585749 GCGGCGTTTA
* * *
6585759 TTTCTAAAAATGCCGTTAAAGGTCATGGTCTTTAGCAGCGCTTACCACACAAACGCCGCTAAAGG
1 TTTCTAAAAATGCCGCTAAAGGTCATGGACTTTAGCAGCGCTTACCAAACAAACGCCGCTAAAGG
* * ** ** *
6585824 TCATGGTCTTTAGCGGCGCTTACCACACAAACACCGCTAAAGGTCATGGTCTTTAGCGGAGC
66 ACACGACCTTTAGCGGCGCTTACCACACAAACACCGCTAAAGACCATGATCTTTAGCGGAGC
* * * * *
6585886 TTACAAAACAAACT-CCGCTGAAGGTCATGGACTTTAGCGGCGCTTACCAAACAAATGCCGCTAA
1 TTTC-TAA-AAA-TGCCGCTAAAGGTCATGGACTTTAGCAGCGCTTACCAAACAAACGCCGCTAA
* ** * * * *
6585950 A-GACAACGACCTTTAGCGGCGCTTCCCTTACAAACGCCGCTAAATACCCTGATCTTTAGCGGCG
63 AGGAC-ACGACCTTTAGCGGCGCTTACCACACAAACACCGCTAAAGACCATGATCTTTAGCGGAG
6586014 C
127 C
6586015 TTCTCTATAAAATGCCGCTAAAG
1 TT-TCTA-AAAATGCCGCTAAAG
6586038 ACCCTGATCT
Statistics
Matches: 120, Mismatches: 25, Indels: 12
0.76 0.16 0.08
Matches are distributed among these distances:
127 3 0.03
128 5 0.04
129 109 0.91
130 3 0.03
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.23
Consensus pattern (127 bp):
TTTCTAAAAATGCCGCTAAAGGTCATGGACTTTAGCAGCGCTTACCAAACAAACGCCGCTAAAGG
ACACGACCTTTAGCGGCGCTTACCACACAAACACCGCTAAAGACCATGATCTTTAGCGGAGC
Found at i:6586128 original size:43 final size:43
Alignment explanation
Indices: 6585782--6586142 Score: 229
Period size: 43 Copynumber: 8.4 Consensus size: 43
6585772 CGTTAAAGGT
* * * **
6585782 CATGGTCTTTAGCAGCGCTTAC-CACACAAACGCCGCTAAAGGT
1 CATGATCTTTAGCGGCGCTTTCAC-CACAAACGCCGCTAAAGAC
* * * **
6585825 CATGGTCTTTAGCGGCGCTTAC-CACACAAACACCGCTAAAGGT
1 CATGATCTTTAGCGGCGCTTTCAC-CACAAACGCCGCTAAAGAC
* * * ** * * **
6585868 CATGGTCTTTAGCGGAGCTTACAAAACAAACTCCGCTGAAGGT
1 CATGATCTTTAGCGGCGCTTTCACCACAAACGCCGCTAAAGAC
*
6585911 CATGGA-CTTTAGCGGCGC-TT-ACCAAACAAATGCCGCTAAAGAC
1 CAT-GATCTTTAGCGGCGCTTTCACC--ACAAACGCCGCTAAAGAC
* * * *
6585954 AACGACCTTTAGCGGCGC-TTC-CCTTACAAACGCCGCTAAATAC
1 CATGATCTTTAGCGGCGCTTTCACC--ACAAACGCCGCTAAAGAC
* * *
6585997 CCTGATCTTTAGCGGCGCTTCTCTA-TA-AAATGCCGCTAAAGAC
1 CATGATCTTTAGCGGCGCTT-TC-ACCACAAACGCCGCTAAAGAC
* * * * *
6586040 CCTGATCTTTAGCGGTGTTTTTCTCCA-AAACGCCGCTAAATAC
1 CATGATCTTTAGCGGCG-CTTTCACCACAAACGCCGCTAAAGAC
* *
6586083 CATGATCTTTAGCGGTGCTTTCACCACAAACGCCGCTATAGAC
1 CATGATCTTTAGCGGCGCTTTCACCACAAACGCCGCTAAAGAC
* * *
6586126 CATTACCTTTAGTGGCG
1 CATGATCTTTAGCGGCG
6586143 TTTTTTTAAA
Statistics
Matches: 260, Mismatches: 45, Indels: 26
0.79 0.14 0.08
Matches are distributed among these distances:
41 1 0.00
42 10 0.04
43 242 0.93
44 5 0.02
45 2 0.01
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.24
Consensus pattern (43 bp):
CATGATCTTTAGCGGCGCTTTCACCACAAACGCCGCTAAAGAC
Found at i:6586642 original size:66 final size:66
Alignment explanation
Indices: 6586476--6586643 Score: 207
Period size: 66 Copynumber: 2.5 Consensus size: 66
6586466 CTCACTACAG
* * *
6586476 CCTCTGCTTCTCTC-ACTGTCGCATCTGCTTTAAGCTGCTGCTGGAGTTCTTCATGCTTTCGTTG
1 CCTCAGCTTCTCTCGA-TGTTGCATCTGCTTTAAGTTGCTGCTGGAGTTCTTCATGCTTTCGTTG
6586540 AA
65 AA
* * * *
6586542 CCTCAGCTTCTCTCGCTGCTGCATCTGCTTTAAGTTG-TAGCTGGAGTTCTTCATATCTTT-TTT
1 CCTCAGCTTCTCTCGATGTTGCATCTGCTTTAAGTTGCT-GCTGGAGTTCTTCAT-GCTTTCGTT
6586605 GAA
64 GAA
* *
6586608 CCTCAGCTTCTCTCGATGTTGCCTCCGCTTTAAGTT
1 CCTCAGCTTCTCTCGATGTTGCATCTGCTTTAAGTT
6586644 TTGTAATTTG
Statistics
Matches: 88, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
65 1 0.01
66 83 0.94
67 4 0.05
ACGTcount: A:0.13, C:0.28, G:0.18, T:0.40
Consensus pattern (66 bp):
CCTCAGCTTCTCTCGATGTTGCATCTGCTTTAAGTTGCTGCTGGAGTTCTTCATGCTTTCGTTGA
A
Found at i:6590685 original size:23 final size:22
Alignment explanation
Indices: 6590646--6590706 Score: 81
Period size: 23 Copynumber: 2.8 Consensus size: 22
6590636 ACATTATTTA
6590646 TATATTTTT--AATTTAATCTC
1 TATATTTTTAAAATTTAATCTC
*
6590666 TTTATTTTTAAAAATTTAATCTC
1 TATATTTTT-AAAATTTAATCTC
*
6590689 TATATTTTTCAAATTTAA
1 TATATTTTTAAAATTTAA
6590707 AAATTTAGGT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
20 8 0.23
22 8 0.23
23 19 0.54
ACGTcount: A:0.34, C:0.08, G:0.00, T:0.57
Consensus pattern (22 bp):
TATATTTTTAAAATTTAATCTC
Found at i:6591048 original size:22 final size:23
Alignment explanation
Indices: 6591000--6591042 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
6590990 TCCTATACAC
* *
6591000 AATTTATATTATTTTTAATAAAA
1 AATTCATATTATTTTCAATAAAA
6591023 AATTCATATTA-TTTCAATAA
1 AATTCATATTATTTTCAATAA
6591043 TTAATTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.49
Consensus pattern (23 bp):
AATTCATATTATTTTCAATAAAA
Found at i:6612361 original size:20 final size:20
Alignment explanation
Indices: 6612337--6612411 Score: 96
Period size: 20 Copynumber: 3.8 Consensus size: 20
6612327 GAAAATAAGA
* *
6612337 GCACCGAAGTGCGAATAGGG
1 GCACCGAAGTGCAAACAGGG
* * * *
6612357 ACACCAAAGTGTATACAGGG
1 GCACCGAAGTGCAAACAGGG
6612377 GCACCGAAGTGCAAACAGGG
1 GCACCGAAGTGCAAACAGGG
6612397 GCACCGAAGTGCAAA
1 GCACCGAAGTGCAAA
6612412 ATCCCGTACA
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.36, C:0.23, G:0.32, T:0.09
Consensus pattern (20 bp):
GCACCGAAGTGCAAACAGGG
Found at i:6613786 original size:11 final size:11
Alignment explanation
Indices: 6613766--6613799 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
6613756 TTAAAATTTC
*
6613766 TTAATGAAACT
1 TTAATAAAACT
*
6613777 TTAATAAAACC
1 TTAATAAAACT
6613788 TTAATAAAACT
1 TTAATAAAACT
6613799 T
1 T
6613800 CGTAAGTATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.50, C:0.12, G:0.03, T:0.35
Consensus pattern (11 bp):
TTAATAAAACT
Found at i:6617164 original size:105 final size:105
Alignment explanation
Indices: 6616947--6617172 Score: 244
Period size: 105 Copynumber: 2.2 Consensus size: 105
6616937 CACACACCCA
* * * * *
6616947 TGTCCTTGCCCATGTGGCTCACATATCCTAGGCACATGCCCATGTCCTCTACCTGTGTGGTTCTA
1 TGTCCTTGCCCATGTGACTCACATAGCCTAGGCACACGCCCATGTCCTCTACCTGTATGGTCCTA
* * * * *
6617012 AAGCATAAGTAGTGAGTTACACGGCCTAGGCACATGTCTG
66 AAGCACAAATAGAGAGTTACACGGCCTAGGCAAACGTCTG
* * * *
6617052 TGTCCTTGCCCGTGTGACTCACATGGCCTGGGCACACGCCCATGTCC-CTGGCC-GTATGGTCCT
1 TGTCCTTGCCCATGTGACTCACATAGCCTAGGCACACGCCCATGTCCTCT-ACCTGTATGGTCCT
* *
6617115 AAATCACAAATAGAGAGTTACACGG-CTTGGACAAACG-CTGG
65 AAAGCACAAATAGAGAGTTACACGGCCTAGG-CAAACGTCT-G
6617156 TGTGCCTTGCCCATGTG
1 TGT-CCTTGCCCATGTG
6617173 GCTCCAAATC
Statistics
Matches: 100, Mismatches: 17, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
103 6 0.06
104 39 0.39
105 55 0.55
ACGTcount: A:0.20, C:0.29, G:0.25, T:0.26
Consensus pattern (105 bp):
TGTCCTTGCCCATGTGACTCACATAGCCTAGGCACACGCCCATGTCCTCTACCTGTATGGTCCTA
AAGCACAAATAGAGAGTTACACGGCCTAGGCAAACGTCTG
Found at i:6619890 original size:90 final size:88
Alignment explanation
Indices: 6619556--6620016 Score: 536
Period size: 90 Copynumber: 5.2 Consensus size: 88
6619546 AACAAAATAA
* * * *
6619556 ATTTATAGATACAAGAAAATACGAAAATTCTAGAAAACTAATATACGAAAATATAAAATTTGACC
1 ATTTACAGATACAA-AAAATACGAACATTCTAGAAAACTGATATACGAAAATATAAAATTCGACC
* *
6619621 AACATATAATACAGGCTAAAATTG
65 AACAAATAATACAGACTAAAATTG
* * * *
6619645 ATTTACAGATACAAAAAATACAAATATTTTAGAAAATTGATATACGAAAATATAAAATTCGACCA
1 ATTTACAGATACAAAAAATACGAACATTCTAGAAAACTGATATACGAAAATATAAAATTCGACCA
* *
6619710 ACAAATAATA-GGGCTAAAATTG
66 ACAAATAATACAGACTAAAATTG
* *
6619732 ATTTACAGATACAAAAAATATGATCATTCTAGAAAACTGATATACGAAAATATAAAATTCGACCA
1 ATTTACAGATACAAAAAATACGAACATTCTAGAAAACTGATATACGAAAATATAAAATTCGACCA
6619797 ACAAATAATACAGACTAAAATAT-
66 ACAAATAATACAGACTAAAAT-TG
* * * * *
6619820 TTTTACAAAT-CTAAAATTATTACGAACATTCTAGAAAACTAATATACAAAAATATAAAATTCGA
1 ATTTACAGATAC-AAAA--AATACGAACATTCTAGAAAACTGATATACGAAAATATAAAATTCGA
*
6619884 CAAACAAATAATAC-GAACTAAAATAT-
63 CCAACAAATAATACAG-ACTAAAAT-TG
* ** * * * * * * *
6619910 TTTTATTGATCCAAAAATAATTCTATCATTTTACAAAACTGATATATGAAAATATAAAATTCGAC
1 ATTTACAGATAC-AAAA-AATACGAACATTCTAGAAAACTGATATACGAAAATATAAAATTCGAC
6619975 CAACAAATAATACAGACTAAAATTG
64 CAACAAATAATACAGACTAAAATTG
6620000 ATTTACAGATACAAAAA
1 ATTTACAGATACAAAAA
6620017 TAATAAGAAA
Statistics
Matches: 320, Mismatches: 43, Indels: 19
0.84 0.11 0.05
Matches are distributed among these distances:
87 81 0.25
88 75 0.23
89 20 0.06
90 138 0.43
91 6 0.02
ACGTcount: A:0.52, C:0.12, G:0.08, T:0.27
Consensus pattern (88 bp):
ATTTACAGATACAAAAAATACGAACATTCTAGAAAACTGATATACGAAAATATAAAATTCGACCA
ACAAATAATACAGACTAAAATTG
Found at i:6619986 original size:180 final size:175
Alignment explanation
Indices: 6619556--6620016 Score: 534
Period size: 175 Copynumber: 2.6 Consensus size: 175
6619546 AACAAAATAA
* * ** * * *
6619556 ATTTATAGATACAAGAAAATACGAAAATTCTAGAAAACTAATATACGAAAATATAAAATTTGACC
1 ATTTACAGATACAA-AAAATATGATCATTCTACAAAACTGATATACGAAAATATAAAATTCGACC
* * * * * * *
6619621 AACATATAATACAGGCTAAAATTGATTTACAGATACAAAAAATACAAATATTTTAGAAAATTGAT
65 AACAAATAATACAGACTAAAATTGATTTACAAATACAAAAAATACAAACATTCTAGAAAACTAAT
* * **
6619686 ATACGAAAATATAAAATTCGACCAACAAATAATAGGGCTAAAATTG
130 ATACAAAAATATAAAATTCGACAAACAAATAATAGAACTAAAATTG
*
6619732 ATTTACAGATACAAAAAATATGATCATTCTAGAAAACTGATATACGAAAATATAAAATTCGACCA
1 ATTTACAGATACAAAAAATATGATCATTCTACAAAACTGATATACGAAAATATAAAATTCGACCA
* * *
6619797 ACAAATAATACAGACTAAAATAT-TTTTACAAAT-CTAAAATTATTACGAACATTCTAGAAAACT
66 ACAAATAATACAGACTAAAAT-TGATTTACAAATAC-AAAA--AATACAAACATTCTAGAAAACT
6619860 AATATACAAAAATATAAAATTCGACAAACAAATAATACGAACTAAAATAT-
127 AATATACAAAAATATAAAATTCGACAAACAAATAATA-GAACTAAAAT-TG
* ** * * * *
6619910 TTTTATTGAT-CCAAAAATAATTCTATCATTTTACAAAACTGATATATGAAAATATAAAATTCGA
1 ATTTACAGATACAAAAAAT-A-T-GATCATTCTACAAAACTGATATACGAAAATATAAAATTCGA
*
6619974 CCAACAAATAATACAGACTAAAATTGATTTACAGATACAAAAA
63 CCAACAAATAATACAGACTAAAATTGATTTACAAATACAAAAA
6620017 TAATAAGAAA
Statistics
Matches: 244, Mismatches: 30, Indels: 20
0.83 0.10 0.07
Matches are distributed among these distances:
174 1 0.00
175 77 0.32
176 14 0.06
177 58 0.24
178 17 0.07
179 3 0.01
180 73 0.30
181 1 0.00
ACGTcount: A:0.52, C:0.12, G:0.08, T:0.27
Consensus pattern (175 bp):
ATTTACAGATACAAAAAATATGATCATTCTACAAAACTGATATACGAAAATATAAAATTCGACCA
ACAAATAATACAGACTAAAATTGATTTACAAATACAAAAAATACAAACATTCTAGAAAACTAATA
TACAAAAATATAAAATTCGACAAACAAATAATAGAACTAAAATTG
Found at i:6620490 original size:57 final size:58
Alignment explanation
Indices: 6620429--6620553 Score: 139
Period size: 58 Copynumber: 2.2 Consensus size: 58
6620419 GGGATGCTGA
** * *
6620429 CCATCAGTGTCCCAGTGCCCAAA-AATATATTTTTT-AATTCTGGTACAAGGGTG-TCGG
1 CCATCAGTGTCCCAGCACCAAAAGAAT-TATTTTTTAAATTCTGGTACAAGGGTGCT-AG
* * * *
6620486 CCATCTGTGTCCTAGCACCAAAAGAATTATTTTTTAAATTTTGGTATAAGGGTGCTAG
1 CCATCAGTGTCCCAGCACCAAAAGAATTATTTTTTAAATTCTGGTACAAGGGTGCTAG
6620544 CCATCAGTGT
1 CCATCAGTGT
6620554 GTTAGCACCC
Statistics
Matches: 56, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
57 26 0.46
58 29 0.52
59 1 0.02
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (58 bp):
CCATCAGTGTCCCAGCACCAAAAGAATTATTTTTTAAATTCTGGTACAAGGGTGCTAG
Found at i:6622832 original size:2 final size:2
Alignment explanation
Indices: 6622825--6622850 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
6622815 AACCTATCTC
6622825 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
6622851 GTGAAGTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6628232 original size:27 final size:26
Alignment explanation
Indices: 6628192--6628248 Score: 69
Period size: 27 Copynumber: 2.2 Consensus size: 26
6628182 CACAAAGAAA
*
6628192 AGTTCAGTGCCTGGAGAAAAGCTTGG
1 AGTTCAGTGCCTGGACAAAAGCTTGG
* * *
6628218 AGTTCTAGTTCCTGGACTAAAGCTTGT
1 AGTTC-AGTGCCTGGACAAAAGCTTGG
6628245 AGTT
1 AGTT
6628249 GTGCTGATTG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
26 5 0.19
27 21 0.81
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.32
Consensus pattern (26 bp):
AGTTCAGTGCCTGGACAAAAGCTTGG
Found at i:6633997 original size:17 final size:18
Alignment explanation
Indices: 6633965--6634009 Score: 56
Period size: 17 Copynumber: 2.5 Consensus size: 18
6633955 TTAAGAATTT
6633965 AAAAATTAAATAAATTAAC
1 AAAAA-TAAATAAATTAAC
*
6633984 AAAAATAAAT-AATTAAG
1 AAAAATAAATAAATTAAC
*
6634001 ATAAATAAA
1 AAAAATAAA
6634010 AGAGAACAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 14 0.58
18 5 0.21
19 5 0.21
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.24
Consensus pattern (18 bp):
AAAAATAAATAAATTAAC
Found at i:6634053 original size:12 final size:12
Alignment explanation
Indices: 6634036--6634060 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
6634026 AAGATTAGAC
6634036 AATAAAGAAGAT
1 AATAAAGAAGAT
6634048 AATAAAGAAGAT
1 AATAAAGAAGAT
6634060 A
1 A
6634061 GATGGAAAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.00, G:0.16, T:0.16
Consensus pattern (12 bp):
AATAAAGAAGAT
Found at i:6640733 original size:31 final size:31
Alignment explanation
Indices: 6640693--6640752 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
6640683 TTGGTGATTT
* *
6640693 AAATGAAAACTTTC-TACTAATTTAGTGACCA
1 AAATAAAAACTTACTTA-TAATTTAGTGACCA
*
6640724 AAATAAAAACTTACTTATAGTTTAGTGAC
1 AAATAAAAACTTACTTATAATTTAGTGAC
6640753 TAATAATGTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 23 0.92
32 2 0.08
ACGTcount: A:0.43, C:0.13, G:0.10, T:0.33
Consensus pattern (31 bp):
AAATAAAAACTTACTTATAATTTAGTGACCA
Found at i:6642213 original size:132 final size:132
Alignment explanation
Indices: 6641976--6642253 Score: 547
Period size: 132 Copynumber: 2.1 Consensus size: 132
6641966 TTTTTTCAGG
6641976 TCTTTAGCGGCGCTTTTTAGCGCCACTAAAAGTATTTGCGGCGCTTTCACAAGTGCTGCAAAAAA
1 TCTTTAGCGGCGCTTTTTAGCGCCACTAAAAGTATTTGCGGCGCTTTCACAAGTGCTGCAAAAAA
6642041 TACCGCTATTGACAACGCCGGTAACATTTGCGGCGTTTATTTTTATAAACGCCACTAAAGGTCAT
66 TACCGCTATTGACAACGCCGGTAACATTTGCGGCGTTTATTTTTATAAACGCCACTAAAGGTCAT
6642106 GT
131 GT
6642108 TCTTTAGCGGCGCTTTTTAGCGCCACTAAAAGTATTTGCGGCGCTTTCACAAGTGCTGCAAAAAA
1 TCTTTAGCGGCGCTTTTTAGCGCCACTAAAAGTATTTGCGGCGCTTTCACAAGTGCTGCAAAAAA
6642173 TACCGCTATTGACAACGCCGGTAACATTTGCGGCGTTTATTTTTATAAACGCCACTAAAGGTCAT
66 TACCGCTATTGACAACGCCGGTAACATTTGCGGCGTTTATTTTTATAAACGCCACTAAAGGTCAT
6642238 GT
131 GT
*
6642240 TCTTCAGCGGCGCT
1 TCTTTAGCGGCGCT
6642254 ACAAAAAAAA
Statistics
Matches: 145, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
132 145 1.00
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (132 bp):
TCTTTAGCGGCGCTTTTTAGCGCCACTAAAAGTATTTGCGGCGCTTTCACAAGTGCTGCAAAAAA
TACCGCTATTGACAACGCCGGTAACATTTGCGGCGTTTATTTTTATAAACGCCACTAAAGGTCAT
GT
Found at i:6642320 original size:43 final size:42
Alignment explanation
Indices: 6642219--6642564 Score: 377
Period size: 43 Copynumber: 8.1 Consensus size: 42
6642209 TTATTTTTAT
* * * ***** *
6642219 AAACGCCACTAAAGGTCATGTTCTTCAGCGGCGCTACAAAAA
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTTCCAC
* * *
6642261 AAACGCCGCTAAAGGTCAGGGTCTTTAGCGGCGCTTTTCCTAC
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTTCC-AC
* * *
6642304 AAACACCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTTTCAAC
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGC-TTTTCCAC
* * *
6642347 AAACACCGCTGAAGATCATGTTCCTTAGCGGCGCTTGTTCCAC
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTT-TTCCAC
* *
6642390 AAACGCCGCTAAAGATCATGTTCCTTAGCGGCGATTTTTCCAC
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCG-CTTTTCCAC
*
6642433 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTTTCCAT
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGC-TTTTCCAC
*
6642476 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTCTTCCGC
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTT-TTCCAC
* * * * * *
6642519 AAATGCCACTAAAGGTCATGTTATTTTAGCGGCGTTTTTACAC
1 AAACGCCGCTAAAGATCATGTT-CTTTAGCGGCGCTTTTCCAC
6642562 AAA
1 AAA
6642565 TGCCTCTATT
Statistics
Matches: 264, Mismatches: 33, Indels: 13
0.85 0.11 0.04
Matches are distributed among these distances:
42 35 0.13
43 210 0.80
44 19 0.07
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.28
Consensus pattern (42 bp):
AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTTCCAC
Found at i:6642568 original size:43 final size:43
Alignment explanation
Indices: 6642261--6642564 Score: 396
Period size: 43 Copynumber: 7.1 Consensus size: 43
6642251 GCTACAAAAA
* * *
6642261 AAACGCCGCTAAAGGTCAGGGTCTTTAGCGGCGC-TTTTCCTAC
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTTTCC-AC
* * *
6642304 AAACACCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTTTCAAC
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTTTCCAC
* * * *
6642347 AAACACCGCTGAAGATCATGTTCCTTAGCGGCGCTTGTTCCAC
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTTTCCAC
* *
6642390 AAACGCCGCTAAAGATCATGTTCCTTAGCGGCGATTTTTCCAC
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTTTCCAC
*
6642433 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTTTCCAT
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTTTCCAC
* *
6642476 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTCTTCCGC
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTTTCCAC
* * * * *
6642519 AAATGCCACTAAAGGTCATGTTATTTTAGCGGCG-TTTTTACAC
1 AAACGCCGCTAAAGATCATGTT-CTTTAGCGGCGCTTTTTCCAC
6642562 AAA
1 AAA
6642565 TGCCTCTATT
Statistics
Matches: 233, Mismatches: 26, Indels: 4
0.89 0.10 0.02
Matches are distributed among these distances:
43 218 0.94
44 15 0.06
ACGTcount: A:0.25, C:0.26, G:0.20, T:0.29
Consensus pattern (43 bp):
AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTTTCCAC
Found at i:6643036 original size:21 final size:21
Alignment explanation
Indices: 6643012--6643052 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
6643002 TGAACCTTTG
*
6643012 CTTCTCTCGCTGCAGCCTCTA
1 CTTCCCTCGCTGCAGCCTCTA
*
6643033 CTTCCCTCGCTGCCGCCTCT
1 CTTCCCTCGCTGCAGCCTCT
6643053 GCTTTAAGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.05, C:0.49, G:0.15, T:0.32
Consensus pattern (21 bp):
CTTCCCTCGCTGCAGCCTCTA
Found at i:6646560 original size:22 final size:22
Alignment explanation
Indices: 6646534--6646579 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
6646524 AAACTCTATT
6646534 CCTTAGACCC-TAAACCGTAAAC
1 CCTTA-ACCCTTAAACCGTAAAC
*
6646556 CCTTAACCCTTAAACCTTAAAC
1 CCTTAACCCTTAAACCGTAAAC
6646578 CC
1 CC
6646580 ACGAACCCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.35, C:0.39, G:0.04, T:0.22
Consensus pattern (22 bp):
CCTTAACCCTTAAACCGTAAAC
Found at i:6646591 original size:22 final size:21
Alignment explanation
Indices: 6646540--6646592 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 21
6646530 TATTCCTTAG
**
6646540 ACCCTAAACCGTAAACCCTTA
1 ACCCTAAACCGTAAACCCCGA
*
6646561 ACCCTTAAACCTTAAACCCACGA
1 ACCC-TAAACCGTAAACCC-CGA
6646584 ACCCTAAAC
1 ACCCTAAAC
6646593 AATAATGTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 4 0.15
22 18 0.67
23 5 0.19
ACGTcount: A:0.40, C:0.40, G:0.04, T:0.17
Consensus pattern (21 bp):
ACCCTAAACCGTAAACCCCGA
Found at i:6646842 original size:21 final size:22
Alignment explanation
Indices: 6646800--6646844 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
6646790 ATTAACTGTA
* **
6646800 AACCCTCAAACCCTTAGCCCTT
1 AACCCTCAAACACTTAAACCTT
6646822 AACCCT-AAACACTTAAACCTT
1 AACCCTCAAACACTTAAACCTT
6646843 AA
1 AA
6646845 ATCCCAACTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.38, C:0.38, G:0.02, T:0.22
Consensus pattern (22 bp):
AACCCTCAAACACTTAAACCTT
Found at i:6646940 original size:14 final size:14
Alignment explanation
Indices: 6646920--6646952 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
6646910 TAGAACATAT
6646920 ATAAACCCTAAATC
1 ATAAACCCTAAATC
*
6646934 CTAAACCCTAAATC
1 ATAAACCCTAAATC
6646948 ATAAA
1 ATAAA
6646953 ATATATATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.52, C:0.27, G:0.00, T:0.21
Consensus pattern (14 bp):
ATAAACCCTAAATC
Found at i:6646978 original size:39 final size:40
Alignment explanation
Indices: 6646892--6646979 Score: 108
Period size: 39 Copynumber: 2.2 Consensus size: 40
6646882 CTGGCCATAT
* * *
6646892 TCCTTAAACCCCGAATCATAGAACATATATAAACCCTAAA
1 TCCTTAAACCCCAAATCATAAAACATATATAAACCATAAA
* * *
6646932 TCC-TAAACCCTAAATCATAAAATATATATAAACTATAAA
1 TCCTTAAACCCCAAATCATAAAACATATATAAACCATAAA
6646971 -CCTTAAACC
1 TCCTTAAACC
6646980 TCAACCCTTA
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
38 2 0.05
39 36 0.88
40 3 0.07
ACGTcount: A:0.48, C:0.25, G:0.02, T:0.25
Consensus pattern (40 bp):
TCCTTAAACCCCAAATCATAAAACATATATAAACCATAAA
Found at i:6647629 original size:208 final size:207
Alignment explanation
Indices: 6647369--6648026 Score: 996
Period size: 208 Copynumber: 3.2 Consensus size: 207
6647359 TTTTGGCAAT
* * * * * ** * * *
6647369 GCGCCACTAATGTCTCTAAATCTGAAAAAGAAAACACTATCGTTTGCCTAAAACTATTATCGATA
1 GCGCCACTATTGTGTCTAAAACTCAACAAGAAAACGTTGTCATTTGCCTAAAACTATTACCGATA
*
6647434 ATGCTTGAATTTTACTGCGTTTTTCGCGAAGCGCCACTAATGTCCCTAAGCACAACAGAAAACGA
66 ATGCTTGAATTTTACCGCGTTTTTCGCGAAGCGCCACTAATGTCCCTAAGCACAACAGAAAACGA
** * *
6647499 CGGCGTATGCTTAAAACTTTTTGCGGCGCTT-TAGAGGAAGCGCTGCTAATGATTGACTTTAGCG
131 CGGCGTATGCTTAAAACTTTTTGCGGCGCTTCTCTA--AAGCGCCGCTAATGATTGACTTCAGCG
*
6647563 GCGATTTCTTCGAA
194 GCGATTTCTTTGAA
6647577 GCGCCACTATTGTGTCTAAAACTCAACAAGAAAACGTTGTCATTTGCCTAAAACTATTACCGATA
1 GCGCCACTATTGTGTCTAAAACTCAACAAGAAAACGTTGTCATTTGCCTAAAACTATTACCGATA
* * * *
6647642 ATGCTTGATTTTTGCCGCATTTTTCGCGAAGCGCCACTAATGTCCCTAAGCACAACAAAAAACGA
66 ATGCTTGAATTTTACCGCGTTTTTCGCGAAGCGCCACTAATGTCCCTAAGCACAACAGAAAACGA
*
6647707 CGGCGTATGCTTAAAACTTTTTGCGGCGCTTCCTCTAAAGCGCCGCTAATGATTGACTTCAGCAG
131 CGGCGTATGCTTAAAACTTTTTGCGGCGCTT-CTCTAAAGCGCCGCTAATGATTGACTTCAGCGG
6647772 CGATTTCTTTGAA
195 CGATTTCTTTGAA
*
6647785 GCGTCACTATTGTGTCTAAAACTCAACAAGAAAACGTTGTCATTTGCCTAAAACTATTACCGATA
1 GCGCCACTATTGTGTCTAAAACTCAACAAGAAAACGTTGTCATTTGCCTAAAACTATTACCGATA
* * * * *
6647850 ATGCTTGACTTTTACGGCGTTTTTTGCAAAGCGTCACTAATGTCCCTAAGCACAACAGAAAACGA
66 ATGCTTGAATTTTACCGCGTTTTTCGCGAAGCGCCACTAATGTCCCTAAGCACAACAGAAAACGA
*
6647915 CGGCGTATGCTTAAAACTTTTTGCGGCGCTTCCTCTAAAGCACCGCTAATGATTGACTTCAGCGG
131 CGGCGTATGCTTAAAACTTTTTGCGGCGCTT-CTCTAAAGCGCCGCTAATGATTGACTTCAGCGG
*
6647980 CGATTTCTTTGTA
195 CGATTTCTTTGAA
6647993 GCGCCACTATTG-GTTCTAAAACTCAACAAGAAAA
1 GCGCCACTATTGTG-TCTAAAACTCAACAAGAAAA
6648027 TGACGTCGTT
Statistics
Matches: 413, Mismatches: 34, Indels: 6
0.91 0.08 0.01
Matches are distributed among these distances:
207 1 0.00
208 410 0.99
210 2 0.00
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (207 bp):
GCGCCACTATTGTGTCTAAAACTCAACAAGAAAACGTTGTCATTTGCCTAAAACTATTACCGATA
ATGCTTGAATTTTACCGCGTTTTTCGCGAAGCGCCACTAATGTCCCTAAGCACAACAGAAAACGA
CGGCGTATGCTTAAAACTTTTTGCGGCGCTTCTCTAAAGCGCCGCTAATGATTGACTTCAGCGGC
GATTTCTTTGAA
Found at i:6650077 original size:8 final size:9
Alignment explanation
Indices: 6650005--6650096 Score: 96
Period size: 9 Copynumber: 10.2 Consensus size: 9
6649995 TTGGGTAATT
6650005 TTCGGGTAA
1 TTCGGGTAA
6650014 TTCGGGTAA
1 TTCGGGTAA
**
6650023 TTTATGGTAA
1 -TTCGGGTAA
*
6650033 TTCGGTTAA
1 TTCGGGTAA
* *
6650042 TTTGGTTAA
1 TTCGGGTAA
*
6650051 TTCGGTTAA
1 TTCGGGTAA
*
6650060 TTCGGTTAA
1 TTCGGGTAA
6650069 -TCGGGTAA
1 TTCGGGTAA
*
6650077 TTCTGGTAA
1 TTCGGGTAA
6650086 TTCGGGTAA
1 TTCGGGTAA
6650095 TT
1 TT
6650097 TTTAACCAAA
Statistics
Matches: 71, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
8 7 0.10
9 57 0.80
10 7 0.10
ACGTcount: A:0.23, C:0.09, G:0.26, T:0.42
Consensus pattern (9 bp):
TTCGGGTAA
Found at i:6652241 original size:17 final size:16
Alignment explanation
Indices: 6652216--6652252 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
6652206 TAATAATCAA
6652216 TATTAGTCAAAAAATTT
1 TATTAGTC-AAAAATTT
*
6652233 TATTGGTCAAAAATTT
1 TATTAGTCAAAAATTT
6652249 TATT
1 TATT
6652253 TTTATTCTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.63
17 7 0.37
ACGTcount: A:0.41, C:0.05, G:0.08, T:0.46
Consensus pattern (16 bp):
TATTAGTCAAAAATTT
Done.