Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D01
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: 64473564
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1880000 characters in sequence are not A, C, G, or T
File 175 of 213
Found at i:52710992 original size:12 final size:14
Alignment explanation
Indices: 52710956--52710990 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
52710946 AGGCCTTAAC
*
52710956 TTGATTTTTAGTTA
1 TTGATTTTTAATTA
52710970 TTGATTTTTAATTA
1 TTGATTTTTAATTA
52710984 TT-ATTTT
1 TTGATTTT
52710991 AACCTTAGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 5 0.25
14 15 0.75
ACGTcount: A:0.23, C:0.00, G:0.09, T:0.69
Consensus pattern (14 bp):
TTGATTTTTAATTA
Found at i:52714081 original size:36 final size:36
Alignment explanation
Indices: 52714031--52714108 Score: 147
Period size: 36 Copynumber: 2.2 Consensus size: 36
52714021 TACTAAGAAT
*
52714031 GAAAAACCTAATCTAAAAAGTAAACTAAAACGAAGG
1 GAAATACCTAATCTAAAAAGTAAACTAAAACGAAGG
52714067 GAAATACCTAATCTAAAAAGTAAACTAAAACGAAGG
1 GAAATACCTAATCTAAAAAGTAAACTAAAACGAAGG
52714103 GAAATA
1 GAAATA
52714109 GTCCCTTTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.58, C:0.13, G:0.14, T:0.15
Consensus pattern (36 bp):
GAAATACCTAATCTAAAAAGTAAACTAAAACGAAGG
Found at i:52716765 original size:22 final size:22
Alignment explanation
Indices: 52716735--52716789 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
52716725 CCAATTTGGA
* * * *
52716735 TGTCGAGACATGACATGGCTGG
1 TGTCAAGACATCACATGACTAG
52716757 TGTCAAGACATCACATGACTAG
1 TGTCAAGACATCACATGACTAG
*
52716779 TGTCATGACAT
1 TGTCAAGACAT
52716790 TGATGGCAGA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.25
Consensus pattern (22 bp):
TGTCAAGACATCACATGACTAG
Found at i:52719735 original size:26 final size:26
Alignment explanation
Indices: 52719699--52719749 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
52719689 TCTATTAAAA
52719699 AAAATAAGTTTCTAATCTGATGGATC
1 AAAATAAGTTTCTAATCTGATGGATC
52719725 AAAATAAGTTTCTAATCTGATGGAT
1 AAAATAAGTTTCTAATCTGATGGAT
52719750 TAGTGATAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (26 bp):
AAAATAAGTTTCTAATCTGATGGATC
Found at i:52733925 original size:3 final size:3
Alignment explanation
Indices: 52733912--52733941 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
52733902 TACAATATAT
52733912 ATA ATA A-A ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
52733942 AAGAGAACGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:52736835 original size:28 final size:28
Alignment explanation
Indices: 52736804--52736863 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
52736794 TTCGTCAAGG
*
52736804 CTATCTTATATGTGGAAGCCCATTAGAA
1 CTATCTTATATGTGAAAGCCCATTAGAA
** *
52736832 CTATCTTATATGTGAAAGTTCATTGGAA
1 CTATCTTATATGTGAAAGCCCATTAGAA
52736860 CTAT
1 CTAT
52736864 ATTGTAAGTG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.37
Consensus pattern (28 bp):
CTATCTTATATGTGAAAGCCCATTAGAA
Found at i:52742260 original size:20 final size:20
Alignment explanation
Indices: 52742237--52742343 Score: 81
Period size: 20 Copynumber: 5.3 Consensus size: 20
52742227 TACACTTTGG
*
52742237 TGCCCCTGTTTGCACTTCGA
1 TGCCCCTATTTGCACTTCGA
* * *
52742257 TGCCCTTATATACACTTCGA
1 TGCCCCTATTTGCACTTCGA
* * *
52742277 TGTCTCTATTTGCACTACGA
1 TGCCCCTATTTGCACTTCGA
* * * *
52742297 TGCCTCTGTTTGCATATTTG-
1 TGCCCCTATTTGCA-CTTCGA
* *
52742317 TGCCCCTATTTGCACTTTGG
1 TGCCCCTATTTGCACTTCGA
52742337 TGCCCCT
1 TGCCCCT
52742344 GTTATGCATC
Statistics
Matches: 67, Mismatches: 18, Indels: 4
0.75 0.20 0.04
Matches are distributed among these distances:
19 4 0.06
20 61 0.91
21 2 0.03
ACGTcount: A:0.14, C:0.30, G:0.17, T:0.39
Consensus pattern (20 bp):
TGCCCCTATTTGCACTTCGA
Found at i:52742494 original size:7 final size:7
Alignment explanation
Indices: 52742482--52742508 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
52742472 AAGATATTAG
52742482 TAAATGT
1 TAAATGT
52742489 TAAATGT
1 TAAATGT
52742496 TAAATGT
1 TAAATGT
52742503 TAAATG
1 TAAATG
52742509 AATTACTTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.15, T:0.41
Consensus pattern (7 bp):
TAAATGT
Found at i:52744882 original size:13 final size:13
Alignment explanation
Indices: 52744866--52744894 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
52744856 ATAATAAAAA
52744866 ATATATTTATTAT
1 ATATATTTATTAT
52744879 ATATATTTATTAT
1 ATATATTTATTAT
52744892 ATA
1 ATA
52744895 AATACTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
ATATATTTATTAT
Found at i:52745343 original size:16 final size:16
Alignment explanation
Indices: 52745322--52745357 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
52745312 CACTTCTTCT
52745322 TTTCTTTTCATTTT-TA
1 TTTCTTTT-ATTTTATA
52745338 TTTCTTTTATTTTATA
1 TTTCTTTTATTTTATA
52745354 TTTC
1 TTTC
52745358 GTATTTCTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 5 0.26
16 14 0.74
ACGTcount: A:0.14, C:0.11, G:0.00, T:0.75
Consensus pattern (16 bp):
TTTCTTTTATTTTATA
Found at i:52753756 original size:14 final size:14
Alignment explanation
Indices: 52753718--52753760 Score: 54
Period size: 13 Copynumber: 3.1 Consensus size: 14
52753708 CAAAATGTAC
52753718 AATATAATTAAA-T
1 AATATAATTAAATT
52753731 AATATAAATTAAATT
1 AATAT-AATTAAATT
*
52753746 AA-ATAATTTAATT
1 AATATAATTAAATT
52753759 AA
1 AA
52753761 CTGTTTACCC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
13 15 0.56
14 9 0.33
15 3 0.11
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
AATATAATTAAATT
Found at i:52759117 original size:25 final size:24
Alignment explanation
Indices: 52759065--52759137 Score: 85
Period size: 25 Copynumber: 3.0 Consensus size: 24
52759055 GTGCATGTAT
* *
52759065 GCTCATACGAGCTGTGAACGGTAA
1 GCTCATAAGAGCTGAGAACGGTAA
* *
52759089 GCTCATATGAGCTGAGTATCGGTAA
1 GCTCATAAGAGCTGAG-AACGGTAA
52759114 GCTCATAAGAGCTGA-AACCGGTAA
1 GCTCATAAGAGCTGAGAA-CGGTAA
52759138 CCCTAATGAC
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
23 1 0.02
24 20 0.48
25 21 0.50
ACGTcount: A:0.32, C:0.19, G:0.27, T:0.22
Consensus pattern (24 bp):
GCTCATAAGAGCTGAGAACGGTAA
Found at i:52772301 original size:22 final size:22
Alignment explanation
Indices: 52772261--52772302 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
52772251 CCATAATCAT
52772261 AACACTTTAAACACATTTAACC
1 AACACTTTAAACACATTTAACC
*
52772283 AACACATTTACACAC-TTTAA
1 AACAC-TTTAAACACATTTAA
52772303 TTTGATACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.45, C:0.26, G:0.00, T:0.29
Consensus pattern (22 bp):
AACACTTTAAACACATTTAACC
Found at i:52772675 original size:3 final size:3
Alignment explanation
Indices: 52772667--52772765 Score: 189
Period size: 3 Copynumber: 33.0 Consensus size: 3
52772657 TGATTACCAA
52772667 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
*
52772715 TTC TTC TTC TTC TTC TTC TTC TTT TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
52772763 TTC
1 TTC
52772766 ATTATCATCA
Statistics
Matches: 94, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
3 94 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:52772812 original size:21 final size:21
Alignment explanation
Indices: 52772788--52772827 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
52772778 GACATCATCA
52772788 TCATCATCGTCATATTCATTG
1 TCATCATCGTCATATTCATTG
** *
52772809 TCATTGTCGTCATCTTCAT
1 TCATCATCGTCATATTCAT
52772828 CTTCTTTTTC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.20, C:0.25, G:0.10, T:0.45
Consensus pattern (21 bp):
TCATCATCGTCATATTCATTG
Found at i:52779808 original size:21 final size:22
Alignment explanation
Indices: 52779776--52779827 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 22
52779766 CAATTGAATC
52779776 TATTTT-TTATTTTTAAATA-T
1 TATTTTATTATTTTTAAATATT
*
52779796 TATTTTATTATTTTTAATTATT
1 TATTTTATTATTTTTAAATATT
*
52779818 TATTTAATTA
1 TATTTTATTA
52779828 AACCGTATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 6 0.21
21 12 0.43
22 10 0.36
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (22 bp):
TATTTTATTATTTTTAAATATT
Found at i:52782704 original size:54 final size:54
Alignment explanation
Indices: 52782643--52782875 Score: 225
Period size: 54 Copynumber: 4.1 Consensus size: 54
52782633 AGTATCATAT
* *
52782643 ATTATGATTTGAGTAAATTCATATAAAAATATTAATTATTATGAATTTTATTAA
1 ATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAA
*
52782697 ATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAA
1 ATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAA
* * * * * * * * *
52782751 ATTATATATTTTAATTATAATAT-ATTTAATAATAATTATGTTAATTTATATTTTATAGTATCAT
1 ATTAT-GA-TTTGAGTA-AAT-TCATATAAGAAT-ATTA-ATT-ATTAAGAATTT-TA-T-T-A-
52782815 A
54 A
*
52782816 TATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAA
1 -ATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAA
52782871 ATTAT
1 ATTAT
52782876 ATATTTTAAT
Statistics
Matches: 142, Mismatches: 23, Indels: 28
0.74 0.12 0.15
Matches are distributed among these distances:
54 61 0.43
55 2 0.01
56 7 0.05
57 12 0.08
58 5 0.04
59 4 0.03
60 16 0.11
61 4 0.03
62 5 0.04
63 12 0.08
64 7 0.05
65 2 0.01
66 5 0.04
ACGTcount: A:0.42, C:0.02, G:0.08, T:0.48
Consensus pattern (54 bp):
ATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAA
Found at i:52782780 original size:15 final size:15
Alignment explanation
Indices: 52782745--52782796 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
52782735 TTAAGAATTT
*
52782745 TATTAAATTAT-ATA
1 TATTTAATTATAATA
52782759 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
52782773 TATTTAATAATAAT-
1 TATTTAATTATAATA
52782787 TATGTTAATT
1 TAT-TTAATT
52782797 TATATTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:52782822 original size:120 final size:120
Alignment explanation
Indices: 52782697--52782912 Score: 432
Period size: 120 Copynumber: 1.8 Consensus size: 120
52782687 ATTTTATTAA
52782697 ATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTATATATTT
1 ATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTATATATTT
52782762 TAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTATAGTATCATAT
66 TAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTATAGTATCATAT
52782817 ATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTATATATTT
1 ATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTATATATTT
52782882 TAATTATAATATATTTAATAATAATTATGTT
66 TAATTATAATATATTTAATAATAATTATGTT
52782913 TAAATATGAT
Statistics
Matches: 96, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
120 96 1.00
ACGTcount: A:0.42, C:0.01, G:0.07, T:0.50
Consensus pattern (120 bp):
ATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTATATATTT
TAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTATAGTATCATAT
Found at i:52782895 original size:16 final size:16
Alignment explanation
Indices: 52782874--52782915 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
52782864 TTATTAAATT
*
52782874 ATATATTTTAATTATA
1 ATATATTTTAATAATA
52782890 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
52782905 AT-TATGTTTAA
1 ATATAT-TTTAA
52782916 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:52782900 original size:15 final size:15
Alignment explanation
Indices: 52782865--52782906 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
52782855 TTAAGAATTT
*
52782865 TATTAAATTAT-ATA
1 TATTTAATTATAATA
52782879 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
52782893 TATTTAATAATAAT
1 TATTTAATTATAAT
52782907 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:52783140 original size:16 final size:16
Alignment explanation
Indices: 52783116--52783167 Score: 86
Period size: 16 Copynumber: 3.2 Consensus size: 16
52783106 GATTTGCTAT
*
52783116 TACACCTCTATTCCAA
1 TACACCTCTAATCCAA
*
52783132 TATACCTCTAATCCAA
1 TACACCTCTAATCCAA
52783148 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
52783164 TACA
1 TACA
52783168 GCGAACCAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.37, C:0.35, G:0.00, T:0.29
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:52784121 original size:25 final size:25
Alignment explanation
Indices: 52784084--52784132 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
52784074 CAGTTAGGGA
52784084 AATTATAAAAAATATATATT-TTTAT
1 AATTATAAAAAAT-TATATTATTTAT
52784109 AATTA-AAATAAATTATATTATTTA
1 AATTATAAA-AAATTATATTATTTA
52784133 AGGGTATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 9 0.41
25 13 0.59
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (25 bp):
AATTATAAAAAATTATATTATTTAT
Found at i:52785324 original size:20 final size:21
Alignment explanation
Indices: 52785299--52785343 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
52785289 GTTCAACTAA
52785299 TTTTGGGTT-TCGATCTCAAT
1 TTTTGGGTTCTCGATCTCAAT
*
52785319 TTTT-GGTTCTCGATTTCAAT
1 TTTTGGGTTCTCGATCTCAAT
52785339 TTTTG
1 TTTTG
52785344 ATCTCAAGTC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.13, C:0.13, G:0.18, T:0.56
Consensus pattern (21 bp):
TTTTGGGTTCTCGATCTCAAT
Found at i:52787253 original size:45 final size:45
Alignment explanation
Indices: 52787203--52787365 Score: 168
Period size: 45 Copynumber: 3.6 Consensus size: 45
52787193 CCAGAAACAA
* * *
52787203 TAAGACCGTAGCTAAAAGACGTTATGGCATCATGATTCTATCAAG
1 TAAGACCATAGCTGAAAGACATTATGGCATCATGATTCTATCAAG
* * **
52787248 TAAGACCATACCTGAAAGACATTATGGCATCATGATTTTATTGAG
1 TAAGACCATAGCTGAAAGACATTATGGCATCATGATTCTATCAAG
* * * * * *
52787293 TAAGACCATAGTTGAAAGACATTATGGCATAACGAATCAAATGAA-
1 TAAGACCATAGCTGAAAGACATTATGGCATCATGATTC-TATCAAG
* *
52787338 -AAGACCATAGTTGAAAGACACTATGGCA
1 TAAGACCATAGCTGAAAGACATTATGGCA
52787366 ACACGACGGA
Statistics
Matches: 100, Mismatches: 17, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
44 27 0.27
45 70 0.70
46 3 0.03
ACGTcount: A:0.40, C:0.16, G:0.19, T:0.25
Consensus pattern (45 bp):
TAAGACCATAGCTGAAAGACATTATGGCATCATGATTCTATCAAG
Found at i:52787355 original size:44 final size:46
Alignment explanation
Indices: 52787248--52787494 Score: 204
Period size: 45 Copynumber: 5.5 Consensus size: 46
52787238 TTCTATCAAG
** * * * ** * *
52787248 TAAGACCATACCTGAAAGACATTATGGCAT-CATGATTTTATTGAG
1 TAAGACCATAGTTGAAAGACACTATGGCATACACGAATAAAATGAA
* *
52787293 TAAGACCATAGTTGAAAGACATTATGGCATA-ACGAATCAAATGAA
1 TAAGACCATAGTTGAAAGACACTATGGCATACACGAATAAAATGAA
**
52787338 -AAGACCATAGTTGAAAGACACTATGGCA-ACACGACGGAAAATGAA
1 TAAGACCATAGTTGAAAGACACTATGGCATACACGA-ATAAAATGAA
* * *
52787383 TAAGATCATAATTGAAAGACACTGTGGCA-ACACG-ATGAAAAATGAA
1 TAAGACCATAGTTGAAAGACACTATGGCATACACGAAT--AAAATGAA
* * *** *
52787429 TAAGACCATGGTTGAAAGACACTATGGCAT-CAAGTCGAGAATGAA
1 TAAGACCATAGTTGAAAGACACTATGGCATACACGAATAAAATGAA
52787474 TAAGACCAT-GTTTGAAAGACA
1 TAAGACCATAG-TTGAAAGACA
52787495 ATAACTCCCT
Statistics
Matches: 168, Mismatches: 25, Indels: 18
0.80 0.12 0.09
Matches are distributed among these distances:
43 1 0.01
44 32 0.19
45 69 0.41
46 66 0.39
ACGTcount: A:0.43, C:0.15, G:0.20, T:0.21
Consensus pattern (46 bp):
TAAGACCATAGTTGAAAGACACTATGGCATACACGAATAAAATGAA
Found at i:52787423 original size:45 final size:45
Alignment explanation
Indices: 52787248--52787494 Score: 225
Period size: 46 Copynumber: 5.5 Consensus size: 45
52787238 TTCTATCAAG
** * * * *** * *
52787248 TAAGACCATACCTGAAAGACATTATGGCATCATGATTTTATTGAG
1 TAAGACCATAGTTGAAAGACACTATGGCAACACGATGAAAATGAA
* *
52787293 TAAGACCATAGTTGAAAGACATTATGGCATA-ACGAAT-CAAATGAA
1 TAAGACCATAGTTGAAAGACACTATGGCA-ACACG-ATGAAAATGAA
*
52787338 -AAGACCATAGTTGAAAGACACTATGGCAACACGACGGAAAATGAA
1 TAAGACCATAGTTGAAAGACACTATGGCAACACGA-TGAAAATGAA
* * *
52787383 TAAGATCATAATTGAAAGACACTGTGGCAACACGATGAAAAATGAA
1 TAAGACCATAGTTGAAAGACACTATGGCAACACGATG-AAAATGAA
* * * *
52787429 TAAGACCATGGTTGAAAGACACTATGGCATCAAG-TCGAGAATGAA
1 TAAGACCATAGTTGAAAGACACTATGGCAACACGAT-GAAAATGAA
52787474 TAAGACCAT-GTTTGAAAGACA
1 TAAGACCATAG-TTGAAAGACA
52787495 ATAACTCCCT
Statistics
Matches: 171, Mismatches: 22, Indels: 18
0.81 0.10 0.09
Matches are distributed among these distances:
43 2 0.01
44 31 0.18
45 68 0.40
46 70 0.41
ACGTcount: A:0.43, C:0.15, G:0.20, T:0.21
Consensus pattern (45 bp):
TAAGACCATAGTTGAAAGACACTATGGCAACACGATGAAAATGAA
Found at i:52788852 original size:26 final size:27
Alignment explanation
Indices: 52788821--52788890 Score: 108
Period size: 26 Copynumber: 2.7 Consensus size: 27
52788811 CATTCTGACC
52788821 CACAACTCGTATGAGCAAGG-CCATTT
1 CACAACTCGTATGAGCAAGGCCCATTT
52788847 CACAACTCGTATGAGC-AGGCCCATTT
1 CACAACTCGTATGAGCAAGGCCCATTT
* *
52788873 CACAGCTCGTGTGAGCAA
1 CACAACTCGTATGAGCAA
52788891 TGTAAAGTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
25 3 0.08
26 36 0.90
27 1 0.03
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (27 bp):
CACAACTCGTATGAGCAAGGCCCATTT
Found at i:52799084 original size:21 final size:21
Alignment explanation
Indices: 52799060--52799104 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
52799050 AGGACTAAAT
*
52799060 TGTAAAAATATAAAAGTGTTA
1 TGTAAAAATATAAAAGTGATA
* *
52799081 TGTAAAAGTGTAAAAGTGATA
1 TGTAAAAATATAAAAGTGATA
52799102 TGT
1 TGT
52799105 GTGCATGATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.47, C:0.00, G:0.20, T:0.33
Consensus pattern (21 bp):
TGTAAAAATATAAAAGTGATA
Found at i:52799723 original size:16 final size:16
Alignment explanation
Indices: 52799702--52799737 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
52799692 GGGAATTATG
52799702 GAATTTAATAGATTTT
1 GAATTTAATAGATTTT
52799718 GAATTTAATAGATTTT
1 GAATTTAATAGATTTT
52799734 GAAT
1 GAAT
52799738 ATCAAGGGTA
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:0.39, C:0.00, G:0.14, T:0.47
Consensus pattern (16 bp):
GAATTTAATAGATTTT
Found at i:52805202 original size:26 final size:26
Alignment explanation
Indices: 52805159--52805230 Score: 81
Period size: 26 Copynumber: 2.8 Consensus size: 26
52805149 TCTCGTCCCT
* ** *
52805159 ATTTTACCCCCAACAAAATTTTGACG
1 ATTTTACCCCTAGTAAAATTTTGACA
* *
52805185 ATTTTACCCTTGGTAAAATTTTGACA
1 ATTTTACCCCTAGTAAAATTTTGACA
*
52805211 ATTTTGCCCCTAGTAAAATT
1 ATTTTACCCCTAGTAAAATT
52805231 CTAAGAAAAT
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.32, C:0.21, G:0.10, T:0.38
Consensus pattern (26 bp):
ATTTTACCCCTAGTAAAATTTTGACA
Found at i:52812163 original size:15 final size:15
Alignment explanation
Indices: 52812145--52812174 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
52812135 TAACCCTAAT
*
52812145 CCTATTAGACACATC
1 CCTATCAGACACATC
52812160 CCTATCAGACACATC
1 CCTATCAGACACATC
52812175 AAAATCAGAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.37, G:0.07, T:0.23
Consensus pattern (15 bp):
CCTATCAGACACATC
Found at i:52813613 original size:104 final size:104
Alignment explanation
Indices: 52813486--52813679 Score: 388
Period size: 104 Copynumber: 1.9 Consensus size: 104
52813476 TTCTTATATA
52813486 TATATATATTTACTTTTTTTTCATCCATATATAAGACTAATTTTAATATAAAATTTTAGAAATAC
1 TATATATATTTACTTTTTTTTCATCCATATATAAGACTAATTTTAATATAAAATTTTAGAAATAC
52813551 ACTCGATGACTCGAATCAATTGGAATTTACTCACTTTCT
66 ACTCGATGACTCGAATCAATTGGAATTTACTCACTTTCT
52813590 TATATATATTTACTTTTTTTTCATCCATATATAAGACTAATTTTAATATAAAATTTTAGAAATAC
1 TATATATATTTACTTTTTTTTCATCCATATATAAGACTAATTTTAATATAAAATTTTAGAAATAC
52813655 ACTCGATGACTCGAATCAATTGGAA
66 ACTCGATGACTCGAATCAATTGGAA
52813680 ACCAAATTCA
Statistics
Matches: 90, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
104 90 1.00
ACGTcount: A:0.37, C:0.13, G:0.07, T:0.42
Consensus pattern (104 bp):
TATATATATTTACTTTTTTTTCATCCATATATAAGACTAATTTTAATATAAAATTTTAGAAATAC
ACTCGATGACTCGAATCAATTGGAATTTACTCACTTTCT
Found at i:52816221 original size:3 final size:3
Alignment explanation
Indices: 52816200--52816325 Score: 117
Period size: 3 Copynumber: 42.0 Consensus size: 3
52816190 TTTAAGATTT
* * ** * *
52816200 TTA TTA TTG TTA TTG TTA TTA TTA TTA TTA TTA TTA TTA CCA TCA TCA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* ** * * **
52816248 TTA TTA TTA ATA CCA TTA TTC TTA TTA TTA TTA ATA CCA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
52816296 TTA TTG TTA TTA TTA TTA TTA TTG TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
52816326 AATTGTTTTA
Statistics
Matches: 99, Mismatches: 24, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 99 1.00
ACGTcount: A:0.31, C:0.07, G:0.03, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:52821874 original size:74 final size:74
Alignment explanation
Indices: 52821787--52821925 Score: 174
Period size: 74 Copynumber: 1.9 Consensus size: 74
52821777 CTCATTTGAG
52821787 CTTCACTCAGTATAAC-AGTA-GAATTTGATCAATTAAACATCAGTCAGTATAACAGTAAGATTT
1 CTTCACTCAGTATAACGA-TATG-ATTTGATCAATTAAACATCAGTCAGTATAACAGTAAGATTT
52821850 GCTCAATTAAA
64 GCTCAATTAAA
* * * * * * * *
52821861 CTTCATTCGGTATAACGATATGATTTGCTCGATTGAGCTTCATTCAGTATAACAGTAAGATTTGC
1 CTTCACTCAGTATAACGATATGATTTGATCAATTAAACATCAGTCAGTATAACAGTAAGATTTGC
52821926 CTCGATAGAG
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
74 53 0.96
75 2 0.04
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.34
Consensus pattern (74 bp):
CTTCACTCAGTATAACGATATGATTTGATCAATTAAACATCAGTCAGTATAACAGTAAGATTTGC
TCAATTAAA
Found at i:52821925 original size:37 final size:37
Alignment explanation
Indices: 52821777--52821925 Score: 158
Period size: 37 Copynumber: 4.0 Consensus size: 37
52821767 TAGATTTCTA
* *
52821777 CTCATTTGAGCTTCACTCAGTATAACAGT-AGAATTTG
1 CTCAATTGAGCTTCATTCAGTATAACAGTAAG-ATTTG
* * * * *
52821814 ATCAATTAAACATCAGTCAGTATAACAGTAAGATTTG
1 CTCAATTGAGCTTCATTCAGTATAACAGTAAGATTTG
* * * *
52821851 CTCAATTAAACTTCATTCGGTATAAC-GATATGATTTG
1 CTCAATTGAGCTTCATTCAGTATAACAG-TAAGATTTG
*
52821888 CTCGATTGAGCTTCATTCAGTATAACAGTAAGATTTG
1 CTCAATTGAGCTTCATTCAGTATAACAGTAAGATTTG
52821925 C
1 C
52821926 CTCGATAGAG
Statistics
Matches: 93, Mismatches: 16, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
36 1 0.01
37 89 0.96
38 3 0.03
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (37 bp):
CTCAATTGAGCTTCATTCAGTATAACAGTAAGATTTG
Found at i:52830105 original size:47 final size:47
Alignment explanation
Indices: 52830040--52830181 Score: 198
Period size: 47 Copynumber: 3.1 Consensus size: 47
52830030 TACTATGGCA
* * * *
52830040 TTTTGATCATGACACCATAACATCTTTCAGTTATGGTCTTACTCATT
1 TTTTCATCATGACGCCATAGCATCTTTCAGCTATGGTCTTACTCATT
* *
52830087 TTTTTATCATGATGCCATAGCATCTTTCAGCTATGGTCTTACTCA--
1 TTTTCATCATGACGCCATAGCATCTTTCAGCTATGGTCTTACTCATT
* *
52830132 TTTACATTATGACGCCATAGCATCTTTCAGCTATGGTCTTACTCATT
1 TTTTCATCATGACGCCATAGCATCTTTCAGCTATGGTCTTACTCATT
52830179 TTT
1 TTT
52830182 AGGCGTATAG
Statistics
Matches: 84, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
45 41 0.49
47 43 0.51
ACGTcount: A:0.23, C:0.22, G:0.12, T:0.43
Consensus pattern (47 bp):
TTTTCATCATGACGCCATAGCATCTTTCAGCTATGGTCTTACTCATT
Found at i:52830163 original size:45 final size:45
Alignment explanation
Indices: 52830045--52830179 Score: 189
Period size: 45 Copynumber: 3.0 Consensus size: 45
52830035 TGGCATTTTG
* * * **
52830045 ATCATGACACCATAACATCTTTCAGTTATGGTCTTACTCATTTTTTT
1 ATCATGACGCCATAGCATCTTTCAGCTATGGTCTTACTCA--TTTAC
*
52830092 ATCATGATGCCATAGCATCTTTCAGCTATGGTCTTACTCATTTAC
1 ATCATGACGCCATAGCATCTTTCAGCTATGGTCTTACTCATTTAC
*
52830137 ATTATGACGCCATAGCATCTTTCAGCTATGGTCTTACTCATTT
1 ATCATGACGCCATAGCATCTTTCAGCTATGGTCTTACTCATTT
52830180 TTAGGCGTAT
Statistics
Matches: 80, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
45 44 0.55
47 36 0.45
ACGTcount: A:0.24, C:0.23, G:0.12, T:0.41
Consensus pattern (45 bp):
ATCATGACGCCATAGCATCTTTCAGCTATGGTCTTACTCATTTAC
Found at i:52831564 original size:23 final size:22
Alignment explanation
Indices: 52831512--52831570 Score: 95
Period size: 21 Copynumber: 2.7 Consensus size: 22
52831502 ACACATAAGA
52831512 GCCTGAA-ACGACACACGAGGT
1 GCCTGAATACGACACACGAGGT
52831533 GCCTG-ATACGACACACGAGGT
1 GCCTGAATACGACACACGAGGT
52831554 GCCTGAAATACGACACA
1 GCCTG-AATACGACACA
52831571 TAAAGTGCCT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.03
21 24 0.69
23 10 0.29
ACGTcount: A:0.34, C:0.29, G:0.25, T:0.12
Consensus pattern (22 bp):
GCCTGAATACGACACACGAGGT
Found at i:52831606 original size:23 final size:23
Alignment explanation
Indices: 52831496--52831606 Score: 88
Period size: 23 Copynumber: 5.0 Consensus size: 23
52831486 ACTTGATCAG
*
52831496 TATACGACACAT-AAGAGCCTGA
1 TATACGACACATAAAGTGCCTGA
** *
52831518 -A-ACGACACACGAGGTGCCTG-
1 TATACGACACATAAAGTGCCTGA
** *
52831538 -ATACGACACACGAGGTGCCTGA
1 TATACGACACATAAAGTGCCTGA
*
52831560 AATACGACACATAAAGTGCCTGA
1 TATACGACACATAAAGTGCCTGA
* * *
52831583 TATATGACGCATAAAGTTCCTGA
1 TATACGACACATAAAGTGCCTGA
52831606 T
1 T
52831607 CGGTAGATTC
Statistics
Matches: 75, Mismatches: 10, Indels: 7
0.82 0.11 0.08
Matches are distributed among these distances:
20 9 0.12
21 27 0.36
23 39 0.52
ACGTcount: A:0.36, C:0.23, G:0.22, T:0.19
Consensus pattern (23 bp):
TATACGACACATAAAGTGCCTGA
Found at i:52831918 original size:51 final size:51
Alignment explanation
Indices: 52831863--52831964 Score: 186
Period size: 51 Copynumber: 2.0 Consensus size: 51
52831853 TCTTATGTTC
*
52831863 ACAATTCAAATCACTTTTTCAACCCAATATGCATTTCAAAACCACATTAAT
1 ACAATTCAAATCAATTTTTCAACCCAATATGCATTTCAAAACCACATTAAT
*
52831914 ACAATTCAAATCAATTTTTCAATCCAATATGCATTTCAAAACCACATTAAT
1 ACAATTCAAATCAATTTTTCAACCCAATATGCATTTCAAAACCACATTAAT
52831965 TCTTTTAATT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.42, C:0.24, G:0.02, T:0.32
Consensus pattern (51 bp):
ACAATTCAAATCAATTTTTCAACCCAATATGCATTTCAAAACCACATTAAT
Found at i:52832467 original size:41 final size:42
Alignment explanation
Indices: 52832374--52832488 Score: 128
Period size: 41 Copynumber: 2.8 Consensus size: 42
52832364 AAAGGTGCCG
** * * *
52832374 CTAATGCTCATGGTTTTAGCAGCGTTTTTGAAAAAAGTACCG
1 CTAATGCTCGGGGTTTTAGCGGCGTTTTTGAAAAAAGCACCA
* *
52832416 CTAATGCTCGGGGTTTTAGCGGCGTTTTT-ATAAAAGCGCCA
1 CTAATGCTCGGGGTTTTAGCGGCGTTTTTGAAAAAAGCACCA
* *
52832457 CTAATTCTCGGGATTTTAGC-G-GTTTTTGAAAA
1 CTAATGCTCGGGGTTTTAGCGGCGTTTTTGAAAA
52832489 TGCGCCGCAA
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
39 6 0.10
40 4 0.06
41 26 0.42
42 26 0.42
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.35
Consensus pattern (42 bp):
CTAATGCTCGGGGTTTTAGCGGCGTTTTTGAAAAAAGCACCA
Found at i:52836439 original size:124 final size:124
Alignment explanation
Indices: 52836218--52836563 Score: 595
Period size: 124 Copynumber: 2.8 Consensus size: 124
52836208 TTATTTCGAG
* *
52836218 TTGACGTTTCTG-GTGAAATAGTATAAAATCGCTTCTAACATGATGCTATTTGAGAAGAAATTAT
1 TTGACGTTTCTGAGT-AAATAGTATAAAATCGCTTCTACCATGATGCTATTTGAGAAGAAATTGT
**
52836282 GAAATCGCGCCCTCGTGGACGCGATTTCCCTACAGTAGGTCATGTAAGAAATAATTTTTT
65 GAAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAATTTTTT
*
52836342 TTGACGTTTCTGAGTAAATAGTATAAAATCGCTTCTTCCATGATGCTATTTGAGAAGAAATTGTG
1 TTGACGTTTCTGAGTAAATAGTATAAAATCGCTTCTACCATGATGCTATTTGAGAAGAAATTGTG
* *
52836407 AAATCGTGCCCTCGTGGACGCGATTTTGCTACAGTTGGTCATGTAAGAAATAATTTTTT
66 AAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAATTTTTT
* *
52836466 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTG
1 TTGACGTTTCTGAGTAAATAGTATAAAATCGCTTCTACCATGATGCTATTTGAGAAGAAATTGTG
52836531 AAATCGCGCCCTCGTGGACGCGATTTTGCTACA
66 AAATCGCGCCCTCGTGGACGCGATTTTGCTACA
52836564 ATAGCAAGTT
Statistics
Matches: 210, Mismatches: 11, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
124 208 0.99
125 2 0.01
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.33
Consensus pattern (124 bp):
TTGACGTTTCTGAGTAAATAGTATAAAATCGCTTCTACCATGATGCTATTTGAGAAGAAATTGTG
AAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAATTTTTT
Found at i:52839783 original size:55 final size:55
Alignment explanation
Indices: 52839679--52839858 Score: 299
Period size: 55 Copynumber: 3.3 Consensus size: 55
52839669 GTTATGTAAC
* *
52839679 ATTATGTAAAATTATTAAG-CCAAAAAAATTTTGTTAATGGTTAGTAAAATTATCAA
1 ATTATGTAAAATTATTAAGTCC--AATAATTGTGTTAATGGTTAGTAAAATTATCAA
*
52839735 ATTATGTAAAATTATTAAGTCCAATAAGTGTGTTAATGGTTAGTAAAATTATCAA
1 ATTATGTAAAATTATTAAGTCCAATAATTGTGTTAATGGTTAGTAAAATTATCAA
52839790 ATTATGTAAAATTATTAAGTCCAATAATTGTGTTAATGGTTAGTAAAATTATCAA
1 ATTATGTAAAATTATTAAGTCCAATAATTGTGTTAATGGTTAGTAAAATTATCAA
*
52839845 ATTATATAAAATTA
1 ATTATGTAAAATTA
52839859 GGTTAGGGTT
Statistics
Matches: 118, Mismatches: 5, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
55 97 0.82
56 19 0.16
57 2 0.02
ACGTcount: A:0.44, C:0.05, G:0.12, T:0.39
Consensus pattern (55 bp):
ATTATGTAAAATTATTAAGTCCAATAATTGTGTTAATGGTTAGTAAAATTATCAA
Found at i:52839887 original size:29 final size:29
Alignment explanation
Indices: 52839853--52840205 Score: 554
Period size: 29 Copynumber: 12.3 Consensus size: 29
52839843 AAATTATATA
*
52839853 AAATTAGGTTAGGGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTAAGGGTTTTTAATT
*
52839882 AAATTAGGTTAGTGTAAGGGTTTTTAATT
1 AAATTAGGTTAGGGTAAGGGTTTTTAATT
* *
52839911 AAATTATGTTAGGGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTAAGGGTTTTTAATT
*
52839940 -AA--A--TTAGGGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTAAGGGTTTTTAATT
*
52839964 AAATTAGGTTAGTGTAAGGGTTTTTAATT
1 AAATTAGGTTAGGGTAAGGGTTTTTAATT
52839993 AAATTAGGTTAGGGTAAGGGTTTTTAATT
1 AAATTAGGTTAGGGTAAGGGTTTTTAATT
*
52840022 AAATTAGGTTAGTGTAAGGGTTTTTAATT
1 AAATTAGGTTAGGGTAAGGGTTTTTAATT
*
52840051 AAAATTAGGTTAGTGTAAGGGTTTTTAATT
1 -AAATTAGGTTAGGGTAAGGGTTTTTAATT
52840081 AAATTAGGTTAGGGTAAGGGTTTTTAATT
1 AAATTAGGTTAGGGTAAGGGTTTTTAATT
*
52840110 AAAATTAGGTTAGTGTAAGGGTTTTTAATT
1 -AAATTAGGTTAGGGTAAGGGTTTTTAATT
*
52840140 AAATTAGGTTAGTGTAAGGGTTTTTAATT
1 AAATTAGGTTAGGGTAAGGGTTTTTAATT
*
52840169 AAATTAGGTTAGGGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTAAGGGTTTTTAATT
52840198 AAATTAGG
1 AAATTAGG
52840206 ATTTTTATTA
Statistics
Matches: 304, Mismatches: 13, Indels: 14
0.92 0.04 0.04
Matches are distributed among these distances:
24 21 0.07
25 2 0.01
26 1 0.00
27 1 0.00
28 2 0.01
29 220 0.72
30 57 0.19
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (29 bp):
AAATTAGGTTAGGGTAAGGGTTTTTAATT
Found at i:52840078 original size:88 final size:87
Alignment explanation
Indices: 52839853--52840205 Score: 608
Period size: 88 Copynumber: 4.1 Consensus size: 87
52839843 AAATTATATA
* * *
52839853 AAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGTGTAAGGGTTTTTAATTAAATTAT
1 AAATTAGGTTAGTGTAAGGGTTTTTAATTAAATTAGGTTAGTGTAAGGGTTTTTAATTAAATTAG
*
52839918 GTTAGGGTTAGGGTTTTTAATT
66 GTTAGGGTAAGGGTTTTTAATT
52839940 AAATTAGG---GT-T-AGGGTTTTTAATTAAATTAGGTTAGTGTAAGGGTTTTTAATTAAATTAG
1 AAATTAGGTTAGTGTAAGGGTTTTTAATTAAATTAGGTTAGTGTAAGGGTTTTTAATTAAATTAG
52840000 GTTAGGGTAAGGGTTTTTAATT
66 GTTAGGGTAAGGGTTTTTAATT
52840022 AAATTAGGTTAGTGTAAGGGTTTTTAATTAAAATTAGGTTAGTGTAAGGGTTTTTAATTAAATTA
1 AAATTAGGTTAGTGTAAGGGTTTTTAATT-AAATTAGGTTAGTGTAAGGGTTTTTAATTAAATTA
52840087 GGTTAGGGTAAGGGTTTTTAATT
65 GGTTAGGGTAAGGGTTTTTAATT
52840110 AAAATTAGGTTAGTGTAAGGGTTTTTAATTAAATTAGGTTAGTGTAAGGGTTTTTAATTAAATTA
1 -AAATTAGGTTAGTGTAAGGGTTTTTAATTAAATTAGGTTAGTGTAAGGGTTTTTAATTAAATTA
*
52840175 GGTTAGGGTTAGGGTTTTTAATT
65 GGTTAGGGTAAGGGTTTTTAATT
52840198 AAATTAGG
1 AAATTAGG
52840206 ATTTTTATTA
Statistics
Matches: 255, Mismatches: 4, Indels: 14
0.93 0.01 0.05
Matches are distributed among these distances:
82 77 0.30
83 1 0.00
84 1 0.00
85 2 0.01
86 1 0.00
87 29 0.11
88 115 0.45
89 29 0.11
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (87 bp):
AAATTAGGTTAGTGTAAGGGTTTTTAATTAAATTAGGTTAGTGTAAGGGTTTTTAATTAAATTAG
GTTAGGGTAAGGGTTTTTAATT
Found at i:52840085 original size:59 final size:58
Alignment explanation
Indices: 52839853--52840205 Score: 572
Period size: 59 Copynumber: 6.1 Consensus size: 58
52839843 AAATTATATA
*
52839853 AAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGTGTAAGGGTTTTTAATT
1 AAATTAGGTTAGGGTAAGGGTTTTTAATTAAATTAGGTTAGTGTAAGGGTTTTTAATT
* *
52839911 AAATTATGTTAGGGTTAGGGTTTTTAATTAAATTAGG---GT-T-AGGGTTTTTAATT
1 AAATTAGGTTAGGGTAAGGGTTTTTAATTAAATTAGGTTAGTGTAAGGGTTTTTAATT
* *
52839964 AAATTAGGTTAGTGTAAGGGTTTTTAATTAAATTAGGTTAGGGTAAGGGTTTTTAATT
1 AAATTAGGTTAGGGTAAGGGTTTTTAATTAAATTAGGTTAGTGTAAGGGTTTTTAATT
*
52840022 AAATTAGGTTAGTGTAAGGGTTTTTAATTAAAATTAGGTTAGTGTAAGGGTTTTTAATT
1 AAATTAGGTTAGGGTAAGGGTTTTTAATT-AAATTAGGTTAGTGTAAGGGTTTTTAATT
52840081 AAATTAGGTTAGGGTAAGGGTTTTTAATTAAAATTAGGTTAGTGTAAGGGTTTTTAATT
1 AAATTAGGTTAGGGTAAGGGTTTTTAATT-AAATTAGGTTAGTGTAAGGGTTTTTAATT
* * *
52840140 AAATTAGGTTAGTGTAAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTAAGGGTTTTTAATTAAATTAGGTTAGTGTAAGGGTTTTTAATT
52840198 AAATTAGG
1 AAATTAGG
52840206 ATTTTTATTA
Statistics
Matches: 279, Mismatches: 10, Indels: 12
0.93 0.03 0.04
Matches are distributed among these distances:
53 47 0.17
54 1 0.00
55 2 0.01
56 1 0.00
57 1 0.00
58 113 0.41
59 114 0.41
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (58 bp):
AAATTAGGTTAGGGTAAGGGTTTTTAATTAAATTAGGTTAGTGTAAGGGTTTTTAATT
Found at i:52842552 original size:31 final size:30
Alignment explanation
Indices: 52842517--52842582 Score: 114
Period size: 31 Copynumber: 2.2 Consensus size: 30
52842507 GCCATTAATG
*
52842517 AAAATATAAAAGAATTTAAAATTATTTTTAA
1 AAAATATAAAAAAATTTAAAATTA-TTTTAA
52842548 AAAATATAAAAAAATTTAAAATTATTTTAA
1 AAAATATAAAAAAATTTAAAATTATTTTAA
52842578 AAAAT
1 AAAAT
52842583 GAAATTGAGG
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 11 0.32
31 23 0.68
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (30 bp):
AAAATATAAAAAAATTTAAAATTATTTTAA
Found at i:52842649 original size:51 final size:51
Alignment explanation
Indices: 52842583--52842695 Score: 199
Period size: 51 Copynumber: 2.2 Consensus size: 51
52842573 TTTAAAAAAT
*
52842583 GAAATTGAGGGGAAATTGAAATTAAATATGGATTTGAGAGAATTTTGGAAG
1 GAAATTGAGAGGAAATTGAAATTAAATATGGATTTGAGAGAATTTTGGAAG
* *
52842634 GAAATTGAGAGGAAATTTAAATTAAATATGGGTTTGAGAGAATTTTGGAAG
1 GAAATTGAGAGGAAATTGAAATTAAATATGGATTTGAGAGAATTTTGGAAG
52842685 GAAATTGAGAG
1 GAAATTGAGAG
52842696 AATTAGAGAG
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
51 59 1.00
ACGTcount: A:0.42, C:0.00, G:0.29, T:0.29
Consensus pattern (51 bp):
GAAATTGAGAGGAAATTGAAATTAAATATGGATTTGAGAGAATTTTGGAAG
Found at i:52843140 original size:43 final size:43
Alignment explanation
Indices: 52843047--52843244 Score: 202
Period size: 43 Copynumber: 4.5 Consensus size: 43
52843037 AATAATTTTT
* * * *
52843047 TAAAAGTCATG-TTTTTAGCAGCATTTGTGGTAGAAGCGCCGCGAAGC
1 TAAAGGTCATGATCTTTAGCGGCGTTTGTGGTAGAAGCG-C-C---GC
* * *
52843094 TAAAGGTCATAATCTTTTGCGGCGTTTGTGGTAGAAGC-CTTGC
1 TAAAGGTCATGATCTTTAGCGGCGTTTGTGGTAGAAGCGC-CGC
* * *
52843137 TAAATGTCATGATCCTTAGCTGCGTTTGTGGTAGAAGCGCCGC
1 TAAAGGTCATGATCTTTAGCGGCGTTTGTGGTAGAAGCGCCGC
* *
52843180 TAAAGGTCATGATCTTTAGCGGCGTTTGTGGTAGAAGTGCCGT
1 TAAAGGTCATGATCTTTAGCGGCGTTTGTGGTAGAAGCGCCGC
* *
52843223 TAAAGGTCATAATCCTTAGCGG
1 TAAAGGTCATGATCTTTAGCGG
52843245 TATTTTTTCA
Statistics
Matches: 128, Mismatches: 21, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
43 95 0.74
44 1 0.01
46 1 0.01
47 9 0.07
48 22 0.17
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.31
Consensus pattern (43 bp):
TAAAGGTCATGATCTTTAGCGGCGTTTGTGGTAGAAGCGCCGC
Found at i:52848595 original size:27 final size:27
Alignment explanation
Indices: 52848537--52848588 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
52848527 ATAGTCCCAA
* *
52848537 CGGACTATCTCCTATTTATTGTCCCGT
1 CGGACTATCTCATATTTAGTGTCCCGT
*
52848564 CGGACTATCTCATGTTTAGTGTCCC
1 CGGACTATCTCATATTTAGTGTCCC
52848589 AGTGGACAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.15, C:0.29, G:0.17, T:0.38
Consensus pattern (27 bp):
CGGACTATCTCATATTTAGTGTCCCGT
Found at i:52848817 original size:45 final size:45
Alignment explanation
Indices: 52848692--52848843 Score: 173
Period size: 47 Copynumber: 3.4 Consensus size: 45
52848682 TCAGCTATAG
* *
52848692 TCTTACTCATTTTTATCATGACACCATAGCATCTTTCAACCATGG
1 TCTTACTCATTTTTATCATGACACCAAAGCATCTTTCAACCATGA
* * * * * *
52848737 TCTTAATCATATTTTTATCATGACTCC-ATGTCATCTTTTAGCTATGA
1 TCTTACTC--ATTTTTATCATGACACCAAAG-CATCTTTCAACCATGA
* *
52848784 TCTTACTCATTTTTATCATGACGCCAAAGCATC-TTCAACCATGG
1 TCTTACTCATTTTTATCATGACACCAAAGCATCTTTCAACCATGA
52848828 TCTTACTCATTTTTAT
1 TCTTACTCATTTTTAT
52848844 GGGTATAGCC
Statistics
Matches: 88, Mismatches: 15, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
44 23 0.26
45 27 0.31
46 3 0.03
47 35 0.40
ACGTcount: A:0.26, C:0.24, G:0.09, T:0.42
Consensus pattern (45 bp):
TCTTACTCATTTTTATCATGACACCAAAGCATCTTTCAACCATGA
Found at i:52865523 original size:41 final size:41
Alignment explanation
Indices: 52865461--52865569 Score: 146
Period size: 41 Copynumber: 2.7 Consensus size: 41
52865451 TGATCGAATG
* *
52865461 TAATACAGACTTTACGTCTAGCAGGCTTGATGCCGGTGAAA
1 TAATTCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAA
*
52865502 TAATTCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGATA
1 TAATTCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAA
* * * * *
52865543 CATTTCGGACTATAGGTCTAGCAGGCT
1 TAATTCAGACTTTACGTCTAGCAGGCT
52865570 AAAAGCTGGT
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 60 1.00
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (41 bp):
TAATTCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAA
Found at i:52865952 original size:18 final size:18
Alignment explanation
Indices: 52865929--52865997 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
52865919 TATGATGAAT
52865929 ATGTATATATATATTCGA
1 ATGTATATATATATTCGA
52865947 ATGTATGTATTAGCTATGTATTCGAA
1 ATGTA--TA-TA--TA--TATTCG-A
52865973 TATGTATATATATATTCGA
1 -ATGTATATATATATTCGA
52865992 ATGTAT
1 ATGTAT
52865998 GTATTAGCTA
Statistics
Matches: 42, Mismatches: 0, Indels: 18
0.70 0.00 0.30
Matches are distributed among these distances:
18 11 0.26
19 1 0.02
20 8 0.19
21 2 0.05
22 2 0.05
23 2 0.05
24 2 0.05
25 8 0.19
26 1 0.02
27 5 0.12
ACGTcount: A:0.35, C:0.06, G:0.14, T:0.45
Consensus pattern (18 bp):
ATGTATATATATATTCGA
Found at i:52865971 original size:25 final size:25
Alignment explanation
Indices: 52865940--52866014 Score: 106
Period size: 25 Copynumber: 3.2 Consensus size: 25
52865930 TGTATATATA
52865940 TATTCGAATGTATGTATTAGCTATG
1 TATTCGAATGTATGTATTAGCTATG
*
52865965 TATTCGAA--TATGTA-TA--TATA
1 TATTCGAATGTATGTATTAGCTATG
52865985 TATTCGAATGTATGTATTAGCTATG
1 TATTCGAATGTATGTATTAGCTATG
52866010 TATTC
1 TATTC
52866015 AGGTATAAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
20 11 0.26
22 8 0.19
23 8 0.19
25 16 0.37
ACGTcount: A:0.31, C:0.08, G:0.16, T:0.45
Consensus pattern (25 bp):
TATTCGAATGTATGTATTAGCTATG
Found at i:52865974 original size:45 final size:45
Alignment explanation
Indices: 52865925--52866014 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
52865915 TGTATATGAT
52865925 GAATATGTATATATATATTCGAATGTATGTATTAGCTATGTATTC
1 GAATATGTATATATATATTCGAATGTATGTATTAGCTATGTATTC
52865970 GAATATGTATATATATATTCGAATGTATGTATTAGCTATGTATTC
1 GAATATGTATATATATATTCGAATGTATGTATTAGCTATGTATTC
52866015 AGGTATAAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.33, C:0.07, G:0.16, T:0.44
Consensus pattern (45 bp):
GAATATGTATATATATATTCGAATGTATGTATTAGCTATGTATTC
Found at i:52865990 original size:20 final size:20
Alignment explanation
Indices: 52865925--52865993 Score: 84
Period size: 20 Copynumber: 3.2 Consensus size: 20
52865915 TGTATATGAT
52865925 GAATATGTATATATATATTC
1 GAATATGTATATATATATTC
*
52865945 GAATGTATGTATTAGCTATGTATTC
1 GAA--TATGTA-TA--TATATATTC
52865970 GAATATGTATATATATATTC
1 GAATATGTATATATATATTC
52865990 GAAT
1 GAAT
52865994 GTATGTATTA
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
20 15 0.36
22 8 0.19
23 8 0.19
25 11 0.26
ACGTcount: A:0.36, C:0.06, G:0.14, T:0.43
Consensus pattern (20 bp):
GAATATGTATATATATATTC
Found at i:52867570 original size:5 final size:5
Alignment explanation
Indices: 52867531--52867555 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
52867521 GTATTGCAAC
52867531 TTTTA TTTTA TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA
52867556 CTCAAATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:52874285 original size:53 final size:53
Alignment explanation
Indices: 52874222--52874328 Score: 198
Period size: 53 Copynumber: 2.0 Consensus size: 53
52874212 TACTTCTACT
52874222 CCAAGAGTTTGATCTAGAAATTCAGGATCGAAAGGGT-GTAGAAAATCAAGTAG
1 CCAAGAGTTTGATCTAGAAATTCAGGATCGAAA-GGTAGTAGAAAATCAAGTAG
52874275 CCAAGAGTTTGATCTAGAAATTCAGGATCGAAAGGTAGTAGAAAATCAAGTAG
1 CCAAGAGTTTGATCTAGAAATTCAGGATCGAAAGGTAGTAGAAAATCAAGTAG
52874328 C
1 C
52874329 AGACCACTTA
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
52 3 0.06
53 50 0.94
ACGTcount: A:0.40, C:0.12, G:0.25, T:0.22
Consensus pattern (53 bp):
CCAAGAGTTTGATCTAGAAATTCAGGATCGAAAGGTAGTAGAAAATCAAGTAG
Found at i:52880802 original size:5 final size:5
Alignment explanation
Indices: 52880759--52880783 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
52880749 GCATTGAAAC
52880759 TTTTA TTTTA TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA
52880784 CTCAGTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:52881206 original size:2 final size:2
Alignment explanation
Indices: 52881199--52881244 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
52881189 ATATCTTTAT
52881199 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
52881241 AC AC
1 AC AC
52881245 CATAGAACCA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:52882240 original size:41 final size:41
Alignment explanation
Indices: 52882162--52882301 Score: 194
Period size: 41 Copynumber: 3.4 Consensus size: 41
52882152 TCATTACTAA
* *
52882162 CCTTTTCGACCTTTTCA-TTGATAT-TTTCTTCAAATATCGT
1 CCTTTTCAACCTTTTCATTTGATATCTTT-TTCAGATATCGT
* * * *
52882202 CATTTCCAACCTTTTCATTTGATATCCTTTTCGGATATCGT
1 CCTTTTCAACCTTTTCATTTGATATCTTTTTCAGATATCGT
*
52882243 CCTTTTCAACCTTTTCATTTGATATCTTTTTCAGATATCAT
1 CCTTTTCAACCTTTTCATTTGATATCTTTTTCAGATATCGT
52882284 CCTTTTCAACCTTTTCAT
1 CCTTTTCAACCTTTTCAT
52882302 AGATTCAGGA
Statistics
Matches: 87, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
40 14 0.16
41 71 0.82
42 2 0.02
ACGTcount: A:0.20, C:0.24, G:0.06, T:0.49
Consensus pattern (41 bp):
CCTTTTCAACCTTTTCATTTGATATCTTTTTCAGATATCGT
Found at i:52882501 original size:20 final size:20
Alignment explanation
Indices: 52882463--52882501 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
52882453 AGATATCAAT
*
52882463 TAATATTATAAATTCAAATG
1 TAATATTATAAAATCAAATG
* *
52882483 TAATATTTTAAAATGAAAT
1 TAATATTATAAAATCAAAT
52882502 ACGAACTTAC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.41
Consensus pattern (20 bp):
TAATATTATAAAATCAAATG
Found at i:52886469 original size:17 final size:17
Alignment explanation
Indices: 52886430--52886472 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
52886420 AACAGAAGTT
52886430 TGCGAGCTCACCAAGAC
1 TGCGAGCTCACCAAGAC
* * *
52886447 TACGAGCTCACCAATAG
1 TGCGAGCTCACCAAGAC
52886464 TGCGAGCTC
1 TGCGAGCTC
52886473 TTTACCTTGC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.28, C:0.33, G:0.23, T:0.16
Consensus pattern (17 bp):
TGCGAGCTCACCAAGAC
Found at i:52890718 original size:15 final size:15
Alignment explanation
Indices: 52890698--52890726 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
52890688 ATGCCTCACA
52890698 CACCGTGTTATCAAT
1 CACCGTGTTATCAAT
52890713 CACCGTGTTATCAA
1 CACCGTGTTATCAA
52890727 GCAACAGTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.31
Consensus pattern (15 bp):
CACCGTGTTATCAAT
Found at i:52891584 original size:15 final size:15
Alignment explanation
Indices: 52891564--52891592 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
52891554 ATGCCTCACA
52891564 CACCGTGTTATCAAT
1 CACCGTGTTATCAAT
52891579 CACCGTGTTATCAA
1 CACCGTGTTATCAA
52891593 GCAACAGTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.31
Consensus pattern (15 bp):
CACCGTGTTATCAAT
Found at i:52892451 original size:15 final size:15
Alignment explanation
Indices: 52892431--52892459 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
52892421 ATGCCTCACA
52892431 CACCGTGTTATCAAT
1 CACCGTGTTATCAAT
52892446 CACCGTGTTATCAA
1 CACCGTGTTATCAA
52892460 GCAACAGTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.31
Consensus pattern (15 bp):
CACCGTGTTATCAAT
Found at i:52892668 original size:867 final size:867
Alignment explanation
Indices: 52890400--52893866 Score: 6722
Period size: 866 Copynumber: 4.0 Consensus size: 867
52890390 AGCCTTGGAT
52890400 AATTTCCAATAAAATCAAAATTATGATTTTTTGCGAAAAACTCATTTTAAAATTTGATTTTGCAT
1 AATTTCCAATAAAATCAAAATTATGATTTTTTGCGAAAAACTCATTTTAAAATTTGATTTTGCAT
52890465 ATTTTAATGGTCAATTAAACTCGATTTAACTACGATTAATTAACATGCATATACATACACCTTCA
66 ATTTTAATGGTCAATTAAACTCGATTTAACTACGATTAATTAACATGCATATACATACACCTTCA
52890530 ATTGAGTTTATTGACATCAATCAAGCCTCAATTATATAGAACTAGGCAATCAATTTCATGCATAT
131 ATTGAGTTTATTGACATCAATCAAGCCTCAATTATATAGAACTAGGCAATCAATTTCATGCATAT
52890595 CAAACACTGAATAAATCAAACAAGTGATGTACCTTAGTTGCTAGTAAACGTCTCCATGGAAGCTT
196 CAAACACTGAATAAATCAAACAAGTGATGTACCTTAGTTGCTAGTAAACGTCTCCATGGAAGCTT
*
52890660 CATTTAAACAATTGTTAGTACAAATTTCATGCCTCACACACCGTGTTATCAATCACCGTGTTATC
261 CATTTAAACAATCGTTAGTACAAATTTCATGCCTCACACACCGTGTTATCAATCACCGTGTTATC
52890725 AAGCAACAGTACAATGTAAACCATTCAATAATTAAACTCAAACATGCCTAAAAATTATTATAAAA
326 AAGCAACAGTACAATGTAAACCATTCAATAATTAAACTCAAACATGCCTAAAAATTATTATAAAA
52890790 CCATCCAAAATAAAATGTCCAATGTCCAAAATCCAATTACAACCAAAATTAAACTAATTCCCGGG
391 CCATCCAAAATAAAATGTCCAATGTCCAAAATCCAATTACAACCAAAATTAAACTAATTCCCGGG
52890855 AGTTCCAGAATGTCCGATTACAGTCTCTAAAACATGTAATAAAGTATCTACCAAGTCTAAAACTC
456 AGTTCCAGAATGTCCGATTACAGTCTCTAAAACATGTAATAAAGTATCTACCAAGTCTAAAACTC
* *
52890920 TTGGAACTCTCTTGCTTTGCTCCTCAACTCCTCAAGCCCGATGATTATCTGTACAAATTGTGAGG
521 TTGGAACTCTCTTGCTTGGCTCCTCAACTCCTCAAGCCCGATGATTATCTGCACAAATTGTGAGG
52890985 GTGTGAGCTCTAAAACTCTCAGTGAATGTTAATAAAAACGACTAGTAAATCAACATCCAAACCAT
586 GTGTGAGCTCTAAAACTCTCAGTGAATGTTAATAAAAACGACTAGTAAATCAACATCCAAACCAT
52891050 GCTTATATCTCATCCAATCAATCACCAATTATCAACCATAATAATGAAACATGTCAATTTAATTT
651 GCTTATATCTCATCCAATCAATCACCAATTATCAACCATAATAATGAAACATGTCAATTTAATTT
* *
52891115 CTATATGCTTTATCAATATCACGAATCAATTATTTATGGTTTACAAACATCGAATGATATAACAA
716 CCATATGCTTTATCAATATCAAGAATCAATTATTTATGGTTTACAAACATCGAATGATATAACAA
52891180 TAATCACACATAAATATATTGGCATACACTTCTCATGGCTTAATTGGGTGATCATACATCGGATA
781 TAATCACACATAAATATATTGGCATACACTTCTCATGGCTTAATTGGGTGATCATACATCGGATA
*
52891245 AATGAATTTCCAAACTCCGAAA
846 AACGAATTTCCAAACTCCGAAA
52891267 AATTTCCAATAAAATCAAAATTATGA-TTTTTGCGAAAAACTCATTTTAAAATTTGATTTTGCAT
1 AATTTCCAATAAAATCAAAATTATGATTTTTTGCGAAAAACTCATTTTAAAATTTGATTTTGCAT
*
52891331 ATTTTAACGGTCAATTAAACTCGATTTAACTACGATTAATTAACATGCATATACATACACCTTCA
66 ATTTTAATGGTCAATTAAACTCGATTTAACTACGATTAATTAACATGCATATACATACACCTTCA
52891396 ATTGAGTTTATTGACATCAATCAAGCCTCAATTATATAGAACTAGGCAATCAATTTCATGCATAT
131 ATTGAGTTTATTGACATCAATCAAGCCTCAATTATATAGAACTAGGCAATCAATTTCATGCATAT
52891461 CAAACACTGAATAAATCAAACAAGTGATGTACCTTAGTTGCTAGTAAACGTCTCCATGGAAGCTT
196 CAAACACTGAATAAATCAAACAAGTGATGTACCTTAGTTGCTAGTAAACGTCTCCATGGAAGCTT
52891526 CATTTAAACAATCGTTAGTACAAATTTCATGCCTCACACACCGTGTTATCAATCACCGTGTTATC
261 CATTTAAACAATCGTTAGTACAAATTTCATGCCTCACACACCGTGTTATCAATCACCGTGTTATC
52891591 AAGCAACAGTACAATGTAAACCATTCAATAATTAAACTCAAACATGCCTAAAAATTATTATAAAA
326 AAGCAACAGTACAATGTAAACCATTCAATAATTAAACTCAAACATGCCTAAAAATTATTATAAAA
52891656 CCATCCAAAATAAAATGTCCAATGTCCAAAATCCAATTACAACCAAAATTAAACTAATTCCCGGG
391 CCATCCAAAATAAAATGTCCAATGTCCAAAATCCAATTACAACCAAAATTAAACTAATTCCCGGG
52891721 AGTTCCAGAATGTCCGATTACAGTCTCTAAAACATGTAATAAAGTATCTACCAAGTCTAAAACTC
456 AGTTCCAGAATGTCCGATTACAGTCTCTAAAACATGTAATAAAGTATCTACCAAGTCTAAAACTC
52891786 TTGGAACTCTCTTGCTTGGCTCCTCAACTCCTCAAGCCCGATGATTATCTGCACAAATTGTGAGG
521 TTGGAACTCTCTTGCTTGGCTCCTCAACTCCTCAAGCCCGATGATTATCTGCACAAATTGTGAGG
*
52891851 GTGTGAGCTCTAAAACTCTTAGTGAATGTTAATAAAAACGACTAGTAAATCAACATCCAAACCAT
586 GTGTGAGCTCTAAAACTCTCAGTGAATGTTAATAAAAACGACTAGTAAATCAACATCCAAACCAT
52891916 GCTTATATCTCATCCAATCAATCACCAATTATCAACCATAATAATGAAACATGTCAATTTAATTT
651 GCTTATATCTCATCCAATCAATCACCAATTATCAACCATAATAATGAAACATGTCAATTTAATTT
*
52891981 CCATATGCTTTATCAATATCAAGAATCAATTATTTATGGTTTACAAACATCGAATAATATAACAA
716 CCATATGCTTTATCAATATCAAGAATCAATTATTTATGGTTTACAAACATCGAATGATATAACAA
* *
52892046 TAATAACACATAAATATATTGGCATACACTTCTCATGGCTTAATTGGGTGATCATACATCAGATA
781 TAATCACACATAAATATATTGGCATACACTTCTCATGGCTTAATTGGGTGATCATACATCGGATA
52892111 AACGAATTTCCAAACTCCGAAA
846 AACGAATTTCCAAACTCCGAAA
*
52892133 AATTTCCAATAAAATCAAAATTATGATTTTTTACGAAAAACTCATTTTAAAATTTGATTTTGCAT
1 AATTTCCAATAAAATCAAAATTATGATTTTTTGCGAAAAACTCATTTTAAAATTTGATTTTGCAT
*
52892198 ATTTTAATGGTCAATTAAACTCGATTTAACTACGATTAATTAACATGTATATACATACACCTTCA
66 ATTTTAATGGTCAATTAAACTCGATTTAACTACGATTAATTAACATGCATATACATACACCTTCA
52892263 ATTGAGTTTATTGACATCAATCAAGCCTCAATTATATAGAACTAGGCAATCAATTTCATGCATAT
131 ATTGAGTTTATTGACATCAATCAAGCCTCAATTATATAGAACTAGGCAATCAATTTCATGCATAT
52892328 CAAACACTGAATAAATCAAACAAGTGATGTACCTTAGTTGCTAGTAAACGTCTCCATGGAAGCTT
196 CAAACACTGAATAAATCAAACAAGTGATGTACCTTAGTTGCTAGTAAACGTCTCCATGGAAGCTT
52892393 CATTTAAACAATCGTTAGTACAAATTTCATGCCTCACACACCGTGTTATCAATCACCGTGTTATC
261 CATTTAAACAATCGTTAGTACAAATTTCATGCCTCACACACCGTGTTATCAATCACCGTGTTATC
52892458 AAGCAACAGTACAATGTAAACCATTCAATAATTAAACTCAAACATGCCTAAAAATTATTATAAAA
326 AAGCAACAGTACAATGTAAACCATTCAATAATTAAACTCAAACATGCCTAAAAATTATTATAAAA
52892523 CCATCCAAAATAAAATGTCCAATGTCCAAAATCCAATTACAACCAAAATTAAACTAATTCCCGGG
391 CCATCCAAAATAAAATGTCCAATGTCCAAAATCCAATTACAACCAAAATTAAACTAATTCCCGGG
52892588 AGTTCCAGAATGTCCGATTACAGTCTCTAAAACATGTAATAAAGTATCTACCAAGTCTAAAACTC
456 AGTTCCAGAATGTCCGATTACAGTCTCTAAAACATGTAATAAAGTATCTACCAAGTCTAAAACTC
52892653 TTGGAACTCTCTTGCTTGGCTCCTCAACTCCTCAAGCCCGATGATTATCTGCACAAATTGTGAGG
521 TTGGAACTCTCTTGCTTGGCTCCTCAACTCCTCAAGCCCGATGATTATCTGCACAAATTGTGAGG
52892718 GTGTGAGCTCTAAAACTCTCAGTGAATGTTAATAAAAACGACTAGTAAATCAACATCCAAACCAT
586 GTGTGAGCTCTAAAACTCTCAGTGAATGTTAATAAAAACGACTAGTAAATCAACATCCAAACCAT
52892783 GCTTATATCTCATCCAATCAATCACCAATTATCAACCATAATAATGAAACATGTCAATTTAATTT
651 GCTTATATCTCATCCAATCAATCACCAATTATCAACCATAATAATGAAACATGTCAATTTAATTT
*
52892848 TCATATGCTTTATCAATATCAAGAATCAATTATTTATGGTTTACAAACATCGAATGATATAACAA
716 CCATATGCTTTATCAATATCAAGAATCAATTATTTATGGTTTACAAACATCGAATGATATAACAA
52892913 TAATCACACATAAATATATTGGCATACACTTCTCATGGCTTAATTGGGTGATCATACATCGGATA
781 TAATCACACATAAATATATTGGCATACACTTCTCATGGCTTAATTGGGTGATCATACATCGGATA
52892978 AACGAATTTCCAAACTCCGAAA
846 AACGAATTTCCAAACTCCGAAA
52893000 AATTTCCAATAAAATCAAAATTATGATTTTTTGCGAAAAACTCATTTTAAAATTTGATTTTGCAT
1 AATTTCCAATAAAATCAAAATTATGATTTTTTGCGAAAAACTCATTTTAAAATTTGATTTTGCAT
52893065 ATTTTAATGGTCAATTAAACTCGATTTAACTACGATTAATTAACATGCATATACATACACCTTCA
66 ATTTTAATGGTCAATTAAACTCGATTTAACTACGATTAATTAACATGCATATACATACACCTTCA
*
52893130 ATTGAGTTTATTGACATCGATCAAGCCTCAATTATATAGAACTAGGCAATCAATTTCATGCATAT
131 ATTGAGTTTATTGACATCAATCAAGCCTCAATTATATAGAACTAGGCAATCAATTTCATGCATAT
52893195 CAAACACTGAATAAATCAAACAAGTGATGTACCTTAGTTGCTAGTAAACGTCTCCATGGAAGCTT
196 CAAACACTGAATAAATCAAACAAGTGATGTACCTTAGTTGCTAGTAAACGTCTCCATGGAAGCTT
52893260 CATTTAAACAATCGTTAGTACAAATTTCATGCCTCACACACCGTGTTATCAATCACCGTGTTATC
261 CATTTAAACAATCGTTAGTACAAATTTCATGCCTCACACACCGTGTTATCAATCACCGTGTTATC
52893325 AAGCAACAGTACAATGTAAACCATTCAATAATTAAACTCAAACATGCCT-AAAATTATTATAAAA
326 AAGCAACAGTACAATGTAAACCATTCAATAATTAAACTCAAACATGCCTAAAAATTATTATAAAA
*
52893389 CCATCCAAAATAAAATGTCCAATGTCCAAAATCCAATTACAACCAAAATTAAACTAATTCCCAGG
391 CCATCCAAAATAAAATGTCCAATGTCCAAAATCCAATTACAACCAAAATTAAACTAATTCCCGGG
*
52893454 AGTTCCAGAATGTCCGATTACAGTCTCTAAAACATGTAATAAAGTGTCTACCAAGTCTAAAACTC
456 AGTTCCAGAATGTCCGATTACAGTCTCTAAAACATGTAATAAAGTATCTACCAAGTCTAAAACTC
52893519 TTGGAACTCTCTTGCTTGGCTCCTCAACTCCTCAAGCCCGATGATTATCTGCACAAATTGTGAGG
521 TTGGAACTCTCTTGCTTGGCTCCTCAACTCCTCAAGCCCGATGATTATCTGCACAAATTGTGAGG
* * *
52893584 GTGTGAGCTCTAAAACTCTCAATGAATGTTAATAAAAACAACTAGTAAATCAACATCCAAAGCAT
586 GTGTGAGCTCTAAAACTCTCAGTGAATGTTAATAAAAACGACTAGTAAATCAACATCCAAACCAT
52893649 GCTTATATCTCATCCAATCAATCACCAATTATCAACCATAATAATGAAACATGTCAATTTAATTT
651 GCTTATATCTCATCCAATCAATCACCAATTATCAACCATAATAATGAAACATGTCAATTTAATTT
*
52893714 CTATATGCTTTATCAATATCAAGAATCAATTATTTATGGTTTACAAACATCGAATGATATAACAA
716 CCATATGCTTTATCAATATCAAGAATCAATTATTTATGGTTTACAAACATCGAATGATATAACAA
*
52893779 TAATCACACATAAATATATTGGCATACACTTCTCATGGCTTAATTGGGTGATCATACACCGGATA
781 TAATCACACATAAATATATTGGCATACACTTCTCATGGCTTAATTGGGTGATCATACATCGGATA
52893844 AACGAATTTCCAAACTCCGAAA
846 AACGAATTTCCAAACTCCGAAA
52893866 A
1 A
52893867 TATCAAATAT
Statistics
Matches: 2569, Mismatches: 30, Indels: 3
0.99 0.01 0.00
Matches are distributed among these distances:
866 1340 0.52
867 1229 0.48
ACGTcount: A:0.39, C:0.20, G:0.11, T:0.31
Consensus pattern (867 bp):
AATTTCCAATAAAATCAAAATTATGATTTTTTGCGAAAAACTCATTTTAAAATTTGATTTTGCAT
ATTTTAATGGTCAATTAAACTCGATTTAACTACGATTAATTAACATGCATATACATACACCTTCA
ATTGAGTTTATTGACATCAATCAAGCCTCAATTATATAGAACTAGGCAATCAATTTCATGCATAT
CAAACACTGAATAAATCAAACAAGTGATGTACCTTAGTTGCTAGTAAACGTCTCCATGGAAGCTT
CATTTAAACAATCGTTAGTACAAATTTCATGCCTCACACACCGTGTTATCAATCACCGTGTTATC
AAGCAACAGTACAATGTAAACCATTCAATAATTAAACTCAAACATGCCTAAAAATTATTATAAAA
CCATCCAAAATAAAATGTCCAATGTCCAAAATCCAATTACAACCAAAATTAAACTAATTCCCGGG
AGTTCCAGAATGTCCGATTACAGTCTCTAAAACATGTAATAAAGTATCTACCAAGTCTAAAACTC
TTGGAACTCTCTTGCTTGGCTCCTCAACTCCTCAAGCCCGATGATTATCTGCACAAATTGTGAGG
GTGTGAGCTCTAAAACTCTCAGTGAATGTTAATAAAAACGACTAGTAAATCAACATCCAAACCAT
GCTTATATCTCATCCAATCAATCACCAATTATCAACCATAATAATGAAACATGTCAATTTAATTT
CCATATGCTTTATCAATATCAAGAATCAATTATTTATGGTTTACAAACATCGAATGATATAACAA
TAATCACACATAAATATATTGGCATACACTTCTCATGGCTTAATTGGGTGATCATACATCGGATA
AACGAATTTCCAAACTCCGAAA
Found at i:52893318 original size:15 final size:15
Alignment explanation
Indices: 52893298--52893326 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
52893288 ATGCCTCACA
52893298 CACCGTGTTATCAAT
1 CACCGTGTTATCAAT
52893313 CACCGTGTTATCAA
1 CACCGTGTTATCAA
52893327 GCAACAGTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.31
Consensus pattern (15 bp):
CACCGTGTTATCAAT
Found at i:52921406 original size:45 final size:45
Alignment explanation
Indices: 52921337--52921427 Score: 155
Period size: 45 Copynumber: 2.0 Consensus size: 45
52921327 AGATACTCGA
* *
52921337 TGGATTCAGCACATAGCAACCACCTTATTAATCAATGATGTCCGG
1 TGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTCCGG
*
52921382 TGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTTCGG
1 TGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTCCGG
52921427 T
1 T
52921428 TCACATAGTA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (45 bp):
TGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTCCGG
Found at i:52921491 original size:51 final size:52
Alignment explanation
Indices: 52921433--52921568 Score: 197
Period size: 50 Copynumber: 2.7 Consensus size: 52
52921423 TCGGTTCACA
52921433 TAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATCT-GATACACG
1 TAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATCTCGATACACG
* * * *
52921484 TAGTAGCCTGCACATAGTACTACACATGCGACC--TATCATTTCGGTACACG
1 TAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATCTCGATACACG
* *
52921534 TAGTAGCCTGCACATAGTAGTACACACGTGACCAT
1 TAGTAGCCTGCACATAGTACTACACATGTGACCAT
52921569 CACTTTCACC
Statistics
Matches: 75, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
49 6 0.08
50 37 0.49
51 32 0.43
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (52 bp):
TAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATCTCGATACACG
Found at i:52921558 original size:50 final size:51
Alignment explanation
Indices: 52921422--52921568 Score: 190
Period size: 51 Copynumber: 2.9 Consensus size: 51
52921412 ATCAATGATG
* * *
52921422 TTCGGTTCACATAGTAGCCTGCACATAGTACTACACATGTGACCATTACCAT
1 TTCGGTACACGTAGTAGCCTGCACATAGTACTACACATGCGACCA-TACCAT
* * *
52921474 CT-GATACACGTAGTAGCCTGCACATAGTACTACACATGCGACC-TATCAT
1 TTCGGTACACGTAGTAGCCTGCACATAGTACTACACATGCGACCATACCAT
* * *
52921523 TTCGGTACACGTAGTAGCCTGCACATAGTAGTACACACGTGACCAT
1 TTCGGTACACGTAGTAGCCTGCACATAGTACTACACATGCGACCAT
52921569 CACTTTCACC
Statistics
Matches: 82, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
49 6 0.07
50 37 0.45
51 38 0.46
52 1 0.01
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.26
Consensus pattern (51 bp):
TTCGGTACACGTAGTAGCCTGCACATAGTACTACACATGCGACCATACCAT
Found at i:52929802 original size:13 final size:13
Alignment explanation
Indices: 52929784--52929826 Score: 61
Period size: 13 Copynumber: 3.4 Consensus size: 13
52929774 GTTTGCACTT
52929784 CGGTCTAACCACA
1 CGGTCTAACCACA
**
52929797 CGGTCT-TTCACA
1 CGGTCTAACCACA
52929809 CGGTCTAACCACA
1 CGGTCTAACCACA
52929822 CGGTC
1 CGGTC
52929827 GTGTGAATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
12 10 0.40
13 15 0.60
ACGTcount: A:0.23, C:0.37, G:0.19, T:0.21
Consensus pattern (13 bp):
CGGTCTAACCACA
Found at i:52931299 original size:13 final size:13
Alignment explanation
Indices: 52931281--52931306 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
52931271 GAAAATGTGG
52931281 ATCAGGTTTGGAA
1 ATCAGGTTTGGAA
52931294 ATCAGGTTTGGAA
1 ATCAGGTTTGGAA
52931307 CTCATAGTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.08, G:0.31, T:0.31
Consensus pattern (13 bp):
ATCAGGTTTGGAA
Found at i:52936236 original size:16 final size:16
Alignment explanation
Indices: 52936215--52936246 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
52936205 ATTTTGTTGC
*
52936215 TAATTTTACTTTTTCA
1 TAATTTCACTTTTTCA
52936231 TAATTTCACTTTTTCA
1 TAATTTCACTTTTTCA
52936247 CTTTCAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.16, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTTCACTTTTTCA
Found at i:52936463 original size:46 final size:45
Alignment explanation
Indices: 52936383--52936470 Score: 108
Period size: 46 Copynumber: 1.9 Consensus size: 45
52936373 ACACGATGGA
*
52936383 ATCAGCACACAGCAACCACCCTTTGTAATCAATGATATCCGGTGGG
1 ATCAGCACACAGCAACCACCCTTTATAATCAATGATA-CCGGTGGG
* *
52936429 ATCAGCACATAGCAACC-CTACC-TTATAATTAATGATACCGGT
1 ATCAGCACACAGCAACCAC--CCTTTATAATCAATGATACCGGT
52936471 TCACATAGTA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
45 6 0.16
46 29 0.78
47 2 0.05
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.24
Consensus pattern (45 bp):
ATCAGCACACAGCAACCACCCTTTATAATCAATGATACCGGTGGG
Found at i:52936534 original size:51 final size:51
Alignment explanation
Indices: 52936476--52936662 Score: 222
Period size: 51 Copynumber: 3.7 Consensus size: 51
52936466 CCGGTTCACA
* *
52936476 TAGTAGCCTGCACATAGTACTACACATGTGACCATCACTATTC-GATACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCAT-ACTATTCTGGTACACG
* * *
52936527 TAGTAGCCTGCACATAGTACTACACACGTGATCGA-AGCTA-TCTGGTACGCA
1 TAGTAGCCTGCACATAGTACTACACACGTGA-CCATA-CTATTCTGGTACACG
** * *
52936578 TAGTAGCCTATACATAGTACTACACATGCGACC-TA-TCATTCTGGTACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATACT-ATTCTGGTACACG
52936628 TAGTAGCCTGCACATAGTACTACACACGTGACCAT
1 TAGTAGCCTGCACATAGTACTACACACGTGACCAT
52936663 CACTTTCACT
Statistics
Matches: 113, Mismatches: 16, Indels: 14
0.79 0.11 0.10
Matches are distributed among these distances:
48 1 0.01
49 1 0.01
50 43 0.38
51 66 0.58
52 2 0.02
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (51 bp):
TAGTAGCCTGCACATAGTACTACACACGTGACCATACTATTCTGGTACACG
Found at i:52936650 original size:101 final size:102
Alignment explanation
Indices: 52936474--52936658 Score: 295
Period size: 101 Copynumber: 1.8 Consensus size: 102
52936464 TACCGGTTCA
* *
52936474 CATAGTAGCCTGCACATAGTACTACACATGTGACCATCACTATTCGATACACGTAGTAGCCTGCA
1 CATAGTAGCCTACACATAGTACTACACATGCGACCATCACTATTCGATACACGTAGTAGCCTGCA
52936539 CATAGTACTACACACGTGATCGAAGCTATCTGGTACG
66 CATAGTACTACACACGTGATCGAAGCTATCTGGTACG
* *
52936576 CATAGTAGCCTATACATAGTACTACACATGCGACC-T-A-TCATTCTGGTACACGTAGTAGCCTG
1 CATAGTAGCCTACACATAGTACTACACATGCGACCATCACT-ATTC-GATACACGTAGTAGCCTG
52936638 CACATAGTACTACACACGTGA
64 CACATAGTACTACACACGTGA
52936659 CCATCACTTT
Statistics
Matches: 77, Mismatches: 4, Indels: 5
0.90 0.05 0.06
Matches are distributed among these distances:
99 1 0.01
100 5 0.06
101 39 0.51
102 32 0.42
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (102 bp):
CATAGTAGCCTACACATAGTACTACACATGCGACCATCACTATTCGATACACGTAGTAGCCTGCA
CATAGTACTACACACGTGATCGAAGCTATCTGGTACG
Found at i:52936681 original size:101 final size:102
Alignment explanation
Indices: 52936469--52936692 Score: 269
Period size: 101 Copynumber: 2.2 Consensus size: 102
52936459 AATGATACCG
* *
52936469 GTTCACATAGTAGCCTGCACATAGTACTACACATGTGACCATCACTATTCGATACACGTAGTAGC
1 GTTCACATAGTAGCCTACACATAGTACTACACATGCGACCATCACTATTCGATACACGTAGTAGC
* **
52936534 CTGCACATAGTACTACACACGTGATCGAAGCTATCTG
66 CTGCACATAGTACTACACACGTGATCCAAGCTATCAC
* * * *
52936571 GTACGCATAGTAGCCTATACATAGTACTACACATGCGACC-T-A-TCATTCTGGTACACGTAGTA
1 GTTCACATAGTAGCCTACACATAGTACTACACATGCGACCATCACT-ATTC-GATACACGTAGTA
*
52936633 GCCTGCACATAGTACTACACACGTGA-CCATCA-CTTTCAC
64 GCCTGCACATAGTACTACACACGTGATCCA--AGCTATCAC
* *
52936672 TTTCACATAGTGGCCTACACA
1 GTTCACATAGTAGCCTACACA
52936693 CAGTCCATGC
Statistics
Matches: 103, Mismatches: 15, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
99 1 0.01
100 7 0.07
101 59 0.57
102 36 0.35
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.26
Consensus pattern (102 bp):
GTTCACATAGTAGCCTACACATAGTACTACACATGCGACCATCACTATTCGATACACGTAGTAGC
CTGCACATAGTACTACACACGTGATCCAAGCTATCAC
Found at i:52948597 original size:19 final size:21
Alignment explanation
Indices: 52948575--52948614 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
52948565 TTCTATCCAT
52948575 AAAATA-T-TAAACCATAATC
1 AAAATAGTCTAAACCATAATC
52948594 AAAATATGTCTAAACCATAAT
1 AAAATA-GTCTAAACCATAAT
52948615 TCACTCAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.33
21 1 0.06
22 11 0.61
ACGTcount: A:0.55, C:0.15, G:0.03, T:0.28
Consensus pattern (21 bp):
AAAATAGTCTAAACCATAATC
Found at i:52949376 original size:43 final size:43
Alignment explanation
Indices: 52949269--52949385 Score: 123
Period size: 43 Copynumber: 2.7 Consensus size: 43
52949259 TTCGTACAAC
* * * *
52949269 GCCAACGTCCCAGACGTGATCTTACATGTAATCACAGATCGAT
1 GCCAACGTCCCAGACGTGGTCTTACACGAAAACACAGATCGAT
* * *
52949312 GCC-GCTATCCCGGACAG-GGTCTTACACGAAAACACA-AGTCGAT
1 GCCAAC-GTCCCAGAC-GTGGTCTTACACGAAAACACAGA-TCGAT
52949355 GCCAACGTCCCAGACGTGGTCTTACACGAAA
1 GCCAACGTCCCAGACGTGGTCTTACACGAAA
52949386 TCACTTATCA
Statistics
Matches: 59, Mismatches: 10, Indels: 10
0.75 0.13 0.13
Matches are distributed among these distances:
42 3 0.05
43 54 0.92
44 2 0.03
ACGTcount: A:0.30, C:0.30, G:0.21, T:0.19
Consensus pattern (43 bp):
GCCAACGTCCCAGACGTGGTCTTACACGAAAACACAGATCGAT
Found at i:52955508 original size:26 final size:26
Alignment explanation
Indices: 52955472--52955563 Score: 130
Period size: 26 Copynumber: 3.5 Consensus size: 26
52955462 CATTAGGACA
*
52955472 TAGCAGGCTTCGAGTTGGTGTATATT
1 TAGCAGGCTTCGAGCTGGTGTATATT
* *
52955498 TAGCCGGCTTCGAGCTGGTGTATTTT
1 TAGCAGGCTTCGAGCTGGTGTATATT
* * *
52955524 TAGTAGGTTTCGTGCTGGTGTATATT
1 TAGCAGGCTTCGAGCTGGTGTATATT
52955550 TAGCAGGCTTCGAG
1 TAGCAGGCTTCGAG
52955564 TCATTGTTTT
Statistics
Matches: 55, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 55 1.00
ACGTcount: A:0.16, C:0.14, G:0.32, T:0.38
Consensus pattern (26 bp):
TAGCAGGCTTCGAGCTGGTGTATATT
Found at i:52960506 original size:12 final size:12
Alignment explanation
Indices: 52960472--52960584 Score: 55
Period size: 12 Copynumber: 9.8 Consensus size: 12
52960462 ATTCTAAAAA
*
52960472 TAATA-TTATTT
1 TAATATTTAATT
52960483 TAATAGTTTAATAT
1 TAATA-TTTAAT-T
52960497 TAA-ATTTAATT
1 TAATATTTAATT
52960508 TAATATTT-ATCT
1 TAATATTTAAT-T
*
52960520 TAATA-GT-ATT
1 TAATATTTAATT
52960530 T--TA-TTAATT
1 TAATATTTAATT
* *
52960539 TAATATTAAAGT
1 TAATATTTAATT
* *
52960551 GATTATCTTAATAT
1 TAATAT-TTAAT-T
52960565 TAA-ATTTAATT
1 TAATATTTAATT
*
52960576 TAATGTTTA
1 TAATATTTA
52960585 TCTTGTAGAT
Statistics
Matches: 78, Mismatches: 12, Indels: 23
0.69 0.11 0.20
Matches are distributed among these distances:
8 3 0.04
9 4 0.05
10 2 0.03
11 20 0.26
12 33 0.42
13 10 0.13
14 6 0.08
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (12 bp):
TAATATTTAATT
Found at i:52960525 original size:37 final size:37
Alignment explanation
Indices: 52960472--52960588 Score: 99
Period size: 37 Copynumber: 3.4 Consensus size: 37
52960462 ATTCTAAAAA
*
52960472 TAATA-TTATTTTAATAGTTTAATATTAAATTTAATT
1 TAATATTTATCTTAATAGTTTAATATTAAATTTAATT
*
52960508 TAATATTTATCTTAATAGTATT-TTATT-AATTTAATAT
1 TAATATTTATCTTAATAGT-TTAATATTAAATTTAAT-T
* * *
52960545 TAA-AGTGA--TT-AT--CTTAATATTAAATTTAATT
1 TAATATTTATCTTAATAGTTTAATATTAAATTTAATT
*
52960576 TAATGTTTATCTT
1 TAATATTTATCTT
52960589 GTAGATAAAC
Statistics
Matches: 64, Mismatches: 9, Indels: 18
0.70 0.10 0.20
Matches are distributed among these distances:
30 2 0.03
31 8 0.12
32 10 0.16
33 2 0.03
34 4 0.06
36 16 0.25
37 20 0.31
38 2 0.03
ACGTcount: A:0.38, C:0.03, G:0.04, T:0.55
Consensus pattern (37 bp):
TAATATTTATCTTAATAGTTTAATATTAAATTTAATT
Found at i:52960547 original size:11 final size:11
Alignment explanation
Indices: 52960472--52960547 Score: 52
Period size: 11 Copynumber: 6.8 Consensus size: 11
52960462 ATTCTAAAAA
*
52960472 TAATATTATTT
1 TAATATTAATT
52960483 TAATAGTTTAATAT
1 TAATA--TTAAT-T
52960497 TAA-ATTTAATT
1 TAATA-TTAATT
*
52960508 TAATATTTATCT
1 TAATATTAAT-T
*
52960520 TAATAGT-ATT
1 TAATATTAATT
52960530 T--TATTAATT
1 TAATATTAATT
52960539 TAATATTAA
1 TAATATTAA
52960548 AGTGATTATC
Statistics
Matches: 53, Mismatches: 4, Indels: 16
0.73 0.05 0.22
Matches are distributed among these distances:
8 3 0.06
9 4 0.08
10 2 0.04
11 21 0.40
12 14 0.26
13 5 0.09
14 4 0.08
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (11 bp):
TAATATTAATT
Found at i:52962607 original size:9 final size:9
Alignment explanation
Indices: 52962593--52962624 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
52962583 ACATATATTA
52962593 AATTTGGTT
1 AATTTGGTT
52962602 AATTTGGTT
1 AATTTGGTT
*
52962611 AATTCGGTT
1 AATTTGGTT
52962620 AATTT
1 AATTT
52962625 TTTTATCTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.25, C:0.03, G:0.19, T:0.53
Consensus pattern (9 bp):
AATTTGGTT
Found at i:52962756 original size:91 final size:90
Alignment explanation
Indices: 52962600--52962770 Score: 272
Period size: 91 Copynumber: 1.9 Consensus size: 90
52962590 TTAAATTTGG
** * *
52962600 TTAATTTGGTTAATTCGGTTAATTTTTTTATCTGTTTTATACTTGTTTTAACCAAAAAACAAAAA
1 TTAATTTGGTTAATTCAATTAATTTTTTTATATGTGTTATACTTGTTTTAACCAAAAAAC-AAAA
52962665 AATATAAATTTTGGTTATTTCATTCGA
65 AATATAAA-TTTGGTTATTTCATTCGA
*
52962692 TTAATTTGGTTAATTCAATTAA-TTTTTTATATGTGTTATACTTGTTTTAACCAAAAAATAAAAA
1 TTAATTTGGTTAATTCAATTAATTTTTTTATATGTGTTATACTTGTTTTAACCAAAAAACAAAAA
52962756 ATATAAATTTGGTTA
66 ATATAAATTTGGTTA
52962771 AATCGACCGA
Statistics
Matches: 74, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
89 8 0.11
90 12 0.16
91 34 0.46
92 20 0.27
ACGTcount: A:0.36, C:0.07, G:0.09, T:0.47
Consensus pattern (90 bp):
TTAATTTGGTTAATTCAATTAATTTTTTTATATGTGTTATACTTGTTTTAACCAAAAAACAAAAA
ATATAAATTTGGTTATTTCATTCGA
Found at i:52963513 original size:27 final size:27
Alignment explanation
Indices: 52963473--52963525 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
52963463 GCAATCAGTA
*
52963473 TAGTCCACTGAGACAGTAAACATGAGG
1 TAGTCCACTAAGACAGTAAACATGAGG
* *
52963500 TAGTCCGCTAAGACATTAAACATGAG
1 TAGTCCACTAAGACAGTAAACATGAG
52963526 AATTTTAGGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.38, C:0.19, G:0.23, T:0.21
Consensus pattern (27 bp):
TAGTCCACTAAGACAGTAAACATGAGG
Found at i:52967186 original size:24 final size:24
Alignment explanation
Indices: 52967139--52967186 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
52967129 GATGAATTAT
* *
52967139 AATTTAAAGTATATTGGTTGAATA
1 AATTTAAAGTATAATGATTGAATA
52967163 AATTTAAAGTATGAATGATT-AATA
1 AATTTAAAGTAT-AATGATTGAATA
52967187 TATTGTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 16 0.76
25 5 0.24
ACGTcount: A:0.46, C:0.00, G:0.15, T:0.40
Consensus pattern (24 bp):
AATTTAAAGTATAATGATTGAATA
Found at i:52971256 original size:37 final size:36
Alignment explanation
Indices: 52971192--52971330 Score: 197
Period size: 37 Copynumber: 3.8 Consensus size: 36
52971182 AGCTCAGACG
* * *
52971192 AAATCTCCACACGAAGTTATCGAGTCTTACCCAGAAA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCC-GAAA
52971229 AAATCTCCACACGTAGTCATCGGGTCTTACCCGAACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGAA-A
* *
52971266 TAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCC-GAAA
*
52971303 TAATCTCCACACGTAGTCATCGGGTCTT
1 AAATCTCCACACGTAGTCATCGGGTCTT
52971331 TAGAGCTCGG
Statistics
Matches: 95, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
36 3 0.03
37 90 0.95
38 2 0.02
ACGTcount: A:0.29, C:0.30, G:0.17, T:0.24
Consensus pattern (36 bp):
AAATCTCCACACGTAGTCATCGGGTCTTACCCGAAA
Found at i:52971293 original size:74 final size:74
Alignment explanation
Indices: 52971193--52971330 Score: 222
Period size: 74 Copynumber: 1.9 Consensus size: 74
52971183 GCTCAGACGA
*
52971193 AATCTCCACACGAAGTTATCGAGTCTTACCCAGAAAAAATCTCCACACGTAGTCATCGGGTCTTA
1 AATCTCCACACGAAGTCATCGAGTCTTACCCAGAAAAAATCTCCACACGTAGTCATCGGGTCTTA
52971258 CCCGAACAT
66 CCCGAACAT
* * * * *
52971267 AATCTCCACACGTAGTCATCGGGTCTTACCCGGACATAATCTCCACACGTAGTCATCGGGTCTT
1 AATCTCCACACGAAGTCATCGAGTCTTACCCAGAAAAAATCTCCACACGTAGTCATCGGGTCTT
52971331 TAGAGCTCGG
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
74 58 1.00
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.25
Consensus pattern (74 bp):
AATCTCCACACGAAGTCATCGAGTCTTACCCAGAAAAAATCTCCACACGTAGTCATCGGGTCTTA
CCCGAACAT
Found at i:52971522 original size:47 final size:47
Alignment explanation
Indices: 52971449--52972149 Score: 1125
Period size: 47 Copynumber: 14.7 Consensus size: 47
52971439 CCCTTCGGGA
* * * * * *
52971449 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * * * * * *
52971496 CCTGTCACATATATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * * *
52971543 CCTGTCACATATATACACTTTCATATTCATCACATCGGCCATTAGGT
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
52971590 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
52971637 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
52971684 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
52971731 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
52971778 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
52971827 CTTATCAAATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATC--ACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
52971876 CTTATCACATATATATACACTTTCAAATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
52971925 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
52971972 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
52972019 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
52972068 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
52972115 CTTATCACATATATACA-TGTTCACATCCATCACAT
1 CTTATCACATATATACACT-TTCACATTCATCACAT
52972150 AGAATCCTAA
Statistics
Matches: 624, Mismatches: 21, Indels: 18
0.94 0.03 0.03
Matches are distributed among these distances:
46 1 0.00
47 439 0.70
49 183 0.29
51 1 0.00
ACGTcount: A:0.30, C:0.30, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:52971839 original size:143 final size:141
Alignment explanation
Indices: 52971449--52972149 Score: 1125
Period size: 143 Copynumber: 4.9 Consensus size: 141
52971439 CCCTTCGGGA
* * * * * * * *
52971449 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
* * * * * * * *
52971514 TTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATACACTTTCATATTCATCACATC
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
*
52971579 GGCCATTAGGT
131 GGCCATTAGGC
52971590 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
*
52971655 TTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
52971720 GGCCATTAGGC
131 GGCCATTAGGC
52971731 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATAC
*
52971796 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAAATATATATACACTTTCACATTCATCA
64 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATC--ACATATATACACTTTCACATTCATCA
52971861 CATCGGCCATTAGGC
127 CATCGGCCATTAGGC
*
52971876 CTTATCACATATATATACACTTTCAAATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
52971941 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
64 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
52972006 TCGGCCATTAGGC
129 TCGGCCATTAGGC
52972019 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
*
52972084 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACA-TGTTCACATCCATCAC
64 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACT-TTCACATTCATCAC
52972148 AT
128 AT
52972150 AGAATCCTAA
Statistics
Matches: 529, Mismatches: 24, Indels: 12
0.94 0.04 0.02
Matches are distributed among these distances:
141 178 0.34
142 1 0.00
143 211 0.40
145 93 0.18
147 46 0.09
ACGTcount: A:0.30, C:0.30, G:0.09, T:0.32
Consensus pattern (141 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
GGCCATTAGGC
Found at i:52975354 original size:25 final size:24
Alignment explanation
Indices: 52975318--52975376 Score: 93
Period size: 25 Copynumber: 2.5 Consensus size: 24
52975308 ATAGAAATAA
*
52975318 ATTAA-AAAATGATTATCAATATC
1 ATTAATAAAATGATTATAAATATC
52975341 ATTAATAACAATGATTATAAATATC
1 ATTAATAA-AATGATTATAAATATC
52975366 ATTAATAAAAT
1 ATTAATAAAAT
52975377 CACAATAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
23 5 0.15
24 5 0.15
25 23 0.70
ACGTcount: A:0.54, C:0.07, G:0.03, T:0.36
Consensus pattern (24 bp):
ATTAATAAAATGATTATAAATATC
Found at i:52975672 original size:27 final size:27
Alignment explanation
Indices: 52975626--52975677 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
52975616 TATTAGAGTA
*
52975626 GCCCACGACCGTCTGAGAATTGGGGTT
1 GCCCACGACCCTCTGAGAATTGGGGTT
* *
52975653 GCCCACGACCCTTTGGGAATTGGGG
1 GCCCACGACCCTCTGAGAATTGGGG
52975678 CTAATAATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.17, C:0.27, G:0.35, T:0.21
Consensus pattern (27 bp):
GCCCACGACCCTCTGAGAATTGGGGTT
Found at i:52976908 original size:18 final size:17
Alignment explanation
Indices: 52976870--52976919 Score: 64
Period size: 18 Copynumber: 2.9 Consensus size: 17
52976860 TGTATTATAA
52976870 TATTAATTAATAAAAAT
1 TATTAATTAATAAAAAT
* *
52976887 TATTAGTTATTAAAATAT
1 TATTAATTAATAAAA-AT
*
52976905 TATTATTTAATAAAA
1 TATTAATTAATAAAA
52976920 GTTTAGGGAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
17 13 0.46
18 15 0.54
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (17 bp):
TATTAATTAATAAAAAT
Found at i:52995122 original size:63 final size:63
Alignment explanation
Indices: 52995005--52995146 Score: 149
Period size: 63 Copynumber: 2.3 Consensus size: 63
52994995 AATGATTGCA
* * ** * * * * *
52995005 CGTGTTGTGGTGCTTGTGTAAAATAAAATGGTGCTGAATATGTTGATGTAGGGAATGATTATG
1 CGTGTTGTGGTGCTTGCGTAAAATAAAACGGAACTAAAGATGATGATATAGGGAATGAGTATG
* * * *
52995068 CGTGTTGTGGTGGTTGCGTAAAATAAAACGGAACTAAAGGTGATGATATGGGGAATGAGTGTG
1 CGTGTTGTGGTGCTTGCGTAAAATAAAACGGAACTAAAGATGATGATATAGGGAATGAGTATG
* *
52995131 CATGTTGTGATGCTTG
1 CGTGTTGTGGTGCTTG
52995147 TGACAAAAAA
Statistics
Matches: 63, Mismatches: 16, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
63 63 1.00
ACGTcount: A:0.27, C:0.06, G:0.34, T:0.33
Consensus pattern (63 bp):
CGTGTTGTGGTGCTTGCGTAAAATAAAACGGAACTAAAGATGATGATATAGGGAATGAGTATG
Found at i:52998468 original size:28 final size:28
Alignment explanation
Indices: 52998428--52998485 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
52998418 ATACATAGTC
52998428 GATTGCTATGTTACTCAAACTCAAATGT
1 GATTGCTATGTTACTCAAACTCAAATGT
52998456 GATTGCTATGTTACTCAAACTCAAATGT
1 GATTGCTATGTTACTCAAACTCAAATGT
52998484 GA
1 GA
52998486 GCTTCAAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Consensus pattern (28 bp):
GATTGCTATGTTACTCAAACTCAAATGT
Found at i:53000768 original size:12 final size:12
Alignment explanation
Indices: 53000751--53000775 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
53000741 GGTGTTTATT
53000751 CGGTTAACCGAC
1 CGGTTAACCGAC
53000763 CGGTTAACCGAC
1 CGGTTAACCGAC
53000775 C
1 C
53000776 CGAAATTACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.36, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTTAACCGAC
Found at i:53000950 original size:9 final size:9
Alignment explanation
Indices: 53000936--53000990 Score: 85
Period size: 9 Copynumber: 6.2 Consensus size: 9
53000926 TTTGGTTAAA
*
53000936 AATTACCCG
1 AATTAACCG
*
53000945 AATTACCCG
1 AATTAACCG
53000954 AATTAACCG
1 AATTAACCG
53000963 AATTAACCG
1 AATTAACCG
53000972 AATTAACCG
1 AATTAACCG
53000981 AATT-ACCG
1 AATTAACCG
53000989 AA
1 AA
53000991 AAATACCCGA
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
8 6 0.13
9 39 0.87
ACGTcount: A:0.42, C:0.25, G:0.11, T:0.22
Consensus pattern (9 bp):
AATTAACCG
Found at i:53011055 original size:15 final size:15
Alignment explanation
Indices: 53011035--53011064 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
53011025 TTTCATTTGG
53011035 CCCTCTAAGCAGTAA
1 CCCTCTAAGCAGTAA
53011050 CCCTCTAAGCAGTAA
1 CCCTCTAAGCAGTAA
53011065 ATAGTTAAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.33, G:0.13, T:0.20
Consensus pattern (15 bp):
CCCTCTAAGCAGTAA
Found at i:53018052 original size:21 final size:21
Alignment explanation
Indices: 53018028--53018068 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
53018018 TTAATTGGGG
53018028 AAAGGTATGAAATTTCCCTCC
1 AAAGGTATGAAATTTCCCTCC
53018049 AAAGGTATGAAATTTCCCTC
1 AAAGGTATGAAATTTCCCTC
53018069 TAAATAGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.29
Consensus pattern (21 bp):
AAAGGTATGAAATTTCCCTCC
Found at i:53018278 original size:2 final size:2
Alignment explanation
Indices: 53018271--53018318 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
53018261 ACGTACATGT
53018271 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
53018313 TC TC TC
1 TC TC TC
53018319 AAGCTTTAGC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:53018448 original size:21 final size:21
Alignment explanation
Indices: 53018423--53018464 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
53018413 ACGAAAAGCT
*
53018423 CCTCTTGTGAAACTAAAGCAA
1 CCTCTTGCGAAACTAAAGCAA
53018444 CCTCTTGCGAAACTAAAGCAA
1 CCTCTTGCGAAACTAAAGCAA
53018465 TCATTTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.38, C:0.26, G:0.14, T:0.21
Consensus pattern (21 bp):
CCTCTTGCGAAACTAAAGCAA
Found at i:53023362 original size:16 final size:18
Alignment explanation
Indices: 53023322--53023367 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
53023312 ATTAAACTAA
*
53023322 ATATATCTTGAATTGATC
1 ATATATCTTGAATTGAGC
53023340 ATATATCTTGAATTGAGC
1 ATATATCTTGAATTGAGC
53023358 -T-TATCTTGAA
1 ATATATCTTGAA
53023368 GATGTTTGTG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 9 0.33
17 1 0.04
18 17 0.63
ACGTcount: A:0.33, C:0.11, G:0.13, T:0.43
Consensus pattern (18 bp):
ATATATCTTGAATTGAGC
Found at i:53026733 original size:19 final size:20
Alignment explanation
Indices: 53026711--53026763 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 20
53026701 ACTCAAGGGG
*
53026711 ACTT-TACCGATACAAGTCC
1 ACTTCTACCCATACAAGTCC
* *
53026730 ACTTCTA-CTATACAGGTCC
1 ACTTCTACCCATACAAGTCC
53026749 ACTTCTACCCATACA
1 ACTTCTACCCATACA
53026764 TCTTGTGAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
19 21 0.72
20 8 0.28
ACGTcount: A:0.30, C:0.34, G:0.08, T:0.28
Consensus pattern (20 bp):
ACTTCTACCCATACAAGTCC
Found at i:53027183 original size:28 final size:29
Alignment explanation
Indices: 53027140--53027194 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
53027130 GATTGTAAAA
*
53027140 GGTTTCTAGTTGAGCCACAAAAGCTAGAT
1 GGTTTCTAGTTGAGCCACAAAAACTAGAT
* *
53027169 GGTTT-TAGTTTAGCCATAAAAACTAG
1 GGTTTCTAGTTGAGCCACAAAAACTAG
53027195 GGGAGAAGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 18 0.78
29 5 0.22
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.31
Consensus pattern (29 bp):
GGTTTCTAGTTGAGCCACAAAAACTAGAT
Found at i:53037964 original size:23 final size:23
Alignment explanation
Indices: 53037934--53037977 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
53037924 TAAATGTTTC
53037934 ATAATATAAATAAGAATATTTTA
1 ATAATATAAATAAGAATATTTTA
* *
53037957 ATAATATAAATATGAGTATTT
1 ATAATATAAATAAGAATATTT
53037978 ATCCCATCCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (23 bp):
ATAATATAAATAAGAATATTTTA
Found at i:53038670 original size:24 final size:25
Alignment explanation
Indices: 53038638--53038687 Score: 84
Period size: 24 Copynumber: 2.0 Consensus size: 25
53038628 AAACTATGGT
*
53038638 ATTCTTATGAAGTGAGTCTT-TTTA
1 ATTCTTATGAAGTGAATCTTATTTA
53038662 ATTCTTATGAAGTGAATCTTATTTA
1 ATTCTTATGAAGTGAATCTTATTTA
53038687 A
1 A
53038688 AAACTTTTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 19 0.79
25 5 0.21
ACGTcount: A:0.30, C:0.08, G:0.14, T:0.48
Consensus pattern (25 bp):
ATTCTTATGAAGTGAATCTTATTTA
Found at i:53040641 original size:41 final size:41
Alignment explanation
Indices: 53040596--53040790 Score: 250
Period size: 41 Copynumber: 4.8 Consensus size: 41
53040586 CACTGGTACA
*
53040596 AAGCCTTCTAGGCTCAAGGCCTGATACAATACACCGACACG
1 AAGCCTACTAGGCTCAAGGCCTGATACAATACACCGACACG
* * *
53040637 AAGCCTACTAGGCTCACA-GCTTGATACAATACACCGGCATG
1 AAGCCTACTAGGCTCA-AGGCCTGATACAATACACCGACACG
* * * *
53040678 AAGCCTGCTAGGCTCAAGGCCTGATATAATACATCGACACA
1 AAGCCTACTAGGCTCAAGGCCTGATACAATACACCGACACG
* * *
53040719 AAGCCTGCTAGGCTCAAGTCCTGATACAATAGACC-AGCACG
1 AAGCCTACTAGGCTCAAGGCCTGATACAATACACCGA-CACG
*
53040760 AAGCCTACTAGGCTCAAGGCCTGACACAATA
1 AAGCCTACTAGGCTCAAGGCCTGATACAATA
53040791 TCTCCGGTAT
Statistics
Matches: 132, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
40 2 0.02
41 129 0.98
42 1 0.01
ACGTcount: A:0.33, C:0.29, G:0.20, T:0.18
Consensus pattern (41 bp):
AAGCCTACTAGGCTCAAGGCCTGATACAATACACCGACACG
Found at i:53055204 original size:22 final size:22
Alignment explanation
Indices: 53055179--53055220 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
53055169 TATTGTTCGG
53055179 ATGACTAAT-AGAAAAGCAATAA
1 ATGACTAATGA-AAAAGCAATAA
53055201 ATGACTAATGAAAAAGCAAT
1 ATGACTAATGAAAAAGCAAT
53055221 TCAACATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 18 0.95
23 1 0.05
ACGTcount: A:0.57, C:0.10, G:0.14, T:0.19
Consensus pattern (22 bp):
ATGACTAATGAAAAAGCAATAA
Found at i:53056753 original size:24 final size:24
Alignment explanation
Indices: 53056594--53056754 Score: 112
Period size: 24 Copynumber: 6.6 Consensus size: 24
53056584 TCCCGTAAAC
* *
53056594 CCACCTGTTCCAATCTATAAACCT
1 CCACCAGTTCCAGTCTATAAACCT
53056618 CCACCAGTTCCAGTCTATAAACCT
1 CCACCAGTTCCAGTCTATAAACCT
* *
53056642 CCTCCAGTTCCAG--TAAAACCACTTCCT
1 CCACCAGTTCCAGTCTATAA--A---CCT
* * *
53056669 CCACCTGTTCCAATCTACAAACCT
1 CCACCAGTTCCAGTCTATAAACCT
** ** * * *
53056693 CCACCAGTTGAAAAACCA-CATCCT
1 CCACCAGTT-CCAGTCTATAAACCT
*
53056717 CCACCTGTTCCAGTCTATAAACCT
1 CCACCAGTTCCAGTCTATAAACCT
53056741 CCACCAGTTCCAGT
1 CCACCAGTTCCAGT
53056755 ATACAAGAAG
Statistics
Matches: 104, Mismatches: 24, Indels: 18
0.71 0.16 0.12
Matches are distributed among these distances:
22 4 0.04
23 3 0.03
24 75 0.72
25 4 0.04
27 14 0.13
29 4 0.04
ACGTcount: A:0.29, C:0.39, G:0.07, T:0.25
Consensus pattern (24 bp):
CCACCAGTTCCAGTCTATAAACCT
Found at i:53056784 original size:57 final size:56
Alignment explanation
Indices: 53056615--53057105 Score: 304
Period size: 48 Copynumber: 8.9 Consensus size: 56
53056605 AATCTATAAA
*
53056615 CCTCCACCAGTTCCAGTCTATAAACCTCCTCCAGTTCCAG--T--AA-AACCACT-T
1 CCTCCACCAGTTCCAGTCTATAAACCTCCACCAGTTCCAGTATACAAGAACCA-TAT
* * * *
53056666 CCTCCACCTGTTCCAATCTACAAACCTCCACCAGTT---G---A-AA-AACCACAT
1 CCTCCACCAGTTCCAGTCTATAAACCTCCACCAGTTCCAGTATACAAGAACCATAT
* *
53056714 CCTCCACCTGTTCCAGTCTATAAACCTCCACCAGTTCCAGTATACAAGAAGCCATGT
1 CCTCCACCAGTTCCAGTCTATAAACCTCCACCAGTTCCAGTATACAAGAA-CCATAT
* * * **
53056771 CCTCCACCAGTTCCAGTCTATAAATCTCCTCCGGTTCCAGTATACAAGAAACCGCAT
1 CCTCCACCAGTTCCAGTCTATAAACCTCCACCAGTTCCAGTATACAAG-AACCATAT
* *
53056828 CCTCCTCCAGTTCCAGTCTATAAGAAACCACATCCACCTCCAGTTCCAGTATACAAGAAACCATG
1 CCTCCACCAGTTCCAGTCTAT---AAA-C-C-TCCA---CCAGTTCCAGTATACAAG-AACCATA
53056893 T
56 T
* * * *
53056894 CCTCCCCCAGTTCCAGTCTATAAATCTCCTCCAGTTCC-G-------GAACCACAT
1 CCTCCACCAGTTCCAGTCTATAAACCTCCACCAGTTCCAGTATACAAGAACCATAT
* *
53056942 CCTCCGCCAGTTCCAGTCTATAAGAAACCACATCCACCTCCAGTTCCAGTATACAAGAAACCATG
1 CCTCCACCAGTTCCAGTCTAT---AAA-C-C-TCCA---CCAGTTCCAGTATACAAG-AACCATA
53057007 T
56 T
* * * *
53057008 CCTCCCCCAGTTCCAGTCTATAAATCTCCTCCAGTTCC-G-------GAACCACAT
1 CCTCCACCAGTTCCAGTCTATAAACCTCCACCAGTTCCAGTATACAAGAACCATAT
* * * * *
53057056 CCTCCGCCAGTTCCAGTCCATAAGCCTCCTCCAGTTCCGGTATACAAGAA
1 CCTCCACCAGTTCCAGTCTATAAACCTCCACCAGTTCCAGTATACAAGAA
53057106 AAGAGTCCCT
Statistics
Matches: 351, Mismatches: 42, Indels: 89
0.73 0.09 0.18
Matches are distributed among these distances:
48 109 0.31
49 3 0.01
51 36 0.10
53 1 0.00
54 4 0.01
55 2 0.01
56 7 0.02
57 95 0.27
58 3 0.01
60 9 0.03
61 2 0.01
62 1 0.00
63 9 0.03
65 1 0.00
66 69 0.20
ACGTcount: A:0.28, C:0.37, G:0.11, T:0.23
Consensus pattern (56 bp):
CCTCCACCAGTTCCAGTCTATAAACCTCCACCAGTTCCAGTATACAAGAACCATAT
Found at i:53056841 original size:33 final size:33
Alignment explanation
Indices: 53056796--53056910 Score: 158
Period size: 33 Copynumber: 3.5 Consensus size: 33
53056786 GTCTATAAAT
* *
53056796 CTCCTCCGGTTCCAGTATACAAGAAACCGCATC
1 CTCCTCCAGTTCCAGTATACAAGAAACCACATC
* *
53056829 CTCCTCCAGTTCCAGTCTATAAGAAACCACATC
1 CTCCTCCAGTTCCAGTATACAAGAAACCACATC
* **
53056862 CACCTCCAGTTCCAGTATACAAGAAACCATGTC
1 CTCCTCCAGTTCCAGTATACAAGAAACCACATC
*
53056895 CTCCCCCAGTTCCAGT
1 CTCCTCCAGTTCCAGT
53056911 CTATAAATCT
Statistics
Matches: 71, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 71 1.00
ACGTcount: A:0.28, C:0.37, G:0.12, T:0.23
Consensus pattern (33 bp):
CTCCTCCAGTTCCAGTATACAAGAAACCACATC
Found at i:53056847 original size:114 final size:110
Alignment explanation
Indices: 53056706--53057078 Score: 486
Period size: 114 Copynumber: 3.3 Consensus size: 110
53056696 CCAGTTGAAA
* * *
53056706 AACCACATCCTCCACCTGTTCCAGTCTAT-AAA-C-C-TCCA-CCAGTTCCAGTATACAAGAAGC
1 AACCACATCCTCCGCCAGTTCCAGTCTATAAAACCACATCCACCCAGTTCCAGTATACAAGAAAC
* *
53056766 CATGTCCTCCACCAGTTCCAGTCTATAAATCTCCTCCGGTTCCAGTATACAAG
66 CATGTCCTCCCCCAGTTCCAGTCTATAAATCTCCTCCAGTTCC-G-------G
* *
53056819 AAACCGCATCCTCCTCCAGTTCCAGTCTATAAGAAACCACATCCACCTCCAGTTCCAGTATACAA
1 -AACCACATCCTCCGCCAGTTCCAGTCTAT-A-AAACCACATCCA-C-CCAGTTCCAGTATACAA
53056884 GAAACCATGTCCTCCCCCAGTTCCAGTCTATAAATCTCCTCCAGTTCCGG
61 GAAACCATGTCCTCCCCCAGTTCCAGTCTATAAATCTCCTCCAGTTCCGG
53056934 AACCACATCCTCCGCCAGTTCCAGTCTATAAGAAACCACATCCACCTCCAGTTCCAGTATACAAG
1 AACCACATCCTCCGCCAGTTCCAGTCTAT-A-AAACCACATCCA-C-CCAGTTCCAGTATACAAG
53056999 AAACCATGTCCTCCCCCAGTTCCAGTCTATAAATCTCCTCCAGTTCCGG
62 AAACCATGTCCTCCCCCAGTTCCAGTCTATAAATCTCCTCCAGTTCCGG
*
53057048 AACCACATCCTCCGCCAGTTCCAGTCCATAA
1 AACCACATCCTCCGCCAGTTCCAGTCTATAA
53057079 GCCTCCTCCA
Statistics
Matches: 241, Mismatches: 9, Indels: 20
0.89 0.03 0.07
Matches are distributed among these distances:
112 1 0.00
113 1 0.00
114 166 0.69
115 1 0.00
117 3 0.01
118 1 0.00
119 1 0.00
120 4 0.02
122 1 0.00
123 62 0.26
ACGTcount: A:0.28, C:0.37, G:0.11, T:0.23
Consensus pattern (110 bp):
AACCACATCCTCCGCCAGTTCCAGTCTATAAAACCACATCCACCCAGTTCCAGTATACAAGAAAC
CATGTCCTCCCCCAGTTCCAGTCTATAAATCTCCTCCAGTTCCGG
Found at i:53056972 original size:33 final size:33
Alignment explanation
Indices: 53056934--53057030 Score: 131
Period size: 33 Copynumber: 2.9 Consensus size: 33
53056924 CCAGTTCCGG
*
53056934 AACCACATCCTCCGCCAGTTCCAGTCTATAAGA
1 AACCACATCCTCCCCCAGTTCCAGTCTATAAGA
* * * *
53056967 AACCACATCCACCTCCAGTTCCAGTATACAAGA
1 AACCACATCCTCCCCCAGTTCCAGTCTATAAGA
**
53057000 AACCATGTCCTCCCCCAGTTCCAGTCTATAA
1 AACCACATCCTCCCCCAGTTCCAGTCTATAA
53057031 ATCTCCTCCA
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 54 1.00
ACGTcount: A:0.31, C:0.37, G:0.10, T:0.22
Consensus pattern (33 bp):
AACCACATCCTCCCCCAGTTCCAGTCTATAAGA
Found at i:53057060 original size:24 final size:24
Alignment explanation
Indices: 53057033--53057095 Score: 65
Period size: 24 Copynumber: 2.6 Consensus size: 24
53057023 GTCTATAAAT
* *
53057033 CTCCTCCAGTTCCGGAACCA-CATC
1 CTCCTCCAGTTCCGG-ACCATAAGC
* * *
53057057 CTCCGCCAGTTCCAGTCCATAAGC
1 CTCCTCCAGTTCCGGACCATAAGC
53057081 CTCCTCCAGTTCCGG
1 CTCCTCCAGTTCCGG
53057096 TATACAAGAA
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
23 3 0.10
24 28 0.90
ACGTcount: A:0.17, C:0.44, G:0.16, T:0.22
Consensus pattern (24 bp):
CTCCTCCAGTTCCGGACCATAAGC
Found at i:53057079 original size:114 final size:114
Alignment explanation
Indices: 53056744--53057079 Score: 537
Period size: 114 Copynumber: 2.9 Consensus size: 114
53056734 TAAACCTCCA
* * *
53056744 CCAGTTCCAGTATACAAGAAGCCATGTCCTCCACCAGTTCCAGTCTATAAATCTCCTCCGGTTCC
1 CCAGTTCCAGTATACAAGAAACCATGTCCTCCCCCAGTTCCAGTCTATAAATCTCCTCCAGTTCC
* *
53056809 AGTATACAAGAAACCGCATCCTCCTCCAGTTCCAGTCTATAAGAAACCACATCCACCT
66 -G-------G-AACCACATCCTCCGCCAGTTCCAGTCTATAAGAAACCACATCCACCT
53056867 CCAGTTCCAGTATACAAGAAACCATGTCCTCCCCCAGTTCCAGTCTATAAATCTCCTCCAGTTCC
1 CCAGTTCCAGTATACAAGAAACCATGTCCTCCCCCAGTTCCAGTCTATAAATCTCCTCCAGTTCC
53056932 GGAACCACATCCTCCGCCAGTTCCAGTCTATAAGAAACCACATCCACCT
66 GGAACCACATCCTCCGCCAGTTCCAGTCTATAAGAAACCACATCCACCT
53056981 CCAGTTCCAGTATACAAGAAACCATGTCCTCCCCCAGTTCCAGTCTATAAATCTCCTCCAGTTCC
1 CCAGTTCCAGTATACAAGAAACCATGTCCTCCCCCAGTTCCAGTCTATAAATCTCCTCCAGTTCC
*
53057046 GGAACCACATCCTCCGCCAGTTCCAGTCCATAAG
66 GGAACCACATCCTCCGCCAGTTCCAGTCTATAAG
53057080 CCTCCTCCAG
Statistics
Matches: 207, Mismatches: 6, Indels: 9
0.93 0.03 0.04
Matches are distributed among these distances:
114 143 0.69
115 1 0.00
122 1 0.00
123 62 0.30
ACGTcount: A:0.28, C:0.37, G:0.12, T:0.23
Consensus pattern (114 bp):
CCAGTTCCAGTATACAAGAAACCATGTCCTCCCCCAGTTCCAGTCTATAAATCTCCTCCAGTTCC
GGAACCACATCCTCCGCCAGTTCCAGTCTATAAGAAACCACATCCACCT
Found at i:53057174 original size:57 final size:57
Alignment explanation
Indices: 53057077--53057184 Score: 144
Period size: 57 Copynumber: 1.9 Consensus size: 57
53057067 TCCAGTCCAT
* * * * * *
53057077 AAGCCTCCTCCAGTTCCGGTATACAAGAAAAGAGTCCCTCCTCCGGTTCCAATCTAC
1 AAGCCCCCTCCAGTTCCGGTATACAACAAAACACTACCTCCCCCGGTTCCAATCTAC
* *
53057134 AAGCCCCCTCCAGTTCCTGTATACAACAAACCACTACCTCCCCCGGTTCCA
1 AAGCCCCCTCCAGTTCCGGTATACAACAAAACACTACCTCCCCCGGTTCCA
53057185 GTGTATACGA
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
57 43 1.00
ACGTcount: A:0.26, C:0.40, G:0.13, T:0.21
Consensus pattern (57 bp):
AAGCCCCCTCCAGTTCCGGTATACAACAAAACACTACCTCCCCCGGTTCCAATCTAC
Found at i:53057284 original size:18 final size:18
Alignment explanation
Indices: 53057261--53057296 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
53057251 TACAAGCCAC
53057261 TCCCTCCACTTCCC-AAGA
1 TCCCTCCA-TTCCCTAAGA
53057279 TCCCTCCATTCCCTAAGA
1 TCCCTCCATTCCCTAAGA
53057297 AGCCATGCCC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.22, C:0.47, G:0.06, T:0.25
Consensus pattern (18 bp):
TCCCTCCATTCCCTAAGA
Done.