Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D10
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: 67973905
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1760000 characters in sequence are not A, C, G, or T
File 175 of 228
Found at i:52393743 original size:20 final size:20
Alignment explanation
Indices: 52393701--52393741 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
52393691 TACAACACAA
*
52393701 TTCAATTTCATATTGAATAT
1 TTCAATTTCATATTCAATAT
*
52393721 TTCAATTT-TTATTCAATAT
1 TTCAATTTCATATTCAATAT
52393740 TT
1 TT
52393742 TCCTAAATTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.32, C:0.10, G:0.02, T:0.56
Consensus pattern (20 bp):
TTCAATTTCATATTCAATAT
Found at i:52394236 original size:22 final size:25
Alignment explanation
Indices: 52394211--52394266 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 25
52394201 CTTTATTTCT
*
52394211 TTTACTTA-T-TTATTTTAT-TATA
1 TTTACTTATTATTATATTATATATA
52394233 TTTACTTTATTATTATATTATATATA
1 TTTAC-TTATTATTATATTATATATA
52394259 TTTACTTA
1 TTTACTTA
52394267 AATATTAAGC
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
22 5 0.17
23 3 0.10
24 1 0.03
25 11 0.38
26 9 0.31
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.64
Consensus pattern (25 bp):
TTTACTTATTATTATATTATATATA
Found at i:52394258 original size:26 final size:27
Alignment explanation
Indices: 52394211--52394265 Score: 78
Period size: 26 Copynumber: 2.1 Consensus size: 27
52394201 CTTTATTTCT
*
52394211 TTTACTTATTTATTTTATTATATTTAC
1 TTTACTTATTTATTATATTATATTTAC
52394238 TTTA-TTATTATATTATA-TATATTTAC
1 TTTACTTATT-TATTATATTATATTTAC
52394264 TT
1 TT
52394266 AAATATTAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 16 0.62
27 10 0.38
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.65
Consensus pattern (27 bp):
TTTACTTATTTATTATATTATATTTAC
Found at i:52394272 original size:26 final size:25
Alignment explanation
Indices: 52394220--52394273 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 25
52394210 TTTTACTTAT
* * *
52394220 TTATTTTATTATATTTACTTTATTA
1 TTATATTATTATATTTACTTAAATA
52394245 TTATATTATATATATTTACTTAAATA
1 TTATATTAT-TATATTTACTTAAATA
52394271 TTA
1 TTA
52394274 AGCAAAATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
25 8 0.32
26 17 0.68
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (25 bp):
TTATATTATTATATTTACTTAAATA
Found at i:52399061 original size:18 final size:19
Alignment explanation
Indices: 52399038--52399073 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
52399028 ACAAAAAAAA
*
52399038 TTTAAGTA-TTAAATAAAG
1 TTTAAGTACCTAAATAAAG
52399056 TTTAAGTACCTAAATAAA
1 TTTAAGTACCTAAATAAA
52399074 TAACCTTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.50, C:0.06, G:0.08, T:0.36
Consensus pattern (19 bp):
TTTAAGTACCTAAATAAAG
Found at i:52404670 original size:23 final size:23
Alignment explanation
Indices: 52404601--52404673 Score: 71
Period size: 23 Copynumber: 3.3 Consensus size: 23
52404591 GTATATTAAA
52404601 ATATAATTAAAATCATTTTGATT
1 ATATAATTAAAATCATTTTGATT
*** * * *
52404624 ATATAA-TATTTTTA-ATTGA-A
1 ATATAATTAAAATCATTTTGATT
52404644 ATATAATTAAAATCATTTTGATT
1 ATATAATTAAAATCATTTTGATT
52404667 ATATAAT
1 ATATAAT
52404674 ATTAATATAA
Statistics
Matches: 35, Mismatches: 12, Indels: 6
0.66 0.23 0.11
Matches are distributed among these distances:
20 6 0.17
21 8 0.23
22 8 0.23
23 13 0.37
ACGTcount: A:0.45, C:0.03, G:0.04, T:0.48
Consensus pattern (23 bp):
ATATAATTAAAATCATTTTGATT
Found at i:52404700 original size:43 final size:41
Alignment explanation
Indices: 52404595--52404700 Score: 142
Period size: 43 Copynumber: 2.5 Consensus size: 41
52404585 TTTAAGGTAT
52404595 ATTAAAATATAATTAAAATCATTTTGATTATATAATATTTTTA
1 ATTAAAATATAATTAAAATCATTTTGATTATATAATA--TTTA
*
52404638 ATTGAAATATAATTAAAATCATTTTGATTATATAATA-TTA
1 ATTAAAATATAATTAAAATCATTTTGATTATATAATATTTA
*
52404678 ATATAAAACTATACATTTAAATC
1 AT-TAAAA-TATA-ATTAAAATC
52404701 CAAAATATAA
Statistics
Matches: 57, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
40 5 0.09
41 4 0.07
42 4 0.07
43 44 0.77
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (41 bp):
ATTAAAATATAATTAAAATCATTTTGATTATATAATATTTA
Found at i:52406607 original size:91 final size:91
Alignment explanation
Indices: 52406481--52406689 Score: 303
Period size: 91 Copynumber: 2.3 Consensus size: 91
52406471 TTAATTTTAG
* *
52406481 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCACTATTAAATTAT
1 TAAATTCATATAAGAA-AATTTATTATCAAGAATTTTATGAAATTATATATCACTATTAAATTAT
* *
52406546 ATTTAAT-ATTAATTATTTTAAATTGTA
65 ATGTAATAATT-ATTATTTTAAATTATA
* *
52406573 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATTATTATTAAATTATA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCACTATTAAATTATA
52406638 TGTAATAATTATTATTTTAAATTATA
66 TGTAATAATTATTATTTTAAATTATA
* * * *
52406664 CAAATTCATAAAATATAATTTATTAT
1 TAAATTCATATAAGAAAATTTATTAT
52406690 TTATAATTGT
Statistics
Matches: 106, Mismatches: 10, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
91 87 0.82
92 19 0.18
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCACTATTAAATTATA
TGTAATAATTATTATTTTAAATTATA
Found at i:52406831 original size:120 final size:120
Alignment explanation
Indices: 52406704--52406996 Score: 500
Period size: 120 Copynumber: 2.4 Consensus size: 120
52406694 AATTGTTTTA
* * *
52406704 AATTTTATTAAATCATATATTTTAATTATAATATATTTAATATTAATTAT-TTCAAATTT-TCTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT--AATTTATATT
*
52406767 TTATAGTATAATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
64 TTACAGTATAATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
52406824 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
*
52406889 ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
66 ACAGTATAATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
*
52406944 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
52406997 TAAATATGAT
Statistics
Matches: 165, Mismatches: 6, Indels: 4
0.94 0.03 0.02
Matches are distributed among these distances:
119 5 0.03
120 158 0.96
121 2 0.01
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
ACAGTATAATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:52406864 original size:15 final size:15
Alignment explanation
Indices: 52406829--52406880 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
52406819 TTAAGAATTT
*
52406829 TATTAAATTAT-ATA
1 TATTTAATTATAATA
52406843 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
52406857 TATTTAATAATAAT-
1 TATTTAATTATAATA
52406871 TATGTTAATT
1 TAT-TTAATT
52406881 TATATTTTAC
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:52406973 original size:18 final size:17
Alignment explanation
Indices: 52406945--52406979 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
52406935 ATTATTAAGA
*
52406945 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
52406962 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
52406980 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:52407097 original size:157 final size:157
Alignment explanation
Indices: 52406933--52407249 Score: 589
Period size: 157 Copynumber: 2.0 Consensus size: 157
52406923 ATAAGAATAT
52406933 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
* *
52406998 AAATATGATTAAATTATTTATTATTGATATTAATAATCTTATTAAAATTTAAATAATAATAACAA
66 AAATATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
*
52407063 TAATAATTTACCAAAACAAATTTCTGC
131 TAATAATTTACCAAAACAAATTTATGC
52407090 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
*
52407155 AAATATGATTAAATTATTTATTATTGATAATAATAATCTTATTGAAATTTAAATAACAATAACAA
66 AAATATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
*
52407220 TAATCATTTACCAAAACAAATTTATGC
131 TAATAATTTACCAAAACAAATTTATGC
52407247 TAA
1 TAA
52407250 AGGTATTCTA
Statistics
Matches: 155, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
157 155 1.00
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.44
Consensus pattern (157 bp):
TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
AAATATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
TAATAATTTACCAAAACAAATTTATGC
Found at i:52407130 original size:18 final size:17
Alignment explanation
Indices: 52407102--52407136 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
52407092 ATTATTAAGA
*
52407102 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
52407119 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
52407137 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:52407170 original size:75 final size:75
Alignment explanation
Indices: 52406934--52407172 Score: 207
Period size: 76 Copynumber: 3.1 Consensus size: 75
52406924 TAAGAATATT
52406934 AATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTA
1 AATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTA
52406999 AATATGATTA
66 AATATGATTA
* ** * * * ** * * * *
52407009 AATTATTTATTATTGATATT-AATAATCTTATTAAAATTTAAATA-ATAATAACAATAATAAT-T
1 AATTATTAAGAATT-TTATTAAATTAT-ATATTTTAATTAAAATATAT-TTAATAATAATTATGT
* * * *
52407071 TACCAAAACAAAT-TTCTGCT
63 T----TAA-ATATGAT-T--A
52407091 AATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTA
1 AATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTA
52407156 AATATGATTA
66 AATATGATTA
52407166 AATTATT
1 AATTATT
52407173 TATTATTGAT
Statistics
Matches: 117, Mismatches: 32, Indels: 30
0.65 0.18 0.17
Matches are distributed among these distances:
75 27 0.23
76 28 0.24
77 4 0.03
78 3 0.03
79 3 0.03
80 4 0.03
81 28 0.24
82 20 0.17
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (75 bp):
AATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTA
AATATGATTA
Found at i:52407327 original size:39 final size:40
Alignment explanation
Indices: 52407284--52407388 Score: 113
Period size: 44 Copynumber: 2.5 Consensus size: 40
52407274 TTCCATTATG
52407284 CTATTACACCTCTATTCCATTCAACCAAACACAAGA-TTA
1 CTATTACACCTCTATTCCATTCAACCAAACACAAGATTTA
* *** *
52407323 CTATTACGCCTCTATTCCATTACATTCAACCAAACAGTTGATTTG
1 CTATTACACCTCTATT-C----CATTCAACCAAACACAAGATTTA
52407368 CTATTACACCTCTATTCCATT
1 CTATTACACCTCTATTCCATT
52407389 ACACCTCTAA
Statistics
Matches: 54, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
39 15 0.28
40 5 0.09
44 17 0.31
45 17 0.31
ACGTcount: A:0.31, C:0.30, G:0.05, T:0.34
Consensus pattern (40 bp):
CTATTACACCTCTATTCCATTCAACCAAACACAAGATTTA
Found at i:52407382 original size:45 final size:44
Alignment explanation
Indices: 52407282--52407391 Score: 131
Period size: 45 Copynumber: 2.6 Consensus size: 44
52407272 TTTTCCATTA
52407282 TGCTATTACACCTCTATT-C----CATTCAACCAAACACAAGAT
1 TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGAT
* * ***
52407321 TACTATTACGCCTCTATTCCATTACATTCAACCAAACAGTTGATT
1 TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGA-T
52407366 TGCTATTACACCTCTATTCCATTACA
1 TGCTATTACACCTCTATTCCATTACA
52407392 CCTCTAATCC
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
39 16 0.28
40 1 0.02
44 16 0.28
45 25 0.43
ACGTcount: A:0.32, C:0.29, G:0.05, T:0.34
Consensus pattern (44 bp):
TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGAT
Found at i:52407391 original size:16 final size:16
Alignment explanation
Indices: 52407370--52407407 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
52407360 TTGATTTGCT
*
52407370 ATTACACCTCTATTCC
1 ATTACACCTCTAATCC
52407386 ATTACACCTCTAATCC
1 ATTACACCTCTAATCC
*
52407402 AATACA
1 ATTACA
52407408 GCGAACCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.34, C:0.34, G:0.00, T:0.32
Consensus pattern (16 bp):
ATTACACCTCTAATCC
Found at i:52407537 original size:24 final size:24
Alignment explanation
Indices: 52407521--52407584 Score: 110
Period size: 24 Copynumber: 2.7 Consensus size: 24
52407511 ATAAACTATG
52407521 CTAATAAATACTAAATATATTATA
1 CTAATAAATACTAAATATATTATA
**
52407545 CTAATAAATGTTAAATATATTATA
1 CTAATAAATACTAAATATATTATA
52407569 CTAATAAATACTAAAT
1 CTAATAAATACTAAAT
52407585 CTTCTAGAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.53, C:0.08, G:0.02, T:0.38
Consensus pattern (24 bp):
CTAATAAATACTAAATATATTATA
Found at i:52408850 original size:27 final size:28
Alignment explanation
Indices: 52408820--52408877 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 28
52408810 CTCGTTTAGG
52408820 TTTAGGTTTA-GTTATTTGTTTT-TTTAA
1 TTTA-GTTTATGTTATTTGTTTTATTTAA
* *
52408847 TTTAGTTTATTTTTTTTGTTTTATTTAA
1 TTTAGTTTATGTTATTTGTTTTATTTAA
52408875 TTT
1 TTT
52408878 TCCACATAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
26 5 0.19
27 14 0.52
28 8 0.30
ACGTcount: A:0.17, C:0.00, G:0.10, T:0.72
Consensus pattern (28 bp):
TTTAGTTTATGTTATTTGTTTTATTTAA
Found at i:52411928 original size:34 final size:34
Alignment explanation
Indices: 52411882--52411948 Score: 116
Period size: 34 Copynumber: 2.0 Consensus size: 34
52411872 TATGTCAGGC
*
52411882 CAAAGAGTAAACTGGTCCTACTGTTAAAACTTAT
1 CAAAGAGCAAACTGGTCCTACTGTTAAAACTTAT
*
52411916 CAAAGAGCAAACTGGTTCTACTGTTAAAACTTA
1 CAAAGAGCAAACTGGTCCTACTGTTAAAACTTA
52411949 CATCCATTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.39, C:0.18, G:0.15, T:0.28
Consensus pattern (34 bp):
CAAAGAGCAAACTGGTCCTACTGTTAAAACTTAT
Found at i:52412688 original size:34 final size:32
Alignment explanation
Indices: 52412588--52412699 Score: 118
Period size: 34 Copynumber: 3.4 Consensus size: 32
52412578 TTTTTTTAAA
* * *
52412588 AAAAAATTAATTAAATTAAGTTTTTGGGGTTTT
1 AAAAAATTAATTAAATT-AGGTTTAGGGTTTTT
*
52412621 AAATAAATTAATTAAATTAGAGATTAGGGTTTTT
1 AAA-AAATTAATTAAATTAG-GTTTAGGGTTTTT
**
52412655 AAGAAAATTAATTAAATTATGGTTTAGTTTTTTT
1 AA-AAAATTAATTAAATTA-GGTTTAGGGTTTTT
52412689 AAAAAA-TAATT
1 AAAAAATTAATT
52412700 TTGTGTTTAG
Statistics
Matches: 68, Mismatches: 7, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
32 5 0.07
33 9 0.13
34 52 0.76
35 2 0.03
ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (32 bp):
AAAAAATTAATTAAATTAGGTTTAGGGTTTTT
Found at i:52412911 original size:126 final size:126
Alignment explanation
Indices: 52412753--52413017 Score: 336
Period size: 126 Copynumber: 2.1 Consensus size: 126
52412743 CTTTTGTTTT
* * *
52412753 TTTTTCTACAGTAGTTTCTGAAAAAATAATTTTGAGAAGACGGTTCT-GAAAATATAATGTAAAA
1 TTTTTCTACAGTAGTTCCTAAAAAAATAATTTTGAGAAGACGATTCTGGAAAA-ATAATGTAAAA
* ** * *
52412817 AACGCTTAAAGCAAGATGCGTTGTCAGCAAAATT-ACTGAAAATAGCTCCCATGTAGACGTTC
65 AACACTTAAAGCAAGATGCACTGTCAGCAAAATTGA-TGAAAAAAGCTCCCATGTAGACGCTC
* * * **
52412879 TTTTTCTATAGTAGTTCCTAAAAAAATAATTTTGAGAAGATGATTCTGGACAAATGGTGTAAAAA
1 TTTTTCTACAGTAGTTCCTAAAAAAATAATTTTGAGAAGACGATTCTGGAAAAATAATGTAAAAA
* * * * *
52412944 ACATTTCAAGCAGGATGCACTGTCAGTAAAATTGATGAAAAAAGCTCCCATGTGGACGCTC
66 ACACTTAAAGCAAGATGCACTGTCAGCAAAATTGATGAAAAAAGCTCCCATGTAGACGCTC
52413005 TTTTTCTACAGTA
1 TTTTTCTACAGTA
52413018 TTTCTTGTTT
Statistics
Matches: 118, Mismatches: 19, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
126 113 0.96
127 5 0.04
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.31
Consensus pattern (126 bp):
TTTTTCTACAGTAGTTCCTAAAAAAATAATTTTGAGAAGACGATTCTGGAAAAATAATGTAAAAA
ACACTTAAAGCAAGATGCACTGTCAGCAAAATTGATGAAAAAAGCTCCCATGTAGACGCTC
Found at i:52416564 original size:18 final size:18
Alignment explanation
Indices: 52416541--52416579 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
52416531 GGAAAAGAAA
*
52416541 ACATATAAGGGTTAGGAT
1 ACATATAAGGGCTAGGAT
52416559 ACATATAAGGGCTAGGAT
1 ACATATAAGGGCTAGGAT
52416577 ACA
1 ACA
52416580 CACCTGGTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.41, C:0.10, G:0.26, T:0.23
Consensus pattern (18 bp):
ACATATAAGGGCTAGGAT
Found at i:52417877 original size:14 final size:14
Alignment explanation
Indices: 52417811--52417880 Score: 50
Period size: 14 Copynumber: 4.6 Consensus size: 14
52417801 ACTGTTATAA
* *
52417811 AAAATTATAAAATA
1 AAAATTAAAAAATT
52417825 AAAATTAATTAAAATT
1 AAAATTAA--AAAATT
*
52417841 ACATAAATGAAAAAATAT
1 --A-AAATTAAAAAAT-T
*
52417859 TAAATTAAAAAATT
1 AAAATTAAAAAATT
52417873 AAAATTAA
1 AAAATTAA
52417881 CCCTTACTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
14 15 0.34
15 11 0.25
16 5 0.11
17 5 0.11
18 2 0.05
19 6 0.14
ACGTcount: A:0.67, C:0.01, G:0.01, T:0.30
Consensus pattern (14 bp):
AAAATTAAAAAATT
Found at i:52418990 original size:6 final size:6
Alignment explanation
Indices: 52418981--52419007 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
52418971 AAGAAGAAGA
52418981 AGAAAG AGAAAG AGAAAG AGAAAG AGA
1 AGAAAG AGAAAG AGAAAG AGAAAG AGA
52419008 GAAAATGTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (6 bp):
AGAAAG
Found at i:52419059 original size:17 final size:18
Alignment explanation
Indices: 52419037--52419070 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
52419027 TATTAAATGA
52419037 TAATTT-TATTTTATTTG
1 TAATTTATATTTTATTTG
*
52419054 TAATTTATTTTTTATTT
1 TAATTTATATTTTATTT
52419071 AATAAAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (18 bp):
TAATTTATATTTTATTTG
Found at i:52419353 original size:15 final size:15
Alignment explanation
Indices: 52419333--52419362 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
52419323 TTTTTATTTT
52419333 TGAAATATAAAATCA
1 TGAAATATAAAATCA
*
52419348 TGAAATATAATATCA
1 TGAAATATAAAATCA
52419363 ACATCAAGGA
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:0.57, C:0.07, G:0.07, T:0.30
Consensus pattern (15 bp):
TGAAATATAAAATCA
Found at i:52431392 original size:20 final size:21
Alignment explanation
Indices: 52431354--52431392 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
52431344 AAACAAATAC
52431354 TCATATTTATATAATAAAAAT
1 TCATATTTATATAATAAAAAT
*
52431375 TCATATTT-TATTATAAAA
1 TCATATTTATATAATAAAA
52431393 TATTTATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (21 bp):
TCATATTTATATAATAAAAAT
Found at i:52431481 original size:12 final size:11
Alignment explanation
Indices: 52431429--52431522 Score: 50
Period size: 12 Copynumber: 8.2 Consensus size: 11
52431419 AATATATATT
52431429 TATTATTAAAA
1 TATTATTAAAA
*
52431440 TATTAATATAAA
1 TATTATTA-AAA
*
52431452 TATT-TTCAGTAA
1 TATTATT-A-AAA
52431464 TA-TATTAAGAA
1 TATTATTAA-AA
52431475 TATTATTTAAAA
1 TATTA-TTAAAA
* *
52431487 TA-TAATAATAT
1 TATTATTAA-AA
* *
52431498 TATTGTTAAATT
1 TATTATTAAA-A
52431510 TATTATTAAAA
1 TATTATTAAAA
52431521 TA
1 TA
52431523 AAATTATAAA
Statistics
Matches: 63, Mismatches: 11, Indels: 18
0.68 0.12 0.20
Matches are distributed among these distances:
10 3 0.05
11 22 0.35
12 34 0.54
13 4 0.06
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.47
Consensus pattern (11 bp):
TATTATTAAAA
Found at i:52436903 original size:41 final size:41
Alignment explanation
Indices: 52436856--52437002 Score: 206
Period size: 41 Copynumber: 3.6 Consensus size: 41
52436846 CATTGAATGT
* * *
52436856 AAGGGGTCGCTAAGTGTAGATTCCCTGAATCATTGATCAAA
1 AAGGGGTTGCTAAGTGCAGATTCCCCGAATCATTGATCAAA
*
52436897 AAGGGGTTGCTAAGTGCAGATTCCCCGAATCACTGATCAAA
1 AAGGGGTTGCTAAGTGCAGATTCCCCGAATCATTGATCAAA
* *
52436938 AAGGGGTTGCTAAGTGCAGATTCCCCGAAAC-TCTGATAAAA
1 AAGGGGTTGCTAAGTGCAGATTCCCCGAATCAT-TGATCAAA
* *
52436979 AAGGTGTTACTAAGTGCAGATTCC
1 AAGGGGTTGCTAAGTGCAGATTCC
52437003 TCAAGGGGTT
Statistics
Matches: 96, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
41 96 1.00
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.24
Consensus pattern (41 bp):
AAGGGGTTGCTAAGTGCAGATTCCCCGAATCATTGATCAAA
Found at i:52437017 original size:26 final size:26
Alignment explanation
Indices: 52436979--52437028 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
52436969 TCTGATAAAA
*
52436979 AAGGTGTTACTAAGTGCAGATTCCTC
1 AAGGGGTTACTAAGTGCAGATTCCTC
* *
52437005 AAGGGGTTGCTAAGTGCTGATTCC
1 AAGGGGTTACTAAGTGCAGATTCC
52437029 CCGAATTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.30
Consensus pattern (26 bp):
AAGGGGTTACTAAGTGCAGATTCCTC
Found at i:52437154 original size:41 final size:43
Alignment explanation
Indices: 52437005--52437155 Score: 116
Period size: 42 Copynumber: 3.6 Consensus size: 43
52436995 CAGATTCCTC
* * * * **
52437005 AAGG-GGTTGCTAAGTGCTGATTCC-CCGAATTATTGATTCCA
1 AAGGTGGTTGCTAAGTGCTAATTCCACCGTATCATTGAATATA
* * *
52437046 AAGGTGGTTGCTAAGTGCTAATTCCACCGTATCCTTGATTGTGA
1 AAGGTGGTTGCTAAGTGCTAATTCCACCGTATCATTGAATAT-A
* * * **
52437090 AAGG-GGTTGATATGTG-TCGATTCC-TTGTATCATTGAATAT-
1 AAGGTGGTTGCTAAGTGCT-AATTCCACCGTATCATTGAATATA
52437130 AAGGTGGTTGCTAAGTGCTAATTCCA
1 AAGGTGGTTGCTAAGTGCTAATTCCA
52437156 TCGAGTAACG
Statistics
Matches: 86, Mismatches: 17, Indels: 13
0.74 0.15 0.11
Matches are distributed among these distances:
40 4 0.05
41 19 0.22
42 32 0.37
43 26 0.30
44 5 0.06
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.34
Consensus pattern (43 bp):
AAGGTGGTTGCTAAGTGCTAATTCCACCGTATCATTGAATATA
Found at i:52440170 original size:43 final size:43
Alignment explanation
Indices: 52440052--52440196 Score: 131
Period size: 42 Copynumber: 3.5 Consensus size: 43
52440042 CCGTTACTCG
*
52440052 GTGGAATCAACACTTAGCAACCACC-TTATATTC-AGTGATAC
1 GTGGAATCAACACTTAGCAACCACCTTTATAATCAAGTGATAC
* * * *
52440093 G-GGAAATCAGCACATAGAAACC-CCTTCATAATCAAG-GATAC
1 GTGG-AATCAACACTTAGCAACCACCTTTATAATCAAGTGATAC
* * * *
52440134 GATGGAATCAACACTTAGCACCCACCTTTAAAATCAA-TAATTC
1 G-TGGAATCAACACTTAGCAACCACCTTTATAATCAAGTGATAC
* *
52440177 GGGGAATCAGCACTTAGCAA
1 GTGGAATCAACACTTAGCAA
52440197 TCCCTCAGGG
Statistics
Matches: 81, Mismatches: 16, Indels: 13
0.74 0.15 0.12
Matches are distributed among these distances:
40 4 0.05
41 28 0.35
42 32 0.40
43 17 0.21
ACGTcount: A:0.38, C:0.24, G:0.16, T:0.22
Consensus pattern (43 bp):
GTGGAATCAACACTTAGCAACCACCTTTATAATCAAGTGATAC
Found at i:52440207 original size:26 final size:26
Alignment explanation
Indices: 52440178--52440227 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
52440168 CAATAATTCG
* *
52440178 GGGAATCAGCACTTAGCAATCCCTCA
1 GGGAATCAGCACTTACCAACCCCTCA
*
52440204 GGGAATCTGCACTTACCAACCCCT
1 GGGAATCAGCACTTACCAACCCCT
52440228 TTTTGATCAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.28, C:0.34, G:0.18, T:0.20
Consensus pattern (26 bp):
GGGAATCAGCACTTACCAACCCCTCA
Found at i:52440270 original size:41 final size:40
Alignment explanation
Indices: 52440204--52440351 Score: 181
Period size: 41 Copynumber: 3.6 Consensus size: 40
52440194 CAATCCCTCA
*
52440204 GGGAATCTGCACTTACCAACCCCTTTTTGATCAAAGTTTCG
1 GGGAATCTGCACTTAGCAACCCCTTTTTGATC-AAGTTTCG
* * * *
52440245 GGGAATCTGCACTTAGCAACTCCTTTTTGATCATTGATTCA
1 GGGAATCTGCACTTAGCAACCCCTTTTTGATCA-AGTTTCG
* *
52440286 GGGAATATTCACTTAGCAACCCCTTTTTGATC-AGTTATTCG
1 GGGAATCTGCACTTAGCAACCCCTTTTTGATCAAG-T-TTCG
*
52440327 GGGAATCTGTACTTAGCAACCCCTT
1 GGGAATCTGCACTTAGCAACCCCTT
52440352 ACATTCAATG
Statistics
Matches: 90, Mismatches: 14, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
39 1 0.01
40 1 0.01
41 88 0.98
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.34
Consensus pattern (40 bp):
GGGAATCTGCACTTAGCAACCCCTTTTTGATCAAGTTTCG
Found at i:52440341 original size:82 final size:81
Alignment explanation
Indices: 52440201--52440351 Score: 223
Period size: 82 Copynumber: 1.8 Consensus size: 81
52440191 TAGCAATCCC
* *
52440201 TCAGGGAATCTGCACTTACCAACCCCTTTTTGATCAAAGTTTCGGGGAATCTGCACTTAGCAACT
1 TCAGGGAATATGCACTTACCAACCCCTTTTTGATC-AAGTTTCGGGGAATCTGCACTTAGCAACC
52440266 CCTTTTTGATCATTGAT
65 CCTTTTTGATCATTGAT
* * *
52440283 TCAGGGAATATTCACTTAGCAACCCCTTTTTGATC-AGTTATTCGGGGAATCTGTACTTAGCAAC
1 TCAGGGAATATGCACTTACCAACCCCTTTTTGATCAAG-T-TTCGGGGAATCTGCACTTAGCAAC
52440347 CCCTT
64 CCCTT
52440352 ACATTCAATG
Statistics
Matches: 62, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
80 2 0.03
81 1 0.02
82 59 0.95
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.34
Consensus pattern (81 bp):
TCAGGGAATATGCACTTACCAACCCCTTTTTGATCAAGTTTCGGGGAATCTGCACTTAGCAACCC
CTTTTTGATCATTGAT
Found at i:52451515 original size:26 final size:26
Alignment explanation
Indices: 52451486--52451558 Score: 101
Period size: 26 Copynumber: 2.8 Consensus size: 26
52451476 CCTCATCCTT
*
52451486 ATTTTACCCTTAGTAAAATTTTGACA
1 ATTTTACCCCTAGTAAAATTTTGACA
* **
52451512 ATTTTACCCCTGGTAAAATTTTGATG
1 ATTTTACCCCTAGTAAAATTTTGACA
*
52451538 ACTTTACCCCTAGTAAAATTT
1 ATTTTACCCCTAGTAAAATTT
52451559 CGAGAAAGTA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 41 1.00
ACGTcount: A:0.32, C:0.18, G:0.10, T:0.41
Consensus pattern (26 bp):
ATTTTACCCCTAGTAAAATTTTGACA
Found at i:52453536 original size:8 final size:8
Alignment explanation
Indices: 52453484--52453538 Score: 58
Period size: 8 Copynumber: 6.8 Consensus size: 8
52453474 TTTTTTTAAG
52453484 TATATTAT
1 TATATTAT
*
52453492 TATTTTAT
1 TATATTAT
*
52453500 TATATT-G
1 TATATTAT
*
52453507 TAAATTATAT
1 TATA-T-TAT
52453517 TATATTAT
1 TATATTAT
52453525 TATATTAT
1 TATATTAT
52453533 TATATT
1 TATATT
52453539 TTAAATAAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
7 3 0.08
8 30 0.79
9 2 0.05
10 3 0.08
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (8 bp):
TATATTAT
Found at i:52454915 original size:41 final size:37
Alignment explanation
Indices: 52454869--52454973 Score: 93
Period size: 37 Copynumber: 2.7 Consensus size: 37
52454859 TTGACCTTGA
52454869 GTCGATGAGACACTGGGTGTCATACTGTTACTTCGGATAG
1 GTCGATGAGACACTGGGTGTCA-AC--TTACTTCGGATAG
* ** ** * *
52454909 ATTCGATGAGGTACTGGGTACCAACTTACTTCGGCTTG
1 -GTCGATGAGACACTGGGTGTCAACTTACTTCGGATAG
* *
52454947 GCCGATGAGACACTGGGTGTCACCTTA
1 GTCGATGAGACACTGGGTGTCAACTTA
52454974 TTGCTTCGAA
Statistics
Matches: 50, Mismatches: 14, Indels: 4
0.74 0.21 0.06
Matches are distributed among these distances:
37 20 0.40
38 11 0.22
40 2 0.04
41 17 0.34
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.29
Consensus pattern (37 bp):
GTCGATGAGACACTGGGTGTCAACTTACTTCGGATAG
Found at i:52460106 original size:57 final size:58
Alignment explanation
Indices: 52459997--52460114 Score: 157
Period size: 57 Copynumber: 2.1 Consensus size: 58
52459987 ATACAAATGG
* * * *
52459997 TGAAAATGGAGAAATGAGAAACATTTGAAAATGATTATAGTTTTTTCTAAAATGAAAA
1 TGAAAATGGAGAAATGAGAAACATTTGAAAATAAATATAGTTTTCTCCAAAATGAAAA
* * * *
52460055 TGAAAATGGAGAAATG-GAATCATTTGGAAATAAATGTGGTTTTCTCCAAAATGAAAA
1 TGAAAATGGAGAAATGAGAAACATTTGAAAATAAATATAGTTTTCTCCAAAATGAAAA
52460112 TGA
1 TGA
52460115 CCTAAGAAGA
Statistics
Matches: 52, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
57 36 0.69
58 16 0.31
ACGTcount: A:0.46, C:0.05, G:0.19, T:0.30
Consensus pattern (58 bp):
TGAAAATGGAGAAATGAGAAACATTTGAAAATAAATATAGTTTTCTCCAAAATGAAAA
Found at i:52468291 original size:12 final size:12
Alignment explanation
Indices: 52468274--52468309 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
52468264 ATATACACAT
*
52468274 TAAAAATATATA
1 TAAAAATATAAA
*
52468286 TAAAAATAAAAA
1 TAAAAATATAAA
52468298 TAAAAATATAAA
1 TAAAAATATAAA
52468310 AATTCAGAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (12 bp):
TAAAAATATAAA
Found at i:52468308 original size:20 final size:22
Alignment explanation
Indices: 52468294--52468351 Score: 75
Period size: 21 Copynumber: 2.6 Consensus size: 22
52468284 TATAAAAATA
52468294 AAAATAAAAATATAAAAATTCAG
1 AAAA-AAAAATATAAAAATTCAG
52468317 AAAAAAAAATAT-AAAA-TCTAG
1 AAAAAAAAATATAAAAATTC-AG
*
52468338 AAAAAAACATATAA
1 AAAAAAAAATATAA
52468352 TTTATAAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
20 2 0.06
21 17 0.53
22 9 0.28
23 4 0.12
ACGTcount: A:0.72, C:0.05, G:0.03, T:0.19
Consensus pattern (22 bp):
AAAAAAAAATATAAAAATTCAG
Found at i:52478231 original size:15 final size:16
Alignment explanation
Indices: 52478211--52478248 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
52478201 GTTTAGTCCC
*
52478211 TAGGGTTTTT-TGGTT
1 TAGGGTTTTTAGGGTT
52478226 TAGGGTTTTTAGGGTT
1 TAGGGTTTTTAGGGTT
52478242 TAGGGTT
1 TAGGGTT
52478249 AGAGTTTTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 10 0.48
16 11 0.52
ACGTcount: A:0.11, C:0.00, G:0.37, T:0.53
Consensus pattern (16 bp):
TAGGGTTTTTAGGGTT
Found at i:52478312 original size:34 final size:34
Alignment explanation
Indices: 52478233--52478312 Score: 90
Period size: 34 Copynumber: 2.3 Consensus size: 34
52478223 GTTTAGGGTT
*
52478233 TTTAGGGTTTAGGGTTAGAGTTTTGTTAAAAATAA
1 TTTA-GGTTTAGGGTTAGAGTTTTGATAAAAATAA
* * *
52478268 TTTAGATTTAGGGCTTAGGGTTTT-ATCAAAATAA
1 TTTAGGTTTAGGG-TTAGAGTTTTGATAAAAATAA
*
52478302 TTTTGGTTTAG
1 TTTAGGTTTAG
52478313 AGTGTAGGGT
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
34 25 0.66
35 13 0.34
ACGTcount: A:0.29, C:0.03, G:0.24, T:0.45
Consensus pattern (34 bp):
TTTAGGTTTAGGGTTAGAGTTTTGATAAAAATAA
Found at i:52478393 original size:34 final size:33
Alignment explanation
Indices: 52478349--52478471 Score: 101
Period size: 34 Copynumber: 3.7 Consensus size: 33
52478339 ATAAATCAAG
*
52478349 TTTAGAGTTTTTTTAAAATTAATTAAATTAGGT
1 TTTAGAGTTTTTATAAAATTAATTAAATTAGGT
* * *
52478382 TTTAGAAG-TTTTAAATAAATAAATAAAATTA-GT
1 TTTAG-AGTTTTTATA-AAATTAATTAAATTAGGT
* * *
52478415 GTTTAGAGTTTTTAAGAAAATTGATTAAATTAGGG
1 -TTTAGAGTTTTT-ATAAAATTAATTAAATTAGGT
* *
52478450 TTTAG-TTTTTTTTAAAA-TAATT
1 TTTAGAGTTTTTATAAAATTAATT
52478472 GTGTTTAGGT
Statistics
Matches: 71, Mismatches: 13, Indels: 14
0.72 0.13 0.14
Matches are distributed among these distances:
31 4 0.06
32 4 0.06
33 19 0.27
34 41 0.58
35 3 0.04
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.47
Consensus pattern (33 bp):
TTTAGAGTTTTTATAAAATTAATTAAATTAGGT
Found at i:52478924 original size:126 final size:125
Alignment explanation
Indices: 52478549--52478926 Score: 485
Period size: 125 Copynumber: 3.0 Consensus size: 125
52478539 AATAGTTTTA
* * * *
52478549 GAAAAATTAATTTTGAGAATACGGTTCTGAA-AAGATAATGTCAATAATACTTCAAGCAGGATGC
1 GAAAAA-TAATTTTGAGAAGACGGTTCTGAACAA-ATAGTGT-AAAAACACTTCAAGCAGGATGC
* *
52478613 ACTGCCAGCAAAATTACTGAAAAAAGCTCTCACGTGGACGCTCTTTTTCTACAGTAGTTCTTG
63 ACTGTCAGCAAAATTACTGAAAAAAGCTCTCACGTGGACGCTCTTTTTCTACAGTAGTTCCTG
* * *
52478676 GAAAAATAATTTTGAGAAGACGGTTCTGAACAAATAGTGTAAAAACGCTTCAAGTAGGATGCATT
1 GAAAAATAATTTTGAGAAGACGGTTCTGAACAAATAGTGTAAAAACACTTCAAGCAGGATGCACT
* * * *
52478741 GTCAACAAAAATATTGAAAAAAGCTCTCACGTGGACGGTCTTTTTCTACAGTAGTTCCTG
66 GTCAGCAAAATTACTGAAAAAAGCTCTCACGTGGACGCTCTTTTTCTACAGTAGTTCCTG
* * * * *
52478801 GAAAAATAATTTTGAGAAGACGTTTTTGAACAAATGGTATTAAAAGCACTTCAAGCAGGATGCAC
1 GAAAAATAATTTTGAGAAGACGGTTCTGAACAAATAGT-GTAAAAACACTTCAAGCAGGATGCAC
* *
52478866 TGTCAGTAAAATTGA-TGAGAAAAA-CT-TCCACGTGGACGCTTTTTTTCTACAGTAGTTCCTG
65 TGTCAGCAAAATT-ACTGA-AAAAAGCTCT-CACGTGGACGCTCTTTTTCTACAGTAGTTCCTG
52478927 TTTGGCCTTA
Statistics
Matches: 220, Mismatches: 26, Indels: 11
0.86 0.10 0.04
Matches are distributed among these distances:
125 110 0.50
126 96 0.44
127 14 0.06
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.29
Consensus pattern (125 bp):
GAAAAATAATTTTGAGAAGACGGTTCTGAACAAATAGTGTAAAAACACTTCAAGCAGGATGCACT
GTCAGCAAAATTACTGAAAAAAGCTCTCACGTGGACGCTCTTTTTCTACAGTAGTTCCTG
Found at i:52481977 original size:25 final size:25
Alignment explanation
Indices: 52481931--52481978 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
52481921 ACTTCTATTT
*
52481931 TATTAAAAATATAAAAATAATTTAC
1 TATTAAAAATATAAAAAAAATTTAC
*
52481956 TATTAAATAT-TAAAAACAAATTT
1 TATTAAAAATATAAAAA-AAATTT
52481979 TATTTTATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 6 0.30
25 14 0.70
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (25 bp):
TATTAAAAATATAAAAAAAATTTAC
Found at i:52481982 original size:23 final size:23
Alignment explanation
Indices: 52481927--52481982 Score: 60
Period size: 25 Copynumber: 2.3 Consensus size: 23
52481917 AAGAACTTCT
*
52481927 ATTTTATTAAAAATATAAAAATA
1 ATTTTATTAAAAATATAAAAAAA
*
52481950 ATTTACTATTAAATAT-TAAAAACAA
1 ATTT--TATTAAAAATATAAAAA-AA
52481975 ATTTTATT
1 ATTTTATT
52481983 TTATTAAATG
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
23 8 0.29
24 6 0.21
25 14 0.50
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.43
Consensus pattern (23 bp):
ATTTTATTAAAAATATAAAAAAA
Found at i:52482434 original size:18 final size:18
Alignment explanation
Indices: 52482398--52482434 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
52482388 AGAAATTGAA
* *
52482398 ACATATAAGGGTTATGAT
1 ACATATAAGGGCTAGGAT
52482416 ACATATAAGGGCTAGGAT
1 ACATATAAGGGCTAGGAT
52482434 A
1 A
52482435 TGCACTTGGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.41, C:0.08, G:0.24, T:0.27
Consensus pattern (18 bp):
ACATATAAGGGCTAGGAT
Found at i:52484003 original size:25 final size:24
Alignment explanation
Indices: 52483966--52484017 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 24
52483956 ACTGTTATAA
* *
52483966 AAAATTATAAAAT-AAAAATTAATT
1 AAAATTACAAAATGAAAAAAT-ATT
52483990 AAAATTACATAAATGAAAAAATATT
1 AAAATTACA-AAATGAAAAAATATT
52484015 AAA
1 AAA
52484018 TAATATTCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 8 0.33
25 10 0.42
26 6 0.25
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (24 bp):
AAAATTACAAAATGAAAAAATATT
Found at i:52487827 original size:19 final size:18
Alignment explanation
Indices: 52487787--52487830 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
52487777 AAAATTCAAA
*
52487787 TATCAATGCAAATTAAGC
1 TATCAATGCAAATCAAGC
* *
52487805 TATCATATGCAAATCATGT
1 TATCA-ATGCAAATCAAGC
52487824 TATCAAT
1 TATCAAT
52487831 TACATAATCT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.41, C:0.16, G:0.09, T:0.34
Consensus pattern (18 bp):
TATCAATGCAAATCAAGC
Found at i:52489884 original size:68 final size:68
Alignment explanation
Indices: 52489775--52489930 Score: 197
Period size: 68 Copynumber: 2.3 Consensus size: 68
52489765 TGAAATTGGA
* * * *
52489775 AGTCTATTAGAAGATTAAACATGATATGATATTGTGTAAGACCATAGCTA-GAGTATGGCAACAT
1 AGTCTATTAGGACATTAAACATGAGATCATATTGTGTAAGACCATAGCTAGGA-TATGGCAACAT
52489839 ATGG
65 ATGG
* * *
52489843 AGTCTATTAGGACATTAAACATTAGATCATATTGTGTAAGACCATAGCTAGGATTTGGTAACATA
1 AGTCTATTAGGACATTAAACATGAGATCATATTGTGTAAGACCATAGCTAGGATATGGCAACATA
52489908 TGG
66 TGG
* ***
52489911 AGACCGCTAGGACATTAAAC
1 AGTCTATTAGGACATTAAAC
52489931 CAGGAGTCCT
Statistics
Matches: 76, Mismatches: 11, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
68 74 0.97
69 2 0.03
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.29
Consensus pattern (68 bp):
AGTCTATTAGGACATTAAACATGAGATCATATTGTGTAAGACCATAGCTAGGATATGGCAACATA
TGG
Found at i:52505472 original size:22 final size:21
Alignment explanation
Indices: 52505426--52505472 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
52505416 GACTGCTTGT
* *
52505426 GATGTCGCAACACAACCTGAG
1 GATGTCACAACACAACCTGAA
*
52505447 GATGTCACAACACACCCCTGAA
1 GATGTCACAACACA-ACCTGAA
52505469 GATG
1 GATG
52505473 AGCATACTGC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 13 0.59
22 9 0.41
ACGTcount: A:0.34, C:0.30, G:0.21, T:0.15
Consensus pattern (21 bp):
GATGTCACAACACAACCTGAA
Found at i:52509221 original size:67 final size:67
Alignment explanation
Indices: 52509113--52509243 Score: 235
Period size: 67 Copynumber: 2.0 Consensus size: 67
52509103 TTTCCAATTT
*
52509113 AGAGAGCACACTCCAGCGAACCTCATTTCTTACAGCGGGATTACCAATCCAGGCTAAATCCCCTG
1 AGAGAGCACACTCCAGCGAACCTCATTTCTTACAGCGGGATTACCAATCCAAGCTAAATCCCCTG
52509178 CA
66 CA
* *
52509180 AGAGAGCACACTCCCGCGAACCTCATTTCTTACAGCGGGATTACCAGTCCAAGCTAAATCCCCT
1 AGAGAGCACACTCCAGCGAACCTCATTTCTTACAGCGGGATTACCAATCCAAGCTAAATCCCCT
52509244 ATAATATAAA
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
67 61 1.00
ACGTcount: A:0.29, C:0.34, G:0.18, T:0.20
Consensus pattern (67 bp):
AGAGAGCACACTCCAGCGAACCTCATTTCTTACAGCGGGATTACCAATCCAAGCTAAATCCCCTG
CA
Found at i:52509459 original size:57 final size:57
Alignment explanation
Indices: 52509371--52509479 Score: 184
Period size: 57 Copynumber: 1.9 Consensus size: 57
52509361 AATTCGGATT
52509371 ACCCGTCCGGGCTAAATCCATTTTCCACATATTCTTCGGGAGGGCTATATCAAGATC
1 ACCCGTCCGGGCTAAATCCATTTTCCACATATTCTTCGGGAGGGCTATATCAAGATC
* *
52509428 ACCCGTCCGGGCTAGAT-CTTTTTCACACATATTCTTCGGGAGGGCTATATCA
1 ACCCGTCCGGGCTAAATCCATTTTC-CACATATTCTTCGGGAGGGCTATATCA
52509480 TGATAGGATC
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
56 6 0.12
57 43 0.88
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.29
Consensus pattern (57 bp):
ACCCGTCCGGGCTAAATCCATTTTCCACATATTCTTCGGGAGGGCTATATCAAGATC
Found at i:52511032 original size:36 final size:36
Alignment explanation
Indices: 52510985--52511058 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
52510975 TGTAACTTGA
52510985 TTTTCTAGCTCCCCATTGTCTCCTTAATATTTTTCT
1 TTTTCTAGCTCCCCATTGTCTCCTTAATATTTTTCT
52511021 TTTTCTAGCTCCCCATTGTCTCCTTAATATTTTTCT
1 TTTTCTAGCTCCCCATTGTCTCCTTAATATTTTTCT
52511057 TT
1 TT
52511059 CTTTCTTTCT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.14, C:0.27, G:0.05, T:0.54
Consensus pattern (36 bp):
TTTTCTAGCTCCCCATTGTCTCCTTAATATTTTTCT
Found at i:52512561 original size:21 final size:21
Alignment explanation
Indices: 52512520--52512562 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
52512510 AAACATGAAG
*
52512520 AAGAGAAGCAAGAGAGTGATA
1 AAGAGAAGAAAGAGAGTGATA
*
52512541 AAGAGGAAGAAAGCGAG-GATA
1 AAGA-GAAGAAAGAGAGTGATA
52512562 A
1 A
52512563 TGAAGGAGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.53, C:0.05, G:0.35, T:0.07
Consensus pattern (21 bp):
AAGAGAAGAAAGAGAGTGATA
Found at i:52523913 original size:11 final size:11
Alignment explanation
Indices: 52523897--52523972 Score: 51
Period size: 10 Copynumber: 7.5 Consensus size: 11
52523887 TGTTCAAAAA
52523897 TAATATTATTT
1 TAATATTATTT
52523908 TAATA-TA-TT
1 TAATATTATTT
52523917 TAA-A--A-TT
1 TAATATTATTT
*
52523924 TAAT-TTAATT
1 TAATATTATTT
*
52523934 TAATACTTATCT
1 TAATA-TTATTT
*
52523946 TAATAGTATTT
1 TAATATTATTT
*
52523957 T-ATATTAATT
1 TAATATTATTT
52523967 TAATAT
1 TAATAT
52523973 GAAAGTGATT
Statistics
Matches: 52, Mismatches: 6, Indels: 14
0.72 0.08 0.19
Matches are distributed among these distances:
7 6 0.12
8 1 0.02
9 6 0.12
10 16 0.31
11 14 0.27
12 9 0.17
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.55
Consensus pattern (11 bp):
TAATATTATTT
Found at i:52523949 original size:38 final size:37
Alignment explanation
Indices: 52523897--52523970 Score: 96
Period size: 38 Copynumber: 2.0 Consensus size: 37
52523887 TGTTCAAAAA
*
52523897 TAATATTATTTTAATA-TATTTAAAATTTAATTTAATT
1 TAATATTATCTTAATAGTATTTAAAA-TTAATTTAATT
* *
52523934 TAATACTTATCTTAATAGTATTTTATATTAATTTAAT
1 TAATA-TTATCTTAATAGTATTTAAAATTAATTTAAT
52523971 ATGAAAGTGA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
37 5 0.16
38 20 0.62
39 7 0.22
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.55
Consensus pattern (37 bp):
TAATATTATCTTAATAGTATTTAAAATTAATTTAATT
Found at i:52526885 original size:40 final size:39
Alignment explanation
Indices: 52526809--52526885 Score: 93
Period size: 40 Copynumber: 1.9 Consensus size: 39
52526799 GAATCAGTTT
**
52526809 GGGCCTTAGCCCATTCAGATACAGTCTCAGAAATACATTA
1 GGGCCTTAGCCCATTCAGATACAGAATCAG-AATACATTA
*
52526849 GGGCCTTAGCCCATATTAGATACAGAATGCAG-ATACA
1 GGGCCTTAGCCCAT-TCAGATACAGAAT-CAGAATACA
52526886 GTAAATCAGA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 19 0.59
41 10 0.31
42 3 0.09
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.23
Consensus pattern (39 bp):
GGGCCTTAGCCCATTCAGATACAGAATCAGAATACATTA
Found at i:52526918 original size:14 final size:14
Alignment explanation
Indices: 52526899--52526936 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
52526889 AATCAGAATC
52526899 CTACCCACCAGCCT
1 CTACCCACCAGCCT
52526913 CTACCCACCAGCCT
1 CTACCCACCAGCCT
*
52526927 CTACACACCA
1 CTACCCACCA
52526937 TCTCCGTCCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.26, C:0.55, G:0.05, T:0.13
Consensus pattern (14 bp):
CTACCCACCAGCCT
Found at i:52530661 original size:18 final size:18
Alignment explanation
Indices: 52530633--52530715 Score: 87
Period size: 18 Copynumber: 4.6 Consensus size: 18
52530623 AATTTATGAG
*
52530633 AAGCTAGCAAAACATATA
1 AAGCTCGCAAAACATATA
* *
52530651 AAGCTCACAAAACACATA
1 AAGCTCGCAAAACATATA
*
52530669 GAGCTCGCAAAACACT-TA
1 AAGCTCGCAAAACA-TATA
* * *
52530687 GAGCTTGCAAAACATACA
1 AAGCTCGCAAAACATATA
52530705 AAGCTCGCAAA
1 AAGCTCGCAAA
52530716 TCATGTTTAT
Statistics
Matches: 53, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
17 1 0.02
18 52 0.98
ACGTcount: A:0.48, C:0.24, G:0.13, T:0.14
Consensus pattern (18 bp):
AAGCTCGCAAAACATATA
Found at i:52534019 original size:29 final size:29
Alignment explanation
Indices: 52533986--52534045 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
52533976 AACTAAAATA
*
52533986 TTAATTAACCTAA-ATTAACCTAATGGAAT
1 TTAATTAACCTAAGA-TAACCAAATGGAAT
*
52534015 TTAATTAACCTAAGATATCCAAATGGAAT
1 TTAATTAACCTAAGATAACCAAATGGAAT
52534044 TT
1 TT
52534046 CCTATTCCTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 27 0.96
30 1 0.04
ACGTcount: A:0.43, C:0.13, G:0.08, T:0.35
Consensus pattern (29 bp):
TTAATTAACCTAAGATAACCAAATGGAAT
Found at i:52534094 original size:19 final size:19
Alignment explanation
Indices: 52534070--52534106 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
52534060 CGGCCTATGA
52534070 TCAATTAAATCCCTAATTG
1 TCAATTAAATCCCTAATTG
* *
52534089 TCAATTAAGTCGCTAATT
1 TCAATTAAATCCCTAATT
52534107 ACCCTCAACT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.35, C:0.19, G:0.08, T:0.38
Consensus pattern (19 bp):
TCAATTAAATCCCTAATTG
Found at i:52551895 original size:16 final size:17
Alignment explanation
Indices: 52551867--52551918 Score: 63
Period size: 18 Copynumber: 3.1 Consensus size: 17
52551857 CCCCTATTTA
52551867 ATTTCCCTC-AAACTTTT
1 ATTTCCC-CAAAACTTTT
52551884 A-TTCCCCAAAACTTTT
1 ATTTCCCCAAAACTTTT
*
52551900 ATTTTCCCCCAAACTTTT
1 A-TTTCCCCAAAACTTTT
52551918 A
1 A
52551919 CTTCTCACCC
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
15 1 0.03
16 14 0.45
17 1 0.03
18 15 0.48
ACGTcount: A:0.27, C:0.31, G:0.00, T:0.42
Consensus pattern (17 bp):
ATTTCCCCAAAACTTTT
Found at i:52551908 original size:18 final size:16
Alignment explanation
Indices: 52551867--52551918 Score: 61
Period size: 16 Copynumber: 3.1 Consensus size: 16
52551857 CCCCTATTTA
52551867 ATTTCCCTCAAACTTTT
1 ATTTCCC-CAAACTTTT
52551884 A-TTCCCCAAAACTTTT
1 ATTTCCCC-AAACTTTT
52551900 ATTTTCCCCCAAACTTTT
1 A-TTT-CCCCAAACTTTT
52551918 A
1 A
52551919 CTTCTCACCC
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
15 1 0.03
16 14 0.45
17 1 0.03
18 11 0.35
19 4 0.13
ACGTcount: A:0.27, C:0.31, G:0.00, T:0.42
Consensus pattern (16 bp):
ATTTCCCCAAACTTTT
Found at i:52559065 original size:19 final size:19
Alignment explanation
Indices: 52559041--52559078 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
52559031 CTTTGGTGTC
52559041 TCGTGCAACATTATACATA
1 TCGTGCAACATTATACATA
*
52559060 TCGTGCAATATTATACATA
1 TCGTGCAACATTATACATA
52559079 CTTGTGGGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.37, C:0.18, G:0.11, T:0.34
Consensus pattern (19 bp):
TCGTGCAACATTATACATA
Found at i:52560372 original size:6 final size:6
Alignment explanation
Indices: 52560361--52560385 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
52560351 ATTTATGGCT
52560361 GGCAGG GGCAGG GGCAGG GGCAGG G
1 GGCAGG GGCAGG GGCAGG GGCAGG G
52560386 TCTTTAGACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.16, G:0.68, T:0.00
Consensus pattern (6 bp):
GGCAGG
Found at i:52564029 original size:18 final size:18
Alignment explanation
Indices: 52564008--52564047 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
52563998 TAATACATTT
*
52564008 TATTTTAATTT-TTAAAAA
1 TATTTAAATTTATT-AAAA
52564026 TATTTAAATTTATTAAAA
1 TATTTAAATTTATTAAAA
52564044 TATT
1 TATT
52564048 AATATAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 18 0.90
19 2 0.10
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TATTTAAATTTATTAAAA
Found at i:52566812 original size:3 final size:3
Alignment explanation
Indices: 52566804--52566832 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
52566794 TCCTCTATCT
52566804 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
52566833 TTTTAAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:52567846 original size:21 final size:21
Alignment explanation
Indices: 52567822--52567862 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
52567812 CATGTCAAAA
52567822 TATT-ATTGTCATATGTTATGC
1 TATTGATTGTCA-ATGTTATGC
52567843 TATTGATTGTCAATGTTATG
1 TATTGATTGTCAATGTTATG
52567863 TTAACGTCAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.24, C:0.07, G:0.17, T:0.51
Consensus pattern (21 bp):
TATTGATTGTCAATGTTATGC
Found at i:52571367 original size:10 final size:10
Alignment explanation
Indices: 52571352--52571385 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
52571342 AAATACAATA
52571352 ATAATACTAT
1 ATAATACTAT
52571362 ATAATACTAT
1 ATAATACTAT
52571372 ATAATA-TA-
1 ATAATACTAT
52571380 ATAATA
1 ATAATA
52571386 AACTAACAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 6 0.25
9 2 0.08
10 16 0.67
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (10 bp):
ATAATACTAT
Found at i:52578396 original size:42 final size:42
Alignment explanation
Indices: 52578349--52578430 Score: 130
Period size: 42 Copynumber: 2.0 Consensus size: 42
52578339 ACAACGGTCC
52578349 CGGATGAACATTTCCCTAATTTCAAAGTAA-AATTCTAAAGCA
1 CGGATGAACATTTCCCTAATTTC-AAGTAACAATTCTAAAGCA
* *
52578391 CGGATGAACATTTCTCTAATTTCAAGTAACAATTTTAAAG
1 CGGATGAACATTTCCCTAATTTCAAGTAACAATTCTAAAG
52578431 AATCCTAACT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
41 6 0.16
42 31 0.84
ACGTcount: A:0.39, C:0.17, G:0.12, T:0.32
Consensus pattern (42 bp):
CGGATGAACATTTCCCTAATTTCAAGTAACAATTCTAAAGCA
Found at i:52579892 original size:26 final size:25
Alignment explanation
Indices: 52579847--52579897 Score: 59
Period size: 26 Copynumber: 2.0 Consensus size: 25
52579837 ATTATTTTAT
* *
52579847 TAAATAAATAATTTTTAAAATATAA
1 TAAATAAATAATTTTAAAAACATAA
52579872 TAAATTAAATACA-TTTAAAAACATAA
1 TAAA-TAAATA-ATTTTAAAAACATAA
52579898 AAACATACAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
25 4 0.18
26 17 0.77
27 1 0.05
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (25 bp):
TAAATAAATAATTTTAAAAACATAA
Found at i:52580169 original size:12 final size:12
Alignment explanation
Indices: 52580152--52580189 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
52580142 AAACAACACC
52580152 AAACAACACAAA
1 AAACAACACAAA
*
52580164 AAACAACAC-TA
1 AAACAACACAAA
52580175 AAACAACACAAA
1 AAACAACACAAA
52580187 AAA
1 AAA
52580190 TAGCACCACC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
11 10 0.43
12 13 0.57
ACGTcount: A:0.74, C:0.24, G:0.00, T:0.03
Consensus pattern (12 bp):
AAACAACACAAA
Found at i:52580182 original size:23 final size:22
Alignment explanation
Indices: 52580141--52580189 Score: 80
Period size: 23 Copynumber: 2.2 Consensus size: 22
52580131 AAGTAGCATC
*
52580141 AAAACAACACCAAACAACACAA
1 AAAACAACACAAAACAACACAA
52580163 AAAACAACACTAAAACAACACAA
1 AAAACAACAC-AAAACAACACAA
52580186 AAAA
1 AAAA
52580190 TAGCACCACC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
22 10 0.40
23 15 0.60
ACGTcount: A:0.71, C:0.27, G:0.00, T:0.02
Consensus pattern (22 bp):
AAAACAACACAAAACAACACAA
Found at i:52581193 original size:30 final size:30
Alignment explanation
Indices: 52581153--52581209 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
52581143 GGGATGTGAG
*
52581153 GGGAGAAAAAGTTATGGGGGGAAAGTGGGA
1 GGGAGAAAAAGTTATGGGAGGAAAGTGGGA
* *
52581183 GGGAGTAAAAGTTTTGGGAGGAAAGTG
1 GGGAGAAAAAGTTATGGGAGGAAAGTG
52581210 AAAAGGTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.35, C:0.00, G:0.47, T:0.18
Consensus pattern (30 bp):
GGGAGAAAAAGTTATGGGAGGAAAGTGGGA
Found at i:52585417 original size:17 final size:17
Alignment explanation
Indices: 52585395--52585431 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
52585385 ATATTGATGA
*
52585395 TAAGTTTAAAAATATAT
1 TAAGTTTAAAAATAAAT
*
52585412 TAAGTTTAAATATAAAT
1 TAAGTTTAAAAATAAAT
52585429 TAA
1 TAA
52585432 TGTCAGATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (17 bp):
TAAGTTTAAAAATAAAT
Found at i:52586901 original size:50 final size:50
Alignment explanation
Indices: 52586838--52587362 Score: 385
Period size: 50 Copynumber: 10.5 Consensus size: 50
52586828 TGGAAAGTAG
*
52586838 GATTCGCTATTGTGG-TTTCAATCTTTTTAACTGCAATGTCGGGGAAGCAA
1 GATTCGCTGTTGTGGCTTT-AATCTTTTTAACTGCAATGTCGGGGAAGCAA
* *
52586888 GATTCGCTGTTGTGGCTTTAATATTTTTAACTGCAATGTCGAGGAAGCAA
1 GATTCGCTGTTGTGGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAA
* * ** * * * * *
52586938 GATTCGCCGTTGTGGCTTTAATCTGTTCCATTGCACTGCCTGGGAGAGTAA
1 GATTCGCTGTTGTGGCTTTAATCTTTTTAACTGCAATGTCGGGGA-AGCAA
* * ** * *
52586989 GATTCG-TCGTTGTGACTTTATTCCATTTAACTGCAATGTTGGGAAAGCAA
1 GATTCGCT-GTTGTGGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAA
* * * ** ** * * * * *
52587039 GATTCACCGTTGTGGCTTTAATCTGTTCCACTGCACCGCCTGAGAGGTAA
1 GATTCGCTGTTGTGGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAA
* * * *
52587089 AATTTGCTGCTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAA
1 GATTCGCTGTTGTGGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAA
* * * * * * ** *
52587139 GATTCGCCGTTGTGGCTTTAATCTGTTTCATTGCACTGCCTAGGAGAGTAA
1 GATTCGCTGTTGTGGCTTTAATCTTTTTAACTGCAATGTCGGGGA-AGCAA
* * *
52587190 GATTCG-TCGTTGTGAC-TTAATCCTTTTAACTGCAATGTCGGGAAAGCAA
1 GATTCGCT-GTTGTGGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAA
* * * ** * ** * * *
52587239 GATTCACCGTTGTGGCTTTAATCTGTTCCATTGCACCGTCTGGGAGGTAA
1 GATTCGCTGTTGTGGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAA
* * * * *
52587289 GATTCGCTGCTGTAGCTTTCATCTTTTTAACCGCAATGTCAGGG-AGACAA
1 GATTCGCTGTTGTGGCTTTAATCTTTTTAACTGCAATGTCGGGGAAG-CAA
* *
52587339 GATTCACCGTTGTGGCTTTAATCT
1 GATTCGCTGTTGTGGCTTTAATCT
52587363 GTTCCACTGC
Statistics
Matches: 346, Mismatches: 120, Indels: 18
0.71 0.25 0.04
Matches are distributed among these distances:
49 17 0.05
50 274 0.79
51 55 0.16
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.34
Consensus pattern (50 bp):
GATTCGCTGTTGTGGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAA
Found at i:52587153 original size:100 final size:99
Alignment explanation
Indices: 52586886--52587394 Score: 666
Period size: 100 Copynumber: 5.1 Consensus size: 99
52586876 TCGGGGAAGC
* * *
52586886 AAGATTCGCTGTTGTGGCTTTAATATTTTTAACTGCAATGTCGAGGAAGCAAGATTCGCCGTTGT
1 AAGATTCGCTGTTGT-GCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGTTGT
*
52586951 GGCTTTAATCTGTTCCATTGCACTGCCTGGGAGAGT
65 GGCTTTAATCTGTTCCATTGCACCGCCTGGGAG-GT
* ** * *
52586987 AAGATTCG-TCGTTGTGACTTTATTCCATTTAACTGCAATGTTGGGAAAGCAAGATTCACCGTTG
1 AAGATTCGCT-GTTGTG-CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGTTG
* *
52587051 TGGCTTTAATCTGTTCCACTGCACCGCCTGAGAGGT
64 TGGCTTTAATCTGTTCCATTGCACCGCCTGGGAGGT
* * * *
52587087 AAAATTTGCTGCTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCGCCGTTGT
1 AAGATTCGCTGTTGT-GCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGTTGT
* * *
52587152 GGCTTTAATCTGTTTCATTGCACTGCCTAGGAGAGT
65 GGCTTTAATCTGTTCCATTGCACCGCCTGGGAG-GT
* *
52587188 AAGATTCG-TCGTTGTGAC-TTAATCCTTTTAACTGCAATGTCGGGAAAGCAAGATTCACCGTTG
1 AAGATTCGCT-GTTGTG-CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGTTG
*
52587251 TGGCTTTAATCTGTTCCATTGCACCGTCTGGGAGGT
64 TGGCTTTAATCTGTTCCATTGCACCGCCTGGGAGGT
* * * *
52587287 AAGATTCGCTGCTGTAGCTTTCATCTTTTTAACCGCAATGTCAGGG-AGACAAGATTCACCGTTG
1 AAGATTCGCTGTTGT-GCTTTAATCTTTTTAACTGCAATGTCGGGGAAG-CAAGATTCACCGTTG
*
52587351 TGGCTTTAATCTGTTCCACTGCACCGCCTGGGAGGT
64 TGGCTTTAATCTGTTCCATTGCACCGCCTGGGAGGT
52587387 AAGATTCG
1 AAGATTCG
52587395 TAATCTTCAA
Statistics
Matches: 354, Mismatches: 43, Indels: 23
0.84 0.10 0.05
Matches are distributed among these distances:
99 17 0.05
100 239 0.68
101 98 0.28
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.33
Consensus pattern (99 bp):
AAGATTCGCTGTTGTGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGTTGTG
GCTTTAATCTGTTCCATTGCACCGCCTGGGAGGT
Found at i:52587319 original size:200 final size:201
Alignment explanation
Indices: 52586886--52587395 Score: 810
Period size: 200 Copynumber: 2.5 Consensus size: 201
52586876 TCGGGGAAGC
* * * *
52586886 AAGATTCGCTGTTGTGGCTTTAATATTTTTAACTGCAATGTCGAGGAAGCAAGATTCGCCGTTGT
1 AAGATTCGCTGCTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCGCCGTTGT
*
52586951 GGCTTTAATCTGTTCCATTGCACTGCCTGGGAGAGTAAGATTCGTCGTTGTGACTTTATTCCATT
66 GGCTTTAATCTGTTCCATTGCACTGCCTGGGAGAGTAAGATTCGTCGTTGTGACTTTAATCCATT
*
52587016 TAACTGCAATGTTGGGAAAGCAAGATTCACCGTTGTGGCTTTAATCTGTTCCACTGCACCGCCTG
131 TAACTGCAATGTCGGGAAAGCAAGATTCACCGTTGTGGCTTTAATCTGTTCCACTGCACCGCCTG
52587081 AGAGGT
196 AGAGGT
* *
52587087 AAAATTTGCTGCTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCGCCGTTGT
1 AAGATTCGCTGCTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCGCCGTTGT
* * *
52587152 GGCTTTAATCTGTTTCATTGCACTGCCTAGGAGAGTAAGATTCGTCGTTGTGAC-TTAATCCTTT
66 GGCTTTAATCTGTTCCATTGCACTGCCTGGGAGAGTAAGATTCGTCGTTGTGACTTTAATCCATT
* *
52587216 TAACTGCAATGTCGGGAAAGCAAGATTCACCGTTGTGGCTTTAATCTGTTCCATTGCACCGTCTG
131 TAACTGCAATGTCGGGAAAGCAAGATTCACCGTTGTGGCTTTAATCTGTTCCACTGCACCGCCTG
*
52587281 GGAGGT
196 AGAGGT
* * * *
52587287 AAGATTCGCTGCTGTAGCTTTCATCTTTTTAACCGCAATGTCAGGG-AGACAAGATTCACCGTTG
1 AAGATTCGCTGCTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAG-CAAGATTCGCCGTTG
* *
52587351 TGGCTTTAATCTGTTCCACTGCACCGCCTGGGAG-GTAAGATTCGT
65 TGGCTTTAATCTGTTCCATTGCACTGCCTGGGAGAGTAAGATTCGT
52587396 AATCTTCAAC
Statistics
Matches: 284, Mismatches: 24, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
199 13 0.05
200 160 0.56
201 111 0.39
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.34
Consensus pattern (201 bp):
AAGATTCGCTGCTGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCGCCGTTGT
GGCTTTAATCTGTTCCATTGCACTGCCTGGGAGAGTAAGATTCGTCGTTGTGACTTTAATCCATT
TAACTGCAATGTCGGGAAAGCAAGATTCACCGTTGTGGCTTTAATCTGTTCCACTGCACCGCCTG
AGAGGT
Found at i:52587644 original size:131 final size:131
Alignment explanation
Indices: 52587380--52588510 Score: 1828
Period size: 131 Copynumber: 8.8 Consensus size: 131
52587370 TGCACCGCCT
* *
52587380 GGGAGGTAAGAT-TCGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTAGTGGCT
1 GGGAGATAAGATCT-GTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTGGTGGCT
* *
52587444 TAAATC-GTTTCCCTACTCCTGGGGAAGATAAGATTTGCCGTCTTCGATCTGCTTCACTATTGCT
65 TAAATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTATTGCT
52587508 TA
130 TA
*
52587510 GGGAGATAAGATCTGTAATCTTCAACCTATCCCACTGTTGACCAGGGAGATAGGACTGGTGGCTT
1 GGGAGATAAGATCTGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTGGTGGCTT
52587575 AAATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTATTGCTT
66 AAATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTATTGCTT
52587640 A
131 A
* * *
52587641 GGGAGATAAGATCTGTAATCTTCAACCTATCCCACTACTGACCAGGGAGATAGGAATAGTGGCTT
1 GGGAGATAAGATCTGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTGGTGGCTT
** * * * *
52587706 AAATCTACTGCCCTACTTCTTGGGAAGATAAGATTCGCCGTTTTCGATCTGCTCCACTATTGCTT
66 AAATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTATTGCTT
52587771 A
131 A
52587772 GGGAGATAAGATCTGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTGGTGGCTT
1 GGGAGATAAGATCTGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTGGTGGCTT
* * *
52587837 AAATCTGTTTCCCTACTCCTAGGGAAGATAAGATTTGCCGTCTTTGATCTGCTCCACTATTGCTT
66 AAATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTATTGCTT
52587902 A
131 A
*
52587903 AGGAGATAAGATCTGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTGGTGGCTT
1 GGGAGATAAGATCTGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTGGTGGCTT
*
52587968 AAATCTGTTTCCCTACTCTTGGGGAAGATAAGATT---CG-C--CG---T-CT----T-TTGCTT
66 AAATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTATTGCTT
52588018 A
131 A
* *
52588019 GGGAGATAAAATCTGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTAGTGGCTT
1 GGGAGATAAGATCTGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTGGTGGCTT
* *
52588084 AAATCTGCTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTT
66 AAATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTATTGCTT
52588149 A
131 A
52588150 GGGAGATAAGATCTGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTGGTGGCTT
1 GGGAGATAAGATCTGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTGGTGGCTT
* * *
52588215 AAATTTGTTTCCCTACTCCTGGGGAAGATAAGATTCGTCGTCTTCGATCTTCTCCACTATTGCTT
66 AAATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTATTGCTT
52588280 A
131 A
*
52588281 GGGAGATAAGATCTGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTTGTGGCTT
1 GGGAGATAAGATCTGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTGGTGGCTT
* * *
52588346 AAATCTGTTTCCCTACTCTTGGGGAAGATAAGATTCGCCGTCTTCGATTTGCTCCACAATTGCTT
66 AAATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTATTGCTT
52588411 A
131 A
* * *
52588412 GGGAGATAAGATCCGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGATTGATGGCTT
1 GGGAGATAAGATCTGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTGGTGGCTT
*
52588477 AAATCTGCTTCCCTACTCCTGGGGAAGATAAGAT
66 AAATCTGTTTCCCTACTCCTGGGGAAGATAAGAT
52588511 CCGTAATCTT
Statistics
Matches: 928, Mismatches: 56, Indels: 33
0.91 0.06 0.03
Matches are distributed among these distances:
116 102 0.11
117 1 0.00
119 2 0.00
120 1 0.00
121 2 0.00
122 3 0.00
125 2 0.00
126 2 0.00
127 1 0.00
128 2 0.00
130 66 0.07
131 744 0.80
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.30
Consensus pattern (131 bp):
GGGAGATAAGATCTGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTGGTGGCTT
AAATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTATTGCTT
A
Found at i:52587650 original size:44 final size:45
Alignment explanation
Indices: 52587600--52587783 Score: 107
Period size: 44 Copynumber: 4.2 Consensus size: 45
52587590 CTCCTGGGGA
*
52587600 AGATAAGATTCGCCGTCTTCGATCTGCT-CCACTATTGCTTAGGG
1 AGATAAGATTCGCCGTCTTCAATCTGCTCCCACTATTGCTTAGGG
*** * * * *
52587644 AGATAAGA-TCTGTAATCTTCAACCT-ATCCCACTACTGAC-CAGGG
1 AGATAAGATTC-GCCGTCTTCAATCTGCTCCCACTATTG-CTTAGGG
* * * * * * * *
52587688 AGATAGGAATAG-TGGCTTAAATCTACTGCC-CTACTT-CTT-GGG
1 AGATAAGATTCGCCGTCTTCAATCTGCTCCCACTA-TTGCTTAGGG
* *
52587730 AAGATAAGATTCGCCGTTTTCGATCTGCT-CCACTATTGCTTAGGG
1 -AGATAAGATTCGCCGTCTTCAATCTGCTCCCACTATTGCTTAGGG
52587775 AGATAAGAT
1 AGATAAGAT
52587784 CTGTAATCTT
Statistics
Matches: 100, Mismatches: 28, Indels: 24
0.66 0.18 0.16
Matches are distributed among these distances:
42 4 0.04
43 26 0.26
44 65 0.65
45 5 0.05
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.30
Consensus pattern (45 bp):
AGATAAGATTCGCCGTCTTCAATCTGCTCCCACTATTGCTTAGGG
Found at i:52588100 original size:116 final size:116
Alignment explanation
Indices: 52587896--52588127 Score: 419
Period size: 116 Copynumber: 2.0 Consensus size: 116
52587886 TGCTCCACTA
* *
52587896 TTGCTTAAGGAGATAAGATCTGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTG
1 TTGCTTAAGGAGATAAAATCTGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTA
* *
52587961 GTGGCTTAAATCTGTTTCCCTACTCTTGGGGAAGATAAGATTCGCCGTCTT
66 GTGGCTTAAATCTGCTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTT
*
52588012 TTGCTTAGGGAGATAAAATCTGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTA
1 TTGCTTAAGGAGATAAAATCTGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTA
52588077 GTGGCTTAAATCTGCTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTT
66 GTGGCTTAAATCTGCTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTT
52588128 CGATCTGCTC
Statistics
Matches: 111, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
116 111 1.00
ACGTcount: A:0.25, C:0.22, G:0.23, T:0.29
Consensus pattern (116 bp):
TTGCTTAAGGAGATAAAATCTGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTA
GTGGCTTAAATCTGCTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTT
Found at i:52588185 original size:44 final size:45
Alignment explanation
Indices: 52588137--52588316 Score: 99
Period size: 44 Copynumber: 4.1 Consensus size: 45
52588127 TCGATCTGCT
52588137 CCACTACTGCTTAGGGAGATAAGATCT-GTAATCTTCAACCTATC
1 CCACTACTGCTTAGGGAGATAAGATCTCGTAATCTTCAACCTATC
* * * * ** * ** * *
52588181 CCACTGCTGAC-CAGGGAGATAGGA-CTGGT-GGCTTAAATTTGTTT
1 CCACTACTG-CTTAGGGAGATAAGATCTCGTAATCTTCAACCT-ATC
* * ** * *
52588225 CC-CTACT-CCTGGGGAAGATAAGAT-TCGTCGTCTTCGATCT-TC
1 CCACTACTGCTTAGGG-AGATAAGATCTCGTAATCTTCAACCTATC
*
52588267 TCCACTATTGCTTAGGGAGATAAGATCT-GTAATCTTCAACCTATC
1 -CCACTACTGCTTAGGGAGATAAGATCTCGTAATCTTCAACCTATC
52588312 CCACT
1 CCACT
52588317 GCTGACCAGG
Statistics
Matches: 97, Mismatches: 27, Indels: 24
0.66 0.18 0.16
Matches are distributed among these distances:
41 1 0.01
42 4 0.04
43 24 0.25
44 59 0.61
45 9 0.09
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.31
Consensus pattern (45 bp):
CCACTACTGCTTAGGGAGATAAGATCTCGTAATCTTCAACCTATC
Found at i:52588459 original size:44 final size:44
Alignment explanation
Indices: 52588411--52588550 Score: 116
Period size: 44 Copynumber: 3.2 Consensus size: 44
52588401 ACAATTGCTT
52588411 AGGGAGATAAGATCCGTAATCTTCAACCTATCCCACTGCTGACC
1 AGGGAGATAAGATCCGTAATCTTCAACCTATCCCACTGCTGACC
* * * *
52588455 AGGGAGATAGGAT---TGATGGCTTAAATCTGCT-TCCCTACTCCTG---
1 AGGGAGATAAGATCCGTAAT--CTTCAA-C--CTATCCC-ACTGCTGACC
*
52588498 -GGGAAGATAAGATCCGTAATCTTCAACCTATCCTACTGCTGACC
1 AGGG-AGATAAGATCCGTAATCTTCAACCTATCCCACTGCTGACC
52588542 AGGGAGATA
1 AGGGAGATA
52588551 GGACTAGTGG
Statistics
Matches: 72, Mismatches: 9, Indels: 30
0.65 0.08 0.27
Matches are distributed among these distances:
41 11 0.15
42 6 0.08
43 14 0.19
44 23 0.32
45 7 0.10
46 11 0.15
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.25
Consensus pattern (44 bp):
AGGGAGATAAGATCCGTAATCTTCAACCTATCCCACTGCTGACC
Found at i:52588460 original size:509 final size:517
Alignment explanation
Indices: 52587380--52588514 Score: 1840
Period size: 509 Copynumber: 2.2 Consensus size: 517
52587370 TGCACCGCCT
* * *
52587380 GGGAGGTAAGATTCGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTAGTGGCTT
1 GGGAGATAAGATCCGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTGGTGGCTT
52587445 AAATC-GTTTCCCTACTCCTGGGGAAGATAAGATTTGCCGTCTTCGATCTGCTTCACTATTGCTT
66 AAATCTGTTTCCCTACTCCTGGGGAAGATAAGA-TT-CCGTC-TCGA--TGCTT--CTATTGCTT
* * *
52587509 AGGGAGATAAGATCTGTAATCTTCAACCTATCCCACTGTTGACCAGGGAGATAGGACTGGTGGCT
124 AGGGAGATAAAATCTGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTAGTGGCT
* *
52587574 TAAATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTATTGCT
189 TAAATCTGCTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCT
52587639 TAGGGAGATAAGATCTGTAATCTTCAACCTATCCCACTACTGACCAGGGAGATAGGAATAGTGGC
254 TAGGGAGATAAGATCTGTAATCTTCAACCTATCCCACTACTGACCAGGGAGATAGGAATAGTGGC
* * *
52587704 TTAAATCTACTGCCCTACTTCTTGGGAAGATAAGATTCGCCGTTTTCGATCTGCTCCACTATTGC
319 TTAAATCTACTGCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTATTGC
52587769 TTAGGGAGATAAGATCTGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTGGTGG
384 TTAGGGAGATAAGATCTGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTGGTGG
* * *
52587834 CTTAAATCTGTTTCCCTACTCCTAGGGAAGATAAGATTTGCCGTCTTTGATCTGCTCCACTATTG
449 CTTAAATCTGTTTCCCTACTCCTAGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACAATTG
52587899 CTTA
514 CTTA
* *
52587903 AGGAGATAAGATCTGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTGGTGGCTT
1 GGGAGATAAGATCCGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTGGTGGCTT
*
52587968 AAATCTGTTTCCCTACTCTTGGGGAAGATAAGATT-CG-C-CG-T-C-T-T-TTGCTTAGGGAGA
66 AAATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCCGTCTCGATGCTTCTATTGCTTAGGGAGA
52588025 TAAAATCTGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTAGTGGCTTAAATCT
131 TAAAATCTGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTAGTGGCTTAAATCT
52588090 GCTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAG
196 GCTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAG
* * * *
52588155 ATAAGATCTGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTGGTGGCTTAAATT
261 ATAAGATCTGTAATCTTCAACCTATCCCACTACTGACCAGGGAGATAGGAATAGTGGCTTAAATC
** * * *
52588220 TGTTTCCCTACTCCTGGGGAAGATAAGATTCGTCGTCTTCGATCTTCTCCACTATTGCTTAGGGA
326 TACTGCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTATTGCTTAGGGA
*
52588285 GATAAGATCTGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTTGTGGCTTAAAT
391 GATAAGATCTGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTGGTGGCTTAAAT
* * *
52588350 CTGTTTCCCTACTCTTGGGGAAGATAAGATTCGCCGTCTTCGATTTGCTCCACAATTGCTTA
456 CTGTTTCCCTACTCCTAGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACAATTGCTTA
* *
52588412 GGGAGATAAGATCCGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGATTGATGGCTT
1 GGGAGATAAGATCCGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTGGTGGCTT
*
52588477 AAATCTGCTTCCCTACTCCTGGGGAAGATAAGA-TCCGT
66 AAATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCCGT
52588515 AATCTTCAAC
Statistics
Matches: 573, Mismatches: 36, Indels: 19
0.91 0.06 0.03
Matches are distributed among these distances:
508 1 0.00
509 470 0.82
510 1 0.00
513 1 0.00
514 1 0.00
515 1 0.00
518 2 0.00
520 1 0.00
521 2 0.00
523 67 0.12
524 26 0.05
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.30
Consensus pattern (517 bp):
GGGAGATAAGATCCGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTGGTGGCTT
AAATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCCGTCTCGATGCTTCTATTGCTTAGGGAGA
TAAAATCTGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTAGTGGCTTAAATCT
GCTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAG
ATAAGATCTGTAATCTTCAACCTATCCCACTACTGACCAGGGAGATAGGAATAGTGGCTTAAATC
TACTGCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTATTGCTTAGGGA
GATAAGATCTGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTGGTGGCTTAAAT
CTGTTTCCCTACTCCTAGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACAATTGCTTA
Found at i:52588549 original size:218 final size:218
Alignment explanation
Indices: 52588284--52588728 Score: 737
Period size: 218 Copynumber: 2.0 Consensus size: 218
52588274 TTGCTTAGGG
* *
52588284 AGATAAGATCTGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTTGTGGCTTAAA
1 AGATAAGATCCGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTAGTGGCTTAAA
* ** *
52588349 TCTGTTTCCCTACTCTTGGGGAAGATAAGATTCGCCGTCTTCGATTTGCTCCACAATTGCTTAGG
66 TCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCCACCTTCGATCTGCTCCACAATTGCTTAGG
* *
52588414 GAGATAAGATCCGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGATTGATGGCTTAA
131 GAGATAAGATCCGTAATCTTCAACCCATCCCACTGCTGACCAGGGAGATAGGACTGATGGCTTAA
52588479 ATCTGCTTCCCTACTCCTGGGGA
196 ATCTGCTTCCCTACTCCTGGGGA
*
52588502 AGATAAGATCCGTAATCTTCAACCTATCCTACTGCTGACCAGGGAGATAGGACTAGTGGCTTAAA
1 AGATAAGATCCGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTAGTGGCTTAAA
* * *
52588567 TCTGTTTCCTTACTCCTGGGGAAGATAAGATTCGCCACCTTCTATCTGCTCCACTATTGCTTAGG
66 TCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCCACCTTCGATCTGCTCCACAATTGCTTAGG
* * *
52588632 GAGATAAGATCCGTAATCTTCAACCCATCCCACTGCTTACTAGGGAGATAGGACTGGTGGCTTAA
131 GAGATAAGATCCGTAATCTTCAACCCATCCCACTGCTGACCAGGGAGATAGGACTGATGGCTTAA
* *
52588697 ATCTGTTTCCCTACTTCTGGGGA
196 ATCTGCTTCCCTACTCCTGGGGA
52588720 AGATAAGAT
1 AGATAAGAT
52588729 TCACCGTCTT
Statistics
Matches: 210, Mismatches: 17, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
218 210 1.00
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.29
Consensus pattern (218 bp):
AGATAAGATCCGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTAGTGGCTTAAA
TCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCCACCTTCGATCTGCTCCACAATTGCTTAGG
GAGATAAGATCCGTAATCTTCAACCCATCCCACTGCTGACCAGGGAGATAGGACTGATGGCTTAA
ATCTGCTTCCCTACTCCTGGGGA
Found at i:52588562 original size:87 final size:87
Alignment explanation
Indices: 52588415--52588597 Score: 314
Period size: 87 Copynumber: 2.1 Consensus size: 87
52588405 TTGCTTAGGG
*
52588415 AGATAAGATCCGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGATTGATGGCTTAAA
1 AGATAAGATCCGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGATAGATGGCTTAAA
52588480 TCTGCTTCCCTACTCCTGGGGA
66 TCTGCTTCCCTACTCCTGGGGA
*
52588502 AGATAAGATCCGTAATCTTCAACCTATCCTACTGCTGACCAGGGAGATAGGACTAG-TGGCTTAA
1 AGATAAGATCCGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGA-TAGATGGCTTAA
* *
52588566 ATCTGTTTCCTTACTCCTGGGGA
65 ATCTGCTTCCCTACTCCTGGGGA
52588589 AGATAAGAT
1 AGATAAGAT
52588598 TCGCCACCTT
Statistics
Matches: 91, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
87 89 0.98
88 2 0.02
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.27
Consensus pattern (87 bp):
AGATAAGATCCGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGATAGATGGCTTAAA
TCTGCTTCCCTACTCCTGGGGA
Found at i:52588614 original size:131 final size:131
Alignment explanation
Indices: 52588502--52589213 Score: 1091
Period size: 131 Copynumber: 5.4 Consensus size: 131
52588492 CTCCTGGGGA
*
52588502 AGATAAGATCCGTAATCTTCAACCTATCCTACTGCTGACCAGGGAGATAGGACTAGTGGCTTAAA
1 AGATAAGATCCGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTAGTGGCTTAAA
* ** * *
52588567 TCTGTTTCCTTACTCCTGGGGAAGATAAGATTCGCCACCTTCTATCTGCTCCACTATTGCTTAGG
66 TCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTATTGCCTAGG
52588632 G
131 G
* * * *
52588633 AGATAAGATCCGTAATCTTCAACCCATCCCACTGCTTACTAGGGAGATAGGACTGGTGGCTTAAA
1 AGATAAGATCCGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTAGTGGCTTAAA
* * *
52588698 TCTGTTTCCCTACTTCTGGGGAAGATAAGATTCACCGTCTTCGATCTGCTCCACTATTGCTTAGG
66 TCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTATTGCCTAGG
52588763 G
131 G
* * *
52588764 AGATAAGATCTGTGATCTTCAACCTATCCCACTGCTGACCAGGGAGATAAGACTAGTGGCTTAAA
1 AGATAAGATCCGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTAGTGGCTTAAA
* * * ** *
52588829 TCTGCTTCCCTACTCCTGGAGAAGATAAGATTCGCCGTCTTCGATCTGTTCCACTATCACTTAGG
66 TCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTATTGCCTAGG
52588894 G
131 G
* * * *
52588895 AGATAAGATCTGTAATCTTCAAGCTATCACACTGCTGACCAGGGAGATAGGACTGGTGGCTTAAA
1 AGATAAGATCCGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTAGTGGCTTAAA
* * ** * * *
52588960 TCTGCTTCCCTACTCCTAGGGAAGATAAGATTCGTTGCCTTCGATCTGCTCCACTATTGCTTAGA
66 TCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTATTGCCTAGG
52589025 G
131 G
*
52589026 AGATAAGATCCGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTGGTGGCTTAAA
1 AGATAAGATCCGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTAGTGGCTTAAA
* *
52589091 TCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTCGATCTGTTCCACTATTGCTTAGG
66 TCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTATTGCCTAGG
52589156 G
131 G
*
52589157 AGATAAGATCTGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTAGT
1 AGATAAGATCCGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTAGT
52589214 AGTCTTCCAC
Statistics
Matches: 530, Mismatches: 51, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
131 530 1.00
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (131 bp):
AGATAAGATCCGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTAGTGGCTTAAA
TCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTATTGCCTAGG
G
Found at i:52588639 original size:262 final size:258
Alignment explanation
Indices: 52588371--52589165 Score: 761
Period size: 262 Copynumber: 3.0 Consensus size: 258
52588361 CTCTTGGGGA
** * * *
52588371 AGATAAGATTCGCCGTCTTCGATTTGCTCCACAATTGCT-TAGGGAGATAAGA-TCCGTAATCTT
1 AGATAAGATTCGCAATCTTC-A--TGCTCCAC-ACTGCTATAGGGAGATAAGACT-GGT-AGCTT
* *
52588434 CAACCTATCCCACTGCTGACCAGGG-AGATAGGATTGATGGCTTAAATCTGCTTCC-CTACTCCT
60 AAACCTATCCCACTGCTG-CCAGGGAAGATAAGATTGATGGCTTAAATCTGC-TCCACTACTCCT
* *
52588497 GGGGAAGATAAGATCCGTAATCTTCAACCTATCCTACTGCTGACCAGGGAGATAGGACTAGTGGC
123 GGGGAAGATAAGATCCGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAAGACTAGTGGC
* ** * *
52588562 TTAAATCTGTTTCCTTACTCCTGGGGAAGATAAGATTCGCCACCTTCTATCTGCTCCACTATTGC
188 TTAAATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTCGATCTGTTCCACTATTGC
52588627 TTAGGG
253 TTAGGG
* * ** * *
52588633 AGATAAGATCCGTAATCTTCAACCCATCC-CACTGCTTACTAGGGAGATAGGACTGGTGGCTTAA
1 AGATAAGATTCGCAATCTTC-ATGC-TCCACACTGC-TA-TAGGGAGATAAGACTGGTAGCTTAA
* * * * * * ** * *
52588697 ATCTGTTTCCCTACTTCTG---GGGAAGATAAGATTCACCGTCTTCGATCTGCTCCACTATTGCT
62 A-C-CTATCCC-ACTGCTGCCAGGGAAGATAAGATTGA-TGGCTTAAATCTGCTCCACTACT-CC
* * *
52588759 TAGGG-AGATAAGATCTGTGATCTTCAACCTATCCCACTGCTGACCAGGGAGATAAGACTAGTGG
122 TGGGGAAGATAAGATCCGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAAGACTAGTGG
* * **
52588823 CTTAAATCTGCTTCCCTACTCCTGGAGAAGATAAGATTCGCCGTCTTCGATCTGTTCCACTATCA
187 CTTAAATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTCGATCTGTTCCACTATTG
52588888 CTTAGGG
252 CTTAGGG
* * * * * *
52588895 AGATAAGA-TCTGTAATCTTCAAGCTATCACACTGCTGACCAGGGAGATAGGACTGGTGGCTTAA
1 AGATAAGATTC-GCAATCTTCATGCT-CCACACTGCT-A-TAGGGAGATAAGACTGGTAGCTTAA
* * * * * * ** * *
52588959 ATCTGCTTCC-CTACT-CCTAGGGAAGATAAGATTCGTTGCCTTCGATCTGCTCCACTATTGCT-
62 ACCT-ATCCCACTGCTGCC-AGGGAAGATAAGATT-GATGGCTTAAATCTGCTCCACTACTCCTG
** * *
52589021 TAGAGAGATAAGATCCGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTGGTGGC
124 GGGA-AGATAAGATCCGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAAGACTAGTGGC
52589086 TTAAATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTCGATCTGTTCCACTATTGC
188 TTAAATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTCGATCTGTTCCACTATTGC
52589151 TTAGGG
253 TTAGGG
52589157 AGATAAGAT
1 AGATAAGAT
52589166 CTGTAATCTT
Statistics
Matches: 444, Mismatches: 64, Indels: 49
0.80 0.11 0.09
Matches are distributed among these distances:
259 8 0.02
260 9 0.02
261 30 0.07
262 380 0.86
263 11 0.02
264 6 0.01
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.29
Consensus pattern (258 bp):
AGATAAGATTCGCAATCTTCATGCTCCACACTGCTATAGGGAGATAAGACTGGTAGCTTAAACCT
ATCCCACTGCTGCCAGGGAAGATAAGATTGATGGCTTAAATCTGCTCCACTACTCCTGGGGAAGA
TAAGATCCGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAAGACTAGTGGCTTAAATCT
GTTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTCGATCTGTTCCACTATTGCTTAGGG
Found at i:52588701 original size:349 final size:349
Alignment explanation
Indices: 52588153--52588859 Score: 1175
Period size: 349 Copynumber: 2.0 Consensus size: 349
52588143 CTGCTTAGGG
* *
52588153 AGATAAGATCTGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTGGTGGCTTAAA
1 AGATAAGATCCGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTAGTGGCTTAAA
* * ** *
52588218 TTTGTTTCCCTACTCCTGGGGAAGATAAGATTCGTCGTCTTCGATCTTCTCCACTATTGCTTAGG
66 TCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCCACCTTCGATCTGCTCCACTATTGCTTAGG
* * *
52588283 GAGATAAGATCTGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTTGTGGCTTAA
131 GAGATAAGATCCGTAATCTTCAACCCATCCCACTGCTGACCAGGGAGATAGGACTGGTGGCTTAA
* *
52588348 ATCTGTTTCCCTAC-TCTTGGGGAAGATAAGATTCGCCGTCTTCGATTTGCTCCACAATTGCTTA
196 ATCTGTTTCCCTACTTC-TGGGGAAGATAAGATTCACCGTCTTCGATCTGCTCCACAATTGCTTA
* *
52588412 GGGAGATAAGATCCGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGA-TTGATGGCT
260 GGGAGATAAGATCCGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAAGACTAG-TGGCT
*
52588476 TAAATCTGCTTCCCTACTCCTGGGGA
324 TAAATCTGCTTCCCTACTCCTGGAGA
*
52588502 AGATAAGATCCGTAATCTTCAACCTATCCTACTGCTGACCAGGGAGATAGGACTAGTGGCTTAAA
1 AGATAAGATCCGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTAGTGGCTTAAA
* *
52588567 TCTGTTTCCTTACTCCTGGGGAAGATAAGATTCGCCACCTTCTATCTGCTCCACTATTGCTTAGG
66 TCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCCACCTTCGATCTGCTCCACTATTGCTTAGG
* *
52588632 GAGATAAGATCCGTAATCTTCAACCCATCCCACTGCTTACTAGGGAGATAGGACTGGTGGCTTAA
131 GAGATAAGATCCGTAATCTTCAACCCATCCCACTGCTGACCAGGGAGATAGGACTGGTGGCTTAA
*
52588697 ATCTGTTTCCCTACTTCTGGGGAAGATAAGATTCACCGTCTTCGATCTGCTCCACTATTGCTTAG
196 ATCTGTTTCCCTACTTCTGGGGAAGATAAGATTCACCGTCTTCGATCTGCTCCACAATTGCTTAG
* *
52588762 GGAGATAAGATCTGTGATCTTCAACCTATCCCACTGCTGACCAGGGAGATAAGACTAGTGGCTTA
261 GGAGATAAGATCCGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAAGACTAGTGGCTTA
52588827 AATCTGCTTCCCTACTCCTGGAGA
326 AATCTGCTTCCCTACTCCTGGAGA
52588851 AGATAAGAT
1 AGATAAGAT
52588860 TCGCCGTCTT
Statistics
Matches: 333, Mismatches: 23, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
349 329 0.99
350 4 0.01
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.29
Consensus pattern (349 bp):
AGATAAGATCCGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTAGTGGCTTAAA
TCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCCACCTTCGATCTGCTCCACTATTGCTTAGG
GAGATAAGATCCGTAATCTTCAACCCATCCCACTGCTGACCAGGGAGATAGGACTGGTGGCTTAA
ATCTGTTTCCCTACTTCTGGGGAAGATAAGATTCACCGTCTTCGATCTGCTCCACAATTGCTTAG
GGAGATAAGATCCGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAAGACTAGTGGCTTA
AATCTGCTTCCCTACTCCTGGAGA
Found at i:52588934 original size:480 final size:480
Alignment explanation
Indices: 52588017--52588990 Score: 1626
Period size: 480 Copynumber: 2.0 Consensus size: 480
52588007 GTCTTTTGCT
* *
52588017 TAGGG-AGATAAAATCTGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTAGTGG
1 TAGGGAAGATAAGATCCGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTAGTGG
**
52588081 CTTAAATCTGCTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTG
66 CTTAAATCTGCTTCCCTACTCCTGGGGAAGATAAGATTCGCCACCTTCGATCTGCTCCACTACTG
* *
52588146 CTTAGGGAGATAAGATCTGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTGGTG
131 CTTAGGGAGATAAGATCCGTAATCTTCAACCCATCCCACTGCTGACCAGGGAGATAGGACTGGTG
* ** *
52588211 GCTTAAATTTGTTTCCCTACTCCTGGGGAAGATAAGATTCGTCGTCTTCGATCTTCTCCACTATT
196 GCTTAAATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCACCGTCTTCGATCTGCTCCACTATT
* *
52588276 GCTTAGGGAGATAAGATCTGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTTGT
261 GCTTAGGGAGATAAGATCTGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAAGACTAGT
* * * *
52588341 GGCTTAAATCTGTTTCCCTACTCTTGGGGAAGATAAGATTCGCCGTCTTCGATTTGCTCCACAAT
326 GGCTTAAATCTGCTTCCCTACTCCTGGAGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACAAT
** * *
52588406 TGCTTAGGGAGATAAGATCCGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGATTGA
391 CACTTAGGGAGATAAGATCCGTAATCTTCAACCTATCACACTGCTGACCAGGGAGATAGGACTGA
52588471 TGGCTTAAATCTGCTTCCCTACTCC
456 TGGCTTAAATCTGCTTCCCTACTCC
* *
52588496 TGGGGAAGATAAGATCCGTAATCTTCAACCTATCCTACTGCTGACCAGGGAGATAGGACTAGTGG
1 TAGGGAAGATAAGATCCGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTAGTGG
* * * *
52588561 CTTAAATCTGTTTCCTTACTCCTGGGGAAGATAAGATTCGCCACCTTCTATCTGCTCCACTATTG
66 CTTAAATCTGCTTCCCTACTCCTGGGGAAGATAAGATTCGCCACCTTCGATCTGCTCCACTACTG
* *
52588626 CTTAGGGAGATAAGATCCGTAATCTTCAACCCATCCCACTGCTTACTAGGGAGATAGGACTGGTG
131 CTTAGGGAGATAAGATCCGTAATCTTCAACCCATCCCACTGCTGACCAGGGAGATAGGACTGGTG
*
52588691 GCTTAAATCTGTTTCCCTACTTCTGGGGAAGATAAGATTCACCGTCTTCGATCTGCTCCACTATT
196 GCTTAAATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCACCGTCTTCGATCTGCTCCACTATT
*
52588756 GCTTAGGGAGATAAGATCTGTGATCTTCAACCTATCCCACTGCTGACCAGGGAGATAAGACTAGT
261 GCTTAGGGAGATAAGATCTGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAAGACTAGT
* *
52588821 GGCTTAAATCTGCTTCCCTACTCCTGGAGAAGATAAGATTCGCCGTCTTCGATCTGTTCCACTAT
326 GGCTTAAATCTGCTTCCCTACTCCTGGAGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACAAT
* * *
52588886 CACTTAGGGAGATAAGATCTGTAATCTTCAAGCTATCACACTGCTGACCAGGGAGATAGGACTGG
391 CACTTAGGGAGATAAGATCCGTAATCTTCAACCTATCACACTGCTGACCAGGGAGATAGGACTGA
52588951 TGGCTTAAATCTGCTTCCCTACTCC
456 TGGCTTAAATCTGCTTCCCTACTCC
52588976 TAGGGAAGATAAGAT
1 TAGGGAAGATAAGAT
52588991 TCGTTGCCTT
Statistics
Matches: 458, Mismatches: 36, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
479 4 0.01
480 454 0.99
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.29
Consensus pattern (480 bp):
TAGGGAAGATAAGATCCGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTAGTGG
CTTAAATCTGCTTCCCTACTCCTGGGGAAGATAAGATTCGCCACCTTCGATCTGCTCCACTACTG
CTTAGGGAGATAAGATCCGTAATCTTCAACCCATCCCACTGCTGACCAGGGAGATAGGACTGGTG
GCTTAAATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCACCGTCTTCGATCTGCTCCACTATT
GCTTAGGGAGATAAGATCTGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAAGACTAGT
GGCTTAAATCTGCTTCCCTACTCCTGGAGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACAAT
CACTTAGGGAGATAAGATCCGTAATCTTCAACCTATCACACTGCTGACCAGGGAGATAGGACTGA
TGGCTTAAATCTGCTTCCCTACTCC
Found at i:52589244 original size:44 final size:43
Alignment explanation
Indices: 52589172--52589562 Score: 415
Period size: 44 Copynumber: 8.9 Consensus size: 43
52589162 AGATCTGTAA
* * ** *
52589172 TCTTCAACCTATCCCACTGCTGACCAGGGAGA-TAGGACTAGTAG
1 TCTTCCACCTATTCCACTGCTGGTCAGGGA-ACTAGGACTA-CAG
* * * *
52589216 TCTTCCACCTATTACACTACTGGTCAGGGAACTAGGACTTGCGG
1 TCTTCCACCTATTCCACTGCTGGTCAGGGAACTAGGAC-TACAG
* * * *
52589260 TCTTCCGCCTATTCCACTGCTGGTCAAGGAACTAGGACTTGCGG
1 TCTTCCACCTATTCCACTGCTGGTCAGGGAACTAGGAC-TACAG
* ** *
52589304 TCTTCCGCCTATTCCACTGCTGGTCAGGGAACTAGGTTTTACAA
1 TCTTCCACCTATTCCACTGCTGGTCAGGGAACTAGG-ACTACAG
* * *
52589348 TCTTTCGCCTATTCCACTGCTGGTGAGGGAACTAGGACTTACAG
1 TCTTCCACCTATTCCACTGCTGGTCAGGGAACTAGGAC-TACAG
** *
52589392 TCTTCCACCTATTCCACTGCTGGTCAGGGAACTAGGTTTTACAA
1 TCTTCCACCTATTCCACTGCTGGTCAGGGAACTAGG-ACTACAG
*
52589436 TCTTTCACCTATTCCACTGCTGGTCAGGGAACTAGGACTTACAG
1 TCTTCCACCTATTCCACTGCTGGTCAGGGAACTAGGAC-TACAG
* ** *
52589480 TCTTCCACCTATTCCACTGCTAGTCAGGGAACTAGGTTTTACAA
1 TCTTCCACCTATTCCACTGCTGGTCAGGGAACTAGG-ACTACAG
* * *
52589524 TCTTTCGCCTATTCCACTACTGGTCAGGGAACTAGGACT
1 TCTTCCACCTATTCCACTGCTGGTCAGGGAACTAGGACT
52589563 TATCTTTGAT
Statistics
Matches: 295, Mismatches: 45, Indels: 15
0.83 0.13 0.04
Matches are distributed among these distances:
43 2 0.01
44 292 0.99
45 1 0.00
ACGTcount: A:0.22, C:0.27, G:0.21, T:0.29
Consensus pattern (43 bp):
TCTTCCACCTATTCCACTGCTGGTCAGGGAACTAGGACTACAG
Found at i:52589277 original size:88 final size:88
Alignment explanation
Indices: 52589179--52589564 Score: 560
Period size: 88 Copynumber: 4.4 Consensus size: 88
52589169 TAATCTTCAA
* ** * * *
52589179 CCTATCCCACTGCTGACCAGGGAGA-TAGGAC-TAGTAGTCTTCCACCTATTACACTACTGGTCA
1 CCTATTCCACTGCTGGTCAGGGA-ACTAGGACTTA-CAGTCTTCCACCTATTCCACTGCTGGTCA
** * ** *
52589242 GGGAACTAGGACTTGCGGTCTTCCG
64 GGGAACTAGGTTTTACAATCTTTCG
* * * *
52589267 CCTATTCCACTGCTGGTCAAGGAACTAGGACTTGCGGTCTTCCGCCTATTCCACTGCTGGTCAGG
1 CCTATTCCACTGCTGGTCAGGGAACTAGGACTTACAGTCTTCCACCTATTCCACTGCTGGTCAGG
52589332 GAACTAGGTTTTACAATCTTTCG
66 GAACTAGGTTTTACAATCTTTCG
*
52589355 CCTATTCCACTGCTGGTGAGGGAACTAGGACTTACAGTCTTCCACCTATTCCACTGCTGGTCAGG
1 CCTATTCCACTGCTGGTCAGGGAACTAGGACTTACAGTCTTCCACCTATTCCACTGCTGGTCAGG
*
52589420 GAACTAGGTTTTACAATCTTTCA
66 GAACTAGGTTTTACAATCTTTCG
*
52589443 CCTATTCCACTGCTGGTCAGGGAACTAGGACTTACAGTCTTCCACCTATTCCACTGCTAGTCAGG
1 CCTATTCCACTGCTGGTCAGGGAACTAGGACTTACAGTCTTCCACCTATTCCACTGCTGGTCAGG
52589508 GAACTAGGTTTTACAATCTTTCG
66 GAACTAGGTTTTACAATCTTTCG
*
52589531 CCTATTCCACTACTGGTCAGGGAACTAGGACTTA
1 CCTATTCCACTGCTGGTCAGGGAACTAGGACTTA
52589565 TCTTTGATCT
Statistics
Matches: 270, Mismatches: 26, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
87 1 0.00
88 268 0.99
89 1 0.00
ACGTcount: A:0.22, C:0.27, G:0.22, T:0.29
Consensus pattern (88 bp):
CCTATTCCACTGCTGGTCAGGGAACTAGGACTTACAGTCTTCCACCTATTCCACTGCTGGTCAGG
GAACTAGGTTTTACAATCTTTCG
Found at i:52589333 original size:132 final size:131
Alignment explanation
Indices: 52589170--52589564 Score: 477
Period size: 132 Copynumber: 3.0 Consensus size: 131
52589160 TAAGATCTGT
* * ** * *
52589170 AATCTTCAACCTATCCCACTGCTGACCAGGGAGA-TAGGACTAGTAGTCTTCCACCTATTACACT
1 AATCTTCCACCTATTCCACTGCTGGTCAGGGA-ACTAGGACTA-CAGTCTTCCACCTATTCCACT
* * * *
52589234 ACTGGTCAGGGAACTAGGACTTGCGGTCTTCCGCCTATTCCACTGCTGGTCAAGGAACTAGGACT
64 GCTGGTCAGGGAACTAGGACTTACAGTCTTCCGCCTATTCCACTGCTGGTCAGGGAACTAGGACT
*
52589299 TGC
129 TAC
** * ** * * *
52589302 GGTCTTCCGCCTATTCCACTGCTGGTCAGGGAACTAGGTTTTACAATCTTTCGCCTATTCCACTG
1 AATCTTCCACCTATTCCACTGCTGGTCAGGGAACTAGG-ACTACAGTCTTCCACCTATTCCACTG
* * **
52589367 CTGGTGAGGGAACTAGGACTTACAGTCTTCCACCTATTCCACTGCTGGTCAGGGAACTAGGTTTT
65 CTGGTCAGGGAACTAGGACTTACAGTCTTCCGCCTATTCCACTGCTGGTCAGGGAACTAGGACTT
52589432 AC
130 AC
*
52589434 AATCTTTCACCTATTCCACTGCTGGTCAGGGAACTAGGACTTACAGTCTTCCACCTATTCCACTG
1 AATCTTCCACCTATTCCACTGCTGGTCAGGGAACTAGGAC-TACAGTCTTCCACCTATTCCACTG
* ** * * *
52589499 CTAGTCAGGGAACTAGGTTTTACAATCTTTCGCCTATTCCACTACTGGTCAGGGAACTAGGACTT
65 CTGGTCAGGGAACTAGGACTTACAGTCTTCCGCCTATTCCACTGCTGGTCAGGGAACTAGGACTT
52589564 A
130 A
52589565 TCTTTGATCT
Statistics
Matches: 218, Mismatches: 42, Indels: 6
0.82 0.16 0.02
Matches are distributed among these distances:
131 1 0.00
132 215 0.99
133 2 0.01
ACGTcount: A:0.23, C:0.27, G:0.21, T:0.29
Consensus pattern (131 bp):
AATCTTCCACCTATTCCACTGCTGGTCAGGGAACTAGGACTACAGTCTTCCACCTATTCCACTGC
TGGTCAGGGAACTAGGACTTACAGTCTTCCGCCTATTCCACTGCTGGTCAGGGAACTAGGACTTA
C
Found at i:52590892 original size:15 final size:15
Alignment explanation
Indices: 52590858--52590891 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
52590848 AGCCTCTCTA
*
52590858 TTTTTACTTTTTCAT
1 TTTTTACTTTTTAAT
52590873 TTTTTA-TTTTTAAT
1 TTTTTACTTTTTAAT
52590887 TTTTT
1 TTTTT
52590892 TTGACTCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.15, C:0.06, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTTTACTTTTTAAT
Found at i:52596160 original size:17 final size:17
Alignment explanation
Indices: 52596138--52596174 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
52596128 ATATTGATGA
*
52596138 TAAGTTTAAAAATATAT
1 TAAGTTTAAAAATAAAT
*
52596155 TAAGTTTAAATATAAAT
1 TAAGTTTAAAAATAAAT
52596172 TAA
1 TAA
52596175 TGTCAGATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (17 bp):
TAAGTTTAAAAATAAAT
Found at i:52607422 original size:77 final size:77
Alignment explanation
Indices: 52607295--52607449 Score: 301
Period size: 77 Copynumber: 2.0 Consensus size: 77
52607285 GTAGTTCTAG
52607295 CTGATAGGTGACAAGTCTGATGCCTTTTAGAATATAGTAAGGTCTAATGAACCTCGGACTCAACT
1 CTGATAGGTGACAAGTCTGATGCCTTTTAGAATATAGTAAGGTCTAATGAACCTCGGACTCAACT
52607360 TACCTTTACGCT
66 TACCTTTACGCT
*
52607372 CTGATAGGTGACAAGTCTGATGCGTTTTAGAATATAGTAAGGTCTAATGAACCTCGGACTCAACT
1 CTGATAGGTGACAAGTCTGATGCCTTTTAGAATATAGTAAGGTCTAATGAACCTCGGACTCAACT
52607437 TACCTTTACGCT
66 TACCTTTACGCT
52607449 C
1 C
52607450 AAACCAGAGA
Statistics
Matches: 77, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
77 77 1.00
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (77 bp):
CTGATAGGTGACAAGTCTGATGCCTTTTAGAATATAGTAAGGTCTAATGAACCTCGGACTCAACT
TACCTTTACGCT
Found at i:52608997 original size:34 final size:35
Alignment explanation
Indices: 52608959--52609025 Score: 127
Period size: 35 Copynumber: 1.9 Consensus size: 35
52608949 TACCAGATTC
52608959 AGGCTATA-TAGAATAGGTGGCTGAGTCAAAACGG
1 AGGCTATACTAGAATAGGTGGCTGAGTCAAAACGG
52608993 AGGCTATACTAGAATAGGTGGCTGAGTCAAAAC
1 AGGCTATACTAGAATAGGTGGCTGAGTCAAAAC
52609026 AGACTTTAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
34 8 0.25
35 24 0.75
ACGTcount: A:0.36, C:0.13, G:0.30, T:0.21
Consensus pattern (35 bp):
AGGCTATACTAGAATAGGTGGCTGAGTCAAAACGG
Found at i:52617867 original size:59 final size:60
Alignment explanation
Indices: 52617798--52617914 Score: 164
Period size: 62 Copynumber: 1.9 Consensus size: 60
52617788 ATCACTTTAA
* * *
52617798 TATTAAATTAATATAATACTTATC-AAGATAAATATTAGATTAAATTTAATATTAAATCT
1 TATTAAATTAATAGAATACTTATCTAAGATAAACATTAAATTAAATTTAATATTAAATCT
* *
52617857 TATTAAATTAATAGAATATTTATCTATAAGATAAACATTAAATTAAATTTAATCTTAA
1 TATTAAATTAATAGAATACTTATC--TAAGATAAACATTAAATTAAATTTAATATTAA
52617915 GATAATCACT
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
59 22 0.44
62 28 0.56
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (60 bp):
TATTAAATTAATAGAATACTTATCTAAGATAAACATTAAATTAAATTTAATATTAAATCT
Found at i:52617907 original size:29 final size:31
Alignment explanation
Indices: 52617874--52617937 Score: 80
Period size: 29 Copynumber: 2.1 Consensus size: 31
52617864 TTAATAGAAT
52617874 ATTT-ATCTATAAGATAA-ACATTAA-ATTAA
1 ATTTAATCT-TAAGATAACACATTAATATTAA
*
52617903 ATTTAATCTTAAGATAATCACTTTAATATTAA
1 ATTTAATCTTAAGATAA-CACATTAATATTAA
52617935 ATT
1 ATT
52617938 AATAAAATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
29 12 0.40
30 4 0.13
31 6 0.20
32 8 0.27
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.42
Consensus pattern (31 bp):
ATTTAATCTTAAGATAACACATTAATATTAA
Found at i:52617998 original size:68 final size:71
Alignment explanation
Indices: 52617857--52618001 Score: 163
Period size: 68 Copynumber: 2.1 Consensus size: 71
52617847 TATTAAATCT
* *
52617857 TATTAAATTAATAGAATATTTATCTATAAGATAAACATTAAATTAAATTTAATCTTAAGATAATC
1 TATTAAATTAATAAAATATTTA-CTATAAGATAAACATTAAATTAAATTTAATATTAAGATAATC
***
52617922 ACTTTAA
65 AAAATAA
** * *
52617929 TATTAAATTAATAAAATA-TTA-T-TAAGATAAGTATTAAATTTAATTTAATATTAAAGAT-ATT
1 TATTAAATTAATAAAATATTTACTATAAGATAAACATTAAATTAAATTTAATATT-AAGATAATC
52617990 AAAATAA
65 AAAATAA
52617997 TATTA
1 TATTA
52618002 TTTTTGGAAT
Statistics
Matches: 63, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
68 37 0.59
69 6 0.10
71 3 0.05
72 17 0.27
ACGTcount: A:0.51, C:0.03, G:0.04, T:0.41
Consensus pattern (71 bp):
TATTAAATTAATAAAATATTTACTATAAGATAAACATTAAATTAAATTTAATATTAAGATAATCA
AAATAA
Found at i:52621941 original size:10 final size:10
Alignment explanation
Indices: 52621926--52621954 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
52621916 TTCAATCGGT
52621926 GACTGGACTA
1 GACTGGACTA
52621936 GACTGGACTA
1 GACTGGACTA
52621946 GACTGGACT
1 GACTGGACT
52621955 GGTCGGGCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.28, C:0.21, G:0.31, T:0.21
Consensus pattern (10 bp):
GACTGGACTA
Found at i:52622480 original size:11 final size:11
Alignment explanation
Indices: 52622466--52622495 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
52622456 AAAGAAATTA
52622466 TTTTAGAAAAT
1 TTTTAGAAAAT
52622477 TTTTCAGAAAAT
1 TTTT-AGAAAAT
52622489 TTTTAGA
1 TTTTAGA
52622496 GATATTTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.40, C:0.03, G:0.10, T:0.47
Consensus pattern (11 bp):
TTTTAGAAAAT
Found at i:52627949 original size:40 final size:39
Alignment explanation
Indices: 52627904--52628040 Score: 123
Period size: 40 Copynumber: 3.4 Consensus size: 39
52627894 ACAAGAGAAT
* *
52627904 GTATGTGCAATCAGGGATACCGAAGTAAAAACAAAGTCA-
1 GTATGTGCATTCAGGG-TACCGAAGTAAAAACAAAGGCAC
* * * **
52627943 GCTATGTGCATTCAAAGGTATCGAAGTAGAAACAGGGGCAC
1 G-TATGTGCATTC-AGGGTACCGAAGTAAAAACAAAGGCAC
* * *
52627984 GTATGTGCATTCAGGGGTACCGAAGTACAAACAAGGGCAT
1 GTATGTGCATTCA-GGGTACCGAAGTAAAAACAAAGGCAC
* *
52628024 GCAAGTGCATTCAGGGT
1 GTATGTGCATTCAGGGT
52628041 CATTTCTTCA
Statistics
Matches: 80, Mismatches: 14, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
39 6 0.08
40 70 0.88
41 4 0.05
ACGTcount: A:0.35, C:0.17, G:0.28, T:0.20
Consensus pattern (39 bp):
GTATGTGCATTCAGGGTACCGAAGTAAAAACAAAGGCAC
Found at i:52633788 original size:18 final size:18
Alignment explanation
Indices: 52633767--52633806 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
52633757 AAATTGAATC
52633767 AAAACAT-AAAATTTAGGA
1 AAAACATAAAAATTT-GGA
52633785 AAAACATAGAAAATTTGGA
1 AAAACATA-AAAATTTGGA
52633804 AAA
1 AAA
52633807 CAGGGGTCAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 7 0.35
19 6 0.30
20 7 0.35
ACGTcount: A:0.62, C:0.05, G:0.12, T:0.20
Consensus pattern (18 bp):
AAAACATAAAAATTTGGA
Found at i:52634794 original size:40 final size:40
Alignment explanation
Indices: 52634688--52634852 Score: 154
Period size: 40 Copynumber: 4.2 Consensus size: 40
52634678 AATGTGTGTT
* * * * *
52634688 AAGGGTATCAAGGTACAAACAAGAGCACATATGTGCAATC
1 AAGGGTACCAAAGTACAAACAGGGGCACATATGTGCATTC
** * * * *
52634728 -AGGGATACTGAAGTACAAATAAGGGCACTTATGTGCATTT
1 AAGGG-TACCAAAGTACAAACAGGGGCACATATGTGCATTC
* *
52634768 AAGGGTACCAAAGTTCAAACAGGGGCACGTATGTGCATTC
1 AAGGGTACCAAAGTACAAACAGGGGCACATATGTGCATTC
* * * *
52634808 AGGGGTACCAATGTACAAATAGGGGCACATGTGTGCATTC
1 AAGGGTACCAAAGTACAAACAGGGGCACATATGTGCATTC
52634848 -AGGGT
1 AAGGGT
52634853 CATTTTCTTC
Statistics
Matches: 100, Mismatches: 23, Indels: 5
0.78 0.18 0.04
Matches are distributed among these distances:
39 8 0.08
40 88 0.88
41 4 0.04
ACGTcount: A:0.35, C:0.16, G:0.27, T:0.22
Consensus pattern (40 bp):
AAGGGTACCAAAGTACAAACAGGGGCACATATGTGCATTC
Found at i:52634801 original size:80 final size:80
Alignment explanation
Indices: 52634686--52634846 Score: 198
Period size: 80 Copynumber: 2.0 Consensus size: 80
52634676 TGAATGTGTG
* * *
52634686 TTAAGGGTATCAAGGTACAAACAAGAGCACATATGTGCAATCAGGGATACTGAA-GTACAAATAA
1 TTAAGGGTACCAAAGTACAAACAAGAGCACATATGTGCAATCAGGGATAC-CAATGTACAAATAA
*
52634750 GGGCACTTATGTGCAT
65 GGGCACATATGTGCAT
* * * * * * *
52634766 TTAAGGGTACCAAAGTTCAAACAGGGGCACGTATGTGCATTCAGGGGTACCAATGTACAAATAGG
1 TTAAGGGTACCAAAGTACAAACAAGAGCACATATGTGCAATCAGGGATACCAATGTACAAATAAG
*
52634831 GGCACATGTGTGCAT
66 GGCACATATGTGCAT
52634846 T
1 T
52634847 CAGGGTCATT
Statistics
Matches: 68, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
79 2 0.03
80 66 0.97
ACGTcount: A:0.35, C:0.16, G:0.26, T:0.23
Consensus pattern (80 bp):
TTAAGGGTACCAAAGTACAAACAAGAGCACATATGTGCAATCAGGGATACCAATGTACAAATAAG
GGCACATATGTGCAT
Found at i:52639757 original size:15 final size:15
Alignment explanation
Indices: 52639739--52639777 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
52639729 AAATTTTAGT
52639739 AAATAAAAAATATAA
1 AAATAAAAAATATAA
** *
52639754 AAATATTAAATATCA
1 AAATAAAAAATATAA
52639769 AAATAAAAA
1 AAATAAAAA
52639778 TAATATAAAT
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (15 bp):
AAATAAAAAATATAA
Found at i:52647654 original size:2 final size:2
Alignment explanation
Indices: 52647647--52647671 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
52647637 CTATACACAA
52647647 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
52647672 TGTATGCTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:52648637 original size:103 final size:103
Alignment explanation
Indices: 52648494--52648702 Score: 316
Period size: 103 Copynumber: 2.0 Consensus size: 103
52648484 ACAATTACCC
52648494 GTATCATTGTTTAAATCAAGTATTTAGCATAAGAAGAGTTGTTTTAAGTACATATTAACTTAGTC
1 GTATCATTGTTTAAATCAAGTATTTAGCATAAGAAGAGTTGTTTTAAGTACATATTAACTTAGTC
*
52648559 TTTC-TATCTCTCATTT-CCCTTCGCTTTTGCATGCATT
66 TTTCATATCTCTC-TTTACCCTTCCCTTTTGCATGCATT
* *
52648596 GTATCATTGTTTAAATCAAAGTATTTAGCATAGGGAA-AGTTGTTTTAAGTACATATTAAGTTAG
1 GTATCATTGTTTAAATC-AAGTATTTAGCATA-AGAAGAGTTGTTTTAAGTACATATTAACTTAG
52648660 TCTTTCTATATATCTCTCTTTACCCTTCCCTTTTGCATGCATT
64 TCTTTC---ATATCTCTCTTTACCCTTCCCTTTTGCATGCATT
52648703 TCAACAGATA
Statistics
Matches: 97, Mismatches: 3, Indels: 9
0.89 0.03 0.08
Matches are distributed among these distances:
102 17 0.18
103 46 0.47
104 3 0.03
106 3 0.03
107 28 0.29
ACGTcount: A:0.27, C:0.16, G:0.13, T:0.44
Consensus pattern (103 bp):
GTATCATTGTTTAAATCAAGTATTTAGCATAAGAAGAGTTGTTTTAAGTACATATTAACTTAGTC
TTTCATATCTCTCTTTACCCTTCCCTTTTGCATGCATT
Found at i:52657390 original size:25 final size:26
Alignment explanation
Indices: 52657353--52657408 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 26
52657343 AACTTTTTAG
* *
52657353 TAATTATATAATTTTACATTTACAAA
1 TAATAATATAATTTGACATTTACAAA
* *
52657379 TAATAATA-AATTTGATATTTAGAAA
1 TAATAATATAATTTGACATTTACAAA
52657404 -AATAA
1 TAATAA
52657409 AATCTTTTTC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 5 0.19
25 14 0.54
26 7 0.27
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.41
Consensus pattern (26 bp):
TAATAATATAATTTGACATTTACAAA
Found at i:52658688 original size:21 final size:21
Alignment explanation
Indices: 52658659--52658706 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
52658649 ATGACAATGT
52658659 AAATAAATAAATAA-ATGAATA
1 AAATAAATAAA-AATATGAATA
*
52658680 AAATGAATAAAAATATGAA-A
1 AAATAAATAAAAATATGAATA
*
52658700 ATATAAA
1 AAATAAA
52658707 AAGATACATA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 8 0.35
21 15 0.65
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.23
Consensus pattern (21 bp):
AAATAAATAAAAATATGAATA
Found at i:52658800 original size:10 final size:10
Alignment explanation
Indices: 52658785--52658819 Score: 61
Period size: 10 Copynumber: 3.5 Consensus size: 10
52658775 ATATGTATTA
52658785 AAATATATAT
1 AAATATATAT
52658795 AAATATATAT
1 AAATATATAT
*
52658805 AAAAATATAT
1 AAATATATAT
52658815 AAATA
1 AAATA
52658820 CACATACAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (10 bp):
AAATATATAT
Found at i:52658800 original size:22 final size:21
Alignment explanation
Indices: 52658765--52658838 Score: 69
Period size: 22 Copynumber: 3.5 Consensus size: 21
52658755 GGGTATTTAG
* * *
52658765 ATATATGTAGATATGTATTAAA
1 ATATATATAAATATATA-TAAA
52658787 ATATATATAAATATATATAAA
1 ATATATATAAATATATATAAA
* *
52658808 A-ATATATAAATACACATACAA
1 ATATATATAAATATATATA-AA
*
52658829 ATATAAATAA
1 ATATATATAA
52658839 GTTACAAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
20 15 0.34
21 8 0.18
22 21 0.48
ACGTcount: A:0.58, C:0.04, G:0.04, T:0.34
Consensus pattern (21 bp):
ATATATATAAATATATATAAA
Found at i:52658802 original size:12 final size:12
Alignment explanation
Indices: 52658765--52658815 Score: 52
Period size: 12 Copynumber: 4.4 Consensus size: 12
52658755 GGGTATTTAG
* *
52658765 ATATATGTAGAT
1 ATATATATAAAT
*
52658777 ATGTAT-TAAA-
1 ATATATATAAAT
52658787 ATATATATAAAT
1 ATATATATAAAT
*
52658799 ATATATAAAAAT
1 ATATATATAAAT
52658811 ATATA
1 ATATA
52658816 AATACACATA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
10 5 0.15
11 7 0.21
12 21 0.64
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (12 bp):
ATATATATAAAT
Found at i:52658814 original size:20 final size:20
Alignment explanation
Indices: 52658783--52658833 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
52658773 AGATATGTAT
* *
52658783 TAAAATATATATAAATATATA
1 TAAAA-ATATATAAATACACA
52658804 TAAAAATATATAAATACACA
1 TAAAAATATATAAATACACA
*
52658824 TACAAATATA
1 TAAAAATATA
52658834 AATAAGTTAC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 22 0.81
21 5 0.19
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (20 bp):
TAAAAATATATAAATACACA
Found at i:52659307 original size:18 final size:18
Alignment explanation
Indices: 52659286--52659368 Score: 53
Period size: 18 Copynumber: 4.3 Consensus size: 18
52659276 TAAGAATAAT
52659286 AATAATAATAGTAGTAAA
1 AATAATAATAGTAGTAAA
* *
52659304 AATATATAA-AATA-AAAA
1 AATA-ATAATAGTAGTAAA
*
52659321 AATAATAGTGATAACAGTATTAAA
1 AATAATA---AT---AGTAGTAAA
*
52659345 CATAATAATAGTAGTAAA
1 AATAATAATAGTAGTAAA
52659363 AATAAT
1 AATAAT
52659369 GATAACATTA
Statistics
Matches: 49, Mismatches: 7, Indels: 18
0.66 0.09 0.24
Matches are distributed among these distances:
16 3 0.06
17 7 0.14
18 20 0.41
19 5 0.10
21 2 0.04
23 3 0.06
24 9 0.18
ACGTcount: A:0.61, C:0.02, G:0.08, T:0.28
Consensus pattern (18 bp):
AATAATAATAGTAGTAAA
Found at i:52661088 original size:47 final size:44
Alignment explanation
Indices: 52660938--52661181 Score: 203
Period size: 44 Copynumber: 5.6 Consensus size: 44
52660928 TTCTTTCGTT
* * * * *
52660938 TGCTCCACTGTAACTTCAGGGAGATAAGA-C--TGGATGTGATC
1 TGCTCTACTGCAACTTCAGGGAGATAAGATCTGTGGTTTTAATC
*
52660979 TGCTCTACTGCAACTTTCAGAGAGATAAGATCTGTGGTTTTAATC
1 TGCTCTACTGCAAC-TTCAGGGAGATAAGATCTGTGGTTTTAATC
* * * * * * **
52661024 CGCTCCACTGTAACTTCAGGGAGATAGGATTTGTAGCTTTTTTTGTC
1 TGCTCTACTGCAACTTCAGGGAGATAAGATCTGT-G--GTTTTAATC
* * ***
52661071 TGCTCTACTGCAACTTCAGGGAGATAAGA-C-G-AGATGCGATC
1 TGCTCTACTGCAACTTCAGGGAGATAAGATCTGTGGTTTTAATC
* *
52661112 TGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGATTTTAATC
1 TGCTCTACTGCAACTTCAGGGAGATAAGATCTGTGGTTTTAATC
* *
52661156 TGCTCCACTGTAACTTCAGGGAGATA
1 TGCTCTACTGCAACTTCAGGGAGATA
52661182 GGGCTAGTAA
Statistics
Matches: 156, Mismatches: 37, Indels: 17
0.74 0.18 0.08
Matches are distributed among these distances:
41 43 0.28
42 15 0.10
43 2 0.01
44 44 0.28
45 21 0.13
47 31 0.20
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.31
Consensus pattern (44 bp):
TGCTCTACTGCAACTTCAGGGAGATAAGATCTGTGGTTTTAATC
Done.