Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A03
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: 105315579
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1369460 characters in sequence are not A, C, G, or T
File 129 of 325
Found at i:41272997 original size:41 final size:41
Alignment explanation
Indices: 41272939--41273038 Score: 155
Period size: 41 Copynumber: 2.4 Consensus size: 41
41272929 GATGAATTAT
*
41272939 ACATACATGCCCCTGTTTGTACTTCAGTACCCCTAAATTGC
1 ACATACGTGCCCCTGTTTGTACTTCAGTACCCCTAAATTGC
* * *
41272980 ACATACGTGCCCTTGTTTGTACTTCGGTACCCCTGAATTGC
1 ACATACGTGCCCCTGTTTGTACTTCAGTACCCCTAAATTGC
*
41273021 ACACACGTGCCCCTGTTT
1 ACATACGTGCCCCTGTTT
41273039 AGACTTCGAA
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.20, C:0.32, G:0.16, T:0.32
Consensus pattern (41 bp):
ACATACGTGCCCCTGTTTGTACTTCAGTACCCCTAAATTGC
Found at i:41275665 original size:56 final size:56
Alignment explanation
Indices: 41275579--41275754 Score: 325
Period size: 56 Copynumber: 3.1 Consensus size: 56
41275569 ACAAGGGATG
* *
41275579 ATGGGCAAAACATGTCATTAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
*
41275635 ATGGGCAAAACATGTCATGAAACTTGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
41275691 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
41275747 ATGGGCAA
1 ATGGGCAA
41275755 TAAAGTAATA
Statistics
Matches: 116, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
56 116 1.00
ACGTcount: A:0.44, C:0.09, G:0.23, T:0.24
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
Found at i:41277040 original size:41 final size:40
Alignment explanation
Indices: 41276883--41277068 Score: 227
Period size: 40 Copynumber: 4.7 Consensus size: 40
41276873 TCGAATGATG
* * * *
41276883 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* *
41276923 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
41276963 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
41277002 TCCGGGTTAAGTCCCGAAGGCATTGTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATT-TGTGCGAGTTACTA-AA
*
41277044 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
41277069 AACGAGTAGC
Statistics
Matches: 127, Mismatches: 13, Indels: 12
0.84 0.09 0.08
Matches are distributed among these distances:
39 35 0.28
40 48 0.38
41 42 0.33
42 2 0.02
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:41277048 original size:80 final size:81
Alignment explanation
Indices: 41276884--41277066 Score: 223
Period size: 79 Copynumber: 2.3 Consensus size: 81
41276874 CGAATGATGT
* *
41276884 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 CCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
*
41276948 GTGCGAGTTACTAATT
66 GTGCGAGTTACTAATA
* * * **
41276964 CCGGGCTAAG-CCCGAAGGCATTGGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCATT
1 CCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCATT
41277026 GTGTGCGAGTTACT-ATAA
65 -TGTGCGAGTTACTAAT-A
*
41277044 CCGGGCTATGTCCCGAAGGCATT
1 CCGGGCTAAGTCCCGAAGGCATT
41277067 TGAACGAGTA
Statistics
Matches: 89, Mismatches: 9, Indels: 9
0.83 0.08 0.08
Matches are distributed among these distances:
78 1 0.01
79 38 0.43
80 38 0.43
81 12 0.13
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
CCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
GTGCGAGTTACTAATA
Found at i:41277090 original size:80 final size:79
Alignment explanation
Indices: 41276936--41277101 Score: 203
Period size: 80 Copynumber: 2.1 Consensus size: 79
41276926 GGACTAAGAT
* **
41276936 CCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
*
41277001 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
41277015 CCGAAGGCATTGTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAG
1 CCGAAGGCATT-TGTGCGAGTTACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGAGTTA-
* *
41277078 CTATATCC-GGTTAAATT
62 CTAAATCCGGGTTAAATC
41277095 CCGAAGG
1 CCGAAGG
41277102 TACGTGATTT
Statistics
Matches: 75, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
79 13 0.17
80 38 0.51
81 24 0.32
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:41283641 original size:56 final size:56
Alignment explanation
Indices: 41283555--41283730 Score: 343
Period size: 56 Copynumber: 3.1 Consensus size: 56
41283545 ACAAGGGATG
*
41283555 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
41283611 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
41283667 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
41283723 ATGGGCAA
1 ATGGGCAA
41283731 TAAACTAATA
Statistics
Matches: 119, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
56 119 1.00
ACGTcount: A:0.45, C:0.09, G:0.23, T:0.23
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
Found at i:41284992 original size:79 final size:81
Alignment explanation
Indices: 41284856--41285038 Score: 232
Period size: 79 Copynumber: 2.3 Consensus size: 81
41284846 TCGAATGATG
* *
41284856 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
41284920 TGTGCGAGTTACTA-A
66 TGTGCGAGTTACTATA
* * * **
41284935 TTCCGGGCTAAG-CCCGAAGGCATTGGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
41284997 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGTTACTATA
* *
41285015 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
41285039 TGAACGAGTA
Statistics
Matches: 90, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 1 0.01
79 59 0.66
80 30 0.33
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGTTACTATA
Found at i:41285054 original size:40 final size:40
Alignment explanation
Indices: 41284857--41285040 Score: 216
Period size: 40 Copynumber: 4.6 Consensus size: 40
41284847 CGAATGATGT
* * * *
41284857 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* *
41284897 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
*
41284937 CCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
41284975 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
41285016 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
41285041 AACGAGTAGC
Statistics
Matches: 126, Mismatches: 11, Indels: 14
0.83 0.07 0.09
Matches are distributed among these distances:
39 35 0.28
40 81 0.64
41 10 0.08
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:41285062 original size:79 final size:79
Alignment explanation
Indices: 41284909--41285073 Score: 210
Period size: 79 Copynumber: 2.1 Consensus size: 79
41284899 GGACTAAGAT
* **
41284909 CCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
*
41284974 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
41284988 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGTTACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGAGTTA-C
* *
41285051 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
41285067 CCGAAGG
1 CCGAAGG
41285074 TACGTGATTT
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
78 2 0.03
79 49 0.65
80 24 0.32
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:41288537 original size:66 final size:66
Alignment explanation
Indices: 41288431--41288558 Score: 238
Period size: 66 Copynumber: 1.9 Consensus size: 66
41288421 GAAGAAGAAA
* *
41288431 GGCTTTGTTTATGGGATATTTTTGTTTAAGGTGATAGAAAGGTTATCCAAATGGATTTTTATGGA
1 GGCTTTATTTATGGGATATTTTTGTTTAAGATGATAGAAAGGTTATCCAAATGGATTTTTATGGA
41288496 T
66 T
41288497 GGCTTTATTTATGGGATATTTTTGTTTAAGATGATAGAAAGGTTATCCAAATGGATTTTTAT
1 GGCTTTATTTATGGGATATTTTTGTTTAAGATGATAGAAAGGTTATCCAAATGGATTTTTAT
41288559 AGTGCTCTTT
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 60 1.00
ACGTcount: A:0.27, C:0.05, G:0.23, T:0.45
Consensus pattern (66 bp):
GGCTTTATTTATGGGATATTTTTGTTTAAGATGATAGAAAGGTTATCCAAATGGATTTTTATGGA
T
Found at i:41289228 original size:27 final size:27
Alignment explanation
Indices: 41289184--41289254 Score: 97
Period size: 27 Copynumber: 2.6 Consensus size: 27
41289174 AGCATGCCAA
* *
41289184 AAAATTGAAGTCTTTGTGGCAATTTAT
1 AAAATGGAAGCCTTTGTGGCAATTTAT
* *
41289211 AAAGTGGAAGCGTTTGTGGCAATTTAT
1 AAAATGGAAGCCTTTGTGGCAATTTAT
*
41289238 AAAATTGAAGCCTTTGT
1 AAAATGGAAGCCTTTGT
41289255 AGCGATCTAT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.32, C:0.08, G:0.23, T:0.37
Consensus pattern (27 bp):
AAAATGGAAGCCTTTGTGGCAATTTAT
Found at i:41289447 original size:27 final size:27
Alignment explanation
Indices: 41289424--41289517 Score: 134
Period size: 27 Copynumber: 3.5 Consensus size: 27
41289414 AGGTATGGTA
* * *
41289424 AACTCTGAAAGAATGGTACATATGACG
1 AACTCTAAAAGAATAGTACATATGGCG
41289451 AACTCTAAAAGAATAGTACATATGGCG
1 AACTCTAAAAGAATAGTACATATGGCG
* *
41289478 AACTCCAAAAGAATAGTACATATGACG
1 AACTCTAAAAGAATAGTACATATGGCG
*
41289505 AACTCTAAGAGAA
1 AACTCTAAAAGAA
41289518 ACGATTCCGT
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 60 1.00
ACGTcount: A:0.46, C:0.16, G:0.18, T:0.20
Consensus pattern (27 bp):
AACTCTAAAAGAATAGTACATATGGCG
Found at i:41290591 original size:23 final size:24
Alignment explanation
Indices: 41290548--41290601 Score: 58
Period size: 23 Copynumber: 2.2 Consensus size: 24
41290538 TTACATATTT
* *
41290548 AAAATTATTCTTGAGT-TTTTTAA
1 AAAATTATTCATGAGTATTTTCAA
41290571 AAAATTATTCATG-GTAATTTTCAA
1 AAAATTATTCATGAGT-ATTTTCAA
41290595 ACAAATT
1 A-AAATT
41290602 TAAAAAGCTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
22 2 0.08
23 12 0.46
24 7 0.27
25 5 0.19
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.44
Consensus pattern (24 bp):
AAAATTATTCATGAGTATTTTCAA
Found at i:41293962 original size:16 final size:17
Alignment explanation
Indices: 41293931--41293963 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
41293921 TTTAATATGT
41293931 ATAATAAATATATAAAA
1 ATAATAAATATATAAAA
*
41293948 ATAAT-AATTTATAAAA
1 ATAATAAATATATAAAA
41293964 TTAAACTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
ATAATAAATATATAAAA
Found at i:41294074 original size:26 final size:26
Alignment explanation
Indices: 41294042--41294103 Score: 72
Period size: 26 Copynumber: 2.3 Consensus size: 26
41294032 ACTAAATTAG
41294042 AATATATATCTACTACATAA-ACTAACAT
1 AATATATA-CTACTA-ATAATA-TAACAT
* *
41294070 AATATATACTATTAATAATATAATAT
1 AATATATACTACTAATAATATAACAT
41294096 AATATATA
1 AATATATA
41294104 ATTATTACTA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
26 17 0.55
27 6 0.19
28 8 0.26
ACGTcount: A:0.53, C:0.10, G:0.00, T:0.37
Consensus pattern (26 bp):
AATATATACTACTAATAATATAACAT
Found at i:41294125 original size:26 final size:26
Alignment explanation
Indices: 41294070--41294126 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
41294060 AAACTAACAT
*
41294070 AATATATACTATTAATAATATAATAT
1 AATATATACTATTAATAATATAATAA
* * *
41294096 AATATATAATTATTACTAATA-CATAA
1 AATATAT-ACTATTAATAATATAATAA
41294122 AATAT
1 AATAT
41294127 TATTAATTGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
26 15 0.58
27 11 0.42
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.40
Consensus pattern (26 bp):
AATATATACTATTAATAATATAATAA
Found at i:41294625 original size:14 final size:14
Alignment explanation
Indices: 41294590--41294632 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
41294580 AGCATATTTC
41294590 AATTAATATAATAA-
1 AATTAATAT-ATAAT
*
41294604 ACAATAATATATAAT
1 A-ATTAATATATAAT
41294619 AATTAATATATAAT
1 AATTAATATATAAT
41294633 GTACATCTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
14 17 0.68
15 8 0.32
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (14 bp):
AATTAATATATAAT
Found at i:41294757 original size:7 final size:7
Alignment explanation
Indices: 41294726--41294751 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
41294716 CATTGGTGCA
41294726 TATATAT
1 TATATAT
41294733 TATATAT
1 TATATAT
41294740 TATATAT
1 TATATAT
41294747 TATAT
1 TATAT
41294752 GATATAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (7 bp):
TATATAT
Found at i:41294809 original size:240 final size:240
Alignment explanation
Indices: 41294384--41294841 Score: 554
Period size: 240 Copynumber: 1.9 Consensus size: 240
41294374 AAACAATAAC
* *
41294384 ATATAATGTACTACTATTATATATAACTTTTATATTACAGATTATAATAGAAGATATAGTATTAC
1 ATATAATGTACTACTATTATATATAACTTTTATATTACAGATTATAATAAAAAATATAGTATTAC
** * * * * *
41294449 ATTATATTATATGTTTAATTATTGATGCATATATAACTATTAATATTTTGTATACTATATGGCAT
66 AAGATATTATATGTTCAATCATTGATGCA-ATATAACTATTAATATATTATATACTATATGACAT
* * * * *
41294514 GATATAGCATTATATAATATTGAGCAAGTGCTAACTTTCAAATGTACGAAAAGTA-TAGGGACTT
130 AATATAACATTATATAATA-TAAGCAAGGGCTAACTTTCAAATGTACAAAAAGTATTA-GGACTT
*
41294578 AGAGCATATTTCAATTAATATAATAAACAATAATATATAATAATTAAT
193 AGAGCATATTTCAATCAATATAATAAACAATAATATATAATAATTAAT
* *
41294626 ATATAATGTAC-ATCTATTATATATAGCTATTATTATATTATAGATTATAATAAAAAAAATATAG
1 ATATAATGTACTA-CTATTATATATAAC--TT-TTATATTACAGATTATAAT--AAAAAATATAG
* *
41294690 TATTACAAGATATTATAGTGTTCAATCATTGGTGC-ATAT-A-TATT-ATATATTATATATTATA
60 TATTACAAGATATTATA-TGTTCAATCATTGATGCAATATAACTATTAATATATTATATACTATA
* *
41294751 TGATATAATATAACATTATATAATA-AAG-AAGGGCTAACTTTCAAATGTGCAAAAAGTATTAGG
124 TGACATAATATAACATTATATAATATAAGCAAGGGCTAACTTTCAAATGTACAAAAAGTATTAGG
* * *
41294814 TCTTAGAGTATATTTCAATCAGTATAAT
189 ACTTAGAGCATATTTCAATCAATATAAT
41294842 GACCGAGCCT
Statistics
Matches: 184, Mismatches: 24, Indels: 18
0.81 0.11 0.08
Matches are distributed among these distances:
240 53 0.29
241 5 0.03
242 24 0.13
243 35 0.19
244 6 0.03
245 19 0.10
246 4 0.02
247 24 0.13
248 14 0.08
ACGTcount: A:0.43, C:0.07, G:0.10, T:0.40
Consensus pattern (240 bp):
ATATAATGTACTACTATTATATATAACTTTTATATTACAGATTATAATAAAAAATATAGTATTAC
AAGATATTATATGTTCAATCATTGATGCAATATAACTATTAATATATTATATACTATATGACATA
ATATAACATTATATAATATAAGCAAGGGCTAACTTTCAAATGTACAAAAAGTATTAGGACTTAGA
GCATATTTCAATCAATATAATAAACAATAATATATAATAATTAAT
Found at i:41298932 original size:47 final size:46
Alignment explanation
Indices: 41298864--41299127 Score: 209
Period size: 47 Copynumber: 5.7 Consensus size: 46
41298854 ATTGTTGGCT
* *
41298864 AGTGTAAGACATGT-TCAGGACAT-GCATCGACCACATTATGAGAGCC
1 AGTGTAAGACATGTCT-GGGACATGGCATCGACCACA-GATGAGAGCC
* * ** * *
41298910 AGTGTAAGACCATGTCTGGGACATGGCATCG-GCATTGAGACAATAGCT
1 AGTGTAAGA-CATGTCTGGGACATGGCATCGACCA--CAGATGAGAGCC
* * *
41298958 AGTGTAAGACATGTTTGGGACAT-GCATCGGCCTCGAGATGTA-AGCC
1 AGTGTAAGACATGTCTGGGACATGGCATCGACCAC-AGATG-AGAGCC
* *** * *
41299004 AGTGTAAGACATGTCTAGGACAT-GCATCGGTTACGAGATGATAGTC
1 AGTGTAAGACATGTCTGGGACATGGCATCGACCAC-AGATGAGAGCC
* *
41299050 AGTGTAAGACCATGTCTGGGACATGGCATCGACTTA-AGATGTGAGCC
1 AGTGTAAGA-CATGTCTGGGACATGGCATCGAC-CACAGATGAGAGCC
41299097 AGTGTAAGACCATGTCTGGGACATGGCATCG
1 AGTGTAAGA-CATGTCTGGGACATGGCATCG
41299128 GCACCTTACC
Statistics
Matches: 179, Mismatches: 27, Indels: 23
0.78 0.12 0.10
Matches are distributed among these distances:
45 1 0.01
46 68 0.38
47 80 0.45
48 27 0.15
49 3 0.02
ACGTcount: A:0.29, C:0.19, G:0.29, T:0.23
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGGCATCGACCACAGATGAGAGCC
Found at i:41299008 original size:46 final size:48
Alignment explanation
Indices: 41298901--41299129 Score: 258
Period size: 47 Copynumber: 4.9 Consensus size: 48
41298891 CGACCACATT
* * *
41298901 ATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAG
1 ATGATAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGAG
** * *
41298949 ACAATAGCTAGTGTAAGA-CATGTTTGGGACAT-GCATCGGCCTCGAG
1 ATGATAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGAG
* *
41298995 ATG-TAAGCCAGTGTAAGA-CATGTCTAGGACAT-GCATCGG-TTACGAG
1 ATGAT-AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCT-CGAG
* * **
41299041 ATGATAGTCAGTGTAAGACCATGTCTGGGACATGGCATC-GACTTAAG
1 ATGATAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGAG
41299088 ATG-TGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGC
1 ATGAT-AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGC
41299130 ACCTTACCCA
Statistics
Matches: 153, Mismatches: 20, Indels: 16
0.81 0.11 0.08
Matches are distributed among these distances:
45 2 0.01
46 64 0.42
47 66 0.43
48 21 0.14
ACGTcount: A:0.28, C:0.19, G:0.30, T:0.23
Consensus pattern (48 bp):
ATGATAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGAG
Found at i:41299117 original size:140 final size:141
Alignment explanation
Indices: 41298864--41299129 Score: 353
Period size: 140 Copynumber: 1.9 Consensus size: 141
41298854 ATTGTTGGCT
*
41298864 AGTGTAAGACATGTTCAGGACATGCATCGACCACATTATGAGAGCCAGTGTAAGACCATGTCTGG
1 AGTGTAAGACATGTTCAGGACATGCATCGACCACATGATGAGAGCCAGTGTAAGACCATGTCTGG
* * * *
41298929 GACATGGCATCGGCATTGAGACAATAGCTAGTGTAAGACATGTTTGGGACAT-GCATCGGCCTCG
66 GACATGGCATCGACATTAAGACAATAGCCAGTGTAAGACATGTCTGGGACATGGCATCGGCCTCG
41298993 AGATGTAAGCC
131 AGATGTAAGCC
*** * *
41299004 AGTGTAAGACATG-TCTAGGACATGCATCGGTTACGA-GATGATAGTCAGTGTAAGACCATGTCT
1 AGTGTAAGACATGTTC-AGGACATGCATCGACCAC-ATGATGAGAGCCAGTGTAAGACCATGTCT
**
41299067 GGGACATGGCATCGAC-TTAAGA-TGTGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGC
64 GGGACATGGCATCGACATTAAGACAAT-AGCCAGTGTAAGA-CATGTCTGGGACATGGCATCGGC
41299130 ACCTTACCCA
Statistics
Matches: 109, Mismatches: 12, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
138 1 0.01
139 19 0.17
140 80 0.73
141 9 0.08
ACGTcount: A:0.29, C:0.19, G:0.29, T:0.23
Consensus pattern (141 bp):
AGTGTAAGACATGTTCAGGACATGCATCGACCACATGATGAGAGCCAGTGTAAGACCATGTCTGG
GACATGGCATCGACATTAAGACAATAGCCAGTGTAAGACATGTCTGGGACATGGCATCGGCCTCG
AGATGTAAGCC
Found at i:41306187 original size:27 final size:28
Alignment explanation
Indices: 41306148--41306242 Score: 79
Period size: 27 Copynumber: 3.5 Consensus size: 28
41306138 TTTGAGAGAT
** *
41306148 GCACTAAACGTGC-AAATTTGATACCGA
1 GCACTAAGTGTGCGAAATTCGATACCGA
* **
41306175 GCACTAAGTGTGCGAAA-TCGGTATTGA
1 GCACTAAGTGTGCGAAATTCGATACCGA
* **
41306202 GCACTAAGTGTGCGAAA-TCGGTCATTGA
1 GCACTAAGTGTGCGAAATTCGAT-ACCGA
41306230 GCACTAAGTGTGC
1 GCACTAAGTGTGC
41306243 AAGTTGGTTT
Statistics
Matches: 60, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
27 39 0.65
28 21 0.35
ACGTcount: A:0.31, C:0.19, G:0.26, T:0.24
Consensus pattern (28 bp):
GCACTAAGTGTGCGAAATTCGATACCGA
Found at i:41306237 original size:28 final size:27
Alignment explanation
Indices: 41306173--41306326 Score: 152
Period size: 28 Copynumber: 5.6 Consensus size: 27
41306163 ATTTGATACC
41306173 GAGCACTAAGTGTGCGAAATCGGTATT
1 GAGCACTAAGTGTGCGAAATCGGTATT
41306200 GAGCACTAAGTGTGCGAAATCGGTCATT
1 GAGCACTAAGTGTGCGAAATCGGT-ATT
* * *
41306228 GAGCACTAAGTGTGC-AAGTTGGTTTT
1 GAGCACTAAGTGTGCGAAATCGGTATT
* * * * *
41306254 AAGCATTAAGTGTG-TAATTTGG-ATTT
1 GAGCACTAAGTGTGCGAAATCGGTA-TT
* *
41306280 CCGAGCACTAAATGTGTGAAATCGGTTATT
1 --GAGCACTAAGTGTGCGAAATCGG-TATT
41306310 GAGCACTAAGTGTGCGA
1 GAGCACTAAGTGTGCGA
41306327 GAAAATTTTT
Statistics
Matches: 104, Mismatches: 15, Indels: 15
0.78 0.11 0.11
Matches are distributed among these distances:
26 22 0.21
27 30 0.29
28 44 0.42
29 5 0.05
30 2 0.02
31 1 0.01
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.30
Consensus pattern (27 bp):
GAGCACTAAGTGTGCGAAATCGGTATT
Found at i:41313703 original size:28 final size:27
Alignment explanation
Indices: 41313671--41313825 Score: 127
Period size: 28 Copynumber: 5.6 Consensus size: 27
41313661 ATTTGATACC
*
41313671 GAGCACTAAGTGTGCGAAATCGGTCATT
1 GAGCACTAAGTGTGCGAAATTGGT-ATT
41313699 GAGCACTAAGTGTGCGAAATTGGTCATT
1 GAGCACTAAGTGTGCGAAATTGGT-ATT
* * * * *
41313727 GAGCACTGAGTATGC-AAGTTTGTTTT
1 GAGCACTAAGTGTGCGAAATTGGTATT
* * * *
41313753 AAGCATTAAGTGTG-TAATTTGG-ATTT
1 GAGCACTAAGTGTGCGAAATTGGTA-TT
*
41313779 CCGAGCACTAAGTGTGCGAAATCGGTTATT
1 --GAGCACTAAGTGTGCGAAATTGG-TATT
*
41313809 GGGCACTAAGTGTGCGA
1 GAGCACTAAGTGTGCGA
41313826 GAAAATTTTT
Statistics
Matches: 101, Mismatches: 19, Indels: 14
0.75 0.14 0.10
Matches are distributed among these distances:
26 19 0.19
27 6 0.06
28 68 0.67
29 5 0.05
30 2 0.02
31 1 0.01
ACGTcount: A:0.27, C:0.14, G:0.28, T:0.30
Consensus pattern (27 bp):
GAGCACTAAGTGTGCGAAATTGGTATT
Found at i:41316787 original size:48 final size:47
Alignment explanation
Indices: 41316735--41317007 Score: 236
Period size: 48 Copynumber: 5.8 Consensus size: 47
41316725 GCCATATTAT
* *
41316735 GAGAGCCAGTGTAAGACCATGTTTGGGACATGGCATCAGCATTAAGAA
1 GAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATC-GCATTGAGAA
* * *
41316783 GAGAGCTAGTGTAAGACCATGTCTGGGGCATGGCATCGGCATTGAGAC
1 GAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATC-GCATTGAGAA
* * * *
41316831 GAGAGCTAGTGTAAGA-CATGTCTGGGACAT-GTATCGGCCTCGAGAA
1 GAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATC-GCATTGAGAA
* * * * *
41316877 GTA-AGCCAGTATAAGA-AATGTCTAGGACAT-GCATCG-GTTACGAGAT
1 G-AGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGCATT--GAGAA
* * * * * *
41316923 GATAGTCAATGTAAGACTATGTCTGGGACATGACATCG-ACTTGAGAT
1 GAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGCA-TTGAGAA
* *
41316970 GTGAGCCAGTGTAAGACCATGTCTAGGACATGGCATCG
1 GAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCG
41317008 GCACCTTACC
Statistics
Matches: 185, Mismatches: 33, Indels: 15
0.79 0.14 0.06
Matches are distributed among these distances:
44 1 0.01
45 2 0.01
46 55 0.30
47 62 0.34
48 63 0.34
49 2 0.01
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (47 bp):
GAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGCATTGAGAA
Found at i:41316921 original size:46 final size:46
Alignment explanation
Indices: 41316738--41317008 Score: 162
Period size: 47 Copynumber: 5.8 Consensus size: 46
41316728 ATATTATGAG
* * * * *
41316738 AGCCAGTGTAAGACCATGTTTGGGACATGGCATCAGCATT-AAGAAG-A
1 AGCCAGTGTAAGACCATGTCTAGGACAT-GCATC-G-GTTCGAGATGTA
* * * *
41316785 GAGCTAGTGTAAGACCATGTCTGGGGCATGGCATCGGCATT-GAGACG-A
1 -AGCCAGTGTAAGACCATGTCTAGGACAT-GCATCGG--TTCGAGATGTA
* * * * *
41316833 GAGCTAGTGTAAGA-CATGTCTGGGACATGTATCGGCCTCGAGAAGTA
1 -AGCCAGTGTAAGACCATGTCTAGGACATGCATCGG-TTCGAGATGTA
* *
41316880 AGCCAGTATAAGA-AATGTCTAGGACATGCATCGGTTACGAGATG-A
1 AGCCAGTGTAAGACCATGTCTAGGACATGCATCGGTT-CGAGATGTA
* * * * * *
41316925 TAGTCAATGTAAGACTATGTCTGGGACATGACATCGACTT-GAGATGTG
1 -AGCCAGTGTAAGACCATGTCTAGGACATG-CATCG-GTTCGAGATGTA
41316973 AGCCAGTGTAAGACCATGTCTAGGACATGGCATCGG
1 AGCCAGTGTAAGACCATGTCTAGGACAT-GCATCGG
41317009 CACCTTACCC
Statistics
Matches: 182, Mismatches: 30, Indels: 24
0.77 0.13 0.10
Matches are distributed among these distances:
45 3 0.02
46 56 0.31
47 63 0.35
48 58 0.32
49 2 0.01
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (46 bp):
AGCCAGTGTAAGACCATGTCTAGGACATGCATCGGTTCGAGATGTA
Found at i:41317970 original size:29 final size:28
Alignment explanation
Indices: 41317917--41317972 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
41317907 ACACTGGCTA
41317917 GGACACGGGCCTGTTCTGACCGTGTGAG
1 GGACACGGGCCTGTTCTGACCGTGTGAG
* *
41317945 GGACACGGGCGTGTGTCTGGCCGTGTGA
1 GGACACGGGCCTGT-TCTGACCGTGTGA
41317973 AAACCCCTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 13 0.52
29 12 0.48
ACGTcount: A:0.12, C:0.23, G:0.43, T:0.21
Consensus pattern (28 bp):
GGACACGGGCCTGTTCTGACCGTGTGAG
Found at i:41323205 original size:46 final size:46
Alignment explanation
Indices: 41323101--41323272 Score: 190
Period size: 46 Copynumber: 3.7 Consensus size: 46
41323091 GGGGCAGGAT
* * *
41323101 GCCGATGCCATGTCCTAGACATGGTTTTACACTGGC-TCATCTCGTA
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTTCATCTC-AA
* *
41323147 GTCGATGCCATGTCCCAGACAT-GTCTTGCACTGGCTTACATCTCAA
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTT-CATCTCAA
* * *
41323193 GGCCGATG-CATGTCCCAGATAT-GTCTTACACTAGCTCTCGTCTCAA
1 -GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCT-TCATCTCAA
*
41323239 TGTCGATGCCATGTCCCAGACATGGTCTTACACT
1 -GCCGATGCCATGTCCCAGACATGGTCTTACACT
41323273 AGCTCACAAT
Statistics
Matches: 107, Mismatches: 13, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
45 11 0.10
46 60 0.56
47 26 0.24
48 10 0.09
ACGTcount: A:0.21, C:0.30, G:0.20, T:0.29
Consensus pattern (46 bp):
GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTTCATCTCAA
Found at i:41326656 original size:35 final size:35
Alignment explanation
Indices: 41326610--41326701 Score: 175
Period size: 35 Copynumber: 2.6 Consensus size: 35
41326600 TCCTCATTGA
41326610 AATACCATACCTACATTTCACAAGTCAGTATGGTT
1 AATACCATACCTACATTTCACAAGTCAGTATGGTT
41326645 AATACCATACCTACATTTCACAAGTCAGTATGGTT
1 AATACCATACCTACATTTCACAAGTCAGTATGGTT
*
41326680 AATACCATACCTACGTTTCACA
1 AATACCATACCTACATTTCACA
41326702 CTTTTCCATG
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 56 1.00
ACGTcount: A:0.35, C:0.25, G:0.10, T:0.30
Consensus pattern (35 bp):
AATACCATACCTACATTTCACAAGTCAGTATGGTT
Found at i:41328171 original size:6 final size:7
Alignment explanation
Indices: 41328149--41328174 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
41328139 GGTTTATAGA
41328149 TTTGCTT
1 TTTGCTT
41328156 TTTGCTT
1 TTTGCTT
41328163 TTTGCTT
1 TTTGCTT
41328170 TTTGC
1 TTTGC
41328175 GTTTATAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.00, C:0.15, G:0.15, T:0.69
Consensus pattern (7 bp):
TTTGCTT
Found at i:41329020 original size:64 final size:64
Alignment explanation
Indices: 41328947--41329080 Score: 241
Period size: 64 Copynumber: 2.1 Consensus size: 64
41328937 TAATATTTCT
* *
41328947 ATATTTCTATCACGATTTTTAATAAATTTATTTATTGATATAATATGTCCCATCTAATATACAA
1 ATATTTCTATCACGAGTTTTAATAAATTTATTTATTAATATAATATGTCCCATCTAATATACAA
*
41329011 ATATTTCTATCACGAGTTTTAATAAATTTATTTATTAATATAATATGTCTCATCTAATATACAA
1 ATATTTCTATCACGAGTTTTAATAAATTTATTTATTAATATAATATGTCCCATCTAATATACAA
41329075 ATATTT
1 ATATTT
41329081 AATAAAATAT
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
64 67 1.00
ACGTcount: A:0.38, C:0.11, G:0.04, T:0.46
Consensus pattern (64 bp):
ATATTTCTATCACGAGTTTTAATAAATTTATTTATTAATATAATATGTCCCATCTAATATACAA
Found at i:41329155 original size:24 final size:24
Alignment explanation
Indices: 41329128--41329198 Score: 99
Period size: 24 Copynumber: 3.0 Consensus size: 24
41329118 ATTATTATTG
*
41329128 AAATATTCTCGTCTGTTTTATCAC
1 AAATATTATCGTCTGTTTTATCAC
*
41329152 AAATATTATTGT-TCGTTTTATCAC
1 AAATATTATCGTCT-GTTTTATCAC
*
41329176 AAATATTATCGTCCGTTTTATCA
1 AAATATTATCGTCTGTTTTATCA
41329199 TTTAAGTTAA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
23 1 0.02
24 40 0.98
ACGTcount: A:0.28, C:0.17, G:0.08, T:0.46
Consensus pattern (24 bp):
AAATATTATCGTCTGTTTTATCAC
Found at i:41329404 original size:29 final size:29
Alignment explanation
Indices: 41329372--41329442 Score: 124
Period size: 29 Copynumber: 2.4 Consensus size: 29
41329362 AACGACATGT
* *
41329372 ATATTATTTAATTAAAATAATTTTTTTCA
1 ATATTATTTAATTAAAATAATTTTTATAA
41329401 ATATTATTTAATTAAAATAATTTTTATAA
1 ATATTATTTAATTAAAATAATTTTTATAA
41329430 ATATTATTTAATT
1 ATATTATTTAATT
41329443 CGCAACTTAC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (29 bp):
ATATTATTTAATTAAAATAATTTTTATAA
Found at i:41329426 original size:16 final size:16
Alignment explanation
Indices: 41329378--41329426 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
41329368 ATGTATATTA
41329378 TTTAATTAAAATAATT
1 TTTAATTAAAATAATT
*
41329394 TTT--TT-CAAT-ATT
1 TTTAATTAAAATAATT
41329406 ATTTAATTAAAATAATT
1 -TTTAATTAAAATAATT
41329423 TTTA
1 TTTA
41329427 TAAATATTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 10
0.68 0.05 0.26
Matches are distributed among these distances:
12 3 0.12
13 6 0.23
14 2 0.08
15 2 0.08
16 10 0.38
17 3 0.12
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (16 bp):
TTTAATTAAAATAATT
Found at i:41329584 original size:9 final size:9
Alignment explanation
Indices: 41329554--41329928 Score: 424
Period size: 9 Copynumber: 42.4 Consensus size: 9
41329544 AATATTTAAC
*
41329554 ATAACTTAC
1 ATAACTTAT
* *
41329563 AAAACTTAC
1 ATAACTTAT
41329572 ATAACTTAT
1 ATAACTTAT
*
41329581 ATAACTTAG
1 ATAACTTAT
*
41329590 ATAA-ATAT
1 ATAACTTAT
*
41329598 ATAAATTAT
1 ATAACTTAT
*
41329607 ATAACTTAC
1 ATAACTTAT
41329616 ATAACTTAT
1 ATAACTTAT
*
41329625 ATAACTTAG
1 ATAACTTAT
*
41329634 ATAA-ATAT
1 ATAACTTAT
*
41329642 ATAACTTAC
1 ATAACTTAT
41329651 ATAACTTAT
1 ATAACTTAT
*
41329660 ATAACTTAG
1 ATAACTTAT
*
41329669 ATAA-ATAT
1 ATAACTTAT
41329677 ATAACTTAT
1 ATAACTTAT
*
41329686 ATAACTTAC
1 ATAACTTAT
41329695 ATAACTTAT
1 ATAACTTAT
*
41329704 ATAACTTAG
1 ATAACTTAT
*
41329713 ATAA-ATAT
1 ATAACTTAT
41329721 ATAACTTAT
1 ATAACTTAT
*
41329730 ATAACTTAG
1 ATAACTTAT
*
41329739 ATAA-ATAT
1 ATAACTTAT
41329747 ATAACTTAT
1 ATAACTTAT
41329756 ATAACTTAT
1 ATAACTTAT
*
41329765 ATAACTTAC
1 ATAACTTAT
41329774 ATAACTTAT
1 ATAACTTAT
41329783 ATAACTTAT
1 ATAACTTAT
*
41329792 ATAACTTAC
1 ATAACTTAT
41329801 ATAACTTAT
1 ATAACTTAT
*
41329810 ATAACTTAG
1 ATAACTTAT
*
41329819 ATAA-ATAT
1 ATAACTTAT
41329827 ATAACTTAT
1 ATAACTTAT
41329836 ATAACTTAT
1 ATAACTTAT
*
41329845 ATAACTTAC
1 ATAACTTAT
41329854 ATAACTTAT
1 ATAACTTAT
41329863 ATAACTTAT
1 ATAACTTAT
*
41329872 ATAACTTAG
1 ATAACTTAT
*
41329881 ATAA-ATAT
1 ATAACTTAT
*
41329889 ATAACTTAC
1 ATAACTTAT
*
41329898 ATAA-ATAT
1 ATAACTTAT
* *
41329906 ATATCATAT
1 ATAACTTAT
*
41329915 CATAACTTAC
1 -ATAACTTAT
41329925 ATAA
1 ATAA
41329929 TACTTAAATA
Statistics
Matches: 306, Mismatches: 51, Indels: 18
0.82 0.14 0.05
Matches are distributed among these distances:
8 47 0.15
9 253 0.83
10 6 0.02
ACGTcount: A:0.48, C:0.12, G:0.02, T:0.38
Consensus pattern (9 bp):
ATAACTTAT
Found at i:41329613 original size:44 final size:44
Alignment explanation
Indices: 41329554--41329901 Score: 410
Period size: 44 Copynumber: 8.3 Consensus size: 44
41329544 AATATTTAAC
* *
41329554 ATAACTTACAAAACTTACATAACTTATATAACTTAGATAAATAT
1 ATAACTTATATAACTTACATAACTTATATAACTTAGATAAATAT
*
41329598 ATAAATTATATAACTTACATAACTTATATAACTTAG------AT
1 ATAACTTATATAACTTACATAACTTATATAACTTAGATAAATAT
41329636 A-AA--TATATAACTTACATAACTTATATAACTTAGATAAATAT
1 ATAACTTATATAACTTACATAACTTATATAACTTAGATAAATAT
41329677 ATAACTTATATAACTTACATAACTTATATAACTTAGATAAATAT
1 ATAACTTATATAACTTACATAACTTATATAACTTAGATAAATAT
* *
41329721 ATAACTTATATAACTTAGATAA-ATATATAAC-----T---TAT
1 ATAACTTATATAACTTACATAACTTATATAACTTAGATAAATAT
* * *
41329756 ATAACTTATATAACTTACATAACTTATATAACTTATATAACTTAC
1 ATAACTTATATAACTTACATAACTTATATAACTTAGATAA-ATAT
* * * *
41329801 ATAACTTATATAACTTAGATAA-ATATATAACTTATATAACTTAT
1 ATAACTTATATAACTTACATAACTTATATAACTTAGATAA-ATAT
* *
41329845 ATAACTTACATAACTTATATAACTTATATAACTTAGATAAATAT
1 ATAACTTATATAACTTACATAACTTATATAACTTAGATAAATAT
*
41329889 ATAACTTACATAA
1 ATAACTTATATAA
41329902 ATATATATCA
Statistics
Matches: 268, Mismatches: 16, Indels: 40
0.83 0.05 0.12
Matches are distributed among these distances:
35 54 0.20
36 8 0.03
37 2 0.01
38 4 0.01
41 4 0.01
42 2 0.01
43 8 0.03
44 148 0.55
45 38 0.14
ACGTcount: A:0.48, C:0.11, G:0.02, T:0.38
Consensus pattern (44 bp):
ATAACTTATATAACTTACATAACTTATATAACTTAGATAAATAT
Found at i:41329620 original size:35 final size:35
Alignment explanation
Indices: 41329572--41329901 Score: 405
Period size: 35 Copynumber: 9.4 Consensus size: 35
41329562 CAAAACTTAC
* * *
41329572 ATAACTTATATAACTTAGATAA-ATATATAAATTAT
1 ATAACTTATATAACTTATATAACTTAGATAAA-TAT
*
41329607 ATAACTTACATAACTTATATAACTTAGATAAATAT
1 ATAACTTATATAACTTATATAACTTAGATAAATAT
*
41329642 ATAACTTACATAACTTATATAACTTAGATAAATAT
1 ATAACTTATATAACTTATATAACTTAGATAAATAT
* * * *
41329677 ATAACTTATATAACTTACATAACTTATATAACTTAG
1 ATAACTTATATAACTTATATAACTTAGATAA-ATAT
*
41329713 ATAA-ATATATAACTTATATAACTTAGATAAATAT
1 ATAACTTATATAACTTATATAACTTAGATAAATAT
* *
41329747 ATAACTTATATAACTTATATAACTTACATAACTTAT
1 ATAACTTATATAACTTATATAACTTAGATAA-ATAT
* * * *
41329783 ATAACTTATATAACTTACATAACTTATATAACTTAG
1 ATAACTTATATAACTTATATAACTTAGATAA-ATAT
* * * *
41329819 ATAA-ATATATAACTTATATAACTTATATAACTTAC
1 ATAACTTATATAACTTATATAACTTAGATAA-ATAT
41329854 ATAACTTATATAACTTATATAACTTAGATAAATAT
1 ATAACTTATATAACTTATATAACTTAGATAAATAT
*
41329889 ATAACTTACATAA
1 ATAACTTATATAA
41329902 ATATATATCA
Statistics
Matches: 262, Mismatches: 28, Indels: 10
0.87 0.09 0.03
Matches are distributed among these distances:
34 6 0.02
35 179 0.68
36 77 0.29
ACGTcount: A:0.48, C:0.11, G:0.02, T:0.39
Consensus pattern (35 bp):
ATAACTTATATAACTTATATAACTTAGATAAATAT
Found at i:41331814 original size:12 final size:12
Alignment explanation
Indices: 41331797--41331821 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
41331787 AAGATCGAGG
41331797 GATGAATCTGAT
1 GATGAATCTGAT
41331809 GATGAATCTGAT
1 GATGAATCTGAT
41331821 G
1 G
41331822 GAGAGGATGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.08, G:0.28, T:0.32
Consensus pattern (12 bp):
GATGAATCTGAT
Found at i:41335152 original size:13 final size:14
Alignment explanation
Indices: 41335136--41335164 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
41335126 TTCTAAATAT
41335136 TTATAA-TGTTTAA
1 TTATAATTGTTTAA
41335149 TTATAATTGTTTAA
1 TTATAATTGTTTAA
41335163 TT
1 TT
41335165 CAATTCATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (14 bp):
TTATAATTGTTTAA
Found at i:41335652 original size:21 final size:21
Alignment explanation
Indices: 41335578--41335653 Score: 91
Period size: 21 Copynumber: 3.6 Consensus size: 21
41335568 ACTTAGAGCG
*
41335578 GAGGCAGCAGAGAGGGAGGCA
1 GAGGCAGCAGCGAGGGAGGCA
* * *
41335599 GCGGCAACAGCGAGAGAGGCA
1 GAGGCAGCAGCGAGGGAGGCA
41335620 GAGGCA-CGAGCGAGGGAGGCA
1 GAGGCAGC-AGCGAGGGAGGCA
*
41335641 GAGGTAGCAGCGA
1 GAGGCAGCAGCGA
41335654 TGGCAGCAGA
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
20 1 0.02
21 44 0.96
22 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.49, T:0.01
Consensus pattern (21 bp):
GAGGCAGCAGCGAGGGAGGCA
Found at i:41335921 original size:32 final size:32
Alignment explanation
Indices: 41335885--41335970 Score: 93
Period size: 31 Copynumber: 2.7 Consensus size: 32
41335875 TTAGAATTAA
*
41335885 TGTTTTTGGTTGTATTTTTATGCTAAATTTGC
1 TGTTTTTGGTTGCATTTTTATGCTAAATTTGC
* * * *
41335917 TGTTTTTGGCTGCA-TTTTATACTATATTTGT
1 TGTTTTTGGTTGCATTTTTATGCTAAATTTGC
* * *
41335948 TGTATTTGGTTGGATTTTAATGC
1 TGTTTTTGGTTGCATTTTTATGC
41335971 AGGAAGGGCT
Statistics
Matches: 43, Mismatches: 10, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
31 25 0.58
32 18 0.42
ACGTcount: A:0.16, C:0.07, G:0.20, T:0.57
Consensus pattern (32 bp):
TGTTTTTGGTTGCATTTTTATGCTAAATTTGC
Found at i:41337228 original size:19 final size:19
Alignment explanation
Indices: 41337201--41337265 Score: 60
Period size: 19 Copynumber: 3.2 Consensus size: 19
41337191 AAAATTATAA
*
41337201 AAAAATCAAAATAATTTTT
1 AAAATTCAAAATAATTTTT
*
41337220 AAAATTCAAAAT-ATTTATA
1 AAAATTCAAAATAATTT-TT
41337239 AAAATTCTAAAATTTATATTTTT
1 AAAATTC-AAAA--TA-ATTTTT
41337262 AAAA
1 AAAA
41337266 AATTATAATT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
18 4 0.11
19 19 0.51
20 4 0.11
22 1 0.03
23 5 0.14
24 4 0.11
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (19 bp):
AAAATTCAAAATAATTTTT
Found at i:41337283 original size:18 final size:18
Alignment explanation
Indices: 41337247--41337289 Score: 63
Period size: 17 Copynumber: 2.4 Consensus size: 18
41337237 TAAAAATTCT
41337247 AAAATT-TATATTTTTAA
1 AAAATTATATATTTTTAA
41337264 AAAATTATA-ATTTTTAAA
1 AAAATTATATATTTTT-AA
41337282 AAAATTAT
1 AAAATTAT
41337290 CTAAAGAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 12 0.50
18 12 0.50
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
AAAATTATATATTTTTAA
Found at i:41338205 original size:41 final size:41
Alignment explanation
Indices: 41338148--41338232 Score: 145
Period size: 41 Copynumber: 2.1 Consensus size: 41
41338138 GACAGATTAC
*
41338148 ATTCTTAGAAAAACTCAAGTTTGAAATTTGAAAATGACATT
1 ATTCTTAGAAAAACTCAAGTTTAAAATTTGAAAATGACATT
41338189 ATTCTTA-AAAAGACTCAAGTTTAAAATTTGAAAATGACATT
1 ATTCTTAGAAAA-ACTCAAGTTTAAAATTTGAAAATGACATT
41338230 ATT
1 ATT
41338233 AAAAATGTCA
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
40 4 0.10
41 38 0.90
ACGTcount: A:0.45, C:0.09, G:0.11, T:0.35
Consensus pattern (41 bp):
ATTCTTAGAAAAACTCAAGTTTAAAATTTGAAAATGACATT
Found at i:41338988 original size:2 final size:2
Alignment explanation
Indices: 41338981--41339006 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
41338971 CTATGGCCCC
41338981 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
41339007 TAATCAATGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:41343194 original size:20 final size:20
Alignment explanation
Indices: 41343169--41343218 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
41343159 GTAAGACCAC
*
41343169 TATTGGTAAATTATTAAAAA
1 TATTGGTAAATAATTAAAAA
* *
41343189 TATTGGTAAATAATTAGATA
1 TATTGGTAAATAATTAAAAA
*
41343209 TTTTGGTAAA
1 TATTGGTAAA
41343219 AGAATTTTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.44, C:0.00, G:0.14, T:0.42
Consensus pattern (20 bp):
TATTGGTAAATAATTAAAAA
Found at i:41350038 original size:20 final size:20
Alignment explanation
Indices: 41350015--41350078 Score: 62
Period size: 20 Copynumber: 3.2 Consensus size: 20
41350005 TATATTTCTA
41350015 TAAATTGAATTATTAGCCAT
1 TAAATTGAATTATTAGCCAT
* * *
41350035 TAAATCGCATATT-TTA--AAA
1 TAAATTG-A-ATTATTAGCCAT
41350054 TAAATTGAATTATTAGCCAT
1 TAAATTGAATTATTAGCCAT
41350074 TAAAT
1 TAAAT
41350079 CGCATGTTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 10
0.67 0.12 0.20
Matches are distributed among these distances:
17 3 0.09
18 4 0.12
19 7 0.21
20 12 0.36
21 4 0.12
22 3 0.09
ACGTcount: A:0.44, C:0.09, G:0.08, T:0.39
Consensus pattern (20 bp):
TAAATTGAATTATTAGCCAT
Found at i:41350057 original size:39 final size:38
Alignment explanation
Indices: 41350014--41350095 Score: 146
Period size: 39 Copynumber: 2.1 Consensus size: 38
41350004 TTATATTTCT
41350014 ATAAATTGAATTATTAGCCATTAAATCGCATATTTTAAA
1 ATAAATTGAATTATTAGCCATTAAATCGCATATTTT-AA
*
41350053 ATAAATTGAATTATTAGCCATTAAATCGCATGTTTTAA
1 ATAAATTGAATTATTAGCCATTAAATCGCATATTTTAA
41350091 ATAAA
1 ATAAA
41350096 ACCTGAAAAT
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
38 7 0.17
39 35 0.83
ACGTcount: A:0.44, C:0.10, G:0.09, T:0.38
Consensus pattern (38 bp):
ATAAATTGAATTATTAGCCATTAAATCGCATATTTTAA
Found at i:41350764 original size:8 final size:8
Alignment explanation
Indices: 41350751--41350784 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
41350741 ATATGTATAC
41350751 TTGTGAAA
1 TTGTGAAA
41350759 TTGTGAAA
1 TTGTGAAA
*
41350767 CTGTGAAA
1 TTGTGAAA
*
41350775 CTGTGAAA
1 TTGTGAAA
41350783 TT
1 TT
41350785 ATAAATATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.35, C:0.06, G:0.24, T:0.35
Consensus pattern (8 bp):
TTGTGAAA
Found at i:41356868 original size:46 final size:46
Alignment explanation
Indices: 41356695--41356868 Score: 176
Period size: 46 Copynumber: 3.8 Consensus size: 46
41356685 TAACCCACCC
* * *
41356695 ATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCC
1 ATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCT
* * *
41356741 ATAAGTGAACTTGGACTCAACTCAACGAGCTCAGATGCCTAGTT-ACATCT
1 ATAAGTGAACTCGGACTCAACTCAACGAGCTC-G--GAC-A-TTCGCATCT
* * *
41356791 CT---CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCT
1 ATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCT
* *
41356834 ATAAGTGAACTCGGACTCAACTCAATGAGTTCGGA
1 ATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
41356869 TGCTCAACCA
Statistics
Matches: 105, Mismatches: 14, Indels: 18
0.77 0.10 0.13
Matches are distributed among these distances:
42 2 0.02
43 7 0.07
44 2 0.02
46 60 0.57
47 25 0.24
49 2 0.02
50 5 0.05
51 2 0.02
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.23
Consensus pattern (46 bp):
ATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCT
Found at i:41360750 original size:5 final size:5
Alignment explanation
Indices: 41360740--41360832 Score: 145
Period size: 5 Copynumber: 18.8 Consensus size: 5
41360730 TTTAGAAGAA
* *
41360740 AATAC AATAC AATTC AGA-A- AATAC AATTC AATAC AATAC AATAC AATAC
1 AATAC AATAC AATAC A-ATAC AATAC AATAC AATAC AATAC AATAC AATAC
41360789 AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATA
1 AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATAC AATA
41360833 GAATTTAGTT
Statistics
Matches: 81, Mismatches: 4, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
3 1 0.01
4 2 0.02
5 77 0.95
6 1 0.01
ACGTcount: A:0.59, C:0.18, G:0.01, T:0.22
Consensus pattern (5 bp):
AATAC
Found at i:41364220 original size:40 final size:40
Alignment explanation
Indices: 41364160--41364306 Score: 186
Period size: 40 Copynumber: 3.7 Consensus size: 40
41364150 GCGTTTGACA
* * * *
41364160 AAAAAGCCGCTATGGATTGAGCATTAGTGTCGCTTTTTGG
1 AAAACGCCGCTATAGATCGAGCATTAGTGACGCTTTTTGG
* *
41364200 AAAACGCCGCTATAGATTGAGCATTAGTGGCGCTTTTTGG
1 AAAACGCCGCTATAGATCGAGCATTAGTGACGCTTTTTGG
* * *
41364240 AAAATGCCGCTATAGATCGAGCATTAGCGACGCTTTTTAG
1 AAAACGCCGCTATAGATCGAGCATTAGTGACGCTTTTTGG
* * *
41364280 AAAACACCACTATAAATCGAGCATTAG
1 AAAACGCCGCTATAGATCGAGCATTAG
41364307 GTTTGAGAAA
Statistics
Matches: 95, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 95 1.00
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28
Consensus pattern (40 bp):
AAAACGCCGCTATAGATCGAGCATTAGTGACGCTTTTTGG
Found at i:41364438 original size:40 final size:41
Alignment explanation
Indices: 41364383--41364487 Score: 122
Period size: 41 Copynumber: 2.6 Consensus size: 41
41364373 AGCTTTAGTG
* **
41364383 GCATTAGCGGCGCTTTATG-GGAAACGCCGCTATAGATCGA
1 GCATTAGCGGTGCTTTATGAAAAAACGCCGCTATAGATCGA
* * *
41364423 GCATTAGCGGTGCTTTTTGAAAAAACGCCGTTATAGGTCGA
1 GCATTAGCGGTGCTTTATGAAAAAACGCCGCTATAGATCGA
* * *
41364464 GCTTTAGCGATGCTTTTTGAAAAA
1 GCATTAGCGGTGCTTTATGAAAAA
41364488 TGCCAAAAAA
Statistics
Matches: 56, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
40 17 0.30
41 39 0.70
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.29
Consensus pattern (41 bp):
GCATTAGCGGTGCTTTATGAAAAAACGCCGCTATAGATCGA
Found at i:41364464 original size:41 final size:41
Alignment explanation
Indices: 41364404--41364487 Score: 132
Period size: 41 Copynumber: 2.0 Consensus size: 41
41364394 GCTTTATGGG
*
41364404 AAACGCCGCTATAGATCGAGCATTAGCGGTGCTTTTTGAAA
1 AAACGCCGCTATAGATCGAGCATTAGCGATGCTTTTTGAAA
* * *
41364445 AAACGCCGTTATAGGTCGAGCTTTAGCGATGCTTTTTGAAA
1 AAACGCCGCTATAGATCGAGCATTAGCGATGCTTTTTGAAA
41364486 AA
1 AA
41364488 TGCCAAAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.29
Consensus pattern (41 bp):
AAACGCCGCTATAGATCGAGCATTAGCGATGCTTTTTGAAA
Found at i:41364821 original size:14 final size:14
Alignment explanation
Indices: 41364804--41364852 Score: 62
Period size: 14 Copynumber: 3.5 Consensus size: 14
41364794 TATAGTTTTG
41364804 GGTTTAGGGTTTAT
1 GGTTTAGGGTTTAT
* *
41364818 GGTTTAAGGTATAT
1 GGTTTAGGGTTTAT
* *
41364832 AGTTTAGGGTTTAA
1 GGTTTAGGGTTTAT
41364846 GGTTTAG
1 GGTTTAG
41364853 AAGTTACTAT
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.22, C:0.00, G:0.33, T:0.45
Consensus pattern (14 bp):
GGTTTAGGGTTTAT
Found at i:41364888 original size:22 final size:21
Alignment explanation
Indices: 41364863--41364915 Score: 70
Period size: 22 Copynumber: 2.5 Consensus size: 21
41364853 AAGTTACTAT
*
41364863 TTTAAGGTTTATGGATTATGAG
1 TTTAAGGATTATGGATTAT-AG
* *
41364885 TTTAGGGATTATGGTTTATAG
1 TTTAAGGATTATGGATTATAG
41364906 TTTAAGGATT
1 TTTAAGGATT
41364916 GGGGTTTAGG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
21 11 0.41
22 16 0.59
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.47
Consensus pattern (21 bp):
TTTAAGGATTATGGATTATAG
Found at i:41364893 original size:15 final size:14
Alignment explanation
Indices: 41364868--41364902 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
41364858 ACTATTTTAA
*
41364868 GGTTTATGGATTAT
1 GGTTTAGGGATTAT
41364882 GAGTTTAGGGATTAT
1 G-GTTTAGGGATTAT
41364897 GGTTTA
1 GGTTTA
41364903 TAGTTTAAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.23, C:0.00, G:0.31, T:0.46
Consensus pattern (14 bp):
GGTTTAGGGATTAT
Found at i:41364921 original size:21 final size:22
Alignment explanation
Indices: 41364863--41364923 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 22
41364853 AAGTTACTAT
* * *
41364863 TTTAAGGTTTATGGATTATGAG
1 TTTAAGGATTAGGGTTTATGAG
* *
41364885 TTTAGGGATTATGGTTTAT-AG
1 TTTAAGGATTAGGGTTTATGAG
*
41364906 TTTAAGGATTGGGGTTTA
1 TTTAAGGATTAGGGTTTA
41364924 GGGGCTAGGG
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 17 0.52
22 16 0.48
ACGTcount: A:0.25, C:0.00, G:0.30, T:0.46
Consensus pattern (22 bp):
TTTAAGGATTAGGGTTTATGAG
Found at i:41365668 original size:14 final size:14
Alignment explanation
Indices: 41365640--41365689 Score: 57
Period size: 13 Copynumber: 3.6 Consensus size: 14
41365630 AGTTTTTTTA
*
41365640 TTATAAAAATCTAAT
1 TTATAAAAA-ATAAT
41365655 TTATAAAAAATAA-
1 TTATAAAAAATAAT
* *
41365668 TAATAAAAAATATT
1 TTATAAAAAATAAT
41365682 TTATAAAA
1 TTATAAAA
41365690 TCACTTAACT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
13 11 0.37
14 10 0.33
15 9 0.30
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (14 bp):
TTATAAAAAATAAT
Found at i:41366779 original size:13 final size:12
Alignment explanation
Indices: 41366748--41366780 Score: 57
Period size: 12 Copynumber: 2.7 Consensus size: 12
41366738 ACAGGTTGGC
41366748 TTTTTACTTTGT
1 TTTTTACTTTGT
41366760 TTTTTACTTTGT
1 TTTTTACTTTGT
41366772 TTTATTACT
1 TTT-TTACT
41366781 GAGTTGTTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 15 0.75
13 5 0.25
ACGTcount: A:0.12, C:0.09, G:0.06, T:0.73
Consensus pattern (12 bp):
TTTTTACTTTGT
Found at i:41370314 original size:84 final size:85
Alignment explanation
Indices: 41370204--41370392 Score: 245
Period size: 84 Copynumber: 2.2 Consensus size: 85
41370194 ATTTGATATG
* * *
41370204 GTCTTTAGTGGCGTTTTTGGGGAAAGCGTCGTTAAAGGTCAT-ATCTTTAGCGGCGTTTAAAGAG
1 GTCTTTAGTGGCGTTTTTGGGGAAAGCGACGCTAAAGGTCATGATCTTTAGCGACGTTTAAAGAG
* * *
41370268 AAAGTGCCGTTAAATATCAT
66 AAAGCGCCGCTAAAGATCAT
* * *** *
41370288 GTCTTTAGCGGCGTTTTTGGGGAAAGCGACGCTAAAGGTCATGTTCTTTAGCGACGTTTCTGGGG
1 GTCTTTAGTGGCGTTTTTGGGGAAAGCGACGCTAAAGGTCATGATCTTTAGCGACGTTTAAAGAG
*
41370353 AAAGCGCCGCTAAAGGTCAT
66 AAAGCGCCGCTAAAGATCAT
41370373 GTTCTTTAGTGGCGTTTTTG
1 G-TCTTTAGTGGCGTTTTTG
41370393 ACAAATAAAC
Statistics
Matches: 89, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
84 39 0.44
85 33 0.37
86 17 0.19
ACGTcount: A:0.22, C:0.15, G:0.30, T:0.33
Consensus pattern (85 bp):
GTCTTTAGTGGCGTTTTTGGGGAAAGCGACGCTAAAGGTCATGATCTTTAGCGACGTTTAAAGAG
AAAGCGCCGCTAAAGATCAT
Found at i:41370346 original size:43 final size:43
Alignment explanation
Indices: 41370205--41370392 Score: 218
Period size: 42 Copynumber: 4.4 Consensus size: 43
41370195 TTTGATATGG
* * * *
41370205 TCTTTAGTGGCGTTTTTGGGGAAAGCGTCGTTAAAGGTCAT-A
1 TCTTTAGCGGCGTTTTTGGGGAAAGCGCCGCTAAAGGTCATGT
*** * * * **
41370247 TCTTTAGCGGCGTTTAAAGAGAAAGTGCCGTTAAATATCATG-
1 TCTTTAGCGGCGTTTTTGGGGAAAGCGCCGCTAAAGGTCATGT
*
41370289 TCTTTAGCGGCGTTTTTGGGGAAAGCGACGCTAAAGGTCATGT
1 TCTTTAGCGGCGTTTTTGGGGAAAGCGCCGCTAAAGGTCATGT
* *
41370332 TCTTTAGCGACGTTTCTGGGGAAAGCGCCGCTAAAGGTCATGT
1 TCTTTAGCGGCGTTTTTGGGGAAAGCGCCGCTAAAGGTCATGT
*
41370375 TCTTTAGTGGCGTTTTTG
1 TCTTTAGCGGCGTTTTTG
41370393 ACAAATAAAC
Statistics
Matches: 120, Mismatches: 24, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
42 65 0.54
43 55 0.46
ACGTcount: A:0.22, C:0.15, G:0.29, T:0.34
Consensus pattern (43 bp):
TCTTTAGCGGCGTTTTTGGGGAAAGCGCCGCTAAAGGTCATGT
Found at i:41371336 original size:23 final size:24
Alignment explanation
Indices: 41371310--41371366 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
41371300 ATAATTTTAA
41371310 TAAATAATTATGG-ATTTTGAACC
1 TAAATAATTATGGAATTTTGAACC
* *
41371333 TAAAAGAATT-TGGAATTTTGAACG
1 T-AAATAATTATGGAATTTTGAACC
*
41371357 TAAATTATTA
1 TAAATAATTA
41371367 ATGTATATGC
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
23 10 0.37
24 17 0.63
ACGTcount: A:0.42, C:0.05, G:0.14, T:0.39
Consensus pattern (24 bp):
TAAATAATTATGGAATTTTGAACC
Found at i:41371342 original size:24 final size:24
Alignment explanation
Indices: 41371315--41371360 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
41371305 TTTAATAAAT
41371315 AATTATGG-ATTTTGAACCTAAAAG
1 AATT-TGGAATTTTGAACCTAAAAG
*
41371339 AATTTGGAATTTTGAACGTAAA
1 AATTTGGAATTTTGAACCTAAA
41371361 TTATTAATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 3 0.15
24 17 0.85
ACGTcount: A:0.41, C:0.07, G:0.17, T:0.35
Consensus pattern (24 bp):
AATTTGGAATTTTGAACCTAAAAG
Found at i:41373053 original size:21 final size:22
Alignment explanation
Indices: 41373015--41373055 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
41373005 TTTTTGCGTA
* *
41373015 TTAATTTTTTATTCAAATATTC
1 TTAAATTTTGATTCAAATATTC
41373037 TTAAATTTTGATT-AAATAT
1 TTAAATTTTGATTCAAATAT
41373056 CTGCATCTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.56
Consensus pattern (22 bp):
TTAAATTTTGATTCAAATATTC
Found at i:41380516 original size:17 final size:18
Alignment explanation
Indices: 41380484--41380523 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
41380474 TTGGTAAAAC
*
41380484 ATTTTATTGGAAACAACG
1 ATTTTATTGCAAACAACG
*
41380502 ATTTTA-TGCAAACAATG
1 ATTTTATTGCAAACAACG
41380519 ATTTT
1 ATTTT
41380524 CTTAAAAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 14 0.70
18 6 0.30
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.40
Consensus pattern (18 bp):
ATTTTATTGCAAACAACG
Found at i:41384670 original size:14 final size:14
Alignment explanation
Indices: 41384651--41384679 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
41384641 TTTGGGTTAT
41384651 CGTGGATTGATTGA
1 CGTGGATTGATTGA
41384665 CGTGGATTGATTGA
1 CGTGGATTGATTGA
41384679 C
1 C
41384680 CAAGTCTGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.10, G:0.34, T:0.34
Consensus pattern (14 bp):
CGTGGATTGATTGA
Found at i:41403701 original size:6 final size:6
Alignment explanation
Indices: 41403679--41403860 Score: 339
Period size: 6 Copynumber: 30.2 Consensus size: 6
41403669 AAAGTGCTTT
41403679 TATATG -ATATG TATATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG --TATATG TATATG TATATG TATATG TATATG TATATG
41403728 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
41403776 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
41403824 TATATG TATATG TATATG TATATG TATATG TATATG T
1 TATATG TATATG TATATG TATATG TATATG TATATG T
41403861 TAATGGCTTC
Statistics
Matches: 173, Mismatches: 0, Indels: 6
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.03
6 163 0.94
8 5 0.03
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.50
Consensus pattern (6 bp):
TATATG
Found at i:41407788 original size:15 final size:15
Alignment explanation
Indices: 41407770--41407801 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
41407760 AGCTGTATTT
41407770 ATATATGCCCAATCA
1 ATATATGCCCAATCA
41407785 ATATATGCCCAATCA
1 ATATATGCCCAATCA
41407800 AT
1 AT
41407802 CCCTCTACTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.41, C:0.25, G:0.06, T:0.28
Consensus pattern (15 bp):
ATATATGCCCAATCA
Found at i:41412931 original size:16 final size:16
Alignment explanation
Indices: 41412912--41412945 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
41412902 ATTAAAAATC
41412912 AAAATTA-AAAATATTG
1 AAAATTATAAAA-ATTG
41412928 AAAATTATAAAAATTG
1 AAAATTATAAAAATTG
41412944 AA
1 AA
41412946 TCATATACAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (16 bp):
AAAATTATAAAAATTG
Found at i:41414061 original size:24 final size:24
Alignment explanation
Indices: 41414033--41414085 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
41414023 ATTTTGTTAA
41414033 CATTTTCTCATATTATAAAATTAT
1 CATTTTCTCATATTATAAAATTAT
41414057 CATTTTCTCATATTATAAAATTAT
1 CATTTTCTCATATTATAAAATTAT
41414081 C-TTTT
1 CATTTT
41414086 GAGATATTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
23 4 0.14
24 25 0.86
ACGTcount: A:0.34, C:0.13, G:0.00, T:0.53
Consensus pattern (24 bp):
CATTTTCTCATATTATAAAATTAT
Found at i:41414748 original size:15 final size:15
Alignment explanation
Indices: 41414718--41414746 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
41414708 ACTATTAGTA
41414718 ATTTTTTAAATATTT
1 ATTTTTTAAATATTT
41414733 ATTTTTT-AATATTT
1 ATTTTTTAAATATTT
41414747 TACCATACTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
ATTTTTTAAATATTT
Found at i:41416697 original size:62 final size:62
Alignment explanation
Indices: 41416600--41416726 Score: 209
Period size: 62 Copynumber: 2.0 Consensus size: 62
41416590 TATTAATGTA
** * *
41416600 ACACCCCTTACCCGCATCCGACTCTGGGACAGGGTACGAGGCATTACCAAACTTCTACTCAT
1 ACACCCCTTACCCGCATCCGAAGCCGGGACAGGGTACGAGGCATTACCAAACTTATACTCAT
*
41416662 ACACCCCTTATCCGCATCCGAAGCCGGGACAGGGTACGAGGCATTACCAAACTTATACTCAT
1 ACACCCCTTACCCGCATCCGAAGCCGGGACAGGGTACGAGGCATTACCAAACTTATACTCAT
41416724 ACA
1 ACA
41416727 TTCATGCAAA
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
62 60 1.00
ACGTcount: A:0.28, C:0.34, G:0.18, T:0.20
Consensus pattern (62 bp):
ACACCCCTTACCCGCATCCGAAGCCGGGACAGGGTACGAGGCATTACCAAACTTATACTCAT
Found at i:41418051 original size:21 final size:21
Alignment explanation
Indices: 41418027--41418070 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
41418017 ACACTGGTGC
41418027 CTCAGTCAATAACATTTTCAA
1 CTCAGTCAATAACATTTTCAA
41418048 CTCAGTCAATAACATTTTCAA
1 CTCAGTCAATAACATTTTCAA
41418069 CT
1 CT
41418071 TCTCAAAGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.36, C:0.25, G:0.05, T:0.34
Consensus pattern (21 bp):
CTCAGTCAATAACATTTTCAA
Found at i:41418857 original size:22 final size:19
Alignment explanation
Indices: 41418831--41418877 Score: 51
Period size: 18 Copynumber: 2.4 Consensus size: 19
41418821 GTAAATCTGG
*
41418831 TTAAATTATTGTCGAAAAATAA
1 TTAAATTATTAT--AAAAA-AA
41418853 TTAAA-TATTATAAAAAAA
1 TTAAATTATTATAAAAAAA
41418871 TTAAATT
1 TTAAATT
41418878 GTGTTAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
18 7 0.30
19 6 0.26
21 5 0.22
22 5 0.22
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.38
Consensus pattern (19 bp):
TTAAATTATTATAAAAAAA
Found at i:41425915 original size:33 final size:34
Alignment explanation
Indices: 41425867--41425934 Score: 93
Period size: 33 Copynumber: 2.0 Consensus size: 34
41425857 TGGAGAATCC
*
41425867 AAGAAATCCGAGGAAGGAATATT-CAAAGCGTTA
1 AAGAAATCCGAGGAAGGAACATTGCAAAGCGTTA
* * *
41425900 AAGAAATCTGGGGAAGGAACATTGTAAAGCGTTA
1 AAGAAATCCGAGGAAGGAACATTGCAAAGCGTTA
41425934 A
1 A
41425935 CATTGAGGAG
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
33 20 0.67
34 10 0.33
ACGTcount: A:0.44, C:0.10, G:0.26, T:0.19
Consensus pattern (34 bp):
AAGAAATCCGAGGAAGGAACATTGCAAAGCGTTA
Found at i:41427322 original size:40 final size:40
Alignment explanation
Indices: 41427285--41427389 Score: 160
Period size: 40 Copynumber: 2.6 Consensus size: 40
41427275 GCTACTCGTT
*
41427285 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
41427325 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
*
41427365 CCAATGCCTTCGGG-CTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
41427390 CATCATTCGA
Statistics
Matches: 60, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
39 10 0.17
40 48 0.80
41 2 0.03
ACGTcount: A:0.25, C:0.30, G:0.23, T:0.23
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:41441228 original size:13 final size:13
Alignment explanation
Indices: 41441210--41441234 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41441200 CAATTTAGGG
41441210 TCACACGCCCGTA
1 TCACACGCCCGTA
41441223 TCACACGCCCGT
1 TCACACGCCCGT
41441235 GTGACCAGAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.48, G:0.16, T:0.16
Consensus pattern (13 bp):
TCACACGCCCGTA
Found at i:41441637 original size:24 final size:24
Alignment explanation
Indices: 41441609--41441665 Score: 114
Period size: 24 Copynumber: 2.4 Consensus size: 24
41441599 TGGCACTTTC
41441609 ACACATTCATAATGTCGTTCTATT
1 ACACATTCATAATGTCGTTCTATT
41441633 ACACATTCATAATGTCGTTCTATT
1 ACACATTCATAATGTCGTTCTATT
41441657 ACACATTCA
1 ACACATTCA
41441666 ATTAGTCACA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.32, C:0.23, G:0.07, T:0.39
Consensus pattern (24 bp):
ACACATTCATAATGTCGTTCTATT
Found at i:41442435 original size:15 final size:15
Alignment explanation
Indices: 41442415--41442444 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
41442405 CATTGCATTA
41442415 CCCGTTGAACACTTG
1 CCCGTTGAACACTTG
41442430 CCCGTTGAACACTTG
1 CCCGTTGAACACTTG
41442445 GAATACTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.33, G:0.20, T:0.27
Consensus pattern (15 bp):
CCCGTTGAACACTTG
Found at i:41446343 original size:23 final size:23
Alignment explanation
Indices: 41446311--41446376 Score: 66
Period size: 23 Copynumber: 3.0 Consensus size: 23
41446301 TGACATAATA
* *
41446311 ATATAGAATAATATATAATATGT
1 ATATAAAATAATATATAATATAT
* *
41446334 ATATAAAATAATGTATAGTATAT
1 ATATAAAATAATATATAATATAT
41446357 ATAT---ATCAATATATAATATA
1 ATATAAAAT-AATATATAATATA
41446377 AGCACAAATA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
20 2 0.06
21 11 0.31
23 23 0.64
ACGTcount: A:0.53, C:0.02, G:0.06, T:0.39
Consensus pattern (23 bp):
ATATAAAATAATATATAATATAT
Found at i:41446420 original size:30 final size:30
Alignment explanation
Indices: 41446386--41446446 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
41446376 AAGCACAAAT
*
41446386 ATAATAACCATATATAAATAATA-ATGTAAA
1 ATAATAACAATATA-AAATAATATATGTAAA
* *
41446416 ATAATAATAATATAAAATAATATATTTAAA
1 ATAATAACAATATAAAATAATATATGTAAA
41446446 A
1 A
41446447 CGTAAGATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 8 0.30
30 19 0.70
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.33
Consensus pattern (30 bp):
ATAATAACAATATAAAATAATATATGTAAA
Found at i:41446423 original size:16 final size:16
Alignment explanation
Indices: 41446402--41446437 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
41446392 ACCATATATA
*
41446402 AATAATAATGTAAAAT
1 AATAATAATATAAAAT
41446418 AATAATAATATAAAAT
1 AATAATAATATAAAAT
41446434 AATA
1 AATA
41446438 TATTTAAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (16 bp):
AATAATAATATAAAAT
Found at i:41446524 original size:13 final size:14
Alignment explanation
Indices: 41446492--41446538 Score: 53
Period size: 13 Copynumber: 3.4 Consensus size: 14
41446482 TAAGTGATAA
*
41446492 AATATAGTATAAAT
1 AATATAGGATAAAT
41446506 ATATATAGGA-AAAT
1 A-ATATAGGATAAAT
*
41446520 AATATACGATAAA-
1 AATATAGGATAAAT
41446533 AATATA
1 AATATA
41446539 AGTAGTATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
13 13 0.45
14 9 0.31
15 7 0.24
ACGTcount: A:0.60, C:0.02, G:0.09, T:0.30
Consensus pattern (14 bp):
AATATAGGATAAAT
Found at i:41455370 original size:15 final size:15
Alignment explanation
Indices: 41455328--41455377 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
41455318 ATAACTTTGC
* *
41455328 ATGCAAACG-ATGTG
1 ATGCAAATGCATGAG
41455342 ATG-AAATGCTATGAG
1 ATGCAAATGC-ATGAG
41455357 ATGCAAATGCATGA-
1 ATGCAAATGCATGAG
41455371 ATGCAAA
1 ATGCAAA
41455378 AAGGATATCG
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
13 4 0.13
14 10 0.32
15 11 0.35
16 6 0.19
ACGTcount: A:0.42, C:0.12, G:0.24, T:0.22
Consensus pattern (15 bp):
ATGCAAATGCATGAG
Found at i:41455376 original size:14 final size:16
Alignment explanation
Indices: 41455341--41455377 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
41455331 CAAACGATGT
41455341 GATG-AAATGCTATGA
1 GATGCAAATGCTATGA
41455356 GATGCAAATGC-ATGA
1 GATGCAAATGCTATGA
41455371 -ATGCAAA
1 GATGCAAA
41455378 AAGGATATCG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 7 0.33
15 8 0.38
16 6 0.29
ACGTcount: A:0.43, C:0.11, G:0.24, T:0.22
Consensus pattern (16 bp):
GATGCAAATGCTATGA
Found at i:41459321 original size:24 final size:24
Alignment explanation
Indices: 41459270--41459315 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
41459260 AATAATATAG
*
41459270 AATAATATATAATATGTATATAAA
1 AATAATATATAATATATATATAAA
* *
41459294 AATAATGTATAGTATATATATA
1 AATAATATATAATATATATATA
41459316 TCAATATATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.54, C:0.00, G:0.07, T:0.39
Consensus pattern (24 bp):
AATAATATATAATATATATATAAA
Found at i:41459377 original size:16 final size:16
Alignment explanation
Indices: 41459356--41459391 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
41459346 ACCATATATA
*
41459356 AATAATAATGTAAAAT
1 AATAATAATATAAAAT
41459372 AATAATAATATAAAAT
1 AATAATAATATAAAAT
41459388 AATA
1 AATA
41459392 TATTCAAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (16 bp):
AATAATAATATAAAAT
Found at i:41460521 original size:13 final size:13
Alignment explanation
Indices: 41460503--41460528 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
41460493 TGATTCGAAA
41460503 CCTGGAATCACGG
1 CCTGGAATCACGG
41460516 CCTGGAATCACGG
1 CCTGGAATCACGG
41460529 TGCTGATGGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.31, G:0.31, T:0.15
Consensus pattern (13 bp):
CCTGGAATCACGG
Found at i:41469632 original size:40 final size:40
Alignment explanation
Indices: 41469538--41469747 Score: 282
Period size: 40 Copynumber: 5.3 Consensus size: 40
41469528 ACCCAATTAT
* *** *
41469538 CTTCGGGATTTAG-CCGGATATAACCACTCGCAC-AAGGC
1 CTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGC
* * * ** *
41469576 CGTCGGGTCTTAGCCCGGATATGGTCGCTAGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGC
41469616 CTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGC
*
41469656 CTTCGGGACTTAGCCCAGATATAGTAACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGC
41469696 CTTCGGGACTTAGCCCGGA-ATTAGTAACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATGC
41469736 CTTCGGGACTTA
1 CTTCGGGACTTA
41469748 ACCCCGTTAG
Statistics
Matches: 152, Mismatches: 17, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
38 10 0.07
39 16 0.11
40 126 0.83
ACGTcount: A:0.26, C:0.28, G:0.24, T:0.23
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGC
Found at i:41474853 original size:14 final size:14
Alignment explanation
Indices: 41474834--41474864 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
41474824 CTCACTTTCT
41474834 ATCTATGTCACGAC
1 ATCTATGTCACGAC
41474848 ATCTATGTCACGAC
1 ATCTATGTCACGAC
41474862 ATC
1 ATC
41474865 GTGGACTCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.29, C:0.29, G:0.13, T:0.29
Consensus pattern (14 bp):
ATCTATGTCACGAC
Found at i:41477694 original size:21 final size:21
Alignment explanation
Indices: 41477668--41477707 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
41477658 ACACAATAGA
* *
41477668 CCTAGGGTAGGTATGTCATTT
1 CCTAGGATAAGTATGTCATTT
41477689 CCTAGGATAAGTATGTCAT
1 CCTAGGATAAGTATGTCAT
41477708 CTACATACAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (21 bp):
CCTAGGATAAGTATGTCATTT
Found at i:41481695 original size:48 final size:48
Alignment explanation
Indices: 41481624--41481729 Score: 176
Period size: 48 Copynumber: 2.2 Consensus size: 48
41481614 CAAGATAAAT
* * *
41481624 ATATATATGTGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
41481672 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
*
41481720 ATGTGTATAT
1 ATATGTATAT
41481730 ATTGTGGCCG
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 54 1.00
ACGTcount: A:0.34, C:0.06, G:0.27, T:0.33
Consensus pattern (48 bp):
ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
Found at i:41489391 original size:40 final size:40
Alignment explanation
Indices: 41489285--41489374 Score: 128
Period size: 40 Copynumber: 2.2 Consensus size: 40
41489275 GCTACTCATT
* * *
41489285 CAAATACCTTCGGGACATACCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
41489325 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
41489365 CTAATGCCTT
1 CAAATGCCTT
41489375 TGGATCTTAG
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
40 43 0.96
41 2 0.04
ACGTcount: A:0.28, C:0.29, G:0.18, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:41491251 original size:39 final size:39
Alignment explanation
Indices: 41491193--41491392 Score: 312
Period size: 39 Copynumber: 5.1 Consensus size: 39
41491183 TACGGGACTT
*
41491193 TATAACACCAGCA-GAAATGCCTTCGGGGCTTAGCCCGGA
1 TATAACACCAGCACG-AATGCCTTCGGGACTTAGCCCGGA
41491232 TATAACACCAGCACGAATGCCTTCGGGACTTAGCCCGGA
1 TATAACACCAGCACGAATGCCTTCGGGACTTAGCCCGGA
* * * * *
41491271 TATAACACCAACACGAATGCCTTTGGTACTTAGCTCAGA
1 TATAACACCAGCACGAATGCCTTCGGGACTTAGCCCGGA
*
41491310 TATAACACCAGCACGAATGCCTTTGGGACTTAGCCCGGA
1 TATAACACCAGCACGAATGCCTTCGGGACTTAGCCCGGA
*
41491349 TATAACACCAGCACGAATGCCTTCGGAACTTAGCCCGGA
1 TATAACACCAGCACGAATGCCTTCGGGACTTAGCCCGGA
41491388 TATAA
1 TATAA
41491393 TTCTCCATTA
Statistics
Matches: 148, Mismatches: 12, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
39 147 0.99
40 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.21, T:0.20
Consensus pattern (39 bp):
TATAACACCAGCACGAATGCCTTCGGGACTTAGCCCGGA
Found at i:41492686 original size:39 final size:39
Alignment explanation
Indices: 41492632--41492709 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
41492622 CTCTCCCTAA
41492632 ATCCAAATTCAGCATATTCAACAACCCAAATGCTAACCT
1 ATCCAAATTCAGCATATTCAACAACCCAAATGCTAACCT
*
41492671 ATCCAAATTCGGCATATTCAACAACCCAAATGCTAACCT
1 ATCCAAATTCAGCATATTCAACAACCCAAATGCTAACCT
41492710 CAACGTTTAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.40, C:0.31, G:0.06, T:0.23
Consensus pattern (39 bp):
ATCCAAATTCAGCATATTCAACAACCCAAATGCTAACCT
Found at i:41498693 original size:25 final size:27
Alignment explanation
Indices: 41498665--41498727 Score: 69
Period size: 26 Copynumber: 2.4 Consensus size: 27
41498655 AGTTATAAAT
41498665 ATTTTAATTTTGA-ATG-TAAAAATTC
1 ATTTTAATTTTGATATGATAAAAATTC
* * *
41498690 ATTTTACTTTT-ATATGATTACAATTC
1 ATTTTAATTTTGATATGATAAAAATTC
*
41498716 AATTTAATTTTG
1 ATTTTAATTTTG
41498728 TCTTACAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
24 1 0.03
25 13 0.43
26 16 0.53
ACGTcount: A:0.35, C:0.06, G:0.06, T:0.52
Consensus pattern (27 bp):
ATTTTAATTTTGATATGATAAAAATTC
Found at i:41498885 original size:24 final size:24
Alignment explanation
Indices: 41498858--41498911 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
41498848 TATTGTTCAC
41498858 TATTATATTATATTGATAATTAAA
1 TATTATATTATATTGATAATTAAA
* * * *
41498882 TATTTTTTTATATTTATTATTAAA
1 TATTATATTATATTGATAATTAAA
41498906 T-TTATA
1 TATTATA
41498912 AAACCTAATA
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
23 3 0.12
24 21 0.88
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (24 bp):
TATTATATTATATTGATAATTAAA
Found at i:41501226 original size:40 final size:40
Alignment explanation
Indices: 41501171--41501312 Score: 216
Period size: 40 Copynumber: 3.6 Consensus size: 40
41501161 TATTTGAATG
*
41501171 ATATCTGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
*
41501211 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTAACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* *
41501251 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGACT
*
41501291 ATATCC-GGCTAAATCCCGAAGG
1 ATATCCGGGCTAAGTCCCGAAGG
41501313 TACTTGGGTT
Statistics
Matches: 94, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
39 14 0.15
40 79 0.84
41 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
Found at i:41502708 original size:5 final size:5
Alignment explanation
Indices: 41502698--41502738 Score: 52
Period size: 5 Copynumber: 8.8 Consensus size: 5
41502688 AAACATTATA
*
41502698 ATATT ATATT ATATT ATATT AT-TT AT-TT -TATT ATAAT ATAT
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATAT
41502739 AATTAATAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
3 1 0.03
4 8 0.25
5 23 0.72
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
ATATT
Found at i:41503066 original size:17 final size:16
Alignment explanation
Indices: 41503036--41503069 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
41503026 AGCCGTACAC
41503036 TATATATTACTTATTA
1 TATATATTACTTATTA
*
41503052 TATATCATTATTTATTA
1 TATAT-ATTACTTATTA
41503069 T
1 T
41503070 TATGCTAGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (16 bp):
TATATATTACTTATTA
Found at i:41503455 original size:16 final size:17
Alignment explanation
Indices: 41503434--41503466 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
41503424 ATAATTATAG
41503434 TATTAAA-AATATTTTA
1 TATTAAATAATATTTTA
41503450 TATTAAATTAATATTTT
1 TATTAAA-TAATATTTT
41503467 TTAAATTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
18 8 0.53
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TATTAAATAATATTTTA
Found at i:41504948 original size:5 final size:5
Alignment explanation
Indices: 41504935--41504967 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
41504925 TTGTGTGTTC
*
41504935 TTTAT TTTAC TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
41504968 TTCATAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTAT
Found at i:41505209 original size:28 final size:28
Alignment explanation
Indices: 41505169--41505252 Score: 159
Period size: 28 Copynumber: 3.0 Consensus size: 28
41505159 AGATGAAGAG
*
41505169 AAGAAGCGTAAGGATCGGAAGGCGTTAA
1 AAGAAGCGTAAGGATCGAAAGGCGTTAA
41505197 AAGAAGCGTAAGGATCGAAAGGCGTTAA
1 AAGAAGCGTAAGGATCGAAAGGCGTTAA
41505225 AAGAAGCGTAAGGATCGAAAGGCGTTAA
1 AAGAAGCGTAAGGATCGAAAGGCGTTAA
41505253 CACAATTACA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 55 1.00
ACGTcount: A:0.42, C:0.11, G:0.33, T:0.14
Consensus pattern (28 bp):
AAGAAGCGTAAGGATCGAAAGGCGTTAA
Found at i:41511818 original size:36 final size:36
Alignment explanation
Indices: 41511771--41511845 Score: 132
Period size: 36 Copynumber: 2.1 Consensus size: 36
41511761 GCCCAAAGTT
* *
41511771 AATCACACAAATTCTTAACATGTTTTCTAGGAATTG
1 AATCACACAAATTCTTAACATGTCTTCCAGGAATTG
41511807 AATCACACAAATTCTTAACATGTCTTCCAGGAATTG
1 AATCACACAAATTCTTAACATGTCTTCCAGGAATTG
41511843 AAT
1 AAT
41511846 AACTCTTTCA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (36 bp):
AATCACACAAATTCTTAACATGTCTTCCAGGAATTG
Found at i:41519253 original size:46 final size:46
Alignment explanation
Indices: 41519178--41519330 Score: 171
Period size: 47 Copynumber: 3.2 Consensus size: 46
41519168 TGCACATAGT
* * ** * *
41519178 CACATATCACACACCGAGGCCATAGCCCAGCCATGGTCTTACACGGAT
1 CACATAT--CACACCGATGCCATATCCCAGAAATGGTCTTATACGGAG
* * *
41519226 CACGTATCACACTGATGCCATATCCCAGAAATGGTCTTATACAGTAG
1 CACATATCACACCGATGCCATATCCCAGAAATGGTCTTATAC-GGAG
* *
41519273 CACATATCACACCGATGCCATATCCCGGATATGGTCTTATACGGAAG
1 CACATATCACACCGATGCCATATCCCAGAAATGGTCTTATACGG-AG
41519320 CACATATCACA
1 CACATATCACA
41519331 TTTCTCCGAA
Statistics
Matches: 89, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
46 30 0.34
47 53 0.60
48 6 0.07
ACGTcount: A:0.31, C:0.30, G:0.17, T:0.22
Consensus pattern (46 bp):
CACATATCACACCGATGCCATATCCCAGAAATGGTCTTATACGGAG
Found at i:41519361 original size:52 final size:48
Alignment explanation
Indices: 41519178--41519384 Score: 168
Period size: 47 Copynumber: 4.2 Consensus size: 48
41519168 TGCACATAGT
* * * ** * *
41519178 CACATATCACACACCGAGGCCATAGCCCAGCCATGGTCTTACACGG-AT
1 CACATATCACA-TCCGAAGCCATATCCCAGATATGGTCTTATACGGAAG
* * * * * *
41519226 CACGTATCACA-CTGATGCCATATCCCAGAAATGGTCTTATACAGTAG
1 CACATATCACATCCGAAGCCATATCCCAGATATGGTCTTATACGGAAG
* *
41519273 CACATATCACA-CCGATGCCATATCCCGGATATGGTCTTATACGGAAG
1 CACATATCACATCCGAAGCCATATCCCAGATATGGTCTTATACGGAAG
* * *
41519320 CACATATCACATTTCTCCGAAGCCATAGCCCAGTTATGGTCTTATACGGAAAT
1 CACATATCACA----TCCGAAGCCATATCCCAGATATGGTCTTATACGG-AAG
*
41519373 CACATTTCACAT
1 CACATATCACAT
41519385 GCTGCCATGG
Statistics
Matches: 131, Mismatches: 21, Indels: 13
0.79 0.13 0.08
Matches are distributed among these distances:
46 26 0.20
47 53 0.40
48 10 0.08
49 1 0.01
52 29 0.22
53 12 0.09
ACGTcount: A:0.30, C:0.29, G:0.16, T:0.24
Consensus pattern (48 bp):
CACATATCACATCCGAAGCCATATCCCAGATATGGTCTTATACGGAAG
Found at i:41521733 original size:30 final size:30
Alignment explanation
Indices: 41521681--41521777 Score: 99
Period size: 30 Copynumber: 3.2 Consensus size: 30
41521671 TTATGGAGCA
41521681 AAGATAAGAAGAAAACC-GAATAAAGAAATCC
1 AAGAT-AG-AGAAAACCAGAATAAAGAAATCC
*
41521712 AAGATAGAGAAACCCAGAATAAAGAAATCC
1 AAGATAGAGAAAACCAGAATAAAGAAATCC
* * * * *
41521742 -AGAATAAAGAGATCCAGGATAAAGAAACCC
1 AAG-ATAGAGAAAACCAGAATAAAGAAATCC
41521772 AAGATA
1 AAGATA
41521778 CGATACTATG
Statistics
Matches: 57, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
29 9 0.16
30 41 0.72
31 7 0.12
ACGTcount: A:0.58, C:0.14, G:0.18, T:0.10
Consensus pattern (30 bp):
AAGATAGAGAAAACCAGAATAAAGAAATCC
Found at i:41521737 original size:15 final size:15
Alignment explanation
Indices: 41521689--41521768 Score: 92
Period size: 15 Copynumber: 5.4 Consensus size: 15
41521679 CAAAGATAAG
*
41521689 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
41521703 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
* *
41521718 GAGAAACCCAGAATA
1 AAGAAATCCAGAATA
41521733 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
* *
41521748 AAGAGATCCAGGATA
1 AAGAAATCCAGAATA
41521763 AAGAAA
1 AAGAAA
41521769 CCCAAGATAC
Statistics
Matches: 55, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
14 9 0.16
15 45 0.82
16 1 0.02
ACGTcount: A:0.59, C:0.14, G:0.17, T:0.10
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:41521777 original size:15 final size:15
Alignment explanation
Indices: 41521700--41521777 Score: 79
Period size: 15 Copynumber: 5.2 Consensus size: 15
41521690 AGAAAACCGA
41521700 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
* *
41521715 ATAGAGAAA-CCCAG
1 ATAAAGAAATCCAAG
41521729 AATAAAGAAATCC-AG
1 -ATAAAGAAATCCAAG
* *
41521744 AATAAAGAGATCCAGG
1 -ATAAAGAAATCCAAG
*
41521760 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
41521775 ATA
1 ATA
41521778 CGATACTATG
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
14 4 0.08
15 45 0.87
16 3 0.06
ACGTcount: A:0.56, C:0.15, G:0.17, T:0.12
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:41525494 original size:52 final size:48
Alignment explanation
Indices: 41525311--41525517 Score: 168
Period size: 47 Copynumber: 4.2 Consensus size: 48
41525301 TGCACATAGT
* * ** * *
41525311 CACATATCACATACCGAGGCCATAGCCCAGCCATGGTCTTACACGG-AT
1 CACATATCACAT-CCGAAGCCATATCCCAGATATGGTCTTATACGGAAG
* * * * * *
41525359 CACGTATCACA-CTGATGCCATATCCCAGAAATGGTCTTATACAGTAG
1 CACATATCACATCCGAAGCCATATCCCAGATATGGTCTTATACGGAAG
* *
41525406 CACATATCACA-CCGATGCCATATCCCGGATATGGTCTTATACGGAAG
1 CACATATCACATCCGAAGCCATATCCCAGATATGGTCTTATACGGAAG
* * * *
41525453 CACATATCACATTTCTCCGAAGCCATAGCCCAGTTATGGTCTTATACAGAAAT
1 CACATATCACA----TCCGAAGCCATATCCCAGATATGGTCTTATAC-GGAAG
*
41525506 CACATTTCACAT
1 CACATATCACAT
41525518 GCTGCCATGG
Statistics
Matches: 130, Mismatches: 22, Indels: 13
0.79 0.13 0.08
Matches are distributed among these distances:
46 26 0.20
47 53 0.41
48 10 0.08
49 1 0.01
52 27 0.21
53 13 0.10
ACGTcount: A:0.31, C:0.29, G:0.16, T:0.25
Consensus pattern (48 bp):
CACATATCACATCCGAAGCCATATCCCAGATATGGTCTTATACGGAAG
Found at i:41531491 original size:40 final size:40
Alignment explanation
Indices: 41531446--41531637 Score: 226
Period size: 40 Copynumber: 4.8 Consensus size: 40
41531436 ATAACCACAA
* * *
41531446 GCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAGCAACTC
*
41531486 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAGCAACTC
* * *
41531526 GCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATC-ACTA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGAT-ATAGCAACTC
* * * * *
41531566 GCATAAATGCCTTCGGGACTTAGCCCGGATAAAATC-ACTA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGAT-ATAGCAACTC
* *
41531606 GCATAAATGCCTTCGGGACTTAGCCCGGATAT
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATAT
41531638 CATTCAAATG
Statistics
Matches: 142, Mismatches: 9, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
39 1 0.01
40 137 0.96
41 4 0.03
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAGCCCGGATATAGCAACTC
Found at i:41531530 original size:80 final size:80
Alignment explanation
Indices: 41531417--41531636 Score: 248
Period size: 80 Copynumber: 2.8 Consensus size: 80
41531407 ACCCAAGTTT
* * * * * * * * *
41531417 CTTCGGAATTTAG-CCGGATATAACCACAAGCACAATTGCCTTCGGGTCTTAACCCGGGT-ATAG
1 CTTCGGGACTTAGCCCGGATAAAATCACTAGCACAAATGCCTTCGGGTCTTAGCCCGGATAAAAG
*
41531480 CAACTCGCACAAATGC
66 C-ACTAGCACAAATGC
* * *
41531496 CTTCGGGTCTTAGCCCGGAT-ATATCAACTCGCACAAATGCCTTCGGGTCTTAGCCCGGATAAAA
1 CTTCGGGACTTAGCCCGGATAAAATC-ACTAGCACAAATGCCTTCGGGTCTTAGCCCGGATAAAA
* *
41531560 TCACTAGCATAAATGC
65 GCACTAGCACAAATGC
* *
41531576 CTTCGGGACTTAGCCCGGATAAAATCACTAGCATAAATGCCTTCGGGACTTAGCCCGGATA
1 CTTCGGGACTTAGCCCGGATAAAATCACTAGCACAAATGCCTTCGGGTCTTAGCCCGGATA
41531637 TCATTCAAAT
Statistics
Matches: 117, Mismatches: 20, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
79 12 0.10
80 98 0.84
81 7 0.06
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (80 bp):
CTTCGGGACTTAGCCCGGATAAAATCACTAGCACAAATGCCTTCGGGTCTTAGCCCGGATAAAAG
CACTAGCACAAATGC
Found at i:41535762 original size:16 final size:16
Alignment explanation
Indices: 41535741--41535772 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
41535731 TCACAAAAAC
41535741 ACAAAAATTTCAAGAA
1 ACAAAAATTTCAAGAA
41535757 ACAAAAATTTCAAGAA
1 ACAAAAATTTCAAGAA
41535773 TTAATCAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.62, C:0.12, G:0.06, T:0.19
Consensus pattern (16 bp):
ACAAAAATTTCAAGAA
Found at i:41537478 original size:12 final size:12
Alignment explanation
Indices: 41537446--41537484 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
41537436 TAAAATTAAA
41537446 AAATTAA-AAC-
1 AAATTAAGAACT
41537456 AAATT-AGAACT
1 AAATTAAGAACT
41537467 AAATTAAGAACT
1 AAATTAAGAACT
41537479 AAATTA
1 AAATTA
41537485 TATTAATAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
9 1 0.04
10 8 0.31
11 5 0.19
12 12 0.46
ACGTcount: A:0.62, C:0.08, G:0.05, T:0.26
Consensus pattern (12 bp):
AAATTAAGAACT
Found at i:41537553 original size:15 final size:15
Alignment explanation
Indices: 41537533--41537562 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
41537523 AAAAACAACA
41537533 AAAAAAAAGTAAAGT
1 AAAAAAAAGTAAAGT
*
41537548 AAAAAAAATTAAAGT
1 AAAAAAAAGTAAAGT
41537563 TACTTAAAAT
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:0.73, C:0.00, G:0.10, T:0.17
Consensus pattern (15 bp):
AAAAAAAAGTAAAGT
Found at i:41541673 original size:18 final size:18
Alignment explanation
Indices: 41541639--41541673 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
41541629 AAATAGTTCG
*
41541639 AGTTATTTGAGTTAATTA
1 AGTTATTTGAGTCAATTA
*
41541657 AGTTATTTGGGTCAATT
1 AGTTATTTGAGTCAATT
41541674 CGAATAAAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.03, G:0.20, T:0.49
Consensus pattern (18 bp):
AGTTATTTGAGTCAATTA
Found at i:41542262 original size:11 final size:11
Alignment explanation
Indices: 41542223--41542263 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
41542213 ACAATAATAA
41542223 CAAAATAGTAG
1 CAAAATAGTAG
* *
41542234 CAACATAATAG
1 CAAAATAGTAG
*
41542245 TAAAATAGTAG
1 CAAAATAGTAG
41542256 CAAAATAG
1 CAAAATAG
41542264 GGAGAAAACT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.56, C:0.10, G:0.15, T:0.20
Consensus pattern (11 bp):
CAAAATAGTAG
Found at i:41544526 original size:2 final size:2
Alignment explanation
Indices: 41544519--41544546 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
41544509 GGCTTAAAGT
41544519 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
41544547 ATTAAAAAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.