Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A13
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: 109233746
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2708888 characters in sequence are not A, C, G, or T
File 196 of 332
Found at i:65259033 original size:29 final size:28
Alignment explanation
Indices: 65258970--65259067 Score: 96
Period size: 29 Copynumber: 3.5 Consensus size: 28
65258960 CATGAGATTG
* * * *
65258970 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
65258999 GC-CTAAAGTGTGCGAGTTTGATTATATA
1 GCACT-AAGTGTGCGAGTTTGATTATATA
65259027 GCACTAAGTGTGCCGAG-TTG-TTATATA
1 GCACTAAGTGTG-CGAGTTTGATTATATA
*
65259054 GCA-TGAGTGTGCGA
1 GCACTAAGTGTGCGA
65259068 ACTTAATATA
Statistics
Matches: 61, Mismatches: 5, Indels: 10
0.80 0.07 0.13
Matches are distributed among these distances:
25 3 0.05
26 7 0.11
27 10 0.16
28 20 0.33
29 21 0.34
ACGTcount: A:0.27, C:0.13, G:0.29, T:0.32
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:65267191 original size:27 final size:28
Alignment explanation
Indices: 65267107--65267204 Score: 135
Period size: 27 Copynumber: 3.5 Consensus size: 28
65267097 CATGAGATTG
* * * *
65267107 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
65267136 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
65267164 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
65267191 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
65267205 GACTTAATAT
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 24 0.38
28 22 0.34
29 18 0.28
ACGTcount: A:0.27, C:0.13, G:0.29, T:0.32
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:65267215 original size:27 final size:27
Alignment explanation
Indices: 65267135--65267217 Score: 96
Period size: 27 Copynumber: 3.0 Consensus size: 27
65267125 TAAATTGTAC
* *
65267135 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
65267163 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTGAATATAT
*
65267190 AGCACTGAGTGTGCGGACTT-AATATAT
1 AGCACTAAGTGTGC-GACTTGAATATAT
65267217 A
1 A
65267218 TTTTGAATCA
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
27 30 0.60
28 20 0.40
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTGAATATAT
Found at i:65267218 original size:29 final size:27
Alignment explanation
Indices: 65267107--65267218 Score: 98
Period size: 28 Copynumber: 4.0 Consensus size: 27
65267097 CATGAGATTG
** * *
65267107 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGC-GACTT-AATTATATA
* *
65267136 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGA-CTTAATTATATA
* *
65267164 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGACTTAATTATATA
*
65267191 GCACTGAGTGTGCGGACTTAATATATAT
1 GCACTAAGTGTGC-GACTTAAT-TATAT
65267219 TTTGAATCAC
Statistics
Matches: 72, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
27 23 0.32
28 28 0.39
29 21 0.29
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (27 bp):
GCACTAAGTGTGCGACTTAATTATATA
Found at i:65272183 original size:32 final size:32
Alignment explanation
Indices: 65272146--65272207 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 32
65272136 AGAATATTGC
65272146 TTATAA-ATCTCAAATGACTACATGTAAAATAT
1 TTATAACATCTC-AATGACTACATGTAAAATAT
* *
65272178 TTATAACGTTTCAATGACTACATGTAAAAT
1 TTATAACATCTCAATGACTACATGTAAAAT
65272208 GTTATAAGTG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
32 24 0.89
33 3 0.11
ACGTcount: A:0.44, C:0.13, G:0.08, T:0.35
Consensus pattern (32 bp):
TTATAACATCTCAATGACTACATGTAAAATAT
Found at i:65272996 original size:26 final size:25
Alignment explanation
Indices: 65272963--65273014 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 25
65272953 TAAGATTTTT
* *
65272963 ATTAAATT-ATATATCATTTTATTAA
1 ATTAAATTAATA-ATAATTATATTAA
65272988 ATTATAATTAATAATAATTATATTAA
1 ATTA-AATTAATAATAATTATATTAA
65273014 A
1 A
65273015 ATATGGTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
25 4 0.17
26 16 0.70
27 3 0.13
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (25 bp):
ATTAAATTAATAATAATTATATTAA
Found at i:65273042 original size:58 final size:57
Alignment explanation
Indices: 65272964--65273074 Score: 143
Period size: 58 Copynumber: 1.9 Consensus size: 57
65272954 AAGATTTTTA
65272964 TTAAATTATATATCATTTTATTAAATTATAATTAATAATAAT-TATATTAAAATATGG
1 TTAAATTATATATCATTTTATTAAATTATAATTAATAATAATCT-TATTAAAATATGG
* * * ** *
65273021 TTAAATTATTTATTATATTTATTATATTATTTTTGATAATAATCTTATTAAAAT
1 TTAAATTATATATCAT-TTTATTAAATTATAATTAATAATAATCTTATTAAAAT
65273075 TTAATAAGAA
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
57 14 0.30
58 31 0.67
59 1 0.02
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.52
Consensus pattern (57 bp):
TTAAATTATATATCATTTTATTAAATTATAATTAATAATAATCTTATTAAAATATGG
Found at i:65273258 original size:16 final size:16
Alignment explanation
Indices: 65273236--65273307 Score: 92
Period size: 16 Copynumber: 4.5 Consensus size: 16
65273226 TGAATTATTG
*
65273236 ATTACAGCTTTATTCC
1 ATTACAGCTCTATTCC
*
65273252 GTTACAGCTCTATTCC
1 ATTACAGCTCTATTCC
*
65273268 ATTACAGCTCTATTCA
1 ATTACAGCTCTATTCC
65273284 ATTACAGCAT-TATTCC
1 ATTACAGC-TCTATTCC
*
65273300 ATAACAGC
1 ATTACAGC
65273308 CAACCAAATA
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
16 48 0.98
17 1 0.02
ACGTcount: A:0.29, C:0.26, G:0.08, T:0.36
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:65288042 original size:44 final size:43
Alignment explanation
Indices: 65287989--65288087 Score: 110
Period size: 42 Copynumber: 2.3 Consensus size: 43
65287979 TGGCAAGTTT
* * * *
65287989 GTCTTGAGACATAAAGTGTCTAAGTTTCAAGACATGGTTACATC
1 GTCTCGAGACATAAAGGGT-TAAATCTCAAGACATGGTTACATC
* * *
65288033 GTCTCGAGACAT-AAGGGTTAAATCTCGAGACATGGTTCCATT
1 GTCTCGAGACATAAAGGGTTAAATCTCAAGACATGGTTACATC
*
65288075 ATCTCGAGACATA
1 GTCTCGAGACATA
65288088 GAACTTCAAA
Statistics
Matches: 46, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
42 30 0.65
43 5 0.11
44 11 0.24
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.29
Consensus pattern (43 bp):
GTCTCGAGACATAAAGGGTTAAATCTCAAGACATGGTTACATC
Found at i:65288044 original size:21 final size:20
Alignment explanation
Indices: 65288018--65288086 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 20
65288008 CTAAGTTTCA
*
65288018 AGACATGGTTACATCGTCTCG
1 AGACATGGTTACAT-ATCTCG
65288039 AGACATAAGGGTTA-A-ATCTCG
1 AGACAT---GGTTACATATCTCG
*
65288060 AGACATGGTTCCATTATCTCG
1 AGACATGGTTACA-TATCTCG
65288081 AGACAT
1 AGACAT
65288087 AGAACTTCAA
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
18 4 0.10
19 1 0.03
21 29 0.73
23 1 0.03
24 5 0.12
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (20 bp):
AGACATGGTTACATATCTCG
Found at i:65288788 original size:27 final size:27
Alignment explanation
Indices: 65288758--65288813 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 27
65288748 AAAAATAAGC
*
65288758 AAGGACAAATGCACAAAGACTAGTTAT
1 AAGGACAAATCCACAAAGACTAGTTAT
* * * *
65288785 AAGGTCGAATCCACAAAGAGTCGTTAT
1 AAGGACAAATCCACAAAGACTAGTTAT
65288812 AA
1 AA
65288814 TATTTCTTTA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.45, C:0.16, G:0.20, T:0.20
Consensus pattern (27 bp):
AAGGACAAATCCACAAAGACTAGTTAT
Found at i:65291110 original size:22 final size:22
Alignment explanation
Indices: 65291084--65291128 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
65291074 CTAAACATTT
65291084 CCTTAGTCTAATAGGAAATGAG
1 CCTTAGTCTAATAGGAAATGAG
*
65291106 CCTTAGTCTAGTAGGAAATGAG
1 CCTTAGTCTAATAGGAAATGAG
65291128 C
1 C
65291129 AAATCGATTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.27
Consensus pattern (22 bp):
CCTTAGTCTAATAGGAAATGAG
Found at i:65300826 original size:228 final size:227
Alignment explanation
Indices: 65300387--65300853 Score: 691
Period size: 228 Copynumber: 2.1 Consensus size: 227
65300377 CACGGCCAAC
* * * *
65300387 CACACGCTCGTGCAACCAGCCCGTGTGCCCTTAGAAATGCCACACATACCCATGTTCCAGGCCAT
1 CACACGCCCGTGCAACCAACCCGTCTGCCCTTAGAAATGCCACACATACCCATGTGCCAGGCCAT
* * * *
65300452 GTGATAGGCCATGCCAAAACTGTAGGGTATATTGACTTATGCTACACGGCCAAGTTACATGCCAG
66 GTGATAGGCCATGCCAAAACTGTAGGGTATACTGACTTATGCCACACGGCCAAGTCACATGCCAA
* *
65300517 TGTGCTGGGCCGTGTAGAGCATACTGACTTGGTTTCTAATTAAACACCAGGTGACACACGACCGT
131 TGTGCTGGGCCGTATAGAGCATACTGACTTGGTTTCTAATTAAACACCAGGGGACACACGACCGT
* * * *
65300582 GTCACTTGACCGAGTGTCACATACGGTTGAGA
196 GTCACCTAACCGAGTGTCACACACGGCTGAGA
* * * * *
65300614 CACATGCCCGTGCGACCAACCCGTCTGCCCTTAGAAATGGCCACACATGCCCGTGTGCCAGGCCG
1 CACACGCCCGTGCAACCAACCCGTCTGCCCTTAGAAAT-GCCACACATACCCATGTGCCAGGCCA
* **
65300679 TGTGCTAGGCTGTGCCAAAACTGTAGGGTATACTGACTTATGCCACACGGCCAAGTCACATGCCA
65 TGTGATAGGCCATGCCAAAACTGTAGGGTATACTGACTTATGCCACACGGCCAAGTCACATGCCA
* *
65300744 ATGTGCTGGGCCGTATGGAGCATACTGACTTGGTTTCTAATTAAACACCAGGGGACACACGATCG
130 ATGTGCTGGGCCGTATAGAGCATACTGACTTGGTTTCTAATTAAACACCAGGGGACACACGACCG
* *
65300809 TGTCACCTAATCGAGTGTCACACATGGCTGAGA
195 TGTCACCTAACCGAGTGTCACACACGGCTGAGA
65300842 CACACGCCCGTG
1 CACACGCCCGTG
65300854 TCTTTACCCG
Statistics
Matches: 212, Mismatches: 27, Indels: 1
0.88 0.11 0.00
Matches are distributed among these distances:
227 33 0.16
228 179 0.84
ACGTcount: A:0.25, C:0.28, G:0.25, T:0.22
Consensus pattern (227 bp):
CACACGCCCGTGCAACCAACCCGTCTGCCCTTAGAAATGCCACACATACCCATGTGCCAGGCCAT
GTGATAGGCCATGCCAAAACTGTAGGGTATACTGACTTATGCCACACGGCCAAGTCACATGCCAA
TGTGCTGGGCCGTATAGAGCATACTGACTTGGTTTCTAATTAAACACCAGGGGACACACGACCGT
GTCACCTAACCGAGTGTCACACACGGCTGAGA
Found at i:65305387 original size:21 final size:21
Alignment explanation
Indices: 65305363--65305404 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
65305353 TTGAACCTAG
65305363 GACCTAGAGAAATTAATTAAA
1 GACCTAGAGAAATTAATTAAA
65305384 GACCTAGAGAAATTAATTAAA
1 GACCTAGAGAAATTAATTAAA
65305405 CACTTAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.52, C:0.10, G:0.14, T:0.24
Consensus pattern (21 bp):
GACCTAGAGAAATTAATTAAA
Found at i:65309342 original size:96 final size:93
Alignment explanation
Indices: 65309229--65309724 Score: 362
Period size: 96 Copynumber: 5.4 Consensus size: 93
65309219 TTTAAATTAA
*
65309229 ATTTTAGGTTTTT-ATATTTTAATATTAAGTTTAAACATTAAATTAATTAGATTTTTATTTTAGG
1 ATTTTAGATTTTTAATATTTTAATATTAAGTTTAAA-ATT-AATT-ATTAGATTTTTATTTTAGG
* *
65309293 TTTTTATATTAAGTTTTAAATTAATTTTTTG
63 TTTTGATATTAAGTTTTAAATTAATTTTTCG
* * ** ** *
65309324 ATTTTCGATTTTTAATATTTTAATATTAAGTAT-ATTTTTTTCTTTTAGA-TTTTAGGTTTTAGG
1 ATTTTAGATTTTTAATATTTTAATATTAAGTTTAAAATTAAT-TATTAGATTTTTA--TTTTAGG
*
65309387 TTTTGATATT-AGATTTTAAATTAGATATTTCG
63 TTTTGATATTAAG-TTTTAAATTA-ATTTTTCG
** * * * * * * * *
65309419 AAATTATATTTTTAATATTTTAATATTAAATTTTAAATTAGTCATTTATATTTTAGATTTTGGGT
1 ATTTTAGATTTTTAATATTTTAATATTAAGTTTAAAATTAATTA-TTAGATTTT-TATTTTAGGT
* * * *
65309484 TTTGACATTAGGTTTTAAATTAAAATTTTCA
64 TTTGATATTAAGTTTTAAATT-AATTTTTCG
* *
65309515 ATTTTAGATTTTTAAGATTTTAATATTAA-TTT---A-T--TT-TTAG------ATTTTAGATTT
1 ATTTTAGATTTTTAATATTTTAATATTAAGTTTAAAATTAATTATTAGATTTTTATTTTAGGTTT
* *
65309566 TGATATTAAGTTTTAAATTATATCTTTGG
66 TGATATTAAGTTTTAAATTA-ATTTTTCG
* * * * * * *
65309595 ATTTTATATTTTTAATATTTTAATGTTAAGTTTTAAATTAAACTTTTTAGATTTTAAATGTTGGG
1 ATTTTAGATTTTTAATATTTTAATATTAAGTTTAAAATT-AA-TTATTAGATTTT-TATTTTAGG
* *
65309660 TTTTGATATTAGGTTTTAAATTAAATTGTTCG
63 TTTTGATATTAAGTTTTAAATT-AATTTTTCG
* *
65309692 ATTTTATATTTTTAGTATTTTAATATTAAGTTT
1 ATTTTAGATTTTTAATATTTTAATATTAAGTTT
65309725 TTAGATTTTA
Statistics
Matches: 313, Mismatches: 57, Indels: 60
0.73 0.13 0.14
Matches are distributed among these distances:
79 1 0.00
80 56 0.18
81 3 0.01
84 1 0.00
85 1 0.00
87 3 0.01
89 3 0.01
90 4 0.01
91 1 0.00
92 6 0.02
93 8 0.03
94 29 0.09
95 48 0.15
96 80 0.26
97 67 0.21
98 2 0.01
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.57
Consensus pattern (93 bp):
ATTTTAGATTTTTAATATTTTAATATTAAGTTTAAAATTAATTATTAGATTTTTATTTTAGGTTT
TGATATTAAGTTTTAAATTAATTTTTCG
Found at i:65309350 original size:48 final size:50
Alignment explanation
Indices: 65309223--65309354 Score: 125
Period size: 48 Copynumber: 2.7 Consensus size: 50
65309213 TTAAGCTTTA
* *
65309223 AATTAAATTTTAGGTTTTT-ATATTTTAATATTAAGTTTAAACATTAAATT
1 AATTAGATTTT-GATTTTTAATATTTTAATATTAAGTTTAAACATTAAATT
* * *
65309273 AATTAGATTTTTA-TTTTAGGT-TTTT-ATATTAAGTTTTAA-ATT-AATT
1 AATTAGATTTTGATTTTTA-ATATTTTAATATTAAGTTTAAACATTAAATT
* *
65309319 -TTTTGATTTTCGATTTTTAATATTTTAATATTAAGT
1 AATTAGATTTT-GATTTTTAATATTTTAATATTAAGT
65309355 ATATTTTTTT
Statistics
Matches: 67, Mismatches: 9, Indels: 14
0.74 0.10 0.16
Matches are distributed among these distances:
45 8 0.12
46 6 0.09
47 12 0.18
48 26 0.39
49 4 0.06
50 11 0.16
ACGTcount: A:0.34, C:0.02, G:0.08, T:0.57
Consensus pattern (50 bp):
AATTAGATTTTGATTTTTAATATTTTAATATTAAGTTTAAACATTAAATT
Found at i:65309554 original size:80 final size:81
Alignment explanation
Indices: 65309462--65309623 Score: 211
Period size: 80 Copynumber: 2.0 Consensus size: 81
65309452 TAAATTAGTC
* * *
65309462 ATTTATATTTTAGATTTTGGGTTTTGACATTAGGTTTTAAATTAAAAT-TTTCAATTTTAGATTT
1 ATTTATATTTTAGATTTTAGATTTTGACATTAAGTTTTAAATT-AAATCTTTCAATTTTAGATTT
65309526 TTAAGATTTTAATATTA
65 TTAAGATTTTAATATTA
* * ** *
65309543 ATTTAT-TTTTAGATTTTAGATTTTGATATTAAGTTTTAAATTATATCTTTGGATTTTATATTTT
1 ATTTATATTTTAGATTTTAGATTTTGACATTAAGTTTTAAATTAAATCTTTCAATTTTAGATTTT
* *
65309607 TAATATTTTAATGTTA
66 TAAGATTTTAATATTA
65309623 A
1 A
65309624 GTTTTAAATT
Statistics
Matches: 70, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
79 3 0.04
80 61 0.87
81 6 0.09
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.57
Consensus pattern (81 bp):
ATTTATATTTTAGATTTTAGATTTTGACATTAAGTTTTAAATTAAATCTTTCAATTTTAGATTTT
TAAGATTTTAATATTA
Found at i:65309607 original size:176 final size:174
Alignment explanation
Indices: 65309373--65309810 Score: 578
Period size: 176 Copynumber: 2.5 Consensus size: 174
65309363 TTCTTTTAGA
* * **
65309373 TTTTAGGTTTTAGGTTTTGATATT-AGATTTTAAATTAGATATTTCGAAATTATATTTTTAATAT
1 TTTTAGATTTTAGGTTTTGATATTAAG-TTTTAAATTAGATCTTTCGATTTTATATTTTTAATAT
* * * * *
65309437 TTTAATATTAAATTTTAAATTAGTC-ATTTATATTTTAGATTTTGGGTTTTGACATTAGGTTTTA
65 TTTAATATTAAGTTTTAAATTAGACTATTTAGATTTTAAATGTTGGGTTTTGACATTAGGTTTTA
65309501 AATTAAAATT-TTCAATTTTAGATTTTTAAG-ATTTTAATATTAATTTAT
130 AATT-AAATTGTTCAATTTTAGATTTTT-AGTATTTTAATATTAA---AT
* * *
65309549 TTTTAGATTTTAGATTTTGATATTAAGTTTTAAATTATATCTTTGGATTTTATATTTTTAATATT
1 TTTTAGATTTTAGGTTTTGATATTAAGTTTTAAATTAGATCTTTCGATTTTATATTTTTAATATT
* * * *
65309614 TTAATGTTAAGTTTTAAATTAAACTTTTTAGATTTTAAATGTTGGGTTTTGATATTAGGTTTTAA
66 TTAATATTAAGTTTTAAATTAGACTATTTAGATTTTAAATGTTGGGTTTTGACATTAGGTTTTAA
* * *
65309679 ATTAAATTGTTCGATTTTATATTTTTAGTATTTTAATATTAAGT
131 ATTAAATTGTTCAATTTTAGATTTTTAGTATTTTAATATTAAAT
* * *
65309723 TTTTAGATTTTAGGTTTTGATATTAGGTTTTAAATTAGATCTTTCAATTTTATATTTTTAAAATT
1 TTTTAGATTTTAGGTTTTGATATTAAGTTTTAAATTAGATCTTTCGATTTTATATTTTTAATATT
* *
65309788 TAAATATTAAGTGTTAAATTAGA
66 TTAATATTAAGTTTTAAATTAGA
65309811 TTTTTTTTAT
Statistics
Matches: 229, Mismatches: 29, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
174 79 0.34
176 82 0.36
177 68 0.30
ACGTcount: A:0.32, C:0.02, G:0.11, T:0.55
Consensus pattern (174 bp):
TTTTAGATTTTAGGTTTTGATATTAAGTTTTAAATTAGATCTTTCGATTTTATATTTTTAATATT
TTAATATTAAGTTTTAAATTAGACTATTTAGATTTTAAATGTTGGGTTTTGACATTAGGTTTTAA
ATTAAATTGTTCAATTTTAGATTTTTAGTATTTTAATATTAAAT
Found at i:65309624 original size:49 final size:48
Alignment explanation
Indices: 65309556--65309725 Score: 175
Period size: 49 Copynumber: 3.5 Consensus size: 48
65309546 TATTTTTAGA
* * *
65309556 TTTTAG-ATTTTGATATTAAGTTTTAAATTATATCTTTGGATTTTATAT
1 TTTTAGTATTTTAATATTAAGTTTTAAATTAAAT-TTTAGATTTTATAT
* * *
65309604 TTTTAATATTTTAATGTTAAGTTTTAAATTAAACTTTTTAGATTTTA-AA
1 TTTTAGTATTTTAATATTAAGTTTTAAATTAAA--TTTTAGATTTTATAT
* ** * * *
65309653 TGTT-GGGTTTTGATATTAGGTTTTAAATTAAATTGTTCGATTTTATAT
1 TTTTAGTATTTTAATATTAAGTTTTAAATTAAATT-TTAGATTTTATAT
65309701 TTTTAGTATTTTAATATTAAGTTTT
1 TTTTAGTATTTTAATATTAAGTTTT
65309726 TAGATTTTAG
Statistics
Matches: 96, Mismatches: 20, Indels: 11
0.76 0.16 0.09
Matches are distributed among these distances:
46 2 0.02
47 9 0.09
48 31 0.32
49 43 0.45
50 10 0.10
51 1 0.01
ACGTcount: A:0.30, C:0.02, G:0.11, T:0.57
Consensus pattern (48 bp):
TTTTAGTATTTTAATATTAAGTTTTAAATTAAATTTTAGATTTTATAT
Found at i:65309823 original size:77 final size:73
Alignment explanation
Indices: 65309660--65309823 Score: 186
Period size: 77 Copynumber: 2.1 Consensus size: 73
65309650 AAATGTTGGG
* * ** *
65309660 TTTTGATATTAGGTTTTAAATTAAATTGTTCGATTTTATATTTTTAGTATTTTAATATTAAGTTT
1 TTTTTATATTAGGTTTTAAATTAAATTGTTCAATTTTATATTTTTAAAATTTAAATATTAAGTTT
65309725 TTAGATTT
66 TTAGATTT
*
65309733 TAGGTTTTGATATTAGGTTTTAAATTAGATCT-TTCAATTTTATATTTTTAAAATTTAAATATTA
1 T---TTTT-ATATTAGGTTTTAAATTAAAT-TGTTCAATTTTATATTTTTAAAATTTAAATATTA
65309797 AGTGTTAAATTAGATTT
61 AGT-TT---TTAGATTT
65309814 TTTTTATATT
1 TTTTTATATT
65309824 TTAAGATTTT
Statistics
Matches: 76, Mismatches: 6, Indels: 14
0.79 0.06 0.15
Matches are distributed among these distances:
73 1 0.01
76 3 0.04
77 56 0.74
78 7 0.09
81 9 0.12
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.57
Consensus pattern (73 bp):
TTTTTATATTAGGTTTTAAATTAAATTGTTCAATTTTATATTTTTAAAATTTAAATATTAAGTTT
TTAGATTT
Found at i:65316561 original size:48 final size:48
Alignment explanation
Indices: 65316483--65316910 Score: 240
Period size: 50 Copynumber: 8.8 Consensus size: 48
65316473 AGGGTTATTC
* *
65316483 GAGAGCTAGTGTAAGACCATGTTTGGGACATGGCATCAACCTGGACAT
1 GAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCAACCTGGACAT
* ** * * *
65316531 GTGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGATAT
1 GAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCAACCTGGACAT
* * * * * *
65316579 GAGTGCTAGTGTAAGACCATGTTTGGAACATGGCATCGACACC-GATAGAT
1 GAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATC-A-ACCTG-GACAT
* * * * ** * *
65316629 GAGAGCCATTATAAGATCATGTCTGGTACATGGCATC-GGCTATGAGAT
1 GAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCAACCT-GGACAT
* * * * * **
65316677 --GTGTCAGTGTAAGACCATCTCTAGGATATGGCATTGGCACAAATGGAC--
1 GAGAGCCAGTGTAAGACCATGTCTGGGACATGGCA-T--CA-ACCTGGACAT
* ** * *
65316725 GAGAGTCAGTGTAAGACCATG-CTTGGGACATGGCATCGGCCTCGATAT
1 GAGAGCCAGTGTAAGACCATGTC-TGGGACATGGCATCAACCTGGACAT
** * * *
65316773 ACGAGAGTTAGTGTAAGACCATGTCTGGGACATGGCATCAGCCTCGATACAC
1 --GAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCAACCT-G-GACAT
* * * * * * * * *
65316825 AATAGTCAGTGTAAGACCATGTCTAGGACATGGCATCGACTTTGATAC
1 GAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCAACCTGGACAT
* *
65316873 GTGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCA
1 GAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCA
65316911 GCTTTCTACC
Statistics
Matches: 283, Mismatches: 77, Indels: 40
0.71 0.19 0.10
Matches are distributed among these distances:
46 27 0.10
47 3 0.01
48 110 0.39
49 3 0.01
50 136 0.48
51 2 0.01
52 2 0.01
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.24
Consensus pattern (48 bp):
GAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCAACCTGGACAT
Found at i:65316686 original size:96 final size:96
Alignment explanation
Indices: 65316487--65316910 Score: 308
Period size: 98 Copynumber: 4.4 Consensus size: 96
65316477 TTATTCGAGA
* * *
65316487 GCTAGTGTAAGACCATGTTTGGGACATGGCATCAACCTGGACATGTGAGCCAGTGTAAGACCATG
1 GCTAGTGTAAGACCATGTTTGGAACATGGCATCAACCTGGACATGAGAGCCAGTATAAGACCATG
*
65316552 TCTGGGACATGGCATCGGCATTGATATGAGT
66 TCTGGGACATGGCATCGGCATTGAGATGAGT
* * * *
65316583 GCTAGTGTAAGACCATGTTTGGAACATGGCATCGACACC-GATAGATGAGAGCCATTATAAGATC
1 GCTAGTGTAAGACCATGTTTGGAACATGGCATC-A-ACCTG-GACATGAGAGCCAGTATAAGACC
* *
65316647 ATGTCTGGTACATGGCATCGGC-TATGAGATGTGT
63 ATGTCTGGGACATGGCATCGGCAT-TGAGATGAGT
* * * * *
65316681 -C-AGTGTAAGACCATCTCTAGGATATGGCATTGGCA-CAA-ATGGAC--GAGAGTCAGTGTAAG
1 GCTAGTGTAAGACCATGT-TTGGA-A---CA-TGGCATCAACCTGGACATGAGAGCCAGTATAAG
* * * *
65316740 ACCATG-CTTGGGACATGGCATCGGCCTCGATATACGAGA
60 ACCATGTC-TGGGACATGGCATCGGCATTGAGAT--GAGT
* * * * * ** * * *
65316779 GTTAGTGTAAGACCATGTCTGGGACATGGCATCAGCCTCGATACACAATAGTCAGTGTAAGACCA
1 GCTAGTGTAAGACCATGTTTGGAACATGGCATCAACCT-G-GACATGAGAGCCAGTATAAGACCA
* * * * * * *
65316844 TGTCTAGGACATGGCATCGACTTTGATACGTGA
64 TGTCTGGGACATGGCATCGGCATTGAGATGAGT
* *
65316877 GCTAGTGTAAGACCATGTCTGGGACATGGCATCA
1 GCTAGTGTAAGACCATGTTTGGAACATGGCATCA
65316911 GCTTTCTACC
Statistics
Matches: 263, Mismatches: 41, Indels: 46
0.75 0.12 0.13
Matches are distributed among these distances:
94 5 0.02
95 5 0.02
96 84 0.32
97 10 0.04
98 92 0.35
99 4 0.02
100 54 0.21
101 4 0.02
102 5 0.02
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.25
Consensus pattern (96 bp):
GCTAGTGTAAGACCATGTTTGGAACATGGCATCAACCTGGACATGAGAGCCAGTATAAGACCATG
TCTGGGACATGGCATCGGCATTGAGATGAGT
Found at i:65320891 original size:130 final size:126
Alignment explanation
Indices: 65320684--65320936 Score: 319
Period size: 130 Copynumber: 2.0 Consensus size: 126
65320674 AATTAACAAA
* * * * *
65320684 ATTATTAATATATACAATTGATGGAGATCATAAATTGTGCTATTAAAATAAAAATGTATAGAACT
1 ATTACTAATATATACAACTGAGGGAGATAATAAATTATGCTATTAAAATAAAAATGTATAGAACT
* * * * *
65320749 TATCAAGATGAAGTTTTGGTTGAGTGGTAAATTTAAGTTTTTACCAATCCAATTGGTGCAC
66 TATCAAAATGAAGCTTTGGTTGACTGGTAAATTTAAGGTTTTACCAATCCAACTGGTGCAC
*
65320810 ATTACTAATATATGCAACTGAGGGAGATAATAAATTATGCATATTAAAATAAAGAAAATGTATA-
1 ATTACTAATATATACAACTGAGGGAGATAATAAATTATGC-TATTAAAAT--A-AAAATGTATAG
* * * *
65320874 AATTATATTAAAATGAAGCTTTGGTTGACTGGTAAATTTAAGGTTTTACTAATTCAACTGGTG
62 AACT-TATCAAAATGAAGCTTTGGTTGACTGGTAAATTTAAGGTTTTACCAATCCAACTGGTG
65320937 TAGGTTTAAA
Statistics
Matches: 107, Mismatches: 15, Indels: 6
0.84 0.12 0.05
Matches are distributed among these distances:
126 34 0.32
127 9 0.08
129 4 0.04
130 60 0.56
ACGTcount: A:0.40, C:0.08, G:0.17, T:0.36
Consensus pattern (126 bp):
ATTACTAATATATACAACTGAGGGAGATAATAAATTATGCTATTAAAATAAAAATGTATAGAACT
TATCAAAATGAAGCTTTGGTTGACTGGTAAATTTAAGGTTTTACCAATCCAACTGGTGCAC
Found at i:65321606 original size:22 final size:21
Alignment explanation
Indices: 65321581--65321628 Score: 53
Period size: 22 Copynumber: 2.3 Consensus size: 21
65321571 TTGTTTTATA
*
65321581 CTTTTTAAATTTTTTATATATT
1 CTTTTTAAACTTTTTATA-ATT
**
65321603 CTTTAGAAACTTTTTATAATT
1 CTTTTTAAACTTTTTATAATT
65321624 -TTTTT
1 CTTTTT
65321629 GAGTTATAAA
Statistics
Matches: 21, Mismatches: 5, Indels: 2
0.75 0.18 0.07
Matches are distributed among these distances:
20 3 0.14
21 3 0.14
22 15 0.71
ACGTcount: A:0.27, C:0.06, G:0.02, T:0.65
Consensus pattern (21 bp):
CTTTTTAAACTTTTTATAATT
Found at i:65325116 original size:6 final size:6
Alignment explanation
Indices: 65325095--65325157 Score: 51
Period size: 6 Copynumber: 10.5 Consensus size: 6
65325085 TTATCCATTA
* *
65325095 TTTTA- TTTTA- TTTTAT TTTTAT ATTTT-T TTTTAA TTTAAT TTTTAT
1 TTTTAT TTTTAT TTTTAT TTTTAT -TTTTAT TTTTAT TTTTAT TTTTAT
*
65325141 ATTTTAAT TTTTCT TTT
1 -TTTT-AT TTTTAT TTT
65325158 GTTTGCTTCT
Statistics
Matches: 48, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
5 14 0.29
6 20 0.42
7 12 0.25
8 2 0.04
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.78
Consensus pattern (6 bp):
TTTTAT
Found at i:65325121 original size:13 final size:13
Alignment explanation
Indices: 65325103--65325152 Score: 68
Period size: 12 Copynumber: 3.9 Consensus size: 13
65325093 TATTTTATTT
65325103 TATTTTATTTTTA
1 TATTTTATTTTTA
65325116 TATTTT-TTTTTA
1 TATTTTATTTTTA
*
65325128 -ATTTAATTTTTA
1 TATTTTATTTTTA
65325140 TATTTTAATTTTT
1 TATTTT-ATTTTT
65325153 CTTTTGTTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
11 4 0.12
12 12 0.38
13 10 0.31
14 6 0.19
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
TATTTTATTTTTA
Found at i:65325126 original size:23 final size:24
Alignment explanation
Indices: 65325093--65325151 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
65325083 ATTTATCCAT
*
65325093 TATTTTATTTT-ATTTTATTTTTA
1 TATTTTATTTTAATTTAATTTTTA
*
65325116 TATTTTTTTTTAATTTAATTTTTA
1 TATTTTATTTTAATTTAATTTTTA
65325140 TATTTTAATTTT
1 TATTTT-ATTTT
65325152 TCTTTTGTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
23 10 0.32
24 17 0.55
25 4 0.13
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (24 bp):
TATTTTATTTTAATTTAATTTTTA
Found at i:65325137 original size:14 final size:14
Alignment explanation
Indices: 65325104--65325152 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 14
65325094 ATTTTATTTT
*
65325104 ATTTTATTTTTAT-
1 ATTTAATTTTTATA
65325117 ATTT--TTTTT-TA
1 ATTTAATTTTTATA
65325128 ATTTAATTTTTATA
1 ATTTAATTTTTATA
*
65325142 TTTTAATTTTT
1 ATTTAATTTTT
65325153 CTTTTGTTTG
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
10 1 0.03
11 9 0.29
13 9 0.29
14 12 0.39
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (14 bp):
ATTTAATTTTTATA
Found at i:65331534 original size:16 final size:16
Alignment explanation
Indices: 65331499--65331545 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
65331489 GCTCCTCCCC
65331499 ATTTATTA-TTTTA-T
1 ATTTATTATTTTTATT
65331513 -TTTATT-TTATTTATT
1 ATTTATTATT-TTTATT
65331528 ATTTATTATTTTTATT
1 ATTTATTATTTTTATT
65331544 AT
1 AT
65331546 ACTGTTATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
13 7 0.25
14 4 0.14
15 1 0.04
16 14 0.50
17 2 0.07
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (16 bp):
ATTTATTATTTTTATT
Found at i:65331540 original size:25 final size:22
Alignment explanation
Indices: 65331499--65331543 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
65331489 GCTCCTCCCC
65331499 ATTTATTATTTTATTTTATTTT
1 ATTTATTATTTTATTTTATTTT
*
65331521 ATTTATTA-TTTATTAT-TTTT
1 ATTTATTATTTTATTTTATTTT
65331541 ATT
1 ATT
65331544 ATACTGTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 7 0.32
21 7 0.32
22 8 0.36
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (22 bp):
ATTTATTATTTTATTTTATTTT
Found at i:65331607 original size:3 final size:3
Alignment explanation
Indices: 65331501--65331590 Score: 73
Period size: 3 Copynumber: 31.0 Consensus size: 3
65331491 TCCTCCCCAT
*
65331501 TTA TTA TT- TTA TT- TTA TT- TTA TTTA TTA TTTA TTA TTT TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA -TTA TTA TTA TTA TTA
* * * * *
65331545 -TA CTG TTA TTA CTA GT- TTG TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
65331591 GGTTTCATAT
Statistics
Matches: 71, Mismatches: 9, Indels: 14
0.76 0.10 0.15
Matches are distributed among these distances:
2 9 0.13
3 56 0.79
4 6 0.08
ACGTcount: A:0.27, C:0.02, G:0.03, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:65333216 original size:6 final size:6
Alignment explanation
Indices: 65333205--65333265 Score: 52
Period size: 6 Copynumber: 9.8 Consensus size: 6
65333195 TTCTTTTCAA
* ** *
65333205 TTTTAT TTTTA- TTTTAT TTTAAT TTTTAT TTTGCT TCTTAGTT GTTTTAT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTA--T -TTTTAT
65333255 TTTTAT TTTTA
1 TTTTAT TTTTA
65333266 GACTTCTTTC
Statistics
Matches: 43, Mismatches: 8, Indels: 8
0.73 0.14 0.14
Matches are distributed among these distances:
5 5 0.12
6 32 0.74
7 1 0.02
8 1 0.02
9 4 0.09
ACGTcount: A:0.16, C:0.03, G:0.05, T:0.75
Consensus pattern (6 bp):
TTTTAT
Found at i:65333220 original size:11 final size:11
Alignment explanation
Indices: 65333193--65333236 Score: 52
Period size: 12 Copynumber: 3.8 Consensus size: 11
65333183 TATTTATTTC
*
65333193 TTTTCTTTTCAA
1 TTTTATTTT-AA
*
65333205 TTTTATTTTTA
1 TTTTATTTTAA
65333216 TTTTATTTTAA
1 TTTTATTTTAA
65333227 TTTTTATTTT
1 -TTTTATTTT
65333237 GCTTCTTAGT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
11 11 0.39
12 17 0.61
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.77
Consensus pattern (11 bp):
TTTTATTTTAA
Found at i:65334036 original size:26 final size:26
Alignment explanation
Indices: 65334005--65334060 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
65333995 CCTATTGAAT
65334005 TAACCCTTAGTCAACCTCGTTGAGCC
1 TAACCCTTAGTCAACCTCGTTGAGCC
*
65334031 TAACCCTTAGTTAACCTCGTTGAGCC
1 TAACCCTTAGTCAACCTCGTTGAGCC
65334057 TAAC
1 TAAC
65334061 ACACCCATTC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.25, C:0.32, G:0.14, T:0.29
Consensus pattern (26 bp):
TAACCCTTAGTCAACCTCGTTGAGCC
Found at i:65341001 original size:16 final size:17
Alignment explanation
Indices: 65340971--65341005 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
65340961 ACAACATCCA
65340971 TTTTTATAATATTCATT
1 TTTTTATAATATTCATT
*
65340988 TTTTTA-AATTTTCATT
1 TTTTTATAATATTCATT
65341004 TT
1 TT
65341006 AAGCTATGCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.69
Consensus pattern (17 bp):
TTTTTATAATATTCATT
Found at i:65345363 original size:21 final size:23
Alignment explanation
Indices: 65345334--65345375 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
65345324 TTCTAAATAA
*
65345334 AGACTAATG-AATAAAAAAAATT
1 AGACTAATGAAACAAAAAAAATT
65345356 AGAC-AATGAAACAAAAAAAA
1 AGACTAATGAAACAAAAAAAA
65345376 AACTTTTAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.69, C:0.07, G:0.10, T:0.14
Consensus pattern (23 bp):
AGACTAATGAAACAAAAAAAATT
Found at i:65346058 original size:16 final size:16
Alignment explanation
Indices: 65346033--65346067 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
65346023 TTATAAGAAA
* *
65346033 AAATTTTAAAATAGAC
1 AAATTATAAAATAAAC
65346049 AAATTATAAAATAAAC
1 AAATTATAAAATAAAC
65346065 AAA
1 AAA
65346068 ATTTTTTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.66, C:0.06, G:0.03, T:0.26
Consensus pattern (16 bp):
AAATTATAAAATAAAC
Found at i:65346235 original size:19 final size:19
Alignment explanation
Indices: 65346211--65346250 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
65346201 AAAATAAAAG
65346211 AAAAAAATAAATTGAAATA
1 AAAAAAATAAATTGAAATA
* *
65346230 AAAAAACTCAATTGAAATA
1 AAAAAAATAAATTGAAATA
65346249 AA
1 AA
65346251 GATAAAATCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.70, C:0.05, G:0.05, T:0.20
Consensus pattern (19 bp):
AAAAAAATAAATTGAAATA
Found at i:65349191 original size:14 final size:14
Alignment explanation
Indices: 65349138--65349182 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
65349128 TATGAGTATT
* * *
65349138 TATATCTATATTTC
1 TATATCTGTATCTA
*
65349152 TATATCTGTATCTG
1 TATATCTGTATCTA
65349166 TATATCTGTATCTA
1 TATATCTGTATCTA
65349180 TAT
1 TAT
65349183 TTTTGTATCA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.27, C:0.13, G:0.07, T:0.53
Consensus pattern (14 bp):
TATATCTGTATCTA
Found at i:65350195 original size:24 final size:24
Alignment explanation
Indices: 65350161--65350212 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
65350151 TTTTTATAAG
* *
65350161 ATTTAGTATTTATTAGTATAATAT
1 ATTTAGCATTTATTAGCATAATAT
*
65350185 ATTTAGCATTTATTAGCATAATTT
1 ATTTAGCATTTATTAGCATAATAT
65350209 ATTT
1 ATTT
65350213 GACCTACGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.35, C:0.04, G:0.08, T:0.54
Consensus pattern (24 bp):
ATTTAGCATTTATTAGCATAATAT
Found at i:65351219 original size:13 final size:13
Alignment explanation
Indices: 65351201--65351225 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
65351191 AAATTAAGAG
65351201 TTATTTTTTTAAT
1 TTATTTTTTTAAT
65351214 TTATTTTTTTAA
1 TTATTTTTTTAA
65351226 CTTCAATAAT
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:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
TTATTTTTTTAAT
Found at i:65351239 original size:34 final size:33
Alignment explanation
Indices: 65351178--65351263 Score: 91
Period size: 34 Copynumber: 2.5 Consensus size: 33
65351168 AGATAATTAC
* *
65351178 ATTTATTTTCTTTAAATTAAGAGTTATTTTTTTA
1 ATTTATTTT-TTTAAATTAAGAATTATTTATTTA
* *
65351212 ATTTATTTTTTTAACTTCAATAATTATTTATTTA
1 ATTTATTTTTTTAAATT-AAGAATTATTTATTTA
*
65351246 TTTTATTATTTTTCAAAT
1 ATTTATT-TTTTT-AAAT
65351264 GTAATTAATT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
33 7 0.16
34 28 0.65
35 5 0.12
36 3 0.07
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.63
Consensus pattern (33 bp):
ATTTATTTTTTTAAATTAAGAATTATTTATTTA
Found at i:65352730 original size:38 final size:39
Alignment explanation
Indices: 65352688--65352781 Score: 109
Period size: 40 Copynumber: 2.4 Consensus size: 39
65352678 CCATCTCCAA
* * *
65352688 CCAACCCAACACACCA-TGTGGGGATAGAATCGACCCAC
1 CCAACCCTACACACCAGTATGGGGATAGAATCAACCCAC
* * *
65352726 CCAACCTTACACACCAAGTATGGGGATATAATCAACCCAT
1 CCAACCCTACACACC-AGTATGGGGATAGAATCAACCCAC
*
65352766 CCAACCCTACAAACCA
1 CCAACCCTACACACCA
65352782 AAAGGTACCG
Statistics
Matches: 46, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
38 13 0.28
39 2 0.04
40 31 0.67
ACGTcount: A:0.37, C:0.36, G:0.13, T:0.14
Consensus pattern (39 bp):
CCAACCCTACACACCAGTATGGGGATAGAATCAACCCAC
Found at i:65353151 original size:13 final size:13
Alignment explanation
Indices: 65353133--65353166 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
65353123 AGGCTCACAC
65353133 GCCCGTGTGCCCT
1 GCCCGTGTGCCCT
65353146 GCCCGTGTGCCCT
1 GCCCGTGTGCCCT
*
65353159 ACCCGTGT
1 GCCCGTGT
65353167 AGATCACACG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.03, C:0.44, G:0.29, T:0.24
Consensus pattern (13 bp):
GCCCGTGTGCCCT
Found at i:65355006 original size:14 final size:16
Alignment explanation
Indices: 65354987--65355018 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
65354977 CATTGTTTCA
65354987 TTCATTT-T-ATTTTT
1 TTCATTTGTAATTTTT
65355001 TTCATTTGTAATTTTT
1 TTCATTTGTAATTTTT
65355017 TT
1 TT
65355019 TTTACAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 1 0.06
16 8 0.50
ACGTcount: A:0.16, C:0.06, G:0.03, T:0.75
Consensus pattern (16 bp):
TTCATTTGTAATTTTT
Found at i:65357774 original size:19 final size:19
Alignment explanation
Indices: 65357739--65357777 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
65357729 AAATAGTGAG
65357739 AATTTATTTTCTAAGAATA
1 AATTTATTTTCTAAGAATA
*
65357758 AATTCTATTTT-TCAGAATA
1 AATT-TATTTTCTAAGAATA
65357777 A
1 A
65357778 CAATTTGATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.46
Consensus pattern (19 bp):
AATTTATTTTCTAAGAATA
Found at i:65368620 original size:27 final size:26
Alignment explanation
Indices: 65368603--65368672 Score: 95
Period size: 27 Copynumber: 2.6 Consensus size: 26
65368593 ATATTAAGTC
65368603 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTCAGTGCTATAT-ATCAACT
*
65368630 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTCAGTGCTATAT-ATC-AACT
*
65368658 CGCACACTTAGTGCT
1 CGCACACTCAGTGCT
65368673 GTACAATTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (26 bp):
CGCACACTCAGTGCTATATATCAACT
Found at i:65368666 original size:28 final size:28
Alignment explanation
Indices: 65368603--65368700 Score: 135
Period size: 28 Copynumber: 3.5 Consensus size: 28
65368593 ATATTAAGTC
*
65368603 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
65368630 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
65368658 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
65368687 CGCACACTTAGTGC
1 CGCACACTTAGTGC
65368701 CAATCTCATG
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 22 0.34
28 23 0.36
29 19 0.30
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:65369164 original size:12 final size:12
Alignment explanation
Indices: 65369147--65369173 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
65369137 TGGGCATACT
65369147 TATGTATATATA
1 TATGTATATATA
65369159 TATGTATATATA
1 TATGTATATATA
65369171 TAT
1 TAT
65369174 ACTTCGGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (12 bp):
TATGTATATATA
Found at i:65371565 original size:46 final size:46
Alignment explanation
Indices: 65371514--65371734 Score: 197
Period size: 47 Copynumber: 4.8 Consensus size: 46
65371504 ATGGTTGAGC
*
65371514 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T-G
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA--AATG-GAACTAG
* * *
65371561 -TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGAAATGTAACTAGG
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTAAATGGAACTA-G
* * *
65371606 CATCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGAAATGTAACTAGG
1 -ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTAAATGGAACTA-G
*
65371653 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAC--G
1 -ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA--AATG-GAACTAG
* * *
65371701 -CCCGAGCTCGTTGGGTTGAGTCCGAGTTCACTTA
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
65371735 GGGGCGGGTT
Statistics
Matches: 154, Mismatches: 11, Indels: 19
0.84 0.06 0.10
Matches are distributed among these distances:
42 2 0.01
43 4 0.03
45 3 0.02
46 60 0.39
47 76 0.49
48 3 0.02
50 3 0.02
51 3 0.02
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.29
Consensus pattern (46 bp):
ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTAAATGGAACTAG
Found at i:65371630 original size:47 final size:47
Alignment explanation
Indices: 65371561--65371683 Score: 246
Period size: 47 Copynumber: 2.6 Consensus size: 47
65371551 GATGCGAATG
65371561 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAAATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAAATGTAACTAGGCA
65371608 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAAATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAAATGTAACTAGGCA
65371655 TCCGAACTCGTTGAGTTGAGTCCGAGTTC
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC
65371684 ACTTATGGAT
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 76 1.00
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (47 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAAATGTAACTAGGCA
Found at i:65375470 original size:27 final size:27
Alignment explanation
Indices: 65375449--65375502 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
65375439 GACCTTTTGC
65375449 TGTACACCAGCTCGCCAAACCTACTAG
1 TGTACACCAGCTCGCCAAACCTACTAG
65375476 TGTACACCAGCTCGCCAAACCTACTAG
1 TGTACACCAGCTCGCCAAACCTACTAG
65375503 CAAATACAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.30, C:0.37, G:0.15, T:0.19
Consensus pattern (27 bp):
TGTACACCAGCTCGCCAAACCTACTAG
Found at i:65375983 original size:19 final size:20
Alignment explanation
Indices: 65375955--65375993 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
65375945 TCCCATTATT
65375955 TATTTATTTTT-TGTTTTAA
1 TATTTATTTTTATGTTTTAA
*
65375974 TATTTGTTTTTATGTTTTAA
1 TATTTATTTTTATGTTTTAA
65375994 ATGTATTTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.21, C:0.00, G:0.08, T:0.72
Consensus pattern (20 bp):
TATTTATTTTTATGTTTTAA
Found at i:65376011 original size:25 final size:23
Alignment explanation
Indices: 65375974--65376019 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
65375964 TTTGTTTTAA
*
65375974 TATTTGTTTTTATGTTTTAAATG
1 TATTTGTTTTTATATTTTAAATG
65375997 TATTTGATTTATTATATTTTAAA
1 TATTTG-TTT-TTATATTTTAAA
65376020 GTTTTTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 3 0.15
25 11 0.55
ACGTcount: A:0.28, C:0.00, G:0.09, T:0.63
Consensus pattern (23 bp):
TATTTGTTTTTATATTTTAAATG
Found at i:65379471 original size:57 final size:56
Alignment explanation
Indices: 65379388--65379503 Score: 223
Period size: 57 Copynumber: 2.1 Consensus size: 56
65379378 TTCCAATCAG
65379388 TTTTCTCATTTCCGATTAGACTAATGACATGCTTAGATTATCTACGAATATAAGTT
1 TTTTCTCATTTCCGATTAGACTAATGACATGCTTAGATTATCTACGAATATAAGTT
65379444 TTTTGCTCATTTCCGATTAGACTAATGACATGCTTAGATTATCTACGAATATAAGTT
1 TTTT-CTCATTTCCGATTAGACTAATGACATGCTTAGATTATCTACGAATATAAGTT
65379501 TTT
1 TTT
65379504 ATTCTATATT
Statistics
Matches: 59, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
56 4 0.07
57 55 0.93
ACGTcount: A:0.29, C:0.16, G:0.13, T:0.42
Consensus pattern (56 bp):
TTTTCTCATTTCCGATTAGACTAATGACATGCTTAGATTATCTACGAATATAAGTT
Found at i:65380061 original size:22 final size:22
Alignment explanation
Indices: 65380036--65380077 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
65380026 CTTGAAAAAA
* *
65380036 TAGTTTAATTGATAAATTAATT
1 TAGTTAAATTAATAAATTAATT
*
65380058 TAGTTAAATTAATTAATTAA
1 TAGTTAAATTAATAAATTAA
65380078 CTAATATTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (22 bp):
TAGTTAAATTAATAAATTAATT
Found at i:65394499 original size:46 final size:46
Alignment explanation
Indices: 65394438--65394528 Score: 155
Period size: 46 Copynumber: 2.0 Consensus size: 46
65394428 GCAACAAAAA
* *
65394438 AAAAACAACATTCTAGAGAAGTATATATACTACACTCTTAAACAAG
1 AAAAACAACATTCTAGAGAAGTATATAAAATACACTCTTAAACAAG
*
65394484 AAAATCAACATTCTAGAGAAGTATATAAAATACACTCTTAAACAA
1 AAAAACAACATTCTAGAGAAGTATATAAAATACACTCTTAAACAA
65394529 CAGTAACCAC
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 42 1.00
ACGTcount: A:0.52, C:0.16, G:0.08, T:0.24
Consensus pattern (46 bp):
AAAAACAACATTCTAGAGAAGTATATAAAATACACTCTTAAACAAG
Found at i:65394871 original size:3 final size:3
Alignment explanation
Indices: 65394837--65394886 Score: 55
Period size: 3 Copynumber: 16.7 Consensus size: 3
65394827 TTCAAATTCC
* * * * *
65394837 TCT TCT TGT TCT TGT TCT TCA TCA TCT CCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
65394885 TC
1 TC
65394887 GACTATTAAA
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.04, C:0.32, G:0.04, T:0.60
Consensus pattern (3 bp):
TCT
Found at i:65395563 original size:22 final size:23
Alignment explanation
Indices: 65395538--65395584 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
65395528 AGATTCATTT
*
65395538 ATATATTTATAAA-ATAAATTAA
1 ATATATTTATAAATATAAAGTAA
* *
65395560 ATATTTTTTTAAATATAAAGTAA
1 ATATATTTATAAATATAAAGTAA
65395583 AT
1 AT
65395585 TAAATACTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 11 0.52
23 10 0.48
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (23 bp):
ATATATTTATAAATATAAAGTAA
Found at i:65406705 original size:13 final size:12
Alignment explanation
Indices: 65406682--65406707 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
65406672 GATTGTGATT
65406682 TTGTCAAAAAAA
1 TTGTCAAAAAAA
65406694 TTGTCAAAAAAA
1 TTGTCAAAAAAA
65406706 TT
1 TT
65406708 CATCATCAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.54, C:0.08, G:0.08, T:0.31
Consensus pattern (12 bp):
TTGTCAAAAAAA
Found at i:65407618 original size:6 final size:6
Alignment explanation
Indices: 65407609--65407654 Score: 56
Period size: 6 Copynumber: 7.5 Consensus size: 6
65407599 GAGATACGAG
* * *
65407609 AGAAAA AGAAATA AAAAAA AGAAAA AGAAAT TGAAAA AGAAAA AGA
1 AGAAAA AGAAA-A AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGA
65407655 GAGTGAGATT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
6 28 0.85
7 5 0.15
ACGTcount: A:0.78, C:0.00, G:0.15, T:0.07
Consensus pattern (6 bp):
AGAAAA
Found at i:65407645 original size:18 final size:19
Alignment explanation
Indices: 65407609--65407654 Score: 67
Period size: 18 Copynumber: 2.5 Consensus size: 19
65407599 GAGATACGAG
65407609 AGAAAAAGAAATAAAAAAA
1 AGAAAAAGAAATAAAAAAA
**
65407628 AGAAAAAGAAAT-TGAAAA
1 AGAAAAAGAAATAAAAAAA
65407646 AGAAAAAGA
1 AGAAAAAGA
65407655 GAGTGAGATT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 13 0.52
19 12 0.48
ACGTcount: A:0.78, C:0.00, G:0.15, T:0.07
Consensus pattern (19 bp):
AGAAAAAGAAATAAAAAAA
Found at i:65410849 original size:33 final size:33
Alignment explanation
Indices: 65410793--65410860 Score: 93
Period size: 33 Copynumber: 2.1 Consensus size: 33
65410783 TCAACCGAGT
* * *
65410793 TCGTATCAGAAGTCATGTAGAGATGTTGTGTAC
1 TCGTATCAAAAGACATGTAGAGATGTTGTATAC
65410826 TCGTATCAAAAGACATGCT-GAGATGTTGTATAC
1 TCGTATCAAAAGACATG-TAGAGATGTTGTATAC
65410859 TC
1 TC
65410861 TAGTTTGGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
33 30 0.97
34 1 0.03
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.32
Consensus pattern (33 bp):
TCGTATCAAAAGACATGTAGAGATGTTGTATAC
Found at i:65412569 original size:39 final size:42
Alignment explanation
Indices: 65412508--65412597 Score: 96
Period size: 42 Copynumber: 2.2 Consensus size: 42
65412498 CTGTGTTAGC
* * *
65412508 TTTCTGTTTAGCTCACATGAGC-TGT-TT-AACCCTTATGGG
1 TTTCTGTTAAGCTCACACGAGCTTCTATTCAACCCTTATGGG
** *
65412547 TTTCTGTTAAGCTCTTACGAGCTTCTATTCCACCCTTATGGG
1 TTTCTGTTAAGCTCACACGAGCTTCTATTCAACCCTTATGGG
*
65412589 TTTCCGTTA
1 TTTCTGTTA
65412598 GCACTTATGT
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
39 18 0.44
40 2 0.05
41 2 0.05
42 19 0.46
ACGTcount: A:0.17, C:0.23, G:0.18, T:0.42
Consensus pattern (42 bp):
TTTCTGTTAAGCTCACACGAGCTTCTATTCAACCCTTATGGG
Found at i:65417723 original size:30 final size:30
Alignment explanation
Indices: 65417687--65417801 Score: 185
Period size: 30 Copynumber: 3.8 Consensus size: 30
65417677 ATCCATATTT
* *
65417687 ATGGAAAATTAAAGATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
65417717 ATGGAAAGTCAAAGATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
* *
65417747 TTGGAAAGTCAAATATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
*
65417777 TTGGAAAGTCAAAGATATGGGTATC
1 ATGGAAAGTCAAAGATATGGGTATC
65417802 GAGATATTGG
Statistics
Matches: 80, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 80 1.00
ACGTcount: A:0.44, C:0.06, G:0.23, T:0.27
Consensus pattern (30 bp):
ATGGAAAGTCAAAGATATGGGTATCAAATA
Found at i:65417743 original size:15 final size:15
Alignment explanation
Indices: 65417701--65417801 Score: 82
Period size: 15 Copynumber: 6.7 Consensus size: 15
65417691 AAAATTAAAG
65417701 ATATGGGTATCAAAT
1 ATATGGGTATCAAAT
** *
65417716 A-ATGGAAAGTCAAAG
1 ATATGGGTA-TCAAAT
65417731 ATATGGGTATCAAAT
1 ATATGGGTATCAAAT
**
65417746 AT-TGGAAAGTCAAAT
1 ATATGGGTA-TCAAAT
65417761 ATATGGGTATCAAAT
1 ATATGGGTATCAAAT
** *
65417776 AT-TGGAAAGTCAAAG
1 ATATGGGTA-TCAAAT
65417791 ATATGGGTATC
1 ATATGGGTATC
65417802 GAGATATTGG
Statistics
Matches: 65, Mismatches: 15, Indels: 12
0.71 0.16 0.13
Matches are distributed among these distances:
14 13 0.20
15 39 0.60
16 13 0.20
ACGTcount: A:0.43, C:0.07, G:0.23, T:0.28
Consensus pattern (15 bp):
ATATGGGTATCAAAT
Found at i:65422410 original size:30 final size:30
Alignment explanation
Indices: 65422376--65422490 Score: 185
Period size: 30 Copynumber: 3.8 Consensus size: 30
65422366 ATCCATATTT
* *
65422376 ATGGAAAATTAAAGATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
65422406 ATGGAAAGTCAAAGATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
* *
65422436 TTGGAAAGTCAAATATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
*
65422466 TTGGAAAGTCAAAGATATGGGTATC
1 ATGGAAAGTCAAAGATATGGGTATC
65422491 GAGATATTGA
Statistics
Matches: 80, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 80 1.00
ACGTcount: A:0.44, C:0.06, G:0.23, T:0.27
Consensus pattern (30 bp):
ATGGAAAGTCAAAGATATGGGTATCAAATA
Found at i:65422432 original size:15 final size:15
Alignment explanation
Indices: 65422390--65422490 Score: 82
Period size: 15 Copynumber: 6.7 Consensus size: 15
65422380 AAAATTAAAG
65422390 ATATGGGTATCAAAT
1 ATATGGGTATCAAAT
** *
65422405 A-ATGGAAAGTCAAAG
1 ATATGGGTA-TCAAAT
65422420 ATATGGGTATCAAAT
1 ATATGGGTATCAAAT
**
65422435 AT-TGGAAAGTCAAAT
1 ATATGGGTA-TCAAAT
65422450 ATATGGGTATCAAAT
1 ATATGGGTATCAAAT
** *
65422465 AT-TGGAAAGTCAAAG
1 ATATGGGTA-TCAAAT
65422480 ATATGGGTATC
1 ATATGGGTATC
65422491 GAGATATTGA
Statistics
Matches: 65, Mismatches: 15, Indels: 12
0.71 0.16 0.13
Matches are distributed among these distances:
14 13 0.20
15 39 0.60
16 13 0.20
ACGTcount: A:0.43, C:0.07, G:0.23, T:0.28
Consensus pattern (15 bp):
ATATGGGTATCAAAT
Found at i:65427403 original size:23 final size:23
Alignment explanation
Indices: 65427375--65427420 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
65427365 AACGGGTAGA
65427375 ATTATTTTAGTGAAAAATATTTT
1 ATTATTTTAGTGAAAAATATTTT
65427398 ATTATTTTAGTGAAAAATATTTT
1 ATTATTTTAGTGAAAAATATTTT
65427421 GTTAGCTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.39, C:0.00, G:0.09, T:0.52
Consensus pattern (23 bp):
ATTATTTTAGTGAAAAATATTTT
Found at i:65439558 original size:27 final size:28
Alignment explanation
Indices: 65439513--65439571 Score: 68
Period size: 26 Copynumber: 2.1 Consensus size: 28
65439503 TTATATAAAT
* *
65439513 AATTTATATATTTTATAAAGTCATACAAA
1 AATTTATATATATTATAAAGTC-TAAAAA
*
65439542 AATTTATAT-TATT-TAAATTCTAAAAA
1 AATTTATATATATTATAAAGTCTAAAAA
65439568 AATT
1 AATT
65439572 CTAAATTTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 9 0.33
27 6 0.22
28 3 0.11
29 9 0.33
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (28 bp):
AATTTATATATATTATAAAGTCTAAAAA
Found at i:65445716 original size:6 final size:6
Alignment explanation
Indices: 65445705--65445746 Score: 66
Period size: 6 Copynumber: 7.0 Consensus size: 6
65445695 CTTAATTATA
* *
65445705 AATATT AATATT AATATT AATATT AATATG AAAATT AATATT
1 AATATT AATATT AATATT AATATT AATATT AATATT AATATT
65445747 CTTTTACTTG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (6 bp):
AATATT
Found at i:65447697 original size:12 final size:13
Alignment explanation
Indices: 65447680--65447710 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
65447670 AAGTCATATA
65447680 AAATAACTAA-AT
1 AAATAACTAAGAT
65447692 AAATAACTAAGAT
1 AAATAACTAAGAT
65447705 AAATAA
1 AAATAA
65447711 AATAGAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 10 0.56
13 8 0.44
ACGTcount: A:0.68, C:0.06, G:0.03, T:0.23
Consensus pattern (13 bp):
AAATAACTAAGAT
Found at i:65447959 original size:25 final size:26
Alignment explanation
Indices: 65447930--65448004 Score: 102
Period size: 24 Copynumber: 3.0 Consensus size: 26
65447920 AACTCTTCTA
65447930 AAAG-AAAACTCAAAAGAAATTTTTG
1 AAAGAAAAACTCAAAAGAAATTTTTG
*
65447955 AAAGAAAAACTC--GAGAAATTTTTG
1 AAAGAAAAACTCAAAAGAAATTTTTG
*
65447979 AAAGAAAAAATCAAAGAGAAATTTTT
1 AAAGAAAAACTCAAA-AGAAATTTTT
65448005 AACTCAAAAG
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
24 22 0.51
25 4 0.09
26 7 0.16
27 10 0.23
ACGTcount: A:0.56, C:0.07, G:0.13, T:0.24
Consensus pattern (26 bp):
AAAGAAAAACTCAAAAGAAATTTTTG
Found at i:65455723 original size:27 final size:27
Alignment explanation
Indices: 65455686--65455830 Score: 195
Period size: 27 Copynumber: 5.4 Consensus size: 27
65455676 AGCATGGCTG
* *
65455686 CCAGAACAGATA-ATGTGACAGAGTCA
1 CCAGAACAGATATATGTGGCAGAGCCA
65455712 CCAGATACAGATA-ATCGTGGCAGAGCCA
1 CCAGA-ACAGATATAT-GTGGCAGAGCCA
65455740 CCAGAACAGATATATGTGGCAGAGCCA
1 CCAGAACAGATATATGTGGCAGAGCCA
* * *
65455767 CCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATATATGTGGCAGAGCCA
*
65455794 CCAGAACAGATATATGTAGCAGAGCCA
1 CCAGAACAGATATATGTGGCAGAGCCA
*
65455821 CCAGATCAGA
1 CCAGAACAGA
65455831 AAATTATGGC
Statistics
Matches: 106, Mismatches: 10, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
26 5 0.05
27 84 0.79
28 17 0.16
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (27 bp):
CCAGAACAGATATATGTGGCAGAGCCA
Found at i:65455745 original size:54 final size:54
Alignment explanation
Indices: 65455686--65455851 Score: 237
Period size: 54 Copynumber: 3.1 Consensus size: 54
65455676 AGCATGGCTG
* * *
65455686 CCAGAACAGATA-ATGTGACAGAGTCACCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGAT-CAGATAATTGTGGCATAGCCA
* *
65455740 CCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATTGTGGCATAGCCA
* *
65455794 CCAGAACAGATATATGT-AGCAGAGCCACCAGATCAGAAAATTATGGCATAGCCA
1 CCAGAACAGATATATGTGA-CAGAGCCACCAGATCAGATAATTGTGGCATAGCCA
65455848 CCAG
1 CCAG
65455852 GACGCTTCCT
Statistics
Matches: 101, Mismatches: 9, Indels: 4
0.89 0.08 0.04
Matches are distributed among these distances:
54 83 0.82
55 18 0.18
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (54 bp):
CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATTGTGGCATAGCCA
Found at i:65455846 original size:27 final size:27
Alignment explanation
Indices: 65455686--65455851 Score: 140
Period size: 27 Copynumber: 6.1 Consensus size: 27
65455676 AGCATGGCTG
* * * *
65455686 CCAGAACAGATAA-TGTGACAGAGTCA
1 CCAGATCAGAAAATTGTGGCAGAGCCA
* *
65455712 CCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGAT-CAGAAAATTGTGGCAGAGCCA
* *
65455740 CCAGAACAG-ATATATGTGGCAGAGCCA
1 CCAGATCAGAAAAT-TGTGGCAGAGCCA
* * *
65455767 CCAGATCAGATATTTGTGGCATAGCCA
1 CCAGATCAGAAAATTGTGGCAGAGCCA
* * *
65455794 CCAGAACAG-ATATATGTAGCAGAGCCA
1 CCAGATCAGAAAAT-TGTGGCAGAGCCA
* *
65455821 CCAGATCAGAAAATTATGGCATAGCCA
1 CCAGATCAGAAAATTGTGGCAGAGCCA
65455848 CCAG
1 CCAG
65455852 GACGCTTCCT
Statistics
Matches: 110, Mismatches: 24, Indels: 11
0.76 0.17 0.08
Matches are distributed among these distances:
26 8 0.07
27 83 0.75
28 19 0.17
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (27 bp):
CCAGATCAGAAAATTGTGGCAGAGCCA
Found at i:65457477 original size:26 final size:26
Alignment explanation
Indices: 65457441--65457550 Score: 184
Period size: 26 Copynumber: 4.2 Consensus size: 26
65457431 CATGAAATTC
65457441 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
65457467 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
65457493 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
* *
65457519 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
65457545 TTATCA
1 TTATCA
65457551 ATTTGTATCA
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 82 1.00
ACGTcount: A:0.36, C:0.25, G:0.05, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:65461532 original size:27 final size:27
Alignment explanation
Indices: 65461495--65461659 Score: 212
Period size: 27 Copynumber: 6.2 Consensus size: 27
65461485 AGCATGGCTG
* *
65461495 CCAGAACAGATA-ATGTGACAGAGTCA
1 CCAGAACAGATATATGTGGCAGAGCCA
65461521 CCAGATACAGATA-ATCGTGGCAGAGCCA
1 CCAGA-ACAGATATAT-GTGGCAGAGCCA
65461549 CCAGAACAGATATATGTGGCAGAGCCA
1 CCAGAACAGATATATGTGGCAGAGCCA
* * *
65461576 CCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATATATGTGGCAGAGCCA
65461603 CCAGAACAGATATATGT-GCAGAGCCA
1 CCAGAACAGATATATGTGGCAGAGCCA
* * *
65461629 TCAGATCAGATAT-TGTGGCATAGCCA
1 CCAGAACAGATATATGTGGCAGAGCCA
65461655 CCAGA
1 CCAGA
65461660 CGCTTCCTCC
Statistics
Matches: 123, Mismatches: 12, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
25 3 0.02
26 36 0.29
27 67 0.54
28 17 0.14
ACGTcount: A:0.36, C:0.22, G:0.24, T:0.18
Consensus pattern (27 bp):
CCAGAACAGATATATGTGGCAGAGCCA
Found at i:65461554 original size:54 final size:53
Alignment explanation
Indices: 65461495--65461659 Score: 244
Period size: 54 Copynumber: 3.1 Consensus size: 53
65461485 AGCATGGCTG
* * *
65461495 CCAGAACAGATA-ATGTGACAGAGTCACCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGAACAGATATATGTG-CAGAGCCACCAGAT-CAGATAATTGTGGCATAGCCA
*
65461549 CCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATATATGT-GCAGAGCCACCAGATCAGATAATTGTGGCATAGCCA
*
65461603 CCAGAACAGATATATGTGCAGAGCCATCAGATCAGAT-ATTGTGGCATAGCCA
1 CCAGAACAGATATATGTGCAGAGCCACCAGATCAGATAATTGTGGCATAGCCA
65461655 CCAGA
1 CCAGA
65461660 CGCTTCCTCC
Statistics
Matches: 103, Mismatches: 6, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
52 19 0.18
53 19 0.18
54 47 0.46
55 17 0.17
56 1 0.01
ACGTcount: A:0.36, C:0.22, G:0.24, T:0.18
Consensus pattern (53 bp):
CCAGAACAGATATATGTGCAGAGCCACCAGATCAGATAATTGTGGCATAGCCA
Found at i:65463265 original size:26 final size:26
Alignment explanation
Indices: 65463229--65463338 Score: 184
Period size: 26 Copynumber: 4.2 Consensus size: 26
65463219 CATGAAATTC
65463229 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
65463255 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
65463281 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
* *
65463307 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
65463333 TTATCA
1 TTATCA
65463339 ATTTGTATCA
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 82 1.00
ACGTcount: A:0.36, C:0.25, G:0.05, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:65465445 original size:26 final size:26
Alignment explanation
Indices: 65465415--65465496 Score: 146
Period size: 26 Copynumber: 3.2 Consensus size: 26
65465405 TGAAATGCCC
65465415 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
65465441 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
65465467 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
65465493 ATCA
1 ATCA
65465497 ATTTGTACCA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 52 1.00
ACGTcount: A:0.35, C:0.24, G:0.07, T:0.33
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:65483147 original size:39 final size:39
Alignment explanation
Indices: 65483104--65483199 Score: 147
Period size: 39 Copynumber: 2.5 Consensus size: 39
65483094 TTTTTGAATT
* *
65483104 TTGTGATAGATGCTTGAATGTTATGTGATTATATGAGTA
1 TTGTGATATATGCTTAAATGTTATGTGATTATATGAGTA
* *
65483143 TTGTGATATATGCTTAAATGTTATGTGGTTATATGTGTA
1 TTGTGATATATGCTTAAATGTTATGTGATTATATGAGTA
*
65483182 ATGTGATATATGCTTAAA
1 TTGTGATATATGCTTAAA
65483200 CCCTTGTAGA
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 52 1.00
ACGTcount: A:0.29, C:0.03, G:0.23, T:0.45
Consensus pattern (39 bp):
TTGTGATATATGCTTAAATGTTATGTGATTATATGAGTA
Found at i:65491140 original size:17 final size:17
Alignment explanation
Indices: 65491118--65491152 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
65491108 AATATAGAAA
*
65491118 GTAATCTTAGAAGATTT
1 GTAATCTGAGAAGATTT
*
65491135 GTAATCTGATAAGATTT
1 GTAATCTGAGAAGATTT
65491152 G
1 G
65491153 ATTTTGTAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.34, C:0.06, G:0.20, T:0.40
Consensus pattern (17 bp):
GTAATCTGAGAAGATTT
Found at i:65494943 original size:47 final size:47
Alignment explanation
Indices: 65494885--65495570 Score: 1176
Period size: 47 Copynumber: 14.5 Consensus size: 47
65494875 ATTCAGCCAA
65494885 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
1 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
65494932 GAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
1 GAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
65494981 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
1 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
65495028 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
1 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
65495075 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
1 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
*
65495122 GAAAGTGTATATATATGTGATAAGGTCTAATGGCCGATGTGATGAATGT
1 GAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
65495171 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
1 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
65495218 GAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
1 GAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
* *
65495267 GAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAACGT
1 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
*
65495314 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAACGT
1 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
65495361 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAACT-T
1 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAA-TGT
*
65495408 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAACGT
1 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
*
65495455 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGCGATGAATGT
1 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
* * * * * * *
65495502 GAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGT
1 GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
*
65495549 GAAAGTGTATAAATGTGATAAG
1 GAAAGTGTATATATGTGATAAG
65495571 TCCCGAAGGG
Statistics
Matches: 611, Mismatches: 20, Indels: 16
0.94 0.03 0.02
Matches are distributed among these distances:
47 471 0.77
49 140 0.23
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29
Consensus pattern (47 bp):
GAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
Found at i:65495745 original size:37 final size:37
Alignment explanation
Indices: 65495689--65495767 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
65495679 CCGAGCTCTA
* * *
65495689 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
65495726 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
65495763 AAGAC
1 AAGAC
65495768 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:65501978 original size:13 final size:13
Alignment explanation
Indices: 65501960--65501984 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
65501950 GAATTAGTAT
65501960 GTGTGAAAATTTC
1 GTGTGAAAATTTC
65501973 GTGTGAAAATTT
1 GTGTGAAAATTT
65501985 AATCGTTTGT
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:0.32, C:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:65506969 original size:33 final size:33
Alignment explanation
Indices: 65506927--65506993 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
65506917 ATGGATTTGA
*
65506927 TGAACATAATTTTTAGACCTTATTTAGATCGAT
1 TGAACATAATTTTTAGACCCTATTTAGATCGAT
65506960 TGAACATAATTTTTAGACCCTATTTAGATCGAT
1 TGAACATAATTTTTAGACCCTATTTAGATCGAT
65506993 T
1 T
65506994 TGTTGTTGTA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.42
Consensus pattern (33 bp):
TGAACATAATTTTTAGACCCTATTTAGATCGAT
Found at i:65507723 original size:15 final size:15
Alignment explanation
Indices: 65507691--65507719 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
65507681 ATTTTTAGTG
65507691 TTTATTATGTGTGAA
1 TTTATTATGTGTGAA
65507706 TTTA-TATGTGTGAA
1 TTTATTATGTGTGAA
65507720 ATTTTCGTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.28, C:0.00, G:0.21, T:0.52
Consensus pattern (15 bp):
TTTATTATGTGTGAA
Found at i:65508253 original size:15 final size:15
Alignment explanation
Indices: 65508233--65508263 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
65508223 AAATATGAAG
65508233 GATATGTTTTGGATT
1 GATATGTTTTGGATT
*
65508248 GATATGTTTTGTATT
1 GATATGTTTTGGATT
65508263 G
1 G
65508264 GAATTTTTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.19, C:0.00, G:0.26, T:0.55
Consensus pattern (15 bp):
GATATGTTTTGGATT
Found at i:65508931 original size:44 final size:44
Alignment explanation
Indices: 65508811--65509032 Score: 243
Period size: 45 Copynumber: 5.0 Consensus size: 44
65508801 TAGGATTTCG
* * * **
65508811 ATATGTGTTTTCATGTAAGACCACGTTTGGGACGTCAGCATCGAT
1 ATATGTG-TTTCGTGTAAGACCATGTCTGGGACGTTGGCATCGAT
* *
65508856 ATATGTGTTTTTGTGTAAGACCACGTCTGGGACGTTGGCATCGAT
1 ATATGTG-TTTCGTGTAAGACCATGTCTGGGACGTTGGCATCGAT
*
65508901 ATATGTGTTTCGTGTAAGACCATGTCTGGGATGTTGGCATCGAT
1 ATATGTGTTTCGTGTAAGACCATGTCTGGGACGTTGGCATCGAT
* * * * *
65508945 ATATGTGGTTACGTGTAAGACCATGTTTGGGACATCGACATC-AT
1 ATATGT-GTTTCGTGTAAGACCATGTCTGGGACGTTGGCATCGAT
* * **
65508989 AT-T-TGATTCGTGTAAGACCCTGTCTGGGACAATGGCATCGAT
1 ATATGTGTTTCGTGTAAGACCATGTCTGGGACGTTGGCATCGAT
65509031 AT
1 AT
65509033 GAGATAGCAT
Statistics
Matches: 154, Mismatches: 21, Indels: 7
0.85 0.12 0.04
Matches are distributed among these distances:
41 28 0.18
42 5 0.03
43 1 0.01
44 44 0.29
45 76 0.49
ACGTcount: A:0.23, C:0.16, G:0.27, T:0.34
Consensus pattern (44 bp):
ATATGTGTTTCGTGTAAGACCATGTCTGGGACGTTGGCATCGAT
Found at i:65508976 original size:89 final size:88
Alignment explanation
Indices: 65508811--65509032 Score: 250
Period size: 89 Copynumber: 2.5 Consensus size: 88
65508801 TAGGATTTCG
* * * ** * **
65508811 ATATGTGTTTTCATGTAAGACCACGTTTGGGACGTCAGCATCGATATATGTGTTTTTGTGTAAGA
1 ATATGTG-TTTCGTGTAAGACCATGTCTGGGACGTTGGCATCGATATATGTGGTTACGTGTAAGA
* * *
65508876 CCACGTCTGGGACGTTGGCATCGAT
65 CCACGTCTGGGACATCGACATC-AT
*
65508901 ATATGTGTTTCGTGTAAGACCATGTCTGGGATGTTGGCATCGATATATGTGGTTACGTGTAAGAC
1 ATATGTGTTTCGTGTAAGACCATGTCTGGGACGTTGGCATCGATATATGTGGTTACGTGTAAGAC
* *
65508966 CATGTTTGGGACATCGACATCAT
66 CACGTCTGGGACATCGACATCAT
* * **
65508989 AT-T-TGATTCGTGTAAGACCCTGTCTGGGACAATGGCATCGATAT
1 ATATGTGTTTCGTGTAAGACCATGTCTGGGACGTTGGCATCGATAT
65509033 GAGATAGCAT
Statistics
Matches: 113, Mismatches: 19, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
86 36 0.32
87 1 0.01
88 4 0.04
89 65 0.58
90 7 0.06
ACGTcount: A:0.23, C:0.16, G:0.27, T:0.34
Consensus pattern (88 bp):
ATATGTGTTTCGTGTAAGACCATGTCTGGGACGTTGGCATCGATATATGTGGTTACGTGTAAGAC
CACGTCTGGGACATCGACATCAT
Found at i:65519533 original size:15 final size:15
Alignment explanation
Indices: 65519501--65519529 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
65519491 ATTTTCTGTG
65519501 TTTATTATGTGTGAA
1 TTTATTATGTGTGAA
65519516 TTTA-TATGTGTGAA
1 TTTATTATGTGTGAA
65519530 ATTTTCGTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.28, C:0.00, G:0.21, T:0.52
Consensus pattern (15 bp):
TTTATTATGTGTGAA
Found at i:65520065 original size:15 final size:15
Alignment explanation
Indices: 65520045--65520074 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
65520035 AATATGAAAT
65520045 ATATGTTTTGCATTG
1 ATATGTTTTGCATTG
*
65520060 ATATGTTTTGTATTG
1 ATATGTTTTGCATTG
65520075 GAATTTTTGA
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:0.20, C:0.03, G:0.20, T:0.57
Consensus pattern (15 bp):
ATATGTTTTGCATTG
Found at i:65520681 original size:23 final size:23
Alignment explanation
Indices: 65520651--65520696 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
65520641 AGACCACGTC
65520651 TGGGATGTCAGCATCTATAACAG
1 TGGGATGTCAGCATCTATAACAG
* *
65520674 TGGGATGTCGGCATCTGTAACAG
1 TGGGATGTCAGCATCTATAACAG
65520697 CCCGATTTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.26, C:0.17, G:0.30, T:0.26
Consensus pattern (23 bp):
TGGGATGTCAGCATCTATAACAG
Found at i:65524134 original size:45 final size:45
Alignment explanation
Indices: 65524065--65524164 Score: 173
Period size: 45 Copynumber: 2.2 Consensus size: 45
65524055 TTACAGTATT
* * *
65524065 GATACATGTGTTTTCGTGTAAGACCATGTCTGGGATGTTGGCATC
1 GATATATGTGTTTTCGTGTAAGACCACGTCTGGGACGTTGGCATC
65524110 GATATATGTGTTTTCGTGTAAGACCACGTCTGGGACGTTGGCATC
1 GATATATGTGTTTTCGTGTAAGACCACGTCTGGGACGTTGGCATC
65524155 GATATATGTG
1 GATATATGTG
65524165 GTTACGTGGT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 52 1.00
ACGTcount: A:0.21, C:0.15, G:0.29, T:0.35
Consensus pattern (45 bp):
GATATATGTGTTTTCGTGTAAGACCACGTCTGGGACGTTGGCATC
Found at i:65527956 original size:13 final size:13
Alignment explanation
Indices: 65527938--65527962 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
65527928 GAATTAGTAT
65527938 GTGTGAAAATTTC
1 GTGTGAAAATTTC
65527951 GTGTGAAAATTT
1 GTGTGAAAATTT
65527963 AATCGTTTGT
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:0.32, C:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:65529115 original size:43 final size:44
Alignment explanation
Indices: 65528971--65529124 Score: 176
Period size: 43 Copynumber: 3.6 Consensus size: 44
65528961 TGTGTTATCG
*
65528971 TGTAAGACCACGTCTGGGACGTTGGCATCGACT-TATGATTTACA
1 TGTAAGACCACGTCTGGGACGTTGGCATCGA-TATTTGATTTACA
* * * *
65529015 TGTAAGGCCACGTTTGGGACGTTGACATCG-TATTTGATTT-CG
1 TGTAAGACCACGTCTGGGACGTTGGCATCGATATTTGATTTACA
*
65529057 TGTAAGATCC-TGTCTGGGACAG-TGGCATCGATATTTG-TTTACA
1 TGTAAGA-CCACGTCTGGGAC-GTTGGCATCGATATTTGATTTACA
*
65529100 TGTAAGACCACGTCTGGGATGTTGG
1 TGTAAGACCACGTCTGGGACGTTGG
65529125 AATTGTACGA
Statistics
Matches: 91, Mismatches: 12, Indels: 15
0.77 0.10 0.13
Matches are distributed among these distances:
42 29 0.32
43 35 0.38
44 27 0.30
ACGTcount: A:0.22, C:0.18, G:0.28, T:0.32
Consensus pattern (44 bp):
TGTAAGACCACGTCTGGGACGTTGGCATCGATATTTGATTTACA
Found at i:65534051 original size:30 final size:30
Alignment explanation
Indices: 65534015--65534077 Score: 126
Period size: 30 Copynumber: 2.1 Consensus size: 30
65534005 AAGGGTTAGA
65534015 ATCGAGATAATTTCAATATATTACCCCACT
1 ATCGAGATAATTTCAATATATTACCCCACT
65534045 ATCGAGATAATTTCAATATATTACCCCACT
1 ATCGAGATAATTTCAATATATTACCCCACT
65534075 ATC
1 ATC
65534078 AAAAACTTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.37, C:0.24, G:0.06, T:0.33
Consensus pattern (30 bp):
ATCGAGATAATTTCAATATATTACCCCACT
Found at i:65535307 original size:5 final size:5
Alignment explanation
Indices: 65535294--65535375 Score: 73
Period size: 5 Copynumber: 16.0 Consensus size: 5
65535284 AAGAAATTTG
*
65535294 AAATGA AAATAA AAATCA AAAGA AAATA AGAATA AAAT- AAATA AAATA
1 AAAT-A AAAT-A AAAT-A AAATA AAATA A-AATA AAATA AAATA AAATA
65535342 AAATA AGAATA AGAAT- AAAT- AAA-A AAATA AAATA
1 AAATA A-AATA A-AATA AAATA AAATA AAATA AAATA
65535376 GGAGGATTCA
Statistics
Matches: 67, Mismatches: 4, Indels: 11
0.82 0.05 0.13
Matches are distributed among these distances:
4 13 0.19
5 27 0.40
6 27 0.40
ACGTcount: A:0.76, C:0.01, G:0.06, T:0.17
Consensus pattern (5 bp):
AAATA
Found at i:65535320 original size:17 final size:16
Alignment explanation
Indices: 65535298--65535360 Score: 58
Period size: 17 Copynumber: 3.9 Consensus size: 16
65535288 AATTTGAAAT
65535298 GAAAATAAAAATCAAAA
1 GAAAATAAAAAT-AAAA
*
65535315 GAAAATAAGAATAAAA
1 GAAAATAAAAATAAAA
*
65535331 -TAAAT-AAAATAAAA
1 GAAAATAAAAATAAAA
* *
65535345 TAAGAATAAGAATAAA
1 GAA-AATAAAAATAAA
65535361 TAAAAAAATA
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
14 8 0.21
15 5 0.13
16 7 0.18
17 18 0.47
ACGTcount: A:0.75, C:0.02, G:0.08, T:0.16
Consensus pattern (16 bp):
GAAAATAAAAATAAAA
Found at i:65535344 original size:25 final size:26
Alignment explanation
Indices: 65535306--65535365 Score: 95
Period size: 25 Copynumber: 2.3 Consensus size: 26
65535296 ATGAAAATAA
65535306 AAATCAAAAGAAAATAAGAATAA-AAT
1 AAAT-AAAAGAAAATAAGAATAAGAAT
*
65535332 AAATAAAATAAAATAAGAATAAGAAT
1 AAATAAAAGAAAATAAGAATAAGAAT
65535358 AAATAAAA
1 AAATAAAA
65535366 AAATAAAATA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
25 17 0.53
26 15 0.47
ACGTcount: A:0.75, C:0.02, G:0.07, T:0.17
Consensus pattern (26 bp):
AAATAAAAGAAAATAAGAATAAGAAT
Found at i:65535353 original size:31 final size:29
Alignment explanation
Indices: 65535300--65535375 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 29
65535290 TTTGAAATGA
*
65535300 AAATAAAAATCAAAAGAAAATAAGAATAAAAT
1 AAAT-AAAAT-AAAATAAAATAAGAAT-AAAT
65535332 AAATAAAATAAAATAAGAATAAGAATAAAT
1 AAATAAAATAAAATAA-AATAAGAATAAAT
65535362 AAA-AAAATAAAATA
1 AAATAAAATAAAATA
65535376 GGAGGATTCA
Statistics
Matches: 42, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
29 11 0.26
30 13 0.31
31 14 0.33
32 4 0.10
ACGTcount: A:0.76, C:0.01, G:0.05, T:0.17
Consensus pattern (29 bp):
AAATAAAATAAAATAAAATAAGAATAAAT
Found at i:65540635 original size:13 final size:13
Alignment explanation
Indices: 65540617--65540642 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
65540607 AAAGGGTTTG
65540617 TTTAAACTAATTA
1 TTTAAACTAATTA
65540630 TTTAAACTAATTA
1 TTTAAACTAATTA
65540643 AATAATTTAA
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:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (13 bp):
TTTAAACTAATTA
Found at i:65542015 original size:60 final size:60
Alignment explanation
Indices: 65541945--65542063 Score: 202
Period size: 60 Copynumber: 2.0 Consensus size: 60
65541935 TGCAATTAGG
*
65541945 AGCACGAATGTGCAATCAAAGGCACCGAAGTGAAAACAGGGGCACGTAAGTGTAATCAGA
1 AGCACAAATGTGCAATCAAAGGCACCGAAGTGAAAACAGGGGCACGTAAGTGTAATCAGA
** *
65542005 AGCACAAATGTGCAATCAAAGGCATTGAAGTGCAAACAGGGGCACGTAAGTGTAATCAG
1 AGCACAAATGTGCAATCAAAGGCACCGAAGTGAAAACAGGGGCACGTAAGTGTAATCAG
65542064 GGGTACTGAT
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
60 55 1.00
ACGTcount: A:0.39, C:0.18, G:0.28, T:0.15
Consensus pattern (60 bp):
AGCACAAATGTGCAATCAAAGGCACCGAAGTGAAAACAGGGGCACGTAAGTGTAATCAGA
Found at i:65542062 original size:40 final size:40
Alignment explanation
Indices: 65542031--65542295 Score: 311
Period size: 40 Copynumber: 6.7 Consensus size: 40
65542021 CAAAGGCATT
* *
65542031 GAAGTGCAAACAGGGGCACGTAAGTGTAATCAGGGGTA-C
1 GAAGTACAAACAGGGGCACGTAAGTGCAATCAGGGGTATC
* * *
65542070 TGATGTACAAATAGAGGCACGTAAGTGCAATCAGGGGTATC
1 -GAAGTACAAACAGGGGCACGTAAGTGCAATCAGGGGTATC
* * *
65542111 GAAGTACAAACAAGGGCACGTAAGTGAAACCAGGGGTATC
1 GAAGTACAAACAGGGGCACGTAAGTGCAATCAGGGGTATC
* * * *
65542151 GAAGTAC-AACATGGGCACGTAAGTGCTATCAGGGATACC
1 GAAGTACAAACAGGGGCACGTAAGTGCAATCAGGGGTATC
* * *
65542190 GAAGTACAAATAGGGGCACATAAGTGCAATCAGGGGTACC
1 GAAGTACAAACAGGGGCACGTAAGTGCAATCAGGGGTATC
** * *
65542230 GAAGTACAAACAAAGACACGTAAGTGCAATCAAGGGTA-C
1 GAAGTACAAACAGGGGCACGTAAGTGCAATCAGGGGTATC
*
65542269 TGAAGTACAAATAGGGGCACGTAAGTG
1 -GAAGTACAAACAGGGGCACGTAAGTG
65542296 TAATAATTTA
Statistics
Matches: 190, Mismatches: 32, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
39 34 0.18
40 155 0.82
41 1 0.01
ACGTcount: A:0.37, C:0.17, G:0.30, T:0.16
Consensus pattern (40 bp):
GAAGTACAAACAGGGGCACGTAAGTGCAATCAGGGGTATC
Found at i:65542064 original size:20 final size:20
Alignment explanation
Indices: 65541932--65542295 Score: 135
Period size: 20 Copynumber: 18.2 Consensus size: 20
65541922 AGTGGCACCA
* *
65541932 AAGTGCAATTAGGAGCACG-
1 AAGTGCAATCAGGGGCACGT
**
65541951 AATGTGCAATCAAAGGCACCG-
1 AA-GTGCAATCAGGGGCA-CGT
* *
65541972 AAGTGAAAACAGGGGCACGT
1 AAGTGCAATCAGGGGCACGT
* ** *
65541992 AAGTGTAATCAGAAGCAC-A
1 AAGTGCAATCAGGGGCACGT
** *
65542011 AATGTGCAATCAAAGGCA-TT
1 AA-GTGCAATCAGGGGCACGT
*
65542031 GAAGTGCAAACAGGGGCACGT
1 -AAGTGCAATCAGGGGCACGT
* *
65542052 AAGTGTAATCAGGGGTAC-T
1 AAGTGCAATCAGGGGCACGT
* * *
65542071 GATGTACAAAT-AGAGGCACGT
1 -AAGTGC-AATCAGGGGCACGT
*
65542092 AAGTGCAATCAGGGGTATCG-
1 AAGTGCAATCAGGGGCA-CGT
* * *
65542112 AAGTACAAACAAGGGCACGT
1 AAGTGCAATCAGGGGCACGT
* * *
65542132 AAGTGAAACCAGGGGTATCG-
1 AAGTGCAATCAGGGGCA-CGT
* *
65542152 AAGTACAA-CATGGGCACGT
1 AAGTGCAATCAGGGGCACGT
* **
65542171 AAGTGCTATCAGGGATACCG-
1 AAGTGCAATCAGGGGCA-CGT
* *
65542191 AAGTACAAAT-AGGGGCACAT
1 AAGTGC-AATCAGGGGCACGT
*
65542211 AAGTGCAATCAGGGGTACCG-
1 AAGTGCAATCAGGGGCA-CGT
* * ** *
65542231 AAGTACAAACAAAGACACGT
1 AAGTGCAATCAGGGGCACGT
* *
65542251 AAGTGCAATCAAGGGTAC-T
1 AAGTGCAATCAGGGGCACGT
*
65542270 GAAGTACAAAT-AGGGGCACGT
1 -AAGTGC-AATCAGGGGCACGT
65542291 AAGTG
1 AAGTG
65542296 TAATAATTTA
Statistics
Matches: 246, Mismatches: 74, Indels: 49
0.67 0.20 0.13
Matches are distributed among these distances:
18 2 0.01
19 31 0.13
20 189 0.77
21 24 0.10
ACGTcount: A:0.38, C:0.17, G:0.29, T:0.16
Consensus pattern (20 bp):
AAGTGCAATCAGGGGCACGT
Found at i:65542096 original size:60 final size:60
Alignment explanation
Indices: 65541945--65542106 Score: 168
Period size: 60 Copynumber: 2.7 Consensus size: 60
65541935 TGCAATTAGG
* * *
65541945 AGCACGAATGTGCAATCAAAGGCACCG-AAGTGAAAACAGGGGCACGTAAGTGTAATCAGA
1 AGCACAAATGTACAATCAAAGGCA-CGTAAGTGCAAACAGGGGCACGTAAGTGTAATCAGA
* * *
65542005 AGCACAAATGTGCAATCAAAGGCA-TTGAAGTGCAAACAGGGGCACGTAAGTGTAATCAGG
1 AGCACAAATGTACAATCAAAGGCACGT-AAGTGCAAACAGGGGCACGTAAGTGTAATCAGA
* * ** * *
65542065 GGTACTGATGTACAAAT-AGAGGCACGTAAGTGCAATCAGGGG
1 AGCACAAATGTAC-AATCAAAGGCACGTAAGTGCAAACAGGGG
65542107 TATCGAAGTA
Statistics
Matches: 86, Mismatches: 12, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
60 82 0.95
61 4 0.05
ACGTcount: A:0.38, C:0.17, G:0.30, T:0.16
Consensus pattern (60 bp):
AGCACAAATGTACAATCAAAGGCACGTAAGTGCAAACAGGGGCACGTAAGTGTAATCAGA
Found at i:65542198 original size:119 final size:119
Alignment explanation
Indices: 65542030--65542299 Score: 357
Period size: 119 Copynumber: 2.3 Consensus size: 119
65542020 TCAAAGGCAT
* * * * * *
65542030 TGAAGTGCAAACAGGGGCACGTAAGTGTAATCAGGGGTACTGATGTACAAATAGAGGCACGTAAG
1 TGAAGTAC-AACATGGGCACGTAAGTGTAATCAGGGATACCGAAGTACAAATAGAGGCACATAAG
* * * *
65542095 TGCAATCAGGGGTATCGAAGTACAAACAAGGGCACGTAAGTGAAACCAGGGGTA-
65 TGCAATCAGGGGTACCGAAGTACAAACAAAGACACGTAAGTGAAACCAAGGGTAC
*
65542149 TCGAAGTACAACATGGGCACGTAAGTGCT-ATCAGGGATACCGAAGTACAAATAGGGGCACATAA
1 T-GAAGTACAACATGGGCACGTAAGTG-TAATCAGGGATACCGAAGTACAAATAGAGGCACATAA
* *
65542213 GTGCAATCAGGGGTACCGAAGTACAAACAAAGACACGTAAGTGCAATCAAGGGTAC
64 GTGCAATCAGGGGTACCGAAGTACAAACAAAGACACGTAAGTGAAACCAAGGGTAC
65542269 TGAAGTACAA-ATAGGGGCACGTAAGTGTAAT
1 TGAAGTACAACAT--GGGCACGTAAGTGTAAT
65542300 AATTTAATAA
Statistics
Matches: 132, Mismatches: 13, Indels: 11
0.85 0.08 0.07
Matches are distributed among these distances:
118 2 0.02
119 107 0.81
120 23 0.17
ACGTcount: A:0.37, C:0.16, G:0.29, T:0.17
Consensus pattern (119 bp):
TGAAGTACAACATGGGCACGTAAGTGTAATCAGGGATACCGAAGTACAAATAGAGGCACATAAGT
GCAATCAGGGGTACCGAAGTACAAACAAAGACACGTAAGTGAAACCAAGGGTAC
Found at i:65545117 original size:104 final size:105
Alignment explanation
Indices: 65544937--65545204 Score: 432
Period size: 104 Copynumber: 2.6 Consensus size: 105
65544927 TAACCGTTAT
* **
65544937 TGGTGGATCTCGCACTTAGCACCACCGCTGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
65545002 AATCAGCACATAGCAACCCCC-TTTCACATTTCAAAGATA
66 AATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATA
*
65545041 TGGTGGATATCGCACTTAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
65545106 AATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATA
66 AATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATA
* * * **
65545146 TGGTGGCTCA-CGCACATAGCACCACCAATGTATCGGGGAATCAGCACACAGCAACCCCT
1 TGGTGGAT-ATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCT
65545205 TTATATACAA
Statistics
Matches: 152, Mismatches: 10, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
104 82 0.54
105 69 0.45
106 1 0.01
ACGTcount: A:0.29, C:0.31, G:0.21, T:0.19
Consensus pattern (105 bp):
TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
AATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATA
Found at i:65545561 original size:29 final size:29
Alignment explanation
Indices: 65545528--65545591 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
65545518 TAATCCACCA
65545528 CCCAACTTTTTG-AAAATTACAATTTTGCC
1 CCCAAC-TTTTGCAAAATTACAATTTTGCC
* * *
65545557 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGCAAAATTACAATTTTGCC
65545587 CCCAA
1 CCCAA
65545592 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (29 bp):
CCCAACTTTTGCAAAATTACAATTTTGCC
Found at i:65545565 original size:30 final size:30
Alignment explanation
Indices: 65545535--65545591 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
65545525 CCACCCAACT
65545535 TTTTG-AAAATTACAATTTTGCCCCCAAAC
1 TTTTGCAAAATTACAATTTTGCCCCCAAAC
* * *
65545564 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGCAAAATTACAATTTTGCCCCCAA
65545592 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTGCCCCCAAAC
Found at i:65552592 original size:104 final size:104
Alignment explanation
Indices: 65552412--65552678 Score: 455
Period size: 104 Copynumber: 2.6 Consensus size: 104
65552402 TAACCGTTAT
* **
65552412 TGGTGGATCTCGCACTTAGCACCACCGCTGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
65552477 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
66 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
*
65552516 TGGTGGATATCGCACTTAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
65552581 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
66 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
* **
65552620 TGGTGGATCA-CGCACATAGCACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCT
1 TGGTGGAT-ATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCT
65552679 TTATATACAA
Statistics
Matches: 154, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
104 153 0.99
105 1 0.01
ACGTcount: A:0.30, C:0.31, G:0.21, T:0.18
Consensus pattern (104 bp):
TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
Found at i:65553037 original size:28 final size:29
Alignment explanation
Indices: 65553005--65553067 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
65552995 TAATCCACCA
65553005 CCCAACTTTTTG-AAAATTACAATTTTG-C
1 CCCAAC-TTTTGCAAAATTACAATTTTGTC
* *
65553033 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGCAAAATTACAATTTTGTC
65553063 CCCAA
1 CCCAA
65553068 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
28 8 0.27
29 18 0.60
30 4 0.13
ACGTcount: A:0.30, C:0.27, G:0.06, T:0.37
Consensus pattern (29 bp):
CCCAACTTTTGCAAAATTACAATTTTGTC
Found at i:65553041 original size:29 final size:30
Alignment explanation
Indices: 65553012--65553067 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
65553002 CCACCCAACT
65553012 TTTTG-AAAATTACAATTTTG-CCCCAAAC
1 TTTTGCAAAATTACAATTTTGTCCCCAAAC
* *
65553040 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGCAAAATTACAATTTTGTCCCCAA
65553068 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 5 0.21
29 13 0.54
30 6 0.25
ACGTcount: A:0.30, C:0.23, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTGTCCCCAAAC
Found at i:65561919 original size:21 final size:18
Alignment explanation
Indices: 65561876--65561923 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
65561866 GTTACTGCTA
*
65561876 CAGAAGAGGAAGTTGTTG
1 CAGAAGAGGAAGTGGTTG
65561894 CAGAAGAGGAAGTGGTTG
1 CAGAAGAGGAAGTGGTTG
* *
65561912 CTGAAGAAGAAG
1 CAGAAGAGGAAG
65561924 AAGTTGCTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.38, C:0.06, G:0.40, T:0.17
Consensus pattern (18 bp):
CAGAAGAGGAAGTGGTTG
Found at i:65569966 original size:61 final size:61
Alignment explanation
Indices: 65569859--65569975 Score: 173
Period size: 61 Copynumber: 1.9 Consensus size: 61
65569849 ACACGGCTTG
* * * *
65569859 GACTTCCTTACACAGGTAGACCACACGCCCGTGTAGTTTTAGCAGACTCTAACACGACCTA
1 GACTTCCTTACACAGGTAGACCACACGCCCGTGTACTTTCAACAGACTCGAACACGACCTA
*
65569920 GACTTCCTTACACGGGTAGACCACACGCCCGTGT-CTATTCAACAGACTCGAACACG
1 GACTTCCTTACACAGGTAGACCACACGCCCGTGTACT-TTCAACAGACTCGAACACG
65569976 GGTTGAAGCA
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
60 1 0.02
61 49 0.98
ACGTcount: A:0.27, C:0.32, G:0.19, T:0.21
Consensus pattern (61 bp):
GACTTCCTTACACAGGTAGACCACACGCCCGTGTACTTTCAACAGACTCGAACACGACCTA
Found at i:65574562 original size:19 final size:21
Alignment explanation
Indices: 65574538--65574579 Score: 70
Period size: 19 Copynumber: 2.1 Consensus size: 21
65574528 CTTCATGAAA
65574538 ATATAAAATT-A-ATTCTACC
1 ATATAAAATTAATATTCTACC
65574557 ATATAAAATTAATATTCTACC
1 ATATAAAATTAATATTCTACC
65574578 AT
1 AT
65574580 GACATCTTCC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 10 0.48
20 1 0.05
21 10 0.48
ACGTcount: A:0.48, C:0.14, G:0.00, T:0.38
Consensus pattern (21 bp):
ATATAAAATTAATATTCTACC
Found at i:65579264 original size:37 final size:36
Alignment explanation
Indices: 65579201--65579270 Score: 104
Period size: 37 Copynumber: 1.9 Consensus size: 36
65579191 AAATAAAAAT
*
65579201 CGTGAATTCGAGCTATTCAACATCGATTTTATCAAC
1 CGTGAATTCGAGCTACTCAACATCGATTTTATCAAC
* *
65579237 CGTGGATTCTGAGCTACTCAACGTCGATTTTATC
1 CGTGAATTC-GAGCTACTCAACATCGATTTTATC
65579271 TTTCCTTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
36 8 0.27
37 22 0.73
ACGTcount: A:0.26, C:0.23, G:0.17, T:0.34
Consensus pattern (36 bp):
CGTGAATTCGAGCTACTCAACATCGATTTTATCAAC
Found at i:65599375 original size:19 final size:20
Alignment explanation
Indices: 65599347--65599385 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
65599337 GATATAGGTA
*
65599347 GTATGTTGCTAGGT-CACAT
1 GTATGGTGCTAGGTGCACAT
*
65599366 GTATGGTGCTGGGTGCACAT
1 GTATGGTGCTAGGTGCACAT
65599386 CATGTGTACA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.18, C:0.15, G:0.33, T:0.33
Consensus pattern (20 bp):
GTATGGTGCTAGGTGCACAT
Found at i:65606838 original size:40 final size:40
Alignment explanation
Indices: 65606764--65606935 Score: 215
Period size: 40 Copynumber: 4.3 Consensus size: 40
65606754 GATAACCGAA
* *
65606764 CTAAGATCCGAAGGCATTCATGCGAGTTGCTATATCCGGG
1 CTAAGACCCGAAGGCATTTATGCGAGTTGCTATATCCGGG
* * * * *
65606804 CTATGTCCCGAAGGCATTTATGCTAG-TGATTATATTCGGG
1 CTAAGACCCGAAGGCATTTATGCGAGTTG-CTATATCCGGG
*
65606844 CTAAGACCCGAAGGCATTTGTGCGAGTTGCTATATCCGGG
1 CTAAGACCCGAAGGCATTTATGCGAGTTGCTATATCCGGG
* *
65606884 CTAAGACCCGAAGGCATTTGTGCGAGTTGTTATATCC-GG
1 CTAAGACCCGAAGGCATTTATGCGAGTTGCTATATCCGGG
65606923 CTAA-ATCCCGAAG
1 CTAAGA-CCCGAAG
65606936 ATACTTGGGT
Statistics
Matches: 115, Mismatches: 14, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
38 1 0.01
39 15 0.13
40 97 0.84
41 2 0.02
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (40 bp):
CTAAGACCCGAAGGCATTTATGCGAGTTGCTATATCCGGG
Done.