Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D12
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: 58873029
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 639818 characters in sequence are not A, C, G, or T
File 21 of 196
Found at i:6054166 original size:19 final size:19
Alignment explanation
Indices: 6054131--6054170 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
6054121 TTACAGTAAC
*
6054131 AATTAAATAAATTTTTTGAA
1 AATTAAATAAATATTTT-AA
6054151 AATTAAA-AAATATTTTAA
1 AATTAAATAAATATTTTAA
6054169 AA
1 AA
6054171 GATATATGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 4 0.21
19 8 0.42
20 7 0.37
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (19 bp):
AATTAAATAAATATTTTAA
Found at i:6056212 original size:22 final size:23
Alignment explanation
Indices: 6056181--6056227 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
6056171 ATGATATAAT
**
6056181 AATATTAAAATTCTAATTAAAAC
1 AATATTAAAATAATAATTAAAAC
*
6056204 AATA-TAAAATAATAATTATAAC
1 AATATTAAAATAATAATTAAAAC
6056226 AA
1 AA
6056228 AACAAATAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (23 bp):
AATATTAAAATAATAATTAAAAC
Found at i:6065072 original size:13 final size:13
Alignment explanation
Indices: 6065054--6065080 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
6065044 GCCAAAATAC
6065054 ACCATGTGATCAA
1 ACCATGTGATCAA
6065067 ACCATGTGATCAA
1 ACCATGTGATCAA
6065080 A
1 A
6065081 AAACATATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.22, G:0.15, T:0.22
Consensus pattern (13 bp):
ACCATGTGATCAA
Found at i:6065590 original size:67 final size:67
Alignment explanation
Indices: 6065444--6065575 Score: 192
Period size: 67 Copynumber: 2.0 Consensus size: 67
6065434 ATTTGAACCA
* ** * * *
6065444 TTCAAACATGAATTCGTTTATATGCCAATTTCACATATTTCATTTCTATACATACATGTTTCAAA
1 TTCAAACATGAATTCATTTATATGCCAATAGCACAGATTTCATTTCTATACACACACGTTTCAAA
6065509 GG
66 GG
* *
6065511 TTCAAACATGAATTCATTTATATGCCAATAGCACAGCTTTCGTTTCTATACACACACGTTTCAAA
1 TTCAAACATGAATTCATTTATATGCCAATAGCACAGATTTCATTTCTATACACACACGTTTCAAA
6065576 TGTTAGCAAA
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
67 57 1.00
ACGTcount: A:0.33, C:0.20, G:0.09, T:0.37
Consensus pattern (67 bp):
TTCAAACATGAATTCATTTATATGCCAATAGCACAGATTTCATTTCTATACACACACGTTTCAAA
GG
Found at i:6066650 original size:10 final size:10
Alignment explanation
Indices: 6066637--6066661 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
6066627 TAATTCAATT
6066637 AAAAAATTAA
1 AAAAAATTAA
6066647 AAAAAATTAA
1 AAAAAATTAA
6066657 AAAAA
1 AAAAA
6066662 CTAATTCAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (10 bp):
AAAAAATTAA
Found at i:6068921 original size:41 final size:40
Alignment explanation
Indices: 6068853--6068996 Score: 209
Period size: 41 Copynumber: 3.5 Consensus size: 40
6068843 TTTAACATAT
* *
6068853 TCACCGGCA-TTAACCTGCTAAGCTTATAGCCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCT-ATTCAGA
* *
6068893 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTAATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCT-ATTCAGA
*
6068934 TCACCGGCACTTAGCCTGCTAGACTTATAGCCTATTTCAGA
1 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTA-TTCAGA
6068975 TCACCGGCACTTAGCCTGCTAG
1 TCACCGGCACTTAGCCTGCTAG
6068997 ACGTAAATTC
Statistics
Matches: 94, Mismatches: 8, Indels: 3
0.90 0.08 0.03
Matches are distributed among these distances:
40 10 0.11
41 84 0.89
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.28
Consensus pattern (40 bp):
TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTATTCAGA
Found at i:6069582 original size:114 final size:115
Alignment explanation
Indices: 6069464--6069706 Score: 404
Period size: 114 Copynumber: 2.1 Consensus size: 115
6069454 CTCAAGATCT
6069464 TATACATATTCATATATAC-T-TATTCGAACTTCATTTATGCATATATATAACATTCATACTTAA
1 TATACATATT-ATATATACATATATTCGAACTTCATTTATGCATATATATAACATTCATACTTAA
*
6069527 CTAATTTCAATTTATATACTTTCAATTATAGCTCATCAAATATACAATAGA
65 CTAATTTCAATTCATATACTTTCAATTATAGCTCATCAAATATACAATAGA
*
6069578 TATACATA-TATATTTACATATATTCGAACTTCATTTATGCATATATATAACATTCATACTTAAC
1 TATACATATTATATATACATATATTCGAACTTCATTTATGCATATATATAACATTCATACTTAAC
* * *
6069642 TAATTTCAATTCATATATTTTTAATTATAGCTCATCAAATATACAATATA
66 TAATTTCAATTCATATACTTTCAATTATAGCTCATCAAATATACAATAGA
6069692 TATACATA-TATATAT
1 TATACATATTATATAT
6069707 TCTGATTTAA
Statistics
Matches: 121, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
112 7 0.06
113 2 0.02
114 112 0.93
ACGTcount: A:0.40, C:0.14, G:0.03, T:0.42
Consensus pattern (115 bp):
TATACATATTATATATACATATATTCGAACTTCATTTATGCATATATATAACATTCATACTTAAC
TAATTTCAATTCATATACTTTCAATTATAGCTCATCAAATATACAATAGA
Found at i:6071138 original size:11 final size:11
Alignment explanation
Indices: 6071122--6071148 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
6071112 CTATATAATG
6071122 CCATAGCTTTT
1 CCATAGCTTTT
6071133 CCATAGCTTTT
1 CCATAGCTTTT
6071144 CCATA
1 CCATA
6071149 CCATATATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.22, C:0.30, G:0.07, T:0.41
Consensus pattern (11 bp):
CCATAGCTTTT
Found at i:6072643 original size:26 final size:26
Alignment explanation
Indices: 6072614--6072663 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
6072604 AATTTTAAAC
6072614 CTATGAATTTTAA-ATTGTATTAATTA
1 CTAT-AATTTTAATATTGTATTAATTA
* *
6072640 CTATACTTTTAATTTTGTATTAAT
1 CTATAATTTTAATATTGTATTAAT
6072664 CATGAATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 7 0.33
26 14 0.67
ACGTcount: A:0.34, C:0.06, G:0.06, T:0.54
Consensus pattern (26 bp):
CTATAATTTTAATATTGTATTAATTA
Found at i:6073222 original size:19 final size:20
Alignment explanation
Indices: 6073193--6073237 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
6073183 TGTGTTTAAT
*
6073193 TATTCTTTTAAAATTAT-TTA
1 TATT-TTTTAAAAATATATTA
6073213 TATTTTTTAAAAATATATTA
1 TATTTTTTAAAAATATATTA
6073233 TATTT
1 TATTT
6073238 AAAATTTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 11 0.48
20 12 0.52
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (20 bp):
TATTTTTTAAAAATATATTA
Found at i:6073853 original size:6 final size:6
Alignment explanation
Indices: 6073808--6073910 Score: 50
Period size: 6 Copynumber: 16.5 Consensus size: 6
6073798 TGTTAGTTAA
* * * *
6073808 TTTTTC TTTCTT- TCTTTC CTTTTC CTTTTC CTTTTC -TTTTC TTTTTAC
1 TTTTTC TTT-TTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTT-C
* * * *
6073856 GTTTTC -TATCC TTCTTTC TTTTTC TCTGTTTC TTTTTAT TATTTTC TTTTTC
1 TTTTTC TTTTTC TT-TTTC TTTTTC T-T-TTTC TTTTT-C T-TTTTC TTTTTC
6073908 TTT
1 TTT
6073911 GCATTTTCTT
Statistics
Matches: 77, Mismatches: 10, Indels: 20
0.72 0.09 0.19
Matches are distributed among these distances:
5 10 0.13
6 43 0.56
7 15 0.19
8 9 0.12
ACGTcount: A:0.04, C:0.21, G:0.02, T:0.73
Consensus pattern (6 bp):
TTTTTC
Found at i:6074558 original size:63 final size:63
Alignment explanation
Indices: 6074447--6074609 Score: 191
Period size: 63 Copynumber: 2.6 Consensus size: 63
6074437 CCGTGTTATT
* * * ** * * *
6074447 GGCCGTGTAACCCACTATTTGTGAATTAAGGTCACATGGGCTAGGGACACGAGTGTGTATCTA
1 GGCCGTGTAACTCACTGTTTGTGAATTAGGGTCACACAGGCCAAGGACACGAGTGTGTATCCA
* * *
6074510 GGCCGTGTAACTCACTGTTTGTGAATTAGGGTCACGCAGGCCAAGGACACGGGTGTGTGTCCA
1 GGCCGTGTAACTCACTGTTTGTGAATTAGGGTCACACAGGCCAAGGACACGAGTGTGTATCCA
* * * *
6074573 GGCCATGTAACTCATTGTTTGTGAACTAGTGTCACAC
1 GGCCGTGTAACTCACTGTTTGTGAATTAGGGTCACAC
6074610 TGGCTAGAGA
Statistics
Matches: 84, Mismatches: 16, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
63 84 1.00
ACGTcount: A:0.23, C:0.21, G:0.29, T:0.27
Consensus pattern (63 bp):
GGCCGTGTAACTCACTGTTTGTGAATTAGGGTCACACAGGCCAAGGACACGAGTGTGTATCCA
Found at i:6076906 original size:11 final size:11
Alignment explanation
Indices: 6076892--6076958 Score: 56
Period size: 11 Copynumber: 6.6 Consensus size: 11
6076882 CGGCCCGAAT
6076892 TATATATTAAA
1 TATATATTAAA
6076903 TATATATT---
1 TATATATTAAA
**
6076911 TATATATTATT
1 TATATATTAAA
* *
6076922 TTTA-ATCAAA
1 TATATATTAAA
6076932 TATATATT--A
1 TATATATTAAA
6076941 TATATATTAAA
1 TATATATTAAA
6076952 TATATAT
1 TATATAT
6076959 AATATGGGCC
Statistics
Matches: 44, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
8 8 0.18
9 9 0.20
10 6 0.14
11 21 0.48
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.52
Consensus pattern (11 bp):
TATATATTAAA
Found at i:6079511 original size:17 final size:18
Alignment explanation
Indices: 6079476--6079513 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
6079466 CCCGGCGCAG
6079476 AGGAACAAAACACGAACA
1 AGGAACAAAACACGAACA
6079494 AGGAAGCAAAA-A-GAACA
1 AGGAA-CAAAACACGAACA
6079511 AGG
1 AGG
6079514 CTAACAGTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 8 0.42
18 6 0.32
19 5 0.26
ACGTcount: A:0.61, C:0.16, G:0.24, T:0.00
Consensus pattern (18 bp):
AGGAACAAAACACGAACA
Found at i:6080030 original size:26 final size:26
Alignment explanation
Indices: 6079994--6080044 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
6079984 AGATTAAACA
*
6079994 CTTAATTTGTTCTTTCCATCAAAGAT
1 CTTAACTTGTTCTTTCCATCAAAGAT
*
6080020 CTTAACTTGTTCTTTCCATTAAAGA
1 CTTAACTTGTTCTTTCCATCAAAGA
6080045 AAATTTTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.27, C:0.20, G:0.08, T:0.45
Consensus pattern (26 bp):
CTTAACTTGTTCTTTCCATCAAAGAT
Found at i:6081860 original size:35 final size:35
Alignment explanation
Indices: 6081771--6081860 Score: 85
Period size: 35 Copynumber: 2.6 Consensus size: 35
6081761 GTATATTCTA
* *
6081771 TTTTGTCGATTTCTTAATCATATATATATCATTCT
1 TTTTGTCGATTTCTTAATCATATATATATCAATAT
* * * * *
6081806 TTTTGTCG-TAATATAAATCAT-TAATGTATTAATAT
1 TTTTGTCGAT-TTCTTAATCATAT-ATATATCAATAT
6081841 TTTTGTCGATTTCTTAATCA
1 TTTTGTCGATTTCTTAATCA
6081861 CACATTTAAC
Statistics
Matches: 42, Mismatches: 10, Indels: 6
0.72 0.17 0.10
Matches are distributed among these distances:
34 2 0.05
35 39 0.93
36 1 0.02
ACGTcount: A:0.29, C:0.11, G:0.08, T:0.52
Consensus pattern (35 bp):
TTTTGTCGATTTCTTAATCATATATATATCAATAT
Found at i:6082024 original size:20 final size:21
Alignment explanation
Indices: 6081996--6082038 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
6081986 TAATTAAGTA
*
6081996 TTTACTTTA-GTGGTTAAGTGT
1 TTTACTTTATGTGCTTAAG-GT
6082017 TTTA-TTTATGTGCTTAAGGT
1 TTTACTTTATGTGCTTAAGGT
6082037 TT
1 TT
6082039 GGGGTTCAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.19, C:0.05, G:0.21, T:0.56
Consensus pattern (21 bp):
TTTACTTTATGTGCTTAAGGT
Found at i:6082530 original size:273 final size:273
Alignment explanation
Indices: 6082043--6082583 Score: 920
Period size: 273 Copynumber: 2.0 Consensus size: 273
6082033 AGGTTTGGGG
* *
6082043 TTCAAGTCCCATTTTTGGAAATTTTGCTTTTTGTTTTGAATCAACCCTCACTTTCAAACTTTTGA
1 TTCAAGTCCCATTTTTGGAAATTTTGCTATTTGTTTTGAATCAACCCTCACTTTCAAACTTTCGA
** **
6082108 CTTAAGATTAATTTTGTGTAAACTTATATTAAGAATGAGCTTGTTGGTTTAATAGTTAAACTTTT
66 CTTAAGATTAATTTTGCATAAACTTATATTAAGAATGAGCTTACTGGTTTAATAGTTAAACTTTT
* * * *
6082173 GTATACCCTTTGGTCTTATGTTCGAGTTTCTGCAAAAGCTATGAGAAAATATCTTATGCTAGTTT
131 GTATACCCTTTGCTCTTATGTTCAAGTTTCTGCAAAAGCTATGAGAAAACATCTTATACTAGTTT
* * *
6082238 ATAAAAATTAGTTTATTTTAAGGTAATTAAATTCCTTTATTTTTGTTAAATTTTTTTTCACGTTT
196 ATAAAAATTAGTCTATTTTAAGGTAATTAAATTCCTTTATTTTTGTTAAAATTTCTTTCACGTTT
6082303 TATTTCTTTCACA
261 TATTTCTTTCACA
*
6082316 TTCAAGTCCCATTTTTGGAAATTTTGCTATTTGTTTTGAATCAACCCTCACTTTTAAACTTTCGA
1 TTCAAGTCCCATTTTTGGAAATTTTGCTATTTGTTTTGAATCAACCCTCACTTTCAAACTTTCGA
* * *
6082381 CTTAAGATTAATTTTGCATAAACTTGTGTTAAGAATGAGCTTACTGGTTTAATGGTTAAACTTTT
66 CTTAAGATTAATTTTGCATAAACTTATATTAAGAATGAGCTTACTGGTTTAATAGTTAAACTTTT
*
6082446 GTATACCCTTTGCTCTTGTGTTCAAGTTTCTGCAAAAGCTATGAGAAAACATCTTATACTAGTTT
131 GTATACCCTTTGCTCTTATGTTCAAGTTTCTGCAAAAGCTATGAGAAAACATCTTATACTAGTTT
6082511 ATAAAAATTAGTCTATTTTAAGGTAATTAAATTCCTTTATTTTTGTTAAAATTTCTTTCACGTTT
196 ATAAAAATTAGTCTATTTTAAGGTAATTAAATTCCTTTATTTTTGTTAAAATTTCTTTCACGTTT
6082576 TATTTCTT
261 TATTTCTT
6082584 CCTTTATCCT
Statistics
Matches: 250, Mismatches: 18, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
273 250 1.00
ACGTcount: A:0.28, C:0.13, G:0.12, T:0.46
Consensus pattern (273 bp):
TTCAAGTCCCATTTTTGGAAATTTTGCTATTTGTTTTGAATCAACCCTCACTTTCAAACTTTCGA
CTTAAGATTAATTTTGCATAAACTTATATTAAGAATGAGCTTACTGGTTTAATAGTTAAACTTTT
GTATACCCTTTGCTCTTATGTTCAAGTTTCTGCAAAAGCTATGAGAAAACATCTTATACTAGTTT
ATAAAAATTAGTCTATTTTAAGGTAATTAAATTCCTTTATTTTTGTTAAAATTTCTTTCACGTTT
TATTTCTTTCACA
Found at i:6083320 original size:42 final size:43
Alignment explanation
Indices: 6083231--6083321 Score: 105
Period size: 42 Copynumber: 2.1 Consensus size: 43
6083221 ATGACATGGG
* * * * *
6083231 TGTGTATCTAGACCGTGTGACTCTCTAACTTGAGTAACATGGT
1 TGTGTGTCTAGACCGTATAACTCTCTAACTTGAGTAACACGGC
*
6083274 TGTGTGTC-AGACCGTATAACTCTCTAACTT-AGGTCACACGGC
1 TGTGTGTCTAGACCGTATAACTCTCTAACTTGA-GTAACACGGC
6083316 TGTGTG
1 TGTGTG
6083322 CCAGGTCGTG
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
41 1 0.02
42 33 0.80
43 7 0.17
ACGTcount: A:0.22, C:0.21, G:0.24, T:0.33
Consensus pattern (43 bp):
TGTGTGTCTAGACCGTATAACTCTCTAACTTGAGTAACACGGC
Found at i:6085263 original size:20 final size:20
Alignment explanation
Indices: 6085224--6085269 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 20
6085214 CCAATATGAT
*
6085224 GTTCTTCAGGATTTCTTCAA
1 GTTCTTCAGAATTTCTTCAA
6085244 GTTCTTCAGAAATTTC-TCAA
1 GTTCTTCAG-AATTTCTTCAA
6085264 GATTCT
1 G-TTCT
6085270 AAAAAGAGCT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 14 0.61
21 9 0.39
ACGTcount: A:0.24, C:0.20, G:0.13, T:0.43
Consensus pattern (20 bp):
GTTCTTCAGAATTTCTTCAA
Found at i:6091972 original size:12 final size:12
Alignment explanation
Indices: 6091955--6091979 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
6091945 ACATCAATTC
6091955 AATAATATACCA
1 AATAATATACCA
6091967 AATAATATACCA
1 AATAATATACCA
6091979 A
1 A
6091980 TTGCATTCAA
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:0.60, C:0.16, G:0.00, T:0.24
Consensus pattern (12 bp):
AATAATATACCA
Found at i:6092910 original size:19 final size:19
Alignment explanation
Indices: 6092882--6092939 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 19
6092872 TACTAGCGTG
*
6092882 CAAAACGCATCCTGGCGCA
1 CAAAATGCATCCTGGCGCA
* *
6092901 -AAAAGTGCATACTGGCACA
1 CAAAA-TGCATCCTGGCGCA
*
6092920 CAAAATACATCCTGGCGCA
1 CAAAATGCATCCTGGCGCA
6092939 C
1 C
6092940 GAAGCGCATA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
18 4 0.13
19 23 0.74
20 4 0.13
ACGTcount: A:0.36, C:0.31, G:0.19, T:0.14
Consensus pattern (19 bp):
CAAAATGCATCCTGGCGCA
Found at i:6092980 original size:19 final size:19
Alignment explanation
Indices: 6092903--6093064 Score: 94
Period size: 19 Copynumber: 8.4 Consensus size: 19
6092893 CTGGCGCAAA
*
6092903 AAGTGCATAC-TGGCACACA
1 AAGTGCAT-CTTGGCACACG
* * * *
6092922 AAATACATCCTGGCGCACG
1 AAGTGCATCTTGGCACACG
* * *
6092941 AAGCGCATATCTGGAACACG
1 AAGTGCATCT-TGGCACACG
*
6092961 ATGTGCATCTTGGCACACG
1 AAGTGCATCTTGGCACACG
* *
6092980 AAGTGCATAC-TGGCATACA
1 AAGTGCAT-CTTGGCACACG
* * **
6092999 AAGTGCATCCTAGTGCACG
1 AAGTGCATCTTGGCACACG
* * *
6093018 AAGCGTATATTTGGCACACG
1 AAGTGCAT-CTTGGCACACG
* *
6093038 ATGTGTATCTTGGCACACG
1 AAGTGCATCTTGGCACACG
6093057 AAGTGCAT
1 AAGTGCAT
6093065 TATGAAGAAT
Statistics
Matches: 103, Mismatches: 35, Indels: 10
0.70 0.24 0.07
Matches are distributed among these distances:
18 2 0.02
19 74 0.72
20 27 0.26
ACGTcount: A:0.30, C:0.24, G:0.24, T:0.22
Consensus pattern (19 bp):
AAGTGCATCTTGGCACACG
Found at i:6092984 original size:77 final size:77
Alignment explanation
Indices: 6092903--6093064 Score: 243
Period size: 77 Copynumber: 2.1 Consensus size: 77
6092893 CTGGCGCAAA
*
6092903 AAGTGCATACTGGCACACAAAATACATCCTGGCGCACGAAGCGCATATCTGGAACACGATGTGCA
1 AAGTGCATACTGGCACACAAAATACATCCTAGCGCACGAAGCGCATATCTGGAACACGATGTGCA
6092968 TCTTGGCACACG
66 TCTTGGCACACG
* * * * * * * *
6092980 AAGTGCATACTGGCATACAAAGTGCATCCTAGTGCACGAAGCGTATATTTGGCACACGATGTGTA
1 AAGTGCATACTGGCACACAAAATACATCCTAGCGCACGAAGCGCATATCTGGAACACGATGTGCA
6093045 TCTTGGCACACG
66 TCTTGGCACACG
6093057 AAGTGCAT
1 AAGTGCAT
6093065 TATGAAGAAT
Statistics
Matches: 76, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
77 76 1.00
ACGTcount: A:0.30, C:0.24, G:0.24, T:0.22
Consensus pattern (77 bp):
AAGTGCATACTGGCACACAAAATACATCCTAGCGCACGAAGCGCATATCTGGAACACGATGTGCA
TCTTGGCACACG
Found at i:6098099 original size:89 final size:89
Alignment explanation
Indices: 6097971--6098440 Score: 705
Period size: 89 Copynumber: 5.3 Consensus size: 89
6097961 CCTCACGCCA
* * * * * * * * *
6097971 ATGAAGACAAGGTCTG-TTCTCTTCGATCTACTCCACCACCAGTATGGGGAGACAAGATCTATTG
1 ATGAAGACAAGATCTGCTT-TCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGTTA
*
6098035 TCT-TCGATCTACTTCACGCCAGTAT
65 TCTCT-GATCTACTTCACGCCAGTAC
*
6098060 ATGAAGACAAGATCTACTTTCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTCG-TA
1 ATGAAGACAAGATCTGCTTTCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCT-GTTA
6098124 TCTCTGATCTACTTCACGCCAGTAC
65 TCTCTGATCTACTTCACGCCAGTAC
* *
6098149 ATGAAGACAAGAT-TGTTTTCTTTGATCTGCTTTGCCACCAGTATGGGAAGGCAAGATCTGTTAT
1 ATGAAGACAAGATCTGCTTTCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGTTAT
*
6098213 CTTTGATCTACTTCACGCCAGTAC
66 CTCTGATCTACTTCACGCCAGTAC
* ** *
6098237 ATGAAGACAATATCTATTTTCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGGTAT
1 ATGAAGACAAGATCTGCTTTCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGTTAT
6098302 CTCTGATCTACTTCACGCCAGTAC
66 CTCTGATCTACTTCACGCCAGTAC
* *
6098326 ATGAAGATAAGATCTGCTTTCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATTTGTTAT
1 ATGAAGACAAGATCTGCTTTCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGTTAT
6098391 CTCTGATCTACTTCACGCCAGTAC
66 CTCTGATCTACTTCACGCCAGTAC
6098415 ATGAAGACAAGATCTGCTTTCTTTGA
1 ATGAAGACAAGATCTGCTTTCTTTGA
6098441 ACCTGCTCCA
Statistics
Matches: 349, Mismatches: 27, Indels: 10
0.90 0.07 0.03
Matches are distributed among these distances:
87 1 0.00
88 81 0.23
89 264 0.76
90 3 0.01
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.31
Consensus pattern (89 bp):
ATGAAGACAAGATCTGCTTTCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGTTAT
CTCTGATCTACTTCACGCCAGTAC
Found at i:6098304 original size:177 final size:178
Alignment explanation
Indices: 6097971--6098440 Score: 737
Period size: 177 Copynumber: 2.6 Consensus size: 178
6097961 CCTCACGCCA
* * * * * * * * *
6097971 ATGAAGACAAGGTCTG-TTCTCTTCGATCTACTCCACCACCAGTATGGGGAGACAAGATCTATTG
1 ATGAAGACAAGATCTGCTT-TCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGTTA
* *
6098035 TCTTCGATCTACTTCACGCCAGTATATGAAGACAAGATCTACTTTCTTTGATCTGCTTCGCCACC
65 TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTACTTTCTTTGATCTGCTTCGCCACC
6098100 AGTATGGGAAGGCAAGATCTCGTATCTCTGATCTACTTCACGCCAGTAC
130 AGTATGGGAAGGCAAGATCTCGTATCTCTGATCTACTTCACGCCAGTAC
* *
6098149 ATGAAGACAAGAT-TGTTTTCTTTGATCTGCTTTGCCACCAGTATGGGAAGGCAAGATCTGTTAT
1 ATGAAGACAAGATCTGCTTTCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGTTAT
* *
6098213 CTTTGATCTACTTCACGCCAGTACATGAAGACAATATCTATTTTCTTTGATCTGCTTCGCCACCA
66 CTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTACTTTCTTTGATCTGCTTCGCCACCA
*
6098278 GTATGGGAAGGCAAGATCTGGTATCTCTGATCTACTTCACGCCAGTAC
131 GTATGGGAAGGCAAGATCTCGTATCTCTGATCTACTTCACGCCAGTAC
* *
6098326 ATGAAGATAAGATCTGCTTTCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATTTGTTAT
1 ATGAAGACAAGATCTGCTTTCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGTTAT
* *
6098391 CTCTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTTGA
66 CTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTACTTTCTTTGA
6098441 ACCTGCTCCA
Statistics
Matches: 267, Mismatches: 23, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
177 159 0.60
178 108 0.40
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.31
Consensus pattern (178 bp):
ATGAAGACAAGATCTGCTTTCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGTTAT
CTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTACTTTCTTTGATCTGCTTCGCCACCA
GTATGGGAAGGCAAGATCTCGTATCTCTGATCTACTTCACGCCAGTAC
Found at i:6105422 original size:19 final size:17
Alignment explanation
Indices: 6105388--6105428 Score: 55
Period size: 19 Copynumber: 2.3 Consensus size: 17
6105378 TTTTCCTTAA
*
6105388 AAAAATGAAACAGAAAG
1 AAAAATGAAAAAGAAAG
6105405 AAAAATGAAAAAATGAAAG
1 AAAAATG-AAAAA-GAAAG
6105424 AAAAA
1 AAAAA
6105429 AGATAGAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.33
18 4 0.19
19 10 0.48
ACGTcount: A:0.76, C:0.02, G:0.15, T:0.07
Consensus pattern (17 bp):
AAAAATGAAAAAGAAAG
Found at i:6105752 original size:23 final size:23
Alignment explanation
Indices: 6105726--6105774 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
6105716 AAAGAAAAGA
6105726 ATCTAAAAATCAAAGATCAATCT
1 ATCTAAAAATCAAAGATCAATCT
6105749 ATCTAAAAATCAAAGATCAATCT
1 ATCTAAAAATCAAAGATCAATCT
6105772 ATC
1 ATC
6105775 CTGTTGTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.51, C:0.18, G:0.04, T:0.27
Consensus pattern (23 bp):
ATCTAAAAATCAAAGATCAATCT
Found at i:6106155 original size:43 final size:43
Alignment explanation
Indices: 6106085--6106232 Score: 206
Period size: 43 Copynumber: 3.4 Consensus size: 43
6106075 TGTCCCAAAC
* ***
6106085 ATGGTCTTACATGGAAATCTTGTATCGATGCCAATAGCCCAGCT
1 ATGGTCTTACA-CGAAATCTCAAATCGATGCCAATAGCCCAGCT
* * *
6106129 ATAGTCTTACATGAAATCTCAAATCGATGCCAATAGCCCAGTT
1 ATGGTCTTACACGAAATCTCAAATCGATGCCAATAGCCCAGCT
**
6106172 ATGGTCTTACACGAAATCTCAAATCGATGCCAATAGCGTAGCT
1 ATGGTCTTACACGAAATCTCAAATCGATGCCAATAGCCCAGCT
6106215 ATGGTCTTACACGAAATC
1 ATGGTCTTACACGAAATC
6106233 ACACCTCAGA
Statistics
Matches: 93, Mismatches: 11, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
43 83 0.89
44 10 0.11
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.28
Consensus pattern (43 bp):
ATGGTCTTACACGAAATCTCAAATCGATGCCAATAGCCCAGCT
Found at i:6106447 original size:31 final size:31
Alignment explanation
Indices: 6106342--6106450 Score: 166
Period size: 31 Copynumber: 3.5 Consensus size: 31
6106332 AACTAGTCTC
* * *
6106342 AATTCGGCAATATATATCCATATACAAATCA
1 AATTCGACAATGTATATCTATATACAAATCA
*
6106373 AATTCGACAATGAATATCTATATACAAATCA
1 AATTCGACAATGTATATCTATATACAAATCA
6106404 AATTCGACAATGTATATCTATATACAAATCA
1 AATTCGACAATGTATATCTATATACAAATCA
6106435 AATTCGGA-AATGTATA
1 AATTC-GACAATGTATA
6106451 AAACATATAC
Statistics
Matches: 72, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
31 70 0.97
32 2 0.03
ACGTcount: A:0.46, C:0.16, G:0.08, T:0.30
Consensus pattern (31 bp):
AATTCGACAATGTATATCTATATACAAATCA
Found at i:6110690 original size:6 final size:6
Alignment explanation
Indices: 6110681--6110745 Score: 64
Period size: 6 Copynumber: 11.3 Consensus size: 6
6110671 CTAAGAAAAT
* * * * *
6110681 AATAAA AAT--A ACTAAA AATAAC AATAAA CATAAT CAT-AA AATAAA
1 AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA
6110726 AATAAA AATAAA AATAAA AA
1 AATAAA AATAAA AATAAA AA
6110746 AACTTAATGG
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
4 3 0.06
5 3 0.06
6 42 0.88
ACGTcount: A:0.75, C:0.06, G:0.00, T:0.18
Consensus pattern (6 bp):
AATAAA
Found at i:6110742 original size:23 final size:23
Alignment explanation
Indices: 6110681--6110744 Score: 67
Period size: 23 Copynumber: 2.8 Consensus size: 23
6110671 CTAAGAAAAT
** *
6110681 AATAAAAATAACTA-AAAATAAC
1 AATAAAAATAAAAATAAAATAAA
* **
6110703 AATAAACATAATCATAAAATAAA
1 AATAAAAATAAAAATAAAATAAA
6110726 AATAAAAATAAAAATAAAA
1 AATAAAAATAAAAATAAAA
6110745 AAACTTAATG
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
22 11 0.32
23 23 0.68
ACGTcount: A:0.75, C:0.06, G:0.00, T:0.19
Consensus pattern (23 bp):
AATAAAAATAAAAATAAAATAAA
Found at i:6112597 original size:12 final size:12
Alignment explanation
Indices: 6112582--6112614 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
6112572 AAAAGACAAA
6112582 AAAAAAAAAAAG
1 AAAAAAAAAAAG
*
6112594 AAAAAGAAAAAG
1 AAAAAAAAAAAG
6112606 AAAAAAAAA
1 AAAAAAAAA
6112615 GCTGAAGATG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAAG
Found at i:6112600 original size:23 final size:22
Alignment explanation
Indices: 6112572--6112615 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
6112562 GTTGACCTCT
6112572 AAAAGACAAAAAAAAAAAAAAGA
1 AAAAGA-AAAAAAAAAAAAAAGA
*
6112595 AAAAGAAAAAGAAAAAAAAAG
1 AAAAGAAAAAAAAAAAAAAAG
6112616 CTGAAGATGC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.86, C:0.02, G:0.11, T:0.00
Consensus pattern (22 bp):
AAAAGAAAAAAAAAAAAAAAGA
Found at i:6116289 original size:22 final size:22
Alignment explanation
Indices: 6116260--6116313 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
6116250 GATATGCAAG
6116260 GGTT-GAATGCCCTAATGTTTT
1 GGTTCGAATGCCCTAATGTTTT
6116281 GGTTCGAATGCCCTAATGTTTT
1 GGTTCGAATGCCCTAATGTTTT
*
6116303 GGGTCGAATGC
1 GGTTCGAATGC
6116314 TCGATTTGAG
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 4 0.13
22 27 0.87
ACGTcount: A:0.19, C:0.17, G:0.28, T:0.37
Consensus pattern (22 bp):
GGTTCGAATGCCCTAATGTTTT
Found at i:6121244 original size:27 final size:27
Alignment explanation
Indices: 6121195--6121253 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
6121185 AGTGAATTCA
* * *
6121195 AAATATATTTTAATTAGGAAATTGATT
1 AAATTTATTTTAATTAGAAAATTAATT
6121222 AAATTTATTTTAATTA-AACAATTAATT
1 AAATTTATTTTAATTAGAA-AATTAATT
*
6121249 TAATT
1 AAATT
6121254 AAAATATTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 1 0.04
27 26 0.96
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.47
Consensus pattern (27 bp):
AAATTTATTTTAATTAGAAAATTAATT
Found at i:6121252 original size:17 final size:17
Alignment explanation
Indices: 6121230--6121270 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
6121220 TTAAATTTAT
6121230 TTTAATTAAACA-ATTAA
1 TTTAATTAAA-ATATTAA
6121247 TTTAATTAAAATATTAA
1 TTTAATTAAAATATTAA
6121264 -TTAATTA
1 TTTAATTA
6121271 GATTAATTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 8 0.35
17 15 0.65
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (17 bp):
TTTAATTAAAATATTAA
Found at i:6121284 original size:17 final size:17
Alignment explanation
Indices: 6121264--6121298 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
6121254 AAAATATTAA
*
6121264 TTAATTAGATTAATTTC
1 TTAATTAAATTAATTTC
*
6121281 TTAATTAAATTATTTTC
1 TTAATTAAATTAATTTC
6121298 T
1 T
6121299 CAACCCAATT
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:0.03, T:0.57
Consensus pattern (17 bp):
TTAATTAAATTAATTTC
Found at i:6122299 original size:17 final size:17
Alignment explanation
Indices: 6122279--6122315 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
6122269 AATTTTTGAA
6122279 TTAGTGAATTCTGTGAT
1 TTAGTGAATTCTGTGAT
*
6122296 TTAGTGAATTTTGTGAT
1 TTAGTGAATTCTGTGAT
6122313 TTA
1 TTA
6122316 AAAAGAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.24, C:0.03, G:0.22, T:0.51
Consensus pattern (17 bp):
TTAGTGAATTCTGTGAT
Found at i:6123591 original size:46 final size:46
Alignment explanation
Indices: 6123538--6123677 Score: 253
Period size: 46 Copynumber: 3.0 Consensus size: 46
6123528 CCATTGCAAA
*
6123538 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAATCATACTGAG
1 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
6123584 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
1 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
* *
6123630 TTGTGAAAAGTATGTATGGTATTTCAGTGAAGAAAACCATACTGAG
1 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
6123676 TT
1 TT
6123678 ATAGCATTGT
Statistics
Matches: 91, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
46 91 1.00
ACGTcount: A:0.35, C:0.08, G:0.26, T:0.31
Consensus pattern (46 bp):
TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
Found at i:6130894 original size:5 final size:5
Alignment explanation
Indices: 6130884--6130912 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
6130874 TACGGTCTAT
6130884 GGGTC GGGTC GGGTC GGGTC GGGTC GGGT
1 GGGTC GGGTC GGGTC GGGTC GGGTC GGGT
6130913 AGCGCCTATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.00, C:0.17, G:0.62, T:0.21
Consensus pattern (5 bp):
GGGTC
Found at i:6131061 original size:21 final size:22
Alignment explanation
Indices: 6131036--6131148 Score: 117
Period size: 26 Copynumber: 4.9 Consensus size: 22
6131026 TGGATTAGTA
6131036 TTTTGTATGAATATTGTAAT-T
1 TTTTGTATGAATATTGTAATAT
6131057 TTTTGTATGAATATTGT-A-AT
1 TTTTGTATGAATATTGTAATAT
6131077 TTTT-TATGAATATTGTAATATTAT
1 TTTTGTATGAATATTGT-A-A-TAT
6131101 AATTTTGTATGAATATTGTAATAT
1 --TTTTGTATGAATATTGTAATAT
6131125 TGTAACTTGTATGAATATTGTAAT
1 T-T---TTGTATGAATATTGTAAT
6131149 GTCGGGATAT
Statistics
Matches: 79, Mismatches: 0, Indels: 21
0.79 0.00 0.21
Matches are distributed among these distances:
19 12 0.15
20 6 0.08
21 17 0.22
22 2 0.03
23 1 0.01
24 5 0.06
25 1 0.01
26 23 0.29
27 12 0.15
ACGTcount: A:0.33, C:0.01, G:0.13, T:0.53
Consensus pattern (22 bp):
TTTTGTATGAATATTGTAATAT
Found at i:6131103 original size:27 final size:27
Alignment explanation
Indices: 6131045--6131148 Score: 132
Period size: 27 Copynumber: 4.1 Consensus size: 27
6131035 ATTTTGTATG
6131045 AATATTGTAATTTT-T-TG--TA-TG-
1 AATATTGTAATTTTGTATGAATATTGT
*
6131066 AATATTGTAATTTTTTATGAATATTGT
1 AATATTGTAATTTTGTATGAATATTGT
*
6131093 AATATTATAATTTTGTATGAATATTGT
1 AATATTGTAATTTTGTATGAATATTGT
*
6131120 AATATTGTAA-CTTGTATGAATATTGT
1 AATATTGTAATTTTGTATGAATATTGT
6131146 AAT
1 AAT
6131149 GTCGGGATAT
Statistics
Matches: 73, Mismatches: 4, Indels: 7
0.87 0.05 0.08
Matches are distributed among these distances:
21 14 0.19
22 1 0.01
23 2 0.03
25 2 0.03
26 20 0.27
27 34 0.47
ACGTcount: A:0.35, C:0.01, G:0.12, T:0.52
Consensus pattern (27 bp):
AATATTGTAATTTTGTATGAATATTGT
Found at i:6131122 original size:19 final size:19
Alignment explanation
Indices: 6130962--6131095 Score: 96
Period size: 19 Copynumber: 6.7 Consensus size: 19
6130952 AGAGGCGCCA
6130962 ATGAATATTGTAATTTTGT
1 ATGAATATTGTAATTTTGT
* *
6130981 ATTAATATTGTAATTATTTT
1 ATGAATATTGTAATT-TTGT
6131001 AT-AATTAAATTTGT-ATTTATAGTT
1 ATGAA-T--A-TTGTAATTT-T-G-T
* * *
6131025 TTGGAT-TAGT-ATTTTGT
1 ATGAATATTGTAATTTTGT
6131042 ATGAATATTGTAATTTTTTGT
1 ATGAATATTGTAA--TTTTGT
*
6131063 ATGAATATTGTAATTTTTT
1 ATGAATATTGTAATTTTGT
6131082 ATGAATATTGTAAT
1 ATGAATATTGTAAT
6131096 ATTATAATTT
Statistics
Matches: 92, Mismatches: 10, Indels: 26
0.72 0.08 0.20
Matches are distributed among these distances:
17 5 0.05
18 4 0.04
19 37 0.40
20 13 0.14
21 20 0.22
22 5 0.05
23 4 0.04
24 3 0.03
25 1 0.01
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (19 bp):
ATGAATATTGTAATTTTGT
Found at i:6131127 original size:19 final size:19
Alignment explanation
Indices: 6131038--6131148 Score: 83
Period size: 19 Copynumber: 5.9 Consensus size: 19
6131028 GATTAGTATT
*
6131038 TTGTATGAATATTGTAATTTT
1 TTGTATGAATATTGTAA--TA
*
6131059 TTGTATGAATATTGTAATT
1 TTGTATGAATATTGTAATA
*
6131078 TTTTATGAATATTGTAATA
1 TTGTATGAATATTGTAATA
*
6131097 -T-TAT-AATTTTGTATGAATA
1 TTGTATGAATATTG--T-AATA
*
6131116 TTG--T-AATATTGTAA-C
1 TTGTATGAATATTGTAATA
6131131 TTGTATGAATATTGTAAT
1 TTGTATGAATATTGTAAT
6131149 GTCGGGATAT
Statistics
Matches: 76, Mismatches: 5, Indels: 20
0.75 0.05 0.20
Matches are distributed among these distances:
15 3 0.04
16 8 0.11
17 5 0.07
18 12 0.16
19 30 0.39
20 1 0.01
21 17 0.22
ACGTcount: A:0.33, C:0.01, G:0.14, T:0.52
Consensus pattern (19 bp):
TTGTATGAATATTGTAATA
Found at i:6131377 original size:16 final size:16
Alignment explanation
Indices: 6131334--6131377 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
6131324 AAAATCAAAT
*
6131334 AAAATTTAATTATATA
1 AAAATTAAATTATATA
* *
6131350 AAAGTTACATTATATA
1 AAAATTAAATTATATA
6131366 AAAATTAAATTA
1 AAAATTAAATTA
6131378 GTTAACAACA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (16 bp):
AAAATTAAATTATATA
Found at i:6131453 original size:38 final size:38
Alignment explanation
Indices: 6131410--6131491 Score: 155
Period size: 38 Copynumber: 2.2 Consensus size: 38
6131400 AAAAAGTCAG
6131410 TTATAATTAAACTTTTAATAAAATGATTTTTAATTTTT
1 TTATAATTAAACTTTTAATAAAATGATTTTTAATTTTT
*
6131448 TTATAATTAAACTTTTAATAAGATGATTTTTAATTTTT
1 TTATAATTAAACTTTTAATAAAATGATTTTTAATTTTT
6131486 TTATAA
1 TTATAA
6131492 ACTTTATATG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 43 1.00
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (38 bp):
TTATAATTAAACTTTTAATAAAATGATTTTTAATTTTT
Found at i:6131617 original size:60 final size:60
Alignment explanation
Indices: 6131524--6131645 Score: 174
Period size: 60 Copynumber: 2.0 Consensus size: 60
6131514 ATATTAAACT
* * * * *
6131524 AAACACAACAACTTATAGCTTAATCCTAAATTACTAATAAATTAAATT-TTAAATAATTAC
1 AAACACAAAAACTTATAACATAATCCTAAATTACTAACAAATT-AATTATAAAATAATTAC
*
6131584 AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTATAAAATAATTAC
1 AAACACAAAAACTTATAACATAATCCTAAATTACTAACAAATTAATTATAAAATAATTAC
6131644 AA
1 AA
6131646 TATTCATACA
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
59 4 0.07
60 51 0.93
ACGTcount: A:0.54, C:0.14, G:0.01, T:0.31
Consensus pattern (60 bp):
AAACACAAAAACTTATAACATAATCCTAAATTACTAACAAATTAATTATAAAATAATTAC
Found at i:6131672 original size:8 final size:8
Alignment explanation
Indices: 6131659--6131768 Score: 58
Period size: 8 Copynumber: 12.4 Consensus size: 8
6131649 TCATACAAAA
6131659 ATTACAAT
1 ATTACAAT
6131667 ATTACAAT
1 ATTACAAT
* * *
6131675 ATATCCCGAC
1 AT-T-ACAAT
6131685 ATTACAAT
1 ATTACAAT
*
6131693 ATTCATACAAA
1 A-T--TACAAT
6131704 ATTACAAT
1 ATTACAAT
6131712 ATTACAAT
1 ATTACAAT
*
6131720 ATTCATACAAA
1 A-T--TACAAT
*
6131731 ATTATAAT
1 ATTACAAT
6131739 ATTACAAT
1 ATTACAAT
*
6131747 ATTCATACAAA
1 A-T--TACAAT
6131758 ATTACAAT
1 ATTACAAT
6131766 ATT
1 ATT
6131769 CATACAAAAA
Statistics
Matches: 77, Mismatches: 14, Indels: 22
0.68 0.12 0.19
Matches are distributed among these distances:
8 47 0.61
9 5 0.06
10 7 0.09
11 18 0.23
ACGTcount: A:0.49, C:0.15, G:0.01, T:0.35
Consensus pattern (8 bp):
ATTACAAT
Found at i:6131709 original size:19 final size:19
Alignment explanation
Indices: 6131685--6131799 Score: 107
Period size: 19 Copynumber: 6.1 Consensus size: 19
6131675 ATATCCCGAC
6131685 ATTACAATATTCATACAAA
1 ATTACAATATTCATACAAA
6131704 ATTACAATA-T--TACAATA
1 ATTACAATATTCATACAA-A
* * *
6131721 TTCATACAAAATT-AT--AAT
1 AT--TACAATATTCATACAAA
6131739 ATTACAATATTCATACAAA
1 ATTACAATATTCATACAAA
6131758 ATTACAATATTCATACAAAAA
1 ATTACAATATTCATAC--AAA
*
6131779 ATTACAATATTCATATAAA
1 ATTACAATATTCATACAAA
6131798 AT
1 AT
6131800 ACTAATCCAA
Statistics
Matches: 79, Mismatches: 7, Indels: 20
0.75 0.07 0.19
Matches are distributed among these distances:
16 13 0.16
17 4 0.05
18 2 0.03
19 40 0.51
20 1 0.01
21 19 0.24
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (19 bp):
ATTACAATATTCATACAAA
Found at i:6131721 original size:27 final size:27
Alignment explanation
Indices: 6131685--6131983 Score: 195
Period size: 27 Copynumber: 11.8 Consensus size: 27
6131675 ATATCCCGAC
6131685 ATTACAATATTCATACAAAATTACAAT
1 ATTACAATATTCATACAAAATTACAAT
*
6131712 ATTACAATATTCATACAAAATTATAAT
1 ATTACAATATTCATACAAAATTACAAT
6131739 ATTACAATATTCATACAAAATTACAAT
1 ATTACAATATTCATACAAAATTACAAT
6131766 ATT-C-ATA--CA-A-AAAATTACAAT
1 ATTACAATATTCATACAAAATTACAAT
* * * *
6131787 ATT-CATATAAAATACTAATCCAAAACTATAA-
1 ATTACA-AT---AT--TCATACAAAATTACAAT
** *
6131818 A-TACAA-ATT--TA-ATTA-TAAAAT
1 ATTACAATATTCATACAAAATTACAAT
6131839 AATTACAATATTCATACAAAAAATTACAAT
1 -ATTACAATATTCATAC--AAAATTACAAT
* * *
6131869 ATTACAATA-T-AT-C------CCGAC
1 ATTACAATATTCATACAAAATTACAAT
*
6131887 ATTACAATATTCATACAAAATTACAAA
1 ATTACAATATTCATACAAAATTACAAT
*
6131914 ATTACAATATTCATACAAAATTATAAT
1 ATTACAATATTCATACAAAATTACAAT
6131941 ATTACAATATTCATACAAAA--A-AA-
1 ATTACAATATTCATACAAAATTACAAT
*
6131964 A-TACAATATTTATACAAAAT
1 ATTACAATATTCATACAAAAT
6131984 ACTAATCCAA
Statistics
Matches: 218, Mismatches: 22, Indels: 68
0.71 0.07 0.22
Matches are distributed among these distances:
18 11 0.05
19 1 0.00
20 6 0.03
21 18 0.08
22 20 0.09
23 10 0.05
24 6 0.03
25 4 0.02
26 7 0.03
27 104 0.48
28 1 0.00
29 11 0.05
30 8 0.04
31 3 0.01
32 8 0.04
ACGTcount: A:0.54, C:0.14, G:0.00, T:0.32
Consensus pattern (27 bp):
ATTACAATATTCATACAAAATTACAAT
Found at i:6131740 original size:46 final size:46
Alignment explanation
Indices: 6131638--6131799 Score: 163
Period size: 46 Copynumber: 3.5 Consensus size: 46
6131628 ATTATAAAAT
* *
6131638 AATTACAATATTCATACAAAAATTACAATATTACAATA-T-ATCCCGA
1 AATTACAATATTCATAC-AAAATTACAATATTACAATATTCAT-ACAA
*
6131684 CATTACAATATTCATACAAAATTACAATATTACAATATTCATACAA
1 AATTACAATATTCATACAAAATTACAATATTACAATATTCATACAA
* * *
6131730 AATTATAATA-T--TACAATATTCATACAAAATTACAATATTCATACAAAA
1 AATTACAATATTCATACAA-AAT--TACAATATTACAATATTCATAC--AA
*
6131778 AATTACAATATTCATATAAAAT
1 AATTACAATATTCATACAAAAT
6131800 ACTAATCCAA
Statistics
Matches: 96, Mismatches: 10, Indels: 16
0.79 0.08 0.13
Matches are distributed among these distances:
43 5 0.05
44 2 0.02
45 21 0.22
46 48 0.50
47 2 0.02
48 11 0.11
49 1 0.01
50 2 0.02
51 4 0.04
ACGTcount: A:0.52, C:0.15, G:0.01, T:0.33
Consensus pattern (46 bp):
AATTACAATATTCATACAAAATTACAATATTACAATATTCATACAA
Found at i:6132090 original size:27 final size:27
Alignment explanation
Indices: 6132052--6132118 Score: 125
Period size: 27 Copynumber: 2.5 Consensus size: 27
6132042 AATTACAATA
6132052 TTCATTGGCGCCTCTCTATGAGGCACC
1 TTCATTGGCGCCTCTCTATGAGGCACC
*
6132079 TTCATTGGCGCCTCTCTGTGAGGCACC
1 TTCATTGGCGCCTCTCTATGAGGCACC
6132106 TTCATTGGCGCCT
1 TTCATTGGCGCCT
6132119 ACTTGATAGG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.12, C:0.33, G:0.24, T:0.31
Consensus pattern (27 bp):
TTCATTGGCGCCTCTCTATGAGGCACC
Found at i:6132216 original size:18 final size:18
Alignment explanation
Indices: 6132195--6132231 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
6132185 TTAAAAAATA
6132195 TAAAAAAAATATT-TTATT
1 TAAAAAAAA-ATTATTATT
6132213 TAAAAAAAAATTATTATT
1 TAAAAAAAAATTATTATT
6132231 T
1 T
6132232 TTTTATTCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 3 0.17
18 15 0.83
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TAAAAAAAAATTATTATT
Found at i:6138269 original size:16 final size:17
Alignment explanation
Indices: 6138244--6138276 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
6138234 TGTCTCCCCC
*
6138244 TCTTCCCCAT-ATTCCT
1 TCTTCACCATCATTCCT
6138260 TCTTCACCATCATTCCT
1 TCTTCACCATCATTCCT
6138277 CTCACCCTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.15, C:0.42, G:0.00, T:0.42
Consensus pattern (17 bp):
TCTTCACCATCATTCCT
Found at i:6141820 original size:18 final size:18
Alignment explanation
Indices: 6141799--6141835 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
6141789 TGAGTTTTCG
6141799 AATTCGAATAATTTAAAT
1 AATTCGAATAATTTAAAT
*
6141817 AATTCGAATAATTTGAAT
1 AATTCGAATAATTTAAAT
6141835 A
1 A
6141836 TCAAACTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.49, C:0.05, G:0.08, T:0.38
Consensus pattern (18 bp):
AATTCGAATAATTTAAAT
Found at i:6145970 original size:14 final size:15
Alignment explanation
Indices: 6145951--6145982 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
6145941 TTTTGATCAC
6145951 ATAAAATTAA-ATTA
1 ATAAAATTAATATTA
6145965 ATAAAATTAATATTA
1 ATAAAATTAATATTA
6145980 ATA
1 ATA
6145983 TAATATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
ATAAAATTAATATTA
Found at i:6146505 original size:17 final size:17
Alignment explanation
Indices: 6146459--6146509 Score: 57
Period size: 20 Copynumber: 2.8 Consensus size: 17
6146449 ATAGTATTTT
*
6146459 ATTAATTTGATATTAAA
1 ATTAATTTAATATTAAA
*
6146476 CTTATTATCTTAATATTAAA
1 ATTA--AT-TTAATATTAAA
6146496 ATTAATTTAATATT
1 ATTAATTTAATATT
6146510 TATCTTGTAG
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
17 11 0.39
18 2 0.07
19 2 0.07
20 13 0.46
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.51
Consensus pattern (17 bp):
ATTAATTTAATATTAAA
Found at i:6146742 original size:13 final size:13
Alignment explanation
Indices: 6146710--6146743 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
6146700 ATTTGTGTAG
6146710 AGAAAATTATTTA
1 AGAAAATTATTTA
6146723 A-AGAAATTATTTA
1 AGA-AAATTATTTA
6146736 AGAAAATT
1 AGAAAATT
6146744 TCTAGAGATA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
12 1 0.05
13 17 0.89
14 1 0.05
ACGTcount: A:0.56, C:0.00, G:0.09, T:0.35
Consensus pattern (13 bp):
AGAAAATTATTTA
Found at i:6151885 original size:34 final size:34
Alignment explanation
Indices: 6151842--6151909 Score: 86
Period size: 34 Copynumber: 2.0 Consensus size: 34
6151832 GCATTTTTGA
* *
6151842 CACTGTACTGAGATGGGC-TAGGGCCCAA-ACTGT
1 CACTGTACTGAAAAGGGCTTA-GGCCCAAGACTGT
6151875 CACTGATACTGAAAAGGGCTTAGGCCCAAGACTGT
1 CACTG-TACTGAAAAGGGCTTAGGCCCAAGACTGT
6151910 TCAACTGTGC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
33 5 0.17
34 18 0.60
35 7 0.23
ACGTcount: A:0.28, C:0.24, G:0.28, T:0.21
Consensus pattern (34 bp):
CACTGTACTGAAAAGGGCTTAGGCCCAAGACTGT
Found at i:6154702 original size:17 final size:17
Alignment explanation
Indices: 6154676--6154774 Score: 59
Period size: 17 Copynumber: 5.8 Consensus size: 17
6154666 ATTTATCTAC
*
6154676 AAATTAAATATTAAATT
1 AAATTTAATATTAAATT
6154693 AAATTTAATATTAAGA-T
1 AAATTTAATATTAA-ATT
6154710 AACCACTTTAATATTAAATTT
1 AA--A-TTTAATATTAAA-TT
* *
6154731 AAA---AA-ATTACTATC
1 AAATTTAATATTA-AATT
6154745 AAA--TAAGTATTAAATT
1 AAATTTAA-TATTAAATT
6154761 AAATTTAATATTAA
1 AAATTTAATATTAA
6154775 TTTATTAAAA
Statistics
Matches: 65, Mismatches: 5, Indels: 24
0.69 0.05 0.26
Matches are distributed among these distances:
14 8 0.12
15 5 0.08
16 5 0.08
17 26 0.40
18 4 0.06
19 3 0.05
20 11 0.17
21 3 0.05
ACGTcount: A:0.54, C:0.05, G:0.02, T:0.39
Consensus pattern (17 bp):
AAATTTAATATTAAATT
Found at i:6157994 original size:14 final size:14
Alignment explanation
Indices: 6157956--6157988 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
6157946 TACATGTATG
*
6157956 TAATTTAACAAATA
1 TAATCTAACAAATA
6157970 TAATCTAACAAATA
1 TAATCTAACAAATA
6157984 TAATC
1 TAATC
6157989 ATACAATTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (14 bp):
TAATCTAACAAATA
Found at i:6160328 original size:27 final size:29
Alignment explanation
Indices: 6160298--6160353 Score: 71
Period size: 27 Copynumber: 2.0 Consensus size: 29
6160288 GCAAAGTCAC
*
6160298 ATGTGCATATTTG-AC-AATCAAAATTTT
1 ATGTGCATAATTGCACAAATCAAAATTTT
*
6160325 ATGTTCATAATTGCACAAAATCAAAATTT
1 ATGTGCATAATTGCAC-AAATCAAAATTT
6160354 ACAAATCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 11 0.46
28 2 0.08
30 11 0.46
ACGTcount: A:0.41, C:0.12, G:0.09, T:0.38
Consensus pattern (29 bp):
ATGTGCATAATTGCACAAATCAAAATTTT
Found at i:6161224 original size:2 final size:2
Alignment explanation
Indices: 6161217--6161245 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
6161207 GATTTGGGTT
6161217 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
6161246 TTTTTTTACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:6172942 original size:6 final size:6
Alignment explanation
Indices: 6172931--6172961 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
6172921 AGATATGCCG
6172931 ATATGT ATATGT ATATGT ATATGT ATATGT A
1 ATATGT ATATGT ATATGT ATATGT ATATGT A
6172962 CGTATGTATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.35, C:0.00, G:0.16, T:0.48
Consensus pattern (6 bp):
ATATGT
Found at i:6174356 original size:2 final size:2
Alignment explanation
Indices: 6174349--6174397 Score: 62
Period size: 2 Copynumber: 24.5 Consensus size: 2
6174339 ATACATACAT
* * *
6174349 AC AC AC AC AC GC AC GC AC GC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
*
6174391 AC GC AC A
1 AC AC AC A
6174398 TACATACATG
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.43, C:0.49, G:0.08, T:0.00
Consensus pattern (2 bp):
AC
Found at i:6174990 original size:1 final size:1
Alignment explanation
Indices: 6174984--6175012 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
6174974 ATTCTAAAGC
6174984 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
6175013 GGAAGGGAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:6176132 original size:9 final size:9
Alignment explanation
Indices: 6176114--6176162 Score: 71
Period size: 9 Copynumber: 5.4 Consensus size: 9
6176104 TTTGGTTAAA
*
6176114 AATTAACCG
1 AATTACCCG
6176123 AATTACCCG
1 AATTACCCG
*
6176132 AATTACCTG
1 AATTACCCG
*
6176141 AATTAACCG
1 AATTACCCG
6176150 AATTACCCG
1 AATTACCCG
6176159 AATT
1 AATT
6176163 GAATCATTAT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 35 1.00
ACGTcount: A:0.39, C:0.24, G:0.10, T:0.27
Consensus pattern (9 bp):
AATTACCCG
Found at i:6176411 original size:39 final size:39
Alignment explanation
Indices: 6176326--6176442 Score: 200
Period size: 39 Copynumber: 3.0 Consensus size: 39
6176316 ACTTAAGAGT
*
6176326 TAGACTTTAGTTTTATTTTTATTGGGTT-GGTAATTGGG
1 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
*
6176364 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGAAATTGGG
1 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
*
6176403 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTATTTGGG
1 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
6176442 T
1 T
6176443 TGGTTGGTAA
Statistics
Matches: 74, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
38 27 0.36
39 47 0.64
ACGTcount: A:0.18, C:0.03, G:0.29, T:0.50
Consensus pattern (39 bp):
TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
Found at i:6176442 original size:13 final size:13
Alignment explanation
Indices: 6176423--6176472 Score: 64
Period size: 13 Copynumber: 3.6 Consensus size: 13
6176413 TTTTAGTTTT
6176423 ATTGGGTTGGGTA
1 ATTGGGTTGGGTA
*
6176436 TTTGGGTTGGTTGGTA
1 ATTGGGTT-G--GGTA
6176452 ATTGGGTTGGGTA
1 ATTGGGTTGGGTA
6176465 ATTGGGTT
1 ATTGGGTT
6176473 TGGTTGGATA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
13 19 0.59
14 1 0.03
15 1 0.03
16 11 0.34
ACGTcount: A:0.12, C:0.00, G:0.44, T:0.44
Consensus pattern (13 bp):
ATTGGGTTGGGTA
Found at i:6176449 original size:17 final size:16
Alignment explanation
Indices: 6176427--6176485 Score: 61
Period size: 16 Copynumber: 3.7 Consensus size: 16
6176417 AGTTTTATTG
*
6176427 GGTTGGGTATTTGGGTT
1 GGTT-GGTAATTGGGTT
6176444 GGTTGGTAATTGGGTT
1 GGTTGGTAATTGGGTT
6176460 -G--GGTAATTGGGTTT
1 GGTTGGTAATTGGG-TT
6176474 GGTTGGATAATT
1 GGTTGG-TAATT
6176486 TTATTTATTA
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
13 10 0.28
14 2 0.06
15 2 0.06
16 11 0.31
17 6 0.17
18 5 0.14
ACGTcount: A:0.14, C:0.00, G:0.42, T:0.44
Consensus pattern (16 bp):
GGTTGGTAATTGGGTT
Found at i:6176458 original size:29 final size:31
Alignment explanation
Indices: 6176423--6176485 Score: 103
Period size: 29 Copynumber: 2.1 Consensus size: 31
6176413 TTTTAGTTTT
*
6176423 ATTGGGTTGGGTATTTGGG-TTGGTTGG-TA
1 ATTGGGTTGGGTAATTGGGTTTGGTTGGATA
6176452 ATTGGGTTGGGTAATTGGGTTTGGTTGGATA
1 ATTGGGTTGGGTAATTGGGTTTGGTTGGATA
6176483 ATT
1 ATT
6176486 TTATTTATTA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 18 0.58
30 8 0.26
31 5 0.16
ACGTcount: A:0.14, C:0.00, G:0.41, T:0.44
Consensus pattern (31 bp):
ATTGGGTTGGGTAATTGGGTTTGGTTGGATA
Found at i:6177110 original size:9 final size:9
Alignment explanation
Indices: 6177093--6177129 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
6177083 TGAGTTTTTG
6177093 AATTCGAAT
1 AATTCGAAT
*
6177102 AACTCGAAT
1 AATTCGAAT
6177111 AATTCGAAT
1 AATTCGAAT
6177120 AATTCGAAT
1 AATTCGAAT
6177129 A
1 A
6177130 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:6179550 original size:19 final size:20
Alignment explanation
Indices: 6179522--6179571 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
6179512 TTAAATTTTT
*
6179522 AAAA-ATTAAAAATCAT-TA
1 AAAATATTAAAAATAATATA
*
6179540 AAATTATT-AAAATAATATA
1 AAAATATTAAAAATAATATA
6179559 AAAATATTAAAAA
1 AAAATATTAAAAA
6179572 ATATCTTTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 10 0.38
19 12 0.46
20 4 0.15
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (20 bp):
AAAATATTAAAAATAATATA
Found at i:6179575 original size:10 final size:9
Alignment explanation
Indices: 6179522--6179571 Score: 50
Period size: 9 Copynumber: 5.4 Consensus size: 9
6179512 TTAAATTTTT
6179522 AAAA-ATTA
1 AAAATATTA
6179530 AAAATCATTA
1 AAAAT-ATTA
*
6179540 AAATTATT-
1 AAAATATTA
6179548 AAAATAATATA
1 AAAAT-AT-TA
6179559 AAAATATTA
1 AAAATATTA
6179568 AAAA
1 AAAA
6179572 ATATCTTTTC
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
8 8 0.23
9 11 0.31
10 11 0.31
11 5 0.14
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (9 bp):
AAAATATTA
Found at i:6190704 original size:16 final size:17
Alignment explanation
Indices: 6190685--6190721 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
6190675 TGCTTGATAG
6190685 AGAAAAGAAAA-TAAAA
1 AGAAAAGAAAAGTAAAA
6190701 AGAAAAGAAAAGTTAAAA
1 AGAAAAGAAAAG-TAAAA
6190719 AGA
1 AGA
6190722 GGGAGGCTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 11 0.58
18 8 0.42
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (17 bp):
AGAAAAGAAAAGTAAAA
Found at i:6201313 original size:27 final size:27
Alignment explanation
Indices: 6201254--6201313 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
6201244 AAAATGTCAA
* *
6201254 AATTTTTAATATTTATTGGATTAGATT
1 AATTTTTAATATTTATGGGATTAGATC
** * *
6201281 TTTTTTTAATATTTGTGGGATTAGGTC
1 AATTTTTAATATTTATGGGATTAGATC
6201308 AATTTT
1 AATTTT
6201314 CTCATTCTCC
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.27, C:0.02, G:0.15, T:0.57
Consensus pattern (27 bp):
AATTTTTAATATTTATGGGATTAGATC
Found at i:6208261 original size:30 final size:31
Alignment explanation
Indices: 6208225--6208282 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 31
6208215 GGTTACCCAC
**
6208225 ACGGCCTGGTGACACGGCCGTGT-GCGGCAT
1 ACGGCCTGGACACACGGCCGTGTCGCGGCAT
*
6208255 ACGGCCTGGACACACGGGCGTGTCGCGG
1 ACGGCCTGGACACACGGCCGTGTCGCGG
6208283 GCCGTGTGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 20 0.83
31 4 0.17
ACGTcount: A:0.14, C:0.31, G:0.41, T:0.14
Consensus pattern (31 bp):
ACGGCCTGGACACACGGCCGTGTCGCGGCAT
Found at i:6211243 original size:13 final size:13
Alignment explanation
Indices: 6211205--6211282 Score: 60
Period size: 13 Copynumber: 6.3 Consensus size: 13
6211195 AGCACTTAAA
*
6211205 ATTTATGCATTTT
1 ATTTATACATTTT
*
6211218 ATTT-T-TA-TTT
1 ATTTATACATTTT
6211228 ATTTATACATTTT
1 ATTTATACATTTT
*
6211241 ATTT-TATCAATTT
1 ATTTATA-CATTTT
*
6211254 A-CTATATCA-TTT
1 ATTTATA-CATTTT
6211266 ATTTATACATTTT
1 ATTTATACATTTT
6211279 ATTT
1 ATTT
6211283 TTATTTTATC
Statistics
Matches: 53, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
10 7 0.13
11 2 0.04
12 11 0.21
13 33 0.62
ACGTcount: A:0.28, C:0.08, G:0.01, T:0.63
Consensus pattern (13 bp):
ATTTATACATTTT
Found at i:6211253 original size:22 final size:23
Alignment explanation
Indices: 6211204--6211254 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
6211194 TAGCACTTAA
* *
6211204 AATTTATGCATTTTATTTTTATT
1 AATTTATACATTTTATTTTTATC
*
6211227 TATTTATACATTTTA-TTTTATC
1 AATTTATACATTTTATTTTTATC
6211249 AATTTA
1 AATTTA
6211255 CTATATCATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 11 0.46
23 13 0.54
ACGTcount: A:0.29, C:0.06, G:0.02, T:0.63
Consensus pattern (23 bp):
AATTTATACATTTTATTTTTATC
Found at i:6211487 original size:16 final size:15
Alignment explanation
Indices: 6211468--6211497 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
6211458 TCTTCATCTA
6211468 TTTATTTATTCATTTG
1 TTTATTTA-TCATTTG
6211484 TTTATTTATCATTT
1 TTTATTTATCATTT
6211498 AAACGTCATC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.20, C:0.07, G:0.03, T:0.70
Consensus pattern (15 bp):
TTTATTTATCATTTG
Found at i:6217464 original size:20 final size:20
Alignment explanation
Indices: 6217437--6217476 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
6217427 GCATCTTCAG
*
6217437 CTTTTTTTTCTTTTTCTTTTT
1 CTTTTTTTT-TTTGTCTTTTT
6217458 CTTTTTTTTTTTGTCTTTT
1 CTTTTTTTTTTTGTCTTTT
6217477 AGAGGTTAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.00, C:0.12, G:0.03, T:0.85
Consensus pattern (20 bp):
CTTTTTTTTTTTGTCTTTTT
Found at i:6217469 original size:12 final size:12
Alignment explanation
Indices: 6217438--6217469 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
6217428 CATCTTCAGC
6217438 TTTTTTTTCTTT
1 TTTTTTTTCTTT
*
6217450 TTCTTTTTCTTT
1 TTTTTTTTCTTT
6217462 TTTTTTTT
1 TTTTTTTT
6217470 GTCTTTTAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (12 bp):
TTTTTTTTCTTT
Found at i:6218516 original size:21 final size:24
Alignment explanation
Indices: 6218465--6218516 Score: 58
Period size: 23 Copynumber: 2.2 Consensus size: 24
6218455 CGAAAATATA
6218465 TTAA-ATAATATATATTTTTATTT
1 TTAATATAATATATATTTTTATTT
6218488 TTAAAATATAATA-AT-TTTTTA-TT
1 TT--AATATAATATATATTTTTATTT
6218511 TTAATA
1 TTAATA
6218517 CTTTACTTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
21 4 0.15
23 6 0.23
24 6 0.23
25 4 0.15
26 6 0.23
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (24 bp):
TTAATATAATATATATTTTTATTT
Found at i:6219265 original size:9 final size:9
Alignment explanation
Indices: 6219251--6219292 Score: 70
Period size: 9 Copynumber: 4.9 Consensus size: 9
6219241 TTGTTATAAT
6219251 AATTAATAC
1 AATTAATAC
6219260 AATTAATAC
1 AATTAATAC
6219269 AATT-A-AC
1 AATTAATAC
6219276 AATTAATAC
1 AATTAATAC
6219285 AATTAATA
1 AATTAATA
6219293 ATTTGATAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
7 6 0.19
8 2 0.06
9 23 0.74
ACGTcount: A:0.57, C:0.10, G:0.00, T:0.33
Consensus pattern (9 bp):
AATTAATAC
Found at i:6219277 original size:16 final size:16
Alignment explanation
Indices: 6219258--6219295 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
6219248 AATAATTAAT
6219258 ACAATTAATACAATTA
1 ACAATTAATACAATTA
6219274 ACAATTAATACAATTA
1 ACAATTAATACAATTA
*
6219290 ATAATT
1 ACAATT
6219296 TGATAATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.55, C:0.11, G:0.00, T:0.34
Consensus pattern (16 bp):
ACAATTAATACAATTA
Found at i:6226214 original size:44 final size:44
Alignment explanation
Indices: 6226112--6226214 Score: 134
Period size: 44 Copynumber: 2.3 Consensus size: 44
6226102 TCTTATCTCT
* * * *
6226112 CTGAAGTTACAGTGGAACGAGATGAAGTTACAAGTCCTATATCC
1 CTGAAGTTACAGTGGAACAAGATGAAGCTACAAATCCTATACCC
* ** *
6226156 CAGAAGTTGTAGTGGAACAAGATGAAGCTATAAATCCTATACCC
1 CTGAAGTTACAGTGGAACAAGATGAAGCTACAAATCCTATACCC
6226200 CTGAAGTTACAGTGG
1 CTGAAGTTACAGTGG
6226215 GTTGGAATGA
Statistics
Matches: 48, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
44 48 1.00
ACGTcount: A:0.35, C:0.17, G:0.23, T:0.24
Consensus pattern (44 bp):
CTGAAGTTACAGTGGAACAAGATGAAGCTACAAATCCTATACCC
Found at i:6227567 original size:30 final size:27
Alignment explanation
Indices: 6227532--6227588 Score: 69
Period size: 30 Copynumber: 2.0 Consensus size: 27
6227522 CTTTTTTTTC
*
6227532 TTTTTAATTTTGTCCTATTTCATCTTTATT
1 TTTTTAATTTTATCCT-TTT-AT-TTTATT
*
6227562 TTTTTATTTTTATCCTTTTATTTTATT
1 TTTTTAATTTTATCCTTTTATTTTATT
6227589 CTTGTGCAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 6 0.24
28 2 0.08
29 3 0.12
30 14 0.56
ACGTcount: A:0.16, C:0.11, G:0.02, T:0.72
Consensus pattern (27 bp):
TTTTTAATTTTATCCTTTTATTTTATT
Found at i:6228782 original size:27 final size:27
Alignment explanation
Indices: 6228743--6228795 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
6228733 GTTACCGTTT
6228743 TTGGGCGTCATGAAGGCACTTAGGTTG
1 TTGGGCGTCATGAAGGCACTTAGGTTG
*
6228770 TTGGGCGTTATGAAGGCACTTAGGTT
1 TTGGGCGTCATGAAGGCACTTAGGTT
6228796 TTAACCCACT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.19, C:0.13, G:0.36, T:0.32
Consensus pattern (27 bp):
TTGGGCGTCATGAAGGCACTTAGGTTG
Found at i:6229109 original size:45 final size:45
Alignment explanation
Indices: 6229055--6229146 Score: 184
Period size: 45 Copynumber: 2.0 Consensus size: 45
6229045 AAATTGATTA
6229055 TTATTTAGTTCTATGTTAATTGAGCTTGAACAGTTAAATTCATAG
1 TTATTTAGTTCTATGTTAATTGAGCTTGAACAGTTAAATTCATAG
6229100 TTATTTAGTTCTATGTTAATTGAGCTTGAACAGTTAAATTCATAG
1 TTATTTAGTTCTATGTTAATTGAGCTTGAACAGTTAAATTCATAG
6229145 TT
1 TT
6229147 TGACAATAAG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.30, C:0.09, G:0.15, T:0.46
Consensus pattern (45 bp):
TTATTTAGTTCTATGTTAATTGAGCTTGAACAGTTAAATTCATAG
Found at i:6230220 original size:17 final size:17
Alignment explanation
Indices: 6230178--6230221 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
6230168 CTTTTTGTTG
6230178 TATTTTATTTTATTTAA
1 TATTTTATTTTATTTAA
* * * *
6230195 TACTATATTTTTTTTAT
1 TATTTTATTTTATTTAA
6230212 TATTTTATTT
1 TATTTTATTT
6230222 ATTATGATGA
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (17 bp):
TATTTTATTTTATTTAA
Found at i:6235209 original size:18 final size:18
Alignment explanation
Indices: 6235188--6235230 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
6235178 TTTAGCCATT
*
6235188 TTTATTTCTATTATAATA
1 TTTATTTCTAGTATAATA
*
6235206 TTTATTTCTAGTATAATT
1 TTTATTTCTAGTATAATA
6235224 TTTATTT
1 TTTATTT
6235231 TGTTTTTAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.65
Consensus pattern (18 bp):
TTTATTTCTAGTATAATA
Found at i:6239146 original size:6 final size:6
Alignment explanation
Indices: 6239137--6239251 Score: 155
Period size: 6 Copynumber: 19.3 Consensus size: 6
6239127 TTTATTTTCT
* * * *
6239137 TTTTAG TTTTAG TTTTA- TTTTA- TGTCTA- TGATTAT TTTTAT TTTTAG
1 TTTTAG TTTTAG TTTTAG TTTTAG T-TTTAG T-TTTAG TTTTAG TTTTAG
6239184 TTTTAG TTTTAG TTTTAG TTTTAG TTTTAG TTTTAG TTTTAG TTTTAG
1 TTTTAG TTTTAG TTTTAG TTTTAG TTTTAG TTTTAG TTTTAG TTTTAG
6239232 TTTTAG TTTTAG TTTTAG TT
1 TTTTAG TTTTAG TTTTAG TT
6239252 GTTTTAGTCT
Statistics
Matches: 102, Mismatches: 5, Indels: 4
0.92 0.05 0.04
Matches are distributed among these distances:
5 6 0.06
6 95 0.93
7 1 0.01
ACGTcount: A:0.17, C:0.01, G:0.14, T:0.68
Consensus pattern (6 bp):
TTTTAG
Found at i:6240879 original size:22 final size:23
Alignment explanation
Indices: 6240853--6240899 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
6240843 TTCCTAATTA
* *
6240853 ATGGCTCTC-TGAGCTTCCCGAT
1 ATGGCTCGCTTGAACTTCCCGAT
6240875 ATGGCTCGCTTGAACTTCCCGAT
1 ATGGCTCGCTTGAACTTCCCGAT
6240898 AT
1 AT
6240900 ATGGTTATCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 8 0.36
23 14 0.64
ACGTcount: A:0.17, C:0.30, G:0.21, T:0.32
Consensus pattern (23 bp):
ATGGCTCGCTTGAACTTCCCGAT
Found at i:6244140 original size:30 final size:30
Alignment explanation
Indices: 6244104--6244192 Score: 142
Period size: 30 Copynumber: 3.0 Consensus size: 30
6244094 AGCTTCAGGG
* *
6244104 GCCACACGGGTTGGGCACATGCCCATGTGA
1 GCCACACGGGCTGGCCACATGCCCATGTGA
*
6244134 GCCACACGGGCTGGCCATATGCCCATGTGA
1 GCCACACGGGCTGGCCACATGCCCATGTGA
*
6244164 GCCACACGAGCTGGCCACATGCCCATGTG
1 GCCACACGGGCTGGCCACATGCCCATGTG
6244193 CCAGCCCGTT
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 54 1.00
ACGTcount: A:0.20, C:0.34, G:0.30, T:0.16
Consensus pattern (30 bp):
GCCACACGGGCTGGCCACATGCCCATGTGA
Found at i:6254313 original size:14 final size:14
Alignment explanation
Indices: 6254294--6254320 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
6254284 ACCTAAACTA
6254294 TTTATAGAAGAAAT
1 TTTATAGAAGAAAT
6254308 TTTATAGAAGAAA
1 TTTATAGAAGAAA
6254321 ATCCTTAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.15, T:0.33
Consensus pattern (14 bp):
TTTATAGAAGAAAT
Found at i:6255862 original size:14 final size:14
Alignment explanation
Indices: 6255841--6255874 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
6255831 TGGTATGGGT
6255841 TTAT-GGGTTTTGG
1 TTATAGGGTTTTGG
6255854 TTATAGGGTTTTGG
1 TTATAGGGTTTTGG
6255868 TTATAGG
1 TTATAGG
6255875 CAAATGATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.20
14 16 0.80
ACGTcount: A:0.15, C:0.00, G:0.35, T:0.50
Consensus pattern (14 bp):
TTATAGGGTTTTGG
Found at i:6266078 original size:19 final size:20
Alignment explanation
Indices: 6266054--6266113 Score: 79
Period size: 19 Copynumber: 3.0 Consensus size: 20
6266044 ATTCTTTACA
6266054 TTTTATAATTTTTTAC-AAT
1 TTTTATAATTTTTTACTAAT
6266073 TTTTATAATTTTTT-CTAAT
1 TTTTATAATTTTTTACTAAT
* *
6266092 TTTTAATAAATTTTTAATAAT
1 TTTT-ATAATTTTTTACTAAT
6266113 T
1 T
6266114 GAATTTTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
18 1 0.03
19 21 0.58
20 9 0.25
21 5 0.14
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (20 bp):
TTTTATAATTTTTTACTAAT
Found at i:6266086 original size:11 final size:10
Alignment explanation
Indices: 6266054--6266113 Score: 68
Period size: 10 Copynumber: 6.0 Consensus size: 10
6266044 ATTCTTTACA
6266054 TTTTATAATT
1 TTTTATAATT
*
6266064 TTTTACAA-T
1 TTTTATAATT
6266073 TTTTATAATT
1 TTTTATAATT
*
6266083 TTTTCTAATT
1 TTTTATAATT
*
6266093 TTTAATAAATT
1 TTTTAT-AATT
*
6266104 TTTAATAATT
1 TTTTATAATT
6266114 GAATTTTTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
9 8 0.19
10 25 0.58
11 10 0.23
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (10 bp):
TTTTATAATT
Found at i:6266403 original size:92 final size:92
Alignment explanation
Indices: 6266193--6266425 Score: 248
Period size: 92 Copynumber: 2.6 Consensus size: 92
6266183 AATTTTTAAT
* *
6266193 AAAAGCATGGGCTTAATTGC-TTTTTTTTGAAAAGGTTTGAGGGTCTTTTTGATGCATTTTGAAA
1 AAAAGCAAGGGCTTAATTGCTTTTTTTTTGAAAAGGTTTGAGAGTCTTTTTGATGCATTTTGAAA
* *
6266257 GATCAAGTGCCTAATTGAGTGTAAAAA
66 GATCAAGTGCCTAAATGAGTGCAAAAA
* * **
6266284 AAAA-TAAGGGCTTAATTTCTTTCTTTTTTTTTAAA-GTTTGAGAG-CATTTTTGATGCATTTTG
1 AAAAGCAAGGGCTTAATTGC-TT-TTTTTTTGAAAAGGTTTGAGAGTC-TTTTTGATGCATTTTG
* *
6266346 AAAGTTCAAGTATCC-AAATGAGTGCAAAAA
63 AAAGATCAAGT-GCCTAAATGAGTGCAAAAA
* * *
6266376 AAAGAGCAGGGGCTTAATTGC--TTTTTTTGAAAATGTTTGAGTG-CTTTTTG
1 AAA-AGCAAGGGCTTAATTGCTTTTTTTTTGAAAAGGTTTGAGAGTCTTTTTG
6266426 CACCCTTAAG
Statistics
Matches: 118, Mismatches: 16, Indels: 17
0.78 0.11 0.11
Matches are distributed among these distances:
90 28 0.24
91 14 0.12
92 51 0.43
93 13 0.11
94 12 0.10
ACGTcount: A:0.30, C:0.09, G:0.21, T:0.39
Consensus pattern (92 bp):
AAAAGCAAGGGCTTAATTGCTTTTTTTTTGAAAAGGTTTGAGAGTCTTTTTGATGCATTTTGAAA
GATCAAGTGCCTAAATGAGTGCAAAAA
Found at i:6269469 original size:27 final size:26
Alignment explanation
Indices: 6269439--6269494 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 26
6269429 AGGCTATCCC
6269439 TTCATAATT-CACCACAAAGGCATTCAT
1 TTCAT-ATTGCACCACAAAGGCATTC-T
* *
6269466 TTCATATTGCGCCACAAAGGCTTTCT
1 TTCATATTGCACCACAAAGGCATTCT
6269492 TTC
1 TTC
6269495 TTTCCTGACA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 7 0.27
27 19 0.73
ACGTcount: A:0.29, C:0.27, G:0.11, T:0.34
Consensus pattern (26 bp):
TTCATATTGCACCACAAAGGCATTCT
Found at i:6273606 original size:22 final size:22
Alignment explanation
Indices: 6273563--6273606 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
6273553 TATATAAATT
* **
6273563 AAGTTAAAATTATTGTGGGTCA
1 AAGTCAAAATTATCATGGGTCA
*
6273585 AAGTCAAAATTATCATGTGTCA
1 AAGTCAAAATTATCATGGGTCA
6273607 TAATTAATTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.39, C:0.09, G:0.18, T:0.34
Consensus pattern (22 bp):
AAGTCAAAATTATCATGGGTCA
Found at i:6277007 original size:12 final size:12
Alignment explanation
Indices: 6276990--6277032 Score: 77
Period size: 12 Copynumber: 3.6 Consensus size: 12
6276980 TAAGGGAAGA
6276990 GAGCCCAAGCAT
1 GAGCCCAAGCAT
*
6277002 GAGCCCAAGTAT
1 GAGCCCAAGCAT
6277014 GAGCCCAAGCAT
1 GAGCCCAAGCAT
6277026 GAGCCCA
1 GAGCCCA
6277033 GGTATGTCGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.33, C:0.33, G:0.26, T:0.09
Consensus pattern (12 bp):
GAGCCCAAGCAT
Found at i:6277022 original size:24 final size:24
Alignment explanation
Indices: 6276990--6277038 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
6276980 TAAGGGAAGA
6276990 GAGCCCAAGCATGAGCCCAAGTAT
1 GAGCCCAAGCATGAGCCCAAGTAT
*
6277014 GAGCCCAAGCATGAGCCCAGGTAT
1 GAGCCCAAGCATGAGCCCAAGTAT
6277038 G
1 G
6277039 TCGCCTTTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.31, C:0.29, G:0.29, T:0.12
Consensus pattern (24 bp):
GAGCCCAAGCATGAGCCCAAGTAT
Found at i:6283594 original size:19 final size:22
Alignment explanation
Indices: 6283556--6283604 Score: 61
Period size: 20 Copynumber: 2.4 Consensus size: 22
6283546 AAATAGTGAG
*
6283556 AATT-TATTTTCTAAGTAT-A-
1 AATTCTATTTTCTAAGAATAAC
6283575 AATTCTATTTTCT-AGAATAAC
1 AATTCTATTTTCTAAGAATAAC
6283596 AATTCTATT
1 AATTCTATT
6283605 GGTTTATATT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
19 8 0.31
20 9 0.35
21 9 0.35
ACGTcount: A:0.37, C:0.10, G:0.04, T:0.49
Consensus pattern (22 bp):
AATTCTATTTTCTAAGAATAAC
Found at i:6286162 original size:17 final size:17
Alignment explanation
Indices: 6286131--6286163 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
6286121 TAGAATTGAG
6286131 TTGAGATAATTATTTAA
1 TTGAGATAATTATTTAA
6286148 TTGAG-TAATTAATTTA
1 TTGAGATAATT-ATTTA
6286164 GTTAATTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.48
Consensus pattern (17 bp):
TTGAGATAATTATTTAA
Found at i:6286171 original size:13 final size:13
Alignment explanation
Indices: 6286144--6286185 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
6286134 AGATAATTAT
*
6286144 TTAATTGAG-TAA
1 TTAATTTAGTTAA
6286156 TTAATTTAGTTAA
1 TTAATTTAGTTAA
* *
6286169 TTAAATTAATTAA
1 TTAATTTAGTTAA
6286182 TTAA
1 TTAA
6286186 ATAATATTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
12 8 0.31
13 18 0.69
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (13 bp):
TTAATTTAGTTAA
Found at i:6286186 original size:13 final size:13
Alignment explanation
Indices: 6286153--6286187 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
6286143 TTTAATTGAG
* *
6286153 TAATTAATTTAGT
1 TAATTAAATTAAT
6286166 TAATTAAATTAAT
1 TAATTAAATTAAT
6286179 TAATTAAAT
1 TAATTAAAT
6286188 AATATTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (13 bp):
TAATTAAATTAAT
Found at i:6287607 original size:14 final size:16
Alignment explanation
Indices: 6287578--6287610 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
6287568 ACGTGTGTGC
6287578 ATAAAACAACAAATTT
1 ATAAAACAACAAATTT
6287594 ATAAAA-AA-AAATTT
1 ATAAAACAACAAATTT
6287608 ATA
1 ATA
6287611 GCAAGGTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 9 0.53
15 2 0.12
16 6 0.35
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (16 bp):
ATAAAACAACAAATTT
Found at i:6289781 original size:19 final size:19
Alignment explanation
Indices: 6289751--6289800 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
6289741 AAAATATAGA
6289751 AAAAGTAAAAAGTA-AAAAT
1 AAAAG-AAAAAGTACAAAAT
6289770 AAGAAGAAAAAGTACAAAAT
1 AA-AAGAAAAAGTACAAAAT
*
6289790 AAAAGCAAAAG
1 AAAAGAAAAAG
6289801 CCTTATGAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 18 0.64
20 10 0.36
ACGTcount: A:0.72, C:0.04, G:0.14, T:0.10
Consensus pattern (19 bp):
AAAAGAAAAAGTACAAAAT
Found at i:6296458 original size:26 final size:27
Alignment explanation
Indices: 6296397--6296455 Score: 100
Period size: 27 Copynumber: 2.2 Consensus size: 27
6296387 GTCAGGAAAT
6296397 GAAGCCTTTGTGGATAACTCTAAAAAG
1 GAAGCCTTTGTGGATAACTCTAAAAAG
* *
6296424 AAAGCCTTTGTGGCTAACTCTAAAAAG
1 GAAGCCTTTGTGGATAACTCTAAAAAG
6296451 GAAGC
1 GAAGC
6296456 TTTCATGGCG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.24
Consensus pattern (27 bp):
GAAGCCTTTGTGGATAACTCTAAAAAG
Found at i:6296464 original size:27 final size:27
Alignment explanation
Indices: 6296398--6296470 Score: 85
Period size: 27 Copynumber: 2.7 Consensus size: 27
6296388 TCAGGAAATG
* *
6296398 AAGCCTTTGTGGATAACTCTAAAAAGA
1 AAGCCTTTATGGCTAACTCTAAAAAGA
* *
6296425 AAGCCTTTGTGGCTAACTCTAAAAAGG
1 AAGCCTTTATGGCTAACTCTAAAAAGA
*
6296452 AAG-CTTTCATGGCGAACTC
1 AAGCCTTT-ATGGCTAACTC
6296471 CAAAGGAATA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
26 4 0.10
27 37 0.90
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26
Consensus pattern (27 bp):
AAGCCTTTATGGCTAACTCTAAAAAGA
Found at i:6296523 original size:28 final size:28
Alignment explanation
Indices: 6296488--6296571 Score: 77
Period size: 27 Copynumber: 3.1 Consensus size: 28
6296478 ATAACCTCTA
*
6296488 TGGC-CAATTGTAATAGGATAGCCTTTG
1 TGGCGCAATTGTAAAAGGATAGCCTTTG
* *
6296515 TGGCGCAA-TGTAAAAGGA-ACACCTGTG
1 TGGCGCAATTGTAAAAGGATA-GCCTTTG
* *
6296542 TGGCG-AATTATGAAAAGAATAGCCTTTG
1 TGGCGCAATTGT-AAAAGGATAGCCTTTG
6296570 TG
1 TG
6296572 ATGGATTATG
Statistics
Matches: 45, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
26 3 0.07
27 25 0.56
28 16 0.36
29 1 0.02
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.27
Consensus pattern (28 bp):
TGGCGCAATTGTAAAAGGATAGCCTTTG
Found at i:6298652 original size:11 final size:11
Alignment explanation
Indices: 6298636--6298661 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
6298626 TAGAAGAGAC
6298636 GAAACAGGGGA
1 GAAACAGGGGA
6298647 GAAACAGGGGA
1 GAAACAGGGGA
6298658 GAAA
1 GAAA
6298662 GAAGAAAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.50, C:0.08, G:0.42, T:0.00
Consensus pattern (11 bp):
GAAACAGGGGA
Found at i:6305678 original size:11 final size:11
Alignment explanation
Indices: 6305662--6305687 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
6305652 TAGAAGAGAC
6305662 GAAACAGGGGA
1 GAAACAGGGGA
6305673 GAAACAGGGGA
1 GAAACAGGGGA
6305684 GAAA
1 GAAA
6305688 GAAGAAAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.50, C:0.08, G:0.42, T:0.00
Consensus pattern (11 bp):
GAAACAGGGGA
Found at i:6312345 original size:126 final size:125
Alignment explanation
Indices: 6312110--6312675 Score: 598
Period size: 126 Copynumber: 4.5 Consensus size: 125
6312100 GATAAAATCA
* * * * * * *
6312110 AAGCAGGATGATTTATCAGAAGGATTTTTGAAGTCGCACCCACGTGTACGCGCTTTTGCTACAGT
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
* * *** * * * *
6312175 AGGTCTTGGGAAAATAATTTCGACTTGATGTTTTTGAGCAAATAGTTTAAAAAACATTTC
66 TGGTCCTAAAAAAATAATTTCGACTTGACGTTTCTGAGCAAATAGTATAAAAAACACTTC
* * ** *
6312235 AAGCAGAATGCTTTGTGAGAAGAATTTGTGAAATCGCGCCGTCGTGGACGCGCTTTTACTACAGT
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
* * * * *
6312300 TGGTCCTAAAAGAAATAATTTCGAGTTGATGTTTTTGAGCAAATAGTTTAAAAAACGCTTC
66 TGGTCCTAAAA-AAATAATTTCGACTTGACGTTTCTGAGCAAATAGTATAAAAAACACTTC
* * * * * *
6312361 AAACAGGATGCTTTATAATAAGAATTTGTGAAGTCGTGCCCACGTGGATGCGCTTTTGCTACAGT
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
* * * * * * *
6312426 AGGTCCTAAAAAAATAATTTTGAGTTAACGTTTCTGAGCAAATAATATAAAACAACGCTGC
66 TGGTCCTAAAAAAATAATTTCGACTTGACGTTTCTGAGCAAATAGTATAAAA-AACACTTC
* * * * * * *
6312487 AAGTAGCATGCTATT-TGAGAAGAATTTGTGAAATTGTGCCCTCGTGAACGTGCTTTTGCTACAG
1 AAGCAGGATGCT-TTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAG
** * *
6312551 TTGGTCCTGGAAAAATAATTTTGACTTGACGTTTCTGAGCAAATAGTAT-AAAATCGA-TTC
65 TTGGTCCTAAAAAAATAATTTCGACTTGACGTTTCTGAGCAAATAGTATAAAAAAC-ACTTC
* * *
6312611 TAGAAGGATGCTTTATGAGAAGAATTTGTGAAATCACGCCCACGTGGACGCGCTTTTGCTACAGT
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
6312676 AACATGTTTG
Statistics
Matches: 368, Mismatches: 68, Indels: 11
0.82 0.15 0.02
Matches are distributed among these distances:
123 2 0.01
124 57 0.15
125 97 0.26
126 210 0.57
127 2 0.01
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (125 bp):
AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
TGGTCCTAAAAAAATAATTTCGACTTGACGTTTCTGAGCAAATAGTATAAAAAACACTTC
Found at i:6312569 original size:251 final size:250
Alignment explanation
Indices: 6312107--6312676 Score: 678
Period size: 251 Copynumber: 2.3 Consensus size: 250
6312097 TAAGATAAAA
* * * * * *
6312107 TCAAAGCAGGATGATTTATCAGAAGGATTTTTGAAGTCGCACCCACGTGTACGCGCTTTTGCTAC
1 TCAAA-CAGGATGCTTTATAAGAAGAATTTGTGAAGTCGCGCCCACGTGGACGCGCTTTTGCTAC
* *** * * * * * * *
6312172 AGTAGGTCTTGGGAAAATAATTTCGACTTGATGTTTTTGAGCAAATAGTTTAAAAAACATTTCAA
65 AGTAGGTCCTAAAAAAATAATTTCGACTTAACGTTTCTGAGCAAATAATATAAAAAACACTGCAA
* *
6312237 GCAGAATGCTTTGTGAGAAGAATTTGTGAAATCGCGCCGTCGTGGACGCGCTTTTACTACAGTTG
130 GCAGAATGCTTTGTGAGAAGAATTTGTGAAATCGCGCCCTCGTGAACGCGCTTTTACTACAGTTG
* * * * *
6312302 GTCCTAAAAGAAATAATTTCGAGTTGATGTTTTTGAGCAAATAGTTTAAAAAACGCT
195 GTCCTAAAAGAAATAATTTCGACTTGACGTTTCTGAGCAAATAGTAT-AAAAACGAT
* * *
6312359 TCAAACAGGATGCTTTATAATAAGAATTTGTGAAGTCGTGCCCACGTGGATGCGCTTTTGCTACA
1 TCAAACAGGATGCTTTATAAGAAGAATTTGTGAAGTCGCGCCCACGTGGACGCGCTTTTGCTACA
* * *
6312424 GTAGGTCCTAAAAAAATAATTTTGAGTTAACGTTTCTGAGCAAATAATATAAAACAACGCTGCAA
66 GTAGGTCCTAAAAAAATAATTTCGACTTAACGTTTCTGAGCAAATAATATAAAA-AACACTGCAA
* * * * * *
6312489 GTAGCATGCTATT-TGAGAAGAATTTGTGAAATTGTGCCCTCGTGAACGTGCTTTTGCTACAGTT
130 GCAGAATGCT-TTGTGAGAAGAATTTGTGAAATCGCGCCCTCGTGAACGCGCTTTTACTACAGTT
** * *
6312553 GGTCCTGGAA-AAATAATTTTGACTTGACGTTTCTGAGCAAATAGTATAAAATCGAT
194 GGTCCTAAAAGAAATAATTTCGACTTGACGTTTCTGAGCAAATAGTATAAAAACGAT
* * * *
6312609 TCTAGA-AGGATGCTTTATGAGAAGAATTTGTGAAATCACGCCCACGTGGACGCGCTTTTGCTAC
1 TC-AAACAGGATGCTTTATAAGAAGAATTTGTGAAGTCGCGCCCACGTGGACGCGCTTTTGCTAC
6312673 AGTA
65 AGTA
6312677 ACATGTTTGG
Statistics
Matches: 268, Mismatches: 47, Indels: 8
0.83 0.15 0.02
Matches are distributed among these distances:
250 65 0.24
251 128 0.48
252 73 0.27
253 2 0.01
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (250 bp):
TCAAACAGGATGCTTTATAAGAAGAATTTGTGAAGTCGCGCCCACGTGGACGCGCTTTTGCTACA
GTAGGTCCTAAAAAAATAATTTCGACTTAACGTTTCTGAGCAAATAATATAAAAAACACTGCAAG
CAGAATGCTTTGTGAGAAGAATTTGTGAAATCGCGCCCTCGTGAACGCGCTTTTACTACAGTTGG
TCCTAAAAGAAATAATTTCGACTTGACGTTTCTGAGCAAATAGTATAAAAACGAT
Found at i:6315843 original size:21 final size:21
Alignment explanation
Indices: 6315817--6317048 Score: 1160
Period size: 21 Copynumber: 56.8 Consensus size: 21
6315807 TCAAATTATA
6315817 TTTAAGTTAAGGGTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTT
6315838 TTTAAGTTAAGGGTTAAGGGTTAAGGAT
1 TTTAAGTTAAGGGTT-AGGG-T-----T
6315866 TTTAAAGTTAAGGGTCTAGGGTT
1 TTT-AAGTTAAGGGT-TAGGGTT
*
6315889 TTAAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGG-TTAGGGTT
*
6315911 TTTAGGTTAAGGGTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTT
* * *
6315932 TTTAGGTTTAGGGTTTATGGTT
1 TTTAAGTTAAGGG-TTAGGGTT
* *
6315954 TTTAATTTAAGGGTTATGGTT
1 TTTAAGTTAAGGGTTAGGGTT
*
6315975 TTTAAGTTAAAGGTCTAGGGTT
1 TTTAAGTTAAGGGT-TAGGGTT
* *
6315997 TTAAAGTTAAGGGTCTATGGTT
1 TTTAAGTTAAGGGT-TAGGGTT
*
6316019 TTAAAGTTAAGGGTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTT
*
6316040 TTTAGGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGG-TTAGGGTT
6316062 TTTAAGTTAAGGGTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTT
*
6316083 TTTAAGTTAAGGGTTTATGGTT
1 TTTAAGTTAAGGG-TTAGGGTT
* *
6316105 TTAAAGTTAAGGGTCTATGGTT
1 TTTAAGTTAAGGGT-TAGGGTT
* * *
6316127 TTAAAGTTAAGGTTTAAGGTT
1 TTTAAGTTAAGGGTTAGGGTT
* *
6316148 TTTAGGTTAAGGGTTATGGTT
1 TTTAAGTTAAGGGTTAGGGTT
* *
6316169 TTTAGGTTAAGGTTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTT
*
6316190 TTTAATTTAAGGGTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTT
* *
6316211 TTTAAGTTAAAGTTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTT
* *
6316232 TTCAGGTTAAGGGTTAGGGTTTT
1 TTTAAGTTAAGGGTTAGGG--TT
*
6316255 TAGGTTAAGGTTTAGGGTTTAGGGTT
1 T---TTAA-GTTAAGGG-TTAGGGTT
* * * * *
6316281 TTTAATTTAATGATTATGATT
1 TTTAAGTTAAGGGTTAGGGTT
*
6316302 TTTAAGTTAAGCGTTTAGGGTT
1 TTTAAGTTAAG-GGTTAGGGTT
*
6316324 TTTAAGTTAAGGGTCTAAGGTT
1 TTTAAGTTAAGGGT-TAGGGTT
* *
6316346 TTAAAGTTAAGGTTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTT
* *
6316367 TTCAGGTTAAGGGTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTT
* * *
6316388 TTTAGGTTAAATGTTTAGGG-T
1 TTTAAGTT-AAGGGTTAGGGTT
* *
6316409 TTTAATTTAAGGGTTAAGGTT
1 TTTAAGTTAAGGGTTAGGGTT
6316430 TTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGG-TTAGGGTT
*
6316452 TTTAAGTTAAGGGTCTATGGTT
1 TTTAAGTTAAGGGT-TAGGGTT
* * *
6316474 TTAAAGTTAAGGTTTATGGTT
1 TTTAAGTTAAGGGTTAGGGTT
*
6316495 TTTAGGTTAAGGGTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTT
* *
6316516 TTTAGGTTAAGGGTTTAAGGTT
1 TTTAAGTTAAGGG-TTAGGGTT
6316538 TTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGG-TTAGGGTT
** *
6316560 TAAAAGTTAAGGTTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTT
** *
6316581 TTTGGGTTAAGAGTTAGGG-T
1 TTTAAGTTAAGGGTTAGGGTT
*
6316601 TTTAGGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGG-TTAGGGTT
*
6316623 TTTAATTTAAGGGTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTT
*
6316644 TTTAAGTTAAGGGTTTATGGTT
1 TTTAAGTTAAGGG-TTAGGGTT
* *
6316666 TCTAAGTTAAGGGTCTATGGTT
1 TTTAAGTTAAGGGT-TAGGGTT
** * *
6316688 TAAAAGTTAAAGTTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTT
*
6316709 TTTAGGTTAAGGGTTAGGG-T
1 TTTAAGTTAAGGGTTAGGGTT
* **
6316729 TTTATGTTAAAGATTTAGGGTT
1 TTTAAGTT-AAGGGTTAGGGTT
* * * *
6316751 TTAAATTTAAGGATTAGTGTT
1 TTTAAGTTAAGGGTTAGGGTT
6316772 TTTAAGTTAAGGGTTTAGGG-T
1 TTTAAGTTAAGGG-TTAGGGTT
*
6316793 TTTAAGTTAAGGGTCTAAGGTT
1 TTTAAGTTAAGGGT-TAGGGTT
* * *
6316815 TTAAACTTAAGGGTTATGGTT
1 TTTAAGTTAAGGGTTAGGGTT
* * *
6316836 TTTAGGTTTAGGGGTTATGGTT
1 TTTAAG-TTAAGGGTTAGGGTT
* *
6316858 TTTAATTTAAGGGTTTATGGTT
1 TTTAAGTTAAGGG-TTAGGGTT
*
6316880 TTTAATTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGG-TTAGGGTT
* * *
6316902 TTTAATTTAAAAGTTTAGGGTTT
1 TTTAAGTT-AAGGGTTAGGG-TT
*
6316925 TTTAAGTTAAGGGTTTAAGG-T
1 TTTAAGTTAAGGG-TTAGGGTT
*
6316946 TTTAAGGTTAAGGGTTAAGGTT
1 TTTAA-GTTAAGGGTTAGGGTT
*
6316968 TTTAGGTTAAGGGGTTAGGGTT
1 TTTAAGTTAA-GGGTTAGGGTT
* *
6316990 TTAAAGTTAATGGTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTT
* *
6317011 TTTAGGTTAATGGTTTAGGGTT
1 TTTAAGTTAA-GGGTTAGGGTT
* *
6317033 TTAAAGTTAAAGGTTA
1 TTTAAGTTAAGGGTTA
6317049 ATGAGTTAGG
Statistics
Matches: 1014, Mismatches: 150, Indels: 94
0.81 0.12 0.07
Matches are distributed among these distances:
20 29 0.03
21 462 0.46
22 455 0.45
23 29 0.03
26 5 0.00
27 7 0.01
28 11 0.01
29 15 0.01
30 1 0.00
ACGTcount: A:0.25, C:0.01, G:0.30, T:0.45
Consensus pattern (21 bp):
TTTAAGTTAAGGGTTAGGGTT
Found at i:6315875 original size:22 final size:22
Alignment explanation
Indices: 6315850--6317049 Score: 954
Period size: 22 Copynumber: 55.5 Consensus size: 22
6315840 TAAGTTAAGG
* *
6315850 GTTAAGGGTTAAGGATTTTAAA
1 GTTAAGGGTTAAGGGTTTTTAA
*
6315872 GTTAAGGGTCT-AGGGTTTTAAA
1 GTTAAGGGT-TAAGGGTTTTTAA
* *
6315894 GTTAAGGGTTTAGGGTTTTTAG
1 GTTAAGGGTTAAGGGTTTTTAA
*
6315916 GTTAAGGGTT-AGGGTTTTTAG
1 GTTAAGGGTTAAGGGTTTTTAA
* * *
6315937 GTTTAGGGTTTATGGTTTTTAA
1 GTTAAGGGTTAAGGGTTTTTAA
* *
6315959 TTTAAGGGTT-ATGGTTTTTAA
1 GTTAAGGGTTAAGGGTTTTTAA
* *
6315980 GTTAAAGGTCT-AGGGTTTTAAA
1 GTTAAGGGT-TAAGGGTTTTTAA
* *
6316002 GTTAAGGGTCT-ATGGTTTTAAA
1 GTTAAGGGT-TAAGGGTTTTTAA
*
6316024 GTTAAGGGTT-AGGGTTTTTAG
1 GTTAAGGGTTAAGGGTTTTTAA
*
6316045 GTTAAGGGTTTAGGGTTTTTAA
1 GTTAAGGGTTAAGGGTTTTTAA
6316067 GTTAAGGGTT-AGGGTTTTTAA
1 GTTAAGGGTTAAGGGTTTTTAA
* * *
6316088 GTTAAGGGTTTATGGTTTTAAA
1 GTTAAGGGTTAAGGGTTTTTAA
* *
6316110 GTTAAGGGTCT-ATGGTTTTAAA
1 GTTAAGGGT-TAAGGGTTTTTAA
* *
6316132 GTTAAGGTTTAA-GGTTTTTAG
1 GTTAAGGGTTAAGGGTTTTTAA
* *
6316153 GTTAAGGGTT-ATGGTTTTTAG
1 GTTAAGGGTTAAGGGTTTTTAA
*
6316174 GTTAA-GGTTTAGGGTTTTTAA
1 GTTAAGGGTTAAGGGTTTTTAA
*
6316195 TTTAAGGGTT-AGGGTTTTTAA
1 GTTAAGGGTTAAGGGTTTTTAA
* * * *
6316216 GTTAA-AGTTTAGGGTTTTCAG
1 GTTAAGGGTTAAGGGTTTTTAA
6316237 GTTAAGGGTT-AGGGTTTTTAGGTTAA
1 GTTAAGGGTTAAGGG--TTT---TTAA
* *
6316263 GGTTTAGGGTTTAGGGTTTTTAA
1 -GTTAAGGGTTAAGGGTTTTTAA
* * * * *
6316286 TTTAATGATT-ATGATTTTTAA
1 GTTAAGGGTTAAGGGTTTTTAA
* *
6316307 GTTAAGCGTTTAGGGTTTTTAA
1 GTTAAGGGTTAAGGGTTTTTAA
*
6316329 GTTAAGGGTCTAA-GGTTTTAAA
1 GTTAAGGGT-TAAGGGTTTTTAA
* * *
6316351 GTTAA-GGTTTAGGGTTTTCAG
1 GTTAAGGGTTAAGGGTTTTTAA
*
6316372 GTTAAGGGTT-AGGGTTTTTAG
1 GTTAAGGGTTAAGGGTTTTTAA
** *
6316393 GTTAAATGTTTAGGG-TTTTAA
1 GTTAAGGGTTAAGGGTTTTTAA
*
6316414 TTTAAGGGTTAA-GGTTTTTAA
1 GTTAAGGGTTAAGGGTTTTTAA
*
6316435 GTTAAGGGTTTAGGGTTTTTAA
1 GTTAAGGGTTAAGGGTTTTTAA
* *
6316457 GTTAAGGGTCT-ATGGTTTTAAA
1 GTTAAGGGT-TAAGGGTTTTTAA
* * *
6316479 GTTAA-GGTTTATGGTTTTTAG
1 GTTAAGGGTTAAGGGTTTTTAA
*
6316500 GTTAAGGGTT-AGGGTTTTTAG
1 GTTAAGGGTTAAGGGTTTTTAA
6316521 GTTAAGGGTTTAA-GGTTTTTAA
1 GTTAAGGG-TTAAGGGTTTTTAA
* **
6316543 GTTAAGGGTTTAGGGTTTAAAA
1 GTTAAGGGTTAAGGGTTTTTAA
* **
6316565 GTTAA-GGTTTAGGGTTTTTGG
1 GTTAAGGGTTAAGGGTTTTTAA
* *
6316586 GTTAAGAGTT-AGGG-TTTTAG
1 GTTAAGGGTTAAGGGTTTTTAA
*
6316606 GTTAAGGGTTTAGGGTTTTTAA
1 GTTAAGGGTTAAGGGTTTTTAA
*
6316628 TTTAAGGGTT-AGGGTTTTTAA
1 GTTAAGGGTTAAGGGTTTTTAA
* * *
6316649 GTTAAGGGTTTATGGTTTCTAA
1 GTTAAGGGTTAAGGGTTTTTAA
* **
6316671 GTTAAGGGTCT-ATGGTTTAAAA
1 GTTAAGGGT-TAAGGGTTTTTAA
* * *
6316693 GTTAA-AGTTTAGGGTTTTTAG
1 GTTAAGGGTTAAGGGTTTTTAA
*
6316714 GTTAAGGGTT-AGGG-TTTTAT
1 GTTAAGGGTTAAGGGTTTTTAA
* * * *
6316734 GTTAAAGATTTAGGGTTTTAAA
1 GTTAAGGGTTAAGGGTTTTTAA
* * *
6316756 TTTAAGGATT-AGTGTTTTTAA
1 GTTAAGGGTTAAGGGTTTTTAA
*
6316777 GTTAAGGGTTTAGGG-TTTTAA
1 GTTAAGGGTTAAGGGTTTTTAA
*
6316798 GTTAAGGGTCTAA-GGTTTTAAA
1 GTTAAGGGT-TAAGGGTTTTTAA
* * *
6316820 CTTAAGGGTT-ATGGTTTTTAG
1 GTTAAGGGTTAAGGGTTTTTAA
* *
6316841 GTTTAGGGGTT-ATGGTTTTTAA
1 G-TTAAGGGTTAAGGGTTTTTAA
* * *
6316863 TTTAAGGGTTTATGGTTTTTAA
1 GTTAAGGGTTAAGGGTTTTTAA
* *
6316885 TTTAAGGGTTTAGGGTTTTTAA
1 GTTAAGGGTTAAGGGTTTTTAA
* ** *
6316907 TTTAAAAGTTTAGGGTTTTTTAA
1 GTTAAGGGTTAAGGG-TTTTTAA
6316930 GTTAAGGGTTTAA-GG-TTTTAA
1 GTTAAGGG-TTAAGGGTTTTTAA
*
6316951 GGTTAAGGGTTAA-GGTTTTTAG
1 -GTTAAGGGTTAAGGGTTTTTAA
*
6316973 GTTAAGGGGTT-AGGGTTTTAAA
1 GTTAA-GGGTTAAGGGTTTTTAA
* *
6316995 GTTAATGGTT-AGGGTTTTTAG
1 GTTAAGGGTTAAGGGTTTTTAA
* * *
6317016 GTTAATGGTTTAGGGTTTTAAA
1 GTTAAGGGTTAAGGGTTTTTAA
*
6317038 GTTAAAGGTTAA
1 GTTAAGGGTTAA
6317050 TGAGTTAGGG
Statistics
Matches: 992, Mismatches: 131, Indels: 110
0.80 0.11 0.09
Matches are distributed among these distances:
20 42 0.04
21 429 0.43
22 472 0.48
23 28 0.03
24 3 0.00
26 5 0.01
27 9 0.01
28 4 0.00
ACGTcount: A:0.25, C:0.01, G:0.29, T:0.45
Consensus pattern (22 bp):
GTTAAGGGTTAAGGGTTTTTAA
Found at i:6315878 original size:29 final size:28
Alignment explanation
Indices: 6315822--6315888 Score: 91
Period size: 29 Copynumber: 2.4 Consensus size: 28
6315812 TTATATTTAA
* *
6315822 GTTAAGGGTTAGGGTTTTTAAGTTAAGG
1 GTTAAGGGTTAGGATTTTAAAGTTAAGG
6315850 GTTAAGGGTTAAGGATTTTAAAGTTAAGG
1 GTTAAGGGTT-AGGATTTTAAAGTTAAGG
6315879 GTCT-AGGGTT
1 GT-TAAGGGTT
6315889 TTAAAGTTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
28 10 0.29
29 24 0.69
30 1 0.03
ACGTcount: A:0.27, C:0.01, G:0.34, T:0.37
Consensus pattern (28 bp):
GTTAAGGGTTAGGATTTTAAAGTTAAGG
Done.