Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D06
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: 68668488
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1920000 characters in sequence are not A, C, G, or T
File 137 of 230
Found at i:40216170 original size:27 final size:26
Alignment explanation
Indices: 40216130--40216209 Score: 142
Period size: 27 Copynumber: 3.0 Consensus size: 26
40216120 CACCAATGAG
40216130 TTGGGGAATCAGCACTTAGCAACCCC
1 TTGGGGAATCAGCACTTAGCAACCCC
40216156 TTGGGGAAATCAGCACTTAGCAACCCC
1 TTGGGG-AATCAGCACTTAGCAACCCC
40216183 TTGGGGGAATCAGCACTTAGCAACCCC
1 TT-GGGGAATCAGCACTTAGCAACCCC
40216210 CTTCACATTT
Statistics
Matches: 52, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
26 6 0.12
27 42 0.81
28 4 0.08
ACGTcount: A:0.28, C:0.30, G:0.24, T:0.19
Consensus pattern (26 bp):
TTGGGGAATCAGCACTTAGCAACCCC
Found at i:40216247 original size:42 final size:41
Alignment explanation
Indices: 40216188--40216324 Score: 146
Period size: 42 Copynumber: 3.5 Consensus size: 41
40216178 ACCCCTTGGG
40216188 GGAATCAGCACTTAGCAACCCCCTTCACATTTAAAATACGGT
1 GGAATCAGCACTTAGCAA-CCCCTTCACATTTAAAATACGGT
* * * *
40216230 GGAATCAGCATTTAGCAACCAC--CA-A--T-GAGT-CGG-
1 GGAATCAGCACTTAGCAACCCCTTCACATTTAAAATACGGT
*
40216263 GGAATCAGCACTTAGCAACCCCTTGCACATTTAAAATATGGT
1 GGAATCAGCACTTAGCAACCCCTT-CACATTTAAAATACGGT
*
40216305 GGAATCAGCACCTAGCAACC
1 GGAATCAGCACTTAGCAACC
40216325 ACCAATGATT
Statistics
Matches: 76, Mismatches: 10, Indels: 18
0.73 0.10 0.17
Matches are distributed among these distances:
33 20 0.26
34 3 0.04
35 2 0.03
36 3 0.04
37 1 0.01
38 1 0.01
39 3 0.04
40 2 0.03
41 5 0.07
42 36 0.47
ACGTcount: A:0.34, C:0.27, G:0.18, T:0.21
Consensus pattern (41 bp):
GGAATCAGCACTTAGCAACCCCTTCACATTTAAAATACGGT
Found at i:40216360 original size:75 final size:75
Alignment explanation
Indices: 40216186--40216362 Score: 293
Period size: 75 Copynumber: 2.4 Consensus size: 75
40216176 CAACCCCTTG
**
40216186 GGGGAATCAGCACTTAGCAACCCCCTT-CACATTTAAAATACGGTGGAATCAGCATTTAGCAACC
1 GGGGAATCAGCACTTAGCAA-CCCCTTGCACATTTAAAATACGGTGGAATCAGCACCTAGCAACC
40216250 ACCAATGAGTC
65 ACCAATGAGTC
*
40216261 GGGGAATCAGCACTTAGCAACCCCTTGCACATTTAAAATATGGTGGAATCAGCACCTAGCAACCA
1 GGGGAATCAGCACTTAGCAACCCCTTGCACATTTAAAATACGGTGGAATCAGCACCTAGCAACCA
*
40216326 CCAATGATTC
66 CCAATGAGTC
*
40216336 GGGGAATTAGCACTTAGCAACCCCTTG
1 GGGGAATCAGCACTTAGCAACCCCTTG
40216363 GGGGAACCAG
Statistics
Matches: 96, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
74 6 0.06
75 90 0.94
ACGTcount: A:0.32, C:0.27, G:0.20, T:0.21
Consensus pattern (75 bp):
GGGGAATCAGCACTTAGCAACCCCTTGCACATTTAAAATACGGTGGAATCAGCACCTAGCAACCA
CCAATGAGTC
Found at i:40220643 original size:4 final size:4
Alignment explanation
Indices: 40220634--40220658 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
40220624 ATTTATATAG
40220634 AGAT AGAT AGAT AGAT AGAT AGAT A
1 AGAT AGAT AGAT AGAT AGAT AGAT A
40220659 ATATGACATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.24, T:0.24
Consensus pattern (4 bp):
AGAT
Found at i:40236575 original size:39 final size:40
Alignment explanation
Indices: 40236482--40236705 Score: 269
Period size: 40 Copynumber: 5.7 Consensus size: 40
40236472 GCTCCTCGTT
*
40236482 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
* *
40236522 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACT-GTA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
*
40236561 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * *
40236601 CCAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * * *
40236640 CAAATACCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
40236681 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
40236706 CATCATTCAA
Statistics
Matches: 159, Mismatches: 19, Indels: 12
0.84 0.10 0.06
Matches are distributed among these distances:
38 2 0.01
39 69 0.43
40 75 0.47
41 13 0.08
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:40236585 original size:79 final size:80
Alignment explanation
Indices: 40236482--40236705 Score: 269
Period size: 79 Copynumber: 2.8 Consensus size: 80
40236472 GCTCCTCGTT
* *
40236482 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG
* *
40236547 ATTTAGTAACT-GTA
66 AATTAGTAACTCGCA
* *
40236561 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCACCAATGCCTTCGGG-CTTAGCCCG
1 CAAATGCCTTCGGGACTTAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCG
*
40236624 GAATTAGTATCTCGCA
65 GAATTAGTAACTCGCA
* * * * * *
40236640 CAAATACCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCC
1 CAAATGCCTTCGGGA-CTTAGCCCGGTTATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGCCC
40236703 GGA
64 GGA
40236706 CATCATTCAA
Statistics
Matches: 124, Mismatches: 15, Indels: 11
0.83 0.10 0.07
Matches are distributed among these distances:
78 22 0.18
79 82 0.66
80 20 0.16
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (80 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG
AATTAGTAACTCGCA
Found at i:40244694 original size:119 final size:120
Alignment explanation
Indices: 40244512--40244734 Score: 283
Period size: 119 Copynumber: 1.9 Consensus size: 120
40244502 TCCTCGTTCA
** *
40244512 AATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
1 AATGCCTTCGGGACATAGCCCGAATATAGTAACTCGCACAAATACCTTCGGGACTTAACCCGGAT
* *
40244577 TTAGTAAC-TCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
66 ATAGTAACTTAGCACAAA-GCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
* * **
40244632 AATGCCTTCGGG-CTTAGCCCGAA-ATTAGTATCTCGCACAAATACCTTC-GGATCTTAGTCCGG
1 AATGCCTTCGGGACATAGCCCGAATA-TAGTAACTCGCACAAATACCTTCGGGA-CTTAACCCGG
* * *
40244694 ATATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
64 ATATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGA
40244735 CATCATTCAA
Statistics
Matches: 88, Mismatches: 12, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
118 4 0.05
119 64 0.73
120 20 0.23
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (120 bp):
AATGCCTTCGGGACATAGCCCGAATATAGTAACTCGCACAAATACCTTCGGGACTTAACCCGGAT
ATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
Found at i:40244734 original size:40 final size:40
Alignment explanation
Indices: 40244510--40244734 Score: 269
Period size: 40 Copynumber: 5.7 Consensus size: 40
40244500 GCTCCTCGTT
* *
40244510 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
40244550 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
40244590 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* * *
40244630 CCAATGCCTTCGGG-CTTAGCCC-GAAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA
* * * * *
40244669 CAAATACCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA
40244710 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
40244735 CATCATTCAA
Statistics
Matches: 160, Mismatches: 19, Indels: 12
0.84 0.10 0.06
Matches are distributed among these distances:
38 4 0.03
39 27 0.17
40 115 0.72
41 14 0.09
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:40254727 original size:54 final size:54
Alignment explanation
Indices: 40254633--40254739 Score: 126
Period size: 54 Copynumber: 2.0 Consensus size: 54
40254623 TCTAAGTTGG
* * * * *
40254633 GACACACGACTATGTCCCAACTCGTGTCCTTACCCGTGTAACTTATTGACTTGA
1 GACACACGACCATGTCCCAACCCGTGTCCTTACCCATGTAACTCACTGACTTGA
* * *
40254687 GACACACGACCGTGTCCCAACCCGTGT-CTCTGCTCATGTAACTCACTGACTTG
1 GACACACGACCATGTCCCAACCCGTGTCCT-TACCCATGTAACTCACTGACTTG
40254740 GGTCACATGG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
53 2 0.05
54 42 0.95
ACGTcount: A:0.22, C:0.33, G:0.18, T:0.27
Consensus pattern (54 bp):
GACACACGACCATGTCCCAACCCGTGTCCTTACCCATGTAACTCACTGACTTGA
Found at i:40256270 original size:19 final size:18
Alignment explanation
Indices: 40256232--40256270 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
40256222 TATTACACAA
*
40256232 TTCAATTTCACATTAAAT
1 TTCAATTTCACACTAAAT
*
40256250 TTCAATTTTCACACTATAT
1 TTCAA-TTTCACACTAAAT
40256269 TT
1 TT
40256271 TACTTATTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.33, C:0.18, G:0.00, T:0.49
Consensus pattern (18 bp):
TTCAATTTCACACTAAAT
Found at i:40259278 original size:27 final size:27
Alignment explanation
Indices: 40259246--40259415 Score: 214
Period size: 27 Copynumber: 6.3 Consensus size: 27
40259236 ACCATATAGA
* *
40259246 CTATTCTTTCAGAGTTCGCCATAAAGG
1 CTATTCTTTCAGAGTTCACCAAAAAGG
* *
40259273 CCATTCTTTCAAAGTTCACCAAAAAGG
1 CTATTCTTTCAGAGTTCACCAAAAAGG
* * *
40259300 CTATTCTTTCAGAGTTCGCCACAACGG
1 CTATTCTTTCAGAGTTCACCAAAAAGG
* *
40259327 CTATTCTTTCAAAGTTCACCAAAAACG
1 CTATTCTTTCAGAGTTCACCAAAAAGG
* *
40259354 CTATTATTTCAGAGTTCACCAAAAATG
1 CTATTCTTTCAGAGTTCACCAAAAAGG
* *
40259381 CTATTCTTTTAGAGTTCACCAGAAAGG
1 CTATTCTTTCAGAGTTCACCAAAAAGG
*
40259408 TTATTCTT
1 CTATTCTT
40259416 AGTTGTCGTG
Statistics
Matches: 121, Mismatches: 22, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 121 1.00
ACGTcount: A:0.31, C:0.23, G:0.14, T:0.33
Consensus pattern (27 bp):
CTATTCTTTCAGAGTTCACCAAAAAGG
Found at i:40262323 original size:18 final size:19
Alignment explanation
Indices: 40262289--40262326 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
40262279 AGAATTTCAT
40262289 AACTTAAGATAACATAAAA
1 AACTTAAGATAACATAAAA
40262308 AACTT-AGATTAA-ATAAAA
1 AACTTAAGA-TAACATAAAA
40262326 A
1 A
40262327 TCATGCTTGC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.63, C:0.08, G:0.05, T:0.24
Consensus pattern (19 bp):
AACTTAAGATAACATAAAA
Found at i:40262467 original size:27 final size:27
Alignment explanation
Indices: 40262432--40262483 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
40262422 GAAAAAAATT
40262432 TAAAATTCATGCAAATATTCCCTTAAA
1 TAAAATTCATGCAAATATTCCCTTAAA
* * *
40262459 TAAATTTCATGCTAATATTGCCTTA
1 TAAAATTCATGCAAATATTCCCTTA
40262484 CCCCCACCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.38, C:0.17, G:0.06, T:0.38
Consensus pattern (27 bp):
TAAAATTCATGCAAATATTCCCTTAAA
Found at i:40270117 original size:27 final size:27
Alignment explanation
Indices: 40270049--40270202 Score: 130
Period size: 27 Copynumber: 5.7 Consensus size: 27
40270039 ATATAAAACA
*
40270049 CACCACAAAGACTATTCTTTTAGAGTT
1 CACCACAAAGGCTATTCTTTTAGAGTT
** * **
40270076 TGCAACAAATACTATTCTTTTAGAGTT
1 CACCACAAAGGCTATTCTTTTAGAGTT
* * **
40270103 TACCAAAAAGGCTATTCTTTCGGAGTT
1 CACCACAAAGGCTATTCTTTTAGAGTT
* * *
40270130 CGCCACCAAGGCTATT-TTTTCAGTGTT
1 CACCACAAAGGCTATTCTTTT-AGAGTT
* * * *
40270157 CACCATAAAGGCTAATCTATCAGAGTT
1 CACCACAAAGGCTATTCTTTTAGAGTT
*
40270184 CGCCACAAAGGCTATTCTT
1 CACCACAAAGGCTATTCTT
40270203 AGCTGTCGTG
Statistics
Matches: 96, Mismatches: 29, Indels: 4
0.74 0.22 0.03
Matches are distributed among these distances:
26 3 0.03
27 91 0.95
28 2 0.02
ACGTcount: A:0.30, C:0.22, G:0.15, T:0.33
Consensus pattern (27 bp):
CACCACAAAGGCTATTCTTTTAGAGTT
Found at i:40270145 original size:54 final size:55
Alignment explanation
Indices: 40270087--40270202 Score: 155
Period size: 54 Copynumber: 2.1 Consensus size: 55
40270077 GCAACAAATA
* * * * *
40270087 CTATTCTTTT-AGAGTTTACCAAAAAGGCTATTCTTTCGGAGTTCGCCACCAAGG
1 CTATTCTTTTCAGAGTTCACCAAAAAGGCTAATCTATCAGAGTTCGCCACAAAGG
* *
40270141 CTATT-TTTTCAGTGTTCACCATAAAGGCTAATCTATCAGAGTTCGCCACAAAGG
1 CTATTCTTTTCAGAGTTCACCAAAAAGGCTAATCTATCAGAGTTCGCCACAAAGG
40270195 CTATTCTT
1 CTATTCTT
40270203 AGCTGTCGTG
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
53 4 0.08
54 47 0.89
55 2 0.04
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.34
Consensus pattern (55 bp):
CTATTCTTTTCAGAGTTCACCAAAAAGGCTAATCTATCAGAGTTCGCCACAAAGG
Found at i:40275260 original size:331 final size:332
Alignment explanation
Indices: 40274634--40275298 Score: 1278
Period size: 331 Copynumber: 2.0 Consensus size: 332
40274624 ATTTGAATTT
40274634 ATTGTTTTTTTTGCTGACTTTGTTTTTTTTTTGTGTCTGTGTCTCTCCTTGGCATAATTCATGCA
1 ATTGTTTTTTTTGCTGACTTTG-TTTTTTTTTGTGTCTGTGTCTCTCCTTGGCATAATTCATGCA
*
40274699 TCATTTAAATCCCTGGGGCACAGTGTCACATCTATATTCACATGAACATACTTCAAAAAGATTTA
65 TCATTTAAATACCTGGGGCACAGTGTCACATCTATATTCACATGAACATACTTCAAAAAGATTTA
40274764 GTTGTTCGGCATGGGGTAGAAAATATAGGGATAATAGCAAGAATGTCAAAGGATACTCAAAGCAG
130 GTTGTTCGGCATGGGGTAGAAAATATAGGGATAATAGCAAGAATGTCAAAGGATACTCAAAGCAG
*
40274829 AGAAGGTGATTGCTAGATAGCTTATTTTGGCTTGAGCCTACCTTAGATAGTTCGCATGGATTGTA
195 AGAAGGTGATCGCTAGATAGCTTATTTTGGCTTGAGCCTACCTTAGATAGTTCGCATGGATTGTA
40274894 GGAGGAATTGCGAAGATGAGTTAAAGGGAATATGGCAATCAAGTAATGATGCTAAAAAAAAGGTA
260 GGAGGAATTGCGAAGATGAGTTAAAGGGAATATGGCAATCAAGTAATGATGCTAAAAAAAAGGTA
40274959 CTTCTATG
325 CTTCTATG
40274967 ATTGTTTTTTTTGCTGACTTTG-TTTTTTTTGTGTCTGTGTCTCTCCTTGGCATAATTCATGCAT
1 ATTGTTTTTTTTGCTGACTTTGTTTTTTTTTGTGTCTGTGTCTCTCCTTGGCATAATTCATGCAT
*
40275031 CATTTAAATACCTGGGGCACAGTGTCGCATCTATATTCACATGAACATACTTCAAAAAGATTTAG
66 CATTTAAATACCTGGGGCACAGTGTCACATCTATATTCACATGAACATACTTCAAAAAGATTTAG
*
40275096 TTGTTCGGCATGGGGTAGAAAATATAGGGATAATAGCGAGAATGTCAAAGGATACTCAAAGCAGA
131 TTGTTCGGCATGGGGTAGAAAATATAGGGATAATAGCAAGAATGTCAAAGGATACTCAAAGCAGA
40275161 GAAGGTGATCGCTAGATAGCTTATTTTGGCTTGAGCCTACCTTAGATAGTTCGCATGGATTGTAG
196 GAAGGTGATCGCTAGATAGCTTATTTTGGCTTGAGCCTACCTTAGATAGTTCGCATGGATTGTAG
40275226 GAGGAATTGCGAAGATGAGTTAAAGGGAATATGGCAATCAAGTAATGATGCTAAAAAAAAGGTAC
261 GAGGAATTGCGAAGATGAGTTAAAGGGAATATGGCAATCAAGTAATGATGCTAAAAAAAAGGTAC
40275291 TTCTATG
326 TTCTATG
40275298 A
1 A
40275299 CAAGTATGGC
Statistics
Matches: 328, Mismatches: 4, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
331 306 0.93
333 22 0.07
ACGTcount: A:0.30, C:0.14, G:0.23, T:0.33
Consensus pattern (332 bp):
ATTGTTTTTTTTGCTGACTTTGTTTTTTTTTGTGTCTGTGTCTCTCCTTGGCATAATTCATGCAT
CATTTAAATACCTGGGGCACAGTGTCACATCTATATTCACATGAACATACTTCAAAAAGATTTAG
TTGTTCGGCATGGGGTAGAAAATATAGGGATAATAGCAAGAATGTCAAAGGATACTCAAAGCAGA
GAAGGTGATCGCTAGATAGCTTATTTTGGCTTGAGCCTACCTTAGATAGTTCGCATGGATTGTAG
GAGGAATTGCGAAGATGAGTTAAAGGGAATATGGCAATCAAGTAATGATGCTAAAAAAAAGGTAC
TTCTATG
Found at i:40277144 original size:12 final size:13
Alignment explanation
Indices: 40277122--40277162 Score: 52
Period size: 12 Copynumber: 3.4 Consensus size: 13
40277112 GTGCCCTAAT
*
40277122 TTCAT-TCATTCA
1 TTCATCTCATTCG
40277134 TTCATCT-ATTCG
1 TTCATCTCATTCG
40277146 TTCA-CTCATTCG
1 TTCATCTCATTCG
40277158 TTCAT
1 TTCAT
40277163 TTGTTTATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
11 2 0.08
12 22 0.88
13 1 0.04
ACGTcount: A:0.20, C:0.27, G:0.05, T:0.49
Consensus pattern (13 bp):
TTCATCTCATTCG
Found at i:40285169 original size:42 final size:42
Alignment explanation
Indices: 40285110--40285361 Score: 312
Period size: 42 Copynumber: 6.1 Consensus size: 42
40285100 AAGGAAAACA
* * * *
40285110 TTCATTGCATTTAGAGGCCCAGGTGTCGAGCTCTATTTACTT
1 TTCATTGCATTTAGAGACCCAGGTGTGGAGGTCCATTTACTT
* *
40285152 TTCATTGCATTTAGAGGCTCAGGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGACCCAGGTGTGGAGGTCCATTTACTT
* * *
40285194 TTCATTGCATTTAGAGTCCCAGGTGCGGAGGTCCATTCACTT
1 TTCATTGCATTTAGAGACCCAGGTGTGGAGGTCCATTTACTT
*
40285236 TTCATTGCATTTAGAGACCCAGGTGTGGAGGTCCATTCACTT
1 TTCATTGCATTTAGAGACCCAGGTGTGGAGGTCCATTTACTT
* * ***
40285278 TTCATTACATTTAGAGACCCAAGTGTGGAGGTTTGTTTACTT
1 TTCATTGCATTTAGAGACCCAGGTGTGGAGGTCCATTTACTT
* * * *
40285320 TTC-TAG--TTTAAAGACCCAGGTGTGGAGGCCCGTTTACTT
1 TTCATTGCATTTAGAGACCCAGGTGTGGAGGTCCATTTACTT
40285359 TTC
1 TTC
40285362 TAGTTTACTT
Statistics
Matches: 187, Mismatches: 23, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
39 31 0.17
41 1 0.01
42 155 0.83
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.37
Consensus pattern (42 bp):
TTCATTGCATTTAGAGACCCAGGTGTGGAGGTCCATTTACTT
Found at i:40285389 original size:16 final size:16
Alignment explanation
Indices: 40285368--40285398 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
40285358 TTTCTAGTTT
40285368 ACTTTTCATTGCATTG
1 ACTTTTCATTGCATTG
40285384 ACTTTTCATTGCATT
1 ACTTTTCATTGCATT
40285399 TAGAGGCCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.19, G:0.10, T:0.52
Consensus pattern (16 bp):
ACTTTTCATTGCATTG
Found at i:40286248 original size:145 final size:147
Alignment explanation
Indices: 40285998--40286401 Score: 513
Period size: 145 Copynumber: 2.8 Consensus size: 147
40285988 AAATTTTTGA
* * *
40285998 TTTTTTTTAAAAAAAGAGAAAATTTAGATTTT-AACAAATAAAAATCTATTTTTTTAGTTATTAT
1 TTTTTTTTAAAAAAAGAGAAAGTTTAGATTTTGAA-AAATAAAAA--TA-TTTTTTAGTCATTTT
* * *
40286062 AAAGAAAAGTTTAAATTTTTAAAACAAAATTTTGATTTTTTTCAACTATTTC-AAAGTAAAAGCT
62 AAAGGAAAGTTTAAAATTTTAAAACAAAATTTTGATTTTTTT-AACTATTTCAAAAATAAAAGCT
40286126 TTAATCTTTAAGAAAAATAGTG
126 TTAATCTTTAAGAAAAATAGTG
***
40286148 TTTTTTTTAAAAAAAGAGAAAGTTTAGATTTTGAAAAATAAAAA-A-AAATTAGTCATTTTAAAG
1 TTTTTTTTAAAAAAAGAGAAAGTTTAGATTTTGAAAAATAAAAATATTTTTTAGTCATTTTAAAG
*
40286211 GAAAGTTTAAAATTTTAAAACAAAAATTTGA-TTTTTT---T-TTTCAAAAATAAAAGCTTTAAT
66 GAAAGTTTAAAATTTTAAAACAAAATTTTGATTTTTTTAACTATTTCAAAAATAAAAGCTTTAAT
*
40286271 TTTTAAGAAAAATAGTG
131 CTTTAAGAAAAATAGTG
* * *
40286288 -TTTTTTTAAAGAATGAAAAAGTTTAGATTTTGAAAAATAAAAATATGTTTTTTAAGTCATTTTA
1 TTTTTTTTAAAAAAAGAGAAAGTTTAGATTTTGAAAAATAAAAATA--TTTTTT-AGTCATTTTA
* * *
40286352 AAGGAAATTTTAAAATTTTAAAACAAATTTTTTATTTTTTTAACTATTTC
63 AAGGAAAGTTTAAAATTTTAAAACAAAATTTTGATTTTTTTAACTATTTC
40286402 GAAATAAGGT
Statistics
Matches: 221, Mismatches: 21, Indels: 25
0.83 0.08 0.09
Matches are distributed among these distances:
139 44 0.20
140 34 0.15
143 2 0.01
144 46 0.21
145 47 0.21
147 1 0.00
148 1 0.00
149 4 0.02
150 40 0.18
151 2 0.01
ACGTcount: A:0.45, C:0.04, G:0.09, T:0.42
Consensus pattern (147 bp):
TTTTTTTTAAAAAAAGAGAAAGTTTAGATTTTGAAAAATAAAAATATTTTTTAGTCATTTTAAAG
GAAAGTTTAAAATTTTAAAACAAAATTTTGATTTTTTTAACTATTTCAAAAATAAAAGCTTTAAT
CTTTAAGAAAAATAGTG
Found at i:40286390 original size:139 final size:137
Alignment explanation
Indices: 40285998--40286390 Score: 375
Period size: 139 Copynumber: 2.7 Consensus size: 137
40285988 AAATTTTTGA
*** * *
40285998 TTTTTTTTAAAAAAAGAGAAAA-TTTAGATTTT-AACAAATAAAAATCTATTTTTTTAGTTATTA
1 TTTTTTTTAAAAAAAGA-AAAAGTTTAGATTTTGAA-AAATAAAAA---A--AAATTAGTCATTT
* * * *
40286061 TAAAGAAAAGTTTAAATTTTTAAAACAAAATTTTGATTTTTTTCAACTATTTCAAAGTAAAAGCT
59 TAAAGGAAAGTTTAAAATTTTAAAACAAAA-TTT-A---TTTT--A-TTTTTCAAAATAAAAGCT
40286126 TTAATCTTTAAGAAAAATAGTG
116 TTAATCTTTAAGAAAAATAGTG
*
40286148 TTTTTTTTAAAAAAAGAGAAAGTTTAGATTTTGAAAAATAAAAAAAAATTAGTCATTTTAAAGGA
1 TTTTTTTTAAAAAAAGAAAAAGTTTAGATTTTGAAAAATAAAAAAAAATTAGTCATTTTAAAGGA
* *
40286213 AAGTTTAAAATTTTAAAACAAAAATTTGATTTTTTTTTTCAAAAATAAAAGCTTTAATTTTTAAG
66 AAGTTTAAAATTTTAAAAC-AAAATTT-ATTTTATTTTTC-AAAATAAAAGCTTTAATCTTTAAG
40286278 AAAAATAGTG
128 AAAAATAGTG
* * ***
40286288 -TTTTTTTAAAGAATGAAAAAGTTTAGATTTTGAAAAATAAAAATATGTTTTTTAAGTCATTTTA
1 TTTTTTTTAAAAAAAGAAAAAGTTTAGATTTTGAAAAATAAAAA-A---AAATT-AGTCATTTTA
*
40286352 AAGGAAATTTTAAAATTTTAAAAC-AAA-TT-TTTTATTTTT
61 AAGGAAAGTTTAAAATTTTAAAACAAAATTTATTTTATTTTT
40286391 TTAACTATTT
Statistics
Matches: 214, Mismatches: 20, Indels: 29
0.81 0.08 0.11
Matches are distributed among these distances:
139 54 0.25
140 33 0.15
141 2 0.01
142 7 0.03
143 2 0.01
144 33 0.15
145 37 0.17
146 4 0.02
147 1 0.00
149 3 0.01
150 36 0.17
151 2 0.01
ACGTcount: A:0.46, C:0.04, G:0.09, T:0.42
Consensus pattern (137 bp):
TTTTTTTTAAAAAAAGAAAAAGTTTAGATTTTGAAAAATAAAAAAAAATTAGTCATTTTAAAGGA
AAGTTTAAAATTTTAAAACAAAATTTATTTTATTTTTCAAAATAAAAGCTTTAATCTTTAAGAAA
AATAGTG
Found at i:40287918 original size:25 final size:25
Alignment explanation
Indices: 40287885--40287935 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
40287875 TTAAAAGTAA
40287885 AAATCTCTAATTTAAGTTTCAAATT
1 AAATCTCTAATTTAAGTTTCAAATT
40287910 AAATCTCTAATTTAAGTTTCAAATT
1 AAATCTCTAATTTAAGTTTCAAATT
40287935 A
1 A
40287936 GATAAGTTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.41, C:0.12, G:0.04, T:0.43
Consensus pattern (25 bp):
AAATCTCTAATTTAAGTTTCAAATT
Found at i:40287934 original size:13 final size:13
Alignment explanation
Indices: 40287893--40287934 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
40287883 AAAAATCTCT
40287893 AATTTAAGTTTCA
1 AATTTAAGTTTCA
* * *
40287906 AA-TTAAATCTCT
1 AATTTAAGTTTCA
40287918 AATTTAAGTTTCA
1 AATTTAAGTTTCA
40287931 AATT
1 AATT
40287935 AGATAAGTTT
Statistics
Matches: 22, Mismatches: 6, Indels: 2
0.73 0.20 0.07
Matches are distributed among these distances:
12 9 0.41
13 13 0.59
ACGTcount: A:0.40, C:0.10, G:0.05, T:0.45
Consensus pattern (13 bp):
AATTTAAGTTTCA
Found at i:40291866 original size:25 final size:25
Alignment explanation
Indices: 40291820--40291867 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
40291810 ATTTATTGTC
**
40291820 TTTAGTTTTTATTTCTTTTTAGATG
1 TTTAGTTTTTATTTCTAGTTAGATG
40291845 TTTAG-TTTTATTTCCTAGTTAGA
1 TTTAGTTTTTATTT-CTAGTTAGA
40291868 ATTTTTTCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.19, C:0.06, G:0.12, T:0.62
Consensus pattern (25 bp):
TTTAGTTTTTATTTCTAGTTAGATG
Found at i:40292764 original size:32 final size:32
Alignment explanation
Indices: 40292720--40292780 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
40292710 AAAGCACAGA
*
40292720 AAAGATTGCTCAAATTCTCAAAAATAAAGATT
1 AAAGATTGCTCAAAGTCTCAAAAATAAAGATT
* * *
40292752 AAAGTTTGCTCAAAGTCTGAAAATTAAAG
1 AAAGATTGCTCAAAGTCTCAAAAATAAAG
40292781 GTTGAACATG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.48, C:0.11, G:0.13, T:0.28
Consensus pattern (32 bp):
AAAGATTGCTCAAAGTCTCAAAAATAAAGATT
Found at i:40301037 original size:20 final size:20
Alignment explanation
Indices: 40300997--40301089 Score: 87
Period size: 20 Copynumber: 4.7 Consensus size: 20
40300987 GGATTTGTAG
* * *
40300997 TTCGGTGCCTATGTATACAC
1 TTCGGTGTCTCTGTTTACAC
* *
40301017 TTCGATGTCTCTGTTTGCAC
1 TTCGGTGTCTCTGTTTACAC
* * *
40301037 TTTGGTGCCTCTGTATACAC
1 TTCGGTGTCTCTGTTTACAC
*
40301057 TTCGGTGTCCCTGTTTACAC
1 TTCGGTGTCTCTGTTTACAC
* *
40301077 TACGGTGCCTCTG
1 TTCGGTGTCTCTG
40301090 CTTGCTCAAT
Statistics
Matches: 56, Mismatches: 17, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 56 1.00
ACGTcount: A:0.13, C:0.27, G:0.22, T:0.39
Consensus pattern (20 bp):
TTCGGTGTCTCTGTTTACAC
Found at i:40301087 original size:40 final size:40
Alignment explanation
Indices: 40300999--40301089 Score: 128
Period size: 40 Copynumber: 2.3 Consensus size: 40
40300989 ATTTGTAGTT
* * * *
40300999 CGGTGCCTATGTATACACTTCGATGTCTCTGTTTGCACTT
1 CGGTGCCTCTGTATACACTTCGATGTCCCTGTTTACACTA
* *
40301039 TGGTGCCTCTGTATACACTTCGGTGTCCCTGTTTACACTA
1 CGGTGCCTCTGTATACACTTCGATGTCCCTGTTTACACTA
40301079 CGGTGCCTCTG
1 CGGTGCCTCTG
40301090 CTTGCTCAAT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.13, C:0.27, G:0.22, T:0.37
Consensus pattern (40 bp):
CGGTGCCTCTGTATACACTTCGATGTCCCTGTTTACACTA
Found at i:40302601 original size:50 final size:50
Alignment explanation
Indices: 40302489--40302729 Score: 338
Period size: 50 Copynumber: 4.8 Consensus size: 50
40302479 TAATAACTTA
* ** *
40302489 CCAAAGCCATGCCCCAGACATGGTCTTACATGGGATGTTCTCATATCGGTG
1 CCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGGTG
* * * **
40302540 CCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTTAGTG
1 CCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTG
* *
40302590 CCAACGCCATGTCCCAGACACGGTCTTACATGGGACCTCTCATCTCGGTG
1 CCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTG
*
40302640 CCAAAGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATCTCGGTG
1 CCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTG
* * *
40302690 CCAACGCCATGTCCCAAACATGGTCTTACATGAGACCTCT
1 CCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
40302730 TTACCCAAAT
Statistics
Matches: 170, Mismatches: 20, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
50 139 0.82
51 31 0.18
ACGTcount: A:0.23, C:0.32, G:0.21, T:0.24
Consensus pattern (50 bp):
CCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTG
Found at i:40305964 original size:27 final size:27
Alignment explanation
Indices: 40305934--40306111 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
40305924 ATATTGAGTC
* * * *
40305934 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
40305961 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
40305988 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
40306016 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
40306043 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
40306070 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
40306097 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
40306112 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:40306073 original size:82 final size:81
Alignment explanation
Indices: 40305955--40306110 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
40305945 TGCTATATAA
* *
40305955 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
40306020 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
40306037 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
40306101 CACTTAGTGC
65 CACTTAGTGC
40306111 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:40306614 original size:12 final size:12
Alignment explanation
Indices: 40306597--40306623 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
40306587 ATGGCATACT
40306597 TATGTATATATA
1 TATGTATATATA
40306609 TATGTATATATA
1 TATGTATATATA
40306621 TAT
1 TAT
40306624 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:40309133 original size:6 final size:6
Alignment explanation
Indices: 40309124--40309152 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
40309114 AAAACCCAAC
40309124 TTAAAA TTAAAA TTAAAA TTAAAA -TAAAA
1 TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA
40309153 GCAAGCGTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.22
6 18 0.78
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (6 bp):
TTAAAA
Found at i:40309378 original size:28 final size:28
Alignment explanation
Indices: 40309346--40309427 Score: 128
Period size: 28 Copynumber: 2.9 Consensus size: 28
40309336 AACAGTACAG
*
40309346 TGTGGGCCTTAGCCCAAAATAGTAACAA
1 TGTGGGCCTTAGCCCAATATAGTAACAA
* * *
40309374 TGTGGGCCTTAGCCCAATACAATAATAA
1 TGTGGGCCTTAGCCCAATATAGTAACAA
40309402 TGTGGGCCTTAGCCCAATATAGTAAC
1 TGTGGGCCTTAGCCCAATATAGTAAC
40309428 CAATACAGTG
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 47 1.00
ACGTcount: A:0.33, C:0.22, G:0.21, T:0.24
Consensus pattern (28 bp):
TGTGGGCCTTAGCCCAATATAGTAACAA
Found at i:40309829 original size:27 final size:27
Alignment explanation
Indices: 40309779--40310186 Score: 308
Period size: 27 Copynumber: 15.1 Consensus size: 27
40309769 GGGTATAACA
* * *
40309779 GTCATTTTACCCTATGGGGGTATTTCA
1 GTCATTTTACCCTTTAGGGGTATTTCG
*
40309806 GTCATTTTACCCTTTAGGGCTATTTCG
1 GTCATTTTACCCTTTAGGGGTATTTCG
* * * * *
40309833 ATCATTTTA-CCGTTCGAGGTTATTTCA
1 GTCATTTTACCCTTTAG-GGGTATTTCG
* * * *
40309860 GCCATTTTA-CCTTTCGAAGGTATTTTG
1 GTCATTTTACCCTTTAG-GGGTATTTCG
* *
40309887 GTCATTTTACCCTTCAAGGGTATTTCG
1 GTCATTTTACCCTTTAGGGGTATTTCG
*
40309914 GCCATTTTACCCTTTAGGGGTATTTCG
1 GTCATTTTACCCTTTAGGGGTATTTCG
* * ***
40309941 ATCATTTTACACTCCGGGGGTA-TTCG
1 GTCATTTTACCCTTTAGGGGTATTTCG
* **
40309967 GTCATTTTA-CCTTTTGAGGGTATTTTA
1 GTCATTTTACCCTTTAG-GGGTATTTCG
* **
40309994 GTCATTTTATCCTACAGGGGTATTTCG
1 GTCATTTTACCCTTTAGGGGTATTTCG
* *
40310021 GTCATTTTA-TCTTTCGAGGGTATTTCG
1 GTCATTTTACCCTTTAG-GGGTATTTCG
* * **
40310048 ATCATTTTACCCTTCGAGGGGTATTTTA
1 GTCATTTTACCCTT-TAGGGGTATTTCG
* **
40310076 GTCATTTTAGCCTTCGGGGGTATTTCG
1 GTCATTTTACCCTTTAGGGGTATTTCG
*
40310103 GTCATTTTA-CCTTTCGGGGGTATTTCG
1 GTCATTTTACCCTTT-AGGGGTATTTCG
* * ***
40310130 ATCATTTTACACTACGGGGGTATTTCG
1 GTCATTTTACCCTTTAGGGGTATTTCG
* *
40310157 GTCATTTTACCCTCT-GAGGGTATTTTG
1 GTCATTTTACCCTTTAG-GGGTATTTCG
40310184 GTC
1 GTC
40310187 GTTTACCTAC
Statistics
Matches: 301, Mismatches: 69, Indels: 22
0.77 0.18 0.06
Matches are distributed among these distances:
25 3 0.01
26 30 0.10
27 234 0.78
28 33 0.11
29 1 0.00
ACGTcount: A:0.17, C:0.19, G:0.21, T:0.43
Consensus pattern (27 bp):
GTCATTTTACCCTTTAGGGGTATTTCG
Found at i:40316124 original size:21 final size:22
Alignment explanation
Indices: 40316098--40316146 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 22
40316088 ACAAGTGACT
*
40316098 ACATAATTGCCAAT-AACGGCC
1 ACATAATTGCAAATAAACGGCC
*
40316119 ACATAATTGCAAATAAACTGCC
1 ACATAATTGCAAATAAACGGCC
40316141 ACATAA
1 ACATAA
40316147 CTTCAACCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 13 0.52
22 12 0.48
ACGTcount: A:0.45, C:0.24, G:0.10, T:0.20
Consensus pattern (22 bp):
ACATAATTGCAAATAAACGGCC
Found at i:40317583 original size:20 final size:21
Alignment explanation
Indices: 40317538--40317593 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 21
40317528 CAAGCTGACT
*
40317538 TTAGCTCAATTCCAGCTCCACA
1 TTAGCTC-ATTTCAGCTCCACA
40317560 --AGCTCATTTCAGCTCCA-A
1 TTAGCTCATTTCAGCTCCACA
*
40317578 TTAGCTCATTTGAGCT
1 TTAGCTCATTTCAGCT
40317594 TAAATCAGCT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
18 1 0.03
19 11 0.37
20 18 0.60
ACGTcount: A:0.25, C:0.30, G:0.12, T:0.32
Consensus pattern (21 bp):
TTAGCTCATTTCAGCTCCACA
Found at i:40317603 original size:20 final size:20
Alignment explanation
Indices: 40317560--40317616 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 20
40317550 CAGCTCCACA
* *
40317560 AGCTCATTTCAGCTCCAATT
1 AGCTCATTTCAGCTCAAATC
* *
40317580 AGCTCATTTGAGCTTAAATC
1 AGCTCATTTCAGCTCAAATC
* *
40317600 AGCTCGTTTAAGCTCAA
1 AGCTCATTTCAGCTCAA
40317617 CCTAAACTAT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.33
Consensus pattern (20 bp):
AGCTCATTTCAGCTCAAATC
Found at i:40322309 original size:27 final size:27
Alignment explanation
Indices: 40322278--40322455 Score: 196
Period size: 27 Copynumber: 6.6 Consensus size: 27
40322268 TAAATTGTAC
40322278 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* *** *
40322305 TGCACTAAGTGTGCGAAACGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
40322331 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
40322359 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
40322387 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
40322414 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
40322441 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
40322456 GACTCAATAT
Statistics
Matches: 127, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
27 104 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:40322419 original size:82 final size:81
Alignment explanation
Indices: 40322279--40322434 Score: 224
Period size: 82 Copynumber: 1.9 Consensus size: 81
40322269 AAATTGTACA
* *
40322279 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAACGAATATGATGCACTAAGTGT
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAACGAATACGATGCACTAAGTGT
40322344 GCGAATTGACCATGCG
66 GCGAATTGACCATGCG
*** *
40322360 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACTAAGT
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAACGAATACGAT-GCACTAAGT
*
40322424 GTGCGAGTTGA
64 GTGCGAATTGA
40322435 TTATATAGCA
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 16 0.24
82 50 0.76
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAACGAATACGATGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:40322446 original size:82 final size:81
Alignment explanation
Indices: 40322275--40322455 Score: 220
Period size: 82 Copynumber: 2.2 Consensus size: 81
40322265 GATTAAATTG
* *
40322275 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAACGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAACGAATACGATGCACTAA
40322340 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * *** *
40322356 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAACGAATACGAT-GCACT
* **
40322420 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
40322438 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
40322456 GACTCAATAT
Statistics
Matches: 83, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
81 18 0.22
82 65 0.78
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAACGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:40324912 original size:28 final size:28
Alignment explanation
Indices: 40324880--40324939 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
40324870 TATTATTTTT
*
40324880 TCTTAGCACGCTACATATTTAAA-TCATG
1 TCTTAGCACACTACATA-TTAAATTCATG
* * *
40324908 TCTTAGTATATTACATATTAAATTCATG
1 TCTTAGCACACTACATATTAAATTCATG
40324936 TCTT
1 TCTT
40324940 TGTTTGTCCA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 5 0.19
28 22 0.81
ACGTcount: A:0.32, C:0.17, G:0.08, T:0.43
Consensus pattern (28 bp):
TCTTAGCACACTACATATTAAATTCATG
Found at i:40325882 original size:19 final size:19
Alignment explanation
Indices: 40325854--40325900 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 19
40325844 CAAAAATAAC
40325854 AAAATAAAAATAAAATTTAT
1 AAAATAAAAATAAAA-TTAT
40325874 AAAATAAAAATAAAATTAT
1 AAAATAAAAATAAAATTAT
40325893 AAACATAA
1 AAA-ATAA
40325901 TATACTAGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 7 0.27
20 19 0.73
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (19 bp):
AAAATAAAAATAAAATTAT
Found at i:40326207 original size:3 final size:3
Alignment explanation
Indices: 40326199--40326258 Score: 52
Period size: 3 Copynumber: 19.7 Consensus size: 3
40326189 TGCGGTAAGT
* *
40326199 ATA ATA ATA AAA ATA TATA AT- ATA ATA ATA ATA A-A CTA ATA ATA
1 ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
40326243 ATTCA GTA ATA ATA AT
1 A-T-A ATA ATA ATA AT
40326259 GTAATATATA
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
2 3 0.07
3 37 0.80
4 5 0.11
5 1 0.02
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:40326232 original size:14 final size:14
Alignment explanation
Indices: 40326199--40326244 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
40326189 TGCGGTAAGT
40326199 ATAATAATA-AA-A
1 ATAATAATATAATA
40326211 ATATATAATATAATA
1 ATA-ATAATATAATA
40326226 ATAATAA-ACTAATA
1 ATAATAATA-TAATA
40326240 ATAAT
1 ATAAT
40326245 TCAGTAATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
12 3 0.10
13 7 0.23
14 16 0.53
15 4 0.13
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (14 bp):
ATAATAATATAATA
Found at i:40326243 original size:11 final size:10
Alignment explanation
Indices: 40326201--40326243 Score: 52
Period size: 11 Copynumber: 4.1 Consensus size: 10
40326191 CGGTAAGTAT
40326201 AATAATAA-A
1 AATAATAATA
40326210 AATATATAATA
1 AATA-ATAATA
40326221 TAATAATAATA
1 -AATAATAATA
40326232 AACTAATAATA
1 AA-TAATAATA
40326243 A
1 A
40326244 TTCAGTAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
9 4 0.13
10 6 0.20
11 16 0.53
12 4 0.13
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (10 bp):
AATAATAATA
Found at i:40326854 original size:41 final size:41
Alignment explanation
Indices: 40326807--40326889 Score: 157
Period size: 41 Copynumber: 2.0 Consensus size: 41
40326797 GAACAAAGAA
40326807 AAAGAAAACCAAATCCCACCTTCAAAAATACTTTTCTGTAT
1 AAAGAAAACCAAATCCCACCTTCAAAAATACTTTTCTGTAT
*
40326848 AAAGAAAACCAAATCCCACCTTCAAAAATATTTTTCTGTAT
1 AAAGAAAACCAAATCCCACCTTCAAAAATACTTTTCTGTAT
40326889 A
1 A
40326890 TTTTCTTTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.45, C:0.23, G:0.05, T:0.28
Consensus pattern (41 bp):
AAAGAAAACCAAATCCCACCTTCAAAAATACTTTTCTGTAT
Found at i:40327790 original size:127 final size:127
Alignment explanation
Indices: 40327565--40328192 Score: 965
Period size: 127 Copynumber: 5.0 Consensus size: 127
40327555 TTTACTCCGT
* * * *
40327565 TGCAACTTCGGGGAGATAGGACTTCATGCGATCTGCTCTCTGCAACCTCAGAAAGATAAGATCTG
1 TGCAACTTCAGGGAGATAAGACTTAATGTGATCTGCTCTCTGCAACCTCAGAAAGATAAGATCTG
* *
40327630 GATGTTAATCCGCTCCACTGCAACTTCAGGGAGAGAGGATTAGTTTCTTCTGTCTGCTCCAT
66 GATGTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTAGTTTCTTCTGTCTGCTCCAC
*
40327692 TGCAACTTCAGGGAGATAAGACTTAATGTGATCTGCTTTCTGCAACCTCAGAAAGATAAGATCTG
1 TGCAACTTCAGGGAGATAAGACTTAATGTGATCTGCTCTCTGCAACCTCAGAAAGATAAGATCTG
40327757 GATGTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTAGTTTCTTCTGTCTGCTCCAC
66 GATGTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTAGTTTCTTCTGTCTGCTCCAC
*
40327819 TGCAACTTCAGGGAGATAAGACTTGATGTGATCTGCTCTCTGCAACCTCAGAAAGATAAGATCTG
1 TGCAACTTCAGGGAGATAAGACTTAATGTGATCTGCTCTCTGCAACCTCAGAAAGATAAGATCTG
*
40327884 GATGTTAATCCACTCCACTGCAACTTCAGGGAGATAGGATTAGTTTCTTCTGTCTGCTCCAC
66 GATGTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTAGTTTCTTCTGTCTGCTCCAC
* * * **
40327946 TGCAACTTCAAGGAGATAAGACTTGATGTGATCTGCTCTATATAACCTCAGAAAGATAAGATCTG
1 TGCAACTTCAGGGAGATAAGACTTAATGTGATCTGCTCTCTGCAACCTCAGAAAGATAAGATCTG
* * * * *
40328011 TGAT-TTAATCCACTCCACCGCAACTTCAGGGAGATATGATTAGGTTT-TT-AGTCTACTCCAC
66 -GATGTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTA-GTTTCTTCTGTCTGCTCCAC
* * * *
40328072 TGCAACTTCAGGGAGATAAGACTTAACGTAATCTGCTCTCTGCAACCTCAGAGAGATAAGATCCG
1 TGCAACTTCAGGGAGATAAGACTTAATGTGATCTGCTCTCTGCAACCTCAGAAAGATAAGATCTG
* * * * *
40328137 AATGTCAATCTGCTCCACTGCAACCTCAGGGAGATAGGATTAGTTTCTTCAGTCTG
66 GATGTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTAGTTTCTTCTGTCTG
40328193 TTCTCTAGGG
Statistics
Matches: 461, Mismatches: 35, Indels: 10
0.91 0.07 0.02
Matches are distributed among these distances:
125 6 0.01
126 100 0.22
127 348 0.75
128 7 0.02
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (127 bp):
TGCAACTTCAGGGAGATAAGACTTAATGTGATCTGCTCTCTGCAACCTCAGAAAGATAAGATCTG
GATGTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTAGTTTCTTCTGTCTGCTCCAC
Found at i:40327831 original size:44 final size:44
Alignment explanation
Indices: 40327641--40327966 Score: 205
Period size: 44 Copynumber: 7.6 Consensus size: 44
40327631 ATGTTAATCC
* *
40327641 GCTCCACTGCAACTTCAGGGAGAGAGGATTAGTTTCTTCTGTCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATTAGTTTCTTCTGTCT
* * * **
40327685 GCTCCATTGCAACTTCAGGGAGATAAGACTTAATGTGATCTG-CT
1 GCTCCACTGCAACTTCAGGGAGATAAGA-TTAGTTTCTTCTGTCT
* * ** ** * ** *
40327729 --T--TCTGCAACCTCAGAAAGATAAGATCT-GGATGTT-AATCC
1 GCTCCACTGCAACTTCAGGGAGATAAGAT-TAGTTTCTTCTGTCT
*
40327768 GCTCCACTGCAACTTCAGGGAGATAGGATTAGTTTCTTCTGTCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATTAGTTTCTTCTGTCT
* *
40327812 GCTCCACTGCAACTTCAGGGAGATAAGACTT-G----ATGTGATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGA-TTAGTTTCTTCTG-TCT
* * ** ** * ** *
40327853 GCT-CTCTGCAACCTCAGAAAGATAAGATCT-GGATGTT-AATCC
1 GCTCCACTGCAACTTCAGGGAGATAAGAT-TAGTTTCTTCTGTCT
* *
40327895 ACTCCACTGCAACTTCAGGGAGATAGGATTAGTTTCTTCTGTCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATTAGTTTCTTCTGTCT
*
40327939 GCTCCACTGCAACTTCAAGGAGATAAGA
1 GCTCCACTGCAACTTCAGGGAGATAAGA
40327967 CTTGATGTGA
Statistics
Matches: 207, Mismatches: 56, Indels: 38
0.69 0.19 0.13
Matches are distributed among these distances:
39 6 0.03
40 44 0.21
41 7 0.03
42 7 0.03
43 47 0.23
44 85 0.41
45 11 0.05
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (44 bp):
GCTCCACTGCAACTTCAGGGAGATAAGATTAGTTTCTTCTGTCT
Found at i:40327876 original size:40 final size:41
Alignment explanation
Indices: 40327578--40328165 Score: 169
Period size: 40 Copynumber: 14.0 Consensus size: 41
40327568 AACTTCGGGG
* * * *
40327578 AGATAGGACTTCATGCGATCTGCT-CTCTGCAACCTCAGAA
1 AGATAAGACTTGATGTGATCTGCTCCACTGCAACCTCAGAA
* * * *
40327618 AGATAAGATCTGGATGTTAATCCGCTCCACTGCAACTTCAGGGAGA
1 AGATAAGA-CTTGATG-TGATCTGCTCCACTGCAACCTCA--GA-A
* * ** * * * **
40327664 GAGGATTAG-TTTCTTCTG-TCTGCTCCATTGCAACTTCAGGG
1 -A-GATAAGACTTGATGTGATCTGCTCCACTGCAACCTCAGAA
* **
40327705 AGATAAGACTTAATGTGATCTGCT-TTCTGCAACCTCAGAA
1 AGATAAGACTTGATGTGATCTGCTCCACTGCAACCTCAGAA
* * * *
40327745 AGATAAGATCTGGATGTTAATCCGCTCCACTGCAACTTCAGGGAGA
1 AGATAAGA-CTTGATG-TGATCTGCTCCACTGCAACCTCA--GA-A
* * ** * * **
40327791 TAGGATTAG-TTTCTTCTG-TCTGCTCCACTGCAACTTCAGGG
1 -A-GATAAGACTTGATGTGATCTGCTCCACTGCAACCTCAGAA
*
40327832 AGATAAGACTTGATGTGATCTGCT-CTCTGCAACCTCAGAA
1 AGATAAGACTTGATGTGATCTGCTCCACTGCAACCTCAGAA
* * ** *
40327872 AGATAAGATCTGGATGTTAATCCACTCCACTGCAACTTCAGGGAGA
1 AGATAAGA-CTTGATG-TGATCTGCTCCACTGCAACCTCA--GA-A
* * ** * * *
40327918 TAGGATTAG-TTTCTTCTG-TCTGCTCCACTGCAACTTCA-AGG
1 -A-GATAAGACTTGATGTGATCTGCTCCACTGCAACCTCAGA-A
* **
40327959 AGATAAGACTTGATGTGATCTGCTCTA-TATAACCTCAGAA
1 AGATAAGACTTGATGTGATCTGCTCCACTGCAACCTCAGAA
* * ** * * **
40327999 AGATAAGATCTGTGATTTAATCCACTCCACCGCAACTTCAGGG
1 AGATAAGA-CT-TGATGTGATCTGCTCCACTGCAACCTCAGAA
* * * * * * **
40328042 AGATATGA-TTAGGTTTTTAGTCTACTCCACTGCAACTTCAGGG
1 AGATAAGACTT--GATGTGA-TCTGCTCCACTGCAACCTCAGAA
* * * * *
40328085 AGATAAGACTTAACGTAATCTGCT-CTCTGCAACCTCAGAG
1 AGATAAGACTTGATGTGATCTGCTCCACTGCAACCTCAGAA
* *
40328125 AGATAAGA-TCCGAATGTCAATCTGCTCCACTGCAACCTCAG
1 AGATAAGACT-TG-ATGT-GATCTGCTCCACTGCAACCTCAG
40328166 GGAGATAGGA
Statistics
Matches: 394, Mismatches: 112, Indels: 81
0.67 0.19 0.14
Matches are distributed among these distances:
39 16 0.04
40 100 0.25
41 50 0.13
42 48 0.12
43 87 0.22
44 57 0.14
45 9 0.02
46 9 0.02
47 3 0.01
48 15 0.04
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (41 bp):
AGATAAGACTTGATGTGATCTGCTCCACTGCAACCTCAGAA
Found at i:40327910 original size:83 final size:84
Alignment explanation
Indices: 40327565--40328172 Score: 260
Period size: 83 Copynumber: 7.2 Consensus size: 84
40327555 TTTACTCCGT
* * * *
40327565 TGCAACTTCGGGGAGATAGGACTTCATGCGATCTGCT-CTCTGCAACCTCAGAAAGATAAGATCT
1 TGCAACTTCAGGGAGATAAGACTTGATGTGATCTGCTCCTCTGCAACCTCAGAAAGATAAGATCT
40327629 GGATGTTAATCCGCTCCAC
66 GGATGTTAATCCGCTCCAC
* * * * * **
40327648 TGCAACTTCAGGGAGAGAGGA-TTAGTTTCTTCTG-TCTGCTCCAT-TGCAACTTCAGGGAGATA
1 TGCAACTTCAGGGAGATAAGACTT-G----ATGTGATCTGCTCC-TCTGCAACCTCAGAAAGATA
** * * **
40327710 AGA-CTTAATG-TGATCTGCT-TTC
60 AGATCTGGATGTTAATCCGCTCCAC
* ** * * * * * ** *
40327732 TGCAACCTCAGAAAGATAAGATCTGGATGTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGAT
1 TGCAACTTCAGGGAGATAAGA-CTTGATG-TGATCTGCTCCTCTGCAACCTCAGAAAGATAAGAT
** * ** *
40327797 -TAGTTTCTTCTGTCTGCTCCAC
64 CT-GGATGTT-AATCCGCTCCAC
40327819 TGCAACTTCAGGGAGATAAGACTTGATGTGATCTGCT-CTCTGCAACCTCAGAAAGATAAGATCT
1 TGCAACTTCAGGGAGATAAGACTTGATGTGATCTGCTCCTCTGCAACCTCAGAAAGATAAGATCT
*
40327883 GGATGTTAATCCACTCCAC
66 GGATGTTAATCCGCTCCAC
* * * * * *
40327902 TGCAACTTCAGGGAGATAGGA-TTAGTTTCTTCTG-TCTGCTCCACTGCAACTTCA-AGGAGATA
1 TGCAACTTCAGGGAGATAAGACTT-G----ATGTGATCTGCTCCTCTGCAACCTCAGA-AAGATA
* * * *
40327964 AGA-CTTGATG-TGATCTGCTCTA-
60 AGATCTGGATGTTAATCCGCTCCAC
** * ** * * ** * * * ** *
40327986 TATAACCTCAGAAAGATAAGATCTGTGATTTAATCCACTCCACCGCAACTTCAGGGAGATATGAT
1 TGCAACTTCAGGGAGATAAGA-CT-TGATGTGATCTGCTCCTCTGCAACCTCAGAAAGATAAGAT
* * * **
40328051 -TAGGTTTTTAGTCTACTCCAC
64 CT-GGATGTTAATCCGCTCCAC
* * * * *
40328072 TGCAACTTCAGGGAGATAAGACTTAACGTAATCTGCT-CTCTGCAACCTCAGAGAGATAAGATCC
1 TGCAACTTCAGGGAGATAAGACTTGATGTGATCTGCTCCTCTGCAACCTCAGAAAGATAAGATCT
* * *
40328136 GAATGTCAATCTGCTCCAC
66 GGATGTTAATCCGCTCCAC
*
40328155 TGCAACCTCAGGGAGATA
1 TGCAACTTCAGGGAGATA
40328173 GGATTAGTTT
Statistics
Matches: 382, Mismatches: 108, Indels: 70
0.68 0.19 0.12
Matches are distributed among these distances:
81 1 0.00
82 7 0.02
83 152 0.40
84 68 0.18
85 35 0.09
86 55 0.14
87 63 0.16
88 1 0.00
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (84 bp):
TGCAACTTCAGGGAGATAAGACTTGATGTGATCTGCTCCTCTGCAACCTCAGAAAGATAAGATCT
GGATGTTAATCCGCTCCAC
Found at i:40333934 original size:12 final size:12
Alignment explanation
Indices: 40333917--40333943 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
40333907 ATTCCGAAGT
40333917 ATATATATATAC
1 ATATATATATAC
40333929 ATATATATATAC
1 ATATATATATAC
40333941 ATA
1 ATA
40333944 AGTATGCCAT
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:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (12 bp):
ATATATATATAC
Found at i:40334456 original size:27 final size:27
Alignment explanation
Indices: 40334425--40334602 Score: 196
Period size: 27 Copynumber: 6.6 Consensus size: 27
40334415 TAAATTGTAC
40334425 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* *** *
40334452 TGCACTAAGTGTGCGAAACGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
40334478 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
40334506 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
40334534 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
40334561 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
40334588 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
40334603 GACTCAATAT
Statistics
Matches: 127, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
27 104 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:40334566 original size:82 final size:81
Alignment explanation
Indices: 40334426--40334581 Score: 224
Period size: 82 Copynumber: 1.9 Consensus size: 81
40334416 AAATTGTACA
* *
40334426 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAACGAATATGATGCACTAAGTGT
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAACGAATACGATGCACTAAGTGT
40334491 GCGAATTGACCATGCG
66 GCGAATTGACCATGCG
*** *
40334507 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACTAAGT
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAACGAATACGAT-GCACTAAGT
*
40334571 GTGCGAGTTGA
64 GTGCGAATTGA
40334582 TTATATAGCA
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 16 0.24
82 50 0.76
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAACGAATACGATGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:40334593 original size:82 final size:81
Alignment explanation
Indices: 40334422--40334602 Score: 220
Period size: 82 Copynumber: 2.2 Consensus size: 81
40334412 GATTAAATTG
* *
40334422 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAACGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAACGAATACGATGCACTAA
40334487 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * *** *
40334503 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAACGAATACGAT-GCACT
* **
40334567 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
40334585 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
40334603 GACTCAATAT
Statistics
Matches: 83, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
81 18 0.22
82 65 0.78
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAACGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:40339396 original size:12 final size:12
Alignment explanation
Indices: 40339379--40339406 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
40339369 GACTAGGTAT
40339379 AAAACAAAGAAG
1 AAAACAAAGAAG
40339391 AAAACAAAGAAG
1 AAAACAAAGAAG
40339403 AAAA
1 AAAA
40339407 GAAATGGAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.79, C:0.07, G:0.14, T:0.00
Consensus pattern (12 bp):
AAAACAAAGAAG
Found at i:40344681 original size:43 final size:40
Alignment explanation
Indices: 40344612--40344728 Score: 128
Period size: 43 Copynumber: 2.9 Consensus size: 40
40344602 AACTGAAGAA
* * *
40344612 ATCGATCCTATCTCCCTGAGGTTGCAGTGGAGCGGATTGAC
1 ATCGATCTTATCTCCCTGAGGTTGCAGTGGAGCAGA-TCAC
* *
40344653 ATACGGATCTTATCTCTCTGAGGTTGCAG-AGAGCAGATCAC
1 AT-C-GATCTTATCTCCCTGAGGTTGCAGTGGAGCAGATCAC
* *
40344694 ATCAACTCTTATTTCCCTGAGGTTGCAGTGGAGCA
1 ATCGA-TCTTATCTCCCTGAGGTTGCAGTGGAGCA
40344729 AACTAAAAAC
Statistics
Matches: 63, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
39 1 0.02
40 21 0.33
41 12 0.19
42 7 0.11
43 22 0.35
ACGTcount: A:0.23, C:0.23, G:0.26, T:0.28
Consensus pattern (40 bp):
ATCGATCTTATCTCCCTGAGGTTGCAGTGGAGCAGATCAC
Found at i:40345063 original size:42 final size:43
Alignment explanation
Indices: 40345005--40345274 Score: 229
Period size: 40 Copynumber: 6.5 Consensus size: 43
40344995 TGTCTAATCC
*
40345005 TATCTCCCTGAAGTTGCAGTGGAGTGGAT-TAATCACAGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGTGGATCGAATCACAGATCT
* * * ** * *
40345047 TATCTCTCTGAGGTTGCAG-AGAGCAGATCGCATCA-A-ATCC
1 TATCTCCCTGAAGTTGCAGTGGAGTGGATCGAATCACAGATCT
*
40345087 TATCTCCCTGAAGTTGCAGTGGAGTGGAT-TAATCACAGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGTGGATCGAATCACAGATCT
* * * ** * *
40345129 TATCTCTCTGAGGTTGCAG-AGAGCAGATCGCATCA-A-ATCC
1 TATCTCCCTGAAGTTGCAGTGGAGTGGATCGAATCACAGATCT
*
40345169 TATCTCCCTGAAGTTGCAGTGGAGTGGATCAAATCACAGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGTGGATCGAATCACAGATCT
* * * ** *
40345212 TATCTCTCTGAGGTTGCAG-AGAGCAGATCGCATCA-AG-TCT
1 TATCTCCCTGAAGTTGCAGTGGAGTGGATCGAATCACAGATCT
* * *
40345252 TATCTCCCAGAGGTTACAGTGGA
1 TATCTCCCTGAAGTTGCAGTGGA
40345275 ATGGGTTGAA
Statistics
Matches: 176, Mismatches: 43, Indels: 19
0.74 0.18 0.08
Matches are distributed among these distances:
40 63 0.36
41 36 0.20
42 57 0.32
43 20 0.11
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.28
Consensus pattern (43 bp):
TATCTCCCTGAAGTTGCAGTGGAGTGGATCGAATCACAGATCT
Found at i:40345256 original size:83 final size:82
Alignment explanation
Indices: 40345000--40345274 Score: 487
Period size: 82 Copynumber: 3.3 Consensus size: 82
40344990 TGAAATGTCT
40345000 AATCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTAATCACAGATCTTATCTCTCTGAGGTTGCA
1 AATCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTAATCACAGATCTTATCTCTCTGAGGTTGCA
40345065 GAGAGCAGATCGCATCA
66 GAGAGCAGATCGCATCA
40345082 AATCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTAATCACAGATCTTATCTCTCTGAGGTTGCA
1 AATCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTAATCACAGATCTTATCTCTCTGAGGTTGCA
40345147 GAGAGCAGATCGCATCA
66 GAGAGCAGATCGCATCA
*
40345164 AATCCTATCTCCCTGAAGTTGCAGTGGAGTGGATCAAATCACAGATCTTATCTCTCTGAGGTTGC
1 AATCCTATCTCCCTGAAGTTGCAGTGGAGTGGAT-TAATCACAGATCTTATCTCTCTGAGGTTGC
40345229 AGAGAGCAGATCGCATCA
65 AGAGAGCAGATCGCATCA
* * * * *
40345247 AGTCTTATCTCCCAGAGGTTACAGTGGA
1 AATCCTATCTCCCTGAAGTTGCAGTGGA
40345275 ATGGGTTGAA
Statistics
Matches: 186, Mismatches: 6, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
82 116 0.62
83 70 0.38
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.28
Consensus pattern (82 bp):
AATCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTAATCACAGATCTTATCTCTCTGAGGTTGCA
GAGAGCAGATCGCATCA
Found at i:40361251 original size:20 final size:20
Alignment explanation
Indices: 40361218--40361259 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
40361208 TACTAGTATA
40361218 TTATGTTTATAATTTTATTT
1 TTATGTTTATAATTTTATTT
40361238 TTAT-TTTATAAATTTTATTT
1 TTATGTTTAT-AATTTTATTT
40361258 TT
1 TT
40361260 TTATTTTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.71
Consensus pattern (20 bp):
TTATGTTTATAATTTTATTT
Found at i:40361263 original size:8 final size:8
Alignment explanation
Indices: 40361250--40361290 Score: 59
Period size: 8 Copynumber: 5.2 Consensus size: 8
40361240 ATTTTATAAA
40361250 TTTTATTT
1 TTTTATTT
40361258 TTTTA--T
1 TTTTATTT
40361264 TTTTATTT
1 TTTTATTT
40361272 TTTTATTT
1 TTTTATTT
40361280 TTGTTATTT
1 TT-TTATTT
40361289 TT
1 TT
40361291 GTATACATGT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
6 6 0.20
8 16 0.53
9 8 0.27
ACGTcount: A:0.12, C:0.00, G:0.02, T:0.85
Consensus pattern (8 bp):
TTTTATTT
Found at i:40361274 original size:14 final size:14
Alignment explanation
Indices: 40361230--40361281 Score: 77
Period size: 14 Copynumber: 3.7 Consensus size: 14
40361220 ATGTTTATAA
40361230 TTTTATTTTTATTT
1 TTTTATTTTTATTT
* * *
40361244 TATAAATTTTATTT
1 TTTTATTTTTATTT
40361258 TTTTATTTTTATTT
1 TTTTATTTTTATTT
40361272 TTTTATTTTT
1 TTTTATTTTT
40361282 GTTATTTTTG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 32 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTTATTTTTATTT
Found at i:40361281 original size:28 final size:29
Alignment explanation
Indices: 40361230--40361290 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 29
40361220 ATGTTTATAA
40361230 TTTTATTTTTATTTTATAAATTTTATT-T
1 TTTTATTTTTATTTTATAAATTTTATTAT
* * * *
40361258 TTTTATTTTTATTTTTTTATTTTTGTTAT
1 TTTTATTTTTATTTTATAAATTTTATTAT
40361287 TTTT
1 TTTT
40361291 GTATACATGT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 23 0.82
29 5 0.18
ACGTcount: A:0.18, C:0.00, G:0.02, T:0.80
Consensus pattern (29 bp):
TTTTATTTTTATTTTATAAATTTTATTAT
Found at i:40361289 original size:14 final size:14
Alignment explanation
Indices: 40361218--40361289 Score: 65
Period size: 14 Copynumber: 5.1 Consensus size: 14
40361208 TACTAGTATA
* *
40361218 TTATGTTTATAATT
1 TTATTTTTATTATT
40361232 TTATTTTTATT-TT
1 TTATTTTTATTATT
* * *
40361245 ATAAATTTTATTTTT
1 -TTATTTTTATTATT
*
40361260 TTATTTTTATTTTT
1 TTATTTTTATTATT
*
40361274 TTATTTTTGTTATT
1 TTATTTTTATTATT
40361288 TT
1 TT
40361290 TGTATACATG
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
13 2 0.04
14 44 0.92
15 2 0.04
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (14 bp):
TTATTTTTATTATT
Found at i:40368068 original size:82 final size:81
Alignment explanation
Indices: 40367952--40368107 Score: 215
Period size: 82 Copynumber: 1.9 Consensus size: 81
40367942 AAATTGTACA
* * * *
40367952 GCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATGAT-GCACTAAGTG
1 GCACTAAGTGTGCGAGTCAACTATGTAGCACTAAGTGTGCGAAATGAATACG-TGGCACTAAGTG
40368016 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
40368033 GCACTAAGTGTGCGAGTCTAACTATGTAGCACTAAGTGTGCGATTTGATTACGTGGCACTAAGTG
1 GCACTAAGTGTGCGAGTC-AACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTG
*
40368098 TGCGAGTTGA
65 TGCGAATTGA
40368108 TTGTATAGCA
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
81 18 0.28
82 47 0.72
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (81 bp):
GCACTAAGTGTGCGAGTCAACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:40368075 original size:55 final size:52
Alignment explanation
Indices: 40367951--40368104 Score: 175
Period size: 55 Copynumber: 2.9 Consensus size: 52
40367941 TAAATTGTAC
* *
40367951 AGCACTAAGTGTGCG-ATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATG
1 AGCACTAAGTGTGCGAATT-GACTATGTGGCACTAAGTGTGCG-AGTGAATATG
* * *
40368004 ATGCACTAAGTGTGCGAATTGACCATGCGGCACTAAGTGTGCGAGTCTAACTATG
1 A-GCACTAAGTGTGCGAATTGACTATGTGGCACTAAGTGTGCGAGT-GAA-TATG
* * *
40368059 TAGCACTAAGTGTGCGATTTGATTACGTGGCACTAAGTGTGCGAGT
1 -AGCACTAAGTGTGCGAATTGACTATGTGGCACTAAGTGTGCGAGT
40368105 TGATTGTATA
Statistics
Matches: 86, Mismatches: 10, Indels: 8
0.83 0.10 0.08
Matches are distributed among these distances:
53 3 0.03
54 36 0.42
55 46 0.53
56 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (52 bp):
AGCACTAAGTGTGCGAATTGACTATGTGGCACTAAGTGTGCGAGTGAATATG
Found at i:40368109 original size:27 final size:27
Alignment explanation
Indices: 40367952--40368107 Score: 163
Period size: 27 Copynumber: 5.7 Consensus size: 27
40367942 AAATTGTACA
*
40367952 GCACTAAGTGTGCG-ATTCGACTATGTT
1 GCACTAAGTGTGCGAATT-GACTATGTG
* *
40367979 GCACTAAGTGTGCGAAATGAATATGAT-
1 GCACTAAGTGTGCGAATTGACTATG-TG
* *
40368006 GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCGAATTGACTATGTG
* * *
40368033 GCACTAAGTGTGCGAGTCTAACTATGTA
1 GCACTAAGTGTGCGAAT-TGACTATGTG
* * *
40368061 GCACTAAGTGTGCGATTTGATTACGTG
1 GCACTAAGTGTGCGAATTGACTATGTG
*
40368088 GCACTAAGTGTGCGAGTTGA
1 GCACTAAGTGTGCGAATTGA
40368108 TTGTATAGCA
Statistics
Matches: 108, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
27 83 0.77
28 25 0.23
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (27 bp):
GCACTAAGTGTGCGAATTGACTATGTG
Found at i:40368118 original size:27 final size:27
Alignment explanation
Indices: 40367944--40368128 Score: 101
Period size: 27 Copynumber: 6.8 Consensus size: 27
40367934 GCGGGATTAA
*
40367944 ATTGTACAGCACTAAGTGTGCG-ATTCG
1 ATTGTATAGCACTAAGTGTGCGAATT-G
*
40367971 ACTATGT-T-GCACTAAGTGTGCGAAATG
1 A-T-TGTATAGCACTAAGTGTGCGAATTG
40367998 AATATG-AT-GCACTAAGTGTGCGAATTG
1 -AT-TGTATAGCACTAAGTGTGCGAATTG
*** *** * *
40368025 ACCATGCGGCACTAAGTGTGCGAGTCTA
1 ATTGTATAGCACTAAGTGTGCGAAT-TG
* * * *
40368053 ACTATGTAGCACTAAGTGTGCGATTTG
1 ATTGTATAGCACTAAGTGTGCGAATTG
*** * *
40368080 ATTACGTGGCACTAAGTGTGCGAGTTG
1 ATTGTATAGCACTAAGTGTGCGAATTG
*
40368107 ATTGTATAGCACTGAGTGTGCG
1 ATTGTATAGCACTAAGTGTGCG
40368129 GGCTCAATAT
Statistics
Matches: 126, Mismatches: 24, Indels: 16
0.76 0.14 0.10
Matches are distributed among these distances:
26 1 0.01
27 96 0.76
28 26 0.21
29 3 0.02
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.29
Consensus pattern (27 bp):
ATTGTATAGCACTAAGTGTGCGAATTG
Found at i:40368119 original size:82 final size:81
Alignment explanation
Indices: 40367944--40368128 Score: 210
Period size: 82 Copynumber: 2.3 Consensus size: 81
40367934 GCGGGATTAA
* * * *
40367944 ATTGTACAGCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCA
1 ATTGTACAGCACTAAGTGTGCGAGTCAACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCA
40368009 CTAAGTGTGCGAATTG
66 CTAAGTGTGCGAATTG
*** * * ** *
40368025 ACCATGCGGCACTAAGTGTGCGAGTCTAACTATGTAGCACTAAGTGTGCGATTTGATTACG-TGG
1 ATTGTACAGCACTAAGTGTGCGAGTC-AACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-G
*
40368089 CACTAAGTGTGCGAGTTG
64 CACTAAGTGTGCGAATTG
* *
40368107 ATTGTATAGCACTGAGTGTGCG
1 ATTGTACAGCACTAAGTGTGCG
40368129 GGCTCAATAT
Statistics
Matches: 82, Mismatches: 20, Indels: 3
0.78 0.19 0.03
Matches are distributed among these distances:
81 21 0.26
82 61 0.74
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.29
Consensus pattern (81 bp):
ATTGTACAGCACTAAGTGTGCGAGTCAACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCA
CTAAGTGTGCGAATTG
Found at i:40376032 original size:82 final size:81
Alignment explanation
Indices: 40375916--40376071 Score: 215
Period size: 82 Copynumber: 1.9 Consensus size: 81
40375906 AAATTGTACA
* * * *
40375916 GCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATGAT-GCACTAAGTG
1 GCACTAAGTGTGCGAGTCAACTATGTAGCACTAAGTGTGCGAAATGAATACG-TGGCACTAAGTG
40375980 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
40375997 GCACTAAGTGTGCGAGTCTAACTATGTAGCACTAAGTGTGCGATTTGATTACGTGGCACTAAGTG
1 GCACTAAGTGTGCGAGTC-AACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTG
*
40376062 TGCGAGTTGA
65 TGCGAATTGA
40376072 TTGTATAGCA
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
81 18 0.28
82 47 0.72
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (81 bp):
GCACTAAGTGTGCGAGTCAACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:40376039 original size:55 final size:52
Alignment explanation
Indices: 40375915--40376068 Score: 175
Period size: 55 Copynumber: 2.9 Consensus size: 52
40375905 TAAATTGTAC
* *
40375915 AGCACTAAGTGTGCG-ATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATG
1 AGCACTAAGTGTGCGAATT-GACTATGTGGCACTAAGTGTGCG-AGTGAATATG
* * *
40375968 ATGCACTAAGTGTGCGAATTGACCATGCGGCACTAAGTGTGCGAGTCTAACTATG
1 A-GCACTAAGTGTGCGAATTGACTATGTGGCACTAAGTGTGCGAGT-GAA-TATG
* * *
40376023 TAGCACTAAGTGTGCGATTTGATTACGTGGCACTAAGTGTGCGAGT
1 -AGCACTAAGTGTGCGAATTGACTATGTGGCACTAAGTGTGCGAGT
40376069 TGATTGTATA
Statistics
Matches: 86, Mismatches: 10, Indels: 8
0.83 0.10 0.08
Matches are distributed among these distances:
53 3 0.03
54 36 0.42
55 46 0.53
56 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (52 bp):
AGCACTAAGTGTGCGAATTGACTATGTGGCACTAAGTGTGCGAGTGAATATG
Found at i:40376073 original size:27 final size:27
Alignment explanation
Indices: 40375916--40376071 Score: 163
Period size: 27 Copynumber: 5.7 Consensus size: 27
40375906 AAATTGTACA
*
40375916 GCACTAAGTGTGCG-ATTCGACTATGTT
1 GCACTAAGTGTGCGAATT-GACTATGTG
* *
40375943 GCACTAAGTGTGCGAAATGAATATGAT-
1 GCACTAAGTGTGCGAATTGACTATG-TG
* *
40375970 GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCGAATTGACTATGTG
* * *
40375997 GCACTAAGTGTGCGAGTCTAACTATGTA
1 GCACTAAGTGTGCGAAT-TGACTATGTG
* * *
40376025 GCACTAAGTGTGCGATTTGATTACGTG
1 GCACTAAGTGTGCGAATTGACTATGTG
*
40376052 GCACTAAGTGTGCGAGTTGA
1 GCACTAAGTGTGCGAATTGA
40376072 TTGTATAGCA
Statistics
Matches: 108, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
27 83 0.77
28 25 0.23
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (27 bp):
GCACTAAGTGTGCGAATTGACTATGTG
Found at i:40376082 original size:27 final size:27
Alignment explanation
Indices: 40375908--40376092 Score: 101
Period size: 27 Copynumber: 6.8 Consensus size: 27
40375898 GCGGGATTAA
*
40375908 ATTGTACAGCACTAAGTGTGCG-ATTCG
1 ATTGTATAGCACTAAGTGTGCGAATT-G
*
40375935 ACTATGT-T-GCACTAAGTGTGCGAAATG
1 A-T-TGTATAGCACTAAGTGTGCGAATTG
40375962 AATATG-AT-GCACTAAGTGTGCGAATTG
1 -AT-TGTATAGCACTAAGTGTGCGAATTG
*** *** * *
40375989 ACCATGCGGCACTAAGTGTGCGAGTCTA
1 ATTGTATAGCACTAAGTGTGCGAAT-TG
* * * *
40376017 ACTATGTAGCACTAAGTGTGCGATTTG
1 ATTGTATAGCACTAAGTGTGCGAATTG
*** * *
40376044 ATTACGTGGCACTAAGTGTGCGAGTTG
1 ATTGTATAGCACTAAGTGTGCGAATTG
*
40376071 ATTGTATAGCACTGAGTGTGCG
1 ATTGTATAGCACTAAGTGTGCG
40376093 GGCTCAATAT
Statistics
Matches: 126, Mismatches: 24, Indels: 16
0.76 0.14 0.10
Matches are distributed among these distances:
26 1 0.01
27 96 0.76
28 26 0.21
29 3 0.02
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.29
Consensus pattern (27 bp):
ATTGTATAGCACTAAGTGTGCGAATTG
Found at i:40376083 original size:82 final size:81
Alignment explanation
Indices: 40375908--40376092 Score: 210
Period size: 82 Copynumber: 2.3 Consensus size: 81
40375898 GCGGGATTAA
* * * *
40375908 ATTGTACAGCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCA
1 ATTGTACAGCACTAAGTGTGCGAGTCAACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCA
40375973 CTAAGTGTGCGAATTG
66 CTAAGTGTGCGAATTG
*** * * ** *
40375989 ACCATGCGGCACTAAGTGTGCGAGTCTAACTATGTAGCACTAAGTGTGCGATTTGATTACG-TGG
1 ATTGTACAGCACTAAGTGTGCGAGTC-AACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-G
*
40376053 CACTAAGTGTGCGAGTTG
64 CACTAAGTGTGCGAATTG
* *
40376071 ATTGTATAGCACTGAGTGTGCG
1 ATTGTACAGCACTAAGTGTGCG
40376093 GGCTCAATAT
Statistics
Matches: 82, Mismatches: 20, Indels: 3
0.78 0.19 0.03
Matches are distributed among these distances:
81 21 0.26
82 61 0.74
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.29
Consensus pattern (81 bp):
ATTGTACAGCACTAAGTGTGCGAGTCAACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCA
CTAAGTGTGCGAATTG
Found at i:40378729 original size:14 final size:14
Alignment explanation
Indices: 40378699--40378749 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
40378689 AAAAATAACA
*
40378699 AAAATAACA-AAATT
1 AAAATAA-ATAAAAT
40378713 AAAATAAATAAAAT
1 AAAATAAATAAAAT
**
40378727 AAAATTTATAAAAT
1 AAAATAAATAAAAT
40378741 AAAAATAAA
1 -AAAATAAA
40378750 ATTATAAACA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
13 1 0.03
14 23 0.77
15 6 0.20
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.24
Consensus pattern (14 bp):
AAAATAAATAAAAT
Found at i:40378732 original size:20 final size:20
Alignment explanation
Indices: 40378707--40378753 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
40378697 CAAAAATAAC
40378707 AAAATTAAAATAAAT-AAAAT
1 AAAATTAAAA-AAATAAAAAT
* *
40378727 AAAATTTATAAAATAAAAAT
1 AAAATTAAAAAAATAAAAAT
40378747 AAAATTA
1 AAAATTA
40378754 TAAACATAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 4 0.17
20 19 0.83
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (20 bp):
AAAATTAAAAAAATAAAAAT
Found at i:40378742 original size:19 final size:18
Alignment explanation
Indices: 40378718--40378762 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 18
40378708 AAATTAAAAT
40378718 AAATAAAATAAAATTTATA
1 AAATAAAATAAAA-TTATA
40378737 AAATAAAAATAAAATTATA
1 AAAT-AAAATAAAATTATA
40378756 AACATAA
1 AA-ATAA
40378763 TATACTAGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 13 0.54
20 11 0.46
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (18 bp):
AAATAAAATAAAATTATA
Found at i:40378762 original size:20 final size:20
Alignment explanation
Indices: 40378718--40378762 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
40378708 AAATTAAAAT
40378718 AAAT-AAAATAAAATTTATA
1 AAATAAAAATAAAATTTATA
40378737 AAATAAAAATAAAA-TTATA
1 AAATAAAAATAAAATTTATA
40378756 AACATAA
1 AA-ATAA
40378763 TATACTAGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 11 0.46
20 13 0.54
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (20 bp):
AAATAAAAATAAAATTTATA
Found at i:40379090 original size:18 final size:19
Alignment explanation
Indices: 40379067--40379104 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
40379057 GGTAAGTATA
40379067 ATAATAAAAATAAA-TAAT
1 ATAATAAAAATAAACTAAT
*
40379085 ATAATAATAATAAACTAAT
1 ATAATAAAAATAAACTAAT
40379104 A
1 A
40379105 ATCATTCAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (19 bp):
ATAATAAAAATAAACTAAT
Found at i:40390541 original size:171 final size:171
Alignment explanation
Indices: 40390256--40390597 Score: 675
Period size: 171 Copynumber: 2.0 Consensus size: 171
40390246 TAGGCAATTG
40390256 GGGTTGAACCACTATAAATCCTTGTGTTCTTTGTTGCACAATTTTTGTTGCTTCCACCACAACTT
1 GGGTTGAACCACTATAAATCCTTGTGTTCTTTGTTGCACAATTTTTGTTGCTTCCACCACAACTT
40390321 ATCAAAGGTTGATTCAACCTCCCTATAGTCGATCTCAAGTTGATCCTTTCGAGCTAACAAATTGT
66 ATCAAAGGTTGATTCAACCTCCCTATAGTCGATCTCAAGTTGATCCTTTCGAGCTAACAAATTGT
40390386 CCTTTTGTGAAATAATGATGCTGTCAAATGAATCTAGTAGT
131 CCTTTTGTGAAATAATGATGCTGTCAAATGAATCTAGTAGT
*
40390427 GGGTTGAACCACTATAAATCCTTGTGTTCTTTGTTGCATAATTTTTGTTGCTTCCACCACAACTT
1 GGGTTGAACCACTATAAATCCTTGTGTTCTTTGTTGCACAATTTTTGTTGCTTCCACCACAACTT
40390492 ATCAAAGGTTGATTCAACCTCCCTATAGTCGATCTCAAGTTGATCCTTTCGAGCTAACAAATTGT
66 ATCAAAGGTTGATTCAACCTCCCTATAGTCGATCTCAAGTTGATCCTTTCGAGCTAACAAATTGT
40390557 CCTTTTGTGAAATAATGATGCTGTCAAATGAATCTAGTAGT
131 CCTTTTGTGAAATAATGATGCTGTCAAATGAATCTAGTAGT
40390598 AAAACTTGAA
Statistics
Matches: 170, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
171 170 1.00
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.37
Consensus pattern (171 bp):
GGGTTGAACCACTATAAATCCTTGTGTTCTTTGTTGCACAATTTTTGTTGCTTCCACCACAACTT
ATCAAAGGTTGATTCAACCTCCCTATAGTCGATCTCAAGTTGATCCTTTCGAGCTAACAAATTGT
CCTTTTGTGAAATAATGATGCTGTCAAATGAATCTAGTAGT
Found at i:40390773 original size:21 final size:21
Alignment explanation
Indices: 40390747--40390792 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
40390737 CTTGTTTCGT
40390747 AACACAATAACCCTATGTCGC
1 AACACAATAACCCTATGTCGC
* *
40390768 AACACAGTAACCCTGTGTCGC
1 AACACAATAACCCTATGTCGC
40390789 AACA
1 AACA
40390793 TCAAAGGTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.37, C:0.33, G:0.13, T:0.17
Consensus pattern (21 bp):
AACACAATAACCCTATGTCGC
Found at i:40408417 original size:24 final size:25
Alignment explanation
Indices: 40408357--40408434 Score: 79
Period size: 25 Copynumber: 3.2 Consensus size: 25
40408347 ACACACCACA
* *
40408357 GCTCTTATGAGCATCCCGATATATG
1 GCTCTTATGAGCTTCACGATATATG
*
40408382 GCTCTCCA-GAGCTTCACGA-ATATG
1 GCTCT-TATGAGCTTCACGATATATG
** *
40408406 GCTCTTATGAGCTTTTCGTTATATG
1 GCTCTTATGAGCTTCACGATATATG
40408431 GCTC
1 GCTC
40408435 ACATCCCGTT
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
23 1 0.02
24 18 0.42
25 23 0.53
26 1 0.02
ACGTcount: A:0.21, C:0.24, G:0.21, T:0.35
Consensus pattern (25 bp):
GCTCTTATGAGCTTCACGATATATG
Found at i:40408476 original size:27 final size:26
Alignment explanation
Indices: 40408438--40408508 Score: 106
Period size: 27 Copynumber: 2.6 Consensus size: 26
40408428 ATGGCTCACA
*
40408438 TCCCGTTATATGGCTTGAAAGAGAGCT
1 TCCCGTT-TATGGCTCGAAAGAGAGCT
40408465 TCCCGTTGTATGGCTCGAAAGAGAGCT
1 TCCCGTT-TATGGCTCGAAAGAGAGCT
40408492 TCCCGTTTATGTGCTCG
1 TCCCGTTTATG-GCTCG
40408509 TATTAGCATT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
26 4 0.10
27 37 0.90
ACGTcount: A:0.20, C:0.23, G:0.27, T:0.31
Consensus pattern (26 bp):
TCCCGTTTATGGCTCGAAAGAGAGCT
Found at i:40410966 original size:15 final size:16
Alignment explanation
Indices: 40410946--40410978 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
40410936 ACATATAACC
40410946 ATATATT-TATTACAA
1 ATATATTATATTACAA
*
40410961 ATATATTATATTTCAA
1 ATATATTATATTACAA
40410977 AT
1 AT
40410979 TATGTTTGCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.48
Consensus pattern (16 bp):
ATATATTATATTACAA
Found at i:40413645 original size:46 final size:46
Alignment explanation
Indices: 40413593--40413682 Score: 144
Period size: 46 Copynumber: 2.0 Consensus size: 46
40413583 GAAGGAAATA
* *
40413593 AAAACCTAATATAATAGAGAAAATAAGTAAAACTAAAACTCTTAAT
1 AAAACCTAATATAATAAAGAAAATAAATAAAACTAAAACTCTTAAT
* *
40413639 AAAACCTGATATAGTAAAGAAAATAAATAAAACTAAAACTCTTA
1 AAAACCTAATATAATAAAGAAAATAAATAAAACTAAAACTCTTA
40413683 TTGCAATAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 40 1.00
ACGTcount: A:0.59, C:0.11, G:0.07, T:0.23
Consensus pattern (46 bp):
AAAACCTAATATAATAAAGAAAATAAATAAAACTAAAACTCTTAAT
Found at i:40425909 original size:74 final size:75
Alignment explanation
Indices: 40425760--40425928 Score: 259
Period size: 74 Copynumber: 2.3 Consensus size: 75
40425750 AAGGAAAACC
* * * *
40425760 ATGATTATTCTCTTATTAATAGAGAAGGCAAATGGAAATTTAGAAAAATGAAGTATATTCTTTCC
1 ATGATTATTCCCTTATTAATAGAGAAGGAAAATGGAAAGTTAGAAAAATAAAGTATATTCTTTCC
40425825 AAAAGAATAT
66 AAAAGAATAT
* *
40425835 ATGATTATTCCCTTTTTAATAGAGAAGGAAAAT-GAAAGTTAGAAAAATAAATTATATTCTTTCC
1 ATGATTATTCCCTTATTAATAGAGAAGGAAAATGGAAAGTTAGAAAAATAAAGTATATTCTTTCC
*
40425899 AAAAGGATAT
66 AAAAGAATAT
*
40425909 AGGATTATTCCCTTATTAAT
1 ATGATTATTCCCTTATTAAT
40425929 TTTGTAAAAT
Statistics
Matches: 85, Mismatches: 9, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
74 55 0.65
75 30 0.35
ACGTcount: A:0.43, C:0.09, G:0.14, T:0.35
Consensus pattern (75 bp):
ATGATTATTCCCTTATTAATAGAGAAGGAAAATGGAAAGTTAGAAAAATAAAGTATATTCTTTCC
AAAAGAATAT
Found at i:40430742 original size:43 final size:43
Alignment explanation
Indices: 40430681--40430767 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
40430671 AGAAAAAGAT
40430681 AGAATTTTTCACACTACAGGGGTCACAGAGCCGTGTGACTCAC
1 AGAATTTTTCACACTACAGGGGTCACAGAGCCGTGTGACTCAC
40430724 AGAATTTTTCACACTACAGGGGTCACAGAGCCGTGTGACTCAC
1 AGAATTTTTCACACTACAGGGGTCACAGAGCCGTGTGACTCAC
40430767 A
1 A
40430768 CGGCTGAGAC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.29, C:0.25, G:0.23, T:0.23
Consensus pattern (43 bp):
AGAATTTTTCACACTACAGGGGTCACAGAGCCGTGTGACTCAC
Found at i:40433194 original size:12 final size:12
Alignment explanation
Indices: 40433171--40433204 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
40433161 TATATATTTT
40433171 AAAATT-ATATA
1 AAAATTAATATA
40433182 AAAATTAATATA
1 AAAATTAATATA
40433194 AAAATTAATAT
1 AAAATTAATAT
40433205 GGGTAGGTCG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 6 0.27
12 16 0.73
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (12 bp):
AAAATTAATATA
Found at i:40435750 original size:50 final size:50
Alignment explanation
Indices: 40435642--40435888 Score: 210
Period size: 50 Copynumber: 4.8 Consensus size: 50
40435632 ATTTGGGTAA
* * *
40435642 AGAGATCCCATGTAAGACCATGTCTGGGACATGACATTGGCATCATTGAGGTTATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGA-G--ATG
* *
40435698 AGAGGTCCCATGTAAGCCCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * * *
40435748 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCAATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * * * * * *
40435798 AGAACTCCCATGTAAGACCATATCTGGGATATGTCATTGG-A-AGTACAAG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATG
* ** * *
40435847 AAACATCCTATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
40435889 TGTTATTATC
Statistics
Matches: 157, Mismatches: 32, Indels: 10
0.79 0.16 0.05
Matches are distributed among these distances:
49 36 0.23
50 79 0.50
52 1 0.01
53 2 0.01
55 1 0.01
56 38 0.24
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.23
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:40437490 original size:69 final size:69
Alignment explanation
Indices: 40437374--40437509 Score: 209
Period size: 69 Copynumber: 2.0 Consensus size: 69
40437364 ACTAAAATAG
*
40437374 AATCCATTAATTTTCACTTTGTTTCTCTAGATAACAATGTATCAGCTCTTCTAGATCCTTGTACC
1 AATCCATTAATTATCACTTTGTTTCTCTAGATAACAATGTATCAGCTCTTCTAGATCCTTGTACC
40437439 ACAT
66 ACAT
* * * * * *
40437443 AATCCATTAATTATCACTTTGTTTCTTTGGATAATAATGTATTAGCTCTTTTGGATCCTTGTACC
1 AATCCATTAATTATCACTTTGTTTCTCTAGATAACAATGTATCAGCTCTTCTAGATCCTTGTACC
40437508 AC
66 AC
40437510 GAAAGATTAA
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
69 60 1.00
ACGTcount: A:0.26, C:0.21, G:0.10, T:0.43
Consensus pattern (69 bp):
AATCCATTAATTATCACTTTGTTTCTCTAGATAACAATGTATCAGCTCTTCTAGATCCTTGTACC
ACAT
Found at i:40441413 original size:44 final size:44
Alignment explanation
Indices: 40441352--40441605 Score: 126
Period size: 44 Copynumber: 5.5 Consensus size: 44
40441342 ATCTACTCTG
* * *
40441352 CTGTAA-CTTCAGAGAGATAAGATCCT-TTA-TTTTAATCCGCTCCA
1 CTGTAATC-TCAGAGAGATAAGAT--TATTAGCTTCAATCAGCTCCA
* * *
40441396 CTGTAATCTCAGTGAGATAGGATTATTAGCTTCAATCAGCTCCG
1 CTGTAATCTCAGAGAGATAAGATTATTAGCTTCAATCAGCTCCA
*
40441440 CTGTAATCTCAGGGAGATAAGATT-TCT-GACTTCAATCTGATGCGATCTACTCTA
1 CTGTAATCTCAGAGAGATAAGATTAT-TAG-CTTCAATC--A---G--CT-C-C-A
* ** * ** *
40441494 CTGTAA-CTTCAAAGAGATAAGATCCTCCATTTTC-ATCCGCTCCA
1 CTGTAATC-TCAGAGAGATAAGATTAT-TAGCTTCAATCAGCTCCA
* * * * *
40441538 CTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCG
1 CTGTAATCTCAGAGAGATAAGATTATTAGCTTCAATCAGCTCCA
*
40441582 CTGTAATCTCAGGGAGATAAGATT
1 CTGTAATCTCAGAGAGATAAGATT
40441606 TCTGGCTTCC
Statistics
Matches: 162, Mismatches: 28, Indels: 40
0.70 0.12 0.17
Matches are distributed among these distances:
42 1 0.01
43 9 0.06
44 111 0.69
45 3 0.02
46 2 0.01
47 2 0.01
49 2 0.01
51 2 0.01
52 1 0.01
53 2 0.01
54 22 0.14
55 5 0.03
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.31
Consensus pattern (44 bp):
CTGTAATCTCAGAGAGATAAGATTATTAGCTTCAATCAGCTCCA
Found at i:40441590 original size:142 final size:142
Alignment explanation
Indices: 40441334--40442040 Score: 1164
Period size: 142 Copynumber: 5.0 Consensus size: 142
40441324 GAGATAAGAC
** **
40441334 CTGATGCGATCTACTCTGCTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTG
1 CTGATGCGATCTACTCTATTGTAACTTCAGAGAGATAAGATCCTCCATTTTAATCCGCTCCACTG
* * *
40441399 TAATCTCAGTGAGATAGGATTATTAGCTTCAATCAGCTCCGCTGTAATCTCAGGGAGATAAGATT
66 TAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATT
* *
40441464 TCTGACTTCAAT
131 TCTGGCTTCCAT
* * *
40441476 CTGATGCGATCTACTCTACTGTAACTTCAAAGAGATAAGATCCTCCATTTTCATCCGCTCCACTG
1 CTGATGCGATCTACTCTATTGTAACTTCAGAGAGATAAGATCCTCCATTTTAATCCGCTCCACTG
40441541 TAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATT
66 TAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATT
40441606 TCTGGCTTCCAT
131 TCTGGCTTCCAT
40441618 CTGATGCGATCTACTCTATTGTAACTTCAGAGAGATAAGATCCTCCATTTTAATCCGCTCCACTG
1 CTGATGCGATCTACTCTATTGTAACTTCAGAGAGATAAGATCCTCCATTTTAATCCGCTCCACTG
* * *
40441683 TAATCTCAGGGGGGATAGGATTACTAGCTTCAATTTGCTCTGCTGTAATCTCAGGGA-ATTAAGA
66 TAATCTCA-GGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGA-TAAGA
40441747 TTTCTGGCTTCCAT
129 TTTCTGGCTTCCAT
40441761 CTGATGCGATCTACTCTATTGTAACTTCAGAGAGATAAGATCCTCCATTTTAATCCGCTCCACTG
1 CTGATGCGATCTACTCTATTGTAACTTCAGAGAGATAAGATCCTCCATTTTAATCCGCTCCACTG
* *
40441826 TAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTATAATCTCAGGGAGATATGATT
66 TAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATT
40441891 TCTGGCTTCCAT
131 TCTGGCTTCCAT
* * * *
40441903 CTAATGCGATCTACTCTGTTGTAACTTCAGAGAGATAAAATCCTCTATTTTAATCCGCTCCACTG
1 CTGATGCGATCTACTCTATTGTAACTTCAGAGAGATAAGATCCTCCATTTTAATCCGCTCCACTG
* * *
40441968 TAATCTCAGGGAGATAAGATTGCTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATC
66 TAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATT
*
40442033 TGTGGCTT
131 TCTGGCTT
40442041 AAATCTGTTT
Statistics
Matches: 531, Mismatches: 31, Indels: 6
0.93 0.05 0.01
Matches are distributed among these distances:
142 393 0.74
143 138 0.26
ACGTcount: A:0.26, C:0.22, G:0.19, T:0.32
Consensus pattern (142 bp):
CTGATGCGATCTACTCTATTGTAACTTCAGAGAGATAAGATCCTCCATTTTAATCCGCTCCACTG
TAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATT
TCTGGCTTCCAT
Found at i:40441614 original size:44 final size:44
Alignment explanation
Indices: 40441532--40442031 Score: 222
Period size: 44 Copynumber: 10.7 Consensus size: 44
40441522 ATTTTCATCC
* * *
40441532 GCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCT
1 GCTCCGCTGTAATCTCAGGGAGATAAGATTTCTAGCTTCAATCT
* *
40441576 GCTCCGCTGTAATCTCAGGGAGATAAGATTTCTGGCTTCCATCTGAT
1 GCTCCGCTGTAATCTCAGGGAGATAAGATTTCTAGCTTCAATC---T
* * * * * * *
40441623 GCGATCTACTCTATTGTAA-CTTCAGAGAGATAAGATCCTCCA-TTTTAATCC
1 GC--TC--CGC---TGTAATC-TCAGGGAGATAAGAT-TTCTAGCTTCAATCT
* * * * *
40441674 GCTCCACTGTAATCTCAGGGGGGATAGGATTACTAGCTTCAATTT
1 GCTCCGCTGTAATCTCA-GGGAGATAAGATTTCTAGCTTCAATCT
* * *
40441719 GCTCTGCTGTAATCTCAGGGA-ATTAAGATTTCTGGCTTCCATCTGAT
1 GCTCCGCTGTAATCTCAGGGAGA-TAAGATTTCTAGCTTCAATC---T
* * * * * * *
40441766 GCGATCTACTCTATTGTAA-CTTCAGAGAGATAAGATCCTCCA-TTTTAATCC
1 GC--TC--CGC---TGTAATC-TCAGGGAGATAAGAT-TTCTAGCTTCAATCT
* * *
40441817 GCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCT
1 GCTCCGCTGTAATCTCAGGGAGATAAGATTTCTAGCTTCAATCT
* * * *
40441861 GCTCCGCTATAATCTCAGGGAGATATGATTTCTGGCTTCCATCTAAT
1 GCTCCGCTGTAATCTCAGGGAGATAAGATTTCTAGCTTCAATC---T
* * * * * * *
40441908 GCGATCTACTCTGTTGTAA-CTTCAGAGAGATAAAATCCTCTA-TTTTAATCC
1 --G--CT-C-C-GCTGTAATC-TCAGGGAGATAAGAT-TTCTAGCTTCAATCT
* *
40441959 GCTCCACTGTAATCTCAGGGAGATAAGATTGCTAGCTTCAATCT
1 GCTCCGCTGTAATCTCAGGGAGATAAGATTTCTAGCTTCAATCT
40442003 GCTCCGCTGTAATCTCAGGGAGATAAGAT
1 GCTCCGCTGTAATCTCAGGGAGATAAGAT
40442032 CTGTGGCTTA
Statistics
Matches: 332, Mismatches: 79, Indels: 90
0.66 0.16 0.18
Matches are distributed among these distances:
43 6 0.02
44 179 0.54
45 33 0.10
46 1 0.00
47 13 0.04
49 10 0.03
51 9 0.03
52 1 0.00
53 4 0.01
54 68 0.20
55 8 0.02
ACGTcount: A:0.26, C:0.22, G:0.19, T:0.32
Consensus pattern (44 bp):
GCTCCGCTGTAATCTCAGGGAGATAAGATTTCTAGCTTCAATCT
Found at i:40441843 original size:285 final size:284
Alignment explanation
Indices: 40441334--40442047 Score: 1187
Period size: 285 Copynumber: 2.5 Consensus size: 284
40441324 GAGATAAGAC
* *
40441334 CTGATGCGATCTACTCTGCTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTG
1 CTGATGCGATCTACTCTGTTGTAACTTCAGAGAGATAAGATCCTCTATTTTAATCCGCTCCACTG
* * *
40441399 TAATCTCAGTGAGATAGGATTATTAGCTTCAATCAGCTCCGCTGTAATCTCAGGGAGATAAGATT
66 TAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATT
* *
40441464 TCTGACTTCAATCTGATGCGATCTACTCTACTGTAACTTCAAAGAGATAAGATCCTCCATTTTCA
131 TCTGGCTTCAATCTGATGCGATCTACTCTACTGTAACTTCAAAGAGATAAGATCCTCCATTTTAA
*
40441529 TCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAG
196 TCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTATAATCTCAG
40441594 GGAGATAAGATTTCTGGCTTCCAT
261 GGAGATAAGATTTCTGGCTTCCAT
* *
40441618 CTGATGCGATCTACTCTATTGTAACTTCAGAGAGATAAGATCCTCCATTTTAATCCGCTCCACTG
1 CTGATGCGATCTACTCTGTTGTAACTTCAGAGAGATAAGATCCTCTATTTTAATCCGCTCCACTG
* * *
40441683 TAATCTCAGGGGGGATAGGATTACTAGCTTCAATTTGCTCTGCTGTAATCTCAGGGA-ATTAAGA
66 TAATCTCA-GGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGA-TAAGA
* * *
40441747 TTTCTGGCTTCCATCTGATGCGATCTACTCTATTGTAACTTCAGAGAGATAAGATCCTCCATTTT
129 TTTCTGGCTTCAATCTGATGCGATCTACTCTACTGTAACTTCAAAGAGATAAGATCCTCCATTTT
40441812 AATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTATAATCTC
194 AATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTATAATCTC
*
40441877 AGGGAGATATGATTTCTGGCTTCCAT
259 AGGGAGATAAGATTTCTGGCTTCCAT
* *
40441903 CTAATGCGATCTACTCTGTTGTAACTTCAGAGAGATAAAATCCTCTATTTTAATCCGCTCCACTG
1 CTGATGCGATCTACTCTGTTGTAACTTCAGAGAGATAAGATCCTCTATTTTAATCCGCTCCACTG
* * *
40441968 TAATCTCAGGGAGATAAGATTGCTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATC
66 TAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATT
* *
40442033 TGTGGCTTAAATCTG
131 TCTGGCTTCAATCTG
40442048 TTTCCTTACA
Statistics
Matches: 397, Mismatches: 30, Indels: 6
0.92 0.07 0.01
Matches are distributed among these distances:
284 131 0.33
285 266 0.67
ACGTcount: A:0.26, C:0.22, G:0.19, T:0.32
Consensus pattern (284 bp):
CTGATGCGATCTACTCTGTTGTAACTTCAGAGAGATAAGATCCTCTATTTTAATCCGCTCCACTG
TAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATT
TCTGGCTTCAATCTGATGCGATCTACTCTACTGTAACTTCAAAGAGATAAGATCCTCCATTTTAA
TCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTATAATCTCAG
GGAGATAAGATTTCTGGCTTCCAT
Found at i:40442046 original size:44 final size:44
Alignment explanation
Indices: 40441954--40442047 Score: 136
Period size: 44 Copynumber: 2.1 Consensus size: 44
40441944 CCTCTATTTT
* *
40441954 AATCCGCTCCACTGTAATCTCAGGGAGATAAGATTGCTAGCTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTGCTAGCTTA
* *
40441998 AATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTG-TGGCTTA
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGAT-TGCTAGCTTA
40442042 AATCTG
1 AATCTG
40442048 TTTCCTTACA
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
44 43 0.96
45 2 0.04
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (44 bp):
AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTGCTAGCTTA
Found at i:40461768 original size:3 final size:3
Alignment explanation
Indices: 40461760--40461794 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
40461750 AACCGAAATC
40461760 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
40461795 GCATTCCACA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:40464591 original size:50 final size:50
Alignment explanation
Indices: 40464479--40464865 Score: 331
Period size: 51 Copynumber: 7.7 Consensus size: 50
40464469 TCATTCGATA
* * *
40464479 CACGTAGTAGCCTTCACATAGTACTACACACGTGAT-TAGTTTTACAGTT
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTACGGCT
* *
40464528 CACGTAGTAGCCTTCACATAGTACTATACACATGATCAAGTTTTACGGCT
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTACGGCT
* * *
40464578 CCCGTAGTAGCCTTCACATGGTACTACACACGTGATCAAGTTTTACGACT
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTACGGCT
* * * *
40464628 CACGTAGTAACCTTCACATAGTACTACATACGTGACCAAAGCTTTT-TGG-T
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGATC-AAG-TTTTACGGCT
* * * * * * * * *
40464678 ACCCATTGTAGCCTTCACTTAGTACTACACATGTAACCATAG-TTTACTGAT
1 -CACGTAGTAGCCTTCACATAGTACTACACACGTGATCA-AGTTTTACGGCT
* * *
40464729 ACACGTAGTAGCATTCACACAGTACTACACACGTGCTCAAAGCTTTT-CGG-T
1 -CACGTAGTAGCCTTCACATAGTACTACACACGTGATC-AAG-TTTTACGGCT
* * * * * *
40464780 ACACATAGTAGCCTTCACTTAGTACTACACATGTGA-CCATTATTTATC-GAT
1 -CACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGT-TTTA-CGGCT
* *
40464831 ACACGTAGTAGCCTCCACACAGTACTACACACGTG
1 -CACGTAGTAGCCTTCACATAGTACTACACACGTG
40464866 TTCATCGACA
Statistics
Matches: 273, Mismatches: 51, Indels: 26
0.78 0.15 0.07
Matches are distributed among these distances:
48 1 0.00
49 41 0.15
50 92 0.34
51 129 0.47
52 7 0.03
53 3 0.01
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.29
Consensus pattern (50 bp):
CACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTACGGCT
Found at i:40464763 original size:102 final size:103
Alignment explanation
Indices: 40464483--40464865 Score: 407
Period size: 102 Copynumber: 3.8 Consensus size: 103
40464473 TCGATACACG
* * *
40464483 TAGTAGCCTTCACATAGTACTACACACGTGA--TTAGTTTTACAG-TTCACGTAGTAGCCTTCAC
1 TAGTAGCCTTCACATAGTACTACACACGTGACCATAGTTTTACTGATACACGTAGTAGCCTTCAC
* * * * *
40464545 ATAGTACTATACACATGATC-AAG-TTTTACGGCT-CCCG
66 ACAGTACTACACACGTGACCAAAGCTTTT-CGG-TACCCA
* * *
40464582 TAGTAGCCTTCACATGGTACTACACACGTGATCA-AGTTTTAC-GACT-CACGTAGTAACCTTCA
1 TAGTAGCCTTCACATAGTACTACACACGTGACCATAGTTTTACTGA-TACACGTAGTAGCCTTCA
* * *
40464644 CATAGTACTACATACGTGACCAAAGCTTTTTGGTACCCA
65 CACAGTACTACACACGTGACCAAAGCTTTTCGGTACCCA
* * * * *
40464683 TTGTAGCCTTCACTTAGTACTACACATGTAACCATAG-TTTACTGATACACGTAGTAGCATTCAC
1 TAGTAGCCTTCACATAGTACTACACACGTGACCATAGTTTTACTGATACACGTAGTAGCCTTCAC
*
40464747 ACAGTACTACACACGTG-CTCAAAGCTTTTCGGTACACA
66 ACAGTACTACACACGTGAC-CAAAGCTTTTCGGTACCCA
* * *
40464785 TAGTAGCCTTCACTTAGTACTACACATGTGACCAT--TATTTA-TCGATACACGTAGTAGCCTCC
1 TAGTAGCCTTCACATAGTACTACACACGTGACCATAGT-TTTACT-GATACACGTAGTAGCCTTC
40464847 ACACAGTACTACACACGTG
64 ACACAGTACTACACACGTG
40464866 TTCATCGACA
Statistics
Matches: 245, Mismatches: 25, Indels: 25
0.83 0.08 0.08
Matches are distributed among these distances:
99 31 0.13
100 41 0.17
101 45 0.18
102 128 0.52
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.30
Consensus pattern (103 bp):
TAGTAGCCTTCACATAGTACTACACACGTGACCATAGTTTTACTGATACACGTAGTAGCCTTCAC
ACAGTACTACACACGTGACCAAAGCTTTTCGGTACCCA
Found at i:40471787 original size:23 final size:23
Alignment explanation
Indices: 40471761--40471806 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
40471751 TTGCGTCATT
40471761 TTCTTTTTAAGGAATTGTGCCTA
1 TTCTTTTTAAGGAATTGTGCCTA
40471784 TTCTTTTTAAGGAATTGTGCCTA
1 TTCTTTTTAAGGAATTGTGCCTA
40471807 ACCCTGAGAC
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:0.22, C:0.13, G:0.17, T:0.48
Consensus pattern (23 bp):
TTCTTTTTAAGGAATTGTGCCTA
Found at i:40484780 original size:20 final size:20
Alignment explanation
Indices: 40484757--40484811 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 20
40484747 CCCCTATTAG
40484757 CACTTCGATGCCCCTGTATA
1 CACTTCGATGCCCCTGTATA
* * * *
40484777 CACTTTGGTGTCCCTGTTTA
1 CACTTCGATGCCCCTGTATA
* *
40484797 CACATCTATGCCCCT
1 CACTTCGATGCCCCT
40484812 ATTCACACTT
Statistics
Matches: 26, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.16, C:0.35, G:0.15, T:0.35
Consensus pattern (20 bp):
CACTTCGATGCCCCTGTATA
Found at i:40494911 original size:27 final size:26
Alignment explanation
Indices: 40494861--40495384 Score: 449
Period size: 27 Copynumber: 19.6 Consensus size: 26
40494851 AAGACCATAA
* **
40494861 CAGTCATTTCATCTCCTA-GGGGTATAA
1 CAGTCATTTTA-C-CCTATGGGGTATTT
40494888 CAGTCATTTTACCCTATGGAGGTATTT
1 CAGTCATTTTACCCTATGG-GGTATTT
**
40494915 TTGTCATTTTACCCTATGGGGATATTT
1 CAGTCATTTTACCCTATGGGG-TATTT
*
40494942 TAGTCATTTTACCCTATGGAGGTATTT
1 CAGTCATTTTACCCTATGG-GGTATTT
* *
40494969 -TGATTATTTTACCCTATAGGGGTATTT
1 CAG-TCATTTTACCCTAT-GGGGTATTT
** *
40494996 TGGTCATTTTACCCTATGGGGATCTTT
1 CAGTCATTTTACCCTATGGGG-TATTT
*
40495023 CAGTCATTTTATCCTATGGGGGTATTT
1 CAGTCATTTTACCCTAT-GGGGTATTT
* *
40495050 C-GATCA-TTTACCTTATGGGAGTAGTT
1 CAG-TCATTTTACCCTATGGG-GTATTT
* * *
40495076 CAATCATTTTACCTTGTGGGAGTATTT
1 CAGTCATTTTACCCTATGGG-GTATTT
*
40495103 CAGTTATTTTACCCTATGGGGGTATTT
1 CAGTCATTTTACCCTAT-GGGGTATTT
*
40495130 C-GATCA-TTT-CTCTATGGGGGTATTT
1 CAG-TCATTTTACCCTAT-GGGGTATTT
*
40495155 CGGTCATTTTACCCTATGGGGATATTT
1 CAGTCATTTTACCCTATGGGG-TATTT
* *
40495182 CGGTCATTTTACCCTAAGGGGGTATTT
1 CAGTCATTTTACCCT-ATGGGGTATTT
* *
40495209 CGGTTATTTTACCCTATGGGGGTATTT
1 CAGTCATTTTACCCTAT-GGGGTATTT
** *
40495236 TTGTCATTTTACCCTATGAGGATATTT
1 CAGTCATTTTACCCTATG-GGGTATTT
*
40495263 CAGTCATTATACCCTATGGGGGTATTT
1 CAGTCATTTTACCCTAT-GGGGTATTT
* *
40495290 CGGTCA-TTTACCCTATGGGAGAATTT
1 CAGTCATTTTACCCTATGGG-GTATTT
* *
40495316 CAGTCATTTTACCCTGTGGGGGTATTG
1 CAGTCATTTTACCCTAT-GGGGTATTT
*
40495343 C-GATTA-TTTACCCTATGCGGGTATTT
1 CAG-TCATTTTACCCTATG-GGGTATTT
40495369 C-GATCATTTTACCCTA
1 CAG-TCATTTTACCCTA
40495385 AATGGTCATA
Statistics
Matches: 418, Mismatches: 50, Indels: 58
0.79 0.10 0.11
Matches are distributed among these distances:
25 30 0.07
26 83 0.20
27 284 0.68
28 21 0.05
ACGTcount: A:0.20, C:0.17, G:0.21, T:0.42
Consensus pattern (26 bp):
CAGTCATTTTACCCTATGGGGTATTT
Found at i:40505573 original size:6 final size:6
Alignment explanation
Indices: 40505562--40505643 Score: 65
Period size: 6 Copynumber: 13.3 Consensus size: 6
40505552 CTTTTCTTTG
* * * * *
40505562 TTTTAT TTTTAT TTTTAAT TTTTAT CTTTGT CTTTAAT TTTAAT TTTAAT
1 TTTTAT TTTTAT TTTT-AT TTTTAT TTTTAT -TTTTAT TTTTAT TTTTAT
* * * *
40505612 CTTTAT TTTTAA TTTTAA TGTTAT TTTTAT TT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TT
40505644 ATTTTAATAA
Statistics
Matches: 62, Mismatches: 12, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
6 53 0.85
7 9 0.15
ACGTcount: A:0.22, C:0.04, G:0.02, T:0.72
Consensus pattern (6 bp):
TTTTAT
Found at i:40505586 original size:19 final size:18
Alignment explanation
Indices: 40505541--40505643 Score: 68
Period size: 19 Copynumber: 5.7 Consensus size: 18
40505531 AAATTTCAAA
* *
40505541 TTTATTTTAATCTTT-TC
1 TTTATTTTTATTTTTATC
* *
40505558 TTT-GTTTTATTTTTATT
1 TTTATTTTTATTTTTATC
* *
40505575 TTTAATTTTTATCTTTGTC
1 TTT-ATTTTTATTTTTATC
* *
40505594 TTTAATTTTAATTTTAATC
1 TTT-ATTTTTATTTTTATC
*
40505613 TTTATTTTTAATTTTAAT-
1 TTTATTTTT-ATTTTTATC
*
40505631 GTTATTTTTATTT
1 TTTATTTTTATTT
40505644 ATTTTAATAA
Statistics
Matches: 68, Mismatches: 14, Indels: 8
0.76 0.16 0.09
Matches are distributed among these distances:
16 8 0.12
17 11 0.16
18 13 0.19
19 36 0.53
ACGTcount: A:0.20, C:0.05, G:0.03, T:0.72
Consensus pattern (18 bp):
TTTATTTTTATTTTTATC
Found at i:40505603 original size:25 final size:25
Alignment explanation
Indices: 40505563--40505630 Score: 91
Period size: 25 Copynumber: 2.7 Consensus size: 25
40505553 TTTTCTTTGT
* * *
40505563 TTTATTTTTATTTTTAATTTTTATC
1 TTTATCTTTAATTTTAATTTTAATC
*
40505588 TTTGTCTTTAATTTTAATTTTAATC
1 TTTATCTTTAATTTTAATTTTAATC
*
40505613 TTTATTTTTAATTTTAAT
1 TTTATCTTTAATTTTAAT
40505631 GTTATTTTTA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.24, C:0.04, G:0.01, T:0.71
Consensus pattern (25 bp):
TTTATCTTTAATTTTAATTTTAATC
Found at i:40519798 original size:16 final size:17
Alignment explanation
Indices: 40519777--40519812 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
40519767 TCAATCATCC
40519777 CTCATCCCTCATCC-CT
1 CTCATCCCTCATCCTCT
*
40519793 CTCATCTCTCATCCTCT
1 CTCATCCCTCATCCTCT
40519810 CTC
1 CTC
40519813 TCAACTCTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.11, C:0.53, G:0.00, T:0.36
Consensus pattern (17 bp):
CTCATCCCTCATCCTCT
Found at i:40529279 original size:6 final size:6
Alignment explanation
Indices: 40529264--40529301 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
40529254 GCTTTGGTCC
40529264 TTTA-T TTTATT TTTATT TTTATT TTTATT TTTATT TTT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTT
40529302 TCTTTCTAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 4 0.12
6 28 0.88
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTATT
Found at i:40529541 original size:20 final size:20
Alignment explanation
Indices: 40529494--40529567 Score: 62
Period size: 21 Copynumber: 3.5 Consensus size: 20
40529484 TATCATACAT
40529494 TATTATTTTAAGTTTT--TG
1 TATTATTTTAAGTTTTCATG
40529512 TTCATATATTTTAAGTTTTCATG
1 -T-AT-TATTTTAAGTTTTCATG
*
40529535 TATTATTATTCAAGTTCATCATG
1 TATTATT-TT-AAGTT-TTCATG
*
40529558 CATTATTTTA
1 TATTATTTTA
40529568 TATATTTTTA
Statistics
Matches: 46, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
19 1 0.02
20 6 0.13
21 18 0.39
22 8 0.17
23 13 0.28
ACGTcount: A:0.27, C:0.08, G:0.08, T:0.57
Consensus pattern (20 bp):
TATTATTTTAAGTTTTCATG
Found at i:40529775 original size:27 final size:25
Alignment explanation
Indices: 40529722--40529776 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 25
40529712 AAAACCTTAT
40529722 TTTATTATATTTTACTTATTTCAAA
1 TTTATTATATTTTACTTATTTCAAA
*
40529747 TTTATATATATTATTA-TCTATTTCGAA
1 TTTAT-TATATT-TTACT-TATTTCAAA
40529774 TTT
1 TTT
40529777 TTCATTCCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
25 5 0.19
26 7 0.27
27 14 0.54
ACGTcount: A:0.31, C:0.07, G:0.02, T:0.60
Consensus pattern (25 bp):
TTTATTATATTTTACTTATTTCAAA
Found at i:40529834 original size:23 final size:24
Alignment explanation
Indices: 40529784--40529834 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
40529774 TTTTTCATTC
* *
40529784 CATATGTATTATTTATTTAGATTA
1 CATATATATTATTTATGTAGATTA
*
40529808 -ATATATATTATTT-TGTATATTA
1 CATATATATTATTTATGTAGATTA
40529830 CATAT
1 CATAT
40529835 TTTGATTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
22 7 0.30
23 16 0.70
ACGTcount: A:0.35, C:0.04, G:0.06, T:0.55
Consensus pattern (24 bp):
CATATATATTATTTATGTAGATTA
Found at i:40531330 original size:16 final size:16
Alignment explanation
Indices: 40531309--40531342 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
40531299 TGTGTTTTGC
*
40531309 TTTGATTGCATGGCAT
1 TTTGATTGCATGACAT
40531325 TTTGATTGCATGACAT
1 TTTGATTGCATGACAT
40531341 TT
1 TT
40531343 CATCTTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.21, C:0.12, G:0.21, T:0.47
Consensus pattern (16 bp):
TTTGATTGCATGACAT
Found at i:40535778 original size:8 final size:7
Alignment explanation
Indices: 40535753--40535853 Score: 70
Period size: 7 Copynumber: 14.6 Consensus size: 7
40535743 GGCAGTAGAG
*
40535753 AAAAAAT
1 AAAAAAC
*
40535760 AAATAAC
1 AAAAAAC
40535767 AAAAAGAC
1 AAAAA-AC
40535775 AAAATAAC
1 AAAA-AAC
40535783 --AAAA-
1 AAAAAAC
*
40535787 AAATAAC
1 AAAAAAC
40535794 AAAATAAC
1 AAAA-AAC
40535802 AAAATAAC
1 AAAA-AAC
40535810 AAAATAAC
1 AAAA-AAC
*
40535818 AAATAAC
1 AAAAAAC
40535825 --AAAAC
1 AAAAAAC
*
40535830 AAACAAC
1 AAAAAAC
40535837 AAAAAAC
1 AAAAAAC
40535844 AAAAAA-
1 AAAAAAC
40535850 AAAA
1 AAAA
40535854 CAAAAACCTC
Statistics
Matches: 77, Mismatches: 9, Indels: 17
0.75 0.09 0.17
Matches are distributed among these distances:
5 6 0.08
6 9 0.12
7 31 0.40
8 30 0.39
9 1 0.01
ACGTcount: A:0.79, C:0.12, G:0.01, T:0.08
Consensus pattern (7 bp):
AAAAAAC
Found at i:40535781 original size:16 final size:15
Alignment explanation
Indices: 40535760--40535847 Score: 84
Period size: 16 Copynumber: 6.2 Consensus size: 15
40535750 GAGAAAAAAT
40535760 AAATAACAAAAAGACA
1 AAATAACAAAAA-ACA
40535776 AAATAAC---AAA-A
1 AAATAACAAAAAACA
40535787 AAATAACAAAATAACA
1 AAATAACAAAA-AACA
40535803 AAATAACAAAATAAC-
1 AAATAACAAAA-AACA
40535818 AAATAAC--AAAAC-
1 AAATAACAAAAAACA
*
40535830 AAACAACAAAAAACA
1 AAATAACAAAAAACA
40535845 AAA
1 AAA
40535848 AAAAAACAAA
Statistics
Matches: 63, Mismatches: 1, Indels: 17
0.78 0.01 0.21
Matches are distributed among these distances:
11 8 0.13
12 10 0.16
13 4 0.06
14 6 0.10
15 12 0.19
16 23 0.37
ACGTcount: A:0.77, C:0.14, G:0.01, T:0.08
Consensus pattern (15 bp):
AAATAACAAAAAACA
Found at i:40535795 original size:19 final size:19
Alignment explanation
Indices: 40535773--40535858 Score: 86
Period size: 19 Copynumber: 4.3 Consensus size: 19
40535763 TAACAAAAAG
40535773 ACAAAATAACAAAAAAATA
1 ACAAAATAACAAAAAAATA
40535792 ACAAAATAACAAAATAACAAAATA
1 ACAAAATAAC---A-AA-AAAATA
*
40535816 AC-AAATAACAAAACAAACA
1 ACAAAATAACAAAA-AAATA
*
40535835 ACAAAA-AACAAAAAAAAA
1 ACAAAATAACAAAAAAATA
40535853 ACAAAA
1 ACAAAA
40535859 ACCTCTATCG
Statistics
Matches: 58, Mismatches: 2, Indels: 15
0.77 0.03 0.20
Matches are distributed among these distances:
18 11 0.19
19 25 0.43
20 4 0.07
22 1 0.02
23 9 0.16
24 8 0.14
ACGTcount: A:0.79, C:0.14, G:0.00, T:0.07
Consensus pattern (19 bp):
ACAAAATAACAAAAAAATA
Found at i:40535795 original size:27 final size:28
Alignment explanation
Indices: 40535755--40535816 Score: 101
Period size: 27 Copynumber: 2.2 Consensus size: 28
40535745 CAGTAGAGAA
40535755 AAAATAAATAACAAAA-AGACAAAATAAC
1 AAAATAAATAACAAAATA-ACAAAATAAC
40535783 AAAA-AAATAACAAAATAACAAAATAAC
1 AAAATAAATAACAAAATAACAAAATAAC
40535810 AAAATAA
1 AAAATAA
40535817 CAAATAACAA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
27 25 0.78
28 7 0.22
ACGTcount: A:0.77, C:0.10, G:0.02, T:0.11
Consensus pattern (28 bp):
AAAATAAATAACAAAATAACAAAATAAC
Found at i:40535858 original size:8 final size:8
Alignment explanation
Indices: 40535764--40535860 Score: 61
Period size: 8 Copynumber: 11.4 Consensus size: 8
40535754 AAAAATAAAT
40535764 AACAAAAA
1 AACAAAAA
*
40535772 GACAAAATA
1 AACAAAA-A
*
40535781 ACAAAAAAA
1 A-ACAAAAA
*
40535790 TAACAAAAT
1 -AACAAAAA
*
40535799 AACAAAAT
1 AACAAAAA
*
40535807 AACAAAAT
1 AACAAAAA
*
40535815 AAC-AAAT
1 AACAAAAA
40535822 AACAAAACA
1 AACAAAA-A
40535831 AACAACAAAA
1 AAC-A-AAAA
40535841 AACAAAAA
1 AACAAAAA
*
40535849 AAAAACAAA
1 AACAA-AAA
40535858 AAC
1 AAC
40535861 CTCTATCGGG
Statistics
Matches: 73, Mismatches: 8, Indels: 15
0.76 0.08 0.16
Matches are distributed among these distances:
7 7 0.10
8 36 0.49
9 16 0.22
10 11 0.15
11 3 0.04
ACGTcount: A:0.78, C:0.14, G:0.01, T:0.06
Consensus pattern (8 bp):
AACAAAAA
Found at i:40536417 original size:47 final size:47
Alignment explanation
Indices: 40536285--40536423 Score: 154
Period size: 48 Copynumber: 2.9 Consensus size: 47
40536275 AAAGAAGGAG
* * * *
40536285 AAGAGACCAAGGTGAAAACGCGCAAAAGGCGCTTTAAGTCCTAAAAAA
1 AAGAGACCAAGGTGAAAACCCGC-AAAGGCACTTTGAGTCCAAAAAAA
* **
40536333 AAGAGACCAAGGCGAAAACCAACAAATGGCACTTTGAGTCCAAAAAAA
1 AAGAGACCAAGGTGAAAACCCGCAAA-GGCACTTTGAGTCCAAAAAAA
* * *
40536381 AAGAG-CCAATGTGAAAACCCGCAAAGGACACCTTGAGACCAAA
1 AAGAGACCAAGGTGAAAACCCGCAAAGG-CACTTTGAGTCCAAA
40536424 GGGGATTTGA
Statistics
Matches: 76, Mismatches: 13, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
46 2 0.03
47 32 0.42
48 42 0.55
ACGTcount: A:0.47, C:0.22, G:0.21, T:0.11
Consensus pattern (47 bp):
AAGAGACCAAGGTGAAAACCCGCAAAGGCACTTTGAGTCCAAAAAAA
Found at i:40537767 original size:51 final size:51
Alignment explanation
Indices: 40537626--40538432 Score: 863
Period size: 51 Copynumber: 15.9 Consensus size: 51
40537616 AAGTCATTAT
* * * *
40537626 AGCGAATATTATTCCCCTGGTGTTGCAGTGGAACAAATTAAAGCTGAAGGC
1 AGCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGCTGAAGGC
* * * *
40537677 AGCAAATCTTTTTTTCCCTGGTGTTGCAGTGGAATAGATTAAAGCTGAAGGC
1 AGCGAATC-TTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGCTGAAGGC
* * * * * *
40537729 AGCGGATCTTATTTCCTTGGCATTACAGTGGAACAGATTAAAGTTGAAGCC
1 AGCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGCTGAAGGC
*
40537780 AGCGAATCTTATTTCCCTGGCGTTGCAATGGAACAGATTAAAGCTGAAGGC
1 AGCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGCTGAAGGC
* * * * * *
40537831 AGTGAATCTTTTTTCCCTGGCATTGCAATGGAACAAATTAAAGCTAAAGGC
1 AGCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGCTGAAGGC
* * *
40537882 AGCGAATCTTTTTTCCCCGGCGTTACAGTGGAACAGATTAAAGCTGAAGGC
1 AGCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGCTGAAGGC
* * * *
40537933 AGCAAATCTTGTTTCCCTGGCGTTGCAGTGGAATAGATTAAAGCTAAAGGC
1 AGCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGCTGAAGGC
* * * *
40537984 AGCGACTCTTGTTTCCTTGGCGCTGCAGTGGAACAGATTAAAGCTGAAGGC
1 AGCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGCTGAAGGC
*** * * *
40538035 AGCGAATCTTATTTCCCTATTGTTGCAGTGGAACAGATTAAAGCTAAAAGT
1 AGCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGCTGAAGGC
* * * *
40538086 AGTGAATCTTATTTCCCTGGCATTGCAGTGGAGCAGATTAAAGCTAAAGGC
1 AGCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGCTGAAGGC
* **
40538137 AACGAATCTTATTTTTCTGGCGTTGCAGTGGAACAGATTAAAGCTGAAGGC
1 AGCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGCTGAAGGC
* ** *
40538188 AACGAATCTTATTTCCCTGGCGTTGCAGTGGAATGGATTAAAGCTGAAGGT
1 AGCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGCTGAAGGC
* * * * ** * * ***
40538239 AGCGAATCTTATTTTCCTAGCATTGGAGCAGAATAGATTAAAGCTACAAAAT
1 AGCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGCT-GAAGGC
* ** * *
40538291 ATGGCGGATCTTATCTT-CCTGAAGTTGCAGTGGAGCAGACTAAA---G-A--C
1 A--GCGAATCTTAT-TTCCCTGGCGTTGCAGTGGAACAGATTAAAGCTGAAGGC
* * *
40538338 AGCGAATCTTATTTCCCTAGCCTTGTAGTGGAACAGATTAAAGCTGAAGGC
1 AGCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGCTGAAGGC
* * * * *
40538389 AGCAAACCTTATTTCCCTAGCGTTGCAATGGAATAGATTAAAGC
1 AGCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGC
40538433 GAAAAAGTAT
Statistics
Matches: 629, Mismatches: 115, Indels: 24
0.82 0.15 0.03
Matches are distributed among these distances:
44 2 0.00
45 30 0.05
47 1 0.00
48 1 0.00
49 2 0.00
51 515 0.82
52 49 0.08
54 27 0.04
55 2 0.00
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.28
Consensus pattern (51 bp):
AGCGAATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGCTGAAGGC
Found at i:40545896 original size:40 final size:40
Alignment explanation
Indices: 40545812--40546036 Score: 294
Period size: 40 Copynumber: 5.7 Consensus size: 40
40545802 TTGAATGATG
* * * *
40545812 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
40545852 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
40545892 TCCGGGCTAAG-CCCGAAGGCATTTTTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
40545931 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
40545971 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
40546011 GCCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
40546037 AACGAGGAGC
Statistics
Matches: 164, Mismatches: 17, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
39 34 0.21
40 122 0.74
41 8 0.05
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:40546058 original size:119 final size:119
Alignment explanation
Indices: 40545812--40546069 Score: 283
Period size: 119 Copynumber: 2.2 Consensus size: 119
40545802 TTGAATGATG
* *
40545812 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
* *** *
40545877 GTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTTTGCGAGTTACTAAA
66 GTGCGAGATACTAATGCCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAAA
* * * **
40545931 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCAT
* * *
40545994 TTGTGCGAGTTACT-ATAGCCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGCTATA
64 TTGTGCGAGATACTAAT-GCCGGGCTAAG-CCCGAAGGCATTTGAACGAGTGA-CTAAA
* *
40546051 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
40546070 TACGTGATTT
Statistics
Matches: 117, Mismatches: 17, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
118 3 0.03
119 83 0.71
120 31 0.26
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (119 bp):
TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
GTGCGAGATACTAATGCCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAAA
Found at i:40548511 original size:16 final size:17
Alignment explanation
Indices: 40548486--40548520 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
40548476 ACTTTTTCAA
40548486 TCATCCCTCATCC-CTC
1 TCATCCCTCATCCTCTC
*
40548502 TCATCTCTCATCCTCTC
1 TCATCCCTCATCCTCTC
40548519 TC
1 TC
40548521 TCAACTCTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.11, C:0.51, G:0.00, T:0.37
Consensus pattern (17 bp):
TCATCCCTCATCCTCTC
Found at i:40552666 original size:25 final size:25
Alignment explanation
Indices: 40552612--40552666 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
40552602 ACATACTAAA
*
40552612 ATAT-GTCAAAACACAAGCCAAATC
1 ATATGGTCAAAACACAAGCCAAAAC
* *
40552636 AAATGGTCATAACAACAA-CCAAAAC
1 ATATGGTCAAAAC-ACAAGCCAAAAC
40552661 ATATGG
1 ATATGG
40552667 CCAACATTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
24 3 0.12
25 18 0.72
26 4 0.16
ACGTcount: A:0.51, C:0.22, G:0.11, T:0.16
Consensus pattern (25 bp):
ATATGGTCAAAACACAAGCCAAAAC
Done.