Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr5
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: 39371879
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2227820 characters in sequence are not A, C, G, or T
File 78 of 103
Found at i:29204158 original size:31 final size:31
Alignment explanation
Indices: 29204115--29204408 Score: 304
Period size: 31 Copynumber: 9.5 Consensus size: 31
29204105 TGTAAGGAAT
**
29204115 AAATGTTGTGACACGCCATGCATTGCAA-TCA
1 AAATGTTGTGACACGCCATGCATAACAAGT-A
* *
29204146 AAATATTGTGACACACCATGCATAACAAGTA
1 AAATGTTGTGACACGCCATGCATAACAAGTA
*
29204177 AAATGTTGTGACACGTCATGCATAACAAGTA
1 AAATGTTGTGACACGCCATGCATAACAAGTA
* * *
29204208 AAATGCTGTCAAACGCCATGCATAACAAGTA
1 AAATGTTGTGACACGCCATGCATAACAAGTA
* * * *
29204239 AAATTTTGTGACATGACATGCATATCAAGTA
1 AAATGTTGTGACACGCCATGCATAACAAGTA
* * *
29204270 AAATGCTGTCAAACGCCATGCATAACAAGTA
1 AAATGTTGTGACACGCCATGCATAACAAGTA
* * *
29204301 AAATGTTGTCAAACGTCATGCATAACAAGTA
1 AAATGTTGTGACACGCCATGCATAACAAGTA
* * *
29204332 AAAT-TCTGTGACACGACATGCGTATCAAGTA
1 AAATGT-TGTGACACGCCATGCATAACAAGTA
* * * * *
29204363 AAATGCTATCACACGTCATGCATATCAAGTA
1 AAATGTTGTGACACGCCATGCATAACAAGTA
* *
29204394 AAATGCTGTCACACG
1 AAATGTTGTGACACG
29204409 TTAATAACTA
Statistics
Matches: 222, Mismatches: 38, Indels: 6
0.83 0.14 0.02
Matches are distributed among these distances:
30 1 0.00
31 220 0.99
32 1 0.00
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (31 bp):
AAATGTTGTGACACGCCATGCATAACAAGTA
Found at i:29204274 original size:93 final size:92
Alignment explanation
Indices: 29204127--29204404 Score: 378
Period size: 93 Copynumber: 3.0 Consensus size: 92
29204117 ATGTTGTGAC
** * * * * *
29204127 ACGCCATGCATTGCAA-TCAAAATATTGTGACACACCATGCATAACAAGTAAAATGTTGTGACAC
1 ACGCCATGCATAACAAGT-AAAATTTTGTGACAGA-CATGCATATCAAGTAAAATGCTGTCACAC
29204191 GTCATGCATAACAAGTAAAATGCTGTCAA
64 GTCATGCATAACAAGTAAAATGCTGTCAA
*
29204220 ACGCCATGCATAACAAGTAAAATTTTGTGACATGACATGCATATCAAGTAAAATGCTGTCAAACG
1 ACGCCATGCATAACAAGTAAAATTTTGTGACA-GACATGCATATCAAGTAAAATGCTGTCACACG
* *
29204285 CCATGCATAACAAGTAAAATGTTGTCAA
65 TCATGCATAACAAGTAAAATGCTGTCAA
* * * *
29204313 ACGTCATGCATAACAAGTAAAATTCTGTGACACGACATGCGTATCAAGTAAAATGCTATCACACG
1 ACGCCATGCATAACAAGTAAAATTTTGTGACA-GACATGCATATCAAGTAAAATGCTGTCACACG
*
29204378 TCATGCATATCAAGTAAAATGCTGTCA
65 TCATGCATAACAAGTAAAATGCTGTCA
29204405 CACGTTAATA
Statistics
Matches: 164, Mismatches: 19, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
93 162 0.99
94 2 0.01
ACGTcount: A:0.40, C:0.20, G:0.16, T:0.24
Consensus pattern (92 bp):
ACGCCATGCATAACAAGTAAAATTTTGTGACAGACATGCATATCAAGTAAAATGCTGTCACACGT
CATGCATAACAAGTAAAATGCTGTCAA
Found at i:29204408 original size:62 final size:62
Alignment explanation
Indices: 29204161--29204404 Score: 344
Period size: 62 Copynumber: 3.9 Consensus size: 62
29204151 TTGTGACACA
*
29204161 CCATGCATAACAAGTAAAATGTTGTGACACGTCATGCATAACAAGTAAAATGCTGTCAAACG
1 CCATGCATAACAAGTAAAATGTTGTCACACGTCATGCATAACAAGTAAAATGCTGTCAAACG
* * * * *
29204223 CCATGCATAACAAGTAAAATTTTGTGACATGACATGCATATCAAGTAAAATGCTGTCAAACG
1 CCATGCATAACAAGTAAAATGTTGTCACACGTCATGCATAACAAGTAAAATGCTGTCAAACG
* * * *
29204285 CCATGCATAACAAGTAAAATGTTGTCAAACGTCATGCATAACAAGTAAAATTCTGTGACACG
1 CCATGCATAACAAGTAAAATGTTGTCACACGTCATGCATAACAAGTAAAATGCTGTCAAACG
* * * * * *
29204347 ACATGCGTATCAAGTAAAATGCTATCACACGTCATGCATATCAAGTAAAATGCTGTCA
1 CCATGCATAACAAGTAAAATGTTGTCACACGTCATGCATAACAAGTAAAATGCTGTCA
29204405 CACGTTAATA
Statistics
Matches: 160, Mismatches: 22, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
62 160 1.00
ACGTcount: A:0.40, C:0.19, G:0.16, T:0.25
Consensus pattern (62 bp):
CCATGCATAACAAGTAAAATGTTGTCACACGTCATGCATAACAAGTAAAATGCTGTCAAACG
Found at i:29204409 original size:31 final size:31
Alignment explanation
Indices: 29204162--29204409 Score: 307
Period size: 31 Copynumber: 8.0 Consensus size: 31
29204152 TGTGACACAC
* *
29204162 CATGCATAACAAGTAAAATGTTGTGACACGT
1 CATGCATAACAAGTAAAATGCTGTCACACGT
* *
29204193 CATGCATAACAAGTAAAATGCTGTCAAACGC
1 CATGCATAACAAGTAAAATGCTGTCACACGT
** * * *
29204224 CATGCATAACAAGTAAAATTTTGTGACATGA
1 CATGCATAACAAGTAAAATGCTGTCACACGT
* * *
29204255 CATGCATATCAAGTAAAATGCTGTCAAACGC
1 CATGCATAACAAGTAAAATGCTGTCACACGT
* *
29204286 CATGCATAACAAGTAAAATGTTGTCAAACGT
1 CATGCATAACAAGTAAAATGCTGTCACACGT
* * *
29204317 CATGCATAACAAGTAAAATTCTGTGACACGA
1 CATGCATAACAAGTAAAATGCTGTCACACGT
* * *
29204348 CATGCGTATCAAGTAAAATGCTATCACACGT
1 CATGCATAACAAGTAAAATGCTGTCACACGT
*
29204379 CATGCATATCAAGTAAAATGCTGTCACACGT
1 CATGCATAACAAGTAAAATGCTGTCACACGT
29204410 TAATAACTAA
Statistics
Matches: 184, Mismatches: 33, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 184 1.00
ACGTcount: A:0.40, C:0.19, G:0.17, T:0.25
Consensus pattern (31 bp):
CATGCATAACAAGTAAAATGCTGTCACACGT
Found at i:29205055 original size:47 final size:47
Alignment explanation
Indices: 29204986--29205311 Score: 357
Period size: 47 Copynumber: 7.0 Consensus size: 47
29204976 CTAAACATGA
29204986 CCATGGCGTGTCACCAACTCTTAACTCTGGCGTGTCACAGATTCCCT
1 CCATGGCGTGTCACCAACTCTTAACTCTGGCGTGTCACAGATTCCCT
* * * * **
29205033 CCATGACGTGTCACCAACTCTTAACTTTGACGTCTCACAGATTCAAT
1 CCATGGCGTGTCACCAACTCTTAACTCTGGCGTGTCACAGATTCCCT
* * * * * **
29205080 CCGTGGCATCTCACCAACCCTAAAAGCTGGCGTGTCACAGATTCCCT
1 CCATGGCGTGTCACCAACTCTTAACTCTGGCGTGTCACAGATTCCCT
**
29205127 CCATACCGTGTCACCAACTCTTAA-TCTGGCGTGTCACAGATTCCCT
1 CCATGGCGTGTCACCAACTCTTAACTCTGGCGTGTCACAGATTCCCT
* * * * * * * *
29205173 CCATGGCGTCTCACCAACCCTGAACGCTGTCGTGTCACACATTCTCA
1 CCATGGCGTGTCACCAACTCTTAACTCTGGCGTGTCACAGATTCCCT
* * *
29205220 CCATGGCGTGTCACCAACTCTTAACTCTGACGTCTCATAGATTCCCT
1 CCATGGCGTGTCACCAACTCTTAACTCTGGCGTGTCACAGATTCCCT
* * * * * *
29205267 CCATGGCGTCTCACCAACTCTGAGCTGTGCCGTGTCACACATTCC
1 CCATGGCGTGTCACCAACTCTTAACTCTGGCGTGTCACAGATTCC
29205312 AACCATGACA
Statistics
Matches: 223, Mismatches: 55, Indels: 2
0.80 0.20 0.01
Matches are distributed among these distances:
46 40 0.18
47 183 0.82
ACGTcount: A:0.22, C:0.35, G:0.17, T:0.26
Consensus pattern (47 bp):
CCATGGCGTGTCACCAACTCTTAACTCTGGCGTGTCACAGATTCCCT
Found at i:29205118 original size:94 final size:94
Alignment explanation
Indices: 29204986--29205284 Score: 395
Period size: 94 Copynumber: 3.2 Consensus size: 94
29204976 CTAAACATGA
* * * **
29204986 CCATGGCGTGTCACCAACTCTTAACTCTGGCGTGTCACAGATTCCCTCCATGACGTGTCACCAAC
1 CCATGGCGTCTCACCAACCCTAAAAGCTGGCGTGTCACAGATTCCCTCCATGACGTGTCACCAAC
* **
29205051 TCTTAACTTTGACGTCTCACAGATTCAAT
66 TCTTAACTCTGACGTCTCACAGATTCCCT
* *
29205080 CCGTGGCATCTCACCAACCCTAAAAGCTGGCGTGTCACAGATTCCCTCCAT-ACCGTGTCACCAA
1 CCATGGCGTCTCACCAACCCTAAAAGCTGGCGTGTCACAGATTCCCTCCATGA-CGTGTCACCAA
* *
29205144 CTCTTAA-TCTGGCGTGTCACAGATTCCCT
65 CTCTTAACTCTGACGTCTCACAGATTCCCT
* * * * * * *
29205173 CCATGGCGTCTCACCAACCCTGAACGCTGTCGTGTCACACATTCTCACCATGGCGTGTCACCAAC
1 CCATGGCGTCTCACCAACCCTAAAAGCTGGCGTGTCACAGATTCCCTCCATGACGTGTCACCAAC
*
29205238 TCTTAACTCTGACGTCTCATAGATTCCCT
66 TCTTAACTCTGACGTCTCACAGATTCCCT
29205267 CCATGGCGTCTCACCAAC
1 CCATGGCGTCTCACCAAC
29205285 TCTGAGCTGT
Statistics
Matches: 178, Mismatches: 24, Indels: 6
0.86 0.12 0.03
Matches are distributed among these distances:
93 79 0.44
94 99 0.56
ACGTcount: A:0.22, C:0.35, G:0.16, T:0.26
Consensus pattern (94 bp):
CCATGGCGTCTCACCAACCCTAAAAGCTGGCGTGTCACAGATTCCCTCCATGACGTGTCACCAAC
TCTTAACTCTGACGTCTCACAGATTCCCT
Found at i:29205262 original size:140 final size:141
Alignment explanation
Indices: 29204992--29205320 Score: 365
Period size: 140 Copynumber: 2.3 Consensus size: 141
29204982 ATGACCATGG
* * *
29204992 CGTGTCACCAACTCTTAACTCTGGCGTGTCACAGATTCCCTCCATGACGTGTCACCAACTCTTAA
1 CGTGTCACCAACTCTTAACTCTGGCGTGTCACAGATTCCCTCCATGACGTCTCACCAACCCTGAA
** * * * *
29205057 CTTTGACGTCTCACAGATTCAATCCGTGGCATCTCACCAACCCTAAAAGCTGGCGTGTCACAGAT
66 CGCTGACGTCTCACACATTCAATCCATGGCATCTCACCAACCCTAAAAGCTGACGTCTCACAGAT
29205122 TCCCTCCATAC
131 TCCCTCCATAC
*
29205133 CGTGTCACCAACTCTTAA-TCTGGCGTGTCACAGATTCCCTCCATGGCGTCTCACCAACCCTGAA
1 CGTGTCACCAACTCTTAACTCTGGCGTGTCACAGATTCCCTCCATGACGTCTCACCAACCCTGAA
* * * * * * * ** *
29205197 CGCTGTCGTGTCACACATTCTCA-CCATGGCGTGTCACCAACTCTTAACTCTGACGTCTCATAGA
66 CGCTGACGTCTCACACATTC-AATCCATGGCATCTCACCAACCCTAAAAGCTGACGTCTCACAGA
**
29205261 TTCCCTCCATGG
130 TTCCCTCCATAC
* * * * * * **
29205273 CGTCTCACCAACTCTGAGCTGTGCCGTGTCACACATTCCAACCATGAC
1 CGTGTCACCAACTCTTAACTCTGGCGTGTCACAGATTCCCTCCATGAC
29205321 ATTTCACAAA
Statistics
Matches: 155, Mismatches: 31, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
140 113 0.73
141 42 0.27
ACGTcount: A:0.22, C:0.35, G:0.16, T:0.26
Consensus pattern (141 bp):
CGTGTCACCAACTCTTAACTCTGGCGTGTCACAGATTCCCTCCATGACGTCTCACCAACCCTGAA
CGCTGACGTCTCACACATTCAATCCATGGCATCTCACCAACCCTAAAAGCTGACGTCTCACAGAT
TCCCTCCATAC
Found at i:29210176 original size:25 final size:24
Alignment explanation
Indices: 29210147--29210224 Score: 69
Period size: 20 Copynumber: 3.4 Consensus size: 24
29210137 TTTTTTAATT
29210147 TTAATAATTTTGAATAATTTAAATA
1 TTAAT-ATTTTGAATAATTTAAATA
*
29210172 TTAATA-TTT---TAAGTTAAA-A
1 TTAATATTTTGAATAATTTAAATA
*
29210191 -NAATAATTTTGAATAATTTAAATA
1 TTAAT-ATTTTGAATAATTTAAATA
*
29210215 TTCATATTTT
1 TTAATATTTT
29210225 AAGTTAAAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 15
0.67 0.08 0.25
Matches are distributed among these distances:
18 3 0.07
19 2 0.05
20 11 0.27
23 11 0.27
24 7 0.17
25 7 0.17
ACGTcount: A:0.45, C:0.01, G:0.04, T:0.49
Consensus pattern (24 bp):
TTAATATTTTGAATAATTTAAATA
Found at i:29210198 original size:43 final size:42
Alignment explanation
Indices: 29210149--29210236 Score: 158
Period size: 43 Copynumber: 2.1 Consensus size: 42
29210139 TTTTAATTTT
29210149 AATAATTTTGAATAATTTAAATATTAATATTTTAAGTTAAAA
1 AATAATTTTGAATAATTTAAATATTAATATTTTAAGTTAAAA
*
29210191 NAATAATTTTGAATAATTTAAATATTCATATTTTAAGTTAAAA
1 -AATAATTTTGAATAATTTAAATATTAATATTTTAAGTTAAAA
29210234 AAT
1 AAT
29210237 TTTTAAAGTT
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
42 3 0.07
43 41 0.93
ACGTcount: A:0.49, C:0.01, G:0.05, T:0.44
Consensus pattern (42 bp):
AATAATTTTGAATAATTTAAATATTAATATTTTAAGTTAAAA
Found at i:29210249 original size:37 final size:41
Alignment explanation
Indices: 29210153--29210264 Score: 115
Period size: 43 Copynumber: 2.7 Consensus size: 41
29210143 AATTTTAATA
* *
29210153 ATTTTGAATAATTTAAATATTAATATTTTAAGTTAAAANAAT
1 ATTTT-AATAAGTTAAATATTAATATTTTAAGTTAAAAAAAT
* *
29210195 AATTTTGAATAATTTAAATATTCATATTTTAAGTT-AAAAAAT
1 -ATTTT-AATAAGTTAAATATTAATATTTTAAGTTAAAAAAAT
*
29210237 -TTTT-A-AAGTTAAATATTAAGTTTTTTAA
1 ATTTTAATAAGTTAAATATTAA-TATTTTAA
29210265 TATTTTAAAT
Statistics
Matches: 63, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
37 12 0.19
38 8 0.13
40 4 0.06
42 6 0.10
43 33 0.52
ACGTcount: A:0.46, C:0.01, G:0.05, T:0.47
Consensus pattern (41 bp):
ATTTTAATAAGTTAAATATTAATATTTTAAGTTAAAAAAAT
Found at i:29210255 original size:29 final size:29
Alignment explanation
Indices: 29210223--29210284 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
29210213 TATTCATATT
29210223 TTAAGTTAAAAAAT-TTTTAAAGTTAAATA
1 TTAAGTTAAAAAATATTTTAAA-TTAAATA
****
29210252 TTAAGTTTTTTAATATTTTAAATTAAATA
1 TTAAGTTAAAAAATATTTTAAATTAAATA
29210281 TTAA
1 TTAA
29210285 TATTCCTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 21 0.75
30 7 0.25
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.48
Consensus pattern (29 bp):
TTAAGTTAAAAAATATTTTAAATTAAATA
Found at i:29210299 original size:29 final size:29
Alignment explanation
Indices: 29210234--29210317 Score: 102
Period size: 29 Copynumber: 2.9 Consensus size: 29
29210224 TAAGTTAAAA
*
29210234 AATTTTTAAAGTTAAATATTAAGT-TT-TTT
1 AATTTTTAAA-TTAAATATTAA-TATTCCTT
29210263 AATATTTTAAATTAAATATTAATATTCCTT
1 AAT-TTTTAAATTAAATATTAATATTCCTT
*
29210293 AATTTTTAAA-CAAATATTAATATTC
1 AATTTTTAAATTAAATATTAATATTC
29210318 ATTGAACCTA
Statistics
Matches: 50, Mismatches: 2, Indels: 7
0.85 0.03 0.12
Matches are distributed among these distances:
28 15 0.30
29 23 0.46
30 12 0.24
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.50
Consensus pattern (29 bp):
AATTTTTAAATTAAATATTAATATTCCTT
Found at i:29210307 original size:28 final size:30
Alignment explanation
Indices: 29210261--29210317 Score: 91
Period size: 28 Copynumber: 2.0 Consensus size: 30
29210251 ATTAAGTTTT
*
29210261 TTAATATTTTAAATTAAATATTAATATTCC
1 TTAATATTTTAAATCAAATATTAATATTCC
29210291 TTAAT-TTTTAAA-CAAATATTAATATTC
1 TTAATATTTTAAATCAAATATTAATATTC
29210318 ATTGAACCTA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 14 0.54
29 7 0.27
30 5 0.19
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (30 bp):
TTAATATTTTAAATCAAATATTAATATTCC
Found at i:29216220 original size:17 final size:16
Alignment explanation
Indices: 29216180--29216210 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
29216170 TTTTATCCTA
29216180 AAATTTTTATTTTTTG
1 AAATTTTTATTTTTTG
29216196 AAATTTTTATTTTTT
1 AAATTTTTATTTTTT
29216211 TTATATTTTT
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:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (16 bp):
AAATTTTTATTTTTTG
Found at i:29216482 original size:87 final size:87
Alignment explanation
Indices: 29216271--29216487 Score: 251
Period size: 87 Copynumber: 2.5 Consensus size: 87
29216261 ATAATTATTA
** *
29216271 AAAATATTTAGTAATTAAAATTATAATACAATACTA-TATCTAATTAGTTAAAGGTGTACTACAA
1 AAAATATTTAGTAATTAAAATTATAATACAATACTATTATCTAGCTAGTTAAAGGTATACTACAA
* *
29216335 TATTGTTAATTAGAAATTATAT
66 TATTGTTAATTAGAAAGTATAC
* * * * *
29216357 ACAAAT-TTTAGTAACTATAATTATGATACAATACTATTATCTAGCTAGTTAAAGTTATACTATA
1 A-AAATATTTAGTAATTAAAATTATAATACAATACTATTATCTAGCTAGTTAAAGGTATACTACA
29216421 ATACTT-TTAATTAGAAAGTATAC
65 ATA-TTGTTAATTAGAAAGTATAC
* * * * * *
29216444 AAAATATCTAATAATTAGAAGTATAATATAATATTATTATCTAG
1 AAAATATTTAGTAATTAAAATTATAATACAATACTATTATCTAG
29216488 TAATACTGTT
Statistics
Matches: 109, Mismatches: 18, Indels: 7
0.81 0.13 0.05
Matches are distributed among these distances:
86 32 0.29
87 75 0.69
88 2 0.02
ACGTcount: A:0.46, C:0.07, G:0.08, T:0.39
Consensus pattern (87 bp):
AAAATATTTAGTAATTAAAATTATAATACAATACTATTATCTAGCTAGTTAAAGGTATACTACAA
TATTGTTAATTAGAAAGTATAC
Found at i:29218815 original size:63 final size:60
Alignment explanation
Indices: 29218698--29218826 Score: 136
Period size: 62 Copynumber: 2.1 Consensus size: 60
29218688 AACATCATCA
* * *
29218698 CCTACTCGTGGGAAACTGCCCACACCACTATTTATAAATCGGGGCTTCAATTCCCTCTTTTTG
1 CCTACTCGTGGGAAACTGCACACACCACTATATATAAATCGGAGCTTCAATTCCC-C--TTTG
* * * *
29218761 CCTACTCGTGGG-ATCTGCACACGCCA-TCATATATAAATCGGAGTTTCAGGTTCCCCTTTG
1 CCTACTCGTGGGAAACTGCACACACCACT-ATATATAAATCGGAGCTTCA-ATTCCCCTTTG
29218821 CCTACT
1 CCTACT
29218827 TGTGAGAACT
Statistics
Matches: 57, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
60 10 0.18
61 1 0.02
62 29 0.51
63 17 0.30
ACGTcount: A:0.22, C:0.30, G:0.17, T:0.31
Consensus pattern (60 bp):
CCTACTCGTGGGAAACTGCACACACCACTATATATAAATCGGAGCTTCAATTCCCCTTTG
Found at i:29218860 original size:60 final size:60
Alignment explanation
Indices: 29218791--29218943 Score: 164
Period size: 62 Copynumber: 2.5 Consensus size: 60
29218781 ACGCCATCAT
* * ** * *
29218791 ATATAAATCGGAGTTTCAGGTTCCCCTTTGCCTACTTGTGAGAACTGCCCACGTCACCCA
1 ATATGAATCGGGGTTTCAGGTTCCCCTTTGCCTACTCATGAGAACTGCCAACATCACCCA
* * *
29218851 ATATGAATCGGGGCTTT-AGGTCTCCCTTTTTACCTACTCATGGGAACTGCCAACATCACCCA
1 ATATGAATCGGGG-TTTCAGGT-TCCC-CTTTGCCTACTCATGAGAACTGCCAACATCACCCA
* * *
29218913 ATATGAATTGGGGCTTCAGGTCCCCCTTTGC
1 ATATGAATCGGGGTTTCAGGTTCCCCTTTGC
29218944 AATCAAATAT
Statistics
Matches: 75, Mismatches: 14, Indels: 8
0.77 0.14 0.08
Matches are distributed among these distances:
60 19 0.25
61 12 0.16
62 44 0.59
ACGTcount: A:0.22, C:0.29, G:0.20, T:0.29
Consensus pattern (60 bp):
ATATGAATCGGGGTTTCAGGTTCCCCTTTGCCTACTCATGAGAACTGCCAACATCACCCA
Found at i:29219222 original size:2 final size:2
Alignment explanation
Indices: 29219209--29219246 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
29219199 ATTTAAAAAC
* *
29219209 AT AT AG AT AT AT AT AT AT AT AT AT AT TT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29219247 TTTAAAGAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29219542 original size:69 final size:69
Alignment explanation
Indices: 29219469--29219613 Score: 236
Period size: 69 Copynumber: 2.1 Consensus size: 69
29219459 TTTTTCTTTA
* * *
29219469 TTCTCCTCTACCGCTGCTCATTCTCTCATTCTTCTTCTTTTTCTTTCTCTTCTTTCTTCCTTCTC
1 TTCTCCTCTACCGCTGCTCACTCTCTCATTCTTCTTCTCTTTCTTTCTCTTCTTTCTTCCCTCTC
29219534 CTTC
66 CTTC
* * *
29219538 TTCTCCTCTGCCGCTGCTCCCTCTCTCTTTCTTCTTCTCTTTCTTTCTCTTCTTTCTTCCCTCTC
1 TTCTCCTCTACCGCTGCTCACTCTCTCATTCTTCTTCTCTTTCTTTCTCTTCTTTCTTCCCTCTC
29219603 CTTC
66 CTTC
29219607 TTCTCCT
1 TTCTCCT
29219614 AGTCGTTGTG
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
69 70 1.00
ACGTcount: A:0.02, C:0.41, G:0.03, T:0.54
Consensus pattern (69 bp):
TTCTCCTCTACCGCTGCTCACTCTCTCATTCTTCTTCTCTTTCTTTCTCTTCTTTCTTCCCTCTC
CTTC
Found at i:29220106 original size:21 final size:21
Alignment explanation
Indices: 29220076--29220123 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
29220066 TATTTTTGTA
29220076 CATGACGTGTAACAACCTAAC
1 CATGACGTGTAACAACCTAAC
* *
29220097 CATGATGTGTAACAAGCTAAC
1 CATGACGTGTAACAACCTAAC
29220118 CATGAC
1 CATGAC
29220124 TTGTCACATA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.21
Consensus pattern (21 bp):
CATGACGTGTAACAACCTAAC
Found at i:29220110 original size:66 final size:65
Alignment explanation
Indices: 29219973--29220176 Score: 272
Period size: 66 Copynumber: 3.1 Consensus size: 65
29219963 CAACATGGCA
* * *
29219973 TGTAACAATCTAACCATAGCTTGTCACATGTTTTTGTACAT-AGATGTAACAACCTAACCATGGC
1 TGTAACAAGCTAACCATAGCTTGTCACATATTTTTGTACATGAG-TGTAACAACCTAACCATGAC
29220037 G
65 G
* * *
29220038 TGTAACAAGCTAATCATAGTTTGTCACATATTTTTGTACATGACGTGTAACAACCTAACCATGAT
1 TGTAACAAGCTAACCATAGCTTGTCACATATTTTTGTACATGA-GTGTAACAACCTAACCATGAC
29220103 G
65 G
29220104 TGTAACAAGCTAACCAT-GACTTGTCACATATTTTTGTACATG-GTGTATAACAACCTAACCAT-
1 TGTAACAAGCTAACCATAG-CTTGTCACATATTTTTGTACATGAGTG--TAACAACCTAACCATG
29220166 AGCG
63 A-CG
29220170 TGTAACA
1 TGTAACA
29220177 TGTTTTTGTA
Statistics
Matches: 124, Mismatches: 9, Indels: 11
0.86 0.06 0.08
Matches are distributed among these distances:
64 3 0.02
65 39 0.31
66 81 0.65
67 1 0.01
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.31
Consensus pattern (65 bp):
TGTAACAAGCTAACCATAGCTTGTCACATATTTTTGTACATGAGTGTAACAACCTAACCATGACG
Found at i:29220156 original size:45 final size:45
Alignment explanation
Indices: 29220097--29220200 Score: 138
Period size: 45 Copynumber: 2.3 Consensus size: 45
29220087 ACAACCTAAC
* * *
29220097 CATGATGTGTAACAAGCTAACCAT-GACTTGTCACATATTTTTGTA
1 CATGATGTGTAACAACCTAACCATAG-CGTGTAACATATTTTTGTA
* * *
29220142 CATGGTGTATAACAACCTAACCATAGCGTGTAACATGTTTTTGTA
1 CATGATGTGTAACAACCTAACCATAGCGTGTAACATATTTTTGTA
29220187 CATGATGTGTAACA
1 CATGATGTGTAACA
29220201 TCATAGCGTG
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
45 49 0.98
46 1 0.02
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (45 bp):
CATGATGTGTAACAACCTAACCATAGCGTGTAACATATTTTTGTA
Found at i:29220748 original size:61 final size:62
Alignment explanation
Indices: 29220650--29220776 Score: 159
Period size: 61 Copynumber: 2.1 Consensus size: 62
29220640 CGTTTAAGTA
* * *
29220650 TTTTGAGCATTTTGGAGTAATTTTTTGAAACACGAAG-AAAAGCATTTAAGCGTTTTGAGCAT
1 TTTTAAGCATTTTGAAGTAATTTTTTGAAACACGAAGAAAAAGC-TTTAAGCATTTTGAGCAT
* * * * *
29220712 TTTTAAGCATTTTGAAGTGA-TTTTTGATACATGAAGAAAAATCTTTAAGCATTTTGAGTAT
1 TTTTAAGCATTTTGAAGTAATTTTTTGAAACACGAAGAAAAAGCTTTAAGCATTTTGAGCAT
29220773 TTTT
1 TTTT
29220777 CGTCAAGTAG
Statistics
Matches: 56, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
61 34 0.61
62 22 0.39
ACGTcount: A:0.32, C:0.08, G:0.18, T:0.42
Consensus pattern (62 bp):
TTTTAAGCATTTTGAAGTAATTTTTTGAAACACGAAGAAAAAGCTTTAAGCATTTTGAGCAT
Found at i:29220988 original size:22 final size:22
Alignment explanation
Indices: 29220963--29221119 Score: 127
Period size: 22 Copynumber: 7.1 Consensus size: 22
29220953 ACATGGCTAA
*
29220963 TTTTTAAGCATTGCGTGACTAG
1 TTTTTAAGCATTACGTGACTAG
*
29220985 TTTTTAAGTATTACGTGACTAG
1 TTTTTAAGCATTACGTGACTAG
* *
29221007 TTTTTAAGCATTATGTGACTAA
1 TTTTTAAGCATTACGTGACTAG
* *
29221029 TTTTTAAGTATTACATGACT-G
1 TTTTTAAGCATTACGTGACTAG
** *
29221050 ATTGATATGACATTACGTGACTAG
1 -TTTTTAAG-CATTACGTGACTAG
** * * *
29221074 TTGATAGGTATTGCGTGACTAG
1 TTTTTAAGCATTACGTGACTAG
** * *
29221096 TTGATAGGCATTGCGTGACTAG
1 TTTTTAAGCATTACGTGACTAG
29221118 TT
1 TT
29221120 AGTAAGGAAT
Statistics
Matches: 114, Mismatches: 18, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
22 96 0.84
23 17 0.15
24 1 0.01
ACGTcount: A:0.27, C:0.11, G:0.22, T:0.41
Consensus pattern (22 bp):
TTTTTAAGCATTACGTGACTAG
Found at i:29220989 original size:44 final size:44
Alignment explanation
Indices: 29220919--29221048 Score: 161
Period size: 44 Copynumber: 2.9 Consensus size: 44
29220909 TGTGTGACAG
* * ** *
29220919 TTTTAAGGCATTGCTTTACTAATTTTTGGGTATTACATGGCTAAT
1 TTTTAA-GCATTGCGTGACTAATTTTTAAGTATTACATGACTAAT
* * *
29220964 TTTTAAGCATTGCGTGACTAGTTTTTAAGTATTACGTGACTAGT
1 TTTTAAGCATTGCGTGACTAATTTTTAAGTATTACATGACTAAT
**
29221008 TTTTAAGCATTATGTGACTAATTTTTAAGTATTACATGACT
1 TTTTAAGCATTGCGTGACTAATTTTTAAGTATTACATGACT
29221049 GATTGATATG
Statistics
Matches: 73, Mismatches: 12, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
44 67 0.92
45 6 0.08
ACGTcount: A:0.27, C:0.11, G:0.17, T:0.45
Consensus pattern (44 bp):
TTTTAAGCATTGCGTGACTAATTTTTAAGTATTACATGACTAAT
Found at i:29221094 original size:89 final size:88
Alignment explanation
Indices: 29220936--29221097 Score: 207
Period size: 89 Copynumber: 1.8 Consensus size: 88
29220926 GCATTGCTTT
** * ** * **
29220936 ACTAATTTTTGGGTATTACATGGCTAATTTTTAAGCATTGCGTGACTAGTTTTTAAGTATTACGT
1 ACTAATTTTTAAGTATTACATGACTAATTGATAAGCATTACGTGACTAGTTGATAAGTATTACGT
29221001 GACTAGTTTTTAAGCATTATGTG
66 GACTAGTTTTTAAGCATTATGTG
* * * *
29221024 ACTAATTTTTAAGTATTACATGACTGATTGATATGACATTACGTGACTAGTTGATAGGTATTGCG
1 ACTAATTTTTAAGTATTACATGACTAATTGATAAG-CATTACGTGACTAGTTGATAAGTATTACG
29221089 TGACTAGTT
65 TGACTAGTT
29221098 GATAGGCATT
Statistics
Matches: 61, Mismatches: 12, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
88 28 0.46
89 33 0.54
ACGTcount: A:0.28, C:0.10, G:0.20, T:0.42
Consensus pattern (88 bp):
ACTAATTTTTAAGTATTACATGACTAATTGATAAGCATTACGTGACTAGTTGATAAGTATTACGT
GACTAGTTTTTAAGCATTATGTG
Found at i:29221107 original size:89 final size:88
Alignment explanation
Indices: 29220936--29221116 Score: 200
Period size: 89 Copynumber: 2.0 Consensus size: 88
29220926 GCATTGCTTT
** * ** * **
29220936 ACTAATTTTTGGGTATTACATGGCTAATTTTTAAGCATTGCGTGACTAGTTTTTAAGTATTACGT
1 ACTAATTTTTAAGTATTACATGACTAATTGATAAGCATTACGTGACTAGTTGATAAGTATTACGT
** *
29221001 GACTAGTTTTTAAGCATTATGTG
66 GACTAGTTGATAAGCATTACGTG
* * * *
29221024 ACTAATTTTTAAGTATTACATGACTGATTGATATGACATTACGTGACTAGTTGATAGGTATTGCG
1 ACTAATTTTTAAGTATTACATGACTAATTGATAAG-CATTACGTGACTAGTTGATAAGTATTACG
* *
29221089 TGACTAGTTGATAGGCATTGCGTG
65 TGACTAGTTGATAAGCATTACGTG
29221113 ACTA
1 ACTA
29221117 GTTAGTAAGG
Statistics
Matches: 75, Mismatches: 17, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
88 28 0.37
89 47 0.63
ACGTcount: A:0.28, C:0.11, G:0.21, T:0.40
Consensus pattern (88 bp):
ACTAATTTTTAAGTATTACATGACTAATTGATAAGCATTACGTGACTAGTTGATAAGTATTACGT
GACTAGTTGATAAGCATTACGTG
Found at i:29221132 original size:45 final size:45
Alignment explanation
Indices: 29221051--29221139 Score: 119
Period size: 45 Copynumber: 2.0 Consensus size: 45
29221041 ACATGACTGA
*
29221051 TTGATATGACATTACGTGACTAGTTGATAGGTATTGCGTGACTAG
1 TTGATATGACATTACGTGACTAGTTGATAGGAATTGCGTGACTAG
* *
29221096 TTGATA-GGCATTGCGTGACTAGTT-AGTAAGGAATTGCGTGACTA
1 TTGATATGACATTACGTGACTAGTTGA-T-AGGAATTGCGTGACTA
29221140 TTTGCGTGAA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
43 1 0.03
44 17 0.44
45 21 0.54
ACGTcount: A:0.27, C:0.11, G:0.28, T:0.34
Consensus pattern (45 bp):
TTGATATGACATTACGTGACTAGTTGATAGGAATTGCGTGACTAG
Found at i:29221135 original size:23 final size:22
Alignment explanation
Indices: 29221051--29221139 Score: 108
Period size: 22 Copynumber: 4.0 Consensus size: 22
29221041 ACATGACTGA
* *
29221051 TTGATATGACATTACGTGACTAG
1 TTGATAGGA-ATTGCGTGACTAG
*
29221074 TTGATAGGTATTGCGTGACTAG
1 TTGATAGGAATTGCGTGACTAG
*
29221096 TTGATAGGCATTGCGTGACTAG
1 TTGATAGGAATTGCGTGACTAG
29221118 TT-AGTAAGGAATTGCGTGACTA
1 TTGA-T-AGGAATTGCGTGACTA
29221140 TTTGCGTGAA
Statistics
Matches: 59, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
21 1 0.02
22 36 0.61
23 22 0.37
ACGTcount: A:0.27, C:0.11, G:0.28, T:0.34
Consensus pattern (22 bp):
TTGATAGGAATTGCGTGACTAG
Found at i:29221234 original size:21 final size:22
Alignment explanation
Indices: 29221184--29221268 Score: 73
Period size: 22 Copynumber: 3.9 Consensus size: 22
29221174 AAGCATTGCT
* * * *
29221184 TAAAAATCAGTCACACAATGTC
1 TAAAAACCAATCACGCAATGCC
29221206 TAAAAACCAATCACGCAATGCC
1 TAAAAACCAATCACGCAATGCC
* * * * *
29221228 T-AAAACCAGTCATGTAATACA
1 TAAAAACCAATCACGCAATGCC
*
29221249 TAAAAACCAATCATGCAATG
1 TAAAAACCAATCACGCAATG
29221269 ATTAAGTCAC
Statistics
Matches: 50, Mismatches: 12, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
21 16 0.32
22 34 0.68
ACGTcount: A:0.47, C:0.24, G:0.09, T:0.20
Consensus pattern (22 bp):
TAAAAACCAATCACGCAATGCC
Found at i:29225215 original size:20 final size:20
Alignment explanation
Indices: 29225192--29225229 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
29225182 ATAATATTTA
29225192 ATATTAAATTATAATTATGT
1 ATATTAAATTATAATTATGT
* *
29225212 ATATTAATTTATATTTAT
1 ATATTAAATTATAATTAT
29225230 AAAATTTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (20 bp):
ATATTAAATTATAATTATGT
Found at i:29227992 original size:45 final size:44
Alignment explanation
Indices: 29227943--29228041 Score: 114
Period size: 44 Copynumber: 2.2 Consensus size: 44
29227933 TTTTTTCTTT
* *
29227943 TTTTCTCTTATTATATTTTTCAGAA-AATAAAA-TGTATTTTATAAA
1 TTTTCTATT-TTATATTTTTCA-AAGAATAAAACTATATTTT-TAAA
* *
29227988 TTTTCTATTTTTTATTTTTCAAAGTATAAAACTATATTTTTAAA
1 TTTTCTATTTTATATTTTTCAAAGAATAAAACTATATTTTTAAA
29228032 TTTT-TATTTT
1 TTTTCTATTTT
29228042 TAAAATAAAC
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
43 8 0.17
44 25 0.52
45 15 0.31
ACGTcount: A:0.33, C:0.06, G:0.03, T:0.58
Consensus pattern (44 bp):
TTTTCTATTTTATATTTTTCAAAGAATAAAACTATATTTTTAAA
Found at i:29228007 original size:44 final size:43
Alignment explanation
Indices: 29227956--29228042 Score: 115
Period size: 44 Copynumber: 2.0 Consensus size: 43
29227946 TCTCTTATTA
*
29227956 TATTTTTCAGAA-AATAAAA-TGTATTTTATAAATTTTCTATTTTT
1 TATTTTTCA-AAGAATAAAACTATATTTT-TAAATTTT-TATTTTT
*
29228000 TATTTTTCAAAGTATAAAACTATATTTTTAAATTTTTATTTTT
1 TATTTTTCAAAGAATAAAACTATATTTTTAAATTTTTATTTTT
29228043 AAAATAAACA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
43 9 0.23
44 23 0.59
45 7 0.18
ACGTcount: A:0.36, C:0.05, G:0.03, T:0.56
Consensus pattern (43 bp):
TATTTTTCAAAGAATAAAACTATATTTTTAAATTTTTATTTTT
Found at i:29236324 original size:2 final size:2
Alignment explanation
Indices: 29236312--29236354 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
29236302 GTAAACACAA
*
29236312 AG AG AG TG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
29236354 A
1 A
29236355 ACCAAACCAG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.49, T:0.02
Consensus pattern (2 bp):
AG
Found at i:29237886 original size:28 final size:28
Alignment explanation
Indices: 29237852--29237928 Score: 77
Period size: 27 Copynumber: 2.7 Consensus size: 28
29237842 TCACTTTGAA
*
29237852 AAATTTTT-AAGAATTAAAAAT-ACTTTT
1 AAATTTTTGAA-AAATAAAAATAACTTTT
*
29237879 AAATTTTTGAAAAATAAAAATAATTTTT
1 AAATTTTTGAAAAATAAAAATAACTTTT
* *
29237907 TAATTTTTAGAAATTATAAAAA
1 AAATTTTT-GAAA-AATAAAAA
29237929 ATAAAAAATA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
27 17 0.40
28 14 0.33
29 4 0.10
30 7 0.17
ACGTcount: A:0.52, C:0.01, G:0.04, T:0.43
Consensus pattern (28 bp):
AAATTTTTGAAAAATAAAAATAACTTTT
Found at i:29237952 original size:6 final size:7
Alignment explanation
Indices: 29237922--29237949 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
29237912 TTTAGAAATT
29237922 ATAAAAA
1 ATAAAAA
29237929 ATAAAAA
1 ATAAAAA
29237936 ATAAAAA
1 ATAAAAA
29237943 ATAAAAA
1 ATAAAAA
29237950 TAATTCCTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (7 bp):
ATAAAAA
Found at i:29237975 original size:50 final size:52
Alignment explanation
Indices: 29237888--29237986 Score: 139
Period size: 51 Copynumber: 1.9 Consensus size: 52
29237878 TAAATTTTTG
** * * *
29237888 AAAAATAAAAATAATTTTTTAATTTTTAGAAATTATAAAA-AATAAAAAATA
1 AAAAATAAAAATAATTTCCTAATTATTAAAAAATATAAAATAATAAAAAATA
29237939 AAAAATAAAAATAA-TTCCTAATTATTAAAAAATATAAAATAATAAAAA
1 AAAAATAAAAATAATTTCCTAATTATTAAAAAATATAAAATAATAAAAA
29237987 TAGAAATAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
50 20 0.48
51 22 0.52
ACGTcount: A:0.66, C:0.02, G:0.01, T:0.31
Consensus pattern (52 bp):
AAAAATAAAAATAATTTCCTAATTATTAAAAAATATAAAATAATAAAAAATA
Found at i:29237976 original size:43 final size:42
Alignment explanation
Indices: 29237919--29238032 Score: 115
Period size: 43 Copynumber: 2.6 Consensus size: 42
29237909 ATTTTTAGAA
29237919 ATTATAAAAA-ATAAAAAATAAAAAATAAAAATAATTCCTAATT
1 ATTA-AAAAATATAAAAAATAAAAAATAAAAATAATT-CTAATT
* * *
29237962 ATTAAAAAATATAAAATAAT-AAAAATAGAAATAATTTTTATT
1 ATTAAAAAATATAAAA-AATAAAAAATAAAAATAATTCTAATT
* *
29238004 TTTAAGAAATTATAAAAAGATTAAAAAAT
1 ATTAA-AAAATATAAAAA-A-TAAAAAAT
29238033 CCATAAAATA
Statistics
Matches: 60, Mismatches: 5, Indels: 10
0.80 0.07 0.13
Matches are distributed among these distances:
42 14 0.23
43 36 0.60
44 4 0.07
45 6 0.10
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.32
Consensus pattern (42 bp):
ATTAAAAAATATAAAAAATAAAAAATAAAAATAATTCTAATT
Found at i:29242803 original size:91 final size:91
Alignment explanation
Indices: 29242646--29242827 Score: 310
Period size: 91 Copynumber: 2.0 Consensus size: 91
29242636 TATTGACCAG
* * *
29242646 CTGCTCGGGTCTAAACCAGAGGGGAAGGAAAGAAAGCATTGACCATCCAGGCCTGTTGTTTGATG
1 CTGCTCGGGTCTAAACCAGAGGGGAAGGAAAGAAAACATTGACCATCCAAGCCTGTTGTTTCATG
29242711 TCATATGCAATGGGCTTCAATGACAA
66 TCATATGCAATGGGCTTCAATGACAA
* *
29242737 CTGCTCGGGTCTCAATCAGAGGGGAAGGAAAGAAAACATTGACCATCCAAGCCTGTTGTTTCATG
1 CTGCTCGGGTCTAAACCAGAGGGGAAGGAAAGAAAACATTGACCATCCAAGCCTGTTGTTTCATG
*
29242802 TCATATGCAGTGGGCTTCAATGACAA
66 TCATATGCAATGGGCTTCAATGACAA
29242828 TTATGGAAGA
Statistics
Matches: 85, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
91 85 1.00
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.24
Consensus pattern (91 bp):
CTGCTCGGGTCTAAACCAGAGGGGAAGGAAAGAAAACATTGACCATCCAAGCCTGTTGTTTCATG
TCATATGCAATGGGCTTCAATGACAA
Found at i:29244715 original size:3 final size:3
Alignment explanation
Indices: 29244707--29244737 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
29244697 GACAAATTGC
29244707 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
29244738 CCCACGATGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:29248673 original size:18 final size:17
Alignment explanation
Indices: 29248633--29248678 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
29248623 TTTTGTATTT
*
29248633 TCTTAATCATTTTTTTA
1 TCTTAATTATTTTTTTA
29248650 TCTTAATTATTTTCTTTA
1 TCTTAATTATTTT-TTTA
*
29248668 TTTTAA-TATTT
1 TCTTAATTATTT
29248679 GACCGAATGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
17 17 0.65
18 9 0.35
ACGTcount: A:0.24, C:0.09, G:0.00, T:0.67
Consensus pattern (17 bp):
TCTTAATTATTTTTTTA
Found at i:29256891 original size:26 final size:26
Alignment explanation
Indices: 29256862--29257013 Score: 155
Period size: 26 Copynumber: 5.9 Consensus size: 26
29256852 TTACGGTATT
29256862 CATCCACTTCTGGTGGTAAAATTATC
1 CATCCACTTCTGGTGGTAAAATTATC
* * * *
29256888 CATCTACTTTTGGTGGCAAAATCATC
1 CATCCACTTCTGGTGGTAAAATTATC
*
29256914 CATCCACTTCTGGTGGCAAAATTATC
1 CATCCACTTCTGGTGGTAAAATTATC
* ** * ** *
29256940 CTTAGA-TACTAATAGTAAAATTATC
1 CATCCACTTCTGGTGGTAAAATTATC
* *
29256965 GATCCACTTCTGATGGTAAAATTAT-
1 CATCCACTTCTGGTGGTAAAATTATC
*
29256990 TATCCACTTCTGGTGGTAAAATTA
1 CATCCACTTCTGGTGGTAAAATTA
29257014 GAATTAAAAT
Statistics
Matches: 101, Mismatches: 24, Indels: 3
0.79 0.19 0.02
Matches are distributed among these distances:
25 38 0.38
26 63 0.62
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.35
Consensus pattern (26 bp):
CATCCACTTCTGGTGGTAAAATTATC
Found at i:29257009 original size:51 final size:52
Alignment explanation
Indices: 29256862--29257013 Score: 148
Period size: 51 Copynumber: 3.0 Consensus size: 52
29256852 TTACGGTATT
* * * * *
29256862 CATCCACTTCTGGTGGTAAAATTATCCATCTACTTTTGGTGGCAAAATCATC
1 CATCCACTTCTGGTGGTAAAATTATCTATCCACTTCTGGTGGTAAAATTATC
* ** * ** *
29256914 CATCCACTTCTGGTGGCAAAATTATCCT-TAGA-TACTAATAGTAAAATTATC
1 CATCCACTTCTGGTGGTAAAATTAT-CTATCCACTTCTGGTGGTAAAATTATC
* *
29256965 GATCCACTTCTGATGGTAAAATTAT-TATCCACTTCTGGTGGTAAAATTA
1 CATCCACTTCTGGTGGTAAAATTATCTATCCACTTCTGGTGGTAAAATTA
29257014 GAATTAAAAT
Statistics
Matches: 77, Mismatches: 20, Indels: 7
0.74 0.19 0.07
Matches are distributed among these distances:
49 1 0.01
50 2 0.03
51 47 0.61
52 26 0.34
53 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.35
Consensus pattern (52 bp):
CATCCACTTCTGGTGGTAAAATTATCTATCCACTTCTGGTGGTAAAATTATC
Found at i:29257031 original size:77 final size:77
Alignment explanation
Indices: 29256877--29257041 Score: 179
Period size: 77 Copynumber: 2.1 Consensus size: 77
29256867 ACTTCTGGTG
* * * ***
29256877 GTAAAATTATCCATCTACTTTTGGTGGCAAAATCATCCATCCACTTCTGGTGGCAAAATTATCCT
1 GTAAAATTATCCATCCACTTCTGATGGCAAAATCATCCATCCACTTCTGGTGGCAAAATTAGAAT
*
29256942 TAGATACTAATA
66 TAAATACTAATA
* * * * *
29256954 GTAAAATTATCGATCCACTTCTGATGGTAAAATTAT-TATCCACTTCTGGTGGTAAAATTAGAAT
1 GTAAAATTATCCATCCACTTCTGATGGCAAAATCATCCATCCACTTCTGGTGGCAAAATTAGAAT
*
29257018 TAAAATAGTAATA
66 T-AAATACTAATA
*
29257031 GTGTAAATTAT
1 GT-AAAATTAT
29257042 TATAACCACT
Statistics
Matches: 72, Mismatches: 14, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
76 24 0.33
77 41 0.57
78 7 0.10
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35
Consensus pattern (77 bp):
GTAAAATTATCCATCCACTTCTGATGGCAAAATCATCCATCCACTTCTGGTGGCAAAATTAGAAT
TAAATACTAATA
Found at i:29258290 original size:16 final size:16
Alignment explanation
Indices: 29258261--29258299 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
29258251 TCTCTTTTAT
*
29258261 ACACACACAAATACAA
1 ACACATACAAATACAA
* *
29258277 ACACATACACATACAT
1 ACACATACAAATACAA
29258293 ACACATA
1 ACACATA
29258300 TATAAAAATG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.56, C:0.31, G:0.00, T:0.13
Consensus pattern (16 bp):
ACACATACAAATACAA
Found at i:29261273 original size:30 final size:30
Alignment explanation
Indices: 29261248--29261307 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
29261238 TCTTACTCTC
29261248 CACACATGTCTAGCATAAAGCCTTACTAGA
1 CACACATGTCTAGCATAAAGCCTTACTAGA
29261278 CACACATGTCTAGCATAAAGCCTTACTAGA
1 CACACATGTCTAGCATAAAGCCTTACTAGA
29261308 TAGGCATCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.37, C:0.27, G:0.13, T:0.23
Consensus pattern (30 bp):
CACACATGTCTAGCATAAAGCCTTACTAGA
Found at i:29261476 original size:118 final size:118
Alignment explanation
Indices: 29261337--29261590 Score: 280
Period size: 118 Copynumber: 2.2 Consensus size: 118
29261327 TTATCCCCAC
* * ** * * * * *
29261337 CACACATGTTTGGCACCAAACCTTGTTAGCTAAGCTCAAGCATGTGTCTTGCTTC-AGCATACAT
1 CACACATGTCTAGCACCAAACCTTCATAGATAAGCTAAAGCATGTGTCTTAC-TCAAGCACAAAT
* ** * *
29261401 GTGCAACA-CGATA-CCTCTTGCTAGATAGGGATAACAAACATGTGTTTCATTGAG
65 GTCCAACATC-ATAGCCT-TTGCTAGATAGGGATAACAAACAACTGTCTCATCGAG
* * *
29261455 CACACATGTCTAGCACCAAACCTTCATAGATAGGTTAAAGCATGTGTTTTACTCAAGCACAAATG
1 CACACATGTCTAGCACCAAACCTTCATAGATAAGCTAAAGCATGTGTCTTACTCAAGCACAAATG
* *
29261520 TCCACCATCATAGCCTTTGCTAGATAGGGATAACAAGCAACTGTCTCATCGAG
66 TCCAACATCATAGCCTTTGCTAGATAGGGATAACAAACAACTGTCTCATCGAG
*
29261573 CACACATGTCTAACACCA
1 CACACATGTCTAGCACCA
29261591 TGGCTTCTGC
Statistics
Matches: 113, Mismatches: 20, Indels: 6
0.81 0.14 0.04
Matches are distributed among these distances:
117 2 0.02
118 107 0.95
119 4 0.04
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.26
Consensus pattern (118 bp):
CACACATGTCTAGCACCAAACCTTCATAGATAAGCTAAAGCATGTGTCTTACTCAAGCACAAATG
TCCAACATCATAGCCTTTGCTAGATAGGGATAACAAACAACTGTCTCATCGAG
Found at i:29263759 original size:21 final size:21
Alignment explanation
Indices: 29263700--29263761 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 21
29263690 TTTTTGTGTT
* *
29263700 TAAAGTTTG-TATTTTTGCAAG
1 TAAAG-TTGATATTTTTGTAAC
* *
29263721 TAAACTTGATCTTTTTGTAAC
1 TAAAGTTGATATTTTTGTAAC
29263742 TAAAGTTGATATTTTTGTAA
1 TAAAGTTGATATTTTTGTAA
29263762 TTGGTTTGTA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
20 3 0.09
21 31 0.91
ACGTcount: A:0.31, C:0.06, G:0.15, T:0.48
Consensus pattern (21 bp):
TAAAGTTGATATTTTTGTAAC
Found at i:29264101 original size:45 final size:45
Alignment explanation
Indices: 29264046--29264178 Score: 131
Period size: 45 Copynumber: 3.0 Consensus size: 45
29264036 AATTACACGC
* * *
29264046 TATGATGTTACACGTCATGTACAAAAATATATTACACGTCATGAT
1 TATGTTGTTACACGTCATGTACAAAAACATATGACACGTCATGAT
* * * * *
29264091 TATGTTGTTACACTTCATGTGCAAAAACATGTGACACGTTATGGT
1 TATGTTGTTACACGTCATGTACAAAAACATATGACACGTCATGAT
* ** * * * *
29264136 TAGGTTGTTACACACCATGTATAGAAACATGTGACACGCCATG
1 TATGTTGTTACACGTCATGTACAAAAACATATGACACGTCATG
29264179 TACAAAAACA
Statistics
Matches: 72, Mismatches: 16, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
45 72 1.00
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Consensus pattern (45 bp):
TATGTTGTTACACGTCATGTACAAAAACATATGACACGTCATGAT
Found at i:29264172 original size:24 final size:24
Alignment explanation
Indices: 29264145--29264264 Score: 77
Period size: 24 Copynumber: 5.1 Consensus size: 24
29264135 TTAGGTTGTT
* *
29264145 ACACACCATGTATAGAAACATGTG
1 ACACACCATGTACAAAAACATGTG
*
29264169 ACACGCCATGTACAAAAACATGTG
1 ACACACCATGTACAAAAACATGTG
** * *** *
29264193 ACATGCCATGGT----TAGGTTGTT
1 ACACACCAT-GTACAAAAACATGTG
* * *
29264214 AAACACCATGTACAGAAACATATG
1 ACACACCATGTACAAAAACATGTG
*
29264238 ACACGCCATGTACAAAAACATGTG
1 ACACACCATGTACAAAAACATGTG
29264262 ACA
1 ACA
29264265 TGCCATGGTT
Statistics
Matches: 69, Mismatches: 22, Indels: 10
0.68 0.22 0.10
Matches are distributed among these distances:
20 2 0.03
21 10 0.14
24 55 0.80
25 2 0.03
ACGTcount: A:0.40, C:0.22, G:0.17, T:0.21
Consensus pattern (24 bp):
ACACACCATGTACAAAAACATGTG
Found at i:29264187 original size:69 final size:69
Alignment explanation
Indices: 29264106--29264373 Score: 405
Period size: 69 Copynumber: 3.9 Consensus size: 69
29264096 TGTTACACTT
* ** * * *
29264106 CATGTGCAAAAACATGTGACACGTTATGGTTAGGTTGTTACACACCATGTATAGAAACATGTGAC
1 CATGTACAAAAACATGTGACACGCCATGGTTAGGTTGTTAAACACCATGTACAGAAACATATGAC
29264171 ACGC
66 ACGC
*
29264175 CATGTACAAAAACATGTGACATGCCATGGTTAGGTTGTTAAACACCATGTACAGAAACATATGAC
1 CATGTACAAAAACATGTGACACGCCATGGTTAGGTTGTTAAACACCATGTACAGAAACATATGAC
29264240 ACGC
66 ACGC
*
29264244 CATGTACAAAAACATGTGACATGCCATGGTTAGGTTGTTAAACACCATGTACAGAAACATATGAC
1 CATGTACAAAAACATGTGACACGCCATGGTTAGGTTGTTAAACACCATGTACAGAAACATATGAC
*
29264309 ACGT
66 ACGC
* * * *
29264313 CATGTACAAAAACATGTAACACGTCATGGTTAGGTTGTTACACGCCATGTACA-AAA-ATATG
1 CATGTACAAAAACATGTGACACGCCATGGTTAGGTTGTTAAACACCATGTACAGAAACATATG
29264374 TTACATGTCA
Statistics
Matches: 186, Mismatches: 13, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
67 5 0.03
68 3 0.02
69 178 0.96
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (69 bp):
CATGTACAAAAACATGTGACACGCCATGGTTAGGTTGTTAAACACCATGTACAGAAACATATGAC
ACGC
Found at i:29264269 original size:24 final size:24
Alignment explanation
Indices: 29264219--29264271 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
29264209 TTGTTAAACA
*
29264219 CCATGTACAGAAACATATGACACG
1 CCATGTACAAAAACATATGACACG
* *
29264243 CCATGTACAAAAACATGTGACATG
1 CCATGTACAAAAACATATGACACG
29264267 CCATG
1 CCATG
29264272 GTTAGGTTGT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.40, C:0.25, G:0.17, T:0.19
Consensus pattern (24 bp):
CCATGTACAAAAACATATGACACG
Found at i:29264292 original size:114 final size:114
Alignment explanation
Indices: 29264174--29264544 Score: 378
Period size: 114 Copynumber: 3.3 Consensus size: 114
29264164 ATGTGACACG
* *
29264174 CCATGTACAAAAACATGTGACATGCCATGGTTAGGTTGTTAAACACCATGTACAGAAACATATGA
1 CCATGTACAAAAACATATGACACGCCATGGTTAGGTTGTTAAACACCATGTACAGAAACATATGA
29264239 CACGCCATGTACAAAAACATGTGACATGCCATGGTTAGGTTGTTAAACA
66 CACGCCATGTACAAAAACATGTGACATGCCATGGTTAGGTTGTTAAACA
* * * *** *
29264288 CCATGTACAGAAACATATGACACGTCAT-GTACAAAAACATG-T-AACACGTCATGGT-TAG---
1 CCATGTACAAAAACATATGACACGCCATGGT----TAGGTTGTTAAACAC--CAT-GTACAGAAA
** * * * * * * * *
29264346 GTTGTTACACGCCATGTACAAAAATATGTTACATGTCATGATTAGGTTGTTAGACG
59 CATATGACACGCCATGTACAAAAACATGTGACATGCCATGGTTAGGTTGTTAAACA
* * *
29264402 CCATGTGCAAAAACATATGACACGCCATGGTTAGGTTGTTACACACAATGTACAGAAACATATGA
1 CCATGTACAAAAACATATGACACGCCATGGTTAGGTTGTTAAACACCATGTACAGAAACATATGA
* **
29264467 CACGCAATGTACAAAAACATGTGACATGCCATGGTTAGGTTGTTGCACA
66 CACGCCATGTACAAAAACATGTGACATGCCATGGTTAGGTTGTTAAACA
* * *
29264516 CCATGTACAGAAACATGTGACACGTCATG
1 CCATGTACAAAAACATATGACACGCCATG
29264545 CACAAAAACA
Statistics
Matches: 198, Mismatches: 45, Indels: 28
0.73 0.17 0.10
Matches are distributed among these distances:
110 2 0.01
111 7 0.04
112 1 0.01
113 6 0.03
114 164 0.83
115 7 0.04
116 1 0.01
117 8 0.04
118 2 0.01
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.25
Consensus pattern (114 bp):
CCATGTACAAAAACATATGACACGCCATGGTTAGGTTGTTAAACACCATGTACAGAAACATATGA
CACGCCATGTACAAAAACATGTGACATGCCATGGTTAGGTTGTTAAACA
Found at i:29264316 original size:24 final size:24
Alignment explanation
Indices: 29264289--29264340 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
29264279 TGTTAAACAC
* *
29264289 CATGTACAGAAACATATGACACGT
1 CATGTACAAAAACATATAACACGT
*
29264313 CATGTACAAAAACATGTAACACGT
1 CATGTACAAAAACATATAACACGT
29264337 CATG
1 CATG
29264341 GTTAGGTTGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.42, C:0.21, G:0.15, T:0.21
Consensus pattern (24 bp):
CATGTACAAAAACATATAACACGT
Found at i:29264458 original size:228 final size:228
Alignment explanation
Indices: 29264171--29264588 Score: 692
Period size: 228 Copynumber: 1.8 Consensus size: 228
29264161 AACATGTGAC
* * *
29264171 ACGCCATGTACAAAAACATGTGACATGCCATGGTTAGGTTGTTAAACACCATGTACAGAAACATA
1 ACGCCATGTACAAAAACATATGACACGCCATGGTTAGGTTGTTAAACACAATGTACAGAAACATA
*
29264236 TGACACGCCATGTACAAAAACATGTGACATGCCATGGTTAGGTTGTTAAACACCATGTACAGAAA
66 TGACACGCAATGTACAAAAACATGTGACATGCCATGGTTAGGTTGTTAAACACCATGTACAGAAA
* * * *
29264301 CATATGACACGTCATGTACAAAAACATGTAACACGTCATGGTTAGGTTGTTACACGCCATGTACA
131 CATATGACACGTCATGCACAAAAACATGTAACACGCCATAGTTAGATTGTTACACGCCATGTACA
29264366 AAAATATGTTACATGTCATGATTAGGTTGTTAG
196 AAAATATGTTACATGTCATGATTAGGTTGTTAG
* *
29264399 ACGCCATGTGCAAAAACATATGACACGCCATGGTTAGGTTGTTACACACAATGTACAGAAACATA
1 ACGCCATGTACAAAAACATATGACACGCCATGGTTAGGTTGTTAAACACAATGTACAGAAACATA
**
29264464 TGACACGCAATGTACAAAAACATGTGACATGCCATGGTTAGGTTGTTGCACACCATGTACAGAAA
66 TGACACGCAATGTACAAAAACATGTGACATGCCATGGTTAGGTTGTTAAACACCATGTACAGAAA
* ** *
29264529 CATGTGACACGTCATGCACAAAAACATGTGGCATGCCATAGTTAGATTGTTACACGCCAT
131 CATATGACACGTCATGCACAAAAACATGTAACACGCCATAGTTAGATTGTTACACGCCAT
29264589 ATTGAAAAAA
Statistics
Matches: 174, Mismatches: 16, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
228 174 1.00
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.25
Consensus pattern (228 bp):
ACGCCATGTACAAAAACATATGACACGCCATGGTTAGGTTGTTAAACACAATGTACAGAAACATA
TGACACGCAATGTACAAAAACATGTGACATGCCATGGTTAGGTTGTTAAACACCATGTACAGAAA
CATATGACACGTCATGCACAAAAACATGTAACACGCCATAGTTAGATTGTTACACGCCATGTACA
AAAATATGTTACATGTCATGATTAGGTTGTTAG
Found at i:29264463 original size:45 final size:45
Alignment explanation
Indices: 29264307--29264471 Score: 195
Period size: 45 Copynumber: 3.7 Consensus size: 45
29264297 GAAACATATG
* * * *
29264307 ACACGTCATGTACAAAAACATGTAACACGTCATGGTTAGGTTGTT
1 ACACGCCATGTACAAAAACATATGACACGCCATGGTTAGGTTGTT
* * * * * *
29264352 ACACGCCATGTACAAAAATATGTTACATGTCATGATTAGGTTGTT
1 ACACGCCATGTACAAAAACATATGACACGCCATGGTTAGGTTGTT
* *
29264397 AGACGCCATGTGCAAAAACATATGACACGCCATGGTTAGGTTGTT
1 ACACGCCATGTACAAAAACATATGACACGCCATGGTTAGGTTGTT
* * *
29264442 ACACACAATGTACAGAAACATATGACACGC
1 ACACGCCATGTACAAAAACATATGACACGC
29264472 AATGTACAAA
Statistics
Matches: 102, Mismatches: 18, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 102 1.00
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.26
Consensus pattern (45 bp):
ACACGCCATGTACAAAAACATATGACACGCCATGGTTAGGTTGTT
Found at i:29264469 original size:24 final size:24
Alignment explanation
Indices: 29264442--29264492 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
29264432 TTAGGTTGTT
*
29264442 ACACACAATGTACAGAAACATATG
1 ACACACAATGTACAAAAACATATG
* *
29264466 ACACGCAATGTACAAAAACATGTG
1 ACACACAATGTACAAAAACATATG
29264490 ACA
1 ACA
29264493 TGCCATGGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.49, C:0.22, G:0.14, T:0.16
Consensus pattern (24 bp):
ACACACAATGTACAAAAACATATG
Found at i:29264484 original size:69 final size:68
Alignment explanation
Indices: 29264403--29264583 Score: 254
Period size: 69 Copynumber: 2.6 Consensus size: 68
29264393 TGTTAGACGC
* * *
29264403 CATGTGCAAAAACATATGACACGCCATGGTTAGGTTGTTACACACAATGTACAGAAACATATGAC
1 CATGTACAAAAACATGTGACATGCCATGGTTAGGTTGTTACACACAATGTACAGAAACATATGAC
29264468 ACG
66 ACG
* * *
29264471 CAATGTACAAAAACATGTGACATGCCATGGTTAGGTTGTTGCACACCATGTACAGAAACATGTGA
1 C-ATGTACAAAAACATGTGACATGCCATGGTTAGGTTGTTACACACAATGTACAGAAACATATGA
29264536 CACG
65 CACG
* * * *
29264540 TCATGCACAAAAACATGTGGCATGCCATAGTTAGATTGTTACAC
1 -CATGTACAAAAACATGTGACATGCCATGGTTAGGTTGTTACAC
29264584 GCCATATTGA
Statistics
Matches: 100, Mismatches: 11, Indels: 3
0.88 0.10 0.03
Matches are distributed among these distances:
68 1 0.01
69 98 0.98
70 1 0.01
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.24
Consensus pattern (68 bp):
CATGTACAAAAACATGTGACATGCCATGGTTAGGTTGTTACACACAATGTACAGAAACATATGAC
ACG
Found at i:29264486 original size:159 final size:159
Alignment explanation
Indices: 29264240--29264544 Score: 468
Period size: 159 Copynumber: 1.9 Consensus size: 159
29264230 AACATATGAC
* * *
29264240 ACGCCATGTACAAAAACATGTGACATGCCATGGTTAGGTTGTTAAACACCATGTACAGAAACATA
1 ACGCCATGTACAAAAACATATGACACGCCATGGTTAGGTTGTTAAACACAATGTACAGAAACATA
* *
29264305 TGACACGTCATGTACAAAAACATGTAACACGTCATGGTTAGGTTGTTACACGCCATGTACAAAAA
66 TGACACGTCATGTACAAAAACATGTAACACGCCATGGTTAGGTTGTTACACACCATGTACAAAAA
* * *
29264370 TATGTTACATGTCATGATTAGGTTGTTAG
131 CATGTGACACGTCATGATTAGGTTGTTAG
* *
29264399 ACGCCATGTGCAAAAACATATGACACGCCATGGTTAGGTTGTTACACACAATGTACAGAAACATA
1 ACGCCATGTACAAAAACATATGACACGCCATGGTTAGGTTGTTAAACACAATGTACAGAAACATA
* * * *
29264464 TGACACG-CAATGTACAAAAACATGTGACATGCCATGGTTAGGTTGTTGCACACCATGTACAGAA
66 TGACACGTC-ATGTACAAAAACATGTAACACGCCATGGTTAGGTTGTTACACACCATGTACAAAA
29264528 ACATGTGACACGTCATG
130 ACATGTGACACGTCATG
29264545 CACAAAAACA
Statistics
Matches: 131, Mismatches: 14, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
158 1 0.01
159 130 0.99
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.25
Consensus pattern (159 bp):
ACGCCATGTACAAAAACATATGACACGCCATGGTTAGGTTGTTAAACACAATGTACAGAAACATA
TGACACGTCATGTACAAAAACATGTAACACGCCATGGTTAGGTTGTTACACACCATGTACAAAAA
CATGTGACACGTCATGATTAGGTTGTTAG
Found at i:29264610 original size:30 final size:29
Alignment explanation
Indices: 29264574--29264723 Score: 129
Period size: 30 Copynumber: 5.3 Consensus size: 29
29264564 CCATAGTTAG
*
29264574 ATTGTTACACGCCATATTGAAAAAAATACT
1 ATTGTTACACGCCATGTTGAAAAAAATA-T
*
29264604 ATTGTTACACGCCATG-T--ACAAAA-AT
1 ATTGTTACACGCCATGTTGAAAAAAATAT
*
29264629 A-TGTTACACGCCATGGTT---AAAAA-AG
1 ATTGTTACACGCCAT-GTTGAAAAAAATAT
* *
29264654 GTTGTTACATGCCATGTTGAAAAAAAATACT
1 ATTGTTACACGCCATGTTG-AAAAAAATA-T
* *
29264685 GTTGTTACACGTCATGTTGAAAAAAATATT
1 ATTGTTACACGCCATGTTGAAAAAAATA-T
29264715 ATTGTTACA
1 ATTGTTACA
29264724 TATCATATTC
Statistics
Matches: 100, Mismatches: 11, Indels: 18
0.78 0.09 0.14
Matches are distributed among these distances:
24 13 0.13
25 11 0.11
26 14 0.14
27 5 0.05
29 6 0.06
30 34 0.34
31 17 0.17
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.31
Consensus pattern (29 bp):
ATTGTTACACGCCATGTTGAAAAAAATAT
Found at i:29264659 original size:26 final size:23
Alignment explanation
Indices: 29264604--29264678 Score: 80
Period size: 26 Copynumber: 3.0 Consensus size: 23
29264594 AAAAAATACT
29264604 ATTGTTACACGCCATG-TACAAAA
1 ATTGTTACACGCCATGTTA-AAAA
29264627 ATATGTTACACGCCATGGTTAAAAA
1 AT-TGTTACACGCCAT-GTTAAAAA
*
29264652 AGGTTGTTACATGCCATGTTGAAAAA
1 A--TTGTTACACGCCATGTT-AAAAA
29264678 A
1 A
29264679 AATACTGTTG
Statistics
Matches: 45, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
23 2 0.04
24 13 0.29
25 9 0.20
26 20 0.44
27 1 0.02
ACGTcount: A:0.39, C:0.16, G:0.17, T:0.28
Consensus pattern (23 bp):
ATTGTTACACGCCATGTTAAAAA
Found at i:29264738 original size:30 final size:30
Alignment explanation
Indices: 29264674--29264738 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 30
29264664 GCCATGTTGA
* * * *
29264674 AAAAAAATACTGTTGTTACACGTCATGTTG
1 AAAAAAATACTATTGTTACACATCATATTC
* *
29264704 AAAAAAATATTATTGTTACATATCATATTC
1 AAAAAAATACTATTGTTACACATCATATTC
29264734 AAAAA
1 AAAAA
29264739 CATTTTGTTA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.46, C:0.11, G:0.09, T:0.34
Consensus pattern (30 bp):
AAAAAAATACTATTGTTACACATCATATTC
Found at i:29277661 original size:49 final size:49
Alignment explanation
Indices: 29277589--29277683 Score: 154
Period size: 49 Copynumber: 1.9 Consensus size: 49
29277579 ATGGGGCTTT
* *
29277589 TTATAATAGCTAACTAAACCTAAACTTACTTGGTGTGCAAGTAAAGTAC
1 TTATAATAGCCAACTAAACCTAAACCTACTTGGTGTGCAAGTAAAGTAC
* *
29277638 TTATAATAGCCAATTCAACCTAAACCTACTTGGTGTGCAAGTAAAG
1 TTATAATAGCCAACTAAACCTAAACCTACTTGGTGTGCAAGTAAAG
29277684 AAAATAGTAA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
49 42 1.00
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.29
Consensus pattern (49 bp):
TTATAATAGCCAACTAAACCTAAACCTACTTGGTGTGCAAGTAAAGTAC
Found at i:29281955 original size:2 final size:2
Alignment explanation
Indices: 29281948--29281980 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
29281938 ATTAATGATG
29281948 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
29281981 CACAATATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:29287916 original size:20 final size:20
Alignment explanation
Indices: 29287874--29287920 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
29287864 CCAAACTAAT
** *
29287874 TATATATATAATATTTTTTA
1 TATATATATAATATACTTAA
*
29287894 TATATATNTAATATACTTAA
1 TATATATATAATATACTTAA
29287914 TATATAT
1 TATATAT
29287921 TAGGGCATTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.53
Consensus pattern (20 bp):
TATATATATAATATACTTAA
Found at i:29288384 original size:21 final size:23
Alignment explanation
Indices: 29288358--29288405 Score: 75
Period size: 22 Copynumber: 2.2 Consensus size: 23
29288348 TAATTACACT
29288358 TAATAA-GTTTAT-TATAAATTA
1 TAATAATGTTTATATATAAATTA
29288379 TAATAATGTTTATATATAAATTA
1 TAATAATGTTTATATATAAATTA
29288402 -AATA
1 TAATA
29288406 TATATAATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
21 6 0.24
22 10 0.40
23 9 0.36
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (23 bp):
TAATAATGTTTATATATAAATTA
Found at i:29288686 original size:16 final size:16
Alignment explanation
Indices: 29288665--29288698 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
29288655 CTAATATATT
*
29288665 TTAAGTATATTATTAA
1 TTAAGTATATTATCAA
*
29288681 TTAAGTTTATTATCAA
1 TTAAGTATATTATCAA
29288697 TT
1 TT
29288699 CTTCTTAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.03, G:0.06, T:0.53
Consensus pattern (16 bp):
TTAAGTATATTATCAA
Found at i:29294419 original size:45 final size:45
Alignment explanation
Indices: 29294370--29294459 Score: 135
Period size: 45 Copynumber: 2.0 Consensus size: 45
29294360 GTACCTAGAA
29294370 GTTTTGCAAAATATACTTGGAGGTTTTAAAAATGATTACCCAAAG
1 GTTTTGCAAAATATACTTGGAGGTTTTAAAAATGATTACCCAAAG
* * * * *
29294415 GTTTTGGAGAATATACTTGGAGGTTTTTAGAATGATTACTCAAAG
1 GTTTTGCAAAATATACTTGGAGGTTTTAAAAATGATTACCCAAAG
29294460 TATTTAAAGA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.34, C:0.09, G:0.21, T:0.36
Consensus pattern (45 bp):
GTTTTGCAAAATATACTTGGAGGTTTTAAAAATGATTACCCAAAG
Found at i:29294454 original size:23 final size:23
Alignment explanation
Indices: 29294383--29294454 Score: 58
Period size: 23 Copynumber: 3.2 Consensus size: 23
29294373 TTGCAAAATA
*
29294383 TACTTGGAGGTTTTAAAAATGAT
1 TACTTGGAGGTTTTAAGAATGAT
**** *
29294406 TACCCAAAGGTTTTGGAGAAT-A-
1 TACTTGGAGGTTTT-AAGAATGAT
*
29294428 TACTTGGAGGTTTTTAGAATGAT
1 TACTTGGAGGTTTTAAGAATGAT
29294451 TACT
1 TACT
29294455 CAAAGTATTT
Statistics
Matches: 35, Mismatches: 11, Indels: 6
0.67 0.21 0.12
Matches are distributed among these distances:
21 5 0.14
22 11 0.31
23 15 0.43
24 4 0.11
ACGTcount: A:0.32, C:0.08, G:0.22, T:0.38
Consensus pattern (23 bp):
TACTTGGAGGTTTTAAGAATGAT
Found at i:29294471 original size:45 final size:45
Alignment explanation
Indices: 29294379--29294489 Score: 127
Period size: 45 Copynumber: 2.5 Consensus size: 45
29294369 AGTTTTGCAA
**
29294379 AATATACTTGGAGGTTTTAAAAATGATTACCCAAAGGTTTTGGAG
1 AATATACTTGGAGGTTTTAAAAATGATTACCCAAAGGTTTTAAAG
* * *
29294424 AATATACTTGGAGGTTTTTAGAATGATTACTCAAA-GTATTTAAAG
1 AATATACTTGGAGGTTTTAAAAATGATTACCCAAAGGT-TTTAAAG
* *
29294469 AATGTA-TCCGGAGGTTTTAAA
1 AATATACT-TGGAGGTTTTAAA
29294490 GAGTGTTCTT
Statistics
Matches: 55, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
44 3 0.05
45 52 0.95
ACGTcount: A:0.36, C:0.08, G:0.21, T:0.35
Consensus pattern (45 bp):
AATATACTTGGAGGTTTTAAAAATGATTACCCAAAGGTTTTAAAG
Found at i:29294489 original size:22 final size:22
Alignment explanation
Indices: 29294462--29294508 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
29294452 ACTCAAAGTA
29294462 TTTAAAGAATGTATC-CGGAGGT
1 TTTAAAGAATGT-TCTCGGAGGT
* *
29294484 TTTAAAGAGTGTTCTTGGAGGT
1 TTTAAAGAATGTTCTCGGAGGT
29294506 TTT
1 TTT
29294509 GTAAGAAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 2 0.09
22 20 0.91
ACGTcount: A:0.26, C:0.06, G:0.28, T:0.40
Consensus pattern (22 bp):
TTTAAAGAATGTTCTCGGAGGT
Found at i:29294620 original size:23 final size:23
Alignment explanation
Indices: 29294572--29294621 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
29294562 ATCTTCAAGA
*
29294572 TTACCTAGAAGGTTTAAAGATAG
1 TTACCTAGAAGGATTAAAGATAG
*
29294595 TTACCTAGAA-GATTAAATGATGG
1 TTACCTAGAAGGATTAAA-GATAG
29294618 TTAC
1 TTAC
29294622 TTTGATGTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 6 0.25
23 18 0.75
ACGTcount: A:0.38, C:0.10, G:0.20, T:0.32
Consensus pattern (23 bp):
TTACCTAGAAGGATTAAAGATAG
Found at i:29299565 original size:24 final size:24
Alignment explanation
Indices: 29299514--29299574 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
29299504 AAAATAATTT
* *
29299514 CTACACGCCATGTTTAAAATTTTG
1 CTACACGCCATGTTTAAAATGTTC
* *
29299538 CTACACGTCATGTTTACAATGTTC
1 CTACACGCCATGTTTAAAATGTTC
*
29299562 CTACTCGCCATGT
1 CTACACGCCATGT
29299575 ACAGACAAAT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.25, C:0.26, G:0.13, T:0.36
Consensus pattern (24 bp):
CTACACGCCATGTTTAAAATGTTC
Found at i:29299620 original size:27 final size:27
Alignment explanation
Indices: 29299590--29299648 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 27
29299580 CAAATTTTAC
* *
29299590 TACATGTCATATTCAAAAAAATGTTGA
1 TACACGTCATATACAAAAAAATGTTGA
* * *
29299617 TACACGTCATGTACAAAAATATGTTGT
1 TACACGTCATATACAAAAAAATGTTGA
29299644 TACAC
1 TACAC
29299649 ACCATGCCAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.41, C:0.15, G:0.12, T:0.32
Consensus pattern (27 bp):
TACACGTCATATACAAAAAAATGTTGA
Found at i:29299654 original size:27 final size:27
Alignment explanation
Indices: 29299603--29299654 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
29299593 ATGTCATATT
**
29299603 CAAAAAAATGTTGATACACGTCATGTA
1 CAAAAAAATGTTGATACACACCATGTA
* *
29299630 CAAAAATATGTTGTTACACACCATG
1 CAAAAAAATGTTGATACACACCATG
29299655 CCATATTCAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.42, C:0.17, G:0.13, T:0.27
Consensus pattern (27 bp):
CAAAAAAATGTTGATACACACCATGTA
Found at i:29302369 original size:21 final size:22
Alignment explanation
Indices: 29302345--29302385 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
29302335 AAACAACAGA
*
29302345 AATCC-GTAAAAGAAAGAAAAT
1 AATCCTGTAAAAAAAAGAAAAT
*
29302366 AATCCTTTAAAAAAAAGAAA
1 AATCCTGTAAAAAAAAGAAA
29302386 GAAATGAACA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.63, C:0.10, G:0.10, T:0.17
Consensus pattern (22 bp):
AATCCTGTAAAAAAAAGAAAAT
Found at i:29302734 original size:33 final size:33
Alignment explanation
Indices: 29302694--29302756 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
29302684 TGACGTTGAC
* *
29302694 ATGATATGTTAACATATCATAATTGATGATAAT
1 ATGATATGCTAACATATCATAATTAATGATAAT
*
29302727 ATGATATGCTAATATATCATAATTAATGAT
1 ATGATATGCTAACATATCATAATTAATGAT
29302757 GACGTAACAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.43, C:0.06, G:0.11, T:0.40
Consensus pattern (33 bp):
ATGATATGCTAACATATCATAATTAATGATAAT
Found at i:29315392 original size:121 final size:121
Alignment explanation
Indices: 29315257--29315589 Score: 395
Period size: 121 Copynumber: 2.8 Consensus size: 121
29315247 CAACCCAAAT
* * **
29315257 ATTATATCATACAAATCTTAAACCTAAAGCACTAAACCAAGAAATATGAATATAAGCCTGCTATT
1 ATTATATCATACAAATCTTAAACCTAAAACACTAAACCAAGAAATATGAAAATAAGCCTAATATT
* *
29315322 CAACATCTAGAAACAAAAAAGCAAAACCCAATCAAGAAATATATGAACATGAACAA
66 CAACATCTAGAAACAAAAAAGCAAAACCCAACCAAAAAATATATGAACATGAACAA
* * * *
29315378 ATTATATCATACAAATCATAAACCTAAAACGCTAAACCAAGAAATATGAACATGAA-CCTAATAC
1 ATTATATCATACAAATCTTAAACCTAAAACACTAAACCAAGAAATATGAAAAT-AAGCCTAATAT
* * * * *
29315442 TCAACATATAGAAACACAAAAGCAATATCCAACCAAAAAATATATGAACATGAAGAA
65 TCAACATCTAGAAACAAAAAAGCAAAACCCAACCAAAAAATATATGAACATGAACAA
* * * * *
29315499 ATTATATCATACAAAT-TATAAACC-AAAACCCCCAAGCCAACAAATATCAAAATAAGCCTAATA
1 ATTATATCATACAAATCT-TAAACCTAAAA-CACTAAACCAAGAAATATGAAAATAAGCCTAATA
* * *
29315562 TTTAACATCCAGAAGCATAAAAA-CAAAA
64 TTCAACATCTAGAAACA-AAAAAGCAAAA
29315590 TAAATAAAAG
Statistics
Matches: 179, Mismatches: 28, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
120 6 0.03
121 167 0.93
122 6 0.03
ACGTcount: A:0.53, C:0.20, G:0.07, T:0.20
Consensus pattern (121 bp):
ATTATATCATACAAATCTTAAACCTAAAACACTAAACCAAGAAATATGAAAATAAGCCTAATATT
CAACATCTAGAAACAAAAAAGCAAAACCCAACCAAAAAATATATGAACATGAACAA
Found at i:29316839 original size:112 final size:111
Alignment explanation
Indices: 29316695--29316972 Score: 337
Period size: 112 Copynumber: 2.5 Consensus size: 111
29316685 AAAATTCCGA
* * *
29316695 CAAACCCTCTAATTGAATGACAATAGTCATTCAATGATTGGCTAATTAAAGCCAATAACCAAAGT
1 CAAACCCTCTAATTGAATGACAATTGTCATTCAATGATTGGCCAATTAAAGCCAATAACCAAAGC
*
29316760 AATTAAAATGACATCATTTTTATAGACTAAAAGGAAAA-AAATTTTGG
66 AATCAAAATGACATCATTTTTATAGACT-AAA-GAAAATAAATTTTGG
* ** * * *
29316807 CAGACTTTTTAATTGAATGACAATTGTCATTCAATGATTGACCAATTGAAA-CCAAAAACCAAAG
1 CAAACCCTCTAATTGAATGACAATTGTCATTCAATGATTGGCCAATT-AAAGCCAATAACCAAAG
* * * ***
29316871 CAATCAAAATGACATTATTTTTATAGAGTTAAGAAAATTTTTTTTGG
65 CAATCAAAATGACATCATTTTTATAGACTAAAGAAAATAAATTTTGG
* * *
29316918 CAAACCCTCCAATTGAATGACAATTGT-ATTCAATGATTGGCCAATTGAAGTCAAT
1 CAAACCCTCTAATTGAATGACAATTGTCATTCAATGATTGGCCAATTAAAGCCAAT
29316973 TGAAACAGTA
Statistics
Matches: 138, Mismatches: 25, Indels: 8
0.81 0.15 0.05
Matches are distributed among these distances:
109 2 0.01
110 26 0.19
111 30 0.22
112 77 0.56
113 3 0.02
ACGTcount: A:0.41, C:0.15, G:0.13, T:0.31
Consensus pattern (111 bp):
CAAACCCTCTAATTGAATGACAATTGTCATTCAATGATTGGCCAATTAAAGCCAATAACCAAAGC
AATCAAAATGACATCATTTTTATAGACTAAAGAAAATAAATTTTGG
Found at i:29320938 original size:21 final size:21
Alignment explanation
Indices: 29320914--29320981 Score: 75
Period size: 21 Copynumber: 3.1 Consensus size: 21
29320904 TTTTTTGAAG
*
29320914 TTTATTCTTATTTTATTATTT
1 TTTATTATTATTTTATTATTT
*
29320935 TTTATTATTATTGTATT-TTT
1 TTTATTATTATTTTATTATTT
*
29320955 TTTCATTATATCTATTTATTATTT
1 TTT-ATTAT-TAT-TTTATTATTT
29320979 TTT
1 TTT
29320982 TATTTTTGAC
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
20 6 0.15
21 20 0.51
22 2 0.05
23 5 0.13
24 6 0.15
ACGTcount: A:0.21, C:0.04, G:0.01, T:0.74
Consensus pattern (21 bp):
TTTATTATTATTTTATTATTT
Found at i:29320963 original size:24 final size:24
Alignment explanation
Indices: 29320925--29320981 Score: 70
Period size: 24 Copynumber: 2.5 Consensus size: 24
29320915 TTATTCTTAT
29320925 TTTATTATTTTTT-A-T-TAT-TA
1 TTTATTATTTTTTCATTATATCTA
29320945 TTGTATT-TTTTTTCATTATATCTA
1 TT-TATTATTTTTTCATTATATCTA
29320969 TTTATTATTTTTT
1 TTTATTATTTTTT
29320982 TATTTTTGAC
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
20 8 0.26
21 5 0.16
22 1 0.03
23 7 0.23
24 10 0.32
ACGTcount: A:0.21, C:0.04, G:0.02, T:0.74
Consensus pattern (24 bp):
TTTATTATTTTTTCATTATATCTA
Found at i:29320970 original size:19 final size:18
Alignment explanation
Indices: 29320930--29320988 Score: 54
Period size: 18 Copynumber: 3.4 Consensus size: 18
29320920 CTTATTTTAT
*
29320930 TATTTTTTATTATTATTG
1 TATTTTTTATTATTATTC
29320948 TATTTTTT-TTCATTATATC
1 TATTTTTTATT-ATTAT-TC
*
29320967 TATTTATTATT-TT-TT-
1 TATTTTTTATTATTATTC
29320982 TATTTTT
1 TATTTTT
29320989 GACTAAATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
15 6 0.17
16 1 0.03
17 3 0.09
18 15 0.43
19 8 0.23
20 2 0.06
ACGTcount: A:0.20, C:0.03, G:0.02, T:0.75
Consensus pattern (18 bp):
TATTTTTTATTATTATTC
Found at i:29321339 original size:3 final size:3
Alignment explanation
Indices: 29321331--29321367 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
29321321 TAACTTATAA
29321331 ATT ATT ATT ATT ATT ATT ATT ATT ATT -TT ATT -TT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
29321368 TATATATTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 4 0.12
3 28 0.88
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
ATT
Found at i:29321369 original size:9 final size:10
Alignment explanation
Indices: 29321331--29321375 Score: 51
Period size: 9 Copynumber: 4.6 Consensus size: 10
29321321 TAACTTATAA
29321331 ATTATTA-TT
1 ATTATTATTT
29321340 ATTATTA-TT
1 ATTATTATTT
29321349 ATTATTATTTT
1 ATTATTA-TTT
29321360 ATT-TTATTT
1 ATTATTATTT
29321369 ATATATT
1 AT-TATT
29321376 TGTTTTCCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
9 21 0.66
10 4 0.12
11 7 0.22
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (10 bp):
ATTATTATTT
Found at i:29322117 original size:87 final size:87
Alignment explanation
Indices: 29321995--29322159 Score: 276
Period size: 87 Copynumber: 1.9 Consensus size: 87
29321985 TCGTCGGCCT
* *
29321995 TTCTTCCCCTTTTTGACTTCGCAGCCGCCGACCACCCCAAAGAAATCGATCTCCCTCTTTCACTC
1 TTCTTCCCCTTTTTGACTTCGCAACCGCCGACCACCCCAAAGAAACCGATCTCCCTCTTTCACTC
*
29322060 ACTCTTCTCTTACTGACGACCC
66 ACTATTCTCTTACTGACGACCC
* * *
29322082 TTCTTCCCCTTTTTGACTTTGCAACCGTCGGCCACCCCAAAGAAACCGATCTCCCTCTTTCACTC
1 TTCTTCCCCTTTTTGACTTCGCAACCGCCGACCACCCCAAAGAAACCGATCTCCCTCTTTCACTC
29322147 ACTATTCTCTTAC
66 ACTATTCTCTTAC
29322160 CGGCGGCTCA
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
87 72 1.00
ACGTcount: A:0.19, C:0.40, G:0.10, T:0.32
Consensus pattern (87 bp):
TTCTTCCCCTTTTTGACTTCGCAACCGCCGACCACCCCAAAGAAACCGATCTCCCTCTTTCACTC
ACTATTCTCTTACTGACGACCC
Found at i:29326327 original size:34 final size:34
Alignment explanation
Indices: 29326281--29326348 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 34
29326271 TTGCTTCTGG
*
29326281 TTTGTGAGTGATTT-CGTGCTGTTTTGTGAGAGAT
1 TTTGTGAGTGATTTAC-TGCTGGTTTGTGAGAGAT
* *
29326315 TTTGTGATTGATTTACTGCTGGTTTGTGGGAGAT
1 TTTGTGAGTGATTTACTGCTGGTTTGTGAGAGAT
29326349 GATAGTGTTC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
34 29 0.97
35 1 0.03
ACGTcount: A:0.15, C:0.06, G:0.32, T:0.47
Consensus pattern (34 bp):
TTTGTGAGTGATTTACTGCTGGTTTGTGAGAGAT
Found at i:29328464 original size:15 final size:15
Alignment explanation
Indices: 29328440--29328473 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
29328430 TGTTAATATT
29328440 TAAA-TATTTTTTAA
1 TAAATTATTTTTTAA
*
29328454 TAAATTATTTTTTGA
1 TAAATTATTTTTTAA
29328469 TAAAT
1 TAAAT
29328474 CACGTTTACT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 4 0.22
15 14 0.78
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (15 bp):
TAAATTATTTTTTAA
Found at i:29331395 original size:6 final size:6
Alignment explanation
Indices: 29331386--29331412 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
29331376 GGTATATATA
29331386 TATGTT TATGTT TATGTT TATGTT TAT
1 TATGTT TATGTT TATGTT TATGTT TAT
29331413 CTCAATTCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.15, T:0.67
Consensus pattern (6 bp):
TATGTT
Found at i:29332195 original size:5 final size:5
Alignment explanation
Indices: 29332185--29332217 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
29332175 TTAAGGTATT
29332185 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTT
29332218 ATTGATCTCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTA
Found at i:29338607 original size:330 final size:328
Alignment explanation
Indices: 29338007--29338664 Score: 1190
Period size: 330 Copynumber: 2.0 Consensus size: 328
29337997 CTTGGTTGTA
29338007 AGCTTTGGCTTTAGGTGTTTGATGCACATTTGAGATGTTACGAAAATTGTTCAATAAACAATTAA
1 AGCTTTGGCTTTAGGTGTTTGATGCACATTTGAGATGTTACGAAAATTGTTCAATAAACAATTAA
* * * * *
29338072 GATAAAATTCAGAAAAATCAAACAAACAGAAAAATATAAGAATTTACGTGGTTCGGCCTGTTGCC
66 GATAAAATTCAGAAAAATCAAACAAAAAAAAAAATACAAAAATTTACGTGGTTCAGCCTGTTGCC
* * *
29338137 TACGTCCACGGAGTGAAACTGTTCTTCTATTATTGAGAAATTAAAGTGTAATAAATTGATCTCTA
131 TACATCCACGGAATGAAACTGTTCGTCTATTATTGAGAAATTAAAGTGTAATAAATTGATCTCTA
29338202 TGGTTTCCCAAACTAACCTAAAATTCGTTGCACACCTTTTTTCAGTAACCTCCAAAGAACACTCA
196 TGGTTTCCCAAACTAACCTAAAATTCGTTGCACACCTTTTTTCAGTAACCTCCAAAGAACACTCA
29338267 CTCAAACCTAGCTCCACCTAGAGCGAAAGATAAAGTTACAAGATATTCCCTTTCTAGAGCTCACG
261 CTCAAACCTAGCTCCACCTAGAGCGAAAGATAAAGTTACAAGATATTCCCTTTCTAGAGCTCACG
29338332 AAG
326 AAG
29338335 NAGCTTTGGCTTTAGGTGTTTGATGCACATTTGAGATGTTACGAAAATTGTTCAATAAACAATTA
1 -AGCTTTGGCTTTAGGTGTTTGATGCACATTTGAGATGTTACGAAAATTGTTCAATAAACAATTA
*
29338400 AGATAAAATTCAGAAAAATCAAGCAAATAAAAAAAATACAAAAATTTACGTGGTTCAGCCTGTTG
65 AGATAAAATTCAGAAAAATCAAACAAA-AAAAAAAATACAAAAATTTACGTGGTTCAGCCTGTTG
* * *
29338465 CCTACATTCATGGAATGAAATTGTTCGTCTATTATTGAGAAATTAAAGTGTAATAAATTGATCTC
129 CCTACATCCACGGAATGAAACTGTTCGTCTATTATTGAGAAATTAAAGTGTAATAAATTGATCTC
29338530 TATGGTTTCCCAAACTAACCTAAAATTCGTTGCACACCTTTTTTCAGTAACCTCCAAAGAACACT
194 TATGGTTTCCCAAACTAACCTAAAATTCGTTGCACACCTTTTTTCAGTAACCTCCAAAGAACACT
29338595 CACTCAAACCTAGCTCCACCTAGAGCGAAAGATAAAGTTACAAGATATTCCCTTTCTAGAGCTCA
259 CACTCAAACCTAGCTCCACCTAGAGCGAAAGATAAAGTTACAAGATATTCCCTTTCTAGAGCTCA
29338660 CGAAG
324 CGAAG
29338665 CACTACACAC
Statistics
Matches: 316, Mismatches: 12, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
329 90 0.28
330 226 0.72
ACGTcount: A:0.36, C:0.19, G:0.15, T:0.29
Consensus pattern (328 bp):
AGCTTTGGCTTTAGGTGTTTGATGCACATTTGAGATGTTACGAAAATTGTTCAATAAACAATTAA
GATAAAATTCAGAAAAATCAAACAAAAAAAAAAATACAAAAATTTACGTGGTTCAGCCTGTTGCC
TACATCCACGGAATGAAACTGTTCGTCTATTATTGAGAAATTAAAGTGTAATAAATTGATCTCTA
TGGTTTCCCAAACTAACCTAAAATTCGTTGCACACCTTTTTTCAGTAACCTCCAAAGAACACTCA
CTCAAACCTAGCTCCACCTAGAGCGAAAGATAAAGTTACAAGATATTCCCTTTCTAGAGCTCACG
AAG
Found at i:29348799 original size:29 final size:29
Alignment explanation
Indices: 29348757--29348816 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
29348747 ATAACCAATT
*
29348757 TCTCAATTACTGGTTCATGATGGTGTATG
1 TCTCAACTACTGGTTCATGATGGTGTATG
*
29348786 TCTCAACTATTGGTTCATGATGGTGTATG
1 TCTCAACTACTGGTTCATGATGGTGTATG
29348815 TC
1 TC
29348817 AAATTCCAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.20, C:0.15, G:0.23, T:0.42
Consensus pattern (29 bp):
TCTCAACTACTGGTTCATGATGGTGTATG
Found at i:29352079 original size:2 final size:2
Alignment explanation
Indices: 29352072--29352097 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
29352062 CATTATGATG
29352072 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
29352098 NNNNNNNNNN
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29355377 original size:121 final size:121
Alignment explanation
Indices: 29355208--29355537 Score: 315
Period size: 121 Copynumber: 2.7 Consensus size: 121
29355198 CCAAATATTG
* * * * * *
29355208 TATCATCCAAATCTTAAACCTAAAGCACTAAACCAAGACATATAAACATAAGCCTGACATTCAAC
1 TATCATACAAATCATAAACCTAAAACCCTAAACCAAGAAATATAAACATAAGCCTGATATTCAAC
* * * * * *
29355273 ATCCATAAACAAAAAAGCAAAATCCAATAGAGAA-ATATATGAATATGAACAAATTA
66 ATCCAGAAACAAAAAAGCAAAATCCAACACA-AATATAGATGAACATCAACAAATTA
* ** * * *
29355329 TATCATACAAATCGTAAACCTAAAACCCTAAATTAAGAAATATGAACATGAA-CTTGATATCCAA
1 TATCATACAAATCATAAACCTAAAACCCTAAACCAAGAAATATAAACAT-AAGCCTGATATTCAA
** * * * *
29355393 CATATAGAAACACAAAAGCAATATCCAACCCAAATATAGATGAACATCAAGAAATTA
65 CATCCAGAAACAAAAAAGCAAAATCCAACACAAATATAGATGAACATCAACAAATTA
* * * * * *
29355450 TATCATGCAAATCATAAA-CTCAAAACCCTAAACCAACAAATATCAATATAAGCCTAATATTTAA
1 TATCATACAAATCATAAACCT-AAAACCCTAAACCAAGAAATATAAACATAAGCCTGATATTCAA
* * *
29355514 CATCCAGAAGCATAAAATCAAAAT
65 CATCCAGAAACAAAAAAGCAAAAT
29355538 AAATCAAAGT
Statistics
Matches: 165, Mismatches: 40, Indels: 8
0.77 0.19 0.04
Matches are distributed among these distances:
120 6 0.04
121 157 0.95
122 2 0.01
ACGTcount: A:0.52, C:0.20, G:0.07, T:0.22
Consensus pattern (121 bp):
TATCATACAAATCATAAACCTAAAACCCTAAACCAAGAAATATAAACATAAGCCTGATATTCAAC
ATCCAGAAACAAAAAAGCAAAATCCAACACAAATATAGATGAACATCAACAAATTA
Found at i:29356807 original size:100 final size:101
Alignment explanation
Indices: 29356631--29356818 Score: 245
Period size: 100 Copynumber: 1.9 Consensus size: 101
29356621 TTATAGACTG
* *
29356631 AAGAAAAAAATTCCAACAAACCCTTCAATTGAATGAAAATTGTTATTCAATGACTGGCCAATTGA
1 AAGAAAAAAATTCCAACAAACCCTTCAATTGAATGAAAATTGTCATTCAATGACTGACCAATTGA
*
29356696 AGCCAACAACCAAAGCAATCAAATGACATCATTTTA
66 AGCCAACAACCAAAACAATCAAATGACATCATTTTA
* * * * * * * *
29356732 AAGAATAAAATTCTAGCAGACCCTTTAATTG-ATGACAATTGTCATTCAATGATTGATCAATTGA
1 AAGAAAAAAATTCCAACAAACCCTTCAATTGAATGAAAATTGTCATTCAATGACTGACCAATTGA
*
29356796 TA-CCAATAACCAAAACAATCAAA
66 -AGCCAACAACCAAAACAATCAAA
29356819 ACAACGTCGT
Statistics
Matches: 74, Mismatches: 12, Indels: 3
0.83 0.13 0.03
Matches are distributed among these distances:
100 47 0.64
101 27 0.36
ACGTcount: A:0.45, C:0.19, G:0.11, T:0.26
Consensus pattern (101 bp):
AAGAAAAAAATTCCAACAAACCCTTCAATTGAATGAAAATTGTCATTCAATGACTGACCAATTGA
AGCCAACAACCAAAACAATCAAATGACATCATTTTA
Found at i:29358439 original size:40 final size:38
Alignment explanation
Indices: 29358385--29358501 Score: 93
Period size: 33 Copynumber: 3.1 Consensus size: 38
29358375 TAATATCATC
* *
29358385 TTTTAAATAT-ATTTTTAATCTCATATATTTTATTTTTAT
1 TTTTTAATATAATTTTTAAT-T-ATATATTTTATTTTAAT
* *
29358424 TTTTTATTATAA---TT--TTATATATTTTATTTTCAT
1 TTTTTAATATAATTTTTAATTATATATTTTATTTTAAT
* * *
29358457 TTCTTAATATAATTTTCAATATTATATATGTTATTTTAAT
1 TTTTTAATATAATTTT-TA-ATTATATATTTTATTTTAAT
29358497 TTTTT
1 TTTTT
29358502 TAAAAGATAA
Statistics
Matches: 61, Mismatches: 9, Indels: 15
0.72 0.11 0.18
Matches are distributed among these distances:
33 26 0.43
34 1 0.02
35 1 0.02
36 1 0.02
37 2 0.03
39 8 0.13
40 22 0.36
ACGTcount: A:0.30, C:0.04, G:0.01, T:0.65
Consensus pattern (38 bp):
TTTTTAATATAATTTTTAATTATATATTTTATTTTAAT
Found at i:29358479 original size:33 final size:33
Alignment explanation
Indices: 29358407--29358472 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
29358397 TTTTAATCTC
* * *
29358407 ATATATTTTATTTTTATTTTTTATTATAATTTT
1 ATATATTTTATTTTCATTTCTTAATATAATTTT
29358440 ATATATTTTATTTTCATTTCTTAATATAATTTT
1 ATATATTTTATTTTCATTTCTTAATATAATTTT
29358473 CAATATTATA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (33 bp):
ATATATTTTATTTTCATTTCTTAATATAATTTT
Found at i:29364214 original size:20 final size:20
Alignment explanation
Indices: 29364186--29364225 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
29364176 CAATTTAAAG
*
29364186 TGGCTTCAT-TACAATTTTCA
1 TGGCCTCATCTAC-ATTTTCA
29364206 TGGCCTCATCTACATTTTCA
1 TGGCCTCATCTACATTTTCA
29364226 AGACCACAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 15 0.83
21 3 0.17
ACGTcount: A:0.23, C:0.25, G:0.10, T:0.42
Consensus pattern (20 bp):
TGGCCTCATCTACATTTTCA
Found at i:29365714 original size:24 final size:23
Alignment explanation
Indices: 29365655--29365715 Score: 61
Period size: 24 Copynumber: 2.7 Consensus size: 23
29365645 AATCACTTAA
*
29365655 TTAAATGGA-TTTCTTCATTGAG
1 TTAAATGGATTTTTTTCATTGAG
* * *
29365677 TAAAATGAATTTTTTTTCTTTGAG
1 TTAAATGGA-TTTTTTTCATTGAG
*
29365701 TTAAATGGACTTTTT
1 TTAAATGGATTTTTT
29365716 CTTTCAAAGA
Statistics
Matches: 30, Mismatches: 7, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
22 7 0.23
23 5 0.17
24 18 0.60
ACGTcount: A:0.28, C:0.07, G:0.15, T:0.51
Consensus pattern (23 bp):
TTAAATGGATTTTTTTCATTGAG
Found at i:29365714 original size:25 final size:25
Alignment explanation
Indices: 29365664--29365720 Score: 64
Period size: 24 Copynumber: 2.3 Consensus size: 25
29365654 ATTAAATGGA
*
29365664 TTTC-TTCATTGAGTAAAATGAATT
1 TTTCTTTCTTTGAGTAAAATGAATT
* *
29365688 TTT-TTTCTTTGAGTTAAATGGACTT
1 TTTCTTTCTTTGAGTAAAAT-GAATT
29365713 TTTCTTTC
1 TTTCTTTC
29365721 AAAGAAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
24 16 0.59
25 7 0.26
26 4 0.15
ACGTcount: A:0.23, C:0.11, G:0.12, T:0.54
Consensus pattern (25 bp):
TTTCTTTCTTTGAGTAAAATGAATT
Found at i:29368028 original size:32 final size:32
Alignment explanation
Indices: 29367966--29368025 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
29367956 TTTTCTTTAA
* *
29367966 TATTCAAGCCAAAAATTATTTTTTTCAAATAC
1 TATTCAAACCAAAAATTAATTTTTTCAAATAC
*
29367998 TATTCAAATCAAAAA-TAATTTTTTCAAA
1 TATTCAAACCAAAAATTAATTTTTTCAAA
29368026 ATAACATTCG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 12 0.48
32 13 0.52
ACGTcount: A:0.45, C:0.13, G:0.02, T:0.40
Consensus pattern (32 bp):
TATTCAAACCAAAAATTAATTTTTTCAAATAC
Found at i:29368190 original size:43 final size:43
Alignment explanation
Indices: 29368129--29368220 Score: 125
Period size: 43 Copynumber: 2.2 Consensus size: 43
29368119 CATGCTATGC
*
29368129 TGATTTTGAGGATATCTTAGAAATATTAATGAAAA-AAATTAAA
1 TGATTTTGAGGATATCTTAGAAATATGAAT-AAAAGAAATTAAA
* * *
29368172 TGATTTTGAGGTTATCTTAGAATTATGGATAAAAGAAATTAAA
1 TGATTTTGAGGATATCTTAGAAATATGAATAAAAGAAATTAAA
29368215 T-ATTTT
1 TGATTTT
29368221 TTGAATTTCT
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
42 9 0.20
43 35 0.80
ACGTcount: A:0.43, C:0.02, G:0.15, T:0.39
Consensus pattern (43 bp):
TGATTTTGAGGATATCTTAGAAATATGAATAAAAGAAATTAAA
Found at i:29372446 original size:3 final size:3
Alignment explanation
Indices: 29372438--29372462 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
29372428 CCAATAAGAA
29372438 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
29372463 CTTTTTTAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:29373079 original size:15 final size:15
Alignment explanation
Indices: 29373056--29373090 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
29373046 TGCAGTTCAG
*
29373056 CTTTCTTTTTCTCTT
1 CTTTTTTTTTCTCTT
*
29373071 CTTTTTTTTTTTCTT
1 CTTTTTTTTTCTCTT
29373086 CTTTT
1 CTTTT
29373091 ATATTTCTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (15 bp):
CTTTTTTTTTCTCTT
Found at i:29373105 original size:14 final size:14
Alignment explanation
Indices: 29373080--29373109 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
29373070 TCTTTTTTTT
29373080 TTTCTTCTTTTATA
1 TTTCTTCTTTTATA
*
29373094 TTTCTTGTTTTATA
1 TTTCTTCTTTTATA
29373108 TT
1 TT
29373110 AGTACATGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.13, C:0.10, G:0.03, T:0.73
Consensus pattern (14 bp):
TTTCTTCTTTTATA
Found at i:29390862 original size:2 final size:2
Alignment explanation
Indices: 29390850--29390894 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
29390840 TCCAACCCAA
*
29390850 TC TC CC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
29390892 TC T
1 TC T
29390895 TCNNNNNNNN
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
TC
Found at i:29390927 original size:2 final size:2
Alignment explanation
Indices: 29390920--29390948 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
29390910 CCTACTCCTC
29390920 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
29390949 ATTGTCTTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:29391192 original size:51 final size:51
Alignment explanation
Indices: 29391113--29391212 Score: 173
Period size: 51 Copynumber: 2.0 Consensus size: 51
29391103 GTTATTGGAG
* *
29391113 TATAATTTAAAAACGTCTGGTTAGCCTCCTCTTTGGATTTCTTTACCCTTC
1 TATAATTTAAAAACGTCTGGTTAACCTCCTCTTTGGATCTCTTTACCCTTC
*
29391164 TATAATTTAAAAATGTCTGGTTAACCTCCTCTTTGGATCTCTTTACCCT
1 TATAATTTAAAAACGTCTGGTTAACCTCCTCTTTGGATCTCTTTACCCT
29391213 CCAAGCTTTT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 46 1.00
ACGTcount: A:0.23, C:0.23, G:0.11, T:0.43
Consensus pattern (51 bp):
TATAATTTAAAAACGTCTGGTTAACCTCCTCTTTGGATCTCTTTACCCTTC
Found at i:29397095 original size:33 final size:33
Alignment explanation
Indices: 29397058--29397135 Score: 113
Period size: 33 Copynumber: 2.4 Consensus size: 33
29397048 TACTTGAAAG
*
29397058 TGTCTTCAACAGAATACTCTTA-TACTTCATTGA
1 TGTCTTCAACACAATACT-TTATTACTTCATTGA
* *
29397091 TGTCTTCAACACAGTACTTTATTACTTCATTGG
1 TGTCTTCAACACAATACTTTATTACTTCATTGA
29397124 TGTCTTCAACAC
1 TGTCTTCAACAC
29397136 TTTCAATAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
32 3 0.07
33 38 0.93
ACGTcount: A:0.27, C:0.23, G:0.10, T:0.40
Consensus pattern (33 bp):
TGTCTTCAACACAATACTTTATTACTTCATTGA
Found at i:29408147 original size:16 final size:16
Alignment explanation
Indices: 29408126--29408156 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
29408116 TGGGTCATTT
29408126 TCGGGTTCAGGTCATC
1 TCGGGTTCAGGTCATC
*
29408142 TCGGGTTCAGTTCAT
1 TCGGGTTCAGGTCAT
29408157 TTCAAATTCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.13, C:0.23, G:0.29, T:0.35
Consensus pattern (16 bp):
TCGGGTTCAGGTCATC
Found at i:29423036 original size:33 final size:33
Alignment explanation
Indices: 29422998--29423064 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
29422988 ACTTGGAAAG
*
29422998 TATTGTATACGAATGCTTAATCAAATTTAAGTA
1 TATTGTATACGAATGCCTAATCAAATTTAAGTA
* * *
29423031 TATTGTGTATGAATGCCTAATCAGATTTAAGTA
1 TATTGTATACGAATGCCTAATCAAATTTAAGTA
29423064 T
1 T
29423065 GTTGAGAGGG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.36, C:0.09, G:0.15, T:0.40
Consensus pattern (33 bp):
TATTGTATACGAATGCCTAATCAAATTTAAGTA
Found at i:29433502 original size:25 final size:25
Alignment explanation
Indices: 29433472--29433523 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
29433462 CTAATGCAAG
29433472 CATTACCAAATTCAATAAATCCATA
1 CATTACCAAATTCAATAAATCCATA
29433497 CATTACCAAATTCAATAAATCCATA
1 CATTACCAAATTCAATAAATCCATA
29433522 CA
1 CA
29433524 ATCTTATATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.48, C:0.25, G:0.00, T:0.27
Consensus pattern (25 bp):
CATTACCAAATTCAATAAATCCATA
Found at i:29433792 original size:87 final size:87
Alignment explanation
Indices: 29433638--29433796 Score: 250
Period size: 87 Copynumber: 1.8 Consensus size: 87
29433628 CAAAAAAATT
*
29433638 ATGGGCAAATAGTTCATATCCAGCATTTACTTCAGAGAATTTATTCCCAACAGTCAAAAAAGTAA
1 ATGGGCAAATAGTTCATATCCAGCATTTACTTCAGAGAATTTATTCCAAACAGTCAAAAAAGTAA
29433703 AAAGCTACCATTTATAGAACATC
66 AAA-CTACCATTTATAGAACATC
* * *
29433726 ATGGTCAAATAGTTCA-ATCCAGCATTTACTTCAGAGCATTTATTCCAAACAGTC-AATAAGTCA
1 ATGGGCAAATAGTTCATATCCAGCATTTACTTCAGAGAATTTATTCCAAACAGTCAAAAAAGT-A
29433789 AAAACTAC
65 AAAACTAC
29433797 AGTTCCAGGG
Statistics
Matches: 66, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
86 10 0.15
87 41 0.62
88 15 0.23
ACGTcount: A:0.40, C:0.20, G:0.12, T:0.28
Consensus pattern (87 bp):
ATGGGCAAATAGTTCATATCCAGCATTTACTTCAGAGAATTTATTCCAAACAGTCAAAAAAGTAA
AAACTACCATTTATAGAACATC
Found at i:29446747 original size:81 final size:82
Alignment explanation
Indices: 29446662--29447026 Score: 402
Period size: 81 Copynumber: 4.5 Consensus size: 82
29446652 CAAAGTTTCG
*
29446662 GAAGCAAAGCCTCCA-TCATTAGAAGTTGCTCCAACAAACAAAGATAGCGAAGAAGCCACAAAAA
1 GAAGCAAAGCCTCCAGTCATTAGAAGTTGCTCCAACAAACAAAGATAGTGAAGAAGCCACAAAAA
29446726 CTGAAATCAAGGATTCT
66 CTGAAATCAAGGATTCT
* *
29446743 GAAGCAAAG-CTGCAGTCATTAGAAGTTGCACCAACAAACAAAGATAGTGAAGAAGCCACAAAAA
1 GAAGCAAAGCCTCCAGTCATTAGAAGTTGCTCCAACAAACAAAGATAGTGAAGAAGCCACAAAAA
*
29446807 CTGAAATAAAGGATTCT
66 CTGAAATCAAGGATTCT
* * * ***
29446824 GAAGC-AAGGCTGCAGTCATTAGAAGTTGCACCAACAAACAAAGATAGTGAAGAAGCTTTAAAAA
1 GAAGCAAAGCCTCCAGTCATTAGAAGTTGCTCCAACAAACAAAGATAGTGAAGAAGCCACAAAAA
* * *
29446888 TTGAAGTCAAGGATGCT
66 CTGAAATCAAGGATTCT
* * * * * * * ** *
29446905 GAAGCAAAGCCT-CAGTCATCAGAAGATGATACAACAAACGAAGACAGGGAAGAAGCTGCAGAAA
1 GAAGCAAAGCCTCCAGTCATTAGAAGTTGCTCCAACAAACAAAGATAGTGAAGAAGCCACAAAAA
* **
29446969 --GAATAGTTAATTATTCT
66 CTGAA-A-TCAAGGATTCT
* * *
29446986 GAAGCAAGGCCTCCA-TCATTAGAAGTTACTCCAACTAACAA
1 GAAGCAAAGCCTCCAGTCATTAGAAGTTGCTCCAACAAACAA
29447027 GGTTAATGAA
Statistics
Matches: 242, Mismatches: 36, Indels: 12
0.83 0.12 0.04
Matches are distributed among these distances:
79 3 0.01
80 7 0.03
81 225 0.93
82 7 0.03
ACGTcount: A:0.44, C:0.19, G:0.20, T:0.18
Consensus pattern (82 bp):
GAAGCAAAGCCTCCAGTCATTAGAAGTTGCTCCAACAAACAAAGATAGTGAAGAAGCCACAAAAA
CTGAAATCAAGGATTCT
Found at i:29460339 original size:112 final size:111
Alignment explanation
Indices: 29460123--29460408 Score: 299
Period size: 112 Copynumber: 2.5 Consensus size: 111
29460113 TGGGTATTTT
* * ** *
29460123 TGGTGTTTTGTTGTTTTGTTGTTGCATTGATTTGTCAATGTTACAACCCACA-TTTTTGGGTTGG
1 TGGTGTTTTGTTATTTTGTTGTTCCATTGATTTACCAATGTTACAACCCACATTTTTTGTGTTGG
* * ** * ** *
29460187 TTTTTCTCTTTGGATTAAAACTCAAGCGAAGAGATGTTTTGTCTTC
66 TATTTCGCTTTACATTAAAACTCAAGAGAAGAGAAATTTTGTCATC
* * *
29460233 TGGTGTTTTGTTATTTTGTTGTATCCTTTGAGTTACCAATGTTACAACCAACATTTTTTGTGTTG
1 TGGTGTTTTGTTATTTTGTTGT-TCCATTGATTTACCAATGTTACAACCCACATTTTTTGTGTTG
* *
29460298 GTATTTCGCTTTACATTAAAGCT-AATGAGAGGAGAAATTTTGTCATC
65 GTATTTCGCTTTACATTAAAACTCAA-GAGAAGAGAAATTTTGTCATC
* * *
29460345 TGG-GTTTTTGTTACTTATTTTGTTGTTTCATTGCTTTAGCAATGTTACAACCCACATTTTTTGT
1 TGGTG-TTTTG----TTATTTTGTTGTTCCATTGATTTACCAATGTTACAACCCACATTTTTTGT
29460409 TGTTTCATTC
Statistics
Matches: 144, Mismatches: 24, Indels: 11
0.80 0.13 0.06
Matches are distributed among these distances:
110 21 0.15
111 27 0.19
112 52 0.36
115 32 0.22
116 12 0.08
ACGTcount: A:0.20, C:0.13, G:0.19, T:0.48
Consensus pattern (111 bp):
TGGTGTTTTGTTATTTTGTTGTTCCATTGATTTACCAATGTTACAACCCACATTTTTTGTGTTGG
TATTTCGCTTTACATTAAAACTCAAGAGAAGAGAAATTTTGTCATC
Found at i:29475206 original size:5 final size:5
Alignment explanation
Indices: 29475198--29475229 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
29475188 TAAGGGTATT
29475198 TTATA TTATA TTATA TTATA TTATA TTATA TT
1 TTATA TTATA TTATA TTATA TTATA TTATA TT
29475230 TTGAACAAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TTATA
Found at i:29480303 original size:16 final size:16
Alignment explanation
Indices: 29480275--29480307 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
29480265 AATATTAATG
29480275 ATTAAATTATAAAAAT
1 ATTAAATTATAAAAAT
29480291 ATTAATATT-TAAAAAT
1 ATTAA-ATTATAAAAAT
29480307 A
1 A
29480308 AAATAAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.81
17 3 0.19
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
ATTAAATTATAAAAAT
Found at i:29480303 original size:23 final size:22
Alignment explanation
Indices: 29480215--29480299 Score: 66
Period size: 23 Copynumber: 3.7 Consensus size: 22
29480205 AAAAATTAAT
* * *
29480215 TAAAATTATTAATATTTTAATCA
1 TAAAAATATTAATA-TTAAATTA
* *
29480238 TAATAATATTTAA-ATTACAAGTA
1 TAAAAATA-TTAATATTA-AATTA
29480261 -AAATAATATTAATGATTAAATTA
1 TAAA-AATATTAAT-ATTAAATTA
29480284 TAAAAATATTAATATT
1 TAAAAATATTAATATT
29480300 TAAAAATAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 13
0.71 0.10 0.19
Matches are distributed among these distances:
22 11 0.22
23 27 0.55
24 11 0.22
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (22 bp):
TAAAAATATTAATATTAAATTA
Found at i:29490901 original size:153 final size:153
Alignment explanation
Indices: 29490623--29490928 Score: 603
Period size: 153 Copynumber: 2.0 Consensus size: 153
29490613 AAACACTTAT
29490623 CCGGATCCGTATCAACCCAAGATCCGAACCCGAATTTTAAAATTCGAAGACTCGATCTGGAAAAT
1 CCGGATCCGTATCAACCCAAGATCCGAACCCGAATTTTAAAATTCGAAGACTCGATCTGGAAAAT
*
29490688 CCAGACTCCAAAGCTTCGTATTTGCCACCAATTGGTTGTTTCAAGAAGCTAATATTATTTGGATT
66 CCAGACTCCAAAGCTTCGTATTTGCCACCAATTGGTTGTTTCAAGAAGCTAATATTATTTGGACT
29490753 TTTCAAACAAAGTCATCAGTCCA
131 TTTCAAACAAAGTCATCAGTCCA
29490776 CCGGATCCGTATCAACCCAAGATCCGAACCCGAATTTTAAAATTCGAAGACTCGATCTGGAAAAT
1 CCGGATCCGTATCAACCCAAGATCCGAACCCGAATTTTAAAATTCGAAGACTCGATCTGGAAAAT
29490841 CCAGACTCCAAAGCTTCGTATTTGCCACCAATTGGTTGTTTCAAGAAGCTAATATTATTTGGACT
66 CCAGACTCCAAAGCTTCGTATTTGCCACCAATTGGTTGTTTCAAGAAGCTAATATTATTTGGACT
29490906 TTTCAAACAAAGTCATCAGTCCA
131 TTTCAAACAAAGTCATCAGTCCA
29490929 AAGACGAAGG
Statistics
Matches: 152, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
153 152 1.00
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.28
Consensus pattern (153 bp):
CCGGATCCGTATCAACCCAAGATCCGAACCCGAATTTTAAAATTCGAAGACTCGATCTGGAAAAT
CCAGACTCCAAAGCTTCGTATTTGCCACCAATTGGTTGTTTCAAGAAGCTAATATTATTTGGACT
TTTCAAACAAAGTCATCAGTCCA
Found at i:29491986 original size:3 final size:3
Alignment explanation
Indices: 29491978--29492009 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
29491968 AGCCTTTCAA
29491978 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
29492010 AGAGTAAATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:29526213 original size:43 final size:40
Alignment explanation
Indices: 29526165--29526244 Score: 115
Period size: 43 Copynumber: 1.9 Consensus size: 40
29526155 TTTTTAATGA
*
29526165 AATCATTTTCTAGTATCCTTGCTACTATGGGAGAGAACTAGAC
1 AATCATTTTCTAGTATCCTT--T-CTATAGGAGAGAACTAGAC
*
29526208 AATCATTTTCTAGTCTCCTTTCTATAGGAGAGAACTA
1 AATCATTTTCTAGTATCCTTTCTATAGGAGAGAACTA
29526245 TTGTGTGAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
40 15 0.43
41 1 0.03
43 19 0.54
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35
Consensus pattern (40 bp):
AATCATTTTCTAGTATCCTTTCTATAGGAGAGAACTAGAC
Done.