Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 113035596
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: 113035596
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 271 characters in sequence are not A, C, G, or T
File 124 of 378
Found at i:34694105 original size:37 final size:33
Alignment explanation
Indices: 34694036--34694183 Score: 173
Period size: 31 Copynumber: 4.5 Consensus size: 33
34694026 TTGCATTCAC
34694036 ATTCTGATTTTGATTCTGTTACCTGAT-A-CTG
1 ATTCTGATTTTGATTCTGTTACCTGATGATCTG
34694067 ATTCTGATTTTGATTCTGTTACCTGATG-T-TG
1 ATTCTGATTTTGATTCTGTTACCTGATGATCTG
*
34694098 ATTCTGATTTTGATTCGGTTACCTGATACTGATTCTG
1 ATTCTGATTTTGATTCTGTTACCTG--A-TGA-TCTG
* * *
34694135 ATTCTGATTCTGATTCTGTCACCTAAT--TCTG
1 ATTCTGATTTTGATTCTGTTACCTGATGATCTG
*
34694166 ATTCTGATTCTGATTCTG
1 ATTCTGATTTTGATTCTG
34694184 ATTCTGATTC
Statistics
Matches: 104, Mismatches: 5, Indels: 16
0.83 0.04 0.13
Matches are distributed among these distances:
31 75 0.72
33 1 0.01
34 3 0.03
35 1 0.01
36 1 0.01
37 23 0.22
ACGTcount: A:0.18, C:0.17, G:0.17, T:0.48
Consensus pattern (33 bp):
ATTCTGATTTTGATTCTGTTACCTGATGATCTG
Found at i:34694184 original size:37 final size:37
Alignment explanation
Indices: 34694096--34694189 Score: 143
Period size: 37 Copynumber: 2.5 Consensus size: 37
34694086 TACCTGATGT
* * * *
34694096 TGATTCTGATTTTGATTCGGTTACCTGATACTGATTC
1 TGATTCTGATTCTGATTCTGTCACCTAATACTGATTC
*
34694133 TGATTCTGATTCTGATTCTGTCACCTAATTCTGATTC
1 TGATTCTGATTCTGATTCTGTCACCTAATACTGATTC
34694170 TGATTCTGATTCTGATTCTG
1 TGATTCTGATTCTGATTCTG
34694190 ATTCTAGTTC
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 52 1.00
ACGTcount: A:0.18, C:0.18, G:0.17, T:0.47
Consensus pattern (37 bp):
TGATTCTGATTCTGATTCTGTCACCTAATACTGATTC
Found at i:34696159 original size:40 final size:39
Alignment explanation
Indices: 34696114--34696321 Score: 209
Period size: 40 Copynumber: 5.2 Consensus size: 39
34696104 CGGAATACAA
*
34696114 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* * *
34696154 CCGGATAGAACGACTTGCACAAATGCCTTCGGGTATTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* * *
34696194 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* ** * * *
34696234 CCGGATTTAGTCACTAGCATAATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACT-GCACAAATGCCTTCGGGTCTTAGC
* * * * *
34696274 CCGGATTTAACTACTAGCATAAATGTCTTCGGGACTTAGC
1 CCGGATATAACCACT-GCACAAATGCCTTCGGGTCTTAGC
34696314 CCGGATAT
1 CCGGATAT
34696322 CATTTAATTG
Statistics
Matches: 142, Mismatches: 25, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
39 1 0.01
40 141 0.99
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.27
Consensus pattern (39 bp):
CCGGATATAACCACTGCACAAATGCCTTCGGGTCTTAGC
Found at i:34696261 original size:80 final size:81
Alignment explanation
Indices: 34696114--34696319 Score: 247
Period size: 80 Copynumber: 2.6 Consensus size: 81
34696104 CGGAATACAA
* * * *
34696114 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGCCCGGA-TAGAACGACTTGCACAAAT
1 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATTAGAACGACTAGCACAAAT
*
34696178 GCCTTCGGGTATTAGC
66 GCCTTCGGGTATTAAC
* * *
34696194 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATTTAG-TC-ACTAGCATAAT
1 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGA-TTAGAACGACTAGCACAAA
*
34696257 TGCCTTCGGGTCTTAAC
65 TGCCTTCGGGTATTAAC
* * ** * *
34696274 CCGGATTTAACTACTAGCATAAATGTCTTCGGGACTTAGCCCGGAT
1 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGAT
34696320 ATCATTTAAT
Statistics
Matches: 109, Mismatches: 15, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
79 1 0.01
80 104 0.95
81 1 0.01
82 3 0.03
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.27
Consensus pattern (81 bp):
CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATTAGAACGACTAGCACAAAT
GCCTTCGGGTATTAAC
Found at i:34704197 original size:40 final size:39
Alignment explanation
Indices: 34704152--34704358 Score: 200
Period size: 40 Copynumber: 5.2 Consensus size: 39
34704142 CGGAATACAA
*
34704152 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* * *
34704192 CCGGATAGAACGACTTGCACAAATGCCTTCGGGTATTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* * *
34704232 CCGGATTTAACAACTTGCACGAATGCCTT-GGGTCTTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* ** * * *
34704271 CCGGATTTAGTCACTAGCATAATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACT-GCACAAATGCCTTCGGGTCTTAGC
* * * * *
34704311 CCGGATTTAACTACTAGCATAAATGTCTTCGGGACTTAGC
1 CCGGATATAACCACT-GCACAAATGCCTTCGGGTCTTAGC
34704351 CCGGATAT
1 CCGGATAT
34704359 CATTTAATTG
Statistics
Matches: 140, Mismatches: 25, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
38 1 0.01
39 30 0.21
40 109 0.78
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.27
Consensus pattern (39 bp):
CCGGATATAACCACTGCACAAATGCCTTCGGGTCTTAGC
Found at i:34704274 original size:79 final size:78
Alignment explanation
Indices: 34704152--34704357 Score: 234
Period size: 79 Copynumber: 2.6 Consensus size: 78
34704142 CGGAATACAA
* * * *
34704152 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGCCCGGATAGAACGACTTGCACAAATG
1 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATAG-AC-ACTAGCACAAATG
*
34704217 CCTTCGGGTATTAGC
64 CCTTCGGGTATTAAC
* * *
34704232 CCGGATTTAACAACTTGCACGAATGCCTT-GGGTCTTAGCCCGGATTTAGTCACTAGCATAATTG
1 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGA--TAGACACTAGCACAAATG
*
34704296 CCTTCGGGTCTTAAC
64 CCTTCGGGTATTAAC
* * ** * *
34704311 CCGGATTTAACTACTAGCATAAATGTCTTCGGGACTTAGCCCGGATA
1 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATA
34704358 TCATTTAATT
Statistics
Matches: 108, Mismatches: 15, Indels: 8
0.82 0.11 0.06
Matches are distributed among these distances:
78 2 0.02
79 62 0.57
80 41 0.38
81 3 0.03
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.27
Consensus pattern (78 bp):
CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATAGACACTAGCACAAATGCC
TTCGGGTATTAAC
Found at i:34709714 original size:45 final size:46
Alignment explanation
Indices: 34709645--34709763 Score: 181
Period size: 45 Copynumber: 2.6 Consensus size: 46
34709635 AACTAGGCAT
*
34709645 CCGAACTCGTTGAGTTGA-TCCCGAGTTCACTTATGGATGCG-A-GC
1 CCGAGCTCGTTGAGTTGAGT-CCGAGTTCACTTATGGATGCGAACGC
*
34709689 ACCGAGCTCGCTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 -CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
34709736 CCGAGCTCGTTGAGTTGAGTCCGAGTTC
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTC
34709764 GTATATGGGT
Statistics
Matches: 68, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
45 37 0.54
46 29 0.43
47 2 0.03
ACGTcount: A:0.19, C:0.25, G:0.29, T:0.26
Consensus pattern (46 bp):
CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
Found at i:34712078 original size:138 final size:138
Alignment explanation
Indices: 34711657--34712344 Score: 914
Period size: 138 Copynumber: 5.1 Consensus size: 138
34711647 TAGAAAAATG
*** * *
34711657 AATTATATTCTTTTGGAAAAAA-ATTAATTTCCATATCTTTTATATTTTGACTAAAATTATTTAA
1 AATTATATTCTTTCCAAAAAAATATTAATTTCCATGTCTTTTATATTTTGACTAAAATTAATTAA
* * *
34711721 TGTAAC----TAT-TTAATAAATTCAGTAAAAATATATACAATTAATAGTTTATATGAATCAAAT
66 TATAACTGTTTATATTAATAAATTCAGT-AAAATATATACAATTAATATTTTGTATGAATCAAAT
34711781 TCATATATT
130 TCATATATT
** *
34711790 AATTATATTCTTT-CAAACGGAATATTAATTTCCATGTCTTTTATATTTTGACCAAAATTAATTA
1 AATTATATTCTTTCCAAA-AAAATATTAATTTCCATGTCTTTTATATTTTGACTAAAATTAATTA
* * * *
34711854 TTATAACTATTTATATTAATAAATTTAGTAATATATATA-AA-TAATATTTTGTATGAATCAAAT
65 ATATAACTGTTTATATTAATAAATTCAGTAAAATATATACAATTAATATTTTGTATGAATCAAAT
34711917 TCATATATT
130 TCATATATT
* * * * * * *
34711926 AATTATATTATTTCCAAAAAAATAATAATTTTCATATCTTGTATATTTTGATTGAAATTAATTAA
1 AATTATATTCTTTCCAAAAAAATATTAATTTCCATGTCTTTTATATTTTGACTAAAATTAATTAA
* * *
34711991 TATAATTGTGTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
66 TATAACTGTTTATATTAATAAATTCAGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
*
34712056 CATAAATT
131 CATATATT
*
34712064 AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACTAAAATTAATTAA
1 AATTATATTCTTTCCAAAAAAATATTAATTTCCATGTCTTTTATATTTTGACTAAAATTAATTAA
*
34712129 TATAACTGTTTATATTAATAAATTCAGAAAAATATATACAATTAATATTTTGTATGAATCAAATT
66 TATAACTGTTTATATTAATAAATTCAGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
34712194 CATATATT
131 CATATATT
* * * * ** *
34712202 AATTATATTATTTCGAAAATAATATTAACTTCCATGTCTTTTATA-TTTGACCGAAGTTAATTAA
1 AATTATATTCTTTCCAAAAAAATATTAATTTCCATGTCTTTTATATTTTGACTAAAATTAATTAA
* * * * *
34712266 TATAACTGTTTATATTAAAAAATTCGGTAAAATAAATAAAATTAATA-TTTGCATGAATCAAATT
66 TATAACTGTTTATATTAATAAATTCAGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
34712330 CATATATT
131 CATATATT
34712338 -ATTATAT
1 AATTATAT
34712345 CTATGTTCTC
Statistics
Matches: 488, Mismatches: 57, Indels: 18
0.87 0.10 0.03
Matches are distributed among these distances:
132 2 0.00
133 15 0.03
134 43 0.09
135 7 0.01
136 134 0.27
137 66 0.14
138 208 0.43
139 13 0.03
ACGTcount: A:0.42, C:0.08, G:0.06, T:0.44
Consensus pattern (138 bp):
AATTATATTCTTTCCAAAAAAATATTAATTTCCATGTCTTTTATATTTTGACTAAAATTAATTAA
TATAACTGTTTATATTAATAAATTCAGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
CATATATT
Found at i:34712324 original size:274 final size:274
Alignment explanation
Indices: 34711673--34712344 Score: 934
Period size: 274 Copynumber: 2.5 Consensus size: 274
34711663 ATTCTTTTGG
* * ** * *
34711673 AAAAAAAT--TAATTTCCATATCTTTTATATTTTGACTAAAATTATTTAATGTAAC----TAT-T
1 AAAAAAATAATAACTTCCATATCTTGTATATTTTGACCGAAATTAATTAATATAACTGTGTATAT
* *
34711731 TAATAAATTCAGTAAAAATATATACAATTAATAGTTTATATGAATCAAATTCATATATTAATTAT
66 TAATAAATTCGGT-AAAATATATACAATTAATAGTTTGTATGAATCAAATTCATATATTAATTAT
* *
34711796 ATTCTTTCAAACGGAATATTAATTTCCATGTCTTTTATATTTTGACCAAAATTAATTATTATAAC
130 ATTCTTTCAAACAGAATATTAATTTCCATGTCTTTTATATTTTGACCAAAATTAATTAATATAAC
* * *
34711861 TATTTATATTAATAAATTTAGTAATATATATAAATAATATTTTGTATGAATCAAATTCATATATT
195 TATTTATATTAATAAATTCAGAAAAATATATAAATAATATTTTGTATGAATCAAATTCATATATT
34711926 AATTATATTATTTCC
260 AATTATATTATTTCC
* * ** *
34711941 AAAAAAATAATAATTTTCATATCTTGTATATTTTGATTGAAATTAATTAATATAATTGTGTATAT
1 AAAAAAATAATAACTTCCATATCTTGTATATTTTGACCGAAATTAATTAATATAACTGTGTATAT
* *
34712006 TAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATTCATAAATTAATTATA
66 TAATAAATTCGGTAAAATATATACAATTAATAGTTTGTATGAATCAAATTCATATATTAATTATA
*
34712071 TTCTTTCCAAA-AGAATATTAATTTCCATGTCTTTTATATTTTGACTAAAATTAATTAATATAAC
131 TTCTTT-CAAACAGAATATTAATTTCCATGTCTTTTATATTTTGACCAAAATTAATTAATATAAC
*
34712135 TGTTTATATTAATAAATTCAGAAAAATATATACAATTAATATTTTGTATGAATCAAATTCATATA
195 TATTTATATTAATAAATTCAGAAAAATATATA-AA-TAATATTTTGTATGAATCAAATTCATATA
*
34712200 TTAATTATATTATTTCG
258 TTAATTATATTATTTCC
* * * * * *
34712217 AAAATAATATTAACTTCCATGTCTTTTATA-TTTGACCGAAGTTAATTAATATAACTGTTTATAT
1 AAAAAAATAATAACTTCCATATCTTGTATATTTTGACCGAAATTAATTAATATAACTGTGTATAT
* * * *
34712281 TAAAAAATTCGGTAAAATAAATAAAATTAATA-TTTGCATGAATCAAATTCATATATT-ATTATA
66 TAATAAATTCGGTAAAATATATACAATTAATAGTTTGTATGAATCAAATTCATATATTAATTATA
34712344 T
131 T
34712345 CTATGTTCTC
Statistics
Matches: 359, Mismatches: 35, Indels: 15
0.88 0.09 0.04
Matches are distributed among these distances:
268 8 0.02
270 39 0.11
273 7 0.02
274 159 0.44
275 77 0.21
276 69 0.19
ACGTcount: A:0.43, C:0.08, G:0.06, T:0.44
Consensus pattern (274 bp):
AAAAAAATAATAACTTCCATATCTTGTATATTTTGACCGAAATTAATTAATATAACTGTGTATAT
TAATAAATTCGGTAAAATATATACAATTAATAGTTTGTATGAATCAAATTCATATATTAATTATA
TTCTTTCAAACAGAATATTAATTTCCATGTCTTTTATATTTTGACCAAAATTAATTAATATAACT
ATTTATATTAATAAATTCAGAAAAATATATAAATAATATTTTGTATGAATCAAATTCATATATTA
ATTATATTATTTCC
Found at i:34716254 original size:87 final size:87
Alignment explanation
Indices: 34716108--34716281 Score: 339
Period size: 87 Copynumber: 2.0 Consensus size: 87
34716098 GACCATTCCT
34716108 TAGTCAACAGTACACCTTATACATTACCTAATTAACTAACCACATATCAATACCATGTCATTAAA
1 TAGTCAACAGTACACCTTATACATTACCTAATTAACTAACCACATATCAATACCATGTCATTAAA
34716173 CAACTATCAACGCAACACATAA
66 CAACTATCAACGCAACACATAA
*
34716195 TAGTCAACAGTACACCTTATACATTACCTAATTAACTAACCACATATTAATACCATGTCATTAAA
1 TAGTCAACAGTACACCTTATACATTACCTAATTAACTAACCACATATCAATACCATGTCATTAAA
34716260 CAACTATCAACGCAACACATAA
66 CAACTATCAACGCAACACATAA
34716282 AGACCTAATT
Statistics
Matches: 86, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
87 86 1.00
ACGTcount: A:0.44, C:0.26, G:0.05, T:0.26
Consensus pattern (87 bp):
TAGTCAACAGTACACCTTATACATTACCTAATTAACTAACCACATATCAATACCATGTCATTAAA
CAACTATCAACGCAACACATAA
Found at i:34718183 original size:29 final size:29
Alignment explanation
Indices: 34718121--34718223 Score: 118
Period size: 29 Copynumber: 3.6 Consensus size: 29
34718111 GTGACGAGAT
* * *
34718121 TGGCACTGAGTGTGCGAGCTTGTAATGTA
1 TGGCACTAAGTGTGCGAGCTTGGAATATA
* * *
34718150 CGGCACTAAGTGTGCGAGTTTGGACTATA
1 TGGCACTAAGTGTGCGAGCTTGGAATATA
* *
34718179 TGGCACTATGTGTGCGGGCTT-GAATCATA
1 TGGCACTAAGTGTGCGAGCTTGGAAT-ATA
34718208 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
34718224 TGATTGAGTA
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
28 3 0.05
29 58 0.95
ACGTcount: A:0.21, C:0.17, G:0.33, T:0.29
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGCTTGGAATATA
Found at i:34726187 original size:29 final size:29
Alignment explanation
Indices: 34726125--34726227 Score: 118
Period size: 29 Copynumber: 3.6 Consensus size: 29
34726115 GTGACGAGAT
* * *
34726125 TGGCACTGAGTGTGCGAGCTTGTAATGTA
1 TGGCACTAAGTGTGCGAGCTTGGAATATA
* * *
34726154 CGGCACTAAGTGTGCGAGTTTGGACTATA
1 TGGCACTAAGTGTGCGAGCTTGGAATATA
* *
34726183 TGGCACTATGTGTGCGGGCTT-GAATCATA
1 TGGCACTAAGTGTGCGAGCTTGGAAT-ATA
34726212 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
34726228 TGATTGAGTA
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
28 3 0.05
29 58 0.95
ACGTcount: A:0.21, C:0.17, G:0.33, T:0.29
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGCTTGGAATATA
Found at i:34728534 original size:43 final size:44
Alignment explanation
Indices: 34728478--34728605 Score: 140
Period size: 43 Copynumber: 3.0 Consensus size: 44
34728468 CATATCATAA
*
34728478 AATGCCAACGTCCCAGTCGTGGTCTTACATGTAATCACATATA-
1 AATGCCAACGTCCCAGACGTGGTCTTACATGTAATCACATATAC
* * * *
34728521 GATGCC-ACTGTCCCAAACAG-GATCTTACACGTAATCACATA-AC
1 AATGCCAAC-GTCCCAGAC-GTGGTCTTACATGTAATCACATATAC
*
34728564 AATGCCAACGTCCCAGACGTGGTATTACATG-AATACACATAT
1 AATGCCAACGTCCCAGACGTGGTCTTACATGTAAT-CACATAT
34728606 CGAAATCCTA
Statistics
Matches: 68, Mismatches: 10, Indels: 13
0.75 0.11 0.14
Matches are distributed among these distances:
42 7 0.10
43 58 0.85
44 3 0.04
ACGTcount: A:0.34, C:0.27, G:0.16, T:0.24
Consensus pattern (44 bp):
AATGCCAACGTCCCAGACGTGGTCTTACATGTAATCACATATAC
Found at i:34728925 original size:15 final size:15
Alignment explanation
Indices: 34728905--34728940 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
34728895 GTTCTTGATT
34728905 TTCAAATTAAAATCA
1 TTCAAATTAAAATCA
*
34728920 TTCAAATTAAACTCA
1 TTCAAATTAAAATCA
34728935 TTCAAA
1 TTCAAA
34728941 CATAATTTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (15 bp):
TTCAAATTAAAATCA
Found at i:34731345 original size:40 final size:40
Alignment explanation
Indices: 34731254--34731435 Score: 146
Period size: 38 Copynumber: 4.7 Consensus size: 40
34731244 ACGACTCGCT
* *
34731254 CAAATGCCTTCGGGAC-AAAGCCCGG-TTATAGTGAC-T-CA
1 CAAATGCCTTCGGGACTTAA-CCCGGATT-TAGTAACTTGCA
* *
34731292 CGAATGCCTTCGGGACTTAACCCGGGTTTAGTAACTTGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTTGCA
* * *
34731332 CAAATGCCTTCGGG-CTT-AGCCGGATTTATTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTTGCA
* * ** * *
34731370 CGAATGCCTTC-GGATCCTAGTCCGGATATAGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAACTT-GCA
*
34731411 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
34731436 CATCATTCGA
Statistics
Matches: 116, Mismatches: 19, Indels: 16
0.77 0.13 0.11
Matches are distributed among these distances:
37 2 0.02
38 53 0.46
39 10 0.09
40 42 0.36
41 9 0.08
ACGTcount: A:0.25, C:0.27, G:0.24, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTTGCA
Found at i:34738730 original size:19 final size:19
Alignment explanation
Indices: 34738687--34738724 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
34738677 GTTAAAAGTT
34738687 AGTATACTATAAATACTAC
1 AGTATACTATAAATACTAC
34738706 AGTATACTATAAATACTAC
1 AGTATACTATAAATACTAC
34738725 TTTATAAGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.47, C:0.16, G:0.05, T:0.32
Consensus pattern (19 bp):
AGTATACTATAAATACTAC
Found at i:34738800 original size:30 final size:28
Alignment explanation
Indices: 34738764--34738825 Score: 72
Period size: 27 Copynumber: 2.1 Consensus size: 28
34738754 GGCTAACCAT
34738764 TTTTCTTTACTTTCCATATTTTTAGATTA-G
1 TTTTCTTTAC-TT-CATA-TTTTAGATTAGG
* *
34738794 TTTTCTTTTCTTCTTATTTTAGATTAGG
1 TTTTCTTTACTTCATATTTTAGATTAGG
34738822 TTTT
1 TTTT
34738826 TCCTTTCTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 10 0.34
28 8 0.28
29 2 0.07
30 9 0.31
ACGTcount: A:0.16, C:0.11, G:0.08, T:0.65
Consensus pattern (28 bp):
TTTTCTTTACTTCATATTTTAGATTAGG
Found at i:34741515 original size:20 final size:18
Alignment explanation
Indices: 34741465--34741516 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 18
34741455 CTACAAAATA
34741465 AATATTAAATTAA-ATTT
1 AATATTAAATTAATATTT
34741482 AATATTAAGA-TAATCACTTT
1 AATATTAA-ATTAAT-A-TTT
34741502 AATATTAAATTAATA
1 AATATTAAATTAATA
34741517 AATTATTATC
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
17 11 0.37
18 1 0.03
19 3 0.10
20 15 0.50
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.42
Consensus pattern (18 bp):
AATATTAAATTAATATTT
Found at i:34742735 original size:27 final size:26
Alignment explanation
Indices: 34742687--34742738 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
34742677 GCGAGGCTGC
*
34742687 CAGATATTGTGACGAAGTCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
* *
34742713 CAGATATATGTGGCGAGGCCACCAGA
1 CAGATAT-TGTGACGAAGCCACCAGA
34742739 TTGCAGGGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.35, C:0.21, G:0.27, T:0.17
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:34743006 original size:8 final size:8
Alignment explanation
Indices: 34742993--34743032 Score: 71
Period size: 8 Copynumber: 5.0 Consensus size: 8
34742983 TACCAGAGTG
34742993 GGCCCATT
1 GGCCCATT
34743001 GGCCCATT
1 GGCCCATT
34743009 GGCCCATT
1 GGCCCATT
*
34743017 AGCCCATT
1 GGCCCATT
34743025 GGCCCATT
1 GGCCCATT
34743033 TTTGGCCCAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
8 30 1.00
ACGTcount: A:0.15, C:0.38, G:0.23, T:0.25
Consensus pattern (8 bp):
GGCCCATT
Found at i:34749984 original size:28 final size:28
Alignment explanation
Indices: 34749911--34749984 Score: 105
Period size: 28 Copynumber: 2.6 Consensus size: 28
34749901 GTTCAAATTG
* * *
34749911 TATAGCACTAAGTGTGCAAGTTTGATTA
1 TATAGCACTAAGTGTGCGAGTTCGACTA
34749939 TATAGCACTAAGTGTGCGAGTTCGACTA
1 TATAGCACTAAGTGTGCGAGTTCGACTA
34749967 T-TAAGCACTAAGTGTGCG
1 TAT-AGCACTAAGTGTGCG
34749985 GGCTTATTAT
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
27 1 0.02
28 41 0.98
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.31
Consensus pattern (28 bp):
TATAGCACTAAGTGTGCGAGTTCGACTA
Found at i:34757841 original size:25 final size:25
Alignment explanation
Indices: 34757807--34757856 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
34757797 TAAATCGAAA
34757807 TCATGCTCTTTGTGTGTGGATATTG
1 TCATGCTCTTTGTGTGTGGATATTG
34757832 TCATGCTCTTTGTGTGTGGATATTG
1 TCATGCTCTTTGTGTGTGGATATTG
34757857 AACCGAAATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.12, C:0.12, G:0.28, T:0.48
Consensus pattern (25 bp):
TCATGCTCTTTGTGTGTGGATATTG
Found at i:34758065 original size:40 final size:40
Alignment explanation
Indices: 34757969--34758159 Score: 238
Period size: 40 Copynumber: 4.8 Consensus size: 40
34757959 CGAATGGTGT
* * * * * *
34757969 CCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGTGACTAAAT
1 CCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACCAAAA
* * *
34758010 CCGGGTCAATTCCCGAAGGCATTTGTGCTAGTTACCAAAA
1 CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAAA
34758050 CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAAA
1 CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAAA
* * *
34758090 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAT
1 CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAAA
* * *
34758130 CCGGGCTAATTCCCGAAGGCAATTGTGCGA
1 CCGGGTTAAGTCCCGAAGGCATTTGTGCGA
34758160 ATCACTATAA
Statistics
Matches: 132, Mismatches: 18, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
40 108 0.82
41 24 0.18
ACGTcount: A:0.26, C:0.24, G:0.27, T:0.24
Consensus pattern (40 bp):
CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAAA
Found at i:34758134 original size:80 final size:80
Alignment explanation
Indices: 34757968--34758201 Score: 254
Period size: 80 Copynumber: 2.9 Consensus size: 80
34757958 TCGAATGGTG
* * * * *
34757968 TCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGTGACTAAATCCGGGTCAATTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTGACCAAAACCGGGTCAAGTCCCGAAGGCATT
* *
34758033 TGTGCTAGTTACCAAA
65 CGTGCGAGTTACCAAA
* * * *
34758049 ACCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAAACCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACCAAAACCGGGTCAAGTCCCGAAGGCATTC
*
34758114 GTGCGAGTTACTAAA
66 GTGCGAGTTACCAAA
* * * * * * * *
34758129 TCCGGGCTAATTCCCGAAGGCAATTGTGCGAATCACTATAACCGGG-CAATGTCCCGAAGACAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACCAAAACCGGGTCAA-GTCCCGAAGGCATT
*
34758193 CGAGCGAGT
65 CGTGCGAGT
34758202 CGCTATATCC
Statistics
Matches: 128, Mismatches: 24, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
79 2 0.02
80 100 0.78
81 26 0.20
ACGTcount: A:0.27, C:0.24, G:0.26, T:0.23
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACCAAAACCGGGTCAAGTCCCGAAGGCATTC
GTGCGAGTTACCAAA
Found at i:34758174 original size:40 final size:39
Alignment explanation
Indices: 34757969--34758201 Score: 202
Period size: 40 Copynumber: 5.8 Consensus size: 39
34757959 CGAATGGTGT
** * *
34757969 CCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGTGACTAAA
1 CCGGGCTAAGTCCCGAAGGCAATTGTGC-GAGTTACTAAA
* * * *
34758009 TCCGGG-TCAATTCCCGAAGGCATTTGTGCTAGTTACCAAAA
1 -CCGGGCT-AAGTCCCGAAGGCAATTGTGCGAGTTA-CTAAA
* * *
34758050 CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAAA
1 CCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTA-CTAAA
*
34758090 CCGGGTTAAGTCCCGAAGGC-ATTCGTGCGAGTTACTAAA
1 CCGGGCTAAGTCCCGAAGGCAATT-GTGCGAGTTACTAAA
* * *
34758129 TCCGGGCTAATTCCCGAAGGCAATTGTGCGAATCACTATAA
1 -CCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACTA-AA
* * *
34758170 CCGGGC-AATGTCCCGAAGACAATCGAGCGAGT
1 CCGGGCTAA-GTCCCGAAGGCAATTGTGCGAGT
34758202 CGCTATATCC
Statistics
Matches: 166, Mismatches: 18, Indels: 17
0.83 0.09 0.08
Matches are distributed among these distances:
39 8 0.05
40 124 0.75
41 34 0.20
ACGTcount: A:0.27, C:0.24, G:0.26, T:0.23
Consensus pattern (39 bp):
CCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACTAAA
Found at i:34758183 original size:120 final size:121
Alignment explanation
Indices: 34757969--34758187 Score: 291
Period size: 120 Copynumber: 1.8 Consensus size: 121
34757959 CGAATGGTGT
* * *
34757969 CCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGTGACTAAATCCGGGTCAATTCCCGAAGGCATTT
1 CCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGACTAAATCCGGGTCAATTCCCGAAGGCAATT
* * * *
34758034 GTGCTAGTTACCAAAACCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACCAAAA
66 GTGCGAATCACCAAAACCGGGTCAAGTCCCGAAGGCATTTGTGCGAGTTACCAAAA
* * *
34758090 CCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTACTAAATCCGGG-CTAATTCCCGAAGGCAAT
1 CCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGACTAAATCCGGGTC-AATTCCCGAAGGCAAT
* *
34758153 TGTGCGAATCACTATAACCGGG-CAATGTCCCGAAG
65 TGTGCGAATCACCAAAACCGGGTCAA-GTCCCGAAG
34758188 ACAATCGAGC
Statistics
Matches: 84, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
119 3 0.04
120 56 0.67
121 25 0.30
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.23
Consensus pattern (121 bp):
CCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGACTAAATCCGGGTCAATTCCCGAAGGCAATT
GTGCGAATCACCAAAACCGGGTCAAGTCCCGAAGGCATTTGTGCGAGTTACCAAAA
Found at i:34764708 original size:5 final size:5
Alignment explanation
Indices: 34764700--34764724 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
34764690 AAAATAAAAA
34764700 TTTAT TTTAT TTTAT TTTAT TTTAT
1 TTTAT TTTAT TTTAT TTTAT TTTAT
34764725 GGTTGGTATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTAT
Found at i:34764997 original size:15 final size:16
Alignment explanation
Indices: 34764979--34765016 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
34764969 AATTGGAAAG
34764979 ATGAAAAGTT-ATTAA
1 ATGAAAAGTTAATTAA
* *
34764994 ATGATAATTTAATTAA
1 ATGAAAAGTTAATTAA
34765010 ATGAAAA
1 ATGAAAA
34765017 AGAAAACAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 8 0.42
16 11 0.58
ACGTcount: A:0.55, C:0.00, G:0.11, T:0.34
Consensus pattern (16 bp):
ATGAAAAGTTAATTAA
Found at i:34778178 original size:43 final size:43
Alignment explanation
Indices: 34778130--34778295 Score: 192
Period size: 43 Copynumber: 3.9 Consensus size: 43
34778120 GTTATTGAGA
* *
34778130 TGTGATTACATGTAAGACCATGTTTGGGACATTGGCATTGTAT
1 TGTGATTACATGTAAGACCATGTCTGGGACATTGGCATCGTAT
* *
34778173 TGTGATTACGTGTAAGACCATGTCTGGGACATTGGCATCATAT
1 TGTGATTACATGTAAGACCATGTCTGGGACATTGGCATCGTAT
* * * * *
34778216 TATGATTTCATGTAAGACCCTGTCTAGGACAGTGGCATCG-AT
1 TGTGATTACATGTAAGACCATGTCTGGGACATTGGCATCGTAT
* * * *
34778258 ATGTGATAACATGTAAGGCCATATCTGGGATA-TGGCAT
1 -TGTGATTACATGTAAGACCATGTCTGGGACATTGGCAT
34778296 TGTACGAGCT
Statistics
Matches: 103, Mismatches: 19, Indels: 3
0.82 0.15 0.02
Matches are distributed among these distances:
42 8 0.08
43 95 0.92
ACGTcount: A:0.27, C:0.15, G:0.25, T:0.33
Consensus pattern (43 bp):
TGTGATTACATGTAAGACCATGTCTGGGACATTGGCATCGTAT
Found at i:34782705 original size:47 final size:44
Alignment explanation
Indices: 34782602--34782768 Score: 149
Period size: 47 Copynumber: 3.6 Consensus size: 44
34782592 TATGCGTGCT
* *
34782602 GATGCATGTCCCAGACATGTCTTACACTAGCACAACTCTTAGTC
1 GATGCATGTCCCAAACATGTCTTACACTAGCACAACTCTTAGCC
* * * *
34782646 GATGCGTGTCCCAAACACGTCTTACACTAGC-TATCTCTGTCGAGGCC
1 GATGCATGTCCCAAACATGTCTTACACTAGCACAACTCT-T--A-GCC
* * *
34782693 GATGCATGTCCCAAACATGTCTTACTCTGGCACTCATCTCTGTA-CC
1 GATGCATGTCCCAAACATGTCTTACACTAGCA--CAACTCT-TAGCC
*
34782739 GATGCCATGTCCCAGACATGGTCTTACACT
1 GATG-CATGTCCCAAACAT-GTCTTACACT
34782769 GCCTCTCATA
Statistics
Matches: 101, Mismatches: 13, Indels: 14
0.79 0.10 0.11
Matches are distributed among these distances:
43 5 0.05
44 29 0.29
46 7 0.07
47 42 0.42
48 10 0.10
50 8 0.08
ACGTcount: A:0.23, C:0.31, G:0.18, T:0.28
Consensus pattern (44 bp):
GATGCATGTCCCAAACATGTCTTACACTAGCACAACTCTTAGCC
Found at i:34783551 original size:12 final size:12
Alignment explanation
Indices: 34783534--34783558 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
34783524 TAAAAATGTA
34783534 AAAATCATCAAG
1 AAAATCATCAAG
34783546 AAAATCATCAAG
1 AAAATCATCAAG
34783558 A
1 A
34783559 TCACTTACAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.16, G:0.08, T:0.16
Consensus pattern (12 bp):
AAAATCATCAAG
Found at i:34787779 original size:31 final size:31
Alignment explanation
Indices: 34787744--34787807 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
34787734 GAAGTGTCAG
34787744 AATGTTGAGTTACTCCT-GGTTGAATCTAAGA
1 AATGTTGAGTTACT-CTGGGTTGAATCTAAGA
*
34787775 AATGTTGAGTTACTCTGGGTTGAATCTGAGA
1 AATGTTGAGTTACTCTGGGTTGAATCTAAGA
34787806 AA
1 AA
34787808 CTGGATGGGT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 2 0.06
31 29 0.94
ACGTcount: A:0.30, C:0.11, G:0.25, T:0.34
Consensus pattern (31 bp):
AATGTTGAGTTACTCTGGGTTGAATCTAAGA
Found at i:34791990 original size:45 final size:45
Alignment explanation
Indices: 34791940--34792027 Score: 149
Period size: 45 Copynumber: 2.0 Consensus size: 45
34791930 TCAAAACATG
34791940 TGTCACATACATCATGAACTCAGACCACAACTCAATGAGTTCATA
1 TGTCACATACATCATGAACTCAGACCACAACTCAATGAGTTCATA
* * *
34791985 TGTCACATATATCATGAACTCAGACCACAATTCGATGAGTTCA
1 TGTCACATACATCATGAACTCAGACCACAACTCAATGAGTTCA
34792028 AATCATATTG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.36, C:0.25, G:0.12, T:0.26
Consensus pattern (45 bp):
TGTCACATACATCATGAACTCAGACCACAACTCAATGAGTTCATA
Found at i:34792558 original size:16 final size:15
Alignment explanation
Indices: 34792516--34792559 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 15
34792506 TCTAAGATTT
*
34792516 TTATTAATTTATTAA
1 TTATTATTTTATTAA
*
34792531 TTATTATATTATATAA
1 TTATTATTTTAT-TAA
*
34792547 TTATTCTTTTATT
1 TTATTATTTTATT
34792560 TTAAATTATA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
15 11 0.46
16 13 0.54
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (15 bp):
TTATTATTTTATTAA
Found at i:34792711 original size:3 final size:3
Alignment explanation
Indices: 34792703--34792756 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
34792693 TTAAAAAATA
34792703 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
34792751 TAT TAT
1 TAT TAT
34792757 GAAATAAATA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:34792946 original size:16 final size:17
Alignment explanation
Indices: 34792908--34792947 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
34792898 AGTGTATTAT
34792908 TATT-ATTATTAATTTA
1 TATTAATTATTAATTTA
*
34792924 T-TAAATTA-TAATTTA
1 TATTAATTATTAATTTA
34792939 TATTAATTA
1 TATTAATTA
34792948 CATTATGAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 4
0.77 0.08 0.15
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TATTAATTATTAATTTA
Found at i:34793815 original size:17 final size:18
Alignment explanation
Indices: 34793793--34793828 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
34793783 TAAATGAGTT
34793793 AATTAGGAT-TAAATTGG
1 AATTAGGATATAAATTGG
*
34793810 AATTAGGGTATAAATTGG
1 AATTAGGATATAAATTGG
34793828 A
1 A
34793829 TAGAAATTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.42, C:0.00, G:0.25, T:0.33
Consensus pattern (18 bp):
AATTAGGATATAAATTGG
Found at i:34794313 original size:23 final size:26
Alignment explanation
Indices: 34794285--34794339 Score: 71
Period size: 27 Copynumber: 2.2 Consensus size: 26
34794275 TGAAAATTTG
*
34794285 ATTGAAAA-GTG-GAAA-ATGATTGA
1 ATTGAAAATGTGAGAAATATGACTGA
34794308 ATTGAAAATGTGAGAAATTATGACTGA
1 ATTGAAAATGTGAGAAA-TATGACTGA
34794335 ATTGA
1 ATTGA
34794340 GATTTATATG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
23 8 0.30
24 3 0.11
25 4 0.15
27 12 0.44
ACGTcount: A:0.45, C:0.02, G:0.24, T:0.29
Consensus pattern (26 bp):
ATTGAAAATGTGAGAAATATGACTGA
Found at i:34797651 original size:15 final size:16
Alignment explanation
Indices: 34797633--34797670 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
34797623 AATTGAAAAG
34797633 ATGAAAAGTT-ATTAA
1 ATGAAAAGTTAATTAA
* *
34797648 ATGATAATTTAATTAA
1 ATGAAAAGTTAATTAA
34797664 ATGAAAA
1 ATGAAAA
34797671 AGAAAATAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 8 0.42
16 11 0.58
ACGTcount: A:0.55, C:0.00, G:0.11, T:0.34
Consensus pattern (16 bp):
ATGAAAAGTTAATTAA
Found at i:34799711 original size:29 final size:29
Alignment explanation
Indices: 34799678--34799808 Score: 163
Period size: 29 Copynumber: 4.5 Consensus size: 29
34799668 TGACGAGATC
*
34799678 GGCACTAAGTGTGCGTGCTGGAAATATAT
1 GGCACTAAGTGTGCGTGCTGGAAAAATAT
* *
34799707 GGCACTAAGTGTGCGTGCTGGAAATATAA
1 GGCACTAAGTGTGCGTGCTGGAAAAATAT
*
34799736 GGCACTAAGTGTGCATGCTGGAAAAATAT
1 GGCACTAAGTGTGCGTGCTGGAAAAATAT
* * ** *
34799765 GACACTATGTGTGCAAGCTGGAAAAATAC
1 GGCACTAAGTGTGCGTGCTGGAAAAATAT
**
34799794 GGCACTGGGTGTGCG
1 GGCACTAAGTGTGCG
34799809 AGCTCGGAGG
Statistics
Matches: 90, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 90 1.00
ACGTcount: A:0.30, C:0.15, G:0.31, T:0.24
Consensus pattern (29 bp):
GGCACTAAGTGTGCGTGCTGGAAAAATAT
Found at i:34807708 original size:26 final size:26
Alignment explanation
Indices: 34807647--34807716 Score: 90
Period size: 26 Copynumber: 2.7 Consensus size: 26
34807637 GACGAGATCG
* *
34807647 GCACTAAGTGTGTGTGCT-AATATAT
1 GCACTAAGTGTGCGTGCTGAATATAA
34807672 GCACTAAGTGTGCGTGCTGAA-ATAAA
1 GCACTAAGTGTGCGTGCTGAATAT-AA
*
34807698 GCACTAAGTGTGCATGCTG
1 GCACTAAGTGTGCGTGCTG
34807717 GAAAAATATG
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
25 19 0.47
26 21 0.52
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.29
Consensus pattern (26 bp):
GCACTAAGTGTGCGTGCTGAATATAA
Found at i:34807760 original size:29 final size:29
Alignment explanation
Indices: 34807698--34807760 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
34807688 CTGAAATAAA
* *
34807698 GCACTAAGTGTGCATGCTGGAAAAATATG
1 GCACTAAGTGTGCAAGCTGGAAAAATACG
* *
34807727 ACACTATGT-TGCAAGCTGGAAAAAATACG
1 GCACTAAGTGTGCAAGCTGG-AAAAATACG
34807756 GCACT
1 GCACT
34807761 GGGTGTGCGA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
28 9 0.32
29 19 0.68
ACGTcount: A:0.37, C:0.17, G:0.24, T:0.22
Consensus pattern (29 bp):
GCACTAAGTGTGCAAGCTGGAAAAATACG
Found at i:34810363 original size:40 final size:39
Alignment explanation
Indices: 34810198--34810381 Score: 138
Period size: 40 Copynumber: 4.6 Consensus size: 39
34810188 AAATTGAATG
* * *
34810198 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAAT--T
1 ATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATCGT
* * * * * *
34810238 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-T
* * * * *
34810278 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATC-GT
*
34810318 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
* * *
34810357 GATATCCGGGTTAAGTCCCGTAGGC
1 -ATATCCGGGCTAAGACCCGAAGGC
34810382 CTTGGTGTGG
Statistics
Matches: 113, Mismatches: 26, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
37 4 0.04
38 2 0.02
39 3 0.03
40 104 0.92
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (39 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
Found at i:34815956 original size:24 final size:25
Alignment explanation
Indices: 34815929--34815981 Score: 65
Period size: 27 Copynumber: 2.1 Consensus size: 25
34815919 TTTACTTATG
34815929 TTTTTTTATT-A-TAATATTGTTGTA
1 TTTTTTTATTGACTAATATTGTT-TA
*
34815953 TTTTTTTTTTGGACTAATATTGTTTA
1 TTTTTTTATT-GACTAATATTGTTTA
34815979 TTT
1 TTT
34815982 GGGTTGATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
24 9 0.36
26 6 0.24
27 10 0.40
ACGTcount: A:0.21, C:0.02, G:0.09, T:0.68
Consensus pattern (25 bp):
TTTTTTTATTGACTAATATTGTTTA
Found at i:34818222 original size:27 final size:26
Alignment explanation
Indices: 34818192--34818248 Score: 62
Period size: 27 Copynumber: 2.1 Consensus size: 26
34818182 CATACCTTGA
*
34818192 CCCCAAATTTGGTAATA-GACTATTATG
1 CCCC-AATTAGGTAA-AGGACTATTATG
*
34818219 CCCCTATTAGGTAAAGTGACTATTATG
1 CCCCAATTAGGTAAAG-GACTATTATG
34818246 CCC
1 CCC
34818249 TTATGGGATG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
25 1 0.04
26 8 0.31
27 17 0.65
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.32
Consensus pattern (26 bp):
CCCCAATTAGGTAAAGGACTATTATG
Found at i:34823590 original size:37 final size:37
Alignment explanation
Indices: 34823537--34823631 Score: 163
Period size: 37 Copynumber: 2.6 Consensus size: 37
34823527 CGAATAGTCC
* *
34823537 CCACACATAGTTATCGGGTCTTACCCGGACAAAATCT
1 CCACACGTAGTCATCGGGTCTTACCCGGACAAAATCT
*
34823574 CCACACGTAGTCATCGGGTCTTACCCGGACATAATCT
1 CCACACGTAGTCATCGGGTCTTACCCGGACAAAATCT
34823611 CCACACGTAGTCATCGGGTCT
1 CCACACGTAGTCATCGGGTCT
34823632 GTGACAGCCC
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 55 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
CCACACGTAGTCATCGGGTCTTACCCGGACAAAATCT
Found at i:34826114 original size:49 final size:49
Alignment explanation
Indices: 34826037--34826250 Score: 347
Period size: 49 Copynumber: 4.4 Consensus size: 49
34826027 ATCAAGATTC
* * *
34826037 GTGAAAATGTATATATATGTGATGAGGCCTAATGGCCGATGCGATGAAT
1 GTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAAT
* * *
34826086 GCGAAAATGTATGTATATGTGATAAGGCCTAATGGCCGATGTGATGAAT
1 GTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAAT
* *
34826135 GTGAAAGTATATATATATGTGATAAGGCCTAATGGCCGATGTGGTGAAT
1 GTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAAT
*
34826184 GTGAAAGTGTATGTATATGTGATAAGGCCTAATGGCCGATGTGATGAAT
1 GTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAAT
34826233 GTGAAAGTGTATATATAT
1 GTGAAAGTGTATATATAT
34826251 ATGTGGTAAA
Statistics
Matches: 152, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
49 152 1.00
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.30
Consensus pattern (49 bp):
GTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAAT
Found at i:34828276 original size:40 final size:40
Alignment explanation
Indices: 34828230--34828569 Score: 352
Period size: 40 Copynumber: 8.6 Consensus size: 40
34828220 TGAATGATAC
* ** *
34828230 CCGGGCTAAGTCCCGAAG-GCATTTATGCTAGTGAATATAT
1 CCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTG-ATGTAT
** * * * *
34828270 CCGGGCTAAGACCCGAAG-GCATTTGTG-TGAGTTGTTATAC
1 CCGGGCTAAGTTCCGAAGAGCATTCGTGCT-AG-TGATGTAT
* ** * * *
34828310 CCGGGTTAAGACCCGAAG-GCAATT-GTGCTTGTGGTTATAT
1 CCGGGCTAAGTTCCGAAGAGC-ATTCGTGCTAGT-GATGTAT
34828350 CC-GGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTAT
1 CCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTAT
*
34828389 CCGGACTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTAT
1 CCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTAT
* * *
34828429 CCGGACTAAGTTCTGAGGAGCATTCGTGCTAGTGATGTAT
1 CCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTAT
* *
34828469 CC-GACTAAGTTCCGAGGAGCATTCGTGCTAGTGATGTAT
1 CCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTAT
* *
34828508 CCGGACTAAGTTCCGAAGAGCATTCGTGCTAGTGATGCAT
1 CCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTAT
* *
34828548 CCGGGCTAGGTCCCGAAGAGCA
1 CCGGGCTAAGTTCCGAAGAGCA
34828570 ATCATGCTGG
Statistics
Matches: 269, Mismatches: 22, Indels: 18
0.87 0.07 0.06
Matches are distributed among these distances:
39 62 0.23
40 201 0.75
41 6 0.02
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.27
Consensus pattern (40 bp):
CCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTAT
Found at i:34828430 original size:79 final size:80
Alignment explanation
Indices: 34828347--34828569 Score: 369
Period size: 79 Copynumber: 2.8 Consensus size: 80
34828337 CTTGTGGTTA
34828347 TATCCGG-CTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTATCCGGACTAAGTTCCGAAGAGCA
1 TATCCGGACTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTATCCGGACTAAGTTCCGAAGAGCA
34828411 TTCGTGCTAGTGATG
66 TTCGTGCTAGTGATG
* * *
34828426 TATCCGGACTAAGTTCTGAGGAGCATTCGTGCTAGTGATGTATCC-GACTAAGTTCCGAGGAGCA
1 TATCCGGACTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTATCCGGACTAAGTTCCGAAGAGCA
34828490 TTCGTGCTAGTGATG
66 TTCGTGCTAGTGATG
* * * *
34828505 TATCCGGACTAAGTTCCGAAGAGCATTCGTGCTAGTGATGCATCCGGGCTAGGTCCCGAAGAGCA
1 TATCCGGACTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTATCCGGACTAAGTTCCGAAGAGCA
34828570 ATCATGCTGG
Statistics
Matches: 132, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
79 82 0.62
80 50 0.38
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (80 bp):
TATCCGGACTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTATCCGGACTAAGTTCCGAAGAGCA
TTCGTGCTAGTGATG
Found at i:34828569 original size:119 final size:119
Alignment explanation
Indices: 34828347--34828569 Score: 374
Period size: 119 Copynumber: 1.9 Consensus size: 119
34828337 CTTGTGGTTA
*
34828347 TATCCGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTATCCGGACTAAGTTCCGAAGAGCAT
1 TATCCGACTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTATCCGGACTAAGTTCCGAAGAGCAT
* * * *
34828412 TCGTGCTAGTGATGTATCCGGACTAAGTTCTGAGGAGCATTCGTGCTAGTGATG
66 TCGTGCTAGTGATGCATCCGGACTAAGTCCCGAAGAGCATTCGTGCTAGTGATG
*
34828466 TATCCGACTAAGTTCCGAGGAGCATTCGTGCTAGTGATGTATCCGGACTAAGTTCCGAAGAGCAT
1 TATCCGACTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTATCCGGACTAAGTTCCGAAGAGCAT
* *
34828531 TCGTGCTAGTGATGCATCCGGGCTAGGTCCCGAAGAGCA
66 TCGTGCTAGTGATGCATCCGGACTAAGTCCCGAAGAGCA
34828570 ATCATGCTGG
Statistics
Matches: 96, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
119 96 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (119 bp):
TATCCGACTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTATCCGGACTAAGTTCCGAAGAGCAT
TCGTGCTAGTGATGCATCCGGACTAAGTCCCGAAGAGCATTCGTGCTAGTGATG
Found at i:34832573 original size:95 final size:96
Alignment explanation
Indices: 34832416--34832616 Score: 341
Period size: 95 Copynumber: 2.1 Consensus size: 96
34832406 TCGTGAAAAT
*
34832416 GTATATATATGTGATGAGGCCTAATGGCCGATGCGATGAATGCGAAAATGTATGTATATGTGAT-
1 GTATATATATGTGATAAGGCCTAATGGCCGATGCGATGAATGCGAAAATGTATGTATATGTGATA
34832480 AGGCCTAATGGCCGATGTGATGAATGTGAAA
66 AGGCCTAATGGCCGATGTGATGAATGTGAAA
* * * *
34832511 GTATATATATGTGATAAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATGTATATGTGATA
1 GTATATATATGTGATAAGGCCTAATGGCCGATGCGATGAATGCGAAAATGTATGTATATGTGATA
34832576 AGGCCTAATGGCCGATGTGATGAATGTGAAA
66 AGGCCTAATGGCCGATGTGATGAATGTGAAA
*
34832607 GTGTATATAT
1 GTATATATAT
34832617 ATATGTGGTA
Statistics
Matches: 99, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
95 59 0.60
96 40 0.40
ACGTcount: A:0.31, C:0.09, G:0.29, T:0.30
Consensus pattern (96 bp):
GTATATATATGTGATAAGGCCTAATGGCCGATGCGATGAATGCGAAAATGTATGTATATGTGATA
AGGCCTAATGGCCGATGTGATGAATGTGAAA
Found at i:34832646 original size:51 final size:49
Alignment explanation
Indices: 34832408--34832618 Score: 329
Period size: 49 Copynumber: 4.4 Consensus size: 49
34832398 ATCAAGATTC
* * *
34832408 GTGAAAATGTATATATATGTGATGAGGCCTAATGGCCGATGCGATGAAT
1 GTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAAT
* * *
34832457 GCGAAAATGTATGTATATGTGAT-AGGCCTAATGGCCGATGTGATGAAT
1 GTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAAT
*
34832505 GTGAAA--GTATATATATGTGATAAGGCCTAATGGCCGATGTGGTGAAT
1 GTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAAT
*
34832552 GTGAAAGTGTATGTATATGTGATAAGGCCTAATGGCCGATGTGATGAAT
1 GTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAAT
34832601 GTGAAAGTGTATATATAT
1 GTGAAAGTGTATATATAT
34832619 ATGTGGTAAA
Statistics
Matches: 150, Mismatches: 9, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
46 14 0.09
47 30 0.20
48 29 0.19
49 77 0.51
ACGTcount: A:0.32, C:0.09, G:0.29, T:0.30
Consensus pattern (49 bp):
GTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAAT
Found at i:34834361 original size:48 final size:48
Alignment explanation
Indices: 34834304--34834567 Score: 483
Period size: 48 Copynumber: 5.5 Consensus size: 48
34834294 CTAGCCGAAT
*
34834304 CACTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCG
1 CACTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCA
*
34834352 CATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCA
1 CACTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCA
* *
34834400 CACTAGCCATTCGGCTTTACCACGTATACATATCTCATACATAGTTCA
1 CACTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCA
34834448 CACTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCA
1 CACTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCA
34834496 CACTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCA
1 CACTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCA
*
34834544 CATTAGCCATTCGGCTTTACCACA
1 CACTAGCCATTCGGCTTTACCACA
34834568 CACATATATA
Statistics
Matches: 208, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 208 1.00
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.33
Consensus pattern (48 bp):
CACTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCA
Found at i:34841049 original size:16 final size:16
Alignment explanation
Indices: 34841019--34841052 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
34841009 TAGGTCTCCA
*
34841019 AAATTTTTACCTTTTT
1 AAATTTTTAACTTTTT
*
34841035 AAATTTTTAATTTTTT
1 AAATTTTTAACTTTTT
34841051 AA
1 AA
34841053 CTTTCTTTAT
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:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (16 bp):
AAATTTTTAACTTTTT
Found at i:34841108 original size:15 final size:16
Alignment explanation
Indices: 34841082--34841111 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
34841072 TAGAATTTTT
34841082 TATAATATTTTAAAAA
1 TATAATATTTTAAAAA
34841098 TATAA-ATTTTAAAA
1 TATAATATTTTAAAA
34841112 TTTTTATAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
TATAATATTTTAAAAA
Found at i:34841161 original size:20 final size:21
Alignment explanation
Indices: 34841131--34841176 Score: 76
Period size: 20 Copynumber: 2.2 Consensus size: 21
34841121 GTATTTTAAA
*
34841131 ATTTAAAAATTATTTTGAATT
1 ATTTTAAAATTATTTTGAATT
34841152 -TTTTAAAATTATTTTGAATT
1 ATTTTAAAATTATTTTGAATT
34841172 ATTTT
1 ATTTT
34841177 GTAACTTTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 19 0.83
21 4 0.17
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (21 bp):
ATTTTAAAATTATTTTGAATT
Found at i:34841171 original size:10 final size:10
Alignment explanation
Indices: 34841138--34841177 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
34841128 AAAATTTAAA
34841138 AATTATTTTG
1 AATTATTTTG
*
34841148 AATT-TTTTAA
1 AATTATTTT-G
34841158 AATTATTTTG
1 AATTATTTTG
34841168 AATTATTTTG
1 AATTATTTTG
34841178 TAACTTTTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
9 4 0.15
10 18 0.69
11 4 0.15
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (10 bp):
AATTATTTTG
Found at i:34843757 original size:46 final size:46
Alignment explanation
Indices: 34843707--34843879 Score: 210
Period size: 46 Copynumber: 3.7 Consensus size: 46
34843697 TGGTTGAGCA
34843707 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
34843753 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--AATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
34843798 CATCCGAACTCGTTGAGTTGAGTTCGAGTTCACTTATGGATGCGAATG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
34843846 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
34843880 GGGGCGGGTT
Statistics
Matches: 106, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 3 0.03
46 60 0.57
47 28 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:34843863 original size:93 final size:93
Alignment explanation
Indices: 34843704--34843874 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
34843694 GGATGGTTGA
*
34843704 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCCGAACTCGTTGAGT
34843769 TGAGTCCGAGTTCGTGAAATGTAACTAG
66 TGAGTCCGAGTTCGTGAAATGTAACTAG
* *
34843797 GCATCCGAACTCGTTGAGTTGAGTTCGAGTTCACTTATGGATGCGAATGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCCGAACTCGTTGAGT
34843862 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
34843875 ACTTAGGGGC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAAATGTAACTAG
Found at i:34851003 original size:23 final size:23
Alignment explanation
Indices: 34850949--34851004 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
34850939 CGCAGTGTAA
*
34850949 CTGCTAATAGTAACGCAAGAAAG
1 CTGCTAATAGTAACACAAGAAAG
*
34850972 CTACTAATAGTAACAC-AGCAAAG
1 CTGCTAATAGTAACACAAG-AAAG
*
34850995 CTGCAAATAG
1 CTGCTAATAG
34851005 CGGCAAATGC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 2 0.07
23 26 0.93
ACGTcount: A:0.45, C:0.20, G:0.18, T:0.18
Consensus pattern (23 bp):
CTGCTAATAGTAACACAAGAAAG
Found at i:34857210 original size:33 final size:33
Alignment explanation
Indices: 34857162--34857224 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
34857152 TACAATAATG
* * *
34857162 GTCTGGGCTTGAGCCCTATTCAATAACAGTACA
1 GTCTGGGCCTAAGCCCTATGCAATAACAGTACA
*
34857195 GTCTGGGCCTAAGCCCTATGCAGTAACAGT
1 GTCTGGGCCTAAGCCCTATGCAATAACAGT
34857225 GTGGGCCTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.25, C:0.25, G:0.24, T:0.25
Consensus pattern (33 bp):
GTCTGGGCCTAAGCCCTATGCAATAACAGTACA
Found at i:34857392 original size:23 final size:23
Alignment explanation
Indices: 34857366--34857423 Score: 89
Period size: 23 Copynumber: 2.5 Consensus size: 23
34857356 ATCGTAGCGT
*
34857366 AGCTGCTAATAGTAATGCAGTAA
1 AGCTGCTAATAGTAATGCAGCAA
* *
34857389 AGCTGCTAGTAGTAATGTAGCAA
1 AGCTGCTAATAGTAATGCAGCAA
34857412 AGCTGCTAATAG
1 AGCTGCTAATAG
34857424 CGGTAAACGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.36, C:0.14, G:0.24, T:0.26
Consensus pattern (23 bp):
AGCTGCTAATAGTAATGCAGCAA
Found at i:34867970 original size:26 final size:26
Alignment explanation
Indices: 34867927--34867984 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
34867917 CTACCAGTAA
* **
34867927 CAGTATCGCAACAGAGCTTTCAATAT
1 CAGTATCGCAACAAAGCTGCCAATAT
* *
34867953 CAGTATCGCAGCAAAGCTGCCAGTAT
1 CAGTATCGCAACAAAGCTGCCAATAT
34867979 CAGTAT
1 CAGTAT
34867985 ATGTGGCGAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (26 bp):
CAGTATCGCAACAAAGCTGCCAATAT
Found at i:34870368 original size:27 final size:27
Alignment explanation
Indices: 34870350--34870419 Score: 122
Period size: 27 Copynumber: 2.6 Consensus size: 27
34870340 ATAGTGAGTC
34870350 CGCACACTTAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTATATAATCAACT
*
34870377 CGCACACTTAGTGCTATACAATCAAACT
1 CGCACACTTAGTGCTATATAATC-AACT
34870405 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
34870420 GTACAAATTT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTATATAATCAACT
Found at i:34870413 original size:28 final size:27
Alignment explanation
Indices: 34870350--34870425 Score: 125
Period size: 28 Copynumber: 2.8 Consensus size: 27
34870340 ATAGTGAGTC
*
34870350 CGCACACTTAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTATACAATCAACT
34870377 CGCACACTTAGTGCTATACAATCAAACT
1 CGCACACTTAGTGCTATACAATC-AACT
*
34870405 CGCACACTTAGTGCTGTACAA
1 CGCACACTTAGTGCTATACAA
34870426 ATTTTAAACC
Statistics
Matches: 46, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
27 22 0.48
28 24 0.52
ACGTcount: A:0.33, C:0.28, G:0.13, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTATACAATCAACT
Found at i:34878223 original size:28 final size:28
Alignment explanation
Indices: 34878160--34878259 Score: 130
Period size: 27 Copynumber: 3.5 Consensus size: 28
34878150 ATAGTGAGTC
*
34878160 CGCACACTTAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATACAATCAAACT
34878187 CGCACACTTAGTGCTATACAATCAAACT
1 CGCACACTTAGTGCTATACAATCAAACT
* * *
34878215 CGCACACTTAGTGCTGTACAAATTTTAAACC
1 CGCACACTTAGTGCTATAC-AA--TCAAACT
34878246 CGCACACTTAGTGC
1 CGCACACTTAGTGC
34878260 CAATTTCATG
Statistics
Matches: 65, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
27 22 0.34
28 22 0.34
29 2 0.03
31 19 0.29
ACGTcount: A:0.32, C:0.28, G:0.13, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATACAATCAAACT
Found at i:34881810 original size:18 final size:18
Alignment explanation
Indices: 34881772--34881810 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
34881762 TTTGGACTAA
*
34881772 GTTTTGGGTTTCAGTTTT
1 GTTTTGGGTTTCAGTTAT
34881790 GTTTTGGGTTT-ATGTTAT
1 GTTTTGGGTTTCA-GTTAT
34881808 GTT
1 GTT
34881811 CATCGGCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 1 0.05
18 18 0.95
ACGTcount: A:0.08, C:0.03, G:0.28, T:0.62
Consensus pattern (18 bp):
GTTTTGGGTTTCAGTTAT
Found at i:34884243 original size:40 final size:40
Alignment explanation
Indices: 34884116--34884245 Score: 174
Period size: 40 Copynumber: 3.2 Consensus size: 40
34884106 ATGCTGGAAA
* *
34884116 TTATATCCGGGTTAAGACCCGAAGGCAATT-GTGCTAGTGG
1 TTATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTGG
* * *
34884156 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCG
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG
*
34884196 TTCTATCCGGGCTAAGACCCGAAGGCATTCGTGC-ACGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGA-GTGG
34884236 TTATATCCGG
1 TTATATCCGG
34884246 TTGTATTCCG
Statistics
Matches: 78, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
39 4 0.05
40 74 0.95
ACGTcount: A:0.22, C:0.25, G:0.29, T:0.24
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG
Found at i:34892199 original size:40 final size:40
Alignment explanation
Indices: 34892072--34892201 Score: 174
Period size: 40 Copynumber: 3.2 Consensus size: 40
34892062 ATGCTGGAAA
* *
34892072 TTATATCCGGGTTAAGACCCGAAGGCAATT-GTGCTAGTGG
1 TTATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTGG
* * *
34892112 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCG
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG
*
34892152 TTCTATCCGGGCTAAGACCCGAAGGCATTCGTGC-ACGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGA-GTGG
34892192 TTATATCCGG
1 TTATATCCGG
34892202 TTGTATTCCG
Statistics
Matches: 78, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
39 4 0.05
40 74 0.95
ACGTcount: A:0.22, C:0.25, G:0.29, T:0.24
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG
Found at i:34895016 original size:41 final size:41
Alignment explanation
Indices: 34894971--34895088 Score: 98
Period size: 41 Copynumber: 3.1 Consensus size: 41
34894961 TGAAAGATAA
34894971 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
* * * * *
34895012 ATGTAGAC-AAG-AG-A-GC-T-A---C--GTGAAAGATA-A
1 ATGTAG-CTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
34895042 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
34895083 ATGTAG
1 ATGTAG
34895089 ACAAAGAGCT
Statistics
Matches: 54, Mismatches: 10, Indels: 26
0.60 0.11 0.29
Matches are distributed among these distances:
29 1 0.02
30 8 0.15
31 9 0.17
32 1 0.02
33 3 0.06
34 1 0.02
35 1 0.02
36 1 0.02
37 1 0.02
38 3 0.06
39 1 0.02
40 9 0.17
41 14 0.26
42 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (41 bp):
ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
Found at i:34895027 original size:71 final size:71
Alignment explanation
Indices: 34894939--34895101 Score: 319
Period size: 71 Copynumber: 2.3 Consensus size: 71
34894929 GAGATGTATC
34894939 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
34895004 AGGACA
66 AGGACA
34895010 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
34895075 AGGACA
66 AGGACA
34895081 CCATGTAGACAA-AGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
34895102 AGACAAATCG
Statistics
Matches: 92, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
70 9 0.10
71 83 0.90
ACGTcount: A:0.36, C:0.18, G:0.28, T:0.19
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
AGGACA
Found at i:34902587 original size:41 final size:41
Alignment explanation
Indices: 34902542--34902659 Score: 98
Period size: 41 Copynumber: 3.1 Consensus size: 41
34902532 TGAAAGATAA
34902542 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
* * * * *
34902583 ATGTAGAC-AAG-AG-A-GC-T-A---C--GTGAAAGATA-A
1 ATGTAG-CTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
34902613 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
34902654 ATGTAG
1 ATGTAG
34902660 ACAAGAGAGC
Statistics
Matches: 54, Mismatches: 10, Indels: 26
0.60 0.11 0.29
Matches are distributed among these distances:
29 1 0.02
30 8 0.15
31 9 0.17
32 1 0.02
33 3 0.06
34 1 0.02
35 1 0.02
36 1 0.02
37 1 0.02
38 3 0.06
39 1 0.02
40 9 0.17
41 14 0.26
42 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (41 bp):
ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
Found at i:34902598 original size:71 final size:71
Alignment explanation
Indices: 34902510--34902673 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
34902500 GAGATGTATC
34902510 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
34902575 AGGACA
66 AGGACA
34902581 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
34902646 AGGACA
66 AGGACA
34902652 CCATGTAGACAAGAGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
34902674 AGACAAATCG
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
AGGACA
Found at i:34914012 original size:18 final size:18
Alignment explanation
Indices: 34913989--34914029 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
34913979 CATAATGCGG
34913989 GCCCATGTGAGCACACAT-
1 GCCCATGT-AGCACACATA
*
34914007 GCCCATGTAGCCCACATA
1 GCCCATGTAGCACACATA
34914025 GCCCA
1 GCCCA
34914030 GAAATGGCCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.27, C:0.39, G:0.20, T:0.15
Consensus pattern (18 bp):
GCCCATGTAGCACACATA
Found at i:34917323 original size:6 final size:6
Alignment explanation
Indices: 34917312--34917338 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
34917302 ATTCACTTTA
34917312 TCTATC TCTATC TCTATC TCTATC TCT
1 TCTATC TCTATC TCTATC TCTATC TCT
34917339 TACAATTTTA
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:0.15, C:0.33, G:0.00, T:0.52
Consensus pattern (6 bp):
TCTATC
Found at i:34922930 original size:80 final size:80
Alignment explanation
Indices: 34922846--34922994 Score: 183
Period size: 80 Copynumber: 1.9 Consensus size: 80
34922836 TATGGTAACC
* * * *
34922846 CGCACCAAGGCCTACGGGACTTAACCCGGATATCA-CGATTTGCACAAATGCCTTCGGGTCTTAG
1 CGCACCAAGGCCTACGGGACTTAACCCGGATAT-AGCCACTAGCACAAATGCCTTCGGGTCTTAA
34922910 CCCGGATAGAATGACT
65 CCCGGATAGAATGACT
* * * * * * *
34922926 CGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
34922991 CCGG
66 CCGG
34922995 TTATAATTTC
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
79 1 0.02
80 56 0.98
ACGTcount: A:0.23, C:0.30, G:0.25, T:0.22
Consensus pattern (80 bp):
CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
CCGGATAGAATGACT
Found at i:34922936 original size:40 final size:38
Alignment explanation
Indices: 34922887--34922994 Score: 128
Period size: 40 Copynumber: 2.7 Consensus size: 38
34922877 ATCACGATTT
*
34922887 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATG-ACTC
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGAT-GAA-GCACTA
*
34922927 GCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATGAAG-CACTA
*
34922967 GCACAATTGCCTTCGGGTCTTAACCCGG
1 GCACAA-TGCCTTCGGGTCTTAGCCCGG
34922995 TTATAATTTC
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
38 1 0.02
39 4 0.07
40 56 0.92
ACGTcount: A:0.21, C:0.30, G:0.26, T:0.23
Consensus pattern (38 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATGAAGCACTA
Found at i:34931039 original size:80 final size:80
Alignment explanation
Indices: 34930955--34931103 Score: 183
Period size: 80 Copynumber: 1.9 Consensus size: 80
34930945 TATGGTAACC
* * * *
34930955 CGCACCAAGGCCTACGGGACTTAACCCGGATATCA-CGATTTGCACAAATGCCTTCGGGTCTTAG
1 CGCACCAAGGCCTACGGGACTTAACCCGGATAT-AGCCACTAGCACAAATGCCTTCGGGTCTTAA
34931019 CCCGGATAGAATGACT
65 CCCGGATAGAATGACT
* * * * * * *
34931035 CGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
34931100 CCGG
66 CCGG
34931104 TTATAATTTC
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
79 1 0.02
80 56 0.98
ACGTcount: A:0.23, C:0.30, G:0.25, T:0.22
Consensus pattern (80 bp):
CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
CCGGATAGAATGACT
Found at i:34931045 original size:40 final size:38
Alignment explanation
Indices: 34930996--34931103 Score: 128
Period size: 40 Copynumber: 2.7 Consensus size: 38
34930986 ATCACGATTT
*
34930996 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATG-ACTC
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGAT-GAA-GCACTA
*
34931036 GCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATGAAG-CACTA
*
34931076 GCACAATTGCCTTCGGGTCTTAACCCGG
1 GCACAA-TGCCTTCGGGTCTTAGCCCGG
34931104 TTATAATTTC
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
38 1 0.02
39 4 0.07
40 56 0.92
ACGTcount: A:0.21, C:0.30, G:0.26, T:0.23
Consensus pattern (38 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATGAAGCACTA
Found at i:34935990 original size:28 final size:28
Alignment explanation
Indices: 34935944--34935999 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
34935934 CAGTACCAAT
** * *
34935944 ACAGTCTGGGCCTTTGCCCTATACAGTA
1 ACAGTCTGGGCCTAAGCCCAACACAGTA
*
34935972 ACAGTGTGGGCCTAAGCCCAACACAGTA
1 ACAGTCTGGGCCTAAGCCCAACACAGTA
34936000 TTAGTACAGT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.27, C:0.29, G:0.23, T:0.21
Consensus pattern (28 bp):
ACAGTCTGGGCCTAAGCCCAACACAGTA
Found at i:34939908 original size:27 final size:27
Alignment explanation
Indices: 34939866--34939952 Score: 115
Period size: 27 Copynumber: 3.2 Consensus size: 27
34939856 AGGAAGCGTC
*
34939866 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCACAATTATCTGAT
* *
34939893 CTGGTGGCTCTACCAC-ATATATCTGTT
1 CTGGTGGCTCTGCCACAAT-TATCTGAT
34939920 CTGGTGGCTCTGCCACAA-TATCTGTAT
1 CTGGTGGCTCTGCCACAATTATCTG-AT
34939947 CTGGTG
1 CTGGTG
34939953 ACTTCGTCAC
Statistics
Matches: 52, Mismatches: 5, Indels: 6
0.83 0.08 0.10
Matches are distributed among these distances:
26 8 0.15
27 43 0.83
28 1 0.02
ACGTcount: A:0.18, C:0.24, G:0.23, T:0.34
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACAATTATCTGAT
Found at i:34939963 original size:27 final size:26
Alignment explanation
Indices: 34939866--34939970 Score: 104
Period size: 27 Copynumber: 3.9 Consensus size: 26
34939856 AGGAAGCGTC
* * *
34939866 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGACTCTGCCACAA-TATCTGTT
* *
34939893 CTGGTGGCTCTACCACATATATCTGTT
1 CTGGTGACTCTGCCACA-ATATCTGTT
*
34939920 CTGGTGGCTCTGCCACAATATCTGTAT
1 CTGGTGACTCTGCCACAATATCTGT-T
*
34939947 CTGGTGACT-TCGTCACAATATCTG
1 CTGGTGACTCT-GCCACAATATCTG
34939971 GCAGCCTCGC
Statistics
Matches: 69, Mismatches: 6, Indels: 6
0.85 0.07 0.07
Matches are distributed among these distances:
26 9 0.13
27 59 0.86
28 1 0.01
ACGTcount: A:0.20, C:0.25, G:0.21, T:0.34
Consensus pattern (26 bp):
CTGGTGACTCTGCCACAATATCTGTT
Found at i:34941936 original size:39 final size:39
Alignment explanation
Indices: 34941905--34942041 Score: 184
Period size: 39 Copynumber: 3.5 Consensus size: 39
34941895 TAACAATTAG
* *
34941905 TTATTTAGTACAGTAATTTAGTCATTCAGTAACTATCAA
1 TTATTCAGTACAGTAATTTAGTTATTCAGTAACTATCAA
* * * * *
34941944 ATATTCAGTGCAGTAGTTTAGTTATTCAATAATTATCAA
1 TTATTCAGTACAGTAATTTAGTTATTCAGTAACTATCAA
**
34941983 TTATTCAAAACAGTAATTTAGTTATTCAGTAACTATCAA
1 TTATTCAGTACAGTAATTTAGTTATTCAGTAACTATCAA
*
34942022 TTATTCAGTACAGTAGTTTA
1 TTATTCAGTACAGTAATTTA
34942042 CCCCTATTAA
Statistics
Matches: 81, Mismatches: 17, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
39 81 1.00
ACGTcount: A:0.36, C:0.12, G:0.11, T:0.41
Consensus pattern (39 bp):
TTATTCAGTACAGTAATTTAGTTATTCAGTAACTATCAA
Found at i:34943351 original size:21 final size:20
Alignment explanation
Indices: 34943327--34943383 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 20
34943317 AAAATCTTAT
34943327 AATATAATTATTTAATTAATA
1 AATATAATTATTTAA-TAATA
** *
34943348 AATATCTTTAACTTAATAATA
1 AATATAATT-ATTTAATAATA
*
34943369 AATAATAAATATTTA
1 AAT-ATAATTATTTA
34943384 TTTACTTCAA
Statistics
Matches: 27, Mismatches: 7, Indels: 4
0.71 0.18 0.11
Matches are distributed among these distances:
21 19 0.70
22 8 0.30
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.44
Consensus pattern (20 bp):
AATATAATTATTTAATAATA
Found at i:34943398 original size:30 final size:28
Alignment explanation
Indices: 34943343--34943404 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 28
34943333 ATTATTTAAT
34943343 TAATAAATATCTTTAACTTAATAATAAA
1 TAATAAATATCTTTAACTTAATAATAAA
* * *
34943371 TAATAAATATTTATTTACTTCAATAATAAG
1 TAATAAATATCT-TTAACTT-AATAATAAA
34943401 TAAT
1 TAAT
34943405 TTAAATCCAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 11 0.38
29 6 0.21
30 12 0.41
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.42
Consensus pattern (28 bp):
TAATAAATATCTTTAACTTAATAATAAA
Found at i:34945951 original size:32 final size:32
Alignment explanation
Indices: 34945915--34946001 Score: 129
Period size: 32 Copynumber: 2.7 Consensus size: 32
34945905 GTCTCAATTA
*
34945915 GGCCTAGCCCATCTCAGAATCAATATCAGTTG
1 GGCCTAGCCCATATCAGAATCAATATCAGTTG
* *
34945947 GGCCTAGCCCATATCAGAACCAGTATCAGTTG
1 GGCCTAGCCCATATCAGAATCAATATCAGTTG
* *
34945979 GGCCTAGCCCATTTCAGTATCAA
1 GGCCTAGCCCATATCAGAATCAA
34946002 ACCCATATGA
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 48 1.00
ACGTcount: A:0.28, C:0.29, G:0.20, T:0.24
Consensus pattern (32 bp):
GGCCTAGCCCATATCAGAATCAATATCAGTTG
Found at i:34960676 original size:40 final size:39
Alignment explanation
Indices: 34960511--34960694 Score: 138
Period size: 40 Copynumber: 4.6 Consensus size: 39
34960501 AAATTGAATG
* * *
34960511 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAAT--T
1 ATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATCGT
* * * * * *
34960551 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-T
* * * * *
34960591 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATC-GT
*
34960631 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
* * *
34960670 GATATCCGGGTTAAGTCCCGTAGGC
1 -ATATCCGGGCTAAGACCCGAAGGC
34960695 CTTGGTGCGG
Statistics
Matches: 113, Mismatches: 26, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
37 4 0.04
38 2 0.02
39 3 0.03
40 104 0.92
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (39 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
Found at i:34960677 original size:80 final size:80
Alignment explanation
Indices: 34960555--34960703 Score: 183
Period size: 80 Copynumber: 1.9 Consensus size: 80
34960545 GAAATTATAA
* * * *
34960555 CCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCTACATCCGGGCTAAGACCCGAAGGCATTCG
1 CCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCATTCG
34960620 TGCGAGTCATTCTAT
66 TGCGAGTCATTCTAT
* * * * * * *
34960635 CCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-TGATATCCGGGTTAAGTCCCGTAGGCCTTG
1 CCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCT-ACATCCGGGCTAAGACCCGAAGGCATTC
34960699 GTGCG
65 GTGCG
34960704 GGTTACCATA
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
79 1 0.02
80 56 0.98
ACGTcount: A:0.22, C:0.25, G:0.30, T:0.23
Consensus pattern (80 bp):
CCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCATTCG
TGCGAGTCATTCTAT
Found at i:34965792 original size:92 final size:92
Alignment explanation
Indices: 34965681--34965850 Score: 313
Period size: 92 Copynumber: 1.8 Consensus size: 92
34965671 GCCCCTAAGT
* *
34965681 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
34965746 CGAGTTCGGATGCCTAGTTACTCTCAC
66 CGAGTTCGGATGCCTAGTTACTCTCAC
*
34965773 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
34965838 CGAGTTCGGATGC
66 CGAGTTCGGATGC
34965851 TCAACCATCC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
92 75 1.00
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (92 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACTCTCAC
Found at i:34965847 original size:46 final size:46
Alignment explanation
Indices: 34965676--34965847 Score: 210
Period size: 46 Copynumber: 3.7 Consensus size: 46
34965666 AACCCGCCCC
* * *
34965676 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
*
34965722 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGC-CTAGTTACTC-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGC-A--T-C-CA
* *
34965769 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
34965814 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
34965848 TGCTCAACCA
Statistics
Matches: 108, Mismatches: 8, Indels: 20
0.79 0.06 0.15
Matches are distributed among these distances:
43 1 0.01
44 4 0.04
45 3 0.03
46 91 0.84
47 3 0.03
48 5 0.05
49 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
Found at i:34965866 original size:46 final size:47
Alignment explanation
Indices: 34965674--34965866 Score: 168
Period size: 46 Copynumber: 4.2 Consensus size: 47
34965664 GTAACCCGCC
* ** * *
34965674 CCTAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTC--GCAT
1 CCTAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCAT
* **
34965719 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGC-CTA-GTT
1 CC-TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCAT
* * *** *
34965765 ACTCTCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTC--GCAT
1 -C-CTAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCAT
34965811 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCAT
1 CC-TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCAT
34965859 CCT-AGTGA
1 CCTAAGTGA
34965867 CATGTCACTT
Statistics
Matches: 118, Mismatches: 19, Indels: 21
0.75 0.12 0.13
Matches are distributed among these distances:
44 1 0.01
45 6 0.05
46 100 0.85
47 5 0.04
48 6 0.05
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.22
Consensus pattern (47 bp):
CCTAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCAT
Found at i:34966297 original size:30 final size:30
Alignment explanation
Indices: 34966263--34966322 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
34966253 ATTTAATACG
34966263 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
34966293 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
34966323 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:34973294 original size:46 final size:46
Alignment explanation
Indices: 34973227--34973398 Score: 188
Period size: 46 Copynumber: 3.7 Consensus size: 46
34973217 AACCCGCCCC
* * *
34973227 TAAGTGAACTCAGACTCAACTCAACGAGCTCGGGCGTTTGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCATTTGCATCCA
* * *
34973273 TAAGTGAACTCGGACTCAACTCAACGAGTTCAGATGCCTAGTTACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTC-G--GGC-ATTTGCATCCA
* * * *
34973321 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCATTTGCATCCA
*
34973366 TAGGTGAACTCGGACTCAACTCAACGAGTTCGG
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG
34973399 ATGCTCAACC
Statistics
Matches: 104, Mismatches: 15, Indels: 14
0.78 0.11 0.11
Matches are distributed among these distances:
43 5 0.05
44 3 0.03
45 1 0.01
46 58 0.56
47 27 0.26
48 2 0.02
49 3 0.03
50 5 0.05
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCATTTGCATCCA
Found at i:34973340 original size:93 final size:93
Alignment explanation
Indices: 34973232--34973402 Score: 279
Period size: 93 Copynumber: 1.8 Consensus size: 93
34973222 GCCCCTAAGT
* * *
34973232 GAACTCAGACTCAACTCAACGAGCTCGGGCGTTTGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
34973297 CGAGTTCAGATGCCTAGTTACATCTCAC
66 CGAGTTCAGATGCCTAGTTACATCTCAC
* * *
34973325 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAGGTGAACTCGGACTCAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
34973390 CGAGTTCGGATGC
66 CGAGTTCAGATGC
34973403 TCAACCATCC
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.22
Consensus pattern (93 bp):
GAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCAGATGCCTAGTTACATCTCAC
Found at i:34973856 original size:30 final size:30
Alignment explanation
Indices: 34973822--34973881 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
34973812 ATTTAATACG
34973822 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
34973852 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
34973882 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:34984395 original size:16 final size:16
Alignment explanation
Indices: 34984376--34984407 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
34984366 AATTATTTTA
34984376 TTACAAAATTTCACTT
1 TTACAAAATTTCACTT
*
34984392 TTACATAATTTCACTT
1 TTACAAAATTTCACTT
34984408 ACTCCATTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.19, G:0.00, T:0.47
Consensus pattern (16 bp):
TTACAAAATTTCACTT
Found at i:34984681 original size:50 final size:50
Alignment explanation
Indices: 34984606--34985000 Score: 411
Period size: 50 Copynumber: 7.9 Consensus size: 50
34984596 ACCGAAGCTC
* * * *
34984606 TCTGGTACGCATAGTAGCCTGCACTTATTACTACACATGCGACCTATCAA
1 TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGACCTATCAA
* * * * *
34984656 TCTGGTACATGTAGTAGCCTACACTTAGTACTACACATGTGACTTAACCA
1 TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGACCTATCAA
* * * * ** *
34984706 TCTGATACACATAGTAGCCTGCACTTAGTACTACATACGTGATCGAAGT-TA
1 TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGA-CCTA-TCAA
* * *
34984757 T-TGGGTACACATAGTAGGCTGCACTTAGTACTACACATGCGACCTATCAA
1 TCT-GGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGACCTATCAA
* * * *
34984807 TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACTTAACCA
1 TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGACCTATCAA
* * * *
34984857 TCTGATACACGTGGTAGCCTGCACTTAGTACTACACATGTGA-TTGAAGTTAA
1 TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGACCT--A-TCAA
* * * *
34984909 -CGGGTACGCTTAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAA
1 TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGACCTATCAA
* *
34984958 TCTAGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGAC
1 TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGAC
34985001 TCACAATGAA
Statistics
Matches: 281, Mismatches: 54, Indels: 20
0.79 0.15 0.06
Matches are distributed among these distances:
49 6 0.02
50 198 0.70
51 75 0.27
52 2 0.01
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.28
Consensus pattern (50 bp):
TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGACCTATCAA
Found at i:34984874 original size:151 final size:151
Alignment explanation
Indices: 34984609--34985001 Score: 651
Period size: 151 Copynumber: 2.6 Consensus size: 151
34984599 GAAGCTCTCT
* *
34984609 GGTACGCATAGTAGCCTGCACTTATTACTACACATGCGACCTATCAATCTGGTACATGTAGTAGC
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTGGTACACGTAGTAGC
* *
34984674 CTACACTTAGTACTACACATGTGACTTAACCATCTGATACACATAGTAGCCTGCACTTAGTACTA
66 CTGCACTTAGTACTACACACGTGACTTAACCATCTGATACACATAGTAGCCTGCACTTAGTACTA
* **
34984739 CATACGTGATCGAAGTTATTG
131 CACACGTGATCGAAGTTAACG
* *
34984760 GGTACACATAGTAGGCTGCACTTAGTACTACACATGCGACCTATCAATCTGGTACACGTAGTAGC
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTGGTACACGTAGTAGC
* *
34984825 CTGCACTTAGTACTACACACGTGACTTAACCATCTGATACACGTGGTAGCCTGCACTTAGTACTA
66 CTGCACTTAGTACTACACACGTGACTTAACCATCTGATACACATAGTAGCCTGCACTTAGTACTA
* *
34984890 CACATGTGATTGAAGTTAACG
131 CACACGTGATCGAAGTTAACG
* *
34984911 GGTACGCTTAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTAGTACACGTAGTAGC
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTGGTACACGTAGTAGC
34984976 CTGCACTTAGTACTACACACGTGACT
66 CTGCACTTAGTACTACACACGTGACT
34985002 CACAATGAAT
Statistics
Matches: 225, Mismatches: 17, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
151 225 1.00
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27
Consensus pattern (151 bp):
GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTGGTACACGTAGTAGC
CTGCACTTAGTACTACACACGTGACTTAACCATCTGATACACATAGTAGCCTGCACTTAGTACTA
CACACGTGATCGAAGTTAACG
Found at i:34984915 original size:101 final size:100
Alignment explanation
Indices: 34984607--34985001 Score: 411
Period size: 101 Copynumber: 3.9 Consensus size: 100
34984597 CCGAAGCTCT
* * * * * *
34984607 CTGGTACGCATAGTAGCCTGCACTTATTACTACACATGCGACCTATCAATCTGGTACATGTAGTA
1 CTGGTACACATAGTAGCCTGCACTTAGTACTACACACGCGACCTAACAATCTGATACACGTAGTA
* * *
34984672 GCCTACACTTAGTACTACACATGTGACTTAACCAT
66 GCCTGCACTTAGTACTACACATGTGACTTAATCAA
* * * * * ** * *
34984707 CTGATACACATAGTAGCCTGCACTTAGTACTACATACGTGATCGAAGTTAT-TGGGTACACATAG
1 CTGGTACACATAGTAGCCTGCACTTAGTACTACACACGCGACCTAA-CAATCT-GATACACGTAG
* * *
34984771 TAGGCTGCACTTAGTACTACACATGCGACCT-ATCAA
64 TAGCCTGCACTTAGTACTACACATGTGACTTAATCAA
* * * * *
34984807 TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACTTAACCATCTGATACACGTGGT
1 -CTGGTACACATAGTAGCCTGCACTTAGTACTACACACGCGACCTAACAATCTGATACACGTAGT
*
34984872 AGCCTGCACTTAGTACTACACATGTGA-TTGAAGTTAA
65 AGCCTGCACTTAGTACTACACATGTGACTT-AA-TCAA
* * * * *
34984909 CGGGTACGCTTAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCT-AGTACACGTAGT
1 CTGGTACACATAGTAGCCTGCACTTAGTACTACACACGCGACCTAACAATCTGA-TACACGTAGT
*
34984973 AGCCTGCACTTAGTACTACACACGTGACT
65 AGCCTGCACTTAGTACTACACATGTGACT
34985002 CACAATGAAT
Statistics
Matches: 242, Mismatches: 44, Indels: 16
0.80 0.15 0.05
Matches are distributed among these distances:
99 1 0.00
100 78 0.32
101 159 0.66
102 4 0.02
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.28
Consensus pattern (100 bp):
CTGGTACACATAGTAGCCTGCACTTAGTACTACACACGCGACCTAACAATCTGATACACGTAGTA
GCCTGCACTTAGTACTACACATGTGACTTAATCAA
Found at i:34985377 original size:19 final size:20
Alignment explanation
Indices: 34985349--34985395 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
34985339 AAGAACAGGT
34985349 TATATCATCAAAATAATCACA
1 TATAT-ATCAAAATAATCACA
* *
34985370 TA-ATATCAAATTATTCACA
1 TATATATCAAAATAATCACA
34985389 TATATAT
1 TATATAT
34985396 ATTTACAACT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 15 0.65
20 6 0.26
21 2 0.09
ACGTcount: A:0.49, C:0.15, G:0.00, T:0.36
Consensus pattern (20 bp):
TATATATCAAAATAATCACA
Found at i:34987140 original size:37 final size:36
Alignment explanation
Indices: 34987090--34987176 Score: 147
Period size: 37 Copynumber: 2.3 Consensus size: 36
34987080 TACGAAGTCT
34987090 TACCCGGACATAATCTCCACACGTAGTCATCGGGTC
1 TACCCGGACATAATCTCCACACGTAGTCATCGGGTC
34987126 GTACCCGGACATAATCTCCACACGTAGTCATCGGGTC
1 -TACCCGGACATAATCTCCACACGTAGTCATCGGGTC
34987163 TCACCCGGAACATA
1 T-ACCCGG-ACATA
34987177 TTTCTAAGTT
Statistics
Matches: 48, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
36 1 0.02
37 42 0.88
38 5 0.10
ACGTcount: A:0.26, C:0.33, G:0.20, T:0.21
Consensus pattern (36 bp):
TACCCGGACATAATCTCCACACGTAGTCATCGGGTC
Found at i:34987312 original size:49 final size:49
Alignment explanation
Indices: 34987245--34987640 Score: 684
Period size: 49 Copynumber: 8.1 Consensus size: 49
34987235 TTTACCACAT
* *
34987245 ATATATATACACTTTCACATTCATCACGTCGGCCATTAGGCCTTATCAC
1 ATATGTATACATTTTCACATTCATCACGTCGGCCATTAGGCCTTATCAC
* *
34987294 ATATATATACATTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
1 ATATGTATACATTTTCACATTCATCACGTCGGCCATTAGGCCTTATCAC
* * *
34987343 ATATATATACAGTTTCACATTCATCACCTCGGCCATTAGGCCTTATCAC
1 ATATGTATACATTTTCACATTCATCACGTCGGCCATTAGGCCTTATCAC
*
34987392 ATATGTATACAGTTTCACATTCATCACGTCGGCCATTAGGCCTTATCAC
1 ATATGTATACATTTTCACATTCATCACGTCGGCCATTAGGCCTTATCAC
* *
34987441 ATATGTATACAGTTTCACATTCATCACGTCGGCCATTAGGCCTTATCAT
1 ATATGTATACATTTTCACATTCATCACGTCGGCCATTAGGCCTTATCAC
34987490 ATATGTATACATTTTCACATTCATCACGTCGGCCATTAGGCCTTATCAC
1 ATATGTATACATTTTCACATTCATCACGTCGGCCATTAGGCCTTATCAC
*
34987539 ATATGTATACATTTTCACATTCATCATGTCGGCCATTAGGCCTTATCAC
1 ATATGTATACATTTTCACATTCATCACGTCGGCCATTAGGCCTTATCAC
*
34987588 ATATGTATACATTTTCACATTCATCATGTCGGCCATTAGGCCTTATCAC
1 ATATGTATACATTTTCACATTCATCACGTCGGCCATTAGGCCTTATCAC
34987637 ATAT
1 ATAT
34987641 ATTATTATGT
Statistics
Matches: 337, Mismatches: 10, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
49 337 1.00
ACGTcount: A:0.28, C:0.26, G:0.12, T:0.35
Consensus pattern (49 bp):
ATATGTATACATTTTCACATTCATCACGTCGGCCATTAGGCCTTATCAC
Found at i:34994050 original size:21 final size:21
Alignment explanation
Indices: 34994024--34994066 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
34994014 CCTTCATCAT
34994024 TTCTTTTATGAAAAAATAGAC
1 TTCTTTTATGAAAAAATAGAC
34994045 TTCTTTTATGAAAAAATAGAC
1 TTCTTTTATGAAAAAATAGAC
34994066 T
1 T
34994067 CATTAAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.42, C:0.09, G:0.09, T:0.40
Consensus pattern (21 bp):
TTCTTTTATGAAAAAATAGAC
Found at i:34994189 original size:16 final size:16
Alignment explanation
Indices: 34994170--34994201 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
34994160 AATTGTTTTA
34994170 TTACAAAATTTCACTT
1 TTACAAAATTTCACTT
*
34994186 TTACATAATTTCACTT
1 TTACAAAATTTCACTT
34994202 ACTCTATTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.19, G:0.00, T:0.47
Consensus pattern (16 bp):
TTACAAAATTTCACTT
Found at i:34994487 original size:50 final size:50
Alignment explanation
Indices: 34994412--34994743 Score: 323
Period size: 50 Copynumber: 6.6 Consensus size: 50
34994402 CTAGTACGCA
* * * * * *
34994412 TAGTAGCTTGCACTTAGTACTACACATGCGACCTATCAATCTGGTACATG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACTTAACAATCTGATACATG
** * * * *
34994462 TAGTAGAATGCACTTAGTTCTACACACATGACTTAACCATTTGATACATG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACTTAACAATCTGATACATG
* * * *
34994512 TAGTATCCTGCACTTAGTACTACACACGTGACTTAACCATCTAATACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACTTAACAATCTGATACATG
* *
34994562 TAGTAGCCTGCACTTAGTACTACACACGTGA-TCAA-AGT-T-A-ACGGGTATG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACTTAACAATCTGATAC----ATG
* ** * * * **
34994611 CATAGTAGCCTGCACTTAGTACTACACATGCAACCTATCAATCTGGTACACA
1 --TAGTAGCCTGCACTTAGTACTACACACGTGACTTAACAATCTGATACATG
* *
34994663 TAGTAGCCTGCACTTCGTACTACACACGTGACTTAACCATCTGATACATG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACTTAACAATCTGATACATG
34994713 TAGTAGCCTGCACTTAGTACTACACACGTGA
1 TAGTAGCCTGCACTTAGTACTACACACGTGA
34994744 TCGAAGTTAA
Statistics
Matches: 226, Mismatches: 45, Indels: 22
0.77 0.15 0.08
Matches are distributed among these distances:
45 2 0.01
46 1 0.00
47 1 0.00
48 1 0.00
49 5 0.02
50 181 0.80
51 28 0.12
52 2 0.01
53 2 0.01
54 1 0.00
56 2 0.01
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.28
Consensus pattern (50 bp):
TAGTAGCCTGCACTTAGTACTACACACGTGACTTAACAATCTGATACATG
Found at i:34994685 original size:151 final size:151
Alignment explanation
Indices: 34994512--34994786 Score: 505
Period size: 151 Copynumber: 1.8 Consensus size: 151
34994502 TTGATACATG
*
34994512 TAGTATCCTGCACTTAGTACTACACACGTGACTTAACCATCTAATACACGTAGTAGCCTGCACTT
1 TAGTAGCCTGCACTTAGTACTACACACGTGACTTAACCATCTAATACACGTAGTAGCCTGCACTT
34994577 AGTACTACACACGTGATCAAAGTTAACGGGTATGCATAGTAGCCTGCACTTAGTACTACACATGC
66 AGTACTACACACGTGATCAAAGTTAACGGGTATGCATAGTAGCCTGCACTTAGTACTACACATGC
34994642 AACCTATCAATCTGGTACACA
131 AACCTATCAATCTGGTACACA
* * *
34994663 TAGTAGCCTGCACTTCGTACTACACACGTGACTTAACCATCTGATACATGTAGTAGCCTGCACTT
1 TAGTAGCCTGCACTTAGTACTACACACGTGACTTAACCATCTAATACACGTAGTAGCCTGCACTT
*
34994728 AGTACTACACACGTGATCGAAGTTAACGGGTATGCATAGTAGCCTGCACTTAGTACTAC
66 AGTACTACACACGTGATCAAAGTTAACGGGTATGCATAGTAGCCTGCACTTAGTACTAC
34994787 CACGTGACTC
Statistics
Matches: 119, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
151 119 1.00
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.27
Consensus pattern (151 bp):
TAGTAGCCTGCACTTAGTACTACACACGTGACTTAACCATCTAATACACGTAGTAGCCTGCACTT
AGTACTACACACGTGATCAAAGTTAACGGGTATGCATAGTAGCCTGCACTTAGTACTACACATGC
AACCTATCAATCTGGTACACA
Found at i:34994766 original size:101 final size:98
Alignment explanation
Indices: 34994470--34994795 Score: 297
Period size: 101 Copynumber: 3.3 Consensus size: 98
34994460 TGTAGTAGAA
* * * *
34994470 TGCACTTAGTTCTACACACATGACTTAACCATTTGATACATGTAGTATCCTGCACTTAGTACTAC
1 TGCACTTAGTACTACACACGTGACTTAACCATCTGATACATGTAGTAGCCTGCACTTAGTACTAC
**
34994535 ACACGTGAC-TTAACCATCTAATACACGTAGTAGCC
66 ACACGTGACATTAACCAGGT-ATACA--TAGTAGCC
*** *
34994570 TGCACTTAGTACTACACACGTGATCAAAGTTAA-CGGGT-ATGCA--TAGTAGCCTGCACTTAGT
1 TGCACTTAGTACTACACACGTGA-C----TTAACCATCTGATACATGTAGTAGCCTGCACTTAGT
* ** * * * *
34994631 ACTACACATGCAACCTATCAATCTGGTACACATAGTAGCC
61 ACTACACACGTGA-C-ATTAACCAGGTATACATAGTAGCC
*
34994671 TGCACTTCGTACTACACACGTGACTTAACCATCTGATACATGTAGTAGCCTGCACTTAGTACTAC
1 TGCACTTAGTACTACACACGTGACTTAACCATCTGATACATGTAGTAGCCTGCACTTAGTACTAC
* *
34994736 ACACGTGATCGAAGTTAA-CGGGTATGCATAGTAGCC
66 ACACGTGA-C--A-TTAACCAGGTATACATAGTAGCC
34994772 TGCACTTAGTACTAC-CACGTGACT
1 TGCACTTAGTACTACACACGTGACT
34994796 CACAATGAAT
Statistics
Matches: 181, Mismatches: 31, Indels: 28
0.75 0.13 0.12
Matches are distributed among these distances:
96 4 0.02
97 2 0.01
98 4 0.02
100 60 0.33
101 88 0.49
102 4 0.02
103 8 0.04
104 7 0.04
105 4 0.02
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (98 bp):
TGCACTTAGTACTACACACGTGACTTAACCATCTGATACATGTAGTAGCCTGCACTTAGTACTAC
ACACGTGACATTAACCAGGTATACATAGTAGCC
Found at i:34994791 original size:50 final size:50
Alignment explanation
Indices: 34994512--34994793 Score: 240
Period size: 50 Copynumber: 5.6 Consensus size: 50
34994502 TTGATACATG
* ***
34994512 TAGTATCCTGCACTTAGTACTACACACGTGA-C--TTAACCATCTAATACA
1 TAGTAGCCTGCACTTAGTACTACACACGTGATCAATTAACCGGGT-ATACA
*
34994560 CGTAGTAGCCTGCACTTAGTACTACACACGTGATCAAAGTTAA-CGGGTATGCA
1 --TAGTAGCCTGCACTTAGTACTACACACGTGATC-AA-TTAACCGGGTATACA
* ** * * * * * *
34994613 TAGTAGCCTGCACTTAGTACTACACATGCAACCTATCAATCTGGTACACA
1 TAGTAGCCTGCACTTAGTACTACACACGTGATCAATTAACCGGGTATACA
* ***
34994663 TAGTAGCCTGCACTTCGTACTACACACGTGA-C--TTAACCATCTGATACA
1 TAGTAGCCTGCACTTAGTACTACACACGTGATCAATTAACCGGGT-ATACA
*
34994711 TGTAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTTAA-CGGGTATGCA
1 --TAGTAGCCTGCACTTAGTACTACACACGTGATC-AA-TTAACCGGGTATACA
34994764 TAGTAGCCTGCACTTAGTACTAC-CACGTGA
1 TAGTAGCCTGCACTTAGTACTACACACGTGA
34994794 CTCACAATGA
Statistics
Matches: 189, Mismatches: 29, Indels: 28
0.77 0.12 0.11
Matches are distributed among these distances:
47 5 0.03
48 4 0.02
49 4 0.02
50 102 0.54
51 54 0.29
53 8 0.04
54 4 0.02
55 8 0.04
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.27
Consensus pattern (50 bp):
TAGTAGCCTGCACTTAGTACTACACACGTGATCAATTAACCGGGTATACA
Found at i:34994793 original size:201 final size:200
Alignment explanation
Indices: 34994409--34994793 Score: 553
Period size: 201 Copynumber: 1.9 Consensus size: 200
34994399 TCTCTAGTAC
* * **
34994409 GCATAGTAGCTTGCACTTAGTACTACACATGCGACCTATCAATCTGGTACATGTAGTAGAATGCA
1 GCATAGTAGCCTGCACTTAGTACTACACATGCAACCTATCAATCTGGTACACATAGTAGAATGCA
* * *
34994474 CTTAGTTCTACACACATGACTTAACCATTTGATACATGTAGTATCCTGCACTTAGTACTACACAC
66 CTTAGTACTACACACATGACTTAACCATCTGATACATGTAGTAGCCTGCACTTAGTACTACACAC
*
34994539 GTGACTTAACCATCTAATACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCAAAGTTAAC
131 GTGACTTAACCAGCTAATACAC-TAGTAGCCTGCACTTAGTACTACACACGTGATCAAAGTTAAC
34994604 GGGTAT
195 GGGTAT
**
34994610 GCATAGTAGCCTGCACTTAGTACTACACATGCAACCTATCAATCTGGTACACATAGTAGCCTGCA
1 GCATAGTAGCCTGCACTTAGTACTACACATGCAACCTATCAATCTGGTACACATAGTAGAATGCA
* *
34994675 CTTCGTACTACACACGTGACTTAACCATCTGATACATGTAGTAGCCTGCACTTAGTACTACACAC
66 CTTAGTACTACACACATGACTTAACCATCTGATACATGTAGTAGCCTGCACTTAGTACTACACAC
* * *
34994740 GTGATCGAAGTTAA-CGGGT-ATGCA-TAGTAGCCTGCACTTAGTACTAC-CACGTGA
131 GTGA-C----TTAACCAGCTAATACACTAGTAGCCTGCACTTAGTACTACACACGTGA
34994794 CTCACAATGA
Statistics
Matches: 164, Mismatches: 15, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
201 130 0.79
202 24 0.15
204 4 0.02
205 2 0.01
206 4 0.02
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (200 bp):
GCATAGTAGCCTGCACTTAGTACTACACATGCAACCTATCAATCTGGTACACATAGTAGAATGCA
CTTAGTACTACACACATGACTTAACCATCTGATACATGTAGTAGCCTGCACTTAGTACTACACAC
GTGACTTAACCAGCTAATACACTAGTAGCCTGCACTTAGTACTACACACGTGATCAAAGTTAACG
GGTAT
Found at i:34995466 original size:30 final size:30
Alignment explanation
Indices: 34995408--34995463 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
34995398 CAAAAATCAT
* *
34995408 ACTTTTACAAATTTGCATTTTGAGCCCTAA
1 ACTTTCACAAATTTGCACTTTGAGCCCTAA
*
34995438 ACTTTCACATATTTGCACTTTG-GCCC
1 ACTTTCACAAATTTGCACTTTGAGCCC
34995464 CTAGGCTCGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
29 4 0.17
30 19 0.83
ACGTcount: A:0.25, C:0.25, G:0.11, T:0.39
Consensus pattern (30 bp):
ACTTTCACAAATTTGCACTTTGAGCCCTAA
Found at i:35001667 original size:122 final size:122
Alignment explanation
Indices: 35001450--35001706 Score: 372
Period size: 122 Copynumber: 2.1 Consensus size: 122
35001440 AGGCATTTTT
* *
35001450 TGGCCTTTAGCGGCGCTTTTAAGCGCCCCTGTAACTATTTACGGCACAACGCCACTATAGAAAAT
1 TGGCCTTTAGCGACGCTTTTAAGCGCCCCTGTAACTATTTACGGCACAACGCCACTATAGAAAAC
*
35001515 GCCGCAAAAGATCATGACTTTTAGCGGCGTTTGTGGGAGAAGCGCCGCTAAAAGACA
66 GCCGCAAAAGATCATGACTTTTAGCGGCGTTTGTGGGAGAAGCACCGCTAAAAGACA
* * * * * *
35001572 TGGCCTTTAGCGACGCTTTTAAGCGCCCCTAG-AACTATTTGCGGCGCAATGCCGCTGTAGCAAA
1 TGGCCTTTAGCGACGCTTTTAAGCGCCCCT-GTAACTATTTACGGCACAACGCCACTATAGAAAA
* * *
35001636 CGCTGCAAAAGATCATGACTTTTAGCGGCGTTTGTGGGAGAAGCACCGTTAAAAGTCA
65 CGCCGCAAAAGATCATGACTTTTAGCGGCGTTTGTGGGAGAAGCACCGCTAAAAGACA
*
35001694 TGGCTTTTTAGCG
1 TGGC-CTTTAGCG
35001707 GCGTTTGTGG
Statistics
Matches: 120, Mismatches: 13, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
122 112 0.93
123 8 0.07
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.25
Consensus pattern (122 bp):
TGGCCTTTAGCGACGCTTTTAAGCGCCCCTGTAACTATTTACGGCACAACGCCACTATAGAAAAC
GCCGCAAAAGATCATGACTTTTAGCGGCGTTTGTGGGAGAAGCACCGCTAAAAGACA
Found at i:35001733 original size:43 final size:42
Alignment explanation
Indices: 35001642--35001774 Score: 169
Period size: 44 Copynumber: 3.1 Consensus size: 42
35001632 CAAACGCTGC
* *
35001642 AAAAGATCATGACTTTTAGCGGCGTTTGTGGGAGAAGCAC-CG
1 AAAAG-TCATGGCTTTTAGCGGCGTTTGTGGGGGAAGCACGCG
*
35001684 TTAAAAGTCATGGCTTTTTAGCGGCGTTTGTGGGGGAAGCGCGCG
1 --AAAAGTCATGGC-TTTTAGCGGCGTTTGTGGGGGAAGCACGCG
* *
35001729 AAAAGTCATGGCTTTTAGCGGTGTTTTTGGGGGAAGCACTGCG
1 AAAAGTCATGGCTTTTAGCGGCGTTTGTGGGGGAAGCAC-GCG
35001772 AAA
1 AAA
35001775 GGTGCTTTTG
Statistics
Matches: 80, Mismatches: 6, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
42 24 0.30
43 24 0.30
44 30 0.38
45 2 0.03
ACGTcount: A:0.24, C:0.15, G:0.34, T:0.27
Consensus pattern (42 bp):
AAAAGTCATGGCTTTTAGCGGCGTTTGTGGGGGAAGCACGCG
Found at i:35001890 original size:31 final size:31
Alignment explanation
Indices: 35001855--35001915 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
35001845 TTCCTACATT
35001855 AAATCCAACCAAAAACAACAAATATAGCATG
1 AAATCCAACCAAAAACAACAAATATAGCATG
* * *
35001886 AAATCCAACTAAAAACAGCAAATGTAGCAT
1 AAATCCAACCAAAAACAACAAATATAGCAT
35001916 AAAAAATAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.56, C:0.21, G:0.08, T:0.15
Consensus pattern (31 bp):
AAATCCAACCAAAAACAACAAATATAGCATG
Found at i:35003619 original size:41 final size:41
Alignment explanation
Indices: 35003570--35003719 Score: 230
Period size: 41 Copynumber: 3.7 Consensus size: 41
35003560 GTGCGACTCA
*
35003570 AAAAGCCCTTCGAGACCAAGCTCGGATTATGACATTGGCTC
1 AAAAGCCCTTCGAGACCAAGCTCGGATTATGACACTGGCTC
* * * * * *
35003611 GAATGCCCTTCGAAACTAGGTTCGG-TTATGACACTGGCTC
1 AAAAGCCCTTCGAGACCAAGCTCGGATTATGACACTGGCTC
35003651 AAAAGCCCTTCGAGACCAAGCTCGGATTATGACACTGGCTC
1 AAAAGCCCTTCGAGACCAAGCTCGGATTATGACACTGGCTC
35003692 AAAAGCCCTTCGAGACCAAGCTCGGATT
1 AAAAGCCCTTCGAGACCAAGCTCGGATT
35003720 TAAACCCCAA
Statistics
Matches: 95, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
40 33 0.35
41 62 0.65
ACGTcount: A:0.28, C:0.27, G:0.23, T:0.22
Consensus pattern (41 bp):
AAAAGCCCTTCGAGACCAAGCTCGGATTATGACACTGGCTC
Found at i:35011917 original size:40 final size:41
Alignment explanation
Indices: 35011828--35011977 Score: 221
Period size: 41 Copynumber: 3.7 Consensus size: 41
35011818 CGCTGACTCA
* *
35011828 AAAAGCCCTTCGAGACCAAGCTCGGATTATGACATTGGCCC
1 AAAAGCCCTTCGAGACCAAGCTCGGATTATGACACTGGCTC
* * * * * *
35011869 GAAGGCCCTTCGAAACTAGGTTCGG-TTATGACACTGGCTC
1 AAAAGCCCTTCGAGACCAAGCTCGGATTATGACACTGGCTC
35011909 AAAAGCCCTTCGAGACCAAGCTCGGATTATGACACTGGCTC
1 AAAAGCCCTTCGAGACCAAGCTCGGATTATGACACTGGCTC
35011950 AAAAGCCCTTCGAGACCAAGCTCGGATT
1 AAAAGCCCTTCGAGACCAAGCTCGGATT
35011978 TAAACCCCAA
Statistics
Matches: 94, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
40 32 0.34
41 62 0.66
ACGTcount: A:0.28, C:0.28, G:0.23, T:0.21
Consensus pattern (41 bp):
AAAAGCCCTTCGAGACCAAGCTCGGATTATGACACTGGCTC
Found at i:35012403 original size:2 final size:2
Alignment explanation
Indices: 35012396--35012425 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
35012386 GCCTTATAAG
35012396 AT AT 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 AT AT
35012426 TACTAAGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35014362 original size:13 final size:14
Alignment explanation
Indices: 35014336--35014364 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
35014326 ACTAACAACG
35014336 AATTAAACCATTAT
1 AATTAAACCATTAT
35014350 AATTAAA-CATTAT
1 AATTAAACCATTAT
35014363 AA
1 AA
35014365 ATATTTATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.34
Consensus pattern (14 bp):
AATTAAACCATTAT
Found at i:35019447 original size:39 final size:40
Alignment explanation
Indices: 35019389--35019489 Score: 132
Period size: 39 Copynumber: 2.5 Consensus size: 40
35019379 AAATTGAATG
* *
35019389 ATATCCGGGCTAAGCCCCGAAGACAATTATGCT-GAAATT
1 ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
* * * * *
35019428 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTAGCT
1 ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
35019468 ATATCCGGGCTAAGACCCGAAG
1 ATATCCGGGCTAAGACCCGAAG
35019490 GCATTCGTGC
Statistics
Matches: 53, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
39 29 0.55
40 24 0.45
ACGTcount: A:0.31, C:0.23, G:0.25, T:0.22
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
Found at i:35019482 original size:40 final size:40
Alignment explanation
Indices: 35019389--35019539 Score: 180
Period size: 40 Copynumber: 3.8 Consensus size: 40
35019379 AAATTGAATG
* * * * *
35019389 ATATCCGGGCTAAGCCCCGAAGACAATTATGCT-GAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
* *
35019428 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTAGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
* *
35019468 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCAAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTAGTAGTT
* *
35019508 AAATCCGGGCTAAGACCCGAAGGCATTTGTGC
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGC
35019540 AAATCATGAT
Statistics
Matches: 96, Mismatches: 13, Indels: 5
0.84 0.11 0.04
Matches are distributed among these distances:
39 32 0.33
40 62 0.65
41 2 0.02
ACGTcount: A:0.28, C:0.23, G:0.26, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
Found at i:35019554 original size:40 final size:39
Alignment explanation
Indices: 35019386--35019571 Score: 157
Period size: 40 Copynumber: 4.7 Consensus size: 39
35019376 GAGAAATTGA
* *
35019386 ATGATATCCGGGCTAAGCCCCGAAGACAATTATGCTG-AAAT
1 ATGATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAAT
* * * *
35019427 -T-ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGT
1 ATGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAAT
* *
35019464 A-GCTATATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGT
1 ATG--ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAAT
*
35019504 -TGTTAAATCCGGGCTAAGACCCGAAGGCATTTGTGCAAAT
1 ATG--ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAAT
* * *
35019544 CATGATATCCGGGTTAAGTCCCGTAGGC
1 -ATGATATCCGGGCTAAGACCCGAAGGC
35019572 CTTGGTGCGG
Statistics
Matches: 119, Mismatches: 18, Indels: 17
0.77 0.12 0.11
Matches are distributed among these distances:
36 2 0.02
37 4 0.03
38 2 0.02
39 21 0.18
40 88 0.74
42 2 0.02
ACGTcount: A:0.28, C:0.22, G:0.26, T:0.24
Consensus pattern (39 bp):
ATGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAAT
Done.