Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr9
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: 91122320
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2661692 characters in sequence are not A, C, G, or T
File 274 of 279
Found at i:89502294 original size:47 final size:44
Alignment explanation
Indices: 89502191--89502405 Score: 130
Period size: 47 Copynumber: 4.7 Consensus size: 44
89502181 TATGCTGATA
*
89502191 CATGTCCCAGACATGTCTTACACTAGCACAACTCTTAGCTGATG
1 CATGTCCCAGACATGTCTTACACTAGCACAACTCTTAGCCGATG
* * * * *
89502235 CGTGTCCTAGACACGTCTTACACTAGC-TATCTCTGTCGAGGCCGATG
1 CATGTCCCAGACATGTCTTACACTAGCACAACTCT-T--A-GCCGATG
* * * * *
89502282 CATGTCCCAGACATGTCTTACTCTGGCACTCATCTCTGT-TCTGATG
1 CATGTCCCAGACATGTCTTACACTAGCA--CAACTCT-TAGCCGATG
* * * * * * *
89502328 CCATGTCCCAGACATGGCCTTACACTGGCTCTCATAATGTGA-CCGAAG
1 -CATGTCCCAGACAT-GTCTTACACTAG--CACA-ACTCTTAGCCGATG
*
89502376 CATGTCCCAGACATGTCTTACACTGGCACA
1 CATGTCCCAGACATGTCTTACACTAGCACA
89502406 CAACTCACCC
Statistics
Matches: 133, Mismatches: 25, Indels: 26
0.72 0.14 0.14
Matches are distributed among these distances:
43 5 0.04
44 28 0.21
46 17 0.13
47 56 0.42
48 16 0.12
49 2 0.02
50 9 0.07
ACGTcount: A:0.23, C:0.31, G:0.19, T:0.27
Consensus pattern (44 bp):
CATGTCCCAGACATGTCTTACACTAGCACAACTCTTAGCCGATG
Found at i:89502385 original size:94 final size:94
Alignment explanation
Indices: 89502138--89502411 Score: 296
Period size: 94 Copynumber: 2.9 Consensus size: 94
89502128 ATAAATTGTC
*
89502138 ATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATACATGT-ATGCTGATA-CATGTCCCAG
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATA-ATGTGA-GCCGA-AGCATGTCCCAG
*
89502201 ACATGTCTTACACTAGCA-CAACTCTTAGCTG
63 ACATGTCTTACACTGGCACCAACTCTTAGCTG
* * * * * * *
89502232 ATG-CGTGTCCTAGACA-CGTCTTACACTAGCTATC-T-CTGTCGAGGCCGATGCATGTCCCAGA
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGT-GA-GCCGAAGCATGTCCCAGA
* * *
89502293 CATGTCTTACTCTGGCACTCATCTCTGT-TCTG
64 CATGTCTTACACTGGCAC-CAACTCT-TAGCTG
*
89502325 ATGCCATGTCCCAGACATGGCCTTACACTGGCTCTCATAATGTGA-CCGAAGCATGTCCCAGACA
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTGAGCCGAAGCATGTCCCAGACA
89502389 TGTCTTACACTGGCACACAACTC
66 TGTCTTACACTGGCAC-CAACTC
89502412 ACCCAATGTC
Statistics
Matches: 146, Mismatches: 24, Indels: 20
0.77 0.13 0.11
Matches are distributed among these distances:
89 3 0.02
91 32 0.22
92 15 0.10
93 23 0.16
94 53 0.36
95 14 0.10
96 3 0.02
97 3 0.02
ACGTcount: A:0.23, C:0.30, G:0.19, T:0.28
Consensus pattern (94 bp):
ATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTGAGCCGAAGCATGTCCCAGACA
TGTCTTACACTGGCACCAACTCTTAGCTG
Found at i:89503959 original size:11 final size:10
Alignment explanation
Indices: 89503940--89503972 Score: 57
Period size: 10 Copynumber: 3.2 Consensus size: 10
89503930 ATAAAACTTG
89503940 AAATTTTTAT
1 AAATTTTTAT
89503950 AAATTTTTTAT
1 AAA-TTTTTAT
89503961 AAATTTTTAT
1 AAATTTTTAT
89503971 AA
1 AA
89503973 TATTATGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 12 0.55
11 10 0.45
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (10 bp):
AAATTTTTAT
Found at i:89504317 original size:19 final size:18
Alignment explanation
Indices: 89504283--89504318 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
89504273 TTCGAAAAAA
89504283 ATTAATTTACTAATATCC
1 ATTAATTTACTAATATCC
*
89504301 ATTAATTATATTAATATC
1 ATTAATT-TACTAATATC
89504319 TTTTGTATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.47
Consensus pattern (18 bp):
ATTAATTTACTAATATCC
Found at i:89505288 original size:14 final size:14
Alignment explanation
Indices: 89505269--89505295 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
89505259 AGTAATATCT
89505269 TGTCTGACTATTCA
1 TGTCTGACTATTCA
89505283 TGTCTGACTATTC
1 TGTCTGACTATTC
89505296 CGTTAACTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.19, C:0.22, G:0.15, T:0.44
Consensus pattern (14 bp):
TGTCTGACTATTCA
Found at i:89511867 original size:29 final size:29
Alignment explanation
Indices: 89511818--89511874 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
89511808 TCTTTTCTCT
* *
89511818 CTATTTTCTTTAAATATTTTGCCTATTTC
1 CTATTTTCTCTAAATATTTTGACTATTTC
*
89511847 CTATTTTCTCT-AATCTATTTGACTATTT
1 CTATTTTCTCTAAATAT-TTTGACTATTT
89511875 TAAGTGAACA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 4 0.17
29 20 0.83
ACGTcount: A:0.21, C:0.18, G:0.04, T:0.58
Consensus pattern (29 bp):
CTATTTTCTCTAAATATTTTGACTATTTC
Found at i:89518799 original size:52 final size:52
Alignment explanation
Indices: 89518718--89518820 Score: 197
Period size: 52 Copynumber: 2.0 Consensus size: 52
89518708 GTGGTTTGTC
*
89518718 GAGGGTTTCTCTCTGATTGCAACTTATTTGACTAAGCTTCTGTGTAAGGGTT
1 GAGGGTTTCTCTCTGATTGCAACTCATTTGACTAAGCTTCTGTGTAAGGGTT
89518770 GAGGGTTTCTCTCTGATTGCAACTCATTTGACTAAGCTTCTGTGTAAGGGT
1 GAGGGTTTCTCTCTGATTGCAACTCATTTGACTAAGCTTCTGTGTAAGGGT
89518821 GTTCCTTTTG
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.19, C:0.17, G:0.25, T:0.39
Consensus pattern (52 bp):
GAGGGTTTCTCTCTGATTGCAACTCATTTGACTAAGCTTCTGTGTAAGGGTT
Found at i:89525290 original size:13 final size:15
Alignment explanation
Indices: 89525256--89525301 Score: 55
Period size: 13 Copynumber: 3.3 Consensus size: 15
89525246 AGCATGTTTA
89525256 ATCTGTTATTTCTGT
1 ATCTGTTATTTCTGT
*
89525271 ATTTGTT-TTTC-GT
1 ATCTGTTATTTCTGT
89525284 ATCTGTTA--TCTGT
1 ATCTGTTATTTCTGT
89525297 ATCTG
1 ATCTG
89525302 ATTTGGGGTG
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
12 2 0.07
13 15 0.56
14 4 0.15
15 6 0.22
ACGTcount: A:0.13, C:0.13, G:0.15, T:0.59
Consensus pattern (15 bp):
ATCTGTTATTTCTGT
Found at i:89528143 original size:26 final size:26
Alignment explanation
Indices: 89528109--89528161 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
89528099 AGTTGGCATG
89528109 ATATAGGGTTGTGAGTACTTACCTAT
1 ATATAGGGTTGTGAGTACTTACCTAT
89528135 ATATAGGGTTGTGAGTACTTACCTAT
1 ATATAGGGTTGTGAGTACTTACCTAT
89528161 A
1 A
89528162 CGTATTATGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.28, C:0.11, G:0.23, T:0.38
Consensus pattern (26 bp):
ATATAGGGTTGTGAGTACTTACCTAT
Found at i:89536128 original size:40 final size:40
Alignment explanation
Indices: 89536064--89537016 Score: 1799
Period size: 40 Copynumber: 23.9 Consensus size: 40
89536054 CCTTCGGGAT
*
89536064 TTAG-CCGGATATAG-CAACTCGCACAAATGCCTTC-GGGAC
1 TTAGCCCGGATATAGTC-ACTAGCACAAATGCCTTCTGGG-C
* *
89536103 TTAGCCCGGATATAGTAACTAGCACAGATGCCTTC-GGGAC
1 TTAGCCCGGATATAGTCACTAGCACAAATGCCTTCTGGG-C
89536143 TTAGCCCGGATATAGTCACTAGCACAAATGCCTTCTGGGC
1 TTAGCCCGGATATAGTCACTAGCACAAATGCCTTCTGGGC
89536183 TTAGCCCGGATATAGTCACTAGCACAAATGCCTTCTGGGC
1 TTAGCCCGGATATAGTCACTAGCACAAATGCCTTCTGGGC
89536223 TTAGCCCGGATATAGTCACTAGCACAAATGCCTTCTGGGC
1 TTAGCCCGGATATAGTCACTAGCACAAATGCCTTCTGGGC
89536263 TTAGCCCGGATATAGTCACTAGCACAAATGCCTTCTGGGC
1 TTAGCCCGGATATAGTCACTAGCACAAATGCCTTCTGGGC
89536303 TTAGCCCGGATATAGTCACTAGCACAAATGCCTTCTGGGC
1 TTAGCCCGGATATAGTCACTAGCACAAATGCCTTCTGGGC
89536343 TTAGCCCGGATATAGTCACTAGCACAAATGCCTTCTGGGC
1 TTAGCCCGGATATAGTCACTAGCACAAATGCCTTCTGGGC
89536383 TTAGCCCGGATATAGTCACTAGCACAAATGCCTTCTGGGC
1 TTAGCCCGGATATAGTCACTAGCACAAATGCCTTCTGGGC
89536423 TTAGCCCGGATATAGTCACTAGCACAAATGCCTTCTGGGC
1 TTAGCCCGGATATAGTCACTAGCACAAATGCCTTCTGGGC
89536463 TTAGCCCGGATATAGTCACTAGCACAAATGCCTTCTGGGC
1 TTAGCCCGGATATAGTCACTAGCACAAATGCCTTCTGGGC
89536503 TTAGCCCGGATATAGTCACTAGCACAAATGCCTTCTGGGC
1 TTAGCCCGGATATAGTCACTAGCACAAATGCCTTCTGGGC
89536543 TTAGCCCGGATATAGTCACTAGCACAAATGCCTTCTGGGC
1 TTAGCCCGGATATAGTCACTAGCACAAATGCCTTCTGGGC
89536583 TTAGCCCGGATATAGTCACTAGCACAAATGCCTTCTGGGC
1 TTAGCCCGGATATAGTCACTAGCACAAATGCCTTCTGGGC
89536623 TTAGCCCGGATATAGTCACTAGCACAAATGCCTTCTGGGC
1 TTAGCCCGGATATAGTCACTAGCACAAATGCCTTCTGGGC
89536663 TTAGCCCGGATATAGTCACTAGCACAAATGCCTTCTGGGC
1 TTAGCCCGGATATAGTCACTAGCACAAATGCCTTCTGGGC
89536703 TTAGCCCGGATATAGTCACTAGCACAAATGCCTTCTGGGC
1 TTAGCCCGGATATAGTCACTAGCACAAATGCCTTCTGGGC
89536743 TTAGCCCGGATATAGTCACTAGCACAAATGCCTTCTGGGC
1 TTAGCCCGGATATAGTCACTAGCACAAATGCCTTCTGGGC
89536783 TTAGCCCGGATATAGTCACTAGCACAAATGCCTTCTGGGC
1 TTAGCCCGGATATAGTCACTAGCACAAATGCCTTCTGGGC
89536823 TTAGCCCGGATATAGTCACTAGCACAAATGCCTTCTGGGC
1 TTAGCCCGGATATAGTCACTAGCACAAATGCCTTCTGGGC
89536863 TTAGCCCGGATATAGTCACTAGCACAAATGCCTTCTGGGC
1 TTAGCCCGGATATAGTCACTAGCACAAATGCCTTCTGGGC
89536903 TTAGCCCGGATATAGTCACTAGCACAAATGCCTTCTGGGC
1 TTAGCCCGGATATAGTCACTAGCACAAATGCCTTCTGGGC
89536943 TTAGCCCGGATATAGTCACTAGCACAAATGCCTTC-GGGAC
1 TTAGCCCGGATATAGTCACTAGCACAAATGCCTTCTGGG-C
*
89536983 TTAGCCCGGATATAGTAACTAGCACAAATGCCTT
1 TTAGCCCGGATATAGTCACTAGCACAAATGCCTT
89537017 TGAATTTTAG
Statistics
Matches: 904, Mismatches: 6, Indels: 7
0.99 0.01 0.01
Matches are distributed among these distances:
39 7 0.01
40 894 0.99
41 3 0.00
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
TTAGCCCGGATATAGTCACTAGCACAAATGCCTTCTGGGC
Found at i:89538413 original size:13 final size:13
Alignment explanation
Indices: 89538395--89538420 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
89538385 ATTTTTATTT
89538395 TTAACATAAAATA
1 TTAACATAAAATA
89538408 TTAACATAAAATA
1 TTAACATAAAATA
89538421 ATTATAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.31
Consensus pattern (13 bp):
TTAACATAAAATA
Found at i:89541761 original size:19 final size:20
Alignment explanation
Indices: 89541720--89541762 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
89541710 TTTTGTAAAG
* *
89541720 TTTGTAAAATAGATGGTACT
1 TTTGTAAAATAGATGGAAAT
*
89541740 TTTGTGAAATA-ATGGAAAT
1 TTTGTAAAATAGATGGAAAT
89541759 TTTG
1 TTTG
89541763 GGTTTTTATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.35, C:0.02, G:0.21, T:0.42
Consensus pattern (20 bp):
TTTGTAAAATAGATGGAAAT
Found at i:89542334 original size:48 final size:48
Alignment explanation
Indices: 89542272--89542440 Score: 216
Period size: 48 Copynumber: 3.6 Consensus size: 48
89542262 ACATTTTGAG
*
89542272 AGCCAGTGTAAGACATGTCTGGGACATGCATCGACCTCGAGATATACC
1 AGCCAGTGTAAGACATGTCTGGGACATGCATCGACCTCGAGATATACA
* * ** *
89542320 AGCCAGTGTAAGACATGTCTGGGACATGCATCGACATTGAGA-CGA-G
1 AGCCAGTGTAAGACATGTCTGGGACATGCATCGACCTCGAGATATACA
** * *
89542366 AGATAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGTACA
1 AGCCAGTGTAAGACATGTCTGGGACATGCATCGACCTCGAGATATACA
* *
89542414 AGCTAGTGTAAGACCTGTCTGGGACAT
1 AGCCAGTGTAAGACATGTCTGGGACAT
89542441 AGTGTCAGCT
Statistics
Matches: 104, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
46 37 0.36
47 2 0.02
48 65 0.62
ACGTcount: A:0.29, C:0.21, G:0.28, T:0.22
Consensus pattern (48 bp):
AGCCAGTGTAAGACATGTCTGGGACATGCATCGACCTCGAGATATACA
Found at i:89542547 original size:142 final size:138
Alignment explanation
Indices: 89542323--89542582 Score: 310
Period size: 142 Copynumber: 1.9 Consensus size: 138
89542313 ATATACCAGC
** *
89542323 CAGTGTAAGACATGTCTGGGACATGCATCGACATTGAGACGAGAGATAGTGTAAGACATGTCTGG
1 CAGTGTAAGACATGTCTGGGACATGCATCGACACCGAGACGAGAGACAGTGTAAGACATGTCTGG
* *
89542388 GACATGCATCGGCCTCGAGATGT-ACAAG-CTAGTGTAAGACCTGTCTGGGACATAGTGTCAGCT
66 GACATGCATCGGCCTCGAGATATGA-AAGTC-AGTGTAAGACCTGTCTAGGACATAGTGTCAGCT
89542451 TGTTGTGTGT
129 TGTTGTGTGT
* * * * * * *
89542461 CAGTGTAAGACCTGTCTGGGATATGGCATCGACACCGATAGATGAGTGCCAGTGTAAGACCTGTT
1 CAGTGTAAGACATGTCTGGGACAT-GCATCGACACCG--AGACGAGAGACAGTGTAAGACATGTC
* *
89542526 TGGGACATGACATCAGG-CTCGATATATGAAAGTCAGTGTAAGAGCTGTCTAGGACAT
63 TGGGACATG-CATC-GGCCTCGAGATATGAAAGTCAGTGTAAGACCTGTCTAGGACAT
89542583 GGCATTGACT
Statistics
Matches: 101, Mismatches: 14, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
138 22 0.22
139 10 0.10
141 29 0.29
142 36 0.36
143 4 0.04
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.25
Consensus pattern (138 bp):
CAGTGTAAGACATGTCTGGGACATGCATCGACACCGAGACGAGAGACAGTGTAAGACATGTCTGG
GACATGCATCGGCCTCGAGATATGAAAGTCAGTGTAAGACCTGTCTAGGACATAGTGTCAGCTTG
TTGTGTGT
Found at i:89542549 original size:49 final size:49
Alignment explanation
Indices: 89542272--89542631 Score: 153
Period size: 48 Copynumber: 7.6 Consensus size: 49
89542262 ACATTTTGAG
* * * *
89542272 AGCCAGTGTAAGACATGTCTGGGACATG-CATCGAC-CTCGAGATAT-ACC
1 AGCCAGTGTAAGACCTGTCTGGGACATGACATCGACAC-CGATAGATGA-A
* ** * *
89542320 AGCCAGTGTAAGACATGTCTGGGACATG-CATCGACATTG--AGACGAG
1 AGCCAGTGTAAGACCTGTCTGGGACATGACATCGACACCGATAGATGAA
** * *
89542366 AGATAGTGTAAGACATGTCTGGGACATG-CATCGGC-CTCG--AGATGTACA
1 AGCCAGTGTAAGACCTGTCTGGGACATGACATCGACAC-CGATAGATG-A-A
* * * * * * **
89542414 AGCTAGTGTAAGACCTGTCTGGGACAT-A-GT-GTCA--GCTTGTTGTG
1 AGCCAGTGTAAGACCTGTCTGGGACATGACATCGACACCGATAGATGAA
* * * * *
89542458 TGTCAGTGTAAGACCTGTCTGGGATATGGCATCGACACCGATAGATGAG
1 AGCCAGTGTAAGACCTGTCTGGGACATGACATCGACACCGATAGATGAA
* * * * *
89542507 TGCCAGTGTAAGACCTGTTTGGGACATGACATCAGGC-TCGATATATGAA
1 AGCCAGTGTAAGACCTGTCTGGGACATGACATC-GACACCGATAGATGAA
* * * * * *** **
89542556 AGTCAGTGTAAGAGCTGTCTAGGACATGGCATTGACTTTGAT-G-TGTT
1 AGCCAGTGTAAGACCTGTCTGGGACATGACATCGACACCGATAGATGAA
*
89542603 AGCCAGTGTAAGACCATGTCTAGGACATG
1 AGCCAGTGTAAGACC-TGTCTGGGACATG
89542632 GCATTGGCAT
Statistics
Matches: 242, Mismatches: 53, Indels: 34
0.74 0.16 0.10
Matches are distributed among these distances:
44 24 0.10
46 45 0.19
47 21 0.09
48 76 0.31
49 74 0.31
50 2 0.01
ACGTcount: A:0.27, C:0.19, G:0.29, T:0.25
Consensus pattern (49 bp):
AGCCAGTGTAAGACCTGTCTGGGACATGACATCGACACCGATAGATGAA
Found at i:89544089 original size:15 final size:15
Alignment explanation
Indices: 89544069--89544101 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
89544059 GTGTGTTTTA
89544069 AATTTCTAGATTAAG
1 AATTTCTAGATTAAG
89544084 AATTTCTAGATTAAG
1 AATTTCTAGATTAAG
89544099 AAT
1 AAT
89544102 GAAAAGTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.42, C:0.06, G:0.12, T:0.39
Consensus pattern (15 bp):
AATTTCTAGATTAAG
Found at i:89546756 original size:28 final size:27
Alignment explanation
Indices: 89546708--89546760 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 27
89546698 TTGTTTAACT
89546708 AACATCAAATATTCATAATATATCATTA
1 AACATCAAATATTCATAATAT-TCATTA
89546736 AACATCAAA-ATGCTCAT-ATATTCAT
1 AACATCAAATAT--TCATAATATTCAT
89546761 CAATGGTAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
27 6 0.26
28 13 0.57
29 4 0.17
ACGTcount: A:0.47, C:0.17, G:0.02, T:0.34
Consensus pattern (27 bp):
AACATCAAATATTCATAATATTCATTA
Found at i:89548136 original size:37 final size:37
Alignment explanation
Indices: 89548086--89548163 Score: 120
Period size: 37 Copynumber: 2.1 Consensus size: 37
89548076 ATTAGATATA
* **
89548086 TTGTATTAAAAATATGTTTCAAATTTATGAAATTTAT
1 TTGTATGAAAAATATGACTCAAATTTATGAAATTTAT
*
89548123 TTGTATGAAAAATATGACTCAAATTTATTAAATTTAT
1 TTGTATGAAAAATATGACTCAAATTTATGAAATTTAT
89548160 TTGT
1 TTGT
89548164 CTATGATTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.40, C:0.04, G:0.09, T:0.47
Consensus pattern (37 bp):
TTGTATGAAAAATATGACTCAAATTTATGAAATTTAT
Found at i:89548898 original size:22 final size:21
Alignment explanation
Indices: 89548872--89548913 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
89548862 TATGTTTAAA
*
89548872 CAATTAATTACATTATTTTTTT
1 CAATTAATTA-ATGATTTTTTT
*
89548894 CAATTTATTAATGATTTTTT
1 CAATTAATTAATGATTTTTT
89548914 AAATAAATTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.31, C:0.07, G:0.02, T:0.60
Consensus pattern (21 bp):
CAATTAATTAATGATTTTTTT
Found at i:89556974 original size:13 final size:13
Alignment explanation
Indices: 89556947--89556980 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
89556937 TTTAATTTAG
89556947 TTTAATTTGATTT
1 TTTAATTTGATTT
89556960 TTTATATTTGA-TT
1 TTTA-ATTTGATTT
89556973 TTTAATTT
1 TTTAATTT
89556981 AAAGAAAGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 4 0.20
13 10 0.50
14 6 0.30
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.71
Consensus pattern (13 bp):
TTTAATTTGATTT
Found at i:89557048 original size:13 final size:13
Alignment explanation
Indices: 89557021--89557054 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
89557011 TTTAATTTAG
89557021 TTTAATTTGATTT
1 TTTAATTTGATTT
89557034 TTTATATTTGA-TT
1 TTTA-ATTTGATTT
89557047 TTTAATTT
1 TTTAATTT
89557055 AAAAGTGGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 4 0.20
13 10 0.50
14 6 0.30
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.71
Consensus pattern (13 bp):
TTTAATTTGATTT
Found at i:89557075 original size:74 final size:74
Alignment explanation
Indices: 89556910--89557057 Score: 287
Period size: 74 Copynumber: 2.0 Consensus size: 74
89556900 AAATCGTAGG
*
89556910 GAAAGAATGAAAAAAAATTGAAAAAAATTTAATTTAGTTTAATTTGATTTTTTATATTTGATTTT
1 GAAAGAGTGAAAAAAAATTGAAAAAAATTTAATTTAGTTTAATTTGATTTTTTATATTTGATTTT
89556975 TAATTTAAA
66 TAATTTAAA
89556984 GAAAGAGTGAAAAAAAATTGAAAAAAATTTAATTTAGTTTAATTTGATTTTTTATATTTGATTTT
1 GAAAGAGTGAAAAAAAATTGAAAAAAATTTAATTTAGTTTAATTTGATTTTTTATATTTGATTTT
89557049 TAATTTAAA
66 TAATTTAAA
89557058 AGTGGCATGT
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
74 73 1.00
ACGTcount: A:0.45, C:0.00, G:0.10, T:0.45
Consensus pattern (74 bp):
GAAAGAGTGAAAAAAAATTGAAAAAAATTTAATTTAGTTTAATTTGATTTTTTATATTTGATTTT
TAATTTAAA
Found at i:89557627 original size:15 final size:16
Alignment explanation
Indices: 89557607--89557641 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
89557597 TTACAAATCT
89557607 AAATA-TCAAATGAGA
1 AAATAGTCAAATGAGA
89557622 AAATATGTCAAATGAGA
1 AAATA-GTCAAATGAGA
89557639 AAA
1 AAA
89557642 ATAGAAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 5 0.28
17 13 0.72
ACGTcount: A:0.60, C:0.06, G:0.14, T:0.20
Consensus pattern (16 bp):
AAATAGTCAAATGAGA
Found at i:89560830 original size:14 final size:14
Alignment explanation
Indices: 89560800--89560844 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
89560790 AGGCTCCATT
*
89560800 TGTTTGCCAGTAAAA
1 TGTTTTCCAG-AAAA
89560815 TGTTTTCCAGAAAA
1 TGTTTTCCAGAAAA
* *
89560829 TGATTTCTAGAAAA
1 TGTTTTCCAGAAAA
89560843 TG
1 TG
89560845 ATTTACTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
14 18 0.67
15 9 0.33
ACGTcount: A:0.36, C:0.11, G:0.18, T:0.36
Consensus pattern (14 bp):
TGTTTTCCAGAAAA
Found at i:89560845 original size:14 final size:14
Alignment explanation
Indices: 89560806--89560848 Score: 59
Period size: 14 Copynumber: 3.0 Consensus size: 14
89560796 CATTTGTTTG
*
89560806 CCAGTAAAATGTTTT
1 CCAG-AAAATGATTT
89560821 CCAGAAAATGATTT
1 CCAGAAAATGATTT
*
89560835 CTAGAAAATGATTT
1 CCAGAAAATGATTT
89560849 ACTTTTTTGG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
14 22 0.85
15 4 0.15
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.35
Consensus pattern (14 bp):
CCAGAAAATGATTT
Found at i:89562279 original size:32 final size:32
Alignment explanation
Indices: 89562233--89562312 Score: 81
Period size: 32 Copynumber: 2.5 Consensus size: 32
89562223 TGTTAATCAT
*
89562233 TTCAATATCCAACAAGCTT-AAAACATAATAAA
1 TTCAATATCCAACAA-ATTCAAAACATAATAAA
** * *
89562265 TTCAATATGTAACAAATTCAAGACATAATAAT
1 TTCAATATCCAACAAATTCAAAACATAATAAA
* *
89562297 TTCAAAATTCAACAAA
1 TTCAATATCCAACAAA
89562313 ATAAAATTTC
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
31 2 0.05
32 37 0.95
ACGTcount: A:0.53, C:0.16, G:0.04, T:0.28
Consensus pattern (32 bp):
TTCAATATCCAACAAATTCAAAACATAATAAA
Found at i:89564630 original size:48 final size:48
Alignment explanation
Indices: 89564568--89564675 Score: 144
Period size: 48 Copynumber: 2.2 Consensus size: 48
89564558 ATATCTAGAT
* * ** *
89564568 ATGGTCTTATACTGGCACACATATCGATGCTGATGCCATGTCCCAAAC
1 ATGGTCTTACACTGGCACACATATCAACACAGATGCCATGTCCCAAAC
* **
89564616 ATGGTCTTACACTGGCTCTTATATCAACACAGATGCCATGTCCCAAAC
1 ATGGTCTTACACTGGCACACATATCAACACAGATGCCATGTCCCAAAC
89564664 ATGGTCTTACAC
1 ATGGTCTTACAC
89564676 GGGATCTCAT
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
48 52 1.00
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.28
Consensus pattern (48 bp):
ATGGTCTTACACTGGCACACATATCAACACAGATGCCATGTCCCAAAC
Found at i:89568690 original size:19 final size:20
Alignment explanation
Indices: 89568653--89568690 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
89568643 CATAACAACG
* *
89568653 ATCACAAAAAGATAGAAATC
1 ATCACAAAAAGAGAAAAATC
89568673 ATCA-AAAAAGAGAAAAAT
1 ATCACAAAAAGAGAAAAAT
89568691 ACATACCTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.66, C:0.11, G:0.11, T:0.13
Consensus pattern (20 bp):
ATCACAAAAAGAGAAAAATC
Found at i:89572994 original size:13 final size:14
Alignment explanation
Indices: 89572976--89573004 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
89572966 TTATTCATTG
89572976 ATCTCTTCCTC-GA
1 ATCTCTTCCTCTGA
89572989 ATCTCTTCCTCTGA
1 ATCTCTTCCTCTGA
89573003 AT
1 AT
89573005 TAGCCTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.17, C:0.34, G:0.07, T:0.41
Consensus pattern (14 bp):
ATCTCTTCCTCTGA
Found at i:89579131 original size:21 final size:21
Alignment explanation
Indices: 89579090--89579131 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
89579080 TCCCCCACCT
* *
89579090 CCCCCGATTCCTCAACTTGTA
1 CCCCCGATGCCTCAACGTGTA
*
89579111 CCCCCGATGCCTCAAGGTGTA
1 CCCCCGATGCCTCAACGTGTA
89579132 GATCTGATGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.19, C:0.40, G:0.17, T:0.24
Consensus pattern (21 bp):
CCCCCGATGCCTCAACGTGTA
Found at i:89584295 original size:18 final size:18
Alignment explanation
Indices: 89584272--89584308 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
89584262 AAGCAAAGAA
89584272 AGGCATAAAATTTCAGGC
1 AGGCATAAAATTTCAGGC
*
89584290 AGGCATAAAATTTTAGGC
1 AGGCATAAAATTTCAGGC
89584308 A
1 A
89584309 TAAAATCGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.41, C:0.14, G:0.22, T:0.24
Consensus pattern (18 bp):
AGGCATAAAATTTCAGGC
Found at i:89589185 original size:28 final size:27
Alignment explanation
Indices: 89589119--89589218 Score: 164
Period size: 27 Copynumber: 3.7 Consensus size: 27
89589109 NNNNNNNNNN
89589119 ACTCGCACACTTAGTGCTACATAGTCA
1 ACTCGCACACTTAGTGCTACATAGTCA
89589146 ACTCGCACACTTAGTGCTACATAGTCAA
1 ACTCGCACACTTAGTGCTACATAGTC-A
* *
89589174 ACTCGTACACTTAGTGCTACATATTCA
1 ACTCGCACACTTAGTGCTACATAGTCA
*
89589201 ATTCGCACACTTAGTGCT
1 ACTCGCACACTTAGTGCT
89589219 GCACAATTTA
Statistics
Matches: 68, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
27 43 0.63
28 25 0.37
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (27 bp):
ACTCGCACACTTAGTGCTACATAGTCA
Found at i:89597154 original size:27 final size:27
Alignment explanation
Indices: 89597124--89597301 Score: 160
Period size: 27 Copynumber: 6.6 Consensus size: 27
89597114 ATATTGAGCC
* * **
89597124 CGCACACTCAGTGCTATATAATCATCT
1 CGCACACTTAGTGCTACATAATCAAAT
* *
89597151 CGCACACTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAAAT
* *
89597178 CGCACACTTAGTGCTACATAGTCAGACT
1 CGCACACTTAGTGCTACATAATCA-AAT
* ** ** *
89597206 CGCACTCTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAAAT
* **
89597233 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAAAT
* *
89597260 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAATCAAAT
89597287 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
89597302 GTACAATTTA
Statistics
Matches: 124, Mismatches: 24, Indels: 6
0.81 0.16 0.04
Matches are distributed among these distances:
27 101 0.81
28 23 0.19
ACGTcount: A:0.28, C:0.29, G:0.16, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAAAT
Found at i:89597263 original size:82 final size:81
Alignment explanation
Indices: 89597150--89597300 Score: 214
Period size: 82 Copynumber: 1.9 Consensus size: 81
89597140 TATAATCATC
* * * *
89597150 TCGCACACTTAGTGCCACGTAATCAAATCGCACACTTAGTGCTACATAGTCAGACTCGCACTCTT
1 TCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCAACATAGTCA-AATCGCACACTT
89597215 AGTGCCGCATGGTCAAT
65 AGTGCCGCATGGTCAAT
* **
89597232 TCGCACACTTAGTG-CATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCACACTT
1 TCGCACACTTAGTGCCA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCACACTT
89597296 AGTGC
65 AGTGC
89597301 TGTACAATTT
Statistics
Matches: 61, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
81 17 0.28
82 44 0.72
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.27
Consensus pattern (81 bp):
TCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCACACTTA
GTGCCGCATGGTCAAT
Found at i:89606603 original size:13 final size:13
Alignment explanation
Indices: 89606585--89606609 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
89606575 GAGTAATCAC
89606585 ACACGGGCGTGTT
1 ACACGGGCGTGTT
89606598 ACACGGGCGTGT
1 ACACGGGCGTGT
89606610 CCCTGCCGAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.24, G:0.40, T:0.20
Consensus pattern (13 bp):
ACACGGGCGTGTT
Found at i:89620910 original size:27 final size:27
Alignment explanation
Indices: 89620880--89620959 Score: 75
Period size: 27 Copynumber: 3.2 Consensus size: 27
89620870 GTTGAGTTGA
89620880 GTCCGAGTTCGTGAGATGTAACTAGGC
1 GTCCGAGTTCGTGAGATGTAACTAGGC
** * *
89620907 GTCCGAACTCGT-TGA-GT---T--GA
1 GTCCGAGTTCGTGAGATGTAACTAGGC
89620927 GTCCGAGTTCGTGAGATGTAACTAGGC
1 GTCCGAGTTCGTGAGATGTAACTAGGC
89620954 GTCCGA
1 GTCCGA
89620960 ACTCGTTGAG
Statistics
Matches: 38, Mismatches: 8, Indels: 14
0.63 0.13 0.23
Matches are distributed among these distances:
20 11 0.29
21 2 0.05
22 3 0.08
25 3 0.08
26 2 0.05
27 17 0.45
ACGTcount: A:0.21, C:0.20, G:0.33, T:0.26
Consensus pattern (27 bp):
GTCCGAGTTCGTGAGATGTAACTAGGC
Found at i:89620930 original size:47 final size:47
Alignment explanation
Indices: 89620861--89620983 Score: 246
Period size: 47 Copynumber: 2.6 Consensus size: 47
89620851 ATGGTTGAGT
89620861 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCG
89620908 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCG
89620955 TCCGAACTCGTTGAGTTGAGTCCGAGTTC
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC
89620984 ACTTATGGAT
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 76 1.00
ACGTcount: A:0.20, C:0.20, G:0.31, T:0.28
Consensus pattern (47 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCG
Found at i:89630074 original size:48 final size:48
Alignment explanation
Indices: 89630018--89630188 Score: 189
Period size: 48 Copynumber: 3.5 Consensus size: 48
89630008 AGCCAGTGAG
*
89630018 AGACCATGTTTGGAACATGGCATCGGCATTTATATGAGAGCTAGTGTA
1 AGACCATGTCTGGAACATGGCATCGGCATTTATATGAGAGCTAGTGTA
* * * * * * * *
89630066 AGACCATGTCTGGGACAAGGCATTGGCCTTAACATGTGGGCTAGTGTA
1 AGACCATGTCTGGAACATGGCATCGGCATTTATATGAGAGCTAGTGTA
* * ** *
89630114 AGACCATGTTTGGAACATGGCATCGACACCGATATATGAGAGCCAGTGTA
1 AGACCATGTCTGGAACATGGCATCGGCA--TTTATATGAGAGCTAGTGTA
*
89630164 AGACCATGTCTGGGACATGGCATCG
1 AGACCATGTCTGGAACATGGCATCG
89630189 ACATCTTACC
Statistics
Matches: 97, Mismatches: 24, Indels: 2
0.79 0.20 0.02
Matches are distributed among these distances:
48 61 0.63
50 36 0.37
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.25
Consensus pattern (48 bp):
AGACCATGTCTGGAACATGGCATCGGCATTTATATGAGAGCTAGTGTA
Found at i:89641163 original size:17 final size:18
Alignment explanation
Indices: 89641141--89641174 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
89641131 TTCTGGGCTT
89641141 TGTGGG-CCACATGGGCG
1 TGTGGGCCCACATGGGCG
89641158 TGTGGGCCCACATGGGC
1 TGTGGGCCCACATGGGC
89641175 CCATTCTCAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.12, C:0.26, G:0.44, T:0.18
Consensus pattern (18 bp):
TGTGGGCCCACATGGGCG
Found at i:89644199 original size:24 final size:23
Alignment explanation
Indices: 89644121--89644205 Score: 73
Period size: 24 Copynumber: 3.5 Consensus size: 23
89644111 TTTAAAGGTC
* *
89644121 CGCACACATAGTGCTCTTACTCATT
1 CGCACACATAGTGCTATTAATC--T
* *
89644146 CGCACACATAGTGCCATGT-TTCCT
1 CGCACACATAGTGCTAT-TAAT-CT
*
89644170 CACACACATAGTGCTATATAATCT
1 CGCACACATAGTGCTAT-TAATCT
89644194 CGCACACATAGT
1 CGCACACATAGT
89644206 TCCATGTAGT
Statistics
Matches: 49, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
24 30 0.61
25 17 0.35
26 2 0.04
ACGTcount: A:0.28, C:0.31, G:0.13, T:0.28
Consensus pattern (23 bp):
CGCACACATAGTGCTATTAATCT
Found at i:89654860 original size:42 final size:43
Alignment explanation
Indices: 89654790--89654937 Score: 111
Period size: 47 Copynumber: 3.3 Consensus size: 43
89654780 TAGCCCAGCT
* * *
89654790 ATGGTCTTACACGATGC-CTCAT-ACCGATGCAATGTCCCAAAC
1 ATGGTCTTACACTA-GCTCACATAACGGATGCAATGTCCCAAAC
* * *
89654832 ATGGTCTTACGCTAGCTCACATAACGATGTGATGCCATGTTCCAAAC
1 ATGGTCTTACACTAGCTCACATAAC---G-GATGCAATGTCCCAAAC
** *
89654879 ATGGTCTTACACTAGCTCATGTAACAATGCCGATGCCATGTCCCAAAC
1 ATGGTCTTACACTAGCTCACATAAC---G--GATGCAATGTCCCAAAC
89654927 ATGGTCTTACA
1 ATGGTCTTACA
89654938 TTGGCTCATG
Statistics
Matches: 87, Mismatches: 12, Indels: 8
0.81 0.11 0.07
Matches are distributed among these distances:
41 2 0.02
42 16 0.18
43 2 0.02
47 40 0.46
48 27 0.31
ACGTcount: A:0.28, C:0.28, G:0.18, T:0.26
Consensus pattern (43 bp):
ATGGTCTTACACTAGCTCACATAACGGATGCAATGTCCCAAAC
Found at i:89654933 original size:48 final size:48
Alignment explanation
Indices: 89654813--89655064 Score: 299
Period size: 48 Copynumber: 5.3 Consensus size: 48
89654803 ATGCCTCATA
* * * * *
89654813 CCGATGCAATGTCCCAAACATGGTCTTACGCTAGCTCACATAACGATG
1 CCGATGCCATGTCCCAAACATGGTCTTACACTGGCTCACGTAACAATG
* * * *
89654861 -TGATGCCATGTTCCAAACATGGTCTTACACTAGCTCATGTAACAATG
1 CCGATGCCATGTCCCAAACATGGTCTTACACTGGCTCACGTAACAATG
* *
89654908 CCGATGCCATGTCCCAAACATGGTCTTACATTGGCTCATGTAACAATG
1 CCGATGCCATGTCCCAAACATGGTCTTACACTGGCTCACGTAACAATG
* * ** * *
89654956 TCGATGCCATGTCCCAAACATGGCCTTACTTTGGCTTACGTAATAATG
1 CCGATGCCATGTCCCAAACATGGTCTTACACTGGCTCACGTAACAATG
* * * *
89655004 CCAATGCCATGTCCCAGACATGGTCTTCCACTGGCTTACGTAACAATG
1 CCGATGCCATGTCCCAAACATGGTCTTACACTGGCTCACGTAACAATG
*
89655052 TCGATGCCATGTC
1 CCGATGCCATGTC
89655065 TGTAACACCC
Statistics
Matches: 176, Mismatches: 27, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
47 40 0.23
48 136 0.77
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.27
Consensus pattern (48 bp):
CCGATGCCATGTCCCAAACATGGTCTTACACTGGCTCACGTAACAATG
Found at i:89656446 original size:27 final size:27
Alignment explanation
Indices: 89656416--89656647 Score: 198
Period size: 27 Copynumber: 8.6 Consensus size: 27
89656406 ATATCGAGCC
* * *
89656416 CGCACACTCAGTGCTATAAAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* *
89656443 CGCACACTTAGTGCCACATAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
89656470 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
** ** *
89656498 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
89656525 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
** ** *
89656552 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
89656579 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* * *
89656606 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
89656633 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
89656648 GTACAATTTA
Statistics
Matches: 172, Mismatches: 28, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
27 148 0.86
28 24 0.14
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:89656567 original size:54 final size:54
Alignment explanation
Indices: 89656442--89656646 Score: 286
Period size: 54 Copynumber: 3.8 Consensus size: 54
89656432 TAAAATCAAC
* * **
89656442 TCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGC-TACATAGTCAAAC
1 TCGCACACTTAGTGCCACATAGTCAAATCGCACACTTAGTGCAT-CATATTC-ATT
* * *
89656497 TCGCACACTTAGTGCCGCATGGTCAATTCGCACACTTAGTGCATCATATTCATT
1 TCGCACACTTAGTGCCACATAGTCAAATCGCACACTTAGTGCATCATATTCATT
* * *
89656551 TCGCACACTTAGTGCCGCATGGTCAATTCGCACACTTAGTGCATCATATTCATT
1 TCGCACACTTAGTGCCACATAGTCAAATCGCACACTTAGTGCATCATATTCATT
*
89656605 TCGCACACTTAGTGCAACATAGTCAAATCGCACACTTAGTGC
1 TCGCACACTTAGTGCCACATAGTCAAATCGCACACTTAGTGC
89656647 TGTACAATTT
Statistics
Matches: 138, Mismatches: 11, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
54 93 0.67
55 44 0.32
56 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (54 bp):
TCGCACACTTAGTGCCACATAGTCAAATCGCACACTTAGTGCATCATATTCATT
Found at i:89656620 original size:81 final size:81
Alignment explanation
Indices: 89656437--89656646 Score: 260
Period size: 81 Copynumber: 2.6 Consensus size: 81
89656427 TGCTATAAAA
* *
89656437 TCAACTCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAATTCGCACACTTAGTG-CACATAATCAAATCGCACACTTAGTGCCACATAGTCAAACTCGCA
* *
89656502 CACTTAGTGCCGCATGG
65 CACTTAGTGCAGCATAG
* ** * * *
89656519 TCAATTCGCACACTTAGTGCATCATATTCATTTCGCACACTTAGTGCCGCATGGTC-AATTCGCA
1 TCAATTCGCACACTTAGTGCA-CATAATCAAATCGCACACTTAGTGCCACATAGTCAAACTCGCA
* *
89656583 CACTTAGTGCATCATAT
65 CACTTAGTGCAGCATAG
* *
89656600 TCATTTCGCACACTTAGTGCAACATAGTCAAATCGCACACTTAGTGC
1 TCAATTCGCACACTTAGTGC-ACATAATCAAATCGCACACTTAGTGC
89656647 TGTACAATTT
Statistics
Matches: 110, Mismatches: 16, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
81 63 0.57
82 47 0.43
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.28
Consensus pattern (81 bp):
TCAATTCGCACACTTAGTGCACATAATCAAATCGCACACTTAGTGCCACATAGTCAAACTCGCAC
ACTTAGTGCAGCATAG
Found at i:89658402 original size:48 final size:48
Alignment explanation
Indices: 89658327--89658594 Score: 401
Period size: 48 Copynumber: 5.6 Consensus size: 48
89658317 GGCTGTCACA
* * * * *
89658327 ATGTCCAAGACATGGTCTTACACTGGCTTACGCAACAATGCTGATGCC
1 ATGTCCCAGACATGGTCTTACACTGGCTCACGTAACAATACCGATGCC
* ** * *
89658375 ATGTCCCAGACATGGTCTTACATTGGCTCGTGTAACAATGCCAATGCC
1 ATGTCCCAGACATGGTCTTACACTGGCTCACGTAACAATACCGATGCC
* * *
89658423 ATGTACCAGACATGGTCTTACATTGGCTCACATAACAATACCGATGCC
1 ATGTCCCAGACATGGTCTTACACTGGCTCACGTAACAATACCGATGCC
*
89658471 ATGTCCCAGACATAGTCTTACACTGGCTCACGTAACAATACCGATGCC
1 ATGTCCCAGACATGGTCTTACACTGGCTCACGTAACAATACCGATGCC
*
89658519 ATGTCCCAGACATGGTCTTACATTGGCTCACGTAACAATACCGATGCC
1 ATGTCCCAGACATGGTCTTACACTGGCTCACGTAACAATACCGATGCC
89658567 ATGTCCCAGACATGGTCTTACACTGGCT
1 ATGTCCCAGACATGGTCTTACACTGGCT
89658595 TAGATATTGC
Statistics
Matches: 199, Mismatches: 21, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
48 199 1.00
ACGTcount: A:0.27, C:0.28, G:0.19, T:0.25
Consensus pattern (48 bp):
ATGTCCCAGACATGGTCTTACACTGGCTCACGTAACAATACCGATGCC
Found at i:89667217 original size:20 final size:20
Alignment explanation
Indices: 89667194--89667240 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
89667184 AGTTTAATAT
89667194 TGAATTTTGAATTTTATAAA
1 TGAATTTTGAATTTTATAAA
89667214 TGAATTTTGAATTTTATAAA
1 TGAATTTTGAATTTTATAAA
89667234 TGAATTT
1 TGAATTT
89667241 AATCATCATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.38, C:0.00, G:0.11, T:0.51
Consensus pattern (20 bp):
TGAATTTTGAATTTTATAAA
Found at i:89673751 original size:58 final size:58
Alignment explanation
Indices: 89673661--89673777 Score: 225
Period size: 58 Copynumber: 2.0 Consensus size: 58
89673651 AGCTCAAGAG
89673661 CAAAGGGGAAATAAATCCGATAAAGGGAAGGAAAAAGTGGTTGAATAGCTAACAGAAT
1 CAAAGGGGAAATAAATCCGATAAAGGGAAGGAAAAAGTGGTTGAATAGCTAACAGAAT
*
89673719 CAAAGGGGAAATAAATCCGATAAAGGGAAGGAAAAAGTGGTTGAATAGCTAACGGAAT
1 CAAAGGGGAAATAAATCCGATAAAGGGAAGGAAAAAGTGGTTGAATAGCTAACAGAAT
89673777 C
1 C
89673778 GTTCGACAAC
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.47, C:0.09, G:0.28, T:0.15
Consensus pattern (58 bp):
CAAAGGGGAAATAAATCCGATAAAGGGAAGGAAAAAGTGGTTGAATAGCTAACAGAAT
Found at i:89674055 original size:40 final size:40
Alignment explanation
Indices: 89674024--89674233 Score: 271
Period size: 40 Copynumber: 5.3 Consensus size: 40
89674014 GGACTAAGAT
* * *
89674024 CCGAAGGCATTTGTGCGAGATA-CAAATTCCGGGTTAAGCC
1 CCGAAGGCATTCGTGCGAGATATTAAA-TCCGGGTTAAGTC
* *
89674064 CCGAAGGCCTTTGTGCGAGATATTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATATTAAATCCGGGTTAAGTC
*
89674104 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATATTAAATCCGGGTTAAGTC
* *
89674144 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTC
1 CCGAAGGCATTCGTGCGAGATATTAAATCCGGGTTAAGTC
* * * * * *
89674184 CCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTCGTGCGAGATATTAAATCCGGGTTAAGTC
89674223 CCGAAGGCATT
1 CCGAAGGCATT
89674234 TGAACGAGGA
Statistics
Matches: 158, Mismatches: 11, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
39 35 0.22
40 120 0.76
41 3 0.02
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGAAGGCATTCGTGCGAGATATTAAATCCGGGTTAAGTC
Found at i:89674187 original size:120 final size:120
Alignment explanation
Indices: 89673971--89674233 Score: 300
Period size: 120 Copynumber: 2.2 Consensus size: 120
89673961 TTGAATGCTG
* *
89673971 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGATCCGAAGGCATT
* * *
89674035 TGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATATTAAA
66 CGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGG-CATTGTGCGAGATACTAAA
* * * * **
89674091 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGAT-CCGAAGGCAT
* * * * * *
89674154 TCGTGCGAGTTATTAAA-TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
65 TCGTGCGAGATA-CAAATTCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAAA
* *
89674210 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
89674234 TGAACGAGGA
Statistics
Matches: 120, Mismatches: 20, Indels: 7
0.82 0.14 0.05
Matches are distributed among these distances:
119 37 0.31
120 74 0.62
121 9 0.08
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.26
Consensus pattern (120 bp):
TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGATCCGAAGGCATT
CGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAAA
Found at i:89674253 original size:79 final size:80
Alignment explanation
Indices: 89673972--89674268 Score: 221
Period size: 80 Copynumber: 3.7 Consensus size: 80
89673962 TGAATGCTGT
* ** * * * **
89673972 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGACTAAGAT-CCGAAGGCATT
1 CCGGGCTAAGTCCCGAAGGCATTCGAAC-GAGTGACTAAATCCGGGTTAAG-TCCCGAAGGCATT
* * *
89674035 TGTGCGAGATAC-AAATT
64 CGTGCGAGTTACTAAA-A
* * * * ** *
89674052 CCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGAT-ATTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 CCGGGCTAAGTCCCGAAGGCATTCGAACGAG-TGACTAAATCCGGGTTAAGTCCCGAAGGCATTC
* *
89674116 GTGCGAGTTATTAAAT
65 GTGCGAGTTACTAAAA
* ** * * *
89674132 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTCCCGAAGGCATT-G
1 CCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGACTAAATCCGGGTTAAGTCCCGAAGGCATTCG
*
89674196 TGTGAGTTACTAAAA
66 TGCGAGTTACTAAAA
* * * *
89674211 CCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGCTATATCC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGA-CTAAATCCGGGTTAAGTCCCGAAGG
89674269 TACGTGATTT
Statistics
Matches: 184, Mismatches: 27, Indels: 14
0.82 0.12 0.06
Matches are distributed among these distances:
78 15 0.08
79 47 0.26
80 111 0.60
81 11 0.06
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (80 bp):
CCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGACTAAATCCGGGTTAAGTCCCGAAGGCATTCG
TGCGAGTTACTAAAA
Found at i:89701470 original size:201 final size:200
Alignment explanation
Indices: 89701126--89701526 Score: 784
Period size: 201 Copynumber: 2.0 Consensus size: 200
89701116 CTTAATCTCT
89701126 TACACACTTATACAAAATCAAAAGCATATAACATGGTATTCATTTAATGATTAAATATTCTCAAT
1 TACACACTTATACAAAATCAAAAGCATATAACATGGTATTCATTTAATGATTAAATATTCTCAAT
*
89701191 TAAACCACAAACATAGCATTTGTATGTCATTATAGATGTGTCTCTCATACTCATTTTACCTTGTT
66 TAAACCACAAACATAGCATTTGTATGTCATCATAGATGTGTCTCTCATACTCATTTTACCTTGTT
89701256 TATTATAGTACCACTTATACATTTATACCAAGATTATCATCTTACCAAATATCTTCAGCTTAATC
131 TATTATAGTACCACTTATACATTTATACCAAGATTATCATCTTACCAAATATCTTCAGCTTAATC
89701321 ATCAA
196 ATCAA
89701326 TACACACTTATACAAAATCAAAAAGCATATAACATGGTATTCATTTAATGATTAAATATTCTCAA
1 TACACACTTATACAAAATC-AAAAGCATATAACATGGTATTCATTTAATGATTAAATATTCTCAA
89701391 TTAAACCACAAACATAGCATTTGTATGTCATCATAGATGTGTCTCTCATACTCATTTTACCTTGT
65 TTAAACCACAAACATAGCATTTGTATGTCATCATAGATGTGTCTCTCATACTCATTTTACCTTGT
89701456 TTATTATAGTACCACTTATACATTTATACCAAGATTATCATCTTACCAAATATCTTCAGCTTAAT
130 TTATTATAGTACCACTTATACATTTATACCAAGATTATCATCTTACCAAATATCTTCAGCTTAAT
89701521 CATCAA
195 CATCAA
89701527 GCATTCATAT
Statistics
Matches: 199, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
200 19 0.10
201 180 0.90
ACGTcount: A:0.37, C:0.19, G:0.07, T:0.37
Consensus pattern (200 bp):
TACACACTTATACAAAATCAAAAGCATATAACATGGTATTCATTTAATGATTAAATATTCTCAAT
TAAACCACAAACATAGCATTTGTATGTCATCATAGATGTGTCTCTCATACTCATTTTACCTTGTT
TATTATAGTACCACTTATACATTTATACCAAGATTATCATCTTACCAAATATCTTCAGCTTAATC
ATCAA
Found at i:89703297 original size:127 final size:127
Alignment explanation
Indices: 89703071--89703324 Score: 472
Period size: 127 Copynumber: 2.0 Consensus size: 127
89703061 CACTACGAAT
* *
89703071 CAAATTTCTCATTTTACAGAATTCAAAATGTGTTGTATTTGATCTCATTTGAAGCTAGACTCATT
1 CAAATTTCTCATTTTACAGAATTCAAAATGTGTTGTAGTTGATCTCATTTGAAACTAGACTCATT
89703136 AAGGAGTCTAAGCATATAAATTTTATCTTATAATCATTTTTGTACAATTTATAATGATTTTC
66 AAGGAGTCTAAGCATATAAATTTTATCTTATAATCATTTTTGTACAATTTATAATGATTTTC
*
89703198 CAAATTTCTCATTTTACAGAATTCAAAATGTGTTTTAGTTGATCTCATTTGAAACTAGACTCATT
1 CAAATTTCTCATTTTACAGAATTCAAAATGTGTTGTAGTTGATCTCATTTGAAACTAGACTCATT
*
89703263 AAGGATTCTAAGCATATAAATTTTATCTTATAATCATTTTTGTACAATTTATAATGATTTTC
66 AAGGAGTCTAAGCATATAAATTTTATCTTATAATCATTTTTGTACAATTTATAATGATTTTC
89703325 TAAAAACAGA
Statistics
Matches: 123, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
127 123 1.00
ACGTcount: A:0.33, C:0.13, G:0.10, T:0.44
Consensus pattern (127 bp):
CAAATTTCTCATTTTACAGAATTCAAAATGTGTTGTAGTTGATCTCATTTGAAACTAGACTCATT
AAGGAGTCTAAGCATATAAATTTTATCTTATAATCATTTTTGTACAATTTATAATGATTTTC
Found at i:89710623 original size:21 final size:21
Alignment explanation
Indices: 89710573--89710623 Score: 75
Period size: 22 Copynumber: 2.4 Consensus size: 21
89710563 GCATCAAAAT
*
89710573 AACCAACGAAGGACAATTGAG
1 AACCAACGAAGGACAACTGAG
*
89710594 AACCCAACGAAGGATAACTGAG
1 AA-CCAACGAAGGACAACTGAG
89710616 AACCAACG
1 AACCAACG
89710624 GTGAAGGGGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 8 0.30
22 19 0.70
ACGTcount: A:0.47, C:0.24, G:0.22, T:0.08
Consensus pattern (21 bp):
AACCAACGAAGGACAACTGAG
Found at i:89712582 original size:40 final size:41
Alignment explanation
Indices: 89712488--89712708 Score: 246
Period size: 40 Copynumber: 5.6 Consensus size: 41
89712478 TATTCGAATG
*
89712488 ATATCCGGGCTAAG-TCCCGAAGGCTTTTGTGCTAGGTGACT
1 ATATCCGGGCTAAGATCCCGAAGGCATTTGTGCTA-GTGACT
* * * *
89712529 ATAACCGGACTAAGAT-CCGAAGGCATTCGTGCGAGTTG-CT
1 ATATCCGGGCTAAGATCCCGAAGGCATTTGTGCTAG-TGACT
*
89712569 ATATCCGGGCTAAGA-CCCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAGATCCCGAAGGCATTTGTGCTAGTGACT
* *
89712609 ATATCCGGGCTAAG-TCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGATCCCGAAGGCATTTGTGCTAGTGACT
* * *
89712649 ATATCCGGGCTAAGA-CCCGAAGGC-CTTGTGCAAGT-AGTT
1 ATATCCGGGCTAAGATCCCGAAGGCATTTGTGCTAGTGA-CT
89712688 ATATCC-GGCTAA-ATCCCGAAG
1 ATATCCGGGCTAAGATCCCGAAG
89712709 ATTACTTGAG
Statistics
Matches: 154, Mismatches: 18, Indels: 19
0.81 0.09 0.10
Matches are distributed among these distances:
37 1 0.01
38 14 0.09
39 15 0.10
40 94 0.61
41 29 0.19
42 1 0.01
ACGTcount: A:0.25, C:0.24, G:0.27, T:0.24
Consensus pattern (41 bp):
ATATCCGGGCTAAGATCCCGAAGGCATTTGTGCTAGTGACT
Found at i:89715110 original size:27 final size:27
Alignment explanation
Indices: 89715056--89715111 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
89715046 CTGTCGCGCG
* * *
89715056 AACAGGTGACTGGTAGATTGCTTGGCA
1 AACAGGTGACTGATAGATTGCCTAGCA
89715083 AACAGGTGACTGATAGATTGCCTAGCA
1 AACAGGTGACTGATAGATTGCCTAGCA
89715110 AA
1 AA
89715112 TAAGTGATTG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.32, C:0.16, G:0.29, T:0.23
Consensus pattern (27 bp):
AACAGGTGACTGATAGATTGCCTAGCA
Found at i:89715118 original size:27 final size:27
Alignment explanation
Indices: 89715056--89715118 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
89715046 CTGTCGCGCG
* * * *
89715056 AACAGGTGACTGGTAGATTGCTTGGCA
1 AACAAGTGACTGATAGATTGCCTAGCA
*
89715083 AACAGGTGACTGATAGATTGCCTAGCA
1 AACAAGTGACTGATAGATTGCCTAGCA
*
89715110 AATAAGTGA
1 AACAAGTGA
89715119 TTGGCGGGCT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.33, C:0.14, G:0.29, T:0.24
Consensus pattern (27 bp):
AACAAGTGACTGATAGATTGCCTAGCA
Found at i:89715243 original size:27 final size:26
Alignment explanation
Indices: 89715165--89715256 Score: 82
Period size: 27 Copynumber: 3.4 Consensus size: 26
89715155 TATCTTACAG
*
89715165 ACAGGTGACTGG-AAAGCTGTCTGGCA
1 ACAGGTGACTGGCAGA-CTGTCTGGCA
*
89715191 GACAGGTGACTGGC-GAAT-TGCTTGGCGA
1 -ACAGGTGACTGGCAGACTGT-C-TGGC-A
89715219 ACAGGTGACTGGCAGACTGTCTGGCAA
1 ACAGGTGACTGGCAGACTGTCTGGC-A
*
89715246 ACATGTGACTG
1 ACAGGTGACTG
89715257 ATGAGTTGCC
Statistics
Matches: 54, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
25 1 0.02
26 2 0.04
27 45 0.83
28 5 0.09
29 1 0.02
ACGTcount: A:0.25, C:0.20, G:0.35, T:0.21
Consensus pattern (26 bp):
ACAGGTGACTGGCAGACTGTCTGGCA
Found at i:89715284 original size:54 final size:54
Alignment explanation
Indices: 89715181--89715290 Score: 139
Period size: 54 Copynumber: 2.0 Consensus size: 54
89715171 GACTGGAAAG
* * * * *
89715181 CTGTCTGGCAGACAGGTGACTGGCGAATTGCTTGGCGAACAGGTGACTGGCAGA
1 CTGTCTGGCAAACAGGTGACTGACGAATTGCCTGGCAAACAGGTAACTGGCAGA
* * * *
89715235 CTGTCTGGCAAACATGTGACTGATGAGTTGCCTGGCAAATAGGTAACTGGCAGA
1 CTGTCTGGCAAACAGGTGACTGACGAATTGCCTGGCAAACAGGTAACTGGCAGA
89715289 CT
1 CT
89715291 ATCTCACGAA
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
54 47 1.00
ACGTcount: A:0.25, C:0.20, G:0.33, T:0.23
Consensus pattern (54 bp):
CTGTCTGGCAAACAGGTGACTGACGAATTGCCTGGCAAACAGGTAACTGGCAGA
Found at i:89716374 original size:27 final size:27
Alignment explanation
Indices: 89716326--89716377 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
89716316 AAGAACTGCG
*
89716326 AAACAGATGACTGGCGAGCTGCCTGAC
1 AAACAGATGACTGGAGAGCTGCCTGAC
89716353 AAACAGATGACTGGTAGA-CTGCCTG
1 AAACAGATGACTGG-AGAGCTGCCTG
89716378 GCGGACATGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
27 21 0.91
28 2 0.09
ACGTcount: A:0.31, C:0.23, G:0.29, T:0.17
Consensus pattern (27 bp):
AAACAGATGACTGGAGAGCTGCCTGAC
Found at i:89720121 original size:21 final size:20
Alignment explanation
Indices: 89720088--89720126 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
89720078 AATATACGTT
89720088 TGTTTGTCAGAACATTTTGTC
1 TGTTTGTCAGAAC-TTTTGTC
**
89720109 TGTTTGTGTGAACTTTTG
1 TGTTTGTCAGAACTTTTG
89720127 GTTATTGGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.15, C:0.10, G:0.23, T:0.51
Consensus pattern (20 bp):
TGTTTGTCAGAACTTTTGTC
Found at i:89721132 original size:25 final size:25
Alignment explanation
Indices: 89721104--89721174 Score: 59
Period size: 20 Copynumber: 3.2 Consensus size: 25
89721094 GAATAACAAC
89721104 CTAAATCAACTACCTCAATAACTTA
1 CTAAATCAACTACCTCAATAACTTA
* *
89721129 CT-AA-CAAC-A-AT-AACAAC---
1 CTAAATCAACTACCTCAATAACTTA
*
89721146 CTAAATCATCTACCTCAATAACTTA
1 CTAAATCAACTACCTCAATAACTTA
89721171 CTAA
1 CTAA
89721175 CAACCTAACT
Statistics
Matches: 33, Mismatches: 5, Indels: 16
0.61 0.09 0.30
Matches are distributed among these distances:
17 2 0.06
18 2 0.06
19 3 0.09
20 6 0.18
21 2 0.06
22 6 0.18
23 4 0.12
24 2 0.06
25 6 0.18
ACGTcount: A:0.46, C:0.28, G:0.00, T:0.25
Consensus pattern (25 bp):
CTAAATCAACTACCTCAATAACTTA
Found at i:89721142 original size:42 final size:42
Alignment explanation
Indices: 89721095--89721178 Score: 159
Period size: 42 Copynumber: 2.0 Consensus size: 42
89721085 ACAAGAAAAG
89721095 AATAACAACCTAAATCAACTACCTCAATAACTTACTAACAAC
1 AATAACAACCTAAATCAACTACCTCAATAACTTACTAACAAC
*
89721137 AATAACAACCTAAATCATCTACCTCAATAACTTACTAACAAC
1 AATAACAACCTAAATCAACTACCTCAATAACTTACTAACAAC
89721179 CTAACTGTTG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.49, C:0.29, G:0.00, T:0.23
Consensus pattern (42 bp):
AATAACAACCTAAATCAACTACCTCAATAACTTACTAACAAC
Found at i:89721891 original size:18 final size:17
Alignment explanation
Indices: 89721870--89721904 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
89721860 TTATTATTTA
*
89721870 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
89721888 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
89721905 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:89721898 original size:28 final size:27
Alignment explanation
Indices: 89721828--89721900 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 27
89721818 TTTATTATCA
*
89721828 AAAATAAATAATTTAATCATATTTAAAC
1 AAAATATATAATTTAAT-ATATTTAAAC
* * **
89721856 ATAAT-TATTATTTAATATATTTTAATT
1 AAAATATATAATTTAATATA-TTTAAAC
89721883 AAAATATATAATTTAATA
1 AAAATATATAATTTAATA
89721901 AAATTCTTAA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
26 3 0.08
27 18 0.50
28 15 0.42
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (27 bp):
AAAATATATAATTTAATATATTTAAAC
Found at i:89722038 original size:18 final size:17
Alignment explanation
Indices: 89722017--89722051 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
89722007 TTATTATTAA
*
89722017 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
89722035 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
89722052 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:89722063 original size:147 final size:149
Alignment explanation
Indices: 89721789--89722063 Score: 509
Period size: 147 Copynumber: 1.9 Consensus size: 149
89721779 ATGATTATTG
*
89721789 TTATTGTTATTTAAATTTTAATAAGATTATTTATTATCAAAAATAAATAATTTAATCATATTTAA
1 TTATTGTTATTTAAATTTTAATAAGATTATTTAATATCAAAAATAAATAATTTAATCATATTTAA
*
89721854 ACATAATTATTATTTAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGC
66 ACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGC
89721919 AGAAATTTGTTTTGGTAAA
131 AGAAATTTGTTTTGGTAAA
*
89721938 TTATT-TTATTTAAATTTTAATAAGATTA-TTAATATCAATAATAAATAATTTAATCATATTTAA
1 TTATTGTTATTTAAATTTTAATAAGATTATTTAATATCAAAAATAAATAATTTAATCATATTTAA
89722001 ACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTA
66 ACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTA
89722064 ATATTCTTAT
Statistics
Matches: 123, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
147 95 0.77
148 23 0.19
149 5 0.04
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (149 bp):
TTATTGTTATTTAAATTTTAATAAGATTATTTAATATCAAAAATAAATAATTTAATCATATTTAA
ACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGC
AGAAATTTGTTTTGGTAAA
Found at i:89722095 original size:54 final size:54
Alignment explanation
Indices: 89722037--89722215 Score: 128
Period size: 55 Copynumber: 3.1 Consensus size: 54
89722027 ATTAAAATAT
*
89722037 ATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAACC
1 ATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAAAC
** * * * * *
89722091 ATAATATATGATACTGTAAAATAT-AAAATAACATAATTATTATTAAATAT-AATATAATTAAAA
1 ATAAT-T-T-A-A---TAAAAT-TCTTAATAA-TTAA-TATTCTT--ATATGAAT-TTACTCAAA
*
89722154 TAT
53 -AC
*
89722157 ATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATC
1 ATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAAAC
89722211 ATAAT
1 ATAAT
89722216 ATATGATACT
Statistics
Matches: 91, Mismatches: 18, Indels: 32
0.65 0.13 0.23
Matches are distributed among these distances:
54 10 0.11
55 11 0.12
56 4 0.04
57 7 0.08
58 5 0.05
59 11 0.12
61 11 0.12
62 5 0.05
63 7 0.08
64 4 0.04
65 11 0.12
66 5 0.05
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.41
Consensus pattern (54 bp):
ATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAAAC
Found at i:89722158 original size:18 final size:17
Alignment explanation
Indices: 89722137--89722171 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
89722127 TTATTATTAA
89722137 ATATAATATAATTAAAAT
1 ATATAATATAA-TAAAAT
*
89722155 ATATAATTTAATAAAAT
1 ATATAATATAATAAAAT
89722172 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
ATATAATATAATAAAAT
Found at i:89722303 original size:120 final size:120
Alignment explanation
Indices: 89722000--89722292 Score: 491
Period size: 120 Copynumber: 2.4 Consensus size: 120
89721990 ATCATATTTA
89722000 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
*
89722065 TATTCTTATATGAATTTACTCAAACCATAATATATGATACTGTAAAATATAAAAT
66 TATTCTTATATGAATTTACTCAAACCATAATATATGATACTATAAAATATAAAAT
* *
89722120 AACATAATTATTATTAAATATAATATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
* *
89722185 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATA-AAATTTT
66 TATTCTTATATGAATTTACTCAAACCATAATATATGATACTATAAAATATAAA--AT
* *
89722241 AA-ATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATT
89722293 TAAAATAATT
Statistics
Matches: 162, Mismatches: 9, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
119 3 0.02
120 156 0.96
121 3 0.02
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (120 bp):
AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
TATTCTTATATGAATTTACTCAAACCATAATATATGATACTATAAAATATAAAAT
Found at i:89722305 original size:28 final size:27
Alignment explanation
Indices: 89722229--89722305 Score: 70
Period size: 28 Copynumber: 2.9 Consensus size: 27
89722219 TGATACTATA
*
89722229 AAATAAAATTTTAAATAATTA-ATATT
1 AAATAAAATTTAAAATAATTATATATT
* *
89722255 AAATATATTTTAATTAA-AA-TATATGATT
1 AAATAAAATTTAA--AATAATTATAT-ATT
*
89722283 TAATAAAATTTAAAATAATTATA
1 AAATAAAATTTAAAATAATTATA
89722306 ACTAATAAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
26 14 0.36
27 6 0.15
28 19 0.49
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (27 bp):
AAATAAAATTTAAAATAATTATATATT
Found at i:89722403 original size:91 final size:89
Alignment explanation
Indices: 89722308--89722513 Score: 245
Period size: 91 Copynumber: 2.3 Consensus size: 89
89722298 TAATTATAAC
* * * *
89722308 TAATAAATTATATTTTATGAATTTGTATAATTTAAAATAA-TAATTATTACATATAATTTAATAA
1 TAATAAATTATATTATATGAATTTATACAATTTAAAATAATTAA-TATTAAATATAATTTAATAA
*
89722372 TAATATAAAATTTCATAAAATTCTTGA
65 TAATAT--AATTTCATAAAATTCTTAA
* * *
89722399 TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAGT
1 TAATAAATTATATTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
* * *
89722464 GATATAATTTCATGAAATTGTTAA
66 AATATAATTTCATAAAATTCTTAA
*
89722488 TAATAAAATGT-TCTTATATGAATTTA
1 TAAT-AAAT-TATATTATATGAATTTA
89722514 CTAAAATCAA
Statistics
Matches: 101, Mismatches: 11, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
89 20 0.20
90 19 0.19
91 59 0.58
92 3 0.03
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (89 bp):
TAATAAATTATATTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
AATATAATTTCATAAAATTCTTAA
Found at i:89723042 original size:12 final size:12
Alignment explanation
Indices: 89723027--89723056 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
89723017 AATACAAACA
89723027 ACAGAAGCTGCT
1 ACAGAAGCTGCT
89723039 ACAGAAGCTGCT
1 ACAGAAGCTGCT
*
89723051 AAAGAA
1 ACAGAA
89723057 ATTAACCATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.13
Consensus pattern (12 bp):
ACAGAAGCTGCT
Found at i:89723339 original size:14 final size:14
Alignment explanation
Indices: 89723320--89723346 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
89723310 TATTAACAAC
89723320 AAATAGTTCCCAAA
1 AAATAGTTCCCAAA
89723334 AAATAGTTCCCAA
1 AAATAGTTCCCAA
89723347 TTGCCAAGCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.22, G:0.07, T:0.22
Consensus pattern (14 bp):
AAATAGTTCCCAAA
Found at i:89732119 original size:58 final size:58
Alignment explanation
Indices: 89732024--89732140 Score: 171
Period size: 58 Copynumber: 2.0 Consensus size: 58
89732014 GGTAAATCAT
* * *
89732024 ATACTTCGATGCTCACACAGAGCTACGGTAGTCCACAACTTATATAGAATTACTACCA
1 ATACATCGATGCTCACACAGAGCTACGGTAGCCCACAACTTATACAGAATTACTACCA
* * * *
89732082 ATACATCGATGCTCATACAGAGCTATGGTAGCCCACAACTTATGCAGAATTGCTACCA
1 ATACATCGATGCTCACACAGAGCTACGGTAGCCCACAACTTATACAGAATTACTACCA
89732140 A
1 A
89732141 ACACTATATC
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
58 52 1.00
ACGTcount: A:0.34, C:0.26, G:0.15, T:0.25
Consensus pattern (58 bp):
ATACATCGATGCTCACACAGAGCTACGGTAGCCCACAACTTATACAGAATTACTACCA
Found at i:89733072 original size:15 final size:15
Alignment explanation
Indices: 89733050--89733081 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
89733040 ATTTCTCCTT
89733050 TTTCTTTTTC-TTTG
1 TTTCTTTTTCATTTG
89733064 TTTCTTTTTCATTTG
1 TTTCTTTTTCATTTG
89733079 TTT
1 TTT
89733082 TACATCTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.03, C:0.12, G:0.06, T:0.78
Consensus pattern (15 bp):
TTTCTTTTTCATTTG
Found at i:89733101 original size:3 final size:3
Alignment explanation
Indices: 89733093--89733163 Score: 59
Period size: 3 Copynumber: 26.0 Consensus size: 3
89733083 ACATCTATAT
*
89733093 ATA ATA AT- ATA AT- ATA TATA AT- GTA ATA AT- ATA ATA AT- ATA
1 ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
89733134 ATA AT- ATA ATA AT- ATA ATA A-C ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
89733164 TAAATTAATA
Statistics
Matches: 55, Mismatches: 4, Indels: 18
0.71 0.05 0.23
Matches are distributed among these distances:
2 14 0.25
3 38 0.69
4 3 0.05
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.37
Consensus pattern (3 bp):
ATA
Found at i:89733106 original size:5 final size:5
Alignment explanation
Indices: 89733096--89733175 Score: 53
Period size: 5 Copynumber: 15.6 Consensus size: 5
89733086 TCTATATATA
*
89733096 ATAAT ATAAT AT-AT ATAAT GTAAT A-ATAT AATAAT ATAAT A-ATAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATA-AT -ATAAT ATAAT ATA-AT
89733141 AATAAT ATAAT A-ACAT AATAAT ATAA- ATTAAT ATA
1 -ATAAT ATAAT ATA-AT -ATAAT ATAAT A-TAAT ATA
89733176 TTACTTATTT
Statistics
Matches: 61, Mismatches: 2, Indels: 24
0.70 0.02 0.28
Matches are distributed among these distances:
4 8 0.13
5 40 0.66
6 10 0.16
7 3 0.05
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (5 bp):
ATAAT
Found at i:89733178 original size:8 final size:8
Alignment explanation
Indices: 89733091--89733166 Score: 120
Period size: 8 Copynumber: 9.8 Consensus size: 8
89733081 TTACATCTAT
89733091 ATATAATA
1 ATATAATA
89733099 ATATAAT-
1 ATATAATA
89733106 ATAT-ATA
1 ATATAATA
*
89733113 ATGTAATA
1 ATATAATA
89733121 ATATAATA
1 ATATAATA
89733129 ATATAATA
1 ATATAATA
89733137 ATATAATA
1 ATATAATA
89733145 ATATAATA
1 ATATAATA
*
89733153 ACATAATA
1 ATATAATA
89733161 ATATAA
1 ATATAA
89733167 ATTAATATAT
Statistics
Matches: 62, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
6 2 0.03
7 7 0.11
8 53 0.85
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.37
Consensus pattern (8 bp):
ATATAATA
Found at i:89734819 original size:21 final size:21
Alignment explanation
Indices: 89734751--89734819 Score: 59
Period size: 21 Copynumber: 3.3 Consensus size: 21
89734741 AAGCCTGAAG
*
89734751 GCTGAACAGAAGCTCATGAGA
1 GCTGAACAGAAGCTCATAAGA
* * * *
89734772 GCTAAACAAAAAC-CAATAAGG
1 GCTGAACAGAAGCTC-ATAAGA
* *
89734793 GTTGAACGGAAGCTCATAAGA
1 GCTGAACAGAAGCTCATAAGA
89734814 GCTGAA
1 GCTGAA
89734820 TGGAAACAGA
Statistics
Matches: 34, Mismatches: 12, Indels: 4
0.68 0.24 0.08
Matches are distributed among these distances:
20 1 0.03
21 32 0.94
22 1 0.03
ACGTcount: A:0.43, C:0.17, G:0.25, T:0.14
Consensus pattern (21 bp):
GCTGAACAGAAGCTCATAAGA
Found at i:89739395 original size:21 final size:20
Alignment explanation
Indices: 89739342--89739383 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
89739332 TAGGCATAAA
89739342 TGTGTTCAGAAAGTAGATTT
1 TGTGTTCAGAAAGTAGATTT
89739362 TGTGTTCAGAAAGTAGATTT
1 TGTGTTCAGAAAGTAGATTT
89739382 TG
1 TG
89739384 GATTCAAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.29, C:0.05, G:0.26, T:0.40
Consensus pattern (20 bp):
TGTGTTCAGAAAGTAGATTT
Found at i:89740473 original size:24 final size:24
Alignment explanation
Indices: 89740421--89740473 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
89740411 GATGTAGATG
* *
89740421 TAGATGCAGATACCAACACAGATA
1 TAGATGCAGATACAAACACAAATA
* * *
89740445 CAGATGCAGATACAAATACAAATT
1 TAGATGCAGATACAAACACAAATA
89740469 TAGAT
1 TAGAT
89740474 CCTACCCTCA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.47, C:0.17, G:0.15, T:0.21
Consensus pattern (24 bp):
TAGATGCAGATACAAACACAAATA
Found at i:89742048 original size:16 final size:16
Alignment explanation
Indices: 89742027--89742060 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
89742017 AGCGACGATG
89742027 AACAATGAGAGTTTGT
1 AACAATGAGAGTTTGT
89742043 AACAATGAGAGTTTGT
1 AACAATGAGAGTTTGT
89742059 AA
1 AA
89742061 TTGTAGGGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.41, C:0.06, G:0.24, T:0.29
Consensus pattern (16 bp):
AACAATGAGAGTTTGT
Found at i:89742246 original size:27 final size:26
Alignment explanation
Indices: 89742216--89742268 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 26
89742206 GAAGCAGAAG
*
89742216 AGAATGGAAAA-AAAAAAGAAAGTTAAA
1 AGAATAGAAAAGAAAAAA-AAA-TTAAA
*
89742243 AGAATATAAAAGAAAAAAAAATTAAA
1 AGAATAGAAAAGAAAAAAAAATTAAA
89742269 TTACTCAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 5 0.22
27 12 0.52
28 6 0.26
ACGTcount: A:0.74, C:0.00, G:0.13, T:0.13
Consensus pattern (26 bp):
AGAATAGAAAAGAAAAAAAAATTAAA
Found at i:89743061 original size:30 final size:31
Alignment explanation
Indices: 89742998--89743064 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
89742988 TACAATTTGA
**
89742998 TCACTAAGCTATTCAAAAATTTTTATTTAAG
1 TCACTAAGCTATTCAAAAATAATTATTTAAG
*
89743029 TCACTGAA-CTATTCAAAAA-AATTATTTTAG
1 TCACT-AAGCTATTCAAAAATAATTATTTAAG
89743059 TCACTA
1 TCACTA
89743065 GATGGTTAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 1 0.03
30 13 0.41
31 16 0.50
32 2 0.06
ACGTcount: A:0.40, C:0.15, G:0.06, T:0.39
Consensus pattern (31 bp):
TCACTAAGCTATTCAAAAATAATTATTTAAG
Found at i:89746558 original size:16 final size:16
Alignment explanation
Indices: 89746537--89746570 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
89746527 AGCGACGATG
89746537 AACAATGAGAGTTTGT
1 AACAATGAGAGTTTGT
89746553 AACAATGAGAGTTTGT
1 AACAATGAGAGTTTGT
89746569 AA
1 AA
89746571 TTGTAGGGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.41, C:0.06, G:0.24, T:0.29
Consensus pattern (16 bp):
AACAATGAGAGTTTGT
Found at i:89747526 original size:31 final size:31
Alignment explanation
Indices: 89747491--89747557 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
89747481 ACTTAATTAA
*
89747491 AAAAATTTACAATTTGA-TCACTAAACTATTC
1 AAAAATTTAC-ATTTAAGTCACTAAACTATTC
* *
89747522 AAAAATTTTCATTTAAGTCACTGAACTATTC
1 AAAAATTTACATTTAAGTCACTAAACTATTC
89747553 AAAAA
1 AAAAA
89747558 AAATTATTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
30 5 0.16
31 27 0.84
ACGTcount: A:0.46, C:0.15, G:0.04, T:0.34
Consensus pattern (31 bp):
AAAAATTTACATTTAAGTCACTAAACTATTC
Found at i:89751096 original size:29 final size:30
Alignment explanation
Indices: 89751064--89751123 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 30
89751054 ACTTAAGAAG
89751064 CAAATG-CTTCTAAAATAATAA-AAAATTAA
1 CAAATGCCTT-TAAAATAATAAGAAAATTAA
89751093 CAAATGCCTTTAAAATAATAAGAAAATTAA
1 CAAATGCCTTTAAAATAATAAGAAAATTAA
89751123 C
1 C
89751124 TATAAAATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
29 17 0.59
30 12 0.41
ACGTcount: A:0.57, C:0.12, G:0.05, T:0.27
Consensus pattern (30 bp):
CAAATGCCTTTAAAATAATAAGAAAATTAA
Found at i:89765277 original size:11 final size:11
Alignment explanation
Indices: 89765261--89765285 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
89765251 CTGTGTGTTC
89765261 TTTATTTTATT
1 TTTATTTTATT
89765272 TTTATTTTATT
1 TTTATTTTATT
89765283 TTT
1 TTT
89765286 TTCACAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTATTTTATT
Found at i:89771635 original size:21 final size:22
Alignment explanation
Indices: 89771592--89771635 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
89771582 CTAACAAGTG
*
89771592 TTTTCTAAAAAATTATTCAAAT
1 TTTTCTAAAAAAATATTCAAAT
* *
89771614 TTTTC-AAAAAAATCTTCTAAT
1 TTTTCTAAAAAAATATTCAAAT
89771635 T
1 T
89771636 AGAAGCGTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.43, C:0.11, G:0.00, T:0.45
Consensus pattern (22 bp):
TTTTCTAAAAAAATATTCAAAT
Found at i:89773121 original size:26 final size:26
Alignment explanation
Indices: 89773085--89773144 Score: 93
Period size: 26 Copynumber: 2.3 Consensus size: 26
89773075 ACGGATTTTC
* *
89773085 TCAAGATTTTACCAGGGGTAAAATTG
1 TCAAAATTTTACCAGGGGTAAAATTA
*
89773111 TCAAAATTTTATCAGGGGTAAAATTA
1 TCAAAATTTTACCAGGGGTAAAATTA
89773137 TCAAAATT
1 TCAAAATT
89773145 CTACTGAAGT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.33
Consensus pattern (26 bp):
TCAAAATTTTACCAGGGGTAAAATTA
Found at i:89774258 original size:18 final size:19
Alignment explanation
Indices: 89774235--89774272 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
89774225 TGGTTTTCTC
*
89774235 AAAATTGAAATG-GAAATG
1 AAAATTAAAATGAGAAATG
89774253 AAAATTAAAATGAGAAATG
1 AAAATTAAAATGAGAAATG
89774272 A
1 A
89774273 TTCATTTGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.61, C:0.00, G:0.18, T:0.21
Consensus pattern (19 bp):
AAAATTAAAATGAGAAATG
Found at i:89782819 original size:19 final size:20
Alignment explanation
Indices: 89782758--89782824 Score: 75
Period size: 21 Copynumber: 3.2 Consensus size: 20
89782748 AAATATATAC
89782758 ATAATAA-TATTAA-AATAAA
1 ATAATAAGTA-TAATAATAAA
*
89782777 ATAATAAGTGATAATAGTGAAA
1 ATAATAAGT-ATAATAAT-AAA
89782799 ATAATAAGTATAATAATAAA
1 ATAATAAGTATAATAATAAA
89782819 TATAAT
1 -ATAAT
89782825 GATGTATGAA
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
19 7 0.17
20 7 0.17
21 15 0.37
22 12 0.29
ACGTcount: A:0.61, C:0.00, G:0.07, T:0.31
Consensus pattern (20 bp):
ATAATAAGTATAATAATAAA
Found at i:89783522 original size:26 final size:26
Alignment explanation
Indices: 89783470--89783536 Score: 82
Period size: 26 Copynumber: 2.5 Consensus size: 26
89783460 AGTAATAATA
89783470 AAAAAGATTAATAATAGTAATAGAAAAT
1 AAAAAGA-TAATAATAG-AATAGAAAAT
*
89783498 ATAAAGATAATAATA-ACATAGAAAAT
1 AAAAAGATAATAATAGA-ATAGAAAAT
*
89783524 AAAAAGGTAATAA
1 AAAAAGATAATAA
89783537 ATATACAGTA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
25 1 0.03
26 20 0.57
27 8 0.23
28 6 0.17
ACGTcount: A:0.66, C:0.01, G:0.10, T:0.22
Consensus pattern (26 bp):
AAAAAGATAATAATAGAATAGAAAAT
Found at i:89783554 original size:6 final size:6
Alignment explanation
Indices: 89783543--89783567 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
89783533 ATAAATATAC
89783543 AGTAAT AGTAAT AGTAAT AGTAAT A
1 AGTAAT AGTAAT AGTAAT AGTAAT A
89783568 AAATATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.16, T:0.32
Consensus pattern (6 bp):
AGTAAT
Found at i:89784838 original size:23 final size:22
Alignment explanation
Indices: 89784772--89784851 Score: 99
Period size: 23 Copynumber: 3.5 Consensus size: 22
89784762 GGCTTGCTAT
**
89784772 TGGGTTTTAGGTGTTTAATGT-GT
1 TGGGTTTT-GG-GTTTAATGTAAA
89784795 TGGGTTTTGAGGTTTAATGTAAA
1 TGGGTTTTG-GGTTTAATGTAAA
89784818 TGGGTTTTGGGATTTAATGTAAA
1 TGGGTTTTGGG-TTTAATGTAAA
89784841 TGGGTTTTGGG
1 TGGGTTTTGGG
89784852 GTTGGGCTTG
Statistics
Matches: 52, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
22 12 0.23
23 40 0.77
ACGTcount: A:0.19, C:0.00, G:0.35, T:0.46
Consensus pattern (22 bp):
TGGGTTTTGGGTTTAATGTAAA
Found at i:89793714 original size:25 final size:25
Alignment explanation
Indices: 89793686--89793743 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
89793676 AACTTTTTTT
89793686 AAATT-TTAAAATAAAAAAACTATAA
1 AAATTATTAAAA-AAAAAAACTATAA
** *
89793711 AAATTATTTTAAAATAAAACTATAA
1 AAATTATTAAAAAAAAAAACTATAA
*
89793736 AAAATATT
1 AAATTATT
89793744 TTTTTAAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 24 0.86
26 4 0.14
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (25 bp):
AAATTATTAAAAAAAAAAACTATAA
Found at i:89793748 original size:28 final size:28
Alignment explanation
Indices: 89793688--89793751 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 28
89793678 CTTTTTTTAA
*
89793688 ATTTTAAAATAAAAAAACTATAAAAATT
1 ATTTTAAAATAAAAAAACTAAAAAAATT
**
89793716 ATTTTAAAATAAAACTA-TAAAAAATATT
1 ATTTTAAAATAAAAAAACTAAAAAA-ATT
*
89793744 TTTTTAAA
1 ATTTTAAA
89793752 TATTTTAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 6 0.19
28 25 0.81
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (28 bp):
ATTTTAAAATAAAAAAACTAAAAAAATT
Found at i:89796729 original size:3 final size:3
Alignment explanation
Indices: 89796721--89796761 Score: 59
Period size: 3 Copynumber: 14.0 Consensus size: 3
89796711 AGATATTTAC
89796721 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TT- TTA TCTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA
89796762 ATTGAGATAA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
2 4 0.11
3 28 0.80
4 3 0.09
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:89796975 original size:12 final size:12
Alignment explanation
Indices: 89796950--89796984 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
89796940 TTAGGGGAAA
89796950 AAAAGAAGAAAAG
1 AAAAGAA-AAAAG
89796963 AAAAGAAAAAAG
1 AAAAGAAAAAAG
*
89796975 AAAGGAAAAA
1 AAAAGAAAAA
89796985 TTAGGGTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 14 0.67
13 7 0.33
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (12 bp):
AAAAGAAAAAAG
Found at i:89796977 original size:17 final size:16
Alignment explanation
Indices: 89796946--89796984 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
89796936 AAAATTAGGG
*
89796946 GAAAAAAAGAAGAAAA
1 GAAAAAAAAAAGAAAA
*
89796962 GAAAAGAAAAAAGAAAG
1 GAAAA-AAAAAAGAAAA
89796979 GAAAAA
1 GAAAAA
89796985 TTAGGGTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (16 bp):
GAAAAAAAAAAGAAAA
Found at i:89801686 original size:13 final size:13
Alignment explanation
Indices: 89801668--89801693 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
89801658 GATAGACCAT
89801668 TCTGTTAGTATAC
1 TCTGTTAGTATAC
89801681 TCTGTTAGTATAC
1 TCTGTTAGTATAC
89801694 ACTAGTAGTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.15, G:0.15, T:0.46
Consensus pattern (13 bp):
TCTGTTAGTATAC
Found at i:89802433 original size:98 final size:98
Alignment explanation
Indices: 89802262--89802451 Score: 240
Period size: 98 Copynumber: 1.9 Consensus size: 98
89802252 CGACATCCAG
*
89802262 ATATGAAGAGCCATTGGTAGAGCATGTTAGTTGCAAACCAAAATGGCACATATGCTAGGCCACTA
1 ATATGAAGAGCCACTGGTAGAGCATGTTAGTTGCAAACCAAAATGGCACATATGCTAGGCCACTA
*
89802327 GTAGGACATGCTAGTTGTTAACCAGGTGGGAGA
66 GTACGACATGCTAGTTGTTAACCAGGTGGGAGA
* * * * ** * *
89802360 ATATGATA-AGCCACTGGTA-AGGCATGTTAGTTGCTAATCAGATTGGCGTATATGTTGGGCCAC
1 ATATGA-AGAGCCACTGGTAGA-GCATGTTAGTTGCAAACCAAAATGGCACATATGCTAGGCCAC
* *
89802423 TGGTACGACATGCTAGTTGTTAACTAGGT
64 TAGTACGACATGCTAGTTGTTAACCAGGT
89802452 TGGCGACCAC
Statistics
Matches: 78, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
97 1 0.01
98 76 0.97
99 1 0.01
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.27
Consensus pattern (98 bp):
ATATGAAGAGCCACTGGTAGAGCATGTTAGTTGCAAACCAAAATGGCACATATGCTAGGCCACTA
GTACGACATGCTAGTTGTTAACCAGGTGGGAGA
Found at i:89802455 original size:49 final size:49
Alignment explanation
Indices: 89802311--89802457 Score: 143
Period size: 49 Copynumber: 3.0 Consensus size: 49
89802301 AAAATGGCAC
* * * * * *
89802311 ATATGCTAGGCCACTAGTAGGACATGCTAGTTGTTAACCAGGTGGGAGA
1 ATATGATAGGCCACTGGTAAGACATGCTAGTTGTTAACTAGGTTGGCGA
* * * * * *
89802360 ATATGATAAGCCACTGGTAAGGCATGTTAGTTGCTAA-TCAGATTGGCGT
1 ATATGATAGGCCACTGGTAAGACATGCTAGTTGTTAACT-AGGTTGGCGA
* * *
89802409 ATATGTTGGGCCACTGGTACGACATGCTAGTTGTTAACTAGGTTGGCGA
1 ATATGATAGGCCACTGGTAAGACATGCTAGTTGTTAACTAGGTTGGCGA
89802458 CCACTAGTAG
Statistics
Matches: 75, Mismatches: 21, Indels: 4
0.75 0.21 0.04
Matches are distributed among these distances:
49 74 0.99
50 1 0.01
ACGTcount: A:0.27, C:0.16, G:0.29, T:0.29
Consensus pattern (49 bp):
ATATGATAGGCCACTGGTAAGACATGCTAGTTGTTAACTAGGTTGGCGA
Found at i:89802775 original size:48 final size:48
Alignment explanation
Indices: 89802695--89802786 Score: 139
Period size: 48 Copynumber: 1.9 Consensus size: 48
89802685 AAGAAAGGAT
* *
89802695 TTGAAAAGAGTAAGTTAATATGGCTCTGTATGTGATATATGTTATGTG
1 TTGAAAAGAGTAAGTTAATATGACTCTATATGTGATATATGTTATGTG
* * *
89802743 TTGAAAAGAGTACGTTAATTTGACTCTATATGTGTTATATGTTA
1 TTGAAAAGAGTAAGTTAATATGACTCTATATGTGATATATGTTA
89802787 CATATAATTA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 39 1.00
ACGTcount: A:0.32, C:0.05, G:0.22, T:0.41
Consensus pattern (48 bp):
TTGAAAAGAGTAAGTTAATATGACTCTATATGTGATATATGTTATGTG
Found at i:89812255 original size:10 final size:10
Alignment explanation
Indices: 89812240--89812280 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
89812230 TATTTACCTA
89812240 TAATTAAACT
1 TAATTAAACT
* *
89812250 TAATTAATCA
1 TAATTAAACT
89812260 TAATT-AA-T
1 TAATTAAACT
89812268 TAATTAAACT
1 TAATTAAACT
89812278 TAA
1 TAA
89812281 ATTAGCTAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
8 5 0.20
9 3 0.12
10 17 0.68
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.41
Consensus pattern (10 bp):
TAATTAAACT
Found at i:89812280 original size:14 final size:14
Alignment explanation
Indices: 89812240--89812280 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
89812230 TATTTACCTA
89812240 TAATTAAACTTAAT
1 TAATTAAACTTAAT
*
89812254 TAATCATAA-TTAAT
1 TAATTA-AACTTAAT
89812268 TAATTAAACTTAA
1 TAATTAAACTTAA
89812281 ATTAGCTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 2 0.09
14 19 0.83
15 2 0.09
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.41
Consensus pattern (14 bp):
TAATTAAACTTAAT
Found at i:89812310 original size:21 final size:21
Alignment explanation
Indices: 89812271--89812315 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
89812261 AATTAATTAA
89812271 TTAAACTTAAATTAGCTAAACT
1 TTAAACTTAAATTAGCTAAA-T
* *
89812293 TTAAGCTT-AATTATCTAAAT
1 TTAAACTTAAATTAGCTAAAT
89812313 TTA
1 TTA
89812316 GTGGATTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 4 0.19
21 10 0.48
22 7 0.33
ACGTcount: A:0.42, C:0.11, G:0.04, T:0.42
Consensus pattern (21 bp):
TTAAACTTAAATTAGCTAAAT
Found at i:89816573 original size:26 final size:24
Alignment explanation
Indices: 89816526--89816580 Score: 56
Period size: 26 Copynumber: 2.2 Consensus size: 24
89816516 TTTCTAGAAT
* * *
89816526 CTAAAACAATATTATTCTTAAATAAA
1 CTAAAACAATAATATCCCT-AA-AAA
*
89816552 CTAAAACAATAATGTCCCTAAAAA
1 CTAAAACAATAATATCCCTAAAAA
89816576 CTAAA
1 CTAAA
89816581 GGTACATCAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
24 8 0.32
25 2 0.08
26 15 0.60
ACGTcount: A:0.55, C:0.16, G:0.02, T:0.27
Consensus pattern (24 bp):
CTAAAACAATAATATCCCTAAAAA
Found at i:89817696 original size:22 final size:21
Alignment explanation
Indices: 89817661--89817736 Score: 59
Period size: 22 Copynumber: 3.7 Consensus size: 21
89817651 AAAAGGTATC
* * *
89817661 TACAAATTAAATCTCTACGAT
1 TACAAATCATATCTCTAAGAT
89817682 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATC-TCTAAGAT
* *
89817705 TGCATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
*
89817724 TGC-AATCATATCT
1 TACAAATCATATCT
89817737 AAGATTGTAT
Statistics
Matches: 45, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
18 6 0.13
19 11 0.24
20 1 0.02
21 3 0.07
22 15 0.33
23 9 0.20
ACGTcount: A:0.39, C:0.18, G:0.07, T:0.36
Consensus pattern (21 bp):
TACAAATCATATCTCTAAGAT
Found at i:89817721 original size:19 final size:19
Alignment explanation
Indices: 89817697--89817787 Score: 152
Period size: 19 Copynumber: 4.9 Consensus size: 19
89817687 AATCATATCT
89817697 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
89817716 TCTAAGATTGCA-ATCATA
1 TCTAAGATTGCATATCATA
*
89817734 TCTAAGATTG--TATAATA
1 TCTAAGATTGCATATCATA
89817751 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
89817770 TCTAAGATTGCATATCAT
1 TCTAAGATTGCATATCAT
89817788 TGAAGATTAT
Statistics
Matches: 67, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
17 15 0.22
18 16 0.24
19 36 0.54
ACGTcount: A:0.37, C:0.14, G:0.11, T:0.37
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:89817757 original size:35 final size:37
Alignment explanation
Indices: 89817690--89817784 Score: 135
Period size: 35 Copynumber: 2.6 Consensus size: 37
89817680 ATTACAAAAT
*
89817690 CATATC-T-TCTAAGATTGCATATCATATCTAAGATTG
1 CATATCATATCTAAGATTG-ATATAATATCTAAGATTG
89817726 CA-ATCATATCTAAGATTG-TATAATATCTAAGATTG
1 CATATCATATCTAAGATTGATATAATATCTAAGATTG
89817761 CATATCATATCTAAGATTGCATAT
1 CATATCATATCTAAGATTG-ATAT
89817785 CATTGAAGAT
Statistics
Matches: 53, Mismatches: 1, Indels: 8
0.85 0.02 0.13
Matches are distributed among these distances:
35 21 0.40
36 19 0.36
37 10 0.19
38 3 0.06
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.38
Consensus pattern (37 bp):
CATATCATATCTAAGATTGATATAATATCTAAGATTG
Found at i:89817944 original size:21 final size:20
Alignment explanation
Indices: 89817906--89817945 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
89817896 TTGGACTTCG
**
89817906 TTTTTTTTTTGGGTTTATTA
1 TTTTTTTTTTGGACTTATTA
89817926 TTTTTGTTTTTGGACTTATT
1 TTTTT-TTTTTGGACTTATT
89817946 TCTGGGCCCG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.10, C:0.03, G:0.15, T:0.72
Consensus pattern (20 bp):
TTTTTTTTTTGGACTTATTA
Found at i:89818193 original size:45 final size:45
Alignment explanation
Indices: 89818138--89818411 Score: 259
Period size: 45 Copynumber: 6.1 Consensus size: 45
89818128 GGAAGGCGAT
* * * *
89818138 ATCTGCTATCTTTGATCTGCTCCCCGTCTAATATAGAGACGCCAA
1 ATCTGTTATCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAA
*
89818183 ATCTGTTATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAA
1 ATCTGTTATCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAA
* * * * *
89818228 ATCTGTT-TCTTCAATCTACTCCCTGTCTAATACAGAGATACTAA
1 ATCTGTTATCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAA
* * * *
89818272 ATCTGTTAACTCCGATTTGCTCCCTGTCTAATACAGAGATGCCAA
1 ATCTGTTATCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAA
* * * * * * * * *
89818317 ATCTATCATCTTGGATCTGCT--TCGATGTAA-ACAAATGAAGGTCAG
1 ATCTGTTATCTTCGATCTGCTCCCCG-TCTAATACAGA-G-ATGCCAA
*
89818362 ATCTGCTATATCTTTGATCTGCTCCCCGTCTAATACAGAGATGCCAA
1 ATCTG-T-TATCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAA
89818409 ATC
1 ATC
89818412 ATCTTGGATC
Statistics
Matches: 182, Mismatches: 38, Indels: 16
0.77 0.16 0.07
Matches are distributed among these distances:
43 5 0.03
44 43 0.24
45 102 0.56
46 1 0.01
47 20 0.11
48 5 0.03
49 6 0.03
ACGTcount: A:0.27, C:0.26, G:0.15, T:0.32
Consensus pattern (45 bp):
ATCTGTTATCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAA
Found at i:89818274 original size:89 final size:89
Alignment explanation
Indices: 89818152--89818320 Score: 239
Period size: 89 Copynumber: 1.9 Consensus size: 89
89818142 GCTATCTTTG
* * * * *
89818152 ATCTGCTCCCCGTCTAATATAGAGACGCCAAATCTGTTATCTTCGATCTGCTCCCCGTCTAATAC
1 ATCTACTCCCCGTCTAATACAGAGACACCAAATCTGTTAACTCCGATCTGCTCCCCGTCTAATAC
89818217 AGAGACGCCAAATCTGTTTCTTCA
66 AGAGACGCCAAATCTGTTTCTTCA
* * * * *
89818241 ATCTACTCCCTGTCTAATACAGAGATACTAAATCTGTTAACTCCGATTTGCTCCCTGTCTAATAC
1 ATCTACTCCCCGTCTAATACAGAGACACCAAATCTGTTAACTCCGATCTGCTCCCCGTCTAATAC
*
89818306 AGAGATGCCAAATCT
66 AGAGACGCCAAATCT
89818321 ATCATCTTGG
Statistics
Matches: 69, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
89 69 1.00
ACGTcount: A:0.27, C:0.28, G:0.14, T:0.31
Consensus pattern (89 bp):
ATCTACTCCCCGTCTAATACAGAGACACCAAATCTGTTAACTCCGATCTGCTCCCCGTCTAATAC
AGAGACGCCAAATCTGTTTCTTCA
Found at i:89818483 original size:78 final size:78
Alignment explanation
Indices: 89818354--89818879 Score: 802
Period size: 78 Copynumber: 6.7 Consensus size: 78
89818344 TAAACAAATG
* * *
89818354 AAGGTCAGATCTGCTATATCTTTGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGG
1 AAGGTCAGATCTGCTGTGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGG
89818419 ATCTGCTTCAATA
66 ATCTGCTTCAATA
* * * *
89818432 AAGGTCCA-ATCTGTTATGTCTTTGATCTGCTCCCCGTTTAATACAGAGATGCCAAATCATCTTG
1 AAGGT-CAGATCTGCTGTGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTG
*
89818496 GATCTGCTTCAATG
65 GATCTGCTTCAATA
* *
89818510 AAGGTTAGATCTGCTGTGTCTTCGATCTGCTCCCCATCTAATACAGAGATGCCAAATCATCTTGG
1 AAGGTCAGATCTGCTGTGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGG
89818575 ATCTGCTTCAATA
66 ATCTGCTTCAATA
* *
89818588 AAGATCAGATCTGCTGTGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGA
1 AAGGTCAGATCTGCTGTGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGG
*
89818653 ATCTGCTTCAATG
66 ATCTGCTTCAATA
* *
89818666 AAGGTCAAATCTGCTGTGTCTTCGATCTGCTCCCTGTCTAATACAGAGATGCCAAATCATCTTGG
1 AAGGTCAGATCTGCTGTGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGG
* * *
89818731 ATTTGCATCAATG
66 ATCTGCTTCAATA
*
89818744 AAGGTCAGATCTGCTGTGTCTTCGATCTGCTCCTCGTCTAATACAGAGATGCCAAATCATCTTGG
1 AAGGTCAGATCTGCTGTGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGG
89818809 ATCTGCTTCAATA
66 ATCTGCTTCAATA
* * * * * **
89818822 AAGGTCAGATCTGCTATGTCTTCGATCTGTTCTCCGTCGATTATGGAGATGCCAAATC
1 AAGGTCAGATCTGCTGTGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATC
89818880 TGTTTCTTCG
Statistics
Matches: 410, Mismatches: 36, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
77 1 0.00
78 407 0.99
79 2 0.00
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.32
Consensus pattern (78 bp):
AAGGTCAGATCTGCTGTGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGG
ATCTGCTTCAATA
Found at i:89819163 original size:40 final size:40
Alignment explanation
Indices: 89819104--89819181 Score: 120
Period size: 40 Copynumber: 1.9 Consensus size: 40
89819094 CAAATCTGTT
* * * *
89819104 TCTTCGATTTATTCTCTGACAATACAGAGATGCCAAATCA
1 TCTTCGATCTACTCCCTGACAATACAGAGACGCCAAATCA
89819144 TCTTCGATCTACTCCCTGACAATACAGAGACGCCAAAT
1 TCTTCGATCTACTCCCTGACAATACAGAGACGCCAAAT
89819182 TTGCTATCTT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.32, C:0.27, G:0.13, T:0.28
Consensus pattern (40 bp):
TCTTCGATCTACTCCCTGACAATACAGAGACGCCAAATCA
Found at i:89819315 original size:224 final size:219
Alignment explanation
Indices: 89818821--89819380 Score: 734
Period size: 224 Copynumber: 2.5 Consensus size: 219
89818811 CTGCTTCAAT
* * * *
89818821 AAAGGTCAGATCTGCTATGTCTTCGATCTGTTCTCCGTCGATTATGGAGATGCCAAATCTGTTTC
1 AAAGGTTAGATCTGTTATGTCTTCGATCTGCTCTCCGTCGAATATGGAGATGCCAAATCTGTTTC
* ** * *
89818886 TTCGATTTGTTCTCTGACAGTACAGAGATGCCAAATCATCTTAGATCTGTTTCAGCGTAAACACG
66 TTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATCT-ACTCACCGCAAACACG
* * * *
89818951 TGAAAGCCAAATCTGTTATATCTTCGATCTGCTCCTTGTCAACGCAAGGATGCCAAATCATCTTG
130 AGAAAGCCAAATCTGTGATATCTTCAATCTGCTCCTTGTAAACGCAAGGATGCCAAATCATCTTG
*
89819016 AATCTACTTCGATGTGAAGACATCC
195 AATCTACTTCGATGTGAAAACATCC
* * *
89819041 GAAGGTTAGATCTGTTATGTCTTTGATCTGCTCTCCGTCAAATATGGAGATGCCAAATCTGTTTC
1 AAAGGTTAGATCTGTTATGTCTTCGATCTGCTCTCCGTCGAATATGGAGATGCCAAATCTGTTTC
* *
89819106 TTCGATTTATTCTCTGACAATACAGAGATGCCAAATCATCTTCGATCTACTC-CCTGACAATACA
66 TTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATCTACTCACC-G-CAA-ACA
* * *
89819170 -GAG-ACGCCAAAT-T-TGCTATCTTTAATCTGCTCCTTGTAAACGCAAGGATGCCAAATTTGCT
128 CGAGAAAGCCAAATCTGTGATATCTTCAATCTGCTCCTTGTAAACGCAAGGATGCCAAA--T-C-
* **
89819231 ATCTTTGATCTGCTACTTCGATGTGAAAATGTCC
189 ATC-TTGA-AT-CTACTTCGATGTGAAAACATCC
89819265 AAAGGTTAGATCTGTTATGTCTTCGATCTGCTCTCCGTCGAATATGGAGATGCCAAATCTGTTTC
1 AAAGGTTAGATCTGTTATGTCTTCGATCTGCTCTCCGTCGAATATGGAGATGCCAAATCTGTTTC
** *
89819330 TTCGATTTGTTCTCTGACAATACAGAGATGTTAAATCATCTTGGATCTACT
66 TTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATCTACT
89819381 TCAGCGTAAA
Statistics
Matches: 298, Mismatches: 32, Indels: 16
0.86 0.09 0.05
Matches are distributed among these distances:
217 37 0.12
218 2 0.01
219 12 0.04
220 108 0.36
221 6 0.02
222 4 0.01
223 1 0.00
224 128 0.43
ACGTcount: A:0.26, C:0.22, G:0.18, T:0.34
Consensus pattern (219 bp):
AAAGGTTAGATCTGTTATGTCTTCGATCTGCTCTCCGTCGAATATGGAGATGCCAAATCTGTTTC
TTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATCTACTCACCGCAAACACGA
GAAAGCCAAATCTGTGATATCTTCAATCTGCTCCTTGTAAACGCAAGGATGCCAAATCATCTTGA
ATCTACTTCGATGTGAAAACATCC
Found at i:89827911 original size:23 final size:22
Alignment explanation
Indices: 89827883--89827927 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
89827873 AAATTAAATA
89827883 TCTAAGATTACAAAATCATATCT
1 TCTAAGATTAC-AAATCATATCT
* *
89827906 TCTAAGATTGCATATCATATCT
1 TCTAAGATTACAAATCATATCT
89827928 AAGATTATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.38, C:0.18, G:0.07, T:0.38
Consensus pattern (22 bp):
TCTAAGATTACAAATCATATCT
Found at i:89827930 original size:19 final size:19
Alignment explanation
Indices: 89827906--89827978 Score: 123
Period size: 19 Copynumber: 3.9 Consensus size: 19
89827896 AATCATATCT
89827906 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
89827925 TCTAAGATT--ATATCATA
1 TCTAAGATTGCATATCATA
89827942 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
89827961 TCTCAGATTGCATATCAT
1 TCTAAGATTGCATATCAT
89827979 TGAAGATTAT
Statistics
Matches: 51, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
17 17 0.33
19 34 0.67
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Done.