Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 124536837
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: 124536837
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 312 characters in sequence are not A, C, G, or T
File 108 of 427
Found at i:28537584 original size:22 final size:21
Alignment explanation
Indices: 28537554--28537619 Score: 64
Period size: 19 Copynumber: 3.2 Consensus size: 21
28537544 TACAAATTAA
28537554 ATCTCCAAGATTACAAGATCAT
1 ATCTCCAAGATTAC-AGATCAT
* * *
28537576 ATCTTCAAGATTGCATATCAT
1 ATCTCCAAGATTACAGATCAT
* *
28537597 ATCT--AAGATTGCATATCAT
1 ATCTCCAAGATTACAGATCAT
28537616 ATCT
1 ATCT
28537620 AAGATTGCAT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
19 19 0.46
21 10 0.24
22 12 0.29
ACGTcount: A:0.36, C:0.20, G:0.09, T:0.35
Consensus pattern (21 bp):
ATCTCCAAGATTACAGATCAT
Found at i:28537606 original size:19 final size:19
Alignment explanation
Indices: 28537571--28537632 Score: 106
Period size: 19 Copynumber: 3.2 Consensus size: 19
28537561 AGATTACAAG
28537571 ATCATATCTTCAAGATTGCAT
1 ATCATATC-T-AAGATTGCAT
28537592 ATCATATCTAAGATTGCAT
1 ATCATATCTAAGATTGCAT
28537611 ATCATATCTAAGATTGCAT
1 ATCATATCTAAGATTGCAT
28537630 ATC
1 ATC
28537633 CTTCAAGATT
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
19 32 0.78
20 1 0.02
21 8 0.20
ACGTcount: A:0.35, C:0.18, G:0.10, T:0.37
Consensus pattern (19 bp):
ATCATATCTAAGATTGCAT
Found at i:28538077 original size:21 final size:22
Alignment explanation
Indices: 28538051--28538104 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 22
28538041 TTTGTAAACC
28538051 AAAATACAT-ATATAATG-ATAT
1 AAAATACATAATA-AATGAATAT
*
28538072 AAAATATATAATAAATGAAATAT
1 AAAATACATAATAAATG-AATAT
28538095 AAAATA-ATAA
1 AAAATACATAA
28538105 GAATTATATA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
21 12 0.41
22 7 0.24
23 10 0.34
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.30
Consensus pattern (22 bp):
AAAATACATAATAAATGAATAT
Found at i:28538094 original size:16 final size:16
Alignment explanation
Indices: 28538058--28538182 Score: 69
Period size: 17 Copynumber: 7.8 Consensus size: 16
28538048 ACCAAAATAC
*
28538058 ATATATAATGATATAAA
1 ATATATAAT-AAATAAA
*
28538075 ATATATAATAAATGAA
1 ATATATAATAAATAAA
*
28538091 ATATAAAAT-AATAAGA
1 ATATATAATAAATAA-A
* *
28538107 ATTATATATTAAGTAAA
1 A-TATATAATAAATAAA
* * * *
28538124 TTTACATACAAAAATATA
1 -ATATATA-ATAAATAAA
* *
28538142 ATA-A-AATAATTAAT
1 ATATATAATAAATAAA
*
28538156 ATATATAATATA-AAA
1 ATATATAATAAATAAA
28538171 ATATATAATAAA
1 ATATATAATAAA
28538183 ATATAAATGG
Statistics
Matches: 79, Mismatches: 22, Indels: 16
0.68 0.19 0.14
Matches are distributed among these distances:
14 8 0.10
15 19 0.24
16 20 0.25
17 23 0.29
18 9 0.11
ACGTcount: A:0.62, C:0.02, G:0.03, T:0.34
Consensus pattern (16 bp):
ATATATAATAAATAAA
Found at i:28538217 original size:16 final size:16
Alignment explanation
Indices: 28538196--28538260 Score: 60
Period size: 16 Copynumber: 4.1 Consensus size: 16
28538186 TAAATGGAAC
28538196 AAATAACATATAATAA
1 AAATAACATATAATAA
*
28538212 AAATAACATATACTAA
1 AAATAACATATAATAA
* * * * *
28538228 AATTTATAAATAATAT
1 AAATAACATATAATAA
*
28538244 AAATAATATA-AATAA
1 AAATAACATATAATAA
28538259 AA
1 AA
28538261 TAATATAAAG
Statistics
Matches: 38, Mismatches: 11, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
15 6 0.16
16 32 0.84
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (16 bp):
AAATAACATATAATAA
Found at i:28538248 original size:32 final size:32
Alignment explanation
Indices: 28538205--28538281 Score: 84
Period size: 32 Copynumber: 2.4 Consensus size: 32
28538195 CAAATAACAT
* * *
28538205 ATAATAAAAATAACATATACTAAAAT-TTATAA
1 ATAATATAAATAACATA-AATAAAATAATATAA
*
28538237 ATAATATAAATAATATAAATAAAATAATATAA
1 ATAATATAAATAACATAAATAAAATAATATAA
*
28538269 AGAATATATAATA
1 ATAATATA-AATA
28538282 TTTAAAATAT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
31 7 0.18
32 27 0.71
33 4 0.11
ACGTcount: A:0.65, C:0.03, G:0.01, T:0.31
Consensus pattern (32 bp):
ATAATATAAATAACATAAATAAAATAATATAA
Found at i:28538261 original size:14 final size:15
Alignment explanation
Indices: 28538239--28538269 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
28538229 ATTTATAAAT
28538239 AATATAAATAATATA
1 AATATAAATAATATA
28538254 AATA-AAATAATATA
1 AATATAAATAATATA
28538268 AA
1 AA
28538270 GAATATATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
AATATAAATAATATA
Found at i:28538261 original size:23 final size:24
Alignment explanation
Indices: 28538235--28538281 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
28538225 TAAAATTTAT
*
28538235 AAATAATATAAATAATATA-AATA
1 AAATAATATAAAGAATATATAATA
28538258 AAATAATATAAAGAATATATAATA
1 AAATAATATAAAGAATATATAATA
28538282 TTTAAAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 18 0.82
24 4 0.18
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (24 bp):
AAATAATATAAAGAATATATAATA
Found at i:28538276 original size:9 final size:9
Alignment explanation
Indices: 28538136--28538268 Score: 60
Period size: 9 Copynumber: 14.2 Consensus size: 9
28538126 TACATACAAA
28538136 AATAT-AAT
1 AATATAAAT
* *
28538144 AAAATAATT
1 AATATAAAT
*
28538153 AATATATAT
1 AATATAAAT
28538162 AATATAAA-
1 AATATAAAT
28538170 AATATATAAT
1 AATATA-AAT
28538180 AAAATATAAAT
1 --AATATAAAT
* *
28538191 GGA-ACAAAT
1 -AATATAAAT
*
28538200 AACATATAAT
1 AATATA-AAT
*
28538210 AAAAATAACAT
1 -AATATAA-AT
28538221 -ATACTAAA-
1 AATA-TAAAT
*
28538229 ATTTATAAAT
1 A-ATATAAAT
28538239 AATATAAAT
1 AATATAAAT
28538248 AATATAAAT
1 AATATAAAT
*
28538257 AAAATAATAT
1 AATATAA-AT
28538267 AA
1 AA
28538269 AGAATATATA
Statistics
Matches: 95, Mismatches: 16, Indels: 26
0.69 0.12 0.19
Matches are distributed among these distances:
8 11 0.12
9 53 0.56
10 15 0.16
11 10 0.11
12 6 0.06
ACGTcount: A:0.65, C:0.03, G:0.02, T:0.31
Consensus pattern (9 bp):
AATATAAAT
Found at i:28538282 original size:5 final size:5
Alignment explanation
Indices: 28538136--28538268 Score: 51
Period size: 5 Copynumber: 28.4 Consensus size: 5
28538126 TACATACAAA
* *
28538136 AATAT AATA- AA-AT AAT-T AATAT -ATAT AATAT AA-AA ATATAT AATAA
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT A-ATAT AATAT
* * *
28538182 AATAT AA-AT GGAACA- AATA- ACATAT AATA- AAAAT AACAT -ATACT
1 AATAT AATAT --AATAT AATAT A-ATAT AATAT AATAT AATAT AATA-T
* * *
28538226 AAAAT -TTAT AA-AT AATAT AA-AT AATAT AA-AT AAAAT AATAT AA
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AA
28538269 AGAATATATA
Statistics
Matches: 97, Mismatches: 13, Indels: 36
0.66 0.09 0.25
Matches are distributed among these distances:
3 1 0.01
4 39 0.40
5 49 0.51
6 7 0.07
7 1 0.01
ACGTcount: A:0.65, C:0.03, G:0.02, T:0.31
Consensus pattern (5 bp):
AATAT
Found at i:28546920 original size:16 final size:17
Alignment explanation
Indices: 28546893--28546924 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
28546883 GATTCGGCAA
28546893 AAGTATTGATGAATAGC
1 AAGTATTGATGAATAGC
28546910 AAGTA-TGATGAATAG
1 AAGTATTGATGAATAG
28546925 TTTTGAAGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.44, C:0.03, G:0.25, T:0.28
Consensus pattern (17 bp):
AAGTATTGATGAATAGC
Found at i:28551131 original size:12 final size:11
Alignment explanation
Indices: 28551094--28551165 Score: 65
Period size: 12 Copynumber: 6.4 Consensus size: 11
28551084 CATATTATTT
28551094 TTATTTATATA
1 TTATTTATATA
**
28551105 TTATCCATTATA
1 TTATTTA-TATA
28551117 TTATTTATATCA
1 TTATTTATAT-A
* *
28551129 TTATTATACATT
1 TTATT-TATATA
*
28551141 TTATTTATAAA
1 TTATTTATATA
28551152 TT-TTTATATA
1 TTATTTATATA
28551162 TTAT
1 TTAT
28551166 ATTTTACCAT
Statistics
Matches: 47, Mismatches: 10, Indels: 8
0.72 0.15 0.12
Matches are distributed among these distances:
10 9 0.19
11 14 0.30
12 20 0.43
13 4 0.09
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.60
Consensus pattern (11 bp):
TTATTTATATA
Found at i:28551133 original size:27 final size:29
Alignment explanation
Indices: 28551085--28551145 Score: 72
Period size: 27 Copynumber: 2.2 Consensus size: 29
28551075 AAAATAGTAC
* * *
28551085 ATATTATTTTTATTTATATATTATCCATT
1 ATATTATTTATATTCATATATTATACATT
28551114 ATATTATTTATA-TCAT-TATTATACATT
1 ATATTATTTATATTCATATATTATACATT
*
28551141 TTATT
1 ATATT
28551146 TATAAATTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 14 0.50
28 3 0.11
29 11 0.39
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.61
Consensus pattern (29 bp):
ATATTATTTATATTCATATATTATACATT
Found at i:28551168 original size:23 final size:24
Alignment explanation
Indices: 28551118--28551169 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
28551108 TCCATTATAT
* *
28551118 TATTTATATCATTATTATACATTT
1 TATTTATATAATTATTATACATTA
* *
28551142 TATTTATA-AATTTTTATATATTA
1 TATTTATATAATTATTATACATTA
28551165 TATTT
1 TATTT
28551170 TACCATATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 16 0.67
24 8 0.33
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.62
Consensus pattern (24 bp):
TATTTATATAATTATTATACATTA
Found at i:28563790 original size:222 final size:222
Alignment explanation
Indices: 28563173--28563803 Score: 1047
Period size: 222 Copynumber: 2.9 Consensus size: 222
28563163 CAGGATAAAG
* *
28563173 CATAGCAGATCTAACCTTCAGATG-TTTTTGCATCGAAGCAGATCCAAGATG-TTTTGTATCCTT
1 CATAGCAGATCTAACCTTCAGATGTTTTTTGCATCGAAGCAGATCCAAGATGATTTGGCATCCTT
*
28563236 GAGTTTACAAGGAGCAGATCGAAGACAT-AGCAGATTTGGCTTTCACGTGTTTACGCTGAAGCAG
66 GCGTTTACAAGGAGCAGATCGAAGACATAAGCAGATTTGGCTTTCACGTGTTTACGCTGAAGCAG
* * *
28563300 ATCTAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCAAAGAAATAGATTTGGCATCTC
131 ATCTAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGAGACAGATTTGGCATCTC
28563365 CATATTCGACAGAGAGCAGATCGAAGA
196 CATATTCGACAGAGAGCAGATCGAAGA
28563392 CATAGCAGATCTAACCTTCAGATGTTTTTTGCATCGAAGCAGATCCAAGATGATTTGGCATCCTT
1 CATAGCAGATCTAACCTTCAGATGTTTTTTGCATCGAAGCAGATCCAAGATGATTTGGCATCCTT
*
28563457 GCGTTTACAAGGAGCAGATCGAAGACATAAGCAGGTTTGGCTTTCACGTGTTTACGCTGAAGCAG
66 GCGTTTACAAGGAGCAGATCGAAGACATAAGCAGATTTGGCTTTCACGTGTTTACGCTGAAGCAG
28563522 ATCTAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGAGACAGATTTGGCATCTC
131 ATCTAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGAGACAGATTTGGCATCTC
*
28563587 CATATTCGACGGAGAGCAGATCGAAGA
196 CATATTCGACAGAGAGCAGATCGAAGA
* * * *
28563614 CATAGCAAATCTAACCTTCGGATGTTTTTTGCATCGAAACAGATCCAAGTTGATTTGGCATCCTT
1 CATAGCAGATCTAACCTTCAGATGTTTTTTGCATCGAAGCAGATCCAAGATGATTTGGCATCCTT
* *
28563679 GCGTTTAGAAGGAGCAGATCGAAGACATAAGCAGATTTGGCTTTCACGTGTTTACTCTGAAGC-G
66 GCGTTTACAAGGAGCAGATCGAAGACATAAGCAGATTTGGCTTTCACGTGTTTACGCTGAAGCAG
* * *
28563743 AATCTAAGATGATTTGGCATCTTTGTATTGTCAGAGAGCAGATCGAAGTTAG-CAGATTTGG
131 -ATCTAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAG--AGACAGATTTGG
28563804 TGTCTCTCCA
Statistics
Matches: 388, Mismatches: 18, Indels: 8
0.94 0.04 0.02
Matches are distributed among these distances:
219 24 0.06
220 27 0.07
221 38 0.10
222 288 0.74
223 9 0.02
224 2 0.01
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (222 bp):
CATAGCAGATCTAACCTTCAGATGTTTTTTGCATCGAAGCAGATCCAAGATGATTTGGCATCCTT
GCGTTTACAAGGAGCAGATCGAAGACATAAGCAGATTTGGCTTTCACGTGTTTACGCTGAAGCAG
ATCTAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGAGACAGATTTGGCATCTC
CATATTCGACAGAGAGCAGATCGAAGA
Found at i:28563817 original size:44 final size:44
Alignment explanation
Indices: 28563753--28564026 Score: 309
Period size: 44 Copynumber: 6.2 Consensus size: 44
28563743 AATCTAAGAT
* * * *
28563753 GATTTGGCATCTTTGTATTGTCAGAGAGCAGATCGAAGTTAGCA
1 GATTTGGCATCTCTCTATTGTCAGAGAGCAGATCAAAGATAGCA
** * * *
28563797 GATTTGGTGTCTCTCCATTGTCAGAGAACAGATCGAAGATAGCA
1 GATTTGGCATCTCTCTATTGTCAGAGAGCAGATCAAAGATAGCA
* * * * *
28563841 GATTTGGCATCTCTGTATTGTCAGAAAGCAGATCGAAGACAGTA
1 GATTTGGCATCTCTCTATTGTCAGAGAGCAGATCAAAGATAGCA
* * * *
28563885 GATTTGGCATCTCTGTATTGTCAAAGAGCAGGTCAAAGATAGTA
1 GATTTGGCATCTCTCTATTGTCAGAGAGCAGATCAAAGATAGCA
* * * *
28563929 GATTTGGCGTCTC-CATATTGTCAAAGAGCAGGTCAAAGATAGTA
1 GATTTGGCATCTCTC-TATTGTCAGAGAGCAGATCAAAGATAGCA
*
28563973 GATTTGGCATCTC-CATATTGTCAGAGAGCAGATCAAAGATAACA
1 GATTTGGCATCTCTC-TATTGTCAGAGAGCAGATCAAAGATAGCA
28564017 GATTTGGCAT
1 GATTTGGCAT
28564027 TCTTAAGTTT
Statistics
Matches: 202, Mismatches: 27, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
44 202 1.00
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.28
Consensus pattern (44 bp):
GATTTGGCATCTCTCTATTGTCAGAGAGCAGATCAAAGATAGCA
Found at i:28563845 original size:88 final size:88
Alignment explanation
Indices: 28563753--28564026 Score: 343
Period size: 88 Copynumber: 3.1 Consensus size: 88
28563743 AATCTAAGAT
* * * ** *
28563753 GATTTGGCATCTTTGTATTGTCAGAGAGCAGATCGAAGTTAGCAGATTTGGTGTCTCTCCATTGT
1 GATTTGGCATCTCTGTATTGTCAGAGAGCAGATCGAAGATAGTAGATTTGGCATCTCTCTATTGT
* *
28563818 CAGAGAACAGATCGAAGATAGCA
66 CAGAGAGCAGATCAAAGATAGCA
* * *
28563841 GATTTGGCATCTCTGTATTGTCAGAAAGCAGATCGAAGACAGTAGATTTGGCATCTCTGTATTGT
1 GATTTGGCATCTCTGTATTGTCAGAGAGCAGATCGAAGATAGTAGATTTGGCATCTCTCTATTGT
* * *
28563906 CAAAGAGCAGGTCAAAGATAGTA
66 CAGAGAGCAGATCAAAGATAGCA
* ** * * *
28563929 GATTTGGCGTCTCCATATTGTCAAAGAGCAGGTCAAAGATAGTAGATTTGGCATCTC-CATATTG
1 GATTTGGCATCTCTGTATTGTCAGAGAGCAGATCGAAGATAGTAGATTTGGCATCTCTC-TATTG
*
28563993 TCAGAGAGCAGATCAAAGATAACA
65 TCAGAGAGCAGATCAAAGATAGCA
28564017 GATTTGGCAT
1 GATTTGGCAT
28564027 TCTTAAGTTT
Statistics
Matches: 157, Mismatches: 28, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
88 157 1.00
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.28
Consensus pattern (88 bp):
GATTTGGCATCTCTGTATTGTCAGAGAGCAGATCGAAGATAGTAGATTTGGCATCTCTCTATTGT
CAGAGAGCAGATCAAAGATAGCA
Found at i:28564056 original size:88 final size:88
Alignment explanation
Indices: 28563753--28564058 Score: 295
Period size: 88 Copynumber: 3.5 Consensus size: 88
28563743 AATCTAAGAT
* * * ** *
28563753 GATTTGGCATCTTTGTATTGTC-AGAGAGCAGATCGAAGTTAGCAGATTTGGTGTCTCTC-CATT
1 GATTTGGCATCTTAGTATTGTCAAGA-AGCAGATCGAAGATAGTAGATTTGGCATCTC-CATATT
* *
28563816 GTCAGAGAACAGATCGAAGATAGCA
64 GTCAGAGAGCAGATCAAAGATAGCA
* **
28563841 GATTTGGCATCTCT-GTATTGTC-AGAAAGCAGATCGAAGACAGTAGATTTGGCATCTCTGTATT
1 GATTTGGCATCT-TAGTATTGTCAAG-AAGCAGATCGAAGATAGTAGATTTGGCATCTCCATATT
* * *
28563904 GTCAAAGAGCAGGTCAAAGATAGTA
64 GTCAGAGAGCAGATCAAAGATAGCA
* * * *
28563929 GATTTGGCGTCTCCA-TATTGTCAA-AGAGCAGGTCAAAGATAGTAGATTTGGCATCTCCATATT
1 GATTTGGCATCT-TAGTATTGTCAAGA-AGCAGATCGAAGATAGTAGATTTGGCATCTCCATATT
*
28563992 GTCAGAGAGCAGATCAAAGATAACA
64 GTCAGAGAGCAGATCAAAGATAGCA
* *
28564017 GATTTGGCATTCTTAAGT-TTG-CAAGAAGTAGATTGAAGATAG
1 GATTTGGCA-TCTT-AGTATTGTCAAGAAGCAGATCGAAGATAG
28564059 CCAATTTGAC
Statistics
Matches: 179, Mismatches: 29, Indels: 20
0.79 0.13 0.09
Matches are distributed among these distances:
87 1 0.01
88 166 0.93
89 11 0.06
90 1 0.01
ACGTcount: A:0.32, C:0.15, G:0.25, T:0.29
Consensus pattern (88 bp):
GATTTGGCATCTTAGTATTGTCAAGAAGCAGATCGAAGATAGTAGATTTGGCATCTCCATATTGT
CAGAGAGCAGATCAAAGATAGCA
Found at i:28564066 original size:132 final size:132
Alignment explanation
Indices: 28563753--28564026 Score: 352
Period size: 132 Copynumber: 2.1 Consensus size: 132
28563743 AATCTAAGAT
* * * * * *
28563753 GATTTGGCATCTTTGTATTGTCAGAGAGCAGATCGAAGTTAGCAGATTTGGTGTCTCTC-CATTG
1 GATTTGGCATCTCTGTATTGTCAAAGAGCAGATCAAAGATAGCAGATTTGGCGTCTC-CATATTG
* * ** *
28563817 TCAGAGAACAGATCGAAGATAGCAGATTTGGCATCTCTGTATTGTCAGAAAGCAGATCGAAGACA
65 TCAAAGAACAGATCAAAGATAGCAGATTTGGCATCTCCATATTGTCAGAAAGCAGATCAAAGACA
**
28563882 GTA
130 ACA
* *
28563885 GATTTGGCATCTCTGTATTGTCAAAGAGCAGGTCAAAGATAGTAGATTTGGCGTCTCCATATTGT
1 GATTTGGCATCTCTGTATTGTCAAAGAGCAGATCAAAGATAGCAGATTTGGCGTCTCCATATTGT
* * * * *
28563950 CAAAGAGCAGGTCAAAGATAGTAGATTTGGCATCTCCATATTGTCAGAGAGCAGATCAAAGATAA
66 CAAAGAACAGATCAAAGATAGCAGATTTGGCATCTCCATATTGTCAGAAAGCAGATCAAAGACAA
28564015 CA
131 CA
28564017 GATTTGGCAT
1 GATTTGGCAT
28564027 TCTTAAGTTT
Statistics
Matches: 121, Mismatches: 20, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
131 1 0.01
132 120 0.99
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.28
Consensus pattern (132 bp):
GATTTGGCATCTCTGTATTGTCAAAGAGCAGATCAAAGATAGCAGATTTGGCGTCTCCATATTGT
CAAAGAACAGATCAAAGATAGCAGATTTGGCATCTCCATATTGTCAGAAAGCAGATCAAAGACAA
CA
Found at i:28565587 original size:12 final size:11
Alignment explanation
Indices: 28565550--28565623 Score: 58
Period size: 12 Copynumber: 6.4 Consensus size: 11
28565540 CATATTATTT
28565550 TTATTTATATA
1 TTATTTATATA
**
28565561 TTATCCATTATA
1 TTATTTA-TATA
28565573 TTATTTATATCA
1 TTATTTATAT-A
* *
28565585 TTATTATACATT
1 TTATT-TATATA
*
28565597 TTATTTATAAA
1 TTATTTATATA
*
28565608 TTTTATTATATA
1 TTAT-TTATATA
28565620 TTAT
1 TTAT
28565624 ATTTTACCAT
Statistics
Matches: 47, Mismatches: 12, Indels: 7
0.71 0.18 0.11
Matches are distributed among these distances:
11 14 0.30
12 29 0.62
13 4 0.09
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.59
Consensus pattern (11 bp):
TTATTTATATA
Found at i:28565589 original size:27 final size:29
Alignment explanation
Indices: 28565541--28565601 Score: 72
Period size: 27 Copynumber: 2.2 Consensus size: 29
28565531 AAAATAGTAC
* * *
28565541 ATATTATTTTTATTTATATATTATCCATT
1 ATATTATTTATATTCATATATTATACATT
28565570 ATATTATTTATA-TCAT-TATTATACATT
1 ATATTATTTATATTCATATATTATACATT
*
28565597 TTATT
1 ATATT
28565602 TATAAATTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 14 0.50
28 3 0.11
29 11 0.39
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.61
Consensus pattern (29 bp):
ATATTATTTATATTCATATATTATACATT
Found at i:28565600 original size:24 final size:23
Alignment explanation
Indices: 28565548--28565605 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 23
28565538 TACATATTAT
*
28565548 TTTTATTTATATATTATCCATTA
1 TTTTATTTATATATTATCCATCA
* *
28565571 TATTATTTATATCATTAT-TATACA
1 TTTTATTTATAT-ATTATCCAT-CA
28565595 TTTTATTTATA
1 TTTTATTTATA
28565606 AATTTTATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
23 13 0.45
24 16 0.55
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (23 bp):
TTTTATTTATATATTATCCATCA
Found at i:28565978 original size:43 final size:43
Alignment explanation
Indices: 28565863--28565948 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
28565853 GTTTTTAAAT
28565863 ATCTTTATTTTTATTTTAGTTGATGTGTTTATAATTTGCTTAC
1 ATCTTTATTTTTATTTTAGTTGATGTGTTTATAATTTGCTTAC
28565906 ATCTTTATTTTTATTTTAGTTGATGTGTTTATAATTTGCTTAC
1 ATCTTTATTTTTATTTTAGTTGATGTGTTTATAATTTGCTTAC
28565949 TTATTTTTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.21, C:0.07, G:0.12, T:0.60
Consensus pattern (43 bp):
ATCTTTATTTTTATTTTAGTTGATGTGTTTATAATTTGCTTAC
Found at i:28570573 original size:21 final size:21
Alignment explanation
Indices: 28570547--28570587 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
28570537 ATCTGCTCAA
* *
28570547 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
28570568 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
28570588 TCGCTTGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:28575164 original size:5 final size:5
Alignment explanation
Indices: 28575141--28575222 Score: 55
Period size: 5 Copynumber: 16.4 Consensus size: 5
28575131 AAATTGTACG
* *
28575141 TAATAA TAA-A TAA-A TAATA TAATA TAATATA TAATA AAAAA TAATA
1 TAAT-A TAATA TAATA TAATA TAATA T-A-ATA TAATA TAATA TAATA
* * *
28575187 TAAT- GAATA AAATA T-ATA TTAAAA TAATA TAATA TA
1 TAATA TAATA TAATA TAATA -TAATA TAATA TAATA TA
28575223 TAATAAAGCA
Statistics
Matches: 61, Mismatches: 9, Indels: 13
0.73 0.11 0.16
Matches are distributed among these distances:
4 14 0.23
5 36 0.59
6 7 0.11
7 4 0.07
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (5 bp):
TAATA
Found at i:28575169 original size:17 final size:17
Alignment explanation
Indices: 28575143--28575222 Score: 72
Period size: 17 Copynumber: 4.5 Consensus size: 17
28575133 ATTGTACGTA
28575143 ATAATA-AATAAATAAT
1 ATAATATAATAAATAAT
*
28575159 ATAATATAATATATAAT
1 ATAATATAATAAATAAT
* *
28575176 AAAAAATAATATAATGAAT
1 ATAATATAATA-AAT-AAT
*
28575195 AAAATATATATTAAAATAAT
1 ATAATATA-A-T-AAATAAT
28575215 ATAATATA
1 ATAATATA
28575223 TAATAAAGCA
Statistics
Matches: 52, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
16 6 0.12
17 18 0.35
18 2 0.04
19 10 0.19
20 11 0.21
21 4 0.08
22 1 0.02
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (17 bp):
ATAATATAATAAATAAT
Found at i:28575172 original size:12 final size:12
Alignment explanation
Indices: 28575143--28575227 Score: 60
Period size: 12 Copynumber: 7.5 Consensus size: 12
28575133 ATTGTACGTA
*
28575143 ATAATA-AATAA
1 ATAATATAATAT
28575154 ATAATATAATAT
1 ATAATATAATAT
28575166 A-ATATATAATA-
1 ATA-ATATAATAT
*
28575177 A-AAAATAATAT
1 ATAATATAATAT
*
28575188 AATGAATAAAATAT
1 -AT-AATATAATAT
28575202 AT-AT-TAA-A-
1 ATAATATAATAT
28575210 ATAATATAATAT
1 ATAATATAATAT
28575222 ATAATA
1 ATAATA
28575228 AAGCATATAA
Statistics
Matches: 59, Mismatches: 5, Indels: 19
0.71 0.06 0.23
Matches are distributed among these distances:
8 2 0.03
9 3 0.05
10 12 0.20
11 12 0.20
12 20 0.34
13 2 0.03
14 8 0.14
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (12 bp):
ATAATATAATAT
Found at i:28575183 original size:31 final size:31
Alignment explanation
Indices: 28575141--28575242 Score: 102
Period size: 31 Copynumber: 3.2 Consensus size: 31
28575131 AAATTGTACG
* *
28575141 TAATAATAAATAAATAATATAATATAATATA
1 TAATAAAAAATAAATAATATAATAAAATATA
*
28575172 TAATAAAAAATAATATAAT-GAATAAAATATA
1 TAATAAAAAATAA-ATAATATAATAAAATATA
*
28575203 TATTAAAATAATATAAT-ATATAATAAAGCATATA
1 TAATAAAA-AATA-AATAATATAATAAA--ATATA
28575237 -AATAAA
1 TAATAAA
28575243 TGTCTAATAA
Statistics
Matches: 59, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
31 31 0.53
32 17 0.29
33 6 0.10
34 5 0.08
ACGTcount: A:0.65, C:0.01, G:0.02, T:0.32
Consensus pattern (31 bp):
TAATAAAAAATAAATAATATAATAAAATATA
Found at i:28575210 original size:29 final size:27
Alignment explanation
Indices: 28575143--28575227 Score: 100
Period size: 29 Copynumber: 3.0 Consensus size: 27
28575133 ATTGTACGTA
*
28575143 ATAATAAATAAATAATATAATATAATAT
1 ATAATAAA-AAATAATATAATATAAAAT
28575171 ATAATAAAAAATAATATAATGAATAAAAT
1 ATAATAAAAAATAATATAAT--ATAAAAT
* *
28575200 AT-ATATTAAAATAATATAATATATAAT
1 ATAATA-AAAAATAATATAATATAAAAT
28575227 A
1 A
28575228 AAGCATATAA
Statistics
Matches: 51, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
27 19 0.37
28 11 0.22
29 21 0.41
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (27 bp):
ATAATAAAAAATAATATAATATAAAAT
Found at i:28575327 original size:9 final size:9
Alignment explanation
Indices: 28575309--28575347 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
28575299 AAAAATAAAT
28575309 AATATATAA
1 AATATATAA
*
28575318 AATATTTAA
1 AATATATAA
*
28575327 AATAAATAA
1 AATATATAA
*
28575336 ATTATATAA
1 AATATATAA
28575345 AAT
1 AAT
28575348 TTTAAAAAGG
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (9 bp):
AATATATAA
Found at i:28575363 original size:27 final size:27
Alignment explanation
Indices: 28575300--28575354 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
28575290 GTTTGTAGTA
28575300 AAAATAAAT-AA-TATATAAAATATTT
1 AAAATAAATAAATTATATAAAATATTT
28575325 AAAATAAATAAATTATATAAAAT-TTT
1 AAAATAAATAAATTATATAAAATATTT
28575351 AAAA
1 AAAA
28575355 AGGACTAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
25 9 0.32
26 9 0.32
27 10 0.36
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (27 bp):
AAAATAAATAAATTATATAAAATATTT
Found at i:28583451 original size:41 final size:40
Alignment explanation
Indices: 28583383--28583502 Score: 127
Period size: 40 Copynumber: 3.0 Consensus size: 40
28583373 TGTAAAACAC
* * * *
28583383 AGAGCAATAGCGGCGTTTTAAC-AAAAACGCCGTTAAAAACT
1 AGAGAAATAGAGGCGTTTT-TCTAAAAACGCCGCTAAAAA-T
* * *
28583424 -GAGCAATAGAGGCGTTTTTTGTTAAAACGCCGCTAAAAAT
1 AGAGAAATAGAGGCG-TTTTTCTAAAAACGCCGCTAAAAAT
*
28583464 AGAGAAATAGCGGCGTTTTTCTAAAAACGCCGCTAAAAA
1 AGAGAAATAGAGGCGTTTTTCTAAAAACGCCGCTAAAAA
28583503 ATTAGAGCAT
Statistics
Matches: 67, Mismatches: 9, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
40 36 0.54
41 31 0.46
ACGTcount: A:0.39, C:0.17, G:0.21, T:0.23
Consensus pattern (40 bp):
AGAGAAATAGAGGCGTTTTTCTAAAAACGCCGCTAAAAAT
Found at i:28583715 original size:41 final size:41
Alignment explanation
Indices: 28583406--28583719 Score: 346
Period size: 41 Copynumber: 7.7 Consensus size: 41
28583396 CGTTTTAACA
* * * * * *
28583406 AAAACGCCGTTAAAAA-CTGAGCAATAGAGGCGTTTTTTGTT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCG-CTTTTGGT
* * * **
28583447 AAAACGCCGCTAAAAA-TAGAGAAATAGCGGCG-TTTTTCT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGT
** *
28583486 AAAAACGCCGCTAAAAAATTAGAGCATTAGCGGCGCTTCTGGT
1 -AAAACGCCGCT-AAAAACCAGAGCATTAGCGGCGCTTTTGGT
* *
28583529 AAAACGCCGCTAAAAACCAAAGCATTAGCGGCGCTTCTGGT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGT
*
28583570 GAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGT
* * *
28583611 AAAACACCGCTAAAAACCAGAACATTAGCGGCGCTTTTGGC
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGT
* * * *
28583652 AAAATGCCGCTAAAAACTAGAGCATTAGTGGCGCTTTTTGT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGT
* *
28583693 AAAACGACGCTAACAACCAGAGCATTA
1 AAAACGCCGCTAAAAACCAGAGCATTA
28583720 TTTATATTAA
Statistics
Matches: 236, Mismatches: 33, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
39 5 0.02
40 11 0.05
41 191 0.81
42 25 0.11
43 4 0.02
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.21
Consensus pattern (41 bp):
AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGT
Found at i:28583920 original size:14 final size:14
Alignment explanation
Indices: 28583868--28583982 Score: 72
Period size: 14 Copynumber: 8.1 Consensus size: 14
28583858 TTAATTATCA
* *
28583868 TTATAGTTTAGGGT
1 TTATGGTTTAAGGT
*
28583882 TTATGATTTAAGGT
1 TTATGGTTTAAGGT
* *
28583896 ATATGGCTTAAGGT
1 TTATGGTTTAAGGT
*
28583910 TTAAGGTTTAAGAGT
1 TTATGGTTTAAG-GT
28583925 TACTAT--TTTAAGGT
1 T--TATGGTTTAAGGT
* *
28583939 TTATGGATTATGCGT
1 TTATGGTTTAAG-GT
* * *
28583954 TTAGGGATTATGGT
1 TTATGGTTTAAGGT
*
28583968 TTATGGTTTATGGT
1 TTATGGTTTAAGGT
28583982 T
1 T
28583983 CAAGGGTTGG
Statistics
Matches: 80, Mismatches: 15, Indels: 12
0.75 0.14 0.11
Matches are distributed among these distances:
12 3 0.04
14 53 0.66
15 22 0.28
17 2 0.03
ACGTcount: A:0.24, C:0.03, G:0.26, T:0.47
Consensus pattern (14 bp):
TTATGGTTTAAGGT
Found at i:28583949 original size:7 final size:7
Alignment explanation
Indices: 28583931--28583982 Score: 59
Period size: 7 Copynumber: 7.3 Consensus size: 7
28583921 GAGTTACTAT
*
28583931 TTTAAGG
1 TTTATGG
28583938 TTTATGG
1 TTTATGG
*
28583945 ATTATGCG
1 TTTATG-G
*
28583953 TTTAGGG
1 TTTATGG
*
28583960 ATTATGG
1 TTTATGG
28583967 TTTATGG
1 TTTATGG
28583974 TTTATGG
1 TTTATGG
28583981 TT
1 TT
28583983 CAAGGGTTGG
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
7 32 0.86
8 5 0.14
ACGTcount: A:0.19, C:0.02, G:0.29, T:0.50
Consensus pattern (7 bp):
TTTATGG
Found at i:28583956 original size:22 final size:21
Alignment explanation
Indices: 28583873--28583982 Score: 69
Period size: 21 Copynumber: 5.1 Consensus size: 21
28583863 TATCATTATA
* * *
28583873 GTTTAGGGTTTATGATTTAAG
1 GTTTATGGATTATGGTTTAAG
* * *
28583894 GTATATGGCTTAAGGTTTAAG
1 GTTTATGGATTATGGTTTAAG
* **
28583915 GTTTA-AGAGTTACTATTTTAAG
1 GTTTATGGA-TTA-TGGTTTAAG
*
28583937 GTTTATGGATTATGCGTTTAGG
1 GTTTATGGATTATG-GTTTAAG
* * *
28583959 GATTATGGTTTATGGTTTATG
1 GTTTATGGATTATGGTTTAAG
28583980 GTT
1 GTT
28583983 CAAGGGTTGG
Statistics
Matches: 66, Mismatches: 19, Indels: 8
0.71 0.20 0.09
Matches are distributed among these distances:
20 1 0.02
21 32 0.48
22 31 0.47
23 2 0.03
ACGTcount: A:0.24, C:0.03, G:0.27, T:0.46
Consensus pattern (21 bp):
GTTTATGGATTATGGTTTAAG
Found at i:28583996 original size:21 final size:23
Alignment explanation
Indices: 28583972--28584021 Score: 86
Period size: 21 Copynumber: 2.3 Consensus size: 23
28583962 TATGGTTTAT
28583972 GGTTTATGGTTC-AAGGGTT-GG
1 GGTTTATGGTTCAAAGGGTTAGG
28583993 GGTTTATGGTTCAAAGGGTTAGG
1 GGTTTATGGTTCAAAGGGTTAGG
28584016 GGTTTA
1 GGTTTA
28584022 GGCCTAAATC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 12 0.44
22 7 0.26
23 8 0.30
ACGTcount: A:0.18, C:0.04, G:0.40, T:0.38
Consensus pattern (23 bp):
GGTTTATGGTTCAAAGGGTTAGG
Found at i:28585020 original size:14 final size:13
Alignment explanation
Indices: 28584991--28585016 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
28584981 TCTAATTTTT
28584991 TCCCCAAATCAAA
1 TCCCCAAATCAAA
28585004 TCCCCAAATCAAA
1 TCCCCAAATCAAA
28585017 ATCCTTCCAC
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:0.46, C:0.38, G:0.00, T:0.15
Consensus pattern (13 bp):
TCCCCAAATCAAA
Found at i:28585061 original size:19 final size:19
Alignment explanation
Indices: 28585037--28585076 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
28585027 CATTTTTTTG
*
28585037 TCGCCATACTGTTCCGTAA
1 TCGCCATACTGATCCGTAA
28585056 TCGCCATACTGATCCGTAA
1 TCGCCATACTGATCCGTAA
28585075 TC
1 TC
28585077 CTCAGCATCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.23, C:0.33, G:0.15, T:0.30
Consensus pattern (19 bp):
TCGCCATACTGATCCGTAA
Found at i:28585124 original size:14 final size:14
Alignment explanation
Indices: 28585105--28585133 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
28585095 GCATTTCTTG
28585105 CTTCTCTAAATCTC
1 CTTCTCTAAATCTC
28585119 CTTCTCTAAATCTC
1 CTTCTCTAAATCTC
28585133 C
1 C
28585134 ATCCCTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.38, G:0.00, T:0.41
Consensus pattern (14 bp):
CTTCTCTAAATCTC
Found at i:28589610 original size:18 final size:19
Alignment explanation
Indices: 28589589--28589628 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
28589579 TTATTGATAG
28589589 TTTTA-TATTTAATCTAGT
1 TTTTATTATTTAATCTAGT
* *
28589607 TTTTATTATTTATTTTAGT
1 TTTTATTATTTAATCTAGT
28589626 TTT
1 TTT
28589629 GATTCTAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.23, C:0.03, G:0.05, T:0.70
Consensus pattern (19 bp):
TTTTATTATTTAATCTAGT
Found at i:28589834 original size:28 final size:28
Alignment explanation
Indices: 28589802--28589874 Score: 78
Period size: 28 Copynumber: 2.6 Consensus size: 28
28589792 ATATCATTCA
28589802 ATATTTTGATAATGAATTTTA-AAT-TTTT
1 ATATTTT--TAATGAATTTTATAATATTTT
* *
28589830 ATATTTTTCATGACTTTTATAATATTTT
1 ATATTTTTAATGAATTTTATAATATTTT
**
28589858 ATATTTTTTTTGAATTT
1 ATATTTTTAATGAATTT
28589875 CATGACATTT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
26 10 0.26
27 3 0.08
28 25 0.66
ACGTcount: A:0.30, C:0.03, G:0.05, T:0.62
Consensus pattern (28 bp):
ATATTTTTAATGAATTTTATAATATTTT
Found at i:28589847 original size:26 final size:28
Alignment explanation
Indices: 28589813--28589874 Score: 83
Period size: 28 Copynumber: 2.3 Consensus size: 28
28589803 TATTTTGATA
28589813 ATGAATTTTA-AAT-TTTTATATTTTTC
1 ATGAATTTTATAATATTTTATATTTTTC
* *
28589839 ATGACTTTTATAATATTTTATATTTTTT
1 ATGAATTTTATAATATTTTATATTTTTC
*
28589867 TTGAATTT
1 ATGAATTT
28589875 CATGACATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 9 0.30
27 3 0.10
28 18 0.60
ACGTcount: A:0.29, C:0.03, G:0.05, T:0.63
Consensus pattern (28 bp):
ATGAATTTTATAATATTTTATATTTTTC
Found at i:28589884 original size:28 final size:28
Alignment explanation
Indices: 28589826--28589884 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 28
28589816 AATTTTAAAT
* * *
28589826 TTTTATATTTTTCATGACTTTTATAATA
1 TTTTATATTTTTCATGAATTTCATAACA
** *
28589854 TTTTATATTTTTTTTGAATTTCATGACA
1 TTTTATATTTTTCATGAATTTCATAACA
28589882 TTT
1 TTT
28589885 AGCGGCGTTT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.25, C:0.07, G:0.05, T:0.63
Consensus pattern (28 bp):
TTTTATATTTTTCATGAATTTCATAACA
Found at i:28594570 original size:2 final size:2
Alignment explanation
Indices: 28594563--28594603 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
28594553 TACGAATGTA
28594563 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
28594604 AACAGGTAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:28597540 original size:27 final size:27
Alignment explanation
Indices: 28597502--28597556 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
28597492 AAGTCAAGAG
28597502 TGTGTTTGGCTAAGGTTATTGACCTAA
1 TGTGTTTGGCTAAGGTTATTGACCTAA
28597529 TGTGTTTGGCTAAGGTTATTGACCTAA
1 TGTGTTTGGCTAAGGTTATTGACCTAA
28597556 T
1 T
28597557 ATATCCAGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.22, C:0.11, G:0.25, T:0.42
Consensus pattern (27 bp):
TGTGTTTGGCTAAGGTTATTGACCTAA
Found at i:28599224 original size:38 final size:37
Alignment explanation
Indices: 28599173--28599270 Score: 103
Period size: 35 Copynumber: 2.7 Consensus size: 37
28599163 TTTATTGAAG
* *
28599173 GGTTGGCAAAAACCTAGTC-AAGGCCAACCTTTAAAAAA
1 GGTTGGGATAAACCTAGTCTAAGGCCAACC--TAAAAAA
* *
28599211 GGTTGGGATAAACCTA-TCTAATG-CAACCTCAAAAA
1 GGTTGGGATAAACCTAGTCTAAGGCCAACCTAAAAAA
* *
28599246 GGTTGGGATAGACCTTGTCTAAGGC
1 GGTTGGGATAAACCTAGTCTAAGGC
28599271 AAAGGTTGGG
Statistics
Matches: 50, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
35 20 0.40
36 6 0.12
37 7 0.14
38 17 0.34
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.22
Consensus pattern (37 bp):
GGTTGGGATAAACCTAGTCTAAGGCCAACCTAAAAAA
Found at i:28599799 original size:16 final size:16
Alignment explanation
Indices: 28599778--28599836 Score: 57
Period size: 16 Copynumber: 3.7 Consensus size: 16
28599768 TTAATCACTT
28599778 TAATATTAAATTAATA
1 TAATATTAAATTAATA
** *
28599794 TAATATTTATCTTGATA
1 TAATA-TTAAATTAATA
* *
28599811 -AATATTATATTAATT
1 TAATATTAAATTAATA
28599826 TAATATTAAAT
1 TAATATTAAAT
28599837 CTTATTAAAA
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
15 8 0.24
16 18 0.53
17 8 0.24
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (16 bp):
TAATATTAAATTAATA
Found at i:28599843 original size:58 final size:58
Alignment explanation
Indices: 28599781--28599911 Score: 158
Period size: 58 Copynumber: 2.2 Consensus size: 58
28599771 ATCACTTTAA
* * * * *
28599781 TATTAAATTAATATAATATTTATCT-TGATAAATATTATATT-AATTTAATATTAAATC
1 TATTAAAATAATAGAATATTTATCTAAGATAAACATTAAATTAAATTTAATATTAAA-C
28599838 TTATTAAAATAATAGAATATTTATCTACAAGATAAACATTAAATTAAATTTAATATTAAAC
1 -TATTAAAATAATAGAATATTTATCT--AAGATAAACATTAAATTAAATTTAATATTAAAC
*
28599899 TATTAAAACAATA
1 TATTAAAATAATA
28599912 TTATTTTTGG
Statistics
Matches: 63, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
58 23 0.37
60 12 0.19
61 14 0.22
62 14 0.22
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.42
Consensus pattern (58 bp):
TATTAAAATAATAGAATATTTATCTAAGATAAACATTAAATTAAATTTAATATTAAAC
Found at i:28600729 original size:73 final size:73
Alignment explanation
Indices: 28600561--28600723 Score: 181
Period size: 73 Copynumber: 2.3 Consensus size: 73
28600551 TTTTCAACAG
* * * *
28600561 ACCCATTTAAGGCAACCTTAAAAAGATTGAGATAGATTTTATCTAAGGTAACCTTTAAAAAAGGT
1 ACCCGTTTAAGGCAACCTTAAAAAGATAGAGATAGATCTTATCTAAGGCAACCTTTAAAAAAGGT
28600626 TGAGATAA
66 TGAGATAA
* * * *
28600634 GCCCGTCTAAGACAACCTTAAAAATATCAGAG-TAGA-CTTATCTAAGGCAACC-TT-AAAAAGG
1 ACCCGTTTAAGGCAACCTTAAAAAGAT-AGAGATAGATCTTATCTAAGGCAACCTTTAAAAAAGG
*
28600695 TTGGGATAA
65 TTGAGATAA
**
28600704 ACTTTGTTTAAGGCAACCTT
1 AC-CCGTTTAAGGCAACCTT
28600724 TTAAAAAAGG
Statistics
Matches: 74, Mismatches: 14, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
70 16 0.22
71 15 0.20
72 14 0.19
73 26 0.35
74 3 0.04
ACGTcount: A:0.39, C:0.16, G:0.17, T:0.28
Consensus pattern (73 bp):
ACCCGTTTAAGGCAACCTTAAAAAGATAGAGATAGATCTTATCTAAGGCAACCTTTAAAAAAGGT
TGAGATAA
Found at i:28600762 original size:108 final size:108
Alignment explanation
Indices: 28600568--28600765 Score: 281
Period size: 108 Copynumber: 1.8 Consensus size: 108
28600558 CAGACCCATT
* * * *
28600568 TAAGGCAACCTTAAAAAGATTGAGATAGATTTTATCTAAGGTAACCTTTAAAAAAGGTTGAGATA
1 TAAGGCAACCTTAAAAAGATTGAGATAAACTTTATCTAAGGCAACCTTTAAAAAAGGTTAAGATA
* *
28600633 AGCCCGTCTAAGACAACCTTAAAAATATCAGAGTAGACTTATC
66 AGACCATCTAAGACAACCTTAAAAATATCAGAGTAGACTTATC
* * * *
28600676 TAAGGCAACCTTAAAAAGGTTGGGATAAACTTTGTTTAAGGCAACCTTTTAAAAAAGGTTAAGAT
1 TAAGGCAACCTTAAAAAGATTGAGATAAACTTTATCTAAGGCAACC-TTTAAAAAAGGTTAAGAT
*
28600741 AA-ACCATCTAAGACAATCTTAAAAA
65 AAGACCATCTAAGACAACCTTAAAAA
28600766 AGTTGAGATA
Statistics
Matches: 78, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
108 59 0.76
109 19 0.24
ACGTcount: A:0.43, C:0.14, G:0.16, T:0.27
Consensus pattern (108 bp):
TAAGGCAACCTTAAAAAGATTGAGATAAACTTTATCTAAGGCAACCTTTAAAAAAGGTTAAGATA
AGACCATCTAAGACAACCTTAAAAATATCAGAGTAGACTTATC
Found at i:28600775 original size:34 final size:36
Alignment explanation
Indices: 28600724--28600790 Score: 102
Period size: 35 Copynumber: 1.9 Consensus size: 36
28600714 AGGCAACCTT
28600724 TTAAAAAAGGTTAAGATAAAC-CATCTAAGACAATC
1 TTAAAAAAGGTTAAGATAAACACATCTAAGACAATC
* *
28600759 TTAAAAAA-GTTGAGATAGACACATCTAAGACA
1 TTAAAAAAGGTTAAGATAAACACATCTAAGACA
28600791 TTATTTTTCT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 10 0.34
35 19 0.66
ACGTcount: A:0.51, C:0.13, G:0.13, T:0.22
Consensus pattern (36 bp):
TTAAAAAAGGTTAAGATAAACACATCTAAGACAATC
Found at i:28600778 original size:108 final size:108
Alignment explanation
Indices: 28600559--28600787 Score: 266
Period size: 108 Copynumber: 2.1 Consensus size: 108
28600549 ATTTTTCAAC
* * * * *
28600559 AGACCCATTTAAGGCAACCTTAAAAAGATTGAGATAGATTTTATCTAAGGTAACCTTTAAAAAAG
1 AGACACATCTAAGGCAACCTTAAAAAGATTGAGATAAACTTTATCTAAGGCAACCTTTAAAAAAG
* * *
28600624 GTTGAGATAAGCCCGTCTAAGACAACCTTAAAAATATCAGAGT
66 GTTAAGATAAGACCATCTAAGACAACCTTAAAAATATCAGAGT
** * * * *
28600667 AGACTTATCTAAGGCAACCTTAAAAAGGTTGGGATAAACTTTGTTTAAGGCAACCTTTTAAAAAA
1 AGACACATCTAAGGCAACCTTAAAAAGATTGAGATAAACTTTATCTAAGGCAACC-TTTAAAAAA
* *
28600732 GGTTAAGATAA-ACCATCTAAGACAATCTTAAAAA-AGT-TGAGAT
65 GGTTAAGATAAGACCATCTAAGACAACCTTAAAAATA-TCAGAG-T
28600775 AGACACATCTAAG
1 AGACACATCTAAG
28600788 ACATTATTTT
Statistics
Matches: 101, Mismatches: 17, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
107 4 0.04
108 78 0.77
109 19 0.19
ACGTcount: A:0.42, C:0.15, G:0.17, T:0.26
Consensus pattern (108 bp):
AGACACATCTAAGGCAACCTTAAAAAGATTGAGATAAACTTTATCTAAGGCAACCTTTAAAAAAG
GTTAAGATAAGACCATCTAAGACAACCTTAAAAATATCAGAGT
Found at i:28603531 original size:12 final size:12
Alignment explanation
Indices: 28603514--28603544 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
28603504 GATATCGATT
28603514 GTTCAGCTTTCG
1 GTTCAGCTTTCG
28603526 GTTCAGCTTTCG
1 GTTCAGCTTTCG
28603538 GTTCAGC
1 GTTCAGC
28603545 AACCATCGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.10, C:0.26, G:0.26, T:0.39
Consensus pattern (12 bp):
GTTCAGCTTTCG
Found at i:28605669 original size:21 final size:22
Alignment explanation
Indices: 28605643--28605701 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 22
28605633 GTTTTAAGAA
*
28605643 TTGTTTTAGTA-TTATTTTTAT
1 TTGTTTTAATATTTATTTTTAT
*
28605664 TTGTTTTAATATTTGTTTTTAT
1 TTGTTTTAATATTTATTTTTAT
* *
28605686 GT-TTTTAA-ATATATTT
1 TTGTTTTAATATTTATTT
28605702 GATTTATTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
20 6 0.19
21 16 0.50
22 10 0.31
ACGTcount: A:0.22, C:0.00, G:0.08, T:0.69
Consensus pattern (22 bp):
TTGTTTTAATATTTATTTTTAT
Found at i:28605736 original size:24 final size:26
Alignment explanation
Indices: 28605687--28605736 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 26
28605677 TGTTTTTATG
*
28605687 TTTTTAAATATATTTGATTTATTAAA
1 TTTTTAAATATATTTGATTTAATAAA
*
28605713 TTTTTAAAT-T-TTTTATTTAATAAA
1 TTTTTAAATATATTTGATTTAATAAA
28605737 ATAAAAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 12 0.55
25 1 0.05
26 9 0.41
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (26 bp):
TTTTTAAATATATTTGATTTAATAAA
Found at i:28605738 original size:25 final size:26
Alignment explanation
Indices: 28605687--28605738 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
28605677 TGTTTTTATG
*
28605687 TTTTTAAATATATTTGATTTATTAAA
1 TTTTTAAATATATTTGATTTATAAAA
*
28605713 TTTTTAAAT-T-TTTTATTTAATAAAA
1 TTTTTAAATATATTTGATTT-ATAAAA
28605738 T
1 T
28605739 AAAAAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 7 0.30
25 7 0.30
26 9 0.39
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (26 bp):
TTTTTAAATATATTTGATTTATAAAA
Found at i:28608736 original size:2 final size:2
Alignment explanation
Indices: 28608729--28608760 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
28608719 AAACTAGTTT
28608729 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
28608761 AATAAATTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:28608847 original size:19 final size:18
Alignment explanation
Indices: 28608789--28608859 Score: 63
Period size: 19 Copynumber: 3.7 Consensus size: 18
28608779 TTTTACTGAA
28608789 TTAATAAATTTTAATATTT
1 TTAA-AAATTTTAATATTT
* *
28608808 TT-ATAATTTTCTATAATTTT
1 TTAAAAATTTT-AAT-A-TTT
28608828 TTAAAAATTTTAATGATTT
1 TTAAAAATTTTAAT-ATTT
*
28608847 TTAACAATTTTAA
1 TTAAAAATTTTAA
28608860 ACAAAATATT
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
17 6 0.14
18 3 0.07
19 18 0.43
20 8 0.19
21 7 0.17
ACGTcount: A:0.39, C:0.03, G:0.01, T:0.56
Consensus pattern (18 bp):
TTAAAAATTTTAATATTT
Found at i:28612363 original size:2 final size:2
Alignment explanation
Indices: 28612356--28612386 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
28612346 CATTCTGCGC
28612356 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
28612387 CACGAAGAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:28613408 original size:21 final size:21
Alignment explanation
Indices: 28613384--28613430 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 21
28613374 ATCGCTTAGA
28613384 TCTTCCTC-AGAATTTTCAGAT
1 TCTTCC-CAAGAATTTTCAGAT
28613405 TCTTCCCAAGAATTTTCAGAT
1 TCTTCCCAAGAATTTTCAGAT
28613426 TCTTC
1 TCTTC
28613431 TACCATACTA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 1 0.04
21 24 0.96
ACGTcount: A:0.23, C:0.26, G:0.09, T:0.43
Consensus pattern (21 bp):
TCTTCCCAAGAATTTTCAGAT
Found at i:28615849 original size:271 final size:271
Alignment explanation
Indices: 28615402--28615905 Score: 834
Period size: 271 Copynumber: 1.9 Consensus size: 271
28615392 ACGGTAAGAG
28615402 TAGGGAACACCTTAATGCTGTTGTTAATCCTTTCTTCCCCACCTAGTATTCCTTCTATTATGTCT
1 TAGGGAACACCTTAATGCTGTTGTTAATCCTTTCTTCCCCACCTAGTATTCCTTCTATTATGTCT
* *
28615467 TCCATTTCATTACAATGTCTAACCTTTAAGTGTTTTCAGGTTCACAAAGCTTTTAACCATAGAGG
66 TCCATTTCATAACAATGTCTAACCTCTAAGTGTTTTCAGGTTCACAAAGCTTTTAACCATAGAGG
* * *** *
28615532 AAGTAAATACACACTTCAGCTTATGACAATTGGACACTTCCAAATGTGTTAAATTTTGAACACCA
131 AAGTAAATACACACTTCAACTTACGACAATCCCACACTACCAAATGTGTTAAATTTTGAACACCA
* *
28615597 CAAGACACTGTAAGAAGTTGATCATCATGCCATCTTTTGAGATTTAGAAGATTGTAGAGTGCCAC
196 CAAGACACAGTAAGAAGTTGATCATCATGCCATATTTTGAGATTTAGAAGATTGTAGAGTGCCAC
28615662 CGAGTCAAGCT
261 CGAGTCAAGCT
28615673 TAGGGAACACGCTTAA-GCTGTTGTTAATCCTTTCTTCCCCACCTAGTATTCCTTCTATTATGTC
1 TAGGGAACAC-CTTAATGCTGTTGTTAATCCTTTCTTCCCCACCTAGTATTCCTTCTATTATGTC
* *
28615737 TTCC-TTTCCATAACAATTTCTGACCTCTAAGTGTTTTCAGGTTCACAAAGCTTTTAACCATAGA
65 TTCCATTT-CATAACAATGTCTAACCTCTAAGTGTTTTCAGGTTCACAAAGCTTTTAACCATAGA
* *
28615801 GGAAGTAAATACACACTTCAACTTACGGC-ATCCCCACACTAGCAAATGTGTTAAATTTTGAACA
129 GGAAGTAAATACACACTTCAACTTACGACAAT-CCCACACTACCAAATGTGTTAAATTTTGAACA
28615865 CCACAAGACACAGTAAGAAGTTGATCATCATGCCATATTTT
193 CCACAAGACACAGTAAGAAGTTGATCATCATGCCATATTTT
28615906 TTCAATCTCA
Statistics
Matches: 216, Mismatches: 14, Indels: 6
0.92 0.06 0.03
Matches are distributed among these distances:
270 5 0.02
271 206 0.95
272 5 0.02
ACGTcount: A:0.30, C:0.22, G:0.14, T:0.33
Consensus pattern (271 bp):
TAGGGAACACCTTAATGCTGTTGTTAATCCTTTCTTCCCCACCTAGTATTCCTTCTATTATGTCT
TCCATTTCATAACAATGTCTAACCTCTAAGTGTTTTCAGGTTCACAAAGCTTTTAACCATAGAGG
AAGTAAATACACACTTCAACTTACGACAATCCCACACTACCAAATGTGTTAAATTTTGAACACCA
CAAGACACAGTAAGAAGTTGATCATCATGCCATATTTTGAGATTTAGAAGATTGTAGAGTGCCAC
CGAGTCAAGCT
Found at i:28621181 original size:18 final size:18
Alignment explanation
Indices: 28621157--28621198 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
28621147 ATTAATTTTT
*
28621157 TAAAAATATTTTAGAAATA
1 TAAAAATATATTA-AAATA
28621176 -AAAAATATATTAAAATA
1 TAAAAATATATTAAAATA
28621193 TAAAAA
1 TAAAAA
28621199 AATCAACCCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (18 bp):
TAAAAATATATTAAAATA
Found at i:28621910 original size:18 final size:19
Alignment explanation
Indices: 28621870--28621914 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
28621860 TGATTTCTTT
*
28621870 TTTTTTCTAACTTTACCTCC
1 TTTTTT-TAACTCTACCTCC
*
28621890 TTTTTTTAACTCTA-CTGC
1 TTTTTTTAACTCTACCTCC
28621908 TTTTTTT
1 TTTTTTT
28621915 TGGCTGATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 10 0.43
19 7 0.30
20 6 0.26
ACGTcount: A:0.13, C:0.22, G:0.02, T:0.62
Consensus pattern (19 bp):
TTTTTTTAACTCTACCTCC
Found at i:28622041 original size:19 final size:20
Alignment explanation
Indices: 28622019--28622062 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
28622009 GATTTCATTT
*
28622019 TTTTC-TCTGACTTTACCTA
1 TTTTCTTCTAACTTTACCTA
*
28622038 TTTTCTTTTAACTTTACCTA
1 TTTTCTTCTAACTTTACCTA
28622058 TTTTC
1 TTTTC
28622063 ATAACATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.16, C:0.23, G:0.02, T:0.59
Consensus pattern (20 bp):
TTTTCTTCTAACTTTACCTA
Found at i:28623361 original size:35 final size:35
Alignment explanation
Indices: 28623315--28623385 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 35
28623305 TAGTAAGGTA
*
28623315 TGATTTTTTTTAAATGTGTAAAAAGCTCTCAAACT
1 TGATTTTTTTTAAATATGTAAAAAGCTCTCAAACT
*
28623350 TGATTTTTTTTAAATATGTAAAAAGTTCTCAAACT
1 TGATTTTTTTTAAATATGTAAAAAGCTCTCAAACT
28623385 T
1 T
28623386 AAAAAATAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.35, C:0.10, G:0.10, T:0.45
Consensus pattern (35 bp):
TGATTTTTTTTAAATATGTAAAAAGCTCTCAAACT
Found at i:28629075 original size:31 final size:31
Alignment explanation
Indices: 28628953--28629063 Score: 168
Period size: 31 Copynumber: 3.6 Consensus size: 31
28628943 AGATATTTCC
* *
28628953 TTTTCAAGTATCACCCTTACGGGCTACCTCT
1 TTTTCAAGTATCACCCTTACGGGCTACTTCA
* *
28628984 TTTTCAAGTATCACCCTTACGGTCTACTTTA
1 TTTTCAAGTATCACCCTTACGGGCTACTTCA
*
28629015 TTTTCAAGTATCACCCTTTCGGGCTACTTCA
1 TTTTCAAGTATCACCCTTACGGGCTACTTCA
*
28629046 TTTTCATGTATCACCCTT
1 TTTTCAAGTATCACCCTT
28629064 TCAGGCCACT
Statistics
Matches: 72, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 72 1.00
ACGTcount: A:0.20, C:0.29, G:0.11, T:0.41
Consensus pattern (31 bp):
TTTTCAAGTATCACCCTTACGGGCTACTTCA
Found at i:28633104 original size:2 final size:2
Alignment explanation
Indices: 28633097--28633127 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
28633087 CTACCATGTA
28633097 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
28633128 AACCAAATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:28635464 original size:21 final size:21
Alignment explanation
Indices: 28635439--28635503 Score: 75
Period size: 21 Copynumber: 3.2 Consensus size: 21
28635429 TAGCTTTCGG
28635439 GCTTCCGTTTAGCACTTGTGT
1 GCTTCCGTTTAGCACTTGTGT
*
28635460 GCTTCAG-TTAGC-CTTCG-G-
1 GCTTCCGTTTAGCACTT-GTGT
*
28635478 GCTTCCGTTTAGCACTTATGT
1 GCTTCCGTTTAGCACTTGTGT
28635499 GCTTC
1 GCTTC
28635504 AGCTAGACTT
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
18 6 0.17
19 9 0.25
20 10 0.28
21 11 0.31
ACGTcount: A:0.11, C:0.26, G:0.23, T:0.40
Consensus pattern (21 bp):
GCTTCCGTTTAGCACTTGTGT
Found at i:28635467 original size:39 final size:39
Alignment explanation
Indices: 28635421--28635521 Score: 159
Period size: 39 Copynumber: 2.6 Consensus size: 39
28635411 GCTCTGATGA
*
28635421 GCTTCAGTTAGCTTTCGGGCTTCCGTTTAGCACTTGTGT
1 GCTTCAGTTAGCTTTCGGGCTTCCGTTTAGCACTTATGT
*
28635460 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
1 GCTTCAGTTAGCTTTCGGGCTTCCGTTTAGCACTTATGT
*
28635499 GCTTCAGCTAGACTTT-GGGCTTC
1 GCTTCAGTTAG-CTTTCGGGCTTC
28635522 AAATCACAAT
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
39 54 0.95
40 3 0.05
ACGTcount: A:0.12, C:0.25, G:0.25, T:0.39
Consensus pattern (39 bp):
GCTTCAGTTAGCTTTCGGGCTTCCGTTTAGCACTTATGT
Found at i:28638294 original size:5 final size:5
Alignment explanation
Indices: 28638284--28638311 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
28638274 ATAGTTTTGA
28638284 AAAAT AAAAT AAAAT AAAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAA
28638312 GAACACACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:28644879 original size:24 final size:23
Alignment explanation
Indices: 28644822--28644883 Score: 74
Period size: 24 Copynumber: 2.7 Consensus size: 23
28644812 AATTTAACTA
*
28644822 ATAATATTAAAA-ATACATGTTC
1 ATAATATTAAAACATACATATTC
28644844 ATAATATATAAAACATACATATAAT-
1 ATAATAT-TAAAACATACATAT--TC
28644869 ATAATATTAAAACAT
1 ATAATATTAAAACAT
28644884 TTACATAATA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
22 7 0.20
23 5 0.14
24 15 0.43
25 7 0.20
26 1 0.03
ACGTcount: A:0.56, C:0.08, G:0.02, T:0.34
Consensus pattern (23 bp):
ATAATATTAAAACATACATATTC
Found at i:28644891 original size:24 final size:25
Alignment explanation
Indices: 28644844--28644894 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 25
28644834 ATACATGTTC
*
28644844 ATAATATATAAAACATACATATAAT
1 ATAATATATAAAACATACACATAAT
**
28644869 ATAATAT-TAAAACATTTACATAAT
1 ATAATATATAAAACATACACATAAT
28644893 AT
1 AT
28644895 GTACTCACAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 16 0.70
25 7 0.30
ACGTcount: A:0.57, C:0.08, G:0.00, T:0.35
Consensus pattern (25 bp):
ATAATATATAAAACATACACATAAT
Found at i:28644994 original size:21 final size:21
Alignment explanation
Indices: 28644970--28645009 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
28644960 AAGATATACT
*
28644970 TATATAAATATATATTAAAGA
1 TATATAAATATATAATAAAGA
*
28644991 TATATACATATATAATAAA
1 TATATAAATATATAATAAA
28645010 ATACATGAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.38
Consensus pattern (21 bp):
TATATAAATATATAATAAAGA
Found at i:28649112 original size:16 final size:16
Alignment explanation
Indices: 28649082--28649128 Score: 71
Period size: 16 Copynumber: 3.1 Consensus size: 16
28649072 GAAATCTCTT
28649082 TTATTTATA--AAATA
1 TTATTTATATTAAATA
*
28649096 TTATTTATCTTAAATA
1 TTATTTATATTAAATA
28649112 TTATTTATATTAAATA
1 TTATTTATATTAAATA
28649128 T
1 T
28649129 GGTATATATT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
14 8 0.28
16 21 0.72
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (16 bp):
TTATTTATATTAAATA
Found at i:28650186 original size:16 final size:16
Alignment explanation
Indices: 28650165--28650202 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
28650155 GTCAACAAGA
28650165 GAGTCGAAAAATTAAT
1 GAGTCGAAAAATTAAT
28650181 GAGTCGAAAAATTAAT
1 GAGTCGAAAAATTAAT
28650197 GAGTCG
1 GAGTCG
28650203 CTTGTGTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.45, C:0.08, G:0.24, T:0.24
Consensus pattern (16 bp):
GAGTCGAAAAATTAAT
Found at i:28657195 original size:23 final size:23
Alignment explanation
Indices: 28657142--28657196 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
28657132 TTTTTAGAAA
28657142 AAATTAATTAAATCTTTATAATC
1 AAATTAATTAAATCTTTATAATC
** *
28657165 -TTTATAATTAAATCTTTATACTC
1 AAAT-TAATTAAATCTTTATAATC
28657188 AAATTAATT
1 AAATTAATT
28657197 TGATCCCATT
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
22 1 0.04
23 23 0.92
24 1 0.04
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (23 bp):
AAATTAATTAAATCTTTATAATC
Found at i:28661629 original size:4 final size:4
Alignment explanation
Indices: 28661620--28661648 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
28661610 AGCAAACGTG
28661620 AGAA AGAA AGAA AGAA AGAA AGAA AGAA A
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA A
28661649 TAGAAATGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:28662474 original size:47 final size:46
Alignment explanation
Indices: 28662410--28662519 Score: 134
Period size: 47 Copynumber: 2.4 Consensus size: 46
28662400 GACATTGAGT
* *
28662410 CGATG-AGACACTATGTGT-CGACTACTGTTAAAGTTCCGGATTTGTTC
1 CGATGAAG-CACTATGTGTACGA-TAATGTTAAAGTTCC-GATTTATTC
* * *
28662457 CGATGAAGTACTTTGTGTACTATAATGTTAAAGTTCCGATTTATTC
1 CGATGAAGCACTATGTGTACGATAATGTTAAAGTTCCGATTTATTC
28662503 CGATGAAGCACTATGTG
1 CGATGAAGCACTATGTG
28662520 CTTATCCCGG
Statistics
Matches: 54, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
46 23 0.43
47 27 0.50
48 4 0.07
ACGTcount: A:0.26, C:0.16, G:0.22, T:0.35
Consensus pattern (46 bp):
CGATGAAGCACTATGTGTACGATAATGTTAAAGTTCCGATTTATTC
Found at i:28668879 original size:4 final size:4
Alignment explanation
Indices: 28668870--28668898 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
28668860 AGCAAACGTG
28668870 AGAA AGAA AGAA AGAA AGAA AGAA AGAA A
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA A
28668899 TAGAAAAGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:28669724 original size:47 final size:47
Alignment explanation
Indices: 28669660--28669770 Score: 154
Period size: 47 Copynumber: 2.4 Consensus size: 47
28669650 GACATTGAGT
*
28669660 CGATG-AGACACTATGTGT-CGACTACTGTTAAAGTTCCGGATTTGTTC
1 CGATGAAG-CACTATGTGTACGA-TAATGTTAAAGTTCCGGATTTGTTC
* * *
28669707 CGATGAAGTACTTTGTGTACTATAATGTTAAAGTTCCGGATTTGTTC
1 CGATGAAGCACTATGTGTACGATAATGTTAAAGTTCCGGATTTGTTC
28669754 CGATGAAGCACTATGTG
1 CGATGAAGCACTATGTG
28669771 CTTATCCCGG
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
47 52 0.93
48 4 0.07
ACGTcount: A:0.25, C:0.16, G:0.23, T:0.35
Consensus pattern (47 bp):
CGATGAAGCACTATGTGTACGATAATGTTAAAGTTCCGGATTTGTTC
Found at i:28671753 original size:20 final size:22
Alignment explanation
Indices: 28671706--28671755 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 22
28671696 GTAATATATA
*
28671706 TGTTTGAATGATGAATTTATTT
1 TGTTTGAATGATGAATTTACTT
* *
28671728 TATTTGAATG-T-ACTTTACTT
1 TGTTTGAATGATGAATTTACTT
28671748 TGTTTGAA
1 TGTTTGAA
28671756 AATTGGTACA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
20 14 0.58
21 1 0.04
22 9 0.38
ACGTcount: A:0.26, C:0.04, G:0.16, T:0.54
Consensus pattern (22 bp):
TGTTTGAATGATGAATTTACTT
Found at i:28673812 original size:46 final size:46
Alignment explanation
Indices: 28673733--28673845 Score: 131
Period size: 46 Copynumber: 2.4 Consensus size: 46
28673723 TGGTTTATCT
* * * *
28673733 ACATTTCTGTCTAGCAACTTGTCTGCAATTATAGTGGCT-TGACCAC
1 ACATATCTGTCTGGCAGCTTGGCTGCAATTATAGTGG-TGTGACCAC
28673779 ACATATCTGTTCTGGCAGCTTGGCTGCAA-TATAGTGGTGTGACCAC
1 ACATATCTG-TCTGGCAGCTTGGCTGCAATTATAGTGGTGTGACCAC
* *
28673825 ATATATTTGATCTGGCAGCTT
1 ACATATCTG-TCTGGCAGCTT
28673846 AACTGCAACT
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
45 1 0.02
46 41 0.71
47 16 0.28
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.35
Consensus pattern (46 bp):
ACATATCTGTCTGGCAGCTTGGCTGCAATTATAGTGGTGTGACCAC
Found at i:28681138 original size:66 final size:66
Alignment explanation
Indices: 28681025--28681149 Score: 178
Period size: 66 Copynumber: 1.9 Consensus size: 66
28681015 GTCAGTAGCC
* * * * * *
28681025 TCACACGGCCTAGCACATGGGCATGTGGCTTGGCTGTGTGTCACAAGTCAGTATGCTCATCATTT
1 TCACACAGCCTAGCACACGGGCATGTGGCTTGGCAGTGTGACACAAGTCAATAAGCTCATCATTT
28681090 T
66 T
* *
28681091 TCACACAGCCTAGCACACGGGCGTGTGGCTTGGCAGTGTGACCCAAGTCAATAAGCTCA
1 TCACACAGCCTAGCACACGGGCATGTGGCTTGGCAGTGTGACACAAGTCAATAAGCTCA
28681150 CTAGTTTGGA
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
66 51 1.00
ACGTcount: A:0.22, C:0.26, G:0.26, T:0.25
Consensus pattern (66 bp):
TCACACAGCCTAGCACACGGGCATGTGGCTTGGCAGTGTGACACAAGTCAATAAGCTCATCATTT
T
Found at i:28681163 original size:66 final size:66
Alignment explanation
Indices: 28681026--28681183 Score: 165
Period size: 66 Copynumber: 2.4 Consensus size: 66
28681016 TCAGTAGCCT
* * * * * * *
28681026 CACACGGCCTAGCACATGGGCATGTGGCTTGGCTGTGTGTCACAAGTCAGTATGCTCATCATTTT
1 CACACAGCCTAGCACACGGGCATGTGGCTTGGCAGTGTGACACAAGTCAATAAGCTCATCAGTTT
*
28681091 T
66 G
* *
28681092 CACACAGCCTAGCACACGGGCGTGTGGCTTGGCAGTGTGACCCAAGTCAATAAGCTCA-CTAGTT
1 CACACAGCCTAGCACACGGGCATGTGGCTTGGCAGTGTGACACAAGTCAATAAGCTCATC-AGTT
28681156 TG
65 TG
* * ** *
28681158 GACACAGGCTAGGGCACAGGCATGTG
1 CACACAGCCTAGCACACGGGCATGTG
28681184 TCCCTATTTC
Statistics
Matches: 75, Mismatches: 16, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
65 1 0.01
66 74 0.99
ACGTcount: A:0.23, C:0.25, G:0.28, T:0.23
Consensus pattern (66 bp):
CACACAGCCTAGCACACGGGCATGTGGCTTGGCAGTGTGACACAAGTCAATAAGCTCATCAGTTT
G
Found at i:28681831 original size:15 final size:16
Alignment explanation
Indices: 28681813--28681842 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
28681803 ATATTAATGT
28681813 TATTTAAT-TTAAAAA
1 TATTTAATATTAAAAA
28681828 TATTTAATATTAAAA
1 TATTTAATATTAAAA
28681843 TAATGCATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TATTTAATATTAAAAA
Found at i:28681984 original size:23 final size:25
Alignment explanation
Indices: 28681939--28681985 Score: 71
Period size: 23 Copynumber: 1.9 Consensus size: 25
28681929 TTTAATTTTT
28681939 AATTTTTAATATTTGATTTTTGTTGA
1 AATTTTT-ATATTTGATTTTTGTTGA
28681965 AATTTTT-TATTT-ATTTTTGTT
1 AATTTTTATATTTGATTTTTGTT
28681986 CACTTTAGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 9 0.43
24 5 0.24
26 7 0.33
ACGTcount: A:0.23, C:0.00, G:0.09, T:0.68
Consensus pattern (25 bp):
AATTTTTATATTTGATTTTTGTTGA
Found at i:28682353 original size:2 final size:2
Alignment explanation
Indices: 28682305--28682336 Score: 55
Period size: 2 Copynumber: 15.5 Consensus size: 2
28682295 ACTATTTGTT
28682305 TA TA TA TA TA TA TA TA TA TA TA TA TA TCA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA T
28682337 TGCTATAGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:28682701 original size:15 final size:16
Alignment explanation
Indices: 28682681--28682717 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
28682671 TTTTATATTT
28682681 TTTTAATTT-TAAATA
1 TTTTAATTTATAAATA
*
28682696 TTTTAATTTATATATA
1 TTTTAATTTATAAATA
28682712 TTTTAA
1 TTTTAA
28682718 AATTATTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTTAATTTATAAATA
Found at i:28682716 original size:16 final size:16
Alignment explanation
Indices: 28682672--28682717 Score: 60
Period size: 15 Copynumber: 3.0 Consensus size: 16
28682662 TTATGAACTT
*
28682672 TTTATAT-TTTTTTAA
1 TTTATATATATTTTAA
*
28682687 TTT-TAAATATTTTAA
1 TTTATATATATTTTAA
28682702 TTTATATATATTTTAA
1 TTTATATATATTTTAA
28682718 AATTATTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
14 2 0.08
15 13 0.50
16 11 0.42
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTATATATATTTTAA
Found at i:28693228 original size:20 final size:20
Alignment explanation
Indices: 28693203--28693244 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
28693193 CAACTTTGAA
*
28693203 TTTT-AATTAAATTTTGCATT
1 TTTTAAATTAAAATTTG-ATT
28693223 TTTTAAATTAAAATTTGATT
1 TTTTAAATTAAAATTTGATT
28693243 TT
1 TT
28693245 AATGATTTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.33, C:0.02, G:0.05, T:0.60
Consensus pattern (20 bp):
TTTTAAATTAAAATTTGATT
Found at i:28694096 original size:24 final size:24
Alignment explanation
Indices: 28694069--28694125 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
28694059 TATTAAAAAA
*
28694069 ATAAAAAATGAAAATA-ATATATAT
1 ATAAAAAATCAAAATATATATA-AT
28694093 ATAAGAAAA-CAAAATATATATAAT
1 ATAA-AAAATCAAAATATATATAAT
*
28694117 CTAAAAAAT
1 ATAAAAAAT
28694126 ATATATAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
23 4 0.14
24 15 0.54
25 9 0.32
ACGTcount: A:0.67, C:0.04, G:0.04, T:0.26
Consensus pattern (24 bp):
ATAAAAAATCAAAATATATATAAT
Found at i:28694141 original size:18 final size:18
Alignment explanation
Indices: 28694087--28694154 Score: 52
Period size: 18 Copynumber: 3.7 Consensus size: 18
28694077 TGAAAATAAT
28694087 ATATATATAAGAAA-ACAAA
1 ATATATATAA-AAATA-AAA
**
28694106 ATATATAT-AATCTAAAAA
1 ATATATATAAAAAT-AAAA
28694124 ATATATATAAAAAT-AAA
1 ATATATATAAAAATAAAA
*
28694141 ATTTATAATAAAAA
1 ATATAT-ATAAAAA
28694155 ACTGATAATT
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
17 9 0.22
18 19 0.47
19 12 0.30
ACGTcount: A:0.66, C:0.03, G:0.01, T:0.29
Consensus pattern (18 bp):
ATATATATAAAAATAAAA
Found at i:28694638 original size:26 final size:24
Alignment explanation
Indices: 28694601--28694652 Score: 77
Period size: 26 Copynumber: 2.1 Consensus size: 24
28694591 TTTAATATCA
28694601 AAATTTTCTATTTTAAATTTAAATTT
1 AAATTTTCTATTTTAAA--TAAATTT
*
28694627 AAATTTTTTATTTTAAATAAATTT
1 AAATTTTCTATTTTAAATAAATTT
28694651 AA
1 AA
28694653 TTGTCACCTG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 9 0.36
26 16 0.64
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (24 bp):
AAATTTTCTATTTTAAATAAATTT
Found at i:28698079 original size:11 final size:11
Alignment explanation
Indices: 28698054--28698086 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
28698044 TATCATTTGT
28698054 ATTTTAA-TT-
1 ATTTTAATTTC
28698063 ATTTTAATTTC
1 ATTTTAATTTC
28698074 ATTTTAATTTC
1 ATTTTAATTTC
28698085 AT
1 AT
28698087 ATATGCATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 7 0.32
10 2 0.09
11 13 0.59
ACGTcount: A:0.30, C:0.06, G:0.00, T:0.64
Consensus pattern (11 bp):
ATTTTAATTTC
Found at i:28699715 original size:22 final size:21
Alignment explanation
Indices: 28699690--28699731 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
28699680 ATAATTGATT
*
28699690 TAAATTTTTTATGATATAAAAA
1 TAAATATTTTAT-ATATAAAAA
*
28699712 TAAATATTTTATATTTAAAA
1 TAAATATTTTATATATAAAA
28699732 TAATTTAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (21 bp):
TAAATATTTTATATATAAAAA
Found at i:28700350 original size:61 final size:61
Alignment explanation
Indices: 28700253--28700412 Score: 152
Period size: 60 Copynumber: 2.7 Consensus size: 61
28700243 TTACTCTAAT
* * * * *
28700253 AACAAATTTAGTTCTCTAATGTTTTCATATTTTATCAATTTGA-TCTTAAA-TATAAAAAAGCTC
1 AACAAATTTAGTCCTC-AATGTTTACAAAATTTATCAATTTGAGT-TCAAATTAT-AAAAA-CTC
* *
28700316 AACAAATTTAG-CCTCAATGTTTACAAAATTTATC-ATTTTAGTTCAAATTATAAAAATTC
1 AACAAATTTAGTCCTCAATGTTTACAAAATTTATCAATTTGAGTTCAAATTATAAAAACTC
* **
28700375 AATAAATTTAGTCCTCAACATTTACAAAA-TTAT-AATTT
1 AACAAATTTAGTCCTCAATGTTTACAAAATTTATCAATTT
28700413 TTAATTTTTA
Statistics
Matches: 83, Mismatches: 10, Indels: 12
0.79 0.10 0.11
Matches are distributed among these distances:
59 20 0.24
60 29 0.35
61 20 0.24
62 3 0.04
63 11 0.13
ACGTcount: A:0.41, C:0.13, G:0.05, T:0.41
Consensus pattern (61 bp):
AACAAATTTAGTCCTCAATGTTTACAAAATTTATCAATTTGAGTTCAAATTATAAAAACTC
Found at i:28700412 original size:29 final size:29
Alignment explanation
Indices: 28700319--28700409 Score: 73
Period size: 29 Copynumber: 3.1 Consensus size: 29
28700309 AAAGCTCAAC
*
28700319 AAATTTAG-CCTCAATGTTTACAAAATTTAT
1 AAATTTAGTCCTCAA-ATTTACAAAA-TTAT
* *
28700349 CATTTTAGT--TCAAATTATA-AAAATTCAAT
1 AAATTTAGTCCTCAAATT-TACAAAATT--AT
28700378 AAATTTAGTCCTCAACATTTACAAAATTAT
1 AAATTTAGTCCTCAA-ATTTACAAAATTAT
28700408 AA
1 AA
28700410 TTTTTAATTT
Statistics
Matches: 48, Mismatches: 5, Indels: 16
0.70 0.07 0.23
Matches are distributed among these distances:
27 2 0.04
28 6 0.12
29 15 0.31
30 10 0.21
31 6 0.12
32 9 0.19
ACGTcount: A:0.44, C:0.13, G:0.04, T:0.38
Consensus pattern (29 bp):
AAATTTAGTCCTCAAATTTACAAAATTAT
Found at i:28703656 original size:58 final size:58
Alignment explanation
Indices: 28703547--28703657 Score: 195
Period size: 58 Copynumber: 1.9 Consensus size: 58
28703537 TAAAATGTTG
* **
28703547 TTGTAAAAGAATCAATAGATACCAATATATGAATTGAATGGAAAATCTTTTTATATTT
1 TTGTAAAAGAATCAATAGATACCAATATATGAATTAAATGGAAAAAATTTTTATATTT
28703605 TTGTAAAAGAATCAATAGATACCAATATATGAATTAAATGGAAAAAATTTTTA
1 TTGTAAAAGAATCAATAGATACCAATATATGAATTAAATGGAAAAAATTTTTA
28703658 CGTTGTTGTT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
58 50 1.00
ACGTcount: A:0.47, C:0.06, G:0.12, T:0.35
Consensus pattern (58 bp):
TTGTAAAAGAATCAATAGATACCAATATATGAATTAAATGGAAAAAATTTTTATATTT
Found at i:28703687 original size:58 final size:57
Alignment explanation
Indices: 28703544--28703671 Score: 175
Period size: 58 Copynumber: 2.2 Consensus size: 57
28703534 TTGTAAAATG
* ** *
28703544 TTGTTGTAAAAGAATCAATAGATACCAATATATGAATTGAATGGAAAATCTTTTTATA
1 TTGTTGTAAAAGAAT-AATAGATACCAATATATGAATTAAATGGAAAAAATTTTTACA
* *
28703602 TTTTTGTAAAAGAATCAATAGATACCAATATATGAATTAAATGGAAAAAATTTTTACG
1 TTGTTGTAAAAGAAT-AATAGATACCAATATATGAATTAAATGGAAAAAATTTTTACA
*
28703660 TTGTTGTTAAAG
1 TTGTTGTAAAAG
28703672 TATATACCTA
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
58 62 1.00
ACGTcount: A:0.43, C:0.06, G:0.14, T:0.37
Consensus pattern (57 bp):
TTGTTGTAAAAGAATAATAGATACCAATATATGAATTAAATGGAAAAAATTTTTACA
Found at i:28703783 original size:26 final size:26
Alignment explanation
Indices: 28703754--28703807 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
28703744 AGGTTGACAT
* *
28703754 CAACAAAGTAGAACCATCAAATTATC
1 CAACAAAATAGAACAATCAAATTATC
* *
28703780 CAACAAAATATAACAATCAAATTTTC
1 CAACAAAATAGAACAATCAAATTATC
28703806 CA
1 CA
28703808 TTGTATATTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.52, C:0.22, G:0.04, T:0.22
Consensus pattern (26 bp):
CAACAAAATAGAACAATCAAATTATC
Found at i:28703859 original size:17 final size:17
Alignment explanation
Indices: 28703839--28703872 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
28703829 TCAACCGGGA
*
28703839 GGTATGATCAATAACAT
1 GGTATCATCAATAACAT
28703856 GGTATCATCAATAACAT
1 GGTATCATCAATAACAT
28703873 CAAGTGTGTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.29
Consensus pattern (17 bp):
GGTATCATCAATAACAT
Found at i:28704258 original size:21 final size:21
Alignment explanation
Indices: 28704233--28704320 Score: 76
Period size: 21 Copynumber: 4.3 Consensus size: 21
28704223 TAAAGTCAAG
28704233 TACATAATATAAATAGTAATA
1 TACATAATATAAATAGTAATA
* *
28704254 TACATAACATAAATAAT-ATA
1 TACATAATATAAATAGTAATA
* * * *
28704274 AACA-ACA-ATATACA-TAACA
1 TACATA-ATATAAATAGTAATA
*
28704293 TACATGATATAAATAGTAATA
1 TACATAATATAAATAGTAATA
28704314 TACATAA
1 TACATAA
28704321 CATACATAAA
Statistics
Matches: 50, Mismatches: 12, Indels: 10
0.69 0.17 0.14
Matches are distributed among these distances:
18 1 0.02
19 12 0.24
20 12 0.24
21 25 0.50
ACGTcount: A:0.58, C:0.10, G:0.03, T:0.28
Consensus pattern (21 bp):
TACATAATATAAATAGTAATA
Found at i:28704270 original size:30 final size:30
Alignment explanation
Indices: 28704233--28704384 Score: 158
Period size: 30 Copynumber: 5.3 Consensus size: 30
28704223 TAAAGTCAAG
28704233 TACATAATATAAATAGTAATATACATAACA
1 TACATAATATAAATAGTAATATACATAACA
* * **
28704263 TAAATAATATAAACAACAATATACATAACA
1 TACATAATATAAATAGTAATATACATAACA
*
28704293 TACATGATATAAATAGTAATATACATAACA
1 TACATAATATAAATAGTAATATACATAACA
* *
28704323 TACATAA-A-CAATAATAA-ACTACATAACA
1 TACATAATATAAATAGTAATA-TACATAACA
* *
28704351 TAC-----ATAAATAGTATTATAAATAACA
1 TACATAATATAAATAGTAATATACATAACA
28704376 TACATAATA
1 TACATAATA
28704385 GACATACTAA
Statistics
Matches: 98, Mismatches: 16, Indels: 16
0.75 0.12 0.12
Matches are distributed among these distances:
24 1 0.01
25 17 0.17
26 1 0.01
27 1 0.01
28 19 0.19
29 1 0.01
30 58 0.59
ACGTcount: A:0.58, C:0.12, G:0.03, T:0.28
Consensus pattern (30 bp):
TACATAATATAAATAGTAATATACATAACA
Found at i:28704292 original size:15 final size:15
Alignment explanation
Indices: 28704250--28704324 Score: 52
Period size: 15 Copynumber: 5.0 Consensus size: 15
28704240 TATAAATAGT
28704250 AATATACATAACATA
1 AATATACATAACATA
*
28704265 AATA-ATATAAACA-A
1 AATATACAT-AACATA
28704279 CAATATACATAACATA
1 -AATATACATAACATA
*
28704295 CATGAT--ATAA-ATA
1 AAT-ATACATAACATA
28704308 GTAATATACATAACATA
1 --AATATACATAACATA
28704325 CATAAACAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 18
0.68 0.06 0.26
Matches are distributed among these distances:
13 3 0.07
14 10 0.22
15 20 0.43
16 10 0.22
17 3 0.07
ACGTcount: A:0.59, C:0.12, G:0.03, T:0.27
Consensus pattern (15 bp):
AATATACATAACATA
Found at i:28704337 original size:25 final size:25
Alignment explanation
Indices: 28704271--28704382 Score: 98
Period size: 28 Copynumber: 4.2 Consensus size: 25
28704261 CATAAATAAT
*
28704271 ATAAACAACAATATACATAACATAC
1 ATAAACAATAATATACATAACATAC
*
28704296 ATGATATAAATAGTAATATACATAACATAC
1 AT-A-A-ACA-A-TAATATACATAACATAC
28704326 ATAAACAATAATAAACTACATAACATAC
1 ATAAACAATAAT--A-TACATAACATAC
* * * *
28704354 ATAAATAGTATTATAAATAACATAC
1 ATAAACAATAATATACATAACATAC
28704379 ATAA
1 ATAA
28704383 TAGACATACT
Statistics
Matches: 72, Mismatches: 7, Indels: 16
0.76 0.07 0.17
Matches are distributed among these distances:
25 21 0.29
26 3 0.04
27 4 0.06
28 24 0.33
29 2 0.03
30 18 0.25
ACGTcount: A:0.58, C:0.13, G:0.03, T:0.26
Consensus pattern (25 bp):
ATAAACAATAATATACATAACATAC
Found at i:28706841 original size:44 final size:44
Alignment explanation
Indices: 28706778--28706867 Score: 180
Period size: 44 Copynumber: 2.0 Consensus size: 44
28706768 ATACTCTAAG
28706778 ACCAAAGGTGATCATGATGAGCATCTTAGAGTAGTTCTTCAGAT
1 ACCAAAGGTGATCATGATGAGCATCTTAGAGTAGTTCTTCAGAT
28706822 ACCAAAGGTGATCATGATGAGCATCTTAGAGTAGTTCTTCAGAT
1 ACCAAAGGTGATCATGATGAGCATCTTAGAGTAGTTCTTCAGAT
28706866 AC
1 AC
28706868 TCCAAGAGAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.29
Consensus pattern (44 bp):
ACCAAAGGTGATCATGATGAGCATCTTAGAGTAGTTCTTCAGAT
Found at i:28708158 original size:18 final size:18
Alignment explanation
Indices: 28708135--28708169 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
28708125 GAGTTAAACG
*
28708135 AATCGAGTTATTTGAGTT
1 AATCGAGTTATTCGAGTT
28708153 AATCGAGTTATTCGAGT
1 AATCGAGTTATTCGAGT
28708170 CAACTTGAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.09, G:0.23, T:0.40
Consensus pattern (18 bp):
AATCGAGTTATTCGAGTT
Found at i:28708619 original size:15 final size:16
Alignment explanation
Indices: 28708599--28708628 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
28708589 CCATTTATTT
28708599 TCCCTC-AAACTTTTA
1 TCCCTCAAAACTTTTA
28708614 TCCCTCAAAACTTTT
1 TCCCTCAAAACTTTT
28708629 TATTTTCCCC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.27, C:0.33, G:0.00, T:0.40
Consensus pattern (16 bp):
TCCCTCAAAACTTTTA
Found at i:28712964 original size:28 final size:27
Alignment explanation
Indices: 28712933--28712994 Score: 72
Period size: 28 Copynumber: 2.3 Consensus size: 27
28712923 TTTATAATTT
28712933 TTTTCTAATTTTTAATT-AAATTTAAATA
1 TTTTCTAATTTTT-ATTAAAATTT-AATA
* *
28712961 TTTTTTTATTTTTATTAAAATTTAATA
1 TTTTCTAATTTTTATTAAAATTTAATA
*
28712988 ATTTCTA
1 TTTTCTA
28712995 CAACTTTTAT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
27 11 0.39
28 17 0.61
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.61
Consensus pattern (27 bp):
TTTTCTAATTTTTATTAAAATTTAATA
Found at i:28717791 original size:27 final size:27
Alignment explanation
Indices: 28717761--28717814 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
28717751 TCCTACAACC
* *
28717761 CATGTAATAGTAATTTAACATTCAATT
1 CATGTAACAATAATTTAACATTCAATT
**
28717788 CATGTAACAATAATTTTCCATTCAATT
1 CATGTAACAATAATTTAACATTCAATT
28717815 TCACATGACA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.39, C:0.15, G:0.06, T:0.41
Consensus pattern (27 bp):
CATGTAACAATAATTTAACATTCAATT
Found at i:28719741 original size:27 final size:27
Alignment explanation
Indices: 28719711--28719869 Score: 237
Period size: 27 Copynumber: 5.9 Consensus size: 27
28719701 ATTACCAAAG
* *
28719711 TACCCCCGATTTACAGAATTACTGTTT
1 TACCCTCGATTTACAGAATTACTATTT
*
28719738 TACCCTCGATTTATAGAATTACTATTT
1 TACCCTCGATTTACAGAATTACTATTT
* *
28719765 TACCTTTGATTTACAGAATTACTATTT
1 TACCCTCGATTTACAGAATTACTATTT
*
28719792 TACCCTCGATTTATAGAATTACTATTT
1 TACCCTCGATTTACAGAATTACTATTT
* *
28719819 TACCCTTGATTTACAGAATTACTGTTT
1 TACCCTCGATTTACAGAATTACTATTT
*
28719846 TACCCTCGATTTACAAAATTACTA
1 TACCCTCGATTTACAGAATTACTA
28719870 AAATACCCTT
Statistics
Matches: 117, Mismatches: 15, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 117 1.00
ACGTcount: A:0.30, C:0.20, G:0.08, T:0.42
Consensus pattern (27 bp):
TACCCTCGATTTACAGAATTACTATTT
Found at i:28719758 original size:54 final size:54
Alignment explanation
Indices: 28719684--28719894 Score: 260
Period size: 54 Copynumber: 3.9 Consensus size: 54
28719674 ATTATTGAAA
* * * * **
28719684 TACCCTCGACTTGTAAAATTACCAAAGTACCCCCGATTTACAGAATTACTGTTT
1 TACCCTCGATTTATAAAATTACTAAATTACCCTTGATTTACAGAATTACTGTTT
* ** * *
28719738 TACCCTCGATTTATAGAATTACTATTTTACCTTTGATTTACAGAATTACTATTT
1 TACCCTCGATTTATAAAATTACTAAATTACCCTTGATTTACAGAATTACTGTTT
* **
28719792 TACCCTCGATTTATAGAATTACTATTTTACCCTTGATTTACAGAATTACTGTTT
1 TACCCTCGATTTATAAAATTACTAAATTACCCTTGATTTACAGAATTACTGTTT
* * * *
28719846 TACCCTCGATTTACAAAATTACTAAAATACCCTTGGTTTACAAAATTAC
1 TACCCTCGATTTATAAAATTACTAAATTACCCTTGATTTACAGAATTAC
28719895 CAAAATACCC
Statistics
Matches: 137, Mismatches: 20, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
54 137 1.00
ACGTcount: A:0.32, C:0.21, G:0.09, T:0.39
Consensus pattern (54 bp):
TACCCTCGATTTATAAAATTACTAAATTACCCTTGATTTACAGAATTACTGTTT
Found at i:28719876 original size:27 final size:27
Alignment explanation
Indices: 28719681--28720149 Score: 198
Period size: 27 Copynumber: 17.3 Consensus size: 27
28719671 CCAATTATTG
* ** *
28719681 AAATACCCTCGACTTGTAAAATTACCA
1 AAATACCCTCGATTTACAAAATTACTA
* * * *
28719708 AAGTACCCCCGATTTACAGAATTACTG
1 AAATACCCTCGATTTACAAAATTACTA
*** * *
28719735 TTTTACCCTCGATTTATAGAATTACTA
1 AAATACCCTCGATTTACAAAATTACTA
*** * * *
28719762 TTTTACCTTTGATTTACAGAATTACTA
1 AAATACCCTCGATTTACAAAATTACTA
*** * *
28719789 TTTTACCCTCGATTTATAGAATTACTA
1 AAATACCCTCGATTTACAAAATTACTA
*** * * *
28719816 TTTTACCCTTGATTTACAGAATTACTG
1 AAATACCCTCGATTTACAAAATTACTA
***
28719843 TTTTACCCTCGATTTACAAAATTACTA
1 AAATACCCTCGATTTACAAAATTACTA
* * *
28719870 AAATACCCTTGGTTTACAAAATTACCA
1 AAATACCCTCGATTTACAAAATTACTA
* * *
28719897 AAATACCCTCGA-TCAGTAAAATTACCA
1 AAATACCCTCGATTTA-CAAAATTACTA
* * ** *
28719924 AAATACCCT-GGTCTGTAAAATTGCTA
1 AAATACCCTCGATTTACAAAATTACTA
* ** *
28719950 AAATACCC-CTGGTTTGTAAAATTACCA
1 AAATACCCTC-GATTTACAAAATTACTA
* ** * *
28719977 AAATACCC-CTAGTTTGTAAAGTTACCA
1 AAATACCCTCGA-TTTACAAAATTACTA
* ** **
28720004 AAATACCACTAG-TTTGTAAAATTACCG
1 AAATACC-CTCGATTTACAAAATTACTA
* *
28720031 AAATACCCTCAATTT-CTAAAATTACCA
1 AAATACCCTCGATTTAC-AAAATTACTA
* *
28720058 AAATACCCTTGATTTACAAAATTACAA
1 AAATACCCTCGATTTACAAAATTACTA
*
28720085 AAATACCCTTGACTTT-CTAAAAATTA-TA
1 AAATACCCTCGA-TTTAC--AAAATTACTA
* * * *
28720113 GAAATACCATTGGTTTACAAAATTACTG
1 -AAATACCCTCGATTTACAAAATTACTA
28720141 AAATACCCT
1 AAATACCCT
28720150 TGGTTTGTAG
Statistics
Matches: 362, Mismatches: 64, Indels: 32
0.79 0.14 0.07
Matches are distributed among these distances:
26 22 0.06
27 312 0.86
28 10 0.03
29 18 0.05
ACGTcount: A:0.37, C:0.21, G:0.08, T:0.33
Consensus pattern (27 bp):
AAATACCCTCGATTTACAAAATTACTA
Found at i:28719877 original size:81 final size:81
Alignment explanation
Indices: 28719684--28719894 Score: 242
Period size: 81 Copynumber: 2.6 Consensus size: 81
28719674 ATTATTGAAA
* ** * * * *
28719684 TACCCTCGACTTGTAAAATTACCAAAGTACCCCCGATTTACAGAATTACTGTTTTACCCTCGATT
1 TACCCTCGATTTACAAAATTACTAAAATACCCTCGATTTACAGAATTACTATTTTACCCTCGATT
*
28719749 TATAGAATTACTATTT
66 TACAGAATTACTATTT
* * * *** * *
28719765 TACCTTTGATTTACAGAATTACTATTTTACCCTCGATTTATAGAATTACTATTTTACCCTTGATT
1 TACCCTCGATTTACAAAATTACTAAAATACCCTCGATTTACAGAATTACTATTTTACCCTCGATT
*
28719830 TACAGAATTACTGTTT
66 TACAGAATTACTATTT
* * *
28719846 TACCCTCGATTTACAAAATTACTAAAATACCCTTGGTTTACAAAATTAC
1 TACCCTCGATTTACAAAATTACTAAAATACCCTCGATTTACAGAATTAC
28719895 CAAAATACCC
Statistics
Matches: 104, Mismatches: 26, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
81 104 1.00
ACGTcount: A:0.32, C:0.21, G:0.09, T:0.39
Consensus pattern (81 bp):
TACCCTCGATTTACAAAATTACTAAAATACCCTCGATTTACAGAATTACTATTTTACCCTCGATT
TACAGAATTACTATTT
Found at i:28719904 original size:54 final size:54
Alignment explanation
Indices: 28719681--28720155 Score: 235
Period size: 54 Copynumber: 8.8 Consensus size: 54
28719671 CCAATTATTG
* * * * ** * * *
28719681 AAATACCCTCGACTTGTAAAATTACCAAAGTACCCCCGATTTACAGAATTACTG
1 AAATACCCTCGATTTATAAAATTACTAAAATACCCTTGGTTTACAAAATTACTA
*** * *** * * *
28719735 TTTTACCCTCGATTTATAGAATTACTATTTTACCTTTGATTTACAGAATTACTA
1 AAATACCCTCGATTTATAAAATTACTAAAATACCCTTGGTTTACAAAATTACTA
*** * *** * * *
28719789 TTTTACCCTCGATTTATAGAATTACTATTTTACCCTTGATTTACAGAATTACTG
1 AAATACCCTCGATTTATAAAATTACTAAAATACCCTTGGTTTACAAAATTACTA
*** * *
28719843 TTTTACCCTCGATTTACAAAATTACTAAAATACCCTTGGTTTACAAAATTACCA
1 AAATACCCTCGATTTATAAAATTACTAAAATACCCTTGGTTTACAAAATTACTA
* * * ** *
28719897 AAATACCCTCGA-TCAGTAAAATTACCAAAATACCC-TGGTCTGTAAAATTGCTA
1 AAATACCCTCGATTTA-TAAAATTACTAAAATACCCTTGGTTTACAAAATTACTA
* * * * * ** * *
28719950 AAATACCC-CTGGTTTGTAAAATTACCAAAATACCCCTAGTTTGTAAAGTTACCA
1 AAATACCCTC-GATTTATAAAATTACTAAAATACCCTTGGTTTACAAAATTACTA
* * ** *** *
28720004 AAATACCACTAG-TTTGTAAAATTACCGAAATACCCTCAATTT-CTAAAATTACCA
1 AAATACC-CTCGATTTATAAAATTACTAAAATACCCTTGGTTTAC-AAAATTACTA
* * * *
28720058 AAATACCCTTGATTTACAAAATTACAAAAATACCCTTGACTTT-CTAAAAATTA-TA
1 AAATACCCTCGATTTATAAAATTACTAAAATACCCTTG-GTTTAC--AAAATTACTA
* * * * *
28720113 GAAATACCATTGGTTTACAAAATTACTGAAATACCCTTGGTTT
1 -AAATACCCTCGATTTATAAAATTACTAAAATACCCTTGGTTT
28720156 GTAGATTTAC
Statistics
Matches: 344, Mismatches: 66, Indels: 21
0.80 0.15 0.05
Matches are distributed among these distances:
52 1 0.00
53 46 0.13
54 246 0.72
55 10 0.03
56 41 0.12
ACGTcount: A:0.37, C:0.21, G:0.09, T:0.34
Consensus pattern (54 bp):
AAATACCCTCGATTTATAAAATTACTAAAATACCCTTGGTTTACAAAATTACTA
Found at i:28719971 original size:80 final size:81
Alignment explanation
Indices: 28719860--28720204 Score: 252
Period size: 81 Copynumber: 4.2 Consensus size: 81
28719850 CTCGATTTAC
* * *
28719860 AAAATTACTAAAATACCCTTGGTTTACAAAATTACCAAAATACCCTCGA-TCAGTAAAATTACCA
1 AAAATTACTAAAATACCCCTGGTTTATAAAATTACCAAAATACCCTCGAGTTAGTAAAATTACCA
*
28719924 AAATACCCTGGTCTGT
66 AAATACCCTAGTCTGT
* * * * *
28719940 AAAATTGCTAAAATACCCCTGGTTTGTAAAATTACCAAAATACCC-CTAGTTTGTAAAGTTACCA
1 AAAATTACTAAAATACCCCTGGTTTATAAAATTACCAAAATACCCTCGAGTTAGTAAAATTACCA
*
28720004 AAATACCACTAGTTTGT
66 AAATACC-CTAGTCTGT
** ** * * * * *
28720021 AAAATTACCGAAATA-CCCTCAATTTCTAAAATTACCAAAATACCCTTGATTTA-CAAAATTACA
1 AAAATTACTAAAATACCCCT-GGTTTATAAAATTACCAAAATACCCTCGAGTTAGTAAAATTACC
* * *
28720084 AAAATACCCTTGACTTTCT
65 AAAATACCC-T-AGTCTGT
** * ** * * * *
28720103 AAAAATTA-TAGAAATACCATTGGTTTACAAAATTACTGAAATACCCTTG-GTTTGTAGATTTAC
1 -AAAATTACTA-AAATACCCCTGGTTTATAAAATTACCAAAATACCCTCGAGTTAGTAAAATTAC
* * **
28720166 CAAAACACCCTTGTAGGGT
64 CAAAATACCCTAGT-CTGT
* *
28720185 GAAATGACTAAAATACCCCT
1 AAAATTACTAAAATACCCCT
28720205 ATTAGGTAAA
Statistics
Matches: 202, Mismatches: 51, Indels: 23
0.73 0.18 0.08
Matches are distributed among these distances:
79 2 0.01
80 65 0.32
81 71 0.35
82 14 0.07
83 48 0.24
84 2 0.01
ACGTcount: A:0.40, C:0.21, G:0.10, T:0.30
Consensus pattern (81 bp):
AAAATTACTAAAATACCCCTGGTTTATAAAATTACCAAAATACCCTCGAGTTAGTAAAATTACCA
AAATACCCTAGTCTGT
Found at i:28720086 original size:107 final size:107
Alignment explanation
Indices: 28719846--28720092 Score: 271
Period size: 107 Copynumber: 2.3 Consensus size: 107
28719836 ATTACTGTTT
* * * * *
28719846 TACCCTCGATTTACAAAATTACTAAAATACCCTTGGTTTACAAAATTACCAAAATACCCTCGATC
1 TACCCTTGATTTACAAAATTACAAAAATACCCCTAGTTTACAAAATTACCAAAATACCCTAGATC
** * * *
28719911 AGTAAAATTACCAAAATACCCTGGTCTGTAAAATTGCTAAAA
66 AGTAAAATTACCAAAATACCCTAATCTCTAAAATTACCAAAA
* * ** * ** *
28719953 TACCCCTGGTTTGTAAAATTACCAAAATACCCCTAGTTTGTAAAGTTACCAAAATACCACTAG-T
1 TACCCTTGATTTACAAAATTACAAAAATACCCCTAGTTTACAAAATTACCAAAATACC-CTAGAT
** * *
28720017 TTGTAAAATTACCGAAATACCCTCAATTTCTAAAATTACCAAAA
65 CAGTAAAATTACCAAAATACCCT-AATCTCTAAAATTACCAAAA
28720061 TACCCTTGATTTACAAAATTACAAAAATACCC
1 TACCCTTGATTTACAAAATTACAAAAATACCC
28720093 TTGACTTTCT
Statistics
Matches: 112, Mismatches: 26, Indels: 3
0.79 0.18 0.02
Matches are distributed among these distances:
107 68 0.61
108 44 0.39
ACGTcount: A:0.41, C:0.23, G:0.08, T:0.29
Consensus pattern (107 bp):
TACCCTTGATTTACAAAATTACAAAAATACCCCTAGTTTACAAAATTACCAAAATACCCTAGATC
AGTAAAATTACCAAAATACCCTAATCTCTAAAATTACCAAAA
Found at i:28720088 original size:81 final size:80
Alignment explanation
Indices: 28719860--28720093 Score: 224
Period size: 80 Copynumber: 2.9 Consensus size: 80
28719850 CTCGATTTAC
* * ** * *
28719860 AAAATTACTAAAATACCCTTGGTTTAC-AAAATTACCAAAATACCCTCGA-TCAGTAAAATTACC
1 AAAATTACCAAAATACCCCTAATTT-CTAAAATTACCAAAATACCCTTGATTTA-TAAAATTACC
*
28719923 AAAATACCCTGGTCTGT
64 AAAATACCCTAGTCTGT
* * ** * * * *
28719940 AAAATTGCTAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCCT-AGTTTGTAAAGTTACCA
1 AAAATTACCAAAATACCCCTAATTTCTAAAATTACCAAAATACCCTTGA-TTTATAAAATTACCA
*
28720004 AAATACCACTAGTTTGT
65 AAATACC-CTAGTCTGT
* * *
28720021 AAAATTACCGAAATA-CCCTCAATTTCTAAAATTACCAAAATACCCTTGATTTACAAAATTACAA
1 AAAATTACCAAAATACCCCT-AATTTCTAAAATTACCAAAATACCCTTGATTTATAAAATTACCA
28720085 AAATACCCT
65 AAATACCCT
28720094 TGACTTTCTA
Statistics
Matches: 127, Mismatches: 21, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
79 1 0.01
80 64 0.50
81 61 0.48
82 1 0.01
ACGTcount: A:0.42, C:0.22, G:0.08, T:0.29
Consensus pattern (80 bp):
AAAATTACCAAAATACCCCTAATTTCTAAAATTACCAAAATACCCTTGATTTATAAAATTACCAA
AATACCCTAGTCTGT
Found at i:28720152 original size:27 final size:27
Alignment explanation
Indices: 28719846--28720178 Score: 210
Period size: 27 Copynumber: 12.3 Consensus size: 27
28719836 ATTACTGTTT
* * *
28719846 TACCCTCGATTTACAAAATTACTAAAA
1 TACCCTTGGTTTACAAAATTACCAAAA
28719873 TACCCTTGGTTTACAAAATTACCAAAA
1 TACCCTTGGTTTACAAAATTACCAAAA
* * * *
28719900 TACCC-TCGATCAGTAAAATTACCAAAA
1 TACCCTTGGTTTA-CAAAATTACCAAAA
* ** * *
28719927 TACCC-TGGTCTGTAAAATTGCTAAAA
1 TACCCTTGGTTTACAAAATTACCAAAA
* **
28719953 TACCCCTGGTTTGTAAAATTACCAAAA
1 TACCCTTGGTTTACAAAATTACCAAAA
* * ** *
28719980 TACCCCTAGTTTGTAAAGTTACCAAAA
1 TACCCTTGGTTTACAAAATTACCAAAA
* ** *
28720007 TACCAC-TAGTTTGTAAAATTACCGAAA
1 TACC-CTTGGTTTACAAAATTACCAAAA
***
28720034 TACCCTCAATTT-CTAAAATTACCAAAA
1 TACCCTTGGTTTAC-AAAATTACCAAAA
* *
28720061 TACCCTTGATTTACAAAATTACAAAAA
1 TACCCTTGGTTTACAAAATTACCAAAA
* *
28720088 TACCCTTGACTTT-CTAAAAATTA-TAGAAA
1 TACCCTTG-GTTTAC--AAAATTACCA-AAA
* **
28720117 TACCATTGGTTTACAAAATTACTGAAA
1 TACCCTTGGTTTACAAAATTACCAAAA
** * *
28720144 TACCCTTGGTTTGTAGATTTACCAAAA
1 TACCCTTGGTTTACAAAATTACCAAAA
*
28720171 CACCCTTG
1 TACCCTTG
28720179 TAGGGTGAAA
Statistics
Matches: 253, Mismatches: 41, Indels: 24
0.80 0.13 0.08
Matches are distributed among these distances:
26 22 0.09
27 203 0.80
28 10 0.04
29 18 0.07
ACGTcount: A:0.40, C:0.21, G:0.09, T:0.30
Consensus pattern (27 bp):
TACCCTTGGTTTACAAAATTACCAAAA
Done.