Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold565
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: 391512
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
File 2 of 3
Found at i:195698 original size:13 final size:13
Alignment explanation
Indices: 195680--195704 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
195670 ATCACTTAAA
195680 TGTATCGATACAT
1 TGTATCGATACAT
195693 TGTATCGATACA
1 TGTATCGATACA
195705 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:195757 original size:52 final size:51
Alignment explanation
Indices: 195693--195841 Score: 244
Period size: 52 Copynumber: 2.9 Consensus size: 51
195683 ATCGATACAT
**
195693 TGTATCGATACACTGATCTTTGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACT-ATCAATGTATCGATACATGCAGGCAAATTTGCCCAGA
*
195745 TGTATCGATACACTATAAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACTAT-CAATGTATCGATACATGCAGGCAAATTTGCCCAGA
195797 TGTATCGATACACTATTCAATGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACACTA-TCAATGTATCGATACATGCAGGCAAATTT
195842 TCATATTTCG
Statistics
Matches: 91, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
51 2 0.02
52 88 0.97
53 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.30
Consensus pattern (51 bp):
TGTATCGATACACTATCAATGTATCGATACATGCAGGCAAATTTGCCCAGA
Found at i:199801 original size:158 final size:158
Alignment explanation
Indices: 199502--199826 Score: 436
Period size: 158 Copynumber: 2.1 Consensus size: 158
199492 AAAATTAATA
* * * *
199502 ATATTAAACATATTTTGACATATTAAACAAGCATGCCATAAAAAATTAATAATATCATAAATCTT
1 ATATTAAACATATTTTAACATATTAAACAAGCATGCCATAAAAAACTAATAATATCAGAAATCTC
* ** * **
199567 AAACAATATCAATCGGTATTTAAATGAGCATTTCATATTAAACAAAAAATATAATCCAAAACAAC
66 AAACAACATCAAGAGGTATCTAAACAAGCATTTCATATTAAACAAAAAATATAATCCAAAACAAC
199632 GCCAAACTAAG-TTTTTTTATTGTTGAC
131 GCCAAACTAAGTTTTTTTTATTGTTGAC
* *
199659 ATATTAAATATATTTTAACTTATTAAACAAGCATGCCATAAAAAAACTAATAATATCAGAAATCT
1 ATATTAAACATATTTTAACATATTAAACAAGCATGCCAT-AAAAAACTAATAATATCAGAAATCT
* * * *
199724 CAAACAACATCAAGAGTTATCTAAACAAGCATTTTATATTAAACAAAAAATATAATCTAAAACCA
65 CAAACAACATCAAGAGGTATCTAAACAAGCATTTCATATTAAACAAAAAATATAATCCAAAACAA
** * * *
199789 CGTTAAATTAAGTTTTTTTTTTTTTTTGAC
130 CGCCAAACTAAG-TTTTTTTTATTGTTGAC
199819 ATATTAAA
1 ATATTAAA
199827 AAAGTATGCC
Statistics
Matches: 144, Mismatches: 21, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
157 36 0.25
158 86 0.60
160 22 0.15
ACGTcount: A:0.47, C:0.13, G:0.06, T:0.34
Consensus pattern (158 bp):
ATATTAAACATATTTTAACATATTAAACAAGCATGCCATAAAAAACTAATAATATCAGAAATCTC
AAACAACATCAAGAGGTATCTAAACAAGCATTTCATATTAAACAAAAAATATAATCCAAAACAAC
GCCAAACTAAGTTTTTTTTATTGTTGAC
Found at i:199852 original size:140 final size:141
Alignment explanation
Indices: 199679--199953 Score: 383
Period size: 140 Copynumber: 2.0 Consensus size: 141
199669 TATTTTAACT
* **
199679 TATTAAACAAGCATGCCATAAAAAAACTAATAATATCAGAAATCTCAAACAACATCAAGAGTTAT
1 TATTAAAAAAGCATGCCATAAAAAAACTAATAATATCAGAAATCTCAAACAACATCAAGAGACAT
* * * *
199744 CTAAACAAGCATTTTATATTAAACAAAAAATATAA-TCTAAAACCACGTTAAATTAAGTTTTTTT
66 CTAAACAAGCATTTCATATTAAACAAAAAATATAACTC-AAAACCACGTTAAACTAAATCTTTTT
*
199808 TTTTTTTTGACA
130 ATTTTTTTGACA
* * * * * *
199820 TATTAAAAAAGTATGCCAT-AAAAAATTAATAATATCATAAATTTTAAACAATATCAAGAGACAT
1 TATTAAAAAAGCATGCCATAAAAAAACTAATAATATCAGAAATCTCAAACAACATCAAGAGACAT
* *
199884 CTAAACGAGCATTTCATATTAAGCAAAAAATATAACTCAAAACCACGTTAAACTAAATCTTTTTA
66 CTAAACAAGCATTTCATATTAAACAAAAAATATAACTCAAAACCACGTTAAACTAAATCTTTTTA
199949 TTTTT
131 TTTTT
199954 GATATATTAA
Statistics
Matches: 117, Mismatches: 16, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
140 98 0.84
141 19 0.16
ACGTcount: A:0.48, C:0.14, G:0.06, T:0.32
Consensus pattern (141 bp):
TATTAAAAAAGCATGCCATAAAAAAACTAATAATATCAGAAATCTCAAACAACATCAAGAGACAT
CTAAACAAGCATTTCATATTAAACAAAAAATATAACTCAAAACCACGTTAAACTAAATCTTTTTA
TTTTTTTGACA
Found at i:200047 original size:158 final size:157
Alignment explanation
Indices: 199812--200111 Score: 358
Period size: 158 Copynumber: 1.9 Consensus size: 157
199802 TTTTTTTTTT
* * * * *
199812 TTTTGACATATTAAAAAAGTATGCCATAAAAAATTAATAATATCATAAATTTTAAACAATATCAA
1 TTTTGACATATTAAAAAAGTATGCCATAAAAAACTAATAATATCAAAAATCTCAAACAACATCAA
* **
199877 GAGACATCTAAACGAGCATTTCATATTAAGCA-AAAAATAT-AA-CTCAAAACCACGTTAAACTA
66 GAGACATCTAAACAAGCATTTCATATTAA--ATAAAAAT-TCAACCT-AAAACCACGCAAAACTA
199939 AATC-TTTTTATTTTTGATATATTAAATATA
127 AATCTTTTTTATTTTTGATATATTAAATATA
* ** *
199969 TTTTGATATATTAAGTAAGTATGCAGCA-AAAAAACTAATAATATCAAAAATCTCAAACGACATC
1 TTTTGACATATTAAAAAAGTATGC--CATAAAAAACTAATAATATCAAAAATCTCAAACAACATC
** * * *
200033 AAGAGTTATTTAAACAAGTATTTCATATTAAATAAAAATTCAACCTAAAACCACGCAAAACTAAG
64 AAGAGACATCTAAACAAGCATTTCATATTAAATAAAAATTCAACCTAAAACCACGCAAAACTAAA
200098 TCTTTTTTATTTTT
129 TCTTTTTTATTTTT
200112 CTGGTTCAAT
Statistics
Matches: 120, Mismatches: 17, Indels: 11
0.81 0.11 0.07
Matches are distributed among these distances:
156 2 0.02
157 47 0.39
158 69 0.57
159 2 0.02
ACGTcount: A:0.47, C:0.13, G:0.07, T:0.33
Consensus pattern (157 bp):
TTTTGACATATTAAAAAAGTATGCCATAAAAAACTAATAATATCAAAAATCTCAAACAACATCAA
GAGACATCTAAACAAGCATTTCATATTAAATAAAAATTCAACCTAAAACCACGCAAAACTAAATC
TTTTTTATTTTTGATATATTAAATATA
Found at i:200050 original size:298 final size:297
Alignment explanation
Indices: 199514--200111 Score: 817
Period size: 298 Copynumber: 2.0 Consensus size: 297
199504 ATTAAACATA
*
199514 TTTTGACATATTAAACAAGCATGCCATAAAAAATTAATAATATCATAAATCTTAAACAATATCAA
1 TTTTGACATATTAAAAAAGCATGCCATAAAAAATTAATAATATCATAAATCTTAAACAATATCAA
** ** * * *
199579 TCGGTATTTAAATGAGCATTTCATATTAAACAAAAAATATAATCCAAAACAACGCCAAACTAAGT
66 GAGACATCTAAACGAGCATTTCATATTAAACAAAAAATATAATCCAAAACAACGCCAAACTAAAT
* *
199644 TTTTTTATTGTTGACATATTAAATATATTTTAACTTATTAAACAAGCATGCCATAAAAAAACTAA
131 CTTTTTATTGTTGACATATTAAATATATTTTAACTTATTAAACAAGCATGCCACAAAAAAACTAA
* *
199709 TAATATCAGAAATCTCAAACAACATCAAGAGTTATCTAAACAAGCATTTTATATTAAACAAAAAA
196 TAATATCAAAAATCTCAAACAACATCAAGAGTTATCTAAACAAGCATTTCATATTAAA-AAAAAA
* ** * * *
199774 TAT-AATCTAAAACCACGTTAAATTAAGTTTTTTTTTTT
260 T-TCAACCTAAAACCACGCAAAACTAAGTCTTTTTTATT
* *
199812 TTTTGACATATTAAAAAAGTATGCCATAAAAAATTAATAATATCATAAATTTTAAACAATATCAA
1 TTTTGACATATTAAAAAAGCATGCCATAAAAAATTAATAATATCATAAATCTTAAACAATATCAA
* * **
199877 GAGACATCTAAACGAGCATTTCATATTAAGCAAAAAATATAA-CTCAAAACCACGTTAAACTAAA
66 GAGACATCTAAACGAGCATTTCATATTAAACAAAAAATATAATC-CAAAACAACGCCAAACTAAA
* * * ** *
199941 TCTTTTTATTTTTGATATATTAAATATATTTTGA-TATATTAAGTAAGTATG-CAGCAAAAAAAC
130 TCTTTTTATTGTTGACATATTAAATATATTTTAACT-TATTAAACAAGCATGCCA-CAAAAAAAC
* * * *
200004 TAATAATATCAAAAATCTCAAACGACATCAAGAGTTATTTAAACAAGTATTTCATATTAAATAAA
193 TAATAATATCAAAAATCTCAAACAACATCAAGAGTTATCTAAACAAGCATTTCATATTAAAAAAA
200069 AATTCAACCTAAAACCACGCAAAACTAAGTCTTTTTTATT
258 AATTCAACCTAAAACCACGCAAAACTAAGTCTTTTTTATT
200109 TTT
1 TTT
200112 CTGGTTCAAT
Statistics
Matches: 262, Mismatches: 34, Indels: 9
0.86 0.11 0.03
Matches are distributed among these distances:
296 1 0.00
297 42 0.16
298 219 0.84
ACGTcount: A:0.47, C:0.13, G:0.07, T:0.33
Consensus pattern (297 bp):
TTTTGACATATTAAAAAAGCATGCCATAAAAAATTAATAATATCATAAATCTTAAACAATATCAA
GAGACATCTAAACGAGCATTTCATATTAAACAAAAAATATAATCCAAAACAACGCCAAACTAAAT
CTTTTTATTGTTGACATATTAAATATATTTTAACTTATTAAACAAGCATGCCACAAAAAAACTAA
TAATATCAAAAATCTCAAACAACATCAAGAGTTATCTAAACAAGCATTTCATATTAAAAAAAAAT
TCAACCTAAAACCACGCAAAACTAAGTCTTTTTTATT
Found at i:200231 original size:7 final size:7
Alignment explanation
Indices: 200221--200293 Score: 55
Period size: 7 Copynumber: 10.7 Consensus size: 7
200211 AGGCCACTCA
200221 CTTTTCT
1 CTTTTCT
200228 CTTTT-T
1 CTTTTCT
200234 -TTTTCTT
1 CTTTTC-T
* *
200241 TTTTTTT
1 CTTTTCT
200248 CTTTTCT
1 CTTTTCT
200255 CTTTTCT
1 CTTTTCT
200262 C-TTTC-
1 CTTTTCT
200267 CTTCTTCT
1 CTT-TTCT
*
200275 TTTTTCT
1 CTTTTCT
* *
200282 TTTTTTT
1 CTTTTCT
200289 CTTTT
1 CTTTT
200294 TTTCCTTTTT
Statistics
Matches: 54, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
5 5 0.09
6 6 0.11
7 37 0.69
8 6 0.11
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (7 bp):
CTTTTCT
Found at i:200240 original size:10 final size:10
Alignment explanation
Indices: 200222--200312 Score: 87
Period size: 10 Copynumber: 8.9 Consensus size: 10
200212 GGCCACTCAC
*
200222 TTTTCTCTTT
1 TTTTTTCTTT
200232 TTTTTTCTTT
1 TTTTTTCTTT
200242 TTTTTTCTTT
1 TTTTTTCTTT
*
200252 TCTCTTTTCTCT
1 T-T-TTTTCTTT
** *
200264 TTCCTTCTTC
1 TTTTTTCTTT
200274 TTTTTTC-TT
1 TTTTTTCTTT
200283 TTTTTTCTTT
1 TTTTTTCTTT
200293 TTTTCCTT-TTT
1 TTTT--TTCTTT
200304 TTTTTTCTT
1 TTTTTTCTT
200313 CAAAGTTCAC
Statistics
Matches: 66, Mismatches: 9, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
9 10 0.15
10 37 0.56
11 9 0.14
12 10 0.15
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (10 bp):
TTTTTTCTTT
Found at i:200259 original size:27 final size:27
Alignment explanation
Indices: 200221--200307 Score: 86
Period size: 32 Copynumber: 3.0 Consensus size: 27
200211 AGGCCACTCA
200221 CTTTTCTCTTTTTTTTTCTTTTTTTTT
1 CTTTTCTCTTTTTTTTTCTTTTTTTTT
*
200248 CTTTTCTCTTTTCTCTTTCCTTCTTCTTTTTT
1 CTTTTCTC-TTT-T-TTT--TTCTTTTTTTTT
*
200280 CTTTT-TTTTCTTTTTTTCCTTTTTTTTT
1 CTTTTCTCTT-TTTTTTT-CTTTTTTTTT
200308 TTCTTCAAAG
Statistics
Matches: 50, Mismatches: 3, Indels: 13
0.76 0.05 0.20
Matches are distributed among these distances:
27 10 0.20
28 12 0.24
29 4 0.08
30 6 0.12
31 2 0.04
32 16 0.32
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (27 bp):
CTTTTCTCTTTTTTTTTCTTTTTTTTT
Found at i:200294 original size:7 final size:7
Alignment explanation
Indices: 200232--200312 Score: 58
Period size: 7 Copynumber: 11.3 Consensus size: 7
200222 TTTTCTCTTT
200232 TTTTTTC
1 TTTTTTC
*
200239 TTTTTTT
1 TTTTTTC
200246 TTCTTTTC
1 TT-TTTTC
*
200254 TCTTTTC
1 TTTTTTC
*
200261 -TCTTTC
1 TTTTTTC
* *
200267 CTTCTTC
1 TTTTTTC
200274 TTTTTTC
1 TTTTTTC
200281 TTTTTTTTC
1 --TTTTTTC
200290 TTTTTTTC
1 -TTTTTTC
*
200298 CTTTTT-
1 TTTTTTC
200304 TTTTTTC
1 TTTTTTC
200311 TT
1 TT
200313 CAAAGTTCAC
Statistics
Matches: 58, Mismatches: 11, Indels: 10
0.73 0.14 0.13
Matches are distributed among these distances:
6 9 0.16
7 29 0.50
8 13 0.22
9 7 0.12
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (7 bp):
TTTTTTC
Found at i:201236 original size:23 final size:22
Alignment explanation
Indices: 201189--201237 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
201179 AATATTTCTT
*
201189 AAAAAATATATTTTAAGAATTA
1 AAAAAATATATTTTAAGAATAA
*
201211 AAAAAATATTATTATT-ATAATAA
1 AAAAAATA-TATT-TTAAGAATAA
201234 AAAA
1 AAAA
201238 CTAATTATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 8 0.35
23 13 0.57
24 2 0.09
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (22 bp):
AAAAAATATATTTTAAGAATAA
Found at i:202201 original size:35 final size:35
Alignment explanation
Indices: 202083--202277 Score: 149
Period size: 35 Copynumber: 5.7 Consensus size: 35
202073 TATTAAAAAC
** *
202083 ATATTTATATAAAATAATCAAATATAAATAAAATT
1 ATATTTATATTGAATAATAAAATATAAATAAAATT
* *
202118 ATAATTATATTGAATAATAATA-AT-AAT-AAATT
1 ATATTTATATTGAATAATAAAATATAAATAAAATT
* *
202150 ATATTCATATTAAATAATAAAATATAAATAAAATT
1 ATATTTATATTGAATAATAAAATATAAATAAAATT
* * *
202185 ATATTTATGTTGAATAATACTTAAA-AT-TATTAAATT
1 ATATTTATATTGAATAATA---AAATATAAATAAAATT
* * * * *
202221 CTATTTATATT-AAAAAT-AAAT-T-ATTTAAACT
1 ATATTTATATTGAATAATAAAATATAAATAAAATT
202252 ATATTTATATT-AAGTAATAAAATATA
1 ATATTTATATTGAA-TAATAAAATATA
202278 TATTAAAAAC
Statistics
Matches: 127, Mismatches: 22, Indels: 22
0.74 0.13 0.13
Matches are distributed among these distances:
31 22 0.17
32 26 0.20
33 9 0.07
34 6 0.05
35 43 0.34
36 16 0.13
37 2 0.02
38 3 0.02
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.42
Consensus pattern (35 bp):
ATATTTATATTGAATAATAAAATATAAATAAAATT
Found at i:202842 original size:14 final size:15
Alignment explanation
Indices: 202823--202851 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
202813 TTTATTAAAA
202823 ATTTATATA-TGTAT
1 ATTTATATATTGTAT
202837 ATTTATATATTGTAT
1 ATTTATATATTGTAT
202852 TATAGTAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (15 bp):
ATTTATATATTGTAT
Found at i:203352 original size:17 final size:18
Alignment explanation
Indices: 203330--203363 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
203320 AATACATTTC
203330 ATCAATAAAATG-CTTTT
1 ATCAATAAAATGACTTTT
203347 ATCAATAAAATGACTTT
1 ATCAATAAAATGACTTT
203364 GTTTTTGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.44, C:0.12, G:0.06, T:0.38
Consensus pattern (18 bp):
ATCAATAAAATGACTTTT
Found at i:207134 original size:73 final size:73
Alignment explanation
Indices: 207034--207308 Score: 245
Period size: 73 Copynumber: 3.7 Consensus size: 73
207024 AATAGATATG
* * *
207034 TTTAGACACTGAAAGTTCTCATATGATCCTTA-ACTTAATTTTAAGGTGCTATTTTTGAAACCTT
1 TTTAGACA-TAAAAGTTCTCACATGAT-CTTAGACTTAATTTTAAGGTACTATTTTTGAAACCTT
207098 AAT-AGACATA
64 AATGA-ACATA
* * * * ** *
207108 TTTAGACATAAAAGTTCTCATATGATCTTAGGACTTAGTTTTAAGTTGC-ATTACTGATACCTTA
1 TTTAGACATAAAAGTTCTCACATGATCTTA-GACTTAATTTTAAGGTACTATTTTTGAAACCTTA
207172 ATGAACATA
65 ATGAACATA
* * * ** *
207181 CTTCGACATGAAAA-TTCTCACATGATCTTAGACTTAGTTTTAATCTACTATTATTGAGATAACC
1 TTTAGACAT-AAAAGTTCTCACATGATCTTAGACTTAATTTTAAGGTACTATT-TT-TGA-AACC
*
207245 TTAATGAACATG
62 TTAATGAACATA
* * * *
207257 TTTCGACATGAAAGTTCTCACATTAT-TCTAGACTAAATTTTAAGGTACTATT
1 TTTAGACATAAAAGTTCTCACATGATCT-TAGACTTAATTTTAAGGTACTATT
207309 ACGTAAAAAA
Statistics
Matches: 167, Mismatches: 24, Indels: 18
0.80 0.11 0.09
Matches are distributed among these distances:
72 19 0.11
73 61 0.37
74 28 0.17
75 6 0.04
76 53 0.32
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.39
Consensus pattern (73 bp):
TTTAGACATAAAAGTTCTCACATGATCTTAGACTTAATTTTAAGGTACTATTTTTGAAACCTTAA
TGAACATA
Found at i:207289 original size:76 final size:75
Alignment explanation
Indices: 207031--207568 Score: 278
Period size: 76 Copynumber: 7.2 Consensus size: 75
207021 CTTAATAGAT
* * * * ** * **
207031 ATGTTTAGACACTGAAAGTTCTCATATGATCCTTA-ACTTAATTTTAAGGTGCTATTTTTG-A-A
1 ATGTTTCGACA-TGAAAGTTCTCACATGATTC-TAGACTTAGTTTTAATATACTATTACTGAATA
207093 ACCTTAAT-AGAC
64 ACCTTAATGA-AC
* * * * *
207105 ATATTTAGACATAAAAGTTCTCATATGA-TCTTAGGACTTAGTTTTAAGT-TGC-ATTACTG-AT
1 ATGTTTCGACATGAAAGTTCTCACATGATTC-TA-GACTTAGTTTTAA-TATACTATTACTGAAT
207166 -ACCTTAATGAAC
63 AACCTTAATGAAC
** * * *
207178 ATACTTCGACATGAAAATTCTCACATGA-TCTTAGACTTAGTTTTAATCTACTATTATTGAGATA
1 ATGTTTCGACATGAAAGTTCTCACATGATTC-TAGACTTAGTTTTAATATACTATTACTGA-ATA
207242 ACCTTAATGAAC
64 ACCTTAATGAAC
* * * ** * *
207254 ATGTTTCGACATGAAAGTTCTCACATTATTCTAGACTAAATTTTAAGGTACTATTACGTAAAAAA
1 ATGTTTCGACATGAAAGTTCTCACATGATTCTAGACTTAGTTTTAATATACTATTAC-TGAATAA
** * *
207319 TTTTAATGGAT
65 CCTTAATGAAC
** * * * * * *
207330 ATGTTTTAACATAAAAGTTCTCACATAATCCTAGACTTGGTTTTAAGATACTACTACCTGAATAA
1 ATGTTTCGACATGAAAGTTCTCACATGATTCTAGACTTAGTTTTAATATACTATTA-CTGAATAA
* *
207395 -TTGTAATAAAC
65 CCT-TAATGAAC
* * * * * * * *
207406 ATGTTTCGAGATGAAGGTTCTTATATGATCCCAGACTTTGTTTT-ATGATACTATTATCTTAA-A
1 ATGTTTCGACATGAAAGTTCTCACATGATTCTAGACTTAGTTTTAAT-ATACTATTA-CTGAATA
*
207469 A-CTTAATGGAC
64 ACCTTAATGAAC
* * * * * *** **
207480 ATGTTTCAACATGAAAGTTCACACATCG-TCCTAAACTTGGTTTTAAGGCACTATTACCAAAATA
1 ATGTTTCGACATGAAAGTTCTCACAT-GATTCTAGACTTAGTTTTAATATACTATTA-CTGAATA
* *
207544 ACCTTAATGGAT
64 ACCTTAATGAAC
*
207556 ATGTTTCAACATG
1 ATGTTTCGACATG
207569 GAAATCCCTA
Statistics
Matches: 368, Mismatches: 77, Indels: 36
0.77 0.16 0.07
Matches are distributed among these distances:
71 1 0.00
72 19 0.05
73 66 0.18
74 74 0.20
75 12 0.03
76 191 0.52
77 5 0.01
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.37
Consensus pattern (75 bp):
ATGTTTCGACATGAAAGTTCTCACATGATTCTAGACTTAGTTTTAATATACTATTACTGAATAAC
CTTAATGAAC
Found at i:207382 original size:152 final size:149
Alignment explanation
Indices: 207168--207568 Score: 340
Period size: 152 Copynumber: 2.7 Consensus size: 149
207158 TTACTGATAC
* ** * * * * **
207168 CTTAATGAACATACTTCGACATGAAAA-TTCTCACATGATCTTAGACTTAGTTTTAATCTACTAT
1 CTTAATGGACATGTTTCAACAT-AAAAGTTCTCACATAATCCTAGACTTGGTTTTAAGATACTAT
* * * *
207232 TATTGAGATAACCTTAATGAACATGTTTCGACATGAAAGTTCTCACATTATTCTAGACTAAATTT
65 TACTGA-ATAACCTTAATGAACATGTTTCGACATGAAAGTTCTCACATGATCCCAGACTAAATTT
*
207297 TAAGGTACTATTA-CGTAAAAAA
129 TAAGATACTATTATC-T-AAAAA
* * * *
207319 TTTTAATGGATATGTTTTAACATAAAAGTTCTCACATAATCCTAGACTTGGTTTTAAGATACTAC
1 -CTTAATGGACATGTTTCAACATAAAAGTTCTCACATAATCCTAGACTTGGTTTTAAGATACTAT
* * * * * * ***
207384 TACCTGAATAA-TTGTAATAAACATGTTTCGAGATGAAGGTTCTTATATGATCCCAGACTTTGTT
65 TA-CTGAATAACCT-TAATGAACATGTTTCGACATGAAAGTTCTCACATGATCCCAGACTAAATT
* *
207448 TTATGATACTATTATCTTAAAA
128 TTAAGATACTATTATCTAAAAA
* * ** * **
207470 CTTAATGGACATGTTTCAACATGAAAGTTCACACATCGTCCTAAACTTGGTTTTAAGGCACTATT
1 CTTAATGGACATGTTTCAACATAAAAGTTCTCACATAATCCTAGACTTGGTTTTAAGATACTATT
** * * *
207535 ACCAAAATAACCTTAATGGATATGTTTCAACATG
66 A-CTGAATAACCTTAATGAACATGTTTCGACATG
207569 GAAATCCCTA
Statistics
Matches: 196, Mismatches: 48, Indels: 12
0.77 0.19 0.05
Matches are distributed among these distances:
150 78 0.40
151 10 0.05
152 104 0.53
153 4 0.02
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.36
Consensus pattern (149 bp):
CTTAATGGACATGTTTCAACATAAAAGTTCTCACATAATCCTAGACTTGGTTTTAAGATACTATT
ACTGAATAACCTTAATGAACATGTTTCGACATGAAAGTTCTCACATGATCCCAGACTAAATTTTA
AGATACTATTATCTAAAAA
Found at i:208547 original size:10 final size:10
Alignment explanation
Indices: 208531--208566 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
208521 CACTCTATTC
208531 CTTTTTTTTT
1 CTTTTTTTTT
* *
208541 ATTTTTTTCT
1 CTTTTTTTTT
208551 CTTTTTTTTT
1 CTTTTTTTTT
208561 CTTTTT
1 CTTTTT
208567 AGTTCCTCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.03, C:0.11, G:0.00, T:0.86
Consensus pattern (10 bp):
CTTTTTTTTT
Found at i:208712 original size:49 final size:49
Alignment explanation
Indices: 208640--208742 Score: 188
Period size: 49 Copynumber: 2.1 Consensus size: 49
208630 GAAACCCTTT
* *
208640 TTGCTAATCCCTTTATATGTATATCCTCCATTTGACACCTCATGTAAGC
1 TTGCTAATCCCTTTATATGTATATCCTCCATTTGACACCTCATGCAACC
208689 TTGCTAATCCCTTTATATGTATATCCTCCATTTGACACCTCATGCAACC
1 TTGCTAATCCCTTTATATGTATATCCTCCATTTGACACCTCATGCAACC
208738 TTGCT
1 TTGCT
208743 TGTAAGTAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 52 1.00
ACGTcount: A:0.23, C:0.28, G:0.10, T:0.39
Consensus pattern (49 bp):
TTGCTAATCCCTTTATATGTATATCCTCCATTTGACACCTCATGCAACC
Found at i:209579 original size:25 final size:23
Alignment explanation
Indices: 209521--209621 Score: 82
Period size: 25 Copynumber: 4.1 Consensus size: 23
209511 AGATAACAAG
*
209521 AAATAAAGATAAAATAAAGAAAACTA
1 AAATAAA-ATAAAATAAAGATAA--A
209547 AAAT-AAATCAAAATAAGAGATAAA
1 AAATAAAAT-AAAATAA-AGATAAA
209571 AAATAAAATATAGAATAAATG-TAAA
1 AAATAAAATA-A-AATAAA-GATAAA
*
209596 AAATAAAATAAAA-AAATATTAAA
1 AAATAAAATAAAATAAAGA-TAAA
209619 AAA
1 AAA
209622 ATAATATGGG
Statistics
Matches: 65, Mismatches: 2, Indels: 19
0.76 0.02 0.22
Matches are distributed among these distances:
22 3 0.05
23 9 0.14
24 9 0.14
25 29 0.45
26 15 0.23
ACGTcount: A:0.73, C:0.02, G:0.06, T:0.19
Consensus pattern (23 bp):
AAATAAAATAAAATAAAGATAAA
Found at i:209580 original size:19 final size:20
Alignment explanation
Indices: 209551--209589 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
209541 AAACTAAAAT
209551 AAATCAAAATA-AGAGATAAA
1 AAATCAAAATATAGA-ATAAA
209571 AAAT-AAAATATAGAATAAA
1 AAATCAAAATATAGAATAAA
209590 TGTAAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.72, C:0.03, G:0.08, T:0.18
Consensus pattern (20 bp):
AAATCAAAATATAGAATAAA
Found at i:209607 original size:12 final size:13
Alignment explanation
Indices: 209556--209610 Score: 53
Period size: 12 Copynumber: 4.3 Consensus size: 13
209546 AAAATAAATC
209556 AAAATAAGAGATAA
1 AAAATAA-AGATAA
*
209570 AAAATAAA-ATAT
1 AAAATAAAGATAA
*
209582 AGAATAAATG-TAA
1 AAAATAAA-GATAA
209595 AAAATAAA-ATAA
1 AAAATAAAGATAA
209607 AAAA
1 AAAA
209611 ATATTAAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
12 17 0.50
13 10 0.29
14 7 0.21
ACGTcount: A:0.75, C:0.00, G:0.07, T:0.18
Consensus pattern (13 bp):
AAAATAAAGATAA
Found at i:209780 original size:28 final size:29
Alignment explanation
Indices: 209747--209804 Score: 109
Period size: 28 Copynumber: 2.0 Consensus size: 29
209737 AGAAAAAGGC
209747 TTATAAATAATTGACAAGCCTAAA-AAAT
1 TTATAAATAATTGACAAGCCTAAATAAAT
209775 TTATAAATAATTGACAAGCCTAAATAAAT
1 TTATAAATAATTGACAAGCCTAAATAAAT
209804 T
1 T
209805 AAAACTTATC
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 24 0.83
29 5 0.17
ACGTcount: A:0.52, C:0.10, G:0.07, T:0.31
Consensus pattern (29 bp):
TTATAAATAATTGACAAGCCTAAATAAAT
Found at i:215540 original size:20 final size:18
Alignment explanation
Indices: 215506--215542 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
215496 TCAGTTAATG
215506 AATTTATAAAAAATAAAT
1 AATTTATAAAAAATAAAT
215524 AATTTAATAATAAAATAAA
1 AATTT-ATAA-AAAATAAA
215543 GACAGTAAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 4 0.24
20 8 0.47
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
AATTTATAAAAAATAAAT
Found at i:215628 original size:21 final size:22
Alignment explanation
Indices: 215604--215658 Score: 69
Period size: 21 Copynumber: 2.5 Consensus size: 22
215594 TAATAACTTT
215604 TTAAAAACTATCC-ACTTATTC-
1 TTAAAAACTATCCTA-TTATTCA
* *
215625 TTAAGAATTATCCTATTATTCA
1 TTAAAAACTATCCTATTATTCA
215647 TTAAAAACTATC
1 TTAAAAACTATC
215659 ATATATATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
21 17 0.61
22 11 0.39
ACGTcount: A:0.40, C:0.18, G:0.02, T:0.40
Consensus pattern (22 bp):
TTAAAAACTATCCTATTATTCA
Found at i:216672 original size:3 final size:3
Alignment explanation
Indices: 216664--216708 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
216654 ATTACGAGCC
*
216664 ATT ATT ATT ATT ATT ATT ATT ATT ACT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
216709 TCAGAAAAAG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:216737 original size:11 final size:12
Alignment explanation
Indices: 216721--216753 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
216711 AGAAAAAGAT
216721 AAAAAGAAAA-G
1 AAAAAGAAAACG
216732 AAAAAGAAAACG
1 AAAAAGAAAACG
216744 AAAAGAGAAA
1 AAAA-AGAAA
216754 CCAAAATGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 10 0.50
12 5 0.25
13 5 0.25
ACGTcount: A:0.79, C:0.03, G:0.18, T:0.00
Consensus pattern (12 bp):
AAAAAGAAAACG
Found at i:217005 original size:11 final size:11
Alignment explanation
Indices: 216973--217006 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
216963 AATAATATTA
*
216973 ATAATTTTTTG
1 ATAATTTTTTT
*
216984 ATAATTATTTT
1 ATAATTTTTTT
216995 ATAATTTTTTT
1 ATAATTTTTTT
217006 A
1 A
217007 CGTGTTGTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (11 bp):
ATAATTTTTTT
Found at i:217522 original size:18 final size:18
Alignment explanation
Indices: 217496--217534 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
217486 ATATAGATAT
* *
217496 ATTTAATATTTTTTAAAA
1 ATTTAATATATTTAAAAA
*
217514 ATTTTATATATTTAAAAA
1 ATTTAATATATTTAAAAA
217532 ATT
1 ATT
217535 ATATTTTATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
ATTTAATATATTTAAAAA
Found at i:224241 original size:74 final size:74
Alignment explanation
Indices: 224130--224274 Score: 236
Period size: 74 Copynumber: 2.0 Consensus size: 74
224120 AGGAAAATCA
* * * * *
224130 GAACTCAATAGTTTGAAATATAGCTAAGAAAGTTAAAGAGCTAGAATGGCTAAAGGAGGTTAATA
1 GAACTCAATACTTCGAAAGATAGCTAAGAAAGATAAAGAGCTAGAATGGCTAAAGAAGGTTAATA
*
224195 GGATAATAC
66 AGATAATAC
224204 GAACTCAATACTTCGAAAGATAGCTAAGAAAGATAAAGAGCTAGAATGGCTAAAGAAGGTTAATA
1 GAACTCAATACTTCGAAAGATAGCTAAGAAAGATAAAGAGCTAGAATGGCTAAAGAAGGTTAATA
224269 AGATAA
66 AGATAA
224275 AAAGAAGGTT
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
74 65 1.00
ACGTcount: A:0.47, C:0.09, G:0.22, T:0.22
Consensus pattern (74 bp):
GAACTCAATACTTCGAAAGATAGCTAAGAAAGATAAAGAGCTAGAATGGCTAAAGAAGGTTAATA
AGATAATAC
Found at i:224280 original size:20 final size:20
Alignment explanation
Indices: 224255--224294 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
224245 TAGAATGGCT
224255 AAAGAAGGTTAATAAGATAA
1 AAAGAAGGTTAATAAGATAA
*
224275 AAAGAAGGTTAATAGGATAA
1 AAAGAAGGTTAATAAGATAA
224295 TACGAACTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.57, C:0.00, G:0.23, T:0.20
Consensus pattern (20 bp):
AAAGAAGGTTAATAAGATAA
Found at i:224318 original size:94 final size:94
Alignment explanation
Indices: 224181--224352 Score: 292
Period size: 94 Copynumber: 1.8 Consensus size: 94
224171 TAGAATGGCT
* *
224181 AAAGGAGGTTAATAGGATAATACGAACTCAATACTTCGAAAGATAGCTAAGAAAGATAAAGAGCT
1 AAAGAAGGTTAATAGGATAATACGAACTCAATACTTCGAAAGATAGCTAAGAAAGATAAAGAACT
224246 AGAATGGCTAAAGAAGGTTAATAAGATAA
66 AGAATGGCTAAAGAAGGTTAATAAGATAA
* *
224275 AAAGAAGGTTAATAGGATAATACGAACTCAATAGTTC-AGAAGATAGCTAAGAAAGTTAAAGAAC
1 AAAGAAGGTTAATAGGATAATACGAACTCAATACTTCGA-AAGATAGCTAAGAAAGATAAAGAAC
224339 TAGAATGGCTAAAG
65 TAGAATGGCTAAAG
224353 GACACGGGGA
Statistics
Matches: 73, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
93 1 0.01
94 72 0.99
ACGTcount: A:0.49, C:0.09, G:0.22, T:0.20
Consensus pattern (94 bp):
AAAGAAGGTTAATAGGATAATACGAACTCAATACTTCGAAAGATAGCTAAGAAAGATAAAGAACT
AGAATGGCTAAAGAAGGTTAATAAGATAA
Found at i:224485 original size:27 final size:25
Alignment explanation
Indices: 224444--224499 Score: 67
Period size: 27 Copynumber: 2.2 Consensus size: 25
224434 ACACACGTGA
*
224444 TAAAACTTATATAAAATAATATAAAAT
1 TAAAAATTATAT-AAATAATAT-AAAT
* *
224471 TAAAAATTATTTAAATAATATTAAT
1 TAAAAATTATATAAATAATATAAAT
224496 TAAA
1 TAAA
224500 CTCAATAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 7 0.27
26 9 0.35
27 10 0.38
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (25 bp):
TAAAAATTATATAAATAATATAAAT
Found at i:224539 original size:17 final size:18
Alignment explanation
Indices: 224519--224572 Score: 65
Period size: 19 Copynumber: 3.0 Consensus size: 18
224509 TTTAATCATG
224519 ATATAAAAATAAT-TAAA
1 ATATAAAAATAATATAAA
*
224536 ATATAAATATAATATAAA
1 ATATAAAAATAATATAAA
* *
224554 ATAATAACACTAATATAAA
1 AT-ATAAAAATAATATAAA
224573 TAAATATATT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
17 12 0.39
18 6 0.19
19 13 0.42
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.30
Consensus pattern (18 bp):
ATATAAAAATAATATAAA
Found at i:225010 original size:20 final size:22
Alignment explanation
Indices: 224985--225033 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
224975 GGAAATTTTT
* *
224985 ATATTATA-AT-TATATTTAAG
1 ATATTATATATATATAATTAAC
225005 ATATTATATATATATAATTAAC
1 ATATTATATATATATAATTAAC
225027 ATATTAT
1 ATATTAT
225034 TAACACAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 8 0.32
21 2 0.08
22 15 0.60
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (22 bp):
ATATTATATATATATAATTAAC
Found at i:225083 original size:15 final size:17
Alignment explanation
Indices: 225059--225098 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
225049 AAAATAATTA
*
225059 AAACATAATA-TGATAT
1 AAACATAATATTAATAT
225075 AAA-ATAATATTAATAT
1 AAACATAATATTAATAT
225091 AAACATAA
1 AAACATAA
225099 ACATGATGAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 6 0.29
16 11 0.52
17 4 0.19
ACGTcount: A:0.62, C:0.05, G:0.03, T:0.30
Consensus pattern (17 bp):
AAACATAATATTAATAT
Found at i:225217 original size:26 final size:25
Alignment explanation
Indices: 225183--225236 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 25
225173 ACAACATAAT
225183 TATTCAATACA-AACACAATATAAAAA
1 TATTCAATACATAA-A-AATATAAAAA
* *
225209 TATTTAATACATAAAAATATCAAAA
1 TATTCAATACATAAAAATATAAAAA
225234 TAT
1 TAT
225237 AAATAAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 12 0.48
26 11 0.44
27 2 0.08
ACGTcount: A:0.59, C:0.11, G:0.00, T:0.30
Consensus pattern (25 bp):
TATTCAATACATAAAAATATAAAAA
Found at i:225996 original size:100 final size:100
Alignment explanation
Indices: 225816--226026 Score: 332
Period size: 100 Copynumber: 2.1 Consensus size: 100
225806 AGTTGCTTAA
* * *
225816 AGTCAACAATTACGGCCACCTCTCTCTATTGTCAAAGATTGGTGAAGAATAGTTAACAATTACGA
1 AGTCAATAATTACGGCCACCTCTCTCTATTATCAAAGATTGGTGAAGAATAGTCAACAATTACGA
* * *
225881 CCGCCTTTCTCGATTGTCAAACGTTGGTGAAGAAT
66 CCACCTCTCTCGATTGTCAAAAGTTGGTGAAGAAT
* * * *
225916 ATTTAATAATTACGGTCACCTCTCTCTATTATCAAAGGTTGGTGAAGAATAGTCAACAATTACGA
1 AGTCAATAATTACGGCCACCTCTCTCTATTATCAAAGATTGGTGAAGAATAGTCAACAATTACGA
225981 CCACCTCTCTCGATTGTCAAAAGTTGGTGAAGAAT
66 CCACCTCTCTCGATTGTCAAAAGTTGGTGAAGAAT
226016 AGTCAATAATT
1 AGTCAATAATT
226027 CTCCCACTTG
Statistics
Matches: 99, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
100 99 1.00
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (100 bp):
AGTCAATAATTACGGCCACCTCTCTCTATTATCAAAGATTGGTGAAGAATAGTCAACAATTACGA
CCACCTCTCTCGATTGTCAAAAGTTGGTGAAGAAT
Found at i:226019 original size:50 final size:50
Alignment explanation
Indices: 225816--226026 Score: 271
Period size: 50 Copynumber: 4.2 Consensus size: 50
225806 AGTTGCTTAA
* *
225816 AGTCAACAATTACGGCCACCTCTCTCTATTGTC-AAAGATTGGTGAAGAAT
1 AGTCAACAATTACGACCACCTCTCTCGATTGTCAAAAG-TTGGTGAAGAAT
* * * *
225866 AGTTAACAATTACGACCGCCTTTCTCGATTGTCAAACGTTGGTGAAGAAT
1 AGTCAACAATTACGACCACCTCTCTCGATTGTCAAAAGTTGGTGAAGAAT
* * * ** * * *
225916 ATTTAATAATTACGGTCACCTCTCTCTATTATCAAAGGTTGGTGAAGAAT
1 AGTCAACAATTACGACCACCTCTCTCGATTGTCAAAAGTTGGTGAAGAAT
225966 AGTCAACAATTACGACCACCTCTCTCGATTGTCAAAAGTTGGTGAAGAAT
1 AGTCAACAATTACGACCACCTCTCTCGATTGTCAAAAGTTGGTGAAGAAT
*
226016 AGTCAATAATT
1 AGTCAACAATT
226027 CTCCCACTTG
Statistics
Matches: 136, Mismatches: 24, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
50 133 0.98
51 3 0.02
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (50 bp):
AGTCAACAATTACGACCACCTCTCTCGATTGTCAAAAGTTGGTGAAGAAT
Found at i:226539 original size:20 final size:20
Alignment explanation
Indices: 226514--226591 Score: 156
Period size: 20 Copynumber: 3.9 Consensus size: 20
226504 GTATCGATAT
226514 AATGTATCGATACATGAACA
1 AATGTATCGATACATGAACA
226534 AATGTATCGATACATGAACA
1 AATGTATCGATACATGAACA
226554 AATGTATCGATACATGAACA
1 AATGTATCGATACATGAACA
226574 AATGTATCGATACATGAA
1 AATGTATCGATACATGAA
226592 ACTGGCAGTA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 58 1.00
ACGTcount: A:0.45, C:0.14, G:0.15, T:0.26
Consensus pattern (20 bp):
AATGTATCGATACATGAACA
Found at i:231888 original size:13 final size:13
Alignment explanation
Indices: 231870--231894 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
231860 CATAAAGTAT
231870 TGTATCGATACAA
1 TGTATCGATACAA
231883 TGTATCGATACA
1 TGTATCGATACA
231895 TTTTTTTTTG
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:231975 original size:13 final size:13
Alignment explanation
Indices: 231957--231981 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
231947 ATCACTTAAA
231957 TGTATCGATACAT
1 TGTATCGATACAT
231970 TGTATCGATACA
1 TGTATCGATACA
231982 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:232046 original size:52 final size:52
Alignment explanation
Indices: 231990--232118 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
231980 CACTGATCTT
*
231990 TGTATCGATACATGCAGGCAAATTTGCCCAAATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAAATGTATCGATACACTATAAAA
* **
232042 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTCAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAAATGTATCGATACACTATAAAA
232094 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
232119 TCATATTTCG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 73 1.00
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAAATGTATCGATACACTATAAAA
Found at i:242899 original size:50 final size:50
Alignment explanation
Indices: 242838--243042 Score: 263
Period size: 50 Copynumber: 4.2 Consensus size: 50
242828 AGTTGCTTAA
* * * * *
242838 AGTCAATAATTACAGCCACATCTTTCTATTATCAAAGGTTGGTGAAGAAT
1 AGTCAACAATTACGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAAT
* *
242888 AGTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGATGAAGAAT
1 AGTCAACAATTACGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAAT
* *
242938 AGTCAACAATTACGGCCACCTCTCTCTATTGTCAAATGTTAGTGAAGAAT
1 AGTCAACAATTACGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAAT
* * ** *
242988 AGTCAATAATTACGGCTACCTCTCTCGGTTGTCAAAAGTTGGT--A-AAT
1 AGTCAACAATTACGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAAT
243035 AGTCAACA
1 AGTCAACA
243043 TATCTTTGCA
Statistics
Matches: 137, Mismatches: 18, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
47 10 0.07
48 1 0.01
50 126 0.92
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (50 bp):
AGTCAACAATTACGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAAT
Found at i:243523 original size:3 final size:3
Alignment explanation
Indices: 243515--243553 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
243505 CTAAAAATAA
243515 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
243554 TTTGTTTAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:245142 original size:16 final size:16
Alignment explanation
Indices: 245123--245179 Score: 55
Period size: 16 Copynumber: 3.7 Consensus size: 16
245113 AATTTAAACT
245123 TTTTAAATTTTAATTA
1 TTTTAAATTTTAATTA
* * * *
245139 TTTTGAGTTTGAATCA
1 TTTTAAATTTTAATTA
*
245155 TTTTAAA-TTTAAGT-
1 TTTTAAATTTTAATTA
245169 TTTTAAATTTT
1 TTTTAAATTTT
245180 TATCAAATCG
Statistics
Matches: 31, Mismatches: 9, Indels: 3
0.72 0.21 0.07
Matches are distributed among these distances:
14 7 0.23
15 7 0.23
16 17 0.55
ACGTcount: A:0.32, C:0.02, G:0.07, T:0.60
Consensus pattern (16 bp):
TTTTAAATTTTAATTA
Found at i:247522 original size:26 final size:26
Alignment explanation
Indices: 247493--247545 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
247483 CTTTTAAGTG
247493 TAATAGACTTAGATCTTTGGATCATC
1 TAATAGACTTAGATCTTTGGATCATC
247519 TAATAGACTTAGATCTTTGGATCATC
1 TAATAGACTTAGATCTTTGGATCATC
247545 T
1 T
247546 TGGTTTAATT
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:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (26 bp):
TAATAGACTTAGATCTTTGGATCATC
Found at i:249393 original size:22 final size:23
Alignment explanation
Indices: 249351--249399 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
249341 TTTTTTGTGA
* *
249351 TTTATTTTTAGTTTTTGTCAT-T
1 TTTATTTTTACTTTATGTCATAT
249373 TTTATTTTTACTTCTAT-TCATAT
1 TTTATTTTTACTT-TATGTCATAT
249396 TTTA
1 TTTA
249400 ATAAATAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 16 0.70
23 7 0.30
ACGTcount: A:0.18, C:0.08, G:0.04, T:0.69
Consensus pattern (23 bp):
TTTATTTTTACTTTATGTCATAT
Found at i:249883 original size:16 final size:16
Alignment explanation
Indices: 249864--249907 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
249854 ACATGTGTAG
*
249864 AAATCATTAATTATAA
1 AAATTATTAATTATAA
*
249880 AAATTA-TATTTATAA
1 AAATTATTAATTATAA
249895 ATAATTATTAATT
1 A-AATTATTAATT
249908 TTGCATTGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
15 9 0.39
16 10 0.43
17 4 0.17
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
AAATTATTAATTATAA
Found at i:250071 original size:28 final size:29
Alignment explanation
Indices: 250007--250071 Score: 82
Period size: 28 Copynumber: 2.3 Consensus size: 29
249997 AAAATTTAAC
*
250007 ATTAAAATATTAATATTAAATATTTTTATT
1 ATTAAAA-ATTAATATAAAATATTTTTATT
250037 ATT-AAAATTAA-ATAAAAATATTTTTA-T
1 ATTAAAAATTAATAT-AAAATATTTTTATT
250064 ATTAAAAA
1 ATTAAAAA
250072 ATAACCTTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
27 6 0.19
28 20 0.62
29 3 0.09
30 3 0.09
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (29 bp):
ATTAAAAATTAATATAAAATATTTTTATT
Found at i:250248 original size:27 final size:27
Alignment explanation
Indices: 250199--250299 Score: 70
Period size: 27 Copynumber: 3.9 Consensus size: 27
250189 ATTTAAACTT
* *
250199 TAAATTTTATTTAATAA-AATTTTATGA
1 TAAATTTTATTT-TTAATATTTTTATGA
250226 TAAATTTTATTTTTAATATTTTTAT--
1 TAAATTTTATTTTTAATATTTTTATGA
* * *
250251 T-AA--TTATTATTAATTATTTTAAAGA
1 TAAATTTTATTTTTAA-TATTTTTATGA
* * *
250276 TAAAATTAATTTTTAAAATTTTTA
1 TAAATTTTATTTTTAATATTTTTA
250300 AGTTAACAAT
Statistics
Matches: 58, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
22 9 0.16
23 7 0.12
24 2 0.03
25 2 0.03
26 5 0.09
27 25 0.43
28 8 0.14
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (27 bp):
TAAATTTTATTTTTAATATTTTTATGA
Found at i:251545 original size:2 final size:2
Alignment explanation
Indices: 251538--251564 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
251528 CCTCATACAA
251538 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
251565 ATTTATTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:252485 original size:58 final size:57
Alignment explanation
Indices: 252377--252492 Score: 214
Period size: 58 Copynumber: 2.0 Consensus size: 57
252367 TGTAGATAAC
*
252377 ATAATATATCTTTTGATTTGATAGCCTCTTGAATTGTTTGCTTTCAAAATGCAGAAT
1 ATAATATATCTTTTGATTTGATAGCCTCTTGAATTATTTGCTTTCAAAATGCAGAAT
252434 ATAATATATCTTTTGATTTGATAGCCCTCTTGAATTATTTGCTTTCAAAATGCAGAAT
1 ATAATATATCTTTTGATTTGATAG-CCTCTTGAATTATTTGCTTTCAAAATGCAGAAT
252492 A
1 A
252493 CTTAATTTGA
Statistics
Matches: 57, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
57 24 0.42
58 33 0.58
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.43
Consensus pattern (57 bp):
ATAATATATCTTTTGATTTGATAGCCTCTTGAATTATTTGCTTTCAAAATGCAGAAT
Found at i:260417 original size:13 final size:13
Alignment explanation
Indices: 260390--260424 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
260380 TTATGATTTT
260390 TATTT-TTAATAA
1 TATTTATTAATAA
*
260402 TATTTATTATTAA
1 TATTTATTAATAA
260415 TATTTATTAA
1 TATTTATTAA
260425 AATTAATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 5 0.25
13 15 0.75
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TATTTATTAATAA
Found at i:268674 original size:24 final size:24
Alignment explanation
Indices: 268647--268699 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
268637 TGTTTATGTA
* *
268647 TTTATTTAATT-TATTTAGATTTAT
1 TTTATTTAATTATA-TTAAATTAAT
268671 TTTATTTAATTATATTAAATTAAT
1 TTTATTTAATTATATTAAATTAAT
268695 TTTAT
1 TTTAT
268700 AAGTAAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 24 0.92
25 2 0.08
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (24 bp):
TTTATTTAATTATATTAAATTAAT
Found at i:271277 original size:85 final size:84
Alignment explanation
Indices: 271169--271401 Score: 283
Period size: 85 Copynumber: 2.7 Consensus size: 84
271159 TTAAGTCGAC
* * * *
271169 AAGTAAATAAAGGATACAA-AAGTTGATGGGTATTGAACCGACAAGTCAACAAACGATAAAAAGA
1 AAGTAAACAAAGGATA-AAGAAGTTGATAGG-ATTGAACCGACAAATCAACAAAGGATAAAAAGA
271233 TTTAGCCAA-GACTAAGCTAAT
64 TTTA-CCAAGGACTAAGCTAAT
** * * *
271254 GGGTGAACAAAGGATAAAGAAGTTGATCGGAGTTGAACCGACAAATTAACAAAGGATAAAAAGAT
1 AAGTAAACAAAGGATAAAGAAGTTGATAGGA-TTGAACCGACAAATCAACAAAGGATAAAAAGAT
*
271319 TTACCAAGGACTAAGCTGAT
65 TTACCAAGGACTAAGCTAAT
* *
271339 AAGTAAACAAAGGATAAAGAAGTTAACCAAGG-TTGAACCGACAAATCAACAAAGGATAAAAAG
1 AAGTAAACAAAGGATAAAGAAGTTGA--TAGGATTGAACCGACAAATCAACAAAGGATAAAAAG
271402 CTATACCTGA
Statistics
Matches: 127, Mismatches: 16, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
84 7 0.06
85 118 0.93
87 2 0.02
ACGTcount: A:0.49, C:0.12, G:0.21, T:0.18
Consensus pattern (84 bp):
AAGTAAACAAAGGATAAAGAAGTTGATAGGATTGAACCGACAAATCAACAAAGGATAAAAAGATT
TACCAAGGACTAAGCTAAT
Found at i:271564 original size:44 final size:44
Alignment explanation
Indices: 271516--271614 Score: 119
Period size: 44 Copynumber: 2.2 Consensus size: 44
271506 GAATTGAATA
* *
271516 GAGTTTAACTAGGGTAAAACCATCACGTCAAA-AGATAGTGAAAG
1 GAGTTTAACCACGGTAAAACCATCACGTCAAACA-ATAGTGAAAG
* * *
271560 GAGTTTGACCACGGTAGAACCATCATGTCAAACAATAGTGAAAG
1 GAGTTTAACCACGGTAAAACCATCACGTCAAACAATAGTGAAAG
* *
271604 AAGTTTGACCA
1 GAGTTTAACCA
271615 TTGTGGTAAC
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
44 47 0.98
45 1 0.02
ACGTcount: A:0.40, C:0.16, G:0.22, T:0.21
Consensus pattern (44 bp):
GAGTTTAACCACGGTAAAACCATCACGTCAAACAATAGTGAAAG
Found at i:271635 original size:44 final size:43
Alignment explanation
Indices: 271554--272195 Score: 174
Period size: 44 Copynumber: 14.9 Consensus size: 43
271544 CAAAAGATAG
* * *
271554 TGAAAGGAGTTTGACCACGGTAG-AACCAT-CATGTCAAACA-ATA
1 TGAAAGAAGTTTGACCAAGGTGGTAACCATACA--TCAAACAGA-A
**
271597 GTGAAAGAAGTTTGACCATTGTGGTAACCATACATCAAATCAGAA
1 -TGAAAGAAGTTTGACCAAGGTGGTAACCATACATCAAA-CAGAA
* * * * * * *
271642 T-AAAAAAATCTGACCAGGGTGGTAACCATACGTCAGACCGAAA
1 TGAAAGAAGTTTGACCAAGGTGGTAACCATACATCAAACAG-AA
*
271685 TGAGAAG-AGTTTGACCAAGGTGGTAACCATACATCAAATAAGAA
1 TGA-AAGAAGTTTGACCAAGGTGGTAACCATACATCAAA-CAGAA
* * * * **
271729 T-AAGGCAGATTTGACCAAAGTGATAACCATATGTCAAATCAGAA
1 TGAAAGAAG-TTTGACCAAGGTGGTAACCATACATCAAA-CAGAA
* * * **
271773 TGAAA-AGAGTCTGACCAAGGTGGTAACTATACATCAGATTGAAA
1 TGAAAGA-AGTTTGACCAAGGTGGTAACCATACATCAAACAG-AA
* * * * * *
271817 TG--AGAAG--AG-CGTAA-CT-AT-A-CGT-CA--AATCAGAA
1 TGAAAGAAGTTTGAC-CAAGGTGGTAACCATACATCAAACAGAA
* * ** *
271849 TGAAAAGAA-TCTGACTAAGGTGGTAACCATATGTCAGAACAAAA
1 TG-AAAGAAGTTTGACCAAGGTGGTAACCATACATCA-AACAGAA
* * * * * * **
271893 TGAGAAG-TGTTTAACTAGGGTCGTAATCATAGGTCAAACAGGAA
1 TGA-AAGAAGTTTGACCAAGGTGGTAACCATACATCAAACA-GAA
* * * ** *
271937 -GGAGGCAGATTTGACCAAGGTGGTAACCATGTATCAAATCACAA
1 TGAAAGAAG-TTTGACCAAGGTGGTAACCATACATCAAA-CAGAA
* * * * * *
271981 TGAAAAGAA-TCTGACTAGGGTGATGACCATACATTAAAACA-AA
1 TG-AAAGAAGTTTGACCAAGGTGGTAACCATACA-TCAAACAGAA
* * *
272024 TGAGAAG-AGTTTGACTAGGGTGGTAACCATGCATCAAACAGGAA
1 TGA-AAGAAGTTTGACCAAGGTGGTAACCATACATCAAACA-GAA
* * * ** *
272068 -GGAGGCAGATTTGACCAAGGTGGTAACCATATGTCAAATCCGAA
1 TGAAAGAAG-TTTGACCAAGGTGGTAACCATACATCAAA-CAGAA
* * * * *
272112 TAAAAAGAA-TCT-AACTAGAGTGGTAACCATACGTCAAATC-GAAA
1 T-GAAAGAAGTTTGACCAAG-GTGGTAACCATACATCAAA-CAG-AA
*
272156 TGAGAAG-AGTTTGACCAAGGTGGTAACCATACATTAAACA
1 TGA-AAGAAGTTTGACCAAGGTGGTAACCATACATCAAACA
272196 ATAAGAAGAC
Statistics
Matches: 432, Mismatches: 113, Indels: 106
0.66 0.17 0.16
Matches are distributed among these distances:
32 4 0.01
33 2 0.00
35 6 0.01
36 5 0.01
37 3 0.01
38 2 0.00
39 3 0.01
40 5 0.01
42 19 0.04
43 83 0.19
44 263 0.61
45 28 0.06
46 9 0.02
ACGTcount: A:0.41, C:0.16, G:0.22, T:0.21
Consensus pattern (43 bp):
TGAAAGAAGTTTGACCAAGGTGGTAACCATACATCAAACAGAA
Found at i:271788 original size:88 final size:87
Alignment explanation
Indices: 271617--271808 Score: 233
Period size: 88 Copynumber: 2.2 Consensus size: 87
271607 TTTGACCATT
* ** * * *
271617 GTGGTAACCATACATCAAATCAGAATAAAAAAATCTGACCAGGGTGGTAACCATACGTCAGACCG
1 GTGGTAACCATACATCAAATAAGAATAAAAAAATCTGACCAAAGTGATAACCATACGTCAAACAG
* *
271682 AAATGAGAAGAGTTTGACCAAG
66 AAATGAAAAGAGTCTGACCAAG
** * * *
271704 GTGGTAACCATACATCAAATAAGAATAAGGCAGATTTGACCAAAGTGATAACCATATGTCAAATC
1 GTGGTAACCATACATCAAATAAGAATAA-AAAAATCTGACCAAAGTGATAACCATACGTCAAA-C
271769 AG-AATGAAAAGAGTCTGACCAAG
64 AGAAATGAAAAGAGTCTGACCAAG
*
271792 GTGGTAACTATACATCA
1 GTGGTAACCATACATCA
271809 GATTGAAATG
Statistics
Matches: 89, Mismatches: 14, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
87 27 0.30
88 60 0.67
89 2 0.02
ACGTcount: A:0.42, C:0.17, G:0.20, T:0.20
Consensus pattern (87 bp):
GTGGTAACCATACATCAAATAAGAATAAAAAAATCTGACCAAAGTGATAACCATACGTCAAACAG
AAATGAAAAGAGTCTGACCAAG
Found at i:271921 original size:76 final size:76
Alignment explanation
Indices: 271752--271899 Score: 206
Period size: 76 Copynumber: 1.9 Consensus size: 76
271742 ACCAAAGTGA
* * * * ***
271752 TAACCATATGTCAAATCAGAATGAAAAGAGTCTGACCAAGGTGGTAACTATACATCAGATTGAAA
1 TAACTATACGTCAAATCAGAATGAAAAGAATCTGACCAAGGTGGTAACCATACATCAGAACAAAA
271817 TGAGAAGAGCG
66 TGAGAAGAGCG
* **
271828 TAACTATACGTCAAATCAGAATGAAAAGAATCTGACTAAGGTGGTAACCATATGTCAGAACAAAA
1 TAACTATACGTCAAATCAGAATGAAAAGAATCTGACCAAGGTGGTAACCATACATCAGAACAAAA
271893 TGAGAAG
66 TGAGAAG
271900 TGTTTAACTA
Statistics
Matches: 62, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
76 62 1.00
ACGTcount: A:0.44, C:0.14, G:0.21, T:0.21
Consensus pattern (76 bp):
TAACTATACGTCAAATCAGAATGAAAAGAATCTGACCAAGGTGGTAACCATACATCAGAACAAAA
TGAGAAGAGCG
Found at i:272228 original size:132 final size:131
Alignment explanation
Indices: 271827--272603 Score: 756
Period size: 132 Copynumber: 5.8 Consensus size: 131
271817 TGAGAAGAGC
* * * * *
271827 GTAACTATACGTCAAATCAGAATGAAAAGAATCTGACTA-AGGTGGTAACCATATGTCAGAACAA
1 GTAACCATATGTCAAATCAGAATGAAAAGAATCTGACTAGA-GTGATAACCATACGTCA-AACGA
* * * * * ** * * *
271891 AATGAGAAGTGTTTAACTAGGGTCGTAATCATAGGTCAAACAGGAAGGAGGCAGATTTGACCAAG
64 AATGAGAAGAGTTTGACCAGGGTGGTAACCATACATCAAACAGGAAGAAGACAGATTTGACTAAG
271956 GTG
129 GTG
* * * * * * *
271959 GTAACCATGTATCAAATCACAATGAAAAGAATCTGACTAGGGTGATGACCATACATTAAAAC-AA
1 GTAACCATATGTCAAATCAGAATGAAAAGAATCTGACTAGAGTGATAACCATAC-GTCAAACGAA
* * * * *
272023 ATGAGAAGAGTTTGACTAGGGTGGTAACCATGCATCAAACAGGAAGGAGGCAGATTTGACCAAGG
65 ATGAGAAGAGTTTGACCAGGGTGGTAACCATACATCAAACAGGAAGAAGACAGATTTGACTAAGG
272088 TG
130 TG
* * * *
272090 GTAACCATATGTCAAATCCGAATAAAAAGAATCTAACTAGAGTGGTAACCATACGTCAAATCGAA
1 GTAACCATATGTCAAATCAGAATGAAAAGAATCTGACTAGAGTGATAACCATACGTCAAA-CGAA
* * ** * *
272155 ATGAGAAGAGTTTGACCAAGGTGGTAACCATACATTAAACAATAAGAAGACAGATTTGATTAGGG
65 ATGAGAAGAGTTTGACCAGGGTGGTAACCATACATCAAACAGGAAGAAGACAGATTTGACTAAGG
272220 TG
130 TG
* * *
272222 GTAACCATATGTCAAATC-GAAATGAAAATAATCTGACTAGAGTGATAACCATATGTCAGACTGA
1 GTAACCATATGTCAAATCAG-AATGAAAAGAATCTGACTAGAGTGATAACCATACGTCAAAC-GA
* * * **
272286 AATGAGAAAAGTTTGACCAAGGTGGTAACGATATGTCAAACAGGAACGTCAAACATGAAGGAGGC
64 AATGAGAAGAGTTTGACCAGGGTGGTAACCATACATCAAACA-G---G----A-A-GAA-GA--C
272351 AGATTTGACTAAGGTG
116 AGATTTGACTAAGGTG
* * * **
272367 GTAACCATACGTCAAATCAAAATGAAAAGAATCTGACTAGAGTGATAACCATACATCAGATTGAA
1 GTAACCATATGTCAAATCAGAATGAAAAGAATCTGACTAGAGTGATAACCATACGTCA-AACGAA
* * *
272432 ATAAGAAGAGTTTGACCTAGGGTGGTAACCATACATCAAATAGGAAGGAA-ATAGATTTGACTAA
65 ATGAGAAGAGTTTGACC-AGGGTGGTAACCATACATCAAACAGGAA-GAAGACAGATTTGACTAA
272496 GGTG
128 GGTG
* * * *
272500 GTAACCATATGTCAAATCAGAATAAAAAGAATTTAACTAG-GAT-AGTAACCATACGTCATACCG
1 GTAACCATATGTCAAATCAGAATGAAAAGAATCTGACTAGAG-TGA-TAACCATACGTCA-AACG
* *
272563 AAATGAGAAGAGTGTGACCAGGGTGGTAACCATACGTCAAA
63 AAATGAGAAGAGTTTGACCAGGGTGGTAACCATACATCAAA
272604 TATAAATGAA
Statistics
Matches: 537, Mismatches: 84, Indels: 48
0.80 0.13 0.07
Matches are distributed among these distances:
130 4 0.01
131 110 0.20
132 219 0.41
133 85 0.16
135 1 0.00
137 4 0.01
138 1 0.00
140 1 0.00
141 1 0.00
142 4 0.01
143 2 0.00
145 86 0.16
146 19 0.04
ACGTcount: A:0.41, C:0.14, G:0.23, T:0.22
Consensus pattern (131 bp):
GTAACCATATGTCAAATCAGAATGAAAAGAATCTGACTAGAGTGATAACCATACGTCAAACGAAA
TGAGAAGAGTTTGACCAGGGTGGTAACCATACATCAAACAGGAAGAAGACAGATTTGACTAAGGT
G
Found at i:272271 original size:44 final size:44
Alignment explanation
Indices: 272087--272615 Score: 186
Period size: 44 Copynumber: 11.7 Consensus size: 44
272077 TTTGACCAAG
* *
272087 GTGGTAACCATATGTCAAATCCG-AATAAAAAGAATCTAACTAGA
1 GTGGTAACCATATGTCAAAT-CGAAATGAAAAGAATCTGACTAGA
* * * * *
272131 GTGGTAACCATACGTCAAATCGAAATGAGAAGAGTTTGACCA-A
1 GTGGTAACCATATGTCAAATCGAAATGAAAAGAATCTGACTAGA
** * * * * *
272174 GGTGGTAACCATACATTAAA-C-AATAAGAAGACAG-ATTTGATTAGG
1 -GTGGTAACCATATGTCAAATCGAA-ATGAA-A-AGAATCTGACTAGA
*
272219 GTGGTAACCATATGTCAAATCGAAATGAAAATAATCTGACTAGA
1 GTGGTAACCATATGTCAAATCGAAATGAAAAGAATCTGACTAGA
* * * * *
272263 GTGATAACCATATGTCAGA-CTGAAATGAGAAA-AGTTTGACCA-A
1 GTGGTAACCATATGTCAAATC-GAAATGA-AAAGAATCTGACTAGA
* * * * * * *
272306 GGTGGTAACGATATGTCAAA-CAGGAACGTCAAACATGAAGGAGGCAGATTTGACTAA
1 -GTGGTAACCATATGTCAAATC--GAA-ATGAAA-A-G-A--A-TCTGA-CT-A--GA
* *
272363 GGTGGTAACCATACGTCAAATCAAAATGAAAAGAATCTGACTAGA
1 G-TGGTAACCATATGTCAAATCGAAATGAAAAGAATCTGACTAGA
* ** * * * * *
272408 GTGATAACCATACATCAGATTGAAAT-AAGAAGAGTTTGACCTAGG
1 GTGGTAACCATATGTCAAATCGAAATGAA-AAGAATCTGA-CTAGA
** * * * *
272453 GTGGTAACCATACATCAAATAGGAAGGAAATAG-ATTTGACTA-A
1 GTGGTAACCATATGTCAAATCGAAATGAAA-AGAATCTGACTAGA
* * *
272496 GGTGGTAACCATATGTCAAATC-AGAATAAAAAGAATTTAACTAG-
1 -GTGGTAACCATATGTCAAATCGA-AATGAAAAGAATCTGACTAGA
* * * * * * * * *
272540 GATAGTAACCATACGTCATACCGAAATGAGAAGAGTGTGACCAGG
1 G-TGGTAACCATATGTCAAATCGAAATGAAAAGAATCTGACTAGA
* **
272585 GTGGTAACCATACGTCAAATATAAATGAAAA
1 GTGGTAACCATATGTCAAATCGAAATGAAAA
272616 AAACTTAACT
Statistics
Matches: 359, Mismatches: 87, Indels: 78
0.69 0.17 0.15
Matches are distributed among these distances:
42 2 0.01
43 15 0.04
44 245 0.68
45 50 0.14
46 9 0.03
47 1 0.00
48 1 0.00
49 4 0.01
50 1 0.00
52 3 0.01
53 1 0.00
54 2 0.01
55 4 0.01
56 3 0.01
57 17 0.05
58 1 0.00
ACGTcount: A:0.42, C:0.14, G:0.21, T:0.22
Consensus pattern (44 bp):
GTGGTAACCATATGTCAAATCGAAATGAAAAGAATCTGACTAGA
Found at i:272572 original size:133 final size:132
Alignment explanation
Indices: 272351--272605 Score: 361
Period size: 133 Copynumber: 1.9 Consensus size: 132
272341 TGAAGGAGGC
* *
272351 AGATTTGACTAAGGTGGTAACCATACGTCAAATCAAAATGAAAAGAATCTGACTAGAGTGATAAC
1 AGATTTGACTAAGGTGGTAACCATACGTCAAATCAAAATAAAAAGAATCTAACTAGAGTGATAAC
** *
272416 CATACATCAGATTGAAATAAGAAGAGTTTGACCTAGGGTGGTAACCATACATCAAATAGGAAGGA
66 CATACATCAGACCGAAATAAGAAGAGTGTGACC-AGGGTGGTAACCATACATCAAATAGGAAGGA
272481 AAT
130 AAT
* * *
272484 AGATTTGACTAAGGTGGTAACCATATGTCAAATCAGAATAAAAAGAATTTAACTAG-GAT-AGTA
1 AGATTTGACTAAGGTGGTAACCATACGTCAAATCAAAATAAAAAGAATCTAACTAGAG-TGA-TA
* * * *
272547 ACCATACGTCATACCGAAATGAGAAGAGTGTGACCAGGGTGGTAACCATACGTCAAATA
64 ACCATACATCAGACCGAAATAAGAAGAGTGTGACCAGGGTGGTAACCATACATCAAATA
272606 TAAATGAAAA
Statistics
Matches: 108, Mismatches: 12, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
132 25 0.23
133 83 0.77
ACGTcount: A:0.42, C:0.14, G:0.21, T:0.23
Consensus pattern (132 bp):
AGATTTGACTAAGGTGGTAACCATACGTCAAATCAAAATAAAAAGAATCTAACTAGAGTGATAAC
CATACATCAGACCGAAATAAGAAGAGTGTGACCAGGGTGGTAACCATACATCAAATAGGAAGGAA
AT
Found at i:272630 original size:44 final size:43
Alignment explanation
Indices: 272353--272666 Score: 175
Period size: 44 Copynumber: 7.1 Consensus size: 43
272343 AAGGAGGCAG
* * *
272353 ATTTGACTAAGGTGGTAACCATACGTCAAATCAAAATGAAAAGA
1 ATTTAACTAGGGTGGTAACCATACGTCAAAT-AAAATGAAAAAA
* * * * * * * *
272397 ATCTGACTAGAGTGATAACCATACATCAGATTGAAAT-AAGAAGA
1 ATTTAACTAGGGTGGTAACCATACGTCA-AATAAAATGAA-AAAA
* * * * * * *
272441 GTTTGACCTAGGGTGGTAACCATACATCAAATAGGAAGGAAATAG
1 ATTT-AACTAGGGTGGTAACCATACGTCAAATA-AAATGAAAAAA
* * * *
272486 ATTTGACTAAGGTGGTAACCATATGTCAAATCAGAAT-AAAAAGA
1 ATTTAACTAGGGTGGTAACCATACGTCAAAT-AAAATGAAAAA-A
* * *** * *
272530 ATTTAACTAGGATAGTAACCATACGTCATACCGAAATGAGAAGA
1 ATTTAACTAGGGTGGTAACCATACGTCA-AATAAAATGAAAAAA
* * * *
272574 GTGTGACCAGGGTGGTAACCATACGTCAAATATAAATGAAAAAA
1 ATTTAACTAGGGTGGTAACCATACGTCAAATA-AAATGAAAAAA
* * *
272618 ACTTAACTAGGGTGGTGACCACACGTCAAGCA-AAAATGAAAAGAA
1 ATTTAACTAGGGTGGTAACCATACGTCAA--ATAAAATGAAAA-AA
272663 ATTT
1 ATTT
272667 GGTTAGGCAA
Statistics
Matches: 198, Mismatches: 59, Indels: 25
0.70 0.21 0.09
Matches are distributed among these distances:
43 7 0.04
44 149 0.75
45 39 0.20
46 3 0.02
ACGTcount: A:0.43, C:0.14, G:0.20, T:0.22
Consensus pattern (43 bp):
ATTTAACTAGGGTGGTAACCATACGTCAAATAAAATGAAAAAA
Found at i:272655 original size:88 final size:88
Alignment explanation
Indices: 272496--272661 Score: 194
Period size: 88 Copynumber: 1.9 Consensus size: 88
272486 ATTTGACTAA
* * * *
272496 GGTGGTAACCATATGTCAAATCAGAATAAAAAGAATTTAACTAGGATAGTAACCATACGTCATAC
1 GGTGGTAACCATACGTCAAATCAAAATAAAAAGAACTTAACTAGGATAGTAACCACACGTCATAC
** *
272561 CGAAATGAGAAGAGTGTGACCAG
66 AAAAATGAAAAGAGTGTGACCAG
* * *
272584 GGTGGTAACCATACGTCAAAT-ATAAATGAAAAA-AACTTAACTAGGGTGGTGACCACACGTCA-
1 GGTGGTAACCATACGTCAAATCA-AAAT-AAAAAGAACTTAACTAGGATAGTAACCACACGTCAT
272646 AGCAAAAATGAAAAGA
64 A-CAAAAATGAAAAGA
272662 AATTTGGTTA
Statistics
Matches: 65, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
87 2 0.03
88 58 0.89
89 5 0.08
ACGTcount: A:0.44, C:0.15, G:0.21, T:0.20
Consensus pattern (88 bp):
GGTGGTAACCATACGTCAAATCAAAATAAAAAGAACTTAACTAGGATAGTAACCACACGTCATAC
AAAAATGAAAAGAGTGTGACCAG
Found at i:272970 original size:3 final size:3
Alignment explanation
Indices: 272962--273023 Score: 117
Period size: 3 Copynumber: 21.0 Consensus size: 3
272952 TATATGTATG
272962 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
273010 TAT TAT TAT T-T TAT
1 TAT TAT TAT TAT TAT
273024 GATGTGATTT
Statistics
Matches: 58, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 56 0.97
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:276474 original size:26 final size:26
Alignment explanation
Indices: 276445--276494 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
276435 ATGGACAATG
276445 TAATTCAACCTCCCCAATAAACTTCT
1 TAATTCAACCTCCCCAATAAACTTCT
*
276471 TAATTCAACCTCCCTAATAAACTT
1 TAATTCAACCTCCCCAATAAACTT
276495 TTTACTTCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.36, C:0.32, G:0.00, T:0.32
Consensus pattern (26 bp):
TAATTCAACCTCCCCAATAAACTTCT
Found at i:277659 original size:2 final size:2
Alignment explanation
Indices: 277616--277641 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
277606 GGATGATTTG
277616 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
277642 AAGAAAGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:283019 original size:19 final size:20
Alignment explanation
Indices: 282976--283023 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
282966 CACACTCAGA
*
282976 TGTATCGATACATTATGCTT
1 TGTATCGATACATTATGCAT
282996 TGTATCGATACATGT-T-CAT
1 TGTATCGATACAT-TATGCAT
283015 TGTATCGAT
1 TGTATCGAT
283024 GTATACACAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 11 0.42
20 14 0.54
21 1 0.04
ACGTcount: A:0.25, C:0.15, G:0.17, T:0.44
Consensus pattern (20 bp):
TGTATCGATACATTATGCAT
Found at i:283095 original size:43 final size:43
Alignment explanation
Indices: 283034--283133 Score: 200
Period size: 43 Copynumber: 2.3 Consensus size: 43
283024 GTATACACAA
283034 TTGTATCGATACATAAAACTGGTAGTAGCTACCTTACCAGTGT
1 TTGTATCGATACATAAAACTGGTAGTAGCTACCTTACCAGTGT
283077 TTGTATCGATACATAAAACTGGTAGTAGCTACCTTACCAGTGT
1 TTGTATCGATACATAAAACTGGTAGTAGCTACCTTACCAGTGT
283120 TTGTATCGATACAT
1 TTGTATCGATACAT
283134 GGCACATTGT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 57 1.00
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (43 bp):
TTGTATCGATACATAAAACTGGTAGTAGCTACCTTACCAGTGT
Found at i:283176 original size:33 final size:33
Alignment explanation
Indices: 283121--283185 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
283111 TACCAGTGTT
*
283121 TGTATCGATACATGGCACATTGTATTGATACAA
1 TGTATCGATACATGGCACATTGTATCGATACAA
283154 TGTATCGATACATGATG-A-ATTGTATCGATACA
1 TGTATCGATACATG--GCACATTGTATCGATACA
283186 TTGCTTCAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 27 0.93
34 1 0.03
35 1 0.03
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.34
Consensus pattern (33 bp):
TGTATCGATACATGGCACATTGTATCGATACAA
Found at i:289130 original size:13 final size:13
Alignment explanation
Indices: 289112--289138 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
289102 ACAATATTCT
289112 TTGTATCGATACA
1 TTGTATCGATACA
289125 TTGTATCGATACA
1 TTGTATCGATACA
289138 T
1 T
289139 GGGTTACTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:289303 original size:20 final size:20
Alignment explanation
Indices: 289265--289304 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
289255 TTTCAAATTT
289265 CTTCATTTTCACTTCAAAATA
1 CTTCATTTTCAC-TCAAAATA
289286 CTTCATTTTTCA-TCAAAAT
1 CTTCA-TTTTCACTCAAAAT
289305 TATCAACAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.39
21 5 0.28
22 6 0.33
ACGTcount: A:0.33, C:0.23, G:0.00, T:0.45
Consensus pattern (20 bp):
CTTCATTTTCACTCAAAATA
Found at i:291064 original size:22 final size:21
Alignment explanation
Indices: 291039--291084 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 21
291029 TTTAAAACGA
291039 TTATCAAGGGGGAGAAAATTTT
1 TTATCAAGGGGGAG-AAATTTT
291061 TTATCAAGGGGGAGAAATTTT
1 TTATCAAGGGGGAGAAATTTT
291082 TTA
1 TTA
291085 AACGAGAGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 10 0.42
22 14 0.58
ACGTcount: A:0.35, C:0.04, G:0.26, T:0.35
Consensus pattern (21 bp):
TTATCAAGGGGGAGAAATTTT
Found at i:291800 original size:33 final size:32
Alignment explanation
Indices: 291758--291820 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 32
291748 TACCACTGTT
291758 TGTATCGATACATG-GCACATTGTATCGATATAA
1 TGTATCGATACATGAG-A-ATTGTATCGATATAA
291791 TGTATCGATACATGATGAATTGTATCGATA
1 TGTATCGATACATGA-GAATTGTATCGATA
291821 CATTGCTTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
33 26 0.93
34 1 0.04
35 1 0.04
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.35
Consensus pattern (32 bp):
TGTATCGATACATGAGAATTGTATCGATATAA
Found at i:294304 original size:23 final size:23
Alignment explanation
Indices: 294278--294324 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
294268 ACGTCGATAG
294278 TTCAATTTATGTTAAGATAATGT
1 TTCAATTTATGTTAAGATAATGT
294301 TTCAATTTATGTTAAGATAATGT
1 TTCAATTTATGTTAAGATAATGT
294324 T
1 T
294325 GGGACTCTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.34, C:0.04, G:0.13, T:0.49
Consensus pattern (23 bp):
TTCAATTTATGTTAAGATAATGT
Found at i:295035 original size:22 final size:24
Alignment explanation
Indices: 295005--295067 Score: 60
Period size: 23 Copynumber: 2.8 Consensus size: 24
294995 AAGAAAAAAA
* *
295005 AGAAAAAGA-GAAGAAAATAG-AG
1 AGAAAAAGATAAAGAAAAGAGTAG
*
295027 AGAACAAGATAAAGAAAAGAGTAG
1 AGAAAAAGATAAAGAAAAGAGTAG
* *
295051 AGAGAAACAT-AAGAAAA
1 AGAAAAAGATAAAGAAAA
295068 TGAAAAAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
22 8 0.24
23 16 0.48
24 9 0.27
ACGTcount: A:0.67, C:0.03, G:0.24, T:0.06
Consensus pattern (24 bp):
AGAAAAAGATAAAGAAAAGAGTAG
Found at i:296690 original size:55 final size:53
Alignment explanation
Indices: 296598--296819 Score: 185
Period size: 56 Copynumber: 4.0 Consensus size: 53
296588 ATTTTAAATG
* *
296598 TGAAAGCCTAAGAGTAGTTGATT-GTTTTAAACCCAGTCAAAATTGGCACTAAAAA
1 TGAAAGCCCAAGAGTAGTT-ATTGGTTTT--GCCCAGTCAAAATTGGCACTAAAAA
296653 TGAAAGCCCAAGAGTAGTTATTTGGTTTTGCCTCAGTCAAAATTGGCACTAAAATCA
1 TGAAAGCCCAAGAGTAGTTA-TTGGTTTTGCC-CAGTCAAAATTGGCACTAAAA--A
** * * ** * *
296710 AAAAAGCCCAAGAGTAGCTAATTGGTTTTGTCCCAATTGAAATTGGTACTAAAAT
1 TGAAAGCCCAAGAGTAG-TTATTGGTTTTG-CCCAGTCAAAATTGGCACTAAAAA
* * * ** *
296765 TAGAAAGCCCATGAGTATTTGATTGATTTCAACCCAATCAAAATTGGCACTAAAA
1 T-GAAAGCCCAAGAGTAGTT-ATTGGTTT-TGCCCAGTCAAAATTGGCACTAAAA
296820 TGTTTAAGCC
Statistics
Matches: 136, Mismatches: 21, Indels: 19
0.77 0.12 0.11
Matches are distributed among these distances:
54 3 0.02
55 42 0.31
56 45 0.33
57 42 0.31
58 4 0.03
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.28
Consensus pattern (53 bp):
TGAAAGCCCAAGAGTAGTTATTGGTTTTGCCCAGTCAAAATTGGCACTAAAAA
Found at i:296736 original size:57 final size:55
Alignment explanation
Indices: 296631--296739 Score: 164
Period size: 57 Copynumber: 1.9 Consensus size: 55
296621 GTTTTAAACC
** * *
296631 CAGTCAAAATTGGCACTAAAAATGAAAGCCCAAGAGTAGTTATTTGGTTTTGCCT
1 CAGTCAAAATTGGCACTAAAAAAAAAAGCCCAAGAGTAGCTAATTGGTTTTGCCT
296686 CAGTCAAAATTGGCACTAAAATCAAAAAAGCCCAAGAGTAGCTAATTGGTTTTG
1 CAGTCAAAATTGGCACTAAAA--AAAAAAGCCCAAGAGTAGCTAATTGGTTTTG
296740 TCCCAATTGA
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
55 21 0.44
57 27 0.56
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.27
Consensus pattern (55 bp):
CAGTCAAAATTGGCACTAAAAAAAAAAGCCCAAGAGTAGCTAATTGGTTTTGCCT
Found at i:296891 original size:56 final size:55
Alignment explanation
Indices: 296692--297029 Score: 217
Period size: 56 Copynumber: 6.2 Consensus size: 55
296682 GCCTCAGTCA
* * * * **
296692 AAATTGGCACTAAAATCAAAAAAGCCCAAGAGTAGCTAATTGGTTTTGTCCCAATTG
1 AAATTGGCACTAAAATGAAAAAA-CCCAAAAGTAGTTGATTGGTTTCAT-CCAATTG
* * * * ** * * * **
296749 AAATTGGTACTAAAATTAGAAAGCCCATGAGTATTTGATTGATTTCAACCCAATCA
1 AAATTGGCACTAAAATGAAAAAACCCAAAAGTAGTTGATTGGTTTC-ATCCAATTG
*** * *
296805 AAATTGGCACTAAAATGTTTAAGCCTAAAAGTAGTTGATTGGTTTCATCCTAATTG
1 AAATTGGCACTAAAATGAAAAAACCCAAAAGTAGTTGATTGGTTTCATCC-AATTG
* *
296861 AAACTGACACTAAAATGAAAAAACCCAAAAGTA----A-TGGTTTCATCCAATTG
1 AAATTGGCACTAAAATGAAAAAACCCAAAAGTAGTTGATTGGTTTCATCCAATTG
* ** * * ** * *
296911 AAATTAGCGTTAAAATG-GAAAGCCCAGGAGTAGTTGATTGGTTTCATCTTAGTTG
1 AAATTGGCACTAAAATGAAAAAACCCAAAAGTAGTTGATTGGTTTCATC-CAATTG
* * *
296966 AATTTGGCACTAAAAT-AAAAAAGCCTAAGAA-TAGCT-ATTTGGTTTCATCCAATTG
1 AAATTGGCACTAAAATGAAAAAA-CCCAA-AAGTAGTTGA-TTGGTTTCATCCAATTG
297021 AAATTGGCA
1 AAATTGGCA
297030 TCAAATTGAT
Statistics
Matches: 211, Mismatches: 58, Indels: 26
0.72 0.20 0.09
Matches are distributed among these distances:
49 11 0.05
50 17 0.08
51 11 0.05
52 1 0.00
53 1 0.00
54 10 0.05
55 35 0.17
56 105 0.50
57 20 0.09
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (55 bp):
AAATTGGCACTAAAATGAAAAAACCCAAAAGTAGTTGATTGGTTTCATCCAATTG
Found at i:297255 original size:92 final size:93
Alignment explanation
Indices: 297097--297293 Score: 243
Period size: 92 Copynumber: 2.1 Consensus size: 93
297087 TGATCTAATA
* ** * *
297097 ACTAATAAGTTTCACCCAAGTCATCTTTTTTACCAATGATTTTACCCCGATTATCTTCTCGACTA
1 ACTAATAAGTTTCACCCAAGTCATCTCTTCAACCAATGATTTCAACCCGATTATCTTCTCGACTA
*
297162 ATAGGTTTTGTCTTAG-CGTTCCTTTTG
66 ATAGGTTTTGCCTTAGTCGTTCCTTTTG
* ** * * * *
297189 CCTAATAAGTTTCACCTTAGTCATCTCTTCAATCAATGGTTTCAACCCGATTTTTTTCTCGACTA
1 ACTAATAAGTTTCACCCAAGTCATCTCTTCAACCAATGATTTCAACCCGATTATCTTCTCGACTA
* *
297254 ATAGGTTTTGCCTTAGTCTTTTCTTTTG
66 ATAGGTTTTGCCTTAGTCGTTCCTTTTG
*
297282 ACTAATAGGTTT
1 ACTAATAAGTTT
297294 TGCCATAGTT
Statistics
Matches: 87, Mismatches: 17, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
92 68 0.78
93 19 0.22
ACGTcount: A:0.22, C:0.22, G:0.12, T:0.44
Consensus pattern (93 bp):
ACTAATAAGTTTCACCCAAGTCATCTCTTCAACCAATGATTTCAACCCGATTATCTTCTCGACTA
ATAGGTTTTGCCTTAGTCGTTCCTTTTG
Found at i:301571 original size:20 final size:20
Alignment explanation
Indices: 301508--301578 Score: 83
Period size: 20 Copynumber: 3.5 Consensus size: 20
301498 CTGAAAAAAT
*
301508 TGTATTGATACATTAACT-TA
1 TGTATTGATACATT-ACTCAA
*
301528 TGTATCGATACA-TACTGACAA
1 TGTATTGATACATTACT--CAA
301549 TGTATTGATACATTACTCAA
1 TGTATTGATACATTACTCAA
301569 TGTATTGATA
1 TGTATTGATA
301579 TATTCTGGGT
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
18 3 0.07
19 1 0.02
20 24 0.55
21 12 0.27
22 4 0.09
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.39
Consensus pattern (20 bp):
TGTATTGATACATTACTCAA
Found at i:304054 original size:80 final size:80
Alignment explanation
Indices: 303933--304119 Score: 198
Period size: 80 Copynumber: 2.3 Consensus size: 80
303923 AAAACATCAA
* * * * *
303933 AAGGGGTACTCTAACCTCCATTTTCACTTTTAAAACACTAAAATTTTTCAT-TTCTGGGGATACT
1 AAGGGGTACTCCAACC-CCGTTTTTACTTCTAAAACACTAAAATTTTTCATCTT-TAGGGATACT
**
303997 TTAA-CCTCACCATCTAC
64 CCAACCCT-ACCATCTAC
* ** * *
304014 GAGGGGTACTCCAACCCCGTTTTTACTTCTAAAATGCTAAATTTTTTTATCTTTAGGGATACTCC
1 AAGGGGTACTCCAACCCCGTTTTTACTTCTAAAACACTAAAATTTTTCATCTTTAGGGATACTCC
*
304079 AACCCTACCATCTCC
66 AACCCTACCATCTAC
*
304094 AAGGGGATACTCCAACCCCGTATTTA
1 AAGGGG-TACTCCAACCCCGTTTTTA
304120 TTTTCGAAAC
Statistics
Matches: 88, Mismatches: 15, Indels: 6
0.81 0.14 0.06
Matches are distributed among these distances:
80 51 0.58
81 37 0.42
ACGTcount: A:0.28, C:0.26, G:0.12, T:0.34
Consensus pattern (80 bp):
AAGGGGTACTCCAACCCCGTTTTTACTTCTAAAACACTAAAATTTTTCATCTTTAGGGATACTCC
AACCCTACCATCTAC
Found at i:304139 original size:81 final size:78
Alignment explanation
Indices: 303973--304158 Score: 191
Period size: 80 Copynumber: 2.3 Consensus size: 78
303963 TAAAACACTA
* ** * *
303973 AAATTTTTCATTTCTGGGGATACTTTAA-CCTCACCATCTACGAGGGGTACTCCAACCCCGTTTT
1 AAATTTTTTATTTCT-GGGATACTCCAACCCT-ACCATCTACAAGGGGTACTCCAACCCCGTATT
*
304037 TACTTCTAAAATGCT
64 TACTTCGAAAATGCT
*
304052 AAATTTTTTTATCTT-TAGGGATACTCCAACCCTACCATCTCCAAGGGGATACTCCAACCCCGTA
1 AAA-TTTTTTAT-TTCT-GGGATACTCCAACCCTACCATCTACAAGGGG-TACTCCAACCCCGTA
*
304116 TTTATTTTCGAAACAT-C-
62 TTTA-CTTCGAAA-ATGCT
*
304133 GAATTTTTTATTTCTGGGATACTCCA
1 AAATTTTTTATTTCTGGGATACTCCA
304159 CTCACGTTTT
Statistics
Matches: 90, Mismatches: 10, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
79 16 0.18
80 40 0.44
81 25 0.28
82 7 0.08
83 2 0.02
ACGTcount: A:0.26, C:0.25, G:0.13, T:0.36
Consensus pattern (78 bp):
AAATTTTTTATTTCTGGGATACTCCAACCCTACCATCTACAAGGGGTACTCCAACCCCGTATTTA
CTTCGAAAATGCT
Found at i:304284 original size:129 final size:132
Alignment explanation
Indices: 304020--304306 Score: 359
Period size: 129 Copynumber: 2.2 Consensus size: 132
304010 CTACGAGGGG
* *
304020 TACTCCAACCCCGTTTTTACTTCTAAAATGCTAAATTTTTTTATCTTTAGGGATACTCCAACCCT
1 TACTCCAATCACGTTTTTACTTCTAAAATGCTAAATTTTTTTATCTTTAGGGATACTCCAACCCT
* * **
304085 ACCATCTCCAAGGGGATACTCCAACCCCGTATTTATTTTCGAAACATCGAATTTTTTATTTCTGG
66 ACCATCTCCAAGGGGATACTCCAACCCCATATTTATTTTCGAAACATCGAATTTTTTATCTCTCA
*
304150 GA
131 AA
* * * *
304152 TACTCCACTCACGTTTTTACTTCTAAAATGCTGAA-TTTTTTATTTTTAGGGATACTCTAA-CCT
1 TACTCCAATCACGTTTTTACTTCTAAAATGCTAAATTTTTTTATCTTTAGGGATACTCCAACCCT
** * *
304215 -CACA-CTCTGAGGGGATACTCCAACCCCATTTTTACTTTT-GAAACATTGAATTTTTTATCTCT
66 AC-CATCTCCAAGGGGATACTCCAACCCCATATTTA-TTTTCGAAACATCGAATTTTTTATCTCT
304277 CAAA
129 CAAA
* *
304281 TACTCCAATCCCATTTTTTACTTCTA
1 TACTCCAATCAC-GTTTTTACTTCTA
304307 CAATATCAAA
Statistics
Matches: 134, Mismatches: 18, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
129 59 0.44
130 21 0.16
131 23 0.17
132 31 0.23
ACGTcount: A:0.26, C:0.24, G:0.10, T:0.39
Consensus pattern (132 bp):
TACTCCAATCACGTTTTTACTTCTAAAATGCTAAATTTTTTTATCTTTAGGGATACTCCAACCCT
ACCATCTCCAAGGGGATACTCCAACCCCATATTTATTTTCGAAACATCGAATTTTTTATCTCTCA
AA
Found at i:304333 original size:129 final size:129
Alignment explanation
Indices: 304020--304342 Score: 323
Period size: 129 Copynumber: 2.5 Consensus size: 129
304010 CTACGAGGGG
* * * * * *
304020 TACTCCAACCCCGTTTTTACTTCTAAAATGCTAAATTTTTTTATCTTTAGGGATACTCCAACC-C
1 TACTCCAATCACGTTTTTACTTCTAAAATGCTAAA-ATTTTCATCTCTAGGGATACTCTAACCTC
** * * *
304084 TACCATCTCCAAGGGGATACTCCAACCCCGTATTTATTTTCGAAACATCGAATTTTTTATTTCTG
65 -A-CA-CTCTGAGGGGATACTCCAACCCCATATTTATTTTCGAAACATCGAATTTTTTATCTCTC
**
304149 GGA
127 AAA
* * * * * *
304152 TACTCCACTCACGTTTTTACTTCTAAAATGCTGAATTTTTTATTTTTAGGGATACTCTAACCTCA
1 TACTCCAATCACGTTTTTACTTCTAAAATGCTAAAATTTTCATCTCTAGGGATACTCTAACCTCA
* *
304217 CACTCTGAGGGGATACTCCAACCCCATTTTTACTTTT-GAAACATTGAATTTTTTATCTCTCAAA
66 CACTCTGAGGGGATACTCCAACCCCATATTTA-TTTTCGAAACATCGAATTTTTTATCTCTCAAA
* * *
304281 TACTCCAATCCCATTTTTTACTTCTACAATAT-C-AAAATTTTCATCTCT-GGGATACTTTAACC
1 TACTCCAATCAC-GTTTTTACTTCTA-AA-ATGCTAAAATTTTCATCTCTAGGGATACTCTAACC
304343 CCATTTTTAC
Statistics
Matches: 162, Mismatches: 24, Indels: 13
0.81 0.12 0.07
Matches are distributed among these distances:
129 71 0.44
130 28 0.17
131 29 0.18
132 34 0.21
ACGTcount: A:0.27, C:0.24, G:0.10, T:0.39
Consensus pattern (129 bp):
TACTCCAATCACGTTTTTACTTCTAAAATGCTAAAATTTTCATCTCTAGGGATACTCTAACCTCA
CACTCTGAGGGGATACTCCAACCCCATATTTATTTTCGAAACATCGAATTTTTTATCTCTCAAA
Found at i:304371 original size:51 final size:51
Alignment explanation
Indices: 304226--304395 Score: 178
Period size: 52 Copynumber: 3.3 Consensus size: 51
304216 ACACTCTGAG
* * * *
304226 GGGATACTCCAACCCCATTTTTACTTTTGAAACATTGAATTTTTTATCTCT
1 GGGATACTCCAACCCCATTTTTACTTCTAAAACATTGAAATTTTCATCTCT
*** * * * **
304277 CAAATACTCCAATCCCATTTTTTACTTCTACAATATCAAAATTTTCATCTCT
1 GGGATACTCCAACCCCA-TTTTTACTTCTAAAACATTGAAATTTTCATCTCT
** * *
304329 GGGATACTTTAACCCCATTTTTACTTCCAAAACATTGAAATTTTCATCTTT
1 GGGATACTCCAACCCCATTTTTACTTCTAAAACATTGAAATTTTCATCTCT
304380 GGAGATACTCCAACCC
1 GG-GATACTCCAACCC
304396 TCACCCCTAA
Statistics
Matches: 91, Mismatches: 26, Indels: 3
0.76 0.22 0.03
Matches are distributed among these distances:
51 43 0.47
52 48 0.53
ACGTcount: A:0.29, C:0.25, G:0.07, T:0.39
Consensus pattern (51 bp):
GGGATACTCCAACCCCATTTTTACTTCTAAAACATTGAAATTTTCATCTCT
Found at i:304696 original size:45 final size:45
Alignment explanation
Indices: 304632--304722 Score: 166
Period size: 45 Copynumber: 2.0 Consensus size: 45
304622 AACCCTGTTT
304632 CTTTTCAAATTTCTTTTAAATTTCAAACTTTTTCCC-AAGGCATCC
1 CTTTTCAAATTTCTTTTAAATTTCAAAC-TTTTCCCTAAGGCATCC
304677 CTTTTCAAATTTCTTTTAAATTTCAAACTTTTCCCTAAGGCATCC
1 CTTTTCAAATTTCTTTTAAATTTCAAACTTTTCCCTAAGGCATCC
304722 C
1 C
304723 CATGTCATTA
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
44 7 0.16
45 38 0.84
ACGTcount: A:0.26, C:0.25, G:0.04, T:0.44
Consensus pattern (45 bp):
CTTTTCAAATTTCTTTTAAATTTCAAACTTTTCCCTAAGGCATCC
Found at i:308968 original size:32 final size:30
Alignment explanation
Indices: 308932--308990 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 30
308922 GAAATCAAAT
308932 ACAAAGAGCT-TAGAAAAATAATAACAATATGA
1 ACAAA-AGCTCTAGAAAAAT-ATAA-AATATGA
*
308964 ACAAAAGCTCTTGAAAAATATAAAATA
1 ACAAAAGCTCTAGAAAAATATAAAATA
308991 CTTTGATCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 4 0.16
31 8 0.32
32 13 0.52
ACGTcount: A:0.59, C:0.10, G:0.10, T:0.20
Consensus pattern (30 bp):
ACAAAAGCTCTAGAAAAATATAAAATATGA
Found at i:309289 original size:13 final size:13
Alignment explanation
Indices: 309271--309296 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
309261 ATATTTTATG
309271 TGTATCGATACAT
1 TGTATCGATACAT
309284 TGTATCGATACAT
1 TGTATCGATACAT
309297 ATTTTGTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:309308 original size:19 final size:19
Alignment explanation
Indices: 309250--309314 Score: 70
Period size: 19 Copynumber: 3.6 Consensus size: 19
309240 TACAAGCCAA
309250 TGTATCGATACATATTTTATG
1 TGTATCGATACATA-TTT-TG
309271 TGTATCGATAC--A---T-
1 TGTATCGATACATATTTTG
309284 TGTATCGATACATATTTTG
1 TGTATCGATACATATTTTG
309303 TGTATCGATACA
1 TGTATCGATACA
309315 AGTTTGGCTA
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 11 0.29
14 1 0.03
15 1 0.03
18 1 0.03
19 13 0.34
21 11 0.29
ACGTcount: A:0.29, C:0.12, G:0.15, T:0.43
Consensus pattern (19 bp):
TGTATCGATACATATTTTG
Found at i:309310 original size:32 final size:34
Alignment explanation
Indices: 309250--309314 Score: 116
Period size: 32 Copynumber: 2.0 Consensus size: 34
309240 TACAAGCCAA
309250 TGTATCGATACATATTTTATGTGTATCGATACAT
1 TGTATCGATACATATTTTATGTGTATCGATACAT
309284 TGTATCGATACATA-TTT-TGTGTATCGATACA
1 TGTATCGATACATATTTTATGTGTATCGATACA
309315 AGTTTGGCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 14 0.45
33 3 0.10
34 14 0.45
ACGTcount: A:0.29, C:0.12, G:0.15, T:0.43
Consensus pattern (34 bp):
TGTATCGATACATATTTTATGTGTATCGATACAT
Found at i:311870 original size:13 final size:13
Alignment explanation
Indices: 311852--311887 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
311842 AATCCCCCTC
311852 TATCGATACAGTG
1 TATCGATACAGTG
*
311865 TATCGATACATTG
1 TATCGATACAGTG
311878 TATCGATACA
1 TATCGATACA
311888 AAGAAAAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (13 bp):
TATCGATACAGTG
Found at i:311901 original size:20 final size:20
Alignment explanation
Indices: 311876--311952 Score: 66
Period size: 20 Copynumber: 3.6 Consensus size: 20
311866 ATCGATACAT
311876 TGTATCGATACAAAGAAAAA
1 TGTATCGATACAAAGAAAAA
**
311896 TGTATCGATACATTGAATTTCCAAA
1 TGTATCGATACAAAGAA-----AAA
*
311921 TGTATCGATACACAA-AAACA
1 TGTATCGATACA-AAGAAAAA
311941 TGTATCGATACA
1 TGTATCGATACA
311953 TTTTGGACAT
Statistics
Matches: 46, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
20 29 0.63
25 17 0.37
ACGTcount: A:0.44, C:0.16, G:0.13, T:0.27
Consensus pattern (20 bp):
TGTATCGATACAAAGAAAAA
Found at i:313988 original size:15 final size:15
Alignment explanation
Indices: 313968--313998 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
313958 ATTTCGTTTG
*
313968 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
313983 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
313998 G
1 G
313999 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:315844 original size:22 final size:20
Alignment explanation
Indices: 315796--315844 Score: 53
Period size: 22 Copynumber: 2.4 Consensus size: 20
315786 TATGCAAGTT
*
315796 TTTATTTTCTTAGCTAACTC
1 TTTATTTTCTTAGCAAACTC
* *
315816 ATTATTTTCATTAGCCAAATTC
1 TTTATTTTC-TTAG-CAAACTC
315838 TTTATTT
1 TTTATTT
315845 CAAATTGCAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 8 0.35
21 4 0.17
22 11 0.48
ACGTcount: A:0.24, C:0.16, G:0.04, T:0.55
Consensus pattern (20 bp):
TTTATTTTCTTAGCAAACTC
Found at i:317763 original size:32 final size:30
Alignment explanation
Indices: 317727--317785 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 30
317717 GAAATCAAAT
317727 ACAAAGAGCT-TAGAAAAATAATAACAATATGA
1 ACAAA-AGCTCTAGAAAAAT-ATAA-AATATGA
*
317759 ACAAAAGCTCTTGAAAAATATAAAATA
1 ACAAAAGCTCTAGAAAAATATAAAATA
317786 CTTTGATCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 4 0.16
31 8 0.32
32 13 0.52
ACGTcount: A:0.59, C:0.10, G:0.10, T:0.20
Consensus pattern (30 bp):
ACAAAAGCTCTAGAAAAATATAAAATATGA
Found at i:318105 original size:32 final size:34
Alignment explanation
Indices: 318045--318109 Score: 107
Period size: 32 Copynumber: 2.0 Consensus size: 34
318035 TACAAGCCAA
318045 TGTATCGATACATATTTTATGTGTATCGATACAT
1 TGTATCGATACATATTTTATGTGTATCGATACAT
*
318079 TGTATCGATATATA-TTT-TGTGTATCGATACA
1 TGTATCGATACATATTTTATGTGTATCGATACA
318110 AGTTTGGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 14 0.47
33 3 0.10
34 13 0.43
ACGTcount: A:0.29, C:0.11, G:0.15, T:0.45
Consensus pattern (34 bp):
TGTATCGATACATATTTTATGTGTATCGATACAT
Found at i:318967 original size:23 final size:24
Alignment explanation
Indices: 318921--318974 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 24
318911 AATTTTCTTG
* *
318921 TAAAATTTGCCCAACATAATTAAA
1 TAAAATATGCCCAACATAAATAAA
*
318945 TAAAATATGCTCAA-ATAAATAAA
1 TAAAATATGCCCAACATAAATAAA
*
318968 TCAAATA
1 TAAAATA
318975 AGCAAATGGA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
23 14 0.54
24 12 0.46
ACGTcount: A:0.56, C:0.13, G:0.04, T:0.28
Consensus pattern (24 bp):
TAAAATATGCCCAACATAAATAAA
Found at i:320532 original size:13 final size:13
Alignment explanation
Indices: 320514--320570 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
320504 TTCAACAATT
320514 TGTATCGATACAA
1 TGTATCGATACAA
320527 TGTATCGATACATAA
1 TGTATCGATAC--AA
320542 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
320559 TGTATCGATACA
1 TGTATCGATACA
320571 TAAGTTTTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.61
15 2 0.05
17 2 0.05
19 11 0.29
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:320551 original size:19 final size:18
Alignment explanation
Indices: 320527--320589 Score: 73
Period size: 19 Copynumber: 3.7 Consensus size: 18
320517 ATCGATACAA
320527 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGT-T
320546 TGTATCGATAC--AA---
1 TGTATCGATACATAAGTT
320559 TGTATCGATACATAAGTTT
1 TGTATCGATACATAAG-TT
320578 TGTATCGATACA
1 TGTATCGATACA
320590 ATGTATCGCT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.29
15 2 0.05
17 2 0.05
19 23 0.61
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (18 bp):
TGTATCGATACATAAGTT
Found at i:320554 original size:32 final size:32
Alignment explanation
Indices: 320513--320597 Score: 161
Period size: 32 Copynumber: 2.7 Consensus size: 32
320503 TTTCAACAAT
320513 TTGTATCGATACAATGTATCGATACATAAGTG
1 TTGTATCGATACAATGTATCGATACATAAGTG
*
320545 TTGTATCGATACAATGTATCGATACATAAGTT
1 TTGTATCGATACAATGTATCGATACATAAGTG
320577 TTGTATCGATACAATGTATCG
1 TTGTATCGATACAATGTATCG
320598 CTACGAAGCT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 52 1.00
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.36
Consensus pattern (32 bp):
TTGTATCGATACAATGTATCGATACATAAGTG
Found at i:327586 original size:14 final size:14
Alignment explanation
Indices: 327569--327609 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 14
327559 AGTCAAAAGT
327569 AAACACAAAAAACA
1 AAACACAAAAAACA
*
327583 AAACAAAAAAAAACA
1 AAAC-ACAAAAAACA
*
327598 ACACACAAAAAA
1 AAACACAAAAAA
327610 AGTGCAAAGG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
14 11 0.48
15 12 0.52
ACGTcount: A:0.80, C:0.20, G:0.00, T:0.00
Consensus pattern (14 bp):
AAACACAAAAAACA
Found at i:327595 original size:15 final size:17
Alignment explanation
Indices: 327575--327610 Score: 58
Period size: 15 Copynumber: 2.2 Consensus size: 17
327565 AAGTAAACAC
327575 AAAAAACAA-A-ACAAA
1 AAAAAACAACACACAAA
327590 AAAAAACAACACACAAA
1 AAAAAACAACACACAAA
327607 AAAA
1 AAAA
327611 GTGCAAAGGC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 9 0.47
16 1 0.05
17 9 0.47
ACGTcount: A:0.83, C:0.17, G:0.00, T:0.00
Consensus pattern (17 bp):
AAAAAACAACACACAAA
Found at i:328911 original size:30 final size:31
Alignment explanation
Indices: 328877--328965 Score: 112
Period size: 31 Copynumber: 2.9 Consensus size: 31
328867 CTTCAAATAC
*
328877 CTTCTT-AAAGTCCACGACTCAGTGGCATTT
1 CTTCTTCAAAGTCCACGACTCAGTGGCATCT
*
328907 CTTCTTCGAAA-TCCACAACTCAGTGGCAATCT
1 CTTCTTC-AAAGTCCACGACTCAGTGGC-ATCT
*
328939 CTT-TTCAAAGTCCACGACTCCGTGGCA
1 CTTCTTCAAAGTCCACGACTCAGTGGCA
328966 CCCTTTTAAG
Statistics
Matches: 51, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
30 10 0.20
31 32 0.63
32 9 0.18
ACGTcount: A:0.25, C:0.30, G:0.16, T:0.29
Consensus pattern (31 bp):
CTTCTTCAAAGTCCACGACTCAGTGGCATCT
Found at i:329048 original size:34 final size:33
Alignment explanation
Indices: 328968--329270 Score: 290
Period size: 34 Copynumber: 9.0 Consensus size: 33
328958 CCGTGGCACC
* ** *
328968 CTTTTAAGTCCATAACTCCATGGCAC-CTTATT
1 CTTTTAAGTCCACAACTCTGTGGCACTCTTTTT
*
329000 CTTTTTAAGCCCACAACTCTGTGGCACTCTTTTT
1 C-TTTTAAGTCCACAACTCTGTGGCACTCTTTTT
*
329034 CTTTTCAAGTCCACAACTCTGTGGCA-TCTTGTTC
1 CTTTT-AAGTCCACAACTCTGTGGCACTCTT-TTT
* * *
329068 CTTTTAAGCCCATAACTCTGTGGTACTCTTTTT
1 CTTTTAAGTCCACAACTCTGTGGCACTCTTTTT
329101 CTTTTCAAGTCCACAACTCTGTGGCAC-CTTTTT
1 CTTTT-AAGTCCACAACTCTGTGGCACTCTTTTT
* *
329134 CTTTTTAAAGCCCACAACTCCGTGGCACTCTTTTT
1 C-TTTT-AAGTCCACAACTCTGTGGCACTCTTTTT
* *
329169 CTTTTTAAAGTCTACAACTCTGTGGCA-TCTCTTTC
1 C-TTTT-AAGTCCACAACTCTGTGGCACTCT-TTTT
** * * *
329204 CTTCAAAATCCACAACTCAGTGGCATCCCTTTTT
1 CTTTTAAGTCCACAACTCTGTGGCA-CTCTTTTT
* * *
329238 CCTGTAAGTCCACAACTCAGTGGCATCTCTTTT
1 CTTTTAAGTCCACAACTCTGTGGCA-CTCTTTT
329271 CAAATCCACA
Statistics
Matches: 227, Mismatches: 33, Indels: 20
0.81 0.12 0.07
Matches are distributed among these distances:
32 1 0.00
33 77 0.34
34 113 0.50
35 36 0.16
ACGTcount: A:0.20, C:0.29, G:0.12, T:0.39
Consensus pattern (33 bp):
CTTTTAAGTCCACAACTCTGTGGCACTCTTTTT
Found at i:329085 original size:67 final size:65
Alignment explanation
Indices: 328968--329265 Score: 326
Period size: 67 Copynumber: 4.4 Consensus size: 65
328958 CCGTGGCACC
* ** * *
328968 CTTTTAAGTCCATAACTCCATGGCACCTTATTCTTTTTAAGCCCACAACTCTGTGGCACTCTTTT
1 CTTTTAAGTCCACAACTCTGTGGCATCTT-TTCCTTTTAAGCCCACAACTCTGTGGCACTCTTTT
329033 T
65 T
* *
329034 CTTTTCAAGTCCACAACTCTGTGGCATCTTGTTCCTTTTAAGCCCATAACTCTGTGGTACTCTTT
1 CTTTT-AAGTCCACAACTCTGTGGCATCTT-TTCCTTTTAAGCCCACAACTCTGTGGCACTCTTT
329099 TT
64 TT
* * *
329101 CTTTTCAAGTCCACAACTCTGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCCGTGGCACTCTT
1 CTTTT-AAGTCCACAACTCTGTGGCATC-TTTTCCTTTT-AAGCCCACAACTCTGTGGCACTCTT
329166 TTT
63 TTT
* ** ** * *
329169 CTTTTTAAAGTCTACAACTCTGTGGCATCTCTTTCCTTCAAAATCCACAACTCAGTGGCATCCCT
1 C-TTTT-AAGTCCACAACTCTGTGGCATCT-TTTCCTTTTAAGCCCACAACTCTGTGGCA-CTCT
329234 TTTT
62 TTTT
* * *
329238 CCTGTAAGTCCACAACTCAGTGGCATCT
1 CTTTTAAGTCCACAACTCTGTGGCATCT
329266 CTTTTCAAAT
Statistics
Matches: 199, Mismatches: 27, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
66 5 0.03
67 108 0.54
68 48 0.24
69 38 0.19
ACGTcount: A:0.21, C:0.29, G:0.12, T:0.38
Consensus pattern (65 bp):
CTTTTAAGTCCACAACTCTGTGGCATCTTTTCCTTTTAAGCCCACAACTCTGTGGCACTCTTTTT
Found at i:329289 original size:29 final size:28
Alignment explanation
Indices: 329242--329377 Score: 145
Period size: 27 Copynumber: 4.9 Consensus size: 28
329232 CTTTTTCCTG
329242 TAAGTCCACAAC-TCAGTGGCATCTCTTT
1 TAAGTCCACAACTTC-GTGGCATCTCTTT
*
329270 TCAAATCCACAACTTCGTGGCATC-CTTT
1 T-AAGTCCACAACTTCGTGGCATCTCTTT
*
329298 TAAGTCCACAAC-TCAGTGGCATTTCTTT
1 TAAGTCCACAACTTC-GTGGCATCTCTTT
* * *
329326 TCAAGTCCACAACTCCATGGCA-CCCTTT
1 T-AAGTCCACAACTTCGTGGCATCTCTTT
* *
329354 TAAGTCCCCAACTCCGTGGCATCT
1 TAAGTCCACAACTTCGTGGCATCT
329378 TTCTCCTTTT
Statistics
Matches: 91, Mismatches: 10, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
26 2 0.02
27 35 0.38
28 17 0.19
29 34 0.37
30 3 0.03
ACGTcount: A:0.24, C:0.32, G:0.13, T:0.30
Consensus pattern (28 bp):
TAAGTCCACAACTTCGTGGCATCTCTTT
Found at i:329316 original size:27 final size:27
Alignment explanation
Indices: 329242--329376 Score: 157
Period size: 29 Copynumber: 4.9 Consensus size: 27
329232 CTTTTTCCTG
329242 TAAGTCCACAACTCAGTGGCATCTCTTT
1 TAAGTCCACAACTCAGTGGCATC-CTTT
*
329270 TCAAATCCACAACTTC-GTGGCATCCTTT
1 T-AAGTCCACAAC-TCAGTGGCATCCTTT
*
329298 TAAGTCCACAACTCAGTGGCATTTCTTT
1 TAAGTCCACAACTCAGTGGCA-TCCTTT
*
329326 TCAAGTCCACAACTCCA-TGGCACCCTTT
1 T-AAGTCCACAACT-CAGTGGCATCCTTT
* *
329354 TAAGTCCCCAACTCCGTGGCATC
1 TAAGTCCACAACTCAGTGGCATC
329377 TTTCTCCTTT
Statistics
Matches: 92, Mismatches: 8, Indels: 15
0.80 0.07 0.13
Matches are distributed among these distances:
26 3 0.03
27 33 0.36
28 17 0.18
29 35 0.38
30 4 0.04
ACGTcount: A:0.24, C:0.33, G:0.13, T:0.30
Consensus pattern (27 bp):
TAAGTCCACAACTCAGTGGCATCCTTT
Found at i:329328 original size:56 final size:56
Alignment explanation
Indices: 329171--329377 Score: 209
Period size: 56 Copynumber: 3.5 Consensus size: 56
329161 CTCTTTTTCT
* *
329171 TTTTAAAGTCTACAACTCTGTGGCATCTCTTTCCTTCAAAATCCACAACT-CAGTGGCATCCC
1 TTTT-AAGTCCACAACTCAGTGGCATCTC-TT--TTC-AAATCCACAACTCCA-TGGCA-CCC
* * *
329233 TTTTTCCTGTAAGTCCACAACTCAGTGGCATCTCTTTTCAAATCCACAACTTCGTGGCATCC
1 ---TT--T-TAAGTCCACAACTCAGTGGCATCTCTTTTCAAATCCACAACTCCATGGCACCC
* *
329295 TTTTAAGTCCACAACTCAGTGGCATTTCTTTTCAAGTCCACAACTCCATGGCACCC
1 TTTTAAGTCCACAACTCAGTGGCATCTCTTTTCAAATCCACAACTCCATGGCACCC
* *
329351 TTTTAAGTCCCCAACTCCGTGGCATCT
1 TTTTAAGTCCACAACTCAGTGGCATCT
329378 TTCTCCTTTT
Statistics
Matches: 126, Mismatches: 12, Indels: 17
0.81 0.08 0.11
Matches are distributed among these distances:
56 72 0.57
57 1 0.01
59 2 0.02
62 2 0.02
63 17 0.13
64 4 0.03
65 2 0.02
66 2 0.02
67 23 0.18
68 1 0.01
ACGTcount: A:0.24, C:0.31, G:0.13, T:0.32
Consensus pattern (56 bp):
TTTTAAGTCCACAACTCAGTGGCATCTCTTTTCAAATCCACAACTCCATGGCACCC
Found at i:329604 original size:92 final size:92
Alignment explanation
Indices: 329454--330372 Score: 955
Period size: 92 Copynumber: 9.9 Consensus size: 92
329444 TCTTTTAAAC
* * * *
329454 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACATTTGTCTTTAAGACCAATGTCGCTGGCCT
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTTGTCTTTAAGTCCAATATCGCTGGCCT
329519 TGAATCAGCACATTGGCACCTTTAAGT
66 TGAATCAGCACATTGGCACCTTTAAGT
* * *
329546 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCTTTAAGACCAATGTCGCTGGCCT
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTTGTCTTTAAGTCCAATATCGCTGGCCT
*
329611 TAAATCAGCACATTGGCACCTTTAAGT
66 TGAATCAGCACATTGGCACCTTTAAGT
* * *
329638 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCTTTAAGTCCAATGTCGTTGGCCT
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTTGTCTTTAAGTCCAATATCGCTGGCCT
329703 TGAATCAGCACATTGGCACCTTTAAGT
66 TGAATCAGCACATTGGCACCTTTAAGT
* * * * *
329730 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACATTTGTCTTAAAGACCAATGTCGCTGGCCT
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTTGTCTTTAAGTCCAATATCGCTGGCCT
329795 TGAATCAGCACATTGGCACCTTTAAGT
66 TGAATCAGCACATTGGCACCTTTAAGT
* *
329822 CCAATATCGCTGGCCTTGAATCAGCACATTGGCA-C-----C-TTATGTCCAATATCGCTTGCCT
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTTGTCTTTAAGTCCAATATCGCTGGCCT
* * *
329880 TGAATTAGCATATTGGCACCTTTGTCTTTAAGA
66 TGAATCAGCACATTGGCA-C-----CTTTAAGT
*
329913 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCA-C-----CTTTAAGTCCAATATCGCTGGCCT
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTTGTCTTTAAGTCCAATATCGCTGGCCT
* * *
329972 TGAATCGGCATATTGGCACCTTTGTCTTTAAGA
66 TGAATCAGCACATTGGCA-C-----CTTTAAGT
* *
330005 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCA-C----T-TTTAAGTCCAATATCGTTGGCCT
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTTGTCTTTAAGTCCAATATCGCTGGCCT
* *
330064 TGAATCAGCATATTGGCACCTTTGTCTTTAAGA
66 TGAATCAGCACATTGGCA-C-----CTTTAAGT
* *
330097 CCAATGTCACTGGCCTTGAATCAGCACATTGGCA-C-----CTTTAAGTCCAATATCGCTGGCCT
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTTGTCTTTAAGTCCAATATCGCTGGCCT
* *
330156 TGAATCAGCATATTGGCACCTTTGTCTTTAAGA
66 TGAATCAGCACATTGGCA-C-----CTTTAAGT
*
330189 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCA-C-----CTTTAAGTCCAATATCGCTGGCCT
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTTGTCTTTAAGTCCAATATCGCTGGCCT
*
330248 TGAATCAGCATATTGGCACCTTTGTCATCTTTTCAGT
66 TGAATCAGCACATTGGCACC-TT-T-A-------AGT
* ** *
330285 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTTAAGTCCAATGTCGCTGGCC
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTTGTC-TTTAAGTCCAATATCGCTGGCC
330350 TTGAATCAGCACATTGGCACCTT
65 TTGAATCAGCACATTGGCACCTT
330373 CATCTTTAAC
Statistics
Matches: 769, Mismatches: 32, Indels: 42
0.91 0.04 0.05
Matches are distributed among these distances:
85 33 0.04
86 3 0.00
87 2 0.00
88 1 0.00
89 1 0.00
91 43 0.06
92 605 0.79
96 36 0.05
97 1 0.00
102 3 0.00
103 41 0.05
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.31
Consensus pattern (92 bp):
CCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTTGTCTTTAAGTCCAATATCGCTGGCCT
TGAATCAGCACATTGGCACCTTTAAGT
Found at i:329816 original size:21 final size:21
Alignment explanation
Indices: 329792--329859 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 21
329782 ATGTCGCTGG
329792 CCTTGAATCAGCACATTGGCA
1 CCTTGAATCAGCACATTGGCA
* * *
329813 CCTTTAAGTC--CA-ATATCGCTGG
1 CCTTGAA-TCAGCACAT-TGGC--A
329835 CCTTGAATCAGCACATTGGCA
1 CCTTGAATCAGCACATTGGCA
329856 CCTT
1 CCTT
329860 ATGTCCAATA
Statistics
Matches: 34, Mismatches: 6, Indels: 14
0.63 0.11 0.26
Matches are distributed among these distances:
19 2 0.06
20 5 0.15
21 12 0.35
22 8 0.24
23 5 0.15
24 2 0.06
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.28
Consensus pattern (21 bp):
CCTTGAATCAGCACATTGGCA
Found at i:330214 original size:410 final size:415
Alignment explanation
Indices: 329454--330372 Score: 1578
Period size: 410 Copynumber: 2.2 Consensus size: 415
329444 TCTTTTAAAC
*
329454 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACATTTGTCTTTAAGACCAATGTCGCTGGCCT
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCTTTAAGACCAATGTCGCTGGCCT
329519 TGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT
66 TGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT
329584 TGTCTTTAAGACCAATGTCGCTGGCCTTAAATCAGCACATTGGCACCTTTAAGTCCAATATCGCT
131 TGTCTTTAAGACCAATGTCGCTGGCCTTAAATCAGCACATTGGCACCTTTAAGTCCAATATCGCT
* **
329649 GGCCTTGAATCAGCATATTGGCACCTTTGTCTTTAAGTCCAATGTCGTTGGCCTTGAATCAGCAC
196 GGCCTTGAATCAGCATATTGGCACCTTTGTCTTTAAGACCAATGTCACTGGCCTTGAATCAGCAC
329714 ATTGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACATTTGTCTTAAAGA
261 ATTGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACATTTGTCTTAAAGA
329779 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATC
326 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATC
329844 AGCACATTGGCACC-T-T-A-T-GT
391 AGCACATTGGCACCTTGTCATTAGT
* *
329864 CCAATATCGCTTGCCTTGAATTAGCATATTGGCACCTTTGTCTTTAAGACCAATGTCGCTGGCCT
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCTTTAAGACCAATGTCGCTGGCCT
*
329929 TGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATCGGCATATTGGCACCTT
66 TGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT
* * *
329994 TGTCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACTTTTAAGTCCAATATCGTT
131 TGTCTTTAAGACCAATGTCGCTGGCCTTAAATCAGCACATTGGCACCTTTAAGTCCAATATCGCT
330059 GGCCTTGAATCAGCATATTGGCACCTTTGTCTTTAAGACCAATGTCACTGGCCTTGAATCAGCAC
196 GGCCTTGAATCAGCATATTGGCACCTTTGTCTTTAAGACCAATGTCACTGGCCTTGAATCAGCAC
* *
330124 ATTGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCTTTAAGA
261 ATTGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACATTTGTCTTAAAGA
330189 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATC
326 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATC
*
330254 AGCATATTGGCACCTTTGTCATCTTTTCAGT
391 AGCACATTGGCACC-TTGTCA----TT-AGT
* * ** *
330285 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTTAAGTCCAATGTCGCTGGCC
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTC-TTTAAGACCAATGTCGCTGGCC
330350 TTGAATCAGCACATTGGCACCTT
65 TTGAATCAGCACATTGGCACCTT
330373 CATCTTTAAC
Statistics
Matches: 477, Mismatches: 20, Indels: 12
0.94 0.04 0.02
Matches are distributed among these distances:
410 391 0.82
412 1 0.00
413 1 0.00
414 1 0.00
419 1 0.00
421 38 0.08
422 44 0.09
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.31
Consensus pattern (415 bp):
CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCTTTAAGACCAATGTCGCTGGCCT
TGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT
TGTCTTTAAGACCAATGTCGCTGGCCTTAAATCAGCACATTGGCACCTTTAAGTCCAATATCGCT
GGCCTTGAATCAGCATATTGGCACCTTTGTCTTTAAGACCAATGTCACTGGCCTTGAATCAGCAC
ATTGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACATTTGTCTTAAAGA
CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATC
AGCACATTGGCACCTTGTCATTAGT
Found at i:330347 original size:50 final size:50
Alignment explanation
Indices: 330225--330379 Score: 256
Period size: 50 Copynumber: 3.0 Consensus size: 50
330215 CATTGGCACC
* *
330225 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCATCT
1 TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACC--T-TCATCT
*
330278 TTTCAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCT
1 TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCT
330328 TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCT
1 TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCT
330378 TT
1 TT
330380 AACATTCCTA
Statistics
Matches: 98, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
50 57 0.58
51 1 0.01
53 40 0.41
ACGTcount: A:0.21, C:0.27, G:0.17, T:0.34
Consensus pattern (50 bp):
TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCT
Found at i:331246 original size:13 final size:13
Alignment explanation
Indices: 331228--331252 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
331218 TTCAACGATT
331228 TGTATCGATACAA
1 TGTATCGATACAA
331241 TGTATCGATACA
1 TGTATCGATACA
331253 TAAGTGTTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:331286 original size:76 final size:76
Alignment explanation
Indices: 331198--331347 Score: 300
Period size: 76 Copynumber: 2.0 Consensus size: 76
331188 ACAAGGTCCC
331198 AACGGTCAAAAATTTTGAATTTCAACGATTTGTATCGATACAATGTATCGATACATAAGTGTTGT
1 AACGGTCAAAAATTTTGAATTTCAACGATTTGTATCGATACAATGTATCGATACATAAGTGTTGT
331263 ATCGATACAAT
66 ATCGATACAAT
331274 AACGGTCAAAAATTTTGAATTTCAACGATTTGTATCGATACAATGTATCGATACATAAGTGTTGT
1 AACGGTCAAAAATTTTGAATTTCAACGATTTGTATCGATACAATGTATCGATACATAAGTGTTGT
331339 ATCGATACA
66 ATCGATACA
331348 TAAGTTTTGT
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 74 1.00
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.34
Consensus pattern (76 bp):
AACGGTCAAAAATTTTGAATTTCAACGATTTGTATCGATACAATGTATCGATACATAAGTGTTGT
ATCGATACAAT
Found at i:331322 original size:13 final size:13
Alignment explanation
Indices: 331304--331328 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
331294 TTCAACGATT
331304 TGTATCGATACAA
1 TGTATCGATACAA
331317 TGTATCGATACA
1 TGTATCGATACA
331329 TAAGTGTTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:331341 original size:19 final size:19
Alignment explanation
Indices: 331317--331366 Score: 91
Period size: 19 Copynumber: 2.6 Consensus size: 19
331307 ATCGATACAA
331317 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGTGT
*
331336 TGTATCGATACATAAGTTT
1 TGTATCGATACATAAGTGT
331355 TGTATCGATACA
1 TGTATCGATACA
331367 ATGTATCGCT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.38
Consensus pattern (19 bp):
TGTATCGATACATAAGTGT
Found at i:331437 original size:13 final size:13
Alignment explanation
Indices: 331419--331443 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
331409 ATTACTCAAA
331419 TGTATCGATACAT
1 TGTATCGATACAT
331432 TGTATCGATACA
1 TGTATCGATACA
331444 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:331508 original size:20 final size:20
Alignment explanation
Indices: 331483--331553 Score: 103
Period size: 20 Copynumber: 3.6 Consensus size: 20
331473 ATTTGCCCAG
331483 ATGTATCGATACACTATGAA
1 ATGTATCGATACACTATGAA
*
331503 ATGTATCGATACACCCA-G--
1 ATGTATCGATACA-CTATGAA
331521 ATGTATCGATACACTATGAA
1 ATGTATCGATACACTATGAA
331541 ATGTATCGATACA
1 ATGTATCGATACA
331554 TGCAGGCAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
17 2 0.04
18 14 0.31
20 27 0.60
21 2 0.04
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.28
Consensus pattern (20 bp):
ATGTATCGATACACTATGAA
Done.