Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001478.1 Hibiscus syriacus cultivar Beakdansim tig00002868_pilon, whole genome shotgun sequence
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: 623040
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
File 3 of 5
Found at i:236339 original size:11 final size:11
Alignment explanation
Indices: 236327--236369 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
236317 TATCTATTAT
236327 TTTTA-TTTTA
1 TTTTATTTTTA
236337 TTTTATTTTTA
1 TTTTATTTTTA
*
236348 TTTTATTTGTTG
1 TTTTATTT-TTA
*
236360 TTTTCTTTTT
1 TTTTATTTTT
236370 TTATATTTGG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
10 5 0.17
11 15 0.52
12 9 0.31
ACGTcount: A:0.12, C:0.02, G:0.05, T:0.81
Consensus pattern (11 bp):
TTTTATTTTTA
Found at i:236344 original size:16 final size:16
Alignment explanation
Indices: 236323--236355 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
236313 TATATATCTA
236323 TTATTTTTATTTTATT
1 TTATTTTTATTTTATT
236339 TTATTTTTATTTTATT
1 TTATTTTTATTTTATT
236355 T
1 T
236356 GTTGTTTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (16 bp):
TTATTTTTATTTTATT
Found at i:236428 original size:19 final size:18
Alignment explanation
Indices: 236395--236441 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
236385 TTTTCATTAC
*
236395 TTTTTTTCTTCTTTT-TT
1 TTTTTTTATTCTTTTGTT
236412 TATTTTTTATTCATTTTGTT
1 T-TTTTTTATTC-TTTTGTT
*
236432 TTGTTTTATT
1 TTTTTTTATT
236442 TCTATTTTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
17 1 0.04
18 9 0.36
19 12 0.48
20 3 0.12
ACGTcount: A:0.09, C:0.06, G:0.04, T:0.81
Consensus pattern (18 bp):
TTTTTTTATTCTTTTGTT
Found at i:236483 original size:19 final size:19
Alignment explanation
Indices: 236395--236483 Score: 74
Period size: 18 Copynumber: 4.5 Consensus size: 19
236385 TTTTCATTAC
* * *
236395 TTTTTTTCTTCTTTTTTTA
1 TTTTTTTATTCTATTTTCA
**
236414 -TTTTTTATTC-ATTTTGT
1 TTTTTTTATTCTATTTTCA
236431 TTTGTTTTATTTCTATTTTACCA
1 TTT-TTTTA-TTCTATTTT--CA
236454 TTTTATTTATTCTATTTTCA
1 TTTT-TTTATTCTATTTTCA
236474 TTTTTTTATT
1 TTTTTTTATT
236484 TTTCCTTTGT
Statistics
Matches: 57, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
17 4 0.07
18 11 0.19
19 11 0.19
20 9 0.16
21 5 0.09
22 10 0.18
23 7 0.12
ACGTcount: A:0.13, C:0.09, G:0.02, T:0.75
Consensus pattern (19 bp):
TTTTTTTATTCTATTTTCA
Found at i:239465 original size:2 final size:2
Alignment explanation
Indices: 239458--239543 Score: 172
Period size: 2 Copynumber: 43.0 Consensus size: 2
239448 TAAAACATTA
239458 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
239500 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
239542 AT
1 AT
239544 TAGCCATGCA
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 84 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:239783 original size:2 final size:2
Alignment explanation
Indices: 239778--239804 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
239768 TTTATTTCAT
239778 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
239805 TATTACCCAC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:240936 original size:57 final size:57
Alignment explanation
Indices: 240867--240980 Score: 210
Period size: 57 Copynumber: 2.0 Consensus size: 57
240857 TCCACTTATA
*
240867 CTTGTATTGTTGGTGGATATAGTGATTGTAGTGGAGCATGGTGGAAAAATGAGGTGT
1 CTTGTATTGTTGGTGGAGATAGTGATTGTAGTGGAGCATGGTGGAAAAATGAGGTGT
*
240924 CTTGTATTGTTGGTGGAGATAGTGCTTGTAGTGGAGCATGGTGGAAAAATGAGGTGT
1 CTTGTATTGTTGGTGGAGATAGTGATTGTAGTGGAGCATGGTGGAAAAATGAGGTGT
240981 TTACATCTGC
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
57 55 1.00
ACGTcount: A:0.24, C:0.04, G:0.38, T:0.34
Consensus pattern (57 bp):
CTTGTATTGTTGGTGGAGATAGTGATTGTAGTGGAGCATGGTGGAAAAATGAGGTGT
Found at i:241379 original size:134 final size:134
Alignment explanation
Indices: 241140--241904 Score: 1165
Period size: 134 Copynumber: 5.7 Consensus size: 134
241130 TGTTTGATCC
* * * * * *
241140 ATTGAATTGGGGTAGACTTGTTTCGCTGTCACTCA-GGAATATTAAATCTTGGAAGA-TATGAAT
1 ATTGAATCGTGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAATG-AT
* *
241203 CTGTTCCGCTTCTTCTGAAGGGAATATCAGATTTGGATGAGTTGATCAATTCCGCTGTCACTCAG
65 CTGTTCCGCTTCTTCTGAAGGGAATATCAGATCTGGATGAGTTGATCCATTCCGCTGTCACTCAG
241268 GGAAG
130 GGAAG
*
241273 ATTGAATCGTGGTAGACTTGTTCCGCTGTCACTTAGGGAATATCAAATCTTGAAAGAGAATGATC
1 ATTGAATCGTGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAATGATC
* * * *
241338 TATTCCTCCTCTTCTGAAGGAAATATCAGATCTGGATGAGTTGATCCATTCCGCTGTCACTCAGG
66 TGTTCCGCTTCTTCTGAAGGGAATATCAGATCTGGATGAGTTGATCCATTCCGCTGTCACTCAGG
241403 GAAG
131 GAAG
* * * * *
241407 ATTGAATCGTGGTAGACTTGCTCTGTTGTCACTCAGGGAATATCAAATCTTGAAAGAGAATAATA
1 ATTGAATCGTGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAATGATC
* * * * *
241472 TGTTCCACTTCTTCTAAAGAGAATATCAAATCTGGATGAGTTGATCCATTCTGCTGTCACTCAGG
66 TGTTCCGCTTCTTCTGAAGGGAATATCAGATCTGGATGAGTTGATCCATTCCGCTGTCACTCAGG
241537 GAAG
131 GAAG
* *
241541 ATTGAATCGTGGTAGACTTATTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGTGATC
1 ATTGAATCGTGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAATGATC
* * *
241606 TGTTCCGCTTCTTCTGAAGGGAATATCAGATTTAGATGAGTTGATCCATTCTGCTGTCACTCAGG
66 TGTTCCGCTTCTTCTGAAGGGAATATCAGATCTGGATGAGTTGATCCATTCCGCTGTCACTCAGG
241671 GAAG
131 GAAG
* * *
241675 ATTGAATCGTGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCCAATCTTGAAAGAGAGTGATA
1 ATTGAATCGTGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAATGATC
* * * *
241740 TATTTCGCTTCTTCTGAAGGGAATATCATATCTGGATGAGATGATCCATTCCGCTGTCACTCAGG
66 TGTTCCGCTTCTTCTGAAGGGAATATCAGATCTGGATGAGTTGATCCATTCCGCTGTCACTCAGG
241805 GAAG
131 GAAG
*
241809 ATTGAATCGTGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGTGATC
1 ATTGAATCGTGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAATGATC
**
241874 TGTTCTACTTCTTCTGAAGGGAATATCAGAT
66 TGTTCCGCTTCTTCTGAAGGGAATATCAGAT
241905 AGATGGATTT
Statistics
Matches: 573, Mismatches: 57, Indels: 3
0.91 0.09 0.00
Matches are distributed among these distances:
133 31 0.05
134 539 0.94
135 3 0.01
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.32
Consensus pattern (134 bp):
ATTGAATCGTGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAATGATC
TGTTCCGCTTCTTCTGAAGGGAATATCAGATCTGGATGAGTTGATCCATTCCGCTGTCACTCAGG
GAAG
Found at i:242031 original size:79 final size:78
Alignment explanation
Indices: 241933--242140 Score: 337
Period size: 79 Copynumber: 2.6 Consensus size: 78
241923 GTTCTTCCGT
*
241933 GAAGGCTTA-TGATTGATTTGCTTCACTACTCTTCAGTGAAGGCTTAAGATGGCCCGGAGGACTT
1 GAAGGCTTACTGA-TGATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGATGGCCCGGAGGACTT
241997 AATCGTCATGCTCA
65 AATCGTCATGCTCA
242011 GAAGGCTTACTGATGAATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGATGGCCCGGAGGACTT
1 GAAGGCTTACTGATG-ATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGATGGCCCGGAGGACTT
**
242076 AATCGTCATGCTTG
65 AATCGTCATGCTCA
* *
242090 GAAGGCCTACTGATGGATTTGTTTCACTACTCTTCGGTGAAGGCTTAAGAT
1 GAAGGCTTACTGAT-GATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGAT
242141 AGATTTGCTT
Statistics
Matches: 122, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
78 11 0.09
79 110 0.90
80 1 0.01
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.31
Consensus pattern (78 bp):
GAAGGCTTACTGATGATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGATGGCCCGGAGGACTTA
ATCGTCATGCTCA
Found at i:242133 original size:38 final size:37
Alignment explanation
Indices: 242090--242177 Score: 122
Period size: 37 Copynumber: 2.4 Consensus size: 37
242080 GTCATGCTTG
* * *
242090 GAAGGCCTACTGATGGATTTGTTTCACTACTCTTCGGT
1 GAAGGCCTA-AGATAGATTTGCTTCACTACTCTTCGGT
*
242128 GAAGGCTTAAGATAGATTTGCTTCACTACTCTTCGGT
1 GAAGGCCTAAGATAGATTTGCTTCACTACTCTTCGGT
*
242165 GAAGGCTTAAGAT
1 GAAGGCCTAAGAT
242178 GGCCCGAAGG
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
37 38 0.83
38 8 0.17
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (37 bp):
GAAGGCCTAAGATAGATTTGCTTCACTACTCTTCGGT
Found at i:242147 original size:37 final size:37
Alignment explanation
Indices: 242105--242177 Score: 137
Period size: 37 Copynumber: 2.0 Consensus size: 37
242095 CCTACTGATG
*
242105 GATTTGTTTCACTACTCTTCGGTGAAGGCTTAAGATA
1 GATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGATA
242142 GATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGAT
1 GATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGAT
242178 GGCCCGAAGG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.23, C:0.18, G:0.22, T:0.37
Consensus pattern (37 bp):
GATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGATA
Found at i:242147 original size:116 final size:116
Alignment explanation
Indices: 242027--242258 Score: 419
Period size: 116 Copynumber: 2.0 Consensus size: 116
242017 TTACTGATGA
* **
242027 ATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGATGGCCCGGAGGACTTAATCGTCATGCTTGGA
1 ATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGATGGCCCGAAGGACTTAATCGTCATGCTCAGA
*
242092 AGGCCTACTGATGGATTTGTTTCACTACTCTTCGGTGAAGGCTTAAGATAG
66 AGGCCTACTGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGATAG
242143 ATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGATGGCCCGAAGGACTTAATCGTCATGCTCAGA
1 ATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGATGGCCCGAAGGACTTAATCGTCATGCTCAGA
*
242208 AGGCTTACTGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGATAG
66 AGGCCTACTGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGATAG
242259 CCCGGATGAC
Statistics
Matches: 111, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
116 111 1.00
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.31
Consensus pattern (116 bp):
ATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGATGGCCCGAAGGACTTAATCGTCATGCTCAGA
AGGCCTACTGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGATAG
Found at i:242229 original size:79 final size:79
Alignment explanation
Indices: 242128--242304 Score: 284
Period size: 79 Copynumber: 2.3 Consensus size: 79
242118 ACTCTTCGGT
* * *
242128 GAAGGCTTA-AGATAGATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGATGGCCCGAAGGACTT
1 GAAGGCTTACTGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGATAGCCCGAAGGACTT
*
242192 AATCGTCATGCTCA
66 AATCATCATGCTCA
* *
242206 GAAGGCTTACTGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGATAGCCCGGATGACTT
1 GAAGGCTTACTGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGATAGCCCGAAGGACTT
*
242271 AATCATCATGCTCG
66 AATCATCATGCTCA
242285 GAAGGCTTACTGATGGATTT
1 GAAGGCTTACTGATGGATTT
242305 AATCATCATG
Statistics
Matches: 91, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
78 9 0.10
79 82 0.90
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (79 bp):
GAAGGCTTACTGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGATAGCCCGAAGGACTT
AATCATCATGCTCA
Found at i:242238 original size:195 final size:195
Alignment explanation
Indices: 241906--242304 Score: 672
Period size: 195 Copynumber: 2.0 Consensus size: 195
241896 ATATCAGATA
** * *
241906 GATGGATTTGCTTCACTGTTCTTCCGTGAAGGCTTATGATTGATTTGCTTCACTACTCTTCAGTG
1 GATGGATTTGCTTCACTACTCTTCCGTGAAGGCTTAAGATAGATTTGCTTCACTACTCTTCAGTG
*
241971 AAGGCTTAAGATGGCCCGGAGGACTTAATCGTCATGCTCAGAAGGCTTACTGATGAATTTGCTTC
66 AAGGCTTAAGATGGCCCGAAGGACTTAATCGTCATGCTCAGAAGGCTTACTGATGAATTTGCTTC
* * *
242036 ACTACTCTTCGGTGAAGGCTTAAGATGGCCCGGAGGACTTAATCGTCATGCTTGGAAGGCCTACT
131 ACTACTCTTCGGTGAAGGCTTAAGATAGCCCGGAGGACTTAATCATCATGCTCGGAAGGCCTACT
* * *
242101 GATGGATTTGTTTCACTACTCTTCGGTGAAGGCTTAAGATAGATTTGCTTCACTACTCTTCGGTG
1 GATGGATTTGCTTCACTACTCTTCCGTGAAGGCTTAAGATAGATTTGCTTCACTACTCTTCAGTG
*
242166 AAGGCTTAAGATGGCCCGAAGGACTTAATCGTCATGCTCAGAAGGCTTACTGATGGATTTGCTTC
66 AAGGCTTAAGATGGCCCGAAGGACTTAATCGTCATGCTCAGAAGGCTTACTGATGAATTTGCTTC
* *
242231 ACTACTCTTCGGTGAAGGCTTAAGATAGCCCGGATGACTTAATCATCATGCTCGGAAGGCTTACT
131 ACTACTCTTCGGTGAAGGCTTAAGATAGCCCGGAGGACTTAATCATCATGCTCGGAAGGCCTACT
242296 GATGGATTT
1 GATGGATTT
242305 AATCATCATG
Statistics
Matches: 190, Mismatches: 14, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
195 190 1.00
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.32
Consensus pattern (195 bp):
GATGGATTTGCTTCACTACTCTTCCGTGAAGGCTTAAGATAGATTTGCTTCACTACTCTTCAGTG
AAGGCTTAAGATGGCCCGAAGGACTTAATCGTCATGCTCAGAAGGCTTACTGATGAATTTGCTTC
ACTACTCTTCGGTGAAGGCTTAAGATAGCCCGGAGGACTTAATCATCATGCTCGGAAGGCCTACT
Found at i:244881 original size:8 final size:8
Alignment explanation
Indices: 244868--244902 Score: 54
Period size: 8 Copynumber: 4.4 Consensus size: 8
244858 TCAATCCATC
244868 CTTTTTTT
1 CTTTTTTT
244876 CTTTTTTT
1 CTTTTTTT
244884 -TCTTTTTT
1 CT-TTTTTT
244892 CTTTTTTT
1 CTTTTTTT
244900 CTT
1 CTT
244903 CTTACTTCGA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
7 1 0.04
8 23 0.92
9 1 0.04
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (8 bp):
CTTTTTTT
Found at i:250244 original size:17 final size:18
Alignment explanation
Indices: 250200--250244 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
250190 TTAAACATTC
250200 ATACATAAAAATAATATA
1 ATACATAAAAATAATATA
250218 AT-CAT-AAAAT-ATA-A
1 ATACATAAAAATAATATA
250232 ATACATAAGAAAT
1 ATACATAA-AAAT
250245 TTTACTACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
14 3 0.12
15 6 0.25
16 6 0.25
17 7 0.29
18 2 0.08
ACGTcount: A:0.64, C:0.07, G:0.02, T:0.27
Consensus pattern (18 bp):
ATACATAAAAATAATATA
Found at i:250827 original size:2 final size:2
Alignment explanation
Indices: 250820--250861 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
250810 TTTGTGGATC
250820 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
250861 A
1 A
250862 ACACTAAACC
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:251542 original size:57 final size:57
Alignment explanation
Indices: 251472--251587 Score: 205
Period size: 57 Copynumber: 2.0 Consensus size: 57
251462 TCCACTTATA
*
251472 CTTGTATTATTGGTGGAGATAGTGTTTGTAGTGGAGCATGGTGGAAAAACGAGGTGT
1 CTTGTATTATTGGTGGAGATAGTGATTGTAGTGGAGCATGGTGGAAAAACGAGGTGT
* *
251529 CTTGTATTGTTGGTGGAGATAGTGATTGTAGTGGAGCATGGTGGAAAAATGAGGTGT
1 CTTGTATTATTGGTGGAGATAGTGATTGTAGTGGAGCATGGTGGAAAAACGAGGTGT
251586 CT
1 CT
251588 ACAAGAAGAA
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
57 56 1.00
ACGTcount: A:0.24, C:0.05, G:0.37, T:0.34
Consensus pattern (57 bp):
CTTGTATTATTGGTGGAGATAGTGATTGTAGTGGAGCATGGTGGAAAAACGAGGTGT
Found at i:253604 original size:21 final size:21
Alignment explanation
Indices: 253578--253619 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
253568 CAATTGTGTA
253578 TCGATGCACCGCTAAAGTGCT
1 TCGATGCACCGCTAAAGTGCT
* *
253599 TCGATGCACTGCTACAGTGCT
1 TCGATGCACCGCTAAAGTGCT
253620 GCTACAGTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (21 bp):
TCGATGCACCGCTAAAGTGCT
Found at i:254481 original size:31 final size:32
Alignment explanation
Indices: 254443--254550 Score: 114
Period size: 31 Copynumber: 3.4 Consensus size: 32
254433 GAACCTCAGC
* *
254443 AACTGTCCATAGGTCCCGAT-GAACCTAGGTA
1 AACTGTCCATATGTCCCGATAGAACATAGGTA
* *
254474 AACTGTCCATATGTTCC-TTAGAACATAGGTA
1 AACTGTCCATATGTCCCGATAGAACATAGGTA
* *
254505 TACTGTCCATATGTCCCGAAAG-ACATAGGTA
1 AACTGTCCATATGTCCCGATAGAACATAGGTA
* *
254536 ATTCTGCCCATATGT
1 A-ACTGTCCATATGT
254551 TACGTAGAAT
Statistics
Matches: 63, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
30 1 0.02
31 49 0.78
32 13 0.21
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.29
Consensus pattern (32 bp):
AACTGTCCATATGTCCCGATAGAACATAGGTA
Found at i:262140 original size:16 final size:16
Alignment explanation
Indices: 262119--262152 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
262109 ATGGGTGGAG
262119 GTTGCGTCATATGACA
1 GTTGCGTCATATGACA
262135 GTTGCGTCATATGACA
1 GTTGCGTCATATGACA
262151 GT
1 GT
262153 GTCACTTAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.32
Consensus pattern (16 bp):
GTTGCGTCATATGACA
Found at i:264728 original size:21 final size:24
Alignment explanation
Indices: 264702--264754 Score: 69
Period size: 21 Copynumber: 2.4 Consensus size: 24
264692 TCCACCAATA
*
264702 TTATATTAT-ATA-ATAT-ATTTT
1 TTATATTATAATATATATAATTAT
264723 TTATATTATAATATATATAATTAT
1 TTATATTATAATATATATAATTAT
264747 TTAT-TTAT
1 TTATATTAT
264755 TTGGGTTACA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 9 0.32
22 3 0.11
23 8 0.29
24 8 0.29
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (24 bp):
TTATATTATAATATATATAATTAT
Found at i:264755 original size:26 final size:26
Alignment explanation
Indices: 264699--264755 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
264689 TTGTCCACCA
*
264699 ATATTATATTATATAATATATTTTTT
1 ATATTATATTATATAATATATTTATT
264725 ATATTATAATATATATAAT-TATTTATT
1 ATATTAT-AT-TATATAATATATTTATT
264752 -TATT
1 ATATT
264756 TGGGTTACAG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
26 11 0.39
27 9 0.32
28 8 0.29
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (26 bp):
ATATTATATTATATAATATATTTATT
Found at i:268383 original size:15 final size:15
Alignment explanation
Indices: 268363--268405 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
268353 ATTTATCTTT
268363 TTAATTTTATAAAAA
1 TTAATTTTATAAAAA
* *
268378 TTAATTTTAT-GAAT
1 TTAATTTTATAAAAA
268392 TTACATTTTATAAA
1 TTA-ATTTTATAAA
268406 GAAAATATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
14 5 0.22
15 17 0.74
16 1 0.04
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (15 bp):
TTAATTTTATAAAAA
Found at i:274353 original size:19 final size:19
Alignment explanation
Indices: 274329--274368 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
274319 GATTTTCACA
274329 TGACAGGTTCTACATTCAT
1 TGACAGGTTCTACATTCAT
274348 TGACAGGTTCTACATTCAT
1 TGACAGGTTCTACATTCAT
274367 TG
1 TG
274369 TGATGGACTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.25, C:0.20, G:0.17, T:0.38
Consensus pattern (19 bp):
TGACAGGTTCTACATTCAT
Found at i:275030 original size:45 final size:45
Alignment explanation
Indices: 274976--275066 Score: 182
Period size: 45 Copynumber: 2.0 Consensus size: 45
274966 GTGGTGTTTC
274976 TGGCCACAAGTTTGTGGGTTGTCCAATGCCTTGTGGTGTTCAGAT
1 TGGCCACAAGTTTGTGGGTTGTCCAATGCCTTGTGGTGTTCAGAT
275021 TGGCCACAAGTTTGTGGGTTGTCCAATGCCTTGTGGTGTTCAGAT
1 TGGCCACAAGTTTGTGGGTTGTCCAATGCCTTGTGGTGTTCAGAT
275066 T
1 T
275067 ACGAGGATGG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.15, C:0.18, G:0.31, T:0.36
Consensus pattern (45 bp):
TGGCCACAAGTTTGTGGGTTGTCCAATGCCTTGTGGTGTTCAGAT
Found at i:278583 original size:21 final size:21
Alignment explanation
Indices: 278557--278598 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
278547 AGAATAAATA
278557 AATAGTACCATTTGAATGCAT
1 AATAGTACCATTTGAATGCAT
278578 AATAGTACCATTTGAATGCAT
1 AATAGTACCATTTGAATGCAT
278599 TAACCTGGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.33
Consensus pattern (21 bp):
AATAGTACCATTTGAATGCAT
Found at i:279423 original size:22 final size:22
Alignment explanation
Indices: 279398--279480 Score: 166
Period size: 22 Copynumber: 3.8 Consensus size: 22
279388 TAAGGGGTAT
279398 CGATTCCCCTGCTACAGGGAAC
1 CGATTCCCCTGCTACAGGGAAC
279420 CGATTCCCCTGCTACAGGGAAC
1 CGATTCCCCTGCTACAGGGAAC
279442 CGATTCCCCTGCTACAGGGAAC
1 CGATTCCCCTGCTACAGGGAAC
279464 CGATTCCCCTGCTACAG
1 CGATTCCCCTGCTACAG
279481 TACTGCTATA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 61 1.00
ACGTcount: A:0.22, C:0.37, G:0.22, T:0.19
Consensus pattern (22 bp):
CGATTCCCCTGCTACAGGGAAC
Found at i:279488 original size:11 final size:11
Alignment explanation
Indices: 279472--279501 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
279462 ACCGATTCCC
279472 CTGCTACAGTA
1 CTGCTACAGTA
*
279483 CTGCTATAGTA
1 CTGCTACAGTA
279494 CTGCTACA
1 CTGCTACA
279502 ATACCTCGAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.27, C:0.27, G:0.17, T:0.30
Consensus pattern (11 bp):
CTGCTACAGTA
Found at i:280087 original size:31 final size:31
Alignment explanation
Indices: 280050--280174 Score: 135
Period size: 31 Copynumber: 4.0 Consensus size: 31
280040 CCTCGACAAT
* *
280050 TGTCCATAAGTCCCGAAGAACCTAGGTAAAC
1 TGTCCATATGTCCCGAAGAACATAGGTAAAC
* ** * *
280081 TGTCCATATGTTCCTTAGAACATAGGTATAT
1 TGTCCATATGTCCCGAAGAACATAGGTAAAC
*
280112 TGTCCATATGTCCCGAA-AGACATAGGTAATTC
1 TGTCCATATGTCCCGAAGA-ACATAGGTAA-AC
* *
280144 TGTCCATATGTTCCGTAGAACATAGGTAAAC
1 TGTCCATATGTCCCGAAGAACATAGGTAAAC
280175 CCTCGACTCT
Statistics
Matches: 75, Mismatches: 16, Indels: 6
0.77 0.16 0.06
Matches are distributed among these distances:
30 1 0.01
31 48 0.64
32 25 0.33
33 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29
Consensus pattern (31 bp):
TGTCCATATGTCCCGAAGAACATAGGTAAAC
Found at i:280168 original size:63 final size:62
Alignment explanation
Indices: 280048--280171 Score: 187
Period size: 63 Copynumber: 2.0 Consensus size: 62
280038 AACCTCGACA
* *
280048 ATTGTCCATAAGTCCCGAAGAACCTAGGTAAACTGTCCATATGTTCCTTAGAACATAGGTAT
1 ATTGTCCATAAGTCCCGAAGAACATAGGTAAACTGTCCATATGTTCCGTAGAACATAGGTAT
* *
280110 ATTGTCCATATGTCCCGAA-AGACATAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTA
1 ATTGTCCATAAGTCCCGAAGA-ACATAGGTAA-ACTGTCCATATGTTCCGTAGAACATAGGTA
280172 AACCCTCGAC
Statistics
Matches: 56, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
61 1 0.02
62 27 0.48
63 28 0.50
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (62 bp):
ATTGTCCATAAGTCCCGAAGAACATAGGTAAACTGTCCATATGTTCCGTAGAACATAGGTAT
Found at i:283494 original size:20 final size:20
Alignment explanation
Indices: 283469--283507 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
283459 TTTTCAAAGG
*
283469 CATGCACCGATTCATCAATC
1 CATGCACCGATGCATCAATC
*
283489 CATGCATCGATGCATCAAT
1 CATGCACCGATGCATCAAT
283508 GAATAAATTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.31, C:0.31, G:0.13, T:0.26
Consensus pattern (20 bp):
CATGCACCGATGCATCAATC
Found at i:283587 original size:65 final size:65
Alignment explanation
Indices: 283518--283697 Score: 188
Period size: 65 Copynumber: 2.8 Consensus size: 65
283508 GAATAAATTG
* *
283518 AACATCGAATGCATTTCATGCACCGATGTACTCTCCATGCATCGATGCACTC-GGAT-TTTATGA
1 AACATCGAATGCATTTCATGCATCGATGCACTCTCCATGCATCGATGCACTCAGGATATTT-T-A
283581 AA
64 AA
* * * *** **
283583 AACATCAAATGTATTTGATGCATCGATGCACAAGCCATGCATCGATGCAC-CAGGATATTTTTTA
1 AACATCGAATGCATTTCATGCATCGATGCACTCTCCATGCATCGATGCACTCAGGATATTTTAAA
* * *
283647 AACATCGAATGCACTTCATGCATCGATGCACTCT-TAGTGCACCGATGCACT
1 AACATCGAATGCATTTCATGCATCGATGCACTCTCCA-TGCATCGATGCACT
283698 AGAAGTCCAA
Statistics
Matches: 92, Mismatches: 19, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
63 1 0.01
64 41 0.45
65 47 0.51
66 3 0.03
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.28
Consensus pattern (65 bp):
AACATCGAATGCATTTCATGCATCGATGCACTCTCCATGCATCGATGCACTCAGGATATTTTAAA
Found at i:283677 original size:17 final size:19
Alignment explanation
Indices: 283649--283697 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
283639 ATTTTTTAAA
283649 CATCGAATGCACT-TCA-TG
1 CATCG-ATGCACTCTCAGTG
*
283667 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTCAGTG
*
283686 CACCGATGCACT
1 CATCGATGCACT
283698 AGAAGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.31, G:0.18, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTCAGTG
Found at i:289401 original size:44 final size:43
Alignment explanation
Indices: 289353--289436 Score: 123
Period size: 44 Copynumber: 1.9 Consensus size: 43
289343 ATGCATCCCT
* *
289353 TTGAATATGTATCGATGCATCAACATGATGCACCGATGCATGAC
1 TTGAATATGCATCGATGCAT-AACATCATGCACCGATGCATGAC
**
289397 TTGAATATGCATCGATGCATAAGTTCATGCACCGATGCAT
1 TTGAATATGCATCGATGCATAACATCATGCACCGATGCAT
289437 CTATCGGGTT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
43 17 0.47
44 19 0.53
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (43 bp):
TTGAATATGCATCGATGCATAACATCATGCACCGATGCATGAC
Found at i:290981 original size:21 final size:21
Alignment explanation
Indices: 290955--290995 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
290945 CCGGGAGCTT
*
290955 GTTCTTCTCGAGCTGCTCCTA
1 GTTCTTCTCGAGCTCCTCCTA
*
290976 GTTCTTCTCGTGCTCCTCCT
1 GTTCTTCTCGAGCTCCTCCT
290996 CCTCCGGCTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.05, C:0.37, G:0.17, T:0.41
Consensus pattern (21 bp):
GTTCTTCTCGAGCTCCTCCTA
Found at i:292016 original size:20 final size:20
Alignment explanation
Indices: 291991--292029 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
291981 TTTTCAAAGG
291991 CATGCACCGATGCATCAATC
1 CATGCACCGATGCATCAATC
*
292011 CATGCATCGATGCATCAAT
1 CATGCACCGATGCATCAAT
292030 GAATAAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.31, C:0.31, G:0.15, T:0.23
Consensus pattern (20 bp):
CATGCACCGATGCATCAATC
Found at i:294899 original size:31 final size:31
Alignment explanation
Indices: 294862--294989 Score: 132
Period size: 31 Copynumber: 4.1 Consensus size: 31
294852 GAACCTCAGC
* *
294862 AACTGTCCATAAGTCCCGAAGAACCTAGGTA
1 AACTGTCCATATGTCCCGAAGAACATAGGTA
* **
294893 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTCCCGAAGAACATAGGTA
* *
294924 TATTGTCCATATGTCCCGAA-AGACATAGGTA
1 AACTGTCCATATGTCCCGAAGA-ACATAGGTA
* * * *
294955 ATTCTGTCCATATGTTCCGTAGAACATAAGTA
1 A-ACTGTCCATATGTCCCGAAGAACATAGGTA
294987 AAC
1 AAC
294990 CCTCGACTCT
Statistics
Matches: 77, Mismatches: 17, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
30 1 0.01
31 51 0.66
32 24 0.31
33 1 0.01
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (31 bp):
AACTGTCCATATGTCCCGAAGAACATAGGTA
Found at i:294981 original size:63 final size:62
Alignment explanation
Indices: 294865--294982 Score: 175
Period size: 62 Copynumber: 1.9 Consensus size: 62
294855 CCTCAGCAAC
* *
294865 TGTCCATAAGTCCCGAAGAACCTAGGTAAACTGTCCATATGTTCCTTAGAACATAGGTATAT
1 TGTCCATAAGTCCCGAAGAACATAGGTAAACTGTCCATATGTTCCGTAGAACATAGGTATAT
* *
294927 TGTCCATATGTCCCGAA-AGACATAGGTAATTCTGTCCATATGTTCCGTAGAACATA
1 TGTCCATAAGTCCCGAAGA-ACATAGGTAA-ACTGTCCATATGTTCCGTAGAACATA
294983 AGTAAACCCT
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
61 1 0.02
62 25 0.50
63 24 0.48
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.30
Consensus pattern (62 bp):
TGTCCATAAGTCCCGAAGAACATAGGTAAACTGTCCATATGTTCCGTAGAACATAGGTATAT
Found at i:295468 original size:2 final size:2
Alignment explanation
Indices: 295461--295486 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
295451 ACTTATGTTC
295461 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
295487 CACACATACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:295964 original size:21 final size:21
Alignment explanation
Indices: 295940--295979 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
295930 TTTTTCATTT
295940 AGGGGAAATC-GATTCCCCCCC
1 AGGGGAAATCTG-TTCCCCCCC
*
295961 AGGGGGAATCTGTTCCCCC
1 AGGGGAAATCTGTTCCCCC
295980 TGCACAATCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 16 0.94
22 1 0.06
ACGTcount: A:0.20, C:0.35, G:0.28, T:0.17
Consensus pattern (21 bp):
AGGGGAAATCTGTTCCCCCCC
Found at i:304108 original size:20 final size:20
Alignment explanation
Indices: 304079--304119 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
304069 TCACTAAAAT
304079 TTAAAATTTTAATTTACTCA
1 TTAAAATTTTAATTTACTCA
*
304099 TTAAATTTTTAATTTACTCA
1 TTAAAATTTTAATTTACTCA
304119 T
1 T
304120 ATATTGATCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.37, C:0.10, G:0.00, T:0.54
Consensus pattern (20 bp):
TTAAAATTTTAATTTACTCA
Found at i:307543 original size:45 final size:45
Alignment explanation
Indices: 307487--307583 Score: 124
Period size: 45 Copynumber: 2.2 Consensus size: 45
307477 TCAGGGGTTA
* * *
307487 ATGGGAGGCAGCAGGCTGAACTGG-TCATTCCGAGAAGTCTGAGGG
1 ATGGTAGGCAGCAGGCTGAACTGGAGCA-ACCGAGAAGTCTGAGGG
* * *
307532 ATGGTAGGCAGCTGGTTGAACTGGAGGAACCGAGAAGTCTGAGGG
1 ATGGTAGGCAGCAGGCTGAACTGGAGCAACCGAGAAGTCTGAGGG
307577 ATGGTAG
1 ATGGTAG
307584 AACTTATAAG
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
45 44 0.98
46 1 0.02
ACGTcount: A:0.26, C:0.14, G:0.41, T:0.19
Consensus pattern (45 bp):
ATGGTAGGCAGCAGGCTGAACTGGAGCAACCGAGAAGTCTGAGGG
Found at i:311616 original size:28 final size:30
Alignment explanation
Indices: 311570--311630 Score: 108
Period size: 28 Copynumber: 2.1 Consensus size: 30
311560 GCAGTTTTGG
311570 TATTTTGTTGTTTGGGTGTTTATTATCTTT
1 TATTTTGTTGTTTGGGTGTTTATTATCTTT
311600 TATTTTG-T-TTTGGGTGTTTATTATCTTT
1 TATTTTGTTGTTTGGGTGTTTATTATCTTT
311628 TAT
1 TAT
311631 GAATAATCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
28 23 0.74
29 1 0.03
30 7 0.23
ACGTcount: A:0.11, C:0.03, G:0.18, T:0.67
Consensus pattern (30 bp):
TATTTTGTTGTTTGGGTGTTTATTATCTTT
Found at i:316941 original size:88 final size:91
Alignment explanation
Indices: 316805--316969 Score: 264
Period size: 89 Copynumber: 1.8 Consensus size: 91
316795 CAGTCAATAT
* *
316805 TGTGTGAACTAAGCAAAGACCTTTGCTCTCTTAACAAAGGAATGAGT-AATATTTACAAGACATC
1 TGTGTGAACTAAGCAAAGACCTTT-CACTCTTAACAAAGGAATGAGTAAAAATTTACAAGACATC
316869 AAAAGTCCTCGTTTTACACTCGAATGC
65 AAAAGTCCTCGTTTTACACTCGAATGC
* *
316896 TGTGTGAACTAAG-AAAGACCTTT-ACTCTTGACAAAGGAATGAGTAAAAATTTATAAGACATCA
1 TGTGTGAACTAAGCAAAGACCTTTCACTCTTAACAAAGGAATGAGTAAAAATTTACAAGACATCA
316959 AAAGTCCTCGT
66 AAAGTCCTCGT
316970 AGGAAGACAA
Statistics
Matches: 69, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
88 19 0.28
89 27 0.39
90 10 0.14
91 13 0.19
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.28
Consensus pattern (91 bp):
TGTGTGAACTAAGCAAAGACCTTTCACTCTTAACAAAGGAATGAGTAAAAATTTACAAGACATCA
AAAGTCCTCGTTTTACACTCGAATGC
Found at i:320375 original size:3 final size:3
Alignment explanation
Indices: 320367--320398 Score: 55
Period size: 3 Copynumber: 10.3 Consensus size: 3
320357 ACAGGAAAAC
320367 ATT ATT ATT ATT ATT ATT ATT ATT ATTT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT A
320399 ACACAGGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:322541 original size:325 final size:325
Alignment explanation
Indices: 321951--322600 Score: 1273
Period size: 325 Copynumber: 2.0 Consensus size: 325
321941 ATTACAGCCT
321951 AATACTTTGGCGGCGGTGTCGAGAGATTGTATAGGCATTCCTCTTGCAAGCTGACTATAAGCTTC
1 AATACTTTGGCGGCGGTGTCGAGAGATTGTATAGGCATTCCTCTTGCAAGCTGACTATAAGCTTC
322016 CCATGTTAAGCACTTTTCGATATCAGTTTGCCAGTCAATGGCACCTATATTGAAGTATTGATAAG
66 CCATGTTAAGCACTTTTCGATATCAGTTTGCCAGTCAATGGCACCTATATTGAAGTATTGATAAG
*
322081 AAGGGCCATGCAAACCATTTAATTCCACCTTAGATTTAGAATCGATCGAACCTATGTGCAAAATA
131 AAGGGCCATGCAAACCATTTAATTCCACCTTAGATTAAGAATCGATCGAACCTATGTGCAAAATA
322146 TTGCGAAGGACTGATGTGCTGAGAGCTCGAACATGTGCACTTGTATGAGAAAGGCATCGAGTTGT
196 TTGCGAAGGACTGATGTGCTGAGAGCTCGAACATGTGCACTTGTATGAGAAAGGCATCGAGTTGT
322211 AGCTGGTAGACGACACTGCATGGATACAGAGATTAAGGGCTTAAATCAGCTTACGAAAGGAGACC
261 AGCTGGTAGACGACACTGCATGGATACAGAGATTAAGGGCTTAAATCAGCTTACGAAAGGAGACC
322276 AATACTTTGGCGGCGGTGTCGAGAGATTGTATAGGCATTCCTCTTGCAAGCTGACTATAAGCTTC
1 AATACTTTGGCGGCGGTGTCGAGAGATTGTATAGGCATTCCTCTTGCAAGCTGACTATAAGCTTC
322341 CCATGTTAAGCACTTTTCGATATCAGTTTGCCAGTCAATGGCACCTATATTGAAGTATTGATAAG
66 CCATGTTAAGCACTTTTCGATATCAGTTTGCCAGTCAATGGCACCTATATTGAAGTATTGATAAG
*
322406 AAGGGCCATGCAAACCATTTAGTTCCACCTTAGATTAAGAATCGATCGAACCTATGTGCAAAATA
131 AAGGGCCATGCAAACCATTTAATTCCACCTTAGATTAAGAATCGATCGAACCTATGTGCAAAATA
*
322471 TTGCGAAGGACTGATGTTCTGAGAGCTCGAACATGTGCACTTGTATGAGAAAGGCATCGAGTTGT
196 TTGCGAAGGACTGATGTGCTGAGAGCTCGAACATGTGCACTTGTATGAGAAAGGCATCGAGTTGT
322536 AGCTGGTAGACGACACTGCATGGATACAGAGATTAAGGGCTTAAATCAGCTTACGAAAGGAGACC
261 AGCTGGTAGACGACACTGCATGGATACAGAGATTAAGGGCTTAAATCAGCTTACGAAAGGAGACC
322601 TTTGTTCCCG
Statistics
Matches: 322, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
325 322 1.00
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.27
Consensus pattern (325 bp):
AATACTTTGGCGGCGGTGTCGAGAGATTGTATAGGCATTCCTCTTGCAAGCTGACTATAAGCTTC
CCATGTTAAGCACTTTTCGATATCAGTTTGCCAGTCAATGGCACCTATATTGAAGTATTGATAAG
AAGGGCCATGCAAACCATTTAATTCCACCTTAGATTAAGAATCGATCGAACCTATGTGCAAAATA
TTGCGAAGGACTGATGTGCTGAGAGCTCGAACATGTGCACTTGTATGAGAAAGGCATCGAGTTGT
AGCTGGTAGACGACACTGCATGGATACAGAGATTAAGGGCTTAAATCAGCTTACGAAAGGAGACC
Found at i:322857 original size:29 final size:29
Alignment explanation
Indices: 322824--322922 Score: 81
Period size: 29 Copynumber: 3.3 Consensus size: 29
322814 ACAGTAATGT
*
322824 AAGATTACAGTGTTTAGTTTAAGGAATAA
1 AAGATTACAGTGTTTAGTTTAACGAATAA
* * * * * **
322853 AAGATTACTAAAATGTATATTTTATCAAATTGT
1 AAGATTAC---AGTGTTTAGTTTAACGAA-TAA
*
322886 AAGATTACAGTGTTTAGTTTAATGAATAA
1 AAGATTACAGTGTTTAGTTTAACGAATAA
322915 AAGATTAC
1 AAGATTAC
322923 TAAAATGTAT
Statistics
Matches: 50, Mismatches: 16, Indels: 8
0.68 0.22 0.11
Matches are distributed among these distances:
29 17 0.34
30 12 0.24
32 12 0.24
33 9 0.18
ACGTcount: A:0.42, C:0.05, G:0.15, T:0.37
Consensus pattern (29 bp):
AAGATTACAGTGTTTAGTTTAACGAATAA
Found at i:322892 original size:62 final size:62
Alignment explanation
Indices: 322821--322946 Score: 243
Period size: 62 Copynumber: 2.0 Consensus size: 62
322811 TTGACAGTAA
322821 TGTAAGATTACAGTGTTTAGTTTAAGGAATAAAAGATTACTAAAATGTATATTTTATCAAAT
1 TGTAAGATTACAGTGTTTAGTTTAAGGAATAAAAGATTACTAAAATGTATATTTTATCAAAT
*
322883 TGTAAGATTACAGTGTTTAGTTTAATGAATAAAAGATTACTAAAATGTATATTTTATCAAAT
1 TGTAAGATTACAGTGTTTAGTTTAAGGAATAAAAGATTACTAAAATGTATATTTTATCAAAT
322945 TG
1 TG
322947 ACCTTGTTCT
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 63 1.00
ACGTcount: A:0.41, C:0.05, G:0.14, T:0.40
Consensus pattern (62 bp):
TGTAAGATTACAGTGTTTAGTTTAAGGAATAAAAGATTACTAAAATGTATATTTTATCAAAT
Found at i:323002 original size:15 final size:15
Alignment explanation
Indices: 322984--323014 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
322974 AAATTTTAAA
322984 TATTTAAATAAAAAT
1 TATTTAAATAAAAAT
*
322999 TATTTATATAAAAAT
1 TATTTAAATAAAAAT
323014 T
1 T
323015 CATCGATAAT
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:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTTAAATAAAAAT
Found at i:323029 original size:27 final size:27
Alignment explanation
Indices: 322999--323055 Score: 96
Period size: 27 Copynumber: 2.1 Consensus size: 27
322989 AAATAAAAAT
*
322999 TATTTATATAAAAATTCATCGATAATA
1 TATTTAAATAAAAATTCATCGATAATA
*
323026 TATTTAAATAAAAATTCATTGATAATA
1 TATTTAAATAAAAATTCATCGATAATA
323053 TAT
1 TAT
323056 CATTTTATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.49, C:0.05, G:0.04, T:0.42
Consensus pattern (27 bp):
TATTTAAATAAAAATTCATCGATAATA
Found at i:323091 original size:21 final size:21
Alignment explanation
Indices: 323049--323088 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
323039 ATTCATTGAT
*
323049 AATATATCATTTTATTATTTA
1 AATATATCATTGTATTATTTA
323070 AATATATCA-TGTATTATTT
1 AATATATCATTGTATTATTT
323089 TAATTTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.55
Consensus pattern (21 bp):
AATATATCATTGTATTATTTA
Found at i:327188 original size:15 final size:16
Alignment explanation
Indices: 327143--327185 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
327133 GCGGTAAAGT
*
327143 ACAAGCTTCCCCATCA
1 ACAAGCATCCCCATCA
327159 ACAAGCATCCCCATCA
1 ACAAGCATCCCCATCA
*
327175 ATAAGCATCCC
1 ACAAGCATCCC
327186 ATCTGTAGCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.35, C:0.42, G:0.07, T:0.16
Consensus pattern (16 bp):
ACAAGCATCCCCATCA
Found at i:328382 original size:27 final size:27
Alignment explanation
Indices: 328352--328446 Score: 181
Period size: 27 Copynumber: 3.5 Consensus size: 27
328342 AGAAATATAT
*
328352 GATTATGTAAATATCCTTTAATTAAGG
1 GATTCTGTAAATATCCTTTAATTAAGG
328379 GATTCTGTAAATATCCTTTAATTAAGG
1 GATTCTGTAAATATCCTTTAATTAAGG
328406 GATTCTGTAAATATCCTTTAATTAAGG
1 GATTCTGTAAATATCCTTTAATTAAGG
328433 GATTCTGTAAATAT
1 GATTCTGTAAATAT
328447 TCTACAGTCC
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
27 67 1.00
ACGTcount: A:0.35, C:0.09, G:0.15, T:0.41
Consensus pattern (27 bp):
GATTCTGTAAATATCCTTTAATTAAGG
Found at i:333552 original size:17 final size:17
Alignment explanation
Indices: 333522--333565 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
333512 GACCGGTTCT
*
333522 AACCCGACAAGACCGTA
1 AACCCGACCAGACCGTA
* *
333539 AACCCGACCCGACCGTT
1 AACCCGACCAGACCGTA
*
333556 GACCCGACCA
1 AACCCGACCA
333566 TTGACCCGAC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.32, C:0.43, G:0.18, T:0.07
Consensus pattern (17 bp):
AACCCGACCAGACCGTA
Found at i:333559 original size:12 final size:12
Alignment explanation
Indices: 333544--333576 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
333534 CCGTAAACCC
*
333544 GACCCGACCGTT
1 GACCCGACCATT
333556 GACCCGACCATT
1 GACCCGACCATT
333568 GACCCGACC
1 GACCCGACC
333577 CGTAAACCTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.21, C:0.45, G:0.21, T:0.12
Consensus pattern (12 bp):
GACCCGACCATT
Found at i:333647 original size:29 final size:29
Alignment explanation
Indices: 333605--333788 Score: 224
Period size: 29 Copynumber: 6.2 Consensus size: 29
333595 ACCGTTGACT
* *
333605 GGGTGTTAGTTTCGTAATTATTTTTAAAA
1 GGGTGCTATTTTCGTAATTATTTTTAAAA
*
333634 GTGTGCTATTTTCGTAATTATTTTTAAAA
1 GGGTGCTATTTTCGTAATTATTTTTAAAA
*
333663 GGGTGCTAGTTTCGTAATTATTTTTAAAA
1 GGGTGCTATTTTCGTAATTATTTTTAAAA
* * *
333692 AGGTGCTATTTTCTTAATGTTTTTTTAAAA
1 GGGTGCTATTTTCGTAAT-TATTTTTAAAA
* *
333722 GGGTGCTATTTTCGTCAATATGTTTTTTGAAA
1 GGGTGCTATTTTCGT-AAT-T-ATTTTTAAAA
* *
333754 GGGTGTTATTTTCGTAAATATTTTTAAAAA
1 GGGTGCTATTTTCGTAATTATTTTT-AAAA
333784 GGGTG
1 GGGTG
333789 ATAATTGTGT
Statistics
Matches: 134, Mismatches: 17, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
29 73 0.54
30 32 0.24
31 6 0.04
32 23 0.17
ACGTcount: A:0.27, C:0.06, G:0.20, T:0.48
Consensus pattern (29 bp):
GGGTGCTATTTTCGTAATTATTTTTAAAA
Found at i:336916 original size:15 final size:16
Alignment explanation
Indices: 336896--336925 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
336886 AATCTACGTG
336896 AATACATGT-ATATGT
1 AATACATGTGATATGT
336911 AATACATGTGATATG
1 AATACATGTGATATG
336926 ATATGAGATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.40, C:0.07, G:0.17, T:0.37
Consensus pattern (16 bp):
AATACATGTGATATGT
Found at i:337100 original size:31 final size:31
Alignment explanation
Indices: 337062--337162 Score: 193
Period size: 31 Copynumber: 3.3 Consensus size: 31
337052 GAGTCGAGGG
337062 TTTACCTATGTTTAAAGGCACATATGGACAA
1 TTTACCTATGTTTAAAGGCACATATGGACAA
337093 TTTACCTATGTTTAAAGGCACATATGGACAA
1 TTTACCTATGTTTAAAGGCACATATGGACAA
*
337124 TTTACCTATGTTTAAAGGCACATATGGACAG
1 TTTACCTATGTTTAAAGGCACATATGGACAA
337155 TTTACCTA
1 TTTACCTA
337163 GGTTCTTCGG
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
31 69 1.00
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Consensus pattern (31 bp):
TTTACCTATGTTTAAAGGCACATATGGACAA
Found at i:340627 original size:15 final size:16
Alignment explanation
Indices: 340607--340636 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
340597 GATCTACGTG
340607 AATACATGT-ATATGT
1 AATACATGTGATATGT
340622 AATACATGTGATATG
1 AATACATGTGATATG
340637 ATATGAGATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.40, C:0.07, G:0.17, T:0.37
Consensus pattern (16 bp):
AATACATGTGATATGT
Found at i:340811 original size:31 final size:31
Alignment explanation
Indices: 340773--340842 Score: 122
Period size: 31 Copynumber: 2.3 Consensus size: 31
340763 GAGTCGAGGG
*
340773 TTTACCTATGTTTAAAGGCACATATGGACAA
1 TTTACCTATGTTTAAAGGCACATATGAACAA
*
340804 TTTACCTATGTTTAAAGGCACATATGAACAG
1 TTTACCTATGTTTAAAGGCACATATGAACAA
340835 TTTACCTA
1 TTTACCTA
340843 GGTTCTTCGG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.34
Consensus pattern (31 bp):
TTTACCTATGTTTAAAGGCACATATGAACAA
Found at i:342898 original size:13 final size:13
Alignment explanation
Indices: 342880--342910 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
342870 TGATGCGCCA
342880 ATGCACCTTGTGT
1 ATGCACCTTGTGT
342893 ATGCACCTTGTGT
1 ATGCACCTTGTGT
342906 ATGCA
1 ATGCA
342911 TCGATGCATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.19, C:0.23, G:0.23, T:0.35
Consensus pattern (13 bp):
ATGCACCTTGTGT
Found at i:344779 original size:21 final size:21
Alignment explanation
Indices: 344753--344792 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
344743 AAGACTCTAT
344753 TTTCAAAATACAAAAATGATG
1 TTTCAAAATACAAAAATGATG
**
344774 TTTCAAAATTGAAAAATGA
1 TTTCAAAATACAAAAATGA
344793 AAATAGTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.53, C:0.07, G:0.10, T:0.30
Consensus pattern (21 bp):
TTTCAAAATACAAAAATGATG
Found at i:347542 original size:31 final size:31
Alignment explanation
Indices: 347507--347579 Score: 146
Period size: 31 Copynumber: 2.4 Consensus size: 31
347497 TGGGACTCCA
347507 AATCAAGCAAAGAAAAGATGGCATCTTCATC
1 AATCAAGCAAAGAAAAGATGGCATCTTCATC
347538 AATCAAGCAAAGAAAAGATGGCATCTTCATC
1 AATCAAGCAAAGAAAAGATGGCATCTTCATC
347569 AATCAAGCAAA
1 AATCAAGCAAA
347580 ATATGTCAAG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.48, C:0.19, G:0.15, T:0.18
Consensus pattern (31 bp):
AATCAAGCAAAGAAAAGATGGCATCTTCATC
Found at i:352767 original size:19 final size:19
Alignment explanation
Indices: 352743--352780 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
352733 TTTTGGTGCA
*
352743 GAGGGAATCGATCCCCCCT
1 GAGGGAACCGATCCCCCCT
*
352762 GAGGGAACCGATTCCCCCT
1 GAGGGAACCGATCCCCCCT
352781 TTGAATGGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.21, C:0.37, G:0.26, T:0.16
Consensus pattern (19 bp):
GAGGGAACCGATCCCCCCT
Found at i:354595 original size:9 final size:8
Alignment explanation
Indices: 354572--354623 Score: 54
Period size: 9 Copynumber: 6.4 Consensus size: 8
354562 TTGTTTCAAC
354572 TTTTTGGA
1 TTTTTGGA
354580 TATTTTGGA
1 T-TTTTGGA
354589 TTGTTT-GA
1 TT-TTTGGA
354597 TTTTGTGGA
1 TTTT-TGGA
*
354606 TTGTTGGA
1 TTTTTGGA
354614 -TTTTGGA
1 TTTTTGGA
354621 TTT
1 TTT
354624 ATGAATAGTG
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
7 8 0.22
8 13 0.35
9 16 0.43
ACGTcount: A:0.13, C:0.00, G:0.27, T:0.60
Consensus pattern (8 bp):
TTTTTGGA
Found at i:354607 original size:17 final size:17
Alignment explanation
Indices: 354575--354618 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
354565 TTTCAACTTT
354575 TTGGATATTT-TGGATTG
1 TTGGAT-TTTGTGGATTG
*
354592 TTTGATTTTGTGGATTG
1 TTGGATTTTGTGGATTG
354609 TTGGATTTTG
1 TTGGATTTTG
354619 GATTTATGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 3 0.12
17 21 0.88
ACGTcount: A:0.14, C:0.00, G:0.30, T:0.57
Consensus pattern (17 bp):
TTGGATTTTGTGGATTG
Found at i:355333 original size:75 final size:76
Alignment explanation
Indices: 355201--355409 Score: 242
Period size: 75 Copynumber: 2.8 Consensus size: 76
355191 CAAAGCCAAA
* * * * * * **
355201 AATTCCAGATTGCTCAGAGGGAACCGATTCCTCCCCATAGGAGGAACCGATTTCCCCCTGAATGG
1 AATTCCAGAATGCTCGGAGAGAACCGA-TCCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAG
355266 TTTGGCTCCGAG
65 TTTGGCTCCGAG
* ** *
355278 ATTTCCAGAATGCTCGGAGAGAATTGAT-TCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
1 AATTCCAGAATGCTCGGAGAGAACCGATCCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
*
355342 TTTGCTCCGAG
66 TTGGCTCCGAG
* * * *
355353 AATTCCAGTATGCTCGGAGGGAACCGATCCCCCCCA-AGGGGGTACCGATTCCCCCCT
1 AATTCCAGAATGCTCGGAGAGAACCGATCCCCCCCATAGGAGGAACCGATTCCCCCCT
355410 TGTACAACGG
Statistics
Matches: 110, Mismatches: 21, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
75 82 0.75
76 7 0.06
77 21 0.19
ACGTcount: A:0.24, C:0.31, G:0.23, T:0.22
Consensus pattern (76 bp):
AATTCCAGAATGCTCGGAGAGAACCGATCCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
TTGGCTCCGAG
Found at i:359366 original size:64 final size:65
Alignment explanation
Indices: 359295--359424 Score: 201
Period size: 65 Copynumber: 2.0 Consensus size: 65
359285 GATGCACCAA
*
359295 TCCATGCATCGATGCAC-CATTGAATAAATT-AAACATCGAATGCATTTTATGCATCGATGCACT
1 TCCATGCATCGATGCACTC-TGGAATAAATTAAAACATCGAATGCATTTTATGCATCGATGCACT
359358 C
65 C
** *
359359 TCCATGCATCGATGCACTCTGGTTTTAATTAAAACATCGAATGCATTTTATGCATCGATGCACTC
1 TCCATGCATCGATGCACTCTGGAATAAATTAAAACATCGAATGCATTTTATGCATCGATGCACTC
359424 T
1 T
359425 GGTTTTAATT
Statistics
Matches: 60, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
64 24 0.40
65 36 0.60
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.32
Consensus pattern (65 bp):
TCCATGCATCGATGCACTCTGGAATAAATTAAAACATCGAATGCATTTTATGCATCGATGCACTC
Found at i:359414 original size:46 final size:46
Alignment explanation
Indices: 359362--359467 Score: 194
Period size: 46 Copynumber: 2.3 Consensus size: 46
359352 TGCACTCTCC
*
359362 ATGCATCGATGCACTCTGGTTTTAATTAAAACATCGAATGCATTTT
1 ATGCATCGATGCACTCTGGTTTTAATTAAAACATCGAATGCACTTT
359408 ATGCATCGATGCACTCTGGTTTTAATTAAAACATCGAATGCACTTT
1 ATGCATCGATGCACTCTGGTTTTAATTAAAACATCGAATGCACTTT
*
359454 ATCCATCGATGCAC
1 ATGCATCGATGCAC
359468 ATACCATGCA
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
46 58 1.00
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.34
Consensus pattern (46 bp):
ATGCATCGATGCACTCTGGTTTTAATTAAAACATCGAATGCACTTT
Found at i:359464 original size:111 final size:109
Alignment explanation
Indices: 359321--359527 Score: 285
Period size: 111 Copynumber: 1.9 Consensus size: 109
359311 CCATTGAATA
* * * *
359321 AATTAAACATCGAATGCATTTTATGCATCGATGCAC-TCTCCATGCATCGATGCACTCT-GGTTT
1 AATTAAACATCGAATGCACTTTATCCATCGATGCACAT-ACCATGCATCGATGCACT-TAGG-CT
**
359384 TAATT-AAAACATCGAATGCATTTTATGCATCGATGCACTCTGGTTTT
63 T-ATTCAAAACATCGAATGCATTAAATGCATCGATGCACTCTGGTTTT
359431 AATTAAAACATCGAATGCACTTTATCCATCGATGCACATACCATGCATCGATGCACTTAGGCTTA
1 AATT-AAACATCGAATGCACTTTATCCATCGATGCACATACCATGCATCGATGCACTTAGGCTTA
*
359496 TTCAAAACATCGATTGCATTAAATGCATCGAT
65 TTCAAAACATCGAATGCATTAAATGCATCGAT
359528 TCACACTTAG
Statistics
Matches: 86, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
109 3 0.03
110 33 0.38
111 49 0.57
112 1 0.01
ACGTcount: A:0.31, C:0.22, G:0.14, T:0.32
Consensus pattern (109 bp):
AATTAAACATCGAATGCACTTTATCCATCGATGCACATACCATGCATCGATGCACTTAGGCTTAT
TCAAAACATCGAATGCATTAAATGCATCGATGCACTCTGGTTTT
Found at i:359525 original size:64 final size:65
Alignment explanation
Indices: 359408--359532 Score: 150
Period size: 64 Copynumber: 1.9 Consensus size: 65
359398 AATGCATTTT
* *
359408 ATGCATCGATGCACTCTGGTTTTAATTAAAACATCGAATGCACTTTATCCATCGATGCACATACC
1 ATGCATCGATGCACTCTGGTCTTAATTAAAACATCGAATGCACTTAATCCATCGATGCACATACC
* * *
359473 ATGCATCGATGCACT-TAGG-CTT-ATTCAAAACATCGATTGCA-TTAAATGCATCGATTCACA
1 ATGCATCGATGCACTCT-GGTCTTAATT-AAAACATCGAATGCACTT-AATCCATCGATGCACA
359533 CTTAGTGCAC
Statistics
Matches: 52, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
63 5 0.10
64 30 0.58
65 17 0.33
ACGTcount: A:0.32, C:0.23, G:0.14, T:0.30
Consensus pattern (65 bp):
ATGCATCGATGCACTCTGGTCTTAATTAAAACATCGAATGCACTTAATCCATCGATGCACATACC
Found at i:361131 original size:28 final size:29
Alignment explanation
Indices: 361012--361198 Score: 209
Period size: 29 Copynumber: 6.4 Consensus size: 29
361002 ACCGTTGACC
*
361012 GGGTGTTAGTTTT-GTAGTTATTTTTAAAA
1 GGGTGTTA-TTTTCGTAATTATTTTTAAAA
* * *
361041 GGGTGCTATTTTCGTATTTAGTTTTAAAA
1 GGGTGTTATTTTCGTAATTATTTTTAAAA
* *
361070 GGGTGCTATTTTCATAATTATTTTTAAAA
1 GGGTGTTATTTTCGTAATTATTTTTAAAA
* *
361099 AGGTGTTGTGTTT-GTAATTATTTTTAAAA
1 GGGTGTTAT-TTTCGTAATTATTTTTAAAA
361128 -GGTGTTATTTTCGTAATTATTTTTAAAA
1 GGGTGTTATTTTCGTAATTATTTTTAAAA
* * * * *
361156 TGGTGCTATTTTCGAAAATATTTTTTTAAA
1 GGGTGTTATTTTCGTAATTA-TTTTTAAAA
361186 GGGTGTTATTTTC
1 GGGTGTTATTTTC
361199 ATAAATTCTT
Statistics
Matches: 136, Mismatches: 17, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
27 3 0.02
28 27 0.20
29 84 0.62
30 22 0.16
ACGTcount: A:0.26, C:0.04, G:0.19, T:0.51
Consensus pattern (29 bp):
GGGTGTTATTTTCGTAATTATTTTTAAAA
Found at i:361178 original size:86 final size:87
Alignment explanation
Indices: 361013--361197 Score: 243
Period size: 86 Copynumber: 2.1 Consensus size: 87
361003 CCGTTGACCG
* *
361013 GGTGTTAGTTTTGTAGTTATTTTTAAAAGGGTGCTATTTTCGTATTTAGTTTTAAAAGGGTGCTA
1 GGTGTTAGTTTTGTAATTATTTTTAAAAGGGTGCTATTTTCGTAATTAGTTTTAAAAGGGTGCTA
*
361078 TTTTCATAATTATTTTTAAAAA
66 TTTTCATAAATATTTTTAAAAA
* * *
361100 GGTGTT-GTGTTTGTAATTATTTTTAAAA-GGTGTTATTTTCGTAATTATTTTTAAAATGGTGCT
1 GGTGTTAGT-TTTGTAATTATTTTTAAAAGGGTGCTATTTTCGTAATTAGTTTTAAAAGGGTGCT
* *
361163 ATTTTCGA-AAATATTTTTTTAAAG
65 ATTTTC-ATAAATA-TTTTTAAAAA
361187 GGTGTTA-TTTT
1 GGTGTTAGTTTT
361198 CATAAATTCT
Statistics
Matches: 86, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
86 46 0.53
87 40 0.47
ACGTcount: A:0.26, C:0.04, G:0.18, T:0.51
Consensus pattern (87 bp):
GGTGTTAGTTTTGTAATTATTTTTAAAAGGGTGCTATTTTCGTAATTAGTTTTAAAAGGGTGCTA
TTTTCATAAATATTTTTAAAAA
Found at i:361196 original size:30 final size:29
Alignment explanation
Indices: 361062--361214 Score: 111
Period size: 28 Copynumber: 5.3 Consensus size: 29
361052 TCGTATTTAG
* *
361062 TTTTAAAAGGGTGCTATTTTC-ATAATTATT
1 TTTTAAAA-GGTGTTATTTTCGA-AAATATT
* * * *
361092 TTTAAAAAGGTGTTGTGTTT-GTAATTA-T
1 TTTTAAAAGGTGTTAT-TTTCGAAAATATT
* *
361120 TTTTAAAAGGTGTTATTTTCGTAATTA-T
1 TTTTAAAAGGTGTTATTTTCGAAAATATT
*
361148 TTTTAAAATGGTGCTATTTTCGAAAATATTT
1 TTTTAAAA-GGTGTTATTTTCGAAAATA-TT
* *
361179 TTTTAAAGGGTGTTATTTTC-ATAAAT-TC
1 TTTTAAAAGGTGTTATTTTCGA-AAATATT
361207 TTTTAAAA
1 TTTTAAAA
361215 ATGGTTGATC
Statistics
Matches: 103, Mismatches: 13, Indels: 16
0.78 0.10 0.12
Matches are distributed among these distances:
27 3 0.03
28 39 0.38
29 28 0.27
30 25 0.24
31 8 0.08
ACGTcount: A:0.31, C:0.05, G:0.14, T:0.50
Consensus pattern (29 bp):
TTTTAAAAGGTGTTATTTTCGAAAATATT
Found at i:365011 original size:25 final size:24
Alignment explanation
Indices: 364975--365023 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
364965 TAATAAAAAA
364975 AATATTTATCTAATGACAAATATTT
1 AATATTTATCTAATGA-AAATATTT
*
365000 AATATATT-TCTAATGATAATATTT
1 AATAT-TTATCTAATGAAAATATTT
365024 GTAATATCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 7 0.32
25 13 0.59
26 2 0.09
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.47
Consensus pattern (24 bp):
AATATTTATCTAATGAAAATATTT
Found at i:365185 original size:21 final size:21
Alignment explanation
Indices: 365155--365222 Score: 100
Period size: 21 Copynumber: 3.2 Consensus size: 21
365145 ATGTGACAAG
*
365155 GTTTAGGATTTAGGGTTTATA
1 GTTTAGGATTTAAGGTTTATA
* *
365176 GTTTAAGATTTATGGTTTATA
1 GTTTAGGATTTAAGGTTTATA
*
365197 GTTTAGGATTTAAGGTTTAGA
1 GTTTAGGATTTAAGGTTTATA
365218 GTTTA
1 GTTTA
365223 TGTGATATGA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.26, C:0.00, G:0.25, T:0.49
Consensus pattern (21 bp):
GTTTAGGATTTAAGGTTTATA
Found at i:365243 original size:42 final size:40
Alignment explanation
Indices: 365153--365292 Score: 113
Period size: 42 Copynumber: 3.4 Consensus size: 40
365143 TTATGTGACA
* * *
365153 AGGTTTAGGATTTAGGGTTTATAGTTTAAGAT-TTATGGTTT
1 AGGTTTAGGATTTAAGGTTTA-AGTTTAAG-TGATATGATTT
* *
365194 ATAGTTTAGGATTTAAGGTTTAGAGTTTATGTGATATGATTT
1 A-GGTTTAGGATTTAAGGTTTA-AGTTTAAGTGATATGATTT
* **
365236 GAGGTTTA-TAGTTTAAGGTTTAAGGTTTAAGTGATAACATTT
1 -AGGTTTAGGA-TTTAAGGTTTAA-GTTTAAGTGATATGATTT
*
365278 AAGGTTTAGGGTTTA
1 -AGGTTTAGGATTTA
365293 GAGTTTATGT
Statistics
Matches: 79, Mismatches: 14, Indels: 11
0.76 0.13 0.11
Matches are distributed among these distances:
41 4 0.05
42 74 0.94
43 1 0.01
ACGTcount: A:0.28, C:0.01, G:0.26, T:0.46
Consensus pattern (40 bp):
AGGTTTAGGATTTAAGGTTTAAGTTTAAGTGATATGATTT
Found at i:365299 original size:42 final size:43
Alignment explanation
Indices: 365197--365292 Score: 115
Period size: 42 Copynumber: 2.3 Consensus size: 43
365187 ATGGTTTATA
* * ** *
365197 GTTTAGGATTTAAGGTTT-AGAGTTTATGTGATATGATTTGAG
1 GTTTAGGGTTTAAGGTTTAAGAGTTTAAGTGATAACATTTAAG
**
365239 GTTTATAGTTTAAGGTTTAAG-GTTTAAGTGATAACATTTAAG
1 GTTTAGGGTTTAAGGTTTAAGAGTTTAAGTGATAACATTTAAG
365281 GTTTAGGGTTTA
1 GTTTAGGGTTTA
365293 GAGTTTATGT
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
42 42 0.95
43 2 0.05
ACGTcount: A:0.28, C:0.01, G:0.26, T:0.45
Consensus pattern (43 bp):
GTTTAGGGTTTAAGGTTTAAGAGTTTAAGTGATAACATTTAAG
Found at i:367970 original size:20 final size:19
Alignment explanation
Indices: 367947--367987 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
367937 CTAGAAGTCA
367947 TCTTAATTAATTGTATGTAT
1 TCTTAATTAATTGTAT-TAT
* *
367967 TCTTATTTTATTGTATTAT
1 TCTTAATTAATTGTATTAT
367986 TC
1 TC
367988 AGTTTAGCGC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.24, C:0.07, G:0.07, T:0.61
Consensus pattern (19 bp):
TCTTAATTAATTGTATTAT
Found at i:368712 original size:12 final size:12
Alignment explanation
Indices: 368695--368757 Score: 56
Period size: 12 Copynumber: 5.3 Consensus size: 12
368685 ATTTTTGTAG
368695 GTTTAAATTCGA
1 GTTTAAATTCGA
*
368707 GTTTAAGTTCGA
1 GTTTAAATTCGA
* *
368719 GCTTGAA-TCGA
1 GTTTAAATTCGA
* *
368730 GCTCAAATTCGA
1 GTTTAAATTCGA
* *
368742 GTTTGAGTTCGA
1 GTTTAAATTCGA
368754 GTTT
1 GTTT
368758 GAATCAAGTT
Statistics
Matches: 40, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
11 9 0.22
12 31 0.77
ACGTcount: A:0.25, C:0.13, G:0.24, T:0.38
Consensus pattern (12 bp):
GTTTAAATTCGA
Found at i:368740 original size:23 final size:23
Alignment explanation
Indices: 368714--368832 Score: 94
Period size: 23 Copynumber: 4.9 Consensus size: 23
368704 CGAGTTTAAG
368714 TTCGAGCTTGAATCGAGCTCAAA
1 TTCGAGCTTGAATCGAGCTCAAA
* * * *
368737 TTCGAGTTTGAGTTCGAGTTTGAATCAAG
1 TTCGAGCTTGA-ATCGA----G-CTCAAA
368766 TTCGAGCTTGAATCGAGCTCAAA
1 TTCGAGCTTGAATCGAGCTCAAA
* * * *
368789 ATCGAGCTTTAATCGAGCTCGAG
1 TTCGAGCTTGAATCGAGCTCAAA
*
368812 TCTCGAGCTTCAATCGAGCTC
1 T-TCGAGCTTGAATCGAGCTC
368833 TTGAATTTTT
Statistics
Matches: 75, Mismatches: 14, Indels: 13
0.74 0.14 0.13
Matches are distributed among these distances:
23 33 0.44
24 23 0.31
28 5 0.07
29 14 0.19
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (23 bp):
TTCGAGCTTGAATCGAGCTCAAA
Found at i:368769 original size:17 final size:17
Alignment explanation
Indices: 368747--368779 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
368737 TTCGAGTTTG
*
368747 AGTTCGAGTTTGAATCA
1 AGTTCGAGCTTGAATCA
368764 AGTTCGAGCTTGAATC
1 AGTTCGAGCTTGAATC
368780 GAGCTCAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.27, C:0.15, G:0.24, T:0.33
Consensus pattern (17 bp):
AGTTCGAGCTTGAATCA
Found at i:368791 original size:29 final size:29
Alignment explanation
Indices: 368711--368791 Score: 66
Period size: 29 Copynumber: 3.0 Consensus size: 29
368701 ATTCGAGTTT
*
368711 AAGTTCGAGCTTGAATCGAGCTCAAATTC
1 AAGTTCGAGCTTGAATCGAGCTCAAAATC
* * ***
368740 GAGTTTGAG--T---TCGAG-TTTGAATC
1 AAGTTCGAGCTTGAATCGAGCTCAAAATC
368763 AAGTTCGAGCTTGAATCGAGCTCAAAATC
1 AAGTTCGAGCTTGAATCGAGCTCAAAATC
368792 GAGCTTTAAT
Statistics
Matches: 35, Mismatches: 11, Indels: 12
0.60 0.19 0.21
Matches are distributed among these distances:
23 11 0.31
24 5 0.14
25 1 0.03
27 1 0.03
28 5 0.14
29 12 0.34
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (29 bp):
AAGTTCGAGCTTGAATCGAGCTCAAAATC
Found at i:368826 original size:24 final size:23
Alignment explanation
Indices: 368767--368832 Score: 78
Period size: 24 Copynumber: 2.8 Consensus size: 23
368757 TGAATCAAGT
*
368767 TCGAGCTTGAATCGAGCTCAAAA
1 TCGAGCTTCAATCGAGCTCAAAA
* ***
368790 TCGAGCTTTAATCGAGCTCGAGTC
1 TCGAGCTTCAATCGAGCTC-AAAA
368814 TCGAGCTTCAATCGAGCTC
1 TCGAGCTTCAATCGAGCTC
368833 TTGAATTTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
23 18 0.49
24 19 0.51
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.26
Consensus pattern (23 bp):
TCGAGCTTCAATCGAGCTCAAAA
Found at i:368865 original size:16 final size:16
Alignment explanation
Indices: 368841--368872 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
368831 TCTTGAATTT
*
368841 TTTTTGAGTTCGAGTC
1 TTTTCGAGTTCGAGTC
368857 TTTTCGAGTTCGAGTC
1 TTTTCGAGTTCGAGTC
368873 GAGTTTCAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.12, C:0.16, G:0.25, T:0.47
Consensus pattern (16 bp):
TTTTCGAGTTCGAGTC
Found at i:369137 original size:13 final size:13
Alignment explanation
Indices: 369119--369143 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
369109 CATAGTTGAA
369119 CAGTCTTCATATG
1 CAGTCTTCATATG
369132 CAGTCTTCATAT
1 CAGTCTTCATAT
369144 TCGCGTCTGT
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:0.24, C:0.24, G:0.12, T:0.40
Consensus pattern (13 bp):
CAGTCTTCATATG
Found at i:370349 original size:36 final size:36
Alignment explanation
Indices: 370308--370379 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
370298 AAAGTAGAAG
370308 ACCTACACACCAGTCCTAAGAGAAATGCTCACATTT
1 ACCTACACACCAGTCCTAAGAGAAATGCTCACATTT
370344 ACCTACACACCAGTCCTAAGAGAAATGCTCACATTT
1 ACCTACACACCAGTCCTAAGAGAAATGCTCACATTT
370380 GGAACCAATC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.36, C:0.31, G:0.11, T:0.22
Consensus pattern (36 bp):
ACCTACACACCAGTCCTAAGAGAAATGCTCACATTT
Found at i:372356 original size:3 final size:3
Alignment explanation
Indices: 372348--372450 Score: 156
Period size: 3 Copynumber: 34.7 Consensus size: 3
372338 TTTTTATCCA
* * *
372348 TAT TAT TAT TAT TAT TAT TAA TAT TAT TAT TAT CAT TAT TAA TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
372396 TAT TAT TAT TAT TAT TAT TAT TAAT T-T TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT
372441 T-T TAT TAT TA
1 TAT TAT TAT TA
372451 AATATATTAA
Statistics
Matches: 91, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
2 4 0.04
3 84 0.92
4 3 0.03
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:372923 original size:6 final size:6
Alignment explanation
Indices: 372912--372938 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
372902 AAAGAAAAAA
372912 AGAGAC AGAGAC AGAGAC AGAGAC AGA
1 AGAGAC AGAGAC AGAGAC AGAGAC AGA
372939 ACCGGAGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.52, C:0.15, G:0.33, T:0.00
Consensus pattern (6 bp):
AGAGAC
Found at i:372967 original size:16 final size:15
Alignment explanation
Indices: 372946--372979 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
372936 AGAACCGGAG
372946 AAAGAAAAAAAAAGAC
1 AAAGAAAAAAAAA-AC
*
372962 AAAGAAAAGAAAAAC
1 AAAGAAAAAAAAAAC
372977 AAA
1 AAA
372980 CAAACTATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.82, C:0.06, G:0.12, T:0.00
Consensus pattern (15 bp):
AAAGAAAAAAAAAAC
Found at i:373918 original size:24 final size:22
Alignment explanation
Indices: 373870--373918 Score: 53
Period size: 24 Copynumber: 2.1 Consensus size: 22
373860 GTTTTAATAG
* *
373870 TATTTTTATTTTTATGAATAAA
1 TATTTTTATTTTCATAAATAAA
*
373892 TATTTTTATATATTCATAAATATA
1 TATTTTTAT-T-TTCATAAATAAA
373916 TAT
1 TAT
373919 ATAATGGTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 9 0.41
23 1 0.05
24 12 0.55
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (22 bp):
TATTTTTATTTTCATAAATAAA
Found at i:375218 original size:17 final size:16
Alignment explanation
Indices: 375189--375226 Score: 58
Period size: 17 Copynumber: 2.3 Consensus size: 16
375179 TATGTAAATG
*
375189 TTATTATTAAATTTCT
1 TTATTATTAAATTTAT
375205 TTATTATGTAAATTTAT
1 TTATTAT-TAAATTTAT
375222 TTATT
1 TTATT
375227 TTCTTTTTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 7 0.35
17 13 0.65
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.63
Consensus pattern (16 bp):
TTATTATTAAATTTAT
Found at i:385245 original size:6 final size:6
Alignment explanation
Indices: 385221--385328 Score: 82
Period size: 6 Copynumber: 17.5 Consensus size: 6
385211 ATGCTTGAAG
*
385221 AAAAGA AAGAAG- AAGAGA AAAAGA AAAAGA AAAAGA AAAAG- -AAAGA
1 AAAAGA AA-AAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA
* *
385267 AAAA-A AAAAGAA AAAAGGGG AAAAGA AAAA-A AAGAAGA AGAAAAA ATAATAGA
1 AAAAGA AAAAG-A AAAA--GA AAAAGA AAAAGA AA-AAGA A-AAAGA A-AA-AGA
385320 AAAAGA AAA
1 AAAAGA AAA
385329 GGGTCAAGGT
Statistics
Matches: 83, Mismatches: 7, Indels: 24
0.73 0.06 0.21
Matches are distributed among these distances:
4 4 0.05
5 10 0.12
6 42 0.51
7 18 0.22
8 8 0.10
9 1 0.01
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (6 bp):
AAAAGA
Found at i:385291 original size:30 final size:29
Alignment explanation
Indices: 385221--385312 Score: 109
Period size: 30 Copynumber: 3.1 Consensus size: 29
385211 ATGCTTGAAG
385221 AAAAGAAAGAAGAAGAGAAAAAGAAAAAG-A
1 AAAAGAAA-AAGAA-AGAAAAAGAAAAAGAA
385251 AAAAGAAAAAGAAAGAAAAA-AAAAAGAA
1 AAAAGAAAAAGAAAGAAAAAGAAAAAGAA
* *
385279 AAAAGGGGAAAAGAAA-AAAAAGAAGAAGAA
1 AAAA--GAAAAAGAAAGAAAAAGAAAAAGAA
385309 AAAA
1 AAAA
385313 TAATAGAAAA
Statistics
Matches: 56, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
27 6 0.11
28 12 0.21
29 10 0.18
30 28 0.50
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (29 bp):
AAAAGAAAAAGAAAGAAAAAGAAAAAGAA
Found at i:385296 original size:27 final size:24
Alignment explanation
Indices: 385221--385328 Score: 69
Period size: 26 Copynumber: 4.3 Consensus size: 24
385211 ATGCTTGAAG
* *
385221 AAAAGAAAGAAGAAGAGAAAAAGAAA
1 AAAAAAAAGAA-AAAAG-AAAAGAAA
*
385247 AAGAAAAAG-AAAAAG-AAAGAAA
1 AAAAAAAAGAAAAAAGAAAAGAAA
385269 A-AAAAAAGAAAAAAGGGGAAAAGAAAA
1 AAAAAAAAGAAAAAA---GAAAAG-AAA
* *
385296 AAAAGAAGAAGAAAAAATAATAGAAA
1 AAAA-AA-AAGAAAAAAGAAAAGAAA
*
385322 AAGAAAA
1 AAAAAAA
385329 GGGTCAAGGT
Statistics
Matches: 66, Mismatches: 7, Indels: 20
0.71 0.08 0.22
Matches are distributed among these distances:
21 6 0.09
22 13 0.20
24 5 0.08
25 4 0.06
26 17 0.26
27 8 0.12
28 2 0.03
29 2 0.03
30 9 0.14
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (24 bp):
AAAAAAAAGAAAAAAGAAAAGAAA
Found at i:385310 original size:12 final size:11
Alignment explanation
Indices: 385218--385328 Score: 79
Period size: 10 Copynumber: 10.1 Consensus size: 11
385208 ATTATGCTTG
385218 AAGAAAAGAAA
1 AAGAAAAGAAA
*
385229 GAAGAAGAGAAA
1 -AAGAAAAGAAA
385241 AAGAAAAAGAAA
1 AAG-AAAAGAAA
*
385253 AAGAAAA-AGA
1 AAGAAAAGAAA
*
385263 AAGAAAAAAAA
1 AAGAAAAGAAA
*
385274 AAGAAAA-AAG
1 AAGAAAAGAAA
**
385284 GGGAAAAG-AA
1 AAGAAAAGAAA
*
385294 AA-AAAAGAAG
1 AAGAAAAGAAA
385304 AAGAAAA-AATA
1 AAGAAAAGAA-A
385315 ATAGAAAAAGAAA
1 A-AG-AAAAGAAA
385328 A
1 A
385329 GGGTCAAGGT
Statistics
Matches: 78, Mismatches: 12, Indels: 17
0.73 0.11 0.16
Matches are distributed among these distances:
9 5 0.06
10 22 0.28
11 21 0.27
12 22 0.28
13 6 0.08
14 2 0.03
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (11 bp):
AAGAAAAGAAA
Found at i:385320 original size:15 final size:15
Alignment explanation
Indices: 385217--385312 Score: 78
Period size: 15 Copynumber: 6.7 Consensus size: 15
385207 TATTATGCTT
*
385217 GAAGAAAAGAAAGAA
1 GAAGAAAAAAAAGAA
*
385232 GAAG-AGAAAAAGAA
1 GAAGAAAAAAAAGAA
*
385246 AAAGAAAAAGAAA-AA
1 GAAGAAAAA-AAAGAA
385261 GAAAGAAAAAAAA-AA
1 G-AAGAAAAAAAAGAA
***
385276 G-A-AAAAAGGGGAA
1 GAAGAAAAAAAAGAA
385289 -AAGAAAAAAAAGAA
1 GAAGAAAAAAAAGAA
385303 GAAGAAAAAA
1 GAAGAAAAAA
385313 TAATAGAAAA
Statistics
Matches: 63, Mismatches: 11, Indels: 14
0.72 0.12 0.16
Matches are distributed among these distances:
12 5 0.08
13 4 0.06
14 19 0.30
15 24 0.38
16 11 0.17
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (15 bp):
GAAGAAAAAAAAGAA
Found at i:386536 original size:50 final size:50
Alignment explanation
Indices: 386461--386662 Score: 395
Period size: 50 Copynumber: 4.0 Consensus size: 50
386451 GAAAGAGACT
386461 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAG
386511 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAG
386561 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAG
*
386611 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAG
386661 AA
1 AA
386663 CCAATCATTG
Statistics
Matches: 151, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
50 151 1.00
ACGTcount: A:0.22, C:0.14, G:0.24, T:0.40
Consensus pattern (50 bp):
AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAG
Found at i:387712 original size:118 final size:116
Alignment explanation
Indices: 387384--388022 Score: 1080
Period size: 117 Copynumber: 5.4 Consensus size: 116
387374 GAATCAAATC
* * * ** *
387384 CATCATTTGATGGATCAGCTTTTCCAGTTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAA
1 CATCACTTGATGGATCATCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCGTCATCTGAAGAA
*
387449 GGAAGAGGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATT
66 GGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATT
*
387500 CATCACTTGATGGATCATTCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCGTCATCTGAAGA
1 CATCACTTGATGGATCA-TCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCGTCATCTGAAGA
387565 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATT
65 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATT
387617 CATCACTTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAG
1 CATCACTTGATGGATCATCATTTCCAGA-GAA-AGTTCATAATGAGAAGAACTCGTCATCTGAAG
*
387682 AAGGAAGAGGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATT
64 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATT
*
387735 CATCACTTGATGGATCATTCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCGTCATCTGAAGA
1 CATCACTTGATGGATCA-TCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCGTCATCTGAAGA
387800 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATT
65 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATT
387852 CATCACTTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAG
1 CATCACTTGATGGATCATCATTTCCAGA-GAA-AGTTCATAATGAGAAGAACTCGTCATCTGAAG
387917 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATT
64 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATT
* * ** *
387970 CATCATTTGATGGAACATCATCCCCAGCAGAAAGTTCGTAATGAGAAGAACTC
1 CATCACTTGATGGATCATCATTTCCAG-AGAAAGTTCATAATGAGAAGAACTC
388023 ATCTGGAGAA
Statistics
Matches: 500, Mismatches: 16, Indels: 13
0.95 0.03 0.02
Matches are distributed among these distances:
116 36 0.07
117 238 0.48
118 215 0.43
119 11 0.02
ACGTcount: A:0.35, C:0.16, G:0.21, T:0.29
Consensus pattern (116 bp):
CATCACTTGATGGATCATCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCGTCATCTGAAGAA
GGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATT
Found at i:387824 original size:235 final size:235
Alignment explanation
Indices: 387413--388022 Score: 1141
Period size: 235 Copynumber: 2.6 Consensus size: 235
387403 TTTTCCAGTT
387413 AGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAGGAAGTTCATAATGAGAAGAACT
1 AGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAGGAAGTTCATAATGAGAAGAACT
387478 TGTTCAACCTTTTGCTTGAATTCATCACTTGATGGATCATTCTTTTCCAGAGAAAGTTCATAATG
66 TGTTCAACCTTTTGCTTGAATTCATCACTTGATGGATCATTCTTTTCCAGAGAAAGTTCATAATG
387543 AGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTT
131 AGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTT
387608 GCTTGAATTCATCACTTGATGGATCATCATTTCCAGAGGA
196 GCTTGAATTCATCACTTGATGGATCATCATTTCCAGAGGA
387648 AGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAGGAAGTTCATAATGAGAAGAACT
1 AGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAGGAAGTTCATAATGAGAAGAACT
387713 TGTTCAACCTTTTGCTTGAATTCATCACTTGATGGATCATTCTTTTCCAGAGAAAGTTCATAATG
66 TGTTCAACCTTTTGCTTGAATTCATCACTTGATGGATCATTCTTTTCCAGAGAAAGTTCATAATG
387778 AGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTT
131 AGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTT
387843 GCTTGAATTCATCACTTGATGGATCATCATTTCCAGAGGA
196 GCTTGAATTCATCACTTGATGGATCATCATTTCCAGAGGA
*
387883 AGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACT
1 AGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAGGAAGTTCATAATGAGAAGAACT
* * * ** *
387948 TGTTCAACCTTTTGCTTGAATTCATCATTTGATGGAACA-TCATCCCCAGCAGAAAGTTCGTAAT
66 TGTTCAACCTTTTGCTTGAATTCATCACTTGATGGATCATTCTTTTCCAG-AGAAAGTTCATAAT
388012 GAGAAGAACTC
130 GAGAAGAACTC
388023 ATCTGGAGAA
Statistics
Matches: 367, Mismatches: 7, Indels: 2
0.98 0.02 0.01
Matches are distributed among these distances:
234 7 0.02
235 360 0.98
ACGTcount: A:0.35, C:0.16, G:0.21, T:0.28
Consensus pattern (235 bp):
AGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAGGAAGTTCATAATGAGAAGAACT
TGTTCAACCTTTTGCTTGAATTCATCACTTGATGGATCATTCTTTTCCAGAGAAAGTTCATAATG
AGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTT
GCTTGAATTCATCACTTGATGGATCATCATTTCCAGAGGA
Found at i:388185 original size:3 final size:3
Alignment explanation
Indices: 388177--388276 Score: 157
Period size: 3 Copynumber: 33.7 Consensus size: 3
388167 TTTTTATCCA
* * *
388177 TAT TAT TAT TAT TAT TAT TAA TAT TAT TAT CAT TAT TAA TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
388225 TAT TAT TAT TAT TAT TAT TAT TTT TAT TAT TAT TAT TAT TAT T-T TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
388272 TAT TA
1 TAT TA
388277 AATATATTAA
Statistics
Matches: 88, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
2 2 0.02
3 86 0.98
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:388750 original size:6 final size:6
Alignment explanation
Indices: 388739--388765 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
388729 AAGAAAAAAA
388739 AGAGAC AGAGAC AGAGAC AGAGAC AGA
1 AGAGAC AGAGAC AGAGAC AGAGAC AGA
388766 ACCGGAGAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.52, C:0.15, G:0.33, T:0.00
Consensus pattern (6 bp):
AGAGAC
Found at i:389679 original size:19 final size:19
Alignment explanation
Indices: 389641--389678 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
389631 TGTAATTTAG
389641 TCATTTATTTTATATGTTT
1 TCATTTATTTTATATGTTT
389660 TCATTTATTTTAT-TGTTT
1 TCATTTATTTTATATGTTT
389678 T
1 T
389679 TAAATATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.18, C:0.05, G:0.05, T:0.71
Consensus pattern (19 bp):
TCATTTATTTTATATGTTT
Found at i:389747 original size:24 final size:22
Alignment explanation
Indices: 389699--389747 Score: 53
Period size: 24 Copynumber: 2.1 Consensus size: 22
389689 GTTTTAATAG
* *
389699 TATTTTTATTTTTATGAATAAA
1 TATTTTTATTTTCATAAATAAA
*
389721 TATTTTTATATATTCATAAATATA
1 TATTTTTAT-T-TTCATAAATAAA
389745 TAT
1 TAT
389748 ATAATGGTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 9 0.41
23 1 0.05
24 12 0.55
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (22 bp):
TATTTTTATTTTCATAAATAAA
Found at i:392061 original size:2 final size:2
Alignment explanation
Indices: 392056--392080 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
392046 ATAGAGATTT
392056 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
392081 TCTTTACAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:392220 original size:12 final size:12
Alignment explanation
Indices: 392203--392230 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
392193 GAGACAACAT
392203 CATACATATATG
1 CATACATATATG
392215 CATACATATATG
1 CATACATATATG
392227 CATA
1 CATA
392231 TATAATAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.43, C:0.18, G:0.07, T:0.32
Consensus pattern (12 bp):
CATACATATATG
Found at i:397030 original size:3 final size:3
Alignment explanation
Indices: 397022--397046 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
397012 AATATGTAAC
397022 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
397047 ATATATAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:397507 original size:105 final size:105
Alignment explanation
Indices: 397316--397591 Score: 392
Period size: 105 Copynumber: 2.6 Consensus size: 105
397306 ATGTAAGGTT
* *
397316 GAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCGTTA-GATGAGTTCTTCTCATTATGAACT
1 GAACAAGTTCTTCTCATTATGAAC-T-TTC-TCCT--TTAGGACGAGTTCTTCTCATTATGAACT
* *
397380 CTTCTGGAAATGTTGATCCACCTCCTTCTGTGATGGACTTGAAAA
61 CTTCTAGAAATGTTGATCCACCTCCTTCTGTGATGAACTTGAAAA
* *
397425 GAACATGTTTTTCTCATTATGAACTTTCTCCTTTAGGACGAGTTCTTCTCATTATGAACTCTTCT
1 GAACAAGTTCTTCTCATTATGAACTTTCTCCTTTAGGACGAGTTCTTCTCATTATGAACTCTTCT
* * * * * *
397490 AGAAATGTTGGTTCACCTTCTTCTGTGGTGAATTTGAAAG
66 AGAAATGTTGATCCACCTCCTTCTGTGATGAACTTGAAAA
397530 GAACAAGTTCTTCTCATTATGAACTTTCTCCTTTAGGACGAGTTCTTCTCATTATGAACTCT
1 GAACAAGTTCTTCTCATTATGAACTTTCTCCTTTAGGACGAGTTCTTCTCATTATGAACTCT
397592 CCATTAGAAA
Statistics
Matches: 152, Mismatches: 14, Indels: 6
0.88 0.08 0.03
Matches are distributed among these distances:
104 3 0.02
105 120 0.79
106 4 0.03
107 3 0.02
108 1 0.01
109 21 0.14
ACGTcount: A:0.24, C:0.21, G:0.15, T:0.40
Consensus pattern (105 bp):
GAACAAGTTCTTCTCATTATGAACTTTCTCCTTTAGGACGAGTTCTTCTCATTATGAACTCTTCT
AGAAATGTTGATCCACCTCCTTCTGTGATGAACTTGAAAA
Found at i:397728 original size:136 final size:136
Alignment explanation
Indices: 397530--398151 Score: 975
Period size: 136 Copynumber: 4.6 Consensus size: 136
397520 AATTTGAAAG
* * *
397530 GAACAAGTTCTTCTCATTATGAAC-T-TTCT-CCT-T-TAGGACGAGTTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACT
* ** * * *
397590 CTCCATTAGAAATGTCAATCCCTCAAGCGAGGTGTCACTGATTGGAAATGTTGTGAATCGAGTGA
66 CTCCATTGGAAATGTTGATCCCTCAAGCGAGGCGTCACTGATTCGAAATGTCGTGAATCGAGTGA
*
397655 TAGGTT
131 TAGGTC
*
397661 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTTTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACT
* ** **
397726 CTCCATTGGAAATATTGATCCCTCAAGCGAGAAGTCACTGATTCGAAATACCGTGAATCGAGTGA
66 CTCCATTGGAAATGTTGATCCCTCAAGCGAGGCGTCACTGATTCGAAATGTCGTGAATCGAGTGA
397791 TAGGTC
131 TAGGTC
397797 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACT
* * *
397862 CTCTATTGGAAATATTGATCCCTCAAGCGAGGCATCACTGATTCGAAATGTCGTGAATCGAGTGA
66 CTCCATTGGAAATGTTGATCCCTCAAGCGAGGCGTCACTGATTCGAAATGTCGTGAATCGAGTGA
397927 TAGGTC
131 TAGGTC
* *
397933 GAACAAGATCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTATTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACT
* * *
397998 CTCTATTGGAAATGTTGATCCCTCAAGCGAGGCGTCACTGATTTGAAATGTTGTGAATCGAGTGA
66 CTCCATTGGAAATGTTGATCCCTCAAGCGAGGCGTCACTGATTCGAAATGTCGTGAATCGAGTGA
398063 TAGGTC
131 TAGGTC
* *
398069 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTTTCGGATGAGTTCTTCTCATTATGAACC
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACT
398134 CTCCATTGGAAATGTTGA
66 CTCCATTGGAAATGTTGA
398152 AAACATTCTG
Statistics
Matches: 453, Mismatches: 33, Indels: 5
0.92 0.07 0.01
Matches are distributed among these distances:
131 23 0.05
132 1 0.00
133 4 0.01
134 3 0.01
135 1 0.00
136 421 0.93
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.34
Consensus pattern (136 bp):
GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACT
CTCCATTGGAAATGTTGATCCCTCAAGCGAGGCGTCACTGATTCGAAATGTCGTGAATCGAGTGA
TAGGTC
Found at i:398231 original size:42 final size:42
Alignment explanation
Indices: 398184--398264 Score: 117
Period size: 42 Copynumber: 1.9 Consensus size: 42
398174 ATCATCTAGT
* *
398184 TCGAAAGGCTTACAGATAACCCGAAAGATTTAAACATCATGC
1 TCGAAAGACTTACAGATAACCCGAAAGATTTAAAAATCATGC
* * *
398226 TCGAAAGACTTACTGATGACCCGAAGGATTTAAAAATCA
1 TCGAAAGACTTACAGATAACCCGAAAGATTTAAAAATCA
398265 AGAAACCCCC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (42 bp):
TCGAAAGACTTACAGATAACCCGAAAGATTTAAAAATCATGC
Found at i:403694 original size:18 final size:17
Alignment explanation
Indices: 403640--403688 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
403630 TTGTACTCCT
* *
403640 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TGA
403658 GAGTGCATCGATGCATGA
1 -AGTGCATCGATGCATGA
403676 AGTGCATTCGATG
1 AGTGCA-TCGATG
403689 TTTGAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.18, G:0.31, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATGA
Found at i:403773 original size:64 final size:65
Alignment explanation
Indices: 403640--403849 Score: 196
Period size: 64 Copynumber: 3.3 Consensus size: 65
403630 TTGTACTCCT
* * * * *
403640 AGTGCATCGGTGCACT-AAGAGTGCATCGATGCATGAAGTGCATTCGATGTTTGAA--AAATAGC
1 AGTGCATCGATGCA-TGGAGAGTGCATCGATGCATCAAATGCATTCGATGTTTCAATTAAAT--C
*
403702 CTG
63 ATG
*** * *
403705 -GTGCATCGATGCATGGCTTGTGCATTGATGCATCAAATGCATTCGATGTTTTAATTAAATCA-G
1 AGTGCATCGATGCATGGAGAGTGCATCGATGCATCAAATGCATTCGATGTTTCAATTAAATCATG
* ** * * *
403768 AGTGCATCGATGCATGGAGAGTGCATCGGTGCATTGAATGCATTCGATGTTTCAATTTATTCATT
1 AGTGCATCGATGCATGGAGAGTGCATCGATGCATCAAATGCATTCGATGTTTCAATTAAATCATG
*
403833 AATGCATCGATGCATGG
1 AGTGCATCGATGCATGG
403850 TATTGATGCA
Statistics
Matches: 118, Mismatches: 22, Indels: 10
0.79 0.15 0.07
Matches are distributed among these distances:
63 2 0.02
64 96 0.81
65 16 0.14
66 4 0.03
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.31
Consensus pattern (65 bp):
AGTGCATCGATGCATGGAGAGTGCATCGATGCATCAAATGCATTCGATGTTTCAATTAAATCATG
Found at i:404205 original size:19 final size:19
Alignment explanation
Indices: 404181--404217 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
404171 TTTCAATTAG
404181 GGGGAATCGATACCCCCTA
1 GGGGAATCGATACCCCCTA
404200 GGGGAATCGATACCCCCT
1 GGGGAATCGATACCCCCT
404218 GGACATACTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.24, C:0.32, G:0.27, T:0.16
Consensus pattern (19 bp):
GGGGAATCGATACCCCCTA
Found at i:412082 original size:21 final size:21
Alignment explanation
Indices: 412058--412145 Score: 167
Period size: 21 Copynumber: 4.2 Consensus size: 21
412048 GTATATAATT
*
412058 CTTAAGGAATGATATGTGCTC
1 CTTAAGGAATGATATGTGGTC
412079 CTTAAGGAATGATATGTGGTC
1 CTTAAGGAATGATATGTGGTC
412100 CTTAAGGAATGATATGTGGTC
1 CTTAAGGAATGATATGTGGTC
412121 CTTAAGGAATGATATGTGGTC
1 CTTAAGGAATGATATGTGGTC
412142 CTTA
1 CTTA
412146 TGGACATTAT
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
21 66 1.00
ACGTcount: A:0.28, C:0.11, G:0.26, T:0.34
Consensus pattern (21 bp):
CTTAAGGAATGATATGTGGTC
Found at i:417437 original size:21 final size:21
Alignment explanation
Indices: 417412--417499 Score: 167
Period size: 21 Copynumber: 4.2 Consensus size: 21
417402 GTATATGATT
*
417412 CTTAAGGAATGATATGTGCTC
1 CTTAAGGAATGATATGTGGTC
417433 CTTAAGGAATGATATGTGGTC
1 CTTAAGGAATGATATGTGGTC
417454 CTTAAGGAATGATATGTGGTC
1 CTTAAGGAATGATATGTGGTC
417475 CTTAAGGAATGATATGTGGTC
1 CTTAAGGAATGATATGTGGTC
417496 CTTA
1 CTTA
417500 TGGACATTAT
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
21 66 1.00
ACGTcount: A:0.28, C:0.11, G:0.26, T:0.34
Consensus pattern (21 bp):
CTTAAGGAATGATATGTGGTC
Found at i:421875 original size:14 final size:14
Alignment explanation
Indices: 421856--421884 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
421846 TTGGGACCGA
421856 GTTCAATTTCGAGG
1 GTTCAATTTCGAGG
421870 GTTCAATTTCGAGG
1 GTTCAATTTCGAGG
421884 G
1 G
421885 AACACACCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.14, G:0.31, T:0.34
Consensus pattern (14 bp):
GTTCAATTTCGAGG
Found at i:424818 original size:18 final size:18
Alignment explanation
Indices: 424797--424850 Score: 60
Period size: 18 Copynumber: 3.2 Consensus size: 18
424787 TATAATATAA
424797 TTATATAAATATTATTTT
1 TTATATAAATATTATTTT
* *
424815 TTAT-TAAA-A-TAATAT
1 TTATATAAATATTATTTT
*
424830 TTATATAATTATTATTTT
1 TTATATAAATATTATTTT
424848 TTA
1 TTA
424851 AAATTTATTA
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
15 8 0.29
16 4 0.14
17 5 0.18
18 11 0.39
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TTATATAAATATTATTTT
Found at i:426685 original size:21 final size:21
Alignment explanation
Indices: 426655--426706 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
426645 TATGCCATCT
* *
426655 CCGCAGGGTTACATTCCTAGC
1 CCGCAAGGTTACATGCCTAGC
*
426676 CCGCCAGGTTACATGCCTAGC
1 CCGCAAGGTTACATGCCTAGC
426697 CCGCAAGGTT
1 CCGCAAGGTT
426707 TTATACCATA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.19, C:0.35, G:0.25, T:0.21
Consensus pattern (21 bp):
CCGCAAGGTTACATGCCTAGC
Found at i:427284 original size:34 final size:34
Alignment explanation
Indices: 427228--427334 Score: 160
Period size: 34 Copynumber: 3.1 Consensus size: 34
427218 ATAAATGTTT
427228 TTAAAATAAAAATTATAGTATTCGAAATTTAACA
1 TTAAAATAAAAATTATAGTATTCGAAATTTAACA
* * * * *
427262 TTAAAATACAAATAATATTATTCAAAATTTAAAA
1 TTAAAATAAAAATTATAGTATTCGAAATTTAACA
*
427296 TTAAAATATAAATTATAGTATTCGAAATTTAACA
1 TTAAAATAAAAATTATAGTATTCGAAATTTAACA
427330 TTAAA
1 TTAAA
427335 TTCAACTTAA
Statistics
Matches: 63, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 63 1.00
ACGTcount: A:0.54, C:0.06, G:0.04, T:0.36
Consensus pattern (34 bp):
TTAAAATAAAAATTATAGTATTCGAAATTTAACA
Done.