Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold195
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: 1914327
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.29
Warning! 179916 characters in sequence are not A, C, G, or T
File 3 of 12
Found at i:335268 original size:12 final size:11
Alignment explanation
Indices: 335246--335321 Score: 70
Period size: 12 Copynumber: 6.9 Consensus size: 11
335236 AGAGAAAGAA
*
335246 GAGAGAGGAGG
1 GAGATAGGAGG
335257 GATGATAGGAGG
1 GA-GATAGGAGG
335269 AGAGATAGGA--
1 -GAGATAGGAGG
*
335279 GAGATAGTA--
1 GAGATAGGAGG
335288 GAGATAGGAGG
1 GAGATAGGAGG
335299 GATGATAGGAGG
1 GA-GATAGGAGG
335311 AGAGATAGGAG
1 -GAGATAGGAG
335322 AGATAATAGA
Statistics
Matches: 56, Mismatches: 3, Indels: 11
0.80 0.04 0.16
Matches are distributed among these distances:
9 16 0.29
11 4 0.07
12 32 0.57
13 4 0.07
ACGTcount: A:0.39, C:0.00, G:0.49, T:0.12
Consensus pattern (11 bp):
GAGATAGGAGG
Found at i:335280 original size:9 final size:9
Alignment explanation
Indices: 335266--335326 Score: 65
Period size: 9 Copynumber: 7.1 Consensus size: 9
335256 GGATGATAGG
335266 AGGAGAGAT
1 AGGAGAGAT
335275 AGGAGAGAT
1 AGGAGAGAT
*
335284 AGTAGAGAT
1 AGGAGAGAT
*
335293 AGGAGGGAT
1 AGGAGAGAT
* *
335302 --GATAG-G
1 AGGAGAGAT
335308 AGGAGAGAT
1 AGGAGAGAT
335317 AGGAGAGAT
1 AGGAGAGAT
335326 A
1 A
335327 ATAGAGAGAG
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
7 3 0.07
8 4 0.10
9 34 0.83
ACGTcount: A:0.43, C:0.00, G:0.44, T:0.13
Consensus pattern (9 bp):
AGGAGAGAT
Found at i:335282 original size:33 final size:30
Alignment explanation
Indices: 335236--335326 Score: 76
Period size: 33 Copynumber: 2.8 Consensus size: 30
335226 TAGCCCTCAA
* *
335236 AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGG
1 AGAGATAGGAGAGAGAGGA--GA-GATAGGAGG
* *
335269 AGAGATAGGAGAGATAGTAGAGATAGGAGG
1 AGAGATAGGAGAGAGAGGAGAGATAGGAGG
335299 -GATGATAGGAGGAGAGATAGGAGAGATA
1 AGA-GATAGGA-GAGAG--AGGAGAGATA
335327 ATAGAGAGAG
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
29 2 0.04
30 16 0.33
31 6 0.12
33 24 0.50
ACGTcount: A:0.44, C:0.00, G:0.45, T:0.11
Consensus pattern (30 bp):
AGAGATAGGAGAGAGAGGAGAGATAGGAGG
Found at i:335297 original size:42 final size:42
Alignment explanation
Indices: 335236--335354 Score: 202
Period size: 42 Copynumber: 2.8 Consensus size: 42
335226 TAGCCCTCAA
* *
335236 AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAGATAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGATAGG
*
335278 AGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGATAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGATAGG
*
335320 AGAGATAATAGAGAGAGGAGGGATGATAGGAGGAG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAG
335355 GAGGGAAGAA
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 72 1.00
ACGTcount: A:0.43, C:0.00, G:0.46, T:0.11
Consensus pattern (42 bp):
AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGATAGG
Found at i:335330 original size:12 final size:12
Alignment explanation
Indices: 335251--335335 Score: 53
Period size: 12 Copynumber: 7.7 Consensus size: 12
335241 AAGAAGAGAG
*
335251 AGGAGGGATGAT
1 AGGAGAGATGAT
335263 AGGAGGAGA-GAT
1 AGGA-GAGATGAT
335275 A-G-GAGA-GAT
1 AGGAGAGATGAT
*
335284 A-G-TAGA-GAT
1 AGGAGAGATGAT
*
335293 AGGAGGGATGAT
1 AGGAGAGATGAT
335305 AGGAGGAGA-GAT
1 AGGA-GAGATGAT
*
335317 AGGAGAGATAAT
1 AGGAGAGATGAT
335329 A-GAGAGA
1 AGGAGAGA
335336 GGAGGGATGA
Statistics
Matches: 61, Mismatches: 6, Indels: 13
0.76 0.08 0.16
Matches are distributed among these distances:
9 16 0.26
10 1 0.02
11 13 0.21
12 25 0.41
13 6 0.10
ACGTcount: A:0.42, C:0.00, G:0.45, T:0.13
Consensus pattern (12 bp):
AGGAGAGATGAT
Found at i:335338 original size:18 final size:18
Alignment explanation
Indices: 335311--335357 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
335301 TGATAGGAGG
*
335311 AGAGATAGGAGAGATAAT
1 AGAGAGAGGAGAGATAAT
* *
335329 AGAGAGAGGAGGGATGAT
1 AGAGAGAGGAGAGATAAT
335347 AG-GAGGAGGAG
1 AGAGA-GAGGAG
335358 GGAAGAAGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 2 0.08
18 23 0.92
ACGTcount: A:0.43, C:0.00, G:0.47, T:0.11
Consensus pattern (18 bp):
AGAGAGAGGAGAGATAAT
Found at i:335358 original size:18 final size:18
Alignment explanation
Indices: 335250--335360 Score: 64
Period size: 21 Copynumber: 5.5 Consensus size: 18
335240 AAAGAAGAGA
335250 GAGGAGGGATGATAGGAG
1 GAGGAGGGATGATAGGAG
335268 GAGAGATAGGAGA-GATAGTAGAG
1 GAG-G--AGG-GATGATAG--GAG
*
335291 ATAGGAGGGATGATAGGAG
1 -GAGGAGGGATGATAGGAG
*
335310 GAGAGATAGGAGA-GATAATAGAG
1 GAG-G--AGG-GATGAT-A-GGAG
335333 AGAGGAGGGATGATAGGAG
1 -GAGGAGGGATGATAGGAG
335352 GAGGAGGGA
1 GAGGAGGGA
335361 AGAAGATGGA
Statistics
Matches: 73, Mismatches: 4, Indels: 32
0.67 0.04 0.29
Matches are distributed among these distances:
18 14 0.19
19 8 0.11
20 5 0.07
21 28 0.38
22 5 0.07
23 8 0.11
24 5 0.07
ACGTcount: A:0.40, C:0.00, G:0.49, T:0.12
Consensus pattern (18 bp):
GAGGAGGGATGATAGGAG
Found at i:340995 original size:199 final size:203
Alignment explanation
Indices: 340610--340999 Score: 468
Period size: 199 Copynumber: 1.9 Consensus size: 203
340600 TAAAAATTAT
* ** * *
340610 ATTTAACTATTCAAATAGTATTAAAATTAGTTAAAACAACATCTAAAAAGCATTTAAGTTTGACG
1 ATTTAACCATTCAAATAGTATTAAAAAGAGTTAAAACAACATCTAAAAAGCATTTAAGGTAGACG
* * * * ** ** *
340675 TTAAATTATTAATATATTATATTAAATTCAATGAATGAGATAAAAATTTATAAATGGGATGAAAT
66 TTAAATGATTAATATA-TACACTAAATTCAATGAATAAGATAAAAAACTATAAATAAGATGAAAA
* * * **
340740 TAATATATATTATATTAAATTCAATGATTGAGATAAAATTAATTAATTGTAATTTTTATATAATA
130 TAATATATATTATATTAAATTCAATGAATAAAATAAAATTAATTAATAATAATTTTTATATAATA
340805 TTTTTAATA
195 TTTTTAATA
340814 ATTTAACCATTCAAAT-GTTATTAAAAAGAGTTAAATA-AA-ATCTAAAAAGCATTTAAGGTAGA
1 ATTTAACCATTCAAATAG-TATTAAAAAGAGTTAAA-ACAACATCTAAAAAGCATTTAAGGTAGA
* * **
340876 TGTTGAATGATTAATATA-ACACTACTTTCAATGAATAAGATAAAAAACTATAAATAAGAT-AAA
64 CGTTAAATGATTAATATATACACTAAATTCAATGAATAAGATAAAAAACTATAAATAAGATGAAA
* * **
340939 ATCA-ATATATTATATTAAATTTAATGAATAAAATAAAATTAATTGGTAATAATTTTTATAT
129 ATAATATATATTATATTAAATTCAATGAATAAAATAAAATTAATTAATAATAATTTTTATAT
341000 TGTGAATAGT
Statistics
Matches: 157, Mismatches: 27, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
199 49 0.31
200 5 0.03
201 33 0.21
203 37 0.24
204 32 0.20
205 1 0.01
ACGTcount: A:0.48, C:0.05, G:0.08, T:0.38
Consensus pattern (203 bp):
ATTTAACCATTCAAATAGTATTAAAAAGAGTTAAAACAACATCTAAAAAGCATTTAAGGTAGACG
TTAAATGATTAATATATACACTAAATTCAATGAATAAGATAAAAAACTATAAATAAGATGAAAAT
AATATATATTATATTAAATTCAATGAATAAAATAAAATTAATTAATAATAATTTTTATATAATAT
TTTTAATA
Found at i:342366 original size:43 final size:43
Alignment explanation
Indices: 342318--342489 Score: 199
Period size: 43 Copynumber: 3.8 Consensus size: 43
342308 AATGAAACTA
342318 AAAAAGTAATGA-ATAAAATTAATATATTATATTAAATTCAAAG
1 AAAAAG-AATGAGATAAAATTAATATATTATATTAAATTCAAAG
*
342361 AAAAAGAATGAGATAAAATTAATATATTATATTAAAGAT-AATGAGCG
1 AAAAAGAATGAGATAAAATTAATATATTATATTAAA-TTCAA--A--G
*
342408 AGATAAAGTTTATTGA-A-AAAATTAATATATTATATTAAATTCAAAG
1 A-A-AAAG---AATGAGATAAAATTAATATATTATATTAAATTCAAAG
342454 AAAAAGAATGAGATAAAATTAATATATTATATTAAA
1 AAAAAGAATGAGATAAAATTAATATATTATATTAAA
342490 GATAATGAGC
Statistics
Matches: 111, Mismatches: 4, Indels: 28
0.78 0.03 0.20
Matches are distributed among these distances:
41 4 0.04
42 6 0.05
43 54 0.49
44 5 0.05
45 2 0.02
46 2 0.02
47 2 0.02
48 2 0.02
49 5 0.05
50 24 0.22
51 1 0.01
52 4 0.04
ACGTcount: A:0.56, C:0.02, G:0.10, T:0.32
Consensus pattern (43 bp):
AAAAAGAATGAGATAAAATTAATATATTATATTAAATTCAAAG
Found at i:342557 original size:93 final size:93
Alignment explanation
Indices: 342327--342541 Score: 421
Period size: 93 Copynumber: 2.3 Consensus size: 93
342317 AAAAAAGTAA
342327 TGAATAAAATTAATATATTATATTAAATTCAAAGAAAAAGAATGAGATAAAATTAATATATTATA
1 TGAA-AAAATTAATATATTATATTAAATTCAAAGAAAAAGAATGAGATAAAATTAATATATTATA
342392 TTAAAGATAATGAGCGAGATAAAGTTTAT
65 TTAAAGATAATGAGCGAGATAAAGTTTAT
342421 TGAAAAAATTAATATATTATATTAAATTCAAAGAAAAAGAATGAGATAAAATTAATATATTATAT
1 TGAAAAAATTAATATATTATATTAAATTCAAAGAAAAAGAATGAGATAAAATTAATATATTATAT
342486 TAAAGATAATGAGCGAGATAAAGTTTAT
66 TAAAGATAATGAGCGAGATAAAGTTTAT
342514 TGAAAAAATTAATATATTATATTAAATT
1 TGAAAAAATTAATATATTATATTAAATT
342542 TAAATTCAAT
Statistics
Matches: 121, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
93 117 0.97
94 4 0.03
ACGTcount: A:0.53, C:0.02, G:0.11, T:0.34
Consensus pattern (93 bp):
TGAAAAAATTAATATATTATATTAAATTCAAAGAAAAAGAATGAGATAAAATTAATATATTATAT
TAAAGATAATGAGCGAGATAAAGTTTAT
Found at i:343006 original size:3 final size:3
Alignment explanation
Indices: 342998--343023 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
342988 TATCTTTTAT
342998 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
343024 TTATAAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:343730 original size:10 final size:10
Alignment explanation
Indices: 343702--343740 Score: 55
Period size: 10 Copynumber: 4.1 Consensus size: 10
343692 AAATTTATTT
*
343702 TTTAATAAAA
1 TTTATTAAAA
343712 -TTA-TAAAA
1 TTTATTAAAA
343720 TTTATTAAAA
1 TTTATTAAAA
343730 TTTATTAAAA
1 TTTATTAAAA
343740 T
1 T
343741 ATAATTTTGG
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
8 5 0.19
9 6 0.22
10 16 0.59
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (10 bp):
TTTATTAAAA
Found at i:348263 original size:11 final size:11
Alignment explanation
Indices: 348243--348276 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
348233 ATTAATTAAT
*
348243 TATTACTATTA
1 TATTATTATTA
*
348254 TGTTATTATTA
1 TATTATTATTA
348265 TATTATTATTA
1 TATTATTATTA
348276 T
1 T
348277 TATTTATTCA
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:0.03, G:0.03, T:0.62
Consensus pattern (11 bp):
TATTATTATTA
Found at i:348273 original size:14 final size:14
Alignment explanation
Indices: 348241--348284 Score: 54
Period size: 14 Copynumber: 3.0 Consensus size: 14
348231 TAATTAATTA
348241 ATTATTACTATTATGTT
1 ATTATTA-TATTA--TT
348258 ATTATTATATTATT
1 ATTATTATATTATT
348272 ATTATTAT-TTATT
1 ATTATTATATTATT
348285 CATGTTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
13 5 0.19
14 10 0.37
16 5 0.19
17 7 0.26
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (14 bp):
ATTATTATATTATT
Found at i:348732 original size:10 final size:10
Alignment explanation
Indices: 348719--348770 Score: 50
Period size: 10 Copynumber: 5.0 Consensus size: 10
348709 AATAGACTCA
348719 AATTTAAAAT
1 AATTTAAAAT
*
348729 AATTTAAATTT
1 AATTTAAA-AT
**
348740 AAAATAAATAT
1 AATTTAAA-AT
*
348751 AATTTTAAAT
1 AATTTAAAAT
348761 AATTTAAAAT
1 AATTTAAAAT
348771 CAAAATAATA
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
10 19 0.58
11 14 0.42
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (10 bp):
AATTTAAAAT
Found at i:348737 original size:16 final size:16
Alignment explanation
Indices: 348718--348779 Score: 72
Period size: 16 Copynumber: 3.9 Consensus size: 16
348708 AAATAGACTC
348718 AAATTTAAAATAATTT
1 AAATTTAAAATAATTT
*
348734 AAATTTAAAATAA-AT
1 AAATTTAAAATAATTT
*
348749 ATAATTTTAAATAATTT
1 A-AATTTAAAATAATTT
* *
348766 AAAATCAAAATAAT
1 AAATTTAAAATAAT
348780 AAAAACTAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
15 2 0.05
16 34 0.89
17 2 0.05
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.39
Consensus pattern (16 bp):
AAATTTAAAATAATTT
Found at i:352075 original size:22 final size:23
Alignment explanation
Indices: 352021--352076 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 23
352011 AAAATTAAAC
*
352021 AATAAGAATATGATACAAAAAAT
1 AATATGAATATGATACAAAAAAT
* *
352044 AAT-TAAAATATGATA-AAAAATT
1 AATAT-GAATATGATACAAAAAAT
352066 AATATGAATAT
1 AATATGAATAT
352077 TTTAAAATCT
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
22 14 0.52
23 13 0.48
ACGTcount: A:0.62, C:0.02, G:0.07, T:0.29
Consensus pattern (23 bp):
AATATGAATATGATACAAAAAAT
Found at i:353247 original size:21 final size:21
Alignment explanation
Indices: 353221--353263 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
353211 TTAAAATTAT
*
353221 TTTTAT-ATTAATATTTATATA
1 TTTTATAATTAA-ATTTAAATA
353242 TTTTATAATTAAATTTAAATA
1 TTTTATAATTAAATTTAAATA
353263 T
1 T
353264 AAATATATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
TTTTATAATTAAATTTAAATA
Found at i:354217 original size:2 final size:2
Alignment explanation
Indices: 354210--354242 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
354200 TAACATGAAT
354210 TA TA TA 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 TA TA TA T
354243 CTAATGAGTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:358074 original size:8 final size:8
Alignment explanation
Indices: 358063--358124 Score: 92
Period size: 8 Copynumber: 7.8 Consensus size: 8
358053 ATTTTTTTCG
358063 TTTTTTGA
1 TTTTTTGA
358071 TTTTTTGA
1 TTTTTTGA
358079 TTTTTTGA
1 TTTTTTGA
358087 TTTTTTGA
1 TTTTTTGA
358095 -TTTTTGA
1 TTTTTTGA
358102 TTTTTTTTGA
1 --TTTTTTGA
358112 -TTTTTGA
1 TTTTTTGA
358119 TTTTTT
1 TTTTTT
358125 TCTAATTTAA
Statistics
Matches: 50, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
7 14 0.28
8 29 0.58
10 7 0.14
ACGTcount: A:0.11, C:0.00, G:0.11, T:0.77
Consensus pattern (8 bp):
TTTTTTGA
Found at i:358125 original size:16 final size:16
Alignment explanation
Indices: 358053--358125 Score: 96
Period size: 16 Copynumber: 4.5 Consensus size: 16
358043 TGCTTAAATA
*
358053 ATTTTTTTCGTTTTTTG
1 ATTTTTTT-GATTTTTG
358070 A-TTTTTTGATTTTTTG
1 ATTTTTTTGA-TTTTTG
358086 A-TTTTTTGATTTTTG
1 ATTTTTTTGATTTTTG
358101 ATTTTTTTTGATTTTTG
1 A-TTTTTTTGATTTTTG
358118 ATTTTTTT
1 ATTTTTTT
358126 CTAATTTAAA
Statistics
Matches: 52, Mismatches: 1, Indels: 7
0.87 0.02 0.12
Matches are distributed among these distances:
15 8 0.15
16 28 0.54
17 16 0.31
ACGTcount: A:0.11, C:0.01, G:0.11, T:0.77
Consensus pattern (16 bp):
ATTTTTTTGATTTTTG
Found at i:359233 original size:272 final size:272
Alignment explanation
Indices: 358460--359275 Score: 1429
Period size: 272 Copynumber: 3.0 Consensus size: 272
358450 CATAAAAAAA
* *
358460 TATTGCCTTTATCCTTTTCACACATGCATATATCAATGTGATCTTGAAACAGTTTAAAGAAAGTT
1 TATTGCCTTTATCCTTTTCACACATGCATATATCAATGTGATCTTGAAACGGTTTAAAGCAAGTT
* *
358525 CTAGAGATACATTCATATGGAAGAATATCACACAACAAAGAAAACACTTATTCACATGAATGATT
66 CTAGAGATACATTCACATGGAAGAATATCACACAACAAAGAAAACACTCATTCACATGAATGATT
358590 TAATCTCTTTTAGGCTCAAAATCTCACAGGTTGAATTAATTCACCAAGAATTCACACATTACTTT
131 TAATCTCTTTTAGGCTCAAAATCTCACAGGTTGAATTAATTCACCAAGAATTCACACATTACTTT
* *
358655 TTCACTCAACTTTCAAGGTTAACTTAAGGTCTTATCTCTTGTTAATTCAATTACTCGATATATGT
196 TTCACTCAACTTTCAAGGTCAACTTAAGGTTTTATCTCTTGTTAATTCAATTACTCGATATATGT
358720 CACTATTCATGC
261 CACTATTCATGC
*
358732 TATTGCCTTTATCCTTTTCACACATGCATATATCAATGTGATCTTGAAACGGTTCAAAGCAAGTT
1 TATTGCCTTTATCCTTTTCACACATGCATATATCAATGTGATCTTGAAACGGTTTAAAGCAAGTT
*
358797 CTAGAGATACATTCACATGGAAG-ATATCACACAACAAAGAAAACACTCATTCATATGAATGATT
66 CTAGAGATACATTCACATGGAAGAATATCACACAACAAAGAAAACACTCATTCACATGAATGATT
* * *
358861 TAATCTTTTTTAGGCTCAAAATCTCATAGGTTGAATTAATTCACCAAGAATTCAAACATTACTTT
131 TAATCTCTTTTAGGCTCAAAATCTCACAGGTTGAATTAATTCACCAAGAATTCACACATTACTTT
* * **
358926 TTCACTCAACTTTCAAGGTCAACTTAAGATTTTATCTCTTGTTAATTCAATTACACGATATACAT
196 TTCACTCAACTTTCAAGGTCAACTTAAGGTTTTATCTCTTGTTAATTCAATTACTCGATATATGT
358991 CACTATTCATGC
261 CACTATTCATGC
*
359003 TATTGCCTTTATCCTTTTCACACATGCATATATCAATGTGATCTTAAAACGGTTTAAAGCAAGTT
1 TATTGCCTTTATCCTTTTCACACATGCATATATCAATGTGATCTTGAAACGGTTTAAAGCAAGTT
359068 CTAGCA-ATACATTCACATGGAAGAATATCACACAACAAAGAAAACACTCATTCACATGAATGAT
66 CTAG-AGATACATTCACATGGAAGAATATCACACAACAAAGAAAACACTCATTCACATGAATGAT
* *
359132 TTAATCTCTTTTAGGCTCAAAATCTCACAAGTTGAATTAATTCACTAAGAATTCACACATTACTT
130 TTAATCTCTTTTAGGCTCAAAATCTCACAGGTTGAATTAATTCACCAAGAATTCACACATTACTT
*
359197 TTTCACTCAACTTTCAAGGTCAACTTAAGGTTTTATCTCTTGCTAATTCAATTACTCGATATATG
195 TTTCACTCAACTTTCAAGGTCAACTTAAGGTTTTATCTCTTGTTAATTCAATTACTCGATATATG
*
359262 TCACTATTTATGC
260 TCACTATTCATGC
359275 T
1 T
359276 TGACTAATCA
Statistics
Matches: 513, Mismatches: 29, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
271 256 0.50
272 257 0.50
ACGTcount: A:0.35, C:0.20, G:0.11, T:0.35
Consensus pattern (272 bp):
TATTGCCTTTATCCTTTTCACACATGCATATATCAATGTGATCTTGAAACGGTTTAAAGCAAGTT
CTAGAGATACATTCACATGGAAGAATATCACACAACAAAGAAAACACTCATTCACATGAATGATT
TAATCTCTTTTAGGCTCAAAATCTCACAGGTTGAATTAATTCACCAAGAATTCACACATTACTTT
TTCACTCAACTTTCAAGGTCAACTTAAGGTTTTATCTCTTGTTAATTCAATTACTCGATATATGT
CACTATTCATGC
Found at i:361568 original size:21 final size:19
Alignment explanation
Indices: 361544--361597 Score: 72
Period size: 21 Copynumber: 2.7 Consensus size: 19
361534 TTTCAACAAT
361544 TTGTATCGATACAAACAGTAA
1 TTGTATCGATACAAA-AGT-A
* *
361565 TTGTATCGATACATAAGTG
1 TTGTATCGATACAAAAGTA
361584 TTGTATCGATACAA
1 TTGTATCGATACAA
361598 TGTATCGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
19 13 0.43
20 3 0.10
21 14 0.47
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (19 bp):
TTGTATCGATACAAAAGTA
Found at i:361589 original size:19 final size:19
Alignment explanation
Indices: 361544--361692 Score: 100
Period size: 19 Copynumber: 8.7 Consensus size: 19
361534 TTTCAACAAT
* *
361544 TTGTATCGATACAAACAGTAA
1 TTGTATCGATACATA-AGT-G
361565 TTGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
361584 TTGTATCGATAC--AA---
1 TTGTATCGATACATAAGTG
**
361598 -TGTATCGATGGATAAGTG
1 TTGTATCGATACATAAGTG
361616 TTGTATCGATAC--AA---
1 TTGTATCGATACATAAGTG
*
361630 -TGTATCGATGCATAAGTG
1 TTGTATCGATACATAAGTG
361648 TTGTATCGATAC--AA---
1 TTGTATCGATACATAAGTG
*
361662 -TGTATCGATGCATAAGTG
1 TTGTATCGATACATAAGTG
361680 TTGTATCGATACA
1 TTGTATCGATACA
361693 ATGTATCGCT
Statistics
Matches: 100, Mismatches: 10, Indels: 38
0.68 0.07 0.26
Matches are distributed among these distances:
13 29 0.29
15 6 0.06
17 6 0.06
19 42 0.42
20 3 0.03
21 14 0.14
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.34
Consensus pattern (19 bp):
TTGTATCGATACATAAGTG
Found at i:361613 original size:32 final size:32
Alignment explanation
Indices: 361566--361700 Score: 252
Period size: 32 Copynumber: 4.2 Consensus size: 32
361556 AAACAGTAAT
*
361566 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATGCATAAGTGTTGTATCGATACAA
*
361598 TGTATCGATGGATAAGTGTTGTATCGATACAA
1 TGTATCGATGCATAAGTGTTGTATCGATACAA
361630 TGTATCGATGCATAAGTGTTGTATCGATACAA
1 TGTATCGATGCATAAGTGTTGTATCGATACAA
361662 TGTATCGATGCATAAGTGTTGTATCGATACAA
1 TGTATCGATGCATAAGTGTTGTATCGATACAA
361694 TGTATCG
1 TGTATCG
361701 CTACGAAGCT
Statistics
Matches: 100, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 100 1.00
ACGTcount: A:0.31, C:0.12, G:0.22, T:0.35
Consensus pattern (32 bp):
TGTATCGATGCATAAGTGTTGTATCGATACAA
Found at i:362074 original size:19 final size:19
Alignment explanation
Indices: 362050--362117 Score: 67
Period size: 19 Copynumber: 3.9 Consensus size: 19
362040 AATTCAACAA
362050 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
362069 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
*
362084 --TGTATCAATACATAAGT
1 TTTGTATCGATACATAAGT
* *
362101 ATTATATCGATACATAA
1 TTTGTATCGATACATAA
362118 TTAGCTACTG
Statistics
Matches: 40, Mismatches: 3, Indels: 12
0.73 0.05 0.22
Matches are distributed among these distances:
13 10 0.25
15 2 0.05
17 2 0.05
19 26 0.65
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:362095 original size:32 final size:32
Alignment explanation
Indices: 362052--362114 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
362042 TTCAACAATT
* * *
362052 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCAATACATAAGTATTATATCGATACAA
362084 TGTATCAATACATAAGTATTATATCGATACA
1 TGTATCAATACATAAGTATTATATCGATACA
362115 TAATTAGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.37
Consensus pattern (32 bp):
TGTATCAATACATAAGTATTATATCGATACAA
Found at i:362175 original size:13 final size:13
Alignment explanation
Indices: 362157--362182 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
362147 CATTTTTCTG
362157 TGTATCGATACAT
1 TGTATCGATACAT
362170 TGTATCGATACAT
1 TGTATCGATACAT
362183 GGATCTTTGT
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:362179 original size:33 final size:33
Alignment explanation
Indices: 362137--362203 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
362127 GCCAAGGAAA
***
362137 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
362170 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
362203 T
1 T
362204 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:364652 original size:51 final size:49
Alignment explanation
Indices: 364534--364665 Score: 149
Period size: 50 Copynumber: 2.6 Consensus size: 49
364524 GTTGAGTTTC
* * *
364534 TCAATTCTCCACAATCGGGGATATTCCAACTCCGATTTTATTTTCAAAACA
1 TCAATT-TTCACAATC-GGGATACTCCAACTCCGATTTTATTTCCAAAACA
* *
364585 TTAATTTTCTATAATCGGGATACTCCAACTCCGATTTTATTTCCAAAA-A
1 TCAATTTTC-ACAATCGGGATACTCCAACTCCGATTTTATTTCCAAAACA
364634 TACCAATTTTTCACAATCGAGGATACTCCAAC
1 T--CAA-TTTTCACAATCG-GGATACTCCAAC
364666 CTCGTTATTT
Statistics
Matches: 69, Mismatches: 7, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
49 2 0.03
50 32 0.46
51 18 0.26
52 17 0.25
ACGTcount: A:0.33, C:0.24, G:0.09, T:0.34
Consensus pattern (49 bp):
TCAATTTTCACAATCGGGATACTCCAACTCCGATTTTATTTCCAAAACA
Found at i:364688 original size:28 final size:28
Alignment explanation
Indices: 364656--364725 Score: 90
Period size: 28 Copynumber: 2.5 Consensus size: 28
364646 ACAATCGAGG
*
364656 ATACTCCAACCTCGTTA-TTTC-ATTGGGA
1 ATACTCCAACCCCGTTACTTTCGA--GGGA
*
364684 ATACTCCAACCCCGTTACTTTCGAGGGG
1 ATACTCCAACCCCGTTACTTTCGAGGGA
364712 ATACTCCAACCCCG
1 ATACTCCAACCCCG
364726 GCTTTATTCC
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
28 33 0.87
29 4 0.11
30 1 0.03
ACGTcount: A:0.24, C:0.33, G:0.16, T:0.27
Consensus pattern (28 bp):
ATACTCCAACCCCGTTACTTTCGAGGGA
Found at i:375053 original size:46 final size:46
Alignment explanation
Indices: 374986--375075 Score: 180
Period size: 46 Copynumber: 2.0 Consensus size: 46
374976 GATATATTCA
374986 TTATTCTAGAATAAATTGGTTATGGGTTTTGGTACGACCTAACTTC
1 TTATTCTAGAATAAATTGGTTATGGGTTTTGGTACGACCTAACTTC
375032 TTATTCTAGAATAAATTGGTTATGGGTTTTGGTACGACCTAACT
1 TTATTCTAGAATAAATTGGTTATGGGTTTTGGTACGACCTAACT
375076 CCCTACCCTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.27, C:0.12, G:0.20, T:0.41
Consensus pattern (46 bp):
TTATTCTAGAATAAATTGGTTATGGGTTTTGGTACGACCTAACTTC
Found at i:376361 original size:13 final size:13
Alignment explanation
Indices: 376345--376372 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
376335 GCTAATACAT
376345 TTTGTTTTGAATA
1 TTTGTTTTGAATA
376358 TTTGTTTTGAATA
1 TTTGTTTTGAATA
376371 TT
1 TT
376373 CTTTTCTCCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.21, C:0.00, G:0.14, T:0.64
Consensus pattern (13 bp):
TTTGTTTTGAATA
Found at i:389775 original size:21 final size:20
Alignment explanation
Indices: 389751--389824 Score: 60
Period size: 21 Copynumber: 3.6 Consensus size: 20
389741 TTGTACAATT
389751 TGTATCAATACAATAAT-TGAA
1 TGTATCAATAC-AT-ATGTGAA
*
389772 TGTATCGATACATATGTGAA
1 TGTATCAATACATATGTGAA
* * * *
389792 TGTAACGATACATGTTTGAAA
1 TGTATCAATACATATGTG-AA
*
389813 TGTATCGATACA
1 TGTATCAATACA
389825 GGACCATGTC
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
19 2 0.04
20 21 0.46
21 23 0.50
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.34
Consensus pattern (20 bp):
TGTATCAATACATATGTGAA
Found at i:389793 original size:20 final size:20
Alignment explanation
Indices: 389768--389824 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 20
389758 ATACAATAAT
389768 TGAATGTATCGATACATATG
1 TGAATGTATCGATACATATG
* * *
389788 TGAATGTAACGATACATGTT
1 TGAATGTATCGATACATATG
389808 TGAAATGTATCGATACA
1 TG-AATGTATCGATACA
389825 GGACCATGTC
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 19 0.59
21 13 0.41
ACGTcount: A:0.37, C:0.11, G:0.19, T:0.33
Consensus pattern (20 bp):
TGAATGTATCGATACATATG
Found at i:392381 original size:32 final size:32
Alignment explanation
Indices: 392314--392414 Score: 139
Period size: 32 Copynumber: 3.1 Consensus size: 32
392304 TTCAACGATT
* *
392314 TGTATCGATACATAAAGTGTTATATCGATACAA
1 TGTATCGATACAT-AAGTGTTGTATTGATACAA
*
392347 TGTATCGATACATAAGTGTTGTATTGATAGAA
1 TGTATCGATACATAAGTGTTGTATTGATACAA
* * *
392379 TGTATTGATACATAAGTTTTGTGTTGATACAA
1 TGTATCGATACATAAGTGTTGTATTGATACAA
392411 TGTA
1 TGTA
392415 AGCTACTGCC
Statistics
Matches: 61, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
32 48 0.79
33 13 0.21
ACGTcount: A:0.35, C:0.08, G:0.19, T:0.39
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATTGATACAA
Found at i:392470 original size:13 final size:13
Alignment explanation
Indices: 392452--392476 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
392442 ATTACTCAAA
392452 TGTATCGATACAT
1 TGTATCGATACAT
392465 TGTATCGATACA
1 TGTATCGATACA
392477 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:399445 original size:13 final size:13
Alignment explanation
Indices: 399427--399451 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
399417 TACAAAGATC
399427 AATGTATCGATAT
1 AATGTATCGATAT
399440 AATGTATCGATA
1 AATGTATCGATA
399452 CATTCCCTTG
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:0.40, C:0.08, G:0.16, T:0.36
Consensus pattern (13 bp):
AATGTATCGATAT
Found at i:399495 original size:13 final size:13
Alignment explanation
Indices: 399477--399528 Score: 50
Period size: 13 Copynumber: 3.5 Consensus size: 13
399467 AGCTTCATAG
399477 CGATACATTGTAT
1 CGATACATTGTAT
399490 CGATACAACACTTATGTAT
1 CGAT---ACA-TT--GTAT
399509 CGATACATTGTAT
1 CGATACATTGTAT
399522 CGATACA
1 CGATACA
399529 ACTCTTATGT
Statistics
Matches: 33, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
13 15 0.45
15 2 0.06
16 6 0.18
17 2 0.06
19 8 0.24
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.33
Consensus pattern (13 bp):
CGATACATTGTAT
Found at i:399509 original size:19 final size:19
Alignment explanation
Indices: 399485--399547 Score: 75
Period size: 19 Copynumber: 3.6 Consensus size: 19
399475 AGCGATACAT
399485 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
399504 TGTATCGAT---ACA--T-
1 TGTATCGATACAACACTTA
*
399517 TGTATCGATACAACTCTTA
1 TGTATCGATACAACACTTA
399536 TGTATCGATACA
1 TGTATCGATACA
399548 GTTACTTGTT
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
13 9 0.24
14 1 0.03
16 5 0.14
18 1 0.03
19 21 0.57
ACGTcount: A:0.33, C:0.19, G:0.13, T:0.35
Consensus pattern (19 bp):
TGTATCGATACAACACTTA
Found at i:399518 original size:32 final size:32
Alignment explanation
Indices: 399477--399547 Score: 133
Period size: 32 Copynumber: 2.2 Consensus size: 32
399467 AGCTTCATAG
399477 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
*
399509 CGATACATTGTATCGATACAACTCTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
399541 CGATACA
1 CGATACA
399548 GTTACTTGTT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.34, C:0.20, G:0.13, T:0.34
Consensus pattern (32 bp):
CGATACATTGTATCGATACAACACTTATGTAT
Found at i:400436 original size:49 final size:49
Alignment explanation
Indices: 400330--400787 Score: 422
Period size: 49 Copynumber: 9.6 Consensus size: 49
400320 TGTACTAAGA
* * * * * *
400330 CAAGGCCAGCGACATTGGGCTTAGGAATGTTAAAGATGCCAATATGCTGATG
1 CAAGGCCAGCGATATTGGACTTA--AA-GATGAAGGTGCCAATATGCTGATT
* * * * *
400382 CAAGGCCAACGATATTGGAATTAAAGGTGAAGGTGCCAATGTGTTGATT
1 CAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATATGCTGATT
** * **
400431 CAAGGCTGGCGATATTAGTTTTAAAGATGAAGGTGCCAATATGCTGATT
1 CAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATATGCTGATT
* * * *
400480 TAAGGCCAACGATATTGGGC-T-----T--A--TGCCAATGTGCTGATT
1 CAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATATGCTGATT
* * * * *
400519 CAAGGCTAGCGACATTGGTCTTAAAAAT-AAGGTGCTAATATGCTGATT
1 CAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATATGCTGATT
* * * *
400567 CAAGGCCAACGATATTGGACTT--AGAAGAAGGTGCTAATGTGCTGATT
1 CAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATATGCTGATT
* * **
400614 CAAGGCTAGCGACATTGGTTTTAAAGATGAAGGTGCCAATATGCTGATT
1 CAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATATGCTGATT
* * *
400663 CAAGGCCAGCGATATTGGACTTAAGGATGAAAGTGCCAATGTGCTGATT
1 CAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATATGCTGATT
* * * *
400712 CAATGCCAGCGACATTGGTCTTAAAAAT-AAGGTGCCAATATGCTGATT
1 CAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATATGCTGATT
400760 CAAGGCCAGCGATATTGGACTTAGAAGA
1 CAAGGCCAGCGATATTGGACTTA-AAGA
400788 AGATGCCACC
Statistics
Matches: 326, Mismatches: 67, Indels: 29
0.77 0.16 0.07
Matches are distributed among these distances:
39 30 0.09
40 1 0.00
41 1 0.00
43 1 0.00
45 1 0.00
46 3 0.01
47 36 0.11
48 71 0.22
49 161 0.49
50 2 0.01
52 19 0.06
ACGTcount: A:0.31, C:0.16, G:0.26, T:0.27
Consensus pattern (49 bp):
CAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATATGCTGATT
Found at i:400536 original size:39 final size:39
Alignment explanation
Indices: 400464--400541 Score: 102
Period size: 39 Copynumber: 2.0 Consensus size: 39
400454 AAGATGAAGG
* *
400464 TGCCAATATGCTGATTTAAGGCCAACGATATTGGGCTTA
1 TGCCAATATGCTGATTCAAGGCCAACGACATTGGGCTTA
* * * *
400503 TGCCAATGTGCTGATTCAAGGCTAGCGACATTGGTCTTA
1 TGCCAATATGCTGATTCAAGGCCAACGACATTGGGCTTA
400542 AAAATAAGGT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (39 bp):
TGCCAATATGCTGATTCAAGGCCAACGACATTGGGCTTA
Found at i:400871 original size:29 final size:29
Alignment explanation
Indices: 400833--401026 Score: 225
Period size: 29 Copynumber: 6.7 Consensus size: 29
400823 TACCACTAAC
400833 TTGTGGGCTTTGAAAAAGGTGCCA-TAGAT
1 TTGTGGGCTTTGAAAAAGGTGCCACT-GAT
* ** *
400862 TTGTGAGCTTTGAAATGGGTGCCATTGA-
1 TTGTGGGCTTTGAAAAAGGTGCCACTGAT
* * * *
400890 CTATGGGCTTCG-AAAAGGATGCCACTGAC
1 TTGTGGGCTTTGAAAAAGG-TGCCACTGAT
400919 TTGTGGGCTTTG-AAAAGGATGCCACTGAT
1 TTGTGGGCTTTGAAAAAGG-TGCCACTGAT
* * *
400948 TTGTGGGCTTCGAAAAGGGTGCCGCTGAT
1 TTGTGGGCTTTGAAAAAGGTGCCACTGAT
*
400977 TTGTGGGCTTTGAAAAGGGTGCCACTGAT
1 TTGTGGGCTTTGAAAAAGGTGCCACTGAT
401006 TTGTGGGCTTTGAAAAAGGTG
1 TTGTGGGCTTTGAAAAAGGTG
401027 AGGAATGTCT
Statistics
Matches: 141, Mismatches: 20, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
27 4 0.03
28 16 0.11
29 115 0.82
30 6 0.04
ACGTcount: A:0.23, C:0.14, G:0.33, T:0.30
Consensus pattern (29 bp):
TTGTGGGCTTTGAAAAAGGTGCCACTGAT
Found at i:400968 original size:86 final size:86
Alignment explanation
Indices: 400825--401026 Score: 255
Period size: 86 Copynumber: 2.3 Consensus size: 86
400815 TGAAAGGTTA
* * * *
400825 CCACTAACTTGTGGGCTTTGAAAAAGGTGCCATAGATTTGTGAGCTTTGAAATGGGTGCCATTGA
1 CCACTGACTTGTGGGCTTTG-AAAAGGTGCCATAGATTTGTGAGCTTCGAAAAGGGTGCCACTGA
400890 -CTATGGGCTTCGAAAAGGATG
65 TCTATGGGCTTCGAAAAGGATG
* *
400911 CCACTGACTTGTGGGCTTTGAAAAGGATGCCACT-GATTTGTGGGCTTCGAAAAGGGTGCCGCTG
1 CCACTGACTTGTGGGCTTTGAAAAGG-TGCCA-TAGATTTGTGAGCTTCGAAAAGGGTGCCACTG
* * * *
400975 ATTTGTGGGCTTTGAAAAGGGTG
64 ATCTATGGGCTTCGAAAAGGATG
*
400998 CCACTGATTTGTGGGCTTTGAAAAAGGTG
1 CCACTGACTTGTGGGCTTTG-AAAAGGTG
401027 AGGAATGTCT
Statistics
Matches: 101, Mismatches: 11, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
85 6 0.06
86 50 0.50
87 39 0.39
88 6 0.06
ACGTcount: A:0.24, C:0.15, G:0.32, T:0.29
Consensus pattern (86 bp):
CCACTGACTTGTGGGCTTTGAAAAGGTGCCATAGATTTGTGAGCTTCGAAAAGGGTGCCACTGAT
CTATGGGCTTCGAAAAGGATG
Found at i:409079 original size:52 final size:52
Alignment explanation
Indices: 408882--409062 Score: 308
Period size: 52 Copynumber: 3.5 Consensus size: 52
408872 CGAAATATGA
* * * *
408882 AAATTTGCCTGCATGTATTGATACATTTCATAGTATATCGATACATATAGGC
1 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTAGGC
408934 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTAGGC
1 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTAGGC
*
408986 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTAGGC
*
409038 AAACTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
409063 AAGATCAGTG
Statistics
Matches: 123, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 123 1.00
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTAGGC
Found at i:409174 original size:32 final size:33
Alignment explanation
Indices: 409133--409201 Score: 113
Period size: 32 Copynumber: 2.1 Consensus size: 33
409123 GGCAGTAGCT
*
409133 TACATTGTATCGATACAAAAC-TTATGTATTGA
1 TACATTGTATCGATACAAAACTTTATGTATCGA
*
409165 TACATTGTATCGATACAACACTTTATGTATCGA
1 TACATTGTATCGATACAAAACTTTATGTATCGA
409198 TACA
1 TACA
409202 AATCGTTGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
32 20 0.59
33 14 0.41
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.36
Consensus pattern (33 bp):
TACATTGTATCGATACAAAACTTTATGTATCGA
Found at i:411281 original size:13 final size:13
Alignment explanation
Indices: 411263--411319 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
411253 CATAAAGTGT
411263 TGTATCGATACAA
1 TGTATCGATACAA
411276 TGTATCGATACATAA
1 TGTATCGATAC--AA
411291 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
411308 TGTATCGATACA
1 TGTATCGATACA
411320 TAAGTGTTGT
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:411298 original size:32 final size:32
Alignment explanation
Indices: 411243--411373 Score: 226
Period size: 32 Copynumber: 4.1 Consensus size: 32
411233 TTCAACGATT
411243 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACAT-AAGTGTTGTATCGATACAA
411276 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
* *
411308 TGTATCGATACATAAGTGTTGTCTCGATACAT
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
411340 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
411372 TG
1 TG
411374 GAAGCTACTG
Statistics
Matches: 93, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
32 80 0.86
33 13 0.14
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.36
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:411300 original size:19 final size:18
Alignment explanation
Indices: 411241--411370 Score: 101
Period size: 19 Copynumber: 7.8 Consensus size: 18
411231 ATTTCAACGA
411241 TTTGTATCGATACATAAAG
1 TTTGTATCGATACAT-AAG
411260 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
411276 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
411292 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
411308 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
*
411324 TGTTGTCTCGATAC---A-
1 T-TTGTATCGATACATAAG
411339 -TTGTATCGATACATAAG
1 TTTGTATCGATACATAAG
411356 TTTTGTATCGATACA
1 -TTTGTATCGATACA
411371 ATGGAAGCTA
Statistics
Matches: 90, Mismatches: 2, Indels: 38
0.69 0.02 0.29
Matches are distributed among these distances:
13 33 0.37
15 4 0.04
16 2 0.02
17 4 0.04
19 35 0.39
20 12 0.13
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.37
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:411431 original size:13 final size:13
Alignment explanation
Indices: 411413--411437 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
411403 ATTACTCAAA
411413 TGTATCGATACAT
1 TGTATCGATACAT
411426 TGTATCGATACA
1 TGTATCGATACA
411438 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:411483 original size:52 final size:52
Alignment explanation
Indices: 411446--411572 Score: 200
Period size: 52 Copynumber: 2.4 Consensus size: 52
411436 CACTGATCTT
* *
411446 TGTATCAATACATGCAGGCAAATTTTCCTAGATGTATCGATACACTATAAAA
1 TGTATCAATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
* *
411498 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCAATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
* *
411550 TGTATCGATACATACAGGCAAAT
1 TGTATCAATACATGCAGGCAAAT
411573 ATTCATATTT
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 70 1.00
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.28
Consensus pattern (52 bp):
TGTATCAATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:423673 original size:20 final size:20
Alignment explanation
Indices: 423648--423701 Score: 108
Period size: 20 Copynumber: 2.7 Consensus size: 20
423638 ATTTGCTTGC
423648 ATGTATCGATACATTGCATA
1 ATGTATCGATACATTGCATA
423668 ATGTATCGATACATTGCATA
1 ATGTATCGATACATTGCATA
423688 ATGTATCGATACAT
1 ATGTATCGATACAT
423702 CTGGGCAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (20 bp):
ATGTATCGATACATTGCATA
Found at i:423756 original size:13 final size:13
Alignment explanation
Indices: 423738--423765 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
423728 AAACAAAGAT
423738 CAATGTATCGATA
1 CAATGTATCGATA
423751 CAATGTATCGATA
1 CAATGTATCGATA
423764 CA
1 CA
423766 TTTGAGTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:423852 original size:32 final size:32
Alignment explanation
Indices: 423810--423880 Score: 115
Period size: 32 Copynumber: 2.2 Consensus size: 32
423800 AGCTTCGTAG
423810 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
* * *
423842 CGATATATTGTATCGATATAACCCTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
423874 CGATACA
1 CGATACA
423881 GTTACTTGTT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.35
Consensus pattern (32 bp):
CGATACATTGTATCGATACAACACTTATGTAT
Found at i:423855 original size:13 final size:13
Alignment explanation
Indices: 423837--423861 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
423827 ACAACACTTA
423837 TGTATCGATATAT
1 TGTATCGATATAT
423850 TGTATCGATATA
1 TGTATCGATATA
423862 ACCCTTATGT
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:0.08, G:0.16, T:0.44
Consensus pattern (13 bp):
TGTATCGATATAT
Found at i:423874 original size:19 final size:18
Alignment explanation
Indices: 423818--423878 Score: 60
Period size: 19 Copynumber: 3.6 Consensus size: 18
423808 AGCGATACAT
*
423818 TGTATCGATACAACACTTA
1 TGTATCGATATAAC-CTTA
423837 TGTATCGATAT-A---T-
1 TGTATCGATATAACCTTA
423850 TGTATCGATATAACCCTTA
1 TGTATCGATATAA-CCTTA
423869 TGTATCGATA
1 TGTATCGATA
423879 CAGTTACTTG
Statistics
Matches: 35, Mismatches: 1, Indels: 12
0.73 0.02 0.25
Matches are distributed among these distances:
13 11 0.31
14 2 0.06
18 2 0.06
19 20 0.57
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.38
Consensus pattern (18 bp):
TGTATCGATATAACCTTA
Found at i:424640 original size:20 final size:20
Alignment explanation
Indices: 424615--424729 Score: 78
Period size: 20 Copynumber: 5.6 Consensus size: 20
424605 TACCTGCATA
424615 TATCGATACATTAAAGAATG
1 TATCGATACATTAAAGAATG
*
424635 TATCGATACA--AACCCAAAATG
1 TATCGATACATTAA---AGAATG
* * *
424656 TATCAATACAAT-GAGAAATG
1 TATCGATACATTAAAG-AATG
*
424676 TATCGATACAATTATAAGCATG
1 TATCGATAC-ATTA-AAGAATG
424698 TATCGATACACTT--AGTAATG
1 TATCGATACA-TTAAAG-AATG
424718 TATCGATACATT
1 TATCGATACATT
424730 TCCTTGGCAG
Statistics
Matches: 75, Mismatches: 9, Indels: 23
0.70 0.08 0.21
Matches are distributed among these distances:
18 2 0.03
19 5 0.07
20 35 0.47
21 17 0.23
22 14 0.19
23 2 0.03
ACGTcount: A:0.43, C:0.15, G:0.13, T:0.30
Consensus pattern (20 bp):
TATCGATACATTAAAGAATG
Found at i:427303 original size:21 final size:21
Alignment explanation
Indices: 427262--427305 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
427252 CTCCCCTTTA
* *
427262 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
427283 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
427304 TC
1 TC
427306 ATATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:429126 original size:13 final size:13
Alignment explanation
Indices: 429108--429133 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
429098 ATAATCACCC
429108 TGTATCGATACAA
1 TGTATCGATACAA
429121 TGTATCGATACAA
1 TGTATCGATACAA
429134 GGAAAAATGT
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:431228 original size:15 final size:15
Alignment explanation
Indices: 431208--431238 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
431198 ATTTCGTTTG
*
431208 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
431223 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
431238 G
1 G
431239 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:433062 original size:21 final size:21
Alignment explanation
Indices: 433033--433077 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
433023 AAGTTTTCAT
*
433033 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
433053 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
433075 TTT
1 TTT
433078 CATCTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:435317 original size:13 final size:13
Alignment explanation
Indices: 435299--435324 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
435289 CAATTATTTG
435299 TGTATCGATACAT
1 TGTATCGATACAT
435312 TGTATCGATACAT
1 TGTATCGATACAT
435325 ACTTGGTGTA
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:435339 original size:32 final size:33
Alignment explanation
Indices: 435279--435342 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
435269 TACAAGCTAA
*
435279 TGTATCGATACAATTATTTGTGTATCGATACAT
1 TGTATCGATACAATTATTGGTGTATCGATACAT
435312 TGTATCGATAC-A-TACTTGGTGTATCGATACA
1 TGTATCGATACAATTA-TTGGTGTATCGATACA
435343 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 2 0.07
32 16 0.55
33 11 0.38
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.39
Consensus pattern (33 bp):
TGTATCGATACAATTATTGGTGTATCGATACAT
Found at i:439120 original size:104 final size:105
Alignment explanation
Indices: 438992--439255 Score: 257
Period size: 104 Copynumber: 2.5 Consensus size: 105
438982 TATGCGAAGA
* * * * * *
438992 ATGCCAATGTGCTAATTCACGGCCAGCGACATTAGACTTGAAGATGAAAAGAATGCCAATATACT
1 ATGCAAATATGCTGATTCAAGGCCAGCGACATTAGACTTAAAGATGAAAAGAATGCCAATAAACT
* * ****
439057 AATTCAAGGTTAGCGACATTAGGCTT-AGGAATGTTAAAG
66 AATTCAAGGCTAGCGACATTAGGCTTAAGAAAAAAAAAAG
* * * * *
439096 ATGCAAATATGTTGATTCAAGGCCAACGATA-TCGAACTTAAAGATGACAAAG-GTGCCAATAAA
1 ATGCAAATATGCTGATTCAAGGCCAGCGACATTAG-ACTTAAAGATGA-AAAGAATGCCAATAAA
* *
439159 CTGATTCAAGGCTAGCGATATTAGGCTTAAGAAAAAAAAAAG
64 CTAATTCAAGGCTAGCGACATTAGGCTTAAGAAAAAAAAAAG
* * * * *
439201 GTGCTAATGTGCTGACTT-AAGGCCAGCGACATTGGACTTAAAGATGAGAAGAATG
1 ATGCAAATATGCTGA-TTCAAGGCCAGCGACATTAGACTTAAAGATGAAAAGAATG
439256 ATAAAGGTGC
Statistics
Matches: 126, Mismatches: 28, Indels: 11
0.76 0.17 0.07
Matches are distributed among these distances:
103 2 0.02
104 72 0.57
105 48 0.38
106 4 0.03
ACGTcount: A:0.39, C:0.15, G:0.23, T:0.23
Consensus pattern (105 bp):
ATGCAAATATGCTGATTCAAGGCCAGCGACATTAGACTTAAAGATGAAAAGAATGCCAATAAACT
AATTCAAGGCTAGCGACATTAGGCTTAAGAAAAAAAAAAG
Found at i:439188 original size:52 final size:51
Alignment explanation
Indices: 438932--439735 Score: 197
Period size: 52 Copynumber: 15.6 Consensus size: 51
438922 GATGGGAAGA
** * * * * *
438932 ATGATAAAGATGCCAATATGTTGATTTAAGGCCAGCGA-TTTGGGCTTAAAT
1 ATGA-AAAGATGCCAATATACTGATTCAAGGCCAGCGACATTAGACTTAAAG
** * * * * *
438983 ATGCGAAGAATGCCAATGTGCTAATTCACGGCCAGCGACATTAGACTTGAAG
1 ATGAAAAG-ATGCCAATATACTGATTCAAGGCCAGCGACATTAGACTTAAAG
* ** * *
439035 ATGAAAAGAATGCCAATATACTAATTCAAGGTTAGCGACATTAGGCTT-AGG
1 ATGAAAAG-ATGCCAATATACTGATTCAAGGCCAGCGACATTAGACTTAAAG
* * ** * * *
439086 AATGTTAAAGATGCAAATATGTTGATTCAAGGCCAACGATA-TCGAACTTAAAG
1 -ATG-AAAAGATGCCAATATACTGATTCAAGGCCAGCGACATTAG-ACTTAAAG
* * * * * *
439139 ATGACAAAGGTGCCAATAAACTGATTCAAGGCTAGCGATATTAGGCTTAAGAAA
1 ATGA-AAAGATGCCAATATACTGATTCAAGGCCAGCGACATTAGACTT-A-AAG
** * * * * *
439193 AAAAAAAGGTGCTAATGTGCTGACTT-AAGGCCAGCGACATTGGACTTAAAG
1 ATGAAAAGATGCCAATATACTGA-TTCAAGGCCAGCGACATTAGACTTAAAG
* * * * * * *
439244 ATGAGAAGAATGATAAAGGTGCTAATATGCTAATTCAAGGTCAGCGATATTGGGCTTAAAG
1 AT--GAA-AA-G----A--TGCCAATATACTGATTCAAGGCCAGCGACATTAGACTTAAAG
* * * * * *
439305 ATGACAAGGGTGCC---A-A--G-GT---GGCCAACGACATTAGACTTGAGG
1 ATGA-AAAGATGCCAATATACTGATTCAAGGCCAGCGACATTAGACTTAAAG
* * * ** * * * *
439347 ATGAGAGGAATGCCAATGTGTTGATTCAAGGCTAGCGACATTGGGCTT-AGG
1 ATGAAAAG-ATGCCAATATACTGATTCAAGGCCAGCGACATTAGACTTAAAG
* * * *
439398 AATGATAAAGATGCCAATATGCTTATTCAAGGCCAGCGATATCAGACTT-AAG
1 -ATGA-AAAGATGCCAATATACTGATTCAAGGCCAGCGACATTAGACTTAAAG
* * * * * *
439450 AAAGAAATAGGTGCCAATGTACTGATTGAAGGCCAACGACCTTAGACTTAAAG
1 -ATGAAA-AGATGCCAATATACTGATTCAAGGCCAGCGACATTAGACTTAAAG
* * * * * *
439503 ATGGTAAAG--GCATAATTATGCTGATTCAAGGCCAACGATATTGGACTTAAAG
1 AT-GAAAAGATGC-CAA-TATACTGATTCAAGGCCAGCGACATTAGACTTAAAG
* ** * * *
439555 ATGGTAAAG--GCATCAATATGTTGATTCAAGGCCAGTGATATTAAACTT-AAG
1 AT-GAAAAGATGC--CAATATACTGATTCAAGGCCAGCGACATTAGACTTAAAG
* * * * * *
439606 --G--AAG-TGCCAATGTGCAGATTCAAGCCCAGTGACATTGGACTTAAAG
1 ATGAAAAGATGCCAATATACTGATTCAAGGCCAGCGACATTAGACTTAAAG
* * * ** * * * *
439652 ATGACCAAGGTGTCAATATGTTGATTCAAGGTCAGCAATATTGGACTT-AAG
1 ATGA-AAAGATGCCAATATACTGATTCAAGGCCAGCGACATTAGACTTAAAG
* * *
439703 ATAAAAATG-TGTCAATGTACTGATTCAAGGCCA
1 ATGAAAA-GATGCCAATATACTGATTCAAGGCCA
439736 ATGATATTGG
Statistics
Matches: 558, Mismatches: 144, Indels: 103
0.69 0.18 0.13
Matches are distributed among these distances:
41 3 0.01
42 24 0.04
45 29 0.05
46 6 0.01
47 2 0.00
48 3 0.01
49 2 0.00
50 27 0.05
51 54 0.10
52 303 0.54
53 53 0.09
54 8 0.01
55 1 0.00
58 1 0.00
59 3 0.01
60 3 0.01
61 36 0.06
ACGTcount: A:0.36, C:0.15, G:0.24, T:0.25
Consensus pattern (51 bp):
ATGAAAAGATGCCAATATACTGATTCAAGGCCAGCGACATTAGACTTAAAG
Found at i:439845 original size:33 final size:33
Alignment explanation
Indices: 439759--439879 Score: 120
Period size: 33 Copynumber: 3.7 Consensus size: 33
439749 TAGAAGGAGA
*
439759 TGCCACCAACTTGTATGGGCTTTTG-AGAGGGT
1 TGCCACCAACTTGTGTGGGCTTTTGAAGAGGGT
* ** *
439791 TGCCACCAAATTGTGCAGGCTTTTGAAGGGGGT
1 TGCCACCAACTTGTGTGGGCTTTTGAAGAGGGT
* * *
439824 TGCCATCGACTTGTGTGGGCTTTAGAAGA-GGT
1 TGCCACCAACTTGTGTGGGCTTTTGAAGAGGGT
* * *
439856 TGGCACCAAGCTTATGTAGGCTTT
1 TGCCACCAA-CTTGTGTGGGCTTT
439880 AGAGGGGATG
Statistics
Matches: 70, Mismatches: 17, Indels: 3
0.78 0.19 0.03
Matches are distributed among these distances:
32 30 0.43
33 40 0.57
ACGTcount: A:0.20, C:0.18, G:0.31, T:0.31
Consensus pattern (33 bp):
TGCCACCAACTTGTGTGGGCTTTTGAAGAGGGT
Found at i:439886 original size:65 final size:64
Alignment explanation
Indices: 439748--439902 Score: 161
Period size: 65 Copynumber: 2.4 Consensus size: 64
439738 GATATTGGGC
* * * * * *
439748 TTAGAAGGAGATGCCACCAACTTGTATGGGCTTTTGAGAGGGTTGCCACCAAATTGTGCAGGCT
1 TTAGAAGGGGATGCCATCGACTTGTGTGGGCTTTAGAGAGGGTTGCCACCAAATTATGCAGGCT
* * * * *
439812 TTTGAAGGGGGTTGCCATCGACTTGTGTGGGCTTTAGA-AGAGGTTGGCACCAAGCTTATGTAGG
1 TTAGAA-GGGGATGCCATCGACTTGTGTGGGCTTTAGAGAG-GGTTGCCACCAA-ATTATGCAGG
439876 CT
63 CT
*
439878 TTAG-AGGGGATGCCATTGACTTGTG
1 TTAGAAGGGGATGCCATCGACTTGTG
439903 GGCTTTGAAA
Statistics
Matches: 74, Mismatches: 14, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
64 25 0.34
65 37 0.50
66 12 0.16
ACGTcount: A:0.22, C:0.16, G:0.33, T:0.29
Consensus pattern (64 bp):
TTAGAAGGGGATGCCATCGACTTGTGTGGGCTTTAGAGAGGGTTGCCACCAAATTATGCAGGCT
Found at i:439953 original size:27 final size:27
Alignment explanation
Indices: 439915--440983 Score: 361
Period size: 27 Copynumber: 36.2 Consensus size: 27
439905 CTTTGAAAAG
*
439915 AAAAAGGTGCCACGGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
* *
439942 AAAAGGGTGCCACAGAGTTATGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
* *
439969 AAAAAGAAAAAAGG-GCCACGGAGGTGTGGACCT
1 -AAAAG------GGTGCCACGGAGTTGTGGACTT
** *
440002 AAAAGGGTGCCACAAAGTTATGGACTTT
1 AAAAGGGTGCCACGGAGTTGTGGAC-TT
* *
440030 AAGAGAAAAAGGTGCCACGAAGTTGTGGACTTT
1 -----AAAAGGGTGCCACGGAGTTGTGGAC-TT
** *
440063 AAGAGAGAAAAATGCCATGGAGTTGTGGACTT
1 AA-A-AG---GGTGCCACGGAGTTGTGGACTT
* * *
440095 AAAAAGGTGCCAC-AAGGTTGTAGACTT
1 AAAAGGGTGCCACGGA-GTTGTGGACTT
* * ****
440122 AATAGAGTGCCATATTGTTGTGGACTTT
1 AAAAGGGTGCCACGGAGTTGTGGAC-TT
* *
440150 AAGAGAAAAAGGTGCCATGGAGTTGTGGACTT
1 -----AAAAGGGTGCCACGGAGTTGTGGACTT
*
440182 AAAAGGGTGCCACAGAGTTGTGGACATT
1 AAAAGGGTGCCACGGAGTTGTGGAC-TT
* **
440210 AAGAGAAAAAGGTGCCATAGAGTTGTGGACTT
1 -----AAAAGGGTGCCACGGAGTTGTGGACTT
* *
440242 AAAAGGGTGCCACGGAGTTGCGGCCCTTGAAT
1 AAAAGGGTGCCACGGAGTTGTGG-AC-T---T
* ** * *
440274 AGAAAAAGGTGCCATAGAGTTATAGACTT
1 --AAAAGGGTGCCACGGAGTTGTGGACTT
* **
440303 AAAAGGGTGTCACAAAGTTGT-GAGCTTTGT
1 AAAAGGGTGCCACGGAGTTGTGGA-C--T-T
* *
440333 AAAGAAAAAGGTACCACGGAGTTGTGGACTTT
1 ----AAAAGGGTGCCACGGAGTTGTGGAC-TT
* *
440365 GAGAGAAAAGGGTACCACGGAGTTGTTGACTT
1 -----AAAAGGGTGCCACGGAGTTGTGGACTT
* **
440397 AAAAGGGTGCCACAGAGTCATGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
* * * *
440424 AAAAGGAAAAAGGGGCCACGTAGTTGTCGACAT
1 AAAA-G-----GGTGCCACGGAGTTGTGGACTT
* * *
440457 AAAATGGTGCCATGGAGTTGTGGA--G
1 AAAAGGGTGCCACGGAGTTGTGGACTT
* * *
440482 AAAAAGGTGCCATGGATTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
* * *
440509 AAAAAGGTGTCACAGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
* * *
440536 AAAAGGATGCCATGGAGTTATGGACTTT
1 AAAAGGGTGCCACGGAGTTGTGGAC-TT
* *
440564 AAGAGAAAAAGGTGCCATGGAGTTGTGGACTT
1 -----AAAAGGGTGCCACGGAGTTGTGGACTT
* *
440596 AAAAGGGTGCCACAGAGTTGTAGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
* ** *
440623 AATAGGGTGCCACGTTGTTATGGACTTT
1 AAAAGGGTGCCACGGAGTTGTGGAC-TT
* *
440651 AAGAGAAAAAGGTGCCACGAAGTTGTGGACTT
1 -----AAAAGGGTGCCACGGAGTTGTGGACTT
* **
440683 AAAAGGATGCCATAGAGTTGTGGACATT
1 AAAAGGGTGCCACGGAGTTGTGGAC-TT
* * **
440711 AAGAGAAAAAGGTTCCATAGAGTTGTGGACTT
1 -----AAAAGGGTGCCACGGAGTTGTGGACTT
* *
440743 AAAATGGTGCCATGGA-TTGTGGACTTT
1 AAAAGGGTGCCACGGAGTTGTGGAC-TT
* * *
440770 AAGAGAAAAAAGGTGCCACGAAGTTATGGACTT
1 ------AAAAGGGTGCCACGGAGTTGTGGACTT
440803 AAAAGGGTGCCACGGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
** *
440830 AAAAGGGTGCCACAAAATTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
** *
440857 AAAAGGGTGCCATAGAGTTATGG-CTTTGT
1 AAAAGGGTGCCACGGAGTTGTGGAC--T-T
*
440886 AAAGAAAAAGGTGACCACGGAGTTGTGGACTTT
1 ----AAAAGGGTG-CCACGGAGTTGTGGAC-TT
* *
440919 AAGAGAAAAAGGTGCCACAGAGTTGTGGACTT
1 -----AAAAGGGTGCCACGGAGTTGTGGACTT
* *
440951 AAAAGGGTGCCACAGAGTTTTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
440978 AAAAGG
1 AAAAGG
440984 AAAAAGAGGC
Statistics
Matches: 797, Mismatches: 151, Indels: 188
0.70 0.13 0.17
Matches are distributed among these distances:
25 22 0.03
26 14 0.02
27 385 0.48
28 21 0.03
29 5 0.01
30 3 0.00
31 1 0.00
32 26 0.03
33 249 0.31
34 68 0.09
35 3 0.00
ACGTcount: A:0.34, C:0.13, G:0.30, T:0.23
Consensus pattern (27 bp):
AAAAGGGTGCCACGGAGTTGTGGACTT
Found at i:439987 original size:60 final size:60
Alignment explanation
Indices: 439910--440624 Score: 403
Period size: 60 Copynumber: 12.0 Consensus size: 60
439900 GTGGGCTTTG
*
439910 AAAAGAAAAAGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTATGGACTTA
1 AAAAGAAAAAGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTA
* * * * *
439970 AAAAGAAAAAAGG-GCCACGGAGGTGTGGACCTAAAAGGGTGCCACAAAGTTATGGACTTT
1 AAAAG-AAAAAGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTA
* * ** **
440030 AAGAGAAAAAGGTGCCACGAAGTTGTGGACTTTAAGAGAGAAAAATGCCATGGAGTTGTGGACTT
1 AAAAGAAAAAGGTGCCACGGAGTTGTGGAC-TTAA-A-AG---GGTGCCACAGAGTTGTGGACTT
440095 -
60 A
* * * * * ** *
440095 -----AAAAAGGTGCCAC-AAGGTTGTAGACTTAATAGAGTGCCATATTGTTGTGGACTTT
1 AAAAGAAAAAGGTGCCACGGA-GTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTA
* *
440150 AAGAGAAAAAGGTGCCATGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACATT-
1 AAAAGAAAAAGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGAC-TTA
* ** * * * *
440210 AAGAGAAAAAGGTGCCATAGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGCGGCCCTTG
1 AAAAGAAAAAGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGG-ACTTA
* ** * * * * *
440271 AATAGAAAAAGGTGCCATAGAGTTATAGACTTAAAAGGGTGTCACAAAGTTGT-GAGCTTTG
1 AAAAGAAAAAGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGA-C-TTA
* * * * *
440332 TAAAGAAAAAGGTACCACGGAGTTGTGGACTTTGAGAGAAAAGGGTACCACGGAGTTGTTGACTT
1 AAAAGAAAAAGGTGCCACGGAGTTGTGGAC-TT-----AAAAGGGTGCCACAGAGTTGTGGACTT
440397 -
60 A
* ** * *
440397 AAAAG-----GGTGCCACAGAGTCATGGACTTAAAAGGAAAAAGGGGCCAC-GTAGTTGTCGAC-
1 AAAAGAAAAAGGTGCCACGGAGTTGTGGACTTAAAA-G-----GGTGCCACAG-AGTTGTGGACT
440455 --
59 TA
* * * * * ** *
440455 ---ATAAAATGGTGCCATGGAGTTGTGGA--GAAAAAGGTGCCATGGATTTGTGGACTT-
1 AAAAGAAAAAGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTA
* * * ** * *
440509 -----AAAAAGGTGTCACAGAGTTGTGGACTTAAAAGGATGCCATGGAGTTATGGACTTT
1 AAAAGAAAAAGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTA
* * *
440564 AAGAGAAAAAGGTGCCATGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTAGACTTA
1 AAAAGAAAAAGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTA
440624 A
1 A
440625 TAGGGTGCCA
Statistics
Matches: 516, Mismatches: 88, Indels: 102
0.73 0.12 0.14
Matches are distributed among these distances:
52 34 0.07
53 1 0.00
54 45 0.09
55 2 0.00
57 2 0.00
58 4 0.01
59 16 0.03
60 279 0.54
61 86 0.17
62 3 0.01
63 2 0.00
65 4 0.01
66 18 0.03
67 18 0.03
68 2 0.00
ACGTcount: A:0.34, C:0.13, G:0.30, T:0.23
Consensus pattern (60 bp):
AAAAGAAAAAGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTA
Found at i:440079 original size:33 final size:33
Alignment explanation
Indices: 440009--440094 Score: 111
Period size: 33 Copynumber: 2.6 Consensus size: 33
439999 CCTAAAAGGG
* * *
440009 TGCCACAAAGTTATGGACTTTAAGAGAAAAAGG
1 TGCCACGAAGTTGTGGACTTTAAGAGAAAAAGA
440042 TGCCACGAAGTTGTGGACTTTAAGAGAGAAAA-A
1 TGCCACGAAGTTGTGGACTTTAAGAGA-AAAAGA
* *
440075 TGCCATGGAGTTGTGGACTT
1 TGCCACGAAGTTGTGGACTT
440095 AAAAAGGTGC
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
33 43 0.91
34 4 0.09
ACGTcount: A:0.35, C:0.13, G:0.28, T:0.24
Consensus pattern (33 bp):
TGCCACGAAGTTGTGGACTTTAAGAGAAAAAGA
Found at i:440217 original size:180 final size:180
Alignment explanation
Indices: 439915--440241 Score: 453
Period size: 180 Copynumber: 1.8 Consensus size: 180
439905 CTTTGAAAAG
* * *
439915 AAAAAGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTATGGACTTAAAAAGAAAAA
1 AAAAAGGTGCCACAGAGTTGTAGACTTAAAAGAGTGCCACAGAGTTATGGACTTAAAAAGAAAAA
*
439980 AGGGCCACGGAGGTGTGGACCTAAAAGGGTGCCACAAAGTTATGGACTTTAAGAGAAAAAGGTGC
66 AGGGCCACGGAGGTGTGGACCTAAAAGGGTGCCACAAAGTTATGGACATTAAGAGAAAAAGGTGC
440045 CACGA-AGTTGTGGACTTTAAGAGAGAAAAATGCCATGGAGTTGTGGACTT
131 CA-GAGAGTTGTGGACTTTAAGAGAGAAAAATGCCATGGAGTTGTGGACTT
* * ** * * *
440095 AAAAAGGTGCCACA-AGGTTGTAGACTTAATAGAGTGCCATATTGTTGTGGACTTTAAGAG-AAA
1 AAAAAGGTGCCACAGA-GTTGTAGACTTAAAAGAGTGCCACAGAGTTATGGACTTAAAAAGAAAA
* * * * *
440158 AAGGTGCCATGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACATTAAGAGAAAAAGGT
65 AAGG-GCCACGGAGGTGTGGACCTAAAAGGGTGCCACAAAGTTATGGACATTAAGAGAAAAAGGT
*
440223 GCCATAGAGTTGTGGACTT
129 GCCAGAGAGTTGTGGACTT
440242 AAAAGGGTGC
Statistics
Matches: 127, Mismatches: 17, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
179 9 0.07
180 118 0.93
ACGTcount: A:0.35, C:0.13, G:0.30, T:0.22
Consensus pattern (180 bp):
AAAAAGGTGCCACAGAGTTGTAGACTTAAAAGAGTGCCACAGAGTTATGGACTTAAAAAGAAAAA
AGGGCCACGGAGGTGTGGACCTAAAAGGGTGCCACAAAGTTATGGACATTAAGAGAAAAAGGTGC
CAGAGAGTTGTGGACTTTAAGAGAGAAAAATGCCATGGAGTTGTGGACTT
Found at i:440251 original size:87 final size:84
Alignment explanation
Indices: 440155--440983 Score: 372
Period size: 87 Copynumber: 9.4 Consensus size: 84
440145 ACTTTAAGAG
* ** *
440155 AAAAAGGTGCCATGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACATTAAGAGAAAAA
1 AAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGAC-TT-AGA-AAAAA
*
440220 GGTGCCATAGAGTTGTGGACTT
63 GGTGCCACAGAGTTGTGGACTT
* * * * ** * *
440242 AAAAGGGTGCCACGGAGTTGCGGCCCTTGAATAGAAAAAGGTGCCATAGAGTTATAGACTT---A
1 AAAAGGGTGCCACAGAGTTGTGG-AC-T---T--AAAAGGGTGCCACGGAGTTGTGGACTTAGAA
* * *
440304 AAAGGGTGTCACAAAGTTGT-GAGCTTTGT
59 AAAAGGTGCCACAGAGTTGTGGA-C--T-T
* * * * *
440333 AAAGAAAAAGGTACCACGGAGTTGTGGACTTTGAGAGAAAAGGGTACCACGGAGTTGTTGACTT-
1 ----AAAAGGGTGCCACAGAGTTGTGGAC-TT-----AAAAGGGTGCCACGGAGTTGTGGACTTA
* **
440397 --AAAAGGGTGCCACAGAGTCATGGACTT
56 GAAAAAAGGTGCCACAGAGTTGTGGACTT
* * * * *
440424 AAAAGGAAAAAGGGGCCAC-GTAGTTGTCGACATAAAATGGTGCCATGGAGTTGTGG----AG-A
1 AAAA-G-----GGTGCCACAG-AGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAGAA
** *
440483 AAAAGGTGCCATGGATTTGTGGACTT
59 AAAAGGTGCCACAGAGTTGTGGACTT
* * * * *
440509 AAAAAGGTGTCACAGAGTTGTGGACTTAAAAGGATGCCATGGAGTTATGGACTTTAAGAGAAAAA
1 AAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGAC-TT-AGA-AAAAA
**
440574 GGTGCCATGGAGTTGTGGACTT
63 GGTGCCACAGAGTTGTGGACTT
* * ** *
440596 AAAAGGGTGCCACAGAGTTGTAGACTTAATAGGGTGCCACGTTGTTATGGACTTTAAGAGAAAAA
1 AAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGAC-TT-AGA-AAAAA
440661 GGTGCCAC-GAAGTTGTGGACTT
63 GGTGCCACAG-AGTTGTGGACTT
* * * * **
440683 AAAAGGATGCCATAGAGTTGTGGACATTAAGAGAAAAAGGTTCCATAGAGTTGTGGACTT---AA
1 AAAAGGGTGCCACAGAGTTGTGGAC-TT-----AAAAGGGTGCCACGGAGTTGTGGACTTAGAAA
* **
440745 AATGGTGCCATGGA-TTGTGGACTTT
60 AAAGGTGCCACAGAGTTGTGGAC-TT
* *
440770 AAGAGAAAAAAGGTGCCAC-GAAGTTATGGACTTAAAAGGGTGCCACGGAGTTGTGGACTT---A
1 ------AAAAGGGTGCCACAG-AGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAGAA
* * *
440831 AAAGGGTGCCACAAAATTGTGGACTT
59 AAAAGGTGCCACAGAGTTGTGGACTT
* * *
440857 AAAAGGGTGCCATAGAGTTATGG-CTTTGTAAAGAAAAAGGTGACCACGGAGTTGTGGACTTTAA
1 AAAAGGGTGCCACAGAGTTGTGGAC--T-T----AAAAGGGTG-CCACGGAGTTGTGGAC-TT-A
440921 GAGAAAAAGGTGCCACAGAGTTGTGGACTT
56 GA-AAAAAGGTGCCACAGAGTTGTGGACTT
*
440951 AAAAGGGTGCCACAGAGTTTTGGACTTAAAAGG
1 AAAAGGGTGCCACAGAGTTGTGGACTTAAAAGG
440984 AAAAAGAGGC
Statistics
Matches: 579, Mismatches: 93, Indels: 139
0.71 0.11 0.17
Matches are distributed among these distances:
79 36 0.06
80 2 0.00
81 19 0.03
82 2 0.00
83 1 0.00
85 27 0.05
86 9 0.02
87 228 0.39
88 51 0.09
89 3 0.01
90 1 0.00
91 3 0.01
92 10 0.02
93 54 0.09
94 110 0.19
95 23 0.04
ACGTcount: A:0.33, C:0.12, G:0.31, T:0.24
Consensus pattern (84 bp):
AAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAGAAAAAAGGT
GCCACAGAGTTGTGGACTT
Found at i:440357 original size:34 final size:33
Alignment explanation
Indices: 440318--440396 Score: 106
Period size: 33 Copynumber: 2.4 Consensus size: 33
440308 GGTGTCACAA
440318 AGTTGT-GAGCTTTGTAAAGAAAAAGGTACCACGG
1 AGTTGTGGA-CTTTG-AAAGAAAAAGGTACCACGG
* *
440352 AGTTGTGGACTTTGAGAGAAAAGGGTACCACGG
1 AGTTGTGGACTTTGAAAGAAAAAGGTACCACGG
*
440385 AGTTGTTGACTT
1 AGTTGTGGACTT
440397 AAAAGGGTGC
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
33 28 0.68
34 11 0.27
35 2 0.05
ACGTcount: A:0.30, C:0.11, G:0.32, T:0.27
Consensus pattern (33 bp):
AGTTGTGGACTTTGAAAGAAAAAGGTACCACGG
Found at i:440512 original size:52 final size:53
Alignment explanation
Indices: 440429--440981 Score: 169
Period size: 60 Copynumber: 9.6 Consensus size: 53
440419 GACTTAAAAG
* * * * * * **
440429 GAAAAAGGGGCCACGTAGTTGTCGACATAAAATGGTGCCATGGAGTTGTGGA-
1 GAAAAAGGTGCCATGGAGTTGTGGACTTAAAAAGGTGCCACAGAGTTGTGGAC
* *
440481 GAAAAAGGTGCCATGGATTTGTGGACTTAAAAAGGTGTCACAGAGTTGTGGAC
1 GAAAAAGGTGCCATGGAGTTGTGGACTTAAAAAGGTGCCACAGAGTTGTGGAC
** * **
440534 TTAAAAGGATGCCATGGAGTTATGGACTTTAAGAGAAAAAGGTGCCATGGAGTTGTGGAC
1 GAAAAAGG-TGCCATGGAGTTGTGGAC-TT-----AAAAAGGTGCCACAGAGTTGTGGAC
* * ** * * * * *
440594 TTAAAAGGGTGCCACAGAGTTGTAGACTTAATAGGGTGCCAC-GTTGTTATGGAC
1 -GAAAAAGGTGCCATGGAGTTGTGGACTTAAAAAGGTGCCACAG-AGTTGTGGAC
* * *
440648 TTTAAGAGAAAAAGGTGCCACGAAGTTGTGGACTT-AAAAGGATGCCATAGAGTTGTGGAC
1 -------GAAAAAGGTGCCATGGAGTTGTGGACTTAAAAAGG-TGCCACAGAGTTGTGGAC
* * * **
440708 ATTAAGAGAAAAAGGTTCCATAGAGTTGTGGACTTAAAATGGTGCCATGGA-TTGTGGAC
1 -------GAAAAAGGTGCCATGGAGTTGTGGACTTAAAAAGGTGCCACAGAGTTGTGGAC
* * * * *
440767 TTTAAGAGAAAAAAGGTGCCACGAAGTTATGGACTTAAAAGGGTGCCACGGAGTTGTGGAC
1 -------G-AAAAAGGTGCCATGGAGTTGTGGACTTAAAAAGGTGCCACAGAGTTGTGGAC
* * *** * * * * *
440828 TTAAAAGGGTGCCACAAAATTGTGGACTTAAAAGGGTGCCATAGAGTTATGGCTTTGTAAA
1 -GAAAAAGGTGCCATGGAGTTGTGGACTTAAAAAGGTGCCACAGAG-T-T-G---TG-GAC
*
440889 GAAAAAGGTGACCACGGAGTTGTGGACTTTAAGAGAAAAAGGTGCCACAGAGTTGTGGAC
1 GAAAAAGGTG-CCATGGAGTTGTGGAC-TT-----AAAAAGGTGCCACAGAGTTGTGGAC
* * ** *
440949 TTAAAAGGGTGCCACAGAGTTTTGGACTTAAAA
1 -GAAAAAGGTGCCATGGAGTTGTGGACTTAAAA
440982 GGAAAAAGAG
Statistics
Matches: 388, Mismatches: 77, Indels: 70
0.73 0.14 0.13
Matches are distributed among these distances:
52 42 0.11
53 7 0.02
54 76 0.20
55 3 0.01
56 1 0.00
57 1 0.00
59 23 0.06
60 171 0.44
61 44 0.11
62 2 0.01
64 1 0.00
65 1 0.00
66 1 0.00
67 15 0.04
ACGTcount: A:0.33, C:0.12, G:0.30, T:0.24
Consensus pattern (53 bp):
GAAAAAGGTGCCATGGAGTTGTGGACTTAAAAAGGTGCCACAGAGTTGTGGAC
Found at i:440665 original size:60 final size:60
Alignment explanation
Indices: 440596--440917 Score: 292
Period size: 60 Copynumber: 5.5 Consensus size: 60
440586 TTGTGGACTT
* * * * *
440596 AAAAGGGTGCCAC-AGAGTTGTAGACTTAATAGGGTGCCACGTTGTTATGGACTTTAAGAG
1 AAAAAGGTGCCACGA-AGTTGTGGACTTAAAAGGGTGCCACGTAGTTGTGGACTTTAAGAG
* * *
440656 AAAAAGGTGCCACGAAGTTGTGGACTTAAAAGGATGCCATAG-AGTTGTGGACATTAAGAG
1 AAAAAGGTGCCACGAAGTTGTGGACTTAAAAGGGTGCCA-CGTAGTTGTGGACTTTAAGAG
* * * * *
440716 AAAAAGGTTCCA-TAGAGTTGTGGACTTAAAATGGTGCCATGGA-TTGTGGACTTTAAGAG
1 AAAAAGGTGCCACGA-AGTTGTGGACTTAAAAGGGTGCCACGTAGTTGTGGACTTTAAGAG
* *
440775 AAAAAAGGTGCCACGAAGTTATGGACTTAAAAGGGTGCCACGGAGTTGTGGAC-TT-----
1 -AAAAAGGTGCCACGAAGTTGTGGACTTAAAAGGGTGCCACGTAGTTGTGGACTTTAAGAG
* * * * *
440830 AAAAGGGTGCCACAAAATTGTGGACTTAAAAGGGTGCCATAG-AGTTATGG-CTTTGTAA-AG
1 AAAAAGGTGCCACGAAGTTGTGGACTTAAAAGGGTGCCA-CGTAGTTGTGGAC-TT-TAAGAG
*
440890 AAAAAGGTGACCACGGAGTTGTGGACTT
1 AAAAAGGTG-CCACGAAGTTGTGGACTT
440918 TAAGAGAAAA
Statistics
Matches: 217, Mismatches: 29, Indels: 31
0.78 0.10 0.11
Matches are distributed among these distances:
53 1 0.00
54 42 0.19
55 2 0.01
56 1 0.00
59 17 0.08
60 128 0.59
61 26 0.12
ACGTcount: A:0.33, C:0.12, G:0.30, T:0.25
Consensus pattern (60 bp):
AAAAAGGTGCCACGAAGTTGTGGACTTAAAAGGGTGCCACGTAGTTGTGGACTTTAAGAG
Found at i:440742 original size:120 final size:119
Alignment explanation
Indices: 440609--440831 Score: 324
Period size: 120 Copynumber: 1.9 Consensus size: 119
440599 AGGGTGCCAC
* *
440609 AGAGTTGTAGACTTAATAGGGTGCCACGTTG-TTATGGACTTTAAGAG-AAAAAGGTGCCACGAA
1 AGAGTTGTAGACTTAAAAGGGTGCCA--TGGATTATGGACTTTAAGAGAAAAAAGGTGCCACGAA
* *
440672 GTTGTGGACTTAAAAGGATGCCATAGAGTTGTGGACATTAAGAGAAAAAGGTTCCAT
64 GTTATGGACTTAAAAGGATGCCACAGAGTTGTGGAC-TTAAGAGAAAAAGGTTCCAT
* * *
440729 AGAGTTGTGGACTTAAAATGGTGCCATGGATTGTGGACTTTAAGAGAAAAAAGGTGCCACGAAGT
1 AGAGTTGTAGACTTAAAAGGGTGCCATGGATTATGGACTTTAAGAGAAAAAAGGTGCCACGAAGT
* *
440794 TATGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAA
66 TATGGACTTAAAAGGATGCCACAGAGTTGTGGACTTAA
440832 AAGGGTGCCA
Statistics
Matches: 92, Mismatches: 9, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
118 2 0.02
119 19 0.21
120 71 0.77
ACGTcount: A:0.33, C:0.12, G:0.30, T:0.26
Consensus pattern (119 bp):
AGAGTTGTAGACTTAAAAGGGTGCCATGGATTATGGACTTTAAGAGAAAAAAGGTGCCACGAAGT
TATGGACTTAAAAGGATGCCACAGAGTTGTGGACTTAAGAGAAAAAGGTTCCAT
Found at i:440909 original size:34 final size:33
Alignment explanation
Indices: 440857--440950 Score: 102
Period size: 33 Copynumber: 2.8 Consensus size: 33
440847 TTGTGGACTT
* *
440857 AAAAGGGTGCCATAGAGTTATGG-CTTTGTAA-AG
1 AAAAAGGTGCCACAGAGTTATGGAC-TT-TAAGAG
* *
440890 AAAAAGGTGACCACGGAGTTGTGGACTTTAAGAG
1 AAAAAGGTG-CCACAGAGTTATGGACTTTAAGAG
*
440924 AAAAAGGTGCCACAGAGTTGTGGACTT
1 AAAAAGGTGCCACAGAGTTATGGACTT
440951 AAAAGGGTGC
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
33 28 0.53
34 24 0.45
35 1 0.02
ACGTcount: A:0.34, C:0.12, G:0.31, T:0.23
Consensus pattern (33 bp):
AAAAAGGTGCCACAGAGTTATGGACTTTAAGAG
Found at i:440969 original size:60 final size:62
Alignment explanation
Indices: 440890--441042 Score: 156
Period size: 60 Copynumber: 2.5 Consensus size: 62
440880 CTTTGTAAAG
* * *
440890 AAAAA-GGTGACCACGGAGTTGTGGACTTTAAGA-GAAAAAG-GTGCCACAGAGTTGTGGAC-T-
1 AAAAAGGGTG-CCACAGAGTTGTGGACTTTAAAAGGAAAAAGAG-G-CAAAGAGTTGTGGACATA
* *
440950 TAAAAGGGTGCCACAGAGTTTTGGAC-TTAAAAGGAAAAAGAGGCAAAGAGTTGTGGACATACAA
1 AAAAAGGGTGCCACAGAGTTGTGGACTTTAAAAGGAAAAAGAGGCAAAGAGTTGTGGACAT---A
*
441014 AAAAAGGGTGCCACAGAGTTGTGGGCTTT
1 AAAAAGGGTGCCACAGAGTTGTGGACTTT
441043 TGGAAAAAGA
Statistics
Matches: 76, Mismatches: 8, Indels: 13
0.78 0.08 0.13
Matches are distributed among these distances:
59 19 0.25
60 27 0.36
61 5 0.07
64 23 0.30
65 2 0.03
ACGTcount: A:0.37, C:0.12, G:0.31, T:0.20
Consensus pattern (62 bp):
AAAAAGGGTGCCACAGAGTTGTGGACTTTAAAAGGAAAAAGAGGCAAAGAGTTGTGGACATA
Found at i:442101 original size:54 final size:53
Alignment explanation
Indices: 441990--442104 Score: 167
Period size: 54 Copynumber: 2.2 Consensus size: 53
441980 AATTTAGAAT
* ** *
441990 TTTTTTTGTGGAGACCAGGATTGGTGAGTCTCGAAGCTTGTGTCTCATTGAGT
1 TTTTTTTGTAGAGACCAGGATTGGTGAGTCTCGAAGCTTGTGTCTCACCGAGG
* *
442043 TTTTTTTGTAGTGACCAGGATTTGGTGAGTCTCGAAGCTTGTGTCTTACCGAGG
1 TTTTTTTGTAGAGACCAGGA-TTGGTGAGTCTCGAAGCTTGTGTCTCACCGAGG
442097 TTTTTTTG
1 TTTTTTTG
442105 GTGTTATTTT
Statistics
Matches: 55, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
53 18 0.33
54 37 0.67
ACGTcount: A:0.16, C:0.13, G:0.29, T:0.43
Consensus pattern (53 bp):
TTTTTTTGTAGAGACCAGGATTGGTGAGTCTCGAAGCTTGTGTCTCACCGAGG
Found at i:447442 original size:51 final size:50
Alignment explanation
Indices: 447361--447475 Score: 187
Period size: 51 Copynumber: 2.3 Consensus size: 50
447351 AAAATAGCAA
447361 GGTTGGAGTATCCCGATGGTGAGAAATTGATATTTTGAAAATAAAAATGG
1 GGTTGGAGTATCCCGATGGTGAGAAATTGATATTTTGAAAATAAAAATGG
* *
447411 GGTTGGAGTATCCTTGATGGTGA-AAAGTTGATATTTTGGAAATAAAAATGG
1 GGTTGGAGTATCC-CGATGGTGAGAAA-TTGATATTTTGAAAATAAAAATGG
447462 GGTTGGAGTATCCC
1 GGTTGGAGTATCCC
447476 CTCAAAAATA
Statistics
Matches: 60, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
50 16 0.27
51 44 0.73
ACGTcount: A:0.32, C:0.07, G:0.30, T:0.31
Consensus pattern (50 bp):
GGTTGGAGTATCCCGATGGTGAGAAATTGATATTTTGAAAATAAAAATGG
Found at i:447501 original size:79 final size:80
Alignment explanation
Indices: 447409--447900 Score: 405
Period size: 79 Copynumber: 6.2 Consensus size: 80
447399 AAATAAAAAT
** *
447409 GGGGTTGGAGTATCCTTGATGGTGAAAAGTTGA-TATTTTGGAAATAAAAAT-GGGGTTGGAGTA
1 GGGGTTGGAGTATCCCCGATGGTGAAAA-TTGAGTATTTTAGAAATAAAAATCGGGGTTGGAGTA
447472 TCCCCTCAAAAATAAC
65 TCCCCTCAAAAATAAC
* * * * *
447488 GGGGTTGGAGTATCCCCGATGGTGAAAAATCAGTGTTTTCA-AAAT-GAAATCGAGGTTGGAGTA
1 GGGGTTGGAGTATCCCCGATGGTGAAAATTGAGTATTTT-AGAAATAAAAATCGGGGTTGGAGTA
*** *
447551 TCCCCTTGGAAACAAC
65 TCCCCTCAAAAATAAC
** * * *
447567 AAGGTTGAAGTATCCCCGATGATGAAAAATT-AGTATTTTAGAAATAAAAATCGGGGTTGAAGTA
1 GGGGTTGGAGTATCCCCGATGGTG-AAAATTGAGTATTTTAGAAATAAAAATCGGGGTTGGAGTA
*
447631 CCCCCTCAAAAATAAC
65 TCCCCTCAAAAATAAC
* * * * **
447647 GGGGTTGGAGTATCCCCGATGATGGAAAATCGA-TATTTGAGAAAT-AAAATTGGGGTTAAAGTA
1 GGGGTTGGAGTATCCCCGATGGT-GAAAATTGAGTATTTTAGAAATAAAAATCGGGGTTGGAGTA
* ** *
447710 TCCCTTTGAATATAAC
65 TCCCCTCAAAAATAAC
* * * * * * * *
447726 AGGCTTGGAGTATTCCCGATGGTAGAAAA-TCAGTGTTTTAGATAT-AAAATCGAGGTTGGAGAA
1 GGGGTTGGAGTATCCCCGATGGT-GAAAATTGAGTATTTTAGAAATAAAAATCGGGGTTGGAGTA
*
447789 TCCCCTCAGAAATAAC
65 TCCCCTCAAAAATAAC
* * * * ** * *
447805 GGAGTTAGAGTA-CCCCTGATAGTGAAAAATCTGTGTTTTAGAAATAAAACAT--GGGTTAGAGT
1 GGGGTTGGAGTATCCCC-GATGGTGAAAATTGAGTATTTTAGAAATAAAA-ATCGGGGTTGGAGT
* **
447867 ATCCCTTTGAAAATAAC
64 ATCCCCTCAAAAATAAC
447884 GGGGTTGGAGTATCCCC
1 GGGGTTGGAGTATCCCC
447901 CCGAAAATAA
Statistics
Matches: 324, Mismatches: 75, Indels: 27
0.76 0.18 0.06
Matches are distributed among these distances:
78 16 0.05
79 230 0.71
80 74 0.23
81 4 0.01
ACGTcount: A:0.34, C:0.14, G:0.25, T:0.27
Consensus pattern (80 bp):
GGGGTTGGAGTATCCCCGATGGTGAAAATTGAGTATTTTAGAAATAAAAATCGGGGTTGGAGTAT
CCCCTCAAAAATAAC
Found at i:447833 original size:238 final size:237
Alignment explanation
Indices: 447409--447900 Score: 565
Period size: 238 Copynumber: 2.1 Consensus size: 237
447399 AAATAAAAAT
** * * **
447409 GGGGTTGGAGTATCCTTGATGGTGAAAAGTTGATATTTTGGAAATAAAAATGGGGTTGGAGTATC
1 GGGGTTGGAGTATCCCCGATGATGAAAAGTCGATATTTTGGAAATAAAAATGGGGTTAAAGTATC
* * *
447474 CCCTCAAAAATAACGGGGTTGGAGTATCCCCGATGGTGAAAAATCAGTGTTTTCAAAATGAAATC
66 CCCTCAAAAATAACAGGCTTGGAGTATCCCCGATGGTGAAAAATCAGTGTTTTCAAAATAAAATC
* **
447539 GAGGTTGGAGTATCCCCTTGGAAACAACAAGGTTGAAGTATCCCCGATGATGAAAAAT-TAGTAT
131 GAGGTTGGAGAATCCCCTCAGAAACAACAAGGTTGAAGTATCCCCGATGATGAAAAATCT-GTAT
447603 TTTAGAAATAAAA-ATCGGGGTT-GAAGTACCCCCTCAAAAATAAC
195 TTTAGAAATAAAACAT--GGGTTAG-AGTACCCCCTCAAAAATAAC
*
447647 GGGGTTGGAGTATCCCCGATGATGGAAAA-TCGATA-TTTGAGAAATAAAATTGGGGTTAAAGTA
1 GGGGTTGGAGTATCCCCGATGAT-GAAAAGTCGATATTTTG-GAAATAAAAATGGGGTTAAAGTA
* ** * * *
447710 TCCCTTTGAATATAACAGGCTTGGAGTATTCCCGATGGT-AGAAAATCAGTGTTTT-AGATATAA
64 TCCCCTCAAAAATAACAGGCTTGGAGTATCCCCGATGGTGA-AAAATCAGTGTTTTCA-AAATAA
* *
447773 AATCGAGGTTGGAGAATCCCCTCAGAAATAAC-GGAGTT-AGAGTA-CCCCTGAT-AGTGAAAAA
127 AATCGAGGTTGGAGAATCCCCTCAGAAACAACAAG-GTTGA-AGTATCCCC-GATGA-TGAAAAA
* * * **
447834 TCTGTGTTTTAGAAATAAAACATGGGTTAGAGTATCCCTTTGAAAATAAC
188 TCTGTATTTTAGAAATAAAACATGGGTTAGAGTACCCCCTCAAAAATAAC
447884 GGGGTTGGAGTATCCCC
1 GGGGTTGGAGTATCCCC
447901 CCGAAAATAA
Statistics
Matches: 217, Mismatches: 26, Indels: 23
0.82 0.10 0.09
Matches are distributed among these distances:
237 51 0.24
238 158 0.73
239 8 0.04
ACGTcount: A:0.34, C:0.14, G:0.25, T:0.27
Consensus pattern (237 bp):
GGGGTTGGAGTATCCCCGATGATGAAAAGTCGATATTTTGGAAATAAAAATGGGGTTAAAGTATC
CCCTCAAAAATAACAGGCTTGGAGTATCCCCGATGGTGAAAAATCAGTGTTTTCAAAATAAAATC
GAGGTTGGAGAATCCCCTCAGAAACAACAAGGTTGAAGTATCCCCGATGATGAAAAATCTGTATT
TTAGAAATAAAACATGGGTTAGAGTACCCCCTCAAAAATAAC
Found at i:447894 original size:28 final size:28
Alignment explanation
Indices: 447857--447926 Score: 95
Period size: 28 Copynumber: 2.5 Consensus size: 28
447847 AATAAAACAT
* ***
447857 GGGTTAGAGTATCCCTTTGAAAATAACG
1 GGGTTGGAGTATCCCCCCGAAAATAACG
*
447885 GGGTTGGAGTATCCCCCCGAAAATAATG
1 GGGTTGGAGTATCCCCCCGAAAATAACG
447913 GGGTTGGAGTATCC
1 GGGTTGGAGTATCC
447927 TCGATGGTGG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.27, C:0.17, G:0.30, T:0.26
Consensus pattern (28 bp):
GGGTTGGAGTATCCCCCCGAAAATAACG
Found at i:447968 original size:79 final size:79
Alignment explanation
Indices: 447883--448039 Score: 224
Period size: 79 Copynumber: 2.0 Consensus size: 79
447873 TTGAAAATAA
* * * *
447883 CGGGGTTGGAGTATCCCCCCGAAAATAATGGGGTTGGAGTATCCTCGATGGTGGAAAATTGGTAT
1 CGGGGTTAGAGTATCCCCCCGAAAATAACGGGGTTGGAGTATCCCCGATGGTGGAAAATCGGTAT
447948 TTTAGAAATAAAAC
66 TTTAGAAATAAAAC
** ** * *
447962 CGGGGTTAGAGTATCTTCTTGGAAATAACGGGGTTGGAGTGTCCCCGATGGTGGAAAATCGGTAT
1 CGGGGTTAGAGTATCCCCCCGAAAATAACGGGGTTGGAGTATCCCCGATGGTGGAAAATCGGTAT
448027 TTTAGAAATAAAA
66 TTTAGAAATAAAA
448040 ACATCAATGA
Statistics
Matches: 68, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
79 68 1.00
ACGTcount: A:0.30, C:0.13, G:0.30, T:0.27
Consensus pattern (79 bp):
CGGGGTTAGAGTATCCCCCCGAAAATAACGGGGTTGGAGTATCCCCGATGGTGGAAAATCGGTAT
TTTAGAAATAAAAC
Found at i:450438 original size:20 final size:20
Alignment explanation
Indices: 450365--450442 Score: 66
Period size: 20 Copynumber: 3.8 Consensus size: 20
450355 AATTGCCTAC
* * **
450365 ATGTATCGATGCATTGAAAA
1 ATGTATCGATACATTTAAGT
450385 ATGTATCGATACAATTATAAGT
1 ATGTATCGATAC-ATT-TAAGT
* * **
450407 ATTTATCAATACATTTACTT
1 ATGTATCGATACATTTAAGT
450427 ATGTATCGATACATTT
1 ATGTATCGATACATTT
450443 CTTTGGCAGT
Statistics
Matches: 46, Mismatches: 10, Indels: 4
0.77 0.17 0.07
Matches are distributed among these distances:
20 28 0.61
21 6 0.13
22 12 0.26
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTAAGT
Found at i:451218 original size:61 final size:61
Alignment explanation
Indices: 451052--451698 Score: 683
Period size: 61 Copynumber: 10.5 Consensus size: 61
451042 AAAAGGAGAG
* * *
451052 AGGCGTCCTGCTCTTTGAGGACTAGAAGGTGCCACCAGCTTGTGTGGGCTTTAAAAGAAAAA
1 AGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAA-AGAAA
* *
451114 AGGAAGCGT-CTCGCTTTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAA
1 A-G--GCGTCCT-GCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAA
* * *
451178 AGGCGTCCTACTCTTT-AGGGACTAAAAGGTGCCACTAACTTGTGTGGGCTTT-AAAAGGAA
1 AGGCGTCCTGCTCTTTGA-GGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAA
* * *
451238 A-GTGTCCTGCTTTTTGAGGACTAGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAA
1 AGGCGTCCTGCTCTTTGAGGACTA-AAAGGTGCCACCAACTTGTGTGGGCTTTAAAA-AGAAA
* * * * * * *
451300 ATGAAAGTGTCTTGCTCTTTGAGGACTGAAAGGTGCCGCCAACTCGTGTGGGTTTTGAAAAGAAA
1 A-G---GCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAA
** * *
451365 AGATGTCCTGCTCTTTGAGTACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAA
1 AGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGA-AA
* ** * * * *
451427 A-GCATCCTGCTCTTTGAGGACTGGAATGTGCCACCAACTCGTGTGGACTTTAAAAGGAAA
1 AGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAA
* * * * ** * * *
451487 AGGCATCCTACTCTTTAAGGACTAAAAGGTCCCATTAACTTGTGCGGGCTTTGAAAAGAGA
1 AGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAA
* * ** * *
451548 AGGCGTCTTGCTCTTTGAGGACTGAAAGGTGCCATTAACTTGTGTGGGCTTTAAAAGGAGA
1 AGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAA
* * * * * *
451609 AGGCATCCTACTCTTTGAGGACTGAAAGATGCCACCAACCTGTGTGGGCTTTAAAAGGAAA
1 AGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAA
*
451670 AGGCATCCTGCTCTTTGAGGACTAAAAGG
1 AGGCGTCCTGCTCTTTGAGGACTAAAAGG
451699 ATAAAAGGTT
Statistics
Matches: 492, Mismatches: 76, Indels: 35
0.82 0.13 0.06
Matches are distributed among these distances:
59 17 0.03
60 40 0.08
61 316 0.64
62 10 0.02
63 2 0.00
64 8 0.02
65 52 0.11
66 28 0.06
67 19 0.04
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.26
Consensus pattern (61 bp):
AGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAA
Found at i:451590 original size:183 final size:184
Alignment explanation
Indices: 451042--451698 Score: 768
Period size: 183 Copynumber: 3.5 Consensus size: 184
451032 TTGAAGATAG
* * * * *
451042 AAAAGGAGAGAGGCGTCCTGCTCTTTGAGGACTAGAAGGTGCCACCAGCTTGTGTGGGCTTTAAA
1 AAAAGGAGA-AAGCATCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTCGTGTGGGCTTTAAA
* * * * *
451107 AGAAAAAAGGAAGCGTCTCGCTTTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAA
65 AGAAAAAAGGCATC--CT-GCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAA
*
451172 AAGAAAAGGCGTCCTACTCTTT-AGGGACTAAAAGGTGCCACTAACTTGTGTGGGCTTT
127 AAGAAAAGGCGTCCTGCTCTTTGA-GGACTAAAAGGTGCCACTAACTTGTGTGGGCTTT
** * * *
451230 AAAA-G-GAAAGTGTCCTGCTTTTTGAGGACTAGAAAGGTGCCACCAACTTGTGTGGGCTTTAAA
1 AAAAGGAGAAAGCATCCTGCTCTTTGAGGACT-GGAAGGTGCCACCAACTCGTGTGGGCTTTAAA
** * * * * *
451293 AGAAAAAATGAAAGTGTCTTGCTCTTTGAGGACTGAAAGGTGCCGCCAACTCGTGTGGGTTTTGA
65 AGAAAAAA-G---GCATCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGA
** * *
451358 AAAGAAAAGATGTCCTGCTCTTTGAGTACTAAAAGGTGCCACCAACTTGTGTGGGCTTT
126 AAAGAAAAGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACTAACTTGTGTGGGCTTT
* *
451417 AAAAGGAGAAAGCATCCTGCTCTTTGAGGACTGGAATGTGCCACCAACTCGTGTGGACTTTAAAA
1 AAAAGGAGAAAGCATCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTCGTGTGGGCTTTAAAA
* * * * ** *
451482 G-GAAAAGGCATCCTACTCTTTAAGGACTAAAAGGTCCCATTAACTTGTGCGGGCTTTGAAAAGA
66 GAAAAAAGGCATCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGA
* * * *
451546 GAAGGCGTCTTGCTCTTTGAGGACTGAAAGGTGCCATTAACTTGTGTGGGCTTT
131 AAAGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACTAACTTGTGTGGGCTTT
* * * *
451600 AAAAGGAGAAGGCATCCTACTCTTTGAGGACTGAAAGATGCCACCAAC-CTGTGTGGGCTTTAAA
1 AAAAGGAGAAAGCATCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTC-GTGTGGGCTTTAAA
*
451664 AG-GAAAAGGCATCCTGCTCTTTGAGGACTAAAAGG
65 AGAAAAAAGGCATCCTGCTCTTTGAGGACTAAAAGG
451699 ATAAAAGGTT
Statistics
Matches: 403, Mismatches: 57, Indels: 23
0.83 0.12 0.05
Matches are distributed among these distances:
182 1 0.00
183 179 0.44
185 20 0.05
186 40 0.10
187 102 0.25
188 37 0.09
189 22 0.05
190 2 0.00
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.26
Consensus pattern (184 bp):
AAAAGGAGAAAGCATCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTCGTGTGGGCTTTAAAA
GAAAAAAGGCATCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGA
AAAGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACTAACTTGTGTGGGCTTT
Found at i:452703 original size:11 final size:11
Alignment explanation
Indices: 452689--452728 Score: 71
Period size: 11 Copynumber: 3.5 Consensus size: 11
452679 TTTCTTTTCA
452689 TTTTTTTGTTT
1 TTTTTTTGTTT
452700 TTTTTTTGTTT
1 TTTTTTTGTTT
452711 TTTTTTTGTTGT
1 TTTTTTTGTT-T
452723 TTTTTT
1 TTTTTT
452729 AAAAGAAAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
11 21 0.75
12 7 0.25
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (11 bp):
TTTTTTTGTTT
Found at i:452711 original size:25 final size:25
Alignment explanation
Indices: 452677--452728 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
452667 TTCTTTTTCC
452677 TTTTTCTTTTCATTTTT-TTGTTTTT
1 TTTTTCTTTT-ATTTTTGTTGTTTTT
* *
452702 TTTTTGTTTTTTTTTTGTTGTTTTT
1 TTTTTCTTTTATTTTTGTTGTTTTT
452727 TT
1 TT
452729 AAAAGAAAGG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 5 0.21
25 19 0.79
ACGTcount: A:0.02, C:0.04, G:0.08, T:0.87
Consensus pattern (25 bp):
TTTTTCTTTTATTTTTGTTGTTTTT
Found at i:454759 original size:49 final size:50
Alignment explanation
Indices: 454650--454780 Score: 192
Period size: 49 Copynumber: 2.6 Consensus size: 50
454640 CACAATTTGT
* * * *
454650 ATCGATACATTGTTTATTGTATCAATACATTTTGGGTTTTACCCAGATGT
1 ATCGATACATTGTTCATTGTATCGATACATTCTGGGTTTTACCCAGATGA
*
454700 ATCGATACATTGTTCATTGTATCGATACATTCTGGG-TTTACCTAGATGA
1 ATCGATACATTGTTCATTGTATCGATACATTCTGGGTTTTACCCAGATGA
* *
454749 ATCGATACATTTTTCAATGTATCGATACATTC
1 ATCGATACATTGTTCATTGTATCGATACATTC
454781 AGGCATTTTT
Statistics
Matches: 74, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
49 41 0.55
50 33 0.45
ACGTcount: A:0.27, C:0.16, G:0.15, T:0.41
Consensus pattern (50 bp):
ATCGATACATTGTTCATTGTATCGATACATTCTGGGTTTTACCCAGATGA
Found at i:457417 original size:79 final size:79
Alignment explanation
Indices: 457079--457461 Score: 361
Period size: 79 Copynumber: 4.9 Consensus size: 79
457069 TTTTTCATCT
** * * * *
457079 CGGGGATACTCCAATTCCGATTTTATTTCCAAAACACCAATTTT-CACAATCAGGGATACTCCAA
1 CGGGGATACTCCAACCCCGATTTTATTTTCAAAACATCGATTTTCCATAATCAGGGATACTCCAA
457143 CCCCGTTA-TTTCA
66 CCCCGTTATTTTCA
* ** * * * * * *
457156 TCGGGGATACTTCAACCCCGGCTTTA-TTTCTAAAATAT-TAATTTCTCACAATCGGGGAAACTC
1 -CGGGGATACTCCAACCCCGATTTTATTTTC-AAAACATCGATTTTC-CATAATCAGGGATACTC
457219 CAACCCCGTTATTTTCA
63 CAACCCCGTTATTTTCA
* ** * * * *
457236 CGGGAATACTCCAACCCCGACCTTA-TGTCTAAAGCATCGATTTTCCATAATC-GATGCTACTCC
1 CGGGGATACTCCAACCCCGATTTTATTTTC-AAAACATCGATTTTCCATAATCAG-GGATACTCC
*
457299 AACCCCATTATTTTCGA
64 AACCCCGTTATTTTC-A
* *
457316 -GGGGATACTCCAACCCCAATTTTATTTTCAAAACATCGATTTTCTATAATCAGGGATACTCCAA
1 CGGGGATACTCCAACCCCGATTTTATTTTCAAAACATCGATTTTCCATAATCAGGGATACTCCAA
*
457380 CCCTGTTATTTTCGA
66 CCCCGTTATTTTC-A
* * * * *
457395 -GGGGATACTCTAACCCCGATTTTATTTTTAGAACATCGA-TTTCCATAATCGGGGATACTCCAG
1 CGGGGATACTCCAACCCCGATTTTATTTTCAAAACATCGATTTTCCATAATCAGGGATACTCCAA
457458 CCCC
66 CCCC
457462 ATTGTTAAAT
Statistics
Matches: 251, Mismatches: 45, Indels: 18
0.80 0.14 0.06
Matches are distributed among these distances:
77 7 0.03
78 50 0.20
79 179 0.71
80 15 0.06
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.31
Consensus pattern (79 bp):
CGGGGATACTCCAACCCCGATTTTATTTTCAAAACATCGATTTTCCATAATCAGGGATACTCCAA
CCCCGTTATTTTCA
Found at i:458591 original size:14 final size:14
Alignment explanation
Indices: 458572--458598 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
458562 CAAATACCTT
458572 TATGTTTAGATACC
1 TATGTTTAGATACC
458586 TATGTTTAGATAC
1 TATGTTTAGATAC
458599 TAGGAACATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.11, G:0.15, T:0.44
Consensus pattern (14 bp):
TATGTTTAGATACC
Found at i:458724 original size:159 final size:157
Alignment explanation
Indices: 458435--458741 Score: 587
Period size: 159 Copynumber: 1.9 Consensus size: 157
458425 AGTGTGTATC
458435 GATACTAGGAACATGTATTGATATAATGTATCAATACTAAGCAATATGTATCGATACATCTGGGT
1 GATACTAGGAACATGTATTGATATAATGTATCAATACTAAGCAATATGTATCGATACATCTGGGT
458500 GTGTATCGATACTTTCTAGAGTTTTGACCTTTATAGCTTAAGTCAACCTTTATGTATCGATACAA
66 GTGTATCGATACTTTCTAGAGTTTTGACCTTTATAGCTTAAGTCAACCTTTATGTATCGATACAA
458565 ATACCTTTATGTTTAGATACCTATGTTTA
131 ATACC--TATGTTTAGATACCTATGTTTA
458594 GATACTAGGAACATGTATTGATATAATGTATCAATACTAAGCAATATGTATCGATACATCTGGGT
1 GATACTAGGAACATGTATTGATATAATGTATCAATACTAAGCAATATGTATCGATACATCTGGGT
*
458659 GTGTATCGATACTTTCTAGGGTTTTGACCTTTATAGCTTAAGTCAACCTTTATGTATCGATACAA
66 GTGTATCGATACTTTCTAGAGTTTTGACCTTTATAGCTTAAGTCAACCTTTATGTATCGATACAA
458724 ATACCTATGTTTAGATAC
131 ATACCTATGTTTAGATAC
458742 TTTGGATTAT
Statistics
Matches: 147, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
157 13 0.09
159 134 0.91
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.37
Consensus pattern (157 bp):
GATACTAGGAACATGTATTGATATAATGTATCAATACTAAGCAATATGTATCGATACATCTGGGT
GTGTATCGATACTTTCTAGAGTTTTGACCTTTATAGCTTAAGTCAACCTTTATGTATCGATACAA
ATACCTATGTTTAGATACCTATGTTTA
Found at i:460328 original size:33 final size:33
Alignment explanation
Indices: 460291--460388 Score: 151
Period size: 33 Copynumber: 3.0 Consensus size: 33
460281 ACAAGCAATA
*
460291 TGTATCGATACAATTTATCATATATCGATACAT
1 TGTATCGATACAATTTATCATGTATCGATACAT
*
460324 TGTATCGATACAATTCATCATGTATCGATACAT
1 TGTATCGATACAATTTATCATGTATCGATACAT
* * *
460357 TGTATCAATACAATGTACCATGTATCGATACA
1 TGTATCGATACAATTTATCATGTATCGATACA
460389 AACAGTGGTA
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.36
Consensus pattern (33 bp):
TGTATCGATACAATTTATCATGTATCGATACAT
Found at i:460347 original size:20 final size:20
Alignment explanation
Indices: 460290--460355 Score: 65
Period size: 20 Copynumber: 3.6 Consensus size: 20
460280 TACAAGCAAT
*
460290 ATGTATCGATACAATTTATC
1 ATGTATCGATACAATTCATC
*
460310 ATATATCGAT---A--CAT-
1 ATGTATCGATACAATTCATC
460324 -TGTATCGATACAATTCATC
1 ATGTATCGATACAATTCATC
460343 ATGTATCGATACA
1 ATGTATCGATACA
460356 TTGTATCAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 14
0.68 0.06 0.26
Matches are distributed among these distances:
13 8 0.22
15 2 0.06
16 1 0.03
17 1 0.03
18 3 0.08
20 21 0.58
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACAATTCATC
Found at i:460363 original size:20 final size:19
Alignment explanation
Indices: 460290--460363 Score: 61
Period size: 20 Copynumber: 4.1 Consensus size: 19
460280 TACAAGCAAT
460290 ATGTATCGATACAATTTATC
1 ATGTATCGATAC-ATTTATC
*
460310 ATATATCGATAC----AT-
1 ATGTATCGATACATTTATC
*
460324 -TGTATCGATACAATTCATC
1 ATGTATCGATAC-ATTTATC
460343 ATGTATCGATACATTGTATC
1 ATGTATCGATACATT-TATC
460363 A
1 A
460364 ATACAATGTA
Statistics
Matches: 43, Mismatches: 3, Indels: 16
0.69 0.05 0.26
Matches are distributed among these distances:
13 10 0.23
15 2 0.05
18 2 0.05
19 3 0.07
20 26 0.60
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.38
Consensus pattern (19 bp):
ATGTATCGATACATTTATC
Found at i:463495 original size:20 final size:22
Alignment explanation
Indices: 463465--463508 Score: 74
Period size: 20 Copynumber: 2.1 Consensus size: 22
463455 TGATTTCCCG
463465 TGTGAATGTATCGATACA-ATT
1 TGTGAATGTATCGATACATATT
463486 TGTG-ATGTATCGATACATATT
1 TGTGAATGTATCGATACATATT
463507 TG
1 TG
463509 AAAATGTACT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.30, C:0.09, G:0.20, T:0.41
Consensus pattern (22 bp):
TGTGAATGTATCGATACATATT
Found at i:463578 original size:19 final size:20
Alignment explanation
Indices: 463535--463586 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
463525 TACAAGCCAA
*
463535 TGTATCGATACAATTTTTGG
1 TGTATCGATACAATCTTTGG
463555 TGTATCGATAC-ATACTTT-G
1 TGTATCGATACAAT-CTTTGG
463574 TGTATCGATACAA
1 TGTATCGATACAA
463587 GTTTGGCTAC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 14 0.48
20 15 0.52
ACGTcount: A:0.29, C:0.13, G:0.17, T:0.40
Consensus pattern (20 bp):
TGTATCGATACAATCTTTGG
Found at i:465688 original size:21 final size:20
Alignment explanation
Indices: 465659--465701 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
465649 GGCTAGTGTG
*
465659 GGGACTGCCCGGTTGCGACCT
1 GGGACTG-CCGGTCGCGACCT
*
465680 GGGAGTGCCGGTCGCGACCT
1 GGGACTGCCGGTCGCGACCT
465700 GG
1 GG
465702 TGGGTGCTGC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.09, C:0.30, G:0.44, T:0.16
Consensus pattern (20 bp):
GGGACTGCCGGTCGCGACCT
Found at i:466162 original size:13 final size:13
Alignment explanation
Indices: 466144--466182 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
466134 ATAATCCCCC
*
466144 TGTATCGATACAG
1 TGTATCGATACAA
466157 TGTATCGATACAA
1 TGTATCGATACAA
466170 TGTATCGATACAA
1 TGTATCGATACAA
466183 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:470111 original size:22 final size:20
Alignment explanation
Indices: 470062--470113 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
470052 ATCATGCAAG
470062 TTTTTATTTTTCTTAGCTAAT
1 TTTTTA-TTTTCTTAGCTAAT
**
470083 TCATTATTTTCATTAGCTAAAT
1 TTTTTATTTTC-TTAGCT-AAT
470105 TTTTTATTT
1 TTTTTATTT
470114 CAACTTGCAA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
20 5 0.20
21 10 0.40
22 10 0.40
ACGTcount: A:0.23, C:0.10, G:0.04, T:0.63
Consensus pattern (20 bp):
TTTTTATTTTCTTAGCTAAT
Found at i:472276 original size:20 final size:22
Alignment explanation
Indices: 472246--472289 Score: 74
Period size: 20 Copynumber: 2.1 Consensus size: 22
472236 TGAATTCCCG
472246 TGTGAATGTATCGATACA-ATT
1 TGTGAATGTATCGATACATATT
472267 TGTG-ATGTATCGATACATATT
1 TGTGAATGTATCGATACATATT
472288 TG
1 TG
472290 AAAATGTAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.30, C:0.09, G:0.20, T:0.41
Consensus pattern (22 bp):
TGTGAATGTATCGATACATATT
Found at i:472361 original size:13 final size:13
Alignment explanation
Indices: 472343--472368 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
472333 CAATTTTTGG
472343 TGTATCGATACAT
1 TGTATCGATACAT
472356 TGTATCGATACAT
1 TGTATCGATACAT
472369 ACTTTGTGTA
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:472365 original size:33 final size:32
Alignment explanation
Indices: 472323--472386 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 32
472313 TACAAGCCAA
*
472323 TGTATCGATACA-ATTTTTGGTGTATCGATACAT
1 TGTATCGATACATA-CTTT-GTGTATCGATACAT
472356 TGTATCGATACATACTTTGTGTATCGATACA
1 TGTATCGATACATACTTTGTGTATCGATACA
472387 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 13 0.45
33 15 0.52
34 1 0.03
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (32 bp):
TGTATCGATACATACTTTGTGTATCGATACAT
Found at i:472383 original size:32 final size:33
Alignment explanation
Indices: 472323--472386 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
472313 TACAAGCCAA
*
472323 TGTATCGATACAATTTTTGGTGTATCGATACAT
1 TGTATCGATACAATCTTTGGTGTATCGATACAT
472356 TGTATCGATAC-ATACTTT-GTGTATCGATACA
1 TGTATCGATACAAT-CTTTGGTGTATCGATACA
472387 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 15 0.52
33 14 0.48
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (33 bp):
TGTATCGATACAATCTTTGGTGTATCGATACAT
Found at i:476794 original size:21 final size:21
Alignment explanation
Indices: 476765--476811 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
476755 AAGTTCTTGT
*
476765 TTTTC-TTAGCTAATTCATTA
1 TTTTCATTAGCCAATTCATTA
**
476785 TTTTCATTAGCCAATTTTTTA
1 TTTTCATTAGCCAATTCATTA
476806 TTTTCA
1 TTTTCA
476812 ACTTGCAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 5 0.22
21 18 0.78
ACGTcount: A:0.23, C:0.15, G:0.04, T:0.57
Consensus pattern (21 bp):
TTTTCATTAGCCAATTCATTA
Found at i:479046 original size:33 final size:33
Alignment explanation
Indices: 479001--479065 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
478991 TTACAAGCAA
*
479001 TGTATCGATACAAT-TCATCATGTATCGATACAT
1 TGTATCGATACAATAT-ACCATGTATCGATACAT
* *
479034 TGTATCGTTACAATATACCATGTATTGATACA
1 TGTATCGATACAATATACCATGTATCGATACA
479066 AATAGTGGCA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 27 0.96
34 1 0.04
ACGTcount: A:0.34, C:0.17, G:0.12, T:0.37
Consensus pattern (33 bp):
TGTATCGATACAATATACCATGTATCGATACAT
Found at i:481829 original size:13 final size:13
Alignment explanation
Indices: 481811--481836 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
481801 CAATTTTTGG
481811 TGTATCGATACAT
1 TGTATCGATACAT
481824 TGTATCGATACAT
1 TGTATCGATACAT
481837 ACTTTGTGTA
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:481854 original size:32 final size:33
Alignment explanation
Indices: 481791--481854 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 33
481781 TACAAGCCAA
* *
481791 TGTATCGATACAATTTTTGGTGTATCGATACAT
1 TGTATCGATACAATCTTTGGTGTATCAATACAT
481824 TGTATCGATAC-ATACTTT-GTGTATCAATACA
1 TGTATCGATACAAT-CTTTGGTGTATCAATACA
481855 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 14 0.50
33 14 0.50
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.41
Consensus pattern (33 bp):
TGTATCGATACAATCTTTGGTGTATCAATACAT
Found at i:483882 original size:22 final size:20
Alignment explanation
Indices: 483833--483884 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
483823 ATCATACAAG
483833 TTTTTATTTTTCTTAGCTAAT
1 TTTTTA-TTTTCTTAGCTAAT
**
483854 TCATTATTTTCATTAGCTAAAT
1 TTTTTATTTTC-TTAGCT-AAT
483876 TTTTTATTT
1 TTTTTATTT
483885 CAACTTGCAA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
20 5 0.20
21 10 0.40
22 10 0.40
ACGTcount: A:0.23, C:0.10, G:0.04, T:0.63
Consensus pattern (20 bp):
TTTTTATTTTCTTAGCTAAT
Found at i:486112 original size:13 final size:13
Alignment explanation
Indices: 486094--486119 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
486084 CAATTTTTGG
486094 TGTATCGATACAT
1 TGTATCGATACAT
486107 TGTATCGATACAT
1 TGTATCGATACAT
486120 ACTTTGTGTA
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:486116 original size:33 final size:32
Alignment explanation
Indices: 486074--486137 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 32
486064 TACAAGCCAA
*
486074 TGTATCGATACA-ATTTTTGGTGTATCGATACAT
1 TGTATCGATACATA-CTTT-GTGTATCGATACAT
486107 TGTATCGATACATACTTTGTGTATCGATACA
1 TGTATCGATACATACTTTGTGTATCGATACA
486138 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 13 0.45
33 15 0.52
34 1 0.03
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (32 bp):
TGTATCGATACATACTTTGTGTATCGATACAT
Found at i:486134 original size:32 final size:33
Alignment explanation
Indices: 486074--486137 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
486064 TACAAGCCAA
*
486074 TGTATCGATACAATTTTTGGTGTATCGATACAT
1 TGTATCGATACAATCTTTGGTGTATCGATACAT
486107 TGTATCGATAC-ATACTTT-GTGTATCGATACA
1 TGTATCGATACAAT-CTTTGGTGTATCGATACA
486138 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 15 0.52
33 14 0.48
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (33 bp):
TGTATCGATACAATCTTTGGTGTATCGATACAT
Found at i:489937 original size:20 final size:19
Alignment explanation
Indices: 489912--489963 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
489902 TTCAACAATT
489912 TGTATCGATACAAACAGTAA
1 TGTATCGATACAAA-AGTAA
* * **
489932 TGTATCGATGCATAAGTGT
1 TGTATCGATACAAAAGTAA
489951 TGTATCGATACAA
1 TGTATCGATACAA
489964 TGTATCGATA
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
19 14 0.54
20 12 0.46
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.31
Consensus pattern (19 bp):
TGTATCGATACAAAAGTAA
Found at i:489969 original size:13 final size:13
Alignment explanation
Indices: 489951--489976 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
489941 GCATAAGTGT
489951 TGTATCGATACAA
1 TGTATCGATACAA
489964 TGTATCGATACAA
1 TGTATCGATACAA
489977 AAGCTACCCT
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:503889 original size:13 final size:13
Alignment explanation
Indices: 503873--503916 Score: 56
Period size: 13 Copynumber: 3.4 Consensus size: 13
503863 AAGAAAGAGA
503873 AAAAAAACAAAAC
1 AAAAAAACAAAAC
503886 AAAAAAACAAAA-
1 AAAAAAACAAAAC
503898 AGAAAAAA-AACAAC
1 A-AAAAAACAA-AAC
503912 AAAAA
1 AAAAA
503917 GGGTCCGGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
12 3 0.11
13 24 0.86
14 1 0.04
ACGTcount: A:0.86, C:0.11, G:0.02, T:0.00
Consensus pattern (13 bp):
AAAAAAACAAAAC
Found at i:503890 original size:15 final size:14
Alignment explanation
Indices: 503870--503910 Score: 57
Period size: 13 Copynumber: 2.9 Consensus size: 14
503860 CAAAAGAAAG
503870 AGAAAAAAAACAAA
1 AGAAAAAAAACAAA
*
503884 A-CAAAAAAACAAAA
1 AGAAAAAAAAC-AAA
503898 AGAAAAAAAACAA
1 AGAAAAAAAACAA
503911 CAAAAAGGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 8 0.35
14 7 0.30
15 8 0.35
ACGTcount: A:0.85, C:0.10, G:0.05, T:0.00
Consensus pattern (14 bp):
AGAAAAAAAACAAA
Found at i:503907 original size:18 final size:19
Alignment explanation
Indices: 503875--503917 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
503865 GAAAGAGAAA
*
503875 AAAAACAAAACAAAAAAAC
1 AAAAAGAAAACAAAAAAAC
*
503894 AAAAAGAAAA-AAAACAAC
1 AAAAAGAAAACAAAAAAAC
503912 AAAAAG
1 AAAAAG
503918 GGTCCGGATG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 13 0.59
19 9 0.41
ACGTcount: A:0.84, C:0.12, G:0.05, T:0.00
Consensus pattern (19 bp):
AAAAAGAAAACAAAAAAAC
Found at i:504993 original size:37 final size:37
Alignment explanation
Indices: 504943--505023 Score: 144
Period size: 37 Copynumber: 2.2 Consensus size: 37
504933 ACAATCATGA
*
504943 ATTTGTGACATTCATAACATTTCTTTTTGCAGGATGC
1 ATTTGTGACATTCATAACATTTCATTTTGCAGGATGC
*
504980 ATTTGTGACATTCATAACATTTCATTTTGCATGATGC
1 ATTTGTGACATTCATAACATTTCATTTTGCAGGATGC
505017 ATTTGTG
1 ATTTGTG
505024 CTTCATCTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 42 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.44
Consensus pattern (37 bp):
ATTTGTGACATTCATAACATTTCATTTTGCAGGATGC
Done.