Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr9
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 48574783
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2023350 characters in sequence are not A, C, G, or T
File 2 of 135
Found at i:240593 original size:16 final size:16
Alignment explanation
Indices: 240569--240609 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
240559 TGTTTTATGT
240569 ATATAATAATAATATA
1 ATATAATAATAATATA
*
240585 ATATTATAATAATATA
1 ATATAATAATAATATA
240601 ATATAATAA
1 ATATAATAA
240610 CTTACTTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
ATATAATAATAATATA
Found at i:240609 original size:8 final size:8
Alignment explanation
Indices: 240574--240603 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
240564 TATGTATATA
240574 ATAATAAT
1 ATAATAAT
*
240582 ATAATATT
1 ATAATAAT
240590 ATAATAAT
1 ATAATAAT
240598 ATAATA
1 ATAATA
240604 TAATAACTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (8 bp):
ATAATAAT
Found at i:243217 original size:26 final size:28
Alignment explanation
Indices: 243188--243248 Score: 101
Period size: 26 Copynumber: 2.3 Consensus size: 28
243178 TTTTTTTGGT
243188 ATATTTTGA-TAAATAAAAAAA-TTATA
1 ATATTTTGAGTAAATAAAAAAAGTTATA
243214 ATATTTT-AGTAAATAAAAAAAGTTATA
1 ATATTTTGAGTAAATAAAAAAAGTTATA
243241 ATATTTTG
1 ATATTTTG
243249 GTTATTTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
25 1 0.03
26 19 0.59
27 12 0.38
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (28 bp):
ATATTTTGAGTAAATAAAAAAAGTTATA
Found at i:262156 original size:6 final size:6
Alignment explanation
Indices: 262142--262176 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
262132 ATTATTGAGT
*
262142 GAGGGG GAGGCG GAGGCG GAGGCG GAAGGCG GAGG
1 GAGGCG GAGGCG GAGGCG GAGGCG G-AGGCG GAGG
262177 GAGGAAAGCA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
6 21 0.78
7 6 0.22
ACGTcount: A:0.20, C:0.11, G:0.69, T:0.00
Consensus pattern (6 bp):
GAGGCG
Found at i:275931 original size:13 final size:13
Alignment explanation
Indices: 275915--275941 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
275905 TAAAAAATAA
275915 ATATTTATTATAT
1 ATATTTATTATAT
275928 ATATTTATTATAT
1 ATATTTATTATAT
275941 A
1 A
275942 AGTACTAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
ATATTTATTATAT
Found at i:277258 original size:70 final size:71
Alignment explanation
Indices: 277184--277318 Score: 229
Period size: 70 Copynumber: 1.9 Consensus size: 71
277174 AATTAATCTC
* *
277184 ATTTTATTACATCAAATAATATCAAAA-TAACTCAAAAAAA-TTTCTATTTTATTACGTCAAATA
1 ATTTTATTACATCAAATAATATCAAAATTAA-TCAAAAAAATTTTCTATTTTATTACATAAAATA
277247 AACTTCT
65 AACTTCT
277254 ATTTTATTACATCAAATAATATCAAAATTAATCAAAAAAATTTTCTATTTTATTACATAAAATAA
1 ATTTTATTACATCAAATAATATCAAAATTAATCAAAAAAATTTTCTATTTTATTACATAAAATAA
277319 TATCAAAATA
Statistics
Matches: 61, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
70 36 0.59
71 25 0.41
ACGTcount: A:0.48, C:0.12, G:0.01, T:0.39
Consensus pattern (71 bp):
ATTTTATTACATCAAATAATATCAAAATTAATCAAAAAAATTTTCTATTTTATTACATAAAATAA
ACTTCT
Found at i:277270 original size:25 final size:25
Alignment explanation
Indices: 277215--277272 Score: 89
Period size: 25 Copynumber: 2.3 Consensus size: 25
277205 TCAAAATAAC
* * *
277215 TCAAAAAAATTTCTATTTTATTACG
1 TCAAATAAACTTCTATTTTATTACA
277240 TCAAATAAACTTCTATTTTATTACA
1 TCAAATAAACTTCTATTTTATTACA
277265 TCAAATAA
1 TCAAATAA
277273 TATCAAAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.43, C:0.14, G:0.02, T:0.41
Consensus pattern (25 bp):
TCAAATAAACTTCTATTTTATTACA
Found at i:277308 original size:25 final size:25
Alignment explanation
Indices: 277215--277315 Score: 88
Period size: 25 Copynumber: 4.2 Consensus size: 25
277205 TCAAAATAAC
*
277215 TCAAAAAAATTTCTATTTTATTACG
1 TCAAAAAAATTTCTATTTTATTACA
* *
277240 TCAAATAAACTTCTATTTTATTACA
1 TCAAAAAAATTTCTATTTTATTACA
* * **
277265 TC-AAATAATATC-A--AAATTA-A
1 TCAAAAAAATTTCTATTTTATTACA
277285 TCAAAAAAATTTTCTATTTTATTACA
1 TCAAAAAAA-TTTCTATTTTATTACA
277311 T-AAAA
1 TCAAAA
277316 TAATATCAAA
Statistics
Matches: 57, Mismatches: 13, Indels: 12
0.70 0.16 0.15
Matches are distributed among these distances:
20 3 0.05
21 9 0.16
22 3 0.05
23 2 0.04
24 6 0.11
25 32 0.56
26 2 0.04
ACGTcount: A:0.47, C:0.12, G:0.01, T:0.41
Consensus pattern (25 bp):
TCAAAAAAATTTCTATTTTATTACA
Found at i:277502 original size:21 final size:21
Alignment explanation
Indices: 277461--277505 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
277451 GACGGTTGTT
*
277461 GTTCCTCCGGTAGGGATTCTG
1 GTTCCTCCGGTAGGCATTCTG
*
277482 GTTCTTCCGGTACGGCA-TCTG
1 GTTCCTCCGGTA-GGCATTCTG
277503 GTT
1 GTT
277506 GTCAGACTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 18 0.86
22 3 0.14
ACGTcount: A:0.09, C:0.24, G:0.31, T:0.36
Consensus pattern (21 bp):
GTTCCTCCGGTAGGCATTCTG
Found at i:281417 original size:20 final size:20
Alignment explanation
Indices: 281380--281417 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
281370 TTTATTTTTA
*
281380 AAAATCTACATAATAATTGT
1 AAAATCTACATAAAAATTGT
281400 AAAATCTA-ATATAAAATT
1 AAAATCTACATA-AAAATT
281418 TACCTCGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.55, C:0.08, G:0.03, T:0.34
Consensus pattern (20 bp):
AAAATCTACATAAAAATTGT
Found at i:282375 original size:11 final size:11
Alignment explanation
Indices: 282361--282437 Score: 72
Period size: 11 Copynumber: 6.9 Consensus size: 11
282351 TTAAATATGG
282361 ATTTGAGAGAA
1 ATTTGAGAGAA
*
282372 ATTTG-GAAGGA
1 ATTTGAG-AGAA
282383 ATTTGAGAGCAA
1 ATTTGAGAG-AA
282395 A-TTGAGAGGAA
1 ATTTGAGA-GAA
282406 ATTT-AGAGGAA
1 ATTTGAGA-GAA
282417 A-TTGAGAGGAA
1 ATTTGAGA-GAA
282428 ATTTGAGAGA
1 ATTTGAGAGA
282438 GGATTAGTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 14
0.78 0.03 0.19
Matches are distributed among these distances:
10 3 0.05
11 42 0.74
12 12 0.21
ACGTcount: A:0.43, C:0.01, G:0.31, T:0.25
Consensus pattern (11 bp):
ATTTGAGAGAA
Found at i:282386 original size:22 final size:22
Alignment explanation
Indices: 282361--282437 Score: 97
Period size: 22 Copynumber: 3.5 Consensus size: 22
282351 TTAAATATGG
282361 ATTTGAGAGAAATTTG-GAAGG-A
1 ATTTGAGAGAAA-TTGAG-AGGAA
282383 ATTTGAGAGCAAATTGAGAGGAA
1 ATTTGAGAG-AAATTGAGAGGAA
282406 ATTT-AGAGGAAATTGAGAGGAA
1 ATTTGAGA-GAAATTGAGAGGAA
282428 ATTTGAGAGA
1 ATTTGAGAGA
282438 GGATTAGTTT
Statistics
Matches: 50, Mismatches: 0, Indels: 10
0.83 0.00 0.17
Matches are distributed among these distances:
22 37 0.74
23 13 0.26
ACGTcount: A:0.43, C:0.01, G:0.31, T:0.25
Consensus pattern (22 bp):
ATTTGAGAGAAATTGAGAGGAA
Found at i:282416 original size:33 final size:35
Alignment explanation
Indices: 282361--282436 Score: 104
Period size: 33 Copynumber: 2.3 Consensus size: 35
282351 TTAAATATGG
* *
282361 ATTTGAGA-GAAATTTGGAAGGAATTTGAGAGCAA
1 ATTTGAGAGGAAATTTAGAAGGAAATTGAGAGCAA
*
282395 A-TTGAGAGGAAATTTAG-AGGAAATTGAGAGGAA
1 ATTTGAGAGGAAATTTAGAAGGAAATTGAGAGCAA
282428 ATTTGAGAG
1 ATTTGAGAG
282437 AGGATTAGTT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
33 21 0.57
34 16 0.43
ACGTcount: A:0.42, C:0.01, G:0.32, T:0.25
Consensus pattern (35 bp):
ATTTGAGAGGAAATTTAGAAGGAAATTGAGAGCAA
Found at i:289380 original size:7 final size:7
Alignment explanation
Indices: 289368--289392 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
289358 GCTGCTTGCT
289368 TTTTGGC
1 TTTTGGC
289375 TTTTGGC
1 TTTTGGC
289382 TTTTGGC
1 TTTTGGC
289389 TTTT
1 TTTT
289393 AGGATCAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.12, G:0.24, T:0.64
Consensus pattern (7 bp):
TTTTGGC
Found at i:290134 original size:21 final size:21
Alignment explanation
Indices: 290110--290151 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
290100 TTGCCGAAAG
*
290110 ATTAAATGAAAGCCGGGTAAT
1 ATTAAATGAAAGCCGGCTAAT
290131 ATTAAATGAAAGCCGGCTAAT
1 ATTAAATGAAAGCCGGCTAAT
290152 CACCTATTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.43, C:0.12, G:0.21, T:0.24
Consensus pattern (21 bp):
ATTAAATGAAAGCCGGCTAAT
Found at i:295672 original size:104 final size:105
Alignment explanation
Indices: 295539--295747 Score: 411
Period size: 104 Copynumber: 2.0 Consensus size: 105
295529 TCCATGGGGA
295539 ACAAATTAAAGAACTTTTGGGCACGTGCATATCAATTCATATAATTTGAATGGGTTACAAAAAAA
1 ACAAATTAAAGAACTTTTGGGCACGTGCATATCAATTCATATAATTTGAATGGGTTACAAAAAAA
295604 AAAAGGCAAGTCAAAAGAGGGGGGCAACATTAGCTTTACT
66 AAAAGGCAAGTCAAAAGAGGGGGGCAACATTAGCTTTACT
295644 ACAAATTAAA-AACTTTTGGGCACGTGCATATCAATTCATATAATTTGAATGGGTTACAAAAAAA
1 ACAAATTAAAGAACTTTTGGGCACGTGCATATCAATTCATATAATTTGAATGGGTTACAAAAAAA
295708 AAAAGGCAAGTCAAAAGAGGGGGGCAACATTAGCTTTACT
66 AAAAGGCAAGTCAAAAGAGGGGGGCAACATTAGCTTTACT
295748 TGCATTTGGA
Statistics
Matches: 104, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
104 94 0.90
105 10 0.10
ACGTcount: A:0.42, C:0.13, G:0.20, T:0.25
Consensus pattern (105 bp):
ACAAATTAAAGAACTTTTGGGCACGTGCATATCAATTCATATAATTTGAATGGGTTACAAAAAAA
AAAAGGCAAGTCAAAAGAGGGGGGCAACATTAGCTTTACT
Found at i:302806 original size:6 final size:6
Alignment explanation
Indices: 302795--302822 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
302785 GTACAATAAT
302795 CTACAC CTACAC CTACAC CTACAC CTAC
1 CTACAC CTACAC CTACAC CTACAC CTAC
302823 TAGTGGGTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.32, C:0.50, G:0.00, T:0.18
Consensus pattern (6 bp):
CTACAC
Found at i:303687 original size:19 final size:19
Alignment explanation
Indices: 303663--303701 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
303653 AATATTTTCT
*
303663 AGTAAATCATTTTACAGAA
1 AGTAAAACATTTTACAGAA
*
303682 AGTAAAACATTTTCCAGAA
1 AGTAAAACATTTTACAGAA
303701 A
1 A
303702 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.49, C:0.13, G:0.10, T:0.28
Consensus pattern (19 bp):
AGTAAAACATTTTACAGAA
Found at i:303704 original size:33 final size:34
Alignment explanation
Indices: 303651--303715 Score: 96
Period size: 33 Copynumber: 1.9 Consensus size: 34
303641 CAAACAGCAG
* *
303651 AAAATATTTTCTAGTAAATCATTTTACAGAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAGT
*
303685 AAAACATTTTCCAG-AAATCATTTTACGGAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAA
303716 ACATTTTACT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 16 0.57
34 12 0.43
ACGTcount: A:0.45, C:0.12, G:0.09, T:0.34
Consensus pattern (34 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAGT
Found at i:303708 original size:14 final size:14
Alignment explanation
Indices: 303685--303724 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
303675 TACAGAAAGT
*
303685 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
303699 AAATCATTTTACGG
1 AAAACATTTTACAG
303713 AAAACATTTTAC
1 AAAACATTTTAC
303725 TGGCAATCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:310331 original size:48 final size:48
Alignment explanation
Indices: 310273--310420 Score: 278
Period size: 48 Copynumber: 3.1 Consensus size: 48
310263 CACCTCGGCT
*
310273 TCTTTTATCCCTATCATGATCATCATCACTTTCAGTTCTCCGGTGCCA
1 TCTTCTATCCCTATCATGATCATCATCACTTTCAGTTCTCCGGTGCCA
310321 TCTTCTATCCCTATCATGATCATCATCACTTTCAGTTCTCCGGTGCCA
1 TCTTCTATCCCTATCATGATCATCATCACTTTCAGTTCTCCGGTGCCA
310369 TCTTCTATCCCTATCATGATCATCATCACTTTCAGTTCTCCGGTGCCTA
1 TCTTCTATCCCTATCATGATCATCATCACTTTCAGTTCTCCGGTGCC-A
310418 TCT
1 TCT
310421 GTCCGTTCTT
Statistics
Matches: 98, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
48 94 0.96
49 4 0.04
ACGTcount: A:0.18, C:0.32, G:0.10, T:0.39
Consensus pattern (48 bp):
TCTTCTATCCCTATCATGATCATCATCACTTTCAGTTCTCCGGTGCCA
Found at i:325610 original size:24 final size:23
Alignment explanation
Indices: 325583--325627 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
325573 GCCAAATGGA
* *
325583 GGATAGCGATGAAGATGATGAAGC
1 GGATAACGAGGAAGAT-ATGAAGC
325607 GGATAACGAGGAAGATATGAA
1 GGATAACGAGGAAGATATGAA
325628 AGAAAGTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.42, C:0.07, G:0.36, T:0.16
Consensus pattern (23 bp):
GGATAACGAGGAAGATATGAAGC
Found at i:325712 original size:22 final size:24
Alignment explanation
Indices: 325687--325733 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 24
325677 ATTATTTTAA
325687 ATTAT-ATTTTA-TAATATT-ATAT
1 ATTATGATTTTAGTAA-ATTCATAT
325709 ATTATGATTTTAGTAAATTCATAT
1 ATTATGATTTTAGTAAATTCATAT
325733 A
1 A
325734 AGAATATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 5 0.23
23 9 0.41
24 8 0.36
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.53
Consensus pattern (24 bp):
ATTATGATTTTAGTAAATTCATAT
Found at i:326064 original size:16 final size:16
Alignment explanation
Indices: 326045--326090 Score: 65
Period size: 16 Copynumber: 2.9 Consensus size: 16
326035 CTATTAGGCC
*
326045 TCTATTCCATTACGCA
1 TCTATTCCATTACACA
* *
326061 TCTATTCTATTACACC
1 TCTATTCCATTACACA
326077 TCTATTCCATTACA
1 TCTATTCCATTACA
326091 GCGAACCAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.26, C:0.30, G:0.02, T:0.41
Consensus pattern (16 bp):
TCTATTCCATTACACA
Found at i:327034 original size:8 final size:8
Alignment explanation
Indices: 327021--327045 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
327011 AGATCTAAAC
327021 AGGCAGTA
1 AGGCAGTA
327029 AGGCAGTA
1 AGGCAGTA
327037 AGGCAGTA
1 AGGCAGTA
327045 A
1 A
327046 AGGAGCTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.40, C:0.12, G:0.36, T:0.12
Consensus pattern (8 bp):
AGGCAGTA
Found at i:328302 original size:123 final size:123
Alignment explanation
Indices: 328078--328302 Score: 378
Period size: 123 Copynumber: 1.8 Consensus size: 123
328068 CTATTTCGAG
* *
328078 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTGGAGAAGAATTTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTGGAGAAGAAATTATG
* *
328143 AAATCGCGCCCTCGTGGACGTGATTTTGTTACAGTAGGTCATGTAAGAAATATTTTTT
66 AAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATATTTTTT
* * *
328201 TTGACGTTTCTGAGCAAATAGTATAAAATTGCTTCTACCAGGATGTTATTTGAGAAGAAATTATG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTGGAGAAGAAATTATG
*
328266 AAATCGCGCCCTCGTGGACGCGATTTTGCTATAGTAG
66 AAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAG
328303 CAAGTTTGGG
Statistics
Matches: 94, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
123 94 1.00
ACGTcount: A:0.29, C:0.15, G:0.23, T:0.33
Consensus pattern (123 bp):
TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTGGAGAAGAAATTATG
AAATCGCGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATATTTTTT
Found at i:331613 original size:55 final size:54
Alignment explanation
Indices: 331478--331657 Score: 229
Period size: 55 Copynumber: 3.2 Consensus size: 54
331468 ATGTAAAATT
* * * *
331478 AAAATTATTAAGTCAAAAATTTGTGTTAATGGTTATTAAAATTATCATGCACA-CA-GT
1 AAAATTATTAAGT-AAAAAATTGTGTTAATGGTTAGTAAAATTATCA---A-ATTATGA
*
331535 AAAATTATTAAGTCAAAAAATTGTGTTAATGATTAGTAAAATTATCAAATTATGA
1 AAAATTATTAAGT-AAAAAATTGTGTTAATGGTTAGTAAAATTATCAAATTATGA
*
331590 AAAATTATTAAGTGTAAAAATTGTGTTAATGGTTAGTAAAATTATCAAATTATGA
1 AAAATTATTAAGT-AAAAAATTGTGTTAATGGTTAGTAAAATTATCAAATTATGA
331645 AAAATTATTAAGT
1 AAAATTATTAAGT
331658 TAGGTTAGGG
Statistics
Matches: 113, Mismatches: 8, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
53 1 0.01
54 2 0.02
55 66 0.58
57 44 0.39
ACGTcount: A:0.46, C:0.04, G:0.12, T:0.37
Consensus pattern (54 bp):
AAAATTATTAAGTAAAAAATTGTGTTAATGGTTAGTAAAATTATCAAATTATGA
Found at i:331685 original size:24 final size:25
Alignment explanation
Indices: 331652--331699 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 25
331642 TGAAAAATTA
331652 TTAAGTTAGGTTAGGGTTAGGGTTT
1 TTAAGTTAGGTTAGGGTTAGGGTTT
*
331677 TTAA-TTAGGTTAGGGTTATGGTT
1 TTAAGTTAGGTTAGGGTTAGGGTT
331700 AGGGTTTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 18 0.82
25 4 0.18
ACGTcount: A:0.21, C:0.00, G:0.33, T:0.46
Consensus pattern (25 bp):
TTAAGTTAGGTTAGGGTTAGGGTTT
Found at i:331707 original size:29 final size:29
Alignment explanation
Indices: 331651--331936 Score: 351
Period size: 29 Copynumber: 9.7 Consensus size: 29
331641 ATGAAAAATT
331651 ATTAAGTTAGGTTAGGGTTAGGGTTTTTA
1 ATTAAGTTAGGTTAGGGTTAGGGTTTTTA
* *
331680 ATTAGGTTAGGGTTATGGTTAGGGTTTTTA
1 ATTAAGTTA-GGTTAGGGTTAGGGTTTTTA
*
331710 ATTAAATTAGGTT-GGAGTTAGGGTTTTTA
1 ATTAAGTTAGGTTAGG-GTTAGGGTTTTTA
* ** *
331739 AATGGGTTATGTTAGGGTTAGGGTTTTTA
1 ATTAAGTTAGGTTAGGGTTAGGGTTTTTA
* * *
331768 ATTAATTTAGGTTAGGGTTAAGGTTTGTA
1 ATTAAGTTAGGTTAGGGTTAGGGTTTTTA
*
331797 ATTAAATTAGGTTAGGGTTAGGGTTTTTTA
1 ATTAAGTTAGGTTAGGGTTAGGG-TTTTTA
*
331827 ATTAAGTTAGGTTAGGGTTAGTGTTTTTA
1 ATTAAGTTAGGTTAGGGTTAGGGTTTTTA
*
331856 ATTAAATTAGGTT-GGAGTTAGGGTTTTTA
1 ATTAAGTTAGGTTAGG-GTTAGGGTTTTTA
*
331885 ATTAGGGTTTAGGTTAGGGTTAGGGTTTTTA
1 ATTA-AG-TTAGGTTAGGGTTAGGGTTTTTA
*
331916 ATTAGGGTTTAGGTTAGGGTT
1 ATTA-AG-TTAGGTTAGGGTT
331937 NNNNNNNNNN
Statistics
Matches: 223, Mismatches: 26, Indels: 14
0.85 0.10 0.05
Matches are distributed among these distances:
28 3 0.01
29 123 0.55
30 54 0.24
31 41 0.18
32 2 0.01
ACGTcount: A:0.24, C:0.00, G:0.31, T:0.45
Consensus pattern (29 bp):
ATTAAGTTAGGTTAGGGTTAGGGTTTTTA
Found at i:331720 original size:59 final size:58
Alignment explanation
Indices: 331651--331936 Score: 360
Period size: 59 Copynumber: 4.8 Consensus size: 58
331641 ATGAAAAATT
*
331651 ATTAAGTTAGGTTAGGGTTAGGGTTTTTAATTAGGTTAGGGTTATGGTTAGGGTTTTTA
1 ATTAAGTTAGGTTAGGGTTAGGGTTTTTAATTAGGTTA-GGTTAGGGTTAGGGTTTTTA
* * * *
331710 ATTAAATTAGGTT-GGAGTTAGGGTTTTTAAATGGGTTATGTTAGGGTTAGGGTTTTTA
1 ATTAAGTTAGGTTAGG-GTTAGGGTTTTTAATTAGGTTAGGTTAGGGTTAGGGTTTTTA
* * * **
331768 ATTAATTTAGGTTAGGGTTAAGGTTTGTAATTAAATTAGGTTAGGGTTAGGGTTTTTTA
1 ATTAAGTTAGGTTAGGGTTAGGGTTTTTAATTAGGTTAGGTTAGGGTTAGGG-TTTTTA
* **
331827 ATTAAGTTAGGTTAGGGTTAGTGTTTTTAATTAAATTAGGTT-GGAGTTAGGGTTTTTA
1 ATTAAGTTAGGTTAGGGTTAGGGTTTTTAATTAGGTTAGGTTAGG-GTTAGGGTTTTTA
*
331885 ATTAGGGTTTAGGTTAGGGTTAGGGTTTTTAATTAGGGTTTAGGTTAGGGTT
1 ATTA-AG-TTAGGTTAGGGTTAGGGTTTTTAATTA-GG-TTAGGTTAGGGTT
331937 NNNNNNNNNN
Statistics
Matches: 197, Mismatches: 21, Indels: 15
0.85 0.09 0.06
Matches are distributed among these distances:
58 73 0.37
59 86 0.44
60 26 0.13
62 10 0.05
63 2 0.01
ACGTcount: A:0.24, C:0.00, G:0.31, T:0.45
Consensus pattern (58 bp):
ATTAAGTTAGGTTAGGGTTAGGGTTTTTAATTAGGTTAGGTTAGGGTTAGGGTTTTTA
Found at i:331757 original size:88 final size:87
Alignment explanation
Indices: 331656--331936 Score: 359
Period size: 88 Copynumber: 3.2 Consensus size: 87
331646 AAATTATTAA
** *
331656 GTTAGGTTAGGGTTAGGGTTTTTAATTAGGTTAGGGTTATGGTTAGGGTTTTTAATTAAATTAGG
1 GTTAGGTTAGGGTTAGGGTTTTTAATTAAATTA-GGTTAGGGTTAGGGTTTTTAATTAAATTAGG
*
331721 TT-GGAGTTAGGGTTTTTAAATGG
65 TTAGG-GTTAGGGTTTTTAATTGG
* * * *
331744 GTTATGTTAGGGTTAGGGTTTTTAATTAATTTAGGTTAGGGTTAAGGTTTGTAATTAAATTAGGT
1 GTTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGT
**
331809 TAGGGTTAGGGTTTTTTAATTAA
66 TAGGGTTAGGG-TTTTTAATTGG
* **
331832 GTTAGGTTAGGGTTAGTGTTTTTAATTAAATTAGGTT-GGAGTTAGGGTTTTTAATTAGGGTTTA
1 GTTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGG-GTTAGGGTTTTTAATTA--AATTA
331896 GGTTAGGGTTAGGGTTTTTAATTAGG
63 GGTTAGGGTTAGGGTTTTTAATT-GG
331922 GTTTAGGTTAGGGTT
1 G-TTAGGTTAGGGTT
331937 NNNNNNNNNN
Statistics
Matches: 168, Mismatches: 18, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
87 39 0.23
88 89 0.53
89 9 0.05
90 18 0.11
91 13 0.08
ACGTcount: A:0.23, C:0.00, G:0.31, T:0.46
Consensus pattern (87 bp):
GTTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGT
TAGGGTTAGGGTTTTTAATTGG
Found at i:331891 original size:13 final size:13
Alignment explanation
Indices: 331873--331925 Score: 52
Period size: 13 Copynumber: 3.7 Consensus size: 13
331863 TAGGTTGGAG
331873 TTAGGGTTTTTAA
1 TTAGGGTTTTTAA
*
331886 TTAGGGTTTAGGTTAGGG
1 TTAGGGTTT---TTA--A
331904 TTAGGGTTTTTAA
1 TTAGGGTTTTTAA
331917 TTAGGGTTT
1 TTAGGGTTT
331926 AGGTTAGGGT
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
13 18 0.55
15 3 0.09
16 3 0.09
18 9 0.27
ACGTcount: A:0.19, C:0.00, G:0.32, T:0.49
Consensus pattern (13 bp):
TTAGGGTTTTTAA
Found at i:334090 original size:307 final size:307
Alignment explanation
Indices: 333536--334147 Score: 999
Period size: 307 Copynumber: 2.0 Consensus size: 307
333526 TCTCCTCGGT
* * * *
333536 CGCGTCGCCCCACACATCTCCCGATACAACGTTGCCAAGATAGCAGACCCCTAACTAAACTCATC
1 CGCGTCGCCCCACACATCTCCCGATACAACATTGCCAAGACAGCAGACCCCCAACTAAACTCACC
333601 GGCTTCTCTAAAATCTACCAATTTCAAGAGCCATCTTAGATGTACGCGGCTCCGTGACGTGTCGG
66 GGCTTCTCTAAAATCTACCAATTTCAAGAGCCATCTTAGATGTACGCGGCTCCGTGACGTGTCGG
* ** *
333666 GCATCAGATAACCTCCAATTATTTGAAGAGTGTATGCCCGAGCATATCGGATTCTTTCAATTTCG
131 GCATCAGATAACCTCCAATTATTTGAAGAATGTATGCCCGAGCATATCAAATTCTTTAAATTTCG
* * * *
333731 GTTGAACCTTCATTCGGATCAGGGAATGTGTCACGTAACTAGCCTATCTCGATCTTACCTCCCTC
196 GTTGAACCTTCATCCGGATCAGAGAATGTGTCACGTAACCAGCCCATCTCGATCTTACCTCCCTC
* *
333796 CATTTTATCCGGAATAACGCCCAAAAGCTCATAGCACACCGCCTCTC
261 CATTTTATCCGGAATAACGCCCAAAAACTCATAACACACCGCCTCTC
* * *
333843 CGCGTCGCCCCGCACATCTCCCGATACAACATTGCCAAGACGGCAGACCCCCAACTAAATTCACC
1 CGCGTCGCCCCACACATCTCCCGATACAACATTGCCAAGACAGCAGACCCCCAACTAAACTCACC
* * * *
333908 GGCTTCTCTAAAATCTACGATTTTCAGGAGCCATCTTAGATGTACGCGGCTCCGTGATGTGTCGG
66 GGCTTCTCTAAAATCTACCAATTTCAAGAGCCATCTTAGATGTACGCGGCTCCGTGACGTGTCGG
333973 GCATCAGATAACCTCCAATTATTTGAAGAATGTATGCCCGAGCATATCAAATTCTTTAAATTTCG
131 GCATCAGATAACCTCCAATTATTTGAAGAATGTATGCCCGAGCATATCAAATTCTTTAAATTTCG
**
334038 GTTGAATTTTCATCCGGATCAGAGAATGTGTCACGTAACCAGCCCATCTCGATCTTACCTCCCTC
196 GTTGAACCTTCATCCGGATCAGAGAATGTGTCACGTAACCAGCCCATCTCGATCTTACCTCCCTC
* *
334103 CATTTTATCCGGAATAGCGCCCAAAAACTCGTAACACACCGCCTC
261 CATTTTATCCGGAATAACGCCCAAAAACTCATAACACACCGCCTC
334148 CCAATTGCTA
Statistics
Matches: 280, Mismatches: 25, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
307 280 1.00
ACGTcount: A:0.26, C:0.30, G:0.17, T:0.26
Consensus pattern (307 bp):
CGCGTCGCCCCACACATCTCCCGATACAACATTGCCAAGACAGCAGACCCCCAACTAAACTCACC
GGCTTCTCTAAAATCTACCAATTTCAAGAGCCATCTTAGATGTACGCGGCTCCGTGACGTGTCGG
GCATCAGATAACCTCCAATTATTTGAAGAATGTATGCCCGAGCATATCAAATTCTTTAAATTTCG
GTTGAACCTTCATCCGGATCAGAGAATGTGTCACGTAACCAGCCCATCTCGATCTTACCTCCCTC
CATTTTATCCGGAATAACGCCCAAAAACTCATAACACACCGCCTCTC
Found at i:337435 original size:30 final size:31
Alignment explanation
Indices: 337401--337458 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 31
337391 CCTTGACTTT
*
337401 AACTTTTTCAAAATTACAATTTT-ACCCTTA
1 AACTTTTACAAAATTACAATTTTGACCCTTA
* *
337431 AACTTTTACATAATTACATTTTTGACCC
1 AACTTTTACAAAATTACAATTTTGACCC
337459 AAGGCTCGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 20 0.83
31 4 0.17
ACGTcount: A:0.34, C:0.21, G:0.02, T:0.43
Consensus pattern (31 bp):
AACTTTTACAAAATTACAATTTTGACCCTTA
Found at i:338666 original size:51 final size:51
Alignment explanation
Indices: 338531--338654 Score: 171
Period size: 51 Copynumber: 2.4 Consensus size: 51
338521 TATTTTAAAA
* *
338531 AAGGAAATTGAGAGCAAATTGAAATTAAATATGGATTTGAGAGATTTTTGG
1 AAGGAAATTGAGAGAAAATTGAAATTAAATATGAATTTGAGAGATTTTTGG
* * *
338582 AATGAAATTGAAAGGAAATTGAAATTAAATATGAATTT-ATGAGAATTTTT-G
1 AAGGAAATTGAGAGAAAATTGAAATTAAATATGAATTTGA-GAG-ATTTTTGG
338633 AAGGAAATTGAGAGAAAATTGA
1 AAGGAAATTGAGAGAAAATTGA
338655 GAGGAAATAT
Statistics
Matches: 64, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
50 1 0.02
51 57 0.89
52 6 0.09
ACGTcount: A:0.46, C:0.01, G:0.23, T:0.31
Consensus pattern (51 bp):
AAGGAAATTGAGAGAAAATTGAAATTAAATATGAATTTGAGAGATTTTTGG
Found at i:338667 original size:12 final size:11
Alignment explanation
Indices: 338630--338669 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
338620 ATGAGAATTT
338630 TTGA-AGGAAA
1 TTGAGAGGAAA
*
338640 TTGAGAGAAAA
1 TTGAGAGGAAA
338651 TTGAGAGGAAA
1 TTGAGAGGAAA
338662 TATGAGAG
1 T-TGAGAG
338670 AGGATTTGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
10 4 0.15
11 16 0.62
12 6 0.23
ACGTcount: A:0.47, C:0.00, G:0.33, T:0.20
Consensus pattern (11 bp):
TTGAGAGGAAA
Found at i:339051 original size:102 final size:101
Alignment explanation
Indices: 338853--339056 Score: 329
Period size: 101 Copynumber: 2.0 Consensus size: 101
338843 ATTTTTATCA
* * *
338853 TTTTATTTTACCCTTTTCACTATTCATCATTTTTTACTCGTAAAATATTTTTTATTTAAATCTTT
1 TTTTATTTCACCCTTTTCACTATTCATCATTTTTTACTCGTAAAAAATTTTCTATTTAAATCTTT
338918 TAAAAAGTTTAAAATAATAAAAATAAAATTATATTT
66 TAAAAAGTTTAAAATAATAAAAATAAAATTATATTT
338954 TTTTATTTCACCCTTTTCACTATTCATCATTTTTTACTCGTAAAAAAGTTTTCTATTTAAATCTT
1 TTTTATTTCACCCTTTTCACTATTCATCATTTTTTACTCGTAAAAAA-TTTTCTATTTAAATCTT
* * *
339019 TTAAAGA-TTTTAAATGGATAAAAATAAAATTATATTT
65 TTAAAAAGTTTAAAAT-AATAAAAATAAAATTATATTT
339056 T
1 T
339057 AATTTCACTA
Statistics
Matches: 95, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
101 52 0.55
102 43 0.45
ACGTcount: A:0.36, C:0.11, G:0.03, T:0.50
Consensus pattern (101 bp):
TTTTATTTCACCCTTTTCACTATTCATCATTTTTTACTCGTAAAAAATTTTCTATTTAAATCTTT
TAAAAAGTTTAAAATAATAAAAATAAAATTATATTT
Found at i:349739 original size:163 final size:163
Alignment explanation
Indices: 349469--349795 Score: 645
Period size: 163 Copynumber: 2.0 Consensus size: 163
349459 CAGGGATCAC
349469 TGCAATGCCTTATCACTCACATGCACCCAAAGTATCCCCAAAACAGACAAACCTAATTATCATCA
1 TGCAATGCCTTATCACTCACATGCACCCAAAGTATCCCCAAAACAGACAAACCTAATTATCATCA
349534 TACAAATTCTAAATATCTATAGGATTCAAATTTATATCAGTCAATTAGAAGTAATATTAAATTCC
66 TACAAATTCTAAATATCTATAGGATTCAAATTTATATCAGTCAATTAGAAGTAATATTAAATTCC
*
349599 TTTCAAACATAGGACGACACAATTAATGCTATA
131 TTTCAAACATAGGACAACACAATTAATGCTATA
349632 TGCAATGCCTTATCACTCACATGCACCCAAAGTATCCCCAAAACAGACAAACCTAATTATCATCA
1 TGCAATGCCTTATCACTCACATGCACCCAAAGTATCCCCAAAACAGACAAACCTAATTATCATCA
349697 TACAAATTCTAAATATCTATAGGATTCAAATTTATATCAGTCAATTAGAAGTAATATTAAATTCC
66 TACAAATTCTAAATATCTATAGGATTCAAATTTATATCAGTCAATTAGAAGTAATATTAAATTCC
349762 TTTCAAACATAGGACAACACAATTAATGCTATA
131 TTTCAAACATAGGACAACACAATTAATGCTATA
349795 T
1 T
349796 TTGAACTGAA
Statistics
Matches: 163, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
163 163 1.00
ACGTcount: A:0.41, C:0.21, G:0.08, T:0.29
Consensus pattern (163 bp):
TGCAATGCCTTATCACTCACATGCACCCAAAGTATCCCCAAAACAGACAAACCTAATTATCATCA
TACAAATTCTAAATATCTATAGGATTCAAATTTATATCAGTCAATTAGAAGTAATATTAAATTCC
TTTCAAACATAGGACAACACAATTAATGCTATA
Found at i:355621 original size:94 final size:95
Alignment explanation
Indices: 355495--355694 Score: 217
Period size: 95 Copynumber: 2.1 Consensus size: 95
355485 GTTTGTCAAT
* * * * * * * **
355495 TAAATTAATTAAAAAATTTTCAAAACTGGATTA-GTTTTCGTGTTTATTATTTTTAAGAAAAAAT
1 TAAATTAATTAAAAAAATTTAAAAACTAGATTAGGATTTAGAGTTAAGGATTTTTAAGAAAAAAT
* * *
355559 CAATTAAATT-AGAGTTTAGGGTTACTTGAG
66 CAAATAAATTAAG-GTTCAGGGTTACTAGAG
** * *
355589 TACTTTAATTAAAAAAATTTAAAAA-TCAGATTAGGATTTAGAGTTAAGGGTTTTTAAGGAAAAA
1 TAAATTAATTAAAAAAATTTAAAAACT-AGATTAGGATTTAGAGTTAAGGATTTTTAAGAAAAAA
355653 TCAAATAAATTAAGGTTCAGGGTTACTAGAG
65 TCAAATAAATTAAGGTTCAGGGTTACTAGAG
355684 TAAATTAATTA
1 TAAATTAATTA
355695 TAAATTTATA
Statistics
Matches: 85, Mismatches: 18, Indels: 5
0.79 0.17 0.05
Matches are distributed among these distances:
93 1 0.01
94 26 0.31
95 56 0.66
96 2 0.02
ACGTcount: A:0.42, C:0.05, G:0.15, T:0.38
Consensus pattern (95 bp):
TAAATTAATTAAAAAAATTTAAAAACTAGATTAGGATTTAGAGTTAAGGATTTTTAAGAAAAAAT
CAAATAAATTAAGGTTCAGGGTTACTAGAG
Found at i:355817 original size:48 final size:48
Alignment explanation
Indices: 355757--355873 Score: 164
Period size: 48 Copynumber: 2.4 Consensus size: 48
355747 TATTTAAAAG
* *
355757 AATTTCTATTATATTAAAAATTGCCTTATTTAAAACGTTATTGTAAAAA
1 AATTTCGATTATATTAAAAATTACCTTATTTAAAACGTTATTGT-AAAA
** *
355806 AATTT-GATTATAAAAAAAATTACCTTATTTAAAACGTTATTGTAAAG
1 AATTTCGATTATATTAAAAATTACCTTATTTAAAACGTTATTGTAAAA
*
355853 AATTTCGACTATATTAAAAAT
1 AATTTCGATTATATTAAAAAT
355874 ATTAAAGTAA
Statistics
Matches: 59, Mismatches: 8, Indels: 3
0.84 0.11 0.04
Matches are distributed among these distances:
47 8 0.14
48 46 0.78
49 5 0.08
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.40
Consensus pattern (48 bp):
AATTTCGATTATATTAAAAATTACCTTATTTAAAACGTTATTGTAAAA
Found at i:356466 original size:18 final size:18
Alignment explanation
Indices: 356440--356482 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
356430 GACTCGAAAA
* * *
356440 AGGAAACATATAAGGGTT
1 AGGATACATAAAAGGGCT
356458 AGGATACATAAAAGGGCT
1 AGGATACATAAAAGGGCT
356476 AGGATAC
1 AGGATAC
356483 GCACCTGGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.44, C:0.09, G:0.28, T:0.19
Consensus pattern (18 bp):
AGGATACATAAAAGGGCT
Found at i:358318 original size:11 final size:11
Alignment explanation
Indices: 358302--358343 Score: 59
Period size: 11 Copynumber: 3.9 Consensus size: 11
358292 AAATAAGGAT
358302 TTGAGAGAAAA
1 TTGAGAGAAAA
*
358313 TTGAGAGGAAA
1 TTGAGAGAAAA
*
358324 TTGAGAGGAAA
1 TTGAGAGAAAA
358335 TT-AGAGAAA
1 TTGAGAGAAA
358344 GGATTTATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
10 6 0.21
11 23 0.79
ACGTcount: A:0.50, C:0.00, G:0.31, T:0.19
Consensus pattern (11 bp):
TTGAGAGAAAA
Found at i:359050 original size:28 final size:29
Alignment explanation
Indices: 358996--359051 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 29
358986 TTATTTAAAG
* * *
358996 TATTTCAAAAATTATAAAAACATTTAATT
1 TATTTAAAAAATTACAAAAACAATTAATT
*
359025 TATTTAAAAAATT-CAAAAATAATTAAT
1 TATTTAAAAAATTACAAAAACAATTAAT
359052 AGTTATTTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
28 11 0.48
29 12 0.52
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.39
Consensus pattern (29 bp):
TATTTAAAAAATTACAAAAACAATTAATT
Found at i:375639 original size:33 final size:34
Alignment explanation
Indices: 375583--375659 Score: 95
Period size: 33 Copynumber: 2.3 Consensus size: 34
375573 TTAAATATGG
* *
375583 ATTTCAGAGAAATTTGGAAGGAAATTGAGAGCAA
1 ATTTGAGAGAAATTTAGAAGGAAATTGAGAGCAA
* *
375617 A-TTGAGAGCAAATTTAG-AGGAAATTTAGAGGAA
1 ATTTGAGAG-AAATTTAGAAGGAAATTGAGAGCAA
375650 ATTTGAGAGA
1 ATTTGAGAGA
375660 GGATTAGTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
33 22 0.59
34 15 0.41
ACGTcount: A:0.44, C:0.04, G:0.27, T:0.25
Consensus pattern (34 bp):
ATTTGAGAGAAATTTAGAAGGAAATTGAGAGCAA
Found at i:375662 original size:14 final size:11
Alignment explanation
Indices: 375591--375658 Score: 73
Period size: 11 Copynumber: 6.0 Consensus size: 11
375581 GGATTTCAGA
*
375591 GAAATTTGGAAG
1 GAAATTTAG-AG
*
375603 GAAATTGAGAG
1 GAAATTTAGAG
* *
375614 CAAATTGAGAG
1 GAAATTTAGAG
*
375625 CAAATTTAGAG
1 GAAATTTAGAG
375636 GAAATTTAGAG
1 GAAATTTAGAG
375647 GAAATTTGAGAG
1 GAAATTT-AGAG
375659 AGGATTAGTT
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
11 39 0.78
12 11 0.22
ACGTcount: A:0.44, C:0.03, G:0.29, T:0.24
Consensus pattern (11 bp):
GAAATTTAGAG
Found at i:391619 original size:7 final size:8
Alignment explanation
Indices: 391589--391618 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
391579 TTAGTCTTAT
391589 ATTTTTTA
1 ATTTTTTA
391597 ATTTTTTA
1 ATTTTTTA
391605 ATTTTTTA
1 ATTTTTTA
391613 ATTTTT
1 ATTTTT
391619 AGTCATCACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (8 bp):
ATTTTTTA
Found at i:394352 original size:31 final size:31
Alignment explanation
Indices: 394310--394382 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 31
394300 ATCAAATGCT
*
394310 CAAATC-AATTCGGTAATATATATCCATATA
1 CAAATCAAATTCGGCAATATATATCCATATA
* * * *
394340 CGAATCAAATTCGGCAGTGTATATCTATATA
1 CAAATCAAATTCGGCAATATATATCCATATA
*
394371 CAAATAAAATTC
1 CAAATCAAATTC
394383 TACAATGTAT
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
30 5 0.14
31 30 0.86
ACGTcount: A:0.42, C:0.16, G:0.10, T:0.32
Consensus pattern (31 bp):
CAAATCAAATTCGGCAATATATATCCATATA
Found at i:394392 original size:31 final size:31
Alignment explanation
Indices: 394328--394393 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
394318 TTCGGTAATA
* * * *
394328 TATATCCATATACGAATCAAATTCGGCAGTG
1 TATATCCATATACAAATAAAATTCGACAATG
* *
394359 TATATCTATATACAAATAAAATTCTACAATG
1 TATATCCATATACAAATAAAATTCGACAATG
394390 TATA
1 TATA
394394 AAACATATAC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.42, C:0.15, G:0.09, T:0.33
Consensus pattern (31 bp):
TATATCCATATACAAATAAAATTCGACAATG
Found at i:397305 original size:11 final size:10
Alignment explanation
Indices: 397291--397335 Score: 54
Period size: 11 Copynumber: 4.3 Consensus size: 10
397281 TTTCTCCCTG
397291 TTTTGTTTCT
1 TTTTGTTTCT
397301 ATTTTGTTTCGT
1 -TTTTGTTTC-T
* *
397313 TTCTATTTCT
1 TTTTGTTTCT
397323 TTTTGTTTCT
1 TTTTGTTTCT
397333 TTT
1 TTT
397336 ATTTCTTATA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
10 12 0.41
11 16 0.55
12 1 0.03
ACGTcount: A:0.04, C:0.11, G:0.09, T:0.76
Consensus pattern (10 bp):
TTTTGTTTCT
Found at i:397330 original size:16 final size:16
Alignment explanation
Indices: 397289--397332 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
397279 TTTTTCTCCC
397289 TGTTTTGTTTCTATTT
1 TGTTTTGTTTCTATTT
*
397305 TGTTTCGTTTCTATTT
1 TGTTTTGTTTCTATTT
397321 CT-TTTTGTTTCT
1 -TGTTTTGTTTCT
397333 TTTATTTCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 24 0.96
17 1 0.04
ACGTcount: A:0.05, C:0.11, G:0.11, T:0.73
Consensus pattern (16 bp):
TGTTTTGTTTCTATTT
Found at i:397425 original size:30 final size:30
Alignment explanation
Indices: 397343--397425 Score: 75
Period size: 30 Copynumber: 2.8 Consensus size: 30
397333 TTTATTTCTT
*
397343 ATATTTACTT-AT-TATAATATATAATATA
1 ATATATACTTAATATATAATATATAATATA
* *
397371 ATATATACTTAATA-ATTAAGATATAATATT
1 ATATATACTTAATATA-TAATATATAATATA
* *
397401 GTA-ATATTGTAATATATAATATATA
1 ATATATACT-TAATATATAATATATA
397426 TTTTCAGCTT
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
28 9 0.20
29 7 0.16
30 27 0.61
31 1 0.02
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (30 bp):
ATATATACTTAATATATAATATATAATATA
Found at i:398945 original size:19 final size:19
Alignment explanation
Indices: 398905--398947 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
398895 GTTTTTTTCC
* *
398905 ATTTTGAATAATTTTTATA
1 ATTTTCAATAATTTTTAAA
398924 ATTTTCAAT-ATTTTTAGAA
1 ATTTTCAATAATTTTTA-AA
398943 ATTTT
1 ATTTT
398948 TCGTACTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.35, C:0.02, G:0.05, T:0.58
Consensus pattern (19 bp):
ATTTTCAATAATTTTTAAA
Found at i:416204 original size:30 final size:30
Alignment explanation
Indices: 416168--416233 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 30
416158 GACAGCTAAA
416168 GCTATCCTTGCCT-AGTCACATGTTAGAATT
1 GCTATCCTTGCCTGA-TCACATGTTAGAATT
*
416198 GCTATCCTTGCCTGATCGCATGTTAGAATT
1 GCTATCCTTGCCTGATCACATGTTAGAATT
*
416228 GTTATC
1 GCTATC
416234 TTAAAGTATT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
30 32 0.97
31 1 0.03
ACGTcount: A:0.21, C:0.23, G:0.18, T:0.38
Consensus pattern (30 bp):
GCTATCCTTGCCTGATCACATGTTAGAATT
Found at i:420943 original size:15 final size:15
Alignment explanation
Indices: 420923--420966 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
420913 GGTTAATAGG
*
420923 AAAGAAAAAAAGGGA
1 AAAGAAAAAAAGGAA
*
420938 AAAGAAAAGAAAAGAA
1 AAAGAAAA-AAAGGAA
420954 AAAGAAAGAAAAG
1 AAAGAAA-AAAAG
420967 AGACGAGACG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
15 8 0.33
16 15 0.62
17 1 0.04
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (15 bp):
AAAGAAAAAAAGGAA
Found at i:420967 original size:15 final size:15
Alignment explanation
Indices: 420923--420967 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 15
420913 GGTTAATAGG
*
420923 AAAGAAA-AAAAGGGA
1 AAAGAAAGAAAA-GAA
420938 AAAGAAAAGAAAAGAA
1 AAAG-AAAGAAAAGAA
420954 AAAGAAAGAAAAGA
1 AAAGAAAGAAAAGA
420968 GACGAGACGA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
15 14 0.52
16 9 0.33
17 4 0.15
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (15 bp):
AAAGAAAGAAAAGAA
Found at i:421219 original size:2 final size:2
Alignment explanation
Indices: 421212--421236 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
421202 CAGGTAGGTA
421212 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
421237 GGGTAGTAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:423141 original size:45 final size:45
Alignment explanation
Indices: 423086--423171 Score: 120
Period size: 45 Copynumber: 1.9 Consensus size: 45
423076 GCAGTAATAG
* *
423086 TAACAATATTCAACACACAAAGT-GCTGAATCTGTAACAGTAACGA
1 TAACAATATTCAACACACAAAGTATC-GAATCAGTAACAGTAACGA
* *
423131 TAACAGTATTCGACACACAAAGTATCGAATCAGTAACAGTA
1 TAACAATATTCAACACACAAAGTATCGAATCAGTAACAGTA
423172 GTCGGCACAT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
45 35 0.97
46 1 0.03
ACGTcount: A:0.44, C:0.20, G:0.14, T:0.22
Consensus pattern (45 bp):
TAACAATATTCAACACACAAAGTATCGAATCAGTAACAGTAACGA
Found at i:449173 original size:75 final size:76
Alignment explanation
Indices: 449049--449202 Score: 301
Period size: 75 Copynumber: 2.0 Consensus size: 76
449039 AAAGGTTTTC
449049 TTTGACTCAATCTTTTACCCGTGAATCAAGTGCATCATGTTTCTATTGATCAAACAAATTAAAAT
1 TTTGACTCAATCTTTTACCCGTGAATCAAGTGCATCATGTTTCTATTGATCAAACAAATTAAAAT
449114 AAAATAAAACA
66 AAAATAAAACA
449125 TTTGACTCAATC-TTTACCCGTGAATCAAGTGCATCATGTTTCTATTGATCAAACAAATTAAAAT
1 TTTGACTCAATCTTTTACCCGTGAATCAAGTGCATCATGTTTCTATTGATCAAACAAATTAAAAT
449189 AAAATAAAACA
66 AAAATAAAACA
449200 TTT
1 TTT
449203 ATTGGTTCAA
Statistics
Matches: 78, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
75 66 0.85
76 12 0.15
ACGTcount: A:0.40, C:0.17, G:0.09, T:0.34
Consensus pattern (76 bp):
TTTGACTCAATCTTTTACCCGTGAATCAAGTGCATCATGTTTCTATTGATCAAACAAATTAAAAT
AAAATAAAACA
Found at i:460081 original size:19 final size:20
Alignment explanation
Indices: 460036--460088 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
460026 TAGGTACGAT
*
460036 AATTTTTATAGTTCTTTTAC
1 AATTTTTATATTTCTTTTAC
*
460056 AAATTTTATATTTC-TTTAC
1 AATTTTTATATTTCTTTTAC
*
460075 ATTTTTTATTATTT
1 AATTTTTA-TATTT
460089 TCTTACGACT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 11 0.39
20 17 0.61
ACGTcount: A:0.26, C:0.08, G:0.02, T:0.64
Consensus pattern (20 bp):
AATTTTTATATTTCTTTTAC
Found at i:460225 original size:28 final size:28
Alignment explanation
Indices: 460151--460227 Score: 84
Period size: 27 Copynumber: 2.8 Consensus size: 28
460141 TGCTTTTTAG
* * *
460151 AATTTCTTTTTAATTTTTAATAAAATTA
1 AATTTTTTTTTTATTTTTATTAAAATTA
* * * *
460179 AATATTTCTTATA-TTTTATTAAAATTT
1 AATTTTTTTTTTATTTTTATTAAAATTA
460206 AATTTTTTTTTTATTTTTATTA
1 AATTTTTTTTTTATTTTTATTA
460228 TTTTATTATC
Statistics
Matches: 38, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
27 22 0.58
28 16 0.42
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.64
Consensus pattern (28 bp):
AATTTTTTTTTTATTTTTATTAAAATTA
Found at i:463909 original size:103 final size:104
Alignment explanation
Indices: 463790--463996 Score: 407
Period size: 103 Copynumber: 2.0 Consensus size: 104
463780 AGACAAAGCA
463790 CCTAGATATGTTGTCTCACACGTATTTTTTTTTTTCAAAATAAAAAACGTGGAAAGAAGAAACAT
1 CCTAGATATGTTGTCTCACACGTATTTTTTTTTTTCAAAATAAAAAACGTGGAAAGAAGAAACAT
463855 TATGCAAGAATACATACATATATATGTCAAAATTTGAAT
66 TATGCAAGAATACATACATATATATGTCAAAATTTGAAT
463894 CCTAGATATG-TGTCTCACACGTATTTTTTTTTTTCAAAATAAAAAACGTGGAAAGAAGAAACAT
1 CCTAGATATGTTGTCTCACACGTATTTTTTTTTTTCAAAATAAAAAACGTGGAAAGAAGAAACAT
463958 TATGCAAGAATACATACATATATATGTCAAAATTTGAAT
66 TATGCAAGAATACATACATATATATGTCAAAATTTGAAT
463997 TCATACCGAA
Statistics
Matches: 103, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
103 93 0.90
104 10 0.10
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.33
Consensus pattern (104 bp):
CCTAGATATGTTGTCTCACACGTATTTTTTTTTTTCAAAATAAAAAACGTGGAAAGAAGAAACAT
TATGCAAGAATACATACATATATATGTCAAAATTTGAAT
Found at i:466004 original size:30 final size:30
Alignment explanation
Indices: 465970--466031 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
465960 AGATATGTTG
465970 CACAACATTCTTGAGTCTTATATAAACCTA
1 CACAACATTCTTGAGTCTTATATAAACCTA
*
466000 CACAACATTCTTGGGTCTTATATAAACCTA
1 CACAACATTCTTGAGTCTTATATAAACCTA
466030 CA
1 CA
466032 AATGTTTTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.35, C:0.24, G:0.08, T:0.32
Consensus pattern (30 bp):
CACAACATTCTTGAGTCTTATATAAACCTA
Found at i:466672 original size:57 final size:59
Alignment explanation
Indices: 466541--466674 Score: 161
Period size: 57 Copynumber: 2.3 Consensus size: 59
466531 GGACTGTTAT
*
466541 AATTATTCTCACATTGGGGCTTAAATTTTTTATTATACAAGTTAAGCCTTGAACTTGAC
1 AATTATTCTCACATTGGGGCTTAAATTTTTTATTATACAAGTTAAGCATTGAACTTGAC
* *
466600 AATTGTTCTCACATTGGGGCTTGAATTTTTT-TT-T-CTAAGTT-AGTCATTGAACTTTG-C
1 AATTATTCTCACATTGGGGCTTAAATTTTTTATTATAC-AAGTTAAG-CATTGAAC-TTGAC
* *
466657 AATTTTTCTCCCATTGGG
1 AATTATTCTCACATTGGG
466675 ATCTAAACTT
Statistics
Matches: 67, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
56 3 0.04
57 30 0.45
58 5 0.07
59 29 0.43
ACGTcount: A:0.25, C:0.16, G:0.16, T:0.44
Consensus pattern (59 bp):
AATTATTCTCACATTGGGGCTTAAATTTTTTATTATACAAGTTAAGCATTGAACTTGAC
Found at i:467484 original size:20 final size:19
Alignment explanation
Indices: 467457--467501 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
467447 TTTTATAATT
467457 TTAA-AAAAATTCTATATTC
1 TTAATAAAAATTCTAT-TTC
*
467476 TTAATAAAATTTCTATTTC
1 TTAATAAAAATTCTATTTC
*
467495 TTTATAA
1 TTAATAA
467502 TTTTTTTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 13 0.57
20 10 0.43
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.49
Consensus pattern (19 bp):
TTAATAAAAATTCTATTTC
Found at i:467829 original size:19 final size:19
Alignment explanation
Indices: 467771--467827 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 19
467761 AATAAACACC
467771 AAAAAAA-ATTTTAGAAAATT
1 AAAAAAATATTTTA-AAAA-T
467791 AAAAAAATATTTTAAAAAT
1 AAAAAAATATTTTAAAAAT
467810 AAAAAAAGTATTTTAAAA
1 AAAAAAA-TATTTTAAAA
467828 TATTTTTACA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
19 8 0.23
20 21 0.60
21 6 0.17
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.30
Consensus pattern (19 bp):
AAAAAAATATTTTAAAAAT
Found at i:470029 original size:57 final size:55
Alignment explanation
Indices: 469932--470065 Score: 166
Period size: 57 Copynumber: 2.4 Consensus size: 55
469922 TTTACCTCGG
* * * *
469932 TAGTCATTCAATTATTATTA-TTTTTTATCATTTAACTATGAAAAA-TTATAAAA
1 TAGTCATTTAATTATTATAATTTTTTTATAATTTAACTATGAAAAAGTTACAAAA
*
469985 TAGTCCATTTAATTATTAATAATTTTTTTGATAATTTAATTATGAAAAAGTTACAAAA
1 TAGT-CATTTAATTATT-ATAATTTTTTT-ATAATTTAACTATGAAAAAGTTACAAAA
*
470043 TAGTCACTTAATTATT-TAATTTT
1 TAGTCATTTAATTATTATAATTTT
470066 ATTTTTTAAA
Statistics
Matches: 70, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
53 4 0.06
54 11 0.16
55 10 0.14
56 6 0.09
57 28 0.40
58 11 0.16
ACGTcount: A:0.40, C:0.07, G:0.05, T:0.48
Consensus pattern (55 bp):
TAGTCATTTAATTATTATAATTTTTTTATAATTTAACTATGAAAAAGTTACAAAA
Found at i:470984 original size:21 final size:21
Alignment explanation
Indices: 470958--470997 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
470948 AAATAATTAT
* *
470958 TTAATATACATTTTAAAATAA
1 TTAATATAAATTTAAAAATAA
470979 TTAATATAAATTTAAAAAT
1 TTAATATAAATTTAAAAAT
470998 TCAATTAGAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (21 bp):
TTAATATAAATTTAAAAATAA
Found at i:475615 original size:5 final size:5
Alignment explanation
Indices: 475605--475636 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
475595 TAGGTAACCC
475605 AACAA AACAA AACAA AACAA AACAA AACAA AA
1 AACAA AACAA AACAA AACAA AACAA AACAA AA
475637 GCTCCTGTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.81, C:0.19, G:0.00, T:0.00
Consensus pattern (5 bp):
AACAA
Found at i:485153 original size:142 final size:142
Alignment explanation
Indices: 484897--485190 Score: 588
Period size: 142 Copynumber: 2.1 Consensus size: 142
484887 AAACCGAAAA
484897 AATTCGGTTAACCGACCGAGTTCGGTTAATCGGTCGGTTAACCGAATTAACCGACCTTCCAAAAA
1 AATTCGGTTAACCGACCGAGTTCGGTTAATCGGTCGGTTAACCGAATTAACCGACCTTCCAAAAA
484962 TTTTAACCGTTAACCGAACCGATTTTTTTTAAAAAAAATCGGTTCGGTTAACGGTTAAAATTTTT
66 TTTTAACCGTTAACCGAACCGATTTTTTTTAAAAAAAATCGGTTCGGTTAACGGTTAAAATTTTT
485027 GGAAGGTCGGTT
131 GGAAGGTCGGTT
485039 AATTCGGTTAACCGACCGAGTTCGGTTAATCGGTCGGTTAACCGAATTAACCGACCTTCCAAAAA
1 AATTCGGTTAACCGACCGAGTTCGGTTAATCGGTCGGTTAACCGAATTAACCGACCTTCCAAAAA
485104 TTTTAACCGTTAACCGAACCGATTTTTTTTAAAAAAAATCGGTTCGGTTAACGGTTAAAATTTTT
66 TTTTAACCGTTAACCGAACCGATTTTTTTTAAAAAAAATCGGTTCGGTTAACGGTTAAAATTTTT
485169 GGAAGGTCGGTT
131 GGAAGGTCGGTT
485181 AATTCGGTTA
1 AATTCGGTTA
485191 TAGTAATTTC
Statistics
Matches: 152, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
142 152 1.00
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (142 bp):
AATTCGGTTAACCGACCGAGTTCGGTTAATCGGTCGGTTAACCGAATTAACCGACCTTCCAAAAA
TTTTAACCGTTAACCGAACCGATTTTTTTTAAAAAAAATCGGTTCGGTTAACGGTTAAAATTTTT
GGAAGGTCGGTT
Found at i:487802 original size:5 final size:5
Alignment explanation
Indices: 487794--487836 Score: 70
Period size: 5 Copynumber: 8.6 Consensus size: 5
487784 AAGAAAGGCC
487794 GAAGA GAAGA GAAGA GAAGA GAAGA GAA-A GGAAGA GAAGA GAA
1 GAAGA GAAGA GAAGA GAAGA GAAGA GAAGA -GAAGA GAAGA GAA
487837 TTATAGAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
4 1 0.03
5 34 0.94
6 1 0.03
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (5 bp):
GAAGA
Found at i:487973 original size:6 final size:6
Alignment explanation
Indices: 487958--487990 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
487948 AAGGTAGAGT
487958 AAAAAG AAAAA- AAAAAG AAAAAG AAAAAG AAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAA
487991 CCCACATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:487974 original size:11 final size:12
Alignment explanation
Indices: 487958--487990 Score: 59
Period size: 11 Copynumber: 2.8 Consensus size: 12
487948 AAGGTAGAGT
487958 AAAAAGAAAAA-
1 AAAAAGAAAAAG
487969 AAAAAGAAAAAG
1 AAAAAGAAAAAG
487981 AAAAAGAAAA
1 AAAAAGAAAA
487991 CCCACATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (12 bp):
AAAAAGAAAAAG
Found at i:488711 original size:45 final size:46
Alignment explanation
Indices: 488600--488717 Score: 141
Period size: 45 Copynumber: 2.6 Consensus size: 46
488590 GTTTGTACAT
* * * * *
488600 AGTTTCAGCCTC-AACATTATTTAAAATGGGTTTTTGTTTATAATA
1 AGTTTCAGCTTCAAACATTCTTGAAAATGGGTTTATGTTTATAAGA
* **
488645 AGTTTTAGCTTCAAATGTTCTTGAAAAT-GGTTTATGTTTATAAGA
1 AGTTTCAGCTTCAAACATTCTTGAAAATGGGTTTATGTTTATAAGA
*
488690 AGTTTCAGCTTCAAACATTCTTGTAAAT
1 AGTTTCAGCTTCAAACATTCTTGAAAAT
488718 ACTTAATGAA
Statistics
Matches: 60, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
45 49 0.82
46 11 0.18
ACGTcount: A:0.31, C:0.11, G:0.14, T:0.43
Consensus pattern (46 bp):
AGTTTCAGCTTCAAACATTCTTGAAAATGGGTTTATGTTTATAAGA
Found at i:491218 original size:26 final size:25
Alignment explanation
Indices: 491168--491219 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 25
491158 GCCGTTCGAA
491168 ATATATAAAAATTTAAAAATCTAAAT
1 ATATATAAAAATTTAAAAA-CTAAAT
*
491194 ATATATTAAAACTTTATAAAA-TAAAT
1 ATATA-TAAAAATTTA-AAAACTAAAT
491220 TTTCAAAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
26 10 0.43
27 9 0.39
28 4 0.17
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.37
Consensus pattern (25 bp):
ATATATAAAAATTTAAAAACTAAAT
Found at i:491476 original size:16 final size:16
Alignment explanation
Indices: 491453--491486 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
491443 TTTCAATAAA
491453 TTTTAATTTTTT-ACT
1 TTTTAATTTTTTAACT
491468 TTTTGAATTTTTTAACT
1 TTTT-AATTTTTTAACT
491485 TT
1 TT
491487 ATATTTTGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 8 0.47
17 5 0.29
ACGTcount: A:0.21, C:0.06, G:0.03, T:0.71
Consensus pattern (16 bp):
TTTTAATTTTTTAACT
Found at i:493482 original size:23 final size:23
Alignment explanation
Indices: 493452--493497 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
493442 TTAAGTACTT
493452 AATTTTCACTTTTACAAATTGCC
1 AATTTTCACTTTTACAAATTGCC
*
493475 AATTTTCACTTTTGCAAATTGCC
1 AATTTTCACTTTTACAAATTGCC
493498 TCCATCGAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.28, C:0.22, G:0.07, T:0.43
Consensus pattern (23 bp):
AATTTTCACTTTTACAAATTGCC
Found at i:510284 original size:15 final size:15
Alignment explanation
Indices: 510264--510297 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
510254 TTAAAAATTT
* *
510264 AAAATAATTATTAAG
1 AAAATAATGATGAAG
510279 AAAATAATGATGAAG
1 AAAATAATGATGAAG
510294 AAAA
1 AAAA
510298 ATAAATAAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.65, C:0.00, G:0.12, T:0.24
Consensus pattern (15 bp):
AAAATAATGATGAAG
Found at i:513682 original size:23 final size:26
Alignment explanation
Indices: 513656--513712 Score: 66
Period size: 25 Copynumber: 2.2 Consensus size: 26
513646 TTTAATTTTA
513656 AAATTTAAAAA-ATAAA-A-AAAATC
1 AAATTTAAAAATATAAATATAAAATC
*
513679 AAATTTTTAAAAATATAAATATAAAATT
1 AAA--TTTAAAAATATAAATATAAAATC
513707 AAATTT
1 AAATTT
513713 CAATTTTATG
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
23 3 0.11
25 8 0.29
26 8 0.29
27 1 0.04
28 8 0.29
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (26 bp):
AAATTTAAAAATATAAATATAAAATC
Found at i:516271 original size:2 final size:2
Alignment explanation
Indices: 516264--516289 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
516254 GCATGAGTTT
516264 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
516290 AAATATCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:522363 original size:17 final size:18
Alignment explanation
Indices: 522341--522374 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
522331 TAAATGAGTT
522341 AATTAGGAT-TAAATTGG
1 AATTAGGATATAAATTGG
*
522358 AATTAGGGTATAAATTG
1 AATTAGGATATAAATTG
522375 AAAAGAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.41, C:0.00, G:0.24, T:0.35
Consensus pattern (18 bp):
AATTAGGATATAAATTGG
Found at i:522789 original size:19 final size:19
Alignment explanation
Indices: 522765--522803 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
522755 TAACCGGGCT
522765 TAGTCGGATATAGTTAGCA
1 TAGTCGGATATAGTTAGCA
522784 TAGTCGGATATAGTTAGCA
1 TAGTCGGATATAGTTAGCA
522803 T
1 T
522804 GCCATAGGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.31, C:0.10, G:0.26, T:0.33
Consensus pattern (19 bp):
TAGTCGGATATAGTTAGCA
Found at i:522875 original size:21 final size:22
Alignment explanation
Indices: 522847--522910 Score: 69
Period size: 21 Copynumber: 3.0 Consensus size: 22
522837 GCTTTGCCGA
522847 TCAGGCACTATATGTGTCGTAT
1 TCAGGCACTATATGTGTCGTAT
* **
522869 T-AGGCACCACGTGTGTCGT-T
1 TCAGGCACTATATGTGTCGTAT
* *
522889 TCAGGCACTTTATGTGTTGTAT
1 TCAGGCACTATATGTGTCGTAT
522911 ACTGCTTCTG
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
20 2 0.06
21 28 0.88
22 2 0.06
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.38
Consensus pattern (22 bp):
TCAGGCACTATATGTGTCGTAT
Found at i:523506 original size:21 final size:22
Alignment explanation
Indices: 523447--523510 Score: 60
Period size: 21 Copynumber: 3.0 Consensus size: 22
523437 CAGAAGCAGT
* * *
523447 ATACAACACATAAAATGCCTGA
1 ATACGACACATATAGTGCCTGA
** *
523469 A-ACGACACACGTGGTGCCT-A
1 ATACGACACATATAGTGCCTGA
523489 ATACGACACATATAGTGCCTGA
1 ATACGACACATATAGTGCCTGA
523511 TCGGCAAAGC
Statistics
Matches: 31, Mismatches: 9, Indels: 4
0.70 0.20 0.09
Matches are distributed among these distances:
20 2 0.06
21 27 0.87
22 2 0.06
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (22 bp):
ATACGACACATATAGTGCCTGA
Found at i:529608 original size:12 final size:12
Alignment explanation
Indices: 529582--529618 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
529572 TAAAAAATTT
529582 AAAATCATTTT-A
1 AAAAT-ATTTTAA
529594 AAAAT-TTTTAA
1 AAAATATTTTAA
529605 AAAATATTTTAA
1 AAAATATTTTAA
529617 AA
1 AA
529619 TGCATAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 4 0.17
11 6 0.26
12 13 0.57
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.41
Consensus pattern (12 bp):
AAAATATTTTAA
Found at i:529618 original size:11 final size:11
Alignment explanation
Indices: 529562--529618 Score: 59
Period size: 11 Copynumber: 5.3 Consensus size: 11
529552 AGCATAAAAT
529562 AAAATAGTTTTA
1 AAAATA-TTTTA
529574 AAAA-A-TTT-
1 AAAATATTTTA
529582 AAAATCATTTTA
1 AAAAT-ATTTTA
529594 AAAAT-TTTTAA
1 AAAATATTTT-A
529605 AAAATATTTTA
1 AAAATATTTTA
529616 AAA
1 AAA
529619 TGCATAAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 13
0.75 0.00 0.25
Matches are distributed among these distances:
8 4 0.10
9 3 0.08
10 5 0.13
11 14 0.36
12 13 0.33
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (11 bp):
AAAATATTTTA
Found at i:529626 original size:21 final size:20
Alignment explanation
Indices: 529602--529647 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 20
529592 TAAAAATTTT
529602 TAAAAAA-TATTTTAAAATGCA
1 TAAAAAATTATTTT-AAA-GCA
529623 TAAAAAAATTATTTTAAAGCA
1 T-AAAAAATTATTTTAAAGCA
529644 TAAA
1 TAAA
529648 CTCGAATCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
20 3 0.13
21 5 0.22
22 9 0.39
23 6 0.26
ACGTcount: A:0.59, C:0.04, G:0.04, T:0.33
Consensus pattern (20 bp):
TAAAAAATTATTTTAAAGCA
Found at i:529629 original size:23 final size:21
Alignment explanation
Indices: 529603--529647 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 21
529593 AAAAATTTTT
529603 AAAAAATATTTTAAAATGCATAA
1 AAAAAATATTTT-AAA-GCATAA
*
529626 AAAAATTATTTTAAAGCATAA
1 AAAAAATATTTTAAAGCATAA
529647 A
1 A
529648 CTCGAATCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 7 0.33
22 3 0.14
23 11 0.52
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.31
Consensus pattern (21 bp):
AAAAAATATTTTAAAGCATAA
Found at i:537177 original size:2 final size:2
Alignment explanation
Indices: 537172--537210 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
537162 TATATATATA
537172 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
537211 TCTATTATTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:537455 original size:101 final size:101
Alignment explanation
Indices: 537322--537550 Score: 404
Period size: 101 Copynumber: 2.3 Consensus size: 101
537312 TGAATTGACG
*
537322 GATAAGACCATAACTGGGTTATGGCACTATGAACGTAAGACCATGGTTGGACCATGGCAGTGTTT
1 GATAAGACCATAACTGGGTTATGGCACGATGAACGTAAGACCATGGTTGGACCATGGCAGTGTTT
537387 ATATATAAGATCATAGCTGGGCTATGACATTCTGAT
66 ATATATAAGATCATAGCTGGGCTATGACATTCTGAT
*
537423 GATAAGACCATAACTAGGTTATGGCACGATGAACGTAAGACCATGGTTGGACCATGGCAGTGTTT
1 GATAAGACCATAACTGGGTTATGGCACGATGAACGTAAGACCATGGTTGGACCATGGCAGTGTTT
* * * *
537488 ATATGTAAGATCATAGCTGGGCTATGGCATTTTGTT
66 ATATATAAGATCATAGCTGGGCTATGACATTCTGAT
537524 GATAAGACCATAACTGGGTTATGGCAC
1 GATAAGACCATAACTGGGTTATGGCAC
537551 TACGAATGTA
Statistics
Matches: 121, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
101 121 1.00
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.28
Consensus pattern (101 bp):
GATAAGACCATAACTGGGTTATGGCACGATGAACGTAAGACCATGGTTGGACCATGGCAGTGTTT
ATATATAAGATCATAGCTGGGCTATGACATTCTGAT
Found at i:537591 original size:24 final size:24
Alignment explanation
Indices: 537555--537605 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
537545 TGGCACTACG
537555 AATGTAAAGGATGAATTGACGGAA
1 AATGTAAAGGATGAATTGACGGAA
* *
537579 AATGTAAATGATGAATTGACGGCA
1 AATGTAAAGGATGAATTGACGGAA
537603 AAT
1 AAT
537606 TACTCAAGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.45, C:0.06, G:0.25, T:0.24
Consensus pattern (24 bp):
AATGTAAAGGATGAATTGACGGAA
Found at i:538176 original size:20 final size:20
Alignment explanation
Indices: 538137--538176 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
538127 GGTTGAATGA
*
538137 TATGCTTATGATTGATGTGT
1 TATGCTTATGAATGATGTGT
538157 TATGCTTATGGAATGA-GTGT
1 TATGCTTAT-GAATGATGTGT
538177 GCAAAGTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.23, C:0.05, G:0.28, T:0.45
Consensus pattern (20 bp):
TATGCTTATGAATGATGTGT
Found at i:539120 original size:40 final size:42
Alignment explanation
Indices: 539076--539159 Score: 154
Period size: 42 Copynumber: 2.0 Consensus size: 42
539066 CTTTTATATA
539076 TTTTTC-TT-TATATATAGTATTTATATGTCAAATATTTATT
1 TTTTTCTTTATATATATAGTATTTATATGTCAAATATTTATT
539116 TTTTTCTTTATATATATAGTATTTATATGTCAAATATTTATT
1 TTTTTCTTTATATATATAGTATTTATATGTCAAATATTTATT
539158 TT
1 TT
539160 CTCCACCTAT
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
40 6 0.14
41 2 0.05
42 34 0.81
ACGTcount: A:0.30, C:0.05, G:0.05, T:0.61
Consensus pattern (42 bp):
TTTTTCTTTATATATATAGTATTTATATGTCAAATATTTATT
Found at i:544947 original size:35 final size:35
Alignment explanation
Indices: 544908--544974 Score: 125
Period size: 35 Copynumber: 1.9 Consensus size: 35
544898 TATGCTGATA
544908 AGCCACTTAAATAAATCTAAATCCCAATATCTATT
1 AGCCACTTAAATAAATCTAAATCCCAATATCTATT
*
544943 AGCCACTTAAATAAATTTAAATCCCAATATCT
1 AGCCACTTAAATAAATCTAAATCCCAATATCT
544975 TTTGAAAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.43, C:0.22, G:0.03, T:0.31
Consensus pattern (35 bp):
AGCCACTTAAATAAATCTAAATCCCAATATCTATT
Found at i:554779 original size:88 final size:89
Alignment explanation
Indices: 554642--554804 Score: 210
Period size: 89 Copynumber: 1.8 Consensus size: 89
554632 AAAAAATTTA
* * * *
554642 AAGGTTTTTTTATGCAATTTGAAAGTTCAAGTATTCAATTGAGTAGAAAAAATTAAGA-GCTTAA
1 AAGGTTTTTTTATACAATTTGAAAGTTAAAGTATTCAATTAAGTAGAAAAAA-AAAGAGGCTTAA
554706 TTACTT-TTTTCTTTAAGAAGTTTG
65 TTACTTATTTTCTTTAAGAAGTTTG
*
554730 AAGGTCTTTTTTATAC-ATTTGAAAAGTTAAAGTGCTT-AATTAAGT-GAAAAAAAAAGAGGCTT
1 AAGGT-TTTTTTATACAATTTG-AAAGTTAAAGT-ATTCAATTAAGTAGAAAAAAAAAGAGGCTT
554792 AATTACTTATTTT
63 AATTACTTATTTT
554805 AAAAATATTT
Statistics
Matches: 65, Mismatches: 5, Indels: 9
0.82 0.06 0.11
Matches are distributed among these distances:
87 4 0.06
88 29 0.45
89 30 0.46
90 2 0.03
ACGTcount: A:0.37, C:0.07, G:0.15, T:0.40
Consensus pattern (89 bp):
AAGGTTTTTTTATACAATTTGAAAGTTAAAGTATTCAATTAAGTAGAAAAAAAAAGAGGCTTAAT
TACTTATTTTCTTTAAGAAGTTTG
Found at i:554925 original size:23 final size:24
Alignment explanation
Indices: 554894--554942 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 24
554884 TACTATTTGT
*
554894 AAACAAAATTACACTTAAATCATA
1 AAACAAAATTACACTGAAATCATA
*
554918 AAAC-AAATTACACTGAAATCGTA
1 AAACAAAATTACACTGAAATCATA
554941 AA
1 AA
554943 TCAGAAGAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 19 0.83
24 4 0.17
ACGTcount: A:0.57, C:0.16, G:0.04, T:0.22
Consensus pattern (24 bp):
AAACAAAATTACACTGAAATCATA
Found at i:557782 original size:2 final size:2
Alignment explanation
Indices: 557775--557811 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
557765 CTAATTTCTA
557775 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
557812 AACTTGACCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:569448 original size:123 final size:123
Alignment explanation
Indices: 569229--569478 Score: 482
Period size: 123 Copynumber: 2.0 Consensus size: 123
569219 CGGCCTTTTT
* *
569229 TTTTTTTTTTTTTTTCAACGTGCATCAGATGGCTTAAAACTAGCATAACATGGACAAAAAATAAA
1 TTTTTTTTTTTTGTACAACGTGCATCAGATGGCTTAAAACTAGCATAACATGGACAAAAAATAAA
569294 GGTTAAATTCTGCTGTTAGTCCCTGTACTTTGCAAAAATTATAAATTTAATCTTTATA
66 GGTTAAATTCTGCTGTTAGTCCCTGTACTTTGCAAAAATTATAAATTTAATCTTTATA
569352 TTTTTTTTTTTTGTACAACGTGCATCAGATGGCTTAAAACTAGCATAACATGGACAAAAAATAAA
1 TTTTTTTTTTTTGTACAACGTGCATCAGATGGCTTAAAACTAGCATAACATGGACAAAAAATAAA
569417 GGTTAAATTCTGCTGTTAGTCCCTGTACTTTGCAAAAATTATAAATTTAATCTTTATA
66 GGTTAAATTCTGCTGTTAGTCCCTGTACTTTGCAAAAATTATAAATTTAATCTTTATA
569475 TTTT
1 TTTT
569479 AATTTAGTTA
Statistics
Matches: 125, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
123 125 1.00
ACGTcount: A:0.34, C:0.14, G:0.12, T:0.40
Consensus pattern (123 bp):
TTTTTTTTTTTTGTACAACGTGCATCAGATGGCTTAAAACTAGCATAACATGGACAAAAAATAAA
GGTTAAATTCTGCTGTTAGTCCCTGTACTTTGCAAAAATTATAAATTTAATCTTTATA
Found at i:585874 original size:19 final size:17
Alignment explanation
Indices: 585833--585875 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
585823 AGATTTTTAA
*
585833 AAAATATATTTAAATTT
1 AAAATATATTCAAATTT
*
585850 AAAATATATTCATATATT
1 AAAATATATTCAAAT-TT
585868 AATAATAT
1 AA-AATAT
585876 TAATAATGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 13 0.59
18 4 0.18
19 5 0.23
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (17 bp):
AAAATATATTCAAATTT
Found at i:597376 original size:6 final size:6
Alignment explanation
Indices: 597365--597392 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
597355 TATGATTTCA
597365 ATATCC ATATCC ATATCC ATATCC ATAT
1 ATATCC ATATCC ATATCC ATATCC ATAT
597393 TAATTATACC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.36, C:0.29, G:0.00, T:0.36
Consensus pattern (6 bp):
ATATCC
Found at i:607999 original size:112 final size:112
Alignment explanation
Indices: 607726--607999 Score: 286
Period size: 112 Copynumber: 2.4 Consensus size: 112
607716 TTAACATCGT
* * *
607726 TTTGGTCTTGATGTATACTATAATTAGTGGCGAC-TATGATAAAACGCCGCTAAAGCAAGTATTA
1 TTTGGTCTTGATGTATATTAGAATTAGTGGCG-CTTATGAGAAAACGCCGCTAAAGCAAGTATTA
* * * **
607790 GCGGCCCATTGTCGAAAGCGCCGCAAAAATCTTAACGAAAACATATCG
65 GCGGCCCATTGACGAAAGCGCCGCAAAAATCTTAACCAAAACACAGAG
* * * * * *
607838 TTTTGTCTTGCTGTATATTAGCATTAGTGGCACTTACGA-AAACCTGCCGCTAAAGCAAGTATTA
1 TTTGGTCTTGATGTATATTAGAATTAGTGGCGCTTATGAGAAAAC-GCCGCTAAAGCAAGTATTA
* * * *
607902 GCGGCGC-TT-ACGAAAAGCGCCGCAATATATGTTAACCAAAACGCAGAG
65 GCGGCCCATTGACG-AAAGCGCCGCAA-AAATCTTAACCAAAACACAGAG
* * * *
607950 TTTGGTCTAGAGGTATATTAGAATTTGTGGCGCTTATGGGAAAACGCCGC
1 TTTGGTCTTGATGTATATTAGAATTAGTGGCGCTTATGAGAAAACGCCGC
608000 AAAATATCCT
Statistics
Matches: 130, Mismatches: 27, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
110 2 0.02
111 19 0.15
112 105 0.81
113 4 0.03
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (112 bp):
TTTGGTCTTGATGTATATTAGAATTAGTGGCGCTTATGAGAAAACGCCGCTAAAGCAAGTATTAG
CGGCCCATTGACGAAAGCGCCGCAAAAATCTTAACCAAAACACAGAG
Found at i:608342 original size:115 final size:114
Alignment explanation
Indices: 607994--608606 Score: 637
Period size: 115 Copynumber: 5.4 Consensus size: 114
607984 TATGGGAAAA
* * ** * ** * *
607994 CGCCGCAAAATATCCTAACCAAAGCGCACCGTTTTGGTCTTGGTGTATGTTACAGTTAGTGGCGC
1 CGCCGCAAAATATCTTAACCAAAACGCAGAGTTTTGGTCTTGATGTATACTAGAATTAGTGGCGC
* * * *
608059 TTAAGGGAAAACACCGCTAAAGCATAATATTAGCGGCG-TTTCGTGAGAAG
66 ATACGGGAAAACGCCGCTAAAGCATACTATTAGCGGCGCTTTC--GAGAAG
* *
608109 CGCCGCAAAATATTTTAACCAAAACGCAGAG-TTTGGTCTTGAGGTATACTAGAATTAGTGGCGC
1 CGCCGCAAAATATCTTAACCAAAACGCAGAGTTTTGGTCTTGATGTATACTAGAATTAGTGGCGC
* * * * *
608173 A-AAGGGAACACGCCGCTAAGGCATACTATTAGCGGCGCGTCTGGAGAAG
66 ATACGGGAAAACGCCGCTAAAGCATACTATTAGCGGCGC-TTTCGAGAAG
* * * *
608222 CGCCGCAAAATTTCTTAACCAAAACGCA-ACGTTTTTGTCTTGATGTATACAACAATTAGTGGCG
1 CGCCGCAAAATATCTTAACCAAAACGCAGA-GTTTTGGTCTTGATGTATACTAGAATTAGTGGCG
* * * * *
608286 CATACTGGAAAACGCTGCTAAAGCATAGTATTAGCGGCGCTTTACAAAAAG
65 CATACGGGAAAACGCCGCTAAAGCATACTATTAGCGGCGCTTT-CGAGAAG
* * *
608337 CGCCGCAAAATATGC-TCACCAAAACGCAGAGTTTT-GTCTTGAGGTATATTAGAATTAGTGGCG
1 CGCCGCAAAATAT-CTTAACCAAAACGCAGAGTTTTGGTCTTGATGTATACTAGAATTAGTGGCG
* * *
608400 CTTACGGGAGAACGCCGCTAAAGCATACTATTAGCGGCGCGTTTTGAGAAG
65 CATACGGGAAAACGCCGCTAAAGCATACTATTAGCGGCGC-TTTCGAGAAG
* ** * ** ** *
608451 CACCATAAAATATATTAACCAAAACGCATCGTTTAAGTCTTGATGTATACTGGAATTAGTGGCGT
1 CGCCGCAAAATATCTTAACCAAAACGCAGAGTTTTGGTCTTGATGTATACTAGAATTAGTGGCG-
* * * * * *
608516 C-CACGAGAAATCACCGCTAAAGCATAGTATTAGCGGCGCTTTTTGAGAAG
65 CATACGGGAAAACGCCGCTAAAGCATACTATTAGCGGCGC-TTTCGAGAAG
*
608566 CGCCGGAAAATATCTTAACCAAAACGCAGAGTTTTGGTCTT
1 CGCCGCAAAATATCTTAACCAAAACGCAGAGTTTTGGTCTT
608607 AACCATGCAT
Statistics
Matches: 412, Mismatches: 74, Indels: 24
0.81 0.15 0.05
Matches are distributed among these distances:
112 1 0.00
113 65 0.16
114 148 0.36
115 195 0.47
116 3 0.01
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.25
Consensus pattern (114 bp):
CGCCGCAAAATATCTTAACCAAAACGCAGAGTTTTGGTCTTGATGTATACTAGAATTAGTGGCGC
ATACGGGAAAACGCCGCTAAAGCATACTATTAGCGGCGCTTTCGAGAAG
Found at i:608392 original size:228 final size:225
Alignment explanation
Indices: 607994--608606 Score: 728
Period size: 229 Copynumber: 2.7 Consensus size: 225
607984 TATGGGAAAA
* * * * * ** *
607994 CGCCGCAAAATATCCTAACCAAAGCGCACCGTTTTGGTCTTGGTGTATGTTACAGTTAGTGGCGC
1 CGCCGCAAAATATCTTAACCAAAACGCAACGTTTTAGTCTTGATGTATACTACAATTAGTGGCGC
* *
608059 TTAAGGGAAAACACCGCTAAAGCATAATATTAGCGGCG-TTTCGTGAGAAGCGCCGCAAAATATT
66 -T-ACGGAAAACACCGCTAAAGCATAGTATTAGCGGCGCTTTC--GAGAAGCGCCGCAAAATA-T
* *
608123 TTAACCAAAACGCAGAGTTTGGTCTTGAGGTATACTAGAATTAGTGGCGC-AAAGGGA-ACACGC
126 CTAACCAAAACGCAGAGTTTTGTCTTGAGGTATACTAGAATTAGTGGCGCTAAAGGGAGA-ACGC
*
608186 CGCTAAGGCATACTATTAGCGGCGCGTCTGGAGAAG
190 CGCTAAAGCATACTATTAGCGGCGCGTCTGGAGAAG
* * *
608222 CGCCGCAAAATTTCTTAACCAAAACGCAACGTTTTTGTCTTGATGTATACAACAATTAGTGGCGC
1 CGCCGCAAAATATCTTAACCAAAACGCAACGTTTTAGTCTTGATGTATACTACAATTAGTGGCGC
* * * *
608287 ATACTGGAAAACGCTGCTAAAGCATAGTATTAGCGGCGCTTTACAAAAAGCGCCGCAAAATATGC
66 -TAC-GGAAAACACCGCTAAAGCATAGTATTAGCGGCGCTTT-CGAGAAGCGCCGCAAAATAT-C
* * * *
608352 TCACCAAAACGCAGAGTTTTGTCTTGAGGTATATTAGAATTAGTGGCGCTTACGGGAGAACGCCG
127 TAACCAAAACGCAGAGTTTTGTCTTGAGGTATACTAGAATTAGTGGCGCTAAAGGGAGAACGCCG
* *
608417 CTAAAGCATACTATTAGCGGCGCGTTTTGAGAAG
192 CTAAAGCATACTATTAGCGGCGCGTCTGGAGAAG
* ** * * * **
608451 CACCATAAAATATATTAACCAAAACGCATCGTTTAAGTCTTGATGTATACTGGAATTAGTGGCGT
1 CGCCGCAAAATATCTTAACCAAAACGCAACGTTTTAGTCTTGATGTATACTACAATTAGTGGCG-
* * * *
608516 CCACGAGAAATCACCGCTAAAGCATAGTATTAGCGGCGCTTTTTGAGAAGCGCCGGAAAATATCT
65 CTACG-GAAAACACCGCTAAAGCATAGTATTAGCGGCGC-TTTCGAGAAGCGCCGCAAAATATC-
608581 TAACCAAAACGCAGAGTTTTGGTCTT
127 TAACCAAAACGCAGAGTTTT-GTCTT
608607 AACCATGCAT
Statistics
Matches: 328, Mismatches: 46, Indels: 20
0.83 0.12 0.05
Matches are distributed among these distances:
227 2 0.01
228 150 0.46
229 165 0.50
230 11 0.03
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.25
Consensus pattern (225 bp):
CGCCGCAAAATATCTTAACCAAAACGCAACGTTTTAGTCTTGATGTATACTACAATTAGTGGCGC
TACGGAAAACACCGCTAAAGCATAGTATTAGCGGCGCTTTCGAGAAGCGCCGCAAAATATCTAAC
CAAAACGCAGAGTTTTGTCTTGAGGTATACTAGAATTAGTGGCGCTAAAGGGAGAACGCCGCTAA
AGCATACTATTAGCGGCGCGTCTGGAGAAG
Found at i:612112 original size:43 final size:43
Alignment explanation
Indices: 612025--612203 Score: 157
Period size: 42 Copynumber: 4.2 Consensus size: 43
612015 CAAAAATAGT
* * * ** * *
612025 GGCGTTTTTGTACAAAAGCGCCTCGAAAGATTATGATCTCTAGC
1 GGCGTTTTTATACAAAA-CGCCGCTAAAGAACATGTTCTTTAGC
* *
612069 GGCGTTTTTATACAAAGCGCCGTTAAAGAACATGTTCTTTAGC
1 GGCGTTTTTATACAAAACGCCGCTAAAGAACATGTTCTTTAGC
* * * * * *
612112 GGCG-CTTAATA-AAAAAGCCACTAAAGATCATTTTCTTTAGC
1 GGCGTTTTTATACAAAACGCCGCTAAAGAACATGTTCTTTAGC
* * * *
612153 GGCGCTTATA-AAAAAACGCCGCTAAAGAACATGGTCTTTAGC
1 GGCGTTTTTATACAAAACGCCGCTAAAGAACATGTTCTTTAGC
612195 GGCGTTTTT
1 GGCGTTTTT
612204 GTTTGTAAAC
Statistics
Matches: 106, Mismatches: 27, Indels: 6
0.76 0.19 0.04
Matches are distributed among these distances:
41 29 0.27
42 39 0.37
43 23 0.22
44 15 0.14
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.30
Consensus pattern (43 bp):
GGCGTTTTTATACAAAACGCCGCTAAAGAACATGTTCTTTAGC
Found at i:612191 original size:42 final size:42
Alignment explanation
Indices: 612086--612198 Score: 158
Period size: 41 Copynumber: 2.7 Consensus size: 42
612076 TTATACAAAG
*
612086 CGCCGTTAAAGAACATGTTCTTTAGCGGCGCTTAATAAAAAA
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAATAAAAAA
* * *
612128 -GCCACTAAAGATCATTTTCTTTAGCGGCGCTT-ATAAAAAAA
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAAT-AAAAAA
*
612169 CGCCGCTAAAGAACATGGTCTTTAGCGGCG
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCG
612199 TTTTTGTTTG
Statistics
Matches: 61, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
40 2 0.03
41 34 0.56
42 25 0.41
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.26
Consensus pattern (42 bp):
CGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAATAAAAAA
Found at i:613726 original size:5 final size:5
Alignment explanation
Indices: 613712--613744 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
613702 AATTATTAAG
613712 TATA- TATAT TATAT TATAT TATAT TATAT TATA
1 TATAT TATAT TATAT TATAT TATAT TATAT TATA
613745 ATGATGAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 4 0.14
5 24 0.86
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
TATAT
Found at i:613736 original size:15 final size:14
Alignment explanation
Indices: 613682--613744 Score: 62
Period size: 13 Copynumber: 4.6 Consensus size: 14
613672 ATATATTAAA
613682 ATATTATA-ATATT
1 ATATTATATATATT
613695 ATATCT-TA-ATTATT
1 ATAT-TATATA-TATT
*
613709 A-AGTATATATATT
1 ATATTATATATATT
613722 ATATTATATTATATT
1 ATATTATA-TATATT
613737 ATATTATA
1 ATATTATA
613745 ATGATGAAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
12 1 0.02
13 15 0.36
14 12 0.29
15 14 0.33
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (14 bp):
ATATTATATATATT
Found at i:613764 original size:4 final size:4
Alignment explanation
Indices: 613750--613801 Score: 63
Period size: 4 Copynumber: 13.2 Consensus size: 4
613740 TTATAATGAT
* *
613750 GAAA TAAA GAAA GAAA GAAA -AAA GAAA GAAA GAAAA GAAA -AAG GAAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA G-AAA GAAA GAAA GAAA
613797 GAAA G
1 GAAA G
613802 GAAGGAAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
3 5 0.12
4 32 0.78
5 4 0.10
ACGTcount: A:0.75, C:0.00, G:0.23, T:0.02
Consensus pattern (4 bp):
GAAA
Found at i:613775 original size:15 final size:15
Alignment explanation
Indices: 613750--613800 Score: 68
Period size: 15 Copynumber: 3.3 Consensus size: 15
613740 TTATAATGAT
613750 GAAATAAAGAAAGAAA
1 GAAA-AAAGAAAGAAA
613766 GAAAAAAGAAAGAAA
1 GAAAAAAGAAAGAAA
613781 GAAAAGAA-AAAGGAAA
1 GAAAA-AAGAAA-GAAA
613797 GAAA
1 GAAA
613801 GGAAGGAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
15 19 0.58
16 14 0.42
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (15 bp):
GAAAAAAGAAAGAAA
Found at i:613788 original size:20 final size:19
Alignment explanation
Indices: 613755--613812 Score: 80
Period size: 20 Copynumber: 3.0 Consensus size: 19
613745 ATGATGAAAT
613755 AAAGAAAGAAAGAAAAAAG
1 AAAGAAAGAAAGAAAAAAG
*
613774 AAAGAAAGAAAAGAAAAAGG
1 AAAGAAAG-AAAGAAAAAAG
* *
613794 AAAGAAAGGAAGGAAAAAG
1 AAAGAAAGAAAGAAAAAAG
613813 TCATTGTTCA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 16 0.47
20 18 0.53
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (19 bp):
AAAGAAAGAAAGAAAAAAG
Found at i:613812 original size:15 final size:13
Alignment explanation
Indices: 613759--613810 Score: 58
Period size: 11 Copynumber: 4.2 Consensus size: 13
613749 TGAAATAAAG
613759 AAAGAAAGAA--A
1 AAAGAAAGAAGGA
*
613770 AAAGAAAGAAAGA
1 AAAGAAAGAAGGA
613783 AAAGAAA-AAGG-
1 AAAGAAAGAAGGA
613794 AAAGAAAGGAAGGA
1 AAAGAAA-GAAGGA
613808 AAA
1 AAA
613811 AGTCATTGTT
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
11 17 0.49
12 3 0.09
13 12 0.34
14 3 0.09
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (13 bp):
AAAGAAAGAAGGA
Found at i:622671 original size:21 final size:21
Alignment explanation
Indices: 622647--622718 Score: 99
Period size: 21 Copynumber: 3.4 Consensus size: 21
622637 GACACCGTCC
*
622647 GTGAAGGCGATGACTCACCTT
1 GTGACGGCGATGACTCACCTT
622668 GTGACGGCGATGACTCACCTT
1 GTGACGGCGATGACTCACCTT
* *
622689 GCGACGTCGATGACTCACCTT
1 GTGACGGCGATGACTCACCTT
**
622710 CCGACGGCG
1 GTGACGGCG
622719 GAGAATCCAT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 46 1.00
ACGTcount: A:0.19, C:0.31, G:0.29, T:0.21
Consensus pattern (21 bp):
GTGACGGCGATGACTCACCTT
Found at i:624696 original size:25 final size:26
Alignment explanation
Indices: 624642--624705 Score: 76
Period size: 25 Copynumber: 2.4 Consensus size: 26
624632 TAAGTTTTTT
* *
624642 ATATATTAAAACTATGCAATTAAGAATA
1 ATATA-TAAAA-TATGCAAATAAAAATA
624670 ATATATAAAATAT-CAAATAAAAATA
1 ATATATAAAATATGCAAATAAAAATA
*
624695 ATAAATAAAAT
1 ATATATAAAAT
624706 CATAAGAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
25 20 0.61
26 3 0.09
27 5 0.15
28 5 0.15
ACGTcount: A:0.62, C:0.05, G:0.03, T:0.30
Consensus pattern (26 bp):
ATATATAAAATATGCAAATAAAAATA
Found at i:625082 original size:23 final size:24
Alignment explanation
Indices: 625034--625080 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
625024 TAAAATATTT
*
625034 TTAATATTAACATTAATTTTTAAA
1 TTAATATTAACATTAATTTATAAA
*
625058 TTAAT-TTAATATTAATTTGATAA
1 TTAATATTAACATTAATTT-ATAA
625081 TTTTAATACT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (24 bp):
TTAATATTAACATTAATTTATAAA
Found at i:630273 original size:8 final size:8
Alignment explanation
Indices: 630260--630284 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
630250 AAATAGCGGA
630260 AGAAATTG
1 AGAAATTG
630268 AGAAATTG
1 AGAAATTG
630276 AGAAATTG
1 AGAAATTG
630284 A
1 A
630285 ACACATAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.24, T:0.24
Consensus pattern (8 bp):
AGAAATTG
Found at i:635149 original size:5 final size:5
Alignment explanation
Indices: 635135--635199 Score: 55
Period size: 5 Copynumber: 12.8 Consensus size: 5
635125 ACAAATAAAT
* *
635135 AAAAG AAAAAG AAAA- AAAAG -AAAG ACAAG CAAAACG AAACAG AAAGG
1 AAAAG -AAAAG AAAAG AAAAG AAAAG AAAAG -AAAA-G AAA-AG AAAAG
635182 AAAAG -AAAG AAAAG AAAA
1 AAAAG AAAAG AAAAG AAAA
635200 AGGGAAAGGG
Statistics
Matches: 49, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
4 12 0.24
5 20 0.41
6 15 0.31
7 2 0.04
ACGTcount: A:0.75, C:0.06, G:0.18, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:635190 original size:10 final size:9
Alignment explanation
Indices: 635136--635198 Score: 54
Period size: 9 Copynumber: 6.3 Consensus size: 9
635126 CAAATAAATA
635136 AAAGAAAAAG
1 AAAG-AAAAG
*
635146 AAAAAAAAG
1 AAAGAAAAG
*
635155 AAAGACAAG
1 AAAGAAAAG
635164 CAAAACGAAACAG
1 --AAA-GAAA-AG
635177 AAAGGAAAAG
1 AAA-GAAAAG
635187 AAAGAAAAG
1 AAAGAAAAG
635196 AAA
1 AAA
635199 AAGGGAAAGG
Statistics
Matches: 44, Mismatches: 5, Indels: 9
0.76 0.09 0.16
Matches are distributed among these distances:
9 21 0.48
10 8 0.18
11 10 0.23
12 3 0.07
13 2 0.05
ACGTcount: A:0.75, C:0.06, G:0.19, T:0.00
Consensus pattern (9 bp):
AAAGAAAAG
Found at i:650721 original size:59 final size:59
Alignment explanation
Indices: 650585--650705 Score: 242
Period size: 59 Copynumber: 2.1 Consensus size: 59
650575 TGTTAACAGC
650585 GATAACAATTGGATAAAAAAATTAAAGTAAAAAAAAGTAAATTCCTAAAAATAAAAAGA
1 GATAACAATTGGATAAAAAAATTAAAGTAAAAAAAAGTAAATTCCTAAAAATAAAAAGA
650644 GATAACAATTGGATAAAAAAATTAAAGTAAAAAAAAGTAAATTCCTAAAAATAAAAAGA
1 GATAACAATTGGATAAAAAAATTAAAGTAAAAAAAAGTAAATTCCTAAAAATAAAAAGA
650703 GAT
1 GAT
650706 GTGTAAATTT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 62 1.00
ACGTcount: A:0.64, C:0.05, G:0.11, T:0.21
Consensus pattern (59 bp):
GATAACAATTGGATAAAAAAATTAAAGTAAAAAAAAGTAAATTCCTAAAAATAAAAAGA
Found at i:668324 original size:14 final size:14
Alignment explanation
Indices: 668305--668335 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
668295 TACTATTTTC
668305 AAAATCTGATTCCA
1 AAAATCTGATTCCA
668319 AAAATCTGATTCCA
1 AAAATCTGATTCCA
668333 AAA
1 AAA
668336 TCAAACATAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.48, C:0.19, G:0.06, T:0.26
Consensus pattern (14 bp):
AAAATCTGATTCCA
Found at i:672755 original size:173 final size:174
Alignment explanation
Indices: 672548--672904 Score: 698
Period size: 173 Copynumber: 2.1 Consensus size: 174
672538 TTTCATATAT
*
672548 TTTAATTTTATTATACACACTTTATTATTTTCATCATTTGTATATATTAAGAATGTGTTTAATTG
1 TTTAATTTCATTATACACACTTTATTATTTTCATCATTTGTATATATTAAGAATGTGTTTAATTG
672613 AGTTGATGTCAGAAATTAACTTAACACCAACTTAAAGTTGATGACAAAACAATGATAAATAATTT
66 AGTTGATGTCAGAAATTAACTTAACACCAACTTAAAGTTGATGACAAAACAATGATAAATAATTT
672678 AATATTTTTTAATTCTAATATCATACATATTTTATGTATTATTA
131 AATATTTTTTAATTCTAATATCATACATATTTTATGTATTATTA
672722 TTTAATTTCATTATACACA-TTTATTATTTTCATCATTTGTATATATTAAGAATGTGTTTAATTG
1 TTTAATTTCATTATACACACTTTATTATTTTCATCATTTGTATATATTAAGAATGTGTTTAATTG
672786 AGTTGATGTCAGAAATTAACTTAACACCAACTTAAAGTTGATGACAAAACAATGATAAATAATTT
66 AGTTGATGTCAGAAATTAACTTAACACCAACTTAAAGTTGATGACAAAACAATGATAAATAATTT
672851 AATATTTTTTAATTCTAATATCATACATATTTTATGTATTATTA
131 AATATTTTTTAATTCTAATATCATACATATTTTATGTATTATTA
672895 TTTAATTTCA
1 TTTAATTTCA
672905 AGTCATACGT
Statistics
Matches: 182, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
173 164 0.90
174 18 0.10
ACGTcount: A:0.38, C:0.09, G:0.08, T:0.45
Consensus pattern (174 bp):
TTTAATTTCATTATACACACTTTATTATTTTCATCATTTGTATATATTAAGAATGTGTTTAATTG
AGTTGATGTCAGAAATTAACTTAACACCAACTTAAAGTTGATGACAAAACAATGATAAATAATTT
AATATTTTTTAATTCTAATATCATACATATTTTATGTATTATTA
Found at i:683955 original size:21 final size:22
Alignment explanation
Indices: 683931--683972 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
683921 ATCAAAAATT
683931 TATTTTAAAAAT-TTTAAAAAG
1 TATTTTAAAAATATTTAAAAAG
*
683952 TATTTTAAAAATATTTTAAAA
1 TATTTTAAAAATATTTAAAAA
683973 TTAAAAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (22 bp):
TATTTTAAAAATATTTAAAAAG
Done.