Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007887.1 Hibiscus syriacus cultivar Beakdansim tig00110267_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 327798
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 2
Found at i:3413 original size:16 final size:17
Alignment explanation
Indices: 3386--3420 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
3376 TATCGCCGAC
3386 CGAAATTTCACTATTCA
1 CGAAATTTCACTATTCA
3403 CGAAA-TTCACTATTCA
1 CGAAATTTCACTATTCA
3419 CG
1 CG
3421 TGAATAGTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.34, C:0.26, G:0.09, T:0.31
Consensus pattern (17 bp):
CGAAATTTCACTATTCA
Found at i:19312 original size:15 final size:15
Alignment explanation
Indices: 19288--19319 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
19278 TGGCAGATCG
*
19288 AAATCCAGAATGGGA
1 AAATCAAGAATGGGA
19303 AAATCAAGAATGGGA
1 AAATCAAGAATGGGA
19318 AA
1 AA
19320 GAAAGATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.53, C:0.09, G:0.25, T:0.12
Consensus pattern (15 bp):
AAATCAAGAATGGGA
Found at i:20036 original size:14 final size:14
Alignment explanation
Indices: 20019--20047 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
20009 CAAGACACCC
20019 AAGGCAGAAAAGTT
1 AAGGCAGAAAAGTT
20033 AAGGCAGAAAAGTT
1 AAGGCAGAAAAGTT
20047 A
1 A
20048 GAGTTGGTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.52, C:0.07, G:0.28, T:0.14
Consensus pattern (14 bp):
AAGGCAGAAAAGTT
Found at i:20756 original size:14 final size:14
Alignment explanation
Indices: 20737--20774 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
20727 GCTTAGGATT
20737 ATTGCACTTTAGTC
1 ATTGCACTTTAGTC
20751 ATTGCACTTTAGTC
1 ATTGCACTTTAGTC
*
20765 ATTGTACTTT
1 ATTGCACTTT
20775 GGGGTATTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.21, C:0.18, G:0.13, T:0.47
Consensus pattern (14 bp):
ATTGCACTTTAGTC
Found at i:24998 original size:16 final size:16
Alignment explanation
Indices: 24977--25010 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
24967 TTACTATTCA
*
24977 CGTGAATAGTGAATTT
1 CGTGAATAGTGAAATT
24993 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
25009 CG
1 CG
25011 GTCGGCGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.32
Consensus pattern (16 bp):
CGTGAATAGTGAAATT
Found at i:31711 original size:183 final size:184
Alignment explanation
Indices: 31398--31784 Score: 631
Period size: 183 Copynumber: 2.1 Consensus size: 184
31388 ATTTCTAATT
* *
31398 TATATAA-AAATTAAATATTTTTTAATTCAAAAAAAGTTTATAATTAATTTAAATAATATATAAT
1 TATATAATATATTTAATATTTTTTAATTCAAAAAAAGTTTATAATTAATTTAAATAATATATAAT
*
31462 TATAAAATAAAAATATTAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATT
66 TATAAAATAAAAATATTAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAATTATT
* * *
31527 GGATCTTAAATTATTAATTGGGTTTGAAATGGTTTGGGCTT-AACCCATATGTTA
131 GGATCTTAAATTATTAATTGGGTTTGAAATGATTTGGG-TTGAACCAATATATTA
31581 TATATAATATATTTAATATTTTTTAATT-AAAAAACAGTTTATAATTAATTTAAATAATATATAA
1 TATATAATATATTTAATATTTTTTAATTCAAAAAA-AGTTTATAATTAATTTAAATAATATATAA
*
31645 TTATAAAATAAAAA-ATT-TATATAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAATTA
65 TTATAAAATAAAAATATTAGATA-AATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAATTA
* *
31708 TTGGATCTTAAATTATTAATTGGGTTTTAAATGATTTGGGTTGAGCCAATATATTA
129 TTGGATCTTAAATTATTAATTGGGTTTGAAATGATTTGGGTTGAACCAATATATTA
31764 TATATAATATATTTAATATTT
1 TATATAATATATTTAATATTT
31785 AAAATTTAAT
Statistics
Matches: 191, Mismatches: 9, Indels: 8
0.92 0.04 0.04
Matches are distributed among these distances:
182 5 0.03
183 125 0.65
184 61 0.32
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.46
Consensus pattern (184 bp):
TATATAATATATTTAATATTTTTTAATTCAAAAAAAGTTTATAATTAATTTAAATAATATATAAT
TATAAAATAAAAATATTAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAATTATT
GGATCTTAAATTATTAATTGGGTTTGAAATGATTTGGGTTGAACCAATATATTA
Found at i:31927 original size:18 final size:18
Alignment explanation
Indices: 31906--31942 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
31896 AATTCGGTTC
*
31906 GATCGGTTAATCGAATTA
1 GATCGGTTAACCGAATTA
31924 GATCGGTTAACCGAATTA
1 GATCGGTTAACCGAATTA
31942 G
1 G
31943 TTGGATTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.32, C:0.14, G:0.24, T:0.30
Consensus pattern (18 bp):
GATCGGTTAACCGAATTA
Found at i:34321 original size:23 final size:23
Alignment explanation
Indices: 34289--34335 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 23
34279 CTTTTAGAAA
34289 TTAATATTTTCTT-ATTTTTATT
1 TTAATATTTTCTTAATTTTTATT
34311 TTAATATTTTTCTTAATTTTTATT
1 TTAATA-TTTTCTTAATTTTTATT
34335 T
1 T
34336 ATTTCTCTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 6 0.26
23 7 0.30
24 10 0.43
ACGTcount: A:0.23, C:0.04, G:0.00, T:0.72
Consensus pattern (23 bp):
TTAATATTTTCTTAATTTTTATT
Found at i:35010 original size:38 final size:37
Alignment explanation
Indices: 34812--35106 Score: 280
Period size: 38 Copynumber: 7.8 Consensus size: 37
34802 ATATCTATAT
* ** *
34812 ATATATATTATATAG-TTTGCAAACAGTTTTTGAAGATAC
1 ATATATAATATATAGTTTTTAAAACA--TTTTGAA-AAAC
* *
34851 ATATATAATATATAGTTTCTAAAAACATTTTG-AAAAT
1 ATATATAATATATAGTTT-TTAAAACATTTTGAAAAAC
*
34888 GTATATAATATATAGTTTTTAAAACACTTTTG-AAAAC
1 ATATATAATATATAGTTTTTAAAACA-TTTTGAAAAAC
*
34925 -TATATAATATATAGTTTTTAAAACATTTT-AGAAA-
1 ATATATAATATATAGTTTTTAAAACATTTTGAAAAAC
34959 ATATATAATATATAGTTTTTAAAATCATTTTGAAAAAC
1 ATATATAATATATAGTTTTTAAAA-CATTTTGAAAAAC
* *
34997 ATATATAATATATATTTTTTGAAAACATATTTTAAAAAAAC
1 ATATATAATATATAGTTTTT-AAAAC--ATTTT-GAAAAAC
* * *
35038 TTATATAATATATAGTTTTTGAAAATACTTTT-TAAAAC
1 ATATATAATATATAGTTTTT-AAAACA-TTTTGAAAAAC
* * *
35076 TTATATAATATATAATTTTAAAAAACATTTT
1 ATATATAATATATAGTTTT-TAAAACATTTT
35107 TTGAAAATTA
Statistics
Matches: 223, Mismatches: 19, Indels: 30
0.82 0.07 0.11
Matches are distributed among these distances:
35 30 0.13
36 38 0.17
37 36 0.16
38 49 0.22
39 24 0.11
40 11 0.05
41 35 0.16
ACGTcount: A:0.46, C:0.05, G:0.06, T:0.43
Consensus pattern (37 bp):
ATATATAATATATAGTTTTTAAAACATTTTGAAAAAC
Found at i:35108 original size:38 final size:37
Alignment explanation
Indices: 34813--35164 Score: 277
Period size: 36 Copynumber: 9.5 Consensus size: 37
34803 TATCTATATA
* ** *
34813 TATATATTATATAG-TTTGCAAACAGTTTTTGAAGATACA
1 TATATAATATATAGTTTTAAAAACA-TTTTTGAA-A-ACT
34852 TATATAATATATAGTTTCTAAAAACA-TTTTGAAAA-T
1 TATATAATATATAGTTT-TAAAAACATTTTTGAAAACT
* *
34888 GTATATAATATATAGTTTTTAAAACACTTTTGAAAAC-
1 -TATATAATATATAGTTTTAAAAACATTTTTGAAAACT
* *
34925 TATATAATATATAGTTTTTAAAACATTTTAGAAAA--
1 TATATAATATATAGTTTTAAAAACATTTTTGAAAACT
* *
34960 TATATAATATATAGTTTTTAAAATCA-TTTTGAAAAACA
1 TATATAATATATAG-TTTTAAAAACATTTTTG-AAAACT
* * *
34998 TATATAATATATATTTTTTGAAAACATATTTTAAAAAAACT
1 TATATAATATATA-GTTTTAAAAACAT-TTTT--GAAAACT
35039 TATATAATATATAGTTTTTGAAAATAC-TTTTT-AAAACT
1 TATATAATATATAG-TTTT-AAAA-ACATTTTTGAAAACT
*
35077 TATATAATATATAATTTTAAAAAACATTTTTTGAAAA-T
1 TATATAATATATAGTTTT-AAAAACA-TTTTTGAAAACT
* * *
35115 TATAT-A-GT-T--TTTAAAAAACATTTTTGAAAATT
1 TATATAATATATAGTTTTAAAAACATTTTTGAAAACT
*
35147 TATAT-GTAATATAGTTTT
1 TATATAAT-ATATAGTTTT
35165 TTAAAATGTT
Statistics
Matches: 263, Mismatches: 24, Indels: 54
0.77 0.07 0.16
Matches are distributed among these distances:
31 10 0.04
32 13 0.05
33 3 0.01
34 1 0.00
35 20 0.08
36 56 0.21
37 39 0.15
38 53 0.20
39 24 0.09
40 6 0.02
41 32 0.12
42 4 0.02
43 2 0.01
ACGTcount: A:0.45, C:0.05, G:0.06, T:0.44
Consensus pattern (37 bp):
TATATAATATATAGTTTTAAAAACATTTTTGAAAACT
Found at i:35128 original size:32 final size:32
Alignment explanation
Indices: 35091--35151 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
35081 TAATATATAA
35091 TTTTAAAAAACATTTTTTGAAAA-TTATATAGT
1 TTTTAAAAAACA-TTTTTGAAAATTTATATAGT
35123 TTTTAAAAAACATTTTTGAAAATTTATAT
1 TTTTAAAAAACATTTTTGAAAATTTATAT
35152 GTAATATAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
31 10 0.36
32 18 0.64
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (32 bp):
TTTTAAAAAACATTTTTGAAAATTTATATAGT
Found at i:35131 original size:31 final size:32
Alignment explanation
Indices: 35084--35151 Score: 95
Period size: 31 Copynumber: 2.2 Consensus size: 32
35074 ACTTATATAA
35084 TATATAATTTT-AAAAAACATTTTTTGAAAA-T
1 TATATAATTTTAAAAAAACA-TTTTTGAAAATT
* *
35115 TATATAGTTTTTAAAAAACATTTTTGAAAATT
1 TATATAATTTTAAAAAAACATTTTTGAAAATT
35147 TATAT
1 TATAT
35152 GTAATATAGT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
31 20 0.59
32 14 0.41
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (32 bp):
TATATAATTTTAAAAAAACATTTTTGAAAATT
Found at i:35143 original size:150 final size:146
Alignment explanation
Indices: 34832--35205 Score: 372
Period size: 148 Copynumber: 2.5 Consensus size: 146
34822 TATAGTTTGC
* * * * *
34832 AAACAGTTTTTGAAGATACATATATAATATATAGTTTCTAAAAACATTTT--GAAAATGTATATA
1 AAACA-TTTTTGAA-AAACATATATAATATATATTTTTTAAAAATATTTTAAAAAAAT-TATATA
* *
34895 ATATATAGTTTTTAAAACACTTTTGAAAACTATATAATATATAGTTTTTAAAACATTTTAGAAAA
63 ATATATAGTTTTTAAAACACTTTTGAAAACTATATAATATATAATTTTAAAAACATTTTAG-AAA
34960 TATATAATATATAGTTTTTAA
127 TATAT-ATATATAGTTTTTAA
*
34981 AATCA-TTTTGAAAAACATATATAATATATATTTTTTGAAAACATATTTTAAAAAAACTTATATA
1 AAACATTTTTGAAAAACATATATAATATATATTTTTT-AAAA-ATATTTTAAAAAAA-TTATATA
* * *
35045 ATATATAGTTTTTGAAAATACTTTTTAAAACTTATATAATATATAATTTTAAAAAACATTTTTTG
63 ATATATAGTTTTT-AAAACACTTTTGAAAAC-TATATAATATATAATTTT-AAAAACA-TTTTAG
35110 -AA-A-AT-TATATAGTTTTTAAA
124 AAATATATATATATAGTTTTT-AA
** * * *
35130 AAACATTTTTGAAAATTTATATGTAATATA-GTTTTTT-AAAATGTTTTTAAAAAAAAGTT-TAT
1 AAACATTTTTGAAAA-ACATATATAATATATATTTTTTAAAAAT-ATTTT-AAAAAAA-TTATAT
*
35192 ATTATATAGTTTTT
62 AATATATAGTTTTT
35206 TTTAAAAAAA
Statistics
Matches: 192, Mismatches: 19, Indels: 29
0.80 0.08 0.12
Matches are distributed among these distances:
146 21 0.11
147 13 0.07
148 41 0.21
149 19 0.10
150 40 0.21
151 28 0.15
152 19 0.10
153 6 0.03
154 5 0.03
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.44
Consensus pattern (146 bp):
AAACATTTTTGAAAAACATATATAATATATATTTTTTAAAAATATTTTAAAAAAATTATATAATA
TATAGTTTTTAAAACACTTTTGAAAACTATATAATATATAATTTTAAAAACATTTTAGAAATATA
TATATATAGTTTTTAA
Found at i:35207 original size:150 final size:148
Alignment explanation
Indices: 34812--35205 Score: 364
Period size: 150 Copynumber: 2.7 Consensus size: 148
34802 ATATCTATAT
** * ** * * *
34812 ATATATATTATATAGTTTGCAAACAGTTTTTGAAGATACATATATAATATATAGTTTCT-AAAA-
1 ATATATA-TATATAGTTTTTAAAAACATTTTGAA-AAACATATATAATATATATTTTTTGAAAAC
* *
34875 ACATTTT--GAAAA-TGTATATAATATATAGTTTTTAAAACACTTTTGAAAACTATATAATATAT
64 ATATTTTAAAAAAACT-TATATAATATATAGTTTTTAAAACACTTTTGAAAACTATATAATATAT
* *
34937 AGTTTTTAAAACATTTTAGAAA
128 AATTTTAAAAACATTTTAG-AA
*
34959 ATATATAATATATAGTTTTTAAAATCATTTTGAAAAACATATATAATATATATTTTTTGAAAACA
1 ATATAT-ATATATAGTTTTTAAAAACATTTTGAAAAACATATATAATATATATTTTTTGAAAACA
* *
35024 TATTTTAAAAAAACTTATATAATATATAGTTTTTGAAAATACTTTTTAAAACTTATATAATATAT
65 TATTTTAAAAAAACTTATATAATATATAGTTTTT-AAAACACTTTTGAAAAC-TATATAATATAT
*
35089 AATTTTAAAAAACATTTTTTG-A
128 AATTTT-AAAAACA-TTTTAGAA
** * *
35111 A-A-AT-TATATAGTTTTTAAAAAACATTTTTGAAAATTTATATGTAATATA-GTTTTTT-AAAA
1 ATATATATATATAGTTTTT-AAAAACA-TTTTGAAAA-ACATATATAATATATATTTTTTGAAAA
** * *
35171 TGT-TTTTAAAAAAAAGTT-TATATTATATAGTTTTT
63 CATATTTT-AAAAAAACTTATATAATATATAGTTTTT
35206 TTTAAAAAAA
Statistics
Matches: 208, Mismatches: 25, Indels: 27
0.80 0.10 0.10
Matches are distributed among these distances:
146 21 0.10
147 30 0.14
148 39 0.19
149 20 0.10
150 40 0.19
151 28 0.13
152 19 0.09
153 6 0.03
154 5 0.02
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (148 bp):
ATATATATATATAGTTTTTAAAAACATTTTGAAAAACATATATAATATATATTTTTTGAAAACAT
ATTTTAAAAAAACTTATATAATATATAGTTTTTAAAACACTTTTGAAAACTATATAATATATAAT
TTTAAAAACATTTTAGAA
Found at i:35235 original size:16 final size:16
Alignment explanation
Indices: 35216--35267 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
35206 TTTAAAAAAA
35216 TATTTTTATTTTTTAT
1 TATTTTTATTTTTTAT
* *
35232 TATTTTTAATTTTTAA
1 TATTTTTATTTTTTAT
*
35248 T-TTTTTATTATTTTTT
1 TATTTTTATT-TTTTAT
35264 TATT
1 TATT
35268 ACTTATATAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
15 7 0.24
16 20 0.69
17 2 0.07
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (16 bp):
TATTTTTATTTTTTAT
Found at i:35238 original size:17 final size:17
Alignment explanation
Indices: 35218--35268 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 17
35208 TAAAAAAATA
35218 TTTTTATTTTTTATTAT
1 TTTTTATTTTTTATTAT
* *
35235 TTTTAATTTTTAATT-T
1 TTTTTATTTTTTATTAT
35251 TTTATTATTTTTTTATTA
1 TTT-TTA-TTTTTTATTA
35269 CTTATATATA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
16 4 0.15
17 15 0.56
18 8 0.30
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTTTATTTTTTATTAT
Found at i:36421 original size:27 final size:27
Alignment explanation
Indices: 36347--36421 Score: 64
Period size: 27 Copynumber: 2.8 Consensus size: 27
36337 ATTTCACCCC
* *
36347 TGTTTTACTATTATTCTAAT-TCATACA
1 TGTTTTA-TATTATTTTAATATTATACA
* * ** *
36374 T-TTTTATGTTTTTTTTGTATTATATA
1 TGTTTTATATTATTTTAATATTATACA
36400 TGTTTTATATTATTTTAATATT
1 TGTTTTATATTATTTTAATATT
36422 TTTTCTTTTT
Statistics
Matches: 35, Mismatches: 11, Indels: 4
0.70 0.22 0.08
Matches are distributed among these distances:
25 7 0.20
26 11 0.31
27 17 0.49
ACGTcount: A:0.25, C:0.05, G:0.05, T:0.64
Consensus pattern (27 bp):
TGTTTTATATTATTTTAATATTATACA
Found at i:37260 original size:2 final size:2
Alignment explanation
Indices: 37253--37277 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
37243 ATCAACGATC
37253 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
37278 ATCAAATGCT
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:38504 original size:13 final size:13
Alignment explanation
Indices: 38486--38512 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
38476 TTACAGACGC
38486 GCATATGAAGACT
1 GCATATGAAGACT
38499 GCATATGAAGACT
1 GCATATGAAGACT
38512 G
1 G
38513 TTCAACTATG
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:0.37, C:0.15, G:0.26, T:0.22
Consensus pattern (13 bp):
GCATATGAAGACT
Found at i:40535 original size:20 final size:21
Alignment explanation
Indices: 40506--40544 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
40496 CTCTTAAATT
*
40506 TCTGATATAAAATT-TACACA
1 TCTGACATAAAATTATACACA
40526 TCTGACATAAAATTATACA
1 TCTGACATAAAATTATACA
40545 TCTATTTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.46, C:0.15, G:0.05, T:0.33
Consensus pattern (21 bp):
TCTGACATAAAATTATACACA
Found at i:40844 original size:20 final size:20
Alignment explanation
Indices: 40819--40868 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
40809 AATTTTGGTT
*
40819 TTGATTAATTCGGTTCGAAA
1 TTGATTAATTCGATTCGAAA
*
40839 TTGATTAATTCGATTCTAAA
1 TTGATTAATTCGATTCGAAA
*
40859 TTGGTTAATT
1 TTGATTAATT
40869 AACTGAATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.30, C:0.08, G:0.16, T:0.46
Consensus pattern (20 bp):
TTGATTAATTCGATTCGAAA
Found at i:42293 original size:18 final size:18
Alignment explanation
Indices: 42270--42308 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
42260 TCAATTTGTA
42270 ACTTATAAAAGTTAAGAG
1 ACTTATAAAAGTTAAGAG
42288 ACTTATAAAAGTTAAGAG
1 ACTTATAAAAGTTAAGAG
42306 ACT
1 ACT
42309 CGACAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.49, C:0.08, G:0.15, T:0.28
Consensus pattern (18 bp):
ACTTATAAAAGTTAAGAG
Found at i:44784 original size:25 final size:25
Alignment explanation
Indices: 44756--44843 Score: 77
Period size: 25 Copynumber: 3.3 Consensus size: 25
44746 AAATCCAAAC
44756 CCGAAACTCAACTTTAAATCTGAAT
1 CCGAAACTCAACTTTAAATCTGAAT
* *
44781 CCGAACCCGACACTCAACTTTAAGTCTGAAC
1 CCG-A----A-ACTCAACTTTAAATCTGAAT
* *
44812 CCGAAGCTCAACTTCAAATCTGAAT
1 CCGAAACTCAACTTTAAATCTGAAT
*
44837 CTGAAAC
1 CCGAAAC
44844 CGACACTCAG
Statistics
Matches: 49, Mismatches: 8, Indels: 12
0.71 0.12 0.17
Matches are distributed among these distances:
25 24 0.49
26 2 0.04
30 2 0.04
31 21 0.43
ACGTcount: A:0.36, C:0.30, G:0.11, T:0.23
Consensus pattern (25 bp):
CCGAAACTCAACTTTAAATCTGAAT
Found at i:44809 original size:31 final size:31
Alignment explanation
Indices: 44721--44885 Score: 153
Period size: 31 Copynumber: 5.5 Consensus size: 31
44711 ACACATATTT
* * * *
44721 GAACCCAAAACTCAACTTTAAGTCTAAATCC
1 GAACCCGACACTCAACTTTAAATCTGAATCC
* *
44752 AAACCCGAAACTCAACTTTAAATCTGAATCC
1 GAACCCGACACTCAACTTTAAATCTGAATCC
* *
44783 GAACCCGACACTCAACTTTAAGTCTGAACCC
1 GAACCCGACACTCAACTTTAAATCTGAATCC
* *
44814 GAA---G---CTCAACTTCAAATCTGAATCT
1 GAACCCGACACTCAACTTTAAATCTGAATCC
* *
44839 GAAACCGACACTCAGAACTTTAAATCCGAATCC
1 GAACCCGACACTC--AACTTTAAATCTGAATCC
*
44872 AAACCCGACACTCA
1 GAACCCGACACTCA
44886 GTCTAAATCC
Statistics
Matches: 109, Mismatches: 17, Indels: 16
0.77 0.12 0.11
Matches are distributed among these distances:
25 20 0.18
28 2 0.02
31 61 0.56
33 26 0.24
ACGTcount: A:0.39, C:0.31, G:0.10, T:0.21
Consensus pattern (31 bp):
GAACCCGACACTCAACTTTAAATCTGAATCC
Found at i:44847 original size:56 final size:57
Alignment explanation
Indices: 44753--44861 Score: 166
Period size: 56 Copynumber: 1.9 Consensus size: 57
44743 TCTAAATCCA
* *
44753 AACCCGAAACTCAACTTTAAATCTGAATCCGAACCCGACACTC-AACTTTAAGTCTG
1 AACCCGAAACTCAACTTCAAATCTGAATCCGAAACCGACACTCAAACTTTAAGTCTG
* *
44809 AACCCGAAGCTCAACTTCAAATCTGAATCTGAAACCGACACTCAGAACTTTAA
1 AACCCGAAACTCAACTTCAAATCTGAATCCGAAACCGACACTCA-AACTTTAA
44862 ATCCGAATCC
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
56 39 0.83
58 8 0.17
ACGTcount: A:0.38, C:0.29, G:0.11, T:0.22
Consensus pattern (57 bp):
AACCCGAAACTCAACTTCAAATCTGAATCCGAAACCGACACTCAAACTTTAAGTCTG
Found at i:44864 original size:33 final size:33
Alignment explanation
Indices: 44821--44886 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
44811 CCCGAAGCTC
* *
44821 AACTTCAAATCTGAATCTGAAA-CCGACACTCAG
1 AACTTCAAATCCGAATC-CAAACCCGACACTCAG
*
44854 AACTTTAAATCCGAATCCAAACCCGACACTCAG
1 AACTTCAAATCCGAATCCAAACCCGACACTCAG
44887 TCTAAATCCA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 3 0.10
33 26 0.90
ACGTcount: A:0.39, C:0.30, G:0.11, T:0.20
Consensus pattern (33 bp):
AACTTCAAATCCGAATCCAAACCCGACACTCAG
Found at i:54200 original size:28 final size:29
Alignment explanation
Indices: 54148--54213 Score: 98
Period size: 28 Copynumber: 2.3 Consensus size: 29
54138 TTAAATTAAA
*
54148 AATATTTAATAAATTATGTTCATATTTAT
1 AATATTTAATAAATTATGTTAATATTTAT
54177 AATATTTAAT-AATTATGTTAATATTTAT
1 AATATTTAATAAATTATGTTAATATTTAT
**
54205 TGTATTTAA
1 AATATTTAA
54214 CCTTACTGTG
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
28 24 0.71
29 10 0.29
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.53
Consensus pattern (29 bp):
AATATTTAATAAATTATGTTAATATTTAT
Found at i:58232 original size:33 final size:35
Alignment explanation
Indices: 58177--58243 Score: 84
Period size: 34 Copynumber: 1.9 Consensus size: 35
58167 TAAGATAATA
* *
58177 AGATAATAGTATAATTACATC-TTATATATATTTAG
1 AGATAATA-TATAATAACATCTTTATACATATTTAG
*
58212 AGATAAT-TATAATAATATCTTTATACATATTT
1 AGATAATATATAATAACATCTTTATACATATTT
58244 TACAAATAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
33 10 0.36
34 11 0.39
35 7 0.25
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.45
Consensus pattern (35 bp):
AGATAATATATAATAACATCTTTATACATATTTAG
Found at i:60883 original size:12 final size:12
Alignment explanation
Indices: 60858--60950 Score: 64
Period size: 12 Copynumber: 7.8 Consensus size: 12
60848 ACGGAGATAT
* *
60858 CAGAAATCAAAA
1 CAGAATTCAGAA
60870 CAGAATTCAGAA
1 CAGAATTCAGAA
60882 CAGATATT-AGAA
1 CAGA-ATTCAGAA
* * * *
60894 CATAATCCATAT
1 CAGAATTCAGAA
*
60906 CAGAAATCAGAA
1 CAGAATTCAGAA
**
60918 CAGAATTCAGGT
1 CAGAATTCAGAA
*
60930 CATGTA-TCAGAA
1 CA-GAATTCAGAA
60942 CAGAATTCA
1 CAGAATTCA
60951 AGTCGAAAAT
Statistics
Matches: 59, Mismatches: 18, Indels: 8
0.69 0.21 0.09
Matches are distributed among these distances:
11 4 0.07
12 50 0.85
13 5 0.08
ACGTcount: A:0.48, C:0.17, G:0.14, T:0.20
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:60885 original size:24 final size:24
Alignment explanation
Indices: 60858--60950 Score: 80
Period size: 24 Copynumber: 3.9 Consensus size: 24
60848 ACGGAGATAT
*
60858 CAGAAATCAAAACAGAATTCAGAA
1 CAGAAATCAGAACAGAATTCAGAA
* * * * * *
60882 CAGATATTAGAACATAATCCATAT
1 CAGAAATCAGAACAGAATTCAGAA
**
60906 CAGAAATCAGAACAGAATTCAGGT
1 CAGAAATCAGAACAGAATTCAGAA
*
60930 CATG-TATCAGAACAGAATTCA
1 CA-GAAATCAGAACAGAATTCA
60951 AGTCGAAAAT
Statistics
Matches: 54, Mismatches: 14, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
24 53 0.98
25 1 0.02
ACGTcount: A:0.48, C:0.17, G:0.14, T:0.20
Consensus pattern (24 bp):
CAGAAATCAGAACAGAATTCAGAA
Found at i:60962 original size:24 final size:24
Alignment explanation
Indices: 60909--60964 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
60899 TCCATATCAG
*
60909 AAATCAGAACAGAATTCAGGTCAT
1 AAATCAGAACAGAATTCAAGTCAT
**
60933 GTATCAGAACAGAATTCAAGTCGA-
1 AAATCAGAACAGAATTCAAGTC-AT
60957 AAATCAGA
1 AAATCAGA
60965 TAAAATAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
24 25 0.96
25 1 0.04
ACGTcount: A:0.46, C:0.16, G:0.18, T:0.20
Consensus pattern (24 bp):
AAATCAGAACAGAATTCAAGTCAT
Found at i:62124 original size:18 final size:18
Alignment explanation
Indices: 62103--62138 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
62093 CTTCCATCCG
*
62103 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
62121 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
62139 GTCCTTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:63479 original size:13 final size:13
Alignment explanation
Indices: 63461--63490 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
63451 AAGGGTCAAC
63461 GGTCAACGGGTCG
1 GGTCAACGGGTCG
63474 GGTCAACGGGTCG
1 GGTCAACGGGTCG
63487 GGTC
1 GGTC
63491 GGGTTGTGAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.13, C:0.23, G:0.47, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:69448 original size:14 final size:13
Alignment explanation
Indices: 69417--69441 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
69407 GTAAATAATT
69417 AATAAAAATTATA
1 AATAAAAATTATA
69430 AATAAAAATTAT
1 AATAAAAATTAT
69442 TTTATAATTA
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
AATAAAAATTATA
Found at i:73925 original size:15 final size:15
Alignment explanation
Indices: 73905--73937 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
73895 AGCGCGACAT
*
73905 CTTTAGAGACTTTGA
1 CTTTAGAGAATTTGA
73920 CTTTAGAGAATTTGA
1 CTTTAGAGAATTTGA
73935 CTT
1 CTT
73938 CCTTTGATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.27, C:0.12, G:0.18, T:0.42
Consensus pattern (15 bp):
CTTTAGAGAATTTGA
Found at i:81271 original size:2 final size:2
Alignment explanation
Indices: 81266--81308 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
81256 AATATATGTT
81266 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
81308 A
1 A
81309 CATACTGCAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:82587 original size:34 final size:32
Alignment explanation
Indices: 82501--82603 Score: 127
Period size: 31 Copynumber: 3.2 Consensus size: 32
82491 ATAAATGTTT
*
82501 TTAAAATACAAATTATATATTCAAAATTTAAAA
1 TTAAAATA-AAATTATATATTCGAAATTTAAAA
* * *
82534 -AAAAATAAAAATATTTATTCGAAATTTAAAA
1 TTAAAATAAAATTATATATTCGAAATTTAAAA
*
82565 TTAAAATATAAATTATAGTATTCGAAATTTAACA
1 TTAAAATA-AAATTATA-TATTCGAAATTTAAAA
82599 TTAAA
1 TTAAA
82604 TTTCAACTTA
Statistics
Matches: 59, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
31 21 0.36
32 12 0.20
33 6 0.10
34 20 0.34
ACGTcount: A:0.56, C:0.05, G:0.03, T:0.36
Consensus pattern (32 bp):
TTAAAATAAAATTATATATTCGAAATTTAAAA
Found at i:83240 original size:126 final size:125
Alignment explanation
Indices: 82945--83256 Score: 488
Period size: 114 Copynumber: 2.6 Consensus size: 125
82935 TTACCTGATT
82945 TACTGATATATCTAGTGTCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCT-T
1 TACTGATATATCTAGTGTCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
*
83009 GAC--AA-AATGGAAGGCGCGCCCCCGGGAACGCCTTCATGTGAATAGTGAAATAATAGG
66 GACAAAATAATGGAAGGCGCGCCCCCGGGAACGCCTTCATGTGAATAGTAAAATAATAGG
83066 TACTGATATA--TAG-G----GAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
1 TACTGATATATCTAGTGTCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
83124 GACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTAAAATAATAGG
66 GACAAAATAATGGAAGGCGCGCCCCCGGGAA--CGCCTTCATGTGAATAGTAAAATAATAGG
* *
83186 TAC-GATATATCTAGTGTCCCGAGGGACATGCGTGACATAATAGGGCAATTATAACATA-TCTCT
1 TACTGATATATCTAGTGTCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
83249 GACAAAAT
66 GACAAAAT
83257 GTGAAGCAAC
Statistics
Matches: 175, Mismatches: 3, Indels: 22
0.88 0.01 0.11
Matches are distributed among these distances:
114 42 0.24
115 4 0.02
117 2 0.01
118 24 0.14
119 9 0.05
120 31 0.18
121 13 0.07
122 1 0.01
125 13 0.07
126 36 0.21
ACGTcount: A:0.35, C:0.18, G:0.24, T:0.23
Consensus pattern (125 bp):
TACTGATATATCTAGTGTCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
GACAAAATAATGGAAGGCGCGCCCCCGGGAACGCCTTCATGTGAATAGTAAAATAATAGG
Found at i:86281 original size:17 final size:17
Alignment explanation
Indices: 86255--86292 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
86245 TTGTGATGGT
*
86255 AATTAACCATAGTTTTG
1 AATTAACCATAATTTTG
*
86272 AATTAGCCATAATTTTG
1 AATTAACCATAATTTTG
86289 AATT
1 AATT
86293 TATTTGTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.37, C:0.11, G:0.11, T:0.42
Consensus pattern (17 bp):
AATTAACCATAATTTTG
Found at i:95995 original size:7 final size:7
Alignment explanation
Indices: 95983--96019 Score: 67
Period size: 7 Copynumber: 5.4 Consensus size: 7
95973 GTCAAAGAAA
95983 GTCAACG
1 GTCAACG
95990 GTCAACG
1 GTCAACG
95997 GTC-ACG
1 GTCAACG
96003 GTCAACG
1 GTCAACG
96010 GTCAACG
1 GTCAACG
96017 GTC
1 GTC
96020 GGGTCGGGTC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 6 0.21
7 23 0.79
ACGTcount: A:0.24, C:0.30, G:0.30, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:96005 original size:13 final size:14
Alignment explanation
Indices: 95983--96019 Score: 67
Period size: 13 Copynumber: 2.7 Consensus size: 14
95973 GTCAAAGAAA
95983 GTCAACGGTCAACG
1 GTCAACGGTCAACG
95997 GTC-ACGGTCAACG
1 GTCAACGGTCAACG
96010 GTCAACGGTC
1 GTCAACGGTC
96020 GGGTCGGGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 13 0.59
14 9 0.41
ACGTcount: A:0.24, C:0.30, G:0.30, T:0.16
Consensus pattern (14 bp):
GTCAACGGTCAACG
Found at i:96031 original size:17 final size:17
Alignment explanation
Indices: 96009--96065 Score: 105
Period size: 17 Copynumber: 3.4 Consensus size: 17
95999 CACGGTCAAC
*
96009 GGTCAACGGTCGGGTCG
1 GGTCAACAGTCGGGTCG
96026 GGTCAACAGTCGGGTCG
1 GGTCAACAGTCGGGTCG
96043 GGTCAACAGTCGGGTCG
1 GGTCAACAGTCGGGTCG
96060 GGTCAA
1 GGTCAA
96066 ACCGGTTCGA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
17 39 1.00
ACGTcount: A:0.18, C:0.23, G:0.42, T:0.18
Consensus pattern (17 bp):
GGTCAACAGTCGGGTCG
Found at i:96080 original size:10 final size:10
Alignment explanation
Indices: 96062--96111 Score: 59
Period size: 9 Copynumber: 5.1 Consensus size: 10
96052 TCGGGTCGGG
96062 TCAAACCGGT
1 TCAAACCGGT
*
96072 TCGAACCGG-
1 TCAAACCGGT
96081 TCAAACCGGT
1 TCAAACCGGT
*
96091 TCAAAACTGG-
1 TC-AAACCGGT
96101 TCAAACCGGT
1 TCAAACCGGT
96111 T
1 T
96112 TTCCAGCAGC
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
9 14 0.42
10 13 0.39
11 6 0.18
ACGTcount: A:0.30, C:0.28, G:0.22, T:0.20
Consensus pattern (10 bp):
TCAAACCGGT
Found at i:96084 original size:19 final size:20
Alignment explanation
Indices: 96060--96111 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
96050 AGTCGGGTCG
*
96060 GGTCAAACCGGTTC-GAACC
1 GGTCAAACCGGTTCAAAACC
*
96079 GGTCAAACCGGTTCAAAACT
1 GGTCAAACCGGTTCAAAACC
96099 GGTCAAACCGGTT
1 GGTCAAACCGGTT
96112 TTCCAGCAGC
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.29, C:0.27, G:0.25, T:0.19
Consensus pattern (20 bp):
GGTCAAACCGGTTCAAAACC
Found at i:103206 original size:17 final size:17
Alignment explanation
Indices: 103184--103255 Score: 117
Period size: 17 Copynumber: 4.2 Consensus size: 17
103174 CAACGGTCAC
*
103184 GGTCAACGGTCGGGTCG
1 GGTCAACAGTCGGGTCG
*
103201 GGTCAACGGTCGGGTCG
1 GGTCAACAGTCGGGTCG
*
103218 GGTCAACAGTTGGGTCG
1 GGTCAACAGTCGGGTCG
103235 GGTCAACAGTCGGGTCG
1 GGTCAACAGTCGGGTCG
103252 GGTC
1 GGTC
103256 GGGTCAACCC
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 52 1.00
ACGTcount: A:0.14, C:0.22, G:0.44, T:0.19
Consensus pattern (17 bp):
GGTCAACAGTCGGGTCG
Found at i:103233 original size:22 final size:20
Alignment explanation
Indices: 103190--103263 Score: 79
Period size: 17 Copynumber: 3.9 Consensus size: 20
103180 TCACGGTCAA
103190 CGGTCGGGTCGGGTC-A-A-
1 CGGTCGGGTCGGGTCAACAG
103207 CGGTCGGGTCGGGTCAACA-
1 CGGTCGGGTCGGGTCAACAG
*
103226 --GTTGGGTCGGGTCAACAG
1 CGGTCGGGTCGGGTCAACAG
103244 TCGGGTCGGGTCGGGTCAAC
1 -C-GGTCGGGTCGGGTCAAC
103264 CCGGTTCAGA
Statistics
Matches: 48, Mismatches: 2, Indels: 9
0.81 0.03 0.15
Matches are distributed among these distances:
17 31 0.65
18 1 0.02
19 1 0.02
22 15 0.31
ACGTcount: A:0.14, C:0.23, G:0.45, T:0.19
Consensus pattern (20 bp):
CGGTCGGGTCGGGTCAACAG
Found at i:103277 original size:10 final size:10
Alignment explanation
Indices: 103259--103327 Score: 63
Period size: 9 Copynumber: 7.1 Consensus size: 10
103249 TCGGGTCGGG
*
103259 TCAACCCGGT
1 TCAAACCGGT
*
103269 TCAGACCGG-
1 TCAAACCGGT
*
103278 TCAAACCAGT
1 TCAAACCGGT
*
103288 TCGAACCGG-
1 TCAAACCGGT
103297 TCAAACCGGT
1 TCAAACCGGT
*
103307 TCAAAACTGG-
1 TC-AAACCGGT
103317 TCAAACCGGT
1 TCAAACCGGT
103327 T
1 T
103328 TTCCAGCAGC
Statistics
Matches: 46, Mismatches: 9, Indels: 8
0.73 0.14 0.13
Matches are distributed among these distances:
9 21 0.46
10 19 0.41
11 6 0.13
ACGTcount: A:0.29, C:0.30, G:0.22, T:0.19
Consensus pattern (10 bp):
TCAAACCGGT
Found at i:103281 original size:19 final size:20
Alignment explanation
Indices: 103257--103327 Score: 92
Period size: 19 Copynumber: 3.6 Consensus size: 20
103247 GGTCGGGTCG
*
103257 GGTCAACCCGGTTCAG-ACC
1 GGTCAAACCGGTTCAGAACC
*
103276 GGTCAAACCAGTTC-GAACC
1 GGTCAAACCGGTTCAGAACC
* *
103295 GGTCAAACCGGTTCAAAACT
1 GGTCAAACCGGTTCAGAACC
103315 GGTCAAACCGGTT
1 GGTCAAACCGGTT
103328 TTCCAGCAGC
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
18 1 0.02
19 28 0.62
20 16 0.36
ACGTcount: A:0.28, C:0.30, G:0.24, T:0.18
Consensus pattern (20 bp):
GGTCAAACCGGTTCAGAACC
Found at i:107972 original size:23 final size:25
Alignment explanation
Indices: 107948--107994 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
107938 ATCTTTTAAA
107948 TTTTATAAAAAAAT-TATATATAAT
1 TTTTATAAAAAAATATATATATAAT
* *
107972 TTTTATTAAAAAGTATATATATA
1 TTTTATAAAAAAATATATATATA
107995 TATATTAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (25 bp):
TTTTATAAAAAAATATATATATAAT
Found at i:108005 original size:23 final size:24
Alignment explanation
Indices: 107955--108005 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
107945 AAATTTTATA
* * *
107955 AAAAAATTATATATAATTTTTATT
1 AAAAAAGTATATATAATATATATT
107979 -AAAAAGTATATAT-ATATATATT
1 AAAAAAGTATATATAATATATATT
108001 AAAAA
1 AAAAA
108006 TAATAAAGTA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
22 7 0.30
23 16 0.70
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (24 bp):
AAAAAAGTATATATAATATATATT
Found at i:109066 original size:25 final size:25
Alignment explanation
Indices: 109037--109084 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
109027 TTAAATACTC
109037 ATGTATTTGATTTTAATGAAAAATT
1 ATGTATTTGATTTTAATGAAAAATT
*
109062 ATGTATTTGTTTTTAATGAAAAA
1 ATGTATTTGATTTTAATGAAAAA
109085 ACTTCATTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.48
Consensus pattern (25 bp):
ATGTATTTGATTTTAATGAAAAATT
Found at i:110372 original size:27 final size:28
Alignment explanation
Indices: 110297--110380 Score: 82
Period size: 28 Copynumber: 3.0 Consensus size: 28
110287 CTATCCGTTT
* * *
110297 ACATTATGA-CGTTGAGTCATTGCATGAA
1 ACATTAT-ACCGTTGAGCCAATGCTTGAA
** *
110325 ACATTATGTCGTCGAGCCAATGCTTGAA
1 ACATTATACCGTTGAGCCAATGCTTGAA
*
110353 ACA-TATACCGTTGAGCCAATTCTTGAA
1 ACATTATACCGTTGAGCCAATGCTTGAA
110380 A
1 A
110381 GCAATGACGG
Statistics
Matches: 46, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
27 21 0.46
28 25 0.54
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (28 bp):
ACATTATACCGTTGAGCCAATGCTTGAA
Found at i:116325 original size:21 final size:22
Alignment explanation
Indices: 116274--116323 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 22
116264 TCAAATGTAA
116274 AATAATTAAATTCTTTTTTATT
1 AATAATTAAATTCTTTTTTATT
116296 AAATAATTAAATTCTTTTTGTATCT
1 -AATAATTAAATTCTTTTT-TAT-T
116321 AAT
1 AAT
116324 TACCTTGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
23 18 0.72
24 6 0.24
25 1 0.04
ACGTcount: A:0.38, C:0.06, G:0.02, T:0.54
Consensus pattern (22 bp):
AATAATTAAATTCTTTTTTATT
Found at i:123785 original size:13 final size:14
Alignment explanation
Indices: 123761--123795 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
123751 AGGGATTAAC
*
123761 ATCATTATTTTCTT
1 ATCATCATTTTCTT
123775 AT-ATCATTTTCTT
1 ATCATCATTTTCTT
123788 ATCATCAT
1 ATCATCAT
123796 ACTCATGAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.26, C:0.17, G:0.00, T:0.57
Consensus pattern (14 bp):
ATCATCATTTTCTT
Found at i:125026 original size:31 final size:31
Alignment explanation
Indices: 124988--125130 Score: 93
Period size: 31 Copynumber: 4.6 Consensus size: 31
124978 ATATTTTTTG
124988 TATCTAAACTATCACTTTTGTTTTATTTTAA
1 TATCTAAACTATCACTTTTGTTTTATTTTAA
* ** *
125019 TGTCTAAACT-T---TTGTT-TTTTCATAATCA
1 TATCTAAACTATCACTT-TTGTTTT-ATTTTAA
* * *
125047 TGAT-TAAAGT-TTACTTTTTGTTTCATTTTAGTA
1 T-ATCTAAACTATCAC-TTTTGTTTTATTTTA--A
*
125080 GTATCTAAACTATCACTTTTGTTTTGTTTTAA
1 -TATCTAAACTATCACTTTTGTTTTATTTTAA
*
125112 TATCTAAACTATCAATTTT
1 TATCTAAACTATCACTTTT
125131 CTCTCGTTTT
Statistics
Matches: 84, Mismatches: 15, Indels: 26
0.67 0.12 0.21
Matches are distributed among these distances:
27 6 0.07
28 13 0.15
29 1 0.01
30 1 0.01
31 32 0.38
32 6 0.07
33 3 0.04
34 19 0.23
35 3 0.04
ACGTcount: A:0.27, C:0.12, G:0.07, T:0.54
Consensus pattern (31 bp):
TATCTAAACTATCACTTTTGTTTTATTTTAA
Found at i:125100 original size:34 final size:31
Alignment explanation
Indices: 125062--125152 Score: 85
Period size: 31 Copynumber: 2.8 Consensus size: 31
125052 AAAGTTTACT
*
125062 TTTTGTTTCATTTTAGTAGTATCTAAACTATCAC
1 TTTTGTTTCATTTTA--A-TATCTAAACTATCAA
**
125096 TTTTGTTTTGTTTTAATATCTAAACTATCAA
1 TTTTGTTTCATTTTAATATCTAAACTATCAA
* * *
125127 TTTTCTCTCGTTTTAATA-CATAAACT
1 TTTTGTTTCATTTTAATATC-TAAACT
125153 TTTTTTTATA
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
30 1 0.02
31 35 0.70
32 1 0.02
34 13 0.26
ACGTcount: A:0.27, C:0.14, G:0.07, T:0.52
Consensus pattern (31 bp):
TTTTGTTTCATTTTAATATCTAAACTATCAA
Found at i:125140 original size:31 final size:31
Alignment explanation
Indices: 125081--125152 Score: 92
Period size: 31 Copynumber: 2.3 Consensus size: 31
125071 ATTTTAGTAG
* * * *
125081 TATCTAAACTATCACTTTTGTTTTGTTTTAA
1 TATCTAAACTATCAATTTTCTCTCGTTTTAA
125112 TATCTAAACTATCAATTTTCTCTCGTTTTAA
1 TATCTAAACTATCAATTTTCTCTCGTTTTAA
125143 TA-CATAAACT
1 TATC-TAAACT
125153 TTTTTTTATA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
30 1 0.03
31 35 0.97
ACGTcount: A:0.31, C:0.17, G:0.04, T:0.49
Consensus pattern (31 bp):
TATCTAAACTATCAATTTTCTCTCGTTTTAA
Found at i:128909 original size:28 final size:28
Alignment explanation
Indices: 128869--128922 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
128859 CCTCTTGTTC
128869 CATCCTTATTTACTATTCAGTTGGTTAG
1 CATCCTTATTTACTATTCAGTTGGTTAG
*
128897 CATCCTTATTTACTATTCATTTGGTT
1 CATCCTTATTTACTATTCAGTTGGTT
128923 GCAAACTCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.20, C:0.19, G:0.11, T:0.50
Consensus pattern (28 bp):
CATCCTTATTTACTATTCAGTTGGTTAG
Found at i:131323 original size:3 final size:3
Alignment explanation
Indices: 131317--131392 Score: 152
Period size: 3 Copynumber: 25.3 Consensus size: 3
131307 ATAGTAGTAG
131317 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
131365 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
131393 TGACAAAAAA
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 73 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:131718 original size:80 final size:79
Alignment explanation
Indices: 131535--131766 Score: 268
Period size: 80 Copynumber: 2.9 Consensus size: 79
131525 TCTTCAAAAG
* * * * * ** * * ** *
131535 TGTTGATCCACCTTATTCTGAGATGGAACCGAGTAAAGGCTGAACAAGTTCTTCTTATTACAAAT
1 TGTTGATCCAACTTCTTCTGTGATGGAATCGAGCAAAGATTGAGCAAGTTCTTCTCATTATGAAC
*
131600 TTCTGCTCTTGAAA
66 TTCTTCTCTTGAAA
* * * *
131614 TGTTGATTCAACTCCTTCTATGATGGAATCGAGCAAAGATTTAGCAAGTTCTTCTCATTATGAAC
1 TGTTGATCCAACTTCTTCTGTGATGGAATCGAGCAAAGATTGAGCAAGTTCTTCTCATTATGAAC
131679 TTCTTCTCTTGGAAA
66 TTCTTCTCTT-GAAA
* *
131694 TGTTGATCCAACTTCTTCTGTGATGGAATCAAGCAAA-AGTTGAGCAAGTTTTTCTCATTATGAA
1 TGTTGATCCAACTTCTTCTGTGATGGAATCGAGCAAAGA-TTGAGCAAGTTCTTCTCATTATGAA
131758 CTTCTTCTC
65 CTTCTTCTC
131767 ATAGAAAACT
Statistics
Matches: 128, Mismatches: 23, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
79 59 0.46
80 69 0.54
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.37
Consensus pattern (79 bp):
TGTTGATCCAACTTCTTCTGTGATGGAATCGAGCAAAGATTGAGCAAGTTCTTCTCATTATGAAC
TTCTTCTCTTGAAA
Found at i:131816 original size:3 final size:3
Alignment explanation
Indices: 131810--131856 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
131800 GGTTCTTCTC
131810 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
131857 CGACAAAAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:132793 original size:19 final size:20
Alignment explanation
Indices: 132769--132806 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
132759 AATTTAATCG
*
132769 AATATATAAT-TTAAAATTC
1 AATATAAAATCTTAAAATTC
132788 AATATAAAATCTTAAAATT
1 AATATAAAATCTTAAAATT
132807 TATTAACACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.39
Consensus pattern (20 bp):
AATATAAAATCTTAAAATTC
Found at i:140815 original size:2 final size:2
Alignment explanation
Indices: 140808--140838 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
140798 ACATTTTATC
140808 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
140839 GGGTTAGAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:145504 original size:17 final size:17
Alignment explanation
Indices: 145466--145503 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
145456 ATAATTCGTC
145466 TTTTTCAATCTCGGGAA
1 TTTTTCAATCTCGGGAA
145483 TTTTTCAATCTCGGG-A
1 TTTTTCAATCTCGGGAA
145499 TTTTT
1 TTTTT
145504 TGGTTGAATC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 6 0.29
17 15 0.71
ACGTcount: A:0.18, C:0.16, G:0.16, T:0.50
Consensus pattern (17 bp):
TTTTTCAATCTCGGGAA
Found at i:146267 original size:28 final size:28
Alignment explanation
Indices: 146208--146273 Score: 73
Period size: 28 Copynumber: 2.4 Consensus size: 28
146198 AAGGTTTATG
* *
146208 GTTTAAGA-TTTGAGGTTAGGTTTTAGA
1 GTTTGAGATTTTGAGGTTAGGTTTGAGA
*
146235 GTTTGAGATTTTGAGGTTTGGGTTTGAGA
1 GTTTGAGATTTTGAGG-TTAGGTTTGAGA
*
146264 -TTTGTGATTT
1 GTTTGAGATTT
146274 GTGATTAGGA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
27 7 0.21
28 16 0.48
29 10 0.30
ACGTcount: A:0.20, C:0.00, G:0.32, T:0.48
Consensus pattern (28 bp):
GTTTGAGATTTTGAGGTTAGGTTTGAGA
Found at i:148608 original size:13 final size:13
Alignment explanation
Indices: 148592--148617 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
148582 GTTATTTATG
148592 TAAAATTTTTAAT
1 TAAAATTTTTAAT
148605 TAAAATTTTTAAT
1 TAAAATTTTTAAT
148618 GTTGAGATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TAAAATTTTTAAT
Found at i:160271 original size:18 final size:18
Alignment explanation
Indices: 160250--160284 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
160240 TTTAAATAAA
*
160250 AATTAAATATTAATATTG
1 AATTAAATAATAATATTG
*
160268 AATTAATTAATAATATT
1 AATTAAATAATAATATT
160285 AATATTGCAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (18 bp):
AATTAAATAATAATATTG
Found at i:162088 original size:71 final size:71
Alignment explanation
Indices: 162013--162153 Score: 183
Period size: 71 Copynumber: 2.0 Consensus size: 71
162003 GTAATGGAGC
* * * * * * * * *
162013 AAGACATTTCTCATCATTTCAATTTGGAGGAGCGATTCATTAAAAGTATTATTTCCTCATGTTAA
1 AAGACATCTCTCACCATGTCAAGTTGGAGAAACGATTCATTAAAAGTATCACTTCCTCAAGTTAA
162078 AAGAGT
66 AAGAGT
* *
162084 AAGACATCTCTCACCATGTCAAGTTGGAGAAACGATTCATTCAAAGTCTCACTTCCTCAAGTTAA
1 AAGACATCTCTCACCATGTCAAGTTGGAGAAACGATTCATTAAAAGTATCACTTCCTCAAGTTAA
162149 AAGAG
66 AAGAG
162154 CAATTAATTC
Statistics
Matches: 59, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
71 59 1.00
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Consensus pattern (71 bp):
AAGACATCTCTCACCATGTCAAGTTGGAGAAACGATTCATTAAAAGTATCACTTCCTCAAGTTAA
AAGAGT
Found at i:164062 original size:41 final size:41
Alignment explanation
Indices: 164000--164081 Score: 146
Period size: 41 Copynumber: 2.0 Consensus size: 41
163990 ACCAACGGTG
164000 CTGAACATTGATACACAAATGTACCAAAGTCGAACTGATAA
1 CTGAACATTGATACACAAATGTACCAAAGTCGAACTGATAA
* *
164041 CTGAACATTGATACACTAATGTACCAAAGTTGAACTGATAA
1 CTGAACATTGATACACAAATGTACCAAAGTCGAACTGATAA
164082 GTACTCACTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.43, C:0.18, G:0.15, T:0.24
Consensus pattern (41 bp):
CTGAACATTGATACACAAATGTACCAAAGTCGAACTGATAA
Found at i:176607 original size:22 final size:23
Alignment explanation
Indices: 176569--176618 Score: 75
Period size: 22 Copynumber: 2.2 Consensus size: 23
176559 ATACATGTCA
176569 TTGTGACATATTTTTCTATGCTT
1 TTGTGACATATTTTTCTATGCTT
* *
176592 TTGTGACGT-TTTTTCTCTGCTT
1 TTGTGACATATTTTTCTATGCTT
176614 TTGTG
1 TTGTG
176619 GTATGTTACT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 17 0.68
23 8 0.32
ACGTcount: A:0.10, C:0.14, G:0.18, T:0.58
Consensus pattern (23 bp):
TTGTGACATATTTTTCTATGCTT
Found at i:178565 original size:31 final size:31
Alignment explanation
Indices: 178466--178557 Score: 152
Period size: 31 Copynumber: 3.0 Consensus size: 31
178456 CAATTTAAGG
*
178466 CAAAATGGTTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GATTTTTGGACTTGAATTGAATTTA
178498 CAAAATGATTTTTGGACTTGAATTGAATTTA
1 CAAAATGATTTTTGGACTTGAATTGAATTTA
178529 CAAAATG-TTTTTGGACTT-AATTGAATTTA
1 CAAAATGATTTTTGGACTTGAATTGAATTTA
178558 TTCAAAATTT
Statistics
Matches: 59, Mismatches: 1, Indels: 3
0.94 0.02 0.05
Matches are distributed among these distances:
29 11 0.19
30 11 0.19
31 31 0.53
32 6 0.10
ACGTcount: A:0.34, C:0.07, G:0.16, T:0.43
Consensus pattern (31 bp):
CAAAATGATTTTTGGACTTGAATTGAATTTA
Found at i:178649 original size:19 final size:19
Alignment explanation
Indices: 178622--178688 Score: 107
Period size: 19 Copynumber: 3.5 Consensus size: 19
178612 AATGTTTTTA
* *
178622 TGAATAGTAATTTACTATT
1 TGAACAGTAAATTACTATT
178641 TGAACAGTAAATTACTATT
1 TGAACAGTAAATTACTATT
*
178660 TGAACAGTAAATCACTATT
1 TGAACAGTAAATTACTATT
178679 TGAACAGTAA
1 TGAACAGTAA
178689 CCCGAGGCTC
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 45 1.00
ACGTcount: A:0.42, C:0.10, G:0.12, T:0.36
Consensus pattern (19 bp):
TGAACAGTAAATTACTATT
Found at i:178820 original size:21 final size:21
Alignment explanation
Indices: 178794--178835 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
178784 ATTTGAATAT
*
178794 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
178815 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
178836 CCCATTCTGG
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:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:178897 original size:21 final size:21
Alignment explanation
Indices: 178864--178903 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
178854 TTTGAGTAGA
*
178864 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
178886 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
178904 ATATACGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:182992 original size:20 final size:20
Alignment explanation
Indices: 182967--183006 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
182957 TACAAATTAA
*
182967 ATTATATTAGTAGTTAAAGG
1 ATTATATTAATAGTTAAAGG
182987 ATTATATTAATAGTTAAAGG
1 ATTATATTAATAGTTAAAGG
183007 GATGTTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.17, T:0.40
Consensus pattern (20 bp):
ATTATATTAATAGTTAAAGG
Found at i:183496 original size:26 final size:25
Alignment explanation
Indices: 183446--183533 Score: 99
Period size: 26 Copynumber: 3.4 Consensus size: 25
183436 ATAAATTCAT
*
183446 AATATTTTATATATATTAACTTTAAAA
1 AATA-TTTAT-TATATTAACTTTTAAA
183473 AATATTT-TTATATTAACTTATTAAA
1 AATATTTATTATATTAACTT-TTAAA
*
183498 TATATTTATTATTAATTAA-TTTTAAA
1 AATATTTATTA-T-ATTAACTTTTAAA
183524 AATATTTATT
1 AATATTTATT
183534 TTTTTTAATA
Statistics
Matches: 54, Mismatches: 3, Indels: 9
0.82 0.05 0.14
Matches are distributed among these distances:
24 11 0.20
25 11 0.20
26 20 0.37
27 7 0.13
28 5 0.09
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (25 bp):
AATATTTATTATATTAACTTTTAAA
Found at i:183554 original size:26 final size:27
Alignment explanation
Indices: 183495--183554 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 27
183485 TTAACTTATT
* *
183495 AAATATATTTATTATTAATTAATTTTA
1 AAATATATTTATTATTAATTAATATAA
**
183522 AAA-ATATTTATT-TTTTTTAATATAA
1 AAATATATTTATTATTAATTAATATAA
183547 AAATATAT
1 AAATATAT
183555 ATTTTATGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
25 12 0.43
26 13 0.46
27 3 0.11
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (27 bp):
AAATATATTTATTATTAATTAATATAA
Found at i:183686 original size:30 final size:29
Alignment explanation
Indices: 183579--183717 Score: 85
Period size: 29 Copynumber: 4.8 Consensus size: 29
183569 TATTTTGAAG
* *
183579 TTAAGATAAGAATAAA-ATATATTTAATAAT
1 TTAAAATAAGAATAAATATAT-TTTAA-AAA
* * * *
183609 TTGAAGTAATAATATAATA-A-TTTAGTAAA
1 TTAAAATAAGAATA-AATATATTTTA-AAAA
* *
183638 TTAAGATAA-AAT--ATATATTTTGAAAAG
1 TTAAAATAAGAATAAATATATTTT-AAAAA
183665 TTAAAAT-AGTAATAAATATATTTTAAAAA
1 TTAAAATAAG-AATAAATATATTTTAAAAA
* *
183694 TTTACATAAGAATAAATATATTTT
1 TTAAAATAAGAATAAATATATTTT
183718 TTAAAAATAT
Statistics
Matches: 83, Mismatches: 15, Indels: 23
0.69 0.12 0.19
Matches are distributed among these distances:
25 3 0.04
26 2 0.02
27 11 0.13
28 7 0.08
29 35 0.42
30 21 0.25
31 3 0.04
32 1 0.01
ACGTcount: A:0.53, C:0.01, G:0.07, T:0.39
Consensus pattern (29 bp):
TTAAAATAAGAATAAATATATTTTAAAAA
Found at i:183772 original size:23 final size:23
Alignment explanation
Indices: 183718--183772 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
183708 AATATATTTT
183718 TTAAAAATATTTTTAAATTAAAA
1 TTAAAAATATTTTTAAATTAAAA
**
183741 CAAAAAATATTTTTAAAATT-AAA
1 TTAAAAATATTTTT-AAATTAAAA
*
183764 TTAATAATA
1 TTAAAAATA
183773 AAATATATTT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
23 21 0.81
24 5 0.19
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (23 bp):
TTAAAAATATTTTTAAATTAAAA
Found at i:183784 original size:28 final size:29
Alignment explanation
Indices: 183730--183784 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
183720 AAAAATATTT
*
183730 TTAAATTAAAACAAAAAATATTTTTAAAA
1 TTAAATTAAAACAAAAAATATATTTAAAA
* *
183759 TTAAATTAATA-ATAAAATATATTTAA
1 TTAAATTAAAACAAAAAATATATTTAA
183785 TAAGTTAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 13 0.57
29 10 0.43
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (29 bp):
TTAAATTAAAACAAAAAATATATTTAAAA
Found at i:184325 original size:12 final size:12
Alignment explanation
Indices: 184292--184325 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
184282 CCGCCGGAGT
*
184292 CGCCGTTGGAGG
1 CGCCGTTGGTGG
*
184304 CGCAGTTGGTGG
1 CGCCGTTGGTGG
184316 CGCCGTTGGT
1 CGCCGTTGGT
184326 AAGTTCCTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.06, C:0.24, G:0.47, T:0.24
Consensus pattern (12 bp):
CGCCGTTGGTGG
Found at i:189985 original size:16 final size:17
Alignment explanation
Indices: 189953--190008 Score: 60
Period size: 16 Copynumber: 3.2 Consensus size: 17
189943 TGATATTAAA
189953 AAAATAATAGAAAAAAT
1 AAAATAATAGAAAAAAT
*
189970 AAAATAA-AGTAAAAAT
1 AAAATAATAGAAAAAAT
* *
189986 ATAATATATATAAATAAAT
1 AAAATA-ATAGAAA-AAAT
190005 AAAA
1 AAAA
190009 ACAAAAATAT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
16 13 0.42
17 8 0.26
18 3 0.10
19 7 0.23
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.23
Consensus pattern (17 bp):
AAAATAATAGAAAAAAT
Found at i:189986 original size:25 final size:25
Alignment explanation
Indices: 189949--190009 Score: 61
Period size: 25 Copynumber: 2.4 Consensus size: 25
189939 TACATGATAT
*
189949 TAAAAAAATAATAGAAAAAATA-AAA
1 TAAATAAA-AATAGAAAAAATATAAA
* * *
189974 TAAAGTAAAAATATAATATATATAAA
1 TAAA-TAAAAATAGAAAAAATATAAA
190000 TAAATAAAAA
1 TAAATAAAAA
190010 CAAAAATATA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
25 20 0.67
26 10 0.33
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (25 bp):
TAAATAAAAATAGAAAAAATATAAA
Found at i:189990 original size:30 final size:31
Alignment explanation
Indices: 189949--190022 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 31
189939 TACATGATAT
* *
189949 TAAAAAAATAATAGA-AAAAATAAA-ATAAAG
1 TAAAAATATAATAGATAAAAATAAATA-AAAA
* *
189979 TAAAAATATAATATATATAAATAAATAAAAA
1 TAAAAATATAATAGATAAAAATAAATAAAAA
*
190010 CAAAAATATAATA
1 TAAAAATATAATA
190023 TTAAGAAAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
30 13 0.35
31 23 0.62
32 1 0.03
ACGTcount: A:0.73, C:0.01, G:0.03, T:0.23
Consensus pattern (31 bp):
TAAAAATATAATAGATAAAAATAAATAAAAA
Found at i:190031 original size:16 final size:16
Alignment explanation
Indices: 190012--190068 Score: 51
Period size: 16 Copynumber: 3.2 Consensus size: 16
190002 AATAAAAACA
190012 AAAATATAATATTAAG
1 AAAATATAATATTAAG
**
190028 AAAATATATATAAAAACG
1 AAAATATA-ATATTAA-G
190046 TATAAAATATAATATTAAG
1 ---AAAATATAATATTAAG
190065 AAAA
1 AAAA
190069 AATATATACA
Statistics
Matches: 32, Mismatches: 4, Indels: 10
0.70 0.09 0.22
Matches are distributed among these distances:
16 12 0.38
17 5 0.16
18 1 0.03
19 1 0.03
20 5 0.16
21 8 0.25
ACGTcount: A:0.65, C:0.02, G:0.05, T:0.28
Consensus pattern (16 bp):
AAAATATAATATTAAG
Found at i:190116 original size:2 final size:2
Alignment explanation
Indices: 190103--190148 Score: 51
Period size: 2 Copynumber: 23.5 Consensus size: 2
190093 AAATAAATAC
* *
190103 AT AT AT AC AT AT AT AT AT AT AT AT AT A- AT GAT AT A- AG AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT
190144 AT AT A
1 AT AT A
190149 ATAAAAATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
1 2 0.05
2 34 0.89
3 2 0.05
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.41
Consensus pattern (2 bp):
AT
Found at i:190161 original size:25 final size:27
Alignment explanation
Indices: 190113--190163 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 27
190103 ATATATACAT
* *
190113 ATATATATATATATATAATGATATAAG
1 ATATATATATATATAAAATAATATAAG
190140 ATATATATA-ATA-AAAATAATATAA
1 ATATATATATATATAAAATAATATAA
190164 TATAAATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 10 0.45
26 3 0.14
27 9 0.41
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (27 bp):
ATATATATATATATAAAATAATATAAG
Found at i:190166 original size:23 final size:23
Alignment explanation
Indices: 190113--190177 Score: 51
Period size: 25 Copynumber: 2.7 Consensus size: 23
190103 ATATATACAT
* *
190113 ATATATATATATATATAATGATATA
1 ATATATATA-ATA-AAAATAATATA
*
190138 AGATATATATAATAAAAATAATATA
1 ATATAT--ATAATAAAAATAATATA
*
190163 ATATAAATAA-AAAAA
1 ATATATATAATAAAAA
190178 GAAGAATATA
Statistics
Matches: 33, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
22 5 0.15
23 4 0.12
25 18 0.55
26 3 0.09
27 3 0.09
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (23 bp):
ATATATATAATAAAAATAATATA
Found at i:190433 original size:21 final size:21
Alignment explanation
Indices: 190403--190556 Score: 131
Period size: 21 Copynumber: 7.4 Consensus size: 21
190393 GATTTACATA
*
190403 TTCGCATTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
** *
190424 TTCGCGTTGCGATTTTCCAAA
1 TTCGCGTTGCGATAGTCCAAG
* *
190445 TT--CGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
*
190466 TT--CGTTGCGATAGTCAAAG
1 TTCGCGTTGCGATAGTCCAAG
*
190485 TTCGCGTTGCGATAGTCAAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
190506 TTTGCGTTGCGATTTATTCCAAG
1 TTCGCGTTGCGA--TAGTCCAAG
*
190529 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
190548 TTCGCGTTG
1 TTCGCGTTG
190557 TGATTTATTC
Statistics
Matches: 112, Mismatches: 13, Indels: 16
0.79 0.09 0.11
Matches are distributed among these distances:
19 25 0.22
21 78 0.70
23 9 0.08
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.36
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCCAAG
Found at i:190452 original size:19 final size:20
Alignment explanation
Indices: 190428--190577 Score: 96
Period size: 21 Copynumber: 7.2 Consensus size: 20
190418 TCCAAGTTCG
190428 CGTTGCGATT-TTCCAAATT
1 CGTTGCGATTATTCCAAATT
190447 CGTTGCGATTTATTCCAAATT
1 CGTTGCGA-TTATTCCAAATT
*
190468 CGTTGCGA-TAGT-CAAAGTT
1 CGTTGCGATTATTCCAAA-TT
*
190487 CGCGTTGCGA-TAGT-CAAAGTTT
1 --CGTTGCGATTATTCCAAA--TT
*
190509 GCGTTGCGATTTATTCCAAGTT
1 -CGTTGCGA-TTATTCCAAATT
* * *
190531 CGTTGCGA-TAGTCGAAGTT
1 CGTTGCGATTATTCCAAATT
*
190550 CGCGTTGTGATTTATTCCAAATT
1 --CGTTGCGA-TTATTCCAAATT
190573 CGTTG
1 CGTTG
190578 TGATAGTCCA
Statistics
Matches: 108, Mismatches: 10, Indels: 24
0.76 0.07 0.17
Matches are distributed among these distances:
18 4 0.04
19 22 0.20
20 2 0.02
21 62 0.57
22 4 0.04
23 11 0.10
24 3 0.03
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.38
Consensus pattern (20 bp):
CGTTGCGATTATTCCAAATT
Found at i:190464 original size:42 final size:42
Alignment explanation
Indices: 190409--190588 Score: 185
Period size: 42 Copynumber: 4.3 Consensus size: 42
190399 CATATTCGCA
190409 TTGCGATAGTCCAAGTTCGCGTTGCGA-TT-TTCCAAATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
* * *
190449 TTGCGATTTATTCCAAATT--CGTTGCGA--TAGT-CAAAGTTCGCG
1 TTGCGA--TAGTCCAAGTTCGCGTTGCGATTTATTCCAAA-TT--CG
* * *
190491 TTGCGATAGTCAAAGTTTGCGTTGCGATTTATTCCAAGTTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
* *
190533 TTGCGATAGTCGAAGTTCGCGTTGTGATTTATTCCAAATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
*
190575 TTGTGATAGTCCAA
1 TTGCGATAGTCCAA
190589 AATCGCAACG
Statistics
Matches: 115, Mismatches: 14, Indels: 20
0.77 0.09 0.13
Matches are distributed among these distances:
39 5 0.04
40 25 0.22
42 77 0.67
44 5 0.04
45 3 0.03
ACGTcount: A:0.22, C:0.18, G:0.23, T:0.37
Consensus pattern (42 bp):
TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
Found at i:190525 original size:63 final size:61
Alignment explanation
Indices: 190409--190577 Score: 223
Period size: 63 Copynumber: 2.7 Consensus size: 61
190399 CATATTCGCA
* **
190409 TTGCGATAGTCCAAGTTCGCGTTGCGATTTTCCAAATTCGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCAAAGTTCGCGTTGCGATAGTCCAAATTCGTTGCGATTTATTCCAAATTCG
*
190470 TTGCGATAGTCAAAGTTCGCGTTGCGATAGT-CAAAGTTTGCGTTGCGATTTATTCCAAGTTCG
1 TTGCGATAGTCAAAGTTCGCGTTGCGATAGTCCAAA--TT-CGTTGCGATTTATTCCAAATTCG
* * *
190533 TTGCGATAGTCGAAGTTCGCGTTGTGATTTATTCCAAATTCGTTG
1 TTGCGATAGTCAAAGTTCGCGTTGCGA--TAGTCCAAATTCGTTG
190578 TGATAGTCCA
Statistics
Matches: 95, Mismatches: 7, Indels: 10
0.85 0.06 0.09
Matches are distributed among these distances:
60 4 0.04
61 28 0.29
62 2 0.02
63 52 0.55
64 2 0.02
65 3 0.03
66 4 0.04
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (61 bp):
TTGCGATAGTCAAAGTTCGCGTTGCGATAGTCCAAATTCGTTGCGATTTATTCCAAATTCG
Found at i:191297 original size:21 final size:21
Alignment explanation
Indices: 191273--191489 Score: 173
Period size: 21 Copynumber: 10.6 Consensus size: 21
191263 TTTGGAATAA
191273 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
* * **
191294 ATCGCAA--CGAATTTGGAAA
1 ATCGCAACGCGAACTTCGACT
*
191313 ATCGCAACGCAAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
* *
191334 ATCGCAA--CGAA-TTTGAAAT
1 ATCGCAACGCGAACTTCG-ACT
191353 AAATCGCAACGCGAACTTCGACT
1 --ATCGCAACGCGAACTTCGACT
* * **
191376 ATCGCAA--CGAATTTGGAAA
1 ATCGCAACGCGAACTTCGACT
191395 ATCGCAACGCGAATCTTCGACT
1 ATCGCAACGCGAA-CTTCGACT
* * **
191417 ATCGCAA--CGAATTTGGAAA
1 ATCGCAACGCGAACTTCGACT
191436 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
* *
191457 ATCACAACGCGAACTTGGACT
1 ATCGCAACGCGAACTTCGACT
*
191478 ATCGCAATGCGA
1 ATCGCAACGCGA
191490 TTTACATATT
Statistics
Matches: 149, Mismatches: 34, Indels: 26
0.71 0.16 0.12
Matches are distributed among these distances:
18 3 0.02
19 46 0.31
20 4 0.03
21 76 0.51
22 11 0.07
23 6 0.04
24 3 0.02
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGAACTTCGACT
Found at i:191328 original size:40 final size:40
Alignment explanation
Indices: 191248--191465 Score: 355
Period size: 40 Copynumber: 5.3 Consensus size: 40
191238 TGGGATTTTG
*
191248 GACTATCGCAATGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGG-A-AAATCGCAACGCGAACTTC
*
191290 GACTATCGCAACGAATTTGGAAAATCGCAACGCAAACTTC
1 GACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTC
*
191330 GACTATCGCAACGAATTTGAAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTG-GA-AAATCGCAACGCGAACTTC
191372 GACTATCGCAACGAATTTGGAAAATCGCAACGCGAATCTTC
1 GACTATCGCAACGAATTTGGAAAATCGCAACGCGAA-CTTC
191413 GACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTC
*
191453 GACTATCACAACG
1 GACTATCGCAACG
191466 CGAACTTGGA
Statistics
Matches: 167, Mismatches: 6, Indels: 8
0.92 0.03 0.04
Matches are distributed among these distances:
40 68 0.41
41 43 0.26
42 56 0.34
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.21
Consensus pattern (40 bp):
GACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTC
Found at i:191385 original size:82 final size:82
Alignment explanation
Indices: 191248--191465 Score: 368
Period size: 82 Copynumber: 2.7 Consensus size: 82
191238 TGGGATTTTG
*
191248 GACTATCGCAATGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAAA
1 GACTATCGCAACGAATTT-GAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAAA
191313 ATCGCAACGC-AAACTTC
65 ATCGCAACGCGAAACTTC
191330 GACTATCGCAACGAATTTGAAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAAA
1 GACTATCGCAACGAATTTG-AATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAAA
*
191395 ATCGCAACGCGAATCTTC
65 ATCGCAACGCGAAACTTC
* *
191413 GACTATCGCAACGAATTTGGA-AAATCGCAACGCGAACTTCGACTATCACAACG
1 GACTATCGCAACGAATTTGAATAAATCGCAACGCGAACTTCGACTATCGCAACG
191466 CGAACTTGGA
Statistics
Matches: 130, Mismatches: 4, Indels: 5
0.94 0.03 0.04
Matches are distributed among these distances:
81 32 0.25
82 73 0.56
83 25 0.19
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.21
Consensus pattern (82 bp):
GACTATCGCAACGAATTTGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAAAA
TCGCAACGCGAAACTTC
Found at i:194204 original size:65 final size:67
Alignment explanation
Indices: 194020--194215 Score: 236
Period size: 65 Copynumber: 2.9 Consensus size: 67
194010 GGAAACGATC
* * *
194020 TCAAAGATATATGTTGTTTCATGA-AAACGGTCTCAAGGGAAACAAAATTTTGTTTTAAGGGAAA
1 TCAAAGAT-TTTG-TGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAA-TTTGTTTTAAGGGAAA
194084 TAAAT
63 TAAAT
** *
194089 TTGAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATTTGTTTTAGGGGAAATAA
1 TCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATTTGTTTTAAGGGAAATAA
194154 AT
66 AT
* * * * * *
194156 TCAAAGA-TTT-TGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAATTTGTTTCAAGAGAAA
1 TCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATTTGTTTTAAGGGAAA
194216 CTGTCTCAAG
Statistics
Matches: 111, Mismatches: 15, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
65 43 0.39
66 3 0.03
67 34 0.31
68 25 0.23
69 6 0.05
ACGTcount: A:0.39, C:0.09, G:0.21, T:0.31
Consensus pattern (67 bp):
TCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATTTGTTTTAAGGGAAATAA
AT
Found at i:194216 original size:36 final size:36
Alignment explanation
Indices: 194164--194389 Score: 168
Period size: 36 Copynumber: 6.4 Consensus size: 36
194154 ATTCAAAGAT
*
194164 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAA
*
194200 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAA
* * * * * *
194236 CTTAGTTCCAAAAGAAATTGTCTCAAGGGAGATGAAA
1 -TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAA
* * * *
194273 TTTATTTCAA-ATAAAACATAT-TC---A-A-A--TAA
1 TTTGTTTCAAGA-GAAAC-TGTCTCAAGAGAGACGAAA
* *
194302 TTTGTTTCAAGGGAAATTGTCTCAAGAGAGAC-ATAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACGA-AA
* *
194338 TTTGTTTCAAG-GAAAACTGTCTGAAGAGAGACGGAA
1 TTTGTTTCAAGAG-AAACTGTCTCAAGAGAGACGAAA
* *
194374 TTTATTTCAAGGGAAA
1 TTTGTTTCAAGAGAAA
194390 TGTTTTCAAT
Statistics
Matches: 148, Mismatches: 27, Indels: 30
0.72 0.13 0.15
Matches are distributed among these distances:
28 2 0.01
29 16 0.11
31 1 0.01
32 2 0.01
33 1 0.01
34 1 0.01
35 2 0.01
36 91 0.61
37 32 0.22
ACGTcount: A:0.40, C:0.12, G:0.20, T:0.28
Consensus pattern (36 bp):
TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAA
Found at i:194261 original size:37 final size:36
Alignment explanation
Indices: 194176--194267 Score: 121
Period size: 37 Copynumber: 2.5 Consensus size: 36
194166 TGTTTCAAGG
* * * *
194176 GAAACTGTCTCAAGAGAGACGAAATTTGTTTCAAGA
1 GAAACTGTCTCAAGAGAGACAAAATTAGTTCCAAAA
194212 GAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAA
1 GAAACTGTCTCAAGAGAGACAAAA-TTAGTTCCAAAA
* *
194249 GAAATTGTCTCAAGGGAGA
1 GAAACTGTCTCAAGAGAGA
194268 TGAAATTTAT
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
36 23 0.47
37 26 0.53
ACGTcount: A:0.41, C:0.15, G:0.22, T:0.22
Consensus pattern (36 bp):
GAAACTGTCTCAAGAGAGACAAAATTAGTTCCAAAA
Found at i:194263 original size:138 final size:138
Alignment explanation
Indices: 194110--194369 Score: 344
Period size: 138 Copynumber: 1.9 Consensus size: 138
194100 GTGTTTCAAG
* * ** * * *
194110 AGAAACTGTCTCAAGGGAAACAAAATTTGTTTTAGGGGAAATAAATTCAAAGATTTTGTTTCAAG
1 AGAAACTGTCTCAAGGGAAACAAAATTTATTTCAAAGAAAACAAATTCAAAGAATTTGTTTCAAG
194175 GGAAACTGTCTCAAGAGAGACGA-AATTTGTTTCAA-GAGAAACTGTCTCAAGAGAGACAAAACT
66 GGAAACTGTCTCAAGAGAGAC-ATAATTTGTTTCAAGGA-AAACTGTCTCAAGAGAGACAAAACT
194238 TAGTTCCAAA
129 TAGTTCCAAA
* * ** * * *
194248 AGAAATTGTCTCAAGGGAGATGAAATTTATTTCAAATAAAACATATTCAAATAATTTGTTTCAAG
1 AGAAACTGTCTCAAGGGAAACAAAATTTATTTCAAAGAAAACAAATTCAAAGAATTTGTTTCAAG
* *
194313 GGAAATTGTCTCAAGAGAGACATAATTTGTTTCAAGGAAAACTGTCTGAAGAGAGAC
66 GGAAACTGTCTCAAGAGAGACATAATTTGTTTCAAGGAAAACTGTCTCAAGAGAGAC
194370 GGAATTTATT
Statistics
Matches: 104, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
137 1 0.01
138 101 0.97
139 2 0.02
ACGTcount: A:0.41, C:0.12, G:0.20, T:0.28
Consensus pattern (138 bp):
AGAAACTGTCTCAAGGGAAACAAAATTTATTTCAAAGAAAACAAATTCAAAGAATTTGTTTCAAG
GGAAACTGTCTCAAGAGAGACATAATTTGTTTCAAGGAAAACTGTCTCAAGAGAGACAAAACTTA
GTTCCAAA
Found at i:196041 original size:69 final size:69
Alignment explanation
Indices: 195921--196058 Score: 240
Period size: 69 Copynumber: 2.0 Consensus size: 69
195911 TGTCTCTCTC
195921 TTGATGCTCTATGATCTTCGAGTGAAGTGGTTAAGTGATTCAGAAAGGATTGTGCTTGATCAATC
1 TTGATGCTCTATGATCTTCGAGTGAAGTGGTTAAGTGATTCAGAAAGGATTGTGCTTGATCAATC
195986 TCAT
66 TCAT
* * * *
195990 TTGATGCTCTATGATCTTTGAGTGAAGTGGTTCAGTGATTCGGAAATGATTGTGCTTGATCAATC
1 TTGATGCTCTATGATCTTCGAGTGAAGTGGTTAAGTGATTCAGAAAGGATTGTGCTTGATCAATC
196055 TCAT
66 TCAT
196059 AGTTTGAATC
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
69 65 1.00
ACGTcount: A:0.25, C:0.13, G:0.25, T:0.38
Consensus pattern (69 bp):
TTGATGCTCTATGATCTTCGAGTGAAGTGGTTAAGTGATTCAGAAAGGATTGTGCTTGATCAATC
TCAT
Found at i:196173 original size:14 final size:13
Alignment explanation
Indices: 196131--196179 Score: 66
Period size: 13 Copynumber: 3.8 Consensus size: 13
196121 TTTTCTTCAA
196131 TTTTC-CTTTGTT
1 TTTTCTCTTTGTT
196143 TTTTCTCTTT-TT
1 TTTTCTCTTTGTT
196155 ATTTTCTCTTTGCTT
1 -TTTTCTCTTTG-TT
196170 TTTTCTCTTT
1 TTTTCTCTTT
196180 TTCTCTTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
12 7 0.21
13 14 0.42
14 10 0.30
15 2 0.06
ACGTcount: A:0.02, C:0.18, G:0.04, T:0.76
Consensus pattern (13 bp):
TTTTCTCTTTGTT
Found at i:196177 original size:27 final size:25
Alignment explanation
Indices: 196130--196181 Score: 86
Period size: 27 Copynumber: 2.0 Consensus size: 25
196120 TTTTTCTTCA
196130 ATTTTCCTTTGTTTTTTCTCTTTTT
1 ATTTTCCTTTGTTTTTTCTCTTTTT
196155 ATTTTCTCTTTGCTTTTTTCTCTTTTT
1 ATTTTC-CTTTG-TTTTTTCTCTTTTT
196182 CTCTTTTTGC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
25 6 0.24
26 5 0.20
27 14 0.56
ACGTcount: A:0.04, C:0.17, G:0.04, T:0.75
Consensus pattern (25 bp):
ATTTTCCTTTGTTTTTTCTCTTTTT
Found at i:197185 original size:21 final size:21
Alignment explanation
Indices: 197152--197192 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
197142 TTCTGGGCAA
* *
197152 GGGAATCGGTACCCATTCAAG
1 GGGAACCGATACCCATTCAAG
*
197173 GGGAACCGATACCCCTTCAA
1 GGGAACCGATACCCATTCAA
197193 ACGAACAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.29, C:0.29, G:0.24, T:0.17
Consensus pattern (21 bp):
GGGAACCGATACCCATTCAAG
Found at i:198709 original size:18 final size:18
Alignment explanation
Indices: 198686--198721 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
198676 AGGAATGATA
198686 TGTGGTCCTTCGGGACAT
1 TGTGGTCCTTCGGGACAT
198704 TGTGGTCCTTCGGGACAT
1 TGTGGTCCTTCGGGACAT
198722 ATATGTATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.11, C:0.22, G:0.33, T:0.33
Consensus pattern (18 bp):
TGTGGTCCTTCGGGACAT
Found at i:198741 original size:121 final size:121
Alignment explanation
Indices: 198583--198824 Score: 448
Period size: 121 Copynumber: 2.0 Consensus size: 121
198573 CGAGGGTCTA
198583 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
1 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
*
198648 GATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
66 GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
198704 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
1 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
* * *
198769 GATCCTTGGCATATGTGTATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
66 GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
198825 ATATGTATTC
Statistics
Matches: 117, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
121 117 1.00
ACGTcount: A:0.24, C:0.15, G:0.26, T:0.36
Consensus pattern (121 bp):
TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
Found at i:198782 original size:59 final size:59
Alignment explanation
Indices: 198598--198788 Score: 137
Period size: 59 Copynumber: 3.2 Consensus size: 59
198588 TCCTTCGGGA
* *
198598 CATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCCCTAG
1 CATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCCTTGG
* * * * * * *
198657 TATATGTATATGATTCTTAAGGAATGATATGTG--GTCCT--TCG-G-GACAT--TGTGGTCCTT
1 CATA--TATGT-ATTCTT-TGGAA-CATGTGTGAAGT-CTGGT-GAGACACATACT-TGATCCTT
198714 CGGG
58 --GG
198718 ACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCCTTGG
1 -CATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCCTTGG
*
198778 CATATGTGTAT
1 CATATATGTAT
198789 GATTCTTAAG
Statistics
Matches: 96, Mismatches: 17, Indels: 38
0.64 0.11 0.25
Matches are distributed among these distances:
57 6 0.06
58 7 0.07
59 28 0.29
60 12 0.12
61 11 0.11
62 19 0.20
63 7 0.07
64 6 0.06
ACGTcount: A:0.25, C:0.15, G:0.24, T:0.36
Consensus pattern (59 bp):
CATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCCTTGG
Found at i:198927 original size:103 final size:103
Alignment explanation
Indices: 198704--198919 Score: 378
Period size: 103 Copynumber: 2.1 Consensus size: 103
198694 TTCGGGACAT
*
198704 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
1 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTAAGACACATACTT
* * *
198769 GATCCTTGGCATATGTGTATGATTCTTAAGGAATGATA
66 GATCCCTAGCATATGTATATGATTCTTAAGGAATGATA
*
198807 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTAAGACGCATACTT
1 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTAAGACACATACTT
*
198872 GATCCCTAGTATATGTATATGATTCTTAAGGAATGATA
66 GATCCCTAGCATATGTATATGATTCTTAAGGAATGATA
198910 TGTGGTCCTT
1 TGTGGTCCTT
198920 ATGGACATTA
Statistics
Matches: 107, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 107 1.00
ACGTcount: A:0.25, C:0.14, G:0.25, T:0.37
Consensus pattern (103 bp):
TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTAAGACACATACTT
GATCCCTAGCATATGTATATGATTCTTAAGGAATGATA
Found at i:199003 original size:23 final size:23
Alignment explanation
Indices: 198935--198995 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 23
198925 CATTATTATA
* *
198935 TGGCACTACGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTATG
*
198958 CGGCACTAT-GGTGCAATTCTATG
1 TGGCACT-TCGGTGCAATTCTATG
198981 TGGCACTTCGGTGCA
1 TGGCACTTCGGTGCA
198996 TTTATATGAG
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
22 1 0.03
23 31 0.97
ACGTcount: A:0.20, C:0.25, G:0.28, T:0.28
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTATG
Found at i:202601 original size:25 final size:23
Alignment explanation
Indices: 202556--202608 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 23
202546 AATAATAAAT
202556 AAAACAAGAAAAAATGGAAAATAA
1 AAAACAAGAAAAAAT-GAAAATAA
202580 CAAAACAAGTAAAAAAAT-AAAATAA
1 -AAAACAAG--AAAAAATGAAAATAA
202605 AAAA
1 AAAA
202609 TAAAAATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
24 4 0.15
25 15 0.58
27 7 0.27
ACGTcount: A:0.77, C:0.06, G:0.08, T:0.09
Consensus pattern (23 bp):
AAAACAAGAAAAAATGAAAATAA
Found at i:202618 original size:26 final size:26
Alignment explanation
Indices: 202546--202632 Score: 63
Period size: 26 Copynumber: 3.3 Consensus size: 26
202536 AAAACGTGAT
*
202546 AATAATAAATAAAACA-AGAAAAAATGGAA
1 AATAAAAAATAAAA-ATA-AAAAAAT--AA
* * *
202575 AATAACAAA-ACAAGTAAAAAAATAA
1 AATAAAAAATAAAAATAAAAAAATAA
*
202600 AATAAAAAATAAAAATAAACAAAAT-G
1 AATAAAAAATAAAAATAAA-AAAATAA
202626 AATAAAA
1 AATAAAA
202633 TGTTAAAAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
25 10 0.21
26 14 0.29
27 12 0.25
28 4 0.08
29 8 0.17
ACGTcount: A:0.76, C:0.05, G:0.06, T:0.14
Consensus pattern (26 bp):
AATAAAAAATAAAAATAAAAAAATAA
Found at i:202716 original size:20 final size:18
Alignment explanation
Indices: 202676--202719 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
202666 ATTAATGGAG
202676 TAAAAAAATAAAAAAAGA
1 TAAAAAAATAAAAAAAGA
* *
202694 TAAAAGAAATTAAAAAGGAA
1 TAAAA-AAATAAAAAAAG-A
202714 TAAAAA
1 TAAAAA
202720 TAATGTGTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 5 0.23
19 11 0.50
20 6 0.27
ACGTcount: A:0.77, C:0.00, G:0.09, T:0.14
Consensus pattern (18 bp):
TAAAAAAATAAAAAAAGA
Found at i:202858 original size:16 final size:17
Alignment explanation
Indices: 202826--202881 Score: 60
Period size: 16 Copynumber: 3.2 Consensus size: 17
202816 TATTAAGAAA
202826 AAAATAATAGAAAAAAT
1 AAAATAATAGAAAAAAT
*
202843 AAAATAA-AGTAAAAAT
1 AAAATAATAGAAAAAAT
* *
202859 ATAATATATATAAATAAAT
1 AAAATA-ATAGAAA-AAAT
202878 AAAA
1 AAAA
202882 ACAAAATAGA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
16 13 0.42
17 8 0.26
18 3 0.10
19 7 0.23
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.23
Consensus pattern (17 bp):
AAAATAATAGAAAAAAT
Found at i:202924 original size:21 final size:21
Alignment explanation
Indices: 202900--202968 Score: 61
Period size: 20 Copynumber: 3.2 Consensus size: 21
202890 GAATATTAAG
* *
202900 AAAATATACATATAAATGTAT
1 AAAATATACATATAAATGAAA
*
202921 AAAATATA-ATATTAA-GAAA
1 AAAATATACATATAAATGAAA
*
202940 AAATATATACATAGTAAATGGAGA
1 AAA-ATATACATA-TAAAT-GAAA
202964 AAAAT
1 AAAAT
202969 TAATACATCT
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
19 5 0.13
20 11 0.29
21 11 0.29
22 3 0.08
23 2 0.05
24 6 0.16
ACGTcount: A:0.61, C:0.03, G:0.09, T:0.28
Consensus pattern (21 bp):
AAAATATACATATAAATGAAA
Found at i:202985 original size:2 final size:2
Alignment explanation
Indices: 202978--203020 Score: 54
Period size: 2 Copynumber: 22.0 Consensus size: 2
202968 TTAATACATC
*
202978 TA TA TA TA TA TA TA TA TA TA TA TA -A TGA TA TA -A GA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA
203019 TA
1 TA
203021 ATAAAAATAA
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
1 2 0.05
2 33 0.89
3 2 0.05
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (2 bp):
TA
Found at i:203024 original size:14 final size:14
Alignment explanation
Indices: 202981--203043 Score: 56
Period size: 14 Copynumber: 4.2 Consensus size: 14
202971 ATACATCTAT
*
202981 ATATATATATATAT
1 ATATATATATATAA
202995 ATATATAATGATATAA
1 ATATAT-AT-ATATAA
203011 GATATATATA-ATAA
1 -ATATATATATATAA
*
203025 AAATAATATAATATAA
1 ATAT-ATAT-ATATAA
203041 ATA
1 ATA
203044 AAAAGAAGAA
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
13 3 0.08
14 14 0.35
15 4 0.10
16 13 0.32
17 6 0.15
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (14 bp):
ATATATATATATAA
Found at i:203033 original size:25 final size:27
Alignment explanation
Indices: 202985--203035 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 27
202975 ATCTATATAT
* *
202985 ATATATATATATATATAATGATATAAG
1 ATATATATATATATAAAATAATATAAG
203012 ATATATATA-ATA-AAAATAATATAA
1 ATATATATATATATAAAATAATATAA
203036 TATAAATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 10 0.45
26 3 0.14
27 9 0.41
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (27 bp):
ATATATATATATATAAAATAATATAAG
Found at i:203060 original size:42 final size:43
Alignment explanation
Indices: 203009--203089 Score: 103
Period size: 42 Copynumber: 1.9 Consensus size: 43
202999 ATAATGATAT
* *
203009 AAGATATATA-TAATAAAAATAATATAATATAAATAAAAAGAAG
1 AAGATATATAGTAA-AAAAATAAAAAAATATAAATAAAAAGAAG
* *
203052 AAGA-ATATAGTAAATAAATAAAAAAATATAATTAAAAA
1 AAGATATATAGTAAAAAAATAAAAAAATATAAATAAAAA
203090 TATATATATA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
42 26 0.79
43 7 0.21
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.25
Consensus pattern (43 bp):
AAGATATATAGTAAAAAAATAAAAAAATATAAATAAAAAGAAG
Found at i:203806 original size:16 final size:16
Alignment explanation
Indices: 203785--203818 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
203775 AAAACTATTA
203785 GTCCGGAATTTGGGGT
1 GTCCGGAATTTGGGGT
203801 GTCCGGAATTTGGGGT
1 GTCCGGAATTTGGGGT
203817 GT
1 GT
203819 TACATCCCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.12, C:0.12, G:0.44, T:0.32
Consensus pattern (16 bp):
GTCCGGAATTTGGGGT
Found at i:214923 original size:3 final size:3
Alignment explanation
Indices: 214915--214939 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
214905 TCCCACTGTT
214915 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
214940 ATTTATATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:217714 original size:31 final size:31
Alignment explanation
Indices: 217678--217858 Score: 236
Period size: 31 Copynumber: 5.8 Consensus size: 31
217668 ATGTTAACAG
* **
217678 TTTGTTATAAATCGATAATGTTATTTACCAA
1 TTTGTTATAAATCGATAATGTTAGTGGCCAA
* * *
217709 TTTGTTATATATCGACAATGTTAGTGGTCAA
1 TTTGTTATAAATCGATAATGTTAGTGGCCAA
*
217740 TTTGTTATAAATCGATAATGTTAGTGGTCAA
1 TTTGTTATAAATCGATAATGTTAGTGGCCAA
* * * **
217771 TTTGTTATAAATCAATAATATTAATGGCTGA
1 TTTGTTATAAATCGATAATGTTAGTGGCCAA
*
217802 TTTGTTATAAATCAATAATGTTAGTGGCCAA
1 TTTGTTATAAATCGATAATGTTAGTGGCCAA
*
217833 TTTGTTATAAATCGATAATATTAGTG
1 TTTGTTATAAATCGATAATGTTAGTG
217859 ATCAATATAT
Statistics
Matches: 130, Mismatches: 20, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 130 1.00
ACGTcount: A:0.34, C:0.08, G:0.15, T:0.43
Consensus pattern (31 bp):
TTTGTTATAAATCGATAATGTTAGTGGCCAA
Done.