Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D02
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: 70731513
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1900000 characters in sequence are not A, C, G, or T
File 173 of 222
Found at i:55677324 original size:116 final size:121
Alignment explanation
Indices: 55677092--55677336 Score: 358
Period size: 116 Copynumber: 2.0 Consensus size: 121
55677082 TTTTAATAAG
*
55677092 ATTATTAGTAAATATAATTTAATAAATATAAAAAGTAAATAATTAAATCATATTTTAATATAATT
1 ATTATTAG-AAATATAATTTAATAAATATAAAAAGTAAATAATTAAATCATATTTTAACATAA-T
* * *
55677157 ATTATTAAATATAATTTAATAAAATAATATATAATTTAATAATATTCTTAATATATTT
64 ATTATTAAATACAATTTAATAAAATAATATATAATTTAATAACATTCTTAATATAATT
* * *
55677215 ATTATTA-AAATATGAA-TTAATAAATATCATAA-TAAATAATTTAATCATATTTTAACAT-A-A
1 ATTATTAGAAATAT-AATTTAATAAATATAAAAAGTAAATAATTAAATCATATTTTAACATAATA
55677275 TTATT-AATACAATTTAATAAAATAATATATAATTTAATAACATTCTTAATATAATT
65 TTATTAAATACAATTTAATAAAATAATATATAATTTAATAACATTCTTAATATAATT
55677331 ATTATT
1 ATTATT
55677337 TTAGATACAT
Statistics
Matches: 114, Mismatches: 7, Indels: 9
0.88 0.05 0.07
Matches are distributed among these distances:
116 54 0.47
117 6 0.05
119 1 0.01
120 24 0.21
121 20 0.18
122 2 0.02
123 7 0.06
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.44
Consensus pattern (121 bp):
ATTATTAGAAATATAATTTAATAAATATAAAAAGTAAATAATTAAATCATATTTTAACATAATAT
TATTAAATACAATTTAATAAAATAATATATAATTTAATAACATTCTTAATATAATT
Found at i:55678189 original size:14 final size:14
Alignment explanation
Indices: 55678170--55678197 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
55678160 TACAATATAT
55678170 ATAAGAATTATACG
1 ATAAGAATTATACG
55678184 ATAAGAATTATACG
1 ATAAGAATTATACG
55678198 GATCCATCTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.14, T:0.29
Consensus pattern (14 bp):
ATAAGAATTATACG
Found at i:55683610 original size:18 final size:18
Alignment explanation
Indices: 55683589--55683632 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
55683579 GATGATATCA
*
55683589 ATATTGTTGATAGTGACG
1 ATATTGATGATAGTGACG
*
55683607 ATATTGATGCTAGTGACG
1 ATATTGATGATAGTGACG
*
55683625 CTATTGAT
1 ATATTGAT
55683633 CATGACCTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.09, G:0.25, T:0.39
Consensus pattern (18 bp):
ATATTGATGATAGTGACG
Found at i:55701132 original size:24 final size:24
Alignment explanation
Indices: 55701100--55701183 Score: 82
Period size: 24 Copynumber: 3.5 Consensus size: 24
55701090 GGCTATATAA
55701100 CAGGAAGCTCATAAGAGCCATATT
1 CAGGAAGCTCATAAGAGCCATATT
** * *
55701124 CAGGAAGCTCATGTGAGTCA-ATAA
1 CAGGAAGCTCATAAGAGCCATAT-T
* *
55701148 CGGGTAGCTC-TGAAGAGCCATATT
1 CAGGAAGCTCAT-AAGAGCCATATT
55701172 CAGGAAGCTCAT
1 CAGGAAGCTCAT
55701184 GTGAGTCAAT
Statistics
Matches: 44, Mismatches: 12, Indels: 7
0.70 0.19 0.11
Matches are distributed among these distances:
23 3 0.07
24 38 0.86
25 3 0.07
ACGTcount: A:0.33, C:0.20, G:0.25, T:0.21
Consensus pattern (24 bp):
CAGGAAGCTCATAAGAGCCATATT
Found at i:55701164 original size:48 final size:48
Alignment explanation
Indices: 55701112--55701226 Score: 212
Period size: 48 Copynumber: 2.4 Consensus size: 48
55701102 GGAAGCTCAT
55701112 AAGAGCCATATTCAGGAAGCTCATGTGAGTCAATAACGGGTAGCTCTG
1 AAGAGCCATATTCAGGAAGCTCATGTGAGTCAATAACGGGTAGCTCTG
55701160 AAGAGCCATATTCAGGAAGCTCATGTGAGTCAATAACGGGTAGCTCTG
1 AAGAGCCATATTCAGGAAGCTCATGTGAGTCAATAACGGGTAGCTCTG
*
55701208 AAGAGCCATTAATCAGGAA
1 AAGAGCCA-TATTCAGGAA
55701227 ACTTCAGATA
Statistics
Matches: 65, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
48 56 0.86
49 9 0.14
ACGTcount: A:0.34, C:0.18, G:0.26, T:0.22
Consensus pattern (48 bp):
AAGAGCCATATTCAGGAAGCTCATGTGAGTCAATAACGGGTAGCTCTG
Found at i:55701204 original size:24 final size:24
Alignment explanation
Indices: 55701129--55701205 Score: 77
Period size: 24 Copynumber: 3.2 Consensus size: 24
55701119 ATATTCAGGA
55701129 AGCTCATGTGAGTCAATAACGGGT
1 AGCTCATGTGAGTCAATAACGGGT
* * * * *
55701153 AGCTC-TGAAGAG-CCATATTCAGGA
1 AGCTCATG-TGAGTCAATA-ACGGGT
55701177 AGCTCATGTGAGTCAATAACGGGT
1 AGCTCATGTGAGTCAATAACGGGT
55701201 AGCTC
1 AGCTC
55701206 TGAAGAGCCA
Statistics
Matches: 39, Mismatches: 10, Indels: 8
0.68 0.18 0.14
Matches are distributed among these distances:
23 6 0.15
24 27 0.69
25 6 0.15
ACGTcount: A:0.30, C:0.19, G:0.27, T:0.23
Consensus pattern (24 bp):
AGCTCATGTGAGTCAATAACGGGT
Found at i:55701313 original size:26 final size:25
Alignment explanation
Indices: 55701282--55701362 Score: 69
Period size: 25 Copynumber: 3.2 Consensus size: 25
55701272 GAAGCTCTGG
55701282 AGAGCCATTAATCAGCAAGCTCATAA
1 AGAGCCATTAATCAG-AAGCTCATAA
* *
55701308 AGAGCCTTTAATCGAGAAGCTC-CAA
1 AGAGCCATTAATC-AGAAGCTCATAA
* *
55701333 AGAGCTA-TATATCAGGATGCTCAT-A
1 AGAGCCATTA-ATCA-GAAGCTCATAA
55701358 AGAGC
1 AGAGC
55701363 TGCATTGTGT
Statistics
Matches: 45, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
24 3 0.07
25 22 0.49
26 18 0.40
27 2 0.04
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.21
Consensus pattern (25 bp):
AGAGCCATTAATCAGAAGCTCATAA
Found at i:55705451 original size:27 final size:28
Alignment explanation
Indices: 55705367--55705464 Score: 135
Period size: 27 Copynumber: 3.5 Consensus size: 28
55705357 CATGAGATTG
* * * *
55705367 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
55705396 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
55705424 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
55705451 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
55705465 GACTTAATAT
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 24 0.38
28 22 0.34
29 18 0.28
ACGTcount: A:0.27, C:0.13, G:0.29, T:0.32
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:55705475 original size:27 final size:27
Alignment explanation
Indices: 55705395--55705477 Score: 96
Period size: 27 Copynumber: 3.0 Consensus size: 27
55705385 TAAATTGTAC
* *
55705395 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
55705423 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTGAATATAT
*
55705450 AGCACTGAGTGTGCGGACTT-AATATAT
1 AGCACTAAGTGTGC-GACTTGAATATAT
55705477 A
1 A
55705478 TTTTTGAATC
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
27 30 0.60
28 20 0.40
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTGAATATAT
Found at i:55705478 original size:29 final size:27
Alignment explanation
Indices: 55705367--55705478 Score: 98
Period size: 28 Copynumber: 4.0 Consensus size: 27
55705357 CATGAGATTG
** * *
55705367 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGC-GACTT-AATTATATA
* *
55705396 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGA-CTTAATTATATA
* *
55705424 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGACTTAATTATATA
*
55705451 GCACTGAGTGTGCGGACTTAATATATAT
1 GCACTAAGTGTGC-GACTTAAT-TATAT
55705479 TTTTGAATCA
Statistics
Matches: 72, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
27 23 0.32
28 28 0.39
29 21 0.29
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (27 bp):
GCACTAAGTGTGCGACTTAATTATATA
Found at i:55710947 original size:41 final size:41
Alignment explanation
Indices: 55710890--55711013 Score: 230
Period size: 41 Copynumber: 3.0 Consensus size: 41
55710880 GAATATTAAG
55710890 AAACATATATGAGCTAATCAATAATCAATTTTCATATACTT
1 AAACATATATGAGCTAATCAATAATCAATTTTCATATACTT
*
55710931 AAACATATATAAGCTAATCAATAATCAATTTTCATATACTT
1 AAACATATATGAGCTAATCAATAATCAATTTTCATATACTT
*
55710972 AAACATATATGAGCTAATAAATAATCAATTTTCATATACTT
1 AAACATATATGAGCTAATCAATAATCAATTTTCATATACTT
55711013 A
1 A
55711014 TACCTTTCAT
Statistics
Matches: 80, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 80 1.00
ACGTcount: A:0.46, C:0.14, G:0.04, T:0.36
Consensus pattern (41 bp):
AAACATATATGAGCTAATCAATAATCAATTTTCATATACTT
Found at i:55711278 original size:25 final size:25
Alignment explanation
Indices: 55711247--55711350 Score: 104
Period size: 25 Copynumber: 4.2 Consensus size: 25
55711237 AGCCCTCTCT
*
55711247 TGAGCCATATAACAGGAAGCTCGTG
1 TGAGCCATATAACAGGAAGCTCATG
* * *
55711272 TGAGCCATGTAACGGGAAGCTTAT-
1 TGAGCCATATAACAGGAAGCTCATG
* * *
55711296 TCGGGCTATATAACAGGAAGCTCATA
1 T-GAGCCATATAACAGGAAGCTCATG
* *
55711322 AGAGCCATAT-TCAGGAAGCTCATG
1 TGAGCCATATAACAGGAAGCTCATG
55711346 TGAGC
1 TGAGC
55711351 TAATAACGGG
Statistics
Matches: 62, Mismatches: 15, Indels: 5
0.76 0.18 0.06
Matches are distributed among these distances:
24 17 0.27
25 45 0.73
ACGTcount: A:0.32, C:0.19, G:0.27, T:0.22
Consensus pattern (25 bp):
TGAGCCATATAACAGGAAGCTCATG
Found at i:55714573 original size:18 final size:18
Alignment explanation
Indices: 55714546--55714588 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
55714536 CGCATAAAAA
* *
55714546 GAAAGTAAATAAATAAAC
1 GAAAGAAAATAAACAAAC
*
55714564 GAAAGAAAATAAACAAAT
1 GAAAGAAAATAAACAAAC
55714582 GAAAGAA
1 GAAAGAA
55714589 GGGGGAAAGG
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:0.70, C:0.05, G:0.14, T:0.12
Consensus pattern (18 bp):
GAAAGAAAATAAACAAAC
Found at i:55714610 original size:19 final size:19
Alignment explanation
Indices: 55714582--55714629 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 19
55714572 ATAAACAAAT
* **
55714582 GAAAGAAGGGGGAAAGGGG
1 GAAAGGAGGGGGAAAAAGG
*
55714601 GAAAGGAGGGAGAAAAAGG
1 GAAAGGAGGGGGAAAAAGG
55714620 G-AAGGAGGGG
1 GAAAGGAGGGG
55714630 AATCCTAATG
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
18 8 0.33
19 16 0.67
ACGTcount: A:0.44, C:0.00, G:0.56, T:0.00
Consensus pattern (19 bp):
GAAAGGAGGGGGAAAAAGG
Found at i:55720704 original size:22 final size:22
Alignment explanation
Indices: 55720660--55720735 Score: 68
Period size: 22 Copynumber: 3.5 Consensus size: 22
55720650 ATTTTAAAAG
* *
55720660 AAAAAT-AAACTAAAAAAGTCT
1 AAAAATAAAAATAAAAAAGACT
*
55720681 AAGAAATAAAATTAAAAAA-ACT
1 AA-AAATAAAAATAAAAAAGACT
*
55720703 AAAAACAAAAAATAAAAAAGGA-T
1 AAAAA-TAAAAATAAAAAA-GACT
55720726 AAAAATAAAA
1 AAAAATAAAA
55720736 GTGAAAAGAA
Statistics
Matches: 45, Mismatches: 5, Indels: 9
0.76 0.08 0.15
Matches are distributed among these distances:
21 5 0.11
22 23 0.51
23 16 0.36
24 1 0.02
ACGTcount: A:0.75, C:0.05, G:0.05, T:0.14
Consensus pattern (22 bp):
AAAAATAAAAATAAAAAAGACT
Found at i:55722250 original size:12 final size:12
Alignment explanation
Indices: 55722222--55722258 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
55722212 AGGTAGTAGG
55722222 AATAATAATATAA
1 AATAATAATA-AA
*
55722235 AATAATACTAAA
1 AATAATAATAAA
55722247 AATAATAATAAA
1 AATAATAATAAA
55722259 TGCTAAATAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 13 0.59
13 9 0.41
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (12 bp):
AATAATAATAAA
Found at i:55722336 original size:27 final size:30
Alignment explanation
Indices: 55722272--55722339 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 30
55722262 TAAATAGCAT
55722272 AAATAAAATTAAATTAAATTAAATTAAGCATA
1 AAATAAAATTAAATTAAATTAAATTAAG-A-A
*
55722304 AGAATAAAA-TAAATT-AATTAATTTAAG-A
1 A-AATAAAATTAAATTAAATTAAATTAAGAA
55722332 AAATAAAA
1 AAATAAAA
55722340 ATATAGGGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
27 7 0.21
28 2 0.06
31 11 0.32
32 7 0.21
33 7 0.21
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.29
Consensus pattern (30 bp):
AAATAAAATTAAATTAAATTAAATTAAGAA
Found at i:55727563 original size:20 final size:20
Alignment explanation
Indices: 55727523--55727574 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
55727513 TTGGAGCCAG
*
55727523 AGATATCGATACCAAAGAAA
1 AGATATTGATACCAAAGAAA
* **
55727543 ATATATTGATACCAATTAAA
1 AGATATTGATACCAAAGAAA
*
55727563 AGGTATTGATAC
1 AGATATTGATAC
55727575 TGGATCGATA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.48, C:0.12, G:0.13, T:0.27
Consensus pattern (20 bp):
AGATATTGATACCAAAGAAA
Found at i:55727733 original size:21 final size:20
Alignment explanation
Indices: 55727709--55727759 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
55727699 GGAGCAATAC
* *
55727709 TAACTTGTTTTAAAGCAATTT
1 TAACTTGATTGAAA-CAATTT
* *
55727730 TAACTCGATTGAAACCATTT
1 TAACTTGATTGAAACAATTT
55727750 TAACTTGATT
1 TAACTTGATT
55727760 AAAAGTTTAT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 14 0.56
21 11 0.44
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.43
Consensus pattern (20 bp):
TAACTTGATTGAAACAATTT
Found at i:55731814 original size:84 final size:83
Alignment explanation
Indices: 55731642--55731799 Score: 223
Period size: 84 Copynumber: 1.9 Consensus size: 83
55731632 AGTGGTGTTG
** * *
55731642 ATACACACCTTGAAGTCTTCATTAATTTCTCATAAGTTCATTTTTATCCCCACACACCAACATAC
1 ATACACACCTTGAAACCTTCATTAATTTCTCATAAGCTCATTTGTAT-CCCACACACCAACATAC
*
55731707 TGTACGTATTAATTATAAA
65 TGTACATATTAATTATAAA
* *
55731726 ATACACACCTTGAAACCTTCGTTAATTTCTCATAAGCTCA-TTGT-T-CTACACACCAACATACT
1 ATACACACCTTGAAACCTTCATTAATTTCTCATAAGCTCATTTGTATCCCACACACCAACATACT
55731788 GTACATATTAAT
66 GTACATATTAAT
55731800 CATAGTAATC
Statistics
Matches: 67, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
80 27 0.40
82 1 0.01
83 3 0.04
84 36 0.54
ACGTcount: A:0.34, C:0.25, G:0.06, T:0.35
Consensus pattern (83 bp):
ATACACACCTTGAAACCTTCATTAATTTCTCATAAGCTCATTTGTATCCCACACACCAACATACT
GTACATATTAATTATAAA
Found at i:55734054 original size:25 final size:25
Alignment explanation
Indices: 55734004--55734056 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
55733994 TAAAGGAAGA
* *
55734004 AAATAATGTCAATAATAGTATTAAT
1 AAATAATGTCAATAATAGAATAAAT
*
55734029 AAATAATGTTATATAATA-AATAAAT
1 AAATAATGTCA-ATAATAGAATAAAT
55734054 AAA
1 AAA
55734057 AAGAAATGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 18 0.75
26 6 0.25
ACGTcount: A:0.58, C:0.02, G:0.06, T:0.34
Consensus pattern (25 bp):
AAATAATGTCAATAATAGAATAAAT
Found at i:55739215 original size:18 final size:19
Alignment explanation
Indices: 55739180--55739216 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
55739170 ATTATTAAGA
55739180 ATTTTATTATAAATTATAT
1 ATTTTATTATAAATTATAT
55739199 ATTTTAATTA-AAA-TATAT
1 ATTTT-ATTATAAATTATAT
55739217 TTAATAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 5 0.29
19 8 0.47
20 4 0.24
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
ATTTTATTATAAATTATAT
Found at i:55739446 original size:44 final size:45
Alignment explanation
Indices: 55739381--55739471 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
55739371 ACCTCTATTC
* * *
55739381 CATTCAACCAAACACAAGATTA-CTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
***
55739425 CATTCAACCAAACAGTGGATTAGCTATTACACCTCTAATCCAATA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
55739470 CA
1 CA
55739472 CCTCTAATCC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.37, C:0.29, G:0.07, T:0.27
Consensus pattern (45 bp):
CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
Found at i:55739473 original size:16 final size:16
Alignment explanation
Indices: 55739452--55739520 Score: 120
Period size: 16 Copynumber: 4.2 Consensus size: 16
55739442 GATTAGCTAT
55739452 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
55739468 TACACCTCTAATCCCAA
1 TACACCTCTAAT-CCAA
55739485 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
55739501 TACACCTCCAATCCAA
1 TACACCTCTAATCCAA
55739517 TACA
1 TACA
55739521 GCGAACCAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
16 35 0.69
17 16 0.31
ACGTcount: A:0.38, C:0.39, G:0.00, T:0.23
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:55739494 original size:33 final size:32
Alignment explanation
Indices: 55739452--55739520 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 32
55739442 GATTAGCTAT
*
55739452 TACACCTCTAATCCAATACACCTCTAATCCCAA
1 TACACCTCTAATCCAATACACCTCCAAT-CCAA
55739485 TACACCTCTAATCCAATACACCTCCAATCCAA
1 TACACCTCTAATCCAATACACCTCCAATCCAA
55739517 TACA
1 TACA
55739521 GCGAACCAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 8 0.23
33 27 0.77
ACGTcount: A:0.38, C:0.39, G:0.00, T:0.23
Consensus pattern (32 bp):
TACACCTCTAATCCAATACACCTCCAATCCAA
Found at i:55740494 original size:27 final size:28
Alignment explanation
Indices: 55740444--55740506 Score: 101
Period size: 27 Copynumber: 2.3 Consensus size: 28
55740434 TACATAGTAC
*
55740444 ATATATATGTGTGGTTTTGCTATATATA
1 ATATATATGTGTGGTTTTACTATATATA
*
55740472 ATATATATGTG-GGTTTTATTATATATA
1 ATATATATGTGTGGTTTTACTATATATA
55740499 ATATATAT
1 ATATATAT
55740507 ATATGCATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
27 22 0.67
28 11 0.33
ACGTcount: A:0.33, C:0.02, G:0.14, T:0.51
Consensus pattern (28 bp):
ATATATATGTGTGGTTTTACTATATATA
Found at i:55740874 original size:17 final size:18
Alignment explanation
Indices: 55740839--55740876 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
55740829 TGTGAGCCAA
**
55740839 TTATATTTGTAAATTATG
1 TTATATTTGTAAACCATG
55740857 TTATATTT-TAAACCATG
1 TTATATTTGTAAACCATG
55740874 TTA
1 TTA
55740877 ACTTGGTGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.34, C:0.05, G:0.08, T:0.53
Consensus pattern (18 bp):
TTATATTTGTAAACCATG
Found at i:55740937 original size:18 final size:18
Alignment explanation
Indices: 55740910--55740950 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
55740900 GGCAACTATG
* **
55740910 TTAATTTGGTGATTTGTA
1 TTAATATGGTGAACTGTA
55740928 TTAATATGGTGAACTGTA
1 TTAATATGGTGAACTGTA
55740946 TTAAT
1 TTAAT
55740951 TTGCCAGACT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.29, C:0.02, G:0.20, T:0.49
Consensus pattern (18 bp):
TTAATATGGTGAACTGTA
Found at i:55740950 original size:36 final size:36
Alignment explanation
Indices: 55740874--55740953 Score: 90
Period size: 36 Copynumber: 2.2 Consensus size: 36
55740864 TTAAACCATG
* * *
55740874 TTAACTTGGTGAATTATATTATTATGGGCAACTATG
1 TTAATTTGGTGAATTATATTAATATGGGCAACTATA
* * *
55740910 TTAATTTGGTGATTTGTATTAATATGGTG-AACTGTA
1 TTAATTTGGTGAATTATATTAATATGG-GCAACTATA
55740946 TTAATTTG
1 TTAATTTG
55740954 CCAGACTATG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
36 36 0.97
37 1 0.03
ACGTcount: A:0.29, C:0.05, G:0.20, T:0.46
Consensus pattern (36 bp):
TTAATTTGGTGAATTATATTAATATGGGCAACTATA
Found at i:55741586 original size:51 final size:51
Alignment explanation
Indices: 55741531--55741639 Score: 159
Period size: 51 Copynumber: 2.1 Consensus size: 51
55741521 TATAATGGAG
* *
55741531 TATGAACTATTATTTTGCATG-GATTGTTATTCGGTATGAATTGTTATT-TCA
1 TATGAACTATTATTTTGCATGAG-TTGTCATTCGGTATGAACTGTTATTAT-A
*
55741582 TATGAACTATTATTTTGCATGAGTTGTCATTTGGTATGAACTGTTATTATA
1 TATGAACTATTATTTTGCATGAGTTGTCATTCGGTATGAACTGTTATTATA
55741633 TATGAAC
1 TATGAAC
55741640 ATATGTTTTA
Statistics
Matches: 53, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
51 51 0.96
52 2 0.04
ACGTcount: A:0.28, C:0.08, G:0.17, T:0.47
Consensus pattern (51 bp):
TATGAACTATTATTTTGCATGAGTTGTCATTCGGTATGAACTGTTATTATA
Found at i:55744441 original size:52 final size:46
Alignment explanation
Indices: 55744422--55744849 Score: 497
Period size: 46 Copynumber: 9.3 Consensus size: 46
55744412 GGACAAGTGG
* * *
55744422 AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGAC
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGAC
*
55744468 AAAGTGATAAGTGATAGCTTCAGCTATACTTATCTGATCAAGTGAC
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGAC
55744514 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGAC
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGAC
*
55744560 AAGTGGAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGAC
1 ------AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGAC
* * *
55744612 AAGTGAAAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGAC
1 ------AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGAC
* * *
55744664 AAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAA
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGAC
55744710 AAAGTGATAA--G-T-GC-T-A--T--ACTTATCTGATCAAGTGAC
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGAC
* *
55744746 AAAGTGATAAGTGTTAGCCTT-AGCTACACTTATCTGATCAAGTGAG
1 AAAGTGATAAGTGATAG-CTTCAGCTACACTTATCTGATCAAGTGAC
* * *
55744792 AAAGTGATAAGTGGTAGCCT-AGCTACACTTATCTGATC-AGGGAC
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGAC
55744836 -AAGTGATAAGTGAT
1 AAAGTGATAAGTGAT
55744850 CATATGTAAG
Statistics
Matches: 346, Mismatches: 20, Indels: 35
0.86 0.05 0.09
Matches are distributed among these distances:
36 28 0.08
38 2 0.01
39 1 0.00
40 2 0.01
41 2 0.01
42 4 0.01
43 14 0.04
44 6 0.02
45 20 0.06
46 173 0.50
52 94 0.27
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.29
Consensus pattern (46 bp):
AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGAC
Found at i:55744476 original size:98 final size:97
Alignment explanation
Indices: 55744356--55744722 Score: 501
Period size: 98 Copynumber: 3.7 Consensus size: 97
55744346 TTTGAGTACT
* * *
55744356 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGGGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGT-
*
55744421 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
65 GAAAGTGATAAGTGATAGCTTCGGCTATACTTA
*
55744454 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTATACTTATCTGATCAAGTGAC-----
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
* *
55744514 AAAGTGATAAGTGATAGCTTCAGCTACACTTA
66 AAAGTGATAAGTGATAGCTTCGGCTATACTTA
*
55744546 TCTGATCAAGTGACAAGTGGAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGA
1 TCTGATCAAGTGAC------AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGA
55744611 CAAGTGAAAAGTGATAAGTGATAGCTTCGGCTATACTTA
60 CAAGTG-AAAGTGATAAGTGATAGCTTCGGCTATACTTA
* * * *
55744650 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTG-ACAAGT
55744715 GATAAGTG
65 GA-AAGTG
55744723 CTATACTTAT
Statistics
Matches: 239, Mismatches: 16, Indels: 27
0.85 0.06 0.10
Matches are distributed among these distances:
92 43 0.18
98 142 0.59
99 11 0.05
104 43 0.18
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (97 bp):
TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
AAAGTGATAAGTGATAGCTTCGGCTATACTTA
Found at i:55744704 original size:196 final size:196
Alignment explanation
Indices: 55744370--55744722 Score: 607
Period size: 196 Copynumber: 1.8 Consensus size: 196
55744360 ATCAAGTGAC
* * *
55744370 AAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGGGACAAGTGGAAAGTGATAAGTA
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGGGACAAGTGAAAAGTGATAAGTA
* *
55744435 ATAGCTTCGGCTATACTTATCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTATACTTA
66 ATAGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTA
*
55744500 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
131 TCTGATCAAGTGAAAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
55744565 G
196 G
* * *
55744566 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGTG
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGGGACAAGTGAAAAGTGATAAGTA
* *
55744631 ATAGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
66 ATAGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTA
55744696 TCTGATCAAGTGAAAAAGTGATAAGTG
131 TCTGATCAAGTGAAAAAGTGATAAGTG
55744723 CTATACTTAT
Statistics
Matches: 146, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
196 146 1.00
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (196 bp):
AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGGGACAAGTGAAAAGTGATAAGTA
ATAGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTA
TCTGATCAAGTGAAAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
G
Found at i:55744732 original size:36 final size:36
Alignment explanation
Indices: 55744686--55744758 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
55744676 GGTAGCTTTA
55744686 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
* *
55744722 GCTATACTTATCTGATCAAGTGACAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
55744758 G
1 G
55744759 TTAGCCTTAG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.29
Consensus pattern (36 bp):
GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
Found at i:55744777 original size:82 final size:82
Alignment explanation
Indices: 55744640--55744804 Score: 294
Period size: 82 Copynumber: 2.0 Consensus size: 82
55744630 GATAGCTTCG
*
55744640 GCTATACTTATCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAA
1 GCTATACTTATCTGATCAAGAGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTGATCAA
55744705 GTGAAAAAGTGATAAGT
66 GTGAAAAAGTGATAAGT
* *
55744722 GCTATACTTATCTGATCAAGTGACAAAGTGATAAGTGTTAGCCTTAGCTACACTTATCTGATCAA
1 GCTATACTTATCTGATCAAGAGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTGATCAA
*
55744787 GTGAGAAAGTGATAAGT
66 GTGAAAAAGTGATAAGT
55744804 G
1 G
55744805 GTAGCCTAGC
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
82 79 1.00
ACGTcount: A:0.35, C:0.14, G:0.21, T:0.30
Consensus pattern (82 bp):
GCTATACTTATCTGATCAAGAGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTGATCAA
GTGAAAAAGTGATAAGT
Found at i:55746382 original size:21 final size:21
Alignment explanation
Indices: 55746344--55746397 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
55746334 AACAGCAGTG
*
55746344 GCGGTGAGATTAATTACTGTA
1 GCGGTGAGATTAATTACTATA
*
55746365 GCGGTGAGATTGGA-TACTATA
1 GCGGTGAGATT-AATTACTATA
* *
55746386 GCAGTAAGATTA
1 GCGGTGAGATTA
55746398 GAAACAGCGG
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
21 26 0.96
22 1 0.04
ACGTcount: A:0.31, C:0.09, G:0.30, T:0.30
Consensus pattern (21 bp):
GCGGTGAGATTAATTACTATA
Found at i:55750007 original size:5 final size:5
Alignment explanation
Indices: 55749970--55750023 Score: 51
Period size: 5 Copynumber: 11.2 Consensus size: 5
55749960 TTTGCTTTAC
* * *
55749970 TGCTT TGCTC TGCTT TG-TT TTC-T T-CTGT TGCTT TGCTT TGCTC TGCTT
1 TGCTT TGCTT TGCTT TGCTT TGCTT TGCT-T TGCTT TGCTT TGCTT TGCTT
55750018 TGCTT T
1 TGCTT T
55750024 TGTTTTTCTA
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
3 1 0.03
4 5 0.12
5 32 0.80
6 2 0.05
ACGTcount: A:0.00, C:0.22, G:0.19, T:0.59
Consensus pattern (5 bp):
TGCTT
Found at i:55753271 original size:13 final size:13
Alignment explanation
Indices: 55753253--55753300 Score: 69
Period size: 13 Copynumber: 3.7 Consensus size: 13
55753243 TTCAAATTTT
*
55753253 TCAAAAACACTTC
1 TCAAAAGCACTTC
55753266 TCAAAAGCACTTC
1 TCAAAAGCACTTC
* *
55753279 TTAAAAGTACTTC
1 TCAAAAGCACTTC
55753292 TCAAAAGCA
1 TCAAAAGCA
55753301 ATGAAGAACT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 30 1.00
ACGTcount: A:0.44, C:0.25, G:0.06, T:0.25
Consensus pattern (13 bp):
TCAAAAGCACTTC
Found at i:55753413 original size:16 final size:17
Alignment explanation
Indices: 55753382--55753414 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
55753372 TTTATTTATA
55753382 TTGTTTCAATTTTTTTT
1 TTGTTTCAATTTTTTTT
*
55753399 TTGTTTTAATTTTTTT
1 TTGTTTCAATTTTTTT
55753415 AATTTTATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.12, C:0.03, G:0.06, T:0.79
Consensus pattern (17 bp):
TTGTTTCAATTTTTTTT
Found at i:55753418 original size:26 final size:25
Alignment explanation
Indices: 55753358--55753442 Score: 82
Period size: 26 Copynumber: 3.3 Consensus size: 25
55753348 CTGATTTCAC
* *
55753358 TTTTGATTTTCTTTTTTATTTATATTG
1 TTTTAATTTT-TTTTTTATTTA-ATTT
* *
55753385 TTTCAATTTTTTTTTTGTTTTAATTT
1 TTTTAATTTTTTTTTT-ATTTAATTT
* *
55753411 TTTTAATTTTATTTTTAATTAA-TT
1 TTTTAATTTTTTTTTTATTTAATTT
55753435 TTTTAATT
1 TTTTAATT
55753443 AATAAACAAG
Statistics
Matches: 49, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
24 10 0.20
25 4 0.08
26 23 0.47
27 12 0.24
ACGTcount: A:0.20, C:0.02, G:0.04, T:0.74
Consensus pattern (25 bp):
TTTTAATTTTTTTTTTATTTAATTT
Found at i:55753437 original size:12 final size:12
Alignment explanation
Indices: 55753404--55753445 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
55753394 TTTTTTTGTT
55753404 TTAATTTTTTTAA
1 TTAA-TTTTTTAA
*
55753417 TT-TTATTTTTAA
1 TTAAT-TTTTTAA
55753429 TTAATTTTTTAA
1 TTAATTTTTTAA
55753441 TTAAT
1 TTAAT
55753446 AAACAAGGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
11 1 0.04
12 21 0.84
13 3 0.12
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
TTAATTTTTTAA
Found at i:55759531 original size:29 final size:29
Alignment explanation
Indices: 55759489--55759547 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
55759479 TAATAATGTT
55759489 AATGATTATTAAGAATTAAATCAAATCAA
1 AATGATTATTAAGAATTAAATCAAATCAA
55759518 AATGATTATTAAGAATTAAATCAAATCAA
1 AATGATTATTAAGAATTAAATCAAATCAA
55759547 A
1 A
55759548 TTTTCATGTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.56, C:0.07, G:0.07, T:0.31
Consensus pattern (29 bp):
AATGATTATTAAGAATTAAATCAAATCAA
Found at i:55769237 original size:209 final size:208
Alignment explanation
Indices: 55768819--55769239 Score: 815
Period size: 209 Copynumber: 2.0 Consensus size: 208
55768809 CAAGAACACC
55768819 TTATCACCTAGCTGCTGTCCAAAAATCAGCTCAATCGAACCACGGATGGACCTTCGATCAAGGAG
1 TTATCACCTAGCTGCTGTCCAAAAATCAGCTCAATCGAACCACGGATGGACCTTCGATCAAGGAG
55768884 TTGATCACTGCTGCACCAAGCTTGAAAAACTGATTTTTTTTCTATTCTCTCTTTTTCTCCAACGA
66 TTGATCACTGCTGCACCAAGCTTGAAAAACTGATTTTTTTTCTATTCTCTCTTTTTCTCCAACGA
55768949 GCTTCAATCTCACTCTCTGTTTTTTTTTCTCTTTTAAATTGAGAATTTGACACTCAATAATAATA
131 GCTTCAATCTCACTCTCTGTTTTTTTTTCTCTTTTAAATTGAGAATTTGACACTCAATAATAATA
55769014 GAAAGACAAAACA
196 GAAAGACAAAACA
* *
55769027 TTATCACCTAGCTGCTGTTCAAAAATCAGCTCAATCGAACCACGGATGGACCTTCGATCGAGGAG
1 TTATCACCTAGCTGCTGTCCAAAAATCAGCTCAATCGAACCACGGATGGACCTTCGATCAAGGAG
55769092 TTGATCACTGCTGCACCAAGCTTGAAAAACTGATTTTTTTTTCTATTCTCTCTTTTTCTCCAACG
66 TTGATCACTGCTGCACCAAGCTTGAAAAACTGA-TTTTTTTTCTATTCTCTCTTTTTCTCCAACG
55769157 AGCTTCAATCTCACTCTCTGTTTTTTTTTCTCTTTTAAATTGAGAATTTGACACTCAATAATAAT
130 AGCTTCAATCTCACTCTCTGTTTTTTTTTCTCTTTTAAATTGAGAATTTGACACTCAATAATAAT
55769222 AGAAAGACAAAACA
195 AGAAAGACAAAACA
55769236 TTAT
1 TTAT
55769240 GGCAGAAAAT
Statistics
Matches: 210, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
208 96 0.46
209 114 0.54
ACGTcount: A:0.29, C:0.23, G:0.13, T:0.35
Consensus pattern (208 bp):
TTATCACCTAGCTGCTGTCCAAAAATCAGCTCAATCGAACCACGGATGGACCTTCGATCAAGGAG
TTGATCACTGCTGCACCAAGCTTGAAAAACTGATTTTTTTTCTATTCTCTCTTTTTCTCCAACGA
GCTTCAATCTCACTCTCTGTTTTTTTTTCTCTTTTAAATTGAGAATTTGACACTCAATAATAATA
GAAAGACAAAACA
Found at i:55770591 original size:34 final size:35
Alignment explanation
Indices: 55770553--55770619 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
55770543 CAGTAAAATA
* *
55770553 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATAATTTACTGGAAAATATTTTAC
*
55770587 TTTTCTGTAAAATAATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATAATTTACTGGAAAATATTTT
55770620 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 16 0.55
35 13 0.45
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATAATTTACTGGAAAATATTTTAC
Found at i:55770605 original size:20 final size:20
Alignment explanation
Indices: 55770568--55770607 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
55770558 CGTAAAATGA
**
55770568 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATAATTTACT
*
55770588 TTTCTGTAAAATAATTTACT
1 TTTCTGGAAAATAATTTACT
55770608 GGAAAATATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.30, C:0.10, G:0.10, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATAATTTACT
Found at i:55778813 original size:30 final size:31
Alignment explanation
Indices: 55778769--55778827 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
55778759 CAATTCATAT
* *
55778769 ATATCTCATGTCACATAGCATGTTTCATTCC
1 ATATCTCATATCACATAGCATGTATCATTCC
*
55778800 ATAT-TCATATCACATATCATGTATCATT
1 ATATCTCATATCACATAGCATGTATCATT
55778828 TATATCATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.31, C:0.22, G:0.07, T:0.41
Consensus pattern (31 bp):
ATATCTCATATCACATAGCATGTATCATTCC
Found at i:55787878 original size:16 final size:17
Alignment explanation
Indices: 55787857--55787890 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
55787847 TCAATGTTGT
55787857 AAAATAAA-CAAGAAAA
1 AAAATAAAGCAAGAAAA
*
55787873 AAAATAAAGGAAGAAAA
1 AAAATAAAGCAAGAAAA
55787890 A
1 A
55787891 GAAGAGGAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.79, C:0.03, G:0.12, T:0.06
Consensus pattern (17 bp):
AAAATAAAGCAAGAAAA
Found at i:55790234 original size:61 final size:59
Alignment explanation
Indices: 55790112--55790249 Score: 168
Period size: 61 Copynumber: 2.3 Consensus size: 59
55790102 TTAATATAAC
* * * ** * * *
55790112 ATTTGGTATTTGAATTTAACACTTTTTCCTAATTTGGTACTTAAACTTTTTTTGGCTCA
1 ATTTGGTACTTGAACTTGACACTTTTTCCTAATTTAATACCTAAACTTTTTTGGGCCCA
*
55790171 ATTTGGTACTTGAACTTGACATTTTTTTCCCTAATTTAATACCTAAACTTTTTTGGGCCCA
1 ATTTGGTACTTGAACTTGACA-CTTTTT-CCTAATTTAATACCTAAACTTTTTTGGGCCCA
*
55790232 ATTTGGTACCTGAACTTG
1 ATTTGGTACTTGAACTTG
55790250 GCACCTAATT
Statistics
Matches: 67, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
59 18 0.27
60 5 0.07
61 44 0.66
ACGTcount: A:0.24, C:0.17, G:0.13, T:0.46
Consensus pattern (59 bp):
ATTTGGTACTTGAACTTGACACTTTTTCCTAATTTAATACCTAAACTTTTTTGGGCCCA
Found at i:55794370 original size:38 final size:38
Alignment explanation
Indices: 55794319--55794397 Score: 158
Period size: 38 Copynumber: 2.1 Consensus size: 38
55794309 ACATGAGGCA
55794319 TTATGTTAACTTGCTATCTTGTTTTTACTTCCTTACGC
1 TTATGTTAACTTGCTATCTTGTTTTTACTTCCTTACGC
55794357 TTATGTTAACTTGCTATCTTGTTTTTACTTCCTTACGC
1 TTATGTTAACTTGCTATCTTGTTTTTACTTCCTTACGC
55794395 TTA
1 TTA
55794398 GACATAATTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.16, C:0.20, G:0.10, T:0.53
Consensus pattern (38 bp):
TTATGTTAACTTGCTATCTTGTTTTTACTTCCTTACGC
Found at i:55809349 original size:44 final size:43
Alignment explanation
Indices: 55809220--55810026 Score: 291
Period size: 44 Copynumber: 18.7 Consensus size: 43
55809210 CCAGTAATCC
* * *
55809220 TATCTCCTTGAAGTTGCAGTGGAGCGGATTAA-AATCACAGATCT
1 TATCTCCTTGAAGTTGCAGTGGAGCAGACTAAGAAGCA-AG-TCT
* * * * * * *
55809264 GATCT-CTCAGAAGTTACAG-GGAGCAGA-T-CGCATCTAGTCT
1 TATCTCCT-TGAAGTTGCAGTGGAGCAGACTAAGAAGCAAGTCT
*
55809304 TATCTCCTTGAAGTTGCAGTGGAGCAAACTAAGTAAGCAAGTCT
1 TATCTCCTTGAAGTTGCAGTGGAGCAGACTAAG-AAGCAAGTCT
* *
55809348 TATCCTCC-TGAAGTTGCAGT-GAGGCAGACTGAAGATGGCAAATCT
1 TAT-CTCCTTGAAGTTGCAGTGGA-GCAGACT-AAGA-AGCAAGTCT
* * * * * *
55809393 TATCTACATGAAGTTGCAATGGAGCAGA-TTA-AAGCTGATAATCC
1 TATCTCCTTGAAGTTGCAGTGGAGCAGACTAAGAAGC--A-AGTCT
* * * * * **
55809437 TATCTCCCTGAAGTTGTAGTGGAGCGGATTAA-AACCTTGGATCT
1 TATCTCCTTGAAGTTGCAGTGGAGCAGACTAAGAAGC-AAG-TCT
* * * * *
55809481 TATCT-CTCTGAAGTTGCAG-AGAGCAGA-T-CGCATCTAGTCT
1 TATCTCCT-TGAAGTTGCAGTGGAGCAGACTAAGAAGCAAGTCT
*
55809521 TATCTCCTTGAAGTTGCAGTGGAGTAGACTAAGTAAGCAAGTCT
1 TATCTCCTTGAAGTTGCAGTGGAGCAGACTAAG-AAGCAAGTCT
* * *
55809565 TATCCTCC-TGAAGATGCAGT-GAGGCAGACTGAAGATGACAAATCT
1 TAT-CTCCTTGAAGTTGCAGTGGA-GCAGACT-AAGAAG-CAAGTCT
* * *
55809610 TATCTCCCTGAAGTTGCAGTGGAGCAGA-TTA-AAGCCGATGATCT
1 TATCTCCTTGAAGTTGCAGTGGAGCAGACTAAGAAG-C-AAG-TCT
* * * * * **
55809654 TATCT-TTCTGAAGTTACAGTGGAGCGGATTAA-AACCTTGGATCT
1 TATCTCCT-TGAAGTTGCAGTGGAGCAGACTAAGAAGC-AAG-TCT
* * * * *
55809698 TATCT-CTCTGAAGTTGCAG-AGAGCAGA-T-CGCATCTAGTCT
1 TATCTCCT-TGAAGTTGCAGTGGAGCAGACTAAGAAGCAAGTCT
* * * *
55809738 TATCTCCCTGAAGTTGTAGTGGAGCAGACTAAGTAAGTAAGCCT
1 TATCTCCTTGAAGTTGCAGTGGAGCAGACTAAG-AAGCAAGTCT
* * *
55809782 TATC-CTTCTGAAGTTGCAGT-GAGGCAGACTGAAGATGGCAAATCT
1 TATCTCCT-TGAAGTTGCAGTGGA-GCAGACT-AAGA-AGCAAGTCT
* * * * *
55809827 TATCTCCCTGAAGTTACAGTGGAGCAG-GTTA-AAGCCGATGATCT
1 TATCTCCTTGAAGTTGCAGTGGAGCAGACTAAGAAG-C-AAG-TCT
* ** * * **
55809871 TATCT-CTCTGAAGTTACAGTGGAGTGGATTAA-AACCTTGGATCT
1 TATCTCCT-TGAAGTTGCAGTGGAGCAGACTAAGAAGC-AAG-TCT
* * * * *
55809915 TATCT-CTCTGAAGTTGCAG-AGAGCAGA-T-CGCATCTAGTCT
1 TATCTCCT-TGAAGTTGCAGTGGAGCAGACTAAGAAGCAAGTCT
* *
55809955 TATCT-CTCTGAAGTTGTAGTGGAGAAGACTAAGTAAGCAAGTCT
1 TATCTCCT-TGAAGTTGCAGTGGAGCAGACTAAG-AAGCAAGTCT
**
55809999 TATCT-CTCTGAAGTTGCAGCAGAGCAGA
1 TATCTCCT-TGAAGTTGCAGTGGAGCAGA
55810027 TCACATCAAA
Statistics
Matches: 578, Mismatches: 128, Indels: 114
0.70 0.16 0.14
Matches are distributed among these distances:
40 74 0.13
41 42 0.07
42 23 0.04
43 45 0.08
44 282 0.49
45 105 0.18
46 7 0.01
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (43 bp):
TATCTCCTTGAAGTTGCAGTGGAGCAGACTAAGAAGCAAGTCT
Found at i:55809535 original size:173 final size:173
Alignment explanation
Indices: 55809343--55809668 Score: 396
Period size: 173 Copynumber: 1.9 Consensus size: 173
55809333 TAAGTAAGCA
*
55809343 AGTCTTATCCTCCTGAAGTTGCAGT-GAGGCAGACTGAAG-ATGGCAAATCTTAT-CTACATGAA
1 AGTCTTATCCTCCTGAAGTTGCAGTGGA-GCAGACT-AAGTA-AGCAAATCTTATCCT-CATGAA
* * * * * *
55809405 GTTGCAATG-GAGCAGATTAAAGCTGA-TAATCCTATCTCCCTGAAGTTGTAGTGGAGCGGATTA
62 GATGCAATGAG-GCAGACTAAAGATGACAAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTA
*
55809468 AAACC-TTGGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCT
126 AAACCGAT-GATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCT
* * *
55809516 AGTCTTAT-CTCCTTGAAGTTGCAGTGGAGTAGACTAAGTAAGCAAGTCTTATCCTCCTGAAGAT
1 AGTCTTATCCTCC-TGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAATCTTATCCTCATGAAGAT
* * * *
55809580 GCAGTGAGGCAGACTGAAGATGACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGC
65 GCAATGAGGCAGACTAAAGATGACAAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAAC
*
55809645 CGATGATCTTATCTTTCTGAAGTT
130 CGATGATCTTATCTCTCTGAAGTT
55809669 ACAGTGGAGC
Statistics
Matches: 130, Mismatches: 16, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
172 41 0.32
173 86 0.66
174 3 0.02
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.29
Consensus pattern (173 bp):
AGTCTTATCCTCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAATCTTATCCTCATGAAGATG
CAATGAGGCAGACTAAAGATGACAAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACC
GATGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCT
Found at i:55809566 original size:84 final size:84
Alignment explanation
Indices: 55809478--55810033 Score: 294
Period size: 84 Copynumber: 6.5 Consensus size: 84
55809468 AAACCTTGGA
55809478 TCTTATCTCTCTGAAGTTGCAG-AGAGCAGATCGCATCTAGTCTTATCTC-CTTGAAGTTGCAGT
1 TCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCTAGTCTTATCTCTC-TGAAGTTGCAGT
*
55809541 GGAGTAGACTAAGTAAGCAAG
65 GGAGCAGACTAAG-AAGCAAG
* * * * *
55809562 TCTTATC-CTCCTGAAGATGCAGT-GAGGCAGA-CTGAAGATGACAAATCTTATCTCCCTGAAGT
1 TCTTATCTCT-CTGAAGTTGCAGTAGA-GCAGATC-G--CAT--CTAGTCTTATCTCTCTGAAGT
* *
55809624 TGCAGTGGAGCAGA-TTA-AAGCCGATG
59 TGCAGTGGAGCAGACTAAGAAG-C-AAG
* * * * *** * *
55809650 ATCTTATCTTTCTGAAGTTACAGTGGAGCGGATTAAAACCTTGGATCTTATCTCTCTGAAGTTGC
1 -TCTTATCTCTCTGAAGTTGCAGTAGAGCAGA-TCGCATC-TAG-TCTTATCTCTCTGAAGTTGC
* * * * *
55809715 AG-AGAGCAGA-T-CGCATCTAG
62 AGTGGAGCAGACTAAGAAGCAAG
* * * * * ** *
55809735 TCTTATCTCCCTGAAGTTGTAGTGGAGCAGACTAAGTAAGTAAGCCTTATC-CTTCTGAAGTTGC
1 TCTTATCTCTCTGAAGTTGCAGTAGAGCAGA-T-CGCATCT-AGTCTTATCTC-TCTGAAGTTGC
* *
55809799 AGT-GAGGCAGACTGAAGATGGCAAA
62 AGTGGA-GCAGACT-AAGA-AGCAAG
* * * * *** * * *
55809824 TCTTATCTCCCTGAAGTTACAGTGGAGCAGGTTAAAGCCGATGATCTTATCTCTCTGAAGTTACA
1 TCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCA-TCTA-G-TCTTATCTCTCTGAAGTTGCA
** * * **
55809889 GTGGAGTGGATTAA-AACCTTGG
63 GTGGAGCAGACTAAGAAGC-AAG
*
55809911 ATCTTATCTCTCTGAAGTTGCAG-AGAGCAGATCGCATCTAGTCTTATCTCTCTGAAGTTGTAGT
1 -TCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCTAGTCTTATCTCTCTGAAGTTGCAGT
*
55809975 GGAGAAGACTAAGTAAGCAAG
65 GGAGCAGACTAAG-AAGCAAG
* *
55809996 TCTTATCTCTCTGAAGTTGCAGCAGAGCAGATCACATC
1 TCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATC
55810034 AAATTCATTT
Statistics
Matches: 354, Mismatches: 80, Indels: 75
0.70 0.16 0.15
Matches are distributed among these distances:
83 3 0.01
84 122 0.34
85 31 0.09
86 12 0.03
87 23 0.06
88 51 0.14
89 105 0.30
90 7 0.02
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.29
Consensus pattern (84 bp):
TCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCTAGTCTTATCTCTCTGAAGTTGCAGTG
GAGCAGACTAAGAAGCAAG
Found at i:55809589 original size:217 final size:217
Alignment explanation
Indices: 55809214--55810017 Score: 1243
Period size: 217 Copynumber: 3.7 Consensus size: 217
55809204 CGGTAGCCAG
* * * *** * *
55809214 TAATCCTATCTCCTTGAAGTTGCAGTGGAGCGGATTAAAATCACAGATCTGATCTCTCAGAAGTT
1 TAATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAACCTTGGATCTTATCTCTCTGAAGTT
* * *
55809279 ACAGGGAGCAGATCGCATCTAGTCTTATCTCCTTGAAGTTGCAGTGGAGCAAACTAAGTAAGCAA
66 GCAGAGAGCAGATCGCATCTAGTCTTATCTCCTTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAA
* *
55809344 GTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTACATGAAGTTG
131 GTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTTG
* *
55809409 CAATGGAGCAGATTAAAGCTGA
196 CAGTGGAGCAGATTAAAGCCGA
**
55809431 TAATCCTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAACCTTGGATCTTATCTCTCTGAAGTT
1 TAATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAACCTTGGATCTTATCTCTCTGAAGTT
*
55809496 GCAGAGAGCAGATCGCATCTAGTCTTATCTCCTTGAAGTTGCAGTGGAGTAGACTAAGTAAGCAA
66 GCAGAGAGCAGATCGCATCTAGTCTTATCTCCTTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAA
* *
55809561 GTCTTATCCTCCTGAAGATGCAGTGAGGCAGACTGAAGATGACAAATCTTATCTCCCTGAAGTTG
131 GTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTTG
55809626 CAGTGGAGCAGATTAAAGCCGA
196 CAGTGGAGCAGATTAAAGCCGA
* * **
55809648 TGATCTTATCTTTCTGAAGTTACAGTGGAGCGGATTAAAACCTTGGATCTTATCTCTCTGAAGTT
1 TAATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAACCTTGGATCTTATCTCTCTGAAGTT
* * *
55809713 GCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGTAGTGGAGCAGACTAAGTAAGTAA
66 GCAGAGAGCAGATCGCATCTAGTCTTATCTCCTTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAA
* * *
55809778 GCCTTATCCTTCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTTA
131 GTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTTG
*
55809843 CAGTGGAGCAGGTTAAAGCCGA
196 CAGTGGAGCAGATTAAAGCCGA
* * * *
55809865 TGATCTTATCTCTCTGAAGTTACAGTGGAGTGGATTAAAACCTTGGATCTTATCTCTCTGAAGTT
1 TAATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAACCTTGGATCTTATCTCTCTGAAGTT
* *
55809930 GCAGAGAGCAGATCGCATCTAGTCTTATCT-CTCTGAAGTTGTAGTGGAGAAGACTAAGTAAGCA
66 GCAGAGAGCAGATCGCATCTAGTCTTATCTCCT-TGAAGTTGCAGTGGAGCAGACTAAGTAAGCA
55809994 AGTCTTAT-CTCTCTGAAGTTGCAG
130 AGTCTTATCCTC-CTGAAGTTGCAG
55810018 CAGAGCAGAT
Statistics
Matches: 544, Mismatches: 41, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
216 3 0.01
217 541 0.99
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.29
Consensus pattern (217 bp):
TAATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAACCTTGGATCTTATCTCTCTGAAGTT
GCAGAGAGCAGATCGCATCTAGTCTTATCTCCTTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAA
GTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTTG
CAGTGGAGCAGATTAAAGCCGA
Found at i:55809739 original size:173 final size:173
Alignment explanation
Indices: 55809560--55809885 Score: 366
Period size: 173 Copynumber: 1.9 Consensus size: 173
55809550 TAAGTAAGCA
* *
55809560 AGTCTTATC-CTCCTGAAGATGCAGT-GAGGCAGACTGAAG-ATGACAAATCTTAT-CTCCCTGA
1 AGTCTTATCTC-CCTGAAGATGCAGTGGA-GCAGACT-AAGTAAG-CAAACCTTATCCT-CCTGA
* * **
55809621 AGTTGCAGTG-GAGCAGA-TTAA-A-GCCGATGATCTTATCTTTCTGAAGTTACAGTGGAGC-GG
61 AGTTGCAGTGAG-GCAGACTGAAGATGCC-A-AATCTTATCTCCCTGAAGTTACAGTGGAGCAGG
*
55809681 ATTAAAACC-TTGGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCT
123 -TTAAAACCGAT-GATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCT
* * * * *
55809733 AGTCTTATCTCCCTGAAGTTGTAGTGGAGCAGACTAAGTAAGTAAGCCTTATCCTTCTGAAGTTG
1 AGTCTTATCTCCCTGAAGATGCAGTGGAGCAGACTAAGTAAGCAAACCTTATCCTCCTGAAGTTG
* *
55809798 CAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTTACAGTGGAGCAGGTTAAAGCC
66 CAGTGAGGCAGACTGAAGATGCCAAATCTTATCTCCCTGAAGTTACAGTGGAGCAGGTTAAAACC
55809863 GATGATCTTATCTCTCTGAAGTT
131 GATGATCTTATCTCTCTGAAGTT
55809886 ACAGTGGAGT
Statistics
Matches: 129, Mismatches: 14, Indels: 20
0.79 0.09 0.12
Matches are distributed among these distances:
172 29 0.22
173 90 0.70
174 8 0.06
175 2 0.02
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.29
Consensus pattern (173 bp):
AGTCTTATCTCCCTGAAGATGCAGTGGAGCAGACTAAGTAAGCAAACCTTATCCTCCTGAAGTTG
CAGTGAGGCAGACTGAAGATGCCAAATCTTATCTCCCTGAAGTTACAGTGGAGCAGGTTAAAACC
GATGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCT
Found at i:55817416 original size:21 final size:21
Alignment explanation
Indices: 55817383--55817429 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
55817373 GTCTGACGAG
55817383 GAGGACGACGATAATGGAGG-A
1 GAGGACGACGATAAT-GAGGAA
* *
55817404 GAGGATGATGATAATGAGGAA
1 GAGGACGACGATAATGAGGAA
55817425 GAGGA
1 GAGGA
55817430 GGAGCCCCGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 4 0.17
21 19 0.83
ACGTcount: A:0.40, C:0.04, G:0.43, T:0.13
Consensus pattern (21 bp):
GAGGACGACGATAATGAGGAA
Found at i:55817431 original size:24 final size:22
Alignment explanation
Indices: 55817380--55817432 Score: 54
Period size: 21 Copynumber: 2.4 Consensus size: 22
55817370 ACCGTCTGAC
*
55817380 GAGGAGGACGACGATAATGGAG
1 GAGGAGGACGACGATAATGGAA
* *
55817402 GA-GAGGATGATGATAATGAGGAA
1 GAGGAGGACGACGATAAT--GGAA
55817425 GAGGAGGA
1 GAGGAGGA
55817433 GCCCCGATCA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
21 13 0.52
22 2 0.08
23 5 0.20
24 5 0.20
ACGTcount: A:0.40, C:0.04, G:0.45, T:0.11
Consensus pattern (22 bp):
GAGGAGGACGACGATAATGGAA
Found at i:55819167 original size:23 final size:24
Alignment explanation
Indices: 55819135--55819179 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
55819125 TGCATGTTTA
55819135 TTTCTTATTTTCAATTTGTTTTGT
1 TTTCTTATTTTCAATTTGTTTTGT
* *
55819159 TTTC-TATTTTTATTTTGTTTT
1 TTTCTTATTTTCAATTTGTTTT
55819180 TAGTTTGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.11, C:0.07, G:0.07, T:0.76
Consensus pattern (24 bp):
TTTCTTATTTTCAATTTGTTTTGT
Found at i:55819180 original size:24 final size:25
Alignment explanation
Indices: 55819135--55819185 Score: 61
Period size: 23 Copynumber: 2.1 Consensus size: 25
55819125 TGCATGTTTA
55819135 TTTCTTATTTTCAATTTGTTTT-GT
1 TTTCTTATTTTCAATTTGTTTTAGT
* *
55819159 TTTC-TATTTTTATTTTGTTTTTAGT
1 TTTCTTATTTTCAATTTG-TTTTAGT
55819184 TT
1 TT
55819186 GTTTAGTTGG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 11 0.48
24 8 0.35
25 4 0.17
ACGTcount: A:0.12, C:0.06, G:0.08, T:0.75
Consensus pattern (25 bp):
TTTCTTATTTTCAATTTGTTTTAGT
Found at i:55820842 original size:31 final size:34
Alignment explanation
Indices: 55820780--55820842 Score: 87
Period size: 35 Copynumber: 1.9 Consensus size: 34
55820770 TAAATCTTAT
*
55820780 TAAATTAATAGAATATTTATTTACAAGATAAAAAA
1 TAAATTAATAAAATATTTATTTA-AAGATAAAAAA
55820815 TAAATTAATAAAATA-TTA-TT-AAGATAAA
1 TAAATTAATAAAATATTTATTTAAAGATAAA
55820843 CATTAACTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
31 8 0.30
33 2 0.07
34 3 0.11
35 14 0.52
ACGTcount: A:0.59, C:0.02, G:0.05, T:0.35
Consensus pattern (34 bp):
TAAATTAATAAAATATTTATTTAAAGATAAAAAA
Found at i:55825334 original size:43 final size:42
Alignment explanation
Indices: 55825287--55825427 Score: 135
Period size: 43 Copynumber: 3.3 Consensus size: 42
55825277 TGGGTAAGTC
*
55825287 GAAGCAATTATACTGACACACGAGGTGCATTATCGAACGAACT
1 GAAGCAATTATACT-ACACACGAGGTGCATCATCGAACGAACT
* * * ** *
55825330 GAAGCAATTATACTA-GCACGTATAGTGCATCATAGAATAAATT
1 GAAGCAATTATACTACACACG-A-GGTGCATCATCGAACGAACT
*
55825373 GAAGCAATTATACTAACACACGAGATGCATCATC-AGACGAACT
1 GAAGCAATTATACT-ACACACGAGGTGCATCATCGA-ACGAACT
55825416 GCAA-CAATTATA
1 G-AAGCAATTATA
55825428 TTGGCACGCT
Statistics
Matches: 78, Mismatches: 14, Indels: 12
0.75 0.13 0.12
Matches are distributed among these distances:
41 4 0.05
42 3 0.04
43 63 0.81
44 4 0.05
45 4 0.05
ACGTcount: A:0.41, C:0.19, G:0.17, T:0.23
Consensus pattern (42 bp):
GAAGCAATTATACTACACACGAGGTGCATCATCGAACGAACT
Found at i:55827836 original size:41 final size:41
Alignment explanation
Indices: 55827736--55827837 Score: 127
Period size: 41 Copynumber: 2.5 Consensus size: 41
55827726 GCAATTATCC
* *
55827736 TGGCACGTAACTGCATCAACGATGTACTAAAGCAAATATAT
1 TGGCACGTAACTGCATCATCGATATACTAAAGCAAATATAT
* * *
55827777 TGGCACGTAAGTGCATCATCGGATATAC-ATAAGTAATTA-AT
1 TGGCACGTAACTGCATCATC-GATATACTA-AAGCAAATATAT
55827818 TGGCACGTAACTGCATCATC
1 TGGCACGTAACTGCATCATC
55827838 ACTAAATCGA
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
41 40 0.75
42 13 0.25
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.26
Consensus pattern (41 bp):
TGGCACGTAACTGCATCATCGATATACTAAAGCAAATATAT
Found at i:55830253 original size:4 final size:4
Alignment explanation
Indices: 55830244--55830271 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
55830234 ACTCAGGGAA
55830244 ATTT ATTT ATTT ATTT ATTT ATTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT
55830272 TTTGTGCGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
ATTT
Found at i:55831974 original size:41 final size:41
Alignment explanation
Indices: 55831912--55832031 Score: 150
Period size: 41 Copynumber: 2.9 Consensus size: 41
55831902 TGATCGAATG
* *
55831912 TAATACAGACTTTACGTCTAGCAGGCTTGATGCCGGTGAAA
1 TAATTCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAA
*
55831953 TAATTCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGATA
1 TAATTCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAA
* * * * * * *
55831994 CATTTCGGACTATAGGTCTAGCAGGCTAAAAGCCGGTG
1 TAATTCAGACTTTACGTCTAGCAGGCTTAATGCCGGTG
55832032 TACTGAATCA
Statistics
Matches: 69, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 69 1.00
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.28
Consensus pattern (41 bp):
TAATTCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAA
Found at i:55839444 original size:41 final size:41
Alignment explanation
Indices: 55839377--55839485 Score: 137
Period size: 41 Copynumber: 2.7 Consensus size: 41
55839367 TGATCGAATG
* * *
55839377 TAATACAGACTTTACGTCTAGTAGGCTTGATGCCGGTGAAA
1 TAATTCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAA
*
55839418 TAATTCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGATA
1 TAATTCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAA
* * * * *
55839459 CATTTCGGACTATAGGTCTAGCAGGCT
1 TAATTCAGACTTTACGTCTAGCAGGCT
55839486 AAAAGCTGGT
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 59 1.00
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30
Consensus pattern (41 bp):
TAATTCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAA
Found at i:55843432 original size:37 final size:37
Alignment explanation
Indices: 55843388--55843473 Score: 95
Period size: 37 Copynumber: 2.3 Consensus size: 37
55843378 ACTCTCTATG
* *
55843388 GCATCAAGATGGTGGTACA-TTTGATC-AACCCTTAGTA
1 GCATCAAGATGGTGGGA-AGTCTGATCGAA-CCTTAGTA
* *
55843425 GCATCAAGATAGTGGGAAGTCTGGTCGAACCTTAGTA
1 GCATCAAGATGGTGGGAAGTCTGATCGAACCTTAGTA
*
55843462 ACATCAAGATGG
1 GCATCAAGATGG
55843474 CAGAGAGATT
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
36 1 0.02
37 38 0.93
38 2 0.05
ACGTcount: A:0.31, C:0.17, G:0.26, T:0.26
Consensus pattern (37 bp):
GCATCAAGATGGTGGGAAGTCTGATCGAACCTTAGTA
Found at i:55844564 original size:57 final size:57
Alignment explanation
Indices: 55844430--55844565 Score: 148
Period size: 57 Copynumber: 2.4 Consensus size: 57
55844420 TAATGAAAAA
* * **
55844430 TTTCAGCTTAACGAGCTTTTTTACCCTAACTTTTGCTTATGTCATCTAACTAAAGAT
1 TTTCAGCTTAACGAGCTTTTTTACCCTAACTTTTGCTTAAGTCATCCAAAGAAAGAT
* * * * ** *
55844487 TTTCAACTTAAC-AGGGTTTTTTTCTCTAACTTTTGCTTAAGTTTTCCAAAGAAGGAT
1 TTTCAGCTTAACGA-GCTTTTTTACCCTAACTTTTGCTTAAGTCATCCAAAGAAAGAT
*
55844544 TTTTAGCTTAACGAGCTTTTTT
1 TTTCAGCTTAACGAGCTTTTTT
55844566 GTGCAGTTTA
Statistics
Matches: 63, Mismatches: 14, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
56 1 0.02
57 61 0.97
58 1 0.02
ACGTcount: A:0.25, C:0.18, G:0.12, T:0.45
Consensus pattern (57 bp):
TTTCAGCTTAACGAGCTTTTTTACCCTAACTTTTGCTTAAGTCATCCAAAGAAAGAT
Found at i:55846347 original size:18 final size:18
Alignment explanation
Indices: 55846324--55846360 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
55846314 AGCAAAGCCA
55846324 TCTCTAACAAAGTTTTCT
1 TCTCTAACAAAGTTTTCT
55846342 TCTCTAACAAAGTTTTCT
1 TCTCTAACAAAGTTTTCT
55846360 T
1 T
55846361 TATCTCTTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.27, C:0.22, G:0.05, T:0.46
Consensus pattern (18 bp):
TCTCTAACAAAGTTTTCT
Found at i:55850096 original size:33 final size:35
Alignment explanation
Indices: 55850008--55850096 Score: 82
Period size: 33 Copynumber: 2.7 Consensus size: 35
55849998 TTAAATAATA
55850008 AATTATATTTATTTATGTTAAATTGTAATTAAAAT
1 AATTATATTTATTTATGTTAAATTGTAATTAAAAT
* ***
55850043 -A-TAT-TTCTATTAAAAATAAATT-T-A-TAAAAT
1 AATTATATT-TATTTATGTTAAATTGTAATTAAAAT
55850073 AATTATATTATATTTATGTTAAAT
1 AATTATATT-TATTTATGTTAAAT
55850097 AATAGTATAT
Statistics
Matches: 41, Mismatches: 9, Indels: 10
0.68 0.15 0.17
Matches are distributed among these distances:
30 6 0.15
31 2 0.05
32 6 0.15
33 26 0.63
34 1 0.02
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.49
Consensus pattern (35 bp):
AATTATATTTATTTATGTTAAATTGTAATTAAAAT
Found at i:55850108 original size:26 final size:24
Alignment explanation
Indices: 55850069--55850117 Score: 62
Period size: 26 Copynumber: 2.0 Consensus size: 24
55850059 TAAATTTATA
* *
55850069 AAATAATTATATTATATTTATGTT
1 AAATAATTATATTAAAATTATGTT
55850093 AAATAATAGTATATTAAAATTATGT
1 AAATAAT--TATATTAAAATTATGT
55850118 CATATTAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 7 0.33
26 14 0.67
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (24 bp):
AAATAATTATATTAAAATTATGTT
Found at i:55852860 original size:18 final size:18
Alignment explanation
Indices: 55852805--55852883 Score: 70
Period size: 20 Copynumber: 4.1 Consensus size: 18
55852795 CCGAGATGCT
*
55852805 AAACAGGGCACAAATGTGC
1 AAACAGGGCACAGA-GTGC
* *
55852824 ATACAGGAGCACCGAAGTGC
1 AAACAGG-GCACAG-AGTGC
55852844 AAA-AGGGCACCAGAGTGC
1 AAACAGGGCA-CAGAGTGC
55852862 ATAACAGGGCACAGATGTGC
1 A-AACAGGGCACAGA-GTGC
55852882 AA
1 AA
55852884 TTAGGGATAC
Statistics
Matches: 49, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
18 9 0.18
19 18 0.37
20 21 0.43
21 1 0.02
ACGTcount: A:0.39, C:0.22, G:0.29, T:0.10
Consensus pattern (18 bp):
AAACAGGGCACAGAGTGC
Found at i:55852862 original size:38 final size:40
Alignment explanation
Indices: 55852789--55852883 Score: 101
Period size: 38 Copynumber: 2.4 Consensus size: 40
55852779 ACAATATCAT
55852789 GGAGCACCG-AGATGCTAAACAGGGCACAAATGTGCAT-ACA
1 GGAGCACCGAAG-TGC-AAACAGGGCACAAATGTGCATAACA
*
55852829 GGAGCACCGAAGTGCAAA-AGGGCACCAGA-GTGCATAACA
1 GGAGCACCGAAGTGCAAACAGGGCA-CAAATGTGCATAACA
* *
55852868 GG-GCACAGATGTGCAA
1 GGAGCACCGAAGTGCAA
55852884 TTAGGGATAC
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
38 24 0.49
39 11 0.22
40 12 0.24
41 2 0.04
ACGTcount: A:0.37, C:0.22, G:0.31, T:0.11
Consensus pattern (40 bp):
GGAGCACCGAAGTGCAAACAGGGCACAAATGTGCATAACA
Found at i:55855017 original size:30 final size:30
Alignment explanation
Indices: 55854983--55855042 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
55854973 ATTGCTTTAG
55854983 GTTATAACTAGATCTAATTAGGGGTCGAGT
1 GTTATAACTAGATCTAATTAGGGGTCGAGT
55855013 GTTATAACTAGATCTAATTAGGGGTCGAGT
1 GTTATAACTAGATCTAATTAGGGGTCGAGT
55855043 CGATGCAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.30, C:0.10, G:0.27, T:0.33
Consensus pattern (30 bp):
GTTATAACTAGATCTAATTAGGGGTCGAGT
Found at i:55856331 original size:15 final size:15
Alignment explanation
Indices: 55856311--55856341 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
55856301 AGTAGTAAAA
55856311 TATTTTTTATTACCT
1 TATTTTTTATTACCT
55856326 TATTTTTTATTACCT
1 TATTTTTTATTACCT
55856341 T
1 T
55856342 CCCTATGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.13, G:0.00, T:0.68
Consensus pattern (15 bp):
TATTTTTTATTACCT
Found at i:55856717 original size:20 final size:20
Alignment explanation
Indices: 55856692--55856754 Score: 81
Period size: 24 Copynumber: 3.0 Consensus size: 20
55856682 TTTTACATAG
55856692 AGATAGTTACTCAATTATAC
1 AGATAGTTACTCAATTATAC
*
55856712 AGATAGTTATCTGGTAAATTATAC
1 AGATAGTTA-C---TCAATTATAC
55856736 AGATAGTTACTCAATTATA
1 AGATAGTTACTCAATTATA
55856755 AAAAAATTTC
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
20 17 0.46
21 1 0.03
23 1 0.03
24 18 0.49
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.37
Consensus pattern (20 bp):
AGATAGTTACTCAATTATAC
Found at i:55857567 original size:7 final size:7
Alignment explanation
Indices: 55857557--55857618 Score: 52
Period size: 7 Copynumber: 8.9 Consensus size: 7
55857547 AATAAAATAA
55857557 AATCCCC
1 AATCCCC
*
55857564 AATCCTC
1 AATCCCC
*
55857571 AATCCTC
1 AATCCCC
*
55857578 AATCCTC
1 AATCCCC
* *
55857585 AATTCCT
1 AATCCCC
*
55857592 AATCCCT
1 AATCCCC
*
55857599 AATCCCT
1 AATCCCC
*
55857606 AATCCCT
1 AATCCCC
55857613 AATCCC
1 AATCCC
55857619 TCCCTCACCA
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 50 1.00
ACGTcount: A:0.29, C:0.44, G:0.00, T:0.27
Consensus pattern (7 bp):
AATCCCC
Found at i:55857587 original size:21 final size:21
Alignment explanation
Indices: 55857557--55857617 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
55857547 AATAAAATAA
55857557 AATCCCCAA-TCCTCAATCCTC
1 AATCCCCAATTCCT-AATCCTC
*
55857578 AATCCTCAATTCCTAATCC-C
1 AATCCCCAATTCCTAATCCTC
* *
55857598 TAATCCCTAATCCCTAATCC
1 -AATCCCCAATTCCTAATCC
55857618 CTCCCTCACC
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
20 1 0.03
21 29 0.85
22 4 0.12
ACGTcount: A:0.30, C:0.43, G:0.00, T:0.28
Consensus pattern (21 bp):
AATCCCCAATTCCTAATCCTC
Found at i:55857619 original size:7 final size:7
Alignment explanation
Indices: 55857589--55857619 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
55857579 ATCCTCAATT
55857589 CCTAATC
1 CCTAATC
55857596 CCTAATC
1 CCTAATC
55857603 CCTAATC
1 CCTAATC
55857610 CCTAATC
1 CCTAATC
55857617 CCT
1 CCT
55857620 CCCTCACCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.26, C:0.45, G:0.00, T:0.29
Consensus pattern (7 bp):
CCTAATC
Found at i:55858039 original size:22 final size:21
Alignment explanation
Indices: 55857991--55858048 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 21
55857981 CAATATTTTT
55857991 TTATTT-TTATA-TTTTTAAA
1 TTATTTATTATATTTTTTAAA
55858010 TT-TATTATTATATTTTTTGAAA
1 TTAT-TTATTATATTTTTT-AAA
55858032 TTATTTA-TATTATTTTT
1 TTATTTATTA-TATTTTT
55858049 ATATTTCTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
18 1 0.03
19 4 0.12
20 5 0.15
21 7 0.21
22 15 0.45
23 1 0.03
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (21 bp):
TTATTTATTATATTTTTTAAA
Found at i:55858046 original size:50 final size:48
Alignment explanation
Indices: 55857904--55858054 Score: 146
Period size: 55 Copynumber: 3.0 Consensus size: 48
55857894 TAATATAAAA
* **
55857904 TTTAAATTTATCATTATACATTTTGAAA-A--TATTTATTTTTATATT
1 TTTAAATTTATTATTATATTTTTTGAAATATTTATTTATTTTTATATT
* * *
55857949 TTAAAATTTTATATATTATTATTTCTTGTCAGCAATATTTTTTTATTTTTATATT
1 TTTAAA-TTTAT-TATTA-TATTT-TT-T--GAAATATTTATTTATTTTTATATT
55858004 TTTAAATTTATTATTATATTTTTTGAAATTATTTATATTATTTTTATATT
1 TTTAAATTTATTATTATATTTTTTGAAA-TATTTAT-TTATTTTTATATT
55858054 T
1 T
55858055 CTTTGAATTT
Statistics
Matches: 85, Mismatches: 9, Indels: 19
0.75 0.08 0.17
Matches are distributed among these distances:
45 5 0.06
46 5 0.06
47 4 0.05
48 6 0.07
49 8 0.09
50 16 0.19
51 2 0.02
52 8 0.09
53 6 0.07
54 5 0.06
55 20 0.24
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (48 bp):
TTTAAATTTATTATTATATTTTTTGAAATATTTATTTATTTTTATATT
Found at i:55864719 original size:24 final size:21
Alignment explanation
Indices: 55864675--55864721 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 21
55864665 TTAAATTTTA
*
55864675 TTTTATTTTATTTGATCTATT
1 TTTTATTTTATTTGATATATT
55864696 TTTTATTTTAATATTGTATATATT
1 TTTTATTTT-AT-TTG-ATATATT
55864720 TT
1 TT
55864722 ATGTACTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 9 0.41
22 2 0.09
23 3 0.14
24 8 0.36
ACGTcount: A:0.23, C:0.02, G:0.04, T:0.70
Consensus pattern (21 bp):
TTTTATTTTATTTGATATATT
Found at i:55865304 original size:6 final size:6
Alignment explanation
Indices: 55865293--55865324 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
55865283 GCAGAATGTA
55865293 AAATTT AAATTT AAATTT AAATTT AAATTT AA
1 AAATTT AAATTT AAATTT AAATTT AAATTT AA
55865325 TATATACAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (6 bp):
AAATTT
Found at i:55867289 original size:2 final size:2
Alignment explanation
Indices: 55867282--55867307 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
55867272 AATATTTTCA
55867282 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
55867308 TTTTAGATTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:55869213 original size:29 final size:31
Alignment explanation
Indices: 55869180--55869240 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 31
55869170 TATATTTGAA
**
55869180 ATTTACTTTT-ATTTTCAAAAATTTT-GTCC
1 ATTTACTTTTCAAATTCAAAAATTTTGGTCC
*
55869209 ATTTATTTTTCAAATTCAAAAATTTTGGTCC
1 ATTTACTTTTCAAATTCAAAAATTTTGGTCC
55869240 A
1 A
55869241 ATCATTAACA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 9 0.33
30 13 0.48
31 5 0.19
ACGTcount: A:0.31, C:0.13, G:0.05, T:0.51
Consensus pattern (31 bp):
ATTTACTTTTCAAATTCAAAAATTTTGGTCC
Found at i:55871072 original size:41 final size:41
Alignment explanation
Indices: 55871015--55871096 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
55871005 TAAAATTAGC
55871015 CATTGGTATGGCTAACAAATCTTGGTTTTGGTATGTGATGA
1 CATTGGTATGGCTAACAAATCTTGGTTTTGGTATGTGATGA
55871056 CATTGGTATGGCTAACAAATCTTGGTTTTGGTATGTGATGA
1 CATTGGTATGGCTAACAAATCTTGGTTTTGGTATGTGATGA
55871097 GGTTATCTTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.24, C:0.10, G:0.27, T:0.39
Consensus pattern (41 bp):
CATTGGTATGGCTAACAAATCTTGGTTTTGGTATGTGATGA
Found at i:55876471 original size:17 final size:17
Alignment explanation
Indices: 55876444--55876476 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
55876434 TCACTACATT
55876444 TTTATTTCACATATTCAC
1 TTTATTTCACA-ATTCAC
55876462 TTTA-TTCACAATTCA
1 TTTATTTCACAATTCA
55876477 TAAAAATACA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 6 0.40
18 4 0.27
ACGTcount: A:0.30, C:0.21, G:0.00, T:0.48
Consensus pattern (17 bp):
TTTATTTCACAATTCAC
Found at i:55877967 original size:17 final size:17
Alignment explanation
Indices: 55877947--55877982 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
55877937 TAAGCTTAGT
55877947 AAGTTCGTATAACTAGA
1 AAGTTCGTATAACTAGA
55877964 AAGTTCGTATAACTAGA
1 AAGTTCGTATAACTAGA
55877981 AA
1 AA
55877983 TACAACTTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.44, C:0.11, G:0.17, T:0.28
Consensus pattern (17 bp):
AAGTTCGTATAACTAGA
Found at i:55879844 original size:8 final size:8
Alignment explanation
Indices: 55879831--55879913 Score: 50
Period size: 8 Copynumber: 10.0 Consensus size: 8
55879821 TAAAATAAAT
55879831 TATTTTAA
1 TATTTTAA
55879839 TATTTTAA
1 TATTTTAA
55879847 TATTTT-A
1 TATTTTAA
55879854 TAATTTTTAAA
1 T-A-TTTT-AA
55879865 TATTATTAA
1 TATT-TTAA
*
55879874 TATATT--
1 TATTTTAA
55879880 T-TTTTAA
1 TATTTTAA
55879887 TAATTTTTAA
1 T-A-TTTTAA
55879897 -ATTTTATA
1 TATTTTA-A
55879905 TAGTTTTAA
1 TA-TTTTAA
55879914 GCTTATCTAA
Statistics
Matches: 60, Mismatches: 2, Indels: 25
0.69 0.02 0.29
Matches are distributed among these distances:
5 3 0.05
6 1 0.02
7 8 0.13
8 19 0.32
9 13 0.22
10 14 0.23
11 2 0.03
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.61
Consensus pattern (8 bp):
TATTTTAA
Found at i:55879850 original size:16 final size:17
Alignment explanation
Indices: 55879833--55879876 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
55879823 AAATAAATTA
55879833 TTTTAATATTTTAATAT
1 TTTTAATATTTTAATAT
55879850 TTTATAAT-TTTTAAATAT
1 TTT-TAATATTTT-AATAT
*
55879868 TATTAATAT
1 TTTTAATAT
55879877 ATTTTTTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
17 11 0.48
18 12 0.52
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TTTTAATATTTTAATAT
Found at i:55879873 original size:10 final size:9
Alignment explanation
Indices: 55879826--55879881 Score: 55
Period size: 8 Copynumber: 6.1 Consensus size: 9
55879816 TTTTTTAAAA
55879826 TAAATTATTT
1 TAAA-TATTT
55879836 T-AATATTT
1 TAAATATTT
55879844 T-AATATTT
1 TAAATATTT
55879852 TATAAT-TTT
1 TA-AATATTT
55879861 TAAATATTAT
1 TAAATATT-T
55879871 TAATATATTT
1 TAA-ATATTT
55879881 T
1 T
55879882 TTTAATAATT
Statistics
Matches: 41, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
8 17 0.41
9 9 0.22
10 10 0.24
11 5 0.12
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (9 bp):
TAAATATTT
Found at i:55880116 original size:28 final size:28
Alignment explanation
Indices: 55880047--55880109 Score: 126
Period size: 28 Copynumber: 2.2 Consensus size: 28
55880037 ATCCTGATGG
55880047 GGCATGCCACATCAGTACCCTTCCATGT
1 GGCATGCCACATCAGTACCCTTCCATGT
55880075 GGCATGCCACATCAGTACCCTTCCATGT
1 GGCATGCCACATCAGTACCCTTCCATGT
55880103 GGCATGC
1 GGCATGC
55880110 TGGATCACGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.21, C:0.35, G:0.21, T:0.24
Consensus pattern (28 bp):
GGCATGCCACATCAGTACCCTTCCATGT
Found at i:55881390 original size:20 final size:18
Alignment explanation
Indices: 55881356--55881392 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
55881346 CCTTAGCCCA
55881356 TAACAGTATCAGTAGCAG
1 TAACAGTATCAGTAGCAG
55881374 TAACAGTTATGCAGTAGCA
1 TAACAG-TAT-CAGTAGCA
55881393 AAATCCTACC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
19 3 0.18
20 8 0.47
ACGTcount: A:0.38, C:0.16, G:0.22, T:0.24
Consensus pattern (18 bp):
TAACAGTATCAGTAGCAG
Found at i:55896814 original size:23 final size:23
Alignment explanation
Indices: 55896787--55896869 Score: 69
Period size: 23 Copynumber: 3.6 Consensus size: 23
55896777 TGGTAGGAGC
**
55896787 TTATTGGCACTTTGGTGCGATTG
1 TTATTGGCACTTCAGTGCGATTG
** *
55896810 TTATTAACACTTCAGTGTGATTG
1 TTATTGGCACTTCAGTGCGATTG
* ***
55896833 TTATTGGCACATC-GATTTAATTG
1 TTATTGGCACTTCAG-TGCGATTG
55896856 TTATTGGCACTTCA
1 TTATTGGCACTTCA
55896870 ATACAATTGA
Statistics
Matches: 47, Mismatches: 11, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
22 1 0.02
23 46 0.98
ACGTcount: A:0.22, C:0.14, G:0.20, T:0.43
Consensus pattern (23 bp):
TTATTGGCACTTCAGTGCGATTG
Found at i:55896877 original size:23 final size:23
Alignment explanation
Indices: 55896829--55896878 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
55896819 CTTCAGTGTG
* **
55896829 ATTGTTATTGGCACATCGATTTA
1 ATTGTTATTGGCACATCAATACA
*
55896852 ATTGTTATTGGCACTTCAATACA
1 ATTGTTATTGGCACATCAATACA
55896875 ATTG
1 ATTG
55896879 ATACTAGCAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (23 bp):
ATTGTTATTGGCACATCAATACA
Found at i:55901807 original size:29 final size:29
Alignment explanation
Indices: 55901765--55901833 Score: 138
Period size: 29 Copynumber: 2.4 Consensus size: 29
55901755 GAAGAGGTGG
55901765 AGAACTTGTTCGTTGAGAGTTTGCGATGA
1 AGAACTTGTTCGTTGAGAGTTTGCGATGA
55901794 AGAACTTGTTCGTTGAGAGTTTGCGATGA
1 AGAACTTGTTCGTTGAGAGTTTGCGATGA
55901823 AGAACTTGTTC
1 AGAACTTGTTC
55901834 ATTAAGAATT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.25, C:0.12, G:0.29, T:0.35
Consensus pattern (29 bp):
AGAACTTGTTCGTTGAGAGTTTGCGATGA
Found at i:55905058 original size:22 final size:20
Alignment explanation
Indices: 55905018--55905058 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
55905008 TATATGTTTG
*
55905018 AATGTGTTTAAATATGCTTA
1 AATGTGTTTAAACATGCTTA
55905038 AATGATGTTTAGAACATGCTT
1 AATG-TGTTTA-AACATGCTT
55905059 TTAGCGTCCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 6 0.33
22 8 0.44
ACGTcount: A:0.34, C:0.07, G:0.17, T:0.41
Consensus pattern (20 bp):
AATGTGTTTAAACATGCTTA
Found at i:55905699 original size:81 final size:81
Alignment explanation
Indices: 55905582--55905822 Score: 286
Period size: 81 Copynumber: 3.0 Consensus size: 81
55905572 GCCTTCGGCA
* * * * * * * *
55905582 CTCCTTCTTCCACCCCTGCCTTTGGCACTCCTTCTTCCACCCCGGCCTTTGGAACTACTCCTTCC
1 CTCCTTCTTCCACACCTGCATTTGGCACTCCGTCTTCGACACCGGCGTTTGGAACTCCTCCTTCG
*
55905647 ACTCCGGCTTTTGGGG
66 ACACCGGCTTTTGGGG
* ** *
55905663 CTCCTTCTTCCACACCGGCATTTGGCACTCCGTCTTCGACACCGGCGTTTGTCACTCCTTCTTCG
1 CTCCTTCTTCCACACCTGCATTTGGCACTCCGTCTTCGACACCGGCGTTTGGAACTCCTCCTTCG
* *
55905728 ACACCTGCGTTTGGGG
66 ACACCGGCTTTTGGGG
* * * **
55905744 CTCCGTCTTCGACACCTGCGTTTGGGGCTCCGTCTTCGACACCGGCGTTTGGAACTCCGTCC-TC
1 CTCCTTCTTCCACACCTGCATTTGGCACTCCGTCTTCGACACCGGCGTTTGGAACTCC-TCCTTC
55905808 GACACCGGCTTTTGG
65 GACACCGGCTTTTGG
55905823 AACTCCATCA
Statistics
Matches: 133, Mismatches: 26, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
81 131 0.98
82 2 0.02
ACGTcount: A:0.10, C:0.39, G:0.21, T:0.30
Consensus pattern (81 bp):
CTCCTTCTTCCACACCTGCATTTGGCACTCCGTCTTCGACACCGGCGTTTGGAACTCCTCCTTCG
ACACCGGCTTTTGGGG
Found at i:55905708 original size:54 final size:54
Alignment explanation
Indices: 55905609--55905822 Score: 232
Period size: 54 Copynumber: 4.0 Consensus size: 54
55905599 GCCTTTGGCA
* * * * * *
55905609 CTCCTTCTTCCACCCCGGCCTTTGGAACTAC-TCCTTCCACTCCGGCTTTTGGGG
1 CTCCTTCTTCCACACCGGCGTTTGGAACTCCGT-CTTCGACACCGGCGTTTGGGG
* * ***
55905663 CTCCTTCTTCCACACCGGCATTTGGCACTCCGTCTTCGACACCGGCGTTTGTCA
1 CTCCTTCTTCCACACCGGCGTTTGGAACTCCGTCTTCGACACCGGCGTTTGGGG
* * ** *
55905717 CTCCTTCTTCGACACCTGCGTTTGGGGCTCCGTCTTCGACACCTGCGTTTGGGG
1 CTCCTTCTTCCACACCGGCGTTTGGAACTCCGTCTTCGACACCGGCGTTTGGGG
* * * *
55905771 CTCCGTCTTCGACACCGGCGTTTGGAACTCCGTCCTCGACACCGGCTTTTGG
1 CTCCTTCTTCCACACCGGCGTTTGGAACTCCGTCTTCGACACCGGCGTTTGG
55905823 AACTCCATCA
Statistics
Matches: 133, Mismatches: 26, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
54 132 0.99
55 1 0.01
ACGTcount: A:0.10, C:0.37, G:0.22, T:0.30
Consensus pattern (54 bp):
CTCCTTCTTCCACACCGGCGTTTGGAACTCCGTCTTCGACACCGGCGTTTGGGG
Found at i:55905737 original size:27 final size:27
Alignment explanation
Indices: 55905578--55905828 Score: 207
Period size: 27 Copynumber: 9.3 Consensus size: 27
55905568 TTCTGCCTTC
* * * * *
55905578 GGCACTCCTTCTTCCACCCCTGCCTTT
1 GGCACTCCGTCTTCGACACCGGCGTTT
* * * *
55905605 GGCACTCCTTCTTCCACCCCGGCCTTT
1 GGCACTCCGTCTTCGACACCGGCGTTT
* * * * *
55905632 GGAACTAC-TCCTTCCACTCCGGCTTTT
1 GGCACTCCGT-CTTCGACACCGGCGTTT
** * * *
55905659 GGGGCTCCTTCTTCCACACCGGCATTT
1 GGCACTCCGTCTTCGACACCGGCGTTT
55905686 GGCACTCCGTCTTCGACACCGGCGTTT
1 GGCACTCCGTCTTCGACACCGGCGTTT
* * *
55905713 GTCACTCCTTCTTCGACACCTGCGTTT
1 GGCACTCCGTCTTCGACACCGGCGTTT
** *
55905740 GGGGCTCCGTCTTCGACACCTGCGTTT
1 GGCACTCCGTCTTCGACACCGGCGTTT
**
55905767 GGGGCTCCGTCTTCGACACCGGCGTTT
1 GGCACTCCGTCTTCGACACCGGCGTTT
* * *
55905794 GGAACTCCGTCCTCGACACCGGCTTTT
1 GGCACTCCGTCTTCGACACCGGCGTTT
*
55905821 GGAACTCC
1 GGCACTCC
55905829 ATCAACGCCG
Statistics
Matches: 195, Mismatches: 27, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
26 1 0.01
27 193 0.99
28 1 0.01
ACGTcount: A:0.11, C:0.39, G:0.21, T:0.29
Consensus pattern (27 bp):
GGCACTCCGTCTTCGACACCGGCGTTT
Found at i:55912659 original size:14 final size:14
Alignment explanation
Indices: 55912621--55912663 Score: 54
Period size: 13 Copynumber: 3.1 Consensus size: 14
55912611 CAAAATGTAC
55912621 AATATAATTAAA-T
1 AATATAATTAAATT
55912634 AATATAAATTAAATT
1 AATAT-AATTAAATT
*
55912649 AA-ATAATTTAATT
1 AATATAATTAAATT
55912662 AA
1 AA
55912664 CTATTTACCC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
13 15 0.56
14 9 0.33
15 3 0.11
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
AATATAATTAAATT
Found at i:55915604 original size:8 final size:8
Alignment explanation
Indices: 55915583--55915622 Score: 62
Period size: 8 Copynumber: 5.0 Consensus size: 8
55915573 CTTTAGATTT
*
55915583 TTTTTAAA
1 TTTTAAAA
*
55915591 TATTAAAA
1 TTTTAAAA
55915599 TTTTAAAA
1 TTTTAAAA
55915607 TTTTAAAA
1 TTTTAAAA
55915615 TTTTAAAA
1 TTTTAAAA
55915623 AATATAAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 29 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (8 bp):
TTTTAAAA
Found at i:55915657 original size:9 final size:9
Alignment explanation
Indices: 55915584--55915666 Score: 61
Period size: 8 Copynumber: 9.8 Consensus size: 9
55915574 TTTAGATTTT
55915584 TTTTAAATA
1 TTTTAAATA
55915593 --TTAAA-A
1 TTTTAAATA
55915599 TTTTAAA-A
1 TTTTAAATA
55915607 TTTTAAA-A
1 TTTTAAATA
*
55915615 TTTTAAAAA
1 TTTTAAATA
* *
55915624 ATATAAAT-
1 TTTTAAATA
** *
55915632 TTTGGAATT
1 TTTTAAATA
55915641 TTTATAAATA
1 TTT-TAAATA
55915651 TTTTAAATA
1 TTTTAAATA
55915660 TTTTAAA
1 TTTTAAA
55915667 ATTATTTTGA
Statistics
Matches: 59, Mismatches: 10, Indels: 10
0.75 0.13 0.13
Matches are distributed among these distances:
6 1 0.02
7 5 0.08
8 25 0.42
9 22 0.37
10 6 0.10
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.49
Consensus pattern (9 bp):
TTTTAAATA
Found at i:55916583 original size:31 final size:27
Alignment explanation
Indices: 55916548--55916611 Score: 74
Period size: 31 Copynumber: 2.2 Consensus size: 27
55916538 TTTAGAAATC
*
55916548 ATTTTTATTTAATTCTAATATATATTTGATA
1 ATTTTTATTTAA-T-TAAAAT-TATTT-ATA
*
55916579 ATTTTTATTTTATTAAAATTATTTATA
1 ATTTTTATTTAATTAAAATTATTTATA
55916606 ATTTTT
1 ATTTTT
55916612 TACTAAAATG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
27 9 0.29
28 5 0.16
29 5 0.16
30 1 0.03
31 11 0.35
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (27 bp):
ATTTTTATTTAATTAAAATTATTTATA
Found at i:55918297 original size:11 final size:11
Alignment explanation
Indices: 55918283--55918343 Score: 54
Period size: 11 Copynumber: 5.6 Consensus size: 11
55918273 AAAAAACTCC
55918283 AAAAATTATAT
1 AAAAATTATAT
55918294 AAAAA-TATAAT
1 AAAAATTAT-AT
**
55918305 ATTAATTAT-T
1 AAAAATTATAT
* *
55918315 AAAAATTTTCT
1 AAAAATTATAT
*
55918326 AAAAAGTATAT
1 AAAAATTATAT
55918337 AAAAATT
1 AAAAATT
55918344 TCAAATATGC
Statistics
Matches: 38, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
10 10 0.26
11 25 0.66
12 3 0.08
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (11 bp):
AAAAATTATAT
Found at i:55920232 original size:19 final size:19
Alignment explanation
Indices: 55920208--55920261 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 19
55920198 AATCTTCAAG
*
55920208 GATATGCAATTTTAGATAT
1 GATATGCAATCTTAGATAT
*
55920227 GATATGTAATCTTAGATAT
1 GATATGCAATCTTAGATAT
* *
55920246 AAAATGCAATCTTAGA
1 GATATGCAATCTTAGA
55920262 AGATATGATT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.41, C:0.07, G:0.15, T:0.37
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:55920512 original size:23 final size:23
Alignment explanation
Indices: 55920468--55920512 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
55920458 TCTTATTTTG
* *
55920468 TTGATTTGTGTATAATTTATTTA
1 TTGATTTGTATATAATTGATTTA
**
55920491 TTGATTTGTATATTGTTGATTT
1 TTGATTTGTATATAATTGATTT
55920513 CAAATCTCTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.16, T:0.62
Consensus pattern (23 bp):
TTGATTTGTATATAATTGATTTA
Found at i:55927405 original size:88 final size:88
Alignment explanation
Indices: 55927256--55928009 Score: 1067
Period size: 88 Copynumber: 8.6 Consensus size: 88
55927246 GTGAAGATAA
* * *
55927256 CAGATCTGGCATTCCTGCACCGACAGCGAAGCAGATCGAAGACACTAGCCTTGCCTCCCTGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
*
55927321 GTAGCAGAGCAGGTTAAAAATAG
66 GTAGCGGAGCAGGTTAAAAATAG
*
55927344 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAGGACACCAGCCTTGCCTCCCTGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
* *
55927409 GCAGCGGAGCAAGTTAAAAATAG
66 GTAGCGGAGCAGGTTAAAAATAG
* * * * * *
55927432 CAGATCTTGCCTTCCTGCACTGGCAGCGAAGCAGATCGAGGACACTAGCCCTGCCTCCCTGAGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
* *
55927497 GCAGTGGAGCAGGTTAAAAATAG
66 GTAGCGGAGCAGGTTAAAAATAG
* * * *
55927520 TAGATCTTGCCTTCCTACACCGACAGCGAAGCAGATCGAAGACACCAGCCCTGCCTCCCTAGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
*
55927585 GTAGCGGAGCAGGTTAAAAATTG
66 GTAGCGGAGCAGGTTAAAAATAG
* * *
55927608 CAGATATTGCCTTCCTGCACCGACAGCGAAGCATATCGAAGACACCAGCCTTGCCTCACTGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
* *
55927673 GTAGCGGAGCAAGTTAAAAATAA
66 GTAGCGGAGCAGGTTAAAAATAG
* * * *
55927696 CAGATATTGCCTTCCTACACCGACAGCGAAGCAGATCGAAGACACCAACCTTGCCTCCTTGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
*
55927761 GTAGTGGAGCAGGTTAAAAATAG
66 GTAGCGGAGCAGGTTAAAAATAG
* * * * *
55927784 CAGATCTTACTTTCTTGCACCGATAGTGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
* *
55927849 GCAGCGGAGTAGGTTAAAAATAG
66 GTAGCGGAGCAGGTTAAAAATAG
* *
55927872 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGTCTTGCCTCTCTGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
*** * *
55927937 GTAGTAAAGCAGTTTAAAAATAA
66 GTAGCGGAGCAGGTTAAAAATAG
* * * * *
55927960 CAGATCTTGTCTTCCTACACCGACAGCGAGGCAGATCGATGACCCCAGCC
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCC
55928010 CTATCTCCCT
Statistics
Matches: 591, Mismatches: 75, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
88 591 1.00
ACGTcount: A:0.28, C:0.27, G:0.24, T:0.21
Consensus pattern (88 bp):
CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
GTAGCGGAGCAGGTTAAAAATAG
Found at i:55927441 original size:44 final size:44
Alignment explanation
Indices: 55927305--55927448 Score: 103
Period size: 44 Copynumber: 3.3 Consensus size: 44
55927295 AGACACTAGC
* * *
55927305 CTTGCCTCCCTGGGTTGTAGCAGAGCAGGTTAAAAATAGCAGAT
1 CTTGCCTCCCTGGGTTGCAGCGGAGCAAGTTAAAAATAGCAGAT
* **** * ** ** * * *
55927349 CTTGCCTTCCTGCACCGACAGCGAAGC-AGATCGAGGACACCAG-C
1 CTTGCCTCCCTGGGTTG-CAGCGGAGCAAG-TTAAAAATAGCAGAT
55927393 CTTGCCTCCCTGGGTTGCAGCGGAGCAAGTTAAAAATAGCAGAT
1 CTTGCCTCCCTGGGTTGCAGCGGAGCAAGTTAAAAATAGCAGAT
*
55927437 CTTGCCTTCCTG
1 CTTGCCTCCCTG
55927449 CACTGGCAGC
Statistics
Matches: 66, Mismatches: 30, Indels: 8
0.63 0.29 0.08
Matches are distributed among these distances:
43 15 0.23
44 38 0.58
45 13 0.20
ACGTcount: A:0.24, C:0.28, G:0.26, T:0.22
Consensus pattern (44 bp):
CTTGCCTCCCTGGGTTGCAGCGGAGCAAGTTAAAAATAGCAGAT
Found at i:55928100 original size:44 final size:44
Alignment explanation
Indices: 55928011--55928108 Score: 135
Period size: 44 Copynumber: 2.2 Consensus size: 44
55928001 ACCCCAGCCC
* *
55928011 TATCTCCCTGGACAACAGTGGAATAGGTTGAAGATTGTAAGTCT
1 TATCTCCCTGGACAACAGTGGAATAGGTTGAAGATGGGAAGTCT
* *
55928055 TATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATGGCGAA-TCT
1 TATCTCCCTGGACAACAGTGGAATAGGTTGAAGATGG-GAAGTCT
*
55928099 TATCTTCCTG
1 TATCTCCCTG
55928109 AAGTTACAGT
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
44 46 0.96
45 2 0.04
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.31
Consensus pattern (44 bp):
TATCTCCCTGGACAACAGTGGAATAGGTTGAAGATGGGAAGTCT
Found at i:55928191 original size:44 final size:44
Alignment explanation
Indices: 55928095--55928604 Score: 263
Period size: 44 Copynumber: 11.8 Consensus size: 44
55928085 AAGATGGCGA
* * * * **
55928095 ATCTTATCTTCCTGAAGTTACAGTGGAACAAATTAAAGCCA-AT
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCACAT
* * **
55928138 AATCATATCTCCCTAAAGTTGCAGTGGAGTGGATTAAAATCACAT
1 -ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCACAT
* * * * **
55928183 ATCTTATCTCTCTGAAGTTGCAG-AGAGCAGA-TCACAT--CGG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCACAT
* * **
55928223 GTCTTATCTCCCTGAAGTTGTAGTGGAGCAGACCCAAGAA--AGCGA-
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TTAA-AATCA-C-AT
* **
55928268 GTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCA-AT
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCACAT
* * *
55928311 AATCCTATCTCCCTGAAGTCGCAGTGGAGC-GAATTAAAATCACAA
1 -ATCTTATCTCCCTGAAGTTGCAGTGGAGCAG-ATTAAAATCACAT
* * ***
55928356 ATCTTATCTCTCTGAAGTTGCAG-AGAGCAGA-TCGCAT--C-T
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCACAT
* * *
55928395 AGTCTTATCTCCCTGAAGTTGCAGTGGAGTAGACTAAGTAAGCA-A-
1 A-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAA--AATCACAT
** * * * * * ***
55928440 GCCTTATC-CTCCTAAAGTTGTAGT-GAGGAAGACTGAAGATGGTGA-
1 ATCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGA-TTAAAAT-CACAT
* **
55928485 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTAAAGCCA-AT
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCACAT
** *
55928528 AATCTTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAATCACAG
1 -ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCACAT
* *
55928573 ATCTTATCTCTCTGAAGTTGCAG-AGAGCAGAT
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGAT
55928605 CGCATCGGGT
Statistics
Matches: 347, Mismatches: 86, Indels: 67
0.69 0.17 0.13
Matches are distributed among these distances:
39 1 0.00
40 43 0.12
41 13 0.04
42 10 0.03
43 23 0.07
44 193 0.56
45 61 0.18
46 3 0.01
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (44 bp):
ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCACAT
Found at i:55928248 original size:84 final size:83
Alignment explanation
Indices: 55928143--55928423 Score: 287
Period size: 84 Copynumber: 3.3 Consensus size: 83
55928133 CCAATAATCA
* *
55928143 TATCTCCCTAAAGTTGCAGTGGAGTGGATTAAAATCACATATCTTATCTCTCTGAAGTTGCAGAG
1 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCACA-ATCTTATCTCTCTGAAGTTGCAGAG
**
55928208 AGCAGATCACATCGGGTCT
65 AGCAGATCACATCTAGTCT
* * ** * *
55928227 TATCTCCCTGAAGTTGTAGTGGAGCAGACCCAAGAA--AGCGAGTCTTATCTCCCTGAAGTTGCA
1 TATCTCCCTGAAGTTGCAGTGGAGCGGA-TTAA-AATCA-C-AATCTTATCTCTCTGAAGTTGCA
* * * * * *
55928290 GTGGAGCAGATTAAAGCCAATAATCC
62 G-AGAGCAGATCACA-TC--TAGTCT
* *
55928316 TATCTCCCTGAAGTCGCAGTGGAGCGAATTAAAATCACAAATCTTATCTCTCTGAAGTTGCAGAG
1 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCAC-AATCTTATCTCTCTGAAGTTGCAGAG
*
55928381 AGCAGATCGCATCTAGTCT
65 AGCAGATCACATCTAGTCT
55928400 TATCTCCCTGAAGTTGCAGTGGAG
1 TATCTCCCTGAAGTTGCAGTGGAG
55928424 TAGACTAAGT
Statistics
Matches: 154, Mismatches: 33, Indels: 20
0.74 0.16 0.10
Matches are distributed among these distances:
84 52 0.34
85 24 0.16
86 14 0.09
87 12 0.08
88 25 0.16
89 27 0.18
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (83 bp):
TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCACAATCTTATCTCTCTGAAGTTGCAGAGA
GCAGATCACATCTAGTCT
Found at i:55928385 original size:173 final size:172
Alignment explanation
Indices: 55928091--55928640 Score: 556
Period size: 173 Copynumber: 3.2 Consensus size: 172
55928081 GTTGAAGATG
* * * * * *
55928091 GCGAATCTTATCTTCCTGAAGTTACAGTGGAACAAATTAAAGCCAATAATCATATCTCCCTAAAG
1 GCGAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCATATCTCCCTGAAG
* * *
55928156 TTGCAGTGGAGTGGATTAAAATCACATATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCACATC
66 TTGCAGTGGAGCGAATTAAAATCACAAATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCACATC
* *
55928221 GGGTCTTATCTCCCTGAAGTTGTAGTGGAGCAGACCCAAGAAA
131 GAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-CCAAGAAA
*
55928264 GCGAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCCTATCTCCCTGAAG
1 GCGAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCATATCTCCCTGAAG
* *
55928329 TCGCAGTGGAGCGAATTAAAATCACAAATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATC
66 TTGCAGTGGAGCGAATTAAAATCACAAATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCACATC
* * * *
55928394 TAGTCTTATCTCCCTGAAGTTGCAGTGGAGTAGACTAAGTAA
131 GAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACCAAGAAA
* * * * * * * **** *
55928436 GCAAGCCTTATC-CTCCTAAAGTTGTAGT-GAGGAAGACTGAAGATGGTGAATCTTATCTCCCTG
1 GCGAGTCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGATTAAAGCCAAT-AATCATATCTCCCTG
* ** * * **
55928499 AAGTTGCAGTGGAGCAAATTAAAGCCA-ATAATCTTATCTCCCTGAAGTTGCAGTGGAGTGGATT
63 AAGTTGCAGTGGAGCGAATTAAAATCACA-AATCTTATCTCTCTGAAGTTGCAG-AGAGCAGA-T
* * * * * * *
55928563 AAAATCACAGATCTTATCTCTCTGAAGTTGCAG-AGAGCAGATC--G-CA
125 CACATC-GAG-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACCAAGAAA
* *
55928609 TCGGGTCTTATCTCCCTGAAGTTGCAGTGGAG
1 GCGAGTCTTATCTCCCTGAAGTTGCAGTGGAG
55928641 TAGACCCAAG
Statistics
Matches: 313, Mismatches: 54, Indels: 20
0.81 0.14 0.05
Matches are distributed among these distances:
171 3 0.01
172 38 0.12
173 230 0.73
174 9 0.03
175 4 0.01
176 8 0.03
177 21 0.07
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.27
Consensus pattern (172 bp):
GCGAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCATATCTCCCTGAAG
TTGCAGTGGAGCGAATTAAAATCACAAATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCACATC
GAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACCAAGAAA
Found at i:55928460 original size:217 final size:218
Alignment explanation
Indices: 55928225--55928732 Score: 727
Period size: 217 Copynumber: 2.3 Consensus size: 218
55928215 CACATCGGGT
* *
55928225 CTTATCTCCCTGAAGTTGTAGTGGAGCAGACCCAAGAAAGCGAGTCTTATCTCCCTGAAGTTGCA
1 CTTATCTCCCTAAAGTTGTAGTGGAGCAGACTCAAGAAAGCGAGTCTTATCTCCCTGAAGTTGCA
*
55928290 GTGGAGCAGATTAAAGCCAATAATCCTATCTCCCTGAAGTCGCAGTGGAGCGAATTAAAATCACA
66 GTGGAGCAAATTAAAGCCAATAATCCTATCTCCCTGAAGTCGCAGTGGAGCGAATTAAAATCACA
*
55928355 AATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGT
131 AATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCGAGTCTTATCTCCCTGAAGTTGCAGT
* *
55928420 GGAGTAGA-CTAAGTAAGCAAGC
196 GGAGTAGACCCAAGAAAGCAAGC
* * ** * *
55928442 CTTATC-CTCCTAAAGTTGTAGT-GAGGAAGACTGAAGATGGTGAATCTTATCTCCCTGAAGTTG
1 CTTATCTC-CCTAAAGTTGTAGTGGA-GCAGACTCAAGAAAGCGAGTCTTATCTCCCTGAAGTTG
* * * *
55928505 CAGTGGAGCAAATTAAAGCCAATAATCTTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAATCA
64 CAGTGGAGCAAATTAAAGCCAATAATCCTATCTCCCTGAAGTCGCAGTGGAGCGAATTAAAATCA
* *
55928570 CAGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCGGGTCTTATCTCCCTGAAGTTGCA
129 CAAATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCGAGTCTTATCTCCCTGAAGTTGCA
* *
55928635 GTGGAGTAGACCCAAGAAAGCGAGT
194 GTGGAGTAGACCCAAGAAAGCAAGC
* * * * * *
55928660 CTTATCTCCCTGAAGTTGCAGTGGACCAGACTCAAGAAATCAAGTCTTATC-CCCTGAAATTGCA
1 CTTATCTCCCTAAAGTTGTAGTGGAGCAGACTCAAGAAAGCGAGTCTTATCTCCCTGAAGTTGCA
*
55928724 GTGGGGCAA
66 GTGGAGCAA
55928733 CTAAATAAAC
Statistics
Matches: 253, Mismatches: 33, Indels: 10
0.85 0.11 0.03
Matches are distributed among these distances:
216 3 0.01
217 202 0.80
218 45 0.18
219 3 0.01
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (218 bp):
CTTATCTCCCTAAAGTTGTAGTGGAGCAGACTCAAGAAAGCGAGTCTTATCTCCCTGAAGTTGCA
GTGGAGCAAATTAAAGCCAATAATCCTATCTCCCTGAAGTCGCAGTGGAGCGAATTAAAATCACA
AATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCGAGTCTTATCTCCCTGAAGTTGCAGT
GGAGTAGACCCAAGAAAGCAAGC
Found at i:55929344 original size:22 final size:22
Alignment explanation
Indices: 55929284--55929341 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 22
55929274 AATCTTCAAG
55929284 GATATGCAATCTT---AGATAT
1 GATATGCAATCTTAGAAGATAT
55929303 GATATGCAATCTTAGAAGATAT
1 GATATGCAATCTTAGAAGATAT
* *
55929325 GATTTTGTAATCTTAGA
1 GA-TATGCAATCTTAGA
55929342 GATTTAATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.39
22 8 0.24
23 12 0.36
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.38
Consensus pattern (22 bp):
GATATGCAATCTTAGAAGATAT
Found at i:55929569 original size:23 final size:23
Alignment explanation
Indices: 55929525--55929569 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
55929515 TCTTATTTTG
* *
55929525 TTGATTTGTGTATAATTTATTTA
1 TTGATTTGTATATAATTGATTTA
**
55929548 TTGATTTGTATATTGTTGATTT
1 TTGATTTGTATATAATTGATTT
55929570 CAAATCTCTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.16, T:0.62
Consensus pattern (23 bp):
TTGATTTGTATATAATTGATTTA
Found at i:55933868 original size:15 final size:15
Alignment explanation
Indices: 55933850--55933878 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
55933840 TTTATAGTTA
55933850 AAAATTTAATTTAAT
1 AAAATTTAATTTAAT
55933865 AAAATTTAATTTAA
1 AAAATTTAATTTAA
55933879 AATTAACTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
AAAATTTAATTTAAT
Found at i:55934559 original size:24 final size:23
Alignment explanation
Indices: 55934515--55934559 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
55934505 GTTTTATGGC
*
55934515 TTTTAGGGTTTAGGGTGCAGGCT
1 TTTTAGGGTTTAGGGTCCAGGCT
55934538 TTTTAGGAG-TTAGGGGTCCAGG
1 TTTTAGG-GTTTA-GGGTCCAGG
55934560 AAAATTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.16, C:0.09, G:0.40, T:0.36
Consensus pattern (23 bp):
TTTTAGGGTTTAGGGTCCAGGCT
Found at i:55934721 original size:126 final size:125
Alignment explanation
Indices: 55934576--55934858 Score: 338
Period size: 126 Copynumber: 2.3 Consensus size: 125
55934566 TTTTTTCGAG
* ** ** * *
55934576 TTGACGTTTCTG-GTTAAATAGTGGGAAATCGCTTCTACTAGGATGCTATTTAAGAAGAAATTGT
1 TTGACGTTTCTGAG-CAAATAGTGTAAAATCGCTGATACCAGGATGCTATATAAGAAGAAATTGT
* *
55934640 GAAATAGTGGCCTCGTGGACAAGATTTCGCTAC-AGTGGTCATGT-GAGAAATAATTTTTTTT
65 GAAATAGCGCCCTCGTGGACAAGATTTCGCTACAAGTGGTCATGTAG-GAAATAA-TTTTTTT
* * * * *
55934701 TTTATGTTTTCTGAGGAAATAGTATAAAATCGCTGATACCAGGATGCTATATGAGAAGAAATTGT
1 TTGACG-TTTCTGAGCAAATAGTGTAAAATCGCTGATACCAGGATGCTATATAAGAAGAAATTGT
* ** *
55934766 GAAATCGCGCCCTCGTGGACGCGATTTCGCTACAATTGGTCATGTAGGAAATAATTTTTTT
65 GAAATAGCGCCCTCGTGGACAAGATTTCGCTACAAGTGGTCATGTAGGAAATAATTTTTTT
*
55934827 TTGACGTTTCTGAGCAAATAGTGTCAAATCGC
1 TTGACGTTTCTGAGCAAATAGTGTAAAATCGC
55934859 GCCCTCGTGG
Statistics
Matches: 132, Mismatches: 22, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
125 27 0.20
126 86 0.65
127 18 0.14
128 1 0.01
ACGTcount: A:0.29, C:0.14, G:0.23, T:0.34
Consensus pattern (125 bp):
TTGACGTTTCTGAGCAAATAGTGTAAAATCGCTGATACCAGGATGCTATATAAGAAGAAATTGTG
AAATAGCGCCCTCGTGGACAAGATTTCGCTACAAGTGGTCATGTAGGAAATAATTTTTTT
Found at i:55938067 original size:29 final size:27
Alignment explanation
Indices: 55938034--55938563 Score: 394
Period size: 29 Copynumber: 20.0 Consensus size: 27
55938024 AACTAGGGTT
55938034 TTTAATTAAGTAGGGTTTAGGGTTTTTAA
1 TTTAATTAAGTA-GG-TTAGGGTTTTTAA
55938063 TTTAATTAA--A--TTAGGGTTTTTAA
1 TTTAATTAAGTAGGTTAGGGTTTTTAA
*
55938086 -TTAAGT-AG--GGTTAGGGTTTTTAA
1 TTTAATTAAGTAGGTTAGGGTTTTTAA
* *
55938109 TTTAATTAAAATAATGTTAGGGTTTTTAA
1 TTTAATT-AAGT-AGGTTAGGGTTTTTAA
*
55938138 TTTAATTAAAATAAGGTTAGGGTTTTTAA
1 TTTAATT-AAGT-AGGTTAGGGTTTTTAA
* *
55938167 TTTAATTAAATTAGGTTAGGGTTAGAGTT--
1 TTTAATT-AAGTAGGTTAGGGTT---TTTAA
55938196 TTTAATTAAGTAGGGTTTAGGGTTTTTAA
1 TTTAATTAAGTA-GG-TTAGGGTTTTTAA
55938225 TTTAATTAA--A--TTAGGGTTTTTAA
1 TTTAATTAAGTAGGTTAGGGTTTTTAA
*
55938248 -TTAAGT-AG--GGTTAGGGTTTTTAA
1 TTTAATTAAGTAGGTTAGGGTTTTTAA
*
55938271 TTTAATTAAAATAAGGTTAGGGTTTTTAA
1 TTTAATT-AAGT-AGGTTAGGGTTTTTAA
55938300 TTTAATTAA--A--TTAGGGTTTTTAA
1 TTTAATTAAGTAGGTTAGGGTTTTTAA
*
55938323 -TTAAGT-AG--GGTTAGGGTTTTTAA
1 TTTAATTAAGTAGGTTAGGGTTTTTAA
*
55938346 TTTAATTAAAATAAGGTTAGGGTTTTTAA
1 TTTAATT-AAGT-AGGTTAGGGTTTTTAA
* * *
55938375 TTTAAGTAGGTTAGGTTAGCGTTTTTAA
1 TTTAATTAAG-TAGGTTAGGGTTTTTAA
* * *
55938403 TTTAATAAAATAAGGTTAGGGTTTTAAA
1 TTTAATTAAGT-AGGTTAGGGTTTTTAA
* *
55938431 TTAAATTAGGTTAGGTTAGGGTTTTTAA
1 TTTAATTAAG-TAGGTTAGGGTTTTTAA
* *
55938459 TTTAATTAAATTAGGTTAGGGTTAGGGTT--
1 TTTAATT-AAGTAGGTTAGGGTT---TTTAA
55938488 TTTAATTAAGTAGGGTTTAGGGTTTTTAA
1 TTTAATTAAGTA-GG-TTAGGGTTTTTAA
55938517 TTTAATTAA--A--TTAGGGTTTTTAA
1 TTTAATTAAGTAGGTTAGGGTTTTTAA
*
55938540 -TTAAGT-AG--GGTTAGGGTTTTTAA
1 TTTAATTAAGTAGGTTAGGGTTTTTAA
55938563 T
1 T
55938564 CAAATAATGT
Statistics
Matches: 415, Mismatches: 37, Indels: 103
0.75 0.07 0.19
Matches are distributed among these distances:
21 4 0.01
22 20 0.05
23 104 0.25
24 15 0.04
25 1 0.00
26 3 0.01
27 8 0.02
28 96 0.23
29 144 0.35
30 16 0.04
31 4 0.01
ACGTcount: A:0.32, C:0.00, G:0.22, T:0.47
Consensus pattern (27 bp):
TTTAATTAAGTAGGTTAGGGTTTTTAA
Found at i:55938096 original size:17 final size:18
Alignment explanation
Indices: 55938063--55938097 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
55938053 GGGTTTTTAA
*
55938063 TTTAATTAAATTAGGGTT
1 TTTAATTAAAGTAGGGTT
55938081 TTTAATT-AAGTAGGGTT
1 TTTAATTAAAGTAGGGTT
55938098 AGGGTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.31, C:0.00, G:0.20, T:0.49
Consensus pattern (18 bp):
TTTAATTAAAGTAGGGTT
Found at i:55938258 original size:17 final size:18
Alignment explanation
Indices: 55938225--55938259 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
55938215 GGGTTTTTAA
*
55938225 TTTAATTAAATTAGGGTT
1 TTTAATTAAAGTAGGGTT
55938243 TTTAATT-AAGTAGGGTT
1 TTTAATTAAAGTAGGGTT
55938260 AGGGTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.31, C:0.00, G:0.20, T:0.49
Consensus pattern (18 bp):
TTTAATTAAAGTAGGGTT
Done.