Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12
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: 24583705
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1509421 characters in sequence are not A, C, G, or T
File 48 of 75
Found at i:15324962 original size:33 final size:33
Alignment explanation
Indices: 15324920--15325124 Score: 115
Period size: 33 Copynumber: 5.6 Consensus size: 33
15324910 CATAAAAAGG
15324920 GGTTGCTAAGTGCTGATTCCCCAAATCATCGGT
1 GGTTGCTAAGTGCTGATTCCCCAAATCATCGGT
*** *
15324953 GGTTGCTAAGTGCTGATTCCACCGTGTCTTCGGATAT
1 GGTTGCTAAGTGCTGATTCC-CCAAATCATCGG---T
*
15324990 GAAAGGGGTTTCTAAGTGCTGATTCCCCAAATCATCGGT
1 ------GGTTGCTAAGTGCTGATTCCCCAAATCATCGGT
* ** * **
15325029 GGTTGCTAAATATTGATTCCACCGTGTCTTCGAATATGAAAGG-
1 GGTTGCTAAGTGCTGATT---CC----C--C-AA-ATCATCGGT
15325072 GGTTGCTAAGTGCTGATTCCCCAAATCATCGGT
1 GGTTGCTAAGTGCTGATTCCCCAAATCATCGGT
15325105 GGTTGCTAAGTGCTGATTCC
1 GGTTGCTAAGTGCTGATTCC
15325125 ACCGTAACGG
Statistics
Matches: 128, Mismatches: 22, Indels: 44
0.66 0.11 0.23
Matches are distributed among these distances:
32 5 0.04
33 56 0.44
34 9 0.07
36 3 0.02
37 1 0.01
39 1 0.01
40 3 0.02
42 9 0.07
43 36 0.28
44 5 0.04
ACGTcount: A:0.22, C:0.21, G:0.25, T:0.32
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCAAATCATCGGT
Found at i:15325007 original size:76 final size:76
Alignment explanation
Indices: 15324915--15325129 Score: 385
Period size: 76 Copynumber: 2.8 Consensus size: 76
15324905 TTGAACATAA
15324915 AAAGGGGTTGCTAAGTGCTGATTCCCCAAATCATCGGTGGTTGCTAAGTGCTGATTCCACCGTGT
1 AAAGGGGTTGCTAAGTGCTGATTCCCCAAATCATCGGTGGTTGCTAAGTGCTGATTCCACCGTGT
*
15324980 CTTCGGATATG
66 CTTCGAATATG
* * **
15324991 AAAGGGGTTTCTAAGTGCTGATTCCCCAAATCATCGGTGGTTGCTAAATATTGATTCCACCGTGT
1 AAAGGGGTTGCTAAGTGCTGATTCCCCAAATCATCGGTGGTTGCTAAGTGCTGATTCCACCGTGT
15325056 CTTCGAATATG
66 CTTCGAATATG
15325067 AAAGGGGTTGCTAAGTGCTGATTCCCCAAATCATCGGTGGTTGCTAAGTGCTGATTCCACCGT
1 AAAGGGGTTGCTAAGTGCTGATTCCCCAAATCATCGGTGGTTGCTAAGTGCTGATTCCACCGT
15325130 AACGGATTGT
Statistics
Matches: 130, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
76 130 1.00
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.31
Consensus pattern (76 bp):
AAAGGGGTTGCTAAGTGCTGATTCCCCAAATCATCGGTGGTTGCTAAGTGCTGATTCCACCGTGT
CTTCGAATATG
Found at i:15325172 original size:27 final size:27
Alignment explanation
Indices: 15325142--15325194 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
15325132 CGGATTGTAT
* * *
15325142 AAGGGGTTGCTAAGTGTTGATTCCCCC
1 AAGGGGTTGCGAAGTGCTAATTCCCCC
15325169 AAGGGGTTGCGAAGTGCTAATTCCCC
1 AAGGGGTTGCGAAGTGCTAATTCCCC
15325195 GACTCACTGG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.21, C:0.23, G:0.30, T:0.26
Consensus pattern (27 bp):
AAGGGGTTGCGAAGTGCTAATTCCCCC
Found at i:15337025 original size:41 final size:40
Alignment explanation
Indices: 15336978--15337061 Score: 98
Period size: 40 Copynumber: 2.1 Consensus size: 40
15336968 GATGAATAGA
* * *
15336978 GGGTTTAATCTAGGGATTTTTTAAGAAGAATAAT-GTATTTG
1 GGGTTTAATCTA-AGATTTTTTAAGAAAAAGAATAG-ATTTG
* *
15337019 GGGTTTAATTTAAGTTTTTTTAAGAAAAAGAATAGATTTG
1 GGGTTTAATCTAAGATTTTTTAAGAAAAAGAATAGATTTG
15337059 GGG
1 GGG
15337062 GTTTGAATTA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
40 25 0.68
41 12 0.32
ACGTcount: A:0.33, C:0.01, G:0.25, T:0.40
Consensus pattern (40 bp):
GGGTTTAATCTAAGATTTTTTAAGAAAAAGAATAGATTTG
Found at i:15351521 original size:44 final size:44
Alignment explanation
Indices: 15351453--15351541 Score: 160
Period size: 44 Copynumber: 2.0 Consensus size: 44
15351443 GTTAAGCTTC
* *
15351453 GGGATCTTCTACATGTATTTATTGATGTCAGATTTAGCGAACTT
1 GGGACCTTCTACATGTATATATTGATGTCAGATTTAGCGAACTT
15351497 GGGACCTTCTACATGTATATATTGATGTCAGATTTAGCGAACTT
1 GGGACCTTCTACATGTATATATTGATGTCAGATTTAGCGAACTT
15351541 G
1 G
15351542 TCAGATATAT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (44 bp):
GGGACCTTCTACATGTATATATTGATGTCAGATTTAGCGAACTT
Found at i:15359786 original size:11 final size:11
Alignment explanation
Indices: 15359770--15359803 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
15359760 GGAAATTGTG
*
15359770 AAAAATTAAAT
1 AAAAATAAAAT
15359781 AAAAATAAAAAT
1 AAAAAT-AAAAT
15359793 AAAAATAAAAT
1 AAAAATAAAAT
15359804 TTTTTATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (11 bp):
AAAAATAAAAT
Found at i:15359788 original size:6 final size:6
Alignment explanation
Indices: 15359777--15359802 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
15359767 GTGAAAAATT
15359777 AAATAA AAATAA AAATAA AAATAA AA
1 AAATAA AAATAA AAATAA AAATAA AA
15359803 TTTTTTATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAATAA
Found at i:15361478 original size:30 final size:30
Alignment explanation
Indices: 15361444--15361500 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
15361434 CTACATGGTT
15361444 GTGCCAAACAACCGTGTGTAACACACGGTC
1 GTGCCAAACAACCGTGTGTAACACACGGTC
** *
15361474 GTGCCAAACAATGGTGTGTGACACACG
1 GTGCCAAACAACCGTGTGTAACACACG
15361501 ATCATGCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.30, C:0.26, G:0.26, T:0.18
Consensus pattern (30 bp):
GTGCCAAACAACCGTGTGTAACACACGGTC
Found at i:15362450 original size:38 final size:38
Alignment explanation
Indices: 15362378--15362452 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 38
15362368 CAATGTTTCA
* ** *
15362378 TTTCATATATCTATTTTCATATAACTGATTCATATAAC
1 TTTCATATATCTATTCTCATATAACCAATACATATAAC
15362416 TTTCATATATCTACTTCT-ATATAACCAATACATATAA
1 TTTCATATATCTA-TTCTCATATAACCAATACATATAA
15362453 TCATTTTATT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
38 29 0.91
39 3 0.09
ACGTcount: A:0.37, C:0.17, G:0.01, T:0.44
Consensus pattern (38 bp):
TTTCATATATCTATTCTCATATAACCAATACATATAAC
Found at i:15369962 original size:28 final size:29
Alignment explanation
Indices: 15369909--15369963 Score: 69
Period size: 28 Copynumber: 1.9 Consensus size: 29
15369899 ATAAAAGATT
*
15369909 AACATAACTTTTTATTAAATTATAAATTA
1 AACATAACTTTTTATAAAATTATAAATTA
*
15369938 AACATAA-TTTTT-TAAAACTTTTAAAT
1 AACATAACTTTTTATAAAA-TTATAAAT
15369964 AGAAAATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 4 0.17
28 12 0.52
29 7 0.30
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.45
Consensus pattern (29 bp):
AACATAACTTTTTATAAAATTATAAATTA
Found at i:15372412 original size:19 final size:19
Alignment explanation
Indices: 15372384--15372437 Score: 83
Period size: 19 Copynumber: 2.8 Consensus size: 19
15372374 CTTGAAAAAG
15372384 GATATGCAATCTTAGATATA
1 GATATGCAATCTTAGATA-A
*
15372404 -ATATACAATCTTAGATAA
1 GATATGCAATCTTAGATAA
15372422 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
15372438 AGATAAGAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
18 1 0.03
19 30 0.97
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.33
Consensus pattern (19 bp):
GATATGCAATCTTAGATAA
Found at i:15372463 original size:22 final size:22
Alignment explanation
Indices: 15372384--15372460 Score: 67
Period size: 19 Copynumber: 3.7 Consensus size: 22
15372374 CTTGAAAAAG
*
15372384 GATATGCAATCTTAG-ATAT-A
1 GATATGCAATCTTAGAAGATAA
*
15372404 -ATATACAATCTT---AGATAA
1 GATATGCAATCTTAGAAGATAA
15372422 GATATGCAATCTTAGAAGATAA
1 GATATGCAATCTTAGAAGATAA
* *
15372444 GAGTTTGTAATCTTAGA
1 GA-TATGCAATCTTAGA
15372461 GATTTAATTT
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
17 3 0.07
18 1 0.02
19 22 0.48
22 8 0.17
23 12 0.26
ACGTcount: A:0.42, C:0.09, G:0.16, T:0.34
Consensus pattern (22 bp):
GATATGCAATCTTAGAAGATAA
Found at i:15372925 original size:21 final size:22
Alignment explanation
Indices: 15372896--15372936 Score: 59
Period size: 20 Copynumber: 1.9 Consensus size: 22
15372886 AACCATTCTT
15372896 ATCATTCTTTTATTT-TTTTTCC
1 ATCATTC-TTTATTTGTTTTTCC
15372918 ATCA-TCTTTATTTGTTTTT
1 ATCATTCTTTATTTGTTTTT
15372937 AATATTATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.15, C:0.15, G:0.02, T:0.68
Consensus pattern (22 bp):
ATCATTCTTTATTTGTTTTTCC
Found at i:15373246 original size:24 final size:23
Alignment explanation
Indices: 15373188--15373246 Score: 59
Period size: 24 Copynumber: 2.4 Consensus size: 23
15373178 CATCAAAATT
15373188 TTTAAATT-TTATATGTATTATTA
1 TTTAAATTATTATA-GTATTATTA
15373211 TTTCAAATTTATTATA-TATTATTTA
1 TTT-AAA-TTATTATAGTATTA-TTA
15373236 TTGTAAATTAT
1 TT-TAAATTAT
15373247 CCAATTCATT
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
23 3 0.10
24 12 0.39
25 10 0.32
26 6 0.19
ACGTcount: A:0.36, C:0.02, G:0.03, T:0.59
Consensus pattern (23 bp):
TTTAAATTATTATAGTATTATTA
Found at i:15373335 original size:23 final size:23
Alignment explanation
Indices: 15373293--15373337 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
15373283 AATTGTACAT
*
15373293 TCATATATATTATTTGTTTTAAC
1 TCATATATATTATTTATTTTAAC
15373316 TCATATATA-TAGTTTATTTTAA
1 TCATATATATTA-TTTATTTTAA
15373338 AATTTTGAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 2 0.10
23 18 0.90
ACGTcount: A:0.33, C:0.07, G:0.04, T:0.56
Consensus pattern (23 bp):
TCATATATATTATTTATTTTAAC
Found at i:15374401 original size:29 final size:29
Alignment explanation
Indices: 15374342--15374402 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
15374332 TTTAAATACA
* * **
15374342 AAAAATAGAGTAATTAAATTTCTTAAAGT
1 AAAAATAGAGAAACTAAATTTCAAAAAGT
15374371 AAAAATAGA-AAACTAAATTTCAAAAATGT
1 AAAAATAGAGAAACTAAATTTCAAAAA-GT
15374400 AAA
1 AAA
15374403 GAAGAGTGTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 13 0.48
29 14 0.52
ACGTcount: A:0.59, C:0.05, G:0.08, T:0.28
Consensus pattern (29 bp):
AAAAATAGAGAAACTAAATTTCAAAAAGT
Found at i:15377656 original size:41 final size:41
Alignment explanation
Indices: 15377598--15377689 Score: 141
Period size: 41 Copynumber: 2.2 Consensus size: 41
15377588 CACTGATCTT
*
15377598 TCCTTAGCTATAAATTAATTACGAAAATAAC-TCAATAATTAA
1 TCCTTA-CTATAAATTAATTACGAAAACAACAT-AATAATTAA
*
15377640 TCCTTACTATAAATTAATTACGAGAACAACATAATAATTAA
1 TCCTTACTATAAATTAATTACGAAAACAACATAATAATTAA
15377681 TCCTTACTA
1 TCCTTACTA
15377690 GTTAAACAAC
Statistics
Matches: 47, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
41 40 0.85
42 7 0.15
ACGTcount: A:0.46, C:0.16, G:0.04, T:0.34
Consensus pattern (41 bp):
TCCTTACTATAAATTAATTACGAAAACAACATAATAATTAA
Found at i:15380726 original size:42 final size:43
Alignment explanation
Indices: 15380626--15380743 Score: 150
Period size: 42 Copynumber: 2.8 Consensus size: 43
15380616 AGCCCGTACA
* * *
15380626 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATTAATTATCG
1 ATGCCAATGTCCCAGACATGGTCTTACACGTAATTAATTATCG
* * *
15380669 ATGCCACTGTCCCAGACAAGGTCTTATACGTAATT-A-TATACG
1 ATGCCAATGTCCCAGACATGGTCTTACACGTAATTAATTAT-CG
*
15380711 ATGTCAATGTCCCAGACATGGTCTTACACGTAA
1 ATGCCAATGTCCCAGACATGGTCTTACACGTAA
15380744 ATCTCAAATC
Statistics
Matches: 64, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
41 3 0.05
42 32 0.50
43 29 0.45
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.29
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACATGGTCTTACACGTAATTAATTATCG
Found at i:15390423 original size:14 final size:14
Alignment explanation
Indices: 15390406--15390450 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
15390396 TTTAGGCCAG
15390406 TTGGGCTAGGTTAA
1 TTGGGCTAGGTTAA
* *
15390420 TTGGGTTAGATT--
1 TTGGGCTAGGTTAA
15390432 TTGGGCTAGGTTAA
1 TTGGGCTAGGTTAA
15390446 TTGGG
1 TTGGG
15390451 TTTGTAAAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
12 10 0.40
14 15 0.60
ACGTcount: A:0.18, C:0.04, G:0.38, T:0.40
Consensus pattern (14 bp):
TTGGGCTAGGTTAA
Found at i:15391951 original size:18 final size:20
Alignment explanation
Indices: 15391910--15391950 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
15391900 AGTATTTGAG
* *
15391910 TTTAGAATATATATTTTATT
1 TTTAAAATATATATTATATT
15391930 TTTAAAATATA-ATTATATT
1 TTTAAAATATATATTATATT
15391949 TT
1 TT
15391951 ATTCTATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (20 bp):
TTTAAAATATATATTATATT
Found at i:15394048 original size:17 final size:17
Alignment explanation
Indices: 15394026--15394061 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
15394016 ATAAAACGAG
15394026 AATAATAAAATTAGTTA
1 AATAATAAAATTAGTTA
15394043 AATAATAAAATTAGTTA
1 AATAATAAAATTAGTTA
15394060 AA
1 AA
15394062 CAAATTTGGA
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:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (17 bp):
AATAATAAAATTAGTTA
Found at i:15394535 original size:30 final size:30
Alignment explanation
Indices: 15394500--15394775 Score: 233
Period size: 30 Copynumber: 9.3 Consensus size: 30
15394490 CTCGTATCAA
* *
15394500 CTTTTCATAGTTCGATAGCCGAAGCTATCC
1 CTTTTCATAATTCGATAGCCGAAGCCATCC
* * * * *
15394530 TTTTTCATAATTTGATGGTCGTTA-CCATCC
1 CTTTTCATAATTCGATAGCCG-AAGCCATCC
* * * ** *
15394560 CTTTTCATTATTCGGTGGTTGTCA-CCATCC
1 CTTTTCATAATTCGATAGCCG-AAGCCATCC
* *
15394590 TTTTTCATAATT-GATAGCCGAAGCTATCC
1 CTTTTCATAATTCGATAGCCGAAGCCATCC
*
15394619 TTTTTCATAGA-TCGATAGCCGAAGCCATCC
1 CTTTTCATA-ATTCGATAGCCGAAGCCATCC
* *
15394649 CTTTTCATTATACGATAGCCGAAGCCATCC
1 CTTTTCATAATTCGATAGCCGAAGCCATCC
* * * *
15394679 CTTTTCATAATTTGATGGTCGTCA-CCATCC
1 CTTTTCATAATTCGATAGCCG-AAGCCATCC
* **
15394709 CTTTTCGTAATT-GATAGCCGAAGTTATCC
1 CTTTTCATAATTCGATAGCCGAAGCCATCC
15394738 CTTTTCAT-ATATCGATAGCCGAAGCCATCC
1 CTTTTCATAAT-TCGATAGCCGAAGCCATCC
15394768 CTTTTCAT
1 CTTTTCAT
15394776 TCGTCGATGA
Statistics
Matches: 197, Mismatches: 40, Indels: 18
0.77 0.16 0.07
Matches are distributed among these distances:
28 4 0.02
29 38 0.19
30 153 0.78
31 2 0.01
ACGTcount: A:0.23, C:0.25, G:0.14, T:0.37
Consensus pattern (30 bp):
CTTTTCATAATTCGATAGCCGAAGCCATCC
Found at i:15394677 original size:89 final size:88
Alignment explanation
Indices: 15394500--15394775 Score: 272
Period size: 89 Copynumber: 3.1 Consensus size: 88
15394490 CTCGTATCAA
* * * *
15394500 CTTTTCATAGTTCGATAGCCGAAGCTATCCTTTTTCATAATTTGATGGTCGTTA-CCATCCCTTT
1 CTTTTCATAATT-GATAGCCGAAGCTATCCTTTTTCATAA-TTGATAGCCG-AAGCCATCCCTTT
* * * ** *
15394564 TCATTATTCGGTGGTTGTCA-CCATCC
63 TCATTATACGATAGCCG-AAGCCATCC
* *
15394590 TTTTTCATAATTGATAGCCGAAGCTATCCTTTTTCATAGATCGATAGCCGAAGCCATCCCTTTTC
1 CTTTTCATAATTGATAGCCGAAGCTATCCTTTTTCATA-ATTGATAGCCGAAGCCATCCCTTTTC
15394655 ATTATACGATAGCCGAAGCCATCC
65 ATTATACGATAGCCGAAGCCATCC
* * * * * * **
15394679 CTTTTCATAATTTGATGGTCGTCA-CCATCCCTTTTCGTAATTGATAGCCGAAGTTATCCCTTTT
1 CTTTTCATAA-TTGATAGCCG-AAGCTATCCTTTTTCATAATTGATAGCCGAAGCCATCCCTTTT
15394743 CA-TATATCGATAGCCGAAGCCATCC
64 CATTATA-CGATAGCCGAAGCCATCC
15394768 CTTTTCAT
1 CTTTTCAT
15394776 TCGTCGATGA
Statistics
Matches: 158, Mismatches: 22, Indels: 13
0.82 0.11 0.07
Matches are distributed among these distances:
88 6 0.04
89 120 0.76
90 31 0.20
91 1 0.01
ACGTcount: A:0.23, C:0.25, G:0.14, T:0.37
Consensus pattern (88 bp):
CTTTTCATAATTGATAGCCGAAGCTATCCTTTTTCATAATTGATAGCCGAAGCCATCCCTTTTCA
TTATACGATAGCCGAAGCCATCC
Found at i:15394714 original size:119 final size:119
Alignment explanation
Indices: 15394500--15394776 Score: 376
Period size: 119 Copynumber: 2.3 Consensus size: 119
15394490 CTCGTATCAA
* * * * ** * * *
15394500 CTTTTCATAGTTCGATAGCCGAAGCTATCCTTTTTCATAATTTGATGGTCGTTACCATCCCTTTT
1 CTTTTCATAGATCGATAGCCGAAGCCATCCCTTTTCATTATACGATAGCCGTAACCATCCCTTTT
* * * *
15394565 CATTATTCGGTGGTTGTCACCATCCTTTTTCATAATTGATAGCCGAAGCTATCC
66 CATAATTCGATGGTCGTCACCATCCCTTTTCATAATTGATAGCCGAAGCTATCC
*
15394619 TTTTTCATAGATCGATAGCCGAAGCCATCCCTTTTCATTATACGATAGCCG-AAGCCATCCCTTT
1 CTTTTCATAGATCGATAGCCGAAGCCATCCCTTTTCATTATACGATAGCCGTAA-CCATCCCTTT
* * *
15394683 TCATAATTTGATGGTCGTCACCATCCCTTTTCGTAATTGATAGCCGAAGTTATCC
65 TCATAATTCGATGGTCGTCACCATCCCTTTTCATAATTGATAGCCGAAGCTATCC
*
15394738 CTTTTCATATATCGATAGCCGAAGCCATCCCTTTTCATT
1 CTTTTCATAGATCGATAGCCGAAGCCATCCCTTTTCATT
15394777 CGTCGATGAT
Statistics
Matches: 138, Mismatches: 19, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
118 1 0.01
119 137 0.99
ACGTcount: A:0.23, C:0.25, G:0.14, T:0.38
Consensus pattern (119 bp):
CTTTTCATAGATCGATAGCCGAAGCCATCCCTTTTCATTATACGATAGCCGTAACCATCCCTTTT
CATAATTCGATGGTCGTCACCATCCCTTTTCATAATTGATAGCCGAAGCTATCC
Found at i:15398292 original size:20 final size:19
Alignment explanation
Indices: 15398238--15398291 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 19
15398228 AATATTTATT
15398238 AATATTTTG-TATTTTAAA
1 AATATTTTGATATTTTAAA
* *
15398256 AATTATTTTAAAATTTTGAAA
1 AA-TATTTTGATATTTT-AAA
15398277 AATATTTTGAT-TTTT
1 AATATTTTGATATTTT
15398292 TTTGTAATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
18 2 0.07
19 10 0.34
20 12 0.41
21 5 0.17
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.56
Consensus pattern (19 bp):
AATATTTTGATATTTTAAA
Found at i:15403658 original size:1 final size:1
Alignment explanation
Indices: 15403652--15403695 Score: 88
Period size: 1 Copynumber: 44.0 Consensus size: 1
15403642 CAATGGAACC
15403652 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
15403696 CTGATTGAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 43 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:15408857 original size:22 final size:22
Alignment explanation
Indices: 15408829--15408890 Score: 106
Period size: 22 Copynumber: 2.8 Consensus size: 22
15408819 GACGCGATTT
15408829 CTTCAAAAATTCTCTCAATTCC
1 CTTCAAAAATTCTCTCAATTCC
*
15408851 CTTCAAAAATTCTCTCAATTTC
1 CTTCAAAAATTCTCTCAATTCC
*
15408873 CTTCCAAAATTCTCTCAA
1 CTTCAAAAATTCTCTCAA
15408891 ACTCTCAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.32, C:0.31, G:0.00, T:0.37
Consensus pattern (22 bp):
CTTCAAAAATTCTCTCAATTCC
Found at i:15408896 original size:30 final size:30
Alignment explanation
Indices: 15408862--15408920 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
15408852 TTCAAAAATT
* *
15408862 CTCTCAATTTCCTTCCAAAATTCTCTCAAA
1 CTCTCAAATTCCTTCCAAAATCCTCTCAAA
15408892 CTCTCAAATTCCTTCCAAAATCCTCTCAA
1 CTCTCAAATTCCTTCCAAAATCCTCTCAA
15408921 TTTCCTTCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.31, C:0.36, G:0.00, T:0.34
Consensus pattern (30 bp):
CTCTCAAATTCCTTCCAAAATCCTCTCAAA
Found at i:15408897 original size:52 final size:51
Alignment explanation
Indices: 15408840--15408942 Score: 145
Period size: 52 Copynumber: 2.0 Consensus size: 51
15408830 TTCAAAAATT
* * *
15408840 CTCTC-AATTCCCTTCAAAAATTCTCTCAATTTCCTTCCAAAATTCTCTCAAA
1 CTCTCAAATT-CCTTCAAAAATCCTCTCAATTTCCTTCAAAAAATCTC-CAAA
*
15408892 CTCTCAAATTCCTTCCAAAATCCTCTCAATTTCCTTCAAAAAATCTCCAAA
1 CTCTCAAATTCCTTCAAAAATCCTCTCAATTTCCTTCAAAAAATCTCCAAA
15408943 TCCATATTAA
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
51 4 0.09
52 38 0.83
53 4 0.09
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.34
Consensus pattern (51 bp):
CTCTCAAATTCCTTCAAAAATCCTCTCAATTTCCTTCAAAAAATCTCCAAA
Found at i:15408931 original size:21 final size:22
Alignment explanation
Indices: 15408892--15408933 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
15408882 TTCTCTCAAA
15408892 CTCTCAAATTCCTTCCAAAATC
1 CTCTCAAATTCCTTCCAAAATC
* *
15408914 CTCTCAATTTCCTTCAAAAA
1 CTCTCAAATTCCTTCCAAAA
15408934 ATCTCCAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (22 bp):
CTCTCAAATTCCTTCCAAAATC
Found at i:15409013 original size:29 final size:29
Alignment explanation
Indices: 15408975--15409031 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
15408965 ATTAAATTTC
*
15408975 ATTTTTTTAAGAA-AATTTTACAATTTTTT
1 ATTTTTTTAA-AATAATTTTAAAATTTTTT
*
15409004 ATTTTTTTAAAATATTTTTAAAATTTTT
1 ATTTTTTTAAAATAATTTTAAAATTTTT
15409032 AATATTTTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 2 0.08
29 23 0.92
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (29 bp):
ATTTTTTTAAAATAATTTTAAAATTTTTT
Found at i:15409159 original size:14 final size:15
Alignment explanation
Indices: 15409130--15409163 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
15409120 AAATTTTATA
15409130 TTTTATTTAAGATAT
1 TTTTATTTAAGATAT
*
15409145 TTTTATTTATG-TAT
1 TTTTATTTAAGATAT
15409159 TTTTA
1 TTTTA
15409164 GATATTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (15 bp):
TTTTATTTAAGATAT
Found at i:15409185 original size:24 final size:23
Alignment explanation
Indices: 15409128--15409185 Score: 64
Period size: 24 Copynumber: 2.3 Consensus size: 23
15409118 TTAAATTTTA
15409128 TATTTTATTTAAGATATTTTTATT
1 TATTTT-TTTAAGATATTTTTATT
15409152 TATGTATTTTT-AGATATTTATTGATT
1 TAT-T-TTTTTAAGATATTT-TT-ATT
15409178 TATTTTTT
1 TATTTTTT
15409186 GTTATAAAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
24 15 0.50
25 7 0.23
26 8 0.27
ACGTcount: A:0.26, C:0.00, G:0.07, T:0.67
Consensus pattern (23 bp):
TATTTTTTTAAGATATTTTTATT
Found at i:15417087 original size:28 final size:28
Alignment explanation
Indices: 15417047--15417578 Score: 246
Period size: 23 Copynumber: 21.0 Consensus size: 28
15417037 NNNACCTAAC
15417047 TTAATTAAAAACCCTAACCTAACTTAAT
1 TTAATTAAAAACCCTAACCTAACTTAAT
*
15417075 TTAATTCAAAACCCTAA-C---C-TAAT
1 TTAATTAAAAACCCTAACCTAACTTAAT
*
15417098 TTAATTAAAAACCCTAACCTAATTGAATTATAAT
1 TTAATTAAAAACCCTAACC----T-AACT-TAAT
*
15417132 TTAATTAAAAACCCTAACCTAATTTAAT
1 TTAATTAAAAACCCTAACCTAACTTAAT
15417160 TTAATTAAAAA---TAA--T---TTAA-
1 TTAATTAAAAACCCTAACCTAACTTAAT
* * *
15417179 TTAAA----AACCCTAACCCTAACCTATT
1 TTAATTAAAAACCCTAA-CCTAACTTAAT
* * *
15417204 TTACA-TGAAAACCCTAACCCTAACATATT
1 TTA-ATTAAAAACCCTAA-CCTAACTTAAT
15417233 TTAATTAAAAACCCTAACCTAACTTAA-
1 TTAATTAAAAACCCTAACCTAACTTAAT
*
15417260 -T--GT-AAAACCCTAA-C---C-TAAT
1 TTAATTAAAAACCCTAACCTAACTTAAT
*
15417279 TGAATTAAAAACCCTAACCTAACTTAAT
1 TTAATTAAAAACCCTAACCTAACTTAAT
* *
15417307 TTAATTAAAAACCCTAACCCTAACCTATT
1 TTAATTAAAAACCCTAA-CCTAACTTAAT
* * *
15417336 TTACA-TGAAAACCCTAACCCTAACATATT
1 TTA-ATTAAAAACCCTAA-CCTAACTTAAT
15417365 TTAATTAAAAACCCTAACCTAAC-----
1 TTAATTAAAAACCCTAACCTAACTTAAT
**
15417388 TTAATGGAAAACCCTAA-C--A--TAAT
1 TTAATTAAAAACCCTAACCTAACTTAAT
* **
15417411 TGAATTAAAAA-CCTAATTTAA-TTAA-
1 TTAATTAAAAACCCTAACCTAACTTAAT
*
15417436 -A-------AACCCTAACCTAACTTAA-
1 TTAATTAAAAACCCTAACCTAACTTAAT
*
15417455 -T--GT-AAAACCCT-ACCTAACTTAAT
1 TTAATTAAAAACCCTAACCTAACTTAAT
*
15417478 TTAATTAAAAACCCTAACTTAACTTAA-
1 TTAATTAAAAACCCTAACCTAACTTAAT
*
15417505 -T--GT-AAAACCCT-ACCTAACTTAAT
1 TTAATTAAAAACCCTAACCTAACTTAAT
15417528 TTAATTAAAAACCCTAACCTAAC-----
1 TTAATTAAAAACCCTAACCTAACTTAAT
*
15417551 TTAATTAAAAATCCTAACCTAACTTAAT
1 TTAATTAAAAACCCTAACCTAACTTAAT
15417579 GTAAAACCCT
Statistics
Matches: 398, Mismatches: 35, Indels: 142
0.69 0.06 0.25
Matches are distributed among these distances:
15 2 0.01
17 2 0.01
18 14 0.04
19 9 0.02
20 5 0.01
21 1 0.00
22 29 0.07
23 100 0.25
24 9 0.02
25 7 0.02
26 8 0.02
27 18 0.05
28 84 0.21
29 85 0.21
30 2 0.01
34 23 0.06
ACGTcount: A:0.45, C:0.22, G:0.02, T:0.31
Consensus pattern (28 bp):
TTAATTAAAAACCCTAACCTAACTTAAT
Found at i:15417137 original size:34 final size:33
Alignment explanation
Indices: 15417094--15417165 Score: 126
Period size: 34 Copynumber: 2.2 Consensus size: 33
15417084 AACCCTAACC
15417094 TAATTTAATTAAAAACCCTAACCTAATTGAATT
1 TAATTTAATTAAAAACCCTAACCTAATTGAATT
*
15417127 ATAATTTAATTAAAAACCCTAACCTAATTTAATT
1 -TAATTTAATTAAAAACCCTAACCTAATTGAATT
15417161 TAATT
1 TAATT
15417166 AAAAATAATT
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
33 5 0.14
34 32 0.86
ACGTcount: A:0.46, C:0.14, G:0.01, T:0.39
Consensus pattern (33 bp):
TAATTTAATTAAAAACCCTAACCTAATTGAATT
Found at i:15417158 original size:23 final size:23
Alignment explanation
Indices: 15417128--15417655 Score: 301
Period size: 23 Copynumber: 22.0 Consensus size: 23
15417118 AATTGAATTA
15417128 TAATTTAATTAAAAACCCTAACC
1 TAATTTAATTAAAAACCCTAACC
15417151 TAATTTAATTTAATTAAA----AA--
1 TAATTTAA-TTAA--AAACCCTAACC
15417171 TAATTTAATTAAAAACCCTAACCC
1 TAATTTAATTAAAAACCCTAA-CC
*
15417195 TAACCTATTTTACA-TGAAAACCCTAACCC
1 T-A---A-TTTA-ATTAAAAACCCTAA-CC
15417224 TAACATATTTTAATTAAAAACCCTAACC
1 T---A-A-TTTAATTAAAAACCCTAACC
*
15417252 TAACTTAATGT-AAAACCCTAACC
1 TAATTTAAT-TAAAAACCCTAACC
*
15417275 TAATTGAATTAAAAACCCTAACCTAAC
1 TAATTTAATTAAAAACCCTAA-C---C
15417302 TTAATTTAATTAAAAACCCTAACCC
1 -TAATTTAATTAAAAACCCTAA-CC
*
15417327 TAACCTATTTTACA-TGAAAACCCTAACCC
1 T-A---A-TTTA-ATTAAAAACCCTAA-CC
15417356 TAACATATTTTAATTAAAAACCCTAACC
1 T---A-A-TTTAATTAAAAACCCTAACC
* ** *
15417384 TAACTTAATGGAAAACCCTAACA
1 TAATTTAATTAAAAACCCTAACC
*
15417407 TAATTGAATT--AAA----AACC
1 TAATTTAATTAAAAACCCTAACC
15417424 TAATTTAATTAAAAACCCTAACC
1 TAATTTAATTAAAAACCCTAACC
* * *
15417447 TAACTTAATGTAAAACCCTACCTAACT
1 TAATTTAAT-TAAAA-AC--CCTAACC
*
15417474 TAATTTAATTAAAAACCCTAACT
1 TAATTTAATTAAAAACCCTAACC
* * *
15417497 TAACTTAATGTAAAACCCTACCTAACT
1 TAATTTAAT-TAAAA-AC--CCTAACC
15417524 TAATTTAATTAAAAACCCTAACC
1 TAATTTAATTAAAAACCCTAACC
* *
15417547 TAACTTAATTAAAAATCCTAACC
1 TAATTTAATTAAAAACCCTAACC
*
15417570 TAACTTAATGT-AAAACCCTAACC
1 TAATTTAAT-TAAAAACCCTAACC
*
15417593 TAATTGAATT--AAA----AACC
1 TAATTTAATTAAAAACCCTAACC
15417610 TAATTTAATTAAAAACCCTAACC
1 TAATTTAATTAAAAACCCTAACC
*
15417633 TAACTTAATGT-AAAACCCTAACC
1 TAATTTAAT-TAAAAACCCTAACC
15417656 CTAAGCTAAT
Statistics
Matches: 412, Mismatches: 36, Indels: 114
0.73 0.06 0.20
Matches are distributed among these distances:
17 28 0.07
19 10 0.02
20 8 0.02
21 8 0.02
22 4 0.01
23 170 0.41
24 22 0.05
25 9 0.02
26 13 0.03
27 30 0.07
28 32 0.08
29 74 0.18
30 2 0.00
31 2 0.00
ACGTcount: A:0.46, C:0.22, G:0.02, T:0.30
Consensus pattern (23 bp):
TAATTTAATTAAAAACCCTAACC
Found at i:15417176 original size:15 final size:15
Alignment explanation
Indices: 15417156--15417185 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
15417146 TAACCTAATT
15417156 TAATTTAATTAAAAA
1 TAATTTAATTAAAAA
15417171 TAATTTAATTAAAAA
1 TAATTTAATTAAAAA
15417186 CCCTAACCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
TAATTTAATTAAAAA
Found at i:15417214 original size:29 final size:28
Alignment explanation
Indices: 15417174--15417387 Score: 211
Period size: 29 Copynumber: 7.9 Consensus size: 28
15417164 TTAAAAATAA
15417174 TTTAATTAAAAACCCTAACCCTAACCTAT
1 TTTAATTAAAAACCCTAA-CCTAACCTAT
* *
15417203 TTTACA-TGAAAACCCTAACCCTAACATAT
1 TTTA-ATTAAAAACCCTAA-CCTAACCTAT
15417232 TTTAATTAAAAACCCTAACCTAA-C---
1 TTTAATTAAAAACCCTAACCTAACCTAT
15417256 -TTAATGT-AAAACCCTAACCT-A---A-
1 TTTAAT-TAAAAACCCTAACCTAACCTAT
* * *
15417278 TTGAATTAAAAACCCTAACCTAACTTAA
1 TTTAATTAAAAACCCTAACCTAACCTAT
15417306 TTTAATTAAAAACCCTAACCCTAACCTAT
1 TTTAATTAAAAACCCTAA-CCTAACCTAT
* *
15417335 TTTACA-TGAAAACCCTAACCCTAACATAT
1 TTTA-ATTAAAAACCCTAA-CCTAACCTAT
15417364 TTTAATTAAAAACCCTAACCTAAC
1 TTTAATTAAAAACCCTAACCTAAC
15417388 TTAATGGAAA
Statistics
Matches: 160, Mismatches: 11, Indels: 29
0.80 0.05 0.14
Matches are distributed among these distances:
22 2 0.01
23 35 0.22
24 2 0.01
27 1 0.01
28 30 0.19
29 88 0.55
30 2 0.01
ACGTcount: A:0.43, C:0.26, G:0.02, T:0.29
Consensus pattern (28 bp):
TTTAATTAAAAACCCTAACCTAACCTAT
Found at i:15417334 original size:132 final size:132
Alignment explanation
Indices: 15417171--15417556 Score: 524
Period size: 132 Copynumber: 3.0 Consensus size: 132
15417161 TAATTAAAAA
15417171 TAATTTAATTAAAAACCCTAACCCTAACCTATTTTACATGAAAACCCTAACCCTAACATATTTTA
1 TAATTTAATTAAAAACCCTAACCCTAACCTATTTTACATGAAAACCCTAACCCTAACATATTTTA
*
15417236 ATTAAAAACCCTAACCTAACTTAATGTAAAACCCTAACCTAATTGAATTAAAAACCCTAACCTAA
66 ATTAAAAACCCTAACCTAACTTAATGTAAAACCCTAACATAATTGAATTAAAAACCCTAACCTAA
15417301 CT
131 CT
15417303 TAATTTAATTAAAAACCCTAACCCTAACCTATTTTACATGAAAACCCTAACCCTAACATATTTTA
1 TAATTTAATTAAAAACCCTAACCCTAACCTATTTTACATGAAAACCCTAACCCTAACATATTTTA
*
15417368 ATTAAAAACCCTAACCTAACTTAATGGAAAACCCTAACATAATTGAATT--AAA----AA-C---
66 ATTAAAAACCCTAACCTAACTTAATGTAAAACCCTAACATAATTGAATTAAAAACCCTAACCTAA
15417423 C-
131 CT
* *
15417424 TAATTTAATTAAAAACCCTAA-CCTAA-C----TTA-ATGTAAAACCCT-A-CCTAACTTAATTT
1 TAATTTAATTAAAAACCCTAACCCTAACCTATTTTACATG-AAAACCCTAACCCTAACATATTTT
* * *
15417480 AATTAAAAACCCTAACTTAACTTAATGTAAAACCCTACCTAACTTAATTTAATTAAAAACCCTAA
65 AATTAAAAACCCTAACCTAACTTAATGTAAAA--C--CCTAACATAATTGAATTAAAAACCCTAA
15417545 CCTAACT
126 CCTAACT
15417552 TAATT
1 TAATT
15417557 AAAAATCCTA
Statistics
Matches: 230, Mismatches: 8, Indels: 36
0.84 0.03 0.13
Matches are distributed among these distances:
113 41 0.18
114 4 0.02
115 12 0.05
117 15 0.07
119 4 0.02
120 5 0.02
121 21 0.09
122 1 0.00
123 2 0.01
124 1 0.00
125 1 0.00
126 2 0.01
127 1 0.00
128 5 0.02
130 3 0.01
132 112 0.49
ACGTcount: A:0.45, C:0.23, G:0.02, T:0.30
Consensus pattern (132 bp):
TAATTTAATTAAAAACCCTAACCCTAACCTATTTTACATGAAAACCCTAACCCTAACATATTTTA
ATTAAAAACCCTAACCTAACTTAATGTAAAACCCTAACATAATTGAATTAAAAACCCTAACCTAA
CT
Found at i:15417444 original size:18 final size:17
Alignment explanation
Indices: 15417407--15417440 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
15417397 AACCCTAACA
15417407 TAATTGAATTAAAAACC
1 TAATTGAATTAAAAACC
*
15417424 TAATTTAATTAAAAACC
1 TAATTGAATTAAAAACC
15417441 CTAACCTAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.53, C:0.12, G:0.03, T:0.32
Consensus pattern (17 bp):
TAATTGAATTAAAAACC
Found at i:15417491 original size:50 final size:50
Alignment explanation
Indices: 15417424--15417652 Score: 292
Period size: 50 Copynumber: 4.9 Consensus size: 50
15417414 ATTAAAAACC
15417424 TAATTTAATTAAAAACCCTAACCTAACTTAATGTAAAACCCTACCTAACT
1 TAATTTAATTAAAAACCCTAACCTAACTTAATGTAAAACCCTACCTAACT
*
15417474 TAATTTAATTAAAAACCCTAACTTAACTTAATGTAAAACCCTACCTAACT
1 TAATTTAATTAAAAACCCTAACCTAACTTAATGTAAAACCCTACCTAACT
* *
15417524 TAATTTAATTAAAAACCCTAACCTAACTTAAT-TAAAA--AT-CCTAACC
1 TAATTTAATTAAAAACCCTAACCTAACTTAATGTAAAACCCTACCTAACT
*
15417570 TAACTTAATGT-AAAACCCTAACCTAA-TTGAAT-TAAAA----A-C---C-
1 TAATTTAAT-TAAAAACCCTAACCTAACTT-AATGTAAAACCCTACCTAACT
15417610 TAATTTAATTAAAAACCCTAACCTAACTTAATGTAAAACCCTA
1 TAATTTAATTAAAAACCCTAACCTAACTTAATGTAAAACCCTA
15417653 ACCCTAAGCT
Statistics
Matches: 163, Mismatches: 6, Indels: 25
0.84 0.03 0.13
Matches are distributed among these distances:
39 1 0.01
40 26 0.16
41 8 0.05
44 1 0.01
45 3 0.02
46 37 0.23
47 2 0.01
49 5 0.03
50 80 0.49
ACGTcount: A:0.46, C:0.22, G:0.02, T:0.30
Consensus pattern (50 bp):
TAATTTAATTAAAAACCCTAACCTAACTTAATGTAAAACCCTACCTAACT
Found at i:15417587 original size:186 final size:193
Alignment explanation
Indices: 15417232--15417652 Score: 605
Period size: 186 Copynumber: 2.2 Consensus size: 193
15417222 CCTAACATAT
15417232 TTTAATTAAAAACCCTAACCTAACTTAATGTAAAA--C--CCTAACCTAATTGAATTAAAAACCC
1 TTTAATTAAAAACCCTAACCTAACTTAATGTAAAACCCTACCTAACCTAATTGAATTAAAAACCC
* * *
15417293 TAACCTAACTTAATTTAATTAAAAACCCTAACCCTAACCTATTTTACATGAAAACCCTAACCCTA
66 TAACCTAACTTAA-TT-AGTAAAAACCCTAACCCTAACCTAATTTACATAAAAACCCTAACCCTA
15417358 ACATATTTTAATTAAAAACCCTAACCTAACTTAATGGAAAACCCTAACATAATTGAATTAAAAAC
129 AC----TTTAATTAAAAACCCTAACCTAACTTAATGGAAAACCCTAACATAATTGAATTAAAAAC
15417423 CTAA
190 CTAA
* *
15417427 TTTAATTAAAAACCCTAACCTAACTTAATGTAAAACCCTACCTAACTTAATTTAATTAAAAACCC
1 TTTAATTAAAAACCCTAACCTAACTTAATGTAAAACCCTACCTAACCTAATTGAATTAAAAACCC
* *
15417492 TAACTTAACTTAA-T-GT-AAAACCCT-A-CCTAACTTAATTTA-ATTAAAAACCCTAA-CCTAA
66 TAACCTAACTTAATTAGTAAAAACCCTAACCCTAACCTAATTTACA-TAAAAACCCTAACCCTAA
* * *
15417550 C-TTAATTAAAAATCCTAACCTAACTTAATGTAAAACCCTAACCTAATTGAATTAAAAACCTAA
130 CTTTAATTAAAAACCCTAACCTAACTTAATGGAAAACCCTAACATAATTGAATTAAAAACCTAA
15417613 TTTAATTAAAAACCCTAACCTAACTTAATGTAAAACCCTA
1 TTTAATTAAAAACCCTAACCTAACTTAATGTAAAACCCTA
15417653 ACCCTAAGCT
Statistics
Matches: 211, Mismatches: 10, Indels: 19
0.88 0.04 0.08
Matches are distributed among these distances:
186 99 0.47
191 7 0.03
192 23 0.11
193 1 0.00
194 8 0.04
195 36 0.17
197 2 0.01
199 35 0.17
ACGTcount: A:0.46, C:0.23, G:0.03, T:0.29
Consensus pattern (193 bp):
TTTAATTAAAAACCCTAACCTAACTTAATGTAAAACCCTACCTAACCTAATTGAATTAAAAACCC
TAACCTAACTTAATTAGTAAAAACCCTAACCCTAACCTAATTTACATAAAAACCCTAACCCTAAC
TTTAATTAAAAACCCTAACCTAACTTAATGGAAAACCCTAACATAATTGAATTAAAAACCTAA
Found at i:15417611 original size:17 final size:17
Alignment explanation
Indices: 15417589--15417626 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
15417579 GTAAAACCCT
15417589 AACCTAATTGAATTAAA
1 AACCTAATTGAATTAAA
*
15417606 AACCTAATTTAATTAAA
1 AACCTAATTGAATTAAA
15417623 AACC
1 AACC
15417627 CTAACCTAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.53, C:0.16, G:0.03, T:0.29
Consensus pattern (17 bp):
AACCTAATTGAATTAAA
Found at i:15417642 original size:63 final size:64
Alignment explanation
Indices: 15417474--15417655 Score: 240
Period size: 63 Copynumber: 2.7 Consensus size: 64
15417464 CTACCTAACT
* * *
15417474 TAATTTAATTAAAAACCCTAACTTAACTTAATGTAAAACCCTACCTAACTTAATTTAATTAAAAA
1 TAATTTAATTAAAAACCCTAACCTAACTTAATGTAAAA--C--CCTAACCTAATTGAATTAAAAA
15417539 CCC
62 CCC
*
15417542 TAACCTAACTTAATTAAAAATCCTAACCTAACTTAATGTAAAACCCTAACCTAATTGAATTAAAA
1 TAA--T---TTAATTAAAAACCCTAACCTAACTTAATGTAAAACCCTAACCTAATTGAATTAAAA
15417607 A-CC
61 ACCC
15417610 TAATTTAATTAAAAACCCTAACCTAACTTAATGTAAAACCCTAACC
1 TAATTTAATTAAAAACCCTAACCTAACTTAATGTAAAACCCTAACC
15417656 CTAAGCTAAT
Statistics
Matches: 104, Mismatches: 5, Indels: 15
0.84 0.04 0.12
Matches are distributed among these distances:
63 41 0.39
66 1 0.01
68 8 0.08
69 20 0.19
70 1 0.01
71 1 0.01
73 32 0.31
ACGTcount: A:0.46, C:0.22, G:0.02, T:0.30
Consensus pattern (64 bp):
TAATTTAATTAAAAACCCTAACCTAACTTAATGTAAAACCCTAACCTAATTGAATTAAAAACCC
Found at i:15421745 original size:39 final size:39
Alignment explanation
Indices: 15421686--15421761 Score: 143
Period size: 39 Copynumber: 1.9 Consensus size: 39
15421676 CCATAAAACC
15421686 CAAACGTAAAATCAGCGTCAAAATCGCGTCCCCGGTATA
1 CAAACGTAAAATCAGCGTCAAAATCGCGTCCCCGGTATA
*
15421725 CAAACGTAAAATCAGTGTCAAAATCGCGTCCCCGGTA
1 CAAACGTAAAATCAGCGTCAAAATCGCGTCCCCGGTA
15421762 CCGCGCTACG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.36, C:0.28, G:0.18, T:0.18
Consensus pattern (39 bp):
CAAACGTAAAATCAGCGTCAAAATCGCGTCCCCGGTATA
Found at i:15429529 original size:44 final size:43
Alignment explanation
Indices: 15429481--15429717 Score: 233
Period size: 44 Copynumber: 5.8 Consensus size: 43
15429471 CTTGGAAAGT
*
15429481 AGTGGAATAGGTTGAAGATTGTAAGTCCTATCTCCCTGGCCAGC
1 AGTGGAATAGGTTGAAGATTGTAA-TCCTATCTCCCTGGTCAGC
15429525 AGTGG-A-A---T-AAG--TG-AATCCTATCTCCCTGGTCAGC
1 AGTGGAATAGGTTGAAGATTGTAATCCTATCTCCCTGGTCAGC
*
15429559 AGTGGAATAGGTTGAAGATTGTAAGTCCTATCTTCCTGGTCAGC
1 AGTGGAATAGGTTGAAGATTGTAA-TCCTATCTCCCTGGTCAGC
*
15429603 AGTGGAATA----G--G--TG-AATCTTATCTCCCTGGTCAGC
1 AGTGGAATAGGTTGAAGATTGTAATCCTATCTCCCTGGTCAGC
15429637 AGTGGAATAGGTTGAAGATTGTAAATCCTATCTCCCTGAG-CAGC
1 AGTGGAATAGGTTGAAGATTGT-AATCCTATCTCCCTG-GTCAGC
* * * *
15429681 AGTGGAGTAGGTTGAAAATTATAGATCTTATCTCCCT
1 AGTGGAATAGGTTGAAGATTGTA-ATCCTATCTCCCT
15429718 AAGCAGTAGT
Statistics
Matches: 162, Mismatches: 9, Indels: 44
0.75 0.04 0.20
Matches are distributed among these distances:
34 49 0.30
35 5 0.03
36 5 0.03
38 5 0.03
39 2 0.01
40 5 0.03
42 5 0.03
43 4 0.02
44 81 0.50
45 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.30
Consensus pattern (43 bp):
AGTGGAATAGGTTGAAGATTGTAATCCTATCTCCCTGGTCAGC
Found at i:15429544 original size:34 final size:34
Alignment explanation
Indices: 15429506--15429645 Score: 154
Period size: 34 Copynumber: 3.8 Consensus size: 34
15429496 AGATTGTAAG
*
15429506 TCCTATCTCCCTGGCCAGCAGTGGAATAAGTGAA
1 TCCTATCTCCCTGGTCAGCAGTGGAATAAGTGAA
15429540 TCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTAA
1 TCCTATCTCCCTGGTCAGCAGTGG-A-A---T-AAG--TG-AA
* *
15429583 GTCCTATCTTCCTGGTCAGCAGTGGAATAGGTGAA
1 -TCCTATCTCCCTGGTCAGCAGTGGAATAAGTGAA
*
15429618 TCTTATCTCCCTGGTCAGCAGTGGAATA
1 TCCTATCTCCCTGGTCAGCAGTGGAATA
15429646 GGTTGAAGAT
Statistics
Matches: 91, Mismatches: 5, Indels: 20
0.78 0.04 0.17
Matches are distributed among these distances:
34 49 0.54
35 3 0.03
36 3 0.03
38 2 0.02
39 2 0.02
40 3 0.03
42 3 0.03
43 3 0.03
44 23 0.25
ACGTcount: A:0.24, C:0.22, G:0.25, T:0.29
Consensus pattern (34 bp):
TCCTATCTCCCTGGTCAGCAGTGGAATAAGTGAA
Found at i:15429692 original size:78 final size:78
Alignment explanation
Indices: 15429481--15429692 Score: 354
Period size: 78 Copynumber: 2.7 Consensus size: 78
15429471 CTTGGAAAGT
*
15429481 AGTGGAATAGGTTGAAGATTGTAAGTCCTATCTCCCTGGCCAGCAGTGGAATAAGTGAATCCTAT
1 AGTGGAATAGGTTGAAGATTGTAAGTCCTATCTCCCTGGCCAGCAGTGGAATAGGTGAATCCTAT
15429546 CTCCCTGGTCAGC
66 CTCCCTGGTCAGC
* * *
15429559 AGTGGAATAGGTTGAAGATTGTAAGTCCTATCTTCCTGGTCAGCAGTGGAATAGGTGAATCTTAT
1 AGTGGAATAGGTTGAAGATTGTAAGTCCTATCTCCCTGGCCAGCAGTGGAATAGGTGAATCCTAT
15429624 CTCCCTGGTCAGC
66 CTCCCTGGTCAGC
* *
15429637 AGTGGAATAGGTTGAAGATTGTAAATCCTATCTCCCTGAG-CAGCAGTGGAGTAGGT
1 AGTGGAATAGGTTGAAGATTGTAAGTCCTATCTCCCTG-GCCAGCAGTGGAATAGGT
15429693 TGAAAATTAT
Statistics
Matches: 126, Mismatches: 7, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
78 125 0.99
79 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.28
Consensus pattern (78 bp):
AGTGGAATAGGTTGAAGATTGTAAGTCCTATCTCCCTGGCCAGCAGTGGAATAGGTGAATCCTAT
CTCCCTGGTCAGC
Found at i:15429723 original size:44 final size:43
Alignment explanation
Indices: 15429616--15429731 Score: 142
Period size: 44 Copynumber: 2.6 Consensus size: 43
15429606 GGAATAGGTG
* * * *
15429616 AATCTTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTA
1 AATCTTATCTCCCTAG-CAGCAGTGGAGTAGGTTGAAAATTATA
*
15429660 AATCCTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATTATA
1 AATCTTATCTCCCT-AGCAGCAGTGGAGTAGGTTGAAAATTATA
* *
15429704 GATCTTATCTCCCTAAGCAGTAGTGGAG
1 AATCTTATCTCCCT-AGCAGCAGTGGAG
15429732 CAGATCGATG
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
44 61 0.98
45 1 0.02
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.29
Consensus pattern (43 bp):
AATCTTATCTCCCTAGCAGCAGTGGAGTAGGTTGAAAATTATA
Found at i:15429944 original size:50 final size:50
Alignment explanation
Indices: 15429864--15430032 Score: 187
Period size: 50 Copynumber: 3.4 Consensus size: 50
15429854 TTTGGCATTA
* *
15429864 CAGTGGAATAGATTGAAGCCACAACGGTGAATCTTTCTTCCCTGGCGGTG
1 CAGTGGAACAGATTGAAGCCACAACGGTGAATCTTTCTTCCCTGGCAGTG
* * * *** *
15429914 CAGTGGAACAGATTGAAGCTACGACAGTGAATCTTGT-TTCCCCAACATTG
1 CAGTGGAACAGATTGAAGCCACAACGGTGAATCTT-TCTTCCCTGGCAGTG
** * *
15429964 CAGTTAAATAGATTGAAGCCACAACGGTGAATCTTACTTCCCTGGCAGTG
1 CAGTGGAACAGATTGAAGCCACAACGGTGAATCTTTCTTCCCTGGCAGTG
* *
15430014 TAGTGGAACAGATTAAAGC
1 CAGTGGAACAGATTGAAGC
15430033 TAAAGGTAGC
Statistics
Matches: 92, Mismatches: 25, Indels: 4
0.76 0.21 0.03
Matches are distributed among these distances:
50 91 0.99
51 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.25
Consensus pattern (50 bp):
CAGTGGAACAGATTGAAGCCACAACGGTGAATCTTTCTTCCCTGGCAGTG
Found at i:15430056 original size:51 final size:51
Alignment explanation
Indices: 15429992--15430114 Score: 117
Period size: 51 Copynumber: 2.4 Consensus size: 51
15429982 CCACAACGGT
* * * *
15429992 GAATCTTACTTCCCTGGCAG-TGTAGTGGAACAGATTAAAGC-TAAAGGTAGC
1 GAATCTTACTTCCCTAGC-GTTGTAGCGGAACAGAATAAAGCAT-AAGGCAGC
** * *
15430043 GAATCTTGTTTCCCTAGCGTTGTAGCGGAGCAGAATAAAGCATAGGGCAGC
1 GAATCTTACTTCCCTAGCGTTGTAGCGGAACAGAATAAAGCATAAGGCAGC
*
15430094 GAATCTTA-TCCCCCTAGCGTT
1 GAATCTTACT-TCCCTAGCGTT
15430115 AAGACTTGGA
Statistics
Matches: 59, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
50 2 0.03
51 56 0.95
52 1 0.02
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.26
Consensus pattern (51 bp):
GAATCTTACTTCCCTAGCGTTGTAGCGGAACAGAATAAAGCATAAGGCAGC
Found at i:15430868 original size:22 final size:21
Alignment explanation
Indices: 15430827--15430887 Score: 72
Period size: 19 Copynumber: 2.9 Consensus size: 21
15430817 AATCTTCAAG
15430827 GATATGCAATCTT--AGATAT
1 GATATGCAATCTTAAAGATAT
15430846 GATATGCAATCTTAGAAGATAT
1 GATATGCAATCTTA-AAGATAT
* *
15430868 GATTTTGTAATCTTAAAGAT
1 GA-TATGCAATCTTAAAGAT
15430888 TTAATTTGTA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
19 13 0.36
22 13 0.36
23 10 0.28
ACGTcount: A:0.38, C:0.08, G:0.16, T:0.38
Consensus pattern (21 bp):
GATATGCAATCTTAAAGATAT
Found at i:15430897 original size:21 final size:23
Alignment explanation
Indices: 15430840--15430897 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 23
15430830 ATGCAATCTT
* *
15430840 AGATATG-ATATGCAATCTTAGA
1 AGATATGAATTTGTAATCTTAGA
*
15430862 AGATATGATTTTGTAATCTTA-A
1 AGATATGAATTTGTAATCTTAGA
*
15430884 AGAT-TTAATTTGTA
1 AGATATGAATTTGTA
15430898 GATATCCTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
21 8 0.27
22 12 0.40
23 10 0.33
ACGTcount: A:0.38, C:0.05, G:0.16, T:0.41
Consensus pattern (23 bp):
AGATATGAATTTGTAATCTTAGA
Found at i:15431132 original size:23 final size:23
Alignment explanation
Indices: 15431088--15431132 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
15431078 TCTTATTTTG
* *
15431088 TTGATTTGTGTATAATTTATTTA
1 TTGATTTGTATATAATTGATTTA
**
15431111 TTGATTTGTATATTGTTGATTT
1 TTGATTTGTATATAATTGATTT
15431133 CGAATCTCTT
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:15438832 original size:31 final size:31
Alignment explanation
Indices: 15438797--15438858 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
15438787 TTCAACACAC
15438797 AAATCATGAATTACATTACCTTATTTAACAA
1 AAATCATGAATTACATTACCTTATTTAACAA
15438828 AAATCATGAATTACATTACCTTATTTAACAA
1 AAATCATGAATTACATTACCTTATTTAACAA
15438859 TATACTAAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.45, C:0.16, G:0.03, T:0.35
Consensus pattern (31 bp):
AAATCATGAATTACATTACCTTATTTAACAA
Found at i:15442812 original size:5 final size:5
Alignment explanation
Indices: 15442746--15442800 Score: 110
Period size: 5 Copynumber: 11.0 Consensus size: 5
15442736 CTTATAATTC
15442746 ATCAT ATCAT ATCAT ATCAT ATCAT ATCAT ATCAT ATCAT ATCAT ATCAT
1 ATCAT ATCAT ATCAT ATCAT ATCAT ATCAT ATCAT ATCAT ATCAT ATCAT
15442796 ATCAT
1 ATCAT
15442801 TTCCATTTCA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 50 1.00
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (5 bp):
ATCAT
Found at i:15443118 original size:29 final size:29
Alignment explanation
Indices: 15442982--15443106 Score: 139
Period size: 29 Copynumber: 4.3 Consensus size: 29
15442972 TGGTATCCAT
* *
15442982 CACCGGTACATAGCACCTGATAAATATAA
1 CACCGGTACAAAGTACCTGATAAATATAA
* * *
15443011 CACCGATATAGAATGT--CTGAT-ACTATAA
1 CACCGGTACA-AA-GTACCTGATAAATATAA
15443039 CACCGGTACAAAGTACCTGATAAATATAA
1 CACCGGTACAAAGTACCTGATAAATATAA
* * *
15443068 TACCAGTACAAAGCACCTGATAAATATAA
1 CACCGGTACAAAGTACCTGATAAATATAA
15443097 CACCGGTACA
1 CACCGGTACA
15443107 GAGTTTCTGA
Statistics
Matches: 78, Mismatches: 13, Indels: 10
0.77 0.13 0.10
Matches are distributed among these distances:
26 2 0.03
27 2 0.03
28 19 0.24
29 53 0.68
30 1 0.01
31 1 0.01
ACGTcount: A:0.42, C:0.22, G:0.14, T:0.22
Consensus pattern (29 bp):
CACCGGTACAAAGTACCTGATAAATATAA
Found at i:15446344 original size:2 final size:2
Alignment explanation
Indices: 15446337--15446361 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
15446327 ATTCATCTAC
15446337 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
15446362 TCATANNNNN
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:15454306 original size:37 final size:37
Alignment explanation
Indices: 15454265--15454340 Score: 152
Period size: 37 Copynumber: 2.1 Consensus size: 37
15454255 TGAAAAGAAT
15454265 ATAATTTTTTTGTTTTATTATTATAATTACTTAAACA
1 ATAATTTTTTTGTTTTATTATTATAATTACTTAAACA
15454302 ATAATTTTTTTGTTTTATTATTATAATTACTTAAACA
1 ATAATTTTTTTGTTTTATTATTATAATTACTTAAACA
15454339 AT
1 AT
15454341 TAAAATAATA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.36, C:0.05, G:0.03, T:0.57
Consensus pattern (37 bp):
ATAATTTTTTTGTTTTATTATTATAATTACTTAAACA
Found at i:15456845 original size:19 final size:19
Alignment explanation
Indices: 15456812--15456851 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
15456802 AAAATATCAT
*
15456812 ATTAATTTTAATTTATTTG
1 ATTAATTTTAATTTACTTG
15456831 ATTAA-TTTAATTTTACTTG
1 ATTAATTTTAA-TTTACTTG
15456850 AT
1 AT
15456852 CAAAATTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.33, C:0.03, G:0.05, T:0.60
Consensus pattern (19 bp):
ATTAATTTTAATTTACTTG
Found at i:15458454 original size:2 final size:2
Alignment explanation
Indices: 15458449--15458487 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
15458439 GGTATATATA
15458449 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
15458488 ACTTAAGATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:15458671 original size:42 final size:42
Alignment explanation
Indices: 15458619--15458791 Score: 242
Period size: 42 Copynumber: 4.1 Consensus size: 42
15458609 CAGTGCCTAT
*
15458619 CAGGTTTAATGCCGGTGAAACAATATCAGACTTTACGTCTAG
1 CAGGCTTAATGCCGGTGAAACAATATCAGACTTTACGTCTAG
* * *
15458661 CAGGCTTAATGCCGGTGAAATAAT-TCCAGACTTTACATTTAG
1 CAGGCTTAATGCCGGTGAAACAATAT-CAGACTTTACGTCTAG
*
15458703 CAGGCTTAATGCCGGTGAAACAATATCAGACTTTACGTCTAC
1 CAGGCTTAATGCCGGTGAAACAATATCAGACTTTACGTCTAG
* * *
15458745 CAGGCTTAATGCCGGTGAAAC-ATTTCAGACTATATGTCTAG
1 CAGGCTTAATGCCGGTGAAACAATATCAGACTTTACGTCTAG
*
15458786 TAGGCT
1 CAGGCT
15458792 AAGTGTCGGT
Statistics
Matches: 116, Mismatches: 13, Indels: 5
0.87 0.10 0.04
Matches are distributed among these distances:
41 22 0.19
42 93 0.80
43 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (42 bp):
CAGGCTTAATGCCGGTGAAACAATATCAGACTTTACGTCTAG
Found at i:15460751 original size:15 final size:15
Alignment explanation
Indices: 15460727--15460758 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
15460717 TATGCATGCA
*
15460727 AAATATAAAAGACAT
1 AAATACAAAAGACAT
15460742 AAATACAAAAGACAT
1 AAATACAAAAGACAT
15460757 AA
1 AA
15460759 TAGTGAAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.69, C:0.09, G:0.06, T:0.16
Consensus pattern (15 bp):
AAATACAAAAGACAT
Found at i:15462189 original size:29 final size:29
Alignment explanation
Indices: 15462153--15462218 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 29
15462143 AAAAAAGTTA
15462153 AATTTTAATTCATATAC-TTTAATTTAATT
1 AATTTTAATTCATATACATTTAA-TTAATT
** *
15462182 AATTTTAATTTTTGTACTATTTAATTAATT
1 AATTTTAATTCATATAC-ATTTAATTAATT
15462212 AATTTTA
1 AATTTTA
15462219 GTTCTTGTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 14 0.44
30 13 0.41
31 5 0.16
ACGTcount: A:0.36, C:0.05, G:0.02, T:0.58
Consensus pattern (29 bp):
AATTTTAATTCATATACATTTAATTAATT
Found at i:15462212 original size:30 final size:30
Alignment explanation
Indices: 15462153--15462250 Score: 105
Period size: 30 Copynumber: 3.3 Consensus size: 30
15462143 AAAAAAGTTA
* *
15462153 AATTTTAATTCATATAC-TTTAATTTAATT
1 AATTTTAATTCTTGTACTTTTAATTTAATT
*
15462182 AATTTTAATTTTTGTACTATTTAA-TTAATT
1 AATTTTAATTCTTGTACT-TTTAATTTAATT
*
15462212 AATTTTAGTTCTTGTACTTTTAAAATTTAA--
1 AATTTTAATTCTTGTACTTTT--AATTTAATT
15462242 AATTTTAAT
1 AATTTTAAT
15462251 CATGACCCTA
Statistics
Matches: 58, Mismatches: 6, Indels: 9
0.79 0.08 0.12
Matches are distributed among these distances:
29 17 0.29
30 30 0.52
31 7 0.12
32 4 0.07
ACGTcount: A:0.36, C:0.05, G:0.03, T:0.56
Consensus pattern (30 bp):
AATTTTAATTCTTGTACTTTTAATTTAATT
Found at i:15463910 original size:2 final size:2
Alignment explanation
Indices: 15463903--15463927 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
15463893 TGATACCATT
15463903 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
15463928 TGAGCTAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:15467317 original size:19 final size:19
Alignment explanation
Indices: 15467293--15467403 Score: 143
Period size: 19 Copynumber: 5.8 Consensus size: 19
15467283 AATCATATAT
*
15467293 TCTAAGATTGCATGTCATA
1 TCTAAGATTGCATATCATA
* * * *
15467312 TCTAAGACT-AAGATTATTA
1 TCTAAGATTGCATATCA-TA
15467331 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
15467350 TCTAAGATTGCATATCAAA
1 TCTAAGATTGCATATCATA
*
15467369 TCTAGGATTGCATATCATA
1 TCTAAGATTGCATATCATA
15467388 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
15467404 CTCAAAAATT
Statistics
Matches: 77, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
18 3 0.04
19 70 0.91
20 4 0.05
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:15468788 original size:16 final size:15
Alignment explanation
Indices: 15468760--15468814 Score: 51
Period size: 16 Copynumber: 3.6 Consensus size: 15
15468750 ATAAGTTAAG
*
15468760 ATTTTT-TAATTTTA
1 ATTTTTATATTTTTA
15468774 ATTTTATATATTTTTA
1 ATTTT-TATATTTTTA
15468790 ATTCTTCT-TATTTTTA
1 ATT-TT-TATATTTTTA
*
15468806 GTTTTTATA
1 ATTTTTATA
15468815 ATAATGTTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
14 6 0.18
15 5 0.15
16 20 0.59
17 3 0.09
ACGTcount: A:0.25, C:0.04, G:0.02, T:0.69
Consensus pattern (15 bp):
ATTTTTATATTTTTA
Found at i:15469624 original size:22 final size:22
Alignment explanation
Indices: 15469599--15469646 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
15469589 AAATAATGAG
* *
15469599 AAAACAACAAGAAAATAACAAC
1 AAAACAACAAAAAAATAACAAA
**
15469621 AAAACATTAAAAAAATAACAAA
1 AAAACAACAAAAAAATAACAAA
15469643 AAAA
1 AAAA
15469647 TCAATAGGTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.77, C:0.12, G:0.02, T:0.08
Consensus pattern (22 bp):
AAAACAACAAAAAAATAACAAA
Found at i:15472145 original size:23 final size:21
Alignment explanation
Indices: 15472115--15472161 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 21
15472105 ATAACAGTTC
* *
15472115 AAAAATTTTCTTTTCATTTATT
1 AAAAATTTT-TCTACATTTATT
15472137 AAAAGATTTTTCTACATTTATT
1 AAAA-ATTTTTCTACATTTATT
15472159 AAA
1 AAA
15472162 TCTATATTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.38, C:0.09, G:0.02, T:0.51
Consensus pattern (21 bp):
AAAAATTTTTCTACATTTATT
Found at i:15475005 original size:22 final size:22
Alignment explanation
Indices: 15474980--15475032 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
15474970 GAAATTAAAT
15474980 TATATATTTATGATATTAAAAA
1 TATATATTTATGATATTAAAAA
* * *
15475002 TATA-ATTTTATTATTTTAATAA
1 TATATA-TTTATGATATTAAAAA
*
15475024 TTTATATTT
1 TATATATTT
15475033 TTATAATTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
21 1 0.04
22 23 0.92
23 1 0.04
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (22 bp):
TATATATTTATGATATTAAAAA
Found at i:15475033 original size:15 final size:16
Alignment explanation
Indices: 15475003--15475041 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
15474993 TATTAAAAAT
15475003 ATAATTTTATTATTTTA
1 ATAA-TTTATTATTTTA
*
15475020 ATAATTTA-TATTTTT
1 ATAATTTATTATTTTA
15475035 ATAATTT
1 ATAATTT
15475042 TTAAAAGATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 13 0.62
16 4 0.19
17 4 0.19
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
ATAATTTATTATTTTA
Found at i:15476253 original size:14 final size:14
Alignment explanation
Indices: 15476234--15476272 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
15476224 TCATTAGTTT
15476234 ATATGTCATAAACC
1 ATATGTCATAAACC
* * *
15476248 ATATGTTATTAAGC
1 ATATGTCATAAACC
15476262 ATATGTCATAA
1 ATATGTCATAA
15476273 TTTATTAAGC
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.41, C:0.13, G:0.10, T:0.36
Consensus pattern (14 bp):
ATATGTCATAAACC
Found at i:15477145 original size:13 final size:13
Alignment explanation
Indices: 15477127--15477151 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
15477117 GGGAAGGAAG
15477127 CGTTTAGAGGGAT
1 CGTTTAGAGGGAT
15477140 CGTTTAGAGGGA
1 CGTTTAGAGGGA
15477152 AGAAAGAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.08, G:0.40, T:0.28
Consensus pattern (13 bp):
CGTTTAGAGGGAT
Found at i:15478049 original size:14 final size:15
Alignment explanation
Indices: 15478030--15478062 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
15478020 CCTATTACAT
15478030 AAAATAAA-ATATTA
1 AAAATAAATATATTA
*
15478044 AAAATAAATATTTTA
1 AAAATAAATATATTA
15478059 AAAA
1 AAAA
15478063 AGACATGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
AAAATAAATATATTA
Found at i:15479020 original size:2 final size:2
Alignment explanation
Indices: 15478968--15479002 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
15478958 TCAATCTCAA
15478968 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
15479003 ACATTCTCAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:15482041 original size:19 final size:19
Alignment explanation
Indices: 15482007--15482062 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 19
15481997 TTACATCTCA
15482007 AAAAAT-TATAAAAAAAC-T
1 AAAAATATAT-AAAAAACTT
15482025 AAAGAATATATAAAAAACACTT
1 AAA-AATATAT-AAAAA-ACTT
15482047 AAAAATATATAAAAAA
1 AAAAATATATAAAAAA
15482063 GACTCAAAAC
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
18 3 0.09
19 4 0.12
20 14 0.41
21 9 0.26
22 4 0.12
ACGTcount: A:0.71, C:0.05, G:0.02, T:0.21
Consensus pattern (19 bp):
AAAAATATATAAAAAACTT
Found at i:15482078 original size:23 final size:21
Alignment explanation
Indices: 15482007--15482071 Score: 82
Period size: 21 Copynumber: 3.2 Consensus size: 21
15481997 TTACATCTCA
15482007 AAAAAT-TATAAAAAA-ACT-
1 AAAAATATATAAAAAACACTC
*
15482025 AAAGAATATATAAAAAACACTT
1 AAA-AATATATAAAAAACACTC
*
15482047 AAAAATATATAAAAAAGACTC
1 AAAAATATATAAAAAACACTC
15482068 AAAA
1 AAAA
15482072 CCCTATACAA
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
18 3 0.07
19 3 0.07
20 9 0.22
21 23 0.56
22 3 0.07
ACGTcount: A:0.69, C:0.08, G:0.03, T:0.20
Consensus pattern (21 bp):
AAAAATATATAAAAAACACTC
Found at i:15482109 original size:21 final size:21
Alignment explanation
Indices: 15482083--15482123 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
15482073 CCTATACAAT
* * *
15482083 CCTAAATCTTAAATCTTAAAC
1 CCTAAACCCTAAATCCTAAAC
15482104 CCTAAACCCTAAATCCTAAA
1 CCTAAACCCTAAATCCTAAA
15482124 ATTCATACAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.44, C:0.29, G:0.00, T:0.27
Consensus pattern (21 bp):
CCTAAACCCTAAATCCTAAAC
Found at i:15488413 original size:28 final size:28
Alignment explanation
Indices: 15488376--15488433 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
15488366 TAATAAATAC
*
15488376 AATATTGAGTTAATATATAATAAAAATT
1 AATATCGAGTTAATATATAATAAAAATT
15488404 AATATCGAGTTAATATATAATAAAAATT
1 AATATCGAGTTAATATATAATAAAAATT
15488432 AA
1 AA
15488434 GCCTAAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.55, C:0.02, G:0.07, T:0.36
Consensus pattern (28 bp):
AATATCGAGTTAATATATAATAAAAATT
Found at i:15505442 original size:20 final size:20
Alignment explanation
Indices: 15505419--15505456 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
15505409 TTAGTTTGGC
*
15505419 TTAATGATGATTAGATTAGT
1 TTAATGATGATTAAATTAGT
15505439 TTAATGATGATTAAATTA
1 TTAATGATGATTAAATTA
15505457 AAGTTAACTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.00, G:0.16, T:0.45
Consensus pattern (20 bp):
TTAATGATGATTAAATTAGT
Found at i:15509906 original size:51 final size:52
Alignment explanation
Indices: 15509849--15509961 Score: 140
Period size: 51 Copynumber: 2.2 Consensus size: 52
15509839 CCAATTCATT
*
15509849 TTCATTTTCATTTTA-AAGAAAACCACATTCATTTACAAATGATT-CCATCTC
1 TTCATTTTCA-TTTAGAAGAAAACCACAATCATTTACAAATGATTCCCATCTC
* * * * * *
15509900 TTCATTTTCATTTAGGAGAAAACCATAATCATTTCCAAATGTTTCCCATTTT
1 TTCATTTTCATTTAGAAGAAAACCACAATCATTTACAAATGATTCCCATCTC
15509952 TTCATTTTCA
1 TTCATTTTCA
15509962 CCATATCTAA
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
50 4 0.08
51 34 0.64
52 15 0.28
ACGTcount: A:0.32, C:0.20, G:0.05, T:0.42
Consensus pattern (52 bp):
TTCATTTTCATTTAGAAGAAAACCACAATCATTTACAAATGATTCCCATCTC
Found at i:15517234 original size:20 final size:20
Alignment explanation
Indices: 15517202--15517322 Score: 118
Period size: 20 Copynumber: 6.0 Consensus size: 20
15517192 AGAATGTGTG
* * *
15517202 CTTCGATGCCTCTATTTGCT
1 CTTCGGTGCCTCTGTTTGCA
*
15517222 CTTCGGTGTCTCTGTTTGCA
1 CTTCGGTGCCTCTGTTTGCA
*
15517242 CTTTGGTGCCTCTGTTTGCA
1 CTTCGGTGCCTCTGTTTGCA
*
15517262 CTTCGGTGCCTCTGATTGCA
1 CTTCGGTGCCTCTGTTTGCA
* * * *
15517282 TATTC-ATGCCCCTGTCTGCA
1 -CTTCGGTGCCTCTGTTTGCA
*
15517302 CTTTGGTGCCTCTGTTATGCA
1 CTTCGGTGCCTCTGTT-TGCA
15517323 TTTATGATGT
Statistics
Matches: 80, Mismatches: 18, Indels: 5
0.78 0.17 0.05
Matches are distributed among these distances:
19 2 0.03
20 71 0.89
21 7 0.09
ACGTcount: A:0.09, C:0.28, G:0.21, T:0.41
Consensus pattern (20 bp):
CTTCGGTGCCTCTGTTTGCA
Found at i:15517843 original size:5 final size:5
Alignment explanation
Indices: 15517833--15517859 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
15517823 TAAATTTTTT
15517833 TGAAA TGAAA TGAAA TGAAA TGAAA TG
1 TGAAA TGAAA TGAAA TGAAA TGAAA TG
15517860 TTTTGTTTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.56, C:0.00, G:0.22, T:0.22
Consensus pattern (5 bp):
TGAAA
Found at i:15518172 original size:27 final size:27
Alignment explanation
Indices: 15518112--15518182 Score: 67
Period size: 27 Copynumber: 2.7 Consensus size: 27
15518102 TGTCAATTGT
15518112 AAAAATG-AATGATATGCGAAGTGTGA
1 AAAAATGTAATGATATGCGAAGTGTGA
**
15518138 AAGTATGTAATGGTATATG-GAAGT-TGA
1 AAAAATGTAAT-G-ATATGCGAAGTGTGA
* *
15518165 AAAAATGTCATGTTATGC
1 AAAAATGTAATGATATGC
15518183 ACCCTGTGCC
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
25 4 0.11
26 6 0.17
27 14 0.40
28 6 0.17
29 5 0.14
ACGTcount: A:0.41, C:0.04, G:0.25, T:0.30
Consensus pattern (27 bp):
AAAAATGTAATGATATGCGAAGTGTGA
Found at i:15532049 original size:22 final size:21
Alignment explanation
Indices: 15531987--15532053 Score: 64
Period size: 22 Copynumber: 3.1 Consensus size: 21
15531977 GGAGGAAGTG
* *
15531987 TATGACTTGTAGCCGTTCTGT
1 TATGGCTTTTAGCCGTTCTGT
* *
15532008 TCAAGGCTTTCT-GCCTTTCTGCT
1 T-ATGGCTTT-TAGCCGTTCTG-T
15532031 TATGGCTTTTAGCCGTTCTGT
1 TATGGCTTTTAGCCGTTCTGT
15532052 TA
1 TA
15532054 ACTGGTAGCG
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
21 5 0.14
22 28 0.78
23 3 0.08
ACGTcount: A:0.12, C:0.22, G:0.21, T:0.45
Consensus pattern (21 bp):
TATGGCTTTTAGCCGTTCTGT
Found at i:15535356 original size:3 final size:3
Alignment explanation
Indices: 15535348--15535421 Score: 148
Period size: 3 Copynumber: 24.7 Consensus size: 3
15535338 CTCTATAGGA
15535348 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
15535396 TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TC
15535422 GCGATCCTCA
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 71 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:15537211 original size:29 final size:30
Alignment explanation
Indices: 15537155--15537213 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
15537145 TACCTTTGAA
* *
15537155 AATATTTACAAAAAGAGACATCTAAAATTT
1 AATATTTACAAAAAGAGACAACCAAAATTT
15537185 AATATTTACAAAAAGA-ACAACCAAAATTT
1 AATATTTACAAAAAGAGACAACCAAAATTT
15537214 TTAAATAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 11 0.41
30 16 0.59
ACGTcount: A:0.56, C:0.12, G:0.05, T:0.27
Consensus pattern (30 bp):
AATATTTACAAAAAGAGACAACCAAAATTT
Found at i:15544395 original size:13 final size:13
Alignment explanation
Indices: 15544377--15544401 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
15544367 ACTAGATTTT
15544377 AACTAAGAAAATC
1 AACTAAGAAAATC
15544390 AACTAAGAAAAT
1 AACTAAGAAAAT
15544402 TAAAAGGTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.12, G:0.08, T:0.16
Consensus pattern (13 bp):
AACTAAGAAAATC
Found at i:15551324 original size:53 final size:52
Alignment explanation
Indices: 15551046--15551321 Score: 188
Period size: 52 Copynumber: 5.1 Consensus size: 52
15551036 TCAATGTCTT
* * *
15551046 AGCACCCAAAAAAACA--TTATCAGATAAAAGGGGTGTCGGA-CATTAATGTCCC
1 AGCACCC-AAAAAACATTTTATCAGAT-AAAGGGGTGTC-AACCATCAGTGTCCC
* * *
15551098 AGCACCCAAAAAACATTTTATCAAATAAAGGGATGTCAACCATCAGTATCCC
1 AGCACCCAAAAAACATTTTATCAGATAAAGGGGTGTCAACCATCAGTGTCCC
* * * ** *
15551150 AACACCCAAAAAATATTTTTTTTAATCAGATAAAGGGGGCGTCGGCCATCAGTGT-GC
1 AGCACCCAAAAAACA----TTTT-ATCAGATAAA-GGGGTGTCAACCATCAGTGTCCC
* *** * *
15551207 AGCACCC-CAAATTTTTTTAAAATCTA-ATAAAAGGGGTGTCGACTATCAGTGTCCC
1 AGCACCCAAAAAACATTTT---ATC-AGAT-AAAGGGGTGTCAACCATCAGTGTCCC
*
15551262 AGCACCCTAAAAAA-ATTTCTATCAGATAAAGGAGTGTCAACCATCAGTGTCCC
1 AGCACCC-AAAAAACATTT-TATCAGATAAAGGGGTGTCAACCATCAGTGTCCC
15551315 AGCACCC
1 AGCACCC
15551322 TAATTTTTTA
Statistics
Matches: 177, Mismatches: 29, Indels: 35
0.73 0.12 0.15
Matches are distributed among these distances:
51 9 0.05
52 43 0.24
53 39 0.22
54 28 0.16
55 12 0.07
56 11 0.06
57 20 0.11
58 15 0.08
ACGTcount: A:0.37, C:0.23, G:0.17, T:0.23
Consensus pattern (52 bp):
AGCACCCAAAAAACATTTTATCAGATAAAGGGGTGTCAACCATCAGTGTCCC
Found at i:15552790 original size:25 final size:25
Alignment explanation
Indices: 15552745--15552842 Score: 94
Period size: 25 Copynumber: 4.0 Consensus size: 25
15552735 GTCATTAGGG
*
15552745 TTACCGAT-TTCAGCTCTTATGAGC
1 TTACCGATATTCAGCTCGTATGAGC
* *
15552769 TTACCGATACTCAGATCGTATGAGC
1 TTACCGATATTCAGCTCGTATGAGC
* * * *
15552794 TTATCGTTATTCAGCTCGGAGGAGC
1 TTACCGATATTCAGCTCGTATGAGC
*
15552819 TTACCG-TTTATC-GCTCGTATGAGC
1 TTACCGATAT-TCAGCTCGTATGAGC
15552843 ATACATATAC
Statistics
Matches: 59, Mismatches: 13, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
24 20 0.34
25 39 0.66
ACGTcount: A:0.21, C:0.23, G:0.21, T:0.34
Consensus pattern (25 bp):
TTACCGATATTCAGCTCGTATGAGC
Found at i:15554029 original size:66 final size:66
Alignment explanation
Indices: 15553918--15554077 Score: 248
Period size: 66 Copynumber: 2.4 Consensus size: 66
15553908 AGTCAGTAGC
* * *
15553918 TTCACATGGCCTAGCACACAGGCGTGTGGCTTGGCCGTGTGGCACAAGTCAGTATACCCTCCAGT
1 TTCACACGGCCTAGCACACGGGCGTGTGGCTTGGCCATGTGGCACAAGTCAGTATACCCTCCAGT
15553983 T
66 T
* * * *
15553984 TTCACACGGCCTAGCATATGGGCGTGTGTCTTGGCCATGTTGCACAAGTCAGTATACCCTCCAGT
1 TTCACACGGCCTAGCACACGGGCGTGTGGCTTGGCCATGTGGCACAAGTCAGTATACCCTCCAGT
15554049 T
66 T
*
15554050 TTCACACGGCCTAACACACGGGCGTGTG
1 TTCACACGGCCTAGCACACGGGCGTGTG
15554078 AGGCCATTTC
Statistics
Matches: 84, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
66 84 1.00
ACGTcount: A:0.20, C:0.29, G:0.26, T:0.25
Consensus pattern (66 bp):
TTCACACGGCCTAGCACACGGGCGTGTGGCTTGGCCATGTGGCACAAGTCAGTATACCCTCCAGT
T
Found at i:15557448 original size:46 final size:46
Alignment explanation
Indices: 15557387--15557494 Score: 135
Period size: 46 Copynumber: 2.3 Consensus size: 46
15557377 TTAAAGGCTA
* *
15557387 TAAATTTGAAGTGTTTAATTGTTGTAAATGGAGGTGTTCAAATCTTG
1 TAAA-TTGAAGTGTTTAAGTGTTGCAAATGGAGGTGTTCAAATCTTG
* * * * *
15557434 TAAATTGAAGTGTTTAGGTGTTGCAATTTGAGGTGTTTAAATGTTG
1 TAAATTGAAGTGTTTAAGTGTTGCAAATGGAGGTGTTCAAATCTTG
*
15557480 GAAATTGAAGTGTTT
1 TAAATTGAAGTGTTT
15557495 TCTTTAAATT
Statistics
Matches: 53, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
46 49 0.92
47 4 0.08
ACGTcount: A:0.29, C:0.03, G:0.26, T:0.43
Consensus pattern (46 bp):
TAAATTGAAGTGTTTAAGTGTTGCAAATGGAGGTGTTCAAATCTTG
Found at i:15557464 original size:23 final size:23
Alignment explanation
Indices: 15557392--15557494 Score: 98
Period size: 23 Copynumber: 4.5 Consensus size: 23
15557382 GGCTATAAAT
* *
15557392 TTGAAGTGTTTAATTGTTGTAAA
1 TTGAAGTGTTTAAATGTTGCAAA
* * * * *
15557415 TGGAGGTGTTCAAATCTTGTAAA
1 TTGAAGTGTTTAAATGTTGCAAA
** *
15557438 TTGAAGTGTTTAGGTGTTGCAAT
1 TTGAAGTGTTTAAATGTTGCAAA
* *
15557461 TTGAGGTGTTTAAATGTTGGAAA
1 TTGAAGTGTTTAAATGTTGCAAA
15557484 TTGAAGTGTTT
1 TTGAAGTGTTT
15557495 TCTTTAAATT
Statistics
Matches: 61, Mismatches: 19, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 61 1.00
ACGTcount: A:0.27, C:0.03, G:0.27, T:0.43
Consensus pattern (23 bp):
TTGAAGTGTTTAAATGTTGCAAA
Found at i:15565488 original size:34 final size:35
Alignment explanation
Indices: 15565390--15565489 Score: 118
Period size: 34 Copynumber: 2.9 Consensus size: 35
15565380 TTTAGAATTT
*
15565390 TTTTTAA-AGAAATTAATT-AATTTAGGTTTTA-AGG
1 TTTTTAAGA-AAATTAATTAAATTAAGG-TTTAGAGG
* * *
15565424 TTTCTAAGTAAATTAATTAAATTAGGGTTTAGA-G
1 TTTTTAAGAAAATTAATTAAATTAAGGTTTAGAGG
15565458 TTTTTAAGAAAATTAATTAAATTAAGGTTTAG
1 TTTTTAAGAAAATTAATTAAATTAAGGTTTAG
15565490 GATTTTTTGA
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
34 49 0.88
35 7 0.12
ACGTcount: A:0.40, C:0.01, G:0.15, T:0.44
Consensus pattern (35 bp):
TTTTTAAGAAAATTAATTAAATTAAGGTTTAGAGG
Found at i:15565980 original size:126 final size:126
Alignment explanation
Indices: 15565594--15565982 Score: 548
Period size: 126 Copynumber: 3.1 Consensus size: 126
15565584 GTTTTTTCTC
* * * *
15565594 CTACAATAGTTTCTGAAAAATTAATTTTGAGAAGACGATTCTGAAAAAATAGTGACAAAAACGTT
1 CTACAGTAGTTTCTGAAAAAATAATTTTGAGAAGACGATTCTGAAAAAATAGTGTCAAAAACGCT
* **
15565659 TCAAGCAGGATGCACTGTCAGCAAAAGTACTGAAAAAAGCTCCTACGTGGACATTCTTTTTT
66 TCAAGCAGGATGCACTGTCAGCAAAAGTACTGAAAAAAGCTCCAACGTGGACGCTC-TTTTT
* * * * * *
15565721 CTATAGTAATTTCTG-AAAAATAATTTTTAGAAGAC-AGTTCTGAAAAAATAATCTTAAAAACGC
1 CTACAGTAGTTTCTGAAAAAATAATTTTGAGAAGACGA-TTCTGAAAAAATAGTGTCAAAAACGC
* * *
15565784 TTCAAGCAGTATGCACTGTCAGCAAAAGTATTGAAAAAAGCTCCCACGTGGACGCTCTTTTT
65 TTCAAGCAGGATGCACTGTCAGCAAAAGTACTGAAAAAAGCTCCAACGTGGACGCTCTTTTT
* * * *
15565846 TTATAGTAGTTTCTGAAAAAATAAATTTGAGAAGACGATTCCGAAAAAATAGTGTCAAAAACGCT
1 CTACAGTAGTTTCTGAAAAAATAATTTTGAGAAGACGATTCTGAAAAAATAGTGTCAAAAACGCT
* *
15565911 TCAAGCAGGATGCACTGTCAGTAAAATTACTGAAAAAAGCTCCAACGTGGACGCTCTTTTT
66 TCAAGCAGGATGCACTGTCAGCAAAAGTACTGAAAAAAGCTCCAACGTGGACGCTCTTTTT
15565972 CTACAGTAGTT
1 CTACAGTAGTT
15565983 CGTGCTTGGC
Statistics
Matches: 229, Mismatches: 30, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
125 19 0.08
126 197 0.86
127 13 0.06
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.29
Consensus pattern (126 bp):
CTACAGTAGTTTCTGAAAAAATAATTTTGAGAAGACGATTCTGAAAAAATAGTGTCAAAAACGCT
TCAAGCAGGATGCACTGTCAGCAAAAGTACTGAAAAAAGCTCCAACGTGGACGCTCTTTTT
Found at i:15567648 original size:21 final size:21
Alignment explanation
Indices: 15567624--15567671 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
15567614 TTTAAGTTCG
15567624 AGTGGTAAAACCCTAAGGTCA
1 AGTGGTAAAACCCTAAGGTCA
* *
15567645 AGTGGTAAGACCCTGAGGTCA
1 AGTGGTAAAACCCTAAGGTCA
15567666 AGTGGT
1 AGTGGT
15567672 TTTAGAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.31, C:0.17, G:0.31, T:0.21
Consensus pattern (21 bp):
AGTGGTAAAACCCTAAGGTCA
Found at i:15569562 original size:14 final size:14
Alignment explanation
Indices: 15569543--15569571 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
15569533 GTCCTATTAC
15569543 TAAATTCATTAGTT
1 TAAATTCATTAGTT
15569557 TAAATTCATTAGTT
1 TAAATTCATTAGTT
15569571 T
1 T
15569572 TTGATTTCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.07, G:0.07, T:0.52
Consensus pattern (14 bp):
TAAATTCATTAGTT
Found at i:15574483 original size:22 final size:22
Alignment explanation
Indices: 15574458--15574641 Score: 224
Period size: 22 Copynumber: 8.1 Consensus size: 22
15574448 TGCACTAATG
15574458 AACAGAGAGCACAGATGTGCTA
1 AACAGAGAGCACAGATGTGCTA
15574480 AACAGAGAGCACAGATGTGCTA
1 AACAGAGAGCACAGATGTGCTA
15574502 AACAGAGAGCACAGATGTGCTA
1 AACAGAGAGCACAGATGTGCTA
* **
15574524 AACAGAGAGCACTGACATGCTAA
1 AACAGAGAGCACAGATGTGCT-A
* *
15574547 TAATCAGAGAGCACAAATTTGCTA
1 -AA-CAGAGAGCACAGATGTGCTA
* *
15574571 AACAGAGAGCACTGACGTGCTAA
1 AACAGAGAGCACAGATGTGCT-A
15574594 ATATCAGAGAGCACAGATGTGCTA
1 A-A-CAGAGAGCACAGATGTGCTA
* * *
15574618 AACAGAAAGCACTGACGTGCTA
1 AACAGAGAGCACAGATGTGCTA
15574640 AA
1 AA
15574642 TATCAGAGAG
Statistics
Matches: 140, Mismatches: 16, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
22 96 0.69
23 6 0.04
24 6 0.04
25 32 0.23
ACGTcount: A:0.41, C:0.19, G:0.24, T:0.16
Consensus pattern (22 bp):
AACAGAGAGCACAGATGTGCTA
Found at i:15574573 original size:47 final size:46
Alignment explanation
Indices: 15574460--15574652 Score: 291
Period size: 47 Copynumber: 4.2 Consensus size: 46
15574450 CACTAATGAA
* *
15574460 CAGAGAGCACAGATGTGCTAAACAGAGAGCACAGATGTGCT-AAA-
1 CAGAGAGCACAGATGTGCTAAACAGAGAGCACTGACGTGCTAAAAT
*
15574504 CAGAGAGCACAGATGTGCTAAACAGAGAGCACTGACATGCTAATAAT
1 CAGAGAGCACAGATGTGCTAAACAGAGAGCACTGACGTGCTAA-AAT
* *
15574551 CAGAGAGCACAAATTTGCTAAACAGAGAGCACTGACGTGCTAAATAT
1 CAGAGAGCACAGATGTGCTAAACAGAGAGCACTGACGTGCTAAA-AT
*
15574598 CAGAGAGCACAGATGTGCTAAACAGAAAGCACTGACGTGCTAAATAT
1 CAGAGAGCACAGATGTGCTAAACAGAGAGCACTGACGTGCTAAA-AT
15574645 CAGAGAGC
1 CAGAGAGC
15574653 GCGCTAGAGT
Statistics
Matches: 136, Mismatches: 9, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
44 38 0.28
45 1 0.01
46 3 0.02
47 94 0.69
ACGTcount: A:0.40, C:0.19, G:0.24, T:0.16
Consensus pattern (46 bp):
CAGAGAGCACAGATGTGCTAAACAGAGAGCACTGACGTGCTAAAAT
Found at i:15574639 original size:69 final size:66
Alignment explanation
Indices: 15574458--15574641 Score: 224
Period size: 69 Copynumber: 2.7 Consensus size: 66
15574448 TGCACTAATG
*
15574458 AACAGAGAGCACAGATGTGCTAAACAGAGAGCACAGATGTGCTAAACAGAGAGCACAGATGTGCT
1 AACAGAGAGCACAGATGTGCTAAACAGAGAGCACAGATGTGCTAAACAGAGAGCACAGACGTGCT
15574523 A
66 A
* ** * * *
15574524 AACAGAGAGCACTGACATGCTAATAATCAGAGAGCACAAATTTGCTAAACAGAGAGCACTGACGT
1 AACAGAGAGCACAGATGTGCT-A-AA-CAGAGAGCACAGATGTGCTAAACAGAGAGCACAGACGT
15574589 GCTAA
63 GCT-A
* * *
15574594 ATATCAGAGAGCACAGATGTGCTAAACAGAAAGCACTGACGTGCTAAA
1 A-A-CAGAGAGCACAGATGTGCTAAACAGAGAGCACAGATGTGCTAAA
15574642 TATCAGAGAG
Statistics
Matches: 97, Mismatches: 15, Indels: 9
0.80 0.12 0.07
Matches are distributed among these distances:
66 18 0.19
67 1 0.01
68 2 0.02
69 54 0.56
70 4 0.04
71 2 0.02
72 16 0.16
ACGTcount: A:0.41, C:0.19, G:0.24, T:0.16
Consensus pattern (66 bp):
AACAGAGAGCACAGATGTGCTAAACAGAGAGCACAGATGTGCTAAACAGAGAGCACAGACGTGCT
A
Found at i:15575024 original size:15 final size:16
Alignment explanation
Indices: 15574997--15575026 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
15574987 AATATAGATA
15574997 TTTAAATAAAATAATT
1 TTTAAATAAAATAATT
15575013 TTTAAA-AAAATAAT
1 TTTAAATAAAATAAT
15575027 CTTGTAGTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
TTTAAATAAAATAATT
Found at i:15575801 original size:29 final size:28
Alignment explanation
Indices: 15575736--15575801 Score: 64
Period size: 29 Copynumber: 2.3 Consensus size: 28
15575726 TCTTTTGTTT
*
15575736 TATATATATAATAATATAATATAATAGCA
1 TATATAT-TAATAATATAATATAATAGAA
*
15575765 TACT-TATTAATTAAGTA-AATATAATATAA
1 TA-TATATTAA-TAA-TATAATATAATAGAA
15575794 TATATATT
1 TATATATT
15575802 TTAAATTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
28 4 0.13
29 24 0.77
30 3 0.10
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (28 bp):
TATATATTAATAATATAATATAATAGAA
Found at i:15576108 original size:19 final size:19
Alignment explanation
Indices: 15576080--15576117 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 19
15576070 CATTTTTTTA
*
15576080 TTTAATCCATTTAAATCAAT
1 TTTAATCCATAT-AATCAAT
15576100 TTTAA-CCATATAATCAAT
1 TTTAATCCATATAATCAAT
15576118 AAAATTTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 7 0.41
19 5 0.29
20 5 0.29
ACGTcount: A:0.42, C:0.16, G:0.00, T:0.42
Consensus pattern (19 bp):
TTTAATCCATATAATCAAT
Found at i:15578109 original size:57 final size:59
Alignment explanation
Indices: 15577989--15578119 Score: 153
Period size: 62 Copynumber: 2.2 Consensus size: 59
15577979 TCTATTGCCT
**
15577989 TATTCAAACGAACTTTTATTTTATTAAATAGGATAAAATATAAAAATAATTGACTATTAAAA
1 TATTCAAAAAAACTTTTATTTTATTAAATA-GATAAAATATAAAAATAATTGA-TA-TAAAA
*
15578051 TATTCAAAAAAACTTTTATTTTATTAAATA-A-AATAATATAAAAATATATTG-TACAAATA
1 TATTCAAAAAAACTTTTATTTTATTAAATAGATAA-AATATAAAAATA-ATTGATATAAA-A
15578110 TATT-AAAAAA
1 TATTCAAAAAA
15578120 TTAATGCATG
Statistics
Matches: 63, Mismatches: 3, Indels: 10
0.83 0.04 0.13
Matches are distributed among these distances:
58 9 0.14
59 9 0.14
60 13 0.21
61 4 0.06
62 28 0.44
ACGTcount: A:0.53, C:0.05, G:0.04, T:0.37
Consensus pattern (59 bp):
TATTCAAAAAAACTTTTATTTTATTAAATAGATAAAATATAAAAATAATTGATATAAAA
Found at i:15578514 original size:18 final size:18
Alignment explanation
Indices: 15578473--15578515 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
15578463 GACTGAGAAA
* *
15578473 AGGAAACATATAAGGGTT
1 AGGATACATATAAGGGCT
*
15578491 AAGATACATATAAGGGCT
1 AGGATACATATAAGGGCT
15578509 AGGATAC
1 AGGATAC
15578516 GCACCTGGCA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.44, C:0.09, G:0.26, T:0.21
Consensus pattern (18 bp):
AGGATACATATAAGGGCT
Found at i:15582805 original size:18 final size:19
Alignment explanation
Indices: 15582759--15582806 Score: 64
Period size: 18 Copynumber: 2.5 Consensus size: 19
15582749 CAATTGATTT
15582759 TTAAAAAATATATTTTAAAA
1 TTAAAAAA-ATATTTTAAAA
15582779 -TATAAAAAATA-TTTAAAA
1 TTA-AAAAAATATTTTAAAA
15582797 TTAAAAAAAT
1 TTAAAAAAAT
15582807 GAAAAGAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
18 14 0.54
19 7 0.27
20 5 0.19
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
TTAAAAAAATATTTTAAAA
Found at i:15582805 original size:19 final size:20
Alignment explanation
Indices: 15582759--15582805 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
15582749 CAATTGATTT
*
15582759 TTAAAAAATATATTTTAAAA
1 TTAAAAAAAATATTTTAAAA
*
15582779 -TATAAAAAATA-TTTAAAA
1 TTAAAAAAAATATTTTAAAA
15582797 TTAAAAAAA
1 TTAAAAAAA
15582806 TGAAAAGAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
18 7 0.30
19 16 0.70
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (20 bp):
TTAAAAAAAATATTTTAAAA
Found at i:15583277 original size:24 final size:24
Alignment explanation
Indices: 15583250--15583316 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
15583240 TTAGTTAACA
15583250 TTGAATTATTTTTATTTTTTATTT
1 TTGAATTATTTTTATTTTTTATTT
***
15583274 TTGAATT-TTAAAGATTTTTTATTT
1 TTGAATTATT-TTTATTTTTTATTT
** *
15583298 TTTCATAATTTTTATTTTT
1 TTGAATTATTTTTATTTTT
15583317 AAAAATTAAA
Statistics
Matches: 32, Mismatches: 9, Indels: 4
0.71 0.20 0.09
Matches are distributed among these distances:
23 2 0.06
24 28 0.88
25 2 0.06
ACGTcount: A:0.24, C:0.01, G:0.04, T:0.70
Consensus pattern (24 bp):
TTGAATTATTTTTATTTTTTATTT
Found at i:15583975 original size:1 final size:1
Alignment explanation
Indices: 15583969--15584002 Score: 68
Period size: 1 Copynumber: 34.0 Consensus size: 1
15583959 TTCTCGCAGC
15583969 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
15584003 CCAACAACAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:15587964 original size:18 final size:18
Alignment explanation
Indices: 15587941--15587975 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
15587931 AGTGAGAACC
*
15587941 TCACAACCACAGCCACAG
1 TCACAACCACAACCACAG
15587959 TCACAACCACAACCACA
1 TCACAACCACAACCACA
15587976 ACCTCATGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.43, C:0.46, G:0.06, T:0.06
Consensus pattern (18 bp):
TCACAACCACAACCACAG
Found at i:15592006 original size:13 final size:13
Alignment explanation
Indices: 15591988--15592021 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
15591978 AACTGAACTG
15591988 AATTATGATGGAC
1 AATTATGATGGAC
15592001 AATTATGATGGAC
1 AATTATGATGGAC
15592014 AATTATGA
1 AATTATGA
15592022 AAAACCAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.41, C:0.06, G:0.21, T:0.32
Consensus pattern (13 bp):
AATTATGATGGAC
Found at i:15595874 original size:62 final size:57
Alignment explanation
Indices: 15595759--15595890 Score: 156
Period size: 62 Copynumber: 2.2 Consensus size: 57
15595749 ATCACTTTAA
* * * * * * *
15595759 TATTAAATTAATATAATATTTATCAAGATAAATATTAGATTAAATTTAATATTAAGTCT
1 TATTAAAATAATAGAATATTTATCAAGATAAAAATAAAATAAAATTTAATATTAA--AT
15595818 TATTAAAATAATAGAATATTTATCTACAAGATAAAAATAAAATAAAATTTAATATTAAAT
1 TATTAAAATAATAGAATATTTA--T-CAAGATAAAAATAAAATAAAATTTAATATTAAAT
15595878 TATTAAAATAATA
1 TATTAAAATAATA
15595891 TTATTTTTGA
Statistics
Matches: 63, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
59 20 0.32
60 14 0.22
61 1 0.02
62 28 0.44
ACGTcount: A:0.54, C:0.03, G:0.04, T:0.39
Consensus pattern (57 bp):
TATTAAAATAATAGAATATTTATCAAGATAAAAATAAAATAAAATTTAATATTAAAT
Found at i:15602232 original size:15 final size:16
Alignment explanation
Indices: 15602212--15602249 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
15602202 TCTAGTTATG
15602212 ATTTTTTGTC-TTTT-C
1 ATTTTTT-TCATTTTAC
15602227 ATTTTTTTCATTTTAC
1 ATTTTTTTCATTTTAC
15602243 ATTTTTT
1 ATTTTTT
15602250 AATAAGCTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 2 0.10
15 11 0.52
16 8 0.38
ACGTcount: A:0.13, C:0.11, G:0.03, T:0.74
Consensus pattern (16 bp):
ATTTTTTTCATTTTAC
Found at i:15610327 original size:7 final size:7
Alignment explanation
Indices: 15610313--15610341 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
15610303 AACACTTTTT
15610313 TCTT-TC
1 TCTTCTC
15610319 TCTTCTC
1 TCTTCTC
15610326 TCTTCTC
1 TCTTCTC
15610333 TCTTCTC
1 TCTTCTC
15610340 TC
1 TC
15610342 GTTTTGTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 4 0.18
7 18 0.82
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (7 bp):
TCTTCTC
Found at i:15614100 original size:24 final size:25
Alignment explanation
Indices: 15614047--15614102 Score: 80
Period size: 24 Copynumber: 2.3 Consensus size: 25
15614037 ATTTAAGGGA
*
15614047 TGCTCCTGTTCCACGACCTCCCCCC
1 TGCTCCTGTTCCACAACCTCCCCCC
*
15614072 T-CTCCTGTTCCACAACCT-CCCTC
1 TGCTCCTGTTCCACAACCTCCCCCC
15614095 TGCTCCTG
1 TGCTCCTG
15614103 CTTCTAAACC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 5 0.18
24 22 0.79
25 1 0.04
ACGTcount: A:0.09, C:0.52, G:0.11, T:0.29
Consensus pattern (25 bp):
TGCTCCTGTTCCACAACCTCCCCCC
Found at i:15627735 original size:30 final size:30
Alignment explanation
Indices: 15627701--15627761 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
15627691 TTTTCTATGA
15627701 TAGAGTTTGTTGGTTTAAGAATTAGGAAGT
1 TAGAGTTTGTTGGTTTAAGAATTAGGAAGT
*
15627731 TAGAGTTTTTTGGTTTAAGAATTAGGAAGT
1 TAGAGTTTGTTGGTTTAAGAATTAGGAAGT
15627761 T
1 T
15627762 TGCCCTTGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.30, C:0.00, G:0.28, T:0.43
Consensus pattern (30 bp):
TAGAGTTTGTTGGTTTAAGAATTAGGAAGT
Found at i:15641084 original size:13 final size:12
Alignment explanation
Indices: 15641047--15641087 Score: 57
Period size: 11 Copynumber: 3.4 Consensus size: 12
15641037 CAACCGGGAA
15641047 TTTTCACTTTT-
1 TTTTCACTTTTC
*
15641058 TTCTCACTTTTC
1 TTTTCACTTTTC
15641070 TTTTCACTATTTC
1 TTTTCACT-TTTC
15641083 TTTTC
1 TTTTC
15641088 CTTATAACCC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
11 10 0.38
12 7 0.27
13 9 0.35
ACGTcount: A:0.10, C:0.24, G:0.00, T:0.66
Consensus pattern (12 bp):
TTTTCACTTTTC
Found at i:15641365 original size:22 final size:22
Alignment explanation
Indices: 15641340--15641427 Score: 79
Period size: 22 Copynumber: 3.9 Consensus size: 22
15641330 ACTATTAAAT
*
15641340 AGAGAGCACTAAAGTGCTATAC
1 AGAGAGCACTAATGTGCTATAC
*
15641362 AGAGAGCAC-AGATGTGCTAAAC
1 AGAGAGCACTA-ATGTGCTATAC
* *
15641384 GGAGAGCACCAATGTGCTAATAATC
1 AGAGAGCACTAATGTGCT-AT-A-C
* *
15641409 GGAGAGCACTAACGTGCTA
1 AGAGAGCACTAATGTGCTA
15641428 GTAATCAAAG
Statistics
Matches: 55, Mismatches: 6, Indels: 8
0.80 0.09 0.12
Matches are distributed among these distances:
21 1 0.02
22 33 0.60
23 2 0.04
24 2 0.04
25 17 0.31
ACGTcount: A:0.38, C:0.19, G:0.26, T:0.17
Consensus pattern (22 bp):
AGAGAGCACTAATGTGCTATAC
Found at i:15641439 original size:25 final size:25
Alignment explanation
Indices: 15641340--15641511 Score: 109
Period size: 25 Copynumber: 7.4 Consensus size: 25
15641330 ACTATTAAAT
*
15641340 AGAGAGCACTAAAGTGCT-AT-A-C
1 AGAGAGCACTAACGTGCTAATAATC
*
15641362 AGAGAGCAC-AGATGTGCT-A-AA-C
1 AGAGAGCACTA-ACGTGCTAATAATC
* * *
15641384 GGAGAGCACCAATGTGCTAATAATC
1 AGAGAGCACTAACGTGCTAATAATC
* *
15641409 GGAGAGCACTAACGTGCTAGTAATC
1 AGAGAGCACTAACGTGCTAATAATC
* *
15641434 A-A-AG----AGCGTGCTATTAATC
1 AGAGAGCACTAACGTGCTAATAATC
* *
15641453 AGAGAGTACTGACGTGCTAATAATC
1 AGAGAGCACTAACGTGCTAATAATC
* * * *
15641478 AGAGAGCATTGATGTGCTACTAATC
1 AGAGAGCACTAACGTGCTAATAATC
15641503 AGAGAGCAC
1 AGAGAGCAC
15641512 GCTAAACTCC
Statistics
Matches: 122, Mismatches: 16, Indels: 21
0.77 0.10 0.13
Matches are distributed among these distances:
19 14 0.11
20 1 0.01
21 3 0.02
22 33 0.27
23 4 0.03
24 3 0.02
25 64 0.52
ACGTcount: A:0.37, C:0.18, G:0.25, T:0.20
Consensus pattern (25 bp):
AGAGAGCACTAACGTGCTAATAATC
Done.