Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D08
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: 65987480
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 223646 characters in sequence are not A, C, G, or T
File 45 of 211
Found at i:13299942 original size:24 final size:23
Alignment explanation
Indices: 13299909--13299962 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
13299899 CCGAGGTTCT
* * *
13299909 TACATACGAACCATGGATTAGTAA
1 TACATGCGAACCATAG-TTAATAA
*
13299933 TACATGCGAACCCTAGTTAATAA
1 TACATGCGAACCATAGTTAATAA
13299956 TACATGC
1 TACATGC
13299963 AAGTCACATA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
23 13 0.50
24 13 0.50
ACGTcount: A:0.39, C:0.20, G:0.15, T:0.26
Consensus pattern (23 bp):
TACATGCGAACCATAGTTAATAA
Found at i:13299997 original size:277 final size:277
Alignment explanation
Indices: 13299503--13300070 Score: 1073
Period size: 277 Copynumber: 2.1 Consensus size: 277
13299493 CCTCTTTGTA
13299503 TGTGAACCCTTATAGGTGCGAACCCTCTTGTATGTGAACCACCTGTGTGTACAAGCCTTGCATGG
1 TGTGAACCCTTATAGGTGCGAACCCTCTTGTATGTGAACCACCTGTGTGTACAAGCCTTGCATGG
13299568 GAACCCCATACTATGAACCCATATGCATAAACATATAAGAATGTTCATGCGAACCCGAGGTTCTT
66 GAACCCCATACTATGAACCCATATGCATAAACATATAAGAATGTTCATGCGAACCCGAGGTTCTT
13299633 ACATACAAACCACGGATTAGTAATACATGCGAACCCTAGTTAATAATACATGCAAGTCACATATT
131 ACATACAAACCACGGATTAGTAATACATGCGAACCCTAGTTAATAATACATGCAAGTCACATATT
13299698 TACATGCAAACCACTACTAGTGAGAGTCAACTATATGATGTCACATGTGAGCCCTAATATTGCAT
196 TACATGCAAACCACTACTAGTGAGAGTCAACTATATGATGTCACATGTGAGCCCTAATATTGCAT
13299763 GTGAACCACCTAAAATG
261 GTGAACCACCTAAAATG
13299780 TGTGAACCCTTATAGGTGCGAACCCTCTTGTATGTGAACCACCTGTGTGTACAAGCCTTGCATGG
1 TGTGAACCCTTATAGGTGCGAACCCTCTTGTATGTGAACCACCTGTGTGTACAAGCCTTGCATGG
*
13299845 GAACCCCATACTATGAACCCATATGCATAAACATATAGGAATGTTCATGCGAACCCGAGGTTCTT
66 GAACCCCATACTATGAACCCATATGCATAAACATATAAGAATGTTCATGCGAACCCGAGGTTCTT
* *
13299910 ACATACGAACCATGGATTAGTAATACATGCGAACCCTAGTTAATAATACATGCAAGTCACATATT
131 ACATACAAACCACGGATTAGTAATACATGCGAACCCTAGTTAATAATACATGCAAGTCACATATT
* * * *
13299975 TACATGCGAACCACTACTAGTGAGAGTCAGCTATATGATGTCACATGTGAGCCTTACTATTGCAT
196 TACATGCAAACCACTACTAGTGAGAGTCAACTATATGATGTCACATGTGAGCCCTAATATTGCAT
13300040 GTGAACCACCTAAAATG
261 GTGAACCACCTAAAATG
13300057 TGTGAACCCTTATA
1 TGTGAACCCTTATA
13300071 TGAATTGTTA
Statistics
Matches: 284, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
277 284 1.00
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.27
Consensus pattern (277 bp):
TGTGAACCCTTATAGGTGCGAACCCTCTTGTATGTGAACCACCTGTGTGTACAAGCCTTGCATGG
GAACCCCATACTATGAACCCATATGCATAAACATATAAGAATGTTCATGCGAACCCGAGGTTCTT
ACATACAAACCACGGATTAGTAATACATGCGAACCCTAGTTAATAATACATGCAAGTCACATATT
TACATGCAAACCACTACTAGTGAGAGTCAACTATATGATGTCACATGTGAGCCCTAATATTGCAT
GTGAACCACCTAAAATG
Found at i:13303538 original size:42 final size:42
Alignment explanation
Indices: 13303475--13303556 Score: 130
Period size: 42 Copynumber: 2.0 Consensus size: 42
13303465 CATTTTAGAA
*
13303475 CCACATGGGCAGAGGACTTGGCGTGTGCCCAAGCTGTGTGAG
1 CCACATGGGCAGAGGACTTGGCGTGTGCCCAAGCTATGTGAG
*
13303517 CCACATGGGCA-AGGACATTGGCGTGTGTCCAAGCTATGTG
1 CCACATGGGCAGAGGAC-TTGGCGTGTGCCCAAGCTATGTG
13303557 GCATATAAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
41 5 0.14
42 32 0.86
ACGTcount: A:0.21, C:0.23, G:0.35, T:0.21
Consensus pattern (42 bp):
CCACATGGGCAGAGGACTTGGCGTGTGCCCAAGCTATGTGAG
Found at i:13307581 original size:21 final size:20
Alignment explanation
Indices: 13307557--13307603 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
13307547 TGAAAGAGGT
*
13307557 TTTATTTTTTTCACTAGTTTA
1 TTTATGTTTTT-ACTAGTTTA
* *
13307578 TTTATGTTTTTGCTTGTTTA
1 TTTATGTTTTTACTAGTTTA
13307598 TTTATG
1 TTTATG
13307604 CTACAAGAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 13 0.57
21 10 0.43
ACGTcount: A:0.15, C:0.06, G:0.11, T:0.68
Consensus pattern (20 bp):
TTTATGTTTTTACTAGTTTA
Found at i:13309213 original size:17 final size:17
Alignment explanation
Indices: 13309191--13309227 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
13309181 AATAAAAATT
13309191 TATTTTATAATAATAAA
1 TATTTTATAATAATAAA
*
13309208 TATTTTGTAATAATAAA
1 TATTTTATAATAATAAA
13309225 TAT
1 TAT
13309228 CATGTATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (17 bp):
TATTTTATAATAATAAA
Found at i:13309233 original size:17 final size:17
Alignment explanation
Indices: 13309198--13309233 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
13309188 ATTTATTTTA
**
13309198 TAATAATAAATATTTTG
1 TAATAATAAATATCATG
13309215 TAATAATAAATATCATG
1 TAATAATAAATATCATG
13309232 TA
1 TA
13309234 TAAACTTAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.50, C:0.03, G:0.06, T:0.42
Consensus pattern (17 bp):
TAATAATAAATATCATG
Found at i:13317840 original size:15 final size:15
Alignment explanation
Indices: 13317820--13317871 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
13317810 ACTACACAAC
13317820 ATTTATTATTAATAT
1 ATTTATTATTAATAT
*
13317835 ATTTATAATTGTAATAAAT
1 ATTTATTA-T-TAAT--AT
*
13317854 ATTTATTATTAAAAT
1 ATTTATTATTAATAT
13317869 ATT
1 ATT
13317872 AATATTGAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
15 12 0.40
16 1 0.03
17 7 0.23
18 1 0.03
19 9 0.30
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
ATTTATTATTAATAT
Found at i:13317936 original size:16 final size:16
Alignment explanation
Indices: 13317905--13317941 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
13317895 ATATGAAGAA
13317905 TATTATTTAAAATTAT
1 TATTATTTAAAATTAT
13317921 TATT-TTTAAAACTTAT
1 TATTATTTAAAA-TTAT
13317937 TATTA
1 TATTA
13317942 AAATAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (16 bp):
TATTATTTAAAATTAT
Found at i:13320561 original size:1 final size:1
Alignment explanation
Indices: 13320555--13320580 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
13320545 GCTCTCTCTC
13320555 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
13320581 AGTAATTAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:13320963 original size:24 final size:25
Alignment explanation
Indices: 13320936--13320992 Score: 66
Period size: 27 Copynumber: 2.3 Consensus size: 25
13320926 ATGTGATACG
13320936 TAATAAAAAA-ATTA-AAATATAATA
1 TAATAAAAAATATTATAAATA-AATA
13320960 TAATATGAAAAATATTATAAATAAATA
1 TAATA--AAAAATATTATAAATAAATA
13320987 T-ATAAA
1 TAATAAA
13320993 TGTTTTGAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
24 7 0.24
26 8 0.28
27 9 0.31
28 5 0.17
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.32
Consensus pattern (25 bp):
TAATAAAAAATATTATAAATAAATA
Found at i:13324152 original size:21 final size:21
Alignment explanation
Indices: 13324104--13324154 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
13324094 GTTTTACTGT
*
13324104 AACAATATTTTAATTTGACATG
1 AACAAT-TTTTAATTTAACATG
** *
13324126 TTCAATTTTTAATTTAACTTG
1 AACAATTTTTAATTTAACATG
13324147 AACAATTT
1 AACAATTT
13324155 CACTATATTC
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.37, C:0.10, G:0.06, T:0.47
Consensus pattern (21 bp):
AACAATTTTTAATTTAACATG
Found at i:13324452 original size:10 final size:9
Alignment explanation
Indices: 13324425--13324460 Score: 56
Period size: 9 Copynumber: 4.0 Consensus size: 9
13324415 TAGAAAATTA
13324425 ATATATTTT
1 ATATATTTT
13324434 ATA-ATTTT
1 ATATATTTT
13324442 ATAATATTTT
1 AT-ATATTTT
13324452 ATATATTTT
1 ATATATTTT
13324461 TGAAAAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 7 0.28
9 11 0.44
10 7 0.28
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (9 bp):
ATATATTTT
Found at i:13326947 original size:3 final size:3
Alignment explanation
Indices: 13326939--13326975 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
13326929 TGTTCTTTGC
* *
13326939 ATT ATT ATT ATT ATT ATT GTT ATT GTT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
13326976 GGGTTTTATA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:13329148 original size:13 final size:13
Alignment explanation
Indices: 13329130--13329154 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13329120 ATAGTGGTAA
13329130 ACATAACATACAC
1 ACATAACATACAC
13329143 ACATAACATACA
1 ACATAACATACA
13329155 TAAACATTAA
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:0.56, C:0.28, G:0.00, T:0.16
Consensus pattern (13 bp):
ACATAACATACAC
Found at i:13329234 original size:57 final size:57
Alignment explanation
Indices: 13329148--13329276 Score: 170
Period size: 57 Copynumber: 2.2 Consensus size: 57
13329138 TACACACATA
* ** *
13329148 ACATACATAAACATTAATAAATAGTCATACACATAACT-GTGATATACCACATAATAT
1 ACATACATAAACATTAATAAACAACCATACACATAA-TAGTAATATACCACATAATAT
* * *
13329205 ACATGCATAAACATTAATAAACAACCATACATATAATAGTAATATGCCACATAATAT
1 ACATACATAAACATTAATAAACAACCATACACATAATAGTAATATACCACATAATAT
13329262 ACATACATTAAACAT
1 ACATACA-TAAACAT
13329277 GGCATACATA
Statistics
Matches: 62, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
56 1 0.02
57 54 0.87
58 7 0.11
ACGTcount: A:0.50, C:0.18, G:0.05, T:0.27
Consensus pattern (57 bp):
ACATACATAAACATTAATAAACAACCATACACATAATAGTAATATACCACATAATAT
Found at i:13329321 original size:27 final size:26
Alignment explanation
Indices: 13329291--13329364 Score: 80
Period size: 27 Copynumber: 2.8 Consensus size: 26
13329281 TACATAGTAT
13329291 ACAAACATAACAGTAATATAACACATA
1 ACAAACATAACA-TAATATAACACATA
*
13329318 ACAAACAT-ACA-AATATACATACATA
1 ACAAACATAACATAATATA-ACACATA
* * *
13329343 ATATACATAACATTATATAACA
1 ACAAACATAACATAATATAACA
13329365 TAATATATAT
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
24 6 0.15
25 12 0.31
26 8 0.21
27 13 0.33
ACGTcount: A:0.58, C:0.18, G:0.01, T:0.23
Consensus pattern (26 bp):
ACAAACATAACATAATATAACACATA
Found at i:13329347 original size:37 final size:36
Alignment explanation
Indices: 13329295--13329513 Score: 162
Period size: 37 Copynumber: 5.8 Consensus size: 36
13329285 TAGTATACAA
*
13329295 ACATAACAGTAATATAACACATAACAAACATACAAATAT
1 ACAT-ACA-TAATATAA-ACATAACATACATACAAATAT
*
13329334 ACATACATAATAT--ACATAACATTATATAACATAATAT
1 ACATACATAATATAAACATAACA-TACAT-ACA-AATAT
*
13329371 ATATACA-AATATACAAACATAACAGTA-A-ACATAATAT
1 ACATACATAATAT--AAACATAACA-TACATACA-AATAT
* * *
13329408 ACATATATAACAATACATAACTTAACATACATACAAATAT
1 ACATACAT---AATATA-AACATAACATACATACAAATAT
*
13329448 ACA-AGCATAACAGTAAACATAACATACATACAAATAT
1 ACATA-CATAATA-TAAACATAACATACATACAAATAT
* *
13329485 ACAAACATAACATTAAACATAACATACAT
1 ACATACATAATA-TAAACATAACATACAT
13329514 GCATAACAGT
Statistics
Matches: 150, Mismatches: 13, Indels: 36
0.75 0.07 0.18
Matches are distributed among these distances:
34 8 0.05
35 3 0.02
36 8 0.05
37 81 0.54
38 5 0.03
39 9 0.06
40 29 0.19
41 7 0.05
ACGTcount: A:0.57, C:0.17, G:0.02, T:0.24
Consensus pattern (36 bp):
ACATACATAATATAAACATAACATACATACAAATAT
Found at i:13329367 original size:15 final size:14
Alignment explanation
Indices: 13329295--13329575 Score: 91
Period size: 12 Copynumber: 21.6 Consensus size: 14
13329285 TAGTATACAA
13329295 ACATAACAGTAATAT
1 ACATAACA-TAATAT
* * *
13329310 A-A-CACATAACAA
1 ACATAACATAATAT
13329322 ACAT-ACA-AATAT
1 ACATAACATAATAT
13329334 ACAT-ACATAATAT
1 ACATAACATAATAT
13329347 ACATAACAT--TAT
1 ACATAACATAATAT
13329359 --ATAACATAATAT
1 ACATAACATAATAT
*
13329371 ATAT-ACA-AATAT
1 ACATAACATAATAT
*
13329383 ACA-AACATAACAGT
1 ACATAACATAATA-T
13329397 --A-AACATAATAT
1 ACATAACATAATAT
* *
13329408 ACAT-ATATAACAAT
1 ACATAACATAA-TAT
* *
13329422 ACATAACTTAACAT
1 ACATAACATAATAT
13329436 ACAT-ACA-AATAT
1 ACATAACATAATAT
* *
13329448 ACA-AGCATAACAGT
1 ACATAACATAATA-T
*
13329462 --A-AACATAACAT
1 ACATAACATAATAT
13329473 ACAT-ACA-AATAT
1 ACATAACATAATAT
*
13329485 ACA-AACATAACAT
1 ACATAACATAATAT
* *
13329498 -TA-AACATAACAT
1 ACATAACATAATAT
* *
13329510 ACAT-GCATAACAGT
1 ACATAACATAATA-T
*
13329524 ACATAGCATACATA-
1 ACATAACATA-ATAT
* *
13329538 ACATAATAGTAAACAT
1 ACATAACA-T-AATAT
13329554 AACAT-ACATAATAT
1 -ACATAACATAATAT
13329568 ACATAACA
1 ACATAACA
13329576 ATTTAAAAAC
Statistics
Matches: 203, Mismatches: 29, Indels: 69
0.67 0.10 0.23
Matches are distributed among these distances:
10 7 0.03
11 2 0.01
12 79 0.39
13 53 0.26
14 39 0.19
15 14 0.07
16 5 0.02
17 4 0.02
ACGTcount: A:0.56, C:0.17, G:0.03, T:0.24
Consensus pattern (14 bp):
ACATAACATAATAT
Found at i:13329387 original size:65 final size:65
Alignment explanation
Indices: 13329289--13329497 Score: 198
Period size: 65 Copynumber: 3.2 Consensus size: 65
13329279 CATACATAGT
* * *
13329289 ATACA-AACATAACAGTAATATAACACATA-ACAAACAT-ACAAATATACATACATA-ATATACA
1 ATACATAACATAACA-T-ATAT-ACAAATATACAAACATAAC-AATAAACATA-ATATACATACA
13329350 TAACA
61 TAACA
* * * * *
13329355 TTATATAACATAATATATATACAAATATACAAACATAACAGTAAACATAATATACATATATAACA
1 ATACATAACATAACATATATACAAATATACAAACATAACAATAAACATAATATACATACATAACA
* * * * * *
13329420 ATACATAACTTAACATACATACAAATATACAAGCATAACAGTAAACATAACATACATACA-AA-T
1 ATACATAACATAACATATATACAAATATACAAACATAACAATAAACATAATATACATACATAACA
13329483 ATACA-AACATAACAT
1 ATACATAACATAACAT
13329498 TAAACATAAC
Statistics
Matches: 121, Mismatches: 18, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
62 9 0.07
63 5 0.04
64 11 0.09
65 82 0.68
66 6 0.05
67 8 0.07
ACGTcount: A:0.57, C:0.17, G:0.02, T:0.24
Consensus pattern (65 bp):
ATACATAACATAACATATATACAAATATACAAACATAACAATAAACATAATATACATACATAACA
Found at i:13329505 original size:65 final size:68
Alignment explanation
Indices: 13329359--13329512 Score: 201
Period size: 65 Copynumber: 2.3 Consensus size: 68
13329349 ATAACATTAT
* * * * *
13329359 ATAACA-TAATATATATACAAATATACAAACATAACAGTAAACATAATATACAT--ATATA-ACA
1 ATAACATTAACATACATACAAATATACAAGCATAACAGTAAACATAACATACATACAAATATACA
13329420 ATAC
66 A-AC
13329424 ATAAC-TTAACATACATACAAATATACAAGCATAACAGTAAACATAACATACATACAAATATACA
1 ATAACATTAACATACATACAAATATACAAGCATAACAGTAAACATAACATACATACAAATATACA
13329488 AAC
66 AAC
13329491 ATAACATTAAACATAACATACA
1 ATAACATT-AACAT-ACATACA
13329513 TGCATAACAG
Statistics
Matches: 77, Mismatches: 5, Indels: 9
0.85 0.05 0.10
Matches are distributed among these distances:
65 48 0.62
67 11 0.14
68 6 0.08
69 5 0.06
70 7 0.09
ACGTcount: A:0.58, C:0.17, G:0.02, T:0.23
Consensus pattern (68 bp):
ATAACATTAACATACATACAAATATACAAGCATAACAGTAAACATAACATACATACAAATATACA
AAC
Found at i:13329537 original size:9 final size:9
Alignment explanation
Indices: 13329313--13329601 Score: 119
Period size: 9 Copynumber: 32.1 Consensus size: 9
13329303 GTAATATAAC
*
13329313 ACATAACAA
1 ACATAACAT
13329322 ACAT-ACA-
1 ACATAACAT
13329329 A-ATATACAT
1 ACATA-ACAT
*
13329338 ACATAATAT
1 ACATAACAT
13329347 ACATAACATT
1 ACATAACA-T
*
13329357 ATATAACAT
1 ACATAACAT
*
13329366 A-ATATATAT
1 ACATA-ACAT
*
13329375 ACA-AATAT
1 ACATAACAT
13329383 ACA-AACAT
1 ACATAACAT
13329391 AACAGTAAACAT
1 -ACA-T-AACAT
13329403 A-ATATACAT
1 ACATA-ACAT
*
13329412 ATATAACAAT
1 ACATAAC-AT
*
13329422 ACATAACTT
1 ACATAACAT
13329431 AACAT-ACAT
1 -ACATAACAT
*
13329440 ACA-AATAT
1 ACATAACAT
*
13329448 ACA-AGCAT
1 ACATAACAT
13329456 AACAGTAAACAT
1 -ACA-T-AACAT
13329468 AACAT-ACAT
1 -ACATAACAT
*
13329477 ACA-AATAT
1 ACATAACAT
13329485 ACA-AACAT
1 ACATAACAT
13329493 AACATTAAACAT
1 -ACA-T-AACAT
13329505 AACAT-ACAT
1 -ACATAACAT
*
13329514 GCATAACAGT
1 ACATAACA-T
*
13329524 ACATAGCAT
1 ACATAACAT
13329533 ACATAACAT
1 ACATAACAT
** *
13329542 A-ATAGTAA
1 ACATAACAT
13329550 ACATAACAT
1 ACATAACAT
*
13329559 ACATAATAT
1 ACATAACAT
13329568 ACATAACA-
1 ACATAACAT
** *
13329576 ATTTAA-AA
1 ACATAACAT
13329584 ACATAACAT
1 ACATAACAT
13329593 ACAT-ACAT
1 ACATAACAT
13329601 A
1 A
13329602 AACAGTAAAG
Statistics
Matches: 219, Mismatches: 31, Indels: 61
0.70 0.10 0.20
Matches are distributed among these distances:
6 2 0.01
7 2 0.01
8 67 0.31
9 88 0.40
10 35 0.16
11 3 0.01
12 22 0.10
ACGTcount: A:0.56, C:0.17, G:0.02, T:0.24
Consensus pattern (9 bp):
ACATAACAT
Found at i:13329562 original size:35 final size:33
Alignment explanation
Indices: 13329515--13329601 Score: 95
Period size: 35 Copynumber: 2.5 Consensus size: 33
13329505 AACATACATG
*
13329515 CATAACAGTACATAGCATACATAAC-ATAATAGTAAA
1 CATAACA-TACATA-CATACATAACAAT-ATA-AAAA
* *
13329551 CATAACATACATAATATACATAACAATTTAAAAA
1 CATAACATACAT-ACATACATAACAATATAAAAA
13329585 CATAACATACATACATA
1 CATAACATACATACATA
13329602 AACAGTAAAG
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
33 4 0.09
34 15 0.33
35 16 0.36
36 10 0.22
ACGTcount: A:0.55, C:0.17, G:0.03, T:0.24
Consensus pattern (33 bp):
CATAACATACATACATACATAACAATATAAAAA
Found at i:13329721 original size:28 final size:29
Alignment explanation
Indices: 13329690--13329748 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 29
13329680 ACAAATGCCA
13329690 ACAAA-AAAAACTAAAAGTCAGATATAAT
1 ACAAATAAAAACTAAAAGTCAGATATAAT
* **
13329718 ACAAATTAAAAATTGGAAGTCAGATATAAT
1 ACAAA-TAAAAACTAAAAGTCAGATATAAT
13329748 A
1 A
13329749 TGTACAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 5 0.19
30 21 0.81
ACGTcount: A:0.59, C:0.08, G:0.10, T:0.22
Consensus pattern (29 bp):
ACAAATAAAAACTAAAAGTCAGATATAAT
Found at i:13343179 original size:25 final size:25
Alignment explanation
Indices: 13343109--13343224 Score: 101
Period size: 25 Copynumber: 4.6 Consensus size: 25
13343099 TTCTGAATAA
* *
13343109 TTCGCCACAAATGTTTCACAGAGAG
1 TTCGCCACAAAGGCTTCACAGAGAG
* * *
13343134 TTCACCATAAAGGCTTCACAGAGGG
1 TTCGCCACAAAGGCTTCACAGAGAG
*
13343159 TTCGCCACAAAGGCTGT-ACAGAATAG
1 TTCGCCACAAAGGCT-TCACAG-AGAG
* ** *
13343185 TT-GCCATAAAATCTTCACAAAGAG
1 TTCGCCACAAAGGCTTCACAGAGAG
*
13343209 TTTGCCACAAAGGCTT
1 TTCGCCACAAAGGCTT
13343225 TACAAAATAC
Statistics
Matches: 70, Mismatches: 17, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
24 6 0.09
25 59 0.84
26 5 0.07
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.23
Consensus pattern (25 bp):
TTCGCCACAAAGGCTTCACAGAGAG
Found at i:13343180 original size:50 final size:50
Alignment explanation
Indices: 13343109--13343228 Score: 127
Period size: 50 Copynumber: 2.4 Consensus size: 50
13343099 TTCTGAATAA
* * * *
13343109 TTCGCCACAAATG-TTTCACAG-AGAGTTCACCATAAAGGCTTCACAGAGGG
1 TTCGCCACAAAGGCTTT-ACAGAAGAGTT-ACCATAAAAGCTTCACAAAGAG
* * * *
13343159 TTCGCCACAAAGGCTGTACAGAATAGTTGCCATAAAATCTTCACAAAGAG
1 TTCGCCACAAAGGCTTTACAGAAGAGTTACCATAAAAGCTTCACAAAGAG
*
13343209 TTTGCCACAAAGGCTTTACA
1 TTCGCCACAAAGGCTTTACA
13343229 AAATACTCAC
Statistics
Matches: 58, Mismatches: 10, Indels: 4
0.81 0.14 0.06
Matches are distributed among these distances:
50 51 0.88
51 7 0.12
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.23
Consensus pattern (50 bp):
TTCGCCACAAAGGCTTTACAGAAGAGTTACCATAAAAGCTTCACAAAGAG
Found at i:13351452 original size:41 final size:42
Alignment explanation
Indices: 13351361--13351465 Score: 113
Period size: 41 Copynumber: 2.5 Consensus size: 42
13351351 GTGGTGCATG
* *
13351361 GGTGGCATTTTGCTAGCCTTTATGGCATAATCTGATTTGGCCTT
1 GGTGGCATTATGCTAGCCTTTATGGC--AATCTGATATGGCCTT
** * *
13351405 TCTGGCATTATGTTAGCCTTTGTGGC-ATCTGATATGGCCTT
1 GGTGGCATTATGCTAGCCTTTATGGCAATCTGATATGGCCTT
* *
13351446 GGTGGCATTCTCCTAGCCTT
1 GGTGGCATTATGCTAGCCTT
13351466 CGTTGTGTAA
Statistics
Matches: 50, Mismatches: 11, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
41 29 0.58
44 21 0.42
ACGTcount: A:0.14, C:0.21, G:0.25, T:0.40
Consensus pattern (42 bp):
GGTGGCATTATGCTAGCCTTTATGGCAATCTGATATGGCCTT
Found at i:13351990 original size:28 final size:28
Alignment explanation
Indices: 13351926--13351996 Score: 79
Period size: 28 Copynumber: 2.5 Consensus size: 28
13351916 ATTAATCAAT
* *
13351926 ATCAACAAGGGTATTCACCAAAACTATT
1 ATCAATAAGGGTATTCACCAAAACTATG
* * * *
13351954 ATTATTAAGGGTATTCACCAAAAGTGTG
1 ATCAATAAGGGTATTCACCAAAACTATG
13351982 ATCAATAAGTGGTAT
1 ATCAATAAG-GGTAT
13351997 CCGCCAAGAA
Statistics
Matches: 34, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
28 29 0.85
29 5 0.15
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.30
Consensus pattern (28 bp):
ATCAATAAGGGTATTCACCAAAACTATG
Found at i:13354965 original size:48 final size:47
Alignment explanation
Indices: 13354846--13354970 Score: 146
Period size: 48 Copynumber: 2.6 Consensus size: 47
13354836 ACGAATTATT
* **
13354846 TTTTCTTTCT-GTCTTTTCTTTTCTTGAAACCCCAAAATCCTTTCCC
1 TTTTCTTTCTAGTCTTTTCTTTGCTTGAAACCCCAAAATCCGGTCCC
* * *
13354892 TTTTCTTTCCCAGAT-TTCTCTTTGCTTGAAACCCCAAAATTCGGTCCC
1 TTTTCTTT-CTAG-TCTTTTCTTTGCTTGAAACCCCAAAATCCGGTCCC
*
13354940 TTTTCTTTCTTAGTCTTTTCGTTGCTTGAAA
1 TTTTCTTTC-TAGTCTTTTCTTTGCTTGAAA
13354971 AAAATATACA
Statistics
Matches: 65, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
46 8 0.12
47 3 0.05
48 53 0.82
49 1 0.02
ACGTcount: A:0.16, C:0.27, G:0.09, T:0.48
Consensus pattern (47 bp):
TTTTCTTTCTAGTCTTTTCTTTGCTTGAAACCCCAAAATCCGGTCCC
Found at i:13358455 original size:24 final size:22
Alignment explanation
Indices: 13358428--13358483 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 22
13358418 AATTTCAAAA
13358428 ATAAAACATAATATAATATTTATC
1 ATAAAA-ATAA-ATAATATTTATC
*
13358452 ATAAAAATAAATATTATTTA--
1 ATAAAAATAAATAATATTTATC
*
13358472 ATTAAAATAAAT
1 ATAAAAATAAAT
13358484 TCTTTAAAGG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 11 0.37
22 9 0.30
23 4 0.13
24 6 0.20
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.38
Consensus pattern (22 bp):
ATAAAAATAAATAATATTTATC
Found at i:13358859 original size:9 final size:9
Alignment explanation
Indices: 13358845--13358916 Score: 69
Period size: 9 Copynumber: 8.2 Consensus size: 9
13358835 AACTTTGGAT
*
13358845 CATAACTTC
1 CATAACTTA
13358854 CATAACTTA
1 CATAACTTA
13358863 CATAA--TA
1 CATAACTTA
*
13358870 CATAA-ATA
1 CATAACTTA
* * *
13358878 TATATCATA
1 CATAACTTA
13358887 CCATAACTTA
1 -CATAACTTA
13358897 CATAACTTA
1 CATAACTTA
13358906 CATAACTTA
1 CATAACTTA
13358915 CA
1 CA
13358917 CCCATTAGAT
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
7 7 0.13
8 5 0.09
9 36 0.67
10 6 0.11
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (9 bp):
CATAACTTA
Found at i:13374246 original size:43 final size:43
Alignment explanation
Indices: 13374131--13374249 Score: 175
Period size: 43 Copynumber: 2.8 Consensus size: 43
13374121 TTACTAAAAA
* * * *
13374131 CGCCGCTAAAGGTCATGTTCTTTAGCGGCATTTGTGGGGAAAG
1 CGCCGCTAAAGGTCATGTTCTATAGTGGCGTTTGTAGGGAAAG
* *
13374174 TGCCGCTAAAGGTCATGTTCTATAATGGCGTTTGTAGGGAAAG
1 CGCCGCTAAAGGTCATGTTCTATAGTGGCGTTTGTAGGGAAAG
*
13374217 CGCTGCTAAAGGTCATGTTCTATAGTGGCGTTT
1 CGCCGCTAAAGGTCATGTTCTATAGTGGCGTTT
13374250 TCCCACATAA
Statistics
Matches: 67, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 67 1.00
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.31
Consensus pattern (43 bp):
CGCCGCTAAAGGTCATGTTCTATAGTGGCGTTTGTAGGGAAAG
Found at i:13377506 original size:11 final size:11
Alignment explanation
Indices: 13377490--13377514 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
13377480 ATAGTTTAGC
13377490 TTATTGAATTT
1 TTATTGAATTT
13377501 TTATTGAATTT
1 TTATTGAATTT
13377512 TTA
1 TTA
13377515 AGGTAAGTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (11 bp):
TTATTGAATTT
Found at i:13393014 original size:28 final size:26
Alignment explanation
Indices: 13392982--13393060 Score: 85
Period size: 25 Copynumber: 3.0 Consensus size: 26
13392972 AACTCAATTT
13392982 TTATTTTTATTATTTATTA-TTT-TT
1 TTATTTTTATTATTTATTACTTTATT
*
13393006 TTCTTTATTTACTTTATTTATTACTTTATT
1 TT-ATT-TTTA--TTATTTATTACTTTATT
13393036 TTA-TTTTATTATTTATTAC-TTATT
1 TTATTTTTATTATTTATTACTTTATT
13393060 T
1 T
13393061 GGATATTAAT
Statistics
Matches: 47, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
24 8 0.17
25 13 0.28
26 4 0.09
27 4 0.09
28 11 0.23
29 3 0.06
30 4 0.09
ACGTcount: A:0.22, C:0.05, G:0.00, T:0.73
Consensus pattern (26 bp):
TTATTTTTATTATTTATTACTTTATT
Found at i:13393016 original size:4 final size:4
Alignment explanation
Indices: 13392981--13393052 Score: 51
Period size: 4 Copynumber: 17.5 Consensus size: 4
13392971 CAACTCAATT
* * *
13392981 TTTA TTTT TATTA TTTA -TTA TTTT TTTC TTTA TTTA CTTTA TTTA -TTA
1 TTTA TTTA T-TTA TTTA TTTA TTTA TTTA TTTA TTTA -TTTA TTTA TTTA
13393029 CTTTA TTTTA TTT- TATTA TTTA TT
1 -TTTA -TTTA TTTA T-TTA TTTA TT
13393053 ACTTATTTGG
Statistics
Matches: 55, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
3 7 0.13
4 33 0.60
5 15 0.27
ACGTcount: A:0.21, C:0.04, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:13393038 original size:17 final size:17
Alignment explanation
Indices: 13392980--13393052 Score: 76
Period size: 17 Copynumber: 4.1 Consensus size: 17
13392970 GCAACTCAAT
13392980 TTTTATTTTTATTATTTA
1 TTTTA-TTTTATTATTTA
* *
13392998 TTATTTTTTTCTTTATTTA
1 TT-TTATTTT-ATTATTTA
*
13393017 CTTTA-TTTATTACTTTA
1 TTTTATTTTATTA-TTTA
13393034 TTTTATTTTATTATTTA
1 TTTTATTTTATTATTTA
13393051 TT
1 TT
13393053 ACTTATTTGG
Statistics
Matches: 45, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
16 3 0.07
17 17 0.38
18 15 0.33
19 10 0.22
ACGTcount: A:0.21, C:0.04, G:0.00, T:0.75
Consensus pattern (17 bp):
TTTTATTTTATTATTTA
Found at i:13403549 original size:35 final size:36
Alignment explanation
Indices: 13403477--13403563 Score: 106
Period size: 35 Copynumber: 2.4 Consensus size: 36
13403467 ATCATCAGAT
* * * *
13403477 CAACCAAAACACACCAGATGCTCATAAGAGCTGGTC
1 CAACCAGAACACACCAGATACTCATAAGAGATAGTC
*
13403513 CAACCAGAACACACC-GATATTCATAAGAGATAGTC
1 CAACCAGAACACACCAGATACTCATAAGAGATAGTC
13403548 CAACC-GAAACACACCA
1 CAACCAG-AACACACCA
13403564 AACAGAGAGT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
34 1 0.02
35 29 0.66
36 14 0.32
ACGTcount: A:0.43, C:0.31, G:0.14, T:0.13
Consensus pattern (36 bp):
CAACCAGAACACACCAGATACTCATAAGAGATAGTC
Found at i:13407355 original size:7 final size:7
Alignment explanation
Indices: 13407343--13407368 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
13407333 TTAAAACTGG
13407343 AAATTGC
1 AAATTGC
13407350 AAATTGC
1 AAATTGC
13407357 AAATTGC
1 AAATTGC
13407364 AAATT
1 AAATT
13407369 TCTTTTGGCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.46, C:0.12, G:0.12, T:0.31
Consensus pattern (7 bp):
AAATTGC
Found at i:13418330 original size:51 final size:51
Alignment explanation
Indices: 13418271--13418564 Score: 301
Period size: 51 Copynumber: 5.8 Consensus size: 51
13418261 TATCGATGAA
* * *
13418271 CACGTGTGTAGCACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATGTTGGT
* * * * * * * *
13418322 CACATGTGTAGTGCTAAGTGAAGGCTACAATGTGTA-CTGAGAAGCT-TTGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATC-GATAA-ATGTTGGT
* *
13418373 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATGTTGGT
* * * * *
13418424 CACATGTGTAGTACTAAGTGAAGGCTACTATGTGTACCGA-AAA-GCTTTGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATG--TTGGT
* * ** *
13418475 CACGTGTGTAGTACTATGTGAATGCTACTACGTGAACCG-TAAAACTTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATGTTGGT
*
13418525 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGA
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGA
13418565 ATGATAAAAG
Statistics
Matches: 196, Mismatches: 38, Indels: 18
0.78 0.15 0.07
Matches are distributed among these distances:
49 1 0.01
50 45 0.23
51 148 0.76
52 2 0.01
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.29
Consensus pattern (51 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATGTTGGT
Found at i:13418447 original size:102 final size:102
Alignment explanation
Indices: 13418271--13418552 Score: 431
Period size: 102 Copynumber: 2.8 Consensus size: 102
13418261 TATCGATGAA
* *
13418271 CACGTGTGTAGCACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTGC
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTAC
* *
13418336 TAAGTGAAGGCTACAATGTGTACTGAGAAGCTTTGGT
66 TAAGTGAAGGCTACAATGTGTACCGAAAAGCTTTGGT
13418373 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTAC
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTAC
*
13418438 TAAGTGAAGGCTACTATGTGTACCGAAAAGCTTTGGT
66 TAAGTGAAGGCTACAATGTGTACCGAAAAGCTTTGGT
* * * *** * *
13418475 CACGTGTGTAGTACTATGTGAATGCTACTACGTGAACCG-TAAAACTTGATCACGTGTGTAGTAC
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTAC
*
13418539 TATGTGAAGGCTAC
66 TAAGTGAAGGCTAC
13418553 TACGTGTATC
Statistics
Matches: 166, Mismatches: 14, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
101 33 0.20
102 133 0.80
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.29
Consensus pattern (102 bp):
CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTAC
TAAGTGAAGGCTACAATGTGTACCGAAAAGCTTTGGT
Found at i:13418596 original size:101 final size:102
Alignment explanation
Indices: 13418278--13418597 Score: 293
Period size: 102 Copynumber: 3.1 Consensus size: 102
13418268 GAACACGTGT
* * ** * *
13418278 GTAGCACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTGCTAAGTGA
1 GTAGTACTGTGTGAAGGCTACTACGTGAACCGATAAAACATGATCACATGTGTAGTACTAAGTGA
* * * * * *** * * *
13418343 AGGCTACAATGTGTACTGAGAAGCTTTGGTCACGTGT
66 AGGCTACTACGTGTACCGAAAAGATAAAGTAACATGG
* ** *
13418380 GTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTACTAAGTGA
1 GTAGTACTGTGTGAAGGCTACTACGTGAACCGATAAAACATGATCACATGTGTAGTACTAAGTGA
* * *** * * *
13418445 AGGCTACTATGTGTACCGAAAAGCTTTGGTCACGTGT
66 AGGCTACTACGTGTACCGAAAAGATAAAGTAACATGG
* * * * *
13418482 GTAGTACTATGTGAATGCTACTACGTGAACCG-TAAAACTTGATCACGTGTGTAGTACTATGTGA
1 GTAGTACTGTGTGAAGGCTACTACGTGAACCGATAAAACATGATCACATGTGTAGTACTAAGTGA
* *
13418546 AGGCTACTACGTGTATCG-AATGATAAAAGTAACATGG
66 AGGCTACTACGTGTACCGAAAAGAT-AAAGTAACATGG
13418583 GTAGTACTGTGTGAA
1 GTAGTACTGTGTGAA
13418598 AAACCCCAAA
Statistics
Matches: 192, Mismatches: 25, Indels: 3
0.87 0.11 0.01
Matches are distributed among these distances:
100 4 0.02
101 62 0.32
102 126 0.66
ACGTcount: A:0.29, C:0.14, G:0.27, T:0.29
Consensus pattern (102 bp):
GTAGTACTGTGTGAAGGCTACTACGTGAACCGATAAAACATGATCACATGTGTAGTACTAAGTGA
AGGCTACTACGTGTACCGAAAAGATAAAGTAACATGG
Found at i:13420578 original size:15 final size:14
Alignment explanation
Indices: 13420558--13420602 Score: 54
Period size: 15 Copynumber: 3.1 Consensus size: 14
13420548 TAAAACGGGG
13420558 AAGAAAAGAATAAGA
1 AAGAAAAGAA-AAGA
*
13420573 AAGAAACGCAAAAGA
1 AAGAAAAG-AAAAGA
*
13420588 AAGGAAAGAAAAGA
1 AAGAAAAGAAAAGA
13420602 A
1 A
13420603 CATGCCAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
14 7 0.27
15 17 0.65
16 2 0.08
ACGTcount: A:0.71, C:0.04, G:0.22, T:0.02
Consensus pattern (14 bp):
AAGAAAAGAAAAGA
Found at i:13420819 original size:18 final size:19
Alignment explanation
Indices: 13420775--13420819 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
13420765 TCTTCTTTAA
13420775 CCTT-TAACCTTCCATCTT
1 CCTTATAACCTTCCATCTT
* *
13420793 CCTCA-AACCTTTCATC-T
1 CCTTATAACCTTCCATCTT
13420810 CCTTATAACC
1 CCTTATAACC
13420820 CTTTTTACTT
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
17 5 0.23
18 17 0.77
ACGTcount: A:0.22, C:0.40, G:0.00, T:0.38
Consensus pattern (19 bp):
CCTTATAACCTTCCATCTT
Found at i:13426822 original size:17 final size:16
Alignment explanation
Indices: 13426784--13426816 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
13426774 TATACCAATC
13426784 AAAATCATGCATCTAAA
1 AAAATCATGCA-CTAAA
13426801 AAAATCATGCA-TAAA
1 AAAATCATGCACTAAA
13426816 A
1 A
13426817 TGAAATTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
17 11 0.69
ACGTcount: A:0.58, C:0.15, G:0.06, T:0.21
Consensus pattern (16 bp):
AAAATCATGCACTAAA
Found at i:13432285 original size:20 final size:20
Alignment explanation
Indices: 13432246--13432300 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
13432236 TTAAATATAT
*
13432246 ATAAATTTGAA-TTTTAAAA
1 ATAATTTTGAATTTTTAAAA
*
13432265 ATAATTTTGAATTTTTGAAA
1 ATAATTTTGAATTTTTAAAA
* *
13432285 ATTATTTTAAATTTTT
1 ATAATTTTGAATTTTT
13432301 TTTTGTAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 10 0.32
20 21 0.68
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (20 bp):
ATAATTTTGAATTTTTAAAA
Found at i:13433159 original size:16 final size:16
Alignment explanation
Indices: 13433110--13433161 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
13433100 AAGTGAAAAG
* *
13433110 AAAATTAGAAGGATGG
1 AAAATTAGAAAGATGA
* * * *
13433126 AAAATTGGAGACACGA
1 AAAATTAGAAAGATGA
13433142 AAAATTAGAAAGATGA
1 AAAATTAGAAAGATGA
13433158 AAAA
1 AAAA
13433162 CAAAAATTTT
Statistics
Matches: 26, Mismatches: 10, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.58, C:0.04, G:0.23, T:0.15
Consensus pattern (16 bp):
AAAATTAGAAAGATGA
Found at i:13433319 original size:20 final size:20
Alignment explanation
Indices: 13433294--13433332 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
13433284 AAATAACATA
13433294 CAATATAGAAAGATTGATTC
1 CAATATAGAAAGATTGATTC
13433314 CAATATAGAAAGATTGATT
1 CAATATAGAAAGATTGATT
13433333 TTTATAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.46, C:0.08, G:0.15, T:0.31
Consensus pattern (20 bp):
CAATATAGAAAGATTGATTC
Found at i:13436107 original size:26 final size:27
Alignment explanation
Indices: 13436078--13436131 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
13436068 ATGCATATAT
* *
13436078 TATAGGAAATGCATGTATA-TATAAAA
1 TATAGAAAATGCATATATATTATAAAA
*
13436104 TATAGAAAATGTATATATATTATAAAA
1 TATAGAAAATGCATATATATTATAAAA
13436131 T
1 T
13436132 GTATATGCAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 16 0.67
27 8 0.33
ACGTcount: A:0.52, C:0.02, G:0.11, T:0.35
Consensus pattern (27 bp):
TATAGAAAATGCATATATATTATAAAA
Found at i:13438068 original size:128 final size:126
Alignment explanation
Indices: 13437861--13438093 Score: 272
Period size: 128 Copynumber: 1.8 Consensus size: 126
13437851 TGCTCCCTGT
* * * * *
13437861 AACTTCAGAGAGGTAAGATCTGCAATTTTAATCCGCTTCGCTGCAACTTCAGAGAGATAGGATTG
1 AACTTCAGAGAGATAAGATCTACAATTTTAATCCGCTCCACTGCAACTTCAGAGAGATAGCATT-
* **
13437926 GATTCTTCTGTCTGCTCAACTGCAGCTTCAA-GGAGATAAGACTGTATGCGATATGTTCTCTGC
65 GATTCCTCAATCTGCTC-ACTGCAGCTT-AAGGGAGATAAGACTGTATGCGATATGTTCTCTGC
*** * *
13437989 AACTTCAGAGAGATAAGATCTATGGTTTTAATCCGCTCCACTGCATCTTCAGGGAGATAGCATT-
1 AACTTCAGAGAGATAAGATCTACAATTTTAATCCGCTCCACTGCAACTTCAGAGAGATAGCATTG
* *
13438053 ATTGGCCTCAATCTGCTCGCTGCATCTTAAGGGAGATAAGA
66 ATT--CCTCAATCTGCTCACTGCAGCTTAAGGGAGATAAGA
13438094 TTCGCCATCT
Statistics
Matches: 87, Mismatches: 15, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
126 5 0.06
127 18 0.21
128 64 0.74
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.30
Consensus pattern (126 bp):
AACTTCAGAGAGATAAGATCTACAATTTTAATCCGCTCCACTGCAACTTCAGAGAGATAGCATTG
ATTCCTCAATCTGCTCACTGCAGCTTAAGGGAGATAAGACTGTATGCGATATGTTCTCTGC
Found at i:13438161 original size:50 final size:50
Alignment explanation
Indices: 13438102--13438261 Score: 171
Period size: 50 Copynumber: 3.2 Consensus size: 50
13438092 GATTCGCCAT
13438102 CTTCAATCTGTTTAACTGCAATGTCTGGGAAACAAGATCCGCCGTCGTGA
1 CTTCAATCTGTTTAACTGCAATGTCTGGGAAACAAGATCCGCCGTCGTGA
** * ** * *** * * *
13438152 CTTCAATCTGTTCCACTACACCGTCAGGGAGGTAAGATTCGCCGTTGTGG
1 CTTCAATCTGTTTAACTGCAATGTCTGGGAAACAAGATCCGCCGTCGTGA
*
13438202 CTTCAATCAT-TTTAATTGCAATGT-TGGGGAAACAAGATCCGCCGTCGTGA
1 CTTCAATC-TGTTTAACTGCAATGTCT-GGGAAACAAGATCCGCCGTCGTGA
13438252 CTTCAATCTG
1 CTTCAATCTG
13438262 CTCTACTACA
Statistics
Matches: 82, Mismatches: 25, Indels: 6
0.73 0.22 0.05
Matches are distributed among these distances:
49 1 0.01
50 80 0.98
51 1 0.01
ACGTcount: A:0.24, C:0.24, G:0.23, T:0.29
Consensus pattern (50 bp):
CTTCAATCTGTTTAACTGCAATGTCTGGGAAACAAGATCCGCCGTCGTGA
Found at i:13438250 original size:100 final size:100
Alignment explanation
Indices: 13438102--13438309 Score: 305
Period size: 100 Copynumber: 2.1 Consensus size: 100
13438092 GATTCGCCAT
*
13438102 CTTCAATCTGTTTAACTGCAATGTCTGGGAAACAAGATCCGCCGTCGTGACTTCAATCTGTTCCA
1 CTTCAATCTGTTTAACTGCAATGTCTGGGAAACAAGATCCGCCGTCGTGACTTCAATCTGCTCCA
* * *
13438167 CTACACC-GTCAGGGAGGTAAGATTCGCCGTTGTGG
66 CTACACCACT-AGAGAAGTAAGATTCGCCGTTGTGG
*
13438202 CTTCAATCAT-TTTAATTGCAATGT-TGGGGAAACAAGATCCGCCGTCGTGACTTCAATCTGCTC
1 CTTCAATC-TGTTTAACTGCAATGTCT-GGGAAACAAGATCCGCCGTCGTGACTTCAATCTGCTC
* *
13438265 TACTACACCACTAGAGAAGTAAGATTTGCCGTTGTGG
64 CACTACACCACTAGAGAAGTAAGATTCGCCGTTGTGG
13438302 CTTCAATC
1 CTTCAATC
13438310 CAATCCACTA
Statistics
Matches: 98, Mismatches: 7, Indels: 6
0.88 0.06 0.05
Matches are distributed among these distances:
99 1 0.01
100 95 0.97
101 2 0.02
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.29
Consensus pattern (100 bp):
CTTCAATCTGTTTAACTGCAATGTCTGGGAAACAAGATCCGCCGTCGTGACTTCAATCTGCTCCA
CTACACCACTAGAGAAGTAAGATTCGCCGTTGTGG
Found at i:13438615 original size:88 final size:88
Alignment explanation
Indices: 13438513--13438681 Score: 275
Period size: 88 Copynumber: 1.9 Consensus size: 88
13438503 AGACTGGTGT
* * * *
13438513 CTTCGATCTGCTTCGCTACCAGTATAGGAAGGCAAGATCTGTCATTTTCAACCTACTCCACTGCT
1 CTTCGATCTACTTCGCTACCAATACAGGAAGACAAGATCTGTCATTTTCAACCTACTCCACTGCT
*
13438578 GCTCAGGGAGATAAGGTTGGTAC
66 ACTCAGGGAGATAAGGTTGGTAC
* *
13438601 CTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGTTATTTTCAACCTACTCCACTGCT
1 CTTCGATCTACTTCGCTACCAATACAGGAAGACAAGATCTGTCATTTTCAACCTACTCCACTGCT
13438666 ACTCAGGGAGATAAGG
66 ACTCAGGGAGATAAGG
13438682 CTGAAGTTTC
Statistics
Matches: 74, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
88 74 1.00
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.28
Consensus pattern (88 bp):
CTTCGATCTACTTCGCTACCAATACAGGAAGACAAGATCTGTCATTTTCAACCTACTCCACTGCT
ACTCAGGGAGATAAGGTTGGTAC
Found at i:13442779 original size:10 final size:10
Alignment explanation
Indices: 13442751--13442798 Score: 51
Period size: 10 Copynumber: 4.8 Consensus size: 10
13442741 TGAATGCTTG
*
13442751 ATGGAATGAA
1 ATGGAATGGA
**
13442761 ATGCTATGGA
1 ATGGAATGGA
* *
13442771 ATGAAATGGT
1 ATGGAATGGA
13442781 ATGGAATGGA
1 ATGGAATGGA
13442791 ATGGAATG
1 ATGGAATG
13442799 AAATAAAATA
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
10 30 1.00
ACGTcount: A:0.40, C:0.02, G:0.33, T:0.25
Consensus pattern (10 bp):
ATGGAATGGA
Found at i:13442794 original size:15 final size:15
Alignment explanation
Indices: 13442751--13442794 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
13442741 TGAATGCTTG
*
13442751 ATGGAATGAAATGCT
1 ATGGAATGAAATGGT
13442766 ATGGAATGAAATGGT
1 ATGGAATGAAATGGT
*
13442781 ATGGAATGGAATGG
1 ATGGAATGAAATGG
13442795 AATGAAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.39, C:0.02, G:0.34, T:0.25
Consensus pattern (15 bp):
ATGGAATGAAATGGT
Found at i:13453436 original size:26 final size:27
Alignment explanation
Indices: 13453392--13453445 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
13453382 ATACATATAT
* *
13453392 TATAGGAAATGCATGTATA-TATAAAA
1 TATAGAAAATGCATATATATTATAAAA
*
13453418 TATAGAAAATGTATATATATTATAAAA
1 TATAGAAAATGCATATATATTATAAAA
13453445 T
1 T
13453446 GTATATGCAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 16 0.67
27 8 0.33
ACGTcount: A:0.52, C:0.02, G:0.11, T:0.35
Consensus pattern (27 bp):
TATAGAAAATGCATATATATTATAAAA
Found at i:13460269 original size:50 final size:49
Alignment explanation
Indices: 13460160--13460341 Score: 168
Period size: 50 Copynumber: 3.7 Consensus size: 49
13460150 AAGAGGTCCA
* * * * *
13460160 ATGTAAGACCATGTTTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCC
1 ATGTAAGACCATGTCTGGGACATGGCATTGGCACCAACATGAGA-CTCCC
** * * *
13460210 CCGTCAGACCATGTCTGGGACATGGCATGGGCACCAATATGAGGACTCCC
1 ATGTAAGACCATGTCTGGGACATGGCATTGGCACCAACATGA-GACTCCC
* * * ** * *
13460260 ATGTAAGACCATATATGGGATATGGCATTGGCA-GTACAGGAAACATCCC
1 ATGTAAGACCATGTCTGGGACATGGCATTGGCACCAACATGAGAC-TCCC
*
13460309 ATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 ATGTAAGACCATGTCTGGGACATGGCATTGGCA
13460342 TGTTATTATC
Statistics
Matches: 105, Mismatches: 25, Indels: 5
0.78 0.19 0.04
Matches are distributed among these distances:
48 2 0.02
49 37 0.35
50 64 0.61
51 2 0.02
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.22
Consensus pattern (49 bp):
ATGTAAGACCATGTCTGGGACATGGCATTGGCACCAACATGAGACTCCC
Found at i:13464564 original size:110 final size:110
Alignment explanation
Indices: 13464271--13464779 Score: 736
Period size: 111 Copynumber: 4.7 Consensus size: 110
13464261 AAAAAAATTC
* * * * * *
13464271 AAATAAAT-AAAAGAACAAATAAAATTACCTT-ATAACAAATCATAATACACATTAAACTAAACA
1 AAATAATTAAAAAAAACAAA-AAAATTACATTCATAAAAAATCATAATAAACACTAAACTAAACA
13464334 -AATAC--TTTATAACCTAATCATAAATTACTAACAAAATAACTTTA
65 CAA-ACAATTTATAACCTAATCATAAATTACTAACAAAATAACTTTA
* * *
13464378 AAGTAATT-GAAAAAAC----AAATTACATTCATAAAAAATCACAATAAACACTAAACTAAACAC
1 AAATAATTAAAAAAAACAAAAAAATTACATTCATAAAAAATCATAATAAACACTAAACTAAACAC
13464438 AAACAATTTATAACCTAATCATAAATTACTAACAAAATAACTTTA
66 AAACAATTTATAACCTAATCATAAATTACTAACAAAATAACTTTA
13464483 AAATAATTAAAAAAAACAAAAAAATTACATTCATAAAAAATCATAATAAACACTAAACTAAACAC
1 AAATAATTAAAAAAAACAAAAAAATTACATTCATAAAAAATCATAATAAACACTAAACTAAACAC
*
13464548 AAAAAATTTATAACCTAATCATAAATTACTAACAAAATAACTTTA
66 AAACAATTTATAACCTAATCATAAATTACTAACAAAATAACTTTA
* *
13464593 AAATAATTTAAAAAACAA-AAAAAAATTACATTCATAAAAAATTACAATAAACACTAAACTAAAC
1 AAATAA-TTAAAAAA-AACAAAAAAATTACATTCATAAAAAATCATAATAAACACTAAACTAAAC
* * *
13464657 ACAAATAATTTATAACATAATCATAAATTACTAACGAAATAACTTTA
64 ACAAACAATTTATAACCTAATCATAAATTACTAACAAAATAACTTTA
*
13464704 AAATAATTAAAAAAATA-AAAAAAATTTACATTCATAAAAAATCATAATATACACTAAACTAAAC
1 AAATAATTAAAAAAA-ACAAAAAAA-TTACATTCATAAAAAATCATAATAAACACTAAACTAAAC
13464768 ACAAACAATTTA
64 ACAAACAATTTA
13464780 CAATAATTAC
Statistics
Matches: 367, Mismatches: 22, Indels: 22
0.89 0.05 0.05
Matches are distributed among these distances:
102 9 0.02
103 30 0.08
104 2 0.01
105 46 0.13
106 7 0.02
107 12 0.03
109 1 0.00
110 109 0.30
111 149 0.41
112 2 0.01
ACGTcount: A:0.60, C:0.14, G:0.01, T:0.26
Consensus pattern (110 bp):
AAATAATTAAAAAAAACAAAAAAATTACATTCATAAAAAATCATAATAAACACTAAACTAAACAC
AAACAATTTATAACCTAATCATAAATTACTAACAAAATAACTTTA
Found at i:13464682 original size:221 final size:215
Alignment explanation
Indices: 13464271--13464779 Score: 758
Period size: 221 Copynumber: 2.3 Consensus size: 215
13464261 AAAAAAATTC
* * * * * *
13464271 AAATAAAT-AAAAGAACAAATAAAATTACCTT-ATAACAAATCATAATACACATTAAACT-AA-A
1 AAATAATTAAAAAAAACAAA-AAAATTACATTCATAAAAAATCATAATAAACACTAAACTAAACA
* * *
13464332 CAAATACTTTATAACCTAATCATAAATTACTAACAAAATAACTTTAAAGTAATTGAAAAAACAAA
65 CAAAAAATTTATAACCTAATCATAAATTACTAACAAAATAACTTTAAAATAATTGAAAAAACAAA
*
13464397 TTACATTCATAAAAAATCACAATAAACACTAAACTAAACACAAACAATTTATAACCTAATCATAA
130 TTACATTCATAAAAAATCACAATAAACACTAAACTAAACACAAACAATTTATAACATAATCATAA
13464462 ATTACTAACAAAATAACTTTA
195 ATTACTAACAAAATAACTTTA
13464483 AAATAATTAAAAAAAACAAAAAAATTACATTCATAAAAAATCATAATAAACACTAAACTAAACAC
1 AAATAATTAAAAAAAACAAAAAAATTACATTCATAAAAAATCATAATAAACACTAAACTAAACAC
*
13464548 AAAAAATTTATAACCTAATCATAAATTACTAACAAAATAACTTTAAAATAATTTAAAAAACAAAA
66 AAAAAATTTATAACCTAATCATAAATTACTAACAAAATAACTTTAAAATAATTGAAAAAAC----
* *
13464613 AAAAATTACATTCATAAAAAATTACAATAAACACTAAACTAAACACAAATAATTTATAACATAAT
127 --AAATTACATTCATAAAAAATCACAATAAACACTAAACTAAACACAAACAATTTATAACATAAT
*
13464678 CATAAATTACTAACGAAATAACTTTA
190 CATAAATTACTAACAAAATAACTTTA
*
13464704 AAATAATTAAAAAAATA-AAAAAAATTTACATTCATAAAAAATCATAATATACACTAAACTAAAC
1 AAATAATTAAAAAAA-ACAAAAAAA-TTACATTCATAAAAAATCATAATAAACACTAAACTAAAC
*
13464768 ACAAACAATTTA
64 ACAAAAAATTTA
13464780 CAATAATTAC
Statistics
Matches: 269, Mismatches: 16, Indels: 14
0.90 0.05 0.05
Matches are distributed among these distances:
212 17 0.06
213 34 0.13
214 2 0.01
215 59 0.22
221 107 0.40
222 50 0.19
ACGTcount: A:0.60, C:0.14, G:0.01, T:0.26
Consensus pattern (215 bp):
AAATAATTAAAAAAAACAAAAAAATTACATTCATAAAAAATCATAATAAACACTAAACTAAACAC
AAAAAATTTATAACCTAATCATAAATTACTAACAAAATAACTTTAAAATAATTGAAAAAACAAAT
TACATTCATAAAAAATCACAATAAACACTAAACTAAACACAAACAATTTATAACATAATCATAAA
TTACTAACAAAATAACTTTA
Found at i:13464881 original size:26 final size:26
Alignment explanation
Indices: 13464825--13464889 Score: 87
Period size: 26 Copynumber: 2.4 Consensus size: 26
13464815 AAAAACAACA
*
13464825 TAAAAAATATTAACTAATCCCTTCTATT
1 TAAAAAA-ATT-ACTAATCCCTTCTAAT
13464853 TAAAAAAATTACTAATCCCTT-TAAAT
1 TAAAAAAATTACTAATCCCTTCT-AAT
13464879 TAAAAAAATTA
1 TAAAAAAATTA
13464890 TAAAATACCT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
25 1 0.03
26 24 0.69
27 3 0.09
28 7 0.20
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (26 bp):
TAAAAAAATTACTAATCCCTTCTAAT
Found at i:13464884 original size:27 final size:27
Alignment explanation
Indices: 13464825--13464886 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
13464815 AAAAACAACA
*
13464825 TAAAAAATATTAACTAATCCCTTCTAT
1 TAAAAAAAATTAACTAATCCCTTCTAT
*
13464852 TTAAAAAAATT-ACTAATCCCTT-TAAAT
1 TAAAAAAAATTAACTAATCCCTTCT--AT
13464879 TAAAAAAA
1 TAAAAAAA
13464887 TTATAAAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
25 1 0.03
26 11 0.37
27 18 0.60
ACGTcount: A:0.52, C:0.15, G:0.00, T:0.34
Consensus pattern (27 bp):
TAAAAAAAATTAACTAATCCCTTCTAT
Found at i:13464963 original size:14 final size:14
Alignment explanation
Indices: 13464904--13464963 Score: 66
Period size: 14 Copynumber: 4.3 Consensus size: 14
13464894 ATACCTTCCA
* *
13464904 TTTCTTTTCTTTTT
1 TTTCCTTTCTTTCT
*
13464918 TTTTCTTTCTTTCT
1 TTTCCTTTCTTTCT
* * *
13464932 TCTCCTTCCTTTCC
1 TTTCCTTTCTTTCT
13464946 TTTCCTTTCTTTCT
1 TTTCCTTTCTTTCT
13464960 TTTC
1 TTTC
13464964 TCCCTCTATT
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
14 36 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (14 bp):
TTTCCTTTCTTTCT
Found at i:13472323 original size:14 final size:14
Alignment explanation
Indices: 13472300--13472338 Score: 60
Period size: 14 Copynumber: 2.7 Consensus size: 14
13472290 GAAATAGGCA
13472300 AGAAAAAGGAAAAG
1 AGAAAAAGGAAAAG
*
13472314 AGAAAGAGGAAAAG
1 AGAAAAAGGAAAAG
13472328 AGAACAAAGGA
1 AGAA-AAAGGA
13472339 GGTGAAACAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 17 0.77
15 5 0.23
ACGTcount: A:0.67, C:0.03, G:0.31, T:0.00
Consensus pattern (14 bp):
AGAAAAAGGAAAAG
Found at i:13489587 original size:23 final size:23
Alignment explanation
Indices: 13489559--13489602 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
13489549 CTTTCTTACT
*
13489559 GTAGTAATTTTCGAGGTATTATA
1 GTAGTAATTTTCGAGATATTATA
13489582 GTAGTAATTTTCGAGATATTA
1 GTAGTAATTTTCGAGATATTA
13489603 CATTTCTCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.32, C:0.05, G:0.20, T:0.43
Consensus pattern (23 bp):
GTAGTAATTTTCGAGATATTATA
Found at i:13490986 original size:35 final size:35
Alignment explanation
Indices: 13490940--13491010 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
13490930 TCCTTATACT
*
13490940 TACCTGAATCTGTTTATTGTACTTTTTCCTGAACA
1 TACCTGAATCTGTTTATTGTACTTTTACCTGAACA
13490975 TACCTGAATCTGTTTATTGTACTTTTACCTGAACA
1 TACCTGAATCTGTTTATTGTACTTTTACCTGAACA
13491010 T
1 T
13491011 TCATGTAACA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.24, C:0.20, G:0.11, T:0.45
Consensus pattern (35 bp):
TACCTGAATCTGTTTATTGTACTTTTACCTGAACA
Found at i:13491158 original size:49 final size:48
Alignment explanation
Indices: 13491094--13491323 Score: 176
Period size: 49 Copynumber: 4.7 Consensus size: 48
13491084 TAATAACATA
*
13491094 CCAAAGCCATGTCCCAGACATGGTCTTACATGAGATGTTTCCTGTACTG
1 CCAATGCCATGTCCCAGACATGGTCTTACATGAGATGTTTCCTGT-CTG
* * * * *
13491143 CCAATGCCATATCCCAGATATGGTCTTACATGGGA-GTTCTCATATCGGTG
1 CCAATGCCATGTCCCAGACATGGTCTTACATGAGATGTT-TCCTGTC--TG
* * * ** * * *
13491193 CCCATGCCATGTCTCAGACATGGTCTTACGAGGACCTCTCATCCTG-GTG
1 CCAATGCCATGTCCCAGACATGGTCTTAC-ATGAGATGT-TTCCTGTCTG
* ** * * *
13491242 CCAACGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATCTCGGTG
1 CCAATGCCATGTCCCAGACATGGTCTTACATGAGATGTTTCCTGTC--TG
* *
13491292 CCAACGCAATGTCCCAGACATGGTCTTACATG
1 CCAATGCCATGTCCCAGACATGGTCTTACATG
13491324 GGACCTCTCA
Statistics
Matches: 141, Mismatches: 31, Indels: 17
0.75 0.16 0.09
Matches are distributed among these distances:
47 3 0.02
48 9 0.06
49 63 0.45
50 60 0.43
51 2 0.01
52 4 0.03
ACGTcount: A:0.23, C:0.30, G:0.21, T:0.27
Consensus pattern (48 bp):
CCAATGCCATGTCCCAGACATGGTCTTACATGAGATGTTTCCTGTCTG
Found at i:13491217 original size:50 final size:50
Alignment explanation
Indices: 13491094--13491423 Score: 289
Period size: 50 Copynumber: 6.6 Consensus size: 50
13491084 TAATAACATA
* * ** * * *
13491094 CCAAAGCCATGTCCCAGACATGGTCTTACATGAGATGTTTCCTGTAC--TG
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAT-CGGTG
* * **
13491143 CCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGGTG
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTG
* * *
13491193 CCCATGCCATGTCTCAGACATGGTCTTAC--GAGGACCTCTCAT-CCTGGTG
1 CCAATGCCATGTCCCAGACATGGTCTTACATG-GGACCTCTCATATC-GGTG
* * *
13491242 CCAACGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATCTCGGTG
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTG
* * *
13491292 CCAACGCAATGTCCCAGACATGGTCTTACATGGGACCTCTCATAATCTCAATGATG
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--TC---GGTG
* *
13491348 CCAATGCCATGTCCCAGACATGGTCTTACACT-GG--CTCACATATCGATG
1 CCAATGCCATGTCCCAGACATGGTCTTACA-TGGGACCTCTCATATCGGTG
* * *
13491396 TCGATGCCATGTCCCAGACATAGTCTTA
1 CCAATGCCATGTCCCAGACATGGTCTTA
13491424 TACGAGATTG
Statistics
Matches: 236, Mismatches: 31, Indels: 29
0.80 0.10 0.10
Matches are distributed among these distances:
48 32 0.14
49 75 0.32
50 82 0.35
51 4 0.02
53 3 0.01
54 6 0.03
56 33 0.14
57 1 0.00
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (50 bp):
CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTG
Found at i:13491244 original size:99 final size:102
Alignment explanation
Indices: 13491141--13491377 Score: 293
Period size: 99 Copynumber: 2.3 Consensus size: 102
13491131 TTTCCTGTAC
* * * ** * * *
13491141 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGGTGCCCATGCCATGTC
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATATCGGTGCCAACGCAATGTC
* *
13491206 TCAGACATGGTCTTAC-GAGGACCTCTC-ATC-C-TGG
66 CCAGACATGGTCTTACAG-GGACCTCTCAATCTCATGA
* *
13491240 TGCCAACGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATCTCGGTGCCAACGCAATGTC
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATATCGGTGCCAACGCAATGTC
13491305 CCAGACATGGTCTTACATGGGACCTCTCATAATCTCAATGA
66 CCAGACATGGTCTTACA-GGGACCTCTC--AATCTC-ATGA
13491346 TGCCAATGCCATGTCCCAGACATGGTCTTACA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACA
13491378 CTGGCTCACA
Statistics
Matches: 117, Mismatches: 13, Indels: 9
0.84 0.09 0.06
Matches are distributed among these distances:
99 70 0.60
100 9 0.08
101 1 0.01
103 3 0.03
104 1 0.01
106 33 0.28
ACGTcount: A:0.24, C:0.30, G:0.20, T:0.26
Consensus pattern (102 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATATCGGTGCCAACGCAATGTC
CCAGACATGGTCTTACAGGGACCTCTCAATCTCATGA
Found at i:13491764 original size:13 final size:13
Alignment explanation
Indices: 13491746--13491770 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13491736 TCTATTTGTG
13491746 CATATTTACTTAC
1 CATATTTACTTAC
13491759 CATATTTACTTA
1 CATATTTACTTA
13491771 ATCAAATATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.20, G:0.00, T:0.48
Consensus pattern (13 bp):
CATATTTACTTAC
Found at i:13494490 original size:23 final size:23
Alignment explanation
Indices: 13494459--13494509 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
13494449 ACCTATTTTC
* *
13494459 TTACTGTAGTAATTTTCGGGGTA
1 TTACAGTAGTAATTTTCGGGATA
13494482 TTACAGTAGTAATTTTCGGGATA
1 TTACAGTAGTAATTTTCGGGATA
13494505 TTACA
1 TTACA
13494510 AATATTGTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.27, C:0.10, G:0.22, T:0.41
Consensus pattern (23 bp):
TTACAGTAGTAATTTTCGGGATA
Found at i:13502714 original size:9 final size:9
Alignment explanation
Indices: 13502698--13502730 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
13502688 TTAATTGAGA
13502698 AATTAATTT
1 AATTAATTT
*
13502707 AGTTAATTT
1 AATTAATTT
13502716 AATTAATTT
1 AATTAATTT
13502725 AATTAA
1 AATTAA
13502731 CTGATTAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (9 bp):
AATTAATTT
Found at i:13505564 original size:39 final size:40
Alignment explanation
Indices: 13505516--13505605 Score: 114
Period size: 39 Copynumber: 2.3 Consensus size: 40
13505506 TTGTTTATTG
* * *
13505516 TTTAAGGTTTAAGG-TTTA-TAGTTTATATATGTTTTATGA
1 TTTAGGGTTTAAGGATTTAGT-GTTTATATATATTCTATGA
13505555 TTTAGGGTTT-AGGATTTAGTGTTTATATATATTCTATGA
1 TTTAGGGTTTAAGGATTTAGTGTTTATATATATTCTATGA
*
13505594 TTCAGGGTTTAA
1 TTTAGGGTTTAA
13505606 AGAATATGAC
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
38 3 0.07
39 39 0.89
40 2 0.05
ACGTcount: A:0.27, C:0.02, G:0.20, T:0.51
Consensus pattern (40 bp):
TTTAGGGTTTAAGGATTTAGTGTTTATATATATTCTATGA
Found at i:13505688 original size:8 final size:8
Alignment explanation
Indices: 13505651--13505703 Score: 58
Period size: 8 Copynumber: 7.0 Consensus size: 8
13505641 TGTAATAGTT
13505651 GGGGTTTA
1 GGGGTTTA
*
13505659 -AGGTTTA
1 GGGGTTTA
* *
13505666 AGTGTTTA
1 GGGGTTTA
13505674 -GGG-TTA
1 GGGGTTTA
13505680 GGGGTTTA
1 GGGGTTTA
13505688 GGGGTTTA
1 GGGGTTTA
13505696 GGGGTTTA
1 GGGGTTTA
13505704 CAGTTAATGT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
6 3 0.08
7 11 0.29
8 24 0.63
ACGTcount: A:0.17, C:0.00, G:0.43, T:0.40
Consensus pattern (8 bp):
GGGGTTTA
Found at i:13505954 original size:21 final size:22
Alignment explanation
Indices: 13505916--13505958 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
13505906 GGGTTTGTGA
13505916 GTTTAAGGTTTAAGGGTTAAGG
1 GTTTAAGGTTTAAGGGTTAAGG
*
13505938 GTTTAGGGTTT-AGGGTTAAGG
1 GTTTAAGGTTTAAGGGTTAAGG
13505959 TCTAAGGAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.23, C:0.00, G:0.40, T:0.37
Consensus pattern (22 bp):
GTTTAAGGTTTAAGGGTTAAGG
Found at i:13508640 original size:17 final size:18
Alignment explanation
Indices: 13508620--13508653 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
13508610 ACATTTTTAA
13508620 TATATATTTTT-AAAATC
1 TATATATTTTTCAAAATC
*
13508637 TATATTTTTTTCAAAAT
1 TATATATTTTTCAAAAT
13508654 TTATCAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (18 bp):
TATATATTTTTCAAAATC
Found at i:13508793 original size:9 final size:9
Alignment explanation
Indices: 13508775--13509382 Score: 559
Period size: 9 Copynumber: 69.2 Consensus size: 9
13508765 CATATATAGA
*
13508775 AACTTGCAT
1 AACTTACAT
13508784 AACTTACAT
1 AACTTACAT
13508793 AACTTACAT
1 AACTTACAT
* *
13508802 AAATTAAAT
1 AACTTACAT
13508811 AACTTACAT
1 AACTTACAT
*
13508820 AACTTAAAT
1 AACTTACAT
13508829 AACTTACAT
1 AACTTACAT
13508838 AA--TACAT
1 AACTTACAT
*
13508845 AACCTT-CCT
1 AA-CTTACAT
13508854 AACTTACAT
1 AACTTACAT
* *
13508863 TATTTACAT
1 AACTTACAT
13508872 AA--TACAT
1 AACTTACAT
13508879 AACTTAGTACAT
1 AAC-T--TACAT
13508891 AACTTACAT
1 AACTTACAT
13508900 AACTTACAT
1 AACTTACAT
13508909 AACTTACAT
1 AACTTACAT
* *
13508918 AAATTAAAT
1 AACTTACAT
13508927 AACTTACAT
1 AACTTACAT
13508936 AACTTACAT
1 AACTTACAT
* *
13508945 AAATTAAAT
1 AACTTACAT
13508954 AACTTACAT
1 AACTTACAT
* *
13508963 AAATTAAAT
1 AACTTACAT
*
13508972 AACTTACAC
1 AACTTACAT
*
13508981 AAATTACAT
1 AACTTACAT
13508990 AACTTACAT
1 AACTTACAT
13508999 AACTTACAT
1 AACTTACAT
13509008 AACTTACAT
1 AACTTACAT
*
13509017 AACTTAAAT
1 AACTTACAT
13509026 AACTTACAT
1 AACTTACAT
13509035 AA--TACAT
1 AACTTACAT
*
13509042 AACCTT-CCT
1 AA-CTTACAT
13509051 AACTTACAT
1 AACTTACAT
* *
13509060 AA--AACAC
1 AACTTACAT
*
13509067 AACCTACAT
1 AACTTACAT
*
13509076 AACTCACAT
1 AACTTACAT
*
13509085 AA--TACAC
1 AACTTACAT
13509092 AACTTACAT
1 AACTTACAT
13509101 AACTTACAT
1 AACTTACAT
*
13509110 AGA-TTAAAT
1 A-ACTTACAT
13509119 AACTTACAT
1 AACTTACAT
* *
13509128 AAATTAAAT
1 AACTTACAT
*
13509137 AA-TTACAC
1 AACTTACAT
*
13509145 AAATTACAT
1 AACTTACAT
13509154 AACTTACAT
1 AACTTACAT
13509163 AACTTACAT
1 AACTTACAT
*
13509172 AACTTACAC
1 AACTTACAT
* *
13509181 AAATTAAAT
1 AACTTACAT
13509190 AACTTACAT
1 AACTTACAT
13509199 AACTTACAT
1 AACTTACAT
*
13509208 AACTTAAAT
1 AACTTACAT
13509217 AACTTACAT
1 AACTTACAT
13509226 AA--TACAT
1 AACTTACAT
*
13509233 AACCTT-CCT
1 AA-CTTACAT
13509242 AACTTACAT
1 AACTTACAT
*
13509251 AA--TACAC
1 AACTTACAT
*
13509258 AACCTACAT
1 AACTTACAT
*
13509267 AACTCACAT
1 AACTTACAT
*
13509276 AA--TACAC
1 AACTTACAT
13509283 AACTTACAT
1 AACTTACAT
13509292 AACTTACAT
1 AACTTACAT
13509301 AA--TACAT
1 AACTTACAT
** *
13509308 AAAAATATAT
1 -AACTTACAT
13509318 AA--TATCAT
1 AACTTA-CAT
13509326 AACTTACAT
1 AACTTACAT
*
13509335 AACTTAAAT
1 AACTTACAT
13509344 AACTTACAT
1 AACTTACAT
13509353 AA--TACAT
1 AACTTACAT
13509360 AACTTAGTACAT
1 AAC-T--TACAT
13509372 AACTTACAT
1 AACTTACAT
13509381 AA
1 AA
13509383 TACATAAAAA
Statistics
Matches: 490, Mismatches: 70, Indels: 78
0.77 0.11 0.12
Matches are distributed among these distances:
7 63 0.13
8 22 0.04
9 377 0.77
10 10 0.02
11 2 0.00
12 16 0.03
ACGTcount: A:0.49, C:0.20, G:0.01, T:0.31
Consensus pattern (9 bp):
AACTTACAT
Found at i:13514860 original size:21 final size:21
Alignment explanation
Indices: 13514834--13514901 Score: 82
Period size: 21 Copynumber: 3.2 Consensus size: 21
13514824 CTACAACTTA
*
13514834 AAGCAGAGGCGGCAGCGAGGG
1 AAGCAGAGGCGGCAGCGAGAG
* *
13514855 AAGCAGAGACTGCAGCGAGAG
1 AAGCAGAGGCGGCAGCGAGAG
** *
13514876 AAGCAGAGGTTGTAGCGAGAG
1 AAGCAGAGGCGGCAGCGAGAG
13514897 AAGCA
1 AAGCA
13514902 AAGGTTCAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.35, C:0.16, G:0.43, T:0.06
Consensus pattern (21 bp):
AAGCAGAGGCGGCAGCGAGAG
Found at i:13514906 original size:21 final size:21
Alignment explanation
Indices: 13514868--13514907 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
13514858 CAGAGACTGC
*
13514868 AGCGAGAGAAGCAGAGGTTGT
1 AGCGAGAGAAGCAAAGGTTGT
13514889 AGCGAGAGAAGCAAAGGTT
1 AGCGAGAGAAGCAAAGGTT
13514908 CAAAAGAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.38, C:0.10, G:0.40, T:0.12
Consensus pattern (21 bp):
AGCGAGAGAAGCAAAGGTTGT
Found at i:13515584 original size:42 final size:41
Alignment explanation
Indices: 13515333--13515583 Score: 288
Period size: 42 Copynumber: 6.0 Consensus size: 41
13515323 TTTGTGAAGA
13515333 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTATTT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTT-TTT
* **
13515375 AAGCGCCGCTAAAGAATAAT-ATCTTTAGCGGCGTTTTTCTCC
1 AAGCGCCGCTAAAGAA-CATGATCTTTAGCGGCGTTTTT-TTT
* * * *
13515417 ATGCGCCACTAAAGAACAAGATCTTTAACGGCGTTTTTCTTT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTT-TTT
* *
13515459 AAGCGCCGCTAAAGAACATGATCTTTAGCGGTGAATTTTTTTA
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCG--TTTTTTTT
* * * *
13515502 AAGCGCCGCTAAAGAACATGACCTTTAGAGGCATTTTTTTCG
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTT-T
* * *
13515544 AAGCGCCGCTAAAAAATATGACCTTTAGCGGCGTTTTTTT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTT
13515584 CTGTAAACGC
Statistics
Matches: 178, Mismatches: 26, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
41 8 0.04
42 132 0.74
43 33 0.19
44 5 0.03
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (41 bp):
AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTT
Found at i:13515673 original size:21 final size:21
Alignment explanation
Indices: 13515649--13515708 Score: 93
Period size: 21 Copynumber: 2.9 Consensus size: 21
13515639 CTTAGCGGCG
* *
13515649 CTAAAAAGCACCGCTAAAGGC
1 CTAAAAAACGCCGCTAAAGGC
*
13515670 CTAAAAAACGCCGCTAAATGC
1 CTAAAAAACGCCGCTAAAGGC
13515691 CTAAAAAACGCCGCTAAA
1 CTAAAAAACGCCGCTAAA
13515709 AACCTGTTCT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.45, C:0.28, G:0.15, T:0.12
Consensus pattern (21 bp):
CTAAAAAACGCCGCTAAAGGC
Found at i:13521398 original size:18 final size:17
Alignment explanation
Indices: 13521357--13521403 Score: 69
Period size: 18 Copynumber: 2.8 Consensus size: 17
13521347 TAATTTTTTT
*
13521357 AAAAAATAA-AAATTGC
1 AAAAAAAAACAAATTGC
13521373 AAAAAAAAACAAATTGC
1 AAAAAAAAACAAATTGC
13521390 AAAAAAAAAACAAA
1 -AAAAAAAAACAAA
13521404 ATAACCAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
16 8 0.29
17 7 0.25
18 13 0.46
ACGTcount: A:0.77, C:0.09, G:0.04, T:0.11
Consensus pattern (17 bp):
AAAAAAAAACAAATTGC
Found at i:13521413 original size:19 final size:18
Alignment explanation
Indices: 13521372--13521416 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
13521362 ATAAAAATTG
**
13521372 CAAAAAAAAACAAATTGC
1 CAAAAAAAAACAAATAAC
*
13521390 AAAAAAAAAACAAAATAAC
1 CAAAAAAAAAC-AAATAAC
13521409 CAAAAAAA
1 CAAAAAAA
13521417 TGAAATTTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 10 0.45
19 12 0.55
ACGTcount: A:0.78, C:0.13, G:0.02, T:0.07
Consensus pattern (18 bp):
CAAAAAAAAACAAATAAC
Found at i:13523595 original size:24 final size:24
Alignment explanation
Indices: 13523568--13523619 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
13523558 TTAGTAAGTC
*
13523568 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
13523592 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
13523616 AAAT
1 AAAT
13523620 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:13525569 original size:24 final size:24
Alignment explanation
Indices: 13525542--13525593 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
13525532 TTAGTAAGTC
*
13525542 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
13525566 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
13525590 AAAT
1 AAAT
13525594 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:13532776 original size:107 final size:103
Alignment explanation
Indices: 13532655--13532908 Score: 438
Period size: 103 Copynumber: 2.4 Consensus size: 103
13532645 AAAATTTTTT
13532655 TTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAATTTAAAAAAAAATTCTTTTTTTTTTC
1 TTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAATTTAAAAAAAAATTC---TTTTTTT-
*
13532720 GTGTCAAAATCAGATATCAGTATACGAAAAACAT-AAAAAAAA
62 GTGTCAAAATCAGATATCAGTATAC-AAAAAAATAAAAAAAAA
13532762 TTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAATTTAAAAAAAAATTCTTTTTTTGTGT
1 TTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAATTTAAAAAAAAATTCTTTTTTTGTGT
13532827 CAAAATCAGATATCAGTATACAAAAAAATAAAAAAAAA
66 CAAAATCAGATATCAGTATACAAAAAAATAAAAAAAAA
*
13532865 TTTAGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAATTTAA
1 TTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAATTTAA
13532909 TTTTTTTTTC
Statistics
Matches: 144, Mismatches: 2, Indels: 6
0.95 0.01 0.04
Matches are distributed among these distances:
102 7 0.05
103 76 0.53
104 7 0.05
107 54 0.38
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29
Consensus pattern (103 bp):
TTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAATTTAAAAAAAAATTCTTTTTTTGTGT
CAAAATCAGATATCAGTATACAAAAAAATAAAAAAAAA
Found at i:13533083 original size:104 final size:106
Alignment explanation
Indices: 13532956--13533300 Score: 563
Period size: 104 Copynumber: 3.3 Consensus size: 106
13532946 TAACACGAAA
* *
13532956 TTTTTTTAAAATTGTACTGGGTGCCGGCCATTGACATGCCAGCACCCAAAATTTTTTTTATTTTT
1 TTTTTTTTAAATTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAATTTTTTTTATTTTT
13533021 TTCGTATACTGATATCTGATTTTGACAC-AAAAAAAAG-AT
66 TTCGTATACTGATATCTGATTTTGACACAAAAAAAAAGAAT
*
13533060 TTTTTTTTAAATTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAATTTTTTTTTATTTTT
1 TTTTTTTTAAATTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAATTTTTTTTATTTTT
13533125 TTCGTATACTGATATCTGATTTTGACACGAAAAAAAAAGAAT
66 TTCGTATACTGATATCTGATTTTGACAC-AAAAAAAAAGAAT
* *
13533167 TTTTTTTTAAATTGTACTGGGTGCCGGCCATTGATAGGCCAACA-CC-AAATTTTTTTTATTTTT
1 TTTTTTTTAAATTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAATTTTTTTTATTTTT
* * *
13533230 TTCGTATACTGATATTTGACTCTGACACAAAAAAAAAGAAAT
66 TTCGTATACTGATATCTGATTTTGACACAAAAAAAAAG-AAT
*
13533272 TTTTTTTTAAATTGTATTGGGTGCCGGCC
1 TTTTTTTTAAATTGTACTGGGTGCCGGCC
13533301 TGTCTTTTTT
Statistics
Matches: 227, Mismatches: 10, Indels: 7
0.93 0.04 0.03
Matches are distributed among these distances:
104 100 0.44
105 72 0.32
106 11 0.05
107 44 0.19
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.40
Consensus pattern (106 bp):
TTTTTTTTAAATTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAAATTTTTTTTATTTTT
TTCGTATACTGATATCTGATTTTGACACAAAAAAAAAGAAT
Found at i:13533327 original size:16 final size:16
Alignment explanation
Indices: 13533306--13533337 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
13533296 CGGCCTGTCT
*
13533306 TTTTTTTTCGTTTTTC
1 TTTTTTTTCCTTTTTC
13533322 TTTTTTTTCCTTTTTC
1 TTTTTTTTCCTTTTTC
13533338 GTATATCAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.00, C:0.16, G:0.03, T:0.81
Consensus pattern (16 bp):
TTTTTTTTCCTTTTTC
Found at i:13533336 original size:17 final size:17
Alignment explanation
Indices: 13533303--13533337 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
13533293 TGCCGGCCTG
*
13533303 TCTTTTTTTTTCGTTTT
1 TCTTTTTTTTCCGTTTT
13533320 TCTTTTTTTTCC-TTTT
1 TCTTTTTTTTCCGTTTT
13533336 TC
1 TC
13533338 GTATATCAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.00, C:0.17, G:0.03, T:0.80
Consensus pattern (17 bp):
TCTTTTTTTTCCGTTTT
Found at i:13534106 original size:13 final size:13
Alignment explanation
Indices: 13534084--13534122 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
13534074 GATCCGACCC
13534084 ATATTAAATATAT
1 ATATTAAATATAT
*
13534097 ATATTTAATATAT
1 ATATTAAATATAT
13534110 ATA--AAATATAT
1 ATATTAAATATAT
13534121 AT
1 AT
13534123 TTTGTCGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 9 0.38
13 15 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
ATATTAAATATAT
Found at i:13537158 original size:88 final size:88
Alignment explanation
Indices: 13537066--13537316 Score: 200
Period size: 88 Copynumber: 2.8 Consensus size: 88
13537056 ACCAGTATGG
* * * *
13537066 GAAGATAAGATAT-GTATATTCGATCCACTTCACTACC-GATATAGGAAGACAGGACCTACTATC
1 GAAGATAAGATATAATATATTCGATCCACTCCACCACCAG-TATAGGAAGACAAGACCT-CTATC
13537129 TTTGATCTACTTCACGCCAGTACAT
64 TTTGATCTACTTCACGCCAGTACAT
* * * * * * * * * *
13537154 GAAGATAATATCTAATTTCTTCGATCTACTCCACCACCAGTATGGGGAGACAAGATCTGTTTCTT
1 GAAGATAAGATATAATATATTCGATCCACTCCACCACCAGTATAGGAAGACAAGACCTCTATCTT
*
13537219 TGATCTTCTTCACGCCAGTACAT
66 TGATCTACTTCACGCCAGTACAT
* * * * ** ** * * * * **
13537242 GAAGACAAGATCTATTTTCCTCGATATACTTCACCACCGGTATGGGAAAACAAGATTTGCTATCT
1 GAAGATAAGATATAATATATTCGATCCACTCCACCACCAGTATAGGAAGACAAGACCT-CTATCT
13537307 TTGATCTACT
65 TTGATCTACT
13537317 CCACCACCAG
Statistics
Matches: 132, Mismatches: 28, Indels: 5
0.80 0.17 0.03
Matches are distributed among these distances:
88 86 0.65
89 45 0.34
90 1 0.01
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.31
Consensus pattern (88 bp):
GAAGATAAGATATAATATATTCGATCCACTCCACCACCAGTATAGGAAGACAAGACCTCTATCTT
TGATCTACTTCACGCCAGTACAT
Found at i:13537248 original size:43 final size:44
Alignment explanation
Indices: 13537127--13537275 Score: 147
Period size: 44 Copynumber: 3.4 Consensus size: 44
13537117 GGACCTACTA
* *
13537127 TCTTTGATCTACTTCACGCCAGTACATGAAGATAATATCTAATT
1 TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTAATT
* * * *** * *
13537171 TCTTCGATCTACTCCACCACCAGTATGGGGAGACAAGATCT-GTT
1 TCTTTGATCTACTTCA-CGCCAGTACATGAAGACAAGATCTAATT
* *
13537215 TCTTTGATCTTCTTCACGCCAGTACATGAAGACAAGATCTATTT
1 TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTAATT
* * *
13537259 TCCTCGATATACTTCAC
1 TCTTTGATCTACTTCAC
13537276 CACCGGTATG
Statistics
Matches: 80, Mismatches: 23, Indels: 4
0.75 0.21 0.04
Matches are distributed among these distances:
43 19 0.24
44 44 0.55
45 17 0.21
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.34
Consensus pattern (44 bp):
TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTAATT
Found at i:13537584 original size:89 final size:90
Alignment explanation
Indices: 13537486--13537744 Score: 321
Period size: 89 Copynumber: 2.9 Consensus size: 90
13537476 ATGTATATTT
* * * * * *
13537486 GATCCACTTCGCTACCGA-TATAGGAAGACAGGACCTACTATCTTTGATCTACTTCATGCCAGTA
1 GATCTACTTCGCCACCGAGTATGGGAAGACAAGATCT-CTATCTTTGATCTACTTCACGCCAGTA
13537550 CATGAAGACAAGATCTG-TTTTCTTC
65 CATGAAGACAAGATCTGTTTTTCTTC
*
13537575 GATCTACTTCGCCACC-AGTATGGGAAGACAAGATCTGCTATCTTTGGTCTACTTCACGCCAGTA
1 GATCTACTTCGCCACCGAGTATGGGAAGACAAGATCT-CTATCTTTGATCTACTTCACGCCAGTA
*
13537639 CATGAAGACAAGATCCGTTTTTCTTC
65 CATGAAGACAAGATCTGTTTTTCTTC
* * * * * * *
13537665 AATCTGCTCCACCA-CGAGTATGGGGAAG-CAAGATCTGTTTCTTTGATCGACTTCACGCCAGTA
1 GATCTACTTCGCCACCGAGTAT-GGGAAGACAAGATCTCTATCTTTGATCTACTTCACGCCAGTA
13537728 CATGAAGACAAGATCTG
65 CATGAAGACAAGATCTG
13537745 CTTTGCCACC
Statistics
Matches: 148, Mismatches: 18, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
88 1 0.01
89 110 0.74
90 31 0.21
91 6 0.04
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29
Consensus pattern (90 bp):
GATCTACTTCGCCACCGAGTATGGGAAGACAAGATCTCTATCTTTGATCTACTTCACGCCAGTAC
ATGAAGACAAGATCTGTTTTTCTTC
Found at i:13537603 original size:45 final size:44
Alignment explanation
Indices: 13537526--13537744 Score: 172
Period size: 44 Copynumber: 4.9 Consensus size: 44
13537516 GGACCTACTA
* ** *
13537526 TCTTTGATCTACTTCATGCCAGTACATGAAGACAAGATCTGTTT
1 TCTTCGATCTACTTCACACCAGTACAGGAAGACAAGATCTGTTT
* ** * *
13537570 TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTA
1 TCTTCGATCTACTTC-ACACCAGTACAGGAAGACAAGATCTGTTT
* * * * *
13537615 TCTTTGGTCTACTTCACGCCAGTACATGAAGACAAGATCCGTTTT
1 TCTTCGATCTACTTCACACCAGTACAGGAAGACAAGATCTG-TTT
* * * * **
13537660 TCTTCAATCTGCTCCACCACGAGTATGGGGAAG-CAAGATCTG-TT
1 TCTTCGATCTACTTCA-CACCAGTA-CAGGAAGACAAGATCTGTTT
* * * *
13537704 TCTTTGATCGACTTCACGCCAGTACATGAAGACAAGATCTG
1 TCTTCGATCTACTTCACACCAGTACAGGAAGACAAGATCTG
13537745 CTTTGCCACC
Statistics
Matches: 130, Mismatches: 40, Indels: 11
0.72 0.22 0.06
Matches are distributed among these distances:
42 4 0.03
43 15 0.12
44 47 0.36
45 46 0.35
46 14 0.11
47 4 0.03
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.30
Consensus pattern (44 bp):
TCTTCGATCTACTTCACACCAGTACAGGAAGACAAGATCTGTTT
Found at i:13537646 original size:133 final size:134
Alignment explanation
Indices: 13537019--13537651 Score: 389
Period size: 133 Copynumber: 4.8 Consensus size: 134
13537009 ACTACTGCTT
* * * * *
13537019 AGGAAGGCAAGATCTGTAATCTTCAATCTACTTCGCCACCAGTATGGGAAGATAAGATATGTATA
1 AGGAAGACAAGATCTGTTATCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATATGTATC
* * * * * *
13537084 TTCGATCCACTTCACTACC-GATATAGGAAGACAGGACCTACTATCTTTGATCTACTTCA-CGCC
66 TTTGATCTACTTCACTGCCAG-TACAGGAAGACAAGACCTACTATCTTCGATCTACTTCACCGCC
13537147 AGTAC
130 AGTAC
* * * * * * * * *
13537152 ATGAAGATAATATCTAATT-TCTTCGATCTACTCCACCACCAGTATGGGGAGACAAGATCTGTTT
1 AGGAAGACAAGATCT-GTTATCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATATGTAT
* * * * * * * *
13537216 CTTTGATCTTCTTCAC-GCCAGTACATGAAGACAAGATCTATTTTCCTCGATATACTTCACCACC
65 CTTTGATCTACTTCACTGCCAGTACAGGAAGACAAGACCTACTATCTTCGATCTACTTCACCGCC
* *
13537280 GGTAT
130 AGTAC
* * * * * * * * *
13537285 GGGAAAACAAGATTTGCTATCTTTGATCTACTCCACCACCAGTATGGGGAGA-TAGA-AT-TACT
1 AGGAAGACAAGATCTGTTATCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATATGTA-T
** * * * * * * * * * *
13537347 GGCTTCAATATACTCCACTGCAACTTCAGAGAGGTA-AA-ATCC-GCCATCTTCGATCTGCTCCA
65 --CTTTGATCTACTTCACTGCCAGTACAG-GAAG-ACAAGA-CCTACTATCTTCGATCTACTTCA
** * *
13537409 -CTACTGCT-T
125 CCGCCAG-TAC
* * * * *
13537418 AGGAAGGCAAGATCTGTAATCTTC-ACTCTGCTTCGCCACCAGTATGGGAAGATAAAATATGTAT
1 AGGAAGACAAGATCTGTTATCTTCGA-TCTACTTCGCCACCAGTATGGGAAGACAAGATATGTAT
* * * * * * * *
13537482 ATTTGATCCACTTCGCTACC-GATATAGGAAGACAGGACCTACTATCTTTGATCTACTTCA-TGC
65 CTTTGATCTACTTCACTGCCAG-TACAGGAAGACAAGACCTACTATCTTCGATCTACTTCACCGC
13537545 CAGTAC
129 CAGTAC
* * *
13537551 ATGAAGACAAGATCTGTTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTAT
1 AGGAAGACAAGATCTGTTATCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATATG-TAT
* *
13537616 CTTTGGTCTACTTCAC-GCCAGTACATGAAGACAAGA
65 CTTTGATCTACTTCACTGCCAGTACAGGAAGACAAGA
13537652 TCCGTTTTTC
Statistics
Matches: 359, Mismatches: 117, Indels: 48
0.69 0.22 0.09
Matches are distributed among these distances:
130 1 0.00
131 3 0.01
132 43 0.12
133 260 0.72
134 40 0.11
135 9 0.03
136 3 0.01
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.29
Consensus pattern (134 bp):
AGGAAGACAAGATCTGTTATCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATATGTATC
TTTGATCTACTTCACTGCCAGTACAGGAAGACAAGACCTACTATCTTCGATCTACTTCACCGCCA
GTAC
Found at i:13550526 original size:25 final size:24
Alignment explanation
Indices: 13550498--13550544 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
13550488 ACTTCTTTTG
13550498 TAAAA-AAAAGAAAAAACAAAAAGCA
1 TAAAAGAAAA-AAAAAA-AAAAAGCA
*
13550523 TAAAAGAACAAAAAAAAAAAAG
1 TAAAAGAAAAAAAAAAAAAAAG
13550545 AATCGAAATC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 6 0.30
25 11 0.55
26 3 0.15
ACGTcount: A:0.81, C:0.06, G:0.09, T:0.04
Consensus pattern (24 bp):
TAAAAGAAAAAAAAAAAAAAAGCA
Found at i:13552156 original size:22 final size:24
Alignment explanation
Indices: 13552129--13552173 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 24
13552119 TTGATACAAC
13552129 ATTATCAAT-AATAATA-TAATAT
1 ATTATCAATAAATAATAGTAATAT
*
13552151 ATTATCATTAAATAATAGTAATA
1 ATTATCAATAAATAATAGTAATA
13552174 ATTTTATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 8 0.40
23 7 0.35
24 5 0.25
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.40
Consensus pattern (24 bp):
ATTATCAATAAATAATAGTAATAT
Found at i:13552192 original size:26 final size:26
Alignment explanation
Indices: 13552163--13552219 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
13552153 TATCATTAAA
* **
13552163 TAATAGTAATAATTTTATTTAAATAT
1 TAATAGTAATAATTATAAATAAATAT
* *
13552189 TAATTGTAATTATTATAAATAAATAT
1 TAATAGTAATAATTATAAATAAATAT
13552215 TAATA
1 TAATA
13552220 ACTCTCGAAT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (26 bp):
TAATAGTAATAATTATAAATAAATAT
Found at i:13552238 original size:7 final size:7
Alignment explanation
Indices: 13552226--13552250 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
13552216 AATAACTCTC
13552226 GAATTTT
1 GAATTTT
13552233 GAATTTT
1 GAATTTT
13552240 GAATTTT
1 GAATTTT
13552247 GAAT
1 GAAT
13552251 CTTGGATCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (7 bp):
GAATTTT
Found at i:13558160 original size:31 final size:30
Alignment explanation
Indices: 13558122--13558187 Score: 87
Period size: 31 Copynumber: 2.2 Consensus size: 30
13558112 CCTAGTAACA
* * * *
13558122 TAAATAAAGACTTTTGCATAGTTCAGTGAC
1 TAAATAAAAACTTTCGAATAGTTCAATGAC
13558152 TTAAATAAAAACTTTCGAATAGTTCAATGAC
1 -TAAATAAAAACTTTCGAATAGTTCAATGAC
13558183 TAAAT
1 TAAAT
13558188 TATAAATTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 5 0.16
31 26 0.84
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.33
Consensus pattern (30 bp):
TAAATAAAAACTTTCGAATAGTTCAATGAC
Found at i:13561696 original size:21 final size:21
Alignment explanation
Indices: 13561667--13561706 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
13561657 TGATCTTGAT
13561667 AATAATAAATAATATTGATTA
1 AATAATAAATAATATTGATTA
*
13561688 AATAGTAAATAATATTGAT
1 AATAATAAATAATATTGAT
13561707 ATTATAAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (21 bp):
AATAATAAATAATATTGATTA
Found at i:13578519 original size:25 final size:25
Alignment explanation
Indices: 13578491--13578687 Score: 173
Period size: 25 Copynumber: 8.2 Consensus size: 25
13578481 GGAGTTTAGC
13578491 GTGCTCTCTGATTATTAGCACATTA
1 GTGCTCTCTGATTATTAGCACATTA
13578516 GTGCTCTCTGATTATTAGCACATTA
1 GTGCTCTCTGATTATTAGCACATTA
* * * *
13578541 GTGCTCTCTAATTACTAGCACGTCA
1 GTGCTCTCTGATTATTAGCACATTA
***
13578566 GTGCTCTCTGATTACTT-GCACGCCA
1 GTGCTCTCTGATTA-TTAGCACATTA
* *
13578591 GTGCTCTCTAATTACTA--AC---A
1 GTGCTCTCTGATTATTAGCACATTA
* *
13578611 -CGCTCTCTGATT-TCTAGCACGTTA
1 GTGCTCTCTGATTAT-TAGCACATTA
*
13578635 GTGCTCTCCGATTATTAGCACATTA
1 GTGCTCTCTGATTATTAGCACATTA
* *
13578660 GTGCTCTAT-A-TATT-GCACTTTA
1 GTGCTCTCTGATTATTAGCACATTA
13578682 GTGCTC
1 GTGCTC
13578688 CCTGTTTAAT
Statistics
Matches: 144, Mismatches: 18, Indels: 23
0.78 0.10 0.12
Matches are distributed among these distances:
19 12 0.08
20 1 0.01
21 2 0.01
22 13 0.09
23 6 0.04
24 3 0.02
25 105 0.73
26 2 0.01
ACGTcount: A:0.22, C:0.25, G:0.16, T:0.37
Consensus pattern (25 bp):
GTGCTCTCTGATTATTAGCACATTA
Found at i:13582808 original size:47 final size:47
Alignment explanation
Indices: 13582755--13582846 Score: 130
Period size: 47 Copynumber: 2.0 Consensus size: 47
13582745 AAGATGTGAC
* * *
13582755 TATGTGTTTTCGTGTAAGACCATATCTGGGATATGACATCGGTGTAA
1 TATGTGTTTCCATGTAAGACCATAGCTGGGATATGACATCGGTGTAA
* * *
13582802 TATGTGTTTCCATGTAAGACCATAGCTGGGCTATGGCTTCGGTGT
1 TATGTGTTTCCATGTAAGACCATAGCTGGGATATGACATCGGTGT
13582847 GTGATATGAG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
47 39 1.00
ACGTcount: A:0.22, C:0.15, G:0.27, T:0.36
Consensus pattern (47 bp):
TATGTGTTTCCATGTAAGACCATAGCTGGGATATGACATCGGTGTAA
Found at i:13585380 original size:12 final size:12
Alignment explanation
Indices: 13585363--13585387 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
13585353 GGTGTTCATT
13585363 CGGTTAACCGAC
1 CGGTTAACCGAC
13585375 CGGTTAACCGAC
1 CGGTTAACCGAC
13585387 C
1 C
13585388 CGAAATAACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.36, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTTAACCGAC
Found at i:13585562 original size:9 final size:9
Alignment explanation
Indices: 13585551--13585626 Score: 107
Period size: 9 Copynumber: 8.4 Consensus size: 9
13585541 TTTGGTTAAA
*
13585551 AATTAACCA
1 AATTAACCG
13585560 AATTAACCG
1 AATTAACCG
13585569 AATTAACCG
1 AATTAACCG
*
13585578 AATTACCCG
1 AATTAACCG
*
13585587 AACTAACCG
1 AATTAACCG
*
13585596 AATTACCCG
1 AATTAACCG
13585605 AATTAACCG
1 AATTAACCG
*
13585614 AATTAACCA
1 AATTAACCG
13585623 AATT
1 AATT
13585627 GAATCACTAC
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 59 1.00
ACGTcount: A:0.45, C:0.25, G:0.08, T:0.22
Consensus pattern (9 bp):
AATTAACCG
Found at i:13588523 original size:6 final size:6
Alignment explanation
Indices: 13588512--13588541 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
13588502 GGAGCCGTGA
13588512 TCAATT TCAATT TCAATT TCAATT TCAATT
1 TCAATT TCAATT TCAATT TCAATT TCAATT
13588542 CATCAAAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.17, G:0.00, T:0.50
Consensus pattern (6 bp):
TCAATT
Found at i:13594540 original size:16 final size:17
Alignment explanation
Indices: 13594519--13594551 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
13594509 TAATTGGTAG
13594519 CTAAT-CACTCTAAACC
1 CTAATCCACTCTAAACC
13594535 CTAATCCACTCTAAACC
1 CTAATCCACTCTAAACC
13594552 ACTCTAAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.36, C:0.39, G:0.00, T:0.24
Consensus pattern (17 bp):
CTAATCCACTCTAAACC
Found at i:13614018 original size:25 final size:24
Alignment explanation
Indices: 13613984--13614035 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 24
13613974 TCTTGAATTG
*
13613984 TTAATGAAGTGATTGCATCGAGCAT
1 TTAATAAAGTGATTGCATCGAGC-T
13614009 TTAATAAAGTGATTGCATCGAGCT
1 TTAATAAAGTGATTGCATCGAGCT
13614033 TTA
1 TTA
13614036 TGGTACCAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
24 4 0.15
25 22 0.85
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.35
Consensus pattern (24 bp):
TTAATAAAGTGATTGCATCGAGCT
Found at i:13620808 original size:20 final size:20
Alignment explanation
Indices: 13620748--13620810 Score: 65
Period size: 20 Copynumber: 3.1 Consensus size: 20
13620738 TTTTTTTTAT
*
13620748 ATTTAA-ATATTTAGTATTATA
1 ATTTAATATTTTTA-TATTA-A
* *
13620769 ATTTTATATTTTTAAATTAA
1 ATTTAATATTTTTATATTAA
*
13620789 ATTTAATATTTTTATTTTAA
1 ATTTAATATTTTTATATTAA
13620809 AT
1 AT
13620811 AAACTTAATT
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
20 20 0.57
21 9 0.26
22 6 0.17
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.59
Consensus pattern (20 bp):
ATTTAATATTTTTATATTAA
Found at i:13625002 original size:17 final size:18
Alignment explanation
Indices: 13624982--13625021 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
13624972 TAAGATGACT
*
13624982 ATAAAAAA-ATTTAATAA
1 ATAAAAAATATTGAATAA
*
13624999 ATAAAAAATATTGAATTA
1 ATAAAAAATATTGAATAA
13625017 ATAAA
1 ATAAA
13625022 TATCAAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (18 bp):
ATAAAAAATATTGAATAA
Found at i:13625022 original size:15 final size:15
Alignment explanation
Indices: 13625012--13625044 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
13625002 AAAAATATTG
13625012 AATTAATAAATATCA
1 AATTAATAAATATCA
13625027 AATTAATATAATAT-A
1 AATTAATA-AATATCA
13625042 AAT
1 AAT
13625045 ATTTTTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (15 bp):
AATTAATAAATATCA
Found at i:13638227 original size:13 final size:13
Alignment explanation
Indices: 13638209--13638239 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
13638199 CAGCCTGCCT
13638209 ACTAAAGACCGTA
1 ACTAAAGACCGTA
13638222 ACTAAAGACCGTA
1 ACTAAAGACCGTA
13638235 ACTAA
1 ACTAA
13638240 CGTAACTCAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.48, C:0.23, G:0.13, T:0.16
Consensus pattern (13 bp):
ACTAAAGACCGTA
Found at i:13651340 original size:26 final size:26
Alignment explanation
Indices: 13651304--13651354 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
13651294 GTAAGTGTTC
13651304 TGAAACTGATACATGCTATGATATTT
1 TGAAACTGATACATGCTATGATATTT
* * *
13651330 TGAAGCTGATATATGTTATGATATT
1 TGAAACTGATACATGCTATGATATT
13651355 CTAAAACTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.33, C:0.08, G:0.18, T:0.41
Consensus pattern (26 bp):
TGAAACTGATACATGCTATGATATTT
Found at i:13664249 original size:16 final size:15
Alignment explanation
Indices: 13664230--13664261 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
13664220 ATTTTAAGCC
13664230 TTTTTACATTTAATAT
1 TTTTTAC-TTTAATAT
13664246 TTTTTACTTTAATAT
1 TTTTTACTTTAATAT
13664261 T
1 T
13664262 ATAATTAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.28, C:0.06, G:0.00, T:0.66
Consensus pattern (15 bp):
TTTTTACTTTAATAT
Found at i:13665402 original size:13 final size:13
Alignment explanation
Indices: 13665384--13665408 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13665374 TAATTTAATA
13665384 TTATTTTGTGTGT
1 TTATTTTGTGTGT
13665397 TTATTTTGTGTG
1 TTATTTTGTGTG
13665409 CATTTTATTG
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:0.08, C:0.00, G:0.24, T:0.68
Consensus pattern (13 bp):
TTATTTTGTGTGT
Found at i:13666622 original size:12 final size:12
Alignment explanation
Indices: 13666605--13666637 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
13666595 TGAAGTTCGA
13666605 ATATGTATATAT
1 ATATGTATATAT
*
13666617 ATATGTATATCT
1 ATATGTATATAT
13666629 AT-TGTATAT
1 ATATGTATAT
13666638 TTGATGAGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 7 0.35
12 13 0.65
ACGTcount: A:0.36, C:0.03, G:0.09, T:0.52
Consensus pattern (12 bp):
ATATGTATATAT
Found at i:13666649 original size:114 final size:114
Alignment explanation
Indices: 13666388--13666818 Score: 733
Period size: 114 Copynumber: 3.8 Consensus size: 114
13666378 TTAGCATAAT
* *
13666388 TATATATGTATAACTATTGTACATTTGATGAGCTATAATTAAAAGTATACAAATTGAAATTAGTT
1 TATATATGTATATCTATTGTATATTTGATGAGCTATAATTAAAAGTATACAAATTGAAATTAGTT
**
13666453 AAGTATGAATG--ATATATATATGCATAAATGAAGTTCGAATATGTATA
66 AAGTATGAATGTTATATATATACACATAAATGAAGTTCGAATATGTATA
* ** *
13666500 TATATATGTATATCTGTTGTATATTTGATGAGCTATAATTAAAAGTATATGAATTGAAATTGGTT
1 TATATATGTATATCTATTGTATATTTGATGAGCTATAATTAAAAGTATACAAATTGAAATTAGTT
13666565 AAGTATGAATGTTATATATATACACATAAATGAAGTTCGAATATGTATA
66 AAGTATGAATGTTATATATATACACATAAATGAAGTTCGAATATGTATA
13666614 TATATATGTATATCTATTGTATATTTGATGAGCTATAATTAAAAGTATACAAATTGAAATTAGTT
1 TATATATGTATATCTATTGTATATTTGATGAGCTATAATTAAAAGTATACAAATTGAAATTAGTT
*
13666679 AAGTATGAATGTTATATATATACACATAAATGAAGTTTGAATATGTATA
66 AAGTATGAATGTTATATATATACACATAAATGAAGTTCGAATATGTATA
**
13666728 TATATATGTATATCTATTGTATATTTGATGAGCTATAATTAAAAGTATATGAATTGAAATTAGTT
1 TATATATGTATATCTATTGTATATTTGATGAGCTATAATTAAAAGTATACAAATTGAAATTAGTT
*
13666793 AAG-ATGAATGTTATATATATGCACAT
66 AAGTATGAATGTTATATATATACACAT
13666819 GTGTGAGGTT
Statistics
Matches: 301, Mismatches: 16, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
112 70 0.23
113 22 0.07
114 209 0.69
ACGTcount: A:0.41, C:0.05, G:0.14, T:0.40
Consensus pattern (114 bp):
TATATATGTATATCTATTGTATATTTGATGAGCTATAATTAAAAGTATACAAATTGAAATTAGTT
AAGTATGAATGTTATATATATACACATAAATGAAGTTCGAATATGTATA
Found at i:13666736 original size:12 final size:12
Alignment explanation
Indices: 13666719--13666751 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
13666709 TGAAGTTTGA
13666719 ATATGTATATAT
1 ATATGTATATAT
*
13666731 ATATGTATATCT
1 ATATGTATATAT
13666743 AT-TGTATAT
1 ATATGTATAT
13666752 TTGATGAGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 7 0.35
12 13 0.65
ACGTcount: A:0.36, C:0.03, G:0.09, T:0.52
Consensus pattern (12 bp):
ATATGTATATAT
Found at i:13667180 original size:40 final size:42
Alignment explanation
Indices: 13667119--13667307 Score: 187
Period size: 41 Copynumber: 4.6 Consensus size: 42
13667109 CAGGCTAAGC
* **
13667119 GCCTAGCAGGCTTAA-TACCGGTGAAT-T-TTTCAGACTT-TAA
1 GCCTAGCAGGC-TAAGTGCCGGTGAATCTGAATCAG-CTTATAA
* *
13667159 GTCTAGCAGGCTAAGTGCCGGTG-ATCTGAATCAGGTTATAA
1 GCCTAGCAGGCTAAGTGCCGGTGAATCTGAATCAGCTTATAA
* *
13667200 GCCTAGCAGGCTAAGTGCCGGTG-ATCTGAATCTGGTTATAA
1 GCCTAGCAGGCTAAGTGCCGGTGAATCTGAATCAGCTTATAA
* * *
13667241 ACCTAGCAAGCTAAGTGTCGGTG-ATCTGAATCAGGC-TATAA
1 GCCTAGCAGGCTAAGTGCCGGTGAATCTGAATCA-GCTTATAA
* *
13667282 GCTTAGCAGGCTAAATGCCGGTGAAT
1 GCCTAGCAGGCTAAGTGCCGGTGAAT
13667308 ATGTTAAATT
Statistics
Matches: 126, Mismatches: 17, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
39 5 0.04
40 20 0.16
41 98 0.78
42 3 0.02
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.27
Consensus pattern (42 bp):
GCCTAGCAGGCTAAGTGCCGGTGAATCTGAATCAGCTTATAA
Found at i:13667210 original size:41 final size:41
Alignment explanation
Indices: 13667156--13667305 Score: 228
Period size: 41 Copynumber: 3.7 Consensus size: 41
13667146 TTTCAGACTT
*
13667156 TAAGTCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTA
1 TAAGCCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTA
*
13667197 TAAGCCTAGCAGGCTAAGTGCCGGTGATCTGAATCTGGTTA
1 TAAGCCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTA
* * * *
13667238 TAAACCTAGCAAGCTAAGTGTCGGTGATCTGAATCAGGCTA
1 TAAGCCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTA
* *
13667279 TAAGCTTAGCAGGCTAAATGCCGGTGA
1 TAAGCCTAGCAGGCTAAGTGCCGGTGA
13667306 ATATGTTAAA
Statistics
Matches: 97, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 97 1.00
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.25
Consensus pattern (41 bp):
TAAGCCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTA
Found at i:13668249 original size:15 final size:15
Alignment explanation
Indices: 13668229--13668257 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
13668219 GAAAGGATAA
13668229 TATTAAAAAAAATTG
1 TATTAAAAAAAATTG
13668244 TATTAAAAAAAATT
1 TATTAAAAAAAATT
13668258 TTAATTTTTC
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:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (15 bp):
TATTAAAAAAAATTG
Found at i:13670935 original size:61 final size:61
Alignment explanation
Indices: 13670866--13670982 Score: 189
Period size: 61 Copynumber: 1.9 Consensus size: 61
13670856 ATTCAAGAGT
* * *
13670866 ACCAAAGTACAAATAGAGGCAGGTATGTGTAATTTAGGGGTACCGAAATACAAACAGGGGC
1 ACCAAAGTACAAACAGAGGCACGTATGTGTAATTCAGGGGTACCGAAATACAAACAGGGGC
* *
13670927 ACCAAAGTACAAACAGCGGCACGTATGTGTAATTCAGGGGTACCGAAGTACAAACA
1 ACCAAAGTACAAACAGAGGCACGTATGTGTAATTCAGGGGTACCGAAATACAAACA
13670983 AGAACACGTA
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
61 51 1.00
ACGTcount: A:0.39, C:0.18, G:0.26, T:0.17
Consensus pattern (61 bp):
ACCAAAGTACAAACAGAGGCACGTATGTGTAATTCAGGGGTACCGAAATACAAACAGGGGC
Found at i:13670937 original size:20 final size:20
Alignment explanation
Indices: 13670901--13670948 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
13670891 TGTGTAATTT
*
13670901 AGGGGTACCGAAATACAAAC
1 AGGGGCACCGAAATACAAAC
13670921 AGGGGCACC-AAAGTACAAAC
1 AGGGGCACCGAAA-TACAAAC
*
13670941 AGCGGCAC
1 AGGGGCAC
13670949 GTATGTGTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 3 0.12
20 22 0.88
ACGTcount: A:0.42, C:0.25, G:0.27, T:0.06
Consensus pattern (20 bp):
AGGGGCACCGAAATACAAAC
Done.