Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr1
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: 37323695
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.32
Warning! 1370832 characters in sequence are not A, C, G, or T
File 26 of 93
Found at i:11013565 original size:47 final size:47
Alignment explanation
Indices: 11013510--11014007 Score: 558
Period size: 47 Copynumber: 10.6 Consensus size: 47
11013500 ACGGAGTTTG
11013510 ACAAACTCTGAACGCTGACGTGTCACAGATTCCCTCCATGGCGTGTC
1 ACAAACTCTGAACGCTGACGTGTCACAGATTCCCTCCATGGCGTGTC
* * * * *
11013557 ATAAACTCTGAACGCTGGCGTGTCACAAATTCCTTCCATGGCGTGTT
1 ACAAACTCTGAACGCTGACGTGTCACAGATTCCCTCCATGGCGTGTC
* *
11013604 ACAAACTCTGAACGCT-AGCGTGTCATAGATTCCCTCTATGGCGTGTC
1 ACAAACTCTGAACGCTGA-CGTGTCACAGATTCCCTCCATGGCGTGTC
* *
11013651 ACAAACTTTGAAC-CTTG-CTGTGTCACAGATTCCCTTCATGGCGTGTC
1 ACAAACTCTGAACGC-TGAC-GTGTCACAGATTCCCTCCATGGCGTGTC
* * *
11013698 ACAAACTCTGAACCCT-ATCGTGTCACAGATTCCCTCTATGGTGTGTC
1 ACAAACTCTGAACGCTGA-CGTGTCACAGATTCCCTCCATGGCGTGTC
* * * * * * *
11013745 CCAAACTCTAAACGTTGGCATGTCACAGATTCCCTCCATCGTGTGTC
1 ACAAACTCTGAACGCTGACGTGTCACAGATTCCCTCCATGGCGTGTC
* *
11013792 ACAAACTCTGAACCCTGTCGTGTCACAGATTCCCTCCATGGCGTGTC
1 ACAAACTCTGAACGCTGACGTGTCACAGATTCCCTCCATGGCGTGTC
* * * **
11013839 TCAAACTCTGAACGCTGGCGTGTCACAGATTCCTTCCATACCGTGTC
1 ACAAACTCTGAACGCTGACGTGTCACAGATTCCCTCCATGGCGTGTC
* * * * * *
11013886 CCAAACTCTGAACGCTGACCTATCACAGATTCCCTCCATGACATATC
1 ACAAACTCTGAACGCTGACGTGTCACAGATTCCCTCCATGGCGTGTC
* * * *
11013933 ACAGACTCTGAAC-CTTGCCGTGTCACAGATTCCTTTCATGGCGTGTC
1 ACAAACTCTGAACGC-TGACGTGTCACAGATTCCCTCCATGGCGTGTC
* *
11013980 ACAAACTCTAAACCCT-ACCGTGTCACAG
1 ACAAACTCTGAACGCTGA-CGTGTCACAG
11014008 TTGTGTAACA
Statistics
Matches: 376, Mismatches: 64, Indels: 22
0.81 0.14 0.05
Matches are distributed among these distances:
46 3 0.01
47 370 0.98
48 3 0.01
ACGTcount: A:0.24, C:0.31, G:0.18, T:0.27
Consensus pattern (47 bp):
ACAAACTCTGAACGCTGACGTGTCACAGATTCCCTCCATGGCGTGTC
Found at i:11013578 original size:24 final size:24
Alignment explanation
Indices: 11013548--11013628 Score: 78
Period size: 24 Copynumber: 3.4 Consensus size: 24
11013538 ATTCCCTCCA
*
11013548 TGGCGTGTCATAAACTCTGAACGC
1 TGGCGTGTCACAAACTCTGAACGC
* *
11013572 TGGCGTGTCACAAATTCCT--TC-C
1 TGGCGTGTCACAAACT-CTGAACGC
*
11013594 ATGGCGTGTTACAAACTCTGAACGC
1 -TGGCGTGTCACAAACTCTGAACGC
*
11013619 TAGCGTGTCA
1 TGGCGTGTCA
11013629 TAGATTCCCT
Statistics
Matches: 44, Mismatches: 8, Indels: 10
0.71 0.13 0.16
Matches are distributed among these distances:
22 3 0.07
23 15 0.34
24 23 0.52
25 3 0.07
ACGTcount: A:0.23, C:0.26, G:0.23, T:0.27
Consensus pattern (24 bp):
TGGCGTGTCACAAACTCTGAACGC
Found at i:11013602 original size:23 final size:23
Alignment explanation
Indices: 11013528--11013608 Score: 67
Period size: 23 Copynumber: 3.5 Consensus size: 23
11013518 TGAACGCTGA
* *
11013528 CGTGTCACAGATTCCCTCCATGG
1 CGTGTCACAAATTCCTTCCATGG
* * *
11013551 CGTGTCATAAACT-CTGAACGC-TGG
1 CGTGTCACAAATTCCT--TC-CATGG
11013575 CGTGTCACAAATTCCTTCCATGG
1 CGTGTCACAAATTCCTTCCATGG
*
11013598 CGTGTTACAAA
1 CGTGTCACAAA
11013609 CTCTGAACGC
Statistics
Matches: 44, Mismatches: 9, Indels: 10
0.70 0.14 0.16
Matches are distributed among these distances:
22 2 0.05
23 24 0.55
24 15 0.34
25 3 0.07
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.27
Consensus pattern (23 bp):
CGTGTCACAAATTCCTTCCATGG
Found at i:11014775 original size:26 final size:26
Alignment explanation
Indices: 11014746--11014799 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
11014736 AATACTCGTA
11014746 TTTTTCATTTAGGAAATCCTTTCAAG
1 TTTTTCATTTAGGAAATCCTTTCAAG
11014772 TTTTTCATTTAGGAAATCCTTTCAAG
1 TTTTTCATTTAGGAAATCCTTTCAAG
11014798 TT
1 TT
11014800 GCAGCTAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.26, C:0.15, G:0.11, T:0.48
Consensus pattern (26 bp):
TTTTTCATTTAGGAAATCCTTTCAAG
Found at i:11018239 original size:25 final size:26
Alignment explanation
Indices: 11018201--11018262 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 26
11018191 CAACTTTTTC
* *
11018201 TTTATTATTATTTA-TATTTTCTGTT
1 TTTATTATTTTTTATTATTTTCAGTT
* *
11018226 TTTCTTATTTTTTATTCTTTTCAGTT
1 TTTATTATTTTTTATTATTTTCAGTT
11018252 TTTATT-TTTTT
1 TTTATTATTTTT
11018263 AAATTTTATC
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
25 17 0.55
26 14 0.45
ACGTcount: A:0.15, C:0.06, G:0.03, T:0.76
Consensus pattern (26 bp):
TTTATTATTTTTTATTATTTTCAGTT
Found at i:11018854 original size:15 final size:15
Alignment explanation
Indices: 11018834--11018863 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
11018824 CACACAATAC
11018834 ATATTTTACTATATG
1 ATATTTTACTATATG
11018849 ATATTTTACTATATG
1 ATATTTTACTATATG
11018864 GGGCACATCG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.53
Consensus pattern (15 bp):
ATATTTTACTATATG
Found at i:11021372 original size:23 final size:23
Alignment explanation
Indices: 11021342--11021385 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
11021332 AGTTTATGAA
*
11021342 ACGACATGTTGGGAATGTGTGAC
1 ACGACATGGTGGGAATGTGTGAC
11021365 ACGACATGGTGGGAATGTGTG
1 ACGACATGGTGGGAATGTGTG
11021386 GTAGGGCTGT
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:0.25, C:0.11, G:0.39, T:0.25
Consensus pattern (23 bp):
ACGACATGGTGGGAATGTGTGAC
Found at i:11021475 original size:33 final size:31
Alignment explanation
Indices: 11021426--11021512 Score: 102
Period size: 33 Copynumber: 2.7 Consensus size: 31
11021416 TTGTGACAGG
* *
11021426 ACATGGTTGGAATGTGTGACACGGCTGTGAC
1 ACATGGTGGGAATGTGTGACACGGCTATGAC
* *
11021457 ACCCATGGTGGGAGTGTGTGGCACGGCTATGAC
1 A--CATGGTGGGAATGTGTGACACGGCTATGAC
* *
11021490 ACATGTTGAGAATGTGTGACACG
1 ACATGGTGGGAATGTGTGACACG
11021513 ACATGGTGGG
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
31 19 0.41
33 27 0.59
ACGTcount: A:0.23, C:0.17, G:0.36, T:0.24
Consensus pattern (31 bp):
ACATGGTGGGAATGTGTGACACGGCTATGAC
Found at i:11021582 original size:58 final size:54
Alignment explanation
Indices: 11021451--11021593 Score: 146
Period size: 58 Copynumber: 2.6 Consensus size: 54
11021441 GTGACACGGC
* *
11021451 TGTGACAC-CCATGGTGGGAGTGTGTGGCACGGCTATGACACATGTTGAGAATG
1 TGTGACACGCCATGGTGGGAATGTGTGGCACGGCTATGACACATGTTCAGAATG
* * * *
11021504 TGTGACACGACATGGTGGGAATGTGTGGCAGGGCTGTGACACGATAGCGTTCAGAGT-
1 TGTGACACGCCATGGTGGGAATGTGTGGCACGGCTATGACAC-AT---GTTCAGAATG
* * *
11021561 TGGTGACACGCCATGGAGGGAATCTGTGACACG
1 T-GTGACACGCCATGGTGGGAATGTGTGGCACG
11021594 TCAGCGTTCA
Statistics
Matches: 73, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
53 8 0.11
54 29 0.40
55 2 0.03
57 1 0.01
58 33 0.45
ACGTcount: A:0.23, C:0.17, G:0.37, T:0.22
Consensus pattern (54 bp):
TGTGACACGCCATGGTGGGAATGTGTGGCACGGCTATGACACATGTTCAGAATG
Found at i:11021591 original size:47 final size:46
Alignment explanation
Indices: 11021537--11021777 Score: 301
Period size: 47 Copynumber: 5.2 Consensus size: 46
11021527 TGTGGCAGGG
11021537 CTGTGACACGATAGCGTTCAGAGTTGGTGACACGCCATGGAGGGAAT
1 CTGTGACACG-TAGCGTTCAGAGTTGGTGACACGCCATGGAGGGAAT
* *
11021584 CTGTGACACGTCAGCGTTCAAAGTTGGTGACACGCCATGGAAGGAAT
1 CTGTGACACGT-AGCGTTCAGAGTTGGTGACACGCCATGGAGGGAAT
*
11021631 CTGTGACATGCTAGCGTTCAGAGTTGGTGACACGCCATGGAGGGAAT
1 CTGTGACACG-TAGCGTTCAGAGTTGGTGACACGCCATGGAGGGAAT
* * * *
11021678 CTGTGAGACGTTAGAGTTCAGA-ATCGTGACACGCCATGGAGGGAAT
1 CTGTGACACG-TAGCGTTCAGAGTTGGTGACACGCCATGGAGGGAAT
* * * * *
11021724 CTATGACACGTCAGCGTTCAGAGTTTGTCAGACTCCATGGA--G-AT
1 CTGTGACACGT-AGCGTTCAGAGTTGGTGACACGCCATGGAGGGAAT
11021768 CTGTGACACG
1 CTGTGACACG
11021778 ACATGGCAAT
Statistics
Matches: 170, Mismatches: 20, Indels: 11
0.85 0.10 0.05
Matches are distributed among these distances:
44 11 0.06
45 2 0.01
46 40 0.24
47 116 0.68
48 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.31, T:0.23
Consensus pattern (46 bp):
CTGTGACACGTAGCGTTCAGAGTTGGTGACACGCCATGGAGGGAAT
Found at i:11022437 original size:31 final size:31
Alignment explanation
Indices: 11022399--11022718 Score: 491
Period size: 31 Copynumber: 10.3 Consensus size: 31
11022389 GTGTCAGCGT
11022399 TGGCGTGTTACCACAGTTTACGTTATATGCA
1 TGGCGTGTTACCACAGTTTACGTTATATGCA
*
11022430 TGGCGTGTTACCACAGTTTACGTTTTATGCA
1 TGGCGTGTTACCACAGTTTACGTTATATGCA
* * * *
11022461 TGGTGTGTTACCATATTTTACATTATATGCA
1 TGGCGTGTTACCACAGTTTACGTTATATGCA
11022492 TGGCGTGTTACCACAGTTTACGTTATATGCA
1 TGGCGTGTTACCACAGTTTACGTTATATGCA
11022523 TGGCGTGTTACCACAGTTTACGTTATATGCA
1 TGGCGTGTTACCACAGTTTACGTTATATGCA
* *
11022554 TGGCGTGTTATCGCAGTTTACGTTATATGCA
1 TGGCGTGTTACCACAGTTTACGTTATATGCA
* * * *
11022585 TGCCGTGTTATCGCAATTTACGTTATATGCA
1 TGGCGTGTTACCACAGTTTACGTTATATGCA
*
11022616 TGGCGTGTTACCACA-TATTACGTTATATACA
1 TGGCGTGTTACCACAGT-TTACGTTATATGCA
11022647 TGGCGTGTTACCACA-TTCTACGTTATATGCA
1 TGGCGTGTTACCACAGTT-TACGTTATATGCA
*
11022678 TGGCGTGTTACCACATTTTACGTTATATGCA
1 TGGCGTGTTACCACAGTTTACGTTATATGCA
11022709 TGGCGTGTTA
1 TGGCGTGTTA
11022719 GCATATTATG
Statistics
Matches: 267, Mismatches: 19, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
30 2 0.01
31 263 0.99
32 2 0.01
ACGTcount: A:0.23, C:0.18, G:0.21, T:0.38
Consensus pattern (31 bp):
TGGCGTGTTACCACAGTTTACGTTATATGCA
Found at i:11029348 original size:118 final size:117
Alignment explanation
Indices: 11029138--11029525 Score: 438
Period size: 118 Copynumber: 3.3 Consensus size: 117
11029128 AACAAGTCAG
* * * * * *
11029138 CGTGTCACGTCAAGTATCTGGCTCCATTCAGTGTGTCACCACAAG-TGGGGCGTGCCGTGCACCC
1 CGTGTCATGCCAAGTATCTAGTTCCACTCAGTGTGTCACCACAAGATGGGGCGTGCCGTTCACCC
*
11029202 CACAATACAGCAAGAAGTCAGTGGGTCACCATAGAAATCTGCATGCACTCAA
66 CACAATACAGCAAGAAGTCAGTGTGTCACCATAGAAATCTGCATGCACTCAA
** * * *
11029254 TATGTCATGCCAAGTTTCTAGTTCCACTTAGTGTGTCACCATAAGATGGGGCGTGCCGTATCACC
1 CGTGTCATGCCAAGTATCTAGTTCCACTCAGTGTGTCACCACAAGATGGGGCGTGCCGT-TCACC
* * *
11029319 CCACAATACAGCAAGAAGTTAGCGTGTCACCATAGAAATCTGCATGCACTCAG
65 CCACAATACAGCAAGAAGTCAGTGTGTCACCATAGAAATCTGCATGCACTCAA
* * * **
11029372 CGTGTCACGCTAAGTATCTGGTTCCACTCAACGTGTCAGCC-CAAGATGGGGCGTGCCGTGTCAC
1 CGTGTCATGCCAAGTATCTAGTTCCACTCAGTGTGTCA-CCACAAGATGGGGCGTGCCGT-TCAC
* * ** * * * * *
11029436 CTCACATTATTGCAAGAAGTCAGTTTGTCACTACAGAAATCTGCATGCCCTGAA
64 CCCACAATACAGCAAGAAGTCAGTGTGTCACCATAGAAATCTGCATGCACTCAA
** * *
11029490 CGTGTCATGCCAACAATCTGGTTTCACTCAGTGTGT
1 CGTGTCATGCCAAGTATCTAGTTCCACTCAGTGTGT
11029526 AAAACGACCC
Statistics
Matches: 224, Mismatches: 45, Indels: 4
0.82 0.16 0.01
Matches are distributed among these distances:
116 35 0.16
117 13 0.06
118 174 0.78
119 2 0.01
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.25
Consensus pattern (117 bp):
CGTGTCATGCCAAGTATCTAGTTCCACTCAGTGTGTCACCACAAGATGGGGCGTGCCGTTCACCC
CACAATACAGCAAGAAGTCAGTGTGTCACCATAGAAATCTGCATGCACTCAA
Found at i:11036206 original size:31 final size:31
Alignment explanation
Indices: 11035987--11036215 Score: 269
Period size: 31 Copynumber: 7.4 Consensus size: 31
11035977 TTTGTCAGTC
* * *
11035987 ATGTTGTAACACGCCATGCATATGACGTATA
1 ATGTGGTAACACGCCATGCATATAACGTAAA
* ** *
11036018 ATGTGGTAACACACCATGCATATAGTGTAGA
1 ATGTGGTAACACGCCATGCATATAACGTAAA
*
11036049 ATGTGGTAACACGCCATGCATATAACGTAGA
1 ATGTGGTAACACGCCATGCATATAACGTAAA
* * * *
11036080 ATGTGGTAACACGCAACGCATATAACATAAT
1 ATGTGGTAACACGCCATGCATATAACGTAAA
* *
11036111 ATGTGGTAACGCGCCATGCATATAACATAAA
1 ATGTGGTAACACGCCATGCATATAACGTAAA
* * *
11036142 ATGTGATAACATGCCATGCATATAACGTCAA
1 ATGTGGTAACACGCCATGCATATAACGTAAA
* *
11036173 ATATGGTAACACGCCATGCATATAACATAAA
1 ATGTGGTAACACGCCATGCATATAACGTAAA
* *
11036204 ATATTGTAACAC
1 ATGTGGTAACAC
11036216 ACCAACGCTG
Statistics
Matches: 169, Mismatches: 29, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 169 1.00
ACGTcount: A:0.38, C:0.19, G:0.18, T:0.25
Consensus pattern (31 bp):
ATGTGGTAACACGCCATGCATATAACGTAAA
Found at i:11037500 original size:15 final size:15
Alignment explanation
Indices: 11037480--11037509 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
11037470 TTCTTTAACG
*
11037480 GTTAAATTAAATATT
1 GTTAAAATAAATATT
11037495 GTTAAAATAAATATT
1 GTTAAAATAAATATT
11037510 AAATTAAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (15 bp):
GTTAAAATAAATATT
Found at i:11037518 original size:17 final size:18
Alignment explanation
Indices: 11037496--11037536 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
11037486 TTAAATATTG
11037496 TTAAAATAAATATT-AAA
1 TTAAAATAAATATTAAAA
* *
11037513 TTAAAATAATTTTTAAAA
1 TTAAAATAAATATTAAAA
11037531 TTAAAA
1 TTAAAA
11037537 AATTAAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 12 0.57
18 9 0.43
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
TTAAAATAAATATTAAAA
Found at i:11037544 original size:31 final size:28
Alignment explanation
Indices: 11037481--11037546 Score: 80
Period size: 31 Copynumber: 2.3 Consensus size: 28
11037471 TCTTTAACGG
*
11037481 TTAAATT-AAATATTGTTAAAATAAATA
1 TTAAATTAAAATATTGTTAAAATAAAAA
*
11037508 TTAAATTAAAATAATTTTTAAAATTAAAAAA
1 TTAAATTAAAAT-ATTGTTAAAA-T-AAAAA
11037539 TTAAATTA
1 TTAAATTA
11037547 CTTCAATTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 7 0.21
28 4 0.12
29 9 0.27
30 1 0.03
31 12 0.36
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.41
Consensus pattern (28 bp):
TTAAATTAAAATATTGTTAAAATAAAAA
Found at i:11046459 original size:4 final size:4
Alignment explanation
Indices: 11046450--11046492 Score: 86
Period size: 4 Copynumber: 10.8 Consensus size: 4
11046440 TTTTATGTTT
11046450 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
11046493 TATATATATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 39 1.00
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:11047019 original size:18 final size:18
Alignment explanation
Indices: 11046988--11047061 Score: 67
Period size: 18 Copynumber: 4.1 Consensus size: 18
11046978 AAGATATGAA
* *
11046988 GATGAAGAATATTATTAT
1 GATGATGAAGATTATTAT
* *
11047006 GATGATGATGATTATGAT
1 GATGATGAAGATTATTAT
** * *
11047024 GATGGGGAGGAATATTAT
1 GATGATGAAGATTATTAT
*
11047042 GATGATGAAGATTATCAT
1 GATGATGAAGATTATTAT
11047060 GA
1 GA
11047062 AGAGAAAGAT
Statistics
Matches: 42, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
18 42 1.00
ACGTcount: A:0.38, C:0.01, G:0.27, T:0.34
Consensus pattern (18 bp):
GATGATGAAGATTATTAT
Found at i:11050143 original size:35 final size:35
Alignment explanation
Indices: 11050114--11050361 Score: 279
Period size: 35 Copynumber: 7.1 Consensus size: 35
11050104 TTAATTGTTT
* * *
11050114 AATTTAATCAATTAGGCCTAATAAATTAATTAAAC
1 AATTTAATTAATTAGGCCCAATAATTTAATTAAAC
*
11050149 AATTTAATTAATTAAGCCC-ATAATTTAATTAAAC
1 AATTTAATTAATTAGGCCCAATAATTTAATTAAAC
* * * *
11050183 AATTTTAATCAATTAGGCCCAATGACTTAATTAAATA
1 AA-TTTAATTAATTAGGCCCAATAATTTAATTAAA-C
* ***
11050220 AATTTAATCAATTAGGCCCAATAATTTAATTATTT
1 AATTTAATTAATTAGGCCCAATAATTTAATTAAAC
* *
11050255 AATTTAATTAATTAGGCCCAATGACTTAATTAAAC
1 AATTTAATTAATTAGGCCCAATAATTTAATTAAAC
* * *
11050290 AATTTAATTAATTAGGCCTAATGATTTAATTAAAT
1 AATTTAATTAATTAGGCCCAATAATTTAATTAAAC
* *
11050325 AATTTAATTAATTATG--C-ATAACTTAATTAAAC
1 AATTTAATTAATTAGGCCCAATAATTTAATTAAAC
11050357 AATTT
1 AATTT
11050362 TAATCAAGTG
Statistics
Matches: 182, Mismatches: 28, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
32 17 0.09
34 16 0.09
35 107 0.59
36 40 0.22
37 2 0.01
ACGTcount: A:0.44, C:0.11, G:0.06, T:0.39
Consensus pattern (35 bp):
AATTTAATTAATTAGGCCCAATAATTTAATTAAAC
Found at i:11050236 original size:106 final size:104
Alignment explanation
Indices: 11050113--11050361 Score: 324
Period size: 106 Copynumber: 2.4 Consensus size: 104
11050103 CTTAATTGTT
*
11050113 TAATTTAATCAATTAGGCCTAATAAATTAATTAAACAATTTAATTAATTAAGCCC-ATAATTTAA
1 TAATTTAATCAATTAGGCC-AATAAATTAATTAAACAATTTAATTAATTAAGCCCAATAACTTAA
11050177 TTAAACAATTTTAATCAATTAGGCCCAATGACTTAATTAAA
65 TTAAACAA-TTTAATCAATTAGGCCCAATGACTTAATTAAA
* *** * *
11050218 TAAATTTAATCAATTAGGCCCAATAATTTAATTATTTAATTTAATTAATTAGGCCCAATGACTTA
1 T-AATTTAATCAATTAGG-CCAATAAATTAATTAAACAATTTAATTAATTAAGCCCAATAACTTA
* * *
11050283 ATTAAACAATTTAATTAATTAGGCCTAATGATTTAATTAAA
64 ATTAAACAATTTAATCAATTAGGCCCAATGACTTAATTAAA
* * *
11050324 TAATTTAATTAATTATG-C-ATAACTTAATTAAACAATTT
1 TAATTTAATCAATTAGGCCAATAAATTAATTAAACAATTT
11050362 TAATCAAGTG
Statistics
Matches: 125, Mismatches: 16, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
102 16 0.13
103 1 0.01
105 15 0.12
106 76 0.61
107 17 0.14
ACGTcount: A:0.44, C:0.11, G:0.06, T:0.39
Consensus pattern (104 bp):
TAATTTAATCAATTAGGCCAATAAATTAATTAAACAATTTAATTAATTAAGCCCAATAACTTAAT
TAAACAATTTAATCAATTAGGCCCAATGACTTAATTAAA
Found at i:11050258 original size:141 final size:139
Alignment explanation
Indices: 11050093--11050368 Score: 367
Period size: 141 Copynumber: 2.0 Consensus size: 139
11050083 TCCTTAAGAA
* *
11050093 GCCCAATTAACTTAATTGTTTAATTTAATCAATTAGGCCTAATAAATTAATTAAACAATTTAATT
1 GCCCAATTAACTTAATTATTTAATTTAATCAATTAGGCCCAATAAATTAATTAAACAATTTAATT
* * *
11050158 AATTAAGCC-CATAATTTAATTAAACAATTTTAATCAATTAGGCCCAATGACTTAATTAAATAAA
66 AATTAAGCCTAATAATTTAATTAAACAA-TTTAATCAATTAGG--C-ATAACTTAATTAAACAAA
11050222 TTTAATCAATTAG
127 TTTAATCAATTAG
* * * *
11050235 GCCCAA-TAATTTAATTATTTAATTTAATTAATTAGGCCCAATGACTTAATTAAACAATTTAATT
1 GCCCAATTAACTTAATTATTTAATTTAATCAATTAGGCCCAATAAATTAATTAAACAATTTAATT
* * * * * *
11050299 AATTAGGCCTAATGATTTAATTAAATAATTTAATTAATTATGCATAACTTAATTAAACAATTTTA
66 AATTAAGCCTAATAATTTAATTAAACAATTTAATCAATTAGGCATAACTTAATTAAACAAATTTA
11050364 ATCAA
131 ATCAA
11050369 GTGCTTGAGA
Statistics
Matches: 118, Mismatches: 15, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
138 24 0.20
139 1 0.01
141 72 0.61
142 21 0.18
ACGTcount: A:0.43, C:0.12, G:0.06, T:0.39
Consensus pattern (139 bp):
GCCCAATTAACTTAATTATTTAATTTAATCAATTAGGCCCAATAAATTAATTAAACAATTTAATT
AATTAAGCCTAATAATTTAATTAAACAATTTAATCAATTAGGCATAACTTAATTAAACAAATTTA
ATCAATTAG
Found at i:11053365 original size:15 final size:15
Alignment explanation
Indices: 11053342--11053390 Score: 80
Period size: 15 Copynumber: 3.3 Consensus size: 15
11053332 ATTTAACGTA
*
11053342 ATTGTAAGTAATGTG
1 ATTGCAAGTAATGTG
11053357 ATTGCAAGTAATGTG
1 ATTGCAAGTAATGTG
*
11053372 ATTGCAAGTAATATG
1 ATTGCAAGTAATGTG
11053387 ATTG
1 ATTG
11053391 TAAGAAAACT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.35, C:0.04, G:0.24, T:0.37
Consensus pattern (15 bp):
ATTGCAAGTAATGTG
Found at i:11053639 original size:33 final size:35
Alignment explanation
Indices: 11053602--11053692 Score: 114
Period size: 33 Copynumber: 2.5 Consensus size: 35
11053592 TTTTAATGTC
*
11053602 ATATATTTTATTTTCATTTC-TTATTATAA-TCTT
1 ATATATTTTATTTTCATTTCTTTAATATAATTCTT
11053635 ATATATTTTATTTTCATTTCTTTAATATAATTTCTT
1 ATATATTTTATTTTCATTTCTTTAATATAA-TTCTT
*
11053671 AGGTTATATTTTATTTTAATTT
1 A---TATATTTTATTTTCATTT
11053693 TTTTCCTATA
Statistics
Matches: 50, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
33 20 0.40
34 8 0.16
36 5 0.10
39 17 0.34
ACGTcount: A:0.27, C:0.07, G:0.02, T:0.64
Consensus pattern (35 bp):
ATATATTTTATTTTCATTTCTTTAATATAATTCTT
Found at i:11056095 original size:2 final size:2
Alignment explanation
Indices: 11056039--11056076 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
11056029 NNNNNNNNNN
11056039 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
11056077 ATTTGTATCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:11066859 original size:25 final size:25
Alignment explanation
Indices: 11066829--11066879 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
11066819 GCATTCATTC
11066829 AAAACTCTCAAAATTCAAATTTCAT
1 AAAACTCTCAAAATTCAAATTTCAT
11066854 AAAACTCTCAAAATTCAAATTTCAT
1 AAAACTCTCAAAATTCAAATTTCAT
11066879 A
1 A
11066880 TAGATTTGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.49, C:0.20, G:0.00, T:0.31
Consensus pattern (25 bp):
AAAACTCTCAAAATTCAAATTTCAT
Found at i:11068627 original size:39 final size:39
Alignment explanation
Indices: 11068541--11068633 Score: 107
Period size: 39 Copynumber: 2.4 Consensus size: 39
11068531 GATTATTTTC
* *
11068541 TGTTTTGGACTTATTCAAATGATGAACATTGATTTCCTAA
1 TGTTTTGG-TTTATTCAAATGATGAACATTGATTTCATAA
** * *
11068581 TAATTTGGTTTATTCATATGATGAACATTG-TTTTATGAA
1 TGTTTTGGTTTATTCAAATGATGAACATTGATTTCAT-AA
11068620 TGTTTTGGTTTATT
1 TGTTTTGGTTTATT
11068634 AACGAGTATT
Statistics
Matches: 44, Mismatches: 8, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
38 4 0.09
39 34 0.77
40 6 0.14
ACGTcount: A:0.27, C:0.08, G:0.16, T:0.49
Consensus pattern (39 bp):
TGTTTTGGTTTATTCAAATGATGAACATTGATTTCATAA
Found at i:11068786 original size:33 final size:33
Alignment explanation
Indices: 11068749--11068834 Score: 109
Period size: 33 Copynumber: 2.6 Consensus size: 33
11068739 TACGGCTTTG
* *
11068749 CTAATAGGTTATAGTAGTTAACATATGACCCTA
1 CTAATAGGTTACAGTAGTTAACATAAGACCCTA
* *
11068782 CTAATAGGTTACAGTAGTTAGCATAAGGCCCTA
1 CTAATAGGTTACAGTAGTTAACATAAGACCCTA
* * *
11068815 TTAATGGGTTACAATAGTTA
1 CTAATAGGTTACAGTAGTTA
11068835 GTAATAATCA
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (33 bp):
CTAATAGGTTACAGTAGTTAACATAAGACCCTA
Found at i:11072569 original size:33 final size:33
Alignment explanation
Indices: 11072532--11072598 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
11072522 ATGTTATGTT
* * *
11072532 ATCATTAATTATGATATGTCAATATGTTACATC
1 ATCATTAATTATAATATATCAATATGTCACATC
*
11072565 ATCATTAATTATAATATATTAATATGTCACATC
1 ATCATTAATTATAATATATCAATATGTCACATC
11072598 A
1 A
11072599 GTATCATATT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.12, G:0.06, T:0.42
Consensus pattern (33 bp):
ATCATTAATTATAATATATCAATATGTCACATC
Found at i:11072686 original size:30 final size:30
Alignment explanation
Indices: 11072659--11072717 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
11072649 ATTTATAACT
11072659 ACTTATTTGACTCAAAATAAAAATATAAAG
1 ACTTATTTGACTCAAAATAAAAATATAAAG
*
11072689 ACTTATTTGACTCAAAATAAAATTATAAA
1 ACTTATTTGACTCAAAATAAAAATATAAA
11072718 AATTTGATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.53, C:0.10, G:0.05, T:0.32
Consensus pattern (30 bp):
ACTTATTTGACTCAAAATAAAAATATAAAG
Found at i:11072851 original size:183 final size:182
Alignment explanation
Indices: 11072543--11072910 Score: 628
Period size: 183 Copynumber: 2.0 Consensus size: 182
11072533 TCATTAATTA
* *
11072543 TGATATGTCAATATGTTACATCATCATTAATTATAATATATTAATATGTCACATCAGTATCATAT
1 TGATATGTCAATATATTACATCATCATTAATTATAATATATTAATATGTCACATCAGTATCATAC
* * * **
11072608 TATATAGAAAGATAAATAACATTTTAACTAGGTCAAAAATTATTTATAACTACTTATTTGACTCA
66 TACATAGAAAGATAAATAACATTTTAACTAGGTCAAAAATTAATCATAAAAACTTATTTGACTC-
11072673 AAATAAAAATATAAAGACTTATTTGACTCAAAATAAAATTATAAAAATTTGAT
130 AAATAAAAATATAAAGACTTATTTGACTCAAAATAAAATTATAAAAATTTGAT
* *
11072726 TGATATGTTAATATATTACATCATCATTAATTATAATATATTAATATGTCTCATCAGTATCATAC
1 TGATATGTCAATATATTACATCATCATTAATTATAATATATTAATATGTCACATCAGTATCATAC
*
11072791 TACATAGAAAGATAAATGACATTTTAACTAGGTCAAAAATTAATCATAAAAACTTATTTGACTCA
66 TACATAGAAAGATAAATAACATTTTAACTAGGTCAAAAATTAATCATAAAAACTTATTTGACTCA
*
11072856 AATAAAAATATGAAGACTTATTTGACTCAAAATAAAATTATAAAAATTTGAT
131 AATAAAAATATAAAGACTTATTTGACTCAAAATAAAATTATAAAAATTTGAT
11072908 TGA
1 TGA
11072911 ATACAATAAA
Statistics
Matches: 174, Mismatches: 11, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
182 55 0.32
183 119 0.68
ACGTcount: A:0.46, C:0.10, G:0.08, T:0.36
Consensus pattern (182 bp):
TGATATGTCAATATATTACATCATCATTAATTATAATATATTAATATGTCACATCAGTATCATAC
TACATAGAAAGATAAATAACATTTTAACTAGGTCAAAAATTAATCATAAAAACTTATTTGACTCA
AATAAAAATATAAAGACTTATTTGACTCAAAATAAAATTATAAAAATTTGAT
Found at i:11073162 original size:24 final size:24
Alignment explanation
Indices: 11073130--11073179 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
11073120 TTGCGCGGGC
* * *
11073130 CTCTTTCTATCTGTTTTTTTCTTT
1 CTCTTTCTACCTCTCTTTTTCTTT
11073154 CTCTTTCTACCTCTCTTTTTCTTT
1 CTCTTTCTACCTCTCTTTTTCTTT
11073178 CT
1 CT
11073180 TTTTTCTCTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.04, C:0.28, G:0.02, T:0.66
Consensus pattern (24 bp):
CTCTTTCTACCTCTCTTTTTCTTT
Found at i:11077339 original size:19 final size:18
Alignment explanation
Indices: 11077288--11077340 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 18
11077278 ACTTTTATAA
*
11077288 AAATTTTAAAATTTTTTT
1 AAATTTTATAATTTTTTT
*
11077306 AACATATTT-TTATTTTTTT
1 AA-AT-TTTATAATTTTTTT
11077325 AGAATTTTATAATTTT
1 A-AATTTTATAATTTT
11077341 GTTTCTATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
18 5 0.18
19 19 0.68
20 4 0.14
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (18 bp):
AAATTTTATAATTTTTTT
Found at i:11081616 original size:27 final size:27
Alignment explanation
Indices: 11081572--11081654 Score: 105
Period size: 27 Copynumber: 3.1 Consensus size: 27
11081562 CTTTTCAATG
*
11081572 TTCATCCA-TTTCGGGTGGTTAAATGTA
1 TTCATCCACTTT-TGGTGGTTAAATGTA
* * *
11081599 TTCGTCCACTTTTTGTGGTTAAATGTC
1 TTCATCCACTTTTGGTGGTTAAATGTA
*
11081626 TTCATCTACTTTTGGTGGTTAAATGTA
1 TTCATCCACTTTTGGTGGTTAAATGTA
11081653 TT
1 TT
11081655 TTTACTATTA
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
27 44 0.94
28 3 0.06
ACGTcount: A:0.19, C:0.14, G:0.19, T:0.47
Consensus pattern (27 bp):
TTCATCCACTTTTGGTGGTTAAATGTA
Found at i:11082203 original size:59 final size:59
Alignment explanation
Indices: 11082093--11082207 Score: 153
Period size: 59 Copynumber: 1.9 Consensus size: 59
11082083 CATAATCTGA
* * * *
11082093 TTTAATAAATTAAGAGACCAAATATAATACATACTACATTATTACAGATTCACATTTCG
1 TTTAATAAATTAAGAGACAAAATATAATACATACTACATCAATACAAATTCACATTTCG
*
11082152 TTTAATAAATTAA-AGAACAAAATATAATATATACTACA-CAATAGCAAATTCACATT
1 TTTAATAAATTAAGAG-ACAAAATATAATACATACTACATCAATA-CAAATTCACATT
11082208 AAAGTTAATT
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
58 5 0.10
59 44 0.90
ACGTcount: A:0.49, C:0.14, G:0.05, T:0.32
Consensus pattern (59 bp):
TTTAATAAATTAAGAGACAAAATATAATACATACTACATCAATACAAATTCACATTTCG
Found at i:11096147 original size:24 final size:24
Alignment explanation
Indices: 11096116--11096221 Score: 103
Period size: 23 Copynumber: 4.5 Consensus size: 24
11096106 NNNNNNNNNN
*
11096116 TTTTATTTTATTTATTTTATTTAT
1 TTTTATTTTATTTAATTTATTTAT
*
11096140 TTTTATTTTATTT-ATTTATTTAA
1 TTTTATTTTATTTAATTTATTTAT
* * *
11096163 TTTGATTTAATTTAATTTAATT-T
1 TTTTATTTTATTTAATTTATTTAT
* * *
11096186 TTTTAATTAATTTTAAATT-TTTA-
1 TTTTATTTTA-TTTAATTTATTTAT
11096209 TTTTATTTTATTT
1 TTTTATTTTATTT
11096222 GAGTGTCTAC
Statistics
Matches: 67, Mismatches: 12, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
22 3 0.04
23 37 0.55
24 27 0.40
ACGTcount: A:0.26, C:0.00, G:0.01, T:0.73
Consensus pattern (24 bp):
TTTTATTTTATTTAATTTATTTAT
Found at i:11096172 original size:10 final size:9
Alignment explanation
Indices: 11096117--11096221 Score: 79
Period size: 9 Copynumber: 11.3 Consensus size: 9
11096107 NNNNNNNNNT
*
11096117 TTTATTTTA
1 TTTATTTAA
*
11096126 TTTATTTTA
1 TTTATTTAA
*
11096135 TTTATTTTTAT
1 TTTA--TTTAA
11096146 TTTATTT-A
1 TTTATTTAA
11096154 TTTATTTAA
1 TTTATTTAA
11096163 TTTGATTTAA
1 TTT-ATTTAA
11096173 TTTAATTTAA
1 TTT-ATTTAA
*
11096183 TTTTTTTAA
1 TTTATTTAA
*
11096192 TTAATTTTAA
1 TTTA-TTTAA
* *
11096202 ATT-TTTAT
1 TTTATTTAA
*
11096210 TTTATTTTA
1 TTTATTTAA
11096219 TTT
1 TTT
11096222 GAGTGTCTAC
Statistics
Matches: 77, Mismatches: 13, Indels: 12
0.75 0.13 0.12
Matches are distributed among these distances:
8 13 0.17
9 33 0.43
10 24 0.31
11 7 0.09
ACGTcount: A:0.27, C:0.00, G:0.01, T:0.72
Consensus pattern (9 bp):
TTTATTTAA
Found at i:11096211 original size:6 final size:5
Alignment explanation
Indices: 11096116--11096221 Score: 71
Period size: 5 Copynumber: 21.6 Consensus size: 5
11096106 NNNNNNNNNN
*
11096116 TTTTA TTTTA -TTTA TTTTA -TTTA TTTTTA TTTTA -TTTA -TTTA TTTAA
1 TTTTA TTTTA TTTTA TTTTA TTTTA -TTTTA TTTTA TTTTA TTTTA TTTTA
* * * * * *
11096163 TTTGA -TTTA ATTTA ATTTA ATTT- TTTTA ATTAA TTTTAAA TTTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT--A -TTTTA
11096209 TTTTA TTTTA TTT
1 TTTTA TTTTA TTT
11096222 GAGTGTCTAC
Statistics
Matches: 84, Mismatches: 8, Indels: 18
0.76 0.07 0.16
Matches are distributed among these distances:
4 22 0.26
5 52 0.62
6 5 0.06
7 1 0.01
8 4 0.05
ACGTcount: A:0.26, C:0.00, G:0.01, T:0.73
Consensus pattern (5 bp):
TTTTA
Found at i:11096750 original size:10 final size:9
Alignment explanation
Indices: 11096731--11096765 Score: 52
Period size: 9 Copynumber: 3.7 Consensus size: 9
11096721 AATGAAGAAG
11096731 AAAAAAAGA
1 AAAAAAAGA
11096740 AAAAAATAGA
1 AAAAAA-AGA
11096750 ATAAAAAAGA
1 A-AAAAAAGA
11096760 AAAAAA
1 AAAAAA
11096766 TTATTTGTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 11 0.46
10 8 0.33
11 5 0.21
ACGTcount: A:0.86, C:0.00, G:0.09, T:0.06
Consensus pattern (9 bp):
AAAAAAAGA
Found at i:11096755 original size:21 final size:20
Alignment explanation
Indices: 11096726--11096766 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
11096716 CGACCAATGA
11096726 AGAAGAAAAAAAGAAAAAAAT
1 AGAAG-AAAAAAGAAAAAAAT
*
11096747 AGAATAAAAAAGAAAAAAAT
1 AGAAGAAAAAAGAAAAAAAT
11096767 TATTTGTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.80, C:0.00, G:0.12, T:0.07
Consensus pattern (20 bp):
AGAAGAAAAAAGAAAAAAAT
Found at i:11096897 original size:16 final size:16
Alignment explanation
Indices: 11096820--11096906 Score: 51
Period size: 16 Copynumber: 5.4 Consensus size: 16
11096810 ACATTATTAA
*
11096820 TATTAATATGATTAAAA
1 TATTAATAT-ATTAAAT
11096837 TATT-ATAATATTAATAT
1 TATTAAT-ATATTAA-AT
11096854 T-TTAA-ACTATT-AAT
1 TATTAATA-TATTAAAT
* *
11096868 GT-TTTATTTATTAAAT
1 -TATTAATATATTAAAT
11096884 TATTAATATATT-AAT
1 TATTAATATATTAAAT
11096899 ATATTAAT
1 -TATTAAT
11096907 TAATGAGTAT
Statistics
Matches: 56, Mismatches: 5, Indels: 19
0.70 0.06 0.24
Matches are distributed among these distances:
14 2 0.04
15 14 0.25
16 31 0.55
17 9 0.16
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.52
Consensus pattern (16 bp):
TATTAATATATTAAAT
Found at i:11096970 original size:40 final size:39
Alignment explanation
Indices: 11096926--11097028 Score: 100
Period size: 40 Copynumber: 2.5 Consensus size: 39
11096916 TAGATAAAAA
*
11096926 ATAAAAAATATTAATATTTCAATCATAATAAT-ATTAAATT
1 ATAAAAAATATTAATATTT-AA-AATAATAATAATTAAATT
* * *
11096966 ATAAATAAAATATTATTAATTAAAATATTAATAATTAAATT
1 AT-AA-AAAATATTAATATTTAAAATAATAATAATTAAATT
* *
11097007 ATACTAAAATATTGATATTTAA
1 ATA-AAAAATATTAATATTTAA
11097029 GTTATTAATT
Statistics
Matches: 51, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
40 24 0.47
41 14 0.27
42 13 0.25
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (39 bp):
ATAAAAAATATTAATATTTAAAATAATAATAATTAAATT
Found at i:11096979 original size:19 final size:19
Alignment explanation
Indices: 11096950--11097019 Score: 63
Period size: 20 Copynumber: 3.5 Consensus size: 19
11096940 TATTTCAATC
11096950 ATAATAATATTAAATTATAA
1 ATAA-AATATTAAATTATAA
11096970 ATAAAATATTATTAATTA-AA
1 ATAAAATATTA--AATTATAA
*
11096990 ATATTAATAATTAAATTAT-A
1 ATA-AAAT-ATTAAATTATAA
*
11097010 CTAAAATATT
1 ATAAAATATT
11097020 GATATTTAAG
Statistics
Matches: 42, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
18 3 0.07
19 10 0.24
20 17 0.40
21 8 0.19
22 4 0.10
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.41
Consensus pattern (19 bp):
ATAAAATATTAAATTATAA
Found at i:11096991 original size:15 final size:15
Alignment explanation
Indices: 11096966--11097004 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
11096956 ATATTAAATT
*
11096966 ATAAATAAAATATTA
1 ATAATTAAAATATTA
*
11096981 TTAATTAAAATATTA
1 ATAATTAAAATATTA
11096996 ATAATTAAA
1 ATAATTAAA
11097005 TTATACTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
ATAATTAAAATATTA
Found at i:11097018 original size:25 final size:25
Alignment explanation
Indices: 11096986--11097033 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
11096976 TATTATTAAT
11096986 TAAAATATTAATAATTAAATTATAC
1 TAAAATATTAATAATTAAATTATAC
* * *
11097011 TAAAATATTGATATTTAAGTTAT
1 TAAAATATTAATAATTAAATTAT
11097034 TAATTATTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (25 bp):
TAAAATATTAATAATTAAATTATAC
Found at i:11097043 original size:40 final size:41
Alignment explanation
Indices: 11096957--11097043 Score: 106
Period size: 40 Copynumber: 2.1 Consensus size: 41
11096947 ATCATAATAA
11096957 TATTAAATTATAAATAAAATATTATTAATTAAAATATTAAT
1 TATTAAATTATAAATAAAATATTATTAATTAAAATATTAAT
* * * **
11096998 AATTAAATTAT-ACTAAAATATTGA-TATTTAAGTTATTAAT
1 TATTAAATTATAAATAAAATATT-ATTAATTAAAATATTAAT
11097038 TATTAA
1 TATTAA
11097044 TGTTTTAATT
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
40 28 0.72
41 11 0.28
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.45
Consensus pattern (41 bp):
TATTAAATTATAAATAAAATATTATTAATTAAAATATTAAT
Found at i:11100605 original size:33 final size:33
Alignment explanation
Indices: 11100568--11100630 Score: 117
Period size: 33 Copynumber: 1.9 Consensus size: 33
11100558 AACAAGTTAT
*
11100568 TGTCAGTTGAAAACAGCAGCACGACTTGTATAC
1 TGTCAGTTGAAAACAGCAGCAAGACTTGTATAC
11100601 TGTCAGTTGAAAACAGCAGCAAGACTTGTA
1 TGTCAGTTGAAAACAGCAGCAAGACTTGTA
11100631 CGTGGAAGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.24
Consensus pattern (33 bp):
TGTCAGTTGAAAACAGCAGCAAGACTTGTATAC
Found at i:11100646 original size:32 final size:32
Alignment explanation
Indices: 11100572--11100646 Score: 98
Period size: 33 Copynumber: 2.3 Consensus size: 32
11100562 AGTTATTGTC
* **
11100572 AGTTGAAAACAGCAGCACGACTTGTATACTGTC
1 AGTTGAAAACAGCAGCAAGACTTG-ATACTGGA
11100605 AGTTGAAAACAGCAGCAAGACTTG-TACGTGGA
1 AGTTGAAAACAGCAGCAAGACTTGATAC-TGGA
11100637 AGTTGAAAAC
1 AGTTGAAAAC
11100647 GTGATGCTGT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
31 3 0.08
32 12 0.32
33 23 0.61
ACGTcount: A:0.37, C:0.17, G:0.24, T:0.21
Consensus pattern (32 bp):
AGTTGAAAACAGCAGCAAGACTTGATACTGGA
Found at i:11104978 original size:33 final size:33
Alignment explanation
Indices: 11104941--11105004 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
11104931 AACAGGTTAT
* * *
11104941 TGTCAGTTGAAAATAGCAGCATGACTTGTATAC
1 TGTCAGTTGAAAACAGCAGAAAGACTTGTATAC
11104974 TGTCAGTTGAAAACAGCAGAAAGACTTGTAT
1 TGTCAGTTGAAAACAGCAGAAAGACTTGTAT
11105005 GTGGAAGTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.28
Consensus pattern (33 bp):
TGTCAGTTGAAAACAGCAGAAAGACTTGTATAC
Found at i:11105019 original size:32 final size:33
Alignment explanation
Indices: 11104945--11105019 Score: 89
Period size: 33 Copynumber: 2.3 Consensus size: 33
11104935 GGTTATTGTC
* * * **
11104945 AGTTGAAAATAGCAGCATGACTTGTATACTGTC
1 AGTTGAAAACAGCAGAAAGACTTGTATACTGGA
*
11104978 AGTTGAAAACAGCAGAAAGACTTGTAT-GTGGA
1 AGTTGAAAACAGCAGAAAGACTTGTATACTGGA
11105010 AGTTGAAAAC
1 AGTTGAAAAC
11105020 GTGATGCTAT
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
32 12 0.33
33 24 0.67
ACGTcount: A:0.39, C:0.12, G:0.24, T:0.25
Consensus pattern (33 bp):
AGTTGAAAACAGCAGAAAGACTTGTATACTGGA
Found at i:11105856 original size:22 final size:21
Alignment explanation
Indices: 11105806--11105858 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 21
11105796 ATCTCACCCA
11105806 ATTTTAATTTTTTTTTCAATTT
1 ATTTT-ATTTTTTTTTCAATTT
* *
11105828 ATATTATTTTTTTTTCATTTCT
1 ATTTTATTTTTTTTTCAATT-T
11105850 ATTTTATTT
1 ATTTTATTT
11105859 GTTCATATGT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 14 0.52
22 13 0.48
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.74
Consensus pattern (21 bp):
ATTTTATTTTTTTTTCAATTT
Found at i:11107735 original size:26 final size:26
Alignment explanation
Indices: 11107658--11107740 Score: 103
Period size: 27 Copynumber: 3.1 Consensus size: 26
11107648 CTTTTCAATG
* *
11107658 TTCATCCACTTCGAGTGGTTAAATGTA
1 TTCATCTACTTTG-GTGGTTAAATGTA
* *
11107685 TTCGTCTACTTTTTGTGGTTAAATGTA
1 TTCATCTAC-TTTGGTGGTTAAATGTA
*
11107712 TTCATCTACTTTGGTGGTTAAATGAA
1 TTCATCTACTTTGGTGGTTAAATGTA
11107738 TTC
1 TTC
11107741 TTACTATTAG
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
26 18 0.38
27 28 0.58
28 2 0.04
ACGTcount: A:0.23, C:0.14, G:0.18, T:0.45
Consensus pattern (26 bp):
TTCATCTACTTTGGTGGTTAAATGTA
Found at i:11108240 original size:60 final size:60
Alignment explanation
Indices: 11108173--11108293 Score: 181
Period size: 60 Copynumber: 2.0 Consensus size: 60
11108163 GCATGCTTAA
* * *
11108173 TCCGATTTAATAAATTAAGAGACCAAATATAATACATACTACATTATTA-CAAATTCACAT
1 TCCGATTTAATAAATTAAGAGACAAAATATAATACATACTACA-CAATAGCAAATTCACAT
* *
11108233 TCCGATTTAATAAATTAAGGGACAAAATATAATATATACTACACAATAGCAAATTCACAT
1 TCCGATTTAATAAATTAAGAGACAAAATATAATACATACTACACAATAGCAAATTCACAT
11108293 T
1 T
11108294 AAAGTTAATT
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
59 3 0.05
60 52 0.95
ACGTcount: A:0.47, C:0.16, G:0.07, T:0.31
Consensus pattern (60 bp):
TCCGATTTAATAAATTAAGAGACAAAATATAATACATACTACACAATAGCAAATTCACAT
Found at i:11119359 original size:3 final size:3
Alignment explanation
Indices: 11119351--11119376 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
11119341 TCTATTTTTG
11119351 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
11119377 TGTTTATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:11124637 original size:20 final size:21
Alignment explanation
Indices: 11124598--11124637 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
11124588 AGATTAAAAT
*
11124598 TCCAAACAAAATATGGAATAC
1 TCCAAACAAAATATGAAATAC
*
11124619 TCCAAA-AACATATGAAATA
1 TCCAAACAAAATATGAAATA
11124638 AATAAAGCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.55, C:0.17, G:0.07, T:0.20
Consensus pattern (21 bp):
TCCAAACAAAATATGAAATAC
Found at i:11125981 original size:2 final size:2
Alignment explanation
Indices: 11125968--11126008 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
11125958 ATTGGTTAAA
* * *
11125968 AT AT AT AC AT AT AT AT AT AC AT AT AT AT AT AC AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
11126009 GAGGTTAAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.41
Consensus pattern (2 bp):
AT
Found at i:11125985 original size:12 final size:12
Alignment explanation
Indices: 11125968--11126008 Score: 82
Period size: 12 Copynumber: 3.4 Consensus size: 12
11125958 ATTGGTTAAA
11125968 ATATATACATAT
1 ATATATACATAT
11125980 ATATATACATAT
1 ATATATACATAT
11125992 ATATATACATAT
1 ATATATACATAT
11126004 ATATA
1 ATATA
11126009 GAGGTTAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.41
Consensus pattern (12 bp):
ATATATACATAT
Found at i:11129133 original size:28 final size:28
Alignment explanation
Indices: 11129099--11129152 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
11129089 GATTGAAATT
*
11129099 TTATTTATGTTTGATGTACTTTATTTTC
1 TTATTTATGTTTGATGTAATTTATTTTC
*
11129127 TTATTTATGTTTGGTGTAATTTATTT
1 TTATTTATGTTTGATGTAATTTATTT
11129153 GTTTGTAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.19, C:0.04, G:0.13, T:0.65
Consensus pattern (28 bp):
TTATTTATGTTTGATGTAATTTATTTTC
Found at i:11132988 original size:97 final size:96
Alignment explanation
Indices: 11132813--11133071 Score: 361
Period size: 97 Copynumber: 2.7 Consensus size: 96
11132803 CACGAGAATG
* *
11132813 ATGGTTTATTTAGAAAGAAAATGAAAAAAAGTCAACATTATACACCCATA-T-TT-TGTTGACAA
1 ATGGTTTATTTA-AAAGAAAAAG-AAAAGAGTCAACATTATACACCCATATTATTATGTTGACAA
*
11132875 AGGGTTCATTTATTACTCTCAATACTTGCTATC
64 AGGGTTCATTTATTACTCTCAATACTCGCTATC
11132908 ATGGTTTATTTTAAAAGAAAAAGAAAAGAGTCAACATTATACACCCATATTATTATGTTGACAAA
1 ATGGTTTA-TTTAAAAGAAAAAGAAAAGAGTCAACATTATACACCCATATTATTATGTTGACAAA
*
11132973 GGGTTCATTTGTTACTCTCAATACTCGCTATC
65 GGGTTCATTTATTACTCTCAATACTCGCTATC
* * *
11133005 ATGGTTTATTT-AAAGTTCAAAAGGAAAGAGTCAACATTATATACCC---TTATTATGTTGACAA
1 ATGGTTTATTTAAAAG--AAAAAGAAAAGAGTCAACATTATACACCCATATTATTATGTTGACAA
11133066 AGGGTT
64 AGGGTT
11133072 AAAGGGTGTT
Statistics
Matches: 151, Mismatches: 7, Indels: 13
0.88 0.04 0.08
Matches are distributed among these distances:
94 46 0.30
95 22 0.15
96 9 0.06
97 74 0.49
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.34
Consensus pattern (96 bp):
ATGGTTTATTTAAAAGAAAAAGAAAAGAGTCAACATTATACACCCATATTATTATGTTGACAAAG
GGTTCATTTATTACTCTCAATACTCGCTATC
Found at i:11144672 original size:31 final size:30
Alignment explanation
Indices: 11144626--11144694 Score: 104
Period size: 30 Copynumber: 2.3 Consensus size: 30
11144616 TTAATTAAGT
*
11144626 ATTTTTAT-TTTTTATTTTTGAGTCAAATAA
1 ATTTTTATATTTTTA-TTTTGAATCAAATAA
*
11144656 ATTTTTATATTTTTATTTTGAATCAAATTA
1 ATTTTTATATTTTTATTTTGAATCAAATAA
11144686 ATTTTTATA
1 ATTTTTATA
11144695 ATTAATGATT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
30 30 0.83
31 6 0.17
ACGTcount: A:0.32, C:0.03, G:0.04, T:0.61
Consensus pattern (30 bp):
ATTTTTATATTTTTATTTTGAATCAAATAA
Found at i:11144892 original size:101 final size:101
Alignment explanation
Indices: 11144712--11144911 Score: 303
Period size: 101 Copynumber: 2.0 Consensus size: 101
11144702 ATTAACTTAA
* * *
11144712 TCAAAATGTCTTTTATCATTCAATACAATATAATATTGACGTGACATATTAAAATGTCATAATTA
1 TCAAAATGCCTCTTATCATTCAATACAATATAATATTGACGTGACATATTAAAATATCATAATTA
* * *
11144777 ATGATTATGTGGTATGCTAACATATTATAATTGAAG
66 ATGATTATGCGGTATACTAACATACTATAATTGAAG
* *
11144813 TCAAAATGCCTCTTATCATTTAATAGC-ATATAATATTGACGTGATATATTAAAATATCATAATT
1 TCAAAATGCCTCTTATCATTCAATA-CAATATAATATTGACGTGACATATTAAAATATCATAATT
*
11144877 AATGATTATGCGGTATATTAACATACTATAATTGA
65 AATGATTATGCGGTATACTAACATACTATAATTGA
11144912 TAATAACGTG
Statistics
Matches: 89, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
101 88 0.99
102 1 0.01
ACGTcount: A:0.40, C:0.10, G:0.11, T:0.39
Consensus pattern (101 bp):
TCAAAATGCCTCTTATCATTCAATACAATATAATATTGACGTGACATATTAAAATATCATAATTA
ATGATTATGCGGTATACTAACATACTATAATTGAAG
Found at i:11147951 original size:228 final size:228
Alignment explanation
Indices: 11147553--11148692 Score: 1146
Period size: 228 Copynumber: 5.0 Consensus size: 228
11147543 TGACCTACCA
* * * * * * *
11147553 GATGCAAATCTTTGTGAAAACCCTAACAGGCAAGACCATCACCCTT-GAGGTTGAGAGCTCTGAT
1 GATGCAAATCTTTGTGAAGACTCTCACAGGAAAGACTATCA-CCTTGGAGGTTGAGAGCTCAGAC
* * *
11147617 ACTATTGACAATGTCAAGGCTAAGATCCAAGACAAGGAAGGAATCCCTCCTGACCAGCAAAGGCT
65 ACTATTGACAATGTCAAGGCAAAGATCCAAGACAAGGAGGGAATCCCTCCAGACCAGCAAAGGCT
* ** *
11147682 TATTTTTGCTGGCAAACAGCTTGAAGATGGTCGAACCCTAGCTGACTATAATATCCAGAAGGAGT
130 TATCTTTGCTGGCAAACAGCTTGAAGATGGAAGAACCCTAGCTGACTATAATATCCAAAAGGAGT
* * *
11147747 CCACCCTCCATTTGGTGCTTCGTCTCCGTGGTGG
195 CCACCCTTCACTTGGTGCTTCGTCTTCGTGGTGG
* * * * *
11147781 TATGCAAATCTTTGTCAAGACACTCACAGGAAAGACTATCACCTTGGAGGTTGAGAGCTCTGATA
1 GATGCAAATCTTTGTGAAGACTCTCACAGGAAAGACTATCACCTTGGAGGTTGAGAGCTCAGACA
* * * * * * * *
11147846 CTATTGACAATGTTAAAGCGAAGATCCAAGACAAGGAAGGAATCCCTCCTGATCAACAAAGACTT
66 CTATTGACAATGTCAAGGCAAAGATCCAAGACAAGGAGGGAATCCCTCCAGACCAGCAAAGGCTT
* ** * *
11147911 ATCTTTGCTGGCAAACAGCTTGAAGACGGTCGCACCCTAGCTGACTATAATATCCAGAAGGAGTC
131 ATCTTTGCTGGCAAACAGCTTGAAGATGGAAGAACCCTAGCTGACTATAATATCCAAAAGGAGTC
* *
11147976 CACCCTTCATTTGGTGCTTCGTCTTCGAGGTGG
196 CACCCTTCACTTGGTGCTTCGTCTTCGTGGTGG
* * * * * *
11148009 CATGCAAATCTTTGTCAAGACTCTCACAGGTAAA-ACGATCACTTTGGAGGTAGAGAGCTCGGAC
1 GATGCAAATCTTTGTGAAGACTCTCACAGG-AAAGACTATCACCTTGGAGGTTGAGAGCTCAGAC
* * * * * * * * *
11148073 ACTATTGACAATGTCAAGGCTAAGATTCAGGATAAAGAGGGTATCCCACCAGATCAGCAGAGG-T
65 ACTATTGACAATGTCAAGGCAAAGATCCAAGACAAGGAGGGAATCCCTCCAGACCAGCAAAGGCT
* * * * * * * * *
11148137 TGATTTTTGCTGGAAAACAACTTGAAGATGGAAGGACACTTGCTGATTATAACATTCAAAAGGAG
130 T-ATCTTTGCTGGCAAACAGCTTGAAGATGGAAGAACCCTAGCTGACTATAATATCCAAAAGGAG
* * *
11148202 TCAACCCTTCACTTGGTTCTCCGTCTTCGTGGTGG
194 TCCACCCTTCACTTGGTGCTTCGTCTTCGTGGTGG
* * * * *
11148237 GATGCAAATTTTTGTGAAGACTCTTACCGGAAAGACTATCACATTGGAGGTTGAGAGTTCAGACA
1 GATGCAAATCTTTGTGAAGACTCTCACAGGAAAGACTATCACCTTGGAGGTTGAGAGCTCAGACA
* * * * * * *
11148302 CCATTGATAATGTGAAGGCAAAGATCCAAGATAAGGAGGGTATCCCACCAGACCAGCAAAGGCTC
66 CTATTGACAATGTCAAGGCAAAGATCCAAGACAAGGAGGGAATCCCTCCAGACCAGCAAAGGCTT
* * * *
11148367 ATCTTTGCTGGCAAGCAGCTTGAAGATGGAAGAACTCTCGCTGACTATAATATCCAAAAGGAATC
131 ATCTTTGCTGGCAAACAGCTTGAAGATGGAAGAACCCTAGCTGACTATAATATCCAAAAGGAGTC
*
11148432 TACCCTTCACTTGGTG-TTGCGT-TTACGTGGTGG
196 CACCCTTCACTTGGTGCTT-CGTCTT-CGTGGTGG
* * * * * * * *
11148465 GATGCAGATATTTGTGAAGAC-CTTGACTGGAAAGACAATAACGTTGGAGGTTGATAGCTCAGAC
1 GATGCAAATCTTTGTGAAGACTC-TCACAGGAAAGACTATCACCTTGGAGGTTGAGAGCTCAGAC
* * * * * *
11148529 ACCATTGATAATGTGAAGGCAAAGATCCAGGACAAGGAGGGGATCCCTCCAGACCAGCAGAGG-T
65 ACTATTGACAATGTCAAGGCAAAGATCCAAGACAAGGAGGGAATCCCTCCAGACCAGCAAAGGCT
* * * * * * * * * * * * *
11148593 TGATTTTTGCTGGGAAGCAGCTGGAGGATGGGAGAACTCTGGCAGACTACAACATCCAGAAGGAA
130 T-ATCTTTGCTGGCAAACAGCTTGAAGATGGAAGAACCCTAGCTGACTATAATATCCAAAAGGAG
* *
11148658 TCCA-CCTTGCATCTT-GTTCTTCGCCTTCGTGGTGG
194 TCCACCCTT-CA-CTTGGTGCTTCGTCTTCGTGGTGG
11148693 CTTTTAAGTT
Statistics
Matches: 779, Mismatches: 120, Indels: 26
0.84 0.13 0.03
Matches are distributed among these distances:
227 18 0.02
228 750 0.96
229 11 0.01
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.25
Consensus pattern (228 bp):
GATGCAAATCTTTGTGAAGACTCTCACAGGAAAGACTATCACCTTGGAGGTTGAGAGCTCAGACA
CTATTGACAATGTCAAGGCAAAGATCCAAGACAAGGAGGGAATCCCTCCAGACCAGCAAAGGCTT
ATCTTTGCTGGCAAACAGCTTGAAGATGGAAGAACCCTAGCTGACTATAATATCCAAAAGGAGTC
CACCCTTCACTTGGTGCTTCGTCTTCGTGGTGG
Found at i:11149297 original size:59 final size:59
Alignment explanation
Indices: 11149205--11149318 Score: 201
Period size: 59 Copynumber: 1.9 Consensus size: 59
11149195 AGCTCTGTTA
* *
11149205 AATCTCCTTGGTTATGTACGTGTAGTTGTGGTCGGTACTTTCTTTGGAGGATTGGAGCC
1 AATCTCCTTGGTTACGTACATGTAGTTGTGGTCGGTACTTTCTTTGGAGGATTGGAGCC
*
11149264 AATCTCCTTGGTTACGTACATGTAGTTGTGGTCGGTACTTTCTTTTGAGGATTGG
1 AATCTCCTTGGTTACGTACATGTAGTTGTGGTCGGTACTTTCTTTGGAGGATTGG
11149319 GGCTCCAGTT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
59 52 1.00
ACGTcount: A:0.16, C:0.15, G:0.29, T:0.40
Consensus pattern (59 bp):
AATCTCCTTGGTTACGTACATGTAGTTGTGGTCGGTACTTTCTTTGGAGGATTGGAGCC
Found at i:11153255 original size:3 final size:3
Alignment explanation
Indices: 11153241--11153297 Score: 55
Period size: 3 Copynumber: 19.7 Consensus size: 3
11153231 TTTCACTCAA
* * * *
11153241 AAT AAC AAT AAT AAT AAT AAT AAT AA- ATT ATT AAT AAT AAC AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
11153288 -AT AAA AAT AA
1 AAT AAT AAT AA
11153298 AAATTTTAAA
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
2 3 0.07
3 41 0.93
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:11157818 original size:21 final size:21
Alignment explanation
Indices: 11157792--11157836 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
11157782 TCATGGACTT
11157792 ATGTTTTTAACTCAAAAAAAC
1 ATGTTTTTAACTCAAAAAAAC
11157813 ATGTTTTTAACTCAAAAAAAC
1 ATGTTTTTAACTCAAAAAAAC
11157834 ATG
1 ATG
11157837 CCTAATAAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.47, C:0.13, G:0.07, T:0.33
Consensus pattern (21 bp):
ATGTTTTTAACTCAAAAAAAC
Found at i:11160028 original size:20 final size:20
Alignment explanation
Indices: 11160003--11160045 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
11159993 TTATTACCAT
11160003 ATTGGTTTTTGGTGAAGTAA
1 ATTGGTTTTTGGTGAAGTAA
11160023 ATTGGTTTTTGGTGAAGTAA
1 ATTGGTTTTTGGTGAAGTAA
11160043 ATT
1 ATT
11160046 TTTATCTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.28, T:0.47
Consensus pattern (20 bp):
ATTGGTTTTTGGTGAAGTAA
Found at i:11160453 original size:53 final size:53
Alignment explanation
Indices: 11160385--11160485 Score: 132
Period size: 52 Copynumber: 1.9 Consensus size: 53
11160375 CTTTATTACA
* * *
11160385 GAAAGAATCAATTCTGAAAATAAAAGAAGTTAGTTCTTAGCAAACAGAAACAGT
1 GAAAGAATCAATTCTGAAAA-AAAAAAAGTCAGTTCTTAGAAAACAGAAACAGT
* * *
11160439 GAAA-AATCGATTCTGAAAAAAAAAAAGTCAGTTTTTTGAAAACAGAA
1 GAAAGAATCAATTCTGAAAAAAAAAAAGTCAGTTCTTAGAAAACAGAA
11160486 CTACTGGAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
52 23 0.56
53 14 0.34
54 4 0.10
ACGTcount: A:0.51, C:0.10, G:0.16, T:0.23
Consensus pattern (53 bp):
GAAAGAATCAATTCTGAAAAAAAAAAAGTCAGTTCTTAGAAAACAGAAACAGT
Found at i:11161582 original size:36 final size:37
Alignment explanation
Indices: 11161519--11161691 Score: 201
Period size: 37 Copynumber: 4.7 Consensus size: 37
11161509 TTTGATTAAG
* * *
11161519 GTTACACCTGATCCT-ATAAAAAGGCATGTTGTG-AA
1 GTTACACTTGATCCTGTTGAAAAGGCATGTTGTGAAA
* * *
11161554 GATTATATTTGATCTTGTTGAAAA-GCATGTTGTGAAA
1 G-TTACACTTGATCCTGTTGAAAAGGCATGTTGTGAAA
*
11161591 GTTACACTTCATCCTGTTGAAAAGGCATGTTGTGAAA
1 GTTACACTTGATCCTGTTGAAAAGGCATGTTGTGAAA
*
11161628 GTTACACTTGATCCTGTTGAAAAGGAATGTTGT-AAA
1 GTTACACTTGATCCTGTTGAAAAGGCATGTTGTGAAA
* * *
11161664 GGTTACGCCTGATCTTGTTGAAAAGGCA
1 -GTTACACTTGATCCTGTTGAAAAGGCA
11161692 AATTGATAGT
Statistics
Matches: 117, Mismatches: 16, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
35 1 0.01
36 41 0.35
37 75 0.64
ACGTcount: A:0.31, C:0.13, G:0.23, T:0.33
Consensus pattern (37 bp):
GTTACACTTGATCCTGTTGAAAAGGCATGTTGTGAAA
Found at i:11161621 original size:73 final size:74
Alignment explanation
Indices: 11161516--11161691 Score: 207
Period size: 73 Copynumber: 2.4 Consensus size: 74
11161506 TGTTTTGATT
* * * * * *
11161516 AAGGTTACACCTGATCCT-ATAAAAAGGCATGTTGTG-AAGATTATATTTGATCTTGTTGAAAA-
1 AAGGTTACACCTCATCCTGTTGAAAAGGCATGTTGTGAAAG-TTACACTTGATCCTGTTGAAAAG
*
11161578 GCATGTTGTGA
65 GAATGTTGT-A
*
11161589 AA-GTTACACTTCATCCTGTTGAAAAGGCATGTTGTGAAAGTTACACTTGATCCTGTTGAAAAGG
1 AAGGTTACACCTCATCCTGTTGAAAAGGCATGTTGTGAAAGTTACACTTGATCCTGTTGAAAAGG
11161653 AATGTTGTA
66 AATGTTGTA
* * *
11161662 AAGGTTACGCCTGATCTTGTTGAAAAGGCA
1 AAGGTTACACCTCATCCTGTTGAAAAGGCA
11161692 AATTGATAGT
Statistics
Matches: 87, Mismatches: 12, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
72 13 0.15
73 40 0.46
74 34 0.39
ACGTcount: A:0.32, C:0.13, G:0.23, T:0.32
Consensus pattern (74 bp):
AAGGTTACACCTCATCCTGTTGAAAAGGCATGTTGTGAAAGTTACACTTGATCCTGTTGAAAAGG
AATGTTGTA
Found at i:11174965 original size:31 final size:31
Alignment explanation
Indices: 11174922--11175030 Score: 164
Period size: 31 Copynumber: 3.5 Consensus size: 31
11174912 ATGACAGTGT
* *
11174922 TGGCATGTTACAACATTTTATGTTATATGCA
1 TGGCGTGTTACAACATTTTACGTTATATGCA
*
11174953 TGGCGTGTTACAACATTTTACGTTATCTGCA
1 TGGCGTGTTACAACATTTTACGTTATATGCA
*
11174984 TGGCGTGTTACAACATTTTACATTATATGCA
1 TGGCGTGTTACAACATTTTACGTTATATGCA
* *
11175015 TGGCGTGCTACCACAT
1 TGGCGTGTTACAACAT
11175031 GACTGACAAA
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 71 1.00
ACGTcount: A:0.26, C:0.18, G:0.18, T:0.38
Consensus pattern (31 bp):
TGGCGTGTTACAACATTTTACGTTATATGCA
Found at i:11179107 original size:117 final size:117
Alignment explanation
Indices: 11178900--11179298 Score: 537
Period size: 117 Copynumber: 3.4 Consensus size: 117
11178890 CAATGACATC
* * * * * *
11178900 TTGTGGTGACACGCTGAGTGGAAGCAGATACTAGGCGTGACATGTTGAGTGCATGCAAATTTCTA
1 TTGTGGTGACACACTGAGTGGAAGCAGATACTTGGCGTGACACGTTGAGTGCATGTAGATTTCTG
* *
11178965 TGGTGACATGTTGACTTCTCACAGTATTGTGGGGTGACACGGCACGCCCCAA
66 TGGTGACACGTTGACTTCTTACAGTATTGTGGGGTGACACGGCACGCCCCAA
* * ** *
11179017 TTGTGATGGCACACTGAGTGGAAATAGATACTTGGCATGACACGTTGAGTGCATGTAGATTTCTG
1 TTGTGGTGACACACTGAGTGGAAGCAGATACTTGGCGTGACACGTTGAGTGCATGTAGATTTCTG
* * **
11179082 TGGTGACACGTTGACTTCTTGCAGTATTGTGGGGTAACACGATACGCCCCAA
66 TGGTGACACGTTGACTTCTTACAGTATTGTGGGGTGACACGGCACGCCCCAA
* * * * *
11179134 TTGTGGTCACACGCTGAGTGGAAGCAGATACTTGGCGTGACACGCTGAGTGCCTGTAGATTTCGG
1 TTGTGGTGACACACTGAGTGGAAGCAGATACTTGGCGTGACACGTTGAGTGCATGTAGATTTCTG
* * * * *
11179199 TGGTAACACGCTAACTTCTTACAGTACTGTGGGGTGACACGGCATGCCCCAA
66 TGGTGACACGTTGACTTCTTACAGTATTGTGGGGTGACACGGCACGCCCCAA
* *
11179251 TTGGGGTGACACACTGAGTGGAAGCAGATACTTGGGGTGACACGTTGA
1 TTGTGGTGACACACTGAGTGGAAGCAGATACTTGGCGTGACACGTTGA
11179299 CTTGTTCTAG
Statistics
Matches: 241, Mismatches: 41, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
117 241 1.00
ACGTcount: A:0.24, C:0.20, G:0.30, T:0.26
Consensus pattern (117 bp):
TTGTGGTGACACACTGAGTGGAAGCAGATACTTGGCGTGACACGTTGAGTGCATGTAGATTTCTG
TGGTGACACGTTGACTTCTTACAGTATTGTGGGGTGACACGGCACGCCCCAA
Found at i:11181706 original size:145 final size:145
Alignment explanation
Indices: 11181373--11181706 Score: 411
Period size: 145 Copynumber: 2.3 Consensus size: 145
11181363 TAAACATATG
* * *** * * *
11181373 TGGAAATGTTGAACACAAACTGTTAGAACCGAT-CTTACCGACAGGTCGTTAGCATTGTACTTTT
1 TGGAATTGTTGAACACAAACTGTTAGAACCG-TCCTTACCGGCTCATCGTTAGCACTGTACGTTA
* * * * * * *
11181437 GAGGATGACTTCTCAGTGGTTGAAGAGTTGTCGTCGCATGGTCCAACTGCAAACACATATATGTT
65 GAGGATGACCTATCAGTGGTTGAAGAGCTATCGTCGCATGATCCAACTACAAACACAGATATGTT
*
11181502 ATTCGATAATCACATA
130 ATTCGATAATCAAATA
* * *
11181518 TAGAATTGTTGAACACAAACTGTTATAACCGTCCTTACTGGCTCATCGTTAGCACTGTGA-GTTA
1 TGGAATTGTTGAACACAAACTGTTAGAACCGTCCTTACCGGCTCATCGTTAGCACTGT-ACGTTA
* ** *
11181582 GAGGATGACCTATCGGTGGTTGTGGAGCTATCGTCGCATGATCCAACTATAAACACAGATATGTT
65 GAGGATGACCTATCAGTGGTTGAAGAGCTATCGTCGCATGATCCAACTACAAACACAGATATGTT
11181647 ATTCGATAATCAAATA
130 ATTCGATAATCAAATA
* *
11181663 TGGAATTGTTGAACTCAAATTGTTAGAACCGTCCTTACCGGCTC
1 TGGAATTGTTGAACACAAACTGTTAGAACCGTCCTTACCGGCTC
11181707 TTCACTGCCA
Statistics
Matches: 159, Mismatches: 28, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
144 1 0.01
145 157 0.99
146 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31
Consensus pattern (145 bp):
TGGAATTGTTGAACACAAACTGTTAGAACCGTCCTTACCGGCTCATCGTTAGCACTGTACGTTAG
AGGATGACCTATCAGTGGTTGAAGAGCTATCGTCGCATGATCCAACTACAAACACAGATATGTTA
TTCGATAATCAAATA
Found at i:11183136 original size:31 final size:31
Alignment explanation
Indices: 11183101--11183236 Score: 202
Period size: 31 Copynumber: 4.4 Consensus size: 31
11183091 TTAACCCATG
*
11183101 ATGTGGTAACACGCCATGCATATAACGTAAA
1 ATGTTGTAACACGCCATGCATATAACGTAAA
*
11183132 ATGTGGTAACACGCCATGCATATAACGTAAA
1 ATGTTGTAACACGCCATGCATATAACGTAAA
*
11183163 ATGTTGTAACACGCCATGCATATAACATAAA
1 ATGTTGTAACACGCCATGCATATAACGTAAA
* * *
11183194 ATGTTGTAACATGCCATGCGTATCAA-GTCAA
1 ATGTTGTAACACGCCATGCATAT-AACGTAAA
11183225 ATGTTGTAACAC
1 ATGTTGTAACAC
11183237 ACCAATGCTG
Statistics
Matches: 97, Mismatches: 7, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
31 95 0.98
32 2 0.02
ACGTcount: A:0.38, C:0.19, G:0.18, T:0.26
Consensus pattern (31 bp):
ATGTTGTAACACGCCATGCATATAACGTAAA
Found at i:11184156 original size:47 final size:47
Alignment explanation
Indices: 11183908--11184159 Score: 252
Period size: 47 Copynumber: 5.4 Consensus size: 47
11183898 TGTCACGAAT
* * * * *
11183908 CTCCATGGAGTTTGACAAACTTTGAACCTTGCCGTGTCACAGATTCC
1 CTCCATGGCGTGTCACAAACTCTGAACCCTGCCGTGTCACAGATTCC
* * * * *
11183955 CTCCATGGCATGTCACAAACTCTTAACACTGACGTGTCTCAGATTCC
1 CTCCATGGCGTGTCACAAACTCTGAACCCTGCCGTGTCACAGATTCC
* * ** * *
11184002 CTCTATGGGGTGTCACAAACTCTGAATGCTGGCATGTCACAGATTCC
1 CTCCATGGCGTGTCACAAACTCTGAACCCTGCCGTGTCACAGATTCC
* * ** * *
11184049 CTCCATGGCATGTCACGAACTCTGAATGCTGGCGTGTCATAGATTCC
1 CTCCATGGCGTGTCACAAACTCTGAACCCTGCCGTGTCACAGATTCC
* * *
11184096 CTCCATGGCGTGTCACAAACTCTAAACCCTGCCATGTCACACATTCC
1 CTCCATGGCGTGTCACAAACTCTGAACCCTGCCGTGTCACAGATTCC
* **
11184143 CACCATGTTGTGTCACA
1 CTCCATGGCGTGTCACA
11184160 CATTCCCAAT
Statistics
Matches: 168, Mismatches: 37, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
47 168 1.00
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.27
Consensus pattern (47 bp):
CTCCATGGCGTGTCACAAACTCTGAACCCTGCCGTGTCACAGATTCC
Found at i:11184158 original size:94 final size:94
Alignment explanation
Indices: 11183908--11184149 Score: 297
Period size: 94 Copynumber: 2.6 Consensus size: 94
11183898 TGTCACGAAT
* * * * *
11183908 CTCCATGGAGTTTGACAAACTTTGAACCTTGCCGTGTCACAGATTCCCTCCATGGCATGTCACAA
1 CTCCATGGAGTGTCACAAACTCTGAACCCTGCCATGTCACAGATTCCCTCCATGGCATGTCACAA
*
11183973 ACTCTTAACACTGACGTGTCTCAGATTCC
66 ACTCTGAACACTGACGTGTCTCAGATTCC
* * ** * *
11184002 CTCTATGGGGTGTCACAAACTCTGAATGCTGGCATGTCACAGATTCCCTCCATGGCATGTCACGA
1 CTCCATGGAGTGTCACAAACTCTGAACCCTGCCATGTCACAGATTCCCTCCATGGCATGTCACAA
** *
11184067 ACTCTGAATGCTGGCGTGTCAT-AGATTCC
66 ACTCTGAACACTGACGTGTC-TCAGATTCC
* * * *
11184096 CTCCATGGCGTGTCACAAACTCTAAACCCTGCCATGTCACACATTCCCACCATG
1 CTCCATGGAGTGTCACAAACTCTGAACCCTGCCATGTCACAGATTCCCTCCATG
11184150 TTGTGTCACA
Statistics
Matches: 124, Mismatches: 23, Indels: 2
0.83 0.15 0.01
Matches are distributed among these distances:
94 123 0.99
95 1 0.01
ACGTcount: A:0.24, C:0.31, G:0.19, T:0.27
Consensus pattern (94 bp):
CTCCATGGAGTGTCACAAACTCTGAACCCTGCCATGTCACAGATTCCCTCCATGGCATGTCACAA
ACTCTGAACACTGACGTGTCTCAGATTCC
Found at i:11188513 original size:2 final size:2
Alignment explanation
Indices: 11188506--11188537 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
11188496 GCCAAAAAGT
11188506 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
11188538 ATAAAAAAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:11193348 original size:13 final size:13
Alignment explanation
Indices: 11193330--11193354 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11193320 ATTTTCAAAA
11193330 ATTTTATAAAATT
1 ATTTTATAAAATT
11193343 ATTTTATAAAAT
1 ATTTTATAAAAT
11193355 CCCATTTTCC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
ATTTTATAAAATT
Found at i:11194569 original size:29 final size:29
Alignment explanation
Indices: 11194508--11194571 Score: 85
Period size: 28 Copynumber: 2.2 Consensus size: 29
11194498 GTAAATTTTT
** *
11194508 AAAAATTACACTTTTACCCCCGTAAAGTG
1 AAAAATTACACTTTTACCCCCAAAAACTG
*
11194537 AAAAATTACATTTTTA-CCCCAAAAACTG
1 AAAAATTACACTTTTACCCCCAAAAACTG
11194565 AAAAATT
1 AAAAATT
11194572 GCCCATAGAC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 16 0.52
29 15 0.48
ACGTcount: A:0.45, C:0.20, G:0.06, T:0.28
Consensus pattern (29 bp):
AAAAATTACACTTTTACCCCCAAAAACTG
Found at i:11198127 original size:13 final size:13
Alignment explanation
Indices: 11198109--11198133 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11198099 ATTTTCAAAA
11198109 ATTTTATAAAATT
1 ATTTTATAAAATT
11198122 ATTTTATAAAAT
1 ATTTTATAAAAT
11198134 CCCATTTTCC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
ATTTTATAAAATT
Found at i:11199347 original size:28 final size:29
Alignment explanation
Indices: 11199287--11199350 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 29
11199277 GTAAATTTTT
** * *
11199287 AAAAATTACACTTTTACCCCCGTAAAGTG
1 AAAAATTACACTTTTACCCCCAAAAACTA
*
11199316 AAAAATTACATTTTTA-CCCCAAAAACTA
1 AAAAATTACACTTTTACCCCCAAAAACTA
11199344 AAAAATT
1 AAAAATT
11199351 GCCCATAGAC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 15 0.50
29 15 0.50
ACGTcount: A:0.47, C:0.20, G:0.05, T:0.28
Consensus pattern (29 bp):
AAAAATTACACTTTTACCCCCAAAAACTA
Found at i:11202123 original size:10 final size:9
Alignment explanation
Indices: 11202090--11202136 Score: 51
Period size: 10 Copynumber: 5.0 Consensus size: 9
11202080 GTAGACACCA
11202090 ATTTTATCTT
1 ATTTTAT-TT
*
11202100 GTTTTATTT
1 ATTTTATTT
11202109 A-TTTATTT
1 ATTTTATTT
11202117 ATTTTTATTT
1 A-TTTTATTT
11202127 CATTTTATTT
1 -ATTTTATTT
11202137 CAGTTTTATC
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
8 8 0.25
9 2 0.06
10 21 0.66
11 1 0.03
ACGTcount: A:0.19, C:0.04, G:0.02, T:0.74
Consensus pattern (9 bp):
ATTTTATTT
Found at i:11202143 original size:11 final size:10
Alignment explanation
Indices: 11202101--11202145 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
11202091 TTTTATCTTG
11202101 TTTTATTT-A
1 TTTTATTTCA
11202110 -TTTATTT-A
1 TTTTATTTCA
11202118 TTTTTATTTCA
1 -TTTTATTTCA
11202129 TTTTATTTCA
1 TTTTATTTCA
11202139 GTTTTAT
1 -TTTTAT
11202146 CATATTATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
8 8 0.25
10 17 0.53
11 7 0.22
ACGTcount: A:0.20, C:0.04, G:0.02, T:0.73
Consensus pattern (10 bp):
TTTTATTTCA
Found at i:11202371 original size:19 final size:20
Alignment explanation
Indices: 11202337--11202374 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
11202327 TGAAAAAATA
11202337 AATACAATATTTTTCGTTAG
1 AATACAATATTTTTCGTTAG
11202357 AATACAATA-TTTTCGTTA
1 AATACAATATTTTTCGTTA
11202375 AAAATGACAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.37, C:0.11, G:0.08, T:0.45
Consensus pattern (20 bp):
AATACAATATTTTTCGTTAG
Found at i:11205592 original size:3 final size:3
Alignment explanation
Indices: 11205578--11205617 Score: 53
Period size: 3 Copynumber: 13.0 Consensus size: 3
11205568 ACATGTTTGA
* *
11205578 ATT ATC ATT ATT ATT ATT ATT ATT ATT TTT ATTT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT
11205618 TTTTGAATGA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:11206350 original size:25 final size:23
Alignment explanation
Indices: 11206304--11206350 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
11206294 CATTCATTCA
* *
11206304 TTCATTTTTTTATATTTTTATTT
1 TTCATTTTTTTATATATATATTT
11206327 TTCATTTTTTTGCATATATATATT
1 TTCATTTTTTT--ATATATATATT
11206351 GCTAAACACT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 11 0.55
25 9 0.45
ACGTcount: A:0.21, C:0.06, G:0.02, T:0.70
Consensus pattern (23 bp):
TTCATTTTTTTATATATATATTT
Found at i:11210148 original size:21 final size:21
Alignment explanation
Indices: 11210122--11210189 Score: 79
Period size: 21 Copynumber: 3.4 Consensus size: 21
11210112 CTCTTACAAA
11210122 AACATAAAAATAAATATTAAT
1 AACATAAAAATAAATATTAAT
* *
11210143 AACATAAAACTAAAT-TTATT
1 AACATAAAAATAAATATTAAT
* *
11210163 AAC-TTAAAATAAATATTTA-
1 AACATAAAAATAAATATTAAT
11210182 AACATAAA
1 AACATAAA
11210190 TTAAACTAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
19 12 0.32
20 12 0.32
21 14 0.37
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.31
Consensus pattern (21 bp):
AACATAAAAATAAATATTAAT
Found at i:11210165 original size:20 final size:20
Alignment explanation
Indices: 11210122--11210194 Score: 78
Period size: 20 Copynumber: 3.6 Consensus size: 20
11210112 CTCTTACAAA
*
11210122 AACATAAAAATAAATATTAAT
1 AACAT-AAAATAAATATTATT
11210143 AACATAAAACTAAAT-TTATT
1 AACATAAAA-TAAATATTATT
* *
11210163 AACTTAAAATAAATATT-TA
1 AACATAAAATAAATATTATT
*
11210182 AACATAAATTAAA
1 AACATAAAATAAA
11210195 CTAAACTAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
19 17 0.38
20 18 0.40
21 10 0.22
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.32
Consensus pattern (20 bp):
AACATAAAATAAATATTATT
Found at i:11210189 original size:19 final size:19
Alignment explanation
Indices: 11210121--11210194 Score: 69
Period size: 19 Copynumber: 3.7 Consensus size: 19
11210111 ACTCTTACAA
*
11210121 AAACATAAAAATAAATATTA
1 AAACAT-AAAATAAATATTT
11210141 ATAACATAAAACTAAAT-TTAT
1 A-AACATAAAA-TAAATATT-T
* *
11210162 TAACTTAAAATAAATATTT
1 AAACATAAAATAAATATTT
*
11210181 AAACATAAATTAAA
1 AAACATAAAATAAA
11210195 CTAAACTAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
19 17 0.39
20 17 0.39
21 10 0.23
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.31
Consensus pattern (19 bp):
AAACATAAAATAAATATTT
Found at i:11211156 original size:30 final size:30
Alignment explanation
Indices: 11211122--11211185 Score: 119
Period size: 30 Copynumber: 2.1 Consensus size: 30
11211112 GGTATACTAG
11211122 GGATAAAAGTTTAACAAGGTTAGCTTGAAA
1 GGATAAAAGTTTAACAAGGTTAGCTTGAAA
*
11211152 GGATAAAAGTTTAACAAGGTTATCTTGAAA
1 GGATAAAAGTTTAACAAGGTTAGCTTGAAA
11211182 GGAT
1 GGAT
11211186 TAAACCTAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.42, C:0.06, G:0.23, T:0.28
Consensus pattern (30 bp):
GGATAAAAGTTTAACAAGGTTAGCTTGAAA
Found at i:11214391 original size:20 final size:19
Alignment explanation
Indices: 11214368--11214421 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 19
11214358 TAAATATAAA
11214368 TAACATAAAACT-AACATTAT
1 TAACATAAAA-TAAACATT-T
*
11214388 TAACTTAAAATAAACATTT
1 TAACATAAAATAAACATTT
* *
11214407 AAACATAAATTAAAC
1 TAACATAAAATAAAC
11214422 TAAACTAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 14 0.48
20 15 0.52
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (19 bp):
TAACATAAAATAAACATTT
Found at i:11220271 original size:54 final size:54
Alignment explanation
Indices: 11220213--11220415 Score: 316
Period size: 54 Copynumber: 3.8 Consensus size: 54
11220203 TCCTGTCGTA
* * *
11220213 AAGCCTCCTTATGTGCCCAAACCTCCAGTTGTAAAGCCTCCGCCTCATATACCG
1 AAGCCTCCCTATGTACCCAAACCTCCAGTTGTAAAGCCTCCGCCTCATACACCG
* *
11220267 AAGCCTCCCTATGTACCCAAACCTCCTGTTGTAAAGCCTCCGCCTCATGCACCG
1 AAGCCTCCCTATGTACCCAAACCTCCAGTTGTAAAGCCTCCGCCTCATACACCG
* * * * *
11220321 AAGCCTCCCTATGTACCCAAACCTCCTGTAGTAAAGCCTCCGCCTTACACCCCG
1 AAGCCTCCCTATGTACCCAAACCTCCAGTTGTAAAGCCTCCGCCTCATACACCG
11220375 AAGCCTCCCTATGTACCCAAACCTCCAGTTGTAAAGCCTCC
1 AAGCCTCCCTATGTACCCAAACCTCCAGTTGTAAAGCCTCC
11220416 ACCCTATACA
Statistics
Matches: 137, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 137 1.00
ACGTcount: A:0.24, C:0.40, G:0.14, T:0.22
Consensus pattern (54 bp):
AAGCCTCCCTATGTACCCAAACCTCCAGTTGTAAAGCCTCCGCCTCATACACCG
Found at i:11220433 original size:36 final size:36
Alignment explanation
Indices: 11220393--11220481 Score: 160
Period size: 36 Copynumber: 2.5 Consensus size: 36
11220383 CTATGTACCC
11220393 AAACCTCCAGTTGTAAAGCCTCCACCCTATACACCA
1 AAACCTCCAGTTGTAAAGCCTCCACCCTATACACCA
* *
11220429 AAACCTCCAGTTGTAAAGCCTCCACCTTATCCACCA
1 AAACCTCCAGTTGTAAAGCCTCCACCCTATACACCA
11220465 AAACCTCCAGTTGTAAA
1 AAACCTCCAGTTGTAAA
11220482 ACCACCCTAC
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 51 1.00
ACGTcount: A:0.34, C:0.36, G:0.09, T:0.21
Consensus pattern (36 bp):
AAACCTCCAGTTGTAAAGCCTCCACCCTATACACCA
Found at i:11220537 original size:21 final size:21
Alignment explanation
Indices: 11220507--11220550 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
11220497 GGTGCCCACG
*
11220507 CCACCATATGTACCCAAGCCC
1 CCACCATATGTACCCAAACCC
* *
11220528 CCACCTTATGTACCGAAACCC
1 CCACCATATGTACCCAAACCC
11220549 CC
1 CC
11220551 CATCGTGCCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.27, C:0.48, G:0.09, T:0.16
Consensus pattern (21 bp):
CCACCATATGTACCCAAACCC
Found at i:11220745 original size:63 final size:63
Alignment explanation
Indices: 11220637--11220886 Score: 383
Period size: 63 Copynumber: 4.0 Consensus size: 63
11220627 CCAGTCATAT
*
11220637 CACCGCCAATTCTGCCTCCAAAGCCTCCTGTATATCCGAGTCCTCCGATTGTGAAGCCACCAA
1 CACCGCCAATCCTGCCTCCAAAGCCTCCTGTATATCCGAGTCCTCCGATTGTGAAGCCACCAA
* * * * *
11220700 CACCACCAGTTCTGCCTCCAACGCCTCCTGTCTATCCGAGTCCTCCGATTGTGAAGCCACCAA
1 CACCGCCAATCCTGCCTCCAAAGCCTCCTGTATATCCGAGTCCTCCGATTGTGAAGCCACCAA
* *
11220763 CACCGCCAATCCTGCCTCCAAAGCCTCCTGTCTATCCGAGTCCTCCGATTGTGAAGCCACCGA
1 CACCGCCAATCCTGCCTCCAAAGCCTCCTGTATATCCGAGTCCTCCGATTGTGAAGCCACCAA
** * * *
11220826 CACCGCCAATCCTGCCTCCAACCCCTCCTATATATCCAAGTCCTCCTATTGTGAAGCCACC
1 CACCGCCAATCCTGCCTCCAAAGCCTCCTGTATATCCGAGTCCTCCGATTGTGAAGCCACC
11220887 TCCCATCGAG
Statistics
Matches: 172, Mismatches: 15, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
63 172 1.00
ACGTcount: A:0.22, C:0.41, G:0.15, T:0.22
Consensus pattern (63 bp):
CACCGCCAATCCTGCCTCCAAAGCCTCCTGTATATCCGAGTCCTCCGATTGTGAAGCCACCAA
Found at i:11221628 original size:40 final size:40
Alignment explanation
Indices: 11221573--11221650 Score: 140
Period size: 40 Copynumber: 1.9 Consensus size: 40
11221563 TCTTCTTAGA
11221573 GATTTTCTAATAATTCATTAAGATAGTAC-GAAATAATAGC
1 GATTTTCTAATAATTCATTAAGATAGT-CTGAAATAATAGC
11221613 GATTTTCTAATAATTCATTAAGATAGTCTGAAATAATA
1 GATTTTCTAATAATTCATTAAGATAGTCTGAAATAATA
11221651 AATTATTGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
39 1 0.03
40 36 0.97
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.37
Consensus pattern (40 bp):
GATTTTCTAATAATTCATTAAGATAGTCTGAAATAATAGC
Found at i:11222348 original size:32 final size:30
Alignment explanation
Indices: 11222312--11222395 Score: 98
Period size: 29 Copynumber: 2.8 Consensus size: 30
11222302 AAGTATAACA
* *
11222312 ATTTTTTGTTGAATATGACGTGTAATAATAAT
1 ATTTTTT-TT-AACATGACGTGTAACAATAAT
11222344 A-TTTTTTTAACATGACGTGTAACAATAAT
1 ATTTTTTTTAACATGACGTGTAACAATAAT
* * *
11222373 ATTTTATTCAGCATGACGTGTAA
1 ATTTTTTTTAACATGACGTGTAA
11222396 TATGTTTTTG
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
29 20 0.43
30 20 0.43
31 5 0.11
32 1 0.02
ACGTcount: A:0.35, C:0.08, G:0.14, T:0.43
Consensus pattern (30 bp):
ATTTTTTTTAACATGACGTGTAACAATAAT
Found at i:11222361 original size:29 final size:30
Alignment explanation
Indices: 11222326--11222397 Score: 110
Period size: 29 Copynumber: 2.4 Consensus size: 30
11222316 TTTGTTGAAT
*
11222326 ATGACGTGTAATAATAATATTTT-TTTAAC
1 ATGACGTGTAATAATAATATTTTATTCAAC
* *
11222355 ATGACGTGTAACAATAATATTTTATTCAGC
1 ATGACGTGTAATAATAATATTTTATTCAAC
11222385 ATGACGTGTAATA
1 ATGACGTGTAATA
11222398 TGTTTTTGTG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
29 22 0.58
30 16 0.42
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.39
Consensus pattern (30 bp):
ATGACGTGTAATAATAATATTTTATTCAAC
Found at i:11222397 original size:24 final size:24
Alignment explanation
Indices: 11222369--11222418 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
11222359 CGTGTAACAA
11222369 TAATAT-TTTATTCAGCATGACGTG
1 TAATATGTTT-TTCAGCATGACGTG
**
11222393 TAATATGTTTTTGTGCATGACGTG
1 TAATATGTTTTTCAGCATGACGTG
11222417 TA
1 TA
11222419 CCAATAACAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 20 0.87
25 3 0.13
ACGTcount: A:0.26, C:0.10, G:0.20, T:0.44
Consensus pattern (24 bp):
TAATATGTTTTTCAGCATGACGTG
Found at i:11222604 original size:23 final size:23
Alignment explanation
Indices: 11222577--11222621 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
11222567 GTAATAACCT
*
11222577 TTTTTAACTATGGTGTATAACATA
1 TTTTGAAC-ATGGTGTATAACATA
* *
11222601 TTTTGTACATGGTGTGTAACA
1 TTTTGAACATGGTGTATAACA
11222622 ACAATAATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 12 0.67
24 6 0.33
ACGTcount: A:0.29, C:0.09, G:0.18, T:0.44
Consensus pattern (23 bp):
TTTTGAACATGGTGTATAACATA
Found at i:11225733 original size:24 final size:24
Alignment explanation
Indices: 11225713--11225759 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
11225703 AAATTTGATT
11225713 GATCCATTTACCAAAACTTTGCCAA
1 GATCCATTTACCAAAACTTTG-CAA
*
11225738 GATTCATTTACCAAAACTTTGC
1 GATCCATTTACCAAAACTTTGC
11225760 CAAAAGAGGC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 1 0.05
25 20 0.95
ACGTcount: A:0.34, C:0.26, G:0.09, T:0.32
Consensus pattern (24 bp):
GATCCATTTACCAAAACTTTGCAA
Found at i:11226412 original size:18 final size:17
Alignment explanation
Indices: 11226386--11226429 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
11226376 TTATTCAAAT
*
11226386 GTGATTATTCAAATTAAA
1 GTGACTATTCAAATT-AA
*
11226404 GTGACTATTTAAATTAA
1 GTGACTATTCAAATTAA
*
11226421 GTGTCTATT
1 GTGACTATT
11226430 TAGATTAAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 10 0.43
18 13 0.57
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.43
Consensus pattern (17 bp):
GTGACTATTCAAATTAA
Found at i:11226428 original size:17 final size:17
Alignment explanation
Indices: 11226386--11226438 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
11226376 TTATTCAAAT
* *
11226386 GTGATTATTCAAATTAAA
1 GTGACTATTTAAATT-AA
11226404 GTGACTATTTAAATTAA
1 GTGACTATTTAAATTAA
* *
11226421 GTGTCTATTTAGATTAA
1 GTGACTATTTAAATTAA
11226438 G
1 G
11226439 ATATGATTCT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
17 18 0.58
18 13 0.42
ACGTcount: A:0.38, C:0.06, G:0.15, T:0.42
Consensus pattern (17 bp):
GTGACTATTTAAATTAA
Found at i:11227333 original size:27 final size:27
Alignment explanation
Indices: 11227288--11227494 Score: 167
Period size: 27 Copynumber: 7.7 Consensus size: 27
11227278 GTTAACGTCG
*
11227288 TGTTGAAAAATGTAG-TGTT-CACGCTA
1 TGTT-AAAAATTTAGTTGTTACACGCTA
* *
11227314 TGTTTTAAAATTTAGTTGTTACATG-TCA
1 TG-TTAAAAATTTAGTTGTTACACGCT-A
* * *
11227342 TGTTGAAAA--TAATTGTTACACGTTA
1 TGTTAAAAATTTAGTTGTTACACGCTA
* * *
11227367 TATTAAAAATATAGTTGTTACATGCTA
1 TGTTAAAAATTTAGTTGTTACACGCTA
11227394 TGTTAAAAATTTAGTTGTTACACG-TCA
1 TGTTAAAAATTTAGTTGTTACACGCT-A
* * * *
11227421 TGTTGAAAATTTACTTGTTACATGCCA
1 TGTTAAAAATTTAGTTGTTACACGCTA
* * *
11227448 TGTTGAAAAATGTAGTTGTTATATGAC-A
1 TGTT-AAAAATTTAGTTGTTACACG-CTA
11227476 TGTTAAAAATTTAGTTGTT
1 TGTTAAAAATTTAGTTGTT
11227495 GCATGCCATT
Statistics
Matches: 147, Mismatches: 23, Indels: 21
0.77 0.12 0.11
Matches are distributed among these distances:
25 19 0.13
26 12 0.08
27 88 0.60
28 27 0.18
29 1 0.01
ACGTcount: A:0.33, C:0.08, G:0.16, T:0.42
Consensus pattern (27 bp):
TGTTAAAAATTTAGTTGTTACACGCTA
Found at i:11227347 original size:54 final size:52
Alignment explanation
Indices: 11227288--11227500 Score: 200
Period size: 54 Copynumber: 4.0 Consensus size: 52
11227278 GTTAACGTCG
*
11227288 TGTTGAAAAATGTAGTGTT-CACGCTATGTTTTAAAATTTAGTTGTTACATGTCA
1 TGTTGAAAAATGTAGTGTTACACG-TATG-TTAAAAATTTAGTTGTTACATG-CA
* * * *
11227342 TGTTG-AAAAT-AATTGTTACACGTTATATTAAAAATATAGTTGTTACATGCTA
1 TGTTGAAAAATGTAGTGTTACACG-TATGTTAAAAATTTAGTTGTTACATGC-A
* * *
11227394 TGTT-AAAAATTTAGTTGTTACACGTCATGTTGAAAATTTACTTGTTACATGCCA
1 TGTTGAAAAATGTAG-TGTTACACGT-ATGTTAAAAATTTAGTTGTTACATG-CA
* * * *
11227448 TGTTGAAAAATGTAGTTGTTATATGACATGTTAAAAATTTAGTTGTTGCATGC
1 TGTTGAAAAATGTAG-TGTTACACG-TATGTTAAAAATTTAGTTGTTACATGC
11227501 CATTCTGAAA
Statistics
Matches: 131, Mismatches: 19, Indels: 18
0.78 0.11 0.11
Matches are distributed among these distances:
51 1 0.01
52 35 0.27
53 14 0.11
54 41 0.31
55 40 0.31
ACGTcount: A:0.33, C:0.09, G:0.17, T:0.41
Consensus pattern (52 bp):
TGTTGAAAAATGTAGTGTTACACGTATGTTAAAAATTTAGTTGTTACATGCA
Found at i:11227412 original size:79 final size:80
Alignment explanation
Indices: 11227290--11227526 Score: 261
Period size: 79 Copynumber: 3.0 Consensus size: 80
11227280 TAACGTCGTG
* *
11227290 TTGAAAAATGTAG-TGTT-CACGCTATGTTTTAAAATTTAGTTGTTACATGTCATGTTGAAAATA
1 TTGAAAAATGTAGTTGTTACATGCTATG-TTAAAAATTTAGTTGTTACATGTCATGTTGAAAATA
**
11227353 ATTGTTACACGTTATA
65 ATTGTTACACGCCATA
* *
11227369 TT-AAAAATATAGTTGTTACATGCTATGTTAAAAATTTAGTTGTTACACGTCATGTTGAAAATTT
1 TTGAAAAATGTAGTTGTTACATGCTATGTTAAAAATTTAGTTGTTACATGTCATGTTGAAAA--T
* * *
11227433 ACTTGTTACATGCCATG
64 AATTGTTACACGCCATA
* * *
11227450 TTGAAAAATGTAGTTGTTATATGAC-ATGTTAAAAATTTAGTTGTTGCATGCCAT-TCTGAAAA-
1 TTGAAAAATGTAGTTGTTACATG-CTATGTTAAAAATTTAGTTGTTACATGTCATGT-TGAAAAT
* *
11227512 AGTTGTTACATGCCA
64 AATTGTTACACGCCA
11227527 CAACATAATT
Statistics
Matches: 136, Mismatches: 15, Indels: 14
0.82 0.09 0.08
Matches are distributed among these distances:
78 9 0.07
79 52 0.38
80 8 0.06
81 16 0.12
82 50 0.37
83 1 0.01
ACGTcount: A:0.33, C:0.10, G:0.16, T:0.40
Consensus pattern (80 bp):
TTGAAAAATGTAGTTGTTACATGCTATGTTAAAAATTTAGTTGTTACATGTCATGTTGAAAATAA
TTGTTACACGCCATA
Found at i:11227479 original size:55 final size:54
Alignment explanation
Indices: 11227288--11227512 Score: 230
Period size: 55 Copynumber: 4.2 Consensus size: 54
11227278 GTTAACGTCG
* *
11227288 TGTTGAAAAATGTAG-TGTT-CACG-CTATGTTTTAAAATTTAGTTGTTACATGTCA
1 TGTTGAAAAAT-TAGTTGTTACACGTC-ATG-TTAAAAATTTAGTTGTTACATGCCA
* * * * *
11227342 TGTTG-AAAA-TAATTGTTACACGTTATATTAAAAATATAGTTGTTACATGCTA
1 TGTTGAAAAATTAGTTGTTACACGTCATGTTAAAAATTTAGTTGTTACATGCCA
* *
11227394 TGTT-AAAAATTTAGTTGTTACACGTCATGTTGAAAATTTACTTGTTACATGCCA
1 TGTTGAAAAA-TTAGTTGTTACACGTCATGTTAAAAATTTAGTTGTTACATGCCA
* * * *
11227448 TGTTGAAAAATGTAGTTGTTATATGACATGTTAAAAATTTAGTTGTTGCATGCCA
1 TGTTGAAAAAT-TAGTTGTTACACGTCATGTTAAAAATTTAGTTGTTACATGCCA
11227503 T-TCTGAAAAA
1 TGT-TGAAAAA
11227513 GTTGTTACAT
Statistics
Matches: 142, Mismatches: 20, Indels: 17
0.79 0.11 0.09
Matches are distributed among these distances:
51 2 0.01
52 33 0.23
53 10 0.07
54 47 0.33
55 50 0.35
ACGTcount: A:0.34, C:0.09, G:0.16, T:0.40
Consensus pattern (54 bp):
TGTTGAAAAATTAGTTGTTACACGTCATGTTAAAAATTTAGTTGTTACATGCCA
Found at i:11227511 original size:27 final size:27
Alignment explanation
Indices: 11227320--11227526 Score: 192
Period size: 27 Copynumber: 7.8 Consensus size: 27
11227310 GCTATGTTTT
*
11227320 AAAATTTAGTTGTTACATGTCATGTTG
1 AAAATTTAGTTGTTACATGCCATGTTG
* * ** * *
11227347 AAAA--TAATTGTTACACGTTATATTA
1 AAAATTTAGTTGTTACATGCCATGTTG
* * *
11227372 AAAATATAGTTGTTACATGCTATGTTA
1 AAAATTTAGTTGTTACATGCCATGTTG
* *
11227399 AAAATTTAGTTGTTACACGTCATGTTG
1 AAAATTTAGTTGTTACATGCCATGTTG
*
11227426 AAAATTTACTTGTTACATGCCATGTTG
1 AAAATTTAGTTGTTACATGCCATGTTG
* * * *
11227453 AAAAATGTAGTTGTTATATGACATGTTA
1 -AAAATTTAGTTGTTACATGCCATGTTG
*
11227481 AAAATTTAGTTGTTGCATGCCAT-TCTG
1 AAAATTTAGTTGTTACATGCCATGT-TG
11227508 AAAA---AGTTGTTACATGCCA
1 AAAATTTAGTTGTTACATGCCA
11227527 CAACATAATT
Statistics
Matches: 148, Mismatches: 28, Indels: 11
0.79 0.15 0.06
Matches are distributed among these distances:
24 14 0.09
25 20 0.14
26 1 0.01
27 91 0.61
28 22 0.15
ACGTcount: A:0.34, C:0.10, G:0.16, T:0.40
Consensus pattern (27 bp):
AAAATTTAGTTGTTACATGCCATGTTG
Found at i:11230035 original size:18 final size:18
Alignment explanation
Indices: 11230012--11230047 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
11230002 ACCTCACCAA
11230012 TAAAAACTGCAGATACTT
1 TAAAAACTGCAGATACTT
*
11230030 TAAAAACTGCCGATACTT
1 TAAAAACTGCAGATACTT
11230048 ATAGCTGGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.42, C:0.19, G:0.11, T:0.28
Consensus pattern (18 bp):
TAAAAACTGCAGATACTT
Found at i:11243705 original size:5 final size:5
Alignment explanation
Indices: 11243691--11243728 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
11243681 GGCTTTTAGC
* *
11243691 TGCC- TGCCA TGCCA TGCCA TGCCA TGTCA TGCCT TGCC
1 TGCCA TGCCA TGCCA TGCCA TGCCA TGCCA TGCCA TGCC
11243729 TTATAGGATT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
4 4 0.13
5 26 0.87
ACGTcount: A:0.13, C:0.39, G:0.21, T:0.26
Consensus pattern (5 bp):
TGCCA
Found at i:11244867 original size:23 final size:24
Alignment explanation
Indices: 11244821--11244867 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
11244811 TTATCAATTG
*
11244821 AACTAACTTCTCCTTGGTTCTATA
1 AACTAACTTCTCCTTGATTCTATA
*
11244845 AACTAAC-TCTCCTTGATTTTATA
1 AACTAACTTCTCCTTGATTCTATA
11244868 GGTAACTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 14 0.67
24 7 0.33
ACGTcount: A:0.28, C:0.23, G:0.06, T:0.43
Consensus pattern (24 bp):
AACTAACTTCTCCTTGATTCTATA
Found at i:11245199 original size:26 final size:25
Alignment explanation
Indices: 11245170--11245221 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 25
11245160 ATGTTTTCAA
* *
11245170 ATTTTATAATTTTTTCTTTTTTTTTT
1 ATTTTATAA-TTTATCTTTATTTTTT
11245196 ATTTTATAATTTATCTTTATTTTTT
1 ATTTTATAATTTATCTTTATTTTTT
11245221 A
1 A
11245222 AAAAATTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 15 0.62
26 9 0.38
ACGTcount: A:0.21, C:0.04, G:0.00, T:0.75
Consensus pattern (25 bp):
ATTTTATAATTTATCTTTATTTTTT
Found at i:11252640 original size:17 final size:20
Alignment explanation
Indices: 11252605--11252642 Score: 55
Period size: 17 Copynumber: 2.0 Consensus size: 20
11252595 ATTGAATATT
11252605 ATAAACAAACAATCTTAATA
1 ATAAACAAACAATCTTAATA
11252625 ATAAA-AAAC-ATC-TAATA
1 ATAAACAAACAATCTTAATA
11252642 A
1 A
11252643 GGTCAAATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.33
18 3 0.17
19 4 0.22
20 5 0.28
ACGTcount: A:0.63, C:0.13, G:0.00, T:0.24
Consensus pattern (20 bp):
ATAAACAAACAATCTTAATA
Found at i:11252818 original size:2 final size:2
Alignment explanation
Indices: 11252797--11252848 Score: 58
Period size: 2 Copynumber: 28.0 Consensus size: 2
11252787 TGAAATTTCA
*
11252797 AT AT A- AT AT A- AT AT -T AT AT AT AT AT AT AT AT AT AT AT GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
11252836 TT AT -T AT AT AT AT
1 AT AT AT AT AT AT AT
11252849 CTAAATTGAA
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
1 4 0.09
2 39 0.91
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (2 bp):
AT
Found at i:11256054 original size:51 final size:51
Alignment explanation
Indices: 11255994--11256095 Score: 186
Period size: 51 Copynumber: 2.0 Consensus size: 51
11255984 TTAGTCTTAA
* *
11255994 TTATATTTTCTTGGCACTTTTCATTTAATTTCTTTGTTTAAAAAGCATCTC
1 TTATATTTTCTTGACACTTTTCATTGAATTTCTTTGTTTAAAAAGCATCTC
11256045 TTATATTTTCTTGACACTTTTCATTGAATTTCTTTGTTTAAAAAGCATCTC
1 TTATATTTTCTTGACACTTTTCATTGAATTTCTTTGTTTAAAAAGCATCTC
11256096 CTGGTCTTTA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.25, C:0.16, G:0.08, T:0.52
Consensus pattern (51 bp):
TTATATTTTCTTGACACTTTTCATTGAATTTCTTTGTTTAAAAAGCATCTC
Found at i:11256563 original size:23 final size:22
Alignment explanation
Indices: 11256520--11256624 Score: 52
Period size: 23 Copynumber: 4.5 Consensus size: 22
11256510 AAATACAAAC
* **
11256520 ATATTTTTATTATAATTTAATA
1 ATATTTTTATTAGAAGATAATA
11256542 ATATTTTGTATTAGAAGATAATTA
1 ATATTTT-TATTAGAAGATAA-TA
* * *
11256566 A-ACCTTTTATTATAA-TTAAATA
1 ATA-TTTTTATTAGAAGAT-AATA
* * *
11256588 ATATTTAATATTAAAAGATAAAA
1 ATATTT-TTATTAGAAGATAATA
11256611 TATATTCTTTATTA
1 -ATATT-TTTATTA
11256625 AATTTAAATA
Statistics
Matches: 62, Mismatches: 12, Indels: 16
0.69 0.13 0.18
Matches are distributed among these distances:
22 13 0.21
23 31 0.50
24 17 0.27
25 1 0.02
ACGTcount: A:0.45, C:0.03, G:0.04, T:0.49
Consensus pattern (22 bp):
ATATTTTTATTAGAAGATAATA
Found at i:11273638 original size:16 final size:17
Alignment explanation
Indices: 11273606--11273638 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
11273596 TGAACTTTAA
*
11273606 AACCAGCACATCTCTAG
1 AACCAGCACAGCTCTAG
11273623 AACCAG-ACAGCTCTAG
1 AACCAGCACAGCTCTAG
11273639 CCCAATCCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.36, C:0.33, G:0.15, T:0.15
Consensus pattern (17 bp):
AACCAGCACAGCTCTAG
Found at i:11292805 original size:27 final size:27
Alignment explanation
Indices: 11292763--11292817 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
11292753 ACCTCATCAT
* *
11292763 TGCCATTCGAAATCTCTAATTTCTCAA
1 TGCCATTCGAAATCTCTAACTCCTCAA
* *
11292790 TGCCATTTGAAGTCTCTAACTCCTCAA
1 TGCCATTCGAAATCTCTAACTCCTCAA
11292817 T
1 T
11292818 TTCTCCCACA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.27, C:0.27, G:0.09, T:0.36
Consensus pattern (27 bp):
TGCCATTCGAAATCTCTAACTCCTCAA
Found at i:11298651 original size:14 final size:14
Alignment explanation
Indices: 11298632--11298661 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
11298622 TATTCCTCCT
11298632 TTTTTTTCTTTCCA
1 TTTTTTTCTTTCCA
*
11298646 TTTTTTTCTTTTCA
1 TTTTTTTCTTTCCA
11298660 TT
1 TT
11298662 ATTCATCCAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTTTTTCTTTCCA
Found at i:11298780 original size:26 final size:26
Alignment explanation
Indices: 11298750--11298864 Score: 112
Period size: 26 Copynumber: 4.5 Consensus size: 26
11298740 TTACAGCATT
*
11298750 CATCCATTTCTAGTGGTAAAATTATC
1 CATCCATTTCTAGTGGAAAAATTATC
*
11298776 CATCCACTTT-TAGTGAAAAAATTATC
1 CATCCA-TTTCTAGTGGAAAAATTATC
11298802 CATCCACTTT-TAGTGGAAAAATTATC
1 CATCCA-TTTCTAGTGGAAAAATTATC
* * * *
11298828 C-T-TATATTCTAATAGTAAAATTATC
1 CATCCAT-TTCTAGTGGAAAAATTATC
*
11298853 CATCCACTTCTA
1 CATCCATTTCTA
11298865 ATAATAAAAT
Statistics
Matches: 75, Mismatches: 9, Indels: 10
0.80 0.10 0.11
Matches are distributed among these distances:
23 1 0.01
24 3 0.04
25 15 0.20
26 52 0.69
27 4 0.05
ACGTcount: A:0.35, C:0.20, G:0.08, T:0.37
Consensus pattern (26 bp):
CATCCATTTCTAGTGGAAAAATTATC
Found at i:11298859 original size:51 final size:51
Alignment explanation
Indices: 11298793--11298927 Score: 157
Period size: 51 Copynumber: 2.7 Consensus size: 51
11298783 TTTTAGTGAA
* *
11298793 AAAATTATCCATCCACTTTTAGTGGAAAAATTATCCTTATATTCTAATAGT
1 AAAATTATCCATCCACTTATAGTGGAAAAATTATCCTTAGATTCTAATAGT
* * * * *
11298844 AAAATTATCCATCCACTTCTAAT-AATAAAATTATTCTTAGATTCTTATAGT
1 AAAATTATCCATCCACTTATAGTGGA-AAAATTATCCTTAGATTCTAATAGT
* * *
11298895 AAAATTAT-TATCCACTTATGGTGGTAAAATTAT
1 AAAATTATCCATCCACTTATAGTGGAAAAATTAT
11298928 TATTAGAATT
Statistics
Matches: 70, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
50 19 0.27
51 51 0.73
ACGTcount: A:0.39, C:0.14, G:0.07, T:0.40
Consensus pattern (51 bp):
AAAATTATCCATCCACTTATAGTGGAAAAATTATCCTTAGATTCTAATAGT
Found at i:11298865 original size:26 final size:26
Alignment explanation
Indices: 11298750--11298911 Score: 107
Period size: 26 Copynumber: 6.3 Consensus size: 26
11298740 TTACAGCATT
* * *
11298750 CATCCATTTCTAGTGGTAAAATTATC
1 CATCCACTTCTAATAGTAAAATTATC
* * *
11298776 CATCCACTTTTAGT-GAAAAAATTATC
1 CATCCACTTCTAATAG-TAAAATTATC
* * * *
11298802 CATCCACTTTTAGTGGAAAAATTATC
1 CATCCACTTCTAATAGTAAAATTATC
* **
11298828 CTTATA-TTCTAATAGTAAAATTATC
1 CATCCACTTCTAATAGTAAAATTATC
* *
11298853 CATCCACTTCTAATAATAAAATTATT
1 CATCCACTTCTAATAGTAAAATTATC
* ** *
11298879 CTTAGA-TTCTTATAGTAAAATTAT-
1 CATCCACTTCTAATAGTAAAATTATC
*
11298903 TATCCACTT
1 CATCCACTT
11298912 ATGGTGGTAA
Statistics
Matches: 108, Mismatches: 24, Indels: 9
0.77 0.17 0.06
Matches are distributed among these distances:
24 2 0.02
25 37 0.34
26 68 0.63
27 1 0.01
ACGTcount: A:0.36, C:0.17, G:0.07, T:0.40
Consensus pattern (26 bp):
CATCCACTTCTAATAGTAAAATTATC
Done.