Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 129486693
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: 129486693
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Warning! 305 characters in sequence are not A, C, G, or T
File 113 of 444
Found at i:28633780 original size:33 final size:33
Alignment explanation
Indices: 28633743--28633806 Score: 128
Period size: 33 Copynumber: 1.9 Consensus size: 33
28633733 TGAGCCTCAG
28633743 GGCACGCTGAGGTATTTTCAATTTCTGTTTTGA
1 GGCACGCTGAGGTATTTTCAATTTCTGTTTTGA
28633776 GGCACGCTGAGGTATTTTCAATTTCTGTTTT
1 GGCACGCTGAGGTATTTTCAATTTCTGTTTT
28633807 TCAATTTCTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.17, C:0.16, G:0.23, T:0.44
Consensus pattern (33 bp):
GGCACGCTGAGGTATTTTCAATTTCTGTTTTGA
Found at i:28633809 original size:14 final size:14
Alignment explanation
Indices: 28633790--28633816 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
28633780 CGCTGAGGTA
28633790 TTTTCAATTTCTGT
1 TTTTCAATTTCTGT
28633804 TTTTCAATTTCTG
1 TTTTCAATTTCTG
28633817 CTCTTCAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.15, G:0.07, T:0.63
Consensus pattern (14 bp):
TTTTCAATTTCTGT
Found at i:28633871 original size:122 final size:122
Alignment explanation
Indices: 28633654--28633891 Score: 424
Period size: 122 Copynumber: 2.0 Consensus size: 122
28633644 TGAGCCTCAG
28633654 GGCACGCTGAGGTAATTTCAATTTATGTTTTTAATTTCTGCTCTTCAAAAAAAATCAACTCATAT
1 GGCACGCTGAGGTAATTTCAATTTATGTTTTTAATTTCTGCTCTTCAAAAAAAATCAACTCATAT
*
28633719 TGTGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTTCTGTTTTGA
66 TGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTTCTGTTTTGA
* *
28633776 GGCACGCTGAGGTATTTTCAATTTCTGTTTTTCAATTTCTGCTCTTC-AAAAAAATCAACTCATA
1 GGCACGCTGAGGTAATTTCAATTTATGTTTTT-AATTTCTGCTCTTCAAAAAAAATCAACTCATA
*
28633840 TTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCGATTTCTG
65 TTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTTCTG
28633892 CTTTCCAATT
Statistics
Matches: 111, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
122 97 0.87
123 14 0.13
ACGTcount: A:0.25, C:0.17, G:0.22, T:0.36
Consensus pattern (122 bp):
GGCACGCTGAGGTAATTTCAATTTATGTTTTTAATTTCTGCTCTTCAAAAAAAATCAACTCATAT
TGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTTCTGTTTTGA
Found at i:28633889 original size:89 final size:89
Alignment explanation
Indices: 28633776--28634004 Score: 395
Period size: 89 Copynumber: 2.6 Consensus size: 89
28633766 TCTGTTTTGA
28633776 GGCACGCTGAGGTATTTTCAATTTCTGTTTTTCAATTTCTGCTCTTCAAAAAAATCAACTCATAT
1 GGCACGCTGAGGTATTTTCAATTTCTGTTTTTCAATTTCTGCTCTTCAAAAAAATCAACTCATAT
28633841 TGCGAGAGGTGAGTTGAGCCTCAG
66 TGCGAGAGGTGAGTTGAGCCTCAG
* * *
28633865 GGCACGCTGAGGTATTTTCGATTTCTGCTTTCCAATTTCTGCTCTTCAAAAAAATCAACTCATAT
1 GGCACGCTGAGGTATTTTCAATTTCTGTTTTTCAATTTCTGCTCTTCAAAAAAATCAACTCATAT
28633930 TGCGAGAGGTGAGTTGAGCCTCAG
66 TGCGAGAGGTGAGTTGAGCCTCAG
* * *
28633954 GGCACGCTGAGGTATTTTCAATTTTTGTTTTTTCAATTTATGCTTTTCAAA
1 GGCACGCTGAGGTATTTTCAATTTCTG-TTTTTCAATTTCTGCTCTTCAAA
28634005 TTCTGCTTTT
Statistics
Matches: 130, Mismatches: 9, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
89 111 0.85
90 19 0.15
ACGTcount: A:0.24, C:0.19, G:0.20, T:0.37
Consensus pattern (89 bp):
GGCACGCTGAGGTATTTTCAATTTCTGTTTTTCAATTTCTGCTCTTCAAAAAAATCAACTCATAT
TGCGAGAGGTGAGTTGAGCCTCAG
Found at i:28633939 original size:211 final size:211
Alignment explanation
Indices: 28633569--28633984 Score: 753
Period size: 211 Copynumber: 2.0 Consensus size: 211
28633559 CCTCAGGGCG
28633569 CGCTGAGGTATTTTCAATTTCTGTTTTTCAATTTCTGCTCTTCAAAAAAATCAACTCATATTGCG
1 CGCTGAGGTATTTTCAATTTCTGTTTTTCAATTTCTGCTCTTCAAAAAAATCAACTCATATTGCG
**
28633634 AGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTAATTTCAATTTATGTTTTTAATTTCTGCTCTT
66 AGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTAATTTCAATTTATGTTTCCAATTTCTGCTCTT
*
28633699 CAAAAAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAA
131 CAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAA
28633764 TTTCTGTTTTGAGGCA
196 TTTCTGTTTTGAGGCA
28633780 CGCTGAGGTATTTTCAATTTCTGTTTTTCAATTTCTGCTCTTCAAAAAAATCAACTCATATTGCG
1 CGCTGAGGTATTTTCAATTTCTGTTTTTCAATTTCTGCTCTTCAAAAAAATCAACTCATATTGCG
* * *
28633845 AGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCGATTTCTGCTTTCCAATTTCTGCTCT
66 AGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTAATTTCAATTTATG-TTTCCAATTTCTGCTCT
28633910 TC-AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCA
130 TCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCA
*
28633974 ATTTTTGTTTT
195 ATTTCTGTTTT
28633985 TTCAATTTAT
Statistics
Matches: 197, Mismatches: 7, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
211 180 0.91
212 17 0.09
ACGTcount: A:0.25, C:0.18, G:0.21, T:0.36
Consensus pattern (211 bp):
CGCTGAGGTATTTTCAATTTCTGTTTTTCAATTTCTGCTCTTCAAAAAAATCAACTCATATTGCG
AGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTAATTTCAATTTATGTTTCCAATTTCTGCTCTT
CAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAA
TTTCTGTTTTGAGGCA
Found at i:28634000 original size:15 final size:15
Alignment explanation
Indices: 28633968--28634015 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
28633958 CGCTGAGGTA
* *
28633968 TTTTCAATTTTTGTT
1 TTTTCAATTTATGCT
28633983 TTTTCAATTTATGC-
1 TTTTCAATTTATGCT
* *
28633997 TTTTCAAATTCTGCT
1 TTTTCAATTTATGCT
28634012 TTTT
1 TTTT
28634016 AAAAAATCAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
14 12 0.43
15 16 0.57
ACGTcount: A:0.17, C:0.12, G:0.06, T:0.65
Consensus pattern (15 bp):
TTTTCAATTTATGCT
Found at i:28634092 original size:103 final size:103
Alignment explanation
Indices: 28633879--28634089 Score: 257
Period size: 103 Copynumber: 2.0 Consensus size: 103
28633869 CGCTGAGGTA
* * *
28633879 TTTTCGATTTCTGCTTTCCAATTTCTGCTCTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGT
1 TTTTCAATTTATGCTTTCCAAATTCTGCTCTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGT
** *
28633944 TGAGCCTCAGGGCACGCTGAGGTATTTTCAATTTTTGTT
66 TGAGCCTCAGGGCACGCTGAGGTATTTTCAAAATCTG-T
* ** *
28633983 TTTTCAATTTATGCTTTTCAAATTCTGCT-TTTTAAAAAATCAACTCATATTGCTAGAGGTGAGT
1 TTTTCAATTTATGCTTTCCAAATTCTGCTCTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGT
*
28634047 TGAGCC-CTGGGTCACATG-TCGAGGTATTTTCAAAATCTGT
66 TGAGCCTCAGGG-CAC--GCT-GAGGTATTTTCAAAATCTGT
28634087 TTT
1 TTT
28634090 CAAATTAAGT
Statistics
Matches: 92, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
102 4 0.04
103 41 0.45
104 30 0.33
105 17 0.18
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.40
Consensus pattern (103 bp):
TTTTCAATTTATGCTTTCCAAATTCTGCTCTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGT
TGAGCCTCAGGGCACGCTGAGGTATTTTCAAAATCTGT
Found at i:28634909 original size:30 final size:30
Alignment explanation
Indices: 28634873--28635007 Score: 157
Period size: 30 Copynumber: 4.5 Consensus size: 30
28634863 TAAATCTTAG
*
28634873 CATTTTCCACCACCAACTCCACTAGCCACT
1 CATTTTCCACCACCAACTCCACTAGCCACA
*
28634903 CCTTTTCCACCACCAACTCCACTAGCCACA
1 CATTTTCCACCACCAACTCCACTAGCCACA
*
28634933 CATTTTCCACCACCAAATCCACTAGCCACA
1 CATTTTCCACCACCAACTCCACTAGCCACA
* ** * *
28634963 C-TTGCTCCATTACCTACTCCACTAACCACA
1 CATT-TTCCACCACCAACTCCACTAGCCACA
*
28634993 C-TTGCTCCACCACCA
1 CATT-TTCCACCACCA
28635008 CTTGTACCTA
Statistics
Matches: 91, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
29 2 0.02
30 89 0.98
ACGTcount: A:0.27, C:0.47, G:0.04, T:0.22
Consensus pattern (30 bp):
CATTTTCCACCACCAACTCCACTAGCCACA
Found at i:28635521 original size:23 final size:23
Alignment explanation
Indices: 28635484--28635613 Score: 65
Period size: 22 Copynumber: 5.5 Consensus size: 23
28635474 CTTTTTTTGT
28635484 TATTAT-TATATTTCTTAATATTA
1 TATTATATATA-TTCTTAATATTA
* *
28635507 TATTATATATATTCTT-TTAATA
1 TATTATATATATTCTTAATATTA
**
28635529 TATTAGGTATATT-TTAA-ATTCTA
1 TATTATATATATTCTTAATA-T-TA
* * *
28635552 TATTACGTATATATATATTTTACTATTT
1 TA-T---TATATATAT-TCTTAATATTA
28635580 TATT-TATATA-TCTTTAATATTA
1 TATTATATATATTC-TTAATATTA
*
28635602 TATTATTTATAT
1 TATTATATATAT
28635614 ATATAAATTT
Statistics
Matches: 79, Mismatches: 14, Indels: 27
0.66 0.12 0.22
Matches are distributed among these distances:
21 4 0.05
22 26 0.33
23 26 0.33
24 6 0.08
27 8 0.10
28 4 0.05
29 4 0.05
30 1 0.01
ACGTcount: A:0.35, C:0.05, G:0.02, T:0.58
Consensus pattern (23 bp):
TATTATATATATTCTTAATATTA
Found at i:28635587 original size:25 final size:26
Alignment explanation
Indices: 28635549--28635618 Score: 72
Period size: 25 Copynumber: 2.8 Consensus size: 26
28635539 ATTTTAAATT
** *
28635549 CTATATTACGTATATATATATT-TTA
1 CTATATTATTTATATATATATTAATA
* *
28635574 CTATTTTATTTATATATCT-TTAATA
1 CTATATTATTTATATATATATTAATA
*
28635599 TTATATTATTTATATATATA
1 CTATATTATTTATATATATA
28635619 AATTTTTTTC
Statistics
Matches: 35, Mismatches: 8, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
24 2 0.06
25 33 0.94
ACGTcount: A:0.36, C:0.06, G:0.01, T:0.57
Consensus pattern (26 bp):
CTATATTATTTATATATATATTAATA
Found at i:28635669 original size:22 final size:24
Alignment explanation
Indices: 28635641--28635699 Score: 68
Period size: 25 Copynumber: 2.5 Consensus size: 24
28635631 ACATGTTATC
28635641 TTATGTATATATCTT-A-ACTATA
1 TTATGTATATATCTTAACACTATA
* *
28635663 TTATGTATGTATTTTTAACACTATA
1 TTATGTATATA-TCTTAACACTATA
*
28635688 TTATGTACATAT
1 TTATGTATATAT
28635700 TTTTAATATT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
22 10 0.33
23 3 0.10
24 2 0.07
25 15 0.50
ACGTcount: A:0.34, C:0.08, G:0.07, T:0.51
Consensus pattern (24 bp):
TTATGTATATATCTTAACACTATA
Found at i:28635689 original size:25 final size:25
Alignment explanation
Indices: 28635657--28635705 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
28635647 ATATATCTTA
**
28635657 ACTATATTATGTATGTATTTTTAAC
1 ACTATATTATGTACATATTTTTAAC
28635682 ACTATATTATGTACATATTTTTAA
1 ACTATATTATGTACATATTTTTAA
28635706 TATTATCACG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.35, C:0.08, G:0.06, T:0.51
Consensus pattern (25 bp):
ACTATATTATGTACATATTTTTAAC
Found at i:28635882 original size:16 final size:15
Alignment explanation
Indices: 28635858--28635905 Score: 69
Period size: 16 Copynumber: 3.1 Consensus size: 15
28635848 TAATTATTAC
*
28635858 TATTCTAATATTTTGA
1 TATTTTAATATTTT-A
28635874 TATTTTAATATTTTA
1 TATTTTAATATTTTA
28635889 TATTTTATATATTTTA
1 TATTTTA-ATATTTTA
28635905 T
1 T
28635906 TATTCACATC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 8 0.27
16 22 0.73
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (15 bp):
TATTTTAATATTTTA
Found at i:28635893 original size:7 final size:8
Alignment explanation
Indices: 28635858--28635909 Score: 61
Period size: 8 Copynumber: 6.5 Consensus size: 8
28635848 TAATTATTAC
*
28635858 TATTCTAA
1 TATTTTAA
*
28635866 TATTTTGA
1 TATTTTAA
28635874 TATTTTAA
1 TATTTTAA
28635882 TATTTT-A
1 TATTTTAA
28635889 TATTTTATA
1 TATTTTA-A
*
28635898 TATTTTAT
1 TATTTTAA
28635906 TATT
1 TATT
28635910 CACATCATTG
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
7 7 0.18
8 23 0.61
9 8 0.21
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (8 bp):
TATTTTAA
Found at i:28637547 original size:14 final size:14
Alignment explanation
Indices: 28637528--28637569 Score: 75
Period size: 14 Copynumber: 3.0 Consensus size: 14
28637518 AACCAAGATA
28637528 TAAAGTTTAAAATT
1 TAAAGTTTAAAATT
*
28637542 TAAAGTTCAAAATT
1 TAAAGTTTAAAATT
28637556 TAAAGTTTAAAATT
1 TAAAGTTTAAAATT
28637570 CAAGATAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.50, C:0.02, G:0.07, T:0.40
Consensus pattern (14 bp):
TAAAGTTTAAAATT
Found at i:28637559 original size:21 final size:21
Alignment explanation
Indices: 28637533--28637572 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
28637523 AGATATAAAG
*
28637533 TTTAAAATTTAAAGTTCAAAA
1 TTTAAAATTTAAAATTCAAAA
*
28637554 TTTAAAGTTTAAAATTCAA
1 TTTAAAATTTAAAATTCAA
28637573 GATAAAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.40
Consensus pattern (21 bp):
TTTAAAATTTAAAATTCAAAA
Found at i:28637581 original size:28 final size:28
Alignment explanation
Indices: 28637528--28637585 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
28637518 AACCAAGATA
* **
28637528 TAAAGTTTAAAATTTAAAGTTCAAAATT
1 TAAAGTTTAAAATTCAAAGTAAAAAATT
28637556 TAAAGTTTAAAATTC-AAGATAAAAAATT
1 TAAAGTTTAAAATTCAAAG-TAAAAAATT
28637584 TA
1 TA
28637586 TTAAAATAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 3 0.12
28 23 0.88
ACGTcount: A:0.53, C:0.03, G:0.07, T:0.36
Consensus pattern (28 bp):
TAAAGTTTAAAATTCAAAGTAAAAAATT
Found at i:28637585 original size:21 final size:21
Alignment explanation
Indices: 28637536--28637585 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
28637526 TATAAAGTTT
* **
28637536 AAAATTTAAAGTTCAAAATTT
1 AAAATTTAAAATTCAAAATAA
* *
28637557 AAAGTTTAAAATTCAAGATAA
1 AAAATTTAAAATTCAAAATAA
28637578 AAAATTTA
1 AAAATTTA
28637586 TTAAAATAAT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.56, C:0.04, G:0.06, T:0.34
Consensus pattern (21 bp):
AAAATTTAAAATTCAAAATAA
Found at i:28642202 original size:57 final size:56
Alignment explanation
Indices: 28642086--28642231 Score: 163
Period size: 57 Copynumber: 2.6 Consensus size: 56
28642076 CATTAGAGAA
* *
28642086 AGGATTTAGCCTGGACTGGTAATCCTGATATAAGCCCTCTTGAGCATATGTACAGAT
1 AGGATTTAGCCTGGACAGGTAATCCTGATATAAG-CCTCTTGAGCATATGTACAAAT
* *
28642143 AGGATTTAGCCCGGACAGGTAATCTTGAT-TAAG-CTCTTGTAAGCATATGTTGA-AAAT
1 AGGATTTAGCCTGGACAGGTAATCCTGATATAAGCCTCTTG--AGCATATG-T-ACAAAT
* * *
28642200 AGGATTTAGCTTGGACAAGTAATCCTGTTATA
1 AGGATTTAGCCTGGACAGGTAATCCTGATATA
28642232 TGATATGTGG
Statistics
Matches: 75, Mismatches: 9, Indels: 9
0.81 0.10 0.10
Matches are distributed among these distances:
54 6 0.08
56 12 0.16
57 54 0.72
58 3 0.04
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.32
Consensus pattern (56 bp):
AGGATTTAGCCTGGACAGGTAATCCTGATATAAGCCTCTTGAGCATATGTACAAAT
Found at i:28644858 original size:19 final size:19
Alignment explanation
Indices: 28644804--28644849 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
28644794 TGTGGGCCCA
28644804 CTTGGGCCAAGTAATAGGC
1 CTTGGGCCAAGTAATAGGC
28644823 CTTGGGCCAAGTAATAGGC
1 CTTGGGCCAAGTAATAGGC
28644842 CTTGGGCC
1 CTTGGGCC
28644850 CATCTATAGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.22, C:0.24, G:0.33, T:0.22
Consensus pattern (19 bp):
CTTGGGCCAAGTAATAGGC
Found at i:28647579 original size:93 final size:93
Alignment explanation
Indices: 28647467--28647638 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
28647457 GCCCATAAGT
* *
28647467 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
28647532 CGAGCTCGGATGCCTAGTTACATCTCTC
66 CGAGCTCGGATGCCTAGTTACATCTCTC
*
28647560 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
28647625 CGAGTTCGGATGCC
66 CGAGCTCGGATGCC
28647639 CAAATATCCT
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCTC
Found at i:28647634 original size:46 final size:46
Alignment explanation
Indices: 28647459--28647634 Score: 214
Period size: 46 Copynumber: 3.8 Consensus size: 46
28647449 TGTAACCCGC
* *
28647459 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
*
28647505 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--ATGC-CTAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGC-A--T
* *** *
28647551 ACATCTCTCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
*
28647598 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
28647635 TGCCCAAATA
Statistics
Matches: 111, Mismatches: 12, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
46 70 0.63
47 32 0.29
49 4 0.04
50 1 0.01
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
Found at i:28650039 original size:30 final size:30
Alignment explanation
Indices: 28649995--28650083 Score: 101
Period size: 30 Copynumber: 3.0 Consensus size: 30
28649985 CAAAGATAAT
28649995 AAGAAAACC-GAATAAAGAAATCCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
* *
28650024 GAGAAACCCAGAATAAAGAAATCC-AGAATA
1 AAGAAAACCAGAATAAAGAAATCCAAG-ATA
* * * *
28650054 AAGAGATCCAGGATAAAGAAACCCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
28650084 CGATACTATG
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
29 9 0.18
30 39 0.78
31 2 0.04
ACGTcount: A:0.57, C:0.16, G:0.17, T:0.10
Consensus pattern (30 bp):
AAGAAAACCAGAATAAAGAAATCCAAGATA
Found at i:28650043 original size:15 final size:15
Alignment explanation
Indices: 28649995--28650074 Score: 92
Period size: 15 Copynumber: 5.4 Consensus size: 15
28649985 CAAAGATAAT
*
28649995 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
28650009 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
* *
28650024 GAGAAACCCAGAATA
1 AAGAAATCCAGAATA
28650039 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
* *
28650054 AAGAGATCCAGGATA
1 AAGAAATCCAGAATA
28650069 AAGAAA
1 AAGAAA
28650075 CCCAAGATAC
Statistics
Matches: 55, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
14 9 0.16
15 45 0.82
16 1 0.02
ACGTcount: A:0.59, C:0.14, G:0.17, T:0.10
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:28650083 original size:15 final size:15
Alignment explanation
Indices: 28650006--28650083 Score: 79
Period size: 15 Copynumber: 5.2 Consensus size: 15
28649996 AGAAAACCGA
28650006 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
* *
28650021 ATAGAGAAA-CCCAG
1 ATAAAGAAATCCAAG
28650035 AATAAAGAAATCC-AG
1 -ATAAAGAAATCCAAG
* *
28650050 AATAAAGAGATCCAGG
1 -ATAAAGAAATCCAAG
*
28650066 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
28650081 ATA
1 ATA
28650084 CGATACTATG
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
14 4 0.08
15 45 0.87
16 3 0.06
ACGTcount: A:0.56, C:0.15, G:0.17, T:0.12
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:28653119 original size:93 final size:93
Alignment explanation
Indices: 28653007--28653178 Score: 299
Period size: 93 Copynumber: 1.8 Consensus size: 93
28652997 CCCCATAAGT
* *
28653007 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
28653072 CGAGCTCGGATGCCTAGTTACATCTCTC
66 CGAGCTCGGATGCCTAGTTACATCTCTC
*
28653100 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
* *
28653165 CGAGTTTGGATGCC
66 CGAGCTCGGATGCC
28653179 CAAATATCCT
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCTC
Found at i:28653170 original size:46 final size:45
Alignment explanation
Indices: 28652999--28653168 Score: 209
Period size: 46 Copynumber: 3.7 Consensus size: 45
28652989 ATGTAACCCC
*
28652999 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTC-GGCATTCGCAT
*
28653045 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG-ATGC-CTAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGCATTCGC-A--T
* *** *
28653091 ACATCTCTCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGG-CATTCGCAT
28653138 CCATAAGTGAACTCGGACTCAACTCAACGAG
1 CCATAAGTGAACTCGGACTCAACTCAACGAG
28653169 TTTGGATGCC
Statistics
Matches: 105, Mismatches: 12, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 2 0.02
46 62 0.59
47 32 0.30
49 4 0.04
50 1 0.01
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.21
Consensus pattern (45 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGCATTCGCAT
Found at i:28653193 original size:46 final size:44
Alignment explanation
Indices: 28653004--28653193 Score: 118
Period size: 46 Copynumber: 4.1 Consensus size: 44
28652994 ACCCCCCATA
* ** ** **
28653004 AGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCAT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCAAATCC-T
* *
28653049 AAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCT
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCA---A-ATC-CT
* * *
28653099 --CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGC--ATCCAT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGCCCAAATCC-T
*
28653142 AAGTGAACTCGGACTCAACTCAACGAGTTTGGATGCCCAAATATCCT
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCC-AA-ATCCT
28653189 AGTGA
1 AGTGA
28653194 CATGTCACTT
Statistics
Matches: 113, Mismatches: 16, Indels: 30
0.71 0.10 0.19
Matches are distributed among these distances:
42 1 0.01
43 4 0.04
44 4 0.04
46 64 0.57
47 28 0.25
48 4 0.04
49 3 0.03
50 4 0.04
51 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.22
Consensus pattern (44 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCAAATCCT
Found at i:28662822 original size:10 final size:10
Alignment explanation
Indices: 28662807--28662831 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
28662797 CATTTAAAAC
28662807 ATGTCTAAAT
1 ATGTCTAAAT
28662817 ATGTCTAAAT
1 ATGTCTAAAT
28662827 ATGTC
1 ATGTC
28662832 CACTCATTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.40
Consensus pattern (10 bp):
ATGTCTAAAT
Found at i:28665228 original size:15 final size:17
Alignment explanation
Indices: 28665203--28665236 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
28665193 GCTAAGGACT
28665203 AAATTAGAAAG-TGATA
1 AAATTAGAAAGATGATA
28665219 AAATTA-AAAGATGATA
1 AAATTAGAAAGATGATA
28665235 AA
1 AA
28665237 TAATTAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.62, C:0.00, G:0.15, T:0.24
Consensus pattern (17 bp):
AAATTAGAAAGATGATA
Found at i:28666388 original size:57 final size:57
Alignment explanation
Indices: 28666288--28666395 Score: 141
Period size: 57 Copynumber: 1.9 Consensus size: 57
28666278 TAGAATGGAC
*
28666288 TGGTAATCCTGATGTAAGCCTTCTTGAGCATATGTATAGATAGGATTTAGCCCGGAT
1 TGGTAATCCTGATGTAAGCCTTCTTGAGCATATGTATAAATAGGATTTAGCCCGGAT
* *
28666345 TGGTAATCTTGAT-TAAG-CTTTTGTGAGCATATGT-TGAAAATAGGATTTAGC
1 TGGTAATCCTGATGTAAGCCTTCT-TGAGCATATGTAT--AAATAGGATTTAGC
28666396 TTGGACAAGT
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
55 5 0.11
56 15 0.33
57 25 0.56
ACGTcount: A:0.28, C:0.12, G:0.24, T:0.36
Consensus pattern (57 bp):
TGGTAATCCTGATGTAAGCCTTCTTGAGCATATGTATAAATAGGATTTAGCCCGGAT
Found at i:28669567 original size:42 final size:42
Alignment explanation
Indices: 28669507--28669619 Score: 147
Period size: 43 Copynumber: 2.7 Consensus size: 42
28669497 TTGAGATTAT
*
28669507 GTGTAAGACCATATCTAGGATATGGCATCAATACGAGA-CTTC
1 GTGTAAGACCATATCTAGGATATGGCATCAATACGAGATC-CC
* * * *
28669549 GTGTAAGACCACAGCTAGGCTATTGGCATCAATATGAGATCCC
1 GTGTAAGACCATATCTAGGATA-TGGCATCAATACGAGATCCC
*
28669592 ATGTAAGACCATATCTAGGATATGGCAT
1 GTGTAAGACCATATCTAGGATATGGCAT
28669620 TGGTACGGTA
Statistics
Matches: 60, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
42 25 0.42
43 34 0.57
44 1 0.02
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.26
Consensus pattern (42 bp):
GTGTAAGACCATATCTAGGATATGGCATCAATACGAGATCCC
Found at i:28681345 original size:40 final size:39
Alignment explanation
Indices: 28681301--28681482 Score: 247
Period size: 39 Copynumber: 4.6 Consensus size: 39
28681291 GTTCAAAACA
* * ** * *
28681301 CCTTCGGGACATAGCCCGGTTATGGTAACCCGCACAAATG
1 CCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATTG
* *
28681341 CCTTCGGGACTTAACCCGGATATCACAACTCGCACAATTG
1 CCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATTG
*
28681381 CCTTCGGGCTTAGCCCGGATATCATAGCTCGCACAATTG
1 CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
* *
28681420 CCTTCGGGCTTAGCCCGGATATCACAATTCGCACAATTG
1 CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
28681459 CCTTCGGGCTTAGCCCGGATATCA
1 CCTTCGGGCTTAGCCCGGATATCA
28681483 CTCGAACATT
Statistics
Matches: 128, Mismatches: 14, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
39 88 0.69
40 40 0.31
ACGTcount: A:0.23, C:0.31, G:0.22, T:0.24
Consensus pattern (39 bp):
CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
Found at i:28681412 original size:39 final size:39
Alignment explanation
Indices: 28681331--28681483 Score: 252
Period size: 39 Copynumber: 3.9 Consensus size: 39
28681321 TATGGTAACC
* *
28681331 CGCACAAATGCCTTCGGGACTTAACCCGGATATCACAACT
1 CGCACAATTGCCTTCGGG-CTTAGCCCGGATATCACAACT
* *
28681371 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAGCT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
*
28681410 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
28681449 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCAC
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCAC
28681484 TCGAACATTC
Statistics
Matches: 106, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
39 89 0.84
40 17 0.16
ACGTcount: A:0.24, C:0.32, G:0.21, T:0.24
Consensus pattern (39 bp):
CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
Found at i:28689414 original size:40 final size:39
Alignment explanation
Indices: 28689370--28689551 Score: 247
Period size: 39 Copynumber: 4.6 Consensus size: 39
28689360 GTTCAAAACA
* * ** * *
28689370 CCTTCGGGACATAGCCCGGTTATGGTAACCCGCACAAATG
1 CCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATTG
* *
28689410 CCTTCGGGACTTAACCCGGATATCACAACTCGCACAATTG
1 CCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATTG
*
28689450 CCTTCGGGCTTAGCCCGGATATCATAGCTCGCACAATTG
1 CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
* *
28689489 CCTTCGGGCTTAGCCCGGATATCACAATTCGCACAATTG
1 CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
28689528 CCTTCGGGCTTAGCCCGGATATCA
1 CCTTCGGGCTTAGCCCGGATATCA
28689552 CTCGAACATT
Statistics
Matches: 128, Mismatches: 14, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
39 88 0.69
40 40 0.31
ACGTcount: A:0.23, C:0.31, G:0.22, T:0.24
Consensus pattern (39 bp):
CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
Found at i:28689481 original size:39 final size:39
Alignment explanation
Indices: 28689400--28689552 Score: 252
Period size: 39 Copynumber: 3.9 Consensus size: 39
28689390 TATGGTAACC
* *
28689400 CGCACAAATGCCTTCGGGACTTAACCCGGATATCACAACT
1 CGCACAATTGCCTTCGGG-CTTAGCCCGGATATCACAACT
* *
28689440 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAGCT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
*
28689479 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
28689518 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCAC
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCAC
28689553 TCGAACATTC
Statistics
Matches: 106, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
39 89 0.84
40 17 0.16
ACGTcount: A:0.24, C:0.32, G:0.21, T:0.24
Consensus pattern (39 bp):
CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
Found at i:28696828 original size:2 final size:2
Alignment explanation
Indices: 28696821--28696851 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
28696811 TTGTACATGT
28696821 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
28696852 TTATTAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:28699228 original size:18 final size:18
Alignment explanation
Indices: 28699201--28699239 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
28699191 TCAGTTGTAA
*
28699201 TTTAGATTTTCTTTTAGT
1 TTTAGATTTTCTTTCAGT
*
28699219 TTTAGTTTTTCTTTCAGT
1 TTTAGATTTTCTTTCAGT
28699237 TTT
1 TTT
28699240 CTATTTTGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.13, C:0.08, G:0.10, T:0.69
Consensus pattern (18 bp):
TTTAGATTTTCTTTCAGT
Found at i:28699246 original size:18 final size:19
Alignment explanation
Indices: 28699206--28699246 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
28699196 TGTAATTTAG
* *
28699206 ATTTTCTTTTAGTTTTAGT
1 ATTTTCTTTCAGTTTTACT
28699225 -TTTTCTTTCAGTTTT-CT
1 ATTTTCTTTCAGTTTTACT
28699242 ATTTT
1 ATTTT
28699247 GTTCTTCACG
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
17 1 0.05
18 18 0.95
ACGTcount: A:0.12, C:0.10, G:0.07, T:0.71
Consensus pattern (19 bp):
ATTTTCTTTCAGTTTTACT
Found at i:28706574 original size:9 final size:9
Alignment explanation
Indices: 28706560--28706589 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
28706550 GGAATTTAGA
28706560 AAAATAATT
1 AAAATAATT
28706569 AAAATAATT
1 AAAATAATT
28706578 AAAATAA-T
1 AAAATAATT
28706586 AAAA
1 AAAA
28706590 GATATTAACC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 5 0.24
9 16 0.76
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (9 bp):
AAAATAATT
Found at i:28713383 original size:24 final size:24
Alignment explanation
Indices: 28713355--28713427 Score: 119
Period size: 24 Copynumber: 3.0 Consensus size: 24
28713345 GGGCCTTGTA
28713355 GGCCCAAAATTAGGACACTACAAT
1 GGCCCAAAATTAGGACACTACAAT
*
28713379 GGCCCAAACTTAGGACACTACAAT
1 GGCCCAAAATTAGGACACTACAAT
* *
28713403 GGCTCAAAATTGGGACACTACAAT
1 GGCCCAAAATTAGGACACTACAAT
28713427 G
1 G
28713428 TTAGTGAGTT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.18
Consensus pattern (24 bp):
GGCCCAAAATTAGGACACTACAAT
Found at i:28732281 original size:26 final size:25
Alignment explanation
Indices: 28732252--28732303 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 25
28732242 ACTTTTGTTA
28732252 AGGGACT-TTTGATGAAAATGTGAAAT
1 AGGGACTATTTG-T-AAAATGTGAAAT
28732278 AGGGACTAATTTGTAAAATGTGAAAT
1 AGGGACT-ATTTGTAAAATGTGAAAT
28732304 TTATGAGTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
26 19 0.79
27 1 0.04
28 4 0.17
ACGTcount: A:0.40, C:0.04, G:0.25, T:0.31
Consensus pattern (25 bp):
AGGGACTATTTGTAAAATGTGAAAT
Found at i:28732830 original size:42 final size:43
Alignment explanation
Indices: 28732783--28732905 Score: 135
Period size: 42 Copynumber: 2.9 Consensus size: 43
28732773 GTACTACCGA
* *
28732783 GATTTCGTATAAGACCATATCTGGGATATGGCATCGATATG-T
1 GATTTCATATAAGACCATATCAGGGATATGGCATCGATATGAT
* * * *
28732825 GATTTCATATAAGACCATGTCAGGAACATGGCGTCGATATGAT
1 GATTTCATATAAGACCATATCAGGGATATGGCATCGATATGAT
* * *
28732868 G-TTTCATGTAAGACCATATCCGAGG-TATGGCATTGATA
1 GATTTCATATAAGACCATATCAG-GGATATGGCATCGATA
28732906 CAGTACTAAG
Statistics
Matches: 66, Mismatches: 13, Indels: 4
0.80 0.16 0.05
Matches are distributed among these distances:
42 63 0.95
43 3 0.05
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.31
Consensus pattern (43 bp):
GATTTCATATAAGACCATATCAGGGATATGGCATCGATATGAT
Found at i:28749140 original size:32 final size:32
Alignment explanation
Indices: 28749104--28749175 Score: 112
Period size: 32 Copynumber: 2.3 Consensus size: 32
28749094 CCACACGGGT
*
28749104 AGGCACATGGGCGTGTGTCTAGGCCGTATGTG
1 AGGCACACGGGCGTGTGTCTAGGCCGTATGTG
*
28749136 AGGCACACGGGCGTGTGTCTAGGCCGTGTGTG
1 AGGCACACGGGCGTGTGTCTAGGCCGTATGTG
28749168 A--CACACGG
1 AGGCACACGG
28749176 TTTACCACAT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
30 7 0.18
32 31 0.82
ACGTcount: A:0.17, C:0.22, G:0.40, T:0.21
Consensus pattern (32 bp):
AGGCACACGGGCGTGTGTCTAGGCCGTATGTG
Found at i:28750887 original size:35 final size:35
Alignment explanation
Indices: 28750848--28750917 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
28750838 ACAGAACTAG
28750848 AGGGCTTCGAATCTCTCTTATTCTTACCTCTCTTA
1 AGGGCTTCGAATCTCTCTTATTCTTACCTCTCTTA
28750883 AGGGCTTCGAATCTCTCTTATTCTTACCTCTCTTA
1 AGGGCTTCGAATCTCTCTTATTCTTACCTCTCTTA
28750918 CGGTCCCTGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.17, C:0.29, G:0.11, T:0.43
Consensus pattern (35 bp):
AGGGCTTCGAATCTCTCTTATTCTTACCTCTCTTA
Found at i:28755800 original size:50 final size:48
Alignment explanation
Indices: 28755554--28755875 Score: 240
Period size: 46 Copynumber: 6.8 Consensus size: 48
28755544 TCACTGGTGT
* * * * *
28755554 GAGCTAGTATAAGA-CATGTCTGGGACAT-GCATCGGC-CAAATTATGA
1 GAGCCAGTGTAAGACCATGTCTAGGACATGGCATCGGCAC-GATGATGA
** *
28755600 GATTCAGTGTAAGACCATGTCTAGGACATGGCATCGGCATTGA-GATGA
1 GAGCCAGTGTAAGACCATGTCTAGGACATGGCATCGGCA-CGATGATGA
* * * * * * *
28755648 GTGCTAGTGTAAGA-CATGTCTGGGATAT-GCATCAGCCTCGA-GACGTA
1 GAGCCAGTGTAAGACCATGTCTAGGACATGGCATC-GGCACGATGATG-A
*
28755695 -AGCCAGTGTAAGA-TATGTCTAGGACAT-GCATCGGCTACGA-GAT--
1 GAGCCAGTGTAAGACCATGTCTAGGACATGGCATCGGC-ACGATGATGA
* * * *
28755738 GTGTCAGTGTAAGACCATGTTTGGGACATGGCATCGGCACGAATAGGA-GA
1 GAGCCAGTGTAAGACCATGTCTAGGACATGGCATCGGCACG-AT--GATGA
* * *
28755788 GAGCTAGTGTAAGACCATGTCTAGCACATGGCATCGGCCTCGATGATGA
1 GAGCCAGTGTAAGACCATGTCTAGGACATGGCATCGG-CACGATGATGA
* *
28755837 TAGCCAGTGTAAGACCATGTCCAGGACATGGCATCGGCA
1 GAGCCAGTGTAAGACCATGTCTAGGACATGGCATCGGCA
28755876 ACTTGCCCCA
Statistics
Matches: 215, Mismatches: 43, Indels: 34
0.74 0.15 0.12
Matches are distributed among these distances:
44 11 0.05
45 16 0.07
46 61 0.28
47 28 0.13
48 25 0.12
49 38 0.18
50 33 0.15
51 3 0.01
ACGTcount: A:0.29, C:0.19, G:0.29, T:0.23
Consensus pattern (48 bp):
GAGCCAGTGTAAGACCATGTCTAGGACATGGCATCGGCACGATGATGA
Found at i:28756940 original size:20 final size:21
Alignment explanation
Indices: 28756899--28756940 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
28756889 TAGAAATTAA
28756899 TTCCACATGGGCGTGTTGCCC
1 TTCCACATGGGCGTGTTGCCC
28756920 TTCCACATGGGCGTG-TGCCC
1 TTCCACATGGGCGTGTTGCCC
28756940 T
1 T
28756941 GTTTTAAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.10, C:0.33, G:0.29, T:0.29
Consensus pattern (21 bp):
TTCCACATGGGCGTGTTGCCC
Found at i:28764803 original size:7 final size:7
Alignment explanation
Indices: 28764791--28764829 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
28764781 TATCTTGAAT
28764791 TTTAAAC
1 TTTAAAC
*
28764798 TTTAAAT
1 TTTAAAC
*
28764805 TTTGAAC
1 TTTAAAC
*
28764812 TTTAAAT
1 TTTAAAC
28764819 TTTAAAC
1 TTTAAAC
28764826 TTTA
1 TTTA
28764830 TATCTTGGTT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.38, C:0.08, G:0.03, T:0.51
Consensus pattern (7 bp):
TTTAAAC
Found at i:28764805 original size:14 final size:14
Alignment explanation
Indices: 28764788--28764829 Score: 75
Period size: 14 Copynumber: 3.0 Consensus size: 14
28764778 TTTTATCTTG
28764788 AATTTTAAACTTTA
1 AATTTTAAACTTTA
*
28764802 AATTTTGAACTTTA
1 AATTTTAAACTTTA
28764816 AATTTTAAACTTTA
1 AATTTTAAACTTTA
28764830 TATCTTGGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.40, C:0.07, G:0.02, T:0.50
Consensus pattern (14 bp):
AATTTTAAACTTTA
Found at i:28764809 original size:21 final size:21
Alignment explanation
Indices: 28764785--28764824 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
28764775 ATTTTTTATC
*
28764785 TTGAATTTTAAACTTTAAATT
1 TTGAACTTTAAACTTTAAATT
*
28764806 TTGAACTTTAAATTTTAAA
1 TTGAACTTTAAACTTTAAA
28764825 CTTTATATCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.50
Consensus pattern (21 bp):
TTGAACTTTAAACTTTAAATT
Found at i:28766480 original size:16 final size:15
Alignment explanation
Indices: 28766459--28766506 Score: 69
Period size: 16 Copynumber: 3.1 Consensus size: 15
28766449 GATGTGAATA
28766459 ATAAAATATATAAAAT
1 ATAAAATAT-TAAAAT
28766475 ATAAAATATTAAAAT
1 ATAAAATATTAAAAT
*
28766490 ATCAAAATATTAGAAT
1 AT-AAAATATTAAAAT
28766506 A
1 A
28766507 GTAATAATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 8 0.27
16 22 0.73
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (15 bp):
ATAAAATATTAAAAT
Found at i:28766489 original size:8 final size:8
Alignment explanation
Indices: 28766455--28766506 Score: 61
Period size: 8 Copynumber: 6.5 Consensus size: 8
28766445 CAATGATGTG
*
28766455 AATAATAA
1 AATATTAA
28766463 AATATATAA
1 AATAT-TAA
28766472 AATA-TAA
1 AATATTAA
28766479 AATATTAA
1 AATATTAA
*
28766487 AATATCAA
1 AATATTAA
*
28766495 AATATTAG
1 AATATTAA
28766503 AATA
1 AATA
28766507 GTAATAATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
7 7 0.18
8 24 0.63
9 7 0.18
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (8 bp):
AATATTAA
Found at i:28766724 original size:22 final size:24
Alignment explanation
Indices: 28766661--28766725 Score: 80
Period size: 25 Copynumber: 2.8 Consensus size: 24
28766651 CGTGATAATA
*
28766661 TTAAAAATATGTACATAATATAGTG
1 TTAAAAATATATACATAATATAG-G
*
28766686 TTAAAAATACATACATAATATA-G
1 TTAAAAATATATACATAATATAGG
*
28766709 TT-AAGATATATACATAA
1 TTAAAAATATATACATAA
28766726 GATAACATGT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
22 13 0.36
23 3 0.08
25 20 0.56
ACGTcount: A:0.52, C:0.06, G:0.08, T:0.34
Consensus pattern (24 bp):
TTAAAAATATATACATAATATAGG
Found at i:28766779 original size:25 final size:25
Alignment explanation
Indices: 28766751--28766884 Score: 86
Period size: 25 Copynumber: 5.6 Consensus size: 25
28766741 AAAAATTTAT
28766751 ATATATAAATAATATAATATTAAAG
1 ATATATAAATAATATAATATTAAAG
* * * *
28766776 ATATATAAATAAAATAGTATAAAAT
1 ATATATAAATAATATAATATTAAAG
* *
28766801 ATATATATACGTAATATAGA-ATTTAA-
1 ATATATA-A-ATAATATA-ATATTAAAG
** *
28766827 A-ATATACCTAATAT-AT-TAAAAG
1 ATATATAAATAATATAATATTAAAG
*
28766849 A-ATATATATAATATAATATT-AAG
1 ATATATAAATAATATAATATTAAAG
*
28766872 AAATAT-AATAATA
1 ATATATAAATAATA
28766885 ACAAAAAAGA
Statistics
Matches: 84, Mismatches: 17, Indels: 18
0.71 0.14 0.15
Matches are distributed among these distances:
21 4 0.05
22 12 0.14
23 18 0.21
24 5 0.06
25 33 0.39
26 2 0.02
27 10 0.12
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.35
Consensus pattern (25 bp):
ATATATAAATAATATAATATTAAAG
Found at i:28767443 original size:30 final size:30
Alignment explanation
Indices: 28767365--28767499 Score: 157
Period size: 30 Copynumber: 4.5 Consensus size: 30
28767355 TAGGTACAAG
* *
28767365 TGGTGGTGGAGCAA-GTGTGGTTAGTGGAGT
1 TGGTGGTGGA-AAATGTGTGGCTAGTGGAGT
* ** * *
28767395 AGGTAATGGAGCAA-GTGTGGCTAGTGGATT
1 TGGTGGTGGA-AAATGTGTGGCTAGTGGAGT
28767425 TGGTGGTGGAAAATGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAATGTGTGGCTAGTGGAGT
* *
28767455 TGGTGGTGGAAAAGGAGTGGCTAGTGGAGT
1 TGGTGGTGGAAAATGTGTGGCTAGTGGAGT
28767485 TGGTGGTGGAAAATG
1 TGGTGGTGGAAAATG
28767500 CTAAGATTTA
Statistics
Matches: 91, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
29 2 0.02
30 89 0.98
ACGTcount: A:0.22, C:0.04, G:0.47, T:0.27
Consensus pattern (30 bp):
TGGTGGTGGAAAATGTGTGGCTAGTGGAGT
Found at i:28768393 original size:15 final size:15
Alignment explanation
Indices: 28768360--28768407 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
28768350 TTGATTTTTT
* *
28768360 AAAAAGCAGAATTTG
1 AAAAAGCAAAAATTG
*
28768375 -AAAAGCATAAATTG
1 AAAAAGCAAAAATTG
*
28768389 AAAAAACAAAAATTG
1 AAAAAGCAAAAATTG
28768404 AAAA
1 AAAA
28768408 TACCTCAGCG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
14 12 0.43
15 16 0.57
ACGTcount: A:0.65, C:0.06, G:0.12, T:0.17
Consensus pattern (15 bp):
AAAAAGCAAAAATTG
Found at i:28768405 original size:105 final size:104
Alignment explanation
Indices: 28768296--28768496 Score: 273
Period size: 103 Copynumber: 1.9 Consensus size: 104
28768286 AAAACAGATT
28768296 TTGAAAATACCTC-GACATGTGACCCAG-GGCTCAACTCACCTCTAGCAATATGAGTTGA-TTTT
1 TTGAAAATACCTCAG-C--GTG-CCCAGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTT
* * *
28768358 TTAAAAAGCAGAATTTGAAAAGCATAAATTGAAAAAACAAAAA
62 TTAAAAAGCAGAAATTGAAAAGCAGAAATCGAAAAAACAAAAA
* * *
28768401 TTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGA
1 TTGAAAATACCTCAGCGTGCCCAGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTTTTAA
* *
28768466 AGAGCAGAAATTGGAAAGCAGAAATCGAAAA
66 AAAGCAGAAATTGAAAAGCAGAAATCGAAAA
28768497 TACCTCAGCG
Statistics
Matches: 85, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
102 4 0.05
103 33 0.39
104 33 0.39
105 14 0.16
106 1 0.01
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.25
Consensus pattern (104 bp):
TTGAAAATACCTCAGCGTGCCCAGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTTTTAA
AAAGCAGAAATTGAAAAGCAGAAATCGAAAAAACAAAAA
Found at i:28768523 original size:89 final size:89
Alignment explanation
Indices: 28768371--28768599 Score: 395
Period size: 89 Copynumber: 2.6 Consensus size: 89
28768361 AAAAGCAGAA
* * *
28768371 TTTGAAAAGCATAAATTGAAAAAACAAAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTC
1 TTTGAAGAGCAGAAATTG-AAAAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTC
28768436 ACCTCTCGCAATATGAGTTGATTTT
65 ACCTCTCGCAATATGAGTTGATTTT
* * *
28768461 TTTGAAGAGCAGAAATTGGAAAGCAGAAATCGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCA
1 TTTGAAGAGCAGAAATTGAAAAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCA
28768526 CCTCTCGCAATATGAGTTGATTTT
66 CCTCTCGCAATATGAGTTGATTTT
28768550 TTTGAAGAGCAGAAATTGAAAAACAGAAATTGAAAATACCTCAGCGTGCC
1 TTTGAAGAGCAGAAATTGAAAAACAGAAATTGAAAATACCTCAGCGTGCC
28768600 TCAAAACAGA
Statistics
Matches: 130, Mismatches: 9, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
89 114 0.88
90 16 0.12
ACGTcount: A:0.37, C:0.20, G:0.19, T:0.24
Consensus pattern (89 bp):
TTTGAAGAGCAGAAATTGAAAAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCA
CCTCTCGCAATATGAGTTGATTTT
Found at i:28768576 original size:14 final size:14
Alignment explanation
Indices: 28768559--28768585 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
28768549 TTTTGAAGAG
28768559 CAGAAATTGAAAAA
1 CAGAAATTGAAAAA
28768573 CAGAAATTGAAAA
1 CAGAAATTGAAAA
28768586 TACCTCAGCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.63, C:0.07, G:0.15, T:0.15
Consensus pattern (14 bp):
CAGAAATTGAAAAA
Found at i:28768611 original size:33 final size:33
Alignment explanation
Indices: 28768569--28768632 Score: 128
Period size: 33 Copynumber: 1.9 Consensus size: 33
28768559 CAGAAATTGA
28768569 AAAACAGAAATTGAAAATACCTCAGCGTGCCTC
1 AAAACAGAAATTGAAAATACCTCAGCGTGCCTC
28768602 AAAACAGAAATTGAAAATACCTCAGCGTGCC
1 AAAACAGAAATTGAAAATACCTCAGCGTGCC
28768633 CTGAGGCTCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.44, C:0.23, G:0.16, T:0.17
Consensus pattern (33 bp):
AAAACAGAAATTGAAAATACCTCAGCGTGCCTC
Found at i:28768764 original size:212 final size:211
Alignment explanation
Indices: 28768391--28768807 Score: 753
Period size: 212 Copynumber: 2.0 Consensus size: 211
28768381 ATAAATTGAA
*
28768391 AAAACAAAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG
1 AAAACAAAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCACAATATGAGTTG
** *
28768456 ATTTTTTTGAAGAGCAGAAATTGGAAAGCAGAAATCGAAAATACCTCAGCGTGCCCTGAGGCTCA
66 ATTTTTTTGAAGAGCAGAAATTAAAAAACAGAAATCGAAAATACCTCAGCGTGCCCTGAGGCTCA
28768521 ACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAGAGCAGAAATTGAAAAACAGAAATTGAAAA
131 ACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAGAGCAGAAATTGAAAAACAGAAATTGAAAA
28768586 TACCTCAGCGTGCCTC
196 TACCTCAGCGTGCCTC
*
28768602 AAAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCACAATATGAGTTG
1 AAAACAAAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCACAATATGAGTTG
* * *
28768667 ATTTTTTTTGAAGAGCAGAAATTAAAAAACATAAATTGAAATTACCTCAGCGTGCCCTGAGGCTC
66 A-TTTTTTTGAAGAGCAGAAATTAAAAAACAGAAATCGAAAATACCTCAGCGTGCCCTGAGGCTC
28768732 AACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAGAGCAGAAATTGAAAAACAGAAATTGAAA
130 AACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAGAGCAGAAATTGAAAAACAGAAATTGAAA
28768797 ATACCTCAGCG
195 ATACCTCAGCG
28768808 CGCCCTGAGG
Statistics
Matches: 197, Mismatches: 8, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
211 64 0.32
212 133 0.68
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.25
Consensus pattern (211 bp):
AAAACAAAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCACAATATGAGTTG
ATTTTTTTGAAGAGCAGAAATTAAAAAACAGAAATCGAAAATACCTCAGCGTGCCCTGAGGCTCA
ACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAGAGCAGAAATTGAAAAACAGAAATTGAAAA
TACCTCAGCGTGCCTC
Found at i:28768788 original size:14 final size:14
Alignment explanation
Indices: 28768771--28768797 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
28768761 TTTTGAAGAG
28768771 CAGAAATTGAAAAA
1 CAGAAATTGAAAAA
28768785 CAGAAATTGAAAA
1 CAGAAATTGAAAA
28768798 TACCTCAGCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.63, C:0.07, G:0.15, T:0.15
Consensus pattern (14 bp):
CAGAAATTGAAAAA
Found at i:28768825 original size:89 final size:89
Alignment explanation
Indices: 28768602--28769025 Score: 749
Period size: 89 Copynumber: 4.8 Consensus size: 89
28768592 AGCGTGCCTC
*
28768602 AAAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCACAATATGAGTTG
1 AAAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG
*
28768667 ATTTTTTTTGAAGAGCAGAAATTAA
66 A-TTTTTTTGAAGAGCAGAAATTGA
* *
28768692 AAAACATAAATTGAAATTACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG
1 AAAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG
28768757 ATTTTTTTGAAGAGCAGAAATTGA
66 ATTTTTTTGAAGAGCAGAAATTGA
* *
28768781 AAAACAGAAATTGAAAATACCTCAGCGCGCCCTGAGGCTTAACTCACCTCTCGCAATATGAGTTG
1 AAAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG
28768846 ATTTTTTTGAAGAGCAGAAATTGA
66 ATTTTTTTGAAGAGCAGAAATTGA
*
28768870 AAAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGTAATATGAGTTG
1 AAAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG
*
28768935 ATTTTTTTGAAGAGCAAAAATTGA
66 ATTTTTTTGAAGAGCAGAAATTGA
* *
28768959 AAAACATAAATTGAAATTACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG
1 AAAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG
28769024 AT
66 AT
28769026 CTTTGGAACA
Statistics
Matches: 319, Mismatches: 15, Indels: 1
0.95 0.04 0.00
Matches are distributed among these distances:
89 256 0.80
90 63 0.20
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.27
Consensus pattern (89 bp):
AAAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG
ATTTTTTTGAAGAGCAGAAATTGA
Found at i:28768877 original size:14 final size:14
Alignment explanation
Indices: 28768860--28768886 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
28768850 TTTTGAAGAG
28768860 CAGAAATTGAAAAA
1 CAGAAATTGAAAAA
28768874 CAGAAATTGAAAA
1 CAGAAATTGAAAA
28768887 TACCTCAGCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.63, C:0.07, G:0.15, T:0.15
Consensus pattern (14 bp):
CAGAAATTGAAAAA
Found at i:28782510 original size:13 final size:13
Alignment explanation
Indices: 28782492--28782516 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28782482 AAATTGGAAA
28782492 GATGATAAATAAG
1 GATGATAAATAAG
28782505 GATGATAAATAA
1 GATGATAAATAA
28782517 TAAAATAAAG
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:0.00, G:0.20, T:0.24
Consensus pattern (13 bp):
GATGATAAATAAG
Found at i:28783675 original size:57 final size:56
Alignment explanation
Indices: 28783559--28783704 Score: 163
Period size: 57 Copynumber: 2.6 Consensus size: 56
28783549 CATTAGAGAA
* *
28783559 AGGATTTAGCCTGGACTGGTAATCCTGATATAAGCCCTCTTGAGCATATGTACAGAT
1 AGGATTTAGCCTGGACAGGTAATCCTGATATAAG-CCTCTTGAGCATATGTACAAAT
* *
28783616 AGGATTTAGCCCGGACAGGTAATCTTGAT-TAAG-CTCTTGTAAGCATATGTTGA-AAAT
1 AGGATTTAGCCTGGACAGGTAATCCTGATATAAGCCTCTTG--AGCATATG-T-ACAAAT
* * *
28783673 AGGATTTAGCTTGGACAAGTAATCCTGTTATA
1 AGGATTTAGCCTGGACAGGTAATCCTGATATA
28783705 TGATNACATG
Statistics
Matches: 75, Mismatches: 9, Indels: 9
0.81 0.10 0.10
Matches are distributed among these distances:
54 6 0.08
56 12 0.16
57 54 0.72
58 3 0.04
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.32
Consensus pattern (56 bp):
AGGATTTAGCCTGGACAGGTAATCCTGATATAAGCCTCTTGAGCATATGTACAAAT
Found at i:28785191 original size:40 final size:39
Alignment explanation
Indices: 28785147--28785328 Score: 247
Period size: 39 Copynumber: 4.6 Consensus size: 39
28785137 GTTCAAAACA
* * ** * *
28785147 CCTTCGGGACATAGCCCGGTTATGGTAACCCGCACAAATG
1 CCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATTG
* *
28785187 CCTTCGGGACTTAACCCGGATATCACAACTCGCACAATTG
1 CCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATTG
*
28785227 CCTTCGGGCTTAGCCCGGATATCATAGCTCGCACAATTG
1 CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
* *
28785266 CCTTCGGGCTTAGCCCGGATATCACAATTCGCACAATTG
1 CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
28785305 CCTTCGGGCTTAGCCCGGATATCA
1 CCTTCGGGCTTAGCCCGGATATCA
28785329 CTCGAACATT
Statistics
Matches: 128, Mismatches: 14, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
39 88 0.69
40 40 0.31
ACGTcount: A:0.23, C:0.31, G:0.22, T:0.24
Consensus pattern (39 bp):
CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
Found at i:28785258 original size:39 final size:39
Alignment explanation
Indices: 28785177--28785329 Score: 252
Period size: 39 Copynumber: 3.9 Consensus size: 39
28785167 TATGGTAACC
* *
28785177 CGCACAAATGCCTTCGGGACTTAACCCGGATATCACAACT
1 CGCACAATTGCCTTCGGG-CTTAGCCCGGATATCACAACT
* *
28785217 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAGCT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
*
28785256 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
28785295 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCAC
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCAC
28785330 TCGAACATTC
Statistics
Matches: 106, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
39 89 0.84
40 17 0.16
ACGTcount: A:0.24, C:0.32, G:0.21, T:0.24
Consensus pattern (39 bp):
CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
Found at i:28793278 original size:40 final size:39
Alignment explanation
Indices: 28793234--28793414 Score: 238
Period size: 39 Copynumber: 4.6 Consensus size: 39
28793224 GTTCAAAACA
* * ** * *
28793234 CCTTCGGGACATAGCCCGGTTATGGTAACCCGCACAAATG
1 CCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATTG
* *
28793274 CCTTCGGGACTTAACCCGGATATCACAACTCGCACAATTG
1 CCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATTG
*
28793314 CCTTCGGGCTTAGCCCGGATATCATAGCTCGCACAATTG
1 CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
* *
28793353 CCTTCGGGCTTAGCCCGGATATCACAA-TTGCACAATTG
1 CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
28793391 CCTTCGGGCTTAGCCCGGATATCA
1 CCTTCGGGCTTAGCCCGGATATCA
28793415 CTCGAACATT
Statistics
Matches: 127, Mismatches: 14, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
38 34 0.27
39 53 0.42
40 40 0.31
ACGTcount: A:0.23, C:0.31, G:0.22, T:0.24
Consensus pattern (39 bp):
CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
Found at i:28793406 original size:77 final size:79
Alignment explanation
Indices: 28793264--28793414 Score: 261
Period size: 77 Copynumber: 1.9 Consensus size: 79
28793254 TATGGTAACC
28793264 CGCACAAATGCCTTCGGGACTTAACCCGGATATCACAACTCGCACAATTGCCTTCGGGCTTAGCC
1 CGCACAAATGCCTTCGGGACTTAACCCGGATATCACAACTCGCACAATTGCCTTCGGGCTTAGCC
28793329 CGGATATCATAGCT
66 CGGATATCATAGCT
* * *
28793343 CGCACAATTGCCTTCGGG-CTTAGCCCGGATATCACAA-TTGCACAATTGCCTTCGGGCTTAGCC
1 CGCACAAATGCCTTCGGGACTTAACCCGGATATCACAACTCGCACAATTGCCTTCGGGCTTAGCC
28793406 CGGATATCA
66 CGGATATCA
28793415 CTCGAACATT
Statistics
Matches: 69, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
77 34 0.49
78 18 0.26
79 17 0.25
ACGTcount: A:0.24, C:0.31, G:0.21, T:0.24
Consensus pattern (79 bp):
CGCACAAATGCCTTCGGGACTTAACCCGGATATCACAACTCGCACAATTGCCTTCGGGCTTAGCC
CGGATATCATAGCT
Found at i:28795391 original size:31 final size:31
Alignment explanation
Indices: 28795356--28795419 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
28795346 GACAAGAGAA
28795356 CTTACCCAATTAGGCCTTGAAAGTTTCCCCT
1 CTTACCCAATTAGGCCTTGAAAGTTTCCCCT
*
28795387 CTTACCCAATTAGGCCTTTAAAGTTTCCCCT
1 CTTACCCAATTAGGCCTTGAAAGTTTCCCCT
28795418 CT
1 CT
28795420 CTGTCTTAGG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.22, C:0.33, G:0.11, T:0.34
Consensus pattern (31 bp):
CTTACCCAATTAGGCCTTGAAAGTTTCCCCT
Found at i:28805935 original size:11 final size:12
Alignment explanation
Indices: 28805913--28805946 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
28805903 TATATATTTT
*
28805913 AAATTTATATAA
1 AAATTAATATAA
28805925 AAA-TAATATAA
1 AAATTAATATAA
28805936 AAATTAATATA
1 AAATTAATATA
28805947 GGCAGCCGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (12 bp):
AAATTAATATAA
Found at i:28806108 original size:28 final size:28
Alignment explanation
Indices: 28806068--28806123 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
28806058 ATTTTAGGCC
28806068 CAGCCCATGCTCACCTTTACACTCACCT
1 CAGCCCATGCTCACCTTTACACTCACCT
28806096 CAGCCCATGCTCACCTTTACACTCACCT
1 CAGCCCATGCTCACCTTTACACTCACCT
28806124 AACATGCCAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.21, C:0.46, G:0.07, T:0.25
Consensus pattern (28 bp):
CAGCCCATGCTCACCTTTACACTCACCT
Found at i:28807635 original size:6 final size:6
Alignment explanation
Indices: 28807624--28807649 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
28807614 AATAAAGTAG
28807624 AAAAAT AAAAAT AAAAAT AAAAAT AA
1 AAAAAT AAAAAT AAAAAT AAAAAT AA
28807650 GAGCATAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:28808213 original size:21 final size:21
Alignment explanation
Indices: 28808170--28808213 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
28808160 TGTCATCCAC
* * *
28808170 CTCTTCTTCCTCATTTTCATT
1 CTCTTCCTCATCATTCTCATT
*
28808191 CTCTTCCTCATCATTCTCGTT
1 CTCTTCCTCATCATTCTCATT
28808212 CT
1 CT
28808214 TCTCAAGGTG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.09, C:0.36, G:0.02, T:0.52
Consensus pattern (21 bp):
CTCTTCCTCATCATTCTCATT
Found at i:28812050 original size:25 final size:25
Alignment explanation
Indices: 28812013--28812181 Score: 99
Period size: 25 Copynumber: 6.8 Consensus size: 25
28812003 TTAAGTTGAG
* *
28812013 AATTCTCTAGAAAGCCTTTATGGAA
1 AATTCTTTGGAAAGCCTTTATGGAA
* * *
28812038 AATTCTTTGGAAATCCTTTGTGGCA
1 AATTCTTTGGAAAGCCTTTATGGAA
* **
28812063 AATTCTTTGGCAAA-CCTTTATAGTG
1 AATTCTTTGG-AAAGCCTTTATGGAA
* * * **
28812088 AATTCTCTAGAAAACCTTTATGGTG
1 AATTCTTTGGAAAGCCTTTATGGAA
* * * * *
28812113 ACTTCTTAGGAAAGCCCTTGTGGCA
1 AATTCTTTGGAAAGCCTTTATGGAA
* * * *
28812138 TA-TCATTTGGAAAGTCTTTTTGGAG
1 AATTC-TTTGGAAAGCCTTTATGGAA
*
28812163 AATTCTTTGGAAATCCTTT
1 AATTCTTTGGAAAGCCTTT
28812182 GTGGTAAGTT
Statistics
Matches: 108, Mismatches: 32, Indels: 8
0.73 0.22 0.05
Matches are distributed among these distances:
24 5 0.05
25 98 0.91
26 5 0.05
ACGTcount: A:0.28, C:0.16, G:0.18, T:0.38
Consensus pattern (25 bp):
AATTCTTTGGAAAGCCTTTATGGAA
Found at i:28812842 original size:13 final size:13
Alignment explanation
Indices: 28812824--28812852 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
28812814 TATTATTTTC
28812824 TTTCATTCTTAGG
1 TTTCATTCTTAGG
28812837 TTTCATTCTTAGG
1 TTTCATTCTTAGG
28812850 TTT
1 TTT
28812853 TAGATTTCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.14, C:0.14, G:0.14, T:0.59
Consensus pattern (13 bp):
TTTCATTCTTAGG
Found at i:28818294 original size:23 final size:23
Alignment explanation
Indices: 28818268--28818338 Score: 71
Period size: 23 Copynumber: 3.2 Consensus size: 23
28818258 TTACTTGTTT
28818268 TGGCACACTATGGTAGAATTGTC
1 TGGCACACTATGGTAGAATTGTC
* *
28818291 TGGCAAATTATAGGCT---ATT-T-
1 TGGCACACTAT-GG-TAGAATTGTC
28818311 TGGCACACTATGGTAGAATTGTC
1 TGGCACACTATGGTAGAATTGTC
28818334 TGGCA
1 TGGCA
28818339 AATTATAGGC
Statistics
Matches: 37, Mismatches: 4, Indels: 14
0.67 0.07 0.25
Matches are distributed among these distances:
18 1 0.03
19 2 0.05
20 9 0.24
21 4 0.11
22 4 0.11
23 14 0.38
24 2 0.05
25 1 0.03
ACGTcount: A:0.27, C:0.15, G:0.25, T:0.32
Consensus pattern (23 bp):
TGGCACACTATGGTAGAATTGTC
Found at i:28818326 original size:43 final size:43
Alignment explanation
Indices: 28818265--28818352 Score: 176
Period size: 43 Copynumber: 2.0 Consensus size: 43
28818255 ATGTTACTTG
28818265 TTTTGGCACACTATGGTAGAATTGTCTGGCAAATTATAGGCTA
1 TTTTGGCACACTATGGTAGAATTGTCTGGCAAATTATAGGCTA
28818308 TTTTGGCACACTATGGTAGAATTGTCTGGCAAATTATAGGCTA
1 TTTTGGCACACTATGGTAGAATTGTCTGGCAAATTATAGGCTA
28818351 TT
1 TT
28818353 GGCCAACTAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (43 bp):
TTTTGGCACACTATGGTAGAATTGTCTGGCAAATTATAGGCTA
Found at i:28820297 original size:43 final size:43
Alignment explanation
Indices: 28820207--28820302 Score: 129
Period size: 43 Copynumber: 2.2 Consensus size: 43
28820197 AATGAACTCG
* *
28820207 CACACTTAATGCCAATTAATTAGTCAAAGCTATAATTGTATCA
1 CACACTTAGTGCCAAATAATTAGTCAAAGCTATAATTGTATCA
* * * **
28820250 CACACTTAGTGCCAAATAATTAGTCGAATCTATAATTGTGTTT
1 CACACTTAGTGCCAAATAATTAGTCAAAGCTATAATTGTATCA
28820293 CACACTTAGT
1 CACACTTAGT
28820303 ACCATTACAT
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 46 1.00
ACGTcount: A:0.35, C:0.19, G:0.11, T:0.34
Consensus pattern (43 bp):
CACACTTAGTGCCAAATAATTAGTCAAAGCTATAATTGTATCA
Found at i:28822897 original size:23 final size:23
Alignment explanation
Indices: 28822870--28822961 Score: 105
Period size: 23 Copynumber: 4.0 Consensus size: 23
28822860 CTCTCGGAAA
*
28822870 CCTTTGTGGTGTATTCTGTAATG
1 CCTTTGTGGCGTATTCTGTAATG
* *
28822893 CCTTTGTGGCATATTCTGTGATG
1 CCTTTGTGGCGTATTCTGTAATG
* * *
28822916 CCTTTGTGCCGT-TTTTGTGATG
1 CCTTTGTGGCGTATTCTGTAATG
* *
28822938 CCTTTTTGGTGTATTCTGTAATG
1 CCTTTGTGGCGTATTCTGTAATG
28822961 C
1 C
28822962 TCTTGCGGTG
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
22 18 0.32
23 39 0.68
ACGTcount: A:0.11, C:0.16, G:0.25, T:0.48
Consensus pattern (23 bp):
CCTTTGTGGCGTATTCTGTAATG
Found at i:28842163 original size:54 final size:53
Alignment explanation
Indices: 28842049--28842181 Score: 223
Period size: 54 Copynumber: 2.5 Consensus size: 53
28842039 CATTTCATGG
28842049 CAGGATTACCAGTCCAGGCTAAATCCCCCAATCATGAACACATAAGGTGATGT
1 CAGGATTACCAGTCCAGGCTAAATCCCCCAATCATGAACACATAAGGTGATGT
* *
28842102 CAAGATTACCAGTCCAGGCTAAATCCCCCATATCATGAACTCATAAGGTGATGT
1 CAGGATTACCAGTCCAGGCTAAATCCCCCA-ATCATGAACACATAAGGTGATGT
*
28842156 CGGGATTACCAGTCCAGGCT-AATCCC
1 CAGGATTACCAGTCCAGGCTAAATCCC
28842182 TTACAACGAC
Statistics
Matches: 75, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
53 35 0.47
54 40 0.53
ACGTcount: A:0.32, C:0.28, G:0.19, T:0.22
Consensus pattern (53 bp):
CAGGATTACCAGTCCAGGCTAAATCCCCCAATCATGAACACATAAGGTGATGT
Found at i:28844124 original size:25 final size:24
Alignment explanation
Indices: 28844096--28844172 Score: 77
Period size: 25 Copynumber: 3.1 Consensus size: 24
28844086 GAAAAGTCTA
28844096 TGTGGCGTATTATTTAGGAAGCCTT
1 TGTGGCGTATTATTT-GGAAGCCTT
* *
28844121 TGTGGC-TAGTTACTTGGAAAGCCTA
1 TGTGGCGTA-TTATTTGG-AAGCCTT
*
28844146 TGTGGTGTA-TATTTGGGAAGCCTT
1 TGTGGCGTATTATTT-GGAAGCCTT
28844170 TGT
1 TGT
28844173 AACTAGTTAT
Statistics
Matches: 43, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
24 17 0.40
25 24 0.56
26 2 0.05
ACGTcount: A:0.19, C:0.12, G:0.30, T:0.39
Consensus pattern (24 bp):
TGTGGCGTATTATTTGGAAGCCTT
Found at i:28844179 original size:49 final size:50
Alignment explanation
Indices: 28844076--28844222 Score: 165
Period size: 50 Copynumber: 3.0 Consensus size: 50
28844066 GCTTATGTGG
* **
28844076 CTAGTTA-TCTGAAAAGTCTATGTGGCGTATTATTTAGGAAGCCTTTGTGG
1 CTAGTTACT-TGAAAAGCCTATGTGGCGTATTATTTAGGAAGCCTTTGTAA
* * *
28844126 CTAGTTACTTGGAAAGCCTATGTGGTGTA-TATTTGGGAAGCCTTTGTAA
1 CTAGTTACTTGAAAAGCCTATGTGGCGTATTATTTAGGAAGCCTTTGTAA
* * * *
28844175 CTAGTTATTTGAAAAGTCC-ATGTGGCATATTATTTAGAAAGCTTTTGT
1 CTAGTTACTTGAAAAG-CCTATGTGGCGTATTATTTAGGAAGCCTTTGT
28844223 GGCAAGTCCT
Statistics
Matches: 81, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
49 39 0.48
50 41 0.51
51 1 0.01
ACGTcount: A:0.26, C:0.12, G:0.24, T:0.39
Consensus pattern (50 bp):
CTAGTTACTTGAAAAGCCTATGTGGCGTATTATTTAGGAAGCCTTTGTAA
Found at i:28844183 original size:25 final size:24
Alignment explanation
Indices: 28844105--28844185 Score: 74
Period size: 25 Copynumber: 3.3 Consensus size: 24
28844095 ATGTGGCGTA
*
28844105 TTATTTAGGAAGCCTTTGTGGCTAG
1 TTATTTGGGAAGCCTTTGT-GCTAG
* * * *
28844130 TTACTTGGAAAGCCTATGTGGT-G
1 TTATTTGGGAAGCCTTTGTGCTAG
*
28844153 TATATTTGGGAAGCCTTTGTAACTAG
1 T-TATTTGGGAAGCCTTTGT-GCTAG
28844179 TTATTTG
1 TTATTTG
28844186 AAAAGTCCAT
Statistics
Matches: 43, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
23 2 0.05
24 17 0.40
25 22 0.51
26 2 0.05
ACGTcount: A:0.22, C:0.11, G:0.26, T:0.41
Consensus pattern (24 bp):
TTATTTGGGAAGCCTTTGTGCTAG
Found at i:28846849 original size:39 final size:39
Alignment explanation
Indices: 28846795--28846872 Score: 111
Period size: 39 Copynumber: 2.0 Consensus size: 39
28846785 GGCATAGACA
*
28846795 TAGTCCACATATCTCATAGAAGAAAAAAGAAGGTTCCCT
1 TAGTCCACATATCTCATAGAAGAAAAAAGAAGGCTCCCT
* * **
28846834 TAGTCTACATGTCTCATAGAAGAAGGAAGAAGGCTCCCT
1 TAGTCCACATATCTCATAGAAGAAAAAAGAAGGCTCCCT
28846873 CATCCTCCCC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.23
Consensus pattern (39 bp):
TAGTCCACATATCTCATAGAAGAAAAAAGAAGGCTCCCT
Found at i:28852390 original size:27 final size:27
Alignment explanation
Indices: 28852358--28852436 Score: 113
Period size: 27 Copynumber: 2.9 Consensus size: 27
28852348 AAGGGCAAAA
*
28852358 CAGTCATTTTACCCTATAAGGGTATGT
1 CAGTCATTTTACACTATAAGGGTATGT
* * *
28852385 CGGTCATTTTACACTACAAGGGTATTT
1 CAGTCATTTTACACTATAAGGGTATGT
*
28852412 CAGTAATTTTACACTATAAGGGTAT
1 CAGTCATTTTACACTATAAGGGTAT
28852437 TTCGATAATT
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 45 1.00
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.37
Consensus pattern (27 bp):
CAGTCATTTTACACTATAAGGGTATGT
Found at i:28852437 original size:27 final size:26
Alignment explanation
Indices: 28852403--28852875 Score: 379
Period size: 27 Copynumber: 17.7 Consensus size: 26
28852393 TTACACTACA
* *
28852403 AGGGTATTTCAGTAATTTTACACTATA
1 AGGGTATTTCAGTAATTTTACA-AATG
*
28852430 AGGGTATTTC-GATAATTTTAAAAATCG
1 AGGGTATTTCAG-TAATTTTACAAAT-G
* *
28852457 -GGCGTGTTTCAGTAATTTTACAAACG
1 AGG-GTATTTCAGTAATTTTACAAATG
* **
28852483 AAGGTATTTTGGTAATTTTACAAATCG
1 AGGGTATTTCAGTAATTTTACAAAT-G
*
28852510 AGGGTATTT-TGATAATTTTACAAATCG
1 AGGGTATTTCAG-TAATTTTACAAAT-G
*
28852537 AGGGTGTTTCAGTAATTTTACAAATCG
1 AGGGTATTTCAGTAATTTTACAAAT-G
* * * *
28852564 AGGGTGTTTCGGTAATTTCAAAAATTG
1 AGGGTATTTCAGTAATTTTACAAA-TG
* * *
28852591 -GGGTATATCGGTAATTTTACAAATCA
1 AGGGTATTTCAGTAATTTTACAAAT-G
* * *
28852617 AGGATATTTCAATAATTTTACAAATT
1 AGGGTATTTCAGTAATTTTACAAATG
*
28852643 AGGGGTATTTCAATAATTTTACAAATCG
1 A-GGGTATTTCAGTAATTTTACAAAT-G
* * *
28852671 AGGGTGTTTCGGTAATTTCACAAATTG
1 AGGGTATTTCAGTAATTTTACAAA-TG
* * *
28852698 GGGGTATTT-TGATAATTTTACAAATTA
1 AGGGTATTTCAG-TAATTTTACAAA-TG
*
28852725 AGGGTATTTC-GATAATTTCAC-AATCG
1 AGGGTATTTCAG-TAATTTTACAAAT-G
*
28852751 AGGGTATTTC-GATAGTTTTACAAATCG
1 AGGGTATTTCAG-TAATTTTACAAAT-G
* *
28852778 ATGGTATTTCAGTAATTTCAC-AATAG
1 AGGGTATTTCAGTAATTTTACAAAT-G
*
28852804 AGGGTATTTCAGTAATTTTATAAATCG
1 AGGGTATTTCAGTAATTTTACAAAT-G
* *
28852831 GGGGTATTTCGGTAATTTTACAAATCG
1 AGGGTATTTCAGTAATTTTACAAAT-G
28852858 AGGGTATTTCAGTAATTT
1 AGGGTATTTCAGTAATTT
28852876 CTCTTTATTA
Statistics
Matches: 369, Mismatches: 57, Indels: 40
0.79 0.12 0.09
Matches are distributed among these distances:
25 2 0.01
26 89 0.24
27 272 0.74
28 6 0.02
ACGTcount: A:0.32, C:0.10, G:0.20, T:0.38
Consensus pattern (26 bp):
AGGGTATTTCAGTAATTTTACAAATG
Found at i:28852571 original size:107 final size:108
Alignment explanation
Indices: 28852376--28852875 Score: 545
Period size: 107 Copynumber: 4.7 Consensus size: 108
28852366 TTACCCTATA
* * * * *
28852376 AGGGTATGTCGGTCATTTTAC-ACTACAAGGGTATTTC-AGTAATTTTACACTAT-AAGGGTATT
1 AGGGTATTTCGGTAATTTTACAAAT-CAAGGGTATTTCGA-TAATTTTACA-AATCGAGGGTATT
* * *
28852438 TC-GATAATTTTAAAAATCG-GGCGTGTTTCAGTAATTTTACAAA-CG
63 TCAG-TAATTTTACAAATCGAGG-GTGTTTCAGTAATTTCACAAATTG
* * * * *
28852483 AAGGTATTTTGGTAATTTTACAAATCGAGGGTATTTTGATAATTTTACAAATCGAGGGTGTTTCA
1 AGGGTATTTCGGTAATTTTACAAATCAAGGGTATTTCGATAATTTTACAAATCGAGGGTATTTCA
* *
28852548 GTAATTTTACAAATCGAGGGTGTTTCGGTAATTTCAAAAATTG
66 GTAATTTTACAAATCGAGGGTGTTTCAGTAATTTCACAAATTG
* * * *
28852591 -GGGTATATCGGTAATTTTACAAATCAAGGATATTTCAATAATTTTACAAAT-TAGGGGTATTTC
1 AGGGTATTTCGGTAATTTTACAAATCAAGGGTATTTCGATAATTTTACAAATCGA-GGGTATTTC
* *
28852654 AATAATTTTACAAATCGAGGGTGTTTCGGTAATTTCACAAATTG
65 AGTAATTTTACAAATCGAGGGTGTTTCAGTAATTTCACAAATTG
* * * * *
28852698 GGGGTATTTTGATAATTTTACAAATTAAGGGTATTTCGATAATTTCAC-AATCGAGGGTATTTC-
1 AGGGTATTTCGGTAATTTTACAAATCAAGGGTATTTCGATAATTTTACAAATCGAGGGTATTTCA
* * * *
28852761 GATAGTTTTACAAATCGATGGTATTTCAGTAATTTCAC-AATAG
66 G-TAATTTTACAAATCGAGGGTGTTTCAGTAATTTCACAAATTG
* * ** *
28852804 AGGGTATTTCAGTAATTTTATAAATCGGGGGTATTTCGGTAATTTTACAAATCGAGGGTATTTCA
1 AGGGTATTTCGGTAATTTTACAAATCAAGGGTATTTCGATAATTTTACAAATCGAGGGTATTTCA
28852869 GTAATTT
66 GTAATTT
28852876 CTCTTTATTA
Statistics
Matches: 330, Mismatches: 51, Indels: 24
0.81 0.13 0.06
Matches are distributed among these distances:
106 45 0.14
107 236 0.72
108 49 0.15
ACGTcount: A:0.32, C:0.10, G:0.20, T:0.38
Consensus pattern (108 bp):
AGGGTATTTCGGTAATTTTACAAATCAAGGGTATTTCGATAATTTTACAAATCGAGGGTATTTCA
GTAATTTTACAAATCGAGGGTGTTTCAGTAATTTCACAAATTG
Found at i:28852876 original size:80 final size:81
Alignment explanation
Indices: 28852403--28852875 Score: 507
Period size: 80 Copynumber: 5.9 Consensus size: 81
28852393 TTACACTACA
* * * *
28852403 AGGGTATTTCAGTAATTTTACACTAT-AAGGGTATTTCGATAATTTTAAAAATCG-GGCGTGTTT
1 AGGGTATTTCAGTAATTTTACA-AATCGAGGGTATTTCGATAATTTTACAAATCGAGG-GTATTT
*
28852466 CAGTAATTTTACAAA-CG
64 CAGTAATTTTACAAATAG
* ** * *
28852483 AAGGTATTTTGGTAATTTTACAAATCGAGGGTATTTTGATAATTTTACAAATCGAGGGTGTTTCA
1 AGGGTATTTCAGTAATTTTACAAATCGAGGGTATTTCGATAATTTTACAAATCGAGGGTATTTCA
*
28852548 GTAATTTTACAAATCG
66 GTAATTTTACAAATAG
* * * * * * * * *
28852564 AGGGTGTTTCGGTAATTTCAAAAATTG-GGGTATATCGGTAATTTTACAAATCAAGGATATTTCA
1 AGGGTATTTCAGTAATTTTACAAATCGAGGGTATTTCGATAATTTTACAAATCGAGGGTATTTCA
*
28852628 ATAATTTTACAAATTAG
66 GTAATTTTACAAA-TAG
* * * * * * *
28852645 -GGGTATTTCAATAATTTTACAAATCGAGGGTGTTTCGGTAATTTCACAAATTGGGGGTATTT-T
1 AGGGTATTTCAGTAATTTTACAAATCGAGGGTATTTCGATAATTTTACAAATCGAGGGTATTTCA
28852708 GATAATTTTACAAATTA-
66 G-TAATTTTACAAA-TAG
* * *
28852725 AGGGTATTTC-GATAATTTCAC-AATCGAGGGTATTTCGATAGTTTTACAAATCGATGGTATTTC
1 AGGGTATTTCAG-TAATTTTACAAATCGAGGGTATTTCGATAATTTTACAAATCGAGGGTATTTC
*
28852788 AGTAATTTCAC-AATAG
65 AGTAATTTTACAAATAG
* * *
28852804 AGGGTATTTCAGTAATTTTATAAATCGGGGGTATTTCGGTAATTTTACAAATCGAGGGTATTTCA
1 AGGGTATTTCAGTAATTTTACAAATCGAGGGTATTTCGATAATTTTACAAATCGAGGGTATTTCA
28852869 GTAATTT
66 GTAATTT
28852876 CTCTTTATTA
Statistics
Matches: 328, Mismatches: 53, Indels: 24
0.81 0.13 0.06
Matches are distributed among these distances:
78 2 0.01
79 21 0.06
80 217 0.66
81 88 0.27
ACGTcount: A:0.32, C:0.10, G:0.20, T:0.38
Consensus pattern (81 bp):
AGGGTATTTCAGTAATTTTACAAATCGAGGGTATTTCGATAATTTTACAAATCGAGGGTATTTCA
GTAATTTTACAAATAG
Found at i:28871743 original size:18 final size:20
Alignment explanation
Indices: 28871701--28871748 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 20
28871691 TAAGTAAAAG
28871701 AAAATAAAAATAAAGCAGCTA
1 AAAATAAAAATAAAGCA-CTA
*
28871722 AAAATAAAAATATAG-A-TA
1 AAAATAAAAATAAAGCACTA
28871740 AAAATAAAA
1 AAAATAAAA
28871749 TGAAAATGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 11 0.42
20 1 0.04
21 14 0.54
ACGTcount: A:0.73, C:0.04, G:0.06, T:0.17
Consensus pattern (20 bp):
AAAATAAAAATAAAGCACTA
Found at i:28871754 original size:12 final size:11
Alignment explanation
Indices: 28871722--28871780 Score: 57
Period size: 12 Copynumber: 5.3 Consensus size: 11
28871712 AAAGCAGCTA
28871722 AAAATAAAAAT
1 AAAATAAAAAT
*
28871733 ATAGATAAAAAT
1 A-AAATAAAAAT
*
28871745 AAAATGAAAAT
1 AAAATAAAAAT
*
28871756 GAAAATGAAAAT
1 -AAAATAAAAAT
*
28871768 GAAAT-AAAAT
1 AAAATAAAAAT
28871778 AAA
1 AAA
28871781 CTCAATGATA
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
10 7 0.17
11 13 0.32
12 21 0.51
ACGTcount: A:0.73, C:0.00, G:0.08, T:0.19
Consensus pattern (11 bp):
AAAATAAAAAT
Found at i:28871959 original size:10 final size:10
Alignment explanation
Indices: 28871943--28872015 Score: 98
Period size: 10 Copynumber: 7.4 Consensus size: 10
28871933 ATGGATCAGT
28871943 AAAAT-AATA
1 AAAATAAATA
28871952 ACAAATAAATA
1 A-AAATAAATA
28871963 AAAATAAATA
1 AAAATAAATA
28871973 AAAATAAATA
1 AAAATAAATA
28871983 AAAATAAA-A
1 AAAATAAATA
*
28871992 GAAACTAAAT-
1 -AAAATAAATA
28872002 AAAATAAATA
1 AAAATAAATA
28872012 AAAA
1 AAAA
28872016 GGTAAAAGGG
Statistics
Matches: 57, Mismatches: 2, Indels: 9
0.84 0.03 0.13
Matches are distributed among these distances:
9 10 0.18
10 42 0.74
11 5 0.09
ACGTcount: A:0.78, C:0.03, G:0.01, T:0.18
Consensus pattern (10 bp):
AAAATAAATA
Found at i:28871963 original size:14 final size:13
Alignment explanation
Indices: 28871944--28872013 Score: 63
Period size: 14 Copynumber: 5.2 Consensus size: 13
28871934 TGGATCAGTA
*
28871944 AAATAATAACAAAT
1 AAATAA-AATAAAT
28871958 AAATAAAAATAAAT
1 AAAT-AAAATAAAT
*
28871972 AAAAATAAAT-AA-
1 AAATA-AAATAAAT
*
28871984 AAATAAAAGAAACT
1 AAATAAAATAAA-T
28871998 AAATAAAATAAAT
1 AAATAAAATAAAT
28872011 AAA
1 AAA
28872014 AAGGTAAAAG
Statistics
Matches: 46, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
11 3 0.07
12 6 0.13
13 7 0.15
14 28 0.61
15 2 0.04
ACGTcount: A:0.77, C:0.03, G:0.01, T:0.19
Consensus pattern (13 bp):
AAATAAAATAAAT
Found at i:28876781 original size:26 final size:26
Alignment explanation
Indices: 28876749--28876801 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
28876739 AGTATTTTAA
28876749 AGTGGAATTCCTTATATAGTAATTAG
1 AGTGGAATTCCTTATATAGTAATTAG
28876775 AGTGGAATTCCTTATATAGTAATTAG
1 AGTGGAATTCCTTATATAGTAATTAG
28876801 A
1 A
28876802 CCATAAATAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.36, C:0.08, G:0.19, T:0.38
Consensus pattern (26 bp):
AGTGGAATTCCTTATATAGTAATTAG
Found at i:28877607 original size:2 final size:2
Alignment explanation
Indices: 28877600--28877643 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
28877590 TATGAAATGC
28877600 TA TA 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 TA TA
28877642 TA
1 TA
28877644 CTGATTACAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:28877877 original size:25 final size:25
Alignment explanation
Indices: 28877848--28877917 Score: 97
Period size: 25 Copynumber: 2.8 Consensus size: 25
28877838 TGTTCCGACC
28877848 CACAGCTCGTGTGAGCATACCGA-T
1 CACAGCTCGTGTGAGCATACCGATT
*
28877872 CTACAGCTCGAGTGAGCATACCGATT
1 C-ACAGCTCGTGTGAGCATACCGATT
* *
28877898 CAAAGCTCGTATGAGCATAC
1 CACAGCTCGTGTGAGCATAC
28877918 ATGTACATGA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
24 1 0.03
25 37 0.93
26 2 0.05
ACGTcount: A:0.29, C:0.27, G:0.23, T:0.21
Consensus pattern (25 bp):
CACAGCTCGTGTGAGCATACCGATT
Found at i:28878566 original size:14 final size:15
Alignment explanation
Indices: 28878545--28878583 Score: 55
Period size: 13 Copynumber: 2.7 Consensus size: 15
28878535 AGTAAATAAT
28878545 AATAATAATTACTAA
1 AATAATAATTACTAA
28878560 AAT-ATAA-TACTAA
1 AATAATAATTACTAA
*
28878573 TATAATAATTA
1 AATAATAATTA
28878584 AAAGTAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
13 8 0.38
14 8 0.38
15 5 0.24
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (15 bp):
AATAATAATTACTAA
Found at i:28880556 original size:47 final size:46
Alignment explanation
Indices: 28880363--28880580 Score: 169
Period size: 47 Copynumber: 4.7 Consensus size: 46
28880353 TATACGTGCT
** *
28880363 GATGCATGTCCTGGACATGTCTTACACTAGCA--CA-ACTCTTA-GCC
1 GATGCATGTCCCAGACATGTCTTACACTGGCACTCATA-TC-TACGCC
* * * * * *
28880407 GATGCATGTCCCAGACACGTCTTACACTGG-ATATCTTCGTCGAGGCC
1 GATGCATGTCCCAGACATGTCTTACACTGGCA-CTCAT-ATCTACGCC
* * * *
28880454 AATGCATGTCCCAGACATGTCTCACATTGGCACTCATCTCTACGCC
1 GATGCATGTCCCAGACATGTCTTACACTGGCACTCATATCTACGCC
* * * *
28880500 GATGCCATGTCCCAGACATGGTCTTACACTAGCACTCATAATGT-GGCT
1 GATG-CATGTCCCAGACAT-GTCTTACACTGGCACTCAT-ATCTACGCC
*
28880548 GATGCATGTCCCTGACATGTCTTACACTGGCAC
1 GATGCATGTCCCAGACATGTCTTACACTGGCAC
28880581 ACAAGAAATT
Statistics
Matches: 138, Mismatches: 26, Indels: 18
0.76 0.14 0.10
Matches are distributed among these distances:
43 1 0.01
44 26 0.19
46 25 0.18
47 61 0.44
48 23 0.17
49 2 0.01
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.27
Consensus pattern (46 bp):
GATGCATGTCCCAGACATGTCTTACACTGGCACTCATATCTACGCC
Found at i:28880960 original size:30 final size:30
Alignment explanation
Indices: 28880919--28880976 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
28880909 AAATTCACAT
* *
28880919 CTTTGGTAAAATGACCATTTTGCCCCTAGA
1 CTTTGGCAAAATGACCATTTTACCCCTAGA
28880949 CTTTGGCAAAATGACCATTTTACCCCTA
1 CTTTGGCAAAATGACCATTTTACCCCTA
28880977 TGCTCGAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.33
Consensus pattern (30 bp):
CTTTGGCAAAATGACCATTTTACCCCTAGA
Found at i:28885396 original size:43 final size:43
Alignment explanation
Indices: 28885348--28885437 Score: 180
Period size: 43 Copynumber: 2.1 Consensus size: 43
28885338 GTGTACATTT
28885348 TGTGCTTATATTCGAATGAAGCAATTAAATTGCTAATGTGAAA
1 TGTGCTTATATTCGAATGAAGCAATTAAATTGCTAATGTGAAA
28885391 TGTGCTTATATTCGAATGAAGCAATTAAATTGCTAATGTGAAA
1 TGTGCTTATATTCGAATGAAGCAATTAAATTGCTAATGTGAAA
28885434 TGTG
1 TGTG
28885438 TTAACATGTG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 47 1.00
ACGTcount: A:0.36, C:0.09, G:0.20, T:0.36
Consensus pattern (43 bp):
TGTGCTTATATTCGAATGAAGCAATTAAATTGCTAATGTGAAA
Found at i:28885523 original size:39 final size:39
Alignment explanation
Indices: 28885469--28885669 Score: 348
Period size: 39 Copynumber: 5.2 Consensus size: 39
28885459 AAGACACTGA
28885469 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
1 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
*
28885508 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCATGCTGG
1 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
*
28885547 AAATATATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
1 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
* * *
28885586 AAATATATCTGGGCCAAAGTCCCGCAGGCTTCGTGCTGG
1 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
*
28885625 AAATGTATCCGGACTAAAGTCCCGCAGGCTTCGTGCTGG
1 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
28885664 AAATGT
1 AAATGT
28885670 GTAACACCCC
Statistics
Matches: 153, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 153 1.00
ACGTcount: A:0.23, C:0.25, G:0.28, T:0.23
Consensus pattern (39 bp):
AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
Found at i:28887114 original size:40 final size:40
Alignment explanation
Indices: 28887055--28887256 Score: 271
Period size: 40 Copynumber: 5.0 Consensus size: 40
28887045 GAATTTAGCT
* ** * *
28887055 GGATATAACCACAAGCACAATTGCCTTCGGGTCTTAACCC
1 GGATATAACAACTCGCACAAATGCCTTCGGGTCTTAGCCC
* *
28887095 GGGTATAGCAACTCGCACAAATGCCTTCGGGTCTTAGCCC
1 GGATATAACAACTCGCACAAATGCCTTCGGGTCTTAGCCC
*
28887135 GGATATAACAACTCGCGCAAATGCCTTCGGGTCTTAGCCC
1 GGATATAACAACTCGCACAAATGCCTTCGGGTCTTAGCCC
* *
28887175 GGATATAACAACTTGTACAAATGCCTTCGGGTCTTAGCCC
1 GGATATAACAACTCGCACAAATGCCTTCGGGTCTTAGCCC
* * *
28887215 GGATATAATC-ACTAGCATAAATGCCTTCGGGACTTAGCCC
1 GGATATAA-CAACTCGCACAAATGCCTTCGGGTCTTAGCCC
28887255 GG
1 GG
28887257 GTATCATTCA
Statistics
Matches: 144, Mismatches: 17, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
40 143 0.99
41 1 0.01
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
GGATATAACAACTCGCACAAATGCCTTCGGGTCTTAGCCC
Found at i:28899207 original size:39 final size:39
Alignment explanation
Indices: 28899104--28899413 Score: 453
Period size: 39 Copynumber: 8.0 Consensus size: 39
28899094 AAGACACTGA
* ** *
28899104 AAATGTATCCAGGCTAAAGTCCCATAGGCTTCATGCTGG
1 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
28899143 AAATGTATCC-GGCTAAAGTCCCGCAGGCTTCGTGCTGG
1 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
*
28899181 AAATATATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
1 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
* * * *
28899220 AAATATATCTGGG-TCAAAGTCCAGCGGGCTTCGTGCTGG
1 AAATGTATCCGGGCT-AAAGTCCCGCAGGCTTCGTGCTGG
*
28899259 AAATGTATCCGGACTAAAGTCCCGCAGGCTTCGTGCTGG
1 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
* *
28899298 AAATGTATCCGGGCCAAAGTCCCGTAGGCTTCGTGCTGG
1 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
* *
28899337 AAATGTATCCGAGCCAAAGTCCCGCAGGCTTCGTGCTGG
1 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
* *
28899376 AAATGTATCCGGGTTAAAGTCCCGCAGGCTTTGTGCTG
1 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTG
28899414 ATAATATAAT
Statistics
Matches: 247, Mismatches: 21, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
38 35 0.14
39 211 0.85
40 1 0.00
ACGTcount: A:0.23, C:0.25, G:0.28, T:0.24
Consensus pattern (39 bp):
AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
Found at i:28901176 original size:24 final size:24
Alignment explanation
Indices: 28901132--28901178 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
28901122 AACTGTATGT
* *
28901132 GAATTTCCTGATGTGTTTCCTGAA
1 GAATTTCCTGATGTATCTCCTGAA
28901156 GAATTTCCTAGAT-TATCTCCTGA
1 GAATTTCCT-GATGTATCTCCTGA
28901179 TCGGGAAGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 17 0.85
25 3 0.15
ACGTcount: A:0.23, C:0.19, G:0.17, T:0.40
Consensus pattern (24 bp):
GAATTTCCTGATGTATCTCCTGAA
Found at i:28903548 original size:46 final size:46
Alignment explanation
Indices: 28903426--28903548 Score: 210
Period size: 46 Copynumber: 2.7 Consensus size: 46
28903416 TACATTTCAC
* *
28903426 GAACTCGGACTCAACTCAACGAGTTTGGACGTTCTCATCCATAAGT
1 GAACTCGGACTCAACTCAACGAGTTTGGATGTTCGCATCCATAAGT
* *
28903472 GAACTCGGACTCAGCTCAACGAGTTCGGATGTTCGCATCCATAAGT
1 GAACTCGGACTCAACTCAACGAGTTTGGATGTTCGCATCCATAAGT
28903518 GAACTCGGACTCAACTCAACGAGTTTGGATG
1 GAACTCGGACTCAACTCAACGAGTTTGGATG
28903549 CCCAAATATC
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 71 1.00
ACGTcount: A:0.28, C:0.25, G:0.23, T:0.24
Consensus pattern (46 bp):
GAACTCGGACTCAACTCAACGAGTTTGGATGTTCGCATCCATAAGT
Found at i:28906015 original size:30 final size:30
Alignment explanation
Indices: 28905971--28906039 Score: 88
Period size: 30 Copynumber: 2.3 Consensus size: 30
28905961 TAAAGATAAC
*
28905971 AAGAAAACC-GAATAAAGAAATCTAAG-ATA
1 AAGAAACCCAGAATAAAGAAATC-AAGAATA
* *
28906000 GAGAAACCCAGAATAAAGAAATCCAGAATA
1 AAGAAACCCAGAATAAAGAAATCAAGAATA
28906030 AAGAAACCCA
1 AAGAAACCCA
28906040 AGATACGATA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
29 9 0.26
30 25 0.74
ACGTcount: A:0.59, C:0.16, G:0.14, T:0.10
Consensus pattern (30 bp):
AAGAAACCCAGAATAAAGAAATCAAGAATA
Found at i:28906019 original size:15 final size:15
Alignment explanation
Indices: 28905971--28906039 Score: 70
Period size: 15 Copynumber: 4.7 Consensus size: 15
28905961 TAAAGATAAC
*
28905971 AAGAAAACC-GAATA
1 AAGAAACCCAGAATA
* *
28905985 AAGAAATCTA-AGATA
1 AAGAAACCCAGA-ATA
*
28906000 GAGAAACCCAGAATA
1 AAGAAACCCAGAATA
*
28906015 AAGAAATCCAGAATA
1 AAGAAACCCAGAATA
28906030 AAGAAACCCA
1 AAGAAACCCA
28906040 AGATACGATA
Statistics
Matches: 44, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
14 8 0.18
15 35 0.80
16 1 0.02
ACGTcount: A:0.59, C:0.16, G:0.14, T:0.10
Consensus pattern (15 bp):
AAGAAACCCAGAATA
Found at i:28908878 original size:46 final size:46
Alignment explanation
Indices: 28908756--28908878 Score: 183
Period size: 46 Copynumber: 2.7 Consensus size: 46
28908746 TACATTTCAC
* * * *
28908756 GAACTCGAACTCAACTCAACTAGTTCAGACGTTCGCATCCATAAGT
1 GAACTCGGACTCAACTCAACGAGTTCGGATGTTCGCATCCATAAGT
* *
28908802 GAACTCGGACTCAGCTCAACGAGTTCGGATGTTCGTATCCATAAGT
1 GAACTCGGACTCAACTCAACGAGTTCGGATGTTCGCATCCATAAGT
*
28908848 GAACTCGGACTCAACTCAACGAGTTTGGATG
1 GAACTCGGACTCAACTCAACGAGTTCGGATG
28908879 CCCAAATATC
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 69 1.00
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.24
Consensus pattern (46 bp):
GAACTCGGACTCAACTCAACGAGTTCGGATGTTCGCATCCATAAGT
Found at i:28912123 original size:3 final size:3
Alignment explanation
Indices: 28912115--28912161 Score: 53
Period size: 3 Copynumber: 16.0 Consensus size: 3
28912105 ATTATAAGTA
* *
28912115 AAT AAT AAT AATT ACT AAA AAT AAT AAT AAT AAT -AT AAT -AT AAT
1 AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
28912159 AAT
1 AAT
28912162 TAAAAGTAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
2 4 0.11
3 31 0.84
4 2 0.05
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:28912665 original size:6 final size:6
Alignment explanation
Indices: 28912656--28912694 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
28912646 TCACTACTAC
* * *
28912656 TACTGT TACTGT TGCTGT TACTGT TACTAT TACTAT TAC
1 TACTGT TACTGT TACTGT TACTGT TACTGT TACTGT TAC
28912695 AGTGTATTCC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.21, C:0.18, G:0.13, T:0.49
Consensus pattern (6 bp):
TACTGT
Found at i:28912694 original size:18 final size:18
Alignment explanation
Indices: 28912650--28912694 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
28912640 TGTGTATCAC
* *
28912650 TACTACTACTGTTACTGT
1 TACTATTACTGTTACTAT
* *
28912668 TGCTGTTACTGTTACTAT
1 TACTATTACTGTTACTAT
28912686 TACTATTAC
1 TACTATTAC
28912695 AGTGTATTCC
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.22, C:0.20, G:0.11, T:0.47
Consensus pattern (18 bp):
TACTATTACTGTTACTAT
Found at i:28914677 original size:12 final size:12
Alignment explanation
Indices: 28914660--28914689 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
28914650 TAAGGTTGTT
28914660 ACACGGCCTAGC
1 ACACGGCCTAGC
*
28914672 ACACGGCCTGGC
1 ACACGGCCTAGC
28914684 ACACGG
1 ACACGG
28914690 GCATTTGGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.23, C:0.40, G:0.30, T:0.07
Consensus pattern (12 bp):
ACACGGCCTAGC
Found at i:28917958 original size:48 final size:50
Alignment explanation
Indices: 28917902--28918002 Score: 143
Period size: 48 Copynumber: 2.0 Consensus size: 50
28917892 CAAACCAAAC
*
28917902 AAGCATTTGTGTATAGTTATCT-GAAAAGCCTA-TGGTGTATTATTTGGG
1 AAGCATTTGTGTATAGTTATCTCAAAAAGCCTAGTGGTGTATTATTTGGG
* * *
28917950 AAGCATTTGTGTCTAGTTATCTCAAAAAGTCTATGTGGTGTATTGTTTGGG
1 AAGCATTTGTGTATAGTTATCTCAAAAAGCCTA-GTGGTGTATTATTTGGG
28918001 AA
1 AA
28918003 TCTTATTGGG
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
48 21 0.46
49 8 0.17
51 17 0.37
ACGTcount: A:0.27, C:0.09, G:0.25, T:0.40
Consensus pattern (50 bp):
AAGCATTTGTGTATAGTTATCTCAAAAAGCCTAGTGGTGTATTATTTGGG
Found at i:28917969 original size:25 final size:25
Alignment explanation
Indices: 28917902--28917976 Score: 64
Period size: 25 Copynumber: 3.1 Consensus size: 25
28917892 CAAACCAAAC
28917902 AAGCATTTGTGTATAGTTATCTGAA
1 AAGCATTTGTGTATAGTTATCTGAA
* * * * **
28917927 AAGCCTATG-GTGTA-TTATTTGGG
1 AAGCATTTGTGTATAGTTATCTGAA
* *
28917950 AAGCATTTGTGTCTAGTTATCTCAA
1 AAGCATTTGTGTATAGTTATCTGAA
28917975 AA
1 AA
28917977 AGTCTATGTG
Statistics
Matches: 35, Mismatches: 13, Indels: 4
0.67 0.25 0.08
Matches are distributed among these distances:
23 13 0.37
24 8 0.23
25 14 0.40
ACGTcount: A:0.29, C:0.11, G:0.21, T:0.39
Consensus pattern (25 bp):
AAGCATTTGTGTATAGTTATCTGAA
Found at i:28918062 original size:25 final size:25
Alignment explanation
Indices: 28918034--28918094 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 25
28918024 GGAAGTGCTT
* *
28918034 TGTGGCTTGTTATCTAAAAAGCCTA
1 TGTGGCATATTATCTAAAAAGCCTA
* *
28918059 TGTGGCATATTATTTGAAAAGCCTA
1 TGTGGCATATTATCTAAAAAGCCTA
28918084 --TGGCATATTAT
1 TGTGGCATATTAT
28918095 TTGGGAAGCA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
23 11 0.34
25 21 0.66
ACGTcount: A:0.30, C:0.13, G:0.20, T:0.38
Consensus pattern (25 bp):
TGTGGCATATTATCTAAAAAGCCTA
Found at i:28918103 original size:23 final size:24
Alignment explanation
Indices: 28918050--28918097 Score: 80
Period size: 23 Copynumber: 2.0 Consensus size: 24
28918040 TTGTTATCTA
28918050 AAAAGCCTATGTGGCATATTATTTG
1 AAAAGCCTA-GTGGCATATTATTTG
28918075 AAAAGCCTA-TGGCATATTATTTG
1 AAAAGCCTAGTGGCATATTATTTG
28918098 GGAAGCATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 14 0.61
25 9 0.39
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.35
Consensus pattern (24 bp):
AAAAGCCTAGTGGCATATTATTTG
Found at i:28918205 original size:25 final size:25
Alignment explanation
Indices: 28918147--28918205 Score: 82
Period size: 25 Copynumber: 2.4 Consensus size: 25
28918137 GTGCATTATT
*
28918147 TGGAAAGCATTTATGGCAAGTCCTC
1 TGGAAAGCCTTTATGGCAAGTCCTC
* * *
28918172 TAGAAAGCCTTTGTGGCGAGTCCTC
1 TGGAAAGCCTTTATGGCAAGTCCTC
28918197 TGGAAAGCC
1 TGGAAAGCC
28918206 CATATACAGA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.25
Consensus pattern (25 bp):
TGGAAAGCCTTTATGGCAAGTCCTC
Found at i:28923514 original size:43 final size:43
Alignment explanation
Indices: 28923406--28923541 Score: 152
Period size: 43 Copynumber: 3.2 Consensus size: 43
28923396 AAGACCACAC
* *
28923406 CTGGGACGTTGGCATCGACT-TATGATTTACGTGTAAGACCATGT
1 CTGGGACGTTGGCATCGA-TATTTGATTT-CATGTAAGACCATGT
* *
28923450 CTGGGATGTTGGCATCG-TATTTGATTTCATGTAAGACCCTGT
1 CTGGGACGTTGGCATCGATATTTGATTTCATGTAAGACCATGT
* * *
28923492 CTGGGACAG-TGGCATCGATATTTGATTACATGTATGACCACGT
1 CTGGGAC-GTTGGCATCGATATTTGATTTCATGTAAGACCATGT
*
28923535 CTAGGAC
1 CTGGGAC
28923542 ATTAGCATTG
Statistics
Matches: 79, Mismatches: 10, Indels: 7
0.82 0.10 0.07
Matches are distributed among these distances:
42 28 0.35
43 35 0.44
44 16 0.20
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.32
Consensus pattern (43 bp):
CTGGGACGTTGGCATCGATATTTGATTTCATGTAAGACCATGT
Found at i:28927684 original size:210 final size:210
Alignment explanation
Indices: 28927322--28927742 Score: 797
Period size: 210 Copynumber: 2.0 Consensus size: 210
28927312 AAACAAGTGC
*
28927322 TCAATTGATCCATCATATTCTTGCATCTATGGCATTTGTCCATCCTATTTTTATGTCTTTCTATC
1 TCAATTGATCCATCATATTATTGCATCTATGGCATTTGTCCATCCTATTTTTATGTCTTTCTATC
28927387 AGATTCTCCTTTGAGGCAATGAAATTTCGACAACATCTCCAAATGAATATTTATAATTTTGGTAG
66 AGATTCTCCTTTGAGGCAATGAAATTTCGACAACATCTCCAAATGAATATTTATAATTTTGGTAG
*
28927452 ACATTTGAGCTTTTAGATATTCTTGCAAACTACTTGATTATCTTGAAAATTTCATAAAGCATAGG
131 ACATTTGAGCTTTTAGATATTCTTGCAAACTACTTGATTATCTTGAAAACTTCATAAAGCATAGG
28927517 AGCTTGTTGAATGCT
196 AGCTTGTTGAATGCT
* *
28927532 TCAATTGATCCATCATATTATTGCATCTATGGCATTTGTCCATCCTATTTTTATGTCTTTTTATG
1 TCAATTGATCCATCATATTATTGCATCTATGGCATTTGTCCATCCTATTTTTATGTCTTTCTATC
*
28927597 AGATTCTCCTTTGAGGCAATGAAATTTTGACAACATCTCCAAATGAATATTTATAATTTTGGTAG
66 AGATTCTCCTTTGAGGCAATGAAATTTCGACAACATCTCCAAATGAATATTTATAATTTTGGTAG
28927662 ACATTTGAGCTTTTAGATATTCTTGCAAACTACTTGATTATCTTGAAAACTTCATAAAGCATAGG
131 ACATTTGAGCTTTTAGATATTCTTGCAAACTACTTGATTATCTTGAAAACTTCATAAAGCATAGG
28927727 AGCTTGTTGAATGCT
196 AGCTTGTTGAATGCT
28927742 T
1 T
28927743 ATCATCCTAG
Statistics
Matches: 206, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
210 206 1.00
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.41
Consensus pattern (210 bp):
TCAATTGATCCATCATATTATTGCATCTATGGCATTTGTCCATCCTATTTTTATGTCTTTCTATC
AGATTCTCCTTTGAGGCAATGAAATTTCGACAACATCTCCAAATGAATATTTATAATTTTGGTAG
ACATTTGAGCTTTTAGATATTCTTGCAAACTACTTGATTATCTTGAAAACTTCATAAAGCATAGG
AGCTTGTTGAATGCT
Done.