Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168159.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_4, whole genome shotgun sequence
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: 33012953
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 65000 characters in sequence are not A, C, G, or T
File 148 of 160
Found at i:28641037 original size:58 final size:59
Alignment explanation
Indices: 28640975--28641094 Score: 190
Period size: 59 Copynumber: 2.1 Consensus size: 59
28640965 TAGAAATAAA
* *
28640975 TTTCCTT-AGAAATAAATTTCAAAAAAA-ATATTTTTGGGGAAAAGTTGAAAGTATCAAT
1 TTTCCTTAAAAAATAAATTTCAAAAAAATA-ATTTTTGGGGAAAAATTGAAAGTATCAAT
*
28641033 TTTCCTTAAAAAATAAATTTCAGAAAAATAATTTTTGGGGAAAAATTGAAAGTATCAAT
1 TTTCCTTAAAAAATAAATTTCAAAAAAATAATTTTTGGGGAAAAATTGAAAGTATCAAT
28641092 TTT
1 TTT
28641095 TCCTACACAA
Statistics
Matches: 57, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
58 7 0.12
59 49 0.86
60 1 0.02
ACGTcount: A:0.45, C:0.07, G:0.12, T:0.36
Consensus pattern (59 bp):
TTTCCTTAAAAAATAAATTTCAAAAAAATAATTTTTGGGGAAAAATTGAAAGTATCAAT
Found at i:28646174 original size:118 final size:116
Alignment explanation
Indices: 28646011--28646290 Score: 319
Period size: 117 Copynumber: 2.4 Consensus size: 116
28646001 GACCAAGTCC
* * * * * *
28646011 AGGTCAAAGATGAATGATCGAAATGAAATTGTGAGTCAAAAAAATAATATAGATTGAGTTGAAAT
1 AGGTCGAAGATGAATGAT-GAGATGAAATCGCGAGTCAAAAAAAT-ATATAAATTGAGTCGAAAT
* * *
28646076 CAAATGATCAAGATAAAATCAG-GAGTCAAGATAAAGCAACTATGATCGAATCG
64 CAAATAATCAAGATAAAA-CAGTGAGTCAAGATAAAACAACTAGGATCGAATCG
* * * *
28646129 AGGTCGAAGATGAATGATTAGGATGAAATCGCGAGTCAAAAAAATATCTAAATTGAGTCGAGATT
1 AGGTCGAAGATGAATGATGA-GATGAAATCGCGAGTCAAAAAAATATATAAATTGAGTCGAAATC
* * * * *
28646194 GAATAATCAAGATGAAACTGTGAGTCAAGATAAAACAATTAGGATCGAGTCG
65 AAATAATCAAGATAAAACAGTGAGTCAAGATAAAACAACTAGGATCGAATCG
* * *
28646246 AGGTTGAAGATAAATGACTGAGACGAAATCGCGAGTCAAAAAAAT
1 AGGTCGAAGATGAATGA-TGAGATGAAATCGCGAGTCAAAAAAAT
28646291 GATCTGAACT
Statistics
Matches: 137, Mismatches: 22, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
116 2 0.01
117 95 0.69
118 40 0.29
ACGTcount: A:0.45, C:0.10, G:0.23, T:0.22
Consensus pattern (116 bp):
AGGTCGAAGATGAATGATGAGATGAAATCGCGAGTCAAAAAAATATATAAATTGAGTCGAAATCA
AATAATCAAGATAAAACAGTGAGTCAAGATAAAACAACTAGGATCGAATCG
Found at i:28646380 original size:118 final size:118
Alignment explanation
Indices: 28646123--28646547 Score: 432
Period size: 118 Copynumber: 3.6 Consensus size: 118
28646113 AACTATGATC
* * *
28646123 GAATCGAGGTCGAAGATGAATGA-TTAGGATGAAATCGCGAGTCAAAAAAAT-ATCTAAATTGAG
1 GAATCGAGGTCGAAGATGAATGACTCA-GATGAAATCACGAGTCAAAAAAATGATCTAAACTGAG
* * * * *
28646186 TCGAGATTGAATAATCAAGATGAAACTGTGAGTCAAGATAAAACAATTAGGA-T
65 TCGAGATCGAATGATCAGGATGAAACTGTGAGTCGAGATAAAACAATCAGGACT
* * * * * * *
28646239 CGAGTCGAGGTTGAAGATAAATGACTGAGACGAAATCGCGAGTCAAAAAAATGATCTGAACTGAG
1 -GAATCGAGGTCGAAGATGAATGACTCAGATGAAATCACGAGTCAAAAAAATGATCTAAACTGAG
* * *
28646304 TCGAGATCGAATGATCAGGACGAAACTGCGAGTCGAGATAAAGCAATCAGGACT
65 TCGAGATCGAATGATCAGGATGAAACTGTGAGTCGAGATAAAACAATCAGGACT
* * * * * * ** *
28646358 GATTCAAGGTCAAATATGAATGAC-CAGAATGAAATTACAAGTCAAAAAAATGATCTGGACTAAG
1 GAATCGAGGTCGAAGATGAATGACTCAG-ATGAAATCACGAGTCAAAAAAATGATCTAAACTGAG
* * * * * **
28646422 CCGAGATCGAATGA-CTGAGATGAAACTGTAAGTCGAGATAAAATAACCAAAACT
65 TCGAGATCGAATGATCAG-GATGAAACTGTGAGTCGAGATAAAACAATCAGGACT
*
28646476 GAATCGAGGTCGAAGATGAATGA-TCAGGATAAAATCACGAGTCAAAAAAATGATCTAAACTGAG
1 GAATCGAGGTCGAAGATGAATGACTCA-GATGAAATCACGAGTCAAAAAAATGATCTAAACTGAG
28646540 -CTGAGATC
65 TC-GAGATC
28646548 TATGACTGGG
Statistics
Matches: 252, Mismatches: 48, Indels: 15
0.80 0.15 0.05
Matches are distributed among these distances:
117 48 0.19
118 202 0.80
119 2 0.01
ACGTcount: A:0.43, C:0.13, G:0.24, T:0.20
Consensus pattern (118 bp):
GAATCGAGGTCGAAGATGAATGACTCAGATGAAATCACGAGTCAAAAAAATGATCTAAACTGAGT
CGAGATCGAATGATCAGGATGAAACTGTGAGTCGAGATAAAACAATCAGGACT
Found at i:28646720 original size:65 final size:65
Alignment explanation
Indices: 28646643--28646778 Score: 227
Period size: 65 Copynumber: 2.1 Consensus size: 65
28646633 GTTAAAAAAA
*
28646643 TAATCTGAACTAAGCTGAGATCAAAATAAGTAATAAATGATAATGTAACGTTGCAAATACATGTC
1 TAATCTGAACTAAGCTGAGATCAAAATAAGTAATAAATGATAATGTAACGCTGCAAATACATGTC
* * * *
28646708 TAATCTGGACTAAGCTGAGATCGAAATAAGTAATAAATGATAATGTAACGCTGCAAATGCATGTT
1 TAATCTGAACTAAGCTGAGATCAAAATAAGTAATAAATGATAATGTAACGCTGCAAATACATGTC
28646773 TAATCT
1 TAATCT
28646779 AGGATGTAAA
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
65 66 1.00
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (65 bp):
TAATCTGAACTAAGCTGAGATCAAAATAAGTAATAAATGATAATGTAACGCTGCAAATACATGTC
Found at i:28647517 original size:53 final size:52
Alignment explanation
Indices: 28647460--28647602 Score: 142
Period size: 52 Copynumber: 2.7 Consensus size: 52
28647450 ATCTAATTAT
* * * *
28647460 TTCACCATTAGGGCCAAATTATAAATATTTTTTTGTTTTGAATTTTTAAATTC
1 TTCACCATTTGGGCCAAATTAGAAAT-TTTTTTTATTTTGAATTTCTAAATTC
* * ** * ** *
28647513 TTCACAATTTGGACGTATTTAGAAATTTTTTTTATTTTTTATTTCTAAATTT
1 TTCACCATTTGGGCCAAATTAGAAATTTTTTTTATTTTGAATTTCTAAATTC
* * *
28647565 TTCACCATTTGGGCCTATTTAGAAATTCTTTTTATTTT
1 TTCACCATTTGGGCCAAATTAGAAATTTTTTTTATTTT
28647603 TTTTGAAAGA
Statistics
Matches: 74, Mismatches: 16, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
52 55 0.74
53 19 0.26
ACGTcount: A:0.27, C:0.11, G:0.09, T:0.53
Consensus pattern (52 bp):
TTCACCATTTGGGCCAAATTAGAAATTTTTTTTATTTTGAATTTCTAAATTC
Found at i:28647562 original size:52 final size:52
Alignment explanation
Indices: 28647482--28647604 Score: 156
Period size: 52 Copynumber: 2.3 Consensus size: 52
28647472 GCCAAATTAT
* ** * *
28647482 AAATATTTTTTTGTTTTGAATTTTTAAATTCTTCACAATTTGGACGTATTTAG
1 AAAT-TTTTTTTATTTTTTATTTCTAAATTCTTCACAATTTGGACCTATTTAG
* * *
28647535 AAATTTTTTTTATTTTTTATTTCTAAATTTTTCACCATTTGGGCCTATTTAG
1 AAATTTTTTTTATTTTTTATTTCTAAATTCTTCACAATTTGGACCTATTTAG
*
28647587 AAATTCTTTTTATTTTTT
1 AAATTTTTTTTATTTTTT
28647605 TTGAAAGAAA
Statistics
Matches: 61, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
52 57 0.93
53 4 0.07
ACGTcount: A:0.25, C:0.09, G:0.08, T:0.58
Consensus pattern (52 bp):
AAATTTTTTTTATTTTTTATTTCTAAATTCTTCACAATTTGGACCTATTTAG
Found at i:28649021 original size:23 final size:23
Alignment explanation
Indices: 28648995--28649043 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
28648985 TTTAAGTTTT
28648995 AACTC-TAATTTTAATCCCACATA
1 AACTCTTAA-TTTAATCCCACATA
*
28649018 AACTCTTAATTTAATCCCACTTA
1 AACTCTTAATTTAATCCCACATA
28649041 AAC
1 AAC
28649044 CCCTCCTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 21 0.88
24 3 0.12
ACGTcount: A:0.39, C:0.27, G:0.00, T:0.35
Consensus pattern (23 bp):
AACTCTTAATTTAATCCCACATA
Found at i:28649338 original size:41 final size:41
Alignment explanation
Indices: 28649293--28649433 Score: 160
Period size: 41 Copynumber: 3.4 Consensus size: 41
28649283 GAGTCACTAT
28649293 AACTTTGAAAAATAAAATATTCTTCTAAACTA-AGGCATCAC
1 AACTTTGAAAAATAAAATATTCTTCTAAAC-AGAGGCATCAC
* * * * * *
28649334 AACTTTGAAAAATAAATTACTCCTCTAAACATAGGTACCAC
1 AACTTTGAAAAATAAAATATTCTTCTAAACAGAGGCATCAC
* * *
28649375 AACTTTTGAAAATTAAAATGCTTCTT-TAAACAGAGGCATAAC
1 AAC-TTTGAAAAATAAAAT-ATTCTTCTAAACAGAGGCATCAC
28649417 AACTTTGAAAAATAAAA
1 AACTTTGAAAAATAAAA
28649434 GGCTCATCGA
Statistics
Matches: 82, Mismatches: 15, Indels: 6
0.80 0.15 0.06
Matches are distributed among these distances:
40 1 0.01
41 50 0.61
42 28 0.34
43 3 0.04
ACGTcount: A:0.47, C:0.16, G:0.09, T:0.28
Consensus pattern (41 bp):
AACTTTGAAAAATAAAATATTCTTCTAAACAGAGGCATCAC
Found at i:28649905 original size:21 final size:21
Alignment explanation
Indices: 28649875--28649915 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
28649865 GATTTCACAC
*
28649875 CTCAAGGATTCTCATTTGAGA
1 CTCAAAGATTCTCATTTGAGA
*
28649896 CTCAAAGATTCTTATTTGAG
1 CTCAAAGATTCTCATTTGAG
28649916 GATTTCTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.37
Consensus pattern (21 bp):
CTCAAAGATTCTCATTTGAGA
Found at i:28649962 original size:10 final size:10
Alignment explanation
Indices: 28649947--28649977 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
28649937 TGAAAAACTT
28649947 AAAGATTCTC
1 AAAGATTCTC
*
28649957 AAAGATTCTT
1 AAAGATTCTC
28649967 AAAGATTCTC
1 AAAGATTCTC
28649977 A
1 A
28649978 TTTGAAATTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.42, C:0.16, G:0.10, T:0.32
Consensus pattern (10 bp):
AAAGATTCTC
Found at i:28650536 original size:79 final size:79
Alignment explanation
Indices: 28650451--28650617 Score: 176
Period size: 79 Copynumber: 2.1 Consensus size: 79
28650441 ATTAGTAATC
* * *
28650451 TCAAAATAAATTCTATCAGT-TGATTCAAATTATGTTCATCACTTGATCACCATTCACAGGCTTC
1 TCAAAATAAATTATATC-GTCTGATCCAAATTATGTTCATCACTTGATCACCAATCACAGGCTTC
*
28650515 TCAGCATTAACCA-T
65 TCAGCACTAACCATT
* * * * ** * * *
28650529 TCTAAAATGAATTATGTCTTCTGATCCACATTATGTTTGTCACTTGATTACCAATCATAGGTTTC
1 TC-AAAATAAATTATATCGTCTGATCCAAATTATGTTCATCACTTGATCACCAATCACAGGCTTC
*
28650594 TCAGTACTAACCATT
65 TCAGCACTAACCATT
28650609 TCAAAATAA
1 TCAAAATAA
28650618 GTTTCATCCT
Statistics
Matches: 71, Mismatches: 15, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
78 3 0.04
79 65 0.92
80 3 0.04
ACGTcount: A:0.33, C:0.21, G:0.10, T:0.37
Consensus pattern (79 bp):
TCAAAATAAATTATATCGTCTGATCCAAATTATGTTCATCACTTGATCACCAATCACAGGCTTCT
CAGCACTAACCATT
Found at i:28651336 original size:18 final size:18
Alignment explanation
Indices: 28651315--28651362 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
28651305 TAAGTCTTTT
*
28651315 TTTTCTCTTTTTTCCATC
1 TTTTCTATTTTTTCCATC
* * *
28651333 TTTTTTATTTTTTTCATG
1 TTTTCTATTTTTTCCATC
28651351 TTTTC-ATTTTTT
1 TTTTCTATTTTTT
28651363 TATTTTTTCT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
17 7 0.28
18 18 0.72
ACGTcount: A:0.08, C:0.15, G:0.02, T:0.75
Consensus pattern (18 bp):
TTTTCTATTTTTTCCATC
Found at i:28651354 original size:9 final size:8
Alignment explanation
Indices: 28651322--28651388 Score: 55
Period size: 8 Copynumber: 8.0 Consensus size: 8
28651312 TTTTTTTCTC
28651322 TTTTTTCCA
1 TTTTTT-CA
*
28651331 TCTTTTTTA
1 T-TTTTTCA
28651340 TTTTTTTCA
1 -TTTTTTCA
*
28651349 TGTTTTCA
1 TTTTTTCA
*
28651357 TTTTTTTA
1 TTTTTTCA
28651365 TTTTTTC-
1 TTTTTTCA
28651372 TTTCTTTCA
1 TTT-TTTCA
*
28651381 TTCTTTCA
1 TTTTTTCA
28651389 CCTATTATTG
Statistics
Matches: 47, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
7 3 0.06
8 28 0.60
9 10 0.21
10 6 0.13
ACGTcount: A:0.10, C:0.15, G:0.01, T:0.73
Consensus pattern (8 bp):
TTTTTTCA
Found at i:28657062 original size:24 final size:24
Alignment explanation
Indices: 28657024--28657077 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
28657014 TCTAACTTTT
28657024 AACTC-TAATTCTAATCCCACCTA
1 AACTCTTAATTCTAATCCCACCTA
* **
28657047 AACTCTTAATTTTAATCCCATTTA
1 AACTCTTAATTCTAATCCCACCTA
28657071 AACTCTT
1 AACTCTT
28657078 TTTATTTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 5 0.19
24 22 0.81
ACGTcount: A:0.33, C:0.28, G:0.00, T:0.39
Consensus pattern (24 bp):
AACTCTTAATTCTAATCCCACCTA
Found at i:28657699 original size:28 final size:27
Alignment explanation
Indices: 28657668--28657728 Score: 86
Period size: 27 Copynumber: 2.2 Consensus size: 27
28657658 TCCTTTCCTT
*
28657668 TTTTTTCTCTTTTTTTTTATTTTTGTAA
1 TTTTTTCTC-TTTTTTTAATTTTTGTAA
* *
28657696 TTTTTTCTCTTTTTTTAATTTTTTTAT
1 TTTTTTCTCTTTTTTTAATTTTTGTAA
28657723 TTTTTT
1 TTTTTT
28657729 TTGGGTACAC
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 21 0.70
28 9 0.30
ACGTcount: A:0.10, C:0.07, G:0.02, T:0.82
Consensus pattern (27 bp):
TTTTTTCTCTTTTTTTAATTTTTGTAA
Found at i:28657717 original size:9 final size:8
Alignment explanation
Indices: 28657679--28657728 Score: 55
Period size: 9 Copynumber: 5.9 Consensus size: 8
28657669 TTTTTCTCTT
28657679 TTTTTTTA
1 TTTTTTTA
*
28657687 TTTTTGTAA
1 TTTTT-TTA
*
28657696 TTTTTTCTC
1 TTTTTT-TA
28657705 TTTTTTTAA
1 TTTTTTT-A
28657714 TTTTTTTA
1 TTTTTTTA
28657722 TTTTTTT
1 TTTTTTT
28657729 TTGGGTACAC
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
8 15 0.43
9 20 0.57
ACGTcount: A:0.12, C:0.04, G:0.02, T:0.82
Consensus pattern (8 bp):
TTTTTTTA
Found at i:28657729 original size:18 final size:17
Alignment explanation
Indices: 28657679--28657728 Score: 73
Period size: 18 Copynumber: 2.9 Consensus size: 17
28657669 TTTTTCTCTT
*
28657679 TTTTTTTATTTTTGTAA
1 TTTTTTTATTTTTTTAA
*
28657696 TTTTTTCTCTTTTTTTAA
1 TTTTTT-TATTTTTTTAA
28657714 TTTTTTTATTTTTTT
1 TTTTTTTATTTTTTT
28657729 TTGGGTACAC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
17 14 0.48
18 15 0.52
ACGTcount: A:0.12, C:0.04, G:0.02, T:0.82
Consensus pattern (17 bp):
TTTTTTTATTTTTTTAA
Found at i:28662322 original size:16 final size:16
Alignment explanation
Indices: 28662292--28662321 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
28662282 TTGAAAATAT
28662292 TTTTTTTTATCTTTTA
1 TTTTTTTTATCTTTTA
28662308 TTTTTTTTAT-TTTT
1 TTTTTTTTATCTTTT
28662322 TTCTTTATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.10, C:0.03, G:0.00, T:0.87
Consensus pattern (16 bp):
TTTTTTTTATCTTTTA
Found at i:28662389 original size:20 final size:19
Alignment explanation
Indices: 28662366--28662433 Score: 64
Period size: 21 Copynumber: 3.4 Consensus size: 19
28662356 AGATTTTTTT
28662366 AAATAAAAATCAATAAAATTA
1 AAATAAAAATCAA-AAAA-TA
* * *
28662387 AATTAAAAAACTAAAAATA
1 AAATAAAAATCAAAAAATA
*
28662406 AAATAAAAACTTAAGAAAATA
1 AAATAAAAA-TCAA-AAAATA
28662427 AAATAAA
1 AAATAAA
28662434 TAAAATGAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
19 10 0.26
20 5 0.13
21 23 0.61
ACGTcount: A:0.74, C:0.04, G:0.01, T:0.21
Consensus pattern (19 bp):
AAATAAAAATCAAAAAATA
Found at i:28662458 original size:18 final size:18
Alignment explanation
Indices: 28662435--28662474 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
28662425 TAAAATAAAT
28662435 AAAATG-AAATCGAAAAAC
1 AAAATGAAAAT-GAAAAAC
*
28662453 AAAATGAAAATGAAAAAG
1 AAAATGAAAATGAAAAAC
28662471 AAAA
1 AAAA
28662475 AAACCTGTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.72, C:0.05, G:0.12, T:0.10
Consensus pattern (18 bp):
AAAATGAAAATGAAAAAC
Found at i:28662473 original size:24 final size:23
Alignment explanation
Indices: 28662431--28662475 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
28662421 AAAATAAAAT
**
28662431 AAATAAAATGAAATCGAAAAACA
1 AAATAAAATGAAAAAGAAAAACA
28662454 AAATGAAAATGAAAAAGAAAAA
1 AAAT-AAAATGAAAAAGAAAAA
28662476 AACCTGTGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.73, C:0.04, G:0.11, T:0.11
Consensus pattern (23 bp):
AAATAAAATGAAAAAGAAAAACA
Found at i:28667080 original size:18 final size:18
Alignment explanation
Indices: 28667057--28667091 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
28667047 GTACTTTTTT
*
28667057 AGTCTAATTATAAAAAAG
1 AGTCTAATAATAAAAAAG
28667075 AGTCTAATAATAAAAAA
1 AGTCTAATAATAAAAAA
28667092 AGTTCATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.60, C:0.06, G:0.09, T:0.26
Consensus pattern (18 bp):
AGTCTAATAATAAAAAAG
Found at i:28667914 original size:30 final size:30
Alignment explanation
Indices: 28667874--28667985 Score: 100
Period size: 30 Copynumber: 3.7 Consensus size: 30
28667864 TGTTTTTTTA
28667874 TTACACTCAAATAAATTATTAACTTTTAAT
1 TTACACTCAAATAAATTATTAACTTTTAAT
* * * *
28667904 TTACATTCAAATAAACTCTTAACATTT-AT
1 TTACACTCAAATAAATTATTAACTTTTAAT
* * * *
28667933 TATATACCCAAATAAATTTTTAATTTTTAAT
1 T-TACACTCAAATAAATTATTAACTTTTAAT
** * *
28667964 TTGTACTTAAATAAATTTTTAA
1 TTACACTCAAATAAATTATTAA
28667986 TAAAAATAAA
Statistics
Matches: 66, Mismatches: 14, Indels: 4
0.79 0.17 0.05
Matches are distributed among these distances:
29 3 0.05
30 60 0.91
31 3 0.05
ACGTcount: A:0.42, C:0.12, G:0.01, T:0.46
Consensus pattern (30 bp):
TTACACTCAAATAAATTATTAACTTTTAAT
Found at i:28670087 original size:27 final size:28
Alignment explanation
Indices: 28670056--28670110 Score: 94
Period size: 27 Copynumber: 2.0 Consensus size: 28
28670046 GTGTTGTTTG
*
28670056 AGAAAATATTTTTTA-TTTTTATTTTTT
1 AGAAAATAGTTTTTATTTTTTATTTTTT
28670083 AGAAAATAGTTTTTATTTTTTATTTTTT
1 AGAAAATAGTTTTTATTTTTTATTTTTT
28670111 GTTTAACAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 14 0.54
28 12 0.46
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.65
Consensus pattern (28 bp):
AGAAAATAGTTTTTATTTTTTATTTTTT
Found at i:28672059 original size:2 final size:2
Alignment explanation
Indices: 28672054--28672078 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
28672044 ACACACACAC
28672054 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
28672079 GAAGAAGAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:28673296 original size:42 final size:42
Alignment explanation
Indices: 28673250--28673331 Score: 110
Period size: 42 Copynumber: 2.0 Consensus size: 42
28673240 TACCAGATCT
* *
28673250 AACATCATTGTCATATATACTATACGGATCATTCCAAAAACA
1 AACATCATTGTCATACATACTATACAGATCATTCCAAAAACA
* * * *
28673292 AACATCGTTTTCATACGTACTATATAGATCATTCCAAAAA
1 AACATCATTGTCATACATACTATACAGATCATTCCAAAAA
28673332 TATTCATCAA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.41, C:0.21, G:0.07, T:0.30
Consensus pattern (42 bp):
AACATCATTGTCATACATACTATACAGATCATTCCAAAAACA
Found at i:28674973 original size:28 final size:28
Alignment explanation
Indices: 28674933--28675031 Score: 144
Period size: 28 Copynumber: 3.5 Consensus size: 28
28674923 GTATAATTAA
28674933 ATGTGTGTTAGTGGTTTATGGAAGTTAG
1 ATGTGTGTTAGTGGTTTATGGAAGTTAG
*
28674961 ATGTTTGTTAGTGGTTTATGGAAGTTAG
1 ATGTGTGTTAGTGGTTTATGGAAGTTAG
* *
28674989 ATGCGTGTTAGTGGTTTATGAAAGTTAG
1 ATGTGTGTTAGTGGTTTATGGAAGTTAG
* * *
28675017 TTGTGAGTAAGTGGT
1 ATGTGTGTTAGTGGT
28675032 ATTTGTTTAT
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 63 1.00
ACGTcount: A:0.22, C:0.01, G:0.34, T:0.42
Consensus pattern (28 bp):
ATGTGTGTTAGTGGTTTATGGAAGTTAG
Found at i:28677895 original size:21 final size:21
Alignment explanation
Indices: 28677870--28677909 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
28677860 ATTTAACTAA
*
28677870 GATGATGGATCAG-ACAAAATT
1 GATGAAGG-TCAGTACAAAATT
28677891 GATGAAGGTCAGTACAAAA
1 GATGAAGGTCAGTACAAAA
28677910 GTTTGATTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.45, C:0.10, G:0.25, T:0.20
Consensus pattern (21 bp):
GATGAAGGTCAGTACAAAATT
Found at i:28678699 original size:28 final size:28
Alignment explanation
Indices: 28678635--28678794 Score: 196
Period size: 28 Copynumber: 5.8 Consensus size: 28
28678625 TGATGAATAA
*
28678635 TTAGATGTGTGTTAGTGGTTTAT-CAAG
1 TTAGATGTGTGTTAGTGGTTTATGAAAG
*
28678662 TTAGATGTTTGTTAGTGGTTTATGAAAG
1 TTAGATGTGTGTTAGTGGTTTATGAAAG
* * * *
28678690 TTCGATGTTTTTTAGTGGTTTATGGAAG
1 TTAGATGTGTGTTAGTGGTTTATGAAAG
* *
28678718 TTAGATATGTGTTAGTGGGTTATGAAAG
1 TTAGATGTGTGTTAGTGGTTTATGAAAG
* * *
28678746 TTAGTTGGGTGTTAGTGGGTTATGAAAG
1 TTAGATGTGTGTTAGTGGTTTATGAAAG
* *
28678774 TTAGTTGTGTGTTAATGGTTT
1 TTAGATGTGTGTTAGTGGTTT
28678795 TTGTTTATGG
Statistics
Matches: 115, Mismatches: 17, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
27 22 0.19
28 93 0.81
ACGTcount: A:0.22, C:0.01, G:0.31, T:0.46
Consensus pattern (28 bp):
TTAGATGTGTGTTAGTGGTTTATGAAAG
Found at i:28684297 original size:42 final size:42
Alignment explanation
Indices: 28684235--28684318 Score: 125
Period size: 42 Copynumber: 2.0 Consensus size: 42
28684225 TGTCGGATCG
* *
28684235 AACATCGTTGTCATATGTACTATGTAAATCA-TTCTAAAAATA
1 AACATCGTTGTCATACGTACTATATAAATCATTTC-AAAAATA
*
28684277 AACATCGTTTTCATACGTACTATATAAATCATTTCAAAAATA
1 AACATCGTTGTCATACGTACTATATAAATCATTTCAAAAATA
28684319 TTCATCAAAC
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
42 35 0.92
43 3 0.08
ACGTcount: A:0.42, C:0.15, G:0.07, T:0.36
Consensus pattern (42 bp):
AACATCGTTGTCATACGTACTATATAAATCATTTCAAAAATA
Found at i:28690215 original size:18 final size:20
Alignment explanation
Indices: 28690192--28690230 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
28690182 CGGTGGAGGA
*
28690192 ATCGAAC-C-GAGTTTCGAG
1 ATCGAACACGGAGTTTAGAG
28690210 ATCGAACACGGAGTTTAGAG
1 ATCGAACACGGAGTTTAGAG
28690230 A
1 A
28690231 AGGATCCTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 7 0.39
19 1 0.06
20 10 0.56
ACGTcount: A:0.33, C:0.18, G:0.28, T:0.21
Consensus pattern (20 bp):
ATCGAACACGGAGTTTAGAG
Found at i:28694985 original size:21 final size:21
Alignment explanation
Indices: 28694954--28694995 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 21
28694944 GCAAAAAATT
28694954 TCTTAAATAAT-A-AAAAAAA
1 TCTTAAATAATCATAAAAAAA
28694973 TCTTATAAGTAATCATAAAAAAA
1 TCTTA-AA-TAATCATAAAAAAA
28694996 AAGGACTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
19 5 0.26
20 2 0.11
21 4 0.21
22 1 0.05
23 7 0.37
ACGTcount: A:0.62, C:0.07, G:0.02, T:0.29
Consensus pattern (21 bp):
TCTTAAATAATCATAAAAAAA
Found at i:28695320 original size:16 final size:16
Alignment explanation
Indices: 28695301--28695342 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
28695291 ATTATTTAAG
*
28695301 ATATTTTTTATTAAAA
1 ATATTATTTATTAAAA
28695317 ATATATATTT-TTAAAA
1 ATAT-TATTTATTAAAA
*
28695333 GTATTATTTA
1 ATATTATTTA
28695343 ATGTATTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 5 0.23
16 13 0.59
17 4 0.18
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (16 bp):
ATATTATTTATTAAAA
Found at i:28695509 original size:14 final size:14
Alignment explanation
Indices: 28695488--28695522 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
28695478 AGAAACCTCT
*
28695488 TAAATAATTTTTTA
1 TAAATAATATTTTA
*
28695502 TTAATAATATTTTA
1 TAAATAATATTTTA
28695516 TAAATAA
1 TAAATAA
28695523 AAATAACAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
TAAATAATATTTTA
Found at i:28697737 original size:13 final size:13
Alignment explanation
Indices: 28697699--28697737 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
28697689 GGTTTTACTT
*
28697699 TGCCTTCATCAGT
1 TGCCTTCATCAGC
28697712 TGCCTTCATCAGC
1 TGCCTTCATCAGC
28697725 TGCCTTCATCAGC
1 TGCCTTCATCAGC
28697738 ATGCATATAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.15, C:0.36, G:0.15, T:0.33
Consensus pattern (13 bp):
TGCCTTCATCAGC
Found at i:28698995 original size:252 final size:252
Alignment explanation
Indices: 28698550--28699020 Score: 680
Period size: 252 Copynumber: 1.9 Consensus size: 252
28698540 GAAATATAAG
* * * * *
28698550 TTTTGGTGTCAAATGTGTTTGGTTGGTGCGCATTCTGAGGTTGTAATGGAAGCTCATAAAAAGGG
1 TTTTGGTGTCAAATGTGTTTAGTTGGTGCACAATCTGAGGTGGTAATGGAAACTCATAAAAAGGG
* * *
28698615 GAAGAGGCATATTGCTCGACTCCTGGATCTTGACGAAAATAATGCAGCTGCCCCTGCTACCTCCA
66 GAAGAGGCACATTGCTCGACTCCTGGAACTTGACGAAAATAATGCAGCTGCCCCTGCTACCTCAA
* *
28698680 CCAACAATAAAGTCACTGAGCTGGCAAGATTTGATGGTAGTCAGATGCCAAAAGTCACTGATGTG
131 CCAACAATAAAGTCACTGAGCAGGCAAGATTAGATGGTAGTCAGATGCCAAAAGTCACTGATGTG
* **
28698745 GT-GGTCGATGAAGCAAATGAGAAGATAACGAATGCTCCAGGGTCTGTTAGTTCTAAA
196 GTAGCT-GACAAAGCAAATGAGAAGATAACGAATGCTCCAGGGTCTGTTAGTTCTAAA
* *
28698802 TTTTGGTGTCAAATGTGTTTATTTGGTGCACAATCTGAGGTGGTACTGGAAACTCATAAAAAGGG
1 TTTTGGTGTCAAATGTGTTTAGTTGGTGCACAATCTGAGGTGGTAATGGAAACTCATAAAAAGGG
* *
28698867 GAAGAGGCACATTGCTCGACTTCTGGAACTTGATGAAAATAGA-GCAGCTGCCCCTGCTACCTCA
66 GAAGAGGCACATTGCTCGACTCCTGGAACTTGACGAAAATA-ATGCAGCTGCCCCTGCTACCTCA
** * * *
28698931 ACCATTAATACAA-TCACTGAGCAGGCAAGATTAGATGG-CGTTCAGATGCCCAAAGTCGCTGAT
130 ACCAACAATA-AAGTCACTGAGCAGGCAAGATTAGATGGTAG-TCAGATGCCAAAAGTCACTGAT
28698994 GTGGTAGCTGACAAAGCAAATGAGAAG
193 GTGGTAGCTGACAAAGCAAATGAGAAG
28699021 CTAATGGATG
Statistics
Matches: 193, Mismatches: 22, Indels: 8
0.87 0.10 0.04
Matches are distributed among these distances:
251 1 0.01
252 187 0.97
253 5 0.03
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26
Consensus pattern (252 bp):
TTTTGGTGTCAAATGTGTTTAGTTGGTGCACAATCTGAGGTGGTAATGGAAACTCATAAAAAGGG
GAAGAGGCACATTGCTCGACTCCTGGAACTTGACGAAAATAATGCAGCTGCCCCTGCTACCTCAA
CCAACAATAAAGTCACTGAGCAGGCAAGATTAGATGGTAGTCAGATGCCAAAAGTCACTGATGTG
GTAGCTGACAAAGCAAATGAGAAGATAACGAATGCTCCAGGGTCTGTTAGTTCTAAA
Found at i:28713682 original size:2 final size:2
Alignment explanation
Indices: 28713666--28713709 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
28713656 CAAAGAAACA
*
28713666 AG AG A- AG AA AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
28713707 AG A
1 AG A
28713710 ATTGGAGGGG
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (2 bp):
AG
Found at i:28715683 original size:2 final size:2
Alignment explanation
Indices: 28715676--28715704 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
28715666 CAGGGGAACA
28715676 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
28715705 GGCTTTTGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:28730872 original size:13 final size:13
Alignment explanation
Indices: 28730854--28730880 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
28730844 ACTTACATGA
28730854 ATAATTTTTTTTT
1 ATAATTTTTTTTT
28730867 ATAATTTTTTTTT
1 ATAATTTTTTTTT
28730880 A
1 A
28730881 ACACTCGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (13 bp):
ATAATTTTTTTTT
Found at i:28732470 original size:24 final size:24
Alignment explanation
Indices: 28732436--28732482 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
28732426 TCAATTCTTT
28732436 CTTAAGATATTTCAATACTTTTTA
1 CTTAAGATATTTCAATACTTTTTA
* *
28732460 CTTAAGGTATTTCGATACTTTTT
1 CTTAAGATATTTCAATACTTTTT
28732483 TTATGATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.28, C:0.13, G:0.09, T:0.51
Consensus pattern (24 bp):
CTTAAGATATTTCAATACTTTTTA
Found at i:28738558 original size:19 final size:19
Alignment explanation
Indices: 28738536--28738598 Score: 56
Period size: 19 Copynumber: 3.2 Consensus size: 19
28738526 AGGAACAGAG
28738536 AAAGGAAACAAACATCATT
1 AAAGGAAACAAACATCATT
* **
28738555 AAAGGAAGGAACAAA-AACAGAG
1 AAAGG-A--AACAAACATCA-TT
28738577 AAAGGAAACAAACATCATT
1 AAAGGAAACAAACATCATT
28738596 AAA
1 AAA
28738599 AGAAGAAATA
Statistics
Matches: 33, Mismatches: 6, Indels: 10
0.67 0.12 0.20
Matches are distributed among these distances:
19 14 0.42
20 4 0.12
21 4 0.12
22 11 0.33
ACGTcount: A:0.62, C:0.13, G:0.16, T:0.10
Consensus pattern (19 bp):
AAAGGAAACAAACATCATT
Found at i:28764622 original size:14 final size:14
Alignment explanation
Indices: 28764603--28764654 Score: 54
Period size: 14 Copynumber: 3.7 Consensus size: 14
28764593 TAAATTTTAA
28764603 ATTTATTAAATAAT
1 ATTTATTAAATAAT
28764617 ATTTATTAAA-AAT
1 ATTTATTAAATAAT
* *
28764630 AATTATATAAATTA-
1 ATTTAT-TAAATAAT
28764644 ATTTAGTTAAA
1 ATTTA-TTAAA
28764655 CCAAATTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
13 8 0.25
14 22 0.69
15 2 0.06
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (14 bp):
ATTTATTAAATAAT
Found at i:28776614 original size:4 final size:4
Alignment explanation
Indices: 28776605--28776669 Score: 62
Period size: 4 Copynumber: 16.8 Consensus size: 4
28776595 TATTGGCCAT
* * * * * *
28776605 ATAC ATAC ATGC ATGC ATGC ATAC ATAC ATGC ATAC ATAT ATAT ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
28776653 AT-- ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATA
28776670 TATATATATA
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
2 2 0.04
4 51 0.96
ACGTcount: A:0.45, C:0.20, G:0.06, T:0.29
Consensus pattern (4 bp):
ATAC
Found at i:28776648 original size:2 final size:2
Alignment explanation
Indices: 28776641--28776683 Score: 50
Period size: 2 Copynumber: 21.5 Consensus size: 2
28776631 ACATGCATAC
* * * *
28776641 AT AT AT AT AT AC AT AT AC AT AC AT AC AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28776683 A
1 A
28776684 GATGTATAAT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (2 bp):
AT
Found at i:28776661 original size:30 final size:30
Alignment explanation
Indices: 28776625--28776681 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
28776615 GCATGCATGC
*
28776625 ATACATACATGCATACATATATATATACAT
1 ATACATACATACATACATATATATATACAT
*
28776655 ATACATACATACATATATATATATATA
1 ATACATACATACATACATATATATATA
28776682 TAGATGTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.49, C:0.14, G:0.02, T:0.35
Consensus pattern (30 bp):
ATACATACATACATACATATATATATACAT
Found at i:28776664 original size:22 final size:22
Alignment explanation
Indices: 28776636--28776679 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
28776626 TACATACATG
*
28776636 CATACATATATATATACATATA
1 CATACATACATATATACATATA
*
28776658 CATACATACATATATATATATA
1 CATACATACATATATACATATA
28776680 TATAGATGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.50, C:0.14, G:0.00, T:0.36
Consensus pattern (22 bp):
CATACATACATATATACATATA
Found at i:28776665 original size:26 final size:26
Alignment explanation
Indices: 28776629--28776683 Score: 92
Period size: 26 Copynumber: 2.1 Consensus size: 26
28776619 GCATGCATAC
*
28776629 ATACATGCATACATATATATATACAT
1 ATACATACATACATATATATATACAT
*
28776655 ATACATACATACATATATATATATAT
1 ATACATACATACATATATATATACAT
28776681 ATA
1 ATA
28776684 GATGTATAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.49, C:0.13, G:0.02, T:0.36
Consensus pattern (26 bp):
ATACATACATACATATATATATACAT
Found at i:28786011 original size:30 final size:31
Alignment explanation
Indices: 28785970--28786028 Score: 102
Period size: 30 Copynumber: 1.9 Consensus size: 31
28785960 AGACTGCTGT
*
28785970 AACCTTTTAGTATTAATTGTCATCAAACTGG
1 AACCTTTTAGTATTAATTGTCATAAAACTGG
28786001 AACC-TTTAGTATTAATTGTCATAAAACT
1 AACCTTTTAGTATTAATTGTCATAAAACT
28786029 CCATGGCACG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 23 0.85
31 4 0.15
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.39
Consensus pattern (31 bp):
AACCTTTTAGTATTAATTGTCATAAAACTGG
Found at i:28787974 original size:50 final size:50
Alignment explanation
Indices: 28787899--28787994 Score: 156
Period size: 50 Copynumber: 1.9 Consensus size: 50
28787889 GAGACCAAAG
28787899 GCCTCATTGGCTACTCGTGCAATGCTAAGATACAATAAGAATTTTAGAAT
1 GCCTCATTGGCTACTCGTGCAATGCTAAGATACAATAAGAATTTTAGAAT
* * * *
28787949 GCCTCATTGGCTACTTGTGTAATGCTAAGATACACTATGAATTTTA
1 GCCTCATTGGCTACTCGTGCAATGCTAAGATACAATAAGAATTTTA
28787995 ATCCTTGATT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 42 1.00
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (50 bp):
GCCTCATTGGCTACTCGTGCAATGCTAAGATACAATAAGAATTTTAGAAT
Found at i:28788139 original size:50 final size:50
Alignment explanation
Indices: 28788060--28788160 Score: 193
Period size: 50 Copynumber: 2.0 Consensus size: 50
28788050 ACCATGCATA
28788060 ATAAGCAAGGGGAAACTGGGAGACAAGAAGCATTTGATGTGTCACTCAAC
1 ATAAGCAAGGGGAAACTGGGAGACAAGAAGCATTTGATGTGTCACTCAAC
*
28788110 ATAAGCAAGGGGAAACTGGGAGACGAGAAGCATTTGATGTGTCACTCAAC
1 ATAAGCAAGGGGAAACTGGGAGACAAGAAGCATTTGATGTGTCACTCAAC
28788160 A
1 A
28788161 CAATATTTCA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.38, C:0.16, G:0.29, T:0.18
Consensus pattern (50 bp):
ATAAGCAAGGGGAAACTGGGAGACAAGAAGCATTTGATGTGTCACTCAAC
Found at i:28788453 original size:50 final size:50
Alignment explanation
Indices: 28788378--28788474 Score: 158
Period size: 50 Copynumber: 1.9 Consensus size: 50
28788368 AGGACCAAAG
28788378 GCCTCATTGGCTACTCGTGCAATGCTAAGATACAATAAGAATTTTAAAAT
1 GCCTCATTGGCTACTCGTGCAATGCTAAGATACAATAAGAATTTTAAAAT
* * * *
28788428 GCCTCATTGGCTACTTGTGTAATGCTAAGATACACTATGAATTTTAA
1 GCCTCATTGGCTACTCGTGCAATGCTAAGATACAATAAGAATTTTAA
28788475 TCCTTGATTA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 43 1.00
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (50 bp):
GCCTCATTGGCTACTCGTGCAATGCTAAGATACAATAAGAATTTTAAAAT
Found at i:28789253 original size:6 final size:6
Alignment explanation
Indices: 28789239--28789311 Score: 65
Period size: 6 Copynumber: 11.7 Consensus size: 6
28789229 CGACTCACTC
* * * * *
28789239 CTTCTT CTTCCT CTTCCT CTTCCT CCTCCACCT CGTCCT CGTCCT CTTCTT
1 CTTCCT CTTCCT CTTCCT CTTCCT -CT--TCCT CTTCCT CTTCCT CTTCCT
*
28789290 CTTCCT CTTCCT CCTCCT CTTC
1 CTTCCT CTTCCT CTTCCT CTTC
28789312 TCCTTCTAAA
Statistics
Matches: 55, Mismatches: 9, Indels: 6
0.79 0.13 0.09
Matches are distributed among these distances:
6 49 0.89
7 2 0.04
8 1 0.02
9 3 0.05
ACGTcount: A:0.01, C:0.51, G:0.03, T:0.45
Consensus pattern (6 bp):
CTTCCT
Found at i:28796716 original size:22 final size:24
Alignment explanation
Indices: 28796691--28796749 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 24
28796681 TTTTTATTTT
28796691 TATTTTTATTATTTAATATA-T-A
1 TATTTTTATTATTTAATATATTAA
* *
28796713 TA-TTTTATT-TTTCATCTATTAA
1 TATTTTTATTATTTAATATATTAA
28796735 TATTTTTATTATTTA
1 TATTTTTATTATTTA
28796750 TCTACTTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
20 7 0.23
21 8 0.27
22 5 0.17
23 7 0.23
24 3 0.10
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (24 bp):
TATTTTTATTATTTAATATATTAA
Found at i:28796744 original size:28 final size:27
Alignment explanation
Indices: 28796681--28796744 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 27
28796671 CCTCAATAGG
28796681 TTTTTATTTTTATTTTTATTATTTAATA
1 TTTTTA-TTTTATTTTTATTATTTAATA
* *
28796709 TATATATTTTATTTTTCATCTA-TTAATA
1 TTTTTATTTTATTTTT-AT-TATTTAATA
28796737 TTTTTATT
1 TTTTTATT
28796745 ATTTATCTAC
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
27 10 0.33
28 18 0.60
29 2 0.07
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (27 bp):
TTTTTATTTTATTTTTATTATTTAATA
Found at i:28796778 original size:27 final size:26
Alignment explanation
Indices: 28796735--28796793 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 26
28796725 CATCTATTAA
*
28796735 TATTT-TTATTATTTATCTACTTTTATT
1 TATTTATTATTACTTATCTA-TTTT-TT
28796762 T-TTTATTATTACTTATCTATTTTTT
1 TATTTATTATTACTTATCTATTTTTT
28796787 TATTTAT
1 TATTTAT
28796794 CTAATTATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
25 3 0.10
26 12 0.41
27 14 0.48
ACGTcount: A:0.22, C:0.07, G:0.00, T:0.71
Consensus pattern (26 bp):
TATTTATTATTACTTATCTATTTTTT
Found at i:28796801 original size:24 final size:23
Alignment explanation
Indices: 28796684--28796839 Score: 94
Period size: 24 Copynumber: 6.7 Consensus size: 23
28796674 CAATAGGTTT
* *
28796684 TTATTTTTATTTTTA-TTATTTAA
1 TTATTATT-TTTTTATTTATCTAA
*
28796707 TATATATATTTTATTT-TTCATCT-A
1 T-TAT-TATTTT-TTTATTTATCTAA
* *
28796731 TTAATATTTTTATTATTTATCTAC
1 TTATTATTTTT-TTATTTATCTAA
*
28796755 TT-TTA-TTTTTTA-TTAT-TAC
1 TTATTATTTTTTTATTTATCTAA
28796774 TTATCTATTTTTTTATTTATCTAA
1 TTAT-TATTTTTTTATTTATCTAA
* *
28796798 TTATTTTTTTTGTTATCTAT-TAA
1 TTATTATTTTT-TTATTTATCTAA
*
28796821 TATATTTATCTTTTTATTT
1 T-TA-TTATTTTTTTATTT
28796840 TGATTAATTT
Statistics
Matches: 105, Mismatches: 13, Indels: 29
0.71 0.09 0.20
Matches are distributed among these distances:
19 5 0.05
20 5 0.05
21 6 0.06
22 19 0.18
23 25 0.24
24 29 0.28
25 16 0.15
ACGTcount: A:0.25, C:0.06, G:0.01, T:0.69
Consensus pattern (23 bp):
TTATTATTTTTTTATTTATCTAA
Found at i:28796802 original size:20 final size:20
Alignment explanation
Indices: 28796735--28796816 Score: 69
Period size: 20 Copynumber: 3.9 Consensus size: 20
28796725 CATCTATTAA
*
28796735 TATTTTTATTATTTATCTACT
1 TATTTTT-TTATTTATCTAAT
* *
28796756 TTTATTTTTTA-TTATTACTTAT
1 TAT-TTTTTTATTTA-T-CTAAT
28796778 CTATTTTTTTATTTATCTAAT
1 -TATTTTTTTATTTATCTAAT
28796799 TATTTTTTT-TGTTATCTA
1 TATTTTTTTAT-TTATCTA
28796817 TTAATATATT
Statistics
Matches: 50, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
19 1 0.02
20 19 0.38
21 10 0.20
22 15 0.30
23 5 0.10
ACGTcount: A:0.22, C:0.07, G:0.01, T:0.70
Consensus pattern (20 bp):
TATTTTTTTATTTATCTAAT
Found at i:28797248 original size:5 final size:5
Alignment explanation
Indices: 28797225--28797313 Score: 76
Period size: 5 Copynumber: 16.8 Consensus size: 5
28797215 TTTAATATTC
*
28797225 TTTTA CTTTTA TCTTTA TTTTA TTTTTA TTTTA CTTTT- CTTTA TTTTTAA
1 TTTTA -TTTTA T-TTTA TTTTA -TTTTA TTTTA -TTTTA TTTTA -TTTT-A
28797275 TTTTA TTTTCA CTTTTA TTTTA TTTTA --TTA TTTTA TTTT
1 TTTTA TTTT-A -TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
28797314 CTTTAAATAA
Statistics
Matches: 71, Mismatches: 2, Indels: 21
0.76 0.02 0.22
Matches are distributed among these distances:
3 3 0.04
4 3 0.04
5 32 0.45
6 28 0.39
7 5 0.07
ACGTcount: A:0.18, C:0.07, G:0.00, T:0.75
Consensus pattern (5 bp):
TTTTA
Found at i:28797250 original size:22 final size:20
Alignment explanation
Indices: 28797238--28797313 Score: 77
Period size: 22 Copynumber: 3.6 Consensus size: 20
28797228 TACTTTTATC
28797238 TTTATTTTATTTTTATTTTA
1 TTTATTTTATTTTTATTTTA
28797258 CTTT-TCTTTATTTTTAATTTTA
1 -TTTAT-TTTATTTTT-ATTTTA
28797280 TTTTCACTTTTA-TTTTATTTTA
1 -TTT-A-TTTTATTTTTATTTTA
28797302 -TTATTTTATTTT
1 TTTATTTTATTTT
28797314 CTTTAAATAA
Statistics
Matches: 48, Mismatches: 1, Indels: 14
0.76 0.02 0.22
Matches are distributed among these distances:
18 5 0.10
19 4 0.08
20 3 0.06
21 12 0.25
22 15 0.31
23 4 0.08
24 4 0.08
25 1 0.02
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.76
Consensus pattern (20 bp):
TTTATTTTATTTTTATTTTA
Found at i:28797318 original size:17 final size:17
Alignment explanation
Indices: 28797233--28797318 Score: 79
Period size: 17 Copynumber: 5.0 Consensus size: 17
28797223 TCTTTTACTT
28797233 TTATCTTTATTTTATTT-
1 TTAT-TTTATTTTATTTA
*
28797250 TTATTTTACTTTTCTTTA
1 TTATTTTA-TTTTATTTA
*
28797268 TT-TTTAATTTTATTT-
1 TTATTTTATTTTATTTA
*
28797283 TCACTTTTATTTTATTTTA
1 TTA-TTTTATTTTA-TTTA
*
28797302 TTATTTTATTTTCTTTA
1 TTATTTTATTTTATTTA
28797319 AATAAAATCT
Statistics
Matches: 56, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
15 1 0.02
16 11 0.20
17 28 0.50
18 14 0.25
19 2 0.04
ACGTcount: A:0.19, C:0.07, G:0.00, T:0.74
Consensus pattern (17 bp):
TTATTTTATTTTATTTA
Found at i:28797318 original size:22 final size:24
Alignment explanation
Indices: 28797225--28797318 Score: 84
Period size: 27 Copynumber: 3.6 Consensus size: 24
28797215 TTTAATATTC
28797225 TTTTACTTTTATCTTTATTTTATTTTTA
1 TTTTAC-TTT-TCTTTATTTTA--TTTA
28797253 TTTTACTTTTCTTTATTTTTAATTTTA
1 TTTTACTTTTCTTTA-TTTT-A-TTTA
*
28797280 TTTTCACTTTTATTTTATTTTA-TTA
1 TTTT-ACTTTT-CTTTATTTTATTTA
28797305 TTTTA-TTTTCTTTA
1 TTTTACTTTTCTTTA
28797319 AATAAAATCT
Statistics
Matches: 60, Mismatches: 2, Indels: 14
0.79 0.03 0.18
Matches are distributed among these distances:
22 4 0.07
23 4 0.07
24 1 0.02
25 7 0.12
26 6 0.10
27 17 0.28
28 17 0.28
29 4 0.07
ACGTcount: A:0.18, C:0.07, G:0.00, T:0.74
Consensus pattern (24 bp):
TTTTACTTTTCTTTATTTTATTTA
Found at i:28797485 original size:60 final size:60
Alignment explanation
Indices: 28797339--28797552 Score: 310
Period size: 60 Copynumber: 3.6 Consensus size: 60
28797329 AAAAAAAATA
* * * * *
28797339 TTTTTGAAAAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAACTTTTCAAAAAA-A-TA
1 TTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAA-TTTTTAAAAAAGATTT
28797398 TTTTT-AGAAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTTAAAAAAGATTT
1 TTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTTAAAAAAGATTT
*
28797457 TTTTTGAGAAAAAGTTGAAAGTATCAA-TTTTCTTTAAAAATAAATTTTTAAAAAAGGTTT
1 TTTTTGAGAAAAAGTTGAAAGTATCAATTTTTC-TTAAAAATAAATTTTTAAAAAAGATTT
* *
28797517 TTTTTAAGAAAAAATTGAAAGTATCAATTTTTCTTA
1 TTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTA
28797553 CACAAAAGCA
Statistics
Matches: 142, Mismatches: 8, Indels: 9
0.89 0.05 0.06
Matches are distributed among these distances:
57 10 0.07
58 36 0.25
59 16 0.11
60 75 0.53
61 5 0.04
ACGTcount: A:0.45, C:0.05, G:0.09, T:0.41
Consensus pattern (60 bp):
TTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTTAAAAAAGATTT
Found at i:28801106 original size:14 final size:15
Alignment explanation
Indices: 28801083--28801115 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
28801073 AAAAGGTCTC
*
28801083 AAAAATGAAAAA-AA
1 AAAAAAGAAAAAGAA
28801097 AAAAAAGAAAAAGAA
1 AAAAAAGAAAAAGAA
28801112 AAAA
1 AAAA
28801116 TAAATGTCAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.88, C:0.00, G:0.09, T:0.03
Consensus pattern (15 bp):
AAAAAAGAAAAAGAA
Found at i:28801284 original size:18 final size:18
Alignment explanation
Indices: 28801263--28801301 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
28801253 GTTTTGAGCC
28801263 TATTATATCTATTTCTTT
1 TATTATATCTATTTCTTT
28801281 TATTATATCTATTTCTTT
1 TATTATATCTATTTCTTT
28801299 TAT
1 TAT
28801302 GACCCCTCAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.23, C:0.10, G:0.00, T:0.67
Consensus pattern (18 bp):
TATTATATCTATTTCTTT
Found at i:28801514 original size:8 final size:8
Alignment explanation
Indices: 28801501--28801578 Score: 79
Period size: 8 Copynumber: 9.6 Consensus size: 8
28801491 GAAGATGATG
28801501 AAAAATGA
1 AAAAATGA
28801509 AAAAATGA
1 AAAAATGA
28801517 AAAAATGAA
1 AAAAATG-A
28801526 AAAAATAGA
1 AAAAAT-GA
*
28801535 GAAAA--A
1 AAAAATGA
* *
28801541 AAGAAGGAA
1 AAAAATG-A
*
28801550 AAAAAAGA
1 AAAAATGA
28801558 AAAAATGA
1 AAAAATGA
28801566 AAAAATGA
1 AAAAATGA
28801574 AAAAA
1 AAAAA
28801579 AATTTAAATT
Statistics
Matches: 59, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
6 4 0.07
8 36 0.61
9 18 0.31
10 1 0.02
ACGTcount: A:0.78, C:0.00, G:0.14, T:0.08
Consensus pattern (8 bp):
AAAAATGA
Found at i:28802720 original size:22 final size:22
Alignment explanation
Indices: 28802695--28802744 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
28802685 ATTTTGATTT
*
28802695 TTTGAGAACTC-AAATGAGAATC
1 TTTGAG-ACTCAAAATGAAAATC
**
28802717 TTTGAGTTTCAAAATGAAAATC
1 TTTGAGACTCAAAATGAAAATC
28802739 TTTGAG
1 TTTGAG
28802745 GAGTAAAACC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 2 0.08
22 22 0.92
ACGTcount: A:0.38, C:0.10, G:0.18, T:0.34
Consensus pattern (22 bp):
TTTGAGACTCAAAATGAAAATC
Found at i:28803617 original size:43 final size:41
Alignment explanation
Indices: 28803306--28803678 Score: 315
Period size: 41 Copynumber: 9.0 Consensus size: 41
28803296 TCAAGGAGTA
* * *
28803306 ATTTACTTTTCAAAGTTTCGTT--GCCTCTGTTTAGAGGAGCA
1 ATTTATTTTTCAAAG--TCGTTGAGCCTCTGATTAGAGGAGCC
* * *
28803347 ATTTATTTTTCAAAGTCGTGGTGCCTCT-ATTTAGAGGAGCA
1 ATTTATTTTTCAAAGTCGTTGAGCCTCTGA-TTAGAGGAGCC
* ** * * *
28803388 ATTTACTTTTCAAAGTTATGGTGCCTCTGTTTAGAGGAG-C
1 ATTTATTTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAGCC
* * * * * * * * ***
28803428 ATTTATTTTT-GAAGTCATGGTGCTTTTGCTTAGAGAATTT
1 ATTTATTTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAGCC
* *
28803468 ATTTATTTTTCAAAGTCATTGAGCCTTTGATTAGAGGAGCC
1 ATTTATTTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAGCC
* *
28803509 ATTTACTTTTCAAAGTTGTTGAGCCTCTGATTAGAGGAGCC
1 ATTTATTTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAGCC
*
28803550 ATTTATTTTTTCAAAGTCGTTGAGCCTTTGATTAGAGGAGCC
1 ATTTA-TTTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAGCC
* * *
28803592 TTGTTTATTTTTCAAAATCGTTGAGCCTCTGATTAGAGGAGCTTT
1 --ATTTATTTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAGC--C
* * *
28803637 GTTTATGTTTCTCAAAGTCGTTAAGCCTCTGCTTAGAGGAGC
1 ATTTAT-TTT-TCAAAGTCGTTGAGCCTCTGATTAGAGGAGC
28803679 TTTGATCAAA
Statistics
Matches: 279, Mismatches: 40, Indels: 22
0.82 0.12 0.06
Matches are distributed among these distances:
39 25 0.09
40 19 0.07
41 128 0.46
42 33 0.12
43 39 0.14
44 7 0.03
45 28 0.10
ACGTcount: A:0.23, C:0.15, G:0.21, T:0.41
Consensus pattern (41 bp):
ATTTATTTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAGCC
Found at i:28803734 original size:16 final size:16
Alignment explanation
Indices: 28803694--28803727 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
28803684 TCAAAATTTT
28803694 AACAAAAAAAAAAGAA
1 AACAAAAAAAAAAGAA
*
28803710 AACAAAAAAAAAATAA
1 AACAAAAAAAAAAGAA
28803726 AA
1 AA
28803728 ATAAAAACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.88, C:0.06, G:0.03, T:0.03
Consensus pattern (16 bp):
AACAAAAAAAAAAGAA
Found at i:28803967 original size:22 final size:23
Alignment explanation
Indices: 28803942--28804000 Score: 61
Period size: 22 Copynumber: 2.6 Consensus size: 23
28803932 TTTTTATTTT
28803942 TATTTTCATTATTTAATATA-T-A
1 TATTTT-ATTATTTAATATATTAA
* *
28803964 TATTTTATT-TTTCATCTATTAA
1 TATTTTATTATTTAATATATTAA
28803986 TATTTTTATTATTTA
1 TA-TTTTATTATTTA
28804001 TCTATTTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
20 7 0.23
21 4 0.13
22 9 0.30
23 7 0.23
24 3 0.10
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (23 bp):
TATTTTATTATTTAATATATTAA
Found at i:28803995 original size:23 final size:23
Alignment explanation
Indices: 28803961--28804076 Score: 72
Period size: 21 Copynumber: 5.2 Consensus size: 23
28803951 TATTTAATAT
28803961 ATATATTTTATT-TTTCATCTATTA
1 ATAT-TTTTATTATTT-ATCTATTA
*
28803985 ATATTTTTATTATTTATCTATTT
1 ATATTTTTATTATTTATCTATTA
*
28804008 TTATTTTTTATTA-TTA-CTTATCT-
1 ATA-TTTTTATTATTTATC-TAT-TA
*
28804031 AT-TTCTT-TTATTTATCTAATT-
1 ATATTTTTATTATTTATCT-ATTA
28804052 AT-TTTTT-TT-TGTTATCTATTA
1 ATATTTTTATTAT-TTATCTATTA
28804073 ATAT
1 ATAT
28804077 ATTTGTCTTT
Statistics
Matches: 77, Mismatches: 5, Indels: 22
0.74 0.05 0.21
Matches are distributed among these distances:
20 7 0.09
21 25 0.32
22 5 0.06
23 23 0.30
24 17 0.22
ACGTcount: A:0.25, C:0.07, G:0.01, T:0.67
Consensus pattern (23 bp):
ATATTTTTATTATTTATCTATTA
Found at i:28803995 original size:28 final size:28
Alignment explanation
Indices: 28803932--28804001 Score: 81
Period size: 28 Copynumber: 2.5 Consensus size: 28
28803922 CCCTGATGGG
28803932 TTTTTATTTTTATTTTCATTATTTAATA
1 TTTTTATTTTTATTTTCATTATTTAATA
* *
28803960 TATATA-TTTTATTTTTCATCTA-TTAATA
1 TTTTTATTTTTA-TTTTCAT-TATTTAATA
28803988 TTTTTATTATTTAT
1 TTTTTATT-TTTAT
28804002 CTATTTTTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
27 5 0.15
28 21 0.62
29 4 0.12
30 4 0.12
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (28 bp):
TTTTTATTTTTATTTTCATTATTTAATA
Found at i:28804006 original size:17 final size:16
Alignment explanation
Indices: 28803935--28804022 Score: 65
Period size: 17 Copynumber: 5.3 Consensus size: 16
28803925 TGATGGGTTT
*
28803935 TTATTTTTATT-TTCA
1 TTATTTTTATTATTTA
*
28803950 TTATTTAATATATATATT-
1 TTATTT-TTAT-TAT-TTA
28803968 TTATTTTTCATCTA-TTA
1 TTATTTTT-AT-TATTTA
*
28803985 ATATTTTTATTATTTA
1 TTATTTTTATTATTTA
*
28804001 TCTATTTTTATTTTTTA
1 T-TATTTTTATTATTTA
28804018 TTATT
1 TTATT
28804023 ACTTATCTAT
Statistics
Matches: 58, Mismatches: 7, Indels: 15
0.73 0.09 0.19
Matches are distributed among these distances:
15 8 0.14
16 14 0.24
17 24 0.41
18 11 0.19
19 1 0.02
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.69
Consensus pattern (16 bp):
TTATTTTTATTATTTA
Found at i:28804020 original size:24 final size:24
Alignment explanation
Indices: 28803961--28804022 Score: 74
Period size: 24 Copynumber: 2.6 Consensus size: 24
28803951 TATTTAATAT
28803961 ATATATTTTATT-TTTCATCTATTA
1 ATAT-TTTTATTATTTCATCTATTA
*
28803985 ATATTTTTATTATTT-ATCTATTT
1 ATATTTTTATTATTTCATCTATTA
*
28804008 TTATTTTTTATTATT
1 ATA-TTTTTATTATT
28804023 ACTTATCTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
23 16 0.47
24 18 0.53
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.69
Consensus pattern (24 bp):
ATATTTTTATTATTTCATCTATTA
Found at i:28804494 original size:17 final size:17
Alignment explanation
Indices: 28804474--28804552 Score: 83
Period size: 17 Copynumber: 4.6 Consensus size: 17
28804464 TTTAATATTC
*
28804474 TTTTACTTTTATCTTTA
1 TTTTACTTTTATTTTTA
*
28804491 TTTTATTTTTATTTTTA
1 TTTTACTTTTATTTTTA
28804508 TTTTACTTTT-TTTTTCA
1 TTTTACTTTTATTTTT-A
28804525 CTTTTA-TTTTATTTTATTA
1 -TTTTACTTTTA-TTT-TTA
28804544 TTTTA-TTTT
1 TTTTACTTTT
28804553 CTTTAAATAA
Statistics
Matches: 54, Mismatches: 3, Indels: 9
0.82 0.05 0.14
Matches are distributed among these distances:
16 5 0.09
17 29 0.54
18 14 0.26
19 4 0.07
20 2 0.04
ACGTcount: A:0.16, C:0.06, G:0.00, T:0.77
Consensus pattern (17 bp):
TTTTACTTTTATTTTTA
Found at i:28804497 original size:5 final size:5
Alignment explanation
Indices: 28804474--28804552 Score: 72
Period size: 5 Copynumber: 14.8 Consensus size: 5
28804464 TTTAATATTC
*
28804474 TTTTA CTTTTA TCTTTA TTTTA TTTTTA TTTTTA TTTTA CTTTTT TTTTCA
1 TTTTA -TTTTA T-TTTA TTTTA -TTTTA -TTTTA TTTTA -TTTTA TTTT-A
28804525 CTTTTA TTTTA TTTTA --TTA TTTTA TTTT
1 -TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
28804553 CTTTAAATAA
Statistics
Matches: 64, Mismatches: 2, Indels: 15
0.79 0.02 0.19
Matches are distributed among these distances:
3 3 0.05
5 31 0.48
6 26 0.41
7 4 0.06
ACGTcount: A:0.16, C:0.06, G:0.00, T:0.77
Consensus pattern (5 bp):
TTTTA
Found at i:28804500 original size:23 final size:22
Alignment explanation
Indices: 28804474--28804542 Score: 95
Period size: 23 Copynumber: 3.0 Consensus size: 22
28804464 TTTAATATTC
28804474 TTTTACTTTTATCTTTATTTTAT
1 TTTTACTTTTAT-TTTATTTTAT
*
28804497 TTTTATTTTTATTTTACTTTT-T
1 TTTTACTTTTATTTTA-TTTTAT
28804519 TTTTCACTTTTATTTTATTTTAT
1 TTTT-ACTTTTATTTTATTTTAT
28804542 T
1 T
28804543 ATTTTATTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
22 13 0.32
23 28 0.68
ACGTcount: A:0.16, C:0.07, G:0.00, T:0.77
Consensus pattern (22 bp):
TTTTACTTTTATTTTATTTTAT
Found at i:28804544 original size:13 final size:13
Alignment explanation
Indices: 28804528--28804552 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28804518 TTTTTCACTT
28804528 TTATTTTATTTTA
1 TTATTTTATTTTA
28804541 TTATTTTATTTT
1 TTATTTTATTTT
28804553 CTTTAAATAA
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:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (13 bp):
TTATTTTATTTTA
Found at i:28804547 original size:18 final size:16
Alignment explanation
Indices: 28804487--28804552 Score: 78
Period size: 18 Copynumber: 3.8 Consensus size: 16
28804477 TACTTTTATC
28804487 TTTATTTTATTTTTATT
1 TTTATTTTATTTTT-TT
28804504 TTTATTTTACTTTTTTT
1 TTTATTTTA-TTTTTTT
*
28804521 TTCACTTTTATTTTATTT
1 TTTA-TTTTATTTT-TTT
28804539 TATTATTTTATTTT
1 T-TTATTTTATTTT
28804553 CTTTAAATAA
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
17 18 0.42
18 23 0.53
19 2 0.05
ACGTcount: A:0.17, C:0.05, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTATTTTATTTTTTT
Found at i:28804552 original size:23 final size:23
Alignment explanation
Indices: 28804469--28804552 Score: 93
Period size: 23 Copynumber: 3.6 Consensus size: 23
28804459 ATTTGTTTAA
28804469 TATTCTTTTACTTTTATCTTTATTT
1 TATT-TTTTACTTTTAT-TTTATTT
*
28804494 TA-TTTTTATTTTTATTTTACTTT
1 TATTTTTTACTTTTATTTTA-TTT
*
28804517 T-TTTTTCACTTTTATTTTATTT
1 TATTTTTTACTTTTATTTTATTT
28804539 TATTATTTTA-TTTT
1 TATT-TTTTACTTTT
28804553 CTTTAAATAA
Statistics
Matches: 51, Mismatches: 4, Indels: 10
0.78 0.06 0.15
Matches are distributed among these distances:
22 8 0.16
23 36 0.71
24 5 0.10
25 2 0.04
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.76
Consensus pattern (23 bp):
TATTTTTTACTTTTATTTTATTT
Found at i:28804719 original size:58 final size:58
Alignment explanation
Indices: 28804557--28804729 Score: 165
Period size: 58 Copynumber: 2.9 Consensus size: 58
28804547 TATTTTCTTT
*
28804557 AAATAAAA-TCCAAAAAAATTATTTTTAGAGAAAAGTTGAAAGTATCAATTTTTTAAGCCTTAA
1 AAATAAAATTTCAAAAAAA-TATTTTT-GAGAAAAGTTGAAAGTATCAATTTTTT-A--C-TAA
* * * * *
28804620 AAATAAATTTTCAAAAAAA-AGTTTTAAGGAAAAGTTTAAAGTATCAATTTTCTT-C-GA
1 AAATAAAATTTCAAAAAAATATTTTTGA-GAAAAGTTGAAAGTATCAATTTT-TTACTAA
* *
28804677 AATTAAAATTTCTAAAAAAATATTTTTGAGAATAGTTGAAAGTATCAATTTTT
1 AAATAAAATTTC-AAAAAAATATTTTTGAGAAAAGTTGAAAGTATCAATTTTT
28804730 CTGCACAAAA
Statistics
Matches: 93, Mismatches: 12, Indels: 16
0.77 0.10 0.13
Matches are distributed among these distances:
57 12 0.13
58 28 0.30
59 7 0.08
61 1 0.01
62 27 0.29
63 9 0.10
64 9 0.10
ACGTcount: A:0.47, C:0.06, G:0.10, T:0.36
Consensus pattern (58 bp):
AAATAAAATTTCAAAAAAATATTTTTGAGAAAAGTTGAAAGTATCAATTTTTTACTAA
Found at i:28808424 original size:2 final size:2
Alignment explanation
Indices: 28808417--28808444 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
28808407 AAAATACTTA
28808417 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28808445 TTTACGTGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28812820 original size:14 final size:15
Alignment explanation
Indices: 28812786--28812836 Score: 52
Period size: 14 Copynumber: 3.5 Consensus size: 15
28812776 AGAGTTAAAA
*
28812786 TTTAAATTTTAGATTT
1 TTTAAATATT-GATTT
*
28812802 ATTAAATATT-ATTT
1 TTTAAATATTGATTT
28812816 TTTAAA-ATTGATTT
1 TTTAAATATTGATTT
*
28812830 TATAAAT
1 TTTAAAT
28812837 TGAATGAGTT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
13 3 0.10
14 18 0.62
16 8 0.28
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (15 bp):
TTTAAATATTGATTT
Found at i:28814003 original size:18 final size:18
Alignment explanation
Indices: 28813973--28814010 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
28813963 TTTAATTTTA
28813973 ATAATAAAAATTTTAAAT
1 ATAATAAAAATTTTAAAT
*
28813991 ATAA-AAAATATTTTATAT
1 ATAATAAAA-ATTTTAAAT
28814009 AT
1 AT
28814011 GAATTTAGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
ATAATAAAAATTTTAAAT
Found at i:28829762 original size:21 final size:22
Alignment explanation
Indices: 28829737--28829780 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
28829727 TGAGATAAAA
28829737 ATATAAATTTT-TT-AAAAATTT
1 ATAT-AATTTTATTAAAAAATTT
28829758 ATATAATTTTATTAAAAAATTT
1 ATATAATTTTATTAAAAAATTT
28829780 A
1 A
28829781 ATCATATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 6 0.29
21 6 0.29
22 9 0.43
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
ATATAATTTTATTAAAAAATTT
Found at i:28829790 original size:21 final size:22
Alignment explanation
Indices: 28829737--28829792 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 22
28829727 TGAGATAAAA
* *
28829737 ATATAA-ATTTTTTAAAAATTT
1 ATATAATATTATTAAAAAATTT
*
28829758 ATATAATTTTATTAAAAAATTT
1 ATATAATATTATTAAAAAATTT
*
28829780 A-ATCATATTATTA
1 ATATAATATTATTA
28829793 TTTTCTATTA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
21 16 0.55
22 13 0.45
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (22 bp):
ATATAATATTATTAAAAAATTT
Found at i:28831724 original size:115 final size:115
Alignment explanation
Indices: 28831522--28831753 Score: 349
Period size: 115 Copynumber: 2.0 Consensus size: 115
28831512 TTTCTAACAT
* *
28831522 AAAATAATGAGTATAAACATATTGAATTTAGTTCAGTAGTTAAATCACGTATTCTCTGTTACATG
1 AAAATAATGAATATAAACATATTGAATTTAGTTCAGTAGTTAAATCACGAATTCTCTGTTACATG
* * *
28831587 CTCAAAGAACAAAGATTGAATTCAATTTTTTTAAATA-TAAAACAAGATTA
66 CTCAAAGAACAAAGATCGAATTCAA-TTTTTTAAATACGAAAACAAAATTA
* * *
28831637 AAAATAATGAATATAAACATATTGCATTTAGTTCAGTAGTTAAATCATGAATTCTCTGTTATATG
1 AAAATAATGAATATAAACATATTGAATTTAGTTCAGTAGTTAAATCACGAATTCTCTGTTACATG
* * *
28831702 TTCAAAGAACAGAGATCGAATTCTATTTTTTAAATACGAAAACAAAATTA
66 CTCAAAGAACAAAGATCGAATTCAATTTTTTAAATACGAAAACAAAATTA
28831752 AA
1 AA
28831754 CCCATACTAT
Statistics
Matches: 105, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
114 11 0.10
115 94 0.90
ACGTcount: A:0.44, C:0.10, G:0.11, T:0.34
Consensus pattern (115 bp):
AAAATAATGAATATAAACATATTGAATTTAGTTCAGTAGTTAAATCACGAATTCTCTGTTACATG
CTCAAAGAACAAAGATCGAATTCAATTTTTTAAATACGAAAACAAAATTA
Found at i:28857069 original size:2 final size:2
Alignment explanation
Indices: 28857064--28857099 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
28857054 TCTCTGTGTT
*
28857064 TC TC TC TC TC TC TC TC AC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
28857100 AAGAGCTTAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.03, C:0.50, G:0.00, T:0.47
Consensus pattern (2 bp):
TC
Found at i:28858389 original size:45 final size:46
Alignment explanation
Indices: 28858302--28858424 Score: 137
Period size: 45 Copynumber: 2.7 Consensus size: 46
28858292 ACCAGAGGAG
*
28858302 AAGCCTAACAAAGTTG-CTAATGAAGTGAAGAAATTGGCAGAAGA-A
1 AAGCCTAACAAAGTTGTC-AATGAAGTGAAGAAATTGACAGAAGATA
* * *
28858347 AAGCCCAACAAAGCTGTCAATGAAGTGAAGAAGTT-ACAAGAAGATA
1 AAGCCTAACAAAGTTGTCAATGAAGTGAAGAAATTGAC-AGAAGATA
* * *
28858393 AA-CCTAGCAATGTTGTTAATGAAGTGAAGAAA
1 AAGCCTAACAAAGTTGTCAATGAAGTGAAGAAA
28858425 ATTAGCCAAT
Statistics
Matches: 65, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
44 1 0.02
45 60 0.92
46 4 0.06
ACGTcount: A:0.46, C:0.12, G:0.23, T:0.19
Consensus pattern (46 bp):
AAGCCTAACAAAGTTGTCAATGAAGTGAAGAAATTGACAGAAGATA
Found at i:28863322 original size:23 final size:23
Alignment explanation
Indices: 28863278--28863322 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
28863268 GGCCTACTAA
* *
28863278 TCGATTTAATTATTTGAAAAGAC
1 TCGATTCAATTATTTAAAAAGAC
28863301 TCGATTCAATTA-TTAAACAAGA
1 TCGATTCAATTATTTAAA-AAGA
28863323 ACTCCGCAGC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.36
Consensus pattern (23 bp):
TCGATTCAATTATTTAAAAAGAC
Found at i:28868577 original size:13 final size:13
Alignment explanation
Indices: 28868561--28868585 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28868551 AAAAAATATA
28868561 TATTTAATTTTAT
1 TATTTAATTTTAT
28868574 TATTTAATTTTA
1 TATTTAATTTTA
28868586 ATAAATAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TATTTAATTTTAT
Found at i:28868715 original size:22 final size:22
Alignment explanation
Indices: 28868666--28868707 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
28868656 CAAAGACAAA
28868666 AATTAAAACATAAATTTATATT
1 AATTAAAACATAAATTTATATT
*
28868688 AATTAAAA-AT-AATTTTTATT
1 AATTAAAACATAAATTTATATT
28868708 TTTATTAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 9 0.47
21 2 0.11
22 8 0.42
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (22 bp):
AATTAAAACATAAATTTATATT
Found at i:28871111 original size:21 final size:24
Alignment explanation
Indices: 28871068--28871114 Score: 64
Period size: 21 Copynumber: 2.1 Consensus size: 24
28871058 ATTATAAATT
*
28871068 TTAATTGATTAAATCGATTATTTA
1 TTAATTGATTAAATCGATCATTTA
28871092 TTAATT-ATT-AAT-GATCATTTA
1 TTAATTGATTAAATCGATCATTTA
28871113 TT
1 TT
28871115 CAAAAATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 10 0.45
22 3 0.14
23 3 0.14
24 6 0.27
ACGTcount: A:0.36, C:0.04, G:0.06, T:0.53
Consensus pattern (24 bp):
TTAATTGATTAAATCGATCATTTA
Found at i:28876112 original size:12 final size:11
Alignment explanation
Indices: 28876095--28876159 Score: 55
Period size: 12 Copynumber: 5.9 Consensus size: 11
28876085 ATAAAAAATG
*
28876095 TATTTAATTATT
1 TATTTAA-TATA
28876107 TATTTAATATA
1 TATTTAATATA
28876118 TATTTACATATA
1 TATTTA-ATATA
28876130 TA-TT-ATAT-
1 TATTTAATATA
* *
28876138 TAGTAAATATA
1 TATTTAATATA
28876149 TTATTTAATAT
1 -TATTTAATAT
28876160 TTTAATTTAA
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
8 2 0.05
9 5 0.11
10 4 0.09
11 11 0.25
12 22 0.50
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (11 bp):
TATTTAATATA
Found at i:28883499 original size:7 final size:7
Alignment explanation
Indices: 28883487--28883511 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
28883477 TCACTATCAT
28883487 CCATTTC
1 CCATTTC
28883494 CCATTTC
1 CCATTTC
28883501 CCATTTC
1 CCATTTC
28883508 CCAT
1 CCAT
28883512 AGAAACAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.16, C:0.44, G:0.00, T:0.40
Consensus pattern (7 bp):
CCATTTC
Found at i:28884389 original size:3 final size:3
Alignment explanation
Indices: 28884381--28884409 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
28884371 GACAAAAATT
28884381 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
28884410 CTTCCTCTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:28887303 original size:13 final size:14
Alignment explanation
Indices: 28887277--28887305 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
28887267 TGTAAAATCA
28887277 AATCAATAACTCAT
1 AATCAATAACTCAT
28887291 AATCAAT-ACTCAT
1 AATCAATAACTCAT
28887304 AA
1 AA
28887306 ATATTTTCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.52, C:0.21, G:0.00, T:0.28
Consensus pattern (14 bp):
AATCAATAACTCAT
Found at i:28892763 original size:12 final size:12
Alignment explanation
Indices: 28892731--28892756 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
28892721 CATAAATTAA
28892731 TTAAATTAAATT
1 TTAAATTAAATT
28892743 TTAAATTAAATT
1 TTAAATTAAATT
28892755 TT
1 TT
28892757 CTATTAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (12 bp):
TTAAATTAAATT
Found at i:28896761 original size:31 final size:31
Alignment explanation
Indices: 28896720--28896789 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 31
28896710 TGATTGTCTA
*
28896720 ATTA-TATTTTAAT-TA-ATTAACAATATATT
1 ATTATTATTTTAATATATAATAACAATA-ATT
*
28896749 ATATATTATTTTAATATATAATAATAATAATT
1 AT-TATTATTTTAATATATAATAACAATAATT
28896781 ATTATTATT
1 ATTATTATT
28896790 ATTATTATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
29 2 0.06
30 2 0.06
31 16 0.46
32 7 0.20
33 8 0.23
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (31 bp):
ATTATTATTTTAATATATAATAACAATAATT
Found at i:28907943 original size:23 final size:23
Alignment explanation
Indices: 28907903--28907948 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
28907893 TCGAAATAAA
28907903 AAATATGACTTTTCAAGAATCCC
1 AAATATGACTTTTCAAGAATCCC
*
28907926 AAATATGCCATTTT-AAGAATCCC
1 AAATATGAC-TTTTCAAGAATCCC
28907949 TTGAATGTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 17 0.81
24 4 0.19
ACGTcount: A:0.39, C:0.22, G:0.09, T:0.30
Consensus pattern (23 bp):
AAATATGACTTTTCAAGAATCCC
Found at i:28915928 original size:3 final size:3
Alignment explanation
Indices: 28915920--28915977 Score: 98
Period size: 3 Copynumber: 19.3 Consensus size: 3
28915910 GTCATTTCTT
* *
28915920 TTA TTA TTA TTA TTA TTA TTA TTA TTG TTA TTA TTA TTA TTC TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
28915968 TTA TTA TTA T
1 TTA TTA TTA T
28915978 GATGTTCGGG
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:28918024 original size:17 final size:17
Alignment explanation
Indices: 28918002--28918035 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
28917992 TTAGTTTGAC
28918002 GTATGTCATTATAAGTG
1 GTATGTCATTATAAGTG
28918019 GTATGTCATTATAAGTG
1 GTATGTCATTATAAGTG
28918036 ATAAGTGGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.06, G:0.24, T:0.41
Consensus pattern (17 bp):
GTATGTCATTATAAGTG
Found at i:28919920 original size:16 final size:17
Alignment explanation
Indices: 28919888--28919928 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
28919878 AATTAGGTTT
*
28919888 TTAAATTTTTTTATAAA
1 TTAAATTTTTATATAAA
28919905 TTAAATTTTTAT-TAAA
1 TTAAATTTTTATATAAA
*
28919921 TAAAATTT
1 TTAAATTT
28919929 GATTAATCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 11 0.50
17 11 0.50
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTAAATTTTTATATAAA
Found at i:28920433 original size:16 final size:16
Alignment explanation
Indices: 28920412--28920447 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
28920402 ATTCGAATCT
28920412 TTTTAAA-TTTAAATTA
1 TTTTAAATTTTAAA-TA
28920428 TTTTAAATTTTAAATA
1 TTTTAAATTTTAAATA
28920444 TTTT
1 TTTT
28920448 TTAATTTGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTTAAATTTTAAATA
Found at i:28920448 original size:17 final size:16
Alignment explanation
Indices: 28920411--28920454 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 16
28920401 GATTCGAATC
28920411 TTTTTAAA-TTTAAAT
1 TTTTTAAATTTTAAAT
28920426 TATTTTAAATTTTAAAT
1 T-TTTTAAATTTTAAAT
*
28920443 ATTTTTTAATTT
1 -TTTTTAAATTT
28920455 GAATCATTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
15 1 0.04
16 7 0.28
17 16 0.64
18 1 0.04
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
TTTTTAAATTTTAAAT
Found at i:28921796 original size:17 final size:16
Alignment explanation
Indices: 28921759--28921796 Score: 67
Period size: 16 Copynumber: 2.3 Consensus size: 16
28921749 TTTTCCAATT
28921759 AACTTTGTAGGCAAAA
1 AACTTTGTAGGCAAAA
28921775 AACTTTGTAGGCAAAA
1 AACTTTGTAGGCAAAA
28921791 ACACTT
1 A-ACTT
28921797 GCCTAAACTC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 17 0.81
17 4 0.19
ACGTcount: A:0.42, C:0.16, G:0.16, T:0.26
Consensus pattern (16 bp):
AACTTTGTAGGCAAAA
Found at i:28929880 original size:3 final size:3
Alignment explanation
Indices: 28929867--28929914 Score: 78
Period size: 3 Copynumber: 16.0 Consensus size: 3
28929857 ATAATTGCTG
* *
28929867 TTA TCA TTA TTA TTA CTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
28929915 CCCTTTGCAT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:28954721 original size:28 final size:28
Alignment explanation
Indices: 28954689--28954743 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
28954679 TTACATTTAA
28954689 TATGGATCTCTTTGTAGAAATTTGTTAT
1 TATGGATCTCTTTGTAGAAATTTGTTAT
28954717 TATGGATCTCTTTGTAGAAATTTGTTA
1 TATGGATCTCTTTGTAGAAATTTGTTA
28954744 AACTTTGTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.25, C:0.07, G:0.18, T:0.49
Consensus pattern (28 bp):
TATGGATCTCTTTGTAGAAATTTGTTAT
Found at i:28966706 original size:18 final size:18
Alignment explanation
Indices: 28966672--28966706 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
28966662 TTAAAGCCTG
*
28966672 TTTTCTTTTTCTTTTTTA
1 TTTTCTTTTTCTGTTTTA
*
28966690 TTTTCTTTTTGTGTTTT
1 TTTTCTTTTTCTGTTTT
28966707 TAAAGTAGTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.03, C:0.09, G:0.06, T:0.83
Consensus pattern (18 bp):
TTTTCTTTTTCTGTTTTA
Found at i:28968688 original size:33 final size:33
Alignment explanation
Indices: 28968626--28968694 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
28968616 TTATGAAAAA
* * *
28968626 TTGAAAATACATATTCAATAAGGTTAAAATTTT
1 TTGAAAATACAAATTCAATAAGATTAAAATGTT
*
28968659 TTGAAAATACAAATTCGATAA-ATTAAAAATGTT
1 TTGAAAATACAAATTCAATAAGATT-AAAATGTT
28968692 TTG
1 TTG
28968695 GATATGTATT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 2 0.06
33 29 0.94
ACGTcount: A:0.46, C:0.06, G:0.10, T:0.38
Consensus pattern (33 bp):
TTGAAAATACAAATTCAATAAGATTAAAATGTT
Found at i:28973801 original size:15 final size:15
Alignment explanation
Indices: 28973781--28973811 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
28973771 AATCTGAAAT
*
28973781 TCAAATATTAACAGC
1 TCAAATACTAACAGC
28973796 TCAAATACTAACAGC
1 TCAAATACTAACAGC
28973811 T
1 T
28973812 ATAGGACTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.23, G:0.06, T:0.26
Consensus pattern (15 bp):
TCAAATACTAACAGC
Found at i:28978727 original size:4 final size:4
Alignment explanation
Indices: 28978718--28978742 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
28978708 CCTTCTCTCT
28978718 TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA T
28978743 CTATCTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:28986360 original size:2 final size:2
Alignment explanation
Indices: 28986353--28986381 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
28986343 TTTAAAGGTG
28986353 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 T
28986382 TAACATGTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:28993589 original size:18 final size:18
Alignment explanation
Indices: 28993566--28993603 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
28993556 TTTTTTGCGC
28993566 ATTGCATACGGCTTTACA
1 ATTGCATACGGCTTTACA
28993584 ATTGCATACGGCTTTACA
1 ATTGCATACGGCTTTACA
28993602 AT
1 AT
28993604 GGAATTCTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.34
Consensus pattern (18 bp):
ATTGCATACGGCTTTACA
Found at i:28999623 original size:19 final size:20
Alignment explanation
Indices: 28999584--28999627 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
28999574 CTAACGCCTC
*
28999584 TACTTCTCACGGCGGCTGTT
1 TACTTCTCACGGCGACTGTT
*
28999604 TACTTCTCA-GTCGACTGTT
1 TACTTCTCACGGCGACTGTT
28999623 T-CTTC
1 TACTTC
28999628 GATGAAGTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 4 0.18
19 9 0.41
20 9 0.41
ACGTcount: A:0.11, C:0.30, G:0.18, T:0.41
Consensus pattern (20 bp):
TACTTCTCACGGCGACTGTT
Found at i:29006053 original size:35 final size:35
Alignment explanation
Indices: 29005977--29006053 Score: 102
Period size: 35 Copynumber: 2.2 Consensus size: 35
29005967 GTTTAATTAT
* * *
29005977 ATATGTGAAGTCAGTTGTAGGTTTATACTCATAAA
1 ATATTTGAAGTCAGTTATAGGTTTATACTCAAAAA
*
29006012 ACATTTGAAGTCAGTTATAGGTTTATA-TCCAAAAA
1 ATATTTGAAGTCAGTTATAGGTTTATACT-CAAAAA
29006047 ATATTTG
1 ATATTTG
29006054 GTTTATATAT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
34 1 0.03
35 35 0.97
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.38
Consensus pattern (35 bp):
ATATTTGAAGTCAGTTATAGGTTTATACTCAAAAA
Found at i:29008391 original size:29 final size:29
Alignment explanation
Indices: 29008359--29008416 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
29008349 ATCCCTTTCT
29008359 TGCTGTCCGATGGTGATATATTTGTTTGG
1 TGCTGTCCGATGGTGATATATTTGTTTGG
29008388 TGCTGTCCGATGGTGATATATTTGTTTGG
1 TGCTGTCCGATGGTGATATATTTGTTTGG
29008417 CCCAAATGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.14, C:0.10, G:0.31, T:0.45
Consensus pattern (29 bp):
TGCTGTCCGATGGTGATATATTTGTTTGG
Found at i:29009286 original size:12 final size:13
Alignment explanation
Indices: 29009260--29009324 Score: 71
Period size: 13 Copynumber: 5.2 Consensus size: 13
29009250 CAGCAATGTG
*
29009260 TTCAGAAACACCA
1 TTCAAAAACACCA
*
29009273 TTCAATAA-ACCA
1 TTCAAAAACACCA
* *
29009285 TTTAGAAACACCA
1 TTCAAAAACACCA
29009298 TTCAAAAA-ACCA
1 TTCAAAAACACCA
*
29009310 TTCAAAAATACCA
1 TTCAAAAACACCA
29009323 TT
1 TT
29009325 TAGCAAACCA
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
12 21 0.49
13 22 0.51
ACGTcount: A:0.49, C:0.25, G:0.03, T:0.23
Consensus pattern (13 bp):
TTCAAAAACACCA
Found at i:29009322 original size:25 final size:25
Alignment explanation
Indices: 29009260--29009324 Score: 94
Period size: 25 Copynumber: 2.6 Consensus size: 25
29009250 CAGCAATGTG
*
29009260 TTCAGAAACACCATTCAATAAACCA
1 TTCAGAAACACCATTCAAAAAACCA
*
29009285 TTTAGAAACACCATTCAAAAAACCA
1 TTCAGAAACACCATTCAAAAAACCA
* *
29009310 TTCAAAAATACCATT
1 TTCAGAAACACCATT
29009325 TAGCAAACCA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.49, C:0.25, G:0.03, T:0.23
Consensus pattern (25 bp):
TTCAGAAACACCATTCAAAAAACCA
Found at i:29009334 original size:12 final size:12
Alignment explanation
Indices: 29009319--29009370 Score: 59
Period size: 12 Copynumber: 4.3 Consensus size: 12
29009309 ATTCAAAAAT
29009319 ACCATTTAGCAA
1 ACCATTTAGCAA
* *
29009331 ACCATTTCGTAA
1 ACCATTTAGCAA
*
29009343 ACCATTAAGCAA
1 ACCATTTAGCAA
* *
29009355 ACCATTCAGCAT
1 ACCATTTAGCAA
29009367 ACCA
1 ACCA
29009371 ATATCGTACA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.40, C:0.29, G:0.08, T:0.23
Consensus pattern (12 bp):
ACCATTTAGCAA
Found at i:29009370 original size:24 final size:24
Alignment explanation
Indices: 29009317--29009370 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
29009307 CCATTCAAAA
* *
29009317 ATACCATTTAGCAAACCATTTCGT
1 ATACCATTAAGCAAACCATTTCGC
*
29009341 AAACCATTAAGCAAACCA-TTCAGC
1 ATACCATTAAGCAAACCATTTC-GC
29009365 ATACCA
1 ATACCA
29009371 ATATCGTACA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
23 3 0.12
24 22 0.88
ACGTcount: A:0.41, C:0.28, G:0.07, T:0.24
Consensus pattern (24 bp):
ATACCATTAAGCAAACCATTTCGC
Done.