Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167826.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_1, 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: 36299135
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Warning! 357000 characters in sequence are not A, C, G, or T
File 22 of 402
Found at i:5128234 original size:263 final size:263
Alignment explanation
Indices: 5127736--5128250 Score: 752
Period size: 263 Copynumber: 2.0 Consensus size: 263
5127726 ATATGATTGG
* * *
5127736 TCAATTAGGTGAATTTATTCTTTCAATGAAAATCTAAGCTTGACTATGACTCCTTAAAAAAATAG
1 TCAATTAAGTGAATTCATTCCTTCAATGAAAATCTAAGCTTGACTATGACTCCTTAAAAAAATAG
* *
5127801 GTATAGCTATGCATTACAAAATTAAATACAGTATAAGAAAATTATAACATCCTCACACACCCATT
66 GTATAGCTATACATTACAAAATTAAATACAGTATAAGAAAATTATAAAATCCTCACACACCCATT
* **
5127866 CAAAGAAATGTATCAATTTATCTTAAATTATTTTAAAAATTTTAGTATAAATGGTTTTGTATTTT
131 CAAAGAAATGTACCAATTTATCTTAAATTATTCAAAAAATTTTAGTATAAATGGTTTTGTATTTT
*
5127931 GTTAAGTTTTGGTATTTAAATATTGAATATAACTTTTAAGTTGTCTCTAATATGATAAGTGTGAT
196 GTTAAGTTTTGGTATTTAAATATTGAAAATAACTTTTAAGTTGTCTCTAATATGATAAGTGTGAT
5127996 TAA
261 TAA
* *
5127999 TCAATTAAGTGAATTCATTCCTTCAATGGAAATCTAAGCTTGACTATGACT-TTCTAAAAAAATA
1 TCAATTAAGTGAATTCATTCCTTCAATGAAAATCTAAGCTTGACTATGACTCCT-TAAAAAAATA
* * * * * * * *
5128063 GGTTTCA-CTCTACATTTCAGAATTAAGTACAGTATAGGAAAAGTTATAAAATCCTTACACGCCC
65 GGTAT-AGCTATACATTACAAAATTAAATACAGTATAAGAAAA-TTATAAAATCCTCACACACCC
*
5128127 ATTTAAAGGAAAT-TACCAATTTATCTTAAATTATTCAAAAAATTTTAGTATAAATGGTCTTT-T
128 ATTCAAA-GAAATGTACCAATTTATCTTAAATTATTCAAAAAATTTTAGTATAAATGGT-TTTGT
* *
5128190 ATTTTGTTAAGTTTTGGTATTTAAATATTGAAAATAA-TTTTAAGTTGTTTTTAATATGATA
191 ATTTTGTTAAGTTTTGGTATTTAAATATTGAAAATAACTTTTAAGTTGTCTCTAATATGATA
5128251 GAATTCGTAA
Statistics
Matches: 225, Mismatches: 22, Indels: 10
0.88 0.09 0.04
Matches are distributed among these distances:
262 1 0.00
263 112 0.50
264 104 0.46
265 8 0.04
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.39
Consensus pattern (263 bp):
TCAATTAAGTGAATTCATTCCTTCAATGAAAATCTAAGCTTGACTATGACTCCTTAAAAAAATAG
GTATAGCTATACATTACAAAATTAAATACAGTATAAGAAAATTATAAAATCCTCACACACCCATT
CAAAGAAATGTACCAATTTATCTTAAATTATTCAAAAAATTTTAGTATAAATGGTTTTGTATTTT
GTTAAGTTTTGGTATTTAAATATTGAAAATAACTTTTAAGTTGTCTCTAATATGATAAGTGTGAT
TAA
Found at i:5129511 original size:11 final size:12
Alignment explanation
Indices: 5129484--5129520 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
5129474 AATTTAATAA
5129484 AAAAATTATTTT
1 AAAAATTATTTT
5129496 AAAAATTATTTT
1 AAAAATTATTTT
*
5129508 AAAAATAATTTT
1 AAAAATTATTTT
5129520 A
1 A
5129521 GAATTTCATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (12 bp):
AAAAATTATTTT
Found at i:5131268 original size:31 final size:31
Alignment explanation
Indices: 5131233--5131297 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
5131223 GTTTGACATA
** *
5131233 ATGCTGTTTAGTCCTTATTTGGTGTTTGCTG
1 ATGCTGTCGAGTCCTTATTTGGTGGTTGCTG
5131264 ATGCTGTCGAGTCCTTATTTGGTGGTTGCTG
1 ATGCTGTCGAGTCCTTATTTGGTGGTTGCTG
5131295 ATG
1 ATG
5131298 TGCTAATCTC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.11, C:0.14, G:0.29, T:0.46
Consensus pattern (31 bp):
ATGCTGTCGAGTCCTTATTTGGTGGTTGCTG
Found at i:5149032 original size:126 final size:126
Alignment explanation
Indices: 5148787--5149020 Score: 287
Period size: 126 Copynumber: 1.9 Consensus size: 126
5148777 TAATTTATAG
* * * * * *
5148787 AAAAAATTTGAAATGGACTCTTAAAGGCGTTTTTGGCCGAAAGCGCTTTCAATAATCCAATTAAT
1 AAAAAAGTTGAAACGGACTCTTAAAGGCATTTTTAGCCCAAAACGCTTTCAATAATCCAATTAAT
*
5148852 AAATTTTTATAAGAGATTATTAAAGGCAGTTTTGATCAAAAATACCTTAAATAATCCATAC
66 AAATTTTTATAAGAGATTATTAAAGGCAGTTTTAATCAAAAATACCTTAAATAATCCATAC
* * * *
5148913 AAAAAAGTTGAAACGGATTTTTAAAGGTATTTTTAGCCCAAAACGTCTTT-AATAATTCACA-TA
1 AAAAAAGTTGAAACGGACTCTTAAAGGCATTTTTAGCCCAAAACG-CTTTCAATAATCCA-ATTA
* *
5148976 ATAAGTTTTTATTAAG-GATTATTGAAGGC-GATTTTAATCAAAAAT
64 ATAAATTTTTA-TAAGAGATTATTAAAGGCAG-TTTTAATCAAAAAT
5149021 GTCTTTAATA
Statistics
Matches: 91, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
125 1 0.01
126 81 0.89
127 9 0.10
ACGTcount: A:0.41, C:0.12, G:0.14, T:0.34
Consensus pattern (126 bp):
AAAAAAGTTGAAACGGACTCTTAAAGGCATTTTTAGCCCAAAACGCTTTCAATAATCCAATTAAT
AAATTTTTATAAGAGATTATTAAAGGCAGTTTTAATCAAAAATACCTTAAATAATCCATAC
Found at i:5154115 original size:20 final size:20
Alignment explanation
Indices: 5154055--5154115 Score: 54
Period size: 20 Copynumber: 3.0 Consensus size: 20
5154045 ACACTTTTTT
*
5154055 ATTTATTTA-TAAATTTA-A
1 ATTTATATATTAAATTTATA
* **
5154073 TATTATATAAATTAAATAAATA
1 -ATT-TATATATTAAATTTATA
5154095 ATTTATATATTAAATTTATA
1 ATTTATATATTAAATTTATA
5154115 A
1 A
5154116 ATCATTTACA
Statistics
Matches: 32, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
19 3 0.09
20 19 0.59
21 9 0.28
22 1 0.03
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
ATTTATATATTAAATTTATA
Found at i:5154409 original size:48 final size:48
Alignment explanation
Indices: 5154286--5154385 Score: 141
Period size: 48 Copynumber: 2.1 Consensus size: 48
5154276 TAAGATTTTT
*
5154286 TATA-AAAAAAAATTATTATATTTAACATTTAAATTATTTATTTGTTTA
1 TATATAAAAAAATTTATT-TATTTAACATTTAAATTATTTATTTGTTTA
* * *
5154334 TTTATAAAAAAATTAATATATTTAACATTTAAATTATTTATTTGTTTA
1 TATATAAAAAAATTTATTTATTTAACATTTAAATTATTTATTTGTTTA
5154382 -ATAT
1 TATAT
5154386 GCAAGTTATT
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
47 3 0.07
48 33 0.72
49 10 0.22
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (48 bp):
TATATAAAAAAATTTATTTATTTAACATTTAAATTATTTATTTGTTTA
Found at i:5154418 original size:24 final size:24
Alignment explanation
Indices: 5154364--5154426 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
5154354 TTTAACATTT
* * *
5154364 AAATTATTTATTTGTTTAATATGC
1 AAATTATTTATTTATGTAACATGC
* *
5154388 AAGTTATTTATTTATGTAACATGG
1 AAATTATTTATTTATGTAACATGC
5154412 AAATTATTTTATTTA
1 AAATTA-TTTATTTA
5154427 ACATATAAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
24 24 0.75
25 8 0.25
ACGTcount: A:0.35, C:0.03, G:0.10, T:0.52
Consensus pattern (24 bp):
AAATTATTTATTTATGTAACATGC
Found at i:5154436 original size:21 final size:21
Alignment explanation
Indices: 5154398--5154437 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
5154388 AAGTTATTTA
*
5154398 TTTATGTAACATGGAAATTAT
1 TTTATGTAACATAGAAATTAT
* *
5154419 TTTATTTAACATATAAATT
1 TTTATGTAACATAGAAATT
5154438 GTTATATAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.40, C:0.05, G:0.07, T:0.47
Consensus pattern (21 bp):
TTTATGTAACATAGAAATTAT
Found at i:5164643 original size:24 final size:21
Alignment explanation
Indices: 5164605--5164657 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 21
5164595 AATTTTATTT
5164605 ATTTATTGTT-TATTTATAATAA
1 ATTTATT-TTATATTTAT-ATAA
5164627 TATTTCATTTTATATTTATATAA
1 -ATTT-ATTTTATATTTATATAA
5164650 ATTTATTT
1 ATTTATTT
5164658 AATTATAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
21 4 0.14
22 4 0.14
23 10 0.36
24 10 0.36
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (21 bp):
ATTTATTTTATATTTATATAA
Found at i:5164674 original size:11 final size:12
Alignment explanation
Indices: 5164626--5164705 Score: 69
Period size: 12 Copynumber: 6.7 Consensus size: 12
5164616 ATTTATAATA
5164626 ATATTTCATTT-T
1 ATATTT-ATTTAT
5164638 ATATTTA--TAT
1 ATATTTATTTAT
*
5164648 AAATTTATTTAATT
1 ATATTTATTT-A-T
5164662 ATAATTTATTTAT
1 AT-ATTTATTTAT
* *
5164675 -TATTTATTAAC
1 ATATTTATTTAT
5164686 ATATTTATTTAT
1 ATATTTATTTAT
5164698 ATATTTAT
1 ATATTTAT
5164706 GAATACGTTT
Statistics
Matches: 55, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
9 1 0.02
10 7 0.13
11 9 0.16
12 25 0.45
13 2 0.04
14 3 0.05
15 8 0.15
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (12 bp):
ATATTTATTTAT
Found at i:5164676 original size:14 final size:15
Alignment explanation
Indices: 5164639--5164677 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
5164629 TTTCATTTTA
5164639 TATTTA-TATAAATT
1 TATTTATTATAAATT
5164653 TATTTAATTAT-AATT
1 TATTT-ATTATAAATT
5164668 TATTTATTAT
1 TATTTATTAT
5164678 TTATTAACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 10 0.43
15 10 0.43
16 3 0.13
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TATTTATTATAAATT
Found at i:5166011 original size:20 final size:20
Alignment explanation
Indices: 5165973--5166012 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
5165963 ATATTTTGAG
**
5165973 ATTCATTTATATTTGTTTAA
1 ATTCATTTATATTCATTTAA
*
5165993 ATTCATTTATGTTCATTTAA
1 ATTCATTTATATTCATTTAA
5166013 GGTTTTTTTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.30, C:0.07, G:0.05, T:0.57
Consensus pattern (20 bp):
ATTCATTTATATTCATTTAA
Found at i:5166517 original size:13 final size:13
Alignment explanation
Indices: 5166499--5166537 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
5166489 GTTACCTCTT
5166499 ATAAATTTATAAA
1 ATAAATTTATAAA
5166512 ATAAATTTATAAA
1 ATAAATTTATAAA
* *
5166525 ATATACTTATAAA
1 ATAAATTTATAAA
5166538 TTTTAAGAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (13 bp):
ATAAATTTATAAA
Found at i:5167580 original size:28 final size:28
Alignment explanation
Indices: 5167549--5167602 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
5167539 ATATATTAAT
5167549 AATTAAGATATCATATTATAA-ATTTTTA
1 AATTAAGATATCATATTA-AATATTTTTA
* *
5167577 AATTCATATATCATATTAAATATTTT
1 AATTAAGATATCATATTAAATATTTT
5167603 ATTATAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 2 0.09
28 21 0.91
ACGTcount: A:0.44, C:0.06, G:0.02, T:0.48
Consensus pattern (28 bp):
AATTAAGATATCATATTAAATATTTTTA
Found at i:5171787 original size:66 final size:66
Alignment explanation
Indices: 5171681--5171813 Score: 232
Period size: 66 Copynumber: 2.0 Consensus size: 66
5171671 ACTTGACATT
* *
5171681 AAGTTGATTCACTCACAACATTAAATGTAGTTACACCTGCAAAGGTTTGAGTCTTGAGATTGTAT
1 AAGTTGATTCACTCACAACATCAAATGTAGTTACACCTGCAAAGGTTTCAGTCTTGAGATTGTAT
5171746 A
66 A
5171747 AAGTTGATGT-ACTCACAACATCAAATGTAGTTACACCTGCAAAGGTTTCAGTCTTGAGATTGTA
1 AAGTTGAT-TCACTCACAACATCAAATGTAGTTACACCTGCAAAGGTTTCAGTCTTGAGATTGTA
5171811 TA
65 TA
5171813 A
1 A
5171814 GGTTTAAGAG
Statistics
Matches: 64, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
66 63 0.98
67 1 0.02
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (66 bp):
AAGTTGATTCACTCACAACATCAAATGTAGTTACACCTGCAAAGGTTTCAGTCTTGAGATTGTAT
A
Found at i:5172755 original size:19 final size:19
Alignment explanation
Indices: 5172731--5172769 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
5172721 TAGAACTAAG
*
5172731 ATACAACCACTGTCCTTGC
1 ATACAACCACTGCCCTTGC
5172750 ATACAACCACTGCCCTTGC
1 ATACAACCACTGCCCTTGC
5172769 A
1 A
5172770 ATACCATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.28, C:0.38, G:0.10, T:0.23
Consensus pattern (19 bp):
ATACAACCACTGCCCTTGC
Found at i:5180594 original size:29 final size:31
Alignment explanation
Indices: 5180548--5180619 Score: 103
Period size: 29 Copynumber: 2.4 Consensus size: 31
5180538 TTATTAGAAA
*
5180548 ATTAAAAATATAAGAATCAATA-AATATTTT
1 ATTAAAAATATAAGAATCAAAATAATATTTT
*
5180578 -TTAAAAATATAATAATCAAAATAATATTTT
1 ATTAAAAATATAAGAATCAAAATAATATTTT
*
5180608 ATTTAAAATATA
1 ATTAAAAATATA
5180620 CGTATTTTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
29 19 0.51
30 8 0.22
31 10 0.27
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (31 bp):
ATTAAAAATATAAGAATCAAAATAATATTTT
Found at i:5180735 original size:26 final size:25
Alignment explanation
Indices: 5180684--5180746 Score: 65
Period size: 26 Copynumber: 2.5 Consensus size: 25
5180674 TATTTATTTC
*
5180684 AAAAT-TTAATATTAATTTATTAAT
1 AAAATATTAATATTAATTTAATAAT
* *
5180708 AAAATATTATTATCTAATTTAATGAT
1 AAAATATTAATAT-TAATTTAATAAT
* *
5180734 AATATATGAATAT
1 AAAATATTAATAT
5180747 ATGATATTTA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
24 5 0.16
25 6 0.19
26 20 0.65
ACGTcount: A:0.49, C:0.02, G:0.03, T:0.46
Consensus pattern (25 bp):
AAAATATTAATATTAATTTAATAAT
Found at i:5181158 original size:17 final size:17
Alignment explanation
Indices: 5181138--5181171 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
5181128 TTTTAAAAAA
5181138 TTAAAAAATAAATATTT
1 TTAAAAAATAAATATTT
**
5181155 TTAAAATTTAAATATTT
1 TTAAAAAATAAATATTT
5181172 AATTATATTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TTAAAAAATAAATATTT
Found at i:5187736 original size:2 final size:2
Alignment explanation
Indices: 5187731--5187775 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
5187721 TTATATAACT
5187731 AG AG AG AG AG 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
5187773 AG A
1 AG A
5187776 TGATGCAACA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5190527 original size:6 final size:6
Alignment explanation
Indices: 5190516--5190546 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
5190506 CAACTTGAGT
*
5190516 ATAATC ATAATC ATAATC ATAATC ATCATC A
1 ATAATC ATAATC ATAATC ATAATC ATAATC A
5190547 GGTACTGCAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.48, C:0.19, G:0.00, T:0.32
Consensus pattern (6 bp):
ATAATC
Found at i:5191331 original size:116 final size:115
Alignment explanation
Indices: 5191119--5191399 Score: 352
Period size: 116 Copynumber: 2.4 Consensus size: 115
5191109 TTCTTTGGCA
** * * **
5191119 CCAAACAAAGATGTCCTCGTCAAATCTCTCTTTGTAAGTTTATTCTTTTTTTCCTGGACGAGTCT
1 CCAAACAAAGATGTCCT-GTCAAATCTCTCCGTGTAAGTTTATTCTCTTCTTCCTAAACGAGTCT
*
5191184 ACATTGCAACTCATCTCTGGAATTAGCACCAAACTCGGACAACTCGCTCGC
65 ACATTGCAACTCATCTCTGGAATCAGCACCAAACTCGGACAACTCGCTCGC
5191235 CCAAACAAAGATGTCCTTGTCAAAATCTCTCCGTGTAAGTTTATTCTCTTCTT-CTAAACGAGTC
1 CCAAACAAAGATGTCC-TGTC-AAATCTCTCCGTGTAAGTTTATTCTCTTCTTCCTAAACGAGTC
* * * * *
5191299 TACATTGCAACTCATCTCTGGAATCGGTACCAAACTCGGCCATCTCGCTTGC
64 TACATTGCAACTCATCTCTGGAATCAGCACCAAACTCGGACAACTCGCTCGC
* * * * *
5191351 CCTAACAAAGAAGT-C-GTCAAATCTATCCGTGGAAGTTTCTTCTTCTTCT
1 CCAAACAAAGATGTCCTGTCAAATCTCTCCGTGTAAGTTTATTC-TCTTCT
5191400 CTGGACTTGC
Statistics
Matches: 145, Mismatches: 17, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
112 21 0.14
113 9 0.06
115 1 0.01
116 86 0.59
117 28 0.19
ACGTcount: A:0.26, C:0.27, G:0.15, T:0.32
Consensus pattern (115 bp):
CCAAACAAAGATGTCCTGTCAAATCTCTCCGTGTAAGTTTATTCTCTTCTTCCTAAACGAGTCTA
CATTGCAACTCATCTCTGGAATCAGCACCAAACTCGGACAACTCGCTCGC
Found at i:5192291 original size:18 final size:18
Alignment explanation
Indices: 5192268--5192302 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
5192258 TGCTTATTGC
5192268 TTCA-TTACTACTATTGTT
1 TTCATTTACTACT-TTGTT
5192286 TTCATTTACTACTTTGT
1 TTCATTTACTACTTTGT
5192303 ATATTCTATG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.20, C:0.17, G:0.06, T:0.57
Consensus pattern (18 bp):
TTCATTTACTACTTTGTT
Found at i:5194502 original size:7 final size:7
Alignment explanation
Indices: 5194490--5194514 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
5194480 GTAAATTTTT
5194490 AAATATA
1 AAATATA
5194497 AAATATA
1 AAATATA
5194504 AAATATA
1 AAATATA
5194511 AAAT
1 AAAT
5194515 TATTGCTATT
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:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (7 bp):
AAATATA
Found at i:5195564 original size:32 final size:32
Alignment explanation
Indices: 5195488--5195565 Score: 77
Period size: 32 Copynumber: 2.4 Consensus size: 32
5195478 AATAGATATA
*
5195488 AATAATTTTTATATTATTAATTTTTTAAATTTT
1 AATAATTTTT-TATTATTAATTTTTTAAATTTG
** ** *
5195521 TTTAAAATTTTAGTT-TTAATTTTTTACATTTG
1 AATAATTTTTTA-TTATTAATTTTTTAAATTTG
5195553 AATAATTTTTTAT
1 AATAATTTTTTAT
5195566 AAATATGTAT
Statistics
Matches: 34, Mismatches: 10, Indels: 4
0.71 0.21 0.08
Matches are distributed among these distances:
31 1 0.03
32 25 0.74
33 8 0.24
ACGTcount: A:0.33, C:0.01, G:0.03, T:0.63
Consensus pattern (32 bp):
AATAATTTTTTATTATTAATTTTTTAAATTTG
Found at i:5195651 original size:19 final size:20
Alignment explanation
Indices: 5195627--5195675 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
5195617 AAATTTTATA
5195627 TTATTAAATAAAAAT-TAAT
1 TTATTAAATAAAAATATAAT
* *
5195646 TTATT-AATATATATATAAT
1 TTATTAAATAAAAATATAAT
5195665 TTAATTAAATA
1 TT-ATTAAATA
5195676 TTTTAAAATC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
18 7 0.28
19 11 0.44
20 3 0.12
21 4 0.16
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TTATTAAATAAAAATATAAT
Found at i:5195951 original size:15 final size:16
Alignment explanation
Indices: 5195931--5195960 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
5195921 AACAAACATA
5195931 AAATAATTT-AAATTC
1 AAATAATTTGAAATTC
5195946 AAATAATTTGAAATT
1 AAATAATTTGAAATT
5195961 TAGTTTGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.40
Consensus pattern (16 bp):
AAATAATTTGAAATTC
Found at i:5195960 original size:22 final size:21
Alignment explanation
Indices: 5195935--5195987 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 21
5195925 AACATAAAAT
5195935 AATTTAAATTCAAATAATTTG
1 AATTTAAATTCAAATAATTTG
** * *
5195956 AAATTTAGTTTGAAATTATTTG
1 -AATTTAAATTCAAATAATTTG
5195978 AATTTAAATT
1 AATTTAAATT
5195988 AATTTAATTT
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
21 8 0.32
22 17 0.68
ACGTcount: A:0.43, C:0.02, G:0.08, T:0.47
Consensus pattern (21 bp):
AATTTAAATTCAAATAATTTG
Found at i:5196271 original size:29 final size:30
Alignment explanation
Indices: 5196203--5196298 Score: 133
Period size: 30 Copynumber: 3.3 Consensus size: 30
5196193 AATTTATAAA
5196203 AAAAATAATATTATAAAAATTAAAATTTTT
1 AAAAATAATATTATAAAAATTAAAATTTTT
*
5196233 AAAAATAATATTATAAAGATTAAAATTTTT
1 AAAAATAATATTATAAAAATTAAAATTTTT
* * * *
5196263 -TAAATAATACTATAAAAACT-AAATTTAT
1 AAAAATAATATTATAAAAATTAAAATTTTT
5196291 AAAAATAA
1 AAAAATAA
5196299 AAAATATCAA
Statistics
Matches: 58, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
28 7 0.12
29 22 0.38
30 29 0.50
ACGTcount: A:0.60, C:0.02, G:0.01, T:0.36
Consensus pattern (30 bp):
AAAAATAATATTATAAAAATTAAAATTTTT
Found at i:5196651 original size:5 final size:5
Alignment explanation
Indices: 5196625--5196663 Score: 51
Period size: 5 Copynumber: 7.2 Consensus size: 5
5196615 GAAAGAGTTG
5196625 TATTAA TATATA TATATA TATTA TATTA TATTA TATTA T
1 TATT-A TAT-TA TAT-TA TATTA TATTA TATTA TATTA T
5196664 GAAAGAGTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
5 18 0.56
6 13 0.41
7 1 0.03
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (5 bp):
TATTA
Found at i:5200385 original size:2 final size:2
Alignment explanation
Indices: 5200378--5200420 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
5200368 TAAATGAGGT
5200378 TC TC TC TC TC TC TC TC TC TC TC TC 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 TC TC TC
5200420 T
1 T
5200421 GTATGCACAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:5206880 original size:2 final size:2
Alignment explanation
Indices: 5206873--5206905 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
5206863 GGGTTTTAAC
*
5206873 AT AT AT AT AT AT AC AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5206906 ACATGTTATA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:5213247 original size:34 final size:34
Alignment explanation
Indices: 5213156--5213247 Score: 80
Period size: 33 Copynumber: 2.6 Consensus size: 34
5213146 AAAAATGTTA
* *
5213156 TATTTTTTAAAAAATAGAGATTTTTTGTTATTTGAAT
1 TATTTTTT-AAAAATA-TG-TTTTTTCTTATTTGAAT
* ** *
5213193 AATTTAATAAAAA-ATATTTTTTCTTATTTG-AT
1 TATTTTTTAAAAATATGTTTTTTCTTATTTGAAT
5213225 TATTTTTTGAAAAATATGTTTTT
1 TATTTTTT-AAAAATATGTTTTT
5213248 AAAATAATAT
Statistics
Matches: 43, Mismatches: 10, Indels: 7
0.72 0.17 0.12
Matches are distributed among these distances:
32 7 0.16
33 18 0.42
34 7 0.16
35 1 0.02
36 5 0.12
37 5 0.12
ACGTcount: A:0.36, C:0.01, G:0.08, T:0.55
Consensus pattern (34 bp):
TATTTTTTAAAAATATGTTTTTTCTTATTTGAAT
Found at i:5213388 original size:19 final size:18
Alignment explanation
Indices: 5213353--5213397 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
5213343 TAATTATGTT
5213353 TTAATAATAATATTTAATA
1 TTAA-AATAATATTTAATA
*
5213372 TTAAAATATTATATTAATA
1 TTAAAATAATAT-TTAATA
5213391 -TAAAATA
1 TTAAAATA
5213398 CTTAAAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 14 0.58
19 10 0.42
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TTAAAATAATATTTAATA
Found at i:5213678 original size:29 final size:29
Alignment explanation
Indices: 5213641--5213745 Score: 95
Period size: 29 Copynumber: 3.4 Consensus size: 29
5213631 TTTAACATTA
5213641 ATTATTAAAATAATAAAATATTA-TTATAT
1 ATTATTAAAATAATAAAATATTACTT-TAT
* * *
5213670 ATTATTAAAATAATAATATAATACTTTTT
1 ATTATTAAAATAATAAAATATTACTTTAT
* *
5213699 ATTATTGAAATATTAAAAATATTTACGTTTAAT
1 ATTATTAAAATAAT-AAAATA-TTAC-TTT-AT
*
5213732 AATATATAAAATAA
1 ATTAT-TAAAATAA
5213746 AATATTTAAA
Statistics
Matches: 59, Mismatches: 11, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
29 35 0.59
30 7 0.12
31 3 0.05
32 3 0.05
33 5 0.08
34 6 0.10
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (29 bp):
ATTATTAAAATAATAAAATATTACTTTAT
Found at i:5213846 original size:17 final size:18
Alignment explanation
Indices: 5213809--5213848 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
5213799 TTAAAATTAA
5213809 ATAA-AATATTTTATTAGT
1 ATAATAATATTTTA-TAGT
5213827 ATAATAATATTTTA-AGT
1 ATAATAATATTTTATAGT
5213844 ATAAT
1 ATAAT
5213849 CAAATCTCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 8 0.38
18 4 0.19
19 9 0.43
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (18 bp):
ATAATAATATTTTATAGT
Found at i:5220330 original size:10 final size:10
Alignment explanation
Indices: 5220317--5220345 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
5220307 CAACCTTGAC
5220317 TTTTCATGCA
1 TTTTCATGCA
5220327 TTTTCATGCA
1 TTTTCATGCA
5220337 TTTT-ATGCA
1 TTTTCATGCA
5220346 CATATGTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 5 0.26
10 14 0.74
ACGTcount: A:0.21, C:0.17, G:0.10, T:0.52
Consensus pattern (10 bp):
TTTTCATGCA
Found at i:5220885 original size:20 final size:19
Alignment explanation
Indices: 5220844--5220882 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 19
5220834 TATTATTTAT
5220844 TATTATTTTAAATATAAAA
1 TATTATTTTAAATATAAAA
5220863 TATTAATTTTAAAATATAAA
1 TATT-ATTTT-AAATATAAA
5220883 TATAAAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 4 0.22
20 5 0.28
21 9 0.50
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
TATTATTTTAAATATAAAA
Found at i:5220910 original size:9 final size:9
Alignment explanation
Indices: 5220882--5220961 Score: 75
Period size: 9 Copynumber: 9.3 Consensus size: 9
5220872 TAAAATATAA
5220882 ATATAAAAT
1 ATATAAAAT
5220891 -TA-AATAA-
1 ATATAA-AAT
5220898 ATATAAAAT
1 ATATAAAAT
5220907 ATATAAAAT
1 ATATAAAAT
5220916 ATATAAAA-
1 ATATAAAAT
5220924 ATATAAAAT
1 ATATAAAAT
*
5220933 -TAAATAAAT
1 ATATA-AAAT
5220942 A-ATATAAAT
1 ATATA-AAAT
5220951 ATAT-AAAT
1 ATATAAAAT
5220959 ATA
1 ATA
5220962 AAGACGAGTC
Statistics
Matches: 61, Mismatches: 2, Indels: 17
0.76 0.03 0.21
Matches are distributed among these distances:
7 2 0.03
8 26 0.43
9 31 0.51
10 2 0.03
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (9 bp):
ATATAAAAT
Found at i:5220935 original size:42 final size:43
Alignment explanation
Indices: 5220880--5220961 Score: 141
Period size: 42 Copynumber: 1.9 Consensus size: 43
5220870 TTTAAAATAT
5220880 AAATATAAAATTAAATAAAT-ATA-AAATATATAAAATATATAA
1 AAATATAAAATTAAATAAATAATATAAATATAT-AAATATATAA
5220922 AAATATAAAATTAAATAAATAATATAAATATATAAATATA
1 AAATATAAAATTAAATAAATAATATAAATATATAAATATA
5220962 AAGACGAGTC
Statistics
Matches: 38, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
42 20 0.53
43 10 0.26
44 8 0.21
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (43 bp):
AAATATAAAATTAAATAAATAATATAAATATATAAATATATAA
Found at i:5220947 original size:27 final size:26
Alignment explanation
Indices: 5220880--5220957 Score: 65
Period size: 25 Copynumber: 3.0 Consensus size: 26
5220870 TTTAAAATAT
5220880 AAATATAAAATTAAAT-AAATATA-AA
1 AAATATAAAA-TAAATAAAATATATAA
* *
5220905 ATATATAAAATATATAAAA-ATATAA
1 AAATATAAAATAAATAAAATATATAA
* *
5220930 AATTAAATAAAT-AATATAAATATATAA
1 AAATATA-AAATAAATA-AAATATATAA
5220957 A
1 A
5220958 TATAAAGACG
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
24 7 0.17
25 21 0.50
26 7 0.17
27 7 0.17
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (26 bp):
AAATATAAAATAAATAAAATATATAA
Found at i:5220963 original size:27 final size:25
Alignment explanation
Indices: 5220875--5220963 Score: 64
Period size: 25 Copynumber: 3.6 Consensus size: 25
5220865 TTAATTTTAA
5220875 AATATAAATATAAAAT-TAAATAAAT
1 AATATAAATATAAAATATAAA-AAAT
*
5220900 -ATAAAATATATAAAATATATAAAAAT
1 AATATAA-ATATAAAATATA-AAAAAT
*
5220926 -ATA-AAAT-TAAATAAATAATATAAAT
1 AATATAAATATAAA-ATATAA-A-AAAT
5220951 -ATATAAATATAAA
1 AATATAAATATAAA
5220964 GACGAGTCAA
Statistics
Matches: 54, Mismatches: 2, Indels: 14
0.77 0.03 0.20
Matches are distributed among these distances:
23 5 0.09
24 12 0.22
25 18 0.33
26 13 0.24
27 6 0.11
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (25 bp):
AATATAAATATAAAATATAAAAAAT
Found at i:5221473 original size:24 final size:23
Alignment explanation
Indices: 5221418--5221473 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 23
5221408 TTTAAAATTT
*
5221418 TTTAATAAAAAATTTATATTAAA
1 TTTAATAAAAAATTAATATTAAA
**
5221441 TAAATATAAAAAATTAATATTTAAA
1 TTTA-ATAAAAAATTAATA-TTAAA
5221466 TTTAATAA
1 TTTAATAA
5221474 TATCGTAATA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
23 2 0.08
24 17 0.65
25 7 0.27
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (23 bp):
TTTAATAAAAAATTAATATTAAA
Found at i:5227933 original size:18 final size:17
Alignment explanation
Indices: 5227903--5227937 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
5227893 TTTACCAACA
5227903 TAAAAAAATTTAAATAG
1 TAAAAAAATTTAAATAG
*
5227920 TAAATAAATATTAAATAG
1 TAAAAAAAT-TTAAATAG
5227938 ATTAGATAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (17 bp):
TAAAAAAATTTAAATAG
Found at i:5234856 original size:46 final size:46
Alignment explanation
Indices: 5234804--5234894 Score: 173
Period size: 46 Copynumber: 2.0 Consensus size: 46
5234794 TAGCAGGCAA
*
5234804 AAAATTACATTCTCTTTCAAGTCCATTCAACAATATACTAAAAAGG
1 AAAATTACATTCTCTTTCAAGTACATTCAACAATATACTAAAAAGG
5234850 AAAATTACATTCTCTTTCAAGTACATTCAACAATATACTAAAAAG
1 AAAATTACATTCTCTTTCAAGTACATTCAACAATATACTAAAAAG
5234895 AAGTTAATTT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.45, C:0.19, G:0.05, T:0.31
Consensus pattern (46 bp):
AAAATTACATTCTCTTTCAAGTACATTCAACAATATACTAAAAAGG
Found at i:5235844 original size:1 final size:1
Alignment explanation
Indices: 5235838--5235868 Score: 53
Period size: 1 Copynumber: 31.0 Consensus size: 1
5235828 TTATTTTCCC
*
5235838 TTTTTTTTTTTTTTTTTTTTTTTTTTCTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
5235869 CCTTCTTTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.03, G:0.00, T:0.97
Consensus pattern (1 bp):
T
Found at i:5236869 original size:45 final size:43
Alignment explanation
Indices: 5236748--5236869 Score: 113
Period size: 45 Copynumber: 2.7 Consensus size: 43
5236738 TATATATATA
* * **
5236748 TTTTTTTATCTATTAATATTTTTATTATTTATCTGTTTTATTT
1 TTTTTTTATCTATTAATATATTTATTTTTTATCTGAATTATTT
* * *
5236791 TTTTTATTAT-TATTTATCTATTTCTTTTATTTATCT-AATTACTTT
1 TTTTT-TTATCTATTAATATATTT-ATTT-TTTATCTGAATTA-TTT
5236836 TTTTTGTTATCTATTAATATATTTATCTTTTTAT
1 TTTTT-TTATCTATTAATATATTTAT-TTTTTAT
5236870 TTTGATTAAT
Statistics
Matches: 62, Mismatches: 11, Indels: 10
0.75 0.13 0.12
Matches are distributed among these distances:
43 15 0.24
44 9 0.15
45 25 0.40
46 13 0.21
ACGTcount: A:0.22, C:0.07, G:0.02, T:0.70
Consensus pattern (43 bp):
TTTTTTTATCTATTAATATATTTATTTTTTATCTGAATTATTT
Found at i:5237434 original size:20 final size:20
Alignment explanation
Indices: 5237395--5237434 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
5237385 GTTTTAGAGA
* *
5237395 GAAGAGAGAGAATAGGAAGG
1 GAAGAGAGAGAAAAGAAAGG
5237415 GAAGAGAGAGAAAAGAAAGG
1 GAAGAGAGAGAAAAGAAAGG
5237435 CTCGATTTGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.42, T:0.03
Consensus pattern (20 bp):
GAAGAGAGAGAAAAGAAAGG
Found at i:5237886 original size:59 final size:59
Alignment explanation
Indices: 5237815--5238499 Score: 855
Period size: 59 Copynumber: 11.7 Consensus size: 59
5237805 ATAAAATGTA
* *
5237815 AAAAAAAATATTTTTAAGGAAAAGTTAAAAGTATCAATTTTTCTTGAAAATAAGCTTTC
1 AAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAGCTTTC
* *
5237874 AAAAAAAATATTTTTAAGAAAAAGTTGAAAGTATCAA-TTTTCTTTGAAAATAAGCTTTC
1 AAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTC-TTGAAAATAAGCTTTC
* * *
5237933 TAAAAAAAATATTTTTG-GGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAGTTTTC
1 -AAAAAAAATATTTTTGAGG-AAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAGCTTTC
*
5237993 AAAAAAAA-GTTTTTGAGGAAAAGTTGAAAGTATCAA-TTTTCTTTGAAAATAAGCTTTC
1 AAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTC-TTGAAAATAAGCTTTC
* * * *
5238051 TAAAAAAAATATTTTAG-GAGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAGTTTTC
1 -AAAAAAAATATTTTTGAG-GAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAGCTTTC
* *
5238111 AAAAAAGA-ATTTTTGAGGAAAAGTTGAAAGTATCAA-TTTTCTTTGAAAATAAACTTTC
1 AAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTC-TTGAAAATAAGCTTTC
* * * * *
5238169 TAAAAAAATATTTTTG-GAAAAAAATTGAAAGTATCAATTTTT-TTAAAAATAAGTTTTC
1 AAAAAAAATATTTTTGAG-GAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAGCTTTC
*
5238227 ---AAAAATATTTTTGAAGAAAAGTTGAAAGTATCAA-TTTTCTTTGAAAATAAGCTTTC
1 AAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTC-TTGAAAATAAGCTTTC
* * *
5238283 AAAAAAAATATCTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAGTTTTTC
1 AAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAG-CTTTC
* * * * *
5238343 TAAAAAATTATTTTTGAGGAAAAGTTAAAAATATCAATTTTCCTTGAAAATAAGCTTTC
1 AAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAGCTTTC
* * * *
5238402 AAAAAAAATATCTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTCGAAATTAAGGTTTC
1 AAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAGCTTTC
*
5238461 -TAAAAAATA--TTTG-GGAAAAAGTTGAAAGTATCAATTTTT
1 AAAAAAAATATTTTTGAGG-AAAAGTTGAAAGTATCAATTTTT
5238500 TCTGTACAAA
Statistics
Matches: 548, Mismatches: 54, Indels: 51
0.84 0.08 0.08
Matches are distributed among these distances:
54 4 0.01
55 32 0.06
56 41 0.07
57 8 0.01
58 109 0.20
59 200 0.36
60 146 0.27
61 8 0.01
ACGTcount: A:0.45, C:0.07, G:0.12, T:0.36
Consensus pattern (59 bp):
AAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAGCTTTC
Found at i:5238022 original size:118 final size:116
Alignment explanation
Indices: 5237815--5238498 Score: 941
Period size: 118 Copynumber: 5.8 Consensus size: 116
5237805 ATAAAATGTA
* * * * *
5237815 AAAAAAAATATTTTTAAGGAAAAGTTAAAAGTATCAATTTTTCTTGAAAATAAGCTTTCAAAAAA
1 AAAAAAAATATTTTT-GGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAGTTTTC-AAAAA
* *
5237880 AATATTTTTAAGAAAAAGTTGAAAGTATCAATTTTCTTTGAAAATAAGCTTTCT
64 AA-ATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCTTTGAAAATAAGCTTTCT
5237934 AAAAAAAATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAGTTTTCAAAAAA
1 AAAAAAAATATTTTTGGG-AAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAGTTTTCAAAAAA
5237999 AAGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCTTTGAAAATAAGCTTTCT
65 AA-TTTTTGAGGAAAAGTTGAAAGTATCAATTTTCTTTGAAAATAAGCTTTCT
*
5238052 AAAAAAAATATTTTAGGAGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAGTTTTCAAAAAA
1 AAAAAAAATATTTTTGG-GAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAGTTTTCAAAAAA
*
5238117 GAATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCTTTGAAAATAAACTTTCT
65 -AATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCTTTGAAAATAAGCTTTCT
* * *
5238170 -AAAAAAATATTTTTGGAAAAAAATTGAAAGTATCAATTTT-TTTAAAAATAAGTTTTC-AAAAA
1 AAAAAAAATATTTTTGG-GAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAGTTTTCAAAAAA
* *
5238232 TATTTTTGAAGAAAAGTTGAAAGTATCAATTTTCTTTGAAAATAAGCTTTC-
65 AATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCTTTGAAAATAAGCTTTCT
* *
5238283 AAAAAAAATATCTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAGTTTTTCTAAAA
1 AAAAAAAATATTTTTG-GGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAG-TTTTC-AAAA
* * * *
5238348 AATTATTTTTGAGGAAAAGTTAAAAATATCAATTTTCCTTGAAAATAAGCTTTC-
63 AA-AATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCTTTGAAAATAAGCTTTCT
* * ** * * *
5238402 AAAAAAAATATCTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTCGAAATTAAGGTTTC-TAAAA
1 AAAAAAAATATTTTTG-GGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAGTTTTCAAAAAA
*
5238466 AATATTTG-GGAAAAAGTTGAAAGTATCAATTTT
65 AATTTTTGAGG-AAAAGTTGAAAGTATCAATTTT
5238499 TTCTGTACAA
Statistics
Matches: 519, Mismatches: 34, Indels: 28
0.89 0.06 0.05
Matches are distributed among these distances:
114 85 0.16
115 42 0.08
116 25 0.05
117 38 0.07
118 177 0.34
119 152 0.29
ACGTcount: A:0.45, C:0.07, G:0.12, T:0.36
Consensus pattern (116 bp):
AAAAAAAATATTTTTGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAGTTTTCAAAAAAA
ATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCTTTGAAAATAAGCTTTCT
Found at i:5238270 original size:30 final size:30
Alignment explanation
Indices: 5238236--5238338 Score: 81
Period size: 30 Copynumber: 3.5 Consensus size: 30
5238226 CAAAAATATT
5238236 TTTGAAGAA-AAGTTGAAAGTATCAATTTTC
1 TTTGAA-AATAAGTTGAAAGTATCAATTTTC
* * * *
5238266 TTTGAAAATAAGCTTTCAAA--A-AAAATATC
1 TTTGAAAATAAG--TTGAAAGTATCAATTTTC
*
5238295 TTTGAGGAA-AAGTTGAAAGTATCAATTTTC
1 TTTGA-AAATAAGTTGAAAGTATCAATTTTC
*
5238325 CTTGAAAATAAGTT
1 TTTGAAAATAAGTT
5238339 TTTCTAAAAA
Statistics
Matches: 54, Mismatches: 11, Indels: 16
0.67 0.14 0.20
Matches are distributed among these distances:
27 5 0.09
29 18 0.33
30 26 0.48
32 5 0.09
ACGTcount: A:0.43, C:0.08, G:0.15, T:0.35
Consensus pattern (30 bp):
TTTGAAAATAAGTTGAAAGTATCAATTTTC
Found at i:5242477 original size:13 final size:13
Alignment explanation
Indices: 5242455--5242497 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
5242445 ACAATGGATG
*
5242455 AAAAATGAGAAAA
1 AAAAAAGAGAAAA
*
5242468 AAAAAAGAGAGAA
1 AAAAAAGAGAAAA
*
5242481 AAAATAGAGGAAAA
1 AAAAAAGA-GAAAA
5242495 AAA
1 AAA
5242498 TGAGAAAATG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
13 18 0.72
14 7 0.28
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.05
Consensus pattern (13 bp):
AAAAAAGAGAAAA
Found at i:5244331 original size:83 final size:83
Alignment explanation
Indices: 5244188--5244377 Score: 301
Period size: 83 Copynumber: 2.3 Consensus size: 83
5244178 CATGTTGTCA
* * * * **
5244188 AGGAACAATTTACTTTTC-AAAGTTGTGGTGCCTTTGTTTAGAGGAGTAATTTGTTTTTCAAAGT
1 AGGAACAATTTACTTTCCAAAAGTTGAGGTGCCTTTATTTAGAGGAGCAATTTACTTTTCAAAGT
5244252 TGTGGTGCCTCTATTTAG
66 TGTGGTGCCTCTATTTAG
* *
5244270 ATGAGCAATTTACTTTCCAAAAGTTGAGGTGCCTTTATTTAGAGGAGCAATTTACTTTTCAAAGT
1 AGGAACAATTTACTTTCCAAAAGTTGAGGTGCCTTTATTTAGAGGAGCAATTTACTTTTCAAAGT
5244335 TGTGGTGCCTCTATTTAG
66 TGTGGTGCCTCTATTTAG
5244353 AGGAACAATTTACTTTCCAAAAGTT
1 AGGAACAATTTACTTTCCAAAAGTT
5244378 AAGCCTCTGA
Statistics
Matches: 97, Mismatches: 10, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
82 15 0.15
83 82 0.85
ACGTcount: A:0.27, C:0.13, G:0.21, T:0.39
Consensus pattern (83 bp):
AGGAACAATTTACTTTCCAAAAGTTGAGGTGCCTTTATTTAGAGGAGCAATTTACTTTTCAAAGT
TGTGGTGCCTCTATTTAG
Found at i:5244447 original size:42 final size:41
Alignment explanation
Indices: 5244195--5244695 Score: 343
Period size: 42 Copynumber: 12.0 Consensus size: 41
5244185 TCAAGGAACA
* * * * *
5244195 ATTTACTTTTCAAAGTTGTGGTGCCTTTGTTTAGAGGAG-T
1 ATTTACTTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAGCT
** * * * * *
5244235 AATTTGTTTTTCAAAGTTGTGGTGCCTCT-ATTTAGATGAGCA
1 -ATTTACTTTTCAAAGTCGTTGAGCCTCTGA-TTAGAGGAGCT
* * ** * * *
5244277 ATTTACTTTCCAAAAGTTGAGGTGCCT-TTATTTAGAGGAGCA
1 ATTTACTTTTC-AAAGTCGTTGAGCCTCTGA-TTAGAGGAGCT
* * * * *
5244319 ATTTACTTTTCAAAGTTGTGGTGCCTCT-ATTTAGAGGAACA
1 ATTTACTTTTCAAAGTCGTTGAGCCTCTGA-TTAGAGGAGCT
* * * *
5244360 ATTTACTTTCCAAA--AGTTAAGCCTCTGATTAG-GAGAGCC
1 ATTTACTTTTCAAAGTCGTTGAGCCTCTGATTAGAG-GAGCT
*
5244399 ATTTACTTTTCAAAAGTCGTTGAGCCTTTGATTAGAGGAGCT
1 ATTTACTTTTC-AAAGTCGTTGAGCCTCTGATTAGAGGAGCT
* * *
5244441 ACTTACTTTCCAAAAGTTGTTGAGCCTCTGATTAGAGGAGCTTT
1 ATTTACTTTTC-AAAGTCGTTGAGCCTCTGATTAGAGGAGC--T
* * * * * *
5244485 AGTTA-TTTTCAAAGTTGTTAAGCCTCTGATTAAAGAAGCC
1 ATTTACTTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAGCT
*
5244525 ATTTACTTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAGCC
1 ATTTACTTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAGCT
* *
5244566 ATTTATTTTTTCAAAGTCGTTGAGCCTCTGATTAGATGAGCTT
1 ATTTA-CTTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAGC-T
* * * * *
5244609 GTTTATTTTTCAAAAGTCTTTGAACCTCTGATTAAAGGAGCTTT
1 ATTTACTTTTC-AAAGTCGTTGAGCCTCTGATTAGAGGAGC--T
* * * *
5244653 GTTTATGTTTCTCAAAGTCGTTAAGCCTCTGCTTAGAGGAGCT
1 ATTTA-CTTT-TCAAAGTCGTTGAGCCTCTGATTAGAGGAGCT
5244696 TGGATCAAAA
Statistics
Matches: 385, Mismatches: 55, Indels: 38
0.81 0.12 0.08
Matches are distributed among these distances:
38 1 0.00
39 25 0.06
40 8 0.02
41 117 0.30
42 158 0.41
43 35 0.09
44 12 0.03
45 27 0.07
46 2 0.01
ACGTcount: A:0.26, C:0.15, G:0.20, T:0.39
Consensus pattern (41 bp):
ATTTACTTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAGCT
Found at i:5244559 original size:83 final size:83
Alignment explanation
Indices: 5244405--5244683 Score: 296
Period size: 83 Copynumber: 3.3 Consensus size: 83
5244395 AGCCATTTAC
* * * * * *
5244405 TTTTCAAAAGTCGTTGAGCCTTTGATTAGAGGAGCTACTTACTTTCCAAAAGTTGTTGAGCCTCT
1 TTTTC-AAAGTCGTTAAGCCTCTGATTA-AAGAGCTATTTACTTTTCAAAAGTCGTTGAGCCTCT
5244470 GATTAGAGGAGCTTTAGTTA
64 GATTAGAGGAGCTTTAGTTA
* *
5244490 TTTTCAAAGTTGTTAAGCCTCTGATTAAAGAAGCCATTTACTTTTC-AAAGTCGTTGAGCCTCTG
1 TTTTCAAAGTCGTTAAGCCTCTGATTAAAG-AGCTATTTACTTTTCAAAAGTCGTTGAGCCTCTG
5244554 ATTAGAGGAGCCATTTA-TT-
65 ATTAGAGGAG-C-TTTAGTTA
* * * * * *
5244573 TTTTCAAAGTCGTTGAGCCTCTGATTAGATGAGCTTGTTTATTTTTCAAAAGTCTTTGAACCTCT
1 TTTTCAAAGTCGTTAAGCCTCTGATTA-AAGAGC-TATTTACTTTTCAAAAGTCGTTGAGCCTCT
*
5244638 GATTAAAGGAGCTTT-GTTTA
64 GATTAGAGGAGCTTTAG-TTA
5244658 TGTTTCTCAAAGTCGTTAAGCCTCTG
1 --TTT-TCAAAGTCGTTAAGCCTCTG
5244684 CTTAGAGGAG
Statistics
Matches: 164, Mismatches: 18, Indels: 21
0.81 0.09 0.10
Matches are distributed among these distances:
83 60 0.37
84 48 0.29
85 34 0.21
87 3 0.02
88 19 0.12
ACGTcount: A:0.25, C:0.16, G:0.20, T:0.39
Consensus pattern (83 bp):
TTTTCAAAGTCGTTAAGCCTCTGATTAAAGAGCTATTTACTTTTCAAAAGTCGTTGAGCCTCTGA
TTAGAGGAGCTTTAGTTA
Found at i:5244588 original size:125 final size:127
Alignment explanation
Indices: 5244375--5244694 Score: 368
Period size: 125 Copynumber: 2.5 Consensus size: 127
5244365 CTTTCCAAAA
* *
5244375 GTTAAGCCTCTGATT-AGGAGAGCCATTTACTTTTCAAAAGTCGTTGAGCCTTTGATTAGAGGAG
1 GTTAAGCCTCTGATTAAAGA-AGCCATTTACTTTTC-AAAGTCGTTGAGCCTCTGATTAGAGGAG
* *
5244439 CTACTTACTTTCCAAAAGTTGTTGAGCCTCTGATTAGAGGAGCTT-TAGTTA-TTTTC-AAAGT-
64 CCACTTACTTTCCAAAAGTCGTTGAGCCTCTGATTAGAGGAGCTTGT--TTATTTTTCAAAAGTC
5244500 T
127 T
5244501 GTTAAGCCTCTGATTAAAGAAGCCATTTACTTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAGCC
1 GTTAAGCCTCTGATTAAAGAAGCCATTTACTTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAGCC
* * * *
5244566 ATTTATTTTTTC-AAAGTCGTTGAGCCTCTGATTAGATGAGCTTGTTTATTTTTCAAAAGTCT
66 ACTTA-CTTTCCAAAAGTCGTTGAGCCTCTGATTAGAGGAGCTTGTTTATTTTTCAAAAGTCT
* ** * * *
5244628 -TTGAA-CCTCTGATTAAAGGAGCTTTGTTTATGTTTCTCAAAGTCGTTAAGCCTCTGCTTAGAG
1 GTT-AAGCCTCTGATTAAAGAAGC--CATTTA-CTTT-TCAAAGTCGTTGAGCCTCTGATTAGAG
5244691 GAGC
61 GAGC
5244695 TTGGATCAAA
Statistics
Matches: 169, Mismatches: 14, Indels: 18
0.84 0.07 0.09
Matches are distributed among these distances:
124 3 0.02
125 66 0.39
126 58 0.34
127 6 0.04
128 4 0.02
129 3 0.02
130 29 0.17
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.37
Consensus pattern (127 bp):
GTTAAGCCTCTGATTAAAGAAGCCATTTACTTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAGCC
ACTTACTTTCCAAAAGTCGTTGAGCCTCTGATTAGAGGAGCTTGTTTATTTTTCAAAAGTCT
Found at i:5244733 original size:22 final size:21
Alignment explanation
Indices: 5244708--5244749 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
5244698 GATCAAAATT
5244708 TTAACAAAAAAAAAATAAAAAA
1 TTAA-AAAAAAAAAATAAAAAA
*
5244730 TTAAAACAAAAAAATAAAAA
1 TTAAAAAAAAAAAATAAAAA
5244750 CAAAAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.81, C:0.05, G:0.00, T:0.14
Consensus pattern (21 bp):
TTAAAAAAAAAAAATAAAAAA
Found at i:5244757 original size:14 final size:14
Alignment explanation
Indices: 5244724--5244757 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
5244714 AAAAAAAAAT
*
5244724 AAAAAATTAAAACA
1 AAAAAATAAAAACA
5244738 AAAAAATAAAAACA
1 AAAAAATAAAAACA
5244752 AAAAAA
1 AAAAAA
5244758 ATGTCTAGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.85, C:0.06, G:0.00, T:0.09
Consensus pattern (14 bp):
AAAAAATAAAAACA
Found at i:5245005 original size:22 final size:22
Alignment explanation
Indices: 5244971--5245086 Score: 64
Period size: 22 Copynumber: 5.3 Consensus size: 22
5244961 TTCATTATAT
*
5244971 TTTTTATTTTTTATCTATTAATA
1 TTTTTA-TATTTATCTATTAATA
* **
5244994 TTTTTATATTTATCTGTTTTTA
1 TTTTTATATTTATCTATTAATA
* *
5245016 TTTTTTTA-TTAT-TATTTATCTA
1 TTTTTATATTTATCTA-TTA-ATA
*
5245038 TTTCTTTTATTTATCTAATT-AT-
1 TTT-TTATATTTATCT-ATTAATA
*
5245060 TTTTT-T-GTTATCTATTAATA
1 TTTTTATATTTATCTATTAATA
*
5245080 TATTTAT
1 TTTTTAT
5245087 TTTTTTATTT
Statistics
Matches: 73, Mismatches: 11, Indels: 20
0.70 0.11 0.19
Matches are distributed among these distances:
18 3 0.04
19 8 0.11
20 6 0.08
21 9 0.12
22 27 0.37
23 12 0.16
24 4 0.05
25 3 0.04
26 1 0.01
ACGTcount: A:0.23, C:0.05, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTTTATATTTATCTATTAATA
Found at i:5245108 original size:44 final size:43
Alignment explanation
Indices: 5244959--5245113 Score: 118
Period size: 43 Copynumber: 3.6 Consensus size: 43
5244949 TTTCTTTTTA
* * * * *
5244959 TTTTCATTATATT-TTTTATTTTTTATCTATTAATATTTTTATA
1 TTTTTATTTTATTATTTT-TTTGTTATCTATTAATATATTTATT
* * * * * *
5245002 TTTATCTGTTT-TTATTTTTTTATTAT-TATTTATCTATTTCTT
1 TTTTTAT-TTTATTATTTTTTTGTTATCTATTAATATATTTATT
* *
5245044 TTATTTATCTAATTATTTTTTTGTTATCTATTAATATATTTATT
1 TT-TTTATTTTATTATTTTTTTGTTATCTATTAATATATTTATT
* *
5245088 TTTTTATTTTGATTAATTTTTGGTTA
1 TTTTTATTTT-ATTATTTTTTTGTTA
5245114 ATATTAGGAT
Statistics
Matches: 84, Mismatches: 22, Indels: 11
0.72 0.19 0.09
Matches are distributed among these distances:
42 14 0.17
43 36 0.43
44 34 0.40
ACGTcount: A:0.23, C:0.05, G:0.03, T:0.70
Consensus pattern (43 bp):
TTTTTATTTTATTATTTTTTTGTTATCTATTAATATATTTATT
Found at i:5245445 original size:19 final size:19
Alignment explanation
Indices: 5245423--5245459 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
5245413 TTTAGATTTC
* *
5245423 GGTTGAATTTTTTGGTGAA
1 GGTTAAATTTTTCGGTGAA
5245442 GGTTAAATTTTTCGGTGA
1 GGTTAAATTTTTCGGTGA
5245460 CTTTTTCGGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.22, C:0.03, G:0.30, T:0.46
Consensus pattern (19 bp):
GGTTAAATTTTTCGGTGAA
Found at i:5245652 original size:15 final size:16
Alignment explanation
Indices: 5245618--5245661 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
5245608 TTTGGGTTTT
*
5245618 AGAGAGAGGGGAGAGA
1 AGAGAGAGGGAAGAGA
5245634 AGAG-GAAGGGAAGAG-
1 AGAGAG-AGGGAAGAGA
5245649 AGAGAGAGGGAAG
1 AGAGAGAGGGAAG
5245662 GCTCGGTCTG
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
15 12 0.48
16 13 0.52
ACGTcount: A:0.45, C:0.00, G:0.55, T:0.00
Consensus pattern (16 bp):
AGAGAGAGGGAAGAGA
Found at i:5245971 original size:19 final size:19
Alignment explanation
Indices: 5245934--5245971 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
5245924 GGTTTTTTAT
*
5245934 TTATTTATTATTATTATTA
1 TTATTTATTATTATGATTA
5245953 TTATTTATTGATTA-GATTA
1 TTATTTATT-ATTATGATTA
5245972 GATTTGTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (19 bp):
TTATTTATTATTATGATTA
Found at i:5245997 original size:5 final size:5
Alignment explanation
Indices: 5245987--5246051 Score: 71
Period size: 5 Copynumber: 12.8 Consensus size: 5
5245977 GTTTAATACT
* *
5245987 TTTTA TTTTA TTTTA TTTTA -TTT- CTTTA TTTTTA TTTCCA TTTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA -TTTTA TTT-TA -TTTTA
5246033 TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTT
5246052 CTTTAAATAA
Statistics
Matches: 52, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
4 6 0.12
5 37 0.71
6 6 0.12
7 3 0.06
ACGTcount: A:0.17, C:0.05, G:0.00, T:0.78
Consensus pattern (5 bp):
TTTTA
Found at i:5246198 original size:29 final size:29
Alignment explanation
Indices: 5246111--5246200 Score: 73
Period size: 29 Copynumber: 3.1 Consensus size: 29
5246101 TCAATTTTCC
**
5246111 TTGAAAATAAGCTTTCAAAAAAAATATTT
1 TTGAAAATAAGCTTTTTAAAAAAATATTT
*
5246140 TTGAAGAA-AAG----TTAAAATTATCAATTTTT
1 TTGAA-AATAAGCTTTTTAAAA--A--AATATTT
5246169 TTGAAAATAAGCTTTTTAAAAAAATATTT
1 TTGAAAATAAGCTTTTTAAAAAAATATTT
5246198 TTG
1 TTG
5246201 GGAAAAAATT
Statistics
Matches: 47, Mismatches: 4, Indels: 20
0.66 0.06 0.28
Matches are distributed among these distances:
25 4 0.09
27 1 0.02
28 2 0.04
29 31 0.66
30 2 0.04
31 1 0.02
33 6 0.13
ACGTcount: A:0.47, C:0.04, G:0.09, T:0.40
Consensus pattern (29 bp):
TTGAAAATAAGCTTTTTAAAAAAATATTT
Found at i:5246200 original size:58 final size:59
Alignment explanation
Indices: 5246064--5246629 Score: 547
Period size: 58 Copynumber: 9.7 Consensus size: 59
5246054 TTAAATAAAA
* * * *
5246064 TTAAAAAATATATATTTTTATGAAAAAGTTGAAAGGATCAATTTTCCTTGAAAATAAGCTTT
1 TTAAAAAA-ATAT-TTTTGAAG-AAAAGTTGAAAGTATCAATTTTCTTTGAAAATAAGCTTT
** * *
5246126 CAAAAAAAATATTTTTGAAGAAAAGTTAAAATTATCAATTTT-TTTGAAAATAAGCTTT
1 TTAAAAAAATATTTTTGAAGAAAAGTTGAAAGTATCAATTTTCTTTGAAAATAAGCTTT
* *
5246184 TTAAAAAAATATTTTTGGGAA-AAAA-TTGAAAGTATCAATTTTCCTTAAAAATAAG-TTT
1 TTAAAAAAATATTTTT--GAAGAAAAGTTGAAAGTATCAATTTTCTTTGAAAATAAGCTTT
* *** **
5246242 TCAAAAAAGGGTTTTTG-AGAAAAAGTTGAAAGTATCAATTTTCTTCAAAAATAAGCTTT
1 TTAAAAAAATATTTTTGAAG-AAAAGTTGAAAGTATCAATTTTCTTTGAAAATAAGCTTT
* * *
5246301 CTAAAAAAAATATTTTTGGAGAAAAGTTGAAAGTATCAATTTT-TTTAAAAATAAG--TT
1 -TTAAAAAAATATTTTTGAAGAAAAGTTGAAAGTATCAATTTTCTTTGAAAATAAGCTTT
* * * * ** *
5246358 TT-CAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTCGAAGTTAAGGTTT
1 TTAAAAAAATATTTTTGAAGAAAAGTTGAAAGTATCAATTTTCTTTGAAAATAAGCTTT
* * *
5246416 TT-AAAAAATA-TTTTGAGGAAAAGTTGAAAGTATTAATTTT-TCTTGAAAATAAGTTTT
1 TTAAAAAAATATTTTTGAAGAAAAGTTGAAAGTATCAATTTTCT-TTGAAAATAAGCTTT
* *
5246473 TTTAAAAAATATTTTTG-AGAAAAAGTTGAAAGTATCAATTTTGC-TTAAAAATAAGC-TT
1 TTAAAAAAATATTTTTGAAG-AAAAGTTGAAAGTATCAATTTT-CTTTGAAAATAAGCTTT
* * * * * * *
5246531 TAAAAAAAATATCTTTGAGGAAAAGTTGAAAGTATAAATTTT-TCTCGAAATTAAGGTTT
1 TTAAAAAAATATTTTTGAAGAAAAGTTGAAAGTATCAATTTTCT-TTGAAAATAAGCTTT
* *
5246590 TT-AAAAAATATTTTGGAA-AAAAGTTGAAAATATCAATTTT
1 TTAAAAAAATATTTTTGAAGAAAAGTTGAAAGTATCAATTTT
5246630 TCCTGTACAA
Statistics
Matches: 422, Mismatches: 60, Indels: 49
0.79 0.11 0.09
Matches are distributed among these distances:
55 37 0.09
56 9 0.02
57 68 0.16
58 165 0.39
59 87 0.21
60 44 0.10
61 6 0.01
62 6 0.01
ACGTcount: A:0.44, C:0.05, G:0.13, T:0.38
Consensus pattern (59 bp):
TTAAAAAAATATTTTTGAAGAAAAGTTGAAAGTATCAATTTTCTTTGAAAATAAGCTTT
Found at i:5246224 original size:117 final size:117
Alignment explanation
Indices: 5246064--5246629 Score: 604
Period size: 117 Copynumber: 4.9 Consensus size: 117
5246054 TTAAATAAAA
** * *
5246064 TTAAAAAATATATATTTTTATGAAAAAGTTGAAAGGATCAATTTTCCTTGAAAATAAGCTTTCAA
1 TTAAAAAA-A-ATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAGTTTTC-A
* * **
5246129 AAAAAATATTTTTGAAGAAAAGTTAAAATTATCAATTTT-TTTGAAAATAAGCTT
63 AAAAAATATTTTTGAAGAAAAGTTGAAAGTATCAATTTTCTTCAAAAATAAGCTT
* * *
5246183 TTTAAAAAAATATTTTTGGGAAAAAATTGAAAGTATCAATTTTCCTTAAAAATAAGTTTTCAAAA
1 TTAAAAAAAATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAGTTTTCAAAA
***
5246248 AAGGGTTTTTG-AGAAAAAGTTGAAAGTATCAATTTTCTTCAAAAATAAGCTT
66 AAATATTTTTGAAG-AAAAGTTGAAAGTATCAATTTTCTTCAAAAATAAGCTT
* *
5246300 TCTAAAAAAAATATTTTT-GGAGAAAAGTTGAAAGTATCAATTTT-TTTAAAAATAAGTTTTC--
1 T-TAAAAAAAATATTTTTGGGA-AAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAGTTTTCAA
* * * ** *
5246361 AAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTCGAAGTTAAGGTT
64 AAAAATATTTTTGAAGAAAAGTTGAAAGTATCAATTTTCTTCAAAAATAAGCTT
* * * **
5246415 TT-TAAAAAATA-TTTTGAGG-AAAAGTTGAAAGTATTAATTTTTCTTGAAAATAAGTTTTTTTA
1 TTAAAAAAAATATTTTTG-GGAAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAG-TTTTCAA
5246477 AAAAATATTTTTG-AGAAAAAGTTGAAAGTATCAATTTTGCTT-AAAAATAAGC-T
64 AAAAATATTTTTGAAG-AAAAGTTGAAAGTATCAATTTT-CTTCAAAAATAAGCTT
* * * * * *
5246530 TTAAAAAAAATATCTTTGAGG-AAAAGTTGAAAGTATAAATTTTTCTCGAAATTAAGGTTTT-TA
1 TTAAAAAAAATATTTTTG-GGAAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAA-GTTTTCAA
* *
5246593 AAAAATATTTTGGAA-AAAAGTTGAAAATATCAATTTT
64 AAAAATATTTTTGAAGAAAAGTTGAAAGTATCAATTTT
5246630 TCCTGTACAA
Statistics
Matches: 386, Mismatches: 44, Indels: 38
0.82 0.09 0.08
Matches are distributed among these distances:
112 25 0.06
113 18 0.05
114 7 0.02
115 71 0.18
116 96 0.25
117 124 0.32
118 38 0.10
119 7 0.02
ACGTcount: A:0.44, C:0.05, G:0.13, T:0.38
Consensus pattern (117 bp):
TTAAAAAAAATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAGTTTTCAAAA
AAATATTTTTGAAGAAAAGTTGAAAGTATCAATTTTCTTCAAAAATAAGCTT
Found at i:5246512 original size:116 final size:114
Alignment explanation
Indices: 5246087--5246629 Score: 612
Period size: 116 Copynumber: 4.7 Consensus size: 114
5246077 ATTTTTATGA
* * **
5246087 AAAAGTTGAAAGGATCAATTTTCCTTGAAAATAAGCTTTCAAAAAAAATATTTTTGA-AGAAAAG
1 AAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAG-TTT-TTAAAAAATATTTTTGAGA-AAAAG
* * * **
5246151 TTAAAATTATCAATTTT-TTTGAAAATAAGCTTTTTAAAAAAATATTTTTGGG
63 TTGAAAGTATCAATTTTCCTCAAAAATAAGC-TTTTAAAAAAATATTTTTGGG
* * * * **
5246203 AAAAAATTGAAAGTATCAATTTTCCTTAAAAATAAGTTTTCAAAAAAGGGTTTTTGAGAAAAAGT
1 -AAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAGTTTTTAAAAAA-TATTTTTGAGAAAAAGT
*
5246268 TGAAAGTATCAATTTTCTTCAAAAATAAGCTTTCTAAAAAAAATATTTTTGGAG
64 TGAAAGTATCAATTTTCCTCAAAAATAAGCTTT-T-AAAAAAATATTTTTGG-G
* * *
5246322 AAAAGTTGAAAGTATCAATTTTT-TTAAAAATAAG-TTTTCAAAAATATTTTTGAGGAAAAGTTG
1 AAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAGTTTTTAAAAAATATTTTTGAGAAAAAGTTG
* ** * *
5246385 AAAGTATCAATTTTCCTCGAAGTTAAGGTTTTTAAAAAATA-TTTTGAGG
66 AAAGTATCAATTTTCCTCAAAAATAAGCTTTTAAAAAAATATTTTTG-GG
*
5246434 AAAAGTTGAAAGTATTAATTTTTCTTGAAAATAAGTTTTTTTAAAAAATATTTTTGAGAAAAAGT
1 AAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAG--TTTTTAAAAAATATTTTTGAGAAAAAGT
* * * *
5246499 TGAAAGTATCAATTTTGCTTAAAAATAAGCTTTAAAAAAAATATCTTTGAGG
64 TGAAAGTATCAATTTTCCTCAAAAATAAGCTTTTAAAAAAATATTTTTG-GG
* * * *
5246551 AAAAGTTGAAAGTATAAATTTTTCTCGAAATTAAGGTTTTTAAAAAATATTTTGGA-AAAAAGTT
1 AAAAGTTGAAAGTATCAATTTTTCTTGAAAATAA-GTTTTTAAAAAATATTTTTGAGAAAAAGTT
*
5246615 GAAAATATCAATTTT
65 GAAAGTATCAATTTT
5246630 TCCTGTACAA
Statistics
Matches: 371, Mismatches: 42, Indels: 28
0.84 0.10 0.06
Matches are distributed among these distances:
112 28 0.08
113 19 0.05
114 1 0.00
115 70 0.19
116 120 0.32
117 94 0.25
118 38 0.10
119 1 0.00
ACGTcount: A:0.44, C:0.06, G:0.13, T:0.37
Consensus pattern (114 bp):
AAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAGTTTTTAAAAAATATTTTTGAGAAAAAGTTG
AAAGTATCAATTTTCCTCAAAAATAAGCTTTTAAAAAAATATTTTTGGG
Found at i:5257357 original size:25 final size:25
Alignment explanation
Indices: 5257329--5257378 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
5257319 GGTGAACTTC
*
5257329 TGTTAGTGTGTTAGTGGTTGAAGCA
1 TGTTAGTCTGTTAGTGGTTGAAGCA
5257354 TGTTAGTCTGTTAGTGGTTGAAGCA
1 TGTTAGTCTGTTAGTGGTTGAAGCA
5257379 ACTAAGTATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.20, C:0.06, G:0.34, T:0.40
Consensus pattern (25 bp):
TGTTAGTCTGTTAGTGGTTGAAGCA
Found at i:5270402 original size:80 final size:80
Alignment explanation
Indices: 5270244--5270393 Score: 237
Period size: 80 Copynumber: 1.9 Consensus size: 80
5270234 CACAAAATAA
*
5270244 AACAATATTCACCAGGCTAAGAGCATTATATCCCAATAGTTTGATGTAGCATACTTCCAAACTCT
1 AACAATATTCACCAGGCTAAGAGCATTATATCCCAATAGTTTGATCTAGCATACTTCCAAACTCT
5270309 CTCTTCCTTTTTTCT
66 CTCTTCCTTTTTTCT
* * * * *
5270324 AACAATATTCAGCAGGCTAGGAGCATTATATCCCAGTAGTTTGATCTAGCATATTTCCTAACTCT
1 AACAATATTCACCAGGCTAAGAGCATTATATCCCAATAGTTTGATCTAGCATACTTCCAAACTCT
*
5270389 TTCTT
66 CTCTT
5270394 TTTATTTTCA
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
80 63 1.00
ACGTcount: A:0.29, C:0.23, G:0.12, T:0.36
Consensus pattern (80 bp):
AACAATATTCACCAGGCTAAGAGCATTATATCCCAATAGTTTGATCTAGCATACTTCCAAACTCT
CTCTTCCTTTTTTCT
Found at i:5274464 original size:4 final size:4
Alignment explanation
Indices: 5274457--5274501 Score: 72
Period size: 4 Copynumber: 11.2 Consensus size: 4
5274447 TCTTTCTTTT
* *
5274457 ATAC ATAC ATAT ATAT ATAC ATAC ATAC ATAC ATAC ATAC ATAC A
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC A
5274502 CATATATAGG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 39 1.00
ACGTcount: A:0.51, C:0.20, G:0.00, T:0.29
Consensus pattern (4 bp):
ATAC
Found at i:5274476 original size:12 final size:12
Alignment explanation
Indices: 5274456--5274507 Score: 68
Period size: 12 Copynumber: 4.3 Consensus size: 12
5274446 ATCTTTCTTT
5274456 TATACATACATA
1 TATACATACATA
*
5274468 TATATATACATA
1 TATACATACATA
*
5274480 CATACATACATA
1 TATACATACATA
* *
5274492 CATACATACACA
1 TATACATACATA
5274504 TATA
1 TATA
5274508 TAGGCATTTC
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 35 1.00
ACGTcount: A:0.50, C:0.19, G:0.00, T:0.31
Consensus pattern (12 bp):
TATACATACATA
Found at i:5283262 original size:20 final size:21
Alignment explanation
Indices: 5283232--5283273 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
5283222 ATGGATATAA
5283232 ATTTCAATTTTTCATTTAAAT
1 ATTTCAATTTTTCATTTAAAT
* *
5283253 ATTT-AATTTTTTATTTTAAT
1 ATTTCAATTTTTCATTTAAAT
5283273 A
1 A
5283274 AAGATCTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (21 bp):
ATTTCAATTTTTCATTTAAAT
Found at i:5285703 original size:19 final size:18
Alignment explanation
Indices: 5285679--5285747 Score: 68
Period size: 19 Copynumber: 3.7 Consensus size: 18
5285669 TATGATTATT
*
5285679 TTTTTTATATTAACACTTA
1 TTTTTTATATTAA-AATTA
5285698 TTTTTTGAT-TTAAAATTA
1 TTTTTT-ATATTAAAATTA
* *
5285716 TTTTTTATTTATAATAATAA
1 TTTTTTATAT-TAA-AATTA
5285736 TTTTTTATATTA
1 TTTTTTATATTA
5285748 CCAATTTAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
17 2 0.05
18 11 0.26
19 15 0.35
20 15 0.35
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.62
Consensus pattern (18 bp):
TTTTTTATATTAAAATTA
Found at i:5286198 original size:18 final size:18
Alignment explanation
Indices: 5286175--5286221 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
5286165 ATTATTATCA
5286175 TATTTTTATATTAACAAT
1 TATTTTTATATTAACAAT
* * *
5286193 TATTTTTAGATTTAGAAT
1 TATTTTTATATTAACAAT
5286211 TATTTTT-TATT
1 TATTTTTATATT
5286222 TATAATAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
17 3 0.12
18 22 0.88
ACGTcount: A:0.32, C:0.02, G:0.04, T:0.62
Consensus pattern (18 bp):
TATTTTTATATTAACAAT
Found at i:5286912 original size:20 final size:20
Alignment explanation
Indices: 5286845--5286921 Score: 66
Period size: 20 Copynumber: 3.8 Consensus size: 20
5286835 TTGATTTAGA
*
5286845 AATATTATTTAT-TTGTAAT
1 AATATTATTTATATTATAAT
* * * *
5286864 AATAATTGTTTTATGTTGCTAAA
1 AAT-ATT-ATTTATATT-ATAAT
5286887 AATATTATTTATATTATAAT
1 AATATTATTTATATTATAAT
*
5286907 AATATTTTTTATATT
1 AATATTATTTATATT
5286922 TGTTCCTATT
Statistics
Matches: 46, Mismatches: 8, Indels: 7
0.75 0.13 0.11
Matches are distributed among these distances:
19 3 0.07
20 20 0.43
21 12 0.26
22 5 0.11
23 6 0.13
ACGTcount: A:0.38, C:0.01, G:0.05, T:0.56
Consensus pattern (20 bp):
AATATTATTTATATTATAAT
Found at i:5287337 original size:19 final size:19
Alignment explanation
Indices: 5287309--5287372 Score: 57
Period size: 16 Copynumber: 3.5 Consensus size: 19
5287299 TACGATTATT
5287309 CTTATATTTTTATATTAACA
1 CTTAT-TTTTTATATTAACA
*
5287329 CTTA-TTTTT-TATTGA-A
1 CTTATTTTTTATATTAACA
5287345 -TTATTTTTTAT-TTATACA
1 CTTATTTTTTATATTA-ACA
*
5287363 CTAATTTTTT
1 CTTATTTTTT
5287373 TATGTTACAA
Statistics
Matches: 36, Mismatches: 3, Indels: 11
0.72 0.06 0.22
Matches are distributed among these distances:
15 3 0.08
16 8 0.22
17 7 0.19
18 6 0.17
19 8 0.22
20 4 0.11
ACGTcount: A:0.28, C:0.08, G:0.02, T:0.62
Consensus pattern (19 bp):
CTTATTTTTTATATTAACA
Found at i:5290966 original size:23 final size:22
Alignment explanation
Indices: 5290940--5290985 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
5290930 TAAAATTAAA
5290940 TATTATAATT-TGATTTTATTATT
1 TATTA-AATTATGATTTTA-TATT
*
5290963 TATTAATTTATGATTTTATATT
1 TATTAAATTATGATTTTATATT
5290985 T
1 T
5290986 GAAATTTAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 8 0.38
23 13 0.62
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.65
Consensus pattern (22 bp):
TATTAAATTATGATTTTATATT
Found at i:5295019 original size:33 final size:33
Alignment explanation
Indices: 5294982--5295044 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
5294972 TTTTAATTTA
5294982 AAAAATA-AGTTTAATAAATATTTTTA-AAACTAT
1 AAAAATATA-TTT-ATAAATATTTTTATAAACTAT
*
5295015 AAAAATATATTTTTAAATATTTTTATAAAC
1 AAAAATATATTTATAAATATTTTTATAAAC
5295045 GAGATCCACT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
32 12 0.44
33 14 0.52
34 1 0.04
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (33 bp):
AAAAATATATTTATAAATATTTTTATAAACTAT
Found at i:5295237 original size:12 final size:12
Alignment explanation
Indices: 5295215--5295245 Score: 55
Period size: 11 Copynumber: 2.7 Consensus size: 12
5295205 TTTAGAATAA
5295215 TAAAATATTTTT
1 TAAAATATTTTT
5295227 T-AAATATTTTT
1 TAAAATATTTTT
5295238 TAAAATAT
1 TAAAATAT
5295246 GGAATTCACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 11 0.61
12 7 0.39
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
TAAAATATTTTT
Found at i:5295458 original size:22 final size:22
Alignment explanation
Indices: 5295430--5295486 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 22
5295420 TTAATTTTTT
** *
5295430 TATTTTTAAAAATATTTAATTA
1 TATTTTTAAAAATATAAAAATA
* *
5295452 TATTTTTTAAATTATAAAAATA
1 TATTTTTAAAAATATAAAAATA
5295474 TATTTTTAAAAAT
1 TATTTTTAAAAAT
5295487 TTTGTTTTTT
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
TATTTTTAAAAATATAAAAATA
Found at i:5296516 original size:22 final size:22
Alignment explanation
Indices: 5296474--5296537 Score: 74
Period size: 22 Copynumber: 2.8 Consensus size: 22
5296464 TTACGAACTT
*
5296474 TTTTGTTTCATTTTTTATTTTTTA
1 TTTT-TTTCAATTTTT-TTTTTTA
5296498 TTTTTTTCAATTTTTTTTTTTA
1 TTTTTTTCAATTTTTTTTTTTA
* * *
5296520 CTTTTTACAATTTATTTT
1 TTTTTTTCAATTTTTTTT
5296538 GTTTGAGATT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
22 22 0.61
23 10 0.28
24 4 0.11
ACGTcount: A:0.16, C:0.06, G:0.02, T:0.77
Consensus pattern (22 bp):
TTTTTTTCAATTTTTTTTTTTA
Found at i:5298063 original size:20 final size:20
Alignment explanation
Indices: 5298024--5298063 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
5298014 CATGTAAGAG
*
5298024 TATCATGCAGATATATTAAT
1 TATCATGCAGATATAATAAT
5298044 TATCATGCA-ATAATAATAAT
1 TATCATGCAGAT-ATAATAAT
5298064 CATATAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 2 0.11
20 16 0.89
ACGTcount: A:0.45, C:0.10, G:0.07, T:0.38
Consensus pattern (20 bp):
TATCATGCAGATATAATAAT
Found at i:5298065 original size:17 final size:17
Alignment explanation
Indices: 5298024--5298088 Score: 60
Period size: 17 Copynumber: 3.6 Consensus size: 17
5298014 CATGTAAGAG
5298024 TATCATGCAGATATATTAA
1 TATCATGCA-ATATA-TAA
5298043 TTATCATGCAATA-ATAA
1 -TATCATGCAATATATAA
**
5298060 TAATCATATAAATATATAA
1 T-ATCAT-GCAATATATAA
5298079 TATCATGCAA
1 TATCATGCAA
5298089 ATCAAATATA
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
16 1 0.03
17 10 0.26
18 10 0.26
19 8 0.21
20 9 0.24
ACGTcount: A:0.48, C:0.11, G:0.06, T:0.35
Consensus pattern (17 bp):
TATCATGCAATATATAA
Found at i:5298066 original size:37 final size:37
Alignment explanation
Indices: 5298025--5298114 Score: 98
Period size: 37 Copynumber: 2.4 Consensus size: 37
5298015 ATGTAAGAGT
*
5298025 ATCATGCAGATATATTAATTATCATGC-AAT--AATAATA
1 ATCATACA-ATATATTAA-TATCATGCAAATCAAAT-ATA
*
5298062 ATCATATAA-ATATATAATATCATGCAAATCAAATATA
1 ATCATACAATATAT-TAATATCATGCAAATCAAATATA
5298099 ATCATACAATATATTA
1 ATCATACAATATATTA
5298115 GTAATTAAAT
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
35 12 0.27
36 7 0.16
37 19 0.42
38 7 0.16
ACGTcount: A:0.50, C:0.11, G:0.04, T:0.34
Consensus pattern (37 bp):
ATCATACAATATATTAATATCATGCAAATCAAATATA
Found at i:5298377 original size:20 final size:18
Alignment explanation
Indices: 5298352--5298441 Score: 63
Period size: 20 Copynumber: 4.5 Consensus size: 18
5298342 ATAAAACATA
5298352 CAATTAAATCTCTAATCATG
1 CAATTAAAT-T-TAATCATG
* *
5298372 CAATTAACAATTAAAACATG
1 CAATT-A-AATTTAATCATG
*
5298392 CAAATAAATATATAATCATG
1 CAATTAAAT-T-TAATCATG
*
5298412 CAATTAATAATTTACATCATA
1 CAATT-A-AATTTA-ATCATG
5298433 CAATTAAAT
1 CAATTAAAT
5298442 ATATTATCTA
Statistics
Matches: 56, Mismatches: 7, Indels: 15
0.72 0.09 0.19
Matches are distributed among these distances:
18 3 0.05
19 5 0.09
20 28 0.50
21 14 0.25
22 6 0.11
ACGTcount: A:0.50, C:0.14, G:0.03, T:0.32
Consensus pattern (18 bp):
CAATTAAATTTAATCATG
Found at i:5298472 original size:41 final size:41
Alignment explanation
Indices: 5298316--5298468 Score: 164
Period size: 41 Copynumber: 3.7 Consensus size: 41
5298306 ACATGTAATC
***
5298316 AAATATATAATTGCGCAATTAACAATATAAAACATACAATT
1 AAATATATAATCATGCAATTAACAATATAAAACATACAATT
* * * *
5298357 AAATCTCTAATCATGCAATTAACAAT-TAAAACATGCAAAT
1 AAATATATAATCATGCAATTAACAATATAAAACATACAATT
* * * *
5298397 AAATATATAATCATGCAATTAATAATTTACATCATACAATT
1 AAATATATAATCATGCAATTAACAATATAAAACATACAATT
* * *
5298438 AAATATATTATCTATGTAATTAAAAATATAA
1 AAATATATAATC-ATGCAATTAACAATATAA
5298469 TCATGCAGTC
Statistics
Matches: 91, Mismatches: 19, Indels: 3
0.81 0.17 0.03
Matches are distributed among these distances:
40 35 0.38
41 42 0.46
42 14 0.15
ACGTcount: A:0.52, C:0.12, G:0.04, T:0.33
Consensus pattern (41 bp):
AAATATATAATCATGCAATTAACAATATAAAACATACAATT
Found at i:5298529 original size:29 final size:29
Alignment explanation
Indices: 5298496--5298613 Score: 124
Period size: 29 Copynumber: 4.2 Consensus size: 29
5298486 TAAAACAAGC
5298496 AATTAAATATATAATCATGCAAAAAATAT
1 AATTAAATATATAATCATGCAAAAAATAT
* *
5298525 AATTAAATGTATAATCATGC-AAATA-AT
1 AATTAAATATATAATCATGCAAAAAATAT
* *
5298552 -ACT--ATATA-AATCATGCAAAAAAAAT
1 AATTAAATATATAATCATGCAAAAAATAT
5298577 GCAATTAAATATATAATCATGCAAATAAATAT
1 --AATTAAATATATAATCATGCAAA-AAATAT
5298609 -ATTAA
1 AATTAA
5298614 TAATCATGCA
Statistics
Matches: 73, Mismatches: 7, Indels: 18
0.74 0.07 0.18
Matches are distributed among these distances:
23 8 0.11
24 8 0.11
25 2 0.03
26 2 0.03
27 2 0.03
28 6 0.08
29 24 0.33
30 5 0.07
31 11 0.15
32 5 0.07
ACGTcount: A:0.56, C:0.08, G:0.05, T:0.31
Consensus pattern (29 bp):
AATTAAATATATAATCATGCAAAAAATAT
Found at i:5298566 original size:52 final size:52
Alignment explanation
Indices: 5298502--5298625 Score: 171
Period size: 54 Copynumber: 2.3 Consensus size: 52
5298492 AAGCAATTAA
* *
5298502 ATATATAATCATGCAAAAAATAT-AATTAAATGTATAATCATGCAAAT-AAT
1 ATATATAATCATGCAAAAAAAATCAATTAAATATATAATCATGCAAATAAAT
5298552 ACTATATAAATCATGCAAAAAAAATGCAATTAAATATATAATCATGCAAATAAAT
1 A-TATAT-AATCATGCAAAAAAAAT-CAATTAAATATATAATCATGCAAATAAAT
5298607 ATATTAATAATCATGCAAA
1 ATA-T-ATAATCATGCAAA
5298626 TATACTAATA
Statistics
Matches: 65, Mismatches: 2, Indels: 9
0.86 0.03 0.12
Matches are distributed among these distances:
50 1 0.02
51 5 0.08
52 16 0.25
54 25 0.38
55 16 0.25
56 2 0.03
ACGTcount: A:0.55, C:0.10, G:0.06, T:0.30
Consensus pattern (52 bp):
ATATATAATCATGCAAAAAAAATCAATTAAATATATAATCATGCAAATAAAT
Found at i:5298581 original size:83 final size:76
Alignment explanation
Indices: 5298494--5298640 Score: 215
Period size: 83 Copynumber: 1.8 Consensus size: 76
5298484 TATAAAACAA
5298494 GCAATTAAATATATAATCATGCAAA-AAATATAATTAAATGTATAATCATGCAAATAATACTATA
1 GCAATTAAATATATAATCATGCAAATAAATAT-ATT--A---ATAATCATGCAAAT-ATACTA-A
5298558 TAAATCATGCAAAAAAAAT
58 TAAATCATGCAAAAAAAAT
5298577 GCAATTAAATATATAATCATGCAAATAAATATATTAATAATCATGCAAATATACTAATAAATCA
1 GCAATTAAATATATAATCATGCAAATAAATATATTAATAATCATGCAAATATACTAATAAATCA
5298641 CACAAATAAA
Statistics
Matches: 63, Mismatches: 0, Indels: 9
0.88 0.00 0.12
Matches are distributed among these distances:
76 8 0.13
77 6 0.10
78 14 0.22
81 1 0.02
83 28 0.44
84 6 0.10
ACGTcount: A:0.54, C:0.10, G:0.05, T:0.30
Consensus pattern (76 bp):
GCAATTAAATATATAATCATGCAAATAAATATATTAATAATCATGCAAATATACTAATAAATCAT
GCAAAAAAAAT
Found at i:5298616 original size:24 final size:24
Alignment explanation
Indices: 5298589--5298659 Score: 78
Period size: 20 Copynumber: 3.1 Consensus size: 24
5298579 AATTAAATAT
5298589 ATAATCATGCAAATAAATATATTA
1 ATAATCATGCAAATAAATATATTA
*
5298613 ATAATCATGC----AAATATACTA
1 ATAATCATGCAAATAAATATATTA
**
5298633 ATAAATCACACAAATAAATATATTA
1 AT-AATCATGCAAATAAATATATTA
5298658 AT
1 AT
5298660 CAAATATATT
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
20 11 0.29
21 6 0.16
24 10 0.26
25 11 0.29
ACGTcount: A:0.55, C:0.11, G:0.03, T:0.31
Consensus pattern (24 bp):
ATAATCATGCAAATAAATATATTA
Found at i:5298664 original size:13 final size:14
Alignment explanation
Indices: 5298648--5298698 Score: 52
Period size: 13 Copynumber: 3.6 Consensus size: 14
5298638 TCACACAAAT
5298648 AAATATATTAAT-C
1 AAATATATTAATGC
5298661 AAATATATT-ATGC
1 AAATATATTAATGC
* *
5298674 AAATAAATTATCTTGC
1 AAATATATTA--ATGC
5298690 AAATATATT
1 AAATATATT
5298699 GTTAGTCAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
12 2 0.06
13 18 0.58
16 11 0.35
ACGTcount: A:0.49, C:0.08, G:0.04, T:0.39
Consensus pattern (14 bp):
AAATATATTAATGC
Found at i:5299340 original size:12 final size:12
Alignment explanation
Indices: 5299323--5299352 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
5299313 ACTAAAAAAA
5299323 CAAAAATTAAAC
1 CAAAAATTAAAC
5299335 CAAAAATTAAAC
1 CAAAAATTAAAC
*
5299347 TAAAAA
1 CAAAAA
5299353 AATAAAATAC
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:0.70, C:0.13, G:0.00, T:0.17
Consensus pattern (12 bp):
CAAAAATTAAAC
Found at i:5299701 original size:85 final size:83
Alignment explanation
Indices: 5299629--5300040 Score: 462
Period size: 85 Copynumber: 4.9 Consensus size: 83
5299619 TTTTTTTTGA
5299629 AAAATGCTACCCCATAATTGAAGCTTTGAAACTTTTGAAAAATAAAATGCTCCTCCACAACTAAG
1 AAAATGCT-CCCCATAATTGAAGCTTTGAAACTTTTGAAAAATAAAATGCTCC-CCACAACTAAG
* * *
5299694 ACTTTGAAACTTCTGAAAAT
64 GCTTTGAAACTTTTAAAAAT
* * * * *
5299714 AAAATGCTTTCCTACAATTGAGGCTTTGAAATTTTTGAAAAATAAAATGCTCCCCACAACTAAGG
1 AAAATGC-TCCCCATAATTGAAGCTTTGAAACTTTTGAAAAATAAAATGCTCCCCACAACTAAGG
* *
5299779 CTTTGAAACTTTGAAGAAT
65 CTTTGAAACTTTTAAAAAT
5299798 AAAATGCTCCCCCCATAATTG-AGACTTTGAAACTTTTGAAAAATAAAATGCTTCCCCACAACTA
1 AAAATGCT--CCCCATAATTGAAG-CTTTGAAACTTTTGAAAAATAAAATGC-TCCCCACAACTA
* * *
5299862 GGGGTTTGGAA-TTTTGGAAAAAT
62 AGGCTTTGAAACTTTT--AAAAAT
* * * *
5299885 AAAATGCTCTCCCATAATTGAGGC-TTAAAAC-TTT---AAATAACATGCTCCCCACAACTTAGG
1 AAAATGCTC-CCCATAATTGAAGCTTTGAAACTTTTGAAAAATAAAATGCTCCCCACAACTAAGG
*
5299945 CTTTGAAACTTTGAAAAAT
65 CTTTGAAACTTTTAAAAAT
* * *
5299964 AAAATGCTCTCCCACAACTGAAGCTTTGAAAC-TTTGAAAAATAAAATGCTCTCTCACAACTAAG
1 AAAATGCTC-CCCATAATTGAAGCTTTGAAACTTTTGAAAAATAAAATGCTC-CCCACAACTAAG
*
5300028 ACTTTGAAACTTT
64 GCTTTGAAACTTT
5300041 GCTTCCCACA
Statistics
Matches: 276, Mismatches: 36, Indels: 31
0.80 0.10 0.09
Matches are distributed among these distances:
79 27 0.10
80 28 0.10
81 13 0.05
83 13 0.05
84 59 0.21
85 90 0.33
86 32 0.12
87 14 0.05
ACGTcount: A:0.39, C:0.20, G:0.13, T:0.29
Consensus pattern (83 bp):
AAAATGCTCCCCATAATTGAAGCTTTGAAACTTTTGAAAAATAAAATGCTCCCCACAACTAAGGC
TTTGAAACTTTTAAAAAT
Found at i:5299741 original size:42 final size:42
Alignment explanation
Indices: 5299629--5300041 Score: 416
Period size: 42 Copynumber: 9.9 Consensus size: 42
5299619 TTTTTTTTGA
* * *
5299629 AAAATGCTAC-CCCATAATTGAAGCTTTGAAACTTTTGAAAAAT
1 AAAATGCT-CTCCCACAACTGAGGCTTTGAAAC-TTTGAAAAAT
* *
5299672 AAAATGCTC-CTCCACAACTAAGACTTTGAAACTTCTG-AAAAT
1 AAAATGCTCTC-CCACAACTGAGGCTTTGAAACTT-TGAAAAAT
* * * *
5299714 AAAATGCTTTCCTACAATTGAGGCTTTGAAATTTTTGAAAAAT
1 AAAATGCTCTCCCACAACTGAGGCTTTGAAA-CTTTGAAAAAT
* *
5299757 AAAATGCTC-CCCACAACTAAGGCTTTGAAACTTTGAAGAAT
1 AAAATGCTCTCCCACAACTGAGGCTTTGAAACTTTGAAAAAT
* * * *
5299798 AAAATGCTCCCCCCATAATTGAGACTTTGAAACTTTTGAAAAAT
1 AAAATGCT-CTCCCACAACTGAGGCTTTGAAAC-TTTGAAAAAT
* * *
5299842 AAAATGCT-TCCCCACAACT-AGGGGTTTGGAATTTTGGAAAAAT
1 AAAATGCTCT-CCCACAACTGA-GGCTTTGAAACTTT-GAAAAAT
* * *
5299885 AAAATGCTCTCCCATAATTGAGGC-TTAAAACTTT---AAAT
1 AAAATGCTCTCCCACAACTGAGGCTTTGAAACTTTGAAAAAT
* *
5299923 AACATGCTC-CCCACAACTTAGGCTTTGAAACTTTGAAAAAT
1 AAAATGCTCTCCCACAACTGAGGCTTTGAAACTTTGAAAAAT
*
5299964 AAAATGCTCTCCCACAACTGAAGCTTTGAAACTTTGAAAAAT
1 AAAATGCTCTCCCACAACTGAGGCTTTGAAACTTTGAAAAAT
* * *
5300006 AAAATGCTCTCTCACAACTAAGACTTTGAAACTTTG
1 AAAATGCTCTCCCACAACTGAGGCTTTGAAACTTTG
5300042 CTTCCCACAA
Statistics
Matches: 305, Mismatches: 47, Indels: 37
0.78 0.12 0.10
Matches are distributed among these distances:
37 11 0.04
38 21 0.07
41 29 0.10
42 127 0.42
43 98 0.32
44 19 0.06
ACGTcount: A:0.38, C:0.20, G:0.13, T:0.29
Consensus pattern (42 bp):
AAAATGCTCTCCCACAACTGAGGCTTTGAAACTTTGAAAAAT
Found at i:5307568 original size:19 final size:20
Alignment explanation
Indices: 5307526--5307568 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
5307516 TAGTTTCTTT
* *
5307526 CCTTCATTTCTTTTTTACAT
1 CCTTCATTTCTTTTCTACAA
*
5307546 CCTTC-TTTCTTTTCTCCAA
1 CCTTCATTTCTTTTCTACAA
5307565 CCTT
1 CCTT
5307569 TTATTCTTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.12, C:0.33, G:0.00, T:0.56
Consensus pattern (20 bp):
CCTTCATTTCTTTTCTACAA
Found at i:5308815 original size:37 final size:36
Alignment explanation
Indices: 5308765--5308860 Score: 99
Period size: 36 Copynumber: 2.6 Consensus size: 36
5308755 TTTTTTTTAT
* * *
5308765 AATTTTGAAAATGGCTTCCCCC-AAATAGAGATTTTGA
1 AATTTTAAAAATGGC-TCCCCCTAAACA-AGACTTTGA
*
5308802 AATTTTAAAAATGGCTCCCCCTAAACAAGGCTTTGA
1 AATTTTAAAAATGGCTCCCCCTAAACAAGACTTTGA
5308838 AACTTTT-AAAATAGG-TCCCCCTA
1 AA-TTTTAAAAAT-GGCTCCCCCTA
5308861 TATAGAGGCT
Statistics
Matches: 52, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
36 28 0.54
37 24 0.46
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (36 bp):
AATTTTAAAAATGGCTCCCCCTAAACAAGACTTTGA
Found at i:5308837 original size:36 final size:37
Alignment explanation
Indices: 5308767--5308881 Score: 130
Period size: 37 Copynumber: 3.1 Consensus size: 37
5308757 TTTTTTATAA
**
5308767 TTTTGAAAATGGCTTCCCCC-AAATAGAGATTTTGAAA-
1 TTTT-AAAATGGC-TCCCCCTAAATAGAGGCTTTGAAAC
*
5308804 TTTTAAAAATGGCTCCCCCTAAACA-AGGCTTTGAAAC
1 TTTT-AAAATGGCTCCCCCTAAATAGAGGCTTTGAAAC
*
5308841 TTTTAAAATAGG-TCCCCCTATATAGAGGCTTTGAAAC
1 TTTTAAAAT-GGCTCCCCCTAAATAGAGGCTTTGAAAC
5308878 TTTT
1 TTTT
5308882 TTTTTTTTTA
Statistics
Matches: 68, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
36 30 0.44
37 38 0.56
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Consensus pattern (37 bp):
TTTTAAAATGGCTCCCCCTAAATAGAGGCTTTGAAAC
Found at i:5308870 original size:37 final size:37
Alignment explanation
Indices: 5308797--5308881 Score: 113
Period size: 36 Copynumber: 2.3 Consensus size: 37
5308787 AAATAGAGAT
5308797 TTTGAAA-TTTTAAAAATGGCTCCCCCTAAACAAGGC
1 TTTGAAACTTTTAAAAATGGCTCCCCCTAAACAAGGC
* *
5308833 TTTGAAACTTTT-AAAATAGG-TCCCCCTATATAGAGGC
1 TTTGAAACTTTTAAAAAT-GGCTCCCCCTAAACA-AGGC
5308870 TTTGAAACTTTT
1 TTTGAAACTTTT
5308882 TTTTTTTTTA
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
36 22 0.50
37 22 0.50
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.34
Consensus pattern (37 bp):
TTTGAAACTTTTAAAAATGGCTCCCCCTAAACAAGGC
Found at i:5309067 original size:97 final size:94
Alignment explanation
Indices: 5308866--5309072 Score: 238
Period size: 97 Copynumber: 2.2 Consensus size: 94
5308856 CCCTATATAG
* * * * *
5308866 AGGCTTTGAAACTTTTTTTTTTTTTAAATCTTGTTTGAAAATTGCTCTTTATAAACAAAGGTTTT
1 AGGCTTTGAAACTTTTTTTTTTTTAAAATCTTGTTTGAAAAGTGCTATCTATAAACAAAGATTTT
*
5308931 AAAACTTTAAAAATGGCTTCCCTAAACAT
66 AAAACTTTAAAAATGGCTTCCCTAAACAA
* * * *
5308960 AGGCTATGAAACTTTTTTTCATTTTTAAAAATCTTGTTTGAAAAGTGCTATCTCTAAATAGAGAT
1 AGGCTTTGAAACTTTTTTT--TTTTT-AAAATCTTGTTTGAAAAGTGCTATCTATAAACAAAGAT
* * *
5309025 TTTGAAACTTTTAAAACT-GCTCTCTCTAAACAA
63 TTTAAAAC-TTTAAAAATGGCT-TCCCTAAACAA
5309058 AGG-TTTGAAACTTTT
1 AGGCTTTGAAACTTTT
5309073 AAAATAGCTC
Statistics
Matches: 94, Mismatches: 14, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
94 18 0.19
96 5 0.05
97 51 0.54
98 20 0.21
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.42
Consensus pattern (94 bp):
AGGCTTTGAAACTTTTTTTTTTTTAAAATCTTGTTTGAAAAGTGCTATCTATAAACAAAGATTTT
AAAACTTTAAAAATGGCTTCCCTAAACAA
Found at i:5309068 original size:36 final size:37
Alignment explanation
Indices: 5309025--5309114 Score: 121
Period size: 36 Copynumber: 2.4 Consensus size: 37
5309015 AAATAGAGAT
* *
5309025 TTTGAAACTTTTAAAACT-GCTCTCTCTAAACAAAGG-
1 TTTGAAACTTTTAAAA-TAGCTCCCCCTAAACAAAGGC
*
5309061 TTTGAAACTTTTAAAATAGCTCCCCCTAAACAGAGGC
1 TTTGAAACTTTTAAAATAGCTCCCCCTAAACAAAGGC
5309098 TTTGAAACTTTTTAAAA
1 TTTGAAAC-TTTTAAAA
5309115 AATCTTGTGT
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
35 1 0.02
36 31 0.65
37 8 0.17
38 8 0.17
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (37 bp):
TTTGAAACTTTTAAAATAGCTCCCCCTAAACAAAGGC
Found at i:5309190 original size:36 final size:36
Alignment explanation
Indices: 5309151--5309271 Score: 134
Period size: 37 Copynumber: 3.3 Consensus size: 36
5309141 AAACAAAGAT
* * *
5309151 TTTGAAACTTGAAAATGGCTCCCCTTAAATAGAGGT
1 TTTGAAACTTTAAAATGACTCCCCTTAAATAGAGGC
* * * *
5309187 TTTGAAAATTTTAAAACGACTCCCGTTAAATAGATGC
1 TTTG-AAACTTTAAAATGACTCCCCTTAAATAGAGGC
* *
5309224 TTTGAAACTTTTAAAATGACTCCCTTTAGATAGAGGC
1 TTTGAAAC-TTTAAAATGACTCCCCTTAAATAGAGGC
*
5309261 TTTAAAACTTT
1 TTTGAAACTTT
5309272 TTAAAAAATC
Statistics
Matches: 70, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
36 10 0.14
37 60 0.86
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.35
Consensus pattern (36 bp):
TTTGAAACTTTAAAATGACTCCCCTTAAATAGAGGC
Found at i:5309271 original size:163 final size:161
Alignment explanation
Indices: 5309013--5309404 Score: 450
Period size: 163 Copynumber: 2.4 Consensus size: 161
5309003 AGTGCTATCT
* * * *
5309013 CTAAATAGAGATTTTGAAACTTTTAAAACTGCTCTCTCTAAACAAAGGTTTGAAACTTTTAAAAT
1 CTAAATAGAGGTTTTGAAACTTTTAAAAC-GCTCCCT-TAAATAAAGCTTTGAAACTTTTAAAAT
*
5309078 AGCTCCCCCTAAACAGAGGCTTTGAAACTTTTTAAAAAATCTTGTGTGAAAATTAATCCCTCTAA
64 AGCTCCCCCTAAACAGAGGCTTTAAAACTTTTTAAAAAATCTTGTGTGAAAATTAATCCCTCTAA
5309143 AC-AAAGATTTTGAAAC-TTGAAAATGGCTC-CC
129 ACAAAAG-TTTTGAAACTTTGAAAATGGCTCACC
* *
5309174 CTTAAATAGAGGTTTTGAAAATTTTAAAACGACTCCCGTTAAATAGATGCTTTGAAACTTTTAAA
1 C-TAAATAGAGGTTTTGAAACTTTTAAAACG-CTCCC-TTAAATA-AAGCTTTGAAACTTTTAAA
** * * * ** *
5309239 AT-GACTCCCTTTAGATAGAGGCTTTAAAACTTTTTAAAAAATCTTGTTTGAAAATTGCTCCCTT
62 ATAG-CTCCCCCTAAACAGAGGCTTTAAAACTTTTTAAAAAATCTTGTGTGAAAATTAATCCCTC
* * *
5309303 TAAATAAAAGTTTTGAAACTTTGAATATGGCTCATC
126 TAAACAAAAGTTTTGAAACTTTGAAAATGGCTCACC
* * * *
5309339 CTAAATAGAGGCTTTGAAACTTTGAAAATGGCTCCCTTTAAATAAAGGCTTTGAATCTTTTTAAA
1 CTAAATAGAGGTTTTGAAACTTTTAAAA-CGCTCCC-TTAAATAAA-GCTTTGAAAC-TTTTAAA
5309404 A
62 A
5309405 AATCTTGTTT
Statistics
Matches: 195, Mismatches: 25, Indels: 18
0.82 0.11 0.08
Matches are distributed among these distances:
161 2 0.01
162 36 0.18
163 85 0.44
164 61 0.31
165 11 0.06
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.34
Consensus pattern (161 bp):
CTAAATAGAGGTTTTGAAACTTTTAAAACGCTCCCTTAAATAAAGCTTTGAAACTTTTAAAATAG
CTCCCCCTAAACAGAGGCTTTAAAACTTTTTAAAAAATCTTGTGTGAAAATTAATCCCTCTAAAC
AAAAGTTTTGAAACTTTGAAAATGGCTCACC
Found at i:5309344 original size:127 final size:127
Alignment explanation
Indices: 5309213--5309461 Score: 390
Period size: 127 Copynumber: 2.0 Consensus size: 127
5309203 CGACTCCCGT
* * * *
5309213 TAAATAGATGCTTTGAAACTTTTAAAATGACTCCCTTTAGATAGAGGCTTTAAAACTTTTTAAAA
1 TAAATAGAGGCTTTGAAACTTTGAAAATGACTCCCTTTAAATAAAGGCTTTAAAACTTTTTAAAA
* * *
5309278 AATCTTGTTTGAAAATTGCTCCCTTTAAATAAAAGTTTTGAAACTTTGAATATGGCTCATCC
66 AATCTTGTTTAAAAATTACTCCCTTTAAATAAAAGTTTTGAAACTTTGAAAATGGCTCATCC
* * *
5309340 TAAATAGAGGCTTTGAAACTTTGAAAATGGCTCCCTTTAAATAAAGGCTTTGAATCTTTTTAAAA
1 TAAATAGAGGCTTTGAAACTTTGAAAATGACTCCCTTTAAATAAAGGCTTTAAAACTTTTTAAAA
* *
5309405 AATCTTGTTTAAAAATTACTCCCTTTAAATATAGGTTTTGAAACTTTGAAAATGGCT
66 AATCTTGTTTAAAAATTACTCCCTTTAAATAAAAGTTTTGAAACTTTGAAAATGGCT
5309462 TTGAAACTTT
Statistics
Matches: 110, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
127 110 1.00
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.38
Consensus pattern (127 bp):
TAAATAGAGGCTTTGAAACTTTGAAAATGACTCCCTTTAAATAAAGGCTTTAAAACTTTTTAAAA
AATCTTGTTTAAAAATTACTCCCTTTAAATAAAAGTTTTGAAACTTTGAAAATGGCTCATCC
Found at i:5309381 original size:37 final size:37
Alignment explanation
Indices: 5309285--5309398 Score: 142
Period size: 37 Copynumber: 3.1 Consensus size: 37
5309275 AAAAATCTTG
* * *
5309285 TTTGAAAATTGCTCCCTTTAAATAAAAGTTTTGAAAC
1 TTTGAAAATGGCTCCCTTTAAATAAAGGCTTTGAAAC
* *
5309322 TTTGAATATGGCTCATCC--TAAATAGAGGCTTTGAAAC
1 TTTGAAAATGGCTC--CCTTTAAATAAAGGCTTTGAAAC
*
5309359 TTTGAAAATGGCTCCCTTTAAATAAAGGCTTTGAATC
1 TTTGAAAATGGCTCCCTTTAAATAAAGGCTTTGAAAC
5309396 TTT
1 TTT
5309399 TTAAAAAATC
Statistics
Matches: 65, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
35 2 0.03
37 61 0.94
39 2 0.03
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (37 bp):
TTTGAAAATGGCTCCCTTTAAATAAAGGCTTTGAAAC
Found at i:5309514 original size:73 final size:73
Alignment explanation
Indices: 5309374--5309533 Score: 232
Period size: 73 Copynumber: 2.2 Consensus size: 73
5309364 AAATGGCTCC
* * *
5309374 CTTTAAATAAAGGCTTTGAATCTTTTTAAAAAATCTTGTTTAAAAATTACTCCCTTTAAATATAG
1 CTTTAAA-AATGGCTTTGAAACTTTTTAAAAAATCTTGTTTAAAAATTACTCCCTTTAAATAGAG
5309439 GTTTTGAAA
65 GTTTTGAAA
* * * *
5309448 CTTTGAAAATGGCTTTGAAACTTTTTAAAAAATCTTGTTTGAAAATTGCTTCCTCTT-AATAGAG
1 CTTTAAAAATGGCTTTGAAACTTTTTAAAAAATCTTGTTTAAAAATTACTCCCT-TTAAATAGAG
5309512 GTTTTGAAA
65 GTTTTGAAA
5309521 CTTTAAAAATGGC
1 CTTTAAAAATGGC
5309534 ACCACTAAAT
Statistics
Matches: 77, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
73 69 0.90
74 8 0.10
ACGTcount: A:0.36, C:0.11, G:0.12, T:0.41
Consensus pattern (73 bp):
CTTTAAAAATGGCTTTGAAACTTTTTAAAAAATCTTGTTTAAAAATTACTCCCTTTAAATAGAGG
TTTTGAAA
Found at i:5309567 original size:89 final size:90
Alignment explanation
Indices: 5309458--5309651 Score: 257
Period size: 89 Copynumber: 2.2 Consensus size: 90
5309448 CTTTGAAAAT
* * *
5309458 GGCTTTGAAACTTTTTAAAAAATCTTGTTTGAAAATTGCTTCCTCTTAATAGA-GGTTTTGAAAC
1 GGCTTTGAAACTTTTAAAAAAATCTTGTTTGAAAATT-ATTCCTCTTAACAGACGGTTTTGAAAC
*
5309522 TTTAAAAATGG-CACCACTAAATAGA
65 TTTAAAAATGGTCACCACTAAACAGA
* * *
5309547 GGCTTTGAAACTTTTAAAAAAATCTTGTTTGGAAATTATTCCTTTTAACAGACGTTTTTGAAACT
1 GGCTTTGAAACTTTTAAAAAAATCTTGTTTGAAAATTATTCCTCTTAACAGACGGTTTTGAAACT
* ** *
5309612 TTGAAAATGGTTTCCCCTAAACAGA
66 TTAAAAATGGTCACCACTAAACAGA
*
5309637 GTCTTTGAAACTTTT
1 GGCTTTGAAACTTTT
5309652 TTCTTTTTTT
Statistics
Matches: 91, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
88 12 0.13
89 55 0.60
90 24 0.26
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.38
Consensus pattern (90 bp):
GGCTTTGAAACTTTTAAAAAAATCTTGTTTGAAAATTATTCCTCTTAACAGACGGTTTTGAAACT
TTAAAAATGGTCACCACTAAACAGA
Found at i:5309685 original size:102 final size:102
Alignment explanation
Indices: 5309564--5309753 Score: 258
Period size: 102 Copynumber: 1.9 Consensus size: 102
5309554 AAACTTTTAA
* * * * *
5309564 AAAAATCTTGTTTGGAAATTATTCCTT-TTAACAGACGTTTTTGAAACTTTGAAAATGGTTTCC-
1 AAAAATCTTGTTTGAAAATTACTCCTTCTAAACAGA-GGTTTTGAAACTTTGAAAATGG-CTCCT
*
5309627 CCTAAACAGAGTCTTTGAAACTTTTTTCTTTTTTTTTTT
64 CCTAAACAGAGGCTTTGAAACTTTTTTCTTTTTTTTTTT
* * *
5309666 AAAAATCTTGTTTGAAAATTGCTCCTTCTAAATAGAGGTTTTGAAACTTTGAAAATGGCTCCTCT
1 AAAAATCTTGTTTGAAAATTACTCCTTCTAAACAGAGGTTTTGAAACTTTGAAAATGGCTCCTCC
*
5309731 TAAATAGAGGCTTTGAAACTTTT
66 TAAACAGAGGCTTTGAAACTTTT
5309754 AAAATTGCCC
Statistics
Matches: 76, Mismatches: 10, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
101 3 0.04
102 67 0.88
103 6 0.08
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.43
Consensus pattern (102 bp):
AAAAATCTTGTTTGAAAATTACTCCTTCTAAACAGAGGTTTTGAAACTTTGAAAATGGCTCCTCC
TAAACAGAGGCTTTGAAACTTTTTTCTTTTTTTTTTT
Found at i:5309727 original size:37 final size:37
Alignment explanation
Indices: 5309676--5309825 Score: 185
Period size: 37 Copynumber: 4.1 Consensus size: 37
5309666 AAAAATCTTG
* ** *
5309676 TTTGAAAATTGCTCCTTCTAAATAGAGGTTTTGAAAC
1 TTTGAAAATGGCTCCCCCTAAATAGAGGCTTTGAAAC
* *
5309713 TTTGAAAATGGCTCCTCTTAAATAGAGGCTTTGAAAC
1 TTTGAAAATGGCTCCCCCTAAATAGAGGCTTTGAAAC
* * *
5309750 TTTTAAAATTGC-CCCCCTAAATAGAGGTTTTGAAAC
1 TTTGAAAATGGCTCCCCCTAAATAGAGGCTTTGAAAC
* **
5309786 TTTGAAAATGGTTCCCCCTAAGCAGAGGCTTTGAAAC
1 TTTGAAAATGGCTCCCCCTAAATAGAGGCTTTGAAAC
5309823 TTT
1 TTT
5309826 TTTCTTTCTT
Statistics
Matches: 97, Mismatches: 15, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
36 30 0.31
37 67 0.69
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34
Consensus pattern (37 bp):
TTTGAAAATGGCTCCCCCTAAATAGAGGCTTTGAAAC
Found at i:5309917 original size:37 final size:36
Alignment explanation
Indices: 5309859--5309972 Score: 120
Period size: 37 Copynumber: 3.1 Consensus size: 36
5309849 TTAAATCTTG
* * *
5309859 TTTGAAAATTGCTCTCTCTAAACAGAGGTTTTGAAAC
1 TTTGAAAA-TGCTCCCCCTAAACAGAGGCTTTGAAAC
* *
5309896 TTTGAAAATAGCTCCCCCTAAACAAAGGCTTTGAAGC
1 TTTGAAAAT-GCTCCCCCTAAACAGAGGCTTTGAAAC
* * * *
5309933 TTTTAAAATGACTTCCGCTAAACAGAAGCTTTGAAAC
1 TTTGAAAATG-CTCCCCCTAAACAGAGGCTTTGAAAC
5309970 TTT
1 TTT
5309973 TTTTTTTTTA
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
36 2 0.03
37 62 0.97
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32
Consensus pattern (36 bp):
TTTGAAAATGCTCCCCCTAAACAGAGGCTTTGAAAC
Found at i:5310014 original size:133 final size:133
Alignment explanation
Indices: 5309837--5310204 Score: 451
Period size: 133 Copynumber: 2.8 Consensus size: 133
5309827 TTCTTTCTTT
** *
5309837 TTTTTTTTTTTTTTAAATCTTGTTTGAAAATTGCTCTCTCTAAACAGAGGTTTTGAAACTTTGAA
1 TTTTTTTTTTTTAAAAATCTTGTTTGAAAATTGCTCCCTCTAAACAGAGGTTTTGAAACTTTGAA
* * *
5309902 AATAGCTCCCCCTAAACAAAGGCTTTGAAGCTTTTAAAATGACTTCCGCTAAACAGAA-GCTTTG
66 AATGGCTCCCCCTAAATAAAGGCTTTGAAACTTTTAAAATGACTTCCGCTAAACA-AAGGCTTTG
5309966 AAAC
130 AAAC
* * * *
5309970 TTTTTTTTTTTTAAAAATCTTGTTTGAAAATTGCTCCCTTTAAACAAAGGTTTTAAAACTTTGAT
1 TTTTTTTTTTTTAAAAATCTTGTTTGAAAATTGCTCCCTCTAAACAGAGGTTTTGAAACTTTGAA
* * * * * * **
5310035 AATGGCTCCTCCTAAATAGAGGTTTTAAAACTTTGAAAATGGCTTCTTCTAAACAAAGGCTTTGA
66 AATGGCTCCCCCTAAATAAAGGCTTTGAAACTTTTAAAATGACTTCCGCTAAACAAAGGCTTTGA
5310100 AAC
131 AAC
** * *
5310103 -----TTTTTAAAAAAATCTTGTTTGAAAATTTCTCCCTCTAAAAAGAGGTTTTGAAACTTTGAA
1 TTTTTTTTTTTTAAAAATCTTGTTTGAAAATTGCTCCCTCTAAACAGAGGTTTTGAAACTTTGAA
* **
5310163 AATGGCTTTCCTTTAAATAAAGGCTTTGAAACTTTTAAAATG
66 AATGGC-TCCCCCTAAATAAAGGCTTTGAAACTTTTAAAATG
5310205 GCTCTCTTTA
Statistics
Matches: 199, Mismatches: 34, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
128 58 0.29
129 27 0.14
132 2 0.01
133 112 0.56
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.39
Consensus pattern (133 bp):
TTTTTTTTTTTTAAAAATCTTGTTTGAAAATTGCTCCCTCTAAACAGAGGTTTTGAAACTTTGAA
AATGGCTCCCCCTAAATAAAGGCTTTGAAACTTTTAAAATGACTTCCGCTAAACAAAGGCTTTGA
AAC
Found at i:5310043 original size:37 final size:36
Alignment explanation
Indices: 5309992--5310105 Score: 129
Period size: 37 Copynumber: 3.1 Consensus size: 36
5309982 AAAAATCTTG
*
5309992 TTTGAAAATTGCTCCCTTTAAACAAAGGTTTTAAAAC
1 TTTGAAAATGGCT-CCTTTAAACAAAGGTTTTAAAAC
* * * *
5310029 TTTGATAATGGCTCCTCCTAAATAGAGGTTTTAAAAC
1 TTTGAAAATGGCTCCT-TTAAACAAAGGTTTTAAAAC
* * *
5310066 TTTGAAAATGGCTTCTTCTAAACAAAGGCTTTGAAAC
1 TTTGAAAATGGCTCCTT-TAAACAAAGGTTTTAAAAC
5310103 TTT
1 TTT
5310106 TTAAAAAAAT
Statistics
Matches: 63, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
36 3 0.05
37 60 0.95
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (36 bp):
TTTGAAAATGGCTCCTTTAAACAAAGGTTTTAAAAC
Found at i:5310228 original size:37 final size:37
Alignment explanation
Indices: 5310131--5310328 Score: 171
Period size: 37 Copynumber: 5.1 Consensus size: 37
5310121 TTGAAAATTT
* * *
5310131 CTCCCTCTAAAAAGAGGTTTTGAAACTTTGAAAATGG
1 CTCCCTTTAAACAGAGGTTTTGAAACTTTTAAAATGG
* * * *
5310168 CTTTCCTTTAAATAAAGGCTTTGAAACTTTTAAAATGG
1 C-TCCCTTTAAACAGAGGTTTTGAAACTTTTAAAATGG
* * *
5310206 CTCTCTTTAAATAGAGGTTTTGAAACTTTTTTAAAAAATCATTG
1 CTCCCTTTAAACAGAGGTTTTGAAAC--TTTT---AAA--ATGG
* * * *
5310250 TTCCCTCTAAACAAAGGTTTTGAAAATTTTAAAATGG
1 CTCCCTTTAAACAGAGGTTTTGAAACTTTTAAAATGG
* * *
5310287 ATCCCCTTAAACAGAGGTTTTGAAACTTTTAAAATAG
1 CTCCCTTTAAACAGAGGTTTTGAAACTTTTAAAATGG
5310324 CTCCC
1 CTCCC
5310329 CCCAAGCAGA
Statistics
Matches: 128, Mismatches: 25, Indels: 16
0.76 0.15 0.09
Matches are distributed among these distances:
37 60 0.47
38 31 0.24
39 7 0.05
42 7 0.05
44 23 0.18
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.36
Consensus pattern (37 bp):
CTCCCTTTAAACAGAGGTTTTGAAACTTTTAAAATGG
Found at i:5310469 original size:18 final size:18
Alignment explanation
Indices: 5310442--5310487 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
5310432 CTCATCAAAT
* * *
5310442 GATGCTAATGGAAATGTC
1 GATGCAAATGCAAATATC
5310460 GATGCAAATGCAAATATC
1 GATGCAAATGCAAATATC
*
5310478 AATGCAAATG
1 GATGCAAATG
5310488 TAAGAATACG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.41, C:0.13, G:0.22, T:0.24
Consensus pattern (18 bp):
GATGCAAATGCAAATATC
Found at i:5310711 original size:41 final size:41
Alignment explanation
Indices: 5310659--5310741 Score: 130
Period size: 41 Copynumber: 2.0 Consensus size: 41
5310649 ACAAGTGCAA
* *
5310659 ATGCAAGTGATGCAAATGTGAATGTCTTTCTTATGATGTAG
1 ATGCAAGTGATGCAAATGTAAATATCTTTCTTATGATGTAG
* *
5310700 ATGCAATTGATGCAAATGTAAATATCTTTTTTATGATGTAG
1 ATGCAAGTGATGCAAATGTAAATATCTTTCTTATGATGTAG
5310741 A
1 A
5310742 CATGAATGCA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.39
Consensus pattern (41 bp):
ATGCAAGTGATGCAAATGTAAATATCTTTCTTATGATGTAG
Found at i:5310766 original size:32 final size:32
Alignment explanation
Indices: 5310714--5310776 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
5310704 AATTGATGCA
* * *
5310714 AATGTAAATATCTTTTTTATGATGTAGACATG
1 AATGCAAATATCTTTCTTATGATGTACACATG
*
5310746 AATGCAAATGTCTTTCTTATGATGTACACAT
1 AATGCAAATATCTTTCTTATGATGTACACAT
5310777 AAGTATGAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.33, C:0.11, G:0.14, T:0.41
Consensus pattern (32 bp):
AATGCAAATATCTTTCTTATGATGTACACATG
Found at i:5311056 original size:35 final size:36
Alignment explanation
Indices: 5311017--5311111 Score: 86
Period size: 35 Copynumber: 2.6 Consensus size: 36
5311007 ATTCAAAGGC
*
5311017 CGGGATGACCCTGCAAGTTAAAAAAT-AAGAACAAT
1 CGGGATGACCCTGCAAGTTAAAAAATAAAAAACAAT
* *** *
5311052 CGGGACGATGTTGCAAGTAAAAAAATAAAAAACAAT
1 CGGGATGACCCTGCAAGTTAAAAAATAAAAAACAAT
* *
5311088 GGGGATAACACC-GCAAGTCTAAAA
1 CGGGATGAC-CCTGCAAGT-TAAAA
5311112 TAAGAAAACG
Statistics
Matches: 44, Mismatches: 13, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
35 21 0.48
36 19 0.43
37 4 0.09
ACGTcount: A:0.47, C:0.16, G:0.21, T:0.16
Consensus pattern (36 bp):
CGGGATGACCCTGCAAGTTAAAAAATAAAAAACAAT
Found at i:5311120 original size:36 final size:35
Alignment explanation
Indices: 5311073--5311142 Score: 88
Period size: 36 Copynumber: 2.0 Consensus size: 35
5311063 TGCAAGTAAA
**
5311073 AAAATAAAAAAC-AATGGGGATAACACCGCAAGTCT
1 AAAATAAAAAACGAAT-AAGATAACACCGCAAGTCT
*
5311108 AAAATAAGAAAACGACTAAGATAACACCGCAAGTC
1 AAAATAA-AAAACGAATAAGATAACACCGCAAGTC
5311143 GGATAAAATG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
35 7 0.23
36 21 0.70
37 2 0.07
ACGTcount: A:0.53, C:0.19, G:0.16, T:0.13
Consensus pattern (35 bp):
AAAATAAAAAACGAATAAGATAACACCGCAAGTCT
Found at i:5311507 original size:33 final size:32
Alignment explanation
Indices: 5311392--5311562 Score: 128
Period size: 32 Copynumber: 5.2 Consensus size: 32
5311382 GCTGGGCATA
* * * *
5311392 AAAATTTCATTAG-GCTAAATAAATTGAGCTT
1 AAAATTTCATTGGTGCCAGATAAATTGGGCTT
* * *
5311423 AAAATTTTCATCAGGGGTCAGATAAATTGGGCTTT
1 AAAA-TTTCAT-TGGTGCCAGATAAATTGGGC-TT
* ** * *
5311458 AAATCTTTTTTTGGTGCCAAATAAATTGAGCTT
1 AAA-ATTTCATTGGTGCCAGATAAATTGGGCTT
* * *
5311491 AAAATTTCATTGGGTGCTAGCTAAGTTGGGCTT
1 AAAATTTCATT-GGTGCCAGATAAATTGGGCTT
* * *
5311524 AAACTTTCATTGGTGTCAGGTAAATTGGGCTT
1 AAAATTTCATTGGTGCCAGATAAATTGGGCTT
5311556 AAAATTT
1 AAAATTT
5311563 TCACTAAAGG
Statistics
Matches: 106, Mismatches: 28, Indels: 11
0.73 0.19 0.08
Matches are distributed among these distances:
31 4 0.04
32 34 0.32
33 32 0.30
34 27 0.25
35 9 0.08
ACGTcount: A:0.32, C:0.11, G:0.20, T:0.37
Consensus pattern (32 bp):
AAAATTTCATTGGTGCCAGATAAATTGGGCTT
Found at i:5311565 original size:33 final size:33
Alignment explanation
Indices: 5311410--5311565 Score: 138
Period size: 34 Copynumber: 4.7 Consensus size: 33
5311400 ATTAGGCTAA
* * *
5311410 ATAAATTGAGCTTAAAATTTTCATCAGGGGTCAG
1 ATAAATTGGGCTTAAAATTTTCAT-TGGTGTCAG
* ** * *
5311444 ATAAATTGGGCTTTAAATCTTTTTTTGGTGCCAA
1 ATAAATTGGGCTTAAAAT-TTTCATTGGTGTCAG
*
5311478 ATAAATTGAGCTTAAAA-TTTCATTGG-GTGCTAG
1 ATAAATTGGGCTTAAAATTTTCATTGGTGT-C-AG
* * *
5311511 CTAAGTTGGGCTT-AAACTTTCATTGGTGTCAG
1 ATAAATTGGGCTTAAAATTTTCATTGGTGTCAG
*
5311543 GTAAATTGGGCTTAAAATTTTCA
1 ATAAATTGGGCTTAAAATTTTCA
5311566 CTAAAGGCTA
Statistics
Matches: 96, Mismatches: 20, Indels: 13
0.74 0.16 0.10
Matches are distributed among these distances:
31 1 0.01
32 24 0.25
33 29 0.30
34 38 0.40
35 4 0.04
ACGTcount: A:0.30, C:0.12, G:0.21, T:0.38
Consensus pattern (33 bp):
ATAAATTGGGCTTAAAATTTTCATTGGTGTCAG
Done.