Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167982.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_24, 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: 18142777
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 63000 characters in sequence are not A, C, G, or T
File 23 of 84
Found at i:4828187 original size:20 final size:21
Alignment explanation
Indices: 4828162--4828202 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
4828152 TAGAGATACG
*
4828162 TAAATGCAC-TTGGCAAGAAA
1 TAAATGAACTTTGGCAAGAAA
*
4828182 TAAATGAACTTTGGGAAGAAA
1 TAAATGAACTTTGGCAAGAAA
4828203 CCATAAAGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.46, C:0.10, G:0.22, T:0.22
Consensus pattern (21 bp):
TAAATGAACTTTGGCAAGAAA
Found at i:4834639 original size:36 final size:36
Alignment explanation
Indices: 4834599--4834670 Score: 110
Period size: 36 Copynumber: 2.0 Consensus size: 36
4834589 AAAATTTAAA
* *
4834599 ATATGCATGCA-TGAAAAAAGTTTAAATTAATTCAAG
1 ATATGCATGCACAG-AAAAAGTTCAAATTAATTCAAG
4834635 ATATGCATGCACAGAAAAAGTTCAAATTAATTCAAG
1 ATATGCATGCACAGAAAAAGTTCAAATTAATTCAAG
4834671 TGGCTGATCG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
36 32 0.97
37 1 0.03
ACGTcount: A:0.47, C:0.11, G:0.14, T:0.28
Consensus pattern (36 bp):
ATATGCATGCACAGAAAAAGTTCAAATTAATTCAAG
Found at i:4837836 original size:13 final size:12
Alignment explanation
Indices: 4837770--4837837 Score: 55
Period size: 13 Copynumber: 4.9 Consensus size: 12
4837760 CATTATTTCC
4837770 TAAAAAAATCAAAT
1 TAAAAAAA--AAAT
4837784 TAAAAGAAAAAAT
1 TAAAA-AAAAAAT
4837797 TAAAAAATTAAAGAT
1 TAAAAAA--AAA-AT
4837812 TAAAGGAAAAAAAT
1 TAAA--AAAAAAAT
4837826 TAAATAAAAAAA
1 TAAA-AAAAAAA
4837838 GACCTATAAA
Statistics
Matches: 47, Mismatches: 1, Indels: 13
0.77 0.02 0.21
Matches are distributed among these distances:
12 2 0.04
13 16 0.34
14 14 0.30
15 12 0.26
17 3 0.06
ACGTcount: A:0.74, C:0.01, G:0.06, T:0.19
Consensus pattern (12 bp):
TAAAAAAAAAAT
Found at i:4837838 original size:29 final size:28
Alignment explanation
Indices: 4837782--4837839 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 28
4837772 AAAAAATCAA
*
4837782 ATTAAAAGAAAAAATTAAAAAATTAAAG
1 ATTAAAAGAAAAAATTAAAAAATAAAAG
*
4837810 ATTAAAGGAAAAAAATTAAATAAA-AAAAG
1 ATTAAAAG-AAAAAATTAAA-AAATAAAAG
4837839 A
1 A
4837840 CCTATAAATG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 7 0.27
29 16 0.62
30 3 0.12
ACGTcount: A:0.72, C:0.00, G:0.09, T:0.19
Consensus pattern (28 bp):
ATTAAAAGAAAAAATTAAAAAATAAAAG
Found at i:4838803 original size:22 final size:22
Alignment explanation
Indices: 4838778--4838833 Score: 67
Period size: 24 Copynumber: 2.5 Consensus size: 22
4838768 TCTCACAATA
4838778 ATAAAAATTTTTATCTTTTAAG
1 ATAAAAATTTTTATCTTTTAAG
* *
4838800 ATAAAAATTAAATTATTTTTTAAG
1 ATAAAAATT--TTTATCTTTTAAG
*
4838824 ATAATAATTT
1 ATAAAAATTT
4838834 AAAATTATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
22 9 0.32
24 19 0.68
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (22 bp):
ATAAAAATTTTTATCTTTTAAG
Found at i:4838820 original size:24 final size:26
Alignment explanation
Indices: 4838788--4838842 Score: 78
Period size: 24 Copynumber: 2.2 Consensus size: 26
4838778 ATAAAAATTT
*
4838788 TTATCTTTTAAGATAA-AAATT-AAA
1 TTATTTTTTAAGATAATAAATTAAAA
*
4838812 TTATTTTTTAAGATAATAATTTAAAA
1 TTATTTTTTAAGATAATAAATTAAAA
4838838 TTATT
1 TTATT
4838843 ATCACATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
24 15 0.56
25 4 0.15
26 8 0.30
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (26 bp):
TTATTTTTTAAGATAATAAATTAAAA
Found at i:4838875 original size:24 final size:23
Alignment explanation
Indices: 4838819--4838878 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 23
4838809 AAATTATTTT
*
4838819 TTAAGATAATAATTTAAAATTATTA
1 TTAA-ATAA-AATTTAAAATTACTA
* *
4838844 TCACATAAAATTTATAAATTACTA
1 TTAAATAAAATTTA-AAATTACTA
4838868 TTAAATAAAAT
1 TTAAATAAAAT
4838879 CATATAGTTA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
23 6 0.21
24 21 0.72
25 2 0.07
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (23 bp):
TTAAATAAAATTTAAAATTACTA
Found at i:4840147 original size:263 final size:260
Alignment explanation
Indices: 4839808--4840300 Score: 655
Period size: 263 Copynumber: 1.9 Consensus size: 260
4839798 CATCAACAAT
* ** * *
4839808 ATTCAAATTTAAAATTTAAAGTCAAGATGAATGGTTTATTAAACATTAACTCTATTAATATTTAT
1 ATTCAAATTTAAAATTTAAAGTCAAGATGAATGATCAATTAAACATTAACTCTATTAATATCTAG
* ** * * ** * *
4839873 GTCAATTAAGTTTTTGAAAGTTAAAATTTTGAAAAATTTAAACATGTAATGCATTTTAATTAAAA
66 GTCAATTAAGTTATCAAAAATTAAAAATTCAAAAAATTTAAACATATAATACATTTTAATTAAAA
* *
4839938 AACTTTAAAAAAGTAAACAACTTTATCTA-TTGAATTAATCTTTATTGGTTAAATAAAAACATGA
131 AAATTT-AAAAAGTAAACAAATTT-TCTATTTGAATTAATCTTTATTGGTTAAATAAAAACATGA
*
4840002 GATAAATAAATTATTCACTATTTTTAGTCAATTTTAAGGGAAGTTATCTGAATAATTAATGGGCA
194 GATAAATAAATTATTCACTATTTTTAATCAATTTTAAGGGAAGTTATCTGAATAATTAATGGGCA
4840067 AG
259 AG
* * * *
4840069 ATTCAAATTTAAAATTATTAAAGTTAAGATGAATGATCAATTGAACATTAGCTTTATTAATATCT
1 ATTCAAATTTAAAA-T-TTAAAGTCAAGATGAATGATCAATTAAACATTAACTCTATTAATATCT
* * **
4840134 GGGTCAATTAAGTTATCAAAAATTAAAAATTCAAAAAATTTAAACGTATAATATGTTTTAATTAA
64 AGGTCAATTAAGTTATCAAAAATTAAAAATTCAAAAAATTTAAACATATAATACATTTTAATTAA
* * * *
4840199 AAAAATTTAAAAAGTAAACAAATTTTTTATTTGATTTGATTTTTATTGGTTAAATAAAAACATGA
129 AAAAATTTAAAAAGTAAACAAATTTTCTATTTGAATTAATCTTTATTGGTTAAATAAAAACATGA
***
4840264 GATTGGTAAATTATTCACTATTTTTAATCAATTTTAA
194 GATAAATAAATTATTCACTATTTTTAATCAATTTTAA
4840301 AGGAGGCATT
Statistics
Matches: 197, Mismatches: 32, Indels: 5
0.84 0.14 0.02
Matches are distributed among these distances:
261 17 0.09
262 82 0.42
263 98 0.50
ACGTcount: A:0.44, C:0.07, G:0.10, T:0.40
Consensus pattern (260 bp):
ATTCAAATTTAAAATTTAAAGTCAAGATGAATGATCAATTAAACATTAACTCTATTAATATCTAG
GTCAATTAAGTTATCAAAAATTAAAAATTCAAAAAATTTAAACATATAATACATTTTAATTAAAA
AAATTTAAAAAGTAAACAAATTTTCTATTTGAATTAATCTTTATTGGTTAAATAAAAACATGAGA
TAAATAAATTATTCACTATTTTTAATCAATTTTAAGGGAAGTTATCTGAATAATTAATGGGCAAG
Found at i:4842244 original size:258 final size:254
Alignment explanation
Indices: 4841872--4842354 Score: 594
Period size: 258 Copynumber: 1.9 Consensus size: 254
4841862 TAATCAATTT
* * * *
4841872 TAAAAGAGACATTGTATCTGAATAATAATTCATCAACAAGATTCAAATTTAAAATTATTAACGCT
1 TAAAAAAGACATTGTATCTAAACAATAATTCATCAACAAGATTCAAATTTAAAATTATTAAAGCT
* * * *
4841937 AAGATGAATAGTCAATCGAACGTTAATTATATTAATAATCATGTCAATTAAGTTTTTCAAAGTTA
66 AAAATGAATAGTCAATCGAACATTAACTATATTAATAATCATGTCAATTAAGTTTTTAAAAGTTA
** *
4842002 AAAATTTTAAAAAAAAATTTAAGTGTGTAATACATTTTAACAAAAAAAATCTT-AAA-TATACTA
131 AAAA--TT--AAAAAAATTTAAACGTGTAATACATTTTAA-AAAAAAAATCTTAAAAGTAAAC-A
4842065 A-TTTATCTATTGAATTAATCTTTATTGGTTAAATGTTTATGGCTTTCACGTTATATAGAAGTTA
190 ATTTTATCTATTGAATTAATCTTTATTGGTTAAATGTTTATGGCTTTCACGTTATATAGAAGTTA
* ** * *
4842129 TAAAAAAGGCATTGTATCTAAACAATAATTCATGGACAATATTCAAATTTAAAAGTTATTAAAGT
1 TAAAAAAGACATTGTATCTAAACAATAATTCATCAACAAGATTCAAATTTAAAA-TTATTAAAGC
** * * * * *
4842194 TAAAATGAATAGTTGATTGAACATTAGCTCTATTAATATTCGTGTCAATTAAGTTTTTAAAAGTT
65 TAAAATGAATAGTCAATCGAACATTAACTATATTAATAATCATGTCAATTAAGTTTTTAAAAGTT
* * * * ** * *
4842259 AAAAATTCATAAAATTTAAACGTGTAGTTCATTTTAATTAAAAATTTTTAAAAAGTAAACAATTT
130 AAAAATTAAAAAAATTTAAACGTGTAATACATTTTAAAAAAAAAATCTT-AAAAGTAAACAATTT
4842324 TATCTATTGAATTAATCTTTATTGGTTAAAT
194 TATCTATTGAATTAATCTTTATTGGTTAAAT
4842355 AAAAACACGA
Statistics
Matches: 190, Mismatches: 31, Indels: 11
0.82 0.13 0.05
Matches are distributed among these distances:
253 8 0.04
254 24 0.13
255 5 0.03
256 39 0.21
257 47 0.25
258 67 0.35
ACGTcount: A:0.43, C:0.08, G:0.10, T:0.39
Consensus pattern (254 bp):
TAAAAAAGACATTGTATCTAAACAATAATTCATCAACAAGATTCAAATTTAAAATTATTAAAGCT
AAAATGAATAGTCAATCGAACATTAACTATATTAATAATCATGTCAATTAAGTTTTTAAAAGTTA
AAAATTAAAAAAATTTAAACGTGTAATACATTTTAAAAAAAAAATCTTAAAAGTAAACAATTTTA
TCTATTGAATTAATCTTTATTGGTTAAATGTTTATGGCTTTCACGTTATATAGAAGTTA
Found at i:4844337 original size:26 final size:27
Alignment explanation
Indices: 4844308--4844371 Score: 71
Period size: 26 Copynumber: 2.4 Consensus size: 27
4844298 TTACATTGAT
4844308 AAATAATATTTTAT-TAAT-TTCAGATC
1 AAATAATATTTTATATAATATT-AGATC
4844334 AAAT-ATAATTTTATATAATATTAGATC
1 AAATAAT-ATTTTATATAATATTAGATC
*
4844361 AATTTAATATT
1 AA-ATAATATT
4844372 AAAAAAAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
25 2 0.06
26 11 0.34
27 11 0.34
28 6 0.19
29 2 0.06
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (27 bp):
AAATAATATTTTATATAATATTAGATC
Found at i:4844390 original size:25 final size:24
Alignment explanation
Indices: 4844362--4844409 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
4844352 TATTAGATCA
*
4844362 ATTTAATATTAAAAAAAAATCATCG
1 ATTTAA-AATAAAAAAAAATCATCG
* *
4844387 ATTTAAAATAAGAAAAACTCATC
1 ATTTAAAATAAAAAAAAATCATC
4844410 CCGATTCAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.56, C:0.10, G:0.04, T:0.29
Consensus pattern (24 bp):
ATTTAAAATAAAAAAAAATCATCG
Found at i:4853036 original size:19 final size:18
Alignment explanation
Indices: 4853012--4853058 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
4853002 AGAATAAATA
4853012 AATAATTTTTAAATATTAT
1 AATAATTTTTAAAT-TTAT
* **
4853031 ATTAATTAATAAATTTAT
1 AATAATTTTTAAATTTAT
4853049 AATAATTTTT
1 AATAATTTTT
4853059 TTATATATTT
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
AATAATTTTTAAATTTAT
Found at i:4855868 original size:4 final size:4
Alignment explanation
Indices: 4855847--4855890 Score: 56
Period size: 4 Copynumber: 11.5 Consensus size: 4
4855837 TATAGAATAC
* *
4855847 ATGT GTGT ATGC ATGT ATGT A--T ATGT ATGT ATGT ATGT ATGT AT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
4855891 CTCATGGATC
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
2 2 0.06
4 32 0.94
ACGTcount: A:0.25, C:0.02, G:0.25, T:0.48
Consensus pattern (4 bp):
ATGT
Found at i:4855875 original size:18 final size:18
Alignment explanation
Indices: 4855852--4855886 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
4855842 AATACATGTG
4855852 TGTATGCATGTATGTATA
1 TGTATGCATGTATGTATA
*
4855870 TGTATGTATGTATGTAT
1 TGTATGCATGTATGTAT
4855887 GTATCTCATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.03, G:0.23, T:0.49
Consensus pattern (18 bp):
TGTATGCATGTATGTATA
Found at i:4855877 original size:22 final size:22
Alignment explanation
Indices: 4855847--4855890 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
4855837 TATAGAATAC
*
4855847 ATGTGTGTATGCATGTATGTAT
1 ATGTATGTATGCATGTATGTAT
*
4855869 ATGTATGTATGTATGTATGTAT
1 ATGTATGTATGCATGTATGTAT
4855891 CTCATGGATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.25, C:0.02, G:0.25, T:0.48
Consensus pattern (22 bp):
ATGTATGTATGCATGTATGTAT
Found at i:4857823 original size:2 final size:2
Alignment explanation
Indices: 4857816--4857840 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4857806 CTAAATCTTC
4857816 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
4857841 CACACACATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4858031 original size:15 final size:15
Alignment explanation
Indices: 4858011--4858040 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
4858001 CGCCCATGAT
4858011 GTGAAAAAAAAAAAA
1 GTGAAAAAAAAAAAA
4858026 GTGAAAAAAAAAAAA
1 GTGAAAAAAAAAAAA
4858041 TTAACATCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.80, C:0.00, G:0.13, T:0.07
Consensus pattern (15 bp):
GTGAAAAAAAAAAAA
Found at i:4859962 original size:10 final size:10
Alignment explanation
Indices: 4859947--4859977 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
4859937 TTTCACACCC
4859947 TAGAGAGAGA
1 TAGAGAGAGA
4859957 TAGAGAGAGA
1 TAGAGAGAGA
4859967 TAGAGAGAGA
1 TAGAGAGAGA
4859977 T
1 T
4859978 GCCTCTGCTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.39, T:0.13
Consensus pattern (10 bp):
TAGAGAGAGA
Found at i:4864495 original size:5 final size:5
Alignment explanation
Indices: 4864485--4864512 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
4864475 AAATCTCTCT
4864485 TTTCC TTTCC TTTCC TTTCC TTTCC TTT
1 TTTCC TTTCC TTTCC TTTCC TTTCC TTT
4864513 TTGTCCTTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (5 bp):
TTTCC
Found at i:4880135 original size:45 final size:44
Alignment explanation
Indices: 4880071--4880159 Score: 133
Period size: 44 Copynumber: 2.0 Consensus size: 44
4880061 CATCTGCGGA
4880071 GCCTGTCTCCTTTAAAGTTCTATTCAAATCAAAGAGAAAAGATTT
1 GCCTGTCTCCTTTAAAGTTC-ATTCAAATCAAAGAGAAAAGATTT
* ** *
4880116 GCCTGTCTCCTTTAGAGTTCATTTGAATCAAAGAGAAAGGATTT
1 GCCTGTCTCCTTTAAAGTTCATTCAAATCAAAGAGAAAAGATTT
4880160 AAATTCTTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
44 21 0.52
45 19 0.47
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Consensus pattern (44 bp):
GCCTGTCTCCTTTAAAGTTCATTCAAATCAAAGAGAAAAGATTT
Found at i:4890670 original size:28 final size:27
Alignment explanation
Indices: 4890621--4890682 Score: 63
Period size: 28 Copynumber: 2.3 Consensus size: 27
4890611 AATTCTTAAA
* *
4890621 AAATAATATTATAAAAATTAAAATTTTT
1 AAATAATATTATAAAAACT-AAATTCTT
***
4890649 AAATAATATTATAGGGACTAAATTCTT
1 AAATAATATTATAAAAACTAAATTCTT
4890676 AAA-AATA
1 AAATAATA
4890683 AAAAATACAT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
26 4 0.14
27 10 0.34
28 15 0.52
ACGTcount: A:0.55, C:0.03, G:0.05, T:0.37
Consensus pattern (27 bp):
AAATAATATTATAAAAACTAAATTCTT
Found at i:4892770 original size:18 final size:19
Alignment explanation
Indices: 4892734--4892772 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
4892724 TAAAATTAAA
*
4892734 AAATAATAAAAATATATTT
1 AAATAATAAAAATAAATTT
*
4892753 AAAT-ATAAATATAAATTT
1 AAATAATAAAAATAAATTT
4892771 AA
1 AA
4892773 TGATAAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
AAATAATAAAAATAAATTT
Found at i:4897825 original size:14 final size:15
Alignment explanation
Indices: 4897806--4897839 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
4897796 ATTATAAACT
4897806 TTTTCAAAAA-TAAA
1 TTTTCAAAAAGTAAA
4897820 TTTTCAAAAAGTTAAA
1 TTTTCAAAAAG-TAAA
4897836 TTTT
1 TTTT
4897840 TAGAAAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 10 0.56
16 8 0.44
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (15 bp):
TTTTCAAAAAGTAAA
Found at i:4897858 original size:18 final size:17
Alignment explanation
Indices: 4897837--4897938 Score: 70
Period size: 18 Copynumber: 6.0 Consensus size: 17
4897827 AAAGTTAAAT
4897837 TTTTAGAAAAATTTATGA
1 TTTTA-AAAAATTTATGA
* *
4897855 TTTTTCAAAAATCTAT--
1 -TTTTAAAAAATTTATGA
*
4897871 TTCTAAAAAATTATATGA
1 TTTTAAAAAATT-TATGA
*
4897889 TTTTTTAAAAATTTAT-A
1 -TTTTAAAAAATTTATGA
**
4897906 -TTTAAAAAATTATAAAA
1 TTTTAAAAAATT-TATGA
4897923 TTTTAAAAAA-TTATGA
1 TTTTAAAAAATTTATGA
4897939 AAATGATTAT
Statistics
Matches: 65, Mismatches: 11, Indels: 17
0.70 0.12 0.18
Matches are distributed among these distances:
15 19 0.29
16 8 0.12
17 3 0.05
18 21 0.32
19 14 0.22
ACGTcount: A:0.48, C:0.03, G:0.04, T:0.45
Consensus pattern (17 bp):
TTTTAAAAAATTTATGA
Found at i:4897893 original size:34 final size:34
Alignment explanation
Indices: 4897838--4897919 Score: 114
Period size: 34 Copynumber: 2.4 Consensus size: 34
4897828 AAGTTAAATT
4897838 TTTAGAAAAATT-TATGATTTTTCAAAAATCTAT-
1 TTTA-AAAAATTATATGATTTTTCAAAAATCTATA
* *
4897871 TTCTAAAAAATTATATGATTTTTTAAAAATTTATA
1 TT-TAAAAAATTATATGATTTTTCAAAAATCTATA
4897906 TTTAAAAAATTATA
1 TTTAAAAAATTATA
4897920 AAATTTTAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
33 9 0.20
34 33 0.75
35 2 0.05
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (34 bp):
TTTAAAAAATTATATGATTTTTCAAAAATCTATA
Found at i:4897926 original size:34 final size:34
Alignment explanation
Indices: 4897854--4897934 Score: 94
Period size: 34 Copynumber: 2.4 Consensus size: 34
4897844 AAAATTTATG
* * **
4897854 ATTTTTCAAAAATCTATTTCTAAAAAATTATATG
1 ATTTTTAAAAAATTTATTTCTAAAAAATTATAAA
*
4897888 ATTTTTTAAAAATTTATATT-TAAAAAATTATAAA
1 ATTTTTAAAAAATTTAT-TTCTAAAAAATTATAAA
4897922 A-TTTTAAAAAATT
1 ATTTTTAAAAAATT
4897935 ATGAAAATGA
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
33 11 0.27
34 28 0.68
35 2 0.05
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.46
Consensus pattern (34 bp):
ATTTTTAAAAAATTTATTTCTAAAAAATTATAAA
Found at i:4897932 original size:33 final size:34
Alignment explanation
Indices: 4897815--4897934 Score: 93
Period size: 34 Copynumber: 3.5 Consensus size: 34
4897805 TTTTTCAAAA
* * *
4897815 ATAAATTTTCAAAAAGTTAAATTTTTAGAAAAATT-T
1 ATAAATTTT-AAAAAATT-TATTTCTA-AAAAATTAT
* * * *
4897851 ATGATTTTTCAAAAATCTATTTCTAAAAAATTAT
1 ATAAATTTTAAAAAATTTATTTCTAAAAAATTAT
* * *
4897885 ATGATTTTTTAAAAATTTATATT-TAAAAAATTAT
1 ATAAATTTTAAAAAATTTAT-TTCTAAAAAATTAT
4897919 A-AAATTTTAAAAAATT
1 ATAAATTTTAAAAAATT
4897935 ATGAAAATGA
Statistics
Matches: 70, Mismatches: 12, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
33 19 0.27
34 37 0.53
35 7 0.10
36 7 0.10
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.44
Consensus pattern (34 bp):
ATAAATTTTAAAAAATTTATTTCTAAAAAATTAT
Found at i:4898286 original size:3 final size:3
Alignment explanation
Indices: 4898278--4898304 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
4898268 ATTTTGTGTT
4898278 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
4898305 AAAGATTGCG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:4898440 original size:14 final size:14
Alignment explanation
Indices: 4898421--4898453 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
4898411 ATCTCTTATC
4898421 TAATT-ATTATATTA
1 TAATTAATTA-ATTA
4898435 TAATTAATTAATTA
1 TAATTAATTAATTA
4898449 TAATT
1 TAATT
4898454 TAAAATTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
TAATTAATTAATTA
Found at i:4907906 original size:2 final size:2
Alignment explanation
Indices: 4907901--4907927 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4907891 TCTCTCTCTC
4907901 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
4907928 CATAAAATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4933074 original size:117 final size:117
Alignment explanation
Indices: 4932842--4933067 Score: 292
Period size: 117 Copynumber: 1.9 Consensus size: 117
4932832 GCAAGCCCAT
* * * * ** *
4932842 ACAGTAAAGTTTTAATAACCCAACTTGGAATATGACATCTTACTTAATTGGGCTTCAGTTATTTC
1 ACAGCAAAGTTTTAATAAACCAACTTGCAATATGACATCTTAATTAATTGGGCTAAAATTATTTC
** * **
4932907 TGTAGTAATTCACATTGTATGCAACAATGTGAAAATTTCAACAACTAGCAAC
66 TAAAGTAATGCACATCATATGCAACAATGTGAAAATTTCAACAACTAGCAAC
*
4932959 ACAGCAAAG-TTTAATAAACCAACTGTTCAATATGACATCTTAATTAATTGGGCTAAAATTATTT
1 ACAGCAAAGTTTTAATAAACCAACT-TGCAATATGACATCTTAATTAATTGGGCTAAAATTATTT
* * *
4933023 TTAAAGTAATGCACATCATATGCAACAATTTGAAATTTTCAACAA
65 CTAAAGTAATGCACATCATATGCAACAATGTGAAAATTTCAACAA
4933068 GCAGCAAGAC
Statistics
Matches: 92, Mismatches: 16, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
116 14 0.15
117 78 0.85
ACGTcount: A:0.39, C:0.16, G:0.12, T:0.33
Consensus pattern (117 bp):
ACAGCAAAGTTTTAATAAACCAACTTGCAATATGACATCTTAATTAATTGGGCTAAAATTATTTC
TAAAGTAATGCACATCATATGCAACAATGTGAAAATTTCAACAACTAGCAAC
Found at i:4939352 original size:40 final size:40
Alignment explanation
Indices: 4939272--4939351 Score: 110
Period size: 39 Copynumber: 2.0 Consensus size: 40
4939262 TTTTATACAG
*
4939272 TGCCCAATCATGTTCTGCCAAATCATGAAAAGCGATTTTT
1 TGCCCAATCATGTTCTGCCAAAGCATGAAAAGCGATTTTT
* *
4939312 TGCCCAATTAT-TTCTGCTAAAGCATGTAAAAG-GATTTTT
1 TGCCCAATCATGTTCTGCCAAAGCATG-AAAAGCGATTTTT
4939351 T
1 T
4939352 TTACTCCGAG
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
39 21 0.58
40 15 0.42
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.36
Consensus pattern (40 bp):
TGCCCAATCATGTTCTGCCAAAGCATGAAAAGCGATTTTT
Found at i:4939808 original size:2 final size:2
Alignment explanation
Indices: 4939797--4939833 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
4939787 AATGGCACTC
4939797 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4939834 CAAACAATGC
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 31 0.94
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:4940270 original size:17 final size:17
Alignment explanation
Indices: 4940250--4940309 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 17
4940240 ATATTACAGA
*
4940250 TTTATTTTTATTTTTATT
1 TTTA-TTTTATTATTATT
* * *
4940268 TTAATATTATTATTCTT
1 TTTATTTTATTATTATT
*
4940285 TTTCTTTTATTATTATTT
1 TTTATTTTATTATTA-TT
4940303 TTTATTT
1 TTTATTT
4940310 GTTAAAATTT
Statistics
Matches: 32, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
17 21 0.66
18 11 0.34
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (17 bp):
TTTATTTTATTATTATT
Found at i:4940277 original size:23 final size:23
Alignment explanation
Indices: 4940251--4940309 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 23
4940241 TATTACAGAT
4940251 TTATTTTTATTTTTATTTTAATA
1 TTATTTTTATTTTTATTTTAATA
* * * *
4940274 TTATTATTCTTTTTCTTTTATTA
1 TTATTTTTATTTTTATTTTAATA
4940297 TTATTTTTTATTT
1 TTA-TTTTTATTT
4940310 GTTAAAATTT
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
23 22 0.76
24 7 0.24
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.76
Consensus pattern (23 bp):
TTATTTTTATTTTTATTTTAATA
Found at i:4941573 original size:16 final size:15
Alignment explanation
Indices: 4941542--4941575 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
4941532 TATTTTGAGA
*
4941542 AAAAAATATATTTTT
1 AAAAAATATATATTT
4941557 AAAAAATATAATATTT
1 AAAAAATAT-ATATTT
4941573 AAA
1 AAA
4941576 TTTTTTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
AAAAAATATATATTT
Found at i:4948207 original size:2 final size:2
Alignment explanation
Indices: 4948200--4948227 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4948190 CGGTCTATCC
4948200 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
4948228 TATTTATCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:4954724 original size:2 final size:2
Alignment explanation
Indices: 4954719--4954759 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
4954709 AGGAGAAAGT
* *
4954719 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4954760 GTACACCCAT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4963845 original size:19 final size:19
Alignment explanation
Indices: 4963823--4963875 Score: 54
Period size: 23 Copynumber: 2.6 Consensus size: 19
4963813 TTTGTTAATT
4963823 TAATATAATAAAAATAAAA
1 TAATATAATAAAAATAAAA
*
4963842 TAATATTTGAATCAAAAATAAAT
1 TAATA--T-AAT-AAAAATAAAA
4963865 TAAT-TAATAAA
1 TAATATAATAAA
4963876 TGTTATAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 9
0.74 0.03 0.23
Matches are distributed among these distances:
18 3 0.10
19 8 0.28
20 1 0.03
21 1 0.03
22 3 0.10
23 13 0.45
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (19 bp):
TAATATAATAAAAATAAAA
Found at i:4973552 original size:24 final size:24
Alignment explanation
Indices: 4973516--4973568 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
4973506 AATTGCATGA
*
4973516 TAGT-ATCGATGTTCTAATTAAAT
1 TAGTAATCGATGTTCTAAGTAAAT
* *
4973539 TAGTAATCGCTGTTCTTAGTAAAT
1 TAGTAATCGATGTTCTAAGTAAAT
4973563 TAGTAA
1 TAGTAA
4973569 GATGTTATCC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 4 0.15
24 22 0.85
ACGTcount: A:0.34, C:0.09, G:0.15, T:0.42
Consensus pattern (24 bp):
TAGTAATCGATGTTCTAAGTAAAT
Found at i:4975176 original size:10 final size:10
Alignment explanation
Indices: 4975159--4975193 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
4975149 AAAATATATC
4975159 AAAATTTTTT
1 AAAATTTTTT
4975169 -AAA-TTTTT
1 AAAATTTTTT
4975177 AAAATTTTTT
1 AAAATTTTTT
4975187 AAAATTT
1 AAAATTT
4975194 AATTTATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
8 5 0.22
9 6 0.26
10 12 0.52
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (10 bp):
AAAATTTTTT
Found at i:4975177 original size:8 final size:9
Alignment explanation
Indices: 4975159--4975193 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
4975149 AAAATATATC
4975159 AAAATTTTT
1 AAAATTTTT
*
4975168 TAAATTTTT
1 AAAATTTTT
4975177 AAAATTTTTT
1 AAAA-TTTTT
4975187 AAAATTT
1 AAAATTT
4975194 AATTTATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
9 14 0.61
10 9 0.39
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (9 bp):
AAAATTTTT
Found at i:4977541 original size:30 final size:31
Alignment explanation
Indices: 4977507--4977578 Score: 80
Period size: 30 Copynumber: 2.4 Consensus size: 31
4977497 TAAATTTGAT
*
4977507 ATTAAAAATTAATATAGTTATATA-ATA-TAA
1 ATTAAAAATTAATATA-TTAAATACATATTAA
4977537 ATTAAAAA-TATATATATTAAATACATATTAA
1 ATTAAAAATTA-ATATATTAAATACATATTAA
*
4977568 A-TAAATATTAA
1 ATTAAAAATTAA
4977579 AATTTTTTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
29 8 0.22
30 22 0.61
31 6 0.17
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.39
Consensus pattern (31 bp):
ATTAAAAATTAATATATTAAATACATATTAA
Found at i:4977566 original size:11 final size:11
Alignment explanation
Indices: 4977550--4977579 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
4977540 AAAAATATAT
*
4977550 ATATTAAATAC
1 ATATTAAATAA
4977561 ATATTAAATAA
1 ATATTAAATAA
4977572 ATATTAAA
1 ATATTAAA
4977580 ATTTTTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (11 bp):
ATATTAAATAA
Found at i:4977596 original size:26 final size:27
Alignment explanation
Indices: 4977562--4977622 Score: 65
Period size: 26 Copynumber: 2.3 Consensus size: 27
4977552 ATTAAATACA
4977562 TATTAAATAAATATTAA-AATTTTT-TAT
1 TATT-AAT-AATATTAATAATTTTTATAT
* *
4977589 TTTTAAT-ATATTAATACTTTTTATAT
1 TATTAATAATATTAATAATTTTTATAT
4977615 TATTAATA
1 TATTAATA
4977623 TGTCAAATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
24 7 0.25
25 6 0.21
26 12 0.43
27 3 0.11
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.56
Consensus pattern (27 bp):
TATTAATAATATTAATAATTTTTATAT
Found at i:4977599 original size:24 final size:26
Alignment explanation
Indices: 4977572--4977623 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
4977562 TATTAAATAA
*
4977572 ATATTAA-AATTTTT-TATTTTTAAT
1 ATATTAATAATTTTTATATTATTAAT
*
4977596 ATATTAATACTTTTTATATTATTAAT
1 ATATTAATAATTTTTATATTATTAAT
4977622 AT
1 AT
4977624 GTCAAATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 7 0.29
25 6 0.25
26 11 0.46
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (26 bp):
ATATTAATAATTTTTATATTATTAAT
Found at i:4977611 original size:18 final size:18
Alignment explanation
Indices: 4977588--4977622 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
4977578 AAATTTTTTA
4977588 TTTTTA-ATATATTAATAC
1 TTTTTATAT-TATTAATAC
4977606 TTTTTATATTATTAATA
1 TTTTTATATTATTAATA
4977623 TGTCAAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTTTATATTATTAATAC
Found at i:4977885 original size:18 final size:17
Alignment explanation
Indices: 4977859--4977923 Score: 51
Period size: 18 Copynumber: 3.7 Consensus size: 17
4977849 CATATTTATA
*
4977859 TTTAAAATTATAATATAT
1 TTTATAATTATAATA-AT
* *
4977877 TTTATAATTTATATTAAA
1 TTTATAA-TTATAATAAT
*
4977895 TTTAT-ATTTTAATAAT
1 TTTATAATTATAATAAT
*
4977911 TTATATCATTATA
1 TT-TATAATTATA
4977924 CGTATCAAAT
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
16 9 0.24
17 4 0.11
18 17 0.46
19 7 0.19
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (17 bp):
TTTATAATTATAATAAT
Found at i:4985902 original size:77 final size:77
Alignment explanation
Indices: 4985775--4985927 Score: 306
Period size: 77 Copynumber: 2.0 Consensus size: 77
4985765 ATTTAACAAT
4985775 GATAATATTGAAATAATGATTCATTGAAATATTTAAAGATATTAACAGAGAAATCACATATTATA
1 GATAATATTGAAATAATGATTCATTGAAATATTTAAAGATATTAACAGAGAAATCACATATTATA
4985840 ACCTGCAAAAGA
66 ACCTGCAAAAGA
4985852 GATAATATTGAAATAATGATTCATTGAAATATTTAAAGATATTAACAGAGAAATCACATATTATA
1 GATAATATTGAAATAATGATTCATTGAAATATTTAAAGATATTAACAGAGAAATCACATATTATA
4985917 ACCTGCAAAAG
66 ACCTGCAAAAG
4985928 TATCTTGATT
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
77 76 1.00
ACGTcount: A:0.49, C:0.09, G:0.12, T:0.30
Consensus pattern (77 bp):
GATAATATTGAAATAATGATTCATTGAAATATTTAAAGATATTAACAGAGAAATCACATATTATA
ACCTGCAAAAGA
Found at i:4986496 original size:2 final size:2
Alignment explanation
Indices: 4986489--4986513 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4986479 AAAACAACTT
4986489 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
4986514 TATATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:4997922 original size:2 final size:2
Alignment explanation
Indices: 4997915--4997946 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
4997905 GAATTCATGA
4997915 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
4997947 CCTTTTGGAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:4999850 original size:16 final size:16
Alignment explanation
Indices: 4999815--4999861 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
4999805 GCTAAGATTG
*
4999815 AAATATTATA-TTTATT
1 AAATATTATATTTTA-A
4999831 AAATATTATATTTTAA
1 AAATATTATATTTTAA
*
4999847 AAATAAT-TATTTTAA
1 AAATATTATATTTTAA
4999862 TCAATTGAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 8 0.29
16 16 0.57
17 4 0.14
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
AAATATTATATTTTAA
Found at i:5011565 original size:2 final size:2
Alignment explanation
Indices: 5011554--5011584 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
5011544 CAAAAAAAAA
*
5011554 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5011585 ATCTTAATGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:5013310 original size:2 final size:2
Alignment explanation
Indices: 5013303--5013331 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5013293 CATCAGCCAA
5013303 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5013332 GAGAGAGAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5013336 original size:2 final size:2
Alignment explanation
Indices: 5013331--5013365 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
5013321 ATATATATAT
5013331 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
5013366 TAAAATTTAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5014703 original size:15 final size:15
Alignment explanation
Indices: 5014667--5014708 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
5014657 ATATCATAAC
* *
5014667 AATATAATTTGAAAA
1 AATATAAATTAAAAA
5014682 AA-A-AAATTAAAAA
1 AATATAAATTAAAAA
5014695 AATATAAATTAAAA
1 AATATAAATTAAAA
5014709 TTTTAATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 10 0.43
14 2 0.09
15 11 0.48
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.26
Consensus pattern (15 bp):
AATATAAATTAAAAA
Found at i:5025430 original size:20 final size:20
Alignment explanation
Indices: 5025394--5025431 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
5025384 AACTTATATG
*
5025394 TTTTATTATATTATTAAAAA
1 TTTTATTATAATATTAAAAA
5025414 TTTTATTAATAAT-TTAAA
1 TTTTATT-ATAATATTAAA
5025432 TTGTATAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TTTTATTATAATATTAAAAA
Found at i:5027341 original size:13 final size:13
Alignment explanation
Indices: 5027323--5027347 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5027313 GCTATAAATA
5027323 TTGCAGTTTTTTG
1 TTGCAGTTTTTTG
5027336 TTGCAGTTTTTT
1 TTGCAGTTTTTT
5027348 ACCTTTTTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.08, G:0.20, T:0.64
Consensus pattern (13 bp):
TTGCAGTTTTTTG
Found at i:5033769 original size:69 final size:69
Alignment explanation
Indices: 5033658--5033794 Score: 229
Period size: 69 Copynumber: 2.0 Consensus size: 69
5033648 GTGAAGTTAC
* *
5033658 AACATACAAAAATGCAATAAGCATCTCAAACTAAGTTCAACTGATTCTCAGATTTTGAACATTAA
1 AACATACAAAAATGAAATAAGCATCTCAAACTAAATTCAACTGATTCTCAGATTTTGAACATTAA
5033723 CTTA
66 CTTA
* * *
5033727 AACATACAGAAATGAAATAAGCATCTCAAACTAAATTCAACTGATTGTCGGATTTTGAACATTAA
1 AACATACAAAAATGAAATAAGCATCTCAAACTAAATTCAACTGATTCTCAGATTTTGAACATTAA
5033792 CTT
66 CTT
5033795 GGTATTCCTC
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
69 63 1.00
ACGTcount: A:0.43, C:0.18, G:0.10, T:0.29
Consensus pattern (69 bp):
AACATACAAAAATGAAATAAGCATCTCAAACTAAATTCAACTGATTCTCAGATTTTGAACATTAA
CTTA
Found at i:5043008 original size:14 final size:14
Alignment explanation
Indices: 5042989--5043018 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5042979 TTAACAAACT
*
5042989 AATGGATGAAGAAG
1 AATGGAAGAAGAAG
5043003 AATGGAAGAAGAAG
1 AATGGAAGAAGAAG
5043017 AA
1 AA
5043019 AGAAAATATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.57, C:0.00, G:0.33, T:0.10
Consensus pattern (14 bp):
AATGGAAGAAGAAG
Found at i:5048139 original size:20 final size:21
Alignment explanation
Indices: 5048116--5048157 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
5048106 AAAGTTCGTA
5048116 TATATTCATTT-AGGTTCATT
1 TATATTCATTTAAGGTTCATT
* *
5048136 TATATTTATTTAAGGTTTATT
1 TATATTCATTTAAGGTTCATT
5048157 T
1 T
5048158 GTTTAACATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.26, C:0.05, G:0.10, T:0.60
Consensus pattern (21 bp):
TATATTCATTTAAGGTTCATT
Found at i:5049364 original size:30 final size:30
Alignment explanation
Indices: 5049328--5049386 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
5049318 TTTGATCATA
5049328 TACAGAAGAATAATAGATTATTAAAATTTT
1 TACAGAAGAATAATAGATTATTAAAATTTT
5049358 TACAGAAGAATAATAGATTATTAAAATTT
1 TACAGAAGAATAATAGATTATTAAAATTT
5049387 AAGCCAAATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.51, C:0.03, G:0.10, T:0.36
Consensus pattern (30 bp):
TACAGAAGAATAATAGATTATTAAAATTTT
Found at i:5049972 original size:27 final size:27
Alignment explanation
Indices: 5049942--5049993 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
5049932 TAATTTTACA
* *
5049942 TATTTATATGTGTTATTTTAATAAAAT
1 TATTTATATATGTTAATTTAATAAAAT
* *
5049969 TATTTATTTATTTTAATTTAATAAA
1 TATTTATATATGTTAATTTAATAAA
5049994 TTAATATTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (27 bp):
TATTTATATATGTTAATTTAATAAAAT
Found at i:5051733 original size:14 final size:15
Alignment explanation
Indices: 5051708--5051749 Score: 54
Period size: 14 Copynumber: 3.0 Consensus size: 15
5051698 CAACCGAGTA
5051708 AATTAT-TTATAATT
1 AATTATATTATAATT
5051722 -ATTATATTATAATT
1 AATTATATTATAATT
*
5051736 AATTA-ATCATAATT
1 AATTATATTATAATT
5051750 TAAAATTATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
13 5 0.20
14 16 0.64
15 4 0.16
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (15 bp):
AATTATATTATAATT
Found at i:5057770 original size:2 final size:2
Alignment explanation
Indices: 5057763--5057795 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
5057753 TAGCAACTTA
5057763 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5057796 AAAGTTGTCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5060122 original size:20 final size:20
Alignment explanation
Indices: 5060073--5060127 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
5060063 TTTATGTTAA
5060073 ATAAAAATATTAAATTTTAT
1 ATAAAAATATTAAATTTTAT
***
5060093 ATATTTATATTAAATTTTAT
1 ATAAAAATATTAAATTTTAT
*
5060113 ATAAAAATATAAAAT
1 ATAAAAATATTAAAT
5060128 ATATATTTTT
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
ATAAAAATATTAAATTTTAT
Found at i:5060206 original size:29 final size:29
Alignment explanation
Indices: 5060174--5060229 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
5060164 TTATTAAAAT
*
5060174 TTTAAATCATATT-ATTTTTATATTTTATA
1 TTTAAATCATATTCA-TTTCATATTTTATA
* *
5060203 TTTATATTATATTCATTTCATATTTTA
1 TTTAAATCATATTCATTTCATATTTTA
5060230 AATTGTCAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 22 0.96
30 1 0.04
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.62
Consensus pattern (29 bp):
TTTAAATCATATTCATTTCATATTTTATA
Found at i:5061588 original size:23 final size:22
Alignment explanation
Indices: 5061542--5061588 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 22
5061532 TTCTCTCTTC
5061542 TTCTCTCTCTTTCTTCCTCTACT
1 TTCTCTCTCTTTC-TCCTCTACT
5061565 TTCTCTACTCTTTC-CCTCTCACT
1 TTCTCT-CTCTTTCTCCTCT-ACT
5061588 T
1 T
5061589 GCTCCTTGCA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 5 0.23
23 10 0.45
24 7 0.32
ACGTcount: A:0.06, C:0.40, G:0.00, T:0.53
Consensus pattern (22 bp):
TTCTCTCTCTTTCTCCTCTACT
Found at i:5064390 original size:21 final size:21
Alignment explanation
Indices: 5064365--5064415 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
5064355 TAAATTTTTA
5064365 AATTTTATATTAT-TTTAATAT
1 AATTTTATATTATATTTAA-AT
*
5064386 AATTTT-TAATATATTTAAAT
1 AATTTTATATTATATTTAAAT
*
5064406 AAATTTATAT
1 AATTTTATAT
5064416 ATAAAATGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
20 12 0.48
21 13 0.52
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
AATTTTATATTATATTTAAAT
Found at i:5064400 original size:22 final size:21
Alignment explanation
Indices: 5064363--5064417 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 21
5064353 TTTAAATTTT
*
5064363 TAAA-TTTTATATTATTTTAA
1 TAAATTTTTATATTATTTAAA
5064383 TATAATTTTTA-ATATATTTAAA
1 TA-AATTTTTATAT-TATTTAAA
*
5064405 TAAATTTATATAT
1 TAAATTTTTATAT
5064418 AAAATGATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
20 2 0.07
21 11 0.38
22 16 0.55
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TAAATTTTTATATTATTTAAA
Found at i:5069060 original size:19 final size:17
Alignment explanation
Indices: 5069033--5069071 Score: 51
Period size: 19 Copynumber: 2.2 Consensus size: 17
5069023 TTTACACCTC
5069033 AAATATAAAAAATAAAATA
1 AAATATAAAAAA-AAAA-A
*
5069052 AAATGTAAAAAAAAAAA
1 AAATATAAAAAAAAAAA
5069069 AAA
1 AAA
5069072 AGCCCATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 4 0.21
18 4 0.21
19 11 0.58
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (17 bp):
AAATATAAAAAAAAAAA
Found at i:5069380 original size:16 final size:17
Alignment explanation
Indices: 5069359--5069400 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
5069349 TTCATTTATA
5069359 AAAACAAA-GCACAACC
1 AAAACAAAGGCACAACC
*
5069375 AAAACAAAGGCATAACC
1 AAAACAAAGGCACAACC
5069392 AAAAGCAAA
1 AAAA-CAAA
5069401 AGCAATCAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 8 0.35
17 11 0.48
18 4 0.17
ACGTcount: A:0.64, C:0.24, G:0.10, T:0.02
Consensus pattern (17 bp):
AAAACAAAGGCACAACC
Found at i:5071439 original size:13 final size:13
Alignment explanation
Indices: 5071421--5071450 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
5071411 ATTATTCCTA
5071421 ATTTTTTATTTTT
1 ATTTTTTATTTTT
5071434 ATTTTTTATTTTT
1 ATTTTTTATTTTT
5071447 -TTTT
1 ATTTT
5071451 GTTTTTGAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (13 bp):
ATTTTTTATTTTT
Found at i:5086959 original size:8 final size:8
Alignment explanation
Indices: 5086936--5086986 Score: 59
Period size: 8 Copynumber: 6.5 Consensus size: 8
5086926 TAAATTAATT
*
5086936 TTTATTTA
1 TTTATATA
*
5086944 TATATATA
1 TTTATATA
5086952 TTTATATA
1 TTTATATA
*
5086960 ATTATATA
1 TTTATATA
*
5086968 TTTAAATA
1 TTTATATA
5086976 TTT-TATA
1 TTTATATA
5086983 TTTA
1 TTTA
5086987 AAAAAATAAA
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
7 6 0.17
8 29 0.83
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (8 bp):
TTTATATA
Found at i:5086984 original size:15 final size:16
Alignment explanation
Indices: 5086946--5086988 Score: 61
Period size: 15 Copynumber: 2.8 Consensus size: 16
5086936 TTTATTTATA
*
5086946 TATATATTTATATAAT
1 TATATATTTAAATAAT
5086962 TATATATTTAAAT-AT
1 TATATATTTAAATAAT
*
5086977 TTTATATTTAAA
1 TATATATTTAAA
5086989 AAAATAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 13 0.52
16 12 0.48
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TATATATTTAAATAAT
Found at i:5088599 original size:19 final size:19
Alignment explanation
Indices: 5088577--5088613 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
5088567 ATATAAATTT
*
5088577 TAATTTTTTATAAATAAAA
1 TAATTATTTATAAATAAAA
*
5088596 TAATTATTTATATATAAA
1 TAATTATTTATAAATAAA
5088614 TTTATTTAAA
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TAATTATTTATAAATAAAA
Found at i:5089245 original size:18 final size:19
Alignment explanation
Indices: 5089201--5089248 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 19
5089191 ATTTTTAATT
*
5089201 ACTATTTAAATTTGAATAA
1 ACTATTTTAATTTGAATAA
* *
5089220 AATATTTTAATTTTAA-AA
1 ACTATTTTAATTTGAATAA
5089238 ACTATTTTAAT
1 ACTATTTTAAT
5089249 ATTTTTGATT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
18 12 0.48
19 13 0.52
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (19 bp):
ACTATTTTAATTTGAATAA
Found at i:5090523 original size:2 final size:2
Alignment explanation
Indices: 5090510--5090548 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
5090500 AACCTGCTTG
*
5090510 GA GA GA GC GA GA GA GA GA GA GA GA GA GA G- GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
5090549 AACTTCAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.46, C:0.03, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:5097403 original size:28 final size:28
Alignment explanation
Indices: 5097342--5097404 Score: 99
Period size: 28 Copynumber: 2.2 Consensus size: 28
5097332 AGTTACTATA
* *
5097342 CTTAACTACAATTCCTTTAAAGATGATC
1 CTTAATTACAATTCCTTTAAAGAGGATC
*
5097370 CTTAATTACAATTCCTTTTAAGAGGATC
1 CTTAATTACAATTCCTTTAAAGAGGATC
5097398 CTTAATT
1 CTTAATT
5097405 TGCTTGCATA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.33, C:0.19, G:0.08, T:0.40
Consensus pattern (28 bp):
CTTAATTACAATTCCTTTAAAGAGGATC
Found at i:5098472 original size:1 final size:1
Alignment explanation
Indices: 5098466--5098492 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
5098456 ATTCTTAGTG
5098466 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
5098493 CAGATCCAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:5106479 original size:18 final size:18
Alignment explanation
Indices: 5106456--5106492 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
5106446 AGAATAGAAG
5106456 GACAAGAAACAGAGCAAA
1 GACAAGAAACAGAGCAAA
5106474 GACAAGAAACAGAGCAAA
1 GACAAGAAACAGAGCAAA
5106492 G
1 G
5106493 TGAACCAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.59, C:0.16, G:0.24, T:0.00
Consensus pattern (18 bp):
GACAAGAAACAGAGCAAA
Found at i:5118188 original size:80 final size:80
Alignment explanation
Indices: 5118051--5118199 Score: 262
Period size: 80 Copynumber: 1.9 Consensus size: 80
5118041 TTCGCAGTTT
* * *
5118051 ATTTCAAGTTAGCTTGTTATAAAACATTAAAGTATATGATATTCTGATGCTGGTATACTTCTGCA
1 ATTTCAAGTTAGCTTGTTAGAAAACATTAAACTATATGATATTCTGATGCTGATATACTTCTGCA
5118116 TGTCCTTCACAGTGC
66 TGTCCTTCACAGTGC
*
5118131 ATTTCAAGTTAGCTTGTTAGAAAACATTAAACTATATGATGTTCTGATGCTGATATACTTCTGCA
1 ATTTCAAGTTAGCTTGTTAGAAAACATTAAACTATATGATATTCTGATGCTGATATACTTCTGCA
5118196 TGTC
66 TGTC
5118200 AAAGTTCAGC
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
80 65 1.00
ACGTcount: A:0.30, C:0.15, G:0.16, T:0.39
Consensus pattern (80 bp):
ATTTCAAGTTAGCTTGTTAGAAAACATTAAACTATATGATATTCTGATGCTGATATACTTCTGCA
TGTCCTTCACAGTGC
Found at i:5120587 original size:120 final size:122
Alignment explanation
Indices: 5120427--5120669 Score: 400
Period size: 120 Copynumber: 2.0 Consensus size: 122
5120417 TACTGGTAAT
* * *
5120427 GTGGTCTTCATGTTTCTTGTTATTGTTGCCTGTAGTTAAAGGATTGTGCCAATGTTTGTGGGTTT
1 GTGGTCTTCATGTTTCTTGTTATTGTTGCCTGTAGGTAAAGGACTGTGCCAATATTTGTGGGTTT
*
5120492 GT-GCGT-TTATAGTTCACATGAACGACTAACCATGGCTGTGGCTTGGCATTGGCAA
66 GTAGCGTCTTATAGTTCACATGAACAACTAACCATGGCTGTGGCTTGGCATTGGCAA
*
5120547 GTGGTCTTCATGTTTCTTGTTATTGTTGCTTGTAGGTAAAGGACTGTGCCAATATTTGTGGGTTT
1 GTGGTCTTCATGTTTCTTGTTATTGTTGCCTGTAGGTAAAGGACTGTGCCAATATTTGTGGGTTT
*
5120612 GTGAGTGTGCTTATAGTTCACATGAACAACTAACCATGGCTGTGGCTTGGCATTGGCA
66 GT-AGCGT-CTTATAGTTCACATGAACAACTAACCATGGCTGTGGCTTGGCATTGGCA
5120670 CAACTTAGTT
Statistics
Matches: 113, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
120 63 0.56
122 3 0.03
124 47 0.42
ACGTcount: A:0.19, C:0.15, G:0.28, T:0.39
Consensus pattern (122 bp):
GTGGTCTTCATGTTTCTTGTTATTGTTGCCTGTAGGTAAAGGACTGTGCCAATATTTGTGGGTTT
GTAGCGTCTTATAGTTCACATGAACAACTAACCATGGCTGTGGCTTGGCATTGGCAA
Found at i:5141286 original size:2 final size:2
Alignment explanation
Indices: 5141279--5141306 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5141269 TTCCATACTG
5141279 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5141307 TTTGTGTCCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5143700 original size:16 final size:16
Alignment explanation
Indices: 5143666--5143699 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
5143656 TCTCACAAAA
5143666 TTTATTTTTCTGATTT
1 TTTATTTTTCTGATTT
*
5143682 TTTATTTTT-TTATTT
1 TTTATTTTTCTGATTT
5143697 TTT
1 TTT
5143700 TGACGTTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.12, C:0.03, G:0.03, T:0.82
Consensus pattern (16 bp):
TTTATTTTTCTGATTT
Found at i:5146727 original size:24 final size:23
Alignment explanation
Indices: 5146676--5146738 Score: 117
Period size: 23 Copynumber: 2.7 Consensus size: 23
5146666 TTATTTTTAA
5146676 TAAAAAATTTTACTAATTTTACT
1 TAAAAAATTTTACTAATTTTACT
5146699 TAAAAAATTTTACTAATTTTACT
1 TAAAAAATTTTACTAATTTTACT
5146722 TAAAAAATTTTATCTAA
1 TAAAAAATTTTA-CTAA
5146739 ATCTTTCACA
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
23 35 0.90
24 4 0.10
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (23 bp):
TAAAAAATTTTACTAATTTTACT
Found at i:5146739 original size:14 final size:14
Alignment explanation
Indices: 5146690--5146733 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 14
5146680 AAATTTTACT
5146690 AATTTTACTTAAAA
1 AATTTTACTTAAAA
5146704 AATTTTAC-T----
1 AATTTTACTTAAAA
5146713 AATTTTACTTAAAA
1 AATTTTACTTAAAA
5146727 AATTTTA
1 AATTTTA
5146734 TCTAAATCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 10
0.71 0.00 0.29
Matches are distributed among these distances:
9 8 0.32
10 1 0.04
13 1 0.04
14 15 0.60
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (14 bp):
AATTTTACTTAAAA
Found at i:5160274 original size:2 final size:2
Alignment explanation
Indices: 5160267--5160293 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5160257 AGTTTATCAA
5160267 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
5160294 AAAGCAAGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5164110 original size:21 final size:21
Alignment explanation
Indices: 5164086--5164129 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
5164076 TATAGTCAAC
5164086 TTGTGATGGAGGGAAGATATA
1 TTGTGATGGAGGGAAGATATA
5164107 TTGTGATGGAGGGAAGATATA
1 TTGTGATGGAGGGAAGATATA
5164128 TT
1 TT
5164130 CCTGAGTTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.32, C:0.00, G:0.36, T:0.32
Consensus pattern (21 bp):
TTGTGATGGAGGGAAGATATA
Found at i:5177867 original size:66 final size:66
Alignment explanation
Indices: 5177785--5178049 Score: 530
Period size: 66 Copynumber: 4.0 Consensus size: 66
5177775 TAACAACAAG
5177785 TTGAACTAACCAAAGATAATATTTGGAATGTTTTGTCTAAAGAAATTATTACAACTGCTATAGCT
1 TTGAACTAACCAAAGATAATATTTGGAATGTTTTGTCTAAAGAAATTATTACAACTGCTATAGCT
5177850 A
66 A
5177851 TTGAACTAACCAAAGATAATATTTGGAATGTTTTGTCTAAAGAAATTATTACAACTGCTATAGCT
1 TTGAACTAACCAAAGATAATATTTGGAATGTTTTGTCTAAAGAAATTATTACAACTGCTATAGCT
5177916 A
66 A
5177917 TTGAACTAACCAAAGATAATATTTGGAATGTTTTGTCTAAAGAAATTATTACAACTGCTATAGCT
1 TTGAACTAACCAAAGATAATATTTGGAATGTTTTGTCTAAAGAAATTATTACAACTGCTATAGCT
5177982 A
66 A
5177983 TTGAACTAACCAAAGATAATATTTGGAATGTTTTGTCTAAAGAAATTATTACAACTGCTATAGCT
1 TTGAACTAACCAAAGATAATATTTGGAATGTTTTGTCTAAAGAAATTATTACAACTGCTATAGCT
5178048 A
66 A
5178049 T
1 T
5178050 ACTAACTTCA
Statistics
Matches: 199, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 199 1.00
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35
Consensus pattern (66 bp):
TTGAACTAACCAAAGATAATATTTGGAATGTTTTGTCTAAAGAAATTATTACAACTGCTATAGCT
A
Found at i:5185829 original size:3 final size:3
Alignment explanation
Indices: 5185821--5185850 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
5185811 ACCGTTGCCA
5185821 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
5185851 CTTTCCTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:5187933 original size:15 final size:16
Alignment explanation
Indices: 5187913--5187942 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
5187903 TAATTGTGTA
5187913 ATTTTTA-AATAAAAT
1 ATTTTTATAATAAAAT
5187928 ATTTTTATAATAAAA
1 ATTTTTATAATAAAA
5187943 ATTAAAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
ATTTTTATAATAAAAT
Found at i:5189727 original size:27 final size:27
Alignment explanation
Indices: 5189682--5189733 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
5189672 CACTCTCAAT
* *
5189682 AAATTTTTTGTATTTTTTTTCTTTTTC
1 AAATTTTTGGTATTTTTTTTATTTTTC
5189709 AAATTTTTGGT-TTTATTTTTATTTT
1 AAATTTTTGGTATTT-TTTTTATTTT
5189734 ATTAAAACAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 3 0.14
27 19 0.86
ACGTcount: A:0.17, C:0.04, G:0.06, T:0.73
Consensus pattern (27 bp):
AAATTTTTGGTATTTTTTTTATTTTTC
Found at i:5190558 original size:25 final size:25
Alignment explanation
Indices: 5190528--5190605 Score: 75
Period size: 25 Copynumber: 3.0 Consensus size: 25
5190518 AAATCAATCG
*
5190528 AATTAATTTTTTTATTAAATTTTAA
1 AATTAATTTTTTAATTAAATTTTAA
** *
5190553 AATTAAAATTTTAATTAAATTAATAA
1 AATTAATTTTTTAATTAAATT-TTAA
* * *
5190579 AAATAATTTAATTAATTTAATTTTAA
1 AATTAATTT-TTTAATTAAATTTTAA
5190605 A
1 A
5190606 TAATTCAATT
Statistics
Matches: 41, Mismatches: 10, Indels: 3
0.76 0.19 0.06
Matches are distributed among these distances:
25 18 0.44
26 13 0.32
27 10 0.24
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (25 bp):
AATTAATTTTTTAATTAAATTTTAA
Found at i:5196067 original size:27 final size:25
Alignment explanation
Indices: 5196016--5196078 Score: 81
Period size: 27 Copynumber: 2.4 Consensus size: 25
5196006 GTTTTTTAAA
* *
5196016 AAATAACAAAAATTATTATAGTTAT
1 AAATAAAAAAAATTATTATAATTAT
5196041 AAATAAAAAATAATTTATTATAATTAT
1 AAATAAAAAA-AA-TTATTATAATTAT
*
5196068 AATTAAAAAAA
1 AAATAAAAAAA
5196079 TAAAAATAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
25 9 0.27
26 3 0.09
27 21 0.64
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (25 bp):
AAATAAAAAAAATTATTATAATTAT
Found at i:5204654 original size:3 final size:3
Alignment explanation
Indices: 5204646--5204676 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
5204636 AAAGTTTTCC
5204646 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
5204677 TTTCTATAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:5214215 original size:17 final size:17
Alignment explanation
Indices: 5214191--5214225 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
5214181 TGATATTATT
5214191 TAATTTATTTTAT-TTA
1 TAATTTATTTTATCTTA
5214207 TAATATTATTTTATCTTA
1 TAAT-TTATTTTATCTTA
5214225 T
1 T
5214226 CTTTTCATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.24
17 9 0.53
18 4 0.24
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (17 bp):
TAATTTATTTTATCTTA
Found at i:5214235 original size:26 final size:26
Alignment explanation
Indices: 5214183--5214236 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
5214173 AAATAGAATG
* *
5214183 ATATTATTTAATTTATTTTATTTATA
1 ATATTATTTAATTTATCTTATTCATA
*
5214209 ATATTATTTTATCTTATCTT-TTCATA
1 ATATTATTTAAT-TTATCTTATTCATA
5214235 AT
1 AT
5214237 TTTGTATAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 18 0.75
27 6 0.25
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (26 bp):
ATATTATTTAATTTATCTTATTCATA
Found at i:5214642 original size:22 final size:21
Alignment explanation
Indices: 5214612--5214653 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
5214602 ATTTATACCA
*
5214612 ATTTATAACTCTTTAATTTTAC
1 ATTTATAAC-CATTAATTTTAC
*
5214634 ATTTTTAACCATTAATTTTA
1 ATTTATAACCATTAATTTTA
5214654 ATAGATTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.33, C:0.12, G:0.00, T:0.55
Consensus pattern (21 bp):
ATTTATAACCATTAATTTTAC
Found at i:5215282 original size:22 final size:22
Alignment explanation
Indices: 5215243--5215311 Score: 72
Period size: 22 Copynumber: 3.2 Consensus size: 22
5215233 TATCTTATAT
* *
5215243 TAAAA-AAAATGATGAATTAAA
1 TAAAACAAAATAATTAATTAAA
5215264 TAAAACAAAATAATTAATTAAA
1 TAAAACAAAATAATTAATTAAA
*
5215286 GAACCAAC-AAATAATT-ATTAAA
1 TAA--AACAAAATAATTAATTAAA
5215308 TAAA
1 TAAA
5215312 TCTAATATAA
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
20 1 0.02
21 5 0.12
22 24 0.59
23 8 0.20
24 3 0.07
ACGTcount: A:0.65, C:0.06, G:0.04, T:0.25
Consensus pattern (22 bp):
TAAAACAAAATAATTAATTAAA
Found at i:5215424 original size:45 final size:45
Alignment explanation
Indices: 5215353--5215439 Score: 156
Period size: 45 Copynumber: 1.9 Consensus size: 45
5215343 ATATAATAAA
* *
5215353 ACTTAGAATTTTCATATGCAATCATAAATTAATTTGCATACGGAC
1 ACTTAGAATTTTCATATACAAGCATAAATTAATTTGCATACGGAC
5215398 ACTTAGAATTTTCATATACAAGCATAAATTAATTTGCATACG
1 ACTTAGAATTTTCATATACAAGCATAAATTAATTTGCATACG
5215440 TCCACATATG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.39, C:0.15, G:0.10, T:0.36
Consensus pattern (45 bp):
ACTTAGAATTTTCATATACAAGCATAAATTAATTTGCATACGGAC
Found at i:5239042 original size:22 final size:22
Alignment explanation
Indices: 5239014--5239064 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
5239004 AGGGAAGACA
5239014 GTTGACCAACAGATTTAGATTC
1 GTTGACCAACAGATTTAGATTC
*
5239036 GTTGACCAACATATTTAGATTC
1 GTTGACCAACAGATTTAGATTC
*
5239058 ATTGACC
1 GTTGACC
5239065 CGAACTTCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (22 bp):
GTTGACCAACAGATTTAGATTC
Found at i:5240598 original size:3 final size:3
Alignment explanation
Indices: 5240577--5240689 Score: 51
Period size: 3 Copynumber: 36.3 Consensus size: 3
5240567 TCTTCTTTTG
5240577 TAT T-T TAT GTAT T-T TAT TAT TAT TAT TAT TAT GTAT ATATT TATT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT -TAT -TA-T TA-T
* * *
5240622 TAT T-T T-T TTT TAT TA- GAT TA- GAT T-T ATAT GTAT ATAGT TAT ATATT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT -TAT -TA-T TAT -TA-T
5240668 TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT T
5240690 TTTAATTATC
Statistics
Matches: 89, Mismatches: 8, Indels: 26
0.72 0.07 0.21
Matches are distributed among these distances:
2 11 0.12
3 49 0.55
4 26 0.29
5 3 0.03
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:5240796 original size:11 final size:12
Alignment explanation
Indices: 5240776--5240808 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
5240766 TTATCTAGAT
*
5240776 TTTTTTTTTTAA
1 TTTTTATTTTAA
5240788 -TTTTATTTTAA
1 TTTTTATTTTAA
5240799 TTTTTATTTT
1 TTTTTATTTT
5240809 GGAGGGCTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (12 bp):
TTTTTATTTTAA
Found at i:5241195 original size:31 final size:31
Alignment explanation
Indices: 5241123--5241195 Score: 94
Period size: 31 Copynumber: 2.4 Consensus size: 31
5241113 AATTTCCAGA
* *
5241123 TTCCGGCGAAAATTCCGGCGACTTTTGAATT
1 TTCCGGCGACAATTCCGGCGACTTTTGAAGT
* *
5241154 TTCCGACGACAATTCCGGTGAAC-TTTGAAGT
1 TTCCGGCGACAATTCCGGCG-ACTTTTGAAGT
5241185 TTCCGGCGACA
1 TTCCGGCGACA
5241196 GACCCAGTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
31 34 0.94
32 2 0.06
ACGTcount: A:0.23, C:0.25, G:0.23, T:0.29
Consensus pattern (31 bp):
TTCCGGCGACAATTCCGGCGACTTTTGAAGT
Found at i:5241281 original size:19 final size:19
Alignment explanation
Indices: 5241257--5241301 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
5241247 TCCGGCCAAT
5241257 TTCCGGCGAAATTCCCAGA
1 TTCCGGCGAAATTCCCAGA
*
5241276 TTCCGGCGAAATTTCCAGA
1 TTCCGGCGAAATTCCCAGA
*
5241295 ATCCGGC
1 TTCCGGC
5241302 ACCGGCGTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.24, C:0.31, G:0.22, T:0.22
Consensus pattern (19 bp):
TTCCGGCGAAATTCCCAGA
Found at i:5242053 original size:156 final size:155
Alignment explanation
Indices: 5241604--5242053 Score: 732
Period size: 156 Copynumber: 2.9 Consensus size: 155
5241594 TTTTTCTTTA
* *
5241604 TTCTTTAATTAATCCGACGACGGAGCCTCTACAAGTAAAAACAGTAGTTTTTCTTGCATACTCCT
1 TTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGT-GAAACAGTAGTTTTTCTTGCATACTCCT
*
5241669 GAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATTTCCGAT
65 GAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATTTTCGAT
* *
5241734 AATTAATTACTTGGCTGATTTTGATT
130 AATTAATTACTTGGTTGATCTTGATT
*
5241760 TT-TTT--TT--T-CGACGACGGAGCCTTTGCAAGTGAAACAGTAGTTTTTCTTGCATACTCCTG
1 TTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTTTTCTTGCATACTCCTG
5241819 AGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATTTTCGATA
66 AGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATTTTCGATA
*
5241884 ATTAATTAATTGGTTGATCTTGATTT
131 ATTAATTACTTGGTTGATCTTGA-TT
*
5241910 TTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTTTTCTTGCATACTCTTG
1 TTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTTTTCTTGCATACTCCTG
* *
5241975 AGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATTTTCAACA
66 AGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATTTTCGATA
* *
5242040 ACTAACTACTTGGT
131 ATTAATTACTTGGT
5242054 AAAATTTTAA
Statistics
Matches: 273, Mismatches: 14, Indels: 14
0.91 0.05 0.05
Matches are distributed among these distances:
149 112 0.41
150 24 0.09
151 4 0.01
153 4 0.01
155 4 0.01
156 125 0.46
ACGTcount: A:0.29, C:0.15, G:0.18, T:0.38
Consensus pattern (155 bp):
TTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTTTTCTTGCATACTCCTG
AGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAATAATTTTCGATA
ATTAATTACTTGGTTGATCTTGATT
Found at i:5250225 original size:8 final size:8
Alignment explanation
Indices: 5250212--5250300 Score: 56
Period size: 8 Copynumber: 10.6 Consensus size: 8
5250202 CTATGCTTGA
5250212 AAAAAAAT
1 AAAAAAAT
5250220 AAAAAAAT
1 AAAAAAAT
5250228 --AAAAAT
1 AAAAAAAT
5250234 GAGAAAAAAT
1 -A-AAAAAAT
5250244 GAAAAAAAT
1 -AAAAAAAT
*
5250253 GAAAAAAT
1 AAAAAAAT
*
5250261 GAAAAATGAT
1 -AAAAA-AAT
*
5250271 GAAAAAAT
1 AAAAAAAT
*
5250279 GAAAAAAT
1 AAAAAAAT
* *
5250287 GGAAAAAAG
1 -AAAAAAAT
5250296 AAAAA
1 AAAAA
5250301 GTGAATGAAA
Statistics
Matches: 67, Mismatches: 7, Indels: 14
0.76 0.08 0.16
Matches are distributed among these distances:
6 6 0.09
8 29 0.43
9 22 0.33
10 10 0.15
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.11
Consensus pattern (8 bp):
AAAAAAAT
Found at i:5250291 original size:17 final size:18
Alignment explanation
Indices: 5250213--5250300 Score: 95
Period size: 16 Copynumber: 5.3 Consensus size: 18
5250203 TATGCTTGAA
5250213 AAAAAAT-A-AAAAAAT-
1 AAAAAATGAGAAAAAATG
5250228 -AAAAATGAGAAAAAATG
1 AAAAAATGAGAAAAAATG
5250245 AAAAAA--ATGAAAAAATG
1 AAAAAATGA-GAAAAAATG
5250262 -AAAAATGATGAAAAAATG
1 AAAAAATGA-GAAAAAATG
5250280 AAAAAATG-GAAAAAA-G
1 AAAAAATGAGAAAAAATG
5250296 AAAAA
1 AAAAA
5250301 GTGAATGAAA
Statistics
Matches: 65, Mismatches: 0, Indels: 15
0.81 0.00 0.19
Matches are distributed among these distances:
14 6 0.09
15 1 0.02
16 19 0.29
17 16 0.25
18 16 0.25
19 7 0.11
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.11
Consensus pattern (18 bp):
AAAAAATGAGAAAAAATG
Found at i:5250293 original size:18 final size:16
Alignment explanation
Indices: 5250214--5250305 Score: 84
Period size: 17 Copynumber: 5.6 Consensus size: 16
5250204 ATGCTTGAAA
5250214 AAAAAT-AAAAAAAT-
1 AAAAATGAAAAAAATG
5250228 AAAAATGAGAAAAAATG
1 AAAAATGA-AAAAAATG
5250245 AAAAAAATG-AAAAAATG
1 --AAAAATGAAAAAAATG
5250262 AAAAATGATGAAAAAATG
1 AAAAATGA--AAAAAATG
*
5250280 AAAAAATGGAAAAAA-G
1 -AAAAATGAAAAAAATG
5250296 AAAAAGTGAA
1 AAAAA-TGAA
5250306 TGAAAAAGGA
Statistics
Matches: 66, Mismatches: 2, Indels: 18
0.77 0.02 0.21
Matches are distributed among these distances:
14 6 0.09
15 13 0.20
16 11 0.17
17 14 0.21
18 8 0.12
19 14 0.21
ACGTcount: A:0.74, C:0.00, G:0.14, T:0.12
Consensus pattern (16 bp):
AAAAATGAAAAAAATG
Found at i:5250294 original size:9 final size:9
Alignment explanation
Indices: 5250228--5250294 Score: 70
Period size: 8 Copynumber: 7.6 Consensus size: 9
5250218 ATAAAAAAAT
5250228 AAAAATGAGA
1 AAAAATG-GA
*
5250238 AAAAATGAA
1 AAAAATGGA
5250247 AAAAAT-GA
1 AAAAATGGA
5250255 AAAAAT-G-
1 AAAAATGGA
5250262 AAAAATGATGA
1 AAAAATG--GA
5250273 AAAAAT-GA
1 AAAAATGGA
5250281 AAAAATGGA
1 AAAAATGGA
5250290 AAAAA
1 AAAAA
5250295 GAAAAAGTGA
Statistics
Matches: 50, Mismatches: 2, Indels: 11
0.79 0.03 0.17
Matches are distributed among these distances:
7 6 0.12
8 16 0.32
9 14 0.28
10 8 0.16
11 6 0.12
ACGTcount: A:0.73, C:0.00, G:0.15, T:0.12
Consensus pattern (9 bp):
AAAAATGGA
Found at i:5250312 original size:35 final size:35
Alignment explanation
Indices: 5250212--5250312 Score: 138
Period size: 34 Copynumber: 2.9 Consensus size: 35
5250202 CTATGCTTGA
*
5250212 AAAAAAATAAAAAAAT-AAAAATGA-GAAAAAATG
1 AAAAAAATGAAAAAATGAAAAATGATGAAAAAATG
5250245 AAAAAAATGAAAAAATGAAAAATGATGAAAAAATG
1 AAAAAAATGAAAAAATGAAAAATGATGAAAAAATG
5250280 -AAAAAATGGAAAAAA-GAAAAAGTGAATGAAAAA
1 AAAAAAAT-GAAAAAATGAAAAA-TG-ATGAAAAA
5250313 GGAGGACTCA
Statistics
Matches: 62, Mismatches: 1, Indels: 7
0.89 0.01 0.10
Matches are distributed among these distances:
33 15 0.24
34 21 0.34
35 18 0.29
36 8 0.13
ACGTcount: A:0.74, C:0.00, G:0.14, T:0.12
Consensus pattern (35 bp):
AAAAAAATGAAAAAATGAAAAATGATGAAAAAATG
Found at i:5251483 original size:42 final size:41
Alignment explanation
Indices: 5251323--5251731 Score: 582
Period size: 41 Copynumber: 10.0 Consensus size: 41
5251313 GTCTAGGAGT
* * *
5251323 ATTTACTTTCCAAAGTTCGT--TGCCTCTGTTGAGAGGAGCA
1 ATTTACTTTTCAAAG-TCGTGGTACCTCTGTTTAGAGGAGCA
*
5251363 ATTTACTTTTCAAAGTCGTGGTACCTCTGTTGAGAGGAGCA
1 ATTTACTTTTCAAAGTCGTGGTACCTCTGTTTAGAGGAGCA
* *
5251404 ATTTATTTTTCAAAGTTCGT--TGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCAAAG-TCGTGGTACCTCTGTTTAGAGGAGCA
* *
5251444 ATTTATTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTT-CAAAGTCGTGGTACCTCTGTTTAGAGGAGCA
* *
5251486 ATTTATTTTTCCAAAGTCGTGGTACCTCTGTTGAGAGGAGCA
1 ATTTACTTTT-CAAAGTCGTGGTACCTCTGTTTAGAGGAGCA
5251528 ATTTACTTTTCAAAGTCGTGGTACCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCAAAGTCGTGGTACCTCTGTTTAGAGGAGCA
* *
5251569 ATTTATTTTTCCAAAGTCGTGGTACCTCTGTTGAGAGGAGCA
1 ATTTACTTTT-CAAAGTCGTGGTACCTCTGTTTAGAGGAGCA
5251611 ATTTACTTTTCAAAGTCGTGGTACCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCAAAGTCGTGGTACCTCTGTTTAGAGGAGCA
5251652 ATTTA-TTTTCCAAAGTCGTGGT-CCTCTGTTTAGAGGAGCA
1 ATTTACTTTT-CAAAGTCGTGGTACCTCTGTTTAGAGGAGCA
5251692 ATTTACTTTTCAAAGTCGTTGAGT--CTCTGTTTAGAGGAGC
1 ATTTACTTTTCAAAGTCG-TG-GTACCTCTGTTTAGAGGAGC
5251732 TTCGGCAAAA
Statistics
Matches: 345, Mismatches: 13, Indels: 21
0.91 0.03 0.06
Matches are distributed among these distances:
39 4 0.01
40 81 0.23
41 146 0.42
42 114 0.33
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.37
Consensus pattern (41 bp):
ATTTACTTTTCAAAGTCGTGGTACCTCTGTTTAGAGGAGCA
Found at i:5251559 original size:83 final size:83
Alignment explanation
Indices: 5251329--5251731 Score: 635
Period size: 83 Copynumber: 4.9 Consensus size: 83
5251319 GAGTATTTAC
*
5251329 TTTCCAAAGTTCGT--TGCCTCTGTTGAGAGGAGCAATTTACTTTTCAAAGTCGTGGTACCTCTG
1 TTTCCAAAG-TCGTGGTACCTCTGTTGAGAGGAGCAATTTACTTTTCAAAGTCGTGGTACCTCTG
*
5251392 TTGAGAGGAGCAATTTATT
65 TTTAGAGGAGCAATTTATT
* * * *
5251411 TTT-CAAAGTTCGT--TGCCTCTGTTTAGAGGAGCAATTTATTTTTCCAAAGTCGTGGTGCCTCT
1 TTTCCAAAG-TCGTGGTACCTCTGTTGAGAGGAGCAATTTACTTTT-CAAAGTCGTGGTACCTCT
5251473 GTTTAGAGGAGCAATTTATT
64 GTTTAGAGGAGCAATTTATT
5251493 TTTCCAAAGTCGTGGTACCTCTGTTGAGAGGAGCAATTTACTTTTCAAAGTCGTGGTACCTCTGT
1 TTTCCAAAGTCGTGGTACCTCTGTTGAGAGGAGCAATTTACTTTTCAAAGTCGTGGTACCTCTGT
5251558 TTAGAGGAGCAATTTATT
66 TTAGAGGAGCAATTTATT
5251576 TTTCCAAAGTCGTGGTACCTCTGTTGAGAGGAGCAATTTACTTTTCAAAGTCGTGGTACCTCTGT
1 TTTCCAAAGTCGTGGTACCTCTGTTGAGAGGAGCAATTTACTTTTCAAAGTCGTGGTACCTCTGT
5251641 TTAGAGGAGCAATTTA-T
66 TTAGAGGAGCAATTTATT
*
5251658 TTTCCAAAGTCGTGGT-CCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGTTGAGT--CTCT
1 TTTCCAAAGTCGTGGTACCTCTGTTGAGAGGAGCAATTTACTTTTCAAAGTCG-TG-GTACCTCT
5251720 GTTTAGAGGAGC
64 GTTTAGAGGAGC
5251732 TTCGGCAAAA
Statistics
Matches: 306, Mismatches: 9, Indels: 13
0.93 0.03 0.04
Matches are distributed among these distances:
81 89 0.29
82 65 0.21
83 125 0.41
84 27 0.09
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.37
Consensus pattern (83 bp):
TTTCCAAAGTCGTGGTACCTCTGTTGAGAGGAGCAATTTACTTTTCAAAGTCGTGGTACCTCTGT
TTAGAGGAGCAATTTATT
Found at i:5251744 original size:1 final size:1
Alignment explanation
Indices: 5251738--5251866 Score: 114
Period size: 1 Copynumber: 129.0 Consensus size: 1
5251728 GAGCTTCGGC
* * * * * *
5251738 AAAAAAACAAAAAAAACAAAAAAAAAAACAAAAAAAACAAAAAAAAAAAAAAATAAAAACAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * *** * ** *
5251803 AAAACAAAAAAACAAAAAAAACAAAAATTTAAAAAAAAAAAACAAAAAAATCAAAAAATAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
5251867 TGTTGAGTTG
Statistics
Matches: 101, Mismatches: 27, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 101 1.00
ACGTcount: A:0.88, C:0.08, G:0.00, T:0.05
Consensus pattern (1 bp):
A
Found at i:5251752 original size:9 final size:9
Alignment explanation
Indices: 5251738--5251860 Score: 130
Period size: 9 Copynumber: 13.6 Consensus size: 9
5251728 GAGCTTCGGC
5251738 AAAAAAACA
1 AAAAAAACA
5251747 AAAAAAACA
1 AAAAAAACA
5251756 AAAAAAA-A
1 AAAAAAACA
5251764 AACAAAAA-A
1 AA-AAAAACA
5251773 AACAAAAA-A
1 AA-AAAAACA
5251782 AAAAAAA-A
1 AAAAAAACA
*
5251790 ATAAAAACA
1 AAAAAAACA
5251799 AAAAAAA-A
1 AAAAAAACA
5251807 CAAAAAAACA
1 -AAAAAAACA
5251817 AAAAAAACA
1 AAAAAAACA
*
5251826 AAAATTTAAAAA
1 AAAA---AAACA
5251838 AAAAAAACA
1 AAAAAAACA
*
5251847 AAAAAATCA
1 AAAAAAACA
5251856 AAAAA
1 AAAAA
5251861 TAAAAATGTT
Statistics
Matches: 102, Mismatches: 5, Indels: 14
0.84 0.04 0.12
Matches are distributed among these distances:
8 16 0.16
9 77 0.75
10 1 0.01
12 8 0.08
ACGTcount: A:0.88, C:0.08, G:0.00, T:0.04
Consensus pattern (9 bp):
AAAAAAACA
Found at i:5252072 original size:3 final size:3
Alignment explanation
Indices: 5252051--5252161 Score: 54
Period size: 3 Copynumber: 35.3 Consensus size: 3
5252041 TCTTCTTTTG
5252051 TAT T-T TAT GTAT T-T TAT TAT TAT TAT TAT TAT GTAT ATATT TATT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT -TAT -TA-T TA-T
* * *
5252096 TAT T-T TTT TAT TA- GAT TA- GAT T-T ATAT GTAT ATAGT TAT ATATT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT -TAT -TA-T TAT -TA-T
5252140 TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT T
5252162 TTTAATTATC
Statistics
Matches: 87, Mismatches: 8, Indels: 26
0.72 0.07 0.21
Matches are distributed among these distances:
2 9 0.10
3 49 0.56
4 26 0.30
5 3 0.03
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:5252632 original size:31 final size:32
Alignment explanation
Indices: 5252597--5252658 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 32
5252587 TCCAGATTCC
5252597 GGCGAAAATTCCGGCG-ACTTTTGAA-TTTTCT
1 GGCGAAAATTCCGGCGAAC-TTTGAAGTTTTCT
* *
5252628 GGCGACAATTCCGGTGAACTTTGAAGTTTTC
1 GGCGAAAATTCCGGCGAACTTTGAAGTTTTC
5252659 GACGACAGAC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
31 20 0.74
32 7 0.26
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.34
Consensus pattern (32 bp):
GGCGAAAATTCCGGCGAACTTTGAAGTTTTCT
Found at i:5252665 original size:31 final size:31
Alignment explanation
Indices: 5252603--5252665 Score: 76
Period size: 31 Copynumber: 2.0 Consensus size: 31
5252593 TTCCGGCGAA
*
5252603 AATTCCGGCGACTTTTGAATTTTCTGGCGAC
1 AATTCCGGCGACTTTTGAATTTTCTGACGAC
*
5252634 AATTCCGGTGAAC-TTTGAAGTTTTC-GACGAC
1 AATTCCGGCG-ACTTTTGAA-TTTTCTGACGAC
5252665 A
1 A
5252666 GACCCAGTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
31 21 0.75
32 7 0.25
ACGTcount: A:0.24, C:0.21, G:0.22, T:0.33
Consensus pattern (31 bp):
AATTCCGGCGACTTTTGAATTTTCTGACGAC
Found at i:5252755 original size:19 final size:19
Alignment explanation
Indices: 5252727--5252769 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
5252717 TCCGGCCAAT
*
5252727 TTCCGGCGAAATTCCCAGA
1 TTCCGACGAAATTCCCAGA
*
5252746 TTCCGACGAAATTTCCAGA
1 TTCCGACGAAATTCCCAGA
*
5252765 ATCCG
1 TTCCG
5252770 GCACCGGCGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.28, C:0.30, G:0.19, T:0.23
Consensus pattern (19 bp):
TTCCGACGAAATTCCCAGA
Done.