Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold74
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: 4633657
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 25 characters in sequence are not A, C, G, or T
File 9 of 24
Found at i:1797956 original size:3 final size:3
Alignment explanation
Indices: 1797948--1797973 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1797938 GACCCAAATG
1797948 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
1797974 AAGATGCCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1799334 original size:35 final size:33
Alignment explanation
Indices: 1799281--1799352 Score: 81
Period size: 34 Copynumber: 2.1 Consensus size: 33
1799271 GGCATGAATT
* *
1799281 AAAAAATAATTAAAATTTAATATAAAATATAATA
1 AAAAAATAATGAAAATTTAAAAT-AAATATAATA
* **
1799315 AAAAAATATATGAATATTTAAAATTTATATAATA
1 AAAAAATA-ATGAAAATTTAAAATAAATATAATA
1799349 AAAA
1 AAAA
1799353 TTATTAACAC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
34 20 0.62
35 12 0.38
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.33
Consensus pattern (33 bp):
AAAAAATAATGAAAATTTAAAATAAATATAATA
Found at i:1801092 original size:17 final size:15
Alignment explanation
Indices: 1801059--1801101 Score: 50
Period size: 17 Copynumber: 2.7 Consensus size: 15
1801049 TCTTTGCAAG
1801059 TTTAAATATTATAAA
1 TTTAAATATTATAAA
*
1801074 TTTAAATAATTTATGAA
1 TTTAAAT-A-TTATAAA
*
1801091 TTTAGATATTA
1 TTTAAATATTA
1801102 AATTTACTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
15 10 0.42
16 2 0.08
17 12 0.50
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.49
Consensus pattern (15 bp):
TTTAAATATTATAAA
Found at i:1801609 original size:13 final size:11
Alignment explanation
Indices: 1801587--1801625 Score: 60
Period size: 11 Copynumber: 3.4 Consensus size: 11
1801577 TTTTTATCAA
1801587 ATTTAAATTTT
1 ATTTAAATTTT
1801598 ATTTAAAAATTTT
1 ATTT--AAATTTT
1801611 ATTTAAATTTT
1 ATTTAAATTTT
1801622 ATTT
1 ATTT
1801626 TGAATTGATT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
11 15 0.58
13 11 0.42
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
ATTTAAATTTT
Found at i:1802055 original size:17 final size:18
Alignment explanation
Indices: 1802035--1802072 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
1802025 TATAAAAAAT
1802035 TATAAAAT-ATATATTAA
1 TATAAAATAATATATTAA
*
1802052 TATAAAATAATTTATTAA
1 TATAAAATAATATATTAA
1802070 TAT
1 TAT
1802073 TTTAATATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
TATAAAATAATATATTAA
Found at i:1802569 original size:2 final size:2
Alignment explanation
Indices: 1802562--1802588 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1802552 TAACAATAAC
1802562 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
1802589 TAAAATCCAA
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:1802966 original size:3 final size:3
Alignment explanation
Indices: 1802958--1802992 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
1802948 TACATAATTT
1802958 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1802993 TAATTTATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1809506 original size:24 final size:25
Alignment explanation
Indices: 1809475--1809540 Score: 82
Period size: 24 Copynumber: 2.7 Consensus size: 25
1809465 TTATAAATAA
1809475 TATATTATATTAAATA-ATTTTAAG
1 TATATTATATTAAATATATTTTAAG
* **
1809499 TATATTATA-TAAAAATATTTTATT
1 TATATTATATTAAATATATTTTAAG
*
1809523 TATATTATATAAAATATA
1 TATATTATATTAAATATA
1809541 ATTAAAAATA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
23 5 0.14
24 24 0.69
25 6 0.17
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (25 bp):
TATATTATATTAAATATATTTTAAG
Found at i:1811171 original size:7 final size:7
Alignment explanation
Indices: 1811159--1811183 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1811149 TTAAAAAGAA
1811159 TAAATTT
1 TAAATTT
1811166 TAAATTT
1 TAAATTT
1811173 TAAATTT
1 TAAATTT
1811180 TAAA
1 TAAA
1811184 ATCCAAATAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (7 bp):
TAAATTT
Found at i:1811656 original size:15 final size:16
Alignment explanation
Indices: 1811636--1811669 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
1811626 ATTTAAAAAA
1811636 ATTAAAC-ATACTTAT
1 ATTAAACGATACTTAT
1811651 ATTAAACGTATACTTAT
1 ATTAAACG-ATACTTAT
1811668 AT
1 AT
1811670 CCAGTCCAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
17 10 0.59
ACGTcount: A:0.44, C:0.12, G:0.03, T:0.41
Consensus pattern (16 bp):
ATTAAACGATACTTAT
Found at i:1812087 original size:45 final size:46
Alignment explanation
Indices: 1812026--1812113 Score: 133
Period size: 45 Copynumber: 1.9 Consensus size: 46
1812016 TACAAAAAAA
1812026 TTAATATTAAAAGAAAACCATAAAATTAAATATATTTA-AAAATAT
1 TTAATATTAAAAGAAAACCATAAAATTAAATATATTTAGAAAATAT
* ** *
1812071 TTAATATTAAATGAAAATTATAAAATTAAATGTATTTAGAAAA
1 TTAATATTAAAAGAAAACCATAAAATTAAATATATTTAGAAAA
1812114 AAATAAATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
45 34 0.89
46 4 0.11
ACGTcount: A:0.58, C:0.02, G:0.05, T:0.35
Consensus pattern (46 bp):
TTAATATTAAAAGAAAACCATAAAATTAAATATATTTAGAAAATAT
Found at i:1814812 original size:7 final size:7
Alignment explanation
Indices: 1814796--1814831 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
1814786 ATCTAATTGA
*
1814796 TTTAGTG
1 TTTAGGG
1814803 TTTAGGG
1 TTTAGGG
*
1814810 TTTAGAG
1 TTTAGGG
1814817 TTTAGGG
1 TTTAGGG
1814824 TTTAGGG
1 TTTAGGG
1814831 T
1 T
1814832 AATGGCTATG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.17, C:0.00, G:0.36, T:0.47
Consensus pattern (7 bp):
TTTAGGG
Found at i:1815919 original size:1 final size:1
Alignment explanation
Indices: 1815913--1815938 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
1815903 GAAGAAAATG
1815913 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
1815939 GAGAGAGAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:1822556 original size:2 final size:2
Alignment explanation
Indices: 1822544--1822578 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1822534 ACGGCGATAC
*
1822544 AT AT AT CT 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 AT A
1822579 GAGCTAGAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1823585 original size:2 final size:2
Alignment explanation
Indices: 1823578--1823628 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
1823568 CGGACAGATC
1823578 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1823620 TA TA TA TA T
1 TA TA TA TA T
1823629 CGTGGTGACC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1828291 original size:20 final size:19
Alignment explanation
Indices: 1828266--1828318 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
1828256 ATTATAATAC
*
1828266 ATAATAATTTA-ATTAATT
1 ATAATAATTTATATTAAAT
1828284 CAATAATAATTTTATATTAAAT
1 --ATAATAA-TTTATATTAAAT
1828306 ATAATAATTTATA
1 ATAATAATTTATA
1828319 ATTTTATTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
19 6 0.20
20 14 0.47
21 4 0.13
22 6 0.20
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (19 bp):
ATAATAATTTATATTAAAT
Found at i:1828760 original size:18 final size:17
Alignment explanation
Indices: 1828720--1828766 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 17
1828710 TTATATTTTA
*
1828720 AATTTAATAAAAATAAT
1 AATTAAATAAAAATAAT
*
1828737 ATATTAAATATAAAATATT
1 A-ATTAAATA-AAAATAAT
1828756 AATTAAATAAA
1 AATTAAATAAA
1828767 TTTTAGATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 3 0.12
18 15 0.58
19 8 0.31
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
AATTAAATAAAAATAAT
Found at i:1829399 original size:15 final size:14
Alignment explanation
Indices: 1829379--1829409 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
1829369 TACACATATA
1829379 ATTTTTAAAAATAAT
1 ATTTTTAAAAA-AAT
1829394 ATTTTTAAAAAAAT
1 ATTTTTAAAAAAAT
1829408 AT
1 AT
1829410 ATAAAAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTTTTAAAAAAAT
Found at i:1829411 original size:16 final size:16
Alignment explanation
Indices: 1829374--1829411 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
1829364 TAATATACAC
*
1829374 ATATAATTTTTAAAAAT
1 ATAT-ATTTTTAAAAAA
1829391 A-ATATTTTTAAAAAA
1 ATATATTTTTAAAAAA
1829406 ATATAT
1 ATATAT
1829412 AAAAATAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 12 0.63
16 6 0.32
17 1 0.05
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
ATATATTTTTAAAAAA
Found at i:1829445 original size:19 final size:20
Alignment explanation
Indices: 1829396--1829446 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 20
1829386 AAAATAATAT
1829396 TTTTAAAAAAA-TATATAAA
1 TTTTAAAAAAATTATATAAA
** *
1829415 -AATAAAATAATTAT-TAAA
1 TTTTAAAAAAATTATATAAA
1829433 TTTTAAAAAAATTA
1 TTTTAAAAAAATTA
1829447 ATTCTAAATA
Statistics
Matches: 24, Mismatches: 6, Indels: 4
0.71 0.18 0.12
Matches are distributed among these distances:
18 11 0.46
19 13 0.54
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
TTTTAAAAAAATTATATAAA
Found at i:1829831 original size:12 final size:12
Alignment explanation
Indices: 1829805--1829866 Score: 56
Period size: 11 Copynumber: 5.0 Consensus size: 12
1829795 TTTAATTTAA
1829805 TTTAGATTAAA-T
1 TTTA-ATTAAATT
*
1829817 TTTAATAAAATTT
1 TTTAATTAAA-TT
1829830 TTATAATTTAAATT
1 TT-TAA-TTAAATT
1829844 TTTAATTAAATT
1 TTTAATTAAATT
*
1829856 ATT-ATTAAATT
1 TTTAATTAAATT
1829867 AATAAATATT
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
11 13 0.30
12 13 0.30
13 6 0.14
14 7 0.16
15 4 0.09
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (12 bp):
TTTAATTAAATT
Found at i:1830079 original size:20 final size:20
Alignment explanation
Indices: 1830054--1830166 Score: 66
Period size: 20 Copynumber: 6.0 Consensus size: 20
1830044 AAGTACATCT
1830054 TATAATTTTTATTATATTTA
1 TATAATTTTTATTATATTTA
*
1830074 TATAATATTTTTTTAT-TTTA
1 TATAAT-TTTTATTATATTTA
* * *
1830094 TGT-ATTATAATTATGA-TTA
1 TATAATTTTTATTAT-ATTTA
*
1830113 -A-AA-TATTA-TATATTTA
1 TATAATTTTTATTATATTTA
*
1830129 -AT-ATATTTA-TATATTTA
1 TATAATTTTTATTATATTTA
* *
1830146 TATTATTTTTATGATATTTA
1 TATAATTTTTATTATATTTA
1830166 T
1 T
1830167 TTATATTGAA
Statistics
Matches: 72, Mismatches: 11, Indels: 20
0.70 0.11 0.19
Matches are distributed among these distances:
15 1 0.01
16 8 0.11
17 15 0.21
18 9 0.12
19 11 0.15
20 20 0.28
21 8 0.11
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (20 bp):
TATAATTTTTATTATATTTA
Found at i:1830140 original size:17 final size:19
Alignment explanation
Indices: 1830118--1830173 Score: 73
Period size: 19 Copynumber: 3.1 Consensus size: 19
1830108 GATTAAAATA
1830118 TTATATATTTA-A-TATAT
1 TTATATATTTATATTATAT
*
1830135 TTATATATTTATATTATTT
1 TTATATATTTATATTATAT
1830154 TTATGATATTTAT-TTATAT
1 TTAT-ATATTTATATTATAT
1830173 T
1 T
1830174 GAATTAAACT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
17 11 0.32
18 1 0.03
19 14 0.41
20 8 0.24
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
TTATATATTTATATTATAT
Found at i:1830142 original size:8 final size:8
Alignment explanation
Indices: 1830118--1830153 Score: 54
Period size: 8 Copynumber: 4.2 Consensus size: 8
1830108 GATTAAAATA
1830118 TTATATAT
1 TTATATAT
1830126 TTAATATAT
1 TT-ATATAT
1830135 TTATATAT
1 TTATATAT
1830143 TTATATTAT
1 TTATA-TAT
1830152 TT
1 TT
1830154 TTATGATATT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
8 13 0.50
9 13 0.50
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (8 bp):
TTATATAT
Found at i:1833411 original size:16 final size:16
Alignment explanation
Indices: 1833392--1833427 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
1833382 TAAATTAAAA
1833392 ATAAT-TAAAATATAAT
1 ATAATATAAAA-ATAAT
1833408 ATAATATAAAAATAAT
1 ATAATATAAAAATAAT
1833424 ATAA
1 ATAA
1833428 ATATTATTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
ATAATATAAAAATAAT
Found at i:1833959 original size:18 final size:19
Alignment explanation
Indices: 1833931--1833966 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1833921 TTAAATATAC
*
1833931 ATAACTTTTAAATATAATT
1 ATAACTTTTAAAAATAATT
1833950 ATAA-TTTTAAAAATAAT
1 ATAACTTTTAAAAATAAT
1833967 GCAATTATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (19 bp):
ATAACTTTTAAAAATAATT
Found at i:1835195 original size:23 final size:23
Alignment explanation
Indices: 1835151--1835234 Score: 65
Period size: 23 Copynumber: 3.8 Consensus size: 23
1835141 TTTTTACACA
* *
1835151 AAAAATTTATAATCTA-AAAAATT
1 AAAAATTTA-AATTTATATAAATT
1835174 AAAAATTTAAATTTATATAAATT
1 AAAAATTTAAATTTATATAAATT
1835197 AATTAAA-TTAAA--T-TATAAATT
1 AA--AAATTTAAATTTATATAAATT
*
1835218 TAAAATTT--ATTTATATA
1 AAAAATTTAAATTTATATA
1835235 TAATACTTGT
Statistics
Matches: 51, Mismatches: 3, Indels: 16
0.73 0.04 0.23
Matches are distributed among these distances:
18 1 0.02
19 3 0.06
20 3 0.06
21 13 0.25
22 6 0.12
23 17 0.33
24 5 0.10
25 3 0.06
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (23 bp):
AAAAATTTAAATTTATATAAATT
Found at i:1836269 original size:11 final size:11
Alignment explanation
Indices: 1836243--1836289 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 11
1836233 ATTATACTAC
*
1836243 ATAAATAATAAT
1 ATAAAT-ATTAT
1836255 ATAAATATTAT
1 ATAAATATTAT
1836266 ATAAATA-TAT
1 ATAAATATTAT
*
1836276 -TAAATTTTAT
1 ATAAATATTAT
1836286 ATAA
1 ATAA
1836290 TATAAATGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
9 5 0.16
10 6 0.19
11 14 0.45
12 6 0.19
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (11 bp):
ATAAATATTAT
Found at i:1836305 original size:32 final size:32
Alignment explanation
Indices: 1836254--1836333 Score: 105
Period size: 32 Copynumber: 2.6 Consensus size: 32
1836244 TAAATAATAA
*
1836254 TATAAATAT-T-ATATAAATATATT-AAATTT
1 TATAAATATATAATATTAATATATTAAAATTT
1836283 TATATAATATA-AATGATTAATATATTAAAATTT
1 TATA-AATATATAAT-ATTAATATATTAAAATTT
1836316 TATAAATATATAATATTA
1 TATAAATATATAATATTA
1836334 TAATAAATAA
Statistics
Matches: 44, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
29 4 0.09
30 5 0.11
31 2 0.05
32 20 0.45
33 13 0.30
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (32 bp):
TATAAATATATAATATTAATATATTAAAATTT
Found at i:1836335 original size:49 final size:52
Alignment explanation
Indices: 1836248--1836344 Score: 123
Period size: 51 Copynumber: 1.9 Consensus size: 52
1836238 ACTACATAAA
*
1836248 TAATAATATAAATATTATATAAATATATTAAATTTTAT-ATAATATAAATGAT
1 TAATAATATAAATATTATATAAATATATTAAATATTATAATAA-ATAAATGAT
*
1836300 TAAT-ATATTAAA-ATTTTATAAATATA-T-AATATTATAATAAATAAA
1 TAATAATA-TAAATATTATATAAATATATTAAATATTATAATAAATAAA
1836345 AATATATATA
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
49 12 0.29
50 5 0.12
51 16 0.39
52 8 0.20
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (52 bp):
TAATAATATAAATATTATATAAATATATTAAATATTATAATAAATAAATGAT
Found at i:1836339 original size:19 final size:18
Alignment explanation
Indices: 1836248--1836342 Score: 55
Period size: 19 Copynumber: 5.5 Consensus size: 18
1836238 ACTACATAAA
1836248 TAAT-AATATA-AATA-T
1 TAATAAATATATAATATT
1836263 TATATAAATATATTAA-ATT
1 TA-ATAAATATA-TAATATT
*
1836282 TTATATAATATA-AATGA-T
1 TAATA-AATATATAAT-ATT
*
1836300 TAAT--ATAT-TAAAATT
1 TAATAAATATATAATATT
*
1836315 TTATAAATATATAATATT
1 TAATAAATATATAATATT
1836333 ATAATAAATA
1 -TAATAAATA
1836343 AAAATATATA
Statistics
Matches: 60, Mismatches: 6, Indels: 24
0.67 0.07 0.27
Matches are distributed among these distances:
14 1 0.02
15 12 0.20
16 2 0.03
17 12 0.20
18 14 0.23
19 19 0.32
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (18 bp):
TAATAAATATATAATATT
Found at i:1836347 original size:34 final size:34
Alignment explanation
Indices: 1836250--1836347 Score: 105
Period size: 36 Copynumber: 2.9 Consensus size: 34
1836240 TACATAAATA
1836250 ATAATATAAATATTAT-ATAAATATATTAAATTTTAT
1 ATAATATAAATATTATAATAAATA-A--AAATTTTAT
* *
1836286 ATAATATAAATGA-T-TAATATATTAAAATTTTAT
1 ATAATATAAAT-ATTATAATAAATAAAAATTTTAT
1836319 A-AATATATAATATTATAATAAATAAAAAT
1 ATAATATA-AATATTATAATAAATAAAAAT
1836348 ATATATATTA
Statistics
Matches: 53, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
32 7 0.13
33 14 0.26
34 12 0.23
35 2 0.04
36 17 0.32
37 1 0.02
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (34 bp):
ATAATATAAATATTATAATAAATAAAAATTTTAT
Found at i:1836471 original size:23 final size:21
Alignment explanation
Indices: 1836445--1836503 Score: 57
Period size: 23 Copynumber: 2.7 Consensus size: 21
1836435 ATTTACTTTC
1836445 AATTTTTTAAAAAATAATAAAAT
1 AATTTTTTAAAAAATAAT--AAT
*
1836468 AATTATTTAAATAAA-AATAAT
1 AATTTTTTAAA-AAATAATAAT
* *
1836489 AAATTTTAAAAAAAT
1 AATTTTTTAAAAAAT
1836504 TAAATTACGA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
20 3 0.10
21 11 0.37
23 13 0.43
24 3 0.10
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (21 bp):
AATTTTTTAAAAAATAATAAT
Found at i:1839152 original size:21 final size:21
Alignment explanation
Indices: 1839110--1839152 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1839100 ATATATATAT
* ** *
1839110 ATATATTAAAAGTTTTATTTA
1 ATATATTAAAAATAATAATTA
1839131 ATATATTAAAAATAATAATTA
1 ATATATTAAAAATAATAATTA
1839152 A
1 A
1839153 AATTATAAAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (21 bp):
ATATATTAAAAATAATAATTA
Found at i:1840200 original size:15 final size:15
Alignment explanation
Indices: 1840167--1840200 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1840157 CTCTTTTCAT
* *
1840167 TATTTTTTAATTTAT
1 TATTTTTTAATATAA
1840182 TATTTTTTAATATAA
1 TATTTTTTAATATAA
1840197 TATT
1 TATT
1840201 AATTATATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
TATTTTTTAATATAA
Found at i:1842125 original size:21 final size:22
Alignment explanation
Indices: 1842080--1842129 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
1842070 GAATTGAATT
* * *
1842080 ATTTATGAATTATTTAAATTTA
1 ATTTATTAAATATTTAAATTAA
1842102 ATTTATTAAATATTT-AATTAA
1 ATTTATTAAATATTTAAATTAA
1842123 ATTTATT
1 ATTTATT
1842130 TATTTAAGTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 12 0.48
22 13 0.52
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (22 bp):
ATTTATTAAATATTTAAATTAA
Found at i:1842135 original size:18 final size:18
Alignment explanation
Indices: 1842089--1842142 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 18
1842079 TATTTATGAA
*
1842089 TTATTTAAATTTAATTTAT
1 TTATTT-AATTAAATTTAT
1842108 TAAATATTTAATTAAATTTAT
1 T---TATTTAATTAAATTTAT
*
1842129 TTATTTAAGTAAAT
1 TTATTTAATTAAAT
1842143 AAAAAAATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
18 12 0.40
19 1 0.03
21 12 0.40
22 5 0.17
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (18 bp):
TTATTTAATTAAATTTAT
Found at i:1842136 original size:14 final size:14
Alignment explanation
Indices: 1842089--1842136 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
1842079 TATTTATGAA
1842089 TTATTTAAATTTAAT
1 TTATTTAAATTT-AT
1842104 TTA-TTAAA--TAT
1 TTATTTAAATTTAT
*
1842115 TTAATTAAATTTAT
1 TTATTTAAATTTAT
1842129 TTATTTAA
1 TTATTTAA
1842137 GTAAATAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
11 5 0.17
12 6 0.21
14 15 0.52
15 3 0.10
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
TTATTTAAATTTAT
Found at i:1845651 original size:2 final size:2
Alignment explanation
Indices: 1845644--1845668 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1845634 CTTTAGATTT
1845644 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 T
1845669 GCAAAGAAGA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1851998 original size:21 final size:18
Alignment explanation
Indices: 1851974--1852039 Score: 59
Period size: 15 Copynumber: 3.7 Consensus size: 18
1851964 AAAACGTGTC
1851974 AATTATTTTAAATATCAATAT
1 AATTATTTTAAA-A-C-ATAT
*
1851995 AATTAATTTAAAACATAT
1 AATTATTTTAAAACATAT
*
1852013 AA-TATTTTAATA-ATA-
1 AATTATTTTAAAACATAT
1852028 AA-TATTTTAAAA
1 AATTATTTTAAAA
1852040 TTAATTTTAT
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
15 11 0.27
16 3 0.07
17 8 0.20
18 6 0.15
19 1 0.02
20 1 0.02
21 11 0.27
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (18 bp):
AATTATTTTAAAACATAT
Found at i:1852058 original size:18 final size:20
Alignment explanation
Indices: 1852037--1852073 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1852027 AAATATTTTA
1852037 AAATTAA-T-TTTATATAAC
1 AAATTAATTATTTATATAAC
1852055 AAATTAATTATTTATATAA
1 AAATTAATTATTTATATAA
1852074 ATATAAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
19 1 0.06
20 9 0.53
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (20 bp):
AAATTAATTATTTATATAAC
Found at i:1852103 original size:14 final size:14
Alignment explanation
Indices: 1852086--1852123 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
1852076 ATAAAATTTA
1852086 ATAAATAAATTATT
1 ATAAATAAATTATT
1852100 ATAAATAACA-TATT
1 ATAAATAA-ATTATT
1852114 AT-AATAAATT
1 ATAAATAAATT
1852124 TTTACTTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 1 0.05
13 6 0.27
14 14 0.64
15 1 0.05
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (14 bp):
ATAAATAAATTATT
Found at i:1852279 original size:16 final size:16
Alignment explanation
Indices: 1852258--1852307 Score: 64
Period size: 16 Copynumber: 3.1 Consensus size: 16
1852248 ACTCGAACTT
* *
1852258 AAAAAATTTAGATTTA
1 AAAAAATTCAAATTTA
1852274 AAAAAATTCAAATTTA
1 AAAAAATTCAAATTTA
* *
1852290 AAAAAACTCAAACTTA
1 AAAAAATTCAAATTTA
1852306 AA
1 AA
1852308 TAGATCAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.62, C:0.08, G:0.02, T:0.28
Consensus pattern (16 bp):
AAAAAATTCAAATTTA
Found at i:1852307 original size:32 final size:31
Alignment explanation
Indices: 1852271--1852332 Score: 72
Period size: 32 Copynumber: 2.0 Consensus size: 31
1852261 AAATTTAGAT
*
1852271 TTAAAAAAATTC-AAATTTAAAAAAACTCAAAC
1 TTAAAAAAA-TCAAAATCTAAAAAAAC-CAAAC
* *
1852303 TTAAATAGATCAAAATCTAAAAAAACCAAA
1 TTAAAAAAATCAAAATCTAAAAAAACCAAA
1852333 TCCAAATAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
31 6 0.23
32 20 0.77
ACGTcount: A:0.63, C:0.13, G:0.02, T:0.23
Consensus pattern (31 bp):
TTAAAAAAATCAAAATCTAAAAAAACCAAAC
Found at i:1852378 original size:16 final size:17
Alignment explanation
Indices: 1852359--1852395 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
1852349 CTCGAAAAAT
1852359 TTTAAAAT-TAAAATAA
1 TTTAAAATATAAAATAA
1852375 TTT-AAATATAAAATAA
1 TTTAAAATATAAAATAA
1852391 TTTAA
1 TTTAA
1852396 CCTAACCTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 4 0.21
16 14 0.74
17 1 0.05
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TTTAAAATATAAAATAA
Found at i:1855730 original size:2 final size:2
Alignment explanation
Indices: 1855723--1855775 Score: 88
Period size: 2 Copynumber: 26.5 Consensus size: 2
1855713 ACCGCACTGT
* *
1855723 GA GA GA GA GA GA GT GA GT GA GA GA GA GA GA GA 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 GA
1855765 GA GA GA GA GA G
1 GA GA GA GA GA G
1855776 GGGTCAGTCA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.45, C:0.00, G:0.51, T:0.04
Consensus pattern (2 bp):
GA
Found at i:1863443 original size:5 final size:5
Alignment explanation
Indices: 1863432--1863462 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
1863422 ATATAGTATA
*
1863432 AAATT AATTT AAATT AAATT AAATT AAATT A
1 AAATT AAATT AAATT AAATT AAATT AAATT A
1863463 TTTTTTTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
AAATT
Found at i:1863523 original size:22 final size:24
Alignment explanation
Indices: 1863480--1863523 Score: 56
Period size: 22 Copynumber: 1.9 Consensus size: 24
1863470 TAAAAAAAAA
*
1863480 TTTAAAATATATATTTAATAATAT
1 TTTAAAATATATATTCAATAATAT
*
1863504 TTTAAAAT-T-TATTCATTAAT
1 TTTAAAATATATATTCAATAAT
1863524 TTAAAAATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 9 0.50
23 1 0.06
24 8 0.44
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (24 bp):
TTTAAAATATATATTCAATAATAT
Found at i:1863572 original size:17 final size:17
Alignment explanation
Indices: 1863551--1863585 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1863541 TTATATTATA
1863551 AAAAATTAAAAATTAAAT
1 AAAAA-TAAAAATTAAAT
*
1863569 AAAAATAAAATTTAAAT
1 AAAAATAAAAATTAAAT
1863586 TGATTGAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
AAAAATAAAAATTAAAT
Found at i:1866272 original size:2 final size:2
Alignment explanation
Indices: 1866265--1866300 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
1866255 TTTTGTAATT
*
1866265 TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1866301 TTTTTATTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1866349 original size:18 final size:18
Alignment explanation
Indices: 1866326--1866374 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 18
1866316 TTATTTGAAT
1866326 AATTATAAATATAATAAA
1 AATTATAAATATAATAAA
* *
1866344 AATTATTAAATGTATTAAA
1 AATTA-TAAATATAATAAA
* *
1866363 ATTTTTAAATAT
1 AATTATAAATAT
1866375 GAAGCTACAT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
18 11 0.44
19 14 0.56
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (18 bp):
AATTATAAATATAATAAA
Found at i:1866362 original size:19 final size:18
Alignment explanation
Indices: 1866326--1866374 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
1866316 TTATTTGAAT
1866326 AATTA-TAAATATAATAAA
1 AATTATTAAATATAAT-AA
* *
1866344 AATTATTAAATGTATTAA
1 AATTATTAAATATAATAA
*
1866362 AATTTTTAAATAT
1 AATTATTAAATAT
1866375 GAAGCTACAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
18 18 0.69
19 8 0.31
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (18 bp):
AATTATTAAATATAATAA
Found at i:1870146 original size:60 final size:60
Alignment explanation
Indices: 1870074--1870194 Score: 224
Period size: 60 Copynumber: 2.0 Consensus size: 60
1870064 TCTAAAAGCT
1870074 ATTTAAGGGTGATTACATGAAATAACTGAATTAAACTTTACGACATAAATAAACCATAGC
1 ATTTAAGGGTGATTACATGAAATAACTGAATTAAACTTTACGACATAAATAAACCATAGC
* *
1870134 ATTTAAGGGTGATTACATGAAATAACTGAATTAAACTTTGCGACGTAAATAAACCATAGC
1 ATTTAAGGGTGATTACATGAAATAACTGAATTAAACTTTACGACATAAATAAACCATAGC
1870194 A
1 A
1870195 AGAGAACAAA
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 59 1.00
ACGTcount: A:0.44, C:0.13, G:0.15, T:0.28
Consensus pattern (60 bp):
ATTTAAGGGTGATTACATGAAATAACTGAATTAAACTTTACGACATAAATAAACCATAGC
Found at i:1879009 original size:16 final size:15
Alignment explanation
Indices: 1878986--1879071 Score: 76
Period size: 15 Copynumber: 6.1 Consensus size: 15
1878976 TTATAAAATT
1878986 TTTAATTAAATAAAA
1 TTTAATTAAATAAAA
1879001 TTATAATT-AATAAAA
1 TT-TAATTAAATAAAA
* **
1879016 TTTATTTAAA-ATTA
1 TTTAATTAAATAAAA
1879030 TTTAA-TAAAT-AAA
1 TTTAATTAAATAAAA
*
1879043 TTTAA--AATTAAAA
1 TTTAATTAAATAAAA
*
1879056 TTTAATTATATAAAA
1 TTTAATTAAATAAAA
1879071 T
1 T
1879072 ATAAAATAAA
Statistics
Matches: 56, Mismatches: 9, Indels: 12
0.73 0.12 0.16
Matches are distributed among these distances:
12 3 0.05
13 18 0.32
14 10 0.18
15 20 0.36
16 5 0.09
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
TTTAATTAAATAAAA
Found at i:1879041 original size:28 final size:25
Alignment explanation
Indices: 1878996--1879046 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 25
1878986 TTTAATTAAA
*
1878996 TAAAATTATAATTAATAAAATTTATT
1 TAAAATTATAATAAAT-AAATTTATT
1879022 TAAAATTATTTAATAAATAAATTTA
1 TAAAATTA--TAATAAATAAATTTA
1879047 AAATTAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 8 0.36
27 7 0.32
28 7 0.32
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (25 bp):
TAAAATTATAATAAATAAATTTATT
Found at i:1879045 original size:23 final size:25
Alignment explanation
Indices: 1878996--1879052 Score: 73
Period size: 23 Copynumber: 2.3 Consensus size: 25
1878986 TTTAATTAAA
**
1878996 TAAAATTATAATTAATAAAATTTATT
1 TAAAATTAT-ATTAATAAAATAAATT
1879022 TAAAATTAT-TTAAT-AAATAAATT
1 TAAAATTATATTAATAAAATAAATT
1879045 TAAAATTA
1 TAAAATTA
1879053 AAATTTAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 15 0.52
24 5 0.17
26 9 0.31
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (25 bp):
TAAAATTATATTAATAAAATAAATT
Found at i:1879082 original size:11 final size:12
Alignment explanation
Indices: 1879069--1879201 Score: 75
Period size: 11 Copynumber: 11.1 Consensus size: 12
1879059 AATTATATAA
1879069 AATATAAAATA-
1 AATATAAAATAT
*
1879080 AAT-TAAAACAT
1 AATATAAAATAT
*
1879091 AATAT-AAACAT
1 AATATAAAATAT
1879102 AATATTAAAA-AT
1 AATA-TAAAATAT
*
1879114 AAT-TAAAACAT
1 AATATAAAATAT
*
1879125 AATAT-AAATAC
1 AATATAAAATAT
1879136 AATATTAAAA-AT
1 AATA-TAAAATAT
*
1879148 AAT-TAAAATAC
1 AATATAAAATAT
*
1879159 AATATGACACAAAAAT
1 AATAT---A-AAATAT
*
1879175 AATATAACATAT
1 AATATAAAATAT
1879187 CAATATCAAAATAT
1 -AATAT-AAAATAT
1879201 A
1 A
1879202 GATAAATGAA
Statistics
Matches: 96, Mismatches: 10, Indels: 30
0.71 0.07 0.22
Matches are distributed among these distances:
10 16 0.17
11 33 0.34
12 18 0.19
13 13 0.14
14 6 0.06
15 1 0.01
16 9 0.09
ACGTcount: A:0.64, C:0.08, G:0.01, T:0.28
Consensus pattern (12 bp):
AATATAAAATAT
Found at i:1879083 original size:21 final size:21
Alignment explanation
Indices: 1879045--1879084 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1879035 TAAATAAATT
*
1879045 TAAAATTAAAATTTAATTATA
1 TAAAATTAAAATTAAATTATA
1879066 TAAAATATAAAA-TAAATTA
1 TAAAAT-TAAAATTAAATTA
1879085 AAACATAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
TAAAATTAAAATTAAATTATA
Found at i:1879115 original size:23 final size:24
Alignment explanation
Indices: 1879069--1879129 Score: 85
Period size: 23 Copynumber: 2.7 Consensus size: 24
1879059 AATTATATAA
1879069 AATATAAA-ATAA-ATTAAAACAT
1 AATATAAACATAATATTAAAACAT
1879091 AATATAAACATAATATTAAAA-AT
1 AATATAAACATAATATTAAAACAT
1879114 AAT-TAAAACATAATAT
1 AATAT-AAACATAATAT
1879130 AAATACAATA
Statistics
Matches: 36, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
22 9 0.25
23 20 0.56
24 7 0.19
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.30
Consensus pattern (24 bp):
AATATAAACATAATATTAAAACAT
Found at i:1879149 original size:23 final size:23
Alignment explanation
Indices: 1879091--1879163 Score: 73
Period size: 23 Copynumber: 3.2 Consensus size: 23
1879081 ATTAAAACAT
* *
1879091 AATA-TAAACATAATATTAA-A-
1 AATATTAAAAATAATATAAATAC
1879111 AATAATTAAAACATAATATAAATAC
1 AAT-ATTAAAA-ATAATATAAATAC
1879136 AATATTAAAAATAAT-TAAAATAC
1 AATATTAAAAATAATAT-AAATAC
1879159 AATAT
1 AATAT
1879164 GACACAAAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
20 3 0.07
21 1 0.02
22 5 0.11
23 25 0.56
24 8 0.18
25 3 0.07
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.30
Consensus pattern (23 bp):
AATATTAAAAATAATATAAATAC
Found at i:1879163 original size:34 final size:34
Alignment explanation
Indices: 1879074--1879155 Score: 137
Period size: 34 Copynumber: 2.4 Consensus size: 34
1879064 TATAAAATAT
*
1879074 AAAATAAATTAAAACATAATATAAACATAATATTA
1 AAAAT-AATTAAAACATAATATAAACACAATATTA
*
1879109 AAAATAATTAAAACATAATATAAATACAATATTA
1 AAAATAATTAAAACATAATATAAACACAATATTA
1879143 AAAATAATTAAAA
1 AAAATAATTAAAA
1879156 TACAATATGA
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
34 40 0.89
35 5 0.11
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (34 bp):
AAAATAATTAAAACATAATATAAACACAATATTA
Found at i:1879420 original size:21 final size:20
Alignment explanation
Indices: 1879390--1879428 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
1879380 ATGTAAAAAA
*
1879390 TATATAAAAATATAATATTT
1 TATATAAAAAAATAATATTT
1879410 TATATACAAAAAATAATAT
1 TATATA-AAAAAATAATAT
1879429 AAATACGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (20 bp):
TATATAAAAAAATAATATTT
Found at i:1879460 original size:8 final size:7
Alignment explanation
Indices: 1879446--1879513 Score: 75
Period size: 8 Copynumber: 9.0 Consensus size: 7
1879436 AATACATAAT
1879446 TTTTTTC
1 TTTTTTC
1879453 TCTTTTTC
1 T-TTTTTC
1879461 TTTCTTTC
1 TTT-TTTC
1879469 TTTTTTC
1 TTTTTTC
1879476 TTTTTT-
1 TTTTTTC
1879482 TATCTTTTC
1 T-T-TTTTC
1879491 TTTCTTTC
1 TTT-TTTC
1879499 TTTCTTTC
1 TTT-TTTC
1879507 TTTTTTC
1 TTTTTTC
1879514 CAACCTTGCC
Statistics
Matches: 55, Mismatches: 0, Indels: 12
0.82 0.00 0.18
Matches are distributed among these distances:
6 1 0.02
7 19 0.35
8 34 0.62
9 1 0.02
ACGTcount: A:0.01, C:0.19, G:0.00, T:0.79
Consensus pattern (7 bp):
TTTTTTC
Found at i:1879466 original size:4 final size:4
Alignment explanation
Indices: 1879457--1879513 Score: 68
Period size: 4 Copynumber: 15.0 Consensus size: 4
1879447 TTTTTCTCTT
*
1879457 TTTC TTTC TTTC TTT- TTTC TTT- TTT- TATC TTTTC TTTC TTTC TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC -TTTC TTTC TTTC TTTC
1879503 TTTC TTT- TTTC
1 TTTC TTTC TTTC
1879514 CAACCTTGCC
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
3 11 0.23
4 33 0.70
5 3 0.06
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (4 bp):
TTTC
Found at i:1879490 original size:30 final size:32
Alignment explanation
Indices: 1879445--1879512 Score: 113
Period size: 31 Copynumber: 2.2 Consensus size: 32
1879435 GAATACATAA
*
1879445 TTTTTTTCTCTTTTTCTTTCTTTCTTT-TTTC
1 TTTTTTTATCTTTTTCTTTCTTTCTTTCTTTC
1879476 TTTTTTTATC-TTTTCTTTCTTTCTTTCTTTC
1 TTTTTTTATCTTTTTCTTTCTTTCTTTCTTTC
1879507 TTTTTT
1 TTTTTT
1879513 CCAACCTTGC
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
30 16 0.46
31 19 0.54
ACGTcount: A:0.01, C:0.18, G:0.00, T:0.81
Consensus pattern (32 bp):
TTTTTTTATCTTTTTCTTTCTTTCTTTCTTTC
Found at i:1880985 original size:13 final size:13
Alignment explanation
Indices: 1880967--1880991 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1880957 CAAATATATA
1880967 TTTTTTTTCTTTC
1 TTTTTTTTCTTTC
1880980 TTTTTTTTCTTT
1 TTTTTTTTCTTT
1880992 TTTCTCTGCC
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:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTTTTCTTTC
Found at i:1881226 original size:2 final size:2
Alignment explanation
Indices: 1881221--1881263 Score: 54
Period size: 2 Copynumber: 22.5 Consensus size: 2
1881211 TATCTTTATC
* *
1881221 TA TA TA AA TA T- TA TA CA TA TA TA TA TA TA TA TA TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1881261 TA T
1 TA T
1881264 TAAAGTAATC
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
1 2 0.06
2 33 0.94
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1881517 original size:23 final size:23
Alignment explanation
Indices: 1881491--1881541 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 23
1881481 TATTTATGAA
*
1881491 ATTATATC-ATGTTTAATTTTTTT
1 ATTATATCGAT-TTTAATTATTTT
*
1881514 ATTATGTCGTATTTTAATTATTTT
1 ATTATATCG-ATTTTAATTATTTT
1881538 ATTA
1 ATTA
1881542 ATGTTGTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 7 0.29
24 15 0.62
25 2 0.08
ACGTcount: A:0.27, C:0.04, G:0.06, T:0.63
Consensus pattern (23 bp):
ATTATATCGATTTTAATTATTTT
Found at i:1881529 original size:24 final size:25
Alignment explanation
Indices: 1881502--1881552 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 25
1881492 TTATATCATG
*
1881502 TTTAATTTTTTTATT-ATGTCGTAT
1 TTTAATTATTTTATTAATGTCGTAT
*
1881526 TTTAATTATTTTATTAATGTTGTAT
1 TTTAATTATTTTATTAATGTCGTAT
1881551 TT
1 TT
1881553 GCATCGTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 14 0.58
25 10 0.42
ACGTcount: A:0.24, C:0.02, G:0.08, T:0.67
Consensus pattern (25 bp):
TTTAATTATTTTATTAATGTCGTAT
Found at i:1888076 original size:18 final size:18
Alignment explanation
Indices: 1888050--1888088 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
1888040 TACCCGACTG
*
1888050 AATACTAAAAACAATAAT
1 AATAATAAAAACAATAAT
**
1888068 AATAATAAAATGAATAAT
1 AATAATAAAAACAATAAT
1888086 AAT
1 AAT
1888089 TGGCCCAGTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.67, C:0.05, G:0.03, T:0.26
Consensus pattern (18 bp):
AATAATAAAAACAATAAT
Found at i:1888578 original size:25 final size:27
Alignment explanation
Indices: 1888530--1888579 Score: 77
Period size: 25 Copynumber: 1.9 Consensus size: 27
1888520 TAATTATTAG
*
1888530 ACATTGATATTTTAAAAAATATATCAA
1 ACATTAATATTTTAAAAAATATATCAA
1888557 ACATTAATA-TTT-AAAAATATATC
1 ACATTAATATTTTAAAAAATATATC
1888580 TAATAATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 11 0.50
26 3 0.14
27 8 0.36
ACGTcount: A:0.52, C:0.08, G:0.02, T:0.38
Consensus pattern (27 bp):
ACATTAATATTTTAAAAAATATATCAA
Found at i:1889565 original size:2 final size:2
Alignment explanation
Indices: 1889558--1889596 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1889548 CAACTTACAC
1889558 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1889597 TCTAAAACAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1897792 original size:15 final size:16
Alignment explanation
Indices: 1897764--1897796 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1897754 ATATGTATAT
1897764 TATATACTAAAAAATTA
1 TATATACT-AAAAATTA
1897781 TATATACT-AAAATTA
1 TATATACTAAAAATTA
1897796 T
1 T
1897797 TTTTGTGAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
17 8 0.50
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (16 bp):
TATATACTAAAAATTA
Found at i:1898303 original size:20 final size:20
Alignment explanation
Indices: 1898277--1898317 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
1898267 AATTCGATTT
1898277 TTTAAAAAT-AAATTTAAAA
1 TTTAAAAATCAAATTTAAAA
*
1898296 TTTAAAAATCAAATTTTAAA
1 TTTAAAAATCAAATTTAAAA
1898316 TT
1 TT
1898318 AAACACTAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (20 bp):
TTTAAAAATCAAATTTAAAA
Found at i:1898656 original size:12 final size:12
Alignment explanation
Indices: 1898636--1898679 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
1898626 TCGACAATGG
1898636 GTATATATGTAT
1 GTATATATGTAT
*
1898648 GTATGTATGTAT
1 GTATATATGTAT
1898660 GTATATA-GATAT
1 GTATATATG-TAT
*
1898672 ATATATAT
1 GTATATAT
1898680 ACATACATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
11 1 0.04
12 26 0.96
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.48
Consensus pattern (12 bp):
GTATATATGTAT
Found at i:1903423 original size:6 final size:6
Alignment explanation
Indices: 1903412--1903503 Score: 57
Period size: 6 Copynumber: 14.8 Consensus size: 6
1903402 TATTTATTAA
* * *
1903412 AAATAT AAATAT -AATAT ATATTACA AAATAT TAATAT --ATAT AAATAT
1 AAATAT AAATAT AAATAT A-AATA-T AAATAT AAATAT AAATAT AAATAT
*
1903459 ATAATATTTT AAATAT AATTAT AATATAT AAATAT -AATAT AAATA
1 A-AATA---T AAATAT AAATAT AA-ATAT AAATAT AAATAT AAATA
1903504 AAAGAATGAT
Statistics
Matches: 68, Mismatches: 7, Indels: 22
0.70 0.07 0.23
Matches are distributed among these distances:
4 4 0.06
5 10 0.15
6 32 0.47
7 15 0.22
8 1 0.01
9 4 0.06
10 2 0.03
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (6 bp):
AAATAT
Found at i:1903452 original size:24 final size:23
Alignment explanation
Indices: 1903374--1903453 Score: 78
Period size: 24 Copynumber: 3.5 Consensus size: 23
1903364 GGATATTTAA
1903374 TAAT-TATATA-ATTAAAAAGTTAT
1 TAATATATATATATTAAAAA--TAT
*
1903397 TAA-A-ATATTTATTAAAAATAT
1 TAATATATATATATTAAAAATAT
*
1903418 AAATATAATATATATTACAAAATAT
1 TAATAT-ATATATATTA-AAAATAT
1903443 TAATATATATA
1 TAATATATATA
1903454 AATATATAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 11
0.76 0.06 0.18
Matches are distributed among these distances:
21 5 0.11
22 5 0.11
23 11 0.23
24 14 0.30
25 12 0.26
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.41
Consensus pattern (23 bp):
TAATATATATATATTAAAAATAT
Found at i:1903474 original size:22 final size:20
Alignment explanation
Indices: 1903412--1903503 Score: 81
Period size: 19 Copynumber: 4.8 Consensus size: 20
1903402 TATTTATTAA
1903412 AAATATAA-ATATAATATAT
1 AAATATAATATATAATATAT
* * *
1903431 -ATTACAAAATATTAATATAT
1 AAATATAATATA-TAATATAT
*
1903451 --ATA-AATATATAATATTTT
1 AAATATAATATATAATA-TAT
1903469 AAATATAAT-TATAATATAT
1 AAATATAATATATAATATAT
1903488 AAATATAATATA-AATA
1 AAATATAATATATAATA
1903504 AAAGAATGAT
Statistics
Matches: 60, Mismatches: 6, Indels: 14
0.75 0.08 0.17
Matches are distributed among these distances:
17 5 0.08
18 12 0.20
19 20 0.33
20 20 0.33
21 3 0.05
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (20 bp):
AAATATAATATATAATATAT
Found at i:1903495 original size:33 final size:35
Alignment explanation
Indices: 1903406--1903499 Score: 106
Period size: 35 Copynumber: 2.7 Consensus size: 35
1903396 TTAAAATATT
*
1903406 TATTAA-AAATATAAATATAATATATATTACAAAA
1 TATTAATATATATAAATATAATATATATTACAAAA
* *
1903440 TATTAATATATATAAATAT-ATAATATTTTA-AATA
1 TATTAATATATATAAATATAAT-ATATATTACAAAA
1903474 TAATT-ATAATATATAAATATAATATA
1 T-ATTAAT-ATATATAAATATAATATA
1903500 AATAAAAGAA
Statistics
Matches: 52, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
34 14 0.27
35 36 0.69
36 2 0.04
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.41
Consensus pattern (35 bp):
TATTAATATATATAAATATAATATATATTACAAAA
Found at i:1903701 original size:15 final size:17
Alignment explanation
Indices: 1903682--1903722 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 17
1903672 TTATATTTGT
1903682 AATTATTTAAT-TTA-A
1 AATTATTTAATATTATA
* *
1903697 TATTATTAAATATTATA
1 AATTATTTAATATTATA
1903714 AATTATTTA
1 AATTATTTA
1903723 TAAATATAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 2
0.77 0.15 0.08
Matches are distributed among these distances:
15 9 0.45
16 3 0.15
17 8 0.40
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
AATTATTTAATATTATA
Found at i:1905936 original size:2 final size:2
Alignment explanation
Indices: 1905929--1905967 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1905919 AGTCGTAAGT
1905929 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1905968 TACAAAAAAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1910430 original size:2 final size:2
Alignment explanation
Indices: 1910423--1910450 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1910413 TTCTAAGGGA
1910423 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
1910451 GTAATGTATA
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:1915035 original size:10 final size:9
Alignment explanation
Indices: 1915009--1915041 Score: 50
Period size: 10 Copynumber: 3.7 Consensus size: 9
1914999 AATTTTCATA
1915009 ATATAAAAT
1 ATATAAAAT
1915018 AT-TAAAAT
1 ATATAAAAT
1915026 ATATATAAAT
1 ATATA-AAAT
1915036 ATATAA
1 ATATAA
1915042 TATTTTAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
8 8 0.36
9 5 0.23
10 9 0.41
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (9 bp):
ATATAAAAT
Found at i:1915063 original size:27 final size:24
Alignment explanation
Indices: 1915010--1915063 Score: 54
Period size: 25 Copynumber: 2.1 Consensus size: 24
1915000 ATTTTCATAA
1915010 TATAAAATATTAAAATATATATAAA
1 TATAAAATATTAAAATATATAT-AA
* *
1915035 TATATAATATTTTAAATATTATTATAA
1 TATAAAATA-TTAAAATA-TA-TATAA
1915062 TA
1 TA
1915064 CGTAAATCTA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
25 8 0.33
26 7 0.29
27 6 0.25
28 3 0.12
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (24 bp):
TATAAAATATTAAAATATATATAA
Found at i:1916165 original size:8 final size:8
Alignment explanation
Indices: 1916154--1916264 Score: 53
Period size: 8 Copynumber: 14.4 Consensus size: 8
1916144 ATATTTATAT
1916154 TATATTTA
1 TATATTTA
*
1916162 TATATTTT
1 TATATTTA
1916170 TATATATTA
1 TATAT-TTA
1916179 TA-A-TTA
1 TATATTTA
1916185 TAT-TTTA
1 TATATTTA
*
1916192 -A-ATAT-
1 TATATTTA
1916197 TATATTTA
1 TATATTTA
*
1916205 TATATTTT
1 TATATTTA
1916213 TAATATATTA
1 T-ATAT-TTA
1916223 T-TATTT-
1 TATATTTA
*
1916229 TAT-GTTA
1 TATATTTA
1916236 TAATATTTTAA
1 T-ATA-TTT-A
1916247 TATATTTA
1 TATATTTA
*
1916255 TTTA-TTA
1 TATATTTA
1916262 TAT
1 TAT
1916265 TCATATCTTC
Statistics
Matches: 78, Mismatches: 10, Indels: 31
0.66 0.08 0.26
Matches are distributed among these distances:
6 12 0.15
7 15 0.19
8 30 0.38
9 11 0.14
10 8 0.10
11 2 0.03
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (8 bp):
TATATTTA
Found at i:1916167 original size:13 final size:13
Alignment explanation
Indices: 1916149--1916270 Score: 76
Period size: 13 Copynumber: 9.2 Consensus size: 13
1916139 TTTGTATATT
1916149 TATATTATATTTA
1 TATATTATATTTA
1916162 TATATTTTTATATATTA
1 TATA---TTATAT-TTA
1916179 TA-ATTATATTTTA
1 TATATTATA-TTTA
*
1916192 AATATTATATTTA
1 TATATTATATTTA
*
1916205 TATATT-T-TTAA
1 TATATTATATTTA
1916216 TATATTATTATTT-
1 TATATTA-TATTTA
*
1916229 TATGTTATAATATT-
1 TATATTAT-AT-TTA
*
1916243 T-TAATATATTTA
1 TATATTATATTTA
* *
1916255 TTTATTATATTCA
1 TATATTATATTTA
1916268 TAT
1 TAT
1916271 CTTCTATACA
Statistics
Matches: 86, Mismatches: 10, Indels: 26
0.70 0.08 0.21
Matches are distributed among these distances:
11 11 0.13
12 5 0.06
13 46 0.53
14 12 0.14
16 7 0.08
17 5 0.06
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.61
Consensus pattern (13 bp):
TATATTATATTTA
Found at i:1916197 original size:43 final size:45
Alignment explanation
Indices: 1916150--1916242 Score: 145
Period size: 43 Copynumber: 2.1 Consensus size: 45
1916140 TTGTATATTT
*
1916150 ATATTATATTTATATATTTTT-ATATATTATAATTATATTTTA-A
1 ATATTATATTTATATATTTTTAATATATTATAATTATATGTTATA
* *
1916193 ATATTATATTTATATATTTTTAATATATTATTATTTTATGTTATA
1 ATATTATATTTATATATTTTTAATATATTATAATTATATGTTATA
1916238 ATATT
1 ATATT
1916243 TTAATATATT
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
43 21 0.47
44 18 0.40
45 6 0.13
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (45 bp):
ATATTATATTTATATATTTTTAATATATTATAATTATATGTTATA
Found at i:1916203 original size:54 final size:54
Alignment explanation
Indices: 1916143--1916265 Score: 139
Period size: 54 Copynumber: 2.3 Consensus size: 54
1916133 TAATAATTTG
* *
1916143 TATATTTATATTATATTT-ATATATTTTTATATATTA-TAATTATATTTTAA-ATAT
1 TATATTTATA-TATATTTAATATATTATTAT-T-TTAGTAATAATATTTTAATATAT
* *
1916197 TATATTTATATATTTTTAATATATTATTATTTTATGTTATAATATTTTAATATAT
1 TATATTTATATATATTTAATATATTATTATTTTA-GTAATAATATTTTAATATAT
1916252 T-TATTTAT-TATATT
1 TATATTTATATATATT
1916266 CATATCTTCT
Statistics
Matches: 60, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
52 3 0.05
53 12 0.20
54 40 0.67
55 5 0.08
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.63
Consensus pattern (54 bp):
TATATTTATATATATTTAATATATTATTATTTTAGTAATAATATTTTAATATAT
Found at i:1916237 original size:31 final size:30
Alignment explanation
Indices: 1916194--1916265 Score: 92
Period size: 31 Copynumber: 2.3 Consensus size: 30
1916184 ATATTTTAAA
1916194 TATTATATTTAT-ATATTTTTAATATATTAT
1 TATTATATTTATAATA-TTTTAATATATTAT
*
1916224 TATTTTATGTTATAATATTTTAATATATTTATT
1 TATTATAT-TTATAATATTTTAATATA-TTA-T
1916257 TATTATATT
1 TATTATATT
1916266 CATATCTTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
30 7 0.19
31 14 0.39
32 7 0.19
33 8 0.22
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (30 bp):
TATTATATTTATAATATTTTAATATATTAT
Found at i:1916251 original size:44 final size:44
Alignment explanation
Indices: 1916150--1916265 Score: 130
Period size: 44 Copynumber: 2.7 Consensus size: 44
1916140 TTGTATATTT
* *
1916150 ATATTATATTTATATATTTTT-ATATATTATAATTATATTTTAA
1 ATATTATATATATATATTTTTAATATATTATAATTATATGTTAA
* * *
1916193 ATATTATATTTATATATTTTTAATATATTATTATTTTATGTTATA
1 ATATTATATATATATATTTTTAATATATTATAATTATATGTTA-A
* *
1916238 ATATTTTA-ATATAT-TTATTTATTATATT
1 ATATTATATATATATATT-TTTAATATATT
1916266 CATATCTTCT
Statistics
Matches: 64, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
43 23 0.36
44 33 0.52
45 8 0.12
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (44 bp):
ATATTATATATATATATTTTTAATATATTATAATTATATGTTAA
Found at i:1916259 original size:23 final size:23
Alignment explanation
Indices: 1916145--1916265 Score: 71
Period size: 23 Copynumber: 5.6 Consensus size: 23
1916135 ATAATTTGTA
*
1916145 TATTTATATTATATTT-ATATA-T
1 TATTTATAATAT-TTTAATATATT
* *
1916167 T-TTTAT-ATATTATAAT-TATA
1 TATTTATAATATTTTAATATATT
* * *
1916187 T-TTTA-AATATTAT-ATTTATA
1 TATTTATAATATTTTAATATATT
* * *
1916207 TATTTTTAATATATTATTAT-TT
1 TATTTATAATATTTTAATATATT
1916229 TATGTTATAATATTTTAATATATT
1 TAT-TTATAATATTTTAATATATT
*
1916253 TATTTATTATATT
1 TATTTATAATATT
1916266 CATATCTTCT
Statistics
Matches: 77, Mismatches: 13, Indels: 17
0.72 0.12 0.16
Matches are distributed among these distances:
19 6 0.08
20 22 0.29
21 8 0.10
22 11 0.14
23 25 0.32
24 5 0.06
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.63
Consensus pattern (23 bp):
TATTTATAATATTTTAATATATT
Found at i:1917584 original size:11 final size:12
Alignment explanation
Indices: 1917568--1917605 Score: 53
Period size: 11 Copynumber: 3.3 Consensus size: 12
1917558 TTTTTATGTC
1917568 ATATTATATTTT
1 ATATTATATTTT
*
1917580 A-ATTATTTTTT
1 ATATTATATTTT
1917591 ATATTATA-TTT
1 ATATTATATTTT
1917602 ATAT
1 ATAT
1917606 CGTGTCTCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
11 17 0.74
12 6 0.26
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (12 bp):
ATATTATATTTT
Found at i:1927641 original size:2 final size:2
Alignment explanation
Indices: 1927634--1927663 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1927624 GTAGGTGGTT
1927634 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
1927664 TTACCAAATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1929983 original size:14 final size:13
Alignment explanation
Indices: 1929958--1929995 Score: 67
Period size: 13 Copynumber: 2.8 Consensus size: 13
1929948 TTAAACGTAA
1929958 TATAAAAATTTTT
1 TATAAAAATTTTT
1929971 TATAAAAATTTTT
1 TATAAAAATTTTT
1929984 TATCAAAAATTT
1 TAT-AAAAATTT
1929996 AAATTTTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 16 0.67
14 8 0.33
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (13 bp):
TATAAAAATTTTT
Found at i:1930322 original size:50 final size:53
Alignment explanation
Indices: 1930239--1930341 Score: 142
Period size: 50 Copynumber: 2.0 Consensus size: 53
1930229 AGGATAAGTA
*
1930239 TTTTATTAGGAGTTATTTAGATACATTACAGTAAAATAATTATTATAA-ACATT
1 TTTTATTAGGAGTCATTTAGATACATTACAGTAAAATAATTATT-TAATACATT
* *
1930292 TTTTA-TA-GAGTCATTT-GATACGTTATAGTAAAATAATTATTTAATACATT
1 TTTTATTAGGAGTCATTTAGATACATTACAGTAAAATAATTATTTAATACATT
1930342 AAACGTTTAA
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
49 3 0.07
50 28 0.61
51 8 0.17
52 2 0.04
53 5 0.11
ACGTcount: A:0.40, C:0.06, G:0.10, T:0.45
Consensus pattern (53 bp):
TTTTATTAGGAGTCATTTAGATACATTACAGTAAAATAATTATTTAATACATT
Found at i:1930802 original size:21 final size:20
Alignment explanation
Indices: 1930773--1930811 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1930763 TTTGATGTGT
1930773 TATAATAAAATAATTATTTGA
1 TATAAT-AAATAATTATTTGA
* *
1930794 TATATTAAATATTTATTT
1 TATAATAAATAATTATTT
1930812 TATAAATTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (20 bp):
TATAATAAATAATTATTTGA
Found at i:1931314 original size:26 final size:26
Alignment explanation
Indices: 1931285--1931372 Score: 72
Period size: 26 Copynumber: 3.2 Consensus size: 26
1931275 TAAAAGAAAT
1931285 TAAATTAATATTAATTATAAATTTAA
1 TAAATTAATATTAATTATAAATTTAA
**
1931311 TAAATTAA-ATATAATTACT-CGTTTAA
1 TAAATTAATAT-TAATTA-TAAATTTAA
*
1931337 TAATATTAAACTAAATTATTTATAAATTTAA
1 TAA-ATT-AA-T--ATTAATTATAAATTTAA
1931368 TAAAT
1 TAAAT
1931373 ATTAAACATA
Statistics
Matches: 48, Mismatches: 5, Indels: 14
0.72 0.07 0.21
Matches are distributed among these distances:
25 2 0.04
26 22 0.46
27 4 0.08
28 2 0.04
30 3 0.06
31 13 0.27
32 2 0.04
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.44
Consensus pattern (26 bp):
TAAATTAATATTAATTATAAATTTAA
Found at i:1931374 original size:32 final size:32
Alignment explanation
Indices: 1931301--1931403 Score: 98
Period size: 32 Copynumber: 3.5 Consensus size: 32
1931291 AATATTAATT
*
1931301 ATAAATTTAAT-AA-ATTAAATATAATTACTC
1 ATAAATTTAATAAATATTAAACATAATTACTC
* * *
1931331 ----GTTTAAT-AATATTAAAC-TAAATTATTT
1 ATAAATTTAATAAATATTAAACAT-AATTACTC
1931358 ATAAATTTAATAAATATTAAACATAATTACTC
1 ATAAATTTAATAAATATTAAACATAATTACTC
1931390 ATAAATTTAA-AAAT
1 ATAAATTTAATAAAT
1931404 TACTAAAATA
Statistics
Matches: 58, Mismatches: 7, Indels: 15
0.73 0.09 0.19
Matches are distributed among these distances:
26 9 0.16
27 12 0.21
31 10 0.17
32 26 0.45
33 1 0.02
ACGTcount: A:0.52, C:0.06, G:0.01, T:0.41
Consensus pattern (32 bp):
ATAAATTTAATAAATATTAAACATAATTACTC
Found at i:1935424 original size:20 final size:18
Alignment explanation
Indices: 1935414--1935459 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 18
1935404 ATATAATATA
1935414 ATTTTTTAAAAGATAAAT
1 ATTTTTTAAAAGATAAAT
* *
1935432 TTTTTTTAAAA-A-AATT
1 ATTTTTTAAAAGATAAAT
1935448 ATGTTTTTAAAA
1 AT-TTTTTAAAA
1935460 TTATTATTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
16 4 0.17
17 10 0.42
18 10 0.42
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (18 bp):
ATTTTTTAAAAGATAAAT
Found at i:1935618 original size:29 final size:27
Alignment explanation
Indices: 1935572--1935626 Score: 74
Period size: 29 Copynumber: 2.0 Consensus size: 27
1935562 TTTAATAACA
1935572 ATAAATATATTTTAAAAATAAAAAAAG
1 ATAAATATATTTTAAAAATAAAAAAAG
* *
1935599 ATAAATAATAATTTTTAAAATATAAAAA
1 ATAAAT-AT-ATTTTAAAAATAAAAAAA
1935627 TTAATTAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 6 0.25
28 2 0.08
29 16 0.67
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (27 bp):
ATAAATATATTTTAAAAATAAAAAAAG
Found at i:1935644 original size:28 final size:29
Alignment explanation
Indices: 1935586--1935653 Score: 75
Period size: 28 Copynumber: 2.3 Consensus size: 29
1935576 ATATATTTTA
* *
1935586 AAAATAAAAAAAGATAAATAATAATTTTT
1 AAAATATAAAAAGATAAATAATAATTATT
* * *
1935615 AAAATATAAAAA-TTAATTAATTATTATT
1 AAAATATAAAAAGATAAATAATAATTATT
1935643 AAAATCATAAA
1 AAAAT-ATAAA
1935654 TTTTTTTAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
28 17 0.52
29 16 0.48
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.34
Consensus pattern (29 bp):
AAAATATAAAAAGATAAATAATAATTATT
Found at i:1936437 original size:14 final size:14
Alignment explanation
Indices: 1936409--1936449 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
1936399 TTGTTTAAGG
*
1936409 TTTTTATTATGTTA
1 TTTTTATTATTTTA
1936423 TTTTGTA-TATTTTA
1 TTTT-TATTATTTTA
1936437 TTTTTATTATTTT
1 TTTTTATTATTTT
1936450 TTATAATATT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
13 2 0.08
14 20 0.83
15 2 0.08
ACGTcount: A:0.20, C:0.00, G:0.05, T:0.76
Consensus pattern (14 bp):
TTTTTATTATTTTA
Found at i:1936451 original size:25 final size:29
Alignment explanation
Indices: 1936409--1936465 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 29
1936399 TTGTTTAAGG
*
1936409 TTTTTATTATGTTATTTTGT-ATATTT-TA
1 TTTTTATTA-GTTATTTTATAATATTTATA
1936437 TTTTTATTA-TT-TTTTATAATATTTATA
1 TTTTTATTAGTTATTTTATAATATTTATA
1936464 TT
1 TT
1936466 GTATAATTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
25 5 0.19
26 8 0.31
27 4 0.15
28 9 0.35
ACGTcount: A:0.25, C:0.00, G:0.04, T:0.72
Consensus pattern (29 bp):
TTTTTATTAGTTATTTTATAATATTTATA
Found at i:1944636 original size:3 final size:3
Alignment explanation
Indices: 1944628--1944665 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
1944618 ATTCCCACAT
1944628 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1944666 TGCTATCTCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:1945229 original size:23 final size:24
Alignment explanation
Indices: 1945201--1945247 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
1945191 ATTTATATTA
1945201 TTTAATA-AATAATTATTTTTTAG
1 TTTAATATAATAATTATTTTTTAG
*
1945224 TTTAATATTTATAATTATTTTTTA
1 TTTAATA-TAATAATTATTTTTTA
1945248 TTTTTAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 7 0.33
25 14 0.67
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (24 bp):
TTTAATATAATAATTATTTTTTAG
Found at i:1947804 original size:20 final size:20
Alignment explanation
Indices: 1947775--1947815 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
1947765 ATTTTTATAC
*
1947775 TATTTGATATGATTCAATAA
1 TATTTAATATGATTCAATAA
*
1947795 TATTTAATATGATTTAATAA
1 TATTTAATATGATTCAATAA
1947815 T
1 T
1947816 CTTTGATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.49
Consensus pattern (20 bp):
TATTTAATATGATTCAATAA
Found at i:1948078 original size:14 final size:16
Alignment explanation
Indices: 1948061--1948093 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
1948051 TAATTTATCT
1948061 TATATTTA-T-ATTTA
1 TATATTTAGTAATTTA
1948075 TATATTTAGTAATTTA
1 TATATTTAGTAATTTA
1948091 TAT
1 TAT
1948094 CATATAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.47
15 1 0.06
16 8 0.47
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (16 bp):
TATATTTAGTAATTTA
Found at i:1948815 original size:2 final size:2
Alignment explanation
Indices: 1948808--1948871 Score: 71
Period size: 2 Copynumber: 32.5 Consensus size: 2
1948798 GAACTTATCA
* *
1948808 AT AT AT AT AT AT AT A- AT AT GAT TT AT GA- AT AT AT -T AA AT AT
1 AT AT AT AT AT AT AT AT AT AT -AT AT AT -AT AT AT AT AT AT AT AT
1948849 AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
1948872 CACACATATA
Statistics
Matches: 53, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
1 3 0.06
2 47 0.89
3 3 0.06
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1951024 original size:20 final size:21
Alignment explanation
Indices: 1950999--1951041 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
1950989 TAAATTAATA
1950999 AATTTAAATAAATATTT-TAT
1 AATTTAAATAAATATTTATAT
* *
1951019 AATTTAAATTATTATTTATAT
1 AATTTAAATAAATATTTATAT
1951040 AA
1 AA
1951042 AAAATTATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
AATTTAAATAAATATTTATAT
Found at i:1951095 original size:18 final size:18
Alignment explanation
Indices: 1951052--1951122 Score: 62
Period size: 18 Copynumber: 4.1 Consensus size: 18
1951042 AAAATTATTA
1951052 AATAATA-AAA-TTTAAT
1 AATAATATAAATTTTAAT
*
1951068 -ATAAAAATAAATTTTAAT
1 AAT-AATATAAATTTTAAT
1951086 AATAATATAAATTCTTAA-
1 AATAATATAAATT-TTAAT
* *
1951104 ACTAAT-CAAATTTTAAT
1 AATAATATAAATTTTAAT
1951121 AA
1 AA
1951123 AATTTTCACA
Statistics
Matches: 44, Mismatches: 5, Indels: 11
0.73 0.08 0.18
Matches are distributed among these distances:
15 2 0.05
16 7 0.16
17 9 0.20
18 20 0.45
19 6 0.14
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (18 bp):
AATAATATAAATTTTAAT
Found at i:1951585 original size:20 final size:21
Alignment explanation
Indices: 1951559--1951613 Score: 69
Period size: 20 Copynumber: 2.6 Consensus size: 21
1951549 TAATTTTTAA
1951559 ATTTAAAAATATAATAAATTT
1 ATTTAAAAATATAATAAATTT
1951580 -TTTAAAAAT-TAAATAAATTT
1 ATTTAAAAATAT-AATAAATTT
*
1951600 ATATTAAATATATA
1 AT-TTAAAAATATA
1951614 TTTATATTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
19 1 0.03
20 18 0.62
21 1 0.03
22 8 0.28
23 1 0.03
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
ATTTAAAAATATAATAAATTT
Found at i:1951607 original size:15 final size:17
Alignment explanation
Indices: 1951587--1951621 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
1951577 TTTTTTAAAA
1951587 ATTAAATA-A-ATTTAT
1 ATTAAATATATATTTAT
1951602 ATTAAATATATATTTAT
1 ATTAAATATATATTTAT
1951619 ATT
1 ATT
1951622 TAAAATAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 8 0.44
16 1 0.06
17 9 0.50
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
ATTAAATATATATTTAT
Found at i:1951766 original size:2 final size:2
Alignment explanation
Indices: 1951759--1951786 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1951749 TTTATCTTTT
1951759 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1951787 CATGTTTGAA
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):
TA
Found at i:1952043 original size:27 final size:26
Alignment explanation
Indices: 1952013--1952080 Score: 75
Period size: 28 Copynumber: 2.5 Consensus size: 26
1952003 TACAATTTAA
1952013 AATTTTAAAATTTTAAAT-TGTTAATAT
1 AATTTTAAAATTTTAAATAT-TT-ATAT
*
1952040 AATTTATAAAATTTAAAATATTTATAT
1 AATTT-TAAAATTTTAAATATTTATAT
* *
1952067 AATTATATAATTTT
1 AATTTTAAAATTTT
1952081 TAAGTCATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
26 7 0.20
27 13 0.37
28 14 0.40
29 1 0.03
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (26 bp):
AATTTTAAAATTTTAAATATTTATAT
Found at i:1952075 original size:35 final size:34
Alignment explanation
Indices: 1952006--1952079 Score: 87
Period size: 35 Copynumber: 2.1 Consensus size: 34
1951996 TTTAGTGTAC
* **
1952006 AATTTAAAATTTTAAAATTTTAAATTGTTAATAT
1 AATTTAAAAATTTAAAATTTTAAATAATTAATAT
*
1952040 AATTTATAAAATTTAAAATATTTATATAATT-ATAT
1 AATTTA-AAAATTTAAAAT-TTTAAATAATTAATAT
1952075 AATTT
1 AATTT
1952080 TTAAGTCATT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
34 6 0.18
35 20 0.59
36 8 0.24
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (34 bp):
AATTTAAAAATTTAAAATTTTAAATAATTAATAT
Found at i:1954168 original size:18 final size:18
Alignment explanation
Indices: 1954132--1954169 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
1954122 ATTAATTTTT
1954132 TTTTTAAAAAAAATCTAAA
1 TTTTTAAAAAAAA-CTAAA
1954151 TTTTTAATAAAAAA-TAAA
1 TTTTTAA-AAAAAACTAAA
1954169 T
1 T
1954170 AGTTTATTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.28
19 7 0.39
20 6 0.33
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (18 bp):
TTTTTAAAAAAAACTAAA
Found at i:1954225 original size:65 final size:67
Alignment explanation
Indices: 1954160--1954308 Score: 177
Period size: 67 Copynumber: 2.3 Consensus size: 67
1954150 ATTTTTAATA
* * *
1954160 AAAAATAAATAGTTTATTTGAT-TA-AATA-TATATATAATTTTTAATATTT-TATATAATTATA
1 AAAAAT-AATAGTTTATATAATATATAATATTATATATAATTTATAATATTTATATATAATTATA
1954221 AAT
65 AAT
* *
1954224 AAAAATAATATTTTATATAATATATAATATTTATATGTAATTTATAATATTTATATATAATTAT-
1 AAAAATAATAGTTTATATAATATATAATA-TTATATATAATTTATAATATTTATATATAATTATA
1954288 -AT
65 AAT
1954290 AAAATATAATA-TTTATATA
1 AAAA-ATAATAGTTTATATA
1954309 TAAATGTAAT
Statistics
Matches: 74, Mismatches: 5, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
63 12 0.16
64 8 0.11
65 4 0.05
66 14 0.19
67 25 0.34
68 11 0.15
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (67 bp):
AAAAATAATAGTTTATATAATATATAATATTATATATAATTTATAATATTTATATATAATTATAA
AT
Found at i:1954266 original size:11 final size:11
Alignment explanation
Indices: 1954188--1954311 Score: 66
Period size: 9 Copynumber: 12.8 Consensus size: 11
1954178 TGATTAAATA
1954188 TATATATAATT
1 TATATATAATT
*
1954199 TTTA-AT-ATT
1 TATATATAATT
1954208 T-TATATAA-T
1 TATATATAATT
* *
1954217 TATAAATAA-A
1 TATATATAATT
*
1954227 AATA-AT-ATT
1 TATATATAATT
*
1954236 T-TATATAATA
1 TATATATAATT
1954246 TATA-AT-ATT
1 TATATATAATT
*
1954255 TATATGTAATT
1 TATATATAATT
1954266 TATA-AT-ATT
1 TATATATAATT
1954275 TATATATAA-T
1 TATATATAATT
*
1954285 TATATA-AA-A
1 TATATATAATT
1954294 TATA-AT-ATT
1 TATATATAATT
1954303 TATATATAA
1 TATATATAA
1954312 ATGTAATAAT
Statistics
Matches: 86, Mismatches: 12, Indels: 30
0.67 0.09 0.23
Matches are distributed among these distances:
8 7 0.08
9 35 0.41
10 30 0.35
11 14 0.16
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (11 bp):
TATATATAATT
Found at i:1954274 original size:67 final size:67
Alignment explanation
Indices: 1954188--1954319 Score: 189
Period size: 67 Copynumber: 2.0 Consensus size: 67
1954178 TGATTAAATA
*
1954188 TATATATAATTTTTAATATTT-TATATAATTATAAATAAAA-ATAATATTT-TATATAATATATA
1 TATATATAATTTATAATATTTATATATAATTAT--ATAAAATATAATATTTATATATAA-ATATA
1954250 ATATT
63 ATATT
* *
1954255 TATATGTAATTTATAATATTTATATATAATTATATAAAATATAATATTTATATATAAATGTAATA
1 TATATATAATTTATAATATTTATATATAATTATATAAAATATAATATTTATATATAAATATAATA
1954320 ATAATAATAA
Statistics
Matches: 59, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
66 6 0.10
67 35 0.59
68 18 0.31
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (67 bp):
TATATATAATTTATAATATTTATATATAATTATATAAAATATAATATTTATATATAAATATAATA
TT
Found at i:1954312 original size:20 final size:20
Alignment explanation
Indices: 1954228--1954291 Score: 94
Period size: 20 Copynumber: 3.2 Consensus size: 20
1954218 ATAAATAAAA
1954228 ATAATATTT-TATATAATAT
1 ATAATATTTATATATAATAT
* *
1954247 ATAATATTTATATGTAATTT
1 ATAATATTTATATATAATAT
1954267 ATAATATTTATATATAATTAT
1 ATAATATTTATATATAA-TAT
1954288 ATAA
1 ATAA
1954292 AATATAATAT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
19 9 0.23
20 24 0.62
21 6 0.15
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (20 bp):
ATAATATTTATATATAATAT
Done.