Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold153
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: 3137677
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Warning! 499 characters in sequence are not A, C, G, or T
File 12 of 24
Found at i:1628830 original size:22 final size:19
Alignment explanation
Indices: 1628783--1628835 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 19
1628773 ATAATTTTTA
1628783 TATTTATATTATATTTATGT
1 TATTTA-ATTATATTTATGT
1628803 TA--TAATTATATTTAAAATGT
1 TATTTAATTATATTT---ATGT
1628823 TATTTAATTATAT
1 TATTTAATTATAT
1628836 AAAATTTTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
17 9 0.32
18 2 0.07
20 8 0.29
22 9 0.32
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
TATTTAATTATATTTATGT
Found at i:1628838 original size:20 final size:22
Alignment explanation
Indices: 1628805--1628854 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
1628795 ATTTATGTTA
1628805 TAATTATATTTAAAATGTT-ATT
1 TAATTATA-TTAAAATGTTGATT
*
1628827 TAATTATA-TAAAATTTTGATT
1 TAATTATATTAAAATGTTGATT
*
1628848 TATTTAT
1 TAATTAT
1628855 TTATTTATGT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 8 0.32
21 9 0.36
22 8 0.32
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (22 bp):
TAATTATATTAAAATGTTGATT
Found at i:1629598 original size:14 final size:16
Alignment explanation
Indices: 1629569--1629602 Score: 54
Period size: 14 Copynumber: 2.2 Consensus size: 16
1629559 TTTTAAATAC
1629569 AAATACTATATATATT
1 AAATACTATATATATT
1629585 AAATA-TAT-TATATT
1 AAATACTATATATATT
1629599 AAAT
1 AAAT
1629603 TATACCATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 10 0.56
15 3 0.17
16 5 0.28
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (16 bp):
AAATACTATATATATT
Found at i:1630331 original size:17 final size:17
Alignment explanation
Indices: 1630309--1630341 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1630299 TTGTAAAATT
1630309 TTAATTTAAACTTGAAA
1 TTAATTTAAACTTGAAA
*
1630326 TTAATTTAAGCTTGAA
1 TTAATTTAAACTTGAA
1630342 CACAAATTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.42, C:0.06, G:0.09, T:0.42
Consensus pattern (17 bp):
TTAATTTAAACTTGAAA
Found at i:1630968 original size:21 final size:24
Alignment explanation
Indices: 1630942--1630989 Score: 66
Period size: 21 Copynumber: 2.1 Consensus size: 24
1630932 ATTTTTAATT
*
1630942 TTATTTAT-TTT-CATTGTTTA-A
1 TTATTTATATTTAAATTGTTTATA
1630963 TTATTTATATTTAAATTGTTTATA
1 TTATTTATATTTAAATTGTTTATA
1630987 TTA
1 TTA
1630990 ATTTTACTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 8 0.35
22 3 0.13
23 8 0.35
24 4 0.17
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.65
Consensus pattern (24 bp):
TTATTTATATTTAAATTGTTTATA
Found at i:1631948 original size:2 final size:2
Alignment explanation
Indices: 1631941--1631980 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1631931 CTTGGCATCA
1631941 AT AT AT AT AT AT 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 AT AT AT AT AT AT
1631981 TCAATGAATT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1632451 original size:2 final size:2
Alignment explanation
Indices: 1632439--1632474 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
1632429 TAACTCTTAA
1632439 AT AT A- 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 AT AT A
1632475 CACGCACATT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1633050 original size:20 final size:21
Alignment explanation
Indices: 1633011--1633061 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 21
1633001 ACATACTCTT
1633011 TAAAATATATTTAAAAAATTA
1 TAAAATATATTTAAAAAATTA
* * *
1633032 TAAAAAATATTT-TAAAATTT
1 TAAAATATATTTAAAAAATTA
1633052 TAAAATATAT
1 TAAAATATAT
1633062 AATAAACTCT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 15 0.58
21 11 0.42
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
TAAAATATATTTAAAAAATTA
Found at i:1633067 original size:20 final size:20
Alignment explanation
Indices: 1633009--1633067 Score: 57
Period size: 20 Copynumber: 2.9 Consensus size: 20
1632999 ATACATACTC
1633009 TTTAAAATATATTTAA-AAAAT
1 TTTAAAATATA--TAATAAAAT
* * **
1633030 TATAAAAAATATTTTAAAAT
1 TTTAAAATATATAATAAAAT
1633050 TTTAAAATATATAATAAA
1 TTTAAAATATATAATAAA
1633068 CTCTTAATAT
Statistics
Matches: 29, Mismatches: 8, Indels: 3
0.73 0.20 0.08
Matches are distributed among these distances:
19 1 0.03
20 19 0.66
21 9 0.31
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
TTTAAAATATATAATAAAAT
Found at i:1633602 original size:47 final size:44
Alignment explanation
Indices: 1633510--1633603 Score: 102
Period size: 47 Copynumber: 2.1 Consensus size: 44
1633500 TTTATTTATT
* *
1633510 ATTTCAAAAAATATATATTTTTATATTTAATATATTTTTATTAA
1 ATTTCAAAAAATATATATTATTATATTTAATATATTATTATTAA
*
1633554 ATTTTAAAAAATAATATATTAATTATTCATTT-ATATA-TATTATCTAA
1 ATTTCAAAAAAT-ATATATT-ATTA-T-ATTTAATATATTATTAT-TAA
1633601 ATT
1 ATT
1633604 CGTGCTAATC
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
44 11 0.26
45 7 0.17
46 8 0.19
47 12 0.29
48 4 0.10
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (44 bp):
ATTTCAAAAAATATATATTATTATATTTAATATATTATTATTAA
Found at i:1633974 original size:16 final size:15
Alignment explanation
Indices: 1633944--1633978 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
1633934 GATTTTAAAT
*
1633944 AATTATTTGTTAGTA
1 AATTATTTGTAAGTA
1633959 AATTACTTTGTAAGTA
1 AATTA-TTTGTAAGTA
1633975 AATT
1 AATT
1633979 TTATAATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.37, C:0.03, G:0.11, T:0.49
Consensus pattern (15 bp):
AATTATTTGTAAGTA
Found at i:1634067 original size:33 final size:35
Alignment explanation
Indices: 1634030--1634128 Score: 98
Period size: 32 Copynumber: 2.8 Consensus size: 35
1634020 TAAAATGTGG
*
1634030 TATAAAAATATAAATATT-TTAAATTTTATAT-AA
1 TATAAAAATATAAATATTATTAAAATTTATATAAA
* *
1634063 TAT-AAATTATTAAT-TTATTAAAATTTATATAAA
1 TATAAAAATATAAATATTATTAAAATTTATATAAA
*
1634096 TATAAAATATATTAAATATAATTATAAAATTTA
1 TATAAAA-ATA-TAAATATTA-T-TAAAATTTA
1634129 ACATGAATAC
Statistics
Matches: 52, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
31 2 0.04
32 21 0.40
33 8 0.15
34 3 0.06
35 2 0.04
36 4 0.08
37 2 0.04
38 1 0.02
39 9 0.17
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (35 bp):
TATAAAAATATAAATATTATTAAAATTTATATAAA
Found at i:1634113 original size:16 final size:17
Alignment explanation
Indices: 1634081--1634116 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
1634071 ATTAATTTAT
*
1634081 TAAAATTTATATAAATA
1 TAAAATATATATAAATA
1634098 TAAAATATAT-TAAATA
1 TAAAATATATATAAATA
1634114 TAA
1 TAA
1634117 TTATAAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
TAAAATATATATAAATA
Found at i:1634121 original size:15 final size:15
Alignment explanation
Indices: 1634049--1634125 Score: 52
Period size: 16 Copynumber: 4.9 Consensus size: 15
1634039 ATAAATATTT
*
1634049 TAAATTTTATATAATA
1 TAAATTATATA-AATA
*
1634065 TAAATTAT-TAATTTA
1 TAAATTATATAA-ATA
1634080 TTAAAATTTATATAAATA
1 -T-AAA-TTATATAAATA
*
1634098 TAAAATATATTAAATA
1 TAAATTATA-TAAATA
1634114 T-AATTATA-AAAT
1 TAAATTATATAAAT
1634126 TTAACATGAA
Statistics
Matches: 50, Mismatches: 5, Indels: 15
0.71 0.07 0.21
Matches are distributed among these distances:
13 4 0.08
14 1 0.02
15 14 0.28
16 18 0.36
17 4 0.08
18 6 0.12
19 3 0.06
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TAAATTATATAAATA
Found at i:1634278 original size:5 final size:5
Alignment explanation
Indices: 1634262--1634321 Score: 63
Period size: 5 Copynumber: 12.6 Consensus size: 5
1634252 TGCTACTCTG
* * * *
1634262 AAATA AATTA AAAT- AAATA AATTA AAATT AAA-A AATTA AAAT- AAATA
1 AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAATA
1634309 AAATA AAATA AAA
1 AAATA AAATA AAA
1634322 GCACAATCTG
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
4 10 0.23
5 34 0.77
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (5 bp):
AAATA
Found at i:1634281 original size:14 final size:14
Alignment explanation
Indices: 1634262--1634320 Score: 93
Period size: 14 Copynumber: 4.2 Consensus size: 14
1634252 TGCTACTCTG
1634262 AAATAAATTAAAAT
1 AAATAAATTAAAAT
1634276 AAATAAATTAAAATT
1 AAATAAATTAAAA-T
1634291 AAA-AAATTAAAAT
1 AAATAAATTAAAAT
*
1634304 AAATAAAATAAAAT
1 AAATAAATTAAAAT
1634318 AAA
1 AAA
1634321 AGCACAATCT
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
13 4 0.10
14 34 0.81
15 4 0.10
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (14 bp):
AAATAAATTAAAAT
Found at i:1639307 original size:15 final size:15
Alignment explanation
Indices: 1639287--1639317 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1639277 TCTCACCCTC
1639287 AAGTTTAAATAACAT
1 AAGTTTAAATAACAT
1639302 AAGTTTAAATAACAT
1 AAGTTTAAATAACAT
1639317 A
1 A
1639318 GTTAACAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.55, C:0.06, G:0.06, T:0.32
Consensus pattern (15 bp):
AAGTTTAAATAACAT
Found at i:1642017 original size:36 final size:36
Alignment explanation
Indices: 1641949--1642021 Score: 94
Period size: 36 Copynumber: 2.0 Consensus size: 36
1641939 AAATAAAAAT
* * *
1641949 TTTTTAATTTAAAATTAGTTTAATTAATTTTAATTA
1 TTTTTAATATAAAAATAGTTTAATTAAATTTAATTA
*
1641985 TTTTTAATAATAAAAATA-TTTATTTAAATTTAATTA
1 TTTTTAAT-ATAAAAATAGTTTAATTAAATTTAATTA
1642021 T
1 T
1642022 AAATTATATA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
36 25 0.78
37 7 0.22
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.56
Consensus pattern (36 bp):
TTTTTAATATAAAAATAGTTTAATTAAATTTAATTA
Found at i:1643819 original size:24 final size:25
Alignment explanation
Indices: 1643792--1643839 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
1643782 TAAATAATTT
*
1643792 TTATATAAAAT-TTAAAGTTTTATA
1 TTATATAAAATATTAAAATTTTATA
*
1643816 TTATATAATATATTAAAATTTTAT
1 TTATATAAAATATTAAAATTTTAT
1643840 CAATATTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 10 0.48
25 11 0.52
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (25 bp):
TTATATAAAATATTAAAATTTTATA
Found at i:1643893 original size:17 final size:20
Alignment explanation
Indices: 1643821--1643895 Score: 72
Period size: 20 Copynumber: 4.0 Consensus size: 20
1643811 TTATATTATA
1643821 TAATA-TATTAA-AATTTTAT
1 TAATATTATTAATAATTTT-T
* *
1643840 CAATATT-TAAATAATTTTT
1 TAATATTATTAATAATTTTT
*
1643859 TAATATTATTAATTATTTTT
1 TAATATTATTAATAATTTTT
1643879 T-AT-TTATT-ATAATTTTT
1 TAATATTATTAATAATTTTT
1643896 AAAATATAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
17 8 0.17
18 5 0.11
19 16 0.34
20 18 0.38
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (20 bp):
TAATATTATTAATAATTTTT
Found at i:1644276 original size:23 final size:23
Alignment explanation
Indices: 1644247--1644293 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
1644237 TAAATAAAAA
*
1644247 TTTTAATTTAATTTATATTTATT
1 TTTTAATTTAATTTATAATTATT
*
1644270 TTTTAATTTAATTTTTAATTATT
1 TTTTAATTTAATTTATAATTATT
1644293 T
1 T
1644294 AATATTTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (23 bp):
TTTTAATTTAATTTATAATTATT
Found at i:1644284 original size:12 final size:12
Alignment explanation
Indices: 1644247--1644289 Score: 61
Period size: 12 Copynumber: 3.7 Consensus size: 12
1644237 TAAATAAAAA
1644247 TTTTAATTTAAT
1 TTTTAATTTAAT
* *
1644259 TTAT-ATTTATT
1 TTTTAATTTAAT
1644270 TTTTAATTTAAT
1 TTTTAATTTAAT
1644282 TTTTAATT
1 TTTTAATT
1644290 ATTTAATATT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
11 9 0.35
12 17 0.65
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (12 bp):
TTTTAATTTAAT
Found at i:1644377 original size:24 final size:24
Alignment explanation
Indices: 1644353--1644410 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 24
1644343 ATTTTACATA
*
1644353 ATAATATAT-TATA-AAAATT-AT
1 ATAATATATAAATATAAAATTAAT
1644374 ATAATATATAAATATAAAATTAAT
1 ATAATATATAAATATAAAATTAAT
1644398 ATATATCATATAA
1 ATA-AT-ATATAA
1644411 CTAAAACTTG
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
21 9 0.29
22 3 0.10
23 6 0.19
24 5 0.16
25 2 0.06
26 6 0.19
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.40
Consensus pattern (24 bp):
ATAATATATAAATATAAAATTAAT
Found at i:1644594 original size:28 final size:32
Alignment explanation
Indices: 1644563--1644628 Score: 97
Period size: 28 Copynumber: 2.2 Consensus size: 32
1644553 ATCTTATATT
1644563 ATATATTTTTAATTT-ATTTT-T-TAAAA-AA
1 ATATATTTTTAATTTAATTTTATGTAAAATAA
1644591 ATATATTTTTAATTTAATTTTATGTAAAATAA
1 ATATATTTTTAATTTAATTTTATGTAAAATAA
1644623 AT-TATT
1 ATATATT
1644629 AATATATAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
28 15 0.44
29 5 0.15
30 1 0.03
31 9 0.26
32 4 0.12
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (32 bp):
ATATATTTTTAATTTAATTTTATGTAAAATAA
Found at i:1644639 original size:15 final size:16
Alignment explanation
Indices: 1644618--1644654 Score: 67
Period size: 15 Copynumber: 2.4 Consensus size: 16
1644608 TTTTATGTAA
1644618 AATAAATTATTAATAT
1 AATAAATTATTAATAT
1644634 -ATAAATTATTAATAT
1 AATAAATTATTAATAT
1644649 AATAAA
1 AATAAA
1644655 ATTTATATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 15 0.75
16 5 0.25
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
AATAAATTATTAATAT
Found at i:1644660 original size:18 final size:17
Alignment explanation
Indices: 1644621--1644670 Score: 61
Period size: 15 Copynumber: 3.0 Consensus size: 17
1644611 TATGTAAAAT
1644621 AAATTATTAATAT-AT-
1 AAATTATTAATATAATA
1644636 AAATTATTAATATAATA
1 AAATTATTAATATAATA
1644653 AAATTTATATAA-ATAATA
1 AAA-TTAT-TAATATAATA
1644671 TATTAAAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
15 13 0.42
16 2 0.06
17 3 0.10
18 10 0.32
19 3 0.10
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
AAATTATTAATATAATA
Found at i:1645216 original size:32 final size:34
Alignment explanation
Indices: 1645178--1645265 Score: 110
Period size: 32 Copynumber: 2.7 Consensus size: 34
1645168 TTTATGATTT
*
1645178 TTTATATTATATAAAATTT-AATATT-TTAATAA
1 TTTATATTATATAAAATTTAAAAATTATTAATAA
* * *
1645210 TTTATATTATATAAATTTTAAAAATTATTATTTA
1 TTTATATTATATAAAATTTAAAAATTATTAATAA
*
1645244 TTTATATTATAT-ATATTTAAAA
1 TTTATATTATATAAAATTTAAAA
1645266 TAATAATTAT
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
32 18 0.38
33 13 0.27
34 17 0.35
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (34 bp):
TTTATATTATATAAAATTTAAAAATTATTAATAA
Found at i:1645226 original size:15 final size:15
Alignment explanation
Indices: 1645178--1645227 Score: 57
Period size: 15 Copynumber: 3.2 Consensus size: 15
1645168 TTTATGATTT
1645178 TTTATATTATATAAAA
1 TTTATATTATAT-AAA
*
1645194 TTTAATATTTTA-ATAA
1 TTT-ATATTATATA-AA
1645210 TTTATATTATATAAA
1 TTTATATTATATAAA
1645225 TTT
1 TTT
1645228 TAAAAATTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
15 13 0.45
16 9 0.31
17 7 0.24
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TTTATATTATATAAA
Found at i:1645252 original size:34 final size:34
Alignment explanation
Indices: 1645169--1645277 Score: 116
Period size: 34 Copynumber: 3.3 Consensus size: 34
1645159 TAATTATTTT
* * *
1645169 TTATGATTT-TTTATATTATATAAAATTT-AATA
1 TTATTATTTATTTATATTATATAAATTTTAAAAA
* *
1645201 TT-TTAATAATTTATATTATATAAATTTTAAAAA
1 TTATTATTTATTTATATTATATAAATTTTAAAAA
* *
1645234 TTATTATTTATTTATATTATATATATTTAAAATAA
1 TTATTATTTATTTATATTATATAAATTTTAAA-AA
*
1645269 TAATTATTT
1 TTATTATTT
1645278 TTGATTTTAT
Statistics
Matches: 63, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
31 3 0.05
32 20 0.32
33 5 0.08
34 25 0.40
35 10 0.16
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (34 bp):
TTATTATTTATTTATATTATATAAATTTTAAAAA
Found at i:1645288 original size:34 final size:34
Alignment explanation
Indices: 1645213--1645295 Score: 96
Period size: 34 Copynumber: 2.4 Consensus size: 34
1645203 TTAATAATTT
* * * *
1645213 ATATTATATAAATTTTAAAAATTATTATTTATTT
1 ATATTATATATATTTAAAAAATAATTATTTATTG
1645247 ATATTATATATATTTAAAATAATAATTATTT-TTG
1 ATATTATATATATTTAAAA-AATAATTATTTATTG
* *
1645281 ATTTTATATTTATTT
1 ATATTATATATATTT
1645296 TATATTTATT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
34 32 0.76
35 10 0.24
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (34 bp):
ATATTATATATATTTAAAAAATAATTATTTATTG
Found at i:1645302 original size:18 final size:20
Alignment explanation
Indices: 1645272--1645330 Score: 63
Period size: 18 Copynumber: 3.0 Consensus size: 20
1645262 AAAATAATAA
1645272 TTATTTT-TGATTTTA-T-AT
1 TTATTTTAT-ATTTTATTAAT
1645290 TTATTTTATA-TTTATTAAT
1 TTATTTTATATTTTATTAAT
*
1645309 TATATTTTATATTGTATTAAT
1 T-TATTTTATATTTTATTAAT
1645330 T
1 T
1645331 AAGTCAAATT
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
17 4 0.11
18 9 0.26
19 4 0.11
20 9 0.26
21 9 0.26
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (20 bp):
TTATTTTATATTTTATTAAT
Found at i:1645313 original size:13 final size:11
Alignment explanation
Indices: 1645281--1645326 Score: 53
Period size: 11 Copynumber: 4.3 Consensus size: 11
1645271 ATTATTTTTG
1645281 ATTTTATATTT
1 ATTTTATATTT
1645292 ATTTTATATTT
1 ATTTTATATTT
1645303 A--TTA-ATTAT
1 ATTTTATATT-T
1645312 ATTTTATATTGT
1 ATTTTATATT-T
1645324 ATT
1 ATT
1645327 AATTAAGTCA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
8 3 0.10
9 5 0.17
11 15 0.50
12 7 0.23
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (11 bp):
ATTTTATATTT
Found at i:1645317 original size:25 final size:24
Alignment explanation
Indices: 1645284--1645332 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
1645274 ATTTTTGATT
* *
1645284 TTATATTTATTTTATATTTATTAA
1 TTATATTTATATTATATTAATTAA
*
1645308 TTATATTTTATATTGTATTAATTAA
1 TTATA-TTTATATTATATTAATTAA
1645333 GTCAAATTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 5 0.24
25 16 0.76
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (24 bp):
TTATATTTATATTATATTAATTAA
Found at i:1645328 original size:21 final size:20
Alignment explanation
Indices: 1645291--1645331 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
1645281 ATTTTATATT
1645291 TATTTTATATTTATTAATTA
1 TATTTTATATTTATTAATTA
1645311 TATTTTATATTGTATTAATTA
1 TATTTTATATT-TATTAATTA
1645332 AGTCAAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.63
Consensus pattern (20 bp):
TATTTTATATTTATTAATTA
Found at i:1645727 original size:4 final size:4
Alignment explanation
Indices: 1645718--1645769 Score: 59
Period size: 4 Copynumber: 13.0 Consensus size: 4
1645708 TGTTCTTTTG
* * * * *
1645718 ATAT ATAT ATAT ATAT GTAT ATAT GTAT GTAT GTAT ATAT GTAT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
1645766 ATAT
1 ATAT
1645770 TATGGACCTG
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 42 1.00
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (4 bp):
ATAT
Found at i:1645729 original size:8 final size:8
Alignment explanation
Indices: 1645719--1645765 Score: 76
Period size: 8 Copynumber: 5.9 Consensus size: 8
1645709 GTTCTTTTGA
*
1645719 TATATATA
1 TATATATG
1645727 TATATATG
1 TATATATG
1645735 TATATATG
1 TATATATG
*
1645743 TATGTATG
1 TATATATG
1645751 TATATATG
1 TATATATG
1645759 TATATAT
1 TATATAT
1645766 ATATTATGGA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 36 1.00
ACGTcount: A:0.38, C:0.00, G:0.11, T:0.51
Consensus pattern (8 bp):
TATATATG
Found at i:1645738 original size:12 final size:12
Alignment explanation
Indices: 1645718--1645769 Score: 77
Period size: 12 Copynumber: 4.3 Consensus size: 12
1645708 TGTTCTTTTG
*
1645718 ATATATATATAT
1 ATATGTATATAT
1645730 ATATGTATATAT
1 ATATGTATATAT
* *
1645742 GTATGTATGTAT
1 ATATGTATATAT
1645754 ATATGTATATAT
1 ATATGTATATAT
1645766 ATAT
1 ATAT
1645770 TATGGACCTG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 35 1.00
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (12 bp):
ATATGTATATAT
Found at i:1646180 original size:20 final size:20
Alignment explanation
Indices: 1646149--1646198 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
1646139 ATATATCCTT
1646149 TAAAATATATTTAAAAAATTA
1 TAAAATATATTT-AAAAATTA
* *
1646170 TAAAA-ATATTTTAAAATTT
1 TAAAATATATTTAAAAATTA
1646189 TAAAATATAT
1 TAAAATATAT
1646199 AATAAATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 11 0.42
20 10 0.38
21 5 0.19
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
TAAAATATATTTAAAAATTA
Found at i:1646204 original size:20 final size:20
Alignment explanation
Indices: 1646147--1646211 Score: 62
Period size: 20 Copynumber: 3.2 Consensus size: 20
1646137 ATATATATCC
1646147 TTTAAAATATATTTAA-AAAAT
1 TTTAAAATATA--TAATAAAAT
* **
1646168 TATAAAA-ATATTTTAAAAT
1 TTTAAAATATATAATAAAAT
*
1646187 TTTAAAATATATAATAAATT
1 TTTAAAATATATAATAAAAT
1646207 TTTAA
1 TTTAA
1646212 TCTTTAAAAA
Statistics
Matches: 35, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
18 1 0.03
19 11 0.31
20 17 0.49
21 6 0.17
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TTTAAAATATATAATAAAAT
Found at i:1646205 original size:19 final size:19
Alignment explanation
Indices: 1646147--1646208 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
1646137 ATATATATCC
*
1646147 TTTAAAATATATTTAAAAAAT
1 TTTAAAATATA--TAATAAAT
* **
1646168 TATAAAA-ATATTTTAAAAT
1 TTTAAAATATATAAT-AAAT
1646187 TTTAAAATATATAATAAAT
1 TTTAAAATATATAATAAAT
1646206 TTT
1 TTT
1646209 TAATCTTTAA
Statistics
Matches: 32, Mismatches: 7, Indels: 6
0.71 0.16 0.13
Matches are distributed among these distances:
18 1 0.03
19 17 0.53
20 8 0.25
21 6 0.19
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
TTTAAAATATATAATAAAT
Found at i:1646229 original size:27 final size:29
Alignment explanation
Indices: 1646157--1646235 Score: 83
Period size: 28 Copynumber: 2.8 Consensus size: 29
1646147 TTTAAAATAT
*
1646157 ATTTAAAAAATTATAA-AAATATTTTAAA
1 ATTTAAAAATTTATAATAAATATTTTAAA
* * *
1646185 ATTTTAAAATATATAATAAAT-TTTTAAT
1 ATTTAAAAATTTATAATAAATATTTTAAA
*
1646213 CTTTAAAAATTTA-AATAATATAT
1 ATTTAAAAATTTATAATAA-ATAT
1646236 CAAAAACGAA
Statistics
Matches: 41, Mismatches: 7, Indels: 5
0.77 0.13 0.09
Matches are distributed among these distances:
27 5 0.12
28 31 0.76
29 5 0.12
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.44
Consensus pattern (29 bp):
ATTTAAAAATTTATAATAAATATTTTAAA
Found at i:1647134 original size:26 final size:27
Alignment explanation
Indices: 1647081--1647139 Score: 68
Period size: 26 Copynumber: 2.2 Consensus size: 27
1647071 TTAAATTTAT
*
1647081 TATTTTAATCTTATTAAATATATTATA
1 TATTTTAATCTTATTAAATATATCATA
* *
1647108 T-TTTTATAT-TTATTAAATGTGTCATA
1 TATTTTA-ATCTTATTAAATATATCATA
1647134 TATTTT
1 TATTTT
1647140 GACGTGAGGT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
26 20 0.74
27 7 0.26
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.59
Consensus pattern (27 bp):
TATTTTAATCTTATTAAATATATCATA
Found at i:1651381 original size:24 final size:25
Alignment explanation
Indices: 1651354--1651402 Score: 73
Period size: 27 Copynumber: 1.9 Consensus size: 25
1651344 AATCCAAAGG
1651354 AAAT-CACCATTTTTGACAAACACA
1 AAATACACCATTTTTGACAAACACA
1651378 AAATAACCACCATTTTTGACAAACA
1 AAAT-A-CACCATTTTTGACAAACA
1651403 AATGGGTGGC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 4 0.18
27 18 0.82
ACGTcount: A:0.47, C:0.24, G:0.04, T:0.24
Consensus pattern (25 bp):
AAATACACCATTTTTGACAAACACA
Found at i:1655963 original size:27 final size:28
Alignment explanation
Indices: 1655902--1655972 Score: 101
Period size: 27 Copynumber: 2.6 Consensus size: 28
1655892 AAACAAGCCT
*
1655902 CCATATTTGACAAATC-CAAAAGAAACCA
1 CCATTTTTGACAAA-CACAAAAGAAACCA
*
1655930 CCATTTTTGACAAACACAAAA-TAACCA
1 CCATTTTTGACAAACACAAAAGAAACCA
1655957 CCATTTTTGACAAACA
1 CCATTTTTGACAAACA
1655973 AATGGGTGGC
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
27 22 0.55
28 18 0.45
ACGTcount: A:0.46, C:0.25, G:0.06, T:0.23
Consensus pattern (28 bp):
CCATTTTTGACAAACACAAAAGAAACCA
Found at i:1657217 original size:21 final size:21
Alignment explanation
Indices: 1657176--1657219 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1657166 TAATAAAAAT
* *
1657176 AATTATTTAAATTTAATTATA
1 AATTATATAAATATAATTATA
1657197 AATTATATAAATAATAA-TATA
1 AATTATATAAAT-ATAATTATA
1657218 AA
1 AA
1657220 ATTAATTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
AATTATATAAATATAATTATA
Found at i:1657222 original size:34 final size:35
Alignment explanation
Indices: 1657157--1657259 Score: 86
Period size: 34 Copynumber: 3.0 Consensus size: 35
1657147 AATTTAAATT
* * * * *
1657157 ATTATTTAATAATAAAAATAATTAT-TTAAATTTA
1 ATTATATAATTATATAAATAATAATATAAAATTTA
1657191 ATTATA-AATTATATAAATAATAATATAAAA-TTA
1 ATTATATAATTATATAAATAATAATATAAAATTTA
* * * * * *
1657224 ATTTTATAATTTTATAATTTATAATTTATAATTTA
1 ATTATATAATTATATAAATAATAATATAAAATTTA
1657259 A
1 A
1657260 AATTTTAAAT
Statistics
Matches: 55, Mismatches: 11, Indels: 5
0.77 0.15 0.07
Matches are distributed among these distances:
33 23 0.42
34 28 0.51
35 4 0.07
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (35 bp):
ATTATATAATTATATAAATAATAATATAAAATTTA
Found at i:1657239 original size:22 final size:22
Alignment explanation
Indices: 1657192--1657257 Score: 55
Period size: 22 Copynumber: 3.0 Consensus size: 22
1657182 TTAAATTTAA
** *
1657192 TTATAAATTAT-ATAAATAATA
1 TTATAAATTATAATTTATAATT
* *
1657213 ATATAAAATTA-ATTTTATAATT
1 TTAT-AAATTATAATTTATAATT
*
1657235 TTATAATTTATAATTTATAATT
1 TTATAAATTATAATTTATAATT
1657257 T
1 T
1657258 AAAATTTTAA
Statistics
Matches: 34, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
21 8 0.24
22 26 0.76
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
TTATAAATTATAATTTATAATT
Found at i:1657269 original size:7 final size:8
Alignment explanation
Indices: 1657222--1657270 Score: 61
Period size: 7 Copynumber: 6.6 Consensus size: 8
1657212 AATATAAAAT
1657222 TAATTTTA
1 TAATTTTA
1657230 TAATTTTA
1 TAATTTTA
1657238 TAA-TTTA
1 TAATTTTA
1657245 TAA-TTTA
1 TAATTTTA
1657252 TAA-TTTA
1 TAATTTTA
*
1657259 AAATTTTA
1 TAATTTTA
1657267 -AATT
1 TAATT
1657271 AATTCCAATT
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
7 24 0.62
8 15 0.38
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (8 bp):
TAATTTTA
Found at i:1657674 original size:22 final size:22
Alignment explanation
Indices: 1657636--1657714 Score: 58
Period size: 22 Copynumber: 3.5 Consensus size: 22
1657626 TTAATTAAAA
*
1657636 ATTAA-AA-AAATTATTTTTAT
1 ATTAATAATAAATAATTTTTAT
1657656 ATTAATAATAAAT-ATTTTTAT
1 ATTAATAATAAATAATTTTTAT
*
1657677 AATTAA-ATTTAAATAAATTTTTTATT
1 -ATTAATA-ATAAAT-AA-TTTTTA-T
1657703 ATTAAATAATAA
1 ATT-AATAATAA
1657715 TTCAAATTAA
Statistics
Matches: 47, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
20 5 0.11
21 11 0.23
22 14 0.30
24 1 0.02
25 9 0.19
26 6 0.13
27 1 0.02
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
ATTAATAATAAATAATTTTTAT
Found at i:1658630 original size:30 final size:30
Alignment explanation
Indices: 1658582--1658639 Score: 75
Period size: 29 Copynumber: 1.9 Consensus size: 30
1658572 GTTAATTTGA
*
1658582 AAAATGTTTGGTTTTAATT-TAAATAAAAT
1 AAAATGTTTGGTTTTAATTGAAAATAAAAT
1658611 AAAATGTTAT-GTCTTTAATTGAAAATAAA
1 AAAATGTT-TGGT-TTTAATTGAAAATAAA
1658640 TTTATATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
29 10 0.40
30 8 0.32
31 7 0.28
ACGTcount: A:0.47, C:0.02, G:0.10, T:0.41
Consensus pattern (30 bp):
AAAATGTTTGGTTTTAATTGAAAATAAAAT
Found at i:1658801 original size:20 final size:22
Alignment explanation
Indices: 1658776--1658816 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
1658766 ACTATCATAA
*
1658776 AAAATT-ATTTTAAT-TTTTAT
1 AAAATTAAATTTAATATTTTAT
1658796 AAAATTAAATTTAATATTTTA
1 AAAATTAAATTTAATATTTTA
1658817 ATTTAATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 7 0.39
22 5 0.28
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
AAAATTAAATTTAATATTTTAT
Found at i:1658821 original size:13 final size:13
Alignment explanation
Indices: 1658803--1658830 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1658793 TATAAAATTA
1658803 AATTTAATATTTT
1 AATTTAATATTTT
1658816 AATTTAATATTTT
1 AATTTAATATTTT
1658829 AA
1 AA
1658831 AAATTATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
AATTTAATATTTT
Found at i:1658855 original size:20 final size:19
Alignment explanation
Indices: 1658832--1658870 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1658822 ATATTTTAAA
*
1658832 AATTATAATAATTAAAAAAT
1 AATTATAAT-ATAAAAAAAT
*
1658852 AATTATTATATAAAAAAAT
1 AATTATAATATAAAAAAAT
1658871 TAATATATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
AATTATAATATAAAAAAAT
Found at i:1658907 original size:19 final size:19
Alignment explanation
Indices: 1658880--1658970 Score: 51
Period size: 19 Copynumber: 4.5 Consensus size: 19
1658870 TTAATATATT
*
1658880 ATTTGATATAAAATTATAA
1 ATTTTATATAAAATTATAA
*
1658899 ATTTTATATCAAAATAAATTTAA
1 ATTTTATAT-AAAAT---TATAA
** * *
1658922 ATTACATGTTAAATT-TAA
1 ATTTTATATAAAATTATAA
1658940 ATTTTTTATATAAAACTTA-AA
1 A--TTTTATATAAAA-TTATAA
1658961 ATTTTATATA
1 ATTTTATATA
1658971 GTATAATATA
Statistics
Matches: 54, Mismatches: 10, Indels: 16
0.68 0.12 0.20
Matches are distributed among these distances:
18 4 0.07
19 18 0.33
20 13 0.24
21 5 0.09
22 4 0.07
23 10 0.19
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.46
Consensus pattern (19 bp):
ATTTTATATAAAATTATAA
Found at i:1659035 original size:14 final size:14
Alignment explanation
Indices: 1659016--1659075 Score: 61
Period size: 15 Copynumber: 4.2 Consensus size: 14
1659006 TTTTATTTAT
1659016 TATAAAATTTAAAA
1 TATAAAATTTAAAA
1659030 TATAAAAATTT-AAA
1 TAT-AAAATTTAAAA
*
1659044 T-TAAAATTTTAATAT
1 TATAAAA-TTTAA-AA
*
1659059 TATAAAAATTAAAA
1 TATAAAATTTAAAA
1659073 TAT
1 TAT
1659076 TTTTTTATTA
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
12 4 0.11
13 4 0.11
14 12 0.32
15 13 0.34
16 5 0.13
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
TATAAAATTTAAAA
Found at i:1659063 original size:29 final size:27
Alignment explanation
Indices: 1659018--1659073 Score: 76
Period size: 29 Copynumber: 2.0 Consensus size: 27
1659008 TTATTTATTA
*
1659018 TAAAATTTAAAATATAAAAATTTAAAT
1 TAAAATTTAAAATATAAAAATTAAAAT
*
1659045 TAAAATTTTAATATTATAAAAATTAAAAT
1 TAAAA-TTTAA-AATATAAAAATTAAAAT
1659074 ATTTTTTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 5 0.20
28 5 0.20
29 15 0.60
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (27 bp):
TAAAATTTAAAATATAAAAATTAAAAT
Found at i:1659065 original size:28 final size:27
Alignment explanation
Indices: 1659018--1659071 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
1659008 TTATTTATTA
*
1659018 TAAAATTTAAAATATAAAAATTTAAAT
1 TAAAATTTAAAATATAAAAAATTAAAT
*
1659045 TAAAATTT-TAATATTATAAAAATTAAA
1 TAAAATTTAAAATA-TA-AAAAATTAAA
1659072 ATATTTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 4 0.17
27 10 0.43
28 9 0.39
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (27 bp):
TAAAATTTAAAATATAAAAAATTAAAT
Found at i:1659326 original size:10 final size:10
Alignment explanation
Indices: 1659311--1659370 Score: 50
Period size: 10 Copynumber: 5.8 Consensus size: 10
1659301 TCTTTAAAAT
1659311 TTTATTTAAA
1 TTTATTTAAA
1659321 TTTATTTAAAA
1 TTTATTT-AAA
*
1659332 TTTATAAATAAA
1 TTTAT--TTAAA
* *
1659344 -TAATTTAAT
1 TTTATTTAAA
1659353 TTTATTTAAA
1 TTTATTTAAA
*
1659363 TATATTTA
1 TTTATTTA
1659371 TATTAATCTT
Statistics
Matches: 39, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
9 3 0.08
10 21 0.54
11 11 0.28
12 3 0.08
13 1 0.03
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (10 bp):
TTTATTTAAA
Found at i:1659420 original size:21 final size:21
Alignment explanation
Indices: 1659394--1659460 Score: 73
Period size: 21 Copynumber: 3.0 Consensus size: 21
1659384 TATTTTATAT
*
1659394 TATAATATATTATAAAAATTA
1 TATAATATATAATAAAAATTA
1659415 TATAATATA-AATATAAAATTAA
1 TATAATATATAATA-AAAATT-A
1659437 TATATATCATATAATTAAAAATTA
1 TATA-AT-ATATAA-TAAAAATTA
1659461 AATTGAATTT
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
20 3 0.08
21 15 0.38
22 5 0.13
23 2 0.05
24 4 0.10
25 8 0.21
26 2 0.05
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.40
Consensus pattern (21 bp):
TATAATATATAATAAAAATTA
Found at i:1659442 original size:26 final size:25
Alignment explanation
Indices: 1659413--1659461 Score: 71
Period size: 26 Copynumber: 1.9 Consensus size: 25
1659403 TTATAAAAAT
1659413 TATATAATATAAATATAAAATTAATA
1 TATATAATATAAATA-AAAATTAATA
* *
1659439 TATATCATATAATTAAAAATTAA
1 TATATAATATAAATAAAAATTAA
1659462 ATTGAATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 8 0.38
26 13 0.62
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (25 bp):
TATATAATATAAATAAAAATTAATA
Found at i:1659623 original size:32 final size:33
Alignment explanation
Indices: 1659561--1659648 Score: 78
Period size: 32 Copynumber: 2.8 Consensus size: 33
1659551 AATTTTTATC
* *
1659561 TAAATTTATTT-ATATTTATA-AATAAAAAATT-
1 TAAATTAATTTAATTTTTATATAA-AAAAAATTA
*
1659592 TAAATTAATTTAATTTTTATATAAAATAAATTA
1 TAAATTAATTTAATTTTTATATAAAAAAAATTA
* *
1659625 TTAATATAA--TAAATTTTATATAAA
1 TAAAT-TAATTTAATTTTTATATAAA
1659649 TAATATATTT
Statistics
Matches: 48, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
31 10 0.21
32 29 0.60
33 6 0.12
34 3 0.06
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (33 bp):
TAAATTAATTTAATTTTTATATAAAAAAAATTA
Found at i:1659651 original size:18 final size:18
Alignment explanation
Indices: 1659606--1659658 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 18
1659596 TTAATTTAAT
1659606 TTTTATAT-AA-AATAAA
1 TTTTATATAAATAATAAA
1659622 --TTAT-TAATATAATAAA
1 TTTTATATAA-ATAATAAA
*
1659638 TTTTATATAAATAATATA
1 TTTTATATAAATAATAAA
1659656 TTT
1 TTT
1659659 AAAACAATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 10
0.73 0.02 0.24
Matches are distributed among these distances:
13 1 0.03
14 5 0.17
15 1 0.03
16 6 0.20
18 14 0.47
19 3 0.10
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TTTTATATAAATAATAAA
Found at i:1660678 original size:60 final size:60
Alignment explanation
Indices: 1660470--1660675 Score: 213
Period size: 60 Copynumber: 3.4 Consensus size: 60
1660460 TATGTTTCGC
* *
1660470 AAATTTTTCTTC--ACGACTTTTTCACTCATGGCGTGCACCATACTCATTTCAATGCTCTTA
1 AAATTTTTCTTCTGA-GAC-TTTTCACTCATGGCGTGCACCATACTCATTTTAATGCCCTTA
* * * * *
1660530 AATTTTTTTTTTCTTTCTGAGACTTTTCACACATGGCGTGCTCAATACTCATTTTTAATGTCC-T
1 AA----ATTTTTC-TTCTGAGACTTTTCACTCATGGCGTGCACCATACTCA-TTTTAATGCCCTT
1660594 A
60 A
* * *
1660595 AAATTTTTCTTTTGAGACTTTTCACTTATGGCGTACACCATACTCATTTTAATGCCCTTA
1 AAATTTTTCTTCTGAGACTTTTCACTCATGGCGTGCACCATACTCATTTTAATGCCCTTA
*
1660655 AAGTTTTTC-TCTGAGACTTTT
1 AAATTTTTCTTCTGAGACTTTT
1660676 TCAGAATCAT
Statistics
Matches: 120, Mismatches: 17, Indels: 19
0.77 0.11 0.12
Matches are distributed among these distances:
59 21 0.17
60 43 0.36
61 6 0.05
64 6 0.05
65 32 0.27
66 11 0.09
67 1 0.01
ACGTcount: A:0.23, C:0.22, G:0.11, T:0.45
Consensus pattern (60 bp):
AAATTTTTCTTCTGAGACTTTTCACTCATGGCGTGCACCATACTCATTTTAATGCCCTTA
Found at i:1662133 original size:45 final size:45
Alignment explanation
Indices: 1662049--1662134 Score: 138
Period size: 45 Copynumber: 1.9 Consensus size: 45
1662039 CAAGGTATCC
*
1662049 TTTTCTAATCTTTCTTTTACTTCTTTATTTGGTACGCGATTTTTT
1 TTTTCTAATCTTTCTTTTACTTCTTTATTTGATACGCGATTTTTT
*
1662094 TTTTCTAATCTTTCTTTTACTTCTTTTTTTGAT-CTGCGATT
1 TTTTCTAATCTTTCTTTTACTTCTTTATTTGATAC-GCGATT
1662135 GCCGTTTATC
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
44 1 0.03
45 37 0.97
ACGTcount: A:0.13, C:0.16, G:0.08, T:0.63
Consensus pattern (45 bp):
TTTTCTAATCTTTCTTTTACTTCTTTATTTGATACGCGATTTTTT
Found at i:1662147 original size:17 final size:17
Alignment explanation
Indices: 1662125--1662160 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
1662115 TCTTTTTTTG
1662125 ATCTGCGATTGCCGTTT
1 ATCTGCGATTGCCGTTT
1662142 ATCTGCGATTGCCGTTT
1 ATCTGCGATTGCCGTTT
1662159 AT
1 AT
1662161 GCTAACATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.14, C:0.22, G:0.22, T:0.42
Consensus pattern (17 bp):
ATCTGCGATTGCCGTTT
Found at i:1668136 original size:17 final size:17
Alignment explanation
Indices: 1668098--1668130 Score: 50
Period size: 16 Copynumber: 1.9 Consensus size: 17
1668088 TTATTTTATT
1668098 TAAAT-TTAATTAAAAA
1 TAAATATTAATTAAAAA
1668114 TAAATATTAATATAAAA
1 TAAATATTAAT-TAAAA
1668131 CTAATACTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 5 0.33
18 5 0.33
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
TAAATATTAATTAAAAA
Found at i:1669150 original size:3 final size:3
Alignment explanation
Indices: 1669142--1669168 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1669132 TATAATATAG
1669142 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1669169 TGTTTTTATT
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1669632 original size:21 final size:22
Alignment explanation
Indices: 1669589--1669632 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
1669579 TTTTTTATTT
***
1669589 ATTTATAAAAATAAAATTTTAA
1 ATTTATAAAAATAAAAGAATAA
1669611 ATTT-TAAAAATAAAAGAATAA
1 ATTTATAAAAATAAAAGAATAA
1669632 A
1 A
1669633 AAGGAAAATC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (22 bp):
ATTTATAAAAATAAAAGAATAA
Found at i:1677610 original size:24 final size:24
Alignment explanation
Indices: 1677547--1677611 Score: 62
Period size: 24 Copynumber: 2.7 Consensus size: 24
1677537 TAAAACATAT
1677547 TTTTTTATGGAAAAGAT-TGCCATTA
1 TTTTTTATGG-AAAG-TCTGCCATTA
* *
1677572 CTATTTAT-GATAAGTCTGCCATTA
1 TTTTTTATGGA-AAGTCTGCCATTA
*
1677596 TTTTTTATGGCAAGTC
1 TTTTTTATGGAAAGTC
1677612 ATATATATGG
Statistics
Matches: 32, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
23 2 0.06
24 23 0.72
25 7 0.22
ACGTcount: A:0.28, C:0.12, G:0.15, T:0.45
Consensus pattern (24 bp):
TTTTTTATGGAAAGTCTGCCATTA
Found at i:1681578 original size:13 final size:13
Alignment explanation
Indices: 1681560--1681587 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1681550 ATACAAAGAT
1681560 CAATGTATCGATA
1 CAATGTATCGATA
1681573 CAATGTATCGATA
1 CAATGTATCGATA
1681586 CA
1 CA
1681588 TTTGAGTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:1681669 original size:13 final size:13
Alignment explanation
Indices: 1681651--1681675 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1681641 AAAAAAAATA
1681651 TGTATCGATACAT
1 TGTATCGATACAT
1681664 TGTATCGATACA
1 TGTATCGATACA
1681676 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1687239 original size:51 final size:51
Alignment explanation
Indices: 1687179--1687276 Score: 162
Period size: 51 Copynumber: 1.9 Consensus size: 51
1687169 TTTTCGAGGG
1687179 GATACTCCAACCCTAGTTTTATTTTCAAAACA-CTGATTTTTCACAATCGGA
1 GATACTCCAACCCTAGTTTTATTTTCAAAACATC-GATTTTTCACAATCGGA
* *
1687230 GATACTCCAACCTTGGTTTTATTTTCAAAACATCGATTTTTCACAAT
1 GATACTCCAACCCTAGTTTTATTTTCAAAACATCGATTTTTCACAAT
1687277 TGGGGATATT
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
51 43 0.98
52 1 0.02
ACGTcount: A:0.31, C:0.22, G:0.09, T:0.38
Consensus pattern (51 bp):
GATACTCCAACCCTAGTTTTATTTTCAAAACATCGATTTTTCACAATCGGA
Found at i:1687319 original size:79 final size:80
Alignment explanation
Indices: 1687230--1687557 Score: 319
Period size: 79 Copynumber: 4.1 Consensus size: 80
1687220 CACAATCGGA
* * * *
1687230 GATACTCCAACCTTGGTTTTATTTTC-AAAACATCGATTTTTCACAATTGGGGATATTCTAACCC
1 GATACTCCAACCTTGATTTTATTTTCTAAAACATCGATTTTTCACAATCGGGGATACTCCAACCC
*
1687294 CGTTATTTTCAAGGG
66 CGTTATTTTCAAGAG
* * * * *
1687309 GGTACTCCAACCTTGATTTTA-TTTCTAAAACA-CTAATTTTTCACCATCGAGGATACTCCAATC
1 GATACTCCAACCTTGATTTTATTTTCTAAAACATC-GATTTTTCACAATCGGGGATACTCCAACC
*
1687372 CCGTTATTTTCGAGAG
65 CCGTTATTTTCAAGAG
*** * * *
1687388 GATACTCCAACCCAAATTTT-TATTTCTAAAACACCGATTTTTCACAATCGGAGATACTCCAATC
1 GATACTCCAACCTTGATTTTAT-TTTCTAAAACATCGATTTTTCACAATCGGGGATACTCCAACC
** * * *
1687452 TTGTTATTTCCGAGGG
65 CCGTTATTTTCAAGAG
** * * * *
1687468 GATGTTCCAACCCT-ACCTTTA-TTTCTAAAACATCAATTTTTCAAAATCGGGGATACTCCAACC
1 GATACTCCAACCTTGA-TTTTATTTTCTAAAACATCGATTTTTCACAATCGGGGATACTCCAACC
1687531 CCGTTATTTTCGAA-AG
65 CCGTTATTTTC-AAGAG
1687547 GATACTCCAAC
1 GATACTCCAAC
1687558 TCCGGTTTTA
Statistics
Matches: 202, Mismatches: 39, Indels: 16
0.79 0.15 0.06
Matches are distributed among these distances:
78 5 0.02
79 133 0.66
80 63 0.31
81 1 0.00
ACGTcount: A:0.29, C:0.24, G:0.13, T:0.34
Consensus pattern (80 bp):
GATACTCCAACCTTGATTTTATTTTCTAAAACATCGATTTTTCACAATCGGGGATACTCCAACCC
CGTTATTTTCAAGAG
Found at i:1687339 original size:130 final size:128
Alignment explanation
Indices: 1687101--1687369 Score: 357
Period size: 130 Copynumber: 2.1 Consensus size: 128
1687091 ATTTCTAAGG
* * *
1687101 GGATACTCTAACCTTGATTTTATTTTCAAAACACTGATTTTTACAATTGGGGATACCCAGCCCTG
1 GGATACTCCAACCTTGATTTTATTTTCAAAACACTGATTTTTACAATTGGGGATACCCAACCCCG
* *
1687166 TTATTTTCGAGGGGATACTCCAACCCTAGTTTTATTTTCAAAACACTGATTTTTCACAATCG-
66 TTATTTTCAAGGGGATACTCCAACCCTAGTTTTATTTTCAAAACACTAATTTTTCACAATCGA
* * *
1687228 GAGATACTCCAACCTTGGTTTTATTTTCAAAACA-TCGATTTTTCACAATTGGGGATATTCTAAC
1 G-GATACTCCAACCTTGATTTTATTTTCAAAACACT-GATTTTT-ACAATTGGGGATA-CCCAAC
* * *
1687292 CCCGTTATTTTCAAGGGGGTACTCCAA-CCTTGATTTTA-TTTCTAAAACACTAATTTTTCACCA
62 CCCGTTATTTTCAAGGGGATACTCCAACCCTAG-TTTTATTTTC-AAAACACTAATTTTTCACAA
1687355 TCGA
125 TCGA
1687359 GGATACTCCAA
1 GGATACTCCAA
1687370 TCCCGTTATT
Statistics
Matches: 124, Mismatches: 11, Indels: 11
0.85 0.08 0.08
Matches are distributed among these distances:
127 2 0.02
128 37 0.30
129 21 0.17
130 63 0.51
131 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.36
Consensus pattern (128 bp):
GGATACTCCAACCTTGATTTTATTTTCAAAACACTGATTTTTACAATTGGGGATACCCAACCCCG
TTATTTTCAAGGGGATACTCCAACCCTAGTTTTATTTTCAAAACACTAATTTTTCACAATCGA
Found at i:1691985 original size:28 final size:28
Alignment explanation
Indices: 1691929--1692005 Score: 77
Period size: 28 Copynumber: 2.8 Consensus size: 28
1691919 AAAAAAAAAT
* *
1691929 CGGGATTGGAGTATCCCTTCG--GAAGTAA
1 CGGGGTTGGAGTATCCC--CGATGAAATAA
1691957 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
** *
1691985 CAAGGTTGGAGTATCCTCGAT
1 CGGGGTTGGAGTATCCCCGAT
1692006 TGTGAAAAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
26 2 0.05
28 40 0.95
ACGTcount: A:0.26, C:0.18, G:0.31, T:0.25
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:1692129 original size:52 final size:52
Alignment explanation
Indices: 1691990--1692158 Score: 175
Period size: 52 Copynumber: 3.2 Consensus size: 52
1691980 AATAACAAGG
* * * * *
1691990 TTGGAGTATCCTCGATTGT-GAAAAATTGGTATTTTTGGAAATAAAATC-AGA
1 TTGGAGTATCCCCGATTGTGGAAAAATTGGT-GTTTTGAAAATAAAACCGGGA
** *
1692041 GTTGGAGTATCCCCGATTAAAGG-AAAATTGGCGTTTTGAAAATAAAACCGGGA
1 -TTGGAGTATCCCCGATT-GTGGAAAAATTGGTGTTTTGAAAATAAAACCGGGA
* **
1692094 TTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTT-AGTGATAAAACCGGGA
1 TTGGAGTATCCCCGATTGTGGAAAAATTGGTGTTTTGA-AAATAAAACCGGGA
1692146 TTGGAGTATCCCC
1 TTGGAGTATCCCC
1692159 TCGGAAATAA
Statistics
Matches: 98, Mismatches: 14, Indels: 10
0.80 0.11 0.08
Matches are distributed among these distances:
51 3 0.03
52 84 0.86
53 10 0.10
54 1 0.01
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (52 bp):
TTGGAGTATCCCCGATTGTGGAAAAATTGGTGTTTTGAAAATAAAACCGGGA
Found at i:1692181 original size:28 final size:27
Alignment explanation
Indices: 1692142--1692215 Score: 85
Period size: 27 Copynumber: 2.7 Consensus size: 27
1692132 TGATAAAACC
**
1692142 GGGATTGGAGTATCCCCTCGGAAATAACG
1 GGGA-TGGAGTATCCCCGAGG-AATAACG
* *
1692171 GGGATGGAGTATCCCCGATGATTAACG
1 GGGATGGAGTATCCCCGAGGAATAACG
*
1692198 GGGTTGGAGTATCCCCGA
1 GGGATGGAGTATCCCCGA
1692216 TTGTGAAGAA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
27 23 0.57
28 13 0.32
29 4 0.10
ACGTcount: A:0.24, C:0.20, G:0.34, T:0.22
Consensus pattern (27 bp):
GGGATGGAGTATCCCCGAGGAATAACG
Found at i:1692230 original size:212 final size:212
Alignment explanation
Indices: 1691924--1692327 Score: 616
Period size: 212 Copynumber: 1.9 Consensus size: 212
1691914 AGAAGAAAAA
* * * *
1691924 AAAATCGGGATTGGAGTATCCCTTCGGAAGTAACGGGGTTGGAGTATCCCCGATGAAATAACAAG
1 AAAACCGGGATTGGAGTATCCCCTCGGAAATAACGGGGATGGAGTATCCCCGATGAAATAACAAG
* *
1691989 GTTGGAGTATCCTCGATTGTGAAAAATTGGT-ATTTTTGGAAATAAAATCAGAGTTGGAGTATCC
66 GTTGGAGTATCCCCGATTGTGAAAAATTGGTGATTTTTGGAAATAAAATCAGAGTTAGAGTATCC
* *
1692053 CCGATTAAAGGAAAATTGGCGTTTTGAAAATAAAACCGG-GATTGGAGTATCCCCGATTGTGGAA
131 CCGATTAAA-GAAAATTAGCGTTTTGAAAATAAAACCGGAG-TTGGAATATCCCCGATTGTGGAA
1692117 AAATTAGTGTTTTAGTGAT
194 AAATTAGTGTTTTAGTGAT
* **
1692136 AAAACCGGGATTGGAGTATCCCCTCGGAAATAACGGGGATGGAGTATCCCCGATG-ATTAACGGG
1 AAAACCGGGATTGGAGTATCCCCTCGGAAATAACGGGGATGGAGTATCCCCGATGAAATAACAAG
* *
1692200 GTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTAGAGTATC
66 GTTGGAGTATCCCCGATTGTGAA-AAATTGGTGATTTTTGGAAATAAAATCAGAGTTAGAGTATC
* * *
1692265 CCCGATTATAGAAAATTAGTGTTTTGAAAATAAAATCGGAGTTGGAATATCCCCGATTGTGGA
130 CCCGATTAAAGAAAATTAGCGTTTTGAAAATAAAACCGGAGTTGGAATATCCCCGATTGTGGA
1692328 GAATTGAGAA
Statistics
Matches: 173, Mismatches: 16, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
211 28 0.16
212 106 0.61
213 39 0.23
ACGTcount: A:0.32, C:0.13, G:0.27, T:0.28
Consensus pattern (212 bp):
AAAACCGGGATTGGAGTATCCCCTCGGAAATAACGGGGATGGAGTATCCCCGATGAAATAACAAG
GTTGGAGTATCCCCGATTGTGAAAAATTGGTGATTTTTGGAAATAAAATCAGAGTTAGAGTATCC
CCGATTAAAGAAAATTAGCGTTTTGAAAATAAAACCGGAGTTGGAATATCCCCGATTGTGGAAAA
ATTAGTGTTTTAGTGAT
Found at i:1692300 original size:51 final size:53
Alignment explanation
Indices: 1692204--1692322 Score: 154
Period size: 51 Copynumber: 2.3 Consensus size: 53
1692194 AACGGGGTTG
* * *
1692204 GAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTA
1 GAGTATCCCCGATTATGAAGAAATTAGTG-TTTTTGAAAATAAAATCGGAGTTA
*
1692258 GAGTATCCCCGATTAT--AGAAAATTAGTG-TTTTGAAAATAAAATCGGAGTTG
1 GAGTATCCCCGATTATGAAG-AAATTAGTGTTTTTGAAAATAAAATCGGAGTTA
*
1692309 GAATATCCCCGATT
1 GAGTATCCCCGATT
1692323 GTGGAGAATT
Statistics
Matches: 59, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
51 34 0.58
52 2 0.03
53 8 0.14
54 15 0.25
ACGTcount: A:0.34, C:0.12, G:0.23, T:0.32
Consensus pattern (53 bp):
GAGTATCCCCGATTATGAAGAAATTAGTGTTTTTGAAAATAAAATCGGAGTTA
Found at i:1694709 original size:13 final size:13
Alignment explanation
Indices: 1694691--1694716 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1694681 ACAAAGATCC
1694691 ATGTATCGATACA
1 ATGTATCGATACA
1694704 ATGTATCGATACA
1 ATGTATCGATACA
1694717 CAAAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1694780 original size:19 final size:18
Alignment explanation
Indices: 1694756--1694823 Score: 74
Period size: 19 Copynumber: 3.9 Consensus size: 18
1694746 CAGTAGCTAA
1694756 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
1694775 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
*
1694790 -T-TGTATCGATGCAAAAC
1 TTATGTATCGATAC-AAAC
1694807 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
1694824 TTGTTGAATT
Statistics
Matches: 41, Mismatches: 2, Indels: 13
0.73 0.04 0.23
Matches are distributed among these distances:
13 10 0.24
14 1 0.02
16 2 0.05
18 4 0.10
19 24 0.59
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:1694809 original size:32 final size:32
Alignment explanation
Indices: 1694759--1694821 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
1694749 TAGCTAATTA
*
1694759 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
*
1694791 TGTATCGATGCAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
1694822 AATTGTTGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:1698990 original size:21 final size:20
Alignment explanation
Indices: 1698959--1699005 Score: 55
Period size: 18 Copynumber: 2.5 Consensus size: 20
1698949 ATGTTAATAT
1698959 AATTTTTTAAT-AT--TTTA
1 AATTTTTTAATAATAATTTA
1698976 ATATTTTTTAATAATAATTTA
1 A-ATTTTTTAATAATAATTTA
*
1698997 AGTTTTTTA
1 AATTTTTTA
1699006 GGTCTGTCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 1 0.04
18 10 0.40
19 2 0.08
20 7 0.28
21 5 0.20
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (20 bp):
AATTTTTTAATAATAATTTA
Found at i:1700889 original size:2 final size:2
Alignment explanation
Indices: 1700882--1700907 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1700872 AGCGTTTTTA
1700882 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
1700908 GTTGTATCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1702045 original size:21 final size:19
Alignment explanation
Indices: 1701996--1702048 Score: 54
Period size: 21 Copynumber: 2.7 Consensus size: 19
1701986 ATAATTCAAA
1701996 TAATAAAAAA-AATTAATT
1 TAATAAAAAATAATTAATT
**
1702014 TAATTGTAAAATATATTAATAT
1 TAA-TAAAAAATA-ATTAAT-T
1702036 TAATAAAAAATAA
1 TAATAAAAAATAA
1702049 AAATAATATT
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
18 3 0.11
19 5 0.19
20 2 0.07
21 13 0.48
22 4 0.15
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (19 bp):
TAATAAAAAATAATTAATT
Found at i:1702307 original size:14 final size:14
Alignment explanation
Indices: 1702287--1702320 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
1702277 AAAAATTGTG
*
1702287 TTTAAAAGATATAA
1 TTTAAAAAATATAA
1702301 -TTAAAAAATATAA
1 TTTAAAAAATATAA
1702314 TTTAAAA
1 TTTAAAA
1702321 TTTTTTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (14 bp):
TTTAAAAAATATAA
Found at i:1707940 original size:12 final size:12
Alignment explanation
Indices: 1707923--1707947 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1707913 CCCCCCCCCC
1707923 AAAAAAAAACAA
1 AAAAAAAAACAA
1707935 AAAAAAAAACAA
1 AAAAAAAAACAA
1707947 A
1 A
1707948 GAGTGAAAGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAAAAAAACAA
Found at i:1708645 original size:17 final size:18
Alignment explanation
Indices: 1708609--1708646 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
1708599 ATTATTATTT
*
1708609 ATTTAAATATTTTTTATA
1 ATTTAAATATTTTATATA
*
1708627 ATTTAAA-ATTTTATGTA
1 ATTTAAATATTTTATATA
1708644 ATT
1 ATT
1708647 GAATTTAAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (18 bp):
ATTTAAATATTTTATATA
Found at i:1709082 original size:11 final size:11
Alignment explanation
Indices: 1709053--1709083 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
1709043 TTAAAATACT
*
1709053 ATATAAAAATA
1 ATATAAATATA
1709064 ATATAAATATA
1 ATATAAATATA
1709075 ATATAAATA
1 ATATAAATA
1709084 CATAAATATG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
ATATAAATATA
Found at i:1709408 original size:14 final size:14
Alignment explanation
Indices: 1709389--1709418 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1709379 ATATATAAAG
1709389 AAAAAATTAATATA
1 AAAAAATTAATATA
*
1709403 AAAAAATTTATATA
1 AAAAAATTAATATA
1709417 AA
1 AA
1709419 TTTTTAATAC
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:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
AAAAAATTAATATA
Found at i:1709743 original size:23 final size:23
Alignment explanation
Indices: 1709717--1709783 Score: 57
Period size: 23 Copynumber: 2.9 Consensus size: 23
1709707 TTTTAAATAT
1709717 ATTAAAAATAATATATATTAAAA
1 ATTAAAAATAATATATATTAAAA
* *
1709740 ATTAATTAA-AAT-TAAATATAAAA
1 ATTAA-AAATAATATATAT-TAAAA
* *
1709763 ATATAAAAATTATAAATATTA
1 AT-TAAAAATAATATATATTA
1709784 TATACATTTA
Statistics
Matches: 33, Mismatches: 6, Indels: 9
0.69 0.12 0.19
Matches are distributed among these distances:
22 4 0.12
23 17 0.52
24 9 0.27
25 3 0.09
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (23 bp):
ATTAAAAATAATATATATTAAAA
Found at i:1709840 original size:22 final size:22
Alignment explanation
Indices: 1709802--1709856 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
1709792 TATTATATTT
*
1709802 TAAATAATAAAAAATATGAATAA
1 TAAATAA-AAAAAATATAAATAA
*
1709825 TAAATAAAAAATATATAAATAA
1 TAAATAAAAAAAATATAAATAA
*
1709847 CAAATAAAAA
1 TAAATAAAAA
1709857 TAAAAAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
22 22 0.76
23 7 0.24
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.24
Consensus pattern (22 bp):
TAAATAAAAAAAATATAAATAA
Found at i:1709845 original size:19 final size:20
Alignment explanation
Indices: 1709802--1709846 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
1709792 TATTATATTT
1709802 TAAAT-AATAAAAAATATGA
1 TAAATAAATAAAAAATATGA
1709821 -ATAATAAATAAAAAATAT-A
1 TA-AATAAATAAAAAATATGA
1709840 TAAATAA
1 TAAATAA
1709847 CAAATAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
18 1 0.04
19 9 0.39
20 13 0.57
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (20 bp):
TAAATAAATAAAAAATATGA
Found at i:1709853 original size:11 final size:11
Alignment explanation
Indices: 1709802--1709860 Score: 50
Period size: 11 Copynumber: 5.4 Consensus size: 11
1709792 TATTATATTT
1709802 TAAAT-AATAA
1 TAAATAAATAA
*
1709812 AAAATATGAATAA
1 TAAATA--AATAA
*
1709825 TAAATAAAAAA
1 TAAATAAATAA
*
1709836 TATATAAATAA
1 TAAATAAATAA
*
1709847 CAAATAAA-AA
1 TAAATAAATAA
1709857 TAAA
1 TAAA
1709861 AAAAAAATTT
Statistics
Matches: 38, Mismatches: 8, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
10 9 0.24
11 19 0.50
13 10 0.26
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.24
Consensus pattern (11 bp):
TAAATAAATAA
Found at i:1710213 original size:29 final size:27
Alignment explanation
Indices: 1710170--1710306 Score: 101
Period size: 26 Copynumber: 5.1 Consensus size: 27
1710160 AATACGTTTT
*
1710170 ATATTAAATACAATAT-ATATA--AAA
1 ATATTAAATATAATATAATATATTAAA
*
1710194 TTATTAAATATAATATAATATCTAATTAAA
1 ATATTAAATATAATATAATA--T-ATTAAA
* *
1710224 AT-TTAACTATAATATAA-ATATTAAT
1 ATATTAAATATAATATAATATATTAAA
*
1710249 ATATT-AATATTTATATAA-ATATTAAA
1 ATATTAAATA-TAATATAATATATTAAA
* *
1710275 TATATTAAATATATTA-AATATAATTATA
1 -ATATTAAATATAATATAATAT-ATTAAA
1710303 ATAT
1 ATAT
1710307 AATAAAATAT
Statistics
Matches: 90, Mismatches: 11, Indels: 21
0.74 0.09 0.17
Matches are distributed among these distances:
24 14 0.16
25 13 0.14
26 19 0.21
27 15 0.17
28 11 0.12
29 14 0.16
30 4 0.04
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (27 bp):
ATATTAAATATAATATAATATATTAAA
Found at i:1710247 original size:18 final size:17
Alignment explanation
Indices: 1710181--1710316 Score: 65
Period size: 18 Copynumber: 7.9 Consensus size: 17
1710171 TATTAAATAC
1710181 AATAT-ATATAAAATTATT
1 AATATAATAT-AAA-TATT
1710199 AAATATAATAT-AATATCT
1 -AATATAATATAAATAT-T
* * *
1710217 AATTAAAATTTAACTA-T
1 AA-TATAATATAAATATT
1710234 AATATAAATATTAATATATT
1 AATAT-AATA-TAA-ATATT
*
1710254 AATATTTATATAAATATT
1 AATA-TAATATAAATATT
1710272 AA-AT-ATATTAAATA-T
1 AATATAATA-TAAATATT
* *
1710287 ATTA-AATATAATTA-T
1 AATATAATATAAATATT
1710302 AATATAATA-AAATAT
1 AATATAATATAAATAT
1710317 ATAAATTATC
Statistics
Matches: 92, Mismatches: 11, Indels: 31
0.69 0.08 0.23
Matches are distributed among these distances:
15 18 0.20
16 17 0.18
17 12 0.13
18 19 0.21
19 13 0.14
20 12 0.13
21 1 0.01
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (17 bp):
AATATAATATAAATATT
Found at i:1710258 original size:20 final size:19
Alignment explanation
Indices: 1710233--1710307 Score: 66
Period size: 20 Copynumber: 3.9 Consensus size: 19
1710223 AATTTAACTA
1710233 TAATATAAATATTAATATAT
1 TAATATAAATA-TAATATAT
**
1710253 TAATATTTATATAA-ATAT
1 TAATATAAATATAATATAT
*
1710271 TAA-ATATAT-TAAATATAT
1 TAATATAAATAT-AATATAT
*
1710289 TAAATATAATTATAATATA
1 T-AATATAAATATAATATA
1710308 ATAAAATATA
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
16 1 0.02
17 7 0.16
18 12 0.27
19 5 0.11
20 19 0.42
21 1 0.02
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
TAATATAAATATAATATAT
Found at i:1710261 original size:33 final size:33
Alignment explanation
Indices: 1710181--1710310 Score: 99
Period size: 32 Copynumber: 3.8 Consensus size: 33
1710171 TATTAAATAC
* * *
1710181 AATATATATAAAATTATTA-AATATAATATAATA
1 AATATAT-TAAATTTAATATAATATAATATATTA
**
1710214 TCTA-ATTAAAATTTAACTATAATATAA-ATATT-
1 AATATATT-AAATTTAA-TATAATATAATATATTA
1710246 AATATATTAATATTT-ATATAAATATTAAATATATTA
1 AATATATTAA-ATTTAATAT-AATA-T-AATATATTA
*
1710282 AATATATTAAATATAATTATAATATAATA
1 AATATATTAAATTTAA-TATAATATAATA
1710311 AAATATATAA
Statistics
Matches: 77, Mismatches: 8, Indels: 23
0.71 0.07 0.21
Matches are distributed among these distances:
31 4 0.05
32 17 0.22
33 16 0.21
34 13 0.17
35 9 0.12
36 15 0.19
37 3 0.04
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (33 bp):
AATATATTAAATTTAATATAATATAATATATTA
Found at i:1710278 original size:73 final size:72
Alignment explanation
Indices: 1710181--1710316 Score: 170
Period size: 73 Copynumber: 1.9 Consensus size: 72
1710171 TATTAAATAC
*
1710181 AATATATATAAAATTATTAAATATAATATAATAT-CTAATTAAAATT-TAACTATAATATAAATA
1 AATATATATAAAATTATTAAATATAATA-AATATACTAAATAAAATTATAA-TATAATA-AAATA
1710244 TTAATATATT
63 TTAATATATT
* * * *
1710254 AATATTTATATAAA-TATTAAATATATTAAATATATTAAATATAATTATAATATAATAAAATAT
1 AATATATATA-AAATTATTAAATATAATAAATATACTAAATAAAATTATAATATAATAAAATAT
1710317 ATAAATTATC
Statistics
Matches: 55, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
72 11 0.20
73 38 0.69
74 6 0.11
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (72 bp):
AATATATATAAAATTATTAAATATAATAAATATACTAAATAAAATTATAATATAATAAAATATTA
ATATATT
Found at i:1710307 original size:29 final size:28
Alignment explanation
Indices: 1710169--1710320 Score: 114
Period size: 29 Copynumber: 5.7 Consensus size: 28
1710159 AAATACGTTT
*
1710169 TATATTAAATACAATAT-ATATA--AAA
1 TATATTAAATATAATATAATATATTAAA
1710194 T-TATTAAATATAATATAATATCTAATTAAA
1 TATATTAAATATAATATAATA--T-ATTAAA
*
1710224 -AT-TTAACTATAATATAA-ATATT-AA
1 TATATTAAATATAATATAATATATTAAA
*
1710248 TATATT-AATATTTATATAA-ATATTAAA
1 TATATTAAATA-TAATATAATATATTAAA
*
1710275 TATATTAAATATATTA-AATATAATTATAA
1 TATATTAAATATAATATAATAT-ATTA-AA
*
1710304 TATAATAAA-AT-ATATAA
1 TATATTAAATATAATATAA
1710321 ATTATCAAAT
Statistics
Matches: 103, Mismatches: 8, Indels: 29
0.74 0.06 0.21
Matches are distributed among these distances:
24 16 0.16
25 12 0.12
26 17 0.17
27 16 0.16
28 14 0.14
29 24 0.23
30 4 0.04
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (28 bp):
TATATTAAATATAATATAATATATTAAA
Found at i:1710995 original size:20 final size:19
Alignment explanation
Indices: 1710963--1711022 Score: 63
Period size: 19 Copynumber: 3.2 Consensus size: 19
1710953 AAATTTATGT
1710963 AAAATAT-AAAATATTTTA
1 AAAATATAAAAATATTTTA
*
1710981 AAAATA-AATATAATA-TATA
1 AAAATATAA-A-AATATTTTA
1711000 AAAATATAAAAATATTATTA
1 AAAATATAAAAATATT-TTA
1711020 AAA
1 AAA
1711023 TATGCTAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
18 11 0.32
19 12 0.35
20 11 0.32
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
AAAATATAAAAATATTTTA
Found at i:1711025 original size:27 final size:30
Alignment explanation
Indices: 1710946--1711025 Score: 80
Period size: 29 Copynumber: 2.8 Consensus size: 30
1710936 TATAATGTAA
* *
1710946 ATTATTAAAAT-TTATGTAAAATATAAAAT
1 ATTATAAAAATATTATATAAAATATAAAAT
* * *
1710975 ATTTTAAAAATA-AATATAATATATAAAA-
1 ATTATAAAAATATTATATAAAATATAAAAT
1711003 A-TATAAAAATATTAT-TAAAATAT
1 ATTATAAAAATATTATATAAAATAT
1711026 GCTAATTATC
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
27 16 0.39
28 3 0.07
29 22 0.54
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (30 bp):
ATTATAAAAATATTATATAAAATATAAAAT
Found at i:1711648 original size:19 final size:19
Alignment explanation
Indices: 1711624--1711660 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1711614 AAAATGCTTA
* *
1711624 AAAAATTTAGATATAATAG
1 AAAAATATAAATATAATAG
1711643 AAAAATATAAATATAATA
1 AAAAATATAAATATAATA
1711661 TATTTAATAA
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:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (19 bp):
AAAAATATAAATATAATAG
Found at i:1713448 original size:6 final size:6
Alignment explanation
Indices: 1713434--1713495 Score: 61
Period size: 6 Copynumber: 10.0 Consensus size: 6
1713424 TAAAAACTTT
* * * *
1713434 AATTCA AATTTA AATTTA AATATA AATAATTA AATTTA AAATTA AATATA
1 AATTTA AATTTA AATTTA AATTTA AAT--TTA AATTTA AATTTA AATTTA
*
1713484 AAATTA AATTTA
1 AATTTA AATTTA
1713496 TTTTTTATTA
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
6 40 0.89
8 5 0.11
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (6 bp):
AATTTA
Found at i:1713764 original size:2 final size:2
Alignment explanation
Indices: 1713757--1713782 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1713747 CCCTTTTTGG
1713757 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
1713783 AATTAATACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1715337 original size:25 final size:24
Alignment explanation
Indices: 1715309--1715366 Score: 73
Period size: 25 Copynumber: 2.4 Consensus size: 24
1715299 ATATTTAAAA
*
1715309 AATTATATATATTTTTTAATATATT
1 AATTATATATATTTTATAA-ATATT
* *
1715334 AATTATTTATATTTTATAAATTTT
1 AATTATATATATTTTATAAATATT
1715358 AA-TATATAT
1 AATTATATAT
1715367 TTATTAGACT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
23 6 0.21
24 6 0.21
25 17 0.59
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (24 bp):
AATTATATATATTTTATAAATATT
Found at i:1715460 original size:16 final size:16
Alignment explanation
Indices: 1715439--1715469 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1715429 GGATTTAAAT
1715439 GTTATATTTTGTGAAC
1 GTTATATTTTGTGAAC
1715455 GTTATATTTTGTGAA
1 GTTATATTTTGTGAA
1715470 TCAAGTGAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.26, C:0.03, G:0.19, T:0.52
Consensus pattern (16 bp):
GTTATATTTTGTGAAC
Found at i:1715535 original size:22 final size:23
Alignment explanation
Indices: 1715507--1715550 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
1715497 ATAAAATAAT
*
1715507 TATATAAAT-TTAATTATAAAAA
1 TATATAAATATTAATAATAAAAA
1715529 TATATAAATATTAATAATAAAA
1 TATATAAATATTAATAATAAAA
1715551 TAATTTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (23 bp):
TATATAAATATTAATAATAAAAA
Found at i:1715713 original size:11 final size:12
Alignment explanation
Indices: 1715694--1715728 Score: 54
Period size: 11 Copynumber: 3.0 Consensus size: 12
1715684 TTTATCATAA
1715694 TTTATATTATAT
1 TTTATATTATAT
*
1715706 TTTA-ATTATTT
1 TTTATATTATAT
1715717 TTTATATTATAT
1 TTTATATTATAT
1715729 AATAAAAGCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
TTTATATTATAT
Found at i:1717255 original size:15 final size:14
Alignment explanation
Indices: 1717226--1717275 Score: 57
Period size: 15 Copynumber: 3.5 Consensus size: 14
1717216 TTATTTAATA
*
1717226 ATAATATTATGTAT
1 ATAATATTATATAT
1717240 ATAATAATTATATAT
1 ATAAT-ATTATATAT
*
1717255 ATAAT-TGATATAT
1 ATAATATTATATAT
1717268 ATATATAT
1 ATA-ATAT
1717276 ACAAATAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
13 10 0.32
14 7 0.23
15 14 0.45
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (14 bp):
ATAATATTATATAT
Found at i:1717269 original size:13 final size:12
Alignment explanation
Indices: 1717237--1717270 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
1717227 TAATATTATG
1717237 TATATA-ATAAT
1 TATATATATAAT
1717248 TATATATATAAT
1 TATATATATAAT
1717260 TGATATATATA
1 T-ATATATATA
1717271 TATATACAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 6 0.29
12 6 0.29
13 9 0.43
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (12 bp):
TATATATATAAT
Found at i:1720547 original size:11 final size:11
Alignment explanation
Indices: 1720531--1720555 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1720521 TTTTGATTAC
1720531 ATTACATCAGA
1 ATTACATCAGA
1720542 ATTACATCAGA
1 ATTACATCAGA
1720553 ATT
1 ATT
1720556 TGAGGAAAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.16, G:0.08, T:0.32
Consensus pattern (11 bp):
ATTACATCAGA
Found at i:1721293 original size:39 final size:38
Alignment explanation
Indices: 1721250--1721360 Score: 102
Period size: 39 Copynumber: 3.2 Consensus size: 38
1721240 AAAATAATAT
1721250 TTAATTAAATTTTAAAAAATTAAGGTATGATTTGTAAAA
1 TTAATTAAATTTTAAAAAATTAAGGTAT-ATTTGTAAAA
*
1721289 TTAA-T---TGTT-AAAAA-TAA---A-A-TT-TAATAA
1 TTAATTAAATTTTAAAAAATTAAGGTATATTTGTAA-AA
1721316 TTAATTAAATTTTAAAAAATTAAGGTATAATTTGTAAAA
1 TTAATTAAATTTTAAAAAATTAAGGTAT-ATTTGTAAAA
1721355 TTAATT
1 TTAATT
1721361 GTTAAAATAA
Statistics
Matches: 56, Mismatches: 2, Indels: 28
0.65 0.02 0.33
Matches are distributed among these distances:
26 3 0.05
27 8 0.14
28 2 0.04
30 1 0.02
31 3 0.05
32 5 0.09
33 6 0.11
34 5 0.09
35 3 0.05
36 1 0.02
38 2 0.04
39 14 0.25
40 3 0.05
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.42
Consensus pattern (38 bp):
TTAATTAAATTTTAAAAAATTAAGGTATATTTGTAAAA
Found at i:1721393 original size:66 final size:66
Alignment explanation
Indices: 1721221--1721367 Score: 240
Period size: 66 Copynumber: 2.2 Consensus size: 66
1721211 TATATTAATT
* ** * *
1721221 ATTATTTGTTATAAAATAAAAAATAATATTTAATTAAATTTTAAAAAATTAAGGTATGATTTGTA
1 ATTAATTGTTA-AAAATAAAATTTAATAATTAATTAAATTTTAAAAAATTAAGGTATAATTTGTA
1721286 AA
65 AA
1721288 ATTAATTGTTAAAAATAAAATTTAATAATTAATTAAATTTTAAAAAATTAAGGTATAATTTGTAA
1 ATTAATTGTTAAAAATAAAATTTAATAATTAATTAAATTTTAAAAAATTAAGGTATAATTTGTAA
1721353 A
66 A
1721354 ATTAATTGTTAAAA
1 ATTAATTGTTAAAA
1721368 TAATTTTTAT
Statistics
Matches: 75, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
66 65 0.87
67 10 0.13
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (66 bp):
ATTAATTGTTAAAAATAAAATTTAATAATTAATTAAATTTTAAAAAATTAAGGTATAATTTGTAA
A
Found at i:1721482 original size:15 final size:15
Alignment explanation
Indices: 1721462--1721490 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1721452 AAATTAATTT
1721462 AATTTATTTTTATTA
1 AATTTATTTTTATTA
1721477 AATTTATTTTTATT
1 AATTTATTTTTATT
1721491 TTATTATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
AATTTATTTTTATTA
Found at i:1721482 original size:20 final size:20
Alignment explanation
Indices: 1721457--1721496 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1721447 TTATAAAATT
1721457 AATTTAATTTAT-TTTTATTA
1 AATTT-ATTTATATTTTATTA
*
1721477 AATTTATTTTTATTTTATTA
1 AATTTATTTATATTTTATTA
1721497 TATATAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (20 bp):
AATTTATTTATATTTTATTA
Found at i:1721488 original size:26 final size:26
Alignment explanation
Indices: 1721459--1721508 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
1721449 ATAAAATTAA
*
1721459 TTTAATTTATT-TTTATTAAATTTATT
1 TTTAATTTATTATATA-TAAATTTATT
*
1721485 TTTATTTTATTATATATAAATTTA
1 TTTAATTTATTATATATAAATTTA
1721509 AAATATTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 18 0.86
27 3 0.14
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (26 bp):
TTTAATTTATTATATATAAATTTATT
Found at i:1721508 original size:20 final size:21
Alignment explanation
Indices: 1721462--1721508 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 21
1721452 AAATTAATTT
*
1721462 AATTTATTTTTATTAAATTTA
1 AATTTATTTTTATTAAATATA
** *
1721483 TTTTTA-TTTTATTATATATA
1 AATTTATTTTTATTAAATATA
1721503 AATTTA
1 AATTTA
1721509 AAATATTAAT
Statistics
Matches: 20, Mismatches: 6, Indels: 1
0.74 0.22 0.04
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
AATTTATTTTTATTAAATATA
Found at i:1721522 original size:22 final size:22
Alignment explanation
Indices: 1721497--1721550 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
1721487 TATTTTATTA
*
1721497 TATATAAATTTAAAATATTAAT
1 TATAAAAATTTAAAATATTAAT
* * *
1721519 TATAAAAATTTTAAATTTTAAA
1 TATAAAAATTTAAAATATTAAT
1721541 T-TAAAAATTT
1 TATAAAAATTT
1721551 TCCCCCAACC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
21 9 0.32
22 19 0.68
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
TATAAAAATTTAAAATATTAAT
Found at i:1725240 original size:61 final size:61
Alignment explanation
Indices: 1725167--1725365 Score: 371
Period size: 61 Copynumber: 3.3 Consensus size: 61
1725157 TCACAAATTT
* *
1725167 TATAACTTTCAAATTTCAATGGTTTTTTTTGAACATTAAATTTACAATTATATAATTTTTA
1 TATAACTTTCAAATTTCAATGGCTTTTTTCGAACATTAAATTTACAATTATATAATTTTTA
*
1725228 TATAACTTTCAAATTTCAATGGCTTTTTTCAAACATTAAATTTACAATTATATAATTTTTA
1 TATAACTTTCAAATTTCAATGGCTTTTTTCGAACATTAAATTTACAATTATATAATTTTTA
1725289 TATAACTTTCAAATTTCAATGGCTTTTTTCGAACATTAAATTTACAATTATATAATTTTTA
1 TATAACTTTCAAATTTCAATGGCTTTTTTCGAACATTAAATTTACAATTATATAATTTTTA
1725350 TATAACTTTCAAATTT
1 TATAACTTTCAAATTT
1725366 ACCATTTGAA
Statistics
Matches: 134, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
61 134 1.00
ACGTcount: A:0.37, C:0.11, G:0.04, T:0.49
Consensus pattern (61 bp):
TATAACTTTCAAATTTCAATGGCTTTTTTCGAACATTAAATTTACAATTATATAATTTTTA
Done.