Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold92
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: 2337674
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 499 characters in sequence are not A, C, G, or T
File 13 of 19
Found at i:1582581 original size:3 final size:3
Alignment explanation
Indices: 1582575--1582625 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
1582565 CTACTACTAC
1582575 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1582623 TAT
1 TAT
1582626 GTTTTGTATT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1583195 original size:18 final size:20
Alignment explanation
Indices: 1583172--1583209 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1583162 GTTTTAGATT
1583172 TTTTAA-AT-TATATATGTA
1 TTTTAATATATATATATGTA
1583190 TTTTAATATATATATATGTA
1 TTTTAATATATATATATGTA
1583210 ATTAATTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 6 0.33
19 2 0.11
20 10 0.56
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.55
Consensus pattern (20 bp):
TTTTAATATATATATATGTA
Found at i:1583380 original size:19 final size:20
Alignment explanation
Indices: 1583339--1583382 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
1583329 CAGACAGTTT
*
1583339 AAAAATTAACTTAGAAAATA
1 AAAAATTAACTAAGAAAATA
1583359 AAAAATTAA-TAAGGAAAA-A
1 AAAAATTAACTAA-GAAAATA
1583378 AAAAA
1 AAAAA
1583383 GCAACAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.73, C:0.02, G:0.07, T:0.18
Consensus pattern (20 bp):
AAAAATTAACTAAGAAAATA
Found at i:1583458 original size:2 final size:2
Alignment explanation
Indices: 1583451--1583522 Score: 50
Period size: 2 Copynumber: 38.5 Consensus size: 2
1583441 CGAAAAGTGG
*
1583451 TA TA TA TA CT- TA TA TT TA T- TA -A TA T- TA -A TA TA TA TA -A
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
1583488 TA T- TGA TA AA TT TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1583523 GATTTTAGTG
Statistics
Matches: 55, Mismatches: 6, Indels: 18
0.70 0.08 0.23
Matches are distributed among these distances:
1 7 0.13
2 46 0.84
3 2 0.04
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1584268 original size:2 final size:2
Alignment explanation
Indices: 1584256--1584308 Score: 88
Period size: 2 Copynumber: 26.5 Consensus size: 2
1584246 TGTCATCATA
* *
1584256 AT AT AT TT AT AT AT AC 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 AT
1584298 AT AT AT AT AT A
1 AT AT AT AT AT A
1584309 ATCAAGTAAT
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:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1589918 original size:29 final size:29
Alignment explanation
Indices: 1589859--1589941 Score: 87
Period size: 29 Copynumber: 2.8 Consensus size: 29
1589849 TATTTGACAT
* *
1589859 TAAACAAAATTACATAAATACAATAAAATA
1 TAAA-AAAATTATATAAATATAATAAAATA
* * **
1589889 TTAAAATATTATATAAATATAATACGATA
1 TAAAAAAATTATATAAATATAATAAAATA
1589918 TAAAAAAATTAT-TATAATATAATA
1 TAAAAAAATTATATA-AATATAATA
1589942 TACAACATAA
Statistics
Matches: 44, Mismatches: 8, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
28 2 0.05
29 39 0.89
30 3 0.07
ACGTcount: A:0.61, C:0.05, G:0.01, T:0.33
Consensus pattern (29 bp):
TAAAAAAATTATATAAATATAATAAAATA
Found at i:1591073 original size:14 final size:14
Alignment explanation
Indices: 1591056--1591090 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
1591046 AATTTTATTT
1591056 AAAT-TTAATTATAA
1 AAATATTAA-TATAA
1591070 AAATATTAATATAA
1 AAATATTAATATAA
1591084 AAATATT
1 AAATATT
1591091 TTTAATATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 16 0.80
15 4 0.20
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
AAATATTAATATAA
Found at i:1591320 original size:9 final size:8
Alignment explanation
Indices: 1591258--1591330 Score: 50
Period size: 7 Copynumber: 9.5 Consensus size: 8
1591248 CATATACAAT
1591258 TAAAT-TA
1 TAAATATA
1591265 TATAA-ATA
1 TA-AATATA
1591273 T-AATATA
1 TAAATATA
*
1591280 TAAA-AAA
1 TAAATATA
* *
1591287 TAATTAAAA
1 TAAAT-ATA
1591296 TAAA-ATA
1 TAAATATA
1591303 T-AATATA
1 TAAATATA
1591310 TAAATTATA
1 TAAA-TATA
1591319 TAAATATA
1 TAAATATA
1591327 TAAA
1 TAAA
1591331 AGATTTATAA
Statistics
Matches: 53, Mismatches: 4, Indels: 17
0.72 0.05 0.23
Matches are distributed among these distances:
6 4 0.08
7 18 0.34
8 17 0.32
9 14 0.26
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (8 bp):
TAAATATA
Found at i:1591377 original size:32 final size:34
Alignment explanation
Indices: 1591309--1591374 Score: 102
Period size: 31 Copynumber: 2.0 Consensus size: 34
1591299 AATATAATAT
1591309 ATAAATTATATAAATATATAAAAGATTTATAAAA
1 ATAAATTATATAAATATATAAAAGATTTATAAAA
*
1591343 ATAAATTAT-T-AATATATTAAA-ATTTATAAAA
1 ATAAATTATATAAATATATAAAAGATTTATAAAA
1591374 A
1 A
1591375 ATATAATATT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
31 11 0.35
32 10 0.32
33 1 0.03
34 9 0.29
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (34 bp):
ATAAATTATATAAATATATAAAAGATTTATAAAA
Found at i:1591686 original size:16 final size:14
Alignment explanation
Indices: 1591656--1591682 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1591646 ATGATAGAAA
1591656 ATTAAATGAAAAAT
1 ATTAAATGAAAAAT
1591670 ATTAAATGAAAAA
1 ATTAAATGAAAAA
1591683 AATAATTATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (14 bp):
ATTAAATGAAAAAT
Found at i:1593373 original size:16 final size:18
Alignment explanation
Indices: 1593338--1593374 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
1593328 ATTAATCAAT
1593338 ATTTCATTTGAAATAAAA
1 ATTTCATTTGAAATAAAA
*
1593356 ATTT-ATTT-AAATACAA
1 ATTTCATTTGAAATAAAA
1593372 ATT
1 ATT
1593375 AAAATATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 10 0.56
17 4 0.22
18 4 0.22
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.43
Consensus pattern (18 bp):
ATTTCATTTGAAATAAAA
Found at i:1596192 original size:20 final size:20
Alignment explanation
Indices: 1596165--1596208 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
1596155 ATTATAATTA
*
1596165 TAAT-TATAATATTATATAT
1 TAATATATAATATTAGATAT
* *
1596184 TAATATATATTTTTAGATAT
1 TAATATATAATATTAGATAT
1596204 TAATA
1 TAATA
1596209 ATTTATTTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (20 bp):
TAATATATAATATTAGATAT
Found at i:1596255 original size:27 final size:27
Alignment explanation
Indices: 1596225--1596277 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
1596215 TTTATATAAA
1596225 TTTTAAAATATTTTTAA-TATTTTTATG
1 TTTTAAAATA-TTTTAATTATTTTTATG
**
1596252 TTTTATTATATTTTAATTATTTTTAT
1 TTTTAAAATATTTTAATTATTTTTAT
1596278 ATTATATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 6 0.26
27 17 0.74
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (27 bp):
TTTTAAAATATTTTAATTATTTTTATG
Found at i:1596277 original size:17 final size:18
Alignment explanation
Indices: 1596233--1596280 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
1596223 AATTTTAAAA
*
1596233 TATTTTTAATATTTTTATG
1 TATTTTT-ATATTTTAATG
1596252 T-TTTATTATATTTTAAT-
1 TATTT-TTATATTTTAATG
1596269 TATTTTTATATT
1 TATTTTTATATT
1596281 ATATTATATA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 8 0.31
18 15 0.58
19 3 0.12
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (18 bp):
TATTTTTATATTTTAATG
Found at i:1596285 original size:27 final size:26
Alignment explanation
Indices: 1596236--1596289 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 26
1596226 TTTAAAATAT
* *
1596236 TTTTAATATTTTTATGTTTTATTATA
1 TTTTAATATTTTTATATTATATTATA
1596262 TTTTAATTATTTTTATATTATATTATA
1 TTTTAA-TATTTTTATATTATATTATA
1596289 T
1 T
1596290 AATTTAATGA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 6 0.24
27 19 0.76
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.69
Consensus pattern (26 bp):
TTTTAATATTTTTATATTATATTATA
Found at i:1596823 original size:24 final size:24
Alignment explanation
Indices: 1596757--1596824 Score: 68
Period size: 24 Copynumber: 2.8 Consensus size: 24
1596747 GTAGACAATT
* *
1596757 TATAATGTTAAATATAATATAATAA
1 TATAAT-TAAAATATAATATAAAAA
*
1596782 TATAATTAAAATAAAATATAAAAA
1 TATAATTAAAATATAATATAAAAA
1596806 TGAT-A-TAAATATATAATAT
1 T-ATAATTAAA-ATATAATAT
1596825 TTTAAAATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
23 4 0.11
24 25 0.68
25 8 0.22
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (24 bp):
TATAATTAAAATATAATATAAAAA
Found at i:1596845 original size:30 final size:27
Alignment explanation
Indices: 1596808--1596933 Score: 96
Period size: 27 Copynumber: 4.5 Consensus size: 27
1596798 TATAAAAATG
1596808 ATATAAATATATAATATTTTAAAATTTA
1 ATATAAATATATAATATTTT-AAATTTA
* *
1596836 TATTATAAAT-TATTAAAATATTAAATTTA
1 -A-TATAAATATA-TAATATTTTAAATTTA
* * * *
1596865 ATATTAATATATTATATTTTTAATATA
1 ATATAAATATATAATATTTTAAATTTA
* *
1596892 ATTATAATATAATATAA-A-TATAAATATA
1 A-TATAA-AT-ATATAATATTTTAAATTTA
1596920 ATATAAATATATAA
1 ATATAAATATATAA
1596934 ATTATCATAT
Statistics
Matches: 79, Mismatches: 12, Indels: 16
0.74 0.11 0.15
Matches are distributed among these distances:
25 6 0.08
26 2 0.03
27 23 0.29
28 16 0.20
29 13 0.16
30 19 0.24
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (27 bp):
ATATAAATATATAATATTTTAAATTTA
Found at i:1596871 original size:20 final size:20
Alignment explanation
Indices: 1596846--1596883 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1596836 TATTATAAAT
1596846 TATTAAAATATTAAATTTAA
1 TATTAAAATATTAAATTTAA
* *
1596866 TATTAATATATTATATTT
1 TATTAAAATATTAAATTT
1596884 TTAATATAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
TATTAAAATATTAAATTTAA
Found at i:1596899 original size:11 final size:11
Alignment explanation
Indices: 1596767--1596945 Score: 76
Period size: 11 Copynumber: 16.6 Consensus size: 11
1596757 TATAATGTTA
1596767 AATATAATATAAT
1 AATATAAT-T-AT
*
1596780 AATATAATTAA
1 AATATAATTAT
*
1596791 AATA-AAATAT
1 AATATAATTAT
*
1596801 AA-A-AATGAT
1 AATATAATTAT
1596810 -ATA-AATATAT
1 AATATAAT-TAT
* *
1596820 AATAT-TTTAA
1 AATATAATTAT
*
1596830 AATTTATATTAT
1 AATATA-ATTAT
* *
1596842 AA-ATTATTAA
1 AATATAATTAT
1596852 AATATTAAATT-T
1 AATA-T-AATTAT
1596864 AATATTAA-TAT
1 AATA-TAATTAT
* * *
1596875 ATTATATTTTT
1 AATATAATTAT
1596886 AATATAATTAT
1 AATATAATTAT
1596897 AATATAA-TAT
1 AATATAATTAT
*
1596907 AAATATAAATAT
1 -AATATAATTAT
*
1596919 AATATAAATAT
1 AATATAATTAT
1596930 -ATA-AATTAT
1 AATATAATTAT
*
1596939 CATATAA
1 AATATAA
1596946 ATACATGCAC
Statistics
Matches: 128, Mismatches: 23, Indels: 32
0.70 0.13 0.17
Matches are distributed among these distances:
8 1 0.01
9 14 0.11
10 32 0.25
11 54 0.42
12 16 0.12
13 11 0.09
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (11 bp):
AATATAATTAT
Found at i:1596930 original size:6 final size:6
Alignment explanation
Indices: 1596886--1596930 Score: 60
Period size: 6 Copynumber: 8.0 Consensus size: 6
1596876 TTATATTTTT
*
1596886 AATATA ATTAT- AATAT- AATATA AATATA AATAT- AATATA AATATA
1 AATATA AATATA AATATA AATATA AATATA AATATA AATATA AATATA
1596931 TAAATTATCA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
5 14 0.40
6 21 0.60
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (6 bp):
AATATA
Found at i:1597088 original size:19 final size:20
Alignment explanation
Indices: 1597049--1597093 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
1597039 AATTCTATAA
1597049 TTTATATATTTATATTAAAT
1 TTTATATATTTATATTAAAT
*
1597069 TTTATATTTTTATATT-AAT
1 TTTATATATTTATATTAAAT
1597088 TTTATA
1 TTTATA
1597094 AATATAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 9 0.38
20 15 0.62
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTATATATTTATATTAAAT
Found at i:1597160 original size:22 final size:22
Alignment explanation
Indices: 1597135--1597183 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
1597125 AAATATTTTG
*
1597135 ATATTTA-ATTTTAAATATAA-
1 ATATTTATATATTAAATATAAT
*
1597155 ATATATTATATATTAAATATATT
1 ATAT-TTATATATTAAATATAAT
1597178 ATATTT
1 ATATTT
1597184 GTGTTATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 4 0.17
21 3 0.12
22 13 0.54
23 4 0.17
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
ATATTTATATATTAAATATAAT
Found at i:1597170 original size:28 final size:28
Alignment explanation
Indices: 1597079--1597170 Score: 84
Period size: 28 Copynumber: 3.3 Consensus size: 28
1597069 TTTATATTTT
1597079 TATATTAATTTTATAAATATAAATATA--A
1 TATATTAA-TTT-TAAATATAAATATATTA
** * *
1597107 TA-AAAAATTTTAAAAAATAAATATTTTGA
1 TATATTAATTTT-AAATATAAATATATT-A
1597136 TAT-TTAATTTTAAATATAAATATATTA
1 TATATTAATTTTAAATATAAATATATTA
1597163 TATATTAA
1 TATATTAA
1597171 ATATATTATA
Statistics
Matches: 50, Mismatches: 8, Indels: 12
0.71 0.11 0.17
Matches are distributed among these distances:
25 1 0.02
26 14 0.28
27 7 0.14
28 19 0.38
29 9 0.18
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (28 bp):
TATATTAATTTTAAATATAAATATATTA
Found at i:1597312 original size:12 final size:13
Alignment explanation
Indices: 1597295--1597326 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
1597285 ATTCCAGACA
1597295 AAATAAAAT-AAT
1 AAATAAAATAAAT
1597307 AAAT-AAATAAAT
1 AAATAAAATAAAT
1597319 AAATAAAA
1 AAATAAAA
1597327 CCCCAAAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 4 0.22
12 11 0.61
13 3 0.17
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (13 bp):
AAATAAAATAAAT
Found at i:1598086 original size:20 final size:20
Alignment explanation
Indices: 1598061--1598103 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
1598051 AAATAGGTCT
*
1598061 ATAAATATCATATAAATAAG
1 ATAAATATAATATAAATAAG
*
1598081 ATAAATATAATATAAATATG
1 ATAAATATAATATAAATAAG
1598101 ATA
1 ATA
1598104 TTATAAGTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (20 bp):
ATAAATATAATATAAATAAG
Found at i:1598149 original size:23 final size:23
Alignment explanation
Indices: 1598116--1598186 Score: 65
Period size: 24 Copynumber: 3.0 Consensus size: 23
1598106 ATAAGTGAAA
*
1598116 TTAAA-AAATAATTAT-ATATTT
1 TTAAATAAATAATTATAATATAT
* *
1598137 TTAAATATGATAAATATAATATAT
1 TTAAATA-AATAATTATAATATAT
*
1598161 TTATATAAATAATTATTAAGTATAT
1 TTAAATAAATAATTA-TAA-TATAT
1598186 T
1 T
1598187 GATAATATTT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
21 5 0.13
22 1 0.03
23 13 0.33
24 14 0.36
25 6 0.15
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (23 bp):
TTAAATAAATAATTATAATATAT
Found at i:1598696 original size:20 final size:22
Alignment explanation
Indices: 1598671--1598715 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
1598661 TAAGTTTTAA
*
1598671 ATAT-AATTTTAA-ATAAAAAT
1 ATATAAATATTAATATAAAAAT
1598691 ATATAAATATTAATATAAAAAT
1 ATATAAATATTAATATAAAAAT
1598713 ATA
1 ATA
1598716 ATTTTAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 4 0.18
21 7 0.32
22 11 0.50
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
ATATAAATATTAATATAAAAAT
Found at i:1598716 original size:20 final size:20
Alignment explanation
Indices: 1598669--1598716 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
1598659 ATTAAGTTTT
*
1598669 AAATAT-AATTTTAAATAAA
1 AAATATAAATATTAAATAAA
1598688 AATATATAAATATT-AATATAA
1 AA-ATATAAATATTAAATA-AA
1598709 AAATATAA
1 AAATATAA
1598717 TTTTAATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 2 0.08
20 14 0.56
21 9 0.36
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (20 bp):
AAATATAAATATTAAATAAA
Found at i:1598735 original size:31 final size:32
Alignment explanation
Indices: 1598698--1598759 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 32
1598688 AATATATAAA
*
1598698 TATTAATATAAAAAT-ATAATTTTAATTTTTT
1 TATTAATATAAAAATAATAATTTTAAATTTTT
* **
1598729 TATTAATTTATCAATAATAATTTTAAATTTT
1 TATTAATATAAAAATAATAATTTTAAATTTT
1598760 AATTCGGACC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
31 12 0.46
32 14 0.54
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (32 bp):
TATTAATATAAAAATAATAATTTTAAATTTTT
Found at i:1600154 original size:20 final size:19
Alignment explanation
Indices: 1600129--1600166 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1600119 TTAACCAGTG
1600129 ATTTTTATAATTATTATAAT
1 ATTTTTATAATT-TTATAAT
*
1600149 ATTTTTTTAATTTTATAA
1 ATTTTTATAATTTTATAA
1600167 AAATAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (19 bp):
ATTTTTATAATTTTATAAT
Found at i:1600462 original size:21 final size:22
Alignment explanation
Indices: 1600424--1600468 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
1600414 TCGATTAATG
*
1600424 ATTATTTATAAATATTTT-TAA
1 ATTATTTAAAAATATTTTATAA
1600445 ATTATTTAAATAAT-TTTTATAA
1 ATTATTTAAA-AATATTTTATAA
1600467 AT
1 AT
1600469 AAATGAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
ATTATTTAAAAATATTTTATAA
Found at i:1602040 original size:2 final size:2
Alignment explanation
Indices: 1602033--1602058 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1602023 GATTATGATG
1602033 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
1602059 GTAGGATGAA
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:1602173 original size:1 final size:1
Alignment explanation
Indices: 1602167--1602197 Score: 53
Period size: 1 Copynumber: 31.0 Consensus size: 1
1602157 GGAGGGGTTC
*
1602167 GGGGGGGGGGGGGGGGGGGGGGGGAGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
1602198 AGAGCATAGC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.03, C:0.00, G:0.97, T:0.00
Consensus pattern (1 bp):
G
Found at i:1602595 original size:14 final size:14
Alignment explanation
Indices: 1602549--1602597 Score: 53
Period size: 14 Copynumber: 3.3 Consensus size: 14
1602539 AGTTATAATT
1602549 ATATATAAATTTTA
1 ATATATAAATTTTA
*
1602563 ATATTTAATAATTTATA
1 ATATAT-A-AATTT-TA
*
1602580 ATATATAAATATTA
1 ATATATAAATTTTA
1602594 ATAT
1 ATAT
1602598 TTTTTAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
14 11 0.38
15 5 0.17
16 6 0.21
17 7 0.24
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
ATATATAAATTTTA
Found at i:1603987 original size:2 final size:2
Alignment explanation
Indices: 1603980--1604007 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1603970 CCTGGCTTTC
1603980 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
1604008 TTCACTTTAG
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:1606942 original size:49 final size:51
Alignment explanation
Indices: 1606870--1606965 Score: 169
Period size: 49 Copynumber: 1.9 Consensus size: 51
1606860 CTTCTTTTTT
1606870 TAATTTTCTTTTATTAATGAATTATAT-ATA-ATATATACATATATACATA
1 TAATTTTCTTTTATTAATGAATTATATAATATATATATACATATATACATA
*
1606919 TAATTTTCTTTTATTAATGAATTATATAATATATATATATATATATA
1 TAATTTTCTTTTATTAATGAATTATATAATATATATATACATATATA
1606966 GTTTTCATGA
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
49 27 0.61
50 3 0.07
51 14 0.32
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.51
Consensus pattern (51 bp):
TAATTTTCTTTTATTAATGAATTATATAATATATATATACATATATACATA
Found at i:1607106 original size:10 final size:10
Alignment explanation
Indices: 1607087--1607146 Score: 59
Period size: 10 Copynumber: 5.8 Consensus size: 10
1607077 GGAAAATCCA
1607087 ATAT-CATAC
1 ATATACATAC
1607096 ATATACATAC
1 ATATACATAC
*
1607106 ATATATATATAC
1 --ATATACATAC
1607118 ATATACATAC
1 ATATACATAC
* *
1607128 ATATATATAT
1 ATATACATAC
1607138 ATATCACAT
1 ATAT-ACAT
1607147 CTTGATATAA
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
9 4 0.10
10 26 0.62
11 3 0.07
12 9 0.21
ACGTcount: A:0.48, C:0.15, G:0.00, T:0.37
Consensus pattern (10 bp):
ATATACATAC
Found at i:1607117 original size:22 final size:22
Alignment explanation
Indices: 1607087--1607138 Score: 95
Period size: 22 Copynumber: 2.3 Consensus size: 22
1607077 GGAAAATCCA
1607087 ATATCATACATATACATACATAT
1 ATAT-ATACATATACATACATAT
1607110 ATATATACATATACATACATAT
1 ATATATACATATACATACATAT
1607132 ATATATA
1 ATATATA
1607139 TATCACATCT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 25 0.86
23 4 0.14
ACGTcount: A:0.50, C:0.13, G:0.00, T:0.37
Consensus pattern (22 bp):
ATATATACATATACATACATAT
Found at i:1607125 original size:18 final size:18
Alignment explanation
Indices: 1607102--1607140 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
1607092 ATACATATAC
*
1607102 ATACATATATATATACAT
1 ATACATACATATATACAT
*
1607120 ATACATACATATATATAT
1 ATACATACATATATACAT
1607138 ATA
1 ATA
1607141 TCACATCTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.51, C:0.10, G:0.00, T:0.38
Consensus pattern (18 bp):
ATACATACATATATACAT
Found at i:1607227 original size:2 final size:2
Alignment explanation
Indices: 1607207--1607255 Score: 73
Period size: 2 Copynumber: 25.0 Consensus size: 2
1607197 GGAAAATCCA
* *
1607207 AT AT -T AT AC AT AC 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 AT
1607248 AT AT AT AT
1 AT AT AT AT
1607256 CACATCTTGA
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1607257 original size:114 final size:118
Alignment explanation
Indices: 1607053--1607291 Score: 371
Period size: 114 Copynumber: 2.0 Consensus size: 118
1607043 ATTCAAGTCT
1607053 AATTTAAAAGATAGCTTGTGATAGGGAAAATCCAATATCATACATATACATACATATATATATAC
1 AATTTAAAAGATAGCTTGTGATAGGGAAAATCCAATATCAT--ATATACATACATATATATATAC
1607118 ATATACATACATATATATATATATCACATCTTGATATAAAAGGTAGGTCGTATAA
64 ATATACATACATATATATATATATCACATCTTGATATAAAAGGTAGGTCGTATAA
*
1607173 AATTTAAAAAGATAGCTTGTGAT-GGGAAAATCC-A-AT-AT-TATACATACATATATATATATA
1 AATTT-AAAAGATAGCTTGTGATAGGGAAAATCCAATATCATATATACATACATATATATATACA
* * * *
1607233 TATATATATATATATATATATATCACATCTTGATGTAAAAGGTAGGTCGTATAC
65 TATACATACATATATATATATATCACATCTTGATATAAAAGGTAGGTCGTATAA
1607287 AATTT
1 AATTT
1607292 TTGACATCCT
Statistics
Matches: 113, Mismatches: 5, Indels: 8
0.90 0.04 0.06
Matches are distributed among these distances:
114 76 0.67
117 2 0.02
118 2 0.02
119 1 0.01
120 15 0.13
121 17 0.15
ACGTcount: A:0.44, C:0.10, G:0.11, T:0.35
Consensus pattern (118 bp):
AATTTAAAAGATAGCTTGTGATAGGGAAAATCCAATATCATATATACATACATATATATATACAT
ATACATACATATATATATATATCACATCTTGATATAAAAGGTAGGTCGTATAA
Found at i:1607421 original size:11 final size:12
Alignment explanation
Indices: 1607407--1607454 Score: 53
Period size: 12 Copynumber: 3.9 Consensus size: 12
1607397 ATTTGGTTCG
*
1607407 ATTTTGATTT-A
1 ATTTTAATTTAA
1607418 ATTTTAATTTAA
1 ATTTTAATTTAA
*
1607430 ATTTTAATTAAA
1 ATTTTAATTTAA
1607442 TATATTTAATTTA
1 -AT-TTTAATTTA
1607455 TTTTGATTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
11 9 0.29
12 12 0.39
13 2 0.06
14 8 0.26
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (12 bp):
ATTTTAATTTAA
Found at i:1608601 original size:40 final size:40
Alignment explanation
Indices: 1608538--1608629 Score: 130
Period size: 40 Copynumber: 2.3 Consensus size: 40
1608528 AGTATATATT
* * *
1608538 ATTTTAATATCAGGTTATCATTTTTTTAATTTATTTAATA
1 ATTTTAAAATTAGATTATCATTTTTTTAATTTATTTAATA
* * *
1608578 ATTTTAAAATTAGATTATTATTTTTTTAGTTTATTTAATG
1 ATTTTAAAATTAGATTATCATTTTTTTAATTTATTTAATA
1608618 ATTTTAAAATTA
1 ATTTTAAAATTA
1608630 ATATAATTTA
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 46 1.00
ACGTcount: A:0.35, C:0.02, G:0.05, T:0.58
Consensus pattern (40 bp):
ATTTTAAAATTAGATTATCATTTTTTTAATTTATTTAATA
Found at i:1609939 original size:91 final size:89
Alignment explanation
Indices: 1609819--1610048 Score: 261
Period size: 90 Copynumber: 2.6 Consensus size: 89
1609809 ATCATTTTCT
* *
1609819 TTCTTGCTACTTTGGCTATTTGTTTTCTTATTTTCAAAACTTTATTAATTTAAACATCAAAGCAT
1 TTCTTGCTACTTTGACTATTTG--TTCTTATTTTCAAAACTTTATTAATTTAAACATCAAAACAT
* *
1609884 GTTTCGAAGTATAAACTCCGACATCA
64 ATTTCAAAGTATAAACTCCGACATCA
* ** * *
1609910 TTCTTGCTATTTTGACTATTTGCTCTCTTATCCTC-AAACTTTATTAATTTAAATATCAAAATAT
1 TTCTTGCTACTTTGACTATTTG-T-TCTTATTTTCAAAACTTTATTAATTTAAACATCAAAACAT
* *
1609974 ATTTTAAAGTATAAACTCCGACTTCA
64 ATTTCAAAGTATAAACTCCGACATCA
* * *
1610000 TTCTT-ATCACTTTAACTATTT-TTTTTA-TTTCAAAACTTTATTAATTTAA
1 TTCTTGCT-ACTTTGACTATTTGTTCTTATTTTCAAAACTTTATTAATTTAA
1610049 TTATTAAAGT
Statistics
Matches: 118, Mismatches: 18, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
86 2 0.02
87 21 0.18
88 1 0.01
89 1 0.01
90 65 0.55
91 28 0.24
ACGTcount: A:0.31, C:0.17, G:0.06, T:0.47
Consensus pattern (89 bp):
TTCTTGCTACTTTGACTATTTGTTCTTATTTTCAAAACTTTATTAATTTAAACATCAAAACATAT
TTCAAAGTATAAACTCCGACATCA
Found at i:1610681 original size:21 final size:21
Alignment explanation
Indices: 1610647--1610706 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
1610637 TAAATATAAT
* *
1610647 ATAATTATATTATATTAAATA
1 ATAATTAAAATATATTAAATA
*
1610668 ATAATTAAAATATAATAAA-A
1 ATAATTAAAATATATTAAATA
1610688 AT-A-TATAAATATATTAAAT
1 ATAATTA-AAATATATTAAAT
1610707 TTTAAAATTA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
18 2 0.06
19 12 0.36
20 3 0.09
21 16 0.48
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
ATAATTAAAATATATTAAATA
Found at i:1611415 original size:15 final size:15
Alignment explanation
Indices: 1611395--1611424 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1611385 CAAACTCAAA
*
1611395 AAACTCTAATACCAT
1 AAACTCAAATACCAT
1611410 AAACTCAAATACCAT
1 AAACTCAAATACCAT
1611425 GTAAGTTACT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.27, G:0.00, T:0.23
Consensus pattern (15 bp):
AAACTCAAATACCAT
Found at i:1611606 original size:2 final size:2
Alignment explanation
Indices: 1611599--1611644 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
1611589 TGTAAGATGC
1611599 AT 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 AT
1611641 AT AT
1 AT AT
1611645 TTGTGTAAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1611704 original size:19 final size:18
Alignment explanation
Indices: 1611662--1611704 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
1611652 AAATTAAATA
1611662 ATTTT-ATTTAATTATAT
1 ATTTTAATTTAATTATAT
*
1611679 TTGTTTAATTTAATTATTAT
1 AT-TTTAATTTAATTA-TAT
1611699 ATTTTA
1 ATTTTA
1611705 TGTTTTATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
17 1 0.05
18 3 0.14
19 13 0.62
20 4 0.19
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (18 bp):
ATTTTAATTTAATTATAT
Found at i:1613191 original size:22 final size:20
Alignment explanation
Indices: 1613166--1613220 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 20
1613156 TTTTTAAAAA
*
1613166 AATATTTTAAATTTATTATATT
1 AATATTTTAAA-TT-TTATAAT
1613188 AATATTTATATAATTTTATAAT
1 AATATTT-TA-AATTTTATAAT
*
1613210 AAAATTTTAAA
1 AATATTTTAAA
1613221 AAATAATTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
20 2 0.07
21 2 0.07
22 19 0.66
23 4 0.14
24 2 0.07
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
AATATTTTAAATTTTATAAT
Found at i:1614095 original size:11 final size:13
Alignment explanation
Indices: 1614043--1614099 Score: 66
Period size: 13 Copynumber: 4.5 Consensus size: 13
1614033 AAAATGGAAA
1614043 ATAT-ATTTTTAT
1 ATATAATTTTTAT
* *
1614055 -TATTATCTTTA-
1 ATATAATTTTTAT
1614066 ATAATAATTTTTAT
1 AT-ATAATTTTTAT
1614080 ATATAATTTTTAT
1 ATATAATTTTTAT
1614093 ATATAAT
1 ATATAAT
1614100 CAGAAAATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
11 3 0.08
12 7 0.18
13 26 0.68
14 2 0.05
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.60
Consensus pattern (13 bp):
ATATAATTTTTAT
Found at i:1614152 original size:2 final size:2
Alignment explanation
Indices: 1614141--1614173 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1614131 AAGCCATTAG
1614141 TA TA TA -A 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
1614174 CACACGAATG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1614340 original size:2 final size:2
Alignment explanation
Indices: 1614333--1614377 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1614323 TTTTGATTAT
1614333 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
1614375 TA T
1 TA T
1614378 TCTTTTACAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1614808 original size:22 final size:20
Alignment explanation
Indices: 1614783--1614837 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 20
1614773 TTTTTAGAAA
*
1614783 AATATTTTAAATTTATTATATT
1 AATATTTTAAA-TT-TTATAAT
1614805 AATATTTATACAATTTTATAAT
1 AATATTT-TA-AATTTTATAAT
*
1614827 AAAATTTTAAA
1 AATATTTTAAA
1614838 AAATAATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
20 2 0.07
21 2 0.07
22 19 0.66
23 4 0.14
24 2 0.07
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (20 bp):
AATATTTTAAATTTTATAAT
Found at i:1614845 original size:13 final size:13
Alignment explanation
Indices: 1614816--1614864 Score: 57
Period size: 13 Copynumber: 3.8 Consensus size: 13
1614806 ATATTTATAC
1614816 AATTTTATAATAA-
1 AATTTTA-AATAAT
*
1614829 AATTTTAAAAAAT
1 AATTTTAAATAAT
1614842 AATTTATAAATAAT
1 AATTT-TAAATAAT
1614856 AA-TTTAAAT
1 AATTTTAAAT
1614865 TTAGTCGAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
12 9 0.28
13 14 0.44
14 9 0.28
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
AATTTTAAATAAT
Found at i:1614856 original size:14 final size:14
Alignment explanation
Indices: 1614819--1614861 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
1614809 TTTATACAAT
1614819 TTTAT-AATAA-AA
1 TTTATAAATAATAA
*
1614831 TTT-TAAAAAATAA
1 TTTATAAATAATAA
1614844 TTTATAAATAATAA
1 TTTATAAATAATAA
1614858 TTTA
1 TTTA
1614862 AATTTAGTCG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
11 1 0.04
12 7 0.27
13 5 0.19
14 13 0.50
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
TTTATAAATAATAA
Found at i:1615604 original size:33 final size:33
Alignment explanation
Indices: 1615510--1615608 Score: 111
Period size: 33 Copynumber: 3.1 Consensus size: 33
1615500 TTAAAGATAA
*
1615510 TTAATAATTATTTTTAAAAGTAAAAAATCATCT
1 TTAATAATTATTTTTAAAAGTAAAAAATTATCT
* *
1615543 TTAA-AAGTTA----TAGAA-TGAAAAAAATATCT
1 TTAATAA-TTATTTTTAAAAGT-AAAAAATTATCT
1615572 TTAATAATTATTTTTAAAAGTAAAAAATTATCT
1 TTAATAATTATTTTTAAAAGTAAAAAATTATCT
1615605 TTAA
1 TTAA
1615609 AAGTTATAGA
Statistics
Matches: 53, Mismatches: 5, Indels: 16
0.72 0.07 0.22
Matches are distributed among these distances:
28 1 0.02
29 21 0.40
30 2 0.04
32 2 0.04
33 26 0.49
34 1 0.02
ACGTcount: A:0.51, C:0.04, G:0.05, T:0.40
Consensus pattern (33 bp):
TTAATAATTATTTTTAAAAGTAAAAAATTATCT
Found at i:1615607 original size:62 final size:62
Alignment explanation
Indices: 1615510--1615645 Score: 263
Period size: 62 Copynumber: 2.2 Consensus size: 62
1615500 TTAAAGATAA
1615510 TTAATAATTATTTTTAAAAGTAAAAAATCATCTTTAAAAGTTATAGAATGAAAAAAATATCT
1 TTAATAATTATTTTTAAAAGTAAAAAATCATCTTTAAAAGTTATAGAATGAAAAAAATATCT
*
1615572 TTAATAATTATTTTTAAAAGTAAAAAATTATCTTTAAAAGTTATAGAATGAAAAAAATATCT
1 TTAATAATTATTTTTAAAAGTAAAAAATCATCTTTAAAAGTTATAGAATGAAAAAAATATCT
1615634 TTAATAATTATT
1 TTAATAATTATT
1615646 CTCTAAAATT
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
62 73 1.00
ACGTcount: A:0.51, C:0.04, G:0.06, T:0.40
Consensus pattern (62 bp):
TTAATAATTATTTTTAAAAGTAAAAAATCATCTTTAAAAGTTATAGAATGAAAAAAATATCT
Found at i:1615644 original size:29 final size:29
Alignment explanation
Indices: 1615531--1615637 Score: 119
Period size: 29 Copynumber: 3.5 Consensus size: 29
1615521 TTTTAAAAGT
1615531 AAAAAATCATCTTTAAAAGTTATAGAATGA
1 AAAAAAT-ATCTTTAAAAGTTATAGAATGA
*
1615561 AAAAAATATCTTTAATAA-TTATTTTTA-AAAGTA
1 AAAAAATATCTTTAA-AAGTTA----TAGAATG-A
*
1615594 AAAAATTATCTTTAAAAGTTATAGAATGA
1 AAAAAATATCTTTAAAAGTTATAGAATGA
1615623 AAAAAATATCTTTAA
1 AAAAAATATCTTTAA
1615638 TAATTATTCT
Statistics
Matches: 65, Mismatches: 4, Indels: 17
0.76 0.05 0.20
Matches are distributed among these distances:
29 28 0.43
30 12 0.18
32 5 0.08
33 20 0.31
ACGTcount: A:0.53, C:0.05, G:0.07, T:0.36
Consensus pattern (29 bp):
AAAAAATATCTTTAAAAGTTATAGAATGA
Found at i:1615811 original size:29 final size:29
Alignment explanation
Indices: 1615778--1615841 Score: 119
Period size: 29 Copynumber: 2.2 Consensus size: 29
1615768 ATATAAATTG
1615778 AGTTATAGAATGAAAAAAATATCTTTAAA
1 AGTTATAGAATGAAAAAAATATCTTTAAA
*
1615807 AGTTATAGAATGAAAAAAATATCTTTAAT
1 AGTTATAGAATGAAAAAAATATCTTTAAA
1615836 AGTTAT
1 AGTTAT
1615842 TCTCTAAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.52, C:0.03, G:0.11, T:0.34
Consensus pattern (29 bp):
AGTTATAGAATGAAAAAAATATCTTTAAA
Found at i:1616752 original size:22 final size:22
Alignment explanation
Indices: 1616720--1616773 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
1616710 TTATATAATT
*
1616720 ATTTTTATAAAATAATATTTTATA
1 ATTTTTA-AATATAA-ATTTTATA
* *
1616744 ATTTTTAAATTTAAATTTTATT
1 ATTTTTAAATATAAATTTTATA
1616766 ATTTTTAA
1 ATTTTTAA
1616774 TTATTTTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 15 0.56
23 5 0.19
24 7 0.26
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
ATTTTTAAATATAAATTTTATA
Found at i:1618046 original size:20 final size:20
Alignment explanation
Indices: 1618009--1618047 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1617999 TTTTTAATTT
* *
1618009 TAATTTCAATTATCAAAATA
1 TAATTTCAAATATAAAAATA
*
1618029 TAATTTTAAATATAAAAAT
1 TAATTTCAAATATAAAAAT
1618048 TAAATTTTTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (20 bp):
TAATTTCAAATATAAAAATA
Found at i:1618361 original size:18 final size:18
Alignment explanation
Indices: 1618335--1618401 Score: 56
Period size: 15 Copynumber: 3.9 Consensus size: 18
1618325 TTTTTAAAAT
1618335 ATTTT-ATATTTATATAA
1 ATTTTAATATTTATATAA
1618352 ATTTTAATATATTA-AT-A
1 ATTTTAATAT-TTATATAA
1618369 A--TTAATA-TTATATAA
1 ATTTTAATATTTATATAA
*
1618384 ATATTAAAATATTTATAT
1 AT-TT-TAATATTTATAT
1618402 TATATTATTT
Statistics
Matches: 40, Mismatches: 1, Indels: 15
0.71 0.02 0.27
Matches are distributed among these distances:
13 3 0.08
14 2 0.05
15 8 0.20
17 7 0.17
18 7 0.17
19 7 0.17
20 6 0.15
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
ATTTTAATATTTATATAA
Found at i:1618389 original size:17 final size:17
Alignment explanation
Indices: 1618318--1618390 Score: 57
Period size: 18 Copynumber: 4.4 Consensus size: 17
1618308 TTATTACGTT
*
1618318 ATATTAAT-TTTTA-AA
1 ATATTAATATTATATAA
*
1618333 ATATTTTATATTTATATAA
1 ATA-TTAATA-TTATATAA
*
1618352 ATTTTAATA-TAT-T-A
1 ATATTAATATTATATAA
1618366 ATAATTAATATTATATAA
1 AT-ATTAATATTATATAA
1618384 ATATTAA
1 ATATTAA
1618391 AATATTTATA
Statistics
Matches: 45, Mismatches: 5, Indels: 14
0.70 0.08 0.22
Matches are distributed among these distances:
14 3 0.07
15 10 0.22
16 10 0.22
17 6 0.13
18 12 0.27
19 4 0.09
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
ATATTAATATTATATAA
Found at i:1618406 original size:25 final size:24
Alignment explanation
Indices: 1618360--1618406 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
1618350 AAATTTTAAT
*
1618360 ATATTAATAATTAATATTATATAA
1 ATATTAAAAATTAATATTATATAA
*
1618384 ATATTAAAATATTTATATTATAT
1 ATATTAAAA-ATTAATATTATAT
1618407 TATTTTTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
ATATTAAAAATTAATATTATATAA
Found at i:1621344 original size:14 final size:13
Alignment explanation
Indices: 1621325--1621389 Score: 61
Period size: 11 Copynumber: 5.4 Consensus size: 13
1621315 TTAGTAAAAT
1621325 TAAATATAATTATA
1 TAAATATAA-TATA
1621339 TAAATATAATA-A
1 TAAATATAATATA
*
1621351 TAAA-ATTAT-TA
1 TAAATATAATATA
1621362 -AAATATAATATA
1 TAAATATAATATA
*
1621374 -ATATA-AATATA
1 TAAATATAATATA
1621385 TAAAT
1 TAAAT
1621390 TTTTTAAAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
10 3 0.07
11 15 0.35
12 14 0.33
13 2 0.05
14 9 0.21
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
TAAATATAATATA
Found at i:1621390 original size:33 final size:35
Alignment explanation
Indices: 1621326--1621449 Score: 105
Period size: 33 Copynumber: 3.5 Consensus size: 35
1621316 TAGTAAAATT
*
1621326 AAATATAATTATATAAATATAATAATAAAA-TTATTA
1 AAATATAA-TATA-ATATATAATAATAAAATTTATTA
*
1621362 AAATATAATATAATATA-AAT-ATATAAATTTTTTA
1 AAATATAATATAATATATAATAATA-AAATTTATTA
* *
1621396 AAAT-TTATATAATATATTAATGTATTAAAATTTA-TA
1 AAATATAATATAATATA-TAA--TAATAAAATTTATTA
*
1621432 TAAATATAAAATAATATA
1 -AAATATAATATAATATA
1621450 ATTATGATAT
Statistics
Matches: 72, Mismatches: 7, Indels: 16
0.76 0.07 0.17
Matches are distributed among these distances:
32 3 0.04
33 17 0.24
34 13 0.18
35 6 0.08
36 10 0.14
37 11 0.15
38 12 0.17
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (35 bp):
AAATATAATATAATATATAATAATAAAATTTATTA
Found at i:1621423 original size:27 final size:28
Alignment explanation
Indices: 1621374--1621443 Score: 99
Period size: 27 Copynumber: 2.6 Consensus size: 28
1621364 ATATAATATA
* *
1621374 ATATAAATATATAAATTTTTTAAAATTT
1 ATATAAATATATAAATGTATTAAAATTT
*
1621402 ATAT-AATATATTAATGTATTAAAATTT
1 ATATAAATATATAAATGTATTAAAATTT
1621429 ATATAAATATA-AAAT
1 ATATAAATATATAAAT
1621444 AATATAATTA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
27 27 0.73
28 10 0.27
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (28 bp):
ATATAAATATATAAATGTATTAAAATTT
Found at i:1624006 original size:9 final size:9
Alignment explanation
Indices: 1623992--1624024 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
1623982 TTTCTCTCTT
*
1623992 TCTGCTATC
1 TCTGCTGTC
1624001 TCTGCTGTC
1 TCTGCTGTC
1624010 TCTGCTGTC
1 TCTGCTGTC
1624019 TCTGCT
1 TCTGCT
1624025 TGAGCCTTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.03, C:0.33, G:0.18, T:0.45
Consensus pattern (9 bp):
TCTGCTGTC
Found at i:1624121 original size:27 final size:26
Alignment explanation
Indices: 1624083--1624134 Score: 95
Period size: 27 Copynumber: 2.0 Consensus size: 26
1624073 TGCAACTTTT
1624083 ACTATTTCAAATTGAATTTCAAAATTA
1 ACTATTTCAAATTGAA-TTCAAAATTA
1624110 ACTATTTCAAATTGAATTCAAAATT
1 ACTATTTCAAATTGAATTCAAAATT
1624135 GGCTGCACAG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 9 0.36
27 16 0.64
ACGTcount: A:0.44, C:0.12, G:0.04, T:0.40
Consensus pattern (26 bp):
ACTATTTCAAATTGAATTCAAAATTA
Found at i:1624135 original size:12 final size:13
Alignment explanation
Indices: 1624086--1624135 Score: 52
Period size: 12 Copynumber: 3.9 Consensus size: 13
1624076 AACTTTTACT
1624086 ATTTC-AAATTGA
1 ATTTCAAAATTGA
*
1624098 ATTTCAAAATTAA
1 ATTTCAAAATTGA
1624111 CTATTTC-AAATTGA
1 --ATTTCAAAATTGA
1624125 A-TTCAAAATTG
1 ATTTCAAAATTG
1624136 GCTGCACAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
11 3 0.09
12 12 0.38
13 6 0.19
14 6 0.19
15 5 0.16
ACGTcount: A:0.44, C:0.10, G:0.06, T:0.40
Consensus pattern (13 bp):
ATTTCAAAATTGA
Found at i:1628781 original size:9 final size:9
Alignment explanation
Indices: 1628767--1628799 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
1628757 TTTCTCTCTT
*
1628767 TCTGCTATC
1 TCTGCTGTC
1628776 TCTGCTGTC
1 TCTGCTGTC
1628785 TCTGCTGTC
1 TCTGCTGTC
1628794 TCTGCT
1 TCTGCT
1628800 TGAGCCTTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.03, C:0.33, G:0.18, T:0.45
Consensus pattern (9 bp):
TCTGCTGTC
Found at i:1628896 original size:27 final size:26
Alignment explanation
Indices: 1628858--1628909 Score: 95
Period size: 27 Copynumber: 2.0 Consensus size: 26
1628848 TGCAACTTTT
1628858 ACTATTTCAAATTGAATTTCAAAATTA
1 ACTATTTCAAATTGAA-TTCAAAATTA
1628885 ACTATTTCAAATTGAATTCAAAATT
1 ACTATTTCAAATTGAATTCAAAATT
1628910 GGCTGCACAG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 9 0.36
27 16 0.64
ACGTcount: A:0.44, C:0.12, G:0.04, T:0.40
Consensus pattern (26 bp):
ACTATTTCAAATTGAATTCAAAATTA
Found at i:1628910 original size:12 final size:13
Alignment explanation
Indices: 1628861--1628910 Score: 52
Period size: 12 Copynumber: 3.9 Consensus size: 13
1628851 AACTTTTACT
1628861 ATTTC-AAATTGA
1 ATTTCAAAATTGA
*
1628873 ATTTCAAAATTAA
1 ATTTCAAAATTGA
1628886 CTATTTC-AAATTGA
1 --ATTTCAAAATTGA
1628900 A-TTCAAAATTG
1 ATTTCAAAATTG
1628911 GCTGCACAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
11 3 0.09
12 12 0.38
13 6 0.19
14 6 0.19
15 5 0.16
ACGTcount: A:0.44, C:0.10, G:0.06, T:0.40
Consensus pattern (13 bp):
ATTTCAAAATTGA
Found at i:1629115 original size:14 final size:13
Alignment explanation
Indices: 1629078--1629111 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
1629068 TATCATTTAA
1629078 ATTAAATTAATTT
1 ATTAAATTAATTT
*
1629091 ATTAAAATAATTT
1 ATTAAATTAATTT
*
1629104 TTTAAATT
1 ATTAAATT
1629112 TAATATAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
ATTAAATTAATTT
Found at i:1629177 original size:22 final size:22
Alignment explanation
Indices: 1629122--1629177 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 22
1629112 TAATATAAAA
*
1629122 TATATAA-ATATTAATATATTT
1 TATATAATATTTTAATATATTT
* * *
1629143 TTTTTAATGTTTTAATATATTT
1 TATATAATATTTTAATATATTT
*
1629165 TATATATTATTTT
1 TATATAATATTTT
1629178 GATCATTTAA
Statistics
Matches: 26, Mismatches: 8, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
21 5 0.19
22 21 0.81
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (22 bp):
TATATAATATTTTAATATATTT
Found at i:1629467 original size:19 final size:19
Alignment explanation
Indices: 1629444--1629481 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
1629434 AAATTGATAA
*
1629444 AAAAATCAAAATAATATTAT
1 AAAAAT-AAAATAAAATTAT
1629464 AAAAATAAAATAAAATTA
1 AAAAATAAAATAAAATTA
1629482 CAAATATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (19 bp):
AAAAATAAAATAAAATTAT
Found at i:1631485 original size:28 final size:31
Alignment explanation
Indices: 1631454--1631525 Score: 75
Period size: 28 Copynumber: 2.5 Consensus size: 31
1631444 TAAAATTTTA
1631454 TTTTATTATTTAAAATATT-A-AAAAAT-A-T
1 TTTTATTATTTAAAAT-TTAATAAAAATAATT
*
1631482 TTTTA-TAATT-AAATTTAAATAAAAATAATT
1 TTTTATTATTTAAAATTT-AATAAAAATAATT
1631512 TTTTATTATTTAAA
1 TTTTATTATTTAAA
1631526 TAATTTTAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
25 2 0.06
26 4 0.11
27 5 0.14
28 11 0.31
29 1 0.03
30 6 0.17
31 4 0.11
32 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (31 bp):
TTTTATTATTTAAAATTTAATAAAAATAATT
Found at i:1632484 original size:2 final size:2
Alignment explanation
Indices: 1632479--1632505 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1632469 ACATGTGTGC
1632479 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1632506 CACACACCAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1633346 original size:24 final size:25
Alignment explanation
Indices: 1633319--1633393 Score: 63
Period size: 23 Copynumber: 3.2 Consensus size: 25
1633309 TTTATTAATA
*
1633319 ATAAAAATTAAGTAA-TATAATTT-G
1 ATAAAAATTAA-AAATTATAATTTAG
*
1633343 AT-AAAATTAAAAATTTATAATTTAT
1 ATAAAAATTAAAAA-TTATAATTTAG
*
1633368 ATAAAAATT-AATATTA-AATTTA-
1 ATAAAAATTAAAAATTATAATTTAG
1633390 ATAA
1 ATAA
1633394 TTTAAAATAT
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
22 6 0.14
23 14 0.32
24 13 0.30
25 5 0.11
26 6 0.14
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (25 bp):
ATAAAAATTAAAAATTATAATTTAG
Found at i:1634424 original size:27 final size:28
Alignment explanation
Indices: 1634394--1634477 Score: 77
Period size: 27 Copynumber: 3.0 Consensus size: 28
1634384 AAAATTTATA
*
1634394 TAATAT-AATTTATTAATATATTAAA-AT
1 TAATATAAATTTA-AAATATATTAAATAT
*
1634421 TAATATAAATTTAAAATATTTTAAATAT
1 TAATATAAATTTAAAATATATTAAATAT
*
1634449 TATGATAATAAA-ATAAAATAT-TTAAATAT
1 TA--AT-ATAAATTTAAAATATATTAAATAT
1634478 GATATCATAT
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
27 16 0.33
28 10 0.20
29 8 0.16
30 10 0.20
31 5 0.10
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (28 bp):
TAATATAAATTTAAAATATATTAAATAT
Found at i:1634493 original size:30 final size:30
Alignment explanation
Indices: 1634432--1634491 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 30
1634422 AATATAAATT
*
1634432 TAAAATATTTTAAATATTATGATAATAAAA
1 TAAAATATTTTAAATATTATCATAATAAAA
*
1634462 TAAAATA-TTTAAATATGATATCATATTAAA
1 TAAAATATTTTAAATAT--TATCATAATAAA
1634492 TATATTTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 9 0.35
30 7 0.27
31 10 0.38
ACGTcount: A:0.55, C:0.02, G:0.03, T:0.40
Consensus pattern (30 bp):
TAAAATATTTTAAATATTATCATAATAAAA
Found at i:1636304 original size:13 final size:13
Alignment explanation
Indices: 1636286--1636315 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1636276 AATATATATT
1636286 ATTTTTTACTTCA
1 ATTTTTTACTTCA
*
1636299 ATTTTTTATTTCA
1 ATTTTTTACTTCA
1636312 ATTT
1 ATTT
1636316 ACTTTTTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.23, C:0.10, G:0.00, T:0.67
Consensus pattern (13 bp):
ATTTTTTACTTCA
Found at i:1636462 original size:19 final size:21
Alignment explanation
Indices: 1636425--1636469 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
1636415 GTTGAAAAAG
1636425 TTAAAATTAAAATATAAATTT
1 TTAAAATTAAAATATAAATTT
*
1636446 TTAAAATTAAAATA-AATTTT
1 TTAAAATTAAAATATAAATTT
1636466 TTAA
1 TTAA
1636470 TATTTTTTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 9 0.39
21 14 0.61
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
TTAAAATTAAAATATAAATTT
Found at i:1637932 original size:20 final size:18
Alignment explanation
Indices: 1637909--1637953 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 18
1637899 GTTTAGATTT
1637909 TTTTAATTTAAATTGATCTA
1 TTTTAATTTAAATT-AT-TA
*
1637929 TTTTGATTTAAATTATTA
1 TTTTAATTTAAATTATTA
1637947 -TTTAATT
1 TTTTAATT
1637954 AATAAAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 6 0.26
18 2 0.09
19 2 0.09
20 13 0.57
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.60
Consensus pattern (18 bp):
TTTTAATTTAAATTATTA
Found at i:1641149 original size:5 final size:5
Alignment explanation
Indices: 1641139--1641163 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
1641129 AAAAGGAGAA
1641139 AAAAT AAAAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT
1641164 GGCATGGATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:1644705 original size:14 final size:14
Alignment explanation
Indices: 1644686--1644715 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1644676 GTGCGACGAT
1644686 TAAATCTAAATATA
1 TAAATCTAAATATA
*
1644700 TAAATCTTAATATA
1 TAAATCTAAATATA
1644714 TA
1 TA
1644716 GAGTGACGTG
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:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (14 bp):
TAAATCTAAATATA
Found at i:1647737 original size:11 final size:11
Alignment explanation
Indices: 1647706--1647741 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
1647696 TTATTTTTTA
1647706 TTTTATATTAT
1 TTTTATATTAT
1647717 ATTTTA-ATTAT
1 -TTTTATATTAT
1647728 TTTTATATTAT
1 TTTTATATTAT
1647739 TTT
1 TTT
1647742 ATAATAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 5 0.22
11 13 0.57
12 5 0.22
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
TTTTATATTAT
Found at i:1648473 original size:16 final size:15
Alignment explanation
Indices: 1648446--1648508 Score: 69
Period size: 14 Copynumber: 4.3 Consensus size: 15
1648436 TAGATATCTC
1648446 AAAATT-TATATAAT
1 AAAATTATATATAAT
1648460 ATAAATTATATATAA-
1 A-AAATTATATATAAT
1648475 AAAATTATATA-AAT
1 AAAATTATATATAAT
* *
1648489 AAACTAATAATATAAT
1 AAAATTAT-ATATAAT
1648505 AAAA
1 AAAA
1648509 AACATAAATA
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
13 2 0.05
14 17 0.41
15 9 0.22
16 13 0.32
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (15 bp):
AAAATTATATATAAT
Found at i:1648489 original size:29 final size:30
Alignment explanation
Indices: 1648446--1648528 Score: 75
Period size: 31 Copynumber: 2.8 Consensus size: 30
1648436 TAGATATCTC
*
1648446 AAAATTTATAT-AATATAAATTATAT-ATA
1 AAAAATTATATAAATATAAATTATATAATA
* *
1648474 AAAAATTATATAAATAAACTAATAATATAATA
1 AAAAATTATATAAATATA--AATTATATAATA
*
1648506 AAAAA-CATA-AATATATAAATTAT
1 AAAAATTATATAA-ATATAAATTAT
1648529 CAAATATAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
28 10 0.23
29 10 0.23
30 2 0.05
31 14 0.32
32 8 0.18
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (30 bp):
AAAAATTATATAAATATAAATTATATAATA
Found at i:1648686 original size:9 final size:11
Alignment explanation
Indices: 1648658--1648683 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1648648 ATATGTGTAT
1648658 TTATATTTATA
1 TTATATTTATA
1648669 TTATATTTATA
1 TTATATTTATA
1648680 TTAT
1 TTAT
1648684 TTAGTAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
TTATATTTATA
Found at i:1649025 original size:18 final size:19
Alignment explanation
Indices: 1648983--1649025 Score: 52
Period size: 21 Copynumber: 2.2 Consensus size: 19
1648973 ATTTTTAAAA
*
1648983 TTTTTAAAAATAATTTTTTAT
1 TTTTTAAAAATAA--TTTAAT
1649004 TTTTTAAAAATAA-TTAAT
1 TTTTTAAAAATAATTTAAT
1649022 TTTT
1 TTTT
1649026 CATCTAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 8 0.38
21 13 0.62
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TTTTTAAAAATAATTTAAT
Found at i:1649284 original size:35 final size:34
Alignment explanation
Indices: 1649243--1649324 Score: 87
Period size: 34 Copynumber: 2.4 Consensus size: 34
1649233 ATATTAAAAT
* * *
1649243 TTTATTTTAATTAATAAATA-ATAATTTAATTTAAA
1 TTTA-TTTAAATAA-AAATATAAAATTTAAATTAAA
1649278 TTTATTTAAATAAAAATATTAAAATTTAAATTAAA
1 TTTATTTAAATAAAAATA-TAAAATTTAAATTAAA
*
1649313 -TTAATTAAATAA
1 TTTATTTAAATAA
1649325 CTTTTAAAAC
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
33 5 0.12
34 19 0.46
35 17 0.41
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (34 bp):
TTTATTTAAATAAAAATATAAAATTTAAATTAAA
Found at i:1649306 original size:30 final size:29
Alignment explanation
Indices: 1649231--1649317 Score: 95
Period size: 30 Copynumber: 2.9 Consensus size: 29
1649221 TAAGATTGGT
* *
1649231 AAATATTAAAATTTTATTTTAATTAATAA
1 AAATATTAAAATTTAAATTTAATTAATAA
* *
1649260 ATAATAATT-TAATTTAAATTTATTTAAATAA
1 A-AAT-ATTAAAATTTAAATTTAATT-AATAA
*
1649291 AAATATTAAAATTTAAATTAAATTAAT
1 AAATATTAAAATTTAAATTTAATTAAT
1649318 TAAATAACTT
Statistics
Matches: 47, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
29 7 0.15
30 31 0.66
31 9 0.19
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (29 bp):
AAATATTAAAATTTAAATTTAATTAATAA
Found at i:1649339 original size:60 final size:59
Alignment explanation
Indices: 1649231--1649343 Score: 138
Period size: 60 Copynumber: 1.9 Consensus size: 59
1649221 TAAGATTGGT
* * * ***
1649231 AAATATTAAAATTTTATTTTAATTAATAAATAATAATTTAATTTAAATTTATTTAAATAA
1 AAATATTAAAATTTAAATTAAATTAATAAATAAT-ATTTAAAACAAATTTATTTAAATAA
1649291 AAATATTAAAATTTAAATTAAATTAATTAAATAACT-TTTAAAACAAATTTATT
1 AAATATTAAAATTTAAATTAAATTAA-TAAATAA-TATTTAAAACAAATTTATT
1649344 ATGATGTAAC
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
60 37 0.82
61 7 0.16
62 1 0.02
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (59 bp):
AAATATTAAAATTTAAATTAAATTAATAAATAATATTTAAAACAAATTTATTTAAATAA
Found at i:1649723 original size:18 final size:19
Alignment explanation
Indices: 1649702--1649738 Score: 58
Period size: 18 Copynumber: 1.9 Consensus size: 19
1649692 TTTATAAAAT
1649702 TAAAAAATT-TTAAATTAG
1 TAAAAAATTATTAAATTAG
1649720 TAAAAAATTAATTAAATTA
1 TAAAAAATT-ATTAAATTA
1649739 TTATAAAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.53
20 8 0.47
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (19 bp):
TAAAAAATTATTAAATTAG
Found at i:1649856 original size:17 final size:17
Alignment explanation
Indices: 1649836--1649877 Score: 63
Period size: 15 Copynumber: 2.6 Consensus size: 17
1649826 TATTAAAAAT
1649836 TATATTATTTAATTAAA
1 TATATTATTTAATTAAA
1649853 TATATT-TTT-ATTAAA
1 TATATTATTTAATTAAA
1649868 TAT-TTATTTA
1 TATATTATTTA
1649878 TTATTAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
14 2 0.09
15 12 0.52
16 3 0.13
17 6 0.26
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TATATTATTTAATTAAA
Found at i:1649912 original size:18 final size:17
Alignment explanation
Indices: 1649840--1649912 Score: 59
Period size: 15 Copynumber: 4.5 Consensus size: 17
1649830 AAAAATTATA
*
1649840 TTATTTAATTAA-ATAT
1 TTATTTAATTAATAAAT
*
1649856 ATT-TTT-ATTAA-ATAT
1 -TTATTTAATTAATAAAT
*
1649871 TTATTT-ATTATTAAAT
1 TTATTTAATTAATAAAT
1649887 TT-TTTAATATAATAAAT
1 TTATTTAAT-TAATAAAT
1649904 TTATTTAAT
1 TTATTTAAT
1649913 CAGTTTGATC
Statistics
Matches: 48, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
14 2 0.04
15 19 0.40
16 10 0.21
17 11 0.23
18 6 0.12
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TTATTTAATTAATAAAT
Found at i:1650708 original size:22 final size:23
Alignment explanation
Indices: 1650673--1650724 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
1650663 TATTTTTATT
*
1650673 TATATCAATAA-TTTATATAAAAA
1 TATATTAATAATTTTA-ATAAAAA
*
1650696 TATATTAA-AATTTTAATATAAA
1 TATATTAATAATTTTAATAAAAA
1650718 TATATTA
1 TATATTA
1650725 TATATATTAG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 15 0.58
23 11 0.42
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (23 bp):
TATATTAATAATTTTAATAAAAA
Found at i:1650746 original size:23 final size:24
Alignment explanation
Indices: 1650718--1650764 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
1650708 TTAATATAAA
*
1650718 TATATT-AT-ATATATTAGACATAT
1 TATATTAATAATAT-TTAAACATAT
1650741 TATATTAATAATATTTAAACATAT
1 TATATTAATAATATTTAAACATAT
1650765 ATTACCATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 6 0.29
24 11 0.52
25 4 0.19
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (24 bp):
TATATTAATAATATTTAAACATAT
Found at i:1652052 original size:2 final size:2
Alignment explanation
Indices: 1652045--1652075 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1652035 TGATGATTAA
1652045 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 A
1652076 AACAATAAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1652953 original size:2 final size:2
Alignment explanation
Indices: 1652946--1652984 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1652936 TATATCTTCA
1652946 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1652985 TTTCTGTTTC
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:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1660582 original size:30 final size:30
Alignment explanation
Indices: 1660504--1660614 Score: 114
Period size: 30 Copynumber: 3.7 Consensus size: 30
1660494 ATTTTATTAC
* * *
1660504 ACCCAAATAAGCCTTTAACCTTTAATTTGC
1 ACCCAAATAAGCCCTTAACATTTAATTTGT
* * * * * *
1660534 ACTCAAGTAAGTCATTAACTTTTTATTTGT
1 ACCCAAATAAGCCCTTAACATTTAATTTGT
* *
1660564 ACCCCAATAAGCCCTTAACATTTAATTTAT
1 ACCCAAATAAGCCCTTAACATTTAATTTGT
*
1660594 ACCTAAATAAGCCCTTAACAT
1 ACCCAAATAAGCCCTTAACAT
1660615 AAATCAAACT
Statistics
Matches: 64, Mismatches: 17, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
30 64 1.00
ACGTcount: A:0.35, C:0.23, G:0.06, T:0.35
Consensus pattern (30 bp):
ACCCAAATAAGCCCTTAACATTTAATTTGT
Found at i:1666669 original size:2 final size:2
Alignment explanation
Indices: 1666656--1666707 Score: 70
Period size: 2 Copynumber: 25.5 Consensus size: 2
1666646 TAATGGTTGT
*
1666656 TA TA TA TT TA TA TA TA TA TA TA TA TA TA TCA T- TGA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA T-A TA TA TA TA
1666699 TA TA TA TA T
1 TA TA TA TA T
1666708 CATTGCTGAT
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
1 1 0.02
2 41 0.91
3 3 0.07
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1666696 original size:23 final size:23
Alignment explanation
Indices: 1666667--1666712 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
1666657 ATATATTTAT
1666667 ATATATATATATATATATCATTG
1 ATATATATATATATATATCATTG
1666690 ATATATATATATATATATCATTG
1 ATATATATATATATATATCATTG
1666713 CTGATTTGGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.48
Consensus pattern (23 bp):
ATATATATATATATATATCATTG
Found at i:1668336 original size:20 final size:21
Alignment explanation
Indices: 1668272--1668336 Score: 62
Period size: 23 Copynumber: 3.0 Consensus size: 21
1668262 ACTTTACGTG
*
1668272 TTTAAT-TATATTAAATTAAA
1 TTTAATATATATTTAATTAAA
1668292 TTTAAATATGATATTTATTATTTAAA
1 TTT-AATAT-ATATTTA--A-TTAAA
1668318 TTTAATATA-ATTTAATTAA
1 TTTAATATATATTTAATTAA
1668337 TAAAAAATTT
Statistics
Matches: 38, Mismatches: 1, Indels: 12
0.75 0.02 0.24
Matches are distributed among these distances:
20 7 0.18
21 4 0.11
22 1 0.03
23 11 0.29
24 1 0.03
25 6 0.16
26 8 0.21
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (21 bp):
TTTAATATATATTTAATTAAA
Found at i:1668344 original size:26 final size:24
Alignment explanation
Indices: 1668315--1668390 Score: 77
Period size: 26 Copynumber: 3.1 Consensus size: 24
1668305 TTTATTATTT
1668315 AAATTTAATATAATTTAATTAATAAA
1 AAATTTAATATAA-TTAATT-ATAAA
*
1668341 AAATTTTATTTATAATTAATTATAAA
1 AAA-TTTA-ATATAATTAATTATAAA
1668367 AAATATTAA-AT-ATTAA-TATAAA
1 AAAT-TTAATATAATTAATTATAAA
1668389 AA
1 AA
1668391 TAATATTTTA
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
22 8 0.18
23 5 0.11
24 2 0.04
25 1 0.02
26 14 0.31
27 10 0.22
28 5 0.11
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (24 bp):
AAATTTAATATAATTAATTATAAA
Found at i:1668373 original size:23 final size:23
Alignment explanation
Indices: 1668323--1668390 Score: 59
Period size: 22 Copynumber: 2.8 Consensus size: 23
1668313 TTAAATTTAA
1668323 TATAATTTAATTAATAAAAAATTTTATT
1 TATAA-TTAATT-ATAAAAAA--TTA-T
1668351 TATAATTAATTATAAAAAA-TAT
1 TATAATTAATTATAAAAAATTAT
*
1668373 TAAATATTAA-TATAAAAA
1 TATA-ATTAATTATAAAAA
1668391 TAATATTTTA
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
22 12 0.32
23 7 0.18
26 8 0.21
27 6 0.16
28 5 0.13
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
TATAATTAATTATAAAAAATTAT
Found at i:1669294 original size:36 final size:33
Alignment explanation
Indices: 1669254--1669319 Score: 89
Period size: 33 Copynumber: 1.9 Consensus size: 33
1669244 TCAATTTAAA
1669254 TTAATATTTAATAATATAAAATAT-TTTTATTAAAAT
1 TTAATA-TTAA-AATA-AAAATATATTTT-TTAAAAT
1669290 TTAATATTAAAATAAAAATATATTTTTTAA
1 TTAATATTAAAATAAAAATATATTTTTTAA
1669320 TAATATTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
33 11 0.38
34 8 0.28
35 4 0.14
36 6 0.21
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (33 bp):
TTAATATTAAAATAAAAATATATTTTTTAAAAT
Found at i:1669299 original size:13 final size:13
Alignment explanation
Indices: 1669246--1669302 Score: 53
Period size: 13 Copynumber: 4.2 Consensus size: 13
1669236 TAAATCAATC
1669246 AATTTAA-ATTAA
1 AATTTAATATTAA
*
1669258 TATTTAATAATATAA
1 AATTTAAT-AT-TAA
**
1669273 AATATTTTTATTAA
1 AAT-TTAATATTAA
1669287 AATTTAATATTAA
1 AATTTAATATTAA
1669300 AAT
1 AAT
1669303 AAAAATATAT
Statistics
Matches: 35, Mismatches: 6, Indels: 7
0.73 0.12 0.15
Matches are distributed among these distances:
12 6 0.17
13 11 0.31
14 8 0.23
15 7 0.20
16 3 0.09
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
AATTTAATATTAA
Found at i:1669323 original size:29 final size:30
Alignment explanation
Indices: 1669291--1669358 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 30
1669281 TATTAAAATT
*
1669291 TAATATTAAAATAAAA-ATATATTTTTTAA
1 TAATATTAAAATAAAATATAAATTTTTTAA
** * *
1669320 TAATATTTTAATAAAATTTAAATTTTTTAT
1 TAATATTAAAATAAAATATAAATTTTTTAA
1669350 TAA-ATTAAA
1 TAATATTAAA
1669359 TTCAATTTAA
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
29 18 0.58
30 13 0.42
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (30 bp):
TAATATTAAAATAAAATATAAATTTTTTAA
Found at i:1670041 original size:26 final size:24
Alignment explanation
Indices: 1670005--1670054 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 24
1669995 TTGGATTGTA
1670005 TTTATTTATTTAATAAAAAATATT
1 TTTATTTATTTAATAAAAAATATT
* *
1670029 TTTATTTAAATTTAATTATAAATATT
1 TTTATTT--ATTTAATAAAAAATATT
1670055 AAAAAATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 7 0.32
26 15 0.68
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (24 bp):
TTTATTTATTTAATAAAAAATATT
Found at i:1670539 original size:23 final size:23
Alignment explanation
Indices: 1670407--1670540 Score: 79
Period size: 23 Copynumber: 6.0 Consensus size: 23
1670397 ATAATTTTAT
1670407 AATATAATA--TAAA-ATAATTAA
1 AATATAATATTTAAATATAA-TAA
1670428 AATATAATATTT-AAT-TACAT-A
1 AATATAATATTTAAATATA-ATAA
* * *
1670449 AATATAAAATTTAAA-ATTATAT
1 AATATAATATTTAAATATAATAA
* *
1670471 AATAATAATTATTAAAAT-TATTAA
1 AAT-ATAA-TATTTAAATATAATAA
* * *
1670495 ATATTTTAA-ATATAATTATAATAA
1 A-A-TATAATATTTAAATATAATAA
1670519 AATATAATATTTAAATATAATA
1 AATATAATATTTAAATATAATA
1670541 TAATTACATA
Statistics
Matches: 83, Mismatches: 16, Indels: 26
0.66 0.13 0.21
Matches are distributed among these distances:
21 23 0.28
22 15 0.18
23 24 0.29
24 16 0.19
25 4 0.05
26 1 0.01
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (23 bp):
AATATAATATTTAAATATAATAA
Found at i:1670559 original size:28 final size:29
Alignment explanation
Indices: 1670393--1670544 Score: 93
Period size: 28 Copynumber: 5.0 Consensus size: 29
1670383 AGACAATATT
1670393 AAATATAAT-TTTATAATATAATATAAAATAATTA
1 AAATATAATATTTA-AATATAAT-T---ATAA-TA
*
1670427 AAATATAATATTT-AAT-TACA-TAAATATA
1 AAATATAATATTTAAATATA-ATTATA-ATA
* *
1670455 AAATTTAAAATTATATAATAATAATTAT--TA
1 AAATATAATATT-TA-AAT-ATAATTATAATA
1670485 AAATTATTAAATATTTTAAATATAATTATAATA
1 AAA-TA-T-AATA-TTTAAATATAATTATAATA
1670518 AAATATAATATTTAAATATAA-TATAAT
1 AAATATAATATTTAAATATAATTATAAT
1670545 TACATAAATT
Statistics
Matches: 97, Mismatches: 6, Indels: 36
0.70 0.04 0.26
Matches are distributed among these distances:
28 20 0.21
29 13 0.13
30 9 0.09
31 14 0.14
32 9 0.09
33 18 0.19
34 11 0.11
35 3 0.03
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (29 bp):
AAATATAATATTTAAATATAATTATAATA
Found at i:1670935 original size:18 final size:19
Alignment explanation
Indices: 1670914--1670955 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
1670904 TTTGATTTAG
*
1670914 TTTATAT-ATTAAACAAAT
1 TTTATATGATAAAACAAAT
*
1670932 TTTATATGATAAAATAAAT
1 TTTATATGATAAAACAAAT
1670951 TTTAT
1 TTTAT
1670956 TAATAAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (19 bp):
TTTATATGATAAAACAAAT
Found at i:1671266 original size:14 final size:14
Alignment explanation
Indices: 1671249--1671299 Score: 66
Period size: 14 Copynumber: 3.4 Consensus size: 14
1671239 TATAATAATA
1671249 TATATATTAAAATT
1 TATATATTAAAATT
*
1671263 TATATAATAAAATTAT
1 TATATATTAAAA-T-T
1671279 TAATATATTAAAATT
1 T-ATATATTAAAATT
1671294 TATATA
1 TATATA
1671300 AATATATAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
14 16 0.50
15 3 0.09
16 3 0.09
17 10 0.31
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
TATATATTAAAATT
Found at i:1671271 original size:31 final size:31
Alignment explanation
Indices: 1671236--1671305 Score: 97
Period size: 31 Copynumber: 2.2 Consensus size: 31
1671226 ATGTGAAAGG
1671236 TAATATAATAA-TATATATATTAAAATTTATA
1 TAATATAATAATTA-ATATATTAAAATTTATA
* *
1671267 TAATAAAATTATTAATATATTAAAATTTATA
1 TAATATAATAATTAATATATTAAAATTTATA
1671298 TAAATATA
1 T-AATATA
1671306 TAAAATTTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
31 27 0.79
32 7 0.21
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (31 bp):
TAATATAATAATTAATATATTAAAATTTATA
Found at i:1671311 original size:19 final size:17
Alignment explanation
Indices: 1671250--1671313 Score: 64
Period size: 19 Copynumber: 3.8 Consensus size: 17
1671240 ATAATAATAT
1671250 ATATATTAAAATTTA-T-
1 ATATA-TAAAATTTATTA
1671266 ATA-ATAAAA-TTATTA
1 ATATATAAAATTTATTA
1671281 ATATATTAAAATTTATATAA
1 ATATA-TAAAATTTAT-T-A
1671301 ATATATAAAATTT
1 ATATATAAAATTT
1671314 TAAATATAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 11
0.79 0.00 0.21
Matches are distributed among these distances:
13 3 0.07
14 6 0.15
15 4 0.10
16 4 0.10
17 5 0.12
18 4 0.10
19 9 0.22
20 6 0.15
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
ATATATAAAATTTATTA
Found at i:1671315 original size:20 final size:20
Alignment explanation
Indices: 1671279--1671345 Score: 66
Period size: 20 Copynumber: 3.4 Consensus size: 20
1671269 ATAAAATTAT
*
1671279 TAATATATTAAAATTTATATA
1 TAATATA-TAAAATTTAAATA
1671300 -AATATATAAAATTTTAAATA
1 TAATATATAAAA-TTTAAATA
* * *
1671320 TAAT-TATAATATATAAAAA
1 TAATATATAAAATTTAAATA
1671339 TAATATA
1 TAATATA
1671346 AATACAAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
19 15 0.38
20 21 0.54
21 3 0.08
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
TAATATATAAAATTTAAATA
Found at i:1671322 original size:22 final size:20
Alignment explanation
Indices: 1671264--1671313 Score: 63
Period size: 17 Copynumber: 2.7 Consensus size: 20
1671254 ATTAAAATTT
*
1671264 ATATAATAAAA-TTAT-T-A
1 ATATATTAAAATTTATATAA
1671281 ATATATTAAAATTTATATAA
1 ATATATTAAAATTTATATAA
1671301 ATATA-TAAAATTT
1 ATATATTAAAATTT
1671314 TAAATATAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
17 10 0.34
18 4 0.14
19 9 0.31
20 6 0.21
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
ATATATTAAAATTTATATAA
Found at i:1671340 original size:37 final size:37
Alignment explanation
Indices: 1671237--1671347 Score: 98
Period size: 37 Copynumber: 2.8 Consensus size: 37
1671227 TGTGAAAGGT
* *
1671237 AATATAATAATATATATATTAAAATTTATATAATAAAATTATT
1 AATATAATTATA-ATATA-TAAAA---ATAT-ATAAAATTATA
* * * *
1671280 AATAT-ATTAAAATTTATATAAATATATAAAATTTTA
1 AATATAATTATAATATATAAAAATATATAAAATTATA
1671316 AATATAATTATAATATATAAAAATAATATAAA
1 AATATAATTATAATATATAAAAAT-ATATAAA
1671348 TACAAAAATT
Statistics
Matches: 57, Mismatches: 9, Indels: 9
0.76 0.12 0.12
Matches are distributed among these distances:
36 14 0.25
37 19 0.33
38 7 0.12
40 4 0.07
41 4 0.07
42 4 0.07
43 5 0.09
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (37 bp):
AATATAATTATAATATATAAAAATATATAAAATTATA
Done.