Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold167
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: 4199719
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.33
Warning! 197959 characters in sequence are not A, C, G, or T
File 8 of 22
Found at i:1043926 original size:29 final size:29
Alignment explanation
Indices: 1043858--1043932 Score: 80
Period size: 29 Copynumber: 2.6 Consensus size: 29
1043848 ATTTTTATTT
* * *
1043858 AAAATGAAATTTTATTTAAATATAAATTA
1 AAAATAAAAATTTATTTAAATATAAATAA
* *
1043887 AAAATATAAATTTATTTTAATAT-AATAA
1 AAAATAAAAATTTATTTAAATATAAATAA
1043915 AAACATAAAAATTATATT
1 AAA-ATAAAAATT-TATT
1043933 AAAAATTATT
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
28 7 0.18
29 27 0.71
30 4 0.11
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.40
Consensus pattern (29 bp):
AAAATAAAAATTTATTTAAATATAAATAA
Found at i:1043934 original size:28 final size:29
Alignment explanation
Indices: 1043876--1043934 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 29
1043866 ATTTTATTTA
* * *
1043876 AATATAAATTAAAAATATAAATTTATTTT
1 AATATAAATAAAAAATATAAAATTATATT
1043905 AATAT-AATAAAAACATA-AAAATTATATT
1 AATATAAATAAAAA-ATATAAAATTATATT
1043933 AA
1 AA
1043935 AAATTATTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
28 18 0.69
29 8 0.31
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (29 bp):
AATATAAATAAAAAATATAAAATTATATT
Found at i:1044046 original size:18 final size:18
Alignment explanation
Indices: 1044025--1044074 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
1044015 AATAGAATCA
1044025 TTTAATTTTTAAATTTAT
1 TTTAATTTTTAAATTTAT
*
1044043 TTT-ATTTTTAAAAATTAT
1 TTTAATTTTT-AAATTTAT
*
1044061 TTTAATATTTAAAT
1 TTTAATTTTTAAAT
1044075 ATTTTATAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 6 0.22
18 16 0.59
19 5 0.19
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTAATTTTTAAATTTAT
Found at i:1044065 original size:36 final size:37
Alignment explanation
Indices: 1043998--1044081 Score: 99
Period size: 36 Copynumber: 2.4 Consensus size: 37
1043988 TTAGATTGAA
*
1043998 TTAAATTT-TTTTA-TTTTAATAGAATCATTTAATTT
1 TTAAATTTATTTTATTTTTAATAGAATCATTTAATAT
*
1044033 TTAAATTTATTTTATTTTTAA-A-AATTATTTTAATAT
1 TTAAATTTATTTTATTTTTAATAGAATCA-TTTAATAT
1044069 TTAAA--TATTTTAT
1 TTAAATTTATTTTAT
1044082 AATTAAATAT
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
34 8 0.18
35 12 0.27
36 18 0.41
37 6 0.14
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.61
Consensus pattern (37 bp):
TTAAATTTATTTTATTTTTAATAGAATCATTTAATAT
Found at i:1044089 original size:15 final size:16
Alignment explanation
Indices: 1044058--1044091 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
1044048 TTTTAAAAAT
*
1044058 TATTTTAATATTTAAA
1 TATTTTAATAATTAAA
1044074 TATTTT-ATAATTAAA
1 TATTTTAATAATTAAA
1044089 TAT
1 TAT
1044092 AAATAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TATTTTAATAATTAAA
Found at i:1044101 original size:27 final size:28
Alignment explanation
Indices: 1044071--1044126 Score: 71
Period size: 27 Copynumber: 2.0 Consensus size: 28
1044061 TTTAATATTT
1044071 AAATATTTTA-TAATTAAAT-ATAAATAA
1 AAAT-TTTTATTAATTAAATAATAAATAA
* *
1044098 AAATTTTTATTTATTAAATAATAATTAA
1 AAATTTTTATTAATTAAATAATAAATAA
1044126 A
1 A
1044127 TTAAATCAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 5 0.20
27 12 0.48
28 8 0.32
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (28 bp):
AAATTTTTATTAATTAAATAATAAATAA
Found at i:1044140 original size:15 final size:16
Alignment explanation
Indices: 1044110--1044150 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
1044100 ATTTTTATTT
*
1044110 ATTAAATAATAATTAA
1 ATTAAATCATAATTAA
1044126 ATTAAATCA-AATTAA
1 ATTAAATCATAATTAA
*
1044141 TTTAAATCAT
1 ATTAAATCAT
1044151 TATATACTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 14 0.64
16 8 0.36
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (16 bp):
ATTAAATCATAATTAA
Found at i:1044465 original size:12 final size:12
Alignment explanation
Indices: 1044444--1044476 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1044434 TATAATTATC
1044444 AATAAA-AATAA
1 AATAAATAATAA
*
1044455 AATATATAATAA
1 AATAAATAATAA
1044467 AATAAATAAT
1 AATAAATAAT
1044477 TTTCATAGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 5 0.26
12 14 0.74
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (12 bp):
AATAAATAATAA
Found at i:1044689 original size:18 final size:20
Alignment explanation
Indices: 1044650--1044691 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
1044640 CAATCATATT
1044650 TAAAATATTATATATTTATA
1 TAAAATATTATATATTTATA
1044670 TAAAAT-TTAATATATTTATA
1 TAAAATATT-ATATATTTATA
1044690 TA
1 TA
1044692 TTTATATTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 2 0.10
20 19 0.90
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TAAAATATTATATATTTATA
Found at i:1044697 original size:14 final size:15
Alignment explanation
Indices: 1044680--1044743 Score: 55
Period size: 14 Copynumber: 4.3 Consensus size: 15
1044670 TAAAATTTAA
1044680 TATATTTATA-TATT
1 TATATTTATATTATT
1044694 TATATTTATATTATT
1 TATATTTATATTATT
*
1044709 T-T-TTCATATTATAT
1 TATATTTATATTAT-T
1044723 CGTAT-TTTATATTATAT
1 --TATATTTATATTAT-T
1044740 TATA
1 TATA
1044744 ATTTTTTATA
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
13 9 0.21
14 12 0.29
15 8 0.19
16 1 0.02
17 12 0.29
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.62
Consensus pattern (15 bp):
TATATTTATATTATT
Found at i:1044754 original size:15 final size:17
Alignment explanation
Indices: 1044715--1044770 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 17
1044705 TATTTTTTCA
1044715 TATTATATCGTAT--TTT
1 TATTATATC-TATAATTT
1044731 ATATTATAT-TATAATTT
1 -TATTATATCTATAATTT
1044748 T-TTATATCGTATAATTT
1 TATTATATC-TATAATTT
1044765 TATTAT
1 TATTAT
1044771 GTTGAAAAGT
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
15 9 0.26
16 1 0.03
17 20 0.59
18 4 0.12
ACGTcount: A:0.32, C:0.04, G:0.04, T:0.61
Consensus pattern (17 bp):
TATTATATCTATAATTT
Found at i:1045170 original size:12 final size:11
Alignment explanation
Indices: 1045136--1045176 Score: 50
Period size: 12 Copynumber: 3.8 Consensus size: 11
1045126 CACAACATTT
1045136 ATATAAAAA-A
1 ATATAAAAATA
*
1045146 ATA-AAACATA
1 ATATAAAAATA
1045156 ATATGAAAAATA
1 ATAT-AAAAATA
1045168 ATATAAAAA
1 ATATAAAAA
1045177 CGGTACGAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
9 4 0.15
10 7 0.27
11 5 0.19
12 10 0.38
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.22
Consensus pattern (11 bp):
ATATAAAAATA
Found at i:1045408 original size:25 final size:23
Alignment explanation
Indices: 1045347--1045410 Score: 60
Period size: 25 Copynumber: 2.7 Consensus size: 23
1045337 ATACACGTAC
*
1045347 ATATAAAAA-TATATATGAAATAA
1 ATATAAAAATTA-ATATGAAACAA
*
1045370 A-ATAAATTATTAATATGTAAACAA
1 ATATAAA-AATTAATATG-AAACAA
1045394 ATATAAAAATGTAATAT
1 ATATAAAAAT-TAATAT
1045411 TTTAAATATA
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
22 5 0.15
23 7 0.21
24 10 0.30
25 11 0.33
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.33
Consensus pattern (23 bp):
ATATAAAAATTAATATGAAACAA
Found at i:1045635 original size:10 final size:10
Alignment explanation
Indices: 1045609--1045643 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
1045599 ACACAACATA
1045609 AATAAAAAAT
1 AATAAAAAAT
*
1045619 AATTAAAACAT
1 AA-TAAAAAAT
1045630 AATAAAAAAT
1 AATAAAAAAT
1045640 AATA
1 AATA
1045644 TGAATATGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
10 13 0.59
11 9 0.41
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (10 bp):
AATAAAAAAT
Found at i:1045807 original size:19 final size:19
Alignment explanation
Indices: 1045785--1045821 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1045775 AAAATACAAT
1045785 ATAAAAAAATAAATATAAC
1 ATAAAAAAATAAATATAAC
* *
1045804 ATAAATATATAAATATAA
1 ATAAAAAAATAAATATAA
1045822 AAATATTTAT
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:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (19 bp):
ATAAAAAAATAAATATAAC
Found at i:1045810 original size:25 final size:25
Alignment explanation
Indices: 1045765--1045822 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
1045755 TATAAAATTT
*
1045765 AAAATTAATTAAAATACAATATAAA
1 AAAATAAATTAAAATACAATATAAA
* *
1045790 AAAATAAATATAACATA-AATATATA
1 AAAATAAAT-TAAAATACAATATAAA
*
1045815 AATATAAA
1 AAAATAAA
1045823 AATATTTATA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 22 0.79
26 6 0.21
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (25 bp):
AAAATAAATTAAAATACAATATAAA
Found at i:1045850 original size:19 final size:19
Alignment explanation
Indices: 1045793--1045856 Score: 71
Period size: 18 Copynumber: 3.5 Consensus size: 19
1045783 ATATAAAAAA
* *
1045793 ATAAATATAACATAAATAT
1 ATAAATATTACATAAATTT
*
1045812 ATAAATA-TA-AAAATATTT
1 ATAAATATTACATAA-ATTT
1045830 ATAAATATTACATAAATTT
1 ATAAATATTACATAAATTT
1045849 AT-AATATT
1 ATAAATATT
1045857 TTAAATAATA
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
17 3 0.08
18 17 0.45
19 15 0.39
20 3 0.08
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (19 bp):
ATAAATATTACATAAATTT
Found at i:1045882 original size:21 final size:21
Alignment explanation
Indices: 1045859--1045900 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
1045849 ATAATATTTT
*
1045859 AAATAATAAAAAATATAAATTAA
1 AAAT-ATAAAAACT-TAAATTAA
1045882 AAATATAAAAACTTAAATT
1 AAATATAAAAACTTAAATT
1045901 TTTTTTTCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
22 8 0.44
23 4 0.22
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (21 bp):
AAATATAAAAACTTAAATTAA
Found at i:1045990 original size:4 final size:4
Alignment explanation
Indices: 1045977--1046039 Score: 51
Period size: 4 Copynumber: 15.8 Consensus size: 4
1045967 AAATACATAA
* *
1045977 TTTC -TTC TTTC TTTTCC TTT- TTTT TTTC -TTC TTTC TTTC TTTC TTTT
1 TTTC TTTC TTTC -TTT-C TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
*
1046024 TTTT TTTCC TTTC TTT
1 TTTC TTT-C TTTC TTT
1046040 TCCTTCTTCC
Statistics
Matches: 50, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
3 9 0.18
4 31 0.62
5 9 0.18
6 1 0.02
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (4 bp):
TTTC
Found at i:1046003 original size:12 final size:13
Alignment explanation
Indices: 1045981--1046040 Score: 61
Period size: 12 Copynumber: 4.5 Consensus size: 13
1045971 ACATAATTTC
1045981 TTCTTTCTTTTCCT
1 TTCTTT-TTTTCCT
1045995 TT-TTTTTTTCTTCT
1 TTCTTTTTTTC--CT
*
1046009 TTCTTTCTTT-CT
1 TTCTTTTTTTCCT
*
1046021 TTTTTTTTTTCCT
1 TTCTTTTTTTCCT
1046034 TTCTTTT
1 TTCTTTT
1046041 CCTTCTTCCT
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
12 15 0.39
13 11 0.29
14 6 0.16
15 6 0.16
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (13 bp):
TTCTTTTTTTCCT
Found at i:1046017 original size:28 final size:25
Alignment explanation
Indices: 1045981--1046039 Score: 82
Period size: 26 Copynumber: 2.2 Consensus size: 25
1045971 ACATAATTTC
*
1045981 TTCTTTCTTTTCCTTTTTTTTTTCTTCT
1 TTCTTTC-TTT-CTTTTTTTTTT-TCCT
1046009 TTCTTTCTTTCTTTTTTTTTTTCCT
1 TTCTTTCTTTCTTTTTTTTTTTCCT
1046034 TTCTTT
1 TTCTTT
1046040 TCCTTCTTCC
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
25 9 0.30
26 11 0.37
27 3 0.10
28 7 0.23
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (25 bp):
TTCTTTCTTTCTTTTTTTTTTTCCT
Found at i:1046037 original size:32 final size:30
Alignment explanation
Indices: 1045977--1046047 Score: 83
Period size: 32 Copynumber: 2.3 Consensus size: 30
1045967 AAATACATAA
1045977 TTTCTTCTTTCTTTTCCTTTTTTTTTTCTTC
1 TTTCTTCTTTCTTTT-CTTTTTTTTTTCTTC
1046008 TTTCTTTCTTTCTTTT-TTTTTTTCCTTTCTT-
1 TTTC-TTCTTTCTTTTCTTTTTTT--TTTCTTC
*
1046039 TTCCTTCTT
1 TTTCTTCTT
1046048 CCTCAGCCTA
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
30 12 0.33
31 7 0.19
32 17 0.47
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (30 bp):
TTTCTTCTTTCTTTTCTTTTTTTTTTCTTC
Found at i:1046050 original size:17 final size:16
Alignment explanation
Indices: 1045978--1046048 Score: 56
Period size: 17 Copynumber: 4.4 Consensus size: 16
1045968 AATACATAAT
1045978 TTCTTCTTTCTTTTCC
1 TTCTTCTTTCTTTTCC
* *
1045994 TT-TT-TTTTTTCTTCT
1 TTCTTCTTTCTT-TTCC
**
1046009 TTCTTTCTTTCTTTTTT
1 TTC-TTCTTTCTTTTCC
*
1046026 TTTTTCCTTTCTTTTCC
1 TTCTT-CTTTCTTTTCC
1046043 TTCTTC
1 TTCTTC
1046049 CTCAGCCTAC
Statistics
Matches: 42, Mismatches: 8, Indels: 10
0.70 0.13 0.17
Matches are distributed among these distances:
14 5 0.12
15 7 0.17
16 5 0.12
17 20 0.48
18 5 0.12
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (16 bp):
TTCTTCTTTCTTTTCC
Found at i:1046318 original size:19 final size:20
Alignment explanation
Indices: 1046294--1046352 Score: 59
Period size: 19 Copynumber: 2.9 Consensus size: 20
1046284 ATATATATTG
*
1046294 ATTTCAAAAAAAATT-ATAA
1 ATTTCAAAAAAAATTCAAAA
1046313 ATTTCAAGAATTAAAATTCAAAA
1 ATTTCAA-AA--AAAATTCAAAA
*
1046336 ATTTC-ATAAAAATTCAA
1 ATTTCAAAAAAAATTCAA
1046353 TTTTTTTATT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
19 16 0.47
20 2 0.06
21 1 0.03
22 7 0.21
23 8 0.24
ACGTcount: A:0.58, C:0.08, G:0.02, T:0.32
Consensus pattern (20 bp):
ATTTCAAAAAAAATTCAAAA
Found at i:1046332 original size:14 final size:16
Alignment explanation
Indices: 1046302--1046338 Score: 51
Period size: 14 Copynumber: 2.4 Consensus size: 16
1046292 TGATTTCAAA
1046302 AAAAATTATAAATTTC
1 AAAAATTATAAATTTC
*
1046318 AAGAATTA-AAA-TTC
1 AAAAATTATAAATTTC
1046332 AAAAATT
1 AAAAATT
1046339 TCATAAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
14 9 0.47
15 3 0.16
16 7 0.37
ACGTcount: A:0.59, C:0.05, G:0.03, T:0.32
Consensus pattern (16 bp):
AAAAATTATAAATTTC
Found at i:1050404 original size:21 final size:21
Alignment explanation
Indices: 1050378--1050418 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
1050368 AAGGGTTCCA
1050378 AATAGTGTGGTCTCGGAATTG
1 AATAGTGTGGTCTCGGAATTG
1050399 AATAGTGTGGTCTCGGAATT
1 AATAGTGTGGTCTCGGAATT
1050419 TTGGCTGAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.10, G:0.32, T:0.34
Consensus pattern (21 bp):
AATAGTGTGGTCTCGGAATTG
Found at i:1051232 original size:69 final size:70
Alignment explanation
Indices: 1051121--1051254 Score: 216
Period size: 69 Copynumber: 1.9 Consensus size: 70
1051111 CCAAAAGTCA
* * *
1051121 TACAATCAGACTGCAAGTAATGAAAGCTATGGTAGGACACATTTATTTTATGTG-TGTGTGTGTA
1 TACAATCAGACTGCAAGTAAAGAAAGCTATGGTAGGAAACATTTATTTTATATGATGTGTGTGTA
1051185 TATAT
66 TATAT
*
1051190 TACAATCAGATTGCAAGTAAAGAAAGCTATGGTAGGAAACATTTATTTTATATGCATGTGTGTGT
1 TACAATCAGACTGCAAGTAAAGAAAGCTATGGTAGGAAACATTTATTTTATATG-ATGTGTGTGT
1051255 GTGTGTGTAT
Statistics
Matches: 59, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
69 50 0.85
71 9 0.15
ACGTcount: A:0.34, C:0.10, G:0.22, T:0.35
Consensus pattern (70 bp):
TACAATCAGACTGCAAGTAAAGAAAGCTATGGTAGGAAACATTTATTTTATATGATGTGTGTGTA
TATAT
Found at i:1054470 original size:24 final size:24
Alignment explanation
Indices: 1054443--1054490 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
1054433 TATTTAATTA
1054443 TTATTTAAA-TAATAAATAATTATT
1 TTATTTAAATTAAT-AATAATTATT
*
1054467 TTATTTAAATTAATTATAATTATT
1 TTATTTAAATTAATAATAATTATT
1054491 AATATAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 18 0.82
25 4 0.18
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (24 bp):
TTATTTAAATTAATAATAATTATT
Found at i:1054498 original size:40 final size:39
Alignment explanation
Indices: 1054421--1054506 Score: 95
Period size: 40 Copynumber: 2.2 Consensus size: 39
1054411 TATAATTCAT
* * * *
1054421 ATTAATTTATTTTATTTAATTATTATTTAAATAATAAATA
1 ATTATTTTATTTAAATTAATTATAATTTAAATAATAAA-A
*
1054461 ATTATTTTATTTAAATTAATTATAATTATTAAT-ATAAAA
1 ATTATTTTATTTAAATTAATTATAATT-TAAATAATAAAA
1054500 A-TATTTT
1 ATTATTTT
1054507 TAATATTATT
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
38 6 0.15
39 2 0.05
40 28 0.70
41 4 0.10
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (39 bp):
ATTATTTTATTTAAATTAATTATAATTTAAATAATAAAA
Found at i:1055544 original size:18 final size:18
Alignment explanation
Indices: 1055523--1055557 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
1055513 TTTATTTTTT
1055523 TTAAAATTTAAATAAATA
1 TTAAAATTTAAATAAATA
1055541 TTAAAATTTAAATAAAT
1 TTAAAATTTAAATAAAT
1055558 TTATTTAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
TTAAAATTTAAATAAATA
Found at i:1055569 original size:19 final size:20
Alignment explanation
Indices: 1055523--1055562 Score: 66
Period size: 18 Copynumber: 2.1 Consensus size: 20
1055513 TTTATTTTTT
1055523 TTAAAATTTAAATAAA--TA
1 TTAAAATTTAAATAAATTTA
1055541 TTAAAATTTAAATAAATTTA
1 TTAAAATTTAAATAAATTTA
1055561 TT
1 TT
1055563 TAATTTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 16 0.80
20 4 0.20
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TTAAAATTTAAATAAATTTA
Found at i:1057574 original size:2 final size:2
Alignment explanation
Indices: 1057567--1057598 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1057557 AAACTTAATA
1057567 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1057599 TCGTATTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1058276 original size:34 final size:37
Alignment explanation
Indices: 1058238--1058305 Score: 99
Period size: 37 Copynumber: 1.9 Consensus size: 37
1058228 AAAACAAATC
1058238 AATTTAAA-TT-ATTATA-TAATAAA-AATTATTTTTT
1 AATTTAAATTTAATTATATTAA-AAATAATTATTTTTT
1058272 AATTTAAATTTAATTATATTAAAAATAATTATTT
1 AATTTAAATTTAATTATATTAAAAATAATTATTT
1058306 AATACATTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
34 8 0.27
35 2 0.07
36 9 0.30
37 11 0.37
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (37 bp):
AATTTAAATTTAATTATATTAAAAATAATTATTTTTT
Found at i:1058280 original size:17 final size:17
Alignment explanation
Indices: 1058238--1058281 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
1058228 AAAACAAATC
1058238 AATTTAAATTATTATAT
1 AATTTAAATTATTATAT
** * *
1058255 AATAAAAATTATTTTTT
1 AATTTAAATTATTATAT
1058272 AATTTAAATT
1 AATTTAAATT
1058282 TAATTATATT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
AATTTAAATTATTATAT
Found at i:1058307 original size:34 final size:33
Alignment explanation
Indices: 1058238--1058308 Score: 90
Period size: 34 Copynumber: 2.1 Consensus size: 33
1058228 AAAACAAATC
* *
1058238 AATTTAAATTATTATATAATAAAAATTATTTTTT
1 AATTTAAATTATTATAT-ATAAAAATAATTATTT
1058272 AATTTAAATTTAATTATAT-TAAAAATAATTATTT
1 AATTTAAA-TT-ATTATATATAAAAATAATTATTT
1058306 AAT
1 AAT
1058309 ACATTAATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
34 24 0.73
35 2 0.06
36 7 0.21
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (33 bp):
AATTTAAATTATTATATATAAAAATAATTATTT
Found at i:1060334 original size:2 final size:2
Alignment explanation
Indices: 1060329--1060356 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1060319 TATATCGCAT
1060329 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
1060357 AATTATAGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1060777 original size:35 final size:34
Alignment explanation
Indices: 1060734--1060802 Score: 86
Period size: 34 Copynumber: 2.0 Consensus size: 34
1060724 ATTTTAAATT
*
1060734 TAAATTTAAATATTTATGATTTTTTATT-TTTTCA
1 TAAATTTAAA-ATTTATAATTTTTTATTATTTTCA
* *
1060768 TAAATTTTAAAGTTTATAATTTTTTTTTATTTTCA
1 TAAA-TTTAAAATTTATAATTTTTTATTATTTTCA
1060803 AATTATAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
34 18 0.60
35 12 0.40
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (34 bp):
TAAATTTAAAATTTATAATTTTTTATTATTTTCA
Found at i:1062656 original size:20 final size:20
Alignment explanation
Indices: 1062614--1062656 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
1062604 ATAAAAACTT
* *
1062614 ATTCATCATTTTGTCATTGA
1 ATTCATAATTTTGTCATTAA
* *
1062634 ATTCATAATTTTTTTATTAA
1 ATTCATAATTTTGTCATTAA
1062654 ATT
1 ATT
1062657 TTTTATAATT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.30, C:0.09, G:0.05, T:0.56
Consensus pattern (20 bp):
ATTCATAATTTTGTCATTAA
Found at i:1062658 original size:13 final size:15
Alignment explanation
Indices: 1062640--1062671 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
1062630 TTGAATTCAT
1062640 AATTTTTT-T-ATTA
1 AATTTTTTATAATTA
1062653 AATTTTTTATAATTA
1 AATTTTTTATAATTA
1062668 AATT
1 AATT
1062672 CATAAAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 8 0.47
14 1 0.06
15 8 0.47
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
AATTTTTTATAATTA
Found at i:1064142 original size:19 final size:21
Alignment explanation
Indices: 1064109--1064148 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
1064099 ATAAAAATTA
1064109 TTTTAATAATATAAT-TATTT
1 TTTTAATAATATAATATATTT
*
1064129 TTTTAAT-ATTTAATATATTT
1 TTTTAATAATATAATATATTT
1064149 AAAATTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
TTTTAATAATATAATATATTT
Found at i:1065729 original size:28 final size:27
Alignment explanation
Indices: 1065673--1065741 Score: 72
Period size: 26 Copynumber: 2.6 Consensus size: 27
1065663 ATTATTATTT
*
1065673 AATT-TTTTATAAAATATTAATATAAA
1 AATTATTTTATAAAATATTAAAATAAA
*
1065699 AATTATTTT-TAATATATTAAAATAATAA
1 AATTATTTTATAAAATATTAAAAT-A-AA
*
1065727 AATTAATTTA-AAAAT
1 AATTATTTTATAAAAT
1065742 TAATTTAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
26 16 0.46
27 5 0.14
28 14 0.40
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (27 bp):
AATTATTTTATAAAATATTAAAATAAA
Found at i:1065742 original size:12 final size:12
Alignment explanation
Indices: 1065725--1065750 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1065715 TTAAAATAAT
1065725 AAAATTAATTTA
1 AAAATTAATTTA
1065737 AAAATTAATTTA
1 AAAATTAATTTA
1065749 AA
1 AA
1065751 TCAGGTCAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
AAAATTAATTTA
Found at i:1066141 original size:23 final size:22
Alignment explanation
Indices: 1066115--1066158 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
1066105 ATTATTTTTA
*
1066115 AATAATAATTTAAATTATAAATT
1 AATAATAAATTAAATT-TAAATT
*
1066138 AATATTAAATTAAATTTAAAT
1 AATAATAAATTAAATTTAAAT
1066159 AAAAATTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
AATAATAAATTAAATTTAAATT
Found at i:1066737 original size:15 final size:16
Alignment explanation
Indices: 1066717--1066760 Score: 56
Period size: 15 Copynumber: 2.8 Consensus size: 16
1066707 AATATTATTA
1066717 ATTTTAAATAAA-AAT
1 ATTTTAAATAAATAAT
1066732 ATTTT-AATAAATAAT
1 ATTTTAAATAAATAAT
*
1066747 AATTTAAATTAAAT
1 ATTTTAAA-TAAAT
1066761 CAGTTTGAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
14 6 0.24
15 12 0.48
16 2 0.08
17 5 0.20
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
ATTTTAAATAAATAAT
Found at i:1070202 original size:25 final size:25
Alignment explanation
Indices: 1070173--1070263 Score: 78
Period size: 25 Copynumber: 3.6 Consensus size: 25
1070163 ATAAATAAAT
1070173 ATTTAAATATTTAAATTTATTATTA
1 ATTTAAATATTTAAATTTATTATTA
*
1070198 ATTTATAA-ATTTAAATTTAAT-TTA
1 ATTTA-AATATTTAAATTTATTATTA
* * ** *
1070222 ATTTTATATGTTTAAAAAATATTAATAA
1 A-TTTAAATATTT-AAATTTATT-ATTA
1070250 ATTTAAATATTTAA
1 ATTTAAATATTTAA
1070264 TAAATATTTT
Statistics
Matches: 51, Mismatches: 9, Indels: 11
0.72 0.13 0.15
Matches are distributed among these distances:
24 5 0.10
25 24 0.47
26 10 0.20
27 9 0.18
28 3 0.06
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (25 bp):
ATTTAAATATTTAAATTTATTATTA
Found at i:1071777 original size:2 final size:2
Alignment explanation
Indices: 1071770--1071798 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1071760 CATACAAGAT
1071770 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1071799 AAGGAAAAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1078483 original size:20 final size:18
Alignment explanation
Indices: 1078456--1078499 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
1078446 ATATATTTGT
*
1078456 ATTTATATTTTTTTATAAA
1 ATTTATATTTTTATA-AAA
1078475 ATATTATATTTTTATAAAA
1 AT-TTATATTTTTATAAAA
1078494 ATTTAT
1 ATTTAT
1078500 TTATACATCT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 4 0.17
19 7 0.30
20 12 0.52
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
ATTTATATTTTTATAAAA
Found at i:1078488 original size:18 final size:16
Alignment explanation
Indices: 1078465--1078501 Score: 56
Period size: 18 Copynumber: 2.2 Consensus size: 16
1078455 TATTTATATT
1078465 TTTTTATAAAATATTATA
1 TTTTTATAAAA-ATT-TA
1078483 TTTTTATAAAAATTTA
1 TTTTTATAAAAATTTA
1078499 TTT
1 TTT
1078502 ATACATCTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 5 0.26
17 3 0.16
18 11 0.58
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TTTTTATAAAAATTTA
Found at i:1078650 original size:172 final size:177
Alignment explanation
Indices: 1078327--1078669 Score: 534
Period size: 172 Copynumber: 1.9 Consensus size: 177
1078317 TCTAATGCAG
* * *
1078327 CTAAAATGGACTACAAGGACTCTTTTAAGGCTGACACGTGGAAATTTTTTTCTTTCATTTTTTTT
1 CTAAAATGGACTACAAGGACACTTCTAAGGCTGACACGTGGAAA-TTTTTTCTTT-ATTATTTTT
* *
1078392 TGTTGAATAAGCTGAAAAAAAAAGAAAGAAAGGAGAAAAAATCGAAAAAAAATTATATATTTGTA
64 TGTTGAATAAGCTGAAAAAAAAAGAAACAAAGGAGAAAAAAT--AAAAAAAATTATATATTCGTA
*
1078457 TTTATATTTTTTTATAAAATATTATATTTTTATAAAAATTTATTTATACAT
127 TTTATATTTTTATATAAAATATTATATTTTTATAAAAATTTATTTATACAT
* *
1078508 CTAAAATGGATTATAAGGACACTTCTAAGGCTGACACGTGGAAA-TTTTTC-TT-TTATTTTTT-
1 CTAAAATGGACTACAAGGACACTTCTAAGGCTGACACGTGGAAATTTTTTCTTTATTATTTTTTG
*
1078569 TTGAATAAGCTGAAAAAAAAAGAAACAAAGGAGAAAAAAT-TAAAAAATTATATATTCGTATTTA
66 TTGAATAAGCTGAAAAAAAAAGAAACAAAGGAGAAAAAATAAAAAAAATTATATATTCGTATTTA
1078633 TATTTTTATATAAAATATTATATTTTTATAAAAATTT
131 TATTTTTATATAAAATATTATATTTTTATAAAAATTT
1078670 TATATATTAA
Statistics
Matches: 153, Mismatches: 9, Indels: 9
0.89 0.05 0.05
Matches are distributed among these distances:
172 58 0.38
175 39 0.25
176 8 0.05
178 2 0.01
179 6 0.04
181 40 0.26
ACGTcount: A:0.43, C:0.07, G:0.11, T:0.39
Consensus pattern (177 bp):
CTAAAATGGACTACAAGGACACTTCTAAGGCTGACACGTGGAAATTTTTTCTTTATTATTTTTTG
TTGAATAAGCTGAAAAAAAAAGAAACAAAGGAGAAAAAATAAAAAAAATTATATATTCGTATTTA
TATTTTTATATAAAATATTATATTTTTATAAAAATTTATTTATACAT
Found at i:1078666 original size:19 final size:20
Alignment explanation
Indices: 1078630--1078674 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
1078620 ATATTCGTAT
1078630 TTATATTTTTATATAAAATA
1 TTATATTTTTATATAAAATA
*
1078650 TTATATTTTTATA-AAAATT
1 TTATATTTTTATATAAAATA
1078669 TTATAT
1 TTATAT
1078675 ATTAATAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 11 0.46
20 13 0.54
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
TTATATTTTTATATAAAATA
Found at i:1078915 original size:17 final size:17
Alignment explanation
Indices: 1078878--1078913 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
1078868 TATTATATTC
1078878 ATATTATTTTATGTTAT
1 ATATTATTTTATGTTAT
1078895 ATATTATTTT-T-TTAT
1 ATATTATTTTATGTTAT
1078910 ATAT
1 ATAT
1078914 ATGGAGTTCG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 8 0.42
16 1 0.05
17 10 0.53
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (17 bp):
ATATTATTTTATGTTAT
Found at i:1079626 original size:36 final size:36
Alignment explanation
Indices: 1079549--1079626 Score: 95
Period size: 36 Copynumber: 2.2 Consensus size: 36
1079539 AACTTACCAA
* * *
1079549 AATATATATAATACTAATTATTGACATATAAAAATT
1 AATATATATAATAATAATTATTGACACATAAAAAAT
* *
1079585 TATATATATTCATAATAATT-TTGACACATAAAAAAT
1 AATATATA-TAATAATAATTATTGACACATAAAAAAT
1079621 AATATA
1 AATATA
1079627 AACACAATAT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
36 26 0.74
37 9 0.26
ACGTcount: A:0.53, C:0.06, G:0.03, T:0.38
Consensus pattern (36 bp):
AATATATATAATAATAATTATTGACACATAAAAAAT
Found at i:1080313 original size:4 final size:4
Alignment explanation
Indices: 1080304--1080366 Score: 53
Period size: 4 Copynumber: 16.2 Consensus size: 4
1080294 TACGTTTGCT
* *
1080304 GAAA GAAA GAAA G-AA GAAA G-AA GAAA AAAA GAAA GACAA GGAA -AAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GA-AA GAAA GAAA
*
1080350 -AAA GAAAA GAAA AAAA G
1 GAAA G-AAA GAAA GAAA G
1080367 TTATATAGTG
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
3 11 0.23
4 30 0.62
5 7 0.15
ACGTcount: A:0.76, C:0.02, G:0.22, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:1080324 original size:15 final size:14
Alignment explanation
Indices: 1080304--1080363 Score: 59
Period size: 15 Copynumber: 4.0 Consensus size: 14
1080294 TACGTTTGCT
1080304 GAAAGAAAGAAAGAA
1 GAAAGAAAGAAA-AA
*
1080319 GAAAGAAGAAAAAAA
1 GAAAGAA-AGAAAAA
1080334 GAAAGACAAGGAAAAA
1 GAAAGA-AA-GAAAAA
1080350 -AAAGAAAAGAAAAA
1 GAAAG-AAAGAAAAA
1080364 AAGTTATATA
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
14 6 0.15
15 22 0.56
16 11 0.28
ACGTcount: A:0.77, C:0.02, G:0.22, T:0.00
Consensus pattern (14 bp):
GAAAGAAAGAAAAA
Found at i:1080455 original size:37 final size:38
Alignment explanation
Indices: 1080395--1080472 Score: 99
Period size: 38 Copynumber: 2.1 Consensus size: 38
1080385 ATTATGTTTT
1080395 ATATTAAAATATTATATTTTTATATA-AATTTTT-TAC
1 ATATTAAAATATTATATTTTTATATATAATTTTTATAC
* *
1080431 ATATTAATAATTATTTTA-TTTTATATATAGTTTTTATAC
1 ATATTAA-AA-TATTATATTTTTATATATAATTTTTATAC
1080470 ATA
1 ATA
1080473 GTATATTCGT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
36 7 0.19
37 11 0.31
38 12 0.33
39 6 0.17
ACGTcount: A:0.40, C:0.03, G:0.01, T:0.56
Consensus pattern (38 bp):
ATATTAAAATATTATATTTTTATATATAATTTTTATAC
Found at i:1080673 original size:12 final size:12
Alignment explanation
Indices: 1080641--1080667 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1080631 TCATATAATA
1080641 TTATATTATTTT
1 TTATATTATTTT
1080653 TTATATTATTTT
1 TTATATTATTTT
1080665 TTA
1 TTA
1080668 ATTTATATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (12 bp):
TTATATTATTTT
Found at i:1080796 original size:16 final size:17
Alignment explanation
Indices: 1080767--1080814 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 17
1080757 TCTATGGCAG
* *
1080767 AGAAAAAGATGAAAAGA
1 AGAAAAAAAAGAAAAGA
1080784 A-AAAAAAAAGAAAA-A
1 AGAAAAAAAAGAAAAGA
*
1080799 AGAAAAGAAAGAAAAG
1 AGAAAAAAAAGAAAAG
1080815 GAGAGAGAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 2 0.08
16 23 0.88
17 1 0.04
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (17 bp):
AGAAAAAAAAGAAAAGA
Found at i:1080968 original size:12 final size:12
Alignment explanation
Indices: 1080948--1081007 Score: 50
Period size: 12 Copynumber: 4.8 Consensus size: 12
1080938 CCGTGTCATA
1080948 TATATTTTTATAT
1 TATA-TTTTATAT
*
1080961 TATGTTTTA-AT
1 TATATTTTATAT
*
1080972 TATTTTTTATAT
1 TATATTTTATAT
*
1080984 CATATTTTAATATT
1 TATATTTT-ATA-T
1080998 TATATATTTA
1 TATAT-TTTA
1081008 AAGTAATATA
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
11 10 0.26
12 13 0.34
13 6 0.16
14 6 0.16
15 3 0.08
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (12 bp):
TATATTTTATAT
Found at i:1080978 original size:23 final size:22
Alignment explanation
Indices: 1080947--1080998 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 22
1080937 TCCGTGTCAT
* *
1080947 ATATATTTTTATATTATGTTTTA
1 ATAT-TTTTTATATCATATTTTA
1080970 ATTATTTTTTATATCATATTTTA
1 A-TATTTTTTATATCATATTTTA
1080993 ATATTT
1 ATATTT
1080999 ATATATTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 5 0.19
23 18 0.69
24 3 0.12
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (22 bp):
ATATTTTTTATATCATATTTTA
Found at i:1081935 original size:16 final size:17
Alignment explanation
Indices: 1081908--1081948 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
1081898 ATTTTAAAAT
1081908 AAAA-TTTA-TTAATT-
1 AAAATTTTATTTAATTA
*
1081922 ATAATTTTATTTAATTA
1 AAAATTTTATTTAATTA
1081939 AAAATTTTAT
1 AAAATTTTAT
1081949 AAATATTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
14 3 0.14
15 4 0.18
16 6 0.27
17 9 0.41
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
AAAATTTTATTTAATTA
Found at i:1082129 original size:8 final size:8
Alignment explanation
Indices: 1082118--1082152 Score: 52
Period size: 8 Copynumber: 4.2 Consensus size: 8
1082108 TTTTTATTTT
1082118 TTAAAAAA
1 TTAAAAAA
1082126 TTAAAAATA
1 TTAAAAA-A
*
1082135 TTAAAATA
1 TTAAAAAA
1082143 TTAAAAAA
1 TTAAAAAA
1082151 TT
1 TT
1082153 TTAAAAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
8 17 0.71
9 7 0.29
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (8 bp):
TTAAAAAA
Found at i:1082140 original size:17 final size:18
Alignment explanation
Indices: 1082118--1082160 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
1082108 TTTTTATTTT
1082118 TTAAAAAATT-AAAAATA
1 TTAAAAAATTAAAAAATA
* *
1082135 TTAAAATATTAAAAAATT
1 TTAAAAAATTAAAAAATA
1082153 TTAAAAAA
1 TTAAAAAA
1082161 ATAATAATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
TTAAAAAATTAAAAAATA
Found at i:1082171 original size:17 final size:17
Alignment explanation
Indices: 1082116--1082171 Score: 67
Period size: 17 Copynumber: 3.2 Consensus size: 17
1082106 ATTTTTTATT
1082116 TTTTAAAAAATTAAAAA
1 TTTTAAAAAATTAAAAA
* *
1082133 TATTAAAATATTAAAAAA
1 TTTTAAAAAATT-AAAAA
* *
1082151 TTTTAAAAAAATAATAA
1 TTTTAAAAAATTAAAAA
1082168 TTTT
1 TTTT
1082172 CGTAGTCAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
17 18 0.56
18 14 0.44
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
TTTTAAAAAATTAAAAA
Found at i:1082592 original size:39 final size:40
Alignment explanation
Indices: 1082517--1082592 Score: 93
Period size: 39 Copynumber: 1.9 Consensus size: 40
1082507 ATAAAATTAA
* * *
1082517 TAAAATGATATATGCTTCATTTATTTTTTAAAATATACTT
1 TAAAATGATATATACTTCATTTAATTTTGAAAATATACTT
*
1082557 TAAAA-GATATATTACTTCA-TTAATTTTGAATATATA
1 TAAAATGATATA-TACTTCATTTAATTTTGAAAATATA
1082593 AAATAATTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
39 20 0.65
40 11 0.35
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.47
Consensus pattern (40 bp):
TAAAATGATATATACTTCATTTAATTTTGAAAATATACTT
Found at i:1083274 original size:2 final size:2
Alignment explanation
Indices: 1083269--1083300 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1083259 TATATATATA
1083269 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1083301 CGTGCGCGCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:1088820 original size:28 final size:30
Alignment explanation
Indices: 1088765--1088820 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
1088755 ATTAATATCT
*
1088765 TAAAATTTATATAATAAATTATTAATTTAA
1 TAAAATTTATATAATAAATTATAAATTTAA
*
1088795 TAAAATTTATATAA-ATA-TATAAATTT
1 TAAAATTTATATAATAAATTATAAATTT
1088821 TTAAATATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 8 0.33
29 2 0.08
30 14 0.58
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (30 bp):
TAAAATTTATATAATAAATTATAAATTTAA
Found at i:1089558 original size:28 final size:28
Alignment explanation
Indices: 1089491--1089562 Score: 75
Period size: 28 Copynumber: 2.7 Consensus size: 28
1089481 AATTATATGA
*
1089491 TATAAATATG--ATGTAAATAAAATAAT
1 TATAAATATGAAATATAAATAAAATAAT
1089517 T-TAAATAT-ATAATATAATATAAAA-AAT
1 TATAAATATGA-AATATAA-ATAAAATAAT
1089544 TATAAATATGAAATA-AAAT
1 TATAAATATGAAATATAAAT
1089563 TATTAATTTA
Statistics
Matches: 39, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
25 7 0.18
26 3 0.08
27 11 0.28
28 17 0.44
29 1 0.03
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (28 bp):
TATAAATATGAAATATAAATAAAATAAT
Found at i:1089608 original size:33 final size:33
Alignment explanation
Indices: 1089570--1089633 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
1089560 AATTATTAAT
1089570 TTATTAAAATATTTAAAATTTATAT-AATATAAA
1 TTATTAAAATA-TTAAAATTTATATAAATATAAA
** *
1089603 TTATTAATTTATTAAAATTTTTATAAATATA
1 TTATTAAAATATTAAAATTTATATAAATATA
1089634 TAATATTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
32 12 0.44
33 15 0.56
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (33 bp):
TTATTAAAATATTAAAATTTATATAAATATAAA
Found at i:1089610 original size:41 final size:40
Alignment explanation
Indices: 1089543--1089639 Score: 137
Period size: 41 Copynumber: 2.4 Consensus size: 40
1089533 ATATAAAAAA
1089543 TTATAAATATGA-AATA-AAATTATTAATTTATTAAAATAT
1 TTATAAATAT-ATAATATAAATTATTAATTTATTAAAATAT
*
1089582 TTA-AAATTTATATAATATAAATTATTAATTTATTAAAATTT
1 TTATAAA--TATATAATATAAATTATTAATTTATTAAAATAT
1089623 TTATAAATATATAATAT
1 TTATAAATATATAATAT
1089640 TTTAAAAATA
Statistics
Matches: 52, Mismatches: 1, Indels: 9
0.84 0.02 0.15
Matches are distributed among these distances:
38 3 0.06
39 4 0.08
40 17 0.33
41 25 0.48
42 3 0.06
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (40 bp):
TTATAAATATATAATATAAATTATTAATTTATTAAAATAT
Found at i:1089856 original size:2 final size:2
Alignment explanation
Indices: 1089849--1089895 Score: 60
Period size: 2 Copynumber: 24.0 Consensus size: 2
1089839 AGTGATAACG
* *
1089849 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AA AA 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
*
1089890 AA AT AT
1 AT AT AT
1089896 TAATATAATA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:1089890 original size:25 final size:25
Alignment explanation
Indices: 1089857--1089928 Score: 81
Period size: 26 Copynumber: 2.8 Consensus size: 25
1089847 CGATATATAT
*
1089857 ATATATATATATATATATATAATAAAA
1 ATATATAAATAT-TA-ATATAATAAAA
1089884 ATATATAAATATTAATATAATAAAA
1 ATATATAAATATTAATATAATAAAA
* * *
1089909 TTTAAATAAATATAAATATA
1 -ATATATAAATATTAATATA
1089929 CAAATTAACG
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
25 11 0.28
26 18 0.45
27 11 0.28
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (25 bp):
ATATATAAATATTAATATAATAAAA
Found at i:1089914 original size:22 final size:23
Alignment explanation
Indices: 1089861--1089923 Score: 69
Period size: 23 Copynumber: 2.8 Consensus size: 23
1089851 ATATATATAT
* *
1089861 ATATATATATATATATAATAAAA
1 ATATATAAATAAATATAATAAAA
1089884 ATATATAAATATTAATATAAT-AAA
1 ATATATAAATA--AATATAATAAAA
1089908 AT-T-TAAATAAATATAA
1 ATATATAAATAAATATAA
1089924 ATATACAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
20 7 0.19
22 6 0.17
23 11 0.31
24 5 0.14
25 7 0.19
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (23 bp):
ATATATAAATAAATATAATAAAA
Found at i:1092082 original size:11 final size:12
Alignment explanation
Indices: 1092065--1092101 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
1092055 TACAAATTTT
1092065 TATTTTTAATTA
1 TATTTTTAATTA
1092077 -ATTTTTAA-TA
1 TATTTTTAATTA
*
1092087 TATTTTAAATTA
1 TATTTTTAATTA
1092099 TAT
1 TAT
1092102 GTATTACTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
10 2 0.09
11 15 0.68
12 5 0.23
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
TATTTTTAATTA
Found at i:1093185 original size:3 final size:3
Alignment explanation
Indices: 1093172--1093206 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
1093162 TGTGATGAGG
* *
1093172 AGA AAA AGA AGA AGA AGG AGA AGA AGA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
1093207 CATGAAGATG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:1094784 original size:12 final size:12
Alignment explanation
Indices: 1094763--1094799 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
1094753 TTATATTTCT
*
1094763 TATATATATATA
1 TATATGTATATA
1094775 TATATGTATATA
1 TATATGTATATA
*
1094787 GATATGTATATA
1 TATATGTATATA
1094799 T
1 T
1094800 TACATTATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.43, C:0.00, G:0.08, T:0.49
Consensus pattern (12 bp):
TATATGTATATA
Found at i:1095936 original size:3 final size:3
Alignment explanation
Indices: 1095917--1095969 Score: 81
Period size: 3 Copynumber: 18.0 Consensus size: 3
1095907 TGACATAAAA
* *
1095917 TAT TGT TAT TGT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1095964 TAT TAT
1 TAT TAT
1095970 ATATATAGAC
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
2 2 0.04
3 43 0.96
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:1096447 original size:6 final size:6
Alignment explanation
Indices: 1096419--1096494 Score: 50
Period size: 6 Copynumber: 12.7 Consensus size: 6
1096409 AAAATATATA
* * * *
1096419 ATATTT AAATTT AATAATAT ATATTT ATATGTT TTA-TT ATATTT ATAATT
1 ATATTT ATATTT -AT-ATTT ATATTT ATAT-TT ATATTT ATATTT ATATTT
**
1096469 ATATTT A-AAAT AT-TTT ATATTT ATAT
1 ATATTT ATATTT ATATTT ATATTT ATAT
1096495 AAATTTTAAT
Statistics
Matches: 52, Mismatches: 12, Indels: 12
0.68 0.16 0.16
Matches are distributed among these distances:
5 10 0.19
6 32 0.62
7 7 0.13
8 3 0.06
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (6 bp):
ATATTT
Found at i:1096492 original size:22 final size:22
Alignment explanation
Indices: 1096407--1096494 Score: 65
Period size: 22 Copynumber: 4.0 Consensus size: 22
1096397 AATTTCTTAA
* * *
1096407 TTAAAATATATAATATTTAAAT
1 TTAAAATATTTTATATTTATAT
1096429 TTAATAATA---TATATTTATAT
1 TTAA-AATATTTTATATTTATAT
** * *
1096449 GTTTTATTATATTTATAATTATAT
1 -TTAAAATAT-TTTATATTTATAT
1096473 TTAAAATATTTTATATTTATAT
1 TTAAAATATTTTATATTTATAT
1096495 AAATTTTAAT
Statistics
Matches: 50, Mismatches: 10, Indels: 12
0.69 0.14 0.17
Matches are distributed among these distances:
20 12 0.24
21 2 0.04
22 16 0.32
23 10 0.20
24 10 0.20
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (22 bp):
TTAAAATATTTTATATTTATAT
Found at i:1100747 original size:15 final size:16
Alignment explanation
Indices: 1100721--1100750 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1100711 TAAAATTTTA
1100721 ATATTAAAATAATTAT
1 ATATTAAAATAATTAT
1100737 ATATT-AAATAATTA
1 ATATTAAAATAATTA
1100751 ATAAAAGTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
ATATTAAAATAATTAT
Found at i:1100861 original size:13 final size:14
Alignment explanation
Indices: 1100833--1100859 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1100823 ATCTTGTATA
1100833 AAAATAATATTTTT
1 AAAATAATATTTTT
1100847 AAAATAATATTTT
1 AAAATAATATTTT
1100860 AATATTTTTA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
AAAATAATATTTTT
Found at i:1101197 original size:21 final size:22
Alignment explanation
Indices: 1101172--1101213 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
1101162 AATATGACAC
1101172 ATATAAAATAAATATA-ATTTA
1 ATATAAAATAAATATATATTTA
*
1101193 ATATAATATAAATATATATTT
1 ATATAAAATAAATATATATTT
1101214 TAAAATTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
ATATAAAATAAATATATATTTA
Found at i:1101211 original size:15 final size:15
Alignment explanation
Indices: 1101193--1101264 Score: 57
Period size: 15 Copynumber: 5.1 Consensus size: 15
1101183 ATATAATTTA
1101193 ATATAATATAAATAT
1 ATATAATATAAATAT
** *
1101208 ATATTTTA-AAATTT
1 ATATAATATAAATAT
*
1101222 ATATAACATAAAT-T
1 ATATAATATAAATAT
1101236 AT-T-ATATAAA-ATT
1 ATATAATATAAATA-T
1101249 ATATAATATAAA-AT
1 ATATAATATAAATAT
1101263 AT
1 AT
1101265 TTTAAATATA
Statistics
Matches: 45, Mismatches: 7, Indels: 11
0.71 0.11 0.17
Matches are distributed among these distances:
12 6 0.13
13 4 0.09
14 17 0.38
15 18 0.40
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (15 bp):
ATATAATATAAATAT
Found at i:1101249 original size:13 final size:15
Alignment explanation
Indices: 1101193--1101262 Score: 69
Period size: 13 Copynumber: 4.9 Consensus size: 15
1101183 ATATAATTTA
1101193 ATATAATAT-AAA-T
1 ATATAATATAAAATT
* *
1101206 ATATATTTTAAAATTT
1 ATATAATATAAAA-TT
*
1101222 ATATAACAT-AAATT
1 ATATAATATAAAATT
1101236 AT-T-ATATAAAATT
1 ATATAATATAAAATT
1101249 ATATAATATAAAAT
1 ATATAATATAAAAT
1101263 ATTTTAAATA
Statistics
Matches: 45, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
12 3 0.07
13 15 0.33
14 8 0.18
15 12 0.27
16 7 0.16
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (15 bp):
ATATAATATAAAATT
Found at i:1101250 original size:27 final size:25
Alignment explanation
Indices: 1101172--1101288 Score: 94
Period size: 27 Copynumber: 4.5 Consensus size: 25
1101162 AATATGACAC
* * * *
1101172 ATATAAAATAAATATAATTTAATATA
1 ATATAACATAAA-ATATTTTAAAATT
*
1101198 ATATAA-AT-ATATATTTTAAAATTT
1 ATATAACATAAAATATTTTAAAA-TT
*
1101222 ATATAACATAAATTATTATATAAAATT
1 ATATAACATAAAATATT-T-TAAAATT
* *
1101249 ATATAATATAAAATATTTTAAATATA
1 ATATAACATAAAATATTTTAAA-ATT
1101275 ATTATAACATAAAA
1 A-TATAACATAAAA
1101289 ATATAAAAAT
Statistics
Matches: 74, Mismatches: 10, Indels: 13
0.76 0.10 0.13
Matches are distributed among these distances:
23 9 0.12
24 8 0.11
25 8 0.11
26 15 0.20
27 29 0.39
28 5 0.07
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (25 bp):
ATATAACATAAAATATTTTAAAATT
Found at i:1102352 original size:17 final size:19
Alignment explanation
Indices: 1102326--1102360 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1102316 TTATTTTTAG
1102326 TTTATATTTAAA-TAAATT
1 TTTATATTTAAATTAAATT
1102344 TTTAT-TTTAAATTAAAT
1 TTTATATTTAAATTAAAT
1102361 ATTAATTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TTTATATTTAAATTAAATT
Found at i:1102358 original size:22 final size:23
Alignment explanation
Indices: 1102318--1102361 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1102308 TAAATTTTTT
*
1102318 ATTTTTAGTTTATATTTAAATAA
1 ATTTTTAGTTTATAATTAAATAA
*
1102341 ATTTTTATTTTA-AATTAAATA
1 ATTTTTAGTTTATAATTAAATA
1102362 TTAATTTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (23 bp):
ATTTTTAGTTTATAATTAAATAA
Found at i:1102365 original size:29 final size:30
Alignment explanation
Indices: 1102300--1102363 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 30
1102290 CTACCTAATT
* * *
1102300 TATTTAAATAAATTTTTTATTTTTAGTTTA
1 TATTTAAATAAATTTTTTATTTTAAATTAA
1102330 TATTTAAATAAA-TTTTTATTTTAAATTAAA
1 TATTTAAATAAATTTTTTATTTTAAATT-AA
1102360 TATT
1 TATT
1102364 AATTTATATT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 13 0.43
30 17 0.57
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (30 bp):
TATTTAAATAAATTTTTTATTTTAAATTAA
Found at i:1102435 original size:28 final size:29
Alignment explanation
Indices: 1102404--1102463 Score: 95
Period size: 29 Copynumber: 2.1 Consensus size: 29
1102394 ATTATAAGTT
*
1102404 AAATTTA-TTTGATACAAATTAAATATTA
1 AAATTTATTTTGATACAAATTAAAAATTA
*
1102432 AAATTTATTTTGATATAAATTAAAAATTA
1 AAATTTATTTTGATACAAATTAAAAATTA
1102461 AAA
1 AAA
1102464 GTTGATAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 7 0.24
29 22 0.76
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.42
Consensus pattern (29 bp):
AAATTTATTTTGATACAAATTAAAAATTA
Found at i:1103079 original size:7 final size:7
Alignment explanation
Indices: 1103069--1103100 Score: 50
Period size: 6 Copynumber: 4.9 Consensus size: 7
1103059 TTTAAAACTA
1103069 TTTAAAT
1 TTTAAAT
1103076 TTT-AAT
1 TTTAAAT
1103082 TTT-AAT
1 TTTAAAT
1103088 TTTAAAT
1 TTTAAAT
1103095 TTTAAA
1 TTTAAA
1103101 AATAATTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 12 0.50
7 12 0.50
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
TTTAAAT
Found at i:1103106 original size:19 final size:19
Alignment explanation
Indices: 1103069--1103107 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
1103059 TTTAAAACTA
***
1103069 TTTAAATTTTAATTTTAAT
1 TTTAAATTTTAAAAATAAT
1103088 TTTAAATTTTAAAAATAAT
1 TTTAAATTTTAAAAATAAT
1103107 T
1 T
1103108 CAATAAATTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TTTAAATTTTAAAAATAAT
Found at i:1103675 original size:10 final size:10
Alignment explanation
Indices: 1103645--1103682 Score: 58
Period size: 10 Copynumber: 3.7 Consensus size: 10
1103635 AAATTAAATA
1103645 AAAATAATTT
1 AAAATAATTT
1103655 AATAATAATTT
1 AA-AATAATTT
*
1103666 AAATTAATTT
1 AAAATAATTT
1103676 AAAATAA
1 AAAATAA
1103683 AAATATTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 15 0.60
11 10 0.40
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (10 bp):
AAAATAATTT
Found at i:1103687 original size:37 final size:38
Alignment explanation
Indices: 1103640--1103727 Score: 101
Period size: 37 Copynumber: 2.4 Consensus size: 38
1103630 AGGTAAAATT
1103640 AAATAAAAATAATTTAATAAT-AATTTAAATTAATT-TA
1 AAATAAAAATAATTT-ATAATAAATTTAAATTAATTATA
** * *
1103677 AAATAAAAAT-ATTTATTTTAAATTTAATTTAATTATT
1 AAATAAAAATAATTTATAATAAATTTAAATTAATTATA
*
1103714 AAATAAAATTAATT
1 AAATAAAAATAATT
1103728 ATTTAGAAAG
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
35 3 0.07
36 17 0.40
37 20 0.47
38 3 0.07
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (38 bp):
AAATAAAAATAATTTATAATAAATTTAAATTAATTATA
Found at i:1104052 original size:22 final size:22
Alignment explanation
Indices: 1104027--1104071 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
1104017 TTTTTGAATT
1104027 AGTAAAAATTAAAAAAA-TTAAA
1 AGTAAAAA-TAAAAAAATTTAAA
**
1104049 AGTATGAATAAAAAAATTTAAA
1 AGTAAAAATAAAAAAATTTAAA
1104071 A
1 A
1104072 AAATTAAAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.69, C:0.00, G:0.07, T:0.24
Consensus pattern (22 bp):
AGTAAAAATAAAAAAATTTAAA
Found at i:1104443 original size:10 final size:10
Alignment explanation
Indices: 1104430--1104493 Score: 55
Period size: 10 Copynumber: 6.5 Consensus size: 10
1104420 TTTAGATATA
1104430 ATATAAAAAT
1 ATATAAAAAT
1104440 ATATAAAAA-
1 ATATAAAAAT
1104449 ATA-ATAAAAT
1 ATATA-AAAAT
*
1104459 A-ATATAAAT
1 ATATAAAAAT
*
1104468 ATAAAATAAAT
1 ATATAA-AAAT
1104479 ATA-AAAAATT
1 ATATAAAAA-T
1104489 ATATA
1 ATATA
1104494 TATAATTATA
Statistics
Matches: 44, Mismatches: 3, Indels: 13
0.73 0.05 0.22
Matches are distributed among these distances:
8 1 0.02
9 16 0.36
10 19 0.43
11 8 0.18
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (10 bp):
ATATAAAAAT
Found at i:1104457 original size:20 final size:19
Alignment explanation
Indices: 1104429--1104487 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 19
1104419 TTTTAGATAT
1104429 AATATAAAAATATATAAAA
1 AATATAAAAATATATAAAA
*
1104448 AATA-ATAAAATA-AT-ATA
1 AATATA-AAAATATATAAAA
*
1104465 AATATAAAATAAATATAAAA
1 AATATAAAA-ATATATAAAA
1104485 AAT
1 AAT
1104488 TATATATATA
Statistics
Matches: 32, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
17 9 0.28
18 6 0.19
19 12 0.38
20 5 0.16
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (19 bp):
AATATAAAAATATATAAAA
Found at i:1104464 original size:35 final size:36
Alignment explanation
Indices: 1104425--1104514 Score: 110
Period size: 37 Copynumber: 2.4 Consensus size: 36
1104415 ATAATTTTAG
1104425 ATATAATATAAAAATATATAAAAAATAATA-AAATA
1 ATATAATATAAAAATATATAAAAAATAATATAAATA
* * *
1104460 ATATAAATATAAAATAAATATAAAAAATTATATATATA
1 ATAT-AATATAAAA-ATATATAAAAAATAATATAAATA
*
1104498 ATTATAATATATAAATA
1 A-TATAATATAAAAATA
1104515 ACACAAAAAC
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
35 4 0.09
36 9 0.20
37 17 0.37
38 13 0.28
39 3 0.07
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (36 bp):
ATATAATATAAAAATATATAAAAAATAATATAAATA
Found at i:1104491 original size:27 final size:27
Alignment explanation
Indices: 1104429--1104483 Score: 53
Period size: 26 Copynumber: 2.1 Consensus size: 27
1104419 TTTTAGATAT
*
1104429 AATATAAAA-ATATATAAAA-AATAATA
1 AATATAAAATAAATATAAAATAAT-ATA
*
1104455 AA-ATAATATAAATATAAAATAAATATA
1 AATATAAAATAAATATAAAAT-AATATA
1104482 AA
1 AA
1104484 AAATTATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
25 5 0.21
26 11 0.46
27 5 0.21
28 3 0.12
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (27 bp):
AATATAAAATAAATATAAAATAATATA
Found at i:1104509 original size:29 final size:28
Alignment explanation
Indices: 1104440--1104512 Score: 82
Period size: 27 Copynumber: 2.7 Consensus size: 28
1104430 ATATAAAAAT
1104440 ATATAAAA-AATA-ATAAAATAATATAA
1 ATATAAAATAATATATAAAATAATATAA
*
1104466 ATATAAAATAA-ATATAAAA-AATTATAT
1 ATATAAAATAATATATAAAATAA-TATAA
*
1104493 ATATAATTATAATATATAAA
1 ATATAA-AATAATATATAAA
1104513 TAACACAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
26 11 0.28
27 18 0.45
28 4 0.10
29 7 0.17
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (28 bp):
ATATAAAATAATATATAAAATAATATAA
Found at i:1104515 original size:11 final size:11
Alignment explanation
Indices: 1104430--1104515 Score: 51
Period size: 11 Copynumber: 7.9 Consensus size: 11
1104420 TTTAGATATA
1104430 ATATAAA-AAT
1 ATATAAATAAT
*
1104440 ATATAAAAAAT
1 ATATAAATAAT
1104451 A-ATAAAATAAT
1 ATAT-AAATAAT
1104462 ATA-AATATAA-
1 ATATAA-ATAAT
1104472 A-ATAAAT-AT
1 ATATAAATAAT
*
1104481 A-AAAAATTATAT
1 ATATAAA-TA-AT
1104493 ATATAATTATAAT
1 ATATAA--ATAAT
1104506 ATATAAATAA
1 ATATAAATAA
1104516 CACAAAAACA
Statistics
Matches: 61, Mismatches: 3, Indels: 23
0.70 0.03 0.26
Matches are distributed among these distances:
8 1 0.02
9 8 0.13
10 15 0.25
11 19 0.31
12 4 0.07
13 11 0.18
14 2 0.03
15 1 0.02
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
ATATAAATAAT
Found at i:1104828 original size:17 final size:17
Alignment explanation
Indices: 1104806--1104891 Score: 68
Period size: 17 Copynumber: 4.8 Consensus size: 17
1104796 GTAAATTTAT
*
1104806 TAATTATAAATATGATA
1 TAATTATAAATATAATA
*
1104823 TAATTATAAAATATAAAAAA
1 TAATTAT-AAATAT--AATA
1104843 TAATTAT-AATATAATAA
1 TAATTATAAATATAAT-A
*
1104860 TAA-TATAAATATGATA
1 TAATTATAAATATAATA
*
1104876 TGAATATAAAAATATA
1 T-AAT-TATAAATATA
1104892 TTAAAATTTA
Statistics
Matches: 55, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
16 7 0.13
17 20 0.36
18 11 0.20
19 8 0.15
20 9 0.16
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.36
Consensus pattern (17 bp):
TAATTATAAATATAATA
Found at i:1104864 original size:20 final size:20
Alignment explanation
Indices: 1104806--1104864 Score: 56
Period size: 20 Copynumber: 3.1 Consensus size: 20
1104796 GTAAATTTAT
*
1104806 TAATTATAA-AT-ATGAT-A
1 TAATTATAATATAATAATAA
1104823 TAATTATAAAATATAA-AA-AA
1 TAATTAT--AATATAATAATAA
1104843 TAATTATAATATAATAATAA
1 TAATTATAATATAATAATAA
1104863 TA
1 TA
1104865 TAAATATGAT
Statistics
Matches: 34, Mismatches: 1, Indels: 11
0.74 0.02 0.24
Matches are distributed among these distances:
17 7 0.21
18 7 0.21
19 4 0.12
20 15 0.44
21 1 0.03
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (20 bp):
TAATTATAATATAATAATAA
Found at i:1104896 original size:11 final size:11
Alignment explanation
Indices: 1104882--1104931 Score: 50
Period size: 10 Copynumber: 4.6 Consensus size: 11
1104872 GATATGAATA
1104882 TAAAAATATAT
1 TAAAAATATAT
*
1104893 T-AAAATTTAT
1 TAAAAATATAT
*
1104903 ATAAAATTA-AT
1 -TAAAAATATAT
*
1104914 TAATAATATAT
1 TAAAAATATAT
1104925 TAAAAAT
1 TAAAAAT
1104932 TTATATAAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
10 14 0.47
11 12 0.40
12 4 0.13
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
TAAAAATATAT
Found at i:1104904 original size:22 final size:22
Alignment explanation
Indices: 1104820--1104940 Score: 65
Period size: 22 Copynumber: 5.5 Consensus size: 22
1104810 TATAAATATG
1104820 ATATAATTATAAA-ATATA-AAAA
1 ATAT-ATTA-AAATATATATAAAA
* *
1104842 ATA-ATTATAATATA-ATAATA
1 ATATATTAAAATATATATAAAA
* **
1104862 ATATAAATATGATATGAATATAAAA
1 ATAT-ATTAAAATAT--ATATAAAA
*
1104887 ATATATTAAAATTTATATAAAA
1 ATATATTAAAATATATATAAAA
*
1104909 TTA-ATTAATAATATAT-TAAAA
1 ATATATTAA-AATATATATAAAA
*
1104930 ATTTATATAAA
1 ATATAT-TAAA
1104941 TCACTTTTAA
Statistics
Matches: 76, Mismatches: 13, Indels: 20
0.70 0.12 0.18
Matches are distributed among these distances:
19 3 0.04
20 13 0.17
21 11 0.14
22 30 0.39
23 3 0.04
24 7 0.09
25 9 0.12
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (22 bp):
ATATATTAAAATATATATAAAA
Found at i:1105858 original size:26 final size:24
Alignment explanation
Indices: 1105829--1105877 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
1105819 ATATTTTATA
1105829 TTTATAAAATATTAATATATTAATAC
1 TTTATAAAATA-TAA-ATATTAATAC
**
1105855 TTTATATTATATAAATATTAATA
1 TTTATAAAATATAAATATTAATA
1105878 TATTTATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 9 0.43
25 3 0.14
26 9 0.43
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (24 bp):
TTTATAAAATATAAATATTAATAC
Found at i:1105862 original size:32 final size:32
Alignment explanation
Indices: 1105818--1105893 Score: 104
Period size: 32 Copynumber: 2.4 Consensus size: 32
1105808 TAGTATTTAA
1105818 AATATTTTATATTTATA-AAATATTAATATATT
1 AATA-TTTATATTTATATAAATATTAATATATT
1105850 AATACTTTATA-TTATATAAATATTAATATATT
1 AATA-TTTATATTTATATAAATATTAATATATT
*
1105882 TATA-TTATATTT
1 AATATTTATATTT
1105894 TTATTTTTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
30 5 0.12
31 7 0.17
32 28 0.70
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (32 bp):
AATATTTATATTTATATAAATATTAATATATT
Found at i:1105890 original size:11 final size:11
Alignment explanation
Indices: 1105766--1105898 Score: 58
Period size: 11 Copynumber: 11.5 Consensus size: 11
1105756 AAAGATAATA
1105766 ATATATATATTT
1 ATAT-TATATTT
*
1105778 ATATTAAATTT
1 ATATTATATTT
1105789 ATA-TAT-TTT
1 ATATTATATTT
1105798 AT-TTATATGTT
1 ATATTATAT-TT
**
1105809 AGTATT-TAAAAT
1 A-TATTAT-ATTT
*
1105821 ATTTTATATTT
1 ATATTATATTT
**
1105832 ATAAAATATTAAT
1 ATATTATATT--T
1105845 ATATTAATACTTT
1 ATATT-ATA-TTT
*
1105858 ATATTATATAAAT
1 ATATTATAT--TT
*
1105871 ATTAATATATTT
1 A-TATTATATTT
1105883 ATATTATATTT
1 ATATTATATTT
*
1105894 TTATT
1 ATATT
1105899 TTTAAATTAT
Statistics
Matches: 90, Mismatches: 17, Indels: 29
0.66 0.12 0.21
Matches are distributed among these distances:
9 8 0.09
10 3 0.03
11 38 0.42
12 14 0.16
13 15 0.17
14 10 0.11
15 2 0.02
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.56
Consensus pattern (11 bp):
ATATTATATTT
Found at i:1105891 original size:19 final size:19
Alignment explanation
Indices: 1105764--1105918 Score: 52
Period size: 19 Copynumber: 8.5 Consensus size: 19
1105754 CAAAAGATAA
*
1105764 TAATATATATAT-TTATAT
1 TAATATATTTATATTATAT
*
1105782 TAA-AT-TTATATATTTTAT
1 TAATATATT-TATATTATAT
1105800 T--TATATGTTAGTATT-TA-
1 TAATATAT-TTA-TATTATAT
*
1105817 AAATAT-TTTATATT-TA-
1 TAATATATTTATATTATAT
*
1105833 TAAAATA-TTA-A-TATAT
1 TAATATATTTATATTATAT
*
1105849 TAATACTTTATATTATATAAATAT
1 TAATA---TAT-TTATAT-TATAT
1105873 TAATATATTTATATTATAT
1 TAATATATTTATATTATAT
** * *
1105892 TTTTATTTTTAAATTATA-
1 TAATATATTTATATTATAT
1105910 TAAT-TATTT
1 TAATATATTT
1105919 TGTATATTTA
Statistics
Matches: 103, Mismatches: 15, Indels: 39
0.66 0.10 0.25
Matches are distributed among these distances:
14 1 0.01
15 3 0.03
16 18 0.17
17 14 0.14
18 17 0.17
19 28 0.27
20 6 0.06
21 6 0.06
22 1 0.01
24 9 0.09
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (19 bp):
TAATATATTTATATTATAT
Found at i:1105898 original size:25 final size:24
Alignment explanation
Indices: 1105845--1105891 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
1105835 AAATATTAAT
*
1105845 ATATTAATACTTTATATTATATAA
1 ATATTAATAATTTATATTATATAA
1105869 ATATTAATATATTTATATTATAT
1 ATATTAATA-ATTTATATTATAT
1105892 TTTTATTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 9 0.43
25 12 0.57
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (24 bp):
ATATTAATAATTTATATTATATAA
Found at i:1105919 original size:19 final size:19
Alignment explanation
Indices: 1105880--1105919 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1105870 TATTAATATA
* **
1105880 TTTATATTATATTTTTATT
1 TTTAAATTATATAATTATT
1105899 TTTAAATTATATAATTATT
1 TTTAAATTATATAATTATT
1105918 TT
1 TT
1105920 GTATATTTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTAAATTATATAATTATT
Found at i:1105928 original size:26 final size:24
Alignment explanation
Indices: 1105881--1105929 Score: 62
Period size: 26 Copynumber: 2.0 Consensus size: 24
1105871 ATTAATATAT
* *
1105881 TTATATTATATTTTTATTTTTAAA
1 TTATATAATATTTTTATATTTAAA
1105905 TTATATAATTATTTTGTATATTTAA
1 TTATATAA-TATTTT-TATATTTAA
1105930 TTTTTATCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 7 0.33
25 6 0.29
26 8 0.38
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (24 bp):
TTATATAATATTTTTATATTTAAA
Found at i:1106484 original size:19 final size:18
Alignment explanation
Indices: 1106460--1106495 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
1106450 TAAAAAATAA
*
1106460 AAAATAATTAAAGTTTATT
1 AAAATAAATAAA-TTTATT
1106479 AAAATAAATAAATTTAT
1 AAAATAAATAAATTTAT
1106496 ATATTTTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (18 bp):
AAAATAAATAAATTTATT
Found at i:1106688 original size:16 final size:17
Alignment explanation
Indices: 1106667--1106699 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1106657 TATTTAAAAA
*
1106667 TTTAATTTTTA-ATTTT
1 TTTAATTATTATATTTT
1106683 TTTAATTATTATATTTT
1 TTTAATTATTATATTTT
1106700 AAAAATTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTAATTATTATATTTT
Found at i:1113931 original size:2 final size:2
Alignment explanation
Indices: 1113926--1113955 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1113916 TTTTTTGGGA
1113926 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
1113956 GCATGAATGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1114346 original size:15 final size:15
Alignment explanation
Indices: 1114328--1114365 Score: 53
Period size: 13 Copynumber: 2.7 Consensus size: 15
1114318 TTTTTTTTAA
1114328 AAATATTTTAAATAT
1 AAATATTTTAAATAT
1114343 AAATA--TTAAATAT
1 AAATATTTTAAATAT
*
1114356 GAATATTTTA
1 AAATATTTTA
1114366 TATAGTTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
13 12 0.60
15 8 0.40
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (15 bp):
AAATATTTTAAATAT
Found at i:1115976 original size:30 final size:34
Alignment explanation
Indices: 1115912--1115983 Score: 91
Period size: 31 Copynumber: 2.3 Consensus size: 34
1115902 TGACGTTTCA
*
1115912 TAATTA-AAAAATTATTTTATTTAAATTTAATAT
1 TAATTATAAAAATTATTTTATTAAAATTTAATAT
*
1115945 TAA-TATAAAAATTA-TTT-TTAAAATTT-TTAT
1 TAATTATAAAAATTATTTTATTAAAATTTAATAT
1115975 TAATTATAA
1 TAATTATAA
1115984 TAGTAAATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
30 6 0.17
31 13 0.37
32 5 0.14
33 11 0.31
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (34 bp):
TAATTATAAAAATTATTTTATTAAAATTTAATAT
Found at i:1117483 original size:22 final size:24
Alignment explanation
Indices: 1117453--1117498 Score: 69
Period size: 22 Copynumber: 2.0 Consensus size: 24
1117443 GGGTGAATTG
*
1117453 TTTTTATAAAAAAA-AAA-ATAAA
1 TTTTAATAAAAAAATAAAGATAAA
1117475 TTTTAATAAAAAAATAAAGATAAA
1 TTTTAATAAAAAAATAAAGATAAA
1117499 GATGAATTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 13 0.62
23 3 0.14
24 5 0.24
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (24 bp):
TTTTAATAAAAAAATAAAGATAAA
Found at i:1123118 original size:2 final size:2
Alignment explanation
Indices: 1123113--1123138 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1123103 AAAAAAGAAA
1123113 AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC
1123139 TGGAAACACC
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:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1124539 original size:132 final size:132
Alignment explanation
Indices: 1124354--1124620 Score: 444
Period size: 132 Copynumber: 2.0 Consensus size: 132
1124344 AATAGGGGCA
*
1124354 CAATGGTTATTACTCCTACCTACCAAGAACGAGAAGTGCATATTCTCTCATCTTCTAACTTGCCA
1 CAATGGTTATTACTCCTACCCACCAAGAACGAGAAGTGCATATTCTCTCATCTTCTAACTTGCCA
* * * *
1124419 TTAAATGTTAATGCTGATACCCAACCGAATCTTGGATCTAAAGCCTGCACATTGCTTAATCCTCT
66 TCAAATGTCAATGCTGATACCCAACCGAATCTTGGATCCAAAGCCTGCACATTGCTTAATCCTAT
1124484 CT
131 CT
* **
1124486 CAATGGTTATTACTCCTGCCCACCAAGAACGAGAAGTGCATATTCTCTCATCTTCTAACTTGCTG
1 CAATGGTTATTACTCCTACCCACCAAGAACGAGAAGTGCATATTCTCTCATCTTCTAACTTGCCA
* *
1124551 TCAAATGTCAATGCTGATACCCAGCCGAATCTTGGATCCAAAGCCTGCACATTGTTTAATCCTAT
66 TCAAATGTCAATGCTGATACCCAACCGAATCTTGGATCCAAAGCCTGCACATTGCTTAATCCTAT
1124616 CT
131 CT
1124618 CAA
1 CAA
1124621 CTTCACGAAA
Statistics
Matches: 125, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
132 125 1.00
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.31
Consensus pattern (132 bp):
CAATGGTTATTACTCCTACCCACCAAGAACGAGAAGTGCATATTCTCTCATCTTCTAACTTGCCA
TCAAATGTCAATGCTGATACCCAACCGAATCTTGGATCCAAAGCCTGCACATTGCTTAATCCTAT
CT
Found at i:1125667 original size:29 final size:31
Alignment explanation
Indices: 1125639--1125700 Score: 88
Period size: 34 Copynumber: 1.9 Consensus size: 31
1125629 TTTGCTATGC
1125639 CATGCCTAGAATAATCAGTTTTGCCATGCCGTG
1 CATGCCTAGAATAATCAGTTTTGCCATGCC--G
*
1125672 TCATGCCTAGAATAATCAGTTTTGTCATG
1 -CATGCCTAGAATAATCAGTTTTGCCATG
1125701 TTTCAAAGTG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
34 27 1.00
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (31 bp):
CATGCCTAGAATAATCAGTTTTGCCATGCCG
Found at i:1129668 original size:12 final size:13
Alignment explanation
Indices: 1129651--1129683 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
1129641 GAACGCAGGT
1129651 ACAACAACAGA-A
1 ACAACAACAGACA
1129663 ACAACAAC-GACA
1 ACAACAACAGACA
1129675 ACAACAACA
1 ACAACAACA
1129684 ACCTAAGCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 2 0.11
12 17 0.89
ACGTcount: A:0.64, C:0.30, G:0.06, T:0.00
Consensus pattern (13 bp):
ACAACAACAGACA
Done.