Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 113035596
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: 113035596
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 271 characters in sequence are not A, C, G, or T
File 365 of 378
Found at i:109432916 original size:2 final size:2
Alignment explanation
Indices: 109432909--109432933 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
109432899 ATTCAAGTCT
109432909 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 T
109432934 TTCTTTTCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:109436908 original size:8 final size:9
Alignment explanation
Indices: 109436887--109436912 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
109436877 TAAATTTTAA
109436887 AAAAAATTC
1 AAAAAATTC
109436896 AAAAAATTC
1 AAAAAATTC
109436905 AAAAAATT
1 AAAAAATT
109436913 ATTCTTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.23
Consensus pattern (9 bp):
AAAAAATTC
Found at i:109436916 original size:21 final size:18
Alignment explanation
Indices: 109436884--109436941 Score: 53
Period size: 20 Copynumber: 2.9 Consensus size: 18
109436874 TTTTAAATTT
*
109436884 TAAAAAAAATTCAAAAAA
1 TAAAAAATATTCAAAAAA
109436902 TTCAAAAAATTATTCTTAAAAAA
1 -T-AAAAAA-TATTC--AAAAAA
*
109436925 TAAAAAATATTTAAAAA
1 TAAAAAATATTCAAAAA
109436942 GTCTAAATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
18 5 0.15
19 1 0.03
20 10 0.30
21 10 0.30
22 1 0.03
23 6 0.18
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (18 bp):
TAAAAAATATTCAAAAAA
Found at i:109437319 original size:21 final size:21
Alignment explanation
Indices: 109437277--109437319 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
109437267 ATCAACTCTG
* *
109437277 TTAAACATTAAATAATATTTT
1 TTAAACAATAAATAATAATTT
*
109437298 TTAAACAATAAATATTAATTT
1 TTAAACAATAAATAATAATTT
109437319 T
1 T
109437320 AATTTAATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.47
Consensus pattern (21 bp):
TTAAACAATAAATAATAATTT
Found at i:109442383 original size:68 final size:67
Alignment explanation
Indices: 109442311--109442460 Score: 171
Period size: 67 Copynumber: 2.2 Consensus size: 67
109442301 CATCATGTGT
* * * *
109442311 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACC
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACC
109442373 ATGTAG
62 ATGTAG
** * *
109442379 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGT
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
109442444 AG
66 AG
109442446 ACAAGAGAGCTACGA
1 ACAAGAGAGCTACGA
109442461 GATAAACTGG
Statistics
Matches: 70, Mismatches: 9, Indels: 7
0.81 0.10 0.08
Matches are distributed among these distances:
64 20 0.29
65 7 0.10
66 4 0.06
67 26 0.37
68 13 0.19
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (67 bp):
ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
AG
Found at i:109442416 original size:64 final size:64
Alignment explanation
Indices: 109442335--109442518 Score: 194
Period size: 67 Copynumber: 2.8 Consensus size: 64
109442325 AGACATTATG
* *
109442335 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * * *
109442399 ATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
109442464 AA
63 AA
* * * *
109442466 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 A-TGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG-ACAAGAGAGC
109442519 CGAACTATAT
Statistics
Matches: 98, Mismatches: 17, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
62 1 0.01
63 19 0.19
64 21 0.21
65 8 0.08
66 16 0.16
67 31 0.32
68 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:109445549 original size:20 final size:19
Alignment explanation
Indices: 109445524--109445567 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
109445514 GGACTAAATT
109445524 AAAAATATATAAATTTATG-G
1 AAAAAT-TATAAATTT-TGTG
*
109445544 AAAAATTCTAAATTTTGTG
1 AAAAATTATAAATTTTGTG
109445563 AAAAA
1 AAAAA
109445568 CATGGGCTGC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 2 0.09
19 14 0.64
20 6 0.27
ACGTcount: A:0.55, C:0.02, G:0.09, T:0.34
Consensus pattern (19 bp):
AAAAATTATAAATTTTGTG
Found at i:109448979 original size:31 final size:31
Alignment explanation
Indices: 109448901--109448990 Score: 87
Period size: 31 Copynumber: 3.0 Consensus size: 31
109448891 TCAAATGAAT
* *
109448901 GCCAAAC-CTTTCAAAA-TAGTCAAATAAGG
1 GCCAAACATTTTCAAAAGTACTCAAATAAGG
* ** * *
109448930 GCCTAACATTTTTGAAAGTACTCAGATAGGG
1 GCCAAACATTTTCAAAAGTACTCAAATAAGG
*
109448961 GCCAAACATTTTCAAAAGTGCTCAAA-AAGG
1 GCCAAACATTTTCAAAAGTACTCAAATAAGG
109448991 ACTTCTCAAA
Statistics
Matches: 46, Mismatches: 13, Indels: 3
0.74 0.21 0.05
Matches are distributed among these distances:
29 6 0.13
30 9 0.20
31 31 0.67
ACGTcount: A:0.40, C:0.19, G:0.18, T:0.23
Consensus pattern (31 bp):
GCCAAACATTTTCAAAAGTACTCAAATAAGG
Found at i:109450761 original size:21 final size:20
Alignment explanation
Indices: 109450732--109450770 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
109450722 TTAGAGATAA
109450732 TATTATTTAAAAAAATAAATT
1 TATTATTT-AAAAAATAAATT
* *
109450753 TATTTTTTATAAAATAAA
1 TATTATTTAAAAAATAAA
109450771 AATAATATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
TATTATTTAAAAAATAAATT
Found at i:109451032 original size:9 final size:9
Alignment explanation
Indices: 109450998--109451036 Score: 51
Period size: 9 Copynumber: 4.1 Consensus size: 9
109450988 TAATAAATAT
109450998 ATTTATTAA
1 ATTTATTAA
*
109451007 ATTTTATTTAT
1 A-TTTA-TTAA
109451018 ATTTATTAA
1 ATTTATTAA
109451027 ATTTATTAA
1 ATTTATTAA
109451036 A
1 A
109451037 ATACAAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
9 14 0.54
10 8 0.31
11 4 0.15
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (9 bp):
ATTTATTAA
Found at i:109451074 original size:15 final size:15
Alignment explanation
Indices: 109451044--109451072 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
109451034 AAAATACAAA
109451044 AAAATAAATATTTTT
1 AAAATAAATATTTTT
109451059 AAAAT-AATATTTTT
1 AAAATAAATATTTTT
109451073 TATTTTATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
AAAATAAATATTTTT
Found at i:109451330 original size:17 final size:17
Alignment explanation
Indices: 109451304--109451336 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
109451294 ATTGATGTTA
109451304 TATTAATAAAATTATTT
1 TATTAATAAAATTATTT
*
109451321 TATTACTAAAATTATT
1 TATTAATAAAATTATT
109451337 AATTTAATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (17 bp):
TATTAATAAAATTATTT
Found at i:109452366 original size:22 final size:22
Alignment explanation
Indices: 109452336--109452379 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
109452326 GGTCGAAATC
*
109452336 AAAAAATTAAATTATAATTTTT
1 AAAAAATTAAATTAAAATTTTT
*
109452358 AAAAGATTAAATTAAAATTTTT
1 AAAAAATTAAATTAAAATTTTT
109452380 TTTTATTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
AAAAAATTAAATTAAAATTTTT
Found at i:109452400 original size:32 final size:32
Alignment explanation
Indices: 109452354--109452417 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
109452344 AAATTATAAT
*
109452354 TTTTAAAAGATTAAATTAAAATTTT-TTTTTA
1 TTTTAAAAGATTAAAATAAAATTTTATTTTTA
*
109452385 TTTTAAAAGAGTTAAAATATAATTTTATTTTTA
1 TTTTAAAAGA-TTAAAATAAAATTTTATTTTTA
109452418 CTAGTTTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 10 0.34
32 13 0.45
33 6 0.21
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (32 bp):
TTTTAAAAGATTAAAATAAAATTTTATTTTTA
Found at i:109452733 original size:30 final size:32
Alignment explanation
Indices: 109452693--109452755 Score: 85
Period size: 30 Copynumber: 2.0 Consensus size: 32
109452683 AGCCTATATC
109452693 TTTATAATTTTTAAAGAATTAAA-T-TAATTT
1 TTTATAATTTTTAAAGAATTAAAGTGTAATTT
* * *
109452723 TTTATCATTTTTAGAGGATTAAAGTGTAATTT
1 TTTATAATTTTTAAAGAATTAAAGTGTAATTT
109452755 T
1 T
109452756 ATTTTTACTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 20 0.71
31 1 0.04
32 7 0.25
ACGTcount: A:0.37, C:0.02, G:0.10, T:0.52
Consensus pattern (32 bp):
TTTATAATTTTTAAAGAATTAAAGTGTAATTT
Found at i:109462623 original size:33 final size:31
Alignment explanation
Indices: 109462575--109462640 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
109462565 ACATCATGGG
*
109462575 AATTTAAAAAAAAACACAGGTGAACTAGAAAAA
1 AATTT-AAAAAAAA-ACAGGTGAAATAGAAAAA
* * *
109462608 AATTTGAAAAGAAACAGTTGAAATAGAAAAA
1 AATTTAAAAAAAAACAGGTGAAATAGAAAAA
109462639 AA
1 AA
109462641 AAAGGAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 18 0.62
32 6 0.21
33 5 0.17
ACGTcount: A:0.64, C:0.06, G:0.14, T:0.17
Consensus pattern (31 bp):
AATTTAAAAAAAAACAGGTGAAATAGAAAAA
Found at i:109463701 original size:34 final size:34
Alignment explanation
Indices: 109463655--109463721 Score: 107
Period size: 34 Copynumber: 2.0 Consensus size: 34
109463645 GTGTGAGTGT
* **
109463655 GGGTGTTTATATATAGTTTATGTATATATAATGC
1 GGGTGTTCATATATAACTTATGTATATATAATGC
109463689 GGGTGTTCATATATAACTTATGTATATATAATG
1 GGGTGTTCATATATAACTTATGTATATATAATG
109463722 ACAGAGTTGA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.31, C:0.04, G:0.19, T:0.45
Consensus pattern (34 bp):
GGGTGTTCATATATAACTTATGTATATATAATGC
Found at i:109465726 original size:4 final size:4
Alignment explanation
Indices: 109465717--109465752 Score: 72
Period size: 4 Copynumber: 9.0 Consensus size: 4
109465707 ATAACATAAG
109465717 CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA
109465753 TCAGTCACAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:109468035 original size:27 final size:28
Alignment explanation
Indices: 109467988--109468044 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 28
109467978 TGTAATTTAA
**
109467988 ATTAAGTTTTAATTAAGTATTGTTTATT
1 ATTAAGTTTTAATTAAGTATTAATTATT
*
109468016 ATTAAGTTTT-A-TATGATATTAATTATT
1 ATTAAGTTTTAATTAAG-TATTAATTATT
109468043 AT
1 AT
109468045 AAAATATTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
26 3 0.12
27 12 0.48
28 10 0.40
ACGTcount: A:0.35, C:0.00, G:0.09, T:0.56
Consensus pattern (28 bp):
ATTAAGTTTTAATTAAGTATTAATTATT
Found at i:109468051 original size:17 final size:18
Alignment explanation
Indices: 109468031--109468068 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
109468021 GTTTTATATG
*
109468031 ATATTA-ATTATTATAAA
1 ATATTATATTATTAGAAA
*
109468048 ATATTATTTTATTAGAAA
1 ATATTATATTATTAGAAA
109468066 ATA
1 ATA
109468069 AATTTCCATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (18 bp):
ATATTATATTATTAGAAA
Found at i:109469372 original size:14 final size:15
Alignment explanation
Indices: 109469355--109469388 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
109469345 AATTGGACTA
*
109469355 AAAAAATTTAAA-TT
1 AAAAAATATAAATTT
109469369 AAAAAATATAAATTT
1 AAAAAATATAAATTT
109469384 AAAAA
1 AAAAA
109469389 CCAAATAGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
AAAAAATATAAATTT
Found at i:109470356 original size:18 final size:18
Alignment explanation
Indices: 109470335--109470392 Score: 62
Period size: 18 Copynumber: 3.1 Consensus size: 18
109470325 GTTTTTAATT
*
109470335 AATTTTTAAATTTTAAAA
1 AATTTTAAAATTTTAAAA
***
109470353 AATTTTAAAAAAATAAAA
1 AATTTTAAAATTTTAAAA
109470371 AATTATTAAAATTATTAAAA
1 AATT-TTAAAATT-TTAAAA
109470391 AA
1 AA
109470393 CATTAACTTT
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
18 18 0.58
19 6 0.19
20 7 0.23
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
AATTTTAAAATTTTAAAA
Found at i:109472836 original size:29 final size:30
Alignment explanation
Indices: 109472803--109472884 Score: 91
Period size: 29 Copynumber: 2.9 Consensus size: 30
109472793 GCAATTAATT
* *
109472803 AATTATTTTTAAATTTAAAAAATT-TTAAA
1 AATTATTTTAAAAATTAAAAAATTATTAAA
*
109472832 AATTATTTTAAAAATTAAAAAGTTATTAAA
1 AATTATTTTAAAAATTAAAAAATTATTAAA
* *
109472862 AAGTA---TAAATATTAAAAAATTAT
1 AATTATTTTAAAAATTAAAAAATTAT
109472885 AAATATAAGA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
27 16 0.35
29 21 0.46
30 9 0.20
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.41
Consensus pattern (30 bp):
AATTATTTTAAAAATTAAAAAATTATTAAA
Found at i:109472841 original size:12 final size:12
Alignment explanation
Indices: 109472816--109472848 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
109472806 TATTTTTAAA
109472816 TTTAAAAA--AT
1 TTTAAAAATTAT
109472826 TTTAAAAATTAT
1 TTTAAAAATTAT
109472838 TTTAAAAATTA
1 TTTAAAAATTA
109472849 AAAAGTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 8 0.38
12 13 0.62
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
TTTAAAAATTAT
Found at i:109472876 original size:16 final size:17
Alignment explanation
Indices: 109472855--109472890 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
109472845 ATTAAAAAGT
109472855 TATT-AAAAAGTATAAA
1 TATTAAAAAAGTATAAA
*
109472871 TATTAAAAAATTATAAA
1 TATTAAAAAAGTATAAA
109472888 TAT
1 TAT
109472891 AAGATGTCAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (17 bp):
TATTAAAAAAGTATAAA
Found at i:109474021 original size:38 final size:41
Alignment explanation
Indices: 109473959--109474047 Score: 121
Period size: 38 Copynumber: 2.2 Consensus size: 41
109473949 TAAAAAGTAT
*
109473959 TTATATTAAAAAATACTACCATAAATATAATAAATATTTTA
1 TTATATTAAAAAATACTACAATAAATATAATAAATATTTTA
* *
109474000 TTATATTAAAAAA-AC-A-AATAAATGTAATAAGTATTTTA
1 TTATATTAAAAAATACTACAATAAATATAATAAATATTTTA
*
109474038 TTGTATTAAA
1 TTATATTAAA
109474048 TATAATTTTA
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
38 28 0.64
39 1 0.02
40 2 0.05
41 13 0.30
ACGTcount: A:0.53, C:0.04, G:0.03, T:0.39
Consensus pattern (41 bp):
TTATATTAAAAAATACTACAATAAATATAATAAATATTTTA
Found at i:109480143 original size:6 final size:6
Alignment explanation
Indices: 109480132--109480156 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
109480122 GGAAGGTGTG
109480132 GAGGCA GAGGCA GAGGCA GAGGCA G
1 GAGGCA GAGGCA GAGGCA GAGGCA G
109480157 CGGTTTGTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.16, G:0.52, T:0.00
Consensus pattern (6 bp):
GAGGCA
Found at i:109480208 original size:17 final size:17
Alignment explanation
Indices: 109480186--109480218 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
109480176 ATAAAGGAGG
109480186 AAGAGAGAA-AAGAAAAC
1 AAGAGA-AAGAAGAAAAC
109480203 AAGAGAAAGAAGAAAA
1 AAGAGAAAGAAGAAAA
109480219 ATACTAGAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 2 0.13
17 13 0.87
ACGTcount: A:0.73, C:0.03, G:0.24, T:0.00
Consensus pattern (17 bp):
AAGAGAAAGAAGAAAAC
Found at i:109485538 original size:40 final size:41
Alignment explanation
Indices: 109485466--109485556 Score: 123
Period size: 40 Copynumber: 2.2 Consensus size: 41
109485456 AAAAAAATAT
*
109485466 TTATATTAAAAAACACTACCATAAATACAATAAATATTTTA
1 TTATATTAAAAAACACTACAATAAATACAATAAATATTTTA
**
109485507 TTATATTAAAAGAACAC-A-AATAAATGTAATAAATATTTTA
1 TTATATTAAAA-AACACTACAATAAATACAATAAATATTTTA
*
109485547 TTGTATTAAA
1 TTATATTAAA
109485557 TATAATTTTA
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
40 28 0.62
41 12 0.27
42 5 0.11
ACGTcount: A:0.53, C:0.08, G:0.03, T:0.36
Consensus pattern (41 bp):
TTATATTAAAAAACACTACAATAAATACAATAAATATTTTA
Found at i:109486784 original size:6 final size:6
Alignment explanation
Indices: 109486766--109486812 Score: 69
Period size: 6 Copynumber: 7.8 Consensus size: 6
109486756 CAAAATACTA
*
109486766 TAATAA TAA-AT TAATAT TAATAT TAATAT TAATAT TAATAT TGAATA
1 TAATAT TAATAT TAATAT TAATAT TAATAT TAATAT TAATAT T-AATA
109486813 AAATAAAAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
5 4 0.11
6 30 0.79
7 4 0.11
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (6 bp):
TAATAT
Found at i:109492260 original size:137 final size:137
Alignment explanation
Indices: 109492014--109492289 Score: 534
Period size: 137 Copynumber: 2.0 Consensus size: 137
109492004 ACCAAAGATG
*
109492014 AAGATATCTATCTTTTCCCTCCAAATATCATTATTTATCATTTCTCTCGGTGTATCTATTTTATA
1 AAGATATCTATCTTTTCCCTCCAAATATCATTATTTATCATTTCTCTCGGTGTATCCATTTTATA
109492079 AAATTTCTTTAATCATTCTCATAGATTTTTTAAAGAAAGAAGAAAAAATATAAAAATATCATTTT
66 AAATTTCTTTAATCATTCTCATAGATTTTTTAAAGAAAGAAGAAAAAATATAAAAATATCATTTT
109492144 CGATTTT
131 CGATTTT
*
109492151 AAGATATCTATCTTTTCCCTCCAAATATCATTATTTATCATTTTTCTCGGTGTATCCATTTTATA
1 AAGATATCTATCTTTTCCCTCCAAATATCATTATTTATCATTTCTCTCGGTGTATCCATTTTATA
109492216 AAATTTCTTTAATCATTCTCATAGATTTTTTAAAGAAAGAAGAAAAAATATAAAAATATCATTTT
66 AAATTTCTTTAATCATTCTCATAGATTTTTTAAAGAAAGAAGAAAAAATATAAAAATATCATTTT
109492281 CGATTTT
131 CGATTTT
109492288 AA
1 AA
109492290 TTTTCTTGTA
Statistics
Matches: 137, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
137 137 1.00
ACGTcount: A:0.36, C:0.14, G:0.07, T:0.43
Consensus pattern (137 bp):
AAGATATCTATCTTTTCCCTCCAAATATCATTATTTATCATTTCTCTCGGTGTATCCATTTTATA
AAATTTCTTTAATCATTCTCATAGATTTTTTAAAGAAAGAAGAAAAAATATAAAAATATCATTTT
CGATTTT
Found at i:109493307 original size:29 final size:29
Alignment explanation
Indices: 109493251--109493307 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
109493241 TTAACTTTAT
* *
109493251 ATTGAATTTTGTTAATTTACTTTTATTTG
1 ATTGAATTTTGTTAATTTAATTTAATTTG
109493280 ATTGAATTTTGTT-ATTTAATTATAATTT
1 ATTGAATTTTGTTAATTTAATT-TAATTT
109493308 AAAATATTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 7 0.28
29 18 0.72
ACGTcount: A:0.28, C:0.02, G:0.09, T:0.61
Consensus pattern (29 bp):
ATTGAATTTTGTTAATTTAATTTAATTTG
Found at i:109494428 original size:30 final size:30
Alignment explanation
Indices: 109494367--109494430 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 30
109494357 TATTGAGTGT
**
109494367 TAAATTTTAATTAAAAATCAAAATTCTTAA
1 TAAATTTTAATTAAAAATCAAAATTAATAA
*
109494397 TAAATTTTAA-TAAAATTCAAAGATTAATAA
1 TAAATTTTAATTAAAAATCAAA-ATTAATAA
109494427 TAAA
1 TAAA
109494431 ATGTAACCAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.38
Consensus pattern (30 bp):
TAAATTTTAATTAAAAATCAAAATTAATAA
Found at i:109494491 original size:12 final size:12
Alignment explanation
Indices: 109494476--109494517 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
109494466 TAATTTTTTA
109494476 AAATATAATGAT
1 AAATATAATGAT
*
109494488 AAATATCAA-AAT
1 AAATAT-AATGAT
109494500 AAAGTATAATGAT
1 AAA-TATAATGAT
109494513 AAATA
1 AAATA
109494518 ATTACAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
12 15 0.60
13 10 0.40
ACGTcount: A:0.62, C:0.02, G:0.07, T:0.29
Consensus pattern (12 bp):
AAATATAATGAT
Found at i:109496949 original size:19 final size:19
Alignment explanation
Indices: 109496925--109496979 Score: 76
Period size: 18 Copynumber: 2.9 Consensus size: 19
109496915 ATAATGCTAA
109496925 AAAATAAATTATTTTAATT
1 AAAATAAATTATTTTAATT
*
109496944 AAAAT-AACTATTTTAATT
1 AAAATAAATTATTTTAATT
* *
109496962 AAAATATATTATCTTAAT
1 AAAATAAATTATTTTAAT
109496980 CAAATTTAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
18 17 0.55
19 14 0.45
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (19 bp):
AAAATAAATTATTTTAATT
Found at i:109497330 original size:2 final size:2
Alignment explanation
Indices: 109497323--109497350 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
109497313 TGTAGTTAGG
109497323 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
109497351 TATTCTAAAG
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:109499083 original size:3 final size:3
Alignment explanation
Indices: 109499075--109499108 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
109499065 AAAAATCGAA
109499075 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
109499109 TAAGTAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:109501358 original size:20 final size:21
Alignment explanation
Indices: 109501333--109501374 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
109501323 AGTTAATTTT
*
109501333 TTTATTTTA-TTTTACTATTA
1 TTTATTATATTTTTACTATTA
109501353 TTTATTATATTTTTACTATTA
1 TTTATTATATTTTTACTATTA
109501374 T
1 T
109501375 AGTTATTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.69
Consensus pattern (21 bp):
TTTATTATATTTTTACTATTA
Found at i:109501372 original size:18 final size:19
Alignment explanation
Indices: 109501342--109501386 Score: 56
Period size: 21 Copynumber: 2.3 Consensus size: 19
109501332 TTTTATTTTA
109501342 TTTTACTATTATTTA-TTATAT
1 TTTTACTATTA--TAGTTAT-T
109501363 TTTTACTATTATAGTTATT
1 TTTTACTATTATAGTTATT
109501382 TTTTA
1 TTTTA
109501387 TTTTCATTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 8 0.35
20 4 0.17
21 11 0.48
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (19 bp):
TTTTACTATTATAGTTATT
Found at i:109501407 original size:27 final size:26
Alignment explanation
Indices: 109501348--109501408 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 26
109501338 TTTATTTTAC
109501348 TATTATTTATTATATTTTTACTATTA
1 TATTATTTATTATATTTTTACTATTA
*
109501374 TAGTTATTTTTTAT-TTTCATTACTACTT-
1 TA-TTATTTATTATATTT--TTACTA-TTA
109501402 TATTATT
1 TATTATT
109501409 ATTGTAATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
26 5 0.17
27 15 0.50
28 8 0.27
29 2 0.07
ACGTcount: A:0.26, C:0.07, G:0.02, T:0.66
Consensus pattern (26 bp):
TATTATTTATTATATTTTTACTATTA
Found at i:109501520 original size:3 final size:3
Alignment explanation
Indices: 109501501--109501557 Score: 55
Period size: 3 Copynumber: 19.3 Consensus size: 3
109501491 TTTTGAATTG
* * *
109501501 TTA TCA TTA TTA CTA TTA TTA -TA TTA -TA TTTA TTA TTA TTA CTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
*
109501545 TTA TTA CTA TTA T
1 TTA TTA TTA TTA T
109501558 ATTTTAATCT
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
2 4 0.09
3 37 0.86
4 2 0.05
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:109501520 original size:9 final size:9
Alignment explanation
Indices: 109501506--109501557 Score: 61
Period size: 9 Copynumber: 5.6 Consensus size: 9
109501496 AATTGTTATC
109501506 ATTATTACT
1 ATTATTACT
109501515 ATTATTA-T
1 ATTATTACT
*
109501523 ATTATATTTATT
1 A-T-TA-TTACT
109501535 ATTATTACT
1 ATTATTACT
109501544 ATTATTACT
1 ATTATTACT
109501553 ATTAT
1 ATTAT
109501558 ATTTTAATCT
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
8 2 0.05
9 26 0.68
10 4 0.11
11 4 0.11
12 2 0.05
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.60
Consensus pattern (9 bp):
ATTATTACT
Found at i:109501569 original size:15 final size:14
Alignment explanation
Indices: 109501522--109501634 Score: 63
Period size: 15 Copynumber: 7.5 Consensus size: 14
109501512 ACTATTATTA
109501522 TATTATATTTATTAT-
1 TATTATA-TT-TTATC
109501537 TATTACTATTATTA-C
1 TATTA-TATT-TTATC
109501552 TATTATATTTTAATC
1 TATTATATTTT-ATC
*
109501567 TATATTTATTTTATC
1 TAT-TATATTTTATC
*
109501582 TAATTTTA-TTTATC
1 T-ATTATATTTTATC
109501596 TATTTATATCTCTGTTAT-
1 TA-TTATA--T-T-TTATC
*
109501614 TATTATATTTTATG
1 TATTATATTTTATC
109501628 TATTATA
1 TATTATA
109501635 CCTATATTTA
Statistics
Matches: 83, Mismatches: 2, Indels: 27
0.74 0.02 0.24
Matches are distributed among these distances:
13 7 0.08
14 24 0.29
15 29 0.35
16 11 0.13
17 5 0.06
18 3 0.04
19 4 0.05
ACGTcount: A:0.30, C:0.06, G:0.02, T:0.62
Consensus pattern (14 bp):
TATTATATTTTATC
Found at i:109501757 original size:3 final size:3
Alignment explanation
Indices: 109501749--109502174 Score: 224
Period size: 3 Copynumber: 144.0 Consensus size: 3
109501739 TTTATTAAAC
109501749 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
109501797 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATTT GTT AGTT A-T ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT A-TT ATT ATT
* * * * ** *
109501843 ACT ATT ATT GTT A-T ATTT ATT CTT ACT ATT ATT ATT ATT ACC ACT
1 ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * ** * **
109501888 ACT ATG ATT TTT ATT AAC A-T ATT ATT GTT ATT -TT -TT ACC A-T ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * **
109501932 ATT ATT -TCCT ATCT TTT ATAT ATT ATT ATT GTT ATT AAC ATAT ATT
1 ATT ATT AT--T AT-T ATT AT-T ATT ATT ATT ATT ATT ATT AT-T ATT
* * *
109501978 ATT ATT AAT -TT ACT ATT ATT -TT CACTT -TT ATT ATT ATT ATT ACT
1 ATT ATT ATT ATT ATT ATT ATT ATT -A-TT ATT ATT ATT ATT ATT ATT
* * * * ** *
109502022 A-T ATT ATT ATT GTT ATT ATT GTT -TT CTAT ATT ATT AAT ACA AAT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT
* * * * *
109502066 ATT AATT -TT CTT ATT ATT ACT ATT ATT AGT ATC A-T AGGT ATT ATT
1 ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT
* * * *
109502111 -TT ATT ATT ATT -TT -TT A-T ATT ATC CTT -TT ATT ACT ATT ATT TTT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * *
109502154 ATC AAT ATT ATT AAT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT
109502175 GTTTTCATTA
Statistics
Matches: 324, Mismatches: 70, Indels: 58
0.72 0.15 0.13
Matches are distributed among these distances:
2 33 0.10
3 265 0.82
4 23 0.07
5 3 0.01
ACGTcount: A:0.31, C:0.06, G:0.03, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:109502226 original size:4 final size:4
Alignment explanation
Indices: 109502217--109502247 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
109502207 ATGTTTTATG
*
109502217 TTTA TTTA TTTA TTTA TTTA TTTA TGTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
109502248 GCTTATTTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:109507889 original size:2 final size:2
Alignment explanation
Indices: 109507882--109507909 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
109507872 TAAATTAGTC
109507882 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
109507910 TAATATTCTC
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:109515076 original size:27 final size:24
Alignment explanation
Indices: 109515045--109515102 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 24
109515035 TGGGTAATCA
*
109515045 TTTTAGGGGTAAACTTAAATTATAAAT
1 TTTTAGGAGT-AA-TTAAATTA-AAAT
109515072 TTTTAAAGGAGTAATTAAATTAAAAT
1 TTTT--AGGAGTAATTAAATTAAAAT
109515098 TTTTA
1 TTTTA
109515103 TTATCTTTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
24 1 0.04
26 8 0.29
27 12 0.43
28 2 0.07
29 5 0.18
ACGTcount: A:0.43, C:0.02, G:0.12, T:0.43
Consensus pattern (24 bp):
TTTTAGGAGTAATTAAATTAAAAT
Found at i:109531168 original size:2 final size:2
Alignment explanation
Indices: 109531161--109531187 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
109531151 GTTTGCACTA
109531161 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
109531188 ATAGTTGAAA
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:109534309 original size:2 final size:2
Alignment explanation
Indices: 109534302--109534330 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
109534292 ACTAATTAAT
109534302 TA TA TA TA TA -A 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
109534331 AAAAGCATGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:109537001 original size:7 final size:7
Alignment explanation
Indices: 109536989--109537017 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
109536979 CTTTATGTTA
109536989 AAGGTTT
1 AAGGTTT
109536996 AAGGTTT
1 AAGGTTT
109537003 AAGGTTT
1 AAGGTTT
109537010 AAGGTTT
1 AAGGTTT
109537017 A
1 A
109537018 TAATTTGGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.31, C:0.00, G:0.28, T:0.41
Consensus pattern (7 bp):
AAGGTTT
Found at i:109537212 original size:32 final size:32
Alignment explanation
Indices: 109537171--109537237 Score: 125
Period size: 32 Copynumber: 2.1 Consensus size: 32
109537161 TGACATAGAA
109537171 AAAAATTACCTGAATCCTGAACTTTAAATATT
1 AAAAATTACCTGAATCCTGAACTTTAAATATT
*
109537203 AAAAATTACCTGGATCCTGAACTTTAAATATT
1 AAAAATTACCTGAATCCTGAACTTTAAATATT
109537235 AAA
1 AAA
109537238 CCTTGAACCT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.33
Consensus pattern (32 bp):
AAAAATTACCTGAATCCTGAACTTTAAATATT
Found at i:109537807 original size:21 final size:19
Alignment explanation
Indices: 109537775--109537813 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
109537765 AGACTTCACA
*
109537775 TTTTTTTTTTCACTCTCTT
1 TTTTTTTTTTCACACTCTT
109537794 TTTTATTTTCTTCACACTCT
1 TTTT-TTTT-TTCACACTCT
109537814 CTTATTTTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 4 0.24
21 9 0.53
ACGTcount: A:0.10, C:0.23, G:0.00, T:0.67
Consensus pattern (19 bp):
TTTTTTTTTTCACACTCTT
Found at i:109541622 original size:39 final size:39
Alignment explanation
Indices: 109541574--109541656 Score: 130
Period size: 39 Copynumber: 2.1 Consensus size: 39
109541564 ATCATGGCGG
* * *
109541574 TCGGTTTGGTACGTACTGTTTCAGTACTAACATGGAACA
1 TCGGCTTGGTACGCACTGTTTCAGTACTAAAATGGAACA
*
109541613 TCGGCTTGGTGCGCACTGTTTCAGTACTAAAATGGAACA
1 TCGGCTTGGTACGCACTGTTTCAGTACTAAAATGGAACA
109541652 TCGGC
1 TCGGC
109541657 CGTTTTTTAT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.30
Consensus pattern (39 bp):
TCGGCTTGGTACGCACTGTTTCAGTACTAAAATGGAACA
Found at i:109542010 original size:2 final size:2
Alignment explanation
Indices: 109542003--109542040 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
109541993 GACTATCTTG
109542003 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
109542041 TTACTAATAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:109546875 original size:2 final size:2
Alignment explanation
Indices: 109546868--109546892 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
109546858 GATTATTCAG
109546868 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
109546893 GATGTGCCAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:109547148 original size:2 final size:2
Alignment explanation
Indices: 109547141--109547180 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
109547131 GTACATTTTA
* *
109547141 AT AT AT AT AT AT AT GT AT AT AT AT AT AT AT A- AG AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
109547181 AACTATAGCA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (2 bp):
AT
Found at i:109548814 original size:45 final size:45
Alignment explanation
Indices: 109548750--109548842 Score: 168
Period size: 45 Copynumber: 2.1 Consensus size: 45
109548740 AATCCGAGAA
109548750 CTGTGATTGCTTACAAGGTATGCCATTCCTTTTACAGAGTTAGCT
1 CTGTGATTGCTTACAAGGTATGCCATTCCTTTTACAGAGTTAGCT
* *
109548795 CTGTGATTGCTTACAAGGTATGCCGTTCCTTTTAGAGAGTTAGCT
1 CTGTGATTGCTTACAAGGTATGCCATTCCTTTTACAGAGTTAGCT
109548840 CTG
1 CTG
109548843 GTTTATATTT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.38
Consensus pattern (45 bp):
CTGTGATTGCTTACAAGGTATGCCATTCCTTTTACAGAGTTAGCT
Found at i:109552204 original size:22 final size:20
Alignment explanation
Indices: 109552179--109552238 Score: 65
Period size: 16 Copynumber: 3.1 Consensus size: 20
109552169 ATATATATAT
*
109552179 ATATATATTAAAACATATAAAA
1 ATATA-ATTAAAA-AAATAAAA
109552201 ATATAATTAAAAAAATAAAA
1 ATATAATTAAAAAAATAAAA
109552221 A-AT--TT-AAAAAATAAAA
1 ATATAATTAAAAAAATAAAA
109552237 AT
1 AT
109552239 TTTACCTTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
16 12 0.33
17 2 0.06
19 2 0.06
20 8 0.22
21 7 0.19
22 5 0.14
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (20 bp):
ATATAATTAAAAAAATAAAA
Found at i:109552229 original size:16 final size:16
Alignment explanation
Indices: 109552205--109552242 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
109552195 ATAAAAATAT
*
109552205 AATTAAAAAAATAAAA
1 AATTTAAAAAATAAAA
109552221 AATTTAAAAAATAAAA
1 AATTTAAAAAATAAAA
*
109552237 ATTTTA
1 AATTTA
109552243 CCTTTTCTGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
AATTTAAAAAATAAAA
Found at i:109552831 original size:3 final size:3
Alignment explanation
Indices: 109552823--109552874 Score: 95
Period size: 3 Copynumber: 17.0 Consensus size: 3
109552813 TTTTTATTTG
109552823 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TGTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
109552872 TTA
1 TTA
109552875 GTGTATACTT
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 45 0.94
4 3 0.06
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:109552962 original size:41 final size:41
Alignment explanation
Indices: 109552909--109553003 Score: 101
Period size: 41 Copynumber: 2.3 Consensus size: 41
109552899 TATATATATG
* *
109552909 TAGTAATGTTTTATTACTTT-ATTTTTA-TATTTTTATTATTA
1 TAGTAATGTTTTA-TA-TTTCATTATTATTATTATTATTATTA
109552950 TAGTAACT-TTTTATATTTCATTATTATTATTATTATTA-T-
1 TAGTAA-TGTTTTATATTTCATTATTATTATTATTATTATTA
109552989 TAGTATATGTTTTAT
1 TAGTA-ATGTTTTAT
109553004 TATATATGTA
Statistics
Matches: 47, Mismatches: 2, Indels: 11
0.78 0.03 0.18
Matches are distributed among these distances:
39 9 0.19
40 16 0.34
41 21 0.45
42 1 0.02
ACGTcount: A:0.28, C:0.03, G:0.05, T:0.63
Consensus pattern (41 bp):
TAGTAATGTTTTATATTTCATTATTATTATTATTATTATTA
Found at i:109553023 original size:21 final size:20
Alignment explanation
Indices: 109552977--109553045 Score: 61
Period size: 25 Copynumber: 3.2 Consensus size: 20
109552967 TCATTATTAT
109552977 TATTATTATTAT-TA-GTATA
1 TATT-TTATTATATATGTATA
*
109552996 TGTTTTATTATATATGTATA
1 TATTTTATTATATATGTATA
109553016 TATCTTTAATATATATATACGTATA
1 TAT-TTT-AT-TATATAT--GTATA
109553041 TATTT
1 TATTT
109553046 ATGTAGTATT
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
18 7 0.17
19 5 0.12
20 7 0.17
21 3 0.07
22 2 0.05
23 7 0.17
24 2 0.05
25 8 0.20
ACGTcount: A:0.35, C:0.03, G:0.06, T:0.57
Consensus pattern (20 bp):
TATTTTATTATATATGTATA
Found at i:109553158 original size:25 final size:25
Alignment explanation
Indices: 109553123--109553172 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
109553113 TCAAATGTTA
*
109553123 TATTATATATATATGTTTTTCATAT
1 TATTATATATATATGTTTTTAATAT
* *
109553148 TATTATGTATATTTGTTTTTAATAT
1 TATTATATATATATGTTTTTAATAT
109553173 CACATTTTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.30, C:0.02, G:0.06, T:0.62
Consensus pattern (25 bp):
TATTATATATATATGTTTTTAATAT
Found at i:109559142 original size:37 final size:37
Alignment explanation
Indices: 109559099--109559169 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
109559089 CACTGATCAT
109559099 TTTATATCTTTTTGAATTGAGATGACACTGATGGTTA
1 TTTATATCTTTTTGAATTGAGATGACACTGATGGTTA
**
109559136 TTTATATCTTTTTGAATTGAGATGATGCTGATGG
1 TTTATATCTTTTTGAATTGAGATGACACTGATGG
109559170 GTAACCAGGG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.25, C:0.07, G:0.21, T:0.46
Consensus pattern (37 bp):
TTTATATCTTTTTGAATTGAGATGACACTGATGGTTA
Found at i:109560342 original size:2 final size:2
Alignment explanation
Indices: 109560335--109560371 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
109560325 GACTGTGCCT
109560335 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
109560372 GAAGATGAGC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:109560787 original size:11 final size:11
Alignment explanation
Indices: 109560771--109560797 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
109560761 TTTTTTTTTT
109560771 GGGGGGGGAGG
1 GGGGGGGGAGG
109560782 GGGGGGGGAGG
1 GGGGGGGGAGG
109560793 GGGGG
1 GGGGG
109560798 TGTGAGACTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.07, C:0.00, G:0.93, T:0.00
Consensus pattern (11 bp):
GGGGGGGGAGG
Found at i:109561905 original size:31 final size:31
Alignment explanation
Indices: 109561870--109561939 Score: 95
Period size: 31 Copynumber: 2.3 Consensus size: 31
109561860 CTTAACAGCC
* *
109561870 TAGTGACTTGAATAAAAAATTTCAAATAGTT
1 TAGTGACTTAAATAAAAAATTTCAAATAATT
* * *
109561901 TAGTGACTTAAATGAAAACTTTTAAATAATT
1 TAGTGACTTAAATAAAAAATTTCAAATAATT
109561932 TAGTGACT
1 TAGTGACT
109561940 ATTTTGTAAC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.43, C:0.07, G:0.13, T:0.37
Consensus pattern (31 bp):
TAGTGACTTAAATAAAAAATTTCAAATAATT
Found at i:109562767 original size:32 final size:31
Alignment explanation
Indices: 109562731--109562797 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
109562721 AAAGATTGAT
** *
109562731 TAATAACCAAATTTAACGGAATAAAAAAAGAA
1 TAATAACCAAA-TTAACCAAAAAAAAAAAGAA
*
109562763 TAATACCCAAATTAACCAAAAAAAAAAAGAA
1 TAATAACCAAATTAACCAAAAAAAAAAAGAA
109562794 -AATA
1 TAATA
109562798 TTAAAGACTA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 4 0.13
31 17 0.55
32 10 0.32
ACGTcount: A:0.66, C:0.12, G:0.06, T:0.16
Consensus pattern (31 bp):
TAATAACCAAATTAACCAAAAAAAAAAAGAA
Found at i:109565802 original size:31 final size:30
Alignment explanation
Indices: 109565764--109565838 Score: 96
Period size: 31 Copynumber: 2.4 Consensus size: 30
109565754 TTAATATAAT
109565764 ATTTGGTACTTGAACTTGACACTTTTTCTTA
1 ATTTGGTACTT-AACTTGACACTTTTTCTTA
* * *
109565795 ATTTGGTACCTAACCTTGATACTTTTTGTTA
1 ATTTGGTACTTAA-CTTGACACTTTTTCTTA
*
109565826 AGTTGGTACTTAA
1 ATTTGGTACTTAA
109565839 ACTTTTTGGG
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
30 2 0.05
31 36 0.95
ACGTcount: A:0.24, C:0.15, G:0.15, T:0.47
Consensus pattern (30 bp):
ATTTGGTACTTAACTTGACACTTTTTCTTA
Found at i:109567808 original size:22 final size:22
Alignment explanation
Indices: 109567780--109567825 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
109567770 AGGAAGAAAG
109567780 GTTTTATTTCTTTTATTTTGAA
1 GTTTTATTTCTTTTATTTTGAA
109567802 GTTTTATTTCTTTTATTTTGAA
1 GTTTTATTTCTTTTATTTTGAA
109567824 GT
1 GT
109567826 ATATGCCTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.17, C:0.04, G:0.11, T:0.67
Consensus pattern (22 bp):
GTTTTATTTCTTTTATTTTGAA
Found at i:109572347 original size:20 final size:19
Alignment explanation
Indices: 109572324--109572367 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
109572314 TATTTTGCTA
*
109572324 TTGTTTCCACTGTTTTGTT
1 TTGTTTCCACTGTTGTGTT
**
109572343 GTTGTTTTTACTGTTGTGTT
1 -TTGTTTCCACTGTTGTGTT
109572363 TTGTT
1 TTGTT
109572368 ATTATTTTGC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.05, C:0.09, G:0.20, T:0.66
Consensus pattern (19 bp):
TTGTTTCCACTGTTGTGTT
Found at i:109572420 original size:14 final size:14
Alignment explanation
Indices: 109572388--109572464 Score: 57
Period size: 14 Copynumber: 5.1 Consensus size: 14
109572378 TATCATTTCG
*
109572388 TTATTATATTATTA
1 TTATTTTATTATTA
* *
109572402 CTATTTTATTATTT
1 TTATTTTATTATTA
*
109572416 TTATTTGGATATTGTATAA
1 TTATTT---TA-T-TATTA
109572435 TTATTTT-TTATTA
1 TTATTTTATTATTA
109572448 TTAATTTTATTATTA
1 TT-ATTTTATTATTA
109572463 TT
1 TT
109572465 TTAGAGTCAT
Statistics
Matches: 49, Mismatches: 7, Indels: 13
0.71 0.10 0.19
Matches are distributed among these distances:
13 6 0.12
14 22 0.45
15 8 0.16
16 1 0.02
17 2 0.04
18 1 0.02
19 9 0.18
ACGTcount: A:0.29, C:0.01, G:0.04, T:0.66
Consensus pattern (14 bp):
TTATTTTATTATTA
Found at i:109572457 original size:12 final size:11
Alignment explanation
Indices: 109572434--109572467 Score: 52
Period size: 12 Copynumber: 3.1 Consensus size: 11
109572424 ATATTGTATA
109572434 ATTATT-TTTT
1 ATTATTATTTT
109572444 ATTATTAATTTT
1 ATTATT-ATTTT
109572456 ATTATTATTTT
1 ATTATTATTTT
109572467 A
1 A
109572468 GAGTCATTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 6 0.27
11 6 0.27
12 10 0.45
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
ATTATTATTTT
Found at i:109575180 original size:36 final size:37
Alignment explanation
Indices: 109575109--109575182 Score: 87
Period size: 37 Copynumber: 2.0 Consensus size: 37
109575099 ATATTAGAAT
* *
109575109 AAAATAATAAGTATAATAATAAATATAAGGATATATG
1 AAAATAATAAGAATAATAATAAATATAAAGATATATG
* *
109575146 AAAATAATAA-AATAATACTATATATAAAAGTATATAT
1 AAAATAATAAGAATAATAATAAATAT-AAAG-ATATAT
109575183 ATATATACCC
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
36 12 0.39
37 13 0.42
38 6 0.19
ACGTcount: A:0.61, C:0.01, G:0.07, T:0.31
Consensus pattern (37 bp):
AAAATAATAAGAATAATAATAAATATAAAGATATATG
Found at i:109575187 original size:18 final size:17
Alignment explanation
Indices: 109575152--109575189 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
109575142 TATGAAAATA
109575152 ATAAAATAATACTATAT
1 ATAAAATAATACTATAT
109575169 ATAAAAGTATATA-TATAT
1 ATAAAA-TA-ATACTATAT
109575187 ATA
1 ATA
109575190 CCCGTATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.32
18 10 0.53
19 3 0.16
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.37
Consensus pattern (17 bp):
ATAAAATAATACTATAT
Found at i:109575624 original size:43 final size:44
Alignment explanation
Indices: 109575542--109575661 Score: 111
Period size: 43 Copynumber: 2.6 Consensus size: 44
109575532 CATAAGATAG
*
109575542 TACATAAATAATCTAAATAATATAATATTGAAAAAATATATATA
1 TACATAAATAATATAAATAATATAATATTGAAAAAATATATATA
* * *
109575586 TACAT-AATAATATATAA-AATATAATGTT-AAAAGCATATATAACA
1 TACATAAATAATATA-AATAATATAATATTGAAAA-AATATAT-ATA
*
109575630 TATATAAATATATATATATATATATATAATAT
1 TACATAAATA-ATATA-A-ATA-ATATAATAT
109575662 AATACATAAG
Statistics
Matches: 62, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
42 4 0.06
43 24 0.39
44 13 0.21
45 4 0.06
46 7 0.11
47 1 0.02
48 1 0.02
49 8 0.13
ACGTcount: A:0.57, C:0.04, G:0.03, T:0.37
Consensus pattern (44 bp):
TACATAAATAATATAAATAATATAATATTGAAAAAATATATATA
Found at i:109575634 original size:2 final size:2
Alignment explanation
Indices: 109575620--109575696 Score: 56
Period size: 2 Copynumber: 40.5 Consensus size: 2
109575610 TGTTAAAAGC
* *
109575620 AT AT AT A- AC AT AT AT AA AT AT AT AT AT AT AT AT AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
109575660 AT A- AT AC AT A- AGT AT -T AA AT AC AT AT AC AT AT AT AT A
1 AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT A
109575697 AAGATCATAG
Statistics
Matches: 58, Mismatches: 11, Indels: 12
0.72 0.14 0.15
Matches are distributed among these distances:
1 5 0.09
2 52 0.90
3 1 0.02
ACGTcount: A:0.55, C:0.05, G:0.01, T:0.39
Consensus pattern (2 bp):
AT
Found at i:109576399 original size:17 final size:17
Alignment explanation
Indices: 109576379--109576414 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
109576369 CCAAAACCAA
*
109576379 AAAAAAATAAAAAAAAG
1 AAAAAAAGAAAAAAAAG
109576396 AAAAAAAGAAAAAAAAG
1 AAAAAAAGAAAAAAAAG
109576413 AA
1 AA
109576415 TAAGGAGAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.89, C:0.00, G:0.08, T:0.03
Consensus pattern (17 bp):
AAAAAAAGAAAAAAAAG
Found at i:109578000 original size:44 final size:45
Alignment explanation
Indices: 109577890--109578023 Score: 126
Period size: 46 Copynumber: 3.0 Consensus size: 45
109577880 ACAGGACAAA
* * *
109577890 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATAAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* * * *
109577936 ACTGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATAAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
** * * * *
109577980 ACAGGAATAATTCATTTAAGTCCATGTCAAAGACATGGCATTGG
1 ACAGGAATAAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
109578024 CAGGATATTG
Statistics
Matches: 71, Mismatches: 15, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
44 34 0.48
45 1 0.01
46 36 0.51
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.28
Consensus pattern (45 bp):
ACAGGAATAAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:109579817 original size:29 final size:27
Alignment explanation
Indices: 109579783--109579843 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 27
109579773 AAAATGGGGT
109579783 TTGGGCTTCTGTTGGGTTAATTTTGAGTG
1 TTGGGCTTC--TTGGGTTAATTTTGAGTG
109579812 TTGGG---CTTGGGTTAATTTTGAGTG
1 TTGGGCTTCTTGGGTTAATTTTGAGTG
*
109579836 TTGAGCTT
1 TTGGGCTT
109579844 GGGTAGGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
24 22 0.79
26 1 0.04
29 5 0.18
ACGTcount: A:0.11, C:0.07, G:0.34, T:0.48
Consensus pattern (27 bp):
TTGGGCTTCTTGGGTTAATTTTGAGTG
Found at i:109579821 original size:24 final size:24
Alignment explanation
Indices: 109579794--109579847 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
109579784 TGGGCTTCTG
*
109579794 TTGGGTTAATTTTGAGTGTTGGGC
1 TTGGGTTAATTTTGAGTGTTGAGC
109579818 TTGGGTTAATTTTGAGTGTTGAGC
1 TTGGGTTAATTTTGAGTGTTGAGC
109579842 TTGGGT
1 TTGGGT
109579848 AGGTTTAGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.13, C:0.04, G:0.37, T:0.46
Consensus pattern (24 bp):
TTGGGTTAATTTTGAGTGTTGAGC
Found at i:109585109 original size:51 final size:50
Alignment explanation
Indices: 109585001--109585097 Score: 117
Period size: 51 Copynumber: 1.9 Consensus size: 50
109584991 AGTTCACAAA
* * *
109585001 ATTTACACATCGTGTCAATTTGACTTTGATTTAATAAATTTAGTCCATAAC
1 ATTTACACATCGTGTCAATTTGACTTTAATTTAACAAATTTAG-ACATAAC
* *
109585052 ATTTACACATTC-TGTTAATTTGATTTTAATTTAACAAATTTA-ACAT
1 ATTTACACA-TCGTGTCAATTTGACTTTAATTTAACAAATTTAGACAT
109585098 GTAATATTTA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
49 3 0.08
51 35 0.88
52 2 0.05
ACGTcount: A:0.35, C:0.13, G:0.07, T:0.44
Consensus pattern (50 bp):
ATTTACACATCGTGTCAATTTGACTTTAATTTAACAAATTTAGACATAAC
Found at i:109585501 original size:13 final size:13
Alignment explanation
Indices: 109585483--109585509 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
109585473 GATGTCGTAT
109585483 TTAGACTTATTCA
1 TTAGACTTATTCA
109585496 TTAGACTTATTCA
1 TTAGACTTATTCA
109585509 T
1 T
109585510 GAGTCAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.48
Consensus pattern (13 bp):
TTAGACTTATTCA
Found at i:109585605 original size:19 final size:19
Alignment explanation
Indices: 109585581--109585617 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
109585571 ATATGACTTA
109585581 AACTCGAACTTAAACATTG
1 AACTCGAACTTAAACATTG
109585600 AACTCGAACTTAAACATT
1 AACTCGAACTTAAACATT
109585618 TAAGATTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.43, C:0.22, G:0.08, T:0.27
Consensus pattern (19 bp):
AACTCGAACTTAAACATTG
Found at i:109590282 original size:232 final size:227
Alignment explanation
Indices: 109589875--109590553 Score: 776
Period size: 232 Copynumber: 2.9 Consensus size: 227
109589865 GGGGGAATAA
* * * *
109589875 ATTGGAATGTATTCTTATTTATTAATAGGTTTTGGGTTCACGTGACTTGCAGTGGCAAACGCCTG
1 ATTGGAATGTATTCTTATTTATTAATAGGTTTTCGGTTCACATGACTCGCAGTGGCAAACGCTTG
* * * * *
109589940 TCAAAAAGTATTTATAATTAATCAGATAGGCGGTTTTGCG-TTATTGTTAAGGATTTTAGGTTTT
66 TCAAAAAGTATTTGTAATTAATC-GATATGC-GTTTTG-GTTTATTATT-AGGAATTTAGATTTT
* * *
109590004 TATTGGATAATGGGAAGTTTTAAATTTCAAGATTTGTTTGAAATATTTAATAATGTGATTTACAA
127 TATTGGATAATGGGAAGTTTCAAATTTCAAGATTTGTTTAAAATATTTAATAAT-TGATTTATAA
109590069 TAATGAGGTTATTTTTTTCATTTGGTAATAGGTCTTTT-
191 TAATGAGGTTATTTTTTT-ATTTGGTAATA-GTCTTTTC
* * * *
109590107 ATTGGAATGTTTTCTTATTTATTGATAGGTTTTCGGTTCACATGACTCACGGTGGCAAACGCTTG
1 ATTGGAATGTATTCTTATTTATTAATAGGTTTTCGGTTCACATGACTCGCAGTGGCAAACGCTTG
* * * * *
109590172 TCAAAAAGTATTTGTAACTAATTCGATATGCAGTTTCGGTTTATTATTAGGAAACTTCGATTTTA
66 TCAAAAAGTATTTGTAATTAA-TCGATATGC-GTTTTGGTTTATTATTAGG-AATTTAGATTTTT
* *
109590237 ATTGGATAATGGGAAGTTTCAAATTTCAAGATTTGTTCAAAATATTTAATAATTTGATTTTTAAT
128 ATTGGATAATGGGAAGTTTCAAATTTCAAGATTTGTTTAAAATATTTAATAA-TTGATTTATAAT
* * * * *
109590302 ATTGAGGTTCA-GTTTTTATTTGTTAATATTTTTTTC
192 AATGAGGTT-ATTTTTTTATTTGGTAATAGTCTTTTC
* * *** * **
109590338 ACTGGAATGTATTCTTATTTATTAATAGGTTTTTGGTTCACATGACTCGCAACAGTAAATACTTG
1 ATTGGAATGTATTCTTATTTATTAATAGGTTTTCGGTTCACATGACTCGCAGTGGCAAACGCTTG
*
109590403 TCAAAAAGTATTTGTAATTAATC-ATATAGGCGATTTTGGTTTATTATTAGGAATTTATGTTTTT
66 TCAAAAAGTATTTGTAATTAATCGATAT--GCG-TTTTGGTTTATTATTAGGAATTTA-GATTTT
* * * * *
109590467 TATTAGATAATAGAAAGTTTCGAATATCAAGATTTGTTTAAAATATTTAATAACTTGATTTATAA
127 TATTGGATAATGGGAAGTTTCAAATTTCAAGATTTGTTTAAAATATTTAATAA-TTGATTTATAA
109590532 TAATG-GGTT-TATTTTTTATTTG
191 TAATGAGGTTAT-TTTTTTATTTG
109590554 TTACTTTGGT
Statistics
Matches: 378, Mismatches: 57, Indels: 26
0.82 0.12 0.06
Matches are distributed among these distances:
229 4 0.01
230 26 0.07
231 171 0.45
232 173 0.46
233 4 0.01
ACGTcount: A:0.30, C:0.08, G:0.17, T:0.45
Consensus pattern (227 bp):
ATTGGAATGTATTCTTATTTATTAATAGGTTTTCGGTTCACATGACTCGCAGTGGCAAACGCTTG
TCAAAAAGTATTTGTAATTAATCGATATGCGTTTTGGTTTATTATTAGGAATTTAGATTTTTATT
GGATAATGGGAAGTTTCAAATTTCAAGATTTGTTTAAAATATTTAATAATTGATTTATAATAATG
AGGTTATTTTTTTATTTGGTAATAGTCTTTTC
Found at i:109590416 original size:231 final size:227
Alignment explanation
Indices: 109589877--109590556 Score: 792
Period size: 231 Copynumber: 2.9 Consensus size: 227
109589867 GGGAATAAAT
* * * *
109589877 TGGAATGTATTCTTATTTATTAATAGGTTTTGGGTTCACGTGACTTGCAGTGGCAAACGCCTGTC
1 TGGAATGTATTCTTATTTATTAATAGGTTTTCGGTTCACATGACTCGCAGTGGCAAACGCTTGTC
* * * * *
109589942 AAAAAGTATTTATAATTAATCAGATAGGCGGTTTTGCG-TTATTGTTAAGGATTTTAGGTTTTTA
66 AAAAAGTATTTGTAATTAATC-GATATGC-GTTTTG-GTTTATTATT-AGGAATTTAGATTTTTA
* * * *
109590006 TTGGATAATGGGAAGTTTTAAATTTCAAGATTTGTTTGAAATATTTAATAATGTGATTTACAATA
127 TTGGATAATGGGAAGTTTCAAATTTCAAGATTTGTTTAAAATATTTAATAATTTGATTTATAATA
* *
109590071 ATGAGGTTATTTTTTTCATTTGGTAATAGGTCTTTTAT
192 ATGAGGTTA-TTTTTT-ATTTGTTAATAGGTCTTTTAC
* * * *
109590109 TGGAATGTTTTCTTATTTATTGATAGGTTTTCGGTTCACATGACTCACGGTGGCAAACGCTTGTC
1 TGGAATGTATTCTTATTTATTAATAGGTTTTCGGTTCACATGACTCGCAGTGGCAAACGCTTGTC
* * * * *
109590174 AAAAAGTATTTGTAACTAATTCGATATGCAGTTTCGGTTTATTATTAGGAAACTTCGATTTTAAT
66 AAAAAGTATTTGTAATTAA-TCGATATGC-GTTTTGGTTTATTATTAGG-AATTTAGATTTTTAT
* * *
109590239 TGGATAATGGGAAGTTTCAAATTTCAAGATTTGTTCAAAATATTTAATAATTTGATTTTTAATAT
128 TGGATAATGGGAAGTTTCAAATTTCAAGATTTGTTTAAAATATTTAATAATTTGATTTATAATAA
* * *
109590304 TGAGGTTCAGTTTTTATTTGTTAATA-TTTTTTTCAC
193 TGAGGTT-ATTTTTTATTTGTTAATAGGTCTTTT-AC
* *** * **
109590340 TGGAATGTATTCTTATTTATTAATAGGTTTTTGGTTCACATGACTCGCAACAGTAAATACTTGTC
1 TGGAATGTATTCTTATTTATTAATAGGTTTTCGGTTCACATGACTCGCAGTGGCAAACGCTTGTC
*
109590405 AAAAAGTATTTGTAATTAATC-ATATAGGCGATTTTGGTTTATTATTAGGAATTTATGTTTTTTA
66 AAAAAGTATTTGTAATTAATCGATAT--GCG-TTTTGGTTTATTATTAGGAATTTA-GATTTTTA
* * * * * *
109590469 TTAGATAATAGAAAGTTTCGAATATCAAGATTTGTTTAAAATATTTAATAACTTGATTTATAATA
127 TTGGATAATGGGAAGTTTCAAATTTCAAGATTTGTTTAAAATATTTAATAATTTGATTTATAATA
109590534 ATG-GGTTTATTTTTTATTTGTTA
192 ATGAGG-TTATTTTTTATTTGTTA
109590557 CTTTGGTATT
Statistics
Matches: 380, Mismatches: 58, Indels: 22
0.83 0.13 0.05
Matches are distributed among these distances:
229 4 0.01
230 28 0.07
231 173 0.46
232 172 0.45
233 3 0.01
ACGTcount: A:0.30, C:0.08, G:0.17, T:0.45
Consensus pattern (227 bp):
TGGAATGTATTCTTATTTATTAATAGGTTTTCGGTTCACATGACTCGCAGTGGCAAACGCTTGTC
AAAAAGTATTTGTAATTAATCGATATGCGTTTTGGTTTATTATTAGGAATTTAGATTTTTATTGG
ATAATGGGAAGTTTCAAATTTCAAGATTTGTTTAAAATATTTAATAATTTGATTTATAATAATGA
GGTTATTTTTTATTTGTTAATAGGTCTTTTAC
Found at i:109591629 original size:13 final size:13
Alignment explanation
Indices: 109591611--109591649 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 13
109591601 ATGTGGGTGA
109591611 ATAACAAAATTTT
1 ATAACAAAATTTT
109591624 ATAACAAATATATTT
1 ATAACAAA-AT-TTT
109591639 ATAA-AAAATTT
1 ATAACAAAATTT
109591650 GATTTAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 2 0.08
13 10 0.42
14 5 0.21
15 7 0.29
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (13 bp):
ATAACAAAATTTT
Found at i:109592106 original size:78 final size:77
Alignment explanation
Indices: 109591996--109592143 Score: 206
Period size: 78 Copynumber: 1.9 Consensus size: 77
109591986 ATAAGGGCAC
* *
109591996 TATAATAAGTTTAAATAAGAGATGAAATTATGCTAAATCAAAAAAAAAAAATTAAATCTCAAATT
1 TATAATAAGTTTAAATAAGAGATGAAACTATGCCAAATCAAAAAAAAAAAATTAAATCTCAAATT
109592061 TGAACTTGAAAA
66 TGAACTTGAAAA
* ** * * * *
109592073 TATAATAAGTTTAGATAAAGAGATGAAACTATGCCAAATTGAAATAAAAGAATTTACTCTCAAAT
1 TATAATAAGTTTAAAT-AAGAGATGAAACTATGCCAAATCAAAAAAAAAAAATTAAATCTCAAAT
109592138 TTGAAC
65 TTGAAC
109592144 ATAAGTTGTC
Statistics
Matches: 61, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
77 15 0.25
78 46 0.75
ACGTcount: A:0.52, C:0.08, G:0.11, T:0.29
Consensus pattern (77 bp):
TATAATAAGTTTAAATAAGAGATGAAACTATGCCAAATCAAAAAAAAAAAATTAAATCTCAAATT
TGAACTTGAAAA
Found at i:109593809 original size:30 final size:31
Alignment explanation
Indices: 109593769--109593827 Score: 77
Period size: 30 Copynumber: 1.9 Consensus size: 31
109593759 CTTGTTAGGA
*
109593769 GTAACTGTCTTACAGTTAGT-TGGTTAGCTTT
1 GTAACTGTCTT-CAGTTAATATGGTTAGCTTT
*
109593800 GTAAC-GTCTTTAGTTAATATGGTTAGCT
1 GTAACTGTCTTCAGTTAATATGGTTAGCT
109593828 GTTTGCTCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 6 0.24
30 14 0.56
31 5 0.20
ACGTcount: A:0.22, C:0.12, G:0.22, T:0.44
Consensus pattern (31 bp):
GTAACTGTCTTCAGTTAATATGGTTAGCTTT
Found at i:109598342 original size:30 final size:31
Alignment explanation
Indices: 109598302--109598360 Score: 77
Period size: 30 Copynumber: 1.9 Consensus size: 31
109598292 CATGTTAGGA
*
109598302 GTAACTGTCTTACAGTTAGT-TGGTTAGCTTT
1 GTAACTGTCTT-CAGTTAATATGGTTAGCTTT
*
109598333 GTAAC-GTCTTTAGTTAATATGGTTAGCT
1 GTAACTGTCTTCAGTTAATATGGTTAGCT
109598361 GTTAGCTCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 6 0.24
30 14 0.56
31 5 0.20
ACGTcount: A:0.22, C:0.12, G:0.22, T:0.44
Consensus pattern (31 bp):
GTAACTGTCTTCAGTTAATATGGTTAGCTTT
Found at i:109600254 original size:11 final size:11
Alignment explanation
Indices: 109600238--109600267 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
109600228 TAACATTAAG
109600238 AATATATATAT
1 AATATATATAT
*
109600249 AATATAAATAT
1 AATATATATAT
109600260 AATATATA
1 AATATATA
109600268 CAATATACAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
AATATATATAT
Found at i:109600794 original size:17 final size:17
Alignment explanation
Indices: 109600772--109600828 Score: 53
Period size: 16 Copynumber: 3.2 Consensus size: 17
109600762 AATAGATTCG
109600772 AAAAAAATAAAAAAAAT
1 AAAAAAATAAAAAAAAT
109600789 -AAAAAATAAAAATAAGAGT
1 AAAAAAATAAAAA-AA-A-T
* * *
109600808 AAAATAATAAAGAAGAT
1 AAAAAAATAAAAAAAAT
109600825 AAAA
1 AAAA
109600829 TCACCTTTAG
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
16 12 0.36
17 7 0.21
18 2 0.06
19 2 0.06
20 10 0.30
ACGTcount: A:0.79, C:0.00, G:0.07, T:0.14
Consensus pattern (17 bp):
AAAAAAATAAAAAAAAT
Found at i:109600829 original size:17 final size:17
Alignment explanation
Indices: 109600791--109600829 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
109600781 AAAAAAATAA
*
109600791 AAAATAAAAATAAGAGT
1 AAAATAAAAAGAAGAGT
109600808 AAAATAATAAAGAAGA-T
1 AAAATAA-AAAGAAGAGT
109600825 AAAAT
1 AAAAT
109600830 CACCTTTAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.72, C:0.00, G:0.10, T:0.18
Consensus pattern (17 bp):
AAAATAAAAAGAAGAGT
Found at i:109602041 original size:8 final size:8
Alignment explanation
Indices: 109602025--109602055 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
109602015 AGACATTTGC
109602025 AATTGTTG
1 AATTGTTG
*
109602033 AATTATTG
1 AATTGTTG
109602041 AATTGTTG
1 AATTGTTG
109602049 AATTGTT
1 AATTGTT
109602056 AAAGGAGGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.29, C:0.00, G:0.19, T:0.52
Consensus pattern (8 bp):
AATTGTTG
Found at i:109605995 original size:14 final size:14
Alignment explanation
Indices: 109605978--109606004 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
109605968 AAATTAATGT
109605978 TAAAAAATTTAAAA
1 TAAAAAATTTAAAA
109605992 TAAAAAATTTAAA
1 TAAAAAATTTAAA
109606005 TTTATGTTGG
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:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
TAAAAAATTTAAAA
Found at i:109607878 original size:27 final size:28
Alignment explanation
Indices: 109607821--109607884 Score: 103
Period size: 28 Copynumber: 2.3 Consensus size: 28
109607811 ATAAAAAAAG
*
109607821 TAAAATTTTAATATTTATATATTTTGTT
1 TAAATTTTTAATATTTATATATTTTGTT
109607849 TAAATTTTTAATATTTATATATTTTG-T
1 TAAATTTTTAATATTTATATATTTTGTT
*
109607876 TAAGTTTTT
1 TAAATTTTT
109607885 GTTCACTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
27 9 0.26
28 25 0.74
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (28 bp):
TAAATTTTTAATATTTATATATTTTGTT
Found at i:109619399 original size:109 final size:112
Alignment explanation
Indices: 109619181--109619402 Score: 333
Period size: 109 Copynumber: 2.0 Consensus size: 112
109619171 TGAATTTAGC
* * * *
109619181 CCTCATGTATCCCCTTTCAGTCAATTTAGGTATTATAGTATTATTATTCTTTTTTGAGCTAAATT
1 CCTCATGTATACACTTTCAATCAATTTAGCTATTATAGTA-TATTATTCTTTTTTGAGCTAAATT
* * *
109619246 TGACTGATTAACCTTTCAAAAAGTGTCCAATTGCTTTTCTTTAATGGA
65 TGACTGATTAACCTTTCAAAAAGTATCAAATTACTTTTCTTTAATGGA
*
109619294 CCTCATGTATACACTTTCAATCAATTTAGCTATTATAG-A-ATTATTCTTTTTTGAGTTAAATTT
1 CCTCATGTATACACTTTCAATCAATTTAGCTATTATAGTATATTATTCTTTTTTGAGCTAAATTT
*
109619357 GACT-ATTAACCTTTCAAAAAGTATCAAATTATTTTTCTTTAATGGA
66 GACTGATTAACCTTTCAAAAAGTATCAAATTACTTTTCTTTAATGGA
109619403 AATACTAACT
Statistics
Matches: 100, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
109 38 0.38
110 27 0.27
112 1 0.01
113 34 0.34
ACGTcount: A:0.30, C:0.15, G:0.10, T:0.45
Consensus pattern (112 bp):
CCTCATGTATACACTTTCAATCAATTTAGCTATTATAGTATATTATTCTTTTTTGAGCTAAATTT
GACTGATTAACCTTTCAAAAAGTATCAAATTACTTTTCTTTAATGGA
Found at i:109620197 original size:31 final size:31
Alignment explanation
Indices: 109620165--109620225 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 31
109620155 ATTTTCATTA
109620165 AAAGATTGACAGA-TAAATTTAATTT-TTTTT
1 AAAGATTG-CAGACTAAATTTAATTTATTTTT
* *
109620195 AAATATTGTAGACTAAATTTAATTTATTTTT
1 AAAGATTGCAGACTAAATTTAATTTATTTTT
109620226 TTTAAAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
29 3 0.11
30 19 0.70
31 5 0.19
ACGTcount: A:0.39, C:0.03, G:0.08, T:0.49
Consensus pattern (31 bp):
AAAGATTGCAGACTAAATTTAATTTATTTTT
Found at i:109623994 original size:22 final size:22
Alignment explanation
Indices: 109623969--109624014 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
109623959 GATATTTGTG
* * *
109623969 TTTGCAAACTACTCAAATTTAA
1 TTTGAAAAATACTCAAATTCAA
*
109623991 TTTGAAAAATATTCAAATTCAA
1 TTTGAAAAATACTCAAATTCAA
109624013 TT
1 TT
109624015 CCGTAATATC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.43, C:0.13, G:0.04, T:0.39
Consensus pattern (22 bp):
TTTGAAAAATACTCAAATTCAA
Found at i:109625222 original size:33 final size:33
Alignment explanation
Indices: 109625180--109625246 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
109625170 CAGATATTGC
109625180 AGTGAAAAATAAAAGCCGTAGGAGTTAAAGTAT
1 AGTGAAAAATAAAAGCCGTAGGAGTTAAAGTAT
109625213 AGTGAAAAATAAAAGCCGTAGGAGTTAAAGTAT
1 AGTGAAAAATAAAAGCCGTAGGAGTTAAAGTAT
109625246 A
1 A
109625247 CTTACTTCCC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.49, C:0.06, G:0.24, T:0.21
Consensus pattern (33 bp):
AGTGAAAAATAAAAGCCGTAGGAGTTAAAGTAT
Found at i:109629141 original size:14 final size:15
Alignment explanation
Indices: 109629122--109629154 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
109629112 AGTTTCAAAT
109629122 TTATGGATGAAGC-A
1 TTATGGATGAAGCAA
109629136 TTATGGATGAAGCAA
1 TTATGGATGAAGCAA
109629151 TTAT
1 TTAT
109629155 CAAAGGATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.36, C:0.06, G:0.24, T:0.33
Consensus pattern (15 bp):
TTATGGATGAAGCAA
Found at i:109631926 original size:13 final size:14
Alignment explanation
Indices: 109631898--109631927 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
109631888 TCAAAATTCC
109631898 AAAAAAAAAATACA
1 AAAAAAAAAATACA
109631912 AAAAAAAAAAT-CA
1 AAAAAAAAAATACA
109631925 AAA
1 AAA
109631928 TTCAAAACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.87, C:0.07, G:0.00, T:0.07
Consensus pattern (14 bp):
AAAAAAAAAATACA
Found at i:109637757 original size:46 final size:46
Alignment explanation
Indices: 109637690--109637864 Score: 205
Period size: 46 Copynumber: 3.8 Consensus size: 46
109637680 TGTAACCCGC
109637690 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCATTCGCAT
*
109637736 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--G-C-A-TTCGCAT
* * * * **
109637786 -C-TCA-CGAACTCAGACTCAACTCAACGAGTTCGAACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCATTCGCAT
*
109637829 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG
109637865 ATGCTCAACC
Statistics
Matches: 108, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 62 0.57
47 25 0.23
48 3 0.03
49 2 0.02
50 4 0.04
51 2 0.02
ACGTcount: A:0.30, C:0.30, G:0.19, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCATTCGCAT
Found at i:109637806 original size:93 final size:93
Alignment explanation
Indices: 109637698--109637868 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
109637688 GCCCATAAGT
* **
109637698 GAACTCGGACTCAACTCAACGAGCTCGGGCATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
109637763 CGAGCTCGGATGCCTAGTTACATCTCAC
66 CGAGCTCGGATGCCTAGTTACATCTCAC
*
109637791 GAACTCAGACTCAACTCAACGAGTTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
109637856 CGAGTTCGGATGC
66 CGAGCTCGGATGC
109637869 TCAACCATCC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (93 bp):
GAACTCAGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCAC
Found at i:109639087 original size:20 final size:20
Alignment explanation
Indices: 109639062--109639099 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
109639052 TACATGCACT
* *
109639062 TATAAAATTATATTATAACA
1 TATAAAATAATACTATAACA
109639082 TATAAAATAATACTATAA
1 TATAAAATAATACTATAA
109639100 TAATTTTCTC
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:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (20 bp):
TATAAAATAATACTATAACA
Found at i:109641869 original size:11 final size:11
Alignment explanation
Indices: 109641830--109641910 Score: 70
Period size: 11 Copynumber: 7.7 Consensus size: 11
109641820 TGCATATATG
109641830 ATATAATACATGA
1 ATAT-ATACAT-A
109641843 ATA-ATACGAT-
1 ATATATAC-ATA
109641853 ATATATACATA
1 ATATATACATA
109641864 ATATAT--ATA
1 ATATATACATA
109641873 ATA-ATA-ATA
1 ATATATACATA
109641882 ATAATATACATA
1 AT-ATATACATA
109641894 ATATATA-A-A
1 ATATATACATA
109641903 ATATATAC
1 ATATATAC
109641911 GTATATAACA
Statistics
Matches: 60, Mismatches: 0, Indels: 19
0.76 0.00 0.24
Matches are distributed among these distances:
8 2 0.03
9 19 0.32
10 7 0.12
11 22 0.37
12 7 0.12
13 3 0.05
ACGTcount: A:0.57, C:0.06, G:0.02, T:0.35
Consensus pattern (11 bp):
ATATATACATA
Found at i:109641870 original size:36 final size:32
Alignment explanation
Indices: 109641815--109641905 Score: 98
Period size: 30 Copynumber: 2.8 Consensus size: 32
109641805 TATATTGAAG
*
109641815 ATATATGCATATATGATATAATACATGAATAATACGAT
1 ATATATACATA-AT-ATATAATA-AT-AATAATA--AT
109641853 ATATATACATAATATAT-ATAATAATAATAAT
1 ATATATACATAATATATAATAATAATAATAAT
109641884 A-ATATACATAATATATAA-AATA
1 ATATATACATAATATATAATAATA
109641906 TATACGTATA
Statistics
Matches: 51, Mismatches: 1, Indels: 10
0.82 0.02 0.16
Matches are distributed among these distances:
30 19 0.37
31 4 0.08
33 7 0.14
34 2 0.04
35 3 0.06
36 4 0.08
37 2 0.04
38 10 0.20
ACGTcount: A:0.55, C:0.05, G:0.04, T:0.35
Consensus pattern (32 bp):
ATATATACATAATATATAATAATAATAATAAT
Found at i:109641871 original size:15 final size:15
Alignment explanation
Indices: 109641851--109641900 Score: 68
Period size: 15 Copynumber: 3.3 Consensus size: 15
109641841 GAATAATACG
109641851 ATATATATACATAAT
1 ATATATATACATAAT
109641866 ATATATAATA-ATAAT
1 ATATAT-ATACATAAT
109641881 A-ATAATATACATAAT
1 ATAT-ATATACATAAT
109641896 ATATA
1 ATATA
109641901 AAATATATAC
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
14 5 0.16
15 21 0.68
16 5 0.16
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (15 bp):
ATATATATACATAAT
Found at i:109641873 original size:9 final size:9
Alignment explanation
Indices: 109641792--109641909 Score: 58
Period size: 9 Copynumber: 11.8 Consensus size: 9
109641782 AAACATACTT
109641792 ATATATATA
1 ATATATATA
109641801 TATATATATTGA
1 -ATATATA-T-A
*
109641813 AGATATATGCA
1 ATATATAT--A
109641824 TATATGATATA
1 -ATAT-ATATA
*
109641835 ATACATGAATA
1 ATATAT--ATA
*
109641846 ATACGATAT-
1 ATA-TATATA
*
109641855 ATATACATA
1 ATATATATA
109641864 ATATATATA
1 ATATATATA
109641873 ATAATAATAATA
1 AT-AT-AT-ATA
*
109641885 ATATACATA
1 ATATATATA
*
109641894 ATATATAAA
1 ATATATATA
109641903 ATATATA
1 ATATATA
109641910 CGTATATAAC
Statistics
Matches: 85, Mismatches: 11, Indels: 25
0.70 0.09 0.21
Matches are distributed among these distances:
8 3 0.04
9 32 0.38
10 16 0.19
11 19 0.22
12 11 0.13
13 4 0.05
ACGTcount: A:0.53, C:0.04, G:0.05, T:0.37
Consensus pattern (9 bp):
ATATATATA
Found at i:109641876 original size:30 final size:30
Alignment explanation
Indices: 109641842--109641932 Score: 100
Period size: 30 Copynumber: 3.1 Consensus size: 30
109641832 ATAATACATG
109641842 AATAATACGATATATATACATAATATATAT
1 AATAATACGATATATATACATAATATATAT
*
109641872 AATAATA--ATAATAATATACATAATATATAA
1 AATAATACGAT-AT-ATATACATAATATATAT
* *
109641902 AATATATACG-TATATA-ACAAAACATATAT
1 AATA-ATACGATATATATACATAATATATAT
109641931 AA
1 AA
109641933 ATATTGGTAA
Statistics
Matches: 52, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
28 2 0.04
29 14 0.27
30 30 0.58
31 5 0.10
32 1 0.02
ACGTcount: A:0.58, C:0.07, G:0.02, T:0.33
Consensus pattern (30 bp):
AATAATACGATATATATACATAATATATAT
Found at i:109641885 original size:21 final size:19
Alignment explanation
Indices: 109641853--109641909 Score: 71
Period size: 21 Copynumber: 2.9 Consensus size: 19
109641843 ATAATACGAT
109641853 ATATATACATAATATATATA
1 ATATATA-ATAATATATATA
*
109641873 ATAATAATAATAATATACATA
1 AT-AT-ATAATAATATATATA
109641894 ATATATAA-AATATATA
1 ATATATAATAATATATA
109641910 CGTATATAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
18 7 0.21
19 4 0.12
20 4 0.12
21 15 0.45
22 3 0.09
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.37
Consensus pattern (19 bp):
ATATATAATAATATATATA
Found at i:109641898 original size:41 final size:41
Alignment explanation
Indices: 109641823--109641909 Score: 101
Period size: 41 Copynumber: 2.1 Consensus size: 41
109641813 AGATATATGC
*
109641823 ATATATGATATAATACATGAATAATACGATATATATACATAAT
1 ATATATAATATAATACATGAATAATACGATATATATA-A-AAT
109641866 ATATATAATAATAATA-AT-AAT-ATAC-ATAATATATAAAAT
1 ATATATAAT-ATAATACATGAATAATACGAT-ATATATAAAAT
109641905 ATATA
1 ATATA
109641910 CGTATATAAC
Statistics
Matches: 41, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
39 8 0.20
40 3 0.07
41 11 0.27
42 3 0.07
43 10 0.24
44 6 0.15
ACGTcount: A:0.56, C:0.05, G:0.03, T:0.36
Consensus pattern (41 bp):
ATATATAATATAATACATGAATAATACGATATATATAAAAT
Found at i:109643376 original size:16 final size:17
Alignment explanation
Indices: 109643355--109643388 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
109643345 GATTATAATG
109643355 TAAATGGGCTAA-GGTT
1 TAAATGGGCTAATGGTT
*
109643371 TAAATGGGTTAATGGTT
1 TAAATGGGCTAATGGTT
109643388 T
1 T
109643389 TATAAGGCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.29, C:0.03, G:0.29, T:0.38
Consensus pattern (17 bp):
TAAATGGGCTAATGGTT
Found at i:109646948 original size:26 final size:27
Alignment explanation
Indices: 109646912--109646964 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
109646902 TGTCAGCTAG
* *
109646912 TGAAATTTTAA-TGTTCGAATGTATGC
1 TGAAATTTTAAGTGTCCGAATGCATGC
*
109646938 TGAATTTTTAAGTGTCCGAATGCATGC
1 TGAAATTTTAAGTGTCCGAATGCATGC
109646965 CAGAATTCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 10 0.43
27 13 0.57
ACGTcount: A:0.28, C:0.11, G:0.21, T:0.40
Consensus pattern (27 bp):
TGAAATTTTAAGTGTCCGAATGCATGC
Found at i:109648838 original size:45 final size:45
Alignment explanation
Indices: 109648786--109649077 Score: 416
Period size: 45 Copynumber: 6.6 Consensus size: 45
109648776 CGGGCTTCGG
*
109648786 GCCTAGCAGGCTATGATGCCGGTGAAATACTATTCGGGCCTTTGA
1 GCCTAGCAGGCTATGATGCCGGTGAAATATTATTCGGGCCTTTGA
*
109648831 GCCTAGCAGGCTATGATGCCGGTGAAATACTATTCGGGCCTTTGA
1 GCCTAGCAGGCTATGATGCCGGTGAAATATTATTCGGGCCTTTGA
*
109648876 GCCTAGCAGGCTATGATGCCGGTGAGATATTATTCGGGCCTTTGA
1 GCCTAGCAGGCTATGATGCCGGTGAAATATTATTCGGGCCTTTGA
*
109648921 GCCTAGCAGGCTATGATGCCGGTGAGATATTATTCGGGCCTTTGA
1 GCCTAGCAGGCTATGATGCCGGTGAAATATTATTCGGGCCTTTGA
*
109648966 GCCTAGCAGGCTATAATGCCGGT-AAGATATTATTCGGG-CTTTCGA
1 GCCTAGCAGGCTATGATGCCGGTGAA-ATATTATTCGGGCCTTT-GA
* * *
109649011 GCCTAGCAGGCTATAATGTCGGTGAAATGA-TA-TCGGGCC-TCGA
1 GCCTAGCAGGCTATGATGCCGGTGAAAT-ATTATTCGGGCCTTTGA
* * *
109649054 CCCTAGCAGGCGA-AATGCCGGTGA
1 GCCTAGCAGGCTATGATGCCGGTGA
109649078 TTAGAGAAAA
Statistics
Matches: 233, Mismatches: 9, Indels: 13
0.91 0.04 0.05
Matches are distributed among these distances:
42 10 0.04
43 13 0.06
44 11 0.05
45 196 0.84
46 3 0.01
ACGTcount: A:0.23, C:0.22, G:0.30, T:0.26
Consensus pattern (45 bp):
GCCTAGCAGGCTATGATGCCGGTGAAATATTATTCGGGCCTTTGA
Found at i:109649847 original size:30 final size:30
Alignment explanation
Indices: 109649780--109649840 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
109649770 TGTGAAAAGA
109649780 AAAGTTTTAAATTGATTGAAATTTTTCGGC
1 AAAGTTTTAAATTGATTGAAATTTTTCGGC
*
109649810 AAAGTTTTAAATTGATTGAAATTTTTTGGC
1 AAAGTTTTAAATTGATTGAAATTTTTCGGC
109649840 A
1 A
109649841 CGGTTTTTGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.34, C:0.05, G:0.16, T:0.44
Consensus pattern (30 bp):
AAAGTTTTAAATTGATTGAAATTTTTCGGC
Found at i:109660107 original size:21 final size:19
Alignment explanation
Indices: 109660078--109660116 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
109660068 TTTCTTCTAA
109660078 TAATATTATTGAAAAGTAAC
1 TAATATTATT-AAAAGTAAC
*
109660098 TAATCATTATTTAAAGTAA
1 TAAT-ATTATTAAAAGTAA
109660117 ACTGACTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.49, C:0.05, G:0.08, T:0.38
Consensus pattern (19 bp):
TAATATTATTAAAAGTAAC
Found at i:109660390 original size:13 final size:12
Alignment explanation
Indices: 109660370--109660399 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
109660360 TTTTTAATTT
109660370 AAATTTTAAAAA
1 AAATTTTAAAAA
109660382 AAATATTTAAAAA
1 AAAT-TTTAAAAA
109660395 AAATT
1 AAATT
109660400 GGCGATCAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AAATTTTAAAAA
Found at i:109661142 original size:15 final size:15
Alignment explanation
Indices: 109661122--109661151 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
109661112 AGTTTTAATA
*
109661122 AATTACGAAAATAAC
1 AATTACAAAAATAAC
109661137 AATTACAAAAATAAC
1 AATTACAAAAATAAC
109661152 CTACTTTCTT
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:0.63, C:0.13, G:0.03, T:0.20
Consensus pattern (15 bp):
AATTACAAAAATAAC
Found at i:109667541 original size:16 final size:16
Alignment explanation
Indices: 109667520--109667574 Score: 67
Period size: 16 Copynumber: 3.5 Consensus size: 16
109667510 TTATTTTAAC
*
109667520 TTGTTTCAAACATGAG
1 TTGTTTTAAACATGAG
*
109667536 TTGTTTTGAACAT-AG
1 TTGTTTTAAACATGAG
* *
109667551 TTGTTTTTAACAAGAG
1 TTGTTTTAAACATGAG
109667567 TTGTTTTA
1 TTGTTTTA
109667575 TGGTGATACT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
15 13 0.39
16 20 0.61
ACGTcount: A:0.27, C:0.07, G:0.18, T:0.47
Consensus pattern (16 bp):
TTGTTTTAAACATGAG
Done.