Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012777.1 Kokia drynarioides strain JFW-HI SEQ_127789, whole genome shotgun sequence
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: 649601
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Warning! 11 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:11453 original size:48 final size:48
Alignment explanation
Indices: 11397--11492 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
11387 CATCCCCACG
11397 CGTAGCATCATCTCTTCATAGAGATTTTAGCTTATTAAGCCTCTTAAA
1 CGTAGCATCATCTCTTCATAGAGATTTTAGCTTATTAAGCCTCTTAAA
11445 CGTAGCATCATCTCTTCATAGAGATTTTAGCTTATTAAGCCTCTTAAA
1 CGTAGCATCATCTCTTCATAGAGATTTTAGCTTATTAAGCCTCTTAAA
11493 GTATCCTTGG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.38
Consensus pattern (48 bp):
CGTAGCATCATCTCTTCATAGAGATTTTAGCTTATTAAGCCTCTTAAA
Found at i:17935 original size:9 final size:9
Alignment explanation
Indices: 17912--17950 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
17902 TTATCAATAA
*
17912 TTTCTTTCT
1 TTTCTTTTT
*
17921 TCTCTTTTT
1 TTTCTTTTT
17930 TTTCTTTTT
1 TTTCTTTTT
*
17939 CTTCTTTTT
1 TTTCTTTTT
17948 TTT
1 TTT
17951 TTCTCATTTT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (9 bp):
TTTCTTTTT
Found at i:17935 original size:18 final size:18
Alignment explanation
Indices: 17912--17950 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
17902 TTATCAATAA
17912 TTTCTTTCTTC-TCTTTTT
1 TTTCTTT-TTCTTCTTTTT
17930 TTTCTTTTTCTTCTTTTT
1 TTTCTTTTTCTTCTTTTT
17948 TTT
1 TTT
17951 TTCTCATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 3 0.15
18 17 0.85
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (18 bp):
TTTCTTTTTCTTCTTTTT
Found at i:17941 original size:20 final size:20
Alignment explanation
Indices: 17916--17954 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
17906 CAATAATTTC
17916 TTTCTTCTCTTTTTTTTCTT
1 TTTCTTCTCTTTTTTTTCTT
*
17936 TTTCTTCTTTTTTTTTTCT
1 TTTCTTCTCTTTTTTTTCT
17955 CATTTTGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (20 bp):
TTTCTTCTCTTTTTTTTCTT
Found at i:17960 original size:23 final size:21
Alignment explanation
Indices: 17916--17970 Score: 60
Period size: 23 Copynumber: 2.6 Consensus size: 21
17906 CAATAATTTC
*
17916 TTTCTTC-TCTTTTTTTTCTT
1 TTTCTTCTTTTTTTTTTTCTT
17936 TTTCTTCTTTTTTTTTTCTCATT
1 TTTCTTCTTTTTTTTTT-TC-TT
17959 TTGT-TTCTTTTT
1 TT-TCTTCTTTTT
17971 CAAATGACTT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
20 7 0.23
21 8 0.27
22 2 0.07
23 12 0.40
24 1 0.03
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.80
Consensus pattern (21 bp):
TTTCTTCTTTTTTTTTTTCTT
Found at i:17969 original size:18 final size:16
Alignment explanation
Indices: 17912--17971 Score: 61
Period size: 18 Copynumber: 3.6 Consensus size: 16
17902 TTATCAATAA
17912 TTTCTTTCTTCTCTTTTT
1 TTTCTTT-TTCTC-TTTT
*
17930 TTTCTTTTTCT-TCTT
1 TTTCTTTTTCTCTTTT
17945 TTT-TTTTTCTCATTTT
1 TTTCTTTTTCTC-TTTT
17961 GTTTCTTTTTC
1 -TTTCTTTTTC
17972 AAATGACTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
14 7 0.19
15 6 0.17
16 3 0.08
17 7 0.19
18 13 0.36
ACGTcount: A:0.02, C:0.18, G:0.02, T:0.78
Consensus pattern (16 bp):
TTTCTTTTTCTCTTTT
Found at i:26891 original size:13 final size:14
Alignment explanation
Indices: 26873--26902 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
26863 TTCAATGCAA
26873 TCAGA-GTTAAATG
1 TCAGAGGTTAAATG
26886 TCAGAGGTTAAATG
1 TCAGAGGTTAAATG
26900 TCA
1 TCA
26903 ATGTACTTAA
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:0.37, C:0.10, G:0.23, T:0.30
Consensus pattern (14 bp):
TCAGAGGTTAAATG
Found at i:43342 original size:30 final size:30
Alignment explanation
Indices: 43308--43384 Score: 109
Period size: 30 Copynumber: 2.6 Consensus size: 30
43298 TGAATGCTCG
*
43308 CAACATGAGTGTTCGTAGCTCCAATGTTCA
1 CAACATGAGTGTTCGCAGCTCCAATGTTCA
* * *
43338 CAACATGAGTATTTGCAGCTCCAGTGTTCA
1 CAACATGAGTGTTCGCAGCTCCAATGTTCA
*
43368 CAACATGAGTGCTCGCA
1 CAACATGAGTGTTCGCA
43385 TCTTCAAAGC
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.27
Consensus pattern (30 bp):
CAACATGAGTGTTCGCAGCTCCAATGTTCA
Found at i:48909 original size:18 final size:18
Alignment explanation
Indices: 48873--48912 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
48863 CCCAGATAAT
**
48873 ATGCGATCACATGACCAA
1 ATGCGATCACAAAACCAA
*
48891 ATGCGATCACAAAATCAA
1 ATGCGATCACAAAACCAA
48909 ATGC
1 ATGC
48913 ATTCAGATAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.42, C:0.25, G:0.15, T:0.17
Consensus pattern (18 bp):
ATGCGATCACAAAACCAA
Found at i:52506 original size:33 final size:33
Alignment explanation
Indices: 52464--52528 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
52454 TCCATAACAA
52464 TCAAGTGGCGACAGCTCTAAAGCACTACGATGC
1 TCAAGTGGCGACAGCTCTAAAGCACTACGATGC
*
52497 TCAAGTGGCGACAGCTTTAAAGCACTACGATG
1 TCAAGTGGCGACAGCTCTAAAGCACTACGATG
52529 TGAAACATCG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.31, C:0.25, G:0.25, T:0.20
Consensus pattern (33 bp):
TCAAGTGGCGACAGCTCTAAAGCACTACGATGC
Found at i:55542 original size:17 final size:17
Alignment explanation
Indices: 55503--55556 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
55493 ATGCATAGCA
* *
55503 TTTAGTTGTCATTGCATT
1 TTTATTTGTCACTGCA-T
55521 TTTATTTGTCACTGCAT
1 TTTATTTGTCACTGCAT
* *
55538 TTTATTTGTTACTACAT
1 TTTATTTGTCACTGCAT
55555 TT
1 TT
55557 GCATTGTAGT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
17 18 0.56
18 14 0.44
ACGTcount: A:0.19, C:0.13, G:0.11, T:0.57
Consensus pattern (17 bp):
TTTATTTGTCACTGCAT
Found at i:63084 original size:11 final size:11
Alignment explanation
Indices: 63070--63115 Score: 58
Period size: 11 Copynumber: 4.1 Consensus size: 11
63060 AGATAAATAT
63070 TATTTTATTAA
1 TATTTTATTAA
63081 TATTTTAATTAGA
1 TATTTT-ATTA-A
*
63094 TA-TTTATCAA
1 TATTTTATTAA
63104 TATTTTATTAA
1 TATTTTATTAA
63115 T
1 T
63116 TTAAGGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
10 3 0.10
11 17 0.57
12 7 0.23
13 3 0.10
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:64344 original size:20 final size:20
Alignment explanation
Indices: 64312--64350 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
64302 AATAGAAGCA
64312 TATGAATAATAA-TAAATTT
1 TATGAATAATAATTAAATTT
*
64331 TATGATATAGTAATTAAATT
1 TATGA-ATAATAATTAAATT
64351 GCATAAAGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 6 0.35
21 6 0.35
ACGTcount: A:0.49, C:0.00, G:0.08, T:0.44
Consensus pattern (20 bp):
TATGAATAATAATTAAATTT
Found at i:73004 original size:7 final size:7
Alignment explanation
Indices: 72994--73023 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
72984 AATATTAAAT
72994 ATTCAAC
1 ATTCAAC
73001 ATTCAAC
1 ATTCAAC
73008 ATTCAAC
1 ATTCAAC
*
73015 ACTCAAC
1 ATTCAAC
73022 AT
1 AT
73024 AATTAGATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.43, C:0.30, G:0.00, T:0.27
Consensus pattern (7 bp):
ATTCAAC
Found at i:79488 original size:111 final size:111
Alignment explanation
Indices: 79286--79514 Score: 422
Period size: 111 Copynumber: 2.1 Consensus size: 111
79276 AAGAAGCAAA
*
79286 GATTGGGAGAAGTAGAAACAATTGCACTTATTGAAGGGTGCATTGCTATTACAAACAAATTGCTT
1 GATT-GGAGAAGTAGAAACAATTGCACTTACTGAAGGGTGCATTGCTATTACAAACAAATTGCTT
*
79351 CTAGACTTTAAGAACCCGAGAGCTTCACAATACCCCATTCCATTGGT
65 CTAGACTTTAAGAACCCGAGAACTTCACAATACCCCATTCCATTGGT
*
79398 GATTGGAGAAGTAGTAACAATTGCACTTACTGAAGGGTGCATTGCTATTACAAACAAATTGCTTC
1 GATTGGAGAAGTAGAAACAATTGCACTTACTGAAGGGTGCATTGCTATTACAAACAAATTGCTTC
79463 TAGACTTTAAGAACCCGAGAACTTCACAATACCCCATTCCATTGGT
66 TAGACTTTAAGAACCCGAGAACTTCACAATACCCCATTCCATTGGT
79509 GATTGG
1 GATTGG
79515 TATATTGGAA
Statistics
Matches: 114, Mismatches: 3, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
111 110 0.96
112 4 0.04
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.28
Consensus pattern (111 bp):
GATTGGAGAAGTAGAAACAATTGCACTTACTGAAGGGTGCATTGCTATTACAAACAAATTGCTTC
TAGACTTTAAGAACCCGAGAACTTCACAATACCCCATTCCATTGGT
Found at i:80493 original size:20 final size:21
Alignment explanation
Indices: 80468--80506 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
80458 TGCATTTTTA
*
80468 GCATTTT-TAACTTAGTGACT
1 GCATTTTCTAACTCAGTGACT
80488 GCATTTTCTAACTCAGTGA
1 GCATTTTCTAACTCAGTGA
80507 TGCTTGATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.26, C:0.18, G:0.15, T:0.41
Consensus pattern (21 bp):
GCATTTTCTAACTCAGTGACT
Found at i:82682 original size:14 final size:14
Alignment explanation
Indices: 82640--82704 Score: 62
Period size: 15 Copynumber: 4.5 Consensus size: 14
82630 AATTTTTTAA
82640 TTTTATTAAATTTAT
1 TTTTATTAAATTT-T
*
82655 TATTATGT-AATTTT
1 TTTTAT-TAAATTTT
82669 ATTTT-TTAAATTTT
1 -TTTTATTAAATTTT
*
82683 CTTTTATTTAATTTT
1 -TTTTATTAAATTTT
82698 TTTTATT
1 TTTTATT
82705 TCTTATTTGT
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
13 1 0.02
14 19 0.45
15 21 0.50
16 1 0.02
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.71
Consensus pattern (14 bp):
TTTTATTAAATTTT
Found at i:82689 original size:29 final size:30
Alignment explanation
Indices: 82634--82704 Score: 85
Period size: 29 Copynumber: 2.4 Consensus size: 30
82624 GGTAGAAATT
82634 TTTTAATTTTATTAAATTTATTATTATGTAA
1 TTTT-ATTTTATTAAATTTATTATTATGTAA
* *
82665 TTTTATTTT-TTAAATTT-TCTTTTATTTAA
1 TTTTATTTTATTAAATTTAT-TATTATGTAA
82694 TTTT-TTTTATT
1 TTTTATTTTATT
82705 TCTTATTTGT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
28 5 0.14
29 22 0.61
30 5 0.14
31 4 0.11
ACGTcount: A:0.27, C:0.01, G:0.01, T:0.70
Consensus pattern (30 bp):
TTTTATTTTATTAAATTTATTATTATGTAA
Found at i:82705 original size:14 final size:15
Alignment explanation
Indices: 82634--82705 Score: 69
Period size: 14 Copynumber: 4.9 Consensus size: 15
82624 GGTAGAAATT
82634 TTTTAATTTTA-TTAA
1 TTTT-ATTTTATTTAA
* *
82649 ATTTATTATTATGTAA
1 TTTTATT-TTATTTAA
*
82665 TTTTATTTT-TTAAA
1 TTTTATTTTATTTAA
*
82679 TTTTCTTTTATTTAA
1 TTTTATTTTATTTAA
82694 TTTT-TTTTATTT
1 TTTTATTTTATTT
82706 CTTATTTGTT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
14 22 0.47
15 16 0.34
16 9 0.19
ACGTcount: A:0.26, C:0.01, G:0.01, T:0.71
Consensus pattern (15 bp):
TTTTATTTTATTTAA
Found at i:84670 original size:38 final size:38
Alignment explanation
Indices: 84623--84707 Score: 107
Period size: 38 Copynumber: 2.2 Consensus size: 38
84613 CGTTTTTGTG
* * * *
84623 AAATCTGGAAGTGCTCATGCGGCGATAGTTTTGGGTCC
1 AAATTTGGAAGTGCTCACGCGGCGACAATTTTGGGTCC
* * *
84661 AAATTTGGAATTGCTCACGCGTCGACAATTTTGGGTGC
1 AAATTTGGAAGTGCTCACGCGGCGACAATTTTGGGTCC
84699 AAATTTGGA
1 AAATTTGGA
84708 TGTTATTTTG
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.31
Consensus pattern (38 bp):
AAATTTGGAAGTGCTCACGCGGCGACAATTTTGGGTCC
Found at i:90796 original size:17 final size:18
Alignment explanation
Indices: 90774--90807 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
90764 TGTTAATGTA
90774 CATTGTCATTGC-TTTTC
1 CATTGTCATTGCATTTTC
90791 CATTGTCATTGCATTTT
1 CATTGTCATTGCATTTT
90808 AGTGTTAGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.15, C:0.21, G:0.12, T:0.53
Consensus pattern (18 bp):
CATTGTCATTGCATTTTC
Found at i:93253 original size:16 final size:17
Alignment explanation
Indices: 93232--93263 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
93222 TGTCAATATC
93232 ATAATATTA-AATTTTA
1 ATAATATTAGAATTTTA
93248 ATAATATTAGAATTTT
1 ATAATATTAGAATTTT
93264 CTTTTATTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (17 bp):
ATAATATTAGAATTTTA
Found at i:96721 original size:21 final size:21
Alignment explanation
Indices: 96695--96734 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
96685 GTAGGTTCAG
96695 TTTCTTCCTTC-TCTTTTTCCT
1 TTTCTT-CTTCTTCTTTTTCCT
96716 TTTCTTCTTCTTCTTTTTC
1 TTTCTTCTTCTTCTTTTTC
96735 TTCATCCTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTCTTCTTCTTCTTTTTCCT
Found at i:104616 original size:23 final size:24
Alignment explanation
Indices: 104563--104626 Score: 80
Period size: 24 Copynumber: 2.7 Consensus size: 24
104553 AAGATAGATG
*
104563 TAAAAGTAGTCAACAAAAAATAAA
1 TAAAAGTAGTTAACAAAAAATAAA
104587 TAAAAGTAGTTAACAAAAAA-AAA
1 TAAAAGTAGTTAACAAAAAATAAA
104610 -AACAAGTCAG-TAACAAA
1 TAA-AAGT-AGTTAACAAA
104627 TAAAGATTAG
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
22 2 0.05
23 14 0.38
24 21 0.57
ACGTcount: A:0.66, C:0.09, G:0.09, T:0.16
Consensus pattern (24 bp):
TAAAAGTAGTTAACAAAAAATAAA
Found at i:108793 original size:175 final size:166
Alignment explanation
Indices: 108509--108851 Score: 587
Period size: 175 Copynumber: 2.0 Consensus size: 166
108499 TGGAATTTTC
108509 AGTATGTATTGAAACATTATTTTGGACACGTCAAATGAGCCTTGACAACATAACGAAATTGTGAT
1 AGTATGTATTGAAACATTATTTTGGACACGTCAAATGAGCCTTGACAACATAACGAAATTGTGAT
*
108574 TCATTGATGTTATTTAAAGCAACCCCCAAAGTTAAACTTGTAAATGTTTAAATCTTTACTTAAGG
66 TCATTGATGTTATTTAAAGCAACCCCCAAAGTTAAACCTGTAAATGTTTAAATCTTTACTTAAGG
108639 TGAAGTGTTATTCTAAAATCGTGTTTCCAAATTGTT
131 TGAAGTGTTATTCTAAAATCGTGTTTCCAAATTGTT
108675 AGTATGTATTGAAACATTATTTTGGACACGTCAAATATTAAATGGAAGCCTTGACAACATAACGA
1 AGTATGTATTGAAACATTATTTTGGACACGTC-------AAAT-G-AGCCTTGACAACATAACGA
*
108740 AATTGTGATTCATTGATGTTATTTAAAGCAGCCCCCAAAGTTAAACCTGTAAATGTTTAAATCTT
57 AATTGTGATTCATTGATGTTATTTAAAGCAACCCCCAAAGTTAAACCTGTAAATGTTTAAATCTT
108805 TACTTAAGGTGAAGTGTTATTCTAAAATCGTGTTTCCAAATTGTT
122 TACTTAAGGTGAAGTGTTATTCTAAAATCGTGTTTCCAAATTGTT
108850 AG
1 AG
108852 GGATCGACCC
Statistics
Matches: 166, Mismatches: 2, Indels: 9
0.94 0.01 0.05
Matches are distributed among these distances:
166 32 0.19
173 4 0.02
174 1 0.01
175 129 0.78
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.36
Consensus pattern (166 bp):
AGTATGTATTGAAACATTATTTTGGACACGTCAAATGAGCCTTGACAACATAACGAAATTGTGAT
TCATTGATGTTATTTAAAGCAACCCCCAAAGTTAAACCTGTAAATGTTTAAATCTTTACTTAAGG
TGAAGTGTTATTCTAAAATCGTGTTTCCAAATTGTT
Found at i:121431 original size:25 final size:25
Alignment explanation
Indices: 121403--121450 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
121393 ATTAAACAAT
121403 TACTTAGTTTTAACAACGAATTTAA
1 TACTTAGTTTTAACAACGAATTTAA
121428 TACTTAGTTTTAACAACGAATTT
1 TACTTAGTTTTAACAACGAATTT
121451 TAGTAAAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.38, C:0.12, G:0.08, T:0.42
Consensus pattern (25 bp):
TACTTAGTTTTAACAACGAATTTAA
Found at i:123139 original size:18 final size:18
Alignment explanation
Indices: 123116--123154 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
123106 GGAGTTCTAA
*
123116 TCTCTAATGAATGTATTT
1 TCTCTAATGAACGTATTT
123134 TCTCTAATGAACGTATTT
1 TCTCTAATGAACGTATTT
123152 TCT
1 TCT
123155 AAGGTTGTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.26, C:0.15, G:0.10, T:0.49
Consensus pattern (18 bp):
TCTCTAATGAACGTATTT
Found at i:123196 original size:25 final size:25
Alignment explanation
Indices: 123168--123219 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
123158 GTTGTAAAAG
123168 AGCCTATTTATAGATTAAATTTCTA
1 AGCCTATTTATAGATTAAATTTCTA
123193 AGCCTATTTATAGATTAAATTTCTA
1 AGCCTATTTATAGATTAAATTTCTA
123218 AG
1 AG
123220 TCAAATAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.37, C:0.12, G:0.10, T:0.42
Consensus pattern (25 bp):
AGCCTATTTATAGATTAAATTTCTA
Found at i:123563 original size:31 final size:31
Alignment explanation
Indices: 123501--123564 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 31
123491 GCATGGGGTG
* * *
123501 TTATAAAAAAAATATTAAAATTGATATAAAC
1 TTATAAAAAAAATATTAAAAATAATAAAAAC
*
123532 TTAT-AAAAAATTATTAAAAGATAATAAAAAC
1 TTATAAAAAAAATATTAAAA-ATAATAAAAAC
123563 TT
1 TT
123565 GAACTGGGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 14 0.50
31 14 0.50
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.33
Consensus pattern (31 bp):
TTATAAAAAAAATATTAAAAATAATAAAAAC
Found at i:128173 original size:28 final size:28
Alignment explanation
Indices: 128126--128245 Score: 116
Period size: 28 Copynumber: 4.2 Consensus size: 28
128116 TGAAGATGAG
* *
128126 AATTTTGGATACCCGTGGGCAAAATGGT
1 AATTTTGGATACTCGAGGGCAAAATGGT
128154 AATTTTGGATACTCGAGGGCAAAATGGT
1 AATTTTGGATACTCGAGGGCAAAATGGT
* * * *
128182 AATTTGGGAAAGTTCGAGGTCAAAAATGG-
1 AATTTTGGATA-CTCGAGGGC-AAAATGGT
* * * *
128211 AATTTTTAGACATTCGAGGGTAAAATGGT
1 AA-TTTTGGATACTCGAGGGCAAAATGGT
128240 AATTTT
1 AATTTT
128246 TGGAAAGTTC
Statistics
Matches: 77, Mismatches: 11, Indels: 8
0.80 0.11 0.08
Matches are distributed among these distances:
28 46 0.60
29 18 0.23
30 13 0.17
ACGTcount: A:0.33, C:0.09, G:0.27, T:0.31
Consensus pattern (28 bp):
AATTTTGGATACTCGAGGGCAAAATGGT
Found at i:128214 original size:29 final size:30
Alignment explanation
Indices: 128145--128608 Score: 203
Period size: 29 Copynumber: 15.8 Consensus size: 30
128135 TACCCGTGGG
* * *
128145 CAAAATGGTAA-TTTTGGATA-CTCGAGGG
1 CAAAATGGTAATTTTTGGAAAGTTCGAGGT
*
128173 CAAAATGGTAA-TTTGGGAAAGTTCGAGGT
1 CAAAATGGTAATTTTTGGAAAGTTCGAGGT
* *
128202 CAAAAATGG-AATTTTTAGACA-TTCGAGGGT
1 C-AAAATGGTAATTTTTGGAAAGTTCGA-GGT
*
128232 -AAAATGGTAATTTTTGGAAAGTTCGGGGTTT
1 CAAAATGGTAATTTTTGGAAAGTTCGAGG--T
* * * *
128263 AAAAATGG-AATTTTTAGACA-TCCGAGGGT
1 CAAAATGGTAATTTTTGGAAAGTTCGA-GGT
* * *
128292 -AAAATGG-AAATTTTGGAAAAATT-GGGGT
1 CAAAATGGTAATTTTTGG-AAAGTTCGAGGT
*
128320 CAAAAATGG-AATTTTTTGG-AAGTTCAAGGGT
1 C-AAAATGGTAA-TTTTTGGAAAGTTCGA-GGT
* *
128351 -GAAATGGTAATTTTTTGGGAAAATTCGAGGT
1 CAAAATGGTAA-TTTTT-GGAAAGTTCGAGGT
* * *
128382 CAAAAATGG-AA-TTATGG-AAGTTTGGGGGT
1 C-AAAATGGTAATTTTTGGAAAG-TTCGAGGT
* *
128411 -AAAATGGTAATTTTTGGAAAAATTAG-GGT
1 CAAAATGGTAATTTTTGG-AAAGTTCGAGGT
* *
128440 CAAAAATGG-AATTTTT-GAAACTTTGAGGGT
1 C-AAAATGGTAATTTTTGGAAAGTTCGA-GGT
* ** *
128470 AAAAAT-GTAATTTTTAAAAAGTTTGAGGT
1 CAAAATGGTAATTTTTGGAAAGTTCGAGGT
* * *
128499 ATAAAAT-GTAA-TTTTGGAAAGTTTTGGGGT
1 -CAAAATGGTAATTTTTGGAAAG-TTCGAGGT
* * ** *
128529 -AAAATGAT-ATTTTTTGAAAAATCAAGGT
1 CAAAATGGTAATTTTTGGAAAGTTCGAGGT
*
128557 CAAAATGG-AA-TTTTGGAAAGTTTGAGGAT
1 CAAAATGGTAATTTTTGGAAAGTTCGAGG-T
* *
128586 AAAAATGAT-ATTTTTGGAAAGTT
1 CAAAATGGTAATTTTTGGAAAGTT
128609 TAGGGTTAAA
Statistics
Matches: 336, Mismatches: 58, Indels: 82
0.71 0.12 0.17
Matches are distributed among these distances:
27 7 0.02
28 75 0.22
29 104 0.31
30 93 0.28
31 36 0.11
32 15 0.04
33 6 0.02
ACGTcount: A:0.37, C:0.04, G:0.25, T:0.33
Consensus pattern (30 bp):
CAAAATGGTAATTTTTGGAAAGTTCGAGGT
Found at i:128310 original size:59 final size:58
Alignment explanation
Indices: 128167--128455 Score: 237
Period size: 60 Copynumber: 4.9 Consensus size: 58
128157 TTTGGATACT
* * * * *
128167 CGAGGGCAAAATGGTAATTTGGGAAAGTTCGAGGTCAAAAATGGAATTTTTAGACATT
1 CGAGGGTAAAATGGAAATTTTGGAAAGTTCGGGGTCAAAAATGGAATTTTTAGACATC
* *
128225 CGAGGGTAAAATGGTAATTTTTGGAAAGTTCGGGGTTTAAAAATGGAATTTTTAGACATC
1 CGAGGGTAAAATGG-AAATTTTGGAAAGTTCGGGG-TCAAAAATGGAATTTTTAGACATC
* * *
128285 CGAGGGTAAAATGGAAATTTTGGAAAAATT-GGGGTCAAAAATGGAATTTTTTGGA-AGTT
1 CGAGGGTAAAATGGAAATTTTGG-AAAGTTCGGGGTCAAAAATGGAA-TTTTTAGACA-TC
* * * * * * * *
128344 CAAGGGTGAAATGGTAATTTTTTGGGAAAATTCGAGGTCAAAAATGGAA-TTATGGA-AGTT
1 CGAGGGTAAAATGG-AA-ATTTT-GGAAAGTTCGGGGTCAAAAATGGAATTTTTAGACA-TC
* * * * *
128404 TGGGGGTAAAATGGTAATTTTTGGAAAAATT-AGGGTCAAAAATGGAATTTTT
1 CGAGGGTAAAATGG-AAATTTTGG-AAAGTTCGGGGTCAAAAATGGAATTTTT
128456 GAAACTTTGA
Statistics
Matches: 196, Mismatches: 24, Indels: 21
0.81 0.10 0.09
Matches are distributed among these distances:
58 41 0.21
59 62 0.32
60 66 0.34
61 10 0.05
62 17 0.09
ACGTcount: A:0.36, C:0.05, G:0.28, T:0.31
Consensus pattern (58 bp):
CGAGGGTAAAATGGAAATTTTGGAAAGTTCGGGGTCAAAAATGGAATTTTTAGACATC
Found at i:128471 original size:59 final size:59
Alignment explanation
Indices: 128146--128634 Score: 335
Period size: 59 Copynumber: 8.3 Consensus size: 59
128136 ACCCGTGGGC
* * * * * *
128146 AAAATGGTAATTTTGGATAC-TCGAGGGCAAAATGGTAA--TTTGGGAAAGTTCGAGGTCA
1 AAAATGG-AATTTTTGAAACTTCGAGGGTAAAATGGTAATTTTTGGAAAAATTAG-GGTCA
* * * *
128204 AAAATGGAATTTTT-AGACATTCGAGGGTAAAATGGTAATTTTTGG-AAAGTTCGGGGTTTA
1 AAAATGGAATTTTTGAAAC-TTCGAGGGTAAAATGGTAATTTTTGGAAAAATT-AGGG-TCA
* * * *
128264 AAAATGGAATTTTT-AGACATCCGAGGGTAAAATGG-AAATTTTGGAAAAATTGGGGTCA
1 AAAATGGAATTTTTGAAAC-TTCGAGGGTAAAATGGTAATTTTTGGAAAAATTAGGGTCA
* * * * * *
128322 AAAATGGAATTTTTTGGAAGTTCAAGGGTGAAATGGTAATTTTTTGGGAAAATTCGAGGTCA
1 AAAATGGAA-TTTTTGAAACTTCGAGGGTAAAATGGTAA-TTTTTGGAAAAATTAG-GGTCA
* * * * *
128384 AAAATGGAA-TTATGGAAGTTTGGGGGTAAAATGGTAATTTTTGGAAAAATTAGGGTCA
1 AAAATGGAATTTTTGAAACTTCGAGGGTAAAATGGTAATTTTTGGAAAAATTAGGGTCA
* *
128442 AAAATGGAATTTTTGAAACTTTGAGGGTAAAAAT-GTAATTTTT--AAAAAGTTTGAGGT-A
1 AAAATGGAATTTTTGAAACTTCGAGGGT-AAAATGGTAATTTTTGGAAAAA-TTAG-GGTCA
* * * * * * * *
128500 TAAAATGTAATTTTGGAAAGTTTTG-GGGTAAAATGAT-ATTTTTTGAAAAATCAAGGTC-
1 -AAAATGGAATTTTTGAAA-CTTCGAGGGTAAAATGGTAATTTTTGGAAAAATTAGGGTCA
* * * * * ** *
128558 AAAATGGAATTTTGGAAAGTTTGAGGATAAAAATGAT-ATTTTTGGAAAGTTTAGGGTTA
1 AAAATGGAATTTTTGAAACTTCGAGGGT-AAAATGGTAATTTTTGGAAAAATTAGGGTCA
*
128617 AAAATGGAATTTTGGAAA
1 AAAATGGAATTTTTGAAA
128635 AGTTTAGGGG
Statistics
Matches: 360, Mismatches: 46, Indels: 49
0.79 0.10 0.11
Matches are distributed among these distances:
56 7 0.02
57 31 0.09
58 90 0.25
59 118 0.33
60 87 0.24
61 13 0.04
62 14 0.04
ACGTcount: A:0.38, C:0.04, G:0.26, T:0.33
Consensus pattern (59 bp):
AAAATGGAATTTTTGAAACTTCGAGGGTAAAATGGTAATTTTTGGAAAAATTAGGGTCA
Found at i:128619 original size:29 final size:29
Alignment explanation
Indices: 128399--128673 Score: 140
Period size: 29 Copynumber: 9.3 Consensus size: 29
128389 GGAATTATGG
* * *
128399 AAGTTTGGGGGTAAAATGGTAATTTTTGGA
1 AAGTTTAGGGTTAAAATGAT-ATTTTTGGA
** *
128429 AAAATTAGGGTCAAAAATGGA-ATTTTT-GA
1 AAGTTTAGGGT-TAAAAT-GATATTTTTGGA
* * **
128458 AACTTTGAGGGTAAAAATG-TAATTTTTAAA
1 AAGTTT-AGGGTTAAAATGAT-ATTTTTGGA
*
128488 AAGTTT-GAGGTATAAAATG-TAATTTTGGA
1 AAGTTTAG-GGT-TAAAATGATATTTTTGGA
* * *
128517 AAGTTTTGGGGTAAAATGATATTTTTTGA
1 AAGTTTAGGGTTAAAATGATATTTTTGGA
** * * *
128546 AAAATCAAGGTCAAAATGGA-A-TTTTGGA
1 AAGTTTAGGGTTAAAAT-GATATTTTTGGA
* *
128574 AAGTTTGAGGATAAAAATGATATTTTTGGA
1 AAGTTT-AGGGTTAAAATGATATTTTTGGA
128604 AAGTTTAGGGTTAAAAATGGA-A-TTTTGGAA
1 AAGTTTAGGGTT-AAAAT-GATATTTTTGG-A
*
128634 AAGTTTAGGGGTTAAAAT-ATTATTTTT-AA
1 AAGTTTA-GGGTTAAAATGA-TATTTTTGGA
128663 ATAGTTTAGGG
1 A-AGTTTAGGG
128674 ACCTTCAAGG
Statistics
Matches: 189, Mismatches: 34, Indels: 45
0.71 0.13 0.17
Matches are distributed among these distances:
28 21 0.11
29 78 0.41
30 73 0.39
31 16 0.08
32 1 0.01
ACGTcount: A:0.39, C:0.01, G:0.24, T:0.36
Consensus pattern (29 bp):
AAGTTTAGGGTTAAAATGATATTTTTGGA
Found at i:128637 original size:30 final size:28
Alignment explanation
Indices: 128174--128643 Score: 176
Period size: 30 Copynumber: 15.9 Consensus size: 28
128164 ACTCGAGGGC
* *
128174 AAAATGGTAATTTGGGAAAG-TTCGAGGTCA
1 AAAATGG-AATTTTGGAAAGTTTAG-GGT-A
* * *
128204 AAAATGGAATTTTTAGACA-TTCGAGGGT-
1 AAAATGGAA-TTTTGGAAAGTT-TAGGGTA
**
128232 AAAATGGTAATTTTTGGAAAGTTCGGGGTTTA
1 AAAATGG-AA-TTTTGGAAAGTTTAGGG--TA
* * **
128264 AAAATGGAATTTTTAGACA-TCCGAGGGT-
1 AAAATGGAA-TTTTGGAAAGT-TTAGGGTA
** *
128292 AAAATGGAAATTTTGGAAAAATTGGGGTCA
1 AAAATGG-AATTTTGGAAAGTTTAGGGT-A
*
128322 AAAATGGAATTTTTTGG-AAGTTCAAGGGT-
1 AAAATGGAA--TTTTGGAAAGTT-TAGGGTA
* * *
128351 GAAATGGTAATTTTTTGGGAAA-ATTCGAGGTCA
1 AAAATGG-AA--TTTT-GGAAAGTTTAG-GGT-A
* *
128384 AAAATGGAATTATGG-AAGTTTGGGGGT-
1 AAAATGGAATTTTGGAAAGTTT-AGGGTA
**
128411 AAAATGGTAATTTTTGGAAAAATTAGGGTCA
1 AAAATGG-AA-TTTTGGAAAGTTTAGGGT-A
* *
128442 AAAATGGAATTTTTGAAACTTTGAGGGTA
1 AAAATGGAATTTTGGAAAGTTT-AGGGTA
* **
128471 AAAATGTAATTTTTAAAAAGTTT-GAGGTA
1 AAAATGGAA-TTTTGGAAAGTTTAG-GGTA
* *
128500 TAAAATGTAATTTTGGAAAGTTTTGGGGT-
1 -AAAATGGAATTTTGGAAAG-TTTAGGGTA
* ** * * *
128529 AAAAT-GATATTTTTTGAAAAATCAAGGTC
1 AAAATGGA-A-TTTTGGAAAGTTTAGGGTA
*
128558 AAAATGGAATTTTGGAAAGTTTGAGGATA
1 AAAATGGAATTTTGGAAAGTTT-AGGGTA
128587 AAAAT-GATATTTTTGGAAAGTTTAGGGTTA
1 AAAATGGA-A-TTTTGGAAAGTTTAGGG-TA
128617 AAAATGGAATTTTGGAAAAGTTTAGGG
1 AAAATGGAATTTTGG-AAAGTTTAGGG
128644 GTTAAAATAT
Statistics
Matches: 335, Mismatches: 60, Indels: 90
0.69 0.12 0.19
Matches are distributed among these distances:
27 8 0.02
28 51 0.15
29 105 0.31
30 113 0.34
31 41 0.12
32 11 0.03
33 6 0.02
ACGTcount: A:0.38, C:0.03, G:0.26, T:0.33
Consensus pattern (28 bp):
AAAATGGAATTTTGGAAAGTTTAGGGTA
Found at i:129754 original size:15 final size:15
Alignment explanation
Indices: 129734--129768 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
129724 TTATTAATAA
* *
129734 TATTAATGTTATTGT
1 TATTAATATTATTAT
129749 TATTAATATTATTAT
1 TATTAATATTATTAT
129764 TATTA
1 TATTA
129769 TTAATGCTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (15 bp):
TATTAATATTATTAT
Found at i:130488 original size:6 final size:6
Alignment explanation
Indices: 130464--130539 Score: 63
Period size: 6 Copynumber: 13.2 Consensus size: 6
130454 GTTTTAAATC
**
130464 ATTTCAA ATTT-A A-TTAA ATTTAA ATTTAA A-GCAA ATTTAA ATTTAA
1 ATTT-AA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
**
130510 GA--TAA ATTTAA ATTTAA AAATAA ATTTAA A
1 -ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA A
130540 ACCAATTTAA
Statistics
Matches: 55, Mismatches: 8, Indels: 13
0.72 0.11 0.17
Matches are distributed among these distances:
4 3 0.05
5 10 0.18
6 37 0.67
7 5 0.09
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (6 bp):
ATTTAA
Found at i:130499 original size:17 final size:18
Alignment explanation
Indices: 130479--130539 Score: 81
Period size: 17 Copynumber: 3.5 Consensus size: 18
130469 AAATTTAATT
130479 AAATTTAAATTTAAAG-C
1 AAATTTAAATTTAAAGAC
*
130496 AAATTTAAATTT-AAGAT
1 AAATTTAAATTTAAAGAC
* *
130513 AAATTTAAATTTAAAAAT
1 AAATTTAAATTTAAAGAC
130531 AAATTTAAA
1 AAATTTAAA
130540 ACCAATTTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
16 3 0.08
17 24 0.60
18 13 0.32
ACGTcount: A:0.57, C:0.02, G:0.03, T:0.38
Consensus pattern (18 bp):
AAATTTAAATTTAAAGAC
Found at i:131018 original size:49 final size:48
Alignment explanation
Indices: 130951--131367 Score: 278
Period size: 49 Copynumber: 8.6 Consensus size: 48
130941 ATGGTACAAA
* * *
130951 ATTCGCCATTGTGACTTAAACCCTTCCCCTTGTGTCTTCGCGGTACTGG
1 ATTCGCCATTGCGACTTAAA-CCTTTCCCTTGTGTCTTCGAGGTACTGG
* * * * *
131000 ATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTC-TCTAAGGTACTAGG
1 ATTCGCCATTGCGACTTAAACCTTTCCCTT-GTGTCTTC-GAGGTACT-GG
* *
131050 -TTCGCCATTGCGACTTAAACCTTTCCCATGTGTCTTCGTGGTACTGG
1 ATTCGCCATTGCGACTTAAACCTTTCCCTTGTGTCTTCGAGGTACTGG
* * * * *
131097 ATTCGCCATTGCGGCTTAAATCTTTCCCTTCATGTC-TCTAAGGAACTAGG
1 ATTCGCCATTGCGACTTAAACCTTTCCCTT-GTGTCTTC-GAGGTACT-GG
* * * * *
131147 -TTCGTCATTGCAACTTAAACC-TTCCCTCTCTTATCTTC-ACAGTACTGG
1 ATTCGCCATTGCGACTTAAACCTTTCCCT-T-GTGTCTTCGA-GGTACTGG
* * * * * * *
131195 ATTCACTATTACAACTTAAATCTTTCCCTTCATGTC-TCTAAGGTACTAGG
1 ATTCGCCATTGCGACTTAAACCTTTCCCTT-GTGTCTTC-GAGGTACT-GG
* * *
131245 -TTCACCATTGTGACTTAAACCTTTCCCTTGTGTCTTCGTGGTACTGG
1 ATTCGCCATTGCGACTTAAACCTTTCCCTTGTGTCTTCGAGGTACTGG
** * * * *
131292 ATTCATCGTTGCGACTTAAATCTTTCCCTTCATG-CTTCTGAGGTACAAGG
1 ATTCGCCATTGCGACTTAAACCTTTCCCTT-GTGTCTTC-GAGGTAC-TGG
* *
131342 -TTTGCCGTTGCGACTTAAACCTTTCC
1 ATTCGCCATTGCGACTTAAACCTTTCC
131368 TTTTGTGTTT
Statistics
Matches: 290, Mismatches: 57, Indels: 42
0.75 0.15 0.11
Matches are distributed among these distances:
47 4 0.01
48 98 0.34
49 171 0.59
50 17 0.06
ACGTcount: A:0.19, C:0.27, G:0.17, T:0.37
Consensus pattern (48 bp):
ATTCGCCATTGCGACTTAAACCTTTCCCTTGTGTCTTCGAGGTACTGG
Found at i:131110 original size:97 final size:97
Alignment explanation
Indices: 130952--131387 Score: 536
Period size: 97 Copynumber: 4.5 Consensus size: 97
130942 TGGTACAAAA
* * * * *
130952 TTCGCCATTGTGACTTAAACCCTTCCCCTTGTGTCTTCGCGGTACTGGATTCGCCGTTGCGGCTT
1 TTCGCCATTGCGACTTAAA-CCTTTCCCTTGTGTCTTCGCGGTACTGGATTCACCATTGCGACTT
131017 AAATCTTTCCCTTCATGTCTCTAAGGTACTAGG
65 AAATCTTTCCCTTCATGTCTCTAAGGTACTAGG
* * * *
131050 TTCGCCATTGCGACTTAAACCTTTCCCATGTGTCTTCGTGGTACTGGATTCGCCATTGCGGCTTA
1 TTCGCCATTGCGACTTAAACCTTTCCCTTGTGTCTTCGCGGTACTGGATTCACCATTGCGACTTA
*
131115 AATCTTTCCCTTCATGTCTCTAAGGAACTAGG
66 AATCTTTCCCTTCATGTCTCTAAGGTACTAGG
* * * * * * * * *
131147 TTCGTCATTGCAACTTAAACC-TTCCCTCTCTTATCTTCACAGTACTGGATTCACTATTACAACT
1 TTCGCCATTGCGACTTAAACCTTTCCCT-T-GTGTCTTCGCGGTACTGGATTCACCATTGCGACT
131211 TAAATCTTTCCCTTCATGTCTCTAAGGTACTAGG
64 TAAATCTTTCCCTTCATGTCTCTAAGGTACTAGG
* * * * *
131245 TTCACCATTGTGACTTAAACCTTTCCCTTGTGTCTTCGTGGTACTGGATTCATCGTTGCGACTTA
1 TTCGCCATTGCGACTTAAACCTTTCCCTTGTGTCTTCGCGGTACTGGATTCACCATTGCGACTTA
* *
131310 AATCTTTCCCTTCATG-CTTCTGAGGTACAAGG
66 AATCTTTCCCTTCATGTC-TCTAAGGTACTAGG
* * * *
131342 TTTGCCGTTGCGACTTAAACCTTTCCTTTTGTGT-TTCACGGTACTG
1 TTCGCCATTGCGACTTAAACCTTTCC-CTTGTGTCTTCGCGGTACTG
131388 ATACCTGTAG
Statistics
Matches: 290, Mismatches: 43, Indels: 11
0.84 0.12 0.03
Matches are distributed among these distances:
96 6 0.02
97 179 0.62
98 99 0.34
99 6 0.02
ACGTcount: A:0.19, C:0.27, G:0.17, T:0.37
Consensus pattern (97 bp):
TTCGCCATTGCGACTTAAACCTTTCCCTTGTGTCTTCGCGGTACTGGATTCACCATTGCGACTTA
AATCTTTCCCTTCATGTCTCTAAGGTACTAGG
Found at i:131360 original size:195 final size:195
Alignment explanation
Indices: 131014--131364 Score: 560
Period size: 195 Copynumber: 1.8 Consensus size: 195
131004 GCCGTTGCGG
*
131014 CTTAAATCTTTCCCTTCATGTCTCTAAGGTACTAGGTTCGCCATTGCGACTTAAACCTTTCCCAT
1 CTTAAATCTTTCCCTTCATGTCTCTAAGGTACTAGGTTCACCATTGCGACTTAAACCTTTCCCAT
* * *
131079 GTGTCTTCGTGGTACTGGATTCGCCATTGCGGCTTAAATCTTTCCCTTCATGTCTCTAAGGAACT
66 GTGTCTTCGTGGTACTGGATTCACCATTGCGACTTAAATCTTTCCCTTCATGTCTCTAAGGAACA
*
131144 AGGTTCGTCATTGCAACTTAAACCTTCCCTCTCTTATCTTCACAGTACTGGATTCACTATTACAA
131 AGGTTCGCCATTGCAACTTAAACCTTCCCTCTCTTATCTTCACAGTACTGGATTCACTATTACAA
* *
131209 CTTAAATCTTTCCCTTCATGTCTCTAAGGTACTAGGTTCACCATTGTGACTTAAACCTTTCCCTT
1 CTTAAATCTTTCCCTTCATGTCTCTAAGGTACTAGGTTCACCATTGCGACTTAAACCTTTCCCAT
* * * *
131274 GTGTCTTCGTGGTACTGGATTCATCGTTGCGACTTAAATCTTTCCCTTCATG-CTTCTGAGGTAC
66 GTGTCTTCGTGGTACTGGATTCACCATTGCGACTTAAATCTTTCCCTTCATGTC-TCTAAGGAAC
* * *
131338 AAGGTTTGCCGTTGCGACTTAAACCTT
130 AAGGTTCGCCATTGCAACTTAAACCTT
131365 TCCTTTTGTG
Statistics
Matches: 141, Mismatches: 14, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
194 1 0.01
195 140 0.99
ACGTcount: A:0.21, C:0.26, G:0.16, T:0.37
Consensus pattern (195 bp):
CTTAAATCTTTCCCTTCATGTCTCTAAGGTACTAGGTTCACCATTGCGACTTAAACCTTTCCCAT
GTGTCTTCGTGGTACTGGATTCACCATTGCGACTTAAATCTTTCCCTTCATGTCTCTAAGGAACA
AGGTTCGCCATTGCAACTTAAACCTTCCCTCTCTTATCTTCACAGTACTGGATTCACTATTACAA
Found at i:132899 original size:15 final size:15
Alignment explanation
Indices: 132879--132909 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
132869 CAATAACTAC
*
132879 AATATTATTATTATT
1 AATATTAATATTATT
132894 AATATTAATATTATT
1 AATATTAATATTATT
132909 A
1 A
132910 TTAATGCTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AATATTAATATTATT
Found at i:133638 original size:6 final size:6
Alignment explanation
Indices: 133614--133689 Score: 54
Period size: 6 Copynumber: 13.2 Consensus size: 6
133604 GTTTTAAGTC
** *
133614 ATTTCAA ATTT-A A-TTAA ATTTAA ATTTAA A-ACAA CTTTAA ATTTAA
1 ATTT-AA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
**
133660 GA--TAA ATTTAA ATTTAA AAATAA ATTTAA A
1 -ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA A
133690 ACCAATTTAA
Statistics
Matches: 53, Mismatches: 10, Indels: 13
0.70 0.13 0.17
Matches are distributed among these distances:
4 3 0.06
5 9 0.17
6 36 0.68
7 5 0.09
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.41
Consensus pattern (6 bp):
ATTTAA
Found at i:133652 original size:17 final size:17
Alignment explanation
Indices: 133629--133689 Score: 77
Period size: 17 Copynumber: 3.5 Consensus size: 17
133619 AAATTTAATT
133629 AAATTTAAATTTAAAAC
1 AAATTTAAATTTAAAAC
* * *
133646 AACTTTAAATTTAAGAT
1 AAATTTAAATTTAAAAC
*
133663 AAATTTAAATTTAAAAAT
1 AAATTTAAATTT-AAAAC
133681 AAATTTAAA
1 AAATTTAAA
133690 ACCAATTTAA
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
17 25 0.66
18 13 0.34
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (17 bp):
AAATTTAAATTTAAAAC
Found at i:138346 original size:22 final size:22
Alignment explanation
Indices: 138321--138368 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
138311 GTCAAAATAG
*
138321 TTTTAATTAT-AATTTTAAGTCT
1 TTTTAACTATCAATTTT-AGTCT
* *
138343 TTTTTACTATCAATTTTATTCT
1 TTTTAACTATCAATTTTAGTCT
138365 TTTT
1 TTTT
138369 TTTCAATTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.25, C:0.08, G:0.02, T:0.65
Consensus pattern (22 bp):
TTTTAACTATCAATTTTAGTCT
Found at i:141755 original size:21 final size:21
Alignment explanation
Indices: 141731--141776 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
141721 AAATTACTAA
*
141731 ATTTTACTTTTTTACTTTA-TT
1 ATTTTACTTTATTA-TTTATTT
141752 ATTTTACTTTATTATTTATTT
1 ATTTTACTTTATTATTTATTT
141773 ATTT
1 ATTT
141777 GGCCTAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 4 0.17
21 19 0.83
ACGTcount: A:0.22, C:0.07, G:0.00, T:0.72
Consensus pattern (21 bp):
ATTTTACTTTATTATTTATTT
Found at i:141756 original size:13 final size:13
Alignment explanation
Indices: 141740--141768 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
141730 AATTTTACTT
141740 TTTTACTTTATTA
1 TTTTACTTTATTA
141753 TTTTACTTTATTA
1 TTTTACTTTATTA
141766 TTT
1 TTT
141769 ATTTATTTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTTACTTTATTA
Found at i:143388 original size:3 final size:3
Alignment explanation
Indices: 143380--143404 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
143370 TATCAATTAA
143380 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
143405 GCTAAATTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:148199 original size:23 final size:23
Alignment explanation
Indices: 148173--148220 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
148163 CTTCTTACAC
*
148173 TTTTTCTTACTC-TTTTCTTTTTG
1 TTTTTC-TACTCATTTTCATTTTG
148196 TTTTTCTACTCATTTTCATTTTG
1 TTTTTCTACTCATTTTCATTTTG
148219 TT
1 TT
148221 CTTTTCCCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 5 0.22
23 18 0.78
ACGTcount: A:0.08, C:0.17, G:0.04, T:0.71
Consensus pattern (23 bp):
TTTTTCTACTCATTTTCATTTTG
Found at i:157763 original size:25 final size:22
Alignment explanation
Indices: 157745--157790 Score: 65
Period size: 25 Copynumber: 2.0 Consensus size: 22
157735 TTAACAGTTA
157745 AAATAAATTAAAAAGTTAATAAAGT
1 AAATAAATTAAAAA-TT-A-AAAGT
157770 AAATAAATTAAAAATTAAAAG
1 AAATAAATTAAAAATTAAAAG
157791 ATGAATTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 4 0.19
23 1 0.05
24 2 0.10
25 14 0.67
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (22 bp):
AAATAAATTAAAAATTAAAAGT
Found at i:157767 original size:16 final size:16
Alignment explanation
Indices: 157746--157789 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
157736 TAACAGTTAA
*
157746 AATAAATTAAAAAGTT
1 AATAAATTAAAAAATT
*
157762 AATAAAGTAAATAAATT
1 AATAAATTAAA-AAATT
157779 AA-AAATTAAAA
1 AATAAATTAAAA
157790 GATGAATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
15 1 0.04
16 17 0.71
17 6 0.25
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (16 bp):
AATAAATTAAAAAATT
Found at i:166171 original size:16 final size:15
Alignment explanation
Indices: 166144--166180 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 15
166134 TATTCTAAAC
166144 TAAATTAAACTAAGT
1 TAAATTAAACTAAGT
*
166159 TAAATTAAAACTAATT
1 TAAATT-AAACTAAGT
166175 TAAATT
1 TAAATT
166181 CTTATGCACG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.54, C:0.05, G:0.03, T:0.38
Consensus pattern (15 bp):
TAAATTAAACTAAGT
Found at i:168339 original size:21 final size:22
Alignment explanation
Indices: 168308--168349 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
168298 ATTCACATGT
168308 TTTCTTACTCATGATTCTTTTG
1 TTTCTTACTCATGATTCTTTTG
**
168330 TTTC-TACTCATTTTTCTTTT
1 TTTCTTACTCATGATTCTTTT
168350 CTTTTTGATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.12, C:0.19, G:0.05, T:0.64
Consensus pattern (22 bp):
TTTCTTACTCATGATTCTTTTG
Found at i:211586 original size:24 final size:24
Alignment explanation
Indices: 211542--211587 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
211532 GCTAGTTGGT
* * *
211542 TGAAAGGATAAGAAGAGGAAGAGG
1 TGAAAGGACAAGAAAAAGAAGAGG
211566 TGAAAGGACAAGAAAAAGAAGA
1 TGAAAGGACAAGAAAAAGAAGA
211588 AACACTGTGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.57, C:0.02, G:0.35, T:0.07
Consensus pattern (24 bp):
TGAAAGGACAAGAAAAAGAAGAGG
Found at i:223042 original size:17 final size:17
Alignment explanation
Indices: 223020--223061 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
223010 CAGTCACATA
223020 AAAAAAAAGAGAAAAAG
1 AAAAAAAAGAGAAAAAG
* *
223037 AAAAAAAAGGGGAAAAG
1 AAAAAAAAGAGAAAAAG
223054 AAGAAAAA
1 AA-AAAAA
223062 TATATATGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 17 0.77
18 5 0.23
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (17 bp):
AAAAAAAAGAGAAAAAG
Found at i:223051 original size:18 final size:17
Alignment explanation
Indices: 223019--223061 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
223009 TCAGTCACAT
223019 AAAAAAAAAGAGAAAAAG
1 AAAAAAAAAGAG-AAAAG
* *
223037 AAAAAAAAGGGGAAAAG
1 AAAAAAAAAGAGAAAAG
223054 AAGAAAAA
1 AA-AAAAA
223062 TATATATGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAGAGAAAAG
Found at i:228681 original size:106 final size:107
Alignment explanation
Indices: 228563--228766 Score: 302
Period size: 107 Copynumber: 1.9 Consensus size: 107
228553 TAATTTAACA
** * ** *
228563 TAATTATAATTATTAAGTATAATGGTTTCGTTAAATATT-AAAATGTGGAAGTTAATATTCTTTT
1 TAATTATAATTATTAAGTATAATAATTTCGTTAAATATTAAAAATATAAAAGTTAATATCCTTTT
*
228627 GGAAATGATATAATGTTTCAATAAACCTTCCATCATTTAGCG
66 GGAAAGGATATAATGTTTCAATAAACCTTCCATCATTTAGCG
* *
228669 TAATTATAATTATTAATTATATTAATTTCGTTAAATATTAAAAATATAAAAGTTAATATCCTTTT
1 TAATTATAATTATTAAGTATAATAATTTCGTTAAATATTAAAAATATAAAAGTTAATATCCTTTT
* *
228734 GGAAAGGATATTATGTTTTAATAAACCTTCCAT
66 GGAAAGGATATAATGTTTCAATAAACCTTCCAT
228767 ATATTTCTTT
Statistics
Matches: 86, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
106 35 0.41
107 51 0.59
ACGTcount: A:0.39, C:0.08, G:0.10, T:0.43
Consensus pattern (107 bp):
TAATTATAATTATTAAGTATAATAATTTCGTTAAATATTAAAAATATAAAAGTTAATATCCTTTT
GGAAAGGATATAATGTTTCAATAAACCTTCCATCATTTAGCG
Found at i:228835 original size:123 final size:123
Alignment explanation
Indices: 228702--229062 Score: 495
Period size: 123 Copynumber: 3.0 Consensus size: 123
228692 AATTTCGTTA
* *
228702 AATATTAAAAATATAAAAGTTAATATCCTTTTGGAAAGGATATTATGTTTTAATAAACCTTCCAT
1 AATATTAAAAACATAGAAGTTAATATCCTTTTGGAAAGGATATTATGTTTTAATAAACCTTCCAT
* *
228767 ATATTTCTTTAAAGGACTATTTCTATTTTAATATGAGATATTATATAAAAGGAAATTG
66 ATATTTCTTTAAAGAACTATTTCCATTTTAATATGAGATATTATATAAAAGGAAATTG
* * * * *
228825 AATATTAAAAACATTGAAGTTAATATCCATTTCGAAAGGATATAATGTTTTAATAAACCTTTCAT
1 AATATTAAAAACATAGAAGTTAATATCCTTTTGGAAAGGATATTATGTTTTAATAAACCTTCCAT
* * * *
228890 ATATTTCTTTAAACAAATATCTCCATTTTAATATGAGATATTATATAAAAAGAAATTG
66 ATATTTCTTTAAAGAACTATTTCCATTTTAATATGAGATATTATATAAAAGGAAATTG
*
228948 AATATTAAAAACATGGAAGTTAATATCCTTTTGGAAA-GA-A-TA-----TAATAAACCTTCCAT
1 AATATTAAAAACATAGAAGTTAATATCCTTTTGGAAAGGATATTATGTTTTAATAAACCTTCCAT
* *
229005 ATATTTCTCTAAAGATACATATTTCCATTTTAATATGAGATATTAAAATAAAAGGAAA
66 ATATTTCTTTAAAGA-AC-TATTTCCATTTTAATATGAGATATT-ATATAAAAGGAAA
229063 GATAGTAGAA
Statistics
Matches: 211, Mismatches: 24, Indels: 11
0.86 0.10 0.04
Matches are distributed among these distances:
115 27 0.13
116 1 0.00
117 24 0.11
118 11 0.05
120 1 0.00
121 1 0.00
122 2 0.01
123 144 0.68
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.38
Consensus pattern (123 bp):
AATATTAAAAACATAGAAGTTAATATCCTTTTGGAAAGGATATTATGTTTTAATAAACCTTCCAT
ATATTTCTTTAAAGAACTATTTCCATTTTAATATGAGATATTATATAAAAGGAAATTG
Found at i:230400 original size:25 final size:25
Alignment explanation
Indices: 230372--230421 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
230362 TTTCAAAGCT
* *
230372 AACGGTGGTTGCTTACTCCAAACTA
1 AACGGAGGTTCCTTACTCCAAACTA
*
230397 AACGGAGGTTCCTTACTCCACACTA
1 AACGGAGGTTCCTTACTCCAAACTA
230422 TCTTATAACA
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:0.28, C:0.28, G:0.18, T:0.26
Consensus pattern (25 bp):
AACGGAGGTTCCTTACTCCAAACTA
Found at i:263054 original size:20 final size:20
Alignment explanation
Indices: 263016--263054 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
263006 AGAGATTTCA
*
263016 TTTAATTATTTATTTTTTAT
1 TTTAATTATTTATATTTTAT
263036 TTTAATTAATTT-TATTTTA
1 TTTAATT-ATTTATATTTTA
263055 AATTTGATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (20 bp):
TTTAATTATTTATATTTTAT
Found at i:273218 original size:2 final size:2
Alignment explanation
Indices: 273211--273240 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
273201 ATCCAAAATC
273211 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
273241 GAGTTATACT
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:277596 original size:30 final size:29
Alignment explanation
Indices: 277430--277614 Score: 108
Period size: 30 Copynumber: 6.2 Consensus size: 29
277420 CCCAAGAAGT
* * *
277430 CCCTAAACTTTCCAAAA-ATCACATTTTAAC
1 CCCTAAACTTT-CAAAATTTCA-AATTTGAC
* *
277460 CCCTAAACTCTTCAAAAATTT-GAGTTTGAC
1 CCCTAAACT-TTC-AAAATTTCAAATTTGAC
* * * *
277490 TCTTGAACAC-TTCAAAAATTCAAATTTAAC
1 CCCT-AA-ACTTTCAAAATTTCAAATTTGAC
* * *
277520 CCCTAAACTTTCCAAATTTTATATTTTGAC
1 CCCTAAACTTTCAAAATTTCA-AATTTGAC
* * *
277550 CCCTAAACTCTACAAAAGTTCAAATTTGGC
1 CCCTAAACT-TTCAAAATTTCAAATTTGAC
*
277580 CCCTAAACCTTTCAAAATTTC-ATTCTTGAC
1 CCCTAAA-CTTTCAAAATTTCAAAT-TTGAC
277610 CCCTA
1 CCCTA
277615 CTTTTGGTTT
Statistics
Matches: 117, Mismatches: 27, Indels: 22
0.70 0.16 0.13
Matches are distributed among these distances:
28 2 0.02
29 19 0.16
30 75 0.64
31 18 0.15
32 3 0.03
ACGTcount: A:0.35, C:0.26, G:0.05, T:0.34
Consensus pattern (29 bp):
CCCTAAACTTTCAAAATTTCAAATTTGAC
Found at i:277609 original size:60 final size:60
Alignment explanation
Indices: 277430--277614 Score: 162
Period size: 60 Copynumber: 3.1 Consensus size: 60
277420 CCCAAGAAGT
* * * * *
277430 CCCTAAACTTTCCAAAAA-TCACATTTTAACCCCTAAACTCTTCAAAAATTTGA-GT-TTGAC
1 CCCTAAACTCTACAAAAATTCA-AATTTAACCCCTAAACT-TTC-AAAATTTCATATCTTGAC
* * * * * * * *
277490 TCTTGAACACTTCAAAAATTCAAATTTAACCCCTAAACTTTCCAAATTTTATATTTTGAC
1 CCCTAAACTCTACAAAAATTCAAATTTAACCCCTAAACTTTCAAAATTTCATATCTTGAC
* **
277550 CCCTAAACTCTACAAAAGTTCAAATTTGGCCCCTAAACCTTTCAAAATTTCAT-TCTTGAC
1 CCCTAAACTCTACAAAAATTCAAATTTAACCCCTAAA-CTTTCAAAATTTCATATCTTGAC
277610 CCCTA
1 CCCTA
277615 CTTTTGGTTT
Statistics
Matches: 100, Mismatches: 21, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
58 7 0.07
59 4 0.04
60 73 0.73
61 16 0.16
ACGTcount: A:0.35, C:0.26, G:0.05, T:0.34
Consensus pattern (60 bp):
CCCTAAACTCTACAAAAATTCAAATTTAACCCCTAAACTTTCAAAATTTCATATCTTGAC
Found at i:277703 original size:23 final size:24
Alignment explanation
Indices: 277677--277727 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
277667 CTTTTTTTCT
277677 TTTAAAATTCCCTTT-TAT-TTTTA
1 TTTAAAATT-CCTTTATATATTTTA
*
277700 TTT-AAATTCTTTTATATATTTTA
1 TTTAAAATTCCTTTATATATTTTA
277723 TTTAA
1 TTTAA
277728 CCCTTCATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
21 4 0.17
22 8 0.33
23 11 0.46
24 1 0.04
ACGTcount: A:0.29, C:0.08, G:0.00, T:0.63
Consensus pattern (24 bp):
TTTAAAATTCCTTTATATATTTTA
Found at i:280853 original size:12 final size:12
Alignment explanation
Indices: 280809--280854 Score: 51
Period size: 11 Copynumber: 4.0 Consensus size: 12
280799 CCTCCCTAGG
280809 GCCACGTCA-CT
1 GCCACGTCAGCT
* *
280820 GCCACATCAACT
1 GCCACGTCAGCT
*
280832 -CCATGTCAGCT
1 GCCACGTCAGCT
280843 GCCACGTCAGCT
1 GCCACGTCAGCT
280855 ACACAGCTCG
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
11 16 0.57
12 12 0.43
ACGTcount: A:0.22, C:0.41, G:0.17, T:0.20
Consensus pattern (12 bp):
GCCACGTCAGCT
Found at i:281773 original size:29 final size:29
Alignment explanation
Indices: 281740--281795 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
281730 AGCTAGAGAG
* *
281740 AAAAAGGGAGTGAAAAAGAGTTTTTTTTA
1 AAAAAGAGAGTGAAAAAGAATTTTTTTTA
* *
281769 AAAAATAGAGTGAAAATGAATTTTTTT
1 AAAAAGAGAGTGAAAAAGAATTTTTTT
281796 CAGAAAAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.46, C:0.00, G:0.20, T:0.34
Consensus pattern (29 bp):
AAAAAGAGAGTGAAAAAGAATTTTTTTTA
Found at i:281802 original size:29 final size:29
Alignment explanation
Indices: 281747--281803 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
281737 GAGAAAAAGG
* *
281747 GAGTGAAAAAGAGTTTTTTTTAAAAAATA
1 GAGTGAAAAAGAATTTTTTTCAAAAAATA
*
281776 GAGTGAAAATGAATTTTTTTCAGAAAAA
1 GAGTGAAAAAGAATTTTTTTCA-AAAAA
281804 ATAGCCTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 19 0.79
30 5 0.21
ACGTcount: A:0.47, C:0.02, G:0.18, T:0.33
Consensus pattern (29 bp):
GAGTGAAAAAGAATTTTTTTCAAAAAATA
Found at i:282246 original size:30 final size:29
Alignment explanation
Indices: 282140--282287 Score: 122
Period size: 30 Copynumber: 5.0 Consensus size: 29
282130 CCAAAATCAC
*
282140 ATTTGACCCCTAAACTCTT-TAAAAATTTG
1 ATTTGACCCCTAAACT-TTCCAAAAATTTG
* *
282169 ATATTAACCCCTAAACTCTT-TAAAAATTTG
1 AT-TTGACCCCTAAACT-TTCCAAAAATTTG
* *
282199 AATTTAACCCATAAACTTTCCAAAAATTTAG
1 -ATTTGACCCCTAAACTTTCCAAAAATTT-G
* *
282230 ATTTGACCCTTAAACTTTCC-AAAATTTAC
1 ATTTGACCCCTAAACTTTCCAAAAATTT-G
* * *
282259 ATTTTGACACTTAAACTCTCCAAAAATTT
1 A-TTTGACCCCTAAACTTTCCAAAAATTT
282288 TCATGTTTTT
Statistics
Matches: 105, Mismatches: 8, Indels: 10
0.85 0.07 0.08
Matches are distributed among these distances:
29 13 0.12
30 82 0.78
31 10 0.10
ACGTcount: A:0.39, C:0.21, G:0.04, T:0.36
Consensus pattern (29 bp):
ATTTGACCCCTAAACTTTCCAAAAATTTG
Found at i:285338 original size:18 final size:17
Alignment explanation
Indices: 285317--285359 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
285307 AAAATTTTAA
285317 AATAAATTAAAAAAAGTT
1 AATAAATTAAAAAAA-TT
*
285335 AATAAATTAAATAAATT
1 AATAAATTAAAAAAATT
285352 AA-AAATTA
1 AATAAATTA
285360 GAATATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 6 0.25
17 4 0.17
18 14 0.58
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (17 bp):
AATAAATTAAAAAAATT
Found at i:285349 original size:9 final size:9
Alignment explanation
Indices: 285316--285354 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
285306 TAAAATTTTA
285316 AAATAAATT
1 AAATAAATT
*
285325 AAAAAAAGTT
1 AAATAAA-TT
285335 -AATAAATT
1 AAATAAATT
285343 AAATAAATT
1 AAATAAATT
285352 AAA
1 AAA
285355 AATTAGAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
8 2 0.08
9 22 0.85
10 2 0.08
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (9 bp):
AAATAAATT
Found at i:312943 original size:144 final size:144
Alignment explanation
Indices: 312683--312972 Score: 508
Period size: 144 Copynumber: 2.0 Consensus size: 144
312673 CGTTTCTCAA
* *
312683 TTTGAACTAAATCGTAACAAATTGATAAATTTACCTTCATTCCTTTCACTTTGTATCCACATACA
1 TTTGAACTAAATCATAACAAATTGATAAATTTACCATCATTCCTTTCACTTTGTATCCACATACA
*
312748 AGTACTATCGTGACATTTACTACTGAAAATGTCTAAATTAATGTGAAGTTTATAATGACACTAAG
66 AGTACCATCGTGACATTTACTACTGAAAATGTCTAAATTAATGTGAAGTTTATAATGACACTAAG
312813 TCATATAATATAAT
131 TCATATAATATAAT
* * *
312827 TTTGAACTAAATCATAGCAAATTGATAATTTTACCATCATTCCTTTCACTTTGTATCCACATAGA
1 TTTGAACTAAATCATAACAAATTGATAAATTTACCATCATTCCTTTCACTTTGTATCCACATACA
* *
312892 AGTACCATTGTGACATTTACTACTGGAAATGTCTAAATTAATGTGAAGTTTATAATGACACTAAG
66 AGTACCATCGTGACATTTACTACTGAAAATGTCTAAATTAATGTGAAGTTTATAATGACACTAAG
312957 TCATATAATATAAT
131 TCATATAATATAAT
312971 TT
1 TT
312973 CCAAATAATT
Statistics
Matches: 138, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
144 138 1.00
ACGTcount: A:0.37, C:0.16, G:0.10, T:0.37
Consensus pattern (144 bp):
TTTGAACTAAATCATAACAAATTGATAAATTTACCATCATTCCTTTCACTTTGTATCCACATACA
AGTACCATCGTGACATTTACTACTGAAAATGTCTAAATTAATGTGAAGTTTATAATGACACTAAG
TCATATAATATAAT
Found at i:316107 original size:24 final size:24
Alignment explanation
Indices: 316080--316130 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
316070 AAATTGACTC
* *
316080 AAACAACTAAACAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAACTG
*
316104 AAACAAATAAATAGAGTTTAACTG
1 AAACAAATAAACAGAGTTTAACTG
316128 AAA
1 AAA
316131 GATTATTTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.55, C:0.10, G:0.12, T:0.24
Consensus pattern (24 bp):
AAACAAATAAACAGAGTTTAACTG
Found at i:320674 original size:33 final size:33
Alignment explanation
Indices: 320637--320699 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
320627 CCGACAGATG
* *
320637 TTCCAATCAATT-ATGAAGTTGCCTTGATAGTTT
1 TTCCAATC-ATTCATGAAGCTGCCCTGATAGTTT
320670 TTCCAATCATTCATGAAGCTGCCCTGATAG
1 TTCCAATCATTCATGAAGCTGCCCTGATAG
320700 ATGTTGATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
32 3 0.11
33 24 0.89
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.37
Consensus pattern (33 bp):
TTCCAATCATTCATGAAGCTGCCCTGATAGTTT
Found at i:347870 original size:16 final size:16
Alignment explanation
Indices: 347849--347894 Score: 76
Period size: 16 Copynumber: 2.9 Consensus size: 16
347839 TCAGTCACAT
347849 AAAAAGAAAGAAAAAG
1 AAAAAGAAAGAAAAAG
347865 AAAAAGAAAGAAAAAG
1 AAAAAGAAAGAAAAAG
*
347881 -AAAAGGAAGAAAAA
1 AAAAAGAAAGAAAAA
347895 AATTTATGAT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
15 13 0.45
16 16 0.55
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (16 bp):
AAAAAGAAAGAAAAAG
Found at i:347894 original size:10 final size:10
Alignment explanation
Indices: 347849--347896 Score: 51
Period size: 10 Copynumber: 4.5 Consensus size: 10
347839 TCAGTCACAT
*
347849 AAAAAGAAAG
1 AAAAAGAAAA
347859 AAAAAGAAAA
1 AAAAAGAAAA
*
347869 AGAAAGAAAA
1 AAAAAGAAAA
347879 AGAAAAGGAAGAA
1 A-AAAA-GAA-AA
347892 AAAAA
1 AAAAA
347897 TTTATGATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
10 19 0.59
11 3 0.09
12 7 0.22
13 3 0.09
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (10 bp):
AAAAAGAAAA
Found at i:350074 original size:23 final size:24
Alignment explanation
Indices: 350048--350096 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 24
350038 ACAATCATTC
* *
350048 CATTTTCTATTA-ATTTACTCTGA
1 CATTTTATATTACATTTACACTGA
*
350071 CATTTTATATTACATTTGCACTGA
1 CATTTTATATTACATTTACACTGA
350095 CA
1 CA
350097 AGATTTAACT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 11 0.50
24 11 0.50
ACGTcount: A:0.29, C:0.18, G:0.06, T:0.47
Consensus pattern (24 bp):
CATTTTATATTACATTTACACTGA
Found at i:355491 original size:36 final size:35
Alignment explanation
Indices: 355451--355551 Score: 132
Period size: 36 Copynumber: 2.8 Consensus size: 35
355441 TAGTAATAGG
355451 CATGACCTTCAGGTCAACAAGGAGTAAAATGAGAAT
1 CATGACCTT-AGGTCAACAAGGAGTAAAATGAGAAT
* * *
355487 CATGACCTTTGGGTCAATAAGGAGTAAAATGAGCAT
1 CATGACC-TTAGGTCAACAAGGAGTAAAATGAGAAT
355523 CATGACC-TATGTGTCAACAAGGAGTAAAA
1 CATGACCTTA-G-GTCAACAAGGAGTAAAA
355552 CGAATAACGA
Statistics
Matches: 57, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
34 1 0.02
35 1 0.02
36 53 0.93
37 2 0.04
ACGTcount: A:0.40, C:0.16, G:0.23, T:0.22
Consensus pattern (35 bp):
CATGACCTTAGGTCAACAAGGAGTAAAATGAGAAT
Found at i:357161 original size:40 final size:40
Alignment explanation
Indices: 357116--357197 Score: 155
Period size: 40 Copynumber: 2.0 Consensus size: 40
357106 CTTTCTTGTG
357116 TTTATTAACACATTAATTACATAGCTTTCAACATACTTTA
1 TTTATTAACACATTAATTACATAGCTTTCAACATACTTTA
*
357156 TTTATTAACACATTAATTACATATCTTTCAACATACTTTA
1 TTTATTAACACATTAATTACATAGCTTTCAACATACTTTA
357196 TT
1 TT
357198 CACATACAAG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.37, C:0.17, G:0.01, T:0.45
Consensus pattern (40 bp):
TTTATTAACACATTAATTACATAGCTTTCAACATACTTTA
Found at i:363341 original size:26 final size:26
Alignment explanation
Indices: 363279--363343 Score: 76
Period size: 26 Copynumber: 2.5 Consensus size: 26
363269 CCCAATTTTA
*
363279 CTTGGTAAAATTTTGATGATTTTACT
1 CTTGGTAAAATTTTGACGATTTTACT
*** * *
363305 CCCAGTCAAATTTTGACGATTTTATT
1 CTTGGTAAAATTTTGACGATTTTACT
363331 CTTGGTAAAATTT
1 CTTGGTAAAATTT
363344 AGAGAGAATT
Statistics
Matches: 29, Mismatches: 10, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.28, C:0.12, G:0.14, T:0.46
Consensus pattern (26 bp):
CTTGGTAAAATTTTGACGATTTTACT
Found at i:371974 original size:113 final size:113
Alignment explanation
Indices: 371828--372049 Score: 381
Period size: 113 Copynumber: 2.0 Consensus size: 113
371818 AAAAAGAAAC
* *
371828 AGAGACACCCGAACCACATCCATGGATGTAATAAAAATAACAAGTCGATCACCCAAATCACATCC
1 AGAGACACCCGAACCACATCCATGGATGCAATAAAAATAACAAATCGATCACCCAAATCACATCC
371893 ATGGAGACAGTGATGTATGATAGTTTAAAATAATTATCACACCCGAAT
66 ATGGAGACAGTGATGTATGATAGTTTAAAATAATTATCACACCCGAAT
* * * *
371941 AGAGACACCCGAATCACATCCATGGATGCAATAAAAATAATAAATCGATCACTCGAATCACATCC
1 AGAGACACCCGAACCACATCCATGGATGCAATAAAAATAACAAATCGATCACCCAAATCACATCC
*
372006 ATGGAGACAGTGATGTATGATAGTTTAAAATAATTGTCACACCC
66 ATGGAGACAGTGATGTATGATAGTTTAAAATAATTATCACACCC
372050 AAATCTCATT
Statistics
Matches: 102, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
113 102 1.00
ACGTcount: A:0.41, C:0.22, G:0.15, T:0.22
Consensus pattern (113 bp):
AGAGACACCCGAACCACATCCATGGATGCAATAAAAATAACAAATCGATCACCCAAATCACATCC
ATGGAGACAGTGATGTATGATAGTTTAAAATAATTATCACACCCGAAT
Found at i:372717 original size:11 final size:11
Alignment explanation
Indices: 372701--372726 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
372691 ATTTATTGAG
372701 TTATAAAAGAC
1 TTATAAAAGAC
372712 TTATAAAAGAC
1 TTATAAAAGAC
372723 TTAT
1 TTAT
372727 TTTATTGTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.50, C:0.08, G:0.08, T:0.35
Consensus pattern (11 bp):
TTATAAAAGAC
Found at i:375420 original size:22 final size:23
Alignment explanation
Indices: 375378--375422 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
375368 TTTGTTAAGG
375378 TTAGGGTTAAGGTTTTTTTAGGAA
1 TTAGGGTTAAGG-TTTTTTAGGAA
*
375402 TTAGGGTTTAGG-TTTTTAGGA
1 TTAGGGTTAAGGTTTTTTAGGA
375423 GTGAAATCGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 9 0.45
24 11 0.55
ACGTcount: A:0.22, C:0.00, G:0.31, T:0.47
Consensus pattern (23 bp):
TTAGGGTTAAGGTTTTTTAGGAA
Found at i:397994 original size:17 final size:17
Alignment explanation
Indices: 397972--398014 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
397962 ATTTTGTGTT
*
397972 CGAACCTTTACATTGTG
1 CGAACCTTTACATTGAG
* *
397989 CGAACCCTTATATTGAG
1 CGAACCTTTACATTGAG
*
398006 CGAGCCTTT
1 CGAACCTTT
398015 TATACGAGCC
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.23, C:0.26, G:0.19, T:0.33
Consensus pattern (17 bp):
CGAACCTTTACATTGAG
Found at i:398063 original size:33 final size:33
Alignment explanation
Indices: 398021--398090 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
398011 CTTTTATACG
*
398021 AGCCTATATTATGTGCAAGCCTATATGTAAGCA
1 AGCCAATATTATGTGCAAGCCTATATGTAAGCA
* * * **
398054 AGCCAATATTGTGTTCGAGCCTATATGTGTGCA
1 AGCCAATATTATGTGCAAGCCTATATGTAAGCA
398087 AGCC
1 AGCC
398091 TTATGATGTG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.30
Consensus pattern (33 bp):
AGCCAATATTATGTGCAAGCCTATATGTAAGCA
Found at i:398090 original size:16 final size:16
Alignment explanation
Indices: 398021--398101 Score: 74
Period size: 16 Copynumber: 4.9 Consensus size: 16
398011 CTTTTATACG
*
398021 AGCCTATATTATGTGCA
1 AGCCTATA-TGTGTGCA
**
398038 AGCCTATATGTAAGCA
1 AGCCTATATGTGTGCA
* * *
398054 AGCCAATATTGTGTTCG
1 AGCCTATA-TGTGTGCA
398071 AGCCTATATGTGTGCA
1 AGCCTATATGTGTGCA
398087 AGCCT-TATGATGTGC
1 AGCCTATATG-TGTGC
398102 GAACCCTATG
Statistics
Matches: 51, Mismatches: 11, Indels: 5
0.76 0.16 0.07
Matches are distributed among these distances:
15 4 0.08
16 28 0.55
17 19 0.37
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.32
Consensus pattern (16 bp):
AGCCTATATGTGTGCA
Found at i:401714 original size:18 final size:17
Alignment explanation
Indices: 401670--401725 Score: 58
Period size: 18 Copynumber: 3.2 Consensus size: 17
401660 CCATGTTAGT
*
401670 AAAAAAATTTAAAGTTAA
1 AAAAAAAATTAAA-TTAA
*
401688 AAAATAAATTAAATTAA
1 AAAAAAAATTAAATTAA
* *
401705 AAAACAAAATAAAAATAA
1 AAAA-AAAATTAAATTAA
401723 AAA
1 AAA
401726 TTGGCTTAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
17 8 0.25
18 24 0.75
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.21
Consensus pattern (17 bp):
AAAAAAAATTAAATTAA
Found at i:401717 original size:17 final size:18
Alignment explanation
Indices: 401679--401717 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
401669 TAAAAAAATT
* *
401679 TAAAGTTAAAAAATAAAT
1 TAAAGTTAAAAAACAAAA
401697 TAAA-TTAAAAAACAAAA
1 TAAAGTTAAAAAACAAAA
401714 TAAA
1 TAAA
401718 AATAAAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.23
Consensus pattern (18 bp):
TAAAGTTAAAAAACAAAA
Found at i:402243 original size:25 final size:22
Alignment explanation
Indices: 402196--402240 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
402186 TGTTTAATCA
402196 TGTTTAATCGATGTTGTTGTTT
1 TGTTTAATCGATGTTGTTGTTT
*
402218 TGTTTAATCGATATTGTTGTTT
1 TGTTTAATCGATGTTGTTGTTT
402240 T
1 T
402241 TTTTTTATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.16, C:0.04, G:0.20, T:0.60
Consensus pattern (22 bp):
TGTTTAATCGATGTTGTTGTTT
Found at i:402482 original size:22 final size:22
Alignment explanation
Indices: 402456--402500 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
402446 TGTTTAATAA
402456 TGTTTAATCAATGTTGTTGTTT
1 TGTTTAATCAATGTTGTTGTTT
*
402478 TGTTTAATCGATGTTGTTGTTT
1 TGTTTAATCAATGTTGTTGTTT
402500 T
1 T
402501 ACCGAGAGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.16, C:0.04, G:0.20, T:0.60
Consensus pattern (22 bp):
TGTTTAATCAATGTTGTTGTTT
Found at i:403788 original size:9 final size:9
Alignment explanation
Indices: 403775--403805 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
403765 AAAAGTTATC
*
403775 ATTTCAACC
1 ATTTCAACA
403784 ATTTCAACA
1 ATTTCAACA
403793 ATTTCAACA
1 ATTTCAACA
403802 ATTT
1 ATTT
403806 GCAATAAGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.39, C:0.23, G:0.00, T:0.39
Consensus pattern (9 bp):
ATTTCAACA
Found at i:404446 original size:160 final size:160
Alignment explanation
Indices: 404015--404473 Score: 618
Period size: 161 Copynumber: 2.9 Consensus size: 160
404005 GTTCTTGAAA
* * * * * * * *
404015 TGTCATCCTTTTTTGGCTTTTAGTTCTCATACTCATACCCGACT--GATAACAACAATCAGAACC
1 TGTCATTCTTTTTTGGATTGTAGTTCTCATACTCATACCAGACTAAGACAAAAAAAATCAAAACC
* * *
404078 CAAATTAGATT-TAAATAATTTGGAATTGACAATGAGAAAGTGTTTACGATATACCTGTGATCTA
66 GAAATTAGATTAT-TATAATTTGGAATTGACAATGAGAAAGTGTTTACAATATACCTGTGATCTA
* *
404142 GTTGTGTTAGGCTCAATGCATGGTGGTAATC
130 GTTGTGTTAGGCTAAATGCATGATGGTAATC
* * * * *
404173 TGTCATTCTTTTTTTGTTTGTAGTTCTCTTACTCATACCAAACTAAGACACAAAAAAATCAAAAT
1 TGTCATTCTTTTTTGGATTGTAGTTCTCATACTCATACCAGACTAAGACA-AAAAAAATCAAAAC
*
404238 CGAAATTAGATTATTATAATTTGGAATTGACAATGAGAAAGTGTTTACAATATACCTATGATCTA
65 CGAAATTAGATTATTATAATTTGGAATTGACAATGAGAAAGTGTTTACAATATACCTGTGATCTA
* **
404303 GTTGTGTTAGGCTAAATGCATTATGGTGTTC
130 GTTGTGTTAGGCTAAATGCATGATGGTAATC
* * *
404334 TGTCGTTCTTTTTTGGATTGTAGTTCTCATACTCGTGCCAGACTAAGACAAAAAAAATCAAAACC
1 TGTCATTCTTTTTTGGATTGTAGTTCTCATACTCATACCAGACTAAGACAAAAAAAATCAAAACC
* * **
404399 GAAATTAGATTATTATGATTTGGAATTGACAATGAGAAAGTGTTTACAATATACCTGTGTTCCCG
66 GAAATTAGATTATTATAATTTGGAATTGACAATGAGAAAGTGTTTACAATATACCTGTGATCTAG
404464 TTGTGTTAGG
131 TTGTGTTAGG
404474 ATCTTGTTTG
Statistics
Matches: 263, Mismatches: 34, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
158 37 0.14
160 87 0.33
161 138 0.52
162 1 0.00
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (160 bp):
TGTCATTCTTTTTTGGATTGTAGTTCTCATACTCATACCAGACTAAGACAAAAAAAATCAAAACC
GAAATTAGATTATTATAATTTGGAATTGACAATGAGAAAGTGTTTACAATATACCTGTGATCTAG
TTGTGTTAGGCTAAATGCATGATGGTAATC
Found at i:407721 original size:54 final size:54
Alignment explanation
Indices: 407656--407907 Score: 200
Period size: 63 Copynumber: 4.3 Consensus size: 54
407646 TGACCTTCAA
* *
407656 CACCCTCAACACCTTCACTAACAGCACCCTTACCCAAACCCTCACCACCTCCTT
1 CACCCTCAACACCTTTACTAACAACACCCTTACCCAAACCCTCACCACCTCCTT
* * *
407710 CACCCTTAACACCTTTACTAACAACACCCTTACCCGAACCCTCATCACCTCCCTCACCCT
1 CACCCTCAACACCTTTACTAACAACACCCTTACCCAAACCCTCACCACCT-CCT-----T
* * *
407770 CAACACCCTTAACACCTTTACTAACACCACCCTTACCCAAACCCNCACCACCTCCCTCCCCCT
1 ---CACCCTCAACACCTTTACTAACAACACCCTTACCCAAACCCTCACCACCT-CCT-----T
* * * * *
407833 CAACACCCTCAACACCTTCACTAGCAATATCCTTACCTAAACCCTCACCACCT-CTCT
1 ---CACCCTCAACACCTTTACTAACAACACCCTTACCCAAACCCTCACCACCTCCT-T
*
407890 CACCCTCAACACCCTTAC
1 CACCCTCAACACCTTTAC
407908 CCGAACTCTC
Statistics
Matches: 169, Mismatches: 20, Indels: 18
0.82 0.10 0.09
Matches are distributed among these distances:
54 61 0.36
55 3 0.02
57 2 0.01
60 1 0.01
61 2 0.01
63 100 0.59
ACGTcount: A:0.28, C:0.51, G:0.01, T:0.20
Consensus pattern (54 bp):
CACCCTCAACACCTTTACTAACAACACCCTTACCCAAACCCTCACCACCTCCTT
Found at i:407779 original size:63 final size:63
Alignment explanation
Indices: 407710--407906 Score: 286
Period size: 63 Copynumber: 3.1 Consensus size: 63
407700 CCACCTCCTT
* *
407710 CACCCTTAACACCTTTACTAACAACACCCTTACCCGAACCCTCATCACCTCCCTCACCCTCAA
1 CACCCTTAACACCTTTACTAACAACACCCTTACCCAAACCCTCACCACCTCCCTCACCCTCAA
* * *
407773 CACCCTTAACACCTTTACTAACACCACCCTTACCCAAACCCNCACCACCTCCCTCCCCCTCAA
1 CACCCTTAACACCTTTACTAACAACACCCTTACCCAAACCCTCACCACCTCCCTCACCCTCAA
* * * * * * *
407836 CACCCTCAACACCTTCACTAGCAATATCCTTACCTAAACCCTCACCACCTCTCTCACCCTCAA
1 CACCCTTAACACCTTTACTAACAACACCCTTACCCAAACCCTCACCACCTCCCTCACCCTCAA
407899 CACCCTTA
1 CACCCTTA
407907 CCCGAACTCT
Statistics
Matches: 118, Mismatches: 16, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
63 118 1.00
ACGTcount: A:0.28, C:0.50, G:0.01, T:0.20
Consensus pattern (63 bp):
CACCCTTAACACCTTTACTAACAACACCCTTACCCAAACCCTCACCACCTCCCTCACCCTCAA
Found at i:408680 original size:21 final size:21
Alignment explanation
Indices: 408654--408697 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
408644 TCAATAAATT
*
408654 ATCAACATGTCAAATATATAA
1 ATCAACATATCAAATATATAA
408675 ATCAACATATCAAATATATAA
1 ATCAACATATCAAATATATAA
408696 AT
1 AT
408698 TACCAAGTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.55, C:0.14, G:0.02, T:0.30
Consensus pattern (21 bp):
ATCAACATATCAAATATATAA
Found at i:408740 original size:77 final size:78
Alignment explanation
Indices: 408601--408753 Score: 290
Period size: 77 Copynumber: 2.0 Consensus size: 78
408591 CAACCAGTAG
*
408601 ACATGTCAAATATATAAATTACCAAGTTTTAAATTAATACGATTCAATAAATTATCAACATGTCA
1 ACATATCAAATATATAAATTACCAAGTTTTAAATTAATACGATTCAATAAATTATCAACATGTCA
408666 AATATATAAATCA
66 AATATATAAATCA
408679 ACATATCAAATATATAAATTACCAAGTTTTAAA-TAATACGATTCAATAAATTATCAACATGTCA
1 ACATATCAAATATATAAATTACCAAGTTTTAAATTAATACGATTCAATAAATTATCAACATGTCA
408743 AATATATAAAT
66 AATATATAAAT
408754 TACCATTCAA
Statistics
Matches: 74, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
77 42 0.57
78 32 0.43
ACGTcount: A:0.50, C:0.12, G:0.05, T:0.33
Consensus pattern (78 bp):
ACATATCAAATATATAAATTACCAAGTTTTAAATTAATACGATTCAATAAATTATCAACATGTCA
AATATATAAATCA
Found at i:409830 original size:32 final size:30
Alignment explanation
Indices: 409794--409898 Score: 106
Period size: 32 Copynumber: 3.4 Consensus size: 30
409784 AAAAATCCTG
*
409794 AAAATCCCTAAATTTTTAAAATCTAAATCCCC
1 AAAATCCCTAAATTTTT-AAACCTAAA-CCCC
* * * *
409826 AAAATCCCAAAAAATTTGAAACCTAAAACCCA
1 AAAATCCC-TAAATTTTTAAACCT-AAACCCC
409858 AAAATCCCTAAATTATTTAAACCTAAA--CC
1 AAAATCCCTAAATT-TTTAAACCTAAACCCC
409887 AAAATCCCTAAA
1 AAAATCCCTAAA
409899 CTCAAGAACC
Statistics
Matches: 61, Mismatches: 9, Indels: 9
0.77 0.11 0.11
Matches are distributed among these distances:
29 13 0.21
31 7 0.11
32 32 0.52
33 9 0.15
ACGTcount: A:0.50, C:0.25, G:0.01, T:0.24
Consensus pattern (30 bp):
AAAATCCCTAAATTTTTAAACCTAAACCCC
Found at i:410868 original size:31 final size:32
Alignment explanation
Indices: 410806--410876 Score: 83
Period size: 32 Copynumber: 2.2 Consensus size: 32
410796 TAAAATCAGT
**
410806 AATTTTTTTTTTAATTTTTAATAAATCTTATA
1 AATTTTTTTTACAATTTTTAATAAATCTTATA
* *
410838 TATTTTTTTTACAATTTTCTAGT-AAT-TTATA
1 AATTTTTTTTACAATTTT-TAATAAATCTTATA
410869 AATTTTTT
1 AATTTTTT
410877 ATTTTTTTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
31 12 0.36
32 18 0.55
33 3 0.09
ACGTcount: A:0.31, C:0.04, G:0.01, T:0.63
Consensus pattern (32 bp):
AATTTTTTTTACAATTTTTAATAAATCTTATA
Found at i:416742 original size:9 final size:10
Alignment explanation
Indices: 416721--416745 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
416711 TTACTAATTG
416721 AAAATTTTAA
1 AAAATTTTAA
416731 AAAATTTTAA
1 AAAATTTTAA
416741 AAAAT
1 AAAAT
416746 CTAAATAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (10 bp):
AAAATTTTAA
Found at i:429282 original size:93 final size:93
Alignment explanation
Indices: 429123--429308 Score: 363
Period size: 93 Copynumber: 2.0 Consensus size: 93
429113 TTAAAATAGG
429123 TGTGATTGGATCACCTTGTAAAAATTTTAAAATCATTAAAATAATAATTTTGGTCTTTGAAACCA
1 TGTGATTGGATCACCTTGTAAAAATTTTAAAATCATTAAAATAATAATTTTGGTCTTTGAAACCA
429188 TAAAACAGATTCGAGAATCGATTACGAT
66 TAAAACAGATTCGAGAATCGATTACGAT
429216 TGTGATTGGATCACCTTGTAAAAATTTTAAAATCATTAAAATAATAATTTTGGTCTTTGAAACCA
1 TGTGATTGGATCACCTTGTAAAAATTTTAAAATCATTAAAATAATAATTTTGGTCTTTGAAACCA
*
429281 TAAAACGGATTCGAGAATCGATTACGAT
66 TAAAACAGATTCGAGAATCGATTACGAT
429309 GAGGAAGGAT
Statistics
Matches: 92, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 92 1.00
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.34
Consensus pattern (93 bp):
TGTGATTGGATCACCTTGTAAAAATTTTAAAATCATTAAAATAATAATTTTGGTCTTTGAAACCA
TAAAACAGATTCGAGAATCGATTACGAT
Found at i:434444 original size:33 final size:33
Alignment explanation
Indices: 434402--434469 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
434392 TTTGTGCTTC
434402 TTCTTCTTTTTATCTTTGTGCCTCTTCCTCTTT
1 TTCTTCTTTTTATCTTTGTGCCTCTTCCTCTTT
434435 TTCTTCTTTTTATCTTTGTGCCTCTTCCTCTTT
1 TTCTTCTTTTTATCTTTGTGCCTCTTCCTCTTT
434468 TT
1 TT
434470 ATCCGTCGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.03, C:0.26, G:0.06, T:0.65
Consensus pattern (33 bp):
TTCTTCTTTTTATCTTTGTGCCTCTTCCTCTTT
Found at i:456229 original size:19 final size:18
Alignment explanation
Indices: 456200--456247 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
456190 ACTATCAAAG
*
456200 TAAATTAATAAT-TCAAAA
1 TAAAATAATAATAT-AAAA
456218 TCAAAATAATAATAATAAAA
1 T-AAAATAATAAT-ATAAAA
456238 TAAAATAATA
1 TAAAATAATA
456248 TAAATTTGTA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 1 0.04
19 19 0.73
20 5 0.19
21 1 0.04
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (18 bp):
TAAAATAATAATATAAAA
Found at i:457365 original size:224 final size:224
Alignment explanation
Indices: 456975--457425 Score: 893
Period size: 224 Copynumber: 2.0 Consensus size: 224
456965 TCTAACGAAA
456975 TTAGATCCTACAAATACAACTAAATATTATTACAAACCTAGCCACCACTTAAATACAAAACTAAA
1 TTAGATCCTACAAATACAACTAAATATTATTACAAACCTAGCCACCACTTAAATACAAAACTAAA
457040 CTAAAGTAACTTACGTGTAGCTCTCGAAATTGAAGCAGGAACCGGTTTAACAGGTGAAGGAGGTA
66 CTAAAGTAACTTACGTGTAGCTCTCGAAATTGAAGCAGGAACCGGTTTAACAGGTGAAGGAGGTA
457105 AATTGTCTGCCTCGAAATCGTGATCACCTAAACAAGAATATTTCATATTAAAAATCCCCAAATTA
131 AATTGTCTGCCTCGAAATCGTGATCACCTAAACAAGAATATTTCATATTAAAAATCCCCAAATTA
457170 AAACTCTAAAATAACTTAAAATATAAAAT
196 AAACTCTAAAATAACTTAAAATATAAAAT
457199 TTAGATCCTACAAATACAACTAAATATTATTACAAACCTAGCCACCACTTAAATACAAAACTAAA
1 TTAGATCCTACAAATACAACTAAATATTATTACAAACCTAGCCACCACTTAAATACAAAACTAAA
457264 CTAAAGTAACTTACGTGTAGCTCTCGAAATTGAAGCAGGAACCGGTTTAACAGGTGAAGGAGGTA
66 CTAAAGTAACTTACGTGTAGCTCTCGAAATTGAAGCAGGAACCGGTTTAACAGGTGAAGGAGGTA
457329 AATTGTCTGCCTCGAAATCGTGATCACCTAAACAAGAATATTTCATATTAAAAATCCCCAAATTA
131 AATTGTCTGCCTCGAAATCGTGATCACCTAAACAAGAATATTTCATATTAAAAATCCCCAAATTA
*
457394 AAACTCTAAAATAACTTAAAGTATAAAAT
196 AAACTCTAAAATAACTTAAAATATAAAAT
457423 TTA
1 TTA
457426 AGATAAACTA
Statistics
Matches: 226, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
224 226 1.00
ACGTcount: A:0.43, C:0.19, G:0.12, T:0.26
Consensus pattern (224 bp):
TTAGATCCTACAAATACAACTAAATATTATTACAAACCTAGCCACCACTTAAATACAAAACTAAA
CTAAAGTAACTTACGTGTAGCTCTCGAAATTGAAGCAGGAACCGGTTTAACAGGTGAAGGAGGTA
AATTGTCTGCCTCGAAATCGTGATCACCTAAACAAGAATATTTCATATTAAAAATCCCCAAATTA
AAACTCTAAAATAACTTAAAATATAAAAT
Found at i:457562 original size:14 final size:14
Alignment explanation
Indices: 457543--457587 Score: 63
Period size: 14 Copynumber: 3.2 Consensus size: 14
457533 AATGGTCAAA
*
457543 GTCAACGGTCAATG
1 GTCAACGATCAATG
*
457557 GTCAACGATTAATG
1 GTCAACGATCAATG
*
457571 GTCAACGATCAACG
1 GTCAACGATCAATG
457585 GTC
1 GTC
457588 GGTCAACAGC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.31, C:0.22, G:0.24, T:0.22
Consensus pattern (14 bp):
GTCAACGATCAATG
Found at i:463266 original size:3 final size:3
Alignment explanation
Indices: 463260--463291 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
463250 CCAAAATTAA
463260 AAT AAT AAT AAT AAT AAT AA- AAT AAT -AT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
463292 TAAATTTGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
2 4 0.15
3 23 0.85
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:464376 original size:21 final size:21
Alignment explanation
Indices: 464346--464401 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
464336 AAAGTCAAAT
*
464346 GTCAA-AGTCAACGGCCAACG
1 GTCAACAGTCAACGGCCAACA
*
464366 GTCAACAGTCAATGGCCAACA
1 GTCAACAGTCAACGGCCAACA
* *
464387 TTCAACTGTCAACGG
1 GTCAACAGTCAACGG
464402 TCGGTTAACG
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 5 0.17
21 25 0.83
ACGTcount: A:0.34, C:0.29, G:0.21, T:0.16
Consensus pattern (21 bp):
GTCAACAGTCAACGGCCAACA
Found at i:474410 original size:8 final size:9
Alignment explanation
Indices: 474389--474430 Score: 50
Period size: 9 Copynumber: 4.6 Consensus size: 9
474379 ACCTGTGGCA
474389 AAAAATTAT
1 AAAAATTAT
474398 AAAAATTAT
1 AAAAATTAT
*
474407 AAAATTTTAAT
1 AAAA-ATT-AT
474418 AAAAA-TAT
1 AAAAATTAT
474426 AAAAA
1 AAAAA
474431 ACTAAAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
8 7 0.24
9 14 0.48
10 2 0.07
11 6 0.21
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (9 bp):
AAAAATTAT
Found at i:476347 original size:20 final size:20
Alignment explanation
Indices: 476324--476362 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
476314 ATACATACTA
*
476324 TCATTGTTTATGACATGATT
1 TCATTGTTCATGACATGATT
*
476344 TCATTGTTCATGACTTGAT
1 TCATTGTTCATGACATGAT
476363 CCTTATTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.23, C:0.13, G:0.15, T:0.49
Consensus pattern (20 bp):
TCATTGTTCATGACATGATT
Found at i:479746 original size:13 final size:15
Alignment explanation
Indices: 479714--479765 Score: 54
Period size: 15 Copynumber: 3.4 Consensus size: 15
479704 ATAATTTGCA
479714 TTATTTTATTTAGCAT
1 TTATTTTATTTA-CAT
479730 TTATTTT-TTTA-AT
1 TTATTTTATTTACAT
*
479743 TTATTATTATTTATTAT
1 TTATT-TTATTTA-CAT
479760 TTATTT
1 TTATTT
479766 ATGTGTTATT
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
13 7 0.22
14 2 0.06
15 8 0.25
16 8 0.25
17 7 0.22
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.71
Consensus pattern (15 bp):
TTATTTTATTTACAT
Found at i:497744 original size:24 final size:24
Alignment explanation
Indices: 497716--497804 Score: 97
Period size: 24 Copynumber: 3.7 Consensus size: 24
497706 AACCTTTCTG
497716 GGCTCGTAAGAGCTAATCTATCTA
1 GGCTCGTAAGAGCTAATCTATCTA
* * *
497740 GGCTCGGAAGAGCTAAGCTATCTG
1 GGCTCGTAAGAGCTAATCTATCTA
* *
497764 GGCTCGTAAGAGGTAATTCTGTCTA
1 GGCTCGTAAGAGCTAA-TCTATCTA
* * *
497789 GACTTGTATGAGCTAA
1 GGCTCGTAAGAGCTAA
497805 ATTCTAGAAG
Statistics
Matches: 52, Mismatches: 12, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
24 35 0.67
25 17 0.33
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.28
Consensus pattern (24 bp):
GGCTCGTAAGAGCTAATCTATCTA
Found at i:508141 original size:24 final size:24
Alignment explanation
Indices: 508080--508142 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
508070 TAGACTAATA
* * *
508080 AGAGTTTTACTCAAATAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
*
508104 AGAGTTTAATTGAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
*
508128 ATAGTTTAACTGAAA
1 AGAGTTTAACTGAAA
508143 GATTATTTCT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.51, C:0.10, G:0.11, T:0.29
Consensus pattern (24 bp):
AGAGTTTAACTGAAACAAATAAAC
Found at i:510339 original size:43 final size:43
Alignment explanation
Indices: 510212--510322 Score: 168
Period size: 43 Copynumber: 2.6 Consensus size: 43
510202 CTAAAGGATT
* *
510212 TTTTAGGTAACTTTTCTGATTCTTTCCTATTTTAAATATATTG
1 TTTTAGGTAAATTTTCTGATTCTTTCCTATTTTAAATATATTA
* *
510255 TTTTAGGTAAATTTACTGATTATTTCCTATTTTAAATATATTA
1 TTTTAGGTAAATTTTCTGATTCTTTCCTATTTTAAATATATTA
* *
510298 TTTTACGTAAATTTTCTTATTCTTT
1 TTTTAGGTAAATTTTCTGATTCTTT
510323 TGTGTTCTAA
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 60 1.00
ACGTcount: A:0.26, C:0.10, G:0.07, T:0.57
Consensus pattern (43 bp):
TTTTAGGTAAATTTTCTGATTCTTTCCTATTTTAAATATATTA
Found at i:511608 original size:25 final size:21
Alignment explanation
Indices: 511565--511609 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
511555 ATTTTGTCTT
511565 TTTCCCATAAGTTACTATTTA
1 TTTCCCATAAGTTACTATTTA
511586 TTTCCCATAAGTTACTATTTA
1 TTTCCCATAAGTTACTATTTA
511607 TTT
1 TTT
511610 ATTTATGTGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.27, C:0.18, G:0.04, T:0.51
Consensus pattern (21 bp):
TTTCCCATAAGTTACTATTTA
Found at i:513419 original size:27 final size:28
Alignment explanation
Indices: 513389--513458 Score: 79
Period size: 27 Copynumber: 2.5 Consensus size: 28
513379 CGCAAACCTA
513389 AAGGTTAAAGGTTTGGGTTCAA-GATTT
1 AAGGTTAAAGGTTTGGGTTCAAGGATTT
* * * *
513416 AAGGTTCAAGTTTTGGGTTTAAGGGTTT
1 AAGGTTAAAGGTTTGGGTTCAAGGATTT
* *
513444 GAGGTTAGAGGTTTG
1 AAGGTTAAAGGTTTG
513459 TGATTTAATA
Statistics
Matches: 34, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
27 19 0.56
28 15 0.44
ACGTcount: A:0.24, C:0.03, G:0.34, T:0.39
Consensus pattern (28 bp):
AAGGTTAAAGGTTTGGGTTCAAGGATTT
Found at i:513512 original size:21 final size:20
Alignment explanation
Indices: 513488--513561 Score: 60
Period size: 21 Copynumber: 3.5 Consensus size: 20
513478 TTGGGTTATG
*
513488 GGTTATGAGTTTGGGGTTTAA
1 GGTT-TGAGTTTGGGATTTAA
* *
513509 GGTTTGAATTCAT-GGTTTTAA
1 GGTTTGAGTT--TGGGATTTAA
*
513530 GGTTGTGAGTTTGGGATTTAG
1 GGTT-TGAGTTTGGGATTTAA
*
513551 GGTTTGGGTTT
1 GGTTTGAGTTT
513562 TGGTTTTGGT
Statistics
Matches: 43, Mismatches: 6, Indels: 9
0.74 0.10 0.16
Matches are distributed among these distances:
20 12 0.28
21 25 0.58
22 6 0.14
ACGTcount: A:0.16, C:0.01, G:0.36, T:0.46
Consensus pattern (20 bp):
GGTTTGAGTTTGGGATTTAA
Found at i:513937 original size:43 final size:43
Alignment explanation
Indices: 513875--513958 Score: 123
Period size: 43 Copynumber: 2.0 Consensus size: 43
513865 TGAACGATTC
* * * *
513875 TTTATGTAACTTTTCTGATTCTTTCCTATTTTAAATATATTGT
1 TTTAGGTAAATTTACTGATTATTTCCTATTTTAAATATATTGT
*
513918 TTTAGGTAAATTTACTGATTATTTTCTATTTTAAATATATT
1 TTTAGGTAAATTTACTGATTATTTCCTATTTTAAATATATT
513959 TAGGTAAATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.27, C:0.08, G:0.07, T:0.57
Consensus pattern (43 bp):
TTTAGGTAAATTTACTGATTATTTCCTATTTTAAATATATTGT
Found at i:515825 original size:13 final size:14
Alignment explanation
Indices: 515759--515826 Score: 61
Period size: 14 Copynumber: 4.9 Consensus size: 14
515749 CTGGGGTAAT
*
515759 GGGTTACGAGTTTG
1 GGGTTATGAGTTTG
515773 GGGTTTATG-GTTTG
1 GGG-TTATGAGTTTG
* * *
515787 GGCTCATG-GTTTTA
1 GGGTTATGAG-TTTG
515801 GGGTTATGAGTTTG
1 GGGTTATGAGTTTG
515815 GGGTT-TGAGTTT
1 GGGTTATGAGTTT
515827 TTATTTTAGG
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
13 12 0.27
14 27 0.61
15 5 0.11
ACGTcount: A:0.12, C:0.04, G:0.40, T:0.44
Consensus pattern (14 bp):
GGGTTATGAGTTTG
Found at i:516210 original size:43 final size:43
Alignment explanation
Indices: 516149--516231 Score: 130
Period size: 43 Copynumber: 1.9 Consensus size: 43
516139 TAACTCTTTT
*
516149 GATTCTTTTCGATTTTAAATATATTATTTCAGGTAAATTTACC
1 GATTCTTTCCGATTTTAAATATATTATTTCAGGTAAATTTACC
* * *
516192 GATTCTTTCCTATTTTAAATATATTGTTTTAGGTAAATTT
1 GATTCTTTCCGATTTTAAATATATTATTTCAGGTAAATTT
516232 TCTTATTCAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.29, C:0.10, G:0.10, T:0.52
Consensus pattern (43 bp):
GATTCTTTCCGATTTTAAATATATTATTTCAGGTAAATTTACC
Found at i:518447 original size:40 final size:40
Alignment explanation
Indices: 518401--518743 Score: 452
Period size: 40 Copynumber: 8.6 Consensus size: 40
518391 CATCTTGTAA
*
518401 CCTGCTAAGCCGTAGGTTGAATATTAACACCGGCTCATAG
1 CCTGCTAAGCCGTAGCTTGAATATTAACACCGGCTCATAG
** * * * * *
518441 GTTGCTAAGTCGTAACTTGAATATTTACACCAGCTCGTAG
1 CCTGCTAAGCCGTAGCTTGAATATTAACACCGGCTCATAG
* * *
518481 CCTGCTAAGCCGTATCTTGAATATTTACACCGGCTCGTAG
1 CCTGCTAAGCCGTAGCTTGAATATTAACACCGGCTCATAG
* *
518521 CCTGCTAAGCCGTAGCTTAAATATTAACATCGGCTCATAG
1 CCTGCTAAGCCGTAGCTTGAATATTAACACCGGCTCATAG
* * *
518561 CCTGCTAAGTCGTAGCTTGAATATTTACACCAGCTCATAG
1 CCTGCTAAGCCGTAGCTTGAATATTAACACCGGCTCATAG
* *
518601 CCTACTAAGCCGTAGCTTGAATATTAACACCGGCTTATAG
1 CCTGCTAAGCCGTAGCTTGAATATTAACACCGGCTCATAG
* ** * *
518641 CCTGCTAAACCGTAGCTTGAATATTAACATTGTCTCGTAG
1 CCTGCTAAGCCGTAGCTTGAATATTAACACCGGCTCATAG
* *
518681 CCTGCTAAACCGTAGCTTGAATATTAACACCGGCTCGTAG
1 CCTGCTAAGCCGTAGCTTGAATATTAACACCGGCTCATAG
*
518721 CCTGTTAAGCCGTAGCTTGAATA
1 CCTGCTAAGCCGTAGCTTGAATA
518744 ACTCTTATTT
Statistics
Matches: 263, Mismatches: 40, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 263 1.00
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.29
Consensus pattern (40 bp):
CCTGCTAAGCCGTAGCTTGAATATTAACACCGGCTCATAG
Found at i:519437 original size:22 final size:22
Alignment explanation
Indices: 519412--519463 Score: 104
Period size: 22 Copynumber: 2.4 Consensus size: 22
519402 AAACAACTCA
519412 CATTTTACCAAAAAATGTACTT
1 CATTTTACCAAAAAATGTACTT
519434 CATTTTACCAAAAAATGTACTT
1 CATTTTACCAAAAAATGTACTT
519456 CATTTTAC
1 CATTTTAC
519464 ATGCTAAACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.38, C:0.19, G:0.04, T:0.38
Consensus pattern (22 bp):
CATTTTACCAAAAAATGTACTT
Found at i:525157 original size:17 final size:17
Alignment explanation
Indices: 525111--525157 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
525101 CTGTAGTATA
*
525111 ATTGTCCCTGCATTATT
1 ATTGTCACTGCATTATT
* *
525128 AATGTCA-TAGCATTTTT
1 ATTGTCACT-GCATTATT
525145 ATTGTCACTGCAT
1 ATTGTCACTGCAT
525158 CTACATTGTC
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
16 1 0.04
17 22 0.92
18 1 0.04
ACGTcount: A:0.23, C:0.19, G:0.13, T:0.45
Consensus pattern (17 bp):
ATTGTCACTGCATTATT
Done.