Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr2
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: 61750188
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1877335 characters in sequence are not A, C, G, or T
File 55 of 186
Found at i:17004333 original size:22 final size:24
Alignment explanation
Indices: 17004303--17004346 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
17004293 CTATCTAGAT
17004303 ATCAAATC-TCT-AAGATTACAGA
1 ATCAAATCTTCTAAAGATTACAGA
*
17004325 ATCATATCTTCTAAAGATTACA
1 ATCAAATCTTCTAAAGATTACA
17004347 TTTAATGTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
23 3 0.16
24 9 0.47
ACGTcount: A:0.43, C:0.18, G:0.07, T:0.32
Consensus pattern (24 bp):
ATCAAATCTTCTAAAGATTACAGA
Found at i:17011707 original size:31 final size:31
Alignment explanation
Indices: 17011664--17011725 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
17011654 TGTATTGATG
*
17011664 TATTAAATTATTTAAATATATTTTATCATTA
1 TATTAAATTATTTAAATATAATTTATCATTA
*
17011695 TATT-AATGTATTTAAATATAATTTATTATTA
1 TATTAAAT-TATTTAAATATAATTTATCATTA
17011726 GATTTAAGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 3 0.11
31 25 0.89
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (31 bp):
TATTAAATTATTTAAATATAATTTATCATTA
Found at i:17012398 original size:31 final size:30
Alignment explanation
Indices: 17012356--17012466 Score: 84
Period size: 31 Copynumber: 3.6 Consensus size: 30
17012346 AGTGGAAAAG
*
17012356 TTTGAGTAAAAATATAAATTTAAAAATTAGA
1 TTTGAGAAAAAATA-AAATTTAAAAATTAGA
* **
17012387 TTTGAGAAAAAA-AAAGCTCGTTTAGAAAACGAG-
1 TTTGAGAAAAAATAAA----ATTTA-AAAATTAGA
* *
17012420 TTTGAGCAAAAATAAAAACTTAAAAATTAGA
1 TTTGAGAAAAAAT-AAAATTTAAAAATTAGA
17012451 TTTGAGAAAAAA-AAAA
1 TTTGAGAAAAAATAAAA
17012467 GCTCGTTTAG
Statistics
Matches: 62, Mismatches: 10, Indels: 18
0.69 0.11 0.20
Matches are distributed among these distances:
29 6 0.10
30 7 0.11
31 25 0.40
33 15 0.24
34 6 0.10
35 3 0.05
ACGTcount: A:0.56, C:0.05, G:0.14, T:0.26
Consensus pattern (30 bp):
TTTGAGAAAAAATAAAATTTAAAAATTAGA
Found at i:17012455 original size:64 final size:65
Alignment explanation
Indices: 17012354--17012492 Score: 237
Period size: 64 Copynumber: 2.2 Consensus size: 65
17012344 AAAGTGGAAA
* * *
17012354 AGTTTGAGTAAAAATATAAATTTAAAAATTAGATTTGAG-AAAAAAAAAGCTCGTTTAGAAAACG
1 AGTTTGAGCAAAAATAAAAACTTAAAAATTAGATTTGAGAAAAAAAAAAGCTCGTTTAGAAAACG
17012418 AGTTTGAGCAAAAATAAAAACTTAAAAATTAGATTTGAGAAAAAAAAAAGCTCGTTTAGAAAACG
1 AGTTTGAGCAAAAATAAAAACTTAAAAATTAGATTTGAGAAAAAAAAAAGCTCGTTTAGAAAACG
17012483 AGTTTG-GCAA
1 AGTTTGAGCAA
17012493 TATATTTTTA
Statistics
Matches: 71, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
64 40 0.56
65 31 0.44
ACGTcount: A:0.51, C:0.06, G:0.17, T:0.26
Consensus pattern (65 bp):
AGTTTGAGCAAAAATAAAAACTTAAAAATTAGATTTGAGAAAAAAAAAAGCTCGTTTAGAAAACG
Found at i:17022186 original size:2 final size:2
Alignment explanation
Indices: 17022179--17022217 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
17022169 AGTCATGTGA
17022179 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
17022218 AGTGGGTTTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:17023887 original size:202 final size:202
Alignment explanation
Indices: 17023541--17023944 Score: 808
Period size: 202 Copynumber: 2.0 Consensus size: 202
17023531 TTAACGTATG
17023541 TTTGTATTTATTTTATATTTTCATTCATTCATAAGTTATTTTTAATGTTTATTAAAGTAAAAAAC
1 TTTGTATTTATTTTATATTTTCATTCATTCATAAGTTATTTTTAATGTTTATTAAAGTAAAAAAC
17023606 CCTATTTATGTTATGTGTAAAGAATGTGTTATTTTTTTATGTAATTTATTTGTTATGTGTGTTTT
66 CCTATTTATGTTATGTGTAAAGAATGTGTTATTTTTTTATGTAATTTATTTGTTATGTGTGTTTT
17023671 AGGTTGATTAAATTTATTTTTTATGTAATTTATTTCGCATGTTATTTTGATTATTTTAATATATA
131 AGGTTGATTAAATTTATTTTTTATGTAATTTATTTCGCATGTTATTTTGATTATTTTAATATATA
17023736 TTTTTTA
196 TTTTTTA
17023743 TTTGTATTTATTTTATATTTTCATTCATTCATAAGTTATTTTTAATGTTTATTAAAGTAAAAAAC
1 TTTGTATTTATTTTATATTTTCATTCATTCATAAGTTATTTTTAATGTTTATTAAAGTAAAAAAC
17023808 CCTATTTATGTTATGTGTAAAGAATGTGTTATTTTTTTATGTAATTTATTTGTTATGTGTGTTTT
66 CCTATTTATGTTATGTGTAAAGAATGTGTTATTTTTTTATGTAATTTATTTGTTATGTGTGTTTT
17023873 AGGTTGATTAAATTTATTTTTTATGTAATTTATTTCGCATGTTATTTTGATTATTTTAATATATA
131 AGGTTGATTAAATTTATTTTTTATGTAATTTATTTCGCATGTTATTTTGATTATTTTAATATATA
17023938 TTTTTTA
196 TTTTTTA
17023945 ATTTTTTATG
Statistics
Matches: 202, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
202 202 1.00
ACGTcount: A:0.28, C:0.04, G:0.11, T:0.57
Consensus pattern (202 bp):
TTTGTATTTATTTTATATTTTCATTCATTCATAAGTTATTTTTAATGTTTATTAAAGTAAAAAAC
CCTATTTATGTTATGTGTAAAGAATGTGTTATTTTTTTATGTAATTTATTTGTTATGTGTGTTTT
AGGTTGATTAAATTTATTTTTTATGTAATTTATTTCGCATGTTATTTTGATTATTTTAATATATA
TTTTTTA
Found at i:17025536 original size:14 final size:14
Alignment explanation
Indices: 17025517--17025550 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
17025507 GACATTTTTT
*
17025517 TTCTAATGATATTA
1 TTCTAATGATACTA
17025531 TTCTAATGATACTA
1 TTCTAATGATACTA
17025545 TTCTAA
1 TTCTAA
17025551 CATGTAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.35, C:0.12, G:0.06, T:0.47
Consensus pattern (14 bp):
TTCTAATGATACTA
Found at i:17026772 original size:14 final size:14
Alignment explanation
Indices: 17026753--17026781 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
17026743 TGGAACAAAC
17026753 TTTGTAATATAAAT
1 TTTGTAATATAAAT
17026767 TTTGTAATATAAAT
1 TTTGTAATATAAAT
17026781 T
1 T
17026782 AAATACATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (14 bp):
TTTGTAATATAAAT
Found at i:17026819 original size:62 final size:62
Alignment explanation
Indices: 17026662--17026830 Score: 218
Period size: 62 Copynumber: 2.7 Consensus size: 62
17026652 AATTAGATTA
** *
17026662 ATTACAACATTAAAACTTGGAACAAACTTTGTTGTCATAAATTAATTAATTGCAACATTATAAC
1 ATTACAACATTAAAACTTGGAACAAACTTTGTAAT-ATAAATTAATTAATT-CAACATTAAAAC
*
17026726 ATTACAACATTAAAACTTGGAACAAACTTTGTAATATAAATT-TTGTAATAT-AA-ATTAAATAC
1 ATTACAACATTAAAACTTGGAACAAACTTTGTAATATAAATTAAT-TAAT-TCAACATTAAA-AC
* *
17026788 ATTGCAACATTAAAACTTGGAACGAACTTTGTAATATAAATTA
1 ATTACAACATTAAAACTTGGAACAAACTTTGTAATATAAATTA
17026831 GGTACGTTGG
Statistics
Matches: 95, Mismatches: 6, Indels: 9
0.86 0.05 0.08
Matches are distributed among these distances:
61 5 0.05
62 45 0.47
63 11 0.12
64 34 0.36
ACGTcount: A:0.46, C:0.12, G:0.08, T:0.34
Consensus pattern (62 bp):
ATTACAACATTAAAACTTGGAACAAACTTTGTAATATAAATTAATTAATTCAACATTAAAAC
Found at i:17031140 original size:19 final size:19
Alignment explanation
Indices: 17031100--17031141 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
17031090 CATAATTTAA
*
17031100 AATGAAAATTTTAAGAAAT
1 AATGAAAATTGTAAGAAAT
*
17031119 AATGAAAGTTGTAA-AAATT
1 AATGAAAATTGTAAGAAA-T
17031138 AATG
1 AATG
17031142 TTTTAAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 3 0.15
19 17 0.85
ACGTcount: A:0.55, C:0.00, G:0.14, T:0.31
Consensus pattern (19 bp):
AATGAAAATTGTAAGAAAT
Found at i:17031357 original size:21 final size:21
Alignment explanation
Indices: 17031309--17031357 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
17031299 AACAGTTTTA
*
17031309 ATAACGAAAGGACTTGATGAT
1 ATAACGTAAGGACTTGATGAT
17031330 ATAACGTAAGGACTTGATGAT
1 ATAACGTAAGGACTTGATGAT
17031351 ATAACGT
1 ATAACGT
17031358 CAATAGTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.41, C:0.10, G:0.22, T:0.27
Consensus pattern (21 bp):
ATAACGTAAGGACTTGATGAT
Found at i:17036077 original size:20 final size:19
Alignment explanation
Indices: 17036049--17036123 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 19
17036039 TTTTAAAATA
*
17036049 AAGTGAAAATGATTTTAACC
1 AAGTCAAAATGATTTTAA-C
*
17036069 AAGTCAAAATGATTTTCATC
1 AAGTCAAAATGATTTT-AAC
* *
17036089 AAGTTAAAATCATTTTAAC
1 AAGTCAAAATGATTTTAAC
17036108 ATA-TCAAAATGATTTT
1 A-AGTCAAAATGATTTT
17036124 CAAAAAAGTT
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
19 14 0.30
20 31 0.67
21 1 0.02
ACGTcount: A:0.44, C:0.11, G:0.09, T:0.36
Consensus pattern (19 bp):
AAGTCAAAATGATTTTAAC
Found at i:17036123 original size:39 final size:40
Alignment explanation
Indices: 17036049--17036125 Score: 113
Period size: 39 Copynumber: 1.9 Consensus size: 40
17036039 TTTTAAAATA
*
17036049 AAGTGAAAATGATTTTAACCAAGTCAAAATGATTTTCATC
1 AAGTGAAAATCATTTTAACCAAGTCAAAATGATTTTCATC
*
17036089 AAGTTAAAATCATTTTAA-CATA-TCAAAATGATTTTCA
1 AAGTGAAAATCATTTTAACCA-AGTCAAAATGATTTTCA
17036126 AAAAAGTTAG
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
39 17 0.50
40 17 0.50
ACGTcount: A:0.44, C:0.12, G:0.09, T:0.35
Consensus pattern (40 bp):
AAGTGAAAATCATTTTAACCAAGTCAAAATGATTTTCATC
Found at i:17036133 original size:40 final size:41
Alignment explanation
Indices: 17036038--17036134 Score: 110
Period size: 40 Copynumber: 2.4 Consensus size: 41
17036028 TATTGAAACA
* * *
17036038 ATTTTAAAATAAAGTGAAAATGATTTTAACCAAGTCAAAATG
1 ATTTTCAAA-AAAGTTAAAATCATTTTAACCAAGTCAAAATG
**
17036080 ATTTTC-ATCAAGTTAAAATCATTTTAA-CATA-TCAAAATG
1 ATTTTCAAAAAAGTTAAAATCATTTTAACCA-AGTCAAAATG
17036119 ATTTTCAAAAAAGTTA
1 ATTTTCAAAAAAGTTA
17036135 GAATTGCTCT
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
39 16 0.35
40 24 0.52
41 1 0.02
42 5 0.11
ACGTcount: A:0.47, C:0.09, G:0.08, T:0.35
Consensus pattern (41 bp):
ATTTTCAAAAAAGTTAAAATCATTTTAACCAAGTCAAAATG
Found at i:17036301 original size:20 final size:22
Alignment explanation
Indices: 17036278--17036317 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
17036268 TTTTACCGAT
17036278 ATCGATA-CTTTC-TAAAAATA
1 ATCGATACCTTTCTTAAAAATA
17036298 ATCGATACCTTTCTTAAAAA
1 ATCGATACCTTTCTTAAAAA
17036318 CGATACGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 5 0.28
22 6 0.33
ACGTcount: A:0.42, C:0.17, G:0.05, T:0.35
Consensus pattern (22 bp):
ATCGATACCTTTCTTAAAAATA
Found at i:17039294 original size:21 final size:22
Alignment explanation
Indices: 17039268--17039313 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
17039258 TACATATAAA
*
17039268 TAAAAAATTATAAT-TATTTTT
1 TAAAAAATTATAATGAATTTTT
* *
17039289 TAAAAATTTATTATGAATTTTT
1 TAAAAAATTATAATGAATTTTT
17039311 TAA
1 TAA
17039314 TGTCAGAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 12 0.57
22 9 0.43
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (22 bp):
TAAAAAATTATAATGAATTTTT
Found at i:17039856 original size:47 final size:49
Alignment explanation
Indices: 17039774--17039909 Score: 176
Period size: 46 Copynumber: 2.9 Consensus size: 49
17039764 CAGGTGTTCG
*
17039774 CATCCATAAGTGAACTCGGACTCAACTCAAAGAGTTCGGATGCCTAGTTA
1 CATCCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCC-AGTTA
* * * *
17039824 CAT-C-TCA-TGAACTCGGATTCAACTCAACGAGTTCGGA---CATTTG
1 CATCCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCAGTTA
17039867 CATCCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGC
1 CATCCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGC
17039910 TCAACCATCC
Statistics
Matches: 73, Mismatches: 7, Indels: 13
0.78 0.08 0.14
Matches are distributed among these distances:
43 6 0.08
44 2 0.03
45 2 0.03
46 29 0.40
47 28 0.38
48 2 0.03
49 1 0.01
50 3 0.04
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (49 bp):
CATCCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCAGTTA
Found at i:17039895 original size:46 final size:46
Alignment explanation
Indices: 17039734--17039906 Score: 174
Period size: 46 Copynumber: 3.7 Consensus size: 46
17039724 AACCCGCCCC
* * * ** *
17039734 TAAGTGAACTCGGACTGAAATCAACGAGCTCAGG-TGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTC-GGACATTTGCATCCA
* * *
17039780 TAAGTGAACTCGGACTCAACTCAAAGAGTTCGGATGCCTAGTTACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-ATTTGCATCCA
* *
17039828 TCA-TGAACTCGGATTCAACTCAACGAGTTCGGACATTTGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
17039873 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
17039907 TGCTCAACCA
Statistics
Matches: 103, Mismatches: 16, Indels: 16
0.76 0.12 0.12
Matches are distributed among these distances:
43 6 0.06
44 2 0.02
45 4 0.04
46 56 0.54
47 28 0.27
48 2 0.02
49 1 0.01
50 4 0.04
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.24
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
Found at i:17039925 original size:46 final size:45
Alignment explanation
Indices: 17039782--17039925 Score: 127
Period size: 46 Copynumber: 3.1 Consensus size: 45
17039772 CGCATCCATA
*
17039782 AGTGAACTCGGACTCAACTCAAAGAGTTCGGATGC-CTAGTTA-CATCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTC-A---ACCATCT
* * * *
17039829 CA-TGAACTCGGATTCAACTCAACGAGTTCGGACAT-TTGCATCCAT-A
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGCT-CAACCATCT
17039875 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCAT-CT
17039921 AGTGA
1 AGTGA
17039926 CATGTCACTT
Statistics
Matches: 78, Mismatches: 9, Indels: 20
0.73 0.08 0.19
Matches are distributed among these distances:
44 8 0.10
45 2 0.03
46 33 0.42
47 30 0.38
48 1 0.01
49 3 0.04
50 1 0.01
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (45 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCT
Found at i:17040363 original size:30 final size:30
Alignment explanation
Indices: 17040329--17040388 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
17040319 ATTTAATACG
17040329 AACTTTAAAAAAATTACACTTTTGCCCCTA
1 AACTTTAAAAAAATTACACTTTTGCCCCTA
*** *
17040359 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTAAAAAAATTACACTTTTGCCCCTA
17040389 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.33, C:0.25, G:0.05, T:0.37
Consensus pattern (30 bp):
AACTTTAAAAAAATTACACTTTTGCCCCTA
Found at i:17047431 original size:93 final size:93
Alignment explanation
Indices: 17047319--17047490 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
17047309 CGCCCATAAG
* *
17047319 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
17047384 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
17047412 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
17047477 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
17047491 TCAATCATCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:17047487 original size:46 final size:46
Alignment explanation
Indices: 17047312--17047487 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
17047302 TGTAACCCGC
* * *
17047312 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
17047358 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
17047408 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
17047451 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
17047488 TGCTCAATCA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 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 63 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:17060121 original size:162 final size:162
Alignment explanation
Indices: 17059849--17060178 Score: 651
Period size: 162 Copynumber: 2.0 Consensus size: 162
17059839 ATGAAGTGTC
*
17059849 AACTAGTCCATACCCAAAATGACATCAAACTCATTGAATGGTAACAACATCAAATCGGCCGGAAA
1 AACTCGTCCATACCCAAAATGACATCAAACTCATTGAATGGTAACAACATCAAATCGGCCGGAAA
17059914 ATAGTGACCTCTAACTATCAAAGGGCATTTCTTGCATACTTTATCGACTATCACATGCTTGCCTA
66 ATAGTGACCTCTAACTATCAAAGGGCATTTCTTGCATACTTTATCGACTATCACATGCTTGCCTA
17059979 GAGGGTTTGACACCTTAATCATAAACTCTGTA
131 GAGGGTTTGACACCTTAATCATAAACTCTGTA
17060011 AACTCGTCCATACCCAAAATGACATCAAACTCATTGAATGGTAACAACATCAAATCGGCCGGAAA
1 AACTCGTCCATACCCAAAATGACATCAAACTCATTGAATGGTAACAACATCAAATCGGCCGGAAA
17060076 ATAGTGACCTCTAACTATCAAAGGGCATTTCTTGCATACTTTATCGACTATCACATGCTTGCCTA
66 ATAGTGACCTCTAACTATCAAAGGGCATTTCTTGCATACTTTATCGACTATCACATGCTTGCCTA
17060141 GAGGGTTTGACACCTTAATCATAAACTCTGTA
131 GAGGGTTTGACACCTTAATCATAAACTCTGTA
17060173 AACTCG
1 AACTCG
17060179 ACAGGTATGT
Statistics
Matches: 167, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
162 167 1.00
ACGTcount: A:0.34, C:0.24, G:0.15, T:0.27
Consensus pattern (162 bp):
AACTCGTCCATACCCAAAATGACATCAAACTCATTGAATGGTAACAACATCAAATCGGCCGGAAA
ATAGTGACCTCTAACTATCAAAGGGCATTTCTTGCATACTTTATCGACTATCACATGCTTGCCTA
GAGGGTTTGACACCTTAATCATAAACTCTGTA
Found at i:17076005 original size:18 final size:19
Alignment explanation
Indices: 17075978--17076013 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
17075968 ATCAATACCG
17075978 TTTTAAAAA-TATTGATAA
1 TTTTAAAAATTATTGATAA
*
17075996 TTTTATAAATTATTGATA
1 TTTTAAAAATTATTGATA
17076014 CTTATGAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (19 bp):
TTTTAAAAATTATTGATAA
Found at i:17076011 original size:19 final size:18
Alignment explanation
Indices: 17075978--17076013 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
17075968 ATCAATACCG
17075978 TTTTAAAAATATTGATAA
1 TTTTAAAAATATTGATAA
*
17075996 TTTTATAAATTATTGATA
1 TTTTA-AAAATATTGATA
17076014 CTTATGAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (18 bp):
TTTTAAAAATATTGATAA
Found at i:17077035 original size:22 final size:22
Alignment explanation
Indices: 17077010--17077082 Score: 119
Period size: 22 Copynumber: 3.3 Consensus size: 22
17077000 TAGCAATAAG
* *
17077010 GTGCTATATAGAGAGCACGAAT
1 GTGCTAAACAGAGAGCACGAAT
17077032 GTGCTAAACAGAGAGCACGAAT
1 GTGCTAAACAGAGAGCACGAAT
*
17077054 GTGCTAAACAGAGAGCACTAAT
1 GTGCTAAACAGAGAGCACGAAT
17077076 GTGCTAA
1 GTGCTAA
17077083 TAATCAGATA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 48 1.00
ACGTcount: A:0.38, C:0.16, G:0.26, T:0.19
Consensus pattern (22 bp):
GTGCTAAACAGAGAGCACGAAT
Found at i:17080560 original size:20 final size:19
Alignment explanation
Indices: 17080537--17080606 Score: 68
Period size: 20 Copynumber: 3.5 Consensus size: 19
17080527 CAAGTGAAAA
17080537 TCAACCAAGTCAAAATGATT
1 TCAA-CAAGTCAAAATGATT
* *
17080557 TCAATCAAGTTAAAATCATT
1 TCAA-CAAGTCAAAATGATT
* *
17080577 TTAACACGTCAAAATGATTT
1 TCAACAAGTCAAAATGA-TT
17080597 TCAAACAAGT
1 TC-AACAAGT
17080607 TAGAATTGCT
Statistics
Matches: 39, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
19 10 0.26
20 23 0.59
21 6 0.15
ACGTcount: A:0.44, C:0.17, G:0.09, T:0.30
Consensus pattern (19 bp):
TCAACAAGTCAAAATGATT
Found at i:17080596 original size:19 final size:20
Alignment explanation
Indices: 17080542--17080597 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
17080532 GAAAATCAAC
*
17080542 CAAGTCAAAATGATTTCAAT
1 CAAGTCAAAATGATTTTAAT
* *
17080562 CAAGTTAAAATCATTTTAA-
1 CAAGTCAAAATGATTTTAAT
*
17080581 CACGTCAAAATGATTTT
1 CAAGTCAAAATGATTTT
17080598 CAAACAAGTT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.34
Consensus pattern (20 bp):
CAAGTCAAAATGATTTTAAT
Found at i:17083982 original size:16 final size:16
Alignment explanation
Indices: 17083961--17083996 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
17083951 TAGTAGACAT
17083961 TATAATAT-AGTTAACA
1 TATAATATCA-TTAACA
17083977 TATAATATCATTAACA
1 TATAATATCATTAACA
17083993 TATA
1 TATA
17083997 TGAAATTACA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 18 0.95
17 1 0.05
ACGTcount: A:0.50, C:0.08, G:0.03, T:0.39
Consensus pattern (16 bp):
TATAATATCATTAACA
Found at i:17087105 original size:57 final size:57
Alignment explanation
Indices: 17086984--17087103 Score: 163
Period size: 57 Copynumber: 2.1 Consensus size: 57
17086974 TTCTCATTTT
*
17086984 CATTTTCATTTCCATTTTGGAGAAAACCACATTCATTTCCAAATGATTTTATTTCTC
1 CATTTTCATTTCCATTTTGGAGAAAACCACAATCATTTCCAAATGATTTTATTTCTC
* **
17087041 CATTTTCATTTTCC-TTTTGGAGATAACCTTAATCATTTCCAAATG-TTTCATATTTCTC
1 CATTTTCA-TTTCCATTTTGGAGAAAACCACAATCATTTCCAAATGATTT--TATTTCTC
17087099 CATTT
1 CATTT
17087104 CACCATTTCT
Statistics
Matches: 56, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
56 3 0.05
57 35 0.62
58 18 0.32
ACGTcount: A:0.26, C:0.21, G:0.07, T:0.47
Consensus pattern (57 bp):
CATTTTCATTTCCATTTTGGAGAAAACCACAATCATTTCCAAATGATTTTATTTCTC
Found at i:17092924 original size:29 final size:29
Alignment explanation
Indices: 17092870--17092967 Score: 117
Period size: 29 Copynumber: 3.4 Consensus size: 29
17092860 CCTGTATCTA
* * *
17092870 GCCCATTAAGCCC-AATCATATTCATATG
1 GCCCATTAGGCCCAAATCACATGCATATG
* * *
17092898 GCCCATTAGGTCTAAATCACCTGCATATG
1 GCCCATTAGGCCCAAATCACATGCATATG
**
17092927 GCCCATTAGGCCCAAATCACATTTATATG
1 GCCCATTAGGCCCAAATCACATGCATATG
17092956 GCCCATTAGGCC
1 GCCCATTAGGCC
17092968 TAGTCACATT
Statistics
Matches: 58, Mismatches: 11, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
28 10 0.17
29 48 0.83
ACGTcount: A:0.29, C:0.30, G:0.15, T:0.27
Consensus pattern (29 bp):
GCCCATTAGGCCCAAATCACATGCATATG
Found at i:17094319 original size:16 final size:16
Alignment explanation
Indices: 17094292--17094341 Score: 64
Period size: 16 Copynumber: 3.1 Consensus size: 16
17094282 AAAAATTCAA
*
17094292 GATTTCGGGATTTTTG
1 GATTTCGAGATTTTTG
*
17094308 GATTTTGAGATTTTTG
1 GATTTCGAGATTTTTG
* *
17094324 GGTTTCGGGATTTTTG
1 GATTTCGAGATTTTTG
17094340 GA
1 GA
17094342 GCATTACATA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.14, C:0.04, G:0.32, T:0.50
Consensus pattern (16 bp):
GATTTCGAGATTTTTG
Found at i:17095719 original size:30 final size:30
Alignment explanation
Indices: 17095679--17095735 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
17095669 AGACTAATTA
* *
17095679 CACACGGGCTGAG-CACACGCCCGTGTGAGG
1 CACACAGGCTG-GCCACACGCCCATGTGAGG
17095709 CACACAGGCTGGCCACACGCCCATGTG
1 CACACAGGCTGGCCACACGCCCATGTG
17095736 GCAGCCCGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 1 0.04
30 23 0.96
ACGTcount: A:0.21, C:0.37, G:0.32, T:0.11
Consensus pattern (30 bp):
CACACAGGCTGGCCACACGCCCATGTGAGG
Found at i:17098310 original size:166 final size:167
Alignment explanation
Indices: 17098027--17098360 Score: 474
Period size: 166 Copynumber: 2.0 Consensus size: 167
17098017 CTTCACATAG
** * * * *
17098027 ACACTACGAGTTTCTAGCAATGTTGTTTGGGCTAACCAATGCCCAATCCACTTTTATGGATTTGA
1 ACACTACGAGTTTCTAGCAATGTCATTTGGACTAAACAACGCCCAATCCACTTTTATGGATCTGA
** * * * *
17098092 TGAACATAATTTTTCATTTGTATTTTTATAGATTTTTTGTTGTGTTCATAGATTATATATTTATC
66 TGAACATAATTTTTCATTTGTATTTGGATAAATTTGTTGTTGTGTTCATAGATGATATATTAATC
17098157 TACTC-AAAAAATAAAAATGATCATGATCAGCATCTA
131 TACTCAAAAAAATAAAAATGATCATGATCAGCATCTA
* * *
17098193 ACACTAGGGGTTTCTAGTAATGTCATTTGGACTAAACAACGCCCAATCCACTTTTATGGATCTGA
1 ACACTACGAGTTTCTAGCAATGTCATTTGGACTAAACAACGCCCAATCCACTTTTATGGATCTGA
*
17098258 TGAACATAATTTTTCATGTT-TATTTGGATAAATTTGTTGTTGTTTTCATAGATGATATATTAAT
66 TGAACATAATTTTTCAT-TTGTATTTGGATAAATTTGTTGTTGTGTTCATAGATGATATATTAAT
* * *
17098322 CTACTCAAAAAAATGAAAATGATCATGATTAGTATCTA
130 CTACTCAAAAAAATAAAAATGATCATGATCAGCATCTA
17098360 A
1 A
17098361 GAGTTTTACT
Statistics
Matches: 147, Mismatches: 19, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
166 116 0.79
167 31 0.21
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.40
Consensus pattern (167 bp):
ACACTACGAGTTTCTAGCAATGTCATTTGGACTAAACAACGCCCAATCCACTTTTATGGATCTGA
TGAACATAATTTTTCATTTGTATTTGGATAAATTTGTTGTTGTGTTCATAGATGATATATTAATC
TACTCAAAAAAATAAAAATGATCATGATCAGCATCTA
Found at i:17098548 original size:162 final size:163
Alignment explanation
Indices: 17098280--17098609 Score: 617
Period size: 162 Copynumber: 2.0 Consensus size: 163
17098270 TTCATGTTTA
17098280 TTTGGATAAATTTGTTGTTGTTTTCATAGATGATATATTAATCTACTCAAAAAAATGAAAATGAT
1 TTTGGATAAATTTGTTGTTGTTTTCATAGATGATATATTAATCTACTCAAAAAAATGAAAATGAT
*
17098345 CATGATTAGTATCTAAGAGTTTTACTACAAACCTTGCAAGAAAAATAATTGTTTTCAAAAGTCTA
66 CATGATTAGTATCTAAGAGTTTTACAACAAACCTTGCAAGAAAAATAATTGTTTTCAAAAGTCTA
17098410 CAAATGTGAGTTCTGGCTACGAGAAGTGAGATT
131 CAAATGTGAGTTCTGGCTACGAGAAGTGAGATT
17098443 TTTGGATAAATTTGTTGTTGTTTTCATAGATGATATATTAATCTACTC-AAAAAATGAAAATGAT
1 TTTGGATAAATTTGTTGTTGTTTTCATAGATGATATATTAATCTACTCAAAAAAATGAAAATGAT
*
17098507 CATGATTAGTATCTAATAGTTTTACAACAAACCTTGCAAGAAAAATAATTGTTTTCAAAAGTCTA
66 CATGATTAGTATCTAAGAGTTTTACAACAAACCTTGCAAGAAAAATAATTGTTTTCAAAAGTCTA
* *
17098572 CAAATGTGAGTTTTGGCTACGAGAAGTGGGATT
131 CAAATGTGAGTTCTGGCTACGAGAAGTGAGATT
17098605 TTTGG
1 TTTGG
17098610 GTTACCTAAT
Statistics
Matches: 163, Mismatches: 4, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
162 115 0.71
163 48 0.29
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.36
Consensus pattern (163 bp):
TTTGGATAAATTTGTTGTTGTTTTCATAGATGATATATTAATCTACTCAAAAAAATGAAAATGAT
CATGATTAGTATCTAAGAGTTTTACAACAAACCTTGCAAGAAAAATAATTGTTTTCAAAAGTCTA
CAAATGTGAGTTCTGGCTACGAGAAGTGAGATT
Found at i:17101136 original size:14 final size:15
Alignment explanation
Indices: 17101099--17101150 Score: 63
Period size: 15 Copynumber: 3.5 Consensus size: 15
17101089 TGATTAAGAT
17101099 TAATTAATTATAGTT-
1 TAATTAATTA-AGTTA
17101114 TAAATTAATTAA-TTA
1 T-AATTAATTAAGTTA
*
17101129 TGATTAATTAAGTTA
1 TAATTAATTAAGTTA
17101144 TAATTAA
1 TAATTAA
17101151 AGTATATAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
14 11 0.34
15 12 0.38
16 9 0.28
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.48
Consensus pattern (15 bp):
TAATTAATTAAGTTA
Found at i:17102239 original size:19 final size:19
Alignment explanation
Indices: 17102215--17102251 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
17102205 TCTATAAATA
17102215 TCAGCTTGTGTGAGCAATG
1 TCAGCTTGTGTGAGCAATG
17102234 TCAGCTTGTGTGAGCAAT
1 TCAGCTTGTGTGAGCAAT
17102252 ATAGTCTCAT
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:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (19 bp):
TCAGCTTGTGTGAGCAATG
Found at i:17112683 original size:12 final size:12
Alignment explanation
Indices: 17112668--17112694 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
17112658 GTCACACACA
17112668 GCCTACCACATG
1 GCCTACCACATG
17112680 GCCTACCACATG
1 GCCTACCACATG
17112692 GCC
1 GCC
17112695 GTGTGGTGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.22, C:0.44, G:0.19, T:0.15
Consensus pattern (12 bp):
GCCTACCACATG
Found at i:17124449 original size:20 final size:20
Alignment explanation
Indices: 17124411--17124451 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
17124401 CATGAACAAT
**
17124411 TTTGTGCCTACTAACACTAA
1 TTTGTGCCTAAAAACACTAA
*
17124431 TTTGTGCCTAAAAAGACTAA
1 TTTGTGCCTAAAAACACTAA
17124451 T
1 T
17124452 GGCTGATGCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.34, C:0.20, G:0.12, T:0.34
Consensus pattern (20 bp):
TTTGTGCCTAAAAACACTAA
Found at i:17129341 original size:28 final size:29
Alignment explanation
Indices: 17129288--17129369 Score: 114
Period size: 29 Copynumber: 2.8 Consensus size: 29
17129278 CACGGCCAGG
*
17129288 TACATGGGCATGTG-GCTAGGCCGTGTGAGC
1 TACACGGGCATGTGAG--AGGCCGTGTGAGC
17129318 TACA-GGGCATGTGAGAGGCCGTGTGAGC
1 TACACGGGCATGTGAGAGGCCGTGTGAGC
*
17129346 CACACGGGCATGTGAGAGGCCGTG
1 TACACGGGCATGTGAGAGGCCGTG
17129370 CGACTGGCCG
Statistics
Matches: 49, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
28 16 0.33
29 28 0.57
30 5 0.10
ACGTcount: A:0.20, C:0.21, G:0.41, T:0.18
Consensus pattern (29 bp):
TACACGGGCATGTGAGAGGCCGTGTGAGC
Found at i:17141374 original size:43 final size:44
Alignment explanation
Indices: 17141037--17141737 Score: 303
Period size: 44 Copynumber: 15.6 Consensus size: 44
17141027 CTTTGATTTA
* * * *
17141037 CTCCACTGCAACTTCAGGGAGATAAGAATCGTAACTTCAACCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTTAATCTG
* * * * ** *
17141081 CTCTACTACAACTTTAGGGAGATGAGGTTTGTGACTTTAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTTAATCTG
* * * *
17141125 CTCCATTGCAACTTCAGGGAGATAAAATTTGCCATGGTAGA-TTTGATCTG
1 CTCCACTGCAACTTCAGGGAGAT--AA---GAC-TTGTA-ACTTTAATCTG
* * * * * ** * *
17141175 AC-CTACTACGACTTCAGAGG-TATAGGGTTTGTAGCTTTAATCTA
1 -CTCCACTGCAACTTCAG-GGAGATAAGACTTGTAACTTTAATCTG
* * * * ** *
17141219 CTCTATTGCAACTTCAGAGAGATAAGATTTGCTATTTTTAGTCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTG-TAACTTTAATCTG
* * *
17141264 TTCCGCTGCAACTTCAGGGAGATAAGACTTGTAACTTCAA-CTTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTTAATC-TG
* * *
17141308 CTCCACTGCATCTTCAGGAAGATAGGACTTGT-ACTTTAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTTAATCTG
* * * *
17141351 CTCCACTGTAACTTTAGGGAGATAAGATTCGCCATGGTAGA-TTTGATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGA-----C-TTGTA-ACTTTAATCTG
* ** * * ** * * *
17141401 AC-CTACTGCGGCTTCAGAGG-TATAGGGTTTATAGCTTTAATCTA
1 -CTCCACTGCAACTTCAG-GGAGATAAGACTTGTAACTTTAATCTG
* * * * * * * *
17141445 CTCTACTACAACCTGAGAGAGATAAGATTTGCT-ATTTTCAGTCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTG-TAACTTT-AATCTG
* * * * * *
17141490 TTTCACTGCAACTTCAGGGAGATAAAACTTGTAACTTCAACCCG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTTAATCTG
* * * *
17141534 CTCCACTGCATCTTCAAGGAGATAGGACTTGT-ACTTTAACCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTTAATCTG
* * ** * **
17141577 CCCCACTGCAACTTCAGGGGGATAAGGTTTGCTATCTTCGATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTG-TAACTTTAATCTG
* * * * *
17141622 TTCCACTGCAACTTCAGGAATATAAGA-TCTGTGACTTCAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACT-TGTAACTTTAATCTG
* * * *
17141666 CTCCGCTGCAACTTCAGAGAGACAAGA-TT-TACGACTTAAAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGTA--ACTT-TAATCTG
17141711 CTCCACTGCAACTTCAGGGAGATAAGA
1 CTCCACTGCAACTTCAGGGAGATAAGA
17141738 TTCACTATGG
Statistics
Matches: 473, Mismatches: 147, Indels: 73
0.68 0.21 0.11
Matches are distributed among these distances:
42 1 0.00
43 69 0.15
44 217 0.46
45 125 0.26
46 1 0.00
48 2 0.00
49 4 0.01
50 46 0.10
51 8 0.02
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.31
Consensus pattern (44 bp):
CTCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTTAATCTG
Found at i:17141438 original size:226 final size:225
Alignment explanation
Indices: 17141038--17141602 Score: 826
Period size: 226 Copynumber: 2.5 Consensus size: 225
17141028 TTTGATTTAC
* * * * * *
17141038 TCCACTGCAACTTCAGGGAGATAAGAATCGTAACTTCAACCTGCTCTACTACAACTTTAGGGAGA
1 TCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAACCTGCTCCACTGCATCTTCA-GGAGA
* * * *
17141103 TGAGG-TTTGTGACTTTAATCTGCTCCATTGCAACTTCAGGGAGATAAAATTTGCCATGGTAGAT
65 T-AGGACTTGT-ACTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCCATGGTAGAT
* * * *
17141167 TTGATCTGACCTACTACGACTTCAGAGGTATAGGGTTTGTAGCTTTAATCTACTCTATTGCAACT
128 TTGATCTGACCTACTACGACTTCAGAGGTATAGGGTTTATAGCTTTAATCTACTCTACTACAACC
*
17141232 TCAGAGAGATAAGATTTGCTATTTTTAGTCTGT
193 TCAGAGAGATAAGATTTGCTATTTTCAGTCTGT
* *
17141265 TCCGCTGCAACTTCAGGGAGATAAGACTTGTAACTTCAACTTGCTCCACTGCATCTTCAGGAAGA
1 TCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAACCTGCTCCACTGCATCTTCAGG-AGA
* *
17141330 TAGGACTTGTACTTTAATCTGCTCCACTGTAACTTTAGGGAGATAAGATTCGCCATGGTAGATTT
65 TAGGACTTGTACTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCCATGGTAGATTT
* * *
17141395 GATCTGACCTACTGCGGCTTCAGAGGTATAGGGTTTATAGCTTTAATCTACTCTACTACAACCTG
130 GATCTGACCTACTACGACTTCAGAGGTATAGGGTTTATAGCTTTAATCTACTCTACTACAACCTC
17141460 AGAGAGATAAGATTTGCTATTTTCAGTCTGT
195 AGAGAGATAAGATTTGCTATTTTCAGTCTGT
* * *
17141491 TTCACTGCAACTTCAGGGAGATAAAACTTGTAACTTCAACCCGCTCCACTGCATCTTCAAGGAGA
1 TCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAACCTGCTCCACTGCATCTTC-AGGAGA
* * *
17141556 TAGGACTTGTACTTTAACCTGCCCCACTGCAACTTCAGGGGGATAAG
65 TAGGACTTGTACTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAG
17141603 GTTTGCTATC
Statistics
Matches: 303, Mismatches: 32, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
226 241 0.80
227 62 0.20
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.31
Consensus pattern (225 bp):
TCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAACCTGCTCCACTGCATCTTCAGGAGAT
AGGACTTGTACTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCCATGGTAGATTTG
ATCTGACCTACTACGACTTCAGAGGTATAGGGTTTATAGCTTTAATCTACTCTACTACAACCTCA
GAGAGATAAGATTTGCTATTTTCAGTCTGT
Found at i:17141739 original size:45 final size:43
Alignment explanation
Indices: 17141493--17141739 Score: 196
Period size: 45 Copynumber: 5.6 Consensus size: 43
17141483 CAGTCTGTTT
* * *
17141493 CACTGCAACTTCAGGGAGATAAAACTTGTA-ACTTCAACCCGCTC
1 CACTGCAACTTCAGGGAGATAAGA-TT-TAGACTTCAATCTGCTC
* * * * * * *
17141537 CACTGCATCTTCAAGGAGATAGGACTT-GTACTTTAACCTGCCC
1 CACTGCAACTTCAGGGAGATAAGATTTAG-ACTTCAATCTGCTC
* * * *
17141580 CACTGCAACTTCAGGGGGATAAGGTTT-GCTATCTTCGATCTGTTC
1 CACTGCAACTTCAGGGAGATAAGATTTAG--A-CTTCAATCTGCTC
* *
17141625 CACTGCAACTTCAGGAATATAAGATCTGT-GACTTCAATCTGCTC
1 CACTGCAACTTCAGGGAGATAAGAT-T-TAGACTTCAATCTGCTC
* * * *
17141669 CGCTGCAACTTCAGAGAGACAAGATTTACGACTTAAAATCTGCTC
1 CACTGCAACTTCAGGGAGATAAGATTTA-GACTT-CAATCTGCTC
17141714 CACTGCAACTTCAGGGAGATAAGATT
1 CACTGCAACTTCAGGGAGATAAGATT
17141740 CACTATGGTG
Statistics
Matches: 160, Mismatches: 34, Indels: 17
0.76 0.16 0.08
Matches are distributed among these distances:
42 2 0.01
43 35 0.22
44 58 0.36
45 62 0.39
46 1 0.01
47 2 0.01
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27
Consensus pattern (43 bp):
CACTGCAACTTCAGGGAGATAAGATTTAGACTTCAATCTGCTC
Found at i:17153265 original size:25 final size:26
Alignment explanation
Indices: 17153230--17153286 Score: 80
Period size: 25 Copynumber: 2.2 Consensus size: 26
17153220 TTTATTTTAT
*
17153230 TTTGGGTTTTATTTTTGTTTTATTGG
1 TTTGGGTTTTATTTTTGGTTTATTGG
*
17153256 TTTGGG-TTTATTTTTGGTTTGTTGG
1 TTTGGGTTTTATTTTTGGTTTATTGG
*
17153281 TCTGGG
1 TTTGGG
17153287 CCAAAATTGG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
25 22 0.79
26 6 0.21
ACGTcount: A:0.05, C:0.02, G:0.30, T:0.63
Consensus pattern (26 bp):
TTTGGGTTTTATTTTTGGTTTATTGG
Found at i:17154953 original size:20 final size:19
Alignment explanation
Indices: 17154909--17154954 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
17154899 ATAATAATGA
17154909 GAATAAAAAAAATAAAAAT
1 GAATAAAAAAAATAAAAAT
* *
17154928 GAAATAAATACAATAATAAAT
1 G-AATAAAAAAAATAA-AAAT
17154949 GAATAA
1 GAATAA
17154955 TAAATGAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 1 0.04
20 17 0.74
21 5 0.22
ACGTcount: A:0.72, C:0.02, G:0.07, T:0.20
Consensus pattern (19 bp):
GAATAAAAAAAATAAAAAT
Found at i:17154956 original size:23 final size:20
Alignment explanation
Indices: 17154898--17154974 Score: 70
Period size: 21 Copynumber: 3.7 Consensus size: 20
17154888 ATAATAAGAT
*
17154898 AATAAT-AATGAGAATAAAAAA
1 AATAATAAATGA-AAT-AAATA
17154919 AATAA-AAATGAAATAAATA
1 AATAATAAATGAAATAAATA
17154938 CAATAATAAATGAATAATAAATGA
1 -AATAATAAATG-A-AATAAAT-A
17154962 AATAATAAA-GAAA
1 AATAATAAATGAAA
17154975 ATTCTAGTGA
Statistics
Matches: 49, Mismatches: 1, Indels: 13
0.78 0.02 0.21
Matches are distributed among these distances:
19 4 0.08
20 10 0.20
21 16 0.33
22 2 0.04
23 16 0.33
24 1 0.02
ACGTcount: A:0.70, C:0.01, G:0.08, T:0.21
Consensus pattern (20 bp):
AATAATAAATGAAATAAATA
Found at i:17154974 original size:11 final size:11
Alignment explanation
Indices: 17154869--17154974 Score: 53
Period size: 11 Copynumber: 9.3 Consensus size: 11
17154859 ATAGAGACAT
17154869 AAATGAATAAACG
1 AAAT-AATAAA-G
17154882 AAATATATAATAAG
1 AAATA-AT-A-AAG
*
17154896 ATAATAATAATG
1 A-AATAATAAAG
17154908 AGAATAA-AAA-
1 A-AATAATAAAG
17154918 AAATAA-AAATG
1 AAATAATAAA-G
*
17154929 AAATAA-ATA-
1 AAATAATAAAG
*
17154938 CAATAATAAATG
1 AAATAATAAA-G
17154950 -AATAATAAATG
1 AAATAATAAA-G
17154961 AAATAATAAAG
1 AAATAATAAAG
17154972 AAA
1 AAA
17154975 ATTCTAGTGA
Statistics
Matches: 77, Mismatches: 6, Indels: 22
0.73 0.06 0.21
Matches are distributed among these distances:
9 13 0.17
10 3 0.04
11 25 0.32
12 18 0.23
13 7 0.09
14 5 0.06
15 6 0.08
ACGTcount: A:0.68, C:0.02, G:0.08, T:0.22
Consensus pattern (11 bp):
AAATAATAAAG
Found at i:17154976 original size:12 final size:12
Alignment explanation
Indices: 17154869--17154974 Score: 63
Period size: 12 Copynumber: 9.2 Consensus size: 12
17154859 ATAGAGACAT
*
17154869 AAATGAATAAACG
1 AAAT-AATAAATG
*
17154882 AAATATATAATAAG
1 AAATA-ATAA-ATG
17154896 ATAATAAT-AATG
1 A-AATAATAAATG
17154908 AGAATAA-AAA--
1 A-AATAATAAATG
17154918 AAATAA-AAATG
1 AAATAATAAATG
17154929 --A-AATAAAT-
1 AAATAATAAATG
17154937 ACAATAATAAATG
1 A-AATAATAAATG
17154950 -AATAATAAATG
1 AAATAATAAATG
17154961 AAATAATAAA-G
1 AAATAATAAATG
17154972 AAA
1 AAA
17154975 ATTCTAGTGA
Statistics
Matches: 77, Mismatches: 3, Indels: 28
0.71 0.03 0.26
Matches are distributed among these distances:
8 2 0.03
9 13 0.17
10 1 0.01
11 16 0.21
12 27 0.35
13 9 0.12
14 5 0.06
15 4 0.05
ACGTcount: A:0.68, C:0.02, G:0.08, T:0.22
Consensus pattern (12 bp):
AAATAATAAATG
Found at i:17155064 original size:3 final size:3
Alignment explanation
Indices: 17155056--17155240 Score: 138
Period size: 3 Copynumber: 63.7 Consensus size: 3
17155046 ATGGTTTAAA
* * * *
17155056 AAT AAT AAT GAT AAT AAT AAT AAT AGT AAT AAT AAT AAT CAT ACT -AT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * ** *
17155103 AAT GAT AGT AAT AAT GGT AA- AAT AAT AAT AAT GAT AAT AAT AAT AA-
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * *
17155149 AAT -AT AA- AA- AAT -TT AGCA- AAT GAT AAT AAT AAT ATT GAT AAT
1 AAT AAT AAT AAT AAT AAT A--AT AAT AAT AAT AAT AAT AAT AAT AAT
*
17155191 AAAT AAT AAT AGT AA- AAT AAT AAT AAT AAT AAT AAT AAT AACT AA-
1 -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT
17155236 AAT AA
1 AAT AA
17155241 CTAAAAAGGA
Statistics
Matches: 141, Mismatches: 28, Indels: 26
0.72 0.14 0.13
Matches are distributed among these distances:
2 17 0.12
3 117 0.83
4 7 0.05
ACGTcount: A:0.61, C:0.02, G:0.06, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:17156784 original size:14 final size:14
Alignment explanation
Indices: 17156767--17156793 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
17156757 CATAAAATAA
17156767 AGAAAATATTTTAT
1 AGAAAATATTTTAT
17156781 AGAAAATATTTTA
1 AGAAAATATTTTA
17156794 CTGGCAAACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (14 bp):
AGAAAATATTTTAT
Found at i:17158363 original size:21 final size:21
Alignment explanation
Indices: 17158339--17158403 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
17158329 AAATCTAACT
17158339 GAAGCACAAAAGTGCTAAACG
1 GAAGCACAAAAGTGCTAAACG
** *
17158360 GAAGC-CCGAAG-GCT-AACT
1 GAAGCACAAAAGTGCTAAACG
*
17158378 GAAGCACATAAGTGCTAAACG
1 GAAGCACAAAAGTGCTAAACG
17158399 GAAGC
1 GAAGC
17158404 CCGAAGGCTA
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
18 8 0.23
19 7 0.20
20 7 0.20
21 13 0.37
ACGTcount: A:0.42, C:0.22, G:0.26, T:0.11
Consensus pattern (21 bp):
GAAGCACAAAAGTGCTAAACG
Found at i:17158380 original size:39 final size:39
Alignment explanation
Indices: 17158333--17158421 Score: 169
Period size: 39 Copynumber: 2.3 Consensus size: 39
17158323 AAACCGAAAT
17158333 CTAACTGAAGCACAAAAGTGCTAAACGGAAGCCCGAAGG
1 CTAACTGAAGCACAAAAGTGCTAAACGGAAGCCCGAAGG
*
17158372 CTAACTGAAGCACATAAGTGCTAAACGGAAGCCCGAAGG
1 CTAACTGAAGCACAAAAGTGCTAAACGGAAGCCCGAAGG
17158411 CTAACTGAAGC
1 CTAACTGAAGC
17158422 TCATCAGAGC
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 49 1.00
ACGTcount: A:0.39, C:0.24, G:0.25, T:0.12
Consensus pattern (39 bp):
CTAACTGAAGCACAAAAGTGCTAAACGGAAGCCCGAAGG
Found at i:17161922 original size:21 final size:21
Alignment explanation
Indices: 17161898--17161938 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
17161888 ACGTGACAAG
* *
17161898 TTAACTGGCCACGTTAGCTAA
1 TTAACTAGCCACGTCAGCTAA
*
17161919 TTAACTAGCCATGTCAGCTA
1 TTAACTAGCCACGTCAGCTA
17161939 TTCCGTTAAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.29
Consensus pattern (21 bp):
TTAACTAGCCACGTCAGCTAA
Found at i:17162620 original size:12 final size:12
Alignment explanation
Indices: 17162603--17162635 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
17162593 CCGACCTTCC
17162603 ATATTAATTTTT
1 ATATTAATTTTT
17162615 ATATT-ATTTTT
1 ATATTAATTTTT
17162626 ATA-TAATTTT
1 ATATTAATTTT
17162636 AAAATATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 14 0.70
12 5 0.25
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:17162898 original size:22 final size:22
Alignment explanation
Indices: 17162850--17162898 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
17162840 ATATCCAAAC
*
17162850 AATAACAACAAAATAGTAGCAA
1 AATAACAACAAAATAGTAACAA
* * * *
17162872 CATAATAATAAAATGGTAACAA
1 AATAACAACAAAATAGTAACAA
17162894 AATAA
1 AATAA
17162899 GGAGAAAACA
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.63, C:0.10, G:0.08, T:0.18
Consensus pattern (22 bp):
AATAACAACAAAATAGTAACAA
Found at i:17169555 original size:29 final size:28
Alignment explanation
Indices: 17169518--17169572 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
17169508 AGTGGTATAC
17169518 TTTTTAAATAATTTGAATAATTTTTAAT
1 TTTTTAAATAATTTGAATAATTTTTAAT
* **
17169546 TTTTTAAAATATTTTTTATAATTTTTA
1 TTTTT-AAATAATTTGAATAATTTTTA
17169573 TTGAAATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 5 0.22
29 18 0.78
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (28 bp):
TTTTTAAATAATTTGAATAATTTTTAAT
Found at i:17180909 original size:4 final size:4
Alignment explanation
Indices: 17180900--17180926 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
17180890 CATTTGGTCC
17180900 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
17180927 TTACAATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:17181276 original size:3 final size:3
Alignment explanation
Indices: 17181268--17181306 Score: 53
Period size: 3 Copynumber: 12.7 Consensus size: 3
17181258 ATTTAGGCCT
17181268 TTA TTA TTA TTA TTA TTA TT- TTCA TCTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TT-A T-TA TTA TTA TTA TT
17181307 TATTTATTCA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
2 2 0.06
3 27 0.82
4 3 0.09
5 1 0.03
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:17181303 original size:25 final size:25
Alignment explanation
Indices: 17181269--17181322 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
17181259 TTTAGGCCTT
*
17181269 TATTATTATTA-TTATTATTTTCATC
1 TATTATTATTATTTATT-TATTCATC
17181294 TATTATTATTATTTATTTATTCATC
1 TATTATTATTATTTATTTATTCATC
17181319 TATT
1 TATT
17181323 TGTTTATCAC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 22 0.81
26 5 0.19
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.65
Consensus pattern (25 bp):
TATTATTATTATTTATTTATTCATC
Found at i:17181642 original size:11 final size:11
Alignment explanation
Indices: 17181626--17181650 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
17181616 TATGACTATT
17181626 ATAGTACATTA
1 ATAGTACATTA
17181637 ATAGTACATTA
1 ATAGTACATTA
17181648 ATA
1 ATA
17181651 CTATCATAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.48, C:0.08, G:0.08, T:0.36
Consensus pattern (11 bp):
ATAGTACATTA
Found at i:17182125 original size:12 final size:12
Alignment explanation
Indices: 17182108--17182133 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
17182098 AGGGGTCGTA
17182108 TTTTAATTTTTT
1 TTTTAATTTTTT
17182120 TTTTAATTTTTT
1 TTTTAATTTTTT
17182132 TT
1 TT
17182134 AATTTTCGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTTAATTTTTT
Found at i:17184405 original size:26 final size:26
Alignment explanation
Indices: 17184347--17184399 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
17184337 TAAATAATGC
**
17184347 TTAATTAAAATTTAAGTTTTTATACA
1 TTAATTAAAATTTAAGTTTAAATACA
17184373 TTAATTAAAATTTAA-TTTAAATTACA
1 TTAATTAAAATTTAAGTTTAAA-TACA
17184399 T
1 T
17184400 ATATTACAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 4 0.17
26 20 0.83
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (26 bp):
TTAATTAAAATTTAAGTTTAAATACA
Found at i:17184892 original size:15 final size:15
Alignment explanation
Indices: 17184872--17184937 Score: 55
Period size: 14 Copynumber: 4.3 Consensus size: 15
17184862 ACTACAAAAC
17184872 ATTTATTATTAATAT
1 ATTTATTATTAATAT
*
17184887 ATTTATAATTGTAATAAAT
1 ATTTATTA-T-TAAT--AT
*
17184906 ATTTATTATTAAAAT
1 ATTTATTATTAATAT
*
17184921 A-TTAATATTAA-AT
1 ATTTATTATTAATAT
17184934 ATTT
1 ATTT
17184938 TCAACAATAT
Statistics
Matches: 42, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
13 3 0.07
14 11 0.26
15 10 0.24
16 1 0.02
17 7 0.17
18 1 0.02
19 9 0.21
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (15 bp):
ATTTATTATTAATAT
Found at i:17192825 original size:20 final size:18
Alignment explanation
Indices: 17192775--17192826 Score: 54
Period size: 20 Copynumber: 2.8 Consensus size: 18
17192765 TATTAAGATA
17192775 AATAGTAAATTAA-ATTT
1 AATAGTAAATTAATATTT
*
17192792 AATATTAAGA-TAATCACTTT
1 AATAGTAA-ATTAAT-A-TTT
17192812 AATAGTAAATTAATA
1 AATAGTAAATTAATA
17192827 AAATACAATC
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
17 10 0.36
18 1 0.04
19 3 0.11
20 14 0.50
ACGTcount: A:0.52, C:0.04, G:0.06, T:0.38
Consensus pattern (18 bp):
AATAGTAAATTAATATTT
Found at i:17198466 original size:25 final size:25
Alignment explanation
Indices: 17198438--17198502 Score: 103
Period size: 25 Copynumber: 2.6 Consensus size: 25
17198428 CACACCACAA
17198438 CTCGCATGAGCTTCCCGTTATTCAG
1 CTCGCATGAGCTTCCCGTTATTCAG
* *
17198463 CTCGCATGAACTTCCCGTTATTTAG
1 CTCGCATGAGCTTCCCGTTATTCAG
*
17198488 CTCACATGAGCTTCC
1 CTCGCATGAGCTTCC
17198503 TATTTACAGC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.18, C:0.32, G:0.17, T:0.32
Consensus pattern (25 bp):
CTCGCATGAGCTTCCCGTTATTCAG
Found at i:17201985 original size:16 final size:14
Alignment explanation
Indices: 17201961--17201997 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 14
17201951 AAAACAAGAA
17201961 AAAGAAATAGAGAAG
1 AAAGAAATAGA-AAG
17201976 AAACGAAATAGAAAG
1 AAA-GAAATAGAAAG
17201991 AAAGAAA
1 AAAGAAA
17201998 GAAGAAAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 4 0.19
15 9 0.43
16 8 0.38
ACGTcount: A:0.70, C:0.03, G:0.22, T:0.05
Consensus pattern (14 bp):
AAAGAAATAGAAAG
Found at i:17202023 original size:26 final size:26
Alignment explanation
Indices: 17201961--17202013 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
17201951 AAAACAAGAA
* * *
17201961 AAAGAAATAGAGAAGAAACGAAATAG
1 AAAGAAAGAAAGAAGAAAAGAAATAG
17201987 AAAGAAAGAAAGAAGAAAAGAAA-AG
1 AAAGAAAGAAAGAAGAAAAGAAATAG
17202012 AA
1 AA
17202014 GAAGGAGAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
25 4 0.17
26 20 0.83
ACGTcount: A:0.72, C:0.02, G:0.23, T:0.04
Consensus pattern (26 bp):
AAAGAAAGAAAGAAGAAAAGAAATAG
Found at i:17204046 original size:87 final size:87
Alignment explanation
Indices: 17203900--17204072 Score: 319
Period size: 87 Copynumber: 2.0 Consensus size: 87
17203890 AGCCTGCTAT
*
17203900 GTTTAAACCCCGAATTCAATCACTAACACAAAGCCTACGAGACTTTAAGCCCAGATATAGTACCA
1 GTTTAAACCCCGAATTCAATCACCAACACAAAGCCTACGAGACTTTAAGCCCAGATATAGTACCA
17203965 GTACGAAGCCTGCGGACCTTAG
66 GTACGAAGCCTGCGGACCTTAG
*
17203987 GTTTAAACCCCGAATTCAATCACCAACACAAAGCCTACGGGACTTTAAGCCCAGATATAGTACCA
1 GTTTAAACCCCGAATTCAATCACCAACACAAAGCCTACGAGACTTTAAGCCCAGATATAGTACCA
*
17204052 GTACGAAGCCTGTGGACCTTA
66 GTACGAAGCCTGCGGACCTTA
17204073 AGTCCGGATA
Statistics
Matches: 83, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
87 83 1.00
ACGTcount: A:0.34, C:0.28, G:0.17, T:0.21
Consensus pattern (87 bp):
GTTTAAACCCCGAATTCAATCACCAACACAAAGCCTACGAGACTTTAAGCCCAGATATAGTACCA
GTACGAAGCCTGCGGACCTTAG
Found at i:17204074 original size:39 final size:39
Alignment explanation
Indices: 17204008--17204202 Score: 201
Period size: 39 Copynumber: 4.9 Consensus size: 39
17203998 GAATTCAATC
* * * * * * *
17204008 ACCAACACAAAGCCTACGGGACTTTAAGCCCAGATATAGT
1 ACCAGCACGAAGCCTGC-GGACCTTAAGTCCGGATATAAT
* * *
17204048 ACCAGTACGAAGCCTGTGGACCTTAAGTCCGGATATAGT
1 ACCAGCACGAAGCCTGCGGACCTTAAGTCCGGATATAAT
* *
17204087 ACCAGCACGAAGCCTGCGGATCTTAAGTCCGGATACAAT
1 ACCAGCACGAAGCCTGCGGACCTTAAGTCCGGATATAAT
* * * * *
17204126 TCCAGCACGAAGCCTGCGAGTCTTTAAGCCCGGATACAAT
1 ACCAGCACGAAGCCTGCG-GACCTTAAGTCCGGATATAAT
* *
17204166 TCCAGCATGAAGCCTGCGGACCTTAAGTCCGGATATA
1 ACCAGCACGAAGCCTGCGGACCTTAAGTCCGGATATA
17204203 CATCAAATAT
Statistics
Matches: 131, Mismatches: 23, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
39 85 0.65
40 46 0.35
ACGTcount: A:0.30, C:0.27, G:0.23, T:0.20
Consensus pattern (39 bp):
ACCAGCACGAAGCCTGCGGACCTTAAGTCCGGATATAAT
Found at i:17204769 original size:48 final size:48
Alignment explanation
Indices: 17204717--17205045 Score: 541
Period size: 48 Copynumber: 6.9 Consensus size: 48
17204707 CCATGTTAAC
* ** * * * * * * *
17204717 CCGCACACATAGTGCCTTAGTAATTCACATACATATTGACATTCCAAT
1 CCGCACACATAGTGCCATACAAATCCGCACACATAGTGCCATACAAAT
17204765 CCGCACACATAGTGCCATACAAATCCGCACACATAGTGCCATACAAAT
1 CCGCACACATAGTGCCATACAAATCCGCACACATAGTGCCATACAAAT
17204813 CCGCACACATAGTGCCATACAAATCCGCACACATAGTGCCATACAAAT
1 CCGCACACATAGTGCCATACAAATCCGCACACATAGTGCCATACAAAT
17204861 CCGCACACATAGTGCCATACAAATCCGCACACATAGTGCCATACAAAT
1 CCGCACACATAGTGCCATACAAATCCGCACACATAGTGCCATACAAAT
17204909 CCGCACACATAGTGCCATACAAATCCGCACACATAGTGCCATACAAAT
1 CCGCACACATAGTGCCATACAAATCCGCACACATAGTGCCATACAAAT
17204957 CCGCACACATAGTGCCATACAAATCCGCACACATAGTGCCATACAAAT
1 CCGCACACATAGTGCCATACAAATCCGCACACATAGTGCCATACAAAT
* * *
17205005 TCGCACACATAGTGCCATTCAAATTCGCACACATAGTGCCA
1 CCGCACACATAGTGCCATACAAATCCGCACACATAGTGCCA
17205046 AAATCATTTC
Statistics
Matches: 268, Mismatches: 13, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
48 268 1.00
ACGTcount: A:0.36, C:0.32, G:0.12, T:0.19
Consensus pattern (48 bp):
CCGCACACATAGTGCCATACAAATCCGCACACATAGTGCCATACAAAT
Found at i:17204774 original size:24 final size:24
Alignment explanation
Indices: 17204762--17205045 Score: 541
Period size: 24 Copynumber: 11.8 Consensus size: 24
17204752 TTGACATTCC
17204762 AATCCGCACACATAGTGCCATACA
1 AATCCGCACACATAGTGCCATACA
17204786 AATCCGCACACATAGTGCCATACA
1 AATCCGCACACATAGTGCCATACA
17204810 AATCCGCACACATAGTGCCATACA
1 AATCCGCACACATAGTGCCATACA
17204834 AATCCGCACACATAGTGCCATACA
1 AATCCGCACACATAGTGCCATACA
17204858 AATCCGCACACATAGTGCCATACA
1 AATCCGCACACATAGTGCCATACA
17204882 AATCCGCACACATAGTGCCATACA
1 AATCCGCACACATAGTGCCATACA
17204906 AATCCGCACACATAGTGCCATACA
1 AATCCGCACACATAGTGCCATACA
17204930 AATCCGCACACATAGTGCCATACA
1 AATCCGCACACATAGTGCCATACA
17204954 AATCCGCACACATAGTGCCATACA
1 AATCCGCACACATAGTGCCATACA
17204978 AATCCGCACACATAGTGCCATACA
1 AATCCGCACACATAGTGCCATACA
* *
17205002 AATTCGCACACATAGTGCCATTCA
1 AATCCGCACACATAGTGCCATACA
*
17205026 AATTCGCACACATAGTGCCA
1 AATCCGCACACATAGTGCCA
17205046 AAATCATTTC
Statistics
Matches: 258, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
24 258 1.00
ACGTcount: A:0.37, C:0.33, G:0.13, T:0.18
Consensus pattern (24 bp):
AATCCGCACACATAGTGCCATACA
Found at i:17204823 original size:72 final size:72
Alignment explanation
Indices: 17204717--17205045 Score: 541
Period size: 72 Copynumber: 4.6 Consensus size: 72
17204707 CCATGTTAAC
* ** * * * * * * *
17204717 CCGCACACATAGTGCCTTAGTAATTCACATACATATTGACATTCCAATCCGCACACATAGTGCCA
1 CCGCACACATAGTGCCATACAAATCCGCACACATAGTGCCATACAAATCCGCACACATAGTGCCA
17204782 TACAAAT
66 TACAAAT
17204789 CCGCACACATAGTGCCATACAAATCCGCACACATAGTGCCATACAAATCCGCACACATAGTGCCA
1 CCGCACACATAGTGCCATACAAATCCGCACACATAGTGCCATACAAATCCGCACACATAGTGCCA
17204854 TACAAAT
66 TACAAAT
17204861 CCGCACACATAGTGCCATACAAATCCGCACACATAGTGCCATACAAATCCGCACACATAGTGCCA
1 CCGCACACATAGTGCCATACAAATCCGCACACATAGTGCCATACAAATCCGCACACATAGTGCCA
17204926 TACAAAT
66 TACAAAT
17204933 CCGCACACATAGTGCCATACAAATCCGCACACATAGTGCCATACAAATCCGCACACATAGTGCCA
1 CCGCACACATAGTGCCATACAAATCCGCACACATAGTGCCATACAAATCCGCACACATAGTGCCA
17204998 TACAAAT
66 TACAAAT
* * *
17205005 TCGCACACATAGTGCCATTCAAATTCGCACACATAGTGCCA
1 CCGCACACATAGTGCCATACAAATCCGCACACATAGTGCCA
17205046 AAATCATTTC
Statistics
Matches: 244, Mismatches: 13, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
72 244 1.00
ACGTcount: A:0.36, C:0.32, G:0.12, T:0.19
Consensus pattern (72 bp):
CCGCACACATAGTGCCATACAAATCCGCACACATAGTGCCATACAAATCCGCACACATAGTGCCA
TACAAAT
Found at i:17205541 original size:17 final size:17
Alignment explanation
Indices: 17205519--17205552 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
17205509 CCCCACTTAA
*
17205519 TATATTATAACTTATTT
1 TATATTATAACATATTT
17205536 TATATTATAACATATTT
1 TATATTATAACATATTT
17205553 CAATTATATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (17 bp):
TATATTATAACATATTT
Found at i:17210901 original size:17 final size:17
Alignment explanation
Indices: 17210879--17210912 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
17210869 CCCCACTTAA
*
17210879 TATATTATAACTTATTT
1 TATATTATAACATATTT
17210896 TATATTATAACATATTT
1 TATATTATAACATATTT
17210913 CAATTATATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (17 bp):
TATATTATAACATATTT
Found at i:17217230 original size:25 final size:25
Alignment explanation
Indices: 17217193--17217260 Score: 91
Period size: 25 Copynumber: 2.7 Consensus size: 25
17217183 GGACACACCA
17217193 CAACTCGTATGAGCTTCCAGTTATT
1 CAACTCGTATGAGCTTCCAGTTATT
* * * *
17217218 GAGCTCGCATGAGCTTCCTGTTATT
1 CAACTCGTATGAGCTTCCAGTTATT
*
17217243 CAACTCATATGAGCTTCC
1 CAACTCGTATGAGCTTCC
17217261 CATTTACAGC
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.22, C:0.26, G:0.18, T:0.34
Consensus pattern (25 bp):
CAACTCGTATGAGCTTCCAGTTATT
Found at i:17221561 original size:10 final size:10
Alignment explanation
Indices: 17221533--17221572 Score: 53
Period size: 10 Copynumber: 3.8 Consensus size: 10
17221523 TCAATTTAAT
17221533 TAAATAAATTA
1 TAAA-AAATTA
17221544 TAAAAAAATTA
1 T-AAAAAATTA
17221555 TAAAAAATTA
1 TAAAAAATTA
*
17221565 TTAAAAAT
1 TAAAAAAT
17221573 AGAGAAAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
10 16 0.59
11 8 0.30
12 3 0.11
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (10 bp):
TAAAAAATTA
Found at i:17222433 original size:31 final size:29
Alignment explanation
Indices: 17222406--17222484 Score: 95
Period size: 31 Copynumber: 2.6 Consensus size: 29
17222396 ATTTTTTAAA
*
17222406 AATTTTAAAATATTAAAAATATGTTTTTTAT
1 AATTTTAAAAT-TTAAAAATAT-CTTTTTAT
* *
17222437 AATTTTAATGATTTTAAAATATCTTTTTAT
1 AATTTTAA-AATTTAAAAATATCTTTTTAT
*
17222467 AATTTTTAAATTTAAAAA
1 AATTTTAAAATTTAAAAA
17222485 ATTAATTAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
29 8 0.20
30 14 0.34
31 17 0.41
32 2 0.05
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.52
Consensus pattern (29 bp):
AATTTTAAAATTTAAAAATATCTTTTTAT
Found at i:17226558 original size:20 final size:20
Alignment explanation
Indices: 17226521--17226559 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
17226511 TAAATTGGAA
*
17226521 TGAAATTGTGATATTGAATG
1 TGAAATTATGATATTGAATG
17226541 TGAAATTAT-ATATATGAAT
1 TGAAATTATGATAT-TGAAT
17226560 TGGATTGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.41, C:0.00, G:0.18, T:0.41
Consensus pattern (20 bp):
TGAAATTATGATATTGAATG
Found at i:17229742 original size:14 final size:14
Alignment explanation
Indices: 17229723--17229755 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
17229713 ACGAAGTTGG
*
17229723 TGATTTCTTTTTGT
1 TGATTTCCTTTTGT
17229737 TGATTTCCTTTTGT
1 TGATTTCCTTTTGT
17229751 TGATT
1 TGATT
17229756 AAATGACATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.09, C:0.09, G:0.15, T:0.67
Consensus pattern (14 bp):
TGATTTCCTTTTGT
Found at i:17234214 original size:16 final size:16
Alignment explanation
Indices: 17234193--17234231 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
17234183 TATGAATGTT
*
17234193 TTTGAATGATTTTTGA
1 TTTGAATGATATTTGA
*
17234209 TTTGAATGGTATTTGA
1 TTTGAATGATATTTGA
17234225 TTATGAA
1 TT-TGAA
17234232 ATGTTTGATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 16 0.80
17 4 0.20
ACGTcount: A:0.28, C:0.00, G:0.21, T:0.51
Consensus pattern (16 bp):
TTTGAATGATATTTGA
Found at i:17235331 original size:13 final size:13
Alignment explanation
Indices: 17235283--17235334 Score: 50
Period size: 13 Copynumber: 3.7 Consensus size: 13
17235273 CTTAGGACAT
*
17235283 GGCCGTGTGGCCA
1 GGCCGTGGGGCCA
*
17235296 GCCCGTGGGGTTCCCA
1 GGCCGTGGGG---CCA
17235312 TGGCCGTGGGGCCA
1 -GGCCGTGGGGCCA
17235326 GGCCGTGGG
1 GGCCGTGGG
17235335 CAGATCTGAC
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
13 17 0.53
14 3 0.09
16 3 0.09
17 9 0.28
ACGTcount: A:0.06, C:0.31, G:0.48, T:0.15
Consensus pattern (13 bp):
GGCCGTGGGGCCA
Found at i:17237071 original size:16 final size:15
Alignment explanation
Indices: 17237039--17237073 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
17237029 AAACCCTATT
17237039 TTTCCTTTATTTTTC
1 TTTCCTTTATTTTTC
*
17237054 TTTCCTTTTTTCTTTC
1 TTTCCTTTATT-TTTC
17237070 TTTC
1 TTTC
17237074 TTTCCTTGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.03, C:0.23, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTCCTTTATTTTTC
Found at i:17237163 original size:8 final size:8
Alignment explanation
Indices: 17237114--17237176 Score: 56
Period size: 8 Copynumber: 7.9 Consensus size: 8
17237104 TCCTTGTTCT
*
17237114 TTATTATT
1 TTATTATA
17237122 TTATTAT-
1 TTATTATA
* *
17237129 TTCTTTTA
1 TTATTATA
17237137 TTATTATA
1 TTATTATA
**
17237145 ACATATATA
1 TTAT-TATA
17237154 TTATTATA
1 TTATTATA
*
17237162 TTATTAAA
1 TTATTATA
17237170 TTATTAT
1 TTATTAT
17237177 TATTTACTTA
Statistics
Matches: 43, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
7 5 0.12
8 32 0.74
9 6 0.14
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (8 bp):
TTATTATA
Found at i:17243935 original size:6 final size:6
Alignment explanation
Indices: 17243919--17243971 Score: 81
Period size: 6 Copynumber: 9.0 Consensus size: 6
17243909 ATGGAATTTT
* *
17243919 AAAT-A AAATAG AAATAG AAATAA AAATAA AAATAA AAATAA AAATAA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA
17243966 AAATAA
1 AAATAA
17243972 TAGTAAAATA
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
5 4 0.09
6 41 0.91
ACGTcount: A:0.79, C:0.00, G:0.04, T:0.17
Consensus pattern (6 bp):
AAATAA
Found at i:17245834 original size:6 final size:6
Alignment explanation
Indices: 17245823--17245849 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
17245813 TAAGATACAC
17245823 AGAGGA AGAGGA AGAGGA AGAGGA AGA
1 AGAGGA AGAGGA AGAGGA AGAGGA AGA
17245850 CATTCACACC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (6 bp):
AGAGGA
Found at i:17286369 original size:31 final size:31
Alignment explanation
Indices: 17286334--17286396 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
17286324 TGTCAAAGGT
17286334 TAGGAAACTTAAGCTAGAAAAATGAAATGCC
1 TAGGAAACTTAAGCTAGAAAAATGAAATGCC
17286365 TAGGAAACTTAAGCTAGAAAAATGAAATGCC
1 TAGGAAACTTAAGCTAGAAAAATGAAATGCC
17286396 T
1 T
17286397 CTAACCCCTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.48, C:0.13, G:0.19, T:0.21
Consensus pattern (31 bp):
TAGGAAACTTAAGCTAGAAAAATGAAATGCC
Found at i:17286489 original size:19 final size:19
Alignment explanation
Indices: 17286465--17286504 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
17286455 CTTTTGTCTC
*
17286465 ATCATACGATAACGTTTAA
1 ATCATACGATAACATTTAA
17286484 ATCATACGATAACATTTAA
1 ATCATACGATAACATTTAA
17286503 AT
1 AT
17286505 TTTAGTTGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.33
Consensus pattern (19 bp):
ATCATACGATAACATTTAA
Found at i:17288046 original size:6 final size:7
Alignment explanation
Indices: 17288029--17288059 Score: 53
Period size: 7 Copynumber: 4.3 Consensus size: 7
17288019 TACTTTAGCC
17288029 TTTTTTA
1 TTTTTTA
17288036 TTTTTTA
1 TTTTTTA
17288043 TTTTTTTA
1 -TTTTTTA
17288051 TTTTTTA
1 TTTTTTA
17288058 TT
1 TT
17288060 ACATTTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 16 0.70
8 7 0.30
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (7 bp):
TTTTTTA
Found at i:17288049 original size:15 final size:15
Alignment explanation
Indices: 17288029--17288059 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
17288019 TACTTTAGCC
17288029 TTTTTTATTTTTTAT
1 TTTTTTATTTTTTAT
17288044 TTTTTTATTTTTTAT
1 TTTTTTATTTTTTAT
17288059 T
1 T
17288060 ACATTTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (15 bp):
TTTTTTATTTTTTAT
Found at i:17295912 original size:15 final size:16
Alignment explanation
Indices: 17295880--17295912 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
17295870 TCAAACACAC
*
17295880 TCCTTTTTTTTTCCTT
1 TCCTTTTTTTTTCATT
17295896 TCCTTTTTTTTT-ATT
1 TCCTTTTTTTTTCATT
17295911 TC
1 TC
17295913 TTTCCCCCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.76
Consensus pattern (16 bp):
TCCTTTTTTTTTCATT
Found at i:17296960 original size:55 final size:56
Alignment explanation
Indices: 17296875--17297027 Score: 229
Period size: 55 Copynumber: 2.8 Consensus size: 56
17296865 CATGAGATTG
17296875 GCACTAAGTGTGCGGGTTTAAATTGCATAGCACTAAGTGTGCAAGTTTGATTAT-A
1 GCACTAAGTGTGCGGGTTTAAATTGCATAGCACTAAGTGTGCAAGTTTGATTATAA
*
17296930 TCACTAAGTGTGCGGGTTTAAATTGCATAGCACTAAGTGTGCAAGTTTGATTATAAA
1 GCACTAAGTGTGCGGGTTTAAATTGCATAGCACTAAGTGTGCAAGTTTGATTAT-AA
* * ** *
17296987 GCACTAAGTGTGCGAGTTT-GATTATATAACACTAAGTGTGC
1 GCACTAAGTGTGCGGGTTTAAATTGCATAGCACTAAGTGTGC
17297028 GGACTTACTA
Statistics
Matches: 89, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
55 53 0.60
56 18 0.20
57 18 0.20
ACGTcount: A:0.30, C:0.13, G:0.24, T:0.33
Consensus pattern (56 bp):
GCACTAAGTGTGCGGGTTTAAATTGCATAGCACTAAGTGTGCAAGTTTGATTATAA
Found at i:17297028 original size:28 final size:28
Alignment explanation
Indices: 17296876--17297028 Score: 150
Period size: 28 Copynumber: 5.5 Consensus size: 28
17296866 ATGAGATTGG
* * ** *
17296876 CACTAAGTGTGCGGGTTTAAATTGCATAG
1 CACTAAGTGTGCGAGTTT-GATTATATAA
*
17296905 CACTAAGTGTGCAAGTTTGATTATAT--
1 CACTAAGTGTGCGAGTTTGATTATATAA
* * ** *
17296931 CACTAAGTGTGCGGGTTTAAATTGCATAG
1 CACTAAGTGTGCGAGTTT-GATTATATAA
*
17296960 CACTAAGTGTGCAAGTTTGATTATA-AA
1 CACTAAGTGTGCGAGTTTGATTATATAA
17296987 GCACTAAGTGTGCGAGTTTGATTATATAA
1 -CACTAAGTGTGCGAGTTTGATTATATAA
17297016 CACTAAGTGTGCG
1 CACTAAGTGTGCG
17297029 GACTTACTAT
Statistics
Matches: 102, Mismatches: 17, Indels: 11
0.78 0.13 0.08
Matches are distributed among these distances:
26 16 0.16
27 6 0.06
28 46 0.45
29 34 0.33
ACGTcount: A:0.30, C:0.13, G:0.24, T:0.33
Consensus pattern (28 bp):
CACTAAGTGTGCGAGTTTGATTATATAA
Found at i:17300582 original size:4 final size:4
Alignment explanation
Indices: 17300573--17300619 Score: 67
Period size: 4 Copynumber: 11.2 Consensus size: 4
17300563 TTTCTTGTAC
*
17300573 ATAA ATAA ATAA ATAA ATAAA ATTAA AAAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA AT-AA A-TAA ATAA ATAA ATAA ATAA ATAA A
17300620 GGATCAAGTT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
4 32 0.82
5 6 0.15
6 1 0.03
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
ATAA
Found at i:17300599 original size:22 final size:22
Alignment explanation
Indices: 17300574--17300615 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
17300564 TTCTTGTACA
*
17300574 TAAATAAATAAATAAATAAAAT
1 TAAAAAAATAAATAAATAAAAT
17300596 TAAAAAAATAAATAAATAAA
1 TAAAAAAATAAATAAATAAA
17300616 TAAAGGATCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (22 bp):
TAAAAAAATAAATAAATAAAAT
Found at i:17301190 original size:6 final size:6
Alignment explanation
Indices: 17301157--17301183 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
17301147 AGGTTATAAG
17301157 TTTATT TTTATT TTTATT TTTATT TTT
1 TTTATT TTTATT TTTATT TTTATT TTT
17301184 TGTTTTTCCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTATT
Found at i:17325740 original size:18 final size:19
Alignment explanation
Indices: 17325705--17325740 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
17325695 TTTCAAACCA
*
17325705 CCAATATCAAAAAGCATAT
1 CCAACATCAAAAAGCATAT
17325724 CCAACATCAAAAA-CATA
1 CCAACATCAAAAAGCATA
17325741 GAGATTTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (19 bp):
CCAACATCAAAAAGCATAT
Found at i:17326554 original size:14 final size:14
Alignment explanation
Indices: 17326535--17326561 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
17326525 AATATAATTA
17326535 TTACTATTATTATT
1 TTACTATTATTATT
17326549 TTACTATTATTAT
1 TTACTATTATTAT
17326562 CTAATATGTT
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:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (14 bp):
TTACTATTATTATT
Found at i:17326633 original size:3 final size:3
Alignment explanation
Indices: 17326619--17326876 Score: 92
Period size: 3 Copynumber: 85.3 Consensus size: 3
17326609 TTAACGTGTC
* * * ** *
17326619 ATT ATT ACT ATT ATT TTT ATT TTT ATT ACC ATT ATT ATT ATC A-T ACTT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT
* * * *
17326667 -GT ATT -TAT ATT -TT TTT ATT -TT AAT ATT ATT ATT ATT ACT ACTT
1 ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT
* *
17326710 CCATT ATT -TT -TT ATT -TCT AACT ATT ATT ATT TTT ATGT ATAT ATT
1 --ATT ATT ATT ATT ATT AT-T -ATT ATT ATT ATT ATT AT-T AT-T ATT
* * * *
17326755 ATT AATT A-T ATT ATT GTT ATT ATT ACT ATT ATT AAAT ATT CTT ATT
1 ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT
* * * * *
17326801 ATT ACT ATT ATT -TT CATT CCTT -TT ATT ATT GTTT ATT ATC ATT -GT
1 ATT ATT ATT ATT ATT -ATT -ATT ATT ATT ATT -ATT ATT ATT ATT ATT
*
17326846 ATT ATT ATT ATT ACTT -CT ATT ATT ATT ATT A
1 ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT A
17326877 CTTTCTTTGT
Statistics
Matches: 187, Mismatches: 43, Indels: 50
0.67 0.15 0.18
Matches are distributed among these distances:
2 20 0.11
3 140 0.75
4 24 0.13
5 2 0.01
6 1 0.01
ACGTcount: A:0.29, C:0.08, G:0.02, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:17331132 original size:2 final size:2
Alignment explanation
Indices: 17331127--17331155 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
17331117 TTCTCTCTTT
17331127 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
17331156 ATACTTAATA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:17331420 original size:5 final size:5
Alignment explanation
Indices: 17331410--17331436 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
17331400 ATAAATATTC
17331410 TTCTT TTCTT TTCTT TTCTT TTCTT TT
1 TTCTT TTCTT TTCTT TTCTT TTCTT TT
17331437 TTTAAAGTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTCTT
Found at i:17336068 original size:17 final size:18
Alignment explanation
Indices: 17336029--17336069 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
17336019 TTTCAAATAT
* *
17336029 GATTGTTTTTTCGTGTAC
1 GATTGTTTTTTCATGCAC
17336047 GATTGTTTTTTCATGCAC
1 GATTGTTTTTTCATGCAC
17336065 -ATTGT
1 GATTGT
17336070 GCGTATGATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.15, C:0.12, G:0.20, T:0.54
Consensus pattern (18 bp):
GATTGTTTTTTCATGCAC
Found at i:17337883 original size:24 final size:26
Alignment explanation
Indices: 17337847--17337909 Score: 69
Period size: 25 Copynumber: 2.5 Consensus size: 26
17337837 ATATACTTTT
17337847 TATTAT-ATATTTTATTATA-TAAATA
1 TATTATAAT-TTTTATTATATTAAATA
* *
17337872 TATT-TAATTTTTTTTATATTATATA
1 TATTATAATTTTTATTATATTAAATA
17337897 TATTAATAATTTT
1 TATT-ATAATTTT
17337910 ACCATATTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
24 10 0.31
25 15 0.47
27 7 0.22
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (26 bp):
TATTATAATTTTTATTATATTAAATA
Found at i:17337906 original size:27 final size:24
Alignment explanation
Indices: 17337856--17337909 Score: 63
Period size: 24 Copynumber: 2.1 Consensus size: 24
17337846 TTATTATATA
17337856 TTTTATTATATAAATATATTTAAT
1 TTTTATTATATAAATATATTTAAT
* *
17337880 TTTTTTTATATTATATATATTAATAAT
1 TTTTATTATA-TAAATATATT--TAAT
17337907 TTT
1 TTT
17337910 ACCATATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 9 0.36
25 9 0.36
27 7 0.28
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (24 bp):
TTTTATTATATAAATATATTTAAT
Found at i:17337950 original size:11 final size:11
Alignment explanation
Indices: 17337934--17337990 Score: 50
Period size: 11 Copynumber: 5.4 Consensus size: 11
17337924 TGCAAAATAC
17337934 TTATTATATTA
1 TTATTATATTA
*
17337945 TTATTATTTTA
1 TTATTATATTA
17337956 -TATTATATT-
1 TTATTATATTA
17337965 TCT-TTATATT-
1 T-TATTATATTA
*
17337975 TTAGTCATATTA
1 TTA-TTATATTA
17337987 TTAT
1 TTAT
17337991 ACATAACTTA
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
9 1 0.03
10 16 0.42
11 18 0.47
12 3 0.08
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.65
Consensus pattern (11 bp):
TTATTATATTA
Found at i:17337958 original size:16 final size:15
Alignment explanation
Indices: 17337937--17337974 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
17337927 AAAATACTTA
17337937 TTATATTATTATTAT-T
1 TTATATTA-TATT-TCT
17337953 TTATATTATATTTCT
1 TTATATTATATTTCT
17337968 TTATATT
1 TTATATT
17337975 TTAGTCATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 1 0.05
15 12 0.57
16 8 0.38
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (15 bp):
TTATATTATATTTCT
Found at i:17338186 original size:3 final size:3
Alignment explanation
Indices: 17338178--17338285 Score: 216
Period size: 3 Copynumber: 36.0 Consensus size: 3
17338168 ATGTTACTAC
17338178 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
17338226 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
17338274 ATT ATT ATT ATT
1 ATT ATT ATT ATT
17338286 TTGTATATAT
Statistics
Matches: 105, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 105 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:17338378 original size:18 final size:17
Alignment explanation
Indices: 17338355--17338396 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
17338345 TTGTATGTTC
*
17338355 GTATATTTTATATACTAT
1 GTATATTTAATATA-TAT
17338373 GTATATCTTAATATATAT
1 GTATAT-TTAATATATAT
17338391 GT-TATT
1 GTATATT
17338397 ATATTTGCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 1 0.05
17 3 0.14
18 11 0.50
19 7 0.32
ACGTcount: A:0.33, C:0.05, G:0.07, T:0.55
Consensus pattern (17 bp):
GTATATTTAATATATAT
Found at i:17342438 original size:22 final size:23
Alignment explanation
Indices: 17342402--17342445 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
17342392 TATTTAAAAT
*
17342402 TTTTTTAATACTTTTTAATTTTA
1 TTTTTTAATAATTTTTAATTTTA
17342425 TTTTTT-ATAATTTTTAATTTT
1 TTTTTTAATAATTTTTAATTTT
17342446 TTAAAATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (23 bp):
TTTTTTAATAATTTTTAATTTTA
Found at i:17342446 original size:17 final size:17
Alignment explanation
Indices: 17342403--17342461 Score: 61
Period size: 17 Copynumber: 3.6 Consensus size: 17
17342393 ATTTAAAATT
*
17342403 TTTTTAATACTTTT-TAA
1 TTTTTAAT-TTTTTATAA
17342420 -TTTT-ATTTTTTATAA
1 TTTTTAATTTTTTATAA
*
17342435 TTTTTAATTTTTTAAAA
1 TTTTTAATTTTTTATAA
*
17342452 TTTTTTATTT
1 TTTTTAATTT
17342462 AAAAAATTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
14 4 0.11
15 5 0.14
16 8 0.22
17 19 0.53
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTTTAATTTTTTATAA
Found at i:17344997 original size:71 final size:71
Alignment explanation
Indices: 17344841--17345002 Score: 234
Period size: 71 Copynumber: 2.3 Consensus size: 71
17344831 GATTCTCAAT
* ** * * *
17344841 AGCTTGAGTGAGCAACATTGGATCATTATTTAGCGATGGTTGAGATCTAGCATGTGTTGCAGATT
1 AGCTTGAGTGAGCAGCATCAGATAATTATTTAGCGATGGTTGAGATCCAACATGTGTTGCAGATT
17344906 CTAGAC
66 CTAGAC
**
17344912 AGCTTGAGTGAGCAGCATCAGATAATTATTTAGCGATGGTTGAGATCCAACATGTGTTGTGGATT
1 AGCTTGAGTGAGCAGCATCAGATAATTATTTAGCGATGGTTGAGATCCAACATGTGTTGCAGATT
*
17344977 CTTGAC
66 CTAGAC
*
17344983 AGCTTGAGTGAGCAGTATCA
1 AGCTTGAGTGAGCAGCATCA
17345003 CATTATACTT
Statistics
Matches: 81, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
71 81 1.00
ACGTcount: A:0.27, C:0.14, G:0.27, T:0.31
Consensus pattern (71 bp):
AGCTTGAGTGAGCAGCATCAGATAATTATTTAGCGATGGTTGAGATCCAACATGTGTTGCAGATT
CTAGAC
Found at i:17345021 original size:71 final size:71
Alignment explanation
Indices: 17344841--17345040 Score: 231
Period size: 71 Copynumber: 2.8 Consensus size: 71
17344831 GATTCTCAAT
* *** * *
17344841 AGCTTGAGTGAGCAACATTGGATCATTATTTAGCGATGGTTGAGATCTAGCATGTGTTGCAGATT
1 AGCTTGAGTGAGCAGCATCACATAATTATTTAGCGATGGTTGAGATCTAACATGTGTTGCAGATT
17344906 CTAGAC
66 CTAGAC
* * **
17344912 AGCTTGAGTGAGCAGCATCAGATAATTATTTAGCGATGGTTGAGATCCAACATGTGTTGTGGATT
1 AGCTTGAGTGAGCAGCATCACATAATTATTTAGCGATGGTTGAGATCTAACATGTGTTGCAGATT
*
17344977 CTTGAC
66 CTAGAC
* * ** * *
17344983 AGCTTGAGTGAGCAGTATCACATTA-TACTTTATTGATGGTCGAGATCTATCATGTGTT
1 AGCTTGAGTGAGCAGCATCACATAATTA-TTTAGCGATGGTTGAGATCTAACATGTGTT
17345041 CCTGTAGTCT
Statistics
Matches: 111, Mismatches: 17, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
70 2 0.02
71 109 0.98
ACGTcount: A:0.27, C:0.14, G:0.26, T:0.34
Consensus pattern (71 bp):
AGCTTGAGTGAGCAGCATCACATAATTATTTAGCGATGGTTGAGATCTAACATGTGTTGCAGATT
CTAGAC
Found at i:17346423 original size:41 final size:41
Alignment explanation
Indices: 17346372--17346452 Score: 110
Period size: 41 Copynumber: 2.0 Consensus size: 41
17346362 CCAGCATGAG
* * *
17346372 GCCTGTTAGG-CTCAAGGCCCGATACAATACATCGGCATAAA
1 GCCTGCTAGGCCT-AAGGCCCGATACAATACACCGCCATAAA
*
17346413 GCCTGCTAGGCCTAAGGCCCGATATAATACACCGCCATAA
1 GCCTGCTAGGCCTAAGGCCCGATACAATACACCGCCATAA
17346453 CAACTCAGTT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
41 33 0.94
42 2 0.06
ACGTcount: A:0.31, C:0.30, G:0.21, T:0.19
Consensus pattern (41 bp):
GCCTGCTAGGCCTAAGGCCCGATACAATACACCGCCATAAA
Found at i:17353531 original size:50 final size:50
Alignment explanation
Indices: 17353447--17353662 Score: 238
Period size: 50 Copynumber: 4.3 Consensus size: 50
17353437 ATCACTCATT
* * * * * *
17353447 TGGCCAAATGTACAAGATCAAATATAAGAGCACATATGTGCTTACCTATA
1 TGGCCGAATATACAAGATCAAATATAACATCACATATGTACATACCTATA
* * * *
17353497 TGGCCGAATATGCAAGATCAAATTTAACATCACATATGTACTTACTTATA
1 TGGCCGAATATACAAGATCAAATATAACATCACATATGTACATACCTATA
* * *
17353547 TGGCCGAATATACAA-ATTCAAATATAAAATCACATTTGTGCATACCT-TCA
1 TGGCCGAATATACAAGA-TCAAATATAACATCACATATGTACATACCTAT-A
* * * * *
17353597 TGGCCGAATATTCAAGATCCAATACAACATCACATATGTACATACTTATG
1 TGGCCGAATATACAAGATCAAATATAACATCACATATGTACATACCTATA
17353647 TGGCCGAATATACAAG
1 TGGCCGAATATACAAG
17353663 GTCATTTAGC
Statistics
Matches: 138, Mismatches: 24, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
49 2 0.01
50 134 0.97
51 2 0.01
ACGTcount: A:0.39, C:0.19, G:0.13, T:0.28
Consensus pattern (50 bp):
TGGCCGAATATACAAGATCAAATATAACATCACATATGTACATACCTATA
Found at i:17353626 original size:100 final size:100
Alignment explanation
Indices: 17353447--17353662 Score: 292
Period size: 100 Copynumber: 2.2 Consensus size: 100
17353437 ATCACTCATT
* * * *
17353447 TGGCCAAATGTACAAGATCAAATATAAGAGCACATATGTGCTTACCTATATGGCCGAATATGCAA
1 TGGCCGAATATACAAGATCAAATATAAAAGCACATATGTGCATACCTATATGGCCGAATATGCAA
** *
17353512 GATCAAATTTAACATCACATATGTACTTACTTATA
66 GATCAAATACAACATCACATATGTACATACTTATA
* * *
17353547 TGGCCGAATATACAA-ATTCAAATATAAAATCACATTTGTGCATACCT-TCATGGCCGAATATTC
1 TGGCCGAATATACAAGA-TCAAATATAAAAGCACATATGTGCATACCTAT-ATGGCCGAATATGC
* *
17353610 AAGATCCAATACAACATCACATATGTACATACTTATG
64 AAGATCAAATACAACATCACATATGTACATACTTATA
17353647 TGGCCGAATATACAAG
1 TGGCCGAATATACAAG
17353663 GTCATTTAGC
Statistics
Matches: 101, Mismatches: 12, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
99 2 0.02
100 99 0.98
ACGTcount: A:0.39, C:0.19, G:0.13, T:0.28
Consensus pattern (100 bp):
TGGCCGAATATACAAGATCAAATATAAAAGCACATATGTGCATACCTATATGGCCGAATATGCAA
GATCAAATACAACATCACATATGTACATACTTATA
Found at i:17364327 original size:12 final size:12
Alignment explanation
Indices: 17364312--17364354 Score: 59
Period size: 12 Copynumber: 3.5 Consensus size: 12
17364302 AAAAAGAACC
17364312 AAAAAAAAAAGA
1 AAAAAAAAAAGA
*
17364324 AAAAAAGAAAGA
1 AAAAAAAAAAGA
*
17364336 AAAAAAAGAAGA
1 AAAAAAAAAAGA
17364348 AGAAAAA
1 A-AAAAA
17364355 CTAACGTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
12 22 0.81
13 5 0.19
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAGA
Found at i:17364335 original size:27 final size:25
Alignment explanation
Indices: 17364284--17364354 Score: 72
Period size: 26 Copynumber: 2.7 Consensus size: 25
17364274 AATCCTTACG
* * *
17364284 ACAAACAAAGAAGAAAAGAAAAAGA
1 ACAAAAAAAAAAGAAAAAAAAAAGA
17364309 ACCAAAAAAAAAAGAAAAAAAGAAAGA
1 A-CAAAAAAAAAAGAAAAAAA-AAAGA
17364336 A-AAAAAAGAAGAAGAAAAA
1 ACAAAAAA-AA-AAGAAAAA
17364355 CTAACGTTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
25 7 0.18
26 18 0.46
27 14 0.36
ACGTcount: A:0.80, C:0.06, G:0.14, T:0.00
Consensus pattern (25 bp):
ACAAAAAAAAAAGAAAAAAAAAAGA
Found at i:17364921 original size:12 final size:12
Alignment explanation
Indices: 17364904--17364936 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
17364894 CGGCCCGCCC
17364904 ATATTAATTTTT
1 ATATTAATTTTT
17364916 ATATT-ATTTTT
1 ATATTAATTTTT
17364927 ATA-TAATTTT
1 ATATTAATTTT
17364937 AAAATATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 14 0.70
12 5 0.25
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:17365094 original size:30 final size:30
Alignment explanation
Indices: 17365058--17365116 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
17365048 CAACTTAACA
*
17365058 AGCAAATGCCTCTAAAATAATAACAAAATT
1 AGCAAATGCCTCTAAAATAATAAAAAAATT
* *
17365088 AGCAAATGTCTTTAAAATAATAAAAAAAT
1 AGCAAATGCCTCTAAAATAATAAAAAAAT
17365117 AAACAATAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.56, C:0.12, G:0.07, T:0.25
Consensus pattern (30 bp):
AGCAAATGCCTCTAAAATAATAAAAAAATT
Found at i:17365177 original size:22 final size:22
Alignment explanation
Indices: 17365152--17365194 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
17365142 TATCCAAACA
17365152 ATAACAACAAAATAGTAGCAAC
1 ATAACAACAAAATAGTAGCAAC
* **
17365174 ATAATAGTAAAATAGTAGCAA
1 ATAACAACAAAATAGTAGCAA
17365195 AATAGGGAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.58, C:0.12, G:0.12, T:0.19
Consensus pattern (22 bp):
ATAACAACAAAATAGTAGCAAC
Found at i:17365198 original size:11 final size:11
Alignment explanation
Indices: 17365159--17365199 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
17365149 ACAATAACAA
17365159 CAAAATAGTAG
1 CAAAATAGTAG
* *
17365170 CAACATAATAG
1 CAAAATAGTAG
*
17365181 TAAAATAGTAG
1 CAAAATAGTAG
17365192 CAAAATAG
1 CAAAATAG
17365200 GGAGAAAATA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.56, C:0.10, G:0.15, T:0.20
Consensus pattern (11 bp):
CAAAATAGTAG
Done.