Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032244.1 Gossypioides kirkii chromosome KI_01
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: 38174113
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1000 characters in sequence are not A, C, G, or T
File 54 of 126
Found at i:15977221 original size:26 final size:26
Alignment explanation
Indices: 15977192--15977246 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 26
15977182 GTGATTAGTA
*
15977192 TATTAACAGAATTAG-CCTTCAATGTT
1 TATTAACAAAATTAGTCCTT-AATGTT
*
15977218 TATTAACAAAATTAGTTCTTAATGTT
1 TATTAACAAAATTAGTCCTTAATGTT
15977244 TAT
1 TAT
15977247 ATATTTTGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 23 0.88
27 3 0.12
ACGTcount: A:0.36, C:0.11, G:0.09, T:0.44
Consensus pattern (26 bp):
TATTAACAAAATTAGTCCTTAATGTT
Found at i:15978275 original size:82 final size:83
Alignment explanation
Indices: 15978138--15978303 Score: 271
Period size: 82 Copynumber: 2.0 Consensus size: 83
15978128 ATTTAGATTA
* *
15978138 GAGGGATAATTCTTGTCTTTGATTCATTACATTCATCATTGAATCATTGGTGTTTGTTGAATTGT
1 GAGGGATAATTCTCGTCTTTGATTCATTACATTCATCATTGAATCATTGGTGTTTGTTGAATTGA
*
15978203 TTGTGTGAAGATA-TAGG
66 TAGTGTGAAGATATTAGG
* *
15978220 GAGGGATAATTCTCGTCTTTTATTTATTACATTCATCATTGAATCATTGGTGTTTGTTGAATTGA
1 GAGGGATAATTCTCGTCTTTGATTCATTACATTCATCATTGAATCATTGGTGTTTGTTGAATTGA
*
15978285 TAGTGTGAAGTTATTAGG
66 TAGTGTGAAGATATTAGG
15978303 G
1 G
15978304 TGGTTTAGAT
Statistics
Matches: 77, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
82 72 0.94
83 5 0.06
ACGTcount: A:0.25, C:0.08, G:0.23, T:0.44
Consensus pattern (83 bp):
GAGGGATAATTCTCGTCTTTGATTCATTACATTCATCATTGAATCATTGGTGTTTGTTGAATTGA
TAGTGTGAAGATATTAGG
Found at i:15982361 original size:20 final size:19
Alignment explanation
Indices: 15982327--15982365 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
15982317 AATTTAAAGC
15982327 AATAAATTAAATTAAAGAA
1 AATAAATTAAATTAAAGAA
*
15982346 AATAAAGTTTAATTAAAGAA
1 AATAAA-TTAAATTAAAGAA
15982366 GAAATAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.64, C:0.00, G:0.08, T:0.28
Consensus pattern (19 bp):
AATAAATTAAATTAAAGAA
Found at i:15982375 original size:15 final size:15
Alignment explanation
Indices: 15982355--15982390 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
15982345 AAATAAAGTT
15982355 TAATTAAAGAAGAAA
1 TAATTAAAGAAGAAA
*
15982370 TAATTAAAGAATAAA
1 TAATTAAAGAAGAAA
15982385 TCAATT
1 T-AATT
15982391 TAGAGTTGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 15 0.79
16 4 0.21
ACGTcount: A:0.61, C:0.03, G:0.08, T:0.28
Consensus pattern (15 bp):
TAATTAAAGAAGAAA
Found at i:15982845 original size:33 final size:34
Alignment explanation
Indices: 15982795--15982922 Score: 129
Period size: 33 Copynumber: 3.8 Consensus size: 34
15982785 TTTAAACAAC
* *
15982795 CAAAATAACAATCAAAATAGCAGC-AAAACAATAA
1 CAAAA-AACAATAAAAATAGCAACAAAAACAATAA
*
15982829 CAAAAAACAATAAAAATAGCAACAAATAACAGTAA
1 CAAAAAACAATAAAAATAGCAACAAA-AACAATAA
* * *
15982864 -AAATAACAA-AAAAATAGCAACAAAAACAACAG
1 CAAAAAACAATAAAAATAGCAACAAAAACAATAA
* *
15982896 CATCAAAACAGTAAAAA-AGCAACAAAA
1 CA-AAAAACAATAAAAATAGCAACAAAA
15982923 CAGCAATCAA
Statistics
Matches: 79, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
32 5 0.06
33 32 0.41
34 30 0.38
35 12 0.15
ACGTcount: A:0.68, C:0.16, G:0.06, T:0.09
Consensus pattern (34 bp):
CAAAAAACAATAAAAATAGCAACAAAAACAATAA
Found at i:15982852 original size:22 final size:22
Alignment explanation
Indices: 15982827--15983000 Score: 81
Period size: 22 Copynumber: 7.6 Consensus size: 22
15982817 GCAAAACAAT
*
15982827 AACAAAAAACAATAAAAATAGC
1 AACAAAAAACAATAAAAATAAC
* *
15982849 AACAAATAACAGTAAAAATAAC
1 AACAAAAAACAATAAAAATAAC
* *
15982871 AA-AAAAATAGCAACAAAAACAAC
1 AACAAAAA-A-CAATAAAAATAAC
* * * *
15982894 AGCATCAAAACAGTAAAAA-AGC
1 AACA-AAAAACAATAAAAATAAC
*
15982916 AACAAAACAGCAATCAAAACAGTAA-
1 AACAAAA-AACAAT-AAAA-A-TAAC
*
15982941 AAAAAATCAACACAATAAAAA-AAC
1 AACAAA--AA-ACAATAAAAATAAC
*
15982965 -AC-CAAAACAATAAAAAATAAC
1 AACAAAAAACAAT-AAAAATAAC
*
15982986 ACCAAAACAACAATA
1 AACAAAA-AACAATA
15983001 TAATTTTTTA
Statistics
Matches: 111, Mismatches: 23, Indels: 35
0.66 0.14 0.21
Matches are distributed among these distances:
19 5 0.05
20 7 0.06
21 9 0.08
22 33 0.30
23 28 0.25
24 9 0.08
25 9 0.08
26 6 0.05
27 5 0.05
ACGTcount: A:0.69, C:0.18, G:0.05, T:0.09
Consensus pattern (22 bp):
AACAAAAAACAATAAAAATAAC
Found at i:15982888 original size:12 final size:12
Alignment explanation
Indices: 15982789--15982894 Score: 55
Period size: 12 Copynumber: 9.3 Consensus size: 12
15982779 ATAACATTTA
*
15982789 AACAACCAAAAT
1 AACAACAAAAAT
15982801 AACAATC-AAAAT
1 AACAA-CAAAAAT
* * *
15982813 AGCAGC-AAAAC
1 AACAACAAAAAT
*
15982824 AATAAC-AAAA-
1 AACAACAAAAAT
*
15982834 AACAATAAAAAT
1 AACAACAAAAAT
*
15982846 AGCAAC--AAAT
1 AACAACAAAAAT
**
15982856 AACAGTAAAAAT
1 AACAACAAAAAT
15982868 AACAA-AAAAAT
1 AACAACAAAAAT
* *
15982879 AGCAACAAAAAC
1 AACAACAAAAAT
15982891 AACA
1 AACA
15982895 GCATCAAAAC
Statistics
Matches: 71, Mismatches: 17, Indels: 12
0.71 0.17 0.12
Matches are distributed among these distances:
10 11 0.15
11 26 0.37
12 33 0.46
13 1 0.01
ACGTcount: A:0.69, C:0.17, G:0.05, T:0.09
Consensus pattern (12 bp):
AACAACAAAAAT
Found at i:15982917 original size:67 final size:67
Alignment explanation
Indices: 15982796--15982921 Score: 166
Period size: 67 Copynumber: 1.9 Consensus size: 67
15982786 TTAAACAACC
* * *
15982796 AAAATAACAATCAAAATAGCAGCAAAACAATAACAAAAAACAATAAAAATAGCAACAAATAACAG
1 AAAATAACAATAAAAATAGCAACAAAACAACAACAAAAAACAATAAAAATAGCAACAAATAACAG
15982861 TA
66 TA
* * *
15982863 AAAATAACAA-AAAAATAGCAACAAAAACAACAGCATCAAAACAGTAAAAA-AGCAACAAA
1 AAAATAACAATAAAAATAGCAAC-AAAACAACAACA-AAAAACAATAAAAATAGCAACAAA
15982922 ACAGCAATCA
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
66 10 0.20
67 29 0.57
68 12 0.24
ACGTcount: A:0.68, C:0.16, G:0.06, T:0.10
Consensus pattern (67 bp):
AAAATAACAATAAAAATAGCAACAAAACAACAACAAAAAACAATAAAAATAGCAACAAATAACAG
TA
Found at i:15982922 original size:34 final size:31
Alignment explanation
Indices: 15982873--15982944 Score: 99
Period size: 31 Copynumber: 2.2 Consensus size: 31
15982863 AAAATAACAA
15982873 AAAAATAGCAACAAAAACAACAGCATCAAAACAGT
1 AAAAA-AGCAAC-AAAACAACA--ATCAAAACAGT
*
15982908 AAAAAAGCAACAAAACAGCAATCAAAACAGT
1 AAAAAAGCAACAAAACAACAATCAAAACAGT
15982939 AAAAAA
1 AAAAAA
15982945 AATCAACACA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
31 17 0.47
33 8 0.22
34 6 0.17
35 5 0.14
ACGTcount: A:0.67, C:0.18, G:0.08, T:0.07
Consensus pattern (31 bp):
AAAAAAGCAACAAAACAACAATCAAAACAGT
Found at i:15982945 original size:33 final size:34
Alignment explanation
Indices: 15982871--15982997 Score: 100
Period size: 37 Copynumber: 3.6 Consensus size: 34
15982861 TAAAAATAAC
15982871 AAAAAAATAGCAACAAAAACAACAGCATCAAAACAGT
1 AAAAAAA-AGCAAC-AAAACAACA-CATCAAAACAGT
*
15982908 --AAAAAAGCAACAAAACAGCA-ATCAAAACAGT
1 AAAAAAAAGCAACAAAACAACACATCAAAACAGT
* * * * *
15982939 AAAAAAAATCAACACAATAAAAAAACACCAAAACAAT
1 AAAAAAAAGC-A-ACAA-AACAACACATCAAAACAGT
*
15982976 AAAAAATAA-CACCAAAACAACA
1 AAAAAA-AAGCAACAAAACAACA
15982998 ATATAATTTT
Statistics
Matches: 73, Mismatches: 10, Indels: 17
0.73 0.10 0.17
Matches are distributed among these distances:
31 11 0.15
33 15 0.21
34 12 0.16
35 12 0.16
36 5 0.07
37 16 0.22
38 2 0.03
ACGTcount: A:0.69, C:0.20, G:0.05, T:0.07
Consensus pattern (34 bp):
AAAAAAAAGCAACAAAACAACACATCAAAACAGT
Found at i:15982950 original size:18 final size:18
Alignment explanation
Indices: 15982927--15982981 Score: 74
Period size: 18 Copynumber: 3.0 Consensus size: 18
15982917 ACAAAACAGC
*
15982927 AATCAAAACAGTAAAAAA
1 AATCAAAACAATAAAAAA
*
15982945 AATCAACACAATAAAAAA
1 AATCAAAACAATAAAAAA
*
15982963 ACACCAAAACAATAAAAAA
1 A-ATCAAAACAATAAAAAA
15982982 TAACACCAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
18 17 0.53
19 15 0.47
ACGTcount: A:0.73, C:0.16, G:0.02, T:0.09
Consensus pattern (18 bp):
AATCAAAACAATAAAAAA
Found at i:15982963 original size:19 final size:19
Alignment explanation
Indices: 15982930--15982995 Score: 71
Period size: 19 Copynumber: 3.4 Consensus size: 19
15982920 AAACAGCAAT
* *
15982930 CAAAACAGT-AAAAAAAAT
1 CAAAACAATAAAAAAAAAC
* *
15982948 CAACACAATAAAAAAACAC
1 CAAAACAATAAAAAAAAAC
15982967 CAAAACAATAAAAAATAACAC
1 CAAAACAATAAAAAA-AA-AC
15982988 CAAAACAA
1 CAAAACAA
15982996 CAATATAATT
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
18 7 0.18
19 21 0.54
20 1 0.03
21 10 0.26
ACGTcount: A:0.71, C:0.20, G:0.02, T:0.08
Consensus pattern (19 bp):
CAAAACAATAAAAAAAAAC
Found at i:15982973 original size:21 final size:21
Alignment explanation
Indices: 15982949--15982995 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
15982939 AAAAAAAATC
15982949 AACACAATAAAAA-AACACCA
1 AACACAATAAAAATAACACCA
15982969 AA-ACAATAAAAAATAACACCA
1 AACACAAT-AAAAATAACACCA
15982990 AA-ACAA
1 AACACAA
15982996 CAATATAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 5 0.20
20 7 0.28
21 13 0.52
ACGTcount: A:0.72, C:0.21, G:0.00, T:0.06
Consensus pattern (21 bp):
AACACAATAAAAATAACACCA
Found at i:15983264 original size:15 final size:15
Alignment explanation
Indices: 15983238--15983338 Score: 80
Period size: 15 Copynumber: 6.1 Consensus size: 15
15983228 AAATAAAATT
15983238 TAATTAAAAGAATAAA
1 TAATT-AAAGAATAAA
15983254 TAATTAAAGAATAAA
1 TAATTAAAGAATAAA
*
15983269 TAAATTTAAAGCAATATATT
1 T-AA-TTAAAG-AATA-A-A
15983289 TAAATTAAA-AATAAAA
1 T-AATTAAAGAAT-AAA
15983305 TTTAATTTAAAGAA-AAA
1 --TAA-TTAAAGAATAAA
15983322 TAATTAAAGAATAAA
1 TAATTAAAGAATAAA
15983337 TA
1 TA
15983339 TATTTAAATT
Statistics
Matches: 72, Mismatches: 2, Indels: 23
0.74 0.02 0.24
Matches are distributed among these distances:
14 8 0.11
15 19 0.26
16 7 0.10
17 15 0.21
18 11 0.15
19 8 0.11
20 4 0.06
ACGTcount: A:0.63, C:0.01, G:0.05, T:0.31
Consensus pattern (15 bp):
TAATTAAAGAATAAA
Found at i:15983338 original size:37 final size:36
Alignment explanation
Indices: 15983228--15983351 Score: 107
Period size: 37 Copynumber: 3.5 Consensus size: 36
15983218 TAAATTTAAA
*
15983228 AAATAAAATTTAATTAAAAGAATAAATAATTAAAGAAT
1 AAAT-AAATTTAATTTAAAGAA-AAATAATTAAAGAAT
* * * *
15983266 AAAT--A---AATTTAAAGCAATATATTTAAATTAA-
1 AAATAAATTTAATTTAAAGAAAAATAATTAAA-GAAT
15983297 AAATAAAATTTAATTTAAAGAAAAATAATTAAAGAAT
1 AAAT-AAATTTAATTTAAAGAAAAATAATTAAAGAAT
* *
15983334 AAATATATTTAAATTAAA
1 AAATAAATTTAATTTAAA
15983352 AAGTAGAATT
Statistics
Matches: 67, Mismatches: 11, Indels: 18
0.70 0.11 0.19
Matches are distributed among these distances:
31 13 0.19
32 11 0.16
34 1 0.01
35 1 0.01
36 14 0.21
37 23 0.34
38 4 0.06
ACGTcount: A:0.63, C:0.01, G:0.04, T:0.32
Consensus pattern (36 bp):
AAATAAATTTAATTTAAAGAAAAATAATTAAAGAAT
Found at i:15983339 original size:54 final size:56
Alignment explanation
Indices: 15983281--15983402 Score: 187
Period size: 56 Copynumber: 2.2 Consensus size: 56
15983271 AATTTAAAGC
*
15983281 AATATATTTAAATTAAAAA-TAAAATTTAATTTAAAG-AAAAATAATTAAAGAATA
1 AATATATTTAAATTAAAAAGTAAAATTTAATTAAAAGAAAAAATAATTAAAGAATA
* *
15983335 AATATATTTAAATTAAAAAGTAGAATTTAATTAAAAGAAAAAATAATTAGAGAATA
1 AATATATTTAAATTAAAAAGTAAAATTTAATTAAAAGAAAAAATAATTAAAGAATA
15983391 AATCA-ATTTAAA
1 AAT-ATATTTAAA
15983403 GTAATATATT
Statistics
Matches: 62, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
54 19 0.31
55 15 0.24
56 27 0.44
57 1 0.02
ACGTcount: A:0.61, C:0.01, G:0.06, T:0.32
Consensus pattern (56 bp):
AATATATTTAAATTAAAAAGTAAAATTTAATTAAAAGAAAAAATAATTAAAGAATA
Found at i:15983344 original size:68 final size:71
Alignment explanation
Indices: 15983194--15983346 Score: 240
Period size: 68 Copynumber: 2.2 Consensus size: 71
15983184 TGATCAAATC
* *
15983194 TAAATCAATTTAAAGTAATATACTTAAATTTAAAAAATAAAATTTAATTAAAAGAATAAATAATT
1 TAAATAAATTTAAAGCAATATACTTAAATTTAAAAAATAAAATTTAATTAAAAGAATAAATAATT
15983259 AAAGAA
66 AAAGAA
* *
15983265 TAAATAAATTTAAAGCAATATATTTAAA-TT-AAAAATAAAATTTAATTTAAAGAA-AAATAATT
1 TAAATAAATTTAAAGCAATATACTTAAATTTAAAAAATAAAATTTAATTAAAAGAATAAATAATT
15983327 AAAGAA
66 AAAGAA
*
15983333 TAAATATATTTAAA
1 TAAATAAATTTAAA
15983347 TTAAAAAGTA
Statistics
Matches: 77, Mismatches: 5, Indels: 3
0.91 0.06 0.04
Matches are distributed among these distances:
68 27 0.35
69 23 0.30
70 2 0.03
71 25 0.32
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (71 bp):
TAAATAAATTTAAAGCAATATACTTAAATTTAAAAAATAAAATTTAATTAAAAGAATAAATAATT
AAAGAA
Found at i:15983446 original size:64 final size:63
Alignment explanation
Indices: 15983373--15983499 Score: 200
Period size: 64 Copynumber: 2.0 Consensus size: 63
15983363 AATTAAAAGA
* *
15983373 AAAAATAATTAGAGAATAAATCAATTTAAAGTAATATATTTAAATTTAAAAAATAGAATTTAAT
1 AAAAATAATTAAAGAATAAATCAATTTAAAGCAATATATTTAAATTTAAAAAATA-AATTTAAT
* * *
15983437 AAAAATAATTAAAGAATAAATCAGTTTAAAGCAATATATTTCAATTTAAAAAGTAAATTTAAT
1 AAAAATAATTAAAGAATAAATCAATTTAAAGCAATATATTTAAATTTAAAAAATAAATTTAAT
15983500 TGAAAGAAGA
Statistics
Matches: 58, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
63 8 0.14
64 50 0.86
ACGTcount: A:0.57, C:0.03, G:0.06, T:0.34
Consensus pattern (63 bp):
AAAAATAATTAAAGAATAAATCAATTTAAAGCAATATATTTAAATTTAAAAAATAAATTTAAT
Found at i:15983584 original size:134 final size:133
Alignment explanation
Indices: 15983335--15983586 Score: 314
Period size: 134 Copynumber: 1.9 Consensus size: 133
15983325 TTAAAGAATA
15983335 AATATATTTAAATTAAAAAGTAGAATTTAATTAAAAGAAAAAATAATTAGAGAATAAATCAATTT
1 AATATATTTAAATTAAAAAGTAGAATTTAATTAAAAGAAAAAATAATTA-AGAATAAATCAATTT
* * *
15983400 AAAGTAATATATTTAAATTTAAAAAATAGAATTTAATAAAAATAATTAAAGAATAAATCAGTTTA
65 AAAGTAATATATTTAAATTAAAAAAATAGAATTTAATAAAAAAAAATAAAGAATAAATCAGTTTA
15983465 AAGC
130 AAGC
* * * * ** *
15983469 AATATATTTCAATTTAAAAAGTA-AATTTAATTGAAAGAAGAAATAATT-AG-TTATTTGAATTT
1 AATATATTT-AAATTAAAAAGTAGAATTTAATTAAAAGAAAAAATAATTAAGAATAAATCAATTT
* *
15983531 AGAGTGATATATTTAAATTAAAAAAATA-AATTTTAATTAAAAAAGAAAATAAAGAA
65 AAAGTAATATATTTAAATTAAAAAAATAGAA-TTTAA-T-AAAAA-AAAATAAAGAA
15983587 CACGAAATGG
Statistics
Matches: 101, Mismatches: 12, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
130 2 0.02
131 38 0.38
132 3 0.03
133 5 0.05
134 41 0.41
135 12 0.12
ACGTcount: A:0.57, C:0.02, G:0.08, T:0.33
Consensus pattern (133 bp):
AATATATTTAAATTAAAAAGTAGAATTTAATTAAAAGAAAAAATAATTAAGAATAAATCAATTTA
AAGTAATATATTTAAATTAAAAAAATAGAATTTAATAAAAAAAAATAAAGAATAAATCAGTTTAA
AGC
Found at i:15983620 original size:18 final size:18
Alignment explanation
Indices: 15983597--15983631 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
15983587 CACGAAATGG
15983597 GTTGATGAGACTTGACAT
1 GTTGATGAGACTTGACAT
*
15983615 GTTGATGGGACTTGACA
1 GTTGATGAGACTTGACA
15983632 GACCCAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.11, G:0.31, T:0.31
Consensus pattern (18 bp):
GTTGATGAGACTTGACAT
Found at i:15984503 original size:68 final size:69
Alignment explanation
Indices: 15984353--15984508 Score: 206
Period size: 69 Copynumber: 2.3 Consensus size: 69
15984343 GGGTGTAAGG
*
15984353 CCCAACTATTATTCTAAGGACCGCAGGCGAAGAGCCACAACCTCCAACACAGTTAGCGAGAGCAA
1 CCCAACTATTATTCTAAGGACCGCAAGCGAAGAGCCACAACCTCCAACACAGTTAGCGAGAGCAA
15984418 AGCT
66 AGCT
* *** * * * **
15984422 CCCAACTGTTATTCTAAGGTTTGCAAGCGAATAGCCGCAACTTTTAACACA-TTAGCGAGAGCAA
1 CCCAACTATTATTCTAAGGACCGCAAGCGAAGAGCCACAACCTCCAACACAGTTAGCGAGAGCAA
15984486 AGCT
66 AGCT
*
15984490 CCCAACTACTATTCTAAGG
1 CCCAACTATTATTCTAAGG
15984509 CTCGCAGGCA
Statistics
Matches: 75, Mismatches: 12, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
68 34 0.45
69 41 0.55
ACGTcount: A:0.33, C:0.28, G:0.19, T:0.21
Consensus pattern (69 bp):
CCCAACTATTATTCTAAGGACCGCAAGCGAAGAGCCACAACCTCCAACACAGTTAGCGAGAGCAA
AGCT
Found at i:15984529 original size:68 final size:69
Alignment explanation
Indices: 15984353--15984538 Score: 232
Period size: 68 Copynumber: 2.7 Consensus size: 69
15984343 GGGTGTAAGG
*
15984353 CCCAACTATTATTCTAAGGAC-CGCAGGCGAAGAGCCACAACCTCCAACACAGTTAGCGAGAGCA
1 CCCAACTATTATTCTAAGG-CTCGCAGGCGAAGAGCCGCAACCTCCAACACAGTTAGCGAGAGCA
15984417 AAGCT
65 AAGCT
* * * * * * **
15984422 CCCAACTGTTATTCTAAGGTTTGCAAGCGAATAGCCGCAACTTTTAACACA-TTAGCGAGAGCAA
1 CCCAACTATTATTCTAAGGCTCGCAGGCGAAGAGCCGCAACCTCCAACACAGTTAGCGAGAGCAA
15984486 AGCT
66 AGCT
* * * *
15984490 CCCAACTACTATTCTAAGGCTCGCAGGCAAAGAGTCGCAACCTCTAACA
1 CCCAACTATTATTCTAAGGCTCGCAGGCGAAGAGCCGCAACCTCCAACA
15984539 TAATCTAAAA
Statistics
Matches: 97, Mismatches: 19, Indels: 3
0.82 0.16 0.03
Matches are distributed among these distances:
68 56 0.58
69 41 0.42
ACGTcount: A:0.33, C:0.28, G:0.19, T:0.19
Consensus pattern (69 bp):
CCCAACTATTATTCTAAGGCTCGCAGGCGAAGAGCCGCAACCTCCAACACAGTTAGCGAGAGCAA
AGCT
Found at i:15987283 original size:20 final size:20
Alignment explanation
Indices: 15987258--15987301 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
15987248 TGACAAAAGT
15987258 TTTTATT-AATTATTATTTTA
1 TTTTATTGAATTA-TATTTTA
*
15987278 TTTTATTGTATTATATTTTA
1 TTTTATTGAATTATATTTTA
15987298 TTTT
1 TTTT
15987302 TTTTAAAAGG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 18 0.82
21 4 0.18
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (20 bp):
TTTTATTGAATTATATTTTA
Found at i:15999962 original size:28 final size:27
Alignment explanation
Indices: 15999928--16000002 Score: 91
Period size: 28 Copynumber: 2.7 Consensus size: 27
15999918 ATAAATAATT
*
15999928 TTAAAATTATTTTTTTAAATAT-AAAA
1 TTAAAATTATTTTTTAAAATATAAAAA
15999954 TTATTAAATTA-TTTTTAAAATATAAAAA
1 TTA--AAATTATTTTTTAAAATATAAAAA
*
15999982 TTAAAATTATTATATTAAAAT
1 TTAAAATTATT-TTTTAAAAT
16000003 CTATCTTTAA
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
26 9 0.21
27 12 0.29
28 21 0.50
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (27 bp):
TTAAAATTATTTTTTAAAATATAAAAA
Found at i:16004897 original size:2 final size:2
Alignment explanation
Indices: 16004890--16004933 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
16004880 AAATTTTATC
16004890 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16004931 AT A
1 AT A
16004934 CCTGGAAATC
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16006615 original size:35 final size:35
Alignment explanation
Indices: 16006567--16006652 Score: 109
Period size: 35 Copynumber: 2.5 Consensus size: 35
16006557 GGGTGACATT
* * *
16006567 GTGTAAATGGTATATAGGCCCTTCGGGGCGACACC
1 GTGTAAATAGTATATAGGCCCTTCAGGACGACACC
* **
16006602 GTGTAAATTGTATATAGGTTCTTCAGGACGACACC
1 GTGTAAATAGTATATAGGCCCTTCAGGACGACACC
*
16006637 GTGTAAACAGTATATA
1 GTGTAAATAGTATATA
16006653 CAGGTCCTAC
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 44 1.00
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.28
Consensus pattern (35 bp):
GTGTAAATAGTATATAGGCCCTTCAGGACGACACC
Found at i:16007981 original size:24 final size:22
Alignment explanation
Indices: 16007952--16008008 Score: 71
Period size: 21 Copynumber: 2.5 Consensus size: 22
16007942 AACCTTTCTT
16007952 ACTACCGATACATCAGTACCATAA
1 ACTACCGATACATCA-TACC-TAA
* *
16007976 ACTACCGATAC-TTATATCTAA
1 ACTACCGATACATCATACCTAA
16007997 ACTACCGATACA
1 ACTACCGATACA
16008009 ACCCAAGTCA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 14 0.47
22 3 0.10
23 2 0.07
24 11 0.37
ACGTcount: A:0.40, C:0.28, G:0.07, T:0.25
Consensus pattern (22 bp):
ACTACCGATACATCATACCTAA
Found at i:16023654 original size:44 final size:46
Alignment explanation
Indices: 16023566--16023657 Score: 118
Period size: 44 Copynumber: 2.0 Consensus size: 46
16023556 GGTTCGCTAT
*
16023566 AATGTAATAGAGCTGTAATCAGTATTTCAGTTGTTTAGTTGAATGG
1 AATGGAATAGAGCTGTAATCAGTATTTCAGTTGTTTAGTTGAATGG
* * *
16023612 AATGGAATAGAGTTGTAAT-AGTA-TTC-TTGTGTTTGGTTGAATGG
1 AATGGAATAGAGCTGTAATCAGTATTTCAGT-TGTTTAGTTGAATGG
16023656 AA
1 AA
16023658 CGGATGTTAT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
43 1 0.02
44 19 0.46
45 4 0.10
46 17 0.41
ACGTcount: A:0.30, C:0.04, G:0.26, T:0.39
Consensus pattern (46 bp):
AATGGAATAGAGCTGTAATCAGTATTTCAGTTGTTTAGTTGAATGG
Found at i:16023823 original size:57 final size:57
Alignment explanation
Indices: 16023753--16023906 Score: 177
Period size: 57 Copynumber: 2.7 Consensus size: 57
16023743 TGTTATTAAA
*
16023753 TTTTAATAAGATTATTATTAAATATAATTTAATAAAAAAATAAATAATTTAAT-CATT
1 TTTTAATATGATTATTATTAAATATAATTTAATAAAAAAATAAATAATTTAATACA-T
* * * * **
16023810 TTTTAACATGATTATTATTAAATACAATTTAATAAAATATTATGTAATTTAATAACAT
1 TTTTAATATGATTATTATTAAATATAATTTAATAAAAAAATAAATAATTTAAT-ACAT
* *
16023868 TCTTAATATAATTATTATTAAAATATGAA-TTAATAAAAA
1 TTTTAATATGATTATTATT-AAATAT-AATTTAATAAAAA
16023907 TCATAATATA
Statistics
Matches: 81, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
57 46 0.57
58 17 0.21
59 16 0.20
60 2 0.02
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.44
Consensus pattern (57 bp):
TTTTAATATGATTATTATTAAATATAATTTAATAAAAAAATAAATAATTTAATACAT
Found at i:16025352 original size:33 final size:34
Alignment explanation
Indices: 16025315--16025407 Score: 91
Period size: 34 Copynumber: 2.8 Consensus size: 34
16025305 TCAAATCACA
* *
16025315 TTATAAATTTAAT-AAA-TTTAACATATTGTACTG
1 TTATAAATTT-ATGAAACATTAACATACTGTACTG
* *
16025348 TTATAGATTTATGAAACATTAACATACTGTATTG
1 TTATAAATTTATGAAACATTAACATACTGTACTG
* * * *
16025382 TTACAGACTTATGGAACATTAACATA
1 TTATAAATTTATGAAACATTAACATA
16025408 GCTTGAGAAC
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
32 2 0.04
33 12 0.24
34 37 0.73
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.40
Consensus pattern (34 bp):
TTATAAATTTATGAAACATTAACATACTGTACTG
Found at i:16025384 original size:34 final size:34
Alignment explanation
Indices: 16025332--16025407 Score: 107
Period size: 34 Copynumber: 2.2 Consensus size: 34
16025322 TTTAATAAAT
* * *
16025332 TTAACATATTGTACTGTTATAGATTTATGAAACA
1 TTAACATACTGTACTGTTACAGACTTATGAAACA
* *
16025366 TTAACATACTGTATTGTTACAGACTTATGGAACA
1 TTAACATACTGTACTGTTACAGACTTATGAAACA
16025400 TTAACATA
1 TTAACATA
16025408 GCTTGAGAAC
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (34 bp):
TTAACATACTGTACTGTTACAGACTTATGAAACA
Found at i:16033375 original size:37 final size:40
Alignment explanation
Indices: 16033330--16033428 Score: 105
Period size: 38 Copynumber: 2.5 Consensus size: 40
16033320 AGCAATAAAG
* *
16033330 TGACACCCAGTGTCTCATCG-GCCTAGCCGAAGTAAAGT-
1 TGACACCCAGTGTCTCATCGAACCTAGCCGAAGTAAAATA
* ** * *
16033368 TG-TACCCAGTACCTCATCGAATCTATCCGAAGTAAAATAA
1 TGACACCCAGTGTCTCATCGAACCTAGCCGAAGTAAAAT-A
16033408 TGACACCCAGTGTCTCATCGA
1 TGACACCCAGTGTCTCATCGA
16033429 CTCAAGGTCG
Statistics
Matches: 47, Mismatches: 10, Indels: 5
0.76 0.16 0.08
Matches are distributed among these distances:
37 14 0.30
38 16 0.34
40 2 0.04
41 15 0.32
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.23
Consensus pattern (40 bp):
TGACACCCAGTGTCTCATCGAACCTAGCCGAAGTAAAATA
Found at i:16033556 original size:6 final size:6
Alignment explanation
Indices: 16033531--16033569 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
16033521 ACAATTCATA
* * *
16033531 TCACTT TCAATT CCAATT TCACTT TCACTT TCACTT TCA
1 TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCA
16033570 ATTTTGATCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.23, C:0.31, G:0.00, T:0.46
Consensus pattern (6 bp):
TCACTT
Found at i:16037281 original size:23 final size:23
Alignment explanation
Indices: 16037250--16037293 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
16037240 TAGTTTTTGA
16037250 CATTATTGACGTCACAATATATG
1 CATTATTGACGTCACAATATATG
*
16037273 CATTGTTGACGTCACAATATA
1 CATTATTGACGTCACAATATA
16037294 CTATTTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (23 bp):
CATTATTGACGTCACAATATATG
Found at i:16037338 original size:18 final size:18
Alignment explanation
Indices: 16037303--16037356 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
16037293 ACTATTTATT
*
16037303 TTTATCATAAAAATAATTTA
1 TTTATCAT-AAAA-AATTAA
16037323 TTTATCATAAAAAATTAA
1 TTTATCATAAAAAATTAA
* *
16037341 TTTTTCATTAAAAATT
1 TTTATCATAAAAAATT
16037357 CGCTATGAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
18 19 0.61
19 4 0.13
20 8 0.26
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (18 bp):
TTTATCATAAAAAATTAA
Found at i:16039049 original size:12 final size:12
Alignment explanation
Indices: 16039032--16039056 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
16039022 TAGGATTTTT
16039032 TACAAAAAATAA
1 TACAAAAAATAA
16039044 TACAAAAAATAA
1 TACAAAAAATAA
16039056 T
1 T
16039057 TTAGAACCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.08, G:0.00, T:0.20
Consensus pattern (12 bp):
TACAAAAAATAA
Found at i:16039421 original size:20 final size:20
Alignment explanation
Indices: 16039396--16039441 Score: 76
Period size: 20 Copynumber: 2.3 Consensus size: 20
16039386 GCTTAAACAC
16039396 AATTTTTGAAGAAGG-AGACA
1 AATTTTTGAAGAAGGAAGA-A
16039416 AATTTTTGAAGAAGGAAGAA
1 AATTTTTGAAGAAGGAAGAA
16039436 AATTTT
1 AATTTT
16039442 GTTCAAACAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 22 0.88
21 3 0.12
ACGTcount: A:0.46, C:0.02, G:0.22, T:0.30
Consensus pattern (20 bp):
AATTTTTGAAGAAGGAAGAA
Found at i:16041367 original size:42 final size:41
Alignment explanation
Indices: 16041278--16041385 Score: 112
Period size: 42 Copynumber: 2.6 Consensus size: 41
16041268 TTATGCTCCA
* * *
16041278 ACCGAGTCATAAGTCTTCCTTTCTAAACAAATCTTATGCTCT
1 ACCGAGACATAAGTCTTCCATT-TAAACAAATCTCATGCTCT
*
16041320 ACCGAGACATAAGTCTTCC-TTTAAACTTAATCTCATGCTCAT
1 ACCGAGACATAAGTCTTCCATTTAAAC-AAATCTCATGCTC-T
* *
16041362 CCCGAGAGATGAA-TCTTCCATTTA
1 ACCGAGACAT-AAGTCTTCCATTTA
16041386 TACATCAAGT
Statistics
Matches: 57, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
40 5 0.09
41 13 0.23
42 33 0.58
43 6 0.11
ACGTcount: A:0.30, C:0.26, G:0.11, T:0.33
Consensus pattern (41 bp):
ACCGAGACATAAGTCTTCCATTTAAACAAATCTCATGCTCT
Found at i:16048685 original size:26 final size:26
Alignment explanation
Indices: 16048582--16048685 Score: 120
Period size: 25 Copynumber: 4.0 Consensus size: 26
16048572 TTTCATTTTG
* ** *
16048582 AATTAATTAAGTTTATGAATGAATTT
1 AATTAATTATGTTTATGTTTGTATTT
**
16048608 GGAATTAATTATGTTTAAATTTGTATTT
1 --AATTAATTATGTTTATGTTTGTATTT
16048636 AATTAATTAT-TTTATGTTTGTATTT
1 AATTAATTATGTTTATGTTTGTATTT
*
16048661 AATTAATTATGTTGATGTTTGTATT
1 AATTAATTATGTTTATGTTTGTATT
16048686 CAGGGTTTAG
Statistics
Matches: 66, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
25 23 0.35
26 23 0.35
28 20 0.30
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.55
Consensus pattern (26 bp):
AATTAATTATGTTTATGTTTGTATTT
Found at i:16048730 original size:21 final size:21
Alignment explanation
Indices: 16048699--16048757 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
16048689 GGTTTAGGGT
*
16048699 TTTAAGATTTTAAGGTTAAGA
1 TTTATGATTTTAAGGTTAAGA
* *
16048720 TTT-TGAGTTTTAAGTTTAAGC
1 TTTATGA-TTTTAAGGTTAAGA
*
16048741 TTTATGATTTTAGGGTT
1 TTTATGATTTTAAGGTT
16048758 TTAAAGTTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
20 2 0.06
21 26 0.84
22 3 0.10
ACGTcount: A:0.27, C:0.02, G:0.20, T:0.51
Consensus pattern (21 bp):
TTTATGATTTTAAGGTTAAGA
Found at i:16048758 original size:29 final size:28
Alignment explanation
Indices: 16048691--16048766 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 28
16048681 GTATTCAGGG
16048691 TTTAGGGTTTTAAGATTTTAAGGTTAAGAT
1 TTTAGGGTTTTAAG--TTTAAGGTTAAGAT
* * *
16048721 TTT-GAGTTTTAAGTTTAAGCTTTATGAT
1 TTTAGGGTTTTAAGTTTAAG-GTTAAGAT
16048749 TTTAGGGTTTTAAAGTTT
1 TTTAGGGTTTT-AAGTTT
16048767 TTTATTTTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
27 6 0.15
28 9 0.23
29 15 0.38
30 9 0.23
ACGTcount: A:0.26, C:0.01, G:0.21, T:0.51
Consensus pattern (28 bp):
TTTAGGGTTTTAAGTTTAAGGTTAAGAT
Found at i:16048803 original size:14 final size:15
Alignment explanation
Indices: 16048786--16048822 Score: 51
Period size: 13 Copynumber: 2.6 Consensus size: 15
16048776 AGGGTTAAAT
16048786 GTTTAGGGTTTTAGG
1 GTTTAGGGTTTTAGG
*
16048801 TTTTA-GG-TTTAGG
1 GTTTAGGGTTTTAGG
16048814 GTTTAGGGT
1 GTTTAGGGT
16048823 ATAAAGTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 4
0.75 0.08 0.17
Matches are distributed among these distances:
13 10 0.56
14 4 0.22
15 4 0.22
ACGTcount: A:0.14, C:0.00, G:0.38, T:0.49
Consensus pattern (15 bp):
GTTTAGGGTTTTAGG
Found at i:16048831 original size:21 final size:21
Alignment explanation
Indices: 16048772--16048832 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
16048762 AGTTTTTTAT
16048772 TTTTAGGGTTAAATGTTTAGGG
1 TTTTAGGGTTAAA-GTTTAGGG
* * *
16048794 TTTTAGGTTTTAGGTTTAGGG
1 TTTTAGGGTTAAAGTTTAGGG
16048815 -TTTAGGGTATAAAGTTTA
1 TTTTAGGGT-TAAAGTTTA
16048833 TTTAGGGTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
20 7 0.22
21 15 0.47
22 10 0.31
ACGTcount: A:0.23, C:0.00, G:0.30, T:0.48
Consensus pattern (21 bp):
TTTTAGGGTTAAAGTTTAGGG
Found at i:16049893 original size:8 final size:8
Alignment explanation
Indices: 16049848--16049896 Score: 64
Period size: 8 Copynumber: 6.1 Consensus size: 8
16049838 TTTAGGATTT
16049848 AGGTTTT-
1 AGGTTTTA
16049855 AGAGTTTTA
1 AG-GTTTTA
16049864 AGGTTTTA
1 AGGTTTTA
*
16049872 AGGTTATA
1 AGGTTTTA
16049880 AGGTTTTA
1 AGGTTTTA
*
16049888 AAGTTTTA
1 AGGTTTTA
16049896 A
1 A
16049897 CTCCATTAGT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
7 2 0.05
8 33 0.89
9 2 0.05
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (8 bp):
AGGTTTTA
Found at i:16050455 original size:27 final size:27
Alignment explanation
Indices: 16050417--16050468 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
16050407 ATGATACTTC
* *
16050417 TGGCCTGACCAACCCGTATTATATCCA
1 TGGCCTAACCAACCCGTATGATATCCA
*
16050444 TGGCCTAACCAACTCGTATGATATC
1 TGGCCTAACCAACCCGTATGATATC
16050469 TATCATCTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.27, C:0.31, G:0.15, T:0.27
Consensus pattern (27 bp):
TGGCCTAACCAACCCGTATGATATCCA
Found at i:16053541 original size:88 final size:88
Alignment explanation
Indices: 16053392--16053586 Score: 268
Period size: 88 Copynumber: 2.2 Consensus size: 88
16053382 TACACGATGC
* * * **
16053392 TGCTCACATGACCTGCGGAGAATCCACAACATATGCGTGATCTCAGCCATGGGTAGGACATCTAA
1 TGCTCACATGAGCTGTGGAGAATCCACAACATATACGTGATCTCAGCCATCAGTAGGACATCTAA
* *
16053457 GACCAGCA-CTATATAATATGTAA
66 GACCAGCACCCATA-AACATGTAA
* *
16053480 TGCTCACATGAGCTGTGGAGAATCCGCAACATATAC-TGAATCTCCGCCATCAGTAGGACATCTA
1 TGCTCACATGAGCTGTGGAGAATCCACAACATATACGTG-ATCTCAGCCATCAGTAGGACATCTA
16053544 AGACCAGCACCCATAAACATGTAA
65 AGACCAGCACCCATAAACATGTAA
*
16053568 TGCTCACACGAGCTGTGGA
1 TGCTCACATGAGCTGTGGA
16053587 ATGGGTCTGC
Statistics
Matches: 95, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
87 2 0.02
88 89 0.94
89 4 0.04
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.22
Consensus pattern (88 bp):
TGCTCACATGAGCTGTGGAGAATCCACAACATATACGTGATCTCAGCCATCAGTAGGACATCTAA
GACCAGCACCCATAAACATGTAA
Found at i:16056962 original size:27 final size:27
Alignment explanation
Indices: 16056910--16056965 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
16056900 TGAATTAATT
*
16056910 AAAAAAAATTATAAAATAAATCAAAAA
1 AAAAAAAATTATAAAACAAATCAAAAA
*
16056937 AAAAAAAATTATAATAACATAT-AAAAA
1 AAAAAAAATTATAA-AACAAATCAAAAA
16056964 AA
1 AA
16056966 TATAAACACT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 21 0.81
28 5 0.19
ACGTcount: A:0.77, C:0.04, G:0.00, T:0.20
Consensus pattern (27 bp):
AAAAAAAATTATAAAACAAATCAAAAA
Found at i:16057185 original size:22 final size:23
Alignment explanation
Indices: 16057151--16057195 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
16057141 TAAAATCTAC
16057151 AAAATATAAACATTTATCTTAAA
1 AAAATATAAACATTTATCTTAAA
* *
16057174 AAAATAT-TACATTTATGTTAAA
1 AAAATATAAACATTTATCTTAAA
16057196 TAAACCTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.53, C:0.07, G:0.02, T:0.38
Consensus pattern (23 bp):
AAAATATAAACATTTATCTTAAA
Found at i:16068050 original size:10 final size:11
Alignment explanation
Indices: 16068020--16068066 Score: 55
Period size: 12 Copynumber: 4.4 Consensus size: 11
16068010 CTAGTGTTAC
16068020 ATTTAT-TTAT
1 ATTTATATTAT
16068030 ATATT-TATTAT
1 AT-TTATATTAT
16068041 -TTTATATTAT
1 ATTTATATTAT
16068051 ACTTTATATTAT
1 A-TTTATATTAT
16068063 ATTT
1 ATTT
16068067 GTCGCATTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
9 2 0.06
10 10 0.31
11 9 0.28
12 11 0.34
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (11 bp):
ATTTATATTAT
Found at i:16080969 original size:23 final size:25
Alignment explanation
Indices: 16080923--16080970 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
16080913 AGGACTGACG
* *
16080923 ACGACTGGTAAGGGAAAGACAAACA
1 ACGACTGCTAAGGAAAAGACAAACA
16080948 ACGACTGCTAA-GAAAAGA-AAACA
1 ACGACTGCTAAGGAAAAGACAAACA
16080971 GTAGAAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 5 0.24
24 6 0.29
25 10 0.48
ACGTcount: A:0.52, C:0.17, G:0.23, T:0.08
Consensus pattern (25 bp):
ACGACTGCTAAGGAAAAGACAAACA
Found at i:16081003 original size:3 final size:3
Alignment explanation
Indices: 16080997--16081027 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
16080987 GAAAAAAAAA
16080997 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
16081028 TAAAAGTAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:16096185 original size:24 final size:24
Alignment explanation
Indices: 16096153--16096275 Score: 151
Period size: 24 Copynumber: 5.1 Consensus size: 24
16096143 GTATACTGGT
16096153 TAACCATTCTGGGCTCATAAGAGC
1 TAACCATTCTGGGCTCATAAGAGC
*
16096177 TAACCATTCTGGGCTCGTAAGAGC
1 TAACCATTCTGGGCTCATAAGAGC
* * *
16096201 TAAACA-TCTTGAGCTCGTAAGAGC
1 TAACCATTC-TGGGCTCATAAGAGC
16096225 TAACCATTCTGGGCTCATAAGAGC
1 TAACCATTCTGGGCTCATAAGAGC
* * *
16096249 TAAACA-TCTTGGGCTCATGACAGC
1 TAACCATTC-TGGGCTCATAAGAGC
16096273 TAA
1 TAA
16096276 TGTTGTCTGT
Statistics
Matches: 87, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
23 4 0.05
24 81 0.93
25 2 0.02
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.25
Consensus pattern (24 bp):
TAACCATTCTGGGCTCATAAGAGC
Found at i:16096226 original size:48 final size:48
Alignment explanation
Indices: 16096165--16096275 Score: 177
Period size: 48 Copynumber: 2.3 Consensus size: 48
16096155 ACCATTCTGG
*
16096165 GCTCATAAGAGCTAACCATTCTGGGCTCGTAAGAGCTAAACATCTTGA
1 GCTCATAAGAGCTAACCATTCTGGGCTCATAAGAGCTAAACATCTTGA
* *
16096213 GCTCGTAAGAGCTAACCATTCTGGGCTCATAAGAGCTAAACATCTTGG
1 GCTCATAAGAGCTAACCATTCTGGGCTCATAAGAGCTAAACATCTTGA
* *
16096261 GCTCATGACAGCTAA
1 GCTCATAAGAGCTAA
16096276 TGTTGTCTGT
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
48 57 1.00
ACGTcount: A:0.31, C:0.23, G:0.22, T:0.24
Consensus pattern (48 bp):
GCTCATAAGAGCTAACCATTCTGGGCTCATAAGAGCTAAACATCTTGA
Found at i:16097032 original size:21 final size:21
Alignment explanation
Indices: 16096984--16097033 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
16096974 AGAGTTTTTA
*
16096984 GTATCGGTAGAAGCATGACAT
1 GTATCGGTAGAAGCATCACAT
* *
16097005 GTTTCGGTAGAAGTC-TCACTT
1 GTATCGGTAGAAG-CATCACAT
16097026 GTATCGGT
1 GTATCGGT
16097034 TGTACTGTCT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 23 0.96
22 1 0.04
ACGTcount: A:0.24, C:0.16, G:0.28, T:0.32
Consensus pattern (21 bp):
GTATCGGTAGAAGCATCACAT
Found at i:16100987 original size:12 final size:12
Alignment explanation
Indices: 16100964--16100997 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
16100954 AGTATAATTT
*
16100964 AATATAACAAAA
1 AATATAAAAAAA
*
16100976 AGTATAAAAAAA
1 AATATAAAAAAA
16100988 AATATAAAAA
1 AATATAAAAA
16100998 GTGTTATCAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.76, C:0.03, G:0.03, T:0.18
Consensus pattern (12 bp):
AATATAAAAAAA
Found at i:16107824 original size:43 final size:43
Alignment explanation
Indices: 16107754--16107848 Score: 120
Period size: 43 Copynumber: 2.2 Consensus size: 43
16107744 TGTATCACGT
* * ** * * *
16107754 GTTCT-AAAAGTTATTTCTTTTTTAAGGATAGAGTCATATGGG
1 GTTCTGAAAAATTATTTATTTTCCAAGGACAGAGTCACATGGA
16107796 GTTCTGAAAAATTATTTATTTTCCAAGGACAGAGTCACATGGA
1 GTTCTGAAAAATTATTTATTTTCCAAGGACAGAGTCACATGGA
16107839 GTTCTGAAAA
1 GTTCTGAAAA
16107849 GTTTTCTGAA
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
42 5 0.11
43 40 0.89
ACGTcount: A:0.33, C:0.11, G:0.20, T:0.37
Consensus pattern (43 bp):
GTTCTGAAAAATTATTTATTTTCCAAGGACAGAGTCACATGGA
Found at i:16120180 original size:14 final size:14
Alignment explanation
Indices: 16120161--16120194 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
16120151 ATATAGTTAC
16120161 AATGAAAATAAAGA
1 AATGAAAATAAAGA
16120175 AATGAAAATAAAGA
1 AATGAAAATAAAGA
16120189 AA-GAAA
1 AATGAAA
16120195 GAAAACAACT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.20
14 16 0.80
ACGTcount: A:0.74, C:0.00, G:0.15, T:0.12
Consensus pattern (14 bp):
AATGAAAATAAAGA
Found at i:16124218 original size:12 final size:12
Alignment explanation
Indices: 16124201--16124250 Score: 57
Period size: 12 Copynumber: 4.2 Consensus size: 12
16124191 CAGGTTTTGT
16124201 TTCTTCTTTCTC
1 TTCTTCTTTCTC
16124213 TTCTTCCTTTC-C
1 TTCTT-CTTTCTC
*
16124225 TTCTTCTTTTTC
1 TTCTTCTTTCTC
* *
16124237 TTCATCCTTCTC
1 TTCTTCTTTCTC
16124249 TT
1 TT
16124251 GAGCATCTCC
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
11 4 0.12
12 23 0.72
13 5 0.16
ACGTcount: A:0.02, C:0.34, G:0.00, T:0.64
Consensus pattern (12 bp):
TTCTTCTTTCTC
Found at i:16131840 original size:158 final size:158
Alignment explanation
Indices: 16131552--16131868 Score: 589
Period size: 158 Copynumber: 2.0 Consensus size: 158
16131542 AACAAAAGTC
* *
16131552 ATAAACAAGTGACGAAAGCTTCATTTGTACTTTTATGATTCAAGATCATTCCATTTATAAACATG
1 ATAAACAAGTGACGAAAGCTTCATTTCTACTTTTATGATTAAAGATCATTCCATTTATAAACATG
16131617 CATATACATGTTTGTTGCATATTAACTATTAAGGTAAGACTATTACTTGTCTTAAATTGAATTAT
66 CATATACATGTTTGTTGCATATTAACTATTAAGGTAAGACTATTACTTGTCTTAAATTGAATTAT
* *
16131682 GTGATGGTATTGAATGCTGAGATTATGA
131 GTGACGATATTGAATGCTGAGATTATGA
16131710 ATAAACAAGTGACGAAAGCTTCATTTCTACTTTTATGATTAAAGATCATTCCATTTATAAACATG
1 ATAAACAAGTGACGAAAGCTTCATTTCTACTTTTATGATTAAAGATCATTCCATTTATAAACATG
16131775 CATATACATGTTTGTTGCATATTAACTATTAAGGTAAGACTATTACTTGTCTTAAATTGAATTAT
66 CATATACATGTTTGTTGCATATTAACTATTAAGGTAAGACTATTACTTGTCTTAAATTGAATTAT
*
16131840 GTGACGATATTGAATGCTGAGATTGTGA
131 GTGACGATATTGAATGCTGAGATTATGA
16131868 A
1 A
16131869 CTTGTTTGAG
Statistics
Matches: 154, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
158 154 1.00
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (158 bp):
ATAAACAAGTGACGAAAGCTTCATTTCTACTTTTATGATTAAAGATCATTCCATTTATAAACATG
CATATACATGTTTGTTGCATATTAACTATTAAGGTAAGACTATTACTTGTCTTAAATTGAATTAT
GTGACGATATTGAATGCTGAGATTATGA
Found at i:16137234 original size:57 final size:56
Alignment explanation
Indices: 16137173--16137279 Score: 155
Period size: 57 Copynumber: 1.9 Consensus size: 56
16137163 AAAAAAATGA
16137173 AACTTTATTTCTAAA-ATTAAAATGTATTAGATACATAT-TATTCTTAAAATTATTTAT
1 AACTTTATTTCTAAATATTAAAAT-TATTAGATACATATAT-TTC-TAAAATTATTTAT
* *
16137230 AACTTTATTTCTAAATTTTAAAATTATTAGATATATATATTTCTAAAATT
1 AACTTTATTTCTAAATATTAAAATTATTAGATACATATATTTCTAAAATT
16137280 TAAAATGATA
Statistics
Matches: 46, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
56 7 0.15
57 31 0.67
58 8 0.17
ACGTcount: A:0.42, C:0.07, G:0.03, T:0.49
Consensus pattern (56 bp):
AACTTTATTTCTAAATATTAAAATTATTAGATACATATATTTCTAAAATTATTTAT
Found at i:16137254 original size:31 final size:30
Alignment explanation
Indices: 16137216--16137317 Score: 98
Period size: 32 Copynumber: 3.3 Consensus size: 30
16137206 CATATTATTC
16137216 TTAAAATTATTTATAACTTTATTTCTAAATT
1 TTAAAATTATTTATAACTTTATTTCTAAA-T
* *
16137247 TTAAAATTATTAGATATA-TATATTTCTAAAAT
1 TTAAAATTATT-TATA-ACTTTATTTCT-AAAT
* * * * *
16137279 TTAAAATGATATAAAACTTTATTCCTAAAA
1 TTAAAATTATTTATAACTTTATTTCTAAAT
16137309 TTAAAATTA
1 TTAAAATTA
16137318 AAATATATAT
Statistics
Matches: 57, Mismatches: 10, Indels: 9
0.75 0.13 0.12
Matches are distributed among these distances:
30 12 0.21
31 20 0.35
32 21 0.37
33 4 0.07
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.46
Consensus pattern (30 bp):
TTAAAATTATTTATAACTTTATTTCTAAAT
Found at i:16146293 original size:12 final size:12
Alignment explanation
Indices: 16146276--16146300 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
16146266 TCAATCTCCA
16146276 CAGGATCTTCTT
1 CAGGATCTTCTT
16146288 CAGGATCTTCTT
1 CAGGATCTTCTT
16146300 C
1 C
16146301 TTCCTCAGGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.28, G:0.16, T:0.40
Consensus pattern (12 bp):
CAGGATCTTCTT
Found at i:16146296 original size:30 final size:30
Alignment explanation
Indices: 16146262--16146327 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
16146252 TCTAAAGATC
*
16146262 ATCTTCAATC-TCCACAGGATCTTCTTCAGG
1 ATCTTC-ATCTTCCACAGGATCCTCTTCAGG
* * *
16146292 ATCTTCTTCTTCCTCAGGATCCTCTTCTGG
1 ATCTTCATCTTCCACAGGATCCTCTTCAGG
16146322 ATCTTC
1 ATCTTC
16146328 TTCATCTTCA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 2 0.06
30 29 0.94
ACGTcount: A:0.17, C:0.32, G:0.12, T:0.39
Consensus pattern (30 bp):
ATCTTCATCTTCCACAGGATCCTCTTCAGG
Found at i:16146302 original size:18 final size:18
Alignment explanation
Indices: 16146281--16146354 Score: 79
Period size: 18 Copynumber: 4.4 Consensus size: 18
16146271 CTCCACAGGA
16146281 TCTTCTTCAGGATCTTCT
1 TCTTCTTCAGGATCTTCT
*
16146299 TCTTCCTCAGGATC--C-
1 TCTTCTTCAGGATCTTCT
16146314 TCTTC-T--GGATCTTCT
1 TCTTCTTCAGGATCTTCT
* *
16146329 TCATCTTCAGGGTCTTCT
1 TCTTCTTCAGGATCTTCT
16146347 TCTTCTTC
1 TCTTCTTC
16146355 TTTAGCTTGT
Statistics
Matches: 46, Mismatches: 4, Indels: 12
0.74 0.06 0.19
Matches are distributed among these distances:
12 5 0.11
14 2 0.04
15 9 0.20
16 2 0.04
18 28 0.61
ACGTcount: A:0.09, C:0.31, G:0.12, T:0.47
Consensus pattern (18 bp):
TCTTCTTCAGGATCTTCT
Found at i:16146328 original size:30 final size:30
Alignment explanation
Indices: 16146276--16146349 Score: 103
Period size: 30 Copynumber: 2.5 Consensus size: 30
16146266 TCAATCTCCA
* *
16146276 CAGGATCTTCTTCAGGATCTTCTTCTTCCT
1 CAGGATCTTCTTCTGGATCTTCTTCATCCT
* *
16146306 CAGGATCCTCTTCTGGATCTTCTTCATCTT
1 CAGGATCTTCTTCTGGATCTTCTTCATCCT
*
16146336 CAGGGTCTTCTTCT
1 CAGGATCTTCTTCT
16146350 TCTTCTTTAG
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.12, C:0.30, G:0.15, T:0.43
Consensus pattern (30 bp):
CAGGATCTTCTTCTGGATCTTCTTCATCCT
Found at i:16147949 original size:28 final size:28
Alignment explanation
Indices: 16147895--16147950 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
16147885 CTATTTTAAA
* *
16147895 AATATTTACAAAAATGAACAACTATTTT
1 AATATTCACAAAAATGAACAACAATTTT
*
16147923 AATATTCAC-AAAATTAACAACCAATTTT
1 AATATTCACAAAAATGAACAA-CAATTTT
16147951 TACAAAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 10 0.42
28 14 0.58
ACGTcount: A:0.50, C:0.14, G:0.02, T:0.34
Consensus pattern (28 bp):
AATATTCACAAAAATGAACAACAATTTT
Found at i:16151452 original size:12 final size:13
Alignment explanation
Indices: 16151437--16151468 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
16151427 TCACATGTAT
16151437 ATCTCAATA-TTA
1 ATCTCAATACTTA
16151449 ATCTCAA-ACTTA
1 ATCTCAATACTTA
16151461 ATCTCAAT
1 ATCTCAAT
16151469 CTCATTAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 1 0.06
12 17 0.94
ACGTcount: A:0.41, C:0.22, G:0.00, T:0.38
Consensus pattern (13 bp):
ATCTCAATACTTA
Found at i:16152150 original size:19 final size:20
Alignment explanation
Indices: 16152117--16152154 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
16152107 GGGTTTCTCA
16152117 AAAAATTAACTGGTCAACAG
1 AAAAATTAACTGGTCAACAG
*
16152137 AAAAGTTAAC-GGTCAACA
1 AAAAATTAACTGGTCAACA
16152155 TTCAAGTCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.50, C:0.16, G:0.16, T:0.18
Consensus pattern (20 bp):
AAAAATTAACTGGTCAACAG
Found at i:16155785 original size:19 final size:19
Alignment explanation
Indices: 16155763--16155800 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
16155753 CCTTAGGTTC
*
16155763 CATTCCATAAGGTGTCATG
1 CATTCCATAAGGTGCCATG
*
16155782 CATTCGATAAGGTGCCATG
1 CATTCCATAAGGTGCCATG
16155801 GACACATGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (19 bp):
CATTCCATAAGGTGCCATG
Found at i:16159293 original size:33 final size:33
Alignment explanation
Indices: 16159256--16159319 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
16159246 TCAACAATCA
*
16159256 ACGGTCGATGATCAAC-AGTCAAGTCAATGGTTG
1 ACGGTAGATGATCAACGA-TCAAGTCAATGGTTG
* *
16159289 ACGGTAGATGGTCAACGATCAAGTTAATGGT
1 ACGGTAGATGATCAACGATCAAGTCAATGGT
16159320 CAACAGTCAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
33 26 0.96
34 1 0.04
ACGTcount: A:0.31, C:0.16, G:0.28, T:0.25
Consensus pattern (33 bp):
ACGGTAGATGATCAACGATCAAGTCAATGGTTG
Found at i:16161575 original size:21 final size:21
Alignment explanation
Indices: 16161551--16161592 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
16161541 TATTCACCAC
* **
16161551 TTCTGGTTCTGGTGAAGTTGG
1 TTCTAGTTCTGGCAAAGTTGG
16161572 TTCTAGTTCTGGCAAAGTTGG
1 TTCTAGTTCTGGCAAAGTTGG
16161593 AGTTTCAACA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.14, C:0.12, G:0.33, T:0.40
Consensus pattern (21 bp):
TTCTAGTTCTGGCAAAGTTGG
Found at i:16163702 original size:42 final size:42
Alignment explanation
Indices: 16163643--16163730 Score: 158
Period size: 42 Copynumber: 2.1 Consensus size: 42
16163633 AATTTATCGC
*
16163643 TTGAACATACACCTATGCCAATACGACCGACTAAAGTAACCT
1 TTGAACATACACCTATGCCAATACGACCGACTAAACTAACCT
*
16163685 TTGAACATACACCTATGCCAATACGACTGACTAAACTAACCT
1 TTGAACATACACCTATGCCAATACGACCGACTAAACTAACCT
16163727 TTGA
1 TTGA
16163731 TAAGTAAATG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.38, C:0.27, G:0.11, T:0.24
Consensus pattern (42 bp):
TTGAACATACACCTATGCCAATACGACCGACTAAACTAACCT
Found at i:16166645 original size:21 final size:21
Alignment explanation
Indices: 16166629--16166697 Score: 111
Period size: 21 Copynumber: 3.3 Consensus size: 21
16166619 ATAATTAAGG
16166629 ATTGAGGATTGAGAATTGAGA
1 ATTGAGGATTGAGAATTGAGA
*
16166650 ATTGAGGATTGAGAACTGAGA
1 ATTGAGGATTGAGAATTGAGA
* *
16166671 ATTGAGGATTGAGTATTGAGT
1 ATTGAGGATTGAGAATTGAGA
16166692 ATTGAG
1 ATTGAG
16166698 TATTAAGTTG
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.35, C:0.01, G:0.33, T:0.30
Consensus pattern (21 bp):
ATTGAGGATTGAGAATTGAGA
Found at i:16166701 original size:7 final size:7
Alignment explanation
Indices: 16166629--16166697 Score: 84
Period size: 7 Copynumber: 9.9 Consensus size: 7
16166619 ATAATTAAGG
*
16166629 ATTGAGG
1 ATTGAGA
16166636 ATTGAGA
1 ATTGAGA
16166643 ATTGAGA
1 ATTGAGA
*
16166650 ATTGAGG
1 ATTGAGA
16166657 ATTGAGA
1 ATTGAGA
*
16166664 ACTGAGA
1 ATTGAGA
*
16166671 ATTGAGG
1 ATTGAGA
*
16166678 ATTGAGT
1 ATTGAGA
*
16166685 ATTGAGT
1 ATTGAGA
16166692 ATTGAG
1 ATTGAG
16166698 TATTAAGTTG
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 55 1.00
ACGTcount: A:0.35, C:0.01, G:0.33, T:0.30
Consensus pattern (7 bp):
ATTGAGA
Found at i:16166800 original size:15 final size:16
Alignment explanation
Indices: 16166774--16166803 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
16166764 TCTAGCCGGT
16166774 GAAAATGTTATCGTTG
1 GAAAATGTTATCGTTG
16166790 GAAAA-GTTATCGTT
1 GAAAATGTTATCGTT
16166804 AAAAGGAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.33, C:0.07, G:0.23, T:0.37
Consensus pattern (16 bp):
GAAAATGTTATCGTTG
Found at i:16169023 original size:23 final size:23
Alignment explanation
Indices: 16168994--16169040 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
16168984 ATTTGCTTTG
*
16168994 AAATTAAAT-TTATT-TATAATTT
1 AAATTTAATATTATTGTA-AATTT
16169016 AAATTTAATATTATTGTAAATTT
1 AAATTTAATATTATTGTAAATTT
16169039 AA
1 AA
16169041 TGTCCCTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 8 0.36
23 12 0.55
24 2 0.09
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (23 bp):
AAATTTAATATTATTGTAAATTT
Found at i:16171009 original size:29 final size:28
Alignment explanation
Indices: 16170959--16171030 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 28
16170949 GGAGGTTCCT
16170959 AAACTGTCCAAAAAATTTTTTTGACCC-CG
1 AAACT-TCC-AAAAATTTTTTTGACCCTCG
*
16170988 AAACTTCCAAAAATTATATTTTTACCCTCG
1 AAACTTCCAAAAATT-T-TTTTGACCCTCG
16171018 -AACTTCCAAAAAT
1 AAACTTCCAAAAAT
16171031 CCATTTTGAC
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
27 7 0.18
28 4 0.10
29 26 0.67
30 2 0.05
ACGTcount: A:0.39, C:0.24, G:0.06, T:0.32
Consensus pattern (28 bp):
AAACTTCCAAAAATTTTTTTGACCCTCG
Found at i:16171037 original size:28 final size:30
Alignment explanation
Indices: 16170976--16171043 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 30
16170966 CCAAAAAATT
*
16170976 TTTTTGACCC-CGAAACTTCCAAAAATTATA
1 TTTTT-ACCCTCGAAACTTCCAAAAATTACA
*
16171006 TTTTTACCCTCG-AACTTCCAAAAA-TCCA
1 TTTTTACCCTCGAAACTTCCAAAAATTACA
*
16171034 TTTTGACCCT
1 TTTTTACCCT
16171044 AATTTTACCC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
28 11 0.32
29 16 0.47
30 7 0.21
ACGTcount: A:0.31, C:0.28, G:0.06, T:0.35
Consensus pattern (30 bp):
TTTTTACCCTCGAAACTTCCAAAAATTACA
Found at i:16171058 original size:57 final size:58
Alignment explanation
Indices: 16170994--16171130 Score: 161
Period size: 58 Copynumber: 2.4 Consensus size: 58
16170984 CCCGAAACTT
* * *
16170994 CCAAAAATTA-TATTTTTACCCTCGAACTTCCAAAAATCCA-TTTTGACCCTAATTTTA
1 CCAAAAATTACTA-TTTTACCCCCGAACTTCCAAAAATCCATTTTTAACCCCAATTTTA
* * * * ** *
16171051 CCCAAAATTACCATTTTACCCCCGAACTTTCTAAAATTTATTTTTAACCCCGATTTTA
1 CCAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCCATTTTTAACCCCAATTTTA
16171109 CCAAAAATTACTATTTTACCCC
1 CCAAAAATTACTATTTTACCCC
16171131 AGAAAGTCCA
Statistics
Matches: 66, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
57 31 0.47
58 35 0.53
ACGTcount: A:0.34, C:0.27, G:0.03, T:0.36
Consensus pattern (58 bp):
CCAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCCATTTTTAACCCCAATTTTA
Found at i:16171129 original size:29 final size:28
Alignment explanation
Indices: 16170992--16171153 Score: 84
Period size: 28 Copynumber: 5.7 Consensus size: 28
16170982 ACCCCGAAAC
**
16170992 TTCCAAAAATTA-TATTTTTACCCTCGAAC
1 TTCCAAAAATTACTA-TTTTACCC-CGATT
* **
16171021 TTCCAAAAA-T-CCATTTTGACCCTAATT
1 TTCCAAAAATTACTATTTT-ACCCCGATT
* * *
16171048 TTACCCAAAATTACCATTTTACCCCCGAACT
1 TT-CCAAAAATTACTATTTTA-CCCCG-ATT
* *
16171079 TTCTAAAATTTA-T-TTTTAACCCCGATT
1 TTCCAAAAATTACTATTTT-ACCCCGATT
**
16171106 TTACCAAAAATTACTATTTTACCCCAGAAA
1 TT-CCAAAAATTACTATTTTACCCC-GATT
*
16171136 GTCC-AAAATTACTATTTT
1 TTCCAAAAATTACTATTTT
16171154 GCCCACAGGT
Statistics
Matches: 102, Mismatches: 19, Indels: 25
0.70 0.13 0.17
Matches are distributed among these distances:
27 11 0.11
28 43 0.42
29 20 0.20
30 24 0.24
31 4 0.04
ACGTcount: A:0.35, C:0.25, G:0.04, T:0.37
Consensus pattern (28 bp):
TTCCAAAAATTACTATTTTACCCCGATT
Found at i:16171304 original size:17 final size:16
Alignment explanation
Indices: 16171265--16171295 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
16171255 CATGTTCGTT
16171265 TCATTTT-TTTGCTTA
1 TCATTTTATTTGCTTA
16171280 TCATTTTATTTGCTTA
1 TCATTTTATTTGCTTA
16171296 GTTATTTTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.16, C:0.13, G:0.06, T:0.65
Consensus pattern (16 bp):
TCATTTTATTTGCTTA
Found at i:16175349 original size:17 final size:18
Alignment explanation
Indices: 16175328--16175378 Score: 59
Period size: 19 Copynumber: 2.8 Consensus size: 18
16175318 TTATCAAAAC
16175328 AAAAAAGAAAAAAAAAG-
1 AAAAAAGAAAAAAAAAGA
* *
16175345 GAAAAAGAAAAGAAAGAGA
1 AAAAAAGAAAA-AAAAAGA
16175364 AAAAAAGAAGAAAAA
1 AAAAAAGAA-AAAAA
16175379 GGTCAAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
17 10 0.36
18 5 0.18
19 11 0.39
20 2 0.07
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (18 bp):
AAAAAAGAAAAAAAAAGA
Found at i:16175359 original size:11 final size:11
Alignment explanation
Indices: 16175330--16175377 Score: 55
Period size: 11 Copynumber: 4.4 Consensus size: 11
16175320 ATCAAAACAA
16175330 AAAAGAAAAA-
1 AAAAGAAAAAG
16175340 AAAAGGAAAAAG
1 AAAA-GAAAAAG
*
16175352 AAAAGAAAGAG
1 AAAAGAAAAAG
16175363 AAAA-AAAGAAG
1 AAAAGAAA-AAG
16175374 AAAA
1 AAAA
16175378 AGGTCAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
10 7 0.21
11 22 0.67
12 4 0.12
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (11 bp):
AAAAGAAAAAG
Found at i:16177272 original size:101 final size:100
Alignment explanation
Indices: 16177117--16177412 Score: 309
Period size: 101 Copynumber: 3.0 Consensus size: 100
16177107 GAAAGATCTA
* * * * * *
16177117 AGACCGTGTACCTCAAAAGACACGACGGGAAAGATCTAAGATCGCAATGGCGGATCCAGTACTGC
1 AGACCGTATACCTCAGAAGACATGACGAGAAAGATCTAAGACCGCAACGGCGGATCCAGTAC--C
* **
16177182 AAAAAGACA-AAAAGGAAAGGTCTAAGTTGCAACAGC
64 AAAAAGACATAAAAGGAAAGATCTAAGCCGCAACAGC
* *
16177218 AGACCGTATACCTCAGAAGACATGACGAGAAAGATCTAAGACCGCAACGACGGATCCAGTACCAG
1 AGACCGTATACCTCAGAAGACATGACGAGAAAGATCTAAGACCGCAACGGCGGATCCAGTACCAA
* * * *
16177283 GAAGACATGAAGGGAAAGATCTAAGCCGCAACGGC
66 AAAGACATAAAAGGAAAGATCTAAGCCGCAACAGC
* * *
16177318 GGATCC--AGTA-C-CATGAAGACATGAAGAGAAAGATCTAAG-CCGCAACGGCAGATCCAGTAC
1 AGA-CCGTA-TACCTCA-GAAGACATGACGAGAAAGATCTAAGACCGCAACGGCGGATCCAGTAC
* *
16177378 CACAAAA-ACATGAAGGGAAAGATCTAAGCCGCAAC
63 CA-AAAAGACATAAAAGGAAAGATCTAAGCCGCAAC
16177413 GGTAGATCCA
Statistics
Matches: 169, Mismatches: 21, Indels: 13
0.83 0.10 0.06
Matches are distributed among these distances:
98 51 0.30
99 36 0.21
100 25 0.15
101 57 0.34
ACGTcount: A:0.41, C:0.23, G:0.25, T:0.12
Consensus pattern (100 bp):
AGACCGTATACCTCAGAAGACATGACGAGAAAGATCTAAGACCGCAACGGCGGATCCAGTACCAA
AAAGACATAAAAGGAAAGATCTAAGCCGCAACAGC
Found at i:16177330 original size:49 final size:49
Alignment explanation
Indices: 16177233--16177476 Score: 308
Period size: 49 Copynumber: 5.0 Consensus size: 49
16177223 GTATACCTCA
* * * *
16177233 GAAGACATGACGAGAAAGATCTAAGACCGCAACGACGGATCCAGTACCAG
1 GAAGACATGAAGGGAAAGATCTAAG-CCGCAACGGCGGATCCAGTACCAC
*
16177283 GAAGACATGAAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCAT
1 GAAGACATGAAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCAC
* *
16177332 GAAGACATGAAGAGAAAGATCTAAGCCGCAACGGCAGATCCAGTACCAC
1 GAAGACATGAAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCAC
* * **
16177381 AAAAACATGAAGGGAAAGATCTAAGCCGCAACGGTAGATCCAGTACCAC
1 GAAGACATGAAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCAC
** * * ** * *
16177430 GAAGATTTGAAGGGAAAGGTTTAAGTTGCAACGGCGAACCCAGTACC
1 GAAGACATGAAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACC
16177477 TTAGAAACAT
Statistics
Matches: 171, Mismatches: 23, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
49 148 0.87
50 23 0.13
ACGTcount: A:0.39, C:0.22, G:0.26, T:0.13
Consensus pattern (49 bp):
GAAGACATGAAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCAC
Found at i:16177434 original size:147 final size:147
Alignment explanation
Indices: 16177133--16177476 Score: 361
Period size: 147 Copynumber: 2.3 Consensus size: 147
16177123 TGTACCTCAA
* * *
16177133 AAGACACGACGGGAAAGATCTAAGATCGCAATGGCGGATCCAGTACTGCAAAAAGACAAAAAGGA
1 AAGACATGAAGGGAAAGATCTAAG-TCGCAACGGCGGATCCAGTAC--CAAAAAGACAAAAAGGA
* ** * * *
16177198 AAGGTCTAAGTTGCAACAGCAGACCGTATACCTCAGAAGACATGACGAGAAAGATCTAAGACCGC
63 AAGATCTAAGCCGCAACAGCAGACCG-ATACCACAGAAAACATGAAGAGAAAGATCTAAGACCGC
* *
16177263 AACGACGGATCCAGTACCAGG
127 AACGACAGATCCAGTACCACG
* ** **
16177284 AAGACATGAAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCATGAAGACATGAAGAGAAA
1 AAGACATGAAGGGAAAGATCTAAGTCGCAACGGCGGATCCAGTACCAAAAAGACAAAAAG-GAAA
* *
16177349 GATCTAAGCCGCAACGGCAGATCC-AGTACCACA-AAAACATGAAGGGAAAGATCTAAG-CCGCA
65 GATCTAAGCCGCAACAGCAGA-CCGA-TACCACAGAAAACATGAAGAGAAAGATCTAAGACCGCA
**
16177411 ACGGTAGATCCAGTACCACG
128 ACGACAGATCCAGTACCACG
** * * * * *
16177431 AAGATTTGAAGGGAAAGGTTTAAGTTGCAACGGCGAACCCAGTACC
1 AAGACATGAAGGGAAAGATCTAAGTCGCAACGGCGGATCCAGTACC
16177477 TTAGAAACAT
Statistics
Matches: 162, Mismatches: 28, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
147 59 0.36
148 33 0.20
149 27 0.17
150 21 0.13
151 22 0.14
ACGTcount: A:0.40, C:0.22, G:0.26, T:0.13
Consensus pattern (147 bp):
AAGACATGAAGGGAAAGATCTAAGTCGCAACGGCGGATCCAGTACCAAAAAGACAAAAAGGAAAG
ATCTAAGCCGCAACAGCAGACCGATACCACAGAAAACATGAAGAGAAAGATCTAAGACCGCAACG
ACAGATCCAGTACCACG
Found at i:16178195 original size:201 final size:200
Alignment explanation
Indices: 16177851--16178435 Score: 760
Period size: 201 Copynumber: 2.9 Consensus size: 200
16177841 AGTGAGGCGA
* * * *
16177851 TCATCTTCCTGATGAGATACAGAGAAGTATACCAACTCAATGCTCAATGCGAGCAAATCCTC-AA
1 TCATCTTCCTGATGAGATATAGAGAAGAATACCAACTC-ACGCTCAATGCGAGCAAATCTTCGAA
* *
16177915 ACCCAGCTTCCTGATAAGATACTGAGAAGCAAGTCGAAGCAATAAAATGGTTAGCTTCCTGATGA
65 ACCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGA
*
16177980 GACACAGAGAAGTGGACCAAATTCGTCTTCCTGATGAGACACAGAGAAGCGAATTAAAACAGGCA
130 GACACAGAGAAGTGGACCAAATTCGTCTTCCTGATGAGACACAGAGAAGCGAATTAAAACAAGCA
16178045 AAGCGG
195 AAGCGG
*
16178051 TCATCTTCCTGATGAGATATAGAGAAGAATACCAACTCGACGCTCGATGCGAGCAAATCTTCGAA
1 TCATCTTCCTGATGAGATATAGAGAAGAATACCAACTC-ACGCTCAATGCGAGCAAATCTTCGAA
* *
16178116 CCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGA
65 ACCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGA
* ** * * *
16178181 GATACTA-AGAAGTGGACCAAATTTTTCTTCCTGATGAGACACAGAGAAGTGAATTGAAACAAGT
130 GACAC-AGAGAAGTGGACCAAATTCGTCTTCCTGATGAGACACAGAGAAGCGAATTAAAACAAGC
* *
16178245 GATGCGG
194 AAAGCGG
* * * * *
16178252 TCATCTTCCTGATGAGACACTGAGAAGAAGACCAAATCAAACTCAGGCTCAACGCGAGCAAATCT
1 TCATCTTCCTGATGAGATA-T-AG-AGAAGA--ATA-CCAACTCACGCTCAATGCGAGCAAATCT
* * * * **
16178317 TCGAATCCCAGCTTCTTGATGAGATAGTGAGAAGCAGGTAGAAGCAATAAAGCGGTTAGCTTCCT
60 TCGAAACCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCT
* * * * * *
16178382 GATGAGCCACAGAGAAGTGAACCAAATCCGTCTTCCTGTTGAAACATAGAGAAG
125 GATGAGACACAGAGAAGTGGACCAAATTCGTCTTCCTGATGAGACACAGAGAAG
16178436 TGGATCAAAA
Statistics
Matches: 335, Mismatches: 41, Indels: 12
0.86 0.11 0.03
Matches are distributed among these distances:
200 56 0.17
201 141 0.42
202 2 0.01
203 2 0.01
204 6 0.02
205 1 0.00
206 121 0.36
207 6 0.02
ACGTcount: A:0.35, C:0.21, G:0.23, T:0.21
Consensus pattern (200 bp):
TCATCTTCCTGATGAGATATAGAGAAGAATACCAACTCACGCTCAATGCGAGCAAATCTTCGAAA
CCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGAG
ACACAGAGAAGTGGACCAAATTCGTCTTCCTGATGAGACACAGAGAAGCGAATTAAAACAAGCAA
AGCGG
Found at i:16178383 original size:206 final size:204
Alignment explanation
Indices: 16177851--16178498 Score: 774
Period size: 206 Copynumber: 3.2 Consensus size: 204
16177841 AGTGAGGCGA
* * * * * *
16177851 TCATCTTCCTGATGAGATACAGAGAAGTATACCAACTCAA-T--GCTCAATGCGAGCAAATCCTC
1 TCATCTTCCTGATGAGACACTGAGAAGAAGACCAAATCAACTCAGCTCAATGCGAGCAAATCTTC
* *
16177913 -AAACCCAGCTTCCTGATAAGATACTGAGAAGCAAGTCGAAGCAATAAAATGGTTAGCTTCCTGA
66 GAAACCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGA
* *
16177977 TGAGACACAGAGAAGTGGACCAAATTCGTCTTCCTGATGAGACACAGAGAAGCGAATTAAAACAG
131 TGAGACACAGAGAAGTGGACCAAATTCGTCTTCCTGATGAGACACAGAGAAGTGAATTAAAACAA
*
16178042 GCAAAGCGG
196 GCGAAGCGG
* * * * *
16178051 TCATCTTCCTGATGAGATA-TAGAGAAGAATACCAACTCGA--C-GCTCGATGCGAGCAAATCTT
1 TCATCTTCCTGATGAGACACT-GAGAAGAAGACCAAATCAACTCAGCTCAATGCGAGCAAATCTT
* *
16178112 CGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTG
65 CGAAACCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTG
* ** *
16178177 ATGAGATACTA-AGAAGTGGACCAAATTTTTCTTCCTGATGAGACACAGAGAAGTGAATTGAAAC
130 ATGAGACAC-AGAGAAGTGGACCAAATTCGTCTTCCTGATGAGACACAGAGAAGTGAATTAAAAC
* *
16178241 AAGTGATGCGG
194 AAGCGAAGCGG
*
16178252 TCATCTTCCTGATGAGACACTGAGAAGAAGACCAAATCAAACTCAGGCTCAACGCGAGCAAATCT
1 TCATCTTCCTGATGAGACACTGAGAAGAAGACCAAATC-AACTCA-GCTCAATGCGAGCAAATCT
* * * * **
16178317 TCGAATCCCAGCTTCTTGATGAGATAGTGAGAAGCAGGTAGAAGCAATAAAGCGGTTAGCTTCCT
64 TCGAAACCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCT
* * * * * * * *
16178382 GATGAGCCACAGAGAAGTGAACCAAATCCGTCTTCCTGTTGAAACATAGAGAAGTGGATCAAAAC
129 GATGAGACACAGAGAAGTGGACCAAATTCGTCTTCCTGATGAGACACAGAGAAGTGAATTAAAAC
* * *
16178447 AAACGACGCAG
194 AAGCGAAGCGG
* * * * *
16178458 TCACCTTCTTGATGAGACACTGAGAAGGAGGCCAAGTCAAC
1 TCATCTTCCTGATGAGACACTGAGAAGAAGACCAAATCAAC
16178499 AAAACCAAAG
Statistics
Matches: 385, Mismatches: 52, Indels: 17
0.85 0.11 0.04
Matches are distributed among these distances:
200 55 0.14
201 156 0.41
202 3 0.01
204 1 0.00
205 4 0.01
206 166 0.43
ACGTcount: A:0.35, C:0.21, G:0.23, T:0.21
Consensus pattern (204 bp):
TCATCTTCCTGATGAGACACTGAGAAGAAGACCAAATCAACTCAGCTCAATGCGAGCAAATCTTC
GAAACCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGA
TGAGACACAGAGAAGTGGACCAAATTCGTCTTCCTGATGAGACACAGAGAAGTGAATTAAAACAA
GCGAAGCGG
Found at i:16178845 original size:6 final size:6
Alignment explanation
Indices: 16178834--16178912 Score: 60
Period size: 6 Copynumber: 13.8 Consensus size: 6
16178824 TTAAACTTGC
* * *
16178834 TTTAAA TTTAAA TTT-AT TTTAAA TTTAAA TTT--A TTTCTAA TTTGAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA
* * *
16178880 TTT-AA TTTAAG TTTGAA TTT-AA TCTAAA TTTAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA
16178913 TATTATTATA
Statistics
Matches: 59, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
4 4 0.07
5 13 0.22
6 38 0.64
7 4 0.07
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:16178845 original size:17 final size:17
Alignment explanation
Indices: 16178823--16178862 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
16178813 CCCAAACCAT
*
16178823 TTTAAACTTGCTTTAAA
1 TTTAAACTTACTTTAAA
* *
16178840 TTTAAATTTATTTTAAA
1 TTTAAACTTACTTTAAA
16178857 TTTAAA
1 TTTAAA
16178863 TTTATTTCTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.40, C:0.05, G:0.03, T:0.53
Consensus pattern (17 bp):
TTTAAACTTACTTTAAA
Found at i:16178860 original size:23 final size:22
Alignment explanation
Indices: 16178834--16178929 Score: 81
Period size: 23 Copynumber: 4.2 Consensus size: 22
16178824 TTAAACTTGC
*
16178834 TTTAAATTTAAATTTATTTTAAA
1 TTTAAATTT-AATTTAATTTAAA
* *
16178857 TTTAAATTTATTTCTAATTTGAA
1 TTTAAATTTAATT-TAATTTAAA
16178880 TTT-AATTTAAGTTTGAATTT-AA
1 TTTAAATTTAA-TTT-AATTTAAA
*
16178902 TCTAAATTTAATATT-ATTATAAA
1 TTTAAATTTAAT-TTAATT-TAAA
16178925 TTTAA
1 TTTAA
16178930 TGTCCCTTTA
Statistics
Matches: 60, Mismatches: 6, Indels: 14
0.75 0.08 0.17
Matches are distributed among these distances:
21 3 0.05
22 16 0.27
23 41 0.68
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54
Consensus pattern (22 bp):
TTTAAATTTAATTTAATTTAAA
Found at i:16178863 original size:17 final size:17
Alignment explanation
Indices: 16178834--16178929 Score: 97
Period size: 17 Copynumber: 5.6 Consensus size: 17
16178824 TTAAACTTGC
16178834 TTTAAATTTAAATTTAT
1 TTTAAATTTAAATTTAT
16178851 TTTAAATTTAAATTTAT
1 TTTAAATTTAAATTTAT
* *
16178868 TTCT-AATTTGAATTTAA
1 TT-TAAATTTAAATTTAT
* * *
16178885 TTTAAGTTTGAATTTAA
1 TTTAAATTTAAATTTAT
*
16178902 TCTAAATTT-AATATTAT
1 TTTAAATTTAAAT-TTAT
*
16178919 TATAAATTTAA
1 TTTAAATTTAA
16178930 TGTCCCTTTA
Statistics
Matches: 68, Mismatches: 7, Indels: 7
0.83 0.09 0.09
Matches are distributed among these distances:
16 4 0.06
17 62 0.91
18 2 0.03
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54
Consensus pattern (17 bp):
TTTAAATTTAAATTTAT
Found at i:16178885 original size:11 final size:10
Alignment explanation
Indices: 16178838--16178913 Score: 53
Period size: 11 Copynumber: 6.8 Consensus size: 10
16178828 ACTTGCTTTA
16178838 AATTTAAATTT
1 AATTT-AATTT
*
16178849 ATTTTAAATTT
1 AATTT-AATTT
*
16178860 AAATTTATTTCT
1 -AATTTAATT-T
16178872 AATTTGAATTT
1 AATTT-AATTT
16178883 AATTTAAGTTT
1 AATTTAA-TTT
*
16178894 GAATTTAATCTA
1 -AATTTAAT-TT
16178906 AATTTAAT
1 AATTTAAT
16178914 ATTATTATAA
Statistics
Matches: 54, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
10 2 0.04
11 36 0.67
12 16 0.30
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (10 bp):
AATTTAATTT
Found at i:16179233 original size:28 final size:29
Alignment explanation
Indices: 16179176--16179255 Score: 112
Period size: 28 Copynumber: 2.8 Consensus size: 29
16179166 CCCTAAGCTG
16179176 TCCAAAAATT-ATGTTTTGACCCCGAAACT
1 TCCAAAAATTCAT-TTTTGACCCCGAAACT
16179205 TCCAAAAATTACATTTTTG-CCCCG-AACT
1 TCCAAAAATT-CATTTTTGACCCCGAAACT
16179233 TCCAAAAATTCCATTTTTGACCC
1 TCCAAAAATT-CATTTTTGACCC
16179256 TGATTTTACC
Statistics
Matches: 47, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
28 22 0.47
29 18 0.38
30 5 0.11
31 2 0.04
ACGTcount: A:0.33, C:0.28, G:0.07, T:0.33
Consensus pattern (29 bp):
TCCAAAAATTCATTTTTGACCCCGAAACT
Found at i:16179271 original size:58 final size:58
Alignment explanation
Indices: 16179206--16179343 Score: 167
Period size: 58 Copynumber: 2.4 Consensus size: 58
16179196 CCCGAAACTT
**
16179206 CCAAAAATTA-CATTTT-TGCCCCGAAC-TTCCAAAAATTCCATTTTTGACCCTGATTTTA
1 CCAAAAATTACCATTTTACCCCCCGAACTTTCCAAAAATT-CA-TTTTGACCC-GATTTTA
* * *
16179264 CCCAAAATTACCATTTTACCCCCCGAACTTTCTAAAACTTCATTTTGACCCGATTTTA
1 CCAAAAATTACCATTTTACCCCCCGAACTTTCCAAAAATTCATTTTGACCCGATTTTA
*
16179322 TCAAAAATTACCATTTT-CCCCC
1 CCAAAAATTACCATTTTACCCCC
16179344 AAAGTCCAAA
Statistics
Matches: 70, Mismatches: 7, Indels: 7
0.83 0.08 0.08
Matches are distributed among these distances:
57 5 0.07
58 31 0.44
59 15 0.21
60 10 0.14
61 9 0.13
ACGTcount: A:0.30, C:0.30, G:0.05, T:0.35
Consensus pattern (58 bp):
CCAAAAATTACCATTTTACCCCCCGAACTTTCCAAAAATTCATTTTGACCCGATTTTA
Found at i:16179336 original size:29 final size:28
Alignment explanation
Indices: 16179235--16179338 Score: 70
Period size: 27 Copynumber: 3.5 Consensus size: 28
16179225 CCCGAACTTC
*
16179235 CAAAAATTCCATTTTTGACCCTGATTTTAC
1 CAAAAATTCCA-TTTTGACCC-GATTTTAT
* **
16179265 CCAAAATTACCATTTT-ACCCCCCGAACTT-T
1 CAAAAATT-CCATTTTGA---CCCGATTTTAT
*
16179295 CTAAAACTT-CATTTTGACCCGATTTTAT
1 C-AAAAATTCCATTTTGACCCGATTTTAT
16179323 CAAAAATTACCATTTT
1 CAAAAATT-CCATTTT
16179339 CCCCCAAAGT
Statistics
Matches: 56, Mismatches: 9, Indels: 19
0.67 0.11 0.23
Matches are distributed among these distances:
27 13 0.23
28 2 0.04
29 13 0.23
30 13 0.23
31 12 0.21
32 3 0.05
ACGTcount: A:0.32, C:0.26, G:0.05, T:0.38
Consensus pattern (28 bp):
CAAAAATTCCATTTTGACCCGATTTTAT
Found at i:16197152 original size:22 final size:22
Alignment explanation
Indices: 16197127--16197168 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
16197117 ACTAATAATT
16197127 AATT-AAATAATTAAAAATTCAC
1 AATTCAAA-AATTAAAAATTCAC
*
16197149 AATTCAAAAATTCAAAATTC
1 AATTCAAAAATTAAAAATTC
16197169 CATATAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.57, C:0.12, G:0.00, T:0.31
Consensus pattern (22 bp):
AATTCAAAAATTAAAAATTCAC
Found at i:16197157 original size:15 final size:15
Alignment explanation
Indices: 16197135--16197168 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
16197125 TTAATTAAAT
*
16197135 AATT-AAAAATTCAC
1 AATTCAAAAATTCAA
16197149 AATTCAAAAATTCAA
1 AATTCAAAAATTCAA
16197164 AATTC
1 AATTC
16197169 CATATAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 4 0.22
15 14 0.78
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.29
Consensus pattern (15 bp):
AATTCAAAAATTCAA
Found at i:16199549 original size:101 final size:98
Alignment explanation
Indices: 16199373--16199606 Score: 301
Period size: 101 Copynumber: 2.3 Consensus size: 98
16199363 ACATGATGGG
* *
16199373 AAAGATCTAAGACCGCAACGGCGGATCAAGTACCTCAAAGACAAAAGGAAAAGGTCTAAGTCGTA
1 AAAGATCTAAGACCGCAACGGCAGATCCAGTA-CTCAAAGACAAAAGGAAAAGGTCTAAGTCGTA
* **
16199438 ACGGCTGACCGTGTACCTCAAAAGACATGACGAA
65 ACGGCTGACCGTATACCTCAAAAGACACAACGAA
16199472 AAAGATCTAAGACCGCAACGGCAGATCCAGTACTGCAAAATGACAAAAGCG-AAAGGTCTAAGTC
1 AAAGATCTAAGACCGCAACGGCAGATCCAGTACT-C-AAA-GACAAAAG-GAAAAGGTCTAAGTC
* * *
16199536 GTAACGG-TAGACCGTATGCCTCAGAAGACACAACGAG
62 GTAACGGCT-GACCGTATACCTCAAAAGACACAACGAA
* * *
16199573 AAAGATCTAAGACCGTAACGACAGATCCAATACT
1 AAAGATCTAAGACCGCAACGGCAGATCCAGTACT
16199607 ACAGAGATAC
Statistics
Matches: 119, Mismatches: 11, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
98 2 0.02
99 31 0.26
100 4 0.03
101 81 0.68
102 1 0.01
ACGTcount: A:0.41, C:0.23, G:0.22, T:0.15
Consensus pattern (98 bp):
AAAGATCTAAGACCGCAACGGCAGATCCAGTACTCAAAGACAAAAGGAAAAGGTCTAAGTCGTAA
CGGCTGACCGTATACCTCAAAAGACACAACGAA
Found at i:16199640 original size:101 final size:101
Alignment explanation
Indices: 16199373--16199644 Score: 254
Period size: 101 Copynumber: 2.7 Consensus size: 101
16199363 ACATGATGGG
* * **
16199373 AAAGATCTAAGACCGCAACGGCGGAT-CAAGTACCT-C-AAA-GACAAAAG-GAAAAGGTCTAAG
1 AAAGATCTAAGACCGCAACGACAGATCCAA-TA-CTACAAAATGACAAAAGCG-AAAGACCTAAG
* * **
16199433 TCGTAACGGCTGACCGTGTACCTCAAAAGACATGACGAA
63 CCGTAACGGCTGACCGTATACCTCAAAAGACACAACGAA
* * * ** *
16199472 AAAGATCTAAGACCGCAACGGCAGATCCAGTACTGCAAAATGACAAAAGCGAAAGGTCTAAGTCG
1 AAAGATCTAAGACCGCAACGACAGATCCAATACTACAAAATGACAAAAGCGAAAGACCTAAGCCG
* * *
16199537 TAACGG-TAGACCGTATGCCTCAGAAGACACAACGAG
66 TAACGGCT-GACCGTATACCTCAAAAGACACAACGAA
* * *
16199573 AAAGATCTAAGACCGTAACGACAGATCCAATACTACAGAGAT-ACAGAAG-GAAAGACCTAAGAC
1 AAAGATCTAAGACCGCAACGACAGATCCAATACTACA-AAATGACAAAAGCGAAAGACCTAAG-C
16199636 CGTAACGGC
64 CGTAACGGC
16199645 GGATCCAGTT
Statistics
Matches: 147, Mismatches: 17, Indels: 15
0.82 0.09 0.08
Matches are distributed among these distances:
98 2 0.01
99 28 0.19
100 16 0.11
101 97 0.66
102 4 0.03
ACGTcount: A:0.41, C:0.22, G:0.23, T:0.14
Consensus pattern (101 bp):
AAAGATCTAAGACCGCAACGACAGATCCAATACTACAAAATGACAAAAGCGAAAGACCTAAGCCG
TAACGGCTGACCGTATACCTCAAAAGACACAACGAA
Found at i:16199696 original size:49 final size:49
Alignment explanation
Indices: 16199355--16199852 Score: 359
Period size: 49 Copynumber: 10.1 Consensus size: 49
16199345 AAGTCTCAGC
* * *
16199355 ACCATGAA-ACATGATGGGAAAGATCTAAGACCGCAACGGCGGATCAAGT
1 ACCACGAAGACATGAAGGGAAAGATCTAAG-CCGCAACGGCGGATCCAGT
* * * * * * * * *
16199404 ACCTCAAAGACA-AAAGGAAAAGGTCTAAGTCGTAACGGCTGA-CCGTGT
1 ACCACGAAGACATGAAGGGAAAGATCTAAGCCGCAACGGCGGATCC-AGT
* * * ** *
16199452 ACCTCAAAAGACATGACGAAAAAGATCTAAGACCGCAACGGCAGATCCAGT
1 ACCAC-GAAGACATGAAGGGAAAGATCTAAG-CCGCAACGGCGGATCCAGT
* * * * * * **
16199503 ACTGCA-AAATGACA-AAAGCGAAAGGTCTAAGTCGTAACGGTAGA-CC-GT
1 AC--CACGAA-GACATGAAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGT
* * * * * * *
16199551 ATGCCTCAGAAGACA-CAACGAGAAAGATCTAAGACCGTAACGACAGATCCAAT
1 A--CCAC-GAAGACATGAA-GGGAAAGATCTAAG-CCGCAACGGCGGATCCAGT
* * * *
16199604 ACTACAGAGATACA-GAA-GGAAAGACCTAAGACCGTAACGGCGGATCCAGT
1 ACCAC-GA-AGACATGAAGGGAAAGATCTAAG-CCGCAACGGCGGATCCAGT
*
16199654 TCCACGAAGACATGAAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGT
1 ACCACGAAGACATGAAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGT
*
16199703 ACCACGAAGACATGAAGAGAAAGATCTAAGCCGCAACGGCGGATCCAGT
1 ACCACGAAGACATGAAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGT
* *
16199752 ACCACGAAGACATGAAAGGAAAGATCTAAGCCGCAACGGCGGATCTAGT
1 ACCACGAAGACATGAAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGT
** * * * * *
16199801 ACCACGAAGATTTGAAGGGAAAGGTTTAAGTCGCAACGGCGAACCCAGT
1 ACCACGAAGACATGAAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGT
16199850 ACC
1 ACC
16199853 TTAGAAACAT
Statistics
Matches: 363, Mismatches: 66, Indels: 40
0.77 0.14 0.09
Matches are distributed among these distances:
47 1 0.00
48 25 0.07
49 192 0.53
50 84 0.23
51 44 0.12
52 14 0.04
53 3 0.01
ACGTcount: A:0.39, C:0.23, G:0.25, T:0.13
Consensus pattern (49 bp):
ACCACGAAGACATGAAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGT
Found at i:16199757 original size:98 final size:96
Alignment explanation
Indices: 16199355--16199852 Score: 396
Period size: 98 Copynumber: 5.0 Consensus size: 96
16199345 AAGTCTCAGC
* * * * * *
16199355 ACCATGAA-ACATGATGGGAAAGATCTAAGACCGCAACGGCGGATCAAGTACCTCAAAGACAAAA
1 ACCACGAAGACATGAAGGGAAAGATCTAAGACCGCAACGGCGGATCCAGTACCACGAAGACAGAA
* *
16199419 GGAAAAGGTCTAAGTCGTAACGGCTGACCGTGT
66 GG-AAAGGTCTAAGTCGTAACGGCGGACC-AGT
* * * ** * *
16199452 ACCTCAAAAGACATGACGAAAAAGATCTAAGACCGCAACGGCAGATCCAGTACTGCA-AAATGAC
1 ACCAC-GAAGACATGAAGGGAAAGATCTAAGACCGCAACGGCGGATCCAGTAC--CACGAA-GAC
* **
16199516 AAAAGCGAAAGGTCTAAGTCGTAACGGTAGACC-GT
62 AGAAG-GAAAGGTCTAAGTCGTAACGGCGGACCAGT
* * * * * * * * *
16199551 ATGCCTCAGAAGACA-CAACGAGAAAGATCTAAGACCGTAACGACAGATCCAATACTACAGAGAT
1 A--CCAC-GAAGACATGAA-GGGAAAGATCTAAGACCGCAACGGCGGATCCAGTACCAC-GA-AG
** *
16199615 ACAGAAGGAAAGACCTAAGACCGTAACGGCGGATCCAGT
60 ACAGAAGGAAAGGTCTAAG-TCGTAACGGCGGA-CCAGT
*
16199654 TCCACGAAGACATGAAGGGAAAGATCTAAG-CCGCAACGGCGGATCCAGTACCACGAAGACATGA
1 ACCACGAAGACATGAAGGGAAAGATCTAAGACCGCAACGGCGGATCCAGTACCACGAAGACA-GA
* * *
16199718 AGAGAAAGATCTAAGCCGCAACGGCGGATCCAGT
65 AG-GAAAGGTCTAAGTCGTAACGGCGGA-CCAGT
* * **
16199752 ACCACGAAGACATGAAAGGAAAGATCTAAG-CCGCAACGGCGGATCTAGTACCACGAAGATTTGA
1 ACCACGAAGACATGAAGGGAAAGATCTAAGACCGCAACGGCGGATCCAGTACCACGAAGA-CAGA
* * *
16199816 AGGGAAAGGTTTAAGTCGCAACGGCGAACCCAGT
65 A-GGAAAGGTCTAAGTCGTAACGGCGGA-CCAGT
16199850 ACC
1 ACC
16199853 TTAGAAACAT
Statistics
Matches: 332, Mismatches: 49, Indels: 39
0.79 0.12 0.09
Matches are distributed among these distances:
97 7 0.02
98 114 0.34
99 73 0.22
100 34 0.10
101 98 0.30
102 4 0.01
103 2 0.01
ACGTcount: A:0.39, C:0.23, G:0.25, T:0.13
Consensus pattern (96 bp):
ACCACGAAGACATGAAGGGAAAGATCTAAGACCGCAACGGCGGATCCAGTACCACGAAGACAGAA
GGAAAGGTCTAAGTCGTAACGGCGGACCAGT
Found at i:16200571 original size:201 final size:200
Alignment explanation
Indices: 16200227--16200860 Score: 811
Period size: 201 Copynumber: 3.1 Consensus size: 200
16200217 AGTGAGGCGA
* * * *
16200227 TCATCTTCCTGATGAGATACAGAGAAGTATACCAACTCAACGCTCAATGTGAGCAAATCCTC-AA
1 TCATCTTCCTGATGAGACACAGAGAAGAATACCAACTCAACGCTCAATGCGAGCAAATCTTCGAA
*
16200291 ACCCAGCTTCCTGATGAGACACTGAGAAGCAAGTCGAAGCAATAAAATGGTTAGCTTCCTGATGA
66 ACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGA
* *
16200356 GACACAAAGAAGTGGACCAAATTCGTCTTCCTGATGAGACACAGAGAAGCGAATTAAAACAGACA
131 GACACAGAGAAGTGGACCAAATTCGTCTTCCTGATGAGACACAGAGAAGCGAATTAAAACA-ACG
16200421 AAGCGG
195 AAGCGG
* * *
16200427 TCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCGACGCTCGATGCGAGCAAATCTTCGAA
1 TCATCTTCCTGATGAGACACAGAGAAGAATACCAACTCAACGCTCAATGCGAGCAAATCTTCGAA
* * *
16200492 CCCCAGCTTCTTGATGAGACACTGAGGAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGA
66 ACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGA
* * * *
16200557 GATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGACACAGAGAAGCGAATTGAAACAAGTG
131 GACACAGAGAAGTGGACCAAATTCGTCTTCCTGATGAGACACAGAGAAGCGAATTAAAACAA-CG
*
16200622 ATGCGG
195 AAGCGG
* * * *
16200628 TCATCTTCCTGATGAGACACTGAGAAGAAGACCAAATCAAACTCAGTCTCAACGCGAGCAAATCT
1 TCATCTTCCTGATGAGACACAGAGAAGAATACCAACTC-AA--C-G-CTCAATGCGAGCAAATCT
* * * * * * * *
16200693 TTGAATCCCAACTTCCTGATGAGATAGTGAGAAACAGGTAGAAGCAATAAAGTGGTTAGCTTCCT
61 TCGAAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCT
* * * * * * * *
16200758 GATGAGCCACAGAGAAGTGAACCAAATCCGTCTTCCTGTTGAAACACAGAGAAGTGGATCAAAAC
126 GATGAGACACAGAGAAGTGGACCAAATTCGTCTTCCTGATGAGACACAGAGAAGCGAATTAAAAC
* *
16200823 AAACGACGCAG
191 -AACGAAGCGG
* *
16200834 TCACCTTCCTGATGAGACACTGAGAAG
1 TCATCTTCCTGATGAGACACAGAGAAG
16200861 GAGGCCAAGT
Statistics
Matches: 378, Mismatches: 48, Indels: 10
0.87 0.11 0.02
Matches are distributed among these distances:
200 58 0.15
201 159 0.42
202 1 0.00
204 1 0.00
205 1 0.00
206 156 0.41
207 2 0.01
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.20
Consensus pattern (200 bp):
TCATCTTCCTGATGAGACACAGAGAAGAATACCAACTCAACGCTCAATGCGAGCAAATCTTCGAA
ACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGA
GACACAGAGAAGTGGACCAAATTCGTCTTCCTGATGAGACACAGAGAAGCGAATTAAAACAACGA
AGCGG
Found at i:16201238 original size:17 final size:17
Alignment explanation
Indices: 16201218--16201324 Score: 94
Period size: 17 Copynumber: 6.2 Consensus size: 17
16201208 TGCTTTGAAA
16201218 TTAAATTTATTCTAAAT
1 TTAAATTTATTCTAAAT
* *
16201235 TTAAATTTATTTTAATT
1 TTAAATTTATTCTAAAT
16201252 TTAAATTTTTACTTCT-AAT
1 TTAAA--TTTA-TTCTAAAT
*
16201271 TTAAATTTAATT-TAAGT
1 TTAAATTT-ATTCTAAAT
* *
16201288 TTGAATTTAATCTAAAT
1 TTAAATTTATTCTAAAT
* *
16201305 TTATA-TTATTGTAAAT
1 TTAAATTTATTCTAAAT
16201321 TTAA
1 TTAA
16201325 TGTCCCTTTA
Statistics
Matches: 71, Mismatches: 13, Indels: 13
0.73 0.13 0.13
Matches are distributed among these distances:
16 15 0.21
17 41 0.58
18 1 0.01
19 11 0.15
20 3 0.04
ACGTcount: A:0.38, C:0.04, G:0.03, T:0.55
Consensus pattern (17 bp):
TTAAATTTATTCTAAAT
Found at i:16201276 original size:36 final size:36
Alignment explanation
Indices: 16201223--16201307 Score: 104
Period size: 36 Copynumber: 2.4 Consensus size: 36
16201213 TGAAATTAAA
* *
16201223 TTTATTCTAAATTTAAATTTATTTTAATTTTAAATT
1 TTTATTCTAAATTTAAATTTAATTTAAGTTTAAATT
*
16201259 TTTACTTCT-AATTTAAATTTAATTTAAGTTTGAA--
1 TTTA-TTCTAAATTTAAATTTAATTTAAGTTTAAATT
*
16201293 TTTAATCTAAATTTA
1 TTTATTCTAAATTTA
16201308 TATTATTGTA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
33 3 0.07
34 10 0.23
36 26 0.60
37 4 0.09
ACGTcount: A:0.36, C:0.05, G:0.02, T:0.56
Consensus pattern (36 bp):
TTTATTCTAAATTTAAATTTAATTTAAGTTTAAATT
Found at i:16201619 original size:30 final size:30
Alignment explanation
Indices: 16201574--16201656 Score: 107
Period size: 29 Copynumber: 2.8 Consensus size: 30
16201564 CCTAAACTGC
16201574 CCAAAAATTAT-ATTTTGACCCCGAAACTT
1 CCAAAAATTATAATTTTGACCCCGAAACTT
**
16201603 CCAAAAATTATAATTTTTCCCCCG-AACTT
1 CCAAAAATTATAATTTTGACCCCGAAACTT
** *
16201632 CCAAAAATTCCATTTTTGACCCCGA
1 CCAAAAATTATAATTTTGACCCCGA
16201657 TTTTACCCAA
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
29 35 0.78
30 10 0.22
ACGTcount: A:0.35, C:0.28, G:0.06, T:0.31
Consensus pattern (30 bp):
CCAAAAATTATAATTTTGACCCCGAAACTT
Found at i:16201733 original size:57 final size:56
Alignment explanation
Indices: 16201665--16201800 Score: 166
Period size: 57 Copynumber: 2.4 Consensus size: 56
16201655 GATTTTACCC
16201665 AAAATTACCATTTTACCCTCGAACTTTCT-AAATTCCATTTTAAACTCAATTTCACTA
1 AAAATTACCATTTTACCC-CGAACTTTCTAAAATTCCATTTTAAACTCAATTTCAC-A
* * * * * * *
16201722 AAAATTACCATTTTACCCCTAAACTTTCTAAAATTTCATTTTGACCTCGATTTTACC
1 AAAATTACCATTTTACCCC-GAACTTTCTAAAATTCCATTTTAAACTCAATTTCACA
*
16201779 AAAATTACCATTTTCCCCCGAA
1 AAAATTACCATTTTACCCCGAA
16201801 AGTCCAAAAT
Statistics
Matches: 68, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
56 3 0.04
57 44 0.65
58 21 0.31
ACGTcount: A:0.34, C:0.26, G:0.03, T:0.38
Consensus pattern (56 bp):
AAAATTACCATTTTACCCCGAACTTTCTAAAATTCCATTTTAAACTCAATTTCACA
Found at i:16201753 original size:30 final size:29
Alignment explanation
Indices: 16201665--16201754 Score: 80
Period size: 30 Copynumber: 3.1 Consensus size: 29
16201655 GATTTTACCC
*
16201665 AAAATTACCATTTTACCCTCGAACTTTCT-
1 AAAATTACCATTTTACCCT-AAACTTTCTA
** *
16201694 -AAATT-CCATTTTAAACTCAA-TTTCACTA
1 AAAATTACCATTTTACCCTAAACTTT--CTA
16201722 AAAATTACCATTTTACCCCTAAACTTTCTA
1 AAAATTACCATTTTA-CCCTAAACTTTCTA
16201752 AAA
1 AAA
16201755 TTTCATTTTG
Statistics
Matches: 48, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
25 3 0.06
26 2 0.04
27 12 0.25
28 5 0.10
29 5 0.10
30 14 0.29
31 4 0.08
32 3 0.06
ACGTcount: A:0.38, C:0.24, G:0.01, T:0.37
Consensus pattern (29 bp):
AAAATTACCATTTTACCCTAAACTTTCTA
Found at i:16203484 original size:21 final size:22
Alignment explanation
Indices: 16203453--16203493 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
16203443 ATATACAAAA
16203453 TTAATATTTTTAATAAGATATT
1 TTAATATTTTTAATAAGATATT
16203475 TTAA-ATTTTTAATAAGATA
1 TTAATATTTTTAATAAGATA
16203494 AACTTTTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (22 bp):
TTAATATTTTTAATAAGATATT
Found at i:16203919 original size:23 final size:23
Alignment explanation
Indices: 16203867--16203920 Score: 56
Period size: 23 Copynumber: 2.3 Consensus size: 23
16203857 TACATTTTTG
* *
16203867 ATAAAAATTAATTATTATATTAT
1 ATAAAAATGAATTATAATATTAT
* *
16203890 ATTAAAATGAATTTATAAT-TTCT
1 ATAAAAATGAA-TTATAATATTAT
16203913 ATAAAAAT
1 ATAAAAAT
16203921 ATATAGATTT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
23 19 0.76
24 6 0.24
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (23 bp):
ATAAAAATGAATTATAATATTAT
Found at i:16205617 original size:13 final size:13
Alignment explanation
Indices: 16205595--16205627 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
16205585 AGTCAAGGGG
*
16205595 AGTTCACGGTCTC
1 AGTTCGCGGTCTC
16205608 AGTTCGCGGTCTC
1 AGTTCGCGGTCTC
16205621 AGTTCGC
1 AGTTCGC
16205628 CTATATCCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.12, C:0.30, G:0.27, T:0.30
Consensus pattern (13 bp):
AGTTCGCGGTCTC
Found at i:16208361 original size:30 final size:30
Alignment explanation
Indices: 16208321--16208380 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
16208311 AGTGATTTAA
*
16208321 AATTATTCATAATCTTAAATTATGTGTGTT
1 AATTACTCATAATCTTAAATTATGTGTGTT
*
16208351 AATTACTCATAATCTTAAATTTTGTGTGTT
1 AATTACTCATAATCTTAAATTATGTGTGTT
16208381 GGTCTGATGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.32, C:0.08, G:0.10, T:0.50
Consensus pattern (30 bp):
AATTACTCATAATCTTAAATTATGTGTGTT
Found at i:16215728 original size:19 final size:20
Alignment explanation
Indices: 16215704--16215749 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
16215694 CATCCAAACA
16215704 CCAGAAAA-T-ATTAACTTTT
1 CCAGAAAAGTAATTAA-TTTT
*
16215723 CCAGAAAAGTAATTCATTTT
1 CCAGAAAAGTAATTAATTTT
16215743 CCAGAAA
1 CCAGAAA
16215750 TCATTCTCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 8 0.33
20 12 0.50
21 4 0.17
ACGTcount: A:0.43, C:0.17, G:0.09, T:0.30
Consensus pattern (20 bp):
CCAGAAAAGTAATTAATTTT
Found at i:16218569 original size:21 final size:21
Alignment explanation
Indices: 16218545--16218597 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
16218535 AGTGCAAACA
16218545 TCTACCGATACAAGTGACT-CT
1 TCTACCGATACAAGT-ACTACT
* **
16218566 TCTATCGATACAAGTTTTACT
1 TCTACCGATACAAGTACTACT
16218587 TCTACCGATAC
1 TCTACCGATAC
16218598 TAAAAACTCT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 1 0.04
21 26 0.96
ACGTcount: A:0.28, C:0.26, G:0.11, T:0.34
Consensus pattern (21 bp):
TCTACCGATACAAGTACTACT
Found at i:16227581 original size:62 final size:62
Alignment explanation
Indices: 16227512--16227646 Score: 164
Period size: 62 Copynumber: 2.2 Consensus size: 62
16227502 TGGACACACA
* * *
16227512 CCCGTGTGACCCTAATGCACAAACAGTGAGTTACAC-GATCTAGACACACGCCCGTGTGTCAG
1 CCCGTGTGACCCTAATACACAAACAGTGAATTACACAG-CCTAGACACACGCCCGTGTGTCAG
** * *** *
16227574 CCCGTGTGACTTTAATACACAAATAGTGAATTACACAGCCTAGACACACGCTTTTGTGTCTG
1 CCCGTGTGACCCTAATACACAAACAGTGAATTACACAGCCTAGACACACGCCCGTGTGTCAG
16227636 CCCGTGTGACC
1 CCCGTGTGACC
16227647 ACTTCACCTT
Statistics
Matches: 61, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
62 60 0.98
63 1 0.02
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.24
Consensus pattern (62 bp):
CCCGTGTGACCCTAATACACAAACAGTGAATTACACAGCCTAGACACACGCCCGTGTGTCAG
Found at i:16231909 original size:2 final size:2
Alignment explanation
Indices: 16231898--16231933 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
16231888 CTTGCTGCTT
16231898 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
16231934 GGTTGGTCAC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:16233398 original size:18 final size:18
Alignment explanation
Indices: 16233375--16233417 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
16233365 TTTATAGCAC
*
16233375 TAAAAAT-GCTTAAAACAT
1 TAAAAATAG-TTAAAAAAT
16233393 TAAAAATAGTTAAAAAAT
1 TAAAAATAGTTAAAAAAT
*
16233411 AAAAAAT
1 TAAAAAT
16233418 TTACAAGCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 21 0.95
19 1 0.05
ACGTcount: A:0.65, C:0.05, G:0.05, T:0.26
Consensus pattern (18 bp):
TAAAAATAGTTAAAAAAT
Found at i:16233679 original size:43 final size:43
Alignment explanation
Indices: 16233630--16233896 Score: 354
Period size: 43 Copynumber: 6.2 Consensus size: 43
16233620 TTGGAAAAAT
* *
16233630 GCCGCTAAAGAACATGATCGTTAGCGGCGCTTTTCCCACAAAC
1 GCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCACAAAC
* * *
16233673 ACCGCTAAAGAACATGGTCTTTAGTGGCGCTTTTCCCATAAAC
1 GCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCACAAAC
* * * *
16233716 ACCGCTAAAGAACATGTTCTTTAGCGACGCTTTTCTCACAAAC
1 GCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCACAAAC
* ** *
16233759 GCCGCTAAAGAACATGGTCTTTAACGGCGCTTTTTTCACAAAT
1 GCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCACAAAC
** *
16233802 GCCGCTAAAGAACATATTCTTTAGCGGCGCTTTTCTCACAAAC
1 GCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCACAAAC
* * *
16233845 GCCTCTAAAGAACATGGTCTGTAGCAGCGCTTTTCCCACAAAC
1 GCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCACAAAC
*
16233888 GCCACTAAA
1 GCCGCTAAA
16233897 ATTAACAAAT
Statistics
Matches: 196, Mismatches: 28, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 196 1.00
ACGTcount: A:0.29, C:0.28, G:0.18, T:0.26
Consensus pattern (43 bp):
GCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCACAAAC
Found at i:16235586 original size:19 final size:19
Alignment explanation
Indices: 16235531--16235593 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
16235521 TCATTTGTTA
*
16235531 ATTTTTTATAATTTTTTATG
1 ATTTTTTATTA-TTTTTATG
*
16235551 -TTTTATGTA-TATATTTATG
1 ATTTT-T-TATTATTTTTATG
*
16235570 ATTTTTTATTATTTTTATA
1 ATTTTTTATTATTTTTATG
16235589 ATTTT
1 ATTTT
16235594 CTCTATTTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 9
0.73 0.08 0.19
Matches are distributed among these distances:
18 2 0.06
19 25 0.71
20 6 0.17
21 2 0.06
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.70
Consensus pattern (19 bp):
ATTTTTTATTATTTTTATG
Found at i:16240346 original size:41 final size:41
Alignment explanation
Indices: 16240268--16240509 Score: 294
Period size: 41 Copynumber: 6.0 Consensus size: 41
16240258 ATCAATTAAA
* *
16240268 TGACC-TTAGCGGCGC-TTTTGA-AAGCGTCGCTATTGCTC
1 TGACCTTTAGCGGCGCTTTTTCATAAGCGCCGCTATTGCTC
* *
16240306 TGACCTTTAGCGACGCTTTTTCATAAGCGCCGCTACTGCTC
1 TGACCTTTAGCGGCGCTTTTTCATAAGCGCCGCTATTGCTC
* * *
16240347 TGACTTTTAGTGGCGCTTTTTCATAAGCGCCGCTATTGTTC
1 TGACCTTTAGCGGCGCTTTTTCATAAGCGCCGCTATTGCTC
* ***
16240388 TGATCTTTAGCGGCGCTTGCCCATAAGCGCCGCTATTGCTC
1 TGACCTTTAGCGGCGCTTTTTCATAAGCGCCGCTATTGCTC
* ***
16240429 TGACCTTTAGTGGCGCTTGCCCATAAGCGCCGCTATTGCTC
1 TGACCTTTAGCGGCGCTTTTTCATAAGCGCCGCTATTGCTC
* *
16240470 TAACCTTTAGCGGC-ATTTTTCCATAAGCGCCGCTATTGCT
1 TGACCTTTAGCGGCGCTTTTT-CATAAGCGCCGCTATTGCT
16240510 TTATCTTTTG
Statistics
Matches: 176, Mismatches: 24, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
38 5 0.03
39 9 0.05
40 7 0.04
41 155 0.88
ACGTcount: A:0.16, C:0.29, G:0.22, T:0.33
Consensus pattern (41 bp):
TGACCTTTAGCGGCGCTTTTTCATAAGCGCCGCTATTGCTC
Done.