Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008252.1 Hibiscus syriacus cultivar Beakdansim tig00110904_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2928487
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 13
Found at i:446957 original size:15 final size:15
Alignment explanation
Indices: 446928--447036 Score: 73
Period size: 15 Copynumber: 7.1 Consensus size: 15
446918 AGATCCAATC
*
446928 AAAA-CAAAGAGAAA
1 AAAAGCAAAGAAAAA
*
446942 AAAAGTAAAGAAAAA
1 AAAAGCAAAGAAAAA
446957 AAAA-CAAAGAGCAAAGAAA
1 AAAAGC-AA-AG--AA-AAA
*
446976 AAAAGAAAAG-AAAA
1 AAAAGCAAAGAAAAA
* *
446990 AAATGCAAAGAGAAA
1 AAAAGCAAAGAAAAA
*
447005 AAGAGCAAAGAGAAAA
1 AAAAGCAAAGA-AAAA
*
447021 AAAA-CAAAGAGAAA
1 AAAAGCAAAGAAAAA
447035 AA
1 AA
447037 GTAAAGAAAA
Statistics
Matches: 74, Mismatches: 12, Indels: 18
0.71 0.12 0.17
Matches are distributed among these distances:
14 20 0.27
15 33 0.45
16 8 0.11
18 4 0.05
19 9 0.12
ACGTcount: A:0.76, C:0.06, G:0.17, T:0.02
Consensus pattern (15 bp):
AAAAGCAAAGAAAAA
Found at i:446967 original size:29 final size:29
Alignment explanation
Indices: 446928--447070 Score: 132
Period size: 29 Copynumber: 4.8 Consensus size: 29
446918 AGATCCAATC
446928 AAAACAAAGAGAAAAAAAGTAAAGAAAAA
1 AAAACAAAGAGAAAAAAAGTAAAGAAAAA
*
446957 AAAACAAAGAGCAAAGAAAAAAAGAAAAGAAAAA
1 AAAAC-AA-AG---AGAAAAAAAGTAAAGAAAAA
** * *
446991 AATGCAAAGAGAAAAAGAGCAAAGAGAAAA
1 AAAACAAAGAGAAAAAAAGTAAAGA-AAAA
447021 AAAACAAAGAG--AAAAAGTAAAG-AAAA
1 AAAACAAAGAGAAAAAAAGTAAAGAAAAA
*
447047 AGAACAAA-AGAAAAACAAAGTAAA
1 AAAACAAAGAG-AAAA-AAAGTAAA
447071 AGAGAAGACA
Statistics
Matches: 94, Mismatches: 10, Indels: 20
0.76 0.08 0.16
Matches are distributed among these distances:
25 2 0.02
26 11 0.12
28 11 0.12
29 27 0.29
30 15 0.16
31 2 0.02
32 2 0.02
33 2 0.02
34 22 0.23
ACGTcount: A:0.76, C:0.06, G:0.16, T:0.03
Consensus pattern (29 bp):
AAAACAAAGAGAAAAAAAGTAAAGAAAAA
Found at i:446977 original size:34 final size:34
Alignment explanation
Indices: 446937--447061 Score: 108
Period size: 34 Copynumber: 3.6 Consensus size: 34
446927 CAAAACAAAG
*
446937 AGAAAAAAAGTAAAGAAAAAAAAACAAAGAGCAA
1 AGAAAAAAAGAAAAGAAAAAAAAACAAAGAGCAA
** *
446971 AGAAAAAAAGAAAAGAAAAAAATGCAAAGAGAAAA
1 AGAAAAAAAGAAAAGAAAAAAAAACAAAGAG-CAA
* * * * * *
447006 AGAGCAAAGAGAAAA-AAAACAAAGAGAAAAAGTAA
1 AGA-AAAAAAGAAAAGAAAA-AAAAACAAAGAGCAA
*
447041 AGAAAAAGAACAAAAGAAAAA
1 AGAAAAA-AAGAAAAGAAAAA
447062 CAAAGTAAAA
Statistics
Matches: 72, Mismatches: 14, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
34 31 0.43
35 20 0.28
36 21 0.29
ACGTcount: A:0.76, C:0.05, G:0.17, T:0.02
Consensus pattern (34 bp):
AGAAAAAAAGAAAAGAAAAAAAAACAAAGAGCAA
Found at i:446985 original size:20 final size:21
Alignment explanation
Indices: 446948--447031 Score: 73
Period size: 21 Copynumber: 4.0 Consensus size: 21
446938 GAAAAAAAGT
446948 AAAGAAAAAAAAACAAAGAGC
1 AAAGAAAAAAAAACAAAGAGC
* **
446969 AAAGAAAAAAAGA-AAAGAAAA
1 AAAGAAAAAAAAACAAAG-AGC
* * *
446990 AAATGCAAAGAGAA-AAAGAGC
1 AAA-GAAAAAAAAACAAAGAGC
447011 AAAGAGAAAAAAAACAAAGAG
1 AAAGA-AAAAAAAACAAAGAG
447032 AAAAAGTAAA
Statistics
Matches: 47, Mismatches: 12, Indels: 7
0.71 0.18 0.11
Matches are distributed among these distances:
20 5 0.11
21 26 0.55
22 16 0.34
ACGTcount: A:0.75, C:0.06, G:0.18, T:0.01
Consensus pattern (21 bp):
AAAGAAAAAAAAACAAAGAGC
Found at i:447049 original size:49 final size:45
Alignment explanation
Indices: 446928--447057 Score: 124
Period size: 45 Copynumber: 2.8 Consensus size: 45
446918 AGATCCAATC
*
446928 AAAACAAAGAGAAAAAAAGTAAAGAAAAAAAAACAAAGAGCAAAGAAA
1 AAAACAAAGAG--AAAAAGTAAAGAAAAAGAAA-AAAGAGCAAAGAAA
* * *
446976 AAAAGAAA-AGAAAAA--AATG-CAAAGAGAAAAAGAGCAAAGAGAAAA
1 AAAACAAAGAGAAAAAGTAAAGAAAAAGA-AAAAAGAGC-AA-AG-AAA
447021 AAAACAAAGAGAAAAAGTAAAGAAAAAGAACAAAAGA
1 AAAACAAAGAGAAAAAGTAAAGAAAAAGAA-AAAAGA
447058 AAAACAAAGT
Statistics
Matches: 66, Mismatches: 7, Indels: 17
0.73 0.08 0.19
Matches are distributed among these distances:
42 11 0.17
43 7 0.11
44 2 0.03
45 15 0.23
46 7 0.11
47 2 0.03
48 11 0.17
49 11 0.17
ACGTcount: A:0.75, C:0.05, G:0.17, T:0.02
Consensus pattern (45 bp):
AAAACAAAGAGAAAAAGTAAAGAAAAAGAAAAAAGAGCAAAGAAA
Found at i:447063 original size:11 final size:12
Alignment explanation
Indices: 446928--447066 Score: 52
Period size: 13 Copynumber: 10.8 Consensus size: 12
446918 AGATCCAATC
446928 AAAACAAAGAGA
1 AAAACAAAGAGA
*
446940 AAAA-AAGTAAAGA
1 AAAACAA--AGAGA
*
446953 AAAA-AAA-ACA
1 AAAACAAAGAGA
* *
446963 AAGAGCAAAGAAA
1 AA-AACAAAGAGA
* *
446976 AAAAGAAAAGAAA
1 AAAA-CAAAGAGA
446989 AAAATGCAAAGAGAA
1 AAAA--CAAAGAG-A
447004 AAAGAGCAAAGAGAAAA
1 AAA-A-CAAAGAG---A
447021 AAAACAAAGAGA
1 AAAACAAAGAGA
* *
447033 AAAAGTAAAGAAA
1 AAAA-CAAAGAGA
447046 AAGAACAAA-AGA
1 AA-AACAAAGAGA
447058 AAAACAAAG
1 AAAACAAAG
447067 TAAAAGAGAA
Statistics
Matches: 101, Mismatches: 12, Indels: 28
0.72 0.09 0.20
Matches are distributed among these distances:
10 4 0.04
11 10 0.10
12 17 0.17
13 36 0.36
14 8 0.08
15 19 0.19
16 2 0.02
17 5 0.05
ACGTcount: A:0.76, C:0.06, G:0.17, T:0.02
Consensus pattern (12 bp):
AAAACAAAGAGA
Found at i:447076 original size:26 final size:25
Alignment explanation
Indices: 446975--447073 Score: 76
Period size: 26 Copynumber: 3.7 Consensus size: 25
446965 GAGCAAAGAA
*
446975 AAAAAGAAAAGAAAAA-AATGCAAAGAG
1 AAAAAGCAAAGAAAAAGAA--CAAA-AG
*
447002 AAAAAGAGCAAAGAGAAAAAAAACAAAGAG
1 -AAAA-AGC-AA-AGAAAAAGAACAAA-AG
*
447032 AAAAAGTAAAGAAAAAGAACAAAAG
1 AAAAAGCAAAGAAAAAGAACAAAAG
*
447057 AAAAA-CAAAGTAAAAGA
1 AAAAAGCAAAGAAAAAGA
447074 GAAGACAAGA
Statistics
Matches: 62, Mismatches: 5, Indels: 12
0.78 0.06 0.15
Matches are distributed among these distances:
24 10 0.16
25 7 0.11
26 13 0.21
27 2 0.03
28 6 0.10
29 6 0.10
30 9 0.15
31 7 0.11
32 2 0.03
ACGTcount: A:0.75, C:0.05, G:0.17, T:0.03
Consensus pattern (25 bp):
AAAAAGCAAAGAAAAAGAACAAAAG
Found at i:448316 original size:64 final size:67
Alignment explanation
Indices: 448233--448357 Score: 179
Period size: 64 Copynumber: 1.9 Consensus size: 67
448223 CAATATCTTT
* *
448233 TAAGTTGTTTCTTTTGAAACAAA-TTTTGTCTCTC-T-AGACAATTTC-TTTCG-GAAAAAAAAT
1 TAAGTTGTTTCTCTGGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCATTT-GAGAAAAAAAAT
448293 TTG
65 TTG
448296 TAAGTTTGTTTCTCTGGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCATTTGAGAAAAAA
1 TAAG-TTGTTTCTCTGGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCATTTGAGAAAAAA
448358 TCTTTGAGTC
Statistics
Matches: 54, Mismatches: 2, Indels: 7
0.86 0.03 0.11
Matches are distributed among these distances:
63 4 0.07
64 17 0.31
65 11 0.20
66 1 0.02
67 11 0.20
68 10 0.19
ACGTcount: A:0.32, C:0.13, G:0.14, T:0.41
Consensus pattern (67 bp):
TAAGTTGTTTCTCTGGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCATTTGAGAAAAAAAATT
TG
Found at i:448385 original size:66 final size:63
Alignment explanation
Indices: 448233--448385 Score: 170
Period size: 66 Copynumber: 2.4 Consensus size: 63
448223 CAATATCTTT
*
448233 TAAGT-TGTTTCTTTTGAAACAAATTTTGTCTCTCTAGACAATTTCTTTCGGAAAAAAAATTTG
1 TAAGTCTGTTTCTCTTGAAACAAATTTTGTCTCTCTAGACAATTTCTTTC-GAAAAAAAATTTG
* * *
448296 TAAGTTTGTTTCTCTGGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCATTT-GAGAAAAAATC
1 TAAGTCTGTTTCTCTTGAAACAAA-TTTTGTCTCTC-T-AGACAATTTC-TTTCGAAAAAAAAT-
448360 TT-
61 TTG
*
448362 TGAGTCTGTTTC-CATTGAAACAAA
1 TAAGTCTGTTTCTC-TTGAAACAAA
448386 ACAAACATCT
Statistics
Matches: 77, Mismatches: 6, Indels: 11
0.82 0.06 0.12
Matches are distributed among these distances:
63 5 0.06
64 16 0.21
65 12 0.16
66 29 0.38
67 12 0.16
68 3 0.04
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.41
Consensus pattern (63 bp):
TAAGTCTGTTTCTCTTGAAACAAATTTTGTCTCTCTAGACAATTTCTTTCGAAAAAAAATTTG
Found at i:448532 original size:97 final size:96
Alignment explanation
Indices: 448303--448548 Score: 273
Period size: 97 Copynumber: 2.5 Consensus size: 96
448293 TTGTAAGTTT
* *
448303 GTTTCTCTGGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCATTTGAGAAAAAATCTTTGAGTC
1 GTTTC-CTTGAAACAAA-TTTTGTCTCTCTTGAGACAATTTC-TTTGAAAAAAAATCTTTGAGTC
* * *
448368 TGTTTCCATTGAAACAAAACAAACATCTTTGAGATT
63 TGTTTCCATTAAAACAAAAC--ACATATTTGAGATC
* * * *
448404 ATTTCCATTGAAACAAATTTTGTCTCCCTTGAGGCAGTTTCTTTGGAAACACAAAATCTTTGAGT
1 GTTTCC-TTGAAACAAATTTTGTCTCTCTTGAGACAATTTCTTT-GAAA-A-AAAATCTTTGAGT
*
448469 TTGTTTCTC-TTAAAACAAAAC-CATATTTGAG-TC
62 CTGTTTC-CATTAAAACAAAACACATATTTGAGATC
*
448502 GTTTCCTTGAAACAAATTTTGTATCTCTTGAGACAATTTCTCTTGAA
1 GTTTCCTTGAAACAAATTTTGTCTCTCTTGAGACAATTTCT-TTGAA
448549 GGATATCTTT
Statistics
Matches: 124, Mismatches: 15, Indels: 16
0.80 0.10 0.10
Matches are distributed among these distances:
97 34 0.27
98 8 0.06
99 12 0.10
100 25 0.20
101 14 0.11
102 30 0.24
103 1 0.01
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (96 bp):
GTTTCCTTGAAACAAATTTTGTCTCTCTTGAGACAATTTCTTTGAAAAAAAATCTTTGAGTCTGT
TTCCATTAAAACAAAACACATATTTGAGATC
Found at i:450933 original size:23 final size:22
Alignment explanation
Indices: 450907--450958 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
450897 TTTTATTTCA
**
450907 TTATTATTCCTATATTTAGCTAT
1 TTATTATTCCTAT-TTTAAATAT
* *
450930 TTATTAATCTTATTTTAAATAT
1 TTATTATTCCTATTTTAAATAT
450952 TTATTAT
1 TTATTAT
450959 CCAATATCTT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
22 13 0.54
23 11 0.46
ACGTcount: A:0.31, C:0.08, G:0.02, T:0.60
Consensus pattern (22 bp):
TTATTATTCCTATTTTAAATAT
Found at i:454029 original size:44 final size:45
Alignment explanation
Indices: 453943--454032 Score: 130
Period size: 44 Copynumber: 2.0 Consensus size: 45
453933 GAGACCTTGA
* *
453943 AATATTACATTTATCTTTTTTTTTGAGACCAAAGGTCGTACACAT
1 AATATTACATTTATCTTTTTTTTTGAGACCAAAAGTCATACACAT
*
453988 AATATTACCTTTATC-TTTTTTTT-AGACCCAAAAGTCATACACAT
1 AATATTACATTTATCTTTTTTTTTGAGA-CCAAAAGTCATACACAT
454032 A
1 A
454033 CTTTTCTTTG
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
43 3 0.07
44 24 0.59
45 14 0.34
ACGTcount: A:0.33, C:0.18, G:0.08, T:0.41
Consensus pattern (45 bp):
AATATTACATTTATCTTTTTTTTTGAGACCAAAAGTCATACACAT
Found at i:454640 original size:19 final size:19
Alignment explanation
Indices: 454595--454641 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
454585 CAAAACAAAG
*
454595 AGAAAAAAATAAAGAACAA
1 AGAAAAAAACAAAGAACAA
** *
454614 AGTTAAAAACAAAGACCAA
1 AGAAAAAAACAAAGAACAA
454633 AGAAAAAAA
1 AGAAAAAAA
454642 TAAGAAAAAA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.74, C:0.09, G:0.11, T:0.06
Consensus pattern (19 bp):
AGAAAAAAACAAAGAACAA
Found at i:454664 original size:15 final size:15
Alignment explanation
Indices: 454644--454695 Score: 79
Period size: 15 Copynumber: 3.5 Consensus size: 15
454634 GAAAAAAATA
454644 AGAAAAAAAGCAAAG
1 AGAAAAAAAGCAAAG
*
454659 AGAAAAAGAGCAAAG
1 AGAAAAAAAGCAAAG
454674 AGAAAAGAAA-CAAAG
1 AGAAAA-AAAGCAAAG
454689 AGAAAAA
1 AGAAAAA
454696 GTAAAGATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
14 1 0.03
15 31 0.91
16 2 0.06
ACGTcount: A:0.73, C:0.06, G:0.21, T:0.00
Consensus pattern (15 bp):
AGAAAAAAAGCAAAG
Found at i:455992 original size:67 final size:63
Alignment explanation
Indices: 455886--456028 Score: 198
Period size: 67 Copynumber: 2.2 Consensus size: 63
455876 ATCAGTATCA
* * * *
455886 TTTGAG-TTGTTTCTTTTGAAGCAAATTTGTCTCTCGAGACAGTTTCTTTTGAAAAAAAAATTC
1 TTTGAGTTTGTTTCTCTGGAAACAAATTTGTCTCTCGAGACAATTTCTTTTGAAAAAAAAA-TC
*
455949 TTTGAGTTTGTTTCTCTGGAAACAAAGTTTGTCTCTCTTGAGACAATTTCTTTTGAGAAAAAAAT
1 TTTGAGTTTGTTTCTCTGGAAACAAA-TTTGTCTCTC--GAGACAATTTCTTTTGAAAAAAAAAT
456014 C
63 C
456015 TTTGAGTTTGTTTC
1 TTTGAGTTTGTTTC
456029 CATTGAAACA
Statistics
Matches: 71, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
63 6 0.08
64 16 0.23
65 10 0.14
66 16 0.23
67 23 0.32
ACGTcount: A:0.27, C:0.13, G:0.17, T:0.44
Consensus pattern (63 bp):
TTTGAGTTTGTTTCTCTGGAAACAAATTTGTCTCTCGAGACAATTTCTTTTGAAAAAAAAATC
Found at i:456039 original size:66 final size:63
Alignment explanation
Indices: 455886--456040 Score: 197
Period size: 66 Copynumber: 2.4 Consensus size: 63
455876 ATCAGTATCA
* * *
455886 TTTGAG-TTGTTTCTTTTGAAGCAAATTTGTCTCTCGAGACAGTTTCTTTTGAAAAAAAAATTC
1 TTTGAGTTTGTTTC-CTTGAAACAAATTTGTCTCTCGAGACAATTTCTTTTGAAAAAAAAATTC
* *
455949 TTTGAGTTTGTTTCTCTGGAAACAAAGTTTGTCTCTCTTGAGACAATTTCTTTTGAGAAAAAAA-
1 TTTGAGTTTGTTTC-CTTGAAACAAA-TTTGTCTCTC--GAGACAATTTCTTTTGAAAAAAAAAT
456013 TC
62 TC
456015 TTTGAGTTTGTTTCCATTGAAACAAA
1 TTTGAGTTTGTTTCC-TTGAAACAAA
456041 ACAAATATCT
Statistics
Matches: 81, Mismatches: 6, Indels: 7
0.86 0.06 0.07
Matches are distributed among these distances:
63 6 0.07
64 16 0.20
65 11 0.14
66 25 0.31
67 23 0.28
ACGTcount: A:0.29, C:0.13, G:0.16, T:0.42
Consensus pattern (63 bp):
TTTGAGTTTGTTTCCTTGAAACAAATTTGTCTCTCGAGACAATTTCTTTTGAAAAAAAAATTC
Found at i:456063 original size:101 final size:100
Alignment explanation
Indices: 455927--456190 Score: 289
Period size: 101 Copynumber: 2.7 Consensus size: 100
455917 TCTCGAGACA
* * * *
455927 GTTTCTTTTG-AA-AAAA-AAAT-TCTTTGAGTTTGTTTCTCTGGAAACAAAGTTTGTCTCTCTT
1 GTTTCTCTTGAAACAAAACAAATATCTTTGAG-TCGTTTC-CTTGAAACAAAATTTGTCTCTCTT
*
455988 GAGACAATTTCTTTTGAGAA-A-AAAATCTTTGAGTTT
64 GAGACAATTTCTTTGGA-AACACAAAATCTTTGAGTTT
* *
456024 GTTTC-CATTGAAACAAAACAAATATCTTTGAGATCGTTTCCATTGAAA-AAAAATTGTCTCCCT
1 GTTTCTC-TTGAAACAAAACAAATATCTTTGAG-TCGTTTCC-TTGAAACAAAATTTGTCTCTCT
* *
456087 TGAGCCAGTTTCTTTGGAAACACAAAATCTTTGAGTTT
63 TGAGACAATTTCTTTGGAAACACAAAATCTTTGAGTTT
* * *
456125 GTTTCTCTTGAAACAAAAC---CATCTTTGAGTCATTTCCTTGAAACAAATTTTGTCTCTCTTGA
1 GTTTCTCTTGAAACAAAACAAATATCTTTGAGTCGTTTCCTTGAAACAAAATTTGTCTCTCTTGA
456187 GACA
66 GACA
456191 GCTTCTCTTG
Statistics
Matches: 141, Mismatches: 16, Indels: 20
0.80 0.09 0.11
Matches are distributed among these distances:
96 6 0.04
97 33 0.23
98 11 0.08
99 6 0.04
100 33 0.23
101 51 0.36
102 1 0.01
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (100 bp):
GTTTCTCTTGAAACAAAACAAATATCTTTGAGTCGTTTCCTTGAAACAAAATTTGTCTCTCTTGA
GACAATTTCTTTGGAAACACAAAATCTTTGAGTTT
Found at i:456129 original size:31 final size:31
Alignment explanation
Indices: 456094--456171 Score: 83
Period size: 31 Copynumber: 2.5 Consensus size: 31
456084 CCTTGAGCCA
456094 GTTTCT-TTGGAAACACAAA-ATCTTTGAGTTT
1 GTTTCTCTT-GAAACA-AAACATCTTTGAGTTT
*
456125 GTTTCTCTTGAAACAAAACCATCTTTGAG-TC
1 GTTTCTCTTGAAACAAAA-CATCTTTGAGTTT
*
456156 ATTTC-CTTGAAACAAA
1 GTTTCTCTTGAAACAAA
456172 TTTTGTCTCT
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
30 14 0.33
31 17 0.40
32 11 0.26
ACGTcount: A:0.32, C:0.18, G:0.13, T:0.37
Consensus pattern (31 bp):
GTTTCTCTTGAAACAAAACATCTTTGAGTTT
Found at i:456474 original size:130 final size:130
Alignment explanation
Indices: 456238--456496 Score: 299
Period size: 130 Copynumber: 2.0 Consensus size: 130
456228 TGAAACCATA
** * * * * *
456238 ATCCCTAAAGATGGCTTACCGTCCTCATCACATAGGAACCGTGTCATACCCCGGCCAGACGTCTT
1 ATCCCTAAAGATGGCCAACCATCCTCATCACATAGAAACCATGTCATACCCCGACCAGACCTCTT
** * * *
456303 CATCACGTAGGAGTTGTGTCACCCCTGATAACCAGCTGTCCTTATCACGTAAGAACCGTGTTATC
66 CATCACGTAGGAGTCATGTCACCCCTGATAACCAACCGTCCTCATCACGTAAGAACCGTGTTATC
* * *
456368 ATCCCTAAAGATGGCCAACCATCCTCATCATATAGAAATCATGTCATCCCCCGACCAGACCTCCT
1 ATCCCTAAAGATGGCCAACCATCCTCATCACATAGAAACCATGTCATACCCCGACCAGACCT-CT
* * * *
456433 T-ATCACGTAGGAGTCATGTCA-CCGTAGA-ATATCAACCGTCCTCATCGCGTAGGAACCGTGTT
65 TCATCACGTAGGAGTCATGTCACCCCT-GATA-ACCAACCGTCCTCATCACGTAAGAACCGTGTT
456495 AT
128 AT
456497 TGTACTTCCT
Statistics
Matches: 107, Mismatches: 19, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
129 4 0.04
130 100 0.93
131 3 0.03
ACGTcount: A:0.27, C:0.31, G:0.18, T:0.25
Consensus pattern (130 bp):
ATCCCTAAAGATGGCCAACCATCCTCATCACATAGAAACCATGTCATACCCCGACCAGACCTCTT
CATCACGTAGGAGTCATGTCACCCCTGATAACCAACCGTCCTCATCACGTAAGAACCGTGTTATC
Found at i:456799 original size:3 final size:3
Alignment explanation
Indices: 456791--456832 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
456781 ATTATAATAT
456791 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
456833 CAATTTACAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:458548 original size:23 final size:22
Alignment explanation
Indices: 458522--458573 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
458512 TTTTATTTCA
**
458522 TTATTATTCCTATATTTAGCTAT
1 TTATTATTCCTAT-TTTAAATAT
* *
458545 TTATTAATCTTATTTTAAATAT
1 TTATTATTCCTATTTTAAATAT
458567 TTATTAT
1 TTATTAT
458574 CCAATATCTT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
22 13 0.54
23 11 0.46
ACGTcount: A:0.31, C:0.08, G:0.02, T:0.60
Consensus pattern (22 bp):
TTATTATTCCTATTTTAAATAT
Found at i:464979 original size:21 final size:20
Alignment explanation
Indices: 464942--464990 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
464932 ACTAGCATAC
*
464942 TATCGATATTGCTTTAATAGG
1 TATCGATATTGCTTTAACA-G
*
464963 TATCGATATT-TTCTTAACAG
1 TATCGATATTGCT-TTAACAG
464983 TATCGATA
1 TATCGATA
464991 CTCCTTAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 10 0.40
21 15 0.60
ACGTcount: A:0.31, C:0.12, G:0.14, T:0.43
Consensus pattern (20 bp):
TATCGATATTGCTTTAACAG
Found at i:468700 original size:18 final size:18
Alignment explanation
Indices: 468677--468712 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
468667 GAATTTTAAG
468677 ATTTTATATTCGATTCAA
1 ATTTTATATTCGATTCAA
468695 ATTTTATATTCGATTCAA
1 ATTTTATATTCGATTCAA
468713 TTATTGAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.11, G:0.06, T:0.50
Consensus pattern (18 bp):
ATTTTATATTCGATTCAA
Found at i:472692 original size:133 final size:133
Alignment explanation
Indices: 472542--472806 Score: 530
Period size: 133 Copynumber: 2.0 Consensus size: 133
472532 TGAGATCTCT
472542 TTTCTCTCCTTTTTTTTGTGGCAACTTGAAACCATTTGGGAAGCAAATTCGTTGAAGAGGTTGAG
1 TTTCTCTCCTTTTTTTTGTGGCAACTTGAAACCATTTGGGAAGCAAATTCGTTGAAGAGGTTGAG
472607 GTCATCCATGTGCCAGTAGCCACCATTGTGTATGACCTTGTTCTTTCCTAGACTATTCAAGTAAG
66 GTCATCCATGTGCCAGTAGCCACCATTGTGTATGACCTTGTTCTTTCCTAGACTATTCAAGTAAG
472672 GAC
131 GAC
472675 TTTCTCTCCTTTTTTTTGTGGCAACTTGAAACCATTTGGGAAGCAAATTCGTTGAAGAGGTTGAG
1 TTTCTCTCCTTTTTTTTGTGGCAACTTGAAACCATTTGGGAAGCAAATTCGTTGAAGAGGTTGAG
472740 GTCATCCATGTGCCAGTAGCCACCATTGTGTATGACCTTGTTCTTTCCTAGACTATTCAAGTAAG
66 GTCATCCATGTGCCAGTAGCCACCATTGTGTATGACCTTGTTCTTTCCTAGACTATTCAAGTAAG
472805 GA
131 GA
472807 AGCAAAACAA
Statistics
Matches: 132, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
133 132 1.00
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.35
Consensus pattern (133 bp):
TTTCTCTCCTTTTTTTTGTGGCAACTTGAAACCATTTGGGAAGCAAATTCGTTGAAGAGGTTGAG
GTCATCCATGTGCCAGTAGCCACCATTGTGTATGACCTTGTTCTTTCCTAGACTATTCAAGTAAG
GAC
Found at i:473557 original size:13 final size:13
Alignment explanation
Indices: 473536--473565 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
473526 TATAGAGGTC
*
473536 GCATGGTCATGCA
1 GCATAGTCATGCA
473549 GCATAGTCATGCA
1 GCATAGTCATGCA
473562 GCAT
1 GCAT
473566 GGTCTTCGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (13 bp):
GCATAGTCATGCA
Found at i:479447 original size:20 final size:21
Alignment explanation
Indices: 479419--479457 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
479409 ATCTTAACCC
479419 CTAAGCTTAAAACCGTAAACT
1 CTAAGCTTAAAACCGTAAACT
*
479440 CTAA-CTTAAAACCTTAAA
1 CTAAGCTTAAAACCGTAAA
479458 TAATAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.46, C:0.23, G:0.05, T:0.26
Consensus pattern (21 bp):
CTAAGCTTAAAACCGTAAACT
Found at i:481397 original size:3 final size:3
Alignment explanation
Indices: 481389--481506 Score: 178
Period size: 3 Copynumber: 41.3 Consensus size: 3
481379 TTTTTTACCC
481389 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-T ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
481436 ATT ATT ATT -TT A-T ATT A-T ATT ATT ATT ATT A-T ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
481480 ATT -TT ATAT ATT ATT ATT A-T ATT ATT A
1 ATT ATT AT-T ATT ATT ATT ATT ATT ATT A
481507 AATTATATTA
Statistics
Matches: 107, Mismatches: 0, Indels: 16
0.87 0.00 0.13
Matches are distributed among these distances:
2 14 0.13
3 90 0.84
4 3 0.03
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:481438 original size:38 final size:37
Alignment explanation
Indices: 481391--481504 Score: 178
Period size: 38 Copynumber: 3.0 Consensus size: 37
481381 TTTTACCCAT
481391 TATTATTATTATTATTATTATTATTATTATTATTATTA
1 TATTATTATTATTATT-TTATTATTATTATTATTATTA
481429 TATTATTATTATTATTTTA-TATTATATTATTATTATTA
1 TATTATTATTATTATTTTATTA-T-TATTATTATTATTA
481467 TATTATTATTATTATTTTATATATTATTATTA-TATTA
1 TATTATTATTATTATTTTAT-TATTATTATTATTATTA
481504 T
1 T
481505 TAAATTATAT
Statistics
Matches: 72, Mismatches: 0, Indels: 9
0.89 0.00 0.11
Matches are distributed among these distances:
36 2 0.03
37 10 0.14
38 57 0.79
39 1 0.01
40 2 0.03
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (37 bp):
TATTATTATTATTATTTTATTATTATTATTATTATTA
Found at i:481522 original size:14 final size:14
Alignment explanation
Indices: 481495--481537 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
481485 ATATATTATT
*
481495 ATTATATT-ATTAA
1 ATTATATTAAATAA
481508 ATTATATTAAATAA
1 ATTATATTAAATAA
481522 ATCTATA-TAAATAA
1 AT-TATATTAAATAA
481536 AT
1 AT
481538 AATTACAGAC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 8 0.30
14 15 0.56
15 4 0.15
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (14 bp):
ATTATATTAAATAA
Found at i:494367 original size:16 final size:16
Alignment explanation
Indices: 494346--494385 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
494336 ATACAATTCT
494346 ATTTATTTCA-AGTTCA
1 ATTTATTTCAGAG-TCA
*
494362 ATTTATTTGAGAGTCA
1 ATTTATTTCAGAGTCA
494378 ATTTATTT
1 ATTTATTT
494386 TTTTGAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 20 0.91
17 2 0.09
ACGTcount: A:0.30, C:0.07, G:0.10, T:0.53
Consensus pattern (16 bp):
ATTTATTTCAGAGTCA
Found at i:494385 original size:20 final size:20
Alignment explanation
Indices: 494362--494404 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
494352 TTCAAGTTCA
*
494362 ATTTATTTGAGAGTCAATTT
1 ATTTATTTGAAAGTCAATTT
* *
494382 ATTTTTTTGAAATTCAATTT
1 ATTTATTTGAAAGTCAATTT
494402 ATT
1 ATT
494405 CTTTTCTATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.05, G:0.09, T:0.56
Consensus pattern (20 bp):
ATTTATTTGAAAGTCAATTT
Found at i:495308 original size:83 final size:83
Alignment explanation
Indices: 495169--496132 Score: 1546
Period size: 83 Copynumber: 11.7 Consensus size: 83
495159 AATTAAATGA
495169 AAGATGAATTTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
1 AAGATGAATTTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
*
495234 ACCAATCAGTGAATTTAG
66 ACCAATCATTGAATTTAG
495252 AAGATGAATTTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
1 AAGATGAATTTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
*
495317 ACCAATCAGTGAATTTAG
66 ACCAATCATTGAATTTAG
*
495335 AAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
1 AAGATGAATTTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
*
495400 ACCAATCAGTGAATTTAG
66 ACCAATCATTGAATTTAG
*
495418 AAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGACAG
1 AAGATGAATTTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-CAG
*
495482 AA-CAATCATTGAGTTT--
65 AACCAATCATTGAATTTAG
495498 -AGATGAATTTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
1 AAGATGAATTTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
495562 ACCAATCATTGAATTT-G
66 ACCAATCATTGAATTTAG
*
495579 AAAGATGAATGTGTTC-ATAAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGC
1 -AAGATGAATTTG-TCAAT-AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGC
*
495643 AGAACCAATCATTGAATTTGG
63 AGAACCAATCATTGAATTTAG
*
495664 AAGATGAATGTGTTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGACA
1 AAGATGAATTTG-TCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-CA
*
495727 GAA-CAATCATTGAGTTTAG
64 GAACCAATCATTGAATTTAG
495746 AAGATGAATTTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
1 AAGATGAATTTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
495811 ACCAATCATTGAATTT-G
66 ACCAATCATTGAATTTAG
*
495828 AAAGATGAATGTGTTC-ATAAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGC
1 -AAGATGAATTTG-TCAAT-AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGC
*
495892 AGAACCAATCATTGAATTTGG
63 AGAACCAATCATTGAATTTAG
*
495913 AAGATGAATGTGTTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGACA
1 AAGATGAATTTG-TCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-CA
*
495976 GAA-CAATCATTGAGTTTAG
64 GAACCAATCATTGAATTTAG
495995 AAGATGAATTTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
1 AAGATGAATTTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
**
496060 ACCAATCATTGAATTCGG
66 ACCAATCATTGAATTTAG
* *
496078 AACATGAATGTGTTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
1 AAGATGAATTTG-TCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
496133 ATTCAGTAGG
Statistics
Matches: 840, Mismatches: 19, Indels: 44
0.93 0.02 0.05
Matches are distributed among these distances:
79 59 0.07
80 17 0.02
81 4 0.00
82 167 0.20
83 423 0.50
84 168 0.20
85 2 0.00
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37
Consensus pattern (83 bp):
AAGATGAATTTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
ACCAATCATTGAATTTAG
Found at i:497238 original size:229 final size:227
Alignment explanation
Indices: 496782--497515 Score: 1056
Period size: 229 Copynumber: 3.2 Consensus size: 227
496772 GAAAGATCAG
*
496782 CTTTTCCAGAG-AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTTATAATGA
1 CTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
* * *
496846 GAAGAATTTGTTCAACC-TTTTACCTGAATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGT
66 GAAGAATTTGTTCAACCTTTTTATCTGAAT-CATCATTTGATGGATCAACTTTTCCAGAGAAGGT
*
496910 TCATAATGAGAAGAACTCATCT---GAA-GAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAAC
130 TCATAATGAGAAGAACCCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAAC
*
496971 CTTTTACCTGAATTCATCAAATTGATGGATTAT
195 CTTTTTCCTGAATTCATCAAATTGATGGATTAT
497004 CTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
1 CTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
* * * *
497069 GAAGAATTTGTTCAACCTTTTTTTCTGAAGTCATCAAATTGATGGATTATCTTTTCCAGAGAAGG
66 GAAGAATTTGTTCAACCTTTTTATCTGAA-TCATC-ATTTGATGGATCAACTTTTCCAGAGAAGG
497134 TTCATAATGAGAAGAACCCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAA
129 TTCATAATGAGAAGAACCCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAA
*
497199 CCTTTTTTCTGAATTCATCAAATTGATGGATTAT
194 CCTTTTTCCTGAATTCATCAAATTGATGGATTAT
*
497233 CTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
1 CTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
* * ** * * *
497298 GAAGAACTTGTTCAATCTTTTGCT-TGAATTCATCATTTGATGGATCAACATTGCCAG-GTAGAG
66 GAAGAATTTGTTCAACCTTTTTATCTGAA-TCATCATTTGATGGATCAACTTTTCCAGAGAAG-G
*
497361 TTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
129 TTCATAATGAGAAGAAC-C--CATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTT
* * * * *
497426 CAATCTTTTGCTTGAATTCATC-ATTTGATGGATCAT
191 CAACCTTTTTCCTGAATTCATCAAATTGATGGATTAT
* ** *
497462 CATCCCCAGCAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAG-AGAAGAA
1 CTTTTCCAG-AGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAA
497516 TTTATTCAAT
Statistics
Matches: 465, Mismatches: 34, Indels: 19
0.90 0.07 0.04
Matches are distributed among these distances:
222 11 0.02
223 69 0.15
224 13 0.03
225 48 0.10
226 3 0.01
227 36 0.08
228 13 0.03
229 176 0.38
230 96 0.21
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (227 bp):
CTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
GAAGAATTTGTTCAACCTTTTTATCTGAATCATCATTTGATGGATCAACTTTTCCAGAGAAGGTT
CATAATGAGAAGAACCCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACC
TTTTTCCTGAATTCATCAAATTGATGGATTAT
Found at i:497270 original size:114 final size:113
Alignment explanation
Indices: 496776--497515 Score: 1044
Period size: 114 Copynumber: 6.5 Consensus size: 113
496766 TCATTTGAAA
* *
496776 GATCAGCTTTTCCAGAG-AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTTA
1 GATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA
* * *
496840 TAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCATTTGATG
66 TAATGAGAAGAATTTGTTCAACCTTTTTCCTGAATTCATCAATTGATG
*
496888 GATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCT---GAA-GAAGAAGAAGTTCA
1 GATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA
*
496949 TAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTCATCAAATTGATG
66 TAATGAGAAGAATTTGTTCAACCTTTTTCCTGAATTCATC-AATTGATG
*
496998 GATTATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA
1 GATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA
* *
497063 TAATGAGAAGAATTTGTTCAACCTTTTTTTCTGAAGTCATCAAATTGATG
66 TAATGAGAAGAATTTGTTCAACC-TTTTTCCTGAATTCATC-AATTGATG
* * *
497113 GATTATCTTTTCCAGAGAAGGTTCATAATGAGAAGAACCCATCTGAAGAAGGAAGAAGAAGTTCA
1 GATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA
*
497178 TAATGAGAAGAATTTGTTCAACCTTTTTTCTGAATTCATCAAATTGATG
66 TAATGAGAAGAATTTGTTCAACCTTTTTCCTGAATTCATC-AATTGATG
* *
497227 GATTATCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA
1 GATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA
* * * * *
497292 TAATGAGAAGAACTTGTTCAATCTTTTGCTTGAATTCATCATTTGATG
66 TAATGAGAAGAATTTGTTCAACCTTTTTCCTGAATTCATCAATTGATG
* * * *
497340 GATCAACATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAG
1 GATCATCTTTTCCAGAG-AAAGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGAAGAAG
* * * * *
497404 TTCATAATGAGAAGAACTTGTTCAATCTTTTGCTTGAATTCATCATTTGATG
62 TTCATAATGAGAAGAATTTGTTCAACCTTTTTCCTGAATTCATCAATTGATG
* ** *
497456 GATCATCATCCCCAGCAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAG-AGAAGAA
1 GATCATCTTTTCCAG-AGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAA
497516 TTTATTCAAT
Statistics
Matches: 586, Mismatches: 29, Indels: 25
0.92 0.05 0.04
Matches are distributed among these distances:
109 52 0.09
110 52 0.09
112 18 0.03
113 72 0.12
114 174 0.30
115 111 0.19
116 87 0.15
117 19 0.03
118 1 0.00
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (113 bp):
GATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA
TAATGAGAAGAATTTGTTCAACCTTTTTCCTGAATTCATCAATTGATG
Found at i:497659 original size:3 final size:3
Alignment explanation
Indices: 497651--497763 Score: 226
Period size: 3 Copynumber: 37.7 Consensus size: 3
497641 TTTTTACCCA
497651 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
497699 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
497747 TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TA
497764 AATATATATT
Statistics
Matches: 110, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 110 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:497790 original size:14 final size:15
Alignment explanation
Indices: 497762--497796 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
497752 TTATTATTAT
497762 TAAATATATATTAAA
1 TAAATATATATTAAA
*
497777 TAAATCTATA-TAAA
1 TAAATATATATTAAA
497791 TAAATA
1 TAAATA
497797 ATTACAGACC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (15 bp):
TAAATATATATTAAA
Found at i:500168 original size:17 final size:17
Alignment explanation
Indices: 500146--500182 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
500136 ATATAAATAT
*
500146 TTATTTATTTATGATTA
1 TTATTTAATTATGATTA
*
500163 TTATTTAATTATTATTA
1 TTATTTAATTATGATTA
500180 TTA
1 TTA
500183 ATATTTTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (17 bp):
TTATTTAATTATGATTA
Found at i:500168 original size:21 final size:21
Alignment explanation
Indices: 500141--500197 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
500131 AAAAAATATA
*
500141 AATATTTATTTATTTATGATT
1 AATATTTAATTATTTATGATT
* *
500162 ATTATTTAATTA-TTATTATT
1 AATATTTAATTATTTATGATT
500182 AATATTTTAATTATTT
1 AATA-TTTAATTATTT
500198 TTTTCTTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 10 0.33
21 18 0.60
22 2 0.07
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (21 bp):
AATATTTAATTATTTATGATT
Found at i:505822 original size:153 final size:153
Alignment explanation
Indices: 505529--505834 Score: 506
Period size: 153 Copynumber: 2.0 Consensus size: 153
505519 TTAGCCATCC
* *
505529 AAGAGATCCATATGTTCTCTAGGAGATTATGAATATTGAATTATCTGATAGGATTTTTTTATTTT
1 AAGAAATCCATATGTTCTCTAGGAGATTATGAATATTGAATTATCTAATAGGATTTTTTTATTTT
505594 ATTATTTCATTTTGTTGGCATTAACCCTATGGGAATAATAAGCCCATACTGTTACTTTAAGTTGA
66 ATTATTTCATTTTGTTGGCATTAACCCTATGGGAATAATAAGCCCATACTGTTACTTTAAGTTGA
* * *
505659 CTAGAGTTGTATTATTGTGTCAT
131 CTAGACTTGTATCATTCTGTCAT
* * * *
505682 AAGAAATCCTTATGTTCTCTAGTAGATTATGAATATTGATTTATCTAATATGGTTTTTTTTATTT
1 AAGAAATCCATATGTTCTCTAGGAGATTATGAATATTGAATTATCTAATA-GGATTTTTTTATTT
*
505747 TATTATTTCATTTTGTT-GCATTAACCCTATGGGAATAATAAGCCCGTACTGTTACTTTAAGTTG
65 TATTATTTCATTTTGTTGGCATTAACCCTATGGGAATAATAAGCCCATACTGTTACTTTAAGTTG
505811 ACTAGACTTGTATCATTCTGTCAT
130 ACTAGACTTGTATCATTCTGTCAT
505835 TTTTTATCTT
Statistics
Matches: 142, Mismatches: 10, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
153 112 0.79
154 30 0.21
ACGTcount: A:0.28, C:0.12, G:0.15, T:0.44
Consensus pattern (153 bp):
AAGAAATCCATATGTTCTCTAGGAGATTATGAATATTGAATTATCTAATAGGATTTTTTTATTTT
ATTATTTCATTTTGTTGGCATTAACCCTATGGGAATAATAAGCCCATACTGTTACTTTAAGTTGA
CTAGACTTGTATCATTCTGTCAT
Found at i:507884 original size:25 final size:25
Alignment explanation
Indices: 507856--507910 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
507846 ATGTTTTATG
**
507856 TATTACGCATTTATTTTATGTATAT
1 TATTACGCATTTATTTTACATATAT
* *
507881 TATTATGTATTTATTTTACATATAT
1 TATTACGCATTTATTTTACATATAT
507906 TATTA
1 TATTA
507911 TATATATTAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.31, C:0.05, G:0.05, T:0.58
Consensus pattern (25 bp):
TATTACGCATTTATTTTACATATAT
Found at i:507888 original size:12 final size:12
Alignment explanation
Indices: 507867--507941 Score: 50
Period size: 12 Copynumber: 6.2 Consensus size: 12
507857 ATTACGCATT
*
507867 TATT-TTATGTA
1 TATTATTATATA
*
507878 TATTATTATGTA
1 TATTATTATATA
*
507890 T-TTATTTTACATA
1 TATTA--TTATATA
507903 TATTATTATATA
1 TATTATTATATA
507915 TATTACTT-TATTA
1 TATTA-TTATA-TA
507928 TATATATT-TATA
1 TAT-TATTATATA
507940 TA
1 TA
507942 ATACTACATG
Statistics
Matches: 54, Mismatches: 3, Indels: 13
0.77 0.04 0.19
Matches are distributed among these distances:
11 7 0.13
12 25 0.46
13 17 0.31
14 5 0.09
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.60
Consensus pattern (12 bp):
TATTATTATATA
Found at i:507911 original size:25 final size:25
Alignment explanation
Indices: 507864--507911 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
507854 TGTATTACGC
**
507864 ATTTATTTTATGTATATTATTATGT
1 ATTTATTTTACATATATTATTATGT
507889 ATTTATTTTACATATATTATTAT
1 ATTTATTTTACATATATTATTAT
507912 ATATATTACT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.62
Consensus pattern (25 bp):
ATTTATTTTACATATATTATTATGT
Found at i:507929 original size:25 final size:25
Alignment explanation
Indices: 507870--507946 Score: 77
Period size: 25 Copynumber: 3.0 Consensus size: 25
507860 ACGCATTTAT
* *
507870 TTTATGTATATTATTATGTAT-TTAT
1 TTTAT-TATATTATTATATATATTAC
*
507895 TTTACATATATTATTATATATATTAC
1 TTTA-TTATATTATTATATATATTAC
*
507921 TTTATTATATATATT-TATATAATAC
1 TTTATTATAT-TATTATATATATTAC
507946 T
1 T
507947 ACATGTATTG
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
25 33 0.75
26 11 0.25
ACGTcount: A:0.35, C:0.04, G:0.03, T:0.58
Consensus pattern (25 bp):
TTTATTATATTATTATATATATTAC
Found at i:509000 original size:11 final size:11
Alignment explanation
Indices: 508977--509013 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
508967 ATGGCGACTC
508977 CAAAATA-TTT
1 CAAAATATTTT
508987 CAAAATATTTT
1 CAAAATATTTT
*
508998 CAAAACATTTT
1 CAAAATATTTT
509009 CAAAA
1 CAAAA
509014 GAAAAACCCC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
10 7 0.28
11 18 0.72
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (11 bp):
CAAAATATTTT
Found at i:510696 original size:20 final size:20
Alignment explanation
Indices: 510659--510702 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
510649 TTTGCATTTT
* **
510659 GCATCTTTGCATTTGCATGA
1 GCATATTTGCATAAGCATGA
*
510679 GCATATTTGCATAAGCATTA
1 GCATATTTGCATAAGCATGA
510699 GCAT
1 GCAT
510703 CTATACATCG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.36
Consensus pattern (20 bp):
GCATATTTGCATAAGCATGA
Found at i:512045 original size:19 final size:18
Alignment explanation
Indices: 512023--512069 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 18
512013 GAAGAGATAT
512023 AGAAAAAAAACACACAAAA
1 AGAAAAAAAACACA-AAAA
*
512042 AGAAAGTAAAAACAGAAAAA
1 AGAAA--AAAAACACAAAAA
512062 AGAAAAAA
1 AGAAAAAA
512070 GAAAAAAGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 3 0.12
19 5 0.20
20 9 0.36
21 8 0.32
ACGTcount: A:0.79, C:0.09, G:0.11, T:0.02
Consensus pattern (18 bp):
AGAAAAAAAACACAAAAA
Found at i:512061 original size:20 final size:21
Alignment explanation
Indices: 512028--512066 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
512018 GATATAGAAA
512028 AAAAACACACAAAAAGAAAGT
1 AAAAACACACAAAAAGAAAGT
*
512049 AAAAACAGA-AAAAAGAAA
1 AAAAACACACAAAAAGAAA
512067 AAAGAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.77, C:0.10, G:0.10, T:0.03
Consensus pattern (21 bp):
AAAAACACACAAAAAGAAAGT
Found at i:512065 original size:7 final size:7
Alignment explanation
Indices: 512044--512134 Score: 64
Period size: 7 Copynumber: 12.4 Consensus size: 7
512034 ACACAAAAAG
512044 AAAGTAAA
1 AAAG-AAA
512052 AACAGAAA
1 AA-AGAAA
512060 AAAGAAA
1 AAAGAAA
512067 AAAGAAA
1 AAAGAAA
512074 AAAG-AA
1 AAAGAAA
*
512080 AAAG-TA
1 AAAGAAA
*
512086 AGAGAAA
1 AAAGAAA
512093 ACATA-AGAA
1 A-A-AGA-AA
512102 AAAGAGAA
1 AAAGA-AA
512110 AAAGAAA
1 AAAGAAA
512117 AAA-AAA
1 AAAGAAA
512123 GAAAGAAGA
1 -AAAGAA-A
512132 AAA
1 AAA
512135 TAGACATATC
Statistics
Matches: 70, Mismatches: 4, Indels: 18
0.76 0.04 0.20
Matches are distributed among these distances:
6 13 0.19
7 27 0.39
8 23 0.33
9 7 0.10
ACGTcount: A:0.78, C:0.02, G:0.16, T:0.03
Consensus pattern (7 bp):
AAAGAAA
Found at i:512082 original size:40 final size:43
Alignment explanation
Indices: 512038--512129 Score: 111
Period size: 40 Copynumber: 2.2 Consensus size: 43
512028 AAAAACACAC
* *
512038 AAAAAGAAAGTA-AAAACA-GA-AAAAAGA-AAAAAGAAAAAAG
1 AAAAAGAAAG-AGAAAACATAAGAAAAAGAGAAAAAGAAAAAAA
*
512078 AAAAAGTAAGAGAAAACATAAGAAAAAGAGAAAAAGAAAAAAA
1 AAAAAGAAAGAGAAAACATAAGAAAAAGAGAAAAAGAAAAAAA
512121 AAGAAAGAA
1 AA-AAAGAA
512130 GAAAATAGAC
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
39 1 0.02
40 15 0.35
41 1 0.02
42 7 0.16
43 14 0.33
44 5 0.12
ACGTcount: A:0.78, C:0.02, G:0.16, T:0.03
Consensus pattern (43 bp):
AAAAAGAAAGAGAAAACATAAGAAAAAGAGAAAAAGAAAAAAA
Found at i:514244 original size:54 final size:56
Alignment explanation
Indices: 514178--514325 Score: 153
Period size: 58 Copynumber: 2.6 Consensus size: 56
514168 TAAGCTTTCA
514178 AAGAAA-TCAAGCCTGATTTTCAGGGGTTTCTTGATGT-TT-TCAAATG-AA-TTTTT
1 AAGAAACT-AAGCCTGATTTTCAGGGGTTTCTTGATGTATTGT-AAATGAAAGTTTTT
* * * *
514231 AAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATAATAATTGTAAATGAAAGTTTTT
1 -AAGAAACTAAGCCTGATTTTCAGGGGTTTCTTGAT-GT-ATTGTAAATGAAAGTTTTT
* * *
514290 AAGAAACTAAGCTTGGTTTTCAAGGGTTTCTTGATG
1 AAGAAACTAAGCCTGATTTTCAGGGGTTTCTTGATG
514326 AGTAAGTCCT
Statistics
Matches: 76, Mismatches: 11, Indels: 11
0.78 0.11 0.11
Matches are distributed among these distances:
54 30 0.39
55 2 0.03
57 7 0.09
58 32 0.42
59 5 0.07
ACGTcount: A:0.31, C:0.09, G:0.20, T:0.39
Consensus pattern (56 bp):
AAGAAACTAAGCCTGATTTTCAGGGGTTTCTTGATGTATTGTAAATGAAAGTTTTT
Found at i:514546 original size:85 final size:85
Alignment explanation
Indices: 514367--514584 Score: 323
Period size: 84 Copynumber: 2.6 Consensus size: 85
514357 CGATCATGAT
* * *
514367 GCTTAAGTCCTTCGGGAAATCCATAAGACCTTCGGGTAGGATGTTTT-AACATTTCATTTGCTCG
1 GCTTAAGTCCTTCGGGACATCCATAAGACCTTCGGGCAGGATGTTTTCAACATTTCATATGCTCG
514431 ATTCACAACACTTCGAATCA
66 ATTCACAACACTTCGAATCA
* *
514451 GCTTAAGTCCTTCGGGCCATCCATAAGACCTTCGGGCAGGATGTTTTCAACATTTCCTATGCTCG
1 GCTTAAGTCCTTCGGGACATCCATAAGACCTTCGGGCAGGATGTTTTCAACATTTCATATGCTCG
514516 ATTCACAACACTTCGAATCA
66 ATTCACAACACTTCGAATCA
* * * ** *
514536 GTTTAAGTCCTTTGGGTCATCCATAAGA-CTTTAGGCTGGATGTTTTCAA
1 GCTTAAGTCCTTCGGGACATCCATAAGACCTTCGGGCAGGATGTTTTCAA
514585 ATGAGTTTTT
Statistics
Matches: 122, Mismatches: 11, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
84 62 0.51
85 60 0.49
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.33
Consensus pattern (85 bp):
GCTTAAGTCCTTCGGGACATCCATAAGACCTTCGGGCAGGATGTTTTCAACATTTCATATGCTCG
ATTCACAACACTTCGAATCA
Found at i:514733 original size:56 final size:56
Alignment explanation
Indices: 514590--514743 Score: 166
Period size: 58 Copynumber: 2.7 Consensus size: 56
514580 TTCAAATGAG
* * ** *** * *
514590 TTTTTAGAAACTAAACTTGATTTTCAGGGGTTTCTTGATGATTATCTCCAAAGATT
1 TTTTTAGAAACTAAGCCTGATTTTCAGGGGTTTCTTGATGAAAATCAAAAAAAATA
* * *
514646 TTTTTAAGGAAACTAAGCCTAATTTTTAGGGGTTCCTTGATGACAAAT-AAAAAAAATA
1 TTTTT-A-GAAACTAAGCCTGATTTTCAGGGGTTTCTTGATGA-AAATCAAAAAAAATA
514704 TTTTTAGAAACTAAGCCTGATTTTCAGGGGTTTCTTGATG
1 TTTTTAGAAACTAAGCCTGATTTTCAGGGGTTTCTTGATG
514744 TTTTTTGAAT
Statistics
Matches: 80, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
56 36 0.45
57 2 0.03
58 40 0.50
59 2 0.03
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.39
Consensus pattern (56 bp):
TTTTTAGAAACTAAGCCTGATTTTCAGGGGTTTCTTGATGAAAATCAAAAAAAATA
Found at i:515592 original size:17 final size:17
Alignment explanation
Indices: 515570--515614 Score: 72
Period size: 17 Copynumber: 2.6 Consensus size: 17
515560 TCCGGTAAGA
*
515570 GAGAAGAAGTTCATAAT
1 GAGAAGAACTTCATAAT
515587 GAGAAGAACTTCATAAT
1 GAGAAGAACTTCATAAT
*
515604 AAGAAGAACTT
1 GAGAAGAACTT
515615 GTTCAATCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.49, C:0.09, G:0.20, T:0.22
Consensus pattern (17 bp):
GAGAAGAACTTCATAAT
Found at i:515611 original size:20 final size:20
Alignment explanation
Indices: 515565--515611 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 20
515555 ACTCATCCGG
*
515565 TAAGAGAGAAGAAGTTCATAA
1 TAAGA-AGAAGAACTTCATAA
515586 T--G-AGAAGAACTTCATAA
1 TAAGAAGAAGAACTTCATAA
515603 TAAGAAGAA
1 TAAGAAGAA
515612 CTTGTTCAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 7
0.73 0.03 0.23
Matches are distributed among these distances:
17 15 0.68
19 2 0.09
20 4 0.18
21 1 0.05
ACGTcount: A:0.53, C:0.06, G:0.21, T:0.19
Consensus pattern (20 bp):
TAAGAAGAAGAACTTCATAA
Found at i:515837 original size:136 final size:136
Alignment explanation
Indices: 515650--516034 Score: 434
Period size: 136 Copynumber: 2.8 Consensus size: 136
515640 ATATGGAGTT
* * * * * * *
515650 GAATCAACAACACCTCACTCGATGG-ATCAACATTTCTAGTTGAGAGTTCATAATGAGAAGAACT
1 GAATCAGCAACACCTCGCTTGAGGGAAT-AACATTTCCAATGGAGAGTTCATAATGAGAAGAACT
* * ** *
515714 CATCCGACAAAGGGAGAATAAGTTCATAATGAGAAGACCTTGTTCGACCTATCACTTGATTCACT
65 CATCCGACAAAGGGAGAAAAAGTTCATAATGAGAAGAACTTGTTCGACCTATCACTCAATTCACA
* * *
515779 GCATTTT
130 ACACTTC
** * *
515786 GAATCAGTGACGCCTCGCTTGAGGGAATGACATTT-CAGATGGAGAGTTCATAATGAGAAGAACT
1 GAATCAGCAACACCTCGCTTGAGGGAATAACATTTCCA-ATGGAGAGTTCATAATGAGAAGAACT
* * * * * **
515850 CATCTGACAGAGGGAAAAAAAGTTCCTAATGAGAAGAGCTTGTTCGACCTATTGCTCAATTCACA
65 CATCCGACAAAGGGAGAAAAAGTTCATAATGAGAAGAACTTGTTCGACCTATCACTCAATTCACA
*
515915 ATACTTC
130 ACACTTC
* * *
515922 GAGTCAGCAACACCTTGCTTGAGGGATTAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTC
1 GAATCAGCAACACCTCGCTTGAGGGAATAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTC
* * *
515987 ATCCGATAAA-GGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCT
66 ATCCGACAAAGGGAGAAAAAGTTCATAATGAGAAGAACTTGTTCGACCT
516035 TAGCTTGTTT
Statistics
Matches: 205, Mismatches: 41, Indels: 7
0.81 0.16 0.03
Matches are distributed among these distances:
135 34 0.17
136 167 0.81
137 4 0.02
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.25
Consensus pattern (136 bp):
GAATCAGCAACACCTCGCTTGAGGGAATAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTC
ATCCGACAAAGGGAGAAAAAGTTCATAATGAGAAGAACTTGTTCGACCTATCACTCAATTCACAA
CACTTC
Found at i:516029 original size:20 final size:19
Alignment explanation
Indices: 515967--516030 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 19
515957 CCAATGGAGA
515967 GTTCATAATGAGAAGAACT
1 GTTCATAATGAGAAGAACT
* * *
515986 CATCCGATAAAGGAGAAGAA--
1 -GTTC-AT-AATGAGAAGAACT
516006 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAAC-T
516026 GTTCA
1 GTTCA
516031 ACCTTAGCTT
Statistics
Matches: 33, Mismatches: 6, Indels: 10
0.67 0.12 0.20
Matches are distributed among these distances:
17 10 0.30
18 2 0.06
19 2 0.06
20 7 0.21
21 2 0.06
22 10 0.30
ACGTcount: A:0.42, C:0.12, G:0.22, T:0.23
Consensus pattern (19 bp):
GTTCATAATGAGAAGAACT
Found at i:516225 original size:116 final size:114
Alignment explanation
Indices: 515952--516349 Score: 401
Period size: 116 Copynumber: 3.4 Consensus size: 114
515942 GAGGGATTAA
* *
515952 CATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATAAAGGAGAAGAAGTTCATAATGA
1 CATTTCCAATGAAGAGTTCATAATGAGAAGAACTCATCCGAT-AAGAAGAAGAAGTTCATAATGA
* * * * * * *
516017 GAAGAACTTGTTCAACCTTAGCTTGTTTCCATTATAGAAGAAGGTGGACCAA
65 GAAGAACTTGTTCAA-CTTTG-TTGATTCCATCACAGAAGAAGGTAGATCAG
* * * *
516069 CATTT-CAATGAAAGGGTTCATAATGAGAATAAC-CAATCCGATGAGCAAGAATAAGTTCATAAT
1 CATTTCCAATG-AAGAGTTCATAATGAGAAGAACTC-ATCCGATAAG-AAGAAGAAGTTCATAAT
516132 GAGAAGAACTTGTTCAACTTTGTTCGATAT-CATCACAGAAGAAGGTAGATCAG
63 GAGAAGAACTTGTTCAACTTTGTT-GAT-TCCATCACAGAAGAAGGTAGATCAG
* * *
516185 CATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATAAGGAAGAAGAAGTTCATAATAA
1 CATTTCCAATGAAGAGTTCATAATGAGAAGAACTCATCCGATAA-GAAGAAGAAGTTCATAATGA
* * * * * *
516250 GAAGAATTTGTTTAACCTTGGTGATTCCATCACAAAAGGAA-GTAGAT-TG
65 GAAGAACTTGTTCAACTTTGTTGATTCCATCACAGAA-GAAGGTAGATCAG
** ** ** *
516299 ACATCCCCAGCGAAGAGTTCATAATGAGAAGAACTTGTCCGATCAGAAGAA
1 -CATTTCCAATGAAGAGTTCATAATGAGAAGAACTCATCCGATAAGAAGAA
516350 ATTGGAGTTC
Statistics
Matches: 237, Mismatches: 33, Indels: 25
0.80 0.11 0.08
Matches are distributed among these distances:
114 8 0.03
115 57 0.24
116 102 0.43
117 70 0.30
ACGTcount: A:0.39, C:0.15, G:0.21, T:0.25
Consensus pattern (114 bp):
CATTTCCAATGAAGAGTTCATAATGAGAAGAACTCATCCGATAAGAAGAAGAAGTTCATAATGAG
AAGAACTTGTTCAACTTTGTTGATTCCATCACAGAAGAAGGTAGATCAG
Found at i:517523 original size:25 final size:25
Alignment explanation
Indices: 517495--517549 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
517485 ATGTTTTATG
**
517495 TATTACGCATTTATTTTATGTATAT
1 TATTACGCATTTATTTTACATATAT
* *
517520 TATTATGTATTTATTTTACATATAT
1 TATTACGCATTTATTTTACATATAT
517545 TATTA
1 TATTA
517550 TATATATTAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.31, C:0.05, G:0.05, T:0.58
Consensus pattern (25 bp):
TATTACGCATTTATTTTACATATAT
Found at i:517527 original size:12 final size:12
Alignment explanation
Indices: 517506--517580 Score: 50
Period size: 12 Copynumber: 6.2 Consensus size: 12
517496 ATTACGCATT
*
517506 TATT-TTATGTA
1 TATTATTATATA
*
517517 TATTATTATGTA
1 TATTATTATATA
*
517529 T-TTATTTTACATA
1 TATTA--TTATATA
517542 TATTATTATATA
1 TATTATTATATA
517554 TATTACTT-TATTA
1 TATTA-TTATA-TA
517567 TATATATT-TATA
1 TAT-TATTATATA
517579 TA
1 TA
517581 ATACTACATG
Statistics
Matches: 54, Mismatches: 3, Indels: 13
0.77 0.04 0.19
Matches are distributed among these distances:
11 7 0.13
12 25 0.46
13 17 0.31
14 5 0.09
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.60
Consensus pattern (12 bp):
TATTATTATATA
Found at i:517550 original size:25 final size:25
Alignment explanation
Indices: 517503--517550 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
517493 TGTATTACGC
**
517503 ATTTATTTTATGTATATTATTATGT
1 ATTTATTTTACATATATTATTATGT
517528 ATTTATTTTACATATATTATTAT
1 ATTTATTTTACATATATTATTAT
517551 ATATATTACT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.62
Consensus pattern (25 bp):
ATTTATTTTACATATATTATTATGT
Found at i:517568 original size:25 final size:25
Alignment explanation
Indices: 517509--517585 Score: 77
Period size: 25 Copynumber: 3.0 Consensus size: 25
517499 ACGCATTTAT
* *
517509 TTTATGTATATTATTATGTAT-TTAT
1 TTTAT-TATATTATTATATATATTAC
*
517534 TTTACATATATTATTATATATATTAC
1 TTTA-TTATATTATTATATATATTAC
*
517560 TTTATTATATATATT-TATATAATAC
1 TTTATTATAT-TATTATATATATTAC
517585 T
1 T
517586 ACATGTATTG
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
25 33 0.75
26 11 0.25
ACGTcount: A:0.35, C:0.04, G:0.03, T:0.58
Consensus pattern (25 bp):
TTTATTATATTATTATATATATTAC
Found at i:525186 original size:18 final size:17
Alignment explanation
Indices: 525147--525203 Score: 73
Period size: 16 Copynumber: 3.4 Consensus size: 17
525137 GCAAGAGCCC
525147 AGGGGTGACACTT-TTG
1 AGGGGTGACACTTGTTG
525163 AGGGGTGACACTTGGATT-
1 AGGGGTGACACTT-G-TTG
*
525181 AGGGGTGACACTTGTGG
1 AGGGGTGACACTTGTTG
525198 AGGGGT
1 AGGGGT
525204 TGCTTGGGAT
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
16 14 0.39
17 7 0.19
18 13 0.36
19 2 0.06
ACGTcount: A:0.19, C:0.11, G:0.44, T:0.26
Consensus pattern (17 bp):
AGGGGTGACACTTGTTG
Found at i:526177 original size:45 final size:45
Alignment explanation
Indices: 526127--526215 Score: 160
Period size: 45 Copynumber: 2.0 Consensus size: 45
526117 CGGTGCGTCC
*
526127 CTTGCCTGCTTCTTGGTATCTTTGATTGCACCTGCTCCCCATGCA
1 CTTGCCTGCTCCTTGGTATCTTTGATTGCACCTGCTCCCCATGCA
*
526172 CTTGCCTGCTCCTTGGTATCTTTGATTGCACTTGCTCCCCATGC
1 CTTGCCTGCTCCTTGGTATCTTTGATTGCACCTGCTCCCCATGC
526216 TATTTTCAGT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.10, C:0.34, G:0.18, T:0.38
Consensus pattern (45 bp):
CTTGCCTGCTCCTTGGTATCTTTGATTGCACCTGCTCCCCATGCA
Found at i:532637 original size:55 final size:57
Alignment explanation
Indices: 532571--532697 Score: 204
Period size: 55 Copynumber: 2.3 Consensus size: 57
532561 AAAAGTTCAA
* *
532571 GGGTTTCTTGATGATTATTTCCAATGAA-TTTTAAAGAAACTAAGCCTGA-TTTTAG
1 GGGTTTCTTGATGATTATTTCCAAAGAATTTTTAAAGAAACTAAGCCTAATTTTTAG
* *
532626 GGGTTTCTTGATGATTATTTCTAAAGAATTTTTAAAGAAGCTAAGCCTAATTTTTAG
1 GGGTTTCTTGATGATTATTTCCAAAGAATTTTTAAAGAAACTAAGCCTAATTTTTAG
532683 GGGTTTCTTGATGAT
1 GGGTTTCTTGATGAT
532698 AACTATAACC
Statistics
Matches: 66, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
55 26 0.39
56 19 0.29
57 21 0.32
ACGTcount: A:0.29, C:0.09, G:0.20, T:0.42
Consensus pattern (57 bp):
GGGTTTCTTGATGATTATTTCCAAAGAATTTTTAAAGAAACTAAGCCTAATTTTTAG
Found at i:532745 original size:58 final size:56
Alignment explanation
Indices: 532566--532752 Score: 161
Period size: 58 Copynumber: 3.3 Consensus size: 56
532556 AAATGAAAAG
**
532566 TTCAAGGGTTTCTTGATGAT-TATTTCC-AATGAATTTTAAAGAAACTAAGCCTGATT
1 TTCAAGGGTTTCTTGATGATATATAACCAAATG--TTTTAAAGAAACTAAGCCTGATT
* * * *
532622 TT-AGGGGTTTCTTGATGATTATTTCTAA--AGAAT-TTTTAAAGAAGCTAAGCCTAATT
1 TTCAAGGGTTTCTTGATGA-TA--TATAACCA-AATGTTTTAAAGAAACTAAGCCTGATT
* * * *
532678 TTTAGGGGTTTCTTGATGATAACTATAACCAAATGTTTTTAAGAAACTAAGCTTGATT
1 TTCAAGGGTTTCTTGATGAT-A-TATAACCAAATGTTTTAAAGAAACTAAGCCTGATT
*
532736 TTCAAGGGTTTATTGAT
1 TTCAAGGGTTTCTTGAT
532753 TAGTAAGTCC
Statistics
Matches: 105, Mismatches: 15, Indels: 20
0.75 0.11 0.14
Matches are distributed among these distances:
55 15 0.14
56 31 0.30
57 20 0.19
58 34 0.32
59 5 0.05
ACGTcount: A:0.32, C:0.10, G:0.18, T:0.41
Consensus pattern (56 bp):
TTCAAGGGTTTCTTGATGATATATAACCAAATGTTTTAAAGAAACTAAGCCTGATT
Found at i:534959 original size:6 final size:6
Alignment explanation
Indices: 534943--534975 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
534933 AACTATTGGT
*
534943 CGACAA AGACAA CGACAA CGACAA CGACAA CGA
1 CGACAA CGACAA CGACAA CGACAA CGACAA CGA
534976 TGGAGATACG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.52, C:0.30, G:0.18, T:0.00
Consensus pattern (6 bp):
CGACAA
Found at i:536266 original size:16 final size:17
Alignment explanation
Indices: 536238--536270 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
536228 AAAAATTGGG
536238 CCCTTTAACAAAATAAA
1 CCCTTTAACAAAATAAA
536255 CCCTTT-ACAAAATAAA
1 CCCTTTAACAAAATAAA
536271 GCCAAACCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (17 bp):
CCCTTTAACAAAATAAA
Found at i:538916 original size:23 final size:23
Alignment explanation
Indices: 538862--538917 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
538852 AAAAAATTGT
538862 AAAC-TACCA-AAAGACAGAGGA
1 AAACGTACCATAAAGACAGAGGA
*
538883 AAATGTACCATAAAGACAGA-GA
1 AAACGTACCATAAAGACAGAGGA
*
538905 TAAACGTGCCATA
1 -AAACGTACCATA
538918 GGAAATTGAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 3 0.10
22 7 0.24
23 19 0.66
ACGTcount: A:0.52, C:0.18, G:0.18, T:0.12
Consensus pattern (23 bp):
AAACGTACCATAAAGACAGAGGA
Found at i:539211 original size:22 final size:22
Alignment explanation
Indices: 539184--539229 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
539174 ATTATTCTAA
* *
539184 TTTTTAAAATTAGTAATATCAT
1 TTTTTAAAATAAATAATATCAT
* *
539206 TTTTTATAATAAATAATATTAT
1 TTTTTAAAATAAATAATATCAT
539228 TT
1 TT
539230 ATTGTATTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.54
Consensus pattern (22 bp):
TTTTTAAAATAAATAATATCAT
Found at i:539457 original size:31 final size:31
Alignment explanation
Indices: 539422--539490 Score: 95
Period size: 31 Copynumber: 2.2 Consensus size: 31
539412 ATCCAAAATA
*
539422 ATAATATTTATTATTTTAGTAATATAATAG-T
1 ATAATATTTATTATTTTAATAA-ATAATAGAT
*
539453 ATAATATTTTTTATTTTAATAAATAATAGAT
1 ATAATATTTATTATTTTAATAAATAATAGAT
*
539484 ATGATAT
1 ATAATAT
539491 ATACTGTTTC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
30 7 0.21
31 27 0.79
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (31 bp):
ATAATATTTATTATTTTAATAAATAATAGAT
Found at i:539566 original size:19 final size:18
Alignment explanation
Indices: 539539--539577 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
539529 TATTTTAAAC
* *
539539 ATAATAATATTATTTTTT
1 ATAATAATAATATTATTT
539557 ATAATAAATAATATTATTT
1 ATAAT-AATAATATTATTT
539576 AT
1 AT
539578 TGTATTCGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
ATAATAATAATATTATTT
Found at i:540942 original size:2 final size:2
Alignment explanation
Indices: 540935--540965 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
540925 CTCAAATCTA
540935 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
540966 GGGTTAATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:541229 original size:15 final size:14
Alignment explanation
Indices: 541209--541243 Score: 61
Period size: 15 Copynumber: 2.4 Consensus size: 14
541199 TTTTAAATTA
541209 TAAAATTATCAATG
1 TAAAATTATCAATG
541223 TATAAATTATCAATG
1 TA-AAATTATCAATG
541238 TAAAAT
1 TAAAAT
541244 AAAAAAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 6 0.30
15 14 0.70
ACGTcount: A:0.51, C:0.06, G:0.06, T:0.37
Consensus pattern (14 bp):
TAAAATTATCAATG
Found at i:541904 original size:14 final size:14
Alignment explanation
Indices: 541885--541911 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
541875 GGTTTTAAAT
541885 AAATTATTATTATA
1 AAATTATTATTATA
541899 AAATTATTATTAT
1 AAATTATTATTAT
541912 CATGATATTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
AAATTATTATTATA
Found at i:542133 original size:13 final size:13
Alignment explanation
Indices: 542115--542139 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
542105 TCATTTAAAT
542115 AATAAACGAACAC
1 AATAAACGAACAC
542128 AATAAACGAACA
1 AATAAACGAACA
542140 ACACAAAAAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.20, G:0.08, T:0.08
Consensus pattern (13 bp):
AATAAACGAACAC
Found at i:542418 original size:14 final size:14
Alignment explanation
Indices: 542399--542467 Score: 76
Period size: 14 Copynumber: 5.2 Consensus size: 14
542389 GCCATCTGTT
542399 CGAACATAAATGAA
1 CGAACATAAATGAA
542413 CGAACATAAAT---
1 CGAACATAAATGAA
542424 -GAACATAAATGAA
1 CGAACATAAATGAA
*
542437 CGAACATAAACGAA
1 CGAACATAAATGAA
*
542451 CGTAA-ATGAATGAA
1 CG-AACATAAATGAA
542465 CGA
1 CGA
542468 GCCCTTTGTT
Statistics
Matches: 47, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
10 10 0.21
13 1 0.02
14 34 0.72
15 2 0.04
ACGTcount: A:0.55, C:0.14, G:0.16, T:0.14
Consensus pattern (14 bp):
CGAACATAAATGAA
Found at i:542429 original size:24 final size:24
Alignment explanation
Indices: 542399--542465 Score: 107
Period size: 24 Copynumber: 2.8 Consensus size: 24
542389 GCCATCTGTT
542399 CGAACATAAATGAACGAACATAAA
1 CGAACATAAATGAACGAACATAAA
*
542423 TGAACATAAATGAACGAACATAAA
1 CGAACATAAATGAACGAACATAAA
* *
542447 CGAACGTAAATGAATGAAC
1 CGAACATAAATGAACGAAC
542466 GAGCCCTTTG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.55, C:0.15, G:0.15, T:0.15
Consensus pattern (24 bp):
CGAACATAAATGAACGAACATAAA
Found at i:544566 original size:14 final size:14
Alignment explanation
Indices: 544549--544589 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
544539 GTTTGGTTAT
544549 GTTCGTTTATGTTC
1 GTTCGTTTATGTTC
*
544563 GTTCGGTTATGTTC
1 GTTCGTTTATGTTC
*
544577 GTTCATTTATGTT
1 GTTCGTTTATGTT
544590 TAACCCAGTC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.10, C:0.12, G:0.22, T:0.56
Consensus pattern (14 bp):
GTTCGTTTATGTTC
Found at i:545684 original size:16 final size:16
Alignment explanation
Indices: 545663--545703 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
545653 GTCTCCAACG
545663 TTTATGTTCGTGTTCA
1 TTTATGTTCGTGTTCA
*
545679 TTTATGTTCGTGTTCG
1 TTTATGTTCGTGTTCA
545695 TTTATGTTC
1 TTTATGTTC
545704 ATTTATTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.10, C:0.12, G:0.20, T:0.59
Consensus pattern (16 bp):
TTTATGTTCGTGTTCA
Found at i:548947 original size:3 final size:3
Alignment explanation
Indices: 548933--549087 Score: 172
Period size: 3 Copynumber: 51.7 Consensus size: 3
548923 ACTTGCTAAC
* ** * *
548933 TCT TCAT TCT TCT TCT TCT TC- TCC TCAT TCT AAT TCT TCT CCT CCT
1 TCT TC-T TCT TCT TCT TCT TCT TCT TC-T TCT TCT TCT TCT TCT TCT
* * * *
548979 CCT CCT CCT CCT TC- TCTT TCT TCT TCT TC- TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TC-T TCT TCT TCT TCT TCT TCT TCT TCT TCT
*
549023 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TGT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
549071 TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TC
549088 CTATTCAACT
Statistics
Matches: 137, Mismatches: 9, Indels: 12
0.87 0.06 0.08
Matches are distributed among these distances:
2 6 0.04
3 124 0.91
4 7 0.05
ACGTcount: A:0.03, C:0.37, G:0.01, T:0.60
Consensus pattern (3 bp):
TCT
Found at i:551711 original size:19 final size:17
Alignment explanation
Indices: 551669--551714 Score: 69
Period size: 16 Copynumber: 2.8 Consensus size: 17
551659 TCTCTTCAAC
*
551669 TTCTCCTACTCTTCATT
1 TTCTCCTCCTCTTCATT
551686 TTC-CCTCCTCTTCATT
1 TTCTCCTCCTCTTCATT
551702 TTC-CCTCCTCTTC
1 TTCTCCTCCTCTTC
551715 TTCCTCTCCA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
16 25 0.89
17 3 0.11
ACGTcount: A:0.07, C:0.43, G:0.00, T:0.50
Consensus pattern (17 bp):
TTCTCCTCCTCTTCATT
Found at i:551717 original size:19 final size:16
Alignment explanation
Indices: 551677--551714 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
551667 ACTTCTCCTA
551677 CTCTTCATTTTCCCTC
1 CTCTTCATTTTCCCTC
551693 CTCTTCATTTTCCCTC
1 CTCTTCATTTTCCCTC
551709 CTCTTC
1 CTCTTC
551715 TTCCTCTCCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.05, C:0.45, G:0.00, T:0.50
Consensus pattern (16 bp):
CTCTTCATTTTCCCTC
Found at i:552301 original size:91 final size:91
Alignment explanation
Indices: 552193--552393 Score: 285
Period size: 91 Copynumber: 2.2 Consensus size: 91
552183 TTATGGTTCA
* * * * * *
552193 AGTATCGATACTAGATGAACAATATTGATACTGGATTAATTGAGATGAAATTTAGGGTTTTCTAG
1 AGTATCGATAATGGATGAACAATATTGATACTGGATGAATTGAGATAAAATTTAGAGTTTTCCAG
* *
552258 CAGGGAGTATCGATATTAAGGGGAGG
66 CAGGGAGTATCAATAATAAGGGGAGG
* *
552284 AGTATCGATATTGGATGAACAATATTGATACTGGATGAATTGGGATAAAATTTAGAGTTTTCCAG
1 AGTATCGATAATGGATGAACAATATTGATACTGGATGAATTGAGATAAAATTTAGAGTTTTCCAG
* *
552349 TAGGGAGTATCAATAATGAGGGGAGG
66 CAGGGAGTATCAATAATAAGGGGAGG
*
552375 AGTATCAATAATGGATGAA
1 AGTATCGATAATGGATGAA
552394 TTGGGATGAA
Statistics
Matches: 97, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
91 97 1.00
ACGTcount: A:0.36, C:0.07, G:0.27, T:0.30
Consensus pattern (91 bp):
AGTATCGATAATGGATGAACAATATTGATACTGGATGAATTGAGATAAAATTTAGAGTTTTCCAG
CAGGGAGTATCAATAATAAGGGGAGG
Found at i:552396 original size:71 final size:71
Alignment explanation
Indices: 552315--552451 Score: 202
Period size: 71 Copynumber: 1.9 Consensus size: 71
552305 ATATTGATAC
* * *
552315 TGGATGAATTGGGATAAAATTTAGAGTTTTCCAGTAGGGAGTATCAATAATGAGGGGAGGAGTAT
1 TGGATGAATTGGGATAAAATTTAGAGTTTTCCAATAGGAAGTATCAATAATGAGAGGAGGAGTAT
552380 CAATAA
66 CAATAA
* * * * *
552386 TGGATGAATTGGGATGAAATTTAGGGTTTTTCAATAGGAAGTATCGATATTGAGAGGAGGAGTAT
1 TGGATGAATTGGGATAAAATTTAGAGTTTTCCAATAGGAAGTATCAATAATGAGAGGAGGAGTAT
552451 C
66 C
552452 GATACTGAAA
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
71 58 1.00
ACGTcount: A:0.34, C:0.05, G:0.31, T:0.30
Consensus pattern (71 bp):
TGGATGAATTGGGATAAAATTTAGAGTTTTCCAATAGGAAGTATCAATAATGAGAGGAGGAGTAT
CAATAA
Found at i:552546 original size:21 final size:21
Alignment explanation
Indices: 552522--552608 Score: 75
Period size: 21 Copynumber: 4.1 Consensus size: 21
552512 CGATACCCTC
*
552522 GGTCTCTATACCAAATAAATT
1 GGTCTCTATACCGAATAAATT
* * *
552543 GGTCTCAATATCGAATAAATA
1 GGTCTCTATACCGAATAAATT
* *
552564 GATCTTTATACCGAATAAATT
1 GGTCTCTATACCGAATAAATT
* * ** *
552585 AGCCTCTATATTGAATAAACT
1 GGTCTCTATACCGAATAAATT
552606 GGT
1 GGT
552609 GATTATGTGA
Statistics
Matches: 48, Mismatches: 18, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
21 48 1.00
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.33
Consensus pattern (21 bp):
GGTCTCTATACCGAATAAATT
Found at i:557487 original size:21 final size:21
Alignment explanation
Indices: 557434--557508 Score: 75
Period size: 20 Copynumber: 3.7 Consensus size: 21
557424 TTTTTGGCTC
*
557434 AAAGGATCGATCCCCTAG-CA
1 AAAGGATCGATCCCCTTGACA
** * *
557454 AAAGGATTAATCCCTTTGACC
1 AAAGGATCGATCCCCTTGACA
557475 AAAGGATCGATCCCCTT-A-A
1 AAAGGATCGATCCCCTTGACA
557494 AAATGGATCGATCCC
1 AAA-GGATCGATCCC
557509 TTAGATTCCA
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
19 3 0.07
20 26 0.59
21 15 0.34
ACGTcount: A:0.35, C:0.27, G:0.17, T:0.21
Consensus pattern (21 bp):
AAAGGATCGATCCCCTTGACA
Found at i:557508 original size:41 final size:40
Alignment explanation
Indices: 557433--557510 Score: 104
Period size: 41 Copynumber: 1.9 Consensus size: 40
557423 ATTTTTGGCT
*
557433 CAAAGGATCGATCCCCTAGCAAAAGGATTAATCCCTTTGAC
1 CAAAGGATCGATCCCCTA-CAAAAGGATCAATCCCTTTGAC
*
557474 CAAAGGATCGATCCCCTTA-AAAATGGATCGATCCCTT
1 CAAAGGATCGATCCCC-TACAAAA-GGATCAATCCCTT
557511 AGATTCCAGT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
40 4 0.12
41 27 0.82
42 2 0.06
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (40 bp):
CAAAGGATCGATCCCCTACAAAAGGATCAATCCCTTTGAC
Found at i:558608 original size:21 final size:21
Alignment explanation
Indices: 558555--558621 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
558545 AGTGAGTTTT
**
558555 GGATCGATCCCTTTACAAAAA
1 GGATCGATCCCTCAACAAAAA
* * * *
558576 AGATCTAACCCTCAAGAAAAA
1 GGATCGATCCCTCAACAAAAA
*
558597 GGATCGATCCCTTC-ACTAAAA
1 GGATCGATCCC-TCAACAAAAA
558618 GGAT
1 GGAT
558622 TGATTCCTTC
Statistics
Matches: 34, Mismatches: 11, Indels: 2
0.72 0.23 0.04
Matches are distributed among these distances:
21 32 0.94
22 2 0.06
ACGTcount: A:0.40, C:0.24, G:0.15, T:0.21
Consensus pattern (21 bp):
GGATCGATCCCTCAACAAAAA
Found at i:558630 original size:21 final size:20
Alignment explanation
Indices: 558593--558651 Score: 82
Period size: 21 Copynumber: 2.9 Consensus size: 20
558583 ACCCTCAAGA
558593 AAAAGGATCGATCCCTTCACT
1 AAAAGGATCGATCCCTTC-CT
* *
558614 AAAAGGATTGATTCCTTCCT
1 AAAAGGATCGATCCCTTCCT
558634 ATAAAGGATCGATCCCTT
1 A-AAAGGATCGATCCCTT
558652 TGTTACAACG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
20 3 0.09
21 30 0.91
ACGTcount: A:0.32, C:0.24, G:0.15, T:0.29
Consensus pattern (20 bp):
AAAAGGATCGATCCCTTCCT
Found at i:559302 original size:21 final size:20
Alignment explanation
Indices: 559278--559336 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 20
559268 ACCCTCAAGA
559278 AAAAGGATCG-TTCTCTTCACT
1 AAAAGGATCGATTC-CTTC-CT
*
559299 AAAAGGATTGATTCCTTCCT
1 AAAAGGATCGATTCCTTCCT
*
559319 ATAAAGGATCGATCCCTT
1 A-AAAGGATCGATTCCTT
559337 TGTTACAACG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 3 0.09
21 27 0.82
22 3 0.09
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.32
Consensus pattern (20 bp):
AAAAGGATCGATTCCTTCCT
Found at i:559898 original size:685 final size:685
Alignment explanation
Indices: 558549--559927 Score: 2609
Period size: 685 Copynumber: 2.0 Consensus size: 685
558539 GATTTAAGTG
*
558549 AGTTTTGGATCGATCCCTTTACAAAAAAGATCTAACCCTCAAGAAAAAGGATCGATCCCTTCACT
1 AGTTTTGGATCGATCCCTTTACAAAAAAGATCGAACCCTCAAGAAAAAGGATCGATCCCTTCACT
*
558614 AAAAGGATTGATTCCTTCCTATAAAGGATCGATCCCTTTGTTACAACGGTCAAATTTTTTTTAAA
66 AAAAGGATTGATTCCTTCCTATAAAGGATCGATCCCTTTGTTACAACGGTCAAATTTTTTTGAAA
558679 AATGATCGATCCCTTGTGCATTAAATGTTGTTTTTGGTTGTAGGTAACGGCTATAATGATACCCA
131 AATGATCGATCCCTTGTGCATTAAATGTTGTTTTTGGTTGTAGGTAACGGCTATAATGATACCCA
558744 AAGGCTCTAAACAGATAGAATTAATGGATAAGGTATAAATTGAAGGTTAAATCTTCCAAAAGTCA
196 AAGGCTCTAAACAGATAGAATTAATGGATAAGGTATAAATTGAAGGTTAAATCTTCCAAAAGTCA
*
558809 ACAAGAGTCATATTGAACCAACCTACCAACATAAAATATTTTTGTGTGCTTAATTTGTTAAATTA
261 ACAAGAGTCATATTGAACCAACCTACCAACATAAAATATTTTTGTGTGCTTAATTTGTCAAATTA
558874 TTTGTTGTAAACACACTTGTGAGCTTCATTGTTTATTTTGCTCAAGTGTGGTTTGGGTGAGAGCT
326 TTTGTTGTAAACACACTTGTGAGCTTCATTGTTTATTTTGCTCAAGTGTGGTTTGGGTGAGAGCT
*
558939 TAATTAGTGTAAACCCATTTTCCTTGTGAGGTTTTATCTTTTTTTGCTTTATTTGTAATTCCTCT
391 TAATTAGTGTAAACCCATTTTCCTTGTGAGGTTTTATCTTTTTTTGCTTTATTTGTAATTCCTCC
559004 TATGGAAAGAGTGTAAACAAGGATTTGGGGTATAAACCTTATGGGTTTACAAGGTCACACCTTGT
456 TATGGAAAGAGTGTAAACAAGGATTTGGGGTATAAACCTTATGGGTTTACAAGGTCACACCTTGT
559069 CCTCAAAGGTGAGCAAATCTAGTGGATTTGAGAAAATCCTTAGTGTGGATGATAAGGTAGTGGAT
521 CCTCAAAGGTGAGCAAATCTAGTGGATTTGAGAAAATCCTTAGTGTGGATGATAAGGTAGTGGAT
559134 GCAGACTTTGTTTGATAAAGTCAAATCACTCTAAATCTTTGAGCAAAAATTTTAATTTTTTGATT
586 GCAGACTTTGTTTGATAAAGTCAAATCACTCTAAATCTTTGAGCAAAAATTTTAATTTTTTGATT
559199 TAATCCACCAAATTTATTAGAAAGCCAATTCACTC
651 TAATCCACCAAATTTATTAGAAAGCCAATTCACTC
* * *
559234 AGTTTTGGATTGATCCCTTTACAAAAAAGATCGAACCCTCAAGAAAAAGGATCGTTCTCTTCACT
1 AGTTTTGGATCGATCCCTTTACAAAAAAGATCGAACCCTCAAGAAAAAGGATCGATCCCTTCACT
559299 AAAAGGATTGATTCCTTCCTATAAAGGATCGATCCCTTTGTTACAACGGTCAAA-TTTTTTGAAA
66 AAAAGGATTGATTCCTTCCTATAAAGGATCGATCCCTTTGTTACAACGGTCAAATTTTTTTGAAA
* *
559363 AATGATCGATCCCTTGTTCATTAAATGTTGTTTTTGGTTGTAGGTAACGGCTATAATGATCCCCA
131 AATGATCGATCCCTTGTGCATTAAATGTTGTTTTTGGTTGTAGGTAACGGCTATAATGATACCCA
559428 AAGGCTCTAAACAGATAGAATTAATGGATAAGGTATAAATTGAAGGTTAAATCTTCCAAAAGTCA
196 AAGGCTCTAAACAGATAGAATTAATGGATAAGGTATAAATTGAAGGTTAAATCTTCCAAAAGTCA
* *
559493 ACAAGAGTCATATTGAACCAACCTACCAACATAAAATTTTTGTTTTGTGCTTAATTTGTCAAATT
261 ACAAGAGTCATATTGAACCAACCTACCAACATAAAATATTT-TTGTGTGCTTAATTTGTCAAATT
559558 ATTTGTTGTAAACACACTTGTGAGCTTCATTGTTTATTTTGCTCAAGTGTGGTTTGGGTGAGAGC
325 ATTTGTTGTAAACACACTTGTGAGCTTCATTGTTTATTTTGCTCAAGTGTGGTTTGGGTGAGAGC
559623 TTAATTAGTGTAAACCCATTTTCCTTGTGAGGTTTTATCTTTTTTTTGCTTTATTTGTAATTCCT
390 TTAATTAGTGTAAACCCATTTTCCTTGTGAGGTTTTATC-TTTTTTTGCTTTATTTGTAATTCCT
559688 CCTATGGAAAGAGTGTAAACAAGGATTTGGGGTATAAACCTTATGGGTTTACAAGGTCACACCTT
454 CCTATGGAAAGAGTGTAAACAAGGATTTGGGGTATAAACCTTATGGGTTTACAAGGTCACACCTT
559753 GTCCTCAAAGGTGAGCAAATCTAGTGGATTTGAGAAAATCCTTAGTGTGGATGATAAGGTAGTGG
519 GTCCTCAAAGGTGAGCAAATCTAGTGGATTTGAGAAAATCCTTAGTGTGGATGATAAGGTAGTGG
559818 ATGCAGACTTTGTTTGATAAAGTCAAATCACTCTAAATCTTTGAGCAAAAATTTTAATTTTTTGA
584 ATGCAGACTTTGTTTGATAAAGTCAAATCACTCTAAATCTTTGAGCAAAAATTTTAATTTTTTGA
559883 TTTAATCCA-CAAATTTATTAGAAAGCCAATTCACTC
649 TTTAATCCACCAAATTTATTAGAAAGCCAATTCACTC
*
559919 CGTTCTTGG
1 AGTT-TTGG
559928 TATATTTTGG
Statistics
Matches: 679, Mismatches: 12, Indels: 5
0.98 0.02 0.01
Matches are distributed among these distances:
684 177 0.26
685 270 0.40
686 232 0.34
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.36
Consensus pattern (685 bp):
AGTTTTGGATCGATCCCTTTACAAAAAAGATCGAACCCTCAAGAAAAAGGATCGATCCCTTCACT
AAAAGGATTGATTCCTTCCTATAAAGGATCGATCCCTTTGTTACAACGGTCAAATTTTTTTGAAA
AATGATCGATCCCTTGTGCATTAAATGTTGTTTTTGGTTGTAGGTAACGGCTATAATGATACCCA
AAGGCTCTAAACAGATAGAATTAATGGATAAGGTATAAATTGAAGGTTAAATCTTCCAAAAGTCA
ACAAGAGTCATATTGAACCAACCTACCAACATAAAATATTTTTGTGTGCTTAATTTGTCAAATTA
TTTGTTGTAAACACACTTGTGAGCTTCATTGTTTATTTTGCTCAAGTGTGGTTTGGGTGAGAGCT
TAATTAGTGTAAACCCATTTTCCTTGTGAGGTTTTATCTTTTTTTGCTTTATTTGTAATTCCTCC
TATGGAAAGAGTGTAAACAAGGATTTGGGGTATAAACCTTATGGGTTTACAAGGTCACACCTTGT
CCTCAAAGGTGAGCAAATCTAGTGGATTTGAGAAAATCCTTAGTGTGGATGATAAGGTAGTGGAT
GCAGACTTTGTTTGATAAAGTCAAATCACTCTAAATCTTTGAGCAAAAATTTTAATTTTTTGATT
TAATCCACCAAATTTATTAGAAAGCCAATTCACTC
Found at i:565739 original size:18 final size:19
Alignment explanation
Indices: 565713--565797 Score: 74
Period size: 18 Copynumber: 4.8 Consensus size: 19
565703 TTAATCTGTG
*
565713 TCTGCTAACTGTAAAAT-A
1 TCTGATAACTGTAAAATCA
565731 TCTGATAACTGT--AATCA
1 TCTGATAACTGTAAAATCA
* * *
565748 TTTGATATCTAT-AAAT-A
1 TCTGATAACTGTAAAATCA
*
565765 TCTTATAACTG-AAAATCA
1 TCTGATAACTGTAAAATCA
*
565783 TCCGATAACTGTAAA
1 TCTGATAACTGTAAA
565798 CATTTAGAAT
Statistics
Matches: 52, Mismatches: 10, Indels: 9
0.73 0.14 0.13
Matches are distributed among these distances:
16 3 0.06
17 22 0.42
18 24 0.46
19 3 0.06
ACGTcount: A:0.40, C:0.15, G:0.09, T:0.35
Consensus pattern (19 bp):
TCTGATAACTGTAAAATCA
Found at i:569025 original size:2 final size:2
Alignment explanation
Indices: 569020--569045 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
569010 AAAAATTAAA
569020 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
569046 TTAAAAGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:569609 original size:21 final size:19
Alignment explanation
Indices: 569563--569610 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 19
569553 GGGTAAAAAA
*
569563 TAATTTAATTAATTTATTC
1 TAATTTAATTAATTTATAC
569582 TAGAATTTAAGTATAATTTATAC
1 T--AATTTAA-T-TAATTTATAC
569605 TAATTT
1 TAATTT
569611 TTTCTATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
19 1 0.04
21 12 0.50
22 1 0.04
23 10 0.42
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.52
Consensus pattern (19 bp):
TAATTTAATTAATTTATAC
Found at i:573543 original size:10 final size:10
Alignment explanation
Indices: 573528--573587 Score: 59
Period size: 10 Copynumber: 5.7 Consensus size: 10
573518 GCTACACCCG
573528 CAATAGCTCC
1 CAATAGCTCC
*
573538 CAATAGCGGCC
1 CAATAGC-TCC
573549 GCAATAGCTCC
1 -CAATAGCTCC
*
573560 CAATAGCGGCC
1 CAATAGC-TCC
573571 GC-ATAGCTCC
1 -CAATAGCTCC
573581 CAATAGC
1 CAATAGC
573588 GGTCGTAATA
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
9 1 0.02
10 21 0.51
11 11 0.27
12 8 0.20
ACGTcount: A:0.28, C:0.37, G:0.20, T:0.15
Consensus pattern (10 bp):
CAATAGCTCC
Found at i:573553 original size:22 final size:22
Alignment explanation
Indices: 573525--573599 Score: 125
Period size: 22 Copynumber: 3.5 Consensus size: 22
573515 CCCGCTACAC
573525 CCGCAATAGCTCCCAATAGCGG
1 CCGCAATAGCTCCCAATAGCGG
573547 CCGCAATAGCTCCCAATAGCGG
1 CCGCAATAGCTCCCAATAGCGG
573569 CCGC-ATAGCTCCCAATAGCGG
1 CCGCAATAGCTCCCAATAGCGG
* *
573590 TCGTAATAGC
1 CCGCAATAGC
573600 GCCCGCGACG
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
21 19 0.38
22 31 0.62
ACGTcount: A:0.27, C:0.35, G:0.23, T:0.16
Consensus pattern (22 bp):
CCGCAATAGCTCCCAATAGCGG
Found at i:575611 original size:80 final size:80
Alignment explanation
Indices: 575478--575637 Score: 320
Period size: 80 Copynumber: 2.0 Consensus size: 80
575468 TAGGAACTAG
575478 GGTTACTAGGTAGAGTATTCTTTCTAAATTAGTACTTATGATCTAATGATAATAGTAGAATGCTT
1 GGTTACTAGGTAGAGTATTCTTTCTAAATTAGTACTTATGATCTAATGATAATAGTAGAATGCTT
575543 AAATGAGGTTTAGAA
66 AAATGAGGTTTAGAA
575558 GGTTACTAGGTAGAGTATTCTTTCTAAATTAGTACTTATGATCTAATGATAATAGTAGAATGCTT
1 GGTTACTAGGTAGAGTATTCTTTCTAAATTAGTACTTATGATCTAATGATAATAGTAGAATGCTT
575623 AAATGAGGTTTAGAA
66 AAATGAGGTTTAGAA
575638 TGTTCAAATT
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
80 80 1.00
ACGTcount: A:0.35, C:0.07, G:0.20, T:0.38
Consensus pattern (80 bp):
GGTTACTAGGTAGAGTATTCTTTCTAAATTAGTACTTATGATCTAATGATAATAGTAGAATGCTT
AAATGAGGTTTAGAA
Found at i:575646 original size:20 final size:21
Alignment explanation
Indices: 575613--575656 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
575603 ATGATAATAG
*
575613 TAGAATGCTTAAA-TGAGGTT
1 TAGAATGCTTAAATTGAGATT
575633 TAGAATG-TTCAAATTGAGATT
1 TAGAATGCTT-AAATTGAGATT
575654 TAG
1 TAG
575657 CCAAAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 2 0.10
20 10 0.48
21 9 0.43
ACGTcount: A:0.36, C:0.05, G:0.23, T:0.36
Consensus pattern (21 bp):
TAGAATGCTTAAATTGAGATT
Found at i:580271 original size:20 final size:20
Alignment explanation
Indices: 580242--580345 Score: 172
Period size: 20 Copynumber: 5.2 Consensus size: 20
580232 TCCAAATTCA
*
580242 CAACGTGAATCTGTAAATCG
1 CAACGCGAATCTGTAAATCG
580262 CAACGCGAATCTGTAAATCG
1 CAACGCGAATCTGTAAATCG
580282 CAACGCGAATCTGTAAATCG
1 CAACGCGAATCTGTAAATCG
*
580302 TAACGCGAATCTGTAAATCG
1 CAACGCGAATCTGTAAATCG
* *
580322 CAATGCGAATCTGTAATTCG
1 CAACGCGAATCTGTAAATCG
580342 CAAC
1 CAAC
580346 ACAGAAGTCA
Statistics
Matches: 78, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 78 1.00
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (20 bp):
CAACGCGAATCTGTAAATCG
Found at i:580359 original size:20 final size:20
Alignment explanation
Indices: 580336--580404 Score: 111
Period size: 20 Copynumber: 3.5 Consensus size: 20
580326 GCGAATCTGT
580336 AATTCGCAACACAGAAGTCA
1 AATTCGCAACACAGAAGTCA
* *
580356 AATTCGTAACACAAAAGTCA
1 AATTCGCAACACAGAAGTCA
580376 AATTCGCAACACAGAAGTCA
1 AATTCGCAACACAGAAGTCA
*
580396 ATTTCGCAA
1 AATTCGCAA
580405 AGCGCGTTTA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.45, C:0.23, G:0.13, T:0.19
Consensus pattern (20 bp):
AATTCGCAACACAGAAGTCA
Found at i:580363 original size:60 final size:58
Alignment explanation
Indices: 580234--580365 Score: 158
Period size: 60 Copynumber: 2.2 Consensus size: 58
580224 ATTCAGTTTC
** * *
580234 CAAATTCACAACGTGAATCTGTAAATCGCAACGCGAATCTGTAAATCGCAACGCGAAT
1 CAAATTCGTAACGCGAATCTGTAAATCGCAACGCGAATCTGTAAATCGCAACACGAAT
* *
580292 CTGTAAA-TCGTAACGCGAATCTGTAAATCGCAATGCGAATCTGTAATTCGCAACACAGAAGT
1 C---AAATTCGTAACGCGAATCTGTAAATCGCAACGCGAATCTGTAAATCGCAACAC-GAA-T
580354 CAAATTCGTAAC
1 CAAATTCGTAAC
580366 ACAAAAGTCA
Statistics
Matches: 62, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
58 1 0.02
59 3 0.05
60 50 0.81
61 6 0.10
62 2 0.03
ACGTcount: A:0.37, C:0.23, G:0.17, T:0.23
Consensus pattern (58 bp):
CAAATTCGTAACGCGAATCTGTAAATCGCAACGCGAATCTGTAAATCGCAACACGAAT
Found at i:580678 original size:16 final size:16
Alignment explanation
Indices: 580654--580687 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
580644 ATAGTTAATT
* *
580654 TTTTTAAATTTTTTTA
1 TTTTGAAATTTTTGTA
580670 TTTTGAAATTTTTGTA
1 TTTTGAAATTTTTGTA
580686 TT
1 TT
580688 ATTATTAGAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.71
Consensus pattern (16 bp):
TTTTGAAATTTTTGTA
Found at i:580789 original size:21 final size:21
Alignment explanation
Indices: 580765--580811 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
580755 TTCACTTAGA
*
580765 TTGCTTAGTAAATTCATTTGG
1 TTGCTTAGTAAATTCATTCGG
580786 TTGCTTAGTAAATTCATTCGG
1 TTGCTTAGTAAATTCATTCGG
580807 TTGCT
1 TTGCT
580812 GTCAATACTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.21, C:0.13, G:0.19, T:0.47
Consensus pattern (21 bp):
TTGCTTAGTAAATTCATTCGG
Found at i:582721 original size:21 final size:21
Alignment explanation
Indices: 582673--582722 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
582663 GTTAGGTGAG
* **
582673 TTACGTGATGAGGTCAATGTT
1 TTACGTGAGGAGGTCAATACT
* *
582694 TTGCGTGAGGAGGTCAGTACT
1 TTACGTGAGGAGGTCAATACT
582715 TTACGTGA
1 TTACGTGA
582723 CGATAATGGT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.22, C:0.12, G:0.32, T:0.34
Consensus pattern (21 bp):
TTACGTGAGGAGGTCAATACT
Found at i:582762 original size:21 final size:21
Alignment explanation
Indices: 582738--582788 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
582728 ATGGTGCATG
*
582738 ACGTGATGAGGT-GCGGTCTTT
1 ACGTGATGAGGTAGAGGT-TTT
*
582759 ACGTGGTGAGGTAGAGGTTTT
1 ACGTGATGAGGTAGAGGTTTT
*
582780 ACGCGATGA
1 ACGTGATGA
582789 CAATGGTGTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.20, C:0.12, G:0.39, T:0.29
Consensus pattern (21 bp):
ACGTGATGAGGTAGAGGTTTT
Found at i:582969 original size:12 final size:12
Alignment explanation
Indices: 582943--582984 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
582933 TTTTTCGACA
582943 TTATTTATTTG-T
1 TTATTTA-TTGAT
582955 TTATTTATTGAT
1 TTATTTATTGAT
* *
582967 TTATGTATTAAT
1 TTATTTATTGAT
582979 TTATTT
1 TTATTT
582985 TTAGCGGCCC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
11 3 0.12
12 23 0.88
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69
Consensus pattern (12 bp):
TTATTTATTGAT
Found at i:583177 original size:42 final size:42
Alignment explanation
Indices: 583125--583241 Score: 139
Period size: 42 Copynumber: 2.8 Consensus size: 42
583115 AATTCACCTG
* **
583125 TCATCGTTCAAGAGG-CATCTCCTATTGTTCAAGAGGCCCCTA
1 TCATCGTTCAAGAGGCCA-CTCCAACCGTTCAAGAGGCCCCTA
* * *
583167 TCATCCTTCAAGAGGCCACTCCAACCGTTCAAGAGGCCTCTG
1 TCATCGTTCAAGAGGCCACTCCAACCGTTCAAGAGGCCCCTA
*
583209 TCATCGTTCAAGAGGTCC-CTCCCACCGTTCAAG
1 TCATCGTTCAAGAGG-CCACTCCAACCGTTCAAG
583242 TGCCCGATTT
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
42 61 0.94
43 4 0.06
ACGTcount: A:0.23, C:0.33, G:0.19, T:0.25
Consensus pattern (42 bp):
TCATCGTTCAAGAGGCCACTCCAACCGTTCAAGAGGCCCCTA
Found at i:583237 original size:21 final size:21
Alignment explanation
Indices: 583129--583241 Score: 79
Period size: 21 Copynumber: 5.4 Consensus size: 21
583119 CACCTGTCAT
* *
583129 CGTTCAAGAGG-CATCTCCTAT
1 CGTTCAAGAGGCCA-CTCCCAC
* * **
583150 TGTTCAAGAGGCCCCTATCATC
1 CGTTCAAGAGGCCACTCCCA-C
*
583172 C-TTCAAGAGGCCACTCCAAC
1 CGTTCAAGAGGCCACTCCCAC
* ** *
583192 CGTTCAAGAGGCCTCTGTCAT
1 CGTTCAAGAGGCCACTCCCAC
583213 CGTTCAAGAGGTCC-CTCCCAC
1 CGTTCAAGAGG-CCACTCCCAC
583234 CGTTCAAG
1 CGTTCAAG
583242 TGCCCGATTT
Statistics
Matches: 69, Mismatches: 19, Indels: 8
0.72 0.20 0.08
Matches are distributed among these distances:
20 2 0.03
21 64 0.93
22 3 0.04
ACGTcount: A:0.23, C:0.34, G:0.19, T:0.24
Consensus pattern (21 bp):
CGTTCAAGAGGCCACTCCCAC
Found at i:584663 original size:64 final size:64
Alignment explanation
Indices: 584587--584754 Score: 237
Period size: 64 Copynumber: 2.6 Consensus size: 64
584577 GGGGTACACT
* *
584587 TTTTTTGCTTGTTTAATTGATTTGTAAATGTTGATTTGTTTAATTGATAAGGAAATTAGAATTA
1 TTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGATAAGGAAATAAGAATTA
* * ** * ***
584651 TTTTTTGGTTGTTTAATTGATTTGTAAAAGTTAATTTGTTTAATTGATGTGTAAATAATTCTTA
1 TTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGATAAGGAAATAAGAATTA
*
584715 TTTTTTGCTTATTTAATTGATTTGTAAAAGTTGATTTGTT
1 TTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTT
584755 GTTTTAAATT
Statistics
Matches: 91, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
64 91 1.00
ACGTcount: A:0.27, C:0.02, G:0.16, T:0.55
Consensus pattern (64 bp):
TTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGATAAGGAAATAAGAATTA
Found at i:584851 original size:14 final size:14
Alignment explanation
Indices: 584832--584858 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
584822 GAAAATCAAA
584832 TTTGCGTTGCGATT
1 TTTGCGTTGCGATT
584846 TTTGCGTTGCGAT
1 TTTGCGTTGCGAT
584859 GGTTGCGAAA
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:0.07, C:0.15, G:0.30, T:0.48
Consensus pattern (14 bp):
TTTGCGTTGCGATT
Found at i:584943 original size:29 final size:29
Alignment explanation
Indices: 584897--584970 Score: 121
Period size: 29 Copynumber: 2.6 Consensus size: 29
584887 TTTCTCGTTT
584897 CGAATTTGACTTTCGCAACAATCGCAACG
1 CGAATTTGACTTTCGCAACAATCGCAACG
*
584926 CGAATTTGACTTTTGCAACAATCGCAACG
1 CGAATTTGACTTTCGCAACAATCGCAACG
* *
584955 TGAATTTTACTTTCGC
1 CGAATTTGACTTTCGC
584971 GTTGCGAATT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.31
Consensus pattern (29 bp):
CGAATTTGACTTTCGCAACAATCGCAACG
Found at i:585204 original size:18 final size:18
Alignment explanation
Indices: 585181--585217 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
585171 AAGCCGGTTA
585181 TGATTGAGATTTTGATTT
1 TGATTGAGATTTTGATTT
*
585199 TGATTGCGATTTTGATTT
1 TGATTGAGATTTTGATTT
585217 T
1 T
585218 CTTTTGCTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.19, C:0.03, G:0.22, T:0.57
Consensus pattern (18 bp):
TGATTGAGATTTTGATTT
Found at i:587510 original size:24 final size:24
Alignment explanation
Indices: 587476--587529 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
587466 CTGAAACATC
*
587476 ATCAAAATCCGAGTATTTACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
587500 ATCAAAGTCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
587524 ATCAAA
1 ATCAAA
587530 TTTTGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.43, C:0.20, G:0.13, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:587676 original size:12 final size:12
Alignment explanation
Indices: 587655--587688 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
587645 TGTTGTGGGT
*
587655 TTTGAGATTGTG
1 TTTGATATTGTG
587667 TTTGATATTGTG
1 TTTGATATTGTG
*
587679 TTTGGTATTG
1 TTTGATATTG
587689 GAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:588218 original size:14 final size:15
Alignment explanation
Indices: 588182--588219 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
588172 GAAATCATTG
588182 AAAAATTATATAGAA
1 AAAAATTATATAGAA
*
588197 ATAAAATTATGTA-AA
1 A-AAAATTATATAGAA
588212 AAAAATTA
1 AAAAATTA
588220 GAGACGAGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (15 bp):
AAAAATTATATAGAA
Found at i:588373 original size:18 final size:18
Alignment explanation
Indices: 588350--588413 Score: 68
Period size: 18 Copynumber: 3.9 Consensus size: 18
588340 AAAACATTCG
588350 TGTTGCGAAACTAAAACC
1 TGTTGCGAAACTAAAACC
*
588368 TGTTGCGAAATTAAAA--
1 TGTTGCGAAACTAAAACC
588384 ----GCGAAACTAAAACC
1 TGTTGCGAAACTAAAACC
*
588398 TGTTGCGAAATTAAAA
1 TGTTGCGAAACTAAAA
588414 TTCGTGTTGC
Statistics
Matches: 37, Mismatches: 3, Indels: 12
0.71 0.06 0.23
Matches are distributed among these distances:
12 11 0.30
18 26 0.70
ACGTcount: A:0.44, C:0.16, G:0.17, T:0.23
Consensus pattern (18 bp):
TGTTGCGAAACTAAAACC
Found at i:588390 original size:30 final size:30
Alignment explanation
Indices: 588354--588413 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
588344 CATTCGTGTT
588354 GCGAAACTAAAACCTGTTGCGAAATTAAAA
1 GCGAAACTAAAACCTGTTGCGAAATTAAAA
588384 GCGAAACTAAAACCTGTTGCGAAATTAAAA
1 GCGAAACTAAAACCTGTTGCGAAATTAAAA
588414 TTCGTGTTGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.47, C:0.17, G:0.17, T:0.20
Consensus pattern (30 bp):
GCGAAACTAAAACCTGTTGCGAAATTAAAA
Found at i:588423 original size:20 final size:20
Alignment explanation
Indices: 588398--588507 Score: 100
Period size: 20 Copynumber: 5.5 Consensus size: 20
588388 AACTAAAACC
588398 TGTTGCGAAATTAAAATTCG
1 TGTTGCGAAATTAAAATTCG
588418 TGTTGCG-AATTCGAAAA-TCG
1 TGTTGCGAAATT--AAAATTCG
* **
588438 AGTTGCGAAAAAAAAATTCG
1 TGTTGCGAAATTAAAATTCG
* *
588458 CGTTGCGAATTTAGAAA-TCG
1 TGTTGCGAAATTA-AAATTCG
* *
588478 AGTTGCGAATTTAAAATTCAG
1 TGTTGCGAAATTAAAATTC-G
588499 TGTTGCGAA
1 TGTTGCGAA
588508 TTTGGAAAAT
Statistics
Matches: 74, Mismatches: 9, Indels: 13
0.77 0.09 0.14
Matches are distributed among these distances:
19 11 0.15
20 45 0.61
21 18 0.24
ACGTcount: A:0.35, C:0.12, G:0.23, T:0.30
Consensus pattern (20 bp):
TGTTGCGAAATTAAAATTCG
Found at i:588443 original size:40 final size:39
Alignment explanation
Indices: 588399--588519 Score: 152
Period size: 40 Copynumber: 3.0 Consensus size: 39
588389 ACTAAAACCT
588399 GTTGCGAAATTAAAATTCGTGTTGCGAATTCGAAAATCGA
1 GTTGCGAAATTAAAATTCGTGTTGCGAATT-GAAAATCGA
** * *
588439 GTTGCGAAAAAAAAATTCGCGTTGCGAATTTAGAAATCGA
1 GTTGCGAAATTAAAATTCGTGTTGCGAATTGA-AAATCGA
*
588479 GTTGCGAATTTAAAATTCAGTGTTGCGAATTTGGAAAATCG
1 GTTGCGAAATTAAAATTC-GTGTTGCGAA-TT-GAAAATCG
588520 CAACGCGAAT
Statistics
Matches: 68, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
39 1 0.01
40 49 0.72
41 9 0.13
42 8 0.12
43 1 0.01
ACGTcount: A:0.36, C:0.12, G:0.23, T:0.30
Consensus pattern (39 bp):
GTTGCGAAATTAAAATTCGTGTTGCGAATTGAAAATCGA
Found at i:602579 original size:14 final size:14
Alignment explanation
Indices: 602560--602587 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
602550 GGACATCCCA
602560 CCTGTATTTAGTAC
1 CCTGTATTTAGTAC
602574 CCTGTATTTAGTAC
1 CCTGTATTTAGTAC
602588 AAGTTCTTGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.21, G:0.14, T:0.43
Consensus pattern (14 bp):
CCTGTATTTAGTAC
Done.