Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold261
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: 750797
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 32985 characters in sequence are not A, C, G, or T
File 1 of 3
Found at i:4235 original size:16 final size:17
Alignment explanation
Indices: 4206--4237 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
4196 TGAATTGATG
4206 ATATGAAGTTATGTGAA
1 ATATGAAGTTATGTGAA
4223 ATATGAA-TTATGTGA
1 ATATGAAGTTATGTGA
4238 TTGCATATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.41, C:0.00, G:0.22, T:0.38
Consensus pattern (17 bp):
ATATGAAGTTATGTGAA
Found at i:5826 original size:14 final size:16
Alignment explanation
Indices: 5795--5826 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
5785 TTATATACGC
5795 ATGCAGAAGTTATGAA
1 ATGCAGAAGTTATGAA
5811 ATGCA-AAGTT-TGAA
1 ATGCAGAAGTTATGAA
5825 AT
1 AT
5827 TTAAATAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.38
15 5 0.31
16 5 0.31
ACGTcount: A:0.44, C:0.06, G:0.22, T:0.28
Consensus pattern (16 bp):
ATGCAGAAGTTATGAA
Found at i:10019 original size:25 final size:23
Alignment explanation
Indices: 9983--10067 Score: 89
Period size: 25 Copynumber: 3.4 Consensus size: 23
9973 CACCGGCTCA
*
9983 AAGCCTGATAGATGACACTGGCAC
1 AAGCCTAATAGAT-ACACTGGCAC
10007 AAGGCCTAATAGATAACACTGGCAC
1 AA-GCCTAATAGAT-ACACTGGCAC
* *
10032 AAGCCTGATAGATAAACATCGGCAC
1 AAGCCTAATAGATACAC-T-GGCAC
10057 AAAGCCTAATA
1 -AAGCCTAATA
10068 TTTAGTTACA
Statistics
Matches: 52, Mismatches: 5, Indels: 6
0.83 0.08 0.10
Matches are distributed among these distances:
23 3 0.06
24 13 0.25
25 27 0.52
26 9 0.17
ACGTcount: A:0.40, C:0.24, G:0.20, T:0.16
Consensus pattern (23 bp):
AAGCCTAATAGATACACTGGCAC
Found at i:12003 original size:68 final size:68
Alignment explanation
Indices: 11894--12054 Score: 232
Period size: 68 Copynumber: 2.4 Consensus size: 68
11884 CAGTTAAATG
* * * * *
11894 TGGGTTTAATATGTGTAAGACCATAGCTAGTCTATGGCAACATATGGAGTTCGCCAGGACAGTGA
1 TGGGTTTAATATGTGTAAGACCATAGCTAGACTACGGCAACATATAGAGTCCGCCAGGACAGTAA
11959 ACA
66 ACA
* **
11962 TGGGTTTAATATGTGTAAGTCCATAGCTAGACTACGGCAACATATAGAGTCCGTTAGGACAGTAA
1 TGGGTTTAATATGTGTAAGACCATAGCTAGACTACGGCAACATATAGAGTCCGCCAGGACAGTAA
12027 ACA
66 ACA
* *
12030 TGGGTTTAATTTGTGTAAGATCATA
1 TGGGTTTAATATGTGTAAGACCATA
12055 ACTGGGTTAT
Statistics
Matches: 82, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
68 82 1.00
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.29
Consensus pattern (68 bp):
TGGGTTTAATATGTGTAAGACCATAGCTAGACTACGGCAACATATAGAGTCCGCCAGGACAGTAA
ACA
Found at i:12075 original size:68 final size:67
Alignment explanation
Indices: 11894--12085 Score: 197
Period size: 68 Copynumber: 2.8 Consensus size: 67
11884 CAGTTAAATG
* * * * *
11894 TGGGTTTAATATGTGTAAGACCATAGCTAGTCTATGGCAACATATGGAGTTCGCCAGGACAGTGA
1 TGGGTTTAATATGTGTAAGATCATAGCTGGT-TATGGCAACATATAGAGTCCGCCAGGACAGTAA
11959 ACA
65 ACA
** * **
11962 TGGGTTTAATATGTGTAAG-TCCATAGCTAGACTACGGCAACATATAGAGTCCGTTAGGACAGTA
1 TGGGTTTAATATGTGTAAGAT-CATAGCT-GGTTATGGCAACATATAGAGTCCGCCAGGACAGTA
12026 AACA
64 AACA
* * * * * *
12030 TGGGTTTAATTTGTGTAAGATCATAACTGGGTTATGACAATATATAAAGTCTGCCA
1 TGGGTTTAATATGTGTAAGATCATAGCT-GGTTATGGCAACATATAGAGTCCGCCA
12086 TAATGGAAAC
Statistics
Matches: 99, Mismatches: 22, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
68 98 0.99
69 1 0.01
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (67 bp):
TGGGTTTAATATGTGTAAGATCATAGCTGGTTATGGCAACATATAGAGTCCGCCAGGACAGTAAA
CA
Found at i:14262 original size:25 final size:24
Alignment explanation
Indices: 14206--14265 Score: 70
Period size: 25 Copynumber: 2.5 Consensus size: 24
14196 CTTAAACGTT
*
14206 TTTC-TTTTC-TATTTTCTTTTTC
1 TTTCATTTTCTTATTTTCTTTCTC
*
14228 CTTCATTTTTCTTATTTTCTTTGCTC
1 TTTCA-TTTTCTTATTTTCTTT-CTC
14254 TTTCATTTTCTT
1 TTTCATTTTCTT
14266 TCTTTTTGCT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
22 3 0.10
24 5 0.16
25 17 0.55
26 6 0.19
ACGTcount: A:0.07, C:0.20, G:0.02, T:0.72
Consensus pattern (24 bp):
TTTCATTTTCTTATTTTCTTTCTC
Found at i:15468 original size:22 final size:22
Alignment explanation
Indices: 15410--15470 Score: 68
Period size: 22 Copynumber: 2.8 Consensus size: 22
15400 GGGTTAGAAA
*
15410 TCTGCATCTGAATCTGATTTAT
1 TCTGCATCTGAATCTGATATAT
* * * *
15432 TCTACATATAAATCTGATATGT
1 TCTGCATCTGAATCTGATATAT
*
15454 TCTGCATCTGTATCTGA
1 TCTGCATCTGAATCTGA
15471 CAGACCATGT
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.26, C:0.18, G:0.13, T:0.43
Consensus pattern (22 bp):
TCTGCATCTGAATCTGATATAT
Found at i:15768 original size:22 final size:22
Alignment explanation
Indices: 15730--15774 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
15720 AATCTGCATC
*
15730 TAAATCTGATTTATTCTACATA
1 TAAATCTGATATATTCTACATA
* *
15752 TAAATCTGATATGTTCTGCATA
1 TAAATCTGATATATTCTACATA
15774 T
1 T
15775 GTATCTGACA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.33, C:0.13, G:0.09, T:0.44
Consensus pattern (22 bp):
TAAATCTGATATATTCTACATA
Found at i:15930 original size:312 final size:312
Alignment explanation
Indices: 15365--16102 Score: 1332
Period size: 312 Copynumber: 2.4 Consensus size: 312
15355 TCATTACGCA
15365 GTGTTGGGATGGATGGAGATGGTGTGTAATGGATGGGGTTAGAAATCTGCATCTGAATCTGATTT
1 GTGTTGGGATGGATGGAGATGGTGTGTAATGGATGGGGTTAGAAATCTGCATCTGAATCTGATTT
*
15430 ATTCTACATATAAATCTGATATGTTCTGCATCTGTATCTGACAGACCATGTAACTGTATCCGACT
66 ATTCTACATATAAATCTGATATGTTCTGCATCTGTATCTGACATACCATGTAACTGTATCCGACT
*
15495 TTCTTTGTTTCTATTCTGTATCTAATTCTGAGTAACGGATGACCTACGGTAAATGAGATTACAAT
131 TTCTTTGTTTCTATTCTGTATCTAATTCTAAGTAACGGATGACCTACGGTAAATGAGATTACAAT
* *
15560 TGTAGTTTACTAATTTATTGCATTCTGATCTGGCAGCTACGCTACGATTATTCTGAAACGTGAGA
196 TGTAGTTTACCAATTTATTGCATTCTGATCTGGCAGCTACGCTACGATTATTCTGAAACGTGACA
* *
15625 TATAGTCATTACGCAGTGTAGGGATGGACGAGTACTTGATGCCTTATATGGT
261 TATAGTCATTACGCAGTGTAGGGATAGACGAGTACTTGATGCCCTATATGGT
* *
15677 GTGTTGGGATGGATGGAGATGGTGTGTAATGGACGGGGTTAGAAATCTGCATCTAAATCTGATTT
1 GTGTTGGGATGGATGGAGATGGTGTGTAATGGATGGGGTTAGAAATCTGCATCTGAATCTGATTT
*
15742 ATTCTACATATAAATCTGATATGTTCTGCATATGTATCTGACATACCATGTAACTGTATCCGACT
66 ATTCTACATATAAATCTGATATGTTCTGCATCTGTATCTGACATACCATGTAACTGTATCCGACT
* *
15807 TTTTTTGTTTCTATTCTGTATCTAATTCTAAGTAACGGATGATCTACGGTAAATGAGATTACAAT
131 TTCTTTGTTTCTATTCTGTATCTAATTCTAAGTAACGGATGACCTACGGTAAATGAGATTACAAT
* *
15872 TGTAGTTTACCAATTTATTGCATTTTGATCTGGCAGCTACGCTGCGATTATTCTGAAACGTGACA
196 TGTAGTTTACCAATTTATTGCATTCTGATCTGGCAGCTACGCTACGATTATTCTGAAACGTGACA
* *
15937 TATAGTCATTACGTAGTGTAGGGATATACGAGTACTTGATGCCCTATATGGT
261 TATAGTCATTACGCAGTGTAGGGATAGACGAGTACTTGATGCCCTATATGGT
*
15989 GTGTTGAGATGGATGGAGATGGTGTGTAATGGATGGGGTTAGAAATCTGCATCTGAATCTGATTT
1 GTGTTGGGATGGATGGAGATGGTGTGTAATGGATGGGGTTAGAAATCTGCATCTGAATCTGATTT
16054 ATTCTACATATAAATCTGATATGTTCTGCATCTGTATCTGACATACCAT
66 ATTCTACATATAAATCTGATATGTTCTGCATCTGTATCTGACATACCAT
16103 TGAACAGTAG
Statistics
Matches: 407, Mismatches: 19, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
312 407 1.00
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (312 bp):
GTGTTGGGATGGATGGAGATGGTGTGTAATGGATGGGGTTAGAAATCTGCATCTGAATCTGATTT
ATTCTACATATAAATCTGATATGTTCTGCATCTGTATCTGACATACCATGTAACTGTATCCGACT
TTCTTTGTTTCTATTCTGTATCTAATTCTAAGTAACGGATGACCTACGGTAAATGAGATTACAAT
TGTAGTTTACCAATTTATTGCATTCTGATCTGGCAGCTACGCTACGATTATTCTGAAACGTGACA
TATAGTCATTACGCAGTGTAGGGATAGACGAGTACTTGATGCCCTATATGGT
Found at i:16092 original size:22 final size:22
Alignment explanation
Indices: 16034--16094 Score: 68
Period size: 22 Copynumber: 2.8 Consensus size: 22
16024 GGGTTAGAAA
*
16034 TCTGCATCTGAATCTGATTTAT
1 TCTGCATCTGAATCTGATATAT
* * * *
16056 TCTACATATAAATCTGATATGT
1 TCTGCATCTGAATCTGATATAT
*
16078 TCTGCATCTGTATCTGA
1 TCTGCATCTGAATCTGA
16095 CATACCATTG
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.26, C:0.18, G:0.13, T:0.43
Consensus pattern (22 bp):
TCTGCATCTGAATCTGATATAT
Found at i:17470 original size:232 final size:232
Alignment explanation
Indices: 17064--17527 Score: 829
Period size: 232 Copynumber: 2.0 Consensus size: 232
17054 GGATCGAGTT
*
17064 TCTGACACTAAACCTGTAAGTATTCCTGTTCAGTTATTGTGATTTGTTGAGACATAGTAGTGATT
1 TCTGACACTAAACCTGTAAGTATTCCTGTTCAGTTATTATGATTTGTTGAGACATAGTAGTGATT
* *
17129 GAAACTGTGGTTTGGTCAAACATTCTAATATGAATTGACATGAGAACTGTGGTAAAGACTCTGAA
66 GAAACTGTGGTTTGGTCAAACATTCTAATATGAATTGACATGAGAACTGTGGTAAAGACGCTAAA
* * * *
17194 CTGATCTATGCATTTCTGACATTGTAGATAATTTGTTGAAATGAGTTCACATGGTAGTTGTGGAT
131 CTGATCTATGCATTTCTGACATTGTAGATAATTTATTAAAATGAGTTCACATGGTAGTTCTGGAC
17259 GTGAGTTTTGTGGGCTCAAGCTGAGTCTTTCTCGATG
196 GTGAGTTTTGTGGGCTCAAGCTGAGTCTTTCTCGATG
*
17296 TCTGACACTAAACCTGTAAGTATTCCTGTTTAGTTATTATGATTTGTTGAGACATAGTAGTGATT
1 TCTGACACTAAACCTGTAAGTATTCCTGTTCAGTTATTATGATTTGTTGAGACATAGTAGTGATT
17361 GAAACTGTGGTTTGGTCAAACATTCTAATATGAATTGACATGAGAACTGTGGTAAAGACGCTAAA
66 GAAACTGTGGTTTGGTCAAACATTCTAATATGAATTGACATGAGAACTGTGGTAAAGACGCTAAA
* *
17426 CTGATCTGTGCGTTTCTGACATTGTAGATAATTTATTAAAATGAGTTCACATGGTAGTTCTGGAC
131 CTGATCTATGCATTTCTGACATTGTAGATAATTTATTAAAATGAGTTCACATGGTAGTTCTGGAC
*
17491 GTGGGTTTTGTGGGCTCAAGCTGAGTCTTTCTCGATG
196 GTGAGTTTTGTGGGCTCAAGCTGAGTCTTTCTCGATG
17528 GGCAGCTTGC
Statistics
Matches: 221, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
232 221 1.00
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.36
Consensus pattern (232 bp):
TCTGACACTAAACCTGTAAGTATTCCTGTTCAGTTATTATGATTTGTTGAGACATAGTAGTGATT
GAAACTGTGGTTTGGTCAAACATTCTAATATGAATTGACATGAGAACTGTGGTAAAGACGCTAAA
CTGATCTATGCATTTCTGACATTGTAGATAATTTATTAAAATGAGTTCACATGGTAGTTCTGGAC
GTGAGTTTTGTGGGCTCAAGCTGAGTCTTTCTCGATG
Found at i:29542 original size:31 final size:31
Alignment explanation
Indices: 29504--29593 Score: 153
Period size: 32 Copynumber: 2.9 Consensus size: 31
29494 AGGCAAATTA
29504 CAAGAGTAATTGAATCCTAATAAAACTATTT
1 CAAGAGTAATTGAATCCTAATAAAACTATTT
*
29535 CAAGAGTAATTGAATCCTAATAAAAACTCTTT
1 CAAGAGTAATTGAATCCTAAT-AAAACTATTT
*
29567 AAAGAGTAATTGAATCCTAATAAAACT
1 CAAGAGTAATTGAATCCTAATAAAACT
29594 CTTTAAAATT
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
31 27 0.48
32 29 0.52
ACGTcount: A:0.47, C:0.13, G:0.10, T:0.30
Consensus pattern (31 bp):
CAAGAGTAATTGAATCCTAATAAAACTATTT
Found at i:29595 original size:31 final size:31
Alignment explanation
Indices: 29505--29600 Score: 165
Period size: 31 Copynumber: 3.1 Consensus size: 31
29495 GGCAAATTAC
* *
29505 AAGAGTAATTGAATCCTAATAAAACTATTTC
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
29536 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
1 AAGAGTAATTGAATCCTAAT-AAAACTCTTTA
29568 AAGAGTAATTGAATCCTAATAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
29599 AA
1 AA
29601 ATTATCTAAG
Statistics
Matches: 62, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
31 33 0.53
32 29 0.47
ACGTcount: A:0.47, C:0.12, G:0.09, T:0.31
Consensus pattern (31 bp):
AAGAGTAATTGAATCCTAATAAAACTCTTTA
Found at i:45022 original size:29 final size:29
Alignment explanation
Indices: 44969--45029 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
44959 GTGGCACATG
* **
44969 GTCGTGTGCCAGACCGTGTGTGACACACA
1 GTCGTGTGCCAGACCATGTACGACACACA
* *
44998 GTCGTGTGCCAGACTATGTACGACACATA
1 GTCGTGTGCCAGACCATGTACGACACACA
45027 GTC
1 GTC
45030 TGGGCTAATT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.23, C:0.26, G:0.28, T:0.23
Consensus pattern (29 bp):
GTCGTGTGCCAGACCATGTACGACACACA
Found at i:45724 original size:46 final size:47
Alignment explanation
Indices: 45638--45727 Score: 110
Period size: 46 Copynumber: 1.9 Consensus size: 47
45628 AATAGCTTGT
* ** * *
45638 CTGCAATTATGGTAGCTCGACCACATATGTTTGTTCTGGCAATTGGG
1 CTGCAATTATAGTAGCTCGACCACATATGTCCGATATGGCAATTGGG
* *
45685 CTGCAA-TATAGTAGCTTGTCCACATATGTCCGATATGGCAATT
1 CTGCAATTATAGTAGCTCGACCACATATGTCCGATATGGCAATT
45728 TTATCTACAA
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
46 30 0.83
47 6 0.17
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.33
Consensus pattern (47 bp):
CTGCAATTATAGTAGCTCGACCACATATGTCCGATATGGCAATTGGG
Found at i:48582 original size:25 final size:25
Alignment explanation
Indices: 48519--48583 Score: 62
Period size: 25 Copynumber: 2.6 Consensus size: 25
48509 TTATAATAAG
*
48519 TATTTTATGATGTTAATTTTAAATTT
1 TATTTTATCAT-TTAATTTTAAATTT
*
48545 TATTATTA-CATTTTATTTT-AATTAT
1 TATT-TTATCATTTAATTTTAAATT-T
*
48570 TATTTTATTATTTA
1 TATTTTATCATTTA
48584 TCAATTGTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
24 7 0.22
25 16 0.50
26 6 0.19
27 3 0.09
ACGTcount: A:0.31, C:0.02, G:0.03, T:0.65
Consensus pattern (25 bp):
TATTTTATCATTTAATTTTAAATTT
Found at i:50025 original size:28 final size:29
Alignment explanation
Indices: 49983--50037 Score: 85
Period size: 28 Copynumber: 1.9 Consensus size: 29
49973 TTTCAGAGGT
*
49983 TTTTTTTTGACAATTTTTGTATTTTTACA
1 TTTTTTTTGACAATTTATGTATTTTTACA
*
50012 TTTTTTTTGA-AATTTATGTTTTTTTA
1 TTTTTTTTGACAATTTATGTATTTTTA
50038 AAAGAAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 14 0.58
29 10 0.42
ACGTcount: A:0.20, C:0.04, G:0.07, T:0.69
Consensus pattern (29 bp):
TTTTTTTTGACAATTTATGTATTTTTACA
Found at i:50647 original size:13 final size:13
Alignment explanation
Indices: 50629--50653 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
50619 AGACTTGAGC
50629 AATATTTTAAGTT
1 AATATTTTAAGTT
50642 AATATTTTAAGT
1 AATATTTTAAGT
50654 CGAATCAAGC
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:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (13 bp):
AATATTTTAAGTT
Found at i:66447 original size:131 final size:132
Alignment explanation
Indices: 66121--66542 Score: 697
Period size: 132 Copynumber: 3.2 Consensus size: 132
66111 NNNNNNNNNN
66121 TAATTCTATTTCCCTGGGCAACAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAG
1 TAATTCTATTTCCCTGGGCAACAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAG
66186 TAGTGGAGCAGATCAAAGATGGCGGATTTTACCTCCTCGTA-GTTATAGTGGAGTACATTGAAGC
66 TAGTGGAGCAGATCAAAGATGGCGGATTTTACCTCCTCG-AGGTTATAGTGGAGTACATTGAAGC
66250 CAG
130 CAG
* * * *
66253 TAATTCTATCTCCTTGGGCAACAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCCAAGCAA
1 TAATTCTATTTCCCTGGGCAACAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAG
* **
66318 TAGTGGAGCAGATCAAAGATGGCAGATTTT-CCTCC-CTGAGGTTGCAGTGGAGTACATTGAAGC
66 TAGTGGAGCAGATCAAAGATGGCGGATTTTACCTCCTC-GAGGTTATAGTGGAGTACATTGAAGC
66381 CAG
130 CAG
* *
66384 TAATTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAG
1 TAATTCTATTTCCCTGGGCAACAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAG
* * *
66449 TAGCGGAGTAGATCAAAGATGGCGGATTTTACCTCCTCGTGGTTATAGTGGAGTACATTGAAGCC
66 TAGTGGAGCAGATCAAAGATGGCGGATTTTACCTCCTCGAGGTTATAGTGGAGTACATTGAAGCC
66514 AG
131 AG
66516 TAATTCTATTTCCCTGGGCAACAGTGG
1 TAATTCTATTTCCCTGGGCAACAGTGG
66543 NNNNNNNNNN
Statistics
Matches: 265, Mismatches: 21, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
130 2 0.01
131 116 0.44
132 146 0.55
133 1 0.00
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.29
Consensus pattern (132 bp):
TAATTCTATTTCCCTGGGCAACAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAG
TAGTGGAGCAGATCAAAGATGGCGGATTTTACCTCCTCGAGGTTATAGTGGAGTACATTGAAGCC
AG
Found at i:68256 original size:2 final size:2
Alignment explanation
Indices: 68249--68277 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
68239 NNNNNNNNAC
68249 AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
68278 TTTACTTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:68268 original size:13 final size:13
Alignment explanation
Indices: 68250--68275 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
68240 NNNNNNNACA
68250 TATATATATATAT
1 TATATATATATAT
68263 TATATATATATAT
1 TATATATATATAT
68276 ATTTTACTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TATATATATATAT
Found at i:68269 original size:15 final size:15
Alignment explanation
Indices: 68249--68278 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
68239 NNNNNNNNAC
68249 ATATATATATATATT
1 ATATATATATATATT
68264 ATATATATATATATT
1 ATATATATATATATT
68279 TTACTTTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
ATATATATATATATT
Found at i:68913 original size:78 final size:78
Alignment explanation
Indices: 68828--68982 Score: 240
Period size: 78 Copynumber: 2.0 Consensus size: 78
68818 TGGGTTCCGA
* * * *
68828 TTTTCTTTGTTAA-TCTTGAATAACCGAGAATATTCTTTATTCAAAATGCATGAGAATAAAAATC
1 TTTTCTTTGCTAATTCTAG-ATAACCAAGAATATTCTTTAATCAAAATGCATGAGAATAAAAATC
68892 ATTTTTGGGAACTG
65 ATTTTTGGGAACTG
* *
68906 TTTTCTTTGCTAATTCTAGATAACCAAGGATATTCTTTAATCAAAATGCATGAGTATAAAAATCA
1 TTTTCTTTGCTAATTCTAGATAACCAAGAATATTCTTTAATCAAAATGCATGAGAATAAAAATCA
68971 TTTTTGGGAACT
66 TTTTTGGGAACT
68983 TAACTTGTTG
Statistics
Matches: 70, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
78 66 0.94
79 4 0.06
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.39
Consensus pattern (78 bp):
TTTTCTTTGCTAATTCTAGATAACCAAGAATATTCTTTAATCAAAATGCATGAGAATAAAAATCA
TTTTTGGGAACTG
Found at i:76462 original size:23 final size:23
Alignment explanation
Indices: 76436--76480 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
76426 GATAGGAAAT
76436 GTTAA-GTTGTTCATGCTTGAATG
1 GTTAATGTT-TTCATGCTTGAATG
* *
76459 GTTAATGTTTTTATGTTTGAAT
1 GTTAATGTTTTCATGCTTGAAT
76481 TTGTGGTGCC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.22, C:0.04, G:0.22, T:0.51
Consensus pattern (23 bp):
GTTAATGTTTTCATGCTTGAATG
Found at i:78372 original size:34 final size:34
Alignment explanation
Indices: 78261--78365 Score: 149
Period size: 34 Copynumber: 3.1 Consensus size: 34
78251 TACTACTGAG
* *
78261 TTGATCTGTTATAAGCATATTACTTGCTACTTTA
1 TTGAACTGTTATAAGCATATTACTTGCTACTATA
* *
78295 TTGAACCGTTATAAGCATATTATTTGCTACTATA
1 TTGAACTGTTATAAGCATATTACTTGCTACTATA
*
78329 TTGAACTGTTATAAGCATATTGA-TTGCTACTGTA
1 TTGAACTGTTATAAGCATATT-ACTTGCTACTATA
78363 TTG
1 TTG
78366 CTCTGTTGAA
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
34 63 0.98
35 1 0.02
ACGTcount: A:0.29, C:0.13, G:0.14, T:0.44
Consensus pattern (34 bp):
TTGAACTGTTATAAGCATATTACTTGCTACTATA
Found at i:79108 original size:21 final size:22
Alignment explanation
Indices: 79082--79123 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
79072 TTTATTAAAA
79082 ATATTTTAAGA-T-TATTATTTG
1 ATATTTT-AGATTGTATTATTTG
79103 ATATTTTAGATTGTATTATTT
1 ATATTTTAGATTGTATTATTT
79124 TATTTTGAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 3 0.16
21 8 0.42
22 8 0.42
ACGTcount: A:0.31, C:0.00, G:0.10, T:0.60
Consensus pattern (22 bp):
ATATTTTAGATTGTATTATTTG
Found at i:82153 original size:56 final size:57
Alignment explanation
Indices: 82048--82154 Score: 162
Period size: 56 Copynumber: 1.9 Consensus size: 57
82038 AGAAAAATTG
* * *
82048 AAAACATTTGGAAATGAAATATTGTTTTCTCCAAAATGAAAATGAAAATGAGAAATA
1 AAAACATTTGGAAATGAAATATGGTTTCCTCCAAAATGAAAATAAAAATGAGAAATA
* *
82105 AAAACATTTGGAAATG-AATGTGGTTTCCTTCAAAATGAAAATAAAAATGA
1 AAAACATTTGGAAATGAAATATGGTTTCCTCCAAAATGAAAATAAAAATGA
82155 AATTTTGTTT
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
56 29 0.64
57 16 0.36
ACGTcount: A:0.50, C:0.07, G:0.15, T:0.28
Consensus pattern (57 bp):
AAAACATTTGGAAATGAAATATGGTTTCCTCCAAAATGAAAATAAAAATGAGAAATA
Found at i:85428 original size:22 final size:22
Alignment explanation
Indices: 85403--85444 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
85393 AAATACGGAG
*
85403 AAAACAACAAGAAAATAGCATT
1 AAAACAACAAAAAAATAGCATT
*
85425 AAAATAACAAAAAAATAGCA
1 AAAACAACAAAAAAATAGCA
85445 GTTTATTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.69, C:0.12, G:0.07, T:0.12
Consensus pattern (22 bp):
AAAACAACAAAAAAATAGCATT
Found at i:90024 original size:23 final size:24
Alignment explanation
Indices: 89998--90053 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 24
89988 TTATATATTT
89998 ATAAAATTATAAATTAATA-AATG
1 ATAAAATTATAAATTAATACAATG
*
90021 ATAAAGA-TATAAATTAATACAATT
1 ATAAA-ATTATAAATTAATACAATG
*
90045 ATGAAATTA
1 ATAAAATTA
90054 CATTTTAACT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
23 18 0.64
24 10 0.36
ACGTcount: A:0.59, C:0.02, G:0.05, T:0.34
Consensus pattern (24 bp):
ATAAAATTATAAATTAATACAATG
Found at i:94263 original size:12 final size:11
Alignment explanation
Indices: 94246--94276 Score: 53
Period size: 12 Copynumber: 2.7 Consensus size: 11
94236 TAGGTTCGTA
94246 AAAAAAATTTCG
1 AAAAAAATTT-G
94258 AAAAAAATTTG
1 AAAAAAATTTG
94269 AAAAAAAT
1 AAAAAAAT
94277 GAGATATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 9 0.47
12 10 0.53
ACGTcount: A:0.68, C:0.03, G:0.06, T:0.23
Consensus pattern (11 bp):
AAAAAAATTTG
Found at i:95238 original size:18 final size:18
Alignment explanation
Indices: 95215--95278 Score: 76
Period size: 18 Copynumber: 3.5 Consensus size: 18
95205 CATGTTGTAA
95215 TGAAAAAGA-AAAAGAGAT
1 TGAAAAAGAGAAAAGA-AT
*
95233 TGAAAAAGAGGAAAAAAAT
1 TGAAAAAGA-GAAAAGAAT
*
95252 TGAAAGAGAGAAAAGAAT
1 TGAAAAAGAGAAAAGAAT
*
95270 CGAAAAAGA
1 TGAAAAAGA
95279 TTGTGAAAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
18 24 0.62
19 10 0.26
20 5 0.13
ACGTcount: A:0.66, C:0.02, G:0.23, T:0.09
Consensus pattern (18 bp):
TGAAAAAGAGAAAAGAAT
Found at i:95298 original size:12 final size:12
Alignment explanation
Indices: 95283--95316 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
95273 AAAAGATTGT
95283 GAAAAAGAAAAC
1 GAAAAAGAAAAC
**
95295 GAAAAAGAAATT
1 GAAAAAGAAAAC
95307 GAAAAAGAAA
1 GAAAAAGAAA
95317 GTGAGAGTGA
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:0.74, C:0.03, G:0.18, T:0.06
Consensus pattern (12 bp):
GAAAAAGAAAAC
Found at i:103552 original size:87 final size:86
Alignment explanation
Indices: 103398--103561 Score: 224
Period size: 87 Copynumber: 1.9 Consensus size: 86
103388 ATGCATAAGT
* * *
103398 TTGAGTTCTTACTCTTAATGAGTTCATAGCCAAGAGTTTGGGTGGTTCTATTGAGACAGACTTGA
1 TTGAGTTATTACTCTTAATGAGTTCATAGCCAAGAGTGTGGATGGTTCTATTGAGACAGACTTGA
103463 TGAATTCACCGACTTGAGATG
66 TGAATTCACCGACTTGAGATG
** * *
103484 TTGAGTTTATTACTCTTAATGAGTTCATATTCGAGAGTGTGGATGG-TCTTATTGAGA-TGTACT
1 TTGAG-TTATTACTCTTAATGAGTTCATAGCCAAGAGTGTGGATGGTTC-TATTGAGACAG-ACT
103547 TGATGAATTCACCGA
63 TGATGAATTCACCGA
103562 ATCTAAATTT
Statistics
Matches: 68, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
86 8 0.12
87 60 0.88
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.37
Consensus pattern (86 bp):
TTGAGTTATTACTCTTAATGAGTTCATAGCCAAGAGTGTGGATGGTTCTATTGAGACAGACTTGA
TGAATTCACCGACTTGAGATG
Found at i:108000 original size:7 final size:7
Alignment explanation
Indices: 107990--108029 Score: 71
Period size: 7 Copynumber: 5.7 Consensus size: 7
107980 ATTGAAACAT
107990 TATATAG
1 TATATAG
107997 TATATAG
1 TATATAG
*
108004 TATGTAG
1 TATATAG
108011 TATATAG
1 TATATAG
108018 TATATAG
1 TATATAG
108025 TATAT
1 TATAT
108030 CAATTTCAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.40, C:0.00, G:0.15, T:0.45
Consensus pattern (7 bp):
TATATAG
Found at i:109348 original size:28 final size:28
Alignment explanation
Indices: 109308--109364 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
109298 TCCTATACGT
109308 TTCCATTTGAGAGAAAAACAAAATTCTA
1 TTCCATTTGAGAGAAAAACAAAATTCTA
109336 TTCCATTTGAGAGAAAAACAAAATTCTA
1 TTCCATTTGAGAGAAAAACAAAATTCTA
109364 T
1 T
109365 CTTTATTATC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (28 bp):
TTCCATTTGAGAGAAAAACAAAATTCTA
Found at i:110876 original size:6 final size:6
Alignment explanation
Indices: 110865--110898 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
110855 TAAAATATTG
110865 ATGGCA ATGGCA ATGGCA ATGGCA ATGGCA ATGG
1 ATGGCA ATGGCA ATGGCA ATGGCA ATGGCA ATGG
110899 ATGAGCATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.32, C:0.15, G:0.35, T:0.18
Consensus pattern (6 bp):
ATGGCA
Found at i:115688 original size:14 final size:14
Alignment explanation
Indices: 115671--115697 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
115661 AACTATATTT
115671 TCAAAATTATTTTC
1 TCAAAATTATTTTC
115685 TCAAAATTATTTT
1 TCAAAATTATTTT
115698 TTCAGAAACT
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:0.37, C:0.11, G:0.00, T:0.52
Consensus pattern (14 bp):
TCAAAATTATTTTC
Found at i:115880 original size:125 final size:126
Alignment explanation
Indices: 115578--116849 Score: 1556
Period size: 125 Copynumber: 10.1 Consensus size: 126
115568 AACAAAGCAG
* * * *
115578 GAACTACTATAGAAAAAGAACGTCCACGTGTGAGC-TTTTTCAGTAATTTTGCTGACAGTGCATC
1 GAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTTAGTAATTTTGCTGACAGTGCATC
* * * *** *
115642 CTGCTTGAAGCATTTTTGAAACTATATTTTCAAAATTATTTTCTCAAAATTATTTTTTC-A
66 CTGCTTGAAGCATTTTTGACACTATTTTTTCAGAACCGTCTTCTCAAAATTATTTTTTCAA
* ** * * * * *
115702 GAAACTACTGTAGAAAAAGAGCATCCATATGGGAGCCTGTTTCAGTAATTTTGTTGATAGTGCAT
1 G-AACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTTAGTAATTTTGCTGACAGTGCAT
*
115767 CCTGCTTGAAGCATTTTTGACACTATTTTTTCAGAACCGTCTT-TTAAAATTATTTTTTCAA
65 CCTGCTTGAAGCATTTTTGACACTATTTTTTCAGAACCGTCTTCTCAAAATTATTTTTTCAA
* * * * * *
115828 GAACTACTGTAAAAAAAGAGTGTCTACGTGGAAGCTTTTGTTAGTAATTTTGTTGACAGTGCATC
1 GAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTTAGTAATTTTGCTGACAGTGCATC
** * * *
115893 CTGCTTGAAGTGTTTTTGACACTA-TTTTTCAGAACCTTTTTTTCAAAATTATTTTTTCAA
66 CTGCTTGAAGCATTTTTGACACTATTTTTTCAGAACCGTCTTCTCAAAATTATTTTTTCAA
* * *
115953 GAACTACTTTAGAAAAAGAGCATCCATGTGGGAGCTTTTTTTAGTAATTTTGCTGACAGTGCATC
1 GAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTTAGTAATTTTGCTGACAGTGCATC
* *
116018 CTGCTTGAAGCATTTTTGACACTATTTTTTCAGAACCGTCTTCTAAAAATTATTTTTTCAG
66 CTGCTTGAAGCATTTTTGACACTATTTTTTCAGAACCGTCTTCTCAAAATTATTTTTTCAA
* * * *
116079 GAGCTACTGTAGAAAAAGAGCGTCCATGTGGGAGCTTTTTTTAGTACTTTTGCTGACAGTGCATA
1 GAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTTAGTAATTTTGCTGACAGTGCATC
** * * * * *
116144 CTAATTGAAGCATTTTTTTACATTATTTTTTTATAATCGTCTTCTCAAAATTATTTTTTCAA
66 CTGCTTGAAGCA-TTTTTGACACTATTTTTTCAGAACCGTCTTCTCAAAATTATTTTTTCAA
* * * * * * *
116206 AAACTACTATAGAAAAAGAGCATCCACGTGGGAG-ATTTTTCAGTAATTTTGCTGACAATGTATC
1 GAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTTAGTAATTTTGCTGACAGTGCATC
* * ** *
116270 CTACTTGAAGCGTTTTTGACACTATTTTTTCAGAACTATCTTCTCAAAATTATTTTTTCAG
66 CTGCTTGAAGCATTTTTGACACTATTTTTTCAGAACCGTCTTCTCAAAATTATTTTTTCAA
116331 GAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTTAGTAATTTTGCTGACAGTGCATC
1 GAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTTAGTAATTTTGCTGACAGTGCATC
* * **
116396 CTGCTTTAAGCGTTTTTGACACTATTTTTTCAGAATTGTCTTCTCAAAATTA-TTTTTCAA
66 CTGCTTGAAGCATTTTTGACACTATTTTTTCAGAACCGTCTTCTCAAAATTATTTTTTCAA
* * * *
116456 GAACTACTGTAAAAAAAAGAGTGTCCACGTGAGAGCTTTTTTTAGTAATTTTGCTGATAGTGCAT
1 GAACTACTGT-AGAAAAAGAGCGTCCACGTGGGAGCTTTTTTTAGTAATTTTGCTGACAGTGCAT
* * * * * * *
116521 GCTGTTTGAAGCAGTTTTCACACTATTTTTTCAAAACCATCTTCTCAAAATTA-TTTTTCAG
65 CCTGCTTGAAGCATTTTTGACACTATTTTTTCAGAACCGTCTTCTCAAAATTATTTTTTCAA
* * * * *
116582 GAACTACTGTACAAAAAGAGTGTCCACGTGGGAG-TTTTTTTAGTACTTTTGCTAACAGTGCATA
1 GAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTTAGTAATTTTGCTGACAGTGCATC
** * * * *
116646 CTATTTAAAGCATTTTTTACATTATTTTTTTAGAACCGTCTTCTCAAAATTA-TTTTTC-A
66 CTGCTTGAAGCATTTTTGACACTATTTTTTCAGAACCGTCTTCTCAAAATTATTTTTTCAA
* * * *
116705 GAAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAATACTTTTGTTGACAGTGCAT
1 G-AACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTTAGTAATTTTGCTGACAGTGCAT
* * * * * **
116770 CCTGCTTGAAGCATTTTTGTCACTATTTTTTTAGAATCATATTCTCAAAATTATTTTTTTTA
65 CCTGCTTGAAGCATTTTTGACACTATTTTTTCAGAACCGTCTTCTCAAAATTATTTTTTCAA
*
116832 GAAACTGCTGTAGAAAAA
1 G-AACTACTGTAGAAAAA
116850 AAAACAAAAT
Statistics
Matches: 991, Mismatches: 145, Indels: 21
0.86 0.13 0.02
Matches are distributed among these distances:
123 1 0.00
124 123 0.12
125 391 0.39
126 387 0.39
127 89 0.09
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.39
Consensus pattern (126 bp):
GAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTTAGTAATTTTGCTGACAGTGCATC
CTGCTTGAAGCATTTTTGACACTATTTTTTCAGAACCGTCTTCTCAAAATTATTTTTTCAA
Found at i:116980 original size:34 final size:33
Alignment explanation
Indices: 116937--117035 Score: 144
Period size: 34 Copynumber: 2.9 Consensus size: 33
116927 ATTATTTTTA
116937 AAAAACCCTAAACCTTAATTTAATTAATTTTCTT
1 AAAAACCCTAAACC-TAATTTAATTAATTTTCTT
* *
116971 AAAAACCCTAAACCCTAATTTAGTTAATTTACTT
1 AAAAACCCTAAA-CCTAATTTAATTAATTTTCTT
*
117005 AAAACCCCTAAAACCTAATTTAATTAATTTT
1 AAAAACCCT-AAACCTAATTTAATTAATTTT
117036 TAAAAAAATT
Statistics
Matches: 58, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
34 53 0.91
35 5 0.09
ACGTcount: A:0.42, C:0.19, G:0.01, T:0.37
Consensus pattern (33 bp):
AAAAACCCTAAACCTAATTTAATTAATTTTCTT
Found at i:117573 original size:92 final size:90
Alignment explanation
Indices: 117452--117633 Score: 219
Period size: 93 Copynumber: 2.0 Consensus size: 90
117442 GTGTAAAATT
* * * *
117452 CTTCAAATTTTTCAAAACAAAAATAATT-AAGCTC-ATGTTTTCTTTTACACTCAATTAGGTACT
1 CTTCAAATTTTTCAAAAAAAAAATAATTAAACCCCTACGTTTT-TTTTACACTCAATTAGGTACT
*
117515 TAAACTTTCCAAAAATG-TTAAAAAGGG
65 TAAA-TTGCC-AAAATGATTAAAAAGGG
117542 CTTCAAATTTTTTTCAAAAAAAAAACT-ATTAAACCCCTACGTTTTTTTTACACTCAATTAGGTA
1 CTTCAAA--TTTTTCAAAAAAAAAA-TAATTAAACCCCTACGTTTTTTTTACACTCAATTAGGTA
*
117606 CTTGAATTGCCAAAATGTATTAAAAAGG
63 CTTAAATTGCCAAAATG-ATTAAAAAGG
117634 CCCTTTGATC
Statistics
Matches: 79, Mismatches: 6, Indels: 11
0.82 0.06 0.11
Matches are distributed among these distances:
90 7 0.09
91 6 0.08
92 22 0.28
93 38 0.48
94 6 0.08
ACGTcount: A:0.40, C:0.16, G:0.09, T:0.36
Consensus pattern (90 bp):
CTTCAAATTTTTCAAAAAAAAAATAATTAAACCCCTACGTTTTTTTTACACTCAATTAGGTACTT
AAATTGCCAAAATGATTAAAAAGGG
Found at i:117795 original size:10 final size:9
Alignment explanation
Indices: 117717--117897 Score: 70
Period size: 9 Copynumber: 19.4 Consensus size: 9
117707 ATATGTGGAA
*
117717 AAAAATGAT
1 AAAAATTAT
117726 AAAAA--AT
1 AAAAATTAT
*
117733 AAAAATCAAT
1 AAAAAT-TAT
117743 AAAAATTAT
1 AAAAATTAT
117752 -AAAATTATT
1 AAAAATTA-T
* **
117761 GAATTTTAAT
1 AAAAATT-AT
117771 AAAAA-TAT
1 AAAAATTAT
*
117779 CAAAATTATT
1 AAAAATTA-T
*
117789 AAAAATTAGAGGA
1 AAAAATT--A--T
117802 AAAAATTAT
1 AAAAATTAT
*
117811 AAAAATCAT
1 AAAAATTAT
117820 -AAAATATAT
1 AAAAAT-TAT
*
117829 AAAAAATTGT
1 -AAAAATTAT
*
117839 AAAATTTAT
1 AAAAATTAT
* * *
117848 GAACATCAT
1 AAAAATTAT
117857 AAAAAATTAT
1 -AAAAATTAT
117867 -AAAATATAT
1 AAAAAT-TAT
*
117876 AGAAA-TAT
1 AAAAATTAT
117884 AAAAAATTAT
1 -AAAAATTAT
117894 AAAA
1 AAAA
117898 TTTTATAAAT
Statistics
Matches: 128, Mismatches: 25, Indels: 38
0.67 0.13 0.20
Matches are distributed among these distances:
7 7 0.05
8 26 0.20
9 44 0.34
10 36 0.28
11 7 0.05
12 1 0.01
13 7 0.05
ACGTcount: A:0.64, C:0.03, G:0.04, T:0.29
Consensus pattern (9 bp):
AAAAATTAT
Found at i:117904 original size:28 final size:28
Alignment explanation
Indices: 117801--117900 Score: 123
Period size: 28 Copynumber: 3.6 Consensus size: 28
117791 AAATTAGAGG
* * * *
117801 AAAAAATTATAAAAATCATAAAATATAT
1 AAAAAATTATAAAATTTATAGAACATAT
*
117829 AAAAAATTGTAAAATTTAT-GAACATCAT
1 AAAAAATTATAAAATTTATAGAACAT-AT
*
117857 AAAAAATTATAAAATATATAGAA-ATAT
1 AAAAAATTATAAAATTTATAGAACATAT
117884 AAAAAATTATAAAATTT
1 AAAAAATTATAAAATTT
117901 TATAAATTTG
Statistics
Matches: 62, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
27 22 0.35
28 37 0.60
29 3 0.05
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (28 bp):
AAAAAATTATAAAATTTATAGAACATAT
Found at i:146421 original size:11 final size:11
Alignment explanation
Indices: 146407--146431 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
146397 TTTTTTATGA
146407 TTTTTACAATT
1 TTTTTACAATT
146418 TTTTTACAATT
1 TTTTTACAATT
146429 TTT
1 TTT
146432 ATTTATTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (11 bp):
TTTTTACAATT
Found at i:149481 original size:41 final size:41
Alignment explanation
Indices: 149424--149588 Score: 330
Period size: 41 Copynumber: 4.0 Consensus size: 41
149414 AATTTATCAC
149424 TACCATTTTGTTAATCCACTAACATATTGCTGACATAATTT
1 TACCATTTTGTTAATCCACTAACATATTGCTGACATAATTT
149465 TACCATTTTGTTAATCCACTAACATATTGCTGACATAATTT
1 TACCATTTTGTTAATCCACTAACATATTGCTGACATAATTT
149506 TACCATTTTGTTAATCCACTAACATATTGCTGACATAATTT
1 TACCATTTTGTTAATCCACTAACATATTGCTGACATAATTT
149547 TACCATTTTGTTAATCCACTAACATATTGCTGACATAATTT
1 TACCATTTTGTTAATCCACTAACATATTGCTGACATAATTT
149588 T
1 T
149589 TTTAACTTTT
Statistics
Matches: 124, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 124 1.00
ACGTcount: A:0.32, C:0.19, G:0.07, T:0.42
Consensus pattern (41 bp):
TACCATTTTGTTAATCCACTAACATATTGCTGACATAATTT
Found at i:150911 original size:47 final size:47
Alignment explanation
Indices: 150812--150952 Score: 130
Period size: 45 Copynumber: 3.1 Consensus size: 47
150802 GTATTTCTTC
* * * * * *
150812 TTTTTTATCCTTGTAATTTGAATTTTTTGTC--CCTATAATTCTAAT
1 TTTTTTGTCCCTGTAAATTGATTTTTTTTTCTTCCTATAATTCAAAT
* ***
150857 TTGTTTGTCCCTGTTGTTTG-TTTTTTTTTCTTCCTATAATTCAAAAT
1 TTTTTTGTCCCTGTAAATTGATTTTTTTTTCTTCCTATAATTC-AAAT
* *
150904 TTTTTTGTCTCTGTAAATTGATTTTTTTGTC-T-CTATAATTCAAAT
1 TTTTTTGTCCCTGTAAATTGATTTTTTTTTCTTCCTATAATTCAAAT
150949 TTTT
1 TTTT
150953 AGTTCATGTA
Statistics
Matches: 78, Mismatches: 14, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
44 8 0.10
45 23 0.29
46 19 0.24
47 19 0.24
48 9 0.12
ACGTcount: A:0.19, C:0.13, G:0.09, T:0.60
Consensus pattern (47 bp):
TTTTTTGTCCCTGTAAATTGATTTTTTTTTCTTCCTATAATTCAAAT
Found at i:150951 original size:22 final size:22
Alignment explanation
Indices: 150890--150952 Score: 65
Period size: 22 Copynumber: 2.8 Consensus size: 22
150880 TTTTTTCTTC
150890 CTATAATTCAAAATTTTTTTGTCT
1 CTATAATTC-AAA-TTTTTTGTCT
* * *
150914 CTGTAAATT-GATTTTTTTGTCT
1 CTAT-AATTCAAATTTTTTGTCT
150936 CTATAATTCAAATTTTT
1 CTATAATTCAAATTTTT
150953 AGTTCATGTA
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
21 4 0.13
22 19 0.61
23 1 0.03
24 3 0.10
25 4 0.13
ACGTcount: A:0.27, C:0.11, G:0.06, T:0.56
Consensus pattern (22 bp):
CTATAATTCAAATTTTTTGTCT
Found at i:151098 original size:20 final size:21
Alignment explanation
Indices: 151051--151100 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 21
151041 CTGTAATTTG
151051 ATTTGTTTGTCCCTATAAATCA
1 ATTT-TTTGTCCCTATAAATCA
*
151073 ATTTTTTGTCCCTATAATTCA
1 ATTTTTTGTCCCTATAAATCA
*
151094 TTTTTTT
1 ATTTTTT
151101 TATTTTTTCC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
21 22 0.85
22 4 0.15
ACGTcount: A:0.22, C:0.16, G:0.06, T:0.56
Consensus pattern (21 bp):
ATTTTTTGTCCCTATAAATCA
Found at i:152401 original size:55 final size:55
Alignment explanation
Indices: 152337--152543 Score: 405
Period size: 55 Copynumber: 3.8 Consensus size: 55
152327 AGGTCATGTT
152337 AAAATTTCATTAAGAAATTTTGAAGTTTAAATACTTAATTAACTATTTAAACTTC
1 AAAATTTCATTAAGAAATTTTGAAGTTTAAATACTTAATTAACTATTTAAACTTC
152392 AAAATTTCATTAAGAAATTTTGAAGTTTAAATACTTAATTAACTATTTAAACTTC
1 AAAATTTCATTAAGAAATTTTGAAGTTTAAATACTTAATTAACTATTTAAACTTC
152447 AAAATTTCATTAAGAAATTTTGAAGTTTAAATACTTAATTAACTATTTAAACTTC
1 AAAATTTCATTAAGAAATTTTGAAGTTTAAATACTTAATTAACTATTTAAACTTC
*
152502 AAAATTTCATTAAGAAATTTTGAAGTTTAAATAGTTAATTAA
1 AAAATTTCATTAAGAAATTTTGAAGTTTAAATACTTAATTAA
152544 GTAAAAAAAG
Statistics
Matches: 151, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
55 151 1.00
ACGTcount: A:0.44, C:0.08, G:0.06, T:0.42
Consensus pattern (55 bp):
AAAATTTCATTAAGAAATTTTGAAGTTTAAATACTTAATTAACTATTTAAACTTC
Found at i:168502 original size:42 final size:43
Alignment explanation
Indices: 168430--168560 Score: 149
Period size: 43 Copynumber: 3.0 Consensus size: 43
168420 CATAGGGTTC
* * *
168430 CGATATGTGATTTACGTGTAAGACCATGTCTGGGACATTGGCAT
1 CGATATATGATTT-CATGTAAGACCCTGTCTGGGACATTGGCAT
* *
168474 C-ATATATGATTTCATGTAAAACCCTGTCTGGGACAGTGGCAT
1 CGATATATGATTTCATGTAAGACCCTGTCTGGGACATTGGCAT
* * * *
168516 CGTTATTTGATTACATGTAAGACCAC-GTCTGGGACGTTGGCAT
1 CGATATATGATTTCATGTAAGACC-CTGTCTGGGACATTGGCAT
168559 CG
1 CG
168561 TATGAGCTTT
Statistics
Matches: 74, Mismatches: 11, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
42 27 0.36
43 45 0.61
44 2 0.03
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.31
Consensus pattern (43 bp):
CGATATATGATTTCATGTAAGACCCTGTCTGGGACATTGGCAT
Found at i:174244 original size:18 final size:19
Alignment explanation
Indices: 174221--174257 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
174211 GCTCGAATTA
*
174221 TAAAA-TTAATTTTATTTT
1 TAAAATTTAAATTTATTTT
174239 TAAAATTTAAATTTATTTT
1 TAAAATTTAAATTTATTTT
174258 AATTCAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
TAAAATTTAAATTTATTTT
Found at i:178286 original size:24 final size:24
Alignment explanation
Indices: 178254--178301 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
178244 TTCACGAGGT
*
178254 AAGTAAAAAGGAAAA-ATAAAATAG
1 AAGTAAAAAAGAAAAGA-AAAATAG
178278 AAGTAAAAAAGAAAAGAAAAATAG
1 AAGTAAAAAAGAAAAGAAAAATAG
178302 TAGGGAAGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 21 0.95
25 1 0.05
ACGTcount: A:0.73, C:0.00, G:0.17, T:0.10
Consensus pattern (24 bp):
AAGTAAAAAAGAAAAGAAAAATAG
Found at i:180902 original size:28 final size:31
Alignment explanation
Indices: 180837--180915 Score: 92
Period size: 28 Copynumber: 2.6 Consensus size: 31
180827 ATAGGGGTTT
* *
180837 TGTTATTTATATATAATATATATGGGTTTTGG
1 TGTTA-TTATATATAATATATATGGGTGTGGG
*
180869 TGTTA-TATATATAATA-A-ATGTGTGTGGG
1 TGTTATTATATATAATATATATGGGTGTGGG
*
180897 TTTTATTATATATAATATA
1 TGTTATTATATATAATATA
180916 CATGAGTTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
28 12 0.29
29 12 0.29
30 12 0.29
32 5 0.12
ACGTcount: A:0.33, C:0.00, G:0.16, T:0.51
Consensus pattern (31 bp):
TGTTATTATATATAATATATATGGGTGTGGG
Found at i:181324 original size:36 final size:36
Alignment explanation
Indices: 181262--181336 Score: 107
Period size: 36 Copynumber: 2.1 Consensus size: 36
181252 CCATGTTAGC
*
181262 TTGGTGAATTATATTATTATGGCGAACTGTATTAAT
1 TTGGTGAATTATATTATTATGACGAACTGTATTAAT
* *
181298 TTGGTGATTTGTATTCA-TATGACGAACTGTATTAAT
1 TTGGTGAATTATATT-ATTATGACGAACTGTATTAAT
181334 TTG
1 TTG
181337 TCAAACTGTG
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
36 34 0.97
37 1 0.03
ACGTcount: A:0.28, C:0.07, G:0.20, T:0.45
Consensus pattern (36 bp):
TTGGTGAATTATATTATTATGACGAACTGTATTAAT
Found at i:182035 original size:51 final size:51
Alignment explanation
Indices: 181980--182087 Score: 155
Period size: 51 Copynumber: 2.1 Consensus size: 51
181970 ATGATGGAGC
* * *
181980 ATGAACTATTATTTTGCATGAATTGTTATTCGGTATGAACTGA-TATTTCAT
1 ATGAACTATTATTTTGCATGAACTGTCATTCGGTAAGAACT-ATTATTTCAT
* *
182031 ATGAACTATTATTTTGCATGAACTGTCATTTGGTAAGAACTATTATTTTAT
1 ATGAACTATTATTTTGCATGAACTGTCATTCGGTAAGAACTATTATTTCAT
182082 ATGAAC
1 ATGAAC
182088 AAATGTTTGG
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
50 1 0.02
51 50 0.98
ACGTcount: A:0.31, C:0.10, G:0.15, T:0.44
Consensus pattern (51 bp):
ATGAACTATTATTTTGCATGAACTGTCATTCGGTAAGAACTATTATTTCAT
Found at i:182087 original size:17 final size:17
Alignment explanation
Indices: 181980--182087 Score: 83
Period size: 17 Copynumber: 6.4 Consensus size: 17
181970 ATGATGGAGC
*
181980 ATGAACTATTATTTTGC
1 ATGAACTATTATTTTGT
* * **
181997 ATGAATTGTTATTCGGT
1 ATGAACTATTATTTTGT
**
182014 ATGAACTGA-TATTTCAT
1 ATGAACT-ATTATTTTGT
*
182031 ATGAACTATTATTTTGC
1 ATGAACTATTATTTTGT
* * *
182048 ATGAACTGTCATTTGGT
1 ATGAACTATTATTTTGT
* *
182065 AAGAACTATTATTTTAT
1 ATGAACTATTATTTTGT
182082 ATGAAC
1 ATGAAC
182088 AAATGTTTGG
Statistics
Matches: 66, Mismatches: 23, Indels: 4
0.71 0.25 0.04
Matches are distributed among these distances:
16 1 0.02
17 65 0.98
ACGTcount: A:0.31, C:0.10, G:0.15, T:0.44
Consensus pattern (17 bp):
ATGAACTATTATTTTGT
Found at i:185163 original size:20 final size:20
Alignment explanation
Indices: 185140--185179 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
185130 TATATTTAGA
* *
185140 TTTTATATACTTTTTTTTAT
1 TTTTATATACATTTTATTAT
*
185160 TTTTTTATACATTTTATTAT
1 TTTTATATACATTTTATTAT
185180 GTCACATATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (20 bp):
TTTTATATACATTTTATTAT
Found at i:191703 original size:14 final size:15
Alignment explanation
Indices: 191674--191715 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
191664 ACCAAGTGTT
191674 TTTG-TTTT-AATGC
1 TTTGATTTTGAATGC
191687 TTTGATTTTGAAT-C
1 TTTGATTTTGAATGC
191701 TTTAGATTTTGAATG
1 TTT-GATTTTGAATG
191716 GATATTGCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 4 0.16
14 8 0.32
15 13 0.52
ACGTcount: A:0.21, C:0.05, G:0.17, T:0.57
Consensus pattern (15 bp):
TTTGATTTTGAATGC
Found at i:197267 original size:18 final size:17
Alignment explanation
Indices: 197240--197274 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
197230 ATGTATTTTG
197240 AAATTAAAAAATATATT
1 AAATTAAAAAATATATT
197257 AAATGTAAAAAATATATT
1 AAAT-TAAAAAATATATT
197275 TTTTAATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (17 bp):
AAATTAAAAAATATATT
Found at i:208627 original size:11 final size:11
Alignment explanation
Indices: 208605--208635 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
208595 GTTTTATTAT
208605 TATATAATATAA
1 TATAT-ATATAA
208617 TATATATATAA
1 TATATATATAA
208628 TATATATA
1 TATATATA
208636 CTTAAACATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.74
12 5 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (11 bp):
TATATATATAA
Found at i:211532 original size:23 final size:22
Alignment explanation
Indices: 211489--211532 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
211479 TTTCAAGTCA
211489 ATATTCAATTCAATTCCACACAT
1 ATATTCAATTCAATT-CACACAT
211512 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
211533 TTAACCGTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.39, C:0.23, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACAT
Found at i:211657 original size:23 final size:23
Alignment explanation
Indices: 211631--211729 Score: 162
Period size: 23 Copynumber: 4.3 Consensus size: 23
211621 ATAAGTGCCA
211631 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* * *
211654 CACTTAAATGTAGCTGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
211677 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
211700 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
211723 CACTGAT
1 CACTGAT
211730 CAATAACACT
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 70 1.00
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.22
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:217510 original size:21 final size:21
Alignment explanation
Indices: 217484--217556 Score: 110
Period size: 21 Copynumber: 3.5 Consensus size: 21
217474 AACTCTTACA
*
217484 AGCTTCTGTTCAGCTTTTTTG
1 AGCTTCTGTTCAGCTCTTTTG
*
217505 AGCTTCTGTTAAGCTCTTTTG
1 AGCTTCTGTTCAGCTCTTTTG
* *
217526 AGCTTTTGTTCAGCTCTTATG
1 AGCTTCTGTTCAGCTCTTTTG
217547 AGCTTCTGTT
1 AGCTTCTGTT
217557 GGCGTGTTCG
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 46 1.00
ACGTcount: A:0.12, C:0.19, G:0.19, T:0.49
Consensus pattern (21 bp):
AGCTTCTGTTCAGCTCTTTTG
Found at i:223343 original size:17 final size:17
Alignment explanation
Indices: 223308--223344 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
223298 ATATTTGTTC
*
223308 TATTGTTGGAATTAAAT
1 TATTGTTGGAAATAAAT
*
223325 TATTGTTGGAAATATAT
1 TATTGTTGGAAATAAAT
223342 TAT
1 TAT
223345 CGAATTTAAT
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:0.35, C:0.00, G:0.16, T:0.49
Consensus pattern (17 bp):
TATTGTTGGAAATAAAT
Found at i:223562 original size:21 final size:21
Alignment explanation
Indices: 223533--223655 Score: 129
Period size: 21 Copynumber: 5.9 Consensus size: 21
223523 GGTTGATCAA
*
223533 CTCTTACGAGCTTCTGTTCAG
1 CTCTTACGAGCTTCTGTTTAG
*
223554 CTCTCACGAGCTTCTGTTTAG
1 CTCTTACGAGCTTCTGTTTAG
** *
223575 CTCTTTTGAGCTTTTGTTTAG
1 CTCTTACGAGCTTCTGTTTAG
** *
223596 CTCTTTTGAGCTTCTGTTAAG
1 CTCTTACGAGCTTCTGTTTAG
*** *
223617 CTCTTTTAAGCTTTTGTTTAG
1 CTCTTACGAGCTTCTGTTTAG
*
223638 CTCTTATGAGCTTCTGTT
1 CTCTTACGAGCTTCTGTT
223656 GGCTTGCTTG
Statistics
Matches: 88, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 88 1.00
ACGTcount: A:0.13, C:0.21, G:0.18, T:0.48
Consensus pattern (21 bp):
CTCTTACGAGCTTCTGTTTAG
Found at i:223598 original size:42 final size:42
Alignment explanation
Indices: 223540--223655 Score: 169
Period size: 42 Copynumber: 2.8 Consensus size: 42
223530 CAACTCTTAC
* * * * *
223540 GAGCTTCTGTTCAGCTCTCACGAGCTTCTGTTTAGCTCTTTT
1 GAGCTTTTGTTTAGCTCTTATGAGCTTCTGTTAAGCTCTTTT
*
223582 GAGCTTTTGTTTAGCTCTTTTGAGCTTCTGTTAAGCTCTTTT
1 GAGCTTTTGTTTAGCTCTTATGAGCTTCTGTTAAGCTCTTTT
*
223624 AAGCTTTTGTTTAGCTCTTATGAGCTTCTGTT
1 GAGCTTTTGTTTAGCTCTTATGAGCTTCTGTT
223656 GGCTTGCTTG
Statistics
Matches: 66, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 66 1.00
ACGTcount: A:0.13, C:0.20, G:0.19, T:0.48
Consensus pattern (42 bp):
GAGCTTTTGTTTAGCTCTTATGAGCTTCTGTTAAGCTCTTTT
Found at i:223625 original size:10 final size:10
Alignment explanation
Indices: 223573--223642 Score: 50
Period size: 11 Copynumber: 6.7 Consensus size: 10
223563 GCTTCTGTTT
*
223573 AGCTCTTTTG
1 AGCTCTTTTA
* *
223583 AGCTTTTGTTT
1 AGCTCTT-TTA
*
223594 AGCTCTTTTG
1 AGCTCTTTTA
*
223604 AGCTTCTGTTA
1 AGC-TCTTTTA
223615 AGCTCTTTTA
1 AGCTCTTTTA
* *
223625 AGCTTTTGTTT
1 AGCTCTT-TTA
223636 AGCTCTT
1 AGCTCTT
223643 ATGAGCTTCT
Statistics
Matches: 47, Mismatches: 10, Indels: 5
0.76 0.16 0.08
Matches are distributed among these distances:
10 23 0.49
11 24 0.51
ACGTcount: A:0.13, C:0.17, G:0.17, T:0.53
Consensus pattern (10 bp):
AGCTCTTTTA
Found at i:226273 original size:49 final size:49
Alignment explanation
Indices: 226199--226305 Score: 171
Period size: 49 Copynumber: 2.2 Consensus size: 49
226189 CACGGCCTAG
*
226199 CACACAGTC-AAGCACATGCCTGTGTGACTCAAAACCCAAAATAACACT
1 CACACAGTCTAAGCACATGCCAGTGTGACTCAAAACCCAAAATAACACT
* *
226247 CGCACAGTCTAGGCACATGCCAGTGTGACTCAAAACCCAAAATAACACT
1 CACACAGTCTAAGCACATGCCAGTGTGACTCAAAACCCAAAATAACACT
*
226296 CACACGGTCT
1 CACACAGTCT
226306 GGACACACGC
Statistics
Matches: 53, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
48 8 0.15
49 45 0.85
ACGTcount: A:0.36, C:0.32, G:0.15, T:0.17
Consensus pattern (49 bp):
CACACAGTCTAAGCACATGCCAGTGTGACTCAAAACCCAAAATAACACT
Found at i:226322 original size:49 final size:49
Alignment explanation
Indices: 226199--226324 Score: 159
Period size: 49 Copynumber: 2.6 Consensus size: 49
226189 CACGGCCTAG
* * *
226199 CACACAGTC-AAGCACATGCCTGTGTGACTCAAAACCCAAAATAACACT
1 CACACAGTCTAGGCACACGCCAGTGTGACTCAAAACCCAAAATAACACT
* *
226247 CGCACAGTCTAGGCACATGCCAGTGTGACTCAAAACCCAAAATAACACT
1 CACACAGTCTAGGCACACGCCAGTGTGACTCAAAACCCAAAATAACACT
*
226296 CACACGGTCT-GGACACACGCTC-GTGTGAC
1 CACACAGTCTAGG-CACACGC-CAGTGTGAC
226325 CCTAAGCCTA
Statistics
Matches: 69, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
48 10 0.14
49 58 0.84
50 1 0.01
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (49 bp):
CACACAGTCTAGGCACACGCCAGTGTGACTCAAAACCCAAAATAACACT
Found at i:226360 original size:50 final size:50
Alignment explanation
Indices: 226303--226399 Score: 144
Period size: 50 Copynumber: 1.9 Consensus size: 50
226293 ACTCACACGG
226303 TCTGGACACACG-CTCGTGTGACCCT-AAGCCTAAAACAATGAGTTACACAA
1 TCTGGACACACGTC-CGTGTGACCCTAAAGCC-AAAACAATGAGTTACACAA
* *
226353 TCTGGACACATGTCCGTGTGACCCTAAATCCAAAACAATGAGTTACA
1 TCTGGACACACGTCCGTGTGACCCTAAAGCCAAAACAATGAGTTACA
226400 TGGCCTGGAC
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
50 38 0.88
51 5 0.12
ACGTcount: A:0.34, C:0.27, G:0.18, T:0.22
Consensus pattern (50 bp):
TCTGGACACACGTCCGTGTGACCCTAAAGCCAAAACAATGAGTTACACAA
Found at i:226408 original size:50 final size:49
Alignment explanation
Indices: 226304--226421 Score: 139
Period size: 50 Copynumber: 2.3 Consensus size: 49
226294 CTCACACGGT
*
226304 CTGGACACACGCTCGTGTGACCCTAAGCCTAAAACAATGAGTTACACAAT
1 CTGGACACACGC-CGTGTGACCCTAAGCCTAAAACAATGAGTTACACAAC
* * ***
226354 CTGGACACATGTCCGTGTGACCCTAAATCC-AAAACAATGAGTTACATGGC
1 CTGGACACACG-CCGTGTGACCCT-AAGCCTAAAACAATGAGTTACACAAC
226404 CTGGACACACGCCCGTGT
1 CTGGACACACG-CCGTGT
226422 ACCTAGCTCA
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
50 53 0.91
51 5 0.09
ACGTcount: A:0.31, C:0.29, G:0.20, T:0.20
Consensus pattern (49 bp):
CTGGACACACGCCGTGTGACCCTAAGCCTAAAACAATGAGTTACACAAC
Found at i:228441 original size:41 final size:41
Alignment explanation
Indices: 228384--228468 Score: 152
Period size: 41 Copynumber: 2.1 Consensus size: 41
228374 ACATACAACT
*
228384 TAGCCAATTTCTGAAGCGAATAATCAGTCCTGACTGGAAGA
1 TAGCCAATTTCTGAAGCAAATAATCAGTCCTGACTGGAAGA
*
228425 TAGCCAATTTTTGAAGCAAATAATCAGTCCTGACTGGAAGA
1 TAGCCAATTTCTGAAGCAAATAATCAGTCCTGACTGGAAGA
228466 TAG
1 TAG
228469 TGAGCAAACT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (41 bp):
TAGCCAATTTCTGAAGCAAATAATCAGTCCTGACTGGAAGA
Found at i:244418 original size:10 final size:10
Alignment explanation
Indices: 244403--244429 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
244393 AGGAGAAGAG
244403 AAAGAAAAAA
1 AAAGAAAAAA
244413 AAAGAAAAAA
1 AAAGAAAAAA
244423 AAAGAAA
1 AAAGAAA
244430 GTTCAAAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (10 bp):
AAAGAAAAAA
Found at i:255220 original size:27 final size:27
Alignment explanation
Indices: 255182--255238 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
255172 CTTGAGGTAG
**
255182 AAAATATTAAATTGATT-TTATTTTATT
1 AAAATATTAAATAAATTATTATTTT-TT
255209 AAAA-ATTAAAATAAATTATTATTTTTT
1 AAAATATT-AAATAAATTATTATTTTTT
255236 AAA
1 AAA
255239 TAAGAAATTC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
26 3 0.12
27 16 0.62
28 7 0.27
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (27 bp):
AAAATATTAAATAAATTATTATTTTTT
Found at i:258243 original size:15 final size:15
Alignment explanation
Indices: 258223--258252 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
258213 ATTTTTTCAA
*
258223 TTCTTTTTATTTTAT
1 TTCTTTTAATTTTAT
258238 TTCTTTTAATTTTAT
1 TTCTTTTAATTTTAT
258253 CCTTTAAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.77
Consensus pattern (15 bp):
TTCTTTTAATTTTAT
Found at i:266075 original size:21 final size:20
Alignment explanation
Indices: 266051--266097 Score: 60
Period size: 22 Copynumber: 2.3 Consensus size: 20
266041 AAATTGAATT
266051 TTAAAATTTGAAATATAAAAA
1 TTAAAATTTGAAA-ATAAAAA
*
266072 TTAAAAATTTTAAAATAAAAA
1 TT-AAAATTTGAAAATAAAAA
266093 -TAAAA
1 TTAAAA
266098 AATAATAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 4 0.17
20 1 0.04
21 9 0.38
22 10 0.42
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (20 bp):
TTAAAATTTGAAAATAAAAA
Found at i:266098 original size:21 final size:22
Alignment explanation
Indices: 266053--266100 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 22
266043 ATTGAATTTT
*
266053 AAAATTTGAAATATAAAAATTA
1 AAAATTTGAAATATAAAAATAA
*
266075 AAAATTTTAAA-ATAAAAATAA
1 AAAATTTGAAATATAAAAATAA
266096 AAAAT
1 AAAAT
266101 AATAAATTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 14 0.58
22 10 0.42
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (22 bp):
AAAATTTGAAATATAAAAATAA
Found at i:266106 original size:21 final size:21
Alignment explanation
Indices: 266065--266106 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
266055 AATTTGAAAT
* **
266065 ATAAAAATTAAAAATTTTAAA
1 ATAAAAATAAAAAATAATAAA
266086 ATAAAAATAAAAAATAATAAA
1 ATAAAAATAAAAAATAATAAA
266107 TTTCAAAATA
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:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (21 bp):
ATAAAAATAAAAAATAATAAA
Found at i:266704 original size:9 final size:9
Alignment explanation
Indices: 266687--266722 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
266677 ACCGAAGAAA
*
266687 CATCATCCT
1 CATCGTCCT
266696 CATCGTCCT
1 CATCGTCCT
*
266705 CGTCGTCCT
1 CATCGTCCT
266714 CATCGTCCT
1 CATCGTCCT
266723 TTTTGCAACC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.11, C:0.44, G:0.11, T:0.33
Consensus pattern (9 bp):
CATCGTCCT
Found at i:269485 original size:3 final size:3
Alignment explanation
Indices: 269479--269504 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
269469 ATATTAAAAA
269479 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
269505 AGAAAGCCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:271648 original size:13 final size:14
Alignment explanation
Indices: 271609--271655 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
271599 TACGGGCTTA
*
271609 GGGAAATGGGAAAT
1 GGGAAAGGGGAAAT
*
271623 GGGAAATGGGAAAT
1 GGGAAAGGGGAAAT
*
271637 GGG-GAGGGGAAAT
1 GGGAAAGGGGAAAT
*
271650 GAGAAA
1 GGGAAA
271656 TTTATTTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
13 10 0.36
14 18 0.64
ACGTcount: A:0.43, C:0.00, G:0.47, T:0.11
Consensus pattern (14 bp):
GGGAAAGGGGAAAT
Found at i:271648 original size:20 final size:21
Alignment explanation
Indices: 271609--271656 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
271599 TACGGGCTTA
*
271609 GGGAAATGGGAAATGGGAAAT
1 GGGAAATGGGAAAGGGGAAAT
*
271630 GGGAAATGGG-GAGGGGAAAT
1 GGGAAATGGGAAAGGGGAAAT
*
271650 GAGAAAT
1 GGGAAAT
271657 TTATTTTTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 14 0.58
21 10 0.42
ACGTcount: A:0.42, C:0.00, G:0.46, T:0.12
Consensus pattern (21 bp):
GGGAAATGGGAAAGGGGAAAT
Found at i:271656 original size:7 final size:7
Alignment explanation
Indices: 271609--271639 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
271599 TACGGGCTTA
271609 GGGAAAT
1 GGGAAAT
271616 GGGAAAT
1 GGGAAAT
271623 GGGAAAT
1 GGGAAAT
271630 GGGAAAT
1 GGGAAAT
271637 GGG
1 GGG
271640 GAGGGGAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.39, C:0.00, G:0.48, T:0.13
Consensus pattern (7 bp):
GGGAAAT
Found at i:275134 original size:45 final size:45
Alignment explanation
Indices: 275070--275156 Score: 140
Period size: 45 Copynumber: 1.9 Consensus size: 45
275060 ACGAACTTAT
*
275070 TTAGATTATCTACTGAAGTAAGTTTTCTTTCTCGCAATGTAATAG
1 TTAGATTATCTACTGAAGTAAGTTGTCTTTCTCGCAATGTAATAG
*
275115 TTAGATTATCTA-TCGAAGTAAGTTGTCTTTCTTGCAATGTAA
1 TTAGATTATCTACT-GAAGTAAGTTGTCTTTCTCGCAATGTAA
275157 ATGTTATTAC
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
44 1 0.03
45 38 0.97
ACGTcount: A:0.29, C:0.13, G:0.16, T:0.43
Consensus pattern (45 bp):
TTAGATTATCTACTGAAGTAAGTTGTCTTTCTCGCAATGTAATAG
Found at i:277851 original size:117 final size:119
Alignment explanation
Indices: 277544--277862 Score: 358
Period size: 117 Copynumber: 2.7 Consensus size: 119
277534 AATAAAAATT
* * * *
277544 AAAACTCTCAAAAAATTCAACACAATGAGACCATCTATTAAGTACATAAAAAACAAAAAAAAATA
1 AAAA-TCTCAAAAAAATAAACACAATGAGACCATTTATTAAGTAAATAAAAAAC--AAAAAAATA
* *
277609 ATGTTAAAAAAAACACAAACATACTTGCTTCCTTTCTTCCAAACACCCTTCCCACAAAAT
63 ATATT---AAAAACACAAACATACTTGCTTCCTTTCTTCCAAACACCCTTCCCACAAAAC
* * * *
277669 AAACTCTCAAAAAAATAAACACAATGAGACTATTTGTTAAGTAAATAAAAAACAAAAAAACAATA
1 AAAATCTCAAAAAAATAAACACAATGAGACCATTTATTAAGTAAATAAAAAACAAAAAAATAATA
* * * * * * *
277734 TT-AAAAGA-AAAGATACTTGCTTCCTTTCTTCCTAACATCCTTTCTACAATACC
66 TTAAAAACACAAACATACTTGCTTCCTTTCTTCCAAACACCCTTCCCACAA-AAC
* * *
277787 AAAATCTCAAAAAAAT-AAGACAATGGGACCATTTATTAAGTAAATAAAAAACAAAAAATTAATA
1 AAAATCTCAAAAAAATAAACACAATGAGACCATTTATTAAGTAAATAAAAAACAAAAAAATAATA
*
277851 TTCAAAAC-CAAA
66 TTAAAAACACAAA
277863 AAAAAAACCT
Statistics
Matches: 166, Mismatches: 25, Indels: 13
0.81 0.12 0.06
Matches are distributed among these distances:
117 80 0.48
118 28 0.17
122 12 0.07
124 43 0.26
125 3 0.02
ACGTcount: A:0.52, C:0.19, G:0.05, T:0.24
Consensus pattern (119 bp):
AAAATCTCAAAAAAATAAACACAATGAGACCATTTATTAAGTAAATAAAAAACAAAAAAATAATA
TTAAAAACACAAACATACTTGCTTCCTTTCTTCCAAACACCCTTCCCACAAAAC
Found at i:281403 original size:22 final size:21
Alignment explanation
Indices: 281375--281441 Score: 64
Period size: 22 Copynumber: 3.1 Consensus size: 21
281365 CGCTGCCAGT
281375 TAACAGAACGACTAAAAGCCA
1 TAACAGAACGACTAAAAGCCA
* *
281396 TAAGCAGAAAGAC-AATAAGCCT
1 TAA-CAGAACGACTAA-AAGCCA
* *
281418 TGAACAGAACGGCTACAAGCCA
1 T-AACAGAACGACTAAAAGCCA
281440 TA
1 TA
281442 CACTTTCTCC
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
21 6 0.17
22 27 0.75
23 3 0.08
ACGTcount: A:0.48, C:0.22, G:0.18, T:0.12
Consensus pattern (21 bp):
TAACAGAACGACTAAAAGCCA
Found at i:281620 original size:26 final size:27
Alignment explanation
Indices: 281569--281621 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
281559 ACTATAGCAC
* *
281569 AAATCAGTCATTTACCCTCGAGGGGCA
1 AAATCAGTCATTTACCCTAGAAGGGCA
*
281596 AAAT-AGTCATTTACCCTATAAGGGCA
1 AAATCAGTCATTTACCCTAGAAGGGCA
281622 TTACGATTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 19 0.83
27 4 0.17
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.25
Consensus pattern (27 bp):
AAATCAGTCATTTACCCTAGAAGGGCA
Found at i:287085 original size:20 final size:20
Alignment explanation
Indices: 287043--287085 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
287033 TATAACTTAG
* **
287043 TAAGTTCGTCGATTTAATGA
1 TAAGTTCGTCGAATTAAACA
287063 TAAGTTCGTCGAATTAAACA
1 TAAGTTCGTCGAATTAAACA
287083 TAA
1 TAA
287086 TAATTCAAAT
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:0.37, C:0.12, G:0.16, T:0.35
Consensus pattern (20 bp):
TAAGTTCGTCGAATTAAACA
Found at i:289702 original size:5 final size:5
Alignment explanation
Indices: 289692--289724 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
289682 ATAATGCAAT
289692 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAA
289725 GCTCTAATAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:298712 original size:43 final size:42
Alignment explanation
Indices: 298665--298802 Score: 109
Period size: 43 Copynumber: 3.2 Consensus size: 42
298655 TCTTAGACGT
** *
298665 GGTCTTACATGTAATCAAATAACGATGCCATTGTCCCAGACAA
1 GGTCTTACACATAATCAAAT-ACGATGCCAATGTCCCAGACAA
* * *
298708 GGTCTTACGCATAATCATATATGATGCCAATGTCCCAGAC-A
1 GGTCTTACACATAATCAAATACGATGCCAATGTCCCAGACAA
* * * * * **
298749 TGACCTACACGTAAATCTCAAAT-CGATGCCAATGTCCTAGACGT
1 GGTCTTACACAT-AA--TCAAATACGATGCCAATGTCCCAGACAA
298793 GGTCTTACAC
1 GGTCTTACAC
298803 GATATCACAT
Statistics
Matches: 73, Mismatches: 18, Indels: 7
0.74 0.18 0.07
Matches are distributed among these distances:
41 8 0.11
42 20 0.27
43 33 0.45
44 12 0.16
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (42 bp):
GGTCTTACACATAATCAAATACGATGCCAATGTCCCAGACAA
Found at i:302713 original size:50 final size:50
Alignment explanation
Indices: 302659--302795 Score: 206
Period size: 50 Copynumber: 2.7 Consensus size: 50
302649 CGGTGCCCAT
* *
302659 GCCATGTCCTAGACATGGTCTTACAAGGGACCTCTCATCTTGGA-ACCAAC
1 GCCATGTCCCAGACATGGTCTTACAAGGGACCTCTCATC-TCGATACCAAC
*
302709 GCCATGTCCCAGACATGGTCTTACGAGGGACCTCTCATCTCGATACCAAC
1 GCCATGTCCCAGACATGGTCTTACAAGGGACCTCTCATCTCGATACCAAC
*
302759 GCCATGTCCCA-AGCATGGTCTTACATGGGACCTCTCA
1 GCCATGTCCCAGA-CATGGTCTTACAAGGGACCTCTCA
302796 CAACCTCAGT
Statistics
Matches: 80, Mismatches: 5, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
49 4 0.05
50 76 0.95
ACGTcount: A:0.24, C:0.32, G:0.20, T:0.23
Consensus pattern (50 bp):
GCCATGTCCCAGACATGGTCTTACAAGGGACCTCTCATCTCGATACCAAC
Found at i:309932 original size:20 final size:20
Alignment explanation
Indices: 309907--309945 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
309897 TACTTTCTTC
309907 TTTACTTACTCT-CTTACTTG
1 TTTACTTACT-TGCTTACTTG
309927 TTTACTTACTTGCTTACTT
1 TTTACTTACTTGCTTACTT
309946 AAATAACTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.15, C:0.23, G:0.05, T:0.56
Consensus pattern (20 bp):
TTTACTTACTTGCTTACTTG
Found at i:311759 original size:50 final size:50
Alignment explanation
Indices: 311692--311792 Score: 193
Period size: 50 Copynumber: 2.0 Consensus size: 50
311682 ACTGTTTAAA
311692 TCGTTTAATAGTAACCTGATAACCATTCCTTTTGACAATGGATTAAATGT
1 TCGTTTAATAGTAACCTGATAACCATTCCTTTTGACAATGGATTAAATGT
*
311742 TCGTTTAATAGTAACCTGATAACCGTTCCTTTTGACAATGGATTAAATGT
1 TCGTTTAATAGTAACCTGATAACCATTCCTTTTGACAATGGATTAAATGT
311792 T
1 T
311793 AATCATGATG
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.39
Consensus pattern (50 bp):
TCGTTTAATAGTAACCTGATAACCATTCCTTTTGACAATGGATTAAATGT
Found at i:327245 original size:19 final size:19
Alignment explanation
Indices: 327201--327246 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
327191 TTTTTTAGGA
327201 GGGAAGTTAGGGATATGGG
1 GGGAAGTTAGGGATATGGG
* *
327220 AGAAAGTTAGGGGAT-TGGG
1 GGGAAGTTA-GGGATATGGG
327239 GGGAAGTT
1 GGGAAGTT
327247 TATAAAAATC
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 17 0.77
20 5 0.23
ACGTcount: A:0.28, C:0.00, G:0.50, T:0.22
Consensus pattern (19 bp):
GGGAAGTTAGGGATATGGG
Found at i:331813 original size:41 final size:43
Alignment explanation
Indices: 331731--332029 Score: 295
Period size: 43 Copynumber: 7.0 Consensus size: 43
331721 ACGGGTTATA
*
331731 CTTCAGTTTATCCGATGATGCATTGTGTGTGCCAGTATATTTTG
1 CTTCAGTTTATCCGATGATGCACTGTGTGTGCCAGTATA-TTTG
* *
331775 -TTCATTTTATCCGATGATGCACTGTGTG-G-CAGGATATTTG
1 CTTCAGTTTATCCGATGATGCACTGTGTGTGCCAGTATATTTG
* **
331815 CTT-TGATTTATTTGATGATGCACTGTGTGTGCCAGTATATTTG
1 CTTCAG-TTTATCCGATGATGCACTGTGTGTGCCAGTATATTTG
* *
331858 CTTCAGTATATCTGATGATGCACTGTGTGTGCCAGTATATTTG
1 CTTCAGTTTATCCGATGATGCACTGTGTGTGCCAGTATATTTG
* * * * * *
331901 CTTCGGTATATCCGATAATGCACTATGTTTGCCAATATATTTG
1 CTTCAGTTTATCCGATGATGCACTGTGTGTGCCAGTATATTTG
* * * * *
331944 TTTC-GATATATCTGATGATGCACTGTGTGTGCTAGTATATTTT
1 CTTCAG-TTTATCCGATGATGCACTGTGTGTGCCAGTATATTTG
* * * * ** *
331987 CTTTAGGTTATTCGACGATGCACT-TGCATGCCAGTATAATTG
1 CTTCAGTTTATCCGATGATGCACTGTGTGTGCCAGTATATTTG
332029 C
1 C
332030 GTAGGTTCAT
Statistics
Matches: 211, Mismatches: 37, Indels: 16
0.80 0.14 0.06
Matches are distributed among these distances:
40 4 0.02
41 29 0.14
42 17 0.08
43 159 0.75
44 2 0.01
ACGTcount: A:0.21, C:0.16, G:0.22, T:0.41
Consensus pattern (43 bp):
CTTCAGTTTATCCGATGATGCACTGTGTGTGCCAGTATATTTG
Found at i:339568 original size:9 final size:9
Alignment explanation
Indices: 339556--339589 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
339546 CTTGAGAAAA
*
339556 TTGATAGAG
1 TTGAGAGAG
339565 TTGAGAGAG
1 TTGAGAGAG
*
339574 TTGAGAGAA
1 TTGAGAGAG
339583 TTGAGAG
1 TTGAGAG
339590 TTTAGAAAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.38, T:0.26
Consensus pattern (9 bp):
TTGAGAGAG
Found at i:340064 original size:12 final size:13
Alignment explanation
Indices: 340047--340079 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
340037 AAAGCTTCAT
340047 TTATTATTTAT-A
1 TTATTATTTATAA
340059 TTATTATTTATAA
1 TTATTATTTATAA
340072 TTA-TATTT
1 TTATTATTT
340080 GTTACATTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 16 0.80
13 4 0.20
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (13 bp):
TTATTATTTATAA
Found at i:351386 original size:21 final size:21
Alignment explanation
Indices: 351361--351414 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
351351 ACTAAACTGA
351361 TGTCGCGACATAGACTGAGGG
1 TGTCGCGACATAGACTGAGGG
*
351382 TGTCGCGACACAGACTGAGGG
1 TGTCGCGACATAGACTGAGGG
351403 TGTCGCGACATA
1 TGTCGCGACATA
351415 CCCCTAAAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.24, C:0.22, G:0.35, T:0.19
Consensus pattern (21 bp):
TGTCGCGACATAGACTGAGGG
Found at i:360790 original size:23 final size:23
Alignment explanation
Indices: 360760--360810 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
360750 CTCAATAGAC
360760 CACTAGGTCATTGATTCGGGAGT
1 CACTAGGTCATTGATTCGGGAGT
*
360783 CACTAGGTCATTGATTTGGGAGT
1 CACTAGGTCATTGATTCGGGAGT
360806 CACTA
1 CACTA
360811 ATCTTAGAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.31
Consensus pattern (23 bp):
CACTAGGTCATTGATTCGGGAGT
Found at i:363828 original size:34 final size:34
Alignment explanation
Indices: 363785--363853 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
363775 CTATAGAAGA
363785 TGACAACCTATTTGTTTTTCTTTTAGTTTAATTT
1 TGACAACCTATTTGTTTTTCTTTTAGTTTAATTT
363819 TGACAACCTATTTGTTTTTCTTTTAGTTTAATTT
1 TGACAACCTATTTGTTTTTCTTTTAGTTTAATTT
363853 T
1 T
363854 ACTTAATTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.20, C:0.12, G:0.09, T:0.59
Consensus pattern (34 bp):
TGACAACCTATTTGTTTTTCTTTTAGTTTAATTT
Found at i:367113 original size:34 final size:34
Alignment explanation
Indices: 367042--367115 Score: 87
Period size: 34 Copynumber: 2.2 Consensus size: 34
367032 AATGCCAATA
* ** *
367042 ATCAGTAGGGCCTTTGCCCAATTTCAGTAATAGT
1 ATCAGTAGGGCCTTGGCCCAATAACAGTAACAGT
*
367076 ATCAGTGGGGCCTTGGCCC-ATAACAGTAACAGAT
1 ATCAGTAGGGCCTTGGCCCAATAACAGTAACAG-T
367110 ATCAGT
1 ATCAGT
367116 CATGCAGTGA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
33 10 0.29
34 24 0.71
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.27
Consensus pattern (34 bp):
ATCAGTAGGGCCTTGGCCCAATAACAGTAACAGT
Found at i:367597 original size:27 final size:26
Alignment explanation
Indices: 367566--367829 Score: 264
Period size: 27 Copynumber: 9.8 Consensus size: 26
367556 TCATCTCCTA
*
367566 AGGGTATAATAGTCATTTTACCCTATG
1 AGGGTAT-TTAGTCATTTTACCCTATG
*
367593 GGGGTATTTTAGTCATTTTACCCTATG
1 AGGGTA-TTTAGTCATTTTACCCTATG
* *
367620 AGGGTATTTCGGTCATTCTACCCTATG
1 AGGGTATTT-AGTCATTTTACCCTATG
*
367647 GGGGTATTTCTA-TCATTTTACCCTATG
1 AGGGTA-TT-TAGTCATTTTACCCTATG
* *
367674 AAGGTATTTTAGTCATTTTACCCTGTG
1 AGGGTA-TTTAGTCATTTTACCCTATG
* *
367701 -GAGGTATTTCGATCATTTTACCCTATA
1 AG-GGTATTTAG-TCATTTTACCCTATG
* *
367728 AGGGTATTTCGGTCATTTTACCTTATG
1 AGGGTATTT-AGTCATTTTACCCTATG
* *
367755 AGAGTATTTCGGTCATTTTACCCTATG
1 AGGGTATTT-AGTCATTTTACCCTATG
*
367782 AGGGTATTTTGGTCATTTTACCCTATG
1 AGGGTA-TTTAGTCATTTTACCCTATG
*
367809 -GGGTATTTCGATCATTTTACC
1 AGGGTATTTAG-TCATTTTACC
367830 TATTTTGGGG
Statistics
Matches: 204, Mismatches: 22, Indels: 23
0.82 0.09 0.09
Matches are distributed among these distances:
25 4 0.02
26 24 0.12
27 167 0.82
28 8 0.04
29 1 0.00
ACGTcount: A:0.21, C:0.17, G:0.20, T:0.42
Consensus pattern (26 bp):
AGGGTATTTAGTCATTTTACCCTATG
Found at i:367624 original size:54 final size:53
Alignment explanation
Indices: 367577--367829 Score: 298
Period size: 54 Copynumber: 4.7 Consensus size: 53
367567 GGGTATAATA
367577 GTCATTTTACCCTATGGGGGTATTTTAGTCATTTTACCCTATGAGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTTAGTCATTTTACCCTATGAGGGTATTT-G
* * *
367631 GTCATTCTACCCTATGGGGGTATTTCTA-TCATTTTACCCTATGAAGGTATTTTA
1 GTCATTTTACCCTATGGGGGTATTT-TAGTCATTTTACCCTATGAGGGTA-TTTG
* * * *
367685 GTCATTTTACCCTGTGGAGGTA-TTTCGATCATTTTACCCTATAAGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTTAG-TCATTTTACCCTATGAGGGTATTT-G
* * * **
367739 GTCATTTTACCTTATGAGAGTATTTCGGTCATTTTACCCTATGAGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTTAGTCATTTTACCCTATGAGGGTA-TTTG
*
367793 GTCATTTTACCCTAT-GGGGTA-TTTCGATCATTTTACC
1 GTCATTTTACCCTATGGGGGTATTTTAG-TCATTTTACC
367830 TATTTTGGGG
Statistics
Matches: 168, Mismatches: 23, Indels: 17
0.81 0.11 0.08
Matches are distributed among these distances:
52 4 0.02
53 19 0.11
54 134 0.80
55 11 0.07
ACGTcount: A:0.20, C:0.18, G:0.19, T:0.43
Consensus pattern (53 bp):
GTCATTTTACCCTATGGGGGTATTTTAGTCATTTTACCCTATGAGGGTATTTG
Found at i:367685 original size:81 final size:79
Alignment explanation
Indices: 367578--367829 Score: 344
Period size: 81 Copynumber: 3.1 Consensus size: 79
367568 GGTATAATAG
* *
367578 TCATTTTACCCTATGGGGGTATTTTAGTCATTTTACCCTATGAGGGTATTTCGGTCATTCTACCC
1 TCATTTTACCCTAT-GAGGTATTTTAGTCATTTTACCCTATGAGGGTATTTCGGTCATTTTACCC
*
367643 TATGGGGGTATTTCTA
65 TAT-GGGGTATTTCGA
* *
367659 TCATTTTACCCTATGAAGGTATTTTAGTCATTTTACCCTGTG-GAGGTATTTCGATCATTTTACC
1 TCATTTTACCCTATG-AGGTATTTTAGTCATTTTACCCTATGAG-GGTATTTCGGTCATTTTACC
* *
367723 CTATAAGGGTATTTCGG
64 CTAT-GGGGTATTTCGA
* ** *
367740 TCATTTTACCTTATGAGAGTATTTCGGTCATTTTACCCTATGAGGGTATTTTGGTCATTTTACCC
1 TCATTTTACCCTATGAG-GTATTTTAGTCATTTTACCCTATGAGGGTATTTCGGTCATTTTACCC
367805 TATGGGGTATTTCGA
65 TATGGGGTATTTCGA
367820 TCATTTTACC
1 TCATTTTACC
367830 TATTTTGGGG
Statistics
Matches: 151, Mismatches: 16, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
80 24 0.16
81 126 0.83
82 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.19, T:0.43
Consensus pattern (79 bp):
TCATTTTACCCTATGAGGTATTTTAGTCATTTTACCCTATGAGGGTATTTCGGTCATTTTACCCT
ATGGGGTATTTCGA
Found at i:367968 original size:27 final size:27
Alignment explanation
Indices: 367938--368200 Score: 259
Period size: 27 Copynumber: 9.7 Consensus size: 27
367928 CCCAATATTT
367938 GTAAAATGACCGAAATACCCTCGATGG
1 GTAAAATGACCGAAATACCCTCGATGG
* *
367965 GTAAAATAACCAAAATACCCTCGATGG
1 GTAAAATGACCGAAATACCCTCGATGG
* * *
367992 GTAAAATTATCGAAATACCC-CTAATGG
1 GTAAAATGACCGAAATACCCTC-GATGG
*
368019 GTAAAATGACTGAAATACCCTCGATGG
1 GTAAAATGACCGAAATACCCTCGATGG
* *
368046 GTAAAATGGCTGAAATACCCTCGATGG
1 GTAAAATGACCGAAATACCCTCGATGG
** *
368073 GTAAAATGACTAAAATACCCTC-ATAAG
1 GTAAAATGACCGAAATACCCTCGAT-GG
* * *
368100 GTAAAATGATCGAAATTCCC-CTG-TAAG
1 GTAAAATGACCGAAATACCCTC-GAT-GG
* * *
368127 GTAAAATGACCGTAATGCCCTTG-TAGG
1 GTAAAATGACCGAAATACCCTCGAT-GG
*
368154 GTAAAATGACCGTAATACCCTC-ATAGG
1 GTAAAATGACCGAAATACCCTCGAT-GG
*
368181 GTTAAATGACCGAAATACCC
1 GTAAAATGACCGAAATACCC
368201 CTATAAGGTA
Statistics
Matches: 202, Mismatches: 27, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
26 4 0.02
27 197 0.98
28 1 0.00
ACGTcount: A:0.38, C:0.20, G:0.19, T:0.22
Consensus pattern (27 bp):
GTAAAATGACCGAAATACCCTCGATGG
Found at i:368214 original size:27 final size:27
Alignment explanation
Indices: 367938--368243 Score: 232
Period size: 27 Copynumber: 11.4 Consensus size: 27
367928 CCCAATATTT
*
367938 GTAAAATGACCGAAATACCCTCGAT-GG
1 GTAAAATGACCGAAATACCC-CTATAGG
* * *
367965 GTAAAATAACCAAAATACCCTCGAT-GG
1 GTAAAATGACCGAAATACCC-CTATAGG
* *
367992 GTAAAATTATCGAAATACCCCTA-ATGG
1 GTAAAATGACCGAAATACCCCTATA-GG
* *
368019 GTAAAATGACTGAAATACCCTCGAT-GG
1 GTAAAATGACCGAAATACCC-CTATAGG
* * *
368046 GTAAAATGGCTGAAATACCCTCGAT-GG
1 GTAAAATGACCGAAATACCC-CTATAGG
** *
368073 GTAAAATGACTAAAATA-CCCTCATAAG
1 GTAAAATGACCGAAATACCCCT-ATAGG
* * * *
368100 GTAAAATGATCGAAATTCCCCTGTAAG
1 GTAAAATGACCGAAATACCCCTATAGG
* * * *
368127 GTAAAATGACCGTAATGCCCTTGTAGG
1 GTAAAATGACCGAAATACCCCTATAGG
*
368154 GTAAAATGACCGTAATA-CCCTCATAGG
1 GTAAAATGACCGAAATACCCCT-ATAGG
* *
368181 GTTAAATGACCGAAATACCCCTATAAG
1 GTAAAATGACCGAAATACCCCTATAGG
* * * *
368208 GTAAAATGAACGTAATGCCCCTAGAGG
1 GTAAAATGACCGAAATACCCCTATAGG
368235 GT-AAATGAC
1 GTAAAATGAC
368244 TATTTTGCCC
Statistics
Matches: 232, Mismatches: 38, Indels: 19
0.80 0.13 0.07
Matches are distributed among these distances:
25 1 0.00
26 15 0.06
27 206 0.89
28 10 0.04
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.22
Consensus pattern (27 bp):
GTAAAATGACCGAAATACCCCTATAGG
Found at i:368276 original size:26 final size:25
Alignment explanation
Indices: 368223--368323 Score: 82
Period size: 24 Copynumber: 4.0 Consensus size: 25
368213 ATGAACGTAA
*
368223 TGCCCCTAGAGGGTAAATGACT-ATTT
1 TGCCCCT-GAGTGTAAATGACTGA-TT
*
368249 TGCCCCTCGAGTGTAAATGATTGATT
1 TGCCCCT-GAGTGTAAATGACTGATT
* *
368275 TGTCCGTGA-TGTAAATGACTGATT
1 TGCCCCTGAGTGTAAATGACTGATT
* ** *
368299 TGTCTGTGA-TTTAAATGACTGATT
1 TGCCCCTGAGTGTAAATGACTGATT
368323 T
1 T
368324 ATCTGTGATT
Statistics
Matches: 66, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
24 37 0.56
25 2 0.03
26 26 0.39
27 1 0.02
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.38
Consensus pattern (25 bp):
TGCCCCTGAGTGTAAATGACTGATT
Found at i:368292 original size:24 final size:24
Alignment explanation
Indices: 368260--368370 Score: 118
Period size: 24 Copynumber: 4.6 Consensus size: 24
368250 GCCCCTCGAG
* *
368260 TGTAAATGATTGATTTGTCCGTGA
1 TGTAAATGACTGATTTGTCTGTGA
368284 TGTAAATGACTGATTTGTCTGTGA
1 TGTAAATGACTGATTTGTCTGTGA
* *
368308 TTTAAATGACTGATTTATCTGTGA
1 TGTAAATGACTGATTTGTCTGTGA
*
368332 TTGGT--ATGACTGATTTGTCTCTGA
1 -T-GTAAATGACTGATTTGTCTGTGA
* **
368356 TTTGTATGACTGATT
1 TGTAAATGACTGATT
368371 CTGAGCATGG
Statistics
Matches: 75, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
22 1 0.01
23 1 0.01
24 71 0.95
25 1 0.01
26 1 0.01
ACGTcount: A:0.23, C:0.09, G:0.23, T:0.45
Consensus pattern (24 bp):
TGTAAATGACTGATTTGTCTGTGA
Found at i:368322 original size:48 final size:48
Alignment explanation
Indices: 368262--368370 Score: 132
Period size: 48 Copynumber: 2.3 Consensus size: 48
368252 CCCTCGAGTG
* * *
368262 TAAATGATTGATTTGTCCGTGA-T-GTAAATGACTGATTTGTCTGTGATT
1 TAAATGACTGATTTATCCGTGATTGGT--ATGACTGATTTGTCTCTGATT
*
368310 TAAATGACTGATTTATCTGTGATTGGTATGACTGATTTGTCTCTGATT
1 TAAATGACTGATTTATCCGTGATTGGTATGACTGATTTGTCTCTGATT
**
368358 TGTATGACTGATT
1 TAAATGACTGATT
368371 CTGAGCATGG
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
48 50 0.94
49 1 0.02
50 2 0.04
ACGTcount: A:0.24, C:0.09, G:0.22, T:0.45
Consensus pattern (48 bp):
TAAATGACTGATTTATCCGTGATTGGTATGACTGATTTGTCTCTGATT
Found at i:368370 original size:13 final size:13
Alignment explanation
Indices: 368289--368370 Score: 59
Period size: 11 Copynumber: 6.8 Consensus size: 13
368279 CGTGATGTAA
368289 ATGACTGATTTGT
1 ATGACTGATTTGT
* **
368302 CTG--TGATTTAA
1 ATGACTGATTTGT
*
368313 ATGACTGATTTAT
1 ATGACTGATTTGT
* *
368326 CTG--TGATTGGT
1 ATGACTGATTTGT
368337 ATGACTGATTTGT
1 ATGACTGATTTGT
*
368350 CT--CTGATTTGT
1 ATGACTGATTTGT
368361 ATGACTGATT
1 ATGACTGATT
368371 CTGAGCATGG
Statistics
Matches: 51, Mismatches: 12, Indels: 12
0.68 0.16 0.16
Matches are distributed among these distances:
11 26 0.51
13 25 0.49
ACGTcount: A:0.22, C:0.10, G:0.22, T:0.46
Consensus pattern (13 bp):
ATGACTGATTTGT
Found at i:368629 original size:32 final size:32
Alignment explanation
Indices: 368542--368680 Score: 129
Period size: 32 Copynumber: 4.4 Consensus size: 32
368532 GCTGTGATGC
*
368542 TACTGATGGCTTTGTGCCTATCATATTATCGT
1 TACTGATGGCTTTGTGCCTATCATATTACCGT
* * ** *
368574 TACCGATGGCATTGTATCGATCATATTACCGT
1 TACTGATGGCTTTGTGCCTATCATATTACCGT
* ** *
368606 TACTGATGG-TTGTGTGCCTATCATATCATTGC
1 TACTGATGGCTT-TGTGCCTATCATATTACCGT
* * *
368638 TACTAATGGCTTTGTGCCAATCATATTACTG-
1 TACTGATGGCTTTGTGCCTATCATATTACCGT
*
368669 TACTTATGGCTT
1 TACTGATGGCTT
368681 GTAGCAATTC
Statistics
Matches: 85, Mismatches: 20, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
31 12 0.14
32 71 0.84
33 2 0.02
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.40
Consensus pattern (32 bp):
TACTGATGGCTTTGTGCCTATCATATTACCGT
Found at i:368647 original size:64 final size:64
Alignment explanation
Indices: 368542--368680 Score: 156
Period size: 64 Copynumber: 2.2 Consensus size: 64
368532 GCTGTGATGC
* * * * *
368542 TACTGATGGCTTTGTGCCTATCATATTATCGTTACCGATGGCATTGTATCGATCATATTACCGT
1 TACTGATGGCTTTGTGCCTATCATATCATCGCTACCAATGGCATTGTACCAATCATATTACCGT
* * * * *
368606 TACTGATGG-TTGTGTGCCTATCATATCATTGCTACTAATGGCTTTGTGCCAATCATATTACTG-
1 TACTGATGGCTT-TGTGCCTATCATATCATCGCTACCAATGGCATTGTACCAATCATATTACCGT
*
368669 TACTTATGGCTT
1 TACTGATGGCTT
368681 GTAGCAATTC
Statistics
Matches: 62, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
63 10 0.16
64 52 0.84
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.40
Consensus pattern (64 bp):
TACTGATGGCTTTGTGCCTATCATATCATCGCTACCAATGGCATTGTACCAATCATATTACCGT
Found at i:372003 original size:57 final size:57
Alignment explanation
Indices: 371923--372034 Score: 163
Period size: 57 Copynumber: 1.9 Consensus size: 57
371913 AATAGTGAAG
* *
371923 TGGAGAAATAGGAAACATTTGGAAATGATTAAGGTTTTCTCCAAAATGAAAATGAAAA
1 TGGAGAAATA-GAAACATTTGGAAATGAATAAGGTTTTCTACAAAATGAAAATGAAAA
**
371981 TGGAGAAAT-GAAACCATTTGGAAATGAATGTGGTTTTCTACAAAATGAAAATGA
1 TGGAGAAATAGAAA-CATTTGGAAATGAATAAGGTTTTCTACAAAATGAAAATGA
372035 CCTGAAAAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
56 4 0.08
57 36 0.73
58 9 0.18
ACGTcount: A:0.45, C:0.07, G:0.21, T:0.27
Consensus pattern (57 bp):
TGGAGAAATAGAAACATTTGGAAATGAATAAGGTTTTCTACAAAATGAAAATGAAAA
Found at i:376475 original size:6 final size:6
Alignment explanation
Indices: 376464--376489 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
376454 TTAATTTTTG
376464 TTTATT TTTATT TTTATT TTTATT TT
1 TTTATT TTTATT TTTATT TTTATT TT
376490 CTTTTCAGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTATT
Found at i:379951 original size:30 final size:30
Alignment explanation
Indices: 379915--379973 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
379905 TTTGATTTAG
379915 TATTAAACAAGCTACAGTTATGTGTAAAAC
1 TATTAAACAAGCTACAGTTATGTGTAAAAC
379945 TATTAAACAAGCTACAGTTATGTGTAAAA
1 TATTAAACAAGCTACAGTTATGTGTAAAA
379974 GGGATGTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.44, C:0.12, G:0.14, T:0.31
Consensus pattern (30 bp):
TATTAAACAAGCTACAGTTATGTGTAAAAC
Found at i:381683 original size:16 final size:16
Alignment explanation
Indices: 381664--381698 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
381654 TAGTATTTTT
381664 AATGTTAAAG-GACTAA
1 AATGTTAAAGTGA-TAA
381680 AATGTTAAAGTGATAA
1 AATGTTAAAGTGATAA
381696 AAT
1 AAT
381699 TACGAGGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 16 0.89
17 2 0.11
ACGTcount: A:0.51, C:0.03, G:0.17, T:0.29
Consensus pattern (16 bp):
AATGTTAAAGTGATAA
Found at i:382553 original size:40 final size:40
Alignment explanation
Indices: 382379--382553 Score: 199
Period size: 40 Copynumber: 4.4 Consensus size: 40
382369 TTGAGCCTTG
* ** * *
382379 TGCCTAGCAAGCTTCGTGCCGGTGTATCTATTGGGCTTAA
1 TGCCTAGCAGGCTTTATGCCGGTGTATATATCGGGCTTAA
** *
382419 AACCTAGCAGGCTTTATGCCTGTGTATATATCGGGCTTAA
1 TGCCTAGCAGGCTTTATGCCGGTGTATATATCGGGCTTAA
* * * *
382459 TTCCTAGCGGGCTTCATGCCAGTGTATATATCGGGCTTAA
1 TGCCTAGCAGGCTTTATGCCGGTGTATATATCGGGCTTAA
* * *
382499 TGCCTAGCAAGCTTTATGCCGGTGTA-ATTATCTGGCTTAG
1 TGCCTAGCAGGCTTTATGCCGGTGTATA-TATCGGGCTTAA
382539 TGCCTAGCAGGCTTT
1 TGCCTAGCAGGCTTT
382554 GGGCCAGTGT
Statistics
Matches: 113, Mismatches: 21, Indels: 2
0.83 0.15 0.01
Matches are distributed among these distances:
39 1 0.01
40 112 0.99
ACGTcount: A:0.20, C:0.22, G:0.25, T:0.33
Consensus pattern (40 bp):
TGCCTAGCAGGCTTTATGCCGGTGTATATATCGGGCTTAA
Found at i:382560 original size:80 final size:80
Alignment explanation
Indices: 382378--382564 Score: 223
Period size: 80 Copynumber: 2.3 Consensus size: 80
382368 ATTGAGCCTT
* * * * * *
382378 GTGCCTAGCAAGCTTCGTGCCGGTGTATCTATTGGGCTTAAAACCTAGCAGGCTTTATGCCTGTG
1 GTGCCTAGCAGGCTTCGTGCCAGTGTATATATCGGGCTTAAAACCTAGCAAGCTTTATGCCGGTG
382443 TATATATCGGGCTTA
66 TATATATCGGGCTTA
* * * * **
382458 ATTCCTAGCGGGCTTCATGCCAGTGTATATATCGGGCTTAATGCCTAGCAAGCTTTATGCCGGTG
1 GTGCCTAGCAGGCTTCGTGCCAGTGTATATATCGGGCTTAAAACCTAGCAAGCTTTATGCCGGTG
*
382523 TA-ATTATCTGGCTTA
66 TATA-TATCGGGCTTA
* *
382538 GTGCCTAGCAGGCTTTGGGCCAGTGTA
1 GTGCCTAGCAGGCTTCGTGCCAGTGTA
382565 AAAATTTGTA
Statistics
Matches: 87, Mismatches: 19, Indels: 2
0.81 0.18 0.02
Matches are distributed among these distances:
79 1 0.01
80 86 0.99
ACGTcount: A:0.20, C:0.21, G:0.27, T:0.32
Consensus pattern (80 bp):
GTGCCTAGCAGGCTTCGTGCCAGTGTATATATCGGGCTTAAAACCTAGCAAGCTTTATGCCGGTG
TATATATCGGGCTTA
Found at i:383111 original size:13 final size:13
Alignment explanation
Indices: 383093--383117 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
383083 TTTGGCTTGA
383093 ATTTTGGGATAGC
1 ATTTTGGGATAGC
383106 ATTTTGGGATAG
1 ATTTTGGGATAG
383118 AAAATAAGTT
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:0.24, C:0.04, G:0.32, T:0.40
Consensus pattern (13 bp):
ATTTTGGGATAGC
Found at i:388691 original size:28 final size:28
Alignment explanation
Indices: 388623--388692 Score: 122
Period size: 28 Copynumber: 2.5 Consensus size: 28
388613 TCTGGGCGTA
* *
388623 AGCCCTATACAGCAACAGTGTGGGCCTT
1 AGCCCAATACAGTAACAGTGTGGGCCTT
388651 AGCCCAATACAGTAACAGTGTGGGCCTT
1 AGCCCAATACAGTAACAGTGTGGGCCTT
388679 AGCCCAATACAGTA
1 AGCCCAATACAGTA
388693 GAAGTACAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.30, C:0.27, G:0.23, T:0.20
Consensus pattern (28 bp):
AGCCCAATACAGTAACAGTGTGGGCCTT
Found at i:389049 original size:27 final size:26
Alignment explanation
Indices: 389027--389278 Score: 204
Period size: 27 Copynumber: 9.3 Consensus size: 26
389017 AGGGGTATAA
389027 TAGTCATTTTACCCTAT-GAGGGTATTT
1 TAGTCATTTTACCCT-TCGAGGGTA-TT
* *
389054 TAATCATTTTATCCTTCGAGGGTATT
1 TAGTCATTTTACCCTTCGAGGGTATT
389080 TCAGTCATTTTACCCTTC-AGGGGTATT
1 T-AGTCATTTTACCCTTCGA-GGGTATT
* ** *
389107 TCGATTGTTTTACCCTTCGAGGATATT
1 TAG-TCATTTTACCCTTCGAGGGTATT
* * * *
389134 TCGGCCATTTTACCCTTGGAGAGTATT
1 T-AGTCATTTTACCCTTCGAGGGTATT
* *
389161 TCGGTCATTTTACCATTC-AGGGGTATT
1 T-AGTCATTTTACCCTTCGA-GGGTATT
* * *
389188 TCAATCATTTTTCCCTTTGAGGGTATTT
1 T-AGTCATTTTACCCTTCGAGGGTA-TT
* *
389216 TGGTCATTTTACCTTTCGAGGGTATT
1 TAGTCATTTTACCCTTCGAGGGTATT
* *
389242 TCGATCATTTTTCCCTTCGAGGGTATTT
1 TAG-TCATTTTACCCTTCGAGGGTA-TT
389270 TAGTCATTT
1 TAGTCATTT
389279 GCCCACGAAT
Statistics
Matches: 181, Mismatches: 33, Indels: 22
0.77 0.14 0.09
Matches are distributed among these distances:
26 11 0.06
27 160 0.88
28 10 0.06
ACGTcount: A:0.19, C:0.18, G:0.19, T:0.44
Consensus pattern (26 bp):
TAGTCATTTTACCCTTCGAGGGTATT
Done.