Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A11
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: 113101708
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2797742 characters in sequence are not A, C, G, or T
File 89 of 352
Found at i:28164135 original size:22 final size:22
Alignment explanation
Indices: 28164097--28164140 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
28164087 ACTAAATAGA
* *
28164097 TATTTATTATATCTATTGTTAT
1 TATTTATTATATATATTATTAT
28164119 TATTTATT-TAATATATTATTAT
1 TATTTATTAT-ATATATTATTAT
28164141 ATTAATGAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 1 0.05
22 18 0.95
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (22 bp):
TATTTATTATATATATTATTAT
Found at i:28166886 original size:20 final size:21
Alignment explanation
Indices: 28166843--28166888 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
28166833 ACTGTTTTGT
28166843 TATGGG-CCAACTGTATTGAA
1 TATGGGCCCAACTGTATTGAA
*
28166863 -ATGGGCCCAACTGTGTT-AA
1 TATGGGCCCAACTGTATTGAA
28166882 TATGGGC
1 TATGGGC
28166889 AAGGCCCAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.28
Consensus pattern (21 bp):
TATGGGCCCAACTGTATTGAA
Found at i:28172587 original size:32 final size:29
Alignment explanation
Indices: 28172517--28172588 Score: 76
Period size: 28 Copynumber: 2.4 Consensus size: 29
28172507 TATAAAATGA
* *
28172517 AATTTATTATATATTTTTTCATAATTATTT
1 AATTTATTA-ATATTTTTTAATAATCATTT
28172547 -A-TTATTAATATTTTATTAATTCAATCATTT
1 AATTTATTAATATTTT-TTAA-T-AATCATTT
28172577 AATTTATTAATA
1 AATTTATTAATA
28172589 AAATATATAA
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
27 7 0.20
28 9 0.26
29 2 0.06
30 7 0.20
31 1 0.03
32 9 0.26
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (29 bp):
AATTTATTAATATTTTTTAATAATCATTT
Found at i:28178376 original size:26 final size:26
Alignment explanation
Indices: 28178340--28178423 Score: 132
Period size: 26 Copynumber: 3.2 Consensus size: 26
28178330 CATGAAAGTC
28178340 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
28178366 TTATCGTGAAACATTTACCTAATCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
28178392 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
28178418 TTATCA
1 TTATCA
28178424 ATTTGTATCA
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 52 1.00
ACGTcount: A:0.36, C:0.24, G:0.06, T:0.35
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:28183257 original size:12 final size:12
Alignment explanation
Indices: 28183242--28183271 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
28183232 GTATTACCTT
28183242 GGCCTCGACCAC
1 GGCCTCGACCAC
28183254 GGCCTCGACCAC
1 GGCCTCGACCAC
28183266 GGCCTC
1 GGCCTC
28183272 TTCCCCGAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.13, C:0.50, G:0.27, T:0.10
Consensus pattern (12 bp):
GGCCTCGACCAC
Found at i:28186483 original size:26 final size:26
Alignment explanation
Indices: 28186447--28186530 Score: 141
Period size: 26 Copynumber: 3.2 Consensus size: 26
28186437 CATGAAATTC
28186447 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
*
28186473 TTATCATGAAACATTTACCTAATCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
28186499 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
28186525 TTATCA
1 TTATCA
28186531 GTTTGTATCA
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 54 1.00
ACGTcount: A:0.37, C:0.24, G:0.05, T:0.35
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:28186876 original size:45 final size:45
Alignment explanation
Indices: 28186821--28186995 Score: 251
Period size: 45 Copynumber: 3.8 Consensus size: 45
28186811 GACAATGTTA
28186821 TGAGAGCCAGTGTAAGACCATGTTGGACATGGCATCGGCGTTGAT
1 TGAGAGCCAGTGTAAGACCATGTTGGACATGGCATCGGCGTTGAT
28186866 TGAGAGCCAGTGTAAGACCATGTTGGACATGGCATCGGCGTTGAT
1 TGAGAGCCAGTGTAAGACCATGTTGGACATGGCATCGGCGTTGAT
* * * * *
28186911 TGTGAGCCAGTGTAAGACCATGTTGGACACGGCATCTGCGTGGAGA
1 TGAGAGCCAGTGTAAGACCATGTTGGACATGGCATCGGCGTTGA-T
* * *
28186957 CGAGAGCTAGCGTAAGACCATGTCTGGGACATGGCATCG
1 TGAGAGCCAGTGTAAGACCATGT-T-GGACATGGCATCG
28186996 ACCTCGACAT
Statistics
Matches: 116, Mismatches: 11, Indels: 3
0.89 0.08 0.02
Matches are distributed among these distances:
45 85 0.73
46 19 0.16
47 1 0.01
48 11 0.09
ACGTcount: A:0.25, C:0.19, G:0.34, T:0.22
Consensus pattern (45 bp):
TGAGAGCCAGTGTAAGACCATGTTGGACATGGCATCGGCGTTGAT
Found at i:28190522 original size:14 final size:15
Alignment explanation
Indices: 28190484--28190528 Score: 65
Period size: 14 Copynumber: 3.0 Consensus size: 15
28190474 TATAGTATCG
*
28190484 TATCTTGGAATTTCTC
1 TATCTTGG-ATTTCTT
28190500 TATCTTGGATTTCTT
1 TATCTTGGATTTCTT
28190515 TA-CTTGGATTTCTT
1 TATCTTGGATTTCTT
28190529 GTTATCTTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
14 12 0.43
15 8 0.29
16 8 0.29
ACGTcount: A:0.16, C:0.16, G:0.13, T:0.56
Consensus pattern (15 bp):
TATCTTGGATTTCTT
Found at i:28192520 original size:30 final size:30
Alignment explanation
Indices: 28192486--28192543 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 30
28192476 AACCCATATC
*
28192486 TTTCAT-TTATTCACACATTTAA-CCCTAAAT
1 TTTCATATT-TTCACA-AATTAATCCCTAAAT
28192516 TTTCATATTTTCACAAATTAATCCCTAA
1 TTTCATATTTTCACAAATTAATCCCTAA
28192544 TATGCATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
29 5 0.20
30 18 0.72
31 2 0.08
ACGTcount: A:0.34, C:0.22, G:0.00, T:0.43
Consensus pattern (30 bp):
TTTCATATTTTCACAAATTAATCCCTAAAT
Found at i:28194986 original size:48 final size:46
Alignment explanation
Indices: 28194927--28195237 Score: 183
Period size: 45 Copynumber: 6.8 Consensus size: 46
28194917 AGGGCGATAT
* *
28194927 GTGTGCTAGTGTAAGACCATGTCTGGGACATGGCATCAGCCACAT-TT-C
1 GTGTGCCAGTGTAAGACCATGT-T-GGACATGGCATCA-ACA-ATGTTAC
*
28194975 GTGTGCCAGTGTAAGACCATGTTTGGAGCATGGCATCAACAATGTTAT
1 GTGTGCCAGTGTAAGACCATG-TTGGA-CATGGCATCAACAATGTTAC
* * ** **
28195023 GAGAGCCAGTGTAAGACCATGTTGGACATGGCATCGGCGTTGATT--
1 GTGTGCCAGTGTAAGACCATGTTGGACATGGCATCAACAATG-TTAC
* * * ** **
28195068 GAGAGCCAGTGTAAAACCATGTTGGACATGGCATCGGCGTTGATT--
1 GTGTGCCAGTGTAAGACCATGTTGGACATGGCATCAACAATG-TTAC
* * * ** *
28195113 GAGAGCCAGTGTAAGACCATGTTGGACAAGGCATCGGCATTGATT--
1 GTGTGCCAGTGTAAGACCATGTTGGACATGGCATCAACAATG-TTAC
* * ** **
28195158 GAGAGCCAGTGTAAGACCATGTTGGACATGGCATCGGCGTTGATT--
1 GTGTGCCAGTGTAAGACCATGTTGGACATGGCATCAACAATG-TTAC
* * *
28195203 GTGAGCTAGTGGAAGACCATGTTGGACATGGCATC
1 GTGTGCCAGTGTAAGACCATGTTGGACATGGCATC
28195238 GGCATGGAGA
Statistics
Matches: 240, Mismatches: 18, Indels: 13
0.89 0.07 0.05
Matches are distributed among these distances:
45 161 0.67
46 14 0.06
47 14 0.06
48 50 0.21
49 1 0.00
ACGTcount: A:0.26, C:0.18, G:0.31, T:0.25
Consensus pattern (46 bp):
GTGTGCCAGTGTAAGACCATGTTGGACATGGCATCAACAATGTTAC
Found at i:28195303 original size:48 final size:45
Alignment explanation
Indices: 28194979--28195338 Score: 425
Period size: 45 Copynumber: 7.8 Consensus size: 45
28194969 CATTTCGTGT
** * *
28194979 GCCAGTGTAAGACCATGTTTGGAGCATGGCATCAACAATGTTATGAGA
1 GCCAGTGTAAGACCATG-TTGGA-CATGGCATCGGCATTGAT-TGAGA
*
28195027 GCCAGTGTAAGACCATGTTGGACATGGCATCGGCGTTGATTGAGA
1 GCCAGTGTAAGACCATGTTGGACATGGCATCGGCATTGATTGAGA
* *
28195072 GCCAGTGTAAAACCATGTTGGACATGGCATCGGCGTTGATTGAGA
1 GCCAGTGTAAGACCATGTTGGACATGGCATCGGCATTGATTGAGA
*
28195117 GCCAGTGTAAGACCATGTTGGACAAGGCATCGGCATTGATTGAGA
1 GCCAGTGTAAGACCATGTTGGACATGGCATCGGCATTGATTGAGA
* *
28195162 GCCAGTGTAAGACCATGTTGGACATGGCATCGGCGTTGATTGTGA
1 GCCAGTGTAAGACCATGTTGGACATGGCATCGGCATTGATTGAGA
* * * **
28195207 GCTAGTGGAAGACCATGTTGGACATGGCATCGGCATGGAGACGAGA
1 GCCAGTGTAAGACCATGTTGGACATGGCATCGGCATTGA-TTGAGA
* * * *
28195253 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGACAT-ATGA
1 GCCAGTGTAAGACCATGT-T-GGACATGGCATCGGCATTGA-TTGA-GA
* * *
28195301 GCTAGTGTAAGACCATGTCCGGGACATGGCATCAGCAT
1 GCCAGTGTAAGACCATGT--TGGACATGGCATCGGCAT
28195339 CTTACCCTAT
Statistics
Matches: 280, Mismatches: 27, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
45 168 0.60
46 33 0.12
47 7 0.03
48 71 0.25
49 1 0.00
ACGTcount: A:0.27, C:0.19, G:0.31, T:0.23
Consensus pattern (45 bp):
GCCAGTGTAAGACCATGTTGGACATGGCATCGGCATTGATTGAGA
Found at i:28197515 original size:21 final size:21
Alignment explanation
Indices: 28197468--28197518 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
28197458 CTTGCACAAA
*
28197468 GTATCAATATCTTTGTAATAG
1 GTATCGATATCTTTGTAATAG
*
28197489 GTATCGATAT-TTTGTTATTAG
1 GTATCGATATCTTTG-TAATAG
28197510 GTATCGATA
1 GTATCGATA
28197519 CCAAATTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 4 0.15
21 23 0.85
ACGTcount: A:0.29, C:0.08, G:0.18, T:0.45
Consensus pattern (21 bp):
GTATCGATATCTTTGTAATAG
Found at i:28200135 original size:17 final size:17
Alignment explanation
Indices: 28200109--28200142 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
28200099 AAAATTAAAT
* *
28200109 ATTTTGATATGACACTA
1 ATTTTAATATAACACTA
28200126 ATTTTAATATAACACTA
1 ATTTTAATATAACACTA
28200143 GTGACCTCGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.41, C:0.12, G:0.06, T:0.41
Consensus pattern (17 bp):
ATTTTAATATAACACTA
Found at i:28209037 original size:43 final size:43
Alignment explanation
Indices: 28208990--28209144 Score: 156
Period size: 43 Copynumber: 3.7 Consensus size: 43
28208980 TGTGTTCTCA
*
28208990 TGTAAGACCACGTCTGGGACTTTGGCATCGATATGTGATTAAG
1 TGTAAGACCACGTCTGGGACATTGGCATCGATATGTGATTAAG
* * ** * *
28209033 TGTAAGACCATGTCGGGGACATCAGCATCG-TATTTGATT-CG
1 TGTAAGACCACGTCTGGGACATTGGCATCGATATGTGATTAAG
* * * *
28209074 TGTAAGACC-CTATCTGGGGCAGTGACATCGATATGTGATTACA-
1 TGTAAGACCAC-GTCTGGGACATTGGCATCGATATGTGATTA-AG
*
28209117 TGTAAGACCACGTCTGGGACGTTGGCAT
1 TGTAAGACCACGTCTGGGACATTGGCAT
28209145 TGTACGATAT
Statistics
Matches: 85, Mismatches: 22, Indels: 10
0.73 0.19 0.09
Matches are distributed among these distances:
41 22 0.26
42 16 0.19
43 46 0.54
44 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.28
Consensus pattern (43 bp):
TGTAAGACCACGTCTGGGACATTGGCATCGATATGTGATTAAG
Found at i:28229083 original size:18 final size:18
Alignment explanation
Indices: 28229060--28229100 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
28229050 TACTTTTCTC
28229060 TTTCTA-TCACAATTCCAA
1 TTTCTATTCACAATT-CAA
*
28229078 TTTCTATTCATAATTCAA
1 TTTCTATTCACAATTCAA
28229096 TTTCT
1 TTTCT
28229101 TTTTTTATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 14 0.67
19 7 0.33
ACGTcount: A:0.29, C:0.22, G:0.00, T:0.49
Consensus pattern (18 bp):
TTTCTATTCACAATTCAA
Found at i:28229276 original size:39 final size:40
Alignment explanation
Indices: 28229233--28229344 Score: 113
Period size: 38 Copynumber: 2.8 Consensus size: 40
28229223 TTGGATCGTT
*
28229233 CGAAGTAATAGTTGACACCCAGTGTCTCATCG-GCCTAGC
1 CGAAGTAATAGTTGACACCCAGTGTCTCATCGAACCTAGC
** ** * *
28229272 CGAAGTAA-AGTTGGTACCCAGTACCTCATCGAATCTATC
1 CGAAGTAATAGTTGACACCCAGTGTCTCATCGAACCTAGC
*
28229311 CGAAGAAATTTAG-TGACACCCAGTGTCTCATCGA
1 CGAAGTAA--TAGTTGACACCCAGTGTCTCATCGA
28229345 CTCGAGGTCG
Statistics
Matches: 57, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
38 19 0.33
39 19 0.33
41 17 0.30
42 2 0.04
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.24
Consensus pattern (40 bp):
CGAAGTAATAGTTGACACCCAGTGTCTCATCGAACCTAGC
Found at i:28230354 original size:25 final size:25
Alignment explanation
Indices: 28230298--28230344 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
28230288 TGTAACTTTC
*
28230298 TTTCCTTT-TTTTACTTCTTTTACG
1 TTTCATTTGTTTTACTTCTTTTACG
*
28230322 TTTCATTTGTTTTATTTCTTTTA
1 TTTCATTTGTTTTACTTCTTTTA
28230345 TGTTATATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.11, C:0.15, G:0.04, T:0.70
Consensus pattern (25 bp):
TTTCATTTGTTTTACTTCTTTTACG
Found at i:28231132 original size:46 final size:46
Alignment explanation
Indices: 28231083--28231252 Score: 170
Period size: 46 Copynumber: 3.7 Consensus size: 46
28231073 GGCATCTGAG
*
28231083 CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAG
1 CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAA
* * * *
28231129 CTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGGCATCTGAA
1 CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G--TCCGAA
* **
28231176 CTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAA-CACCTGAA
1 CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCC-GAA
*
28231222 CTCGTTGAGTTGAGTCTGAGTTCACTTATGG
1 CTCGTTGAGTTGAGTCCGAGTTCACTTATGG
28231253 GTAGGTTACA
Statistics
Matches: 102, Mismatches: 12, Indels: 20
0.76 0.09 0.15
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 4 0.04
46 57 0.56
47 26 0.25
48 2 0.02
50 4 0.04
51 2 0.02
ACGTcount: A:0.21, C:0.18, G:0.29, T:0.32
Consensus pattern (46 bp):
CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAA
Found at i:28231232 original size:93 final size:93
Alignment explanation
Indices: 28231073--28231244 Score: 274
Period size: 93 Copynumber: 1.8 Consensus size: 93
28231063 AGGATATTTG
* ** *
28231073 GGCATCTGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAGCTCGTTGAG
1 GGCATCTGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATCACCGAACTCGTTGAG
28231138 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
*
28231166 GGCATCTGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAA-CACCTGAACTCGTTGA
1 GGCATCTGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATCACC-GAACTCGTTGA
*
28231230 GTTGAGTCTGAGTTC
65 GTTGAGTCCGAGTTC
28231245 ACTTATGGGT
Statistics
Matches: 72, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
92 2 0.03
93 70 0.97
ACGTcount: A:0.21, C:0.19, G:0.30, T:0.31
Consensus pattern (93 bp):
GGCATCTGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATCACCGAACTCGTTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:28234333 original size:55 final size:54
Alignment explanation
Indices: 28234238--28234387 Score: 149
Period size: 55 Copynumber: 2.8 Consensus size: 54
28234228 CTACTTTGTT
* ** * *
28234238 GCACTAAGTGTGCGAAATGAATATGAT-GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAATGTGCGAGTTGACTAT-ATAGCACTAAGTGTGCGAATTGACCACGCG
* * * * ** *
28234292 GCACTAAGTGTGCGGGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTG
1 GCACTAAATGTGCGAG-TTGACTATATAGCACTAAGTGTGCGAATTGACCACGCG
* *
28234347 GCACTAAATGTGCGAGTTGATTATATAGCACTGAGTGTGCG
1 GCACTAAATGTGCGAGTTGACTATATAGCACTAAGTGTGCG
28234388 GGCTCAATAT
Statistics
Matches: 79, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
54 37 0.47
55 42 0.53
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.29
Consensus pattern (54 bp):
GCACTAAATGTGCGAGTTGACTATATAGCACTAAGTGTGCGAATTGACCACGCG
Found at i:28234350 original size:27 final size:27
Alignment explanation
Indices: 28234210--28234387 Score: 146
Period size: 27 Copynumber: 6.6 Consensus size: 27
28234200 TAAATTGTAC
28234210 AGCACTAAGTGTGCGATTCT-ACTT-TGT
1 AGCACTAAGTGTGCGATT-TGA-TTATGT
* ** *
28234237 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGATTATGT
* ** *
28234263 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGATTATGT
* * *
28234291 GGCACTAAGTGTGCGGGTTTGACTATGT
1 AGCACTAAGTGTGC-GATTTGATTATGT
*
28234319 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGATTATGT
* * * *
28234346 GGCACTAAATGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGATTATGT
*
28234373 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
28234388 GGCTCAATAT
Statistics
Matches: 121, Mismatches: 25, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
26 2 0.02
27 97 0.80
28 22 0.18
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGATTATGT
Found at i:28234351 original size:82 final size:81
Alignment explanation
Indices: 28234211--28234366 Score: 190
Period size: 82 Copynumber: 1.9 Consensus size: 81
28234201 AAATTGTACA
* * * *
28234211 GCACTAAGTGTGCGATTCTACTTTGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAAGTGT
1 GCACTAAGTGTGCGATTCTACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAAATGT
28234276 GCGAATTGACCATGCG
66 GCGAATTGACCATGCG
* ** *
28234292 GCACTAAGTGTGCGGGTT-TGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TGGCACTAAA
1 GCACTAAGTGTGC-GATTCT-ACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACTAAA
*
28234355 TGTGCGAGTTGA
63 TGTGCGAATTGA
28234367 TTATATAGCA
Statistics
Matches: 63, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
81 15 0.24
82 48 0.76
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTCTACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAAATGT
GCGAATTGACCATGCG
Found at i:28242263 original size:27 final size:27
Alignment explanation
Indices: 28242233--28242301 Score: 84
Period size: 27 Copynumber: 2.6 Consensus size: 27
28242223 TCTACTTTGT
*
28242233 TGCACTAAGTGTGCGAAATGAATATGA
1 TGCACTAAGTGTGCGAAATGAACATGA
* * * *
28242260 TGCACTAAGAGTGCGAATTGACCATGC
1 TGCACTAAGTGTGCGAAATGAACATGA
*
28242287 GGCACTAAGTGTGCG
1 TGCACTAAGTGTGCG
28242302 GGTCTAACTA
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.30, C:0.17, G:0.29, T:0.23
Consensus pattern (27 bp):
TGCACTAAGTGTGCGAAATGAACATGA
Found at i:28242347 original size:82 final size:81
Alignment explanation
Indices: 28242207--28242362 Score: 190
Period size: 82 Copynumber: 1.9 Consensus size: 81
28242197 AAATTGTACA
* * * *
28242207 GCACTAAGTGTGCGATTCTACTTTGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAAGA-G
1 GCACTAAGTGTGCGAGTCTACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA-ATG
28242271 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
* ** *
28242288 GCACTAAGTGTGCGGGTCTAACTATGTAGCACTAAGTGTGCGATTTGATTACG-TGGCACTAAAT
1 GCACTAAGTGTGCGAGTCT-ACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACTAAAT
*
28242352 GTGCGAGTTGA
64 GTGCGAATTGA
28242363 TTATATAGCA
Statistics
Matches: 63, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
81 19 0.30
82 44 0.70
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGAGTCTACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAAATGT
GCGAATTGACCATGCG
Found at i:28242373 original size:27 final size:27
Alignment explanation
Indices: 28242314--28242383 Score: 86
Period size: 27 Copynumber: 2.6 Consensus size: 27
28242304 TCTAACTATG
* *
28242314 TAGCACTAAGTGTGCGATTTGATTACG
1 TAGCACTAAGTGTGCGAGTTGATTACA
* * *
28242341 TGGCACTAAATGTGCGAGTTGATTATA
1 TAGCACTAAGTGTGCGAGTTGATTACA
*
28242368 TAGCACTGAGTGTGCG
1 TAGCACTAAGTGTGCG
28242384 GGCTCAATAT
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.26, C:0.14, G:0.29, T:0.31
Consensus pattern (27 bp):
TAGCACTAAGTGTGCGAGTTGATTACA
Found at i:28243968 original size:9 final size:9
Alignment explanation
Indices: 28243950--28243980 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
28243940 GTAGTGATTC
*
28243950 AATTCAGGT
1 AATTCGGGT
28243959 AATTCGGGT
1 AATTCGGGT
28243968 AATTCGGGT
1 AATTCGGGT
28243977 AATT
1 AATT
28243981 TGGTTAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.29, C:0.10, G:0.26, T:0.35
Consensus pattern (9 bp):
AATTCGGGT
Found at i:28244007 original size:17 final size:17
Alignment explanation
Indices: 28243965--28244007 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
28243955 AGGTAATTCG
*
28243965 GGTAATTCGGGTAATTT
1 GGTAATTTGGGTAATTT
* *
28243982 GGTTAATTTGGTTACTTT
1 GG-TAATTTGGGTAATTT
28244000 GGTAATTT
1 GGTAATTT
28244008 TTAACCAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.21, C:0.05, G:0.26, T:0.49
Consensus pattern (17 bp):
GGTAATTTGGGTAATTT
Found at i:28246621 original size:40 final size:40
Alignment explanation
Indices: 28246547--28246811 Score: 374
Period size: 40 Copynumber: 6.6 Consensus size: 40
28246537 AACCCAAGTA
* * *
28246547 CCTTCGGGATTTAG-CCGGATATAG-CAACTCGCACACATG
1 CCTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATG
*
28246586 CCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
28246626 CCTTCGGGACTTAGCCCGGGTATAG-CAACTACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTC-ACTA---GCACAAATG
* *
28246669 CCTTTGGGACTTCGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
28246709 CCTTCGGGACTTAGCCCGGATATGGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
28246749 CCTTCGGGACTTAGCCCGGATATGGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
28246789 CCTTCGGGACTTAGCCTGGATAT
1 CCTTCGGGACTTAGCCCGGATAT
28246812 CATCCGAATA
Statistics
Matches: 206, Mismatches: 13, Indels: 13
0.89 0.06 0.06
Matches are distributed among these distances:
39 13 0.06
40 156 0.76
41 1 0.00
43 35 0.17
44 1 0.00
ACGTcount: A:0.25, C:0.28, G:0.24, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
Found at i:28254559 original size:40 final size:40
Alignment explanation
Indices: 28254485--28254748 Score: 356
Period size: 40 Copynumber: 6.6 Consensus size: 40
28254475 AACCCAAGTA
* * *
28254485 CCTTCGGGATTTAG-CCGGATATAG-CAACTCGCACACATG
1 CCTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATG
*
28254524 CCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
* *
28254564 CCTTCGGGACTTAGCCTGGGTATAG-CAACTACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTC-ACTA---GCACAAATG
*
28254607 CCTTCGGGACTTCGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
28254647 CCTTC-GGACTTAGCCCGGATATGGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
28254686 CCTTCGGGACTTAGCCCGGATATGGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
* *
28254726 CCTTTGGGACTTAGCCTGGATAT
1 CCTTCGGGACTTAGCCCGGATAT
28254749 CATCCGAATA
Statistics
Matches: 203, Mismatches: 14, Indels: 15
0.88 0.06 0.06
Matches are distributed among these distances:
39 50 0.25
40 116 0.57
41 1 0.00
43 35 0.17
44 1 0.00
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
Found at i:28254714 original size:79 final size:80
Alignment explanation
Indices: 28254485--28254748 Score: 372
Period size: 79 Copynumber: 3.3 Consensus size: 80
28254475 AACCCAAGTA
* * * *
28254485 CCTTCGGGATTTAG-CCGGATATAGCAACTCGCACACATGCCTTCGGGTCTTAGCCCGGATATAG
1 CCTTCGGGACTTAGCCCGGATATAGCAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAG
28254549 TCACTAGCACAAATG
66 TCACTAGCACAAATG
* * *
28254564 CCTTCGGGACTTAGCCTGGGTATAGCAACTACTCGCACAAATGCCTTCGGGACTTCGCCCGGATA
1 CCTTCGGGACTTAGCCCGGATATAGCAACTA---GCACAAATGCCTTCGGGACTTAGCCCGGATA
28254629 TAGTCACTAGCACAAATG
63 TAGTCACTAGCACAAATG
* *
28254647 CCTTC-GGACTTAGCCCGGATATGGTC-ACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATG
1 CCTTCGGGACTTAGCCCGGATATAG-CAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATA
28254710 GTCACTAGCACAAATG
65 GTCACTAGCACAAATG
* *
28254726 CCTTTGGGACTTAGCCTGGATAT
1 CCTTCGGGACTTAGCCCGGATAT
28254749 CATCCGAATA
Statistics
Matches: 165, Mismatches: 14, Indels: 11
0.87 0.07 0.06
Matches are distributed among these distances:
79 64 0.39
80 29 0.18
82 20 0.12
83 52 0.32
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (80 bp):
CCTTCGGGACTTAGCCCGGATATAGCAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAG
TCACTAGCACAAATG
Found at i:28262412 original size:19 final size:19
Alignment explanation
Indices: 28262366--28262413 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
28262356 GTATATATTT
28262366 TAAA-TTTATTTAGGTAGA
1 TAAATTTTATTTAGGTAGA
*
28262384 TAAATCTTATTTAGGTAGA
1 TAAATTTTATTTAGGTAGA
28262403 TAAATTTTATT
1 TAAATTTTATT
28262414 CATATTCTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 4 0.15
19 23 0.85
ACGTcount: A:0.38, C:0.02, G:0.12, T:0.48
Consensus pattern (19 bp):
TAAATTTTATTTAGGTAGA
Found at i:28262495 original size:42 final size:42
Alignment explanation
Indices: 28262437--28262516 Score: 151
Period size: 42 Copynumber: 1.9 Consensus size: 42
28262427 TATTTTTATT
28262437 TTATATTTTAGTAGTTTATTAGAATAAGGGAACTATTTTCCC
1 TTATATTTTAGTAGTTTATTAGAATAAGGGAACTATTTTCCC
*
28262479 TTATGTTTTAGTAGTTTATTAGAATAAGGGAACTATTT
1 TTATATTTTAGTAGTTTATTAGAATAAGGGAACTATTT
28262517 CCCCAATTAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.31, C:0.06, G:0.16, T:0.46
Consensus pattern (42 bp):
TTATATTTTAGTAGTTTATTAGAATAAGGGAACTATTTTCCC
Found at i:28266341 original size:19 final size:19
Alignment explanation
Indices: 28266299--28266342 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
28266289 ATATTTTAAA
*
28266299 TTTATTTAGATAGATAAAT
1 TTTATTTAGATAGAAAAAT
*
28266318 CTTATTTAGATAGAAAAAT
1 TTTATTTAGATAGAAAAAT
28266337 TTTATT
1 TTTATT
28266343 CATATTCTAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.41, C:0.02, G:0.09, T:0.48
Consensus pattern (19 bp):
TTTATTTAGATAGAAAAAT
Found at i:28266402 original size:42 final size:42
Alignment explanation
Indices: 28266352--28266445 Score: 136
Period size: 42 Copynumber: 2.3 Consensus size: 42
28266342 TCATATTCTA
**
28266352 GGAA-TATTTTATTTTATCTTTTAGTAGTTTATTAAAATAAG
1 GGAACTATTTTACCTTATCTTTTAGTAGTTTATTAAAATAAG
* * *
28266393 GGAACTATTTTCCCTTATGTTTTAGTAGTTTATTAGAATAAG
1 GGAACTATTTTACCTTATCTTTTAGTAGTTTATTAAAATAAG
28266435 GGAACTATTTT
1 GGAACTATTTT
28266446 CCCAATTAAG
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
41 4 0.09
42 43 0.91
ACGTcount: A:0.31, C:0.06, G:0.15, T:0.48
Consensus pattern (42 bp):
GGAACTATTTTACCTTATCTTTTAGTAGTTTATTAAAATAAG
Found at i:28266446 original size:42 final size:42
Alignment explanation
Indices: 28266365--28266448 Score: 150
Period size: 42 Copynumber: 2.0 Consensus size: 42
28266355 ATATTTTATT
28266365 TTATCTTTTAGTAGTTTATTAAAATAAGGGAACTATTTTCCC
1 TTATCTTTTAGTAGTTTATTAAAATAAGGGAACTATTTTCCC
* *
28266407 TTATGTTTTAGTAGTTTATTAGAATAAGGGAACTATTTTCCC
1 TTATCTTTTAGTAGTTTATTAAAATAAGGGAACTATTTTCCC
28266449 AATTAAGATT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.45
Consensus pattern (42 bp):
TTATCTTTTAGTAGTTTATTAAAATAAGGGAACTATTTTCCC
Found at i:28268517 original size:52 final size:52
Alignment explanation
Indices: 28268434--28268538 Score: 183
Period size: 52 Copynumber: 2.0 Consensus size: 52
28268424 CGCTATACTT
*
28268434 ATATACTTAAGCTCAGAGACAAGGATTAGTGAAAAATTAGATAATTCCACTA
1 ATATACTTAAGCTCAGAGACAAGGATAAGTGAAAAATTAGATAATTCCACTA
**
28268486 ATATACTTAAGCTTGGAGACAAGGATAAGTGAAAAATTAGATAATTCCACTA
1 ATATACTTAAGCTCAGAGACAAGGATAAGTGAAAAATTAGATAATTCCACTA
28268538 A
1 A
28268539 CTCTCTTGAT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.45, C:0.12, G:0.16, T:0.27
Consensus pattern (52 bp):
ATATACTTAAGCTCAGAGACAAGGATAAGTGAAAAATTAGATAATTCCACTA
Found at i:28272411 original size:20 final size:21
Alignment explanation
Indices: 28272385--28272435 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
28272375 ATTGAAAATT
28272385 TTAAAAATAATTT-TTAGAAAA
1 TTAAAAA-AATTTGTTAGAAAA
*
28272406 -TAAAAAAATTTGTTTGAAAA
1 TTAAAAAAATTTGTTAGAAAA
28272426 TTAAAAAAAT
1 TTAAAAAAAT
28272436 AATAAGAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
19 5 0.19
20 13 0.48
21 9 0.33
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (21 bp):
TTAAAAAAATTTGTTAGAAAA
Found at i:28272804 original size:31 final size:31
Alignment explanation
Indices: 28272764--28272824 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
28272754 AGTTGGTCAC
*
28272764 CCAACTTTTAAGG-TGCTTTCATTTTGGTTAT
1 CCAACTTTT-AGGATGCTTTCATTTTAGTTAT
*
28272795 CCAATTTTTAGGATGCTTTCATTTTAGTTA
1 CCAACTTTTAGGATGCTTTCATTTTAGTTA
28272825 CCTAAACGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 3 0.11
31 24 0.89
ACGTcount: A:0.21, C:0.15, G:0.15, T:0.49
Consensus pattern (31 bp):
CCAACTTTTAGGATGCTTTCATTTTAGTTAT
Found at i:28277209 original size:3 final size:3
Alignment explanation
Indices: 28277196--28277241 Score: 74
Period size: 3 Copynumber: 15.3 Consensus size: 3
28277186 TATTTGAGAA
* *
28277196 TAT TTT TAT TAT TAT TAT CAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
28277242 TGGTAGCCCA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:28279180 original size:22 final size:22
Alignment explanation
Indices: 28279139--28279180 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
28279129 AGAAAACAAC
* *
28279139 GGTGAAGCTACTGTTGAATGGT
1 GGTGAAGCTACTGCTAAATGGT
*
28279161 GGTGAAGCTATTGCTAAATG
1 GGTGAAGCTACTGCTAAATG
28279181 TCAATGAACA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.26, C:0.10, G:0.33, T:0.31
Consensus pattern (22 bp):
GGTGAAGCTACTGCTAAATGGT
Found at i:28288938 original size:42 final size:42
Alignment explanation
Indices: 28288874--28288963 Score: 128
Period size: 42 Copynumber: 2.1 Consensus size: 42
28288864 ACGACCTAGC
* *
28288874 ACACGGTCTGACATACGAGTGTGTGAGGCCATTTCGAAGGGT
1 ACACGGTCTGACACACGAGTGTGTAAGGCCATTTCGAAGGGT
* *
28288916 ACACGGTCTGGCACAC-AGGTGTGTAAGGCCATTTCGAATGGT
1 ACACGGTCTGACACACGA-GTGTGTAAGGCCATTTCGAAGGGT
28288958 ACACGG
1 ACACGG
28288964 GCTAGTCACA
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
41 1 0.02
42 42 0.98
ACGTcount: A:0.24, C:0.21, G:0.32, T:0.22
Consensus pattern (42 bp):
ACACGGTCTGACACACGAGTGTGTAAGGCCATTTCGAAGGGT
Found at i:28296433 original size:17 final size:17
Alignment explanation
Indices: 28296411--28296446 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
28296401 GAGACACGGC
28296411 GTCTGTCTTCGTCGTGT
1 GTCTGTCTTCGTCGTGT
28296428 GTCTGTCTTCGTCGTGT
1 GTCTGTCTTCGTCGTGT
28296445 GT
1 GT
28296447 GACATACGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.00, C:0.22, G:0.31, T:0.47
Consensus pattern (17 bp):
GTCTGTCTTCGTCGTGT
Found at i:28301773 original size:43 final size:44
Alignment explanation
Indices: 28301693--28301859 Score: 155
Period size: 43 Copynumber: 3.9 Consensus size: 44
28301683 GGTTATCGAG
* * * *
28301693 ATATGATTACATGTAAGACCATGTCTGGGACATTGGCATTGTAT
1 ATATGATTACATGTAAGACCATGTCTAGGATACTGGCATCGTAT
*
28301737 -TATGATTACGTGTAAGACCATGTCTAGGATACTGGCATCGT-T
1 ATATGATTACATGTAAGACCATGTCTAGGATACTGGCATCGTAT
*** * * *
28301779 ATATGATTTTGTATAAGACCTTGTCTAGGATAGC-GACATCG-AT
1 ATATGATTACATGTAAGACCATGTCTAGGATA-CTGGCATCGTAT
* * * *
28301822 ATGTGATAACATGTAAGACCATATCTGGGATA-TGGCAT
1 ATATGATTACATGTAAGACCATGTCTAGGATACTGGCAT
28301860 TGTACGAGCT
Statistics
Matches: 99, Mismatches: 20, Indels: 10
0.77 0.16 0.08
Matches are distributed among these distances:
42 5 0.05
43 93 0.94
44 1 0.01
ACGTcount: A:0.30, C:0.14, G:0.23, T:0.33
Consensus pattern (44 bp):
ATATGATTACATGTAAGACCATGTCTAGGATACTGGCATCGTAT
Found at i:28306894 original size:11 final size:11
Alignment explanation
Indices: 28306869--28306908 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
28306859 AGGTGTGCAT
*
28306869 GGGCCGGG-CC
1 GGGCCGGGTTC
28306879 GGGCCGGGTTC
1 GGGCCGGGTTC
28306890 GGGCCGGGTTC
1 GGGCCGGGTTC
*
28306901 GGGTCGGG
1 GGGCCGGG
28306909 CCCATAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
10 8 0.30
11 19 0.70
ACGTcount: A:0.00, C:0.28, G:0.60, T:0.12
Consensus pattern (11 bp):
GGGCCGGGTTC
Found at i:28306894 original size:16 final size:16
Alignment explanation
Indices: 28306873--28306910 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
28306863 GTGCATGGGC
28306873 CGGGCCGGG-CCGGGTT
1 CGGGCCGGGTCCGGG-T
*
28306889 CGGGCCGGGTTCGGGT
1 CGGGCCGGGTCCGGGT
28306905 CGGGCC
1 CGGGCC
28306911 CATAAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 16 0.80
17 4 0.20
ACGTcount: A:0.00, C:0.32, G:0.55, T:0.13
Consensus pattern (16 bp):
CGGGCCGGGTCCGGGT
Found at i:28307052 original size:24 final size:25
Alignment explanation
Indices: 28307025--28307073 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
28307015 CTTTTTTTAT
*
28307025 TAAATAAAAAAC-TTTAAAATATAA
1 TAAATAAAAAACATTTAAAACATAA
* *
28307049 TAAATCAAATACATTTAAAACATAA
1 TAAATAAAAAACATTTAAAACATAA
28307074 AAACAAATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 10 0.48
25 11 0.52
ACGTcount: A:0.63, C:0.08, G:0.00, T:0.29
Consensus pattern (25 bp):
TAAATAAAAAACATTTAAAACATAA
Found at i:28307066 original size:25 final size:23
Alignment explanation
Indices: 28307037--28307101 Score: 66
Period size: 25 Copynumber: 2.9 Consensus size: 23
28307027 AATAAAAAAC
*
28307037 TTTAAAATATAATAAATCAAATACA
1 TTTAAAACATAA-AAA-CAAATACA
28307062 TTTAAAACATAAAAACAAAT--A
1 TTTAAAACATAAAAACAAATACA
*
28307083 -TTAAAACA-AAAAATAAATA
1 TTTAAAACATAAAAACAAATA
28307102 AATAATGGGA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
19 9 0.24
20 8 0.22
21 1 0.03
23 5 0.14
24 3 0.08
25 11 0.30
ACGTcount: A:0.66, C:0.08, G:0.00, T:0.26
Consensus pattern (23 bp):
TTTAAAACATAAAAACAAATACA
Found at i:28307100 original size:19 final size:20
Alignment explanation
Indices: 28307063--28307101 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
28307053 TCAAATACAT
28307063 TTAAAACATAAAAACAAATA
1 TTAAAACATAAAAACAAATA
*
28307083 TTAAAACA-AAAAATAAATA
1 TTAAAACATAAAAACAAATA
28307102 AATAATGGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.72, C:0.08, G:0.00, T:0.21
Consensus pattern (20 bp):
TTAAAACATAAAAACAAATA
Found at i:28307312 original size:7 final size:7
Alignment explanation
Indices: 28307300--28307339 Score: 55
Period size: 7 Copynumber: 5.6 Consensus size: 7
28307290 AAAGTTATTT
28307300 AAAATTA
1 AAAATTA
28307307 AAAATTAAA
1 AAAATT--A
28307316 AAAATTA
1 AAAATTA
28307323 AAAATTA
1 AAAATTA
28307330 AAAA-TA
1 AAAATTA
28307336 AAAA
1 AAAA
28307340 AATTTAAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
6 6 0.19
7 18 0.58
9 7 0.23
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.23
Consensus pattern (7 bp):
AAAATTA
Found at i:28307319 original size:16 final size:16
Alignment explanation
Indices: 28307300--28307364 Score: 71
Period size: 16 Copynumber: 4.1 Consensus size: 16
28307290 AAAGTTATTT
28307300 AAAATTAAAAATTAAA
1 AAAATTAAAAATTAAA
28307316 AAAATTAAAAATTAAA
1 AAAATTAAAAATTAAA
28307332 AATAA--AAAAATTTAAA
1 AA-AATTAAAAA-TTAAA
* * *
28307348 ATAATTTAATATTAAA
1 AAAATTAAAAATTAAA
28307364 A
1 A
28307365 TCAGGCCGGG
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
15 7 0.17
16 30 0.71
17 5 0.12
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
AAAATTAAAAATTAAA
Found at i:28307326 original size:23 final size:22
Alignment explanation
Indices: 28307300--28307349 Score: 82
Period size: 22 Copynumber: 2.2 Consensus size: 22
28307290 AAAGTTATTT
28307300 AAAATTAAAAATTAAAAAAATTA
1 AAAATTAAAAA-TAAAAAAATTA
*
28307323 AAAATTAAAAATAAAAAAATTT
1 AAAATTAAAAATAAAAAAATTA
28307345 AAAAT
1 AAAAT
28307350 AATTTAATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
22 15 0.58
23 11 0.42
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (22 bp):
AAAATTAAAAATAAAAAAATTA
Found at i:28309553 original size:45 final size:45
Alignment explanation
Indices: 28309489--28309580 Score: 184
Period size: 45 Copynumber: 2.0 Consensus size: 45
28309479 TTTAAGAGAA
28309489 TAATTGTTCAAACTTAAAAAGGAATAAATGCAATAGGGTTTCTGC
1 TAATTGTTCAAACTTAAAAAGGAATAAATGCAATAGGGTTTCTGC
28309534 TAATTGTTCAAACTTAAAAAGGAATAAATGCAATAGGGTTTCTGC
1 TAATTGTTCAAACTTAAAAAGGAATAAATGCAATAGGGTTTCTGC
28309579 TA
1 TA
28309581 TGATCCTCGT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.40, C:0.11, G:0.17, T:0.32
Consensus pattern (45 bp):
TAATTGTTCAAACTTAAAAAGGAATAAATGCAATAGGGTTTCTGC
Found at i:28312911 original size:17 final size:17
Alignment explanation
Indices: 28312871--28312914 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
28312861 CCACCAATAG
28312871 TGAAAAAAAACAAAAAC
1 TGAAAAAAAACAAAAAC
* * *
28312888 AGTAAAAAAAATAAAAGC
1 TG-AAAAAAAACAAAAAC
28312906 TGAAAAAAA
1 TGAAAAAAA
28312915 GTCTGTAACA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.75, C:0.07, G:0.09, T:0.09
Consensus pattern (17 bp):
TGAAAAAAAACAAAAAC
Found at i:28313106 original size:3 final size:3
Alignment explanation
Indices: 28313086--28313133 Score: 55
Period size: 3 Copynumber: 16.3 Consensus size: 3
28313076 TTCATTATGG
* *
28313086 GAA GAAA GAA GGA GAA GAA GAA -AA GAA G-A GAA GAA GAA GAA GGA
1 GAA G-AA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
28313130 GAA G
1 GAA G
28313134 GAGGCGGCAC
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
2 4 0.11
3 31 0.82
4 3 0.08
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:28313107 original size:16 final size:16
Alignment explanation
Indices: 28313086--28313133 Score: 73
Period size: 16 Copynumber: 3.1 Consensus size: 16
28313076 TTCATTATGG
28313086 GAAGAAAGAAGGAGAA
1 GAAGAAAGAAGGAGAA
28313102 GAAGAAAAGAA-GAGAA
1 GAAG-AAAGAAGGAGAA
28313118 GAAG-AAGAAGGAGAA
1 GAAGAAAGAAGGAGAA
28313133 G
1 G
28313134 GAGGCGGCAC
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
14 5 0.17
15 6 0.20
16 13 0.43
17 6 0.20
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (16 bp):
GAAGAAAGAAGGAGAA
Found at i:28313118 original size:22 final size:21
Alignment explanation
Indices: 28313087--28313127 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
28313077 TCATTATGGG
*
28313087 AAGAAAGAAGGAGAAGAAGAA
1 AAGAAAGAAGAAGAAGAAGAA
28313108 AAGAAGAGAAGAAGAAGAAG
1 AAGAA-AGAAGAAGAAGAAG
28313128 GAGAAGGAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (21 bp):
AAGAAAGAAGAAGAAGAAGAA
Found at i:28313120 original size:25 final size:24
Alignment explanation
Indices: 28313086--28313132 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
28313076 TTCATTATGG
*
28313086 GAAGAAAGAAGGAGAAGAAGAAAA
1 GAAGAAAGAAGAAGAAGAAGAAAA
*
28313110 GAAGAGAAGAAGAAGAAGGAGAA
1 GAAGA-AAGAAGAAGAAGAAGAA
28313133 GGAGGCGGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 5 0.25
25 15 0.75
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (24 bp):
GAAGAAAGAAGAAGAAGAAGAAAA
Found at i:28313659 original size:17 final size:17
Alignment explanation
Indices: 28313637--28313670 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
28313627 ACCTTTTACA
* *
28313637 AAAATAGTATAAAAAAT
1 AAAATACTAAAAAAAAT
28313654 AAAATACTAAAAAAAAT
1 AAAATACTAAAAAAAAT
28313671 CTTAATCAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.21
Consensus pattern (17 bp):
AAAATACTAAAAAAAAT
Found at i:28314186 original size:151 final size:151
Alignment explanation
Indices: 28313776--28314225 Score: 739
Period size: 149 Copynumber: 3.0 Consensus size: 151
28313766 AAATTTAAAA
*
28313776 AAGGTTATTTACTAAATTAATATAAAAAACACTAAAATAATACATTTGAAACATTATGTACTAAA
1 AAGGTTATTTACTAAATTAATATAAAAAACACTAAAATAATACATTTGAAACATTATGTATTAAA
* *
28313841 ATAATAT-AAAAATTAATTACGAAAATAGTATATTTTAAAAAATAAAA-TCTAAAAATTTAAAAA
66 ATAATATAAAAAATAAAATACGAAAATAGTATATTTTAAAAAATAAAATTC-AAAAATTTAAAAA
* *
28313904 ATACAAATAAATGGTCAAAATC
130 ATACAAACAAATGGCCAAAATC
* * * *
28313926 AGGGTTATTTACTAAATTAATAT-AAAAA-ATTAAAATAATACATTCGAAACAATATGTATTAAA
1 AAGGTTATTTACTAAATTAATATAAAAAACACTAAAATAATACATTTGAAACATTATGTATTAAA
28313989 ATAATATAAAAAATAAAATACGAAAATAGTATATTTTAAAAAATAAAATTCAAAAATTTAAAAAA
66 ATAATATAAAAAATAAAATACGAAAATAGTATATTTTAAAAAATAAAATTCAAAAATTTAAAAAA
28314054 TACAAACAAATGGCCAAAATC
131 TACAAACAAATGGCCAAAATC
*
28314075 AAGGTTATTTATTAAATTAATATAAAAAACACTAAAATAATACATTTGAAACATTATGTATTAAA
1 AAGGTTATTTACTAAATTAATATAAAAAACACTAAAATAATACATTTGAAACATTATGTATTAAA
*
28314140 ATAATATAAAAAATAAAATACGAAAATAGTATATTTTAAAAAATAAAATCCAAAAA-TTAAAAAA
66 ATAATATAAAAAATAAAATACGAAAATAGTATATTTTAAAAAATAAAATTCAAAAATTTAAAAAA
* *
28314204 TACCAACAAATGGCAAAAATC
131 TACAAACAAATGGCCAAAATC
28314225 A
1 A
28314226 TCGAAAAAAA
Statistics
Matches: 279, Mismatches: 17, Indels: 8
0.92 0.06 0.03
Matches are distributed among these distances:
148 38 0.14
149 97 0.35
150 57 0.20
151 87 0.31
ACGTcount: A:0.58, C:0.08, G:0.06, T:0.29
Consensus pattern (151 bp):
AAGGTTATTTACTAAATTAATATAAAAAACACTAAAATAATACATTTGAAACATTATGTATTAAA
ATAATATAAAAAATAAAATACGAAAATAGTATATTTTAAAAAATAAAATTCAAAAATTTAAAAAA
TACAAACAAATGGCCAAAATC
Found at i:28315310 original size:31 final size:31
Alignment explanation
Indices: 28315275--28315333 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
28315265 ACTTAATAAG
28315275 CAAATGCCTCTAAAATAATAAAAAAATTTAA
1 CAAATGCCTCTAAAATAATAAAAAAATTTAA
* *
28315306 CAAATGCCTTTAAAATAATAAGAAAATT
1 CAAATGCCTCTAAAATAATAAAAAAATT
28315334 AGCAATAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.56, C:0.12, G:0.05, T:0.27
Consensus pattern (31 bp):
CAAATGCCTCTAAAATAATAAAAAAATTTAA
Found at i:28315410 original size:22 final size:23
Alignment explanation
Indices: 28315376--28315437 Score: 56
Period size: 22 Copynumber: 2.8 Consensus size: 23
28315366 CAATAACAAC
* *
28315376 AAAATAGTTGCAACATAAT-AGT
1 AAAATAGTAGCAAAATAATGAGT
* *
28315398 AAAATGGTAGCAAAATAGTGAGT
1 AAAATAGTAGCAAAATAATGAGT
* *
28315421 AAAA-AATAGAAAAATAA
1 AAAATAGTAGCAAAATAA
28315438 CATTTAAAAA
Statistics
Matches: 31, Mismatches: 8, Indels: 2
0.76 0.20 0.05
Matches are distributed among these distances:
22 24 0.77
23 7 0.23
ACGTcount: A:0.58, C:0.05, G:0.16, T:0.21
Consensus pattern (23 bp):
AAAATAGTAGCAAAATAATGAGT
Found at i:28316998 original size:18 final size:18
Alignment explanation
Indices: 28316951--28317004 Score: 63
Period size: 18 Copynumber: 3.0 Consensus size: 18
28316941 GTAGCCAATA
28316951 TAGAGCCTGAGCCAGAGC
1 TAGAGCCTGAGCCAGAGC
** * *
28316969 TAGCTCCCGAGCCCGAGC
1 TAGAGCCTGAGCCAGAGC
*
28316987 TAGAGCCTGAGCCTGAGC
1 TAGAGCCTGAGCCAGAGC
28317005 CACAGCTAGA
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.22, C:0.33, G:0.31, T:0.13
Consensus pattern (18 bp):
TAGAGCCTGAGCCAGAGC
Found at i:28317028 original size:24 final size:23
Alignment explanation
Indices: 28316975--28317028 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
28316965 GAGCTAGCTC
28316975 CCGAGCCCGAGCTAGAGCCTGAG
1 CCGAGCCCGAGCTAGAGCCTGAG
*
28316998 CCTGAGCCAC-AGCTAGAGGCTGAG
1 CC-GAGCC-CGAGCTAGAGCCTGAG
28317022 TCCGAGC
1 -CCGAGC
28317029 GATCGCATTC
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
23 2 0.07
24 22 0.81
25 3 0.11
ACGTcount: A:0.22, C:0.33, G:0.33, T:0.11
Consensus pattern (23 bp):
CCGAGCCCGAGCTAGAGCCTGAG
Found at i:28321706 original size:19 final size:19
Alignment explanation
Indices: 28321669--28321708 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
28321659 TTTTCAAACA
*
28321669 GTTTTTTTATACAATTTAT
1 GTTTTTTTAAACAATTTAT
28321688 GTTTTTTTAAACTAA-TTAT
1 GTTTTTTTAAAC-AATTTAT
28321707 GT
1 GT
28321709 CAGAAAAGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 17 0.89
20 2 0.11
ACGTcount: A:0.28, C:0.05, G:0.07, T:0.60
Consensus pattern (19 bp):
GTTTTTTTAAACAATTTAT
Found at i:28323254 original size:19 final size:19
Alignment explanation
Indices: 28323231--28323270 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
28323221 TTTGAATATT
*
28323231 TTTTTTAAATTATATCTAAG
1 TTTTATAAATTATAT-TAAG
*
28323251 TTTTATAACTTATATTAAG
1 TTTTATAAATTATATTAAG
28323270 T
1 T
28323271 AAAAATTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.35, C:0.05, G:0.05, T:0.55
Consensus pattern (19 bp):
TTTTATAAATTATATTAAG
Found at i:28330062 original size:26 final size:26
Alignment explanation
Indices: 28330033--28330089 Score: 114
Period size: 26 Copynumber: 2.2 Consensus size: 26
28330023 TGATAAAAAT
28330033 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
28330059 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
28330085 TGATA
1 TGATA
28330090 GGCATTTCAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.32, C:0.07, G:0.26, T:0.35
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:28331618 original size:25 final size:27
Alignment explanation
Indices: 28331576--28331628 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
28331566 TTTACAGTTT
28331576 TACCCCTAAGAGATAAATT-ACCGAAA
1 TACCCCTAAGAGATAAATTGACCGAAA
* *
28331602 TACCCCT-AGAGTTAAATTGACCTAAA
1 TACCCCTAAGAGATAAATTGACCGAAA
28331628 T
1 T
28331629 GCATGTTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 10 0.42
26 14 0.58
ACGTcount: A:0.42, C:0.23, G:0.11, T:0.25
Consensus pattern (27 bp):
TACCCCTAAGAGATAAATTGACCGAAA
Found at i:28333255 original size:12 final size:12
Alignment explanation
Indices: 28333233--28333271 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
28333223 GGGGAAGAGA
*
28333233 CCGTCGTCGAGG
1 CCGTGGTCGAGG
*
28333245 CTGTGGTCGAGG
1 CCGTGGTCGAGG
28333257 CCGTGGTCGAGG
1 CCGTGGTCGAGG
28333269 CCG
1 CCG
28333272 AGGTAGTACT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.08, C:0.28, G:0.46, T:0.18
Consensus pattern (12 bp):
CCGTGGTCGAGG
Found at i:28339511 original size:49 final size:48
Alignment explanation
Indices: 28339458--28339554 Score: 142
Period size: 48 Copynumber: 2.0 Consensus size: 48
28339448 TTAAAGAGGG
* *
28339458 TTTAAAATAAATAATATATAAAATAGTTT-AACTACATAATGTATATAAA
1 TTTAAAATAAATAATATAT-AAA-AGTTTAAAATAAATAATGTATATAAA
*
28339507 TTTAAAATAAATAATATGTAAAAGTTTAAAATAAATAATGTATATAAA
1 TTTAAAATAAATAATATATAAAAGTTTAAAATAAATAATGTATATAAA
28339555 AAGAAAATCA
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
47 5 0.11
48 21 0.48
49 18 0.41
ACGTcount: A:0.57, C:0.02, G:0.05, T:0.36
Consensus pattern (48 bp):
TTTAAAATAAATAATATATAAAAGTTTAAAATAAATAATGTATATAAA
Found at i:28339534 original size:24 final size:24
Alignment explanation
Indices: 28339457--28339555 Score: 103
Period size: 24 Copynumber: 4.0 Consensus size: 24
28339447 ATTAAAGAGG
28339457 GTTTAAAATAAATAATATATAAAATA
1 GTTTAAAATAAATAATATAT-AAA-A
* * *
28339483 GTTT-AACTACATAATGTATATAAA
1 GTTTAAAATAAATAATATATA-AAA
*
28339507 -TTTAAAATAAATAATATGTAAAA
1 GTTTAAAATAAATAATATATAAAA
28339530 GTTTAAAATAAATAATGTATATAAAA
1 GTTTAAAATAAATAA--TATATAAAA
28339556 AGAAAATCAT
Statistics
Matches: 60, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
23 6 0.10
24 28 0.47
25 14 0.23
26 12 0.20
ACGTcount: A:0.57, C:0.02, G:0.06, T:0.35
Consensus pattern (24 bp):
GTTTAAAATAAATAATATATAAAA
Found at i:28345167 original size:21 final size:21
Alignment explanation
Indices: 28345142--28345245 Score: 78
Period size: 19 Copynumber: 5.2 Consensus size: 21
28345132 TAGCCTCCGG
28345142 GCTTCCGTTTAGCACTTGTGT
1 GCTTCCGTTTAGCACTTGTGT
* *
28345163 GCTTCAG-TTAAC-CTTCG-G-
1 GCTTCCGTTTAGCACTT-GTGT
*
28345181 GCTTCCGTTTAACACTTGTGT
1 GCTTCCGTTTAGCACTTGTGT
** **
28345202 GCTTTAG-TTAGC-CTTCAG-
1 GCTTCCGTTTAGCACTTGTGT
*
28345220 GCTTCCGTTTAGCACTTATGT
1 GCTTCCGTTTAGCACTTGTGT
28345241 GCTTC
1 GCTTC
28345246 AGCTAGACTT
Statistics
Matches: 63, Mismatches: 12, Indels: 16
0.69 0.13 0.18
Matches are distributed among these distances:
18 11 0.17
19 19 0.30
20 17 0.27
21 16 0.25
ACGTcount: A:0.13, C:0.25, G:0.21, T:0.40
Consensus pattern (21 bp):
GCTTCCGTTTAGCACTTGTGT
Found at i:28345170 original size:39 final size:39
Alignment explanation
Indices: 28345124--28345263 Score: 208
Period size: 39 Copynumber: 3.6 Consensus size: 39
28345114 GTTCTGATGA
*
28345124 GCTTCAGTTAGCCTCCGGGCTTCCGTTTAGCACTTGTGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTGTGT
* *
28345163 GCTTCAGTTAACCTTCGGGCTTCCGTTTAACACTTGTGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTGTGT
* * *
28345202 GCTTTAGTTAGCCTTCAGGCTTCCGTTTAGCACTTATGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTGTGT
* *
28345241 GCTTCAGCTAGACTTCGGGCTTC
1 GCTTCAGTTAGCCTTCGGGCTTC
28345264 AAATCACGAT
Statistics
Matches: 89, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 89 1.00
ACGTcount: A:0.14, C:0.26, G:0.23, T:0.37
Consensus pattern (39 bp):
GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTGTGT
Found at i:28349652 original size:18 final size:17
Alignment explanation
Indices: 28349623--28349670 Score: 62
Period size: 18 Copynumber: 2.8 Consensus size: 17
28349613 GAAGTGAATG
28349623 AAAAAAAG-AAAAAGAA
1 AAAAAAAGTAAAAAGAA
28349639 AAAAAAAGTTAAAAAGAA
1 AAAAAAAG-TAAAAAGAA
* *
28349657 CATAAAAGTAAAAA
1 AAAAAAAGTAAAAA
28349671 ATTAAATTGC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 8 0.29
17 6 0.21
18 14 0.50
ACGTcount: A:0.79, C:0.02, G:0.10, T:0.08
Consensus pattern (17 bp):
AAAAAAAGTAAAAAGAA
Found at i:28362781 original size:20 final size:20
Alignment explanation
Indices: 28362758--28362807 Score: 50
Period size: 20 Copynumber: 2.6 Consensus size: 20
28362748 AACTATTCAA
*
28362758 ATAATATTATTTGAATAGTT
1 ATAATATTATTTGAATAATT
* **
28362778 ATAAAATTAAATGAATAATT
1 ATAATATTATTTGAATAATT
28362798 AT--TATTATTT
1 ATAATATTATTT
28362808 ATTTATTAAT
Statistics
Matches: 23, Mismatches: 7, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
18 5 0.22
20 18 0.78
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.48
Consensus pattern (20 bp):
ATAATATTATTTGAATAATT
Found at i:28374155 original size:26 final size:26
Alignment explanation
Indices: 28374117--28374224 Score: 198
Period size: 26 Copynumber: 4.2 Consensus size: 26
28374107 TGATACAAAT
*
28374117 TGATAATGAGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
28374143 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
28374169 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
28374195 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
28374221 TGAT
1 TGAT
28374225 GGAAATTTCA
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 79 1.00
ACGTcount: A:0.31, C:0.06, G:0.26, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:28379588 original size:26 final size:26
Alignment explanation
Indices: 28379559--28379640 Score: 155
Period size: 26 Copynumber: 3.2 Consensus size: 26
28379549 TGATACAAAT
28379559 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
28379585 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
28379611 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
28379637 TGAT
1 TGAT
28379641 GGGAATTTCA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 54 1.00
ACGTcount: A:0.30, C:0.06, G:0.27, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:28381267 original size:27 final size:26
Alignment explanation
Indices: 28381225--28381365 Score: 153
Period size: 27 Copynumber: 5.2 Consensus size: 26
28381215 AGGAAACGTC
*
28381225 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCACAATTATCTG-T
* *
28381252 TTGGTGGCTCTACCAC-ATATATCTGT
1 CTGGTGGCTCTGCCACAAT-TATCTGT
*
28381278 CCTGGTGGCTATGCCACAATTATCTGAT
1 -CTGGTGGCTCTGCCACAATTATCTG-T
28381306 CTGGTGGCTCTGCCAC-ATATATCTGTT
1 CTGGTGGCTCTGCCACAAT-TATCTG-T
28381333 CTGGTGGCTCTGCCACAA-TATCTATGT
1 CTGGTGGCTCTGCCACAATTATC--TGT
28381360 CTGGTG
1 CTGGTG
28381366 ACTTCGTCAC
Statistics
Matches: 98, Mismatches: 8, Indels: 16
0.80 0.07 0.13
Matches are distributed among these distances:
26 9 0.09
27 83 0.85
28 6 0.06
ACGTcount: A:0.18, C:0.24, G:0.23, T:0.35
Consensus pattern (26 bp):
CTGGTGGCTCTGCCACAATTATCTGT
Found at i:28381304 original size:54 final size:54
Alignment explanation
Indices: 28381222--28381355 Score: 225
Period size: 54 Copynumber: 2.5 Consensus size: 54
28381212 TGGAGGAAAC
*
28381222 GTCCTGGTGGCTATGCCACAATTATCTGATTTGGTGGCTCTACCACATATATCT
1 GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTACCACATATATCT
*
28381276 GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCT
1 GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTACCACATATATCT
* *
28381330 GTTCTGGTGGCTCTGCCACAA-TATCT
1 GTCCTGGTGGCTATGCCACAATTATCT
28381356 ATGTCTGGTG
Statistics
Matches: 76, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
53 5 0.07
54 71 0.93
ACGTcount: A:0.19, C:0.25, G:0.22, T:0.34
Consensus pattern (54 bp):
GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTACCACATATATCT
Found at i:28381377 original size:81 final size:80
Alignment explanation
Indices: 28381225--28381382 Score: 191
Period size: 81 Copynumber: 2.0 Consensus size: 80
28381215 AGGAAACGTC
*
28381225 CTGGTGGCTATGCCACAATTATCTGATTTGGTGGCTCTACCACATATATCTGTCCTGGTGGCTAT
1 CTGGTGGCTATGCCACAATTATCTGATTTGGTGGCTCTACCACATATATCTGTCCTGGTGACTAT
28381290 GCCACAATTATCTGAT
66 GCCACAA-TATCTGAT
* *
28381306 CTGGTGGCTCTGCCAC-ATATATCTG-TTCTGGTGGCTCTGCCACA-ATATCTATGT-CTGGTGA
1 CTGGTGGCTATGCCACAAT-TATCTGATT-TGGTGGCTCTACCACATATATC--TGTCCTGGTGA
*
28381367 CT-TCGTCACAATATCT
62 CTAT-GCCACAATATCT
28381383 AGCAGCCTTG
Statistics
Matches: 68, Mismatches: 4, Indels: 11
0.82 0.05 0.13
Matches are distributed among these distances:
80 15 0.22
81 50 0.74
82 3 0.04
ACGTcount: A:0.20, C:0.25, G:0.21, T:0.35
Consensus pattern (80 bp):
CTGGTGGCTATGCCACAATTATCTGATTTGGTGGCTCTACCACATATATCTGTCCTGGTGACTAT
GCCACAATATCTGAT
Found at i:28382638 original size:15 final size:15
Alignment explanation
Indices: 28382618--28382648 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
28382608 TTAAGTTACT
28382618 TAAATCGTTTTCGAC
1 TAAATCGTTTTCGAC
*
28382633 TAAATCGTTTTTGAC
1 TAAATCGTTTTCGAC
28382648 T
1 T
28382649 TGAGATTCAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (15 bp):
TAAATCGTTTTCGAC
Found at i:28385003 original size:43 final size:43
Alignment explanation
Indices: 28384954--28385061 Score: 164
Period size: 43 Copynumber: 2.5 Consensus size: 43
28384944 GATTACTGAG
* *
28384954 ATGTGATTACGTGTAAGACCATGTCTGGGACATTGGCATTG-T
1 ATGTGATTACGTGTAAGACCATGTCTGGGACAGTGGCATCGAT
28384996 ATTGTGATTACGTGTAAGACCATGTCTGGGACAGTGGCATCGAT
1 A-TGTGATTACGTGTAAGACCATGTCTGGGACAGTGGCATCGAT
* *
28385040 ATGTGATAACATGTAAGACCAT
1 ATGTGATTACGTGTAAGACCAT
28385062 ATCTAGGATA
Statistics
Matches: 60, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
42 1 0.02
43 57 0.95
44 2 0.03
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.31
Consensus pattern (43 bp):
ATGTGATTACGTGTAAGACCATGTCTGGGACAGTGGCATCGAT
Found at i:28388393 original size:14 final size:14
Alignment explanation
Indices: 28388374--28388401 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
28388364 ACCAATGTAA
28388374 TCATTTATATCATC
1 TCATTTATATCATC
28388388 TCATTTATATCATC
1 TCATTTATATCATC
28388402 ACATAAATGT
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:0.29, C:0.21, G:0.00, T:0.50
Consensus pattern (14 bp):
TCATTTATATCATC
Found at i:28390857 original size:3 final size:3
Alignment explanation
Indices: 28390834--28390886 Score: 70
Period size: 3 Copynumber: 17.3 Consensus size: 3
28390824 ATAAAAAATA
* * *
28390834 TAT TTT TAT TTT TATT TAT TAT TAT TAT TAT TAT TAT TAG TAT TAT
1 TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
28390880 TAT TAT T
1 TAT TAT T
28390887 TTTGACTCAG
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
3 40 0.93
4 3 0.07
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (3 bp):
TAT
Found at i:28393793 original size:47 final size:47
Alignment explanation
Indices: 28393663--28393793 Score: 217
Period size: 47 Copynumber: 2.8 Consensus size: 47
28393653 TTCGAGTAAA
* * * *
28393663 TACCTTGATTTGGTTACGAGCCATGGTATAGGTACTCCGGGATATGT
1 TACCTTGATTTGGCTACGGGCCATGGTATAGGTACTTCGGGATAAGT
28393710 TACCTTGATTTGGCTACGGGCCATGGTATAGGTACTTCGGGATAAGT
1 TACCTTGATTTGGCTACGGGCCATGGTATAGGTACTTCGGGATAAGT
*
28393757 TACCTTGATTTGGCTATGGGCCATGGTATAGGTACTT
1 TACCTTGATTTGGCTACGGGCCATGGTATAGGTACTT
28393794 ATCGATTGTG
Statistics
Matches: 79, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 79 1.00
ACGTcount: A:0.21, C:0.17, G:0.28, T:0.34
Consensus pattern (47 bp):
TACCTTGATTTGGCTACGGGCCATGGTATAGGTACTTCGGGATAAGT
Found at i:28398323 original size:26 final size:26
Alignment explanation
Indices: 28398275--28398398 Score: 83
Period size: 26 Copynumber: 4.8 Consensus size: 26
28398265 AATGCAAGCA
* *
28398275 TTGAGCTGGTGGTTATTTGGTAGG-C
1 TTGAGCTGGTGATTATTTAGTAGGAC
* *
28398300 TTTGAGCTGATGATTTTTTAGTAGGAC
1 -TTGAGCTGGTGATTATTTAGTAGGAC
* *
28398327 TTGAGCCGGTGATTATTTAGCA-GACC
1 TTGAGCTGGTGATTATTTAGTAGGA-C
* * * * **
28398353 TTAAGCCGGTGTTTATTTAGCAGGTT
1 TTGAGCTGGTGATTATTTAGTAGGAC
*
28398379 TTGAGCTAGTG-TATATTTAG
1 TTGAGCTGGTGAT-TATTTAG
28398399 CAGGTACTAT
Statistics
Matches: 79, Mismatches: 15, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
25 3 0.04
26 74 0.94
27 2 0.03
ACGTcount: A:0.20, C:0.10, G:0.29, T:0.40
Consensus pattern (26 bp):
TTGAGCTGGTGATTATTTAGTAGGAC
Found at i:28409907 original size:43 final size:43
Alignment explanation
Indices: 28409846--28409928 Score: 148
Period size: 43 Copynumber: 1.9 Consensus size: 43
28409836 ACATGAATCC
*
28409846 CATCCATTATGAACTCGGACCTCTCAACGAGCTCGGATGCTCG
1 CATCCATAATGAACTCGGACCTCTCAACGAGCTCGGATGCTCG
*
28409889 CATCCATAATGAACTCGGACCTCTCAATGAGCTCGGATGC
1 CATCCATAATGAACTCGGACCTCTCAACGAGCTCGGATGC
28409929 CACATATCTC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.25, C:0.31, G:0.20, T:0.23
Consensus pattern (43 bp):
CATCCATAATGAACTCGGACCTCTCAACGAGCTCGGATGCTCG
Found at i:28416875 original size:26 final size:26
Alignment explanation
Indices: 28416822--28416938 Score: 137
Period size: 26 Copynumber: 4.5 Consensus size: 26
28416812 ATACAAGAAA
* *
28416822 AGCAGGCCTTGACCT-GTGGTTATTT
1 AGCAGGCCTTGAGCTGGTGTTTATTT
* * *
28416847 AGCATGACTTGAGCTGGTGTTGATTT
1 AGCAGGCCTTGAGCTGGTGTTTATTT
* **
28416873 AGCAGGCCTTAAGCCAGTGTTTATTT
1 AGCAGGCCTTGAGCTGGTGTTTATTT
*
28416899 AGTAGGCCTTGAGCTGGTGTTTATTT
1 AGCAGGCCTTGAGCTGGTGTTTATTT
*
28416925 AGCAAGCCTTGAGC
1 AGCAGGCCTTGAGC
28416939 CAGTGGTTAT
Statistics
Matches: 74, Mismatches: 17, Indels: 1
0.80 0.18 0.01
Matches are distributed among these distances:
25 12 0.16
26 62 0.84
ACGTcount: A:0.20, C:0.17, G:0.28, T:0.35
Consensus pattern (26 bp):
AGCAGGCCTTGAGCTGGTGTTTATTT
Found at i:28416910 original size:52 final size:52
Alignment explanation
Indices: 28416822--28416957 Score: 184
Period size: 52 Copynumber: 2.6 Consensus size: 52
28416812 ATACAAGAAA
* * * *
28416822 AGCAGGCCTTGA-CCTGTGGTTATTTAGCATGACTTGAGCTGGTGTTGATTT
1 AGCAGGCCTTGAGCCAGTGGTTATTTAGTAGGCCTTGAGCTGGTGTTGATTT
* * *
28416873 AGCAGGCCTTAAGCCAGTGTTTATTTAGTAGGCCTTGAGCTGGTGTTTATTT
1 AGCAGGCCTTGAGCCAGTGGTTATTTAGTAGGCCTTGAGCTGGTGTTGATTT
* *
28416925 AGCAAGCCTTGAGCCAGTGGTTATCTAGTAGGC
1 AGCAGGCCTTGAGCCAGTGGTTATTTAGTAGGC
28416958 TTTAAGCCAG
Statistics
Matches: 73, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
51 11 0.15
52 62 0.85
ACGTcount: A:0.20, C:0.17, G:0.29, T:0.35
Consensus pattern (52 bp):
AGCAGGCCTTGAGCCAGTGGTTATTTAGTAGGCCTTGAGCTGGTGTTGATTT
Found at i:28416948 original size:26 final size:26
Alignment explanation
Indices: 28416822--28416969 Score: 129
Period size: 26 Copynumber: 5.7 Consensus size: 26
28416812 ATACAAGAAA
*
28416822 AGCAGGCCTTGA-CCTGTGGTTATTT
1 AGCAGGCCTTGAGCCAGTGGTTATTT
* * **
28416847 AGCATGACTTGAGCTGGT-GTTGATTT
1 AGCAGGCCTTGAGCCAGTGGTT-ATTT
* *
28416873 AGCAGGCCTTAAGCCAGTGTTTATTT
1 AGCAGGCCTTGAGCCAGTGGTTATTT
* ** *
28416899 AGTAGGCCTTGAGCTGGTGTTTATTT
1 AGCAGGCCTTGAGCCAGTGGTTATTT
* *
28416925 AGCAAGCCTTGAGCCAGTGGTTATCT
1 AGCAGGCCTTGAGCCAGTGGTTATTT
* * *
28416951 AGTAGGCTTTAAGCCAGTG
1 AGCAGGCCTTGAGCCAGTG
28416970 TATGTTTAAT
Statistics
Matches: 96, Mismatches: 24, Indels: 5
0.77 0.19 0.04
Matches are distributed among these distances:
25 13 0.14
26 81 0.84
27 2 0.02
ACGTcount: A:0.20, C:0.17, G:0.28, T:0.34
Consensus pattern (26 bp):
AGCAGGCCTTGAGCCAGTGGTTATTT
Found at i:28416963 original size:78 final size:77
Alignment explanation
Indices: 28416825--28416970 Score: 186
Period size: 78 Copynumber: 1.9 Consensus size: 77
28416815 CAAGAAAAGC
* ** *
28416825 AGGCCTTGACCTGTGGTTATTTAGCATGACTTGAGCTGGTGTTGATTTAGCAGGCCTTAAGCCAG
1 AGGCCTTGACCTGTGGTTATTTAGCAAGACTTGAGCCAGTGTTGATCTAGCAGGCCTTAAGCCAG
28416890 TGTTTATTTAGT
66 TGTTTATTTAGT
* * * * *
28416902 AGGCCTTGAGCTGGTGTTTATTTAGCAAGCCTTGAGCCAGTGGTT-ATCTAGTAGGCTTTAAGCC
1 AGGCCTTGACCT-GTGGTTATTTAGCAAGACTTGAGCCAGT-GTTGATCTAGCAGGCCTTAAGCC
28416966 AGTGT
64 AGTGT
28416971 ATGTTTAATA
Statistics
Matches: 58, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
77 11 0.19
78 44 0.76
79 3 0.05
ACGTcount: A:0.20, C:0.16, G:0.28, T:0.36
Consensus pattern (77 bp):
AGGCCTTGACCTGTGGTTATTTAGCAAGACTTGAGCCAGTGTTGATCTAGCAGGCCTTAAGCCAG
TGTTTATTTAGT
Found at i:28419259 original size:12 final size:13
Alignment explanation
Indices: 28419237--28419265 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
28419227 AAAATCTTCC
28419237 TTGTGTTTTTTTT
1 TTGTGTTTTTTTT
28419250 TTGT-TTTTTTTT
1 TTGTGTTTTTTTT
28419262 TTGT
1 TTGT
28419266 ACTTTGACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (13 bp):
TTGTGTTTTTTTT
Found at i:28423820 original size:13 final size:13
Alignment explanation
Indices: 28423802--28423828 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
28423792 GGTATACTGA
28423802 CTTATCAATACAG
1 CTTATCAATACAG
28423815 CTTATCAATACAG
1 CTTATCAATACAG
28423828 C
1 C
28423829 GAAGTCACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.26, G:0.07, T:0.30
Consensus pattern (13 bp):
CTTATCAATACAG
Found at i:28426189 original size:47 final size:47
Alignment explanation
Indices: 28426118--28426430 Score: 170
Period size: 47 Copynumber: 6.7 Consensus size: 47
28426108 AGGGTATATT
* * *
28426118 GCCGATGCCATGTCCTAGACATGGTCTTACACTGGCTCATCTATTAA
1 GCCGATGCCATGTCCCAAACATGGTCTTACACTGACTCATCTATTAA
* * * *
28426165 GTCGATGCCATGTCCTAAACATGGTCTTACACTGACT-AT-TGAAATCGAG
1 GCCGATGCCATGTCCCAAACATGGTCTTACACTGACTCATCT---AT-TAA
* * **
28426214 GCCGACGCCATGTCCCAAACATGGTCTTACACTGACACATCTCGT-A
1 GCCGATGCCATGTCCCAAACATGGTCTTACACTGACTCATCTATTAA
* * * *
28426260 GCCGATG-CATGTCCCAGACAT-GTCTTACACTGGCTTACATCT-TGAG
1 GCCGATGCCATGTCCCAAACATGGTCTTACACTGAC-T-CATCTATTAA
** * * * *
28426306 GTTGACG-CATGTCCCAAACAT-GTC-TAAAATTAGCTC-TC-ATCTCAA
1 GCCGATGCCATGTCCCAAACATGGTCTTACACTGA-CTCATCTAT-T-AA
* * * *
28426351 TGCCGATGCCATGTCCCAGACATGTTCTTACACTGTCTC-TCATAATGT-G
1 -GCCGATGCCATGTCCCAAACATGGTCTTACACTGACTCATC-T-AT-TAA
*
28426400 GCCAATG-CATGTCCCAAACAT-GTCTTACACT
1 GCCGATGCCATGTCCCAAACATGGTCTTACACT
28426431 AGCACACAAT
Statistics
Matches: 202, Mismatches: 44, Indels: 41
0.70 0.15 0.14
Matches are distributed among these distances:
43 3 0.01
44 13 0.06
45 20 0.10
46 47 0.23
47 60 0.30
48 15 0.07
49 38 0.19
50 2 0.01
51 4 0.02
ACGTcount: A:0.26, C:0.28, G:0.18, T:0.28
Consensus pattern (47 bp):
GCCGATGCCATGTCCCAAACATGGTCTTACACTGACTCATCTATTAA
Found at i:28427912 original size:23 final size:23
Alignment explanation
Indices: 28427886--28427929 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
28427876 TGAACTAAAA
28427886 CAGTAAGCTC-TGACGAGCTGAAT
1 CAGTAAGCTCAT-ACGAGCTGAAT
28427909 CAGTAAGCTCATACGAGCTGA
1 CAGTAAGCTCATACGAGCTGA
28427930 GAATAGTAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 19 0.95
24 1 0.05
ACGTcount: A:0.32, C:0.23, G:0.25, T:0.20
Consensus pattern (23 bp):
CAGTAAGCTCATACGAGCTGAAT
Found at i:28430654 original size:40 final size:40
Alignment explanation
Indices: 28430567--28430801 Score: 172
Period size: 40 Copynumber: 5.9 Consensus size: 40
28430557 GATTATTGTT
* * *
28430567 TGATTGCACATATGTACCTCTATTTGTACTTTGGTACCTC
1 TGATTGCACATATGTGCCTCTATTTGTACTTCGGTACCCC
* *
28430607 TGATTGCATATATGTGCCTCTATTTGTACTTCGATACCCC
1 TGATTGCACATATGTGCCTCTATTTGTACTTCGGTACCCC
* *
28430647 TGTTTGCACATACGTGTCC-C-ATTTTGTACTTCGGTACCCC
1 TGATTGCACATATGTG-CCTCTA-TTTGTACTTCGGTACCCC
* * * ** * * *
28430687 TAACTACACATACATGCC-CTTGTTTGTACTTCAGTACCCT
1 TGATTGCACATATGTGCCTC-TATTTGTACTTCGGTACCCC
** * * *
28430727 TGATTGCACATACATGCCCCTATTTGTAATTCAGTA-CCC
1 TGATTGCACATATGTGCCTCTATTTGTACTTCGGTACCCC
* * * * * * *
28430766 TGAATGCATATTTGTGCCCCTGTTTATACTCCGGTA
1 TGATTGCACATATGTGCCTCTATTTGTACTTCGGTA
28430802 ACTCTGAATC
Statistics
Matches: 157, Mismatches: 33, Indels: 11
0.78 0.16 0.05
Matches are distributed among these distances:
39 32 0.20
40 122 0.78
41 3 0.02
ACGTcount: A:0.21, C:0.26, G:0.15, T:0.38
Consensus pattern (40 bp):
TGATTGCACATATGTGCCTCTATTTGTACTTCGGTACCCC
Found at i:28437074 original size:42 final size:42
Alignment explanation
Indices: 28437015--28437101 Score: 174
Period size: 42 Copynumber: 2.1 Consensus size: 42
28437005 ATATACCAAA
28437015 AACTTACCAATTTGACCAATTCATTTGGCCATTCAAGAACCT
1 AACTTACCAATTTGACCAATTCATTTGGCCATTCAAGAACCT
28437057 AACTTACCAATTTGACCAATTCATTTGGCCATTCAAGAACCT
1 AACTTACCAATTTGACCAATTCATTTGGCCATTCAAGAACCT
28437099 AAC
1 AAC
28437102 ATATAGGCAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.34, C:0.26, G:0.09, T:0.30
Consensus pattern (42 bp):
AACTTACCAATTTGACCAATTCATTTGGCCATTCAAGAACCT
Found at i:28438260 original size:43 final size:42
Alignment explanation
Indices: 28438213--28438333 Score: 127
Period size: 43 Copynumber: 2.8 Consensus size: 42
28438203 TCAAATATCA
* * * *
28438213 ATGCCACTGTCCCAGACAGGGCCTTACACATAATCTTTAA-TCG
1 ATGCCAATGTCCCAGACACGGTCTTACACAT-ATC-TCAAGTCG
* *
28438256 ATGCCAATGTCTCAGACACGGTCTTACATGATATCTCAAGTCG
1 ATGCCAATGTCCCAGACACGGTCTTACA-CATATCTCAAGTCG
* *
28438299 ATGCCAAAGTCCCAGACATGGTCTTACACGATATC
1 ATGCCAATGTCCCAGACACGGTCTTACAC-ATATC
28438334 ACATATCGGA
Statistics
Matches: 65, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
42 3 0.05
43 60 0.92
44 2 0.03
ACGTcount: A:0.29, C:0.28, G:0.17, T:0.26
Consensus pattern (42 bp):
ATGCCAATGTCCCAGACACGGTCTTACACATATCTCAAGTCG
Found at i:28438635 original size:34 final size:34
Alignment explanation
Indices: 28438592--28438659 Score: 109
Period size: 34 Copynumber: 2.0 Consensus size: 34
28438582 TACTCGACGA
* * *
28438592 CTTTCGACTTTTCCCGGTCTAATTCCATTTTCTT
1 CTTTCGACTTTCCCCAGTATAATTCCATTTTCTT
28438626 CTTTCGACTTTCCCCAGTATAATTCCATTTTCTT
1 CTTTCGACTTTCCCCAGTATAATTCCATTTTCTT
28438660 TGGTTCTTGA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.15, C:0.29, G:0.07, T:0.49
Consensus pattern (34 bp):
CTTTCGACTTTCCCCAGTATAATTCCATTTTCTT
Found at i:28444527 original size:21 final size:21
Alignment explanation
Indices: 28444501--28444540 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
28444491 TGATATCCAG
*
28444501 AAGAGGATATTGCAATACCCA
1 AAGAGGATATCGCAATACCCA
28444522 AAGAGGATATCGCAATACC
1 AAGAGGATATCGCAATACC
28444541 ACTGAAGGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.42, C:0.20, G:0.20, T:0.17
Consensus pattern (21 bp):
AAGAGGATATCGCAATACCCA
Found at i:28447668 original size:10 final size:10
Alignment explanation
Indices: 28447636--28447669 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
28447626 ATTTTGAAAC
28447636 TAATTAATAA
1 TAATTAATAA
*
28447646 TATATTAAAAA
1 TA-ATTAATAA
28447657 TAATTAATAA
1 TAATTAATAA
28447667 TAA
1 TAA
28447670 CATATGAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 12 0.57
11 9 0.43
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (10 bp):
TAATTAATAA
Found at i:28454000 original size:22 final size:23
Alignment explanation
Indices: 28453965--28454008 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
28453955 TTAGCGCACA
28453965 AAATATATAAATAT-AAATAAAT
1 AAATATATAAATATAAAATAAAT
* *
28453987 AAATATTTATATATAAAATAAA
1 AAATATATAAATATAAAATAAA
28454009 ATATAAATTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (23 bp):
AAATATATAAATATAAAATAAAT
Found at i:28454002 original size:14 final size:14
Alignment explanation
Indices: 28453965--28454016 Score: 63
Period size: 14 Copynumber: 3.9 Consensus size: 14
28453955 TTAGCGCACA
28453965 AAATATATAAATAT
1 AAATATATAAATAT
*
28453979 AAATAAATAAATAT
1 AAATATATAAATAT
**
28453993 TTATATATAAA-AT
1 AAATATATAAATAT
28454006 AAA-ATATAAAT
1 AAATATATAAAT
28454017 TGAATAATTT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
12 7 0.23
13 3 0.10
14 21 0.68
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
AAATATATAAATAT
Found at i:28461418 original size:40 final size:40
Alignment explanation
Indices: 28461363--28461583 Score: 349
Period size: 40 Copynumber: 5.6 Consensus size: 40
28461353 TATTCGAATG
*
28461363 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
*
28461403 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
28461443 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* *
28461483 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTATTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* *
28461523 ATATCCGGGCTAA-ACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGACT
*
28461562 ATATCC-GGCTAAATCCCGAAGG
1 ATATCCGGGCTAAGTCCCGAAGG
28461584 TACTTGGGTT
Statistics
Matches: 169, Mismatches: 10, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
38 6 0.04
39 33 0.20
40 130 0.77
ACGTcount: A:0.23, C:0.23, G:0.26, T:0.28
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
Found at i:28476051 original size:38 final size:39
Alignment explanation
Indices: 28475974--28476187 Score: 266
Period size: 38 Copynumber: 5.6 Consensus size: 39
28475964 TATTCGAATG
*
28475974 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCA-TTGTGCTATTGACT
28476014 ATATCCGGGCTAAGT-CCGAAGGCATTGTGCTATTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTGTGCTATTGACT
28476052 ATATCC-GGCTAAGTCCCGAAGGCATT-TGTCTA--GACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTGTG-CTATTGACT
*
28476088 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTATTGACT
1 ATATCCGGGCTAAGTCCCGAAGGC-ATTGTGCTATTGACT
* * *
28476128 ATATCTGGGCTAA--ACCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGTCCCGAAGGCA-TTGTGCTA-TTGACT
*
28476166 ATATCC-GGCTAAATCCCGAAGG
1 ATATCCGGGCTAAGTCCCGAAGG
28476188 TACTTGGGTT
Statistics
Matches: 155, Mismatches: 8, Indels: 23
0.83 0.04 0.12
Matches are distributed among these distances:
36 10 0.06
37 33 0.21
38 60 0.39
39 21 0.14
40 31 0.20
ACGTcount: A:0.24, C:0.22, G:0.26, T:0.28
Consensus pattern (39 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTGTGCTATTGACT
Found at i:28476139 original size:77 final size:76
Alignment explanation
Indices: 28475974--28476187 Score: 276
Period size: 77 Copynumber: 2.8 Consensus size: 76
28475964 TATTCGAATG
28475974 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGT-CCGAAGGCA
1 ATAT-CGGGCTAAGTCCCGAAGGCATTTGTGCTA--GACTATATCCGGGCTAAGTCCCGAAGGCA
28476038 TTGTGCTATTGACT
63 TTGTGCTATTGACT
* *
28476052 ATATCCGGCTAAGTCCCGAAGGCATTTGT-CTAGACTATATCCGGGCTAAGTCCCGAAGGCTTTT
1 ATATCGGGCTAAGTCCCGAAGGCATTTGTGCTAGACTATATCCGGGCTAAGTCCCGAAGGC-ATT
28476116 GTGCTATTGACT
65 GTGCTATTGACT
* * * *
28476128 ATATCTGGGCTAA--ACCGAAGGCATTTGTGCGAGTTGCTATATCC-GGCTAAATCCCGAAGG
1 ATATC-GGGCTAAGTCCCGAAGGCATTTGTGCTAG--ACTATATCCGGGCTAAGTCCCGAAGG
28476188 TACTTGGGTT
Statistics
Matches: 123, Mismatches: 7, Indels: 13
0.86 0.05 0.09
Matches are distributed among these distances:
74 19 0.15
75 22 0.18
76 25 0.20
77 45 0.37
78 12 0.10
ACGTcount: A:0.24, C:0.22, G:0.26, T:0.28
Consensus pattern (76 bp):
ATATCGGGCTAAGTCCCGAAGGCATTTGTGCTAGACTATATCCGGGCTAAGTCCCGAAGGCATTG
TGCTATTGACT
Found at i:28476174 original size:114 final size:114
Alignment explanation
Indices: 28475974--28476187 Score: 342
Period size: 114 Copynumber: 1.9 Consensus size: 114
28475964 TATTCGAATG
*
28475974 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTCCGAAGGCAT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGACCGAAGGCAT
* *
28476039 TGTGCTATTGACTATATCCGGCTAAGTCCCGAAGGCATTTGTCTAGACT
66 TGTGCGATTGACTATATCCGGCTAAATCCCGAAGGCATTTGTCTAGACT
* * *
28476088 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTATTGACTATATCTGGGCTAA-ACCGAAGGCAT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGACCGAAGGCA-
28476152 TTGTGCGAGTTG-CTATATCCGGCTAAATCCCGAAGG
65 TTGTGCGA-TTGACTATATCCGGCTAAATCCCGAAGG
28476188 TACTTGGGTT
Statistics
Matches: 92, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
113 9 0.10
114 80 0.87
115 3 0.03
ACGTcount: A:0.24, C:0.22, G:0.26, T:0.28
Consensus pattern (114 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGACCGAAGGCAT
TGTGCGATTGACTATATCCGGCTAAATCCCGAAGGCATTTGTCTAGACT
Found at i:28484201 original size:31 final size:31
Alignment explanation
Indices: 28484166--28484227 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
28484156 TCAGATAAGA
28484166 GAAAAGAGAAAGTAACCGAGTAGCCACTCCG
1 GAAAAGAGAAAGTAACCGAGTAGCCACTCCG
28484197 GAAAAGAGAAAGTAACCGAGTAGCCACTCCG
1 GAAAAGAGAAAGTAACCGAGTAGCCACTCCG
28484228 CAACTGTACC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.10
Consensus pattern (31 bp):
GAAAAGAGAAAGTAACCGAGTAGCCACTCCG
Found at i:28484612 original size:40 final size:40
Alignment explanation
Indices: 28484557--28484709 Score: 261
Period size: 40 Copynumber: 3.8 Consensus size: 40
28484547 TATTCGAATG
* *
28484557 ATATCCGGGCTAAGTCCAGAAGGCTTTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* *
28484597 ATATCTGGGCTAAGTCCCGAAGGCATTTGTGCTATTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
28484637 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
*
28484677 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCT
28484710 TCGGGCTAAG
Statistics
Matches: 106, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 106 1.00
ACGTcount: A:0.22, C:0.22, G:0.27, T:0.30
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
Found at i:28484724 original size:29 final size:29
Alignment explanation
Indices: 28484682--28484737 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
28484672 TGACTATATC
* *
28484682 CGGGCTAAGTCCCGAAGGCTTTTGTGCTT
1 CGGGCTAAGACCCGAAGGCATTTGTGCTT
28484711 CGGGCTAAGACCCGAAGGCATTTGTGC
1 CGGGCTAAGACCCGAAGGCATTTGTGC
28484738 GAGTTTCTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.18, C:0.25, G:0.32, T:0.25
Consensus pattern (29 bp):
CGGGCTAAGACCCGAAGGCATTTGTGCTT
Found at i:28490518 original size:40 final size:40
Alignment explanation
Indices: 28490386--28490510 Score: 200
Period size: 40 Copynumber: 3.1 Consensus size: 40
28490376 AACCCAAGTA
*
28490386 CCTTCGGGATTTAG-CCGGATATAG-CTACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTC-ACTCGCACAAATG
*
28490425 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTCGCACAAATG
*
28490465 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTCGCACAAATG
28490505 CCTTCG
1 CCTTCG
28490511 AATCTTAGTC
Statistics
Matches: 80, Mismatches: 4, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
39 13 0.16
40 67 0.84
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTCACTCGCACAAATG
Found at i:28497801 original size:17 final size:17
Alignment explanation
Indices: 28497779--28497814 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
28497769 CGATTAGTGA
28497779 TTCTACCTAGTTTTATC
1 TTCTACCTAGTTTTATC
28497796 TTCTACCTAGTTTTATC
1 TTCTACCTAGTTTTATC
28497813 TT
1 TT
28497815 TTATTTATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.17, C:0.22, G:0.06, T:0.56
Consensus pattern (17 bp):
TTCTACCTAGTTTTATC
Found at i:28505755 original size:15 final size:15
Alignment explanation
Indices: 28505735--28505765 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
28505725 TTCAAAACTT
28505735 AATTAAATCATTTCA
1 AATTAAATCATTTCA
*
28505750 AATTAAATCGTTTCA
1 AATTAAATCATTTCA
28505765 A
1 A
28505766 CCACGCCTCG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.13, G:0.03, T:0.39
Consensus pattern (15 bp):
AATTAAATCATTTCA
Found at i:28509689 original size:25 final size:24
Alignment explanation
Indices: 28509652--28509699 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
28509642 ATGGCCCTCT
*
28509652 CGAGCTTCCCGTTATATGGTTCTTG
1 CGAGCTTCCCGTTA-ATAGTTCTTG
**
28509677 CGAGCTTTTCGTTAATAGTTCTT
1 CGAGCTTCCCGTTAATAGTTCTT
28509700 CGGAGCATCC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.15, C:0.21, G:0.21, T:0.44
Consensus pattern (24 bp):
CGAGCTTCCCGTTAATAGTTCTTG
Found at i:28509913 original size:24 final size:24
Alignment explanation
Indices: 28509856--28509941 Score: 77
Period size: 24 Copynumber: 3.6 Consensus size: 24
28509846 TGGTTATCTG
* * **
28509856 GAGCTTCCCGTTAATAGCTCTTCG
1 GAGCTTCCCGTTATTGGCTCTTAA
* *
28509880 GAACTACCCGTTATTGGCT-TGTAA
1 GAGCTTCCCGTTATTGGCTCT-TAA
*
28509904 GAGCTTCCCGATTA-TGGCTCTTAT
1 GAGCTTCCCG-TTATTGGCTCTTAA
28509928 GAGCTTCCCGTTAT
1 GAGCTTCCCGTTAT
28509942 ATAGCCCGAA
Statistics
Matches: 49, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
23 4 0.08
24 41 0.84
25 4 0.08
ACGTcount: A:0.19, C:0.26, G:0.21, T:0.35
Consensus pattern (24 bp):
GAGCTTCCCGTTATTGGCTCTTAA
Found at i:28509995 original size:25 final size:25
Alignment explanation
Indices: 28509905--28510001 Score: 90
Period size: 25 Copynumber: 3.9 Consensus size: 25
28509895 GGCTTGTAAG
* ** *
28509905 AGCTTCCCGAT-TATGGCTCTTATG
1 AGCTTCCCGTTATATGGCTCGAATA
* *
28509929 AGCTTCCCGTTATATAGCCCGAATA
1 AGCTTCCCGTTATATGGCTCGAATA
* *
28509954 AGCTTCCCATTACATGGCTC-ACATA
1 AGCTTCCCGTTATATGGCTCGA-ATA
*
28509979 AGCTTCCTGTTATATGGCTCGAA
1 AGCTTCCCGTTATATGGCTCGAA
28510002 AGAGGGCTTC
Statistics
Matches: 57, Mismatches: 13, Indels: 5
0.76 0.17 0.07
Matches are distributed among these distances:
24 11 0.19
25 45 0.79
26 1 0.02
ACGTcount: A:0.24, C:0.27, G:0.18, T:0.32
Consensus pattern (25 bp):
AGCTTCCCGTTATATGGCTCGAATA
Found at i:28513090 original size:89 final size:89
Alignment explanation
Indices: 28512953--28513115 Score: 317
Period size: 89 Copynumber: 1.8 Consensus size: 89
28512943 TTTCAAATAA
28512953 CCAATTCCAATTCCAATCACAATATACAATATCAAATAAATTAATTTATTTTAACTTTAACCATT
1 CCAATTCCAATTCCAATCACAATATACAATATCAAATAAATTAATTTATTTTAACTTTAACCATT
28513018 TAGCCTCATTTCAAATAACCAATT
66 TAGCCTCATTTCAAATAACCAATT
*
28513042 CCAATTCCAATTCCAATCACAATATACAATATCAAATAAATTAGTTTATTTTAACTTTAACCATT
1 CCAATTCCAATTCCAATCACAATATACAATATCAAATAAATTAATTTATTTTAACTTTAACCATT
28513107 TAGCCTCAT
66 TAGCCTCAT
28513116 GAACTATAAT
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
89 73 1.00
ACGTcount: A:0.40, C:0.21, G:0.02, T:0.36
Consensus pattern (89 bp):
CCAATTCCAATTCCAATCACAATATACAATATCAAATAAATTAATTTATTTTAACTTTAACCATT
TAGCCTCATTTCAAATAACCAATT
Found at i:28513981 original size:12 final size:13
Alignment explanation
Indices: 28513958--28513995 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
28513948 CAACCCGCCC
28513958 ATATTAATTTTTT
1 ATATTAATTTTTT
28513971 ATATT-ATTTTTT
1 ATATTAATTTTTT
*
28513983 ATATAAATTTTTT
1 ATATTAATTTTTT
28513996 TAAAAAATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 11 0.48
13 12 0.52
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
ATATTAATTTTTT
Found at i:28513997 original size:14 final size:12
Alignment explanation
Indices: 28513962--28513995 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
28513952 CCGCCCATAT
28513962 TAATTTTTTATA
1 TAATTTTTTATA
*
28513974 TTATTTTTTATA
1 TAATTTTTTATA
28513986 TAAATTTTTT
1 T-AATTTTTT
28513996 TAAAAAATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 12 0.63
13 7 0.37
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (12 bp):
TAATTTTTTATA
Found at i:28525137 original size:43 final size:43
Alignment explanation
Indices: 28525074--28525183 Score: 175
Period size: 43 Copynumber: 2.6 Consensus size: 43
28525064 GACACCTCAA
* *
28525074 TGCATTATTGGATAAGCCAAAGTAAATATACTAGCACACATAG
1 TGCATCATTGGATAAACCAAAGTAAATATACTAGCACACATAG
*
28525117 TGCATCATTGGATAAACCAAAGTAAATATACTAGCATACATAG
1 TGCATCATTGGATAAACCAAAGTAAATATACTAGCACACATAG
* *
28525160 TGCATCATTTGATAAACCGAAGTA
1 TGCATCATTGGATAAACCAAAGTA
28525184 TAAACTTTTA
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 62 1.00
ACGTcount: A:0.42, C:0.16, G:0.15, T:0.26
Consensus pattern (43 bp):
TGCATCATTGGATAAACCAAAGTAAATATACTAGCACACATAG
Found at i:28535734 original size:28 final size:29
Alignment explanation
Indices: 28535702--28535757 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 29
28535692 ACACGGACGA
* *
28535702 GGACACAGGTGTGT-CTAGGCCGTGTGAG
1 GGACACAGGCGTGTGCTAGGCCATGTGAG
* *
28535730 GGACATAGGCGTGTGCTCGGCCATGTGA
1 GGACACAGGCGTGTGCTAGGCCATGTGA
28535758 AAATCCCTGT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
28 12 0.52
29 11 0.48
ACGTcount: A:0.18, C:0.20, G:0.41, T:0.21
Consensus pattern (29 bp):
GGACACAGGCGTGTGCTAGGCCATGTGAG
Done.