Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 41 of 226
Found at i:17510691 original size:19 final size:19
Alignment explanation
Indices: 17510667--17510703 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
17510657 CTTAGATCAA
*
17510667 TTTTTTATTTTTCCTAATT
1 TTTTTTATTTATCCTAATT
17510686 TTTTTTATTTATCCTAAT
1 TTTTTTATTTATCCTAAT
17510704 CATTAATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.19, C:0.11, G:0.00, T:0.70
Consensus pattern (19 bp):
TTTTTTATTTATCCTAATT
Found at i:17513882 original size:93 final size:94
Alignment explanation
Indices: 17513776--17513968 Score: 234
Period size: 93 Copynumber: 2.1 Consensus size: 94
17513766 TTAATGGTGT
* * *
17513776 AAAAA-GGCTCTCAAACTTTTTCAAAAAAA-CAATTAAG-CCTTTG-CTTTTTCTTTTTTTGCAC
1 AAAAAGGGCTCTCAAAATTTTTCAAAAAAAGCAATTAAGCCCCTAGTC-TTTT-TTTTTTTGCAC
* * * *
17513837 TGAATTGGGTATTTGAACTGTCAAAATGCATA
64 T-AATTGGGTACTTAAACTGCCAAAATACATA
*
17513869 AAAAAGGGC-CTCAAAATTTTTCAAAAAAAGCAATTGAGCCCCTAGTCTTTTTTTTTTTGCACTA
1 AAAAAGGGCTCTCAAAATTTTTCAAAAAAAGCAATTAAGCCCCTAGTCTTTTTTTTTTTGCACTA
* *
17513933 ATTGGGTACTTAAACTGCCAAATTACATC
66 ATTGGGTACTTAAACTGCCAAAATACATA
17513962 AAAAAGG
1 AAAAAGG
17513969 CTAAGGGTGG
Statistics
Matches: 86, Mismatches: 10, Indels: 8
0.83 0.10 0.08
Matches are distributed among these distances:
93 55 0.64
94 22 0.26
95 8 0.09
96 1 0.01
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.34
Consensus pattern (94 bp):
AAAAAGGGCTCTCAAAATTTTTCAAAAAAAGCAATTAAGCCCCTAGTCTTTTTTTTTTTGCACTA
ATTGGGTACTTAAACTGCCAAAATACATA
Found at i:17516045 original size:4 final size:4
Alignment explanation
Indices: 17516038--17516160 Score: 246
Period size: 4 Copynumber: 30.8 Consensus size: 4
17516028 TATCTGTGTG
17516038 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
17516086 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
17516134 TGTA TGTA TGTA TGTA TGTA TGTA TGT
1 TGTA TGTA TGTA TGTA TGTA TGTA TGT
17516161 GTTTTACCTG
Statistics
Matches: 119, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 119 1.00
ACGTcount: A:0.24, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TGTA
Found at i:17516650 original size:9 final size:9
Alignment explanation
Indices: 17516636--17516667 Score: 50
Period size: 8 Copynumber: 3.8 Consensus size: 9
17516626 GATAACTGAT
17516636 AACAAAAAA
1 AACAAAAAA
17516645 AAC-AAAAA
1 AACAAAAAA
17516653 AACAAAAAA
1 AACAAAAAA
17516662 AA-AAAA
1 AACAAAA
17516668 GGTTGGAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 12 0.55
9 10 0.45
ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00
Consensus pattern (9 bp):
AACAAAAAA
Found at i:17516658 original size:17 final size:16
Alignment explanation
Indices: 17516636--17516667 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
17516626 GATAACTGAT
17516636 AACAAAAAAAACAAAAA
1 AACAAAAAAAA-AAAAA
17516653 AACAAAAAAAAAAAA
1 AACAAAAAAAAAAAA
17516668 GGTTGGAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00
Consensus pattern (16 bp):
AACAAAAAAAAAAAAA
Found at i:17517783 original size:18 final size:18
Alignment explanation
Indices: 17517762--17517807 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
17517752 TTAACTGAAC
*
17517762 TAATCGAATTATCCGAAT
1 TAATCGAATTACCCGAAT
*
17517780 TAATCAAATTACCCGAAT
1 TAATCGAATTACCCGAAT
*
17517798 TAACCGAATT
1 TAATCGAATT
17517808 GAATCACTAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.30
Consensus pattern (18 bp):
TAATCGAATTACCCGAAT
Found at i:17517938 original size:13 final size:13
Alignment explanation
Indices: 17517920--17517944 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17517910 TTATGATTGG
17517920 ATTGGGTTGGGTA
1 ATTGGGTTGGGTA
17517933 ATTGGGTTGGGT
1 ATTGGGTTGGGT
17517945 TAGATATTTG
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:0.12, C:0.00, G:0.48, T:0.40
Consensus pattern (13 bp):
ATTGGGTTGGGTA
Found at i:17519156 original size:8 final size:8
Alignment explanation
Indices: 17519143--17519169 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
17519133 TGGAGAGGCT
17519143 TGGGGCAG
1 TGGGGCAG
17519151 TGGGGCAG
1 TGGGGCAG
17519159 TGGGGCAG
1 TGGGGCAG
17519167 TGG
1 TGG
17519170 AATCACTGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.11, C:0.11, G:0.63, T:0.15
Consensus pattern (8 bp):
TGGGGCAG
Found at i:17522518 original size:23 final size:24
Alignment explanation
Indices: 17522473--17522519 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
17522463 AAATGGGCCT
* * *
17522473 AAAAATTTGTCCAAGCTCGGCCCG
1 AAAAAATTGTCCAAGCCCAGCCCG
17522497 AAAAAATTG-CCAAGCCCAGCCCG
1 AAAAAATTGTCCAAGCCCAGCCCG
17522520 GCCCGGCCCA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.34, C:0.32, G:0.19, T:0.15
Consensus pattern (24 bp):
AAAAAATTGTCCAAGCCCAGCCCG
Found at i:17522905 original size:9 final size:8
Alignment explanation
Indices: 17522876--17522907 Score: 55
Period size: 8 Copynumber: 3.9 Consensus size: 8
17522866 CTTTTATTAA
17522876 TTTAAAAT
1 TTTAAAAT
17522884 TTTAAAAT
1 TTTAAAAT
17522892 TTTAAAATT
1 TTTAAAA-T
17522901 TTTAAAA
1 TTTAAAA
17522908 AGTTAAAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 15 0.65
9 8 0.35
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (8 bp):
TTTAAAAT
Found at i:17522913 original size:17 final size:17
Alignment explanation
Indices: 17522877--17522916 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
17522867 TTTTATTAAT
**
17522877 TTAAAA-TTTTAAAATT
1 TTAAAATTTTTAAAAAG
17522893 TTAAAATTTTTAAAAAG
1 TTAAAATTTTTAAAAAG
17522910 TTAAAAT
1 TTAAAAT
17522917 GAAAAAATTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 6 0.29
17 15 0.71
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (17 bp):
TTAAAATTTTTAAAAAG
Found at i:17525261 original size:6 final size:6
Alignment explanation
Indices: 17525230--17525278 Score: 62
Period size: 6 Copynumber: 7.8 Consensus size: 6
17525220 CCAAACACAC
* *
17525230 CAGTAAA CAGTAA TCAGTAA CGGTAA CAGTAA CAGTAA AAGTAA CAGTA
1 CAGT-AA CAGTAA -CAGTAA CAGTAA CAGTAA CAGTAA CAGTAA CAGTA
17525279 TTCAACACAC
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
6 27 0.73
7 10 0.27
ACGTcount: A:0.49, C:0.14, G:0.18, T:0.18
Consensus pattern (6 bp):
CAGTAA
Found at i:17531349 original size:50 final size:50
Alignment explanation
Indices: 17531238--17531486 Score: 327
Period size: 50 Copynumber: 4.8 Consensus size: 50
17531228 ATTTGGGTAA
*
17531238 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CC----GA-CATG
* *
17531294 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGACATG
* *
17531344 AGAGGTCCCATGTAAGACCATGTCTGGGTCATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGACATG
* * * *
17531394 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACCAACATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGACATG
** *
17531444 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
17531487 TGTTATTATC
Statistics
Matches: 175, Mismatches: 17, Indels: 7
0.88 0.09 0.04
Matches are distributed among these distances:
50 97 0.55
51 36 0.21
55 2 0.01
56 40 0.23
ACGTcount: A:0.27, C:0.23, G:0.29, T:0.22
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGACATG
Found at i:17533060 original size:6 final size:6
Alignment explanation
Indices: 17533029--17533077 Score: 62
Period size: 6 Copynumber: 7.8 Consensus size: 6
17533019 CCAAACACAC
* *
17533029 CAGTAAA CAGTAA TCAGTAA CGGTAA CAGTAA CAGTAA AAGTAA CAGTA
1 CAGT-AA CAGTAA -CAGTAA CAGTAA CAGTAA CAGTAA CAGTAA CAGTA
17533078 TTCAACACAC
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
6 27 0.73
7 10 0.27
ACGTcount: A:0.49, C:0.14, G:0.18, T:0.18
Consensus pattern (6 bp):
CAGTAA
Found at i:17533108 original size:33 final size:34
Alignment explanation
Indices: 17533069--17533144 Score: 111
Period size: 34 Copynumber: 2.3 Consensus size: 34
17533059 AACAGTAAAA
*
17533069 GTAACAGTA-TTCAACACACAAAGTGCTGAATCT-
1 GTAACAGTATTTCAACACACAAAGTGCCGAAT-TG
*
17533102 GTAACAGTATTTCGACACACAAAGTGCCGAATTG
1 GTAACAGTATTTCAACACACAAAGTGCCGAATTG
17533136 GTAACAGTA
1 GTAACAGTA
17533145 ACAGTAATCG
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
33 10 0.26
34 29 0.74
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.24
Consensus pattern (34 bp):
GTAACAGTATTTCAACACACAAAGTGCCGAATTG
Found at i:17534930 original size:29 final size:29
Alignment explanation
Indices: 17534876--17534933 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
17534866 GGAAAACGAA
* *
17534876 CCATTTCGGTAAATAATTACATAAAGGGC
1 CCATTTCGGTAAATAATTAAAAAAAGGGC
*
17534905 CCATTTCGGTAAAT-TTTGAAAAAAAGGGC
1 CCATTTCGGTAAATAATT-AAAAAAAGGGC
17534934 TTTTTTTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 2 0.08
29 23 0.92
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.28
Consensus pattern (29 bp):
CCATTTCGGTAAATAATTAAAAAAAGGGC
Found at i:17543949 original size:13 final size:13
Alignment explanation
Indices: 17543931--17543991 Score: 77
Period size: 13 Copynumber: 4.7 Consensus size: 13
17543921 CTCAAAATTT
17543931 TCAAAAGCACTTC
1 TCAAAAGCACTTC
17543944 TCAAAAGCACTTC
1 TCAAAAGCACTTC
* *
17543957 TCGAAAGCACTTT
1 TCAAAAGCACTTC
* * *
17543970 TCTACAGCACTTT
1 TCAAAAGCACTTC
17543983 TCAAAAGCA
1 TCAAAAGCA
17543992 TTGCCAAACT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 42 1.00
ACGTcount: A:0.36, C:0.28, G:0.10, T:0.26
Consensus pattern (13 bp):
TCAAAAGCACTTC
Found at i:17565682 original size:21 final size:23
Alignment explanation
Indices: 17565658--17565705 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
17565648 AAAAAAGAAG
*
17565658 AAAATAGC-AAGAAAA-TAATAA
1 AAAATAGCAAAAAAAAGTAATAA
17565679 AAAATAGCAAAAAAAAGTAATAA
1 AAAATAGCAAAAAAAAGTAATAA
17565702 AAAA
1 AAAA
17565706 ACAGGAGGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 8 0.33
22 6 0.25
23 10 0.42
ACGTcount: A:0.75, C:0.04, G:0.08, T:0.12
Consensus pattern (23 bp):
AAAATAGCAAAAAAAAGTAATAA
Found at i:17566199 original size:16 final size:17
Alignment explanation
Indices: 17566173--17566204 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
17566163 CAAAACTATT
17566173 ATTTTAGAAAATTTTAA
1 ATTTTAGAAAATTTTAA
17566190 ATTTTA-AAAATTTTA
1 ATTTTAGAAAATTTTA
17566205 TAAATATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (17 bp):
ATTTTAGAAAATTTTAA
Found at i:17566219 original size:27 final size:27
Alignment explanation
Indices: 17566173--17566241 Score: 95
Period size: 27 Copynumber: 2.6 Consensus size: 27
17566163 CAAAACTATT
*
17566173 ATTTTAGAAA-ATTTTAAATTTTAAAA
1 ATTTTATAAATATTTTAAATTTTAAAA
*
17566199 ATTTTATAAATATTTTTAATTTTAAAA
1 ATTTTATAAATATTTTAAATTTTAAAA
*
17566226 ATTATATTAAATATTT
1 ATTTTA-TAAATATTT
17566242 GAAAATTATT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
26 9 0.24
27 20 0.53
28 9 0.24
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.52
Consensus pattern (27 bp):
ATTTTATAAATATTTTAAATTTTAAAA
Found at i:17570412 original size:22 final size:22
Alignment explanation
Indices: 17570387--17570467 Score: 117
Period size: 22 Copynumber: 3.7 Consensus size: 22
17570377 GAGTTTCATT
17570387 AGCTTAGTACGTTAGCCATGAG
1 AGCTTAGTACGTTAGCCATGAG
17570409 AGCTTAGTACGTTAGCCATGAG
1 AGCTTAGTACGTTAGCCATGAG
* * * **
17570431 GGTTTAGTTCGTTAAACATGAG
1 AGCTTAGTACGTTAGCCATGAG
17570453 AGCTTAGTACGTTAG
1 AGCTTAGTACGTTAG
17570468 TTACAACTAT
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.31
Consensus pattern (22 bp):
AGCTTAGTACGTTAGCCATGAG
Found at i:17576578 original size:22 final size:22
Alignment explanation
Indices: 17576550--17576593 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
17576540 TATGCTTCTC
*
17576550 GACTTTCCTTGTTTCTGCATGA
1 GACTTTCCTTGCTTCTGCATGA
*
17576572 GACTTTCCTTGCTTCTGTATGA
1 GACTTTCCTTGCTTCTGCATGA
17576594 CATCCCTTCC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.45
Consensus pattern (22 bp):
GACTTTCCTTGCTTCTGCATGA
Found at i:17578749 original size:22 final size:21
Alignment explanation
Indices: 17578712--17578762 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 21
17578702 AATGTAAAAC
17578712 TAAAAAAA-ATTCAAAAATTA
1 TAAAAAAATATTCAAAAATTA
* *
17578732 TAAAAAAATATATTAAAAATTG
1 TAAAAAAATAT-TCAAAAATTA
17578754 TAAAAAAAT
1 TAAAAAAAT
17578763 TTTAGAATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 8 0.30
21 2 0.07
22 17 0.63
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (21 bp):
TAAAAAAATATTCAAAAATTA
Found at i:17581130 original size:17 final size:17
Alignment explanation
Indices: 17581093--17581132 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
17581083 TAATTCTCAA
*
17581093 ATAAATAAATTATGATT
1 ATAAATAAATTATGATG
* *
17581110 ATAATTAAATTATTATG
1 ATAAATAAATTATGATG
17581127 ATAAAT
1 ATAAAT
17581133 TATGAAAAAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (17 bp):
ATAAATAAATTATGATG
Found at i:17593158 original size:18 final size:18
Alignment explanation
Indices: 17593124--17593174 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 18
17593114 AGGGGTGTGC
17593124 AAAATTCGGTTAAAACCGAA
1 AAAATTCGGTT--AACCGAA
*
17593144 AAAATTCGGTTAACCGAC
1 AAAATTCGGTTAACCGAA
**
17593162 TGAATTCGGTTAA
1 AAAATTCGGTTAA
17593175 TCAGTCGGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 17 0.61
20 11 0.39
ACGTcount: A:0.41, C:0.16, G:0.18, T:0.25
Consensus pattern (18 bp):
AAAATTCGGTTAACCGAA
Found at i:17593402 original size:7 final size:7
Alignment explanation
Indices: 17593390--17593434 Score: 54
Period size: 7 Copynumber: 6.3 Consensus size: 7
17593380 CCAAGAATAA
17593390 TTCATGT
1 TTCATGT
17593397 TTCATGTT
1 TTCATG-T
17593405 TTCATGT
1 TTCATGT
**
17593412 TTCATAC
1 TTCATGT
*
17593419 TGCATGT
1 TTCATGT
17593426 TTCATGT
1 TTCATGT
17593433 TT
1 TT
17593435 TCTTCTGTAC
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
7 24 0.77
8 7 0.23
ACGTcount: A:0.16, C:0.16, G:0.13, T:0.56
Consensus pattern (7 bp):
TTCATGT
Found at i:17593706 original size:17 final size:17
Alignment explanation
Indices: 17593684--17593744 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
17593674 TGTTAAAGAC
17593684 TTATGTAATATTTTTAA
1 TTATGTAATATTTTTAA
* ***
17593701 TTATGTAGTGATTCAAAGA
1 TTATGTAAT-ATTTTTA-A
*
17593720 CTTATGTAATATTTTTAG
1 -TTATGTAATATTTTTAA
17593738 TTATGTA
1 TTATGTA
17593745 GTAATTCAAA
Statistics
Matches: 32, Mismatches: 9, Indels: 6
0.68 0.19 0.13
Matches are distributed among these distances:
17 15 0.47
18 4 0.12
19 5 0.16
20 8 0.25
ACGTcount: A:0.33, C:0.03, G:0.13, T:0.51
Consensus pattern (17 bp):
TTATGTAATATTTTTAA
Found at i:17593728 original size:37 final size:37
Alignment explanation
Indices: 17593678--17593786 Score: 173
Period size: 37 Copynumber: 2.9 Consensus size: 37
17593668 TTTATGTGTT
17593678 AAAGACTTATGTAATATTTTTAATTATGTAGTGATTC
1 AAAGACTTATGTAATATTTTTAATTATGTAGTGATTC
* *
17593715 AAAGACTTATGTAATATTTTTAGTTATGTAGTAATTC
1 AAAGACTTATGTAATATTTTTAATTATGTAGTGATTC
* * *
17593752 AAAGACTTGTGTAATTTTTTTAATTATATAGTGAT
1 AAAGACTTATGTAATATTTTTAATTATGTAGTGAT
17593787 CGGTCAAGTC
Statistics
Matches: 65, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 65 1.00
ACGTcount: A:0.35, C:0.05, G:0.14, T:0.47
Consensus pattern (37 bp):
AAAGACTTATGTAATATTTTTAATTATGTAGTGATTC
Found at i:17593807 original size:9 final size:9
Alignment explanation
Indices: 17593785--17593855 Score: 99
Period size: 9 Copynumber: 8.0 Consensus size: 9
17593775 TTATATAGTG
*
17593785 ATCGGTCAA
1 ATCGGTTAA
*
17593794 GTCGGTTAA
1 ATCGGTTAA
17593803 ATCGGTTAA
1 ATCGGTTAA
*
17593812 GTCGGTTAA
1 ATCGGTTAA
17593821 ATCGGTT-A
1 ATCGGTTAA
17593829 ATCGGTTAA
1 ATCGGTTAA
*
17593838 ATAGGTTAA
1 ATCGGTTAA
17593847 ATCGGTTAA
1 ATCGGTTAA
17593856 TTTTTAACCA
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
8 8 0.15
9 46 0.85
ACGTcount: A:0.31, C:0.11, G:0.25, T:0.32
Consensus pattern (9 bp):
ATCGGTTAA
Found at i:17593844 original size:26 final size:26
Alignment explanation
Indices: 17593795--17593856 Score: 97
Period size: 26 Copynumber: 2.3 Consensus size: 26
17593785 ATCGGTCAAG
* *
17593795 TCGGTTAAATCGGTTAAGTCGGTTAAA
1 TCGGTT-AATCGGTTAAATAGGTTAAA
17593822 TCGGTTAATCGGTTAAATAGGTTAAA
1 TCGGTTAATCGGTTAAATAGGTTAAA
17593848 TCGGTTAAT
1 TCGGTTAAT
17593857 TTTTAACCAA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
26 27 0.82
27 6 0.18
ACGTcount: A:0.31, C:0.10, G:0.24, T:0.35
Consensus pattern (26 bp):
TCGGTTAATCGGTTAAATAGGTTAAA
Found at i:17594032 original size:12 final size:12
Alignment explanation
Indices: 17594015--17594039 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
17594005 AACTAATTCG
17594015 GGTCGGTTAACC
1 GGTCGGTTAACC
17594027 GGTCGGTTAACC
1 GGTCGGTTAACC
17594039 G
1 G
17594040 AATGCACACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.36, T:0.24
Consensus pattern (12 bp):
GGTCGGTTAACC
Found at i:17601524 original size:36 final size:36
Alignment explanation
Indices: 17601484--17601671 Score: 232
Period size: 36 Copynumber: 4.9 Consensus size: 36
17601474 GGTAGCTTTA
17601484 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
* *
17601520 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGAT-A-----AG---T
17601565 AGCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 -GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
* *
17601602 GTTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
* *
17601638 GCTATACTTATCTGATCAAGTGACAAAGTGATAA
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAA
17601672 ATGGTAGTTT
Statistics
Matches: 134, Mismatches: 8, Indels: 20
0.83 0.05 0.12
Matches are distributed among these distances:
36 96 0.72
37 2 0.01
40 2 0.01
42 2 0.01
45 2 0.01
46 30 0.22
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.29
Consensus pattern (36 bp):
GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
Found at i:17601585 original size:82 final size:82
Alignment explanation
Indices: 17601448--17601638 Score: 328
Period size: 82 Copynumber: 2.3 Consensus size: 82
17601438 TTTGAGTACT
* *
17601448 TCTGATCAAGAGATAAAGCGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
1 TCTGATCAAGAGAAAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
17601513 GATAAGTGCTACACTTA
66 GATAAGTGCTACACTTA
*
17601530 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
1 TCTGATCAAGAGAAAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
* *
17601595 GATAAGTGTTATACTTA
66 GATAAGTGCTACACTTA
*
17601612 TCTGATCAAGTGAAAAAGTGATAAGTG
1 TCTGATCAAGAGAAAAAGTGATAAGTG
17601639 CTATACTTAT
Statistics
Matches: 103, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
82 103 1.00
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.29
Consensus pattern (82 bp):
TCTGATCAAGAGAAAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
GATAAGTGCTACACTTA
Found at i:17602253 original size:36 final size:36
Alignment explanation
Indices: 17602213--17602400 Score: 225
Period size: 36 Copynumber: 4.9 Consensus size: 36
17602203 GGTAGCTTTA
17602213 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
*
17602249 GCTACACTTATCTGATCAAGAGACAAAA-TGATAAGTGGTAGCTTT
1 GCTACACTTATCTGATCAAGTGA-AAAAGTGAT-A-----AG---T
17602294 AGCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 -GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
* *
17602331 GTTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
* *
17602367 GCTATACTTATCTGATCAAGTGACAAAGTGATAA
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAA
17602401 ATGGTAGTTT
Statistics
Matches: 134, Mismatches: 6, Indels: 24
0.82 0.04 0.15
Matches are distributed among these distances:
36 92 0.69
37 6 0.04
40 2 0.01
42 2 0.01
45 6 0.04
46 26 0.19
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.29
Consensus pattern (36 bp):
GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
Found at i:17602314 original size:82 final size:81
Alignment explanation
Indices: 17602177--17602367 Score: 310
Period size: 82 Copynumber: 2.3 Consensus size: 81
17602167 TTTGAGTACT
**
17602177 TCTGATCAAGAGATAAAGCGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
1 TCTGATCAAGAGA-AAAATGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
17602242 GATAAGTGCTACACTTA
65 GATAAGTGCTACACTTA
17602259 TCTGATCAAGAGACAAAATGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
1 TCTGATCAAGAGA-AAAATGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
* *
17602324 GATAAGTGTTATACTTA
65 GATAAGTGCTACACTTA
*
17602341 TCTGATCAAGTGAAAAAGTGATAAGTG
1 TCTGATCAAGAGAAAAA-TGATAAGTG
17602368 CTATACTTAT
Statistics
Matches: 102, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
81 4 0.04
82 98 0.96
ACGTcount: A:0.38, C:0.13, G:0.21, T:0.29
Consensus pattern (81 bp):
TCTGATCAAGAGAAAAATGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGTG
ATAAGTGCTACACTTA
Found at i:17602603 original size:729 final size:729
Alignment explanation
Indices: 17601201--17602647 Score: 2831
Period size: 729 Copynumber: 2.0 Consensus size: 729
17601191 ATGAATAAAT
17601201 TTGTATTTTATATCGAGAACCCGAAGCAAGCCGAGGAAAAGAAAAAGTAGTTGATTAGTCCCTGA
1 TTGTATTTTATATCGAGAACCCGAAGCAAGCCGAGGAAAAGAAAAAGTAGTTGATTAGTCCCTGA
17601266 ACTTTTACAAATTCAACAAATCGACCCAGGTAAGTTCATATGGCTGAAATTTAATGATTAAATGT
66 ACTTTTACAAATTCAACAAATCGACCCAGGTAAGTTCATATGGCTGAAATTTAATGATTAAATGT
17601331 TAATTTCATGAATTATATAATGTATGATGAAATATATTTAGTGTTGAAAAGAGAGTAAAATAAAA
131 TAATTTCATGAATTATATAATGTATGATGAAATATATTTAGTGTTGAAAAGAGAGTAAAATAAAA
* *
17601396 TGCGAAAATCGAATAAATGATCAAATTAAGCGGAACACTGAATTTGAGTACTTCTGATCAAGAGA
196 TGCAAAAATCGAATAAATGATCAAATTAAGCGGAACACCGAATTTGAGTACTTCTGATCAAGAGA
17601461 TAAAGCGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGTGATAAGTGCTACA
261 TAAAGCGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGTGATAAGTGCTACA
*
17601526 CTTATCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAA
326 CTTATCTGATCAAGAGACAAAATGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAA
17601591 AAGTGATAAGTGTTATACTTATCTGATCAAGTGAAAAAGTGATAAGTGCTATACTTATCTGATCA
391 AAGTGATAAGTGTTATACTTATCTGATCAAGTGAAAAAGTGATAAGTGCTATACTTATCTGATCA
17601656 AGTGACAAAGTGATAAATGGTAGTTTAGCTACACTTATCTGATCAGGGACAAATGATAAGTGATC
456 AGTGACAAAGTGATAAATGGTAGTTTAGCTACACTTATCTGATCAGGGACAAATGATAAGTGATC
17601721 ATACGTAAAACCATAGTTATACTATGGCAAAGTGAAAGTGAAGTACTCAATTTTCCGTGACCGTT
521 ATACGTAAAACCATAGTTATACTATGGCAAAGTGAAAGTGAAGTACTCAATTTTCCGTGACCGTT
17601786 CCTTAATTTTGATCAAGGATGGTAAGTGACGAATGGGCACAAAGGAATTATGGTAAAAGAATAAG
586 CCTTAATTTTGATCAAGGATGGTAAGTGACGAATGGGCACAAAGGAATTATGGTAAAAGAATAAG
*
17601851 TAGTAGTGAGTTTATATCAAGGAACTCACCAAAGATTGTGGTTGACAGGTAAATTTAGTAATGGT
651 TAGTAGTGAGTTTATACCAAGGAACTCACCAAAGATTGTGGTTGACAGGTAAATTTAGTAATGGT
17601916 GTATATTGTATAAG
716 GTATATTGTATAAG
17601930 TTGTATTTTATATCGAGAACCCGAAGCAAGCCGAGGAAAAGAAAAAGTAGTTGATTAGTCCCTGA
1 TTGTATTTTATATCGAGAACCCGAAGCAAGCCGAGGAAAAGAAAAAGTAGTTGATTAGTCCCTGA
17601995 ACTTTTACAAATTCAACAAATCGACCCAGGTAAGTTCATATGGCTGAAATTTAATGATTAAATGT
66 ACTTTTACAAATTCAACAAATCGACCCAGGTAAGTTCATATGGCTGAAATTTAATGATTAAATGT
*
17602060 TAATTTCATGAATTATATAATGTATGATGAAATGTATTTAGTGTTGAAAAGAGAGTAAAATAAAA
131 TAATTTCATGAATTATATAATGTATGATGAAATATATTTAGTGTTGAAAAGAGAGTAAAATAAAA
*
17602125 TGCAAAAATCGAATAAATGATCAAATTAAGCGGAACACCGGATTTGAGTACTTCTGATCAAGAGA
196 TGCAAAAATCGAATAAATGATCAAATTAAGCGGAACACCGAATTTGAGTACTTCTGATCAAGAGA
17602190 TAAAGCGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGTGATAAGTGCTACA
261 TAAAGCGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGTGATAAGTGCTACA
17602255 CTTATCTGATCAAGAGACAAAATGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAA
326 CTTATCTGATCAAGAGACAAAATGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAA
17602320 AAGTGATAAGTGTTATACTTATCTGATCAAGTGAAAAAGTGATAAGTGCTATACTTATCTGATCA
391 AAGTGATAAGTGTTATACTTATCTGATCAAGTGAAAAAGTGATAAGTGCTATACTTATCTGATCA
17602385 AGTGACAAAGTGATAAATGGTAGTTTAGCTACACTTATCTGATCAGGGACAAATGATAAGTGATC
456 AGTGACAAAGTGATAAATGGTAGTTTAGCTACACTTATCTGATCAGGGACAAATGATAAGTGATC
*
17602450 ATACGTAAGACCATAGTTATACTATGGCAAAGTGAAAGTGAAGTACTCAATTTTCCGTGACCGTT
521 ATACGTAAAACCATAGTTATACTATGGCAAAGTGAAAGTGAAGTACTCAATTTTCCGTGACCGTT
17602515 CCTTAATTTTGATCAAGGATGGTAAGTGACGAATGGGCACAAAGGAATTATGGTAAAAGAATAAG
586 CCTTAATTTTGATCAAGGATGGTAAGTGACGAATGGGCACAAAGGAATTATGGTAAAAGAATAAG
17602580 TAGTAGTGAGTTTATACCAAGGAACTCACCAAAGATTGTGGTTGACAGGTAAATTTAGTAATGGT
651 TAGTAGTGAGTTTATACCAAGGAACTCACCAAAGATTGTGGTTGACAGGTAAATTTAGTAATGGT
17602645 GTA
716 GTA
17602648 NNNNNNNNNN
Statistics
Matches: 711, Mismatches: 7, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
729 711 1.00
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.29
Consensus pattern (729 bp):
TTGTATTTTATATCGAGAACCCGAAGCAAGCCGAGGAAAAGAAAAAGTAGTTGATTAGTCCCTGA
ACTTTTACAAATTCAACAAATCGACCCAGGTAAGTTCATATGGCTGAAATTTAATGATTAAATGT
TAATTTCATGAATTATATAATGTATGATGAAATATATTTAGTGTTGAAAAGAGAGTAAAATAAAA
TGCAAAAATCGAATAAATGATCAAATTAAGCGGAACACCGAATTTGAGTACTTCTGATCAAGAGA
TAAAGCGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGTGATAAGTGCTACA
CTTATCTGATCAAGAGACAAAATGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAA
AAGTGATAAGTGTTATACTTATCTGATCAAGTGAAAAAGTGATAAGTGCTATACTTATCTGATCA
AGTGACAAAGTGATAAATGGTAGTTTAGCTACACTTATCTGATCAGGGACAAATGATAAGTGATC
ATACGTAAAACCATAGTTATACTATGGCAAAGTGAAAGTGAAGTACTCAATTTTCCGTGACCGTT
CCTTAATTTTGATCAAGGATGGTAAGTGACGAATGGGCACAAAGGAATTATGGTAAAAGAATAAG
TAGTAGTGAGTTTATACCAAGGAACTCACCAAAGATTGTGGTTGACAGGTAAATTTAGTAATGGT
GTATATTGTATAAG
Found at i:17608226 original size:20 final size:21
Alignment explanation
Indices: 17608201--17608247 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
17608191 TATTTCAATA
17608201 TTTTAAGTATTTTAT-ATTAT
1 TTTTAAGTATTTTATAATTAT
*
17608221 TTTTAA-TTTTTTATAATTAT
1 TTTTAAGTATTTTATAATTAT
*
17608241 TATTAAG
1 TTTTAAG
17608248 AAATACTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (21 bp):
TTTTAAGTATTTTATAATTAT
Found at i:17609121 original size:35 final size:35
Alignment explanation
Indices: 17609082--17609153 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
17609072 TTAATCATGA
17609082 GATCGTTTTTTCATGACAATTTTGTCAAATAATTT
1 GATCGTTTTTTCATGACAATTTTGTCAAATAATTT
17609117 GATCGTTTTTTCATGACAATTTTGTCAAATAATTT
1 GATCGTTTTTTCATGACAATTTTGTCAAATAATTT
17609152 GA
1 GA
17609154 CCTTATTTGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.29, C:0.11, G:0.12, T:0.47
Consensus pattern (35 bp):
GATCGTTTTTTCATGACAATTTTGTCAAATAATTT
Found at i:17609895 original size:19 final size:18
Alignment explanation
Indices: 17609869--17609906 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
17609859 AAAATCTTAT
*
17609869 AAAGTAAAAATACAAATA
1 AAAGTAAAAATAAAAATA
17609887 AAAGATAAAAATAAAAATA
1 AAAG-TAAAAATAAAAATA
17609906 A
1 A
17609907 TTAAATTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.76, C:0.03, G:0.05, T:0.16
Consensus pattern (18 bp):
AAAGTAAAAATAAAAATA
Found at i:17609900 original size:6 final size:6
Alignment explanation
Indices: 17609873--17609906 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
17609863 TCTTATAAAG
*
17609873 TAAAAA TACAAA TAAAAGA TAAAAA TAAAAA TAA
1 TAAAAA TAAAAA TAAAA-A TAAAAA TAAAAA TAA
17609907 TTAAATTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 19 0.76
7 6 0.24
ACGTcount: A:0.76, C:0.03, G:0.03, T:0.18
Consensus pattern (6 bp):
TAAAAA
Found at i:17609900 original size:13 final size:12
Alignment explanation
Indices: 17609873--17609906 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
17609863 TCTTATAAAG
*
17609873 TAAAAATACAAA
1 TAAAAATAAAAA
17609885 TAAAAGATAAAAA
1 TAAAA-ATAAAAA
17609898 TAAAAATAA
1 TAAAAATAA
17609907 TTAAATTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.76, C:0.03, G:0.03, T:0.18
Consensus pattern (12 bp):
TAAAAATAAAAA
Found at i:17610384 original size:22 final size:22
Alignment explanation
Indices: 17610358--17610405 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
17610348 CTTTAATCAA
17610358 TTATTCAAAAGTACCACAAGAT
1 TTATTCAAAAGTACCACAAGAT
17610380 TTATTCAAAAGTACCACAAGAT
1 TTATTCAAAAGTACCACAAGAT
17610402 TTAT
1 TTAT
17610406 CTTGTTGAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.44, C:0.17, G:0.08, T:0.31
Consensus pattern (22 bp):
TTATTCAAAAGTACCACAAGAT
Found at i:17613075 original size:15 final size:15
Alignment explanation
Indices: 17613055--17613083 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
17613045 TCACTTCAAT
17613055 TACTGACAAAAGTAC
1 TACTGACAAAAGTAC
17613070 TACTGACAAAAGTA
1 TACTGACAAAAGTA
17613084 ATTGATGGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.17, G:0.14, T:0.21
Consensus pattern (15 bp):
TACTGACAAAAGTAC
Found at i:17614256 original size:13 final size:13
Alignment explanation
Indices: 17614238--17614262 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17614228 TCAAAGGAGC
17614238 AAAAAGAAAAAAG
1 AAAAAGAAAAAAG
17614251 AAAAAGAAAAAA
1 AAAAAGAAAAAA
17614263 ACAATAGACA
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:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (13 bp):
AAAAAGAAAAAAG
Found at i:17636951 original size:3 final size:3
Alignment explanation
Indices: 17636943--17636986 Score: 52
Period size: 3 Copynumber: 14.3 Consensus size: 3
17636933 GGCAGTTTCT
* * *
17636943 CAC CAC CAC CAC CAC CTC CAC CAC CTTC CTC CAC CAC CAC CAC C
1 CAC CAC CAC CAC CAC CAC CAC CAC C-AC CAC CAC CAC CAC CAC C
17636987 TCCTAATCGT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
3 34 0.94
4 2 0.06
ACGTcount: A:0.25, C:0.66, G:0.00, T:0.09
Consensus pattern (3 bp):
CAC
Found at i:17644421 original size:16 final size:16
Alignment explanation
Indices: 17644400--17644431 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
17644390 CAACTGCAAA
17644400 CACCAAACAGGAAAAG
1 CACCAAACAGGAAAAG
17644416 CACCAAACAGGAAAAG
1 CACCAAACAGGAAAAG
17644432 AACAGTGTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.25, G:0.19, T:0.00
Consensus pattern (16 bp):
CACCAAACAGGAAAAG
Found at i:17648312 original size:63 final size:63
Alignment explanation
Indices: 17648234--17648360 Score: 236
Period size: 63 Copynumber: 2.0 Consensus size: 63
17648224 GTAGCTCTCT
* *
17648234 GGCTAATTATCCTATTCAACACTCGTTTGTTGAAAATTTTGTATCATGTAAAATTTAATATGA
1 GGCTAATTATCCTATTCAACACTAGTTTGTTGAAAATTTTGTATCATGTAAAAATTAATATGA
17648297 GGCTAATTATCCTATTCAACACTAGTTTGTTGAAAATTTTGTATCATGTAAAAATTAATATGA
1 GGCTAATTATCCTATTCAACACTAGTTTGTTGAAAATTTTGTATCATGTAAAAATTAATATGA
17648360 G
1 G
17648361 TTATTAAACA
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 62 1.00
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.40
Consensus pattern (63 bp):
GGCTAATTATCCTATTCAACACTAGTTTGTTGAAAATTTTGTATCATGTAAAAATTAATATGA
Found at i:17652103 original size:54 final size:54
Alignment explanation
Indices: 17652043--17652151 Score: 173
Period size: 54 Copynumber: 2.0 Consensus size: 54
17652033 AACCAAACAA
* *
17652043 TGTTCAAATTCTTTGGCACCGCGTGGCATCCTAAATGATGGATCTCTACAATTC
1 TGTTCAAATTCTATGGCACCGCATGGCATCCTAAATGATGGATCTCTACAATTC
* * *
17652097 TGTTCAAATTCTATGGCACCGTATGGCATCCTAAGTGATGGATCTGTACAATTC
1 TGTTCAAATTCTATGGCACCGCATGGCATCCTAAATGATGGATCTCTACAATTC
17652151 T
1 T
17652152 CGAGGTACTT
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 50 1.00
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.34
Consensus pattern (54 bp):
TGTTCAAATTCTATGGCACCGCATGGCATCCTAAATGATGGATCTCTACAATTC
Found at i:17659611 original size:12 final size:11
Alignment explanation
Indices: 17659587--17659642 Score: 51
Period size: 13 Copynumber: 4.8 Consensus size: 11
17659577 AACATGTTTC
17659587 TTTTATTTTAT
1 TTTTATTTTAT
17659598 TTTTATTCTTATT
1 TTTTATT-TTA-T
* *
17659611 TTTTAATTTCT
1 TTTTATTTTAT
17659622 TCATTTATTTTA-
1 T--TTTATTTTAT
17659634 TTTTATTTT
1 TTTTATTTT
17659643 TTGCTTATTA
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
10 8 0.22
11 9 0.24
12 6 0.16
13 14 0.38
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.77
Consensus pattern (11 bp):
TTTTATTTTAT
Found at i:17662653 original size:25 final size:25
Alignment explanation
Indices: 17662565--17662650 Score: 91
Period size: 30 Copynumber: 3.2 Consensus size: 25
17662555 TAAATGTATA
*
17662565 TGTTTTATACATTGCCGAATTTGAT
1 TGTTTTATATATTGCCGAATTTGAT
* *
17662590 TAATTATAGATATATATTGTCGAATTTGAT
1 T-GTT-T---TATATATTGCCGAATTTGAT
17662620 TGTTTTATATATTGCCGAATTTGAAT
1 TGTTTTATATATTGCCGAATTTG-AT
17662646 TGTTT
1 TGTTT
17662651 ATAGTTATAC
Statistics
Matches: 50, Mismatches: 5, Indels: 11
0.76 0.08 0.17
Matches are distributed among these distances:
25 18 0.36
26 9 0.18
27 1 0.02
28 1 0.02
29 2 0.04
30 19 0.38
ACGTcount: A:0.28, C:0.07, G:0.15, T:0.50
Consensus pattern (25 bp):
TGTTTTATATATTGCCGAATTTGAT
Found at i:17662659 original size:31 final size:29
Alignment explanation
Indices: 17662569--17663131 Score: 169
Period size: 31 Copynumber: 18.8 Consensus size: 29
17662559 TGTATATGTT
*
17662569 TTATACATTGCCGAATTTGATTAATTATAG
1 TTATACATTGCCGAATTTGATT-GTTATAG
* * *
17662599 ATATATATTGTCGAATTTGATTG-T-T--
1 TTATACATTGCCGAATTTGATTGTTATAG
*
17662624 TTATATATTGCCGAATTTGAATTGTTTATAG
1 TTATACATTGCCGAATTTG-ATTG-TTATAG
* * * *
17662655 TTATACATTGTCGAAATTGATTTGCATATGG
1 TTATACATTGCCGAATTTGA-TTG-TTATAG
* *
17662686 TTATA-AGTTGCTGAA-TTGATT-TGTACATG
1 TTATACA-TTGCCGAATTTGATTGT-TATA-G
* * * *
17662715 ATTATACATTGCTGAAATTAATTTGTATATGG
1 -TTATACATTGCCGAATTTGA-TTGT-TATAG
** * *
17662747 TTATACATTGTTGAAATTGAATTGTATATGG
1 TTATACATTGCCGAATTTG-ATTGT-TATAG
* *
17662778 ATATA-AGTTGCCGAA-TTGATTCGTATATGG
1 TTATACA-TTGCCGAATTTGATT-GT-TATAG
* * * * *
17662808 TTGTACATTGCTGAAATTAATTTGTATATGG
1 TTATACATTGCCGAATTTGA-TTGT-TATAG
* ** * *
17662839 TTATATATTGTTGAAATTGAATTGTATATGG
1 TTATACATTGCCGAATTTG-ATTGT-TATAG
*
17662870 ATATA-AGTTGCCGAA-TTGATT-TGTATATG
1 TTATACA-TTGCCGAATTTGATTGT-TATA-G
* * ** * *
17662899 ACTATACATTGCTGAAATTAAATTGTACATGG
1 -TTATACATTGCCG-AATTTGATTGT-TATAG
** * *
17662931 TTATACATTGTTGAAATTGAATTGTATATGG
1 TTATACATTGCCGAATTTG-ATTGT-TATAG
* * *
17662962 ATATA-AGTTGCTGAA-TTGATTCGTATATGG
1 TTATACA-TTGCCGAATTTGATT-GT-TATAG
* *
17662992 TTATACATTGCTGAATTTGA-T-TTGTA-
1 TTATACATTGCCGAATTTGATTGTTATAG
*
17663018 -TATACATTGCCGAACTTT-ATTCGTATATGG
1 TTATACATTGCCGAA-TTTGATT-GT-TATAG
* *
17663048 TTATACATTGTCGAA-TTGATTCGTATATGG
1 TTATACATTGCCGAATTTGATT-GT-TATAG
17663078 TTATACATTGCCGAATTTGATT-TGTATATG
1 TTATACATTGCCGAATTTGATTGT-TATA-G
*
17663108 ATTATACATTGCCGAACTTGATTG
1 -TTATACATTGCCGAATTTGATTG
17663132 GTTTCGTGCA
Statistics
Matches: 422, Mismatches: 65, Indels: 90
0.73 0.11 0.16
Matches are distributed among these distances:
25 31 0.07
26 8 0.02
27 3 0.01
28 10 0.02
29 22 0.05
30 128 0.30
31 202 0.48
32 12 0.03
33 6 0.01
ACGTcount: A:0.30, C:0.08, G:0.18, T:0.44
Consensus pattern (29 bp):
TTATACATTGCCGAATTTGATTGTTATAG
Found at i:17662725 original size:61 final size:60
Alignment explanation
Indices: 17662624--17663130 Score: 407
Period size: 61 Copynumber: 8.3 Consensus size: 60
17662614 TTTGATTGTT
* * * * *
17662624 TTATATATTGCCGAATTTGAATTGTTTAT-AGTTATACATTGTCGAAATTGATTTGCATATGG
1 TTATACATTGCTGAA-TTGATTTGTATATGA-TTATACATTG-CGAAATTGATTTGTATATGG
* *
17662686 TTATA-AGTTGCTGAATTGATTTGTACATGATTATACATTGCTGAAATTAATTTGTATATGG
1 TTATACA-TTGCTGAATTGATTTGTATATGATTATACATTGC-GAAATTGATTTGTATATGG
* * *
17662747 TTATACATTGTTGAAATTGAATTGTATATGGA-TATA-AGTTGCCG-AATTGATTCGTATATGG
1 TTATACATTGCTG-AATTGATTTGTATAT-GATTATACA-TTG-CGAAATTGATTTGTATATGG
* * * * * *
17662808 TTGTACATTGCTGAAATTAATTTGTATATGGTTATATATTGTTGAAATTGAATTGTATATGG
1 TTATACATTGCTG-AATTGATTTGTATATGATTATACATTG-CGAAATTGATTTGTATATGG
* * * * * *
17662870 ATATA-AGTTGCCGAATTGATTTGTATATGACTATACATTGCTGAAATTAAATTGTACATGG
1 TTATACA-TTGCTGAATTGATTTGTATATGATTATACATTGC-GAAATTGATTTGTATATGG
* * *
17662931 TTATACATTGTTGAAATTGAATTGTATATGGA-TATA-AGTTGCTG-AATTGATTCGTATATGG
1 TTATACATTGCTG-AATTGATTTGTATAT-GATTATACA-TTGC-GAAATTGATTTGTATATGG
* * *
17662992 TTATACATTGCTGAATTTGATTTG----T-A-TATACATTGCCGAACTTTATTCGTATATGG
1 TTATACATTGCTGAA-TTGATTTGTATATGATTATACATTG-CGAAATTGATTTGTATATGG
* * * *
17663048 TTATACATTG-TCGAATTGATTCGTATATGGTTATACATTGCCGAATTTGATTTGTATATGA
1 TTATACATTGCT-GAATTGATTTGTATATGATTATACATTG-CGAAATTGATTTGTATATGG
*
17663109 TTATACATTGCCGAACTTGATT
1 TTATACATTGCTGAA-TTGATT
17663131 GGTTTCGTGC
Statistics
Matches: 366, Mismatches: 49, Indels: 60
0.77 0.10 0.13
Matches are distributed among these distances:
55 17 0.05
56 30 0.08
57 1 0.00
59 1 0.00
60 4 0.01
61 218 0.60
62 90 0.25
63 5 0.01
ACGTcount: A:0.30, C:0.08, G:0.19, T:0.43
Consensus pattern (60 bp):
TTATACATTGCTGAATTGATTTGTATATGATTATACATTGCGAAATTGATTTGTATATGG
Found at i:17662750 original size:92 final size:92
Alignment explanation
Indices: 17662645--17663128 Score: 590
Period size: 92 Copynumber: 5.3 Consensus size: 92
17662635 CGAATTTGAA
* * * * * *
17662645 TTGTTTATAGTTATACATTGTCGAAATTGATTTGCATATGGTTATAAGTTGCTGAATTGATTTGT
1 TTGTATATGGTTATACATTGTCGAAATTGAATTGTATATGGATATAAGTTGCTGAATTGATTCGT
* *
17662710 ACATGATTATACATTGCTGAAATTAAT
66 ATATGGTTATACATTGCTGAAATTAAT
* *
17662737 TTGTATATGGTTATACATTGTTGAAATTGAATTGTATATGGATATAAGTTGCCGAATTGATTCGT
1 TTGTATATGGTTATACATTGTCGAAATTGAATTGTATATGGATATAAGTTGCTGAATTGATTCGT
*
17662802 ATATGGTTGTACATTGCTGAAATTAAT
66 ATATGGTTATACATTGCTGAAATTAAT
* * * *
17662829 TTGTATATGGTTATATATTGTTGAAATTGAATTGTATATGGATATAAGTTGCCGAATTGATTTGT
1 TTGTATATGGTTATACATTGTCGAAATTGAATTGTATATGGATATAAGTTGCTGAATTGATTCGT
** *
17662894 ATATGACTATACATTGCTGAAATTAAA
66 ATATGGTTATACATTGCTGAAATTAAT
* *
17662921 TTGTACATGGTTATACATTGTTGAAATTGAATTGTATATGGATATAAGTTGCTGAATTGATTCGT
1 TTGTATATGGTTATACATTGTCGAAATTGAATTGTATATGGATATAAGTTGCTGAATTGATTCGT
* *
17662986 ATATGGTTATACATTGCTGAATTTGAT
66 ATATGGTTATACATTGCTGAAATTAAT
* * * *
17663013 TTG--TA----TATACATTGCCGAACTT-TATTCGTATATGGTTATACA-TTG-TCGAATTGATT
1 TTGTATATGGTTATACATTGTCGAAATTGAATT-GTATATGGATATA-AGTTGCT-GAATTGATT
* * *
17663069 CGTATATGGTTATACATTGCCGAATTTGAT
63 CGTATATGGTTATACATTGCTGAAATTAAT
* * *
17663099 TTGTATATGATTATACATTGCCGAACTTGA
1 TTGTATATGGTTATACATTGTCGAAATTGA
17663129 TTGGTTTCGT
Statistics
Matches: 348, Mismatches: 34, Indels: 19
0.87 0.08 0.05
Matches are distributed among these distances:
85 4 0.01
86 70 0.20
87 1 0.00
88 2 0.01
90 1 0.00
92 270 0.78
ACGTcount: A:0.30, C:0.08, G:0.19, T:0.43
Consensus pattern (92 bp):
TTGTATATGGTTATACATTGTCGAAATTGAATTGTATATGGATATAAGTTGCTGAATTGATTCGT
ATATGGTTATACATTGCTGAAATTAAT
Found at i:17663021 original size:25 final size:25
Alignment explanation
Indices: 17662993--17663045 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 25
17662983 CGTATATGGT
* *
17662993 TATACATTGCTGAA-TTTGATTTGTA
1 TATACATTGCCGAACTTT-ATTCGTA
17663018 TATACATTGCCGAACTTTATTCGTA
1 TATACATTGCCGAACTTTATTCGTA
17663043 TAT
1 TAT
17663046 GGTTATACAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 22 0.88
26 3 0.12
ACGTcount: A:0.28, C:0.13, G:0.13, T:0.45
Consensus pattern (25 bp):
TATACATTGCCGAACTTTATTCGTA
Found at i:17663350 original size:44 final size:43
Alignment explanation
Indices: 17663239--17663400 Score: 234
Period size: 43 Copynumber: 3.7 Consensus size: 43
17663229 GGTGTGATTT
* *
17663239 CGTGTAGGACCATGTCTGGGACATCGGTATCGAAGTAAGGAAA
1 CGTGTAAGACCATGTCTGGGACATCGGCATCGAAGTAAGGAAA
* * *
17663282 CGTGTAGGACCATGTCTGGGACATTGGCATCAAAGTAAGGAAA
1 CGTGTAAGACCATGTCTGGGACATCGGCATCGAAGTAAGGAAA
* * * *
17663325 CGTGTAAAGACCATGCCTGGGACATTGGAATCGAAGTAAGAAAA
1 CGTGT-AAGACCATGTCTGGGACATCGGCATCGAAGTAAGGAAA
17663369 CGTGTAAGACCATGTCTGGGACATCGGCATCG
1 CGTGTAAGACCATGTCTGGGACATCGGCATCG
17663401 TATATGATTC
Statistics
Matches: 107, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
43 69 0.64
44 38 0.36
ACGTcount: A:0.31, C:0.18, G:0.30, T:0.20
Consensus pattern (43 bp):
CGTGTAAGACCATGTCTGGGACATCGGCATCGAAGTAAGGAAA
Found at i:17673168 original size:3 final size:3
Alignment explanation
Indices: 17673160--17673187 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
17673150 CTTTGTAAGC
17673160 TGA TGA TGA TGA TGA TGA TGA TGA TGA T
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA T
17673188 ACATACATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.36
Consensus pattern (3 bp):
TGA
Found at i:17679065 original size:2 final size:2
Alignment explanation
Indices: 17679058--17679092 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
17679048 TTTAATAATT
* *
17679058 TA TA TA TA TA TA TA TA TA TA TA TT TA TA TT TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
17679093 TTACCTTGTC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (2 bp):
TA
Found at i:17679093 original size:6 final size:6
Alignment explanation
Indices: 17679055--17679095 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
17679045 ATCTTTAATA
* * *
17679055 ATTTAT ATATAT ATATAT ATATAT ATTTAT ATTTAT ATTTA
1 ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT ATTTA
17679096 CCTTGTCCAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (6 bp):
ATTTAT
Found at i:17679093 original size:12 final size:12
Alignment explanation
Indices: 17679055--17679095 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
17679045 ATCTTTAATA
17679055 ATTTATATATAT
1 ATTTATATATAT
*
17679067 ATATATATATAT
1 ATTTATATATAT
*
17679079 ATTTATATTTAT
1 ATTTATATATAT
17679091 ATTTA
1 ATTTA
17679096 CCTTGTCCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
ATTTATATATAT
Found at i:17679751 original size:30 final size:30
Alignment explanation
Indices: 17679717--17679776 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
17679707 AATATCAATG
17679717 AAAGTGGTAATAGTTTTGAATATTATATAT
1 AAAGTGGTAATAGTTTTGAATATTATATAT
17679747 AAAGTGGTAATAGTTTTGAATATTATATAT
1 AAAGTGGTAATAGTTTTGAATATTATATAT
17679777 TCATAGTGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.40, C:0.00, G:0.17, T:0.43
Consensus pattern (30 bp):
AAAGTGGTAATAGTTTTGAATATTATATAT
Found at i:17684026 original size:19 final size:18
Alignment explanation
Indices: 17684004--17684061 Score: 55
Period size: 19 Copynumber: 3.0 Consensus size: 18
17683994 AAAATAAATT
17684004 TTAAATATTAAATAATTTA
1 TTAAATATT-AATAATTTA
*
17684023 TTAAA-AATAATAAATTATA
1 TTAAATATTAAT-AATT-TA
17684042 TTAATTATATTAATAATTTA
1 TTAA--ATATTAATAATTTA
17684062 GTATATGACT
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
17 3 0.09
18 6 0.19
19 11 0.34
20 2 0.06
21 5 0.16
22 5 0.16
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAAATATTAATAATTTA
Found at i:17688788 original size:2 final size:2
Alignment explanation
Indices: 17688781--17688813 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
17688771 TGTGTCTAGC
17688781 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
17688814 GATTAGTGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:17697819 original size:17 final size:17
Alignment explanation
Indices: 17697788--17697828 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
17697778 ATGTGTACCA
*
17697788 ATAAATAATTTAAAAATG
1 ATAAA-AATTCAAAAATG
*
17697806 ATAAAAATTCAAAAATT
1 ATAAAAATTCAAAAATG
17697823 ATAAAA
1 ATAAAA
17697829 GTTAATAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 16 0.76
18 5 0.24
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.29
Consensus pattern (17 bp):
ATAAAAATTCAAAAATG
Found at i:17697838 original size:17 final size:16
Alignment explanation
Indices: 17697797--17697839 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
17697787 AATAAATAAT
*
17697797 TTAAAAATGATAAAAA
1 TTAAAAATTATAAAAA
*
17697813 TTCAAAAATTATAAAAG
1 TT-AAAAATTATAAAAA
17697830 TTAATAAATT
1 TTAA-AAATT
17697840 TTTTAAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 4 0.17
17 19 0.83
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (16 bp):
TTAAAAATTATAAAAA
Found at i:17697966 original size:22 final size:22
Alignment explanation
Indices: 17697941--17697983 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
17697931 ATCAAATTTA
17697941 AAAAAATAAAAATTAAATTATT
1 AAAAAATAAAAATTAAATTATT
* * *
17697963 AAAAACTAAAATTTACATTAT
1 AAAAAATAAAAATTAAATTAT
17697984 GGATTAATTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.33
Consensus pattern (22 bp):
AAAAAATAAAAATTAAATTATT
Found at i:17700823 original size:4 final size:4
Alignment explanation
Indices: 17700809--17700838 Score: 51
Period size: 4 Copynumber: 7.2 Consensus size: 4
17700799 CTTTAATCCC
17700809 TACA TTACA TACA TACA TACA TACA TACA T
1 TACA -TACA TACA TACA TACA TACA TACA T
17700839 TTGGATATCA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 21 0.84
5 4 0.16
ACGTcount: A:0.47, C:0.23, G:0.00, T:0.30
Consensus pattern (4 bp):
TACA
Found at i:17701164 original size:4 final size:4
Alignment explanation
Indices: 17701155--17701182 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
17701145 TTTTATTGCA
17701155 AGGC AGGC AGGC AGGC AGGC AGGC AGGC
1 AGGC AGGC AGGC AGGC AGGC AGGC AGGC
17701183 GTGAGTCCCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.25, G:0.50, T:0.00
Consensus pattern (4 bp):
AGGC
Found at i:17707831 original size:19 final size:19
Alignment explanation
Indices: 17707803--17707839 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
17707793 TTTTGGAGAA
17707803 TAAAAGTTT-GAGGGAAAG
1 TAAAAGTTTGGAGGGAAAG
17707821 TAAATAGTTTGGAGGGAAA
1 TAAA-AGTTTGGAGGGAAA
17707840 ATATTAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 5 0.29
20 8 0.47
ACGTcount: A:0.43, C:0.00, G:0.32, T:0.24
Consensus pattern (19 bp):
TAAAAGTTTGGAGGGAAAG
Found at i:17708181 original size:9 final size:9
Alignment explanation
Indices: 17708167--17708203 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
17708157 TATAGTTTGA
17708167 TATTCGAAT
1 TATTCGAAT
17708176 TATTCGAAT
1 TATTCGAAT
*
17708185 TATTCGAGT
1 TATTCGAAT
*
17708194 TATTTGAAT
1 TATTCGAAT
17708203 T
1 T
17708204 CGAAAACTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.30, C:0.08, G:0.14, T:0.49
Consensus pattern (9 bp):
TATTCGAAT
Found at i:17708273 original size:9 final size:9
Alignment explanation
Indices: 17708256--17708286 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
17708246 TCGAGTTGAT
17708256 TCGAATAAC
1 TCGAATAAC
*
17708265 TCGATTAAC
1 TCGAATAAC
17708274 TCGAATAAC
1 TCGAATAAC
17708283 TCGA
1 TCGA
17708287 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:17719842 original size:14 final size:14
Alignment explanation
Indices: 17719823--17719849 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
17719813 GAAATGAATG
17719823 AAAGAAAAAAAGAA
1 AAAGAAAAAAAGAA
17719837 AAAGAAAAAAAGA
1 AAAGAAAAAAAGA
17719850 GTTGATGGGA
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:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (14 bp):
AAAGAAAAAAAGAA
Found at i:17725250 original size:20 final size:20
Alignment explanation
Indices: 17725222--17725259 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
17725212 TATTTTCTAG
*
17725222 TAAATCATTTTACAGAAAAA
1 TAAAACATTTTACAGAAAAA
*
17725242 TAAAACATTTTCCAGAAA
1 TAAAACATTTTACAGAAA
17725260 TCATTTTACG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.53, C:0.13, G:0.05, T:0.29
Consensus pattern (20 bp):
TAAAACATTTTACAGAAAAA
Found at i:17725262 original size:34 final size:35
Alignment explanation
Indices: 17725208--17725274 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
17725198 CAAACAGCAG
* *
17725208 AAAATATTTTCTAGTAAATCATTTTACAGAAAAAT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAAT
*
17725243 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
17725275 TATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.48, C:0.12, G:0.07, T:0.33
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAAT
Found at i:17729562 original size:24 final size:24
Alignment explanation
Indices: 17729535--17729583 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
17729525 AAGAGGAAAG
17729535 TTTAAAGAACATAAAAGAAAAAAA
1 TTTAAAGAACATAAAAGAAAAAAA
** * *
17729559 TTTAAATTACTTAAAAGGAAAAAA
1 TTTAAAGAACATAAAAGAAAAAAA
17729583 T
1 T
17729584 ATGGGATCAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.63, C:0.04, G:0.08, T:0.24
Consensus pattern (24 bp):
TTTAAAGAACATAAAAGAAAAAAA
Found at i:17736114 original size:3 final size:3
Alignment explanation
Indices: 17736106--17736141 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
17736096 TTTACATAGC
17736106 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
17736142 GATATAATGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:17742301 original size:2 final size:2
Alignment explanation
Indices: 17742294--17742323 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
17742284 AATATAAAAG
17742294 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
17742324 GAAGTTGGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:17743761 original size:40 final size:39
Alignment explanation
Indices: 17743712--17743825 Score: 97
Period size: 40 Copynumber: 2.8 Consensus size: 39
17743702 GTTTAGTTAT
17743712 TAATAATTATTGTTACTTAGTATTATTGTTAGTAAAAAAAC
1 TAAT-ATTATT-TTACTTAGTATTATTGTTAGTAAAAAAAC
** * **
17743753 TAATATTATTATGGC-TAGTTATTA-GGATTAGTAAAAACTC
1 TAATATTATT-TTACTTAG-TATTATTG-TTAGTAAAAAAAC
* *
17743793 TAATTATTATTTTAGTTAGTATGATTGTTAGTA
1 TAA-TATTATTTTACTTAGTATTATTGTTAGTA
17743826 TTTTTTTTCC
Statistics
Matches: 57, Mismatches: 11, Indels: 11
0.72 0.14 0.14
Matches are distributed among these distances:
39 4 0.07
40 38 0.67
41 15 0.26
ACGTcount: A:0.37, C:0.04, G:0.13, T:0.46
Consensus pattern (39 bp):
TAATATTATTTTACTTAGTATTATTGTTAGTAAAAAAAC
Found at i:17744017 original size:150 final size:147
Alignment explanation
Indices: 17743828--17744303 Score: 579
Period size: 150 Copynumber: 3.2 Consensus size: 147
17743818 TGTTAGTATT
17743828 TTTTTTC-CGAATTTTATTACTTTAAAAAATATACTATTTTTCAATTTTATTATTTTACATTATT
1 TTTTTTCTCGAATTTTATTACTTT-AAAAATATACTATTTTT-AATTTTATTATTTTACATTATT
17743892 TTAGTACATTATGTTTGAAATTTAAATAAATTTAGTGTGTTTTTTAAATAAATTAAAAAAACCCT
64 TTAGTACATTATGTTTGAAATTT-AAT-AATTTAGTGTGTTTTTTAAATAAATTAAAAAAACCCT
17743957 TATTTCGGCCCTTTACTCGTA
127 TATTTCGGCCCTTTACTCGTA
*
17743978 TTTTTTCTCGAGTTTTATTACTTTAAAAATATACTATTTTATAATTTTATTATTTTACATTATTT
1 TTTTTTCTCGAATTTTATTACTTTAAAAATATACTATTTT-TAATTTTATTATTTTACATTATTT
* * *
17744043 TAGTACATTATGTTTAAAATTTATTAATTTAGTGTG-TTTTTAAATAAATTTAAAAAAAACCTTT
65 TAGTACATTATGTTTGAAATTTAATAATTTAGTGTGTTTTTTAAATAAA-TT-AAAAAAACCCTT
*
17744107 ATTTCGGCCCTTTGCTCGTA
128 ATTTCGGCCCTTTACTCGTA
* * * *
17744127 TTTTTTTCCCAAATTTTATTACTTTCAATAAAAATATATTATTTTTGTATTTTATT-TTTTACAT
1 -TTTTTTCTCGAATTTTATTAC-TT---TAAAAATATACTATTTTT-AATTTTATTATTTTACAT
* * * * * *
17744191 TATTTTAGTACATTATGTTTGAAATGTATTAA-TTATTTCTGTTTTTT--TTAATTTAGTAAAAA
60 TATTTTAGTACATTATGTTTGAAATTTAATAATTTA-GTGTGTTTTTTAAATAAATTA--AAAAA
* *
17744253 ACCCTAACTTCGGCCC-TTAGCTCGTA
122 ACCCTTATTTCGGCCCTTTA-CTCGTA
*
17744279 TTTTTTCTCCACATTTTATTACTTT
1 TTTTTTCTCGA-ATTTTATTACTTT
17744304 CGGTGAATAT
Statistics
Matches: 288, Mismatches: 22, Indels: 34
0.84 0.06 0.10
Matches are distributed among these distances:
147 12 0.04
148 14 0.05
149 32 0.11
150 86 0.30
151 33 0.11
152 40 0.14
153 42 0.15
154 29 0.10
ACGTcount: A:0.30, C:0.11, G:0.07, T:0.52
Consensus pattern (147 bp):
TTTTTTCTCGAATTTTATTACTTTAAAAATATACTATTTTTAATTTTATTATTTTACATTATTTT
AGTACATTATGTTTGAAATTTAATAATTTAGTGTGTTTTTTAAATAAATTAAAAAAACCCTTATT
TCGGCCCTTTACTCGTA
Found at i:17744641 original size:4 final size:4
Alignment explanation
Indices: 17744634--17744738 Score: 69
Period size: 4 Copynumber: 25.5 Consensus size: 4
17744624 TTCCTTTCAT
* *
17744634 TTTC TTTC -TCC TTTCC TTTTC TTTC TTTCC TGT- TTT- TTTC TTCTCC
1 TTTC TTTC TTTC TTT-C T-TTC TTTC TTT-C TTTC TTTC TTTC TT-T-C
17744680 TTTCC TTTTC TTTC TTTC TTCTCC TTTC -TT- TTTC TTTC TTT- TTTC
1 TTT-C -TTTC TTTC TTTC TT-T-C TTTC TTTC TTTC TTTC TTTC TTTC
17744725 TTTC TTTC TTTC TT
1 TTTC TTTC TTTC TT
17744739 CTCCTTTCCC
Statistics
Matches: 84, Mismatches: 4, Indels: 26
0.74 0.04 0.23
Matches are distributed among these distances:
3 14 0.17
4 45 0.54
5 14 0.17
6 11 0.13
ACGTcount: A:0.00, C:0.28, G:0.01, T:0.71
Consensus pattern (4 bp):
TTTC
Found at i:17744647 original size:17 final size:17
Alignment explanation
Indices: 17744625--17744729 Score: 83
Period size: 17 Copynumber: 6.1 Consensus size: 17
17744615 TCTTTTTCCT
*
17744625 TCCTTTCATTTTCTTTC
1 TCCTTTCCTTTTCTTTC
17744642 TCCTTTCCTTTTCTTTC
1 TCCTTTCCTTTTCTTTC
*
17744659 TTTCCTGTT-TTTTTC-TTC
1 --TCCT-TTCCTTTTCTTTC
17744677 TCCTTTCCTTTTCTTTC
1 TCCTTTCCTTTTCTTTC
*
17744694 TTTCTTCTCC-TTTCTTT-
1 -TCCTT-TCCTTTTCTTTC
* *
17744711 TTCTTTCTTTTTTCTTTC
1 TCCTTTC-CTTTTCTTTC
17744729 T
1 T
17744730 TTCTTTCTTC
Statistics
Matches: 73, Mismatches: 5, Indels: 19
0.75 0.05 0.20
Matches are distributed among these distances:
15 4 0.05
16 14 0.19
17 26 0.36
18 15 0.21
19 12 0.16
20 2 0.03
ACGTcount: A:0.01, C:0.29, G:0.01, T:0.70
Consensus pattern (17 bp):
TCCTTTCCTTTTCTTTC
Found at i:17744692 original size:52 final size:53
Alignment explanation
Indices: 17744617--17744736 Score: 140
Period size: 52 Copynumber: 2.3 Consensus size: 53
17744607 TTTTTATTTC
*
17744617 TTTTTCCTTCCTTTCATTTTCTTTC-TCCTT-TCCTTT-TCTTTCTTTCCTGTT
1 TTTTTCTTTCCTTTCATTTTCTTTCTTCCTTCTCCTTTCTCTTTCTTT-CTGTT
* * * *
17744668 TTTTTCTTCTCCTTTCCTTTTCTTTCTTTCTTCTCCTTTCTTTTTCTTTCTTTT
1 TTTTTCTT-TCCTTTCATTTTCTTTCTTCCTTCTCCTTTCTCTTTCTTTCTGTT
17744722 TTCTTTCTTT-CTTTC
1 TT-TTTCTTTCCTTTC
17744737 TTCTCCTTTC
Statistics
Matches: 59, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
51 7 0.12
52 16 0.27
53 9 0.15
54 13 0.22
55 14 0.24
ACGTcount: A:0.01, C:0.28, G:0.01, T:0.70
Consensus pattern (53 bp):
TTTTTCTTTCCTTTCATTTTCTTTCTTCCTTCTCCTTTCTCTTTCTTTCTGTT
Found at i:17744702 original size:24 final size:24
Alignment explanation
Indices: 17744670--17744738 Score: 94
Period size: 24 Copynumber: 3.1 Consensus size: 24
17744660 TTCCTGTTTT
17744670 TTTCTTCTCCTTTCCTTTTCTTTC
1 TTTCTTCTCCTTTCCTTTTCTTTC
*
17744694 TTTCTTCTCCTTTCTTTTTCTTTC
1 TTTCTTCTCCTTTCCTTTTCTTTC
17744718 TTT-TT-T-CTTT-C-TTTCTTTC
1 TTTCTTCTCCTTTCCTTTTCTTTC
17744737 TT
1 TT
17744739 CTCCTTTCCC
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
19 10 0.23
21 4 0.09
22 1 0.02
23 2 0.05
24 26 0.60
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (24 bp):
TTTCTTCTCCTTTCCTTTTCTTTC
Found at i:17744724 original size:35 final size:35
Alignment explanation
Indices: 17744606--17744734 Score: 111
Period size: 39 Copynumber: 3.5 Consensus size: 35
17744596 ATTACCTTAT
* *
17744606 TTTTTTATTTCTTT-TTCCTTCCTTTCATTTTCTTTC
1 TTTTTTCTTTCTTTCTT-C-TCCTTTCTTTTTCTTTC
* *
17744642 TCCTTTCCTTTTCTTTCTT-TCCTGTT-TTTTTCTTCTCC
1 T-TTTTTC-TTTCTTTCTTCTCCT-TTCTTTTTCTT-T-C
17744680 TTTCCTTTTCTTTCTTTCTTCTCCTTTCTTTTTCTTTC
1 -TT--TTTTCTTTCTTTCTTCTCCTTTCTTTTTCTTTC
17744718 TTTTTTCTTTCTTTCTT
1 TTTTTTCTTTCTTTCTT
17744735 TCTTCTCCTT
Statistics
Matches: 76, Mismatches: 6, Indels: 23
0.72 0.06 0.22
Matches are distributed among these distances:
35 15 0.20
36 12 0.16
37 8 0.11
38 9 0.12
39 16 0.21
40 16 0.21
ACGTcount: A:0.02, C:0.26, G:0.01, T:0.71
Consensus pattern (35 bp):
TTTTTTCTTTCTTTCTTCTCCTTTCTTTTTCTTTC
Found at i:17744729 original size:39 final size:39
Alignment explanation
Indices: 17744625--17744746 Score: 137
Period size: 39 Copynumber: 3.2 Consensus size: 39
17744615 TCTTTTTCCT
* * *
17744625 TCCTTTCATTTTCTTTCTCCTTTC-CT-TTTCTTTCTT-
1 TCCTTTCTTTTTCTTTCTCTTTTCTTTCTTTCTTTCTTC
*
17744661 TCCTGTT-TTTTTC-TTCTCCTTTCCTTTTCTTTCTTTCTTC
1 TCCT-TTCTTTTTCTTTCT-CTTTTC-TTTCTTTCTTTCTTC
*
17744701 TCCTTTCTTTTTCTTTCTTTTTTCTTTCTTTCTTTCTTC
1 TCCTTTCTTTTTCTTTCTCTTTTCTTTCTTTCTTTCTTC
17744740 TCCTTTC
1 TCCTTTC
17744747 CCTCTCCTTC
Statistics
Matches: 72, Mismatches: 6, Indels: 13
0.79 0.07 0.14
Matches are distributed among these distances:
35 4 0.06
36 13 0.18
37 2 0.03
38 1 0.01
39 34 0.47
40 14 0.19
41 4 0.06
ACGTcount: A:0.01, C:0.30, G:0.01, T:0.69
Consensus pattern (39 bp):
TCCTTTCTTTTTCTTTCTCTTTTCTTTCTTTCTTTCTTC
Found at i:17747045 original size:5 final size:6
Alignment explanation
Indices: 17747027--17747051 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
17747017 CTGTTTTTAC
17747027 TTATTT TTATTT TTATTT TTATTT T
1 TTATTT TTATTT TTATTT TTATTT T
17747052 GGGTTAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTATTT
Found at i:17748576 original size:7 final size:7
Alignment explanation
Indices: 17748561--17748595 Score: 61
Period size: 7 Copynumber: 5.0 Consensus size: 7
17748551 CTTACATTAA
*
17748561 ATATGTT
1 ATATATT
17748568 ATATATT
1 ATATATT
17748575 ATATATT
1 ATATATT
17748582 ATATATT
1 ATATATT
17748589 ATATATT
1 ATATATT
17748596 TTTAATTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (7 bp):
ATATATT
Found at i:17753006 original size:22 final size:23
Alignment explanation
Indices: 17752953--17753008 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 23
17752943 CCCGTTTTAA
* * *
17752953 ATTAAAATTAAAATTATTTTTTT
1 ATTAAAATTAAAACTATATTGTT
*
17752976 AATAAAATTAAAACTA-ATTGTT
1 ATTAAAATTAAAACTATATTGTT
17752998 ATTAAAATTAA
1 ATTAAAATTAA
17753009 TTGTTAGTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 14 0.50
23 14 0.50
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (23 bp):
ATTAAAATTAAAACTATATTGTT
Found at i:17753021 original size:16 final size:16
Alignment explanation
Indices: 17752984--17753023 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
17752974 TTAATAAAAT
* *
17752984 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
17753000 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
17753016 TAAAATTA
1 TAAAATTA
17753024 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:17753108 original size:9 final size:9
Alignment explanation
Indices: 17753096--17753132 Score: 74
Period size: 9 Copynumber: 4.1 Consensus size: 9
17753086 TTTATCAAAT
17753096 TATTAATTG
1 TATTAATTG
17753105 TATTAATTG
1 TATTAATTG
17753114 TATTAATTG
1 TATTAATTG
17753123 TATTAATTG
1 TATTAATTG
17753132 T
1 T
17753133 TGTAACAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:17753269 original size:22 final size:24
Alignment explanation
Indices: 17753229--17753272 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
17753219 AAATAAACTT
17753229 AAAATAAAAAACTATTATATTTTA
1 AAAATAAAAAACTATTATATTTTA
17753253 AAAATAAAAAA-TA-TATATTT
1 AAAATAAAAAACTATTATATTT
17753273 AATATTTTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 7 0.35
23 2 0.10
24 11 0.55
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (24 bp):
AAAATAAAAAACTATTATATTTTA
Found at i:17762734 original size:15 final size:15
Alignment explanation
Indices: 17762714--17762759 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
17762704 AAATTTAAAA
17762714 TTTAATTTTTATATT
1 TTTAATTTTTATATT
* * *
17762729 TTTAATTTTAAGAGT
1 TTTAATTTTTATATT
17762744 TTT-ATTTTT-TATT
1 TTTAATTTTTATATT
17762757 TTT
1 TTT
17762760 CAGTTGTTAA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
13 5 0.20
14 5 0.20
15 15 0.60
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.72
Consensus pattern (15 bp):
TTTAATTTTTATATT
Found at i:17765427 original size:18 final size:18
Alignment explanation
Indices: 17765404--17765442 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
17765394 GTAATAAAAT
17765404 ATGCAT-AATAAAATTAAA
1 ATGCATAAAT-AAATTAAA
17765422 ATGCATAAATAAATTAAA
1 ATGCATAAATAAATTAAA
17765440 ATG
1 ATG
17765443 GAAGTTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 17 0.85
19 3 0.15
ACGTcount: A:0.59, C:0.05, G:0.08, T:0.28
Consensus pattern (18 bp):
ATGCATAAATAAATTAAA
Found at i:17765728 original size:17 final size:18
Alignment explanation
Indices: 17765706--17765745 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
17765696 GTGATATTTT
17765706 AATTAAATATTT-TTTAA
1 AATTAAATATTTATTTAA
*
17765723 AATTAAATTTTTATTTAA
1 AATTAAATATTTATTTAA
*
17765741 TATTA
1 AATTA
17765746 TATTTGCAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
AATTAAATATTTATTTAA
Found at i:17765745 original size:18 final size:17
Alignment explanation
Indices: 17765706--17765750 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 17
17765696 GTGATATTTT
*
17765706 AATTAAATATTTTTTAA
1 AATTAAATTTTTTTTAA
17765723 AATTAAATTTTTATTTAA
1 AATTAAATTTTT-TTTAA
* *
17765741 TATTATATTT
1 AATTAAATTT
17765751 GCAACTGTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
17 11 0.46
18 13 0.54
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
AATTAAATTTTTTTTAA
Found at i:17768448 original size:116 final size:116
Alignment explanation
Indices: 17768220--17768534 Score: 324
Period size: 116 Copynumber: 2.7 Consensus size: 116
17768210 CCAAACAAGA
* **** * *
17768220 GAAAGGTT-CTTTACTTTCCTCAAAATGTAATTTTTTTTACATGTCTAAAGTTTCCTTCATGTGG
1 GAAAGGTTAC-TTACTTTCCTCAAAATGCAATTTTTTAGGTATGTCCAAAGTTTCCTTCATGTGA
* *
17768284 TGTCAATTGAGTT-AGTGCTCAATCCTCTATGTTTTTTTGGTATGTCTAG-A-
65 TGTCAATTGAGTTAAG-GCTCAATCCTCTATGATTTATTGGTATGTCTAGAAT
*
17768334 GCAAATGGTTACTTACTTTCCTCAAAATGCAATATTTTTAGGTATGTCCAAAGTTTCCTTCATAT
1 G-AAA-GGTTACTTACTTTCCTCAAAATGCAAT-TTTTTAGGTATGTCCAAAGTTTCCTTCATGT
* * *
17768399 GATGCCAATTGAGTTAAGGCT-TATTCTGCTAT-ATTTATTGGTATGTCTAGAAT
63 GATGTCAATTGAGTTAAGGCTCAATCCT-CTATGATTTATTGGTATGTCTAGAAT
* * * * * *
17768452 GAAAGGTTATTTGCTTTCCTCTAAATGC---TTGTTGGGTATGTCCAAAGTTTACTTCATGTGAT
1 GAAAGGTTACTTACTTTCCTCAAAATGCAATTTTTTAGGTATGTCCAAAGTTTCCTTCATGTGAT
* *
17768514 GTAAATTAAGTTAAGGCTCAA
66 GTCAATTGAGTTAAGGCTCAA
17768535 CCTATCAAAT
Statistics
Matches: 168, Mismatches: 24, Indels: 19
0.80 0.11 0.09
Matches are distributed among these distances:
112 45 0.27
113 1 0.01
114 1 0.01
115 3 0.02
116 65 0.39
117 50 0.30
118 3 0.02
ACGTcount: A:0.26, C:0.15, G:0.17, T:0.42
Consensus pattern (116 bp):
GAAAGGTTACTTACTTTCCTCAAAATGCAATTTTTTAGGTATGTCCAAAGTTTCCTTCATGTGAT
GTCAATTGAGTTAAGGCTCAATCCTCTATGATTTATTGGTATGTCTAGAAT
Found at i:17773297 original size:33 final size:35
Alignment explanation
Indices: 17773202--17773298 Score: 89
Period size: 33 Copynumber: 2.8 Consensus size: 35
17773192 TTAATATTTT
*
17773202 AATATATGAAATATAAATTTTAAATATTT--TTAAGC
1 AATATAT-AAAT-TATATTTTAAATATTTAATTAAGC
* *
17773237 AATAAATATTAATTAT-TTATAAA-ATTTAATT-AG-
1 AAT--ATATAAATTATATTTTAAATATTTAATTAAGC
17773270 AATATATAAATTATATTTTAAATATTTAA
1 AATATATAAATTATATTTTAAATATTTAA
17773299 ATATAACCAT
Statistics
Matches: 51, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
31 10 0.20
32 6 0.12
33 13 0.25
34 8 0.16
35 7 0.14
36 3 0.06
37 4 0.08
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (35 bp):
AATATATAAATTATATTTTAAATATTTAATTAAGC
Found at i:17781837 original size:6 final size:6
Alignment explanation
Indices: 17781826--17781856 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
17781816 ATTACTTTTG
*
17781826 ATTTAA ATTTAA ATTTAA ATTTAA TTTTAA A
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA A
17781857 ATTACAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
ATTTAA
Found at i:17782053 original size:7 final size:8
Alignment explanation
Indices: 17782033--17782059 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
17782023 ATTCATGATC
17782033 ATTTTTTA
1 ATTTTTTA
17782041 ATTTTTTA
1 ATTTTTTA
17782049 ATTTTTTA
1 ATTTTTTA
17782057 ATT
1 ATT
17782060 GTCTATTTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (8 bp):
ATTTTTTA
Found at i:17783798 original size:9 final size:9
Alignment explanation
Indices: 17783784--17783854 Score: 54
Period size: 9 Copynumber: 7.3 Consensus size: 9
17783774 ATTGTTATTC
17783784 TAATTTTTT
1 TAATTTTTT
17783793 TAA-TTTTT
1 TAATTTTTT
17783801 TAACTTTCTTT
1 TAA-TTT-TTT
* *
17783812 ATAAATATTT
1 -TAATTTTTT
17783822 TATATTTTTT
1 TA-ATTTTTT
*
17783832 TGAAATTTTTA
1 T--AATTTTTT
17783843 TAATTTTTT
1 TAATTTTTT
17783852 TAA
1 TAA
17783855 AAATATAAAT
Statistics
Matches: 49, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
8 8 0.16
9 15 0.31
10 11 0.22
11 11 0.22
12 4 0.08
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.66
Consensus pattern (9 bp):
TAATTTTTT
Found at i:17783843 original size:19 final size:21
Alignment explanation
Indices: 17783814--17783852 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
17783804 CTTTCTTTAT
17783814 AAATATTTTAT-ATTTTTTTG
1 AAATATTTTATAATTTTTTTG
17783834 AAAT-TTTTATAATTTTTTT
1 AAATATTTTATAATTTTTTT
17783853 AAAAATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (21 bp):
AAATATTTTATAATTTTTTTG
Found at i:17783853 original size:30 final size:29
Alignment explanation
Indices: 17783784--17783854 Score: 74
Period size: 31 Copynumber: 2.4 Consensus size: 29
17783774 ATTGTTATTC
*
17783784 TAATTTTTTTAATTTTTTAACTTTCTTTA
1 TAATTTTTTTAATTTTTTAACATTCTTTA
* *
17783813 TAAATATTTTATATTTTTTTGAA-ATT-TTTA
1 T-AAT-TTTTTTAATTTTTT-AACATTCTTTA
17783843 TAATTTTTTTAA
1 TAATTTTTTTAA
17783855 AAATATAAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
28 6 0.18
29 4 0.12
30 8 0.24
31 14 0.41
32 2 0.06
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.66
Consensus pattern (29 bp):
TAATTTTTTTAATTTTTTAACATTCTTTA
Found at i:17783858 original size:21 final size:21
Alignment explanation
Indices: 17783794--17783858 Score: 64
Period size: 21 Copynumber: 3.1 Consensus size: 21
17783784 TAATTTTTTT
* *
17783794 AATTTTT-TAACTTTCTTTATA
1 AATTTTTATAA-TTTTTTTAAA
*
17783815 AATATTTTAT-ATTTTTTT-GA
1 AAT-TTTTATAATTTTTTTAAA
17783835 AATTTTTATAATTTTTTTAAA
1 AATTTTTATAATTTTTTTAAA
17783856 AAT
1 AAT
17783859 ATAAATTTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
19 6 0.16
20 12 0.32
21 13 0.35
22 5 0.14
23 1 0.03
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.62
Consensus pattern (21 bp):
AATTTTTATAATTTTTTTAAA
Found at i:17784289 original size:2 final size:2
Alignment explanation
Indices: 17784277--17784309 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
17784267 GTCTCCTTCC
*
17784277 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
17784310 GTTGCATGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:17787015 original size:17 final size:18
Alignment explanation
Indices: 17786993--17787029 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
17786983 TTGATTATAT
17786993 AAATATAA-AAAATTAAA
1 AAATATAATAAAATTAAA
*
17787010 AAATATAATAATATTAAA
1 AAATATAATAAAATTAAA
17787028 AA
1 AA
17787030 TTAATAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (18 bp):
AAATATAATAAAATTAAA
Found at i:17787016 original size:25 final size:26
Alignment explanation
Indices: 17786988--17787042 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 26
17786978 TTGTCTTGAT
17786988 TATATA-AATATAAAAAATTAAAAAA
1 TATATATAATATAAAAAATTAAAAAA
* * *
17787013 TATA-ATAATATTAAAAATTAATAAT
1 TATATATAATATAAAAAATTAAAAAA
17787038 TATAT
1 TATAT
17787043 TGATTAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
24 1 0.04
25 24 0.96
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (26 bp):
TATATATAATATAAAAAATTAAAAAA
Found at i:17792286 original size:30 final size:31
Alignment explanation
Indices: 17792234--17792291 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 31
17792224 AGTTACAAAG
*
17792234 TGGTCACTCAATTATTCAATTTTTTCTTGTT
1 TGGTCACTCAACTATTCAATTTTTTCTTGTT
*
17792265 TGGTCAC-CAACTATTCGATTTTTTCTT
1 TGGTCACTCAACTATTCAATTTTTTCTT
17792292 TTGTAGTCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 18 0.72
31 7 0.28
ACGTcount: A:0.19, C:0.19, G:0.10, T:0.52
Consensus pattern (31 bp):
TGGTCACTCAACTATTCAATTTTTTCTTGTT
Found at i:17793669 original size:25 final size:25
Alignment explanation
Indices: 17793614--17793669 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
17793604 ATTTAGAATG
*
17793614 ATCTTTACAAATTTAAATCAAAATA
1 ATCTTTACAAATTTAAACCAAAATA
17793639 AT-TTTA-AAATTGTATAACCAAAAT-
1 ATCTTTACAAATT-TA-AACCAAAATA
17793663 ATCTTTA
1 ATCTTTA
17793670 GTTTTAAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
23 5 0.19
24 8 0.30
25 14 0.52
ACGTcount: A:0.48, C:0.11, G:0.02, T:0.39
Consensus pattern (25 bp):
ATCTTTACAAATTTAAACCAAAATA
Found at i:17794278 original size:28 final size:28
Alignment explanation
Indices: 17794223--17794300 Score: 95
Period size: 28 Copynumber: 2.7 Consensus size: 28
17794213 TATAAAAATG
17794223 TAATATAATAAAG-CTTTAATTTAACCAATT
1 TAATAT-ATAAAGACTTT--TTTAACCAATT
*
17794253 TAATATATAAAGACTTTTTTACCCAATT
1 TAATATATAAAGACTTTTTTAACCAATT
* *
17794281 TAGTATATAATGACTTTTTT
1 TAATATATAAAGACTTTTTT
17794301 TTAGTTGATT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
28 28 0.64
29 6 0.14
30 10 0.23
ACGTcount: A:0.40, C:0.10, G:0.05, T:0.45
Consensus pattern (28 bp):
TAATATATAAAGACTTTTTTAACCAATT
Found at i:17803967 original size:20 final size:20
Alignment explanation
Indices: 17803942--17803985 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
17803932 AGGCTTAGGA
*
17803942 TTTAGGATTTGAGTTCAAGG
1 TTTAGGATTCGAGTTCAAGG
*
17803962 TTTAGGGTTCGAGTTCAAGG
1 TTTAGGATTCGAGTTCAAGG
17803982 TTTA
1 TTTA
17803986 TGGGTAAGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.23, C:0.07, G:0.30, T:0.41
Consensus pattern (20 bp):
TTTAGGATTCGAGTTCAAGG
Found at i:17807112 original size:18 final size:18
Alignment explanation
Indices: 17807089--17807125 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
17807079 GCTGGGCAGT
* *
17807089 AGAAGAAGTAGAAGAGAA
1 AGAAGAAGAAAAAGAGAA
17807107 AGAAGAAGAAAAAGAGAA
1 AGAAGAAGAAAAAGAGAA
17807125 A
1 A
17807126 AAAAAATACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.68, C:0.00, G:0.30, T:0.03
Consensus pattern (18 bp):
AGAAGAAGAAAAAGAGAA
Found at i:17811304 original size:10 final size:10
Alignment explanation
Indices: 17811289--17811313 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
17811279 CAATAGAACC
17811289 AAAAAAAACA
1 AAAAAAAACA
17811299 AAAAAAAACA
1 AAAAAAAACA
17811309 AAAAA
1 AAAAA
17811314 CATATAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (10 bp):
AAAAAAAACA
Found at i:17817895 original size:88 final size:90
Alignment explanation
Indices: 17817741--17817915 Score: 255
Period size: 88 Copynumber: 2.0 Consensus size: 90
17817731 TATATCACTG
*
17817741 GTAAAAAGTTTTAAGGCATATAAAAGAGATGGAAAAATGAATGCAAAAGTAGATAGATCATAGAT
1 GTAAAAAGTTTAAAGGCA-ATAAAAGAGATGGAAAAATGAATGCAAAAGTAGATAGATCATAGAT
17817806 GAGTCTCTGGA-TTGATCTAGAAGCA
65 GAGTCTCTGGATTTGATCTAGAAGCA
* * * * ** *
17817831 GTAAAATGTTTAAAGGC-ATAAACGAGATGGAGATATGAATGTGAAAGTAGATAGATCATGGATG
1 GTAAAAAGTTTAAAGGCAATAAAAGAGATGGAAAAATGAATGCAAAAGTAGATAGATCATAGATG
17817895 AGTCTCTGGATTTGATCTAGA
66 AGTCTCTGGATTTGATCTAGA
17817916 TTCAAGAAAT
Statistics
Matches: 76, Mismatches: 8, Indels: 3
0.87 0.09 0.03
Matches are distributed among these distances:
88 51 0.67
89 10 0.13
90 15 0.20
ACGTcount: A:0.41, C:0.07, G:0.25, T:0.26
Consensus pattern (90 bp):
GTAAAAAGTTTAAAGGCAATAAAAGAGATGGAAAAATGAATGCAAAAGTAGATAGATCATAGATG
AGTCTCTGGATTTGATCTAGAAGCA
Found at i:17821857 original size:21 final size:21
Alignment explanation
Indices: 17821832--17821872 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
17821822 TTGAATTTTA
17821832 AAATTT-AAAAAATCAAAAATT
1 AAATTTCAAAAAAT-AAAAATT
*
17821853 AAATTTCTAAAAATAAAAAT
1 AAATTTCAAAAAATAAAAAT
17821873 ACATGATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (21 bp):
AAATTTCAAAAAATAAAAATT
Found at i:17822713 original size:37 final size:37
Alignment explanation
Indices: 17822672--17822745 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
17822662 TTCTTGAAAC
17822672 TTGTTTTTCAAGTTTAAAATATGTATTAAATGAATGG
1 TTGTTTTTCAAGTTTAAAATATGTATTAAATGAATGG
17822709 TTGTTTTTCAAGTTTAAAATATGTATTAAATGAATGG
1 TTGTTTTTCAAGTTTAAAATATGTATTAAATGAATGG
17822746 CTCAAATTCT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.35, C:0.03, G:0.16, T:0.46
Consensus pattern (37 bp):
TTGTTTTTCAAGTTTAAAATATGTATTAAATGAATGG
Found at i:17825693 original size:18 final size:18
Alignment explanation
Indices: 17825672--17825708 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
17825662 TGTTATATAC
17825672 GAGTACCAACTTATTTCG
1 GAGTACCAACTTATTTCG
*
17825690 GAGTACTAACTTATTTCG
1 GAGTACCAACTTATTTCG
17825708 G
1 G
17825709 CGTTCTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (18 bp):
GAGTACCAACTTATTTCG
Found at i:17832361 original size:45 final size:44
Alignment explanation
Indices: 17832255--17832362 Score: 112
Period size: 45 Copynumber: 2.4 Consensus size: 44
17832245 TATTAAAAGT
* ** *
17832255 ATAATATTGTTTAATAAT-TATTAATAATTTGGTTTAAATATAAT
1 ATAATATTGTTT-ATAATATATTAACAATAGGGTTTAAATATAAC
***
17832299 ATAATAACATATT-TAATATATTAACAATAGGGTATTAAATATAAC
1 ATAATATTGT-TTATAATATATTAACAATAGGGT-TTAAATATAAC
17832344 ATAATATTGTTTATAATAT
1 ATAATATTGTTTATAATAT
17832363 TGCACTTGTA
Statistics
Matches: 50, Mismatches: 10, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
43 4 0.08
44 21 0.42
45 25 0.50
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.44
Consensus pattern (44 bp):
ATAATATTGTTTATAATATATTAACAATAGGGTTTAAATATAAC
Found at i:17833469 original size:2 final size:2
Alignment explanation
Indices: 17833462--17833490 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
17833452 TGCATGAATT
17833462 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
17833491 TAGCATATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:17834015 original size:22 final size:23
Alignment explanation
Indices: 17833990--17834040 Score: 77
Period size: 22 Copynumber: 2.3 Consensus size: 23
17833980 ACAATAAAGA
*
17833990 TAAATAATATTTGTATT-AACAT
1 TAAATAATATTTATATTAAACAT
*
17834012 TAAATAATATTTATATTAAATAT
1 TAAATAATATTTATATTAAACAT
17834035 TAAATA
1 TAAATA
17834041 TTATCTTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 16 0.62
23 10 0.38
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (23 bp):
TAAATAATATTTATATTAAACAT
Found at i:17834082 original size:25 final size:23
Alignment explanation
Indices: 17834054--17834105 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 23
17834044 TCTTTAAGAT
17834054 AAATATTATTTATCTTA-ATATTTAA
1 AAATATTA-TTATC--AGATATTTAA
*
17834079 AAATTTTATTATCAGATATTTAA
1 AAATATTATTATCAGATATTTAA
17834102 AAAT
1 AAAT
17834106 TAAAATCATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
22 1 0.04
23 12 0.48
24 5 0.20
25 7 0.28
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (23 bp):
AAATATTATTATCAGATATTTAA
Found at i:17834098 original size:63 final size:64
Alignment explanation
Indices: 17833986--17834107 Score: 142
Period size: 63 Copynumber: 1.9 Consensus size: 64
17833976 AATTACAATA
* * *
17833986 AAGATAAATAATATTTGTATTAACATTAAATAATATTTATATTAAATA-TTAAATATTATCTTT
1 AAGATAAATAATATTTATATTAACATTAAATAATATTTATATCAAATATTTAAAAATTATCTTT
* * * *
17834049 AAGATAAATATTATTTATCTTAATATTTAAA-AAT-TTTATTATCAGATATTTAAAAATTA
1 AAGATAAATAATATTTATATTAACA-TTAAATAATATTTA-TATCAAATATTTAAAAATTA
17834108 AAATCATAAT
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
62 4 0.08
63 31 0.63
64 14 0.29
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.46
Consensus pattern (64 bp):
AAGATAAATAATATTTATATTAACATTAAATAATATTTATATCAAATATTTAAAAATTATCTTT
Done.