Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007924.1 Hibiscus syriacus cultivar Beakdansim tig00110330_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1741266
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
File 6 of 7
Found at i:1318671 original size:14 final size:13
Alignment explanation
Indices: 1318652--1318700 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 13
1318642 TATTCTCTTT
1318652 TATTTTATTTTCTG
1 TATTTTATTTT-TG
*
1318666 TATTTTTATTTTTT
1 TA-TTTTATTTTTG
*
1318680 TATTTTACTTATTG
1 TATTTTA-TTTTTG
1318694 TATTTTA
1 TATTTTA
1318701 ATATTACTCT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
13 5 0.17
14 16 0.53
15 9 0.30
ACGTcount: A:0.18, C:0.04, G:0.04, T:0.73
Consensus pattern (13 bp):
TATTTTATTTTTG
Found at i:1320644 original size:29 final size:29
Alignment explanation
Indices: 1320583--1320649 Score: 107
Period size: 29 Copynumber: 2.3 Consensus size: 29
1320573 TTAATGGAAT
*
1320583 CATTCAACGTTGAATGCTGAACGGTTCAA
1 CATTCAGCGTTGAATGCTGAACGGTTCAA
**
1320612 CATTCAGCGTTGAATGCTGAACGGTTCTG
1 CATTCAGCGTTGAATGCTGAACGGTTCAA
1320641 CATTCAGCG
1 CATTCAGCG
1320650 CGTTTGTTTC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.25, C:0.22, G:0.24, T:0.28
Consensus pattern (29 bp):
CATTCAGCGTTGAATGCTGAACGGTTCAA
Found at i:1322985 original size:13 final size:13
Alignment explanation
Indices: 1322967--1323008 Score: 68
Period size: 13 Copynumber: 3.3 Consensus size: 13
1322957 AACGGTCAAC
1322967 GGTCAACGGGTCG
1 GGTCAACGGGTCG
1322980 GGTCAAC-GGTCG
1 GGTCAACGGGTCG
*
1322992 GGTAAACGGGTCG
1 GGTCAACGGGTCG
1323005 GGTC
1 GGTC
1323009 GGGTAAACTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
12 11 0.42
13 15 0.58
ACGTcount: A:0.17, C:0.21, G:0.45, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:1323010 original size:18 final size:18
Alignment explanation
Indices: 1322987--1323040 Score: 99
Period size: 18 Copynumber: 3.0 Consensus size: 18
1322977 TCGGGTCAAC
1322987 GGTCGGGTAAACGGGTCG
1 GGTCGGGTAAACGGGTCG
*
1323005 GGTCGGGTAAACTGGTCG
1 GGTCGGGTAAACGGGTCG
1323023 GGTCGGGTAAACGGGTCG
1 GGTCGGGTAAACGGGTCG
1323041 TGACCGGTCA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.17, C:0.17, G:0.48, T:0.19
Consensus pattern (18 bp):
GGTCGGGTAAACGGGTCG
Found at i:1323040 original size:13 final size:13
Alignment explanation
Indices: 1322971--1323007 Score: 58
Period size: 12 Copynumber: 2.9 Consensus size: 13
1322961 GTCAACGGTC
*
1322971 AACGGGTCGGGTC
1 AACGGGTCGGGTA
1322984 AAC-GGTCGGGTA
1 AACGGGTCGGGTA
1322996 AACGGGTCGGGT
1 AACGGGTCGGGT
1323008 CGGGTAAACT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.19, C:0.19, G:0.46, T:0.16
Consensus pattern (13 bp):
AACGGGTCGGGTA
Found at i:1330260 original size:13 final size:13
Alignment explanation
Indices: 1330246--1330292 Score: 78
Period size: 13 Copynumber: 3.7 Consensus size: 13
1330236 GTCAACGGTC
*
1330246 AACGGGTCGGGTC
1 AACGGGTCGGGTA
1330259 AAC-GGTCGGGTA
1 AACGGGTCGGGTA
1330271 AACGGGTCGGGTA
1 AACGGGTCGGGTA
1330284 AACGGGTCG
1 AACGGGTCG
1330293 TGACCGGTCA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
12 11 0.34
13 21 0.66
ACGTcount: A:0.21, C:0.19, G:0.45, T:0.15
Consensus pattern (13 bp):
AACGGGTCGGGTA
Found at i:1330315 original size:10 final size:10
Alignment explanation
Indices: 1330295--1330349 Score: 78
Period size: 10 Copynumber: 5.6 Consensus size: 10
1330285 ACGGGTCGTG
1330295 ACCGGTC-AA
1 ACCGGTCAAA
1330304 ACCGGTCAAA
1 ACCGGTCAAA
1330314 ACCGGTTCAAA
1 ACCGG-TCAAA
*
1330325 ACCGGT-TAA
1 ACCGGTCAAA
1330334 ACCGGTCAAA
1 ACCGGTCAAA
1330344 ACCGGT
1 ACCGGT
1330350 TTCCAGCGTT
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
9 15 0.37
10 16 0.39
11 10 0.24
ACGTcount: A:0.35, C:0.29, G:0.22, T:0.15
Consensus pattern (10 bp):
ACCGGTCAAA
Found at i:1330350 original size:19 final size:19
Alignment explanation
Indices: 1330295--1330350 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
1330285 ACGGGTCGTG
*
1330295 ACCGGTC-AAACCGGTCAAA
1 ACCGGTCAAAACCGGT-TAA
1330314 ACCGGTTCAAAACCGGTTAA
1 ACCGG-TCAAAACCGGTTAA
1330334 ACCGGTCAAAACCGGTT
1 ACCGGTCAAAACCGGTT
1330351 TCCAGCGTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
19 17 0.50
20 9 0.26
21 8 0.24
ACGTcount: A:0.34, C:0.29, G:0.21, T:0.16
Consensus pattern (19 bp):
ACCGGTCAAAACCGGTTAA
Found at i:1335392 original size:11 final size:11
Alignment explanation
Indices: 1335378--1335406 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
1335368 TCGTTAAGAA
1335378 CTCGAGTCGAG
1 CTCGAGTCGAG
1335389 CTCGAGTCGAG
1 CTCGAGTCGAG
1335400 -TCGAGTC
1 CTCGAGTC
1335407 CATTCGATCC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 7 0.39
11 11 0.61
ACGTcount: A:0.17, C:0.28, G:0.34, T:0.21
Consensus pattern (11 bp):
CTCGAGTCGAG
Found at i:1339812 original size:30 final size:28
Alignment explanation
Indices: 1339751--1339899 Score: 101
Period size: 30 Copynumber: 5.1 Consensus size: 28
1339741 TTTTATGTTC
* * *
1339751 TTAACTTTTAAAAATATATT-TTATT-TT
1 TTAA-TTTTAAATATATTTTATTCTTATT
1339778 TTAATGTGTTAAATATATTTTATTCTTATT
1 TTAAT-T-TTAAATATATTTTATTCTTATT
**
1339808 TTAATATAAAAATATATGGTTTAATT-TTATCT
1 TTAAT-TTTAAATATAT--TTT-ATTCTTAT-T
* *
1339840 TT-A-GTTAATTATATTTTATTCTTATT
1 TTAATTTTAAATATATTTTATTCTTATT
*
1339866 TTAATTTTAAAAATATATTTTATTCTTAAT
1 TTAATTTT--AAATATATTTTATTCTTATT
1339896 TTAA
1 TTAA
1339900 AATATATTTT
Statistics
Matches: 96, Mismatches: 13, Indels: 23
0.73 0.10 0.17
Matches are distributed among these distances:
26 7 0.07
27 13 0.14
28 13 0.14
29 19 0.20
30 30 0.31
31 8 0.08
32 6 0.06
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.58
Consensus pattern (28 bp):
TTAATTTTAAATATATTTTATTCTTATT
Found at i:1339905 original size:23 final size:24
Alignment explanation
Indices: 1339856--1339909 Score: 76
Period size: 23 Copynumber: 2.2 Consensus size: 24
1339846 AATTATATTT
1339856 TATTCTTATTTTAATTTTAAAAATA
1 TATT-TTATTTTAATTTTAAAAATA
1339881 TATTTTATTCTTAA-TTT-AAAATA
1 TATTTTATT-TTAATTTTAAAAATA
1339904 TATTTT
1 TATTTT
1339910 GAAGTTAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
23 12 0.43
24 8 0.29
25 8 0.29
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (24 bp):
TATTTTATTTTAATTTTAAAAATA
Found at i:1341471 original size:27 final size:27
Alignment explanation
Indices: 1341421--1341472 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
1341411 CAGATTTATA
* **
1341421 TTATATAAATATTTCTTCTTTATATGC
1 TTATATAAATATTTATTCAATATATGC
*
1341448 TTATATAAATATTTATTGAATATAT
1 TTATATAAATATTTATTCAATATAT
1341473 TATTATTGTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.37, C:0.06, G:0.04, T:0.54
Consensus pattern (27 bp):
TTATATAAATATTTATTCAATATATGC
Found at i:1341478 original size:27 final size:27
Alignment explanation
Indices: 1341419--1341478 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
1341409 AACAGATTTA
* **
1341419 TATTATATAAATATTTCTTCTTTATAT
1 TATTATATAAATATTTATTCAATATAT
** *
1341446 GCTTATATAAATATTTATTGAATATAT
1 TATTATATAAATATTTATTCAATATAT
1341473 TATTAT
1 TATTAT
1341479 TGTAAAATTT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.37, C:0.05, G:0.03, T:0.55
Consensus pattern (27 bp):
TATTATATAAATATTTATTCAATATAT
Found at i:1341783 original size:21 final size:22
Alignment explanation
Indices: 1341742--1341783 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
1341732 TTTAAATTTT
*
1341742 AAATTTTTATTTATTTCATATA
1 AAATTTTTATTTATTTAATATA
1341764 AAATGTTTTA-TTA-TTAATAT
1 AAAT-TTTTATTTATTTAATAT
1341784 TATATATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
21 6 0.33
22 7 0.39
23 5 0.28
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (22 bp):
AAATTTTTATTTATTTAATATA
Found at i:1342745 original size:43 final size:43
Alignment explanation
Indices: 1342698--1342877 Score: 245
Period size: 43 Copynumber: 4.2 Consensus size: 43
1342688 AATTTTTTAA
*
1342698 ACAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTCCC
1 ACAAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCC
* *
1342741 ACAAACGCCGCAATAGGTGTTGAGATTTAGCGACGTTTTTTCC
1 ACAAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCC
* * **
1342784 ACAAACACCGCAATAGGTGTTGAGATTTAGCTGC-TTTTTTAC
1 ACAAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCC
* * * * *
1342826 ACAAACGCCGCAATATGTCTTGAGATTTTGCGGTGTTTTCCCC
1 ACAAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCC
1342869 ACAAACGCC
1 ACAAACGCC
1342878 ACAAAAGATC
Statistics
Matches: 120, Mismatches: 16, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
42 35 0.29
43 85 0.71
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (43 bp):
ACAAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCC
Found at i:1342864 original size:85 final size:86
Alignment explanation
Indices: 1342698--1342874 Score: 239
Period size: 85 Copynumber: 2.1 Consensus size: 86
1342688 AATTTTTTAA
* * * *
1342698 ACAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTCCCACAAACGCCGCAATAGGTGTTG
1 ACAAACACCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCACACAAACGCCGCAATAGGTCTTG
**
1342763 AGATTTAGCGACGTTTTTTCC
66 AGATTTAGCGACGTTTTCCCC
* * *
1342784 ACAAACACCGCAATAGGTGTTGAGATTTAGCTGC-TTTTTTACACAAACGCCGCAATATGTCTTG
1 ACAAACACCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCACACAAACGCCGCAATAGGTCTTG
* **
1342848 AGATTTTGCGGTGTTTTCCCC
66 AGATTTAGCGACGTTTTCCCC
1342869 ACAAAC
1 ACAAAC
1342875 GCCACAAAAG
Statistics
Matches: 79, Mismatches: 12, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
85 48 0.61
86 31 0.39
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.31
Consensus pattern (86 bp):
ACAAACACCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCACACAAACGCCGCAATAGGTCTTG
AGATTTAGCGACGTTTTCCCC
Found at i:1342908 original size:85 final size:86
Alignment explanation
Indices: 1342740--1342929 Score: 188
Period size: 85 Copynumber: 2.2 Consensus size: 86
1342730 GCGTTTTTCC
* ** * * * *
1342740 CACAAACGCCGCAATAGGTGTTGAGATTTAGCGACGTTTTTTCCACAAACACCGCAATAGGTGTT
1 CACAAACGCCGCAATAGGTCTTGAGATTTAGCGACGTTTTCCCCACAAACACCACAAAAGATGCT
* *
1342805 GAGATTTAGCTGCTTTTTTA-
66 GAGATATAGCTGCCTTTTTAG
* * ** *
1342825 CACAAACGCCGCAATATGTCTTGAGATTTTGCGGTGTTTTCCCCACAAACGCCACAAAAGAT-CT
1 CACAAACGCCGCAATAGGTCTTGAGATTTAGCGACGTTTTCCCCACAAACACCACAAAAGATGCT
1342889 G-GTATATAGCTGCGCTTTTTAG
66 GAG-ATATAGCTGC-CTTTTTAG
* * *
1342911 AATAAACGCCGCAAAAGGT
1 CACAAACGCCGCAATAGGT
1342930 TATATCTATA
Statistics
Matches: 84, Mismatches: 18, Indels: 5
0.79 0.17 0.05
Matches are distributed among these distances:
83 1 0.01
84 11 0.13
85 57 0.68
86 15 0.18
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.28
Consensus pattern (86 bp):
CACAAACGCCGCAATAGGTCTTGAGATTTAGCGACGTTTTCCCCACAAACACCACAAAAGATGCT
GAGATATAGCTGCCTTTTTAG
Found at i:1342923 original size:128 final size:128
Alignment explanation
Indices: 1342690--1342929 Score: 270
Period size: 128 Copynumber: 1.9 Consensus size: 128
1342680 TTTAAATAAA
* * * * *
1342690 TTTTTTAAACAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTCCCACAAACGCCGCAAT
1 TTTTTTAAACAAACGCCGCAATAGGTCTTGAGATTTAGCGGCGTTTTCCCCACAAACGCCACAAA
* * * * * *
1342755 AGGTGTTGAGATTTAGCGACGTTTTTTCCACAAACACCGCAATAGGTGTTGAGATTTAGCTGC
66 AGATGCTGAGATATAGCGACGTTTTTACAACAAACACCGCAAAAGGTGTTGAGATTTAGCTGC
* * * *
1342818 TTTTTTACACAAACGCCGCAATATGTCTTGAGATTTTGCGGTGTTTTCCCCACAAACGCCACAAA
1 TTTTTTAAACAAACGCCGCAATAGGTCTTGAGATTTAGCGGCGTTTTCCCCACAAACGCCACAAA
* * *
1342883 AGAT-CTG-GTATATAGCTG-CGCTTTTTAGAATAAACGCCGCAAAAGGT
66 AGATGCTGAG-ATATAGC-GACG-TTTTTACAACAAACACCGCAAAAGGT
1342930 TATATCTATA
Statistics
Matches: 91, Mismatches: 18, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
126 1 0.01
127 10 0.11
128 80 0.88
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.30
Consensus pattern (128 bp):
TTTTTTAAACAAACGCCGCAATAGGTCTTGAGATTTAGCGGCGTTTTCCCCACAAACGCCACAAA
AGATGCTGAGATATAGCGACGTTTTTACAACAAACACCGCAAAAGGTGTTGAGATTTAGCTGC
Found at i:1345994 original size:42 final size:42
Alignment explanation
Indices: 1345948--1346037 Score: 108
Period size: 42 Copynumber: 2.1 Consensus size: 42
1345938 GTATGGATTA
* **
1345948 AAAGTAAAAGTATTTAATGGAGTTTGTGCTTAAAGTGCCACT
1 AAAGTAAAAGTATTTAACGGAGTTTGTGCTTAAAACGCCACT
** ** *
1345990 AAAGTACGAGTATTTGGCGGTGTTTGTGCTTAAAACGCCACT
1 AAAGTAAAAGTATTTAACGGAGTTTGTGCTTAAAACGCCACT
1346032 AAAGTA
1 AAAGTA
1346038 CATTATTTTG
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.33, C:0.12, G:0.23, T:0.31
Consensus pattern (42 bp):
AAAGTAAAAGTATTTAACGGAGTTTGTGCTTAAAACGCCACT
Found at i:1346097 original size:82 final size:81
Alignment explanation
Indices: 1345984--1346357 Score: 301
Period size: 82 Copynumber: 4.6 Consensus size: 81
1345974 TGCTTAAAGT
* * * * *
1345984 GCCACTAAAGTACGAGTATTTGGCGGTGTTTGTGCTTAAAACGCCACTAAAGTACATTATTTTGC
1 GCCACTAAAGTACGAGTCTTTAGCGGCGTTTGT-CTAAAAACGCCACTAAAGTACATTATTTAGC
* * *
1346049 GGCATTTATATAAAAAT
65 GGCGTTTTTATAAAAAC
* * * * * *
1346066 GCCTCTATAGTACGAGTCTTTAGCGGCGTTTGTATAAAAATGCCGCTAAAG-AC-TCGTACTATA
1 GCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTCTAAAAACGCCACTAAAGTACAT--TA-TTTA
* *
1346129 GCGGTGTTTGTAT-AAAAC
63 GCGGCGTTTTTATAAAAAC
* * * * * *
1346147 GTCACTAAATTAC-AGTGTTTCGCGGCGTTTGTATAAAAACGCCACTAAAGTAAATTATTTAGCG
1 GCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTCTAAAAACGCCACTAAAGTACATTATTTAGCG
* *
1346211 GTGTTTTTAGAATAAAC
66 GCGTTTTTATAA-AAAC
* ** ** * * * *
1346228 GTCGGTAAAG-ACTCGTACTATAGCGGCATATGTAC-AAAAACGCCACTAAAGAACATTATTTAG
1 GCCACTAAAGTACGAGT-CTTTAGCGGCGTTTGT-CTAAAAACGCCACTAAAGTACATTATTTAG
1346291 CGGCGTTTTTATAAAAAC
64 CGGCGTTTTTATAAAAAC
* * * *
1346309 ACCGCTATAGTACGAGTCTTTACCGGCGTTTGTTCTAAAAACGCCACTA
1 GCCACTAAAGTACGAGTCTTTAGCGGCGTTTG-TCTAAAAACGCCACTA
1346358 CAAATGCCGC
Statistics
Matches: 228, Mismatches: 51, Indels: 26
0.75 0.17 0.09
Matches are distributed among these distances:
79 15 0.07
80 40 0.18
81 65 0.29
82 108 0.47
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (81 bp):
GCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTCTAAAAACGCCACTAAAGTACATTATTTAGCG
GCGTTTTTATAAAAAC
Found at i:1356873 original size:9 final size:9
Alignment explanation
Indices: 1356859--1356888 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
1356849 AGGAGAAACT
1356859 GGAAGGGGA
1 GGAAGGGGA
1356868 GGAAGGGGA
1 GGAAGGGGA
1356877 GGAAGGGGA
1 GGAAGGGGA
1356886 GGA
1 GGA
1356889 GAAATGGGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.67, T:0.00
Consensus pattern (9 bp):
GGAAGGGGA
Found at i:1358585 original size:19 final size:20
Alignment explanation
Indices: 1358547--1358585 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
1358537 GTCGAAGTTC
*
1358547 TCGTTGCGATTTATTCTAAAT
1 TCGTTGCGA-TTAGTCTAAAT
1358568 TCGTTGCGA-TAGTCTAAA
1 TCGTTGCGATTAGTCTAAA
1358586 ATCGCAACGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
21 9 0.53
ACGTcount: A:0.26, C:0.15, G:0.18, T:0.41
Consensus pattern (20 bp):
TCGTTGCGATTAGTCTAAAT
Found at i:1358681 original size:6 final size:6
Alignment explanation
Indices: 1358670--1358696 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
1358660 CGAAGACACG
1358670 CACTAC CACTAC CACTAC CACTAC CAC
1 CACTAC CACTAC CACTAC CACTAC CAC
1358697 GACACGACCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.52, G:0.00, T:0.15
Consensus pattern (6 bp):
CACTAC
Found at i:1359358 original size:21 final size:21
Alignment explanation
Indices: 1359334--1359408 Score: 98
Period size: 21 Copynumber: 3.6 Consensus size: 21
1359324 TTTGGAATAA
*
1359334 ATCGCAACGCGAACTTCGACT
1 ATCGCAATGCGAACTTCGACT
*
1359355 ATCGCAATGCGATA-GTCGACT
1 ATCGCAATGCGA-ACTTCGACT
*
1359376 ATCGCAATGCGAACTTGGACT
1 ATCGCAATGCGAACTTCGACT
*
1359397 ATCGCATTGCGA
1 ATCGCAATGCGA
1359409 TTTACATATT
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
20 1 0.02
21 45 0.96
22 1 0.02
ACGTcount: A:0.28, C:0.27, G:0.23, T:0.23
Consensus pattern (21 bp):
ATCGCAATGCGAACTTCGACT
Found at i:1359459 original size:29 final size:29
Alignment explanation
Indices: 1359417--1359472 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
1359407 GATTTACATA
* *
1359417 TTCGTATTGCGATAGTCCAAGTTCGCAAG
1 TTCGCATTACGATAGTCCAAGTTCGCAAG
*
1359446 TTCGCATTACGATAGTCGAAGTTCGCA
1 TTCGCATTACGATAGTCCAAGTTCGCA
1359473 TTGCGATAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.30
Consensus pattern (29 bp):
TTCGCATTACGATAGTCCAAGTTCGCAAG
Found at i:1359469 original size:21 final size:21
Alignment explanation
Indices: 1359443--1359520 Score: 129
Period size: 21 Copynumber: 3.7 Consensus size: 21
1359433 CCAAGTTCGC
*
1359443 AAGTTCGCATTACGATAGTCG
1 AAGTTCGCATTGCGATAGTCG
1359464 AAGTTCGCATTGCGATAGTCG
1 AAGTTCGCATTGCGATAGTCG
*
1359485 AAGTTCGCGTTGCGATAGTCG
1 AAGTTCGCATTGCGATAGTCG
*
1359506 AAGTTCGCGTTGCGA
1 AAGTTCGCATTGCGA
1359521 ATCTTGAAAC
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 55 1.00
ACGTcount: A:0.23, C:0.19, G:0.29, T:0.28
Consensus pattern (21 bp):
AAGTTCGCATTGCGATAGTCG
Found at i:1360273 original size:41 final size:41
Alignment explanation
Indices: 1360226--1360307 Score: 114
Period size: 41 Copynumber: 2.0 Consensus size: 41
1360216 ATTCGCGTTG
1360226 CATTTCGCGTTGCGATAGT-TGAAAATCG-CGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTCT-AAAAT-GTCGTTGCGATTTTC
* *
1360267 CATTTCGTGTTGCGATAGTCTACAATGTCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTCTAAAATGTCGTTGCGATTTTC
1360308 TACAGTTGTT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
40 1 0.03
41 35 0.95
42 1 0.03
ACGTcount: A:0.18, C:0.20, G:0.23, T:0.39
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTCTAAAATGTCGTTGCGATTTTC
Found at i:1360324 original size:22 final size:22
Alignment explanation
Indices: 1360275--1360347 Score: 85
Period size: 22 Copynumber: 3.4 Consensus size: 22
1360265 TCCATTTCGT
*
1360275 GTTGCGATAGTCTACA-ATGTC
1 GTTGCGATAGTCTACAGTTGTC
** *
1360296 GTTGCGATTTTCTACAGTTGTT
1 GTTGCGATAGTCTACAGTTGTC
*
1360318 GTTGCGAAAGTCTACAGTTGTC
1 GTTGCGATAGTCTACAGTTGTC
*
1360340 GTAGCGAT
1 GTTGCGAT
1360348 TTTCCAAATT
Statistics
Matches: 41, Mismatches: 10, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
21 14 0.34
22 27 0.66
ACGTcount: A:0.21, C:0.16, G:0.26, T:0.37
Consensus pattern (22 bp):
GTTGCGATAGTCTACAGTTGTC
Found at i:1360330 original size:43 final size:42
Alignment explanation
Indices: 1360254--1360353 Score: 123
Period size: 43 Copynumber: 2.4 Consensus size: 42
1360244 TTGAAAATCG
* *
1360254 CGTTGCGATTTTCCATTTCGTGTTGCGATAGTCTACA-ATGT
1 CGTTGCGATTTTCCAGTTCGTGTTGCGAAAGTCTACAGATGT
*
1360295 CGTTGCGATTTTCTACAGTT-GTTGTTGCGAAAGTCTACAGTTGT
1 CGTTGCGATTTTC--CAGTTCG-TGTTGCGAAAGTCTACAGATGT
*
1360339 CGTAGCGATTTTCCA
1 CGTTGCGATTTTCCA
1360354 AATTCGTTGC
Statistics
Matches: 51, Mismatches: 4, Indels: 7
0.82 0.06 0.11
Matches are distributed among these distances:
41 13 0.25
42 3 0.06
43 20 0.39
44 15 0.29
ACGTcount: A:0.18, C:0.19, G:0.23, T:0.40
Consensus pattern (42 bp):
CGTTGCGATTTTCCAGTTCGTGTTGCGAAAGTCTACAGATGT
Found at i:1361013 original size:12 final size:11
Alignment explanation
Indices: 1360983--1361016 Score: 52
Period size: 12 Copynumber: 3.1 Consensus size: 11
1360973 CCGTCTCGTC
1360983 TCGGGTCG-GG
1 TCGGGTCGTGG
1360993 TCGGGTCGTGG
1 TCGGGTCGTGG
1361004 TCGTGGTCGTGG
1 TCG-GGTCGTGG
1361016 T
1 T
1361017 AATACGTGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 8 0.36
11 5 0.23
12 9 0.41
ACGTcount: A:0.00, C:0.18, G:0.53, T:0.29
Consensus pattern (11 bp):
TCGGGTCGTGG
Found at i:1361160 original size:42 final size:41
Alignment explanation
Indices: 1361112--1361205 Score: 118
Period size: 41 Copynumber: 2.3 Consensus size: 41
1361102 AACGAATTTA
*
1361112 GAAAATCGCAACGACAACTGT-AGACTATCGCAACGCGAAATG
1 GAAAATCGCAACG-CAACTGTCA-ACTACCGCAACGCGAAATG
* * *
1361154 GAAAATCGCAACGCGATTTTCAACTACCGCAACGCGAAATG
1 GAAAATCGCAACGCAACTGTCAACTACCGCAACGCGAAATG
*
1361195 GAAAATTGCAA
1 GAAAATCGCAA
1361206 TGTGATTTTC
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
41 32 0.70
42 14 0.30
ACGTcount: A:0.40, C:0.23, G:0.20, T:0.16
Consensus pattern (41 bp):
GAAAATCGCAACGCAACTGTCAACTACCGCAACGCGAAATG
Found at i:1361186 original size:21 final size:21
Alignment explanation
Indices: 1361158--1361249 Score: 87
Period size: 21 Copynumber: 4.4 Consensus size: 21
1361148 GAAATGGAAA
1361158 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
* ** ** *
1361179 ACCGCAACGCGAAATGGAA-A
1 ATCGCAACGCGATTTTCAACT
* * *
1361199 ATTGCAATGTGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
*
1361220 ATCGCAACGCGATTTTCAATT
1 ATCGCAACGCGATTTTCAACT
1361241 ATCGCAACG
1 ATCGCAACG
1361250 TGAAATGCAA
Statistics
Matches: 51, Mismatches: 19, Indels: 2
0.71 0.26 0.03
Matches are distributed among these distances:
20 11 0.22
21 40 0.78
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (21 bp):
ATCGCAACGCGATTTTCAACT
Found at i:1361193 original size:41 final size:41
Alignment explanation
Indices: 1361135--1361231 Score: 158
Period size: 41 Copynumber: 2.4 Consensus size: 41
1361125 ACAACTGTAG
1361135 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
* * * *
1361176 ACTACCGCAACGCGAAATGGAAAATTGCAATGTGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
1361217 ACTATCGCAACGCGA
1 ACTATCGCAACGCGA
1361232 TTTTCAATTA
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.36, C:0.24, G:0.20, T:0.21
Consensus pattern (41 bp):
ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
Found at i:1361376 original size:21 final size:21
Alignment explanation
Indices: 1361347--1361400 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
1361337 GAACTGGAAA
1361347 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
* *
1361368 ATCGTAACGCGATTTTCAATT
1 ATCGCAACGCGATTTTCAACT
*
1361389 ATCACAACGCGA
1 ATCGCAACGCGA
1361401 AATGCAACAC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.28
Consensus pattern (21 bp):
ATCGCAACGCGATTTTCAACT
Found at i:1361449 original size:148 final size:148
Alignment explanation
Indices: 1361176--1361466 Score: 492
Period size: 148 Copynumber: 2.0 Consensus size: 148
1361166 GCGATTTTCA
* * *
1361176 ACTACCGCAACGCGAAATGGAAAATTGCAATGTGATTTTCAACTATCGCAACGCGATTTTCAATT
1 ACTACCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGATTTTCAATT
* * **
1361241 ATCGCAACGTGAAATGCAACGTGAATTTGCGATAGTGGAGATCGCAATGCGAATTAGAGATCGCA
66 ATCACAACGCGAAATGCAACACGAATTTGCGATAGTGGAGATCGCAATGCGAATTAGAGATCGCA
1361306 TTGCGATTTTGTTTGTAG
131 TTGCGATTTTGTTTGTAG
* * *
1361324 ACTATCGCAACGCGAACTGGAAAATCGCAACGCGATTTTCAACTATCGTAACGCGATTTTCAATT
1 ACTACCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGATTTTCAATT
1361389 ATCACAACGCGAAATGCAACACGAATTTGCGATAGTGGAGATCGCAATGCGAATTAGAGATCGCA
66 ATCACAACGCGAAATGCAACACGAATTTGCGATAGTGGAGATCGCAATGCGAATTAGAGATCGCA
1361454 TTGCGATTTTGTT
131 TTGCGATTTTGTT
1361467 GGTCATTTTC
Statistics
Matches: 133, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
148 133 1.00
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.27
Consensus pattern (148 bp):
ACTACCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGATTTTCAATT
ATCACAACGCGAAATGCAACACGAATTTGCGATAGTGGAGATCGCAATGCGAATTAGAGATCGCA
TTGCGATTTTGTTTGTAG
Found at i:1362192 original size:22 final size:22
Alignment explanation
Indices: 1362164--1362216 Score: 106
Period size: 22 Copynumber: 2.4 Consensus size: 22
1362154 TTCCATTTCG
1362164 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
1362186 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
1362208 CGTTGCGAT
1 CGTTGCGAT
1362217 TTTTCAAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.17, C:0.19, G:0.28, T:0.36
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGTTGT
Found at i:1362340 original size:6 final size:6
Alignment explanation
Indices: 1362329--1362362 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
1362319 GACACGTATT
1362329 ACCACG ACCACG ACCACG ACCACG ACCACG ACCA
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCA
1362363 TGAGACGGAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.35, C:0.50, G:0.15, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:1362849 original size:6 final size:6
Alignment explanation
Indices: 1362840--1362894 Score: 101
Period size: 6 Copynumber: 9.2 Consensus size: 6
1362830 CGCCGCCGTC
*
1362840 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TAGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
1362888 TCGTGG T
1 TCGTGG T
1362895 AATACGTGTC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 47 1.00
ACGTcount: A:0.02, C:0.15, G:0.49, T:0.35
Consensus pattern (6 bp):
TCGTGG
Found at i:1363081 original size:15 final size:15
Alignment explanation
Indices: 1363061--1363094 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1363051 TTTTTTATAT
1363061 TTTTAAAAA-AATTAA
1 TTTTAAAAACAA-TAA
1363076 TTTTAAAAACAATAA
1 TTTTAAAAACAATAA
1363091 TTTT
1 TTTT
1363095 TTCAAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 16 0.89
16 2 0.11
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (15 bp):
TTTTAAAAACAATAA
Found at i:1363132 original size:26 final size:27
Alignment explanation
Indices: 1363087--1363142 Score: 71
Period size: 26 Copynumber: 2.1 Consensus size: 27
1363077 TTTAAAAACA
1363087 ATAATTTTTTCAAAAATATATAAA-ATTT
1 ATAATTTTTT-AAAAATATA-AAATATTT
*
1363115 ATAATTTTTT-AAATTATAAAATATTT
1 ATAATTTTTTAAAAATATAAAATATTT
1363141 AT
1 AT
1363143 CATCATCATC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
25 3 0.12
26 13 0.50
28 10 0.38
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (27 bp):
ATAATTTTTTAAAAATATAAAATATTT
Found at i:1368215 original size:2 final size:2
Alignment explanation
Indices: 1368208--1368261 Score: 101
Period size: 2 Copynumber: 27.5 Consensus size: 2
1368198 AAAACCATAC
1368208 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1368250 AT AT AT AT -T AT A
1 AT AT AT AT AT AT A
1368262 GGAAAACAAC
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 50 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1372845 original size:25 final size:25
Alignment explanation
Indices: 1372811--1372860 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
1372801 TAGTACCAAA
*
1372811 AGCCGAATATTTAGGGATTTAGGAC
1 AGCCGAATATTTAGGAATTTAGGAC
1372836 AGCCGAATATTTAGGAATTTAGGAC
1 AGCCGAATATTTAGGAATTTAGGAC
1372861 TATTTTAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.34, C:0.12, G:0.26, T:0.28
Consensus pattern (25 bp):
AGCCGAATATTTAGGAATTTAGGAC
Found at i:1373248 original size:3 final size:3
Alignment explanation
Indices: 1373235--1373291 Score: 55
Period size: 3 Copynumber: 19.3 Consensus size: 3
1373225 GTAATATGTA
* * *
1373235 AAT AA- AAT AAT AAT AAT AAC ACT AAT AAT AAT AATT AA- AAT AAC
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT
*
1373279 GAT AAT AAT AAT A
1 AAT AAT AAT AAT A
1373292 TACAAAAAAG
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
2 4 0.09
3 36 0.84
4 3 0.07
ACGTcount: A:0.65, C:0.05, G:0.02, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:1373298 original size:24 final size:24
Alignment explanation
Indices: 1373235--1373291 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 24
1373225 GTAATATGTA
1373235 AATAA-AATAAT-AATAATAACACT
1 AATAATAATAATCAA-AATAACACT
*
1373258 AATAATAATAATTAAAATAACGA-T
1 AATAATAATAATCAAAATAAC-ACT
1373282 AATAATAATA
1 AATAATAATA
1373292 TACAAAAAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
23 5 0.16
24 23 0.74
25 3 0.10
ACGTcount: A:0.65, C:0.05, G:0.02, T:0.28
Consensus pattern (24 bp):
AATAATAATAATCAAAATAACACT
Found at i:1373523 original size:43 final size:44
Alignment explanation
Indices: 1373453--1373742 Score: 152
Period size: 46 Copynumber: 6.7 Consensus size: 44
1373443 GGACGCCACT
* * * * * *
1373453 GCTCATACGTGATGAAGAGTTCGGGTCGTCTAAGGG-TGACATG
1 GCTCCTACGTGATGAGGAGATCTGGTCATCTAAGGGATGACACG
* * * * **
1373496 GTTCCTACGTGATGAGGAAATCTGG---TC-GAGGGTTGACATT
1 GCTCCTACGTGATGAGGAGATCTGGTCATCTAAGGGATGACACG
* * * * *
1373536 GCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACG
1 GCTCCTACGTGATGAGGAGATCTGGTCATCT-AAGG-GATGACACG
* * * * *
1373582 GTTCCTACGTGATGAGGACG-GCTGGTTATCT-ATGGTTGACACG
1 GCTCCTACGTGATGAGGA-GATCTGGTCATCTAAGGGATGACACG
* ** *
1373625 GCTCCTACGTGGTGAGGAGATCTGGTC-T-GGA-GAATGACACG
1 GCTCCTACGTGATGAGGAGATCTGGTCATCTAAGGGATGACACG
* * * * *
1373666 GCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACG
1 GCTCCTACGTGATGAGGAGATCTGGTCATCT-AAGG-GATGACACG
* *
1373712 GTTCCTACGTGATGAGGACG-GCTGGTCATCT
1 GCTCCTACGTGATGAGGA-GATCTGGTCATCT
1373743 TTAGGAGTTA
Statistics
Matches: 183, Mismatches: 48, Indels: 29
0.70 0.18 0.11
Matches are distributed among these distances:
39 4 0.02
40 28 0.15
41 30 0.16
42 4 0.02
43 49 0.27
44 3 0.02
45 4 0.02
46 59 0.32
47 2 0.01
ACGTcount: A:0.24, C:0.19, G:0.31, T:0.26
Consensus pattern (44 bp):
GCTCCTACGTGATGAGGAGATCTGGTCATCTAAGGGATGACACG
Found at i:1373560 original size:40 final size:40
Alignment explanation
Indices: 1373452--1373560 Score: 112
Period size: 40 Copynumber: 2.6 Consensus size: 40
1373442 GGGACGCCAC
*
1373452 TGCTCATACGTGATGAAGAGTTCGGGTCGTCTAAGGGTGACAT
1 TGCTCATACGTGATGAAGAGTTCTGGTCG--T-AGGGTGACAT
* * * * **
1373495 GGTTCCTACGTGATGAGGAAATCTGGTCG-AGGGTTGACAT
1 TGCTCATACGTGATGAAGAGTTCTGGTCGTAGGG-TGACAT
1373535 TGCTCATACGTGATGAAGAGTTCTGG
1 TGCTCATACGTGATGAAGAGTTCTGG
1373561 CCATCTAAAG
Statistics
Matches: 52, Mismatches: 13, Indels: 5
0.74 0.19 0.07
Matches are distributed among these distances:
39 4 0.08
40 26 0.50
43 22 0.42
ACGTcount: A:0.23, C:0.16, G:0.33, T:0.28
Consensus pattern (40 bp):
TGCTCATACGTGATGAAGAGTTCTGGTCGTAGGGTGACAT
Found at i:1373795 original size:28 final size:30
Alignment explanation
Indices: 1373755--1373823 Score: 81
Period size: 28 Copynumber: 2.3 Consensus size: 30
1373745 AGGAGTTATG
* *
1373755 GTTTCAAGAGAAACCAAA-TTAAAGAT-T-T
1 GTTTCAAAAGAAA-CAAACCTAAAGATATAT
1373783 GTTTCAAAAGAAACAAACCTAAAGATGATAT
1 GTTTCAAAAGAAACAAACCTAAAGAT-ATAT
1373814 GTTTCAAAAG
1 GTTTCAAAAG
1373824 CAACTGTCTC
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
27 4 0.11
28 19 0.54
30 1 0.03
31 11 0.31
ACGTcount: A:0.48, C:0.12, G:0.14, T:0.26
Consensus pattern (30 bp):
GTTTCAAAAGAAACAAACCTAAAGATATAT
Found at i:1373893 original size:63 final size:62
Alignment explanation
Indices: 1373825--1373942 Score: 177
Period size: 63 Copynumber: 1.9 Consensus size: 62
1373815 TTTCAAAAGC
*
1373825 AACTGTCTCAAAAGAGACAAAATTTTGTTTCAAA-GGAAATGA-CTCAAAGATTGTTTAAAGGAA
1 AACTGTCTCAAAAGAGACAAAA-TTCGTTT-AAAGGGAAATGATCTCAAAGA-TGTTTAAAGGAA
*
1373888 AACTGTCTCAAATGAGACAAAATTCGTTTAAAGGGAAATGATCTCAAAGATGTTT
1 AACTGTCTCAAAAGAGACAAAATTCGTTTAAAGGGAAATGATCTCAAAGATGTTT
1373943 GTTTTGTTTC
Statistics
Matches: 51, Mismatches: 2, Indels: 5
0.88 0.03 0.09
Matches are distributed among these distances:
61 3 0.06
62 19 0.37
63 29 0.57
ACGTcount: A:0.42, C:0.12, G:0.18, T:0.28
Consensus pattern (62 bp):
AACTGTCTCAAAAGAGACAAAATTCGTTTAAAGGGAAATGATCTCAAAGATGTTTAAAGGAA
Found at i:1373901 original size:36 final size:36
Alignment explanation
Indices: 1373861--1373935 Score: 91
Period size: 36 Copynumber: 2.1 Consensus size: 36
1373851 GTTTCAAAGG
*
1373861 AAATGACTCAAAGATT-GTTTAAAGGAAAACTG-TCTC
1 AAATGACACAAA-ATTCGTTTAAAGGAAAA-TGATCTC
* *
1373897 AAATGAGACAAAATTCGTTTAAAGGGAAATGATCTC
1 AAATGACACAAAATTCGTTTAAAGGAAAATGATCTC
1373933 AAA
1 AAA
1373936 GATGTTTGTT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
35 5 0.15
36 29 0.85
ACGTcount: A:0.45, C:0.12, G:0.17, T:0.25
Consensus pattern (36 bp):
AAATGACACAAAATTCGTTTAAAGGAAAATGATCTC
Found at i:1373969 original size:35 final size:35
Alignment explanation
Indices: 1373930--1374009 Score: 92
Period size: 36 Copynumber: 2.3 Consensus size: 35
1373920 GGGAAATGAT
* * *
1373930 CTCAAAGATGTTTG-TTTTGTT-TCAAAGGAAACAGA
1 CTCAAAGATG-GTGATTTTGTTCCCAAA-GAAACAAA
1373965 CTCAAAGATGGTGAATTTTGTTCCCAAAGAAACAAA
1 CTCAAAGATGGTG-ATTTTGTTCCCAAAGAAACAAA
1374001 CTCAAAGAT
1 CTCAAAGAT
1374010 TTTTCTCAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
34 2 0.05
35 10 0.26
36 23 0.59
37 4 0.10
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.29
Consensus pattern (35 bp):
CTCAAAGATGGTGATTTTGTTCCCAAAGAAACAAA
Found at i:1374178 original size:31 final size:30
Alignment explanation
Indices: 1374114--1374188 Score: 82
Period size: 31 Copynumber: 2.4 Consensus size: 30
1374104 TGAAAATTCG
* *
1374114 TTTCAAGGGAAACGACTCAAAGATGGTTTTA
1 TTTCAAGAGAAACAACTCAAAGAT-GTTTTA
1374145 TTTCAAGAGAAACAAACTCAAAGAT-TTTATA
1 TTTCAAGAGAAAC-AACTCAAAGATGTTT-TA
1374176 TTT-ATAGAGAAAC
1 TTTCA-AGAGAAAC
1374189 TGCCTCAAGG
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
30 4 0.10
31 25 0.64
32 10 0.26
ACGTcount: A:0.43, C:0.12, G:0.16, T:0.29
Consensus pattern (30 bp):
TTTCAAGAGAAACAACTCAAAGATGTTTTA
Found at i:1374347 original size:68 final size:67
Alignment explanation
Indices: 1374245--1374370 Score: 189
Period size: 68 Copynumber: 1.9 Consensus size: 67
1374235 GTGGGTGGTT
* * *
1374245 TCAAAAGAAGTTGTCTCGAGAGACAAAATATTGTTTCCAAAGAAACAGACTCAAAGATTTTTTTT
1 TCAAAAGAAATTGTCTCAAGAGACAAAATATTGTTTCAAAAGAAACAGACTCAAAGATTTTTTTT
1374310 TC
66 TC
* * *
1374312 TCAAAAGAAATTGTCTTTAAGAGATAAAATTTTGTTTCAAAAGAAACAGACTCAAAGAT
1 TCAAAAGAAATTGTC-TCAAGAGACAAAATATTGTTTCAAAAGAAACAGACTCAAAGAT
1374371 GGATTACATC
Statistics
Matches: 52, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
67 14 0.27
68 38 0.73
ACGTcount: A:0.43, C:0.13, G:0.14, T:0.30
Consensus pattern (67 bp):
TCAAAAGAAATTGTCTCAAGAGACAAAATATTGTTTCAAAAGAAACAGACTCAAAGATTTTTTTT
TC
Found at i:1374641 original size:69 final size:68
Alignment explanation
Indices: 1374550--1374707 Score: 167
Period size: 69 Copynumber: 2.3 Consensus size: 68
1374540 AAAGATTTAC
* * * * *
1374550 TTCAAGAGAAACTGTCTCAAGAGATACAAAATTCAT-TTT-AAGAGAAACAGATTCAAAGATTTT
1 TTCAAAAGAAACTATCTCAAGAGAGACAAAATT-ATGTTTCAA-AGAAACAAACTCAAAGA-TTT
*
1374613 TTTTTT
63 TTTTGT
* * * *
1374619 TTCAAAAGAAATTATCTTAAGAGAGACAACATTTTGTTTCCAAAGAAACAAACTCAAAGATTTTT
1 TTCAAAAGAAACTATCTCAAGAGAGACAAAATTATGTTT-CAAAGAAACAAACTCAAAGATTTTT
1374684 TTGT
65 TTGT
*
1374688 TTCAAAAGAAACAATCTCAA
1 TTCAAAAGAAACTATCTCAA
1374708 AGATTTTTTT
Statistics
Matches: 73, Mismatches: 13, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
68 1 0.01
69 55 0.75
70 15 0.21
71 2 0.03
ACGTcount: A:0.43, C:0.13, G:0.11, T:0.32
Consensus pattern (68 bp):
TTCAAAAGAAACTATCTCAAGAGAGACAAAATTATGTTTCAAAGAAACAAACTCAAAGATTTTTT
TGT
Found at i:1374687 original size:32 final size:32
Alignment explanation
Indices: 1374650--1374717 Score: 118
Period size: 32 Copynumber: 2.1 Consensus size: 32
1374640 AGAGACAACA
*
1374650 TTTTGTTTCCAAAGAAACAAACTCAAAGATTT
1 TTTTGTTTCAAAAGAAACAAACTCAAAGATTT
*
1374682 TTTTGTTTCAAAAGAAACAATCTCAAAGATTT
1 TTTTGTTTCAAAAGAAACAAACTCAAAGATTT
1374714 TTTT
1 TTTT
1374718 CACAAAATTG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.38, C:0.13, G:0.09, T:0.40
Consensus pattern (32 bp):
TTTTGTTTCAAAAGAAACAAACTCAAAGATTT
Found at i:1374783 original size:52 final size:53
Alignment explanation
Indices: 1374703--1374806 Score: 174
Period size: 52 Copynumber: 2.0 Consensus size: 53
1374693 AAGAAACAAT
*
1374703 CTCAAAGATTTTTTTCACAAAATTGTCTCAAGAGAGACAAAGCTTTGTTTCAGA
1 CTCAAAGA-TTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAGA
*
1374757 CTCAAAGA-TTTTTCACGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCA
1 CTCAAAGATTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCA
1374807 AAATAAATAG
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
52 40 0.83
54 8 0.17
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (53 bp):
CTCAAAGATTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAGA
Found at i:1375014 original size:28 final size:28
Alignment explanation
Indices: 1374817--1375006 Score: 282
Period size: 28 Copynumber: 6.9 Consensus size: 28
1374807 AAATAAATAG
*
1374817 ACTCAAAG--TTTTTTCAA-AAAAAC-A
1 ACTCAAAGATTTTTTTCAAGAGAAACAA
* * *
1374841 ACTCAAAGATTTTTATTCAAAAGGAGCAA
1 ACTCAAAGATTTTT-TTCAAGAGAAACAA
*
1374870 ACTCAAAGA-TTTTTTCAAGAGGAACAA
1 ACTCAAAGATTTTTTTCAAGAGAAACAA
1374897 ACTCAAAGATTTTTTTCAAGAGAAACAA
1 ACTCAAAGATTTTTTTCAAGAGAAACAA
*
1374925 ACTCAAAGATTTTTTTCAAGAGAAACTA
1 ACTCAAAGATTTTTTTCAAGAGAAACAA
1374953 ACTCAAAGATTTTTTTCAAGAGAAACAA
1 ACTCAAAGATTTTTTTCAAGAGAAACAA
1374981 ACTCAAAGATTTTTTTCAAGAGAAAC
1 ACTCAAAGATTTTTTTCAAGAGAAAC
1375007 TGTCTCAAGA
Statistics
Matches: 152, Mismatches: 8, Indels: 8
0.90 0.05 0.05
Matches are distributed among these distances:
24 8 0.05
26 4 0.03
27 26 0.17
28 104 0.68
29 10 0.07
ACGTcount: A:0.45, C:0.15, G:0.11, T:0.29
Consensus pattern (28 bp):
ACTCAAAGATTTTTTTCAAGAGAAACAA
Found at i:1375330 original size:36 final size:36
Alignment explanation
Indices: 1375246--1375349 Score: 115
Period size: 36 Copynumber: 3.0 Consensus size: 36
1375236 GAGAAAATGA
* * *
1375246 TGTCTCAAGCGAGACGAAATTTG-CTTTA-AGATAC
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAC
* ** *
1375280 AGTCTCAAATGAGACAAAATTTGTTTTTAGAGAAAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAC
*
1375316 TGTCTCAAGCGAGACAAAGTTTGTTTTT-GAGAAA
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAA
1375350 ACGATCTCAA
Statistics
Matches: 57, Mismatches: 11, Indels: 3
0.80 0.15 0.04
Matches are distributed among these distances:
34 19 0.33
35 10 0.18
36 28 0.49
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (36 bp):
TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAC
Found at i:1375377 original size:36 final size:36
Alignment explanation
Indices: 1375247--1375365 Score: 111
Period size: 36 Copynumber: 3.4 Consensus size: 36
1375237 AGAAAATGAT
* * * *
1375247 GTCTCAAGCGAGACGAAATTTG-CTTTA-AG-ATAC
1 GTCTCAAGTGAGACAAAATTTGTTTTTAGAGAAAAC
* **
1375280 AGTCTCAAATGAGACAAAATTTGTTTTTAGAGAAATT
1 -GTCTCAAGTGAGACAAAATTTGTTTTTAGAGAAAAC
* *
1375317 GTCTCAAGCGAGACAAAGTTTGTTTTT-GAGAAAAC
1 GTCTCAAGTGAGACAAAATTTGTTTTTAGAGAAAAC
1375352 GATCTCAAGTGAGA
1 G-TCTCAAGTGAGA
1375366 TCAACTTTGT
Statistics
Matches: 68, Mismatches: 13, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
34 19 0.28
35 11 0.16
36 37 0.54
37 1 0.01
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.29
Consensus pattern (36 bp):
GTCTCAAGTGAGACAAAATTTGTTTTTAGAGAAAAC
Found at i:1376016 original size:4 final size:4
Alignment explanation
Indices: 1376007--1376066 Score: 70
Period size: 4 Copynumber: 15.0 Consensus size: 4
1375997 TTTATGTATC
* *
1376007 ATGT ATGT ATG- -TGT ATAT ATGT ATGT ATGCAT ATAT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATG--T ATGT ATGT ATGT ATGT
1376055 ATGT ATGT ATGT
1 ATGT ATGT ATGT
1376067 TTTCTCGATC
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
2 2 0.04
4 43 0.90
6 3 0.06
ACGTcount: A:0.28, C:0.02, G:0.22, T:0.48
Consensus pattern (4 bp):
ATGT
Found at i:1376030 original size:18 final size:18
Alignment explanation
Indices: 1376007--1376066 Score: 79
Period size: 18 Copynumber: 3.4 Consensus size: 18
1375997 TTTATGTATC
1376007 ATGTATGTATGTGTATAT
1 ATGTATGTATGTGTATAT
**
1376025 ATGTATGTATGCATATAT
1 ATGTATGTATGTGTATAT
*
1376043 ATGTATGTA--TGTATGT
1 ATGTATGTATGTGTATAT
1376059 ATGTATGT
1 ATGTATGT
1376067 TTTCTCGATC
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
16 12 0.32
18 25 0.68
ACGTcount: A:0.28, C:0.02, G:0.22, T:0.48
Consensus pattern (18 bp):
ATGTATGTATGTGTATAT
Found at i:1377886 original size:20 final size:20
Alignment explanation
Indices: 1377863--1377903 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
1377853 GGATAAATGC
1377863 AATGTTTCAAGGTCGCAAAG
1 AATGTTTCAAGGTCGCAAAG
*
1377883 AATGTTTCAAGGTCTCAAAG
1 AATGTTTCAAGGTCGCAAAG
1377903 A
1 A
1377904 TAGGGAGTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.27
Consensus pattern (20 bp):
AATGTTTCAAGGTCGCAAAG
Found at i:1383774 original size:25 final size:25
Alignment explanation
Indices: 1383740--1383789 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
1383730 TAGTACCAAA
*
1383740 AGCCGAATATTTAGGGATTTAGGAC
1 AGCCGAATATTTAGGAATTTAGGAC
1383765 AGCCGAATATTTAGGAATTTAGGAC
1 AGCCGAATATTTAGGAATTTAGGAC
1383790 TATTTTAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.34, C:0.12, G:0.26, T:0.28
Consensus pattern (25 bp):
AGCCGAATATTTAGGAATTTAGGAC
Found at i:1384178 original size:3 final size:3
Alignment explanation
Indices: 1384164--1384221 Score: 55
Period size: 3 Copynumber: 19.3 Consensus size: 3
1384154 GTAATATGTA
* * * *
1384164 AAT AAA AAT AAT AAT AAT AAC ACT AAT AAT AAT AATT AA- AAT AAC
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT
*
1384209 GAT AAT AAT AAT A
1 AAT AAT AAT AAT A
1384222 TACAAAAAAG
Statistics
Matches: 43, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
2 2 0.05
3 38 0.88
4 3 0.07
ACGTcount: A:0.66, C:0.05, G:0.02, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:1384228 original size:24 final size:24
Alignment explanation
Indices: 1384164--1384221 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 24
1384154 GTAATATGTA
*
1384164 AATAAAAATAAT-AATAATAACACT
1 AATAATAATAATCAA-AATAACACT
*
1384188 AATAATAATAATTAAAATAACGA-T
1 AATAATAATAATCAAAATAAC-ACT
1384212 AATAATAATA
1 AATAATAATA
1384222 TACAAAAAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
24 28 0.90
25 3 0.10
ACGTcount: A:0.66, C:0.05, G:0.02, T:0.28
Consensus pattern (24 bp):
AATAATAATAATCAAAATAACACT
Found at i:1384831 original size:42 final size:42
Alignment explanation
Indices: 1384771--1384902 Score: 124
Period size: 43 Copynumber: 3.1 Consensus size: 42
1384761 TTATATGAGT
*
1384771 TAAAAA-TGGGATTGAAAAATTAGGAGATTCAATTATAAATG
1 TAAAAAGTGAGATTGAAAAATTAGGAGATTCAATTATAAATG
* * * * *
1384812 TAAAAAGTGAGATTTAAAAAATCATGAGCTT-AATTATAAAGG
1 TAAAAAGTGAGA-TTGAAAAATTAGGAGATTCAATTATAAATG
* * * * * *
1384854 TACAAGGTGTGGTTGAAAAACTTAGGATAATCAATTATAAATG
1 TAAAAAGTGAGATTGAAAAA-TTAGGAGATTCAATTATAAATG
1384897 TAAAAA
1 TAAAAA
1384903 AAAATGGGAT
Statistics
Matches: 68, Mismatches: 19, Indels: 6
0.73 0.20 0.06
Matches are distributed among these distances:
41 13 0.19
42 27 0.40
43 28 0.41
ACGTcount: A:0.48, C:0.05, G:0.18, T:0.29
Consensus pattern (42 bp):
TAAAAAGTGAGATTGAAAAATTAGGAGATTCAATTATAAATG
Found at i:1385218 original size:31 final size:31
Alignment explanation
Indices: 1385183--1385245 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
1385173 ATCGTTCTTC
1385183 ATTTTTTAATGATAAATAACCAATAAAATTA
1 ATTTTTTAATGATAAATAACCAATAAAATTA
1385214 ATTTTTTAATGATAAATAACCAATAAAATTA
1 ATTTTTTAATGATAAATAACCAATAAAATTA
1385245 A
1 A
1385246 AATGTAACGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.52, C:0.06, G:0.03, T:0.38
Consensus pattern (31 bp):
ATTTTTTAATGATAAATAACCAATAAAATTA
Found at i:1387184 original size:56 final size:56
Alignment explanation
Indices: 1387098--1387212 Score: 221
Period size: 56 Copynumber: 2.1 Consensus size: 56
1387088 GATTTTTCAG
1387098 TGTTCTCGATTTCGTTGCTCACCCCGAGTTACAGGTTTCTACATTGGAGTATATAA
1 TGTTCTCGATTTCGTTGCTCACCCCGAGTTACAGGTTTCTACATTGGAGTATATAA
*
1387154 TGTTCTCGATTTCGTTGCTCACCCCGAGTTACAGGTTTCTACATTGGATTATATAA
1 TGTTCTCGATTTCGTTGCTCACCCCGAGTTACAGGTTTCTACATTGGAGTATATAA
1387210 TGT
1 TGT
1387213 ATCTACTATC
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 58 1.00
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.39
Consensus pattern (56 bp):
TGTTCTCGATTTCGTTGCTCACCCCGAGTTACAGGTTTCTACATTGGAGTATATAA
Found at i:1394091 original size:3 final size:3
Alignment explanation
Indices: 1394025--1394074 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
1394015 ATAATATTAA
1394025 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1394073 AT
1 AT
1394075 CACCATCATC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1394205 original size:6 final size:6
Alignment explanation
Indices: 1394196--1394394 Score: 398
Period size: 6 Copynumber: 33.2 Consensus size: 6
1394186 CCATCATTAT
1394196 CATTCC CATTCC CATTCC CATTCC CATTCC CATTCC CATTCC CATTCC
1 CATTCC CATTCC CATTCC CATTCC CATTCC CATTCC CATTCC CATTCC
1394244 CATTCC CATTCC CATTCC CATTCC CATTCC CATTCC CATTCC CATTCC
1 CATTCC CATTCC CATTCC CATTCC CATTCC CATTCC CATTCC CATTCC
1394292 CATTCC CATTCC CATTCC CATTCC CATTCC CATTCC CATTCC CATTCC
1 CATTCC CATTCC CATTCC CATTCC CATTCC CATTCC CATTCC CATTCC
1394340 CATTCC CATTCC CATTCC CATTCC CATTCC CATTCC CATTCC CATTCC
1 CATTCC CATTCC CATTCC CATTCC CATTCC CATTCC CATTCC CATTCC
1394388 CATTCC C
1 CATTCC C
1394395 TTTAGAACTG
Statistics
Matches: 193, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 193 1.00
ACGTcount: A:0.17, C:0.50, G:0.00, T:0.33
Consensus pattern (6 bp):
CATTCC
Found at i:1396968 original size:14 final size:13
Alignment explanation
Indices: 1396943--1396967 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1396933 CATTTTCTAA
1396943 AAAAATGATTTTC
1 AAAAATGATTTTC
1396956 AAAAATGATTTT
1 AAAAATGATTTT
1396968 TTTGTTATTT
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:0.48, C:0.04, G:0.08, T:0.40
Consensus pattern (13 bp):
AAAAATGATTTTC
Found at i:1417105 original size:25 final size:24
Alignment explanation
Indices: 1417077--1417168 Score: 87
Period size: 25 Copynumber: 3.6 Consensus size: 24
1417067 AATAAAATTC
1417077 AAAATATTTTATATATACTAACTTA
1 AAAATATTTTAT-TATACTAACTTA
*
1417102 AAAATATTTT-TTATATTAACTTGTA
1 AAAATATTTTATTATACTAAC-T-TA
* *
1417127 AATATATTTTATTATTAACTTAATTTA
1 AAAATATTTTATTA-T-AC-TAACTTA
*
1417154 AAAATATTTTTTTAT
1 AAAATATTTTATTAT
1417169 TATTTTCAAT
Statistics
Matches: 55, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
23 8 0.15
24 2 0.04
25 21 0.38
26 4 0.07
27 15 0.27
28 2 0.04
29 3 0.05
ACGTcount: A:0.42, C:0.04, G:0.01, T:0.52
Consensus pattern (24 bp):
AAAATATTTTATTATACTAACTTA
Found at i:1417121 original size:23 final size:23
Alignment explanation
Indices: 1417077--1417149 Score: 83
Period size: 23 Copynumber: 3.0 Consensus size: 23
1417067 AATAAAATTC
*
1417077 AAAATATTTTATATATACTAACTTA
1 AAAATATTTT-T-TATATTAACTTA
*
1417102 AAAATATTTTTTATATTAACTTG
1 AAAATATTTTTTATATTAACTTA
* *
1417125 TAAATATATTTTATTATTAACTTA
1 AAAATATTTTTTA-TATTAACTTA
1417149 A
1 A
1417150 TTTAAAAATA
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
23 21 0.51
24 10 0.24
25 10 0.24
ACGTcount: A:0.44, C:0.05, G:0.01, T:0.49
Consensus pattern (23 bp):
AAAATATTTTTTATATTAACTTA
Found at i:1417169 original size:27 final size:27
Alignment explanation
Indices: 1417077--1417218 Score: 98
Period size: 27 Copynumber: 5.3 Consensus size: 27
1417067 AATAAAATTC
* * *
1417077 AAAATATTTTATATA-T-ACTAACTTA
1 AAAATATTTTTTATATTAACTTATTTA
*
1417102 AAAATATTTTTTATATTAAC-T-TGTA
1 AAAATATTTTTTATATTAACTTATTTA
* *
1417127 AATATATTTTAT-TATTAACTTAATTTA
1 AAAATATTTTTTATATTAACTT-ATTTA
** *
1417154 AAAATATTTTTT-TATTATTTTCAATTA
1 AAAATATTTTTTATATTAACTT-ATTTA
*
1417181 AAAATATATATTTTATGTTAAAACTTATTTA
1 AAAATAT-T-TTTTATATT--AACTTATTTA
1417212 AAAATAT
1 AAAATAT
1417219 GACTAAATTG
Statistics
Matches: 90, Mismatches: 17, Indels: 14
0.74 0.14 0.12
Matches are distributed among these distances:
24 7 0.08
25 27 0.30
26 1 0.01
27 33 0.37
28 1 0.01
29 4 0.04
30 3 0.03
31 11 0.12
32 3 0.03
ACGTcount: A:0.44, C:0.04, G:0.01, T:0.51
Consensus pattern (27 bp):
AAAATATTTTTTATATTAACTTATTTA
Found at i:1418537 original size:29 final size:29
Alignment explanation
Indices: 1418502--1418557 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
1418492 TTCGCCCTTG
* * *
1418502 GAATTTTATAAGTTTAAGTTCGCCCCATA
1 GAATTTTATAAGCTCAAGTTCACCCCATA
1418531 GAATTTTATAAGCTCAAGTTCACCCCA
1 GAATTTTATAAGCTCAAGTTCACCCCA
1418558 ACATAAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.32, C:0.21, G:0.12, T:0.34
Consensus pattern (29 bp):
GAATTTTATAAGCTCAAGTTCACCCCATA
Found at i:1422897 original size:19 final size:18
Alignment explanation
Indices: 1422860--1422898 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 18
1422850 TCTTAAACTT
1422860 AACTCGAATGAAGCCTTA
1 AACTCGAATGAAGCCTTA
1422878 AACTCGAACCTGAA-CCTTA
1 AACTCGAA--TGAAGCCTTA
1422897 AA
1 AA
1422899 TGCATGAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 8 0.42
19 7 0.37
20 4 0.21
ACGTcount: A:0.41, C:0.26, G:0.13, T:0.21
Consensus pattern (18 bp):
AACTCGAATGAAGCCTTA
Found at i:1428365 original size:49 final size:49
Alignment explanation
Indices: 1428268--1428366 Score: 144
Period size: 49 Copynumber: 2.0 Consensus size: 49
1428258 AGTGTCAAGA
* *
1428268 TATTATTCACTTACATCGGTGTAACTATATGTTAAGTGATACATTTTTT
1 TATTATTCACTTACATCGGTGTAAATATATGTTAAGTGATACACTTTTT
* * * *
1428317 TATTATTCACTTACATCGGTGTAAATATGTGTTAGGTGCTATACTTTTT
1 TATTATTCACTTACATCGGTGTAAATATATGTTAAGTGATACACTTTTT
1428366 T
1 T
1428367 GTAGTATGAA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
49 44 1.00
ACGTcount: A:0.26, C:0.12, G:0.14, T:0.47
Consensus pattern (49 bp):
TATTATTCACTTACATCGGTGTAAATATATGTTAAGTGATACACTTTTT
Found at i:1434536 original size:29 final size:29
Alignment explanation
Indices: 1434494--1434553 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
1434484 ATTCTACAGT
1434494 GATCTCGTAGGACGCCATGCAATCCAGGC
1 GATCTCGTAGGACGCCATGCAATCCAGGC
*
1434523 GATCTTGTAGGACGCCATGCAATCCAGGC
1 GATCTCGTAGGACGCCATGCAATCCAGGC
1434552 GA
1 GA
1434554 CATACGGGAG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.25, C:0.28, G:0.28, T:0.18
Consensus pattern (29 bp):
GATCTCGTAGGACGCCATGCAATCCAGGC
Found at i:1434685 original size:32 final size:32
Alignment explanation
Indices: 1434644--1434725 Score: 164
Period size: 32 Copynumber: 2.6 Consensus size: 32
1434634 TATTATACGA
1434644 GGAGAGGTCGCCATGCAGACGAGCCAGCCAAT
1 GGAGAGGTCGCCATGCAGACGAGCCAGCCAAT
1434676 GGAGAGGTCGCCATGCAGACGAGCCAGCCAAT
1 GGAGAGGTCGCCATGCAGACGAGCCAGCCAAT
1434708 GGAGAGGTCGCCATGCAG
1 GGAGAGGTCGCCATGCAG
1434726 TCTGGGCGAC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 50 1.00
ACGTcount: A:0.27, C:0.27, G:0.37, T:0.10
Consensus pattern (32 bp):
GGAGAGGTCGCCATGCAGACGAGCCAGCCAAT
Found at i:1434756 original size:29 final size:29
Alignment explanation
Indices: 1434712--1434806 Score: 163
Period size: 29 Copynumber: 3.3 Consensus size: 29
1434702 GCCAATGGAG
* **
1434712 AGGTCGCCATGCAGTCTGGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
1434741 AGGTCGCCATGTAGTCCCGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
1434770 AGGTCGCCATGTAGTCCCGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
1434799 AGGTCGCC
1 AGGTCGCC
1434807 CCGGCGTCAC
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 63 1.00
ACGTcount: A:0.14, C:0.31, G:0.33, T:0.23
Consensus pattern (29 bp):
AGGTCGCCATGTAGTCCCGGCGACCTTGT
Found at i:1435143 original size:16 final size:18
Alignment explanation
Indices: 1435122--1435160 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
1435112 GGAGATAAGG
*
1435122 TAAATTTGTTTA-TATT-
1 TAAATTAGTTTATTATTA
1435138 TAAATTAGTTTATTATTA
1 TAAATTAGTTTATTATTA
1435156 TAAAT
1 TAAAT
1435161 GTTAATTAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 11 0.55
17 4 0.20
18 5 0.25
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.56
Consensus pattern (18 bp):
TAAATTAGTTTATTATTA
Found at i:1435328 original size:46 final size:48
Alignment explanation
Indices: 1435265--1435356 Score: 129
Period size: 46 Copynumber: 2.0 Consensus size: 48
1435255 TTATATAGTT
1435265 AAAAAATAATTAATTAGTTTGTT-TT-GTT-AATAGTT-AGTTATATAA
1 AAAAAATAATTAATTAGTTT-TTGTTAGTTAAATAGTTAAGTTATATAA
*
1435310 AAAAAATTATTTAATTAGTTTTTGTTAGTTAAATAGTTAAGTTATAT
1 AAAAAA-TAATTAATTAGTTTTTGTTAGTTAAATAGTTAAGTTATAT
1435357 TTGTTTGTTG
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
45 8 0.20
46 15 0.37
47 3 0.07
48 7 0.17
49 8 0.20
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.48
Consensus pattern (48 bp):
AAAAAATAATTAATTAGTTTTTGTTAGTTAAATAGTTAAGTTATATAA
Found at i:1435433 original size:32 final size:33
Alignment explanation
Indices: 1435397--1435473 Score: 95
Period size: 34 Copynumber: 2.3 Consensus size: 33
1435387 TTAGTTAGTA
*
1435397 AGTTTATTAGTAG-TATA-TTATAATGAAAAAAT
1 AGTTTATTAGTAGTTATAGTTAT-ATAAAAAAAT
*
1435429 AGTTTATTAGTTAGTTTTAGTTATATAAAAAAAT
1 AGTTTATTAG-TAGTTATAGTTATATAAAAAAAT
*
1435463 ATTTTATTAGT
1 AGTTTATTAGT
1435474 TGTTTAAGGG
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
32 10 0.26
33 4 0.10
34 21 0.54
35 4 0.10
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.47
Consensus pattern (33 bp):
AGTTTATTAGTAGTTATAGTTATATAAAAAAAT
Found at i:1435551 original size:16 final size:16
Alignment explanation
Indices: 1435519--1435565 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
1435509 TTTAAAAAGT
*
1435519 TTAGTTTGTTAGT-TTA
1 TTAGTTTATTA-TATTA
1435535 TTAGTTTATTATATTA
1 TTAGTTTATTATATTA
*
1435551 TAAG-TTATTATATTA
1 TTAGTTTATTATATTA
1435566 AAGTTTAGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 12 0.43
16 16 0.57
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.60
Consensus pattern (16 bp):
TTAGTTTATTATATTA
Found at i:1435560 original size:15 final size:14
Alignment explanation
Indices: 1435540--1435570 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
1435530 GTTTATTAGT
1435540 TTATTATATTATAAG
1 TTATTATATTA-AAG
1435555 TTATTATATTAAAG
1 TTATTATATTAAAG
1435569 TT
1 TT
1435571 TAGTGTTGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (14 bp):
TTATTATATTAAAG
Found at i:1437742 original size:17 final size:17
Alignment explanation
Indices: 1437720--1437752 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1437710 CAATGATGTT
*
1437720 TAGTATCAAATCATTAC
1 TAGTATCAAATAATTAC
1437737 TAGTATCAAATAATTA
1 TAGTATCAAATAATTA
1437753 AATATTTAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.12, G:0.06, T:0.36
Consensus pattern (17 bp):
TAGTATCAAATAATTAC
Found at i:1437981 original size:14 final size:14
Alignment explanation
Indices: 1437962--1438001 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
1437952 TAGTAATAAT
1437962 TATTAAATCATTAG
1 TATTAAATCATTAG
*
1437976 TATTAAATCATTAT
1 TATTAAATCATTAG
*
1437990 TA-TAAATAATTA
1 TATTAAATCATTA
1438002 CTAAATAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 9 0.38
14 15 0.62
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (14 bp):
TATTAAATCATTAG
Found at i:1438051 original size:12 final size:12
Alignment explanation
Indices: 1437944--1438301 Score: 81
Period size: 12 Copynumber: 28.9 Consensus size: 12
1437934 TTAGTATTCT
1437944 ATAATTATTAGTA
1 ATAATTATTA-TA
1437957 ATAATTATTA-A
1 ATAATTATTATA
* *
1437968 ATCATTAGTATTAA
1 ATAATTATTA-T-A
*
1437982 ATCATTATTATAA
1 ATAATTATTAT-A
*
1437995 ATAATTACTA-A
1 ATAATTATTATA
**
1438006 ATAA-TAACATA
1 ATAATTATTATA
1438017 ATAATTATTATAAA
1 ATAATTATTAT--A
*
1438031 ATCATTATTATA
1 ATAATTATTATA
* *
1438043 ATGATTATTATC
1 ATAATTATTATA
*
1438055 A-AATCATTACTAA
1 ATAATTATTA-T-A
* * *
1438068 ATCATCA-AATCA
1 ATAATTATTAT-A
* *
1438080 TTAAATATT-TAA
1 ATAATTATTAT-A
*
1438092 ATCATTATTA-A
1 ATAATTATTATA
* *
1438103 ATCATTTTTATA
1 ATAATTATTATA
*
1438115 ATGATTATTACTAA
1 ATAATTATTA-T-A
*
1438129 ATCATTATTATA
1 ATAATTATTATA
*
1438141 ATGATTATTATCAA
1 ATAATTATTAT--A
* *
1438155 ATCATTACTATA
1 ATAATTATTATA
* *
1438167 ATGATTATTATC
1 ATAATTATTATA
*
1438179 A-AATCATTACTAA
1 ATAATTATTA-T-A
* * *
1438192 ATCATCA-AATCA
1 ATAATTATTAT-A
* *
1438204 TTAAATATT-TAA
1 ATAATTATTAT-A
*
1438216 ATCATTATTA-A
1 ATAATTATTATA
* *
1438227 ATCATTTTTATA
1 ATAATTATTATA
*
1438239 ATTATTATTATTAA
1 ATAATTATTA-T-A
*
1438253 ATCATTATTATA
1 ATAATTATTATA
*
1438265 ATGATTATTATCAA
1 ATAATTATTAT--A
* *
1438279 ATCATTACTATA
1 ATAATTATTATA
*
1438291 ATGATTATTAT
1 ATAATTATTAT
1438302 CAAATCATTA
Statistics
Matches: 257, Mismatches: 61, Indels: 55
0.69 0.16 0.15
Matches are distributed among these distances:
10 3 0.01
11 51 0.20
12 105 0.41
13 29 0.11
14 69 0.27
ACGTcount: A:0.45, C:0.08, G:0.02, T:0.44
Consensus pattern (12 bp):
ATAATTATTATA
Found at i:1438058 original size:26 final size:26
Alignment explanation
Indices: 1437960--1438311 Score: 263
Period size: 26 Copynumber: 14.2 Consensus size: 26
1437950 ATTAGTAATA
* * *
1437960 ATTATTA-AATCATTAGTATTAAATC
1 ATTATTATAATGATTATTATCAAATC
*
1437985 ATTATTATAA--ATAATTA-CTAAAT-
1 ATTATTATAATGATTATTATC-AAATC
* ** * *
1438008 AATAACATAATAATTATTATAAAATC
1 ATTATTATAATGATTATTATCAAATC
1438034 ATTATTATAATGATTATTATCAAATC
1 ATTATTATAATGATTATTATCAAATC
* * * * * *
1438060 ATTACTA-AATCATCA-AATC-ATTA
1 ATTATTATAATGATTATTATCAAATC
* * *
1438083 AATATT-TAA--ATCATTATTAAATC
1 ATTATTATAATGATTATTATCAAATC
*
1438106 ATTTTTATAATGATTATTA-CTAAATC
1 ATTATTATAATGATTATTATC-AAATC
1438132 ATTATTATAATGATTATTATCAAATC
1 ATTATTATAATGATTATTATCAAATC
*
1438158 ATTACTATAATGATTATTATCAAATC
1 ATTATTATAATGATTATTATCAAATC
* * * * * *
1438184 ATTACTA-AATCATCA-AATC-ATTA
1 ATTATTATAATGATTATTATCAAATC
* * *
1438207 AATATT-TAA--ATCATTATTAAATC
1 ATTATTATAATGATTATTATCAAATC
* * *
1438230 ATTTTTATAATTATTATTATTAAATC
1 ATTATTATAATGATTATTATCAAATC
1438256 ATTATTATAATGATTATTATCAAATC
1 ATTATTATAATGATTATTATCAAATC
*
1438282 ATTACTATAATGATTATTATCAAATC
1 ATTATTATAATGATTATTATCAAATC
1438308 ATTA
1 ATTA
1438312 CTAAATCATC
Statistics
Matches: 258, Mismatches: 49, Indels: 39
0.75 0.14 0.11
Matches are distributed among these distances:
21 8 0.03
22 4 0.02
23 35 0.14
24 21 0.08
25 29 0.11
26 160 0.62
27 1 0.00
ACGTcount: A:0.45, C:0.09, G:0.02, T:0.44
Consensus pattern (26 bp):
ATTATTATAATGATTATTATCAAATC
Found at i:1438184 original size:124 final size:124
Alignment explanation
Indices: 1437976--1438369 Score: 677
Period size: 124 Copynumber: 3.2 Consensus size: 124
1437966 AAATCATTAG
* * * ** * *
1437976 TATTAAATCATTATTATAA--ATAATTACTAAAT-AATAACATAATAATTATTATAAAATCATTA
1 TATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTA
*
1438038 TTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
66 CTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
1438097 TATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTA
1 TATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTA
1438162 CTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
66 CTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
* *
1438221 TATTAAATCATTTTTATAATTATTATTATTAAATCATTATTATAATGATTATTATCAAATCATTA
1 TATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTA
1438286 CTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
66 CTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
1438345 TATTAAATCATTTTTATAATGATTA
1 TATTAAATCATTTTTATAATGATTA
1438370 ATAAATACAT
Statistics
Matches: 259, Mismatches: 11, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
121 18 0.07
123 12 0.05
124 229 0.88
ACGTcount: A:0.45, C:0.09, G:0.02, T:0.44
Consensus pattern (124 bp):
TATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTA
CTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
Found at i:1438347 original size:98 final size:95
Alignment explanation
Indices: 1438138--1438369 Score: 236
Period size: 98 Copynumber: 2.4 Consensus size: 95
1438128 AATCATTATT
* * * *
1438138 ATAATGATTATTATCAAATCATTACTATAATGATTATTATCAAATCATTACTAAATCATCAAATC
1 ATAATTATCATTATTAAATCATTATTATAATGATTATTATCAAATCATTACTAAATCAT-AAATC
* * **
1438203 ATTAAATATTTAAATCATTATTAAATCATTTTT
65 ATCAAATATTTAAATC--TATCAAATCATTTAA
* * * *
1438236 ATAATTATTATTATTAAATCATTATTATAATGATTATTATCAAATCATTACTATAATGAT-TATT
1 ATAATTATCATTATTAAATCATTATTATAATGATTATTATCAAATCATTACTA-AATCATAAATC
1438300 ATCAAATCATTACTAAATC-ATCAAATCA-TTAA
65 ATCAAAT-ATT--TAAATCTATCAAATCATTTAA
* *
1438332 ATATTTAAATCATTATTAAATCATTTTTATAATGATTA
1 ATAATT--ATCATTATTAAATCATTATTATAATGATTA
1438370 ATAAATACAT
Statistics
Matches: 115, Mismatches: 13, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
96 7 0.06
97 16 0.14
98 81 0.70
99 5 0.04
100 6 0.05
ACGTcount: A:0.44, C:0.10, G:0.02, T:0.44
Consensus pattern (95 bp):
ATAATTATCATTATTAAATCATTATTATAATGATTATTATCAAATCATTACTAAATCATAAATCA
TCAAATATTTAAATCTATCAAATCATTTAA
Found at i:1441272 original size:26 final size:24
Alignment explanation
Indices: 1441212--1441272 Score: 59
Period size: 26 Copynumber: 2.4 Consensus size: 24
1441202 TACTAATATT
*
1441212 ATTAATAATGATTTAATAATTATT
1 ATTAATAATGATTTAATAATTATG
* *
1441236 ATTAATCTAATGATTTGATATTTAATG
1 ATTAA--TAATGATTTAATAATT-ATG
1441263 ATTTAATAAT
1 A-TTAATAAT
1441273 AATATGATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
24 5 0.17
26 18 0.60
27 3 0.10
28 4 0.13
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.49
Consensus pattern (24 bp):
ATTAATAATGATTTAATAATTATG
Found at i:1441561 original size:17 final size:17
Alignment explanation
Indices: 1441508--1441567 Score: 57
Period size: 17 Copynumber: 3.3 Consensus size: 17
1441498 AATATAAATA
*
1441508 AAACAAAATATTTTTTTT
1 AAACACAATA-TTTTTTT
* *
1441526 AAACAACACTAAATATTTTT
1 AAAC-ACA--ATATTTTTTT
1441546 AAACACAATATTTTTTT
1 AAACACAATATTTTTTT
1441563 AAACA
1 AAACA
1441568 AAAATTATCT
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
17 13 0.38
18 4 0.12
19 5 0.15
20 10 0.29
21 2 0.06
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.40
Consensus pattern (17 bp):
AAACACAATATTTTTTT
Found at i:1441659 original size:14 final size:14
Alignment explanation
Indices: 1441640--1441666 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1441630 CACATACACA
1441640 ACAACAAAAAATAG
1 ACAACAAAAAATAG
1441654 ACAACAAAAAATA
1 ACAACAAAAAATA
1441667 ATAAATTACT
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:0.74, C:0.15, G:0.04, T:0.07
Consensus pattern (14 bp):
ACAACAAAAAATAG
Found at i:1441659 original size:17 final size:17
Alignment explanation
Indices: 1441637--1441669 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1441627 TTACACATAC
1441637 ACAACAACAAAA-AATAG
1 ACAACAA-AAAATAATAG
1441654 ACAACAAAAAATAATA
1 ACAACAAAAAATAATA
1441670 AATTACTCAC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.73, C:0.15, G:0.03, T:0.09
Consensus pattern (17 bp):
ACAACAAAAAATAATAG
Found at i:1442093 original size:21 final size:21
Alignment explanation
Indices: 1442060--1442108 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
1442050 AATATAATAT
*
1442060 ATAACTTAAACTAACCAACTA
1 ATAACTTAAACTAACAAACTA
* *
1442081 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
1442102 ATTAACT
1 A-TAACT
1442109 AGATTTTAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.51, C:0.18, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:1442583 original size:35 final size:35
Alignment explanation
Indices: 1442543--1442610 Score: 118
Period size: 35 Copynumber: 1.9 Consensus size: 35
1442533 TGGATGCAAC
1442543 GCATGCATGAGTGATACAGTTAAAGCTTGGTCGTT
1 GCATGCATGAGTGATACAGTTAAAGCTTGGTCGTT
* *
1442578 GCATGCATGATTGCTACAGTTAAAGCTTGGTCG
1 GCATGCATGAGTGATACAGTTAAAGCTTGGTCG
1442611 CGATGCAGGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.31
Consensus pattern (35 bp):
GCATGCATGAGTGATACAGTTAAAGCTTGGTCGTT
Found at i:1442667 original size:12 final size:12
Alignment explanation
Indices: 1442650--1442674 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1442640 TCCATGGCGA
1442650 CCTACCACCTAC
1 CCTACCACCTAC
1442662 CCTACCACCTAC
1 CCTACCACCTAC
1442674 C
1 C
1442675 ATGTCGTAGG
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:0.24, C:0.60, G:0.00, T:0.16
Consensus pattern (12 bp):
CCTACCACCTAC
Found at i:1442701 original size:29 final size:30
Alignment explanation
Indices: 1442668--1442739 Score: 128
Period size: 30 Copynumber: 2.4 Consensus size: 30
1442658 CTACCCTACC
1442668 ACCTACCATGTCGT-AGGGACTCCATGGCG
1 ACCTACCATGTCGTCAGGGACTCCATGGCG
*
1442697 ACCTACCATGTCGTCGGGGACTCCATGGCG
1 ACCTACCATGTCGTCAGGGACTCCATGGCG
1442727 ACCTACCATGTCG
1 ACCTACCATGTCG
1442740 CGACCTACCA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
29 14 0.34
30 27 0.66
ACGTcount: A:0.19, C:0.33, G:0.26, T:0.21
Consensus pattern (30 bp):
ACCTACCATGTCGTCAGGGACTCCATGGCG
Found at i:1442744 original size:15 final size:15
Alignment explanation
Indices: 1442724--1442755 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
1442714 GGACTCCATG
1442724 GCGACCTACCATGTC
1 GCGACCTACCATGTC
1442739 GCGACCTACCATGTC
1 GCGACCTACCATGTC
1442754 GC
1 GC
1442756 CGGCAACCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.19, C:0.41, G:0.22, T:0.19
Consensus pattern (15 bp):
GCGACCTACCATGTC
Found at i:1443010 original size:29 final size:29
Alignment explanation
Indices: 1442968--1443023 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
1442958 AAATAATGAT
1442968 GGACGCCGGGCGTGCATGGCGACCTATAA
1 GGACGCCGGGCGTGCATGGCGACCTATAA
*
1442997 GGACTCCGGGCGTGCATGGCGACCTAT
1 GGACGCCGGGCGTGCATGGCGACCTAT
1443024 GTTGCCACTG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.18, C:0.29, G:0.38, T:0.16
Consensus pattern (29 bp):
GGACGCCGGGCGTGCATGGCGACCTATAA
Found at i:1446821 original size:14 final size:15
Alignment explanation
Indices: 1446794--1446838 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 15
1446784 AATATAATTA
1446794 ATATAATATAAATTTT
1 ATATAAT-TAAATTTT
*
1446810 A-ATAATTTAATTTT
1 ATATAATTAAATTTT
1446824 ATTATAATTAAATTT
1 A-TATAATTAAATTT
1446839 AAGATGATGC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
14 8 0.32
15 5 0.20
16 12 0.48
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
ATATAATTAAATTTT
Found at i:1450522 original size:45 final size:45
Alignment explanation
Indices: 1450458--1450552 Score: 163
Period size: 45 Copynumber: 2.1 Consensus size: 45
1450448 ATTAATAAAA
*
1450458 TAAATCATGATAATTAAAACAGGAGCAATTTACAAGTTGAGTGAT
1 TAAATCATGATAATTAAAACAGGAGCAATTTAAAAGTTGAGTGAT
* *
1450503 TAAATCATGATAATTAAAACATGAGTAATTTAAAAGTTGAGTGAT
1 TAAATCATGATAATTAAAACAGGAGCAATTTAAAAGTTGAGTGAT
1450548 TAAAT
1 TAAAT
1450553 TGAAAACTTT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.46, C:0.06, G:0.16, T:0.32
Consensus pattern (45 bp):
TAAATCATGATAATTAAAACAGGAGCAATTTAAAAGTTGAGTGAT
Found at i:1450550 original size:15 final size:15
Alignment explanation
Indices: 1450458--1450551 Score: 57
Period size: 16 Copynumber: 6.3 Consensus size: 15
1450448 ATTAATAAAA
*
1450458 TAAATCATGA-TAAT
1 TAAAACATGAGTAAT
* *
1450472 TAAAACAGGAGCAATT
1 TAAAACATGAGTAA-T
* ** *
1450488 TACAAGTTGAGTGAT
1 TAAAACATGAGTAAT
*
1450503 TAAATCATGA-TAAT
1 TAAAACATGAGTAAT
1450517 TAAAACATGAGTAATT
1 TAAAACATGAGTAA-T
** *
1450533 TAAAAGTTGAGTGAT
1 TAAAACATGAGTAAT
1450548 TAAA
1 TAAA
1450552 TTGAAAACTT
Statistics
Matches: 58, Mismatches: 18, Indels: 7
0.70 0.22 0.08
Matches are distributed among these distances:
14 20 0.34
15 17 0.29
16 21 0.36
ACGTcount: A:0.47, C:0.06, G:0.16, T:0.31
Consensus pattern (15 bp):
TAAAACATGAGTAAT
Found at i:1454945 original size:3 final size:3
Alignment explanation
Indices: 1454937--1454971 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
1454927 ATTAACTAAA
*
1454937 ATT ATT ATT ATT ATT ATT AAT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1454972 ATATATATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:1455149 original size:158 final size:161
Alignment explanation
Indices: 1454973--1455290 Score: 439
Period size: 162 Copynumber: 2.0 Consensus size: 161
1454963 TATTATTATA
* *
1454973 TATATATATATATAACTTAGATCTATT-AAAA-AAAACTAATTACATTTTAAT-A-ACACACGAT
1 TATATATATATATAACTTAAATCTATTAAAAAGAAAACTAATTACATTTTAATAACACACACAAT
* *
1455034 CCATTGAACTTTGAAGAATCAATCAAATTTTAGATA-TCAAAATGAGGATATGACTCTCTTGTCC
66 CCATTAAAC-TTGAAGAATCAATCAAATTTTAGA-ACTCAAAATGAGGATATGACTCTCCTGTCC
* *
1455098 ACCGCAAAGGATGAGGGCATGCAATAATGGATC
129 ACCGCAAAAGATGAGGCCATGCAATAATGGATC
*
1455131 TATATATATATATAACTTAAATCTATTAAAAATGAAAACTAATTGCATTTTAATAACACACACAA
1 TATATATATATATAACTTAAATCTATTAAAAA-GAAAACTAATTACATTTTAATAACACACACAA
* ** * **
1455196 TCCATTAAACTTGAAGACTTGATCAATTTTTAGAACTCAAGTTGAGGATATGACTCTCCTGTCCA
65 TCCATTAAACTTGAAGAATCAATCAAATTTTAGAACTCAAAATGAGGATATGACTCTCCTGTCCA
* *
1455261 CCGCAAAAGATGAGGCCATGTAATCATGGA
130 CCGCAAAAGATGAGGCCATGCAATAATGGA
1455291 ACTGGAATTT
Statistics
Matches: 139, Mismatches: 15, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
158 26 0.19
159 4 0.03
161 20 0.14
162 73 0.53
163 16 0.12
ACGTcount: A:0.41, C:0.16, G:0.13, T:0.31
Consensus pattern (161 bp):
TATATATATATATAACTTAAATCTATTAAAAAGAAAACTAATTACATTTTAATAACACACACAAT
CCATTAAACTTGAAGAATCAATCAAATTTTAGAACTCAAAATGAGGATATGACTCTCCTGTCCAC
CGCAAAAGATGAGGCCATGCAATAATGGATC
Found at i:1457710 original size:23 final size:23
Alignment explanation
Indices: 1457680--1457726 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
1457670 ATTATTATTA
1457680 TTTTTTTTATAAAGAATCACAAT
1 TTTTTTTTATAAAGAATCACAAT
1457703 TTTTTTTTATAAAGAATCACAAT
1 TTTTTTTTATAAAGAATCACAAT
1457726 T
1 T
1457727 CTAAAATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.38, C:0.09, G:0.04, T:0.49
Consensus pattern (23 bp):
TTTTTTTTATAAAGAATCACAAT
Found at i:1467333 original size:2 final size:2
Alignment explanation
Indices: 1467326--1467361 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1467316 CTGCTAAGGA
1467326 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1467362 TTATGTATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1471954 original size:17 final size:18
Alignment explanation
Indices: 1471932--1471981 Score: 57
Period size: 17 Copynumber: 2.7 Consensus size: 18
1471922 GGGTATGCTC
1471932 AAATTTTATTTTAACT-T
1 AAATTTTATTTTAACTCT
*
1471949 AAATTTTACTATTAACTCT
1 AAATTTTA-TTTTAACTCT
*
1471968 ATAATTGTATTTTA
1 A-AATTTTATTTTA
1471982 CAATAGTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 8 0.30
18 7 0.26
19 6 0.22
20 6 0.22
ACGTcount: A:0.36, C:0.08, G:0.02, T:0.54
Consensus pattern (18 bp):
AAATTTTATTTTAACTCT
Found at i:1477230 original size:22 final size:20
Alignment explanation
Indices: 1477183--1477232 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 20
1477173 ATGTTGGTGA
1477183 ATTTTTTTTTAAAATGAGTTG
1 ATTTTTTTTTAAAATGAG-TG
1477204 ATTTTTTTTTAAAA-GAAAGTG
1 ATTTTTTTTTAAAATG--AGTG
1477225 ATTTTTTT
1 ATTTTTTT
1477233 AAAAAAATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
20 1 0.04
21 24 0.89
22 2 0.07
ACGTcount: A:0.30, C:0.00, G:0.12, T:0.58
Consensus pattern (20 bp):
ATTTTTTTTTAAAATGAGTG
Found at i:1478756 original size:19 final size:18
Alignment explanation
Indices: 1478734--1478781 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
1478724 TAATTAAATA
1478734 TTTAA-TAAATTATTATATT
1 TTTAATTAAA-TATT-TATT
1478753 TTTAATTTAAATATTTATT
1 TTTAA-TTAAATATTTATT
*
1478772 TTTAAGTAAA
1 TTTAATTAAA
1478782 CCAAAATAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 4 0.15
19 14 0.54
20 4 0.15
21 4 0.15
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (18 bp):
TTTAATTAAATATTTATT
Found at i:1479476 original size:31 final size:30
Alignment explanation
Indices: 1479407--1479478 Score: 90
Period size: 30 Copynumber: 2.4 Consensus size: 30
1479397 AACCATAATA
* *
1479407 ATCACATCTTAAATAAATAAAAATAAAATT
1 ATCATATCTTAAATAAATAAAAATAAAATG
* *
1479437 ATTATATCTTAATTAAATAAAAATAAAAATG
1 ATCATATCTTAAATAAATAAAAAT-AAAATG
*
1479468 ATCGTATCTTA
1 ATCATATCTTA
1479479 TGTATTTTAA
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
30 21 0.60
31 14 0.40
ACGTcount: A:0.54, C:0.08, G:0.03, T:0.35
Consensus pattern (30 bp):
ATCATATCTTAAATAAATAAAAATAAAATG
Found at i:1490137 original size:23 final size:24
Alignment explanation
Indices: 1490091--1490145 Score: 78
Period size: 25 Copynumber: 2.3 Consensus size: 24
1490081 TAAATAAAAT
*
1490091 TATATTATAAAAATAAACGAACAAA
1 TATATTATAAAAACAAAC-AACAAA
1490116 TATATTATAAAAACAAAC-ACAAA
1 TATATTATAAAAACAAACAACAAA
1490139 TA-ATTAT
1 TATATTAT
1490146 GTTCATAACC
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 5 0.17
23 7 0.24
25 17 0.59
ACGTcount: A:0.62, C:0.09, G:0.02, T:0.27
Consensus pattern (24 bp):
TATATTATAAAAACAAACAACAAA
Found at i:1490481 original size:19 final size:20
Alignment explanation
Indices: 1490457--1490502 Score: 76
Period size: 21 Copynumber: 2.3 Consensus size: 20
1490447 GATTATTAAA
1490457 AATTATAAAATA-ATTTTAT
1 AATTATAAAATATATTTTAT
1490476 AATTATAAAATATTATTTTAT
1 AATTATAAAATA-TATTTTAT
1490497 AATTAT
1 AATTAT
1490503 GAGATTATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 12 0.48
21 13 0.52
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
AATTATAAAATATATTTTAT
Found at i:1492367 original size:3 final size:3
Alignment explanation
Indices: 1492359--1492385 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1492349 TCAAATCCTT
1492359 CAG CAG CAG CAG CAG CAG CAG CAG CAG
1 CAG CAG CAG CAG CAG CAG CAG CAG CAG
1492386 GAACTGGAGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.33, G:0.33, T:0.00
Consensus pattern (3 bp):
CAG
Found at i:1494254 original size:26 final size:26
Alignment explanation
Indices: 1494219--1494278 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
1494209 TGGTATTTTT
*
1494219 AAAATATAAATGAATA-AATAATTATTA
1 AAAAT-TAAATGAA-ACAATAATAATTA
* *
1494246 AAAATTAAATTAAACTATAATAATTA
1 AAAATTAAATGAAACAATAATAATTA
1494272 AAAATTA
1 AAAATTA
1494279 TTACGTTAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
25 1 0.03
26 23 0.79
27 5 0.17
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (26 bp):
AAAATTAAATGAAACAATAATAATTA
Found at i:1495098 original size:23 final size:25
Alignment explanation
Indices: 1495055--1495100 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
1495045 ACTGAAAACA
*
1495055 TATTTTTTTTCTTCATATTTTCACT
1 TATTTTTGTTCTTCATATTTTCACT
1495080 TATTTTTGTT-TTCAT-TTTTCA
1 TATTTTTGTTCTTCATATTTTCA
1495101 AAAATCATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 5 0.25
25 9 0.45
ACGTcount: A:0.15, C:0.13, G:0.02, T:0.70
Consensus pattern (25 bp):
TATTTTTGTTCTTCATATTTTCACT
Found at i:1498076 original size:17 final size:17
Alignment explanation
Indices: 1498054--1498087 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1498044 AGCTTATTAA
1498054 ATATTAAATATATATAT
1 ATATTAAATATATATAT
**
1498071 ATATTATTTATATATAT
1 ATATTAAATATATATAT
1498088 TTAGACTAAT
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:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
ATATTAAATATATATAT
Found at i:1498489 original size:16 final size:17
Alignment explanation
Indices: 1498449--1498503 Score: 69
Period size: 16 Copynumber: 3.4 Consensus size: 17
1498439 CATGATTGTT
* *
1498449 TTAAATATTATAAAAAA
1 TTAAATTTTATAAAATA
1498466 TTAAATTTTATAAAATA
1 TTAAATTTTATAAAATA
*
1498483 -TATATTTTATAAAAT-
1 TTAAATTTTATAAAATA
1498498 TTAAAT
1 TTAAAT
1498504 ATATTTTTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
16 18 0.55
17 15 0.45
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
TTAAATTTTATAAAATA
Found at i:1498885 original size:31 final size:30
Alignment explanation
Indices: 1498840--1498921 Score: 107
Period size: 31 Copynumber: 2.8 Consensus size: 30
1498830 TTTATTTACA
* *
1498840 TAAAGTA--TTTTTAGTCAAAATGAGTACC
1 TAAAGTATTTTTTTAGTCAAAATAAATACC
1498868 TAAAGTTATTTTTTTAGTCAAAATAAATACC
1 TAAAG-TATTTTTTTAGTCAAAATAAATACC
*
1498899 TAAAGTATTTTTTGA-TCAAAATA
1 TAAAGTATTTTTTTAGTCAAAATA
1498922 GGCACATAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
28 5 0.10
29 10 0.21
30 9 0.19
31 24 0.50
ACGTcount: A:0.41, C:0.09, G:0.10, T:0.40
Consensus pattern (30 bp):
TAAAGTATTTTTTTAGTCAAAATAAATACC
Found at i:1498931 original size:29 final size:29
Alignment explanation
Indices: 1498836--1498936 Score: 98
Period size: 29 Copynumber: 3.4 Consensus size: 29
1498826 TTCATTTATT
*
1498836 TACATAAAGTATTTTTAG-TCAAAAT-GAG
1 TACATAAAGTATTTTTTGATCAAAATAG-G
* * **
1498864 TACCTAAAGTTATTTTTTTAGTCAAAATAAA
1 TACATAAAG-TATTTTTTGA-TCAAAATAGG
*
1498895 TACCTAAAGTATTTTTTGATCAAAATAGG
1 TACATAAAGTATTTTTTGATCAAAATAGG
*
1498924 CACATAAAGTATT
1 TACATAAAGTATT
1498937 CATTTTTTTT
Statistics
Matches: 59, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
28 8 0.14
29 26 0.44
30 9 0.15
31 16 0.27
ACGTcount: A:0.42, C:0.10, G:0.11, T:0.38
Consensus pattern (29 bp):
TACATAAAGTATTTTTTGATCAAAATAGG
Done.