Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008579.1 Hibiscus syriacus cultivar Beakdansim tig00111513_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: 396338
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
File 1 of 2
Found at i:2516 original size:24 final size:24
Alignment explanation
Indices: 2482--2528 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
2472 CTGAAACATC
2482 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
2506 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
2529 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:3229 original size:20 final size:20
Alignment explanation
Indices: 3201--3567 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
3191 AAATTTCAGT
* * * *
3201 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
3221 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
3241 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
3261 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
3281 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
3301 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
3321 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
3341 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
3361 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
3381 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
3401 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
3421 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
3441 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
3461 ATTGCGATTTAC-CATACGC
1 GTTGCGATTTACGGATACGC
*
3480 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
3500 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
3520 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
** *
3540 GTTGCGATTT-CATATTCGC
1 GTTGCGATTTACGGATACGC
3559 GTTGCGATT
1 GTTGCGATT
3568 ATGGAAAATC
Statistics
Matches: 309, Mismatches: 29, Indels: 19
0.87 0.08 0.05
Matches are distributed among these distances:
19 36 0.12
20 268 0.87
21 5 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:5684 original size:24 final size:27
Alignment explanation
Indices: 5645--5694 Score: 79
Period size: 25 Copynumber: 2.0 Consensus size: 27
5635 TAAGCTCTCT
5645 AAAAAAATAAAGTTTAGAT-CTAAACG
1 AAAAAAATAAAGTTTAGATACTAAACG
5671 AAAAAAAT-AA-TTTAGATACTAAAC
1 AAAAAAATAAAGTTTAGATACTAAAC
5695 ATTTAGTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 7 0.30
25 8 0.35
26 8 0.35
ACGTcount: A:0.60, C:0.08, G:0.08, T:0.24
Consensus pattern (27 bp):
AAAAAAATAAAGTTTAGATACTAAACG
Found at i:12522 original size:32 final size:32
Alignment explanation
Indices: 12471--12557 Score: 122
Period size: 32 Copynumber: 2.8 Consensus size: 32
12461 AACTGTTAGA
* *
12471 ACATAGGT-ATACTGTCCATATGTCTCAAAAG
1 ACATAGGTAATTCTGTCCATATGTCCCAAAAG
12502 ACATAGGTAATTCTGTCCATATGTCCCAAAAG
1 ACATAGGTAATTCTGTCCATATGTCCCAAAAG
* * *
12534 ACATAGGTACTTTTGTTCATATGT
1 ACATAGGTAATTCTGTCCATATGT
12558 TCCGTAGAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
31 8 0.16
32 42 0.84
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.33
Consensus pattern (32 bp):
ACATAGGTAATTCTGTCCATATGTCCCAAAAG
Found at i:14877 original size:18 final size:18
Alignment explanation
Indices: 14854--14906 Score: 72
Period size: 18 Copynumber: 2.9 Consensus size: 18
14844 AGAGAAAAGA
14854 CGTGCCAAAAAGCAGAGG
1 CGTGCCAAAAAGCAGAGG
*
14872 CGTGCC-AATAGACAGAGG
1 CGTGCCAAAAAG-CAGAGG
*
14890 CGTGCTAAAAAGCAGAG
1 CGTGCCAAAAAGCAGAG
14907 AAAATACATG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 4 0.13
18 22 0.73
19 4 0.13
ACGTcount: A:0.38, C:0.21, G:0.32, T:0.09
Consensus pattern (18 bp):
CGTGCCAAAAAGCAGAGG
Found at i:14946 original size:24 final size:24
Alignment explanation
Indices: 14894--14947 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 24
14884 CAGAGGCGTG
* *
14894 CTAAAAAGCAGAGAAAATACATGC
1 CTAAAAGGCAGAGAAAATACATCC
*
14918 C-AAAAGGCAGAGAAAA-ATATACC
1 CTAAAAGGCAGAGAAAATACAT-CC
14941 CTAAAAG
1 CTAAAAG
14948 CCAATAATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
22 3 0.12
23 16 0.64
24 6 0.24
ACGTcount: A:0.56, C:0.17, G:0.17, T:0.11
Consensus pattern (24 bp):
CTAAAAGGCAGAGAAAATACATCC
Found at i:16866 original size:16 final size:17
Alignment explanation
Indices: 16845--16879 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
16835 TACTATTTAC
16845 GTGAATAAT-AAATTTT
1 GTGAATAATAAAATTTT
*
16861 GTGAATAGTAAAATTTT
1 GTGAATAATAAAATTTT
16878 GT
1 GT
16880 CAACGATACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.40, C:0.00, G:0.17, T:0.43
Consensus pattern (17 bp):
GTGAATAATAAAATTTT
Found at i:29460 original size:27 final size:27
Alignment explanation
Indices: 29430--29498 Score: 129
Period size: 27 Copynumber: 2.6 Consensus size: 27
29420 ATACTAATTA
*
29430 GTTTTAAGTTATTTTAATTGTGATAAT
1 GTTTAAAGTTATTTTAATTGTGATAAT
29457 GTTTAAAGTTATTTTAATTGTGATAAT
1 GTTTAAAGTTATTTTAATTGTGATAAT
29484 GTTTAAAGTTATTTT
1 GTTTAAAGTTATTTT
29499 TGTTTATTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.30, C:0.00, G:0.14, T:0.55
Consensus pattern (27 bp):
GTTTAAAGTTATTTTAATTGTGATAAT
Found at i:31184 original size:34 final size:36
Alignment explanation
Indices: 31146--31224 Score: 96
Period size: 34 Copynumber: 2.3 Consensus size: 36
31136 ACTCCAACTA
31146 AATATCTTTTAATATTCAAAT-TT-AAA-TATATAAT
1 AATATCTTTTAAT-TTCAAATATTCAAAGTATATAAT
* *
31180 AATATATTTTAATTTGAAATATTCAAAGTATATAAT
1 AATATCTTTTAATTTCAAATATTCAAAGTATATAAT
31216 --TATCTTTTA
1 AATATCTTTTA
31225 TCAATAATCA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
33 6 0.15
34 22 0.56
35 3 0.08
36 8 0.21
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.48
Consensus pattern (36 bp):
AATATCTTTTAATTTCAAATATTCAAAGTATATAAT
Found at i:42687 original size:3 final size:3
Alignment explanation
Indices: 42679--42728 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
42669 GCTTGTAGAC
42679 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
42727 AT
1 AT
42729 ATAAAATGTG
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:43472 original size:15 final size:15
Alignment explanation
Indices: 43455--43510 Score: 58
Period size: 15 Copynumber: 3.6 Consensus size: 15
43445 TAACCGGTTT
*
43455 CGGTTTTAAAAAAAT
1 CGGTTTTAAAAAAAC
*
43470 CGGTTTTTTTAAAAAAC
1 CGG--TTTTAAAAAAAC
*
43487 CGGTTATAAAAAAAC
1 CGGTTTTAAAAAAAC
*
43502 CGATTTTAA
1 CGGTTTTAA
43511 TATTCCAGAT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
15 20 0.61
17 13 0.39
ACGTcount: A:0.43, C:0.11, G:0.12, T:0.34
Consensus pattern (15 bp):
CGGTTTTAAAAAAAC
Found at i:43483 original size:17 final size:17
Alignment explanation
Indices: 43458--43508 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
43448 CCGGTTTCGG
*
43458 TTTTAAAAAAATCGGTT
1 TTTTAAAAAAACCGGTT
*
43475 TTTTTAAAAAACCGG--
1 TTTTAAAAAAACCGGTT
* *
43490 TTATAAAAAAACCGATT
1 TTTTAAAAAAACCGGTT
43507 TT
1 TT
43509 AATATTCCAG
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
15 12 0.44
17 15 0.56
ACGTcount: A:0.43, C:0.10, G:0.10, T:0.37
Consensus pattern (17 bp):
TTTTAAAAAAACCGGTT
Found at i:43703 original size:21 final size:21
Alignment explanation
Indices: 43679--43731 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
43669 ATACTTAGGG
43679 AACCGATTCCCTATGAGAGGA
1 AACCGATTCCCTATGAGAGGA
*
43700 AACCGATTCCCTATGAGAGGG
1 AACCGATTCCCTATGAGAGGA
*
43721 TACCGATTCCC
1 AACCGATTCCC
43732 CCATGCTCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.28, C:0.28, G:0.23, T:0.21
Consensus pattern (21 bp):
AACCGATTCCCTATGAGAGGA
Found at i:43948 original size:13 final size:13
Alignment explanation
Indices: 43927--43981 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
43917 AAGTTCGATA
*
43927 AATTCAAATACTT
1 AATTGAAATACTT
43940 AATTGAAATACTT
1 AATTGAAATACTT
* *
43953 AATT-AACTCAACAT
1 AATTGAAAT--ACTT
43967 AATTGAAATACTT
1 AATTGAAATACTT
43980 AA
1 AA
43982 ATACTTCCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.35
Consensus pattern (13 bp):
AATTGAAATACTT
Found at i:44063 original size:32 final size:33
Alignment explanation
Indices: 43967--44065 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
43957 AACTCAACAT
* * *
43967 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
44000 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
44033 AATTCAAATACTTAAAAACTT-CAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
44065 A
1 A
44066 TTGAAACAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 12 0.19
33 51 0.81
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.32
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:44084 original size:21 final size:21
Alignment explanation
Indices: 44060--44099 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
44050 ACTTCAAGTT
44060 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
44081 CGATAATTGAAATAAAGTT
1 CGATAATTGAAACAAAGTT
44100 ATAAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.30
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:67578 original size:94 final size:93
Alignment explanation
Indices: 67461--67637 Score: 293
Period size: 93 Copynumber: 1.9 Consensus size: 93
67451 TGAAGAAAGA
*
67461 TTTTCTCATTTGGATAGCTATGGGCTGGATTTTAAATATTTTTTGGGTTTTCCCA-TTAAGCATC
1 TTTTCTCATTTGGATAGCTATGGGCTGGATTTAAAATA-TTTTTGGGTTTT-CCAGTTAAGCATC
67525 GGCCTGTTAACCAATTAAATATTTTTTGAG
64 GGCCTGTTAACCAATTAAATATTTTTTGAG
* * *
67555 TTTTCTCGTTTGGATAGCTATGGGCTGGATTTAAAATATTTTTGGGTTTTCCAGTTACGCATTGG
1 TTTTCTCATTTGGATAGCTATGGGCTGGATTTAAAATATTTTTGGGTTTTCCAGTTAAGCATCGG
67620 CCTGTTAACCAATTAAAT
66 CCTGTTAACCAATTAAAT
67638 TTACACCACT
Statistics
Matches: 78, Mismatches: 4, Indels: 3
0.92 0.05 0.04
Matches are distributed among these distances:
92 3 0.04
93 39 0.50
94 36 0.46
ACGTcount: A:0.23, C:0.14, G:0.19, T:0.44
Consensus pattern (93 bp):
TTTTCTCATTTGGATAGCTATGGGCTGGATTTAAAATATTTTTGGGTTTTCCAGTTAAGCATCGG
CCTGTTAACCAATTAAATATTTTTTGAG
Found at i:69364 original size:28 final size:27
Alignment explanation
Indices: 69332--69399 Score: 86
Period size: 28 Copynumber: 2.5 Consensus size: 27
69322 ATTTTAATTA
69332 AATAAAATTTAAATTAATTATATTTTTT
1 AATAAAA-TTAAATTAATTATATTTTTT
* *
69360 AATAAAAAATAATTTAATTATATTTTTT
1 AAT-AAAATTAAATTAATTATATTTTTT
69388 -AT-AAATTAAATT
1 AATAAAATTAAATT
69400 TTAATAAAAG
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
25 8 0.23
27 2 0.06
28 21 0.60
29 4 0.11
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (27 bp):
AATAAAATTAAATTAATTATATTTTTT
Found at i:70316 original size:18 final size:18
Alignment explanation
Indices: 70269--70317 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
70259 AAATATTAAG
*
70269 TAACTTAAAATAAAAATA
1 TAACTTAAAATTAAAATA
**
70287 TAACTTTGAATTAAAATA
1 TAACTTAAAATTAAAATA
70305 TATA-TTAAAATTA
1 TA-ACTTAAAATTA
70318 TCGATCAAGT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
18 24 0.96
19 1 0.04
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (18 bp):
TAACTTAAAATTAAAATA
Found at i:72305 original size:35 final size:36
Alignment explanation
Indices: 72266--72368 Score: 165
Period size: 35 Copynumber: 2.9 Consensus size: 36
72256 AAGAAAAATA
72266 TATGCATACCTATTATTTTGAAAAGAATATTAAA-C
1 TATGCATACCTATTATTTTGAAAAGAATATTAAAGC
*
72301 TATGCATACCTATTATTTTGCAAAGAATA-TAAAGC
1 TATGCATACCTATTATTTTGAAAAGAATATTAAAGC
* *
72336 TATGCATACCTATTATTTTAAAAAGACTATTAA
1 TATGCATACCTATTATTTTGAAAAGAATATTAA
72369 GTTCAGTTTA
Statistics
Matches: 62, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
34 4 0.06
35 55 0.89
36 3 0.05
ACGTcount: A:0.42, C:0.13, G:0.09, T:0.37
Consensus pattern (36 bp):
TATGCATACCTATTATTTTGAAAAGAATATTAAAGC
Found at i:77693 original size:32 final size:29
Alignment explanation
Indices: 77657--77731 Score: 71
Period size: 29 Copynumber: 2.5 Consensus size: 29
77647 GTCATTAACG
77657 ATTTAATGATATAATTGAAACAAAAATAAAAA
1 ATTTAATGATATAATTG--ACAAAAAT-AAAA
* *
77689 ATTTAGT-ACTATAATTGACAAAACTAAAA
1 ATTTAATGA-TATAATTGACAAAAATAAAA
* *
77718 ATTCAATGGTATAA
1 ATTTAATGATATAA
77732 AGAATATAGT
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
29 14 0.39
30 7 0.19
31 1 0.03
32 14 0.39
ACGTcount: A:0.55, C:0.07, G:0.08, T:0.31
Consensus pattern (29 bp):
ATTTAATGATATAATTGACAAAAATAAAA
Found at i:78364 original size:21 final size:20
Alignment explanation
Indices: 78325--78366 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
78315 TTTTTACTAT
*
78325 ATTATAAAATAATTAAATTA
1 ATTATAAAAAAATTAAATTA
*
78345 ATTATAAATAAAATTCAATTA
1 ATTATAAA-AAAATTAAATTA
78366 A
1 A
78367 ATACACATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (20 bp):
ATTATAAAAAAATTAAATTA
Found at i:88597 original size:68 final size:68
Alignment explanation
Indices: 88488--88614 Score: 227
Period size: 68 Copynumber: 1.9 Consensus size: 68
88478 TGTGCTTGGA
* *
88488 ATGCTAACTTCCATCTGGTCAAGTATTTCTATGTGCAAAGGAAATGATTAGTTGAAAGTTTTGGG
1 ATGCTAACTTCCATCTGGTCAAGCATTTCTATGTGCAAAGGAAATGATTAATTGAAAGTTTTGGG
88553 TGG
66 TGG
*
88556 ATGCTAACTTCCATCTGGTCAAGCATTTCTATGTGCAAAGGAAATGATTAATTGGAAGT
1 ATGCTAACTTCCATCTGGTCAAGCATTTCTATGTGCAAAGGAAATGATTAATTGAAAGT
88615 ACTTGGGAAG
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
68 56 1.00
ACGTcount: A:0.30, C:0.13, G:0.23, T:0.34
Consensus pattern (68 bp):
ATGCTAACTTCCATCTGGTCAAGCATTTCTATGTGCAAAGGAAATGATTAATTGAAAGTTTTGGG
TGG
Found at i:112078 original size:17 final size:17
Alignment explanation
Indices: 112056--112094 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
112046 TCCTGCTAAG
112056 ACAACCAAACACAAAAT
1 ACAACCAAACACAAAAT
*
112073 ACAACCAAACATAAAAT
1 ACAACCAAACACAAAAT
112090 ACAAC
1 ACAAC
112095 ATTCCCAGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.64, C:0.28, G:0.00, T:0.08
Consensus pattern (17 bp):
ACAACCAAACACAAAAT
Found at i:112140 original size:20 final size:20
Alignment explanation
Indices: 112111--112270 Score: 250
Period size: 20 Copynumber: 8.1 Consensus size: 20
112101 AGTAATCCTA
112111 TTCC-CTGGTAATCTTACAT
1 TTCCACTGGTAATCTTACAT
112130 TTCCACTGGTAATCTTACAT
1 TTCCACTGGTAATCTTACAT
112150 TTCCACTGGTAATCTTACAT
1 TTCCACTGGTAATCTTACAT
112170 TTCCACTGGTAATCTTACAT
1 TTCCACTGGTAATCTTACAT
112190 TTCCACTGGTAATCTTACAT
1 TTCCACTGGTAATCTTACAT
* * *
112210 TCCCACTGATAATTTTACAT
1 TTCCACTGGTAATCTTACAT
*
112230 TCCCACTGGTAATCTTACAT
1 TTCCACTGGTAATCTTACAT
* **
112250 TCCCACTAATAATCTTACAT
1 TTCCACTGGTAATCTTACAT
112270 T
1 T
112271 CCGTGAACTA
Statistics
Matches: 133, Mismatches: 7, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
19 4 0.03
20 129 0.97
ACGTcount: A:0.26, C:0.26, G:0.08, T:0.39
Consensus pattern (20 bp):
TTCCACTGGTAATCTTACAT
Found at i:113340 original size:27 final size:27
Alignment explanation
Indices: 113306--113367 Score: 115
Period size: 27 Copynumber: 2.3 Consensus size: 27
113296 ATTAATTTAT
*
113306 ATTATAATTTTTAATAAATAAAAATTA
1 ATTATAATTTTTAATAAATAAAAAGTA
113333 ATTATAATTTTTAATAAATAAAAAGTA
1 ATTATAATTTTTAATAAATAAAAAGTA
113360 ATTATAAT
1 ATTATAAT
113368 ATTTGTATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (27 bp):
ATTATAATTTTTAATAAATAAAAAGTA
Found at i:122219 original size:13 final size:12
Alignment explanation
Indices: 122190--122215 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
122180 TTAATAAAAG
122190 AATTTCATTTTT
1 AATTTCATTTTT
122202 AATTTCATTTTT
1 AATTTCATTTTT
122214 AA
1 AA
122216 ATTTTAGATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.08, G:0.00, T:0.62
Consensus pattern (12 bp):
AATTTCATTTTT
Found at i:126872 original size:30 final size:30
Alignment explanation
Indices: 126836--126902 Score: 125
Period size: 30 Copynumber: 2.2 Consensus size: 30
126826 TTTTGAGATG
126836 GAAAAAGTGTTCCTGAGATGTTTCTGCTTA
1 GAAAAAGTGTTCCTGAGATGTTTCTGCTTA
126866 GAAAAAGTGTTCCTGAGATGTTTCTGCTTA
1 GAAAAAGTGTTCCTGAGATGTTTCTGCTTA
*
126896 GAGAAAG
1 GAAAAAG
126903 CTATCATTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (30 bp):
GAAAAAGTGTTCCTGAGATGTTTCTGCTTA
Found at i:132511 original size:32 final size:32
Alignment explanation
Indices: 132469--132529 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 32
132459 GCTTCAATCA
** * *
132469 AAAATATTAAATTATTATTATTTTAGGTTTTG
1 AAAATATTAAAAGATCAATATTTTAGGTTTTG
*
132501 AAAATGTTAAAAGATCAATATTTTAGGTT
1 AAAATATTAAAAGATCAATATTTTAGGTT
132530 AGGTTCAACC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 24 1.00
ACGTcount: A:0.41, C:0.02, G:0.11, T:0.46
Consensus pattern (32 bp):
AAAATATTAAAAGATCAATATTTTAGGTTTTG
Found at i:135193 original size:10 final size:10
Alignment explanation
Indices: 135157--135222 Score: 75
Period size: 10 Copynumber: 6.7 Consensus size: 10
135147 GGCTGCTGGA
135157 AACCGGTTT-
1 AACCGGTTTG
*
135166 AACCGGTTTTC
1 AACCGG-TTTG
135177 AACCGGTTCTG
1 AACCGGTT-TG
135188 -ACCGGTTTG
1 AACCGGTTTG
*
135197 AACCGGTCTG
1 AACCGGTTTG
135207 AACCGGTTTG
1 AACCGGTTTG
135217 -ACCGGT
1 AACCGGT
135223 CGTACCCGAC
Statistics
Matches: 50, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
9 14 0.28
10 29 0.58
11 7 0.14
ACGTcount: A:0.18, C:0.26, G:0.27, T:0.29
Consensus pattern (10 bp):
AACCGGTTTG
Found at i:135253 original size:22 final size:22
Alignment explanation
Indices: 135226--135267 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
135216 GACCGGTCGT
*
135226 ACCCGACCTGACCGTTGACCCG
1 ACCCGACCCGACCGTTGACCCG
135248 ACCCGACCCGACCGTTGACC
1 ACCCGACCCGACCGTTGACC
135268 GTTGACTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.19, C:0.48, G:0.21, T:0.12
Consensus pattern (22 bp):
ACCCGACCCGACCGTTGACCCG
Found at i:142384 original size:10 final size:9
Alignment explanation
Indices: 142349--142447 Score: 81
Period size: 10 Copynumber: 10.3 Consensus size: 9
142339 GCTGCTGCAT
*
142349 ACCGGTTTA
1 ACCGGTTTG
*
142358 ACCGGTTTTCA
1 ACCGG-TTT-G
142369 ACCGGTTCTG
1 ACCGGTT-TG
142379 ACCGGTTTG
1 ACCGGTTTG
* *
142388 ACTGGTTTCA
1 ACCGGTTT-G
*
142398 ACCGGTTCG
1 ACCGGTTTG
142407 AACCGGTTTG
1 -ACCGGTTTG
*
142417 ACCGGTCTG
1 ACCGGTTTG
142426 AACCGGTTTG
1 -ACCGGTTTG
*
142436 ACCGGTCTG
1 ACCGGTTTG
142445 ACC
1 ACC
142448 CGACCCGACC
Statistics
Matches: 74, Mismatches: 10, Indels: 12
0.77 0.10 0.12
Matches are distributed among these distances:
9 33 0.45
10 34 0.46
11 7 0.09
ACGTcount: A:0.16, C:0.27, G:0.27, T:0.29
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:142405 original size:29 final size:29
Alignment explanation
Indices: 142349--142447 Score: 121
Period size: 29 Copynumber: 3.4 Consensus size: 29
142339 GCTGCTGCAT
*
142349 ACCGGTTTAACCGGTTTTCAACCGGTTCTG
1 ACCGGTTTGACCGG-TTTCAACCGGTTCTG
*
142379 ACCGGTTTGACTGGTTTCAACCGGTTC-G
1 ACCGGTTTGACCGGTTTCAACCGGTTCTG
* *
142407 AACCGGTTTGACCGGTCTGAACCGGTT-TG
1 -ACCGGTTTGACCGGTTTCAACCGGTTCTG
*
142436 ACCGGTCTGACC
1 ACCGGTTTGACC
142448 CGACCCGACC
Statistics
Matches: 61, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
28 12 0.20
29 37 0.61
30 12 0.20
ACGTcount: A:0.16, C:0.27, G:0.27, T:0.29
Consensus pattern (29 bp):
ACCGGTTTGACCGGTTTCAACCGGTTCTG
Found at i:142442 original size:19 final size:19
Alignment explanation
Indices: 142349--142445 Score: 90
Period size: 19 Copynumber: 5.0 Consensus size: 19
142339 GCTGCTGCAT
* * *
142349 ACCGGTTTAACCGGTTTTCA
1 ACCGGTTTGACCGG-TCTGA
*
142369 ACCGGTTCTGACCGGTTTG-
1 ACCGGTT-TGACCGGTCTGA
* *
142388 ACTGGTTTCAACCGGT-TCGA
1 ACCGGTTT-GACCGGTCT-GA
142408 ACCGGTTTGACCGGTCTGA
1 ACCGGTTTGACCGGTCTGA
142427 ACCGGTTTGACCGGTCTGA
1 ACCGGTTTGACCGGTCTGA
142446 CCCGACCCGA
Statistics
Matches: 66, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
18 2 0.03
19 40 0.61
20 18 0.27
21 6 0.09
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (19 bp):
ACCGGTTTGACCGGTCTGA
Found at i:142446 original size:9 final size:9
Alignment explanation
Indices: 142408--142447 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
142398 ACCGGTTCGA
*
142408 ACCGGTTTG
1 ACCGGTCTG
142417 ACCGGTCTG
1 ACCGGTCTG
*
142426 AACCGGTTTG
1 -ACCGGTCTG
142436 ACCGGTCTG
1 ACCGGTCTG
142445 ACC
1 ACC
142448 CGACCCGACC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
9 19 0.70
10 8 0.30
ACGTcount: A:0.15, C:0.30, G:0.30, T:0.25
Consensus pattern (9 bp):
ACCGGTCTG
Found at i:142469 original size:22 final size:22
Alignment explanation
Indices: 142444--142490 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
142434 TGACCGGTCT
142444 GACCCGACCCGACCATTGACCC
1 GACCCGACCCGACCATTGACCC
*
142466 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCATTGACCC
142488 GAC
1 GAC
142491 TCGATCGTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.21, C:0.49, G:0.21, T:0.09
Consensus pattern (22 bp):
GACCCGACCCGACCATTGACCC
Found at i:142486 original size:17 final size:17
Alignment explanation
Indices: 142466--142503 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
142456 CCATTGACCC
142466 GACCCGACCCGACCGTT
1 GACCCGACCCGACCGTT
* *
142483 GACCCGACTCGATCGTT
1 GACCCGACCCGACCGTT
142500 GACC
1 GACC
142504 GTTGACCGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.18, C:0.42, G:0.24, T:0.16
Consensus pattern (17 bp):
GACCCGACCCGACCGTT
Found at i:142508 original size:7 final size:7
Alignment explanation
Indices: 142496--142523 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
142486 CCGACTCGAT
142496 CGTTGAC
1 CGTTGAC
142503 CGTTGAC
1 CGTTGAC
142510 CGTTGAC
1 CGTTGAC
142517 CGTTGAC
1 CGTTGAC
142524 TTTCTTTGAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.14, C:0.29, G:0.29, T:0.29
Consensus pattern (7 bp):
CGTTGAC
Found at i:145987 original size:19 final size:20
Alignment explanation
Indices: 145955--145992 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
145945 TATGTAAATA
145955 AAATAAATACAAAA-AATTG
1 AAATAAATACAAAATAATTG
145974 AAATAAAGTA-AAAATAATT
1 AAATAAA-TACAAAATAATT
145993 AACAAAAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.68, C:0.03, G:0.05, T:0.24
Consensus pattern (20 bp):
AAATAAATACAAAATAATTG
Found at i:150871 original size:60 final size:60
Alignment explanation
Indices: 150778--150895 Score: 184
Period size: 60 Copynumber: 2.0 Consensus size: 60
150768 ACCAGTTTAA
* *
150778 ATCAATAACAACTTTAATTTAGTAGCACAAGATCACAAGGA-TGACCAAAAGAAAAGCTCC
1 ATCAATAACAACTTTAATCTAGTAGCACAAGATCACAA-AATTGACCAAAAGAAAAGCTCC
* *
150838 ATCAATAACAACTTTAGTCTAGTAGCACAAGATCACAAAATTGATCAAAAGAAAAGCT
1 ATCAATAACAACTTTAATCTAGTAGCACAAGATCACAAAATTGACCAAAAGAAAAGCT
150896 TAAAACAGAA
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
59 1 0.02
60 52 0.98
ACGTcount: A:0.47, C:0.19, G:0.13, T:0.21
Consensus pattern (60 bp):
ATCAATAACAACTTTAATCTAGTAGCACAAGATCACAAAATTGACCAAAAGAAAAGCTCC
Found at i:153121 original size:15 final size:15
Alignment explanation
Indices: 153101--153129 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
153091 GAAGATACCA
153101 CTCTTTTACCATATC
1 CTCTTTTACCATATC
153116 CTCTTTTACCATAT
1 CTCTTTTACCATAT
153130 AGATCAATTG
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:0.21, C:0.31, G:0.00, T:0.48
Consensus pattern (15 bp):
CTCTTTTACCATATC
Found at i:153290 original size:18 final size:18
Alignment explanation
Indices: 153251--153286 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
153241 TTAAAAAGAA
*
153251 TAATAGTTTATTGAAAAT
1 TAATAATTTATTGAAAAT
153269 TAATAATTTATT-AAAAT
1 TAATAATTTATTGAAAAT
153286 T
1 T
153287 TAATTTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (18 bp):
TAATAATTTATTGAAAAT
Found at i:160256 original size:85 final size:87
Alignment explanation
Indices: 160111--160271 Score: 308
Period size: 85 Copynumber: 1.9 Consensus size: 87
160101 TTATCCACTT
160111 TCACCATCACTTGTCTCTCGCCAAGGTTCCATATTTATTACACCATCAACAATTTCTTATCTGTT
1 TCACCATCACTTGTCTCTCGCCAAGGTTCCATATTTATTACACCATCAACAATTTCTTATCTGTT
160176 ACACCATCAACCTTCAATCCAC
66 ACACCATCAACCTTCAATCCAC
160198 TCACCATCAC-T-TCTCTCGCCAAGGTTCCATATTTATTACACCATCAACAATTTCTTATCTGTT
1 TCACCATCACTTGTCTCTCGCCAAGGTTCCATATTTATTACACCATCAACAATTTCTTATCTGTT
160261 ACACCATCAAC
66 ACACCATCAAC
160272 AATCTCGATC
Statistics
Matches: 74, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
85 63 0.85
86 1 0.01
87 10 0.14
ACGTcount: A:0.28, C:0.33, G:0.06, T:0.34
Consensus pattern (87 bp):
TCACCATCACTTGTCTCTCGCCAAGGTTCCATATTTATTACACCATCAACAATTTCTTATCTGTT
ACACCATCAACCTTCAATCCAC
Found at i:176287 original size:14 final size:14
Alignment explanation
Indices: 176268--176313 Score: 51
Period size: 13 Copynumber: 3.4 Consensus size: 14
176258 TTGATAGTAT
176268 AAATTATAATTATA
1 AAATTATAATTATA
* *
176282 AAATTATAA-AAAA
1 AAATTATAATTATA
*
176295 AAAAT-TAATTATA
1 AAATTATAATTATA
176308 AAATTA
1 AAATTA
176314 AATAACGTAA
Statistics
Matches: 24, Mismatches: 6, Indels: 4
0.71 0.18 0.12
Matches are distributed among these distances:
12 3 0.12
13 12 0.50
14 9 0.38
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
AAATTATAATTATA
Found at i:177040 original size:2 final size:2
Alignment explanation
Indices: 177033--177067 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
177023 GGATTCAAAT
*
177033 TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
177068 GTATGTGTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:177068 original size:12 final size:12
Alignment explanation
Indices: 177033--177071 Score: 69
Period size: 12 Copynumber: 3.2 Consensus size: 12
177023 GGATTCAAAT
*
177033 TATATATATATA
1 TATATATATATG
177045 TATATATATATG
1 TATATATATATG
177057 TATATATATATG
1 TATATATATATG
177069 TAT
1 TAT
177072 GTGTTAAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (12 bp):
TATATATATATG
Found at i:177401 original size:29 final size:29
Alignment explanation
Indices: 177359--177418 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
177349 CCAAATAAAC
177359 AATAATTCAATTCTGGGAAATTGTTCAAA
1 AATAATTCAATTCTGGGAAATTGTTCAAA
177388 AATAATTCAATTCTGGGAAATTGTTCAAA
1 AATAATTCAATTCTGGGAAATTGTTCAAA
177417 AA
1 AA
177419 GTATTAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.33
Consensus pattern (29 bp):
AATAATTCAATTCTGGGAAATTGTTCAAA
Found at i:177699 original size:28 final size:28
Alignment explanation
Indices: 177667--177721 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
177657 AAAGTAACCC
177667 ATGCCGTTCGAGACATGAACGAAATAAT
1 ATGCCGTTCGAGACATGAACGAAATAAT
177695 ATGCCGTTCGAGACATGAACGAAATAA
1 ATGCCGTTCGAGACATGAACGAAATAA
177722 GTAATTTTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.40, C:0.18, G:0.22, T:0.20
Consensus pattern (28 bp):
ATGCCGTTCGAGACATGAACGAAATAAT
Found at i:179457 original size:62 final size:63
Alignment explanation
Indices: 179362--179479 Score: 204
Period size: 62 Copynumber: 1.9 Consensus size: 63
179352 ATATCGGTAA
*
179362 GATATATATTATAAGTAGATTAAAAAAATTGTAAATATATATTATCTTATAATCATCTCATAT
1 GATATATATTATAAGTAGATTAAAAAAATTGTAAACATATATTATCTTATAATCATCTCATAT
179425 GATATATATTATTAA-TAGATT-AAAAAATTGTAAACATATATTATCTTATAATCAT
1 GATATATATTA-TAAGTAGATTAAAAAAATTGTAAACATATATTATCTTATAATCAT
179480 ATTATATTAT
Statistics
Matches: 53, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
62 33 0.62
63 17 0.32
64 3 0.06
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.42
Consensus pattern (63 bp):
GATATATATTATAAGTAGATTAAAAAAATTGTAAACATATATTATCTTATAATCATCTCATAT
Found at i:180832 original size:13 final size:13
Alignment explanation
Indices: 180811--180844 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
180801 TTTTTAAAAA
*
180811 ATAATTATTTTTT
1 ATAAATATTTTTT
180824 ATAAATATTTTTT
1 ATAAATATTTTTT
*
180837 AAAAATAT
1 ATAAATAT
180845 ATAATGATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
ATAAATATTTTTT
Found at i:185429 original size:59 final size:59
Alignment explanation
Indices: 185320--185431 Score: 154
Period size: 59 Copynumber: 1.9 Consensus size: 59
185310 AAATATTAAA
* * * *
185320 ATAATCAAATAATTATTTTATAATTTTTAATAATTATTAACTCAATAAAATAATATTCT
1 ATAATCAAAAAATTATTTTATAACTTTTAATAATTATGAACTCAAAAAAATAATATTCT
* *
185379 ATAATCAAAAAATTATTTTATAACTTTTAATAGTTA-GAATTCAACAAAAATAA
1 ATAATCAAAAAATTATTTTATAACTTTTAATAATTATGAACTCAA-AAAAATAA
185432 CATCATAGGG
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
58 6 0.13
59 40 0.87
ACGTcount: A:0.50, C:0.07, G:0.02, T:0.41
Consensus pattern (59 bp):
ATAATCAAAAAATTATTTTATAACTTTTAATAATTATGAACTCAAAAAAATAATATTCT
Found at i:185678 original size:2 final size:2
Alignment explanation
Indices: 185673--185698 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
185663 TCTTGTTTAA
185673 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
185699 CGTATTTTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:193873 original size:2 final size:2
Alignment explanation
Indices: 193866--193890 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
193856 TTTAACCCAA
193866 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
193891 AACTTAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:196687 original size:16 final size:17
Alignment explanation
Indices: 196666--196700 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
196656 GAAAGGGAAA
*
196666 GGAGGAGG-GATTTGAG
1 GGAGGAGGAGAGTTGAG
196682 GGAGGAGGAGAGTTGAG
1 GGAGGAGGAGAGTTGAG
196699 GG
1 GG
196701 GGTTGGAGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.26, C:0.00, G:0.60, T:0.14
Consensus pattern (17 bp):
GGAGGAGGAGAGTTGAG
Found at i:198143 original size:2 final size:2
Alignment explanation
Indices: 198136--198193 Score: 100
Period size: 2 Copynumber: 29.5 Consensus size: 2
198126 GTATTTCTTA
198136 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
*
198178 AT AT AT GT AT AT -T AT A
1 AT AT AT AT AT AT AT AT A
198194 GTATTGAGGG
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 52 0.98
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:201508 original size:31 final size:31
Alignment explanation
Indices: 201456--201521 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
201446 AAATTTAAAT
201456 TGGTCACGAACATTATCGATTTATAACAAAA
1 TGGTCACGAACATTATCGATTTATAACAAAA
* * * *
201487 TGGTCACTAACGTTATTGATTTGTAACAAAA
1 TGGTCACGAACATTATCGATTTATAACAAAA
201518 TGGT
1 TGGT
201522 AACTTCACTA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (31 bp):
TGGTCACGAACATTATCGATTTATAACAAAA
Found at i:201747 original size:6 final size:6
Alignment explanation
Indices: 201719--201761 Score: 59
Period size: 6 Copynumber: 6.7 Consensus size: 6
201709 AATTTTTAAA
201719 AAAATT AAAACATT AAAAGTT AAAATT AAAATT AAAATT AAAA
1 AAAATT -AAA-ATT AAAA-TT AAAATT AAAATT AAAATT AAAA
201762 GATCTTGAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
6 19 0.56
7 12 0.35
8 3 0.09
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.28
Consensus pattern (6 bp):
AAAATT
Found at i:202257 original size:31 final size:31
Alignment explanation
Indices: 202182--202259 Score: 104
Period size: 30 Copynumber: 2.5 Consensus size: 31
202172 ATGACGATAG
* *
202182 AGTGATCATTTTGTTATAAATGGATAACGTT
1 AGTGATCATTTTGTTACAAATGGATAACATT
* *
202213 -GTGACCATTTTGTTACAAATTGATAACATT
1 AGTGATCATTTTGTTACAAATGGATAACATT
*
202243 AGTGATCAATTTGTTAC
1 AGTGATCATTTTGTTAC
202260 TTTTAAAACT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
30 26 0.65
31 14 0.35
ACGTcount: A:0.32, C:0.10, G:0.17, T:0.41
Consensus pattern (31 bp):
AGTGATCATTTTGTTACAAATGGATAACATT
Found at i:212727 original size:41 final size:41
Alignment explanation
Indices: 212682--212763 Score: 119
Period size: 41 Copynumber: 2.0 Consensus size: 41
212672 TCGAAATCCT
* * * * *
212682 GTGTTTGTTTCACGTAGTTCGTTTTTTGGAAAATGTTTTCC
1 GTGTTTATTTCACATAATTCGTTTTTCGAAAAATGTTTTCC
212723 GTGTTTATTTCACATAATTCGTTTTTCGAAAAATGTTTTCC
1 GTGTTTATTTCACATAATTCGTTTTTCGAAAAATGTTTTCC
212764 AGTATTTGGT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.20, C:0.13, G:0.17, T:0.50
Consensus pattern (41 bp):
GTGTTTATTTCACATAATTCGTTTTTCGAAAAATGTTTTCC
Found at i:213011 original size:21 final size:23
Alignment explanation
Indices: 212985--213034 Score: 70
Period size: 21 Copynumber: 2.3 Consensus size: 23
212975 TAATTATTAA
212985 AATATTTAAAAT-ATATT-TATT
1 AATATTTAAAATAATATTATATT
*
213006 AATATTTATAATAATATTATATT
1 AATATTTAAAATAATATTATATT
213029 -ATATTT
1 AATATTT
213035 TTAATATTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 11 0.42
22 11 0.42
23 4 0.15
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (23 bp):
AATATTTAAAATAATATTATATT
Found at i:213012 original size:10 final size:10
Alignment explanation
Indices: 212997--213042 Score: 51
Period size: 10 Copynumber: 4.5 Consensus size: 10
212987 TATTTAAAAT
212997 ATATTTATTA
1 ATATTTATTA
213007 ATATTTATAATA
1 ATATTTAT--TA
213019 ATATTATATT-
1 ATATT-TATTA
213029 ATATTT-TTA
1 ATATTTATTA
213038 ATATT
1 ATATT
213043 ATAGTAAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
8 2 0.06
9 6 0.19
10 13 0.41
11 1 0.03
12 7 0.22
13 3 0.09
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (10 bp):
ATATTTATTA
Found at i:213030 original size:26 final size:25
Alignment explanation
Indices: 212968--213030 Score: 71
Period size: 23 Copynumber: 2.6 Consensus size: 25
212958 CATTTTCATC
212968 AAAATATTA-ATTATTAAAATATTT
1 AAAATATTATATTATTAAAATATTT
*
212992 AAAATA-TAT-TTATTAATAT-TTAT
1 AAAATATTATATTATTAAAATATT-T
213015 AATAATATTATATTAT
1 AA-AATATTATATTAT
213031 ATTTTTAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
22 2 0.06
23 14 0.42
24 10 0.30
25 3 0.09
26 4 0.12
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (25 bp):
AAAATATTATATTATTAAAATATTT
Found at i:213062 original size:32 final size:32
Alignment explanation
Indices: 212996--213075 Score: 85
Period size: 32 Copynumber: 2.5 Consensus size: 32
212986 ATATTTAAAA
*
212996 TATATTTATTAATATTTATAATAATATTATAT
1 TATATTTATTAATATTTATAATAATATCATAT
213028 TATATTT-TTAATATTATAGTAA-AATAATCA-AT
1 TATATTTATTAATATT-TA-TAATAAT-ATCATAT
*
213060 TATATTATAATAATAT
1 TATATT-TATTAATAT
213076 AAGATATTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
31 8 0.20
32 20 0.49
33 7 0.17
34 6 0.15
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (32 bp):
TATATTTATTAATATTTATAATAATATCATAT
Found at i:213099 original size:29 final size:29
Alignment explanation
Indices: 213059--213158 Score: 93
Period size: 27 Copynumber: 3.4 Consensus size: 29
213049 AAATAATCAA
*
213059 TTATATTATAATAATATAAGATATTATATT
1 TTATATTTTAATAATAT-AGATATTATATT
*
213089 TT-TATTTTAATAA-ATATATATTATATT
1 TTATATTTTAATAATATAGATATTATATT
213116 TTAATATATTTAATAATGAGTA-ATATTAT-TT
1 TT-ATAT-TTTAATAAT-A-TAGATATTATATT
*
213147 ATATA-TTTAATA
1 TTATATTTTAATA
213159 TTAATATAAT
Statistics
Matches: 61, Mismatches: 3, Indels: 14
0.78 0.04 0.18
Matches are distributed among these distances:
27 13 0.21
28 9 0.15
29 13 0.21
30 13 0.21
31 3 0.05
32 8 0.13
33 2 0.03
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (29 bp):
TTATATTTTAATAATATAGATATTATATT
Found at i:213116 original size:21 final size:20
Alignment explanation
Indices: 213083--213121 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
213073 TATAAGATAT
*
213083 TATATTTTTATTTTAATAAA
1 TATATTTATATTTTAATAAA
213103 TATATATTATATTTTAATA
1 TATAT-TTATATTTTAATA
213122 TATTTAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TATATTTATATTTTAATAAA
Found at i:213382 original size:22 final size:22
Alignment explanation
Indices: 213346--213403 Score: 57
Period size: 22 Copynumber: 2.6 Consensus size: 22
213336 TTTAATAATA
* *
213346 AATAAATTATTTTAATATTTTA-
1 AATAAATAATATTAA-ATTTTAT
*
213368 AAGT-AATAATATTAAGTTTTAT
1 AA-TAAATAATATTAAATTTTAT
213390 AATAAATAATATTA
1 AATAAATAATATTA
213404 TTTATTGTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
21 6 0.20
22 23 0.77
23 1 0.03
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (22 bp):
AATAAATAATATTAAATTTTAT
Found at i:213606 original size:15 final size:15
Alignment explanation
Indices: 213600--213636 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
213590 TTTAAATTTC
213600 AGTAATTCAAATTCT
1 AGTAATTCAAATTCT
213615 AGTAATTCAAATTCT
1 AGTAATTCAAATTCT
213630 AGTAATT
1 AGTAATT
213637 GATTTTCCAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.41, C:0.11, G:0.08, T:0.41
Consensus pattern (15 bp):
AGTAATTCAAATTCT
Found at i:214591 original size:39 final size:40
Alignment explanation
Indices: 214493--214599 Score: 103
Period size: 42 Copynumber: 2.6 Consensus size: 40
214483 AGATGTGGAT
* * * * *
214493 GCTGGTGGCGGAAATGGTGTAAATGAATCTACATATGGTG
1 GCTGGGGGTGGAAATGGTGTAGATGAACCTACAGATGGTG
*
214533 GCACTGGGGGTGGAAATGGTGTAGATGAACCTAGAGATGGTG
1 G--CTGGGGGTGGAAATGGTGTAGATGAACCTACAGATGGTG
214575 G-TGGGGGT-GATAATGGT-TATGATGA
1 GCTGGGGGTGGA-AATGGTGTA-GATGA
214600 CAATGAAAGA
Statistics
Matches: 57, Mismatches: 6, Indels: 9
0.79 0.08 0.12
Matches are distributed among these distances:
38 4 0.07
39 18 0.32
40 1 0.02
42 34 0.60
ACGTcount: A:0.26, C:0.07, G:0.40, T:0.26
Consensus pattern (40 bp):
GCTGGGGGTGGAAATGGTGTAGATGAACCTACAGATGGTG
Found at i:219657 original size:26 final size:26
Alignment explanation
Indices: 219621--219674 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
219611 ACCGAAGTGC
* *
219621 TAATACACATAAGGTTGTGCCCCCCA
1 TAATACACATAAGGTCGTGCCCACCA
219647 TAATACACATAAGGTCGTGCCCACCA
1 TAATACACATAAGGTCGTGCCCACCA
219673 TA
1 TA
219675 TGCACTAAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.33, C:0.30, G:0.15, T:0.22
Consensus pattern (26 bp):
TAATACACATAAGGTCGTGCCCACCA
Found at i:219877 original size:16 final size:16
Alignment explanation
Indices: 219856--219894 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 16
219846 TTCATACCCG
219856 AAATAACATCCA-CTAT
1 AAATAACATCCATC-AT
219872 AAATAACATCCATCAT
1 AAATAACATCCATCAT
219888 AAATAAC
1 AAATAAC
219895 TAGAGATCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 21 0.95
17 1 0.05
ACGTcount: A:0.54, C:0.23, G:0.00, T:0.23
Consensus pattern (16 bp):
AAATAACATCCATCAT
Found at i:222410 original size:341 final size:342
Alignment explanation
Indices: 221443--222453 Score: 1655
Period size: 333 Copynumber: 3.0 Consensus size: 342
221433 AACTCGATAA
* * * *
221443 ATTTTGATTTTTGTATAAAATTACACAATACGTATAATCTAGTATAGGAAAACTATGAGGGTAAG
1 ATTTTGATTTTTGAATGAAATTACACAATACGTATAATCTAGTATAAGAAAACTTTGAGGGTAAG
**
221508 TATTTTAAAATATGAATAATTTTATAAAAAATTTATAACTAATATTTATTTTAC--AA--A--AT
66 TATTTTAAAATATGAATAATTTTATAAAAGTTTTATAACTAATATTTATTTTACAAAATGATGAT
*
221567 GATGATGATGATGATAAATATTTTATAATTTAAAAATTATAAATTTCATATATTTTTGAAAATTT
131 GATGATGATGATGATAAATATTTTATAATTTAAAAATTATAAATTTCATATATTTTTGAAAAATT
221632 TATTGACTTTTAAAATTAATTGTTTAAAAATAT-AAAAAATATTAAAATAAACTTTTAATTACAT
196 TATTGACTTTTAAAATTAATTGTTTAAAAATATAAAAAAATATTAAAATAAACTTTTAATTACAT
*
221696 TTGAGGGATCAAATGAATAATTATTCATTAATTATTA-TTTTTAACAACAGTTAATAATGTTTAT
261 TTGAGGGATCAAATGAATTATTATTCATTAATTATTATTTTTTAACAACAGTTAATAATGTTTAT
221760 TCATTTTTAATAAAATT
326 TCATTTTTAATAAAATT
* * *
221777 ATTTTGATTTTTGCATGAAATTACACAATACATATAATCTAGTAT-AGAAAAACTTTGAAGGTAA
1 ATTTTGATTTTTGAATGAAATTACACAATACGTATAATCTAGTATAAG-AAAACTTTGAGGGTAA
* **
221841 GTATTTCAAAATATGAATAATTTTATAAAAGTTTTATAACTAGGATTTATTTTACAAAATGATGA
65 GTATTTTAAAATATGAATAATTTTATAAAAGTTTTATAACTAATATTTATTTTACAAAATGATGA
*
221906 TGATGAT-A--A--AT--ATA--TTATAATTTTAAAAATTATAAATTTCATATATTTTTGAAAAG
130 TGATGATGATGATGATAAATATTTTATAA-TTTAAAAATTATAAATTTCATATATTTTTGAAAAA
* *
221962 TTTATTGACTTTTAAAATTAATTGTTTAAAAATATAAAAATATATTAAAATAAGCTTTTAATTAC
194 TTTATTGACTTTTAAAATTAATTGTTTAAAAATATAAAAAAATATTAAAATAAACTTTTAATTAC
*
222027 ATTTGAGGGATCAAATGAATTATTATTCATTAATTATTATTTTTTAACAACAATTAATAATGTTT
259 ATTTGAGGGATCAAATGAATTATTATTCATTAATTATTATTTTTTAACAACAGTTAATAATGTTT
222092 ATTCA-TTTTAATAAAATT
324 ATTCATTTTTAATAAAATT
*
222110 ATTTTGATTTTTGAATGAAATTACACAATATGTATAATCTAGTATAAGAAAACTTTGAGGGTAAG
1 ATTTTGATTTTTGAATGAAATTACACAATACGTATAATCTAGTATAAGAAAACTTTGAGGGTAAG
* *
222175 AATTTTAAAATATGAATAATTTTATAAAAGTTTTATAACTATTATTTATTTTACAAAATGATGAT
66 TATTTTAAAATATGAATAATTTTATAAAAGTTTTATAACTAATATTTATTTTACAAAATGATGAT
*
222240 GATGATGATGATGATAAATATTTTATAATTTAAAAAGTATAAATTTCATATATTTTTGAAAAATT
131 GATGATGATGATGATAAATATTTTATAATTTAAAAATTATAAATTTCATATATTTTTGAAAAATT
222305 TATTGACTTTTAAAATTAATTGTTTAAAAATATAAAAAAATATTAAAATAAACTTTTAATTACAT
196 TATTGACTTTTAAAATTAATTGTTTAAAAATATAAAAAAATATTAAAATAAACTTTTAATTACAT
* *
222370 TTGAGGGATCAAATGAATTATTATTCATTAATTATTATTTTTTAACAACAGTTATTAATATTTAT
261 TTGAGGGATCAAATGAATTATTATTCATTAATTATTATTTTTTAACAACAGTTAATAATGTTTAT
222435 TCATTTTTAATAAAATT
326 TCATTTTTAATAAAATT
222452 AT
1 AT
222454 AATTTAATAT
Statistics
Matches: 625, Mismatches: 31, Indels: 34
0.91 0.04 0.05
Matches are distributed among these distances:
331 6 0.01
332 69 0.11
333 207 0.33
334 138 0.22
335 2 0.00
336 3 0.00
337 1 0.00
338 3 0.00
339 1 0.00
340 11 0.02
341 163 0.26
342 21 0.03
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.43
Consensus pattern (342 bp):
ATTTTGATTTTTGAATGAAATTACACAATACGTATAATCTAGTATAAGAAAACTTTGAGGGTAAG
TATTTTAAAATATGAATAATTTTATAAAAGTTTTATAACTAATATTTATTTTACAAAATGATGAT
GATGATGATGATGATAAATATTTTATAATTTAAAAATTATAAATTTCATATATTTTTGAAAAATT
TATTGACTTTTAAAATTAATTGTTTAAAAATATAAAAAAATATTAAAATAAACTTTTAATTACAT
TTGAGGGATCAAATGAATTATTATTCATTAATTATTATTTTTTAACAACAGTTAATAATGTTTAT
TCATTTTTAATAAAATT
Found at i:222575 original size:40 final size:39
Alignment explanation
Indices: 222523--222598 Score: 125
Period size: 39 Copynumber: 1.9 Consensus size: 39
222513 GAGGTGATAT
* *
222523 TTTTTTATCTTTACATTATTTTTTTTATTGAATTTTAATA
1 TTTTTTAGCTTTACATT-CTTTTTTTATTGAATTTTAATA
222563 TTTTTTAGCTTTACATTCTTTTTTTATTGAATTTTA
1 TTTTTTAGCTTTACATTCTTTTTTTATTGAATTTTA
222599 TTCACTTTCA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
39 18 0.53
40 16 0.47
ACGTcount: A:0.22, C:0.07, G:0.04, T:0.67
Consensus pattern (39 bp):
TTTTTTAGCTTTACATTCTTTTTTTATTGAATTTTAATA
Found at i:223827 original size:17 final size:16
Alignment explanation
Indices: 223786--223828 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
223776 ATTTTTTATT
223786 TGGGTTT-AAAATTAA
1 TGGGTTTAAAAATTAA
223801 TCGGGTTTTAAAATATTAA
1 T-GGG-TTTAAAA-ATTAA
223820 TGGGTTTAA
1 TGGGTTTAA
223829 GGTTAAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
15 1 0.04
16 3 0.12
17 8 0.33
18 6 0.25
19 6 0.25
ACGTcount: A:0.35, C:0.02, G:0.21, T:0.42
Consensus pattern (16 bp):
TGGGTTTAAAAATTAA
Found at i:223851 original size:23 final size:23
Alignment explanation
Indices: 223808--223851 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
223798 TAATCGGGTT
*
223808 TTAAAATATTAATGGGTTTAAGG
1 TTAAAATATTAATAGGTTTAAGG
*
223831 TTAAAAT-TTATTAGGTCTTAA
1 TTAAAATATTAATAGGT-TTAA
223852 TATTTTAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.39, C:0.02, G:0.16, T:0.43
Consensus pattern (23 bp):
TTAAAATATTAATAGGTTTAAGG
Found at i:223914 original size:14 final size:14
Alignment explanation
Indices: 223897--223938 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
223887 AATTAACGAG
*
223897 CATAAACGAATAAA
1 CATAAACGAACAAA
*
223911 CATAAATGAACAAA
1 CATAAACGAACAAA
*
223925 CATAAACAAACAAA
1 CATAAACGAACAAA
223939 ATATTGAATG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.67, C:0.17, G:0.05, T:0.12
Consensus pattern (14 bp):
CATAAACGAACAAA
Found at i:226697 original size:18 final size:18
Alignment explanation
Indices: 226656--226698 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
226646 ACCACCACCA
226656 CTATGACACCTCCCCCAG
1 CTATGACACCTCCCCCAG
* *
226674 CCATGACACCTCCCCCGG
1 CTATGACACCTCCCCCAG
226692 CTATGAC
1 CTATGAC
226699 GCCAACTTCG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.21, C:0.49, G:0.14, T:0.16
Consensus pattern (18 bp):
CTATGACACCTCCCCCAG
Found at i:227911 original size:343 final size:339
Alignment explanation
Indices: 227248--227930 Score: 1221
Period size: 343 Copynumber: 2.0 Consensus size: 339
227238 CAAAACACCT
*
227248 TACAGATATACTATTCCAACTCATATCATATGAAGAACAACACACCCTTTCATATAGGAATTTGA
1 TACAGATATACTATTCCAACTCATATCATAGGAAGAACAACACACCCTTTCATATAGGAATTTGA
227313 TCCTCTAAATATATCTTCCCGAATTCGACTAACCTAATAGAGATGTACATTTGCATGAATCCATT
66 TCCTCTAAATATATCTTCCCGAATTCGACTAACCTAATAGAGATGTACATTTGCATGAATCCATT
227378 AAAAACCCATCCTGCAGCTAAAAGTTAGACGAGTATGGGTTGGTGTGGATAAAAGGAATAAGAGC
131 AAAAACCCATCCTGCAGCTAAAAGTTAGACGAGTATGGGTTGGTGTGGATAAAAGGAATAAGAGC
227443 AAGCAATAAGTGGTGGTGAATGGATGATGCCAATGAATATCATCAGTGGAAGAAAAAGGTTAGGT
196 AAGCAATAAGTGGTGGTGAATGGATGATGCCAATGAATATCATCAGTGGAAGAAAAAGGTTAGGT
* *
227508 GCTAGCTGTTATGGTAGACTTTGTGTGGACGACAGATGGGTGAGTAATTAGCTTTGGTGGAAAGG
261 GCTAGCTGTTATGGTAGACTTTGTATGGACGACAGATGGGTGAATAATTAGCTTTGGTGGAAAGG
227573 TGAAACCAAATTGCC
326 TG-AACCAAATTGCC
*
227588 TACAGATATAACTATTCGAACTCATAATCTATAGGAAGAACAACACACCCTTTCATATAGGAATT
1 TACAGATAT-ACTATTCCAACTCAT-ATC-ATAGGAAGAACAACACACCCTTTCATATAGGAATT
227653 TGATCCTCTAAATATATTCTTCCCGAATTCGACTAACCTAATAGAGATGTACATTTGCATGAATC
63 TGATCCTCTAAATATA-TCTTCCCGAATTCGACTAACCTAATAGAGATGTACATTTGCATGAATC
*
227718 CATT-AAAACCCATCCTGCAGCTAAAAGTTAGATGAGTATGGGTTGGTGTGTGGATAAAAGG-AT
127 CATTAAAAACCCATCCTGCAGCTAAAAGTTAGACGAGTATGGGTT-G-GTGTGGATAAAAGGAAT
227781 AAGAGCAAGCAATAAGTGGTGGTGAATGGATGATGCCAATG-A-ATCATCAGTGGAAGAAAAAGG
190 AAGAGCAAGCAATAAGTGGTGGTGAATGGATGATGCCAATGAATATCATCAGTGGAAGAAAAAGG
227844 TTAGGTGCTAGCTGTTATGGTAGACTTTGTATGGACGACAGATGGGTGAATAATTAGCTTTTGGT
255 TTAGGTGCTAGCTGTTATGGTAGACTTTGTATGGACGACAGATGGGTGAATAATTAGC-TTTGGT
227909 GGAAAGGTGAACCAAATTGCC
319 GGAAAGGTGAACCAAATTGCC
227930 T
1 T
227931 TCCTTATTAA
Statistics
Matches: 331, Mismatches: 5, Indels: 12
0.95 0.01 0.03
Matches are distributed among these distances:
340 9 0.03
341 14 0.04
342 93 0.28
343 105 0.32
344 96 0.29
345 14 0.04
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.28
Consensus pattern (339 bp):
TACAGATATACTATTCCAACTCATATCATAGGAAGAACAACACACCCTTTCATATAGGAATTTGA
TCCTCTAAATATATCTTCCCGAATTCGACTAACCTAATAGAGATGTACATTTGCATGAATCCATT
AAAAACCCATCCTGCAGCTAAAAGTTAGACGAGTATGGGTTGGTGTGGATAAAAGGAATAAGAGC
AAGCAATAAGTGGTGGTGAATGGATGATGCCAATGAATATCATCAGTGGAAGAAAAAGGTTAGGT
GCTAGCTGTTATGGTAGACTTTGTATGGACGACAGATGGGTGAATAATTAGCTTTGGTGGAAAGG
TGAACCAAATTGCC
Found at i:230625 original size:15 final size:15
Alignment explanation
Indices: 230581--230649 Score: 61
Period size: 15 Copynumber: 4.7 Consensus size: 15
230571 ATTTTATTAG
*
230581 TATGTGAA-ATATTC
1 TATGTGAATATGTTC
* *
230595 TACGTGAAAATGTTC
1 TATGTGAATATGTTC
*
230610 TATGTGAATATTTTC
1 TATGTGAATATGTTC
*
230625 TA-GATGAATGTGTTC
1 TATG-TGAATATGTTC
*
230640 TAAGTGAATA
1 TATGTGAATA
230650 AACGACACTT
Statistics
Matches: 44, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
14 8 0.18
15 35 0.80
16 1 0.02
ACGTcount: A:0.33, C:0.07, G:0.19, T:0.41
Consensus pattern (15 bp):
TATGTGAATATGTTC
Found at i:234082 original size:21 final size:21
Alignment explanation
Indices: 234058--234131 Score: 105
Period size: 21 Copynumber: 3.5 Consensus size: 21
234048 AACCATTCTC
234058 TTCATGAAAAGATTAAATCCT
1 TTCATGAAAAGATTAAATCCT
234079 TTCATGAAAAGATTAAATCCT
1 TTCATGAAAAGATTAAATCCT
**
234100 TTCATGAAAA-AGTTAAGCCCT
1 TTCATGAAAAGA-TTAAATCCT
*
234121 TTCATCAAAAG
1 TTCATGAAAAG
234132 GAGAAGTCTT
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
20 1 0.02
21 47 0.98
ACGTcount: A:0.42, C:0.16, G:0.11, T:0.31
Consensus pattern (21 bp):
TTCATGAAAAGATTAAATCCT
Found at i:234148 original size:21 final size:21
Alignment explanation
Indices: 234124--234173 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
234114 AAGCCCTTTC
234124 ATCAAAAGGAGAAGTCTTTTA
1 ATCAAAAGGAGAAGTCTTTTA
** *
234145 ATCAAAAGGTTAAGTCTTTTC
1 ATCAAAAGGAGAAGTCTTTTA
*
234166 ATCGAAAG
1 ATCAAAAG
234174 ATCTTAACCT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.40, C:0.12, G:0.18, T:0.30
Consensus pattern (21 bp):
ATCAAAAGGAGAAGTCTTTTA
Found at i:234366 original size:23 final size:23
Alignment explanation
Indices: 234336--234388 Score: 106
Period size: 23 Copynumber: 2.3 Consensus size: 23
234326 AGTAAGGCAA
234336 TATTGTGTTCGACTAATCACTAC
1 TATTGTGTTCGACTAATCACTAC
234359 TATTGTGTTCGACTAATCACTAC
1 TATTGTGTTCGACTAATCACTAC
234382 TATTGTG
1 TATTGTG
234389 CTTACTGTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.25, C:0.19, G:0.15, T:0.42
Consensus pattern (23 bp):
TATTGTGTTCGACTAATCACTAC
Found at i:237109 original size:21 final size:21
Alignment explanation
Indices: 237085--237128 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
237075 TTTTGAAACC
237085 ACCATTTTGGTTTTAAAATTA
1 ACCATTTTGGTTTTAAAATTA
237106 ACCATTTTGGTTTTAAAATTA
1 ACCATTTTGGTTTTAAAATTA
237127 AC
1 AC
237129 GGTGATATCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.34, C:0.11, G:0.09, T:0.45
Consensus pattern (21 bp):
ACCATTTTGGTTTTAAAATTA
Found at i:237670 original size:28 final size:29
Alignment explanation
Indices: 237636--237692 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
237626 TTGAAAATTA
*
237636 TAAAAAT-AATATTATAAT-TTATAAATAT
1 TAAAAATCAATATT-TAATACTATAAATAT
*
237664 TAAAAATCTATATTTAATACTATAAATAT
1 TAAAAATCAATATTTAATACTATAAATAT
237693 AATAAAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 11 0.44
29 14 0.56
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (29 bp):
TAAAAATCAATATTTAATACTATAAATAT
Found at i:254986 original size:139 final size:139
Alignment explanation
Indices: 254736--255075 Score: 421
Period size: 139 Copynumber: 2.4 Consensus size: 139
254726 TTCTTTAAAT
* * * * *
254736 TTAGTCCTTAAATTTA-GAGGAATTTTTAATTTGGTCATCGCTCTTGCTCGATGTTCCATTTTAA
1 TTAGTCATTAAATTTAGGA-GAATTTTTAATTTGGTCATCGCTTTTGCTTGAGGTTCCATTTGAA
** * * * *
254800 TTATTCAAACCAAATAATTGGTCAAAATTGACCAGGTTAATAATTAGAGCCTCTATTTTAAGTTT
65 ACATTCAAACCAAATAATTGGTCAAAATTGACCAAGTTAATAATTAGAGACTCCATTTTAAGTGT
254865 AATTTCAAAC
130 AATTTCAAAC
* *
254875 TTAGTCATTAAATTTAGGAAAATTTTTAATTTGGTCATCGTTTTTGCTTGAGGTTCCATTTGAAA
1 TTAGTCATTAAATTTAGGAGAATTTTTAATTTGGTCATCGCTTTTGCTTGAGGTTCCATTTGAAA
* * * * *
254940 CATTCGAATCACATAATTGGTTAAAATTGACCAAGTTAATAATTAGAGACTCCATTTTACGTGTA
66 CATTCAAACCAAATAATTGGTCAAAATTGACCAAGTTAATAATTAGAGACTCCATTTTAAGTGTA
*
255005 ATTTCATAC
131 ATTTCAAAC
* * * * * * *
255014 CTAGTCCTTTAATTTTAGGAGAATTTTTTATCTGGTCATCGCTTATGCTTTAGGTTCCATTT
1 TTAGT-CATTAAATTTAGGAGAATTTTTAATTTGGTCATCGCTTTTGCTTGAGGTTCCATTT
255076 TGACTGTTCA
Statistics
Matches: 171, Mismatches: 28, Indels: 3
0.85 0.14 0.01
Matches are distributed among these distances:
139 121 0.71
140 50 0.29
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (139 bp):
TTAGTCATTAAATTTAGGAGAATTTTTAATTTGGTCATCGCTTTTGCTTGAGGTTCCATTTGAAA
CATTCAAACCAAATAATTGGTCAAAATTGACCAAGTTAATAATTAGAGACTCCATTTTAAGTGTA
ATTTCAAAC
Found at i:261131 original size:16 final size:16
Alignment explanation
Indices: 261104--261137 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
261094 CCTTTTTGGG
261104 AAGCAGACAAGAAATGC
1 AAGCAGACAAGAAA-GC
261121 AAGCA-ACAAGAAAGC
1 AAGCAGACAAGAAAGC
261136 AA
1 AA
261138 CGATGGAGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 8 0.47
17 5 0.29
ACGTcount: A:0.59, C:0.18, G:0.21, T:0.03
Consensus pattern (16 bp):
AAGCAGACAAGAAAGC
Found at i:269355 original size:30 final size:30
Alignment explanation
Indices: 269310--269394 Score: 95
Period size: 28 Copynumber: 2.9 Consensus size: 30
269300 TGCTCGTATT
* *
269310 GGTCGCCATGAAGTCGGGGCGAAGCAAGTA
1 GGTCGCCATGCAGTCGGGGCGAACCAAGTA
* **
269340 GGTCACCATGCAGTC-GGGCG-ACCTTGTA
1 GGTCGCCATGCAGTCGGGGCGAACCAAGTA
*
269368 GGTCGCCATACAGTCGGGGCG-ACCAAG
1 GGTCGCCATGCAGTCGGGGCGAACCAAG
269395 CATGCTCCCA
Statistics
Matches: 45, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
28 18 0.40
29 14 0.31
30 13 0.29
ACGTcount: A:0.22, C:0.26, G:0.36, T:0.15
Consensus pattern (30 bp):
GGTCGCCATGCAGTCGGGGCGAACCAAGTA
Found at i:269989 original size:21 final size:22
Alignment explanation
Indices: 269949--269989 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
269939 AATAATTTTA
* *
269949 AGCTTTCGTTTATTTTTTAAAT
1 AGCTTTCATTTATATTTTAAAT
269971 AGCTTTCATTTA-ATTTTAA
1 AGCTTTCATTTATATTTTAA
269990 TTGTAAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.27, C:0.10, G:0.07, T:0.56
Consensus pattern (22 bp):
AGCTTTCATTTATATTTTAAAT
Found at i:270960 original size:234 final size:233
Alignment explanation
Indices: 270513--270985 Score: 761
Period size: 234 Copynumber: 2.0 Consensus size: 233
270503 TTTAGGATTT
* * *
270513 AGTGTTTAGGGTTTTCAATAATAACCAAAATATTTTAGGGTTTAGGGTTTAAAGTTCACAAAATC
1 AGTGTTTAGGGTTTTAAATAACAACCAAAATATGTTAGGGTTTAGGG-----AGTTCACAAAATC
270578 AATAGTTACATATATTATTTGTTGTATATTGATTTTGTGAACCCTAAACCCTAATTTTTTTATTA
61 AATAGTTACATATATTATTTGTTGTATATTGATTTTGTGAACCCTAAACCCTAATTTTTTTATTA
270643 TTACTGAAAACCTTTATAAATTCATGGTATGTTGAGGGCAATGAAAGGGATAGAGAATGGTGATA
126 TTACTGAAAACCTTTATAAATTCATGGTATGTTGAGGGCAATGAAAGGGATAGAGAATGGTGATA
*
270708 TCTACCATGATAGTGGTTACATATTTGTTTTTTTATAAGAAGAA
191 TCTACCATGATAGTGGTTACAGATTTG-TTTTTTATAAGAAGAA
*
270752 AGTGTTTAGGGTTTTAAATAACAATCAAAATATGTTAGGGTTTA-GG-GTTCACAAAATCAATAG
1 AGTGTTTAGGGTTTTAAATAACAACCAAAATATGTTAGGGTTTAGGGAGTTCACAAAATCAATAG
* *
270815 TTACTTATATTATTTGTTGTATATTGATTTTGTGAACCCTACACCCTAAATTTTTTTGATTATTA
66 TTACATATATTATTTGTTGTATATTGATTTTGTGAACCCTAAACCCT-AATTTTTTT-ATTATTA
* *
270880 CTGAAAACCTTTATAAATTCATGGTATGTTGAGGGCAATGAAAGGGGTAGAGGATGGTGATATCT
129 CTGAAAACCTTTATAAATTCATGGTATGTTGAGGGCAATGAAAGGGATAGAGAATGGTGATATCT
* *
270945 ACCATGATGGTGGTTATAGATTTGTTTTTTATAAGAAGAA
194 ACCATGATAGTGGTTACAGATTTGTTTTTTATAAGAAGAA
270985 A
1 A
270986 TTGATTGGAG
Statistics
Matches: 221, Mismatches: 11, Indels: 10
0.91 0.05 0.04
Matches are distributed among these distances:
232 62 0.28
233 26 0.12
234 91 0.41
238 2 0.01
239 40 0.18
ACGTcount: A:0.33, C:0.09, G:0.19, T:0.39
Consensus pattern (233 bp):
AGTGTTTAGGGTTTTAAATAACAACCAAAATATGTTAGGGTTTAGGGAGTTCACAAAATCAATAG
TTACATATATTATTTGTTGTATATTGATTTTGTGAACCCTAAACCCTAATTTTTTTATTATTACT
GAAAACCTTTATAAATTCATGGTATGTTGAGGGCAATGAAAGGGATAGAGAATGGTGATATCTAC
CATGATAGTGGTTACAGATTTGTTTTTTATAAGAAGAA
Found at i:271795 original size:30 final size:29
Alignment explanation
Indices: 271728--271810 Score: 112
Period size: 29 Copynumber: 2.8 Consensus size: 29
271718 GAGCAGGCTT
*
271728 GGTCGCCCCGACTGCATAGCGACCTACAA
1 GGTCGCCCCGACTGCATGGCGACCTACAA
* **
271757 GGTCGCCCCGATTGCATGGCGACCTACTT
1 GGTCGCCCCGACTGCATGGCGACCTACAA
*
271786 GCTTCGCCCCGACTGCATGGCGACC
1 G-GTCGCCCCGACTGCATGGCGACC
271811 AATACGAGCA
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
29 26 0.55
30 21 0.45
ACGTcount: A:0.17, C:0.39, G:0.27, T:0.18
Consensus pattern (29 bp):
GGTCGCCCCGACTGCATGGCGACCTACAA
Found at i:272068 original size:31 final size:31
Alignment explanation
Indices: 272033--272093 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
272023 TATAATCTCC
*
272033 CAACATTTAGTCT-GTTTGTAATATGGTCCCT
1 CAACATTT-GTCTCGTTTGCAATATGGTCCCT
* *
272064 CAACATTTTTTTCGTTTGCAATATGGTCCC
1 CAACATTTGTCTCGTTTGCAATATGGTCCC
272094 AGACCTAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 2 0.08
31 24 0.92
ACGTcount: A:0.21, C:0.21, G:0.15, T:0.43
Consensus pattern (31 bp):
CAACATTTGTCTCGTTTGCAATATGGTCCCT
Found at i:273618 original size:30 final size:31
Alignment explanation
Indices: 273582--273650 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 31
273572 TTTTAAAACA
*
273582 TGCAATATAATCCC-AAACATTTATTCCATT
1 TGCAATATAATCCCTAAACATTTAGTCCATT
** * *
273612 TGCAATATGGTCCCTCAACATTTAGTCCGTT
1 TGCAATATAATCCCTAAACATTTAGTCCATT
273643 TGCAATAT
1 TGCAATAT
273651 GGTCCCTGAC
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
30 12 0.36
31 21 0.64
ACGTcount: A:0.30, C:0.23, G:0.10, T:0.36
Consensus pattern (31 bp):
TGCAATATAATCCCTAAACATTTAGTCCATT
Found at i:273635 original size:31 final size:31
Alignment explanation
Indices: 273597--273657 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
273587 TATAATCCCA
*
273597 AACATTTATTCCATTTGCAATATGGTCCCTC
1 AACATTTAGTCCATTTGCAATATGGTCCCTC
*
273628 AACATTTAGTCCGTTTGCAATATGGTCCCT
1 AACATTTAGTCCATTTGCAATATGGTCCCT
273658 GACATAACTG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.25, C:0.25, G:0.13, T:0.38
Consensus pattern (31 bp):
AACATTTAGTCCATTTGCAATATGGTCCCTC
Found at i:274104 original size:24 final size:24
Alignment explanation
Indices: 274072--274120 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
274062 TATCTTCACA
*
274072 TTATTTTCACATTACAATGTTATT
1 TTATTTTCACACTACAATGTTATT
*
274096 TTATTTTCACACTACATTGTTATT
1 TTATTTTCACACTACAATGTTATT
274120 T
1 T
274121 GATATATCAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.27, C:0.14, G:0.04, T:0.55
Consensus pattern (24 bp):
TTATTTTCACACTACAATGTTATT
Found at i:274910 original size:25 final size:27
Alignment explanation
Indices: 274863--274920 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
274853 TTGTAAATTT
* *
274863 AAATATATTAAATTATAAGATAAATAA
1 AAATATATTAAAATATAAGATAAACAA
274890 AAATATATTAAAAT-TAA-ATAAACAA
1 AAATATATTAAAATATAAGATAAACAA
*
274915 ACATAT
1 AAATAT
274921 TAATTTGTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 12 0.43
26 3 0.11
27 13 0.46
ACGTcount: A:0.64, C:0.03, G:0.02, T:0.31
Consensus pattern (27 bp):
AAATATATTAAAATATAAGATAAACAA
Found at i:279758 original size:7 final size:6
Alignment explanation
Indices: 279742--279789 Score: 51
Period size: 6 Copynumber: 7.8 Consensus size: 6
279732 TTATAATTGA
* * * *
279742 TTTAAT TTTAAT ATTTAAT TTTAGT TTAAAT TTTAAT TATAAT ATTAA
1 TTTAAT TTTAAT -TTTAAT TTTAAT TTTAAT TTTAAT TTTAAT TTTAA
279790 GTCATGAATT
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
6 28 0.82
7 6 0.18
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (6 bp):
TTTAAT
Found at i:279759 original size:13 final size:13
Alignment explanation
Indices: 279741--279778 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
279731 TTTATAATTG
279741 ATTTAATTTTAAT
1 ATTTAATTTTAAT
*
279754 ATTTAATTTTAGT
1 ATTTAATTTTAAT
*
279767 -TTAAATTTTAAT
1 ATTTAATTTTAAT
279779 TATAATATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
12 10 0.45
13 12 0.55
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61
Consensus pattern (13 bp):
ATTTAATTTTAAT
Found at i:285218 original size:224 final size:224
Alignment explanation
Indices: 284828--285275 Score: 860
Period size: 224 Copynumber: 2.0 Consensus size: 224
284818 ATCACATTCG
284828 CCATAAAGTTTGACAATGACATTTTGTTTTGCCAACCAAGCTTTTTGATATAAGACATTGTACCC
1 CCATAAAGTTTGACAATGACATTTTGTTTTGCCAACCAAGCTTTTTGATATAAGACATTGTACCC
*
284893 ATACTGCGACTGTATAGCTGAAATCAACACTGTAACAGCTATATGAGAGCTTGCTTTTATATGGG
66 ATACTACGACTGTATAGCTGAAATCAACACTGTAACAGCTATATGAGAGCTTGCTTTTATATGGG
284958 CATGATGGCTTGGCATATCACATCAGATTCCAACTTGGGATGATCTTGGTTGACCCCTCCAGAAC
131 CATGATGGCTTGGCATATCACATCAGATTCCAACTTGGGATGATCTTGGTTGACCCCTCCAGAAC
285023 AACATGTGTGAGGACCATTGTATACTGTT
196 AACATGTGTGAGGACCATTGTATACTGTT
285052 CCATAAAGTTTGACAATGACATTTTGTTTTGCCAACCAAGCTTTTTGATATAAGACATTGTACCC
1 CCATAAAGTTTGACAATGACATTTTGTTTTGCCAACCAAGCTTTTTGATATAAGACATTGTACCC
*
285117 ATACTACGATTGTATAGCTGAAATCAACACTGTAACAGCTATATGAGAGCTTGCTTTTATATGGG
66 ATACTACGACTGTATAGCTGAAATCAACACTGTAACAGCTATATGAGAGCTTGCTTTTATATGGG
* *
285182 CATGATGGCTTGGCATATCACTTCAGATTCCAACTTGGGATGATCTTGGTTGACCCCTCCAGCAC
131 CATGATGGCTTGGCATATCACATCAGATTCCAACTTGGGATGATCTTGGTTGACCCCTCCAGAAC
285247 AACATGTGTGAGGACCATTGTATACTGTT
196 AACATGTGTGAGGACCATTGTATACTGTT
285276 AGTTCACATT
Statistics
Matches: 220, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
224 220 1.00
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.32
Consensus pattern (224 bp):
CCATAAAGTTTGACAATGACATTTTGTTTTGCCAACCAAGCTTTTTGATATAAGACATTGTACCC
ATACTACGACTGTATAGCTGAAATCAACACTGTAACAGCTATATGAGAGCTTGCTTTTATATGGG
CATGATGGCTTGGCATATCACATCAGATTCCAACTTGGGATGATCTTGGTTGACCCCTCCAGAAC
AACATGTGTGAGGACCATTGTATACTGTT
Found at i:290489 original size:23 final size:23
Alignment explanation
Indices: 290459--290559 Score: 148
Period size: 23 Copynumber: 4.4 Consensus size: 23
290449 CAACAAACGA
290459 CAAGCATCAATGTACCAATTCAT
1 CAAGCATCAATGTACCAATTCAT
*
290482 CAAGCATCAATATACCAATTCAT
1 CAAGCATCAATGTACCAATTCAT
290505 CAAGCATCAATGTACCAATTCAT
1 CAAGCATCAATGTACCAATTCAT
* * * * *
290528 CAAGCATTATTGCATCAATTCAG
1 CAAGCATCAATGTACCAATTCAT
290551 CAAGCATCA
1 CAAGCATCA
290560 TGCATTAAGA
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 70 1.00
ACGTcount: A:0.40, C:0.26, G:0.09, T:0.26
Consensus pattern (23 bp):
CAAGCATCAATGTACCAATTCAT
Found at i:290676 original size:20 final size:20
Alignment explanation
Indices: 290651--290695 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
290641 AACCCTTACA
**
290651 AATATCAAGTAGAAGCAAAC
1 AATATCAAACAGAAGCAAAC
290671 AATATCAAACAGAAGCAAAC
1 AATATCAAACAGAAGCAAAC
290691 AATAT
1 AATAT
290696 AAAATAGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.58, C:0.16, G:0.11, T:0.16
Consensus pattern (20 bp):
AATATCAAACAGAAGCAAAC
Found at i:290704 original size:20 final size:20
Alignment explanation
Indices: 290660--290704 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
290650 AAATATCAAG
*
290660 TAGAAGCAAACAATATCAAA
1 TAGAAGCAAACAATATAAAA
*
290680 CAGAAGCAAACAATATAAAA
1 TAGAAGCAAACAATATAAAA
290700 TAGAA
1 TAGAA
290705 TAATGCAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.62, C:0.13, G:0.11, T:0.13
Consensus pattern (20 bp):
TAGAAGCAAACAATATAAAA
Found at i:292041 original size:31 final size:31
Alignment explanation
Indices: 292003--292066 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
291993 CTATTTGTTT
* *
292003 ATTGCTCATATCAAACAAGGACATAATGACA
1 ATTGCTCATACCAAACAAGGAAATAATGACA
* *
292034 ATTGCTCATACCAAACAGGGAAATAATGGCA
1 ATTGCTCATACCAAACAAGGAAATAATGACA
292065 AT
1 AT
292067 CTTTTCGAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.44, C:0.19, G:0.16, T:0.22
Consensus pattern (31 bp):
ATTGCTCATACCAAACAAGGAAATAATGACA
Found at i:293148 original size:28 final size:28
Alignment explanation
Indices: 293116--293262 Score: 192
Period size: 28 Copynumber: 5.2 Consensus size: 28
293106 ATAAACTATT
*
293116 TATAATTAATATTAAAATAATTATATAG
1 TATAATTAATATTAAAATAATTATATAA
293144 TATAATTAATATTAAAATAATTATATAA
1 TATAATTAATATTAAAATAATTATATAA
*
293172 TATAATTAATATTAAAATAATTACATAA
1 TATAATTAATATTAAAATAATTATATAA
*
293200 TATAATTAATATTAATATTAACTTATATTAA
1 TATAATTAATATTAA-AATAA-TTATA-TAA
*
293231 TATAATATAAT-TTATAAT--TTATATTAA
1 TATAAT-TAATATTAAAATAATTATA-TAA
293258 TATAA
1 TATAA
293263 AATATAGTCT
Statistics
Matches: 109, Mismatches: 6, Indels: 9
0.88 0.05 0.07
Matches are distributed among these distances:
27 14 0.13
28 69 0.63
29 4 0.04
30 6 0.06
31 12 0.11
32 4 0.04
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (28 bp):
TATAATTAATATTAAAATAATTATATAA
Found at i:293190 original size:8 final size:9
Alignment explanation
Indices: 293122--293216 Score: 58
Period size: 9 Copynumber: 10.2 Consensus size: 9
293112 TATTTATAAT
293122 TAATATTAA
1 TAATATTAA
293131 -AATAATTATA
1 TAAT-ATTA-A
*
293141 TAGTA-TAA
1 TAATATTAA
293149 TTAATATTAA
1 -TAATATTAA
293159 -AATAATTATA
1 TAAT-ATTA-A
293169 TAATA-TAA
1 TAATATTAA
293177 TTAATATTAA
1 -TAATATTAA
293187 -AATAATTACA
1 TAAT-ATTA-A
293197 TAATA-TAA
1 TAATATTAA
293205 TTAATATTAA
1 -TAATATTAA
293215 TA
1 TA
293217 TTAACTTATA
Statistics
Matches: 69, Mismatches: 2, Indels: 30
0.68 0.02 0.30
Matches are distributed among these distances:
8 12 0.17
9 34 0.49
10 15 0.22
11 8 0.12
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (9 bp):
TAATATTAA
Found at i:293261 original size:22 final size:22
Alignment explanation
Indices: 293200--293262 Score: 85
Period size: 22 Copynumber: 2.9 Consensus size: 22
293190 AATTACATAA
293200 TATAATTAATATTAATATTAACT
1 TATAATTAATATTAATA-TAACT
*
293223 TAT-ATTAATA-TAATATAATT
1 TATAATTAATATTAATATAACT
*
293243 TATAATTTATATTAATATAA
1 TATAATTAATATTAATATAA
293263 AATATAGTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
20 7 0.19
21 11 0.31
22 15 0.42
23 3 0.08
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (22 bp):
TATAATTAATATTAATATAACT
Found at i:293268 original size:22 final size:22
Alignment explanation
Indices: 293165--293268 Score: 77
Period size: 22 Copynumber: 4.5 Consensus size: 22
293155 TTAAAATAAT
*
293165 TATATAATATAATTAATATTAAAA
1 TATAAAATATAATTAATATT--AA
293189 TAATTACATAATATAATTAATATTAA
1 T-A-TA-A-AATATAATTAATATTAA
* *
293215 TATTAACT-TATATTAATA-TAA
1 TATAAAATATA-ATTAATATTAA
** *
293236 TATAATTTATAATTTATATTAA
1 TATAAAATATAATTAATATTAA
293258 TATAAAATATA
1 TATAAAATATA
293269 GTCTATAAAA
Statistics
Matches: 64, Mismatches: 9, Indels: 16
0.72 0.10 0.18
Matches are distributed among these distances:
21 16 0.25
22 23 0.36
23 1 0.02
24 2 0.03
25 2 0.03
26 5 0.08
28 15 0.23
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (22 bp):
TATAAAATATAATTAATATTAA
Found at i:293289 original size:31 final size:31
Alignment explanation
Indices: 293224--293308 Score: 99
Period size: 31 Copynumber: 2.9 Consensus size: 31
293214 ATATTAACTT
* *
293224 ATATTAATATAATATA-AT-TTAT--AATTT
1 ATATTAATATAAAATATATGTTATAAAATTA
293251 ATATTAATATAAAATATA-GTCTATAAAATTA
1 ATATTAATATAAAATATATGT-TATAAAATTA
*
293282 ATATTAATATAAACTATATGTTATAAA
1 ATATTAATATAAAATATATGTTATAAA
293309 TGATATAGTA
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
27 15 0.31
28 2 0.04
29 3 0.06
31 27 0.55
32 2 0.04
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (31 bp):
ATATTAATATAAAATATATGTTATAAAATTA
Found at i:293348 original size:27 final size:26
Alignment explanation
Indices: 293223--293495 Score: 103
Period size: 27 Copynumber: 10.2 Consensus size: 26
293213 AATATTAACT
*
293223 TATATTAATAT-AA-TATAATTTATAA
1 TATATTAATATAAACTATAGTTTAT-A
* *
293248 TTTATATTAATATAAAATATAGTCTATA
1 --TATATTAATATAAACTATAGTTTATA
* * ***
293276 -AAATTAATATTAA-TATAAACTATA
1 TATATTAATATAAACTATAGTTTATA
* * * *
293300 TGTTATAAATGATATAGTATAGTTTATA
1 T-ATATTAAT-ATAAACTATAGTTTATA
* * *
293328 CTATATTAATATAAATTATAGTTAAGA
1 -TATATTAATATAAACTATAGTTTATA
* * * *
293355 TA-ATTAACATTAATA-TAAACTATATA
1 TATATTAATA-TAA-ACTATAGTTTATA
*
293381 GTACATTAATATAAACTATAGTTTATATA
1 -TATATTAATATAAACTATAG-TT-TATA
* *
293410 TATAGTTCATATGTAAACTATAGTTCATA
1 TATA-TT-A-ATATAAACTATAGTTTATA
293439 TATA-TAGTATATAAACTATAGTTTATA
1 TATATTA--ATATAAACTATAGTTTATA
* * * *
293466 TA-AATAGTATAAAATATAGTATATA
1 TATATTAATATAAACTATAGTTTATA
*
293491 AATAT
1 TATAT
293496 AAATTATAGT
Statistics
Matches: 186, Mismatches: 40, Indels: 41
0.70 0.15 0.15
Matches are distributed among these distances:
24 9 0.05
25 34 0.18
26 20 0.11
27 59 0.32
28 27 0.15
29 22 0.12
30 3 0.02
31 12 0.06
ACGTcount: A:0.48, C:0.04, G:0.06, T:0.42
Consensus pattern (26 bp):
TATATTAATATAAACTATAGTTTATA
Found at i:293402 original size:20 final size:21
Alignment explanation
Indices: 293361--293402 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
293351 AAGATAATTA
293361 ACATTAATATAAACTATATAGT
1 ACATTAATATAAAC-ATATAGT
293383 ACATTAATATAAAC-TATAGT
1 ACATTAATATAAACATATAGT
293403 TTATATATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 6 0.30
22 14 0.70
ACGTcount: A:0.50, C:0.10, G:0.05, T:0.36
Consensus pattern (21 bp):
ACATTAATATAAACATATAGT
Found at i:293412 original size:79 final size:79
Alignment explanation
Indices: 293250--293412 Score: 208
Period size: 79 Copynumber: 2.1 Consensus size: 79
293240 ATTTATAATT
* * *
293250 TATATTAATATAAAATATAGTCTATAAAATTAATATTAATATAAACTATATGTTATAAATGATAT
1 TATATTAATATAAAATATAGTCTATAAAATTAACATTAATATAAACTATATGTCATAAATGATAA
*
293315 AGTATAGTTTATAC
66 ACTATAGTTTATAC
* *
293329 TATATTAATATAAATTATAGT-TA-AGATAATTAACATTAATATAAACTATATAGTACATTAAT-
1 TATATTAATATAAAATATAGTCTATA-A-AATTAACATTAATATAAACTATAT-GT-CATAAATG
293391 ATAAACTATAGTTTATA-
62 ATAAACTATAGTTTATAC
293408 TATAT
1 TATAT
293413 AGTTCATATG
Statistics
Matches: 74, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
77 1 0.01
78 3 0.04
79 48 0.65
80 17 0.23
81 5 0.07
ACGTcount: A:0.48, C:0.04, G:0.06, T:0.42
Consensus pattern (79 bp):
TATATTAATATAAAATATAGTCTATAAAATTAACATTAATATAAACTATATGTCATAAATGATAA
ACTATAGTTTATAC
Found at i:293427 original size:31 final size:28
Alignment explanation
Indices: 293389--293496 Score: 125
Period size: 27 Copynumber: 3.9 Consensus size: 28
293379 TAGTACATTA
293389 ATATAAACTATAGTTTATATATATAGTT
1 ATATAAACTATAGTTTATATATATAGTT
*
293417 CATATGTAAACTATAGTTCATATATATAG-T
1 -ATA--TAAACTATAGTTTATATATATAGTT
*
293447 ATATAAACTATAGTTTATATAAATAG-T
1 ATATAAACTATAGTTTATATATATAGTT
* *
293474 ATA-AAA-TATAGTATATAAATATA
1 ATATAAACTATAGTTTATATATATA
293497 AATTATAGTA
Statistics
Matches: 71, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
25 14 0.20
26 3 0.04
27 25 0.35
29 6 0.08
30 1 0.01
31 22 0.31
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.41
Consensus pattern (28 bp):
ATATAAACTATAGTTTATATATATAGTT
Found at i:293449 original size:18 final size:17
Alignment explanation
Indices: 293404--293449 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
293394 AACTATAGTT
293404 TATATATATAGTTCATA
1 TATATATATAGTTCATA
* *
293421 TGTAAACTATAGTTCATA
1 TATATA-TATAGTTCATA
293439 TATATAGTATA
1 TATATA-TATA
293450 TAAACTATAG
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
17 4 0.17
18 19 0.83
ACGTcount: A:0.41, C:0.07, G:0.09, T:0.43
Consensus pattern (17 bp):
TATATATATAGTTCATA
Found at i:293476 original size:25 final size:26
Alignment explanation
Indices: 293389--293494 Score: 101
Period size: 31 Copynumber: 4.0 Consensus size: 26
293379 TAGTACATTA
*
293389 ATATAAACTATAGTTTATATATATAG
1 ATATAAACTATAGTTTATATAAATAG
* *
293415 TTCATATGTAAACTATAGTTCATATATATAG
1 ---ATA--TAAACTATAGTTTATATAAATAG
293446 TATATAAACTATAGTTTATATAAATAG
1 -ATATAAACTATAGTTTATATAAATAG
*
293473 -TATAAAATATAG--TATATAAATA
1 ATATAAACTATAGTTTATATAAATA
293495 TAAATTATAG
Statistics
Matches: 70, Mismatches: 5, Indels: 10
0.82 0.06 0.12
Matches are distributed among these distances:
23 10 0.14
25 11 0.16
27 21 0.30
29 6 0.09
31 22 0.31
ACGTcount: A:0.47, C:0.05, G:0.08, T:0.41
Consensus pattern (26 bp):
ATATAAACTATAGTTTATATAAATAG
Found at i:293496 original size:29 final size:29
Alignment explanation
Indices: 293463--293531 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 29
293453 ACTATAGTTT
293463 ATATAAATAGTATAAAATATAG-TATATAA
1 ATATAAATA-TATAAAATATAGATATATAA
** *
293492 ATATAAAT-TATAGTATGTAGATTATATAA
1 ATATAAATATATAAAATATAGA-TATATAA
293521 ATATAAATATA
1 ATATAAATATA
293532 AATTGTATAG
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
27 9 0.26
29 23 0.68
30 2 0.06
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (29 bp):
ATATAAATATATAAAATATAGATATATAA
Found at i:293498 original size:20 final size:20
Alignment explanation
Indices: 293473--293534 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
293463 ATATAAATAG
293473 TATAAAATATAGTATATAAA
1 TATAAAATATAGTATATAAA
* * *
293493 TATAAATTATAGTATGTAGAT
1 TATAAAATATAGTATATA-AA
*
293514 TATATAAATATA-AATATAAA
1 TATA-AAATATAGTATATAAA
293534 T
1 T
293535 TGTATAGTTT
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
20 18 0.55
21 9 0.27
22 6 0.18
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (20 bp):
TATAAAATATAGTATATAAA
Found at i:293552 original size:20 final size:20
Alignment explanation
Indices: 293527--293639 Score: 86
Period size: 20 Copynumber: 5.6 Consensus size: 20
293517 ATAAATATAA
*
293527 ATATAAATTGTATAGTTTAT
1 ATATAAATTATATAGTTTAT
* *
293547 ATATAATTCATATATAATTTAT
1 ATATAAAT--TATATAGTTTAT
* * *
293569 ATATAAACTATGTAGTTTCT
1 ATATAAATTATATAGTTTAT
* *
293589 ATAT-AGTTCA-ATAGTTCAT
1 ATATAAATT-ATATAGTTTAT
* *
293608 ATATAAACTATATAGTTCAT
1 ATATAAATTATATAGTTTAT
*
293628 ATGTAAATTATA
1 ATATAAATTATA
293640 CTATATAGTA
Statistics
Matches: 71, Mismatches: 17, Indels: 10
0.72 0.17 0.10
Matches are distributed among these distances:
19 13 0.18
20 42 0.59
22 16 0.23
ACGTcount: A:0.42, C:0.06, G:0.07, T:0.45
Consensus pattern (20 bp):
ATATAAATTATATAGTTTAT
Found at i:293572 original size:13 final size:11
Alignment explanation
Indices: 293537--293574 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
293527 ATATAAATTG
*
293537 TATAGTTTATA
1 TATAATTTATA
*
293548 TATAATTCATA
1 TATAATTTATA
293559 TATAATTTATA
1 TATAATTTATA
293570 TATAA
1 TATAA
293575 ACTATGTAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (11 bp):
TATAATTTATA
Found at i:293648 original size:53 final size:53
Alignment explanation
Indices: 293599--293896 Score: 253
Period size: 53 Copynumber: 5.6 Consensus size: 53
293589 ATATAGTTCA
*
293599 ATAGTTCATATATAAACTATATAGTTCATATGTAAATTATACTATATAGTATAT
1 ATAGTTCATATGTAAACTATATAGTTCATATGTAAATTATACTATATA-TATAT
** * *
293653 ATAGTTTTTATATATAA-TATATAG-T-ATA--TAAATATAAACTATAGTATATAT
1 ATAGTTCATATGTA-AACTATATAGTTCATATGTAAAT-TATACTATA-TATATAT
* *
293704 ATAGATCATATGTAAACTATATAGTAT-ATAAATATAAA--ATA-TAGTATATATAT
1 ATAGTTCATATGTAAACTATATAGT-TCAT--ATGTAAATTATACTA-TATATATAT
* * * * * *
293757 ATAGGTCATATGTAAACTATATAGTTTATATATATA-TAGTTC-ATATATAAACT
1 ATAGTTCATATGTAAACTATATAGTTCATATGTAAATTA-TACTATATATATA-T
* *
293810 ATAGTTCATATGTAAACTATATAGTTCATATGTAAACTATATAGTTTATATATAT
1 ATAGTTCATATGTAAACTATATAGTTCATATGTAAA-T-TATACTATATATATAT
*
293865 ATAGTTGATATGTAAACTATA-A-TTCATATGTA
1 ATAGTTCATATGTAAACTATATAGTTCATATGTA
293897 TAGTATATAA
Statistics
Matches: 203, Mismatches: 21, Indels: 41
0.77 0.08 0.15
Matches are distributed among these distances:
50 7 0.03
51 36 0.18
52 14 0.07
53 84 0.41
54 24 0.12
55 25 0.12
56 9 0.04
57 4 0.02
ACGTcount: A:0.44, C:0.06, G:0.08, T:0.42
Consensus pattern (53 bp):
ATAGTTCATATGTAAACTATATAGTTCATATGTAAATTATACTATATATATAT
Found at i:293653 original size:2 final size:2
Alignment explanation
Indices: 293636--293759 Score: 63
Period size: 2 Copynumber: 58.0 Consensus size: 2
293626 ATATGTAAAT
* *
293636 TA TA CTA TA TA GTA TA TA TA GTT TT TA TA TA TA -A TA TA TA GTA
1 TA TA -TA TA TA -TA TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA
* * * * *
293679 TA TA AA TA TA AA CTA TA GTA TA TA TA TA GA TCA TA TG TA AA CTA
1 TA TA TA TA TA TA -TA TA -TA TA TA TA TA TA T-A TA TA TA TA -TA
* *
293723 TA TA GTA TA TA AA TA TA -A AA TA TA GTA TA TA TA TA TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA
293760 GGTCATATGT
Statistics
Matches: 95, Mismatches: 15, Indels: 24
0.71 0.11 0.18
Matches are distributed among these distances:
1 2 0.02
2 76 0.80
3 17 0.18
ACGTcount: A:0.48, C:0.03, G:0.06, T:0.42
Consensus pattern (2 bp):
TA
Found at i:293777 original size:20 final size:20
Alignment explanation
Indices: 293754--293896 Score: 143
Period size: 20 Copynumber: 7.8 Consensus size: 20
293744 ATAGTATATA
*
293754 TATATAGGTCATATGTAAAC
1 TATATAGTTCATATGTAAAC
*
293774 TATATAGTT--TA--TATA-
1 TATATAGTTCATATGTAAAC
*
293789 TATATAGTTCATATATAAAC
1 TATATAGTTCATATGTAAAC
293809 --TATAGTTCATATGTAAAC
1 TATATAGTTCATATGTAAAC
293827 TATATAGTTCATATGTAAAC
1 TATATAGTTCATATGTAAAC
*
293847 TATATAGTT--TA--TATA-
1 TATATAGTTCATATGTAAAC
*
293862 TATATAGTTGATATGTAAAC
1 TATATAGTTCATATGTAAAC
293882 TATA-A-TTCATATGTA
1 TATATAGTTCATATGTA
293897 TAGTATATAA
Statistics
Matches: 104, Mismatches: 7, Indels: 26
0.76 0.05 0.19
Matches are distributed among these distances:
15 18 0.17
16 6 0.06
17 4 0.04
18 30 0.29
19 7 0.07
20 39 0.38
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.43
Consensus pattern (20 bp):
TATATAGTTCATATGTAAAC
Found at i:293794 original size:35 final size:35
Alignment explanation
Indices: 293748--293885 Score: 181
Period size: 35 Copynumber: 3.9 Consensus size: 35
293738 TAAAATATAG
*
293748 TATATATATATAGGTCATATGTAAACTATATAGTT
1 TATATATATATAGTTCATATGTAAACTATATAGTT
*
293783 TATATATATATAGTTCATATATAAAC--TATAGTT
1 TATATATATATAGTTCATATGTAAACTATATAGTT
*
293816 CATATGTAAACTATATAGTTCATATGTAAACTATATAGTT
1 --TA--TATA-TATATAGTTCATATGTAAACTATATAGTT
*
293856 TATATATATATAGTTGATATGTAAACTATA
1 TATATATATATAGTTCATATGTAAACTATA
293886 ATTCATATGT
Statistics
Matches: 90, Mismatches: 6, Indels: 14
0.82 0.05 0.13
Matches are distributed among these distances:
33 7 0.08
35 49 0.54
36 3 0.03
37 3 0.03
38 21 0.23
40 7 0.08
ACGTcount: A:0.41, C:0.07, G:0.09, T:0.43
Consensus pattern (35 bp):
TATATATATATAGTTCATATGTAAACTATATAGTT
Done.