Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009018.1 Hibiscus syriacus cultivar Beakdansim tig00112408_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: 522392
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
File 1 of 2
Found at i:6897 original size:19 final size:19
Alignment explanation
Indices: 6873--6912 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
6863 AATAAATTTA
6873 ATTTAAATAAAAAATATAT
1 ATTTAAATAAAAAATATAT
* * *
6892 ATTTAATTTAAATATATAT
1 ATTTAAATAAAAAATATAT
6911 AT
1 AT
6913 ATACCCGGCC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
ATTTAAATAAAAAATATAT
Found at i:6957 original size:12 final size:12
Alignment explanation
Indices: 6913--6966 Score: 65
Period size: 12 Copynumber: 4.6 Consensus size: 12
6903 ATATATATAT
* *
6913 ATACCCGGCCCG
1 ATACCCGACCCA
* *
6925 ATTCCCGGCCCA
1 ATACCCGACCCA
6937 ATA-CCGACCCA
1 ATACCCGACCCA
6948 ATACCCGACCCA
1 ATACCCGACCCA
6960 ATACCCG
1 ATACCCG
6967 TTTAAATAAC
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
11 10 0.27
12 27 0.73
ACGTcount: A:0.26, C:0.48, G:0.15, T:0.11
Consensus pattern (12 bp):
ATACCCGACCCA
Found at i:10541 original size:17 final size:18
Alignment explanation
Indices: 10507--10545 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
10497 GGAGGTTGTC
10507 TTAAGATCCAACTTAATA
1 TTAAGATCCAACTTAATA
*
10525 TTAATATCCAA-TTAATA
1 TTAAGATCCAACTTAATA
10542 TTAA
1 TTAA
10546 ATAATGTCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.46, C:0.13, G:0.03, T:0.38
Consensus pattern (18 bp):
TTAAGATCCAACTTAATA
Found at i:13652 original size:29 final size:28
Alignment explanation
Indices: 13620--13692 Score: 76
Period size: 29 Copynumber: 2.5 Consensus size: 28
13610 AATAGTATGT
* *
13620 TAATATTTT-TCAATTATTTAATTTTTATA
1 TAATATTTTAT-AATGA-TTAATTTATATA
13649 TAATCATTTTATAATGATTAATTTATATA
1 TAAT-ATTTTATAATGATTAATTTATATA
*
13678 TTATATTTGTATAAT
1 TAATATTT-TATAAT
13693 TAATATAGTA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
28 4 0.11
29 24 0.63
30 9 0.24
31 1 0.03
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.58
Consensus pattern (28 bp):
TAATATTTTATAATGATTAATTTATATA
Found at i:14892 original size:15 final size:15
Alignment explanation
Indices: 14862--14892 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
14852 ATGAAAGTCG
*
14862 AGGAGGAGGAGGAAA
1 AGGAGGAGGAGAAAA
14877 AGGAGGAGGAGAAAA
1 AGGAGGAGGAGAAAA
14892 A
1 A
14893 AAGAAAAAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (15 bp):
AGGAGGAGGAGAAAA
Found at i:17157 original size:28 final size:30
Alignment explanation
Indices: 17126--17188 Score: 78
Period size: 28 Copynumber: 2.2 Consensus size: 30
17116 AAGATACGAG
* *
17126 TATTACAA-ATATAAATAAATTCTAAA-A-T
1 TATTAAAAGATATAAA-AAATTATAAATATT
17154 TATTAAAAGATATAAAAAATTATAAATATT
1 TATTAAAAGATATAAAAAATTATAAATATT
17184 TATTA
1 TATTA
17189 GAGTTCATGG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 16 0.53
29 8 0.27
30 6 0.20
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (30 bp):
TATTAAAAGATATAAAAAATTATAAATATT
Found at i:19571 original size:31 final size:31
Alignment explanation
Indices: 19533--19617 Score: 145
Period size: 31 Copynumber: 2.7 Consensus size: 31
19523 TTAAGCTCAC
*
19533 GAATTTTCGAGTCGAGTTGAGCTTCATTTCA
1 GAATTTTCGAGTCGAGTCGAGCTTCATTTCA
19564 -AAGTTTTCGAGTCGAGTCGAGCTTCATTTCA
1 GAA-TTTTCGAGTCGAGTCGAGCTTCATTTCA
19595 GAATTTTCGAGTCGAGTCGAGCT
1 GAATTTTCGAGTCGAGTCGAGCT
19618 CAGCACTACT
Statistics
Matches: 51, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
30 2 0.04
31 47 0.92
32 2 0.04
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.35
Consensus pattern (31 bp):
GAATTTTCGAGTCGAGTCGAGCTTCATTTCA
Found at i:21193 original size:22 final size:22
Alignment explanation
Indices: 21168--21209 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
21158 ATGTGAAATT
*
21168 TGTCCCGAATGACCTATGTATA
1 TGTCCCGAAGGACCTATGTATA
21190 TGTCCCGAAGGACCTATGTA
1 TGTCCCGAAGGACCTATGTA
21210 ACCCTCGAAT
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:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (22 bp):
TGTCCCGAAGGACCTATGTATA
Found at i:22320 original size:36 final size:35
Alignment explanation
Indices: 22280--22412 Score: 202
Period size: 31 Copynumber: 3.9 Consensus size: 35
22270 ACAGTGCTGG
*
22280 ACATTGATACACAAATGTACCAAAGCTGATATGATA
1 ACATTGATACACGAATGTACC-AAGCTGATATGATA
22316 ACATTGATACACGAATGTACCAAGCTGATATGATA
1 ACATTGATACACGAATGTACCAAGCTGATATGATA
22351 ACATTGAT----GAATGTACCAAGCTGATATGATA
1 ACATTGATACACGAATGTACCAAGCTGATATGATA
*
22382 ACATTGATACACGAATGTATCAAAGCTGATA
1 ACATTGATACACGAATGTA-CCAAGCTGATA
22413 ATACTCAACT
Statistics
Matches: 90, Mismatches: 2, Indels: 10
0.88 0.02 0.10
Matches are distributed among these distances:
31 31 0.34
35 29 0.32
36 30 0.33
ACGTcount: A:0.41, C:0.16, G:0.17, T:0.26
Consensus pattern (35 bp):
ACATTGATACACGAATGTACCAAGCTGATATGATA
Found at i:24803 original size:17 final size:17
Alignment explanation
Indices: 24781--24821 Score: 82
Period size: 17 Copynumber: 2.4 Consensus size: 17
24771 TCTCGTACCA
24781 AAAATCTGATTCCCACT
1 AAAATCTGATTCCCACT
24798 AAAATCTGATTCCCACT
1 AAAATCTGATTCCCACT
24815 AAAATCT
1 AAAATCT
24822 CTGTTTTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.39, C:0.27, G:0.05, T:0.29
Consensus pattern (17 bp):
AAAATCTGATTCCCACT
Found at i:30127 original size:22 final size:21
Alignment explanation
Indices: 30076--30128 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 21
30066 AACGATCTTG
* * *
30076 AAAGTAAAATCAAAGATTTGC
1 AAAGAAAAATAAAAGATTTGA
**
30097 AAATCAAAATAAAAGAGTTTGA
1 AAAGAAAAATAAAAGA-TTTGA
30119 AAAGAAAAAT
1 AAAGAAAAAT
30129 TTGGATTTGC
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
21 13 0.52
22 12 0.48
ACGTcount: A:0.60, C:0.06, G:0.13, T:0.21
Consensus pattern (21 bp):
AAAGAAAAATAAAAGATTTGA
Found at i:33883 original size:24 final size:23
Alignment explanation
Indices: 33855--33934 Score: 78
Period size: 24 Copynumber: 3.5 Consensus size: 23
33845 CACTTAACAA
33855 TGCATCGATGCATCCCTTTGAATG
1 TGCATCGATGCAT-CCTTTGAATG
* *
33879 TGCATCGATTCATCATGTTG-A--
1 TGCATCGATGCATCCT-TTGAATG
*
33900 TGCACCGATGCATGCC-TTGAATG
1 TGCATCGATGCAT-CCTTTGAATG
33923 TGCATCGATGCA
1 TGCATCGATGCA
33935 CAGGGTCATG
Statistics
Matches: 45, Mismatches: 6, Indels: 11
0.73 0.10 0.18
Matches are distributed among these distances:
20 3 0.07
21 12 0.27
22 1 0.02
23 14 0.31
24 15 0.33
ACGTcount: A:0.23, C:0.24, G:0.23, T:0.31
Consensus pattern (23 bp):
TGCATCGATGCATCCTTTGAATG
Found at i:36713 original size:64 final size:65
Alignment explanation
Indices: 36536--36695 Score: 252
Period size: 65 Copynumber: 2.5 Consensus size: 65
36526 GATTTAATTG
* *
36536 AACATTGAATGCATTTGATGCATCGATGCACATACCATGCATCGATGCACTCAGGGTTTTATGAA
1 AACATCGAATGCATTTGATGCATCGATGCACATACCATGCATCGATGCACTCAGGATTTTATGAA
* *
36601 AACATCGAATGCATTTGATGCATCAATGCACATACCATGCATCGATGCAGTCAGGATTTT-TCG-
1 AACATCGAATGCATTTGATGCATCGATGCACATACCATGCATCGATGCACTCAGGATTTTAT-GA
36664 A
65 A
*
36665 AACATCGAATGCATTTTATGCATCGATGCAC
1 AACATCGAATGCATTTGATGCATCGATGCAC
36696 TCTTAGTGCA
Statistics
Matches: 88, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
64 31 0.35
65 57 0.65
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (65 bp):
AACATCGAATGCATTTGATGCATCGATGCACATACCATGCATCGATGCACTCAGGATTTTATGAA
Found at i:40433 original size:22 final size:22
Alignment explanation
Indices: 40408--40449 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
40398 ATGTGAAATT
40408 TGTCCCGAATGACCTATGTATA
1 TGTCCCGAATGACCTATGTATA
40430 TGTCCCGAATGACCTATGTA
1 TGTCCCGAATGACCTATGTA
40450 ACCCTCGACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (22 bp):
TGTCCCGAATGACCTATGTATA
Found at i:44365 original size:20 final size:20
Alignment explanation
Indices: 44337--44395 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
44327 CAATGGGCCA
44337 GACCGATTCGAGTTGACTCAG
1 GACCGATTCGAGTTGACTC-G
*
44358 G-TCGATTCG-GTTGACTCG
1 GACCGATTCGAGTTGACTCG
*
44376 GACCGGTTCGAGTTGACTCG
1 GACCGATTCGAGTTGACTCG
44396 AATCGTTTCT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
18 2 0.06
19 14 0.42
20 16 0.48
21 1 0.03
ACGTcount: A:0.17, C:0.24, G:0.32, T:0.27
Consensus pattern (20 bp):
GACCGATTCGAGTTGACTCG
Found at i:46587 original size:57 final size:58
Alignment explanation
Indices: 46517--46643 Score: 141
Period size: 61 Copynumber: 2.2 Consensus size: 58
46507 CTAGACCCTG
* * *
46517 TAAACGAAC-CGAACGCACACGAACGAA-GGTATGTTCATGTTCGTTCATTTAATAAA
1 TAAACGAACACGAACACAAACGAACAAATGGTATGTTCATGTTCGTTCATTTAATAAA
* * ** *
46573 TAAACGAACACGAACATAAACGAATAAATTTTTTTTTGTTCATGTTCGTTCATTTAATAAA
1 TAAACGAACACGAACACAAACGAACAAA---TGGTATGTTCATGTTCGTTCATTTAATAAA
46634 TAAACGAACA
1 TAAACGAACA
46644 TAAATGAATA
Statistics
Matches: 58, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
56 9 0.16
57 13 0.22
61 36 0.62
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.30
Consensus pattern (58 bp):
TAAACGAACACGAACACAAACGAACAAATGGTATGTTCATGTTCGTTCATTTAATAAA
Found at i:46957 original size:14 final size:14
Alignment explanation
Indices: 46933--47006 Score: 94
Period size: 14 Copynumber: 5.1 Consensus size: 14
46923 GCCCTCTATT
*
46933 CGAATATAAATGAA
1 CGAACATAAATGAA
*
46947 CGAGCATAAATGAA
1 CGAACATAAATGAA
*
46961 CGAACGTAAATGAA
1 CGAACATAAATGAA
*
46975 CGAGCATAAATGAA
1 CGAACATAAATGAA
46989 CGAACATATAATCGAA
1 CGAACATA-AAT-GAA
47005 CG
1 CG
47007 TTCACGAACG
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
14 43 0.84
15 3 0.06
16 5 0.10
ACGTcount: A:0.50, C:0.15, G:0.19, T:0.16
Consensus pattern (14 bp):
CGAACATAAATGAA
Found at i:46973 original size:28 final size:28
Alignment explanation
Indices: 46939--46993 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
46929 TATTCGAATA
46939 TAAATGAACGAGCATAAATGAACGAACG
1 TAAATGAACGAGCATAAATGAACGAACG
46967 TAAATGAACGAGCATAAATGAACGAAC
1 TAAATGAACGAGCATAAATGAACGAAC
46994 ATATAATCGA
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:0.51, C:0.15, G:0.20, T:0.15
Consensus pattern (28 bp):
TAAATGAACGAGCATAAATGAACGAACG
Found at i:47797 original size:2 final size:2
Alignment explanation
Indices: 47790--47815 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
47780 AATATGTGTT
47790 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
47816 TGAAATAACT
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:50474 original size:51 final size:48
Alignment explanation
Indices: 50359--50480 Score: 120
Period size: 51 Copynumber: 2.4 Consensus size: 48
50349 TGGGTTTATT
* * *
50359 TAAATAATATTTTTATTTAAACTTATAATATCAAGATAACAAATGTTAA
1 TAAAAAATATTTTTA-TTAAACTTATAACATCAAGATAAAAAATGTTAA
* * *
50408 TAAAATATAATTTTTTATTAAATTTTATCACATCAGAGATAAAAAAAT-TTAAA
1 TAAAAAAT-A-TTTTTATTAAA-CTTATAACATCA-AGAT-AAAAAATGTT-AA
50461 TAAAAAATATTTTTATTAAA
1 TAAAAAATATTTTTATTAAA
50481 ACTCGTCACA
Statistics
Matches: 60, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
49 6 0.10
50 6 0.10
51 26 0.43
52 7 0.12
53 15 0.25
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (48 bp):
TAAAAAATATTTTTATTAAACTTATAACATCAAGATAAAAAATGTTAA
Found at i:76165 original size:61 final size:64
Alignment explanation
Indices: 76053--76199 Score: 201
Period size: 61 Copynumber: 2.3 Consensus size: 64
76043 TAGCAGGTTT
* *
76053 ATATTAGCACTAGTGTGTAAGGACACTAGGTGCAGGTGGTGGGCACAACCTTATGTTTCATATCC
1 ATATTAGCACTAGAGTGTAA-GACACTAGGTGCAGGTGGTGGGCACAACCTTATGTGTCATATCC
* * *
76118 ATATCAGCACTAGAGTGTAA-AC-CTA-GTGTAGGTGGTGGGCACGACCTTATGTGTCATATCC
1 ATATTAGCACTAGAGTGTAAGACACTAGGTGCAGGTGGTGGGCACAACCTTATGTGTCATATCC
* *
76179 AGATTAGCACTAGAGGGTAAG
1 ATATTAGCACTAGAGTGTAAG
76200 CTCAGTGCAA
Statistics
Matches: 73, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
61 50 0.68
62 3 0.04
63 2 0.03
65 18 0.25
ACGTcount: A:0.28, C:0.18, G:0.27, T:0.27
Consensus pattern (64 bp):
ATATTAGCACTAGAGTGTAAGACACTAGGTGCAGGTGGTGGGCACAACCTTATGTGTCATATCC
Found at i:84058 original size:21 final size:21
Alignment explanation
Indices: 84034--84089 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
84024 CGAAAAATGA
*
84034 AGCAAGGGAAGCAGAGAGAGC
1 AGCAAGGGAAGCAGACAGAGC
* *
84055 AGCAATGGAAGCAGCCAGAGC
1 AGCAAGGGAAGCAGACAGAGC
84076 AGC-AGTGGAAGCAG
1 AGCAAG-GGAAGCAG
84090 TTGCAGCACA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 1 0.03
21 29 0.97
ACGTcount: A:0.39, C:0.18, G:0.39, T:0.04
Consensus pattern (21 bp):
AGCAAGGGAAGCAGACAGAGC
Found at i:84549 original size:44 final size:43
Alignment explanation
Indices: 84448--84566 Score: 114
Period size: 44 Copynumber: 2.7 Consensus size: 43
84438 TTATGTGTTA
**
84448 TTTAGCGGCGTTTGTAACAAAAAACGCTGCTATATACCGGTCC
1 TTTAGCGGCGTTTGTAACAAAAAACGCTGCTATATACCAATCC
** * * * *
84491 TTTAGCATCGTTTGTATCCTAAAAACGCTGGTATATAGCAATCC
1 TTTAGCGGCGTTTGTA-ACAAAAAACGCTGCTATATACCAATCC
* * *
84535 TTTAGCGGCATTTGTGGA-AAAAAACGCCGCTA
1 TTTAGCGGCGTTTGT-AACAAAAAACGCTGCTA
84567 AATCTCAACA
Statistics
Matches: 58, Mismatches: 16, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
43 25 0.43
44 33 0.57
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.29
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTAACAAAAAACGCTGCTATATACCAATCC
Found at i:84633 original size:43 final size:44
Alignment explanation
Indices: 84554--84662 Score: 125
Period size: 43 Copynumber: 2.5 Consensus size: 44
84544 ATTTGTGGAA
* *
84554 AAAAACGCCGCTAAATC-TCAAC-ACTTATTGCAGCGTTTGCGAT
1 AAAAACGCCGCTAAA-CATCAACAACTTACTGCAGCGTTTGCGAG
** * *
84597 AAAAACGCCGCTAAACATCAACAAC-TACTGTGGCGTTTGTGGG
1 AAAAACGCCGCTAAACATCAACAACTTACTGCAGCGTTTGCGAG
*
84640 AAAAATGCCGCTAAACATCAACA
1 AAAAACGCCGCTAAACATCAACA
84663 CCTAATACAA
Statistics
Matches: 57, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
42 1 0.02
43 54 0.95
44 2 0.04
ACGTcount: A:0.37, C:0.25, G:0.17, T:0.21
Consensus pattern (44 bp):
AAAAACGCCGCTAAACATCAACAACTTACTGCAGCGTTTGCGAG
Found at i:85015 original size:25 final size:25
Alignment explanation
Indices: 84960--85015 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 25
84950 ATTTATGTAC
* **
84960 GTATATCATACCTACATACATGTAT
1 GTATATCATACATACATACATACAT
** *
84985 CAATATCATATATACATACATACAT
1 GTATATCATACATACATACATACAT
85010 GTATAT
1 GTATAT
85016 ATGAATAAAT
Statistics
Matches: 23, Mismatches: 8, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.41, C:0.18, G:0.05, T:0.36
Consensus pattern (25 bp):
GTATATCATACATACATACATACAT
Found at i:86461 original size:31 final size:31
Alignment explanation
Indices: 86423--86547 Score: 207
Period size: 31 Copynumber: 4.0 Consensus size: 31
86413 CCCGAAGGAC
* * *
86423 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
86454 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
86485 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
86516 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
86547 C
1 C
86548 CCTTGACCCT
Statistics
Matches: 90, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
31 89 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:88656 original size:41 final size:41
Alignment explanation
Indices: 88586--88668 Score: 112
Period size: 41 Copynumber: 2.0 Consensus size: 41
88576 ATTGTAATTA
* *
88586 ATATAGAAAGTAAATTTATTAACCAAATAATCATTATTAAT
1 ATATAGAAAGTAAATATATTAACCAAATAATCATAATTAAT
* * * *
88627 ATATAGAAAGTAAATATATTGATCTAATAATTATAATTAAT
1 ATATAGAAAGTAAATATATTAACCAAATAATCATAATTAAT
88668 A
1 A
88669 AATTATTCTA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.52, C:0.05, G:0.06, T:0.37
Consensus pattern (41 bp):
ATATAGAAAGTAAATATATTAACCAAATAATCATAATTAAT
Found at i:91875 original size:25 final size:25
Alignment explanation
Indices: 91837--91904 Score: 129
Period size: 25 Copynumber: 2.8 Consensus size: 25
91827 TTTATTTTTG
91837 TTTC-TTAAAATTTTATAAACTATT
1 TTTCTTTAAAATTTTATAAACTATT
91861 TTTCTTTAAAATTTTATAAACTATT
1 TTTCTTTAAAATTTTATAAACTATT
91886 TTTCTTTAAAATTTTATAA
1 TTTCTTTAAAATTTTATAA
91905 GTTTATCTCT
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
24 4 0.09
25 39 0.91
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.56
Consensus pattern (25 bp):
TTTCTTTAAAATTTTATAAACTATT
Found at i:99462 original size:21 final size:20
Alignment explanation
Indices: 99433--99472 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
99423 CATTGCAGGA
99433 ATTTATGGCCTCAACAAAAG
1 ATTTATGGCCTCAACAAAAG
*
99453 ATTTAATGGCTTCAACAAAA
1 ATTT-ATGGCCTCAACAAAA
99473 ACCTTGATGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.42, C:0.17, G:0.12, T:0.28
Consensus pattern (20 bp):
ATTTATGGCCTCAACAAAAG
Found at i:99940 original size:15 final size:15
Alignment explanation
Indices: 99917--99953 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
99907 TAATGTGAGA
*
99917 CCTCCACCACCGTTC
1 CCTCAACCACCGTTC
99932 CCTCAACCACCGTTC
1 CCTCAACCACCGTTC
99947 CCTCAAC
1 CCTCAAC
99954 GATTGAAGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.19, C:0.57, G:0.05, T:0.19
Consensus pattern (15 bp):
CCTCAACCACCGTTC
Found at i:110748 original size:18 final size:18
Alignment explanation
Indices: 110725--110781 Score: 96
Period size: 18 Copynumber: 3.2 Consensus size: 18
110715 AAACCGTCAC
*
110725 AGAGTGAAGGATTTGCAT
1 AGAGTGGAGGATTTGCAT
*
110743 AGAGTGGAGGATTTGCAC
1 AGAGTGGAGGATTTGCAT
110761 AGAGTGGAGGATTTGCAT
1 AGAGTGGAGGATTTGCAT
110779 AGA
1 AGA
110782 CTATCAAAAG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.32, C:0.07, G:0.37, T:0.25
Consensus pattern (18 bp):
AGAGTGGAGGATTTGCAT
Found at i:122860 original size:21 final size:21
Alignment explanation
Indices: 122807--122861 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
122797 TACTTTGGGA
122807 AGTATCGATACTCTCATATAG
1 AGTATCGATACTCTCATATAG
* *
122828 AGGTTTCAATACT-TCATATAGG
1 A-GTATCGATACTCTCATATA-G
122850 AGTATCGATACT
1 AGTATCGATACT
122862 AGGAGAAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
21 17 0.61
22 11 0.39
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (21 bp):
AGTATCGATACTCTCATATAG
Found at i:128993 original size:31 final size:31
Alignment explanation
Indices: 128958--129061 Score: 102
Period size: 31 Copynumber: 3.3 Consensus size: 31
128948 TCATAATTAG
128958 ATGATCATTTATATAGTTTACCCTTAAAAAT
1 ATGATCATTTATATAGTTTACCCTTAAAAAT
* * * ** *
128989 ATGATCATCATATCAATA-TTAATCCTATAATTAG
1 ATGATCAT-TTAT--ATAGTTTACCCT-TAAAAAT
*
129023 ATGATCATTCATATAGTTTACCCTTAAAAAT
1 ATGATCATTTATATAGTTTACCCTTAAAAAT
129054 ATGATCAT
1 ATGATCAT
129062 CATATCAATA
Statistics
Matches: 55, Mismatches: 13, Indels: 10
0.71 0.17 0.13
Matches are distributed among these distances:
31 23 0.42
32 9 0.16
33 8 0.15
34 15 0.27
ACGTcount: A:0.39, C:0.14, G:0.07, T:0.39
Consensus pattern (31 bp):
ATGATCATTTATATAGTTTACCCTTAAAAAT
Found at i:129019 original size:65 final size:65
Alignment explanation
Indices: 128944--129095 Score: 263
Period size: 65 Copynumber: 2.4 Consensus size: 65
128934 TATTGACACA
*
128944 AATCTCATAATTAGATGATCATTTATATAGTTTACCCTTAAAAATATGATCATCATATCAATATT
1 AATCCCATAATTAGATGATCATTTATATAGTTTACCCTTAAAAATATGATCATCATATCAATATT
* *
129009 AATCCTATAATTAGATGATCATTCATATAGTTTACCCTTAAAAATATGATCATCATATCAATATT
1 AATCCCATAATTAGATGATCATTTATATAGTTTACCCTTAAAAATATGATCATCATATCAATATT
129074 AATCCCATAATTA-AT-ATCATTT
1 AATCCCATAATTAGATGATCATTT
129096 GAGCAATTTA
Statistics
Matches: 82, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
63 6 0.07
64 2 0.02
65 74 0.90
ACGTcount: A:0.40, C:0.15, G:0.05, T:0.39
Consensus pattern (65 bp):
AATCCCATAATTAGATGATCATTTATATAGTTTACCCTTAAAAATATGATCATCATATCAATATT
Found at i:129027 original size:34 final size:33
Alignment explanation
Indices: 128989--129093 Score: 103
Period size: 31 Copynumber: 3.2 Consensus size: 33
128979 CCTTAAAAAT
128989 ATGATCATCATATCAATATTAATCCTATAATTA
1 ATGATCATCATATCAATATTAATCCTATAATTA
* * **
129022 GATGATCATTCATAT-AGT-TT-ACCCT-TAAAAA
1 -ATGATCA-TCATATCAATATTAATCCTATAATTA
*
129053 TATGATCATCATATCAATATTAATCCCATAATTA
1 -ATGATCATCATATCAATATTAATCCTATAATTA
129087 AT-ATCAT
1 ATGATCAT
129094 TTGAGCAATT
Statistics
Matches: 56, Mismatches: 10, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
30 6 0.11
31 13 0.23
32 11 0.20
33 7 0.12
34 13 0.23
35 6 0.11
ACGTcount: A:0.41, C:0.16, G:0.05, T:0.38
Consensus pattern (33 bp):
ATGATCATCATATCAATATTAATCCTATAATTA
Found at i:129119 original size:65 final size:64
Alignment explanation
Indices: 128944--129112 Score: 191
Period size: 65 Copynumber: 2.6 Consensus size: 64
128934 TATTGACACA
* * * **
128944 AATCTCATAATTAGATGATCATTTATATAGTTTACCCTTAAAAATATGATCATCATATCAATATT
1 AATCCCATAATTAGATGATCA-TTATACAATTTACCCAAAAAAATATGATCATCATATCAATATT
* * * **
129009 AATCCTATAATTAGATGATCATTCATATAGTTTACCCTTAAAAATATGATCATCATATCAATATT
1 AATCCCATAATTAGATGATCATT-ATACAATTTACCCAAAAAAATATGATCATCATATCAATATT
129074 AATCCCATAATTA-AT-ATCATT-TGAGCAATTTACCCAAAA
1 AATCCCATAATTAGATGATCATTAT-A-CAATTTACCCAAAA
129113 TAAAATAGGC
Statistics
Matches: 94, Mismatches: 7, Indels: 8
0.86 0.06 0.07
Matches are distributed among these distances:
61 1 0.01
62 1 0.01
63 16 0.17
64 4 0.04
65 72 0.77
ACGTcount: A:0.41, C:0.16, G:0.06, T:0.37
Consensus pattern (64 bp):
AATCCCATAATTAGATGATCATTATACAATTTACCCAAAAAAATATGATCATCATATCAATATT
Found at i:135811 original size:18 final size:16
Alignment explanation
Indices: 135788--135836 Score: 55
Period size: 18 Copynumber: 2.9 Consensus size: 16
135778 ATGAAAAATC
135788 TTTAATTAAAAAATAA
1 TTTAATTAAAAAATAA
135804 CTTTTAATTAAAATAA-AA
1 --TTTAATTAAAA-AATAA
135822 TTTAATTACAAAAAT
1 TTTAATTA-AAAAAT
135837 TTCATTCATA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
16 10 0.36
17 3 0.11
18 13 0.46
19 2 0.07
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (16 bp):
TTTAATTAAAAAATAA
Found at i:138269 original size:239 final size:239
Alignment explanation
Indices: 137846--138327 Score: 912
Period size: 239 Copynumber: 2.0 Consensus size: 239
137836 AATTCATATG
*
137846 TCAT-AATTTCATTTAAGCACATGAATTTTTCCCATATAGCTCATCTTGCATATTCGTATTATTA
1 TCATAAATTTCATTTAAGCACATGAATTTTTCCCATATAGCTCATCTTACATATTCGTATTATTA
* * *
137910 TTTATGTATATGTCTCCTAATTGATATATTATTTTCCTATTATTTTATAGGTCCATACTACTTAT
66 TTTATGTACATGTCTCCTAATTGATATATTATTTTCCTATTATTCTATAAGTCCATACTACTTAT
137975 CTTATCTCACTTCTCATTTAATCATATAATTCCATTATATTAGTTCTCATAGATTATCACACCAC
131 CTTATCTCACTTCTCATTTAATCATATAATTCCATTATATTAGTTCTCATAGATTATCACACCAC
*
138040 CATGTACTTTCTTAATTCATGTTCATATTATTTATATCACATTT
196 CATGTACTTGCTTAATTCATGTTCATATTATTTATATCACATTT
138084 TCATAAATTTCATTTAAGCACATGAATTTTTCCCATATAGCTCATCTTACATATTCGTATTATTA
1 TCATAAATTTCATTTAAGCACATGAATTTTTCCCATATAGCTCATCTTACATATTCGTATTATTA
138149 TTTATGTACATGTCTCCTAATTGATATATTATTTTCCTATTATTCTATAAGTCCATACTACTTAT
66 TTTATGTACATGTCTCCTAATTGATATATTATTTTCCTATTATTCTATAAGTCCATACTACTTAT
138214 CTTATCTCACTTCTCATTTAATCATATAATTCCATTATATTAGTTCTCATAGATTATCACACCAC
131 CTTATCTCACTTCTCATTTAATCATATAATTCCATTATATTAGTTCTCATAGATTATCACACCAC
138279 CATGTACTTGCTTAATTCATGTTCATATTATTTATATCACATTT
196 CATGTACTTGCTTAATTCATGTTCATATTATTTATATCACATTT
138323 TCATA
1 TCATA
138328 TACTTACCTA
Statistics
Matches: 238, Mismatches: 5, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
238 4 0.02
239 234 0.98
ACGTcount: A:0.29, C:0.19, G:0.06, T:0.46
Consensus pattern (239 bp):
TCATAAATTTCATTTAAGCACATGAATTTTTCCCATATAGCTCATCTTACATATTCGTATTATTA
TTTATGTACATGTCTCCTAATTGATATATTATTTTCCTATTATTCTATAAGTCCATACTACTTAT
CTTATCTCACTTCTCATTTAATCATATAATTCCATTATATTAGTTCTCATAGATTATCACACCAC
CATGTACTTGCTTAATTCATGTTCATATTATTTATATCACATTT
Found at i:156238 original size:25 final size:25
Alignment explanation
Indices: 156212--156325 Score: 115
Period size: 26 Copynumber: 4.4 Consensus size: 25
156202 AATGAATAAG
*
156212 TTTTGAAAAATGCTTGAT-AAAGAA
1 TTTTGAAAAATGTTTGATGAAAGAA
** *
156236 GTTTTGAAAAAAATTTGATGAAAAAAA
1 -TTTTGAAAAATGTTTGATG-AAAGAA
156263 TTTTGAAAAATGTTTGATGAAA-ATA
1 TTTTGAAAAATGTTTGATGAAAGA-A
*
156288 TTTTGAAAAAATTGTTTGATAAAAGAA
1 TTTTG-AAAAA-TGTTTGATGAAAGAA
*
156315 TTTTTAAAAAT
1 TTTTGAAAAAT
156326 ATTTCCCCTT
Statistics
Matches: 75, Mismatches: 8, Indels: 12
0.79 0.08 0.13
Matches are distributed among these distances:
24 1 0.01
25 25 0.33
26 27 0.36
27 21 0.28
28 1 0.01
ACGTcount: A:0.48, C:0.01, G:0.14, T:0.37
Consensus pattern (25 bp):
TTTTGAAAAATGTTTGATGAAAGAA
Found at i:156246 original size:26 final size:26
Alignment explanation
Indices: 156212--156324 Score: 110
Period size: 27 Copynumber: 4.4 Consensus size: 26
156202 AATGAATAAG
*
156212 TTTTG-AAAAATGCTTGAT-AAAGAA
1 TTTTGAAAAAATGTTTGATGAAAGAA
* *
156236 GTTTTGAAAAAA-ATTTGATGAAAAAAA
1 -TTTTGAAAAAATGTTTGATG-AAAGAA
156263 TTTTG-AAAAATGTTTGATGAAA-ATA
1 TTTTGAAAAAATGTTTGATGAAAGA-A
*
156288 TTTTGAAAAAATTGTTTGATAAAAGAA
1 TTTTGAAAAAA-TGTTTGATGAAAGAA
*
156315 TTTTTAAAAA
1 TTTTGAAAAA
156325 TATTTCCCCT
Statistics
Matches: 74, Mismatches: 6, Indels: 14
0.79 0.06 0.15
Matches are distributed among these distances:
24 1 0.01
25 24 0.32
26 22 0.30
27 26 0.35
28 1 0.01
ACGTcount: A:0.49, C:0.01, G:0.14, T:0.36
Consensus pattern (26 bp):
TTTTGAAAAAATGTTTGATGAAAGAA
Found at i:156251 original size:51 final size:51
Alignment explanation
Indices: 156194--156325 Score: 137
Period size: 51 Copynumber: 2.6 Consensus size: 51
156184 TTTTATTTTC
* *
156194 AAAATTTGAATG-AATAAGTTTTGAAAAATGCTTGAT-AAAGA-AGTTTTGAAA
1 AAAATTTG-ATGAAAAAAATTTTGAAAAATGCTTGATGAAA-ATA-TTTTGAAA
*
156245 AAAATTTGATGAAAAAAATTTTGAAAAATGTTTGATGAAAATATTTTGAAA
1 AAAATTTGATGAAAAAAATTTTGAAAAATGCTTGATGAAAATATTTTGAAA
* * *
156296 AAATTGTTTGAT-AAAAGAATTTTTAAAAAT
1 AAA--ATTTGATGAAAAAAATTTTGAAAAAT
156326 ATTTCCCCTT
Statistics
Matches: 70, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
50 3 0.04
51 41 0.59
52 20 0.29
53 6 0.09
ACGTcount: A:0.49, C:0.01, G:0.14, T:0.36
Consensus pattern (51 bp):
AAAATTTGATGAAAAAAATTTTGAAAAATGCTTGATGAAAATATTTTGAAA
Found at i:156257 original size:14 final size:14
Alignment explanation
Indices: 156240--156285 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
156230 AAAGAAGTTT
156240 TGAAAAAAATTTGA
1 TGAAAAAAATTTGA
156254 TGAAAAAAATTT--
1 TGAAAAAAATTTGA
**
156266 TGAAAAATGTTTGA
1 TGAAAAAAATTTGA
156280 TGAAAA
1 TGAAAA
156286 TATTTTGAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
12 10 0.36
14 18 0.64
ACGTcount: A:0.54, C:0.00, G:0.15, T:0.30
Consensus pattern (14 bp):
TGAAAAAAATTTGA
Found at i:156305 original size:13 final size:12
Alignment explanation
Indices: 156237--156329 Score: 55
Period size: 13 Copynumber: 7.2 Consensus size: 12
156227 GATAAAGAAG
156237 TTTTGAAAAAAAT
1 TTTTG-AAAAAAT
* *
156250 TTGATGAAAAAAA
1 TT-TTGAAAAAAT
156263 TTTTG-AAAAAT
1 TTTTGAAAAAAT
* *
156274 GTTTGATGAAAAT
1 TTTTGA-AAAAAT
156287 ATTTTGAAAAAAT
1 -TTTTGAAAAAAT
156300 TGTTTGATAAAAGAAT
1 T-TTTG--AAAA-AAT
156316 TTTT-AAAAATAT
1 TTTTGAAAAA-AT
156328 TT
1 TT
156330 CCCCTTATTT
Statistics
Matches: 63, Mismatches: 8, Indels: 19
0.70 0.09 0.21
Matches are distributed among these distances:
11 10 0.16
12 11 0.17
13 24 0.38
14 7 0.11
15 7 0.11
16 4 0.06
ACGTcount: A:0.48, C:0.00, G:0.12, T:0.40
Consensus pattern (12 bp):
TTTTGAAAAAAT
Found at i:159403 original size:19 final size:19
Alignment explanation
Indices: 159379--159421 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
159369 ACATCTGTAG
159379 CATGGGCAGCATGGTCCAA
1 CATGGGCAGCATGGTCCAA
* *
159398 CATGGGCGGCATGGTGCAA
1 CATGGGCAGCATGGTCCAA
159417 CATGG
1 CATGG
159422 CCTGTGCAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.23, C:0.23, G:0.37, T:0.16
Consensus pattern (19 bp):
CATGGGCAGCATGGTCCAA
Found at i:165441 original size:63 final size:62
Alignment explanation
Indices: 165366--165524 Score: 201
Period size: 63 Copynumber: 2.5 Consensus size: 62
165356 TGTGTTGAAG
* ** * * *
165366 GTGCATCGATGCATATTGAGTGCATCGATGCATTAATTTTAATACAAACATCGAATGTCGTCA
1 GTGCATCGATGCATA-GGAGTGCATCGATGCATTAATAATAAAACAAACATCGAATGCCCTCA
** **
165429 GTGCATCGATGCATAAGGAGTGCATCGATGCATTTCTAATAAAATGAACATCGAATGCCCTCA
1 GTGCATCGATGCAT-AGGAGTGCATCGATGCATTAATAATAAAACAAACATCGAATGCCCTCA
165492 GTGCATCGATGCATCAGGAGTGCATCGATGCAT
1 GTGCATCGATGCAT-AGGAGTGCATCGATGCAT
165525 GCCTCCATTA
Statistics
Matches: 84, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
63 83 0.99
64 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (62 bp):
GTGCATCGATGCATAGGAGTGCATCGATGCATTAATAATAAAACAAACATCGAATGCCCTCA
Found at i:167080 original size:23 final size:23
Alignment explanation
Indices: 167047--167091 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
167037 ATTATTATAT
*
167047 GGCACTACGGTACAATTCTACGC
1 GGCACTACGGTACAATTATACGC
* *
167070 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTACAATTATACG
167092 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.24
Consensus pattern (23 bp):
GGCACTACGGTACAATTATACGC
Found at i:170529 original size:63 final size:62
Alignment explanation
Indices: 170454--170612 Score: 192
Period size: 63 Copynumber: 2.5 Consensus size: 62
170444 TGTGTTGAAG
* ** * * *
170454 GTGCATCGATGCATATTGAGTGCATCGATGCATTAATTTTAATACAAACATCGAATGTCGACA
1 GTGCATCGATGCATA-GGAGTGCATCGATGCATTAATAATAAAACAAACATCGAATGCCCACA
** ** *
170517 GTGCATCGATGCATAAGGAGTGCATCGATGCATTTCTAATAAAATGAACATCGAATGCCCTCA
1 GTGCATCGATGCAT-AGGAGTGCATCGATGCATTAATAATAAAACAAACATCGAATGCCCACA
170580 GTGCATCGATGCATCAGGAGTGCATCGATGCAT
1 GTGCATCGATGCAT-AGGAGTGCATCGATGCAT
170613 GCCTCCATTA
Statistics
Matches: 83, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
63 82 0.99
64 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.27
Consensus pattern (62 bp):
GTGCATCGATGCATAGGAGTGCATCGATGCATTAATAATAAAACAAACATCGAATGCCCACA
Found at i:172176 original size:23 final size:23
Alignment explanation
Indices: 172143--172187 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
172133 ATTATTATAT
*
172143 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
*
172166 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTATACG
172188 AGCTGTGGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.22, C:0.27, G:0.27, T:0.24
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:175621 original size:63 final size:62
Alignment explanation
Indices: 175546--175704 Score: 201
Period size: 63 Copynumber: 2.5 Consensus size: 62
175536 TGTGTTGAAG
* ** * * *
175546 GTGCATCGATGCATATTGAGTGCATCGATGCATTAATTTTAATACAAACATCGAATGTCGTCA
1 GTGCATCGATGCATA-GGAGTGCATCGATGCATTAATAATAAAACAAACATCGAATGCCCTCA
** **
175609 GTGCATCGATGCATAAGGAGTGCATCGATGCATTTCTAATAAAATGAACATCGAATGCCCTCA
1 GTGCATCGATGCAT-AGGAGTGCATCGATGCATTAATAATAAAACAAACATCGAATGCCCTCA
175672 GTGCATCGATGCATCAGGAGTGCATCGATGCAT
1 GTGCATCGATGCAT-AGGAGTGCATCGATGCAT
175705 GCCTCCATTA
Statistics
Matches: 84, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
63 83 0.99
64 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (62 bp):
GTGCATCGATGCATAGGAGTGCATCGATGCATTAATAATAAAACAAACATCGAATGCCCTCA
Found at i:177262 original size:23 final size:23
Alignment explanation
Indices: 177235--177279 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
177225 ATTATTATAT
177235 GGCACTAT-GGTGCAATTCTACGC
1 GGCACT-TCGGTGCAATTCTACGC
*
177258 GGCACTTCGGTGCAATTTTACG
1 GGCACTTCGGTGCAATTCTACG
177280 AGCTGTGGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 1 0.05
23 19 0.95
ACGTcount: A:0.20, C:0.24, G:0.27, T:0.29
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGC
Found at i:180306 original size:13 final size:12
Alignment explanation
Indices: 180277--180310 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
180267 TAATGGGCGT
*
180277 TTTTGAAAACCA
1 TTTTGAAAACAA
180289 TTTTGAAAACAA
1 TTTTGAAAACAA
180301 TGTTTGAAAA
1 T-TTTGAAAA
180311 ATCATAATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 12 0.60
13 8 0.40
ACGTcount: A:0.44, C:0.09, G:0.12, T:0.35
Consensus pattern (12 bp):
TTTTGAAAACAA
Found at i:187056 original size:115 final size:115
Alignment explanation
Indices: 186844--187058 Score: 279
Period size: 115 Copynumber: 1.9 Consensus size: 115
186834 TTCAATTTAA
* * * * * *
186844 TTTGCCTTTGTTTGGCTATCTGAAGGAATATATCCATAAAACCATGACTTTTAACCAATTGCTTT
1 TTTGCCATTATTTGGCTAGCTAAAGGAATATATCCATAAAACCAAGACTTTTAACCAACTGCTTT
* * * **
186909 AGCAGAATATCTCAGCTTTATTGTATGTATATGTATAGTTTTTCTTTTTC
66 AGCAGAATAGCTCAGCTATATTATATACATATGTATAGTTTTTCTTTTTC
* * *
186959 TTTGCCATTATTTGGCTAGCTAAAGGAATTTATCCATAAAGCCAAGGCTTTTAACCAACTGCTTT
1 TTTGCCATTATTTGGCTAGCTAAAGGAATATATCCATAAAACCAAGACTTTTAACCAACTGCTTT
*
187024 AG-TGAAATAGCTCAGCTATATTATATACATATGTA
66 AGCAG-AATAGCTCAGCTATATTATATACATATGTA
187059 ATTACATTAA
Statistics
Matches: 84, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
114 1 0.01
115 83 0.99
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.40
Consensus pattern (115 bp):
TTTGCCATTATTTGGCTAGCTAAAGGAATATATCCATAAAACCAAGACTTTTAACCAACTGCTTT
AGCAGAATAGCTCAGCTATATTATATACATATGTATAGTTTTTCTTTTTC
Found at i:194655 original size:2 final size:2
Alignment explanation
Indices: 194648--194672 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
194638 AAAGAAATTC
194648 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
194673 ACTTAAAATT
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:195514 original size:24 final size:25
Alignment explanation
Indices: 195450--195518 Score: 70
Period size: 24 Copynumber: 2.7 Consensus size: 25
195440 ATTTCTCGTT
*
195450 TTTCTTTTTCTGTTCTATTTTTTATT
1 TTTCTTTTTCTGTTCT-TTTTTTATC
**
195476 TTTGCTCGATT-TGTTCTTTTTTT-TC
1 TTT-CT-TTTTCTGTTCTTTTTTTATC
195501 TTTCTTTTTCTGTTCTTT
1 TTTCTTTTTCTGTTCTTT
195519 GATTGATGAT
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
23 2 0.06
24 10 0.29
25 4 0.11
26 9 0.26
27 8 0.23
28 2 0.06
ACGTcount: A:0.04, C:0.14, G:0.07, T:0.74
Consensus pattern (25 bp):
TTTCTTTTTCTGTTCTTTTTTTATC
Found at i:197212 original size:20 final size:20
Alignment explanation
Indices: 197187--197224 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
197177 TTTGGTTCAC
197187 GGAATGTAAAATTACCAGTG
1 GGAATGTAAAATTACCAGTG
*
197207 GGAATGTAAGATTACCAG
1 GGAATGTAAAATTACCAG
197225 ATAATAGGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.11, G:0.26, T:0.24
Consensus pattern (20 bp):
GGAATGTAAAATTACCAGTG
Found at i:197429 original size:2 final size:2
Alignment explanation
Indices: 197422--197448 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
197412 TCATAAAATT
197422 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
197449 TTACAAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:199012 original size:35 final size:37
Alignment explanation
Indices: 198942--199014 Score: 98
Period size: 35 Copynumber: 2.0 Consensus size: 37
198932 GTTAGAAAAT
*
198942 ATTTATATATTTTCTTTAAAAAAATTAAATTTATAAA
1 ATTTATATATTTTCTTTAAAAAAATTAAATATATAAA
*
198979 ATTTATATATTTT-TTT-ACAAAATTGAAA-ATATAAA
1 ATTTATATATTTTCTTTAAAAAAATT-AAATATATAAA
199014 A
1 A
199015 AGGTTTAATG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
35 14 0.42
36 6 0.18
37 13 0.39
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAAATTAAATATATAAA
Found at i:199352 original size:3 final size:3
Alignment explanation
Indices: 199344--199377 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
199334 TTTGTCCCAT
199344 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
199378 AAAAAATAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:199435 original size:21 final size:20
Alignment explanation
Indices: 199409--199448 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
199399 TTAATTTTAT
199409 AGGCCCAGATCCAGAACCCGG
1 AGGCCCAGATCCAG-ACCCGG
*
199430 AGGCCCAGATCTAGACCCG
1 AGGCCCAGATCCAGACCCG
199449 ACCCAACACC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.28, C:0.38, G:0.28, T:0.07
Consensus pattern (20 bp):
AGGCCCAGATCCAGACCCGG
Found at i:199512 original size:23 final size:23
Alignment explanation
Indices: 199481--199530 Score: 91
Period size: 23 Copynumber: 2.2 Consensus size: 23
199471 TTAGCATCTT
*
199481 CTCCGCCGCCTCTACTCCAACTG
1 CTCCACCGCCTCTACTCCAACTG
199504 CTCCACCGCCTCTACTCCAACTG
1 CTCCACCGCCTCTACTCCAACTG
199527 CTCC
1 CTCC
199531 GCCGTCATGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.14, C:0.54, G:0.10, T:0.22
Consensus pattern (23 bp):
CTCCACCGCCTCTACTCCAACTG
Found at i:199973 original size:22 final size:22
Alignment explanation
Indices: 199945--199986 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
199935 GACCGACAGC
199945 CGGAATAGTGACCGACGGTGGT
1 CGGAATAGTGACCGACGGTGGT
*
199967 CGGAATAGTGACCGGCGGTG
1 CGGAATAGTGACCGACGGTG
199987 ACCGACTGGT
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:0.21, C:0.19, G:0.43, T:0.17
Consensus pattern (22 bp):
CGGAATAGTGACCGACGGTGGT
Found at i:203171 original size:6 final size:6
Alignment explanation
Indices: 203118--203163 Score: 65
Period size: 6 Copynumber: 7.3 Consensus size: 6
203108 ATTCTTATTG
*
203118 TTACAT TTACATAT TTACAT TTACAT TTACAT TTACAT TTGCAT TT
1 TTACAT TTAC--AT TTACAT TTACAT TTACAT TTACAT TTACAT TT
203164 TTCATTTTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
6 31 0.84
8 6 0.16
ACGTcount: A:0.30, C:0.15, G:0.02, T:0.52
Consensus pattern (6 bp):
TTACAT
Found at i:205962 original size:9 final size:9
Alignment explanation
Indices: 205948--205988 Score: 59
Period size: 9 Copynumber: 4.8 Consensus size: 9
205938 ACTTGAAGAA
205948 GAAAAAAAG
1 GAAAAAAAG
*
205957 GAAAAAAAA
1 GAAAAAAAG
205966 GAAAAAAA-
1 GAAAAAAAG
205974 G-AAAAAAG
1 GAAAAAAAG
205982 GAAAAAA
1 GAAAAAA
205989 GAAAAAATTG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
7 6 0.21
8 2 0.07
9 21 0.72
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (9 bp):
GAAAAAAAG
Found at i:205963 original size:8 final size:8
Alignment explanation
Indices: 205946--205995 Score: 66
Period size: 8 Copynumber: 6.1 Consensus size: 8
205936 ATACTTGAAG
205946 AAGAAAAA
1 AAGAAAAA
205954 AAGGAAAAAA
1 AA-G-AAAAA
205964 AAGAAAAA
1 AAGAAAAA
205972 AAG-AAAA
1 AAGAAAAA
*
205979 AAGGAAAA
1 AAGAAAAA
205987 AAGAAAAA
1 AAGAAAAA
205995 A
1 A
205996 TTGAATCAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
7 7 0.18
8 22 0.58
9 2 0.05
10 7 0.18
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (8 bp):
AAGAAAAA
Found at i:205969 original size:18 final size:17
Alignment explanation
Indices: 205946--205995 Score: 68
Period size: 15 Copynumber: 3.0 Consensus size: 17
205936 ATACTTGAAG
205946 AAGAAAAAAAGGAAAAAA
1 AAGAAAAAAA-GAAAAAA
205964 AAGAAAAAAAG--AAAA
1 AAGAAAAAAAGAAAAAA
*
205979 AAGGAAAAAAGAAAAAA
1 AAGAAAAAAAGAAAAAA
205996 TTGAATCAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
15 14 0.48
17 5 0.17
18 10 0.34
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (17 bp):
AAGAAAAAAAGAAAAAA
Found at i:205983 original size:25 final size:23
Alignment explanation
Indices: 205950--205995 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 23
205940 TTGAAGAAGA
205950 AAAAAAGGAAAAAAAAGAAAAAAAG
1 AAAAAAGG--AAAAAAGAAAAAAAG
205975 AAAAAAGGAAAAAAGAAAAAA
1 AAAAAAGGAAAAAAGAAAAAA
205996 TTGAATCAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 13 0.62
25 8 0.38
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (23 bp):
AAAAAAGGAAAAAAGAAAAAAAG
Found at i:206485 original size:32 final size:32
Alignment explanation
Indices: 206443--206509 Score: 107
Period size: 32 Copynumber: 2.1 Consensus size: 32
206433 AGAGTCTGGA
* * *
206443 AACAATAAGTATCTCTACGAGATGAGCATAAC
1 AACAAGAAGTATCTCTACCAGATAAGCATAAC
206475 AACAAGAAGTATCTCTACCAGATAAGCATAAC
1 AACAAGAAGTATCTCTACCAGATAAGCATAAC
206507 AAC
1 AAC
206510 CATTTCTTCA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.46, C:0.21, G:0.13, T:0.19
Consensus pattern (32 bp):
AACAAGAAGTATCTCTACCAGATAAGCATAAC
Found at i:208945 original size:75 final size:74
Alignment explanation
Indices: 208808--209007 Score: 172
Period size: 75 Copynumber: 2.7 Consensus size: 74
208798 ATCAACAAGA
** * * * * * *
208808 AGCAAATGTTGGGGTATGTTGAAAGGCCATTTCAATCA-TAATCAGGAATATCGACGCGTTTTGA
1 AGCAAATACTGGGGCATGTTGAAAGCCCATTTCAATCAGAAAT-TGGAATATCGACACATTTTGA
*
208872 ATGCTCACGTCA-
65 ACG-TC-CGT-AT
* *
208884 A-CAAATACTGGGGCATGTTGAAAGCCCATTTCAATCAGAAATTGGAATATTGGCACATTTTGAA
1 AGCAAATACTGGGGCATGTTGAAAGCCCATTTCAATCAGAAATTGGAATATCGACACATTTTGAA
*
208948 CGTCTGTATT
66 CGTCCGTA-T
** * * * *
208958 AGCAAATGTTGGGGCATGCTGAAAGCCAATTTCAATAAGAAATTAGAATA
1 AGCAAATACTGGGGCATGTTGAAAGCCCATTTCAATCAGAAATTGGAATA
209008 ACATTTTGAA
Statistics
Matches: 102, Mismatches: 18, Indels: 9
0.79 0.14 0.07
Matches are distributed among these distances:
72 1 0.01
73 2 0.02
74 3 0.03
75 92 0.90
76 4 0.04
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.28
Consensus pattern (74 bp):
AGCAAATACTGGGGCATGTTGAAAGCCCATTTCAATCAGAAATTGGAATATCGACACATTTTGAA
CGTCCGTAT
Found at i:209050 original size:70 final size:71
Alignment explanation
Indices: 208892--209050 Score: 178
Period size: 75 Copynumber: 2.2 Consensus size: 71
208882 CAACAAATAC
* * * * *
208892 TGGGGCATGTTGAAAGCCCATTTCAATCAGAAATTGGAATATTGGCACATTTTGAACGTCTGTAT
1 TGGGGCATGCTGAAAGCCAATTTCAATAAGAAATTAGAATA---G-ACATTTTGAACGTCTATAT
* *
208957 TAGCAAATGT
62 CAGCAAATGA
208967 TGGGGCATGCTGAAAGCCAATTTCAATAAGAAATTAGAATA-ACATTTTGAACGT-TCATATCAG
1 TGGGGCATGCTGAAAGCCAATTTCAATAAGAAATTAGAATAGACATTTTGAACGTCT-ATATCAG
*
209030 TAAATGA
65 CAAATGA
*
209037 TGGGGTATGCTGAA
1 TGGGGCATGCTGAA
209051 GGCCCACATC
Statistics
Matches: 74, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
69 1 0.01
70 36 0.49
75 37 0.50
ACGTcount: A:0.34, C:0.13, G:0.23, T:0.30
Consensus pattern (71 bp):
TGGGGCATGCTGAAAGCCAATTTCAATAAGAAATTAGAATAGACATTTTGAACGTCTATATCAGC
AAATGA
Found at i:210416 original size:22 final size:22
Alignment explanation
Indices: 210391--210475 Score: 116
Period size: 22 Copynumber: 3.9 Consensus size: 22
210381 ATATCTACAT
*
210391 TCTTCAAAGATAATAGATTTTC
1 TCTTCAAAGATAATAGATTCTC
*
210413 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATAATAGATTCTC
*
210435 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATAATAGATTCTC
* * *
210457 TTTTCAAAGAAAAAAGATT
1 TCTTCAAAGATAATAGATT
210476 TATTGGATTT
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 57 1.00
ACGTcount: A:0.38, C:0.14, G:0.12, T:0.36
Consensus pattern (22 bp):
TCTTCAAAGATAATAGATTCTC
Found at i:210982 original size:20 final size:20
Alignment explanation
Indices: 210920--210983 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
210910 TCCAGAGAAA
210920 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
* ***
210940 ATT--TGAA-GAGGAAGAAGAA
1 GTTCAT-AATGA-GAAGAACTT
210959 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
210979 GTTCA
1 GTTCA
210984 ACCTTTTTCA
Statistics
Matches: 31, Mismatches: 8, Indels: 10
0.63 0.16 0.20
Matches are distributed among these distances:
18 3 0.10
19 10 0.32
20 15 0.48
21 3 0.10
ACGTcount: A:0.42, C:0.08, G:0.23, T:0.27
Consensus pattern (20 bp):
GTTCATAATGAGAAGAACTT
Found at i:211080 original size:123 final size:123
Alignment explanation
Indices: 210797--211229 Score: 671
Period size: 122 Copynumber: 3.6 Consensus size: 123
210787 TGCCAGGTAG
* *
210797 AGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAATTTCATAATGAGAAGAACTTGTTCA
1 AGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
* * *
210862 ACCTTTTGCACGACTCTATCACAAAAGGAGATAGAT-AGCATCAACTTTTCCAGAGAA
66 ACCTTTTTCATGACTCTATCACAGAAGGAGATAGATCAGCATCAACTTTTCCAGAGAA
* *
210919 AGTTCATAATGAGAAGAACTTATTTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
1 AGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
210984 ACCTTTTTCATGACTCTATCACAGAAGGAGATAGATCAGCATCAACTTTTCCAGAGAA
66 ACCTTTTTCATGACTCTATCACAGAAGGAGATAGATCAGCATCAACTTTTCCAGAGAA
* * *
211042 AGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAATAGCTTGTTCA
1 AGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
* * * *
211107 ACCTTTGT-ATGACTCTATCACAGAAGAAGATAGATCAGCATCAACATTTCCAGA-AG
66 ACCTTTTTCATGACTCTATCACAGAAGGAGATAGATCAGCATCAACTTTTCCAGAGAA
* * *
211163 TGTTTATAATAAGAAGAACTCATCTG-A-AGG-AGAAGAAGTTCATAATGAGAAGAACTTGTTCA
1 AGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
211225 ACCTT
66 ACCTT
211230 GTCTTAATTC
Statistics
Matches: 290, Mismatches: 20, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
118 35 0.12
119 3 0.01
120 1 0.00
121 23 0.08
122 138 0.48
123 90 0.31
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.26
Consensus pattern (123 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
ACCTTTTTCATGACTCTATCACAGAAGGAGATAGATCAGCATCAACTTTTCCAGAGAA
Found at i:211353 original size:137 final size:136
Alignment explanation
Indices: 211147--211503 Score: 506
Period size: 137 Copynumber: 2.6 Consensus size: 136
211137 TAGATCAGCA
* * * *
211147 TCAACATTTCCAGAA-GTGTTTATAATAAGAAGAACTCATCTG-AAGG-AGAAGAAGTTCATAAT
1 TCAACATTTCCAGAAGGAGTTCATAATGAGAAGAACTCATCTGAAAGGAAGAAGAAATTCATAAT
* * *
211209 GAGAAGAACTTGTTCAACCTTG-TCTTAATTCATTACATATGAAGCCAAATTAACAACCCCTCTT
66 GAGAAGAACTTGTTCAACCTTGCT-TTAATTCATCACATATGAAGCCAAATCAACAACACCTCTT
211273 TTGAGGG
130 TTGAGGG
*
211280 TCAACATTTCCAGAAGGAGTTCATAATGAGAAGAACTCGTCTGAATAGGAAGAAGAAATTCATAA
1 TCAACATTTCCAGAAGGAGTTCATAATGAGAAGAACTCATCTGAA-AGGAAGAAGAAATTCATAA
* *** **
211345 TGAGAAGAACTTGTTCAACCTTGCTTTAATTCATCATATATGAAGTTGAATCAATGACACCTCTT
65 TGAGAAGAACTTGTTCAACCTTGCTTTAATTCATCACATATGAAGCCAAATCAACAACACCTCTT
211410 TTGAGGG
130 TTGAGGG
* *
211417 TCAGCATTTCCAGAAGGAGTTCATAATGAGAAGAAATCATCTGAAGAGGAAGAAGAAATTCATAA
1 TCAACATTTCCAGAAGGAGTTCATAATGAGAAGAACTCATCTGAA-AGGAAGAAGAAATTCATAA
*
211482 TGAGAAAAACTTGTTCAACCTT
65 TGAGAAGAACTTGTTCAACCTT
211504 TTGCTAGATT
Statistics
Matches: 200, Mismatches: 19, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
133 15 0.08
134 23 0.12
135 1 0.00
136 3 0.01
137 157 0.79
138 1 0.00
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.28
Consensus pattern (136 bp):
TCAACATTTCCAGAAGGAGTTCATAATGAGAAGAACTCATCTGAAAGGAAGAAGAAATTCATAAT
GAGAAGAACTTGTTCAACCTTGCTTTAATTCATCACATATGAAGCCAAATCAACAACACCTCTTT
TGAGGG
Found at i:211753 original size:3 final size:3
Alignment explanation
Indices: 211745--211778 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
211735 TTTGTCCCAT
211745 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
211779 AAAAAAATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:211836 original size:21 final size:21
Alignment explanation
Indices: 211812--211893 Score: 139
Period size: 21 Copynumber: 4.0 Consensus size: 21
211802 TTAGTTTTAT
*
211812 AGGCCCAAATCTAGAACCCGG
1 AGGCCCAGATCTAGAACCCGG
211833 AGGCCCAGATCTAGAACCCGG
1 AGGCCCAGATCTAGAACCCGG
*
211854 AGGCCCAGATCCAGAACCCGG
1 AGGCCCAGATCTAGAACCCGG
211875 AGGCCCAGATCTAG-ACCCG
1 AGGCCCAGATCTAGAACCCG
211894 ACCCAACACC
Statistics
Matches: 58, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
20 5 0.09
21 53 0.91
ACGTcount: A:0.29, C:0.35, G:0.27, T:0.09
Consensus pattern (21 bp):
AGGCCCAGATCTAGAACCCGG
Found at i:215798 original size:26 final size:25
Alignment explanation
Indices: 215750--215798 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 25
215740 GAAGAGCTAA
*
215750 ATAATAAATACAAATAAACATATCC
1 ATAATAAATACAAATAAAAATATCC
215775 ATAATATAATAC-AATAAATAATAT
1 ATAATA-AATACAAATAAA-AATAT
215799 AGGTACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 12 0.57
26 9 0.43
ACGTcount: A:0.61, C:0.10, G:0.00, T:0.29
Consensus pattern (25 bp):
ATAATAAATACAAATAAAAATATCC
Found at i:217230 original size:3 final size:3
Alignment explanation
Indices: 217207--217251 Score: 67
Period size: 3 Copynumber: 15.7 Consensus size: 3
217197 ATTGTAAATA
*
217207 AAT AA- AAT -AT AAT AGT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
217252 ATAAAAAAGA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
2 4 0.11
3 34 0.89
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:217695 original size:134 final size:134
Alignment explanation
Indices: 217437--217926 Score: 700
Period size: 134 Copynumber: 3.7 Consensus size: 134
217427 GAAGAGTTTG
* * * * *
217437 GGTTGTCTAAGGGTGACACAGCTCCTACGTGATGA-G-GATCTAGTCAGGGG-ATAACACTACTC
1 GGTTATCTAAGGGTGACACAGCTCCTACGCGATGAGGAGATCTGGTC-GGGGAATGACACGACTC
* * *
217499 ATACGTGATGAAGAGTTCTTGGCCATCTTTAAGAAATG-TGATAACTCAGTTCCTACGCGATGAG
65 ATACGTGATGAAGAGTTC-TGGCCAT-TTTTAGAAATGATGATAACTCGGTTCCTACGTGATGAG
*
217563 GACTGCT
128 GACGGCT
* * * * *
217570 GGTTATCTATGGGTGACACAGCTCCTACGTGATGAGGAGGTTTGGTCGGGGAATGACACGGCTCA
1 GGTTATCTAAGGGTGACACAGCTCCTACGCGATGAGGAGATCTGGTCGGGGAATGACACGACTCA
* *
217635 TACGTGATGAAGAGTTCTAGCCATTTTTAGAAAGGATGATAACTCGGTTCCTACGTGATGAGGAC
66 TACGTGATGAAGAGTTCTGGCCATTTTTAGAAATGATGATAACTCGGTTCCTACGTGATGAGGAC
217700 GGCT
131 GGCT
* * * * *
217704 GGTTATCTAAGTGTGACACGGCTCCTATGCGATGAGGAGATCTGGTCGGGGGATGACACGGCTCA
1 GGTTATCTAAGGGTGACACAGCTCCTACGCGATGAGGAGATCTGGTCGGGGAATGACACGACTCA
217769 TACGTGATGAAGAGTTCTGGCCATTTTTAGAAATGATGATAACTCGGTTCCTACGTGATGAGGAC
66 TACGTGATGAAGAGTTCTGGCCATTTTTAGAAATGATGATAACTCGGTTCCTACGTGATGAGGAC
217834 GGCT
131 GGCT
* **
217838 GGTTATCTAAGGGTGATATGGCTCCTACGCGATGAGGAGATCTGGTCGGGGAATGACACGACTCA
1 GGTTATCTAAGGGTGACACAGCTCCTACGCGATGAGGAGATCTGGTCGGGGAATGACACGACTCA
*
217903 TACGTCATGAAGAGTTCTGGCCAT
66 TACGTGATGAAGAGTTCTGGCCAT
217927 CTATAGGGAT
Statistics
Matches: 322, Mismatches: 31, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
133 42 0.13
134 247 0.77
135 33 0.10
ACGTcount: A:0.25, C:0.18, G:0.30, T:0.27
Consensus pattern (134 bp):
GGTTATCTAAGGGTGACACAGCTCCTACGCGATGAGGAGATCTGGTCGGGGAATGACACGACTCA
TACGTGATGAAGAGTTCTGGCCATTTTTAGAAATGATGATAACTCGGTTCCTACGTGATGAGGAC
GGCT
Found at i:217978 original size:29 final size:29
Alignment explanation
Indices: 217942--218023 Score: 146
Period size: 29 Copynumber: 2.8 Consensus size: 29
217932 GGGATAATGA
*
217942 TTTCAAAAGAAACCGACTCAAAGATGATG
1 TTTCAAAAGAAACAGACTCAAAGATGATG
217971 TTTCAAAAGAAACAGACTCAAAGATGATG
1 TTTCAAAAGAAACAGACTCAAAGATGATG
*
218000 TTTCAAAAGGAACAGACTCAAAGA
1 TTTCAAAAGAAACAGACTCAAAGA
218024 AATTTTTTTT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 51 1.00
ACGTcount: A:0.48, C:0.16, G:0.17, T:0.20
Consensus pattern (29 bp):
TTTCAAAAGAAACAGACTCAAAGATGATG
Found at i:218199 original size:15 final size:15
Alignment explanation
Indices: 218179--218216 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
218169 CAAAGATTTT
218179 TCTCAAGAAAAAATG
1 TCTCAAGAAAAAATG
*
218194 TCTCAAGAAAAACTG
1 TCTCAAGAAAAAATG
218209 TCTCAAGA
1 TCTCAAGA
218217 GAGACAAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.47, C:0.18, G:0.13, T:0.21
Consensus pattern (15 bp):
TCTCAAGAAAAAATG
Found at i:218279 original size:29 final size:28
Alignment explanation
Indices: 218227--218511 Score: 184
Period size: 29 Copynumber: 9.6 Consensus size: 28
218217 GAGACAAAAC
218227 TTTGTTTCAAAAGAAACAAACTCAAAGAT
1 TTTGTTTCAAAAGAAAC-AACTCAAAGAT
**
218256 TTTGGTTTCAAAAGAAATGACTCAAAGA-
1 TTT-GTTTCAAAAGAAACAACTCAAAGAT
* * *
218284 TTT-TTTCACGAAATTGTCTTAAGAGAA-ACAAA-AC
1 TTTGTTTCA--AAA--G----AA-ACAACTCAAAGAT
* * *
218318 TTTGGTTCAAAAGAAATAGACTCAAAGAA
1 TTTGTTTCAAAAGAAACA-ACTCAAAGAT
218347 TTT-TTTCAAAAGAAACAACTCAAAGAT
1 TTTGTTTCAAAAGAAACAACTCAAAGAT
* *
218374 TATTATTTCAAAAGAAACAACTCACAGATT
1 T-TTGTTTCAAAAGAAACAACTCAAAGA-T
* *
218404 TTTATTTCAAAAGAAACAACTCACAGACT
1 TTTGTTTCAAAAGAAACAACTCAAAGA-T
*
218433 TTTGTTTCAAGAGAAACAAACTCAAAGATAGGT
1 TTTGTTTCAAAAGAAAC-AACTCAAAG--A--T
**
218466 TTTGTTTCAAGGGAAACAATCTCAAAGAT
1 TTTGTTTCAAAAGAAACAA-CTCAAAGAT
* *
218495 GTTTGTTTTAAGAGAAA
1 -TTTGTTTCAAAAGAAA
218512 TTGTCTTAAA
Statistics
Matches: 211, Mismatches: 21, Indels: 47
0.76 0.08 0.17
Matches are distributed among these distances:
26 7 0.03
27 13 0.06
28 24 0.11
29 81 0.38
30 38 0.18
31 2 0.01
32 3 0.01
33 28 0.13
34 9 0.04
35 6 0.03
ACGTcount: A:0.44, C:0.13, G:0.13, T:0.29
Consensus pattern (28 bp):
TTTGTTTCAAAAGAAACAACTCAAAGAT
Found at i:218302 original size:91 final size:89
Alignment explanation
Indices: 218207--218374 Score: 246
Period size: 91 Copynumber: 1.9 Consensus size: 89
218197 CAAGAAAAAC
* * *
218207 TGTCTCAAGAGAGACAAAACTTTGTTTCAAAAGAAACAAACTCAAAGATTTTGGTTTCAAAAGAA
1 TGTCTCAAGAGAAACAAAACTTTGGTTCAAAAGAAACAAACTCAAAGAATTT--TTTCAAAAGAA
**
218272 ATGACTCAAAGATTTTTTCACGAAAT
64 ACAACTCAAAGATTTTTTCACGAAAT
* * *
218298 TGTCTTAAGAGAAACAAAACTTTGGTTCAAAAGAAATAGACTCAAAGAATTTTTTCAAAAGAAAC
1 TGTCTCAAGAGAAACAAAACTTTGGTTCAAAAGAAACAAACTCAAAGAATTTTTTCAAAAGAAAC
218363 AACTCAAAGATT
66 AACTCAAAGATT
218375 ATTATTTCAA
Statistics
Matches: 69, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
89 23 0.33
91 46 0.67
ACGTcount: A:0.45, C:0.14, G:0.14, T:0.27
Consensus pattern (89 bp):
TGTCTCAAGAGAAACAAAACTTTGGTTCAAAAGAAACAAACTCAAAGAATTTTTTCAAAAGAAAC
AACTCAAAGATTTTTTCACGAAAT
Found at i:218603 original size:66 final size:65
Alignment explanation
Indices: 218489--218697 Score: 217
Period size: 64 Copynumber: 3.2 Consensus size: 65
218479 AAACAATCTC
* * * * **
218489 AAAGATGTTTGTTTTAAGAGAAATTGTCTTAAAAGAGACAAACCTTTGTTTTCATAA-AAACATA
1 AAAGAT-TTT-TTTCAAAAGAAACTGTCTCAAAAGAGACAAAATTTTGTTTTCA-AAGAAACATA
*
218553 TTT
63 CTT
* * *
218556 AAAGATTTTTCTTCAAAAGGAACTGTCTCAAAAGTGACAAAATTTTGTTTCCAAAGAAACATACT
1 AAAGATTTTT-TTCAAAAGAAACTGTCTCAAAAGAGACAAAATTTTGTTTTCAAAGAAACATACT
218621 T
65 T
* * * *
218622 AAAG-TTTCTTTT-AAAAGAAACTTTCTCAAAAGAGACAAAATTGTGTTATCAAAGAAACAAACT
1 AAAGATTT-TTTTCAAAAGAAACTGTCTCAAAAGAGACAAAATTTTGTTTTCAAAGAAACATACT
*
218685 C
65 T
218686 AAAGATTTTTTT
1 AAAGATTTTTTT
218698 TCATTTTGTT
Statistics
Matches: 120, Mismatches: 18, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
64 52 0.43
65 11 0.09
66 51 0.43
67 6 0.05
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.34
Consensus pattern (65 bp):
AAAGATTTTTTTCAAAAGAAACTGTCTCAAAAGAGACAAAATTTTGTTTTCAAAGAAACATACTT
Found at i:218662 original size:64 final size:63
Alignment explanation
Indices: 218465--218697 Score: 204
Period size: 64 Copynumber: 3.6 Consensus size: 63
218455 CAAAGATAGG
* * * *
218465 TTTTGTTTCAAGGGAAACA-ATCTCAAAGATGTTTGTTTTAAGAGAAA-TTGTCTTAAAAGAGAC
1 TTTTGTTTCAA-AGAAACATA-CTTAAAGA--TTT-TTTTAAAAGAAACTT-TCTCAAAAGAGAC
*
218528 AAAC
60 AAAA
* * * * *
218532 CTTTGTTTTCATAA-AAACATATTTAAAGATTTTTCTTCAAAAGGAACTGTCTCAAAAGTGACAA
1 TTTTG-TTTCA-AAGAAACATACTTAAAGATTTTT-TT-AAAAGAAACTTTCTCAAAAGAGACAA
218596 AA
62 AA
218598 TTTTGTTTCCAAAGAAACATACTTAAAG-TTTCTTTTAAAAGAAACTTTCTCAAAAGAGACAAAA
1 TTTTGTTT-CAAAGAAACATACTTAAAGATTT-TTTTAAAAGAAACTTTCTCAAAAGAGACAAAA
* * *
218662 TTGTGTTATCAAAGAAACAAACTCAAAGATTTTTTT
1 TTTTGTT-TCAAAGAAACATACTTAAAGATTTTTTT
218698 TCATTTTGTT
Statistics
Matches: 137, Mismatches: 18, Indels: 25
0.76 0.10 0.14
Matches are distributed among these distances:
64 54 0.39
65 19 0.14
66 41 0.30
67 16 0.12
68 6 0.04
69 1 0.01
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.34
Consensus pattern (63 bp):
TTTTGTTTCAAAGAAACATACTTAAAGATTTTTTTAAAAGAAACTTTCTCAAAAGAGACAAAA
Found at i:218819 original size:30 final size:31
Alignment explanation
Indices: 218765--218823 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
218755 GAGACAAAGT
218765 TTTGTTTCAAAAGAAATAGACTCAAAGATCC
1 TTTGTTTCAAAAGAAATAGACTCAAAGATCC
*
218796 TTTGTTTCAAAAGAAA-CGACTCAAAGAT
1 TTTGTTTCAAAAGAAATAGACTCAAAGAT
218824 GATTTTTGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 11 0.41
31 16 0.59
ACGTcount: A:0.42, C:0.15, G:0.14, T:0.29
Consensus pattern (31 bp):
TTTGTTTCAAAAGAAATAGACTCAAAGATCC
Found at i:218901 original size:36 final size:35
Alignment explanation
Indices: 218861--218950 Score: 117
Period size: 36 Copynumber: 2.5 Consensus size: 35
218851 ATAATTTGGA
218861 AAATTGTCTCAAGTGAGACAACATTTGTTTTTAGAG
1 AAATTGTCTCAAGTGAGACAACATTTGTTTTT-GAG
** *
218897 AAATTGTCTCAAACGAGACAACGTTTGTTTTTGAG
1 AAATTGTCTCAAGTGAGACAACATTTGTTTTTGAG
**
218932 AAAACGATCTCAAGTGAGA
1 AAATTG-TCTCAAGTGAGA
218951 TCTTCTTTGT
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
35 7 0.15
36 39 0.85
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (35 bp):
AAATTGTCTCAAGTGAGACAACATTTGTTTTTGAG
Found at i:219237 original size:103 final size:102
Alignment explanation
Indices: 218901--219248 Score: 350
Period size: 103 Copynumber: 3.3 Consensus size: 102
218891 TTAGAGAAAT
* * **
218901 TGTCTCAAACGAGAC-AACGTTTGTTTTTG--AGAAAACGATCTCAAGTGAGATCTTCTTTGTTT
1 TGTCTCAAGCGAGACGAA-ATTTG-TTTTGAAAGAAAACGATCTCAAGTGAGATCAACTTTGTTT
* * *
218963 AATGTGAAAACAAATTCGAAATTTGTATTCTCAAAGGAATA
64 AATGTG-AAACAAATTCGAAATTTGTATT-TAAAAGAAAAA
* * * * *
219004 TGTCTCAAACGAGACGAAATTTGTTTTGAAAAAATTAACAATCTCAAGTGAGATTAATTTTTGTT
1 TGTCTCAAGCGAGACGAAATTTGTTTTGAAAGAA--AACGATCTCAAGTGAGATCAA-CTTTGTT
* * *
219069 TCAA-GTGAATCAAATTCGAAATTTGTATATCAAAGAAAAAAA
63 T-AATGTGAAACAAATTCGAAATTTGTAT-TTAAA-AGAAAAA
* * *
219111 TGTCTCAAGCAAGACGAAGTTTGTTTT-AAGAGAAAGCGATCTC-AGCTGAGATCAACTTTGTTT
1 TGTCTCAAGCGAGACGAAATTTGTTTTGAA-AGAAAACGATCTCAAG-TGAGATCAACTTTGTTT
219174 AATGTGAAACAAATTC-AAATTTTGTATCTTAAAAGAAAAA
64 AATGTGAAACAAATTCGAAA-TTTGTAT-TTAAAAGAAAAA
*
219214 TGTCTCAAGTGAGACGAAATTTGTTTTGAAAGAAA
1 TGTCTCAAGCGAGACGAAATTTGTTTTGAAAGAAA
219249 TTGTCTCAAG
Statistics
Matches: 203, Mismatches: 28, Indels: 28
0.78 0.11 0.11
Matches are distributed among these distances:
102 5 0.02
103 59 0.29
104 39 0.19
105 15 0.07
106 41 0.20
107 42 0.21
108 2 0.01
ACGTcount: A:0.39, C:0.12, G:0.17, T:0.32
Consensus pattern (102 bp):
TGTCTCAAGCGAGACGAAATTTGTTTTGAAAGAAAACGATCTCAAGTGAGATCAACTTTGTTTAA
TGTGAAACAAATTCGAAATTTGTATTTAAAAGAAAAA
Found at i:219256 original size:36 final size:37
Alignment explanation
Indices: 219205--219276 Score: 110
Period size: 36 Copynumber: 2.0 Consensus size: 37
219195 TTGTATCTTA
* *
219205 AAAGAAAAATGTCTCAAGTGAGACGAAATTTGTTTTG
1 AAAGAAAAATGTCTCAAGCGAGACAAAATTTGTTTTG
*
219242 AAAG-AAATTGTCTCAAGCGAGACAAAATTTGTTTT
1 AAAGAAAAATGTCTCAAGCGAGACAAAATTTGTTTT
219277 AAAATTCCCA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
36 28 0.88
37 4 0.12
ACGTcount: A:0.40, C:0.10, G:0.19, T:0.31
Consensus pattern (37 bp):
AAAGAAAAATGTCTCAAGCGAGACAAAATTTGTTTTG
Found at i:219659 original size:12 final size:12
Alignment explanation
Indices: 219642--219690 Score: 64
Period size: 12 Copynumber: 4.1 Consensus size: 12
219632 TATATATATG
*
219642 TGTATGTCTGTT
1 TGTATGTATGTT
*
219654 TGTATGTATGTA
1 TGTATGTATGTT
219666 TGTATGTATGTGT
1 TGTATGTATGT-T
219679 TG-ATGTATGTT
1 TGTATGTATGTT
219690 T
1 T
219691 TTCTCAATCT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
11 2 0.06
12 29 0.88
13 2 0.06
ACGTcount: A:0.16, C:0.02, G:0.27, T:0.55
Consensus pattern (12 bp):
TGTATGTATGTT
Found at i:219688 original size:4 final size:4
Alignment explanation
Indices: 219642--219676 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
219632 TATATATATG
* *
219642 TGTA TGTC TGTT TGTA TGTA TGTA TGTA TGTA TGT
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGT
219677 GTTGATGTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.17, C:0.03, G:0.26, T:0.54
Consensus pattern (4 bp):
TGTA
Found at i:226950 original size:3 final size:3
Alignment explanation
Indices: 226934--226969 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
226924 ATTGAAAATA
226934 AAT AA- AAT -AT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
226970 ATAAAAAAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 4 0.13
3 27 0.87
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:229034 original size:22 final size:23
Alignment explanation
Indices: 229008--229057 Score: 75
Period size: 22 Copynumber: 2.2 Consensus size: 23
228998 TTTAAATAAT
229008 CGTTTATACTAAAC-GAGATACC
1 CGTTTATACTAAACGGAGATACC
* *
229030 TGTTTATGCTAAACGGAGATACC
1 CGTTTATACTAAACGGAGATACC
229053 CGTTT
1 CGTTT
229058 TCCCGCAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 12 0.50
23 12 0.50
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (23 bp):
CGTTTATACTAAACGGAGATACC
Found at i:229447 original size:20 final size:20
Alignment explanation
Indices: 229411--229448 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
229401 CAAAAAACAA
229411 TAAAAAAACAATATCTTCCC
1 TAAAAAAACAATATCTTCCC
*
229431 TAAAGAAAA-AATTTCTTC
1 TAAA-AAAACAATATCTTC
229449 AGTTTCAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.50, C:0.18, G:0.03, T:0.29
Consensus pattern (20 bp):
TAAAAAAACAATATCTTCCC
Found at i:229976 original size:9 final size:8
Alignment explanation
Indices: 229961--229987 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
229951 GGTTAAATTT
229961 TAAAAAAA
1 TAAAAAAA
229969 TAAAAAAA
1 TAAAAAAA
229977 TAAAAAAA
1 TAAAAAAA
229985 TAA
1 TAA
229988 TAATAATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (8 bp):
TAAAAAAA
Found at i:230811 original size:22 final size:22
Alignment explanation
Indices: 230786--230837 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
230776 TCTACGGCGG
230786 AATCCGTCCCCATCTCCGACGA
1 AATCCGTCCCCATCTCCGACGA
*
230808 AATCCGTCCCTATCTCCGACGA
1 AATCCGTCCCCATCTCCGACGA
*
230830 AATTCGTC
1 AATCCGTC
230838 TATCTCCATC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.23, C:0.40, G:0.13, T:0.23
Consensus pattern (22 bp):
AATCCGTCCCCATCTCCGACGA
Found at i:230842 original size:20 final size:21
Alignment explanation
Indices: 230786--230844 Score: 75
Period size: 22 Copynumber: 2.8 Consensus size: 21
230776 TCTACGGCGG
*
230786 AATCCGTCCCCATCTCCGACGA
1 AATCCGT-CCTATCTCCGACGA
230808 AATCCGTCCCTATCTCCGACGA
1 AATCCGT-CCTATCTCCGACGA
*
230830 AATTCGT-CTATCTCC
1 AATCCGTCCTATCTCC
230845 ATCTCTCAGA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.23
22 27 0.77
ACGTcount: A:0.22, C:0.41, G:0.12, T:0.25
Consensus pattern (21 bp):
AATCCGTCCTATCTCCGACGA
Found at i:231246 original size:20 final size:20
Alignment explanation
Indices: 231207--231273 Score: 102
Period size: 20 Copynumber: 3.4 Consensus size: 20
231197 AAATCGCAAC
231207 GCGATTTT-AGTTTT-GCGTT
1 GCGATTTTCA-TTTTCGCGTT
231226 GCGATTTTCATTTTCGCGTT
1 GCGATTTTCATTTTCGCGTT
231246 GCGATTTTCATTTTCGCGTT
1 GCGATTTTCATTTTCGCGTT
*
231266 GCAATTTT
1 GCGATTTT
231274 AAGTTTCAGA
Statistics
Matches: 45, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
19 12 0.27
20 33 0.73
ACGTcount: A:0.12, C:0.16, G:0.21, T:0.51
Consensus pattern (20 bp):
GCGATTTTCATTTTCGCGTT
Found at i:232955 original size:21 final size:21
Alignment explanation
Indices: 232928--232980 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
232918 GTTAGGGGAG
*
232928 TTACGTGATGAGGTCAGTGCT
1 TTACGTGATGAGGTCAGTACT
* * **
232949 TTGCGTGAGGAGGTTGGTACT
1 TTACGTGATGAGGTCAGTACT
232970 TTACGTGATGA
1 TTACGTGATGA
232981 CAATGGTGCA
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.19, C:0.11, G:0.36, T:0.34
Consensus pattern (21 bp):
TTACGTGATGAGGTCAGTACT
Found at i:233100 original size:21 final size:21
Alignment explanation
Indices: 233050--233101 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
233040 ATGACAATAG
* *
233050 TGCTTTACGTGGTGAGGTATC
1 TGCTTTACGTGATGAGGTAGC
*
233071 TACTTTACGTGATGAGGTAGC
1 TGCTTTACGTGATGAGGTAGC
*
233092 TGCTCTACGT
1 TGCTTTACGT
233102 AAGATTGTTG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.17, C:0.17, G:0.29, T:0.37
Consensus pattern (21 bp):
TGCTTTACGTGATGAGGTAGC
Found at i:233436 original size:21 final size:21
Alignment explanation
Indices: 233389--233480 Score: 107
Period size: 21 Copynumber: 4.5 Consensus size: 21
233379 CACCTGTCAT
* *
233389 CGTTCAAGAGG-CCC-CCTAT
1 CGTTCAAGAGGCCCCTCCCAC
* *
233408 CTTTCAAGAGGACCCTCCCAC
1 CGTTCAAGAGGCCCCTCCCAC
* * *
233429 CATTCAAGAGGCCCCTCTCAT
1 CGTTCAAGAGGCCCCTCCCAC
233450 CGTTCAAGAGGCCCCTCCCAC
1 CGTTCAAGAGGCCCCTCCCAC
233471 CGTTCAAGAG
1 CGTTCAAGAG
233481 CCTGATCCAT
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
19 10 0.16
20 3 0.05
21 48 0.79
ACGTcount: A:0.23, C:0.39, G:0.18, T:0.20
Consensus pattern (21 bp):
CGTTCAAGAGGCCCCTCCCAC
Found at i:233466 original size:42 final size:40
Alignment explanation
Indices: 233391--233480 Score: 135
Period size: 42 Copynumber: 2.2 Consensus size: 40
233381 CCTGTCATCG
*
233391 TTCAAGAGGCCCCCTATCTTTCAAGAGGACCCTCCCACCA
1 TTCAAGAGGCCCCCTATCGTTCAAGAGGACCCTCCCACCA
* *
233431 TTCAAGAGGCCCCTCTCATCGTTCAAGAGGCCCCTCCCACCG
1 TTCAAGAGGCCCC-CT-ATCGTTCAAGAGGACCCTCCCACCA
233473 TTCAAGAG
1 TTCAAGAG
233481 CCTGATCCAT
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
40 13 0.29
41 2 0.04
42 30 0.67
ACGTcount: A:0.23, C:0.39, G:0.18, T:0.20
Consensus pattern (40 bp):
TTCAAGAGGCCCCCTATCGTTCAAGAGGACCCTCCCACCA
Found at i:234998 original size:20 final size:19
Alignment explanation
Indices: 234944--235003 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 19
234934 AAGGTACACT
234944 TTCGCAACGCAAAGGTCAAA
1 TTCGCAACGCAAA-GTCAAA
***
234964 TTCGCGTTGCAAAAGTCAAA
1 TTCGCAACGC-AAAGTCAAA
234984 TTCGCAACGCGAAAGTCAAA
1 TTCGCAACGC-AAAGTCAAA
235004 CGCGCGTTGC
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
20 29 0.91
21 3 0.09
ACGTcount: A:0.38, C:0.23, G:0.20, T:0.18
Consensus pattern (19 bp):
TTCGCAACGCAAAGTCAAA
Found at i:235002 original size:40 final size:39
Alignment explanation
Indices: 234944--235023 Score: 108
Period size: 40 Copynumber: 2.0 Consensus size: 39
234934 AAGGTACACT
**
234944 TTCGCAACGCAAAGGTCAAATTCGCGTTGCAAAAGTCAAA
1 TTCGCAACGCAAAGGTCAAACGCGCGTTGC-AAAGTCAAA
*
234984 TTCGCAACGCGAAA-GTCAAACGCGCGTTGCGAAGTCAAA
1 TTCGCAACGC-AAAGGTCAAACGCGCGTTGCAAAGTCAAA
235023 T
1 T
235024 GCACGTTGCG
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
39 9 0.25
40 24 0.67
41 3 0.08
ACGTcount: A:0.35, C:0.24, G:0.23, T:0.19
Consensus pattern (39 bp):
TTCGCAACGCAAAGGTCAAACGCGCGTTGCAAAGTCAAA
Found at i:235015 original size:20 final size:20
Alignment explanation
Indices: 234992--235035 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
234982 AATTCGCAAC
*
234992 GCGAAAGTCAAACGCGCGTT
1 GCGAAAGTCAAACGCACGTT
*
235012 GCG-AAGTCAAATGCACGTT
1 GCGAAAGTCAAACGCACGTT
235031 GCGAA
1 GCGAA
235036 TTTTACTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.32, C:0.23, G:0.30, T:0.16
Consensus pattern (20 bp):
GCGAAAGTCAAACGCACGTT
Found at i:235065 original size:20 final size:20
Alignment explanation
Indices: 235027--235067 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
235017 GTCAAATGCA
*
235027 CGTTGCGAATTTTACTTTCG
1 CGTTGCGAATTTGACTTTCG
* *
235047 CGTTTCGAATTTGATTTTCG
1 CGTTGCGAATTTGACTTTCG
235067 C
1 C
235068 AACAATCGCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.15, C:0.20, G:0.20, T:0.46
Consensus pattern (20 bp):
CGTTGCGAATTTGACTTTCG
Found at i:235105 original size:49 final size:49
Alignment explanation
Indices: 235031--235128 Score: 160
Period size: 49 Copynumber: 2.0 Consensus size: 49
235021 AATGCACGTT
* * * *
235031 GCGAATTTTACTTTCGCGTTTCGAATTTGATTTTCGCAACAATCGCAAC
1 GCGAATTTGACTTTCGCGTTGCGAATTTAACTTTCGCAACAATCGCAAC
235080 GCGAATTTGACTTTCGCGTTGCGAATTTAACTTTCGCAACAATCGCAAC
1 GCGAATTTGACTTTCGCGTTGCGAATTTAACTTTCGCAACAATCGCAAC
235129 AAAAAATCGC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
49 45 1.00
ACGTcount: A:0.26, C:0.23, G:0.17, T:0.34
Consensus pattern (49 bp):
GCGAATTTGACTTTCGCGTTGCGAATTTAACTTTCGCAACAATCGCAAC
Found at i:237686 original size:24 final size:24
Alignment explanation
Indices: 237635--237686 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
237625 ATCCGAGTAT
** *
237635 TGACCAAGATCAAAGTCTGGGTAT
1 TGACCAAGATCAAAGTCTGAATAC
* *
237659 TGACCAAGATCAAATTTTGAATAC
1 TGACCAAGATCAAAGTCTGAATAC
237683 TGAC
1 TGAC
237687 TAGTACTCAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.37, C:0.17, G:0.19, T:0.27
Consensus pattern (24 bp):
TGACCAAGATCAAAGTCTGAATAC
Found at i:237810 original size:10 final size:10
Alignment explanation
Indices: 237795--237824 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
237785 AGGTTGTGGT
237795 TTTGATATTG
1 TTTGATATTG
237805 TTTGATATTG
1 TTTGATATTG
*
237815 TTTGGTATTG
1 TTTGATATTG
237825 GAAATGTGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.17, C:0.00, G:0.23, T:0.60
Consensus pattern (10 bp):
TTTGATATTG
Found at i:238628 original size:20 final size:20
Alignment explanation
Indices: 238603--238669 Score: 64
Period size: 20 Copynumber: 3.3 Consensus size: 20
238593 AAAATATACC
238603 TGCGAAATTAAAATTCGTGT
1 TGCGAAATTAAAATTCGTGT
* *
238623 TGCG-AATTCAAAAATCGAGT
1 TGCGAAATT-AAAATTCGTGT
* * *
238643 TGCGAATTTGAAATCCAGTGT
1 TGCGAAATTAAAATTC-GTGT
238664 TGCGAA
1 TGCGAA
238670 TTTGGAAATC
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
19 4 0.11
20 21 0.57
21 12 0.32
ACGTcount: A:0.34, C:0.13, G:0.22, T:0.30
Consensus pattern (20 bp):
TGCGAAATTAAAATTCGTGT
Found at i:239588 original size:2 final size:2
Alignment explanation
Indices: 239548--239574 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
239538 GGTTTAAGCT
239548 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
239575 TAAATTTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:240660 original size:160 final size:162
Alignment explanation
Indices: 240487--240808 Score: 630
Period size: 162 Copynumber: 2.0 Consensus size: 162
240477 GAGGTTAAGA
240487 TGGCTGGGCATAATCTATTTGTTTTCCAATTTCTAAGTTTTG-AGCTTGCGATTGGGTCA-TTCT
1 TGGCTGGGCATAATCTATTTGTTTTCCAATTTCTAAGTTTTGAAGCTTGCGATTGGGTCATTTCT
240550 AATGAACCATGACACCTGCAAAACAAATCGATCATACTCCATAAGTGGGAGCCAAATATGAGGAC
66 AATGAACCATGACACCTGCAAAACAAATCGATCATACTCCATAAGTGGGAGCCAAATATGAGGAC
240615 TTTGGATTTTAGTCTAGAGAAATTGCTTGTAT
131 TTTGGATTTTAGTCTAGAGAAATTGCTTGTAT
240647 TGGCTGGGCATAATCTATTTGTTTTCCAATTTCTAAGTTTTGAAGCTTGCGATTGGGTCATTTCT
1 TGGCTGGGCATAATCTATTTGTTTTCCAATTTCTAAGTTTTGAAGCTTGCGATTGGGTCATTTCT
240712 AATGAACCATGACACCTGCAAAACAAATCGATCATACTCCATAAGTGGGAGCCAAATATGAGGAC
66 AATGAACCATGACACCTGCAAAACAAATCGATCATACTCCATAAGTGGGAGCCAAATATGAGGAC
240777 TTTGGATTTTAGTCTAGAGAAATTGCTTGTAT
131 TTTGGATTTTAGTCTAGAGAAATTGCTTGTAT
240809 GGGTTCATCT
Statistics
Matches: 160, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
160 42 0.26
161 17 0.11
162 101 0.63
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (162 bp):
TGGCTGGGCATAATCTATTTGTTTTCCAATTTCTAAGTTTTGAAGCTTGCGATTGGGTCATTTCT
AATGAACCATGACACCTGCAAAACAAATCGATCATACTCCATAAGTGGGAGCCAAATATGAGGAC
TTTGGATTTTAGTCTAGAGAAATTGCTTGTAT
Found at i:247054 original size:18 final size:18
Alignment explanation
Indices: 247031--247076 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
247021 CTTTAATTTA
*
247031 TTTATTTAATTATTTTCT
1 TTTATTTAATTATTATCT
*
247049 TTTATTTAATTCTTATCT
1 TTTATTTAATTATTATCT
247067 TTTAGTTTAA
1 TTTA-TTTAA
247077 AAACAAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 20 0.80
19 5 0.20
ACGTcount: A:0.24, C:0.07, G:0.02, T:0.67
Consensus pattern (18 bp):
TTTATTTAATTATTATCT
Found at i:250621 original size:34 final size:34
Alignment explanation
Indices: 250578--250651 Score: 121
Period size: 34 Copynumber: 2.2 Consensus size: 34
250568 GTGCAGTGCA
* *
250578 AAAAAATAGCAGTACAATTTTAGTTCGAACAATT
1 AAAAAATAGCAGTACAATTTTAGTTCAAACAATG
*
250612 AAAAAATAGCAGTACAATTTTGGTTCAAACAATG
1 AAAAAATAGCAGTACAATTTTAGTTCAAACAATG
250646 AAAAAA
1 AAAAAA
250652 AGAGAAAAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.51, C:0.11, G:0.12, T:0.26
Consensus pattern (34 bp):
AAAAAATAGCAGTACAATTTTAGTTCAAACAATG
Found at i:258154 original size:25 final size:26
Alignment explanation
Indices: 258121--258175 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 26
258111 TTACTGAATA
*
258121 TTTAGTTCGGAATAA-TAAAAAAGAT
1 TTTAGTTCGAAATAATTAAAAAAGAT
* *
258146 TTTATTTCGAAATAATTAAATAAGAT
1 TTTAGTTCGAAATAATTAAAAAAGAT
258172 TTTA
1 TTTA
258176 ATTAATTCAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 13 0.50
26 13 0.50
ACGTcount: A:0.45, C:0.04, G:0.11, T:0.40
Consensus pattern (26 bp):
TTTAGTTCGAAATAATTAAAAAAGAT
Found at i:259189 original size:16 final size:17
Alignment explanation
Indices: 259164--259198 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
259154 ACAATATCGT
*
259164 ATAAAGACATTAATAAA
1 ATAAAGACATGAATAAA
259181 ATAAA-ACATGAATAAA
1 ATAAAGACATGAATAAA
259197 AT
1 AT
259199 CATATGTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.66, C:0.06, G:0.06, T:0.23
Consensus pattern (17 bp):
ATAAAGACATGAATAAA
Found at i:259904 original size:23 final size:24
Alignment explanation
Indices: 259854--259904 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
259844 ATTTAAACCC
259854 AAAATCATATAAAAATCATTTAAT
1 AAAATCATATAAAAATCATTTAAT
*
259878 -AAATCAGTA-AAAGAT-ATTTAAT
1 AAAATCA-TATAAAAATCATTTAAT
259900 AAAAT
1 AAAAT
259905 AGTTCAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
22 7 0.29
23 15 0.62
24 2 0.08
ACGTcount: A:0.59, C:0.06, G:0.04, T:0.31
Consensus pattern (24 bp):
AAAATCATATAAAAATCATTTAAT
Found at i:267403 original size:23 final size:23
Alignment explanation
Indices: 267371--267429 Score: 91
Period size: 23 Copynumber: 2.6 Consensus size: 23
267361 CATATAAATG
*
267371 CACCGAAGTGCCACGTAGAATTA
1 CACCGTAGTGCCACGTAGAATTA
* *
267394 CACCGTAGTGCCGCGTAGAATTG
1 CACCGTAGTGCCACGTAGAATTA
267417 CACCGTAGTGCCA
1 CACCGTAGTGCCA
267430 TATAATAATG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.27, C:0.29, G:0.25, T:0.19
Consensus pattern (23 bp):
CACCGTAGTGCCACGTAGAATTA
Found at i:269129 original size:21 final size:21
Alignment explanation
Indices: 269105--269149 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
269095 TTTTGTTCGT
* *
269105 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
269126 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
269147 TTG
1 TTG
269150 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:271270 original size:25 final size:24
Alignment explanation
Indices: 271242--271300 Score: 57
Period size: 25 Copynumber: 2.3 Consensus size: 24
271232 TACAACTCTT
*
271242 TTAATGAATATTTAATTT-AGAATAA
1 TTAAT-AAGATTT-ATTTCAGAATAA
*
271267 TTAAATAAGATTTATTTCGGAATAA
1 TT-AATAAGATTTATTTCAGAATAA
271292 TTAAATAAG
1 TT-AATAAG
271301 TTTTGAATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 4 0.13
25 23 0.77
26 3 0.10
ACGTcount: A:0.47, C:0.02, G:0.10, T:0.41
Consensus pattern (24 bp):
TTAATAAGATTTATTTCAGAATAA
Found at i:277196 original size:21 final size:23
Alignment explanation
Indices: 277170--277251 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 23
277160 CCAGAACCGT
*
277170 GGGGGGTATCGATTCCCC-T-AA
1 GGGGGGAATCGATTCCCCTTCAA
*
277191 GGGGGGAATCGGTTCCCCTTCAA
1 GGGGGGAATCGATTCCCCTTCAA
* *
277214 AGGGGGAAT-GGTTCCCCTTCAA
1 GGGGGGAATCGATTCCCCTTCAA
*
277236 -GGGGGTATCGATTCCC
1 GGGGGGAATCGATTCCC
277252 TCTGCACCAA
Statistics
Matches: 53, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
21 23 0.43
22 20 0.38
23 10 0.19
ACGTcount: A:0.18, C:0.24, G:0.34, T:0.23
Consensus pattern (23 bp):
GGGGGGAATCGATTCCCCTTCAA
Done.