Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A09
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: 77927517
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1491452 characters in sequence are not A, C, G, or T
File 41 of 250
Found at i:12361438 original size:28 final size:28
Alignment explanation
Indices: 12361402--12361527 Score: 155
Period size: 28 Copynumber: 4.5 Consensus size: 28
12361392 TCCTGAAGAT
*
12361402 TCTTGCTTGAGAGATAGTCCATGCAGAC
1 TCTTGCTTGAGAGATAGTCCATGTAGAC
* * * *
12361430 TCTTACTTGAGAGATAGTCTATGTGGCC
1 TCTTGCTTGAGAGATAGTCCATGTAGAC
*
12361458 TCTTGCTTGAGAGATAGTCTATGTAGAC
1 TCTTGCTTGAGAGATAGTCCATGTAGAC
* *
12361486 TCTTGCTTGAAAGATAGTCCATGTGGAC
1 TCTTGCTTGAGAGATAGTCCATGTAGAC
* *
12361514 TATTGCATGA-AGAT
1 TCTTGCTTGAGAGAT
12361528 TCTTACCCAA
Statistics
Matches: 85, Mismatches: 13, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
27 4 0.05
28 81 0.95
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (28 bp):
TCTTGCTTGAGAGATAGTCCATGTAGAC
Found at i:12361488 original size:56 final size:56
Alignment explanation
Indices: 12361402--12361511 Score: 175
Period size: 56 Copynumber: 2.0 Consensus size: 56
12361392 TCCTGAAGAT
* *
12361402 TCTTGCTTGAGAGATAGTCCATGCAGACTCTTACTTGAGAGATAGTCTATGTGGCC
1 TCTTGCTTGAGAGATAGTCCATGCAGACTCTTACTTGAAAGATAGTCCATGTGGCC
* * *
12361458 TCTTGCTTGAGAGATAGTCTATGTAGACTCTTGCTTGAAAGATAGTCCATGTGG
1 TCTTGCTTGAGAGATAGTCCATGCAGACTCTTACTTGAAAGATAGTCCATGTGG
12361512 ACTATTGCAT
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
56 49 1.00
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.34
Consensus pattern (56 bp):
TCTTGCTTGAGAGATAGTCCATGCAGACTCTTACTTGAAAGATAGTCCATGTGGCC
Found at i:12361595 original size:18 final size:18
Alignment explanation
Indices: 12361568--12361603 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
12361558 TACTTGAGAA
* *
12361568 ACGACCAAATTACCATTT
1 ACGACAAAATAACCATTT
12361586 ACGACAAAATAACCATTT
1 ACGACAAAATAACCATTT
12361604 TGCCCATTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.44, C:0.25, G:0.06, T:0.25
Consensus pattern (18 bp):
ACGACAAAATAACCATTT
Found at i:12364064 original size:22 final size:22
Alignment explanation
Indices: 12364008--12364064 Score: 78
Period size: 22 Copynumber: 2.6 Consensus size: 22
12363998 TGCAAGGCTT
*
12364008 ACACGCCCGTGTGGTCCAAGGG
1 ACACGCCCGTGTGGTCCAAGGA
* *
12364030 ACCCACCCGTGTGGTCCAAGGA
1 ACACGCCCGTGTGGTCCAAGGA
*
12364052 ACACGCCCATGTG
1 ACACGCCCGTGTG
12364065 ACCTTAGGAC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.21, C:0.35, G:0.30, T:0.14
Consensus pattern (22 bp):
ACACGCCCGTGTGGTCCAAGGA
Found at i:12369232 original size:15 final size:14
Alignment explanation
Indices: 12369188--12369237 Score: 50
Period size: 13 Copynumber: 3.6 Consensus size: 14
12369178 GTCTCTGTAC
12369188 TATATTTAATTTGG
1 TATATTTAATTTGG
* *
12369202 -ATATGT-ATTTGT
1 TATATTTAATTTGG
12369214 TATATTTCAATTTGG
1 TATATTT-AATTTGG
12369229 TATAATTTA
1 TAT-ATTTA
12369238 TTTTTTATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 7
0.72 0.10 0.18
Matches are distributed among these distances:
12 5 0.18
13 10 0.36
15 9 0.32
16 4 0.14
ACGTcount: A:0.30, C:0.02, G:0.12, T:0.56
Consensus pattern (14 bp):
TATATTTAATTTGG
Found at i:12369607 original size:40 final size:40
Alignment explanation
Indices: 12369552--12369647 Score: 129
Period size: 40 Copynumber: 2.4 Consensus size: 40
12369542 CTATTTGTTG
*
12369552 CATATAAATTGTTGAACTATCTATTTTTACTAATTCTTTA
1 CATATAAATTATTGAACTATCTATTTTTACTAATTCTTTA
* * * * *
12369592 TATATAAATTATTGAAGTATTTATTTTTATTGATTCTTTA
1 CATATAAATTATTGAACTATCTATTTTTACTAATTCTTTA
*
12369632 CATATAAATTACTGAA
1 CATATAAATTATTGAA
12369648 TTGTTGATTT
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 48 1.00
ACGTcount: A:0.35, C:0.08, G:0.06, T:0.50
Consensus pattern (40 bp):
CATATAAATTATTGAACTATCTATTTTTACTAATTCTTTA
Found at i:12369658 original size:40 final size:40
Alignment explanation
Indices: 12369552--12369658 Score: 108
Period size: 40 Copynumber: 2.7 Consensus size: 40
12369542 CTATTTGTTG
** *
12369552 CATATAAATTGTTGAACTATCT-ATTTTTACTAATTCTTTA
1 CATATAAATTACTGAAGTAT-TGATTTTTACTAATTCTTTA
* * * * *
12369592 TATATAAATTATTGAAGTATTTATTTTTATTGATTCTTTA
1 CATATAAATTACTGAAGTATTGATTTTTACTAATTCTTTA
* *
12369632 CATATAAATTACTGAATTGTTGATTTT
1 CATATAAATTACTGAAGTATTGATTTT
12369659 CAAGCCATCG
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
39 1 0.02
40 55 0.98
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.52
Consensus pattern (40 bp):
CATATAAATTACTGAAGTATTGATTTTTACTAATTCTTTA
Found at i:12378462 original size:93 final size:93
Alignment explanation
Indices: 12378354--12378525 Score: 301
Period size: 93 Copynumber: 1.8 Consensus size: 93
12378344 CGCCCATAAG
* *
12378354 CGAACTCGGACTCAACTCAACGAGCTCAGG-CGTTCGCATCCATAAGTGAACTCGGACTCAACTC
1 CGAACTCAGACTCAACTCAACGAGCTC-GGACATTCGCATCCATAAGTGAACTCGGACTCAACTC
12378418 AACGAGTTCGGATGCCTAGTTACATCTCA
65 AACGAGTTCGGATGCCTAGTTACATCTCA
*
12378447 CGAACTCAGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
12378512 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
12378526 TCAATCATCC
Statistics
Matches: 75, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
92 2 0.03
93 73 0.97
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (93 bp):
CGAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:12378520 original size:46 final size:46
Alignment explanation
Indices: 12378347--12378522 Score: 200
Period size: 46 Copynumber: 3.8 Consensus size: 46
12378337 TGTAACCCGC
* *
12378347 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCAGG-CGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTC-GGACATTCGCAT
* *
12378393 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
* *
12378443 -C-TCA-CGAACTCAGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
12378486 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
12378523 TGCTCAATCA
Statistics
Matches: 109, Mismatches: 11, Indels: 20
0.78 0.08 0.14
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 4 0.04
46 60 0.55
47 28 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:12385866 original size:46 final size:46
Alignment explanation
Indices: 12385799--12386070 Score: 366
Period size: 46 Copynumber: 5.9 Consensus size: 46
12385789 TTTCTGAAAT
12385799 GAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGATAC
1 GAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGATAC
*
12385845 GAAATGTGTAAAACCATGGTTGAAAGATACCATGGCAACATGATAC
1 GAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGATAC
** *
12385891 GAAATGTGTAAGACCATGGTTGAAAGATAGTATGGCAACATGATAT
1 GAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGATAC
* * * *
12385937 GAAATGTGTAAGACTATGGTTGAAAGATACCATGGCAACGTGACAT
1 GAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGATAC
** * * *
12385983 GAAATGAATAAGTCCATGGTTGAAAGATACCATGACAACATGACA-
1 GAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGATAC
* * * * *
12386028 GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCATCATG
1 G-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATG
12386071 TCGAAGATAA
Statistics
Matches: 202, Mismatches: 23, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
45 1 0.00
46 201 1.00
ACGTcount: A:0.40, C:0.14, G:0.24, T:0.22
Consensus pattern (46 bp):
GAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGATAC
Found at i:12385915 original size:21 final size:21
Alignment explanation
Indices: 12385891--12385961 Score: 54
Period size: 21 Copynumber: 3.2 Consensus size: 21
12385881 AACATGATAC
12385891 GAAATGTGTAAGACCATGGTT
1 GAAATGTGTAAGACCATGGTT
* * *
12385912 GAAA-GATAGTATGGCAACATGATAT
1 GAAATG-T-GTA-AG-ACCATGGT-T
*
12385937 GAAATGTGTAAGACTATGGTT
1 GAAATGTGTAAGACCATGGTT
12385958 GAAA
1 GAAA
12385962 GATACCATGG
Statistics
Matches: 37, Mismatches: 7, Indels: 12
0.66 0.12 0.21
Matches are distributed among these distances:
20 1 0.03
21 10 0.27
22 8 0.22
23 2 0.05
24 9 0.24
25 6 0.16
26 1 0.03
ACGTcount: A:0.39, C:0.07, G:0.27, T:0.27
Consensus pattern (21 bp):
GAAATGTGTAAGACCATGGTT
Found at i:12387835 original size:17 final size:17
Alignment explanation
Indices: 12387791--12387837 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
12387781 ATTTTATACA
* * *
12387791 ATTTATGAACATTTTAT
1 ATTTATAAATATTTAAT
*
12387808 ATTT-GAAATATTTAAT
1 ATTTATAAATATTTAAT
12387824 ATTTATAAATATTT
1 ATTTATAAATATTT
12387838 TTATATAGAT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
16 12 0.50
17 12 0.50
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.53
Consensus pattern (17 bp):
ATTTATAAATATTTAAT
Found at i:12388396 original size:31 final size:31
Alignment explanation
Indices: 12388331--12388407 Score: 84
Period size: 31 Copynumber: 2.5 Consensus size: 31
12388321 ATAAAGTAAT
* * * *
12388331 ATTTAATTCTTAAATTTGATAAATTTTATCA
1 ATTTAATCCTTAAATTTAACAAATTTTATAA
* *
12388362 ATTTAATCCTTAAATTTAACAATTTTTTTAA
1 ATTTAATCCTTAAATTTAACAAATTTTATAA
*
12388393 ATTTGA-CCTTAAATT
1 ATTTAATCCTTAAATT
12388408 AGATTTTTTT
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
30 9 0.23
31 30 0.77
ACGTcount: A:0.38, C:0.09, G:0.03, T:0.51
Consensus pattern (31 bp):
ATTTAATCCTTAAATTTAACAAATTTTATAA
Found at i:12396273 original size:39 final size:39
Alignment explanation
Indices: 12396228--12396328 Score: 157
Period size: 39 Copynumber: 2.6 Consensus size: 39
12396218 ATCGTGATCT
* * * *
12396228 GAAGCCCGAAGTCTAGCTGAAGTACATAAGTGCTAAACG
1 GAAGCCCGAAGGCTAACTGAAGCACACAAGTGCTAAACG
*
12396267 GAAGCCCGAAGGCTAACTGAAGCACACAAGTGTTAAACG
1 GAAGCCCGAAGGCTAACTGAAGCACACAAGTGCTAAACG
12396306 GAAGCCCGAAGGCTAACTGAAGC
1 GAAGCCCGAAGGCTAACTGAAGC
12396329 CCATCAGAGC
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 57 1.00
ACGTcount: A:0.37, C:0.23, G:0.27, T:0.14
Consensus pattern (39 bp):
GAAGCCCGAAGGCTAACTGAAGCACACAAGTGCTAAACG
Found at i:12396329 original size:18 final size:18
Alignment explanation
Indices: 12396226--12396330 Score: 68
Period size: 18 Copynumber: 5.5 Consensus size: 18
12396216 ACATCGTGAT
* *
12396226 CTGAAGCCCGAAGTCTAG
1 CTGAAGCCCGAAGGCTAA
* **
12396244 CTGAAGTACATAAGTGCTAAA
1 CTGAAG-CCCGAAG-GCT-AA
*
12396265 CGGAAGCCCGAAGGCTAA
1 CTGAAGCCCGAAGGCTAA
*
12396283 CTGAAGCACAC-AAGTGTTAAA
1 CTGAAGC-C-CGAAG-GCT-AA
*
12396304 CGGAAGCCCGAAGGCTAA
1 CTGAAGCCCGAAGGCTAA
12396322 CTGAAGCCC
1 CTGAAGCCC
12396331 ATCAGAGCTG
Statistics
Matches: 65, Mismatches: 14, Indels: 16
0.68 0.15 0.17
Matches are distributed among these distances:
18 24 0.37
19 14 0.22
20 13 0.20
21 14 0.22
ACGTcount: A:0.35, C:0.25, G:0.26, T:0.14
Consensus pattern (18 bp):
CTGAAGCCCGAAGGCTAA
Found at i:12402134 original size:34 final size:34
Alignment explanation
Indices: 12402090--12402175 Score: 127
Period size: 34 Copynumber: 2.5 Consensus size: 34
12402080 ACACAATTAA
* *
12402090 CCATCCAGCACACCAGATGCTTATATGAGCTAAT
1 CCATCCAGCACACCAAATGCTCATATGAGCTAAT
* *
12402124 CCATCTAGCACACCAAATGCTCGTATGAGCTAAT
1 CCATCCAGCACACCAAATGCTCATATGAGCTAAT
*
12402158 CCATCCAGCACATCAAAT
1 CCATCCAGCACACCAAAT
12402176 AACACTGTAA
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 46 1.00
ACGTcount: A:0.34, C:0.31, G:0.13, T:0.22
Consensus pattern (34 bp):
CCATCCAGCACACCAAATGCTCATATGAGCTAAT
Found at i:12407624 original size:24 final size:24
Alignment explanation
Indices: 12407597--12407646 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
12407587 CAGACACGGG
*
12407597 CTGGGACACGGCCGTGTGTTCTTA
1 CTGGGACACGACCGTGTGTTCTTA
12407621 CTGGGACACGACCGTGTGTTCTTA
1 CTGGGACACGACCGTGTGTTCTTA
12407645 CT
1 CT
12407647 TCAAATGCCC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.14, C:0.26, G:0.30, T:0.30
Consensus pattern (24 bp):
CTGGGACACGACCGTGTGTTCTTA
Found at i:12411379 original size:16 final size:16
Alignment explanation
Indices: 12411335--12411380 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
12411325 ATTTATCCAA
*
12411335 TTAT-ATTTAATGATT
1 TTATAATTTAATAATT
*
12411350 TTATAATTTTATAATT
1 TTATAATTTAATAATT
12411366 TTATTAA-TTAATAAT
1 TTA-TAATTTAATAAT
12411381 ATATTATGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
15 4 0.15
16 19 0.73
17 3 0.12
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (16 bp):
TTATAATTTAATAATT
Found at i:12418110 original size:153 final size:148
Alignment explanation
Indices: 12417834--12418134 Score: 458
Period size: 153 Copynumber: 2.0 Consensus size: 148
12417824 ATAGTAATGG
* * * *
12417834 TTATTATTATTTTTAAAATAATTATTAATTAAATTTTTTATATTATTATTATATTTCTAGACATA
1 TTATTATTATTTTTAAAACAATTACTAATTAAATTTTTTATATTATTATTATATGTCTAGACACA
* *
12417899 GATGGGTGTGTTAAAGAATTGATCTATACAAAATTAATTGAATTTGACGTCACGAGTTAATTATA
66 AATGGGTGTGTTAAAGAATTGATCTATACAAAATTAATTGAATTTGACGTCACGAGTTAATTAAA
12417964 CACCAAACAGTCTGAATA
131 CACCAAACAGTCTGAATA
*
12417982 TTATTATTATTTTTAAAACAATTACTAATTAAAATTTTATTTTTATATTATTATTATATGTCTGG
1 TTATTATTATTTTTAAAACAATTACTAATT-AAA---T-TTTTTATATTATTATTATATGTCTAG
* * *
12418047 ACACAAATGGGTGTGTTAAAGAATTGATTTATACAAAATTAATTGAGTTTGACGTCACTAGTTAA
61 ACACAAATGGGTGTGTTAAAGAATTGATCTATACAAAATTAATTGAATTTGACGTCACGAGTTAA
*
12418112 TTAAACACCAAACAGTTTGAATA
126 TTAAACACCAAACAGTCTGAATA
12418135 CATCAATTAA
Statistics
Matches: 137, Mismatches: 11, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
148 28 0.20
149 3 0.02
152 1 0.01
153 105 0.77
ACGTcount: A:0.39, C:0.08, G:0.11, T:0.42
Consensus pattern (148 bp):
TTATTATTATTTTTAAAACAATTACTAATTAAATTTTTTATATTATTATTATATGTCTAGACACA
AATGGGTGTGTTAAAGAATTGATCTATACAAAATTAATTGAATTTGACGTCACGAGTTAATTAAA
CACCAAACAGTCTGAATA
Found at i:12426362 original size:6 final size:6
Alignment explanation
Indices: 12426353--12426383 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
12426343 AACCAAAAGC
12426353 ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA A
1 ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA A
12426384 GTTTGGTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
ATAAAA
Found at i:12431117 original size:65 final size:66
Alignment explanation
Indices: 12431035--12431173 Score: 228
Period size: 65 Copynumber: 2.1 Consensus size: 66
12431025 AAGCCAAAAC
*
12431035 ATGTCTGATCAAGAATCACAATCAGTTCTTGCCAGAGATGCAGAAATCGAATGATGTAGGAATAG
1 ATGTCTGATCAAGAATCACAATCAGTTCTTGCCAGAGATACAGAAATCGAATGATGTAGGAATAG
12431100 G
66 G
* * *
12431101 ATGTC-GATCAAGAATCACAATCAGTTCTTGCCAGAGATATAGAAATCGAATGGTGTAGGACTAG
1 ATGTCTGATCAAGAATCACAATCAGTTCTTGCCAGAGATACAGAAATCGAATGATGTAGGAATAG
12431165 G
66 G
12431166 ATGT-TGAT
1 ATGTCTGAT
12431174 ATTTGTCCAT
Statistics
Matches: 68, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
65 63 0.93
66 5 0.07
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.26
Consensus pattern (66 bp):
ATGTCTGATCAAGAATCACAATCAGTTCTTGCCAGAGATACAGAAATCGAATGATGTAGGAATAG
G
Found at i:12434847 original size:14 final size:14
Alignment explanation
Indices: 12434828--12434858 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
12434818 AAATATTATA
12434828 AATATTAAAAAAAT
1 AATATTAAAAAAAT
*
12434842 AATATTATAAAAAT
1 AATATTAAAAAAAT
12434856 AAT
1 AAT
12434859 GTGTTTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (14 bp):
AATATTAAAAAAAT
Found at i:12436623 original size:3 final size:3
Alignment explanation
Indices: 12436579--12436606 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
12436569 TCTAATCACT
12436579 ATG ATG ATG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG A
12436607 ATGTGTAGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.32, T:0.32
Consensus pattern (3 bp):
ATG
Found at i:12437726 original size:17 final size:17
Alignment explanation
Indices: 12437697--12437742 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
12437687 TTTTAAAATA
*
12437697 TATATTTTAAAAT-TTT
1 TATATTTTTAAATATTT
12437713 TATACTTTTTAAATATTT
1 TATA-TTTTTAAATATTT
12437731 T-TAATTTTTAAA
1 TAT-ATTTTTAAA
12437743 AATTAATTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 4 0.15
17 17 0.65
18 5 0.19
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (17 bp):
TATATTTTTAAATATTT
Found at i:12438899 original size:1 final size:1
Alignment explanation
Indices: 12438893--12438917 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
12438883 GTAGCAAAGG
12438893 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
12438918 CCTAATCTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:12448955 original size:18 final size:18
Alignment explanation
Indices: 12448932--12448975 Score: 88
Period size: 18 Copynumber: 2.4 Consensus size: 18
12448922 GGGTATACTG
12448932 AGTTACACCACACGGCCA
1 AGTTACACCACACGGCCA
12448950 AGTTACACCACACGGCCA
1 AGTTACACCACACGGCCA
12448968 AGTTACAC
1 AGTTACAC
12448976 GCCCGTGTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.34, C:0.36, G:0.16, T:0.14
Consensus pattern (18 bp):
AGTTACACCACACGGCCA
Found at i:12451042 original size:43 final size:43
Alignment explanation
Indices: 12450994--12451143 Score: 146
Period size: 43 Copynumber: 3.5 Consensus size: 43
12450984 TTTACGGAGA
12450994 TGTGATTACATGTAAGACCATGTCTGGGACATTGGCATTGTAT
1 TGTGATTACATGTAAGACCATGTCTGGGACATTGGCATTGTAT
* *
12451037 TGTGATTACGTGTAAGATCATGTCTGGGACATTGGCATCAT-TA-
1 TGTGATTACATGTAAGACCATGTCTGGGACATTGGCAT--TGTAT
* * * * * * *
12451080 TATGATTTCGTATAAGACTC-TGTCTGGGATAGTGGCACTG-AT
1 TGTGATTACATGTAAGAC-CATGTCTGGGACATTGGCATTGTAT
*
12451122 ATGTGATAACATGTAAGACCAT
1 -TGTGATTACATGTAAGACCAT
12451144 ATCCGGGATA
Statistics
Matches: 86, Mismatches: 14, Indels: 14
0.75 0.12 0.12
Matches are distributed among these distances:
41 2 0.02
42 1 0.01
43 79 0.92
44 3 0.03
45 1 0.01
ACGTcount: A:0.27, C:0.14, G:0.25, T:0.34
Consensus pattern (43 bp):
TGTGATTACATGTAAGACCATGTCTGGGACATTGGCATTGTAT
Found at i:12452918 original size:18 final size:18
Alignment explanation
Indices: 12452886--12452927 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
12452876 GACAATGTGA
*
12452886 TTATGT-TTGATGGATGT
1 TTATGTGTTAATGGATGT
*
12452903 TTATGTGTTAATGGATTT
1 TTATGTGTTAATGGATGT
12452921 TTATGTG
1 TTATGTG
12452928 AGAAATGTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 6 0.27
18 16 0.73
ACGTcount: A:0.19, C:0.00, G:0.26, T:0.55
Consensus pattern (18 bp):
TTATGTGTTAATGGATGT
Found at i:12454048 original size:22 final size:22
Alignment explanation
Indices: 12454016--12454066 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
12454006 TAATTCAAGC
12454016 AATCTTTATTTGTCGCAAATTCA
1 AATC-TTATTTGTCGCAAATTCA
12454039 AATCTTATTTGTCGCAAATTCA
1 AATCTTATTTGTCGCAAATTCA
*
12454061 AGTCTT
1 AATCTT
12454067 TCTGAGTCAT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
22 23 0.85
23 4 0.15
ACGTcount: A:0.29, C:0.18, G:0.10, T:0.43
Consensus pattern (22 bp):
AATCTTATTTGTCGCAAATTCA
Found at i:12461735 original size:14 final size:14
Alignment explanation
Indices: 12461716--12461744 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
12461706 TATGTCATAT
12461716 TTTTATGTTTGAGA
1 TTTTATGTTTGAGA
12461730 TTTTATGTTTGAGA
1 TTTTATGTTTGAGA
12461744 T
1 T
12461745 GTGACTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.00, G:0.21, T:0.59
Consensus pattern (14 bp):
TTTTATGTTTGAGA
Found at i:12465951 original size:37 final size:37
Alignment explanation
Indices: 12465910--12466017 Score: 94
Period size: 37 Copynumber: 3.1 Consensus size: 37
12465900 TTACATTAAT
12465910 CTTTTAATAAACTTAAGCTTTAAGTTCTTAGTACAAA
1 CTTTTAATAAACTTAAGCTTTAAGTTCTTAGTACAAA
* *
12465947 CTTTT--TAATAC--AA-CATTT-A-TTAC--A-T-TAAT
1 CTTTTAATAA-ACTTAAGC-TTTAAGTT-CTTAGTACAAA
12465976 CTTTTAATAAACTTAAGCTTTAAGTTCTTAGTACAAA
1 CTTTTAATAAACTTAAGCTTTAAGTTCTTAGTACAAA
12466013 CTTTT
1 CTTTT
12466018 TTAATACACC
Statistics
Matches: 53, Mismatches: 4, Indels: 28
0.62 0.05 0.33
Matches are distributed among these distances:
29 7 0.13
30 3 0.06
31 4 0.08
32 7 0.13
33 6 0.11
34 7 0.13
35 4 0.08
36 3 0.06
37 12 0.23
ACGTcount: A:0.36, C:0.14, G:0.06, T:0.44
Consensus pattern (37 bp):
CTTTTAATAAACTTAAGCTTTAAGTTCTTAGTACAAA
Found at i:12465956 original size:66 final size:66
Alignment explanation
Indices: 12465844--12466043 Score: 328
Period size: 66 Copynumber: 3.0 Consensus size: 66
12465834 TTCTTTTTGT
* * * * *
12465844 TTTTAATAAACTTAAGCTTTTAAGTTGTTTGTAGAAACTCTTTAATACAACGTTTATTACATTAA
1 TTTTAATAAACTTAAGC-TTTAAGTTCTTAGTACAAACTTTTTAATACAACATTTATTACATTAA
12465909 TC
65 TC
12465911 TTTTAATAAACTTAAGCTTTAAGTTCTTAGTACAAACTTTTTAATACAACATTTATTACATTAAT
1 TTTTAATAAACTTAAGCTTTAAGTTCTTAGTACAAACTTTTTAATACAACATTTATTACATTAAT
12465976 C
66 C
*
12465977 TTTTAATAAACTTAAGCTTTAAGTTCTTAGTACAAACTTTTTTAATACACCATTTATTACATTAA
1 TTTTAATAAACTTAAGCTTTAAGTTCTTAGTACAAAC-TTTTTAATACAACATTTATTACATTAA
12466042 TC
65 TC
12466044 AATGTATTGT
Statistics
Matches: 126, Mismatches: 6, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
66 81 0.64
67 45 0.36
ACGTcount: A:0.36, C:0.14, G:0.06, T:0.45
Consensus pattern (66 bp):
TTTTAATAAACTTAAGCTTTAAGTTCTTAGTACAAACTTTTTAATACAACATTTATTACATTAAT
C
Found at i:12473533 original size:19 final size:19
Alignment explanation
Indices: 12473509--12473548 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
12473499 TGAAAATGTG
12473509 TAAGTTATGCCTATAAATT
1 TAAGTTATGCCTATAAATT
*
12473528 TAAGTTATGCCTATGAATT
1 TAAGTTATGCCTATAAATT
12473547 TA
1 TA
12473549 TGATGACACA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.35, C:0.10, G:0.12, T:0.42
Consensus pattern (19 bp):
TAAGTTATGCCTATAAATT
Found at i:12477660 original size:40 final size:40
Alignment explanation
Indices: 12477515--12477660 Score: 181
Period size: 40 Copynumber: 3.6 Consensus size: 40
12477505 TACTAGCTCA
* * *
12477515 AAGCCTGCGGAACTTTAAGCCC-GA-ATATAGTACCAGCACT-
1 AAGCCTGCGGGA-TTTAA-CCCAGATATACATTACCAGCA-TG
* *
12477555 AAGCCTGCGGGATTTAACCCTGATATACATTACCAGCACG
1 AAGCCTGCGGGATTTAACCCAGATATACATTACCAGCATG
*
12477595 AAGCCTGCGGGATTTAACCCGGATATACATTACCAGCATG
1 AAGCCTGCGGGATTTAACCCAGATATACATTACCAGCATG
*
12477635 AAGCCTGCAGGATTTAACCCAGATAT
1 AAGCCTGCGGGATTTAACCCAGATAT
12477661 TTAATATATC
Statistics
Matches: 95, Mismatches: 8, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
38 3 0.03
39 7 0.07
40 85 0.89
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.22
Consensus pattern (40 bp):
AAGCCTGCGGGATTTAACCCAGATATACATTACCAGCATG
Found at i:12485564 original size:40 final size:38
Alignment explanation
Indices: 12485519--12485635 Score: 108
Period size: 40 Copynumber: 3.0 Consensus size: 38
12485509 CGAATCCAGT
* *
12485519 TACTAGCTCAAAGCCTACGGAACTTTAAGCCCGGATATAG
1 TACTAGCACAAAGCCTACGGAA-TTTAA-CCCAGATATAG
* * *
12485559 TACTAGCACTAAGCCTACGGGATTTAACCCAGATATACAT
1 TACTAGCACAAAGCCTACGGAATTTAACCCAGATAT--AG
* * * * *
12485599 TACCAGCACGAAGCCTGCGGGATTTAACCCGGATATA
1 TACTAGCACAAAGCCTACGGAATTTAACCCAGATATA
12485636 CATTACCAGC
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
38 9 0.14
39 5 0.08
40 52 0.79
ACGTcount: A:0.32, C:0.26, G:0.20, T:0.22
Consensus pattern (38 bp):
TACTAGCACAAAGCCTACGGAATTTAACCCAGATATAG
Found at i:12485636 original size:40 final size:40
Alignment explanation
Indices: 12485542--12485674 Score: 180
Period size: 40 Copynumber: 3.4 Consensus size: 40
12485532 CCTACGGAAC
* * * *
12485542 TTTAAGCCCGGATAT--AGTACTAGCACTAAGCCTACGGGA
1 TTTAA-CCCGGATATACATTACCAGCACGAAGCCTGCGGGA
*
12485581 TTTAACCCAGATATACATTACCAGCACGAAGCCTGCGGGA
1 TTTAACCCGGATATACATTACCAGCACGAAGCCTGCGGGA
*
12485621 TTTAACCCGGATATACATTACCAGCATGAAGCCTGCGGGA
1 TTTAACCCGGATATACATTACCAGCACGAAGCCTGCGGGA
*
12485661 TTTAACCTGGATAT
1 TTTAACCCGGATAT
12485675 TTAATATATC
Statistics
Matches: 84, Mismatches: 8, Indels: 3
0.88 0.08 0.03
Matches are distributed among these distances:
38 8 0.10
39 5 0.06
40 71 0.85
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.24
Consensus pattern (40 bp):
TTTAACCCGGATATACATTACCAGCACGAAGCCTGCGGGA
Found at i:12496588 original size:37 final size:37
Alignment explanation
Indices: 12496527--12496605 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 37
12496517 TTATTACGAA
* * *
12496527 GTCTTACCCAGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCAGACAAAATCCCCACACGAAGTCATCGG
* *
12496564 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCAGACAAAATCCCCACACGAAGTCATCGG
12496601 GTCTT
1 GTCTT
12496606 TAGAGCTCGG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.27, C:0.32, G:0.18, T:0.24
Consensus pattern (37 bp):
GTCTTACCCAGACAAAATCCCCACACGAAGTCATCGG
Found at i:12496902 original size:51 final size:47
Alignment explanation
Indices: 12496724--12497064 Score: 511
Period size: 47 Copynumber: 7.1 Consensus size: 47
12496714 CCCTTCGGGA
* * * * * *
12496724 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
12496771 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
12496818 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
12496865 CTTATCACATATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC----ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
12496916 CTTATCACATATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC----ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
12496967 CTTATCACGTATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
12497014 CCTATCACGTATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
12497061 CTTA
1 CTTA
12497065 CTATCATTTC
Statistics
Matches: 277, Mismatches: 13, Indels: 8
0.93 0.04 0.03
Matches are distributed among these distances:
47 179 0.65
51 98 0.35
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:12502056 original size:30 final size:30
Alignment explanation
Indices: 12502013--12502075 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
12502003 ACTTATTTTA
12502013 TTGTTAATATTGTTATTATTTTAGAGGCAT
1 TTGTTAATATTGTTATTATTTTAGAGGCAT
* *
12502043 TTGTTATTTTTGTTATTATTTTAGAGGCAT
1 TTGTTAATATTGTTATTATTTTAGAGGCAT
12502073 TTG
1 TTG
12502076 CTTGTTAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.22, C:0.03, G:0.17, T:0.57
Consensus pattern (30 bp):
TTGTTAATATTGTTATTATTTTAGAGGCAT
Found at i:12504161 original size:16 final size:16
Alignment explanation
Indices: 12504140--12504174 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
12504130 CATGTAAGAC
12504140 CATGTCTGGGACATGG
1 CATGTCTGGGACATGG
12504156 CATGTCTGGGACATGG
1 CATGTCTGGGACATGG
12504172 CAT
1 CAT
12504175 TGGCATCGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.20, C:0.20, G:0.34, T:0.26
Consensus pattern (16 bp):
CATGTCTGGGACATGG
Found at i:12506462 original size:40 final size:40
Alignment explanation
Indices: 12506388--12506612 Score: 312
Period size: 40 Copynumber: 5.6 Consensus size: 40
12506378 AACCCAAGTA
* * *
12506388 CCTTCGGGATTTAG-CCGGATATAG-CAATTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATG
*
12506427 CCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
12506467 CCTTCGGGACTTAGCCCGGGTATAG-CAACTACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTC-ACTA---GCACAAATG
*
12506510 CCTTCGGGACTTCGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
12506550 CCTTCGAGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
12506590 CCATCGGGACTTAGCCCGGATAT
1 CCTTCGGGACTTAGCCCGGATAT
12506613 CATCCGAATA
Statistics
Matches: 167, Mismatches: 12, Indels: 13
0.87 0.06 0.07
Matches are distributed among these distances:
39 13 0.08
40 116 0.69
41 1 0.01
43 36 0.22
44 1 0.01
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
Found at i:12506508 original size:83 final size:82
Alignment explanation
Indices: 12506388--12506612 Score: 336
Period size: 83 Copynumber: 2.8 Consensus size: 82
12506378 AACCCAAGTA
* *
12506388 CCTTCGGGATTTAG-CCGGATATAGCAA-T-TCGCACAAATGCCTTCGGGTCTTAGCCCGGATAT
1 CCTTCGGGACTTAGCCCGGATATAGCAACTATCGCACAAATGCCTTCGGGACTTAGCCCGGATAT
12506450 AGTCACTAGCACAAATG
66 AGTCACTAGCACAAATG
* *
12506467 CCTTCGGGACTTAGCCCGGGTATAGCAACTACTCGCACAAATGCCTTCGGGACTTCGCCCGGATA
1 CCTTCGGGACTTAGCCCGGATATAGCAACTA-TCGCACAAATGCCTTCGGGACTTAGCCCGGATA
12506532 TAGTCACTAGCACAAATG
65 TAGTCACTAGCACAAATG
* *
12506550 CCTTCGAGACTTAGCCCGGATATAGTC-ACTA--GCACAAATGCCATCGGGACTTAGCCCGGATA
1 CCTTCGGGACTTAGCCCGGATATAG-CAACTATCGCACAAATGCCTTCGGGACTTAGCCCGGATA
12506612 T
65 T
12506613 CATCCGAATA
Statistics
Matches: 133, Mismatches: 8, Indels: 9
0.89 0.05 0.06
Matches are distributed among these distances:
79 13 0.10
80 42 0.32
81 1 0.01
83 76 0.57
84 1 0.01
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (82 bp):
CCTTCGGGACTTAGCCCGGATATAGCAACTATCGCACAAATGCCTTCGGGACTTAGCCCGGATAT
AGTCACTAGCACAAATG
Found at i:12508770 original size:13 final size:13
Alignment explanation
Indices: 12508748--12508780 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
12508738 TTACTTTAGT
12508748 TTAA-TTAGTTAA
1 TTAATTTAGTTAA
12508760 TTAATTTAGTTAA
1 TTAATTTAGTTAA
*
12508773 TTAGTTTA
1 TTAATTTA
12508781 ATAAACAACC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (13 bp):
TTAATTTAGTTAA
Found at i:12512922 original size:26 final size:26
Alignment explanation
Indices: 12512862--12512933 Score: 72
Period size: 27 Copynumber: 2.7 Consensus size: 26
12512852 ATGAAGTTTT
* *
12512862 CCACAAAGGCATTCCTTTCATACTCTC
1 CCACAAAGGC-TTTCTTTCATACTATC
* * *
12512889 CCAAAAAGGCTTTCTTTCATATTATG
1 CCACAAAGGCTTTCTTTCATACTATC
*
12512915 CCACAAAGGGTTTTCTTTC
1 CCACAAA-GGCTTTCTTTC
12512934 CAAACGTGTT
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
26 18 0.49
27 19 0.51
ACGTcount: A:0.26, C:0.28, G:0.11, T:0.35
Consensus pattern (26 bp):
CCACAAAGGCTTTCTTTCATACTATC
Found at i:12549495 original size:54 final size:54
Alignment explanation
Indices: 12549436--12549547 Score: 224
Period size: 54 Copynumber: 2.1 Consensus size: 54
12549426 ACTTGTACCT
12549436 TCCAATTAAAGTATCTACTACTTCTTACTTTCCTTGTATTCCTTTCCAAAATCA
1 TCCAATTAAAGTATCTACTACTTCTTACTTTCCTTGTATTCCTTTCCAAAATCA
12549490 TCCAATTAAAGTATCTACTACTTCTTACTTTCCTTGTATTCCTTTCCAAAATCA
1 TCCAATTAAAGTATCTACTACTTCTTACTTTCCTTGTATTCCTTTCCAAAATCA
12549544 TCCA
1 TCCA
12549548 TTACTACAGT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 58 1.00
ACGTcount: A:0.28, C:0.27, G:0.04, T:0.42
Consensus pattern (54 bp):
TCCAATTAAAGTATCTACTACTTCTTACTTTCCTTGTATTCCTTTCCAAAATCA
Found at i:12557654 original size:15 final size:15
Alignment explanation
Indices: 12557634--12557662 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
12557624 CAATATCTAA
12557634 ATAAAGCCCTCACTT
1 ATAAAGCCCTCACTT
12557649 ATAAAGCCCTCACT
1 ATAAAGCCCTCACT
12557663 ATTCATCATC
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:0.34, C:0.34, G:0.07, T:0.24
Consensus pattern (15 bp):
ATAAAGCCCTCACTT
Found at i:12561442 original size:68 final size:67
Alignment explanation
Indices: 12561370--12561519 Score: 171
Period size: 67 Copynumber: 2.2 Consensus size: 67
12561360 CATCATGTGT
* * * *
12561370 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACC
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACC
12561432 ATGTAG
62 ATGTAG
** * *
12561438 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGT
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
12561503 AG
66 AG
12561505 ACAAGAGAGCTACGA
1 ACAAGAGAGCTACGA
12561520 GATAAACTGG
Statistics
Matches: 70, Mismatches: 9, Indels: 7
0.81 0.10 0.08
Matches are distributed among these distances:
64 20 0.29
65 7 0.10
66 4 0.06
67 26 0.37
68 13 0.19
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (67 bp):
ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
AG
Found at i:12561475 original size:64 final size:64
Alignment explanation
Indices: 12561394--12561577 Score: 194
Period size: 67 Copynumber: 2.8 Consensus size: 64
12561384 AGACATTATG
* *
12561394 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * * *
12561458 ATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
12561523 AA
63 AA
* * * *
12561525 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 A-TGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG-ACAAGAGAGC
12561578 CGAACTATAT
Statistics
Matches: 98, Mismatches: 17, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
62 1 0.01
63 19 0.19
64 21 0.21
65 8 0.08
66 16 0.16
67 31 0.32
68 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:12565591 original size:43 final size:44
Alignment explanation
Indices: 12565543--12565639 Score: 110
Period size: 43 Copynumber: 2.2 Consensus size: 44
12565533 ATCACATCAG
* *
12565543 GGTCTTACATGA-AAT-TGATTATCAAAGCCAATGTCCCAGACAT
1 GGTCTTACATGATAATCTCAATA-CAAAGCCAATGTCCCAGACAT
* * * *
12565586 GGTCTTACA-CATAATCTCAATACAATGCTAATGTCCCCGACAT
1 GGTCTTACATGATAATCTCAATACAAAGCCAATGTCCCAGACAT
12565629 GGTCTTACATG
1 GGTCTTACATG
12565640 TATTCACATC
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
42 1 0.02
43 39 0.89
44 4 0.09
ACGTcount: A:0.32, C:0.24, G:0.15, T:0.29
Consensus pattern (44 bp):
GGTCTTACATGATAATCTCAATACAAAGCCAATGTCCCAGACAT
Found at i:12568221 original size:29 final size:29
Alignment explanation
Indices: 12568179--12568237 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
12568169 AATTGAAATT
*
12568179 ATTACAGCAAGATCTCTCATTCCCAAACC
1 ATTACAGCAAGATCGCTCATTCCCAAACC
12568208 ATTACAGCAAGATCGCTCATTCCCAAACC
1 ATTACAGCAAGATCGCTCATTCCCAAACC
12568237 A
1 A
12568238 AGTACCTTCG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.36, C:0.34, G:0.08, T:0.22
Consensus pattern (29 bp):
ATTACAGCAAGATCGCTCATTCCCAAACC
Found at i:12568323 original size:40 final size:40
Alignment explanation
Indices: 12568242--12568339 Score: 128
Period size: 40 Copynumber: 2.5 Consensus size: 40
12568232 AAACCAAGTA
* * *
12568242 CCTTCGGGATTTAG-CCGGATATAGCTACTCGCTCAACTG
1 CCTTCGGGACTTAGCCCGGATATAGCTACTCGCACAAATG
*
12568281 CCTTCGGGACTTAGCCCGGATATAG-TAACTTGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGCT-ACTCGCACAAATG
*
12568321 CCTTCGGGGCTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
12568340 TTATCATCCG
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
39 14 0.27
40 38 0.73
ACGTcount: A:0.20, C:0.29, G:0.26, T:0.26
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGCTACTCGCACAAATG
Found at i:12570295 original size:52 final size:52
Alignment explanation
Indices: 12570217--12570321 Score: 210
Period size: 52 Copynumber: 2.0 Consensus size: 52
12570207 TTATCCTTAA
12570217 TTTTGCTATCATTCTGCACTAATATCGCTGCATTAGTTAATTCTAGATTGTG
1 TTTTGCTATCATTCTGCACTAATATCGCTGCATTAGTTAATTCTAGATTGTG
12570269 TTTTGCTATCATTCTGCACTAATATCGCTGCATTAGTTAATTCTAGATTGTG
1 TTTTGCTATCATTCTGCACTAATATCGCTGCATTAGTTAATTCTAGATTGTG
12570321 T
1 T
12570322 CCAAAATTGT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.23, C:0.17, G:0.15, T:0.45
Consensus pattern (52 bp):
TTTTGCTATCATTCTGCACTAATATCGCTGCATTAGTTAATTCTAGATTGTG
Found at i:12572021 original size:5 final size:5
Alignment explanation
Indices: 12572013--12572039 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
12572003 GGAAAGTATT
12572013 TAAAA TAAAA TAAAA TAAAA TAAAA TA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TA
12572040 TTACAACAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (5 bp):
TAAAA
Found at i:12573759 original size:46 final size:46
Alignment explanation
Indices: 12573709--12573881 Score: 208
Period size: 46 Copynumber: 3.7 Consensus size: 46
12573699 TGGTTGAGCA
*
12573709 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * *
12573755 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CG
* *
12573802 TCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* *
12573848 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
12573882 GGGGGGGTTA
Statistics
Matches: 107, Mismatches: 13, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
43 6 0.06
45 3 0.03
46 61 0.57
47 29 0.27
48 3 0.03
50 5 0.05
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:12573865 original size:93 final size:93
Alignment explanation
Indices: 12573706--12573876 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
12573696 GGATGGTTGA
* *
12573706 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
12573771 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * *
12573799 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
12573864 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
12573877 ACTTAGGGGG
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:12574141 original size:19 final size:20
Alignment explanation
Indices: 12574104--12574141 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
12574094 ATAAGGTGGT
12574104 AAGATGATGAATGATGTTTA
1 AAGATGATGAATGATGTTTA
12574124 AAGATG-TGATAT-ATGTTT
1 AAGATGATGA-ATGATGTTT
12574142 TGGTGGTACC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.37, C:0.00, G:0.24, T:0.39
Consensus pattern (20 bp):
AAGATGATGAATGATGTTTA
Found at i:12581318 original size:46 final size:46
Alignment explanation
Indices: 12581268--12581393 Score: 207
Period size: 46 Copynumber: 2.7 Consensus size: 46
12581258 TGGTTGAGCA
*
12581268 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* *
12581314 TCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* *
12581360 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
12581394 GGGGCGGGTT
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
46 74 1.00
ACGTcount: A:0.21, C:0.21, G:0.27, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:12586579 original size:17 final size:17
Alignment explanation
Indices: 12586559--12586591 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
12586549 AACACCTCTA
12586559 ATACCTCTCAAAAACCT
1 ATACCTCTCAAAAACCT
*
12586576 ATACCTCTCGAAAACC
1 ATACCTCTCAAAAACC
12586592 CCTTTTCTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.39, C:0.36, G:0.03, T:0.21
Consensus pattern (17 bp):
ATACCTCTCAAAAACCT
Found at i:12592887 original size:28 final size:28
Alignment explanation
Indices: 12592855--12592909 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
12592845 AAAAGAAATT
12592855 AGCAAGGCTACACAAGAATTCACTATGA
1 AGCAAGGCTACACAAGAATTCACTATGA
12592883 AGCAAGGCTACACAAGAATTCACTATG
1 AGCAAGGCTACACAAGAATTCACTATG
12592910 GCAAATGATC
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:0.42, C:0.22, G:0.18, T:0.18
Consensus pattern (28 bp):
AGCAAGGCTACACAAGAATTCACTATGA
Found at i:12601206 original size:20 final size:21
Alignment explanation
Indices: 12601181--12601219 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
12601171 CCGAATGTAC
12601181 TTTTCATATACA-CATATAAT
1 TTTTCATATACATCATATAAT
*
12601201 TTTTCATTTACATCATATA
1 TTTTCATATACATCATATA
12601220 TGATTTGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.36, C:0.15, G:0.00, T:0.49
Consensus pattern (21 bp):
TTTTCATATACATCATATAAT
Found at i:12601477 original size:41 final size:42
Alignment explanation
Indices: 12601423--12601522 Score: 103
Period size: 41 Copynumber: 2.4 Consensus size: 42
12601413 CGTACATGCT
* *
12601423 ATCACATATCGATGCCGTTGTCCCAGACAGGGTCTTACACGA
1 ATCAAATATCGATGCCGATGTCCCAGACAGGGTCTTACACGA
* * * * *
12601465 ATCAAATA-CGATGCTGATGTCCTAGATATGGTCTTACATGTA
1 ATCAAATATCGATGCCGATGTCCCAGACAGGGTCTTACACG-A
* *
12601507 ATCACATATTGATGCC
1 ATCAAATATCGATGCC
12601523 AACGTCTCAT
Statistics
Matches: 46, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
41 26 0.57
42 15 0.33
43 5 0.11
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (42 bp):
ATCAAATATCGATGCCGATGTCCCAGACAGGGTCTTACACGA
Found at i:12603844 original size:28 final size:28
Alignment explanation
Indices: 12603813--12603867 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
12603803 TGAATTATCA
*
12603813 AGGATGGCACTAAGTGTGCGACACATCT
1 AGGATAGCACTAAGTGTGCGACACATCT
* *
12603841 AGGATAGCACTTAGTGTGCGATACATC
1 AGGATAGCACTAAGTGTGCGACACATC
12603868 CATGAAGGCA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.24
Consensus pattern (28 bp):
AGGATAGCACTAAGTGTGCGACACATCT
Found at i:12605307 original size:14 final size:15
Alignment explanation
Indices: 12605290--12605318 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
12605280 TCACAAAAAT
12605290 TTCACACAT-ATAAA
1 TTCACACATAATAAA
12605304 TTCACACATAATAAA
1 TTCACACATAATAAA
12605319 CACTGAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.52, C:0.21, G:0.00, T:0.28
Consensus pattern (15 bp):
TTCACACATAATAAA
Found at i:12609411 original size:17 final size:17
Alignment explanation
Indices: 12609389--12609422 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
12609379 GCCTTTAGAG
12609389 TTAGCTAATTGCTTGTA
1 TTAGCTAATTGCTTGTA
12609406 TTAGCTAATTGCTTGTA
1 TTAGCTAATTGCTTGTA
12609423 CTTGGGTACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.12, G:0.18, T:0.47
Consensus pattern (17 bp):
TTAGCTAATTGCTTGTA
Found at i:12612088 original size:20 final size:21
Alignment explanation
Indices: 12612051--12612090 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
12612041 GTACTTCGAA
12612051 AAAAGAGGGCCTCAATGGGCC
1 AAAAGAGGGCCTCAATGGGCC
*
12612072 AAAAGTGGGCC-CAATGGGC
1 AAAAGAGGGCCTCAATGGGC
12612091 TTACGGACCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.33, C:0.23, G:0.35, T:0.10
Consensus pattern (21 bp):
AAAAGAGGGCCTCAATGGGCC
Found at i:12627801 original size:43 final size:43
Alignment explanation
Indices: 12627740--12627898 Score: 171
Period size: 43 Copynumber: 3.7 Consensus size: 43
12627730 CAATGTCGTA
* * *
12627740 TCCCAGATATGGTCTTACATGTTATCACATATCGATGCCAATT
1 TCCCAGACATGGTCTTACACGTAATCACATATCGATGCCAATT
* * * * * *
12627783 TCCCAAACAGGGTCTTACACGAAATCGA-TTAAT-GATGCTAATG
1 TCCCAGACATGGTCTTACACGTAATC-ACAT-ATCGATGCCAATT
*
12627826 TCCCAGACATGGTCTTACACGTAATCACA-ATACAATGCCAATT
1 TCCCAGACATGGTCTTACACGTAATCACATAT-CGATGCCAATT
*
12627869 TCCCAGACATGGTCTTACATGTAATCACAT
1 TCCCAGACATGGTCTTACACGTAATCACAT
12627899 CTTTGTAACC
Statistics
Matches: 93, Mismatches: 17, Indels: 11
0.77 0.14 0.09
Matches are distributed among these distances:
41 2 0.02
42 1 0.01
43 87 0.94
44 3 0.03
ACGTcount: A:0.32, C:0.25, G:0.14, T:0.29
Consensus pattern (43 bp):
TCCCAGACATGGTCTTACACGTAATCACATATCGATGCCAATT
Found at i:12633821 original size:40 final size:40
Alignment explanation
Indices: 12633712--12633899 Score: 292
Period size: 40 Copynumber: 4.7 Consensus size: 40
12633702 TATTCGGATG
* *
12633712 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
12633752 A-ATTCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACT
1 ATA-ACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
12633791 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
12633831 ATAACTGGGCTAAGTCCCGAAGGCATTTGTGC-AGGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGA-GTTACT
*
12633871 ATAACCGGGCTAAGTCTCGAAGGCATTTG
1 ATAACCGGGCTAAGTCCCGAAGGCATTTG
12633900 AGCAAGTAGC
Statistics
Matches: 137, Mismatches: 7, Indels: 8
0.90 0.05 0.05
Matches are distributed among these distances:
39 36 0.26
40 101 0.74
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
Found at i:12633913 original size:40 final size:40
Alignment explanation
Indices: 12633712--12633922 Score: 286
Period size: 40 Copynumber: 5.3 Consensus size: 40
12633702 TATTCGGATG
* *
12633712 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
* *
12633752 A-ATTCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACT
1 ATA-ACCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
*
12633791 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
* *
12633831 ATAACTGGGCTAAGTCCCGAAGGCATTTGTGCAGGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
* *
12633871 ATAACCGGGCTAAGTCTCGAAGGCATTTGAGCAAG-TAGCT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTA-CT
*
12633911 ATATCC-GGCTAA
1 ATAACCGGGCTAA
12633923 ATTCTGAAGG
Statistics
Matches: 155, Mismatches: 12, Indels: 9
0.88 0.07 0.05
Matches are distributed among these distances:
39 43 0.28
40 112 0.72
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
Found at i:12637222 original size:34 final size:34
Alignment explanation
Indices: 12637173--12637269 Score: 117
Period size: 34 Copynumber: 2.8 Consensus size: 34
12637163 CTTTGTTTAC
12637173 ATACTG-TACTAAAATGGGCTAAGGCCCAGACTG
1 ATACTGTTACTAAAATGGGCTAAGGCCCAGACTG
* * *
12637206 CCT-CTGTTACTAAAATGGGCTCAGGCCTAGACTG
1 -ATACTGTTACTAAAATGGGCTAAGGCCCAGACTG
*
12637240 ATACTGTTACTAAAAGGGGGGCTAAGGCCC
1 ATACTGTTACTAAAA--TGGGCTAAGGCCC
12637270 TAACTGGAAC
Statistics
Matches: 52, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
33 4 0.08
34 38 0.73
36 10 0.19
ACGTcount: A:0.29, C:0.23, G:0.26, T:0.23
Consensus pattern (34 bp):
ATACTGTTACTAAAATGGGCTAAGGCCCAGACTG
Found at i:12641425 original size:43 final size:43
Alignment explanation
Indices: 12641356--12641522 Score: 196
Period size: 43 Copynumber: 3.9 Consensus size: 43
12641346 AGCTCGTAAA
* * *
12641356 ATGCC-ATTTCCCAGATATGGTCTTACATGTTATCACATATCG
1 ATGCCAATGTCCCAGACATGGTCTTACATGTAATCACATATCG
* * * *** *
12641398 ATCCCACTGTCCCAGACAGGGTCTTACACAAAATCA-ATTAACG
1 ATGCCAATGTCCCAGACATGGTCTTACATGTAATCACA-TATCG
*
12641441 ATGCCAATGTCCCAGACATGGTCTTACATGTAATCACA-ATACA
1 ATGCCAATGTCCCAGACATGGTCTTACATGTAATCACATAT-CG
12641484 ATGCCAATGTCCCAGACATGGTCTTACATGTAATCACAT
1 ATGCCAATGTCCCAGACATGGTCTTACATGTAATCACAT
12641523 CTCGGTAACC
Statistics
Matches: 102, Mismatches: 18, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
42 6 0.06
43 95 0.93
44 1 0.01
ACGTcount: A:0.32, C:0.26, G:0.14, T:0.28
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACATGGTCTTACATGTAATCACATATCG
Found at i:12649448 original size:10 final size:10
Alignment explanation
Indices: 12649433--12649481 Score: 53
Period size: 10 Copynumber: 4.7 Consensus size: 10
12649423 CTTTCAACCG
*
12649433 ATATAATACT
1 ATATAATAAT
*
12649443 ATATAACTATT
1 ATATAA-TAAT
12649454 ATTATAATAAT
1 A-TATAATAAT
*
12649465 AAATAATAAT
1 ATATAATAAT
12649475 ATATAAT
1 ATATAAT
12649482 GTACTACTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
10 20 0.61
11 8 0.24
12 5 0.15
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (10 bp):
ATATAATAAT
Found at i:12650069 original size:238 final size:249
Alignment explanation
Indices: 12649457--12650104 Score: 699
Period size: 252 Copynumber: 2.6 Consensus size: 249
12649447 AACTATTATT
* * * *
12649457 ATAATA-ATAAATAA-TAATATATAATGTACTACTATGATATATAGCTATTATTACATTATAGAT
1 ATAATATAT-AATAATTAACATATAATGTAATACTATTATATATA-CTATTATTATATTATAGAT
* * * * * *
12649520 TATAATAAAAGACATGGTATTACATGATAATATAATGTTTACTCATTGTTGCA-TATATAAACTA
64 TATTATAAAAGATATAGTATTACATGATATTATAATGTTTAATCATTGATGCATTATATAAACTA
* * *
12649584 TTAATATATTATATACCATATGATATGATATAACATTATGTAATATAGTAGCAGGATTAACTTTC
129 TTAATATATTATATACTATATGATATGATATAACATTATATAATATAGTAGCAGGACTAACTTTC
*
12649649 AAAGGTACGAAAAGTATAGAGACTTAGAGAATATTTCAACCAATATAATAATAAAGA
194 AAAGGTACGAAAAGTATAGAGACTCAGAGAATATTTCAACCAATATAATAAT-AAGA
* *
12649706 ATAATATATAATAATTAATATATAATGTACTACTATTATATATAACTATTATTATATTATAG-TT
1 ATAATATATAATAATTAACATATAATGTAATACTATTATATAT-ACTATTATTATATTATAGATT
* * * *
12649770 AATAGTAAAAGATGTAGTATTACATGAT-TTCATAATGCTTAACCATTGATGCATATATATAAA-
65 ATTA-TAAAAGATATAGTATTACATGATATT-ATAATGTTTAATCATTGATGCAT-TATATAAAC
* * * * *
12649833 TGATTAACATATTATATAATAAATGATATAATATAACATTATATAATATAGTAGGA-GAGCTAAC
127 T-ATTAATATATTATATACTATATGATATGATATAACATTATATAATATAGTAGCAGGA-CTAAC
* * * *
12649897 TTTC-AAGTGTATGAAAAGTATA-AGGACTCGGAGAATATTTCAACCAGTATAGTAAT-A-A
190 TTTCAAAG-GTACGAAAAGTATAGA-GACTCAGAGAATATTTCAACCAATATAATAATAAGA
* * *
12649955 A-AATA-AT-AT-A-TGACA-ATAA-GTAATA-TA-TA-ATATACTACTATTATATTATAGAATA
1 ATAATATATAATAATTAACATATAATGTAATACTATTATATATACTATTATTATATTATAGATTA
* * * **
12650010 TTATAAAAGATATAATATTACATTATATTATAATGTTTAATCATTGGTAAATGTATATAAACTAT
66 TTATAAAAGATATAGTATTACATGATATTATAATGTTTAATCATTGATGCAT-TATATAAACTAT
*
12650075 TAATATATTACATACTATATGATATGATAT
130 TAATATATTATATACTATATGATATGATAT
12650105 GTAACACCCT
Statistics
Matches: 340, Mismatches: 45, Indels: 39
0.80 0.11 0.09
Matches are distributed among these distances:
238 90 0.26
239 11 0.03
240 2 0.01
241 2 0.01
242 5 0.01
243 4 0.01
244 3 0.01
245 1 0.00
246 2 0.01
247 2 0.01
248 4 0.01
249 18 0.05
250 84 0.25
251 8 0.02
252 104 0.31
ACGTcount: A:0.46, C:0.07, G:0.10, T:0.37
Consensus pattern (249 bp):
ATAATATATAATAATTAACATATAATGTAATACTATTATATATACTATTATTATATTATAGATTA
TTATAAAAGATATAGTATTACATGATATTATAATGTTTAATCATTGATGCATTATATAAACTATT
AATATATTATATACTATATGATATGATATAACATTATATAATATAGTAGCAGGACTAACTTTCAA
AGGTACGAAAAGTATAGAGACTCAGAGAATATTTCAACCAATATAATAATAAGA
Found at i:12653482 original size:20 final size:19
Alignment explanation
Indices: 12653446--12653496 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
12653436 AAGGGTTATT
*
12653446 TTGTAAA-GTTGTAAAATAA
1 TTGTAAATG-TGTGAAATAA
12653465 GTTGTAAATGTGTGAAATAA
1 -TTGTAAATGTGTGAAATAA
12653485 TTG-AAAT-TGTGA
1 TTGTAAATGTGTGA
12653497 GTTGCTATAG
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
17 5 0.17
18 4 0.14
19 3 0.10
20 16 0.55
21 1 0.03
ACGTcount: A:0.41, C:0.00, G:0.22, T:0.37
Consensus pattern (19 bp):
TTGTAAATGTGTGAAATAA
Found at i:12654212 original size:48 final size:46
Alignment explanation
Indices: 12654152--12654317 Score: 145
Period size: 48 Copynumber: 3.5 Consensus size: 46
12654142 TATGTGTGCT
*
12654152 AGTGTAACACATGTCTGGGACATGCATCAGCCTCTAGATATACAAGGC
1 AGTGTAAGACATGTCTGGGACATGCATC-GCCTCTAGATATACAA-GC
* * * * * * * ***
12654200 AGTGTAAGACATGTCTAGGACATGCATCG-GTATGGAGACGAGATTT
1 AGTGTAAGACATGTCTGGGACATGCATCGCCTCTAGATA-TACAAGC
* *
12654246 AGTGTAAGACATGTTTGGGACATGCATCGACCTCGAGATATACAAGC
1 AGTGTAAGACATGTCTGGGACATGCATCG-CCTCTAGATATACAAGC
* *
12654293 TAGTTTAAGACCTGTCTGGGACATG
1 -AGTGTAAGACATGTCTGGGACATG
12654318 GCGTCAGCTT
Statistics
Matches: 88, Mismatches: 26, Indels: 8
0.72 0.21 0.07
Matches are distributed among these distances:
46 32 0.36
47 5 0.06
48 51 0.58
ACGTcount: A:0.30, C:0.18, G:0.27, T:0.25
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGCATCGCCTCTAGATATACAAGC
Found at i:12659356 original size:19 final size:19
Alignment explanation
Indices: 12659332--12659369 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
12659322 AATCTTACCA
* *
12659332 GTGAATAGGTTAGGGTACT
1 GTGAATACGTCAGGGTACT
12659351 GTGAATACGTCAGGGTACT
1 GTGAATACGTCAGGGTACT
12659370 ATTTTCTCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.26, C:0.11, G:0.34, T:0.29
Consensus pattern (19 bp):
GTGAATACGTCAGGGTACT
Found at i:12665610 original size:19 final size:19
Alignment explanation
Indices: 12665586--12665628 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
12665576 TGTGTGATTA
12665586 TCCGAGTGTCCTATTCCAT
1 TCCGAGTGTCCTATTCCAT
12665605 TCCGAGTGTCCTATTCCAT
1 TCCGAGTGTCCTATTCCAT
12665624 TCCGA
1 TCCGA
12665629 ATGGTTCATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.16, C:0.33, G:0.16, T:0.35
Consensus pattern (19 bp):
TCCGAGTGTCCTATTCCAT
Found at i:12669274 original size:20 final size:21
Alignment explanation
Indices: 12669243--12669286 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
12669233 ATTAAAAGGT
* *
12669243 TAATATAGTAAATTAATGAAA
1 TAATATAGTAAAATAATAAAA
12669264 TAATA-AGTAAAATAATAAAA
1 TAATATAGTAAAATAATAAAA
12669284 TAA
1 TAA
12669287 CCAAAGCTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 16 0.76
21 5 0.24
ACGTcount: A:0.64, C:0.00, G:0.07, T:0.30
Consensus pattern (21 bp):
TAATATAGTAAAATAATAAAA
Found at i:12671529 original size:40 final size:40
Alignment explanation
Indices: 12671470--12671562 Score: 159
Period size: 40 Copynumber: 2.3 Consensus size: 40
12671460 TAGTGTGGGC
*
12671470 GACTTAACCCGGATATAGTAACTCGCACAATTGCCTTCGG
1 GACTTAACCCGGATATAGTAACTCGCACAAATGCCTTCGG
*
12671510 GACTTAACCCGGATTTAGTAACTCGCACAAATGCCTTCGG
1 GACTTAACCCGGATATAGTAACTCGCACAAATGCCTTCGG
*
12671550 GACTTAGCCCGGA
1 GACTTAACCCGGA
12671563 CATCATTCAA
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 50 1.00
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
GACTTAACCCGGATATAGTAACTCGCACAAATGCCTTCGG
Found at i:12679453 original size:39 final size:38
Alignment explanation
Indices: 12679300--12679518 Score: 153
Period size: 40 Copynumber: 5.6 Consensus size: 38
12679290 TACTCGTTCA
* * *
12679300 AATGCTTTCGGGACATAGCCCGG-TTATAGTAACTCGCAC
1 AATGCCTTCGGGACTTAACCCGGATT-TA-TAACTCGCAC
*
12679339 AATTGCCTTCGGGACTTAACCCGGATTTAGTAACTTGCAC
1 AA-TGCCTTCGGGACTTAACCCGGATTTA-TAACTCGCAC
* * ** *
12679379 AAATGCC-T--GG-CTTAGCCCGAAATTCGTATCTCGCCAC
1 -AATGCCTTCGGGACTTAACCCG-GATTTATAACTCG-CAC
*
12679416 AATGCCTTCGGGACTTAACTCGGATTTATAACTCGCCAC
1 AATGCCTTCGGGACTTAACCCGGATTTATAACTCG-CAC
* * *
12679455 AA-GCGCTTCGGGACTTAACCCGGATTTGGTCACTTAGCAC
1 AATGC-CTTCGGGACTTAACCCGGATTT-ATAAC-TCGCAC
* * *
12679495 AAAGGCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
12679519 CATCATTCAA
Statistics
Matches: 145, Mismatches: 22, Indels: 25
0.76 0.11 0.13
Matches are distributed among these distances:
36 19 0.13
37 9 0.06
38 2 0.01
39 41 0.28
40 67 0.46
41 7 0.05
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (38 bp):
AATGCCTTCGGGACTTAACCCGGATTTATAACTCGCAC
Found at i:12682976 original size:79 final size:80
Alignment explanation
Indices: 12682865--12683055 Score: 255
Period size: 79 Copynumber: 2.4 Consensus size: 80
12682855 GGTTATAGTA
* *
12682865 ACTCGCACAATTG-CTTCGGGACTTAACCCGGATTTAGTAACTTGCACAAATGCCTTCGGG-CTT
1 ACTCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACAAATGCCTTCGGGACTT
*
12682928 AGCCCGAAATTCGT-
66 AACCCGAAATTCGTC
*
12682942 ATCTCGCACAAATGCCTTCGGGACTTAACTCGGATTTAGTAACTCGCACAAATGCCTTCGGGACT
1 A-CTCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACAAATGCCTTCGGGACT
* * *
12683007 TAACCCGGATTTGGTC
65 TAACCCGAAATTCGTC
* *
12683023 ACTTAGCACAAA-GCCTTCGGGACTTAGCCCGGA
1 AC-TCGCACAAATGCCTTCGGGACTTAACCCGGA
12683056 CATCATTCAA
Statistics
Matches: 99, Mismatches: 10, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
77 1 0.01
78 11 0.11
79 45 0.45
80 33 0.33
81 9 0.09
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (80 bp):
ACTCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACAAATGCCTTCGGGACTT
AACCCGAAATTCGTC
Found at i:12682999 original size:40 final size:40
Alignment explanation
Indices: 12682840--12683055 Score: 260
Period size: 40 Copynumber: 5.5 Consensus size: 40
12682830 GTTCAAAGCT
* * *
12682840 TTCGGGACATAGCCCGG-TTATAGTAACTCGCACAATTG-C
1 TTCGGGACTTAACCCGGATT-TAGTAACTCGCACAAATGCC
*
12682879 TTCGGGACTTAACCCGGATTTAGTAACTTGCACAAATGCC
1 TTCGGGACTTAACCCGGATTTAGTAACTCGCACAAATGCC
* * * * *
12682919 TTCGGG-CTTAGCCCGAAATTCGTATCTCGCACAAATGCC
1 TTCGGGACTTAACCCGGATTTAGTAACTCGCACAAATGCC
*
12682958 TTCGGGACTTAACTCGGATTTAGTAACTCGCACAAATGCC
1 TTCGGGACTTAACCCGGATTTAGTAACTCGCACAAATGCC
* * *
12682998 TTCGGGACTTAACCCGGATTTGGTCACTTAGCACAAA-GCC
1 TTCGGGACTTAACCCGGATTTAGTAAC-TCGCACAAATGCC
*
12683038 TTCGGGACTTAGCCCGGA
1 TTCGGGACTTAACCCGGA
12683056 CATCATTCAA
Statistics
Matches: 152, Mismatches: 21, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
39 64 0.42
40 80 0.53
41 8 0.05
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
TTCGGGACTTAACCCGGATTTAGTAACTCGCACAAATGCC
Found at i:12686405 original size:39 final size:40
Alignment explanation
Indices: 12686360--12686571 Score: 204
Period size: 39 Copynumber: 5.6 Consensus size: 40
12686350 GCTACTCGTT
*
12686360 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
*
12686400 C-AATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-TTATAGTAACTCGCA
* *
12686439 CAAATGCCTTCGGG-CTTAGCCCGG-AATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTA-TAGTAACTCGCA
* *
12686478 CAAATGCCTTC-GGA-TTA-CTCGGAT-TAGT--CTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
* * *
12686512 CAAATGCCTTC-GGACTTA--CCGG--ATGGTCACTTAGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAAC-TCGCA
12686548 CAAA-GCCTTCGGGACTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGG
12686572 ACATCATTCA
Statistics
Matches: 148, Mismatches: 10, Indels: 30
0.79 0.05 0.16
Matches are distributed among these distances:
33 3 0.02
34 23 0.16
35 10 0.07
36 19 0.13
37 4 0.03
38 9 0.06
39 65 0.44
40 15 0.10
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
Found at i:12699283 original size:40 final size:40
Alignment explanation
Indices: 12699217--12699294 Score: 104
Period size: 40 Copynumber: 1.9 Consensus size: 40
12699207 CGACTATGTT
* *
12699217 TAGCACTTAGTGTGCGTTTCAAAATAGCTTCGGCTATAAA
1 TAGCACTTAGTGTGCGATTCAAAATAGCTTCAGCTATAAA
**
12699257 TAGCACTTAGTGTGCGAATT-GGAATAGCTTCAGCTATA
1 TAGCACTTAGTGTGCG-ATTCAAAATAGCTTCAGCTATA
12699295 TGAGGCACTA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 31 0.94
41 2 0.06
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.32
Consensus pattern (40 bp):
TAGCACTTAGTGTGCGATTCAAAATAGCTTCAGCTATAAA
Found at i:12702579 original size:49 final size:49
Alignment explanation
Indices: 12702507--12702699 Score: 203
Period size: 49 Copynumber: 3.9 Consensus size: 49
12702497 GCCGAAGCTA
* * *
12702507 TCTGGAACGCGTAGTAGCCTGCACTTAGTACTACGCATGCGACCAACAG
1 TCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAACAG
* * *
12702556 TCTGGTACGCGTAGTAGCCTGCACTTAGTACTACACA-GTGACCTCACCA-
1 TCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGA-C-CAACAG
** * * * *
12702605 TCTAATACACATAGTAGCCTGCACTTAGTACTACACACGTGATC-ACAG
1 TCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAACAG
*
12702653 TTTTCGGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACC
1 ---TCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACC
12702700 TCACAATAGA
Statistics
Matches: 120, Mismatches: 17, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
47 2 0.02
48 4 0.03
49 69 0.57
50 8 0.07
51 37 0.31
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.24
Consensus pattern (49 bp):
TCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAACAG
Found at i:12702689 original size:100 final size:99
Alignment explanation
Indices: 12702518--12702703 Score: 268
Period size: 100 Copynumber: 1.9 Consensus size: 99
12702508 CTGGAACGCG
* * * *
12702518 TAGTAGCCTGCACTTAGTACTACGCATGCGACCAACAGTCTGGTACGCGTAGTAGCCTGCACTTA
1 TAGTAGCCTGCACTTAGTACTACACACGCGACCAACAGTCGGGTACGCATAGTAGCCTGCACTTA
*
12702583 GTACTACACA-GTGACCTCACCATCTAATACACA
66 GTACTACACATGCGACCTCACCATCTAATACACA
* *
12702616 TAGTAGCCTGCACTTAGTACTACACACGTGATC-ACAGTTTTCGGGTACGCATAGTAGCCTGCAC
1 TAGTAGCCTGCACTTAGTACTACACACGCGACCAACAG---TCGGGTACGCATAGTAGCCTGCAC
12702680 TTAGTACTACACATGCGACCTCAC
63 TTAGTACTACACATGCGACCTCAC
12702704 AATAGATCAT
Statistics
Matches: 77, Mismatches: 7, Indels: 5
0.87 0.08 0.06
Matches are distributed among these distances:
97 4 0.05
98 29 0.38
100 35 0.45
101 9 0.12
ACGTcount: A:0.27, C:0.29, G:0.19, T:0.25
Consensus pattern (99 bp):
TAGTAGCCTGCACTTAGTACTACACACGCGACCAACAGTCGGGTACGCATAGTAGCCTGCACTTA
GTACTACACATGCGACCTCACCATCTAATACACA
Found at i:12704419 original size:15 final size:15
Alignment explanation
Indices: 12704372--12704427 Score: 71
Period size: 15 Copynumber: 3.7 Consensus size: 15
12704362 ACAAGAAAAC
12704372 GAATAAAGAAATCCA
1 GAATAAAGAAATCCA
*
12704387 -AGATAGAA-AAACCCA
1 GA-ATA-AAGAAATCCA
12704402 GAATAAAGAAATCCA
1 GAATAAAGAAATCCA
12704417 GAATAAAGAAA
1 GAATAAAGAAA
12704428 CCCAAGATAC
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
14 3 0.09
15 29 0.83
16 3 0.09
ACGTcount: A:0.62, C:0.12, G:0.14, T:0.11
Consensus pattern (15 bp):
GAATAAAGAAATCCA
Found at i:12707547 original size:50 final size:49
Alignment explanation
Indices: 12707439--12707568 Score: 181
Period size: 50 Copynumber: 2.6 Consensus size: 49
12707429 CTGGTACGCA
* * * **
12707439 TAGTAGCC-GACACTTAGTACTACACATGCGACCAACAGTCTGGTACACG
1 TAGTAGCCTG-CACTTAGTACTACACACGTGACCAACAATCTAATACACG
*
12707488 TAGTAGCCTGCACTTAGTACTACACACGTGACCTCACAATCTAATACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACC-AACAATCTAATACACG
12707538 TAGTAGCCTGCACTTAGTACTACACACGTGA
1 TAGTAGCCTGCACTTAGTACTACACACGTGA
12707569 TCACAGTTTT
Statistics
Matches: 73, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
49 29 0.40
50 44 0.60
ACGTcount: A:0.31, C:0.28, G:0.18, T:0.23
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACACGTGACCAACAATCTAATACACG
Found at i:12709292 original size:153 final size:152
Alignment explanation
Indices: 12709011--12709320 Score: 471
Period size: 153 Copynumber: 2.0 Consensus size: 152
12709001 ATTTGTATGT
*
12709011 ATTT-GCATTTTGGGTTGGGATTTGATTTTGGAAGTGTGGAAAAATGATTCTACAGTTAAATTGC
1 ATTTGGCATTTTGGGTTGGGATTTGATTTTGGAAGTGAGGAAAAATGATTCTACAGTTAAATTGC
*
12709075 ACTACTATTATCTAGCGATAAAATCGCAATTATGTTAGCAGCCCAACTGTATAAAGATCATGAGG
66 ACTACTATTATCTAGCGATAAAATCGCAATTATGTTAGCAGCCCAACTGCATAAAGATCATGAGG
*
12709140 CAAATGACCTTTTCATGGTGTG
131 CAAATGACCTCTTCATGGTGTG
**
12709162 ATTTGGCATTTTGGGTTGGGATTTGATTTTGGAAGTGAAGGAAGTATGATTCTACAGTTAAATTG
1 ATTTGGCATTTTGGGTTGGGATTTGATTTTGGAAGTG-AGGAAAAATGATTCTACAGTTAAATTG
** * * * * * *
12709227 CGTTATTATTATTTAGTGATAAAA-CTGCAATTATGTTAGCAGCCCGACTGCATAACGGTCATGA
65 CACTACTATTATCTAGCGATAAAATC-GCAATTATGTTAGCAGCCCAACTGCATAAAGATCATGA
12709291 GGCAAATGACCTCTTCATGGTGTG
129 GGCAAATGACCTCTTCATGGTGTG
12709315 ATTTGG
1 ATTTGG
12709321 TTAGATTGGT
Statistics
Matches: 143, Mismatches: 13, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
151 4 0.03
152 33 0.23
153 106 0.74
ACGTcount: A:0.29, C:0.13, G:0.24, T:0.35
Consensus pattern (152 bp):
ATTTGGCATTTTGGGTTGGGATTTGATTTTGGAAGTGAGGAAAAATGATTCTACAGTTAAATTGC
ACTACTATTATCTAGCGATAAAATCGCAATTATGTTAGCAGCCCAACTGCATAAAGATCATGAGG
CAAATGACCTCTTCATGGTGTG
Found at i:12715697 original size:19 final size:20
Alignment explanation
Indices: 12715673--12715710 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
12715663 GGTACCACCA
12715673 AAACAT-ATATCA-CATCTTT
1 AAACATCAT-TCATCATCTTT
12715692 AAACATCATTCATCATCTT
1 AAACATCATTCATCATCTT
12715711 ACCACCTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (20 bp):
AAACATCATTCATCATCTTT
Found at i:12716024 original size:46 final size:46
Alignment explanation
Indices: 12715939--12716060 Score: 181
Period size: 46 Copynumber: 2.7 Consensus size: 46
12715929 CGCCCCTAAG
* * * *
12715939 TGAACTCGGACTCAACTCAATGAGATCGGGCGTTCGCATCCATAAA
1 TGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAA
* *
12715985 TGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAG
1 TGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAA
*
12716031 TGAACTCAGACTCAACTCAACGAGTTCGGA
1 TGAACTCGGACTCAACTCAACGAGTTCGGA
12716061 TGCTCAACCA
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 69 1.00
ACGTcount: A:0.31, C:0.26, G:0.20, T:0.22
Consensus pattern (46 bp):
TGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAA
Found at i:12716517 original size:30 final size:30
Alignment explanation
Indices: 12716483--12716542 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
12716473 ATTTAATATG
12716483 AACTTTTAAAAAAATACACTTTTGCCCCTA
1 AACTTTTAAAAAAATACACTTTTGCCCCTA
** * *
12716513 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTTAAAAAAATACACTTTTGCCCCTA
12716543 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.33, C:0.25, G:0.05, T:0.37
Consensus pattern (30 bp):
AACTTTTAAAAAAATACACTTTTGCCCCTA
Found at i:12723174 original size:19 final size:20
Alignment explanation
Indices: 12723150--12723187 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
12723140 GGTACCACCA
12723150 AAACAT-ATATCA-CATCTTT
1 AAACATCAT-TCATCATCTTT
12723169 AAACATCATTCATCATCTT
1 AAACATCATTCATCATCTT
12723188 ACCACATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (20 bp):
AAACATCATTCATCATCTTT
Found at i:12723560 original size:46 final size:46
Alignment explanation
Indices: 12723412--12723583 Score: 190
Period size: 46 Copynumber: 3.7 Consensus size: 46
12723402 AACCCGCCCC
* *** *
12723412 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGTGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
* * *
12723458 TAAATGAACTC-GACTCAACTCAACGAGTTCGGATGCCTAGTTACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-ATTTGCATCCA
* *
12723505 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
12723550 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
12723584 TGCTCAACCA
Statistics
Matches: 104, Mismatches: 14, Indels: 16
0.78 0.10 0.12
Matches are distributed among these distances:
43 6 0.06
44 2 0.02
45 22 0.21
46 45 0.43
47 24 0.23
48 1 0.01
49 4 0.04
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.23
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
Found at i:12730518 original size:46 final size:46
Alignment explanation
Indices: 12730468--12730640 Score: 217
Period size: 46 Copynumber: 3.7 Consensus size: 46
12730458 TGGTTGAGCA
*
12730468 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * *
12730514 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CG
*
12730561 TCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCAAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* *
12730607 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
12730641 GGGGCGGGTT
Statistics
Matches: 108, Mismatches: 12, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
43 6 0.06
45 3 0.03
46 61 0.56
47 29 0.27
48 3 0.03
50 6 0.06
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:12730624 original size:93 final size:93
Alignment explanation
Indices: 12730465--12730635 Score: 306
Period size: 93 Copynumber: 1.8 Consensus size: 93
12730455 GGATGGTTGA
* *
12730465 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
12730530 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* *
12730558 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCAAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
12730623 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
12730636 ACTTAGGGGC
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:12730902 original size:19 final size:20
Alignment explanation
Indices: 12730865--12730902 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
12730855 ATAAGGTTGT
12730865 AAGATGATGAATGATGTTTA
1 AAGATGATGAATGATGTTTA
12730885 AAGATG-TGATAT-ATGTTT
1 AAGATGATGA-ATGATGTTT
12730903 TGGTGGTACC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.37, C:0.00, G:0.24, T:0.39
Consensus pattern (20 bp):
AAGATGATGAATGATGTTTA
Found at i:12734955 original size:23 final size:22
Alignment explanation
Indices: 12734874--12734944 Score: 74
Period size: 22 Copynumber: 3.2 Consensus size: 22
12734864 CCAGATCTGA
* *
12734874 TGAACAATAAGCTCTATTGAGC
1 TGAACAGTAAGCTCTATCGAGC
*
12734896 T-AAAACGATAAGCTCTATCGAGC
1 TGAACA-G-TAAGCTCTATCGAGC
12734919 TGAACAGTAAGCTC-ATGCGAGC
1 TGAACAGTAAGCTCTAT-CGAGC
12734941 TGAA
1 TGAA
12734945 ATGGTAAGCT
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
21 5 0.12
22 17 0.41
23 16 0.39
24 3 0.07
ACGTcount: A:0.37, C:0.20, G:0.21, T:0.23
Consensus pattern (22 bp):
TGAACAGTAAGCTCTATCGAGC
Found at i:12737425 original size:15 final size:15
Alignment explanation
Indices: 12737405--12737441 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
12737395 ATACCAAGAT
12737405 GAGGCAAGTGATATC
1 GAGGCAAGTGATATC
12737420 GAGGCAAGTGATATC
1 GAGGCAAGTGATATC
*
12737435 AAGGCAA
1 GAGGCAA
12737442 CTCAGTCTGT
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:0.38, C:0.14, G:0.32, T:0.16
Consensus pattern (15 bp):
GAGGCAAGTGATATC
Found at i:12737524 original size:27 final size:27
Alignment explanation
Indices: 12737494--12737551 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
12737484 ACCCCCTAAT
* *
12737494 TGATAAAATGAATGTTATTCCCTTATG
1 TGATAAAATCAATGTTATGCCCTTATG
* *
12737521 TGATAAAATCACTGTTATGCCTTTATG
1 TGATAAAATCAATGTTATGCCCTTATG
12737548 TGAT
1 TGAT
12737552 GTATGATTGT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.31, C:0.12, G:0.16, T:0.41
Consensus pattern (27 bp):
TGATAAAATCAATGTTATGCCCTTATG
Found at i:12744289 original size:25 final size:25
Alignment explanation
Indices: 12744261--12744330 Score: 88
Period size: 25 Copynumber: 2.8 Consensus size: 25
12744251 CTCTTTTAAT
*
12744261 AACTGGGGCAAAGCCCTTTTTGACA
1 AACTGGGGCAAAGCCCTTTTCGACA
* **
12744286 AACTAGGGCAAAGCCCTTTTCGGTA
1 AACTGGGGCAAAGCCCTTTTCGACA
12744311 AA-TCGGGGCAAAGCCCTTTT
1 AACT-GGGGCAAAGCCCTTTT
12744331 GCACTTCCTC
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
24 1 0.03
25 38 0.97
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.24
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTTCGACA
Found at i:12749000 original size:15 final size:16
Alignment explanation
Indices: 12748973--12749002 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
12748963 AGATATTCCA
12748973 ATTTAGTCCCATTTTT
1 ATTTAGTCCCATTTTT
12748989 ATTTAG-CCCATTTT
1 ATTTAGTCCCATTTT
12749003 GGGAATTTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.20, C:0.20, G:0.07, T:0.53
Consensus pattern (16 bp):
ATTTAGTCCCATTTTT
Found at i:12762372 original size:40 final size:39
Alignment explanation
Indices: 12762328--12762419 Score: 105
Period size: 40 Copynumber: 2.3 Consensus size: 39
12762318 TATGATTGGT
*
12762328 ACTAAGTGTGCGGTTTAATATAACTTCGGCTACA-AATGGC
1 ACTAAGTGTGCGG-TTAACATAACTTCGGCTACAGAA-GGC
* ** *
12762368 ACTAAGTGTGCCAGTTGGCATAACTTCGGCTATAGAAGGC
1 ACTAAGTGTG-CGGTTAACATAACTTCGGCTACAGAAGGC
12762408 ACTAAGTGTGCG
1 ACTAAGTGTGCG
12762420 ATACCGATTT
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
39 1 0.02
40 39 0.89
41 4 0.09
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.27
Consensus pattern (39 bp):
ACTAAGTGTGCGGTTAACATAACTTCGGCTACAGAAGGC
Found at i:12763923 original size:5 final size:5
Alignment explanation
Indices: 12763913--12763940 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
12763903 ATTAATCTTA
12763913 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
12763941 TCTTCTTCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:12766094 original size:18 final size:18
Alignment explanation
Indices: 12766071--12766108 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
12766061 TTTTCATACT
12766071 TTAAATAAAT-TAACTTTA
1 TTAAATAAATATAA-TTTA
*
12766089 TTAAATATATATAATTTA
1 TTAAATAAATATAATTTA
12766107 TT
1 TT
12766109 TTTTTTAGGC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (18 bp):
TTAAATAAATATAATTTA
Found at i:12766587 original size:27 final size:29
Alignment explanation
Indices: 12766521--12766593 Score: 78
Period size: 29 Copynumber: 2.5 Consensus size: 29
12766511 AATATTACTC
* *
12766521 AATTATTTATTTATTTTTATTGGTAACAT
1 AATTATTTCTTTATTCTTATTGGTAACAT
* *
12766550 AACTTTTTTTCTTT-TTCTT-TTGTTAACAT
1 AA--TTATTTCTTTATTCTTATTGGTAACAT
12766579 AATTATTTCTTTATT
1 AATTATTTCTTTATT
12766594 TGAAAAATCT
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
27 9 0.25
28 2 0.06
29 13 0.36
30 4 0.11
31 8 0.22
ACGTcount: A:0.25, C:0.08, G:0.04, T:0.63
Consensus pattern (29 bp):
AATTATTTCTTTATTCTTATTGGTAACAT
Found at i:12768117 original size:53 final size:53
Alignment explanation
Indices: 12768032--12768137 Score: 176
Period size: 53 Copynumber: 2.0 Consensus size: 53
12768022 TTGTTCATGT
*
12768032 GTCATCATCGTGTTTAGTCATGTCACGCAACTGTTAAAAAATTAATGGTGTTA
1 GTCAGCATCGTGTTTAGTCATGTCACGCAACTGTTAAAAAATTAATGGTGTTA
* * *
12768085 GTCAGCATCGTGTTTAGTCATGTTACTCAACTGTTAAAAAATTAATTGTGTTA
1 GTCAGCATCGTGTTTAGTCATGTCACGCAACTGTTAAAAAATTAATGGTGTTA
12768138 ATCATAAGAA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
53 49 1.00
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.38
Consensus pattern (53 bp):
GTCAGCATCGTGTTTAGTCATGTCACGCAACTGTTAAAAAATTAATGGTGTTA
Found at i:12775581 original size:25 final size:25
Alignment explanation
Indices: 12775553--12775601 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
12775543 TTATAATATG
* * *
12775553 AAAAATGACTATTTTGCCCTTAGGT
1 AAAAATGACCATTTTACCCCTAGGT
12775578 AAAAATGACCATTTTACCCCTAGG
1 AAAAATGACCATTTTACCCCTAGG
12775602 GTTTAATTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.35, C:0.20, G:0.14, T:0.31
Consensus pattern (25 bp):
AAAAATGACCATTTTACCCCTAGGT
Found at i:12780040 original size:27 final size:27
Alignment explanation
Indices: 12780010--12780098 Score: 99
Period size: 27 Copynumber: 3.3 Consensus size: 27
12780000 GTGCGTATAG
12780010 TGATAGTGACACTTCGGTGCAACTCAA
1 TGATAGTGACACTTCGGTGCAACTCAA
* *
12780037 TGATAGTGACACTAT-GGTGCAACTTAG
1 TGATAGTGACACT-TCGGTGCAACTCAA
* * * *
12780064 TTATAGTGGCACTTCAGTGCAATTCAA
1 TGATAGTGACACTTCGGTGCAACTCAA
*
12780091 TGACAGTG
1 TGATAGTG
12780099 GCTCTTTGGA
Statistics
Matches: 50, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
26 1 0.02
27 48 0.96
28 1 0.02
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (27 bp):
TGATAGTGACACTTCGGTGCAACTCAA
Found at i:12782587 original size:15 final size:15
Alignment explanation
Indices: 12782563--12782602 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
12782553 AAGCAACATC
12782563 AAGA-GAATCACCAA
1 AAGATGAATCACCAA
*
12782577 AAGATGAATCACCTA
1 AAGATGAATCACCAA
12782592 AAGATGAATCA
1 AAGATGAATCA
12782603 TATCATGTAC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 4 0.17
15 20 0.83
ACGTcount: A:0.53, C:0.17, G:0.15, T:0.15
Consensus pattern (15 bp):
AAGATGAATCACCAA
Found at i:12790477 original size:46 final size:45
Alignment explanation
Indices: 12790410--12790501 Score: 175
Period size: 46 Copynumber: 2.0 Consensus size: 45
12790400 CATCACAAGA
12790410 ATAAGCCAAAAATTACAAGATCGTCTCGAAAATCATTCTCATAGAT
1 ATAAGCCAAAAATTACAAGATCGTCTCG-AAATCATTCTCATAGAT
12790456 ATAAGCCAAAAATTACAAGATCGTCTCGAAATCATTCTCATAGAT
1 ATAAGCCAAAAATTACAAGATCGTCTCGAAATCATTCTCATAGAT
12790501 A
1 A
12790502 GAACTTACTC
Statistics
Matches: 46, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
45 18 0.39
46 28 0.61
ACGTcount: A:0.43, C:0.20, G:0.11, T:0.26
Consensus pattern (45 bp):
ATAAGCCAAAAATTACAAGATCGTCTCGAAATCATTCTCATAGAT
Found at i:12804579 original size:46 final size:46
Alignment explanation
Indices: 12804459--12804586 Score: 147
Period size: 46 Copynumber: 2.8 Consensus size: 46
12804449 TAACCCGCCC
12804459 CTAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CTAAGTGAACTCGGACTCAACTCAACGAGTTCGGA--CCTAGTTACAT
* * * *
12804507 CTCA-CGAACTCGGACTCAACTTAACGAGTTCGGA-C-A-TTCGCAT
1 CTAAGTGAACTCGGACTCAACTCAACGAGTTCGGACCTAGTT-ACAT
12804550 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 -C-TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
12804587 TGCTCAACCA
Statistics
Matches: 69, Mismatches: 7, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
42 2 0.03
43 4 0.06
44 2 0.03
45 2 0.03
46 28 0.41
47 28 0.41
48 3 0.04
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.23
Consensus pattern (46 bp):
CTAAGTGAACTCGGACTCAACTCAACGAGTTCGGACCTAGTTACAT
Found at i:12804605 original size:46 final size:44
Alignment explanation
Indices: 12804462--12804605 Score: 132
Period size: 46 Copynumber: 3.1 Consensus size: 44
12804452 CCCGCCCCTA
12804462 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTA-CATCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCC-A---ACCATCT
* * * * *
12804509 CA-CGAACTCGGACTCAACTTAACGAGTTCGGACATTCGCATCCAT-A
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGC-CAACCATCT
12804555 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGC-CAACCAT-CT
12804601 AGTGA
1 AGTGA
12804606 CATGTCACTT
Statistics
Matches: 78, Mismatches: 11, Indels: 16
0.74 0.10 0.15
Matches are distributed among these distances:
44 9 0.12
45 1 0.01
46 32 0.41
47 30 0.38
48 1 0.01
49 4 0.05
50 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.23
Consensus pattern (44 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCAACCATCT
Found at i:12812015 original size:93 final size:93
Alignment explanation
Indices: 12811908--12812078 Score: 324
Period size: 93 Copynumber: 1.8 Consensus size: 93
12811898 GCCCCTAAGT
*
12811908 GAACTCGGACTCAACTCAACGAGCTCGGGCATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
12811973 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
12812001 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
12812066 CGAGTTCGGATGC
66 CGAGTTCGGATGC
12812079 TCAACCATCC
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:12812075 original size:46 final size:46
Alignment explanation
Indices: 12811903--12812075 Score: 228
Period size: 46 Copynumber: 3.7 Consensus size: 46
12811893 AACCCGCCCC
* *
12811903 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
*
12811949 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCATCCA
* *
12811997 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
12812042 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
12812076 TGCTCAACCA
Statistics
Matches: 110, Mismatches: 8, Indels: 18
0.81 0.06 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 61 0.55
47 29 0.26
48 2 0.02
49 2 0.02
50 4 0.04
51 2 0.02
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.21
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
Found at i:12814344 original size:42 final size:42
Alignment explanation
Indices: 12814296--12814399 Score: 104
Period size: 43 Copynumber: 2.5 Consensus size: 42
12814286 GATGCCTCTA
* * *
12814296 TCCCAGACAGGGTCTTACACG-AAA-TCAGATACGATGTCAATG
1 TCCCAGACACGGTCTTACACGTAAACTCA-AT-CGAGGCCAATG
* * * *
12814338 TCCCAGACATGGTCCTATACGTAAATCTCAATCGAGGCCTATG
1 TCCCAGACACGGTCTTACACGTAAA-CTCAATCGAGGCCAATG
12814381 TCCCAGACACGGTCTTACA
1 TCCCAGACACGGTCTTACA
12814400 TGATATCTTA
Statistics
Matches: 50, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
42 18 0.36
43 27 0.54
44 2 0.04
45 3 0.06
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (42 bp):
TCCCAGACACGGTCTTACACGTAAACTCAATCGAGGCCAATG
Found at i:12816524 original size:22 final size:22
Alignment explanation
Indices: 12816499--12816541 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
12816489 TGTTTCCTTG
12816499 TTTGAGCTCTAGAAATTCTTTA
1 TTTGAGCTCTAGAAATTCTTTA
12816521 TTTGAGCTCTAGAAATTCTTT
1 TTTGAGCTCTAGAAATTCTTT
12816542 CTTTTTCTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.26, C:0.14, G:0.14, T:0.47
Consensus pattern (22 bp):
TTTGAGCTCTAGAAATTCTTTA
Found at i:12821938 original size:93 final size:93
Alignment explanation
Indices: 12821774--12821945 Score: 267
Period size: 93 Copynumber: 1.8 Consensus size: 93
12821764 CGCCCATAAG
* *
12821774 CGAACTCGGACTCAACTCAATGAGCTCGAGCGTTCGCATCCATAGCTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGAGCATTCGCATCCATAGCTGAACTCGGACTCAACTCA
12821839 ACGAGTTCGGATGCCTAGTTACATTTCA
66 ACGAGTTCGGATGCCTAGTTACATTTCA
**
12821867 CGAACTCGGACTCAACTCAACGATTTCG-GACATTCGCATCCATAAG-TGAACTCGGACTCAACT
1 CGAACTCGGACTCAACTCAACGAGCTCGAG-CATTCGCATCCAT-AGCTGAACTCGGACTCAACT
*
12821930 CAATGAGTTCGGATGC
64 CAACGAGTTCGGATGC
12821946 TCAACCATCC
Statistics
Matches: 72, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
92 1 0.01
93 69 0.96
94 2 0.03
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.23
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGAGCATTCGCATCCATAGCTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATTTCA
Found at i:12821941 original size:46 final size:47
Alignment explanation
Indices: 12821767--12821942 Score: 177
Period size: 46 Copynumber: 3.8 Consensus size: 47
12821757 TGTAACCCGC
* * *
12821767 CCATAAGCGAACTCGGACTCAACTCAATGAGCTC-GAGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGAGCATTCGCAT
*
12821813 CCAT-AGCTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGC-GAACTCGGACTCAACTCAACGAGTTCGGA-G-C-A-TTCGCAT
* * *
12821863 --TTCA-CGAACTCGGACTCAACTCAACGATTTCGGA-CATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGAGCATTCGCAT
* *
12821906 CCATAAGTGAACTCGGACTCAACTCAATGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
12821943 TGCTCAACCA
Statistics
Matches: 107, Mismatches: 12, Indels: 22
0.76 0.09 0.16
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 1 0.01
45 5 0.05
46 55 0.51
47 30 0.28
48 3 0.03
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.23
Consensus pattern (47 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGAGCATTCGCAT
Found at i:12821961 original size:46 final size:45
Alignment explanation
Indices: 12821820--12821961 Score: 112
Period size: 46 Copynumber: 3.1 Consensus size: 45
12821810 CATCCATAGC
*
12821820 TGAACTCGGACTCAACTCAACGAGTTCGGATGC-CTAGTTA-CATTTCA-
1 TGAACTCGGACTCAACTCAACGAGTTCGGATGCTC-A---ACCATCT-AG
* * * * * *
12821867 CGAACTCGGACTCAACTCAACGATTTCGGACATTCGCATCCAT-AAG
1 TGAACTCGGACTCAACTCAACGAGTTCGG--ATGCTCAACCATCTAG
*
12821913 TGAACTCGGACTCAACTCAATGAGTTCGGATGCTCAACCATCCTAG
1 TGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCAT-CTAG
12821959 TGA
1 TGA
12821962 CATGTCACTT
Statistics
Matches: 76, Mismatches: 12, Indels: 15
0.74 0.12 0.15
Matches are distributed among these distances:
44 9 0.12
45 1 0.01
46 31 0.41
47 30 0.39
49 4 0.05
50 1 0.01
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.25
Consensus pattern (45 bp):
TGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCTAG
Found at i:12825830 original size:51 final size:51
Alignment explanation
Indices: 12825753--12825885 Score: 146
Period size: 51 Copynumber: 2.6 Consensus size: 51
12825743 CGGATACCCG
* * *
12825753 GTGG-CTTGCACATAGTACCACCCTTGT-AGTCAAAGCTACCTTCTT-CACAAA
1 GTGGCCTT-CACATAGTACCACACTTGTGA-TCAAAACCACC-TCTTACACAAA
* *
12825804 GTGGCCTTCACATAGTACCACACTTGTGATCAAAACCATCTCTTACACATA
1 GTGGCCTTCACATAGTACCACACTTGTGATCAAAACCACCTCTTACACAAA
* * *
12825855 GTGGCCTACACTTAGTACCACACATGTGATC
1 GTGGCCTTCACATAGTACCACACTTGTGATC
12825886 GAAGCTATTG
Statistics
Matches: 71, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
50 4 0.06
51 63 0.89
52 4 0.06
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.27
Consensus pattern (51 bp):
GTGGCCTTCACATAGTACCACACTTGTGATCAAAACCACCTCTTACACAAA
Done.