Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr13
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: 55873576
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1239791 characters in sequence are not A, C, G, or T
File 53 of 182
Found at i:16520543 original size:75 final size:74
Alignment explanation
Indices: 16520387--16520558 Score: 170
Period size: 75 Copynumber: 2.4 Consensus size: 74
16520377 AGCCATACAT
* * * * * * **
16520387 GGGAAGCTC--AAGAGTCAAAT-TCGAGAAGCTCATGCGAGCCAATATCGGGAAGCTCTGGAGAG
1 GGGAAGCTCATAAGAGCCAAATAACGGGAAGCTCATGAGAGCCAATAACGGAAAGCTCAAGAGAG
16520449 CCATTAATC
66 CCATTAATC
* * *
16520458 GGGAAGCTCATGAGAGCCAATTAACGGGAAGCTCGTGAGAGCCAAATAACGGAAAGCTCAAGAGA
1 GGGAAGCTCATAAGAGCCAAATAACGGGAAGCTCATGAGAGCC-AATAACGGAAAGCTCAAGAGA
* *
16520523 GCCATTTATT
65 GCCATTAATC
** *
16520533 GGGATTCTCATAAGAGCTAAATAACG
1 GGGAAGCTCATAAGAGCCAAATAACG
16520559 AGACGATCTT
Statistics
Matches: 79, Mismatches: 18, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
71 9 0.11
73 8 0.10
74 16 0.20
75 46 0.58
ACGTcount: A:0.35, C:0.19, G:0.27, T:0.19
Consensus pattern (74 bp):
GGGAAGCTCATAAGAGCCAAATAACGGGAAGCTCATGAGAGCCAATAACGGAAAGCTCAAGAGAG
CCATTAATC
Found at i:16522402 original size:23 final size:24
Alignment explanation
Indices: 16522359--16522403 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
16522349 TATTTATTAT
* *
16522359 TTTTTCTGTTTTTTTTGTTTGTCA
1 TTTTTATGTTTTTTTTATTTGTCA
16522383 TTTTTATG-TTTTTTTATTTGT
1 TTTTTATGTTTTTTTTATTTGT
16522404 TTTAAAATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.07, C:0.04, G:0.11, T:0.78
Consensus pattern (24 bp):
TTTTTATGTTTTTTTTATTTGTCA
Found at i:16522428 original size:13 final size:13
Alignment explanation
Indices: 16522410--16522435 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
16522400 TTGTTTTAAA
16522410 ATATTTTAAATGT
1 ATATTTTAAATGT
16522423 ATATTTTAAATGT
1 ATATTTTAAATGT
16522436 TTTATAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (13 bp):
ATATTTTAAATGT
Found at i:16522474 original size:22 final size:22
Alignment explanation
Indices: 16522403--16522477 Score: 80
Period size: 22 Copynumber: 3.3 Consensus size: 22
16522393 TTTTTATTTG
* *
16522403 TTTTAAAATATTTTAAATGTAT
1 TTTTTAAATATTTTAAATATAT
* *
16522425 ATTTTAAATGTTTTATAATATTAT
1 TTTTTAAATATTTTA-AATA-TAT
16522449 TTTTTAAA-ATTTTAAATATAAT
1 TTTTTAAATATTTTAAATAT-AT
16522471 TTTTTAA
1 TTTTTAA
16522478 TGTTATAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
21 1 0.02
22 25 0.57
23 8 0.18
24 10 0.23
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (22 bp):
TTTTTAAATATTTTAAATATAT
Found at i:16522480 original size:45 final size:46
Alignment explanation
Indices: 16522403--16522491 Score: 110
Period size: 45 Copynumber: 2.0 Consensus size: 46
16522393 TTTTTATTTG
* * *
16522403 TTTTAAAATATTTTAAATGTATATTTTAAATGTTTTATAATATTAT
1 TTTTAAAATATTTTAAATATATATTTTAAATGTTATAAAATATTAT
* *
16522449 TTTTTAAA-ATTTTAAATATA-ATTTTTTAATGTTATAAAATATT
1 TTTTAAAATATTTTAAATATATA-TTTTAAATGTTATAAAATATT
16522492 TAAAATATAT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
44 1 0.03
45 29 0.78
46 7 0.19
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.56
Consensus pattern (46 bp):
TTTTAAAATATTTTAAATATATATTTTAAATGTTATAAAATATTAT
Found at i:16522486 original size:22 final size:22
Alignment explanation
Indices: 16522413--16522486 Score: 69
Period size: 22 Copynumber: 3.3 Consensus size: 22
16522403 TTTTAAAATA
* *
16522413 TTTTAAATGT-ATATTTTAAATG
1 TTTTAAATATAAT-TTTTTAATG
* **
16522435 TTTTATAATATTATTTTTTAAAA
1 TTTTA-AATATAATTTTTTAATG
16522458 TTTTAAATATAATTTTTTAATG
1 TTTTAAATATAATTTTTTAATG
*
16522480 TTATAAA
1 TTTTAAA
16522487 ATATTTAAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
22 25 0.60
23 15 0.36
24 2 0.05
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (22 bp):
TTTTAAATATAATTTTTTAATG
Found at i:16522606 original size:21 final size:21
Alignment explanation
Indices: 16522549--16522606 Score: 64
Period size: 21 Copynumber: 2.7 Consensus size: 21
16522539 TTTTATAACA
* *
16522549 TTTAAATGTATATTTTAAGAAT
1 TTTAAATATA-ATTTTAAAAAT
*
16522571 TTTAAATACT-TTTTTAAAAAT
1 TTTAAATA-TAATTTTAAAAAT
16522592 TTTAAATATAATTTT
1 TTTAAATATAATTTT
16522607 TTAAAATTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
20 1 0.03
21 21 0.70
22 7 0.23
23 1 0.03
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.53
Consensus pattern (21 bp):
TTTAAATATAATTTTAAAAAT
Found at i:16522610 original size:23 final size:21
Alignment explanation
Indices: 16522561--16522612 Score: 68
Period size: 23 Copynumber: 2.4 Consensus size: 21
16522551 TAAATGTATA
* *
16522561 TTTTAAGAATTTTAAATACTT
1 TTTTAAAAATTTTAAATAATT
16522582 TTTTAAAAATTTTAAATATAATT
1 TTTTAAAAATTTT-AA-ATAATT
16522605 TTTTAAAA
1 TTTTAAAA
16522613 TTATTTTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 12 0.44
22 2 0.07
23 13 0.48
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (21 bp):
TTTTAAAAATTTTAAATAATT
Found at i:16522613 original size:22 final size:21
Alignment explanation
Indices: 16522561--16522614 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 21
16522551 TAAATGTATA
16522561 TTTTAAGAATTTTAAATACTTT
1 TTTTAA-AATTTTAAATACTTT
*
16522583 TTTAAAAATTTTAAATA-TAATT
1 TTTTAAAATTTTAAATACT--TT
16522605 TTTTAAAATT
1 TTTTAAAATT
16522615 ATTTTTAAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 1 0.04
21 11 0.39
22 16 0.57
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (21 bp):
TTTTAAAATTTTAAATACTTT
Found at i:16528763 original size:11 final size:10
Alignment explanation
Indices: 16528742--16528785 Score: 52
Period size: 11 Copynumber: 4.1 Consensus size: 10
16528732 TCAATTCAAC
16528742 TTTCAATTTTT
1 TTTC-ATTTTT
16528753 TTCTCATTTTT
1 TT-TCATTTTT
16528764 TTTCAGTTTTT
1 TTTCA-TTTTT
*
16528775 TTTTATTTTT
1 TTTCATTTTT
16528785 T
1 T
16528786 GGTCCTCCAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
10 9 0.30
11 19 0.63
12 2 0.07
ACGTcount: A:0.11, C:0.09, G:0.02, T:0.77
Consensus pattern (10 bp):
TTTCATTTTT
Found at i:16529046 original size:36 final size:35
Alignment explanation
Indices: 16528991--16529141 Score: 166
Period size: 36 Copynumber: 4.7 Consensus size: 35
16528981 AAAAAATAAT
*
16528991 AAACAAAT-AAAAAATAGAAAAATGAAATAAAGAA
1 AAACAAATAAAAAAAGAGAAAAATGAAATAAAGAA
16529025 AAACAAATAAAAAAAAGAGAAAAATGAAATAAAGAA
1 AAACAAAT-AAAAAAAGAGAAAAATGAAATAAAGAA
* *
16529061 AAACAAATAAAAATA-AGAAAAA-G-------GAC
1 AAACAAATAAAAAAAGAGAAAAATGAAATAAAGAA
*
16529087 AAACAAATAAAAAAAGAAAAAAATGAAATAAAGAA
1 AAACAAATAAAAAAAGAGAAAAATGAAATAAAGAA
16529122 AAA-AAAT-AAAAAAG-GAAAAA
1 AAACAAATAAAAAAAGAGAAAAA
16529142 GGACAAACAA
Statistics
Matches: 99, Mismatches: 7, Indels: 24
0.76 0.05 0.18
Matches are distributed among these distances:
26 16 0.16
27 6 0.06
28 1 0.01
32 5 0.05
33 8 0.08
34 19 0.19
35 11 0.11
36 33 0.33
ACGTcount: A:0.78, C:0.03, G:0.10, T:0.09
Consensus pattern (35 bp):
AAACAAATAAAAAAAGAGAAAAATGAAATAAAGAA
Found at i:16529139 original size:17 final size:17
Alignment explanation
Indices: 16529078--16529141 Score: 69
Period size: 18 Copynumber: 3.7 Consensus size: 17
16529068 TAAAAATAAG
*
16529078 AAAAAGGACAAACAAATA
1 AAAAAGGA-AAAAAAATA
*
16529096 AAAAAAG-AAAAAAATGA
1 AAAAAGGAAAAAAAAT-A
16529113 AATAAA-GAAAAAAAATA
1 AA-AAAGGAAAAAAAATA
16529130 AAAAAGGAAAAA
1 AAAAAGGAAAAA
16529142 GGACAAACAA
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
16 10 0.25
17 13 0.32
18 17 0.43
ACGTcount: A:0.80, C:0.03, G:0.11, T:0.06
Consensus pattern (17 bp):
AAAAAGGAAAAAAAATA
Found at i:16529166 original size:59 final size:58
Alignment explanation
Indices: 16528999--16529159 Score: 223
Period size: 62 Copynumber: 2.7 Consensus size: 58
16528989 ATAAACAAAT
* * *
16528999 AAAAAATAGAAAAATGAAATAAAGAAAAACAAATAAAAAAAAGAGAAAAATGAAATAAAGAA
1 AAAAAATA-AAAAAAGAAA-AAGGACAAACAAATAAAAAAAA-A-AAAAATGAAATAAAGAA
16529061 AAACAAATAAAAATAAGAAAAAGGACAAACAAATAAAAAAAGAAAAAAATGAAATAAAGAA
1 AAA-AAATAAAAA-AAGAAAAAGGACAAACAAATAAAAAAA-AAAAAAATGAAATAAAGAA
*
16529122 AAAAAATAAAAAAGGAAAAAGGACAAACAAATAAAAAA
1 AAAAAATAAAAAAAGAAAAAGGACAAACAAATAAAAAA
16529160 TCAAAAAGAT
Statistics
Matches: 92, Mismatches: 4, Indels: 9
0.88 0.04 0.09
Matches are distributed among these distances:
59 25 0.27
60 9 0.10
61 20 0.22
62 27 0.29
63 11 0.12
ACGTcount: A:0.78, C:0.04, G:0.11, T:0.08
Consensus pattern (58 bp):
AAAAAATAAAAAAAGAAAAAGGACAAACAAATAAAAAAAAAAAAAATGAAATAAAGAA
Found at i:16533123 original size:17 final size:18
Alignment explanation
Indices: 16533098--16533131 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
16533088 CTAAAATCCA
16533098 TATTAAATTTC-TTTTTC
1 TATTAAATTTCATTTTTC
*
16533115 TATTCAATTTCATTTTT
1 TATTAAATTTCATTTTT
16533132 TAAGATAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.65
Consensus pattern (18 bp):
TATTAAATTTCATTTTTC
Found at i:16533151 original size:10 final size:10
Alignment explanation
Indices: 16533129--16533178 Score: 55
Period size: 10 Copynumber: 4.8 Consensus size: 10
16533119 CAATTTCATT
16533129 TTTTAAGATAA
1 TTTTAA-ATAA
16533140 TTTTAAATAA
1 TTTTAAATAA
* **
16533150 TTTTATATTT
1 TTTTAAATAA
16533160 TTTTAAAATAA
1 TTTT-AAATAA
16533171 TTTTAAAT
1 TTTTAAAT
16533179 TTTTTAATAT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
10 19 0.59
11 13 0.41
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (10 bp):
TTTTAAATAA
Found at i:16533154 original size:21 final size:22
Alignment explanation
Indices: 16533129--16533176 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 22
16533119 CAATTTCATT
16533129 TTTTAAGATAATTTT-AAATAA
1 TTTTAAGATAATTTTAAAATAA
* **
16533150 TTTT-ATATTTTTTTAAAATAA
1 TTTTAAGATAATTTTAAAATAA
16533171 TTTTAA
1 TTTTAA
16533177 ATTTTTTAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 7 0.32
21 14 0.64
22 1 0.05
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (22 bp):
TTTTAAGATAATTTTAAAATAA
Found at i:16533165 original size:31 final size:31
Alignment explanation
Indices: 16533127--16533191 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
16533117 TTCAATTTCA
*
16533127 TTTTTTAAGATAATTTTAAATAATTTT-ATAT
1 TTTTTTAAAATAATTTTAAAT-ATTTTAATAT
*
16533158 TTTTTTAAAATAATTTTAAATTTTTTAATAT
1 TTTTTTAAAATAATTTTAAATATTTTAATAT
16533189 TTT
1 TTT
16533192 CAACAATGGC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 4 0.13
31 27 0.87
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (31 bp):
TTTTTTAAAATAATTTTAAATATTTTAATAT
Found at i:16533180 original size:21 final size:20
Alignment explanation
Indices: 16533140--16533183 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 20
16533130 TTTAAGATAA
*
16533140 TTTTAAATAATTTTATATTT
1 TTTTAAATAATTTTAAATTT
16533160 TTTTAAAATAATTTTAAATTT
1 TTTT-AAATAATTTTAAATTT
16533181 TTT
1 TTT
16533184 AATATTTTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 4 0.18
21 18 0.82
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTTAAATAATTTTAAATTT
Found at i:16533184 original size:20 final size:21
Alignment explanation
Indices: 16533140--16533185 Score: 69
Period size: 20 Copynumber: 2.3 Consensus size: 21
16533130 TTTAAGATAA
*
16533140 TTTT-AAATAATTTTATATTT
1 TTTTAAAATAATTTTATAATT
16533160 TTTTAAAATAATTTTA-AATT
1 TTTTAAAATAATTTTATAATT
16533180 TTTTAA
1 TTTTAA
16533186 TATTTTCAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 13 0.54
21 11 0.46
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
TTTTAAAATAATTTTATAATT
Found at i:16533313 original size:14 final size:15
Alignment explanation
Indices: 16533284--16533316 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
16533274 ATTTTAAATA
16533284 TTATTTAAGATATTT
1 TTATTTAAGATATTT
*
16533299 TTATTTATG-TATTT
1 TTATTTAAGATATTT
16533313 TTAT
1 TTAT
16533317 ATAATTATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (15 bp):
TTATTTAAGATATTT
Found at i:16535518 original size:26 final size:25
Alignment explanation
Indices: 16535482--16535531 Score: 82
Period size: 26 Copynumber: 2.0 Consensus size: 25
16535472 TAATTTATTT
*
16535482 AAAAACCCTAACCCCTAACCGTAATA
1 AAAAACCCTAAACCCTAACC-TAATA
16535508 AAAAACCCTAAACCCTAACCTAAT
1 AAAAACCCTAAACCCTAACCTAAT
16535532 TTAATTAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 4 0.17
26 19 0.83
ACGTcount: A:0.48, C:0.34, G:0.02, T:0.16
Consensus pattern (25 bp):
AAAAACCCTAAACCCTAACCTAATA
Found at i:16535617 original size:29 final size:29
Alignment explanation
Indices: 16535463--16536183 Score: 848
Period size: 29 Copynumber: 24.1 Consensus size: 29
16535453 ATTATTTGAT
*
16535463 ACCCTAACCTAATTTATTTAAAAACCCTA
1 ACCCTAACCTAATTTAATTAAAAACCCTA
16535492 ACCCCTAACCGTAA--T-A--AAAAACCCTAA
1 A-CCCTAACC-TAATTTAATTAAAAACCCT-A
16535519 ACCCTAACCTAATTTAATTAAAAACCCTA
1 ACCCTAACCTAATTTAATTAAAAACCCTA
** *
16535548 A-CCTAATTTAATTTAATTAAAAATCCTA
1 ACCCTAACCTAATTTAATTAAAAACCCTA
** *
16535576 ACCC-AATTTAATTTATTTAAAAACCCTA
1 ACCCTAACCTAATTTAATTAAAAACCCTA
16535604 ACCCTAACCTAATTTAATTAAAAACCCTA
1 ACCCTAACCTAATTTAATTAAAAACCCTA
*
16535633 ACCCTAGCCTAATTTAATTTAATTAAAAACCCTA
1 ACCCTAACC-----TAATTTAATTAAAAACCCTA
*
16535667 ACCCTTAGCCTAATTTAATTTAATTAAAAACCCTA
1 ACCC-TAACC-----TAATTTAATTAAAAACCCTA
* *
16535702 ACCCTAACCTATTTTAATTAAAAACCGTA
1 ACCCTAACCTAATTTAATTAAAAACCCTA
*
16535731 ACCCTAGCCTAATTTAATTAAAAACCCTA
1 ACCCTAACCTAATTTAATTAAAAACCCTA
16535760 ACCCTAACCTAATTTAATTAAAAACCCTA
1 ACCCTAACCTAATTTAATTAAAAACCCTA
*
16535789 ACCCTAACCTATTTTAATTAAAAA-CCTA
1 ACCCTAACCTAATTTAATTAAAAACCCTA
** *
16535817 A-CCTAATTTAATTTATTTAAAAACCCTA
1 ACCCTAACCTAATTTAATTAAAAACCCTA
*
16535845 ACTCTAACCTAATTTAATTAAAAACCCTA
1 ACCCTAACCTAATTTAATTAAAAACCCTA
16535874 ACCCTAACCTAATTTAATTAAAAACCCTA
1 ACCCTAACCTAATTTAATTAAAAACCCTA
16535903 ACCCTAACCTAATTTAATTTAATTTAAAACCCTA
1 ACCCTAACCTAATTTAA-TT-A---AAAACCCTA
*
16535937 ACCCTAACCTATTTTAATTAAAAACCCTA
1 ACCCTAACCTAATTTAATTAAAAACCCTA
*
16535966 ACCCTAACCTAATTTAATTTAATTAAAAACTCTA
1 ACCCTAACC-----TAATTTAATTAAAAACCCTA
* * *
16536000 ACCCTAACTTATTTTAATTGAAAACCCTA
1 ACCCTAACCTAATTTAATTAAAAACCCTA
16536029 ACCCTAACCTAATTTAATTTAATTAAAAACCCTA
1 ACCCTAACC-----TAATTTAATTAAAAACCCTA
*
16536063 ACTCTAACCTAATTTAATTAAAAACCCTAA
1 ACCCTAACCTAATTTAATTAAAAACCCT-A
* *
16536093 ACCCTAACATATTTTAATTAAAAACCCTA
1 ACCCTAACCTAATTTAATTAAAAACCCTA
*
16536122 ACTCTAACCTAATTTAATTAAAAACCCTAA
1 ACCCTAACCTAATTTAATTAAAAACCCT-A
* *
16536152 ACCCTAACATATTTTAATTAAAAACCCTA
1 ACCCTAACCTAATTTAATTAAAAACCCTA
16536181 ACC
1 ACC
16536184 TAATTTATGT
Statistics
Matches: 610, Mismatches: 47, Indels: 70
0.84 0.06 0.10
Matches are distributed among these distances:
25 3 0.00
26 17 0.03
27 21 0.03
28 62 0.10
29 290 0.48
30 71 0.12
31 4 0.01
32 1 0.00
33 2 0.00
34 105 0.17
35 34 0.06
ACGTcount: A:0.43, C:0.25, G:0.01, T:0.31
Consensus pattern (29 bp):
ACCCTAACCTAATTTAATTAAAAACCCTA
Found at i:16535635 original size:23 final size:23
Alignment explanation
Indices: 16535517--16535560 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
16535507 AAAAAACCCT
16535517 AAACCCTAACCTAATTTAATTAA
1 AAACCCTAACCTAATTTAATTAA
16535540 AAACCCTAACCTAATTTAATT
1 AAACCCTAACCTAATTTAATT
16535561 TAATTAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.45, C:0.23, G:0.00, T:0.32
Consensus pattern (23 bp):
AAACCCTAACCTAATTTAATTAA
Found at i:16535663 original size:63 final size:61
Alignment explanation
Indices: 16535472--16536183 Score: 692
Period size: 63 Copynumber: 11.9 Consensus size: 61
16535462 TACCCTAACC
*
16535472 TAATTTATTTAAAAACCCTAACCCCTAACCGTAA--T-A--AAAAACCCTAAACCCTAACC---
1 TAATTTAATTAAAAACCCTAA-CCCTAACC-TAATTTAATTAAAAACCCT-AACCCTAACCTAA
** * *
16535528 TAATTTAATTAAAAACCCTAA-CCTAATTTAATTTAATTAAAAATCCTAACCC-AA--T-T
1 TAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAA
* *
16535584 TAATTTATTTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAGCCTAA
1 TAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAA
*
16535645 TTTAATTTAATTAAAAACCCTAACCCTTAGCCTAATTTAATTTAATTAAAAACCCTAACCCTAAC
1 --TAATTTAATTAAAAACCCTAACCC-TAACC-----TAATTTAATTAAAAACCCTAACCCTAAC
16535710 CT-A
58 CTAA
* *
16535713 T--TTTAATTAAAAACCGTAACCCTAGCCTAATTTAATTAAAAACCCTAACCCTAACC---
1 TAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAA
* *
16535769 TAATTTAATTAAAAACCCTAACCCTAACCTATTTTAATTAAAAA-CCTAA-CCTAA--T-T
1 TAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAA
* *
16535825 TAATTTATTTAAAAACCCTAACTCTAACCTAATTTAATTAAAAACCCTAACCCTAACC---
1 TAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAA
16535883 TAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTTAATTTAAAACCCTAACCCTAACCT-
1 TAATTTAATTAAAAACCCTAACCCTAACCTAATTTAA-TT-A---AAAACCCTAACCCTAACCTA
16535947 A
61 A
*
16535948 T--TTTAATTAAAAACCCTAACCCTAACCTAATTTAATTTAATTAAAAACTCTAACCCTAA-CT-
1 TAATTTAATTAAAAACCCTAACCCTAACC-----TAATTTAATTAAAAACCCTAACCCTAACCTA
16536009 -
61 A
* * *
16536009 TATTTTAATTGAAAACCCTAACCCTAACCTAATTTAATTTAATTAAAAACCCTAACTCTAACC--
1 TAATTTAATTAAAAACCCTAACCCTAACC-----TAATTTAATTAAAAACCCTAACCCTAACCTA
16536072 -
61 A
* * *
16536072 TAATTTAATTAAAAACCCTAAACCCTAACATATTTTAATTAAAAACCCTAACTCTAACC---
1 TAATTTAATTAAAAACCCT-AACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAA
* *
16536131 TAATTTAATTAAAAACCCTAAACCCTAACATATTTTAATTAAAAACCCTAACC
1 TAATTTAATTAAAAACCCT-AACCCTAACCTAATTTAATTAAAAACCCTAACC
16536184 TAATTTATGT
Statistics
Matches: 581, Mismatches: 31, Indels: 85
0.83 0.04 0.12
Matches are distributed among these distances:
53 3 0.01
54 5 0.01
55 1 0.00
56 90 0.15
57 43 0.07
58 116 0.20
59 82 0.14
60 2 0.00
61 1 0.00
62 2 0.00
63 159 0.27
64 34 0.06
65 1 0.00
66 2 0.00
67 2 0.00
68 9 0.02
69 29 0.05
ACGTcount: A:0.44, C:0.24, G:0.01, T:0.31
Consensus pattern (61 bp):
TAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAA
Found at i:16536118 original size:23 final size:23
Alignment explanation
Indices: 16536091--16536214 Score: 79
Period size: 23 Copynumber: 4.8 Consensus size: 23
16536081 TAAAAACCCT
16536091 AAACCCTAACATATTTTAATTAA
1 AAACCCTAACATATTTTAATTAA
*
16536114 AAACCCTAACTCTAACCTAATTTAATTAA
1 AAACCCTAA--C--A--TATTTTAATTAA
16536143 AAACCCTAAACCCTAACATATTTTAATTAA
1 AAA--C----C-CTAACATATTTTAATTAA
* *
16536173 AAACCCTAACCTAATTT-ATGTAA
1 AAACCCTAACATATTTTAAT-TAA
16536196 AAACCCTAACATAATTTTA
1 AAACCCTAACAT-ATTTTA
16536215 CCTAATTTGA
Statistics
Matches: 79, Mismatches: 6, Indels: 30
0.69 0.05 0.26
Matches are distributed among these distances:
22 2 0.03
23 33 0.42
24 5 0.06
25 1 0.01
27 1 0.01
28 1 0.01
29 14 0.18
30 14 0.18
31 1 0.01
32 1 0.01
34 1 0.01
35 1 0.01
36 4 0.05
ACGTcount: A:0.46, C:0.22, G:0.01, T:0.31
Consensus pattern (23 bp):
AAACCCTAACATATTTTAATTAA
Found at i:16536267 original size:56 final size:56
Alignment explanation
Indices: 16536206--16536330 Score: 189
Period size: 56 Copynumber: 2.2 Consensus size: 56
16536196 AAACCCTAAC
* * * *
16536206 ATAATTTTACCTAATTTGATAATCTTACTAACCATTAAC-ACATTTTTTGGGGCTTA
1 ATAATTTTACATAATTTGATAATCTTACTAACCATTAACAAAAGTTTTT-AGGCTTA
*
16536262 ATAATTTTACATAATTTGATAATTTTACTAACCATTAACAAAAGTTTTTAGGCTTA
1 ATAATTTTACATAATTTGATAATCTTACTAACCATTAACAAAAGTTTTTAGGCTTA
16536318 ATAATTTTACATA
1 ATAATTTTACATA
16536331 GTTTTACATA
Statistics
Matches: 63, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
56 56 0.89
57 7 0.11
ACGTcount: A:0.37, C:0.13, G:0.07, T:0.43
Consensus pattern (56 bp):
ATAATTTTACATAATTTGATAATCTTACTAACCATTAACAAAAGTTTTTAGGCTTA
Found at i:16539906 original size:29 final size:28
Alignment explanation
Indices: 16539848--16539913 Score: 87
Period size: 29 Copynumber: 2.3 Consensus size: 28
16539838 GATTTTCTGG
16539848 AAAATGGCCCATTTCGGTAAATAATAAA
1 AAAATGGCCCATTTCGGTAAATAATAAA
* **
16539876 AAAATCGGCCCATTTTGGTAAATTTTGAAA
1 AAAAT-GGCCCATTTCGGTAAATAAT-AAA
16539906 AAAATGGC
1 AAAATGGC
16539914 TTTTTTTGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
28 5 0.15
29 20 0.61
30 8 0.24
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.27
Consensus pattern (28 bp):
AAAATGGCCCATTTCGGTAAATAATAAA
Found at i:16559742 original size:15 final size:15
Alignment explanation
Indices: 16559724--16559756 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
16559714 AATTCCTTTT
16559724 AGGTGAAATCCTAAG
1 AGGTGAAATCCTAAG
*
16559739 AGGTGAAATCCTAGG
1 AGGTGAAATCCTAAG
16559754 AGG
1 AGG
16559757 CTCAGCGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.36, C:0.12, G:0.33, T:0.18
Consensus pattern (15 bp):
AGGTGAAATCCTAAG
Found at i:16561864 original size:33 final size:33
Alignment explanation
Indices: 16561822--16561888 Score: 118
Period size: 33 Copynumber: 2.0 Consensus size: 33
16561812 CGAAGGTTCA
16561822 AACTTATGTTTTCCTTTT-GGAAGTGCTATGGGC
1 AACTTATGTTTTCCTTTTAGG-AGTGCTATGGGC
16561855 AACTTATGTTTTCCTTTTAGGAGTGCTATGGGC
1 AACTTATGTTTTCCTTTTAGGAGTGCTATGGGC
16561888 A
1 A
16561889 TTACCATTAC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
33 31 0.94
34 2 0.06
ACGTcount: A:0.19, C:0.15, G:0.24, T:0.42
Consensus pattern (33 bp):
AACTTATGTTTTCCTTTTAGGAGTGCTATGGGC
Found at i:16572465 original size:7 final size:7
Alignment explanation
Indices: 16572453--16572477 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
16572443 ATTGTTGGTA
16572453 TTATAAT
1 TTATAAT
16572460 TTATAAT
1 TTATAAT
16572467 TTATAAT
1 TTATAAT
16572474 TTAT
1 TTAT
16572478 TATTGACTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (7 bp):
TTATAAT
Found at i:16577767 original size:37 final size:37
Alignment explanation
Indices: 16577717--16577793 Score: 145
Period size: 37 Copynumber: 2.1 Consensus size: 37
16577707 AAGAAAAAGG
16577717 AAAGGAAAATTCTTTTGTTTCTTTTACAATTTGGTCT
1 AAAGGAAAATTCTTTTGTTTCTTTTACAATTTGGTCT
*
16577754 AAAGGAAAGTTCTTTTGTTTCTTTTACAATTTGGTCT
1 AAAGGAAAATTCTTTTGTTTCTTTTACAATTTGGTCT
16577791 AAA
1 AAA
16577794 ATCCCTAAGG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.29, C:0.10, G:0.14, T:0.47
Consensus pattern (37 bp):
AAAGGAAAATTCTTTTGTTTCTTTTACAATTTGGTCT
Found at i:16584718 original size:41 final size:41
Alignment explanation
Indices: 16584606--16584720 Score: 167
Period size: 41 Copynumber: 2.8 Consensus size: 41
16584596 ACCAGCTTTT
* * * * *
16584606 AGCCTGCTAGACTTATAGTCTGAATTGTATCACCGGCATTA
1 AGCCTGCTAGACGTATAGTCTGAATTATTTCATCGGCATCA
*
16584647 AGCCTGCTAGACGTATAGTCTGAATAATTTCATCGGCATCA
1 AGCCTGCTAGACGTATAGTCTGAATTATTTCATCGGCATCA
*
16584688 AGCCTGCTAGACGTAAAGTCTGAATTATTTCAT
1 AGCCTGCTAGACGTATAGTCTGAATTATTTCAT
16584721 TGACAATAAA
Statistics
Matches: 66, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 66 1.00
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (41 bp):
AGCCTGCTAGACGTATAGTCTGAATTATTTCATCGGCATCA
Found at i:16586125 original size:192 final size:192
Alignment explanation
Indices: 16585798--16586183 Score: 772
Period size: 192 Copynumber: 2.0 Consensus size: 192
16585788 ACAAAATTTG
16585798 TCCATAATAAGCTAGGGCCGAATGTTCCTTGTCTTCATACAAGTCCACACATTTCATTTATTTCA
1 TCCATAATAAGCTAGGGCCGAATGTTCCTTGTCTTCATACAAGTCCACACATTTCATTTATTTCA
16585863 CATTTTAATCCCTCAAAATTTATTTTTACAATTTAGTTCCAATTTCTCAAATTCACTAAAAATTC
66 CATTTTAATCCCTCAAAATTTATTTTTACAATTTAGTTCCAATTTCTCAAATTCACTAAAAATTC
16585928 AAAGACAAAACATGTTAATCTATCACATTTCTTTCATTTTTCATCATCAACAATCATAATGT
131 AAAGACAAAACATGTTAATCTATCACATTTCTTTCATTTTTCATCATCAACAATCATAATGT
16585990 TCCATAATAAGCTAGGGCCGAATGTTCCTTGTCTTCATACAAGTCCACACATTTCATTTATTTCA
1 TCCATAATAAGCTAGGGCCGAATGTTCCTTGTCTTCATACAAGTCCACACATTTCATTTATTTCA
16586055 CATTTTAATCCCTCAAAATTTATTTTTACAATTTAGTTCCAATTTCTCAAATTCACTAAAAATTC
66 CATTTTAATCCCTCAAAATTTATTTTTACAATTTAGTTCCAATTTCTCAAATTCACTAAAAATTC
16586120 AAAGACAAAACATGTTAATCTATCACATTTCTTTCATTTTTCATCATCAACAATCATAATGT
131 AAAGACAAAACATGTTAATCTATCACATTTCTTTCATTTTTCATCATCAACAATCATAATGT
16586182 TC
1 TC
16586184 AAGCATTCAT
Statistics
Matches: 194, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
192 194 1.00
ACGTcount: A:0.34, C:0.22, G:0.06, T:0.39
Consensus pattern (192 bp):
TCCATAATAAGCTAGGGCCGAATGTTCCTTGTCTTCATACAAGTCCACACATTTCATTTATTTCA
CATTTTAATCCCTCAAAATTTATTTTTACAATTTAGTTCCAATTTCTCAAATTCACTAAAAATTC
AAAGACAAAACATGTTAATCTATCACATTTCTTTCATTTTTCATCATCAACAATCATAATGT
Found at i:16593398 original size:16 final size:16
Alignment explanation
Indices: 16593377--16593417 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 16
16593367 GAATTTAGAA
16593377 GAATTTTTAAATTAGT
1 GAATTTTTAAATTAGT
* *
16593393 GAATTTTGTGATTTAGT
1 GAATTTT-TAAATTAGT
16593410 GAATTTTT
1 GAATTTTT
16593418 GCGATTTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 8 0.36
17 14 0.64
ACGTcount: A:0.29, C:0.00, G:0.17, T:0.54
Consensus pattern (16 bp):
GAATTTTTAAATTAGT
Found at i:16594238 original size:46 final size:46
Alignment explanation
Indices: 16594171--16594355 Score: 343
Period size: 46 Copynumber: 4.0 Consensus size: 46
16594161 CATGGCAAAG
16594171 TGTGAAAAGTAGGTATGGTGTTTCGGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTGTTTCGGTGAAGAAAACCATACTGAGT
16594217 TGTGAAAAGTAGGTATGGTGTTTCGGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTGTTTCGGTGAAGAAAACCATACTGAGT
*
16594263 TATGAAAAGTAGGTATGGTGTTTCGGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTGTTTCGGTGAAGAAAACCATACTGAGT
* *
16594309 TGTGAAAAGTAGGTATGGTATTTCCGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTGTTTCGGTGAAGAAAACCATACTGAGT
16594355 T
1 T
16594356 ATAGCAATGT
Statistics
Matches: 135, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
46 135 1.00
ACGTcount: A:0.34, C:0.09, G:0.29, T:0.29
Consensus pattern (46 bp):
TGTGAAAAGTAGGTATGGTGTTTCGGTGAAGAAAACCATACTGAGT
Found at i:16597745 original size:17 final size:17
Alignment explanation
Indices: 16597720--16597753 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
16597710 TTAAAATTGG
16597720 ATTGAGAAAATTATTTA
1 ATTGAGAAAATTATTTA
* *
16597737 ATTGGGAAATTTATTTA
1 ATTGAGAAAATTATTTA
16597754 TTTATTTAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.15, T:0.44
Consensus pattern (17 bp):
ATTGAGAAAATTATTTA
Found at i:16608167 original size:48 final size:48
Alignment explanation
Indices: 16608101--16608257 Score: 237
Period size: 48 Copynumber: 3.3 Consensus size: 48
16608091 GTATTTATTT
*
16608101 AATTAGAT-CAATTTCAACATTAAAACTTGGAACAAACTTTGTAATATA
1 AATTAGATAC-ATTACAACATTAAAACTTGGAACAAACTTTGTAATATA
16608149 AATTAGATACATTACAACATTAAAACTTGGAACAAACTTTGTAATATA
1 AATTAGATACATTACAACATTAAAACTTGGAACAAACTTTGTAATATA
* **
16608197 AATTAGATACATTACAACATTAAAACGAT-GATTAAACTTTGTAATATA
1 AATTAGATACATTACAACATTAAAAC-TTGGAACAAACTTTGTAATATA
*
16608245 AATTAGGTACATT
1 AATTAGATACATT
16608258 GGGTTACATA
Statistics
Matches: 102, Mismatches: 5, Indels: 4
0.92 0.05 0.04
Matches are distributed among these distances:
48 100 0.98
49 2 0.02
ACGTcount: A:0.46, C:0.11, G:0.09, T:0.33
Consensus pattern (48 bp):
AATTAGATACATTACAACATTAAAACTTGGAACAAACTTTGTAATATA
Found at i:16619540 original size:29 final size:29
Alignment explanation
Indices: 16619508--16619569 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 29
16619498 AAAGTTGCCA
*
16619508 AGCACCTAGCGAGCTTGAGATTTAAAAAG
1 AGCACCTAGCAAGCTTGAGATTTAAAAAG
* *
16619537 AGCACCTAGCAAGCTTGAGATTTGAAAGG
1 AGCACCTAGCAAGCTTGAGATTTAAAAAG
16619566 AGCA
1 AGCA
16619570 TCGTTAATAG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.37, C:0.18, G:0.26, T:0.19
Consensus pattern (29 bp):
AGCACCTAGCAAGCTTGAGATTTAAAAAG
Found at i:16624450 original size:14 final size:16
Alignment explanation
Indices: 16624425--16624456 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
16624415 AAAAATAAGG
16624425 AAATATTAACATG-GA
1 AAATATTAACATGAGA
16624440 AAATATT-ACATGAGA
1 AAATATTAACATGAGA
16624455 AA
1 AA
16624457 GGCACCTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.56, C:0.06, G:0.12, T:0.25
Consensus pattern (16 bp):
AAATATTAACATGAGA
Found at i:16624746 original size:127 final size:126
Alignment explanation
Indices: 16624585--16624837 Score: 488
Period size: 127 Copynumber: 2.0 Consensus size: 126
16624575 TTCCTTATGA
16624585 GCAAAAATAATTCCTTCTTTCAATCCACTCATTGACGACTGCTTAGACTTGTTTGGTAAGAAAGA
1 GCAAAAATAATTCCTTCTTTCAATCCACTCATTGACGACTGCTTAGACTTGTTTGGTAAGAAAGA
*
16624650 TGATTTTTAAAAAAAAATCTAAAATAGTTAAAGCTTTTATATAAGAACATGAACTGGAAGTT
66 TGATTTTT-AAAAAAAATCTAAAATAGTTAAAGCTTTTATATAAGAACATGAACTGAAAGTT
16624712 GCAAAAATAATTCCTTCTTTCAATCCACTCATTGACGACTGCTTAGACTTGTTTGGTAAGAAAGA
1 GCAAAAATAATTCCTTCTTTCAATCCACTCATTGACGACTGCTTAGACTTGTTTGGTAAGAAAGA
16624777 TGATTTTTAAAAAAAATCTAAAATAGTTAAAGCTTTTATATAAGAACATGAACTGAAAGTT
66 TGATTTTTAAAAAAAATCTAAAATAGTTAAAGCTTTTATATAAGAACATGAACTGAAAGTT
16624838 TTTATCTTTC
Statistics
Matches: 125, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
126 52 0.42
127 73 0.58
ACGTcount: A:0.40, C:0.13, G:0.14, T:0.33
Consensus pattern (126 bp):
GCAAAAATAATTCCTTCTTTCAATCCACTCATTGACGACTGCTTAGACTTGTTTGGTAAGAAAGA
TGATTTTTAAAAAAAATCTAAAATAGTTAAAGCTTTTATATAAGAACATGAACTGAAAGTT
Found at i:16625086 original size:34 final size:34
Alignment explanation
Indices: 16625043--16625110 Score: 109
Period size: 34 Copynumber: 2.0 Consensus size: 34
16625033 TTGCCTATGT
*
16625043 GTTCTTAACAACCAAGTAAATTAATCTCGAATAA
1 GTTCTTAACAACCAAGTAAATTAATCTCAAATAA
* *
16625077 GTTCTTAACAACTAAGTAAATTCATCTCAAATAA
1 GTTCTTAACAACCAAGTAAATTAATCTCAAATAA
16625111 CAGAGAGTAG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.44, C:0.18, G:0.07, T:0.31
Consensus pattern (34 bp):
GTTCTTAACAACCAAGTAAATTAATCTCAAATAA
Found at i:16631498 original size:17 final size:16
Alignment explanation
Indices: 16631460--16631503 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
16631450 CCTAGAATAT
*
16631460 TTTGATATATTATTAA
1 TTTGATAAATTATTAA
16631476 -TTGATAAATTAGTTAA
1 TTTGATAAATTA-TTAA
*
16631492 TTTGATAGATTA
1 TTTGATAAATTA
16631504 ACTAATTAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 10 0.42
16 4 0.17
17 10 0.42
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (16 bp):
TTTGATAAATTATTAA
Found at i:16632046 original size:19 final size:21
Alignment explanation
Indices: 16632008--16632046 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
16631998 ATTGGGTGGA
*
16632008 TCAGCTCTTACGAGCTTCTGT
1 TCAGCTCTTACGACCTTCTGT
16632029 TCAGCT-TT-CGACCTTCTG
1 TCAGCTCTTACGACCTTCTG
16632047 CTGGCATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 2 0.12
21 6 0.35
ACGTcount: A:0.13, C:0.31, G:0.18, T:0.38
Consensus pattern (21 bp):
TCAGCTCTTACGACCTTCTGT
Found at i:16644230 original size:157 final size:155
Alignment explanation
Indices: 16643936--16644388 Score: 534
Period size: 159 Copynumber: 2.9 Consensus size: 155
16643926 AAGATCATGA
* * * * * *
16643936 ATTCAGCCTAACATAACGGGAACACAGGTATATCATAAACACTTTTTCATTGTCAATTCTAGAAT
1 ATTCAGCCTAACACAACTGGATCACAGGTATATCAT-AACACTTTTTAATT-TCAATTCAAAAAT
* * * * **
16644001 ATTAAAATCTAATTT-GGGTTCTGATTTTTTTGGCCTTTGTCTGGTATGAGTATAGAACTAGAAG
64 ATTTAAATCTAATTTGGGGTTCTGATTTTTTTTGTCTTAGTCTGGTACAAGTATAGAACTAGAAG
* * *
16644065 CCTAAAAAATAACAACATAACACCATGC
129 CC-AAAAAAGAACAACAGAACACCATCC
* * * *
16644093 ATTCAGCCTAATACAATTGGATCATAGGTATATCCTATACACTATTTTAATTTCAATTCAAAAAT
1 ATTCAGCCTAACACAACTGGATCACAGGTATATCATA-ACACT-TTTTAATTTCAATTCAAAAAT
* * *
16644158 ATTTTAATCTAATTTGGGGTTCTAATTTTTTTTTGTCTTAGTCTGGTACAAGTACACGAACTAGA
64 ATTTAAATCTAATTTGGGGTTCTGA-TTTTTTTTGTCTTAGTCTGGTACAAGTATA-GAACTAGA
*
16644223 AGCAAAAAAAGAACAACAGAACACCATCC
127 AGCCAAAAAAGAACAACAGAACACCATCC
* * * * *
16644252 ATTCAGCCTAACACAACTGGATCACGGGTATATCGTAACACTTTTTTAATTTCTATTCCAAATTA
1 ATTCAGCCTAACACAACTGGATCACAGGTATATCATAACAC-TTTTTAATTTCAATTCAAAAATA
* *
16644317 TTTAAATCTAATTTGGGGTTCTGA-TTTTTGT-TCTTAGTCTGGTACAAGTATGGGAACTAGAAG
65 TTTAAATCTAATTTGGGGTTCTGATTTTTTTTGTCTTAGTCTGGTACAAGTAT-AGAACTAGAAG
16644380 CCAAAAAAG
129 CCAAAAAAG
16644389 GGTAGCATAT
Statistics
Matches: 252, Mismatches: 37, Indels: 16
0.83 0.12 0.05
Matches are distributed among these distances:
155 37 0.15
156 7 0.03
157 58 0.23
158 60 0.24
159 79 0.31
160 11 0.04
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (155 bp):
ATTCAGCCTAACACAACTGGATCACAGGTATATCATAACACTTTTTAATTTCAATTCAAAAATAT
TTAAATCTAATTTGGGGTTCTGATTTTTTTTGTCTTAGTCTGGTACAAGTATAGAACTAGAAGCC
AAAAAAGAACAACAGAACACCATCC
Found at i:16644602 original size:83 final size:82
Alignment explanation
Indices: 16644464--16644667 Score: 320
Period size: 83 Copynumber: 2.5 Consensus size: 82
16644454 TTGAGATGGT
* * *
16644464 TAACATATTTTGTTTGTTTTTTGAAATGATTTGTTGAAATGGTTGTTTAACATCTTACTTCTATA
1 TAACATATTTTTTTTGTTTTTTGAAATGATTTGTTGAAATGGTTGGTTAACATCTTACTGCTATA
16644529 GGATCATTTTGTTAGCA
66 GGATCATTTTGTTAGCA
16644546 TAACATATTTCTTTTTGTTTTTTGAAATGATTTGTTGAAATGGTTGGTTAACATCTTACTGCTAT
1 TAACATATTT-TTTTTGTTTTTTGAAATGATTTGTTGAAATGGTTGGTTAACATCTTACTGCTAT
* *
16644611 AGGATTATTTTGTTAGTA
65 AGGATCATTTTGTTAGCA
* *
16644629 TAACAT-TTTTTGTTTATTTTTTGAAATGTTTTGTTGAAA
1 TAACATATTTTT-TTTGTTTTTTGAAATGATTTGTTGAAA
16644668 GATGTATACA
Statistics
Matches: 113, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
81 2 0.02
82 38 0.34
83 73 0.65
ACGTcount: A:0.25, C:0.07, G:0.16, T:0.52
Consensus pattern (82 bp):
TAACATATTTTTTTTGTTTTTTGAAATGATTTGTTGAAATGGTTGGTTAACATCTTACTGCTATA
GGATCATTTTGTTAGCA
Found at i:16647022 original size:6 final size:6
Alignment explanation
Indices: 16647011--16647040 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
16647001 TCATTATGCC
16647011 TATACA TATACA TATACA TATACA TATACA
1 TATACA TATACA TATACA TATACA TATACA
16647041 CTTATAAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (6 bp):
TATACA
Found at i:16651320 original size:30 final size:30
Alignment explanation
Indices: 16651286--16651342 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
16651276 TCAATGCTAC
* *
16651286 TATAT-AAAAATAATATTATTAATATTTTGA
1 TATATGAAAAATAAAATT-TAAATATTTTGA
*
16651316 TATATGAAATATAAAATTTAAATATTT
1 TATATGAAAAATAAAATTTAAATATTT
16651343 CTCATGCAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
30 13 0.57
31 10 0.43
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.46
Consensus pattern (30 bp):
TATATGAAAAATAAAATTTAAATATTTTGA
Found at i:16652698 original size:30 final size:30
Alignment explanation
Indices: 16652632--16652699 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 30
16652622 TTTAATAACC
* * *
16652632 TAAATCTTTATAATTTTTAAAGGATTAAAT
1 TAAATTTTTATAATTTTTAAAGGATCAAAG
* *
16652662 TAAATTTTTAT-ATTTTTAGAGGGTCAAAG
1 TAAATTTTTATAATTTTTAAAGGATCAAAG
16652691 TATAATTTT
1 TA-AATTTT
16652700 ACATTTACTA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
29 16 0.50
30 16 0.50
ACGTcount: A:0.38, C:0.03, G:0.10, T:0.49
Consensus pattern (30 bp):
TAAATTTTTATAATTTTTAAAGGATCAAAG
Found at i:16654543 original size:18 final size:19
Alignment explanation
Indices: 16654522--16654563 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
16654512 TTTTTTTTAC
16654522 TGTTATTT-TGATTTTAAT
1 TGTTATTTATGATTTTAAT
*
16654540 TGTT-TTTATTATTTTAAT
1 TGTTATTTATGATTTTAAT
*
16654558 TTTTAT
1 TGTTAT
16654564 CATATTTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 3 0.15
18 16 0.80
19 1 0.05
ACGTcount: A:0.21, C:0.00, G:0.07, T:0.71
Consensus pattern (19 bp):
TGTTATTTATGATTTTAAT
Found at i:16669149 original size:16 final size:16
Alignment explanation
Indices: 16669124--16669154 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
16669114 TTTTGTTGCC
*
16669124 AATTTTACTTTTTCAT
1 AATTTCACTTTTTCAT
16669140 AATTTCACTTTTTCA
1 AATTTCACTTTTTCA
16669155 CTTTCAATTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.16, G:0.00, T:0.58
Consensus pattern (16 bp):
AATTTCACTTTTTCAT
Found at i:16670730 original size:28 final size:28
Alignment explanation
Indices: 16670692--16670759 Score: 91
Period size: 28 Copynumber: 2.4 Consensus size: 28
16670682 AAATTAGGTA
16670692 TTACAAATATGGTTGTTAGAATCTAACCG
1 TTAC-AATATGGTTGTTAGAATCTAACCG
* * *
16670721 TTACAATATGATTGTTGGAATCTGACCG
1 TTACAATATGGTTGTTAGAATCTAACCG
*
16670749 TTGCAATATGG
1 TTACAATATGG
16670760 CCATTGAATT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 30 0.88
29 4 0.12
ACGTcount: A:0.31, C:0.13, G:0.21, T:0.35
Consensus pattern (28 bp):
TTACAATATGGTTGTTAGAATCTAACCG
Found at i:16672204 original size:27 final size:27
Alignment explanation
Indices: 16672165--16672253 Score: 169
Period size: 27 Copynumber: 3.3 Consensus size: 27
16672155 TAAGCTTTCA
*
16672165 TAATCAAAATCTCAAATGGCATTCGAT
1 TAATCAAAGTCTCAAATGGCATTCGAT
16672192 TAATCAAAGTCTCAAATGGCATTCGAT
1 TAATCAAAGTCTCAAATGGCATTCGAT
16672219 TAATCAAAGTCTCAAATGGCATTCGAT
1 TAATCAAAGTCTCAAATGGCATTCGAT
16672246 TAATCAAA
1 TAATCAAA
16672254 ATCAAAGTGA
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 61 1.00
ACGTcount: A:0.40, C:0.18, G:0.12, T:0.29
Consensus pattern (27 bp):
TAATCAAAGTCTCAAATGGCATTCGAT
Found at i:16672292 original size:24 final size:25
Alignment explanation
Indices: 16672249--16672307 Score: 70
Period size: 24 Copynumber: 2.4 Consensus size: 25
16672239 ATTCGATTAA
*
16672249 TCAAAATCAAAGTGAAATTTC-ATT
1 TCAAAATCAAACTGAAATTTCAATT
16672273 ATC-AAATCAAACT-AACATTTCAATT
1 -TCAAAATCAAACTGAA-ATTTCAATT
16672298 TCAAAATCAA
1 TCAAAATCAA
16672308 GATGGCATGT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
23 2 0.07
24 16 0.53
25 12 0.40
ACGTcount: A:0.49, C:0.17, G:0.03, T:0.31
Consensus pattern (25 bp):
TCAAAATCAAACTGAAATTTCAATT
Found at i:16675215 original size:29 final size:29
Alignment explanation
Indices: 16675173--16675232 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
16675163 GAAATTGATC
16675173 TTTATTCACATCTAATGATCGTACAATCA
1 TTTATTCACATCTAATGATCGTACAATCA
16675202 TTTATTCACATCTAATGATCGTACAATCA
1 TTTATTCACATCTAATGATCGTACAATCA
16675231 TT
1 TT
16675233 GAAGTACTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.33, C:0.20, G:0.07, T:0.40
Consensus pattern (29 bp):
TTTATTCACATCTAATGATCGTACAATCA
Found at i:16679029 original size:15 final size:15
Alignment explanation
Indices: 16679009--16679040 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
16678999 TAAATAACAA
16679009 AAAAAAATTATACAT
1 AAAAAAATTATACAT
16679024 AAAAAAATTATACAT
1 AAAAAAATTATACAT
16679039 AA
1 AA
16679041 TATAACTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.25
Consensus pattern (15 bp):
AAAAAAATTATACAT
Found at i:16684906 original size:25 final size:25
Alignment explanation
Indices: 16684872--16684939 Score: 75
Period size: 25 Copynumber: 2.7 Consensus size: 25
16684862 GAATGTAAGT
* *
16684872 AAGTGTACATTTGGGATA-TAAAACA
1 AAGTATACATTTGGGA-AGAAAAACA
*
16684897 AAGTATACATTTGGGAAGAAAAATA
1 AAGTATACATTTGGGAAGAAAAACA
*
16684922 AAGTATACAATTTAGGAA
1 AAGTATAC-ATTTGGGAA
16684940 AATTACAAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
24 1 0.03
25 28 0.76
26 8 0.22
ACGTcount: A:0.49, C:0.06, G:0.19, T:0.26
Consensus pattern (25 bp):
AAGTATACATTTGGGAAGAAAAACA
Found at i:16687208 original size:7 final size:7
Alignment explanation
Indices: 16687196--16687220 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
16687186 ATTAAAGAAT
16687196 AATTTAG
1 AATTTAG
16687203 AATTTAG
1 AATTTAG
16687210 AATTTAG
1 AATTTAG
16687217 AATT
1 AATT
16687221 GAGGATTGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (7 bp):
AATTTAG
Found at i:16687255 original size:7 final size:7
Alignment explanation
Indices: 16687245--16687334 Score: 83
Period size: 7 Copynumber: 12.9 Consensus size: 7
16687235 GACGATCGAG
16687245 AATTGAA
1 AATTGAA
*
16687252 AATTGGA
1 AATTGAA
*
16687259 AATTGGA
1 AATTGAA
*
16687266 AATTGGA
1 AATTGAA
*
16687273 AATTGAG
1 AATTGAA
16687280 AATTGAA
1 AATTGAA
*
16687287 AATTGAG
1 AATTGAA
* *
16687294 GATTAAA
1 AATTGAA
16687301 AATT-AA
1 AATTGAA
* *
16687307 GGATTGAG
1 -AATTGAA
16687315 AATTGAA
1 AATTGAA
16687322 AATTGAA
1 AATTGAA
16687329 AATTGA
1 AATTGA
16687335 GTATTGAGTT
Statistics
Matches: 68, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
6 2 0.03
7 65 0.96
8 1 0.01
ACGTcount: A:0.49, C:0.00, G:0.22, T:0.29
Consensus pattern (7 bp):
AATTGAA
Found at i:16687256 original size:35 final size:34
Alignment explanation
Indices: 16687208--16687342 Score: 103
Period size: 35 Copynumber: 3.9 Consensus size: 34
16687198 TTTAGAATTT
* * * * *
16687208 AGAATTTAGAATTGAGGATTGAGGATTGACGATCG
1 AGAATTGAAAATTGAGAATTGAGAATTGA-GATTG
*
16687243 AGAATTGAAAATTG-GAAATTG-GAAATTGGAAATTG
1 AGAATTGAAAATTGAG-AATTGAG-AATT-GAGATTG
* * * *
16687278 AGAATTGAAAATTGAGGATTAAAAATTAAGGATTG
1 AGAATTGAAAATTGAGAATTGAGAATTGA-GATTG
* *
16687313 AGAATTGAAAATTGAAAATTGAGTATTGAG
1 AGAATTGAAAATTGAGAATTGAGAATTGAG
16687343 TTAAAAAGAA
Statistics
Matches: 77, Mismatches: 17, Indels: 13
0.72 0.16 0.12
Matches are distributed among these distances:
34 4 0.05
35 70 0.91
36 3 0.04
ACGTcount: A:0.44, C:0.01, G:0.26, T:0.29
Consensus pattern (34 bp):
AGAATTGAAAATTGAGAATTGAGAATTGAGATTG
Found at i:16687335 original size:21 final size:21
Alignment explanation
Indices: 16687280--16687341 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 21
16687270 GGAAATTGAG
* *
16687280 AATTGAAAATTGAGGATTAAA
1 AATTGAAAATTGAGAATTGAA
* **
16687301 AATTAAGGATTGAGAATTGAA
1 AATTGAAAATTGAGAATTGAA
*
16687322 AATTGAAAATTGAGTATTGA
1 AATTGAAAATTGAGAATTGA
16687342 GTTAAAAAGA
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.48, C:0.00, G:0.21, T:0.31
Consensus pattern (21 bp):
AATTGAAAATTGAGAATTGAA
Found at i:16687789 original size:17 final size:17
Alignment explanation
Indices: 16687769--16687801 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
16687759 AGCAAATGCC
16687769 TTTAA-AATAATAACAAA
1 TTTAAGAATAA-AACAAA
16687786 TTTAAGAATAAAACAA
1 TTTAAGAATAAAACAA
16687802 GTATTATACA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.64, C:0.06, G:0.03, T:0.27
Consensus pattern (17 bp):
TTTAAGAATAAAACAAA
Found at i:16688375 original size:3 final size:3
Alignment explanation
Indices: 16688367--16688416 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
16688357 TAGCAACTTG
16688367 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
16688415 AA
1 AA
16688417 ATCTTTCTTA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:16693366 original size:12 final size:12
Alignment explanation
Indices: 16693349--16693378 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
16693339 AGCATCAAGG
*
16693349 TATAAACCAGAT
1 TATAAACCAGAA
16693361 TATAAACCAGAA
1 TATAAACCAGAA
16693373 TATAAA
1 TATAAA
16693379 ATTTCATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.57, C:0.13, G:0.07, T:0.23
Consensus pattern (12 bp):
TATAAACCAGAA
Found at i:16693426 original size:12 final size:12
Alignment explanation
Indices: 16693409--16693438 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
16693399 AGCAACAAGG
*
16693409 TATAAACCAGAT
1 TATAAACCAGAA
16693421 TATAAACCAGAA
1 TATAAACCAGAA
16693433 TATAAA
1 TATAAA
16693439 ATTTCAGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.57, C:0.13, G:0.07, T:0.23
Consensus pattern (12 bp):
TATAAACCAGAA
Found at i:16693483 original size:59 final size:59
Alignment explanation
Indices: 16693327--16693497 Score: 315
Period size: 60 Copynumber: 2.9 Consensus size: 59
16693317 AATGTCACAA
* *
16693327 ATATAAAAAAGAAGCATCAAGGTATAAACCAGATTATAAACCAGAATATAAAATTTCAT
1 ATATAAAAAAGAAGCAACAAGGTATAAACCAGATTATAAACCAGAATATAAAATTTCAG
16693386 ATATAAAAAAAGAAGCAACAAGGTATAAACCAGATTATAAACCAGAATATAAAATTTCAG
1 ATAT-AAAAAAGAAGCAACAAGGTATAAACCAGATTATAAACCAGAATATAAAATTTCAG
16693446 ATATAAAAAAGAAGCAACAAGGTATAAACCAGATTATAAACCAGAATATAAA
1 ATATAAAAAAGAAGCAACAAGGTATAAACCAGATTATAAACCAGAATATAAA
16693498 CCAGAGTATA
Statistics
Matches: 109, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
59 52 0.48
60 57 0.52
ACGTcount: A:0.57, C:0.12, G:0.11, T:0.20
Consensus pattern (59 bp):
ATATAAAAAAGAAGCAACAAGGTATAAACCAGATTATAAACCAGAATATAAAATTTCAG
Found at i:16693485 original size:12 final size:12
Alignment explanation
Indices: 16693468--16693509 Score: 66
Period size: 12 Copynumber: 3.5 Consensus size: 12
16693458 AGCAACAAGG
*
16693468 TATAAACCAGAT
1 TATAAACCAGAA
16693480 TATAAACCAGAA
1 TATAAACCAGAA
*
16693492 TATAAACCAGAG
1 TATAAACCAGAA
16693504 TATAAA
1 TATAAA
16693510 ATTCCAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.55, C:0.14, G:0.10, T:0.21
Consensus pattern (12 bp):
TATAAACCAGAA
Found at i:16693533 original size:10 final size:10
Alignment explanation
Indices: 16693518--16693547 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
16693508 AAATTCCAAA
16693518 TAAGAGAAAG
1 TAAGAGAAAG
*
16693528 TAAGAGAAAT
1 TAAGAGAAAG
16693538 TAAGAGAAAG
1 TAAGAGAAAG
16693548 CAGAAGACAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.27, T:0.13
Consensus pattern (10 bp):
TAAGAGAAAG
Found at i:16694077 original size:58 final size:59
Alignment explanation
Indices: 16694007--16694118 Score: 165
Period size: 58 Copynumber: 1.9 Consensus size: 59
16693997 GGCAACAACG
* *
16694007 AAACAAATGGAACTGTAAGGCAACAAT-AGT-AGGCAACAACGACAAATTATAAACAGCT
1 AAACAAAGGGAACTGTAAGGCAAC-ATCAGTAAGGCAACAACAACAAATTATAAACAGCT
* *
16694065 AAACAAAGGGAACTGTAAGGCAACATCAGTAAGGCAACATCAACAGATTATAAA
1 AAACAAAGGGAACTGTAAGGCAACATCAGTAAGGCAACAACAACAAATTATAAA
16694119 GAAGATTATA
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
57 2 0.04
58 26 0.54
59 20 0.42
ACGTcount: A:0.50, C:0.17, G:0.18, T:0.15
Consensus pattern (59 bp):
AAACAAAGGGAACTGTAAGGCAACATCAGTAAGGCAACAACAACAAATTATAAACAGCT
Found at i:16694098 original size:14 final size:14
Alignment explanation
Indices: 16694079--16694106 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
16694069 AAAGGGAACT
16694079 GTAAGGCAACATCA
1 GTAAGGCAACATCA
16694093 GTAAGGCAACATCA
1 GTAAGGCAACATCA
16694107 ACAGATTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.21, G:0.21, T:0.14
Consensus pattern (14 bp):
GTAAGGCAACATCA
Found at i:16694137 original size:11 final size:11
Alignment explanation
Indices: 16694106--16694143 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
16694096 AGGCAACATC
16694106 AACAGATTATA
1 AACAGATTATA
*
16694117 AAGAAGATTATA
1 AA-CAGATTATA
16694129 AACAGATTATA
1 AACAGATTATA
16694140 AACA
1 AACA
16694144 AAAGACATCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 14 0.58
12 10 0.42
ACGTcount: A:0.58, C:0.08, G:0.11, T:0.24
Consensus pattern (11 bp):
AACAGATTATA
Found at i:16694841 original size:10 final size:11
Alignment explanation
Indices: 16694820--16694881 Score: 60
Period size: 11 Copynumber: 5.9 Consensus size: 11
16694810 GGCCTATTTT
16694820 TATTTT-AAAA
1 TATTTTAAAAA
16694830 T-TTTT-AAAA
1 TATTTTAAAAA
**
16694839 -ATTAAAAAAA
1 TATTTTAAAAA
*
16694849 GTATTTTAAAAG
1 -TATTTTAAAAA
16694861 TATTTTAAAAA
1 TATTTTAAAAA
16694872 TATTTTAAAA
1 TATTTTAAAA
16694882 TTAAAAAAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
9 10 0.24
10 5 0.12
11 20 0.48
12 7 0.17
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (11 bp):
TATTTTAAAAA
Found at i:16694854 original size:22 final size:20
Alignment explanation
Indices: 16694826--16694930 Score: 76
Period size: 22 Copynumber: 5.2 Consensus size: 20
16694816 TTTTTATTTT
16694826 AAAAT-TTTTAAAAATTAAA
1 AAAATATTTTAAAAATTAAA
**
16694845 AAAAGTATTTTAAAAGTATTTTA
1 AAAA-TATTTTAAAA--ATTAAA
16694868 AAAATATTTT-AAAATT-AA
1 AAAATATTTTAAAAATTAAA
** *
16694886 AAAA-ATTAAAAAAAGTATGTAA
1 AAAATATTTTAAAAA-T-T-AAA
16694908 AAAATATTTT-AAAATTAAA
1 AAAATATTTTAAAAATTAAA
16694927 AAAA
1 AAAA
16694931 ATATATTTAT
Statistics
Matches: 68, Mismatches: 8, Indels: 20
0.71 0.08 0.21
Matches are distributed among these distances:
17 3 0.04
18 9 0.13
19 14 0.21
20 3 0.04
21 12 0.18
22 16 0.24
23 11 0.16
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (20 bp):
AAAATATTTTAAAAATTAAA
Found at i:16694861 original size:11 final size:11
Alignment explanation
Indices: 16694845--16694881 Score: 65
Period size: 11 Copynumber: 3.4 Consensus size: 11
16694835 AAAAATTAAA
16694845 AAAAGTATTTT
1 AAAAGTATTTT
16694856 AAAAGTATTTT
1 AAAAGTATTTT
*
16694867 AAAAATATTTT
1 AAAAGTATTTT
16694878 AAAA
1 AAAA
16694882 TTAAAAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (11 bp):
AAAAGTATTTT
Found at i:16694897 original size:51 final size:52
Alignment explanation
Indices: 16694820--16694921 Score: 152
Period size: 51 Copynumber: 2.0 Consensus size: 52
16694810 GGCCTATTTT
** * * *
16694820 TATTTTAAAATTTTTAAAAATTAAAAAAAGTATTTTAAAAGTATTTTAAAAA
1 TATTTTAAAATTTAAAAAAATTAAAAAAAGTATGTAAAAAATATTTTAAAAA
16694872 TATTTTAAAA-TTAAAAAAATTAAAAAAAGTATGTAAAAAATATTTTAAAA
1 TATTTTAAAATTTAAAAAAATTAAAAAAAGTATGTAAAAAATATTTTAAAA
16694922 TTAAAAAAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
51 35 0.78
52 10 0.22
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (52 bp):
TATTTTAAAATTTAAAAAAATTAAAAAAAGTATGTAAAAAATATTTTAAAAA
Found at i:16694900 original size:40 final size:42
Alignment explanation
Indices: 16694820--16694935 Score: 141
Period size: 40 Copynumber: 2.8 Consensus size: 42
16694810 GGCCTATTTT
***
16694820 TATTTT-AAAAT-TTTTAAAAATTAAAAAAAGTATTTTAAAAG
1 TATTTTAAAAATATTTT-AAAATTAAAAAAAGTATAAAAAAAG
16694861 TATTTTAAAAATATTTTAAAATTAAAAAAA-T-TAAAAAAAG
1 TATTTTAAAAATATTTTAAAATTAAAAAAAGTATAAAAAAAG
* * *
16694901 TATGTAAAAAATATTTTAAAATTAAAAAAAATATA
1 TATTTTAAAAATATTTTAAAATTAAAAAAAGTATA
16694936 TTTATTATAT
Statistics
Matches: 66, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
40 34 0.52
41 8 0.12
42 20 0.30
43 4 0.06
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.37
Consensus pattern (42 bp):
TATTTTAAAAATATTTTAAAATTAAAAAAAGTATAAAAAAAG
Found at i:16703442 original size:3 final size:3
Alignment explanation
Indices: 16703436--16703473 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
16703426 ATTATTGAGT
*
16703436 TTA TTA TTA TTA TTA TTA TTA TCA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
16703474 TCTTCCTATT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:16716149 original size:44 final size:43
Alignment explanation
Indices: 16715914--16716237 Score: 159
Period size: 44 Copynumber: 7.5 Consensus size: 43
16715904 AGAATTGCAG
* * * * *
16715914 ATCTTATCTCCCTGAGATTACAGCGGAGCAGGTTGAATATAGTA
1 ATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGACA-AA
* * **
16715958 ATCCTATCTCCCTGA-AGTTACAGTGGAGCGGATT--A-A-AGG
1 ATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTGAAGACAAA
* * * * * * * *
16715997 ATCTTATCTCTCTGA-AGTTACTGTAGAGCGGATCG--CACCAG
1 ATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTGAAGACAAA
* * * * * *
16716038 GTCTTATTTCCCTGAGATTACAGTGGAACAGACTAAAGA-ATGTCAG
1 ATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGACA----AA
* * *
16716084 ATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAGGCCAGAA
1 ATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGACA-AA
* **
16716128 ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGACACT
1 ATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGACAAA
* * * *
16716171 ATCCTATCTCCCTGA-AGTTACAGTGGAGCGGATTCAA-ATAAA
1 ATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTGAAGACAAA
16716213 GGATCTTATCTCCCTGA-AGTTACAG
1 --ATCTTATCTCCCTGAGA-TTACAG
16716238 CAGAGTAGAT
Statistics
Matches: 216, Mismatches: 49, Indels: 30
0.73 0.17 0.10
Matches are distributed among these distances:
39 29 0.13
40 2 0.01
41 25 0.12
42 5 0.02
43 33 0.15
44 88 0.41
46 33 0.15
47 1 0.00
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (43 bp):
ATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGACAAA
Found at i:16716193 original size:43 final size:43
Alignment explanation
Indices: 16716084--16716247 Score: 161
Period size: 44 Copynumber: 3.8 Consensus size: 43
16716074 AGAATGTCAG
* * * *
16716084 ATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAGGCCAGAA
1 ATCTTATCTCCCTGAAGTTACAGCGGAGCAGATTGAAGACA-AA
**
16716128 ATCTTATCTCCCTG-AGATTACAGCGGAGCAGATTGAAGACACT
1 ATCTTATCTCCCTGAAG-TTACAGCGGAGCAGATTGAAGACAAA
* * * * *
16716171 ATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTCAA-ATAAA
1 ATCTTATCTCCCTGAAGTTACAGCGGAGCAGATTGAAGACAAA
* *
16716213 GGATCTTATCTCCCTGAAGTTACAGCAGAGTAGAT
1 --ATCTTATCTCCCTGAAGTTACAGCGGAGCAGAT
16716248 CGCATCAAGT
Statistics
Matches: 98, Mismatches: 18, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
42 2 0.02
43 31 0.32
44 65 0.66
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (43 bp):
ATCTTATCTCCCTGAAGTTACAGCGGAGCAGATTGAAGACAAA
Found at i:16716353 original size:218 final size:214
Alignment explanation
Indices: 16715914--16716319 Score: 487
Period size: 218 Copynumber: 1.9 Consensus size: 214
16715904 AGAATTGCAG
* * * *
16715914 ATCTTATCTCCCTGAGATTACAGCGGAGCAGGTTGAATATAGTAATCCTATCTCCCTGAAGTTAC
1 ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGACACTAATCCTATCTCCCTGAAGTTAC
* * * * *
16715979 AGTGGAGCGGATTAAAGGATCTTATCTCTCTGAAGTTACTGTAGAGCGGATCGCACCAGGTCTTA
66 AGTGGAGCGGATTAAAGGATCTTATCTCCCTGAAGTTACAGCAGAGCAGATCGCACCAAGTCTTA
** * * * * * *
16716044 TTTCCCTGAGATTACAGTGGAACAGACTAAAGAATGTCAGATCTTATCTCCCTGAGGTTACAGTG
131 TTTCCCTGAGATTACAGTGGAACAGACTAAAGAATAACAGATCATACCCCCCTAAAGTTACAGCG
** *
16716109 GAGCAGATTGAGGCCAGAA
196 GAGCAGACAGAGGACAGAA
16716128 ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGACACT-ATCCTATCTCCCTGAAGTTAC
1 ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGACACTAATCCTATCTCCCTGAAGTTAC
* *
16716192 AGTGGAGCGGATTCAAATAAAGGATCTTATCTCCCTGAAGTTACAGCAGAGTAGATCGCATCAAG
66 AGTGGAGCGGA-T----TAAAGGATCTTATCTCCCTGAAGTTACAGCAGAGCAGATCGCACCAAG
* * * *
16716257 TCTTATTTCCCTGAAGA-TGCAGTGGAATAGACTGAA-AATAACA-AGTCATGCCCCCCTAAAGT
126 TCTTATTTCCCTG-AGATTACAGTGGAACAGACTAAAGAATAACAGA-TCATACCCCCCTAAAGT
16716319 T
189 T
16716320 GTAGCGGGGC
Statistics
Matches: 163, Mismatches: 22, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
213 32 0.20
214 40 0.25
216 1 0.01
217 17 0.10
218 70 0.43
219 3 0.02
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (214 bp):
ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGACACTAATCCTATCTCCCTGAAGTTAC
AGTGGAGCGGATTAAAGGATCTTATCTCCCTGAAGTTACAGCAGAGCAGATCGCACCAAGTCTTA
TTTCCCTGAGATTACAGTGGAACAGACTAAAGAATAACAGATCATACCCCCCTAAAGTTACAGCG
GAGCAGACAGAGGACAGAA
Found at i:16717850 original size:3 final size:3
Alignment explanation
Indices: 16717844--16717881 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
16717834 ATTATTGAGT
*
16717844 TTA TTA TTA TTA TTA TTA TTA TCA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
16717882 TCTTCCTATT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:16717909 original size:9 final size:10
Alignment explanation
Indices: 16717828--16717912 Score: 79
Period size: 9 Copynumber: 8.7 Consensus size: 10
16717818 TCCTATCATT
16717828 TTATTTATTA
1 TTATTTATTA
16717838 TTGAGTTTATTA
1 TT-A-TTTATTA
16717850 TTA-TTATTA
1 TTATTTATTA
*
16717859 TTA-TTATCA
1 TTATTTATTA
16717868 TTA-TTATTA
1 TTATTTATTA
* *
16717877 TTATTTCTTC
1 TTATTTATTA
* *
16717887 CTATTTATTT
1 TTATTTATTA
16717897 TTATTTATT-
1 TTATTTATTA
16717906 TTATTTA
1 TTATTTA
16717913 AACCTTTGGT
Statistics
Matches: 64, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
9 32 0.50
10 21 0.33
11 2 0.03
12 9 0.14
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (10 bp):
TTATTTATTA
Found at i:16725906 original size:53 final size:53
Alignment explanation
Indices: 16725825--16725929 Score: 183
Period size: 53 Copynumber: 2.0 Consensus size: 53
16725815 ACTGGTAGTA
* *
16725825 TTAAATATAAACCTATCTTATTATATTTGCATCTTCAAAATTGAGGAAGCTTG
1 TTAAATATAAACCTATCTTACTACATTTGCATCTTCAAAATTGAGGAAGCTTG
*
16725878 TTAAATATAAACCTATGTTACTACATTTGCATCTTCAAAATTGAGGAAGCTT
1 TTAAATATAAACCTATCTTACTACATTTGCATCTTCAAAATTGAGGAAGCTT
16725930 AACATGTTAA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 49 1.00
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.38
Consensus pattern (53 bp):
TTAAATATAAACCTATCTTACTACATTTGCATCTTCAAAATTGAGGAAGCTTG
Found at i:16732035 original size:27 final size:27
Alignment explanation
Indices: 16731997--16732050 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
16731987 AACAGAACAG
*
16731997 AACTCAATTCATGTTAAAAATAAATTT
1 AACTCAATTCATGTCAAAAATAAATTT
*
16732024 AACTCATTTCATGTCAAAAATAAATTT
1 AACTCAATTCATGTCAAAAATAAATTT
16732051 TCTTTAAGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.46, C:0.13, G:0.04, T:0.37
Consensus pattern (27 bp):
AACTCAATTCATGTCAAAAATAAATTT
Found at i:16732260 original size:117 final size:118
Alignment explanation
Indices: 16732104--16732338 Score: 348
Period size: 117 Copynumber: 2.0 Consensus size: 118
16732094 TCACTGTGCA
* * * * *
16732104 CTGCTAGTTATTCTTGGACTACATAGGCTGTAAACAGAAATTTCTAGGTTCAAATCTAGTCATG-
1 CTGCTAATTATTCTTGGACTACATAGGCTGTAAAAAGAAATTTCAAGATTCAAATCTAGCCATGA
*
16732168 TCTTGTGTATGGTATTGAATTTTTATATGCATCATTATTATCTCTGTATTCTTT
66 T-TTGTGTATGGTATTGAATTTTTATATGCATCATTATTATCTCTGAATTCTTT
* * *
16732222 CTGCTAATTATTCTTGG-CTAGATAGGTTGTAAAAAGAAATTTCAAGATTCAAATCTGGCCATGA
1 CTGCTAATTATTCTTGGACTACATAGGCTGTAAAAAGAAATTTCAAGATTCAAATCTAGCCATGA
* *
16732286 TTTGTGTATGGTATTGAATTTTTATATGCCTCTTTATTATCTCTGAATTCTTT
66 TTTGTGTATGGTATTGAATTTTTATATGCATCATTATTATCTCTGAATTCTTT
16732339 TTAGTGGTTG
Statistics
Matches: 105, Mismatches: 11, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
117 88 0.84
118 17 0.16
ACGTcount: A:0.26, C:0.14, G:0.16, T:0.44
Consensus pattern (118 bp):
CTGCTAATTATTCTTGGACTACATAGGCTGTAAAAAGAAATTTCAAGATTCAAATCTAGCCATGA
TTTGTGTATGGTATTGAATTTTTATATGCATCATTATTATCTCTGAATTCTTT
Found at i:16749621 original size:42 final size:42
Alignment explanation
Indices: 16749562--16749670 Score: 191
Period size: 42 Copynumber: 2.6 Consensus size: 42
16749552 ACAGCCTAGC
16749562 ACACGGCTTGGCACACAGGCATGTGAGGCCATTTCGAAAGTT
1 ACACGGCTTGGCACACAGGCATGTGAGGCCATTTCGAAAGTT
*
16749604 ACACGGCTTGGCACACAGGCGTGTGAGGCCATTTCGAAAGTT
1 ACACGGCTTGGCACACAGGCATGTGAGGCCATTTCGAAAGTT
* *
16749646 ACACGGCCTAGCACACAGGCATGTG
1 ACACGGCTTGGCACACAGGCATGTG
16749671 GCTTGGCCGT
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 63 1.00
ACGTcount: A:0.26, C:0.26, G:0.29, T:0.19
Consensus pattern (42 bp):
ACACGGCTTGGCACACAGGCATGTGAGGCCATTTCGAAAGTT
Found at i:16752483 original size:14 final size:14
Alignment explanation
Indices: 16752464--16752490 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
16752454 CCATTGAAAA
16752464 ATGGGTTGTTACAT
1 ATGGGTTGTTACAT
16752478 ATGGGTTGTTACA
1 ATGGGTTGTTACA
16752491 AAGGAAGCAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.07, G:0.30, T:0.41
Consensus pattern (14 bp):
ATGGGTTGTTACAT
Found at i:16763984 original size:62 final size:59
Alignment explanation
Indices: 16763912--16764025 Score: 156
Period size: 62 Copynumber: 1.9 Consensus size: 59
16763902 AGTGATTATC
* * * *
16763912 TTAACATTAAATTTAATTTAATGTTTATCTTGTAGATAAATATTCTATTAATTTAATAAAAT
1 TTAACATTAAATCTAATCTAATATTTATC-T-T-GATAAATATTATATTAATTTAATAAAAT
*
16763974 TTAATATTAAATCTAATCTAATATTTATCTTGATAAATATTATATTAATTTA
1 TTAACATTAAATCTAATCTAATATTTATCTTGATAAATATTATATTAATTTA
16764026 TTTTAAAGTG
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
59 20 0.43
60 1 0.02
61 1 0.02
62 25 0.53
ACGTcount: A:0.42, C:0.05, G:0.04, T:0.49
Consensus pattern (59 bp):
TTAACATTAAATCTAATCTAATATTTATCTTGATAAATATTATATTAATTTAATAAAAT
Found at i:16764831 original size:22 final size:22
Alignment explanation
Indices: 16764806--16764861 Score: 80
Period size: 20 Copynumber: 2.6 Consensus size: 22
16764796 ATCTGTAAAC
16764806 TTTCAATTTACTACAACATGTG
1 TTTCAATTTACTACAACATGTG
*
16764828 TTTCAA--TACTATAACATGTG
1 TTTCAATTTACTACAACATGTG
16764848 TTTCAATTGTACTA
1 TTTCAATT-TACTA
16764862 ATAGTTGTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
20 19 0.63
22 6 0.20
23 5 0.17
ACGTcount: A:0.32, C:0.16, G:0.09, T:0.43
Consensus pattern (22 bp):
TTTCAATTTACTACAACATGTG
Found at i:16767000 original size:16 final size:16
Alignment explanation
Indices: 16766931--16766998 Score: 118
Period size: 16 Copynumber: 4.2 Consensus size: 16
16766921 TTTGGTTCGC
16766931 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
16766947 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
16766963 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
* *
16766979 TGTAATGGAATAGAGG
1 TGTATTGGATTAGAGG
16766995 TGTA
1 TGTA
16766999 ATAGCAAATC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.28, C:0.00, G:0.37, T:0.35
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:16767033 original size:45 final size:44
Alignment explanation
Indices: 16766979--16767073 Score: 136
Period size: 45 Copynumber: 2.1 Consensus size: 44
16766969 GGATTAGAGG
* *
16766979 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAAC-ACTGTTTGGTTGAA
* **
16767024 TGTAATGGAATAGAGGCGTAATAGTAAAACTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
16767068 TGTAAT
1 TGTAAT
16767074 AGAGGTGTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 18 0.40
45 27 0.60
ACGTcount: A:0.35, C:0.05, G:0.27, T:0.33
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
Found at i:16767243 original size:25 final size:25
Alignment explanation
Indices: 16767211--16767265 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
16767201 TAATTTAATC
*
16767211 ATAT-TTAAACATAATTATTATT-AA
1 ATATATTAAACAT-ATTATAATTAAA
*
16767235 ATATATTAAATATATTATAATTAAA
1 ATATATTAAACATATTATAATTAAA
16767260 ATATAT
1 ATATAT
16767266 AATTTAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 12 0.44
25 15 0.56
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (25 bp):
ATATATTAAACATATTATAATTAAA
Found at i:16767447 original size:47 final size:46
Alignment explanation
Indices: 16767396--16767556 Score: 140
Period size: 47 Copynumber: 3.6 Consensus size: 46
16767386 GATTTAATAA
16767396 AATTTAAAATAATTATAACTAATAAATTATCTTATATGAATTTGTAT
1 AATTTAAAATAATTATAA-TAATAAATTATCTTATATGAATTTGTAT
* * * * *
16767443 AATTTAAAATAATTATTATTACATATAAT-TTA-AT-AA---GATAT
1 AATTTAAAATAATTATAATAATAAATTATCTTATATGAATTTG-TAT
* * * *
16767484 AATTTCATAA-AATTATTGATAATAAATTTTCTTATATGAATTTATAT
1 AATTT-AAAATAATTA-TAATAATAAATTATCTTATATGAATTTGTAT
16767531 AATTTAAAATAATT-TATATAATAAAT
1 AATTTAAAATAATTATA-ATAATAAAT
16767557 CTATTGTATA
Statistics
Matches: 88, Mismatches: 15, Indels: 23
0.70 0.12 0.18
Matches are distributed among these distances:
40 1 0.01
41 13 0.15
42 11 0.12
43 5 0.06
44 4 0.05
45 6 0.07
46 19 0.22
47 29 0.33
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.45
Consensus pattern (46 bp):
AATTTAAAATAATTATAATAATAAATTATCTTATATGAATTTGTAT
Found at i:16772049 original size:29 final size:29
Alignment explanation
Indices: 16772004--16772079 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 29
16771994 AATGTAATTT
* * *
16772004 ATATATATGTA-ATTTTTTTATCTATATAT
1 ATATATATTTATA-TTTTTTATATATATAC
* *
16772033 GTATATATTTATATTTTTTATATTTATAC
1 ATATATATTTATATTTTTTATATATATAC
*
16772062 ATATATATTTATGTTTTT
1 ATATATATTTATATTTTT
16772080 AAAATAATTA
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
29 38 0.97
30 1 0.03
ACGTcount: A:0.32, C:0.03, G:0.04, T:0.62
Consensus pattern (29 bp):
ATATATATTTATATTTTTTATATATATAC
Found at i:16772054 original size:23 final size:23
Alignment explanation
Indices: 16772028--16772071 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
16772018 TTTTTATCTA
* *
16772028 TATATGTATATATTTATATTTTT
1 TATATGTATACATATATATTTTT
*
16772051 TATATTTATACATATATATTT
1 TATATGTATACATATATATTT
16772072 ATGTTTTTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.61
Consensus pattern (23 bp):
TATATGTATACATATATATTTTT
Found at i:16772450 original size:15 final size:16
Alignment explanation
Indices: 16772430--16772465 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
16772420 TTTCTATGCC
16772430 ATTGTTATATTTA-TT
1 ATTGTTATATTTATTT
*
16772445 ATTGTTGTATTTATTT
1 ATTGTTATATTTATTT
16772461 ATTGT
1 ATTGT
16772466 GGCATTTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.63
16 7 0.37
ACGTcount: A:0.22, C:0.00, G:0.11, T:0.67
Consensus pattern (16 bp):
ATTGTTATATTTATTT
Found at i:16784737 original size:84 final size:84
Alignment explanation
Indices: 16784635--16784920 Score: 299
Period size: 84 Copynumber: 3.3 Consensus size: 84
16784625 TTAAAGCCAT
*
16784635 TAATCTTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAATCACAGATCTTATCTCTCTGAAGTT
1 TAATCTTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAACCACAGATCTTATCTCTCTGAAGTT
16784700 GCAGAGAGCAGATCGCATC
66 GCAGAGAGCAGATCGCATC
* * *** * * * * *
16784719 TAGTCTTATCTCTCTGAAGTTGCAGTGGAGCAAACTAAGTAAGCAAAG-TCTTATCCCCCTGAAG
1 TAATCTTATCTCCCTGAAGTTGCAGTGGAGTGGATTAA--AACCACAGATCTTATCTCTCTGAAG
* * *
16784783 TTGCAGTGGGGCAGA-CAGAAGATGGC
64 TTGCAG-AGAGCAGATC-G--CAT--C
* * *
16784809 GAATCTTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAACCACGGATCTTATCTTTCTGAAGTT
1 TAATCTTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAACCACAGATCTTATCTCTCTGAAGTT
16784874 GCAGAGAGCAGATCGCATC
66 GCAGAGAGCAGATCGCATC
* *
16784893 TAATCTTATC-CTTCTGAGGTTGCAGTGG
1 TAATCTTATCTC-CCTGAAGTTGCAGTGG
16784921 GGCAGATTAA
Statistics
Matches: 159, Mismatches: 32, Indels: 22
0.75 0.15 0.10
Matches are distributed among these distances:
83 1 0.01
84 56 0.35
85 21 0.13
86 15 0.09
88 14 0.09
89 20 0.13
90 32 0.20
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (84 bp):
TAATCTTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAACCACAGATCTTATCTCTCTGAAGTT
GCAGAGAGCAGATCGCATC
Found at i:16784769 original size:45 final size:44
Alignment explanation
Indices: 16784503--16784838 Score: 230
Period size: 45 Copynumber: 7.7 Consensus size: 44
16784493 GATCGCATCT
*
16784503 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAGCAAGC-A
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAG-AAGCAA
* * * *
16784547 AGTCTTATC-CTCCTGAAGCTACAGT-GAGGCATACTGAAGACGGCAA
1 AGTCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGACT-AAGA-AGCAA
* * * *
16784593 A-TATTATCTCCTTGAAGTTGTAGTGGAGCAGA-TTA-AAGCCATTA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAG-CA--A
** * * *
16784637 A-TCTTATCTCCCTGAAGTTGCAGTGGAGTGGATTAA-AATCAC
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAGCAA
* * * * * *
16784679 AGATCTTATCTCTCTGAAGTTGCAG-AGAGCAGA-T-CGCATC-T
1 AG-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAGCAA
* *
16784720 AGTCTTATCTCTCTGAAGTTGCAGTGGAGCAAACTAAGTAAGCAA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAG-AAGCAA
* * * * *
16784765 AGTCTTATCCCCCTGAAGTTGCAGTGGGGCAGACAGAAGATGGCGA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGAC-TAAGA-AGCAA
16784811 A-TCTTATCTCCCTGAAGTTGCAGTGGAG
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAG
16784839 TGGATTAAAA
Statistics
Matches: 228, Mismatches: 43, Indels: 41
0.73 0.14 0.13
Matches are distributed among these distances:
40 22 0.10
41 9 0.04
42 9 0.04
43 10 0.04
44 82 0.36
45 84 0.37
46 12 0.05
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (44 bp):
AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAGCAA
Found at i:16784829 original size:218 final size:218
Alignment explanation
Indices: 16784417--16784877 Score: 645
Period size: 218 Copynumber: 2.1 Consensus size: 218
16784407 AGTGAAACCG
* *
16784417 TAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAAATCACAGATCTTATATCTTTGAAGT
1 TAATCTTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAAATCACAGATCTTATATCTCTGAAGT
* * *
16784482 TTCAAAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAGCAAGCA
66 TGCAAAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTAAGCAAGCA
* * * *
16784547 AGTCTTATCCTCCTGAAGCTACAGTGAGGCATACTGAAGACGGCAAATATTATCTCCTTGAAGTT
131 AGTCTTATCCCCCTGAAGCTACAGTGAGGCAGACAGAAGACGGCAAATATTATCTCCCTGAAGTT
* * *
16784612 GTAGTGGAGCAGATTAAAGCCAT
196 GCAGTGGAGCAGATTAAAACCAC
* *
16784635 TAATCTTATCTCCCTGAAGTTGCAGTGGAGTGGATT-AAAATCACAGATCTTATCTCTCTGAAGT
1 TAATCTTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAAATCACAGATCTTATATCTCTGAAGT
* * *
16784699 TGCAGAGAGCAGATCGCATCTAGTCTTATCTCTCTGAAGTTGCAGTGGAGCAAACTAAGTAAGCA
66 TGCAAAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTAAGCAAGC-
* * * * * *
16784764 AAGTCTTATCCCCCTGAAGTTGCAGTGGGGCAGACAGAAGATGGCGAATCTTATCTCCCTGAAGT
130 AAGTCTTATCCCCCTGAAGCTACAGTGAGGCAGACAGAAGACGGCAAATATTATCTCCCTGAAGT
**
16784829 TGCAGTGGAGTGGATTAAAACCAC
195 TGCAGTGGAGCAGATTAAAACCAC
** **
16784853 GGATCTTATCTTTCTGAAGTTGCAG
1 TAATCTTATCTCCCTGAAGTTGCAG
16784878 AGAGCAGATC
Statistics
Matches: 213, Mismatches: 29, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
217 84 0.39
218 129 0.61
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (218 bp):
TAATCTTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAAATCACAGATCTTATATCTCTGAAGT
TGCAAAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTAAGCAAGCA
AGTCTTATCCCCCTGAAGCTACAGTGAGGCAGACAGAAGACGGCAAATATTATCTCCCTGAAGTT
GCAGTGGAGCAGATTAAAACCAC
Found at i:16784830 original size:174 final size:173
Alignment explanation
Indices: 16784636--16784964 Score: 507
Period size: 174 Copynumber: 1.9 Consensus size: 173
16784626 TAAAGCCATT
*
16784636 AATCTTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAATCACAGATCTTATCTCTCTGAAGTTG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAACCACAGATCTTATCTCTCTGAAGTTG
* * *
16784701 CAGAGAGCAGATCGCATCTAGTCTTAT-CTCTCTGAAGTTGCAGTGGAGCAAACTAAGTAAGCAA
66 CAGAGAGCAGATCGCATCTAATCTTATCCT-TCTGAAGTTGCAGTGGAGCAAACTAAATAAACAA
* *
16784765 AGTCTTATCCCCCTGAAGTTGCAGTGGGGCAGACAGAAGATGGCG
130 A-TCCTATCCCCCTAAAGTTGCAGTGGGGCAGACAGAAGATGGCG
* *
16784810 AATCTTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAACCACGGATCTTATCTTTCTGAAGTTG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAACCACAGATCTTATCTCTCTGAAGTTG
* * * *
16784875 CAGAGAGCAGATCGCATCTAATCTTATCCTTCTGAGGTTGCAGTGGGGCAGATTAAATAAACAAA
66 CAGAGAGCAGATCGCATCTAATCTTATCCTTCTGAAGTTGCAGTGGAGCAAACTAAATAAACAAA
* *
16784940 TCCTATCTCCCTAAAGTTGTAGTGG
131 TCCTATCCCCCTAAAGTTGCAGTGG
16784965 AGTGGATTAG
Statistics
Matches: 140, Mismatches: 14, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
173 21 0.15
174 117 0.84
175 2 0.01
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (173 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAACCACAGATCTTATCTCTCTGAAGTTG
CAGAGAGCAGATCGCATCTAATCTTATCCTTCTGAAGTTGCAGTGGAGCAAACTAAATAAACAAA
TCCTATCCCCCTAAAGTTGCAGTGGGGCAGACAGAAGATGGCG
Found at i:16786624 original size:19 final size:21
Alignment explanation
Indices: 16786584--16786641 Score: 91
Period size: 21 Copynumber: 2.8 Consensus size: 21
16786574 TTCATTAATA
16786584 ATGTAATTTTTTTATATATAT
1 ATGTAATTTTTTTATATATAT
*
16786605 ATGTAATTTTTTTATCTATAT
1 ATGTAATTTTTTTATATATAT
*
16786626 ATGT-ATATTTTTATAT
1 ATGTAATTTTTTTATAT
16786642 TTTTTATATT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
20 10 0.29
21 24 0.71
ACGTcount: A:0.31, C:0.02, G:0.05, T:0.62
Consensus pattern (21 bp):
ATGTAATTTTTTTATATATAT
Found at i:16786633 original size:29 final size:29
Alignment explanation
Indices: 16786600--16786674 Score: 73
Period size: 29 Copynumber: 2.6 Consensus size: 29
16786590 TTTTTTTATA
*
16786600 TATATATGTA-ATTTTTT-TATCTATATATG
1 TATATATGTATATTTTTTATAT-T-TATACG
* *
16786629 TATATTTTTATATTTTTTATATTTATACG
1 TATATATGTATATTTTTTATATTTATACG
* *
16786658 TATATATTTATGTTTTT
1 TATATATGTATATTTTT
16786675 AAAATAATTA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
29 28 0.72
30 8 0.21
31 3 0.08
ACGTcount: A:0.28, C:0.03, G:0.05, T:0.64
Consensus pattern (29 bp):
TATATATGTATATTTTTTATATTTATACG
Found at i:16787048 original size:15 final size:16
Alignment explanation
Indices: 16787028--16787063 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
16787018 TTTCTATGCC
16787028 ATTGTTATATTTA-TT
1 ATTGTTATATTTATTT
*
16787043 ATTGTTGTATTTATTT
1 ATTGTTATATTTATTT
16787059 ATTGT
1 ATTGT
16787064 GGCATTTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.63
16 7 0.37
ACGTcount: A:0.22, C:0.00, G:0.11, T:0.67
Consensus pattern (16 bp):
ATTGTTATATTTATTT
Found at i:16788732 original size:26 final size:26
Alignment explanation
Indices: 16788698--16788752 Score: 92
Period size: 26 Copynumber: 2.1 Consensus size: 26
16788688 TGTGAAATTT
16788698 AATTCAATAATTAAATAATAGAAATA
1 AATTCAATAATTAAATAATAGAAATA
* *
16788724 AATTCAATAATTAAATAGTAGACATA
1 AATTCAATAATTAAATAATAGAAATA
16788750 AAT
1 AAT
16788753 ATTTTCCTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.58, C:0.05, G:0.05, T:0.31
Consensus pattern (26 bp):
AATTCAATAATTAAATAATAGAAATA
Found at i:16791672 original size:23 final size:22
Alignment explanation
Indices: 16791629--16791687 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
16791619 AAAGGGTATC
* *
16791629 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
16791650 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
* *
16791673 TGCATATCATATCTT
1 TACAAATCATATCTT
16791688 AGATTATATA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
21 3 0.09
22 19 0.59
23 10 0.31
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.37
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:16791698 original size:19 final size:19
Alignment explanation
Indices: 16791642--16791775 Score: 151
Period size: 19 Copynumber: 6.8 Consensus size: 19
16791632 AAATTAAATC
*
16791642 TCTAAGATTACAAAATCATA
1 TCTAAGATTAC-ATATCATA
*
16791662 TCTTCTAAGATTGCATATCATA
1 ---TCTAAGATTACATATCATA
* *
16791684 TCTTAGATTATATATCATA
1 TCTAAGATTACATATCATA
*
16791703 TCTAAGATTGCATATCATA
1 TCTAAGATTACATATCATA
* *
16791722 TCTAAGATTATATATTATA
1 TCTAAGATTACATATCATA
*
16791741 TCTAAGATTGCATATCATA
1 TCTAAGATTACATATCATA
*
16791760 TCTAAGATTGCATATC
1 TCTAAGATTACATATC
16791776 CCTGAAGATT
Statistics
Matches: 97, Mismatches: 14, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
19 80 0.82
22 7 0.07
23 10 0.10
ACGTcount: A:0.38, C:0.14, G:0.08, T:0.40
Consensus pattern (19 bp):
TCTAAGATTACATATCATA
Found at i:16791711 original size:38 final size:38
Alignment explanation
Indices: 16791665--16791768 Score: 190
Period size: 38 Copynumber: 2.7 Consensus size: 38
16791655 AATCATATCT
*
16791665 TCTAAGATTGCATATCATATCTTAGATTATATATCATA
1 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
*
16791703 TCTAAGATTGCATATCATATCTAAGATTATATATTATA
1 TCTAAGATTGCATATCATATCTAAGATTATATATCATA
16791741 TCTAAGATTGCATATCATATCTAAGATT
1 TCTAAGATTGCATATCATATCTAAGATT
16791769 GCATATCCCT
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 64 1.00
ACGTcount: A:0.38, C:0.12, G:0.09, T:0.41
Consensus pattern (38 bp):
TCTAAGATTGCATATCATATCTAAGATTATATATCATA
Found at i:16792309 original size:132 final size:132
Alignment explanation
Indices: 16792072--16792830 Score: 1407
Period size: 132 Copynumber: 5.8 Consensus size: 132
16792062 GCAATATCAA
* * * * ** *
16792072 GGAGATAGGACTTACAATCTTCAACCTATTCCACTGCTGACCAGGG-AGATATG-ATTACTGGCT
1 GGAGATAAGACCTAAAATCTTCAATCTATTCCACTATTGTCCAGGGAAG-TA-GAATTACTGGCT
16792135 TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCACCATCTTCGATATTTTCCACTACTGC
64 TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCACCATCTTCGATATTTTCCACTACTGC
16792200 TTAG
129 TTAG
16792204 GGAGATAAGACCTAAAATCTTCAATCTATTCCACTATTGTCCAGGGAAGTAGAATTACTGGCTTC
1 GGAGATAAGACCTAAAATCTTCAATCTATTCCACTATTGTCCAGGGAAGTAGAATTACTGGCTTC
16792269 AATGTACTCCACTGTAACCACAGGGAGGTAAAATCCACCATCTTCGATATTTTCCACTACTGCTT
66 AATGTACTCCACTGTAACCACAGGGAGGTAAAATCCACCATCTTCGATATTTTCCACTACTGCTT
16792334 AG
131 AG
16792336 GGAGATAAGACCTAAAATCTTCAATCTATTCCACTATTGTCCAGGGAAGTAGAATTACTGGCTTC
1 GGAGATAAGACCTAAAATCTTCAATCTATTCCACTATTGTCCAGGGAAGTAGAATTACTGGCTTC
16792401 AATGTACTCCACTGTAACCACAGGGAGGTAAAATCCACCATCTTCGATATTTTCCACTACTGCTT
66 AATGTACTCCACTGTAACCACAGGGAGGTAAAATCCACCATCTTCGATATTTTCCACTACTGCTT
16792466 AG
131 AG
16792468 GGAGATAAGACCTAAAATCTTCAATCTATTCCACTATTGTCCAGGGAAGTAGAATTACTGGCTTC
1 GGAGATAAGACCTAAAATCTTCAATCTATTCCACTATTGTCCAGGGAAGTAGAATTACTGGCTTC
16792533 AATGTACTCCACTGTAACCACAGGGAGGTAAAATCCACCATCTTCGATATTTTCCACTACTGCTT
66 AATGTACTCCACTGTAACCACAGGGAGGTAAAATCCACCATCTTCGATATTTTCCACTACTGCTT
16792598 AG
131 AG
16792600 GGAGATAAGACCTAAAATCTTCAATCTATTCCACTATTGTCCAGGGAAGTAGAATTACTGGCTTC
1 GGAGATAAGACCTAAAATCTTCAATCTATTCCACTATTGTCCAGGGAAGTAGAATTACTGGCTTC
16792665 AATGTACTCCACTGTAACCACAGGGAGGTAAAATCCACCATCTTCGATATTTTCCACTACTGCTT
66 AATGTACTCCACTGTAACCACAGGGAGGTAAAATCCACCATCTTCGATATTTTCCACTACTGCTT
16792730 AG
131 AG
*
16792732 GGAGATAAGACCTAAAATCTTCAATCTATTCCACTATTGTCCAGGGAAGTAGAATTACTAGCTTC
1 GGAGATAAGACCTAAAATCTTCAATCTATTCCACTATTGTCCAGGGAAGTAGAATTACTGGCTTC
16792797 AATGTACTCCACTGTAACCACA-GGAGGTAAAATC
66 AATGTACTCCACTGTAACCACAGGGAGGTAAAATC
16792831 TGTCATCTTC
Statistics
Matches: 617, Mismatches: 8, Indels: 5
0.98 0.01 0.01
Matches are distributed among these distances:
131 13 0.02
132 602 0.98
133 2 0.00
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.28
Consensus pattern (132 bp):
GGAGATAAGACCTAAAATCTTCAATCTATTCCACTATTGTCCAGGGAAGTAGAATTACTGGCTTC
AATGTACTCCACTGTAACCACAGGGAGGTAAAATCCACCATCTTCGATATTTTCCACTACTGCTT
AG
Found at i:16799511 original size:22 final size:21
Alignment explanation
Indices: 16799486--16799540 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 21
16799476 TATAAATTAA
16799486 ATCTCTAAGATTACAAAATCAT
1 ATCTCTAAGATTAC-AAATCAT
* *
16799508 ATCTTCTAAGATTGCATATCAT
1 ATC-TCTAAGATTACAAATCAT
16799530 A--TCTAAGATTA
1 ATCTCTAAGATTA
16799541 TATATCAAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
19 9 0.31
22 10 0.34
23 10 0.34
ACGTcount: A:0.40, C:0.16, G:0.07, T:0.36
Consensus pattern (21 bp):
ATCTCTAAGATTACAAATCAT
Found at i:16799519 original size:23 final size:22
Alignment explanation
Indices: 16799489--16799533 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
16799479 AAATTAAATC
16799489 TCTAAGATTACAAAATCATATCT
1 TCTAAGATTAC-AAATCATATCT
* *
16799512 TCTAAGATTGCATATCATATCT
1 TCTAAGATTACAAATCATATCT
16799534 AAGATTATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.38, C:0.18, G:0.07, T:0.38
Consensus pattern (22 bp):
TCTAAGATTACAAATCATATCT
Found at i:16799545 original size:19 final size:21
Alignment explanation
Indices: 16799512--16799561 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 21
16799502 AATCATATCT
*
16799512 TCTAAGATTGCATATC-A-TA
1 TCTAAGATTACATATCAAGTA
*
16799531 TCTAAGATTATATATCAAGTA
1 TCTAAGATTACATATCAAGTA
*
16799552 TCTAATATTA
1 TCTAAGATTA
16799562 AGTAAAGTAC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 14 0.54
20 1 0.04
21 11 0.42
ACGTcount: A:0.40, C:0.12, G:0.08, T:0.40
Consensus pattern (21 bp):
TCTAAGATTACATATCAAGTA
Found at i:16799555 original size:21 final size:19
Alignment explanation
Indices: 16799489--16799561 Score: 56
Period size: 19 Copynumber: 3.5 Consensus size: 19
16799479 AAATTAAATC
*
16799489 TCTAAGATTACAAAATCATA
1 TCTAAGATTAC-ATATCATA
*
16799509 TCTTCTAAGATTGCATATCATA
1 ---TCTAAGATTACATATCATA
*
16799531 TCTAAGATTATATATCAAGTA
1 TCTAAGATTACATATC-A-TA
*
16799552 TCTAATATTA
1 TCTAAGATTA
16799562 AGTAAAGTAC
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
19 14 0.33
20 1 0.02
21 11 0.26
22 7 0.16
23 10 0.23
ACGTcount: A:0.41, C:0.14, G:0.07, T:0.38
Consensus pattern (19 bp):
TCTAAGATTACATATCATA
Found at i:16802718 original size:17 final size:16
Alignment explanation
Indices: 16802691--16802737 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
16802681 AAATTTGAGA
16802691 ATAAA-AAATAAAAAT
1 ATAAATAAATAAAAAT
16802706 CATAAATAAATAAGAAAT
1 -ATAAATAAATAA-AAAT
*
16802724 AGAAATAAA-AAAAA
1 ATAAATAAATAAAAA
16802738 AAGAACAAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
15 3 0.11
16 7 0.25
17 14 0.50
18 4 0.14
ACGTcount: A:0.77, C:0.02, G:0.04, T:0.17
Consensus pattern (16 bp):
ATAAATAAATAAAAAT
Found at i:16804922 original size:21 final size:20
Alignment explanation
Indices: 16804892--16804931 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
16804882 TAATTTACAA
*
16804892 TCAAAGACATATATATATAAT
1 TCAAAGACATACA-ATATAAT
*
16804913 TCAAATACATACAATATAA
1 TCAAAGACATACAATATAA
16804932 GTTATAAATG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.55, C:0.12, G:0.03, T:0.30
Consensus pattern (20 bp):
TCAAAGACATACAATATAAT
Found at i:16805689 original size:10 final size:12
Alignment explanation
Indices: 16805658--16805690 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
16805648 ATTAAACTAA
*
16805658 GATTTCTATAAC
1 GATTTATATAAC
16805670 GATTTATATAAC
1 GATTTATATAAC
16805682 GATTTATAT
1 GATTTATAT
16805691 GCAACAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.36, C:0.09, G:0.09, T:0.45
Consensus pattern (12 bp):
GATTTATATAAC
Found at i:16805821 original size:86 final size:86
Alignment explanation
Indices: 16805676--16805938 Score: 339
Period size: 86 Copynumber: 3.1 Consensus size: 86
16805666 TAACGATTTA
* * * *
16805676 TATAACGATTTATATGCAACAAATTAGCAAAAATCAATGGCTCAAGTTCATGTATTTACCAAAAA
1 TATAACAACTTATATGCAACAAATTAGCAAAAATCAATGGTTCAAGTTCATGCATTTACCAAAAA
* *
16805741 TCAGACTAATTTTTCAA-TATT
66 CCAGACTAAATTTTCAACT-TT
* *
16805762 TATAACAACTTATATGCAACAAATTAGCAAAAATAAATGGTTCAAGTTCATGCATTTACCAACAA
1 TATAACAACTTATATGCAACAAATTAGCAAAAATCAATGGTTCAAGTTCATGCATTTACCAAAAA
16805827 CCAGACTAAATTTTCAACTTT
66 CCAGACTAAATTTTCAACTTT
* * * ** * * *
16805848 GATAACAACTTATGTGCAACAAATTAGAAAAAATCAACAGTTCAAGTTCATGCATTCATCAACAA
1 TATAACAACTTATATGCAACAAATTAGCAAAAATCAATGGTTCAAGTTCATGCATTTACCAAAAA
* *
16805913 CCAAACCAAATTTTCAACTTT
66 CCAGACTAAATTTTCAACTTT
*
16805934 AATAA
1 TATAA
16805939 AGTAGAAGGA
Statistics
Matches: 157, Mismatches: 19, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
86 156 0.99
87 1 0.01
ACGTcount: A:0.44, C:0.18, G:0.08, T:0.30
Consensus pattern (86 bp):
TATAACAACTTATATGCAACAAATTAGCAAAAATCAATGGTTCAAGTTCATGCATTTACCAAAAA
CCAGACTAAATTTTCAACTTT
Found at i:16806294 original size:86 final size:86
Alignment explanation
Indices: 16806138--16806305 Score: 219
Period size: 86 Copynumber: 2.0 Consensus size: 86
16806128 ATTTACCAAT
* * * * *
16806138 TTATATACAACAAATTAACACAAATCAACGGTTCAAGTTCATGTATTTACCAAAAGCCGAACTAA
1 TTATATACAACAAATTAACAAAAATCAACGGTTCAAGTGCATGTATTCACCAAAAACCGAACCAA
*
16806203 ATTTTCAATTTTTGTAATAAA
66 ATTTTCAAATTTTGTAATAAA
* * ** * *
16806224 TTATATGCAACAAATTAGCAAAAATCAATTGTTCAGGTGCATGTATTCACCAAAAACCGGACCAA
1 TTATATACAACAAATTAACAAAAATCAACGGTTCAAGTGCATGTATTCACCAAAAACCGAACCAA
*
16806289 TTTTTCAAATTTTGTAA
66 ATTTTCAAATTTTGTAA
16806306 AGTAAGAGTT
Statistics
Matches: 69, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
86 69 1.00
ACGTcount: A:0.41, C:0.17, G:0.10, T:0.32
Consensus pattern (86 bp):
TTATATACAACAAATTAACAAAAATCAACGGTTCAAGTGCATGTATTCACCAAAAACCGAACCAA
ATTTTCAAATTTTGTAATAAA
Found at i:16809153 original size:73 final size:70
Alignment explanation
Indices: 16809075--16809225 Score: 248
Period size: 73 Copynumber: 2.1 Consensus size: 70
16809065 TTATTAAAAA
*
16809075 ATTATTTCATTTTGAAAAAAATGACGCCGTTTTACTATGCTAAAAATTTTTTATTTTGTTTTTTT
1 ATTATTTCATTTTGAAAAAAATGACGCCGTTTTACTATGCTAAAAA--ATTTATTTTG-TTTTTT
16809140 ATAAATTG
63 ATAAATTG
*
16809148 ATTATTTCATTTTGAACAAAATGACGCCGTTTTACTATGCTAAAAAATTTATTTTGTTTTTTATA
1 ATTATTTCATTTTGAAAAAAATGACGCCGTTTTACTATGCTAAAAAATTTATTTTGTTTTTTATA
16809213 AATTG
66 AATTG
16809218 ATTTATTT
1 A-TTATTT
16809226 TTGCAGCGCT
Statistics
Matches: 75, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
70 15 0.20
71 15 0.20
73 45 0.60
ACGTcount: A:0.32, C:0.09, G:0.09, T:0.50
Consensus pattern (70 bp):
ATTATTTCATTTTGAAAAAAATGACGCCGTTTTACTATGCTAAAAAATTTATTTTGTTTTTTATA
AATTG
Found at i:16809622 original size:15 final size:16
Alignment explanation
Indices: 16809586--16809623 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
16809576 TCTTAACCCG
*
16809586 ACTCCTAAATCCCTAA
1 ACTCTTAAATCCCTAA
16809602 AC-CTTAAATCCCT-A
1 ACTCTTAAATCCCTAA
16809616 ACTCTTAA
1 ACTCTTAA
16809624 CCCCTAACGT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 3 0.15
15 15 0.75
16 2 0.10
ACGTcount: A:0.37, C:0.34, G:0.00, T:0.29
Consensus pattern (16 bp):
ACTCTTAAATCCCTAA
Found at i:16809630 original size:14 final size:14
Alignment explanation
Indices: 16809611--16809644 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
16809601 AACCTTAAAT
16809611 CCCTAAC-TCTTAAC
1 CCCTAACGTC-TAAC
16809625 CCCTAACGTCTAAC
1 CCCTAACGTCTAAC
16809639 CCCTAA
1 CCCTAA
16809645 ACCCCTAACC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 17 0.89
15 2 0.11
ACGTcount: A:0.29, C:0.44, G:0.03, T:0.24
Consensus pattern (14 bp):
CCCTAACGTCTAAC
Found at i:16809654 original size:15 final size:15
Alignment explanation
Indices: 16809621--16809662 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
16809611 CCCTAACTCT
**
16809621 TAACCCCT-AACGTC
1 TAACCCCTAAACCCC
16809635 TAACCCCTAAACCCC
1 TAACCCCTAAACCCC
*
16809650 TAACCCTTAAACC
1 TAACCCCTAAACC
16809663 TTAAGTCCCA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
14 8 0.33
15 16 0.67
ACGTcount: A:0.33, C:0.45, G:0.02, T:0.19
Consensus pattern (15 bp):
TAACCCCTAAACCCC
Done.