Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 99090824
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: 99090824
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 317 characters in sequence are not A, C, G, or T
File 95 of 318
Found at i:28688163 original size:12 final size:12
Alignment explanation
Indices: 28688148--28688173 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
28688138 GTTTTTTGGT
28688148 AAAACGCCGCTA
1 AAAACGCCGCTA
28688160 AAAACGCCGCTA
1 AAAACGCCGCTA
28688172 AA
1 AA
28688174 GCCCTGTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.31, G:0.15, T:0.08
Consensus pattern (12 bp):
AAAACGCCGCTA
Found at i:28692763 original size:63 final size:63
Alignment explanation
Indices: 28692664--28692784 Score: 161
Period size: 63 Copynumber: 1.9 Consensus size: 63
28692654 TGTGCTAACC
* ** * *
28692664 CAATTTATTTTACACAAGTAACACAACACGTTCAATCTTTCCCTACATCAACCCCTTCAGCAT
1 CAATTTATTTTACACAAGCAACACAACACGCACAATCATTCCCTACATCAACACCTTCAGCAT
* * * *
28692727 CAATTTATTTTACACAAGCACCATAGCACGCACAATCATTCCCTGCATCAACACCTTC
1 CAATTTATTTTACACAAGCAACACAACACGCACAATCATTCCCTACATCAACACCTTC
28692785 TCTAGGGGTA
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
63 49 1.00
ACGTcount: A:0.33, C:0.33, G:0.06, T:0.28
Consensus pattern (63 bp):
CAATTTATTTTACACAAGCAACACAACACGCACAATCATTCCCTACATCAACACCTTCAGCAT
Found at i:28694305 original size:40 final size:40
Alignment explanation
Indices: 28694237--28694335 Score: 105
Period size: 40 Copynumber: 2.5 Consensus size: 40
28694227 CGGATTAATT
* * **
28694237 CGATGAGGCACTGGGTGCC-AAT--TTACTTCGGTTTAGC
1 CGATGAGACACTAGGTGCCAAATCATTACTTCGAATTAGC
* *
28694274 CGATGAGACACTAGGTGTCAAATCATTACTTCGAATTATC
1 CGATGAGACACTAGGTGCCAAATCATTACTTCGAATTAGC
* *
28694314 CGATGAGGCACTGGGTGCCAAA
1 CGATGAGACACTAGGTGCCAAA
28694336 CTAGTGTGTT
Statistics
Matches: 50, Mismatches: 9, Indels: 3
0.81 0.15 0.05
Matches are distributed among these distances:
37 16 0.32
38 3 0.06
40 31 0.62
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.26
Consensus pattern (40 bp):
CGATGAGACACTAGGTGCCAAATCATTACTTCGAATTAGC
Found at i:28698819 original size:12 final size:12
Alignment explanation
Indices: 28698802--28698826 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28698792 ATCAACATTG
28698802 TTGATATGTATA
1 TTGATATGTATA
28698814 TTGATATGTATA
1 TTGATATGTATA
28698826 T
1 T
28698827 CTGTGAACTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (12 bp):
TTGATATGTATA
Found at i:28701368 original size:9 final size:9
Alignment explanation
Indices: 28701354--28701384 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
28701344 GATCAAGTAA
28701354 AATTAAATT
1 AATTAAATT
28701363 AATTAAATT
1 AATTAAATT
28701372 AATTAAAATT
1 AATT-AAATT
28701382 AAT
1 AAT
28701385 ATGATATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 13 0.62
10 8 0.38
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (9 bp):
AATTAAATT
Found at i:28702259 original size:5 final size:5
Alignment explanation
Indices: 28702232--28702270 Score: 55
Period size: 5 Copynumber: 8.0 Consensus size: 5
28702222 TTTAGGAAAT
28702232 TAATA TAATAA TAATA T-AT- TAATA TAATA TAATA TAATA
1 TAATA TAAT-A TAATA TAATA TAATA TAATA TAATA TAATA
28702271 ATAAAATAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
3 1 0.03
4 4 0.13
5 21 0.68
6 5 0.16
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
TAATA
Found at i:28705733 original size:40 final size:38
Alignment explanation
Indices: 28705650--28705796 Score: 105
Period size: 40 Copynumber: 3.7 Consensus size: 38
28705640 TCGAATGATG
* * * * * *
28705650 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACTATA
1 TCCGGACTAAG-CCTGAAGGCATTGTGC-AAGTTAATAAA
* * *
28705690 TCCGGACTAGGATCTGAAGGCATTTGTGCGAGTTAATAAA
1 TCCGGACTAAG-CCTGAAGGCA-TTGTGCAAGTTAATAAA
* *
28705730 TCCGGGCTAAGCCTGAAGGCATTGTGCAAGTTACTAAA
1 TCCGGACTAAGCCTGAAGGCATTGTGCAAGTTAATAAA
* ** *
28705768 CCCGGGTTAAGTCCCGAAGGCATTCGTGC
1 TCCGGACTAAG-CCTGAAGGCATT-GTGC
28705797 GAGTCGCTAT
Statistics
Matches: 86, Mismatches: 18, Indels: 6
0.78 0.16 0.05
Matches are distributed among these distances:
38 24 0.28
39 20 0.23
40 36 0.42
41 6 0.07
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (38 bp):
TCCGGACTAAGCCTGAAGGCATTGTGCAAGTTAATAAA
Found at i:28713050 original size:5 final size:5
Alignment explanation
Indices: 28713032--28713062 Score: 53
Period size: 5 Copynumber: 6.0 Consensus size: 5
28713022 TTTAAGAAAT
28713032 TAATA TAATAA TAATA TAATA TAATA TAATA
1 TAATA TAAT-A TAATA TAATA TAATA TAATA
28713063 ATAAAATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 20 0.80
6 5 0.20
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
TAATA
Found at i:28713057 original size:21 final size:21
Alignment explanation
Indices: 28713032--28713071 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
28713022 TTTAAGAAAT
*
28713032 TAATATAATAATAATATAATA
1 TAATATAATAATAAAATAATA
28713053 TAATATAATAATAAAATAA
1 TAATATAATAATAAAATAA
28713072 AGCATATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (21 bp):
TAATATAATAATAAAATAATA
Found at i:28713093 original size:20 final size:20
Alignment explanation
Indices: 28713034--28713083 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 20
28713024 TAAGAAATTA
* **
28713034 ATATAATAATAATATAATATA
1 ATATAATAATAAAATAA-AGC
28713055 ATATAATAATAAAATAAAGC
1 ATATAATAATAAAATAAAGC
28713075 ATATAATAA
1 ATATAATAA
28713084 AACATAAAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 10 0.38
21 16 0.62
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (20 bp):
ATATAATAATAAAATAAAGC
Found at i:28714971 original size:16 final size:16
Alignment explanation
Indices: 28714950--28714985 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
28714940 AATTGTATGT
28714950 GTGCATGGATAATGAA
1 GTGCATGGATAATGAA
28714966 GTGCATGGATAATGAA
1 GTGCATGGATAATGAA
28714982 GTGC
1 GTGC
28714986 TTGAAAACTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.33, C:0.08, G:0.33, T:0.25
Consensus pattern (16 bp):
GTGCATGGATAATGAA
Found at i:28724408 original size:3 final size:3
Alignment explanation
Indices: 28724402--28724439 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
28724392 GTTTAAACAA
28724402 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
28724440 AAGAAGGAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:28727590 original size:2 final size:2
Alignment explanation
Indices: 28727579--28727624 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
28727569 AGGAAAAAAA
* *
28727579 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28727621 AT AT
1 AT AT
28727625 GAATATTCAT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:28728282 original size:57 final size:56
Alignment explanation
Indices: 28728215--28728349 Score: 155
Period size: 56 Copynumber: 2.4 Consensus size: 56
28728205 TAAAGTCTGG
* ** * *
28728215 ATTTAGCCTGGATTGGTAATCCAGATTAAGCTCTTAAGAGTAT-TTTTCACAGAAAGA
1 ATTTAGCCTGGACTGGTAATCCAGACAAAGCTCTT-AGAGCATATGTT-ACAGAAAGA
* * * *
28728272 ATTTAGCCTGGACTAGTAATCCTGACAAAGCTCTTAGAGCATATGTTACAGACAGG
1 ATTTAGCCTGGACTGGTAATCCAGACAAAGCTCTTAGAGCATATGTTACAGAAAGA
*
28728328 ATTTAGCCTAGACTGGTAATCC
1 ATTTAGCCTGGACTGGTAATCC
28728350 TGCTGTATGA
Statistics
Matches: 66, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
56 33 0.50
57 33 0.50
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (56 bp):
ATTTAGCCTGGACTGGTAATCCAGACAAAGCTCTTAGAGCATATGTTACAGAAAGA
Found at i:28728347 original size:56 final size:57
Alignment explanation
Indices: 28728195--28728351 Score: 174
Period size: 57 Copynumber: 2.8 Consensus size: 57
28728185 TTGAGCCTTT
* * * * * **
28728195 GAGCATATGTTAAAGTCTGGATTTAGCCTGGATTGGTAATCCAGATTAAGCTCTTAA
1 GAGCATATGTTACAGACAGGATTTAGCCTGGACTGGTAATCCTGACAAAGCTCTTAA
* * * * *
28728252 GAGTAT-TTTTCACAGAAAGAATTTAGCCTGGACTAGTAATCCTGACAAAGCTCTT-A
1 GAGCATATGTT-ACAGACAGGATTTAGCCTGGACTGGTAATCCTGACAAAGCTCTTAA
*
28728308 GAGCATATGTTACAGACAGGATTTAGCCTAGACTGGTAATCCTG
1 GAGCATATGTTACAGACAGGATTTAGCCTGGACTGGTAATCCTG
28728352 CTGTATGATA
Statistics
Matches: 80, Mismatches: 18, Indels: 5
0.78 0.17 0.05
Matches are distributed among these distances:
56 38 0.47
57 42 0.52
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.31
Consensus pattern (57 bp):
GAGCATATGTTACAGACAGGATTTAGCCTGGACTGGTAATCCTGACAAAGCTCTTAA
Found at i:28729711 original size:53 final size:53
Alignment explanation
Indices: 28729630--28729780 Score: 214
Period size: 53 Copynumber: 2.8 Consensus size: 53
28729620 CTTACACGGT
* *
28729630 TCACATATCATACCGAAGCCATATCCCAGAC-ATGGTCTTATACGGAATCACATTA
1 TCACAT-T-ATACCGATGCCATAGCCCAG-CTATGGTCTTATACGGAATCACATTA
*
28729685 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCACATTA
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
** *
28729738 TCACATTGCACCGATGCCATAGCCCAGCTATGGTCTTAAACGG
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGG
28729781 GCGCACTTAT
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
52 1 0.01
53 81 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.26
Consensus pattern (53 bp):
TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
Found at i:28737226 original size:53 final size:53
Alignment explanation
Indices: 28737145--28737295 Score: 214
Period size: 53 Copynumber: 2.8 Consensus size: 53
28737135 CTTACACGGT
* *
28737145 TCACATATCATACCGAAGCCATATCCCAGAC-ATGGTCTTATACGGAATCACATTA
1 TCACAT-T-ATACCGATGCCATAGCCCAG-CTATGGTCTTATACGGAATCACATTA
*
28737200 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCACATTA
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
** *
28737253 TCACATTGCACCGATGCCATAGCCCAGCTATGGTCTTAAACGG
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGG
28737296 GCGCACTTAT
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
52 1 0.01
53 81 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.26
Consensus pattern (53 bp):
TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
Found at i:28742277 original size:15 final size:15
Alignment explanation
Indices: 28742254--28742292 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
28742244 AATTTCTCTT
*
28742254 ACAAAAACAGCAACA
1 ACAACAACAGCAACA
*
28742269 ACAACAACAGCAGCA
1 ACAACAACAGCAACA
*
28742284 ACAGCAACA
1 ACAACAACA
28742293 ACAATTTCTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.59, C:0.31, G:0.10, T:0.00
Consensus pattern (15 bp):
ACAACAACAGCAACA
Found at i:28742558 original size:6 final size:6
Alignment explanation
Indices: 28742549--28742591 Score: 86
Period size: 6 Copynumber: 7.2 Consensus size: 6
28742539 GCCGCCGCCG
28742549 CAGCAA CAGCAA CAGCAA CAGCAA CAGCAA CAGCAA CAGCAA C
1 CAGCAA CAGCAA CAGCAA CAGCAA CAGCAA CAGCAA CAGCAA C
28742592 CAAACCAACA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.49, C:0.35, G:0.16, T:0.00
Consensus pattern (6 bp):
CAGCAA
Found at i:28747191 original size:3 final size:3
Alignment explanation
Indices: 28747185--28747210 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
28747175 AATAATAATA
28747185 ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG AT
28747211 AATAATAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.31, T:0.35
Consensus pattern (3 bp):
ATG
Found at i:28749682 original size:8 final size:9
Alignment explanation
Indices: 28749667--28749691 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
28749657 TATTAAATTT
28749667 TAAAAAAAA
1 TAAAAAAAA
28749676 TAAAAAAAA
1 TAAAAAAAA
28749685 TAAAAAA
1 TAAAAAA
28749692 CCACAATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (9 bp):
TAAAAAAAA
Found at i:28751333 original size:29 final size:30
Alignment explanation
Indices: 28751301--28751360 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
28751291 TAAAATAATC
* * *
28751301 ATATATATTTGAGATAAATATATTA-TATT
1 ATATATATTTAAAATAAATACATTATTATT
*
28751330 ATATTTATTTAAAATAAATACATTATTATT
1 ATATATATTTAAAATAAATACATTATTATT
28751360 A
1 A
28751361 CTTAAAAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 21 0.81
30 5 0.19
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (30 bp):
ATATATATTTAAAATAAATACATTATTATT
Found at i:28751359 original size:25 final size:24
Alignment explanation
Indices: 28751327--28751374 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
28751317 AATATATTAT
*
28751327 ATTATATTTA-TTTAAAATAAATAC
1 ATTATA-TTACTTAAAAATAAATAC
28751351 ATTATTATTACTTAAAAATAAATA
1 ATTA-TATTACTTAAAAATAAATA
28751375 AGTTAAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (24 bp):
ATTATATTACTTAAAAATAAATAC
Found at i:28756466 original size:16 final size:15
Alignment explanation
Indices: 28756414--28756468 Score: 65
Period size: 15 Copynumber: 3.6 Consensus size: 15
28756404 GAGAAAGAAA
*
28756414 TAAAAAATATTTCTT
1 TAAAAAATATTTTTT
* *
28756429 AATAAAAATGTTTTTT
1 TA-AAAAATATTTTTT
28756445 TAAAAAATATTTTTT
1 TAAAAAATATTTTTT
*
28756460 TACAAAATA
1 TAAAAAATA
28756469 AGTTTTATTT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
15 21 0.64
16 12 0.36
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (15 bp):
TAAAAAATATTTTTT
Found at i:28756479 original size:18 final size:16
Alignment explanation
Indices: 28756414--28756479 Score: 57
Period size: 15 Copynumber: 4.1 Consensus size: 16
28756404 GAGAAAGAAA
*
28756414 TAAAAAATA-TTTCTT
1 TAAAAAATAGTTTTTT
*
28756429 AATAAAAAT-GTTTTTT
1 TA-AAAAATAGTTTTTT
28756445 TAAAAAATA-TTTTTT
1 TAAAAAATAGTTTTTT
*
28756460 TACAAAATAAGTTTTATT
1 TAAAAAAT-AGTTTT-TT
28756478 TA
1 TA
28756480 GTATATTAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
15 20 0.49
16 13 0.32
17 4 0.10
18 4 0.10
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.48
Consensus pattern (16 bp):
TAAAAAATAGTTTTTT
Found at i:28774840 original size:24 final size:24
Alignment explanation
Indices: 28774808--28774858 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
28774798 ATGTATCGGC
28774808 AAAAGTCGAAATGCCGAAAAGCTG
1 AAAAGTCGAAATGCCGAAAAGCTG
28774832 AAAAGTCGAAATGCCGAAAAGCTG
1 AAAAGTCGAAATGCCGAAAAGCTG
28774856 AAA
1 AAA
28774859 GTTTGGCTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.49, C:0.16, G:0.24, T:0.12
Consensus pattern (24 bp):
AAAAGTCGAAATGCCGAAAAGCTG
Found at i:28775129 original size:29 final size:28
Alignment explanation
Indices: 28775082--28775181 Score: 85
Period size: 29 Copynumber: 3.5 Consensus size: 28
28775072 TGAATGTGAC
*
28775082 TGGGCCTAACGGGCTATATAAATGTGGTT
1 TGGGCCTAATGGGC-ATATAAATGTGGTT
* * *
28775111 TGGGCCTAATGGGTCATATACAGGTGATT
1 TGGGCCTAATGGG-CATATAAATGTGGTT
* * * *
28775140 TGGTCCTAATGGGCCATATGAATAT-GAT
1 TGGGCCTAATGGG-CATATAAATGTGGTT
*
28775168 TGGGCTTAATGGGC
1 TGGGCCTAATGGGC
28775182 CAGATACAGG
Statistics
Matches: 56, Mismatches: 14, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
27 1 0.02
28 12 0.21
29 42 0.75
30 1 0.02
ACGTcount: A:0.24, C:0.14, G:0.31, T:0.31
Consensus pattern (28 bp):
TGGGCCTAATGGGCATATAAATGTGGTT
Found at i:28776362 original size:141 final size:141
Alignment explanation
Indices: 28776108--28776389 Score: 555
Period size: 141 Copynumber: 2.0 Consensus size: 141
28776098 ATTACGAGAA
28776108 GTTGAACATGGATTTCTTAAATTATAGTATGTTTTCTACGTTTCCACAACTAAGTTTTTTAAAAT
1 GTTGAACATGGATTTCTTAAATTATAGTATGTTTTCTACGTTTCCACAACTAAGTTTTTTAAAAT
28776173 ATCAAATGATTTAAACAAGGCTTTCGTAACTGAAAGGTTTTTCTTTTTTAGTTAATTAGGGTTTT
66 ATCAAATGATTTAAACAAGGCTTTCGTAACTGAAAGGTTTTTCTTTTTTAGTTAATTAGGGTTTT
28776238 TTAAGAAGGGT
131 TTAAGAAGGGT
*
28776249 GTTGAACATGGATTTCTTAAATTATAGTATGTTTTCTACGTTTCCGCAACTAAGTTTTTTAAAAT
1 GTTGAACATGGATTTCTTAAATTATAGTATGTTTTCTACGTTTCCACAACTAAGTTTTTTAAAAT
28776314 ATCAAATGATTTAAACAAGGCTTTCGTAACTGAAAGGTTTTTCTTTTTTAGTTAATTAGGGTTTT
66 ATCAAATGATTTAAACAAGGCTTTCGTAACTGAAAGGTTTTTCTTTTTTAGTTAATTAGGGTTTT
28776379 TTAAGAAGGGT
131 TTAAGAAGGGT
28776390 TTTTAATGAA
Statistics
Matches: 140, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
141 140 1.00
ACGTcount: A:0.30, C:0.10, G:0.17, T:0.43
Consensus pattern (141 bp):
GTTGAACATGGATTTCTTAAATTATAGTATGTTTTCTACGTTTCCACAACTAAGTTTTTTAAAAT
ATCAAATGATTTAAACAAGGCTTTCGTAACTGAAAGGTTTTTCTTTTTTAGTTAATTAGGGTTTT
TTAAGAAGGGT
Found at i:28781827 original size:22 final size:23
Alignment explanation
Indices: 28781801--28781846 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
28781791 CAACCAAACC
28781801 AATTCA-ACATATTT-TCAAGATA
1 AATTCATACATATTTAT-AAGATA
*
28781823 AATTCATGCATATTTATAAGATA
1 AATTCATACATATTTATAAGATA
28781846 A
1 A
28781847 CGTCATTACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 14 0.67
24 1 0.05
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.37
Consensus pattern (23 bp):
AATTCATACATATTTATAAGATA
Found at i:28781852 original size:23 final size:23
Alignment explanation
Indices: 28781808--28781852 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
28781798 ACCAATTCAA
*
28781808 CATATTTTCAAGATAAATTCATG
1 CATATTTTCAAGATAAAGTCATG
*
28781831 CATATTTAT-AAGATAACGTCAT
1 CATATTT-TCAAGATAAAGTCAT
28781853 TACATATCCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (23 bp):
CATATTTTCAAGATAAAGTCATG
Found at i:28793488 original size:43 final size:42
Alignment explanation
Indices: 28793353--28793514 Score: 121
Period size: 43 Copynumber: 3.8 Consensus size: 42
28793343 TGTGATATCA
** * *
28793353 TGTAAGACCATGTCT-GGTACGTTGGCATC-AATTTGGTATTTACG
1 TGTAAGACCATGTCTAGG-ACAATGGCATCGTATTT-G-A-TTACC
* * * * ***
28793397 TGTAAGACCACGTCTGGGGCATTGGCATCGTATTTGATTTTG
1 TGTAAGACCATGTCTAGGACAATGGCATCGTATTTGATTACC
* *
28793439 TGTAAGACCCTGTTTAGGACAATGGCATCGATATTTGATTACC
1 TGTAAGACCATGTCTAGGACAATGGCATCG-TATTTGATTACC
* * *
28793482 TGTAAGACCATGTCTGGGACATTGGCATTGTAT
1 TGTAAGACCATGTCTAGGACAATGGCATCGTAT
28793515 GAACGTTACG
Statistics
Matches: 95, Mismatches: 20, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
42 30 0.32
43 35 0.37
44 24 0.25
45 6 0.06
ACGTcount: A:0.23, C:0.17, G:0.25, T:0.35
Consensus pattern (42 bp):
TGTAAGACCATGTCTAGGACAATGGCATCGTATTTGATTACC
Found at i:28800247 original size:22 final size:23
Alignment explanation
Indices: 28800222--28800269 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
28800212 AGAAATTTTT
28800222 AAAAATAATTCT-AAAAATATCA
1 AAAAATAATTCTAAAAAATATCA
* * *
28800244 AAAAATTATTTTAAAAAATATTA
1 AAAAATAATTCTAAAAAATATCA
28800267 AAA
1 AAA
28800270 TTCATAATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 10 0.45
23 12 0.55
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (23 bp):
AAAAATAATTCTAAAAAATATCA
Found at i:28802728 original size:3 final size:3
Alignment explanation
Indices: 28802720--28802779 Score: 120
Period size: 3 Copynumber: 20.0 Consensus size: 3
28802710 TAAAACATGC
28802720 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
28802768 ATA ATA ATA ATA
1 ATA ATA ATA ATA
28802780 CTCACACCAA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:28803070 original size:2 final size:2
Alignment explanation
Indices: 28803063--28803115 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
28803053 CAAAATGTTG
28803063 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28803105 AT AT AT AT AT A
1 AT AT AT AT AT A
28803116 AATGTTAAAC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:28803250 original size:21 final size:20
Alignment explanation
Indices: 28803224--28803263 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
28803214 CAAGACTTCC
28803224 AAACATCTTA-AAAAATGTTTT
1 AAACAT-TTATAAAAA-GTTTT
28803245 AAACATTTATAAAAAGTTT
1 AAACATTTATAAAAAGTTT
28803264 GGACAAAGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.50, C:0.07, G:0.05, T:0.38
Consensus pattern (20 bp):
AAACATTTATAAAAAGTTTT
Found at i:28803318 original size:20 final size:20
Alignment explanation
Indices: 28803293--28803330 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
28803283 TTTAAACTTT
*
28803293 TTTTTAACTCAATTGAAACA
1 TTTTTAAATCAATTGAAACA
28803313 TTTTTAAATCAATTGAAA
1 TTTTTAAATCAATTGAAA
28803331 AATTGTTCCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.42, C:0.11, G:0.05, T:0.42
Consensus pattern (20 bp):
TTTTTAAATCAATTGAAACA
Found at i:28805867 original size:11 final size:11
Alignment explanation
Indices: 28805851--28805876 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
28805841 TTACTCAAAT
28805851 AATTTTAATAA
1 AATTTTAATAA
28805862 AATTTTAATAA
1 AATTTTAATAA
28805873 AATT
1 AATT
28805877 GACATGCTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
AATTTTAATAA
Found at i:28809999 original size:16 final size:15
Alignment explanation
Indices: 28809980--28810028 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 15
28809970 TTTTAAATTA
28809980 AATAATATATAAAAAT
1 AATAA-ATATAAAAAT
28809996 AATAAATATAAAATAT
1 AATAAATATAAAA-AT
* *
28810012 TATAAATTTAAAAAT
1 AATAAATATAAAAAT
28810027 AA
1 AA
28810029 GTCGAGTTGA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
15 11 0.38
16 18 0.62
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
AATAAATATAAAAAT
Found at i:28810154 original size:21 final size:21
Alignment explanation
Indices: 28810130--28810169 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
28810120 AAATCCTCTC
28810130 AAATTTTACTTAAACCCTTAG
1 AAATTTTACTTAAACCCTTAG
28810151 AAATTTTACTTAAACCCTT
1 AAATTTTACTTAAACCCTT
28810170 CGGAAGGTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.38, C:0.20, G:0.03, T:0.40
Consensus pattern (21 bp):
AAATTTTACTTAAACCCTTAG
Found at i:28812317 original size:16 final size:17
Alignment explanation
Indices: 28812278--28812310 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
28812268 TTAAATTTTT
28812278 TATTAAAAATTTTAGTAC
1 TATTAAAAA-TTTAGTAC
28812296 TATTAAAAA-TTAGTA
1 TATTAAAAATTTAGTA
28812311 TGATTAATAG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.48, C:0.03, G:0.06, T:0.42
Consensus pattern (17 bp):
TATTAAAAATTTAGTAC
Found at i:28815952 original size:21 final size:21
Alignment explanation
Indices: 28815911--28815952 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
28815901 CACCCTGAAA
**
28815911 CTCAATATAACAACCTGATTT
1 CTCAATATAACAACCACATTT
28815932 CTCAAT-TCAACAACCACATTT
1 CTCAATAT-AACAACCACATTT
28815953 AAGGCATCTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.38, C:0.29, G:0.02, T:0.31
Consensus pattern (21 bp):
CTCAATATAACAACCACATTT
Found at i:28818136 original size:40 final size:40
Alignment explanation
Indices: 28818075--28818318 Score: 355
Period size: 40 Copynumber: 6.1 Consensus size: 40
28818065 CGGAATTTAG
* ** *
28818075 CCGGATATAACCACAAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAACAACTCGCACAAATGCCTTCGGGTCTTAAC
* * * *
28818115 CAGGGTATAGCAACTCGCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAACAACTCGCACAAATGCCTTCGGGTCTTAAC
28818155 CCGGATATAACAACTCGCACAAATGCCTTCGGGTCTTAAC
1 CCGGATATAACAACTCGCACAAATGCCTTCGGGTCTTAAC
28818195 CCGGATATAACAACTCGCACAAATGCCTTCGGGTCTTAAC
1 CCGGATATAACAACTCGCACAAATGCCTTCGGGTCTTAAC
*
28818235 CCGGATATAACAACTCGCACAAATGTCTTCGGGTCTTAAC
1 CCGGATATAACAACTCGCACAAATGCCTTCGGGTCTTAAC
* * * *
28818275 CCGGATATAATC-ACTAGCATAAATGCCTTCGGGGCTTAGC
1 CCGGATATAA-CAACTCGCACAAATGCCTTCGGGTCTTAAC
28818315 CCGG
1 CCGG
28818319 GTATCATTCA
Statistics
Matches: 185, Mismatches: 18, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
40 184 0.99
41 1 0.01
ACGTcount: A:0.28, C:0.29, G:0.20, T:0.23
Consensus pattern (40 bp):
CCGGATATAACAACTCGCACAAATGCCTTCGGGTCTTAAC
Found at i:28824212 original size:38 final size:39
Alignment explanation
Indices: 28824160--28824302 Score: 234
Period size: 39 Copynumber: 3.7 Consensus size: 39
28824150 GAATGTTCGA
28824160 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
* *
28824199 GTGATA-CCGGGCTAAGCCCGAAGGCAATTGTGCGAGTT
1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
*
28824237 ATGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
*
28824276 GTGATATCCGGGTTAAGTCCCGAAGGC
1 GTGATATCCGGGCTAAG-CCCGAAGGC
28824303 CTTTGTGCGG
Statistics
Matches: 95, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
38 35 0.37
39 51 0.54
40 9 0.09
ACGTcount: A:0.27, C:0.21, G:0.30, T:0.22
Consensus pattern (39 bp):
GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
Found at i:28824248 original size:77 final size:79
Alignment explanation
Indices: 28824161--28824342 Score: 269
Period size: 77 Copynumber: 2.3 Consensus size: 79
28824151 AATGTTCGAG
28824161 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTGTGATA-CCGGGCTAAG-CCCGAAGGC
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTGTGATATCCGGGCTAAGTCCCGAAGGC
28824224 AATTGTGCGAGTTA
66 AATTGTGCGAGTTA
*
28824238 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTGTGATATCCGGGTTAAGTCCCGAAGGC
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTGTGATATCCGGGCTAAGTCCCGAAGGC
** *
28824303 CTTTGTGCGGGTTA
66 AATTGTGCGAGTTA
** * *
28824317 CCATAACCGGGCTATGTCCCGAAGGC
1 TGATATCCGGGCTAAG-CCCGAAGGC
28824343 GTTTGAACGA
Statistics
Matches: 94, Mismatches: 8, Indels: 3
0.90 0.08 0.03
Matches are distributed among these distances:
77 44 0.47
78 9 0.10
79 32 0.34
80 9 0.10
ACGTcount: A:0.25, C:0.23, G:0.30, T:0.23
Consensus pattern (79 bp):
TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTGTGATATCCGGGCTAAGTCCCGAAGGC
AATTGTGCGAGTTA
Found at i:28832232 original size:38 final size:39
Alignment explanation
Indices: 28832180--28832322 Score: 234
Period size: 39 Copynumber: 3.7 Consensus size: 39
28832170 GAATGTTCGA
28832180 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
* *
28832219 GTGATA-CCGGGCTAAGCCCGAAGGCAATTGTGCGAGTT
1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
*
28832257 ATGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
*
28832296 GTGATATCCGGGTTAAGTCCCGAAGGC
1 GTGATATCCGGGCTAAG-CCCGAAGGC
28832323 CTTTGTGCGG
Statistics
Matches: 95, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
38 35 0.37
39 51 0.54
40 9 0.09
ACGTcount: A:0.27, C:0.21, G:0.30, T:0.22
Consensus pattern (39 bp):
GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
Found at i:28832268 original size:77 final size:79
Alignment explanation
Indices: 28832181--28832362 Score: 269
Period size: 77 Copynumber: 2.3 Consensus size: 79
28832171 AATGTTCGAG
28832181 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTGTGATA-CCGGGCTAAG-CCCGAAGGC
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTGTGATATCCGGGCTAAGTCCCGAAGGC
28832244 AATTGTGCGAGTTA
66 AATTGTGCGAGTTA
*
28832258 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTGTGATATCCGGGTTAAGTCCCGAAGGC
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTGTGATATCCGGGCTAAGTCCCGAAGGC
** *
28832323 CTTTGTGCGGGTTA
66 AATTGTGCGAGTTA
** * *
28832337 CCATAACCGGGCTATGTCCCGAAGGC
1 TGATATCCGGGCTAAG-CCCGAAGGC
28832363 GTTTGAACGA
Statistics
Matches: 94, Mismatches: 8, Indels: 3
0.90 0.08 0.03
Matches are distributed among these distances:
77 44 0.47
78 9 0.10
79 32 0.34
80 9 0.10
ACGTcount: A:0.25, C:0.23, G:0.30, T:0.23
Consensus pattern (79 bp):
TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTGTGATATCCGGGCTAAGTCCCGAAGGC
AATTGTGCGAGTTA
Found at i:28840251 original size:38 final size:39
Alignment explanation
Indices: 28840199--28840341 Score: 234
Period size: 39 Copynumber: 3.7 Consensus size: 39
28840189 GAATGTTCGA
28840199 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
* *
28840238 GTGATA-CCGGGCTAAGCCCGAAGGCAATTGTGCGAGTT
1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
*
28840276 ATGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
*
28840315 GTGATATCCGGGTTAAGTCCCGAAGGC
1 GTGATATCCGGGCTAAG-CCCGAAGGC
28840342 CTTTGTGCGG
Statistics
Matches: 95, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
38 35 0.37
39 51 0.54
40 9 0.09
ACGTcount: A:0.27, C:0.21, G:0.30, T:0.22
Consensus pattern (39 bp):
GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
Found at i:28840287 original size:77 final size:79
Alignment explanation
Indices: 28840200--28840381 Score: 269
Period size: 77 Copynumber: 2.3 Consensus size: 79
28840190 AATGTTCGAG
28840200 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTGTGATA-CCGGGCTAAG-CCCGAAGGC
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTGTGATATCCGGGCTAAGTCCCGAAGGC
28840263 AATTGTGCGAGTTA
66 AATTGTGCGAGTTA
*
28840277 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTGTGATATCCGGGTTAAGTCCCGAAGGC
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTGTGATATCCGGGCTAAGTCCCGAAGGC
** *
28840342 CTTTGTGCGGGTTA
66 AATTGTGCGAGTTA
** * *
28840356 CCATAACCGGGCTATGTCCCGAAGGC
1 TGATATCCGGGCTAAG-CCCGAAGGC
28840382 GTTTGAACGA
Statistics
Matches: 94, Mismatches: 8, Indels: 3
0.90 0.08 0.03
Matches are distributed among these distances:
77 44 0.47
78 9 0.10
79 32 0.34
80 9 0.10
ACGTcount: A:0.25, C:0.23, G:0.30, T:0.23
Consensus pattern (79 bp):
TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTGTGATATCCGGGCTAAGTCCCGAAGGC
AATTGTGCGAGTTA
Found at i:28845806 original size:47 final size:47
Alignment explanation
Indices: 28845692--28845991 Score: 458
Period size: 47 Copynumber: 6.3 Consensus size: 47
28845682 GTATGAGATA
28845692 TATATAT-TGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA--GTG
28845740 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
28845787 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA--GTG
*
28845836 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAGGTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
* *
28845883 TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
* * * * * * *
28845930 TATATATGTGATAGGGCCGAGTGGCCAACGTGATGGATGTGGAAGTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
*
28845977 TATAAATGTGATAAG
1 TATATATGTGATAAG
28845992 TCCCGAAGGG
Statistics
Matches: 238, Mismatches: 11, Indels: 7
0.93 0.04 0.03
Matches are distributed among these distances:
47 149 0.63
48 7 0.03
49 82 0.34
ACGTcount: A:0.31, C:0.08, G:0.31, T:0.29
Consensus pattern (47 bp):
TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
Found at i:28845863 original size:96 final size:96
Alignment explanation
Indices: 28845692--28845991 Score: 480
Period size: 96 Copynumber: 3.2 Consensus size: 96
28845682 GTATGAGATA
28845692 TATATAT-TGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTGTATATATGTGATAAGG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTGTATATATGTGATAAGG
28845756 CCTAATGGCCGATGTGATGAATGTGAAAGTG
66 CCTAATGGCCGATGTGATGAATGTGAAAGTG
28845787 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTGTATATATGTGATAAGG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTGTATATATGTGATAAGG
*
28845852 CCTAATGGCCGATGTGATGAATGTGAAGGTG
66 CCTAATGGCCGATGTGATGAATGTGAAAGTG
* * *
28845883 TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAA--GTGTATATATGTGATAGGG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTGTATATATGTGATAAGG
* * * * * *
28845946 CCGAGTGGCCAACGTGATGGATGTGGAAGTG
66 CCTAATGGCCGATGTGATGAATGTGAAAGTG
*
28845977 TATAAATGTGATAAG
1 TATATATGTGATAAG
28845992 TCCCGAAGGG
Statistics
Matches: 192, Mismatches: 12, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
94 56 0.29
95 7 0.04
96 129 0.67
ACGTcount: A:0.31, C:0.08, G:0.31, T:0.29
Consensus pattern (96 bp):
TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTGTATATATGTGATAAGG
CCTAATGGCCGATGTGATGAATGTGAAAGTG
Found at i:28850573 original size:151 final size:151
Alignment explanation
Indices: 28850299--28850694 Score: 603
Period size: 151 Copynumber: 2.6 Consensus size: 151
28850289 AAAGCTCTCT
* * * * * *
28850299 GGTACGCATAGTAGCCTGCACTTAGTACTACACATACAACCTATCAATCTGGCATATGTACTTGC
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCAACCTATCAATCTGGTACACGTAGTAGC
* * *
28850364 CTGCACTTAGTACTACACACATGACTTATCCATCTGATACACGTAGTAGCCCGCACTTAGTACTA
66 CTGCACTTAGTACTACACACGTGACCTAACCATCTGATACACGTAGTAGCCCGCACTTAGTACTA
**
28850429 CACACGTGATCGAAGTTAACG
131 CACACGTGATCGAAACTAACG
* *
28850450 GGTACGTATAGTAGCCTGCACTTAGTACTACACATGCAACCTATCAATCCGGTACACGTAGTAGC
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCAACCTATCAATCTGGTACACGTAGTAGC
* *
28850515 TTGCACTTAGTACTACACACGTGACCTAACCATCTGATACACGTAGTAGCCTGCACTTAGTACTA
66 CTGCACTTAGTACTACACACGTGACCTAACCATCTGATACACGTAGTAGCCCGCACTTAGTACTA
*
28850580 CACACGTGATCGAAACTATCG
131 CACACGTGATCGAAACTAACG
* * * *
28850601 GGTACGCATAGTAGCCTGCACTTAGTACTACATATGCGACCTAACAATCTTGTACACGTAGTAGC
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCAACCTATCAATCTGGTACACGTAGTAGC
*
28850666 CTGCATTTAGTACTACACACGTGACCTAA
66 CTGCACTTAGTACTACACACGTGACCTAA
28850695 AACTGTCTTA
Statistics
Matches: 221, Mismatches: 24, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
151 221 1.00
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.26
Consensus pattern (151 bp):
GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCAACCTATCAATCTGGTACACGTAGTAGC
CTGCACTTAGTACTACACACGTGACCTAACCATCTGATACACGTAGTAGCCCGCACTTAGTACTA
CACACGTGATCGAAACTAACG
Found at i:28850585 original size:50 final size:50
Alignment explanation
Indices: 28850296--28850694 Score: 368
Period size: 50 Copynumber: 7.9 Consensus size: 50
28850286 ACCAAAGCTC
* * **** *
28850296 TCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATACAACCTATCAA
1 TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAACAA
* * * * * * * * *
28850346 TCTGGCATATGTACTTGCCTGCACTTAGTACTACACACATGACTTATCCA
1 TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAACAA
* * * * *
28850396 TCTGATACACGTAGTAGCCCGCACTTAGTACTACACACGTGATCGAAGTTAA
1 TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAA--CAA
* *** * ** *
28850448 -CGGGTACGTATAGTAGCCTGCACTTAGTACTACACATGCAACCTATCAA
1 TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAACAA
* * *
28850497 TCCGGTACACGTAGTAGCTTGCACTTAGTACTACACACGTGACCTAACCA
1 TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAACAA
* ** *
28850547 TCTGATACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCGAAACTA
1 TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGA-CCTAACAA
* * * * * *
28850598 TCGGGTACGCATAGTAGCCTGCACTTAGTACTACATATGCGACCTAACAA
1 TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAACAA
* *
28850648 TCTTGTACACGTAGTAGCCTGCATTTAGTACTACACACGTGACCTAA
1 TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAA
28850695 AACTGTCTTA
Statistics
Matches: 272, Mismatches: 73, Indels: 8
0.77 0.21 0.02
Matches are distributed among these distances:
49 2 0.01
50 195 0.72
51 74 0.27
52 1 0.00
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.26
Consensus pattern (50 bp):
TCTGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAACAA
Found at i:28850605 original size:101 final size:99
Alignment explanation
Indices: 28850307--28850693 Score: 353
Period size: 101 Copynumber: 3.8 Consensus size: 99
28850297 CTGGTACGCA
**** * * * * * *
28850307 TAGTAGCCTGCACTTAGTACTACACATACAACCTATCAATCTGGCATATGTACTTGCCTGCACTT
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACAATCT-GTACACGTAGTAGCCTGCACTT
* * * * *
28850372 AGTACTACACACATGACTTATCCATCTGATACACG
65 AGTACTACACACGTGACCTATCAATCCGGTACACG
* * * * * ***
28850407 TAGTAGCCCGCACTTAGTACTACACACGTGATCGAAGTTAA-CGGGTACGTATAGTAGCCTGCAC
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAA--CAATC-TGTACACGTAGTAGCCTGCAC
* **
28850471 TTAGTACTACACATGCAACCTATCAATCCGGTACACG
63 TTAGTACTACACACGTGACCTATCAATCCGGTACACG
* *
28850508 TAGTAGCTTGCACTTAGTACTACACACGTGACCTAACCATCTGATACACGTAGTAGCCTGCACTT
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACAATCTG-TACACGTAGTAGCCTGCACTT
** * * * * *
28850573 AGTACTACACACGTGATCGAAACTATCGGGTACGCA
65 AGTACTACACACGTGA-CCTATCAATCCGGTACACG
* * * *
28850609 TAGTAGCCTGCACTTAGTACTACATATGCGACCTAACAATCTTGTACACGTAGTAGCCTGCATTT
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACAATC-TGTACACGTAGTAGCCTGCACTT
28850674 AGTACTACACACGTGACCTA
65 AGTACTACACACGTGACCTA
28850694 AAACTGTCTT
Statistics
Matches: 228, Mismatches: 52, Indels: 14
0.78 0.18 0.05
Matches are distributed among these distances:
99 2 0.01
100 62 0.27
101 160 0.70
102 4 0.02
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.26
Consensus pattern (99 bp):
TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACAATCTGTACACGTAGTAGCCTGCACTTA
GTACTACACACGTGACCTATCAATCCGGTACACG
Found at i:28852431 original size:47 final size:47
Alignment explanation
Indices: 28852297--28852467 Score: 188
Period size: 47 Copynumber: 3.7 Consensus size: 47
28852287 GTAAGGTGCC
*
28852297 GATGCCATGTCCGAGACATGGTCTTACACT-AGCTCACATCTCAAGTC
1 GATGCCATGTCCGAGACATGGTCTTACACTGA-CTCACATCTCAAGTT
* * ** *
28852344 CATGCCATGTTCGAGACACAGTCTTACACTGCCTCACATCTCAAGTT
1 GATGCCATGTCCGAGACATGGTCTTACACTGACTCACATCTCAAGTT
* * * *
28852391 GATGCCATGTACTAGACATGGTCTTACACTGACT-ATCATCTCGTAGCT
1 GATGCCATGTCCGAGACATGGTCTTACACTGACTCA-CATCTC-AAGTT
*
28852439 GATG-CATGTCCCAGACAT-GTCTTACACTG
1 GATGCCATGTCCGAGACATGGTCTTACACTG
28852468 GCTTACGTCT
Statistics
Matches: 105, Mismatches: 16, Indels: 7
0.82 0.12 0.05
Matches are distributed among these distances:
46 12 0.11
47 86 0.82
48 7 0.07
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.28
Consensus pattern (47 bp):
GATGCCATGTCCGAGACATGGTCTTACACTGACTCACATCTCAAGTT
Found at i:28852479 original size:46 final size:45
Alignment explanation
Indices: 28852297--28852508 Score: 142
Period size: 47 Copynumber: 4.5 Consensus size: 45
28852287 GTAAGGTGCC
* * *
28852297 GATGCCATGTCCGAGACATGGTCTTACACT-AGCTCACATCTCAAG-T
1 GATG-CATGTCCCAGACAT-GTCTTACACTGA-CTTACATCTCGAGCT
* * * * * * * *
28852343 CCATGCCATGTTCGAGACACAGTCTTACACTGCCTCACATCTCAAGTT
1 -GATG-CATGTCCCAGACA-TGTCTTACACTGACTTACATCTCGAGCT
* *
28852391 GATGCCATGTACTAGACATGGTCTTACACTGAC-TATCATCTCGTAGCT
1 GATG-CATGTCCCAGACAT-GTCTTACACTGACTTA-CATCTCG-AGCT
* * *
28852439 GATGCATGTCCCAGACATGTCTTACACTGGCTTACGTCTCGAGGCC
1 GATGCATGTCCCAGACATGTCTTACACTGACTTACATCTCGA-GCT
* *
28852485 GATGCATGTCCCAAAAATGTCTTA
1 GATGCATGTCCCAGACATGTCTTA
28852509 TACTAGAACT
Statistics
Matches: 138, Mismatches: 19, Indels: 17
0.79 0.11 0.10
Matches are distributed among these distances:
45 1 0.01
46 43 0.31
47 86 0.62
48 8 0.06
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28
Consensus pattern (45 bp):
GATGCATGTCCCAGACATGTCTTACACTGACTTACATCTCGAGCT
Found at i:28862209 original size:47 final size:45
Alignment explanation
Indices: 28862134--28862396 Score: 215
Period size: 47 Copynumber: 5.6 Consensus size: 45
28862124 GGTAAGGTAC
*
28862134 CGATGCCATGTCCCAAACATGGTCTTACACTGGCTCACATCTCAAGT
1 CGATG-CATGTCCCAGACAT-GTCTTACACTGGCTCACATCTCAAGT
* ** * *
28862181 CGACGACATGTCCCAGACATGGTCTTACACTAACT-ATCATCTCATTGC
1 CGATG-CATGTCCCAGACAT-GTCTTACACTGGCTCA-CATCTCA-AGT
* * *
28862229 CGATGCATGCCCCAGACATGTCTTACACTGGCTTACGTCTCAAGT
1 CGATGCATGTCCCAGACATGTCTTACACTGGCTCACATCTCAAGT
* * * * *
28862274 CGATACCATGT-CCAGACATGTCTTACACTGGCACTCGTCTCAATGC
1 CGAT-GCATGTCCCAGACATGTCTTACACTGGCTCACATCTCAA-GT
* * * * * ***
28862320 CGATGCCATGTCCTAGACACGATCTTACATTGGCTCTCATAATGTGGT
1 CGATG-CATGTCCCAGACATG-TCTTACACTGGCTCACAT-CTCAAGT
28862368 CGATGCATGTCCCAGACATGTCTTACACT
1 CGATGCATGTCCCAGACATGTCTTACACT
28862397 AGCCTACACA
Statistics
Matches: 173, Mismatches: 34, Indels: 19
0.77 0.15 0.08
Matches are distributed among these distances:
45 34 0.20
46 41 0.24
47 71 0.41
48 26 0.15
49 1 0.01
ACGTcount: A:0.24, C:0.30, G:0.18, T:0.27
Consensus pattern (45 bp):
CGATGCATGTCCCAGACATGTCTTACACTGGCTCACATCTCAAGT
Found at i:28862346 original size:93 final size:94
Alignment explanation
Indices: 28862133--28862397 Score: 274
Period size: 93 Copynumber: 2.8 Consensus size: 94
28862123 GGGTAAGGTA
*
28862133 CCGATGCCATGTCCCAAACATGGTCTTACACTGGCTCACATCTCAAGTCGACGACATGTCCCAGA
1 CCGATGCCATGTCCCAGACAT-GTCTTACACTGGCTCACATCTCAAGTCGACGACATGTCCCAGA
*
28862198 CATGGTCTTACACTAACTATCATCTCATTG
65 CATGGTCTTACACTAACTATCATCTCAATG
* * * *
28862228 CCGATG-CATGCCCCAGACATGTCTTACACTGGCTTACGTCTCAAGTCGA-TACCATGT-CCAGA
1 CCGATGCCATGTCCCAGACATGTCTTACACTGGCTCACATCTCAAGTCGACGA-CATGTCCCAGA
** *
28862290 CAT-GTCTTACACTGGC-ACTCGTCTCAATG
65 CATGGTCTTACACTAACTA-TCATCTCAATG
* * * * * *** *
28862319 CCGATGCCATGTCCTAGACACGATCTTACATTGGCTCTCATAATGTGGTCGATG-CATGTCCCAG
1 CCGATGCCATGTCCCAGACATG-TCTTACACTGGCTCACAT-CTCAAGTCGACGACATGTCCCAG
28862383 ACAT-GTCTTACACTA
64 ACATGGTCTTACACTA
28862398 GCCTACACAC
Statistics
Matches: 141, Mismatches: 22, Indels: 15
0.79 0.12 0.08
Matches are distributed among these distances:
90 1 0.01
91 26 0.18
92 21 0.15
93 51 0.36
94 36 0.26
95 6 0.04
ACGTcount: A:0.25, C:0.31, G:0.18, T:0.27
Consensus pattern (94 bp):
CCGATGCCATGTCCCAGACATGTCTTACACTGGCTCACATCTCAAGTCGACGACATGTCCCAGAC
ATGGTCTTACACTAACTATCATCTCAATG
Found at i:28869819 original size:46 final size:46
Alignment explanation
Indices: 28869668--28869978 Score: 227
Period size: 46 Copynumber: 6.7 Consensus size: 46
28869658 GGGTAAGGTA
* * * *
28869668 CCGATGCCATGTCCCAAACACGGTCTTACATTGGCTCACATCTCAAG
1 CCGATGCCATGTCCCAGACA-TGTCTTACACTGGCTTACATCTCAAG
* * * * * *
28869715 TCAATGCCATGCCCCAGACATGGTCTTACATTGAC-TATCATCTCGTAG
1 CCGATGCCATGTCCCAGACAT-GTCTTACACTGGCTTA-CATCTC-AAG
* *
28869763 CCGATG-CATGTCCCAGACATGTCTTACACTAGCTTACGTCTCAAG
1 CCGATGCCATGTCCCAGACATGTCTTACACTGGCTTACATCTCAAG
* * * * *
28869808 TCGATGCCATGTCCTAGACATGTCTTACATTGGCTTACGTCTCGAGG
1 CCGATGCCATGTCCCAGACATGTCTTACACTGGCTTACATCTC-AAG
* * * *
28869855 CCGATG-CATGTCCCACAAATGTCTTACACTAGCACT-CATCTCAATG
1 CCGATGCCATGTCCCAGACATGTCTTACACTGGC-TTACATCTCAA-G
* * * * * ***
28869901 CCGATGCCATGTACTAGACACGGTCTTACACTGGCTTTCATAATGTGG
1 CCGATGCCATGTCCCAGACA-TGTCTTACACTGGCTTACAT-CTCAAG
* *
28869949 CTGATG-CGTGTCCCAGACATGTCTTACACT
1 CCGATGCCATGTCCCAGACATGTCTTACACT
28869979 AGCCCACACA
Statistics
Matches: 206, Mismatches: 46, Indels: 25
0.74 0.17 0.09
Matches are distributed among these distances:
45 8 0.04
46 93 0.45
47 77 0.37
48 27 0.13
49 1 0.00
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.28
Consensus pattern (46 bp):
CCGATGCCATGTCCCAGACATGTCTTACACTGGCTTACATCTCAAG
Found at i:28869961 original size:94 final size:92
Alignment explanation
Indices: 28869668--28869982 Score: 271
Period size: 94 Copynumber: 3.4 Consensus size: 92
28869658 GGGTAAGGTA
* * * * * * ** *
28869668 CCGATGCCATGTCCCAAACACGGTCTTACA-TTGGCTCACATCTCAAGTCAATGCCATGCCCCAG
1 CCGATG-CATGTCCCAGACA-TGTCTTACACTAGCCT-ACATCTCAAGCCGATGCCATGTACTAG
* * *
28869732 ACATGGTCTTACATTGAC-TATCATCTCGTA-G
63 ACA-GGTCTTACACTGGCTTA-CATATCG-AGG
* * * *
28869763 CCGATGCATGTCCCAGACATGTCTTACACTAGCTTACGTCTCAAGTCGATGCCATGTCCTAGACA
1 CCGATGCATGTCCCAGACATGTCTTACACTAGCCTACATCTCAAGCCGATGCCATGTACTAGACA
* * * *
28869828 TGTCTTACATTGGCTTACGTCTCGAGG
66 GGTCTTACACTGGCTTACATATCGAGG
* *
28869855 CCGATGCATGTCCCACAAATGTCTTACACTAGCACT-CATCTCAATGCCGATGCCATGTACTAGA
1 CCGATGCATGTCCCAGACATGTCTTACACTAGC-CTACATCTCAA-GCCGATGCCATGTACTAGA
* *
28869919 CACGGTCTTACACTGGCTTTCATAAT-GTGG
64 CA-GGTCTTACACTGGCTTACAT-ATCGAGG
* *
28869949 CTGATGCGTGTCCCAGACATGTCTTACACTAGCC
1 CCGATGCATGTCCCAGACATGTCTTACACTAGCC
28869983 CACACACAAA
Statistics
Matches: 185, Mismatches: 28, Indels: 16
0.81 0.12 0.07
Matches are distributed among these distances:
91 1 0.01
92 57 0.31
93 57 0.31
94 63 0.34
95 7 0.04
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.28
Consensus pattern (92 bp):
CCGATGCATGTCCCAGACATGTCTTACACTAGCCTACATCTCAAGCCGATGCCATGTACTAGACA
GGTCTTACACTGGCTTACATATCGAGG
Found at i:28877384 original size:46 final size:44
Alignment explanation
Indices: 28877318--28877511 Score: 142
Period size: 46 Copynumber: 4.2 Consensus size: 44
28877308 CCAAGACACG
*
28877318 GTCTTACATTGGCTCA-CATCTAAAGTCGATGCGATGTCCCGACAT
1 GTCTTACACTGGCT-ATCATCTAAAGTCGATGC-ATGTCCCGACAT
* ** * *
28877363 GGTCTTACACTGACTATCATCTCGTAGCCGATGCATGTCCCAGATAT
1 -GTCTTACACTGGCTATCATCT-AAAGTCGATGCATGTCCC-GACAT
* * * *
28877410 GTCTTACACTGGCT-TACGTCTCAAGTTGATGCCATGTCCTAGACAT
1 GTCTTACACTGGCTAT-CATCTAAAGTCGATG-CATGTCC-CGACAT
* * *
28877456 GTCTTACACTGGCT-TACATCTCGAGGCCGATGCATGTCCCAGACAT
1 GTCTTACACTGGCTAT-CATCT-AAAGTCGATGCATGTCCC-GACAT
*
28877502 GTTTTACACT
1 GTCTTACACT
28877512 AGCACTCGTC
Statistics
Matches: 119, Mismatches: 21, Indels: 16
0.76 0.13 0.10
Matches are distributed among these distances:
45 8 0.07
46 93 0.78
47 18 0.15
ACGTcount: A:0.23, C:0.27, G:0.20, T:0.30
Consensus pattern (44 bp):
GTCTTACACTGGCTATCATCTAAAGTCGATGCATGTCCCGACAT
Found at i:28877461 original size:92 final size:91
Alignment explanation
Indices: 28877303--28877605 Score: 281
Period size: 92 Copynumber: 3.3 Consensus size: 91
28877293 GTACCAACGC
* * * * * * * *
28877303 CATGTCCAAGACACGGTCTTACATTGGCTCACATCTAAAGTCGATGCGATGTCC-CGACATGGTC
1 CATGTCCCAGACA-TGTCTTACACTGGCTTACGTCTCAAGTCGATGCCATGTCCTAGACAT-GTC
*
28877367 TTACACTGACTATCATCTCGTAGCCGATG
64 TTACACTGGCT-TCATCTCGTAGCCGATG
* *
28877396 CATGTCCCAGATATGTCTTACACTGGCTTACGTCTCAAGTTGATGCCATGTCCTAGACATGTCTT
1 CATGTCCCAGACATGTCTTACACTGGCTTACGTCTCAAGTCGATGCCATGTCCTAGACATGTCTT
28877461 ACACTGGCTTACATCTCG-AGGCCGATG
66 ACACTGGCTT-CATCTCGTA-GCCGATG
* * * * * ** *
28877488 CATGTCCCAGACATGTTTTACACTAGCACT-CGTCTCAATGCCAATGCCATGGACTAGACACGGT
1 CATGTCCCAGACATGTCTTACACTGGC-TTACGTCTCAA-GTCGATGCCATGTCCTAGACA-TGT
* * * *
28877552 CTTACATTGGCTCTCATAAT-GTGGCTGATG
63 CTTACACTGGCT-TCAT-CTCGTAGCCGATG
28877582 CATGTCCCAGACATGTCTTACACT
1 CATGTCCCAGACATGTCTTACACT
28877606 AGCCCACACA
Statistics
Matches: 175, Mismatches: 26, Indels: 17
0.80 0.12 0.08
Matches are distributed among these distances:
91 2 0.01
92 92 0.53
93 33 0.19
94 46 0.26
95 2 0.01
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.29
Consensus pattern (91 bp):
CATGTCCCAGACATGTCTTACACTGGCTTACGTCTCAAGTCGATGCCATGTCCTAGACATGTCTT
ACACTGGCTTCATCTCGTAGCCGATG
Found at i:28879450 original size:40 final size:40
Alignment explanation
Indices: 28879351--28879581 Score: 322
Period size: 40 Copynumber: 5.8 Consensus size: 40
28879341 TGGATGATAA
* * * **
28879351 CCGGGCTAAGTCCCGAAGGCATCTGTGCTAGTGACTAGTT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
* *
28879391 TCGGGC-AAGTCCCAAAGGCATTTGTGCGAGTTACTAAAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
*
28879430 CCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACTAAAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
*
28879470 CCAGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
* *
28879510 CCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACTCTAA-
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AAAT
* *
28879550 CCGGGCTATGTCCCGAAGGCATTTGAGCGAGT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGT
28879582 AGCTATATCC
Statistics
Matches: 171, Mismatches: 18, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
39 32 0.19
40 137 0.80
41 2 0.01
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
Found at i:28883450 original size:40 final size:40
Alignment explanation
Indices: 28883352--28883569 Score: 275
Period size: 40 Copynumber: 5.5 Consensus size: 40
28883342 TGGATGATAA
* *
28883352 CCGGGCTAAGTCCCGAAGGCATTT-TGCACTAGTGACTAGT-T
1 CCGGGCTAAGTCCCGAAGGCATTTGTG--CGAGTTACTA-TAT
* *
28883393 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTATTACAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
28883433 CCGGGCTAAGTCTCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
28883473 CCGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
28883513 CCGGGCTATGTCCCGAAGGCA-TTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* *
28883552 CC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
28883570 TACTTGGCTT
Statistics
Matches: 159, Mismatches: 15, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
38 15 0.09
39 15 0.09
40 103 0.65
41 24 0.15
42 2 0.01
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:28889835 original size:5 final size:5
Alignment explanation
Indices: 28889825--28889862 Score: 60
Period size: 5 Copynumber: 7.6 Consensus size: 5
28889815 TATAGAGATA
28889825 AAAAT AAAAT AAAAT -AAAT AAAAAT AAAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT -AAAAT AAAAT AAAAT AAA
28889863 TAATAGGTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
4 4 0.13
5 23 0.74
6 4 0.13
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:28889847 original size:20 final size:20
Alignment explanation
Indices: 28889822--28889865 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
28889812 AAATATAGAG
28889822 ATAAAAATAAAATAAAATAA
1 ATAAAAATAAAATAAAATAA
28889842 ATAAAAATAAAATAAAATAA
1 ATAAAAATAAAATAAAATAA
28889862 ATAA
1 ATAA
28889866 TAGGTGTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (20 bp):
ATAAAAATAAAATAAAATAA
Found at i:28895740 original size:19 final size:19
Alignment explanation
Indices: 28895716--28895755 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
28895706 ATCAACTTCG
28895716 CTTAATTATGAAAAATGTA
1 CTTAATTATGAAAAATGTA
*
28895735 CTTAATTATGACAAATGTA
1 CTTAATTATGAAAAATGTA
28895754 CT
1 CT
28895756 CTCAGACAGG
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:0.42, C:0.10, G:0.10, T:0.38
Consensus pattern (19 bp):
CTTAATTATGAAAAATGTA
Found at i:28897866 original size:33 final size:33
Alignment explanation
Indices: 28897822--28897887 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
28897812 GCTTGGGCCC
* *
28897822 ACTCTGCTACTGTATAGGGCTAAAGCCCAGACT
1 ACTCTGCTACTGAATAAGGCTAAAGCCCAGACT
* * *
28897855 ACTCTGTTACTGAATAAGGCTACAGCCTAGACT
1 ACTCTGCTACTGAATAAGGCTAAAGCCCAGACT
28897888 GTTTTGCATA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.29, C:0.26, G:0.20, T:0.26
Consensus pattern (33 bp):
ACTCTGCTACTGAATAAGGCTAAAGCCCAGACT
Found at i:28899676 original size:2 final size:2
Alignment explanation
Indices: 28899669--28899693 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
28899659 AATGTTGTTA
28899669 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
28899694 AGTTTTAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:28911067 original size:44 final size:42
Alignment explanation
Indices: 28911017--28911172 Score: 140
Period size: 44 Copynumber: 3.7 Consensus size: 42
28911007 TGTGTTATCG
*
28911017 TGTAAGACCATGTCTGGGACGTCGGCATCAATTTGTGATTTACA
1 TGTAAGACCATGTCTGGGACGTTGGCATC-ATTT-TGATTTACA
* * * *
28911061 TGTAAGACCATGTCTGGGACATTGGCATCGTATATGATTT-CG
1 TGTAAGACCATGTCTGGGACGTTGGCATCAT-TTTGATTTACA
*** *
28911103 TGTAAGACC-TGTCTAAAATAG-TGGCATCGATATTTGA-TTACA
1 TGTAAGACCATGTCTGGGA-CGTTGGCATC-AT-TTTGATTTACA
*
28911145 TGTAAGACCACGTCTGGGACGTTGGCAT
1 TGTAAGACCATGTCTGGGACGTTGGCAT
28911173 TGTACGAGCT
Statistics
Matches: 88, Mismatches: 18, Indels: 13
0.74 0.15 0.11
Matches are distributed among these distances:
41 15 0.17
42 27 0.31
43 18 0.20
44 28 0.32
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.31
Consensus pattern (42 bp):
TGTAAGACCATGTCTGGGACGTTGGCATCATTTTGATTTACA
Found at i:28918535 original size:40 final size:39
Alignment explanation
Indices: 28918372--28918553 Score: 129
Period size: 40 Copynumber: 4.6 Consensus size: 39
28918362 AAATTGATTG
* *
28918372 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAAT--T
1 ATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATCGT
* * * * * *
28918411 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-T
* * * * *
28918451 ACATCCGGGCTAAGA-CCGAAGGCATTCGTGCGAGTCATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATC-GT
*
28918490 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
* * *
28918529 GATATCCGGGTTAAGTCCCGTAGGC
1 -ATATCCGGGCTAAGACCCGAAGGC
28918554 CTTGGTGCGG
Statistics
Matches: 111, Mismatches: 25, Indels: 13
0.74 0.17 0.09
Matches are distributed among these distances:
37 4 0.04
38 2 0.02
39 46 0.41
40 59 0.53
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (39 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
Found at i:28925876 original size:38 final size:39
Alignment explanation
Indices: 28925824--28925966 Score: 234
Period size: 39 Copynumber: 3.7 Consensus size: 39
28925814 GAATGTTCGA
28925824 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
* *
28925863 GTGATA-CCGGGCTAAGCCCGAAGGCAATTGTGCGAGTT
1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
*
28925901 ATGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
*
28925940 GTGATATCCGGGTTAAGTCCCGAAGGC
1 GTGATATCCGGGCTAAG-CCCGAAGGC
28925967 CTTTGTGCGG
Statistics
Matches: 95, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
38 35 0.37
39 51 0.54
40 9 0.09
ACGTcount: A:0.27, C:0.21, G:0.30, T:0.22
Consensus pattern (39 bp):
GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
Found at i:28925912 original size:77 final size:79
Alignment explanation
Indices: 28925825--28926006 Score: 269
Period size: 77 Copynumber: 2.3 Consensus size: 79
28925815 AATGTTCGAG
28925825 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTGTGATA-CCGGGCTAAG-CCCGAAGGC
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTGTGATATCCGGGCTAAGTCCCGAAGGC
28925888 AATTGTGCGAGTTA
66 AATTGTGCGAGTTA
*
28925902 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTGTGATATCCGGGTTAAGTCCCGAAGGC
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTGTGATATCCGGGCTAAGTCCCGAAGGC
** *
28925967 CTTTGTGCGGGTTA
66 AATTGTGCGAGTTA
** * *
28925981 CCATAACCGGGCTATGTCCCGAAGGC
1 TGATATCCGGGCTAAG-CCCGAAGGC
28926007 GTTTGAACGA
Statistics
Matches: 94, Mismatches: 8, Indels: 3
0.90 0.08 0.03
Matches are distributed among these distances:
77 44 0.47
78 9 0.10
79 32 0.34
80 9 0.10
ACGTcount: A:0.25, C:0.23, G:0.30, T:0.23
Consensus pattern (79 bp):
TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTGTGATATCCGGGCTAAGTCCCGAAGGC
AATTGTGCGAGTTA
Found at i:28932178 original size:38 final size:39
Alignment explanation
Indices: 28932126--28932268 Score: 234
Period size: 39 Copynumber: 3.7 Consensus size: 39
28932116 GAATGTTCGA
28932126 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
* *
28932165 GTGATA-CCGGGCTAAGCCCGAAGGCAATTGTGCGAGTT
1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
*
28932203 ATGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
*
28932242 GTGATATCCGGGTTAAGTCCCGAAGGC
1 GTGATATCCGGGCTAAG-CCCGAAGGC
28932269 CTTTGTGCGG
Statistics
Matches: 95, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
38 35 0.37
39 51 0.54
40 9 0.09
ACGTcount: A:0.27, C:0.21, G:0.30, T:0.22
Consensus pattern (39 bp):
GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
Found at i:28932214 original size:77 final size:79
Alignment explanation
Indices: 28932127--28932308 Score: 269
Period size: 77 Copynumber: 2.3 Consensus size: 79
28932117 AATGTTCGAG
28932127 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTGTGATA-CCGGGCTAAG-CCCGAAGGC
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTGTGATATCCGGGCTAAGTCCCGAAGGC
28932190 AATTGTGCGAGTTA
66 AATTGTGCGAGTTA
*
28932204 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTGTGATATCCGGGTTAAGTCCCGAAGGC
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTGTGATATCCGGGCTAAGTCCCGAAGGC
** *
28932269 CTTTGTGCGGGTTA
66 AATTGTGCGAGTTA
** * *
28932283 CCATAACCGGGCTATGTCCCGAAGGC
1 TGATATCCGGGCTAAG-CCCGAAGGC
28932309 GTTTGAACGA
Statistics
Matches: 94, Mismatches: 8, Indels: 3
0.90 0.08 0.03
Matches are distributed among these distances:
77 44 0.47
78 9 0.10
79 32 0.34
80 9 0.10
ACGTcount: A:0.25, C:0.23, G:0.30, T:0.23
Consensus pattern (79 bp):
TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTGTGATATCCGGGCTAAGTCCCGAAGGC
AATTGTGCGAGTTA
Found at i:28940184 original size:38 final size:39
Alignment explanation
Indices: 28940132--28940274 Score: 234
Period size: 39 Copynumber: 3.7 Consensus size: 39
28940122 GAATGTTCGA
28940132 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
* *
28940171 GTGATA-CCGGGCTAAGCCCGAAGGCAATTGTGCGAGTT
1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
*
28940209 ATGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
*
28940248 GTGATATCCGGGTTAAGTCCCGAAGGC
1 GTGATATCCGGGCTAAG-CCCGAAGGC
28940275 CTTTGTGCGG
Statistics
Matches: 95, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
38 35 0.37
39 51 0.54
40 9 0.09
ACGTcount: A:0.27, C:0.21, G:0.30, T:0.22
Consensus pattern (39 bp):
GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
Found at i:28940220 original size:77 final size:79
Alignment explanation
Indices: 28940133--28940314 Score: 269
Period size: 77 Copynumber: 2.3 Consensus size: 79
28940123 AATGTTCGAG
28940133 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTGTGATA-CCGGGCTAAG-CCCGAAGGC
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTGTGATATCCGGGCTAAGTCCCGAAGGC
28940196 AATTGTGCGAGTTA
66 AATTGTGCGAGTTA
*
28940210 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTGTGATATCCGGGTTAAGTCCCGAAGGC
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTGTGATATCCGGGCTAAGTCCCGAAGGC
** *
28940275 CTTTGTGCGGGTTA
66 AATTGTGCGAGTTA
** * *
28940289 CCATAACCGGGCTATGTCCCGAAGGC
1 TGATATCCGGGCTAAG-CCCGAAGGC
28940315 GTTTGAACGA
Statistics
Matches: 94, Mismatches: 8, Indels: 3
0.90 0.08 0.03
Matches are distributed among these distances:
77 44 0.47
78 9 0.10
79 32 0.34
80 9 0.10
ACGTcount: A:0.25, C:0.23, G:0.30, T:0.23
Consensus pattern (79 bp):
TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTGTGATATCCGGGCTAAGTCCCGAAGGC
AATTGTGCGAGTTA
Found at i:28948209 original size:38 final size:39
Alignment explanation
Indices: 28948157--28948299 Score: 234
Period size: 39 Copynumber: 3.7 Consensus size: 39
28948147 GAATGTTCGA
28948157 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
* *
28948196 GTGATA-CCGGGCTAAGCCCGAAGGCAATTGTGCGAGTT
1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
*
28948234 ATGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
*
28948273 GTGATATCCGGGTTAAGTCCCGAAGGC
1 GTGATATCCGGGCTAAG-CCCGAAGGC
28948300 CTTTGTGCGG
Statistics
Matches: 95, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
38 35 0.37
39 51 0.54
40 9 0.09
ACGTcount: A:0.27, C:0.21, G:0.30, T:0.22
Consensus pattern (39 bp):
GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
Found at i:28948245 original size:77 final size:79
Alignment explanation
Indices: 28948158--28948339 Score: 269
Period size: 77 Copynumber: 2.3 Consensus size: 79
28948148 AATGTTCGAG
28948158 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTGTGATA-CCGGGCTAAG-CCCGAAGGC
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTGTGATATCCGGGCTAAGTCCCGAAGGC
28948221 AATTGTGCGAGTTA
66 AATTGTGCGAGTTA
*
28948235 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTGTGATATCCGGGTTAAGTCCCGAAGGC
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTGTGATATCCGGGCTAAGTCCCGAAGGC
** *
28948300 CTTTGTGCGGGTTA
66 AATTGTGCGAGTTA
** * *
28948314 CCATAACCGGGCTATGTCCCGAAGGC
1 TGATATCCGGGCTAAG-CCCGAAGGC
28948340 GTTTGAACGA
Statistics
Matches: 94, Mismatches: 8, Indels: 3
0.90 0.08 0.03
Matches are distributed among these distances:
77 44 0.47
78 9 0.10
79 32 0.34
80 9 0.10
ACGTcount: A:0.25, C:0.23, G:0.30, T:0.23
Consensus pattern (79 bp):
TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTGTGATATCCGGGCTAAGTCCCGAAGGC
AATTGTGCGAGTTA
Found at i:28953519 original size:40 final size:40
Alignment explanation
Indices: 28953464--28953644 Score: 258
Period size: 40 Copynumber: 4.5 Consensus size: 40
28953454 ATAACCGCAA
* * * *
28953464 GCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTT
1 GCACAAATGCCTTCGGGTCTTAACCCGGATATAACAACTC
*
28953504 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAACAACTC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATATAACAACTC
*
28953544 GCACAAATGCCTTCGGGTCTTAACCCGAATATAACAACTC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATATAACAACTC
* *
28953584 CCACAAATGCCTTCGGGTCTTAACCCGGATATAATC-ACTA
1 GCACAAATGCCTTCGGGTCTTAACCCGGATATAA-CAACTC
*
28953624 GCATAAATGCCTTCGGG-CTTA
1 GCACAAATGCCTTCGGGTCTTA
28953645 GCCCAGGTAT
Statistics
Matches: 128, Mismatches: 12, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
39 4 0.03
40 123 0.96
41 1 0.01
ACGTcount: A:0.28, C:0.29, G:0.19, T:0.25
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAACCCGGATATAACAACTC
Found at i:28955488 original size:46 final size:48
Alignment explanation
Indices: 28955381--28955495 Score: 146
Period size: 46 Copynumber: 2.4 Consensus size: 48
28955371 CTGTCACACT
* * * *
28955381 ATGTCCCAGACAGGTCTTACACTAGCTTGTCCATCGTGAGGCTGATGC
1 ATGTCCCAGACATGTCTTACACTAGCTTCTCCATCGTAACGCTGATGC
*
28955429 ATGTCCCAGACATGTCTTACACTAG-TTCT-CGTC-TCAACGCTGATGC
1 ATGTCCCAGACATGTCTTACACTAGCTTCTCCATCGT-AACGCTGATGC
*
28955475 ATGTCCCAGACATGTTTTACA
1 ATGTCCCAGACATGTCTTACA
28955496 TTGGCTTAAA
Statistics
Matches: 60, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
45 1 0.02
46 32 0.53
47 3 0.05
48 24 0.40
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.30
Consensus pattern (48 bp):
ATGTCCCAGACATGTCTTACACTAGCTTCTCCATCGTAACGCTGATGC
Found at i:28959945 original size:12 final size:12
Alignment explanation
Indices: 28959925--28959955 Score: 53
Period size: 12 Copynumber: 2.5 Consensus size: 12
28959915 TAGTTTATTT
28959925 ATTTCTTGTTTTA
1 ATTT-TTGTTTTA
28959938 ATTTTTGTTTTA
1 ATTTTTGTTTTA
28959950 ATTTTT
1 ATTTTT
28959956 TTAAATGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 14 0.78
13 4 0.22
ACGTcount: A:0.16, C:0.03, G:0.06, T:0.74
Consensus pattern (12 bp):
ATTTTTGTTTTA
Found at i:28975213 original size:14 final size:13
Alignment explanation
Indices: 28975184--28975219 Score: 54
Period size: 14 Copynumber: 2.7 Consensus size: 13
28975174 CGGTGCGTGA
*
28975184 CTTTCTCTTTTTT
1 CTTTCTTTTTTTT
28975197 CTTTCTTTTTCTTT
1 CTTTCTTTTT-TTT
28975211 CTTTCTTTT
1 CTTTCTTTT
28975220 GCATGTCTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 9 0.43
14 12 0.57
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (13 bp):
CTTTCTTTTTTTT
Found at i:28975360 original size:2 final size:2
Alignment explanation
Indices: 28975341--28975386 Score: 60
Period size: 2 Copynumber: 23.5 Consensus size: 2
28975331 TAATATAACT
*
28975341 TA TA TA T- TA TC TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
28975381 TCA TA T
1 T-A TA T
28975387 CATTAATTGT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
1 2 0.05
2 35 0.90
3 2 0.05
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:28981134 original size:40 final size:40
Alignment explanation
Indices: 28981090--28981275 Score: 227
Period size: 40 Copynumber: 4.7 Consensus size: 40
28981080 GCTACTCGTT
* *
28981090 CAAATGCCTCCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
28981130 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
*
28981170 CAAATGCCTTC-GGATCTTAGTCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAACTCGCA
* * * * *
28981210 CGAATGCCTTC-GGATCTTAGTCCGGATATAGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
28981251 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
28981276 CATCATTCGA
Statistics
Matches: 131, Mismatches: 11, Indels: 8
0.87 0.07 0.05
Matches are distributed among these distances:
39 3 0.02
40 116 0.89
41 12 0.09
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:28981990 original size:2 final size:2
Alignment explanation
Indices: 28981983--28982014 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
28981973 ATGTGCAAAC
28981983 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28982015 GTGCAAGAGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28998823 original size:27 final size:28
Alignment explanation
Indices: 28998767--28998836 Score: 124
Period size: 27 Copynumber: 2.5 Consensus size: 28
28998757 AAACTTGTAC
28998767 AGCACTAAGTGTGCGAGTTTGATCATAT
1 AGCACTAAGTGTGCGAGTTTGATCATAT
*
28998795 AGCACTAAGTGTGCGAG-TTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATCATAT
28998822 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
28998837 GACTCACTAT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 24 0.59
28 17 0.41
ACGTcount: A:0.29, C:0.14, G:0.27, T:0.30
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTTTGATCATAT
Found at i:28998847 original size:27 final size:27
Alignment explanation
Indices: 28998767--28998848 Score: 78
Period size: 27 Copynumber: 3.0 Consensus size: 27
28998757 AAACTTGTAC
* *
28998767 AGCACTAAGTGTGCGAGTTTGA-TCATAT
1 AGCACTAAGTGTGCGAG-CTCACT-ATAT
* * *
28998795 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGCTCACTATAT
28998822 AGCACTAAGTGTGCG-GACTCACTATAT
1 AGCACTAAGTGTGCGAG-CTCACTATAT
28998849 GCTTTTGAAT
Statistics
Matches: 49, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
26 1 0.02
27 30 0.61
28 18 0.37
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGCTCACTATAT
Found at i:29012871 original size:21 final size:21
Alignment explanation
Indices: 29012836--29012876 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
29012826 TAAATGAAAA
* *
29012836 CTCATAAGGGTTGAAAGGAAG
1 CTCATAAGAGCTGAAAGGAAG
*
29012857 CTCATAAGAGCTGAACGGAA
1 CTCATAAGAGCTGAAAGGAA
29012877 ACCTAATAGG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.39, C:0.15, G:0.29, T:0.17
Consensus pattern (21 bp):
CTCATAAGAGCTGAAAGGAAG
Found at i:29014778 original size:6 final size:6
Alignment explanation
Indices: 29014762--29014803 Score: 66
Period size: 6 Copynumber: 6.8 Consensus size: 6
29014752 TGGTTTTCTC
*
29014762 AAAATG GAAATG AAAATG AAAATG AAAATG AAAATG AGAAAT
1 AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG A-AAAT
29014804 AATTCATTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
6 29 0.88
7 4 0.12
ACGTcount: A:0.64, C:0.00, G:0.19, T:0.17
Consensus pattern (6 bp):
AAAATG
Found at i:29015478 original size:13 final size:13
Alignment explanation
Indices: 29015460--29015484 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29015450 TATGGTCTAC
29015460 AATTTCATGAAAT
1 AATTTCATGAAAT
29015473 AATTTCATGAAA
1 AATTTCATGAAA
29015485 ATTTCGTTCG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.08, T:0.36
Consensus pattern (13 bp):
AATTTCATGAAAT
Found at i:29016648 original size:25 final size:25
Alignment explanation
Indices: 29016619--29016667 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
29016609 CTTTATTATT
*
29016619 ATCATTATGAAGAATTATGTGATTA
1 ATCATTATCAAGAATTATGTGATTA
* *
29016644 ATCATTATCATGAGTTATGTGATT
1 ATCATTATCAAGAATTATGTGATT
29016668 GGTCTTCTGG
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:0.06, G:0.16, T:0.43
Consensus pattern (25 bp):
ATCATTATCAAGAATTATGTGATTA
Found at i:29016794 original size:20 final size:20
Alignment explanation
Indices: 29016766--29016803 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
29016756 CTAGGAATTA
29016766 TGTGATCTGAGCTCATGAGT
1 TGTGATCTGAGCTCATGAGT
* *
29016786 TGTGGTCTGAGTTCATGA
1 TGTGATCTGAGCTCATGA
29016804 TATATGTGAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.18, C:0.13, G:0.32, T:0.37
Consensus pattern (20 bp):
TGTGATCTGAGCTCATGAGT
Found at i:29027108 original size:40 final size:39
Alignment explanation
Indices: 29026943--29027126 Score: 138
Period size: 40 Copynumber: 4.6 Consensus size: 39
29026933 AAATTGAATG
* * *
29026943 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAAT--T
1 ATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATCGT
* * * * * *
29026983 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-T
* * * * *
29027023 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATC-GT
*
29027063 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
* * *
29027102 GATATCCGGGTTAAGTCCCGTAGGC
1 -ATATCCGGGCTAAGACCCGAAGGC
29027127 CTTGGTGCGG
Statistics
Matches: 113, Mismatches: 26, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
37 4 0.04
38 2 0.02
39 3 0.03
40 104 0.92
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (39 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
Found at i:29027151 original size:80 final size:81
Alignment explanation
Indices: 29026983--29027171 Score: 186
Period size: 80 Copynumber: 2.4 Consensus size: 81
29026973 GCTGGAAATT
* * * *
29026983 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCTACATCCGGGCTAAGACCCGAAGGCA
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
*
29027048 TTCGTGCGAGTCATTC
66 TTCGTGCGAGTCATCC
* * * * * *
29027064 -TATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-TGATATCCGGGTTAAGTCCCGTAGGC
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCT-ACATCCGGGCTAAGACCCGAAGGC
* * * *
29027127 CTTGGTGCGGGTTA-CC
65 ATTCGTGCGAGTCATCC
* * *
29027143 ATAACCGGGCTATGTCCCGAAGGCGATTG
1 ATAACCGGGCTAAGACCCGAAGGCAATTG
29027172 ATCGAGTAGC
Statistics
Matches: 86, Mismatches: 20, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
79 2 0.02
80 84 0.98
ACGTcount: A:0.23, C:0.24, G:0.30, T:0.23
Consensus pattern (81 bp):
ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
TTCGTGCGAGTCATCC
Found at i:29029631 original size:30 final size:30
Alignment explanation
Indices: 29029595--29029660 Score: 123
Period size: 30 Copynumber: 2.2 Consensus size: 30
29029585 TGTAACATAA
29029595 CCGTGTGTCACACACAGCTGAGACACATGC
1 CCGTGTGTCACACACAGCTGAGACACATGC
*
29029625 CCGTGTGTCACACACGGCTGAGACACATGC
1 CCGTGTGTCACACACAGCTGAGACACATGC
29029655 CCGTGT
1 CCGTGT
29029661 CTCTGCCCGT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.23, C:0.33, G:0.26, T:0.18
Consensus pattern (30 bp):
CCGTGTGTCACACACAGCTGAGACACATGC
Found at i:29030608 original size:23 final size:23
Alignment explanation
Indices: 29030582--29030635 Score: 83
Period size: 22 Copynumber: 2.4 Consensus size: 23
29030572 AAGCTTAAAT
29030582 GAGCTGAAACAATAAGCTCTATC
1 GAGCTGAAACAATAAGCTCTATC
* *
29030605 GAGCTG-AACAGTAAGCTCTATT
1 GAGCTGAAACAATAAGCTCTATC
29030627 GAGCTGAAA
1 GAGCTGAAA
29030636 TGGTAAGCTC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 20 0.71
23 8 0.29
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.22
Consensus pattern (23 bp):
GAGCTGAAACAATAAGCTCTATC
Found at i:29044865 original size:13 final size:13
Alignment explanation
Indices: 29044847--29044871 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29044837 CCCGGCAGGC
29044847 ACACGCCCGTGTG
1 ACACGCCCGTGTG
29044860 ACACGCCCGTGT
1 ACACGCCCGTGT
29044872 ACGATTATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.40, G:0.28, T:0.16
Consensus pattern (13 bp):
ACACGCCCGTGTG
Found at i:29048496 original size:55 final size:53
Alignment explanation
Indices: 29048365--29048560 Score: 207
Period size: 55 Copynumber: 3.6 Consensus size: 53
29048355 CTTACCATTT
*
29048365 CCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAACTCACCAATG
1 CCATGTCTTGACATGGTCTTACATGGGATCCTTGCCTTATGAACTCACCAATG
* * * *
29048418 CCATGCCTTGGCATGGTCTTACATGGGA-CCTTTGCCTTATAGTAACTTATCAATG
1 CCATGTCTTGACATGGTCTTACATGGGATCC-TTGCCTTAT-G-AACTCACCAATG
*** *
29048473 CCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTA-GAAACCTTACCAACTG
1 CCATGTCTTGACATGGTCTTACATGGGATCCTTGCCTTATG-AA-CTCACCAA-TG
* * * *
29048528 CGATGCCTTGGCATGGTCTTACATGGTATCCTT
1 CCATGTCTTGACATGGTCTTACATGGGATCCTT
29048561 AAACCCTAAT
Statistics
Matches: 120, Mismatches: 17, Indels: 10
0.82 0.12 0.07
Matches are distributed among these distances:
52 2 0.02
53 37 0.31
54 8 0.07
55 71 0.59
56 2 0.02
ACGTcount: A:0.21, C:0.26, G:0.18, T:0.35
Consensus pattern (53 bp):
CCATGTCTTGACATGGTCTTACATGGGATCCTTGCCTTATGAACTCACCAATG
Found at i:29054705 original size:134 final size:134
Alignment explanation
Indices: 29054465--29054726 Score: 497
Period size: 134 Copynumber: 2.0 Consensus size: 134
29054455 AAAATCGTCA
*
29054465 GGAGTCGTCACACTATCAAAACATAAGTATGGCATGTATAGCTAGAGTCTTACTCATACTAAATA
1 GGAGTCGTCACACTATCAAAACATAAGTATGGCATGTATAGCTAGACTCTTACTCATACTAAATA
*
29054530 TTCTGAGAACTGACTAAACCTTTGCTCTGATACCAATAAATGTAACGCCCCAAACTCGAGACCAT
66 TTCTGAGAACTGACTAAACCTTTACTCTGATACCAATAAATGTAACGCCCCAAACTCGAGACCAT
29054595 CGCC
131 CGCC
29054599 GGAGTCGTCACACTATCAAAACATAAGTATGGCATGTATAGCTAGACTCTTACTCATACTAAATA
1 GGAGTCGTCACACTATCAAAACATAAGTATGGCATGTATAGCTAGACTCTTACTCATACTAAATA
*
29054664 TTTTGAGAACTGACTAAACCTTTACTCTGATACCAATAAATGTAACGCCCCAAACTCGAGACC
66 TTCTGAGAACTGACTAAACCTTTACTCTGATACCAATAAATGTAACGCCCCAAACTCGAGACC
29054727 GTCACCAGAG
Statistics
Matches: 125, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
134 125 1.00
ACGTcount: A:0.35, C:0.24, G:0.15, T:0.26
Consensus pattern (134 bp):
GGAGTCGTCACACTATCAAAACATAAGTATGGCATGTATAGCTAGACTCTTACTCATACTAAATA
TTCTGAGAACTGACTAAACCTTTACTCTGATACCAATAAATGTAACGCCCCAAACTCGAGACCAT
CGCC
Found at i:29055784 original size:16 final size:16
Alignment explanation
Indices: 29055765--29055795 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
29055755 CTTCTTAACT
29055765 TACTCACTTACTTAAA
1 TACTCACTTACTTAAA
*
29055781 TACTTACTTACTTAA
1 TACTCACTTACTTAA
29055796 TCAAATTTAT
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:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (16 bp):
TACTCACTTACTTAAA
Found at i:29055801 original size:20 final size:20
Alignment explanation
Indices: 29055762--29055801 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
29055752 AAACTTCTTA
* *
29055762 ACTTACTCACTTACTTAAAT
1 ACTTACTCACTTAATCAAAT
*
29055782 ACTTACTTACTTAATCAAAT
1 ACTTACTCACTTAATCAAAT
29055802 TTATTAATAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.40
Consensus pattern (20 bp):
ACTTACTCACTTAATCAAAT
Found at i:29056116 original size:53 final size:54
Alignment explanation
Indices: 29055987--29056241 Score: 265
Period size: 55 Copynumber: 4.8 Consensus size: 54
29055977 ATGCGGGTAC
* * * * *
29055987 CTTACCATTGCCATGACATGTCATGGTCTTACGTGGTATCC-T---TT-TGAAA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAAA
* *
29056036 CTTACCATTGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATG-AA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAAA
* * * *
29056089 CTCACCAATGCCATGCCTTGGCATGGTCTTACATGGGA-CCTTTGCCTTATAGTAA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCC-TTGCCTTAT-GAAA
* * * *
29056144 CTTATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTA-GAAA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAAA
* *
29056197 CCTTACCAATTGCCATGCCTTGGCATGCTCTTACATGGTATCCTT
1 -CTTACCAA-TGCCATGCCTTGACATGGTCTTACATGGTATCCTT
29056242 AAACCTTAAT
Statistics
Matches: 172, Mismatches: 23, Indels: 16
0.82 0.11 0.08
Matches are distributed among these distances:
49 37 0.22
50 1 0.01
52 2 0.01
53 49 0.28
54 10 0.06
55 71 0.41
56 2 0.01
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.36
Consensus pattern (54 bp):
CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAAA
Found at i:29056178 original size:108 final size:110
Alignment explanation
Indices: 29056034--29056234 Score: 318
Period size: 108 Copynumber: 1.8 Consensus size: 110
29056024 ATCCTTTTGA
* *
29056034 AACTTACCATTGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATG-AA-CTCACCAA
1 AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTA-GAAACCTCACCAA
*
29056097 -TGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATAGT
65 TTGCCATGCCTTGGCATGCTCTTACATGGGACCTTTGCCTTATAGT
* * *
29056142 AACTTATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTAGAAACCTTACCAAT
1 AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTAGAAACCTCACCAAT
29056207 TGCCATGCCTTGGCATGCTCTTACATGG
66 TGCCATGCCTTGGCATGCTCTTACATGG
29056235 TATCCTTAAA
Statistics
Matches: 84, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
107 1 0.01
108 49 0.58
109 7 0.08
110 27 0.32
ACGTcount: A:0.22, C:0.26, G:0.17, T:0.34
Consensus pattern (110 bp):
AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTAGAAACCTCACCAAT
TGCCATGCCTTGGCATGCTCTTACATGGGACCTTTGCCTTATAGT
Found at i:29061464 original size:22 final size:22
Alignment explanation
Indices: 29061439--29061508 Score: 58
Period size: 22 Copynumber: 3.1 Consensus size: 22
29061429 TAAGCTCCTC
29061439 CTAAGCTGATGAATAGTAAGCT
1 CTAAGCTGATGAATAGTAAGCT
29061461 CTAATAAGCTGA--AATAGTAAGCT
1 C---TAAGCTGATGAATAGTAAGCT
*
29061484 CT-ATC-GAGCTGAATAGTAAGCT
1 CTAAGCTGA--TGAATAGTAAGCT
29061506 CTA
1 CTA
29061509 TTGAGTTGAA
Statistics
Matches: 39, Mismatches: 1, Indels: 15
0.71 0.02 0.27
Matches are distributed among these distances:
18 2 0.05
19 2 0.05
20 1 0.03
22 14 0.36
23 12 0.31
25 8 0.21
ACGTcount: A:0.37, C:0.16, G:0.20, T:0.27
Consensus pattern (22 bp):
CTAAGCTGATGAATAGTAAGCT
Found at i:29061480 original size:23 final size:23
Alignment explanation
Indices: 29061440--29061552 Score: 95
Period size: 23 Copynumber: 4.8 Consensus size: 23
29061430 AAGCTCCTCC
29061440 TAAGCTGATGAATAGTAAGCTCTAA
1 TAAGCTGA--AATAGTAAGCTCTAA
29061465 TAAGCTGAAATAGTAAGCTCT-A
1 TAAGCTGAAATAGTAAGCTCTAA
* *
29061487 TCGAGCTG-AATAGTAAGCTCTAT
1 T-AAGCTGAAATAGTAAGCTCTAA
* * ** * *
29061510 TGAGTTGAAACGGTAAGCTCCAG
1 TAAGCTGAAATAGTAAGCTCTAA
*
29061533 TAAGCTGAAAATGGTAAGCT
1 TAAGCTG-AAATAGTAAGCT
29061553 ATTACGAGTT
Statistics
Matches: 74, Mismatches: 10, Indels: 9
0.80 0.11 0.10
Matches are distributed among these distances:
22 20 0.27
23 35 0.47
24 11 0.15
25 8 0.11
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.27
Consensus pattern (23 bp):
TAAGCTGAAATAGTAAGCTCTAA
Found at i:29061509 original size:22 final size:21
Alignment explanation
Indices: 29061448--29061518 Score: 88
Period size: 22 Copynumber: 3.2 Consensus size: 21
29061438 CCTAAGCTGA
*
29061448 TGAATAGTAAGCTCTAATAAGC
1 TGAATAGTAAGCTCT-ATGAGC
29061470 TGAAATAGTAAGCTCTATCGAGC
1 TG-AATAGTAAGCTCTAT-GAGC
*
29061493 TGAATAGTAAGCTCTATTGAGT
1 TGAATAGTAAGCTCTA-TGAGC
29061515 TGAA
1 TGAA
29061519 ACGGTAAGCT
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
22 25 0.57
23 19 0.43
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.30
Consensus pattern (21 bp):
TGAATAGTAAGCTCTATGAGC
Found at i:29061539 original size:45 final size:45
Alignment explanation
Indices: 29061448--29061541 Score: 109
Period size: 45 Copynumber: 2.1 Consensus size: 45
29061438 CCTAAGCTGA
* * *
29061448 TGAATAGTAAGCTCTAATAAGCTGAAATAGTAAGCTCTATCGAGC
1 TGAATAGTAAGCTCTAATAAGCTGAAACAGTAAGCTCCATCAAGC
* * * *
29061493 TGAATAGTAAGCTCTATTGAGTTGAAACGGTAAGCTCCAGT-AAGC
1 TGAATAGTAAGCTCTAATAAGCTGAAACAGTAAGCTCCA-TCAAGC
29061538 TGAA
1 TGAA
29061542 AATGGTAAGC
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
45 40 0.98
46 1 0.02
ACGTcount: A:0.36, C:0.15, G:0.22, T:0.27
Consensus pattern (45 bp):
TGAATAGTAAGCTCTAATAAGCTGAAACAGTAAGCTCCATCAAGC
Found at i:29068652 original size:40 final size:40
Alignment explanation
Indices: 29068607--29068773 Score: 185
Period size: 40 Copynumber: 4.2 Consensus size: 40
29068597 CGGAATATAA
29068607 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * * *
29068647 CCGGATAGAATAACTCGCACGAATGCCTTCGGGCCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
* * *
29068687 CCGGATATAACCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
29068727 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
29068766 CCGGATAT
1 CCGGATAT
29068774 CATTCAATTT
Statistics
Matches: 107, Mismatches: 19, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
39 14 0.13
40 93 0.87
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:29068757 original size:80 final size:79
Alignment explanation
Indices: 29068607--29068773 Score: 205
Period size: 80 Copynumber: 2.1 Consensus size: 79
29068597 CGGAATATAA
* *
29068607 CCGGATATAATCACGTGCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATAACTCGCACGAATG
1 CCGGATATAACCACGTGCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATG
29068672 CCTTCGGGCCTTAGC
66 CCTTCGGG-CTTAGC
* * ** *
29068687 CCGGATATAACCAC-TAGCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAA
1 CCGGATATAACCACGT-GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTC-GCACGAA
*
29068749 TTGTCTTCGGGCTTAGC
64 -TGCCTTCGGGCTTAGC
29068766 CCGGATAT
1 CCGGATAT
29068774 CATTCAATTT
Statistics
Matches: 76, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
79 18 0.24
80 58 0.76
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (79 bp):
CCGGATATAACCACGTGCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATG
CCTTCGGGCTTAGC
Found at i:29069622 original size:17 final size:19
Alignment explanation
Indices: 29069599--29069644 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
29069589 AAGAAGCATG
29069599 AATCATGCTCAAGAATG-C
1 AATCATGCTCAAGAATGAC
*
29069617 -ATCATGGC-CAAGTATGAC
1 AATCAT-GCTCAAGAATGAC
29069635 AATCATGCTC
1 AATCATGCTC
29069645 CTTTTCAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
17 12 0.52
18 5 0.22
19 6 0.26
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (19 bp):
AATCATGCTCAAGAATGAC
Found at i:29076657 original size:40 final size:40
Alignment explanation
Indices: 29076612--29076778 Score: 185
Period size: 40 Copynumber: 4.2 Consensus size: 40
29076602 CGGAATATAA
29076612 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * * *
29076652 CCGGATAGAATAACTCGCACGAATGCCTTCGGGCCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
* * *
29076692 CCGGATATAACCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
29076732 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
29076771 CCGGATAT
1 CCGGATAT
29076779 CATTCAATTT
Statistics
Matches: 107, Mismatches: 19, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
39 14 0.13
40 93 0.87
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:29076762 original size:80 final size:79
Alignment explanation
Indices: 29076612--29076778 Score: 205
Period size: 80 Copynumber: 2.1 Consensus size: 79
29076602 CGGAATATAA
* *
29076612 CCGGATATAATCACGTGCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATAACTCGCACGAATG
1 CCGGATATAACCACGTGCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATG
29076677 CCTTCGGGCCTTAGC
66 CCTTCGGG-CTTAGC
* * ** *
29076692 CCGGATATAACCAC-TAGCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAA
1 CCGGATATAACCACGT-GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTC-GCACGAA
*
29076754 TTGTCTTCGGGCTTAGC
64 -TGCCTTCGGGCTTAGC
29076771 CCGGATAT
1 CCGGATAT
29076779 CATTCAATTT
Statistics
Matches: 76, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
79 18 0.24
80 58 0.76
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (79 bp):
CCGGATATAACCACGTGCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATG
CCTTCGGGCTTAGC
Found at i:29077626 original size:17 final size:19
Alignment explanation
Indices: 29077603--29077648 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
29077593 AAGAAGCATG
29077603 AATCATGCTCAAGAATG-C
1 AATCATGCTCAAGAATGAC
*
29077621 -ATCATGGC-CAAGTATGAC
1 AATCAT-GCTCAAGAATGAC
29077639 AATCATGCTC
1 AATCATGCTC
29077649 CTTTTCAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
17 12 0.52
18 5 0.22
19 6 0.26
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (19 bp):
AATCATGCTCAAGAATGAC
Found at i:29079835 original size:71 final size:70
Alignment explanation
Indices: 29079679--29079831 Score: 178
Period size: 71 Copynumber: 2.3 Consensus size: 70
29079669 GCTCTCTTGT
* *
29079679 ACACATGCGACCTAGCTAC----AT-TTTCACGTAGCTCTCTTGTCTACATGGTGTCCTTCACTT
1 ACACATGCGACCTAGCTACATTTATCTTTCACGTAGCTCTCTTGTCTACATGGTGTACAT-ACTT
*
29079739 GGAATC
65 CGAATC
*
29079745 ACGCATGCGACCTAGCTACATTTATCTTTCACGTAGCTCTCTTGTCTACATGG-GATACAT-C-T
1 ACACATGCGACCTAGCTACATTTATCTTTCACGTAGCTCTCTTGTCTACATGGTG-TACATACTT
*
29079807 CGTATC
65 CGAATC
*
29079813 ACACATGTGACCTAGCTAC
1 ACACATGCGACCTAGCTAC
29079832 TACAGGGTGT
Statistics
Matches: 74, Mismatches: 7, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
66 18 0.24
68 22 0.30
69 1 0.01
70 3 0.04
71 30 0.41
ACGTcount: A:0.23, C:0.29, G:0.16, T:0.32
Consensus pattern (70 bp):
ACACATGCGACCTAGCTACATTTATCTTTCACGTAGCTCTCTTGTCTACATGGTGTACATACTTC
GAATC
Found at i:29087317 original size:71 final size:71
Alignment explanation
Indices: 29087201--29087400 Score: 391
Period size: 71 Copynumber: 2.8 Consensus size: 71
29087191 CATGGTGCAC
29087201 GAATCACGCATGCGACCTAGCTACATTTATCTTTCACGTAGCTCTCTTGTCTACATGGTGTCCTT
1 GAATCACGCATGCGACCTAGCTACATTTATCTTTCACGTAGCTCTCTTGTCTACATGGTGTCCTT
29087266 CACTTG
66 CACTTG
*
29087272 GAATCACGCATGCGACCTAGCTATATTTATCTTTCACGTAGCTCTCTTGTCTACATGGTGTCCTT
1 GAATCACGCATGCGACCTAGCTACATTTATCTTTCACGTAGCTCTCTTGTCTACATGGTGTCCTT
29087337 CACTTG
66 CACTTG
29087343 GAATCACGCATGCGACCTAGCTACATTTATCTTTCACGTAGCTCTCTTGTCTACATGG
1 GAATCACGCATGCGACCTAGCTACATTTATCTTTCACGTAGCTCTCTTGTCTACATGG
29087401 GATACATCTC
Statistics
Matches: 127, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
71 127 1.00
ACGTcount: A:0.20, C:0.28, G:0.17, T:0.35
Consensus pattern (71 bp):
GAATCACGCATGCGACCTAGCTACATTTATCTTTCACGTAGCTCTCTTGTCTACATGGTGTCCTT
CACTTG
Found at i:29087438 original size:71 final size:70
Alignment explanation
Indices: 29087200--29087434 Score: 350
Period size: 71 Copynumber: 3.4 Consensus size: 70
29087190 ACATGGTGCA
*
29087200 CGAATCACGCATGCGACCTAGCTACATTTATCTTTCACGTAGCTCTCTTGTCTACATGGTGTCCT
1 CGAATCACGCATGCGACCTAGCTACATTTATCTTTCACGTAGCTCTCTTGTCTACATGGTGTCCA
29087265 TCACTT
66 T-ACTT
* * *
29087271 GGAATCACGCATGCGACCTAGCTATATTTATCTTTCACGTAGCTCTCTTGTCTACATGGTGTCCT
1 CGAATCACGCATGCGACCTAGCTACATTTATCTTTCACGTAGCTCTCTTGTCTACATGGTGTCCA
29087336 TCACTT
66 T-ACTT
* *
29087342 GGAATCACGCATGCGACCTAGCTACATTTATCTTTCACGTAGCTCTCTTGTCTACATGG-GATAC
1 CGAATCACGCATGCGACCTAGCTACATTTATCTTTCACGTAGCTCTCTTGTCTACATGGTG-TCC
29087406 AT-C-T
65 ATACTT
* *
29087410 CGTATCACGCATGTGACCTAGCTAC
1 CGAATCACGCATGCGACCTAGCTAC
29087435 TACAGGGTGT
Statistics
Matches: 155, Mismatches: 8, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
68 23 0.15
69 1 0.01
70 1 0.01
71 130 0.84
ACGTcount: A:0.21, C:0.28, G:0.17, T:0.34
Consensus pattern (70 bp):
CGAATCACGCATGCGACCTAGCTACATTTATCTTTCACGTAGCTCTCTTGTCTACATGGTGTCCA
TACTT
Found at i:29089023 original size:33 final size:34
Alignment explanation
Indices: 29088980--29089066 Score: 83
Period size: 33 Copynumber: 2.6 Consensus size: 34
29088970 ACTGTACTAA
*
29088980 TACTGTAATGGGCTTAGGCCC-CACTGA-TACTGC
1 TACTGAAATGGGCTTAGGCCCACACT-ATTACTGC
* *
29089013 TACTGAAAT-GGCTCT-GGCCCAGACTATTACTGT
1 TACTGAAATGGGCT-TAGGCCCACACTATTACTGC
* *
29089046 TACTAAAATGGGCTAAGGCCC
1 TACTGAAATGGGCTTAGGCCC
29089067 TAACTGAGAC
Statistics
Matches: 44, Mismatches: 5, Indels: 9
0.76 0.09 0.16
Matches are distributed among these distances:
32 10 0.23
33 25 0.57
34 9 0.20
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.26
Consensus pattern (34 bp):
TACTGAAATGGGCTTAGGCCCACACTATTACTGC
Found at i:29090493 original size:37 final size:37
Alignment explanation
Indices: 29090443--29090520 Score: 156
Period size: 37 Copynumber: 2.1 Consensus size: 37
29090433 TATAAAAGAA
29090443 GTCTTACCCGGTCATAATCTCCACACGTAGTCATCGG
1 GTCTTACCCGGTCATAATCTCCACACGTAGTCATCGG
29090480 GTCTTACCCGGTCATAATCTCCACACGTAGTCATCGG
1 GTCTTACCCGGTCATAATCTCCACACGTAGTCATCGG
29090517 GTCT
1 GTCT
29090521 CGCCCGGAAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.21, C:0.32, G:0.19, T:0.28
Consensus pattern (37 bp):
GTCTTACCCGGTCATAATCTCCACACGTAGTCATCGG
Found at i:29090683 original size:49 final size:49
Alignment explanation
Indices: 29090623--29090745 Score: 219
Period size: 49 Copynumber: 2.5 Consensus size: 49
29090613 CATATATTTT
*
29090623 ACATTGGCCATTAGGCCTCATCACATATACATACACTTTCACATTCACC
1 ACATCGGCCATTAGGCCTCATCACATATACATACACTTTCACATTCACC
*
29090672 ACATCGGCCATTAGGCCTCATCACATATACGTACACTTTCACATTCACC
1 ACATCGGCCATTAGGCCTCATCACATATACATACACTTTCACATTCACC
*
29090721 ACATCGGCCATTAGGCCTTATCACA
1 ACATCGGCCATTAGGCCTCATCACA
29090746 CATATATGTA
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 71 1.00
ACGTcount: A:0.29, C:0.33, G:0.11, T:0.27
Consensus pattern (49 bp):
ACATCGGCCATTAGGCCTCATCACATATACATACACTTTCACATTCACC
Found at i:29102221 original size:24 final size:24
Alignment explanation
Indices: 29102181--29102242 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 24
29102171 GATTATGTAG
29102181 AAAGAATAAAGAAATGAA-AAAAAA
1 AAAGAA-AAAGAAATGAAGAAAAAA
* *
29102205 AAAGAAAGAGAATATGAAGAAAAAC
1 AAAGAAAAAGAA-ATGAAGAAAAAA
*
29102230 AAAGAAAAGGAAA
1 AAAGAAAAAGAAA
29102243 AAAAAAGTGT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
23 5 0.16
24 12 0.38
25 15 0.47
ACGTcount: A:0.74, C:0.02, G:0.18, T:0.06
Consensus pattern (24 bp):
AAAGAAAAAGAAATGAAGAAAAAA
Done.