Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007999.1 Hibiscus syriacus cultivar Beakdansim tig00110450_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 11700749
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 19 of 50
Found at i:5012439 original size:10 final size:10
Alignment explanation
Indices: 5012391--5012441 Score: 56
Period size: 10 Copynumber: 5.3 Consensus size: 10
5012381 TTGAAAATGT
5012391 ATAATAAAATA
1 ATAAT-AAATA
5012402 A-AATAAATA
1 ATAATAAATA
5012411 ATAAT--ATA
1 ATAATAAATA
5012419 AT-ATAATATA
1 ATAATAA-ATA
5012429 ATAATAAATA
1 ATAATAAATA
5012439 ATA
1 ATA
5012442 GTAGTAAAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
7 2 0.06
8 5 0.14
9 6 0.17
10 17 0.49
11 5 0.14
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (10 bp):
ATAATAAATA
Found at i:5012503 original size:18 final size:18
Alignment explanation
Indices: 5012482--5012524 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
5012472 GTTGTTTTTA
* *
5012482 AAATAAAATATAAGAATT
1 AAATAAAAGAAAAGAATT
*
5012500 AAATAAAAGAAAATAATT
1 AAATAAAAGAAAAGAATT
5012518 AAATAAA
1 AAATAAA
5012525 CAAATTAAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (18 bp):
AAATAAAAGAAAAGAATT
Found at i:5013196 original size:71 final size:75
Alignment explanation
Indices: 5013117--5013305 Score: 246
Period size: 76 Copynumber: 2.6 Consensus size: 75
5013107 AAAACATCTC
* * * *
5013117 AAATCCTAATTAAAACACTTACAA-CTATTTAAACTGAAATACCT-AA-AAA-ATAATAT-TTAA
1 AAATCCTAATTAAAATAC-TAAAACCTATTTAAACTAAAATACCTAAACAAAGATAAAATATTAA
5013177 AATAATA-CTCT
65 AATAATATC-CT
*
5013188 AAATCCTAATTAAAATAATAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATTAA
1 AAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCT-AAACAAAGATAAAATATTAA
5013253 AATAATATCCT
65 AATAATATCCT
* *
5013264 AAAACTTAATTAAAATACTAAAACCTATTTAAACTAAAATAC
1 AAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATAC
5013306 AAAGATAAAA
Statistics
Matches: 103, Mismatches: 8, Indels: 9
0.86 0.07 0.08
Matches are distributed among these distances:
70 4 0.04
71 35 0.34
73 2 0.02
74 3 0.03
75 6 0.06
76 52 0.50
77 1 0.01
ACGTcount: A:0.56, C:0.14, G:0.01, T:0.29
Consensus pattern (75 bp):
AAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAACAAAGATAAAATATTAAA
ATAATATCCT
Found at i:5013214 original size:19 final size:19
Alignment explanation
Indices: 5013187--5013233 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
5013177 AATAATACTC
*
5013187 TAAATCCTAATTAAAATAA
1 TAAAACCTAATTAAAATAA
* *
5013206 TAAAACCTATTTAAACTAA
1 TAAAACCTAATTAAAATAA
*
5013225 -AATACCTAA
1 TAAAACCTAA
5013234 AACAAAGATA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
18 7 0.30
19 16 0.70
ACGTcount: A:0.55, C:0.15, G:0.00, T:0.30
Consensus pattern (19 bp):
TAAAACCTAATTAAAATAA
Found at i:5017156 original size:42 final size:42
Alignment explanation
Indices: 5017097--5017194 Score: 178
Period size: 42 Copynumber: 2.3 Consensus size: 42
5017087 ATGTGTTTGC
*
5017097 AGAGCAAAGCTCAATTAACCAACTTTTCCTCGTAATCTTCTT
1 AGAGCAAAGCTCAATTAACAAACTTTTCCTCGTAATCTTCTT
5017139 AGAGCAAAGCTCAATTAACAAACTTTTCCTCGTAATCTTCTT
1 AGAGCAAAGCTCAATTAACAAACTTTTCCTCGTAATCTTCTT
*
5017181 AGACCAAAGCTCAA
1 AGAGCAAAGCTCAA
5017195 CACACCAACC
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 54 1.00
ACGTcount: A:0.35, C:0.26, G:0.10, T:0.30
Consensus pattern (42 bp):
AGAGCAAAGCTCAATTAACAAACTTTTCCTCGTAATCTTCTT
Found at i:5020254 original size:15 final size:15
Alignment explanation
Indices: 5020234--5020264 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
5020224 AATTACCAAT
*
5020234 TTCCATTGAAATATC
1 TTCCATTAAAATATC
5020249 TTCCATTAAAATATC
1 TTCCATTAAAATATC
5020264 T
1 T
5020265 CATAGTGAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.19, G:0.03, T:0.42
Consensus pattern (15 bp):
TTCCATTAAAATATC
Found at i:5021438 original size:19 final size:21
Alignment explanation
Indices: 5021396--5021455 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
5021386 GATAGCCAAT
**
5021396 AACACTCAAAATCAACACCTA
1 AACACTCAAAATCAACACAAA
5021417 AACACTC-AAAT-AACACAAA
1 AACACTCAAAATCAACACAAA
*
5021436 AACA-ACAATAATCAACACAA
1 AACACTCAA-AATCAACACAA
5021456 TTTCTTGGAT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
18 1 0.03
19 11 0.33
20 7 0.21
21 14 0.42
ACGTcount: A:0.60, C:0.28, G:0.00, T:0.12
Consensus pattern (21 bp):
AACACTCAAAATCAACACAAA
Found at i:5021864 original size:10 final size:11
Alignment explanation
Indices: 5021833--5021866 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
5021823 TAAGGAATGG
*
5021833 ATGGCAATTGG
1 ATGGCAATTGA
5021844 ATGGCAATTGA
1 ATGGCAATTGA
5021855 ATGG-AATTGA
1 ATGGCAATTGA
5021865 AT
1 AT
5021867 CAAGGATGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 8 0.36
11 14 0.64
ACGTcount: A:0.35, C:0.06, G:0.29, T:0.29
Consensus pattern (11 bp):
ATGGCAATTGA
Found at i:5027121 original size:21 final size:22
Alignment explanation
Indices: 5027084--5027124 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
5027074 TTTATTGATA
*
5027084 GTGTCCAACCCTGAAATTTTTC
1 GTGTCCAACCCTAAAATTTTTC
5027106 GTGTCC-ACCCTAAAATTTT
1 GTGTCCAACCCTAAAATTTT
5027125 ATTTTTATCC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.24, C:0.27, G:0.12, T:0.37
Consensus pattern (22 bp):
GTGTCCAACCCTAAAATTTTTC
Found at i:5028187 original size:33 final size:34
Alignment explanation
Indices: 5028124--5028189 Score: 82
Period size: 33 Copynumber: 2.0 Consensus size: 34
5028114 ATTTGAAAAC
* *
5028124 AAAACTTTAAAATAAAATAAATAAATAAATTTTG
1 AAAACTTTAAAAGAAAATAAAGAAATAAATTTTG
*
5028158 AAAACTTT-AAAGAAAATAGAAGAGA-AAATTTT
1 AAAACTTTAAAAGAAAATA-AAGAAATAAATTTT
5028190 ATAAAGCTAG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
33 16 0.57
34 12 0.43
ACGTcount: A:0.61, C:0.03, G:0.08, T:0.29
Consensus pattern (34 bp):
AAAACTTTAAAAGAAAATAAAGAAATAAATTTTG
Found at i:5028402 original size:73 final size:73
Alignment explanation
Indices: 5028322--5028461 Score: 253
Period size: 73 Copynumber: 1.9 Consensus size: 73
5028312 ATAAAGAAAA
*
5028322 TAAATCCTAATTAAAATACTTAAAACTATTTAAACTAAAATACCTAAAACAAAGATAAGATAAAA
1 TAAATCCTAATTAAAATACTTAAAACTATTTAAAATAAAATACCTAAAACAAAGATAAGATAAAA
5028387 TAATATCC
66 TAATATCC
**
5028395 TAAATCCTAATTAAAATACTTAAAACTATTTAAAATAAAATGTCTAAAACAAAGATAAGATAAAA
1 TAAATCCTAATTAAAATACTTAAAACTATTTAAAATAAAATACCTAAAACAAAGATAAGATAAAA
5028460 TA
66 TA
5028462 TAATATTTAA
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
73 64 1.00
ACGTcount: A:0.57, C:0.11, G:0.04, T:0.28
Consensus pattern (73 bp):
TAAATCCTAATTAAAATACTTAAAACTATTTAAAATAAAATACCTAAAACAAAGATAAGATAAAA
TAATATCC
Found at i:5030464 original size:52 final size:51
Alignment explanation
Indices: 5030397--5030513 Score: 198
Period size: 52 Copynumber: 2.3 Consensus size: 51
5030387 TACATTCCAT
*
5030397 TGTTCTGTTCGAATATTTCTGCAATGTTCTAACCAAATCAGTTTTTTTGCAC
1 TGTTCTGTTCGAATATTTCTGCAAAGTTCTAACCAAATCA-TTTTTTTGCAC
* *
5030449 TGTTCAGTTCGAATATTTCTGCAAAGTTCTAACCAAATCATTTTTTTTCAC
1 TGTTCTGTTCGAATATTTCTGCAAAGTTCTAACCAAATCATTTTTTTGCAC
5030500 TGTTCTGTTCGAAT
1 TGTTCTGTTCGAAT
5030514 CTGCTGTGTA
Statistics
Matches: 61, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
51 23 0.38
52 38 0.62
ACGTcount: A:0.24, C:0.19, G:0.13, T:0.44
Consensus pattern (51 bp):
TGTTCTGTTCGAATATTTCTGCAAAGTTCTAACCAAATCATTTTTTTGCAC
Found at i:5035692 original size:27 final size:27
Alignment explanation
Indices: 5035662--5035714 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
5035652 GACTAAGTCT
5035662 GATCGGGTCAGGTCAGCGGGTTGGTCG
1 GATCGGGTCAGGTCAGCGGGTTGGTCG
*
5035689 GATCGGGTTAGGTCAGCGGGTTGGTC
1 GATCGGGTCAGGTCAGCGGGTTGGTC
5035715 AGAAACGGGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.11, C:0.17, G:0.47, T:0.25
Consensus pattern (27 bp):
GATCGGGTCAGGTCAGCGGGTTGGTCG
Found at i:5035716 original size:12 final size:12
Alignment explanation
Indices: 5035672--5035716 Score: 54
Period size: 12 Copynumber: 3.5 Consensus size: 12
5035662 GATCGGGTCA
5035672 GGTCAGCGGGTT
1 GGTCAGCGGGTT
*
5035684 GGTCGGATCGGGTT
1 GGTC--AGCGGGTT
5035698 AGGTCAGCGGGTT
1 -GGTCAGCGGGTT
5035711 GGTCAG
1 GGTCAG
5035717 AAACGGGTCG
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
12 10 0.36
13 7 0.25
14 7 0.25
15 4 0.14
ACGTcount: A:0.11, C:0.16, G:0.49, T:0.24
Consensus pattern (12 bp):
GGTCAGCGGGTT
Found at i:5039034 original size:72 final size:72
Alignment explanation
Indices: 5038956--5039090 Score: 216
Period size: 72 Copynumber: 1.9 Consensus size: 72
5038946 ATAAAGAAAA
* * * * * *
5038956 TAAATCCTTATTAAAATACTTAAAACTATTTAAATTAAAATATCTAAAACAAAGATAAGATAATT
1 TAAATCCTAATCAAAATACATAAAACTATTTAAACTAAAATACCTAAAACAAAAATAAGATAATT
5039021 AATATCC
66 AATATCC
5039028 TAAATCCTAATCAAAATACATAAAACTATTTAAACTAAAATACCTAAAACAAAAATAAGATAA
1 TAAATCCTAATCAAAATACATAAAACTATTTAAACTAAAATACCTAAAACAAAAATAAGATAA
5039091 GATAAAATAT
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
72 57 1.00
ACGTcount: A:0.56, C:0.13, G:0.02, T:0.29
Consensus pattern (72 bp):
TAAATCCTAATCAAAATACATAAAACTATTTAAACTAAAATACCTAAAACAAAAATAAGATAATT
AATATCC
Found at i:5045103 original size:27 final size:27
Alignment explanation
Indices: 5045065--5045118 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
5045055 TTCCAGGGAG
5045065 AATTGTCATGTCACTTTCTCTAGTGGT
1 AATTGTCATGTCACTTTCTCTAGTGGT
5045092 AATTGTCATGTCACTTTCTCTAGTGGT
1 AATTGTCATGTCACTTTCTCTAGTGGT
5045119 GCATACATCG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.44
Consensus pattern (27 bp):
AATTGTCATGTCACTTTCTCTAGTGGT
Found at i:5053067 original size:19 final size:19
Alignment explanation
Indices: 5053039--5053077 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
5053029 ATAAATATGC
*
5053039 ATTAGGCTATGAATATGAA
1 ATTAGACTATGAATATGAA
*
5053058 ATTAGACTATGAATCTGAA
1 ATTAGACTATGAATATGAA
5053077 A
1 A
5053078 ATAAGTTGTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.44, C:0.08, G:0.18, T:0.31
Consensus pattern (19 bp):
ATTAGACTATGAATATGAA
Found at i:5055035 original size:12 final size:12
Alignment explanation
Indices: 5055020--5055084 Score: 51
Period size: 12 Copynumber: 5.4 Consensus size: 12
5055010 AAATGGAGAT
*
5055020 ATCAGAAATCAT
1 ATCAGAAATCAG
*
5055032 ATCAGATATCAG
1 ATCAGAAATCAG
*
5055044 AACA-AAATTCAG
1 ATCAGAAA-TCAG
*
5055056 ATTAGAAATCAG
1 ATCAGAAATCAG
* * *
5055068 AACAGAATTCAT
1 ATCAGAAATCAG
5055080 ATCAG
1 ATCAG
5055085 GTATTATAAC
Statistics
Matches: 40, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
11 2 0.05
12 35 0.88
13 3 0.08
ACGTcount: A:0.49, C:0.15, G:0.12, T:0.23
Consensus pattern (12 bp):
ATCAGAAATCAG
Found at i:5055108 original size:24 final size:24
Alignment explanation
Indices: 5055081--5055132 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
5055071 AGAATTCATA
*
5055081 TCAGGTATTATAA-CAGAATCCAGG
1 TCAGGTATCA-AATCAGAATCCAGG
5055105 TCAGGTATCAAATCAGAATCCAGG
1 TCAGGTATCAAATCAGAATCCAGG
5055129 TCAG
1 TCAG
5055133 AAATCAGATA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 2 0.08
24 24 0.92
ACGTcount: A:0.37, C:0.19, G:0.21, T:0.23
Consensus pattern (24 bp):
TCAGGTATCAAATCAGAATCCAGG
Found at i:5062930 original size:21 final size:22
Alignment explanation
Indices: 5062906--5062953 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
5062896 ATTTCCTTGG
5062906 CTAATTTCTCTC-TTGC-AACTC
1 CTAATTTCTCTCTTTGCAAAC-C
*
5062927 CTAA-TTCTTTCTTTGCAAACC
1 CTAATTTCTCTCTTTGCAAACC
5062948 CTAATT
1 CTAATT
5062954 AACCTTCCAC
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
20 6 0.26
21 13 0.57
22 4 0.17
ACGTcount: A:0.23, C:0.29, G:0.04, T:0.44
Consensus pattern (22 bp):
CTAATTTCTCTCTTTGCAAACC
Found at i:5065859 original size:30 final size:30
Alignment explanation
Indices: 5065823--5065889 Score: 134
Period size: 30 Copynumber: 2.2 Consensus size: 30
5065813 AGAATGCAGT
5065823 TAAATTTTAGGAATTTATGTACTCTTTCTA
1 TAAATTTTAGGAATTTATGTACTCTTTCTA
5065853 TAAATTTTAGGAATTTATGTACTCTTTCTA
1 TAAATTTTAGGAATTTATGTACTCTTTCTA
5065883 TAAATTT
1 TAAATTT
5065890 CATAGTGTTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.31, C:0.09, G:0.09, T:0.51
Consensus pattern (30 bp):
TAAATTTTAGGAATTTATGTACTCTTTCTA
Found at i:5071797 original size:27 final size:28
Alignment explanation
Indices: 5071748--5071802 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 28
5071738 TTTTTAGCTT
5071748 TTATTTTAAAAATTATTTAAAAACTTTA
1 TTATTTTAAAAATTATTTAAAAACTTTA
* *
5071776 TTATTTTAAAAA-TATTTTAAAATTTTA
1 TTATTTTAAAAATTATTTAAAAACTTTA
5071803 AAAATATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 13 0.52
28 12 0.48
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (28 bp):
TTATTTTAAAAATTATTTAAAAACTTTA
Found at i:5072125 original size:16 final size:16
Alignment explanation
Indices: 5072100--5072130 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5072090 TTTTTCAAAG
5072100 TTAAAAAATATTAAAT
1 TTAAAAAATATTAAAT
*
5072116 TTAAAGAATATTAAA
1 TTAAAAAATATTAAA
5072131 ATGTTTTATT
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:0.61, C:0.00, G:0.03, T:0.35
Consensus pattern (16 bp):
TTAAAAAATATTAAAT
Found at i:5072210 original size:27 final size:25
Alignment explanation
Indices: 5072150--5072212 Score: 63
Period size: 27 Copynumber: 2.4 Consensus size: 25
5072140 TTTTTGAACG
* *
5072150 TTTTGAAAATAATAAAAATATTAAT
1 TTTTTAAAATAATAAAAATATCAAT
*
5072175 TATTATTAAAATTATAAAAAATGATCAAT
1 T-TT-TTAAAATAAT-AAAAAT-ATCAAT
5072204 TTTTTAAAA
1 TTTTTAAAA
5072213 ACTCTAAACT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
25 1 0.03
26 2 0.06
27 14 0.45
28 8 0.26
29 6 0.19
ACGTcount: A:0.54, C:0.02, G:0.03, T:0.41
Consensus pattern (25 bp):
TTTTTAAAATAATAAAAATATCAAT
Found at i:5076920 original size:92 final size:91
Alignment explanation
Indices: 5076763--5076939 Score: 266
Period size: 92 Copynumber: 1.9 Consensus size: 91
5076753 GATTCAATCA
*
5076763 GATACAATGGTAAGGGTATCGATACCAAGCAACATCGAATCTAAAATCGATATCAATACCAGAAG
1 GATACAATGGTAAAGGTATCGATACCAAGCAACATCGAATCTAAAATCGATATCAATACCAGAAG
5076828 GGGATATCGATACCATAGTATGGTACC
66 GGG-TATCGATACCATAGTATGGTACC
* * * * * *
5076855 GATACCATGGTAAATGTATCGATACCAGGCAACATCGAA-CTTAAAATCGATATCGATATCGGAA
1 GATACAATGGTAAAGGTATCGATACCAAGCAACATCGAATC-TAAAATCGATATCAATACCAGAA
5076919 GGGGTATCGATACCATAGTAT
65 GGGGTATCGATACCATAGTAT
5076940 ATATGGTAGG
Statistics
Matches: 77, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
91 18 0.23
92 59 0.77
ACGTcount: A:0.38, C:0.18, G:0.21, T:0.23
Consensus pattern (91 bp):
GATACAATGGTAAAGGTATCGATACCAAGCAACATCGAATCTAAAATCGATATCAATACCAGAAG
GGGTATCGATACCATAGTATGGTACC
Found at i:5077386 original size:57 final size:57
Alignment explanation
Indices: 5077284--5078300 Score: 1402
Period size: 57 Copynumber: 17.8 Consensus size: 57
5077274 ATTACCAAAT
* * *
5077284 GGCACTTCGTGTACAAAAATGTTAAG-AATTCATACTAAGTATATGAATTTCCATATTG
1 GGCACTTCGTGTGC-AAAA-GTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTG
* *
5077342 GGCACTTCGTGTGCAAAAGTTAATAAATTCATACTAAGTGTATGAATTTCTGTATTG
1 GGCACTTCGTGTGCAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTG
* *
5077399 GGCACTTCATGTGCAAAAATGTTAAGAAATTCATA-TAAGTGTATGAATTTCCGT-GTG
1 GGCACTTCGTGTGC-AAAA-GTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTG
*
5077456 GGCACTTCGTGTGCAAAAGTTAAGAAATTCATACTAAGTGTATGAACTTCCGTATTG
1 GGCACTTCGTGTGCAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTG
** *
5077513 GGCACTTCGTGTGC-AAAGTTAAGAAATTCATACTAAGTGTAAAAATTTCCGTATTA
1 GGCACTTCGTGTGCAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTG
* *
5077569 GGCAATTCGTGTACAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTG
1 GGCACTTCGTGTGCAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTG
* * * *
5077626 GACACTTCGTGTGTAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCGGTATTA
1 GGCACTTCGTGTGCAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTG
* * * * **
5077683 GACAATTCGTGTGCAAAAGTTAAGAATTTCATACTAAGTGTATGAATTTCTGTATCC
1 GGCACTTCGTGTGCAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTG
* *
5077740 GGAACTTCGTGTGCAAAAGTTAAGAAATTCATACTAAGTGTAAGAATTTCCGTATTG
1 GGCACTTCGTGTGCAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTG
*
5077797 GGCACTTCGTGTACAAAAGTTAAGAAATTCATA-TAAAGTGTATGAATTTCCGTATTG
1 GGCACTTCGTGTGCAAAAGTTAAGAAATTCATACT-AAGTGTATGAATTTCCGTATTG
* * * * * *
5077854 GGCACTTCGTCTGTAAAAGTTAAGAGATTCATACAAAGTTTATGAATTTCCTTATTG
1 GGCACTTCGTGTGCAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTG
* *
5077911 GGCACTCCGTGTGCAAAAGTTAAGATATTCATACTAAGTGTATGAATTTCCGTATTG
1 GGCACTTCGTGTGCAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTG
* * * * *
5077968 GACACTTCTTGTGCAAAAATGTTTAGAAATTCATATTAAGTGTATGAATTTCTGTATTG
1 GGCACTTCGTGTGC-AAAA-GTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTG
* * * **
5078027 GGCACTTCGTGTGCAAAAGTTGAGAAATTCATACTAAGTATACGAATTTCAATATTG
1 GGCACTTCGTGTGCAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTG
* *
5078084 GGCACTTCGTGTGTAAAAGTTAAAAAATTC--A-TAAGTGTATGAATTTCCGTATTG
1 GGCACTTCGTGTGCAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTG
* * *
5078138 GACACTTCGTGTGCAAAAGTTAAGAAATTCATACTAAGTTTATGATTTTCCGTATTG
1 GGCACTTCGTGTGCAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTG
* **
5078195 GGCACTTCGTGTGCAAAAGTTAAGAAATTCATACTAAGTGTATGATTTTTTGTATTG
1 GGCACTTCGTGTGCAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTG
* * * *
5078252 GGTACTTTGTGTGCAAATTGTTAAGAGATTCATACTAAGTGTATGAATT
1 GGCACTTCGTGTGCAAA-AGTTAAGAAATTCATACTAAGTGTATGAATT
5078301 ATCAGATGAG
Statistics
Matches: 851, Mismatches: 94, Indels: 28
0.87 0.10 0.03
Matches are distributed among these distances:
54 46 0.05
55 16 0.02
56 79 0.09
57 578 0.68
58 71 0.08
59 61 0.07
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.35
Consensus pattern (57 bp):
GGCACTTCGTGTGCAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTG
Found at i:5078161 original size:455 final size:454
Alignment explanation
Indices: 5077287--5078300 Score: 1428
Period size: 455 Copynumber: 2.2 Consensus size: 454
5077277 ACCAAATGGC
* * *
5077287 ACTTCGTGTACAAAAATGTTAAG-AATTCATACTAAGTATATGAATTTCCATATTGGGCACTTCG
1 ACTTCGTGTGC-AAAA-GTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTCG
* * *
5077351 TGTGCAAAAGTTAATAAATTCATACTAAGTGTATGAATTTCTGTATTGGGCACTTCATGTGCAAA
64 TGTGCAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTCATCTGCAAA
* *
5077416 AATGTTAAGAAATTCATATAAGTGTATGAATTTCCGTGTGGGCACTTCGTGTGCAAAAGTTAAGA
129 AATGTTAAGAAATTCATAAAAGTGTATGAATTTCCGTGTGGGCACTCCGTGTGCAAAAGTTAAGA
*
5077481 AATTCATACTAAGTGTATGAACTTCCGTATTGGGCACTTCGTGTGCAAAGTTAAGAAATTCATAC
194 AATTCATACTAAGTGTATGAACTTCCGTATTGGACACTTCGTGTGCAAAGTTAAGAAATTCATAC
*
5077546 TAAGTGTAAAAATTTCCGTATTAGGCAATTCGTGTACAAAAGTTAAGAAATTCATACTAAGTGTA
259 TAAGTGTAAAAATTTCCGTATTAGGCAATTCGTGTACAAAAGTTAAGAAATTCATACTAAGTATA
* ** *
5077611 TGAATTTCCGTATTGGACACTTCGTGTGTAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTC
324 CGAATTTCAATATTGGACACTTCGTGTGTAAAAGTTAAAAAATTCA-ACTAAGTGTATGAATTTC
* * *
5077676 GGTATTAGACAATTCGTGTGCAAAAGTTAAGAATTTCATACTAAGTGTATGAATTTCTGTATCCG
388 CGTATTAGACAATTCGTGTGCAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATCCG
5077741 GA
453 GA
*
5077743 ACTTCGTGTGCAAAAGTTAAGAAATTCATACTAAGTGTAAGAATTTCCGTATTGGGCACTTCGTG
1 ACTTCGTGTGCAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTCGTG
* * *
5077808 TACAAAAGTTAAGAAATTCATA-TAAAGTGTATGAATTTCCGTATTGGGCACTTCGTCTG-TAAA
66 TGCAAAAGTTAAGAAATTCATACT-AAGTGTATGAATTTCCGTATTGGGCACTTCATCTGCAAAA
* * * *
5077871 A-GTTAAGAGATTCATACAAAGTTTATGAATTTCCTTATTGGGCACTCCGTGTGCAAAAGTTAAG
130 ATGTTAAGAAATTCATA-AAAGTGTATGAATTTCCGT-GTGGGCACTCCGTGTGCAAAAGTTAAG
* * * *
5077935 ATATTCATACTAAGTGTATGAATTTCCGTATTGGACACTTCTTGTGCAAAAATGTTTAGAAATTC
193 AAATTCATACTAAGTGTATGAACTTCCGTATTGGACACTTCGTGTGC--AAA-GTTAAGAAATTC
* ** * * * * *
5078000 ATATTAAGTGTATGAATTTCTGTATTGGGCACTTCGTGTGCAAAAGTTGAGAAATTCATACTAAG
255 ATACTAAGTGTAAAAATTTCCGTATTAGGCAATTCGTGTACAAAAGTTAAGAAATTCATACTAAG
*
5078065 TATACGAATTTCAATATTGGGCACTTCGTGTGTAAAAGTTAAAAAATTC-A-TAAGTGTATGAAT
320 TATACGAATTTCAATATTGGACACTTCGTGTGTAAAAGTTAAAAAATTCAACTAAGTGTATGAAT
* * * *
5078128 TTCCGTATTGGACACTTCGTGTGCAAAAGTTAAGAAATTCATACTAAGTTTATGATTTTCCGTAT
385 TTCCGTATTAGACAATTCGTGTGCAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTAT
** *
5078193 TGGGC
450 CCGGA
* ** * *
5078198 ACTTCGTGTGCAAAAGTTAAGAAATTCATACTAAGTGTATGATTTTTTGTATTGGGTACTTTGTG
1 ACTTCGTGTGCAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTCGTG
* *
5078263 TGCAAATTGTTAAGAGATTCATACTAAGTGTATGAATT
66 TGCAAA-AGTTAAGAAATTCATACTAAGTGTATGAATT
5078301 ATCAGATGAG
Statistics
Matches: 495, Mismatches: 54, Indels: 18
0.87 0.10 0.03
Matches are distributed among these distances:
453 14 0.03
454 27 0.05
455 301 0.61
456 38 0.08
457 4 0.01
458 111 0.22
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.35
Consensus pattern (454 bp):
ACTTCGTGTGCAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTCGTG
TGCAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTCATCTGCAAAAA
TGTTAAGAAATTCATAAAAGTGTATGAATTTCCGTGTGGGCACTCCGTGTGCAAAAGTTAAGAAA
TTCATACTAAGTGTATGAACTTCCGTATTGGACACTTCGTGTGCAAAGTTAAGAAATTCATACTA
AGTGTAAAAATTTCCGTATTAGGCAATTCGTGTACAAAAGTTAAGAAATTCATACTAAGTATACG
AATTTCAATATTGGACACTTCGTGTGTAAAAGTTAAAAAATTCAACTAAGTGTATGAATTTCCGT
ATTAGACAATTCGTGTGCAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATCCGGA
Found at i:5086583 original size:23 final size:23
Alignment explanation
Indices: 5086557--5086601 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
5086547 CTACTTCGAT
5086557 CTTCAAGAAGTTGTTGACTGGGC
1 CTTCAAGAAGTTGTTGACTGGGC
* *
5086580 CTTCTAGAAGTTGTTGATTGGG
1 CTTCAAGAAGTTGTTGACTGGG
5086602 TACCATGTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.20, C:0.13, G:0.31, T:0.36
Consensus pattern (23 bp):
CTTCAAGAAGTTGTTGACTGGGC
Found at i:5114543 original size:20 final size:20
Alignment explanation
Indices: 5114518--5114557 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
5114508 TATTTGATGT
5114518 TTGTCCTCAAGAATTTCTTA
1 TTGTCCTCAAGAATTTCTTA
5114538 TTGTCCTCAAGAATTTCTTA
1 TTGTCCTCAAGAATTTCTTA
5114558 ATCAACACAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.20, G:0.10, T:0.45
Consensus pattern (20 bp):
TTGTCCTCAAGAATTTCTTA
Found at i:5117696 original size:16 final size:16
Alignment explanation
Indices: 5117675--5117711 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
5117665 ACATATGTAT
5117675 ATATATTAATTAATAA
1 ATATATTAATTAATAA
5117691 ATATATTAATTAATAA
1 ATATATTAATTAATAA
5117707 ATATA
1 ATATA
5117712 AATTTTGCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
ATATATTAATTAATAA
Found at i:5121144 original size:13 final size:13
Alignment explanation
Indices: 5121126--5121151 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5121116 TACAGACGCG
5121126 CATATGAAGACTA
1 CATATGAAGACTA
5121139 CATATGAAGACTA
1 CATATGAAGACTA
5121152 TTCAACTATA
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:0.46, C:0.15, G:0.15, T:0.23
Consensus pattern (13 bp):
CATATGAAGACTA
Found at i:5121950 original size:16 final size:17
Alignment explanation
Indices: 5121929--5121971 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
5121919 TATCAAAATT
5121929 AAATTAAAT-TACTAAA
1 AAATTAAATATACTAAA
*
5121945 AAATTAAAATATATTAAA
1 AAATT-AAATATACTAAA
5121963 AATATTAAA
1 AA-ATTAAA
5121972 AGCATTATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 5 0.22
17 4 0.17
18 11 0.48
19 3 0.13
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (17 bp):
AAATTAAATATACTAAA
Found at i:5121964 original size:19 final size:20
Alignment explanation
Indices: 5121923--5121972 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
5121913 ATCAAATATC
*
5121923 AAAATTAAATTAAATTACTAA
1 AAAATTAAAATAAATTAC-AA
*
5121944 AAAATTAAAATATATTA-AA
1 AAAATTAAAATAAATTACAA
*
5121963 AATATTAAAA
1 AAAATTAAAA
5121973 GCATTATTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 11 0.42
21 15 0.58
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (20 bp):
AAAATTAAAATAAATTACAA
Found at i:5132096 original size:17 final size:17
Alignment explanation
Indices: 5132046--5132100 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
5132036 TTTCACGTTA
5132046 ATAAAGACTAAA-GTATT
1 ATAAA-ACTAAATGTATT
*
5132063 ATAAAACATATATGTATT
1 ATAAAAC-TAAATGTATT
5132081 -TAACAACTAAATGTATT
1 ATAA-AACTAAATGTATT
5132098 ATA
1 ATA
5132101 CCCTTATTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
16 2 0.06
17 20 0.62
18 10 0.31
ACGTcount: A:0.51, C:0.07, G:0.07, T:0.35
Consensus pattern (17 bp):
ATAAAACTAAATGTATT
Found at i:5135561 original size:19 final size:18
Alignment explanation
Indices: 5135531--5135575 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
5135521 GATTTAAACG
*
5135531 AACTATCATGCTAAAATA
1 AACTAACATGCTAAAATA
* *
5135549 AACTTAACATGCTTAAATG
1 AAC-TAACATGCTAAAATA
5135568 AACTAACA
1 AACTAACA
5135576 CACTTAAATG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 8 0.35
19 15 0.65
ACGTcount: A:0.49, C:0.18, G:0.07, T:0.27
Consensus pattern (18 bp):
AACTAACATGCTAAAATA
Found at i:5143484 original size:23 final size:23
Alignment explanation
Indices: 5143430--5143492 Score: 63
Period size: 26 Copynumber: 2.6 Consensus size: 23
5143420 GTCTGTCCGC
5143430 CTTCTAGAAGCTGCTGACAGAAT
1 CTTCTAGAAGCTGCTGACAGAAT
* * *
5143453 CATCATCTAGAAGCTGGTGACTGGAT
1 C-T--TCTAGAAGCTGCTGACAGAAT
*
5143479 CTTCTAGAAACTGC
1 CTTCTAGAAGCTGC
5143493 AACACCATCT
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
23 11 0.34
24 1 0.03
25 1 0.03
26 19 0.59
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (23 bp):
CTTCTAGAAGCTGCTGACAGAAT
Found at i:5145163 original size:24 final size:24
Alignment explanation
Indices: 5145133--5145186 Score: 108
Period size: 24 Copynumber: 2.2 Consensus size: 24
5145123 TCGAGTCAGT
5145133 GTTGCATTTAGATAATGCAAACCA
1 GTTGCATTTAGATAATGCAAACCA
5145157 GTTGCATTTAGATAATGCAAACCA
1 GTTGCATTTAGATAATGCAAACCA
5145181 GTTGCA
1 GTTGCA
5145187 GTCAGTTTGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.30
Consensus pattern (24 bp):
GTTGCATTTAGATAATGCAAACCA
Found at i:5147491 original size:12 final size:12
Alignment explanation
Indices: 5147474--5147512 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
5147464 CAGAGAATGT
5147474 AGATAGTGATTG
1 AGATAGTGATTG
5147486 AGATAGTGATTG
1 AGATAGTGATTG
* *
5147498 AGATAATGACTG
1 AGATAGTGATTG
5147510 AGA
1 AGA
5147513 CAAGGACTGC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.38, C:0.03, G:0.31, T:0.28
Consensus pattern (12 bp):
AGATAGTGATTG
Found at i:5173934 original size:20 final size:22
Alignment explanation
Indices: 5173895--5173935 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
5173885 TCACCATTTG
5173895 TCTTCTTCTTCATCTCCTTGTTT
1 TCTTCTTCTTCA-CTCCTTGTTT
5173918 TCTTCTTCTTC-CT-CTTGT
1 TCTTCTTCTTCACTCCTTGT
5173936 GAGTGAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.28
21 2 0.11
23 11 0.61
ACGTcount: A:0.02, C:0.32, G:0.05, T:0.61
Consensus pattern (22 bp):
TCTTCTTCTTCACTCCTTGTTT
Found at i:5178045 original size:45 final size:45
Alignment explanation
Indices: 5177994--5178315 Score: 357
Period size: 45 Copynumber: 7.1 Consensus size: 45
5177984 AAATGAATGA
* * ** *
5177994 ATAAATGAAATGCATAATGAG-ACATTATCATAATGAAAGGATGAC
1 ATAAATGAAATGCATAACG-GTGCATTATCAGCATGAAAGGATGCC
* * * * *
5178039 ATAAATGAAATGTATAACGATGGATTATCGGCATAAAAGGATGCC
1 ATAAATGAAATGCATAACGGTGCATTATCAGCATGAAAGGATGCC
5178084 ATAAATGAAATGCATAACGGTGCATTAT-AGGCATGAAAGGATGCC
1 ATAAATGAAATGCATAACGGTGCATTATCA-GCATGAAAGGATGCC
*
5178129 ATAAATGAAATGCATAATGGTGCATTAT-AGGCATGAAAGGATGCC
1 ATAAATGAAATGCATAACGGTGCATTATCA-GCATGAAAGGATGCC
* ** *
5178174 ATAAATAAAATAAATAACGGTGCATTATCGGCATGAAAGGATGCC
1 ATAAATGAAATGCATAACGGTGCATTATCAGCATGAAAGGATGCC
* * *
5178219 ATAAATGAAATGTATAACGGTGCATTAAT-GGCATGGAAGGATGCC
1 ATAAATGAAATGCATAACGGTGCATT-ATCAGCATGAAAGGATGCC
* * * *
5178264 GTAAATGAAAATGCATAACAGTGCATTAT-AGGCATGAAATGATGCT
1 ATAAATG-AAATGCATAACGGTGCATTATCA-GCATGAAAGGATGCC
5178310 ATAAAT
1 ATAAAT
5178316 AAAAATAAAG
Statistics
Matches: 238, Mismatches: 33, Indels: 11
0.84 0.12 0.04
Matches are distributed among these distances:
45 202 0.85
46 36 0.15
ACGTcount: A:0.43, C:0.11, G:0.22, T:0.24
Consensus pattern (45 bp):
ATAAATGAAATGCATAACGGTGCATTATCAGCATGAAAGGATGCC
Found at i:5178201 original size:135 final size:135
Alignment explanation
Indices: 5177994--5178324 Score: 443
Period size: 135 Copynumber: 2.4 Consensus size: 135
5177984 AAATGAATGA
* ** * * **
5177994 ATAAATGAAATGCATAATGAG-ACATTATCA-TAATGAAAGGATGACATAAATGAAATGTATAAC
1 ATAAATGAAATGCATAATG-GTGCATTAT-AGGCATGAAAGGATGCCATAAATAAAATAAATAAC
*
5178057 GATGGATTATCGGCATAAAAGGATGCCATAAATGAAATGCATAACGGTGCATT-ATAGGCATGAA
64 GATGCATTATCGGCATAAAAGGATGCCATAAATGAAATGCATAACGGTGCATTAAT-GGCATGAA
5178121 AGGATGCC
128 AGGATGCC
*
5178129 ATAAATGAAATGCATAATGGTGCATTATAGGCATGAAAGGATGCCATAAATAAAATAAATAACGG
1 ATAAATGAAATGCATAATGGTGCATTATAGGCATGAAAGGATGCCATAAATAAAATAAATAACGA
* * *
5178194 TGCATTATCGGCATGAAAGGATGCCATAAATGAAATGTATAACGGTGCATTAATGGCATGGAAGG
66 TGCATTATCGGCATAAAAGGATGCCATAAATGAAATGCATAACGGTGCATTAATGGCATGAAAGG
5178259 ATGCC
131 ATGCC
* ** * *
5178264 GTAAATGAAAATGCATAACAGTGCATTATAGGCATGAAATGATGCTATAAATAAAAATAAA
1 ATAAATG-AAATGCATAATGGTGCATTATAGGCATGAAAGGATGCCATAAAT-AAAATAAA
5178325 GAATAATGGG
Statistics
Matches: 174, Mismatches: 17, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
134 2 0.01
135 122 0.70
136 42 0.24
137 8 0.05
ACGTcount: A:0.44, C:0.11, G:0.21, T:0.24
Consensus pattern (135 bp):
ATAAATGAAATGCATAATGGTGCATTATAGGCATGAAAGGATGCCATAAATAAAATAAATAACGA
TGCATTATCGGCATAAAAGGATGCCATAAATGAAATGCATAACGGTGCATTAATGGCATGAAAGG
ATGCC
Found at i:5193608 original size:23 final size:22
Alignment explanation
Indices: 5193571--5193709 Score: 88
Period size: 24 Copynumber: 6.0 Consensus size: 22
5193561 TATTTCGCTT
5193571 AAAGAAGAAAT-AAAAGAAAAAA
1 AAAGAA-AAATGAAAAGAAAAAA
*
5193593 AAACGAAAAATGAAAA-AAATAAT
1 AAA-GAAAAATGAAAAGAAA-AAA
*
5193616 AATG-AAAATGAGAAA-AAGAAAA
1 AAAGAAAAATGA-AAAGAA-AAAA
*
5193638 AGAAGAAAAGAAGAAAAGAAAAAA
1 A-AAGAAAA-ATGAAAAGAAAAAA
** *
5193662 TGAGAAAAAATAAAAATGAAAAAA
1 AAAG-AAAAATGAAAA-GAAAAAA
* *
5193686 GAAAGAAAAATAAAAAGAGAAAA
1 -AAAGAAAAATGAAAAGAAAAAA
5193709 A
1 A
5193710 TGAAAAAAAG
Statistics
Matches: 93, Mismatches: 12, Indels: 24
0.72 0.09 0.19
Matches are distributed among these distances:
21 7 0.08
22 20 0.22
23 27 0.29
24 32 0.34
25 7 0.08
ACGTcount: A:0.77, C:0.01, G:0.15, T:0.07
Consensus pattern (22 bp):
AAAGAAAAATGAAAAGAAAAAA
Found at i:5193609 original size:8 final size:7
Alignment explanation
Indices: 5193571--5193717 Score: 68
Period size: 8 Copynumber: 19.4 Consensus size: 7
5193561 TATTTCGCTT
*
5193571 AAAGAAG
1 AAAGAAA
*
5193578 AAATAAA
1 AAAGAAA
*
5193585 AGAAAAAA
1 A-AAGAAA
5193593 AAACGAAA
1 AAA-GAAA
*
5193601 AATGAAA
1 AAAGAAA
5193608 AAA-ATAA
1 AAAGA-AA
*
5193615 TAATG-AA
1 -AAAGAAA
*
5193622 AATGAGAA
1 AAAGA-AA
5193630 AAAG-AA
1 AAAGAAA
5193636 AAAGAAGA
1 AAAGAA-A
5193644 AAAGAAGA
1 AAAGAA-A
5193652 AAAGAAA
1 AAAGAAA
5193659 AAATGAGAA
1 AAA-GA-AA
5193668 AAA-ATAA
1 AAAGA-AA
5193675 AAATGAAA
1 AAA-GAAA
5193683 AAAGAAA
1 AAAGAAA
*
5193690 GAAAAATAA
1 -AAAGA-AA
5193699 AAAGAGAA
1 AAAGA-AA
5193707 AAATGAAA
1 AAA-GAAA
5193715 AAA
1 AAA
5193718 AGAGAAATAA
Statistics
Matches: 112, Mismatches: 12, Indels: 31
0.72 0.08 0.20
Matches are distributed among these distances:
6 11 0.10
7 33 0.29
8 58 0.52
9 10 0.09
ACGTcount: A:0.77, C:0.01, G:0.15, T:0.07
Consensus pattern (7 bp):
AAAGAAA
Found at i:5193610 original size:15 final size:14
Alignment explanation
Indices: 5193590--5193717 Score: 75
Period size: 15 Copynumber: 8.4 Consensus size: 14
5193580 ATAAAAGAAA
5193590 AAAAAACGAAAAATG
1 AAAAAA-GAAAAATG
5193605 AAAAAA-ATAATAATG
1 AAAAAAGA-AA-AATG
*
5193620 AAAATGAGAAAAA-G
1 AAAA-AAGAAAAATG
*
5193634 -AAAAAGAAGAAAAG
1 AAAAAAGAA-AAATG
5193648 AAGAAAAGAAAAAATGAG
1 AA-AAAAG-AAAAAT--G
*
5193666 AAAAAATAAAAATG
1 AAAAAAGAAAAATG
5193680 AAAAAAGAAAGAAAAAT-
1 ---AAA-AAAGAAAAATG
5193697 AAAAAGAGAAAAATG
1 AAAAA-AGAAAAATG
5193712 AAAAAA
1 AAAAAA
5193718 AGAGAAATAA
Statistics
Matches: 91, Mismatches: 5, Indels: 35
0.69 0.04 0.27
Matches are distributed among these distances:
12 4 0.04
13 9 0.10
14 17 0.19
15 22 0.24
16 17 0.19
17 10 0.11
18 12 0.13
ACGTcount: A:0.77, C:0.01, G:0.15, T:0.08
Consensus pattern (14 bp):
AAAAAAGAAAAATG
Found at i:5193686 original size:39 final size:40
Alignment explanation
Indices: 5193620--5193720 Score: 124
Period size: 39 Copynumber: 2.6 Consensus size: 40
5193610 AATAATAATG
5193620 AAAATGAG-AAAAAGAAAAAGAAGAAAAG-AAGAAAAGA-A
1 AAAATGAGAAAAAAGAAAAAGAAGAAAAGAAAGAAAA-ATA
*
5193658 AAAATGAGAAAAAATAAAAATGAA-AAAAGAAAGAAAAATA
1 AAAATGAGAAAAAAGAAAAA-GAAGAAAAGAAAGAAAAATA
*
5193698 AAAA-GAGAAAAATGAAAAA-AAGA
1 AAAATGAGAAAAAAGAAAAAGAAGA
5193721 GAAATAAAAG
Statistics
Matches: 55, Mismatches: 3, Indels: 10
0.81 0.04 0.15
Matches are distributed among these distances:
37 2 0.04
38 9 0.16
39 29 0.53
40 15 0.27
ACGTcount: A:0.77, C:0.00, G:0.17, T:0.06
Consensus pattern (40 bp):
AAAATGAGAAAAAAGAAAAAGAAGAAAAGAAAGAAAAATA
Found at i:5193702 original size:47 final size:45
Alignment explanation
Indices: 5193578--5193718 Score: 132
Period size: 47 Copynumber: 3.1 Consensus size: 45
5193568 CTTAAAGAAG
5193578 AAAT-AAAAGAAAAAA-AAACGAAAAATGAAAAA-AATAATAATGAAAA
1 AAATAAAAAGAAAAAAGAAA-GAAAAAT-AAAAAGAA-AA-AATGAAAA
** *
5193624 TGAGAAAAAG-AAAAAG-AAGAAAAGA-AGAAAAGAAAAAATGAGAAA
1 AAATAAAAAGAAAAAAGAAAGAAAA-ATA-AAAAGAAAAAATGA-AAA
5193669 AAATAAAAATGAAAAAAGAAAGAAAAATAAAAAGAGAAAAATGAAAA
1 AAATAAAAA-GAAAAAAGAAAGAAAAATAAAAAGA-AAAAATGAAAA
5193716 AAA
1 AAA
5193719 GAGAAATAAA
Statistics
Matches: 78, Mismatches: 6, Indels: 21
0.74 0.06 0.20
Matches are distributed among these distances:
44 6 0.08
45 20 0.26
46 12 0.15
47 24 0.31
48 16 0.21
ACGTcount: A:0.77, C:0.01, G:0.14, T:0.08
Consensus pattern (45 bp):
AAATAAAAAGAAAAAAGAAAGAAAAATAAAAAGAAAAAATGAAAA
Found at i:5195100 original size:51 final size:51
Alignment explanation
Indices: 5195038--5195452 Score: 551
Period size: 51 Copynumber: 8.0 Consensus size: 51
5195028 AAGCAAATTC
*
5195038 GTTCGTTGAAGATTGAGTCCTGTACTCTCTGAATGAATAGGGAGCGGACAA
1 GTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAA
*
5195089 GTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGTGGACAA
1 GTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAA
5195140 GTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAA
1 GTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAA
5195191 GTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAA
1 GTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAA
* * *
5195242 GTTCGTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGAACAC
1 GTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAA
** * * * * **
5195293 GTTTATTGAAGATCGAGTCTTATACTCTCTAAAGGAATAGGGAGCGGACCC
1 GTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAA
* * * * * *
5195344 GTTTGTTGAAGATTATTCGAGTCTTATACTCCCTGAACGAATAGGGAGCAGACAC
1 GTTCGTTGAAG---ATT-GAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAA
* * * *
5195399 GTTTGTTGAAGATTGTTCAAGTCTTATACTCTCTGAATGAATAGAGAGCAGACA
1 GTTCGTTGAAGATTG----AGTCCTATACTCTCTGAATGAATAGGGAGCGGACA
5195453 CATTTTATGA
Statistics
Matches: 333, Mismatches: 23, Indels: 12
0.90 0.06 0.03
Matches are distributed among these distances:
51 253 0.76
52 3 0.01
54 2 0.01
55 75 0.23
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.28
Consensus pattern (51 bp):
GTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAA
Found at i:5200265 original size:21 final size:21
Alignment explanation
Indices: 5200241--5200307 Score: 107
Period size: 21 Copynumber: 3.1 Consensus size: 21
5200231 AGTGGTAAGG
5200241 CTATAATTTATTGGCATAAAA
1 CTATAATTTATTGGCATAAAA
5200262 CTATAATTTATTGGCATAAAA
1 CTATAATTTATTGGCATAAAA
* *
5200283 ATATAATTTATGTGGCATAAGA
1 CTATAATTTAT-TGGCATAAAA
5200305 CTA
1 CTA
5200308 GCCTTTGGTT
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
21 31 0.74
22 11 0.26
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.37
Consensus pattern (21 bp):
CTATAATTTATTGGCATAAAA
Found at i:5200368 original size:22 final size:21
Alignment explanation
Indices: 5200343--5200399 Score: 51
Period size: 22 Copynumber: 2.6 Consensus size: 21
5200333 AAGACACGCA
*
5200343 AGTGCTAAGGCACTTTATTATT
1 AGTGCT-AGGCACTTTATTATC
* * *
5200365 AGTGAGTATGCACTTTTTTATC
1 AGTG-CTAGGCACTTTATTATC
5200387 AGTGCTGAGGCAC
1 AGTGCT-AGGCAC
5200400 GCCCATAATA
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
21 1 0.04
22 25 0.93
23 1 0.04
ACGTcount: A:0.25, C:0.16, G:0.23, T:0.37
Consensus pattern (21 bp):
AGTGCTAGGCACTTTATTATC
Found at i:5201030 original size:2 final size:2
Alignment explanation
Indices: 5200983--5201012 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5200973 TTCTCTAATC
5200983 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
5201013 CCTTTTCATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5204623 original size:16 final size:16
Alignment explanation
Indices: 5204593--5204625 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
5204583 AATTTATTTC
5204593 ATAAATTTTATTTTTT
1 ATAAATTTTATTTTTT
5204609 ATAATATTTTATTTTTT
1 ATAA-ATTTTATTTTTT
5204626 CACAAATTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
ATAAATTTTATTTTTT
Found at i:5206234 original size:38 final size:39
Alignment explanation
Indices: 5206192--5206277 Score: 88
Period size: 38 Copynumber: 2.3 Consensus size: 39
5206182 AATAACTTAA
***
5206192 AATAATTTTTTTATTATTTATAATTT-ATATATAT-ATTT
1 AATAATTTTTTTA-TACAAATAATTTAATATATATCATTT
**
5206230 AATAAAATTTTTATACAAATAATTTAATATATATCATTT
1 AATAATTTTTTTATACAAATAATTTAATATATATCATTT
*
5206269 -TTAATTTTT
1 AATAATTTTT
5206278 ATTTCTTTTA
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
37 9 0.24
38 25 0.66
39 4 0.11
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (39 bp):
AATAATTTTTTTATACAAATAATTTAATATATATCATTT
Found at i:5213736 original size:25 final size:27
Alignment explanation
Indices: 5213698--5213757 Score: 90
Period size: 26 Copynumber: 2.3 Consensus size: 27
5213688 CCCTATGGGG
*
5213698 AAAATAACCAAAATGCC-CTTAAGTGT
1 AAAATGACCAAAATGCCTCTTAAGTGT
5213724 AAAATGACC-AAATGCCTCTTAAGTGT
1 AAAATGACCAAAATGCCTCTTAAGTGT
5213750 -AAATGACC
1 AAAATGACC
5213758 TAAAGTATAT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
25 15 0.47
26 17 0.53
ACGTcount: A:0.43, C:0.20, G:0.13, T:0.23
Consensus pattern (27 bp):
AAAATGACCAAAATGCCTCTTAAGTGT
Found at i:5216328 original size:40 final size:39
Alignment explanation
Indices: 5216084--5216314 Score: 246
Period size: 39 Copynumber: 5.8 Consensus size: 39
5216074 TCTAAAAAAC
* * * * *
5216084 TAAATCCAATGATTTATTTCCTATTATAAAATAGGAAAAA
1 TAAATCCAACGATTTATTTCCTTTTACAAAACA-GAAAGA
* * * *
5216124 TAAAAAATTCAACAATTTATTTCCTTTTACAAAACATAAATA
1 T---AAATCCAACGATTTATTTCCTTTTACAAAACAGAAAGA
* * *
5216166 TAAATTCAACGATTTATTTTCTTTTACAAAACAAAAAGA
1 TAAATCCAACGATTTATTTCCTTTTACAAAACAGAAAGA
* * * *
5216205 TAAATCTAACGATTTATTTTCTTTTATAAAACAGAATGA
1 TAAATCCAACGATTTATTTCCTTTTACAAAACAGAAAGA
* *
5216244 TAAATCCAACGATTTATTTCCGTTTACAAAACAGAAAAA
1 TAAATCCAACGATTTATTTCCTTTTACAAAACAGAAAGA
*
5216283 TAAATCCAAATGATTTATTTCCTTTTACAAAA
1 TAAATCC-AACGATTTATTTCCTTTTACAAAA
5216315 TGAGGAAATA
Statistics
Matches: 162, Mismatches: 25, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
39 108 0.67
40 23 0.14
42 5 0.03
43 26 0.16
ACGTcount: A:0.45, C:0.13, G:0.05, T:0.36
Consensus pattern (39 bp):
TAAATCCAACGATTTATTTCCTTTTACAAAACAGAAAGA
Found at i:5216334 original size:28 final size:28
Alignment explanation
Indices: 5216302--5216357 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
5216292 ATGATTTATT
** *
5216302 TCCTTTTACAAAATGAGGAAATAAATCA
1 TCCTTTTACAAAACAAGAAAATAAATCA
*
5216330 TCCTTTTACAGAACAAGAAAATAAATCA
1 TCCTTTTACAAAACAAGAAAATAAATCA
5216358 AATGATTTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.48, C:0.16, G:0.09, T:0.27
Consensus pattern (28 bp):
TCCTTTTACAAAACAAGAAAATAAATCA
Found at i:5216448 original size:40 final size:39
Alignment explanation
Indices: 5216377--5216548 Score: 195
Period size: 39 Copynumber: 4.4 Consensus size: 39
5216367 TTTGTTTTAT
* *
5216377 TTTATTTTCTTTTACAAAATAGGAAACTAAATCCAAAGA
1 TTTATTTTCTTTTACAAAATAGGAAAATAAATCCAACGA
* * *
5216416 TTTATTTCCTTTTTACAATATAGAAAAATAAATCCAACGA
1 TTTATTTTC-TTTTACAAAATAGGAAAATAAATCCAACGA
** * * * *
5216456 TTTATTTTCTTTTACAAACCAGTAAACTAAAT-TATATGA
1 TTTATTTTCTTTTACAAAATAGGAAAATAAATCCA-ACGA
* *
5216495 TTTATTTACTTTTTCAAAATAGGAAAATAAATCCAACGA
1 TTTATTTTCTTTTACAAAATAGGAAAATAAATCCAACGA
5216534 TTTA-TTTCTTTTACA
1 TTTATTTTCTTTTACA
5216549 TATAATAATC
Statistics
Matches: 107, Mismatches: 23, Indels: 7
0.78 0.17 0.05
Matches are distributed among these distances:
38 10 0.09
39 62 0.58
40 35 0.33
ACGTcount: A:0.40, C:0.13, G:0.06, T:0.41
Consensus pattern (39 bp):
TTTATTTTCTTTTACAAAATAGGAAAATAAATCCAACGA
Found at i:5216473 original size:79 final size:78
Alignment explanation
Indices: 5216377--5216548 Score: 240
Period size: 79 Copynumber: 2.2 Consensus size: 78
5216367 TTTGTTTTAT
* * *
5216377 TTTATTTTCTTTTACAAAATAGGAAACTAAATCCA-AAGATTTATTTCCTTTTTACAATATAGAA
1 TTTATTTTCTTTTACAAAACAGGAAACTAAAT-CATAAGATTTATTTACTTTTT-CAAAATAGAA
5216441 AAATAAATCCAACGA
64 AAATAAATCCAACGA
* * * * *
5216456 TTTATTTTCTTTTACAAACCAGTAAACTAAATTATATGATTTATTTACTTTTTCAAAATAGGAAA
1 TTTATTTTCTTTTACAAAACAGGAAACTAAATCATAAGATTTATTTACTTTTTCAAAATAGAAAA
5216521 ATAAATCCAACGA
66 ATAAATCCAACGA
5216534 TTTA-TTTCTTTTACA
1 TTTATTTTCTTTTACA
5216549 TATAATAATC
Statistics
Matches: 84, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
77 11 0.13
78 28 0.33
79 45 0.54
ACGTcount: A:0.40, C:0.13, G:0.06, T:0.41
Consensus pattern (78 bp):
TTTATTTTCTTTTACAAAACAGGAAACTAAATCATAAGATTTATTTACTTTTTCAAAATAGAAAA
ATAAATCCAACGA
Found at i:5216674 original size:94 final size:93
Alignment explanation
Indices: 5216534--5216703 Score: 243
Period size: 94 Copynumber: 1.8 Consensus size: 93
5216524 AATCCAACGA
* * * * * *
5216534 TTTATTTCTTTTACATATAATAATCATACTAGATTCTTAGGAAAATAAATTTATCGATTTATTTC
1 TTTATTTCTTTTACATATAAGAATCATACTAGACTCTCAGGAAAATAAATTCAACAATTTATTTC
5216599 CTTTTACAAAACAAAAAAAATTATACAC
66 CTTTTACAAAACAAAAAAAATTATACAC
* *
5216627 TTTATTTCTTTTTACATATTAGAATCAT-GTGAGACTCTCAGGAAAATAAATTCAACAATTTATT
1 TTTATTTC-TTTTACATATAAGAATCATACT-AGACTCTCAGGAAAATAAATTCAACAATTTATT
5216691 TCCTTTTACAAAA
64 TCCTTTTACAAAA
5216704 TAGGAAAATA
Statistics
Matches: 67, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
93 9 0.13
94 58 0.87
ACGTcount: A:0.39, C:0.14, G:0.06, T:0.41
Consensus pattern (93 bp):
TTTATTTCTTTTACATATAAGAATCATACTAGACTCTCAGGAAAATAAATTCAACAATTTATTTC
CTTTTACAAAACAAAAAAAATTATACAC
Found at i:5216733 original size:44 final size:41
Alignment explanation
Indices: 5216676--5216819 Score: 159
Period size: 44 Copynumber: 3.4 Consensus size: 41
5216666 AGGAAAATAA
5216676 ATTCAACAATTTATTTCCTTTTACAAAATAGGAAAATAAAAATT
1 ATTCAACAATTTATTTCCTTTTACAAAATA-GAAAA-AAAAA-T
*
5216720 ATTCAACAATTTATTTCCTTTTACAAAACA-AAAAAAATAA-
1 ATTCAACAATTTATTTCCTTTTACAAAATAGAAAAAAA-AAT
* * *
5216760 ATCCAACGATTTATTTCCTTTTA-AAAATAGATATAAGAAAATAA
1 ATTCAACAATTTATTTCCTTTTACAAAATAGA-A-AA-AAAA-AT
5216804 ATTCAACAATTTATTT
1 ATTCAACAATTTATTT
5216820 TTTATTTAGG
Statistics
Matches: 87, Mismatches: 6, Indels: 14
0.81 0.06 0.13
Matches are distributed among these distances:
39 5 0.06
40 22 0.25
41 4 0.05
42 9 0.10
43 4 0.05
44 43 0.49
ACGTcount: A:0.48, C:0.12, G:0.03, T:0.36
Consensus pattern (41 bp):
ATTCAACAATTTATTTCCTTTTACAAAATAGAAAAAAAAAT
Found at i:5216891 original size:58 final size:59
Alignment explanation
Indices: 5216823--5216959 Score: 179
Period size: 58 Copynumber: 2.3 Consensus size: 59
5216813 TTTATTTTTT
* * * *
5216823 ATTTAGGATTCCCAAAAAAATTAAATTTAACAATTTATT-TCATTTAACAAAATAGAA-C
1 ATTTAAGATTCTCAAAAAAA-TAAATTTAACAATGTATTAACATTTAACAAAATAGAATC
* * * *
5216881 ATTTAAGATTCTTAAGAAAATAAATTTAACAATGTATTAACTTTTTACAAAATAGAATC
1 ATTTAAGATTCTCAAAAAAATAAATTTAACAATGTATTAACATTTAACAAAATAGAATC
5216940 ATTTAAGATTCTCAAAAAAA
1 ATTTAAGATTCTCAAAAAAA
5216960 ATATGAACAT
Statistics
Matches: 67, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
57 17 0.25
58 31 0.46
59 19 0.28
ACGTcount: A:0.49, C:0.10, G:0.06, T:0.35
Consensus pattern (59 bp):
ATTTAAGATTCTCAAAAAAATAAATTTAACAATGTATTAACATTTAACAAAATAGAATC
Found at i:5217088 original size:58 final size:58
Alignment explanation
Indices: 5217026--5217170 Score: 170
Period size: 58 Copynumber: 2.5 Consensus size: 58
5217016 TAATTTGTAG
5217026 AATTTATTTTTCTTACAAAGTTA-AAGTCATTCAAGATT-TCCAAAGAAATAAATTCAAA
1 AATTTATTTTTCTTACAAAGTTAGAA-TCATTCAAGATTCT-CAAAGAAATAAATTCAAA
* * * * * *
5217084 AATTTATTTTAT-TTACCAAGTTAGAATCATTTAATATTCTGAAGGAAATAAATTCAAC
1 AATTTATTTT-TCTTACAAAGTTAGAATCATTCAAGATTCTCAAAGAAATAAATTCAAA
* *
5217142 AATCTATTTTCCTTACAAAGTTAGAATCA
1 AATTTATTTTTCTTACAAAGTTAGAATCA
5217171 ACGCAAGATT
Statistics
Matches: 74, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
58 70 0.95
59 4 0.05
ACGTcount: A:0.42, C:0.12, G:0.08, T:0.38
Consensus pattern (58 bp):
AATTTATTTTTCTTACAAAGTTAGAATCATTCAAGATTCTCAAAGAAATAAATTCAAA
Found at i:5217496 original size:14 final size:15
Alignment explanation
Indices: 5217477--5217509 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
5217467 GTTATATGGT
5217477 AATAATACCAT-AAC
1 AATAATACCATGAAC
*
5217491 AATAATATCATGAAC
1 AATAATACCATGAAC
5217506 AATA
1 AATA
5217510 TAATGATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.58, C:0.15, G:0.03, T:0.24
Consensus pattern (15 bp):
AATAATACCATGAAC
Found at i:5228153 original size:21 final size:21
Alignment explanation
Indices: 5228111--5228154 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
5228101 ACCCCGGGAG
*
5228111 CTAGTTCTTCACGAGCTGCTC
1 CTAGTTCTTCACGAGCTCCTC
*
5228132 CTAGTTCTTCTC-ATGCTCCTC
1 CTAGTTCTTCACGA-GCTCCTC
5228153 CT
1 CT
5228155 CCTCCAGCTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 19 0.95
ACGTcount: A:0.11, C:0.36, G:0.14, T:0.39
Consensus pattern (21 bp):
CTAGTTCTTCACGAGCTCCTC
Found at i:5228967 original size:20 final size:21
Alignment explanation
Indices: 5228930--5228969 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
5228920 AAATTAAGTT
5228930 AAATGAATTTTAAGATTTTAC
1 AAATGAATTTTAAGATTTTAC
5228951 AAATG-ATTTTACA-ATTTTA
1 AAATGAATTTTA-AGATTTTA
5228970 TATTCGATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.45
Consensus pattern (21 bp):
AAATGAATTTTAAGATTTTAC
Found at i:5244715 original size:104 final size:104
Alignment explanation
Indices: 5244501--5244700 Score: 323
Period size: 104 Copynumber: 1.9 Consensus size: 104
5244491 TATTTGCTGA
* *
5244501 AGATGACGTTGTTCCTTTTTGTTGAGGAGGTCGAGTCAATCTAGAGATAATATGGTGTTAAAGAT
1 AGATGACATTGTTCCTTTTTGTTGAGGAAGTCGAGTCAATCTAGAGATAATATGGTGTTAAAGAT
*
5244566 AACATTGTTCATTCATGTTGAAGAGTTATGGCTGCTTTT
66 AACATTGCTCATTCATGTTGAAGAGTTATGGCTGCTTTT
*
5244605 AGATGACATTGTTCCTTCTTT-TTGAGGAAGTCGAGTCAATCTAGAGATAATATGGTGTTGAAGA
1 AGATGACATTGTTCCTT-TTTGTTGAGGAAGTCGAGTCAATCTAGAGATAATATGGTGTTAAAGA
*
5244669 TGACATTGCTCA-TCTATGTTGAAGAGTTATGG
65 TAACATTGCTCATTC-ATGTTGAAGAGTTATGG
5244701 TCATTTTCAT
Statistics
Matches: 89, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
103 2 0.02
104 84 0.94
105 3 0.03
ACGTcount: A:0.27, C:0.11, G:0.25, T:0.37
Consensus pattern (104 bp):
AGATGACATTGTTCCTTTTTGTTGAGGAAGTCGAGTCAATCTAGAGATAATATGGTGTTAAAGAT
AACATTGCTCATTCATGTTGAAGAGTTATGGCTGCTTTT
Found at i:5244722 original size:104 final size:104
Alignment explanation
Indices: 5244501--5244727 Score: 320
Period size: 104 Copynumber: 2.2 Consensus size: 104
5244491 TATTTGCTGA
* *
5244501 AGATGACGTTGTTCCTTTTTGTTGAGGAGGTCGAGTCAATCTAGAGATAATATGGTGTTAAAGAT
1 AGATGACGATGTTCCTTTTTGTTGAGGAAGTCGAGTCAATCTAGAGATAATATGGTGTTAAAGAT
*
5244566 AACATTGTTCATTCATGTTGAAGAGTTATGGCTGCTTTT
66 AACATTGCTCATTCATGTTGAAGAGTTATGGCTGCTTTT
*
5244605 AGATGAC-ATTGTTCCTTCTTT-TTGAGGAAGTCGAGTCAATCTAGAGATAATATGGTGTTGAAG
1 AGATGACGA-TGTTCCTT-TTTGTTGAGGAAGTCGAGTCAATCTAGAGATAATATGGTGTTAAAG
*
5244668 ATGACATTGCTCA-TCTATGTTGAAGAGTTATGG-T-CATTTT
64 ATAACATTGCTCATTC-ATGTTGAAGAGTTATGGCTGC-TTTT
*
5244708 CATATGACGATGTTCCTTTT
1 -AGATGACGATGTTCCTTTT
5244728 CGTTATAGAA
Statistics
Matches: 111, Mismatches: 6, Indels: 13
0.85 0.05 0.10
Matches are distributed among these distances:
102 1 0.01
103 9 0.08
104 97 0.87
105 4 0.04
ACGTcount: A:0.26, C:0.12, G:0.23, T:0.39
Consensus pattern (104 bp):
AGATGACGATGTTCCTTTTTGTTGAGGAAGTCGAGTCAATCTAGAGATAATATGGTGTTAAAGAT
AACATTGCTCATTCATGTTGAAGAGTTATGGCTGCTTTT
Found at i:5244739 original size:104 final size:103
Alignment explanation
Indices: 5244501--5244757 Score: 280
Period size: 104 Copynumber: 2.5 Consensus size: 103
5244491 TATTTGCTGA
* * *
5244501 AGATGACGTTGTTCCTTTTTGTTGA-GGAGGTCGAGTCAATCTAGAGATAATATGGTGTTAAAGA
1 AGATGACGATGTTCC-TTTTGTT-ATAGAAGTCGAGTCAATCTAGAGATAATATGGTGTTAAAGA
*
5244565 TAACATTGTTCATTCATGTTGAAGAGTTATGGCTGCTTTT
64 TAACATTGCTCATTCATGTTGAAGAGTTATGGCTGCTTTT
*
5244605 AGATGAC-ATTGTTCCTTCTT-TT-TGAGGAAGTCGAGTCAATCTAGAGATAATATGGTGTTGAA
1 AGATGACGA-TGTTCCTT-TTGTTAT-A-GAAGTCGAGTCAATCTAGAGATAATATGGTGTTAAA
*
5244667 GATGACATTGCTCA-TCTATGTTGAAGAGTTATGG-T-CATTTT
62 GATAACATTGCTCATTC-ATGTTGAAGAGTTATGGCTGC-TTTT
* **
5244708 CATATGACGATGTTCCTTTTCGTTATAGAAGTTTAGTCAATCT-G-GATAAT
1 -AGATGACGATGTTCCTTTT-GTTATAGAAGTCGAGTCAATCTAGAGATAAT
5244758 TTAAAAATAA
Statistics
Matches: 132, Mismatches: 9, Indels: 26
0.79 0.05 0.16
Matches are distributed among these distances:
102 7 0.05
103 14 0.11
104 106 0.80
105 4 0.03
106 1 0.01
ACGTcount: A:0.27, C:0.12, G:0.23, T:0.39
Consensus pattern (103 bp):
AGATGACGATGTTCCTTTTGTTATAGAAGTCGAGTCAATCTAGAGATAATATGGTGTTAAAGATA
ACATTGCTCATTCATGTTGAAGAGTTATGGCTGCTTTT
Found at i:5245084 original size:139 final size:137
Alignment explanation
Indices: 5244882--5245684 Score: 555
Period size: 139 Copynumber: 5.9 Consensus size: 137
5244872 ACGTATAAAA
* * * *
5244882 GTATTT-GGATATTTTGGAGACAACACAGTTCTTTCATGTTAAGGAAGTCTGATTATCTGAGGAT
1 GTATTTGGGATAATTTGGAGACAACACAGTTCCTTCACGTTGAGGAAGTCTGATTATCTGAGGAT
* * * *
5244946 GATACTGCTCCTCTAAGTTAAGGAGATCTGGTCAGTGGATGACATTATTCCTTTGTCTTGAGGAC
66 GACACTGCTCCTCT-AGTTAAGGAGATCTGGTCAGTGGACGACATTATTCCTTCGTGTTGAGGAC
*
5245011 GTCTAGCC
130 GTCTAGCT
* * * *
5245019 GTATTTGGAGATAATTTGGAGACAACACAGTTCCTTCACATTAAGAAAGTCTAATTATCTGAGGA
1 GTATTTGG-GATAATTTGGAGACAACACAGTTCCTTCACGTTGAGGAAGTCTGATTATCTGAGGA
* * * * * * * ** *
5245084 TGACATTGCTCATTCGTA-TTGAGAAGATCTAGTCAGTGGACAATATTAATT-CTTCAAGTTTAG
65 TGACACTGCTC-CTC-TAGTTAAGGAGATCTGGTCAGTGGACGACATT-ATTCCTTCGTGTTGAG
* *
5245147 G-CGTATAGAT
127 GACGTCTAGCT
* * * ***
5245157 GT-TTTTGGATAATTTGGAGAAAACATAGTTCCTTTGTGTTGAGGAAGT-TGATTATCTGAGGAT
1 GTATTTGGGATAATTTGGAGACAACACAGTTCCTTCACGTTGAGGAAGTCTGATTATCTGAGGAT
* * * * * * *
5245220 GACACTGCTCATTTACGTTAAGGAGATCAGTTTAGTGGACGACATTGTTCCTTCGTGTTAAGGAC
66 GACACTGCTCCTCTA-GTTAAGGAGATCTGGTCAGTGGACGACATTATTCCTTCGTGTTGAGGAC
*
5245285 ATCTAGCT
130 GTCTAGCT
* * * * * ** *
5245293 GTATCTGGAGATAATTTGGATACAACACGGTTCATTCACATTGACAAAG-CTTGATTATCTGAGT
1 GTATTTGG-GATAATTTGGAGACAACACAGTTCCTTCACGTTGAGGAAGTC-TGATTATCTGAGG
* * * *** * * * * ** *
5245357 ATGACA-T--TGCTC-A-TT--CG-CAT-TGAAGAGT-GACAATATTGTTTCTTCGCATTGAGGG
64 ATGACACTGCTCCTCTAGTTAAGGAGATCTGGTCAGTGGACGACATTATTCCTTCGTGTTGAGGA
**
5245412 CGTCTAGAA
129 CGTCTAGCT
* ** * * *
5245421 GTATTT-GGATAATTTGGAGACAACACAGTTCTTTCGTGTTGAGGAAGTCTAATTTTATGAGGAT
1 GTATTTGGGATAATTTGGAGACAACACAGTTCCTTCACGTTGAGGAAGTCTGATTATCTGAGGAT
* * * * * * *
5245485 AACACTGGTCCTTTGCGTTGAGGAGATCTGGTCAGTGTACGACATTGTTCCTTCGTGTTGAGGAC
66 GACACTGCTCCTCT-AGTTAAGGAGATCTGGTCAGTGGACGACATTATTCCTTCGTGTTGAGGAC
5245550 GTCTAGCT
130 GTCTAGCT
* * * * * * * *
5245558 GTATTTGGAGATAATTTTGAGCCAACACGGTTACTTCTCGTTGAGGAAGTCTGGTTGTCTAAGGA
1 GTATTTGG-GATAATTTGGAGACAACACAGTTCCTTCACGTTGAGGAAGTCTGATTATCTGAGGA
* * * * * * *
5245623 TGACACTGCTCCT-TCGCTTTAAGGAGATCTTGCCAATGAATGACATTATTCCTTTGTGTTGA
65 TGACACTGCTCCTCTAG--TTAAGGAGATCTGGTCAGTGGACGACATTATTCCTTCGTGTTGA
5245685 TGGCATCTAT
Statistics
Matches: 500, Mismatches: 137, Indels: 56
0.72 0.20 0.08
Matches are distributed among these distances:
126 46 0.09
127 3 0.01
128 31 0.06
129 7 0.01
130 2 0.00
131 1 0.00
132 2 0.00
133 4 0.01
134 4 0.01
135 57 0.11
136 48 0.10
137 48 0.10
138 41 0.08
139 199 0.40
140 6 0.01
141 1 0.00
ACGTcount: A:0.26, C:0.15, G:0.24, T:0.35
Consensus pattern (137 bp):
GTATTTGGGATAATTTGGAGACAACACAGTTCCTTCACGTTGAGGAAGTCTGATTATCTGAGGAT
GACACTGCTCCTCTAGTTAAGGAGATCTGGTCAGTGGACGACATTATTCCTTCGTGTTGAGGACG
TCTAGCT
Found at i:5245304 original size:274 final size:265
Alignment explanation
Indices: 5244865--5245594 Score: 867
Period size: 274 Copynumber: 2.7 Consensus size: 265
5244855 GCTTATTCAC
* * * * *
5244865 ATTGAGGACGTATAAAAGTATTTGGATATTTTGGAGACAACACAGTTCTTTCATGTTAAGGAAGT
1 ATTGAGGGCGTATAGAAGTATTTGGATAATTTGGAGACAACACAGTTCTTTCGTGTTGAGGAAGT
* * * * *
5244930 CTGATTATCTGAGGATGATACTGCTCCTCTAAGTTAAGGAGATCTGGTCAGTGGATGACATTATT
66 CTGATTATCTGAGGATGACACTGCTCCTTTACGTTAAGGAGATCTGGTCAGTGGACGACATTGTT
* * * *
5244995 CCTTTGTCTTGAGGACGTCTAGCCGTATTTGGAGATAATTTGGAGACAACACAGTTCCTTCACAT
131 CCTTCGTGTTGAGGACGTCTAGCTGTATTTGGAGATAATTTGGAGACAACACGGTTCCTTCACAT
* *
5245060 TAAGAAAG-TCTAATTATCTGAGGATGACATTGCTCATTCGTATTGAGAAGATCTAGTCAGTGGA
196 TAACAAAGCT-TAATTATCTGAGGATGACATTGCTCATTCGCATT-----GA---AG--AGT-GA
5245124 CAATATTAATTCTTC-A
249 CAATATTAATTCTTCGA
* * * * *
5245140 AGTTTA-GGCGTATAGATGTTTTTGGATAATTTGGAGAAAACATAGTTCCTTT-GTGTTGAGGAA
1 A-TTGAGGGCGTATAGAAGTATTTGGATAATTTGGAGACAACACAGTT-CTTTCGTGTTGAGGAA
* * * *
5245203 GT-TGATTATCTGAGGATGACACTGCTCATTTACGTTAAGGAGATCAGTTTAGTGGACGACATTG
64 GTCTGATTATCTGAGGATGACACTGCTCCTTTACGTTAAGGAGATCTGGTCAGTGGACGACATTG
* * * * *
5245267 TTCCTTCGTGTTAAGGACATCTAGCTGTATCTGGAGATAATTTGGATACAACACGGTTCATTCAC
129 TTCCTTCGTGTTGAGGACGTCTAGCTGTATTTGGAGATAATTTGGAGACAACACGGTTCCTTCAC
* * * **
5245332 ATTGACAAAGCTTGATTATCTGAGTATGACATTGCTCATTCGCATTGAAGAGTGACAATATTGTT
194 ATTAACAAAGCTTAATTATCTGAGGATGACATTGCTCATTCGCATTGAAGAGTGACAATATTAAT
*
5245397 TCTTCGC
259 TCTTCGA
*
5245404 ATTGAGGGCGTCTAGAAGTATTTGGATAATTTGGAGACAACACAGTTCTTTCGTGTTGAGGAAGT
1 ATTGAGGGCGTATAGAAGTATTTGGATAATTTGGAGACAACACAGTTCTTTCGTGTTGAGGAAGT
* * * * * * * *
5245469 CTAATTTTATGAGGATAACACTGGTCCTTTGCGTTGAGGAGATCTGGTCAGTGTACGACATTGTT
66 CTGATTATCTGAGGATGACACTGCTCCTTTACGTTAAGGAGATCTGGTCAGTGGACGACATTGTT
* * *
5245534 CCTTCGTGTTGAGGACGTCTAGCTGTATTTGGAGATAATTTTGAGCCAACACGGTTACTTC
131 CCTTCGTGTTGAGGACGTCTAGCTGTATTTGGAGATAATTTGGAGACAACACGGTTCCTTC
5245595 TCGTTGAGGA
Statistics
Matches: 386, Mismatches: 62, Indels: 24
0.82 0.13 0.05
Matches are distributed among these distances:
263 22 0.06
264 53 0.14
265 105 0.27
266 2 0.01
269 2 0.01
274 148 0.38
275 47 0.12
276 7 0.02
ACGTcount: A:0.27, C:0.15, G:0.24, T:0.34
Consensus pattern (265 bp):
ATTGAGGGCGTATAGAAGTATTTGGATAATTTGGAGACAACACAGTTCTTTCGTGTTGAGGAAGT
CTGATTATCTGAGGATGACACTGCTCCTTTACGTTAAGGAGATCTGGTCAGTGGACGACATTGTT
CCTTCGTGTTGAGGACGTCTAGCTGTATTTGGAGATAATTTGGAGACAACACGGTTCCTTCACAT
TAACAAAGCTTAATTATCTGAGGATGACATTGCTCATTCGCATTGAAGAGTGACAATATTAATTC
TTCGA
Found at i:5247853 original size:21 final size:21
Alignment explanation
Indices: 5247829--5247908 Score: 90
Period size: 21 Copynumber: 3.7 Consensus size: 21
5247819 TTTTCGTAAG
*
5247829 AGTACTTTGTGTAGTTGGTGA
1 AGTACTTTGTGTACTTGGTGA
**
5247850 AGTACTTTGTGTACTATGGAAA
1 AGTACTTTGTGTACT-TGGTGA
*
5247872 GAGTACTTTGTGTACTT-GTAGT
1 -AGTACTTTGTGTACTTGGT-GA
5247894 AGTACTTTGTGTACT
1 AGTACTTTGTGTACT
5247909 ATGGCACTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
21 30 0.60
22 5 0.10
23 15 0.30
ACGTcount: A:0.23, C:0.09, G:0.26, T:0.42
Consensus pattern (21 bp):
AGTACTTTGTGTACTTGGTGA
Found at i:5247898 original size:44 final size:44
Alignment explanation
Indices: 5247826--5247912 Score: 140
Period size: 44 Copynumber: 2.0 Consensus size: 44
5247816 GCATTTTCGT
*
5247826 AAGAGTACTTTGTGTAGTTGGTGAAGTACTTTGTGTACTATGGA
1 AAGAGTACTTTGTGTACTTGGTGAAGTACTTTGTGTACTATGGA
*
5247870 AAGAGTACTTTGTGTACTT-GTAGTAGTACTTTGTGTACTATGG
1 AAGAGTACTTTGTGTACTTGGT-GAAGTACTTTGTGTACTATGG
5247913 CACTTTGTGT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
43 2 0.05
44 38 0.95
ACGTcount: A:0.24, C:0.08, G:0.28, T:0.40
Consensus pattern (44 bp):
AAGAGTACTTTGTGTACTTGGTGAAGTACTTTGTGTACTATGGA
Found at i:5255135 original size:23 final size:21
Alignment explanation
Indices: 5255081--5255137 Score: 71
Period size: 21 Copynumber: 2.6 Consensus size: 21
5255071 TGCATTTCGT
5255081 AAGAGTACTTTGTGTACTTAG
1 AAGAGTACTTTGTGTACTTAG
*
5255102 -AGTAGTACTTTGTGTACTATGG
1 AAG-AGTACTTTGTGTACT-TAG
5255124 CAAGAGTACTTTGT
1 -AAGAGTACTTTGT
5255138 AGAACTTTGT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
20 2 0.06
21 15 0.48
22 2 0.06
23 10 0.32
24 2 0.06
ACGTcount: A:0.26, C:0.11, G:0.25, T:0.39
Consensus pattern (21 bp):
AAGAGTACTTTGTGTACTTAG
Found at i:5256454 original size:36 final size:36
Alignment explanation
Indices: 5256359--5256461 Score: 93
Period size: 36 Copynumber: 2.8 Consensus size: 36
5256349 AACAATTTCA
* *
5256359 AAATTTGTGTTTCAAGGGTAAACTATCTCAAGCGAGAC
1 AAATTT-TGTTTCAA-GGAAAACAATCTCAAGCGAGAC
* ** *
5256397 AAAATTTGTTTTTAGGAAAACAATCTCAAGTGAGATC
1 AAATTTTGTTTCAAGGAAAACAATCTCAAGCGAGA-C
*
5256434 -AATTTTGTTTCAAGTG-AAACAATTTCAA
1 AAATTTTGTTTCAAG-GAAAACAATCTCAA
5256462 AATTTGTGTT
Statistics
Matches: 53, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
36 40 0.75
37 8 0.15
38 5 0.09
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.33
Consensus pattern (36 bp):
AAATTTTGTTTCAAGGAAAACAATCTCAAGCGAGAC
Found at i:5256546 original size:97 final size:98
Alignment explanation
Indices: 5256332--5256550 Score: 280
Period size: 102 Copynumber: 2.2 Consensus size: 98
5256322 GGTAAGATAA
* * *
5256332 AATTTTGTTTCGAGGGAAACAATTTCAAAATTTGTGTTTCAAGGGTAAACTATCTCAAGCGAGAC
1 AATTTTGTTTCAAGTGAAACAATTTCAAAATTTGTGTTTCAAGGGAAAACTATCTCAAGCGAGAC
**
5256397 AAAATTTGTTTTTAGGAAAACAATCTCAAGTGAGATC
66 AAAA----TAATTAGGAAAACAATCTCAAGTGAGATC
** * * *
5256434 AATTTTGTTTCAAGTGAAACAATTTCAAAATTTGTGTTTTGAGGGAAAATTGTCTCAAGCGAGAT
1 AATTTTGTTTCAAGTGAAACAATTTCAAAATTTGTGTTTCAAGGGAAAACTATCTCAAGCGAGAC
*
5256499 AAAA-AATTAGGAAAA-AATTCTCAAGTTAGATC
66 AAAATAATTAGGAAAACAA-TCTCAAGTGAGATC
5256531 AATTTTGTTTCAAGTGAAAC
1 AATTTTGTTTCAAGTGAAAC
5256551 TGTCTCAAAC
Statistics
Matches: 105, Mismatches: 11, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
96 2 0.02
97 42 0.40
102 61 0.58
ACGTcount: A:0.38, C:0.11, G:0.18, T:0.33
Consensus pattern (98 bp):
AATTTTGTTTCAAGTGAAACAATTTCAAAATTTGTGTTTCAAGGGAAAACTATCTCAAGCGAGAC
AAAATAATTAGGAAAACAATCTCAAGTGAGATC
Found at i:5258308 original size:25 final size:24
Alignment explanation
Indices: 5258259--5258319 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 24
5258249 TTTTATTTTC
5258259 AAATTTTGAAAAAGATCAATTAAAA
1 AAATTTTGAAAAAGATCAA-TAAAA
* *
5258284 TAATTTTGAAAAATG-TTAATAAAA
1 AAATTTTGAAAAA-GATCAATAAAA
5258308 AAA-TTTGAAAAA
1 AAATTTTGAAAAA
5258320 AATATTGCCT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
23 9 0.28
24 7 0.22
25 15 0.47
26 1 0.03
ACGTcount: A:0.59, C:0.02, G:0.08, T:0.31
Consensus pattern (24 bp):
AAATTTTGAAAAAGATCAATAAAA
Found at i:5259206 original size:14 final size:15
Alignment explanation
Indices: 5259174--5259215 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
5259164 AATAAGTTCT
*
5259174 TTTTC-TTCTTCTTC
1 TTTTCTTTCTTTTTC
5259188 TTTTCTTTCTTTTTC
1 TTTTCTTTCTTTTTC
*
5259203 TTTCCTTT-TTTTT
1 TTTTCTTTCTTTTT
5259216 GTATTCTTGC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTTCTTTCTTTTTC
Found at i:5261843 original size:87 final size:85
Alignment explanation
Indices: 5261593--5261853 Score: 225
Period size: 87 Copynumber: 3.0 Consensus size: 85
5261583 ATATCAACCT
5261593 TTCCATTTAGTTCATAATAATCCTTCACTA-TATGATCATTTCCATAAATTATTAAAATTTCCAA
1 TTCCATTTAGTTCATAATAATCCTTCACTATTATGATCATTTCCATAAATTATTAAAATTTCCAA
*
5261657 CACCTTAATAATATACTCAA
66 CACCTTAATAATAAACTCAA
* * * * * ** * * **
5261677 TT-CA-ATACTTTA-ACATTCAAACACTTGCAAT-TTCATCCTCTATTTCCTTAGACTT-TTCGA
1 TTCCATTTAGTTCATA-A-T-AATC-CTT-CACTATT-ATGATC-ATTTCCATA-AATTATTAAA
*
5261737 A-TT-CAACCACCTCT-TTAATAAACTTGCAA
58 ATTTCCAA-CACCT-TAATAATAAAC-T-CAA
5261766 TTCCATTTAGTTCATAATAATCCTTCACTATTATGATCATTTCCATAAATTATTAAAATTTCCAA
1 TTCCATTTAGTTCATAATAATCCTTCACTATTATGATCATTTCCATAAATTATTAAAATTTCCAA
*
5261831 CACCTTAATAATATACTCAA
66 CACCTTAATAATAAACTCAA
5261851 TTC
1 TTC
5261854 AATACTTTAA
Statistics
Matches: 130, Mismatches: 26, Indels: 41
0.66 0.13 0.21
Matches are distributed among these distances:
81 1 0.01
82 6 0.05
83 3 0.02
84 5 0.04
85 12 0.09
86 21 0.16
87 39 0.30
88 22 0.17
89 11 0.08
90 3 0.02
91 6 0.05
92 1 0.01
ACGTcount: A:0.35, C:0.22, G:0.03, T:0.39
Consensus pattern (85 bp):
TTCCATTTAGTTCATAATAATCCTTCACTATTATGATCATTTCCATAAATTATTAAAATTTCCAA
CACCTTAATAATAAACTCAA
Found at i:5261882 original size:174 final size:174
Alignment explanation
Indices: 5261593--5261940 Score: 680
Period size: 174 Copynumber: 2.0 Consensus size: 174
5261583 ATATCAACCT
5261593 TTCCATTTAGTTCATAATAATCCTTCACTATATGATCATTTCCATAAATTATTAAAATTTCCAAC
1 TTCCATTTAGTTCATAATAATCCTTCACTATATGATCATTTCCATAAATTATTAAAATTTCCAAC
5261658 ACCTTAATAATATACTCAATTCAATACTTTAACATTCAAACACTTGCAATTTCATCCTCTATTTC
66 ACCTTAATAATATACTCAATTCAATACTTTAACATTCAAACACTTGCAATTTCATCCTCTATTTC
5261723 CTTAGACTTTTCGAATTCAACCACCTC-TTTAATAAACTTGCAA
131 CTTAGACTTTTCGAATTCAACCACCTCTTTTAATAAACTTGCAA
5261766 TTCCATTTAGTTCATAATAATCCTTCACTATTATGATCATTTCCATAAATTATTAAAATTTCCAA
1 TTCCATTTAGTTCATAATAATCCTTCACTA-TATGATCATTTCCATAAATTATTAAAATTTCCAA
5261831 CACCTTAATAATATACTCAATTCAATACTTTAACATTCAAACACTTGCAATTTCATCCTCTATTT
65 CACCTTAATAATATACTCAATTCAATACTTTAACATTCAAACACTTGCAATTTCATCCTCTATTT
5261896 CCTTAGACTTTTCGAATTCAACCACCTCTTTTAATAAACTTGCAA
130 CCTTAGACTTTTCGAATTCAACCACCTCTTTTAATAAACTTGCAA
5261941 GTCGCTCCCA
Statistics
Matches: 173, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
173 30 0.17
174 127 0.73
175 16 0.09
ACGTcount: A:0.34, C:0.23, G:0.03, T:0.39
Consensus pattern (174 bp):
TTCCATTTAGTTCATAATAATCCTTCACTATATGATCATTTCCATAAATTATTAAAATTTCCAAC
ACCTTAATAATATACTCAATTCAATACTTTAACATTCAAACACTTGCAATTTCATCCTCTATTTC
CTTAGACTTTTCGAATTCAACCACCTCTTTTAATAAACTTGCAA
Found at i:5263367 original size:29 final size:29
Alignment explanation
Indices: 5263280--5263368 Score: 70
Period size: 29 Copynumber: 3.0 Consensus size: 29
5263270 AAAAATATAT
* * * *
5263280 AACTTTTAGAACTTAAATTTTTTGTCCCTA
1 AACTTTCAAAACTTAAA-TTTTAGTCACTA
* * * *
5263310 AACTTTTCAAAATTTATACTTTAGCCACTA
1 AAC-TTTCAAAACTTAAATTTTAGTCACTA
* *
5263340 AACTTTCAAAACTTACATTTTGGTCACTA
1 AACTTTCAAAACTTAAATTTTAGTCACTA
5263369 CTAAAAATTT
Statistics
Matches: 45, Mismatches: 13, Indels: 3
0.74 0.21 0.05
Matches are distributed among these distances:
29 21 0.47
30 14 0.31
31 10 0.22
ACGTcount: A:0.34, C:0.19, G:0.06, T:0.42
Consensus pattern (29 bp):
AACTTTCAAAACTTAAATTTTAGTCACTA
Found at i:5264271 original size:24 final size:24
Alignment explanation
Indices: 5264244--5264316 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 24
5264234 ATTCGGCCAA
5264244 AGCAACATTTCATCCGTCCAATGC
1 AGCAACATTTCATCCGTCCAATGC
* ** * *
5264268 AGCAA-AATAAATTCGGCCAA---
1 AGCAACATTTCATCCGTCCAATGC
5264288 AGCAACATTTCATCCGTCCAATGC
1 AGCAACATTTCATCCGTCCAATGC
5264312 AGCAA
1 AGCAA
5264317 AATAAATCAT
Statistics
Matches: 35, Mismatches: 10, Indels: 8
0.66 0.19 0.15
Matches are distributed among these distances:
20 5 0.14
21 10 0.29
23 10 0.29
24 10 0.29
ACGTcount: A:0.37, C:0.29, G:0.14, T:0.21
Consensus pattern (24 bp):
AGCAACATTTCATCCGTCCAATGC
Found at i:5264297 original size:44 final size:44
Alignment explanation
Indices: 5264234--5264323 Score: 180
Period size: 44 Copynumber: 2.0 Consensus size: 44
5264224 GGTGAACTTT
5264234 ATTCGGCCAAAGCAACATTTCATCCGTCCAATGCAGCAAAATAA
1 ATTCGGCCAAAGCAACATTTCATCCGTCCAATGCAGCAAAATAA
5264278 ATTCGGCCAAAGCAACATTTCATCCGTCCAATGCAGCAAAATAA
1 ATTCGGCCAAAGCAACATTTCATCCGTCCAATGCAGCAAAATAA
5264322 AT
1 AT
5264324 CATTTCCTCA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.39, C:0.27, G:0.13, T:0.21
Consensus pattern (44 bp):
ATTCGGCCAAAGCAACATTTCATCCGTCCAATGCAGCAAAATAA
Found at i:5265065 original size:17 final size:17
Alignment explanation
Indices: 5265043--5265107 Score: 69
Period size: 17 Copynumber: 3.8 Consensus size: 17
5265033 TGAAGAAAAC
5265043 AAAGAAATAAAGTGTAA
1 AAAGAAATAAAGTGTAA
**
5265060 AAAGAAGA-AAAGTACAA
1 AAAGAA-ATAAAGTGTAA
*
5265077 CAAGTAAATAAAGTGTAA
1 AAAG-AAATAAAGTGTAA
*
5265095 AAAGAAAAAAAGT
1 AAAGAAATAAAGT
5265108 ACAGTAAGTA
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
17 25 0.66
18 13 0.34
ACGTcount: A:0.66, C:0.03, G:0.17, T:0.14
Consensus pattern (17 bp):
AAAGAAATAAAGTGTAA
Found at i:5265086 original size:35 final size:35
Alignment explanation
Indices: 5265047--5265119 Score: 119
Period size: 35 Copynumber: 2.1 Consensus size: 35
5265037 GAAAACAAAG
*
5265047 AAATAAAGTGTAAAAAGAAGAAAAGTACAACAAGT
1 AAATAAAGTGTAAAAAGAAAAAAAGTACAACAAGT
**
5265082 AAATAAAGTGTAAAAAGAAAAAAAGTACAGTAAGT
1 AAATAAAGTGTAAAAAGAAAAAAAGTACAACAAGT
5265117 AAA
1 AAA
5265120 CTCCGACAAC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.64, C:0.04, G:0.16, T:0.15
Consensus pattern (35 bp):
AAATAAAGTGTAAAAAGAAAAAAAGTACAACAAGT
Found at i:5269057 original size:21 final size:20
Alignment explanation
Indices: 5269029--5269068 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
5269019 CATTGGAGGA
*
5269029 ATTTATGGCCTCGACAAAAG
1 ATTTATGGCCTCAACAAAAG
*
5269049 ATTTCATGGCTTCAACAAAA
1 ATTT-ATGGCCTCAACAAAA
5269069 AACTTAATGC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.38, C:0.20, G:0.15, T:0.28
Consensus pattern (20 bp):
ATTTATGGCCTCAACAAAAG
Found at i:5286107 original size:21 final size:21
Alignment explanation
Indices: 5286081--5286120 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
5286071 TATAACAGAG
*
5286081 GGTATCGGTACCCCTTCATAA
1 GGTATCGGTACACCTTCATAA
5286102 GGTATCGGTACACCTTCAT
1 GGTATCGGTACACCTTCAT
5286121 TAAATTCAAA
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:0.23, C:0.28, G:0.20, T:0.30
Consensus pattern (21 bp):
GGTATCGGTACACCTTCATAA
Found at i:5286278 original size:20 final size:19
Alignment explanation
Indices: 5286216--5286284 Score: 67
Period size: 20 Copynumber: 3.7 Consensus size: 19
5286206 AGCAATCATA
5286216 GGTGTATGGATACACCTACAG
1 GGTGTATGGATACA-CT-CAG
5286237 GG-GTATCGG-TACAC-CA-
1 GGTGTAT-GGATACACTCAG
5286253 -GTGTATGGATACACTGCAG
1 GGTGTATGGATACACT-CAG
5286272 GGTGTATGGATAC
1 GGTGTATGGATAC
5286285 CCTTTGATAC
Statistics
Matches: 41, Mismatches: 0, Indels: 15
0.73 0.00 0.27
Matches are distributed among these distances:
15 3 0.07
16 9 0.22
17 2 0.05
18 2 0.05
19 1 0.02
20 20 0.49
21 4 0.10
ACGTcount: A:0.26, C:0.17, G:0.32, T:0.25
Consensus pattern (19 bp):
GGTGTATGGATACACTCAG
Found at i:5286538 original size:21 final size:19
Alignment explanation
Indices: 5286509--5286565 Score: 80
Period size: 21 Copynumber: 2.9 Consensus size: 19
5286499 ATGTTTAATG
5286509 AAAAAGATACCAATTGTTT
1 AAAAAGATACCAATTGTTT
5286528 ACAAAAGGATACCAATTG-TT
1 A-AAAA-GATACCAATTGTTT
*
5286548 AAAAATATACCAATTGTT
1 AAAAAGATACCAATTGTT
5286566 ACTAATTGTT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
18 10 0.29
19 6 0.18
20 7 0.21
21 11 0.32
ACGTcount: A:0.47, C:0.12, G:0.11, T:0.30
Consensus pattern (19 bp):
AAAAAGATACCAATTGTTT
Found at i:5286557 original size:18 final size:18
Alignment explanation
Indices: 5286509--5286566 Score: 80
Period size: 18 Copynumber: 3.1 Consensus size: 18
5286499 ATGTTTAATG
5286509 AAAAAGATACCAATTGTTT
1 AAAAAGATACCAATTG-TT
5286528 ACAAAAGGATACCAATTGTT
1 A-AAAA-GATACCAATTGTT
*
5286548 AAAAATATACCAATTGTT
1 AAAAAGATACCAATTGTT
5286566 A
1 A
5286567 CTAATTGTTG
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
18 13 0.36
19 5 0.14
20 7 0.19
21 11 0.31
ACGTcount: A:0.48, C:0.12, G:0.10, T:0.29
Consensus pattern (18 bp):
AAAAAGATACCAATTGTT
Found at i:5287713 original size:19 final size:19
Alignment explanation
Indices: 5287676--5287738 Score: 67
Period size: 19 Copynumber: 3.4 Consensus size: 19
5287666 TCTAAATCAT
*
5287676 TTTTCAAAATTTCATTTTAA
1 TTTTCAAAA-TTAATTTTAA
*
5287696 TTTTCAAAATTAATTTTAG
1 TTTTCAAAATTAATTTTAA
* *
5287715 CTTTCAAAATCAA-TTT-A
1 TTTTCAAAATTAATTTTAA
5287732 TTTTCAA
1 TTTTCAA
5287739 TTTTGAGTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
17 6 0.16
18 3 0.08
19 19 0.51
20 9 0.24
ACGTcount: A:0.37, C:0.11, G:0.02, T:0.51
Consensus pattern (19 bp):
TTTTCAAAATTAATTTTAA
Found at i:5288633 original size:32 final size:32
Alignment explanation
Indices: 5288591--5288656 Score: 78
Period size: 32 Copynumber: 2.1 Consensus size: 32
5288581 TTACAAACTC
* * *
5288591 CCTAGTTTTTCTCGGGCTAAACTAGAACCTTT
1 CCTAGCTTTTCACGGGATAAACTAGAACCTTT
* **
5288623 CCTAGCTTTTCACGGGATCAGTTAGAACCTTT
1 CCTAGCTTTTCACGGGATAAACTAGAACCTTT
5288655 CC
1 CC
5288657 CCTTTACAAT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.21, C:0.27, G:0.17, T:0.35
Consensus pattern (32 bp):
CCTAGCTTTTCACGGGATAAACTAGAACCTTT
Found at i:5289770 original size:17 final size:18
Alignment explanation
Indices: 5289737--5289770 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
5289727 TAGTGAACAG
*
5289737 TAATGTCTACAGCATCAA
1 TAATGTCTACAGAATCAA
5289755 TAATGT-TACAGAATCA
1 TAATGTCTACAGAATCA
5289771 GCATACCAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.41, C:0.18, G:0.12, T:0.29
Consensus pattern (18 bp):
TAATGTCTACAGAATCAA
Found at i:5295209 original size:21 final size:20
Alignment explanation
Indices: 5295163--5295210 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 20
5295153 TAATGTAAGT
* *
5295163 GTATCGATACTGAGGGTTTG
1 GTATTGATACTGAGGGCTTG
*
5295183 GAATTGATACTGAGGGGCTTG
1 GTATTGATACTGA-GGGCTTG
5295204 GTATTGA
1 GTATTGA
5295211 ACATGGGAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
20 11 0.48
21 12 0.52
ACGTcount: A:0.23, C:0.08, G:0.35, T:0.33
Consensus pattern (20 bp):
GTATTGATACTGAGGGCTTG
Found at i:5303087 original size:14 final size:15
Alignment explanation
Indices: 5302976--5303125 Score: 133
Period size: 15 Copynumber: 9.5 Consensus size: 15
5302966 TAATAAGGTT
5302976 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
5302991 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
5303006 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
*
5303021 ATTTACTTTAAAATA
1 ATTTATTTTAAAATA
* *
5303036 AATTATTATAAAATATGGA
1 ATTTATT-TTAAA-AT--A
5303055 TTGATTTATTTTAAAATA
1 ---ATTTATTTTAAAATA
5303073 ATTTATTTT-AAATA
1 ATTTATTTTAAAATA
* * *
5303087 ATTTATTAGTATGAATTG
1 ATTTATT--T-TAAAATA
5303105 ATTTATTTT-AAATA
1 ATTTATTTTAAAATA
5303119 ATTTATT
1 ATTTATT
5303126 AGTATGGATT
Statistics
Matches: 112, Mismatches: 12, Indels: 23
0.76 0.08 0.16
Matches are distributed among these distances:
14 22 0.20
15 57 0.51
16 6 0.05
17 3 0.03
18 11 0.10
19 1 0.01
20 2 0.02
21 4 0.04
22 6 0.05
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.51
Consensus pattern (15 bp):
ATTTATTTTAAAATA
Found at i:5303110 original size:18 final size:18
Alignment explanation
Indices: 5303087--5303143 Score: 59
Period size: 18 Copynumber: 3.4 Consensus size: 18
5303077 ATTTTAAATA
5303087 ATTTATTAGTATGAATTG
1 ATTTATTAGTATGAATTG
* *
5303105 ATTTATT--T-T-AAATA
1 ATTTATTAGTATGAATTG
*
5303119 ATTTATTAGTATGGATTG
1 ATTTATTAGTATGAATTG
5303137 ATTTATT
1 ATTTATT
5303144 TTAAAATATG
Statistics
Matches: 30, Mismatches: 5, Indels: 8
0.70 0.12 0.19
Matches are distributed among these distances:
14 10 0.33
15 1 0.03
16 2 0.07
17 1 0.03
18 16 0.53
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.54
Consensus pattern (18 bp):
ATTTATTAGTATGAATTG
Found at i:5303112 original size:32 final size:32
Alignment explanation
Indices: 5303073--5303148 Score: 143
Period size: 32 Copynumber: 2.4 Consensus size: 32
5303063 TTTTAAAATA
5303073 ATTTATTTTAAATAATTTATTAGTATGAATTG
1 ATTTATTTTAAATAATTTATTAGTATGAATTG
*
5303105 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGAATTG
5303137 ATTTATTTTAAA
1 ATTTATTTTAAA
5303149 ATATGGATTG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 43 1.00
ACGTcount: A:0.37, C:0.00, G:0.09, T:0.54
Consensus pattern (32 bp):
ATTTATTTTAAATAATTTATTAGTATGAATTG
Found at i:5303165 original size:54 final size:54
Alignment explanation
Indices: 5303096--5303814 Score: 544
Period size: 54 Copynumber: 13.6 Consensus size: 54
5303086 AATTTATTAG
*
5303096 TATGAATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
* *
5303150 TATGGATTGATTTA--TT--AT--TGTAGTT-GTGTGGATTGATTTATTTT-AAA
1 TATGGATTGATTTATTTTAAATAATTTA-TTAGTATGGATTGATTTATTTTAAAA
* * * * * * * *
5303197 TA---ATTTA-TTAGTATAGATTGATTTATTTTAAAATATGGGTTGATTCATTTT-AAA
1 TATGGATTGATTTATTTTA-AATAATTTA--TT--AGTATGGATTGATTTATTTTAAAA
** ** * ** * * * *
5303251 TAATTTATTAGTATGGA-TTGATTTATTTTA-AAATATGAATTGATTTATTTTAAAA
1 T-ATGGATT-G-ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
5303306 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
*
5303360 TATGGATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
* *
5303414 TATAGATTGATTTA--TT--AT--TGTAGTT-GTATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTA-TTAGTATGGATTGATTTATTTTAAAA
5303462 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
* ** ** * ** * * *
5303516 TATGAATTGATTTATTTTAAA-ATATGGATT-G-ATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTTAAATA-ATTTATTAGTATGGA-TTGATTTATTTTA-AAA
* *
5303570 TATAGATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
*
5303624 TATGGATTGATTTA--TT--AT--TGTAGTT-GTATGGATTGATTTATTTTAAATAATTTATTA
1 TATGGATTGATTTATTTTAAATAATTTA-TTAGTATGGATTGATTTA-TTT---TAA---A--A
* * * **
5303681 GTATGGATTGATTTATTTT-AA-AA--TA-TAG-ATTGATTTA-TTATTGTAGTTA
1 -TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTA-AAA
5303730 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
5303784 TATGGATTGATTTATTTTAAATAATTTATTA
1 TATGGATTGATTTATTTTAAATAATTTATTA
5303815 TTGTAGTTGT
Statistics
Matches: 529, Mismatches: 75, Indels: 122
0.73 0.10 0.17
Matches are distributed among these distances:
43 3 0.01
44 4 0.01
45 1 0.00
47 5 0.01
48 97 0.18
49 12 0.02
50 13 0.02
51 2 0.00
52 19 0.04
53 28 0.05
54 271 0.51
55 24 0.05
56 5 0.01
57 4 0.01
58 25 0.05
59 7 0.01
60 7 0.01
61 2 0.00
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.52
Consensus pattern (54 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
Found at i:5303204 original size:80 final size:82
Alignment explanation
Indices: 5303049--5303799 Score: 706
Period size: 80 Copynumber: 9.5 Consensus size: 82
5303039 TATTATAAAA
* * *
5303049 TATGGATTGATTTATTTTAAAATA---ATTTATTT-TAAATAATTTATTAGTATGAATTGATTTA
1 TATGGATTGATTTATTTTAAAATATGGATTGATTTATTAAT-ATTTATTAGTATGGATTGATTTA
5303110 TTTTAAATAATTTATTAG
65 TTTTAAATAATTTATTAG
* *
5303128 TATGGATTGATTTATTTTAAAATATGGATTGATTTATT-AT-TGTAGTT-GTGTGGATTGATTTA
1 TATGGATTGATTTATTTTAAAATATGGATTGATTTATTAATATTTA-TTAGTATGGATTGATTTA
5303190 TTTTAAATAATTTATTAG
65 TTTTAAATAATTTATTAG
* * *
5303208 TATAGATTGATTTATTTTAAAATATGGGTTGATTCATTTTAAATAATTTATTAGTATGGATTGAT
1 TATGGATTGATTTATTTTAAAATATGGATTGATT--TATT-AAT-ATTTATTAGTATGGATTGAT
5303273 TTATTTT-AA-AA--TA-T-G
62 TTATTTTAAATAATTTATTAG
5303288 -A---ATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGAT
1 TATGGATTGATTTATTTTAAAATATGGATTGATTTA--TT-AAT-ATTTATTAGTATGGATTGAT
5303349 TTA-TTT---TAA---A--A-
62 TTATTTTAAATAATTTATTAG
* * * * * * *
5303360 TATGGATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTTAT-TTTA-AAATATAGATTG
1 TATGGATTGATTTATTTT-AA-AA--TA--TGGATTGATTTATTAATATTTATTAGTATGGATTG
*
5303423 ATTTA--TT--AT--TGTAGTT-G
60 ATTTATTTTAAATAATTTA-TTAG
5303440 TATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGAT
1 TATGGATTGATTTATTTTAAAATATGGATTGATTTA--TT-AAT-ATTTATTAGTATGGATTGAT
5303505 TTATTTT-AA-AA--TA-T-G
62 TTATTTTAAATAATTTATTAG
*
5303520 -A---ATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGAT
1 TATGGATTGATTTATTTTAAAATATGGATTGATTTA--TT-AAT-ATTTATTAGTATGGATTGAT
*
5303581 TTATTTTAAATAATTTATTTG
62 TTATTTTAAATAATTTATTAG
*
5303602 TATGGATTGATTTATTTTAAAATATGGATTGATTTATT-AT-TGTAGTT-GTATGGATTGATTTA
1 TATGGATTGATTTATTTTAAAATATGGATTGATTTATTAATATTTA-TTAGTATGGATTGATTTA
5303664 TTTTAAATAATTTATTAG
65 TTTTAAATAATTTATTAG
* *
5303682 TATGGATTGATTTATTTTAAAATATAGATTGATTTATT-AT-TGTAGTTA-TATGGATTGATTTA
1 TATGGATTGATTTATTTTAAAATATGGATTGATTTATTAATATTTA-TTAGTATGGATTGATTTA
5303744 TTTTAAATAATTTATTAG
65 TTTTAAATAATTTATTAG
5303762 TATGGATTGATTTATTTTAAAATATGGATTGATTTATT
1 TATGGATTGATTTATTTTAAAATATGGATTGATTTATT
5303800 TTAAATAATT
Statistics
Matches: 583, Mismatches: 32, Indels: 113
0.80 0.04 0.16
Matches are distributed among these distances:
73 2 0.00
74 12 0.02
75 5 0.01
76 156 0.27
77 11 0.02
78 6 0.01
79 34 0.06
80 256 0.44
81 6 0.01
82 30 0.05
83 3 0.01
84 6 0.01
85 4 0.01
86 52 0.09
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.52
Consensus pattern (82 bp):
TATGGATTGATTTATTTTAAAATATGGATTGATTTATTAATATTTATTAGTATGGATTGATTTAT
TTTAAATAATTTATTAG
Found at i:5303239 original size:22 final size:22
Alignment explanation
Indices: 5303212--5303558 Score: 118
Period size: 22 Copynumber: 13.8 Consensus size: 22
5303202 TATTAGTATA
5303212 GATTGATTTATTTTAAAATATG
1 GATTGATTTATTTTAAAATATG
* *
5303234 GGTTGATTCATTTTAAATAATTTATTAG
1 GATTGATTTATTTT-AA-AA--TA-T-G
* * *
5303262 TATGGATTGATTTATTTTAAAATATG
1 GATTGATTTA-TT--TT-AAAATATG
*
5303288 AATTGATTTATTTTAAAATATG
1 GATTGATTTATTTTAAAATATG
5303310 GATTGATTTATTTTAAATAATTTATTAG
1 GATTGATTTATTTT-AA-AA--TA-T-G
* * *
5303338 TATGGATTGATTTATTTTAAAATATG
1 GATTGATTTA-TT---TTAAAATATG
5303364 GATTGATTTATTTTAAATAATTTATTTG
1 GATTGATTTATTTT-AA-AA--TA--TG
* * * *
5303392 TATGGATTGATTTATTTTAAAATATA
1 GATTGATTTA-TT---TTAAAATATG
***
5303418 GATTGATTTATTATTGTAGTTGTATG
1 GATTGATTTA-T-TT-TA-AAATATG
5303444 GATTGATTTATTTTAAAATATG
1 GATTGATTTATTTTAAAATATG
5303466 GATTGATTTATTTTAAATAATTTATTAG
1 GATTGATTTATTTT-AA-AA--TA-T-G
* * *
5303494 TATGGATTGATTTATTTTAAAATATG
1 GATTGATTTA-TT---TTAAAATATG
*
5303520 AATTGATTTATTTTAAAATATG
1 GATTGATTTATTTTAAAATATG
5303542 GATTGATTTATTTTAAA
1 GATTGATTTATTTTAAA
5303559 TAATTTATTA
Statistics
Matches: 245, Mismatches: 38, Indels: 84
0.67 0.10 0.23
Matches are distributed among these distances:
22 79 0.32
23 12 0.05
24 11 0.04
25 9 0.04
26 55 0.22
27 7 0.03
28 40 0.16
29 8 0.03
30 8 0.03
31 10 0.04
32 6 0.02
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (22 bp):
GATTGATTTATTTTAAAATATG
Found at i:5303334 original size:210 final size:203
Alignment explanation
Indices: 5303096--5303799 Score: 731
Period size: 210 Copynumber: 3.3 Consensus size: 203
5303086 AATTTATTAG
5303096 TATGAATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
1 TATGAATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
* * * * *
5303161 TTATTATTGTAGTTGTGTGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTT
66 TTATTATT-TATTTGTATGGATTGATTTATTTT-AA-AA--TA-TAG-ATTGATTTA-TTATTGT
*** * *
5303226 A-AAATATGGGTTGATTCATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGAA
123 AGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGAA
5303290 TTGATTTATTTTAAAA
188 TTGATTTATTTTAAAA
*
5303306 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
1 TATGAATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
5303371 TTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATAGATTGATTTATTATTGTA
66 TTA---T---T-ATTTATTTGTATGGATTGATTTATTTTAAAATATAGATTGATTTATTATTGTA
** ** * ** * * *
5303436 GTTGTATGGATTGATTTATTTTAAA-ATATGGATT-G-ATTTATTTTAAATAATTTATTAGTATG
124 GTTGTATGGATTGATTTATTTTAAATA-ATTTATTAGTATGGA-TTGATTTATTTTA-AAATATG
*
5303498 GATTGATTTATTTTAAAA
186 AATTGATTTATTTTAAAA
* * ** * * * *
5303516 TATGAATTGATTTATTTTAAAATATGGATTGATTTA-TTTTAAATAATTTATTAGTATAGAT-T-
1 TATGAATTGATTTATTTT-AAATA---ATTTA-TTAGTATGGATTGATTTATT-TTA-AAATATG
* * *
5303578 GATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATT
59 GATTGA-TTT--ATTATTTATTTGTATGGATTGATTTATTTTAAAATATAGATTGATTTATTATT
5303643 GTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATAT-
121 GTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATG
**
5303707 AGATTGATTTATTATTGTAGTTA
186 A-ATTGATTTA-T-TT-TA-AAA
*
5303730 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
1 TATGAATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
5303795 TTATT
66 TTATT
5303800 TTAAATAATT
Statistics
Matches: 404, Mismatches: 58, Indels: 67
0.76 0.11 0.13
Matches are distributed among these distances:
207 2 0.00
208 6 0.01
209 27 0.07
210 252 0.62
211 20 0.05
212 7 0.02
213 8 0.02
214 41 0.10
215 11 0.03
216 26 0.06
217 4 0.01
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.52
Consensus pattern (203 bp):
TATGAATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
TTATTATTTATTTGTATGGATTGATTTATTTTAAAATATAGATTGATTTATTATTGTAGTTGTAT
GGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGAATTGATTTA
TTTTAAAA
Found at i:5303566 original size:14 final size:14
Alignment explanation
Indices: 5303547--5303600 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
5303537 ATATGGATTG
5303547 ATTTATTTTAAATA
1 ATTTATTTTAAATA
* *
5303561 ATTTATTAGTATAGATTG
1 ATTTATT--T-TA-AATA
5303579 ATTTATTTTAAATA
1 ATTTATTTTAAATA
5303593 ATTTATTT
1 ATTTATTT
5303601 GTATGGATTG
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
14 17 0.53
15 2 0.06
16 2 0.06
17 2 0.06
18 9 0.28
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (14 bp):
ATTTATTTTAAATA
Found at i:5303653 original size:26 final size:25
Alignment explanation
Indices: 5303602--5303745 Score: 102
Period size: 26 Copynumber: 5.6 Consensus size: 25
5303592 AATTTATTTG
**
5303602 TATGGATTGATTTA-T-TT-TAAAA
1 TATGGATTGATTTATTATTGTATTA
*
5303624 TATGGATTGATTTATTATTGTAGTTG
1 TATGGATTGATTTATTATTGTA-TTA
*
5303650 TATGGATTGATTTATTTTAAATAATTTATTA
1 TATGGATTGATTTA--TT--AT--TGTATTA
**
5303681 GTATGGATTGATTTA-T-TT-TAAAA
1 -TATGGATTGATTTATTATTGTATTA
*
5303704 TATAGATTGATTTATTATTGTAGTTA
1 TATGGATTGATTTATTATTGTA-TTA
5303730 TATGGATTGATTTATT
1 TATGGATTGATTTATT
5303746 TTAAATAATT
Statistics
Matches: 96, Mismatches: 11, Indels: 26
0.72 0.08 0.20
Matches are distributed among these distances:
22 27 0.28
23 5 0.05
24 5 0.05
25 4 0.04
26 31 0.32
28 2 0.02
29 1 0.01
30 2 0.02
31 2 0.02
32 17 0.18
ACGTcount: A:0.31, C:0.00, G:0.16, T:0.53
Consensus pattern (25 bp):
TATGGATTGATTTATTATTGTATTA
Found at i:5303787 original size:22 final size:22
Alignment explanation
Indices: 5303762--5303804 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
5303752 AATTTATTAG
5303762 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
5303784 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
5303805 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:5303864 original size:31 final size:31
Alignment explanation
Indices: 5303829--5303887 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
5303819 AGTTGTATGG
* *
5303829 ATTATTTAAATTTCAGTATTGTAAAACTAAA
1 ATTATTTAAATCTCAGTATTGCAAAACTAAA
5303860 ATTATTTAAATCTCAGTATTGCAAAACT
1 ATTATTTAAATCTCAGTATTGCAAAACT
5303888 CTTTTAAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.42, C:0.10, G:0.07, T:0.41
Consensus pattern (31 bp):
ATTATTTAAATCTCAGTATTGCAAAACTAAA
Found at i:5303928 original size:16 final size:16
Alignment explanation
Indices: 5303907--5303947 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
5303897 TTAAAAAATC
5303907 AGTTTATTTATATTTT
1 AGTTTATTTATATTTT
5303923 AGTTTATTTATATTTT
1 AGTTTATTTATATTTT
*
5303939 AGTTCATTT
1 AGTTTATTT
5303948 TAGCAGTCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.24, C:0.02, G:0.07, T:0.66
Consensus pattern (16 bp):
AGTTTATTTATATTTT
Found at i:5306659 original size:21 final size:21
Alignment explanation
Indices: 5306635--5306694 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 21
5306625 GCAAATTCGC
5306635 GTTGCATTTCGCGTTGCGAAA
1 GTTGCATTTCGCGTTGCGAAA
* ** *
5306656 GTTGAAAATCGCGTTGCG-AT
1 GTTGCATTTCGCGTTGCGAAA
* *
5306676 TTTTCATTTCGCGTTGCGA
1 GTTGCATTTCGCGTTGCGA
5306695 TAGTCTACAA
Statistics
Matches: 29, Mismatches: 9, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
20 14 0.48
21 15 0.52
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.37
Consensus pattern (21 bp):
GTTGCATTTCGCGTTGCGAAA
Found at i:5307401 original size:5 final size:5
Alignment explanation
Indices: 5307387--5307417 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
5307377 CCGCCGCCGC
5307387 CGTC- CGTCT CGTCT CGTCT CGTCT CGTCT CG
1 CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CG
5307418 GGTCGTGGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.00, C:0.42, G:0.23, T:0.35
Consensus pattern (5 bp):
CGTCT
Found at i:5307429 original size:6 final size:6
Alignment explanation
Indices: 5307418--5307444 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
5307408 TCTCGTCTCG
5307418 GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGT
5307445 AATACGTGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.15, G:0.52, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:5307582 original size:22 final size:22
Alignment explanation
Indices: 5307556--5307609 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
5307546 AATTTGGAAA
5307556 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
*
5307578 ATCGCAACAACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
5307600 ATCGCAACGA
1 ATCGCAACGA
5307610 ATTTGGAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.39, C:0.28, G:0.17, T:0.17
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:5309161 original size:13 final size:13
Alignment explanation
Indices: 5309143--5309172 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
5309133 GCGATAAATG
5309143 GTCAACGGGTCGC
1 GTCAACGGGTCGC
*
5309156 GTCAACGGGTCGG
1 GTCAACGGGTCGC
5309169 GTCA
1 GTCA
5309173 GCCGGTTCAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.17, C:0.27, G:0.40, T:0.17
Consensus pattern (13 bp):
GTCAACGGGTCGC
Found at i:5309470 original size:6 final size:6
Alignment explanation
Indices: 5309454--5309491 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
5309444 TCTCGGGTCA
5309454 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
5309492 AATACGTGTC
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.16
6 27 0.84
ACGTcount: A:0.00, C:0.16, G:0.53, T:0.32
Consensus pattern (6 bp):
GGTCGT
Found at i:5309674 original size:22 final size:22
Alignment explanation
Indices: 5309593--5309667 Score: 141
Period size: 22 Copynumber: 3.4 Consensus size: 22
5309583 AATTTGGAAA
5309593 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
*
5309615 ATCGCAACAACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
5309637 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
5309659 ATCGCAACG
1 ATCGCAACG
5309668 CGAACTGGAA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 51 1.00
ACGTcount: A:0.37, C:0.28, G:0.17, T:0.17
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:5310312 original size:23 final size:23
Alignment explanation
Indices: 5310282--5310328 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
5310272 AGATTAATAA
5310282 TTTTTCTACTAAAATTAAAACAT
1 TTTTTCTACTAAAATTAAAACAT
5310305 TTTTTCTACTAAAATTAAAACAT
1 TTTTTCTACTAAAATTAAAACAT
5310328 T
1 T
5310329 AAACTTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.43, C:0.13, G:0.00, T:0.45
Consensus pattern (23 bp):
TTTTTCTACTAAAATTAAAACAT
Found at i:5311395 original size:39 final size:39
Alignment explanation
Indices: 5311333--5311407 Score: 114
Period size: 39 Copynumber: 1.9 Consensus size: 39
5311323 CACATTTATA
5311333 CAATAATGTCCCACAATTATGAAAACTTATAAAATATCC
1 CAATAATGTCCCACAATTATGAAAACTTATAAAATATCC
** * *
5311372 CAATAATGTCCCATGATTCTGAAAACTTGTAAAATA
1 CAATAATGTCCCACAATTATGAAAACTTATAAAATA
5311408 GCCCCTTTTC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 32 1.00
ACGTcount: A:0.44, C:0.19, G:0.08, T:0.29
Consensus pattern (39 bp):
CAATAATGTCCCACAATTATGAAAACTTATAAAATATCC
Found at i:5313069 original size:76 final size:76
Alignment explanation
Indices: 5312917--5313124 Score: 283
Period size: 76 Copynumber: 2.7 Consensus size: 76
5312907 CAAAGCCAAA
* * * * **
5312917 AATTACAGATTGCTCAGAGGGAACCGATTCCCCTCCATAGGAGGAACCGATTCCCCCCTGAATGG
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCC-CCATAGGAGGAACCGATTCCCCCCTAAACAG
5312982 TTTGGCCCCGAG
65 TTTGGCCCCGAG
*
5312994 ATTTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
* *
5313059 TTTGCTCCGAG
66 TTGGCCCCGAG
* * * *
5313070 AATTCCAGTATGCTTGGAGGGAACCGATTCCCCCCA-AGGGGGTACCGATTCCCCC
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCC
5313125 TTGTACAACG
Statistics
Matches: 117, Mismatches: 14, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
75 17 0.15
76 71 0.61
77 29 0.25
ACGTcount: A:0.24, C:0.31, G:0.24, T:0.21
Consensus pattern (76 bp):
AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
TTGGCCCCGAG
Found at i:5318946 original size:23 final size:21
Alignment explanation
Indices: 5318894--5318955 Score: 81
Period size: 23 Copynumber: 2.9 Consensus size: 21
5318884 TTTTGGTGCA
*
5318894 GAGGGAATCGA-TCCCCCCTT
1 GAGGGAACCGATTCCCCCCTT
*
5318914 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCCTT
5318935 GAAGGGGAACCGATTCCCCCC
1 G-A-GGGAACCGATTCCCCCC
5318956 CACAGGGGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
20 10 0.28
21 9 0.25
22 1 0.03
23 16 0.44
ACGTcount: A:0.21, C:0.35, G:0.26, T:0.18
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCTT
Found at i:5320954 original size:15 final size:15
Alignment explanation
Indices: 5320934--5320975 Score: 57
Period size: 17 Copynumber: 2.7 Consensus size: 15
5320924 CTTTTTGAAT
*
5320934 ATTTTGGATTGTTTG
1 ATTTTGGATTGTTGG
5320949 ATTTTGTGGATTGTTGG
1 A-TTT-TGGATTGTTGG
5320966 ATTTTGGATT
1 ATTTTGGATT
5320976 TATTAATGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 7 0.29
16 6 0.25
17 11 0.46
ACGTcount: A:0.14, C:0.00, G:0.29, T:0.57
Consensus pattern (15 bp):
ATTTTGGATTGTTGG
Found at i:5320960 original size:17 final size:17
Alignment explanation
Indices: 5320938--5320971 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
5320928 TTGAATATTT
*
5320938 TGGATTGTTTGATTTTG
1 TGGATTGTTGGATTTTG
5320955 TGGATTGTTGGATTTTG
1 TGGATTGTTGGATTTTG
5320972 GATTTATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.12, C:0.00, G:0.32, T:0.56
Consensus pattern (17 bp):
TGGATTGTTGGATTTTG
Found at i:5321768 original size:77 final size:76
Alignment explanation
Indices: 5321580--5321790 Score: 280
Period size: 76 Copynumber: 2.8 Consensus size: 76
5321570 CAAAGCCAAA
* * * * **
5321580 AATTACAGATTGCTCAGAGGGAACCGATTCCCCTCCATAGGAGGAACCGATTCCCCCCCTGAATG
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCC-CCATAGGAGGAACCGATT-CCCCCCTAAACA
5321645 GTTTGGCCCCGAG
64 GTTTGGCCCCGAG
* *
5321658 ATTTCCAGAATGCTCGGAGGGAACTGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
* *
5321723 TTTGCTCCGAG
66 TTGGCCCCGAG
* * *
5321734 AATTCCAGTATGCTCGGAGGGAACCGATTCCCCCCA-AGGGGGTACCGATTCCCCCCT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCT
5321791 TGTACAACGG
Statistics
Matches: 118, Mismatches: 15, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
75 19 0.16
76 53 0.45
77 18 0.15
78 28 0.24
ACGTcount: A:0.24, C:0.32, G:0.24, T:0.21
Consensus pattern (76 bp):
AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
TTGGCCCCGAG
Found at i:5322956 original size:30 final size:30
Alignment explanation
Indices: 5322922--5322978 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
5322912 CACTATTGTA
*
5322922 CTTCTTTTTTATTTATTTCTCAAGTGTGTT
1 CTTCTATTTTATTTATTTCTCAAGTGTGTT
5322952 CTTCTATTTTATTTATTTCTCAAGTGT
1 CTTCTATTTTATTTATTTCTCAAGTGT
5322979 TTTTATTTGC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.16, C:0.14, G:0.09, T:0.61
Consensus pattern (30 bp):
CTTCTATTTTATTTATTTCTCAAGTGTGTT
Found at i:5322985 original size:26 final size:29
Alignment explanation
Indices: 5322922--5322986 Score: 91
Period size: 30 Copynumber: 2.3 Consensus size: 29
5322912 CACTATTGTA
*
5322922 CTTCTTTTTTATTTATTTCTCAAGTGTGTT
1 CTTCTATTTTATTTATTTCTCAAG-GTGTT
5322952 CTTCTATTTTATTTATTTCTCAA-GTGTT
1 CTTCTATTTTATTTATTTCTCAAGGTGTT
5322980 -TT-TATTT
1 CTTCTATTT
5322987 GCTCTAGAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
26 5 0.15
27 2 0.06
28 5 0.15
30 22 0.65
ACGTcount: A:0.15, C:0.12, G:0.08, T:0.65
Consensus pattern (29 bp):
CTTCTATTTTATTTATTTCTCAAGGTGTT
Done.