Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 135709677
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: 135709677
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 350 characters in sequence are not A, C, G, or T
File 22 of 438
Found at i:5779960 original size:19 final size:20
Alignment explanation
Indices: 5779934--5779982 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 20
5779924 TAATACAAGT
5779934 AAAA-AATAATAA-CGATGA
1 AAAATAATAATAATCGATGA
**
5779952 AAAATAATAATAATTTATGA
1 AAAATAATAATAATCGATGA
5779972 AAAATAA-AATA
1 AAAATAATAATA
5779983 TAATAAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
18 4 0.15
19 12 0.44
20 11 0.41
ACGTcount: A:0.67, C:0.02, G:0.06, T:0.24
Consensus pattern (20 bp):
AAAATAATAATAATCGATGA
Found at i:5779992 original size:7 final size:7
Alignment explanation
Indices: 5779888--5780038 Score: 52
Period size: 7 Copynumber: 21.4 Consensus size: 7
5779878 TATATATGTA
5779888 AAATAAT
1 AAATAAT
*
5779895 ATATAAT
1 AAATAAT
5779902 --AT-AT
1 AAATAAT
5779906 AAATAAT
1 AAATAAT
*
5779913 TAATAAAT
1 AAAT-AAT
*
5779921 ACATAAT
1 AAATAAT
*
5779928 ACAAGTAAA
1 A-AA-TAAT
5779937 AAATAAT
1 AAATAAT
5779944 AACGATGAA-
1 AA--AT-AAT
5779953 AAATAAT
1 AAATAAT
5779960 -AATAAT
1 AAATAAT
**
5779966 TTATGAA-
1 AAAT-AAT
5779973 AAATAA-
1 AAATAAT
5779979 AATATAAT
1 AA-ATAAT
5779987 AAATAAT
1 AAATAAT
5779994 -AAT-AT
1 AAATAAT
5779999 AAATAAT
1 AAATAAT
*
5780006 ATATAAAT
1 AAAT-AAT
*
5780014 AGATAATT
1 AAATAA-T
*
5780022 ATATAAT
1 AAATAAT
5780029 ATAAT-AT
1 A-AATAAT
5780036 AAA
1 AAA
5780039 AGTAAGGTTT
Statistics
Matches: 111, Mismatches: 14, Indels: 39
0.68 0.09 0.24
Matches are distributed among these distances:
4 2 0.02
5 4 0.04
6 22 0.20
7 47 0.42
8 26 0.23
9 8 0.07
10 2 0.02
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.31
Consensus pattern (7 bp):
AAATAAT
Found at i:5780000 original size:12 final size:12
Alignment explanation
Indices: 5779985--5780038 Score: 67
Period size: 12 Copynumber: 4.4 Consensus size: 12
5779975 ATAAAATATA
5779985 ATAAATAATAAT
1 ATAAATAATAAT
5779997 ATAAATAAT-AT
1 ATAAATAATAAT
5780008 ATAAATAGATAATT
1 ATAAATA-ATAA-T
5780022 ATATAAT-ATAAT
1 ATA-AATAATAAT
5780034 ATAAA
1 ATAAA
5780039 AGTAAGGTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
11 11 0.29
12 15 0.39
13 5 0.13
14 4 0.11
15 3 0.08
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (12 bp):
ATAAATAATAAT
Found at i:5780002 original size:26 final size:26
Alignment explanation
Indices: 5779973--5780037 Score: 78
Period size: 26 Copynumber: 2.5 Consensus size: 26
5779963 AATTTATGAA
5779973 AAATAAAATATAATAAATAATAATAT
1 AAATAAAATATAATAAATAATAATAT
* * *
5779999 AAATAATATATAAATAGATAATTATAT
1 AAATAAAATAT-AATAAATAATAATAT
*
5780026 -AATATAATATAA
1 AAATAAAATATAA
5780038 AAGTAAGGTT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
25 2 0.06
26 18 0.55
27 13 0.39
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.34
Consensus pattern (26 bp):
AAATAAAATATAATAAATAATAATAT
Found at i:5780027 original size:23 final size:23
Alignment explanation
Indices: 5779979--5780031 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
5779969 TGAAAAATAA
5779979 AATATAATAAATAATAATATAAAT
1 AATAT-ATAAATAATAATATAAAT
*
5780003 AATATATAAATAGATAAT-TATAT
1 AATATATAAATA-ATAATATAAAT
5780026 AATATA
1 AATATA
5780032 ATATAAAAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 17 0.63
24 10 0.37
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (23 bp):
AATATATAAATAATAATATAAAT
Found at i:5780038 original size:26 final size:26
Alignment explanation
Indices: 5779974--5780038 Score: 71
Period size: 27 Copynumber: 2.5 Consensus size: 26
5779964 ATTTATGAAA
*
5779974 AATAAAATAT-AATAAATAATAATAT
1 AATATAATATAAATAAATAATAATAT
* *
5779999 AA-ATAATATATAAATAGATAATTATAT
1 AATAT-A-ATATAAATAAATAATAATAT
5780026 AATATAATATAAA
1 AATATAATATAAA
5780039 AGTAAGGTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
24 1 0.03
25 3 0.09
26 11 0.33
27 16 0.48
28 2 0.06
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.34
Consensus pattern (26 bp):
AATATAATATAAATAAATAATAATAT
Found at i:5782054 original size:206 final size:206
Alignment explanation
Indices: 5781700--5782325 Score: 1042
Period size: 206 Copynumber: 3.0 Consensus size: 206
5781690 GAAGGTGAGG
* ** * * *
5781700 TCTGCTATGTATCTGCTTTCCGTTGAAGTGGAGATGCTAGACTTCGATTTGCTCTCTGACAATAC
1 TCTGCTATGTGTCTGCCCTCTGTTGAAGTGGAGATGCCAGACTTCGATTTGCTCTCTGCCAATAC
5781765 A-AAGATGCCAAATCATCTTAGATTTGCTTCATCGTAAACACGTGAAAGCCAAATCAGCTATGTC
66 AGAA-ATGCCAAATCATCTTAGATTTGCTTCATCGTAAACACGTGAAAGCCAAATCAGCTATGTC
*
5781829 TTCGATTTGCTCCTTGTAAGCACAGGGATGCCAAATCATCTTGGATCTTGCTTCAGTCTAATCAT
130 TTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAATCATCTTGGATCTTGCTTCAGTCTAATCAT
5781894 CTGAAGGCCAGA
195 CTGAAGGCCAGA
*
5781906 TCTGCTATGTGTCTGCCCTCTGTCGAAGTGGAGATGCCAGACTTCGATTTGCTCTCTGCCAATAC
1 TCTGCTATGTGTCTGCCCTCTGTTGAAGTGGAGATGCCAGACTTCGATTTGCTCTCTGCCAATAC
5781971 AGAAATGCCAAATCATCTTAGATTTGCTTCATCGTAAACACGTGAAAGCCAAATCAGCTATGTCT
66 AGAAATGCCAAATCATCTTAGATTTGCTTCATCGTAAACACGTGAAAGCCAAATCAGCTATGTCT
5782036 TCGATTTGCTCCTTGTAAGCACAAGGATGCCAAATCATCTTGGATCTTGCTTCAGTCTAATCATC
131 TCGATTTGCTCCTTGTAAGCACAAGGATGCCAAATCATCTTGGATCTTGCTTCAGTCTAATCATC
5782101 TGAAGGCCAGA
196 TGAAGGCCAGA
5782112 TCTGCTATGTGTCTGCCCTCTGTTGAAGTGGAGATGCCAGACTTCGATTTGCTCTCTGCCAATAC
1 TCTGCTATGTGTCTGCCCTCTGTTGAAGTGGAGATGCCAGACTTCGATTTGCTCTCTGCCAATAC
* * * *
5782177 AGAGATGCCAAATCATCTTAGATTCGCTTCATCGTAATCACATGAAAGCCAAATCAGCTATGTCT
66 AGAAATGCCAAATCATCTTAGATTTGCTTCATCGTAAACACGTGAAAGCCAAATCAGCTATGTCT
* * * * *
5782242 TCGATTTGTTCCTTGTAAGCACAAGGATACCAAACCATCTTGGATC-TACTTCAG-CATAAGCAT
131 TCGATTTGCTCCTTGTAAGCACAAGGATGCCAAATCATCTTGGATCTTGCTTCAGTC-TAATCAT
**
5782305 CTGAAGGTGAGA
195 CTGAAGGCCAGA
5782317 TCTGCTATG
1 TCTGCTATG
5782326 CTGCGGCCTA
Statistics
Matches: 398, Mismatches: 20, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
204 1 0.00
205 32 0.08
206 363 0.91
207 2 0.01
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (206 bp):
TCTGCTATGTGTCTGCCCTCTGTTGAAGTGGAGATGCCAGACTTCGATTTGCTCTCTGCCAATAC
AGAAATGCCAAATCATCTTAGATTTGCTTCATCGTAAACACGTGAAAGCCAAATCAGCTATGTCT
TCGATTTGCTCCTTGTAAGCACAAGGATGCCAAATCATCTTGGATCTTGCTTCAGTCTAATCATC
TGAAGGCCAGA
Found at i:5794569 original size:61 final size:61
Alignment explanation
Indices: 5794504--5794640 Score: 167
Period size: 60 Copynumber: 2.3 Consensus size: 61
5794494 CAGTGTTAAC
* * *
5794504 TGGGCCTTAGCCCATATCAATATTAATTTGGGCCATAGCCC-CTTAC-AGTATC-AGAGTATAT
1 TGGGCCTTAGCCCATATCAATATCAATTTGGGCCACAGCCCTATTACAAG--TCGAGA-TATAT
* *
5794565 TGGGCC-TAGCCCATATCAGTATCAATTTGGGCCGCAGCCCTATTACAAGTCGAGATATAT
1 TGGGCCTTAGCCCATATCAATATCAATTTGGGCCACAGCCCTATTACAAGTCGAGATATAT
5794625 TGGGCCTT-GCCCATAT
1 TGGGCCTTAGCCCATAT
5794641 TAACATAGTT
Statistics
Matches: 67, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
60 51 0.76
61 14 0.21
62 2 0.03
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.29
Consensus pattern (61 bp):
TGGGCCTTAGCCCATATCAATATCAATTTGGGCCACAGCCCTATTACAAGTCGAGATATAT
Found at i:5797384 original size:33 final size:32
Alignment explanation
Indices: 5797340--5797407 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 32
5797330 ACCAACATAC
*
5797340 AAAGTATAATTAAATAATGCATAATATACAAA
1 AAAGTATAATTAAATAATGCATAACATACAAA
*
5797372 AAAGTGATAATTAAATAATGCATGACATACAAA
1 AAAGT-ATAATTAAATAATGCATAACATACAAA
5797405 AAA
1 AAA
5797408 AAAAGTAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
32 5 0.15
33 28 0.85
ACGTcount: A:0.59, C:0.07, G:0.09, T:0.25
Consensus pattern (32 bp):
AAAGTATAATTAAATAATGCATAACATACAAA
Found at i:5797768 original size:23 final size:23
Alignment explanation
Indices: 5797733--5797801 Score: 58
Period size: 23 Copynumber: 3.0 Consensus size: 23
5797723 AATTTATATT
5797733 TATA-ATAAA-ATAATTATATAA
1 TATATATAAATATAATTATATAA
*
5797754 TATATATAAATATAAGTT-TAGAA
1 TATATATAAATATAA-TTATATAA
5797777 TA-ATATGAAATAAGTAATTA-ATAA
1 TATATAT-AAAT-A-TAATTATATAA
5797801 T
1 T
5797802 GAAATATACG
Statistics
Matches: 39, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
21 4 0.10
22 9 0.23
23 14 0.36
24 9 0.23
25 3 0.08
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.38
Consensus pattern (23 bp):
TATATATAAATATAATTATATAA
Found at i:5797854 original size:35 final size:35
Alignment explanation
Indices: 5797815--5797886 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
5797805 ATATACGTAT
5797815 TGCACAAATTATTATATTATAATATCCTCAAAATG
1 TGCACAAATTATTATATTATAATATCCTCAAAATG
5797850 TGCACAAATTATTATATTATAATATCCTCAAAATG
1 TGCACAAATTATTATATTATAATATCCTCAAAATG
5797885 TG
1 TG
5797887 TAATAATAGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.42, C:0.14, G:0.07, T:0.38
Consensus pattern (35 bp):
TGCACAAATTATTATATTATAATATCCTCAAAATG
Found at i:5798051 original size:18 final size:18
Alignment explanation
Indices: 5797961--5798064 Score: 61
Period size: 18 Copynumber: 5.3 Consensus size: 18
5797951 TAAAAACTTT
5797961 AATAATA-ATAATATATA
1 AATAATATATAATATATA
* *
5797978 ATAAAAGCATATAATAGTATAA
1 A-ATAA-TATATAATA-TAT-A
5798000 AAGTGACATAGTATAATATATA
1 AA-T-A-ATA-TATAATATATA
*
5798022 ATATAA-AGTAT-ATATGTAA
1 A-ATAATA-TATAATATAT-A
5798041 AATAATATATAATATATA
1 AATAATATATAATATATA
5798059 AATAAT
1 AATAAT
5798065 TAATAAATAC
Statistics
Matches: 68, Mismatches: 6, Indels: 25
0.69 0.06 0.25
Matches are distributed among these distances:
17 1 0.01
18 22 0.32
19 14 0.21
20 7 0.10
21 5 0.07
22 5 0.07
23 6 0.09
24 8 0.12
ACGTcount: A:0.58, C:0.02, G:0.07, T:0.34
Consensus pattern (18 bp):
AATAATATATAATATATA
Found at i:5798070 original size:11 final size:10
Alignment explanation
Indices: 5798041--5798172 Score: 56
Period size: 11 Copynumber: 12.6 Consensus size: 10
5798031 ATATATGTAA
*
5798041 AATAATATAT
1 AATAATAAAT
5798051 AATATATAAAT
1 AATA-ATAAAT
5798062 AATTAATAAAT
1 AA-TAATAAAT
*
5798073 ACATAATACA-
1 A-ATAATAAAT
* *
5798083 AGTAAAAAAT
1 AATAATAAAT
**
5798093 AATAA-CGAT
1 AATAATAAAT
*
5798102 GAAAAAT-AAT
1 -AATAATAAAT
**
5798112 AATAATTTAT
1 AATAATAAAT
*
5798122 GAAAAATAAA-
1 -AATAATAAAT
5798132 ATATAATAAAT
1 A-ATAATAAAT
5798143 AATAATATAAAT
1 AAT-A-ATAAAT
5798155 AATATATAAAT
1 AATA-ATAAAT
5798166 AGATAAT
1 A-ATAAT
5798173 TATATAACAT
Statistics
Matches: 93, Mismatches: 16, Indels: 25
0.69 0.12 0.19
Matches are distributed among these distances:
9 13 0.14
10 26 0.28
11 39 0.42
12 15 0.16
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (10 bp):
AATAATAAAT
Found at i:5798112 original size:19 final size:20
Alignment explanation
Indices: 5798086--5798134 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 20
5798076 TAATACAAGT
5798086 AAAA-AATAATAA-CGATGA
1 AAAATAATAATAATCGATGA
**
5798104 AAAATAATAATAATTTATGA
1 AAAATAATAATAATCGATGA
5798124 AAAATAA-AATA
1 AAAATAATAATA
5798135 TAATAAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
18 4 0.15
19 12 0.44
20 11 0.41
ACGTcount: A:0.67, C:0.02, G:0.06, T:0.24
Consensus pattern (20 bp):
AAAATAATAATAATCGATGA
Found at i:5798144 original size:7 final size:7
Alignment explanation
Indices: 5798040--5798163 Score: 50
Period size: 7 Copynumber: 17.9 Consensus size: 7
5798030 TATATATGTA
5798040 AAATAAT
1 AAATAAT
*
5798047 ATATAAT
1 AAATAAT
5798054 --AT-AT
1 AAATAAT
5798058 AAATAAT
1 AAATAAT
*
5798065 TAATAAAT
1 AAAT-AAT
*
5798073 ACATAAT
1 AAATAAT
*
5798080 ACAAGTAAA
1 A-AA-TAAT
5798089 AAATAAT
1 AAATAAT
5798096 AACGATGAA-
1 AA--AT-AAT
5798105 AAATAAT
1 AAATAAT
5798112 -AATAAT
1 AAATAAT
**
5798118 TTATGAA-
1 AAAT-AAT
5798125 AAATAA-
1 AAATAAT
5798131 AATATAAT
1 AA-ATAAT
5798139 AAATAAT
1 AAATAAT
5798146 -AAT-AT
1 AAATAAT
5798151 AAATAAT
1 AAATAAT
*
5798158 ATATAA
1 AAATAA
5798164 ATAGATAATT
Statistics
Matches: 90, Mismatches: 11, Indels: 32
0.68 0.08 0.24
Matches are distributed among these distances:
4 2 0.02
5 4 0.04
6 20 0.22
7 42 0.47
8 12 0.13
9 8 0.09
10 2 0.02
ACGTcount: A:0.65, C:0.02, G:0.03, T:0.30
Consensus pattern (7 bp):
AAATAAT
Found at i:5798152 original size:12 final size:12
Alignment explanation
Indices: 5798137--5798190 Score: 58
Period size: 12 Copynumber: 4.4 Consensus size: 12
5798127 ATAAAATATA
5798137 ATAAATAATAAT
1 ATAAATAATAAT
5798149 ATAAATAAT-AT
1 ATAAATAATAAT
5798160 ATAAATAGATAATT
1 ATAAATA-ATAA-T
*
5798174 ATATAA-CATAAT
1 ATA-AATAATAAT
5798186 ATAAA
1 ATAAA
5798191 AGTACGGTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
11 11 0.30
12 15 0.41
13 5 0.14
14 4 0.11
15 2 0.05
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (12 bp):
ATAAATAATAAT
Found at i:5802563 original size:25 final size:25
Alignment explanation
Indices: 5802539--5802587 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 25
5802529 TGTACCATCA
*
5802539 AAAATTAAGATAT-TAAATTAAATC
1 AAAATTAAAATATATAAATTAAATC
*
5802563 AAAATTAAAATATATACATTAAATC
1 AAAATTAAAATATATAAATTAAATC
5802588 TCTATTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 12 0.55
25 10 0.45
ACGTcount: A:0.59, C:0.06, G:0.02, T:0.33
Consensus pattern (25 bp):
AAAATTAAAATATATAAATTAAATC
Found at i:5804797 original size:27 final size:27
Alignment explanation
Indices: 5804752--5804807 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
5804742 AGGTGGCTTT
* *
5804752 GGAGCTGGAGGCGGGGGTGGTTTTGGA
1 GGAGCTGGAGGCGGGGGTGGATTCGGA
* *
5804779 GGAGCTGGAGGTGGTGGTGGATTCGGA
1 GGAGCTGGAGGCGGGGGTGGATTCGGA
5804806 GG
1 GG
5804808 TGGGCATGGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.12, C:0.07, G:0.59, T:0.21
Consensus pattern (27 bp):
GGAGCTGGAGGCGGGGGTGGATTCGGA
Found at i:5804890 original size:30 final size:30
Alignment explanation
Indices: 5804856--5804954 Score: 80
Period size: 30 Copynumber: 3.3 Consensus size: 30
5804846 GTGGTGGATA
5804856 TGGTGGTGGGATTGGCAAAGGAGGAGGTGT
1 TGGTGGTGGGATTGGCAAAGGAGGAGGTGT
* * ***
5804886 TGGTGGT-GGATACGG---AGGTGGCATAGGAAA
1 TGGTGGTGGGAT-TGGCAAAGGAGG---AGGTGT
*
5804916 GGGTGGTGGGATTGGCAAAGGAGGAGGTGT
1 TGGTGGTGGGATTGGCAAAGGAGGAGGTGT
5804946 TGGTGGTGG
1 TGGTGGTGG
5804955 AATCGGAAAG
Statistics
Matches: 49, Mismatches: 12, Indels: 16
0.64 0.16 0.21
Matches are distributed among these distances:
27 5 0.10
29 4 0.08
30 31 0.63
31 4 0.08
33 5 0.10
ACGTcount: A:0.20, C:0.04, G:0.54, T:0.22
Consensus pattern (30 bp):
TGGTGGTGGGATTGGCAAAGGAGGAGGTGT
Found at i:5804981 original size:78 final size:78
Alignment explanation
Indices: 5804887--5805094 Score: 382
Period size: 78 Copynumber: 2.7 Consensus size: 78
5804877 AGGAGGTGTT
* *
5804887 GGTGGTGGATACGGAGGTGGCATAGGAAAGGGTGGTGGGATTGGCAAAGGAGGAGGTGTTGGTGG
1 GGTGGAGGATACGGAGGTGGCATAGGAAAAGGTGGTGGGATTGGCAAAGGAGGAGGTGTTGGTGG
5804952 TGGAATCGGAAAG
66 TGGAATCGGAAAG
5804965 GGTGGAGGATACGGAGGTGGCATAGGAAAAGGTGGTGGGATTGGCAAAGGAGGAGGTGTTGGTGG
1 GGTGGAGGATACGGAGGTGGCATAGGAAAAGGTGGTGGGATTGGCAAAGGAGGAGGTGTTGGTGG
5805030 TGGAATCGGAAAG
66 TGGAATCGGAAAG
*
5805043 GGTGGAGGATACGGAGGTGGCGTAGGAAAAGGTGGT-GGATTGGCAAAGGAGG
1 GGTGGAGGATACGGAGGTGGCATAGGAAAAGGTGGTGGGATTGGCAAAGGAGG
5805095 CGGATATGGA
Statistics
Matches: 127, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
77 16 0.13
78 111 0.87
ACGTcount: A:0.26, C:0.05, G:0.51, T:0.18
Consensus pattern (78 bp):
GGTGGAGGATACGGAGGTGGCATAGGAAAAGGTGGTGGGATTGGCAAAGGAGGAGGTGTTGGTGG
TGGAATCGGAAAG
Found at i:5804996 original size:60 final size:57
Alignment explanation
Indices: 5804844--5804984 Score: 167
Period size: 60 Copynumber: 2.4 Consensus size: 57
5804834 GCTTTGGTAA
* *
5804844 AGGTGGTGGATATGGTGGTGGGATTGGCAAAGGAGGAGGTGTTGGTGGTGGATACGG
1 AGGTGGAGGATACGGTGGTGGGATTGGCAAAGGAGGAGGTGTTGGTGGTGGATACGG
* *
5804901 AGGTGGCATAGGAAAGGGTGGTGGGATTGGCAAAGGAGGAGGTGTTGGTGGTGGA-ATCGG
1 AGGTGG---AGGATACGGTGGTGGGATTGGCAAAGGAGGAGGTGTTGGTGGTGGATA-CGG
*
5804961 AAAGGGTGGAGGATACGGAGGTGG
1 --A-GGTGGAGGATACGGTGGTGG
5804985 CATAGGAAAA
Statistics
Matches: 71, Mismatches: 6, Indels: 11
0.81 0.07 0.12
Matches are distributed among these distances:
57 6 0.08
59 1 0.01
60 58 0.82
62 1 0.01
63 5 0.07
ACGTcount: A:0.23, C:0.04, G:0.52, T:0.21
Consensus pattern (57 bp):
AGGTGGAGGATACGGTGGTGGGATTGGCAAAGGAGGAGGTGTTGGTGGTGGATACGG
Found at i:5805299 original size:23 final size:23
Alignment explanation
Indices: 5805269--5805317 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
5805259 GAGGTGGAAA
5805269 GGGCGGTGGTTTTGGAGGTGGTG
1 GGGCGGTGGTTTTGGAGGTGGTG
5805292 GGGCGGTGGTTTTGGAGGTGGTG
1 GGGCGGTGGTTTTGGAGGTGGTG
5805315 GGG
1 GGG
5805318 GTGGTGGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.04, C:0.04, G:0.63, T:0.29
Consensus pattern (23 bp):
GGGCGGTGGTTTTGGAGGTGGTG
Found at i:5805323 original size:24 final size:24
Alignment explanation
Indices: 5805221--5805324 Score: 102
Period size: 24 Copynumber: 4.4 Consensus size: 24
5805211 GATATGGCAA
*
5805221 GGGTGGTGGTTTTGGAGGTGGAGT
1 GGGTGGTGGTTTTGGAGGTGGAGG
* *** **
5805245 AGGTGGTGGAGCTGGAGGTGGAAA
1 GGGTGGTGGTTTTGGAGGTGGAGG
* *
5805269 GGGCGGTGGTTTTGGAGGTGG-TG
1 GGGTGGTGGTTTTGGAGGTGGAGG
* *
5805292 GGGCGGTGGTTTTGGAGGTGGTGG
1 GGGTGGTGGTTTTGGAGGTGGAGG
5805316 GGGTGGTGG
1 GGGTGGTGG
5805325 AAATGGACAC
Statistics
Matches: 64, Mismatches: 15, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
23 21 0.33
24 43 0.67
ACGTcount: A:0.10, C:0.03, G:0.61, T:0.27
Consensus pattern (24 bp):
GGGTGGTGGTTTTGGAGGTGGAGG
Found at i:5808151 original size:15 final size:15
Alignment explanation
Indices: 5808106--5808152 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
5808096 CTCAGATTAC
5808106 GTTTTAGTCACTTAT
1 GTTTTAGTCACTTAT
* *
5808121 GTTTGAAAT-A-TTAT
1 GTTT-TAGTCACTTAT
5808135 GTTTTAGTCACTTAT
1 GTTTTAGTCACTTAT
5808150 GTT
1 GTT
5808153 ATCGTCTTGT
Statistics
Matches: 25, Mismatches: 4, Indels: 6
0.71 0.11 0.17
Matches are distributed among these distances:
13 2 0.08
14 9 0.36
15 12 0.48
16 2 0.08
ACGTcount: A:0.23, C:0.09, G:0.15, T:0.53
Consensus pattern (15 bp):
GTTTTAGTCACTTAT
Found at i:5811596 original size:30 final size:30
Alignment explanation
Indices: 5811562--5811620 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
5811552 AAAAAATTAA
5811562 ATACTAAATTA-AAAAAAGTCAAATTTATAG
1 ATACTAAATTAGAAAAAAGT-AAATTTATAG
* *
5811592 ATACTAAATTAGAAGAATGTAAATTTATA
1 ATACTAAATTAGAAAAAAGTAAATTTATA
5811621 TATGAGAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 20 0.77
31 6 0.23
ACGTcount: A:0.54, C:0.05, G:0.08, T:0.32
Consensus pattern (30 bp):
ATACTAAATTAGAAAAAAGTAAATTTATAG
Found at i:5820870 original size:21 final size:21
Alignment explanation
Indices: 5820846--5820885 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
5820836 GCAAGTATAT
5820846 GTATATA-TATAGATATTTTTA
1 GTATATATTATA-ATATTTTTA
*
5820867 GTATTTATTATAATATTTT
1 GTATATATTATAATATTTT
5820886 CTTACTCTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.57
Consensus pattern (21 bp):
GTATATATTATAATATTTTTA
Found at i:5821413 original size:24 final size:23
Alignment explanation
Indices: 5821368--5821419 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 23
5821358 ATATTTCTAA
5821368 TATATGTTGTATATGTTCA-TTT
1 TATATGTTGTATATGTTCATTTT
5821390 TATATGTTATGTATATGTAT-ATTTT
1 TATATG-T-TGTATATGT-TCATTTT
5821415 TATAT
1 TATAT
5821420 ATATATTGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
22 6 0.23
23 1 0.04
24 10 0.38
25 9 0.35
ACGTcount: A:0.27, C:0.02, G:0.12, T:0.60
Consensus pattern (23 bp):
TATATGTTGTATATGTTCATTTT
Found at i:5821556 original size:14 final size:14
Alignment explanation
Indices: 5821521--5821548 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5821511 TAATATTGTT
5821521 GTTTTAATATTTCA
1 GTTTTAATATTTCA
5821535 GTTTTAATATTTCA
1 GTTTTAATATTTCA
5821549 TTATTAATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.07, G:0.07, T:0.57
Consensus pattern (14 bp):
GTTTTAATATTTCA
Found at i:5833329 original size:26 final size:26
Alignment explanation
Indices: 5833298--5833405 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
5833288 TGAAATTCCC
* *
5833298 ATCATGGAACATTTACTTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
5833324 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
5833350 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
5833376 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
5833402 ATCA
1 ATCA
5833406 ATTTGTACCA
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 76 1.00
ACGTcount: A:0.36, C:0.23, G:0.07, T:0.33
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:5835734 original size:19 final size:19
Alignment explanation
Indices: 5835710--5835778 Score: 58
Period size: 19 Copynumber: 3.8 Consensus size: 19
5835700 TAAAATGTTG
5835710 ATATTTTATAATTAAGATC
1 ATATTTTATAATTAAGATC
* *
5835729 ATATTTAATAATTATA-AAC
1 ATATTTTATAATTA-AGATC
*
5835748 ATGA---TATAATT-AGATG
1 AT-ATTTTATAATTAAGATC
5835764 ATATTTTATAATTAA
1 ATATTTTATAATTAA
5835779 AATCTACATG
Statistics
Matches: 38, Mismatches: 5, Indels: 14
0.67 0.09 0.25
Matches are distributed among these distances:
15 2 0.05
16 3 0.08
17 6 0.16
18 7 0.18
19 18 0.47
20 2 0.05
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.45
Consensus pattern (19 bp):
ATATTTTATAATTAAGATC
Found at i:5837799 original size:3 final size:3
Alignment explanation
Indices: 5837791--5837843 Score: 97
Period size: 3 Copynumber: 17.7 Consensus size: 3
5837781 GTAGATGTGG
*
5837791 ATT ATT ATT ATT ATT ATT ATT ATT GTT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
5837839 ATT AT
1 ATT AT
5837844 ACATTTAATT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:5839806 original size:19 final size:17
Alignment explanation
Indices: 5839784--5839827 Score: 54
Period size: 19 Copynumber: 2.5 Consensus size: 17
5839774 TAATCGTATG
5839784 TTTAA-TTATTTGTTTCTAA
1 TTTAATTTA-TTGTTT-T-A
5839803 TTTAATTTATTGTTTTA
1 TTTAATTTATTGTTTTA
5839820 TTTAATTT
1 TTTAATTT
5839828 TTCACATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 9 0.38
18 1 0.04
19 11 0.46
20 3 0.12
ACGTcount: A:0.25, C:0.02, G:0.05, T:0.68
Consensus pattern (17 bp):
TTTAATTTATTGTTTTA
Found at i:5839943 original size:22 final size:22
Alignment explanation
Indices: 5839918--5839966 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
5839908 TTTATCAATT
5839918 TACTAACGTTGTTAACTCTAGG
1 TACTAACGTTGTTAACTCTAGG
5839940 TACTAACGTTGTTAACTCTAGG
1 TACTAACGTTGTTAACTCTAGG
5839962 TACTA
1 TACTA
5839967 TAATAAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.37
Consensus pattern (22 bp):
TACTAACGTTGTTAACTCTAGG
Found at i:5841053 original size:10 final size:10
Alignment explanation
Indices: 5841038--5841153 Score: 62
Period size: 10 Copynumber: 11.5 Consensus size: 10
5841028 TTTTTAAAAT
5841038 AATTATTAAA
1 AATTATTAAA
*
5841048 AATTATAAAAA
1 AATTAT-TAAA
5841059 AATTA-TAGAA
1 AATTATTA-AA
**
5841069 AACCAATTAAA
1 AA-TTATTAAA
*
5841080 AATTATTAAG
1 AATTATTAAA
*
5841090 AATTATAAAAA
1 AATTAT-TAAA
5841101 AATTA-TAAGA
1 AATTATTAA-A
* *
5841111 GATTGTTAAA
1 AATTATTAAA
5841121 AA-TATTAAA
1 AATTATTAAA
5841130 AA-TATTTAAA
1 AATTA-TTAAA
*
5841140 ACTT-TTAAA
1 AATTATTAAA
*
5841149 TATTA
1 AATTA
5841154 CAGAAAATTC
Statistics
Matches: 79, Mismatches: 17, Indels: 20
0.68 0.15 0.17
Matches are distributed among these distances:
9 20 0.25
10 33 0.42
11 24 0.30
12 2 0.03
ACGTcount: A:0.59, C:0.03, G:0.04, T:0.34
Consensus pattern (10 bp):
AATTATTAAA
Found at i:5841056 original size:21 final size:21
Alignment explanation
Indices: 5841032--5841106 Score: 73
Period size: 21 Copynumber: 3.6 Consensus size: 21
5841022 ATAATTTTTT
*
5841032 TAAAATAATTATTAAAAATTA
1 TAAAAAAATTATTAAAAATTA
**
5841053 TAAAAAAATTA-TAGAAAACCA
1 TAAAAAAATTATTA-AAAATTA
* *
5841074 -ATTAAAAATTATTAAGAATTA
1 TA-AAAAAATTATTAAAAATTA
5841095 TAAAAAAATTAT
1 TAAAAAAATTAT
5841107 AAGAGATTGT
Statistics
Matches: 42, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
20 3 0.07
21 36 0.86
22 3 0.07
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.32
Consensus pattern (21 bp):
TAAAAAAATTATTAAAAATTA
Found at i:5841194 original size:22 final size:22
Alignment explanation
Indices: 5841155--5841199 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 22
5841145 TAAATATTAC
5841155 AGAAAATTCTATAATCCTTGTTAT
1 AGAAAATTC-ATAATCCTT-TTAT
5841179 AGAAAATTC-TAATCCTTTTAT
1 AGAAAATTCATAATCCTTTTAT
5841200 TAATTCTCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 4 0.19
22 8 0.38
24 9 0.43
ACGTcount: A:0.38, C:0.13, G:0.07, T:0.42
Consensus pattern (22 bp):
AGAAAATTCATAATCCTTTTAT
Found at i:5843112 original size:31 final size:33
Alignment explanation
Indices: 5843077--5843141 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 33
5843067 TTAAAATAAC
* *
5843077 TCGATCATTTT-TTAAAA-ATTGATGATTAAAT
1 TCGATCATTTTATTAAAATATTAATGACTAAAT
**
5843108 TCGATTTTTTTATTAAAATATTAATGACTAAAT
1 TCGATCATTTTATTAAAATATTAATGACTAAAT
5843141 T
1 T
5843142 TAACATTTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
31 9 0.32
32 6 0.21
33 13 0.46
ACGTcount: A:0.38, C:0.06, G:0.08, T:0.48
Consensus pattern (33 bp):
TCGATCATTTTATTAAAATATTAATGACTAAAT
Found at i:5844796 original size:2 final size:2
Alignment explanation
Indices: 5844789--5844816 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5844779 GAAAATGCAA
5844789 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
5844817 TGAAGATATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5848644 original size:18 final size:18
Alignment explanation
Indices: 5848621--5848656 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
5848611 ATTTTATTTC
* *
5848621 TAATTAACGTGTTTTTAA
1 TAATTAAAGTGATTTTAA
5848639 TAATTAAAGTGATTTTAA
1 TAATTAAAGTGATTTTAA
5848657 GCCTTTAATC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.39, C:0.03, G:0.11, T:0.47
Consensus pattern (18 bp):
TAATTAAAGTGATTTTAA
Found at i:5861257 original size:22 final size:22
Alignment explanation
Indices: 5861232--5861275 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
5861222 TAATCTTATA
5861232 ATAAATTATTAATATAATAAAT
1 ATAAATTATTAATATAATAAAT
* * *
5861254 ATAATTTATTATTTTAATAAAT
1 ATAAATTATTAATATAATAAAT
5861276 TATTTAATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
ATAAATTATTAATATAATAAAT
Found at i:5861388 original size:15 final size:15
Alignment explanation
Indices: 5861368--5861424 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
5861358 ATTCAATATT
5861368 AATATTTTAATAATA
1 AATATTTTAATAATA
*
5861383 AATATTTATTACAATTATA
1 AATA-TT-TT--AATAATA
*
5861402 AATATATTAATAATA
1 AATATTTTAATAATA
*
5861417 AATGTTTT
1 AATATTTT
5861425 GTAATATAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 16 0.48
16 2 0.06
17 4 0.12
18 1 0.03
19 10 0.30
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:5861703 original size:32 final size:34
Alignment explanation
Indices: 5861665--5861736 Score: 89
Period size: 33 Copynumber: 2.2 Consensus size: 34
5861655 AACTTTTATG
*
5861665 AAATATTTTTA-AGAAA-TCTATC-AAACAACAGA
1 AAATATTTTTACACAAATTC-ATCTAAACAACAGA
*
5861697 AAATA-TTTTACACAAATTCATCTAAACACCAGA
1 AAATATTTTTACACAAATTCATCTAAACAACAGA
5861730 AAATATT
1 AAATATT
5861737 AGCTTTTTCA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
31 5 0.15
32 12 0.35
33 16 0.47
34 1 0.03
ACGTcount: A:0.51, C:0.15, G:0.04, T:0.29
Consensus pattern (34 bp):
AAATATTTTTACACAAATTCATCTAAACAACAGA
Found at i:5872313 original size:31 final size:31
Alignment explanation
Indices: 5872270--5872331 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
5872260 AGTTATAAAA
* * *
5872270 TAGTTATTGAATTATTC-GAAAATTTTCATTT
1 TAGTCATTGAATTACTCAAAAAATTTT-ATTT
5872301 TAGTCATTGAATTACTCAAAAAATTTTATTT
1 TAGTCATTGAATTACTCAAAAAATTTTATTT
5872332 AAGCAATTGG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 19 0.70
32 8 0.30
ACGTcount: A:0.35, C:0.08, G:0.08, T:0.48
Consensus pattern (31 bp):
TAGTCATTGAATTACTCAAAAAATTTTATTT
Found at i:5873219 original size:24 final size:24
Alignment explanation
Indices: 5873179--5873230 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
5873169 TTCTAATTAA
*
5873179 ATTTTATAAATAATTAATATTTATT
1 ATTTTATAAATAATTAAAATTTA-T
*
5873204 ATTTTA-AAATATTTAAAATTTAT
1 ATTTTATAAATAATTAAAATTTAT
5873227 ATTT
1 ATTT
5873231 CATATATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 5 0.20
24 14 0.56
25 6 0.24
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (24 bp):
ATTTTATAAATAATTAAAATTTAT
Found at i:5873229 original size:30 final size:30
Alignment explanation
Indices: 5873190--5873246 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
5873180 TTTTATAAAT
*
5873190 AATTAATATTT-ATTATTTTAAAATATTTAA
1 AATTAATATTTCA-TATATTAAAATATTTAA
*
5873220 AATTTATATTTCATATATTAAAATATT
1 AATTAATATTTCATATATTAAAATATT
5873247 AACAAAAAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 23 0.96
31 1 0.04
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.53
Consensus pattern (30 bp):
AATTAATATTTCATATATTAAAATATTTAA
Found at i:5879053 original size:29 final size:29
Alignment explanation
Indices: 5879013--5879095 Score: 157
Period size: 29 Copynumber: 2.9 Consensus size: 29
5879003 CCGTATTTTT
5879013 TTTCCAGCATGCACACTTAGTGCCATATA
1 TTTCCAGCATGCACACTTAGTGCCATATA
5879042 TTTCCAGCATGCACACTTAGTGCCATATA
1 TTTCCAGCATGCACACTTAGTGCCATATA
*
5879071 TTTCCAGCACGCACACTTAGTGCCA
1 TTTCCAGCATGCACACTTAGTGCCA
5879096 ATCTCGTCAC
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 53 1.00
ACGTcount: A:0.27, C:0.30, G:0.14, T:0.29
Consensus pattern (29 bp):
TTTCCAGCATGCACACTTAGTGCCATATA
Found at i:5883800 original size:13 final size:13
Alignment explanation
Indices: 5883784--5883817 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
5883774 AATAAAATAA
5883784 TAAAATATCTTAT
1 TAAAATATCTTAT
5883797 TAAAATATCTTAT
1 TAAAATATCTTAT
5883810 TAAAATAT
1 TAAAATAT
5883818 TAATAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (13 bp):
TAAAATATCTTAT
Found at i:5884106 original size:31 final size:32
Alignment explanation
Indices: 5884053--5884112 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 32
5884043 CACCCTTAAA
* * *
5884053 ATATTTTCACTATTAATCCTTCAATTTTTTTC
1 ATATTTACACTATTAACCCTTCAAATTTTTTC
5884085 ATATTTACACT-TTAACCCTTCAAATTTT
1 ATATTTACACTATTAACCCTTCAAATTTT
5884113 GAGTATTTAC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 15 0.60
32 10 0.40
ACGTcount: A:0.28, C:0.20, G:0.00, T:0.52
Consensus pattern (32 bp):
ATATTTACACTATTAACCCTTCAAATTTTTTC
Found at i:5888389 original size:3 final size:3
Alignment explanation
Indices: 5888381--5888431 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
5888371 CTACAAAGGT
5888381 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
5888429 ATA
1 ATA
5888432 TAAAATTAAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:5888590 original size:15 final size:15
Alignment explanation
Indices: 5888570--5888599 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5888560 AACAAGACCG
*
5888570 TCTCTAAGGTTCAAA
1 TCTCTAAAGTTCAAA
5888585 TCTCTAAAGTTCAAA
1 TCTCTAAAGTTCAAA
5888600 GACTCTTATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.20, G:0.10, T:0.33
Consensus pattern (15 bp):
TCTCTAAAGTTCAAA
Found at i:5912528 original size:15 final size:17
Alignment explanation
Indices: 5912508--5912540 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
5912498 TTGAAATGAT
5912508 TAAAGT-ATTTT-ATAA
1 TAAAGTGATTTTAATAA
5912523 TAAAGTGATTTTAATAA
1 TAAAGTGATTTTAATAA
5912540 T
1 T
5912541 GGTAACAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 5 0.31
17 5 0.31
ACGTcount: A:0.45, C:0.00, G:0.09, T:0.45
Consensus pattern (17 bp):
TAAAGTGATTTTAATAA
Found at i:5914749 original size:21 final size:21
Alignment explanation
Indices: 5914714--5914764 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
5914704 TATCTTTTAA
5914714 TTATTATTAAAATATA-AAAT
1 TTATTATTAAAATATATAAAT
* *
5914734 TTATTAATTTAAATATATAACT
1 TTATT-ATTAAAATATATAAAT
5914756 TTATATATT
1 TTAT-TATT
5914765 TGATATAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 5 0.19
21 10 0.38
22 10 0.38
23 1 0.04
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (21 bp):
TTATTATTAAAATATATAAAT
Found at i:5914765 original size:22 final size:20
Alignment explanation
Indices: 5914714--5914765 Score: 59
Period size: 22 Copynumber: 2.5 Consensus size: 20
5914704 TATCTTTTAA
*
5914714 TTATTATTAAAATATAAAAT
1 TTATTATTTAAATATAAAAT
*
5914734 TTATTAATTTAAATATATAACT
1 TTATT-ATTTAAATATA-AAAT
5914756 TTATATATTT
1 TTAT-TATTT
5914766 GATATAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 5 0.19
21 10 0.37
22 11 0.41
23 1 0.04
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (20 bp):
TTATTATTTAAATATAAAAT
Found at i:5922319 original size:35 final size:35
Alignment explanation
Indices: 5922275--5922476 Score: 262
Period size: 35 Copynumber: 5.6 Consensus size: 35
5922265 TCCTCATTGA
** *
5922275 AATACCATACCTACATTTTTCAACTCGGTATGGGA-
1 AATACCATACCTACATTTCACAACTCAGTAT-GGAT
* **
5922310 AATGCCATACCTACATTTCTTAACTCAGTATGGATTTGAT
1 AATACCATACCTACATTTCACAACTCAGTAT-G----GAT
*
5922350 AATACCATACCTACATTTCACAGCTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
*
5922385 AATACCATACCTACATTTCACAGCTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
5922420 AATACCATACCTACATTTCACAACTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
*
5922455 GATACCATACCTACATTTCACA
1 AATACCATACCTACATTTCACA
5922477 CTTTGCCATG
Statistics
Matches: 152, Mismatches: 10, Indels: 10
0.88 0.06 0.06
Matches are distributed among these distances:
35 122 0.80
39 3 0.02
40 27 0.18
ACGTcount: A:0.34, C:0.25, G:0.11, T:0.31
Consensus pattern (35 bp):
AATACCATACCTACATTTCACAACTCAGTATGGAT
Found at i:5923890 original size:39 final size:39
Alignment explanation
Indices: 5923845--5924055 Score: 368
Period size: 39 Copynumber: 5.4 Consensus size: 39
5923835 GGCCGTTACA
* *
5923845 ACTTCTGTCCCTCAGTCAGCCTTTGGGCTTCCGTTTAGC
1 ACTTCTGTGCTTCAGTCAGCCTTTGGGCTTCCGTTTAGC
5923884 ACTTCTGTGCTTCAGTCAGCCTTTGGGCTTCCGTTTAGC
1 ACTTCTGTGCTTCAGTCAGCCTTTGGGCTTCCGTTTAGC
*
5923923 ACTTCTGTGCTTCAGTCAGCCTTCGGGCTTCCGTTTAGC
1 ACTTCTGTGCTTCAGTCAGCCTTTGGGCTTCCGTTTAGC
5923962 ACTTCTGTGCTTCAGTCAGCCTTTGGGCTTCCGTTTAGC
1 ACTTCTGTGCTTCAGTCAGCCTTTGGGCTTCCGTTTAGC
* *
5924001 ACTTGTGTGCTTCAGTCAGCCTTCGGGCTTCCGTTTAGC
1 ACTTCTGTGCTTCAGTCAGCCTTTGGGCTTCCGTTTAGC
*
5924040 ACTTATGTGCTTCAGT
1 ACTTCTGTGCTTCAGT
5924056 TAAGCTTCGG
Statistics
Matches: 165, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 165 1.00
ACGTcount: A:0.11, C:0.29, G:0.23, T:0.37
Consensus pattern (39 bp):
ACTTCTGTGCTTCAGTCAGCCTTTGGGCTTCCGTTTAGC
Found at i:5926750 original size:11 final size:12
Alignment explanation
Indices: 5926720--5926752 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
5926710 GTCACAAGTG
5926720 AATTAATTCACA
1 AATTAATTCACA
*
5926732 AATGAATTCA-A
1 AATTAATTCACA
5926743 AATTAATTCA
1 AATTAATTCA
5926753 TTTTGGAACC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.52, C:0.12, G:0.03, T:0.33
Consensus pattern (12 bp):
AATTAATTCACA
Found at i:5929950 original size:3 final size:3
Alignment explanation
Indices: 5929328--5929935 Score: 186
Period size: 3 Copynumber: 203.3 Consensus size: 3
5929318 AAATAAAACA
5929328 AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * **
5929375 AAT AAT AAT AAT AAT AAT AA- AACA AAG AAT AAT TAT AAT GAT ACCGG
1 AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT A--AT
* * * * **
5929422 AAT AAT GAA- GAT AAT ACCTT AAT AAC AAT GAT -AT GTT AAT AAT AAT
1 AAT AAT -AAT AAT AAT A--AT AAT AAT AAT AAT AAT AAT AAT AAT AAT
** * * * ** *
5929468 TGT AAT AGAG AAC AAC AAT ACATT AAT AAT AAT ATAT GTT AAT AAC AAT
1 AAT AAT A-AT AAT AAT AAT A-A-T AAT AAT AAT A-AT AAT AAT AAT AAT
* * * * * *
5929517 AAT AAA AAT ATGT AA- AA- AAGGG AAT AAT AAT -AT AGT AAA AAT GAT
1 AAT AAT AAT A-AT AAT AAT AA--T AAT AAT AAT AAT AAT AAT AAT AAT
* ** * * * * *
5929562 GAT AAT -AT GTT AAT AAG AAT AAT AGT AGT AGT AGT AAT AA- AA- AGAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT
* * * * *
5929608 AAT AGT AAT ACA- AAT AAA AAT AAA AAT AAA AAT AAT AGT AAT AAT
1 AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * * * * * *
5929653 GAT AAT AAT AAC AAT AGT AAT AA- AAC AGAGG AAA AAA AAC AA- CAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A-A-T AAT AAT AAT AAT AAT
* * * * *
5929698 AAC AAT AAG AGT AAT AAT AAT AACT -AT TAT AAT AAT AAA AAT -AT
1 AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT
* **
5929742 AA- AATT AAT GAT -AT AAT AA- AAT AAT AAT AGG AA- AAT AAGT -AT
1 AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT
* * * * ** *
5929784 AAA AAT AA- AAT -AT AAT CAT AGT AAT AAT ATT TGT AGT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * *
5929830 AAT AGT AAG AAT AAT AAT AAT -AT AAC AAT AAT AGT AAT -AT AACT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T
* * * **
5929874 AAAT AAT AAT AAT AAT GAA- AAT AAT ACT GAC GGT AAT AAT AAT AAT
1 -AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
5929920 AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT A
5929936 TAGTTAAAAA
Statistics
Matches: 447, Mismatches: 112, Indels: 92
0.69 0.17 0.14
Matches are distributed among these distances:
2 44 0.10
3 369 0.83
4 24 0.05
5 10 0.02
ACGTcount: A:0.60, C:0.04, G:0.08, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:5929962 original size:21 final size:21
Alignment explanation
Indices: 5929907--5929956 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
5929897 ATACTGACGG
*
5929907 TAATAATAATA-A--TAATAA
1 TAATAATAATATAGTTAAAAA
5929925 TAATAATAATATAGTTAAAAA
1 TAATAATAATATAGTTAAAAA
*
5929946 TAATAGTAATA
1 TAATAATAATA
5929957 GTGTTAGAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
18 11 0.41
19 1 0.04
21 15 0.56
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (21 bp):
TAATAATAATATAGTTAAAAA
Found at i:5930087 original size:14 final size:16
Alignment explanation
Indices: 5930068--5930102 Score: 56
Period size: 14 Copynumber: 2.3 Consensus size: 16
5930058 TAATATAGGC
5930068 AAATAAAT-TAGAT-A
1 AAATAAATATAGATGA
5930082 AAATAAATATAGATGA
1 AAATAAATATAGATGA
5930098 AAATA
1 AAATA
5930103 TACTAATAGC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 8 0.42
15 5 0.26
16 6 0.32
ACGTcount: A:0.66, C:0.00, G:0.09, T:0.26
Consensus pattern (16 bp):
AAATAAATATAGATGA
Found at i:5930132 original size:3 final size:3
Alignment explanation
Indices: 5930126--5930334 Score: 77
Period size: 3 Copynumber: 68.0 Consensus size: 3
5930116 AATACCATAG
* * *
5930126 TAA TAA TGA TAA TAA TAA TGA TAA TAA -AGA TAAA TAA TAA TAA TAC
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A T-AA TAA TAA TAA TAA
** * ** *
5930172 TAA TGT TAA TAA TAA TAA -AA TAA AAA TTG TAA TAA TAG TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * * * * *
5930219 GAA CGTAA TAA AAA GAA AAA GAAA TGA TAA CATG TAAA TAGA -AA TAA
1 TAA --TAA TAA TAA TAA TAA -TAA TAA TAA TA-A T-AA TA-A TAA TAA
* * ** *
5930266 TAG T-A TAT TAA TAA TAA TAA TATA TGT TAA TAA TGA TAA TAA TAGA
1 TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TA-A
* *
5930312 AAA TAA TAA AAA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA
5930335 AAAACTATGT
Statistics
Matches: 147, Mismatches: 44, Indels: 30
0.67 0.20 0.14
Matches are distributed among these distances:
2 7 0.05
3 125 0.85
4 11 0.07
5 4 0.03
ACGTcount: A:0.61, C:0.01, G:0.08, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:5930226 original size:23 final size:23
Alignment explanation
Indices: 5930178--5930229 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
5930168 ATACTAATGT
*
5930178 TAATAATAATAAAATAAAAATTG
1 TAATAATAATAAAATAAAAATCG
* *
5930201 TAATAATAGTAATAATAAGAA-CG
1 TAATAATAATAA-AATAAAAATCG
5930224 TAATAA
1 TAATAA
5930230 AAAGAAAAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 18 0.72
24 7 0.28
ACGTcount: A:0.62, C:0.02, G:0.08, T:0.29
Consensus pattern (23 bp):
TAATAATAATAAAATAAAAATCG
Found at i:5930297 original size:19 final size:20
Alignment explanation
Indices: 5930261--5930306 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 20
5930251 TGTAAATAGA
5930261 AATAATAGTATATTAATAAT
1 AATAATAGTATATTAATAAT
*
5930281 AATAATA-TATGTTAATAAT
1 AATAATAGTATATTAATAAT
*
5930300 GATAATA
1 AATAATA
5930307 ATAGAAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.54, C:0.00, G:0.07, T:0.39
Consensus pattern (20 bp):
AATAATAGTATATTAATAAT
Found at i:5930407 original size:25 final size:23
Alignment explanation
Indices: 5930369--5930417 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 23
5930359 GAAATAACAG
5930369 TAATAAAAAAATAAT-AAATATAA
1 TAATAAAAAAATAATGAAA-ATAA
5930392 TAATAGAAAACAATAATGAAAATAA
1 TAATA-AAAA-AATAATGAAAATAA
5930417 T
1 T
5930418 TAATTTGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 5 0.22
24 4 0.17
25 11 0.48
26 3 0.13
ACGTcount: A:0.69, C:0.02, G:0.04, T:0.24
Consensus pattern (23 bp):
TAATAAAAAAATAATGAAAATAA
Found at i:5930421 original size:13 final size:13
Alignment explanation
Indices: 5930369--5930417 Score: 52
Period size: 12 Copynumber: 4.1 Consensus size: 13
5930359 GAAATAACAG
5930369 TAATA-AAAA-AA
1 TAATAGAAAATAA
*
5930380 TAATA-AATATAA
1 TAATAGAAAATAA
*
5930392 TAATAGAAAACAA
1 TAATAGAAAATAA
5930405 TAAT-GAAAATAA
1 TAATAGAAAATAA
5930417 T
1 T
5930418 TAATTTGAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
11 8 0.25
12 15 0.47
13 9 0.28
ACGTcount: A:0.69, C:0.02, G:0.04, T:0.24
Consensus pattern (13 bp):
TAATAGAAAATAA
Found at i:5942162 original size:16 final size:16
Alignment explanation
Indices: 5942141--5942171 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
5942131 TTTCAAGCAC
5942141 TGTGTATGTATATATG
1 TGTGTATGTATATATG
5942157 TGTGTATGTATATAT
1 TGTGTATGTATATAT
5942172 TTTTTGCTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.52
Consensus pattern (16 bp):
TGTGTATGTATATATG
Found at i:5942275 original size:5 final size:5
Alignment explanation
Indices: 5942265--5942293 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
5942255 ATATATATAA
5942265 CAAAG CAAAG CAAAG CAAAG CAAAG CAAA
1 CAAAG CAAAG CAAAG CAAAG CAAAG CAAA
5942294 ACTGAAAGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.62, C:0.21, G:0.17, T:0.00
Consensus pattern (5 bp):
CAAAG
Found at i:5944565 original size:7 final size:7
Alignment explanation
Indices: 5944537--5944606 Score: 106
Period size: 7 Copynumber: 10.0 Consensus size: 7
5944527 ATTTAGTAAG
5944537 ATATTTT
1 ATATTTT
*
5944544 ATTTTATT
1 ATATT-TT
*
5944552 TTATTTT
1 ATATTTT
5944559 ATATTTT
1 ATATTTT
5944566 ATATTTT
1 ATATTTT
5944573 ATATTTT
1 ATATTTT
5944580 ATATTTT
1 ATATTTT
5944587 ATATTTT
1 ATATTTT
5944594 ATATTTT
1 ATATTTT
5944601 A-ATTTT
1 ATATTTT
5944607 TTAAATCTGA
Statistics
Matches: 58, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
6 5 0.09
7 48 0.83
8 5 0.09
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (7 bp):
ATATTTT
Found at i:5944981 original size:18 final size:18
Alignment explanation
Indices: 5944953--5944996 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
5944943 TTTCTAAATA
5944953 AAAAGAAACATT-TTATTTT
1 AAAA-AAACATTATT-TTTT
5944972 AAAAAAACATTATTTTTT
1 AAAAAAACATTATTTTTT
5944990 AAAAAAA
1 AAAAAAA
5944997 TTGGAATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 18 0.75
19 6 0.25
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.36
Consensus pattern (18 bp):
AAAAAAACATTATTTTTT
Found at i:5945604 original size:18 final size:18
Alignment explanation
Indices: 5945583--5945634 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 18
5945573 TAAATTGCTA
5945583 TTTTAATAATAAAAATAT-
1 TTTTAATAATAAAAAT-TG
5945601 TTTTAAT--TAAAAATTG
1 TTTTAATAATAAAAATTG
*
5945617 TTATAATATATAAAAATT
1 TTTTAATA-ATAAAAATT
5945635 AATATAATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
15 1 0.03
16 13 0.45
18 7 0.24
19 8 0.28
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (18 bp):
TTTTAATAATAAAAATTG
Found at i:5949550 original size:18 final size:19
Alignment explanation
Indices: 5949527--5949562 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
5949517 AGAATTTTTT
5949527 TAAAA-TTATAAAAAATAA
1 TAAAATTTATAAAAAATAA
*
5949545 TAAAATTTATTAAAAATA
1 TAAAATTTATAAAAAATA
5949563 TCAAAAGATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
TAAAATTTATAAAAAATAA
Found at i:5949568 original size:28 final size:28
Alignment explanation
Indices: 5949526--5949598 Score: 87
Period size: 28 Copynumber: 2.6 Consensus size: 28
5949516 TAGAATTTTT
* *
5949526 TTAAAATTATAAAAAATAATAAAATTTA
1 TTAAAAATATCAAAAATAATAAAATTTA
5949554 TTAAAAATATCAAAAGAT-ATAAAATTTA
1 TTAAAAATATCAAAA-ATAATAAAATTTA
* *
5949582 TTAGAAAT-TCTAAAATA
1 TTAAAAATATCAAAAATA
5949599 TTGTAAAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
26 2 0.05
27 5 0.13
28 30 0.77
29 2 0.05
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.34
Consensus pattern (28 bp):
TTAAAAATATCAAAAATAATAAAATTTA
Found at i:5949898 original size:18 final size:18
Alignment explanation
Indices: 5949877--5949933 Score: 53
Period size: 18 Copynumber: 3.1 Consensus size: 18
5949867 TTAGAAATTC
5949877 TAAAATATTGTAAAAAAA
1 TAAAATATTGTAAAAAAA
* **
5949895 TAAAAT-TTATTAGAAATCA
1 TAAAATATT-GTA-AAAAAA
*
5949914 TAAAAGATTGTAAAAAAA
1 TAAAATATTGTAAAAAAA
5949932 TA
1 TA
5949934 TTAATTCTTT
Statistics
Matches: 29, Mismatches: 7, Indels: 6
0.69 0.17 0.14
Matches are distributed among these distances:
17 2 0.07
18 14 0.48
19 11 0.38
20 2 0.07
ACGTcount: A:0.61, C:0.02, G:0.07, T:0.30
Consensus pattern (18 bp):
TAAAATATTGTAAAAAAA
Found at i:5949906 original size:37 final size:37
Alignment explanation
Indices: 5949859--5949933 Score: 116
Period size: 37 Copynumber: 2.0 Consensus size: 37
5949849 CAAAAGATAC
*
5949859 AAAAATTATTAGAAATTC-TAAAATATTGTAAAAAAAT
1 AAAAATTATTAGAAA-TCATAAAAGATTGTAAAAAAAT
*
5949896 AAAATTTATTAGAAATCATAAAAGATTGTAAAAAAAT
1 AAAAATTATTAGAAATCATAAAAGATTGTAAAAAAAT
5949933 A
1 A
5949934 TTAATTCTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
36 2 0.06
37 33 0.94
ACGTcount: A:0.60, C:0.03, G:0.07, T:0.31
Consensus pattern (37 bp):
AAAAATTATTAGAAATCATAAAAGATTGTAAAAAAAT
Found at i:5950054 original size:285 final size:277
Alignment explanation
Indices: 5949562--5950108 Score: 721
Period size: 285 Copynumber: 1.9 Consensus size: 277
5949552 TATTAAAAAT
* * *
5949562 ATCAAAAGATATAAAATTTATTAGAAATTCTAAAATATTGTAAAAAAATATTAAAAATCATCAAA
1 ATCAAAAGATACAAAAATTATTAGAAATTCTAAAATATTGTAAAAAAATATTAAAAATCATAAAA
*
5949627 GATTGTAAAATAATTATTAAAAATTTTAAAAACTAGTTAAAAGAAATTGTATCTTAGAATAAAAT
66 GATTGTAAAATAAATATTAAAAATTTTAAAAACTAGTTAAAAGAAATTGTATCTTAGAATAAAAT
* * * * *
5949692 ATACCTTTGCTAGTGGCATTTAAAATATTAAAAACTTGATATAAAAAATTGTATGTCGTAATACA
131 ATACCTTCGCTAGTAGCATTTAAAATATT----ACTTGATATAAAAAAATGAAAGTCGTAATACA
**
5949757 AACAGTTTTTTATAAAAAAAATATTTTAAAATTTTTGAATAAACATTTTATAT-AAATTTTGTAA
192 AACAG-TTTTTAT--AAAAAATATTTTAAAAAATTTGAATAAACATTTTATATCAAA-TTT-TAA
5949821 TATTTTGAAAAAATAATAAAAAAAGG
252 TATTTTGAAAAAATAATAAAAAAAGG
5949847 ATCAAAAGATACAAAAATTATTAGAAATTCTAAAATATTGTAAAAAAATAAAATTTATTAGAAAT
1 ATCAAAAGATACAAAAATTATTAGAAATTCTAAAATATTGTAAAAAAAT---A-TTA--A-AAAT
*** *
5949912 CATAAAAGATTGTAAAA-AAATATTAATTCTTTTAAAAACTAG-TAAAA-AAGTTGTATCTTAGA
59 CATAAAAGATTGTAAAATAAATATTAAAAATTTTAAAAACTAGTTAAAAGAAATTGTATCTTAGA
*
5949974 ATAAAATATACCTTCGACTAGTAGCATTTTAAAATATT-CTTGATATAAAAAAAT-AAAGATTGT
124 ATAAAATATACCTTCG-CTAGTAGCA-TTTAAAATATTACTTGATATAAAAAAATGAAAG-TCGT
5950037 AATACAAACCA-TTTTTATAAAAAATATTTTAAAAAATTTGAATAAACATTTTATATCAAATTTT
186 AATACAAA-CAGTTTTTATAAAAAATATTTTAAAAAATTTGAATAAACATTTTATATCAAATTTT
5950101 AATATTTT
250 AATATTTT
5950109 AAATCAATTT
Statistics
Matches: 234, Mismatches: 16, Indels: 27
0.84 0.06 0.10
Matches are distributed among these distances:
282 9 0.04
283 39 0.17
284 3 0.01
285 56 0.24
286 26 0.11
287 2 0.01
288 1 0.00
289 32 0.14
290 13 0.06
291 33 0.14
292 20 0.09
ACGTcount: A:0.51, C:0.06, G:0.07, T:0.36
Consensus pattern (277 bp):
ATCAAAAGATACAAAAATTATTAGAAATTCTAAAATATTGTAAAAAAATATTAAAAATCATAAAA
GATTGTAAAATAAATATTAAAAATTTTAAAAACTAGTTAAAAGAAATTGTATCTTAGAATAAAAT
ATACCTTCGCTAGTAGCATTTAAAATATTACTTGATATAAAAAAATGAAAGTCGTAATACAAACA
GTTTTTATAAAAAATATTTTAAAAAATTTGAATAAACATTTTATATCAAATTTTAATATTTTGAA
AAAATAATAAAAAAAGG
Found at i:5952620 original size:2 final size:2
Alignment explanation
Indices: 5952613--5952641 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5952603 TACATGAAAT
5952613 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5952642 GAAGAAAGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5958548 original size:39 final size:39
Alignment explanation
Indices: 5958361--5958537 Score: 300
Period size: 39 Copynumber: 4.5 Consensus size: 39
5958351 ACAAAGCATG
5958361 CGGGACTTTAAGCCCGGATATAATACCAGCACGAATGCCTT
1 CGGGAC-TT-AGCCCGGATATAATACCAGCACGAATGCCTT
** *
5958402 CGGGACTTAGCCCGGATATAGCACTAGCACGAATGCCTT
1 CGGGACTTAGCCCGGATATAATACCAGCACGAATGCCTT
5958441 CGGGACTTAGCCCGGATATAATACCAGCACGAATGCCTT
1 CGGGACTTAGCCCGGATATAATACCAGCACGAATGCCTT
*
5958480 CAGGACTTAGCCCGGATATAATACCAGCACGAATGCCTT
1 CGGGACTTAGCCCGGATATAATACCAGCACGAATGCCTT
5958519 CGGGACTTAGCCCGGATAT
1 CGGGACTTAGCCCGGATAT
5958538 TTTTCCAGCA
Statistics
Matches: 128, Mismatches: 8, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
39 120 0.94
40 2 0.02
41 6 0.05
ACGTcount: A:0.28, C:0.28, G:0.24, T:0.21
Consensus pattern (39 bp):
CGGGACTTAGCCCGGATATAATACCAGCACGAATGCCTT
Found at i:5958573 original size:39 final size:39
Alignment explanation
Indices: 5958530--5958661 Score: 203
Period size: 39 Copynumber: 3.4 Consensus size: 39
5958520 GGGACTTAGC
* * *
5958530 CCGGATATTTTTCCAGCACT-TAGCCTGCGGACTTTAAGT
1 CCGGATATATTTCCAGCA-TAAAGCCTGCGGACTTCAAGT
5958569 CCGGATATATTTCCAGCATAAAGCCTGCGGACTTCAAGT
1 CCGGATATATTTCCAGCATAAAGCCTGCGGACTTCAAGT
*
5958608 CCAGATATATTTCCAGCATAAAGCCTGCGGACTTCAAGT
1 CCGGATATATTTCCAGCATAAAGCCTGCGGACTTCAAGT
*
5958647 CCGGATATTTTTCCA
1 CCGGATATATTTCCA
5958662 ATAGCATGCA
Statistics
Matches: 86, Mismatches: 6, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
38 1 0.01
39 85 0.99
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.30
Consensus pattern (39 bp):
CCGGATATATTTCCAGCATAAAGCCTGCGGACTTCAAGT
Found at i:5958573 original size:78 final size:78
Alignment explanation
Indices: 5958361--5958654 Score: 251
Period size: 78 Copynumber: 3.7 Consensus size: 78
5958351 ACAAAGCATG
* * * * * **
5958361 CGGGACTTTAAGCCCGGATATAATACCAGCACGAATGCCTTCGGGAC-TT-AGCCCGGATATAGC
1 CGGGAC-TT-AGCCCGGATATATTTCCAGCACTAA-GCCTGC-GGACTTTAAGTCCGGATATAAT
*
5958424 ACTAGCACGAATGCCTT
62 ACCAGCACGAATGCCTT
* * * * *
5958441 CGGGACTTAGCCCGGATATAATACCAGCACGAATGCCTTCAGGAC-TT-AGCCCGGATATAATAC
1 CGGGACTTAGCCCGGATATATTTCCAGCACTAA-GCCTGC-GGACTTTAAGTCCGGATATAATAC
5958504 CAGCACGAATGCCTT
64 CAGCACGAATGCCTT
* * * *
5958519 CGGGACTTAGCCCGGATATTTTTCCAGCACTTAGCCTGCGGACTTTAAGTCCGGATATATTTCCA
1 CGGGACTTAGCCCGGATATATTTCCAGCACTAAGCCTGCGGACTTTAAGTCCGGATATAATACCA
* * *
5958584 GCA-TAAAGCCTG
66 GCACGAATGCCTT
* * *
5958596 C-GGACTTCAAGTCCAGATATATTTCCAGCA-TAAAGCCTGCGGACTTCAAGTCCGGATAT
1 CGGGACTT--AGCCCGGATATATTTCCAGCACT-AAGCCTGCGGACTTTAAGTCCGGATAT
5958655 TTTTCCAATA
Statistics
Matches: 188, Mismatches: 21, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
76 10 0.05
77 15 0.08
78 155 0.82
79 2 0.01
80 6 0.03
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24
Consensus pattern (78 bp):
CGGGACTTAGCCCGGATATATTTCCAGCACTAAGCCTGCGGACTTTAAGTCCGGATATAATACCA
GCACGAATGCCTT
Found at i:5958615 original size:117 final size:118
Alignment explanation
Indices: 5958353--5958661 Score: 299
Period size: 117 Copynumber: 2.6 Consensus size: 118
5958343 TCACCACTAC
* *
5958353 AAAGCATGCGGGACTTTAAGCCCGGATATAATACCAGCACGAATGCCTTCGGGACTTAGCCCGGA
1 AAAGCCTGCAGGAC-TTAAGCCCGGATATAATACCAGCACGAATGCCTTCGGGACTTAGCCCGGA
**** * *
5958418 TATAGCACTAGCACGAATGCCTTCGGGACTTAGCCCGGATATAATACCAGCACG
65 TATTTTTCCAGCACGAATGCCTGCGGGACTTAGCCCGGATATAATACCAGCACG
* *
5958472 AATGCCTTCAGGACTT-AGCCCGGATATAATACCAGCACGAATGCCTTCGGGACTTAGCCCGGAT
1 AAAGCCTGCAGGACTTAAGCCCGGATATAATACCAGCACGAATGCCTTCGGGACTTAGCCCGGAT
** * * * *
5958536 ATTTTTCCAGCACTTA-GCCTGC-GGACTTTAAGTCCGGATATATTTCCAGCA-T
66 ATTTTTCCAGCACGAATGCCTGCGGGAC-TT-AGCCCGGATATAATACCAGCACG
* * * * * * * *
5958588 AAAGCCTGC-GGACTTCAAGTCCAGATATATTTCCAGCA-TAAAGCCTGC-GGACTTCAAGTCCG
1 AAAGCCTGCAGGACTT-AAGCCCGGATATAATACCAGCACGAATGCCTTCGGGACTT--AGCCCG
5958650 GATATTTTTCCA
63 GATATTTTTCCA
5958662 ATAGCATGCA
Statistics
Matches: 158, Mismatches: 26, Indels: 14
0.80 0.13 0.07
Matches are distributed among these distances:
115 16 0.10
116 21 0.13
117 109 0.69
118 2 0.01
119 10 0.06
ACGTcount: A:0.28, C:0.27, G:0.22, T:0.24
Consensus pattern (118 bp):
AAAGCCTGCAGGACTTAAGCCCGGATATAATACCAGCACGAATGCCTTCGGGACTTAGCCCGGAT
ATTTTTCCAGCACGAATGCCTGCGGGACTTAGCCCGGATATAATACCAGCACG
Found at i:5970047 original size:60 final size:60
Alignment explanation
Indices: 5969951--5970137 Score: 281
Period size: 60 Copynumber: 3.2 Consensus size: 60
5969941 ATGAATACAG
* * * * *
5969951 ATTCATCAGAAAGTTTTGGTGGAGCCTTAATCGGACTCTGTTCTTCTCTTGCTTCTTGAA
1 ATTCATCAGAAGGTTTTAGTGGAGACTTCATTGGACTCTGTTCTTCTCTTGCTTCTTGAA
* * *
5970011 ATTCATCAGAAGGTTTTAGTGGAGACTTCATTGGACTCTGTTCTTCCCTTGCGTCATGAA
1 ATTCATCAGAAGGTTTTAGTGGAGACTTCATTGGACTCTGTTCTTCTCTTGCTTCTTGAA
5970071 ATTCATC---AGGTTTTAGTGGAGACTTCATTGGACTCTGTTCTTCTCTTGCTTCTTGAA
1 ATTCATCAGAAGGTTTTAGTGGAGACTTCATTGGACTCTGTTCTTCTCTTGCTTCTTGAA
5970128 ATTCATCAGA
1 ATTCATCAGA
5970138 GCTGGTACTC
Statistics
Matches: 113, Mismatches: 11, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
57 54 0.48
60 59 0.52
ACGTcount: A:0.21, C:0.20, G:0.20, T:0.40
Consensus pattern (60 bp):
ATTCATCAGAAGGTTTTAGTGGAGACTTCATTGGACTCTGTTCTTCTCTTGCTTCTTGAA
Found at i:5970109 original size:57 final size:57
Alignment explanation
Indices: 5969963--5970136 Score: 258
Period size: 57 Copynumber: 3.0 Consensus size: 57
5969953 TCATCAGAAA
* * * *
5969963 GTTTTGGTGGAGCCTTAATCGGACTCTGTTCTTCTCTTGCTTCTTGAAATTCATCAGAAG
1 GTTTTAGTGGAGACTTCATTGGACTCTGTTCTTCTCTTGCTTCTTGAAATTCATC---AG
* * *
5970023 GTTTTAGTGGAGACTTCATTGGACTCTGTTCTTCCCTTGCGTCATGAAATTCATCAG
1 GTTTTAGTGGAGACTTCATTGGACTCTGTTCTTCTCTTGCTTCTTGAAATTCATCAG
5970080 GTTTTAGTGGAGACTTCATTGGACTCTGTTCTTCTCTTGCTTCTTGAAATTCATCAG
1 GTTTTAGTGGAGACTTCATTGGACTCTGTTCTTCTCTTGCTTCTTGAAATTCATCAG
5970137 AGCTGGTACT
Statistics
Matches: 104, Mismatches: 10, Indels: 3
0.89 0.09 0.03
Matches are distributed among these distances:
57 56 0.54
60 48 0.46
ACGTcount: A:0.18, C:0.20, G:0.21, T:0.41
Consensus pattern (57 bp):
GTTTTAGTGGAGACTTCATTGGACTCTGTTCTTCTCTTGCTTCTTGAAATTCATCAG
Found at i:5971038 original size:9 final size:9
Alignment explanation
Indices: 5971024--5971050 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
5971014 AAAGATCTGG
5971024 TGGAGAAGA
1 TGGAGAAGA
5971033 TGGAGAAGA
1 TGGAGAAGA
5971042 TGGAGAAGA
1 TGGAGAAGA
5971051 ATGATGAGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.44, T:0.11
Consensus pattern (9 bp):
TGGAGAAGA
Found at i:5972040 original size:22 final size:21
Alignment explanation
Indices: 5972009--5972077 Score: 57
Period size: 22 Copynumber: 3.2 Consensus size: 21
5971999 ATTACTTTTT
* *
5972009 TTTTTGCTATTTTCTTGTTAA
1 TTTTTACTATTTTATTGTTAA
* * *
5972030 TTTTTCACTATTGTGTTGTTAC
1 TTTTT-ACTATTTTATTGTTAA
**
5972052 TATTTTGTTATTTTATTGTTAA
1 T-TTTTACTATTTTATTGTTAA
5972074 TTTT
1 TTTT
5972078 GTTATTTTAG
Statistics
Matches: 37, Mismatches: 9, Indels: 4
0.74 0.18 0.08
Matches are distributed among these distances:
21 8 0.22
22 25 0.68
23 4 0.11
ACGTcount: A:0.16, C:0.07, G:0.10, T:0.67
Consensus pattern (21 bp):
TTTTTACTATTTTATTGTTAA
Found at i:5972235 original size:13 final size:14
Alignment explanation
Indices: 5972211--5972240 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
5972201 TGTTGTACTA
5972211 TATTTTTAAAAAAT
1 TATTTTTAAAAAAT
5972225 TATTTTTAAAAAAT
1 TATTTTTAAAAAAT
5972239 TA
1 TA
5972241 ATACGGGTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TATTTTTAAAAAAT
Found at i:5973527 original size:11 final size:11
Alignment explanation
Indices: 5973511--5973535 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
5973501 ATATCTATAA
5973511 TTCTCTTCATT
1 TTCTCTTCATT
5973522 TTCTCTTCATT
1 TTCTCTTCATT
5973533 TTC
1 TTC
5973536 ATCAGTTGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.28, G:0.00, T:0.64
Consensus pattern (11 bp):
TTCTCTTCATT
Found at i:5981371 original size:13 final size:13
Alignment explanation
Indices: 5981353--5981377 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5981343 TCTAGTCTTT
5981353 TTTTTCTTTTTTC
1 TTTTTCTTTTTTC
5981366 TTTTTCTTTTTT
1 TTTTTCTTTTTT
5981378 ATGTAAAACA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTCTTTTTTC
Found at i:5981954 original size:17 final size:17
Alignment explanation
Indices: 5981931--5981979 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 17
5981921 TTATTTTGAA
5981931 TTTAAAATATATAAAA-
1 TTTAAAATATATAAAAG
5981947 TCTTAAAA-A-ATAAAAG
1 T-TTAAAATATATAAAAG
*
5981963 TTTATAAATTTATAAAA
1 TTTA-AAATATATAAAA
5981980 ATATTAGAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 8
0.75 0.03 0.22
Matches are distributed among these distances:
15 9 0.33
16 6 0.22
17 6 0.22
18 6 0.22
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (17 bp):
TTTAAAATATATAAAAG
Found at i:5981960 original size:24 final size:24
Alignment explanation
Indices: 5981933--5981982 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
5981923 ATTTTGAATT
5981933 TAAAA-TATATAAAATCTTA-AAAAA
1 TAAAAGTATAT-AAAT-TTATAAAAA
*
5981957 TAAAAGTTTATAAATTTATAAAAA
1 TAAAAGTATATAAATTTATAAAAA
5981981 TA
1 TA
5981983 TTAGAAATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
23 3 0.13
24 16 0.70
25 4 0.17
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (24 bp):
TAAAAGTATATAAATTTATAAAAA
Found at i:5983026 original size:13 final size:15
Alignment explanation
Indices: 5982992--5983028 Score: 51
Period size: 13 Copynumber: 2.5 Consensus size: 15
5982982 TAATTATCAC
5982992 TTAATTAATATTAGAG
1 TTAATT-ATATTAGAG
5983008 TTAATTATATTA-A-
1 TTAATTATATTAGAG
5983021 TTAATTAT
1 TTAATTAT
5983029 TATTTTAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 8 0.38
14 1 0.05
15 6 0.29
16 6 0.29
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.51
Consensus pattern (15 bp):
TTAATTATATTAGAG
Found at i:5988827 original size:18 final size:17
Alignment explanation
Indices: 5988804--5988842 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 17
5988794 GCTTAGGTTA
5988804 AAATCATAGTTATCTCAC
1 AAATCATAGTTATCTC-C
5988822 AAATCATAGTTATCTCC
1 AAATCATAGTTATCTCC
5988839 AAAT
1 AAAT
5988843 GTGATGATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.41, C:0.21, G:0.05, T:0.33
Consensus pattern (17 bp):
AAATCATAGTTATCTCC
Found at i:5996880 original size:19 final size:21
Alignment explanation
Indices: 5996843--5996881 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
5996833 TTAATGCATA
5996843 ATTTATATAAAAAATAATAAT
1 ATTTATATAAAAAATAATAAT
*
5996864 ATTTA-ATAAATAA-AATAA
1 ATTTATATAAAAAATAATAA
5996882 AATCTGTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 7 0.41
21 5 0.29
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (21 bp):
ATTTATATAAAAAATAATAAT
Found at i:5999786 original size:88 final size:88
Alignment explanation
Indices: 5999637--5999813 Score: 257
Period size: 88 Copynumber: 2.0 Consensus size: 88
5999627 TGAGAGAAAA
** * *
5999637 GTAAAAATAACTGTAAAGCAAAATCACGAATGCTATTTTGACAAAGCTTTCTCTTTCCTGTTTGT
1 GTAAAAATAACTACAAAGCAAAATCACAAATGCTATTTTGACAAAGCTTTCTCTTTCCTGTTTGC
* * *
5999702 TGCCGAGCCTACCTAGGTAACCC
66 TGACGACCCTACCCAGGTAACCC
* *
5999725 GTAAAAATAACTACAAGGCAAAATCACAAATGCTATTTT-AGCAAAGGTTTCTCTTTCCTGTTTG
1 GTAAAAATAACTACAAAGCAAAATCACAAATGCTATTTTGA-CAAAGCTTTCTCTTTCCTGTTTG
5999789 CTGACGACCCTACCCAGGTAACCC
65 CTGACGACCCTACCCAGGTAACCC
5999813 G
1 G
5999814 ATATATAATT
Statistics
Matches: 79, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
87 1 0.01
88 78 0.99
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.29
Consensus pattern (88 bp):
GTAAAAATAACTACAAAGCAAAATCACAAATGCTATTTTGACAAAGCTTTCTCTTTCCTGTTTGC
TGACGACCCTACCCAGGTAACCC
Found at i:6000981 original size:132 final size:130
Alignment explanation
Indices: 6000713--6001004 Score: 404
Period size: 132 Copynumber: 2.2 Consensus size: 130
6000703 ATTGATTTAG
* * *
6000713 AAGCCTTCCTCCATTGATATCGAGCCTTCATTGGTTTACCCAACCAGCAAAATCTTTCCAGGTTC
1 AAGCCTTCCTCCATTGATATCCAGCCTCCATTGGTTTACCCAACCAGCAAAATCTTTCCACGTTC
* * *
6000778 ATGTCTGGATTATATAGGAGAACTTAACCAGTGAAGCTCATCTCTGGATGCTGCTCTTGTTGTGA
66 ATGCCTGGATTACATAGGAGAACTTAACCAGTGAAACTCATCTCTGGATGCTGCTCTTGTTGTGA
* * * *
6000843 AAGCCTTCCTCCATTGATATCCAACCTCCATTGGTTTGCCCAACCTGCAAAATCTTTCCACGTTT
1 AAGCCTTCCTCCATTGATATCCAGCCTCCATTGGTTTACCCAACCAGCAAAATCTTTCCACGTTC
* * * ** *
6000908 ATGCCTAGGGTTTACATAGGAGAACTTAACTAGTGAAACTCATCTCTGGATGTTTTTTTTGTTGT
66 ATGCCT--GGATTACATAGGAGAACTTAACCAGTGAAACTCATCTCTGGATGCTGCTCTTGTTGT
6000973 GA
129 GA
* *
6000975 AAGCCTTCCGCCATTGATATCTAGCCTCCA
1 AAGCCTTCCTCCATTGATATCCAGCCTCCA
6001005 ACGTTTATGC
Statistics
Matches: 141, Mismatches: 19, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
130 63 0.45
132 78 0.55
ACGTcount: A:0.24, C:0.25, G:0.17, T:0.33
Consensus pattern (130 bp):
AAGCCTTCCTCCATTGATATCCAGCCTCCATTGGTTTACCCAACCAGCAAAATCTTTCCACGTTC
ATGCCTGGATTACATAGGAGAACTTAACCAGTGAAACTCATCTCTGGATGCTGCTCTTGTTGTGA
Found at i:6003733 original size:26 final size:26
Alignment explanation
Indices: 6003697--6003806 Score: 175
Period size: 26 Copynumber: 4.2 Consensus size: 26
6003687 CATGAATTTC
*
6003697 TTATCATGAAACATTTACCTAAACCA
1 TTATCATGAAACATTTACCTAACCCA
6003723 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* * *
6003749 TTATCATGGAATATTTACCTAATCCA
1 TTATCATGAAACATTTACCTAACCCA
*
6003775 TTATCATGGAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
6003801 TTATCA
1 TTATCA
6003807 ATTTGTATCA
Statistics
Matches: 78, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 78 1.00
ACGTcount: A:0.37, C:0.24, G:0.05, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:6009263 original size:19 final size:19
Alignment explanation
Indices: 6009241--6009281 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
6009231 ACCAAGATCT
*
6009241 TAGGCGACTGATACTATGA
1 TAGGCGACTGATACCATGA
6009260 TAGGCGACTGATACCATGA
1 TAGGCGACTGATACCATGA
6009279 TAG
1 TAG
6009282 AAGGTAAACT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.32, C:0.17, G:0.27, T:0.24
Consensus pattern (19 bp):
TAGGCGACTGATACCATGA
Found at i:6010416 original size:76 final size:76
Alignment explanation
Indices: 6010323--6010466 Score: 270
Period size: 76 Copynumber: 1.9 Consensus size: 76
6010313 TATAATTTTA
*
6010323 TTTTACTAATTTAAAATTTTATAAAATTTATAAAATTTAAATAAAAATTTTCTATTTTAAAAAGG
1 TTTTACTAATTTAAAATTTTATAAAATTTATAAAATTTAAATAAAAATTTTCTACTTTAAAAAGG
6010388 AAGATTTTATT
66 AAGATTTTATT
*
6010399 TTTTACTAATTTAAAATTTTATAAATTTTATAAAATTTAAATAAAAATTTTCTACTTTAAAAAGG
1 TTTTACTAATTTAAAATTTTATAAAATTTATAAAATTTAAATAAAAATTTTCTACTTTAAAAAGG
6010464 AAG
66 AAG
6010467 GTTCCTAAAC
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
76 66 1.00
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.46
Consensus pattern (76 bp):
TTTTACTAATTTAAAATTTTATAAAATTTATAAAATTTAAATAAAAATTTTCTACTTTAAAAAGG
AAGATTTTATT
Found at i:6010676 original size:36 final size:36
Alignment explanation
Indices: 6010634--6010704 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
6010624 ATTATTAATG
**
6010634 TTCCCTACTTCAACTTCTAAAGAAAAATTGTTTATT
1 TTCCCTACTTCAACTAATAAAGAAAAATTGTTTATT
6010670 TTCCCTACTTCAACTAATAAAGAAAAATTGTTTAT
1 TTCCCTACTTCAACTAATAAAGAAAAATTGTTTAT
6010705 AACACTTGTC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.37, C:0.18, G:0.06, T:0.39
Consensus pattern (36 bp):
TTCCCTACTTCAACTAATAAAGAAAAATTGTTTATT
Found at i:6013071 original size:28 final size:29
Alignment explanation
Indices: 6013019--6013074 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
6013009 AATTAATTTT
* **
6013019 AAAATTTTAATATATTTTTTAATATATTA
1 AAAATTTTAATATACTTAATAATATATTA
6013048 AAAATTTTAATATACTTAAT-ATATATT
1 AAAATTTTAATATACTTAATAATATATT
6013075 TTTAATAGGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 7 0.29
29 17 0.71
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (29 bp):
AAAATTTTAATATACTTAATAATATATTA
Found at i:6013136 original size:19 final size:19
Alignment explanation
Indices: 6013114--6013186 Score: 67
Period size: 19 Copynumber: 3.6 Consensus size: 19
6013104 TAATATATTT
6013114 AAAATTTTAAATAACTTAA
1 AAAATTTTAAATAACTTAA
*
6013133 AAAAATTTAAATATA-TTAA
1 AAAATTTTAAATA-ACTTAA
*
6013152 AAAATGTTAAGTATAACTTTAA
1 AAAATTTTAA--ATAAC-TTAA
*
6013174 ATATATTTTAAAT
1 A-AAATTTTAAAT
6013187 TTTTAATATA
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
19 24 0.56
20 2 0.05
21 5 0.12
22 5 0.12
23 7 0.16
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.40
Consensus pattern (19 bp):
AAAATTTTAAATAACTTAA
Found at i:6013154 original size:18 final size:18
Alignment explanation
Indices: 6013105--6013166 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 18
6013095 AAGATTTTTT
* *
6013105 AATATATTTAAAATTTTA
1 AATATATTAAAAAATTTA
6013123 AATA-ACTTAAAAAAATTTA
1 AATATA-TT-AAAAAATTTA
6013142 AATATATTAAAAAATGTTA
1 AATATATTAAAAAAT-TTA
*
6013161 AGTATA
1 AATATA
6013167 ACTTTAAATA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
17 1 0.03
18 13 0.35
19 22 0.59
20 1 0.03
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (18 bp):
AATATATTAAAAAATTTA
Found at i:6013248 original size:17 final size:17
Alignment explanation
Indices: 6013226--6013292 Score: 68
Period size: 17 Copynumber: 3.9 Consensus size: 17
6013216 AAAAAAGATT
6013226 TTTTAACATAT-TTAAAA
1 TTTTAA-ATATATTAAAA
6013243 TTTTAAA-A-ACTTAAAAA
1 TTTTAAATATA-TT-AAAA
**
6013260 AATTAAATATATTAAAA
1 TTTTAAATATATTAAAA
6013277 TTTTAAATATATTAAA
1 TTTTAAATATATTAAA
6013293 GAAAATGTTG
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
15 1 0.02
16 3 0.07
17 33 0.80
18 3 0.07
19 1 0.02
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (17 bp):
TTTTAAATATATTAAAA
Found at i:6013400 original size:70 final size:70
Alignment explanation
Indices: 6013265--6013395 Score: 230
Period size: 68 Copynumber: 1.9 Consensus size: 70
6013255 AAAAAAATTA
* *
6013265 AATATATTAAAATTTTAAATATATTAAAGAAAATGTTGAGTATAACCAATTTTAAAATTTTAATA
1 AATATATTAAAATTTTAAACATATTAAAGAAAATGTTAAGTATAACCAATTTTAAAATTTTAATA
6013330 TACTT
66 TACTT
6013335 AATATATTAAAATTTTAAACATATTAAA-AAAAT-TTAAGTATAACCAATTTTAAAATTTTAA
1 AATATATTAAAATTTTAAACATATTAAAGAAAATGTTAAGTATAACCAATTTTAAAATTTTAA
6013396 AATATTTTTT
Statistics
Matches: 59, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
68 27 0.46
69 5 0.08
70 27 0.46
ACGTcount: A:0.51, C:0.05, G:0.04, T:0.40
Consensus pattern (70 bp):
AATATATTAAAATTTTAAACATATTAAAGAAAATGTTAAGTATAACCAATTTTAAAATTTTAATA
TACTT
Found at i:6016161 original size:20 final size:22
Alignment explanation
Indices: 6016117--6016162 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
6016107 TTTTAGTATC
* *
6016117 ATTTTTATTTGTTTTAATATTT
1 ATTTTTATGTGTTTTAATATAT
6016139 ATTTTTATGT-TTTTAA-ATAT
1 ATTTTTATGTGTTTTAATATAT
6016159 ATTT
1 ATTT
6016163 GATTTATTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 7 0.32
21 6 0.27
22 9 0.41
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (22 bp):
ATTTTTATGTGTTTTAATATAT
Found at i:6016177 original size:25 final size:24
Alignment explanation
Indices: 6016133--6016190 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 24
6016123 ATTTGTTTTA
*
6016133 ATATTTATTTTTATGTTTTTAAAT
1 ATATTTATTTTTATGATTTTAAAT
6016157 ATATTTGATTTATTAT-ATTTTAAA-
1 ATATTT-ATTT-TTATGATTTTAAAT
*
6016181 ATTTTTATTT
1 ATATTTATTT
6016191 AATGAAATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
23 4 0.13
24 11 0.37
25 11 0.37
26 4 0.13
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (24 bp):
ATATTTATTTTTATGATTTTAAAT
Found at i:6016182 original size:26 final size:24
Alignment explanation
Indices: 6016133--6016190 Score: 66
Period size: 26 Copynumber: 2.4 Consensus size: 24
6016123 ATTTGTTTTA
* *
6016133 ATATTTATTTTTATGTTTTTAAAT
1 ATATTTATTTTTATATTTTAAAAT
6016157 ATATTTGATTTATTATATTTTAAAAT
1 ATATTT-ATTT-TTATATTTTAAAAT
6016183 -T-TTTATTT
1 ATATTTATTT
6016191 AATGAAATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
23 4 0.13
24 9 0.30
25 5 0.17
26 12 0.40
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (24 bp):
ATATTTATTTTTATATTTTAAAAT
Found at i:6017699 original size:27 final size:26
Alignment explanation
Indices: 6017662--6017776 Score: 149
Period size: 27 Copynumber: 4.3 Consensus size: 26
6017652 AGCATGGCTG
* *
6017662 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
6017688 CCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
6017716 CCAGAACAGATATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* * *
6017743 CCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
6017770 CCAGAAC
1 CCAGAAC
6017777 GCTTCCTCCA
Statistics
Matches: 80, Mismatches: 6, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
26 5 0.06
27 58 0.73
28 17 0.21
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:6017721 original size:54 final size:54
Alignment explanation
Indices: 6017662--6017776 Score: 169
Period size: 54 Copynumber: 2.1 Consensus size: 54
6017652 AGCATGGCTG
*
6017662 CCAGAACAGATA-ATGTGACAGAGTCACCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGAT-CAGATAATCGTGGCAGAGCCA
* * * *
6017716 CCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
6017770 CCAGAAC
1 CCAGAAC
6017777 GCTTCCTCCA
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
54 37 0.67
55 18 0.33
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (54 bp):
CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
Found at i:6019426 original size:26 final size:26
Alignment explanation
Indices: 6019390--6019473 Score: 150
Period size: 26 Copynumber: 3.2 Consensus size: 26
6019380 CATGAAATTC
6019390 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
6019416 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
6019442 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
6019468 TTATCA
1 TTATCA
6019474 ATTTGTATCA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 56 1.00
ACGTcount: A:0.37, C:0.25, G:0.05, T:0.33
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:6024921 original size:27 final size:26
Alignment explanation
Indices: 6024884--6024998 Score: 149
Period size: 27 Copynumber: 4.3 Consensus size: 26
6024874 AGCATGGCTG
* *
6024884 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
6024910 CCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
6024938 CCAGAACAGATATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* * *
6024965 CCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
6024992 CCAGAAC
1 CCAGAAC
6024999 GCTTCCTCCA
Statistics
Matches: 80, Mismatches: 6, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
26 5 0.06
27 58 0.73
28 17 0.21
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:6024943 original size:54 final size:54
Alignment explanation
Indices: 6024884--6024998 Score: 169
Period size: 54 Copynumber: 2.1 Consensus size: 54
6024874 AGCATGGCTG
*
6024884 CCAGAACAGATA-ATGTGACAGAGTCACCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGAT-CAGATAATCGTGGCAGAGCCA
* * * *
6024938 CCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
6024992 CCAGAAC
1 CCAGAAC
6024999 GCTTCCTCCA
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
54 37 0.67
55 18 0.33
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (54 bp):
CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
Found at i:6026649 original size:26 final size:26
Alignment explanation
Indices: 6026613--6026696 Score: 150
Period size: 26 Copynumber: 3.2 Consensus size: 26
6026603 CATGAAATTC
6026613 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
6026639 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
6026665 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
6026691 TTATCA
1 TTATCA
6026697 ATTTGTATCA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 56 1.00
ACGTcount: A:0.37, C:0.25, G:0.05, T:0.33
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:6032157 original size:27 final size:26
Alignment explanation
Indices: 6032120--6032234 Score: 149
Period size: 27 Copynumber: 4.3 Consensus size: 26
6032110 AGCATGGCTG
* *
6032120 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
6032146 CCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
6032174 CCAGAACAGATATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* * *
6032201 CCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
6032228 CCAGAAC
1 CCAGAAC
6032235 GCTTCCTCCA
Statistics
Matches: 80, Mismatches: 6, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
26 5 0.06
27 58 0.73
28 17 0.21
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:6032179 original size:54 final size:54
Alignment explanation
Indices: 6032120--6032234 Score: 169
Period size: 54 Copynumber: 2.1 Consensus size: 54
6032110 AGCATGGCTG
*
6032120 CCAGAACAGATA-ATGTGACAGAGTCACCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGAT-CAGATAATCGTGGCAGAGCCA
* * * *
6032174 CCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
6032228 CCAGAAC
1 CCAGAAC
6032235 GCTTCCTCCA
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
54 37 0.67
55 18 0.33
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (54 bp):
CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
Found at i:6032398 original size:28 final size:25
Alignment explanation
Indices: 6032337--6032399 Score: 81
Period size: 25 Copynumber: 2.4 Consensus size: 25
6032327 AAATTAACCC
* *
6032337 TAGGGGTATAACGTAATTTTGCACC
1 TAGGGGTATAACGTAATTTTCCACA
6032362 TAGGGGTATAACAGTAATTTTCCATACA
1 TAGGGGTATAAC-GTAATTTTCC--ACA
6032390 TAGGGGTATA
1 TAGGGGTATA
6032400 TATAATTTAG
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
25 12 0.36
26 9 0.27
28 12 0.36
ACGTcount: A:0.32, C:0.13, G:0.24, T:0.32
Consensus pattern (25 bp):
TAGGGGTATAACGTAATTTTCCACA
Found at i:6033881 original size:26 final size:26
Alignment explanation
Indices: 6033845--6033928 Score: 150
Period size: 26 Copynumber: 3.2 Consensus size: 26
6033835 CATGAAATTC
6033845 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
6033871 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
6033897 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
6033923 TTATCA
1 TTATCA
6033929 ATTTGTATCA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 56 1.00
ACGTcount: A:0.37, C:0.25, G:0.05, T:0.33
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:6034728 original size:17 final size:19
Alignment explanation
Indices: 6034693--6034729 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
6034683 TTTAATTAGC
6034693 ATTATGAGATAAAATTATT
1 ATTATGAGATAAAATTATT
*
6034712 ATTATTAGA-AAAA-TATT
1 ATTATGAGATAAAATTATT
6034729 A
1 A
6034730 CTGTATGTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 5 0.29
18 4 0.24
19 8 0.47
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.41
Consensus pattern (19 bp):
ATTATGAGATAAAATTATT
Found at i:6036559 original size:28 final size:28
Alignment explanation
Indices: 6036527--6036580 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
6036517 CGTAGATCAC
6036527 GAAATTACCCCTAAAGAGCAAAATTATT
1 GAAATTACCCCTAAAGAGCAAAATTATT
6036555 GAAATTACCCCTAAAGAGCAAAATTA
1 GAAATTACCCCTAAAGAGCAAAATTA
6036581 CCGATATACC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.48, C:0.19, G:0.11, T:0.22
Consensus pattern (28 bp):
GAAATTACCCCTAAAGAGCAAAATTATT
Found at i:6042342 original size:21 final size:21
Alignment explanation
Indices: 6042318--6042358 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
6042308 ATATAAGTAC
* *
6042318 AATAACAATAATGGTAATAAA
1 AATAAAAATAATAGTAATAAA
6042339 AATAAAAATAATAGTAATAA
1 AATAAAAATAATAGTAATAA
6042359 TAGCACGTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.66, C:0.02, G:0.07, T:0.24
Consensus pattern (21 bp):
AATAAAAATAATAGTAATAAA
Found at i:6042552 original size:12 final size:12
Alignment explanation
Indices: 6042508--6042555 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
6042498 TGTTCATGCG
*
6042508 TAAATATAAAGA
1 TAAATATAAACA
**
6042520 TAGGTATAATACA
1 TAAATATAA-ACA
6042533 TAAAATATAAACA
1 T-AAATATAAACA
6042546 TAAATATAAA
1 TAAATATAAA
6042556 GAGATAAATA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
12 16 0.55
13 7 0.24
14 6 0.21
ACGTcount: A:0.62, C:0.04, G:0.06, T:0.27
Consensus pattern (12 bp):
TAAATATAAACA
Found at i:6043259 original size:21 final size:21
Alignment explanation
Indices: 6043229--6043272 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
6043219 TTCGAAAATA
6043229 AAATAAAAAGGAAAA-AATAAT
1 AAATAAAAA-GAAAATAATAAT
*
6043250 AAATAGAAAGAAAATAATAAT
1 AAATAAAAAGAAAATAATAAT
6043271 AA
1 AA
6043273 TGTAATATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.75, C:0.00, G:0.09, T:0.16
Consensus pattern (21 bp):
AAATAAAAAGAAAATAATAAT
Done.