Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 97507971
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: 97507971
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 232 characters in sequence are not A, C, G, or T
File 178 of 328
Found at i:52805200 original size:56 final size:56
Alignment explanation
Indices: 52805114--52805235 Score: 190
Period size: 56 Copynumber: 2.2 Consensus size: 56
52805104 AAATCTGCAA
* * * *
52805114 ACACATTGCTCACTGACCGATCTCGCACACATATTGCTCGGTTAAAGAATTCGCAC
1 ACACAGTGCCCACTGACCGATCTCGCACACATAGTGCTCGGTTAAAGAATTCACAC
* *
52805170 ACACAGTGCCCACTGATCGATCTCGTACACATAGTGCTCGGTTAAAGAATTCACAC
1 ACACAGTGCCCACTGACCGATCTCGCACACATAGTGCTCGGTTAAAGAATTCACAC
52805226 ACACAGTGCC
1 ACACAGTGCC
52805236 TCAATTCATT
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
56 60 1.00
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.23
Consensus pattern (56 bp):
ACACAGTGCCCACTGACCGATCTCGCACACATAGTGCTCGGTTAAAGAATTCACAC
Found at i:52805452 original size:43 final size:43
Alignment explanation
Indices: 52805391--52805533 Score: 187
Period size: 43 Copynumber: 3.3 Consensus size: 43
52805381 CTTTGCTAGT
** * * *
52805391 ATCACCGGCATTAAGCCTGTTAGGCACGAAGACCCAAATACAC
1 ATCACCGGCACGAAGCCTGCTAGGCACGAAGGCCCGAATACAC
*
52805434 ATCACCGGCACGAAGCCTGCTAGGAACGAAGGCCCGAATACAC
1 ATCACCGGCACGAAGCCTGCTAGGCACGAAGGCCCGAATACAC
* * * * *
52805477 ATCACCAGCACAAAGCCTGCTAGGCATGAAGGCCTGATTACAC
1 ATCACCGGCACGAAGCCTGCTAGGCACGAAGGCCCGAATACAC
52805520 ATCACCGGCACGAA
1 ATCACCGGCACGAA
52805534 TGCCCTTCAG
Statistics
Matches: 86, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 86 1.00
ACGTcount: A:0.34, C:0.31, G:0.22, T:0.13
Consensus pattern (43 bp):
ATCACCGGCACGAAGCCTGCTAGGCACGAAGGCCCGAATACAC
Found at i:52805587 original size:40 final size:40
Alignment explanation
Indices: 52805522--52805682 Score: 259
Period size: 40 Copynumber: 4.0 Consensus size: 40
52805512 GATTACACAT
* * * * *
52805522 CACCGGCACGAATGCCCTTCAGGACTTAGCCCAGATGTAA
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
*
52805562 CACCAGCACGAATGCTCTTCGGGACTTAGCTCGGATATAA
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
52805602 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
*
52805642 CACCAGCACGAATGCTCTTTGGGACTTAGCCCGGATATAA
1 CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
52805682 C
1 C
52805683 TCTCAATTCT
Statistics
Matches: 113, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 113 1.00
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.20
Consensus pattern (40 bp):
CACCAGCACGAATGCTCTTCGGGACTTAGCCCGGATATAA
Found at i:52812069 original size:10 final size:10
Alignment explanation
Indices: 52812054--52812102 Score: 71
Period size: 10 Copynumber: 4.8 Consensus size: 10
52812044 GTATAATGTG
52812054 CATATCATAA
1 CATATCATAA
**
52812064 CATATCATGTG
1 CATATCAT-AA
52812075 CATATCATAA
1 CATATCATAA
52812085 CATATCATAA
1 CATATCATAA
52812095 CATATCAT
1 CATATCAT
52812103 GTGCATATCA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
10 26 0.76
11 8 0.24
ACGTcount: A:0.43, C:0.20, G:0.04, T:0.33
Consensus pattern (10 bp):
CATATCATAA
Found at i:52812075 original size:21 final size:21
Alignment explanation
Indices: 52812049--52812092 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
52812039 CATGCGTATA
52812049 ATGTGCATATCATAACATATC
1 ATGTGCATATCATAACATATC
52812070 ATGTGCATATCATAACATATC
1 ATGTGCATATCATAACATATC
52812091 AT
1 AT
52812093 AACATATCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.18, G:0.09, T:0.34
Consensus pattern (21 bp):
ATGTGCATATCATAACATATC
Found at i:52812121 original size:10 final size:11
Alignment explanation
Indices: 52812049--52812125 Score: 63
Period size: 10 Copynumber: 7.4 Consensus size: 11
52812039 CATGCGTATA
52812049 ATGTGCATATC
1 ATGTGCATATC
**
52812060 AT-AACATATC
1 ATGTGCATATC
52812070 ATGTGCATATC
1 ATGTGCATATC
**
52812081 AT-AACATATC
1 ATGTGCATATC
**
52812091 AT-AACATATC
1 ATGTGCATATC
52812101 ATGTGCATATC
1 ATGTGCATATC
*
52812112 ATGT-CCTATC
1 ATGTGCATATC
52812122 ATGT
1 ATGT
52812126 ATATCAATAT
Statistics
Matches: 55, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
10 35 0.64
11 20 0.36
ACGTcount: A:0.35, C:0.19, G:0.10, T:0.35
Consensus pattern (11 bp):
ATGTGCATATC
Found at i:52812123 original size:31 final size:31
Alignment explanation
Indices: 52812054--52812113 Score: 120
Period size: 31 Copynumber: 1.9 Consensus size: 31
52812044 GTATAATGTG
52812054 CATATCATAACATATCATGTGCATATCATAA
1 CATATCATAACATATCATGTGCATATCATAA
52812085 CATATCATAACATATCATGTGCATATCAT
1 CATATCATAACATATCATGTGCATATCAT
52812114 GTCCTATCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.40, C:0.20, G:0.07, T:0.33
Consensus pattern (31 bp):
CATATCATAACATATCATGTGCATATCATAA
Found at i:52814368 original size:27 final size:27
Alignment explanation
Indices: 52814338--52814391 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
52814328 AACAAAGAAA
52814338 ACAT-CCATGGAAGAGTTCTTGGGTTCG
1 ACATACCAT-GAAGAGTTCTTGGGTTCG
*
52814365 ACATACTATGAAGAGTTCTTGGGTTCG
1 ACATACCATGAAGAGTTCTTGGGTTCG
52814392 GTACACTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 22 0.88
28 3 0.12
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.31
Consensus pattern (27 bp):
ACATACCATGAAGAGTTCTTGGGTTCG
Found at i:52814399 original size:27 final size:27
Alignment explanation
Indices: 52814347--52814400 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
52814337 AACATCCATG
*
52814347 GAAGAGTTCTTGGGTTCGACATACTAT
1 GAAGAGTTCTTGGGTTCGACACACTAT
**
52814374 GAAGAGTTCTTGGGTTCGGTACACTAT
1 GAAGAGTTCTTGGGTTCGACACACTAT
52814401 TAGCTTGATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.24, C:0.15, G:0.28, T:0.33
Consensus pattern (27 bp):
GAAGAGTTCTTGGGTTCGACACACTAT
Found at i:52816973 original size:27 final size:27
Alignment explanation
Indices: 52816926--52816986 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
52816916 GGGGTAAAAT
**
52816926 AGTAATTTTACCCCACGAGGGTATCTC
1 AGTAATTTTACCCCAAAAGGGTATCTC
* * *
52816953 GGTAATTTTACCCTAAAAGGGTATTTC
1 AGTAATTTTACCCCAAAAGGGTATCTC
52816980 AGTAATT
1 AGTAATT
52816987 CTCCCTTACA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (27 bp):
AGTAATTTTACCCCAAAAGGGTATCTC
Found at i:52817001 original size:27 final size:27
Alignment explanation
Indices: 52816971--52817032 Score: 97
Period size: 27 Copynumber: 2.3 Consensus size: 27
52816961 TACCCTAAAA
* *
52816971 GGGTATTTCAGTAATTCTCCCTTACAG
1 GGGTATTTCAATAATTCTACCTTACAG
*
52816998 GGGTATTTCAATAATTCTATCTTACAG
1 GGGTATTTCAATAATTCTACCTTACAG
52817025 GGGTATTT
1 GGGTATTT
52817033 TGGTAATTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.24, C:0.16, G:0.19, T:0.40
Consensus pattern (27 bp):
GGGTATTTCAATAATTCTACCTTACAG
Found at i:52817117 original size:27 final size:26
Alignment explanation
Indices: 52817025--52817119 Score: 88
Period size: 27 Copynumber: 3.7 Consensus size: 26
52817015 TATCTTACAG
* *
52817025 GGGTATTTTGGTAATTTTACAAAT-TA
1 GGGTATTTTGGTAATTTT-CTAATCCA
* *
52817051 GGGGTATTTTGGTAATTTTATAAACCA
1 -GGGTATTTTGGTAATTTTCTAATCCA
* *
52817078 --ATATTTTGGTAATTTTGCTAATCGA
1 GGGTATTTTGGTAATTTT-CTAATCCA
52817103 GGGTATTTTGGTAATTT
1 GGGTATTTTGGTAATTT
52817120 GGTAAACTAA
Statistics
Matches: 55, Mismatches: 9, Indels: 8
0.76 0.12 0.11
Matches are distributed among these distances:
24 15 0.27
25 5 0.09
26 2 0.04
27 33 0.60
ACGTcount: A:0.27, C:0.05, G:0.21, T:0.46
Consensus pattern (26 bp):
GGGTATTTTGGTAATTTTCTAATCCA
Found at i:52817126 original size:51 final size:51
Alignment explanation
Indices: 52817028--52817126 Score: 137
Period size: 51 Copynumber: 1.9 Consensus size: 51
52817018 CTTACAGGGG
* *
52817028 TATTTTGGTAATTTTACAAATTAGGGGTATTTTGGTAATTTTATAAACCAA
1 TATTTTGGTAATTTTACAAATGAGGGGTATTTTGGTAATTTGATAAACCAA
* * *
52817079 TATTTTGGTAATTTTGCTAATCGA-GGGTATTTTGGTAATTTGGTAAAC
1 TATTTTGGTAATTTTACAAAT-GAGGGGTATTTTGGTAATTTGATAAAC
52817127 TAAAGTATTC
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
51 41 0.98
52 1 0.02
ACGTcount: A:0.29, C:0.06, G:0.19, T:0.45
Consensus pattern (51 bp):
TATTTTGGTAATTTTACAAATGAGGGGTATTTTGGTAATTTGATAAACCAA
Found at i:52818064 original size:22 final size:22
Alignment explanation
Indices: 52818039--52818097 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 22
52818029 CAACTTGTAT
*
52818039 GAGCTTACTGTTCAGCTCGATA
1 GAGCTTACTGTTCAGCTCAATA
* *
52818061 GAGCTTACCGTTTCAGCTTAATA
1 GAGCTTACTG-TTCAGCTCAATA
*
52818084 GAGCTTACTATTCA
1 GAGCTTACTGTTCA
52818098 TTAGCTCAAG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
22 13 0.42
23 18 0.58
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.34
Consensus pattern (22 bp):
GAGCTTACTGTTCAGCTCAATA
Found at i:52818065 original size:45 final size:45
Alignment explanation
Indices: 52817991--52818097 Score: 119
Period size: 45 Copynumber: 2.3 Consensus size: 45
52817981 GTGTTACATA
* *
52817991 AGAGCTTACTGTTTTCAGCTCATTGGAGCTTACCATTTCAACTT-GT
1 AGAGCTTACTG--TTCAGCTCATTAGAGCTTACCATTTCAACTTAAT
* *
52818037 ATGAGCTTACTGTTCAGCTCGA-TAGAGCTTACCGTTTCAGCTTAAT
1 A-GAGCTTACTGTTCAGCTC-ATTAGAGCTTACCATTTCAACTTAAT
*
52818083 AGAGCTTACTATTCA
1 AGAGCTTACTGTTCA
52818098 TTAGCTCAAG
Statistics
Matches: 53, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
45 39 0.74
46 4 0.08
47 10 0.19
ACGTcount: A:0.24, C:0.21, G:0.18, T:0.36
Consensus pattern (45 bp):
AGAGCTTACTGTTCAGCTCATTAGAGCTTACCATTTCAACTTAAT
Found at i:52818084 original size:23 final size:23
Alignment explanation
Indices: 52817991--52818091 Score: 80
Period size: 23 Copynumber: 4.4 Consensus size: 23
52817981 GTGTTACATA
* *
52817991 AGAGCTTACTGTTTTCAGCTCATT
1 AGAGCTTACCG-TTTCAGCTCAAT
* * * **
52818015 GGAGCTTACCATTTCAACT-TGT
1 AGAGCTTACCGTTTCAGCTCAAT
* *
52818037 ATGAGCTTACTG-TTCAGCTCGAT
1 A-GAGCTTACCGTTTCAGCTCAAT
*
52818060 AGAGCTTACCGTTTCAGCTTAAT
1 AGAGCTTACCGTTTCAGCTCAAT
52818083 AGAGCTTAC
1 AGAGCTTAC
52818092 TATTCATTAG
Statistics
Matches: 59, Mismatches: 15, Indels: 7
0.73 0.19 0.09
Matches are distributed among these distances:
22 16 0.27
23 35 0.59
24 8 0.14
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.36
Consensus pattern (23 bp):
AGAGCTTACCGTTTCAGCTCAAT
Found at i:52820845 original size:6 final size:6
Alignment explanation
Indices: 52820834--52820889 Score: 60
Period size: 6 Copynumber: 9.0 Consensus size: 6
52820824 AAAAGCGTAT
* *
52820834 GAAAAA GAAAAA GAAATA GAAAAA GAAAAAA GAATGAAA G-AAAA CAAAAA
1 GAAAAA GAAAAA GAAAAA GAAAAA G-AAAAA GAA--AAA GAAAAA GAAAAA
52820884 GAAAAA
1 GAAAAA
52820890 AAGAGTGAGA
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
5 3 0.07
6 28 0.67
7 7 0.17
8 4 0.10
ACGTcount: A:0.79, C:0.02, G:0.16, T:0.04
Consensus pattern (6 bp):
GAAAAA
Found at i:52820920 original size:27 final size:27
Alignment explanation
Indices: 52820835--52820909 Score: 93
Period size: 27 Copynumber: 2.9 Consensus size: 27
52820825 AAAGCGTATG
*
52820835 AAAAAGAA--AAAGAAATAGAAAAAGAA
1 AAAAAGAATGAAAGAAA-ACAAAAAGAA
52820861 A-AAAGAATGAAAGAAAACAAAAAGAA
1 AAAAAGAATGAAAGAAAACAAAAAGAA
* *
52820887 AAAAAGAGTGAGAGAAAACAAAA
1 AAAAAGAATGAAAGAAAACAAAA
52820910 TGAGATTAAG
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
25 6 0.14
26 11 0.26
27 26 0.60
ACGTcount: A:0.76, C:0.03, G:0.17, T:0.04
Consensus pattern (27 bp):
AAAAAGAATGAAAGAAAACAAAAAGAA
Found at i:52824587 original size:20 final size:21
Alignment explanation
Indices: 52824562--52824609 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
52824552 TTCTATTCAG
52824562 AGGCATCAGATTG-G-AAACAA
1 AGGCATC-GATTGTGCAAACAA
*
52824582 AGGCAT-GATTGTGCAATCAA
1 AGGCATCGATTGTGCAAACAA
52824602 AGGCATCG
1 AGGCATCG
52824610 GGGTGAAAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
18 5 0.21
19 1 0.04
20 17 0.71
21 1 0.04
ACGTcount: A:0.38, C:0.17, G:0.27, T:0.19
Consensus pattern (21 bp):
AGGCATCGATTGTGCAAACAA
Found at i:52827027 original size:9 final size:9
Alignment explanation
Indices: 52827013--52827043 Score: 62
Period size: 9 Copynumber: 3.4 Consensus size: 9
52827003 CAAACAACTA
52827013 AAAAATAAT
1 AAAAATAAT
52827022 AAAAATAAT
1 AAAAATAAT
52827031 AAAAATAAT
1 AAAAATAAT
52827040 AAAA
1 AAAA
52827044 GAAGGAACGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (9 bp):
AAAAATAAT
Found at i:52827066 original size:23 final size:23
Alignment explanation
Indices: 52827031--52827074 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
52827021 TAAAAATAAT
*
52827031 AAAAATAATAAAAG-AAGGAACG
1 AAAAATAAGAAAAGAAAGGAACG
52827053 AAAAATAAAGAAAAGAAAGGAA
1 AAAAAT-AAGAAAAGAAAGGAA
52827075 ATATCTAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 6 0.32
23 7 0.37
24 6 0.32
ACGTcount: A:0.73, C:0.02, G:0.18, T:0.07
Consensus pattern (23 bp):
AAAAATAAGAAAAGAAAGGAACG
Found at i:52827274 original size:38 final size:38
Alignment explanation
Indices: 52827232--52827307 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
52827222 TTCGAAACCC
52827232 CATTTTCAATATTCGAGTTCGTAAATGTTAACTATTTA
1 CATTTTCAATATTCGAGTTCGTAAATGTTAACTATTTA
*
52827270 CATTTTCAATATTTGAGTTCGTAAATGTTAACTATTTA
1 CATTTTCAATATTCGAGTTCGTAAATGTTAACTATTTA
52827308 ATATTTACAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.32, C:0.12, G:0.11, T:0.46
Consensus pattern (38 bp):
CATTTTCAATATTCGAGTTCGTAAATGTTAACTATTTA
Found at i:52829225 original size:37 final size:37
Alignment explanation
Indices: 52829184--52829296 Score: 96
Period size: 35 Copynumber: 3.2 Consensus size: 37
52829174 TGGTATGTGT
52829184 TATTGGAATGTCGTGATTGAGGTGCCTATGTTAGGTA
1 TATTGGAATGTCGTGATTGAGGTGCCTATGTTAGGTA
* ** *
52829221 TATTGG-TTG-AATGTTTGATGGTG--TGAT-TTA--TCA
1 TATTGGAATGTCGTGATTGA-GGTGCCT-ATGTTAGGT-A
* *
52829254 TACTGGAATGTCGTGATTGAGGTGCCTATGTTAGGCA
1 TATTGGAATGTCGTGATTGAGGTGCCTATGTTAGGTA
52829291 TATTGG
1 TATTGG
52829297 TTGAATGTTT
Statistics
Matches: 55, Mismatches: 11, Indels: 20
0.64 0.13 0.23
Matches are distributed among these distances:
32 1 0.02
33 6 0.11
34 10 0.18
35 16 0.29
36 10 0.18
37 12 0.22
ACGTcount: A:0.21, C:0.08, G:0.31, T:0.40
Consensus pattern (37 bp):
TATTGGAATGTCGTGATTGAGGTGCCTATGTTAGGTA
Found at i:52829234 original size:40 final size:40
Alignment explanation
Indices: 52829189--52829304 Score: 103
Period size: 40 Copynumber: 3.1 Consensus size: 40
52829179 TGTGTTATTG
52829189 GAATGTCGTGATTGAGGTGCCTATGTTAGGTATATTGGTT
1 GAATGTCGTGATTGAGGTGCCTATGTTAGGTATATTGGTT
* *
52829229 GAATGT-TTGA-T--GGTG--TGAT-TTA--TCATACT-G--
1 GAATGTCGTGATTGAGGTGCCT-ATGTTAGGT-ATATTGGTT
*
52829259 GAATGTCGTGATTGAGGTGCCTATGTTAGGCATATTGGTT
1 GAATGTCGTGATTGAGGTGCCTATGTTAGGTATATTGGTT
52829299 GAATGT
1 GAATGT
52829305 TTGATTGTGT
Statistics
Matches: 57, Mismatches: 5, Indels: 28
0.63 0.06 0.31
Matches are distributed among these distances:
30 6 0.11
31 3 0.05
32 3 0.05
33 4 0.07
34 8 0.14
35 4 0.07
36 8 0.14
37 4 0.07
38 2 0.04
39 3 0.05
40 12 0.21
ACGTcount: A:0.22, C:0.08, G:0.31, T:0.40
Consensus pattern (40 bp):
GAATGTCGTGATTGAGGTGCCTATGTTAGGTATATTGGTT
Found at i:52829300 original size:70 final size:70
Alignment explanation
Indices: 52829187--52829327 Score: 264
Period size: 70 Copynumber: 2.0 Consensus size: 70
52829177 TATGTGTTAT
*
52829187 TGGAATGTCGTGATTGAGGTGCCTATGTTAGGTATATTGGTTGAATGTTTGATGGTGTGATTTAT
1 TGGAATGTCGTGATTGAGGTGCCTATGTTAGGCATATTGGTTGAATGTTTGATGGTGTGATTTAT
52829252 CATAC
66 CATAC
*
52829257 TGGAATGTCGTGATTGAGGTGCCTATGTTAGGCATATTGGTTGAATGTTTGATTGTGTGATTTAT
1 TGGAATGTCGTGATTGAGGTGCCTATGTTAGGCATATTGGTTGAATGTTTGATGGTGTGATTTAT
52829322 CATAC
66 CATAC
52829327 T
1 T
52829328 TCGAATAATA
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
70 69 1.00
ACGTcount: A:0.21, C:0.08, G:0.29, T:0.42
Consensus pattern (70 bp):
TGGAATGTCGTGATTGAGGTGCCTATGTTAGGCATATTGGTTGAATGTTTGATGGTGTGATTTAT
CATAC
Found at i:52831582 original size:15 final size:15
Alignment explanation
Indices: 52831562--52831598 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
52831552 GATGATATTG
*
52831562 AGATCGATAAAACAA
1 AGATCGAGAAAACAA
*
52831577 AGATCGAGAAAACGA
1 AGATCGAGAAAACAA
52831592 AGATCGA
1 AGATCGA
52831599 ACTATAAAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.54, C:0.14, G:0.22, T:0.11
Consensus pattern (15 bp):
AGATCGAGAAAACAA
Found at i:52838031 original size:27 final size:27
Alignment explanation
Indices: 52838001--52838198 Score: 243
Period size: 27 Copynumber: 7.3 Consensus size: 27
52837991 TACTGAAATG
* *
52838001 CCCTCGATTTGTAGAATTATCATTTTA
1 CCCTCGATTTATAGAATTACCATTTTA
* *
52838028 CCCTCGATTTATAGAATTACCGTTTCA
1 CCCTCGATTTATAGAATTACCATTTTA
* *
52838055 CCGTCGATTTATAAAATTACCATTTTA
1 CCCTCGATTTATAGAATTACCATTTTA
*
52838082 CCCTTGATTTATAGAATTACCATTTTA
1 CCCTCGATTTATAGAATTACCATTTTA
* *
52838109 CCCTTGATTTGTAGAATTACCATTTTA
1 CCCTCGATTTATAGAATTACCATTTTA
* *
52838136 CCCTCGATTTACAAAATTACCATTTTA
1 CCCTCGATTTATAGAATTACCATTTTA
* * * * *
52838163 CCCTCAATTTACAAAATTATCGTTTTA
1 CCCTCGATTTATAGAATTACCATTTTA
*
52838190 CCCTTGATT
1 CCCTCGATT
52838199 GTGAAATTAC
Statistics
Matches: 150, Mismatches: 21, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 150 1.00
ACGTcount: A:0.29, C:0.22, G:0.08, T:0.41
Consensus pattern (27 bp):
CCCTCGATTTATAGAATTACCATTTTA
Found at i:52838124 original size:81 final size:81
Alignment explanation
Indices: 52838001--52838198 Score: 279
Period size: 81 Copynumber: 2.4 Consensus size: 81
52837991 TACTGAAATG
* * * *
52838001 CCCTCGATTTGTAGAATTATCATTTTACCCTCGATTTATAGAATTACCGTTTCACCGTCGATTTA
1 CCCTCGATTTATAGAATTATCATTTTACCCTTGATTTATAGAATTACCATTTCACCCTCGATTTA
*
52838066 TAAAATTACCATTTTA
66 CAAAATTACCATTTTA
* * * *
52838082 CCCTTGATTTATAGAATTACCATTTTACCCTTGATTTGTAGAATTACCATTTTACCCTCGATTTA
1 CCCTCGATTTATAGAATTATCATTTTACCCTTGATTTATAGAATTACCATTTCACCCTCGATTTA
52838147 CAAAATTACCATTTTA
66 CAAAATTACCATTTTA
* * * *
52838163 CCCTCAATTTACAAAATTATCGTTTTACCCTTGATT
1 CCCTCGATTTATAGAATTATCATTTTACCCTTGATT
52838199 GTGAAATTAC
Statistics
Matches: 102, Mismatches: 15, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
81 102 1.00
ACGTcount: A:0.29, C:0.22, G:0.08, T:0.41
Consensus pattern (81 bp):
CCCTCGATTTATAGAATTATCATTTTACCCTTGATTTATAGAATTACCATTTCACCCTCGATTTA
CAAAATTACCATTTTA
Found at i:52838271 original size:54 final size:54
Alignment explanation
Indices: 52838197--52838326 Score: 165
Period size: 54 Copynumber: 2.4 Consensus size: 54
52838187 TTACCCTTGA
* *
52838197 TTGTGAAATTACTGAAATACCCCT-GTAGGATAGA-ATTACCAAAATACCCCTAGT
1 TTGTGAAATTACCGAAATACCCCTAGTAGG-TA-ATATTACCAAAATACCACTAGT
* * ** *
52838251 TTGTAAAATTACCAAAATACCCCTAGTTTGTAATATTACCGAAATACCACTAGT
1 TTGTGAAATTACCGAAATACCCCTAGTAGGTAATATTACCAAAATACCACTAGT
52838305 TTGTGAAATTACCGAAATACCC
1 TTGTGAAATTACCGAAATACCC
52838327 TCAATTTGTA
Statistics
Matches: 65, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
53 1 0.02
54 61 0.94
55 3 0.05
ACGTcount: A:0.38, C:0.21, G:0.12, T:0.29
Consensus pattern (54 bp):
TTGTGAAATTACCGAAATACCCCTAGTAGGTAATATTACCAAAATACCACTAGT
Found at i:52838360 original size:27 final size:27
Alignment explanation
Indices: 52838230--52838355 Score: 173
Period size: 27 Copynumber: 4.7 Consensus size: 27
52838220 TGTAGGATAG
52838230 AATTACCAAAATACCCCTAGTTTGTAA
1 AATTACCAAAATACCCCTAGTTTGTAA
52838257 AATTACCAAAATACCCCTAGTTTGTAA
1 AATTACCAAAATACCCCTAGTTTGTAA
* * * *
52838284 TATTACCGAAATACCACTAGTTTGTGA
1 AATTACCAAAATACCCCTAGTTTGTAA
* *
52838311 AATTACCGAAATA-CCCTCAATTTGTAA
1 AATTACCAAAATACCCCT-AGTTTGTAA
*
52838338 AATTATCAAAATACCCCT
1 AATTACCAAAATACCCCT
52838356 GATTTACAAA
Statistics
Matches: 87, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
26 3 0.03
27 80 0.92
28 4 0.05
ACGTcount: A:0.40, C:0.22, G:0.08, T:0.30
Consensus pattern (27 bp):
AATTACCAAAATACCCCTAGTTTGTAA
Found at i:52838453 original size:27 final size:27
Alignment explanation
Indices: 52838230--52838466 Score: 129
Period size: 27 Copynumber: 8.7 Consensus size: 27
52838220 TGTAGGATAG
* * *
52838230 AATTACCAAAATACCCCTAGTTTGTAA
1 AATTACCAAAATACCCTTGGTTTATAA
* * *
52838257 AATTACCAAAATACCCCTAGTTTGTAA
1 AATTACCAAAATACCCTTGGTTTATAA
* * * * *
52838284 TATTACCGAAATACCAC-TAGTTTGTGA
1 AATTACCAAAATACC-CTTGGTTTATAA
* *** *
52838311 AATTACCGAAATACCCTCAATTTGTAA
1 AATTACCAAAATACCCTTGGTTTATAA
* * * *
52838338 AATTATCAAAATACCCCTGATTTACAA
1 AATTACCAAAATACCCTTGGTTTATAA
* * * *
52838365 AATTA-GAGAAATTCCCTTGACTTTCTAAA
1 AATTACCA-AAATACCCTTG-GTTTAT-AA
* *
52838394 AATTA-TAGAAATACCATTGGTTTATAA
1 AATTACCA-AAATACCCTTGGTTTATAA
* * *
52838421 AATTACTAAAATACCCTTGGTTTGTAG
1 AATTACCAAAATACCCTTGGTTTATAA
* *
52838448 ATTTACCAAAACACCCTTG
1 AATTACCAAAATACCCTTG
52838467 TAGGATGAAA
Statistics
Matches: 173, Mismatches: 31, Indels: 12
0.80 0.14 0.06
Matches are distributed among these distances:
26 2 0.01
27 143 0.83
28 10 0.06
29 18 0.10
ACGTcount: A:0.39, C:0.19, G:0.09, T:0.32
Consensus pattern (27 bp):
AATTACCAAAATACCCTTGGTTTATAA
Found at i:52839397 original size:25 final size:23
Alignment explanation
Indices: 52839359--52839427 Score: 77
Period size: 25 Copynumber: 2.9 Consensus size: 23
52839349 AGGAAGTGCT
*
52839359 AAAAGGGCTCTGCCCTAGTTTACCG
1 AAAAGGGCTTTGCCCTAGTTTA--G
52839384 AAAAGGGCTTTGCCCTAGTTATTAG
1 AAAAGGGCTTTGCCCTAG-T-TTAG
*
52839409 AAAA-GGCTTTGCCCCAGTT
1 AAAAGGGCTTTGCCCTAGTT
52839428 ATTAAAAGAG
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
22 1 0.03
23 1 0.03
24 12 0.30
25 22 0.55
26 1 0.03
27 3 0.08
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.28
Consensus pattern (23 bp):
AAAAGGGCTTTGCCCTAGTTTAG
Found at i:52839421 original size:24 final size:25
Alignment explanation
Indices: 52839383--52839431 Score: 82
Period size: 24 Copynumber: 2.0 Consensus size: 25
52839373 CTAGTTTACC
*
52839383 GAAAAGGGCTTTGCCCTAGTTATTA
1 GAAAAGGGCTTTGCCCCAGTTATTA
52839408 GAAAA-GGCTTTGCCCCAGTTATTA
1 GAAAAGGGCTTTGCCCCAGTTATTA
52839432 AAAGAGGTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 18 0.78
25 5 0.22
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (25 bp):
GAAAAGGGCTTTGCCCCAGTTATTA
Found at i:52839638 original size:42 final size:42
Alignment explanation
Indices: 52839575--52839708 Score: 241
Period size: 42 Copynumber: 3.2 Consensus size: 42
52839565 TAGTCTCCCC
52839575 AAATGGGCTTGCATACATTCATTGACATTACATGTGATATTG
1 AAATGGGCTTGCATACATTCATTGACATTACATGTGATATTG
*
52839617 AAATGGGCTTGCATACTTTCATTGACATTACATGTGATATTG
1 AAATGGGCTTGCATACATTCATTGACATTACATGTGATATTG
* *
52839659 AAATGGACTTGCATACATCCATTGACATTACATGTGATATTG
1 AAATGGGCTTGCATACATTCATTGACATTACATGTGATATTG
52839701 AAATGGGC
1 AAATGGGC
52839709 CTAAGGGCCA
Statistics
Matches: 87, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 87 1.00
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.34
Consensus pattern (42 bp):
AAATGGGCTTGCATACATTCATTGACATTACATGTGATATTG
Found at i:52839770 original size:31 final size:31
Alignment explanation
Indices: 52839732--52839815 Score: 125
Period size: 31 Copynumber: 2.7 Consensus size: 31
52839722 CGTTTACAGT
*
52839732 AAAGGCTTCGGTCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
* * *
52839763 AAAGGCTTTGGCCCAGTGGTATGATTTATGG
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
52839794 AAAGGCTTCGGCCCAGT-ATATG
1 AAAGGCTTCGGCCCAGTGATATG
52839816 TCAAGACTAA
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
30 4 0.09
31 43 0.91
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.30
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGATATGATTTATGA
Found at i:52851812 original size:71 final size:72
Alignment explanation
Indices: 52851730--52851891 Score: 238
Period size: 71 Copynumber: 2.3 Consensus size: 72
52851720 CATCATGTGT
* * * **
52851730 ACAAGAAAGCTACGAGACACCCTGTA-GTAGCTAGGTCACATGCGTGATTCCAAGTGAAGGACAC
1 ACAAGAGAGCTACGAGACAACATAAATGTAGCTAGGTCACATGCGTGATTCCAAGTGAAGGACAC
52851794 CATGTAG
66 CATGTAG
* * *
52851801 ACAAGAGAGCTACGTGA-AAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACAC
1 ACAAGAGAGCTACGAGACAACATAAATGTAGCTAGGTCACATGCGTGATTCCAAGTGAAGGACAC
52851865 CATGTAG
66 CATGTAG
52851872 ACAAGAGAGCTACGAGACAA
1 ACAAGAGAGCTACGAGACAA
52851892 ATCGGTTGGG
Statistics
Matches: 80, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
70 3 0.04
71 75 0.94
72 2 0.03
ACGTcount: A:0.36, C:0.20, G:0.27, T:0.17
Consensus pattern (72 bp):
ACAAGAGAGCTACGAGACAACATAAATGTAGCTAGGTCACATGCGTGATTCCAAGTGAAGGACAC
CATGTAG
Found at i:52861261 original size:22 final size:19
Alignment explanation
Indices: 52861236--52861277 Score: 57
Period size: 22 Copynumber: 2.1 Consensus size: 19
52861226 TGATAATAAC
52861236 TAATATATAATTATATTTATTA
1 TAATATAT-ATTA-A-TTATTA
52861258 TAATATATATTAATTATTA
1 TAATATATATTAATTATTA
52861277 T
1 T
52861278 CAACTTTGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 7 0.35
20 1 0.05
21 4 0.20
22 8 0.40
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
TAATATATATTAATTATTA
Found at i:52861268 original size:16 final size:15
Alignment explanation
Indices: 52861236--52861274 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
52861226 TGATAATAAC
52861236 TAATATATAATTATAT
1 TAAT-TATAATTATAT
*
52861252 TTATTATAATATATAT
1 TAATTATAAT-TATAT
52861268 TAATTAT
1 TAATTAT
52861275 TATCAACTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
TAATTATAATTATAT
Found at i:52869473 original size:38 final size:39
Alignment explanation
Indices: 52869356--52869517 Score: 263
Period size: 39 Copynumber: 4.2 Consensus size: 39
52869346 TGTGTATGAA
*
52869356 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAAT
52869395 TGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAAT
* *
52869434 TGTGCGAGCTATGATATCCGGGCTAA-CCCGAAGGCAAT
1 TGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAAT
* *
52869472 TGTGCGAGTTGTGATATCCGGGTTAAGTCCCGAAGGCATT
1 TGTGCGAGTTGTGATATCCGGGCTAAG-CCCGAAGGCAAT
52869512 TGTGCG
1 TGTGCG
52869518 GGTTACCATA
Statistics
Matches: 114, Mismatches: 7, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
38 35 0.31
39 62 0.54
40 17 0.15
ACGTcount: A:0.23, C:0.20, G:0.32, T:0.25
Consensus pattern (39 bp):
TGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAAT
Found at i:52869484 original size:77 final size:79
Alignment explanation
Indices: 52869367--52869517 Score: 270
Period size: 77 Copynumber: 1.9 Consensus size: 79
52869357 GTGCGAATTG
52869367 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTGTGATATCCGGGCTAAG-CCCGAAGGC
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTGTGATATCCGGGCTAAGTCCCGAAGGC
52869431 AATTGTGCGAGCTA
66 AATTGTGCGAGCTA
*
52869445 TGATATCCGGGCTAA-CCCGAAGGCAATTGTGCGAGTTGTGATATCCGGGTTAAGTCCCGAAGGC
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTGTGATATCCGGGCTAAGTCCCGAAGGC
*
52869509 ATTTGTGCG
66 AATTGTGCG
52869518 GGTTACCATA
Statistics
Matches: 70, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
77 38 0.54
78 32 0.46
ACGTcount: A:0.23, C:0.21, G:0.32, T:0.24
Consensus pattern (79 bp):
TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTGTGATATCCGGGCTAAGTCCCGAAGGC
AATTGTGCGAGCTA
Found at i:52869533 original size:40 final size:39
Alignment explanation
Indices: 52869356--52869547 Score: 251
Period size: 39 Copynumber: 4.9 Consensus size: 39
52869346 TGTGTATGAA
* *
52869356 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAGTTATGATATCCGGGCTAAGCCCGAAGGCAAT
*
52869395 TGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAGTTATGATATCCGGGCTAAGCCCGAAGGCAAT
*
52869434 TGTGCGAGCTATGATATCCGGGCTAA-CCCGAAGGCAAT
1 TGTGCGAGTTATGATATCCGGGCTAAGCCCGAAGGCAAT
* * *
52869472 TGTGCGAGTTGTGATATCCGGGTTAAGTCCCGAAGGCATT
1 TGTGCGAGTTATGATATCCGGGCTAAG-CCCGAAGGCAAT
* ** * *
52869512 TGTGCGGGTTACCATAACCGGGCTATGTCCCGAAGG
1 TGTGCGAGTTATGATATCCGGGCTAAG-CCCGAAGG
52869548 TTTTGAACAG
Statistics
Matches: 137, Mismatches: 14, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
38 35 0.26
39 62 0.45
40 40 0.29
ACGTcount: A:0.23, C:0.21, G:0.32, T:0.24
Consensus pattern (39 bp):
TGTGCGAGTTATGATATCCGGGCTAAGCCCGAAGGCAAT
Found at i:52877482 original size:40 final size:40
Alignment explanation
Indices: 52877321--52877513 Score: 257
Period size: 39 Copynumber: 4.9 Consensus size: 40
52877311 TGTGTATGAA
*
52877321 TGTGCGAATTGTGATATCCGGGCTAAG-CCCGAAGGCAAT
1 TGTGCGAGTTGTGATATCCGGGCTAAGTCCCGAAGGCAAT
52877360 TGTGCGAGTTGTGATATCCGGGCTAAG-CCCGAAGGCAAT
1 TGTGCGAGTTGTGATATCCGGGCTAAGTCCCGAAGGCAAT
* * * *
52877399 TGTGCGAGCTATGATATCCGGGATAACT-CCGAAGGCAAT
1 TGTGCGAGTTGTGATATCCGGGCTAAGTCCCGAAGGCAAT
* *
52877438 TGTGCGAGTTGTGATATCCGGGTTAAGTCCCGAAGGCATT
1 TGTGCGAGTTGTGATATCCGGGCTAAGTCCCGAAGGCAAT
* * * * *
52877478 TGTGCGGGTTATCATAACCGGGCTATGTCCCGAAGG
1 TGTGCGAGTTGTGATATCCGGGCTAAGTCCCGAAGG
52877514 TGTTTGAACA
Statistics
Matches: 136, Mismatches: 16, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
39 96 0.71
40 40 0.29
ACGTcount: A:0.23, C:0.20, G:0.32, T:0.25
Consensus pattern (40 bp):
TGTGCGAGTTGTGATATCCGGGCTAAGTCCCGAAGGCAAT
Found at i:52882000 original size:27 final size:27
Alignment explanation
Indices: 52881946--52882000 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
52881936 AATATAATGT
*
52881946 AATTATAAAATAATTAAATTGTACTTA
1 AATTATAAAATAATTAAATTGTAATTA
* *
52881973 AATTATTAAAAT-ATTGAATTTTAATTA
1 AATTA-TAAAATAATTAAATTGTAATTA
52882000 A
1 A
52882001 TTTTATAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 18 0.75
28 6 0.25
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.44
Consensus pattern (27 bp):
AATTATAAAATAATTAAATTGTAATTA
Found at i:52889629 original size:39 final size:40
Alignment explanation
Indices: 52889529--52889710 Score: 176
Period size: 40 Copynumber: 4.6 Consensus size: 40
52889519 TCGAATGATG
* * *
52889529 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATA
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGC-AAGTTACTAAA
* * * *
52889569 TCCGGACTAGGAT-CCGAAGGCATTCGTGCGAGTTAATAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTCGTGCAAGTTACTAAA
52889609 TCCGGGCTAAG-CCCGAAGGCATT-GTGCAAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCAAGTTACTAAA
* * * **
52889647 CCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTCGCTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCAAGTTACTA-AA
**
52889688 -CCGGGCTTCGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
52889711 TGAGCGAGTC
Statistics
Matches: 117, Mismatches: 19, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
38 22 0.19
39 23 0.20
40 63 0.54
41 9 0.08
ACGTcount: A:0.24, C:0.25, G:0.28, T:0.23
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTCGTGCAAGTTACTAAA
Found at i:52889674 original size:78 final size:80
Alignment explanation
Indices: 52889529--52889710 Score: 210
Period size: 78 Copynumber: 2.3 Consensus size: 80
52889519 TCGAATGATG
* * * *
52889529 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACTATATCCGGACTAGGATCCGAAGGCATTC
1 TCCGGGCTAAGTCCCGAAGGCATTGTGCTAAGTGACTAAACCCGGACTAAGATCCGAAGGCATTC
52889594 GTGCGAGTTAATAAA
66 GTGCGAGTTAATAAA
* **
52889609 TCCGGGCTAAG-CCCGAAGGCATTGTGC-AAGTTACTAAACCCGGGTTAAG-TCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTGTGCTAAGTGACTAAACCCGGACTAAGAT-CCGAAGGCATT
***
52889671 CGTGCGAGTCGCTATAA
65 CGTGCGAGTTAATA-AA
**
52889688 -CCGGGCTTCGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
52889711 TGAGCGAGTC
Statistics
Matches: 87, Mismatches: 12, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
77 1 0.01
78 46 0.53
79 29 0.33
80 11 0.13
ACGTcount: A:0.24, C:0.25, G:0.28, T:0.23
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTGTGCTAAGTGACTAAACCCGGACTAAGATCCGAAGGCATTC
GTGCGAGTTAATAAA
Found at i:52897672 original size:39 final size:40
Alignment explanation
Indices: 52897572--52897753 Score: 176
Period size: 40 Copynumber: 4.6 Consensus size: 40
52897562 TCGAATGATG
* * *
52897572 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATA
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGC-AAGTTACTAAA
* * * *
52897612 TCCGGACTAGGAT-CCGAAGGCATTCGTGCGAGTTAATAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTCGTGCAAGTTACTAAA
52897652 TCCGGGCTAAG-CCCGAAGGCATT-GTGCAAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCAAGTTACTAAA
* * * **
52897690 CCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTCGCTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCAAGTTACTA-AA
**
52897731 -CCGGGCTTCGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
52897754 TGAGCGAGTC
Statistics
Matches: 117, Mismatches: 19, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
38 22 0.19
39 23 0.20
40 63 0.54
41 9 0.08
ACGTcount: A:0.24, C:0.25, G:0.28, T:0.23
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTCGTGCAAGTTACTAAA
Found at i:52897717 original size:78 final size:80
Alignment explanation
Indices: 52897572--52897753 Score: 210
Period size: 78 Copynumber: 2.3 Consensus size: 80
52897562 TCGAATGATG
* * * *
52897572 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACTATATCCGGACTAGGATCCGAAGGCATTC
1 TCCGGGCTAAGTCCCGAAGGCATTGTGCTAAGTGACTAAACCCGGACTAAGATCCGAAGGCATTC
52897637 GTGCGAGTTAATAAA
66 GTGCGAGTTAATAAA
* **
52897652 TCCGGGCTAAG-CCCGAAGGCATTGTGC-AAGTTACTAAACCCGGGTTAAG-TCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTGTGCTAAGTGACTAAACCCGGACTAAGAT-CCGAAGGCATT
***
52897714 CGTGCGAGTCGCTATAA
65 CGTGCGAGTTAATA-AA
**
52897731 -CCGGGCTTCGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
52897754 TGAGCGAGTC
Statistics
Matches: 87, Mismatches: 12, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
77 1 0.01
78 46 0.53
79 29 0.33
80 11 0.13
ACGTcount: A:0.24, C:0.25, G:0.28, T:0.23
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTGTGCTAAGTGACTAAACCCGGACTAAGATCCGAAGGCATTC
GTGCGAGTTAATAAA
Found at i:52903967 original size:20 final size:20
Alignment explanation
Indices: 52903922--52903963 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
52903912 CTTCATTCGC
*
52903922 TTGTCCCACGCCCGTGTATGT
1 TTGT-CCACACCCGTGTATGT
*
52903943 ATGTCCACACCCGTGT-TGT
1 TTGTCCACACCCGTGTATGT
52903962 TT
1 TT
52903964 TGTCAGTCTT
Statistics
Matches: 18, Mismatches: 3, Indels: 2
0.78 0.13 0.09
Matches are distributed among these distances:
19 4 0.22
20 11 0.61
21 3 0.17
ACGTcount: A:0.12, C:0.31, G:0.21, T:0.36
Consensus pattern (20 bp):
TTGTCCACACCCGTGTATGT
Found at i:52908673 original size:39 final size:40
Alignment explanation
Indices: 52908590--52908764 Score: 225
Period size: 39 Copynumber: 4.5 Consensus size: 40
52908580 CGGATGATAA
* **
52908590 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGAGACTA-AT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
52908629 TCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
52908668 CCGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
52908707 CCGGGCTAAGTCCCGAAGGCATTTGAGCAAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* *
52908747 CC-GGCTAAATTCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
52908765 TACTTGGTTT
Statistics
Matches: 121, Mismatches: 11, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
38 23 0.19
39 74 0.61
40 24 0.20
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:52908748 original size:79 final size:77
Alignment explanation
Indices: 52908590--52908764 Score: 219
Period size: 79 Copynumber: 2.2 Consensus size: 77
52908580 CGGATGATAA
* ** *
52908590 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGAGACTAATTCGGGCTAAGCCCGAAGGCATTTGTG
1 CCGGGCTAAGT-CCGAAGGCATTTGTGCGAGAGACTAAACCGGGCTAAGCCCGAAGGCATTTGAG
*
52908655 CGAGTTACTATAT
65 CAAGTTACTATAT
**
52908668 CCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTTGA
1 CCGGGCTAAGTCCGAAGGCATTTGTGCGAGAGACTA-AACCGGGCTAAG-CCCGAAGGCATTTGA
52908733 GCAAG-TAGCTATAT
64 GCAAGTTA-CTATAT
*
52908747 CC-GGCTAAATTCCGAAGG
1 CCGGGCT-AAGTCCGAAGG
52908765 TACTTGGTTT
Statistics
Matches: 85, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
77 22 0.26
78 27 0.32
79 36 0.42
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (77 bp):
CCGGGCTAAGTCCGAAGGCATTTGTGCGAGAGACTAAACCGGGCTAAGCCCGAAGGCATTTGAGC
AAGTTACTATAT
Found at i:52916724 original size:40 final size:40
Alignment explanation
Indices: 52916623--52916827 Score: 303
Period size: 40 Copynumber: 5.2 Consensus size: 40
52916613 CGGATGATAA
* *
52916623 CCGGGCTAAGT-CCGAAGGCATTTGTGCTAGTGACTA-AT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
52916661 TCGGGCTAAG-CCCGAAGGCATTTGTGTGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
52916700 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
52916740 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
52916780 CCGGGCTAAGTCCCGAAGGCATTTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
52916820 CC-GGCTAA
1 CCGGGCTAA
52916828 ATTCGAAGGT
Statistics
Matches: 154, Mismatches: 9, Indels: 7
0.91 0.05 0.04
Matches are distributed among these distances:
38 31 0.20
39 19 0.12
40 104 0.68
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:52922367 original size:22 final size:22
Alignment explanation
Indices: 52922339--52922383 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
52922329 CTCTAGTGTG
52922339 TTTAAATAGCCTTTAGAATGCC
1 TTTAAATAGCCTTTAGAATGCC
*
52922361 TTTAAATAGGCTTTAGAATGCC
1 TTTAAATAGCCTTTAGAATGCC
52922383 T
1 T
52922384 AAAAGCCCTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.38
Consensus pattern (22 bp):
TTTAAATAGCCTTTAGAATGCC
Found at i:52925418 original size:29 final size:28
Alignment explanation
Indices: 52925386--52925488 Score: 107
Period size: 29 Copynumber: 3.6 Consensus size: 28
52925376 GTGACGAGAT
* *
52925386 TGGCACTGAGTGTGCGAGCTTGTAATGTA
1 TGGCACTAAGTGTGCGAGCTTG-AATATA
* * *
52925415 TGGCACTAAGTGTACGAGTTTGGACTATA
1 TGGCACTAAGTGTGCGAGCTT-GAATATA
* * *
52925444 TGGCACTATGTGTGCGGGCTTGAATCACA
1 TGGCACTAAGTGTGCGAGCTTGAAT-ATA
52925473 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
52925489 TGATTGAGTA
Statistics
Matches: 60, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
28 3 0.05
29 56 0.93
30 1 0.02
ACGTcount: A:0.22, C:0.17, G:0.32, T:0.29
Consensus pattern (28 bp):
TGGCACTAAGTGTGCGAGCTTGAATATA
Found at i:52929402 original size:50 final size:49
Alignment explanation
Indices: 52929339--52929517 Score: 168
Period size: 50 Copynumber: 3.7 Consensus size: 49
52929329 TACGAGATGT
* *
52929339 GTCAGTGTAAGACCATGTCTGGGACATGGCATCAGCAC-AGATATGCCAGA
1 GTCAGTGTAAGACCATGTCTGGGACATGGCATCAGC-CTAGATA-ACAAGA
* ** * * *
52929389 G-CTAGTGTAAGACCAAGTCTGGGACATGGTGTCGGCCTCGATAACAATA
1 GTC-AGTGTAAGACCATGTCTGGGACATGGCATCAGCCTAGATAACAAGA
* * * *
52929438 GTCAGTGTAAGACCATGTCTGGGACATGGCATC-GACTTGA-GACATGA
1 GTCAGTGTAAGACCATGTCTGGGACATGGCATCAGCCTAGATAACAAGA
* * *
52929485 GCCAGTGTAAGACCATGTCTAGGACATGACATC
1 GTCAGTGTAAGACCATGTCTGGGACATGGCATC
52929518 GGCATCATAC
Statistics
Matches: 107, Mismatches: 19, Indels: 9
0.79 0.14 0.07
Matches are distributed among these distances:
47 34 0.32
48 5 0.05
49 33 0.31
50 35 0.33
ACGTcount: A:0.29, C:0.21, G:0.28, T:0.22
Consensus pattern (49 bp):
GTCAGTGTAAGACCATGTCTGGGACATGGCATCAGCCTAGATAACAAGA
Found at i:52936838 original size:53 final size:53
Alignment explanation
Indices: 52936657--52936863 Score: 180
Period size: 53 Copynumber: 3.8 Consensus size: 53
52936647 ATTAGGGTTT
* * * * *
52936657 AAGGATACCAAGTAAGACCATGCCAAGGCATGGCATTGGTAAGTTTTACAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAG-TTCATAAGGC
* * * * * * * *
52936711 AAGGAAATCATGTAAGACCATGTCAAGACATGACACTGATAAACTACGATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGT-AAGTTC-ATAAGGC
* * * * * *
52936766 AAAGATCCCATGTATGACCATGCCAAGGCATGGTAATGGTGAGTTCATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTTCATAAGGC
* ** *
52936819 AAGGATACCACGTAAGACCATATCAAGACATGGAAATGGTAAGTT
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTT
52936864 TAAAAAGGAA
Statistics
Matches: 116, Mismatches: 35, Indels: 5
0.74 0.22 0.03
Matches are distributed among these distances:
53 43 0.37
54 36 0.31
55 37 0.32
ACGTcount: A:0.38, C:0.18, G:0.24, T:0.20
Consensus pattern (53 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTTCATAAGGC
Found at i:52939792 original size:50 final size:49
Alignment explanation
Indices: 52939598--52939860 Score: 167
Period size: 50 Copynumber: 5.6 Consensus size: 49
52939588 GTGAGCTAGA
* * * ** * *
52939598 GTAAGA-CATGTCTGGGACAT-GCATCAGCCAC-ATTATTAGAGCCAGT
1 GTAAGACCATGTCTGGGACATGGCATCGGCCTCGATAACAACAGTCAGT
* **
52939644 GTAAGACCTTGTCTGGGACAT-GCATCGGCCTCG-TAAGGTA-AG-CTAGT
1 GTAAGACCATGTCTGGGACATGGCATCGGCCTCGATAA-CAACAGTC-AGT
* * * * *** *
52939691 ATAAGA-CATGTCAGGGACA-GGCATCGG-CT-G-TGAGATGTGTCAAT
1 GTAAGACCATGTCTGGGACATGGCATCGGCCTCGATAACAACAGTCAGT
* * *
52939735 GTAAGACCATGTCTGGGACATGGCATCGGCGC-GGATAAGCCAGAG-CTAGT
1 GTAAGACCATGTCTGGGACATGGCATCGGC-CTCGATAA-CAACAGTC-AGT
* *
52939785 GTAAGACCATGTCTGGGACATGGCGTCGGCCTCGATGACAACAGTCAGT
1 GTAAGACCATGTCTGGGACATGGCATCGGCCTCGATAACAACAGTCAGT
*
52939834 GTAAGACCATGTCTTGGACATGGCATC
1 GTAAGACCATGTCTGGGACATGGCATC
52939861 AACTTCAGAC
Statistics
Matches: 172, Mismatches: 28, Indels: 31
0.74 0.12 0.13
Matches are distributed among these distances:
43 1 0.01
44 11 0.06
45 15 0.09
46 33 0.19
47 34 0.20
48 4 0.02
49 36 0.21
50 38 0.22
ACGTcount: A:0.27, C:0.21, G:0.30, T:0.22
Consensus pattern (49 bp):
GTAAGACCATGTCTGGGACATGGCATCGGCCTCGATAACAACAGTCAGT
Found at i:52939845 original size:99 final size:92
Alignment explanation
Indices: 52939640--52939860 Score: 239
Period size: 99 Copynumber: 2.3 Consensus size: 92
52939630 TTATTAGAGC
* **
52939640 CAGTGTAAGACCTTGTCTGGGACAT-GCATCGGCCTCGTAAGGTAAGCTAGTATAAGACATGTCA
1 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGTAAGCCAAGCTAGTATAAGACATGTCA
* ***
52939704 GGGACAGGCATCGGCTGTGAGATGTGT
66 GGGACAGGCATCGGCTGTGACAACAGT
* * *
52939731 CAATGTAAGACCATGTCTGGGACATGGCATCGGCGC-GGATAAGCCAGAGCTAGTGTAAGACCAT
1 CAGTGTAAGACCATGTCTGGGACATGGCATCGGC-CTCG-TAAGCCA-AGCTAGTATAAGA-CAT
* *
52939795 GTCTGGGACATGGCGTCGGCCTCGATGACAACAGT
62 GTCAGGGACA-GGCATCGG-CT-G-TGACAACAGT
*
52939830 CAGTGTAAGACCATGTCTTGGACATGGCATC
1 CAGTGTAAGACCATGTCTGGGACATGGCATC
52939861 AACTTCAGAC
Statistics
Matches: 107, Mismatches: 14, Indels: 10
0.82 0.11 0.08
Matches are distributed among these distances:
91 23 0.21
92 9 0.08
93 6 0.06
94 12 0.11
95 12 0.11
96 7 0.07
97 2 0.02
98 1 0.01
99 35 0.33
ACGTcount: A:0.26, C:0.21, G:0.31, T:0.22
Consensus pattern (92 bp):
CAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGTAAGCCAAGCTAGTATAAGACATGTCA
GGGACAGGCATCGGCTGTGACAACAGT
Found at i:52940987 original size:20 final size:21
Alignment explanation
Indices: 52940949--52940987 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
52940939 TCTTAGTGAT
*
52940949 CACATGGGTGTGTTGCCCTTC
1 CACATGGGCGTGTTGCCCTTC
52940970 CACATGGGCGTG-TGCCCT
1 CACATGGGCGTGTTGCCCT
52940988 GTTTCAAGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.10, C:0.31, G:0.31, T:0.28
Consensus pattern (21 bp):
CACATGGGCGTGTTGCCCTTC
Found at i:52942368 original size:28 final size:28
Alignment explanation
Indices: 52942303--52942401 Score: 119
Period size: 28 Copynumber: 3.5 Consensus size: 28
52942293 CCTGAGATTG
* * *
52942303 GCACTAAGTGTGCGGGTTCAAATTGTATA
1 GCACTAAGTGTGCGAGTT-AGATTATATA
*
52942332 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTAGATTATATA
* *
52942360 GCACTAAGTGTGCGAGTTCGACTAT-TAA
1 GCACTAAGTGTGCGAGTTAGATTATAT-A
52942388 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
52942402 GGCTTATTAT
Statistics
Matches: 63, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
27 1 0.02
28 45 0.71
29 17 0.27
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.30
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTAGATTATATA
Found at i:52951149 original size:33 final size:33
Alignment explanation
Indices: 52951107--52951174 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
52951097 GAAATATAAG
52951107 AATGTACATGAAATTATTGTAATATTTACATAC
1 AATGTACATGAAATTATTGTAATATTTACATAC
52951140 AATGTACATGAAATTATTGTAATATTTACATAC
1 AATGTACATGAAATTATTGTAATATTTACATAC
52951173 AA
1 AA
52951175 CTTACCTTGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.38
Consensus pattern (33 bp):
AATGTACATGAAATTATTGTAATATTTACATAC
Found at i:52955206 original size:30 final size:30
Alignment explanation
Indices: 52955172--52955232 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
52955162 TCCTTAACTC
52955172 AAACTTTGGCAAAATTACAATTTTGCCCCT
1 AAACTTTGGCAAAATTACAATTTTGCCCCT
* * * *
52955202 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGCAAAATTACAATTTTGCCCCT
52955232 A
1 A
52955233 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGCAAAATTACAATTTTGCCCCT
Found at i:52961462 original size:44 final size:40
Alignment explanation
Indices: 52961368--52961465 Score: 115
Period size: 40 Copynumber: 2.4 Consensus size: 40
52961358 TAGTATTTGA
** * *
52961368 CACTAAGTGTGCGATTTAAACTAGCTTTGGCTATGTGAGG
1 CACTAAGTGTGCGATACAAACTAGCTTCGGCTATGAGAGG
*
52961408 CACTAAGTGTGCGATACCAACTTAGCTTCGGCTAATTGAGATGG
1 CACTAAGTGTGCGATACAAAC-TAGCTTCGGCT-A-TGAGA-GG
52961452 CACTAAGTGTGCGA
1 CACTAAGTGTGCGA
52961466 AAATTGTTCT
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
40 18 0.37
41 10 0.20
42 1 0.02
43 4 0.08
44 16 0.33
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.29
Consensus pattern (40 bp):
CACTAAGTGTGCGATACAAACTAGCTTCGGCTATGAGAGG
Found at i:52964039 original size:40 final size:39
Alignment explanation
Indices: 52963990--52964197 Score: 224
Period size: 40 Copynumber: 5.2 Consensus size: 39
52963980 TCTTCGGAAT
* *
52963990 TTAG-CCGGATATAACCACAAGCACAATTGCCTTCGGGTC
1 TTAGCCCGGATATAACAACTAGCACAA-TGCCTTCGGGTC
* * *** *
52964029 TTAACCCGGATTTGGTAACTTGCACAAATGCCTTCGGGTC
1 TTAGCCCGGATATAACAACTAGCAC-AATGCCTTCGGGTC
*
52964069 TTAGCCCGGATATAACAACTCGCACGAATGCCTTCGGGTC
1 TTAGCCCGGATATAACAACTAGCAC-AATGCCTTCGGGTC
52964109 TTAGCCCGGATATAACAACTCA-CACGAATGCCTTCGGGTC
1 TTAGCCCGGATATAACAACT-AGCAC-AATGCCTTCGGGTC
* * *
52964149 TTAGCCCGGATATAATC-ATTAGCATAAATGCCTTCGGGAC
1 TTAGCCCGGATATAA-CAACTAGCA-CAATGCCTTCGGGTC
52964189 TTAGCCCGG
1 TTAGCCCGG
52964198 GTATCATTCA
Statistics
Matches: 144, Mismatches: 19, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
39 4 0.03
40 137 0.95
41 3 0.02
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (39 bp):
TTAGCCCGGATATAACAACTAGCACAATGCCTTCGGGTC
Found at i:52966114 original size:33 final size:33
Alignment explanation
Indices: 52966077--52966141 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
52966067 AGATAGTCTT
*
52966077 TCGGGACA-TAAAACATGAAATAGAGAAAGTCCA
1 TCGGGACAGT-AAACACGAAATAGAGAAAGTCCA
* *
52966110 TCGGGACAGTAAACACGGAATAGAGTAAGTCC
1 TCGGGACAGTAAACACGAAATAGAGAAAGTCC
52966142 GCCAGGATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 27 0.96
34 1 0.04
ACGTcount: A:0.43, C:0.17, G:0.25, T:0.15
Consensus pattern (33 bp):
TCGGGACAGTAAACACGAAATAGAGAAAGTCCA
Found at i:52966189 original size:27 final size:27
Alignment explanation
Indices: 52966134--52966194 Score: 86
Period size: 27 Copynumber: 2.3 Consensus size: 27
52966124 ACGGAATAGA
*
52966134 GTAAGTCCGCCAGGATAATAAACATGG
1 GTAAGTCCGCCAGGATAATAAACACGG
* * *
52966161 GTTAGTCCGCCAGGATAGTATACACGG
1 GTAAGTCCGCCAGGATAATAAACACGG
52966188 GTAAGTC
1 GTAAGTC
52966195 TGAAGGGATG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.31, C:0.20, G:0.28, T:0.21
Consensus pattern (27 bp):
GTAAGTCCGCCAGGATAATAAACACGG
Found at i:52967898 original size:20 final size:20
Alignment explanation
Indices: 52967873--52967914 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
52967863 GTCGTTCTAA
*
52967873 GCACCAGCAGCTCCTTTATT
1 GCACCAGCAACTCCTTTATT
52967893 GCACCAGCAACTCCTTTATT
1 GCACCAGCAACTCCTTTATT
52967913 GC
1 GC
52967915 TGCTCTTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.21, C:0.36, G:0.14, T:0.29
Consensus pattern (20 bp):
GCACCAGCAACTCCTTTATT
Found at i:52971006 original size:2 final size:2
Alignment explanation
Indices: 52970999--52971040 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
52970989 AATGACTTTC
52970999 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
52971041 GCTTTCCATA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:52979498 original size:16 final size:17
Alignment explanation
Indices: 52979472--52979507 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
52979462 AAGTAGTCAA
52979472 TTGTGGTATGATAAATG
1 TTGTGGTATGATAAATG
*
52979489 TTGT-GTATGATAGATG
1 TTGTGGTATGATAAATG
52979505 TTG
1 TTG
52979508 ATATTGTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.25, C:0.00, G:0.31, T:0.44
Consensus pattern (17 bp):
TTGTGGTATGATAAATG
Found at i:52982358 original size:45 final size:45
Alignment explanation
Indices: 52982263--52982426 Score: 185
Period size: 45 Copynumber: 3.7 Consensus size: 45
52982253 CCGACATATT
*
52982263 GCCTGCTAGGCTCGAA-GCCTG-ATA-TCAT-TTCACCGGCATTATA
1 GCCTGCTAGGCTCGAAGGCCCGAATAGT-ATCTT-ACCGGCATTATA
*
52982306 GCCTGCTAGGCTCGAAGGCCCGAATAGTATCTTACTGGCATTATA
1 GCCTGCTAGGCTCGAAGGCCCGAATAGTATCTTACCGGCATTATA
* * * *
52982351 GCCTGCTAAGCTC-AAGGGCTCGATTAGTATCTCACCGGCATTATA
1 GCCTGCTAGGCTCGAA-GGCCCGAATAGTATCTTACCGGCATTATA
* * *
52982396 GCCTGCTAGGCTCAAAGGCTCGATTAGTATC
1 GCCTGCTAGGCTCGAAGGCCCGAATAGTATC
52982427 GTACGATATT
Statistics
Matches: 107, Mismatches: 8, Indels: 10
0.86 0.06 0.08
Matches are distributed among these distances:
43 16 0.15
44 6 0.06
45 80 0.75
46 5 0.05
ACGTcount: A:0.24, C:0.26, G:0.23, T:0.27
Consensus pattern (45 bp):
GCCTGCTAGGCTCGAAGGCCCGAATAGTATCTTACCGGCATTATA
Found at i:52986752 original size:50 final size:48
Alignment explanation
Indices: 52986631--52986805 Score: 159
Period size: 47 Copynumber: 3.7 Consensus size: 48
52986621 TAGGGTATAA
**
52986631 TGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCACGTTAAG
1 TGCCGATGCCATGT-CCAGACATGGTCTTACACTAACTCTCACGTTAAG
* * **
52986680 T--CGATGCCATGTCCTAAACATGGTCTTACACTAACTCTTACGTATCTG
1 TGCCGATGCCATGTCC-AGACATGGTCTTACACTAACTCTCACGT-TAAG
* * *
52986728 TGCCGATGCCATATCTCAGACATGGTCTTACACTAACACATCATG-T-A-
1 TGCCGATGCCATGTC-CAGACATGGTCTTACACTAACTC-TCACGTTAAG
52986775 -GCCGATG-CATGTCCCAGACAT-GTCTTACACT
1 TGCCGATGCCATGT-CCAGACATGGTCTTACACT
52986806 GGCTTACATC
Statistics
Matches: 106, Mismatches: 13, Indels: 19
0.77 0.09 0.14
Matches are distributed among these distances:
44 10 0.09
45 11 0.10
46 10 0.09
47 35 0.33
48 3 0.03
49 2 0.02
50 31 0.29
51 4 0.04
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.29
Consensus pattern (48 bp):
TGCCGATGCCATGTCCAGACATGGTCTTACACTAACTCTCACGTTAAG
Found at i:52986815 original size:46 final size:46
Alignment explanation
Indices: 52986632--52986945 Score: 191
Period size: 46 Copynumber: 6.7 Consensus size: 46
52986622 AGGGTATAAT
52986632 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCA-C-GTTAA
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCT-TCATCTG-T-A
* * * **
52986679 GTCGATGCCATGTCCTAAACATGGTCTTACACTAACTCTTACGTATCTGT-
1 GCCGATGCCATGTCCCAGACATGGTCTTACACT--GGCTT-C--ATCTGTA
* * ** *
52986729 GCCGATGCCATATCTCAGACATGGTCTTACACTAAC-ACATCATGTA
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTTCATC-TGTA
52986775 GCCGATG-CATGTCCCAGACAT-GTCTTACACTGGCTTACATCTCG-A
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTT-CATCT-GTA
* * * **
52986820 GGCCGATG-CATGTCCCAGAAAT-GTCTTACACTAGCTCTCGTCTCAA
1 -GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCT-TCATCTGTA
* * * * * * * *
52986866 TGTCAATGCCATGTCCCAGAGATGGTCTTATACTGGATCTCATAATATG
1 -GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCT-TCAT-CTGTA
*
52986915 GCCGATG-CATGTCCCAGACAT-GCCTTACACT
1 GCCGATGCCATGTCCCAGACATGGTCTTACACT
52986946 AGCACACAAT
Statistics
Matches: 210, Mismatches: 39, Indels: 37
0.73 0.14 0.13
Matches are distributed among these distances:
44 14 0.07
45 17 0.08
46 64 0.30
47 57 0.27
48 22 0.10
49 4 0.02
50 28 0.13
51 1 0.00
52 2 0.01
53 1 0.00
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.28
Consensus pattern (46 bp):
GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTTCATCTGTA
Found at i:52989805 original size:24 final size:25
Alignment explanation
Indices: 52989778--52989825 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
52989768 TCAAGCAGCC
*
52989778 ATATTAGGAAGCTCATAAA-AGCTT
1 ATATCAGGAAGCTCATAAAGAGCTT
*
52989802 ATATCAGGACGCTCATAAAGAGCT
1 ATATCAGGAAGCTCATAAAGAGCT
52989826 GCGTTTGTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.40, C:0.17, G:0.19, T:0.25
Consensus pattern (25 bp):
ATATCAGGAAGCTCATAAAGAGCTT
Found at i:52993859 original size:83 final size:83
Alignment explanation
Indices: 52993742--52993904 Score: 299
Period size: 83 Copynumber: 2.0 Consensus size: 83
52993732 AAATAGATAG
* *
52993742 TTAAGCTATTCCGATCTTGAAAATATAAAAATTACTAAAAATGAGGCAAGATTACTTACCCAATT
1 TTAAGCTATTCCGATCTCGAAAATATAAAAATTACTAAAAACGAGGCAAGATTACTTACCCAATT
52993807 AAGCTTGTTTGATTTAGA
66 AAGCTTGTTTGATTTAGA
*
52993825 TTAAGCTATTCTGATCTCGAAAATATAAAAATTACTAAAAACGAGGCAAGATTACTTACCCAATT
1 TTAAGCTATTCCGATCTCGAAAATATAAAAATTACTAAAAACGAGGCAAGATTACTTACCCAATT
52993890 AAGCTTGTTTGATTT
66 AAGCTTGTTTGATTT
52993905 CATTTTTCTT
Statistics
Matches: 77, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
83 77 1.00
ACGTcount: A:0.39, C:0.14, G:0.13, T:0.34
Consensus pattern (83 bp):
TTAAGCTATTCCGATCTCGAAAATATAAAAATTACTAAAAACGAGGCAAGATTACTTACCCAATT
AAGCTTGTTTGATTTAGA
Found at i:53000520 original size:29 final size:30
Alignment explanation
Indices: 53000464--53000525 Score: 90
Period size: 29 Copynumber: 2.1 Consensus size: 30
53000454 ACTTATTTTA
53000464 TTGTTAATTTTGTTATTACTTTAAAGGCAT
1 TTGTTAATTTTGTTATTACTTTAAAGGCAT
* * *
53000494 TTGTTAATTTT-TTATTATTTTAGAGGCTT
1 TTGTTAATTTTGTTATTACTTTAAAGGCAT
53000523 TTG
1 TTG
53000526 CTTGTTAAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 18 0.62
30 11 0.38
ACGTcount: A:0.23, C:0.05, G:0.15, T:0.58
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTACTTTAAAGGCAT
Found at i:53001073 original size:8 final size:8
Alignment explanation
Indices: 53001060--53001086 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
53001050 AATGTTTTTA
53001060 TATGATTT
1 TATGATTT
53001068 TATGATTT
1 TATGATTT
53001076 TATGATTT
1 TATGATTT
53001084 TAT
1 TAT
53001087 TTACAATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.26, C:0.00, G:0.11, T:0.63
Consensus pattern (8 bp):
TATGATTT
Found at i:53003413 original size:20 final size:21
Alignment explanation
Indices: 53003379--53003417 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
53003369 TCGATTAAGT
*
53003379 TAAATTTAAATTATTTTTTTA
1 TAAATTTAAAATATTTTTTTA
53003400 TAAA-TTAAAATATTTTTT
1 TAAATTTAAAATATTTTTT
53003418 GTCATTATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TAAATTTAAAATATTTTTTTA
Found at i:53009976 original size:40 final size:35
Alignment explanation
Indices: 53009910--53010040 Score: 129
Period size: 35 Copynumber: 3.6 Consensus size: 35
53009900 CATGGCAAAG
53009910 TGTGAAATGTAGGTATGGTATCATCCATACTGAGT
1 TGTGAAATGTAGGTATGGTATCATCCATACTGAGT
53009945 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGT
1 TGTGAAATGTAGGTATGG---TATC--ATCCATACTGAGT
** * * *
53009985 TAAGAAATGTAGGTATGGCAT-TTCCCATACCGAGT
1 TGTGAAATGTAGGTATGGTATCAT-CCATACTGAGT
***
53010020 TAAAAAATGTAGGTATGGTAT
1 TGTGAAATGTAGGTATGGTAT
53010041 TTCAATGAGG
Statistics
Matches: 83, Mismatches: 7, Indels: 12
0.81 0.07 0.12
Matches are distributed among these distances:
34 1 0.01
35 47 0.57
37 2 0.02
38 4 0.05
40 29 0.35
ACGTcount: A:0.33, C:0.11, G:0.24, T:0.33
Consensus pattern (35 bp):
TGTGAAATGTAGGTATGGTATCATCCATACTGAGT
Found at i:53017441 original size:40 final size:35
Alignment explanation
Indices: 53017375--53017467 Score: 123
Period size: 40 Copynumber: 2.5 Consensus size: 35
53017365 CATGGCAAAG
53017375 TGTGAAATGTAGGTATGGTATCATCCATACTGAGT
1 TGTGAAATGTAGGTATGGTATCATCCATACTGAGT
53017410 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGT
1 TGTGAAATGTAGGTATGG---TATC--ATCCATACTGAGT
**
53017450 TAAGAAATGTAGGTATGG
1 TGTGAAATGTAGGTATGG
53017468 CATTTCCCAT
Statistics
Matches: 51, Mismatches: 2, Indels: 5
0.88 0.03 0.09
Matches are distributed among these distances:
35 18 0.35
38 4 0.08
40 29 0.57
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.33
Consensus pattern (35 bp):
TGTGAAATGTAGGTATGGTATCATCCATACTGAGT
Found at i:53017465 original size:35 final size:34
Alignment explanation
Indices: 53017378--53017502 Score: 99
Period size: 40 Copynumber: 3.4 Consensus size: 34
53017368 GGCAAAGTGT
**
53017378 GAAATGTAGGTATGGTATCATCCATACTGAGTTGT
1 GAAATGTAGGTAT-GTATCATCCATACTGAGTTAA
53017413 GAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAA
1 GAAATGTAGGTAT-G---TATC--ATCCATACTGAGTTAA
* * *
53017453 GAAATGTAGGTATGGCAT-TTCCCATACCGAGTTAAA
1 GAAATGTAGGTAT-GTATCAT-CCATACTGAGTT-AA
*
53017489 AAAATGTAGGTATG
1 GAAATGTAGGTATG
53017503 GTATTTCAAT
Statistics
Matches: 77, Mismatches: 6, Indels: 14
0.79 0.06 0.14
Matches are distributed among these distances:
34 1 0.01
35 27 0.35
36 14 0.18
37 2 0.03
38 4 0.05
40 29 0.38
ACGTcount: A:0.34, C:0.11, G:0.23, T:0.31
Consensus pattern (34 bp):
GAAATGTAGGTATGTATCATCCATACTGAGTTAA
Found at i:53017501 original size:36 final size:35
Alignment explanation
Indices: 53017439--53017509 Score: 106
Period size: 36 Copynumber: 2.0 Consensus size: 35
53017429 ATTATCAAAT
* *
53017439 CCATACTGAGTTAAGAAATGTAGGTATGGCATTTC
1 CCATACCGAGTTAAAAAATGTAGGTATGGCATTTC
*
53017474 CCATACCGAGTTAAAAAAATGTAGGTATGGTATTTC
1 CCATACCGAGTT-AAAAAATGTAGGTATGGCATTTC
53017510 AATGAGGAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
35 11 0.34
36 21 0.66
ACGTcount: A:0.34, C:0.14, G:0.21, T:0.31
Consensus pattern (35 bp):
CCATACCGAGTTAAAAAATGTAGGTATGGCATTTC
Found at i:53022263 original size:16 final size:15
Alignment explanation
Indices: 53022237--53022275 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
53022227 CCAAATTCGA
*
53022237 TATTTTT-ATATTATT
1 TATTTTTAATA-TAAT
53022252 TATTTTTAATATAAT
1 TATTTTTAATATAAT
53022267 TATTTTTAA
1 TATTTTTAA
53022276 ATTTGTAAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 19 0.86
16 3 0.14
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
TATTTTTAATATAAT
Found at i:53022460 original size:2 final size:2
Alignment explanation
Indices: 53022453--53022495 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
53022443 ACGCAAGTGT
53022453 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
53022495 T
1 T
53022496 TTCCTTTTTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:53030830 original size:29 final size:30
Alignment explanation
Indices: 53030771--53030830 Score: 68
Period size: 30 Copynumber: 2.0 Consensus size: 30
53030761 GATAGGAGGG
* * * **
53030771 GAGTAAAAGTTTTGGGGGGAAAGTGGGAAA
1 GAGTAAAAGTTTTGAGGGAAAAATGAAAAA
53030801 GAGTAAAAGTTTTGAGGGAAAAAT-AAAAA
1 GAGTAAAAGTTTTGAGGGAAAAATGAAAAA
53030830 G
1 G
53030831 GTTTGAGAGT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
29 4 0.16
30 21 0.84
ACGTcount: A:0.45, C:0.00, G:0.35, T:0.20
Consensus pattern (30 bp):
GAGTAAAAGTTTTGAGGGAAAAATGAAAAA
Found at i:53035206 original size:86 final size:86
Alignment explanation
Indices: 53035061--53035224 Score: 267
Period size: 86 Copynumber: 1.9 Consensus size: 86
53035051 ACAAAAAACG
*
53035061 TAAGGTTGTATATGGTATGTTACATTACTTTGATTGGCTCATTTGATTGGAATGTATTATCCAAC
1 TAAGGTTGTAGATGGTATGTTACATTACTTTGATTGGCTCATTTGATTGGAATGTATTATCCAAC
53035126 ACTACGTTTGGTTCGCTGACA
66 ACTACGTTTGGTTCGCTGACA
* * * *
53035147 TAAGGTTGTCGATGGTATGTTACATTA-TCTTGTTTGGTTCATTTGGTTGGAATGTATTATCCAA
1 TAAGGTTGTAGATGGTATGTTACATTACT-TTGATTGGCTCATTTGATTGGAATGTATTATCCAA
53035211 CACTACGTTTGGTT
65 CACTACGTTTGGTT
53035225 TAATGTAATA
Statistics
Matches: 72, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
85 1 0.01
86 71 0.99
ACGTcount: A:0.23, C:0.13, G:0.22, T:0.43
Consensus pattern (86 bp):
TAAGGTTGTAGATGGTATGTTACATTACTTTGATTGGCTCATTTGATTGGAATGTATTATCCAAC
ACTACGTTTGGTTCGCTGACA
Found at i:53035472 original size:37 final size:37
Alignment explanation
Indices: 53035430--53035500 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
53035420 TTGTTATTAA
*
53035430 ATTTTAATAGGATTATTATTAAAAATAATTTAATCAT
1 ATTTTAATAGAATTATTATTAAAAATAATTTAATCAT
*
53035467 ATTTTAATAGAATTATTATTAAATATAATTTAAT
1 ATTTTAATAGAATTATTATTAAAAATAATTTAAT
53035501 AAAAATAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.46, C:0.01, G:0.04, T:0.48
Consensus pattern (37 bp):
ATTTTAATAGAATTATTATTAAAAATAATTTAATCAT
Found at i:53035525 original size:14 final size:16
Alignment explanation
Indices: 53035508--53035587 Score: 71
Period size: 16 Copynumber: 5.1 Consensus size: 16
53035498 AATAAAAATA
53035508 ATAATATTTTTA-A-T
1 ATAATATTTTTATATT
53035522 ATAATTATTTTTATATT
1 ATAA-TATTTTTATATT
* *
53035539 AAAATATTTTTATTTT
1 ATAATATTTTTATATT
53035555 A-AATTATATTTTGATATT
1 ATAA-TAT-TTTT-ATATT
53035573 A-AATA-TTTTATATT
1 ATAATATTTTTATATT
53035587 A
1 A
53035588 AATTATATTA
Statistics
Matches: 57, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
14 10 0.18
15 14 0.25
16 16 0.28
17 10 0.18
18 7 0.12
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (16 bp):
ATAATATTTTTATATT
Found at i:53035525 original size:17 final size:17
Alignment explanation
Indices: 53035505--53035550 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 17
53035495 TTTAATAAAA
53035505 ATAATAATATTTTTAAT
1 ATAATAATATTTTTAAT
53035522 ATAAT--TATTTTT-AT
1 ATAATAATATTTTTAAT
53035536 ATTAA-AATATTTTTA
1 A-TAATAATATTTTTA
53035551 TTTTAAATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
14 3 0.12
15 10 0.40
16 7 0.28
17 5 0.20
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
ATAATAATATTTTTAAT
Found at i:53035582 original size:32 final size:32
Alignment explanation
Indices: 53035524--53035620 Score: 108
Period size: 32 Copynumber: 3.0 Consensus size: 32
53035514 TTTTTAATAT
53035524 AATTAT-TTTTATATTAAAATATTTTTATTTTA
1 AATTATATTTTATATTAAAATA-TTTTATTTTA
*
53035556 AATTATATTTTGATATT-AAATATTTTATATTA
1 AATTATATTTT-ATATTAAAATATTTTATTTTA
** *
53035588 AATTATATTAAAATATTTCAAATATTTTATTTT
1 AATTATATT-TTATA-TTAAAATATTTTATTTT
53035621 TATATTTTCT
Statistics
Matches: 56, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
32 27 0.48
33 11 0.20
34 18 0.32
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (32 bp):
AATTATATTTTATATTAAAATATTTTATTTTA
Found at i:53038067 original size:15 final size:15
Alignment explanation
Indices: 53038047--53038079 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
53038037 AAGTAAAGTG
53038047 ATTTTGGATATACGA
1 ATTTTGGATATACGA
*
53038062 ATTTTGGATATATGA
1 ATTTTGGATATACGA
53038077 ATT
1 ATT
53038080 AATGAAAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.33, C:0.03, G:0.18, T:0.45
Consensus pattern (15 bp):
ATTTTGGATATACGA
Found at i:53038149 original size:26 final size:26
Alignment explanation
Indices: 53038120--53038171 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
53038110 ATGAAAGGAC
53038120 CAAATCACAAATTTCGAGAAGTTTAA
1 CAAATCACAAATTTCGAGAAGTTTAA
53038146 CAAATCACAAATTTCGAGAAGTTTAA
1 CAAATCACAAATTTCGAGAAGTTTAA
53038172 GGACTAAAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.46, C:0.15, G:0.12, T:0.27
Consensus pattern (26 bp):
CAAATCACAAATTTCGAGAAGTTTAA
Found at i:53044898 original size:22 final size:21
Alignment explanation
Indices: 53044873--53044913 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
53044863 TCCACAAGAA
53044873 TAATATAAAATCAAAGAAATAT
1 TAATATAAAAT-AAAGAAATAT
* *
53044895 TAATTTAAAATAAATAAAT
1 TAATATAAAATAAAGAAAT
53044914 TCAAATTAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.32
Consensus pattern (21 bp):
TAATATAAAATAAAGAAATAT
Found at i:53054157 original size:113 final size:113
Alignment explanation
Indices: 53053959--53054187 Score: 413
Period size: 113 Copynumber: 2.0 Consensus size: 113
53053949 AAGTGCAGGG
* *
53053959 TTGGATGGGGTTATCGTGCATTAATCATATGAGATTGTTTTGTTATGGGCCCAACTGTGTTAATA
1 TTGGATGGGGGTATCATGCATTAATCATATGAGATTGTTTTGTTATGGGCCCAACTGTGTTAATA
* *
53054024 TGGGCAAGGCCCAATATATCTCGACTTGTAATAGGGCTACGGCCCAGA
66 TGGGCAAGGCCCAATATATCTCAACTTGTAATAGGGCTACGACCCAGA
53054072 TTGGATGGGGGTATCATGCATTAATCATATGAGATTGTTTTGTTATGGGCCCAACTGTGTTAATA
1 TTGGATGGGGGTATCATGCATTAATCATATGAGATTGTTTTGTTATGGGCCCAACTGTGTTAATA
*
53054137 TGGGCAAGGCCTAATATATCTCAACTTGTAATAGGGCTACGACCCAGA
66 TGGGCAAGGCCCAATATATCTCAACTTGTAATAGGGCTACGACCCAGA
53054185 TTG
1 TTG
53054188 ATATTGATAT
Statistics
Matches: 111, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
113 111 1.00
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32
Consensus pattern (113 bp):
TTGGATGGGGGTATCATGCATTAATCATATGAGATTGTTTTGTTATGGGCCCAACTGTGTTAATA
TGGGCAAGGCCCAATATATCTCAACTTGTAATAGGGCTACGACCCAGA
Found at i:53055413 original size:26 final size:28
Alignment explanation
Indices: 53055383--53055437 Score: 87
Period size: 26 Copynumber: 2.0 Consensus size: 28
53055373 AAACTCTTCT
53055383 AAAAGAAAACTC-AAGAGAA-ATTATTA
1 AAAAGAAAACTCAAAGAGAATATTATTA
*
53055409 AAAAGAAAACTCAAAGAGAATTTTATTA
1 AAAAGAAAACTCAAAGAGAATATTATTA
53055437 A
1 A
53055438 CTCAAAGTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 12 0.46
27 7 0.27
28 7 0.27
ACGTcount: A:0.60, C:0.07, G:0.11, T:0.22
Consensus pattern (28 bp):
AAAAGAAAACTCAAAGAGAATATTATTA
Found at i:53065548 original size:31 final size:30
Alignment explanation
Indices: 53065510--53065626 Score: 103
Period size: 31 Copynumber: 3.8 Consensus size: 30
53065500 TTAATCACAT
*
53065510 TAATATTAAATTAATAAAACATTATCTAAA
1 TAATATTAAATTAATAAAATATTATCTAAA
** * *
53065540 TAAGTATTAAATTAAATTTAATATCA-C-ATAT
1 TAA-TATTAAATT-AATAAAATATTATCTA-AA
* *
53065571 TAATATTAAATTAATAAAATACTATCTAGA
1 TAATATTAAATTAATAAAATATTATCTAAA
*
53065601 TAAATATTAAATTAAATTAAATATTA
1 T-AATATTAAATT-AATAAAATATTA
53065627 AATTTATTAA
Statistics
Matches: 67, Mismatches: 13, Indels: 12
0.73 0.14 0.13
Matches are distributed among these distances:
29 8 0.12
30 15 0.22
31 26 0.39
32 18 0.27
ACGTcount: A:0.54, C:0.05, G:0.02, T:0.39
Consensus pattern (30 bp):
TAATATTAAATTAATAAAATATTATCTAAA
Found at i:53065597 original size:61 final size:61
Alignment explanation
Indices: 53065508--53065624 Score: 189
Period size: 61 Copynumber: 1.9 Consensus size: 61
53065498 AATTAATCAC
* * *
53065508 ATTAATATTAAATTAATAAAACATTATCTAAATAAGTATTAAATTAAATTTAATATCACAT
1 ATTAATATTAAATTAATAAAACACTATCTAAATAAATATTAAATTAAATTAAATATCACAT
* *
53065569 ATTAATATTAAATTAATAAAATACTATCTAGATAAATATTAAATTAAATTAAATAT
1 ATTAATATTAAATTAATAAAACACTATCTAAATAAATATTAAATTAAATTAAATAT
53065625 TAAATTTATT
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
61 51 1.00
ACGTcount: A:0.54, C:0.05, G:0.02, T:0.39
Consensus pattern (61 bp):
ATTAATATTAAATTAATAAAACACTATCTAAATAAATATTAAATTAAATTAAATATCACAT
Found at i:53068767 original size:17 final size:17
Alignment explanation
Indices: 53068721--53068767 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
53068711 TCGTTAAAGG
*
53068721 CCGATAAATGA-AATGC
1 CCGACAAATGATAATGC
*
53068737 CCGATC-AATTATAATGC
1 CCGA-CAAATGATAATGC
53068754 CCGACAAATGATAA
1 CCGACAAATGATAA
53068768 ATGATAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
16 9 0.36
17 16 0.64
ACGTcount: A:0.43, C:0.21, G:0.15, T:0.21
Consensus pattern (17 bp):
CCGACAAATGATAATGC
Found at i:53076084 original size:312 final size:312
Alignment explanation
Indices: 53075486--53076127 Score: 1025
Period size: 312 Copynumber: 2.1 Consensus size: 312
53075476 ATTTTAACTA
*
53075486 ATTAAATAAATCTCAAATGCACGATTTCAAAATATGAGTTTAATCAAGATGACATAATTGTGTTA
1 ATTAATTAAATCT--AATGCACGATTTCAAAATATGAGTTTAATCAAGATGACATAATTGTGTTA
* *
53075551 GATCAATTACATTTCTTAACTTAGAATTATCAAACTCATGTTTATATTGTTACGAACAAATTTAC
64 GATCAATTACATTTCTTAACTTAGAATTATCAAACTCATGCTTATATTGTTACGAACAAATTCAC
* **
53075616 GGCAACTCGGTAATTTGCTAACTTATGAACATACTCACCTACCAAAATCCATTCATCTCTTGACT
129 GACAACTCGAAAATTTGCTAACTTATGAACATACTCACCTACCAAAATCCATTCATCTCTTGACT
* * *
53075681 AGATCCCTATGTCAATCCATCCGATTAAACAAATCTTTAATAGGAAAATATGTTATTGTACATAC
194 AGATCCCTATGTAAATCCAACCGATTAAACAAATCTTTAATAGGAAAATATGTTATTGCACATAC
* * *
53075746 AAATTTATTATATCGAAATGATCTCTTGTACATATCCCTATGTCAATTCAAACG
259 AAACTTATTAGATCGAAATAATCTCTTGTACATATCCCTATGTCAATTCAAACG
*
53075800 ATTAATTAAATCTAATGCATGATTTCAAAATATGA-TTTAAATCAAGATGACATAATTGTGTTAG
1 ATTAATTAAATCTAATGCACGATTTCAAAATATGAGTTT-AATCAAGATGACATAATTGTGTTAG
* * * *
53075864 ATTAATTACATTTCTTAACTTAGAATTATTAAACTCATGCTTATATTGTTACGAATAAATTCATG
65 ATCAATTACATTTCTTAACTTAGAATTATCAAACTCATGCTTATATTGTTACGAACAAATTCACG
*
53075929 ACAACTCGAAAATTTGCTAACTTATGAACATACTTACCTACCAAAATCCATTCATCTCTTGACTA
130 ACAACTCGAAAATTTGCTAACTTATGAACATACTCACCTACCAAAATCCATTCATCTCTTGACTA
* * *
53075994 TATCCCTATGTAAATTCAACCGATTAAACAAATCTTTAATAGGAAAATATGTTATTGCACATTCA
195 GATCCCTATGTAAATCCAACCGATTAAACAAATCTTTAATAGGAAAATATGTTATTGCACATACA
* * * *
53076059 TACTTATTAGATTGAAATAATCTCTTGTACATATCCCTATGTCAATTCCAATG
260 AACTTATTAGATCGAAATAATCTCTTGTACATATCCCTATGTCAATTCAAACG
53076112 ATTAATTAAATCTAAT
1 ATTAATTAAATCTAAT
53076128 AAGCACATAA
Statistics
Matches: 302, Mismatches: 25, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
311 3 0.01
312 287 0.95
314 12 0.04
ACGTcount: A:0.38, C:0.17, G:0.09, T:0.36
Consensus pattern (312 bp):
ATTAATTAAATCTAATGCACGATTTCAAAATATGAGTTTAATCAAGATGACATAATTGTGTTAGA
TCAATTACATTTCTTAACTTAGAATTATCAAACTCATGCTTATATTGTTACGAACAAATTCACGA
CAACTCGAAAATTTGCTAACTTATGAACATACTCACCTACCAAAATCCATTCATCTCTTGACTAG
ATCCCTATGTAAATCCAACCGATTAAACAAATCTTTAATAGGAAAATATGTTATTGCACATACAA
ACTTATTAGATCGAAATAATCTCTTGTACATATCCCTATGTCAATTCAAACG
Found at i:53077360 original size:12 final size:12
Alignment explanation
Indices: 53077343--53077368 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
53077333 AAAATTCATC
53077343 AAAATTAATTAA
1 AAAATTAATTAA
53077355 AAAATTAATTAA
1 AAAATTAATTAA
53077367 AA
1 AA
53077369 TTCAACATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
AAAATTAATTAA
Found at i:53089602 original size:14 final size:14
Alignment explanation
Indices: 53089583--53089610 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
53089573 AATGAAAGTA
53089583 CATAGTATATGATG
1 CATAGTATATGATG
53089597 CATAGTATATGATG
1 CATAGTATATGATG
53089611 AAAGTGATAG
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:0.36, C:0.07, G:0.21, T:0.36
Consensus pattern (14 bp):
CATAGTATATGATG
Found at i:53092134 original size:49 final size:49
Alignment explanation
Indices: 53092062--53092160 Score: 162
Period size: 49 Copynumber: 2.0 Consensus size: 49
53092052 TAGTCAAAAG
* *
53092062 CCTTAGTTTCATGAGTAAATTACATTTAAATTGTGATGTGATGTAATAC
1 CCTTAGCTTCATGAGTAAATTACATTTAAATTGTGACGTGATGTAATAC
* *
53092111 CCTTAGCTTCATGAGTGAATTACATTTAAATTGTGGCGTGATGTAATAC
1 CCTTAGCTTCATGAGTAAATTACATTTAAATTGTGACGTGATGTAATAC
53092160 C
1 C
53092161 TGACAATCTA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
49 46 1.00
ACGTcount: A:0.30, C:0.13, G:0.18, T:0.38
Consensus pattern (49 bp):
CCTTAGCTTCATGAGTAAATTACATTTAAATTGTGACGTGATGTAATAC
Found at i:53094406 original size:8 final size:8
Alignment explanation
Indices: 53094393--53094427 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
53094383 GTAAAAGCCA
53094393 AAATGCCG
1 AAATGCCG
*
53094401 AAATGCTG
1 AAATGCCG
53094409 AAATGCCG
1 AAATGCCG
*
53094417 AAAAGCCG
1 AAATGCCG
53094425 AAA
1 AAA
53094428 GTTTGGCTAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.46, C:0.20, G:0.23, T:0.11
Consensus pattern (8 bp):
AAATGCCG
Found at i:53094427 original size:16 final size:16
Alignment explanation
Indices: 53094385--53094427 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
53094375 ATGAATCGGT
*
53094385 AAAAGCCAAAATGCCG
1 AAAAGCCGAAATGCCG
* *
53094401 AAATGCTGAAATGCCG
1 AAAAGCCGAAATGCCG
53094417 AAAAGCCGAAA
1 AAAAGCCGAAA
53094428 GTTTGGCTAC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.49, C:0.21, G:0.21, T:0.09
Consensus pattern (16 bp):
AAAAGCCGAAATGCCG
Found at i:53094607 original size:29 final size:29
Alignment explanation
Indices: 53094572--53094649 Score: 86
Period size: 29 Copynumber: 2.7 Consensus size: 29
53094562 GCCTAACGGG
*
53094572 CCATATAAATGTGATTTGGTCCCAATGGA
1 CCATATAAATGTGATTTGGGCCCAATGGA
* * * *
53094601 CCATATACAGGTGATTTGGGCCTAATGGG
1 CCATATAAATGTGATTTGGGCCCAATGGA
* *
53094630 CCATATGAATATGA-TTGGGC
1 CCATATAAATGTGATTTGGGC
53094650 TTAATGGGCC
Statistics
Matches: 40, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
28 6 0.15
29 34 0.85
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (29 bp):
CCATATAAATGTGATTTGGGCCCAATGGA
Found at i:53095765 original size:17 final size:18
Alignment explanation
Indices: 53095732--53095765 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
53095722 GTTTAAGAAG
*
53095732 GGTTTTCAGTGAAAACAT
1 GGTTTTCACTGAAAACAT
53095750 GGTTTTCACT-AAAACA
1 GGTTTTCACTGAAAACA
53095766 CTTCAATGTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32
Consensus pattern (18 bp):
GGTTTTCACTGAAAACAT
Found at i:53099086 original size:39 final size:39
Alignment explanation
Indices: 53098952--53099133 Score: 161
Period size: 41 Copynumber: 4.6 Consensus size: 39
53098942 AACATTATTT
* * * * * *
53098952 AGGCTCTGTGTCTAGCAGGCTCTGTGCCGGTGTATTACATT
1 AGGCTTTGTGCCTAGCAGGCTTTGTGCCGATG-A-TATATC
* * * *
53098993 GGGCTCTGTGCCTAGCAGGCTTTGTGCTGGTGATAT-TC
1 AGGCTTTGTGCCTAGCAGGCTTTGTGCCGATGATATATC
* *
53099031 GGGCTTTGTGCCTAGCAAGCTTTGTGCCGATGATATATC
1 AGGCTTTGTGCCTAGCAGGCTTTGTGCCGATGATATATC
* *
53099070 AGGCTTGGTGCCTAGCAGGCTTCGTGCC-AGTGTATTATATC
1 AGGCTTTGTGCCTAGCAGGCTTTGTGCCGA-TG-A-TATATC
* *
53099111 AAGTTTTGTGCCTAGCAGGCTTT
1 AGGCTTTGTGCCTAGCAGGCTTT
53099134 ATGTCGGTGT
Statistics
Matches: 119, Mismatches: 18, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
38 34 0.29
39 30 0.25
40 2 0.02
41 53 0.45
ACGTcount: A:0.15, C:0.21, G:0.30, T:0.34
Consensus pattern (39 bp):
AGGCTTTGTGCCTAGCAGGCTTTGTGCCGATGATATATC
Found at i:53099122 original size:41 final size:39
Alignment explanation
Indices: 53098999--53099132 Score: 137
Period size: 38 Copynumber: 3.4 Consensus size: 39
53098989 CATTGGGCTC
* * * **
53098999 TGTGCCTAGCAGGCTTTGTGCTGGTGATAT-TCGGGCTT
1 TGTGCCTAGCAGGCTTCGTGCCGATGATATATCAAGCTT
* * *
53099037 TGTGCCTAGCAAGCTTTGTGCCGATGATATATCAGGCTT
1 TGTGCCTAGCAGGCTTCGTGCCGATGATATATCAAGCTT
* *
53099076 GGTGCCTAGCAGGCTTCGTGCC-AGTGTATTATATCAAGTTT
1 TGTGCCTAGCAGGCTTCGTGCCGA-TG-A-TATATCAAGCTT
53099117 TGTGCCTAGCAGGCTT
1 TGTGCCTAGCAGGCTT
53099133 TATGTCGGTG
Statistics
Matches: 82, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
38 28 0.34
39 28 0.34
40 1 0.01
41 25 0.30
ACGTcount: A:0.16, C:0.20, G:0.29, T:0.34
Consensus pattern (39 bp):
TGTGCCTAGCAGGCTTCGTGCCGATGATATATCAAGCTT
Found at i:53099343 original size:21 final size:21
Alignment explanation
Indices: 53099319--53099383 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 21
53099309 AAGGAAGGTA
53099319 ATGTTCAACGAAAGTATGTTT
1 ATGTTCAACGAAAGTATGTTT
*
53099340 ATGTTC-ATGAAA-T-TG---
1 ATGTTCAACGAAAGTATGTTT
*
53099355 ATATTCAAACGAAAGTATGTTT
1 ATGTTC-AACGAAAGTATGTTT
53099377 ATGTTCA
1 ATGTTCA
53099384 TGAAATTGAT
Statistics
Matches: 33, Mismatches: 4, Indels: 14
0.65 0.08 0.27
Matches are distributed among these distances:
15 5 0.15
17 5 0.15
18 3 0.09
19 3 0.09
20 5 0.15
21 7 0.21
22 5 0.15
ACGTcount: A:0.35, C:0.09, G:0.17, T:0.38
Consensus pattern (21 bp):
ATGTTCAACGAAAGTATGTTT
Found at i:53100224 original size:18 final size:18
Alignment explanation
Indices: 53100201--53100238 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
53100191 ATGAAAGGTG
*
53100201 TTAAGTATATGTA-TATGT
1 TTAAGTAAAT-TAGTATGT
53100219 TTAAGTAAATTAGTATGT
1 TTAAGTAAATTAGTATGT
53100237 TT
1 TT
53100239 GCTTTTGAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 2 0.11
18 16 0.89
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.50
Consensus pattern (18 bp):
TTAAGTAAATTAGTATGT
Found at i:53108229 original size:25 final size:25
Alignment explanation
Indices: 53108187--53108235 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
53108177 CTTTATTATT
* *
53108187 ATCATTATGAAGAATTATGTGATTA
1 ATCATTATCAAGAATTATATGATTA
* *
53108212 ATCATTATCATGAGTTATATGATT
1 ATCATTATCAAGAATTATATGATT
53108236 GGTCCTCTGG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.37, C:0.06, G:0.14, T:0.43
Consensus pattern (25 bp):
ATCATTATCAAGAATTATATGATTA
Found at i:53114024 original size:46 final size:44
Alignment explanation
Indices: 53113916--53114049 Score: 155
Period size: 46 Copynumber: 3.0 Consensus size: 44
53113906 GGTGGTATGT
**
53113916 GAGCCAGTGTAAGACATGTCTGGGACATGCATAACCACATT-ATGAA
1 GAGCCAGTGTAAGACATGTCTGGGACATGCAT--CGGCATTGA-GAA
* *
53113962 -AGCCAGTGTATGACATGTCTGGGACATTCATCGGCATTGAGACGA
1 GAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCATTGAGA--A
* *
53114007 GAGCCAGTGTAAGACATGTCTTGGACATGCATCGGCGTTGAGA
1 GAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCATTGAGA
53114050 TATGCAAGCT
Statistics
Matches: 76, Mismatches: 8, Indels: 8
0.83 0.09 0.09
Matches are distributed among these distances:
43 7 0.09
44 1 0.01
45 30 0.39
46 38 0.50
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.23
Consensus pattern (44 bp):
GAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCATTGAGAA
Found at i:53115186 original size:43 final size:44
Alignment explanation
Indices: 53115094--53115210 Score: 141
Period size: 43 Copynumber: 2.7 Consensus size: 44
53115084 ATATGCCTCC
*
53115094 TCTGGCCATGGGCGTGTGCCTC-AGCCGTGTGGAGGACACGGCCT
1 TCTGGCCATGGGCGTGTGCCTCGA-CCGTGTGGAGGACACGGACT
*
53115138 T-TGGCCATGGGCGTGTGCCTCGACCGTGTGGAGGATAC-GACT
1 TCTGGCCATGGGCGTGTGCCTCGACCGTGTGGAGGACACGGACT
* * * * *
53115180 TCTGGCCACGAGCATATGCCTCGACCATGTG
1 TCTGGCCATGGGCGTGTGCCTCGACCGTGTG
53115211 CCTCTATTTG
Statistics
Matches: 64, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
42 4 0.06
43 58 0.91
44 2 0.03
ACGTcount: A:0.15, C:0.28, G:0.35, T:0.22
Consensus pattern (44 bp):
TCTGGCCATGGGCGTGTGCCTCGACCGTGTGGAGGACACGGACT
Found at i:53115186 original size:109 final size:109
Alignment explanation
Indices: 53114991--53115201 Score: 341
Period size: 109 Copynumber: 1.9 Consensus size: 109
53114981 CGGACAGAGA
*
53114991 CATGGCCGTGTGCCTCAGCCGTGTAGAGGACATAGCCTCTAGCCATGGGCGTGTGCCTCGACCGT
1 CATGGCCGTGTGCCTCAGCCGTGTAGAGGACACAGCCTCTAGCCATGGGCGTGTGCCTCGACCGT
* *
53115056 GTGGAGGACATGACTTTTGGCCACGAGCATATGCCTCCTCTGGC
66 GTGGAGGACACGACTTCTGGCCACGAGCATATGCCTCCTCTGGC
* * * * *
53115100 CATGGGCGTGTGCCTCAGCCGTGTGGAGGACACGGCCTTTGGCCATGGGCGTGTGCCTCGACCGT
1 CATGGCCGTGTGCCTCAGCCGTGTAGAGGACACAGCCTCTAGCCATGGGCGTGTGCCTCGACCGT
*
53115165 GTGGAGGATACGACTTCTGGCCACGAGCATATGCCTC
66 GTGGAGGACACGACTTCTGGCCACGAGCATATGCCTC
53115202 GACCATGTGC
Statistics
Matches: 93, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
109 93 1.00
ACGTcount: A:0.16, C:0.29, G:0.33, T:0.22
Consensus pattern (109 bp):
CATGGCCGTGTGCCTCAGCCGTGTAGAGGACACAGCCTCTAGCCATGGGCGTGTGCCTCGACCGT
GTGGAGGACACGACTTCTGGCCACGAGCATATGCCTCCTCTGGC
Found at i:53115312 original size:69 final size:69
Alignment explanation
Indices: 53115207--53115335 Score: 231
Period size: 69 Copynumber: 1.9 Consensus size: 69
53115197 GCCTCGACCA
* * *
53115207 TGTGCCTCTATTTGGTTGCTGGCGTCAAAAATAGAATGTCAAGGTTTTTAGACACGGGTGCCTCA
1 TGTGCCTCTATTTGGTTGCTGACATCAAAAACAGAATGTCAAGGTTTTTAGACACGGGTGCCTCA
53115272 GCCG
66 GCCG
53115276 TGTGCCTCTATTTGGTTGCTGACATCAAAAACAGAATGTCAAGGTTTTTAGACACGGGTG
1 TGTGCCTCTATTTGGTTGCTGACATCAAAAACAGAATGTCAAGGTTTTTAGACACGGGTG
53115336 TGTCGTGGCT
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
69 57 1.00
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.31
Consensus pattern (69 bp):
TGTGCCTCTATTTGGTTGCTGACATCAAAAACAGAATGTCAAGGTTTTTAGACACGGGTGCCTCA
GCCG
Found at i:53122929 original size:21 final size:21
Alignment explanation
Indices: 53122854--53122919 Score: 78
Period size: 25 Copynumber: 3.0 Consensus size: 21
53122844 GTCTTGAATT
53122854 TGTTAGATATTGAATTTATTA
1 TGTTAGATATTGAATTTATTA
* *
53122875 TGTTTTAAGCTTGTTGAATTTATTA
1 TG--TT-AG-ATATTGAATTTATTA
53122900 TGTTAGATATTGAATTTATT
1 TGTTAGATATTGAATTTATT
53122920 TAGTTGGATA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
21 14 0.38
22 2 0.05
23 4 0.11
24 2 0.05
25 15 0.41
ACGTcount: A:0.29, C:0.02, G:0.15, T:0.55
Consensus pattern (21 bp):
TGTTAGATATTGAATTTATTA
Found at i:53124377 original size:22 final size:22
Alignment explanation
Indices: 53124352--53124393 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
53124342 ACAATTTAAA
53124352 ATATAAATTTATTAATATATAT
1 ATATAAATTTATTAATATATAT
53124374 ATATAAATTTATTAATATAT
1 ATATAAATTTATTAATATAT
53124394 GTAAAAACAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
ATATAAATTTATTAATATATAT
Found at i:53124517 original size:15 final size:14
Alignment explanation
Indices: 53124484--53124550 Score: 89
Period size: 14 Copynumber: 4.7 Consensus size: 14
53124474 CCAGAAAAGT
*
53124484 AAATAATTTTCCAG
1 AAATCATTTTCCAG
*
53124498 AAATCATTTTCTAGG
1 AAATCATTTTCCA-G
53124513 AAATCATTTTCCAG
1 AAATCATTTTCCAG
*
53124527 AAATCATTTTCCGG
1 AAATCATTTTCCAG
*
53124541 AAAACATTTT
1 AAATCATTTT
53124551 ACCTGCAAAC
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
14 34 0.72
15 13 0.28
ACGTcount: A:0.37, C:0.16, G:0.09, T:0.37
Consensus pattern (14 bp):
AAATCATTTTCCAG
Found at i:53124521 original size:29 final size:28
Alignment explanation
Indices: 53124484--53124550 Score: 98
Period size: 29 Copynumber: 2.4 Consensus size: 28
53124474 CCAGAAAAGT
*
53124484 AAATAATTTTCCAGAAATCATTTTCTAGG
1 AAATCATTTTCCAGAAATCATTTTC-AGG
*
53124513 AAATCATTTTCCAGAAATCATTTTCCGG
1 AAATCATTTTCCAGAAATCATTTTCAGG
*
53124541 AAAACATTTT
1 AAATCATTTT
53124551 ACCTGCAAAC
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
28 11 0.31
29 24 0.69
ACGTcount: A:0.37, C:0.16, G:0.09, T:0.37
Consensus pattern (28 bp):
AAATCATTTTCCAGAAATCATTTTCAGG
Found at i:53130443 original size:42 final size:42
Alignment explanation
Indices: 53130361--53130504 Score: 105
Period size: 42 Copynumber: 3.5 Consensus size: 42
53130351 CAATGTCATG
*
53130361 TCCCAGACATGGTCTTACATGAGATCTCACATCGAAGCCATA
1 TCCCAGACATGGTCTTACACGAGATCTCACATCGAAGCCATA
* * ** * *
53130403 TCCCAGATATGGTCTTATACGA-AGTCTCATTTCGATGCCATG
1 TCCCAGACATGGTCTTACACGAGA-TCTCACATCGAAGCCATA
** * * * * *
53130445 T-CTTGACGTGGTCTTACACGAAATCTCATAT-TAACGTCATA
1 TCCCAGACATGGTCTTACACGAGATCTCACATCGAA-GCCATA
* *
53130486 TCCTAGATATGGTCTTACA
1 TCCCAGACATGGTCTTACA
53130505 TGATAACTCA
Statistics
Matches: 78, Mismatches: 20, Indels: 8
0.74 0.19 0.08
Matches are distributed among these distances:
40 1 0.01
41 28 0.36
42 49 0.63
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.31
Consensus pattern (42 bp):
TCCCAGACATGGTCTTACACGAGATCTCACATCGAAGCCATA
Found at i:53133605 original size:27 final size:27
Alignment explanation
Indices: 53133571--53133640 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
53133561 CTTCATTCAT
* *
53133571 GAAATAATTACATGAATTGGTTATATG
1 GAAATAATTATATGAATTGGTTAAATG
*
53133598 GATATAATTATATGAATTGGTTAAATG
1 GAAATAATTATATGAATTGGTTAAATG
53133625 GAAATAATTATATGAA
1 GAAATAATTATATGAA
53133641 ATGGAACATT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.44, C:0.01, G:0.17, T:0.37
Consensus pattern (27 bp):
GAAATAATTATATGAATTGGTTAAATG
Found at i:53142242 original size:22 final size:22
Alignment explanation
Indices: 53142198--53142238 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
53142188 TTATTTGATA
*
53142198 TTTAAATTTATTTTTGAATTGT
1 TTTAAATTTATTATTGAATTGT
53142220 TTTAAA-TTATTATTGAATT
1 TTTAAATTTATTATTGAATT
53142239 TGTTAACTTT
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:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (22 bp):
TTTAAATTTATTATTGAATTGT
Done.