Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10
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: 48586650
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2183483 characters in sequence are not A, C, G, or T
File 60 of 145
Found at i:19669614 original size:19 final size:20
Alignment explanation
Indices: 19669592--19669639 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
19669582 TTTTTATAGA
19669592 TATTTTGAAT-TTT-AAAATT
1 TATTTTGAATATTTGAAAA-T
19669611 TATTTTGAATATTTGAAAAT
1 TATTTTGAATATTTGAAAAT
19669631 TATTTTGAA
1 TATTTTGAA
19669640 CTTTGTTTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 10 0.37
20 13 0.48
21 4 0.15
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (20 bp):
TATTTTGAATATTTGAAAAT
Found at i:19669960 original size:20 final size:20
Alignment explanation
Indices: 19669923--19669961 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
19669913 AATATAAAAA
* * *
19669923 TAACTAAGTTTTTTATTAAT
1 TAACTAAATTGTTAATTAAT
19669943 TAACTAAATTGTTAATTAA
1 TAACTAAATTGTTAATTAA
19669962 GTAGGAGTGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (20 bp):
TAACTAAATTGTTAATTAAT
Found at i:19671760 original size:21 final size:21
Alignment explanation
Indices: 19671735--19671792 Score: 107
Period size: 21 Copynumber: 2.8 Consensus size: 21
19671725 TATTTGATTC
19671735 CAATCAAATTGATTTAATTTT
1 CAATCAAATTGATTTAATTTT
19671756 CAATCAAATTGATTTAATTTT
1 CAATCAAATTGATTTAATTTT
*
19671777 TAATCAAATTGATTTA
1 CAATCAAATTGATTTA
19671793 TTAGCTCCTT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.40, C:0.09, G:0.05, T:0.47
Consensus pattern (21 bp):
CAATCAAATTGATTTAATTTT
Found at i:19672707 original size:87 final size:85
Alignment explanation
Indices: 19672567--19672797 Score: 212
Period size: 88 Copynumber: 2.6 Consensus size: 85
19672557 TTATTCCCAC
* * * * *
19672567 ACGGTTTTTATTTCATTTTGTTATTTTATTTCCAAACAGGA-AATTAAAGTTAAATAAGATCCGT
1 ACGG-TTTTATTACATTTTG--ATTTTATTTCCAAA-ACGAGAATTAAAATTAAATAAAATACGT
** * ** *
19672631 TTCGGGATTTATTCTCGCTGTTTA
62 TTCAAGATTTATTCCCGCCATTCA
* * *
19672655 ACAGGTTTTATTCCACTTTTGATTTTATTTCCAAAACGAGTATTAAAATTAAAATAAAATATGTT
1 AC-GGTTTTATTACA-TTTTGATTTTATTTCCAAAACGAGAATTAAAATT-AAATAAAATACGTT
19672720 TCAAGATTTATTCCCGCCATTCA
63 TCAAGATTTATTCCCGCCATTCA
* * * *
19672743 ACTGATTTATTACATTTTGATTATGTTTCCAAAAACGAGAAATTAAAATTAAATA
1 ACGGTTTTATTACATTTTGATTTTATTTCC-AAAACGAG-AATTAAAATTAAATA
19672798 CAATTTTTTT
Statistics
Matches: 118, Mismatches: 19, Indels: 13
0.79 0.13 0.09
Matches are distributed among these distances:
86 17 0.14
87 44 0.37
88 50 0.42
89 7 0.06
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.42
Consensus pattern (85 bp):
ACGGTTTTATTACATTTTGATTTTATTTCCAAAACGAGAATTAAAATTAAATAAAATACGTTTCA
AGATTTATTCCCGCCATTCA
Found at i:19672815 original size:87 final size:87
Alignment explanation
Indices: 19672661--19672821 Score: 200
Period size: 87 Copynumber: 1.9 Consensus size: 87
19672651 TTTAACAGGT
* * *
19672661 TTTATTCCACTTTTGATTTTATTTCCAAAACGAGTATTAAAATTAAAATAAAATATGTTTCAAGA
1 TTTATTACACTTTTGATTATATTTCCAAAACGAGAATTAAAATTAAAATAAAATATGTTTCAAGA
*
19672726 TTTATTCCCGCCATTCAACTGA
66 TTTAATCCCGCCATTCAACTGA
* * * * **
19672748 TTTATTACA-TTTTGATTATGTTTCCAAAAACGAGAAATTAAAATT-AAATACAATTTTTTTCGG
1 TTTATTACACTTTTGATTATATTTCC-AAAACGAG-AATTAAAATTAAAATAAAATATGTTTCAA
19672811 GATTTAATCCC
64 GATTTAATCCC
19672822 ATCGTTTAAT
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
86 14 0.23
87 39 0.63
88 9 0.15
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.41
Consensus pattern (87 bp):
TTTATTACACTTTTGATTATATTTCCAAAACGAGAATTAAAATTAAAATAAAATATGTTTCAAGA
TTTAATCCCGCCATTCAACTGA
Found at i:19673093 original size:84 final size:84
Alignment explanation
Indices: 19672608--19673183 Score: 533
Period size: 83 Copynumber: 6.8 Consensus size: 84
19672598 CCAAACAGGA
* * * **
19672608 AATTAAAGTTAAATAAGATCCGTTTCGGGATTTATTCTCGC-T-GTTTAAC-AGGTTTTATTCCA
1 AATTAAA-TTAAATAAAATCTGTTTCGGGATTTATTC-C-CATCGTTTAACAAGATTTTATTTGA
* **
19672670 CTTTTGATTTTATTTCCAAAACGAG
63 -TTTT-ATTTTGTTTCC-AAATTAG
* * ** ** * * * **
19672695 TATTAAAATTAAAATAAAATATGTTTCAAGATTTATTCCCGCCATTCAAC-TGA-TTTATTACAT
1 AATT-AAATT-AAATAAAATCTGTTTCGGGATTTATTCCCATCGTTTAACAAGATTTTATTTGAT
* **
19672758 TTTGATTATGTTTCCAAAAACGAG
64 TTT-ATTTTGTTTCC--AAATTAG
* * * * * * *
19672782 AAATTAAAATTAAATACAATTTTTTTCGGGATTTAATCCCATCGTTTAATAAGATTATATTTTAT
1 -AATT-AAATTAAATAAAATCTGTTTCGGGATTTATTCCCATCGTTTAACAAGATTTTATTTGAT
*
19672847 TTTATTTTGTCTCCAAATTAG
64 TTTATTTTGTTTCCAAATTAG
* *
19672868 AATTAGAATGAAATAAAATCTGTTTCGGGATTTATTACCGC-T-GTTTAACAAAATTTTATTTGA
1 AATTA-AATTAAATAAAATCTGTTTCGGGATTTATT-CC-CATCGTTTAACAAGATTTTATTTGA
*
19672931 TTTTATTTTGTTTCTAAATTAG
63 TTTTATTTTGTTTCCAAATTAG
* * *
19672953 AATTAAATTAAA-AAAATATGTTTCGAGATTTATTCCCGTCGTTTAACAAGATTTTATTTGATTT
1 AATTAAATTAAATAAAATCTGTTTCGGGATTTATTCCCATCGTTTAACAAGATTTTATTTGATTT
19673017 TATTTTGTTTCCAAATTAG
66 TATTTTGTTTCCAAATTAG
* * *
19673036 AATGAAATTAAATAAAATCTGTTTCGAGATTTATTCCCATCGTTTAACAAGATTTTATTTTATTT
1 AATTAAATTAAATAAAATCTGTTTCGGGATTTATTCCCATCGTTTAACAAGATTTTATTTGATTT
19673101 TATTTT-TTTCCAAATTAG
66 TATTTTGTTTCCAAATTAG
* * * * *
19673119 AATTAAATGAAATAAAATCTATTTCGGGATTTATTCCCGTTGTTTAAC-ATATTTTATTTTGATT
1 AATTAAATTAAATAAAATCTGTTTCGGGATTTATTCCCATCGTTTAACAAGATTTTA-TTTGATT
19673183 T
65 T
19673184 AATTATTTAA
Statistics
Matches: 412, Mismatches: 62, Indels: 34
0.81 0.12 0.07
Matches are distributed among these distances:
81 1 0.00
82 10 0.02
83 133 0.32
84 62 0.15
85 71 0.17
86 23 0.06
87 51 0.12
88 51 0.12
89 10 0.02
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.45
Consensus pattern (84 bp):
AATTAAATTAAATAAAATCTGTTTCGGGATTTATTCCCATCGTTTAACAAGATTTTATTTGATTT
TATTTTGTTTCCAAATTAG
Found at i:19673093 original size:167 final size:168
Alignment explanation
Indices: 19672805--19673183 Score: 525
Period size: 167 Copynumber: 2.3 Consensus size: 168
19672795 ATACAATTTT
* * * * *
19672805 TTTCGGGATTTAATCCCATCGTTTAATAAGATTATATTTTATTTTATTTTGTCTCCAAATTAGAA
1 TTTCGGGATTTATTCCCGTCGTTTAACAAGATTTTATTTGATTTTATTTTGTCTCCAAATTAGAA
* *
19672870 TTAGAATGAAATAAAATCTGTTTCGGGATTTATTACCGCTGTTTAACAAAATTTTATTTGATTTT
66 TGAGAATGAAATAAAATCTGTTTCGAGATTTATTACCGCTGTTTAACAAAATTTTATTTGATTTT
* * *
19672935 ATTTTGTTTCTAAATTAGAATTAAATTAAA-AAAATATG
131 ATTTT-TTTCCAAATTAGAATTAAATGAAATAAAATATA
* *
19672973 TTTCGAGATTTATTCCCGTCGTTTAACAAGATTTTATTTGATTTTATTTTGTTTCCAAATTAGAA
1 TTTCGGGATTTATTCCCGTCGTTTAACAAGATTTTATTTGATTTTATTTTGTCTCCAAATTAGAA
* * *
19673038 TGA-AATTAAATAAAATCTGTTTCGAGATTTATT-CC-CATCGTTTAACAAGATTTTATTTTATT
66 TGAGAATGAAATAAAATCTGTTTCGAGATTTATTACCGC-T-GTTTAACAAAATTTTATTTGATT
*
19673100 TTATTTTTTTCCAAATTAGAATTAAATGAAATAAAATCTA
129 TTATTTTTTTCCAAATTAGAATTAAATGAAATAAAATATA
* *
19673140 TTTCGGGATTTATTCCCGTTGTTTAAC-ATATTTTATTTTGATTT
1 TTTCGGGATTTATTCCCGTCGTTTAACAAGATTTTA-TTTGATTT
19673184 AATTATTTAA
Statistics
Matches: 188, Mismatches: 19, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
165 1 0.01
166 32 0.17
167 95 0.51
168 60 0.32
ACGTcount: A:0.32, C:0.10, G:0.11, T:0.47
Consensus pattern (168 bp):
TTTCGGGATTTATTCCCGTCGTTTAACAAGATTTTATTTGATTTTATTTTGTCTCCAAATTAGAA
TGAGAATGAAATAAAATCTGTTTCGAGATTTATTACCGCTGTTTAACAAAATTTTATTTGATTTT
ATTTTTTTCCAAATTAGAATTAAATGAAATAAAATATA
Found at i:19673949 original size:31 final size:31
Alignment explanation
Indices: 19673908--19673973 Score: 123
Period size: 31 Copynumber: 2.1 Consensus size: 31
19673898 TGTTAAGAAA
19673908 ATAATGAAGGAATTATGGACATCGTTGGACC
1 ATAATGAAGGAATTATGGACATCGTTGGACC
*
19673939 ATAATTAAGGAATTATGGACATCGTTGGACC
1 ATAATGAAGGAATTATGGACATCGTTGGACC
19673970 ATAA
1 ATAA
19673974 ATAATTAGTG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.38, C:0.12, G:0.23, T:0.27
Consensus pattern (31 bp):
ATAATGAAGGAATTATGGACATCGTTGGACC
Found at i:19683171 original size:18 final size:18
Alignment explanation
Indices: 19683148--19683183 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
19683138 TGCCAGGTGC
*
19683148 GTATCCTATCCCTTATAT
1 GTATCCTAACCCTTATAT
19683166 GTATCCTAACCCTTATAT
1 GTATCCTAACCCTTATAT
19683184 ATTTCTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.25, C:0.28, G:0.06, T:0.42
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:19683403 original size:21 final size:21
Alignment explanation
Indices: 19683379--19683422 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
19683369 CCCACAACCA
*
19683379 GAGCAACTACAACCCCCGTCG
1 GAGCAACCACAACCCCCGTCG
*
19683400 GAGCAACCAGAACCCCCGTCG
1 GAGCAACCACAACCCCCGTCG
19683421 GA
1 GA
19683423 AGTTGAACCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.41, G:0.23, T:0.07
Consensus pattern (21 bp):
GAGCAACCACAACCCCCGTCG
Found at i:19684170 original size:317 final size:318
Alignment explanation
Indices: 19683584--19684218 Score: 1263
Period size: 317 Copynumber: 2.0 Consensus size: 318
19683574 TAATAGTAAA
19683584 TTATTTTTATATTTTTAATAAAATATAAGTTCTTTTGAATAAGGCAATAGAAATAATGCAACATA
1 TTATTTTTATATTTTTAATAAAATATAAGTTCTTTTGAATAAGGCAATAGAAATAATGCAACATA
19683649 ATTTCATTACAGCAATTATCAACTATTTCAGTTTGGACATGATTGAATTGTATAACCTGGGTTCC
66 ATTTCATTACAGCAATTATCAACTATTTCAGTTTGGACATGATTGAATTGTATAACCTGGGTTCC
19683714 TACACCATCCGTACAACTTCTGTTGGTTCGCTCTTTCCCGAATATCCATATTATTTCGTATTCTA
131 TACACCATCCGTACAACTTCTGTTGGTTCGCTCTTTCCCGAATATCCATATTATTTCGTATTCTA
19683779 CTCGAAAAAGGTCGACCTTTTGGTTTGCGACATAATTCTCTATTCGGTAACAACTTAAACAGAAC
196 CTCGAAAAAGGTCGACCTTTTGGTTTGCGACATAATTCTCTATTCGGTAACAACTTAAACAGAAC
19683844 AAGTGATACCGGAACAAGCATTTTTGACACTATTTGTTCAGAACCGTCTTCTCAAAAT
261 AAGTGATACCGGAACAAGCATTTTTGACACTATTTGTTCAGAACCGTCTTCTCAAAAT
19683902 TTATTTTTAT-TTTTTAATAAAATATAAGTTCTTTTGAATAAGGCAATAGAAATAATGCAACATA
1 TTATTTTTATATTTTTAATAAAATATAAGTTCTTTTGAATAAGGCAATAGAAATAATGCAACATA
19683966 ATTTCATTACAGCAATTATCAACTATTTCAGTTTGGACATGATTGAATTGTATAACCTGGGTTCC
66 ATTTCATTACAGCAATTATCAACTATTTCAGTTTGGACATGATTGAATTGTATAACCTGGGTTCC
19684031 TACACCATCCGTACAACTTCTGTTGGTTCGCTCTTTCCCGAATATCCATATTATTTCGTATTCTA
131 TACACCATCCGTACAACTTCTGTTGGTTCGCTCTTTCCCGAATATCCATATTATTTCGTATTCTA
19684096 CTCGAAAAAGGTCGACCTTTTGGTTTGCGACATAATTCTCTATTCGGTAACAACTTAAACAGAAC
196 CTCGAAAAAGGTCGACCTTTTGGTTTGCGACATAATTCTCTATTCGGTAACAACTTAAACAGAAC
19684161 AAGTGATACCGGAACAAGCATTTTTGACACTATTTGTTCAGAACCGTCTTCTCAAAAT
261 AAGTGATACCGGAACAAGCATTTTTGACACTATTTGTTCAGAACCGTCTTCTCAAAAT
19684219 AATTTTTTCA
Statistics
Matches: 317, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
317 307 0.97
318 10 0.03
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (318 bp):
TTATTTTTATATTTTTAATAAAATATAAGTTCTTTTGAATAAGGCAATAGAAATAATGCAACATA
ATTTCATTACAGCAATTATCAACTATTTCAGTTTGGACATGATTGAATTGTATAACCTGGGTTCC
TACACCATCCGTACAACTTCTGTTGGTTCGCTCTTTCCCGAATATCCATATTATTTCGTATTCTA
CTCGAAAAAGGTCGACCTTTTGGTTTGCGACATAATTCTCTATTCGGTAACAACTTAAACAGAAC
AAGTGATACCGGAACAAGCATTTTTGACACTATTTGTTCAGAACCGTCTTCTCAAAAT
Found at i:19684437 original size:126 final size:125
Alignment explanation
Indices: 19684176--19684496 Score: 489
Period size: 125 Copynumber: 2.6 Consensus size: 125
19684166 ATACCGGAAC
* * **
19684176 AAGCATTTTTGACACTATTTGTTCAGAACCGTCTTCTCAAAATAATTTTTTCAGGAACTGTTGTA
1 AAGCATTTTTGACACTATTTGTTCAGAACCGTATTCTCAAAATTA-TTTTTCAGGAACTACTGTA
*
19684241 GAAAAAGAGCGTCCACGTGGGAGCTTTTTCCAGTAATTTTGCTAACAGTGCATCCTACTTG
65 GAAAAAGAGCGTCCACGTGGGAGCTTTTTCCAGTAATTTTGCTAACAATGCATCCTACTTG
*
19684302 AAGCATTTTTGACACTATTTGTTCAAAACCGTATTCTCAAAATTATTTTTCAGGAACTACTGTAG
1 AAGCATTTTTGACACTATTTGTTCAGAACCGTATTCTCAAAATTATTTTTCAGGAACTACTGTAG
* ** * * * *
19684367 AAAAAGAGCGTCCACGTGGGTGCTTTTTTTAGTAATTTTGCTGACAATGTATCTTGCTTG
66 AAAAAGAGCGTCCACGTGGGAGCTTTTTCCAGTAATTTTGCTAACAATGCATCCTACTTG
* * *
19684427 AAGCGTTTTTTACACTATTTGTTCAGAACCGTATTCTCAAAATTATTTTTTAGGAACTACTGTAG
1 AAGCATTTTTGACACTATTTGTTCAGAACCGTATTCTCAAAATTATTTTTCAGGAACTACTGTAG
19684492 AAAAA
66 AAAAA
19684497 AATCCTTATT
Statistics
Matches: 178, Mismatches: 17, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
125 136 0.76
126 42 0.24
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.37
Consensus pattern (125 bp):
AAGCATTTTTGACACTATTTGTTCAGAACCGTATTCTCAAAATTATTTTTCAGGAACTACTGTAG
AAAAAGAGCGTCCACGTGGGAGCTTTTTCCAGTAATTTTGCTAACAATGCATCCTACTTG
Found at i:19684599 original size:34 final size:33
Alignment explanation
Indices: 19684551--19684660 Score: 132
Period size: 34 Copynumber: 3.3 Consensus size: 33
19684541 CACAATATTA
*
19684551 TTTTAAAAAAACTAAACCTTAATTTAATTAATT
1 TTTTAAAAACACTAAACCTTAATTTAATTAATT
19684584 TTCTTAAAAACACTAAACCCTT-ATTTAATTAATT
1 TT-TTAAAAACACTAAA-CCTTAATTTAATTAATT
* * * *
19684618 TATTTTAAACCCCTAAACCCTAATTTAATTAATT
1 T-TTTAAAAACACTAAACCTTAATTTAATTAATT
*
19684652 TTTAAAAAA
1 TTTTAAAAA
19684661 GAACACTAAA
Statistics
Matches: 65, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
33 10 0.15
34 50 0.77
35 5 0.08
ACGTcount: A:0.45, C:0.15, G:0.00, T:0.41
Consensus pattern (33 bp):
TTTTAAAAACACTAAACCTTAATTTAATTAATT
Found at i:19684761 original size:14 final size:15
Alignment explanation
Indices: 19684724--19684759 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
19684714 TTATTTGAAC
*
19684724 AAAACCCTAACCCTA
1 AAAACCCTAAACCTA
*
19684739 AAAACCCTAAACCAA
1 AAAACCCTAAACCTA
19684754 AAAACC
1 AAAACC
19684760 TAGGGACTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.56, C:0.36, G:0.00, T:0.08
Consensus pattern (15 bp):
AAAACCCTAAACCTA
Found at i:19687776 original size:9 final size:9
Alignment explanation
Indices: 19687762--19687800 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
19687752 GTTTAAGAGG
19687762 AGAAAAAGA
1 AGAAAAAGA
19687771 AGAAAAAGA
1 AGAAAAAGA
**
19687780 AG-AGGAGA
1 AGAAAAAGA
19687788 AGAAAAAGA
1 AGAAAAAGA
19687797 AGAA
1 AGAA
19687801 GAAGGAGAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
8 6 0.24
9 19 0.76
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (9 bp):
AGAAAAAGA
Found at i:19687783 original size:23 final size:23
Alignment explanation
Indices: 19687756--19687817 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 23
19687746 TTTAGGGTTT
19687756 AAGAGGAGAA-AAAGAAGAAAAAG
1 AAGAGGAGAAGAAA-AAGAAAAAG
*
19687779 AAGAGGAGAAGAAAAAGAAGAAG
1 AAGAGGAGAAGAAAAAGAAAAAG
*
19687802 AAGGAGAAG-AGAAAAA
1 AA-GAGGAGAAGAAAAA
19687818 ATGGAGATGC
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
23 27 0.77
24 8 0.23
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (23 bp):
AAGAGGAGAAGAAAAAGAAAAAG
Found at i:19687798 original size:26 final size:26
Alignment explanation
Indices: 19687756--19687818 Score: 83
Period size: 26 Copynumber: 2.5 Consensus size: 26
19687746 TTTAGGGTTT
*
19687756 AAGAGGAGAAAAAGAAGAAAAAGAAG
1 AAGAGAAGAAAAAGAAGAAAAAGAAG
* * *
19687782 AGGAGAAGAAAAAGAAGAAGAAGGAG
1 AAGAGAAGAAAAAGAAGAAAAAGAAG
19687808 AAGAGAA-AAAA
1 AAGAGAAGAAAA
19687819 TGGAGATGCC
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
25 4 0.12
26 28 0.88
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (26 bp):
AAGAGAAGAAAAAGAAGAAAAAGAAG
Found at i:19688340 original size:3 final size:3
Alignment explanation
Indices: 19688332--19688361 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
19688322 GAAAAGAGCC
*
19688332 AAG AAG AAG AAG AAG AGG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
19688362 GGCAAAGACA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:19688655 original size:30 final size:31
Alignment explanation
Indices: 19688602--19688670 Score: 88
Period size: 30 Copynumber: 2.3 Consensus size: 31
19688592 ACTATTAATC
* *
19688602 AGTGGCTGTTTTGTCATTTTTTTATAACGTT-
1 AGTGACTGTTTTGTCATTTTTTTA-AAAGTTG
*
19688633 AGTGACTGTTTTGTTA-TTTTTTAAAAGTTG
1 AGTGACTGTTTTGTCATTTTTTTAAAAGTTG
19688663 AGTGACTG
1 AGTGACTG
19688671 AAATGAAACT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
29 5 0.15
30 15 0.44
31 14 0.41
ACGTcount: A:0.20, C:0.07, G:0.22, T:0.51
Consensus pattern (31 bp):
AGTGACTGTTTTGTCATTTTTTTAAAAGTTG
Found at i:19689661 original size:32 final size:31
Alignment explanation
Indices: 19689614--19689673 Score: 84
Period size: 32 Copynumber: 1.9 Consensus size: 31
19689604 TACTTATCAA
* *
19689614 TTATTTATTATCATTTTAGTATATTTTTATG
1 TTATTAATTATCATTTTAGTAAATTTTTATG
*
19689645 TTATTAATATATCATTTTGGTAAATTTTT
1 TTATTAAT-TATCATTTTAGTAAATTTTT
19689674 TTAATTTGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 7 0.28
32 18 0.72
ACGTcount: A:0.28, C:0.03, G:0.07, T:0.62
Consensus pattern (31 bp):
TTATTAATTATCATTTTAGTAAATTTTTATG
Found at i:19693816 original size:88 final size:87
Alignment explanation
Indices: 19693668--19693834 Score: 246
Period size: 88 Copynumber: 1.9 Consensus size: 87
19693658 AAAATTTAAC
* * * * *
19693668 TTCTTCTGTGCCTAAAAACATTACTCATAAATTGATTTTTCCAATAATTGCTATTAGACCAGGTT
1 TTCTTCTATACCTAAAAACACTACTCATAAATTAATTTTTCCAATAATTGCTATAAGACCAGGTT
19693733 GTG-TCATGTTTATAGTATAAAA
66 GTGCT-ATGTTTATAGTATAAAA
* *
19693755 TTCTTCTATACCTAAAAACACTGCTCACTAAATTAATTTTTCCAATAATTGGTATAAGACCAGGT
1 TTCTTCTATACCTAAAAACACTACTCA-TAAATTAATTTTTCCAATAATTGCTATAAGACCAGGT
19693820 TGTGCTATGTTTATA
65 TGTGCTATGTTTATA
19693835 ATAAATTGAA
Statistics
Matches: 71, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
87 23 0.32
88 47 0.66
89 1 0.01
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.40
Consensus pattern (87 bp):
TTCTTCTATACCTAAAAACACTACTCATAAATTAATTTTTCCAATAATTGCTATAAGACCAGGTT
GTGCTATGTTTATAGTATAAAA
Found at i:19695294 original size:27 final size:27
Alignment explanation
Indices: 19695264--19695336 Score: 83
Period size: 27 Copynumber: 2.7 Consensus size: 27
19695254 GGGGGTGGTG
*
19695264 CCTATCTGATAGGCGGTACTAGTGACC
1 CCTATCTGATAGGCGGCACTAGTGACC
* * * *
19695291 CCTATCTGGTAGGCAGCATTGGTGACC
1 CCTATCTGATAGGCGGCACTAGTGACC
* *
19695318 CCTATTTAATAGGCGGCAC
1 CCTATCTGATAGGCGGCAC
19695337 CAGTATTAAA
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.22, C:0.26, G:0.26, T:0.26
Consensus pattern (27 bp):
CCTATCTGATAGGCGGCACTAGTGACC
Found at i:19695435 original size:22 final size:22
Alignment explanation
Indices: 19695420--19695462 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
19695410 AAGAAGAGAG
19695420 GAAG-AAGAAAGAAAGAAAGGA
1 GAAGAAAGAAAGAAAGAAAGGA
19695441 GAAGAAAGAAAGAAAGGAAAGG
1 GAAGAAAGAAAGAAA-GAAAGG
19695463 TATTTTTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 4 0.20
22 10 0.50
23 6 0.30
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (22 bp):
GAAGAAAGAAAGAAAGAAAGGA
Found at i:19695443 original size:18 final size:18
Alignment explanation
Indices: 19695422--19695458 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
19695412 GAAGAGAGGA
19695422 AGAAGAAAGAAAGAAAGG
1 AGAAGAAAGAAAGAAAGG
19695440 AGAAGAAAGAAAGAAAGG
1 AGAAGAAAGAAAGAAAGG
19695458 A
1 A
19695459 AAGGTATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (18 bp):
AGAAGAAAGAAAGAAAGG
Found at i:19695931 original size:20 final size:19
Alignment explanation
Indices: 19695906--19695943 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
19695896 TTAGCACAAA
19695906 ATGAGA-AAGTTGATAAGATG
1 ATGAGAGAA-TTG-TAAGATG
19695926 ATGAGAGAATTGTAAGAT
1 ATGAGAGAATTGTAAGAT
19695944 TACCATAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 6 0.35
20 9 0.53
21 2 0.12
ACGTcount: A:0.45, C:0.00, G:0.29, T:0.26
Consensus pattern (19 bp):
ATGAGAGAATTGTAAGATG
Found at i:19697055 original size:20 final size:20
Alignment explanation
Indices: 19697000--19697056 Score: 78
Period size: 21 Copynumber: 2.8 Consensus size: 20
19696990 GGTGAAGAAC
*
19697000 ATGGAGCTCAAGAAACGTGT
1 ATGGAGCTCAAGAACCGTGT
* *
19697020 ATGGTGGCTTAAGAACCGTGT
1 ATGG-AGCTCAAGAACCGTGT
19697041 ATGGAGCTCAAGAACC
1 ATGGAGCTCAAGAACC
19697057 ATTGATAGTC
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
20 14 0.45
21 17 0.55
ACGTcount: A:0.32, C:0.18, G:0.30, T:0.21
Consensus pattern (20 bp):
ATGGAGCTCAAGAACCGTGT
Found at i:19699307 original size:49 final size:49
Alignment explanation
Indices: 19699187--19699502 Score: 496
Period size: 49 Copynumber: 6.5 Consensus size: 49
19699177 AATTTAAACT
** * *
19699187 ACAAAGTTTGTTCCTCGTTTTAATGTTGTAATGCATCTAATTTAT-ATT
1 ACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTATCTAATTTATGATC
* * *
19699235 ACAAAATTTTTTCCAAGTTTTAATGTTGTAATGTATCTAATATATGATC
1 ACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTATCTAATTTATGATC
* *
19699284 ACAAAGTTTGTTCCAACTTTTAATGTTGTAATGTATCTAATTTAT-ATT
1 ACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTATCTAATTTATGATC
*
19699332 ACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTATCTAATTTATGACC
1 ACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTATCTAATTTATGATC
19699381 ACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTATCTAATTTATG-TCC
1 ACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTATCTAATTTATGAT-C
19699430 ACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTATCTAATTTATG-TCC
1 ACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTATCTAATTTATGAT-C
19699479 ACAAAGTTTGTTCCAAGTTTTAAT
1 ACAAAGTTTGTTCCAAGTTTTAAT
19699503 ATTTCAATTA
Statistics
Matches: 249, Mismatches: 16, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
48 85 0.34
49 164 0.66
ACGTcount: A:0.30, C:0.12, G:0.13, T:0.45
Consensus pattern (49 bp):
ACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTATCTAATTTATGATC
Found at i:19699353 original size:97 final size:97
Alignment explanation
Indices: 19699187--19699502 Score: 501
Period size: 97 Copynumber: 3.2 Consensus size: 97
19699177 AATTTAAACT
* * * *
19699187 ACAAAGTTTGTTCC-TCGTTTTAATGTTGTAATGCATCTAATTTATATTACAAAATTTTTTCCAA
1 ACAAAGTTTGTTCCAAC-TTTTAATGTTGTAATGTATCTAATTTATATTACAAAGTTTGTTCCAA
*
19699251 GTTTTAATGTTGTAATGTATCTAATATATGATC
65 GTTTTAATGTTGTAATGTATCTAATTTATGATC
19699284 ACAAAGTTTGTTCCAACTTTTAATGTTGTAATGTATCTAATTTATATTACAAAGTTTGTTCCAAG
1 ACAAAGTTTGTTCCAACTTTTAATGTTGTAATGTATCTAATTTATATTACAAAGTTTGTTCCAAG
*
19699349 TTTTAATGTTGTAATGTATCTAATTTATGACC
66 TTTTAATGTTGTAATGTATCTAATTTATGATC
* * *
19699381 ACAAAGTTTGTTCCAAGTTTTAATGTTGTAATGTATCTAATTTATGTCCACAAAGTTTGTTCCAA
1 ACAAAGTTTGTTCCAACTTTTAATGTTGTAATGTATCTAATTTATAT-TACAAAGTTTGTTCCAA
19699446 GTTTTAATGTTGTAATGTATCTAATTTATG-TCC
65 GTTTTAATGTTGTAATGTATCTAATTTATGAT-C
*
19699479 ACAAAGTTTGTTCCAAGTTTTAAT
1 ACAAAGTTTGTTCCAACTTTTAAT
19699503 ATTTCAATTA
Statistics
Matches: 206, Mismatches: 10, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
97 134 0.65
98 72 0.35
ACGTcount: A:0.30, C:0.12, G:0.13, T:0.45
Consensus pattern (97 bp):
ACAAAGTTTGTTCCAACTTTTAATGTTGTAATGTATCTAATTTATATTACAAAGTTTGTTCCAAG
TTTTAATGTTGTAATGTATCTAATTTATGATC
Found at i:19699819 original size:33 final size:33
Alignment explanation
Indices: 19699777--19699839 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
19699767 CGATGAACTT
* * *
19699777 GAGCCGGGAGGAGTGGAGTACTGTGGTGGATAC
1 GAGCCGGGAGGACTGGAGTAATGCGGTGGATAC
19699810 GAGCCGGGAGGACTGGAGTAATGCGGTGGA
1 GAGCCGGGAGGACTGGAGTAATGCGGTGGA
19699840 CATGGGCCTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.22, C:0.13, G:0.49, T:0.16
Consensus pattern (33 bp):
GAGCCGGGAGGACTGGAGTAATGCGGTGGATAC
Found at i:19706792 original size:30 final size:30
Alignment explanation
Indices: 19706758--19706830 Score: 101
Period size: 30 Copynumber: 2.4 Consensus size: 30
19706748 ACAAGCTATC
* * *
19706758 ACACGGCCGTGTGACACACACGGCTTGGTG
1 ACACGGCCGTGTGACACACACGACCTAGTG
* *
19706788 ACACGACCGTGTGACACGCACGACCTAGTG
1 ACACGGCCGTGTGACACACACGACCTAGTG
19706818 ACACGGCCGTGTG
1 ACACGGCCGTGTG
19706831 TCATTTGATA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.22, C:0.32, G:0.32, T:0.15
Consensus pattern (30 bp):
ACACGGCCGTGTGACACACACGACCTAGTG
Found at i:19706809 original size:17 final size:17
Alignment explanation
Indices: 19706789--19706822 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
19706779 GGCTTGGTGA
19706789 CACGACCGT-GTGACACG
1 CACGACC-TAGTGACACG
19706806 CACGACCTAGTGACACG
1 CACGACCTAGTGACACG
19706823 GCCGTGTGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 1 0.06
17 15 0.94
ACGTcount: A:0.26, C:0.35, G:0.26, T:0.12
Consensus pattern (17 bp):
CACGACCTAGTGACACG
Found at i:19714881 original size:17 final size:17
Alignment explanation
Indices: 19714861--19714898 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
19714851 TAGAATTTGG
19714861 TTGAGAAAAAAATTTAA
1 TTGAGAAAAAAATTTAA
*
19714878 TTGAGAAAAAACTTTAA
1 TTGAGAAAAAAATTTAA
19714895 TTGA
1 TTGA
19714899 AGTTAATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.53, C:0.03, G:0.13, T:0.32
Consensus pattern (17 bp):
TTGAGAAAAAAATTTAA
Found at i:19716855 original size:68 final size:68
Alignment explanation
Indices: 19716654--19717048 Score: 414
Period size: 68 Copynumber: 5.8 Consensus size: 68
19716644 AGTTTAATGA
* *** * * * *
19716654 GTAAGACCATAGCTCGACTATGGCAACTAATAGAGTCCAATAGGGCATTAAATAT-GTGTTACAA
1 GTAAGACCATAGCTCGACTATGGCAACCAATAGAGTCCGCCAGGACGTTAAACATGGGGTTACAA
*
19716718 AGT
66 GGT
* * * * ** *
19716721 GTAAGATCATAGCTCGACTATGACAACAAAATAGAGTCTGCCAAAATGTTAAACATGGGGTTACA
1 GTAAGACCATAGCTCGACTATGGCAAC-CAATAGAGTCCGCCAGGACGTTAAACATGGGGTTACA
19716786 AGGT
65 AGGT
*
19716790 GTAAGACCATAGCTCGGCTATGGCAACCAATAGAGTCCGCCAGGACGTTAAACATGGGGTTACAA
1 GTAAGACCATAGCTCGACTATGGCAACCAATAGAGTCCGCCAGGACGTTAAACATGGGGTTACAA
19716855 GGT
66 GGT
* ** ** * *
19716858 GTAAGTCCATAGCTCGGTTATGGCAACCAATAGAGTCCTTCAGGAAGTTAAACATGAGGTTACAA
1 GTAAGACCATAGCTCGACTATGGCAACCAATAGAGTCCGCCAGGACGTTAAACATGGGGTTACAA
19716923 GGT
66 GGT
* * ** * * * *
19716926 GTAAAACCATTGCTCGGTTATGGAAACCAATAAAGTCCTCCAGGATGTTAAACATGGGGTTACAA
1 GTAAGACCATAGCTCGACTATGGCAACCAATAGAGTCCGCCAGGACGTTAAACATGGGGTTACAA
19716991 GGT
66 GGT
* * ** * * **
19716994 GTAAGACCATGGCTCAACCCTGACAACCAATAGAGTTCGCCAAAACGTTAAACAT
1 GTAAGACCATAGCTCGACTATGGCAACCAATAGAGTCCGCCAGGACGTTAAACAT
19717049 AGGTTCAAAT
Statistics
Matches: 274, Mismatches: 52, Indels: 3
0.83 0.16 0.01
Matches are distributed among these distances:
67 25 0.09
68 215 0.78
69 34 0.12
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.23
Consensus pattern (68 bp):
GTAAGACCATAGCTCGACTATGGCAACCAATAGAGTCCGCCAGGACGTTAAACATGGGGTTACAA
GGT
Found at i:19719584 original size:32 final size:32
Alignment explanation
Indices: 19719543--19719604 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
19719533 CATCTATTTT
*
19719543 CATTGTTCAACTCTTTGACAACACGAAAAATC
1 CATTGTTCAACTATTTGACAACACGAAAAATC
* *
19719575 CATTGTTCAACTATTTGACTACATGAAAAA
1 CATTGTTCAACTATTTGACAACACGAAAAA
19719605 AACCAAAAGC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.39, C:0.21, G:0.10, T:0.31
Consensus pattern (32 bp):
CATTGTTCAACTATTTGACAACACGAAAAATC
Found at i:19720834 original size:28 final size:27
Alignment explanation
Indices: 19720792--19720848 Score: 71
Period size: 26 Copynumber: 2.0 Consensus size: 27
19720782 AAATTTTCAA
*
19720792 AAAAAAATTTGATCTATTTTTGTAATATTT
1 AAAAAAA-TTGATCT-TTTTT-TAAAATTT
19720822 AAAAAAA-TGATCTTTTTTTAAAATTT
1 AAAAAAATTGATCTTTTTTTAAAATTT
19720848 A
1 A
19720849 GTCCAAGCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
26 8 0.31
27 5 0.19
28 6 0.23
30 7 0.27
ACGTcount: A:0.44, C:0.04, G:0.05, T:0.47
Consensus pattern (27 bp):
AAAAAAATTGATCTTTTTTTAAAATTT
Found at i:19722450 original size:41 final size:37
Alignment explanation
Indices: 19722376--19722447 Score: 126
Period size: 37 Copynumber: 1.9 Consensus size: 37
19722366 GAACAAAAAA
* *
19722376 AAAAAAAGAGTGGTAAAGGTTATCTAAGTAAGAAACT
1 AAAAAAAGAGTGGGAAAGGTTATATAAGTAAGAAACT
19722413 AAAAAAAGAGTGGGAAAGGTTATATAAGTAAGAAA
1 AAAAAAAGAGTGGGAAAGGTTATATAAGTAAGAAA
19722448 GAACATGGGA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.54, C:0.03, G:0.24, T:0.19
Consensus pattern (37 bp):
AAAAAAAGAGTGGGAAAGGTTATATAAGTAAGAAACT
Found at i:19749914 original size:33 final size:33
Alignment explanation
Indices: 19749872--19749934 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
19749862 TTTATATTTA
19749872 AAATAATTAAAGA-ATTATTAAAATTATAAATAT
1 AAATAATTAAA-ATATTATTAAAATTATAAATAT
* *
19749905 AAATTATTAAAATATTTTTAAAATTATAAA
1 AAATAATTAAAATATTATTAAAATTATAAA
19749935 AAAAATTGCA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
32 1 0.04
33 26 0.96
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.40
Consensus pattern (33 bp):
AAATAATTAAAATATTATTAAAATTATAAATAT
Found at i:19749970 original size:22 final size:22
Alignment explanation
Indices: 19749924--19749970 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
19749914 AAATATTTTT
*
19749924 AAAATTATAAAAAAAATTGCAA
1 AAAATTATAAAAAAAATAGCAA
*
19749946 AAAATTATAAAAGAAACTAGCAA
1 AAAATTATAAAA-AAAATAGCAA
19749969 AA
1 AA
19749971 TAAAAAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 12 0.55
23 10 0.45
ACGTcount: A:0.68, C:0.06, G:0.06, T:0.19
Consensus pattern (22 bp):
AAAATTATAAAAAAAATAGCAA
Found at i:19750016 original size:27 final size:27
Alignment explanation
Indices: 19749967--19750023 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
19749957 AGAAACTAGC
*
19749967 AAAATAAAAAATTATATAGATTAAGAA
1 AAAATAAAAAATTATAAAGATTAAGAA
* * *
19749994 AAAATAAAAAATTGTAAATATTATGAA
1 AAAATAAAAAATTATAAAGATTAAGAA
19750021 AAA
1 AAA
19750024 TGTTTAAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (27 bp):
AAAATAAAAAATTATAAAGATTAAGAA
Found at i:19750085 original size:27 final size:25
Alignment explanation
Indices: 19750028--19750113 Score: 64
Period size: 27 Copynumber: 3.3 Consensus size: 25
19750018 GAAAAATGTT
* * **
19750028 TAAAATATAGAAAATTATTAAAACTA
1 TAAAAAATAGAAAAGTACAAAAAC-A
* *
19750054 TTAAAAAATGGAAAAGTGCAAAAAATCA
1 -TAAAAAATAGAAAAGTAC-AAAAA-CA
* *
19750082 TAAAATATAGAAAATTACAAAAACA
1 TAAAAAATAGAAAAGTACAAAAACA
19750107 TAAAAAA
1 TAAAAAA
19750114 AATGTTCACA
Statistics
Matches: 46, Mismatches: 11, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
25 8 0.17
26 5 0.11
27 27 0.59
28 5 0.11
29 1 0.02
ACGTcount: A:0.65, C:0.06, G:0.07, T:0.22
Consensus pattern (25 bp):
TAAAAAATAGAAAAGTACAAAAACA
Found at i:19758471 original size:14 final size:15
Alignment explanation
Indices: 19758414--19758502 Score: 51
Period size: 15 Copynumber: 5.7 Consensus size: 15
19758404 ATTGGGTTTA
19758414 TTTTATTTAATTTTGAAT
1 TTTTATTT-A-TTT-AAT
*
19758432 TTTGTTTTTATTT-AT
1 TTT-TATTTATTTAAT
*
19758447 TGTTTACTATTATTTGAT
1 T-TTTA-T-TTATTTAAT
19758465 TTTTATTTATTTAAT
1 TTTTATTTATTTAAT
* *
19758480 TTTGAATTA--T-AT
1 TTTTATTTATTTAAT
19758492 TTTTATTTATT
1 TTTTATTTATT
19758503 GCTTACTATT
Statistics
Matches: 57, Mismatches: 7, Indels: 18
0.70 0.09 0.22
Matches are distributed among these distances:
12 9 0.16
13 1 0.02
15 19 0.33
16 4 0.07
17 13 0.23
18 7 0.12
19 4 0.07
ACGTcount: A:0.24, C:0.01, G:0.06, T:0.70
Consensus pattern (15 bp):
TTTTATTTATTTAAT
Found at i:19758493 original size:27 final size:26
Alignment explanation
Indices: 19758410--19758502 Score: 82
Period size: 27 Copynumber: 3.4 Consensus size: 26
19758400 ATCAATTGGG
*
19758410 TTTATTTTATTTAATTTTGAATTTTGTT
1 TTTA-TTTATTTAATTTTGAA-TTTATT
* *
19758438 TTTATTTATTGTTTACTATT--ATTTGATT
1 TTTATTTA---TTTAATTTTGAATTT-ATT
19758466 TTTATTTATTTAATTTTGAATTATATT
1 TTTATTTATTTAATTTTGAATT-TATT
19758493 TTTATTTATT
1 TTTATTTATT
19758503 GCTTACTATT
Statistics
Matches: 53, Mismatches: 5, Indels: 15
0.73 0.07 0.21
Matches are distributed among these distances:
25 7 0.13
27 23 0.43
28 16 0.30
30 7 0.13
ACGTcount: A:0.24, C:0.01, G:0.05, T:0.70
Consensus pattern (26 bp):
TTTATTTATTTAATTTTGAATTTATT
Found at i:19758495 original size:55 final size:55
Alignment explanation
Indices: 19758410--19758536 Score: 200
Period size: 55 Copynumber: 2.3 Consensus size: 55
19758400 ATCAATTGGG
* * *
19758410 TTTATTTTATTTAATTTTGAATTTTGTTTTTATTTATTGTTTACTATTATTTGATT
1 TTTA-TTTATTTAATTTTGAATTATATTTTTATTTATTGCTTACTATTATTTGATT
*
19758466 TTTATTTATTTAATTTTGAATTATATTTTTATTTATTGCTTACTATTCTTTGATT
1 TTTATTTATTTAATTTTGAATTATATTTTTATTTATTGCTTACTATTATTTGATT
*
19758521 TTTATATATTTAATTT
1 TTTATTTATTTAATTT
19758537 CGTATTACTT
Statistics
Matches: 66, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
55 62 0.94
56 4 0.06
ACGTcount: A:0.24, C:0.03, G:0.06, T:0.68
Consensus pattern (55 bp):
TTTATTTATTTAATTTTGAATTATATTTTTATTTATTGCTTACTATTATTTGATT
Found at i:19758522 original size:28 final size:27
Alignment explanation
Indices: 19758432--19758530 Score: 89
Period size: 28 Copynumber: 3.6 Consensus size: 27
19758422 AATTTTGAAT
19758432 TTTG-TTTTTATTTATTGTTTACTATTA
1 TTTGATTTTTATTTATTG-TTACTATTA
* *
19758459 TTTGATTTTTATTTA-T-TTAATTTTGAA
1 TTTGATTTTTATTTATTGTTACTATT--A
*
19758486 TTAT-ATTTTTATTTATTGCTTACTATTC
1 TT-TGATTTTTATTTATTG-TTACTATTA
*
19758514 TTTGATTTTTATATATT
1 TTTGATTTTTATTTATT
19758531 TAATTTCGTA
Statistics
Matches: 58, Mismatches: 6, Indels: 15
0.73 0.08 0.19
Matches are distributed among these distances:
25 6 0.10
27 20 0.34
28 26 0.45
30 6 0.10
ACGTcount: A:0.22, C:0.04, G:0.06, T:0.68
Consensus pattern (27 bp):
TTTGATTTTTATTTATTGTTACTATTA
Found at i:19767190 original size:33 final size:33
Alignment explanation
Indices: 19767118--19767193 Score: 82
Period size: 33 Copynumber: 2.3 Consensus size: 33
19767108 ATGTTTATAT
* * *
19767118 GTAAGATCATAGCTGGGCTATGGCATTTTAATA
1 GTAAGACCATAACTGGGCTATGGCACTTTAATA
** *
19767151 AAAAGACCATAACTGGGTTATGGCACTTTAA-A
1 GTAAGACCATAACTGGGCTATGGCACTTTAATA
19767183 CGTAAGACCAT
1 -GTAAGACCAT
19767194 GGTTAGACCA
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
32 1 0.03
33 33 0.97
ACGTcount: A:0.36, C:0.16, G:0.21, T:0.28
Consensus pattern (33 bp):
GTAAGACCATAACTGGGCTATGGCACTTTAATA
Found at i:19774608 original size:33 final size:33
Alignment explanation
Indices: 19774567--19774723 Score: 95
Period size: 33 Copynumber: 4.7 Consensus size: 33
19774557 GTTTATATGT
19774567 AAGACCATAGCTGGGCTATGGCATTTTAATGAA
1 AAGACCATAGCTGGGCTATGGCATTTTAATGAA
* * * * * *
19774600 AAGACCATAACTGAGTTATGGCACTTTGAACG-T
1 AAGACCATAGCTGGGCTATGGCA-TTTTAATGAA
* * * * *
19774633 AAGACCATGGTTCGACCATGGCAATATTT-AT-AA
1 AAGACCATAGCTGGGCTATGGC-AT-TTTAATGAA
* * * *
19774666 GTAAGACCATAGCTAGGCTATGGCATTCTGATGAT
1 --AAGACCATAGCTGGGCTATGGCATTTTAATGAA
* *
19774701 AAGACCATAACTGGGTTATGGCA
1 AAGACCATAGCTGGGCTATGGCA
19774724 CTACGAATGT
Statistics
Matches: 89, Mismatches: 27, Indels: 16
0.67 0.20 0.12
Matches are distributed among these distances:
33 58 0.65
34 13 0.15
35 18 0.20
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (33 bp):
AAGACCATAGCTGGGCTATGGCATTTTAATGAA
Found at i:19774706 original size:101 final size:101
Alignment explanation
Indices: 19774531--19774758 Score: 321
Period size: 101 Copynumber: 2.3 Consensus size: 101
19774521 AATTGACGGA
* * * * *
19774531 TAAGACCATGGTTGGACCATGGAAATGTTTATATGTAAGACCATAGCTGGGCTATGGCATTTTAA
1 TAAGACCATGGTTGGACCATGGCAATATTTATAAGTAAGACCATAGCTAGGCTATGGCATTCTAA
**
19774596 TGAAAAGACCATAACTGAGTTATGGCACTTTGAACG
66 TGAAAAGACCATAACTGAGTTATGGCACTACGAACG
* *
19774632 TAAGACCATGGTTCGACCATGGCAATATTTATAAGTAAGACCATAGCTAGGCTATGGCATTCTGA
1 TAAGACCATGGTTGGACCATGGCAATATTTATAAGTAAGACCATAGCTAGGCTATGGCATTCTAA
* * *
19774697 TGATAAGACCATAACTGGGTTATGGCACTACGAATG
66 TGAAAAGACCATAACTGAGTTATGGCACTACGAACG
* * *
19774733 TAAGACCTTGGCTGGGCCATGGCAAT
1 TAAGACCATGGTTGGACCATGGCAAT
19774759 GCATGTGTAA
Statistics
Matches: 111, Mismatches: 16, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
101 111 1.00
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (101 bp):
TAAGACCATGGTTGGACCATGGCAATATTTATAAGTAAGACCATAGCTAGGCTATGGCATTCTAA
TGAAAAGACCATAACTGAGTTATGGCACTACGAACG
Found at i:19774737 original size:33 final size:32
Alignment explanation
Indices: 19774666--19774739 Score: 78
Period size: 33 Copynumber: 2.2 Consensus size: 32
19774656 ATATTTATAA
* *
19774666 GTAAGACCATAGCTAGGCTATGGCATTCTGAT
1 GTAAGACCATAACTAGGCTATGGCATACTGAT
* *
19774698 GATAAGACCATAACTGGGTTATGGCACTAC-GAAT
1 G-TAAGACCATAACTAGGCTATGGCA-TACTG-AT
19774732 GTAAGACC
1 GTAAGACC
19774740 TTGGCTGGGC
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
32 1 0.03
33 29 0.83
34 5 0.14
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.24
Consensus pattern (32 bp):
GTAAGACCATAACTAGGCTATGGCATACTGAT
Found at i:19775100 original size:215 final size:216
Alignment explanation
Indices: 19774728--19775165 Score: 770
Period size: 215 Copynumber: 2.0 Consensus size: 216
19774718 ATGGCACTAC
* * *
19774728 GAATGTAAGACCTTGGCTGGGCCATGGCAATGCATGTGTAAGACCATAGTTGGACTATGGCACAA
1 GAATGTAAGACCATGGCTGGGCCATGACAATGCATGTGTAAGACCATAGTTGGACTATCGCACAA
* *
19774793 AAAAAATGATGTACTCATACCCGTAAGTCGTTCATCGATTCAGTAAGAATTGGTAAAAGACCTAT
66 AAAAAACGATGTACTCATACCCGTAAGTCGTTCATCAATTCAGTAAGAATTGGTAAAAGACCTAT
*
19774858 GTGAATGAATTGAAAGATATATTGATTATTAATGATATTGATCTAAAGGAAGTCTGTTCATTGAC
131 GTGAATGAATTAAAAGATATATTGATTATTAATGATATTGATCTAAAGGAAGTCTGTTCATTGAC
19774923 TTATGTTGTATTTGACAAGGA
196 TTATGTTGTATTTGACAAGGA
* *
19774944 GAATGTAAGACCATGGCTGGGTCATGACAATGC-TGTGTAAGACCATAGTTGGACTATCGCCCAA
1 GAATGTAAGACCATGGCTGGGCCATGACAATGCATGTGTAAGACCATAGTTGGACTATCGCACAA
*
19775008 AAAAAACGATGTACTCATACCCGTAAGTCGTTCCTCAATTCAGTAAGAATTGGTAAAAGACCTAT
66 AAAAAACGATGTACTCATACCCGTAAGTCGTTCATCAATTCAGTAAGAATTGGTAAAAGACCTAT
*
19775073 GTGAATGAATTAAAAGATATATTGATTATTAATGATATTGATCTAAAGGAAGTTTGTTCATTGAC
131 GTGAATGAATTAAAAGATATATTGATTATTAATGATATTGATCTAAAGGAAGTCTGTTCATTGAC
*
19775138 TTATGTTGTATTTGACAGGGA
196 TTATGTTGTATTTGACAAGGA
19775159 GAATGTA
1 GAATGTA
19775166 TGATTTATTT
Statistics
Matches: 211, Mismatches: 11, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
215 181 0.86
216 30 0.14
ACGTcount: A:0.34, C:0.13, G:0.22, T:0.31
Consensus pattern (216 bp):
GAATGTAAGACCATGGCTGGGCCATGACAATGCATGTGTAAGACCATAGTTGGACTATCGCACAA
AAAAAACGATGTACTCATACCCGTAAGTCGTTCATCAATTCAGTAAGAATTGGTAAAAGACCTAT
GTGAATGAATTAAAAGATATATTGATTATTAATGATATTGATCTAAAGGAAGTCTGTTCATTGAC
TTATGTTGTATTTGACAAGGA
Found at i:19778407 original size:41 final size:41
Alignment explanation
Indices: 19778350--19778450 Score: 184
Period size: 41 Copynumber: 2.5 Consensus size: 41
19778340 TTTAACATAT
*
19778350 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAGA
*
19778391 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAGA
19778432 TCACCGGCACTTAGCCTGC
1 TCACCGGCACTTAGCCTGC
19778451 CAGACTTAAA
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 58 1.00
ACGTcount: A:0.22, C:0.31, G:0.21, T:0.27
Consensus pattern (41 bp):
TCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAGA
Found at i:19778573 original size:41 final size:41
Alignment explanation
Indices: 19778432--19778576 Score: 175
Period size: 41 Copynumber: 3.5 Consensus size: 41
19778422 CTGATTCAGA
* * * * **
19778432 TCACCGGCACTT-AGCCTGCCAGACTTAAAGTCCGAATTGTT
1 TCACCGGCA-TTAAGCCTGCTAGACATAAAGTCTGAAATAAT
*
19778473 TCACCGGCCTTAAGCCTGCTAGACATAAAGTCTGAAATAAT
1 TCACCGGCATTAAGCCTGCTAGACATAAAGTCTGAAATAAT
*
19778514 TCACCGGCATTTAGCCTGCTAGACATAAAGTCTGAAATAAT
1 TCACCGGCATTAAGCCTGCTAGACATAAAGTCTGAAATAAT
* * *
19778555 TCATCGGTATTAACCCTGCTAG
1 TCACCGGCATTAAGCCTGCTAG
19778577 GCATCGAGCC
Statistics
Matches: 90, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
40 2 0.02
41 88 0.98
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.27
Consensus pattern (41 bp):
TCACCGGCATTAAGCCTGCTAGACATAAAGTCTGAAATAAT
Found at i:19778590 original size:41 final size:41
Alignment explanation
Indices: 19778472--19778590 Score: 139
Period size: 41 Copynumber: 2.9 Consensus size: 41
19778462 TCCGAATTGT
* * *
19778472 TTCACCGGCCTTAAGCCTGCTAGACATAAAGTCTGAAATAA
1 TTCACCGGCATTAACCCTGCTAGACATAAAGCCTGAAATAA
* * *
19778513 TTCACCGGCATTTAGCCTGCTAGACATAAAGTCTGAAATAA
1 TTCACCGGCATTAACCCTGCTAGACATAAAGCCTGAAATAA
* * * **
19778554 TTCATCGGTATTAACCCTGCTAGGCATCGAGCCTGAA
1 TTCACCGGCATTAACCCTGCTAGACATAAAGCCTGAA
19778591 TACCACGGAT
Statistics
Matches: 68, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 68 1.00
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.26
Consensus pattern (41 bp):
TTCACCGGCATTAACCCTGCTAGACATAAAGCCTGAAATAA
Found at i:19787496 original size:30 final size:31
Alignment explanation
Indices: 19787461--19787533 Score: 76
Period size: 32 Copynumber: 2.4 Consensus size: 31
19787451 TTGATACATC
*
19787461 AACTTTAATTTGGTAC-AATTATACACATGA
1 AACTTTAATTTGGTACAAAATATACACATGA
* * * * *
19787491 AACTTTGATTGTGGTTCAAAATGTATATATGA
1 AACTTTAATT-TGGTACAAAATATACACATGA
19787523 AACTTTAATTT
1 AACTTTAATTT
19787534 TTATTTAATT
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
30 9 0.26
31 6 0.18
32 19 0.56
ACGTcount: A:0.37, C:0.10, G:0.12, T:0.41
Consensus pattern (31 bp):
AACTTTAATTTGGTACAAAATATACACATGA
Found at i:19788344 original size:38 final size:38
Alignment explanation
Indices: 19788302--19788381 Score: 99
Period size: 38 Copynumber: 2.1 Consensus size: 38
19788292 ATTTGGTTTT
* * *
19788302 AATACAAAATTGAATATTGA-AACTAAATTTAAGTATCA
1 AATACAAAATTAAACATT-ATAACTAAATTTAAGTATAA
* *
19788340 AATACTAAATTAAACATTATAATTAAATTTAAGTATAA
1 AATACAAAATTAAACATTATAACTAAATTTAAGTATAA
19788378 AATA
1 AATA
19788382 ATATATTAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
37 1 0.03
38 35 0.97
ACGTcount: A:0.55, C:0.06, G:0.05, T:0.34
Consensus pattern (38 bp):
AATACAAAATTAAACATTATAACTAAATTTAAGTATAA
Found at i:19800642 original size:12 final size:12
Alignment explanation
Indices: 19800625--19800649 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
19800615 CGTCGTAGTT
19800625 ATCATCATAATC
1 ATCATCATAATC
19800637 ATCATCATAATC
1 ATCATCATAATC
19800649 A
1 A
19800650 AGTCCATAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.24, G:0.00, T:0.32
Consensus pattern (12 bp):
ATCATCATAATC
Found at i:19803954 original size:25 final size:25
Alignment explanation
Indices: 19803924--19803989 Score: 73
Period size: 25 Copynumber: 2.7 Consensus size: 25
19803914 GCTCTCTCTC
19803924 GAGCCATATAATGGGAAACTCATGT-
1 GAGCCATATAATGGGAAACTCAT-TA
* * *
19803949 GAGCCATGTAACGGGAAGCTCATTA
1 GAGCCATATAATGGGAAACTCATTA
*
19803974 GAGCCATA-ATTGGGAA
1 GAGCCATATAATGGGAA
19803990 GTTAATCGAG
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
24 7 0.21
25 27 0.79
ACGTcount: A:0.35, C:0.17, G:0.27, T:0.21
Consensus pattern (25 bp):
GAGCCATATAATGGGAAACTCATTA
Found at i:19804037 original size:25 final size:25
Alignment explanation
Indices: 19803997--19804110 Score: 81
Period size: 25 Copynumber: 4.5 Consensus size: 25
19803987 GAAGTTAATC
*
19803997 GAGCCA-T-ATCAGGAAGCTC-AGGA
1 GAGCCATTAATCAAGAAGCTCTA-GA
*
19804020 GAGCCATTAATCAAGAAGCTCATAAAA
1 GAGCCATTAATCAAGAAGCTC-T-AGA
* ***
19804047 GAGCCTTTAATTGGGAAGCTCTAGA
1 GAGCCATTAATCAAGAAGCTCTAGA
* *
19804072 GAGCCATTAATCGAGAAGCTCATGAAA
1 GAGCCATTAATCAAGAAGCTC-T-AGA
*
19804099 GAGCCTTTAATC
1 GAGCCATTAATC
19804111 GGGAAGTTTC
Statistics
Matches: 72, Mismatches: 12, Indels: 10
0.77 0.13 0.11
Matches are distributed among these distances:
23 6 0.08
24 1 0.01
25 31 0.43
26 2 0.03
27 31 0.43
28 1 0.01
ACGTcount: A:0.37, C:0.19, G:0.23, T:0.21
Consensus pattern (25 bp):
GAGCCATTAATCAAGAAGCTCTAGA
Found at i:19804057 original size:27 final size:26
Alignment explanation
Indices: 19804019--19804116 Score: 108
Period size: 27 Copynumber: 3.7 Consensus size: 26
19804009 GAAGCTCAGG
*
19804019 AGAGCCATTAATCAAGAAGCTCATAAA
1 AGAGCCATTAATCGAGAAGCTCAT-AA
* * * *
19804046 AGAGCCTTTAATTGGGAAGCTC-TAG
1 AGAGCCATTAATCGAGAAGCTCATAA
19804071 AGAGCCATTAATCGAGAAGCTCATGAA
1 AGAGCCATTAATCGAGAAGCTCAT-AA
* *
19804098 AGAGCCTTTAATCGGGAAG
1 AGAGCCATTAATCGAGAAG
19804117 TTTCGGAGAG
Statistics
Matches: 58, Mismatches: 11, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
25 20 0.34
26 2 0.03
27 36 0.62
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (26 bp):
AGAGCCATTAATCGAGAAGCTCATAA
Found at i:19804065 original size:52 final size:52
Alignment explanation
Indices: 19804008--19804130 Score: 178
Period size: 52 Copynumber: 2.4 Consensus size: 52
19803998 AGCCATATCA
*
19804008 GGAAGCTCAGGAGAGCCATTAATCAAGAAGCTCATAAAAGAGCCTTTAATTG
1 GGAAGCTCAGGAGAGCCATTAATCAAGAAGCTCATAAAAGAGCCTTTAATCG
* *
19804060 GGAAGCTCTA-GAGAGCCATTAATCGAGAAGCTCATGAAAGAGCCTTTAATCG
1 GGAAGCTC-AGGAGAGCCATTAATCAAGAAGCTCATAAAAGAGCCTTTAATCG
*
19804112 GGAAGTTTC-GGAGAGCCAT
1 GGAAG-CTCAGGAGAGCCAT
19804131 ATATCTGGAT
Statistics
Matches: 64, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
52 61 0.95
53 3 0.05
ACGTcount: A:0.35, C:0.18, G:0.26, T:0.21
Consensus pattern (52 bp):
GGAAGCTCAGGAGAGCCATTAATCAAGAAGCTCATAAAAGAGCCTTTAATCG
Found at i:19804230 original size:24 final size:25
Alignment explanation
Indices: 19804203--19804249 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
19804193 GGATGCTTCG
*
19804203 AAGAGCTAT-TAACGGGAAGCTCGC
1 AAGAACTATATAACGGGAAGCTCGC
19804227 AAGAACTATATAACGGGAAGCTC
1 AAGAACTATATAACGGGAAGCTC
19804250 ATGAGAGCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.38, C:0.19, G:0.26, T:0.17
Consensus pattern (25 bp):
AAGAACTATATAACGGGAAGCTCGC
Found at i:19807370 original size:13 final size:13
Alignment explanation
Indices: 19807327--19807403 Score: 70
Period size: 13 Copynumber: 5.9 Consensus size: 13
19807317 TTTAGTATTG
* *
19807327 CTTTTGAGAAGGA
1 CTTTTGAAAAGTA
19807340 C-TTTGAAAAAGTGA
1 CTTTTG-AAAAGT-A
*
19807354 -TTTTGAGAAGTA
1 CTTTTGAAAAGTA
19807366 CTTTTGAAAAGTGA
1 CTTTTGAAAAGT-A
*
19807380 -TTTTGAGAAGTA
1 CTTTTGAAAAGTA
19807392 CTTTTGAAAAGT
1 CTTTTGAAAAGT
19807404 TTAGTTTAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
12 6 0.12
13 40 0.77
14 6 0.12
ACGTcount: A:0.35, C:0.05, G:0.23, T:0.36
Consensus pattern (13 bp):
CTTTTGAAAAGTA
Found at i:19807402 original size:26 final size:26
Alignment explanation
Indices: 19807328--19807403 Score: 127
Period size: 26 Copynumber: 2.9 Consensus size: 26
19807318 TTAGTATTGC
*
19807328 TTTTGAGAAGGAC-TTTGAAAAAGTGA
1 TTTTGAGAAGTACTTTTG-AAAAGTGA
19807354 TTTTGAGAAGTACTTTTGAAAAGTGA
1 TTTTGAGAAGTACTTTTGAAAAGTGA
19807380 TTTTGAGAAGTACTTTTGAAAAGT
1 TTTTGAGAAGTACTTTTGAAAAGT
19807404 TTAGTTTAAA
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
26 44 0.92
27 4 0.08
ACGTcount: A:0.36, C:0.04, G:0.24, T:0.37
Consensus pattern (26 bp):
TTTTGAGAAGTACTTTTGAAAAGTGA
Found at i:19813656 original size:421 final size:421
Alignment explanation
Indices: 19812866--19813707 Score: 1675
Period size: 421 Copynumber: 2.0 Consensus size: 421
19812856 ACCACATTGG
19812866 TAGCACATATTCTCAACAATCTTTGAAGGATTATTTTGACCACTTTTTTCTTATTTTTCATTGTT
1 TAGCACATATTCTCAACAATCTTTGAAGGATTATTTTGACCACTTTTTTCTTATTTTTCATTGTT
19812931 ATTCTTTTTTTGGTGGTTAGAAGTATCATTGTTATGACCGCCATGATAATGATTACTAGTATGTC
66 ATTCTTTTTTTGGTGGTTAGAAGTATCATTGTTATGACCGCCATGATAATGATTACTAGTATGTC
19812996 CTTAACCACGTCTCCCACTATGTCCACGACCGCAACTACTACTGCGACCTCTATATTTTCTATTT
131 CTTAACCACGTCTCCCACTATGTCCACGACCGCAACTACTACTGCGACCTCTATATTTTCTATTT
19813061 TCATAATTATTGTGTACTGCTACATTCACTTCAGGGAATGGTGTAGAACCAGTGGGACGAATTCC
196 TCATAATTATTGTGTACTGCTACATTCACTTCAGGGAATGGTGTAGAACCAGTGGGACGAATTCC
19813126 ATGATTTTTCATCAACAGCTCATTATTTTGTTCAGCCACCAAAATGCATGAAATCAATTCAGAAT
261 ATGATTTTTCATCAACAGCTCATTATTTTGTTCAGCCACCAAAATGCATGAAATCAATTCAGAAT
19813191 ACCTTTTAAAACCTTTTTCACGATATTGCTACTGTAGGAGCACATTAGTTGCATGAAAGGTTGAA
326 ACCTTTTAAAACCTTTTTCACGATATTGCTACTGTAGGAGCACATTAGTTGCATGAAAGGTTGAA
19813256 AATGTTTTCTCTAACAAGTCCTCATCAGTTA
391 AATGTTTTCTCTAACAAGTCCTCATCAGTTA
*
19813287 TAGCATATATTCTCAACAATCTTTGAAGGATTATTTTGACCACTTTTTTCTTATTTTTCATTGTT
1 TAGCACATATTCTCAACAATCTTTGAAGGATTATTTTGACCACTTTTTTCTTATTTTTCATTGTT
19813352 ATTCTTTTTTTGGTGGTTAGAAGTATCATTGTTATGACCGCCATGATAATGATTACTAGTATGTC
66 ATTCTTTTTTTGGTGGTTAGAAGTATCATTGTTATGACCGCCATGATAATGATTACTAGTATGTC
19813417 CTTAACCACGTCTCCCACTATGTCCACGACCGCAACTACTACTGCGACCTCTATATTTTCTATTT
131 CTTAACCACGTCTCCCACTATGTCCACGACCGCAACTACTACTGCGACCTCTATATTTTCTATTT
19813482 TCATAATTATTGTGTACTGCTACATTCACTTCAGGGAATGGTGTAGAACCAGTGGGACGAATTCC
196 TCATAATTATTGTGTACTGCTACATTCACTTCAGGGAATGGTGTAGAACCAGTGGGACGAATTCC
19813547 ATGATTTTTCATCAACAGCTCATTATTTTGTTCAGCCACCAAAATGCATGAAATCAATTCAGAAT
261 ATGATTTTTCATCAACAGCTCATTATTTTGTTCAGCCACCAAAATGCATGAAATCAATTCAGAAT
19813612 ACCTTTTAAAACCTTTTTCACGATATTGCTACTGTAGGAGCACATTAGTTGCATGAAAGGTTGAA
326 ACCTTTTAAAACCTTTTTCACGATATTGCTACTGTAGGAGCACATTAGTTGCATGAAAGGTTGAA
19813677 AATGTTTTCTCTAACAAGTCCTCATCAGTTA
391 AATGTTTTCTCTAACAAGTCCTCATCAGTTA
19813708 CGTTTTCTCC
Statistics
Matches: 420, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
421 420 1.00
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.37
Consensus pattern (421 bp):
TAGCACATATTCTCAACAATCTTTGAAGGATTATTTTGACCACTTTTTTCTTATTTTTCATTGTT
ATTCTTTTTTTGGTGGTTAGAAGTATCATTGTTATGACCGCCATGATAATGATTACTAGTATGTC
CTTAACCACGTCTCCCACTATGTCCACGACCGCAACTACTACTGCGACCTCTATATTTTCTATTT
TCATAATTATTGTGTACTGCTACATTCACTTCAGGGAATGGTGTAGAACCAGTGGGACGAATTCC
ATGATTTTTCATCAACAGCTCATTATTTTGTTCAGCCACCAAAATGCATGAAATCAATTCAGAAT
ACCTTTTAAAACCTTTTTCACGATATTGCTACTGTAGGAGCACATTAGTTGCATGAAAGGTTGAA
AATGTTTTCTCTAACAAGTCCTCATCAGTTA
Found at i:19820265 original size:2 final size:2
Alignment explanation
Indices: 19820258--19820288 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
19820248 CATTACCCAT
19820258 TA 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 TA T
19820289 CTTTTGCTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19824017 original size:7 final size:7
Alignment explanation
Indices: 19824005--19824041 Score: 74
Period size: 7 Copynumber: 5.3 Consensus size: 7
19823995 ATCAACCAAA
19824005 TCAAGAT
1 TCAAGAT
19824012 TCAAGAT
1 TCAAGAT
19824019 TCAAGAT
1 TCAAGAT
19824026 TCAAGAT
1 TCAAGAT
19824033 TCAAGAT
1 TCAAGAT
19824040 TC
1 TC
19824042 CATTAGTATC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.41, C:0.16, G:0.14, T:0.30
Consensus pattern (7 bp):
TCAAGAT
Found at i:19839543 original size:18 final size:18
Alignment explanation
Indices: 19839525--19839558 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
19839515 AATAAAATGA
19839525 AAAATTT-TTATAAATTG
1 AAAATTTATTATAAATTG
*
19839542 AAAATTTATTCTAAATT
1 AAAATTTATTATAAATT
19839559 TGGTTGTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (18 bp):
AAAATTTATTATAAATTG
Found at i:19843129 original size:29 final size:27
Alignment explanation
Indices: 19843071--19843186 Score: 92
Period size: 28 Copynumber: 4.1 Consensus size: 27
19843061 AATTTTTGTA
* * *
19843071 AAAGTGAA-CCTTTGTGGATATCTTTGTT
1 AAAG-GAAGCCTTTGT-GCTATCTCTATT
19843099 AAAGGAAGCCTTTGTGTCTAATCTCTATT
1 AAAGGAAGCCTTTGTG-CT-ATCTCTATT
* * *
19843128 AAATGAAGCTTTTGTGGTGATCTCTATT
1 AAAGGAAGCCTTTGTGCT-ATCTCTATT
*
19843156 AAAGGAATCCCTTATG-GCTATCTCTATT
1 AAAGGAA-GCCTT-TGTGCTATCTCTATT
19843184 AAA
1 AAA
19843187 AAAGATTCCA
Statistics
Matches: 72, Mismatches: 11, Indels: 10
0.77 0.12 0.11
Matches are distributed among these distances:
27 4 0.06
28 40 0.56
29 26 0.36
30 2 0.03
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.39
Consensus pattern (27 bp):
AAAGGAAGCCTTTGTGCTATCTCTATT
Found at i:19843206 original size:30 final size:30
Alignment explanation
Indices: 19843170--19843273 Score: 104
Period size: 30 Copynumber: 3.5 Consensus size: 30
19843160 GAATCCCTTA
19843170 TGGCTATCTCTATTAAAAAAGATTCCATTG
1 TGGCTATCTCTATTAAAAAAGATTCCATTG
* * * * *
19843200 TGGCTATCTCTGTTACAAAGGA-TGCATTTA
1 TGGCTATCTCTATTAAAAAAGATTCCA-TTG
* * *
19843230 TGACTATCTCTATT-AAAAAGATACCTTTG
1 TGGCTATCTCTATTAAAAAAGATTCCATTG
*
19843259 TGGCTATCTCAATTA
1 TGGCTATCTCTATTA
19843274 CATGAATGCC
Statistics
Matches: 56, Mismatches: 15, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
29 22 0.39
30 34 0.61
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (30 bp):
TGGCTATCTCTATTAAAAAAGATTCCATTG
Found at i:19846811 original size:61 final size:62
Alignment explanation
Indices: 19846726--19846850 Score: 243
Period size: 61 Copynumber: 2.0 Consensus size: 62
19846716 TCACCATGCT
19846726 ATCAATTATATTTTTAATTTTAAGGTCTGTTTGATTGGCAGTAAAATGTTTTCCGTAAAATG
1 ATCAATTATATTTTTAATTTTAAGGTCTGTTTGATTGGCAGTAAAATGTTTTCCGTAAAATG
19846788 ATCAATTATA-TTTTAATTTTAAGGTCTGTTTGATTGGCAGTAAAATGTTTTCCGTAAAATG
1 ATCAATTATATTTTTAATTTTAAGGTCTGTTTGATTGGCAGTAAAATGTTTTCCGTAAAATG
19846849 AT
1 AT
19846851 TTCTGGAAAA
Statistics
Matches: 63, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
61 53 0.84
62 10 0.16
ACGTcount: A:0.31, C:0.08, G:0.16, T:0.45
Consensus pattern (62 bp):
ATCAATTATATTTTTAATTTTAAGGTCTGTTTGATTGGCAGTAAAATGTTTTCCGTAAAATG
Found at i:19846846 original size:14 final size:14
Alignment explanation
Indices: 19846827--19846866 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
19846817 TTGATTGGCA
19846827 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
19846841 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
19846855 GGAAAATGTTTT
1 GTAAAATGTTTT
19846867 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:19846879 original size:34 final size:35
Alignment explanation
Indices: 19846835--19846901 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
19846825 CAGTAAAATG
* *
19846835 TTTTCCGTAAAATGA-TTTCTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGACTTACTGGAAAATATTTTAC
*
19846869 TTTTCTGTAAAATGACTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGACTTACTGGAAAATATTTT
19846902 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 14 0.48
35 15 0.52
ACGTcount: A:0.31, C:0.10, G:0.13, T:0.45
Consensus pattern (35 bp):
TTTTCCGTAAAATGACTTACTGGAAAATATTTTAC
Found at i:19846888 original size:20 final size:20
Alignment explanation
Indices: 19846850--19846889 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
19846840 CGTAAAATGA
**
19846850 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGACTTACT
*
19846870 TTTCTGTAAAATGACTTACT
1 TTTCTGGAAAATGACTTACT
19846890 GGAAAATATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.47
Consensus pattern (20 bp):
TTTCTGGAAAATGACTTACT
Found at i:19853764 original size:24 final size:24
Alignment explanation
Indices: 19853732--19853785 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
19853722 TATGCGAATC
19853732 CAGAAACAGACACAAAAACAAAAA
1 CAGAAACAGACACAAAAACAAAAA
* *
19853756 CAGAAACAGACCCAGAAACAAAAA
1 CAGAAACAGACACAAAAACAAAAA
*
19853780 TAGAAA
1 CAGAAA
19853786 ATAAAATCCA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.67, C:0.20, G:0.11, T:0.02
Consensus pattern (24 bp):
CAGAAACAGACACAAAAACAAAAA
Found at i:19860374 original size:17 final size:17
Alignment explanation
Indices: 19860344--19860376 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
19860334 TGACCCTGTC
19860344 TCACTAAAATTAAAATA
1 TCACTAAAATTAAAATA
19860361 TCAC-AAAATATAAAAT
1 TCACTAAAAT-TAAAAT
19860377 TCTTTTGCGT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.61, C:0.12, G:0.00, T:0.27
Consensus pattern (17 bp):
TCACTAAAATTAAAATA
Found at i:19861297 original size:50 final size:50
Alignment explanation
Indices: 19861235--19861363 Score: 150
Period size: 50 Copynumber: 2.6 Consensus size: 50
19861225 CAATGTCATA
* * ** * * * *
19861235 TCCCAGATATGGTCTTACATGGGAGTTTTCATATCGGTGCCTATGCCATG
1 TCCCAGACATGGTCTTACGTGGGACCTCTAATATCGGTGCCAACGCCATG
* * *
19861285 TCCCAGACATGGTCTTACGGGGGACCTCTAATCTTGGTGCCAACGCCATG
1 TCCCAGACATGGTCTTACGTGGGACCTCTAATATCGGTGCCAACGCCATG
*
19861335 TCCCAGACATTGTCTTACGTGGGACCTCT
1 TCCCAGACATGGTCTTACGTGGGACCTCT
19861364 CATAACCTCA
Statistics
Matches: 66, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
50 66 1.00
ACGTcount: A:0.19, C:0.27, G:0.24, T:0.29
Consensus pattern (50 bp):
TCCCAGACATGGTCTTACGTGGGACCTCTAATATCGGTGCCAACGCCATG
Found at i:19865930 original size:22 final size:23
Alignment explanation
Indices: 19865857--19865952 Score: 124
Period size: 23 Copynumber: 4.2 Consensus size: 23
19865847 TTTAAGAGGA
19865857 TGTGTTTGGAGGGTATATTTGGT
1 TGTGTTTGGAGGGTATATTTGGT
* *
19865880 TGTGTTGGGAGGATATATTTGGT
1 TGTGTTTGGAGGGTATATTTGGT
* *
19865903 TGTGTTTGGAGGGTA-AATTGTT
1 TGTGTTTGGAGGGTATATTTGGT
*
19865925 TGTGTTTGGAGGCTATGA-TTGGT
1 TGTGTTTGGAGGGTAT-ATTTGGT
19865948 TGTGT
1 TGTGT
19865953 GGGTGATAGC
Statistics
Matches: 63, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
22 19 0.30
23 43 0.68
24 1 0.02
ACGTcount: A:0.15, C:0.01, G:0.39, T:0.46
Consensus pattern (23 bp):
TGTGTTTGGAGGGTATATTTGGT
Found at i:19865947 original size:45 final size:46
Alignment explanation
Indices: 19865857--19865952 Score: 133
Period size: 45 Copynumber: 2.1 Consensus size: 46
19865847 TTTAAGAGGA
*
19865857 TGTGTTTGGAGGGTATATTTGGTTGTGTTGGGAGGATATATTTGGT
1 TGTGTTTGGAGGGTATAATTGGTTGTGTTGGGAGGATATATTTGGT
* * *
19865903 TGTGTTTGGAGGGTA-AATTGTTTGTGTTTGGAGGCTATGA-TTGGT
1 TGTGTTTGGAGGGTATAATTGGTTGTGTTGGGAGGATAT-ATTTGGT
19865948 TGTGT
1 TGTGT
19865953 GGGTGATAGC
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
45 29 0.64
46 16 0.36
ACGTcount: A:0.15, C:0.01, G:0.39, T:0.46
Consensus pattern (46 bp):
TGTGTTTGGAGGGTATAATTGGTTGTGTTGGGAGGATATATTTGGT
Found at i:19866638 original size:134 final size:134
Alignment explanation
Indices: 19866398--19866665 Score: 527
Period size: 134 Copynumber: 2.0 Consensus size: 134
19866388 TATTCATAAG
19866398 ATAACCTCATCACATACCAAAACCAAAATTTGTTAGCCATACCAATGGCTAGCCATACATTCATT
1 ATAACCTCATCACATACCAAAACCAAAATTTGTTAGCCATACCAATGGCTAGCCATACATTCATT
*
19866463 TCACATTAACATTTGCTTTACTAGCTTATACATGCCATTGATTTCCAAAATAAAGTTTCTTTATA
66 TCACATTAACATTTGCTTTACTAGCTTATACATGCCATTGATTTCCAAAATAAAGTGTCTTTATA
19866528 TACC
131 TACC
19866532 ATAACCTCATCACATACCAAAACCAAAATTTGTTAGCCATACCAATGGCTAGCCATACATTCATT
1 ATAACCTCATCACATACCAAAACCAAAATTTGTTAGCCATACCAATGGCTAGCCATACATTCATT
19866597 TCACATTAACATTTGCTTTACTAGCTTATACATGCCATTGATTTCCAAAATAAAGTGTCTTTATA
66 TCACATTAACATTTGCTTTACTAGCTTATACATGCCATTGATTTCCAAAATAAAGTGTCTTTATA
19866662 TACC
131 TACC
19866666 GAGATCTTGA
Statistics
Matches: 133, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
134 133 1.00
ACGTcount: A:0.35, C:0.24, G:0.08, T:0.33
Consensus pattern (134 bp):
ATAACCTCATCACATACCAAAACCAAAATTTGTTAGCCATACCAATGGCTAGCCATACATTCATT
TCACATTAACATTTGCTTTACTAGCTTATACATGCCATTGATTTCCAAAATAAAGTGTCTTTATA
TACC
Found at i:19871110 original size:17 final size:17
Alignment explanation
Indices: 19871063--19871110 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
19871053 CCTATTCCTA
**
19871063 AAAAATAAAAATTGTCC
1 AAAAATAAAAATAATCC
* **
19871080 AAAATTAATTATAATCC
1 AAAAATAAAAATAATCC
19871097 AAAAATAAAAATAA
1 AAAAATAAAAATAA
19871111 AAAGTTTGGG
Statistics
Matches: 23, Mismatches: 8, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.65, C:0.08, G:0.02, T:0.25
Consensus pattern (17 bp):
AAAAATAAAAATAATCC
Found at i:19879204 original size:29 final size:29
Alignment explanation
Indices: 19879162--19879219 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
19879152 GAAGTAAGTA
19879162 ATAGTGTGTCTATTCCGTGGTATTTTGGT
1 ATAGTGTGTCTATTCCGTGGTATTTTGGT
*
19879191 ATAGTGTGTCTATTCTGTGGTATTTTGGT
1 ATAGTGTGTCTATTCCGTGGTATTTTGGT
19879220 GATGAAATGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.14, C:0.09, G:0.28, T:0.50
Consensus pattern (29 bp):
ATAGTGTGTCTATTCCGTGGTATTTTGGT
Found at i:19882772 original size:31 final size:29
Alignment explanation
Indices: 19882728--19882785 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 29
19882718 ATTTATCTAC
19882728 AAGATAAACATTAA-ATTAAACTTAATATT
1 AAGATAAACATTAATATTAAA-TTAATATT
*
19882757 AAGATAATCACATTAATGTTAAATTAATA
1 AAGATAA--ACATTAATATTAAATTAATA
19882786 AAATCCTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
29 7 0.28
31 13 0.52
32 5 0.20
ACGTcount: A:0.53, C:0.07, G:0.05, T:0.34
Consensus pattern (29 bp):
AAGATAAACATTAATATTAAATTAATATT
Found at i:19882809 original size:12 final size:12
Alignment explanation
Indices: 19882792--19882822 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
19882782 AATAAAATCC
19882792 TATTAAAATAAA
1 TATTAAAATAAA
*
19882804 TATTAAACTAAA
1 TATTAAAATAAA
19882816 TATTAAA
1 TATTAAA
19882823 TCTATTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.35
Consensus pattern (12 bp):
TATTAAAATAAA
Found at i:19895779 original size:21 final size:21
Alignment explanation
Indices: 19895737--19895780 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
19895727 TTGATTCTAC
*
19895737 TTAGGTACATTTAGTAGAATT
1 TTAGGTACATTTACTAGAATT
*
19895758 TTAGG-ACATTTCACTAGTATT
1 TTAGGTACATTT-ACTAGAATT
19895779 TT
1 TT
19895781 TATCATTGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.30, C:0.09, G:0.16, T:0.45
Consensus pattern (21 bp):
TTAGGTACATTTACTAGAATT
Found at i:19896964 original size:36 final size:36
Alignment explanation
Indices: 19896904--19897003 Score: 148
Period size: 36 Copynumber: 2.7 Consensus size: 36
19896894 AGAAAAAGAT
19896904 TAAATTGTAGAACAAATTGT-AAATTTAGTAATAGGGAC
1 TAAATTGT-GAA-AAATT-TAAAATTTAGTAATAGGGAC
*
19896942 TAAATTGTGAAAAATTTAAAATTGAGTAATAGGGAC
1 TAAATTGTGAAAAATTTAAAATTTAGTAATAGGGAC
*
19896978 TAAATTGTGAAAATTTTAAAATTTAG
1 TAAATTGTGAAAAATTTAAAATTTAG
19897004 GGGTTTACTT
Statistics
Matches: 58, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
35 1 0.02
36 46 0.79
37 3 0.05
38 8 0.14
ACGTcount: A:0.46, C:0.03, G:0.17, T:0.34
Consensus pattern (36 bp):
TAAATTGTGAAAAATTTAAAATTTAGTAATAGGGAC
Found at i:19902304 original size:152 final size:153
Alignment explanation
Indices: 19902126--19902430 Score: 603
Period size: 152 Copynumber: 2.0 Consensus size: 153
19902116 AAATGAGGTA
19902126 TGGCAATGTGCTACAATATATATATATATATATATATGAGTGTATAAACTAAGAGAATAGAAAGA
1 TGGCAATGTGCTACAATATATATATATATATATATATGAGTGTATAAACTAAGAGAATAGAAAGA
19902191 CCCATTGGGCTTATTCATCTCCAAAGTGAAAATCTGTGCTGGTCCATTGGGGCAGTGCTTAGACA
66 CCCATTGGGCTTATTCATCTCCAAAGTGAAAATCTGTGCTGGTCCATTGGGGCAGTGCTTAGACA
19902256 GAAGTAGTTTGTTTAAGGAAGGG
131 GAAGTAGTTTGTTTAAGGAAGGG
19902279 TGGCAATGTG-TACAATATATATATATATATATATATGAGTGTATAAACTAAGAGAATAGAAAGA
1 TGGCAATGTGCTACAATATATATATATATATATATATGAGTGTATAAACTAAGAGAATAGAAAGA
19902343 CCCATTGGGCTTATTCATCTCCAAAGTGAAAATCTGTGCTGGTCCATTGGGGCAGTGCTTAGACA
66 CCCATTGGGCTTATTCATCTCCAAAGTGAAAATCTGTGCTGGTCCATTGGGGCAGTGCTTAGACA
19902408 GAAGTAGTTTGTTTAAGGAAGGG
131 GAAGTAGTTTGTTTAAGGAAGGG
19902431 ATAATGATGG
Statistics
Matches: 152, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
152 142 0.93
153 10 0.07
ACGTcount: A:0.34, C:0.12, G:0.24, T:0.30
Consensus pattern (153 bp):
TGGCAATGTGCTACAATATATATATATATATATATATGAGTGTATAAACTAAGAGAATAGAAAGA
CCCATTGGGCTTATTCATCTCCAAAGTGAAAATCTGTGCTGGTCCATTGGGGCAGTGCTTAGACA
GAAGTAGTTTGTTTAAGGAAGGG
Found at i:19906749 original size:12 final size:12
Alignment explanation
Indices: 19906732--19906765 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
19906722 TTCAGCTTTA
*
19906732 GGTTTGGGTTTG
1 GGTTTGGGTCTG
19906744 GGTTTGGGTCTG
1 GGTTTGGGTCTG
*
19906756 GGTCTGGGTC
1 GGTTTGGGTC
19906766 AATCAATGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.00, C:0.09, G:0.50, T:0.41
Consensus pattern (12 bp):
GGTTTGGGTCTG
Found at i:19908105 original size:5 final size:5
Alignment explanation
Indices: 19908095--19908132 Score: 58
Period size: 5 Copynumber: 7.6 Consensus size: 5
19908085 ACTGATATCT
* *
19908095 ATATA ATATA ATATA ATATA GTATA GTATA ATATA ATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATA
19908133 GGCTGGGATG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.39
Consensus pattern (5 bp):
ATATA
Found at i:19908893 original size:21 final size:22
Alignment explanation
Indices: 19908867--19908912 Score: 69
Period size: 21 Copynumber: 2.1 Consensus size: 22
19908857 AGGAATTAAA
19908867 GGTGAGAA-GTAAAAG-TTTGGG
1 GGTGAGAATG-AAAAGTTTTGGG
19908888 GGTGAGAATGAAAAGTTTTGGG
1 GGTGAGAATGAAAAGTTTTGGG
19908910 GGT
1 GGT
19908913 TGAGGGAGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 13 0.57
22 10 0.43
ACGTcount: A:0.30, C:0.00, G:0.43, T:0.26
Consensus pattern (22 bp):
GGTGAGAATGAAAAGTTTTGGG
Found at i:19910877 original size:18 final size:19
Alignment explanation
Indices: 19910851--19910889 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
19910841 CTCATATCCG
*
19910851 ATAATTCCTGAT-AAATGA
1 ATAAGTCCTGATAAAATGA
19910869 ATAAGTCCTGATAAAATGA
1 ATAAGTCCTGATAAAATGA
19910888 AT
1 AT
19910890 GAAACTCGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.46, C:0.10, G:0.13, T:0.31
Consensus pattern (19 bp):
ATAAGTCCTGATAAAATGA
Found at i:19923689 original size:23 final size:23
Alignment explanation
Indices: 19923663--19923710 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
19923653 AATCAGCTTC
19923663 TTTAATAC-ACCTATTAGGACACA
1 TTTAA-ACGACCTATTAGGACACA
*
19923686 TTTAAACGACTTATTAGGACACA
1 TTTAAACGACCTATTAGGACACA
19923709 TT
1 TT
19923711 AATCATACCA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 2 0.09
23 21 0.91
ACGTcount: A:0.38, C:0.19, G:0.10, T:0.33
Consensus pattern (23 bp):
TTTAAACGACCTATTAGGACACA
Found at i:19931770 original size:25 final size:25
Alignment explanation
Indices: 19931742--19931800 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
19931732 CGATTCTCAA
* *
19931742 CTCGTATGAGC-TTATTGATTTATAG
1 CTCGTATGAGCATT-TCGATTCATAG
19931767 CTCGTGA-GAGCATTTCGATTCATAG
1 CTCGT-ATGAGCATTTCGATTCATAG
19931792 CTCGTATGA
1 CTCGTATGA
19931801 ACATACATGT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
24 1 0.03
25 25 0.86
26 3 0.10
ACGTcount: A:0.24, C:0.17, G:0.22, T:0.37
Consensus pattern (25 bp):
CTCGTATGAGCATTTCGATTCATAG
Found at i:19944716 original size:17 final size:17
Alignment explanation
Indices: 19944694--19944730 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
19944684 TAGATAGAGG
19944694 TTTTGGTCGACCTAGTT
1 TTTTGGTCGACCTAGTT
19944711 TTTTGGTCGACCTAGTT
1 TTTTGGTCGACCTAGTT
19944728 TTT
1 TTT
19944731 CACCTTGGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.11, C:0.16, G:0.22, T:0.51
Consensus pattern (17 bp):
TTTTGGTCGACCTAGTT
Found at i:19948579 original size:25 final size:25
Alignment explanation
Indices: 19948514--19948591 Score: 70
Period size: 25 Copynumber: 3.1 Consensus size: 25
19948504 GTCATTAGGG
*
19948514 TTATCTATTCTCAGCTCTTATGAGC
1 TTATCAATTCTCAGCTCTTATGAGC
* *
19948539 TTACCAATT-TGTAGCTCTTGA-GAGC
1 TTATCAATTCT-CAGCTCTT-ATGAGC
* **
19948564 TTATCGATTCTCAGCTCGGATGAGC
1 TTATCAATTCTCAGCTCTTATGAGC
19948589 TTA
1 TTA
19948592 CTGATTTACA
Statistics
Matches: 41, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
24 2 0.05
25 37 0.90
26 2 0.05
ACGTcount: A:0.22, C:0.22, G:0.18, T:0.38
Consensus pattern (25 bp):
TTATCAATTCTCAGCTCTTATGAGC
Found at i:19953597 original size:10 final size:11
Alignment explanation
Indices: 19953548--19953606 Score: 52
Period size: 11 Copynumber: 5.3 Consensus size: 11
19953538 AGATAAATAT
19953548 TATTTTATTAA
1 TATTTTATTAA
19953559 TATTTTGACTTGAA
1 TATTTT-A-TT-AA
*
19953573 -A-TTTATTTA
1 TATTTTATTAA
19953582 TATTTTATTAA
1 TATTTTATTAA
19953593 T-TTTTAGTTAA
1 TATTTTA-TTAA
19953604 TAT
1 TAT
19953607 ATAAGGAATG
Statistics
Matches: 39, Mismatches: 2, Indels: 13
0.72 0.04 0.24
Matches are distributed among these distances:
9 1 0.03
10 8 0.21
11 20 0.51
12 5 0.13
13 3 0.08
14 2 0.05
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:19953938 original size:21 final size:21
Alignment explanation
Indices: 19953909--19953962 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
19953899 AGAGGTTTAT
*
19953909 TAAGTTCAAGTGGTAAGACCC
1 TAAGGTCAAGTGGTAAGACCC
*
19953930 TAAGGTCAAATGGTAAGACCC
1 TAAGGTCAAGTGGTAAGACCC
19953951 TAAGGTCAAGTG
1 TAAGGTCAAGTG
19953963 TTTTAGAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.35, C:0.17, G:0.26, T:0.22
Consensus pattern (21 bp):
TAAGGTCAAGTGGTAAGACCC
Found at i:19958399 original size:19 final size:19
Alignment explanation
Indices: 19958360--19958414 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 19
19958350 TATAAAAATT
* *
19958360 TACAAGAAAATATTGATAAA
1 TACAAGAATATA-TGAAAAA
19958380 TA-AAGAATATAGTGAAAAA
1 TACAAGAATATA-TGAAAAA
19958399 TACAAGAATATATGAA
1 TACAAGAATATATGAA
19958415 TATATTAGTC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 20 0.65
20 11 0.35
ACGTcount: A:0.60, C:0.04, G:0.13, T:0.24
Consensus pattern (19 bp):
TACAAGAATATATGAAAAA
Found at i:19958939 original size:22 final size:22
Alignment explanation
Indices: 19958891--19959011 Score: 107
Period size: 22 Copynumber: 5.5 Consensus size: 22
19958881 AAATTTAGCA
* * *
19958891 TGCTTACTGTCTTGCGCTTTTG
1 TGCTTACTGTTTTGCACTTTGG
* * *
19958913 CGCTTACTGTTTCGCACTTTGT
1 TGCTTACTGTTTTGCACTTTGG
* *
19958935 TGCTTACCGTTTTGCACTTCGG
1 TGCTTACTGTTTTGCACTTTGG
* *
19958957 TACCTACTGTTTTGCACTTTGG
1 TGCTTACTGTTTTGCACTTTGG
* * * *
19958979 TGCTTAGTGATTTGGACTTCGG
1 TGCTTACTGTTTTGCACTTTGG
*
19959001 TGCCTACTGTT
1 TGCTTACTGTT
19959012 CTTATCTCTG
Statistics
Matches: 75, Mismatches: 24, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 75 1.00
ACGTcount: A:0.10, C:0.23, G:0.22, T:0.45
Consensus pattern (22 bp):
TGCTTACTGTTTTGCACTTTGG
Found at i:19958965 original size:44 final size:44
Alignment explanation
Indices: 19958917--19959011 Score: 127
Period size: 44 Copynumber: 2.2 Consensus size: 44
19958907 CTTTTGCGCT
* *
19958917 TACTGTTTCGCACTTTGTTGCTTACCGTTTTGCACTTCGGTACC
1 TACTGTTTCGCACTTTGGTGCTTACCGATTTGCACTTCGGTACC
* ** * *
19958961 TACTGTTTTGCACTTTGGTGCTTAGTGATTTGGACTTCGGTGCC
1 TACTGTTTCGCACTTTGGTGCTTACCGATTTGCACTTCGGTACC
19959005 TACTGTT
1 TACTGTT
19959012 CTTATCTCTG
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.44
Consensus pattern (44 bp):
TACTGTTTCGCACTTTGGTGCTTACCGATTTGCACTTCGGTACC
Found at i:19961868 original size:24 final size:24
Alignment explanation
Indices: 19961841--19961895 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
19961831 AAGAAATAAC
19961841 AAATATTTTATGCTAATAAATGA-T
1 AAATATTTTATGCTAATAAAT-ACT
*
19961865 AAATATATTATGCTAATAAATACT
1 AAATATTTTATGCTAATAAATACT
19961889 AAATATT
1 AAATATT
19961896 CTAGAAACCA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 1 0.04
24 27 0.96
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.40
Consensus pattern (24 bp):
AAATATTTTATGCTAATAAATACT
Found at i:19976665 original size:14 final size:15
Alignment explanation
Indices: 19976646--19976675 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
19976636 CCTTCTTTTC
19976646 TTCTTTCTTTC-TTT
1 TTCTTTCTTTCATTT
19976660 TTCTTTCTTTCATTT
1 TTCTTTCTTTCATTT
19976675 T
1 T
19976676 GCATGTCTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.77
Consensus pattern (15 bp):
TTCTTTCTTTCATTT
Found at i:19978407 original size:13 final size:13
Alignment explanation
Indices: 19978391--19978420 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
19978381 TATAAGAAGG
19978391 AAATAAAATAAAT
1 AAATAAAATAAAT
*
19978404 AAATAAAATGAAT
1 AAATAAAATAAAT
19978417 AAAT
1 AAAT
19978421 CACAAAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.23
Consensus pattern (13 bp):
AAATAAAATAAAT
Found at i:19979514 original size:5 final size:6
Alignment explanation
Indices: 19979496--19979521 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
19979486 AAAGGTAACG
19979496 AATAAA AATAAA AATAAA AATAAA AA
1 AATAAA AATAAA AATAAA AATAAA AA
19979522 ACAAAGTCGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AATAAA
Found at i:19980331 original size:50 final size:49
Alignment explanation
Indices: 19980277--19981211 Score: 317
Period size: 50 Copynumber: 18.7 Consensus size: 49
19980267 GTGATGTCGA
* * * * *
19980277 GGAAGCACGGTTCGCCATTGTGGCTTCAATCTGTTCCACTACACTGTCTG
1 GGAAGCAAGATTCGCCGTTGTGGCTT-AATCTGTTCCACTGCACTGTCAG
* * * * * *
19980327 GGAAGTAAGATTCGCTGTTGTAGCTTTAATCT-TTCTAACTGCAATATCAG
1 GGAAGCAAGATTCGCCGTTGTGGC-TTAATCTGTTC-CACTGCACTGTCAG
*
19980377 GGAAGCAAGATTCGCCGTTGTGGCGTTAATCTGTTCCACTGCACTGTTTA-
1 GGAAGCAAGATTCGCCGTTGTGGC-TTAATCTGTTCCACTGCACTG-TCAG
* * * * * * ** * *
19980427 AGAAGTAAGATTTGCTGTTGTAGCTTTAATCTTTTTAACTGCAATGTCGG
1 GGAAGCAAGATTCGCCGTTGTGGC-TTAATCTGTTCCACTGCACTGTCAG
* * * ** * * *
19980477 GGAAGCAAGGTTCGCCATCGTGGCTTTAATCTACTCTACTGTA-TCGCCAG
1 GGAAGCAAGATTCGCCGTTGTGGC-TTAATCTGTTCCACTGCACT-GTCAG
* * * ** * *
19980527 AGG-AGTAAGATTCGCTGTTGTGGCTTCAATCTTTTTAACTGCAATGTCGG
1 -GGAAGCAAGATTCGCCGTTGTGGCTT-AATCTGTTCCACTGCACTGTCAG
* * * * * * *
19980577 GGAAGCAAGATTCACCGATGTGGCTTTAATCTATTCCACTGTACCGCCTGG
1 GGAAGCAAGATTCGCCGTTGTGGC-TTAATCTGTTCCACTGCACTGTC-AG
* * * * * * * ** * * *
19980628 GGAA-TAAGATTTGCCATTATAGCTTTAGTCTTTTTAACTGCAATGCCGG
1 GGAAGCAAGATTCGCCGTTGTGGC-TTAATCTGTTCCACTGCACTGTCAG
* * * * *
19980677 GGAAGCGAGATTCACTGATGTGGCTTTAATCTGCTCCACTGCA-TCG-CAAG
1 GGAAGCAAGATTCGCCGTTGTGGC-TTAATCTGTTCCACTGCACT-GTC-AG
* * * * * ** * *
19980727 AGAAGTAAGATTCGCTGCTGTGGCTTTAATCTTTTTAACTGCAATGTCGG
1 GGAAGCAAGATTCGCCGTTGTGGC-TTAATCTGTTCCACTGCACTGTCAG
* * * * * *
19980777 GGAAGCAATATTCACCGATGTGGCCTTAATCTGCTCCACGGCA-TCGCCAG
1 GGAAGCAAGATTCGCCGTTGTGG-CTTAATCTGTTCCACTGCACT-GTCAG
* * * * * ** * *
19980827 GGCAGTAGGATTCGTCGCTGTGGCTTTAATCT-TTTTA-TGCAATGTCGG
1 GGAAGCAAGATTCGCCGTTGTGGC-TTAATCTGTTCCACTGCACTGTCAG
* * * * * * *
19980875 GGAAGCAAGATTCACCGATGTAGCTTTAATCTGATCCACTGCACCGCCTG
1 GGAAGCAAGATTCGCCGTTGTGGC-TTAATCTGTTCCACTGCACTGTCAG
* * * * * * ** * * * **
19980925 GGGAGTAAGATTCGCTGTTATAGCTTTAATCTTTTTAAATGAAATGTTGG
1 GGAAGCAAGATTCGCCGTTGTGGC-TTAATCTGTTCCACTGCACTGTCAG
* * * * *
19980975 GGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCACTGTACCG-CTTG
1 GGAAGCAAGATTCGCCGTTGTGGC-TTAATCTGTTCCACTGCACTGTC-AG
* * * ** * * ** * * *
19981025 AGAAGTAAAATTCGTTGTTGTAGCTTTAATCTTTTTAACTGTAATGTCGG
1 GGAAGCAAGATTCGCCGTTGTGGC-TTAATCTGTTCCACTGCACTGTCAG
* * * * * *
19981075 GGAAGCAAGATTCACCGATGTGGCTTTAATCTGCTCCATTGCATTGCCAG
1 GGAAGCAAGATTCGCCGTTGTGGC-TTAATCTGTTCCACTGCACTGTCAG
* * * * ** *
19981125 AGAAGTAAGACTCGCCGTTGTGGCTTCAATCTTTTTAACTGCAATGTCAG
1 GGAAGCAAGATTCGCCGTTGTGGCTT-AATCTGTTCCACTGCACTGTCAG
*
19981175 GGAAGCAAGATTCGCTGTTGTGGCTTTAATCTGTTCC
1 GGAAGCAAGATTCGCCGTTGTGGC-TTAATCTGTTCC
19981212 GTTGCATTAT
Statistics
Matches: 627, Mismatches: 231, Indels: 54
0.69 0.25 0.06
Matches are distributed among these distances:
48 31 0.05
49 26 0.04
50 546 0.87
51 24 0.04
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.33
Consensus pattern (49 bp):
GGAAGCAAGATTCGCCGTTGTGGCTTAATCTGTTCCACTGCACTGTCAG
Found at i:19981219 original size:100 final size:100
Alignment explanation
Indices: 19980250--19981207 Score: 1034
Period size: 100 Copynumber: 9.6 Consensus size: 100
19980240 TAACTCGTAA
* ** * * * * * *
19980250 CTTTAATCTGTTTAACTGTGATGTCGAGGAAGCACGGTTCGCC-ATTGTGGCTTCAATCTGTTCC
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGA-TGTGGCTTTAATCTGCTCC
* * * *
19980314 ACTACA-CTGTCTGGGAAGTAAGATTCGCTGTTGTAG
65 ACTGCATC-GCCAGAGAAGTAAGATTCGCTGTTGTAG
* * * * * * *
19980350 CTTTAATCTTTCTAACTGCAATATCAGGGAAGCAAGATTCGCCGTTGTGGCGTTAATCTGTTCCA
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGCTCCA
** *
19980415 CTGCA-CTGTTTA-AGAAGTAAGATTTGCTGTTGTAG
66 CTGCATC-G-CCAGAGAAGTAAGATTCGCTGTTGTAG
* * * *
19980450 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGGTTCGCC-ATCGTGGCTTTAATCTACTCT
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGAT-GTGGCTTTAATCTGCTCC
* * *
19980514 ACTGTATCGCCAGAGGAGTAAGATTCGCTGTTGTGG
65 ACTGCATCGCCAGAGAAGTAAGATTCGCTGTTGTAG
* **
19980550 CTTCAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTATTCCA
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGCTCCA
* * * * * ** *
19980615 CTGTACCGCCTGGGGAA-TAAGATTTGCCATTATAG
66 CTGCATCGCC-AGAGAAGTAAGATTCGCTGTTGTAG
* * * *
19980650 CTTTAGTCTTTTTAACTGCAATGCCGGGGAAGCGAGATTCACTGATGTGGCTTTAATCTGCTCCA
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGCTCCA
* * *
19980715 CTGCATCGCAAGAGAAGTAAGATTCGCTGCTGTGG
66 CTGCATCGCCAGAGAAGTAAGATTCGCTGTTGTAG
* *
19980750 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAATATTCACCGATGTGGCCTTAATCTGCTCCA
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGCTCCA
* * * * * *
19980815 CGGCATCGCCAGGGCAGTAGGATTCG-TCGCTGTGG
66 CTGCATCGCCAGAGAAGTAAGATTCGCT-GTTGTAG
* *
19980850 CTTTAATCTTTTT-A-TGCAATGTCGGGGAAGCAAGATTCACCGATGTAGCTTTAATCTGATCCA
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGCTCCA
* * * * *
19980913 CTGCACCGCCTGGGGAGTAAGATTCGCTGTTATAG
66 CTGCATCGCCAGAGAAGTAAGATTCGCTGTTGTAG
* * * *
19980948 CTTTAATCTTTTTAAATGAAATGTTGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCA
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGCTCCA
* * ** * *
19981013 CTGTACCGCTTGAGAAGTAAAATTCGTTGTTGTAG
66 CTGCATCGCCAGAGAAGTAAGATTCGCTGTTGTAG
*
19981048 CTTTAATCTTTTTAACTGTAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGCTCCA
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGCTCCA
* * * * *
19981113 TTGCATTGCCAGAGAAGTAAGACTCGCCGTTGTGG
66 CTGCATCGCCAGAGAAGTAAGATTCGCTGTTGTAG
* * * * *
19981148 CTTCAATCTTTTTAACTGCAATGTCAGGGAAGCAAGATTCGCTGTTGTGGCTTTAATCTG
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTG
19981208 TTCCGTTGCA
Statistics
Matches: 727, Mismatches: 119, Indels: 24
0.84 0.14 0.03
Matches are distributed among these distances:
98 83 0.11
99 10 0.01
100 627 0.86
101 7 0.01
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.33
Consensus pattern (100 bp):
CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGCTCCA
CTGCATCGCCAGAGAAGTAAGATTCGCTGTTGTAG
Found at i:19981291 original size:46 final size:46
Alignment explanation
Indices: 19981224--19981331 Score: 180
Period size: 46 Copynumber: 2.3 Consensus size: 46
19981214 TGCATTATCT
* *
19981224 GGGAGATAAGGTCTGAAATTCTTTGGTCTATTCCACTGTAATCTCA
1 GGGAGATAAGATCTGAAATTCTTCGGTCTATTCCACTGTAATCTCA
*
19981270 GGGAGAGAAGATCTGAAATTCTTCGGTCTATTCCACTGTAATCTCA
1 GGGAGATAAGATCTGAAATTCTTCGGTCTATTCCACTGTAATCTCA
*
19981316 GGGAGATAAGACCTGA
1 GGGAGATAAGATCTGA
19981332 TGCGATCTAC
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 57 1.00
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.30
Consensus pattern (46 bp):
GGGAGATAAGATCTGAAATTCTTCGGTCTATTCCACTGTAATCTCA
Found at i:19982760 original size:15 final size:15
Alignment explanation
Indices: 19982740--19982774 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
19982730 TTAGCCTCTC
*
19982740 CATTTTTAC-TTTTT
1 CATTTTTTCATTTTT
19982754 CATTTTTTCATTTTT
1 CATTTTTTCATTTTT
19982769 CATTTT
1 CATTTT
19982775 CATCTTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.42
15 11 0.58
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.71
Consensus pattern (15 bp):
CATTTTTTCATTTTT
Found at i:19988299 original size:30 final size:31
Alignment explanation
Indices: 19988265--19988325 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
19988255 AAAAGATAAA
19988265 AAAGAT-AAAAAACCTAAGGGCTTCGTTCCC
1 AAAGATAAAAAAACCTAAGGGCTTCGTTCCC
19988295 AAAGATAAAAAAACCTAAGGGCTTCGTTCCC
1 AAAGATAAAAAAACCTAAGGGCTTCGTTCCC
19988326 TTCCCAAGCG
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 6 0.20
31 24 0.80
ACGTcount: A:0.41, C:0.23, G:0.16, T:0.20
Consensus pattern (31 bp):
AAAGATAAAAAAACCTAAGGGCTTCGTTCCC
Found at i:19990686 original size:29 final size:29
Alignment explanation
Indices: 19990636--19990691 Score: 78
Period size: 28 Copynumber: 1.9 Consensus size: 29
19990626 ATACTATAAT
*
19990636 AAATCTAAAATATATGATAATTTATAAACA
1 AAATCTAAAATATATGA-AAATTATAAACA
*
19990666 AAATTTAAAA-ATATGAAAATTATAAA
1 AAATCTAAAATATATGAAAATTATAAA
19990692 GGGACGACCG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 9 0.38
29 6 0.25
30 9 0.38
ACGTcount: A:0.61, C:0.04, G:0.04, T:0.32
Consensus pattern (29 bp):
AAATCTAAAATATATGAAAATTATAAACA
Found at i:19991204 original size:14 final size:14
Alignment explanation
Indices: 19991185--19991219 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
19991175 CAGAGTCTAG
19991185 GTTGGTGTTGCTGT
1 GTTGGTGTTGCTGT
*
19991199 GTTGGTTTTGCTGT
1 GTTGGTGTTGCTGT
19991213 GTTGGTG
1 GTTGGTG
19991220 CAACAAACAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.00, C:0.06, G:0.43, T:0.51
Consensus pattern (14 bp):
GTTGGTGTTGCTGT
Found at i:19994593 original size:21 final size:21
Alignment explanation
Indices: 19994567--19994607 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
19994557 TTAAGAGATA
*
19994567 TTACTTGAATAGTTGTATCTC
1 TTACTTGAATAGTTATATCTC
*
19994588 TTACTTTAATAGTTATATCT
1 TTACTTGAATAGTTATATCT
19994608 ATGTAAGAGA
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:0.27, C:0.12, G:0.10, T:0.51
Consensus pattern (21 bp):
TTACTTGAATAGTTATATCTC
Found at i:19997561 original size:6 final size:6
Alignment explanation
Indices: 19997549--19997623 Score: 62
Period size: 6 Copynumber: 12.7 Consensus size: 6
19997539 AAGAAGAAGA
* * * * * *
19997549 AAAAAT AACAAT AAAAAT AAAAGT AAAAAG AAAAAC AAAAAC AAAAAC
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
* * *
19997597 AAAAAC AAAAAC AAAAA- CAAAAT AAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAA
19997624 CTAGGTAAAA
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
5 4 0.07
6 56 0.93
ACGTcount: A:0.81, C:0.09, G:0.03, T:0.07
Consensus pattern (6 bp):
AAAAAT
Found at i:19997588 original size:12 final size:12
Alignment explanation
Indices: 19997573--19997618 Score: 83
Period size: 12 Copynumber: 3.8 Consensus size: 12
19997563 AAATAAAAGT
*
19997573 AAAAAGAAAAAC
1 AAAAACAAAAAC
19997585 AAAAACAAAAAC
1 AAAAACAAAAAC
19997597 AAAAACAAAAAC
1 AAAAACAAAAAC
19997609 AAAAACAAAA
1 AAAAACAAAA
19997619 TAAAACTAGG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.85, C:0.13, G:0.02, T:0.00
Consensus pattern (12 bp):
AAAAACAAAAAC
Found at i:19997594 original size:18 final size:18
Alignment explanation
Indices: 19997573--19997618 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
19997563 AAATAAAAGT
*
19997573 AAAAAGAAAAACAAAAAC
1 AAAAACAAAAACAAAAAC
19997591 AAAAACAAAAACAAAAAC
1 AAAAACAAAAACAAAAAC
19997609 AAAAACAAAA
1 AAAAACAAAA
19997619 TAAAACTAGG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.85, C:0.13, G:0.02, T:0.00
Consensus pattern (18 bp):
AAAAACAAAAACAAAAAC
Found at i:20010275 original size:9 final size:9
Alignment explanation
Indices: 20010263--20010290 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
20010253 GATTAATTCG
20010263 ATTATAGTT
1 ATTATAGTT
20010272 ATTATAGTT
1 ATTATAGTT
20010281 ATTATAGTT
1 ATTATAGTT
20010290 A
1 A
20010291 GTTAATTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.54
Consensus pattern (9 bp):
ATTATAGTT
Found at i:20010315 original size:35 final size:35
Alignment explanation
Indices: 20010275--20010346 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
20010265 TATAGTTATT
*
20010275 ATAGTTATTATAGTTAGTTAATTAAAGTTCCATAA
1 ATAGTTATTATAGTTAGTTAATTAAAGTACCATAA
20010310 ATAGTTATTATAGTTAGTTAATTAAAGTACCATAA
1 ATAGTTATTATAGTTAGTTAATTAAAGTACCATAA
20010345 AT
1 AT
20010347 TAATTCAGTT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.42, C:0.06, G:0.11, T:0.42
Consensus pattern (35 bp):
ATAGTTATTATAGTTAGTTAATTAAAGTACCATAA
Found at i:20010719 original size:13 final size:13
Alignment explanation
Indices: 20010701--20010726 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
20010691 TAAGTTGGAA
20010701 AAATACAAAAGTG
1 AAATACAAAAGTG
20010714 AAATACAAAAGTG
1 AAATACAAAAGTG
20010727 GGAGTTTGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.08, G:0.15, T:0.15
Consensus pattern (13 bp):
AAATACAAAAGTG
Found at i:20011287 original size:21 final size:21
Alignment explanation
Indices: 20011261--20011362 Score: 195
Period size: 21 Copynumber: 4.9 Consensus size: 21
20011251 AAAAAACAAG
20011261 ATCGTCAAGGAGTCCATCGTC
1 ATCGTCAAGGAGTCCATCGTC
20011282 ATCGTCAAGGAGTCCATCGTC
1 ATCGTCAAGGAGTCCATCGTC
20011303 ATCGTCAAGGAGTCCATCGTC
1 ATCGTCAAGGAGTCCATCGTC
20011324 ATCGTCAAGGAGTCCATCGTC
1 ATCGTCAAGGAGTCCATCGTC
*
20011345 ATCGTCAAGGAGTTCATC
1 ATCGTCAAGGAGTCCATC
20011363 TTCCTATGAG
Statistics
Matches: 80, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
21 80 1.00
ACGTcount: A:0.25, C:0.27, G:0.24, T:0.25
Consensus pattern (21 bp):
ATCGTCAAGGAGTCCATCGTC
Found at i:20015593 original size:13 final size:13
Alignment explanation
Indices: 20015575--20015612 Score: 76
Period size: 13 Copynumber: 2.9 Consensus size: 13
20015565 AGTTCTTTAT
20015575 TGCTTTTGAGAAG
1 TGCTTTTGAGAAG
20015588 TGCTTTTGAGAAG
1 TGCTTTTGAGAAG
20015601 TGCTTTTGAGAA
1 TGCTTTTGAGAA
20015613 ATTTGAGTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.24, C:0.08, G:0.29, T:0.39
Consensus pattern (13 bp):
TGCTTTTGAGAAG
Found at i:20016159 original size:12 final size:12
Alignment explanation
Indices: 20016142--20016167 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
20016132 ATTGTTTGAT
20016142 TCACCATCATCA
1 TCACCATCATCA
20016154 TCACCATCATCA
1 TCACCATCATCA
20016166 TC
1 TC
20016168 GTCGTCGTCG
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:0.31, C:0.42, G:0.00, T:0.27
Consensus pattern (12 bp):
TCACCATCATCA
Found at i:20017757 original size:72 final size:72
Alignment explanation
Indices: 20017595--20017731 Score: 238
Period size: 72 Copynumber: 1.9 Consensus size: 72
20017585 CTAATTTAGT
*
20017595 ATAAATAAGTAGAACATAAATTCAATATCCAAAGACCAAACATAAACAACTATTAATAAAACTAG
1 ATAAATAAGTAGAACATAAATTCAATATCCAAAAACCAAACATAAACAACTATTAATAAAACTAG
20017660 ATTACAC
66 ATTACAC
* * *
20017667 ATAAATAAGTAGAACATAAATTCAATGTCCAAAAACCAAACATAAATAACTATTGATAAAACTAG
1 ATAAATAAGTAGAACATAAATTCAATATCCAAAAACCAAACATAAACAACTATTAATAAAACTAG
20017732 TTTAGCATTG
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
72 61 1.00
ACGTcount: A:0.55, C:0.15, G:0.07, T:0.23
Consensus pattern (72 bp):
ATAAATAAGTAGAACATAAATTCAATATCCAAAAACCAAACATAAACAACTATTAATAAAACTAG
ATTACAC
Done.