Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr7
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: 21614486
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1093914 characters in sequence are not A, C, G, or T
File 40 of 54
Found at i:16070183 original size:36 final size:36
Alignment explanation
Indices: 16070143--16070213 Score: 133
Period size: 36 Copynumber: 2.0 Consensus size: 36
16070133 CTAAAGGAAG
*
16070143 AACATTCAATCAATTCAAAGACTTAAAGAGCCATAA
1 AACATTCAATAAATTCAAAGACTTAAAGAGCCATAA
16070179 AACATTCAATAAATTCAAAGACTTAAAGAGCCATA
1 AACATTCAATAAATTCAAAGACTTAAAGAGCCATA
16070214 GTCTACTTTG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.51, C:0.18, G:0.08, T:0.23
Consensus pattern (36 bp):
AACATTCAATAAATTCAAAGACTTAAAGAGCCATAA
Found at i:16070569 original size:4 final size:4
Alignment explanation
Indices: 16070560--16070585 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
16070550 GCCATAGAAG
16070560 CTCA CTCA CTCA CTCA CTCA CTCA CT
1 CTCA CTCA CTCA CTCA CTCA CTCA CT
16070586 TGAAAATCCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.50, G:0.00, T:0.27
Consensus pattern (4 bp):
CTCA
Found at i:16079843 original size:43 final size:43
Alignment explanation
Indices: 16079771--16080068 Score: 298
Period size: 43 Copynumber: 7.1 Consensus size: 43
16079761 ACAATGCAAT
* * *
16079771 ATCATCA--TCATGTGCTCTCCCTAC-TCGCACATAGCTAGGTC
1 ATCATCAGCTCATGTGCACTCCC-ACACCGCACATAGCTGGGTC
* *
16079812 ATCATCAAG-TCATGTGCACTCCGACACCGCACATAACTGGGTC
1 ATCATC-AGCTCATGTGCACTCCCACACCGCACATAGCTGGGTC
* *
16079855 ATCATCAGCTCATTTGCACTCCCACACCGCACATACCTGGGTC
1 ATCATCAGCTCATGTGCACTCCCACACCGCACATAGCTGGGTC
* * **
16079898 ATCATCAACTCATGTGCACTCCCTACA-CGTACAATA-C--AAT-
1 ATCATCAGCTCATGTGCACTCCC-ACACCGCAC-ATAGCTGGGTC
*
16079938 ATCATCA--TCATGTGCACTCCCTAC-TCGCACATAGCTGGGTC
1 ATCATCAGCTCATGTGCACTCCC-ACACCGCACATAGCTGGGTC
* * *
16079979 ATCATCAGCTCATATGCACTCCCACACTGCACATAGTTGGGTC
1 ATCATCAGCTCATGTGCACTCCCACACCGCACATAGCTGGGTC
* * *
16080022 ATCATTAGCTCATGTGCACTCCCACA-CGCACATAGCTAGATC
1 ATCATCAGCTCATGTGCACTCCCACACCGCACATAGCTGGGTC
16080064 ATCAT
1 ATCAT
16080069 TATCACACAA
Statistics
Matches: 217, Mismatches: 26, Indels: 27
0.80 0.10 0.10
Matches are distributed among these distances:
37 3 0.01
38 22 0.10
40 8 0.04
41 14 0.06
42 24 0.11
43 140 0.65
44 6 0.03
ACGTcount: A:0.27, C:0.34, G:0.14, T:0.25
Consensus pattern (43 bp):
ATCATCAGCTCATGTGCACTCCCACACCGCACATAGCTGGGTC
Found at i:16079967 original size:124 final size:124
Alignment explanation
Indices: 16079812--16080049 Score: 356
Period size: 124 Copynumber: 1.9 Consensus size: 124
16079802 TAGCTAGGTC
*
16079812 ATCATCAAGTCATGTGCACTCCGACACCGCACATAACTGGGTCATCATCAGCTCATTTGCACTCC
1 ATCATCAAGTCATGTGCACTCC-ACACCGCACATAACTGGGTCATCATCAGCTCATATGCACTCC
16079877 CACACCGCACATACCTGGGTCATCATCAACTCATGTGCACTCCCTACACGTACAATACAAT
65 CACACCGCACATACCTGGGTCATCATCAACTCATGTGCACTCCC-ACACGTACAATACAAT
*
16079938 ATCATC-A-TCATGTGCACTCC-CTACTCGCACATAGCTGGGTCATCATCAGCTCATATGCACTC
1 ATCATCAAGTCATGTGCACTCCAC-AC-CGCACATAACTGGGTCATCATCAGCTCATATGCACTC
* ** * *
16080000 CCACACTGCACATAGTTGGGTCATCATTAGCTCATGTGCACTCCCACACG
64 CCACACCGCACATACCTGGGTCATCATCAACTCATGTGCACTCCCACACG
16080050 CACATAGCTA
Statistics
Matches: 103, Mismatches: 7, Indels: 7
0.88 0.06 0.06
Matches are distributed among these distances:
122 1 0.01
123 7 0.07
124 88 0.85
125 1 0.01
126 6 0.06
ACGTcount: A:0.26, C:0.34, G:0.15, T:0.24
Consensus pattern (124 bp):
ATCATCAAGTCATGTGCACTCCACACCGCACATAACTGGGTCATCATCAGCTCATATGCACTCCC
ACACCGCACATACCTGGGTCATCATCAACTCATGTGCACTCCCACACGTACAATACAAT
Found at i:16080022 original size:167 final size:166
Alignment explanation
Indices: 16079740--16080055 Score: 508
Period size: 167 Copynumber: 1.9 Consensus size: 166
16079730 CACACTCAGA
* *
16079740 TCATGTGCACTCCCTACACGCACAATGCAATATCATCATCATGTGCTCTCCCTACTCGCACATAG
1 TCATGTGCACTCCCTACACGCACAATACAATATCATCATCATGTGCACTCCCTACTCGCACATAG
* * *
16079805 CTAGGTCATCATCAAGTCATGTGCACTCCGACACCGCACATAACTGGGTCATCATCAGCTCATTT
66 CTAGGTCATCATCAAGTCATATGCACTCCCACACCGCACATAACTGGGTCATCATCAGCTCATGT
16079870 GCACTCCCACACCGCACATACCTGGGTCATCATCAAC
131 GCACTCCCACA-CGCACATACCTGGGTCATCATCAAC
*
16079907 TCATGTGCACTCCCTACACGTACAATACAATATCATCATCATGTGCACTCCCTACTCGCACATAG
1 TCATGTGCACTCCCTACACGCACAATACAATATCATCATCATGTGCACTCCCTACTCGCACATAG
* * ** *
16079972 CTGGGTCATCATC-AGCTCATATGCACTCCCACACTGCACATAGTTGGGTCATCATTAGCTCATG
66 CTAGGTCATCATCAAG-TCATATGCACTCCCACACCGCACATAACTGGGTCATCATCAGCTCATG
16080036 TGCACTCCCACACGCACATA
130 TGCACTCCCACACGCACATA
16080056 GCTAGATCAT
Statistics
Matches: 137, Mismatches: 11, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
166 10 0.07
167 127 0.93
ACGTcount: A:0.27, C:0.34, G:0.14, T:0.25
Consensus pattern (166 bp):
TCATGTGCACTCCCTACACGCACAATACAATATCATCATCATGTGCACTCCCTACTCGCACATAG
CTAGGTCATCATCAAGTCATATGCACTCCCACACCGCACATAACTGGGTCATCATCAGCTCATGT
GCACTCCCACACGCACATACCTGGGTCATCATCAAC
Found at i:16081633 original size:2 final size:2
Alignment explanation
Indices: 16081626--16081654 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
16081616 TCATAACCTC
16081626 TA TA TA TA TA TA TA TA TA -A TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
16081655 AACATACATA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:16081761 original size:43 final size:43
Alignment explanation
Indices: 16081694--16081962 Score: 340
Period size: 43 Copynumber: 6.3 Consensus size: 43
16081684 ACTCTCCCTC
* *
16081694 AGCTAGGTCATCATCAGCTAATGTGCACTCCTACACTGCACAT
1 AGCTAGGTCATCATCAGCTCATGTGCACTCCTACACCGCACAT
* * *
16081737 GGCTAGGTCATCATCAGCTCATGTGCACTCTTACACTGCACAT
1 AGCTAGGTCATCATCAGCTCATGTGCACTCCTACACCGCACAT
* * * * *
16081780 AGCTAGGTCATCATCAACTTATGTACACTTCTACACCACACAT
1 AGCTAGGTCATCATCAGCTCATGTGCACTCCTACACCGCACAT
* * * *
16081823 AGCTGGGTCAACATCAGCTCATGTGCACTCTTACACCGCATAT
1 AGCTAGGTCATCATCAGCTCATGTGCACTCCTACACCGCACAT
* * *
16081866 AGCTAGATCATCATCAGCTCATGTGCACTCTTACACCACACAT
1 AGCTAGGTCATCATCAGCTCATGTGCACTCCTACACCGCACAT
* * *
16081909 AGTTGGGTCATCATCAACTCATGTGCACTCCTACACCGCACAT
1 AGCTAGGTCATCATCAGCTCATGTGCACTCCTACACCGCACAT
* *
16081952 AGTTGGGTCAT
1 AGCTAGGTCAT
16081963 AATTATCACA
Statistics
Matches: 195, Mismatches: 31, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 195 1.00
ACGTcount: A:0.27, C:0.30, G:0.16, T:0.27
Consensus pattern (43 bp):
AGCTAGGTCATCATCAGCTCATGTGCACTCCTACACCGCACAT
Found at i:16081943 original size:129 final size:129
Alignment explanation
Indices: 16081694--16081961 Score: 383
Period size: 129 Copynumber: 2.1 Consensus size: 129
16081684 ACTCTCCCTC
* * * * *
16081694 AGCTAGGTCATCATCAGCTAATGTGCACTCCTACACTGCACATGGCTAGGTCATCATCAGCTCAT
1 AGCTGGGTCAACATCAGCTAATGTGCACTCCTACACCGCACATAGCTAGATCATCATCAGCTCAT
** * *
16081759 GTGCACTCTTACACTGCACATAGCTAGGTCATCATCAACTTATGTACACTTCTACACCACACAT
66 GTGCACTCTTACACCACACATAGCTAGGTCATCATCAACTCATGTACACTCCTACACCACACAT
* * *
16081823 AGCTGGGTCAACATCAGCTCATGTGCACTCTTACACCGCATATAGCTAGATCATCATCAGCTCAT
1 AGCTGGGTCAACATCAGCTAATGTGCACTCCTACACCGCACATAGCTAGATCATCATCAGCTCAT
* * * *
16081888 GTGCACTCTTACACCACACATAGTTGGGTCATCATCAACTCATGTGCACTCCTACACCGCACAT
66 GTGCACTCTTACACCACACATAGCTAGGTCATCATCAACTCATGTACACTCCTACACCACACAT
*
16081952 AGTTGGGTCA
1 AGCTGGGTCA
16081962 TAATTATCAC
Statistics
Matches: 122, Mismatches: 17, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
129 122 1.00
ACGTcount: A:0.27, C:0.30, G:0.16, T:0.26
Consensus pattern (129 bp):
AGCTGGGTCAACATCAGCTAATGTGCACTCCTACACCGCACATAGCTAGATCATCATCAGCTCAT
GTGCACTCTTACACCACACATAGCTAGGTCATCATCAACTCATGTACACTCCTACACCACACAT
Found at i:16082793 original size:20 final size:21
Alignment explanation
Indices: 16082765--16082808 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
16082755 AAGAAGAAGA
*
16082765 AGAAAAAGTTGCTGGAAA-TT
1 AGAAAAAGTTGCTAGAAACTT
*
16082785 AGAATAAGTTGCTAGAAACTT
1 AGAAAAAGTTGCTAGAAACTT
16082806 AGA
1 AGA
16082809 TATTTATGCC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 16 0.76
21 5 0.24
ACGTcount: A:0.45, C:0.07, G:0.23, T:0.25
Consensus pattern (21 bp):
AGAAAAAGTTGCTAGAAACTT
Found at i:16084556 original size:2 final size:2
Alignment explanation
Indices: 16084509--16084543 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
16084499 CATTAGGTCG
16084509 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
16084544 CATACGAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:16084639 original size:43 final size:43
Alignment explanation
Indices: 16084573--16084704 Score: 165
Period size: 43 Copynumber: 3.1 Consensus size: 43
16084563 GTAATGCTAT
* *
16084573 TGACTCGGTTATGTGCGAGTAGGGAGTGCTCATAAGCCGATGA
1 TGACCCGGTTATGTGCGAGTAGGGAGTGCACATAAGCCGATGA
* *
16084616 TGACCCGGTTATGTGCGAGTAGGGAGTGCACATAAACCGGTGA
1 TGACCCGGTTATGTGCGAGTAGGGAGTGCACATAAGCCGATGA
** ** * * *
16084659 TGACCTAGCCATGTGTGAGTAGGGAGTGCACATGAGCTGATGA
1 TGACCCGGTTATGTGCGAGTAGGGAGTGCACATAAGCCGATGA
16084702 TGA
1 TGA
16084705 TGGAATGGTG
Statistics
Matches: 76, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 76 1.00
ACGTcount: A:0.25, C:0.17, G:0.35, T:0.23
Consensus pattern (43 bp):
TGACCCGGTTATGTGCGAGTAGGGAGTGCACATAAGCCGATGA
Found at i:16084739 original size:2 final size:2
Alignment explanation
Indices: 16084732--16084764 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
16084722 TGATGATGGG
*
16084732 TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
16084765 GTAAATATGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:16086045 original size:42 final size:42
Alignment explanation
Indices: 16085999--16086191 Score: 215
Period size: 42 Copynumber: 4.6 Consensus size: 42
16085989 GCTCATGTGC
* * * **
16085999 ACTCCCACTAGCACATGGCTGGGTCATCATCGGCTTATGCGG
1 ACTCCTACTCGCACATGGCCGGGTCATCATCGGCTTATGCAA
* * * * * **
16086041 ACTCCCACTTGCACATTGCCAGGTCATCATCGACTTATGCGT
1 ACTCCTACTCGCACATGGCCGGGTCATCATCGGCTTATGCAA
*
16086083 ACTCCTACTCGCACATAGCCGGGTCATCATCGGCTTATGCAA
1 ACTCCTACTCGCACATGGCCGGGTCATCATCGGCTTATGCAA
* * * *
16086125 ACTCCTACTGGCACATAGCCTGGTCATCATCGGCTTATGCAC
1 ACTCCTACTCGCACATGGCCGGGTCATCATCGGCTTATGCAA
* *
16086167 ACTCCTACTCGCACATAGTCGGGTC
1 ACTCCTACTCGCACATGGCCGGGTC
16086192 CACATCAACA
Statistics
Matches: 132, Mismatches: 19, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 132 1.00
ACGTcount: A:0.21, C:0.33, G:0.20, T:0.25
Consensus pattern (42 bp):
ACTCCTACTCGCACATGGCCGGGTCATCATCGGCTTATGCAA
Found at i:16086110 original size:84 final size:84
Alignment explanation
Indices: 16085998--16086191 Score: 262
Period size: 84 Copynumber: 2.3 Consensus size: 84
16085988 AGCTCATGTG
* * * * ** * *
16085998 CACTCCCACTAGCACATGGCTGGGTCATCATCGGCTTATGCGGACTCCCACTTGCACATTGCCAG
1 CACTCCTACTCGCACATAGCCGGGTCATCATCGGCTTATGCAAACTCCCACTGGCACATAGCCAG
*
16086063 GTCATCATCGACTTATGCG
66 GTCATCATCGACTTATGCA
* * *
16086082 TACTCCTACTCGCACATAGCCGGGTCATCATCGGCTTATGCAAACTCCTACTGGCACATAGCCTG
1 CACTCCTACTCGCACATAGCCGGGTCATCATCGGCTTATGCAAACTCCCACTGGCACATAGCCAG
*
16086147 GTCATCATCGGCTTATGCA
66 GTCATCATCGACTTATGCA
*
16086166 CACTCCTACTCGCACATAGTCGGGTC
1 CACTCCTACTCGCACATAGCCGGGTC
16086192 CACATCAACA
Statistics
Matches: 95, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
84 95 1.00
ACGTcount: A:0.21, C:0.34, G:0.20, T:0.25
Consensus pattern (84 bp):
CACTCCTACTCGCACATAGCCGGGTCATCATCGGCTTATGCAAACTCCCACTGGCACATAGCCAG
GTCATCATCGACTTATGCA
Found at i:16095545 original size:39 final size:39
Alignment explanation
Indices: 16095491--16095587 Score: 185
Period size: 39 Copynumber: 2.5 Consensus size: 39
16095481 TAATTTGCAA
16095491 GATAGAAAGTTTCTCGCTGCAGTAAAATTCAAGCAGTAG
1 GATAGAAAGTTTCTCGCTGCAGTAAAATTCAAGCAGTAG
*
16095530 GATAGAAAGTTTCTCGCTGCAGTAAATTTCAAGCAGTAG
1 GATAGAAAGTTTCTCGCTGCAGTAAAATTCAAGCAGTAG
16095569 GATAGAAAGTTTCTCGCTG
1 GATAGAAAGTTTCTCGCTG
16095588 AGCGAGAAGC
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 57 1.00
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.28
Consensus pattern (39 bp):
GATAGAAAGTTTCTCGCTGCAGTAAAATTCAAGCAGTAG
Found at i:16095957 original size:43 final size:42
Alignment explanation
Indices: 16095897--16095989 Score: 141
Period size: 42 Copynumber: 2.2 Consensus size: 42
16095887 ACCATCCTAC
* *
16095897 CATCATCAGCTCATGTGCACTTCCCACTCACACATGGCTGGGT
1 CATCATCAGCTCATGTGCAC-TCCCACACACACAAGGCTGGGT
* *
16095940 CATCATCAGCTCATGTGCACTCCTACACGCACAAGGCTGGGT
1 CATCATCAGCTCATGTGCACTCCCACACACACAAGGCTGGGT
16095982 CATCATCA
1 CATCATCA
16095990 TCACACCAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
42 26 0.57
43 20 0.43
ACGTcount: A:0.24, C:0.34, G:0.18, T:0.24
Consensus pattern (42 bp):
CATCATCAGCTCATGTGCACTCCCACACACACAAGGCTGGGT
Found at i:16100901 original size:19 final size:19
Alignment explanation
Indices: 16100879--16100923 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
16100869 GAGAATAATA
16100879 AAAATTTAGAGGAAATTTT
1 AAAATTTAGAGGAAATTTT
**
16100898 AAAATTTTTAGGAAATTTT
1 AAAATTTAGAGGAAATTTT
16100917 AAAATTT
1 AAAATTT
16100924 TTAAGCAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.47, C:0.00, G:0.11, T:0.42
Consensus pattern (19 bp):
AAAATTTAGAGGAAATTTT
Found at i:16100924 original size:19 final size:19
Alignment explanation
Indices: 16100888--16100926 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
16100878 AAAAATTTAG
16100888 AGGAAATTTTAAAATTTTT
1 AGGAAATTTTAAAATTTTT
16100907 AGGAAATTTTAAAATTTTT
1 AGGAAATTTTAAAATTTTT
16100926 A
1 A
16100927 AGCAAATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.10, T:0.46
Consensus pattern (19 bp):
AGGAAATTTTAAAATTTTT
Found at i:16100933 original size:20 final size:19
Alignment explanation
Indices: 16100891--16100933 Score: 68
Period size: 19 Copynumber: 2.2 Consensus size: 19
16100881 AATTTAGAGG
*
16100891 AAATTTTAAAATTTTTAGG
1 AAATTTTAAAATTTTTAGC
16100910 AAATTTTAAAATTTTTAAGC
1 AAATTTTAAAATTTTT-AGC
16100930 AAAT
1 AAAT
16100934 AAAGTGAGGC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.47, C:0.02, G:0.07, T:0.44
Consensus pattern (19 bp):
AAATTTTAAAATTTTTAGC
Found at i:16103357 original size:22 final size:22
Alignment explanation
Indices: 16103329--16103377 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
16103319 GAAAAATAGA
* *
16103329 TGCTGATATATTTATGGTACTT
1 TGCTGATATATTCATGGAACTT
* *
16103351 TGCTGATATGTTCATGGAATTT
1 TGCTGATATATTCATGGAACTT
16103373 TGCTG
1 TGCTG
16103378 CTGATAATTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.20, C:0.10, G:0.22, T:0.47
Consensus pattern (22 bp):
TGCTGATATATTCATGGAACTT
Found at i:16112336 original size:22 final size:22
Alignment explanation
Indices: 16112304--16112356 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
16112294 GAAAGCTTTG
*
16112304 TGCTCTTATCTTTAAAACCAAA
1 TGCTCTGATCTTTAAAACCAAA
16112326 TGCTCTGATCTTTAAAACCAAA
1 TGCTCTGATCTTTAAAACCAAA
*
16112348 AGCTCTGAT
1 TGCTCTGAT
16112357 ACCACTTGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.34, C:0.23, G:0.09, T:0.34
Consensus pattern (22 bp):
TGCTCTGATCTTTAAAACCAAA
Found at i:16112770 original size:14 final size:15
Alignment explanation
Indices: 16112745--16112773 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
16112735 AAAATATTCT
16112745 AATTTTTCATAAAAC
1 AATTTTTCATAAAAC
16112760 AATTTTT-ATAAAAC
1 AATTTTTCATAAAAC
16112774 GCTATGTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.41
Consensus pattern (15 bp):
AATTTTTCATAAAAC
Found at i:16116302 original size:37 final size:37
Alignment explanation
Indices: 16116258--16116413 Score: 242
Period size: 37 Copynumber: 4.2 Consensus size: 37
16116248 AACGCAATAT
* *
16116258 CATCATCATGTATGCACTCCCTACTCGTACACTTCAA
1 CATCATCATGTGTGCACTCCCTACTCGCACACTTCAA
* *
16116295 CATCATCATGTGTGCACTCCCTATTTGCACAC-TCTAA
1 CATCATCATGTGTGCACTCCCTACTCGCACACTTC-AA
* *
16116332 CAACATCATGTGTGCATTCCCTACTCGCACACTTCAA
1 CATCATCATGTGTGCACTCCCTACTCGCACACTTCAA
16116369 CATCATCATGTGTGCACTCCCTACTCGCACACTTCAA
1 CATCATCATGTGTGCACTCCCTACTCGCACACTTCAA
16116406 CATCATCA
1 CATCATCA
16116414 CACAACATTA
Statistics
Matches: 107, Mismatches: 10, Indels: 4
0.88 0.08 0.03
Matches are distributed among these distances:
36 2 0.02
37 103 0.96
38 2 0.02
ACGTcount: A:0.26, C:0.35, G:0.10, T:0.29
Consensus pattern (37 bp):
CATCATCATGTGTGCACTCCCTACTCGCACACTTCAA
Found at i:16118447 original size:56 final size:56
Alignment explanation
Indices: 16118374--16118481 Score: 153
Period size: 56 Copynumber: 1.9 Consensus size: 56
16118364 TTATATGGCC
* ****
16118374 ACCCGTTGGAACCAATCACATTTCATGCACAAATTTTCCTTTGTTTTCATTTAGCT
1 ACCCGTTGAAACCAATCACAACAAATGCACAAATTTTCCTTTGTTTTCATTTAGCT
* *
16118430 ACCCTTTGAAACCAATCACAACAAATGCACCAATTTTCCTTTGTTTTCATTT
1 ACCCGTTGAAACCAATCACAACAAATGCACAAATTTTCCTTTGTTTTCATTT
16118482 GACCACTTTG
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
56 45 1.00
ACGTcount: A:0.28, C:0.26, G:0.08, T:0.38
Consensus pattern (56 bp):
ACCCGTTGAAACCAATCACAACAAATGCACAAATTTTCCTTTGTTTTCATTTAGCT
Found at i:16119829 original size:42 final size:42
Alignment explanation
Indices: 16119753--16119878 Score: 146
Period size: 42 Copynumber: 3.0 Consensus size: 42
16119743 GTAATGATAT
* * * * **
16119753 TGACCCGGCTATGTGCAAGTAGGAGTGTGCATAAGCCGTTGC
1 TGACCTGGCTATGTGCGAGTGGGAGAGCACATAAGCCGTTGC
*
16119795 TGACCCT-GCTATGTGCGAGTGGGAGAGCATATAAGCCGTTGC
1 TGA-CCTGGCTATGTGCGAGTGGGAGAGCACATAAGCCGTTGC
* * *
16119837 TGACCTGGCTATGTGTGAGTGGGAGTGCGCATAAGCCGTTGC
1 TGACCTGGCTATGTGCGAGTGGGAGAGCACATAAGCCGTTGC
16119879 ATATGAGCTG
Statistics
Matches: 71, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
41 3 0.04
42 66 0.93
43 2 0.03
ACGTcount: A:0.20, C:0.21, G:0.35, T:0.25
Consensus pattern (42 bp):
TGACCTGGCTATGTGCGAGTGGGAGAGCACATAAGCCGTTGC
Found at i:16121979 original size:11 final size:11
Alignment explanation
Indices: 16121963--16121994 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
16121953 CGATAAAAGT
16121963 ATTATTATTTA
1 ATTATTATTTA
*
16121974 ATTATTATTTT
1 ATTATTATTTA
16121985 ATTATTATTT
1 ATTATTATTT
16121995 CCTCGTGTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (11 bp):
ATTATTATTTA
Found at i:16123784 original size:120 final size:120
Alignment explanation
Indices: 16123564--16123804 Score: 448
Period size: 120 Copynumber: 2.0 Consensus size: 120
16123554 TGAACATAGG
16123564 AAGGAAACAAGCAACGTTAAGGAAAGTTTTTAAAAAAAATCATGATGCATTTAAGTTAAAAAATA
1 AAGGAAACAAGCAACGTTAAGGAAAG-TTTTAAAAAAAATCATGATGCATTTAAGTTAAAAAATA
16123629 ATGCAGTTTAGCTTACCCCTTATTAAAAACCCCTCATTTCAAATCTTGGTCTTTTA
65 ATGCAGTTTAGCTTACCCCTTATTAAAAACCCCTCATTTCAAATCTTGGTCTTTTA
*
16123685 NAAGGGAACAAGCAACGTTAAGGAAAG-TTTAAAAAAAATCATGATGCATTTAAGTTAAAAAATA
1 -AAGGAAACAAGCAACGTTAAGGAAAGTTTTAAAAAAAATCATGATGCATTTAAGTTAAAAAATA
16123749 ATGCAGTTTAGCTTACCCCTTATTAAAAACCCCTCATTTCAAATCTTGGTCTTTTA
65 ATGCAGTTTAGCTTACCCCTTATTAAAAACCCCTCATTTCAAATCTTGGTCTTTTA
16123805 GTCACTTAAT
Statistics
Matches: 118, Mismatches: 1, Indels: 2
0.98 0.01 0.02
Matches are distributed among these distances:
120 93 0.79
122 25 0.21
ACGTcount: A:0.40, C:0.16, G:0.13, T:0.31
Consensus pattern (120 bp):
AAGGAAACAAGCAACGTTAAGGAAAGTTTTAAAAAAAATCATGATGCATTTAAGTTAAAAAATAA
TGCAGTTTAGCTTACCCCTTATTAAAAACCCCTCATTTCAAATCTTGGTCTTTTA
Found at i:16124250 original size:42 final size:42
Alignment explanation
Indices: 16124192--16124314 Score: 149
Period size: 42 Copynumber: 2.9 Consensus size: 42
16124182 GCACAAGGCT
*
16124192 AGGTCATCATCA-GCTTATGTGCACTCCTACTCACACATAGCC
1 AGGTCATCAT-AGGCTTATGCGCACTCCTACTCACACATAGCC
* * * *
16124234 AGGTCATCATAGGCTTATGGGCACTTCTACTCACGCATAGCT
1 AGGTCATCATAGGCTTATGCGCACTCCTACTCACACATAGCC
* * * *
16124276 GGGTCATCATCGGCTTATGCACACTCCTACTCGCACATA
1 AGGTCATCATAGGCTTATGCGCACTCCTACTCACACATA
16124315 TCCGAATCCA
Statistics
Matches: 69, Mismatches: 11, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
41 1 0.01
42 68 0.99
ACGTcount: A:0.24, C:0.31, G:0.18, T:0.27
Consensus pattern (42 bp):
AGGTCATCATAGGCTTATGCGCACTCCTACTCACACATAGCC
Found at i:16127688 original size:28 final size:29
Alignment explanation
Indices: 16127630--16127693 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 29
16127620 GCAAATTTTT
* *
16127630 AAAAATTACACTTTTGCCCCTATAAAGTG
1 AAAAATTACACTTTTGCCCCTAAAAACTG
*
16127659 AAAAATTACATTTTTGCCCC-AAAAACTG
1 AAAAATTACACTTTTGCCCCTAAAAACTG
16127687 AAAAATT
1 AAAAATT
16127694 GTCCATAGAC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
28 13 0.41
29 19 0.59
ACGTcount: A:0.44, C:0.19, G:0.08, T:0.30
Consensus pattern (29 bp):
AAAAATTACACTTTTGCCCCTAAAAACTG
Found at i:16140600 original size:58 final size:58
Alignment explanation
Indices: 16140534--16140745 Score: 322
Period size: 58 Copynumber: 3.7 Consensus size: 58
16140524 AATTTCTAGA
*
16140534 AAATTGTGGGCGTTACGTATCGCCGTCCCCACTTTGCACATGCACGGTAGTAATTAGG
1 AAATTGTGGGCGTTACGTATCGCCGTCCCCACTTTGCACAGGCACGGTAGTAATTAGG
* * * *
16140592 AAATTGTGGGCGTTACGTATCACCGTCTCCACTTTGTATAGGCACGGTAGT-A--AGG
1 AAATTGTGGGCGTTACGTATCGCCGTCCCCACTTTGCACAGGCACGGTAGTAATTAGG
* *
16140647 AAATTGTGGACGATACGTATCGCCGTCCCCACTTTGCACAGGCACGGTAGTAATTAGG
1 AAATTGTGGGCGTTACGTATCGCCGTCCCCACTTTGCACAGGCACGGTAGTAATTAGG
* *
16140705 AAATTGTGGGCATTACGTATCGTCGTCCCCACTTTGCACAG
1 AAATTGTGGGCGTTACGTATCGCCGTCCCCACTTTGCACAG
16140746 TTGCATCAAT
Statistics
Matches: 136, Mismatches: 15, Indels: 6
0.87 0.10 0.04
Matches are distributed among these distances:
55 48 0.35
56 1 0.01
57 1 0.01
58 86 0.63
ACGTcount: A:0.24, C:0.24, G:0.25, T:0.27
Consensus pattern (58 bp):
AAATTGTGGGCGTTACGTATCGCCGTCCCCACTTTGCACAGGCACGGTAGTAATTAGG
Found at i:16140737 original size:113 final size:113
Alignment explanation
Indices: 16140534--16140740 Score: 351
Period size: 113 Copynumber: 1.8 Consensus size: 113
16140524 AATTTCTAGA
* * *
16140534 AAATTGTGGGCGTTACGTATCGCCGTCCCCACTTTGCACATGCACGGTAGTAATTAGGAAATTGT
1 AAATTGTGGACGATACGTATCGCCGTCCCCACTTTGCACAGGCACGGTAGTAATTAGGAAATTGT
* *
16140599 GGGCGTTACGTATCACCGTCTCCACTTTGTATAGGCACGGTAGTAAGG
66 GGGCATTACGTATCACCGTCCCCACTTTGTATAGGCACGGTAGTAAGG
16140647 AAATTGTGGACGATACGTATCGCCGTCCCCACTTTGCACAGGCACGGTAGTAATTAGGAAATTGT
1 AAATTGTGGACGATACGTATCGCCGTCCCCACTTTGCACAGGCACGGTAGTAATTAGGAAATTGT
**
16140712 GGGCATTACGTATCGTCGTCCCCACTTTG
66 GGGCATTACGTATCACCGTCCCCACTTTG
16140741 CACAGTTGCA
Statistics
Matches: 87, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
113 87 1.00
ACGTcount: A:0.23, C:0.23, G:0.26, T:0.28
Consensus pattern (113 bp):
AAATTGTGGACGATACGTATCGCCGTCCCCACTTTGCACAGGCACGGTAGTAATTAGGAAATTGT
GGGCATTACGTATCACCGTCCCCACTTTGTATAGGCACGGTAGTAAGG
Found at i:16144441 original size:58 final size:57
Alignment explanation
Indices: 16144371--16144586 Score: 310
Period size: 58 Copynumber: 3.8 Consensus size: 57
16144361 CTTTGAATTT
* * * *
16144371 TTAGAAAATTGTGGGCATTATGTATCGCCGTCCCCACTTTGAACATGCACGGTAGTAA
1 TTAGGAAATTGTGGGCATTACGTATCGCCGTCCCCACTTTGCACAAGCACGGTAGT-A
* * *
16144429 TTAGGAAATTGTGGGCATTACGTATCACCGTCCCCACTTTGCACAGGCACAGTAGTA
1 TTAGGAAATTGTGGGCATTACGTATCGCCGTCCCCACTTTGCACAAGCACGGTAGTA
*
16144486 --AGGAAATTGTGGGCGTTACGTATCGCCGTCCCCACTTTGCACAAGCACGGTAGTGA
1 TTAGGAAATTGTGGGCATTACGTATCGCCGTCCCCACTTTGCACAAGCACGGTAGT-A
* *
16144542 TTAGGAAATTGTGCGCGTTACGTATCGCCGTCCCCACTTTGCACA
1 TTAGGAAATTGTGGGCATTACGTATCGCCGTCCCCACTTTGCACA
16144587 GTTGCATCAA
Statistics
Matches: 144, Mismatches: 11, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
55 50 0.35
56 1 0.01
57 1 0.01
58 92 0.64
ACGTcount: A:0.25, C:0.25, G:0.24, T:0.27
Consensus pattern (57 bp):
TTAGGAAATTGTGGGCATTACGTATCGCCGTCCCCACTTTGCACAAGCACGGTAGTA
Found at i:16144574 original size:113 final size:113
Alignment explanation
Indices: 16144376--16144587 Score: 352
Period size: 113 Copynumber: 1.9 Consensus size: 113
16144366 AATTTTTAGA
* *
16144376 AAATTGTGGGCATTATGTATCGCCGTCCCCACTTTGAACATGCACGGTAGTAATTAGGAAATTGT
1 AAATTGTGGGCATTACGTATCGCCGTCCCCACTTTGAACAAGCACGGTAGTAATTAGGAAATTGT
*
16144441 GGGCATTACGTATCACCGTCCCCACTTTGCACAGGCACAGTAGTAAGG
66 GCGCATTACGTATCACCGTCCCCACTTTGCACAGGCACAGTAGTAAGG
* * *
16144489 AAATTGTGGGCGTTACGTATCGCCGTCCCCACTTTGCACAAGCACGGTAGTGATTAGGAAATTGT
1 AAATTGTGGGCATTACGTATCGCCGTCCCCACTTTGAACAAGCACGGTAGTAATTAGGAAATTGT
* *
16144554 GCGCGTTACGTATCGCCGTCCCCACTTTGCACAG
66 GCGCATTACGTATCACCGTCCCCACTTTGCACAG
16144588 TTGCATCAAT
Statistics
Matches: 91, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
113 91 1.00
ACGTcount: A:0.24, C:0.25, G:0.25, T:0.26
Consensus pattern (113 bp):
AAATTGTGGGCATTACGTATCGCCGTCCCCACTTTGAACAAGCACGGTAGTAATTAGGAAATTGT
GCGCATTACGTATCACCGTCCCCACTTTGCACAGGCACAGTAGTAAGG
Found at i:16154048 original size:74 final size:73
Alignment explanation
Indices: 16153963--16154139 Score: 189
Period size: 74 Copynumber: 2.4 Consensus size: 73
16153953 AATATACTTT
* * *
16153963 TTAGTTGATTAAGTCGTCTTTGTCTTTTGA-TCCTA-GTTTCTGGTAGTGAGCTCTTAGTCAATT
1 TTAGTTGATTAAGTC-TCTTTGT-TTTTGAGT-CTAGGTTTCTGGCAGTAAGCTCTTAGTCAACT
16154026 AACAATGGTTC
63 AACAATGGTTC
* * * *
16154037 TTAGTTGATTAAGT-TCTTTCTATCTTGTAGTCTAGGTTTCTGGCAGTAAGCTCTTAGTCGACTC
1 TTAGTTGATTAAGTCTCTTTGT-TTTTG-AGTCTAGGTTTCTGGCAGTAAGCTCTTAGTCAACTA
*
16154101 ACAATGTTTC
64 ACAATGGTTC
* *
16154111 TTAGTCGACTAAGTCTTCTTTGTTTTTGA
1 TTAGTTGATTAAGTC-TCTTTGTTTTTGA
16154140 ACTAGCCATC
Statistics
Matches: 85, Mismatches: 13, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
72 10 0.12
73 4 0.05
74 61 0.72
75 4 0.05
76 6 0.07
ACGTcount: A:0.20, C:0.16, G:0.19, T:0.45
Consensus pattern (73 bp):
TTAGTTGATTAAGTCTCTTTGTTTTTGAGTCTAGGTTTCTGGCAGTAAGCTCTTAGTCAACTAAC
AATGGTTC
Found at i:16157872 original size:22 final size:22
Alignment explanation
Indices: 16157833--16157876 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
16157823 CCTAAATTGC
*
16157833 CCCTAAGTTGCTTATACTTTCT
1 CCCTAAATTGCTTATACTTTCT
* *
16157855 CCCTAAATTTCTTTTACTTTCT
1 CCCTAAATTGCTTATACTTTCT
16157877 ATCTCCCTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.18, C:0.27, G:0.05, T:0.50
Consensus pattern (22 bp):
CCCTAAATTGCTTATACTTTCT
Found at i:16159716 original size:21 final size:22
Alignment explanation
Indices: 16159670--16159716 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
16159660 GGTACCCTGC
* *
16159670 TTCTCGCTGTAGCGAGAAAGCA
1 TTCTCGCTGCAACGAGAAAGCA
16159692 TTCTCGCTGCAACGAGAAA-CA
1 TTCTCGCTGCAACGAGAAAGCA
16159713 TTCT
1 TTCT
16159717 ATTTTGGCAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 6 0.26
22 17 0.74
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.26
Consensus pattern (22 bp):
TTCTCGCTGCAACGAGAAAGCA
Found at i:16166172 original size:42 final size:42
Alignment explanation
Indices: 16166113--16166196 Score: 132
Period size: 42 Copynumber: 2.0 Consensus size: 42
16166103 GTAATGATAT
* * **
16166113 TGACCTGGCTATGTGCGAGTGGGAGTGTGCATAAGCCGTTGC
1 TGACCCGGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTGC
16166155 TGACCCGGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTGC
1 TGACCCGGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTGC
16166197 ATATGAGCTA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (42 bp):
TGACCCGGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTGC
Found at i:16177375 original size:37 final size:36
Alignment explanation
Indices: 16177324--16177475 Score: 209
Period size: 37 Copynumber: 4.2 Consensus size: 36
16177314 AATATTGTGT
16177324 GATGATGTTGAAGTGTGCGAGTAGGGAGTGCACACA
1 GATGATGTTGAAGTGTGCGAGTAGGGAGTGCACACA
* *
16177360 GGGTGATGTTGAAGTGTGCGAGTAGGGAGTGTACAC-
1 -GATGATGTTGAAGTGTGCGAGTAGGGAGTGCACACA
* * *
16177396 -TTGATGTTGAAATGTACGAGTAGGGAGTGCACACA
1 GATGATGTTGAAGTGTGCGAGTAGGGAGTGCACACA
*
16177431 TGATGATGTTGAAGTGCGCGAGTAGGGAGTGCACACA
1 -GATGATGTTGAAGTGTGCGAGTAGGGAGTGCACACA
16177468 TGATGATG
1 -GATGATG
16177476 ATATTGCATT
Statistics
Matches: 102, Mismatches: 10, Indels: 6
0.86 0.08 0.05
Matches are distributed among these distances:
34 30 0.29
37 72 0.71
ACGTcount: A:0.27, C:0.11, G:0.38, T:0.24
Consensus pattern (36 bp):
GATGATGTTGAAGTGTGCGAGTAGGGAGTGCACACA
Found at i:16177416 original size:71 final size:71
Alignment explanation
Indices: 16177325--16177472 Score: 233
Period size: 71 Copynumber: 2.1 Consensus size: 71
16177315 ATATTGTGTG
* * * *
16177325 ATGATGTTGAAGTGTGCGAGTAGGGAGTGCACACAGGGTGATGTTGAAGTGTGCGAGTAGGGAGT
1 ATGATGTTGAAATGTACGAGTAGGGAGTGCACACAGGATGATGTTGAAGTGCGCGAGTAGGGAGT
*
16177390 GTACAC
66 GCACAC
* *
16177396 TTGATGTTGAAATGTACGAGTAGGGAGTGCACACATGATGATGTTGAAGTGCGCGAGTAGGGAGT
1 ATGATGTTGAAATGTACGAGTAGGGAGTGCACACAGGATGATGTTGAAGTGCGCGAGTAGGGAGT
16177461 GCACAC
66 GCACAC
16177467 ATGATG
1 ATGATG
16177473 ATGATATTGC
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
71 69 1.00
ACGTcount: A:0.27, C:0.11, G:0.38, T:0.24
Consensus pattern (71 bp):
ATGATGTTGAAATGTACGAGTAGGGAGTGCACACAGGATGATGTTGAAGTGCGCGAGTAGGGAGT
GCACAC
Found at i:16177645 original size:23 final size:24
Alignment explanation
Indices: 16177599--16177645 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
16177589 AATTGCTCCC
* *
16177599 AAATTGCTTTTCATTTTAGCAAGA
1 AAATGGCTTTTCATTGTAGCAAGA
16177623 AAATGGCTTTTCA-TGTAGCAAGA
1 AAATGGCTTTTCATTGTAGCAAGA
16177646 CCCTTTTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.36
Consensus pattern (24 bp):
AAATGGCTTTTCATTGTAGCAAGA
Found at i:16179964 original size:27 final size:29
Alignment explanation
Indices: 16179918--16179971 Score: 85
Period size: 28 Copynumber: 1.9 Consensus size: 29
16179908 GAAAAGTGCT
16179918 AGGGCAAAAAATTTACCGA-TTTGCCCCC
1 AGGGCAAAAAATTTACCGATTTTGCCCCC
*
16179946 AGGGCGAAAAATTTA-CGATTTTGCCC
1 AGGGCAAAAAATTTACCGATTTTGCCC
16179972 TTATCTCCGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 3 0.12
28 21 0.88
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.24
Consensus pattern (29 bp):
AGGGCAAAAAATTTACCGATTTTGCCCCC
Found at i:16189492 original size:74 final size:74
Alignment explanation
Indices: 16189370--16189564 Score: 193
Period size: 74 Copynumber: 2.6 Consensus size: 74
16189360 CAAATAGAAT
* * * *
16189370 GCTCTTAGTTGACTAGC-ATACTTTTTAGTCGATTAAG-TCATCTCTGTCTTTTGATCCCA-GTT
1 GCTCTTAGTTGACTAACAAT-GTTTTTAGTCGATTAAGTTCATCTCTGTCTTGTAAT-CCAGGTT
*
16189432 TCTAGCAGTGA
64 TCTAGCAGTAA
* *
16189443 GCTCTTAGTTGACTAACAATGTTTCTTAGTCGATTAAGTTC-TTTTTGTCTTGTAATCCAGGTTT
1 GCTCTTAGTTGACTAACAATGTTT-TTAGTCGATTAAGTTCATCTCTGTCTTGTAATCCAGGTTT
* *
16189507 TTGGCAGTAA
65 CTAGCAGTAA
* * * * *
16189517 GCTTTTAGTCGATTAACAATGTTTTTTAGTCGACTAAG-TCTTCTCTGT
1 GCTCTTAGTTGACTAACAATG-TTTTTAGTCGATTAAGTTCATCTCTGT
16189565 TTCTGAACCG
Statistics
Matches: 101, Mismatches: 15, Indels: 11
0.80 0.12 0.09
Matches are distributed among these distances:
73 24 0.24
74 72 0.71
75 5 0.05
ACGTcount: A:0.21, C:0.17, G:0.18, T:0.44
Consensus pattern (74 bp):
GCTCTTAGTTGACTAACAATGTTTTTAGTCGATTAAGTTCATCTCTGTCTTGTAATCCAGGTTTC
TAGCAGTAA
Found at i:16212704 original size:21 final size:21
Alignment explanation
Indices: 16212662--16212704 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
16212652 CTTGTACCGA
*
16212662 TGGTGGAACTAAAGGAGTAAC
1 TGGTGGAACTAAAGGAGAAAC
* * *
16212683 TGGTGGTACTATAGGTGAAAC
1 TGGTGGAACTAAAGGAGAAAC
16212704 T
1 T
16212705 TGACCAGTCT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.09, G:0.33, T:0.26
Consensus pattern (21 bp):
TGGTGGAACTAAAGGAGAAAC
Found at i:16221377 original size:16 final size:18
Alignment explanation
Indices: 16221356--16221389 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
16221346 AAGGTGATTT
16221356 TAAAGTGA-AC-TTGGGA
1 TAAAGTGAGACGTTGGGA
16221372 TAAAGTGAGACGTTGGGA
1 TAAAGTGAGACGTTGGGA
16221390 CTCAAGGAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 2 0.12
18 6 0.38
ACGTcount: A:0.35, C:0.06, G:0.35, T:0.24
Consensus pattern (18 bp):
TAAAGTGAGACGTTGGGA
Found at i:16224081 original size:28 final size:28
Alignment explanation
Indices: 16224050--16224104 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
16224040 GACAAAAAGT
16224050 GTAAAATGGTAATTTTGCCACC-CCAGGG
1 GTAAAATGGTAATTTT-CCACCACCAGGG
*
16224078 GTAAAATTGTAATTTTCCACCACCAGG
1 GTAAAATGGTAATTTTCCACCACCAGG
16224105 ATATTTTTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 5 0.20
28 20 0.80
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (28 bp):
GTAAAATGGTAATTTTCCACCACCAGGG
Found at i:16225245 original size:13 final size:13
Alignment explanation
Indices: 16225227--16225251 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16225217 AGAGAAATTG
16225227 TGATTTTATAAAA
1 TGATTTTATAAAA
16225240 TGATTTTATAAA
1 TGATTTTATAAA
16225252 TTTTCTGAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:16227062 original size:38 final size:40
Alignment explanation
Indices: 16226975--16227077 Score: 133
Period size: 38 Copynumber: 2.6 Consensus size: 40
16226965 ACCCGGCTCA
16226975 TGTACATCCCCCCACATCGTGCAC-ATAGACGGCACCATCG
1 TGTACATCCCCCCACATCGTGCACAATAGACGG-ACCATCG
* * *
16227015 TGTGCATCCCCCCACATCGTGCACAATCA-A-TG-CTATCG
1 TGTACATCCCCCCACATCGTGCACAAT-AGACGGACCATCG
16227053 TGTACATCCCCCCACATCGTGCACA
1 TGTACATCCCCCCACATCGTGCACA
16227078 TGGGCACTAT
Statistics
Matches: 57, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
38 29 0.51
40 24 0.42
41 3 0.05
42 1 0.02
ACGTcount: A:0.24, C:0.40, G:0.16, T:0.20
Consensus pattern (40 bp):
TGTACATCCCCCCACATCGTGCACAATAGACGGACCATCG
Found at i:16230855 original size:38 final size:40
Alignment explanation
Indices: 16230769--16230871 Score: 133
Period size: 38 Copynumber: 2.6 Consensus size: 40
16230759 ACCCGGCTCA
16230769 TGTACATCCCCCCACATCGTGCAC-ATAGACGGCACCATCG
1 TGTACATCCCCCCACATCGTGCACAATAGACGG-ACCATCG
* * *
16230809 TGTGCATCCCCCCACATCATGCACAATCA-A-TG-CCATCG
1 TGTACATCCCCCCACATCGTGCACAAT-AGACGGACCATCG
16230847 TGTACATCCCCCCACATCGTGCACA
1 TGTACATCCCCCCACATCGTGCACA
16230872 CGGGCACTAT
Statistics
Matches: 56, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
38 29 0.52
40 23 0.41
41 3 0.05
42 1 0.02
ACGTcount: A:0.25, C:0.41, G:0.15, T:0.19
Consensus pattern (40 bp):
TGTACATCCCCCCACATCGTGCACAATAGACGGACCATCG
Found at i:16237620 original size:40 final size:38
Alignment explanation
Indices: 16237564--16237669 Score: 115
Period size: 38 Copynumber: 2.7 Consensus size: 38
16237554 CTCACCCAGC
16237564 TCATGTGCATCCCCCCACATCGTGCACATAGCTGAAGT-CA
1 TCATGTGCATCCCCCCACATCGTGCACA-A--TGAAGTCCA
* * * * *
16237604 TCATGTGCATCTCCCCATATTGTGCACAATTAATTCCA
1 TCATGTGCATCCCCCCACATCGTGCACAATGAAGTCCA
* *
16237642 TCGTGTGCACCCCCCCACATCGTGCACA
1 TCATGTGCATCCCCCCACATCGTGCACA
16237670 CAGGCATTTT
Statistics
Matches: 55, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
37 4 0.07
38 25 0.45
39 1 0.02
40 25 0.45
ACGTcount: A:0.24, C:0.36, G:0.15, T:0.25
Consensus pattern (38 bp):
TCATGTGCATCCCCCCACATCGTGCACAATGAAGTCCA
Found at i:16242700 original size:2 final size:2
Alignment explanation
Indices: 16242693--16242728 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
16242683 GATGGTGTAC
16242693 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
16242729 GCTATTAGCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16245912 original size:35 final size:35
Alignment explanation
Indices: 16245866--16246002 Score: 195
Period size: 35 Copynumber: 3.9 Consensus size: 35
16245856 ACTCAACCAA
* *
16245866 TGTGCACTCCCTACACACACA-AGGCAATATCATCG
1 TGTGCACTCCCTACTCACACACA-TCAATATCATCG
16245901 TGTGCACTCCCTACTCACACACATCAATATCATCG
1 TGTGCACTCCCTACTCACACACATCAATATCATCG
* * *
16245936 TGTGCACTCCCTACTCGCACACATCAACATCACCG
1 TGTGCACTCCCTACTCACACACATCAATATCATCG
* *
16245971 TGTGCACTCCCTACTCGCACACTTCAATATCA
1 TGTGCACTCCCTACTCACACACATCAATATCA
16246003 CTATCCACAC
Statistics
Matches: 94, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
35 93 0.99
36 1 0.01
ACGTcount: A:0.28, C:0.38, G:0.11, T:0.23
Consensus pattern (35 bp):
TGTGCACTCCCTACTCACACACATCAATATCATCG
Found at i:16247986 original size:2 final size:2
Alignment explanation
Indices: 16247979--16248027 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
16247969 ATGCTTCGCT
16247979 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
16248021 TA TA TA T
1 TA TA TA T
16248028 NNNNNNNNNN
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:16261735 original size:2 final size:2
Alignment explanation
Indices: 16261728--16261783 Score: 58
Period size: 2 Copynumber: 28.0 Consensus size: 2
16261718 ACATACATAC
** * *
16261728 AT AT AT AT AT AT AT AT GC AT AT AA AT AC 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
* *
16261770 AT AC AT AC AT AT AT
1 AT AT AT AT AT AT AT
16261784 TAGTACAATA
Statistics
Matches: 42, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.07, G:0.02, T:0.41
Consensus pattern (2 bp):
AT
Found at i:16261783 original size:18 final size:18
Alignment explanation
Indices: 16261716--16261780 Score: 76
Period size: 18 Copynumber: 3.6 Consensus size: 18
16261706 TCATAAAATA
16261716 ATACATACATACATATAT
1 ATACATACATACATATAT
* * * *
16261734 ATATATATATGCATATAA
1 ATACATACATACATATAT
* *
16261752 ATACATATATATATATAT
1 ATACATACATACATATAT
16261770 ATACATACATA
1 ATACATACATA
16261781 TATTAGTACA
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 38 1.00
ACGTcount: A:0.51, C:0.11, G:0.02, T:0.37
Consensus pattern (18 bp):
ATACATACATACATATAT
Found at i:16261861 original size:2 final size:2
Alignment explanation
Indices: 16261854--16261878 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
16261844 ATTGATTCCA
16261854 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
16261879 GAGAGAGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:16261915 original size:2 final size:2
Alignment explanation
Indices: 16261910--16261965 Score: 58
Period size: 2 Copynumber: 28.0 Consensus size: 2
16261900 AGTTTNATAC
** * *
16261910 AT AT AT AT AT AT AT AT GC AT AT AA AT AC 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
* *
16261952 AT AC AT AC AT AT AT
1 AT AT AT AT AT AT AT
16261966 TAGTACAATA
Statistics
Matches: 42, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.07, G:0.02, T:0.41
Consensus pattern (2 bp):
AT
Found at i:16261926 original size:182 final size:181
Alignment explanation
Indices: 16261724--16262083 Score: 711
Period size: 182 Copynumber: 2.0 Consensus size: 181
16261714 TAATACATAC
16261724 ATACATATATATATATATATGCATATAAATACATATATATATATATATACATACATATATTAGTA
1 ATACATATATATATATATATGCATATAAATACATATATATATATATATACATACATATATTAGTA
16261789 CAATATTGAATTATATAATATGAGCATGTTAAGCTAGAAGGAGCTTCGTTAACAAATTGATTCCA
66 CAATATTGAATTATATAATATGAGCATGTTAAGCTAGAAGGAGCTTCGTTAACAAATTGATTCCA
16261854 ATATATATATATATATATATATATAGAGAGAGAGAGAGAGAGAGAGAGTTT
131 ATATATATATATATATATATATATAGAGAGAGAGAGAGAGAGAGAGAGTTT
16261905 NATACATATATATATATATATGCATATAAATACATATATATATATATATACATACATATATTAGT
1 -ATACATATATATATATATATGCATATAAATACATATATATATATATATACATACATATATTAGT
16261970 ACAATATTGAATTATATAATATGAGCATGTTAAGCTAGAAGGAGCTTCGTTAACAAATTGATTCC
65 ACAATATTGAATTATATAATATGAGCATGTTAAGCTAGAAGGAGCTTCGTTAACAAATTGATTCC
16262035 AATATATATATATATATATATATATAGAGAGAGAGAGAGAGAGAGAGAG
130 AATATATATATATATATATATATATAGAGAGAGAGAGAGAGAGAGAGAG
16262084 AGTTTCTTTT
Statistics
Matches: 178, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
182 178 1.00
ACGTcount: A:0.45, C:0.07, G:0.14, T:0.34
Consensus pattern (181 bp):
ATACATATATATATATATATGCATATAAATACATATATATATATATATACATACATATATTAGTA
CAATATTGAATTATATAATATGAGCATGTTAAGCTAGAAGGAGCTTCGTTAACAAATTGATTCCA
ATATATATATATATATATATATATAGAGAGAGAGAGAGAGAGAGAGAGTTT
Found at i:16261944 original size:22 final size:22
Alignment explanation
Indices: 16261916--16261965 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
16261906 ATACATATAT
*
16261916 ATATATATATGCATATAAATAC
1 ATATATATATACATATAAATAC
* *
16261938 ATATATATATATATATACATAC
1 ATATATATATACATATAAATAC
16261960 ATATAT
1 ATATAT
16261966 TAGTACAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.50, C:0.08, G:0.02, T:0.40
Consensus pattern (22 bp):
ATATATATATACATATAAATAC
Found at i:16262043 original size:2 final size:2
Alignment explanation
Indices: 16262036--16262060 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
16262026 ATTGATTCCA
16262036 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
16262061 GAGAGAGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:16262065 original size:2 final size:2
Alignment explanation
Indices: 16262060--16262085 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
16262050 ATATATATAT
16262060 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
16262086 TTTCTTTTGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:16264437 original size:37 final size:37
Alignment explanation
Indices: 16264389--16264460 Score: 117
Period size: 37 Copynumber: 1.9 Consensus size: 37
16264379 ATCTTATAAT
*
16264389 TGTGTGGTACAATACCCCACATCAAGACCCTCATGTA
1 TGTGTGATACAATACCCCACATCAAGACCCTCATGTA
* *
16264426 TGTGTGATACAATACCCTACATCAAGATCCTCATG
1 TGTGTGATACAATACCCCACATCAAGACCCTCATG
16264461 CTTGTATAGA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.31, C:0.28, G:0.15, T:0.26
Consensus pattern (37 bp):
TGTGTGATACAATACCCCACATCAAGACCCTCATGTA
Found at i:16275929 original size:71 final size:71
Alignment explanation
Indices: 16275851--16276072 Score: 275
Period size: 71 Copynumber: 3.1 Consensus size: 71
16275841 TCTCAAGCAC
* * * *
16275851 TTGATTAAAATTGTTTAATTAAATCATTAGGCCTAATTAATTAAATTATTTAATTAAGTCCTTGG
1 TTGATTAAAATTATTTAATTAAATTATTAGGCCTAATTAATTAAATTGTTTAATTAAGTCATTGG
16275916 GCCTAA
66 GCCTAA
* *** * * * * *
16275922 TTAATT-AAATTACACAATTAAGTTATTGGGTCTAATTGATTAAATTTGTTTGATTAAGTCATTG
1 TTGATTAAAATTATTTAATTAAATTATTAGGCCTAATTAATTAAA-TTGTTTAATTAAGTCATTG
16275986 GGCCTAA
65 GGCCTAA
* * * *
16275993 TTGATTAAAATTATTTAATTAAATTGTTAAGCTTAATTAATTAAATTGTTTAATTAAGTTATTGG
1 TTGATTAAAATTATTTAATTAAATTATTAGGCCTAATTAATTAAATTGTTTAATTAAGTCATTGG
16276058 GCCTAA
66 GCCTAA
16276064 TTGATTAAA
1 TTGATTAAA
16276073 TTAAACAATT
Statistics
Matches: 123, Mismatches: 26, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
70 29 0.24
71 66 0.54
72 28 0.23
ACGTcount: A:0.36, C:0.07, G:0.13, T:0.44
Consensus pattern (71 bp):
TTGATTAAAATTATTTAATTAAATTATTAGGCCTAATTAATTAAATTGTTTAATTAAGTCATTGG
GCCTAA
Found at i:16276085 original size:35 final size:35
Alignment explanation
Indices: 16275858--16276075 Score: 220
Period size: 35 Copynumber: 6.2 Consensus size: 35
16275848 CACTTGATTA
* * * *
16275858 AAATTGTTTAATTAAATCATTAGGCCTAATTAATT
1 AAATTATTTAATTAAGTTATTGGGCCTAATTAATT
**
16275893 AAATTATTTAATTAAGTCCTTGGGCCTAATTAATT
1 AAATTATTTAATTAAGTTATTGGGCCTAATTAATT
*** * *
16275928 AAATTACACAATTAAGTTATTGGGTCTAATTGATT
1 AAATTATTTAATTAAGTTATTGGGCCTAATTAATT
* * * *
16275963 AAATTTGTTTGATTAAGTCATTGGGCCTAATTGATT
1 AAA-TTATTTAATTAAGTTATTGGGCCTAATTAATT
* * ** *
16275999 AAAATTATTTAATTAAATTGTTAAGCTTAATTAATT
1 -AAATTATTTAATTAAGTTATTGGGCCTAATTAATT
* *
16276035 AAATTGTTTAATTAAGTTATTGGGCCTAATTGATT
1 AAATTATTTAATTAAGTTATTGGGCCTAATTAATT
16276070 AAATTA
1 AAATTA
16276076 AACAATTAAG
Statistics
Matches: 146, Mismatches: 35, Indels: 4
0.79 0.19 0.02
Matches are distributed among these distances:
35 95 0.65
36 48 0.33
37 3 0.02
ACGTcount: A:0.37, C:0.07, G:0.12, T:0.44
Consensus pattern (35 bp):
AAATTATTTAATTAAGTTATTGGGCCTAATTAATT
Found at i:16276093 original size:107 final size:106
Alignment explanation
Indices: 16275880--16276095 Score: 245
Period size: 107 Copynumber: 2.0 Consensus size: 106
16275870 TAAATCATTA
* **
16275880 GGCCTAATTAATTAAATTATTTAATTAAGTCCTTGGGCCTAATTAATTAAATTACACAATTAAGT
1 GGCCTAATTAATTAAATTATTTAATTAAATCCTTAAGCCTAATTAATTAAATTACACAATTAAGT
* ***** *
16275945 TATTGGGTCTAATTGATTAAATTTGTTTGATTAAGTCATTG
66 TATTGGGCCTAATTGATTAAATTTAAACAATTAAGTAATTG
* ** * ****
16275986 GGCCTAATTGATTAAAATTATTTAATTAAATTGTTAAGCTTAATTAATTAAATTGTTTAATTAAG
1 GGCCTAATTAATT-AAATTATTTAATTAAATCCTTAAGCCTAATTAATTAAATTACACAATTAAG
16276051 TTATTGGGCCTAATTGATTAAA-TTAAACAATTAAGCTAATTG
65 TTATTGGGCCTAATTGATTAAATTTAAACAATTAAG-TAATTG
16276093 GGC
1 GGC
16276096 TTCTTAAGGA
Statistics
Matches: 90, Mismatches: 18, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
106 20 0.22
107 70 0.78
ACGTcount: A:0.36, C:0.08, G:0.14, T:0.42
Consensus pattern (106 bp):
GGCCTAATTAATTAAATTATTTAATTAAATCCTTAAGCCTAATTAATTAAATTACACAATTAAGT
TATTGGGCCTAATTGATTAAATTTAAACAATTAAGTAATTG
Found at i:16277355 original size:2 final size:2
Alignment explanation
Indices: 16277343--16277373 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
16277333 ACATATTTAC
*
16277343 AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
16277374 CCATCATCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:16277434 original size:20 final size:20
Alignment explanation
Indices: 16277377--16277439 Score: 101
Period size: 20 Copynumber: 3.2 Consensus size: 20
16277367 ATATATACCA
*
16277377 TCATCATCATC-TCACCAAC
1 TCATCATCATCATCACCAGC
*
16277396 CCATCATCATCATCACCAGC
1 TCATCATCATCATCACCAGC
16277416 TCATCATCATCATCACCAGC
1 TCATCATCATCATCACCAGC
16277436 TCAT
1 TCAT
16277440 GCGCACTCCC
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
19 10 0.25
20 30 0.75
ACGTcount: A:0.30, C:0.41, G:0.03, T:0.25
Consensus pattern (20 bp):
TCATCATCATCATCACCAGC
Found at i:16277486 original size:43 final size:43
Alignment explanation
Indices: 16277438--16277547 Score: 159
Period size: 43 Copynumber: 2.6 Consensus size: 43
16277428 TCACCAGCTC
** * *
16277438 ATGCGCACTCCCTACTCGCACATGGCTAGGTCATCAC-CGGGTT
1 ATGCGCACTCCCTACTCGCACATAACCAGGTCATC-CTCGGCTT
*
16277481 ATGCGCACTCCCTACTCGCACATAACCGGGTCATCCTCGGCTT
1 ATGCGCACTCCCTACTCGCACATAACCAGGTCATCCTCGGCTT
16277524 ATGCGCACTCCCTACTCGCACATA
1 ATGCGCACTCCCTACTCGCACATA
16277548 GCCGAGTCAA
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
42 1 0.02
43 60 0.98
ACGTcount: A:0.20, C:0.38, G:0.19, T:0.23
Consensus pattern (43 bp):
ATGCGCACTCCCTACTCGCACATAACCAGGTCATCCTCGGCTT
Found at i:16286031 original size:19 final size:19
Alignment explanation
Indices: 16286007--16286044 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
16285997 CCATTTAACT
*
16286007 TATTGGAGTATGATTTGAG
1 TATTGGAGTATAATTTGAG
16286026 TATTGGAGTATAATTTGAG
1 TATTGGAGTATAATTTGAG
16286045 GGTTTGGCAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.42
Consensus pattern (19 bp):
TATTGGAGTATAATTTGAG
Found at i:16288667 original size:15 final size:16
Alignment explanation
Indices: 16288647--16288687 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 16
16288637 CAGAGATTTT
16288647 GATTTTAAAG-CTTTG
1 GATTTTAAAGTCTTTG
*
16288662 GATTTTAAAGTTTTTG
1 GATTTTAAAGTCTTTG
16288678 G-TTTTAAAGT
1 GATTTTAAAGT
16288688 TGTTTTAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 19 0.79
16 5 0.21
ACGTcount: A:0.27, C:0.02, G:0.20, T:0.51
Consensus pattern (16 bp):
GATTTTAAAGTCTTTG
Found at i:16288688 original size:15 final size:15
Alignment explanation
Indices: 16288643--16288688 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
16288633 AGATCAGAGA
*
16288643 TTTTGATTTTAAAG-
1 TTTTGGTTTTAAAGT
*
16288657 CTTTGGATTTTAAAGT
1 TTTTGG-TTTTAAAGT
16288673 TTTTGGTTTTAAAGT
1 TTTTGGTTTTAAAGT
16288688 T
1 T
16288689 GTTTTAAGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
14 4 0.15
15 18 0.67
16 5 0.19
ACGTcount: A:0.24, C:0.02, G:0.17, T:0.57
Consensus pattern (15 bp):
TTTTGGTTTTAAAGT
Found at i:16305264 original size:19 final size:19
Alignment explanation
Indices: 16305200--16305252 Score: 106
Period size: 19 Copynumber: 2.8 Consensus size: 19
16305190 TTAATATTTT
16305200 AATATTATTTTATTAATAA
1 AATATTATTTTATTAATAA
16305219 AATATTATTTTATTAATAA
1 AATATTATTTTATTAATAA
16305238 AATATTATTTTATTA
1 AATATTATTTTATTA
16305253 TGAAAATTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
AATATTATTTTATTAATAA
Found at i:16307402 original size:35 final size:35
Alignment explanation
Indices: 16307336--16307481 Score: 151
Period size: 35 Copynumber: 4.2 Consensus size: 35
16307326 CACTTGATTA
* *
16307336 AAATTTTTTAATTAAG---TTGTGCCTAATTAATT
1 AAATTATTTAATTAAGTCATTGGGCCTAATTAATT
*
16307368 AAATTATTTAATTAAATCATTGGGCCTAATTAATT
1 AAATTATTTAATTAAGTCATTGGGCCTAATTAATT
* *
16307403 AAATT-TCTTAATTAAGTTATTGGG--TATATTGATT
1 AAATTAT-TTAATTAAGTCATTGGGCCTA-ATTAATT
* *
16307437 AAATTTGTTTAATTAAGTCATTGGGCCTAATTGATT
1 AAA-TTATTTAATTAAGTCATTGGGCCTAATTAATT
16307473 AAAATTATT
1 -AAATTATT
16307482 GAGCTTAATT
Statistics
Matches: 96, Mismatches: 8, Indels: 16
0.80 0.07 0.13
Matches are distributed among these distances:
32 14 0.15
33 2 0.02
34 10 0.10
35 53 0.55
36 12 0.12
37 5 0.05
ACGTcount: A:0.36, C:0.06, G:0.12, T:0.47
Consensus pattern (35 bp):
AAATTATTTAATTAAGTCATTGGGCCTAATTAATT
Found at i:16307502 original size:22 final size:22
Alignment explanation
Indices: 16307445--16307503 Score: 64
Period size: 23 Copynumber: 2.6 Consensus size: 22
16307435 TTAAATTTGT
* * *
16307445 TTAATTAAGTCATTGGGCCTAA
1 TTAATTAAATTATTGAGCCTAA
* *
16307467 TTGATTAAAATTATTGAGCTTAA
1 TTAATT-AAATTATTGAGCCTAA
16307490 TTAATTAAATTATT
1 TTAATTAAATTATT
16307504 TAATTAAGTT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
22 13 0.43
23 17 0.57
ACGTcount: A:0.37, C:0.07, G:0.12, T:0.44
Consensus pattern (22 bp):
TTAATTAAATTATTGAGCCTAA
Found at i:16307544 original size:35 final size:35
Alignment explanation
Indices: 16307477--16307556 Score: 97
Period size: 35 Copynumber: 2.3 Consensus size: 35
16307467 TTGATTAAAA
* * ***
16307477 TTATTGAGCTTAATTAATTAAATTATTTAATTAAG
1 TTATTGGGCCTAATTAATTAAATTAAACAATTAAG
*
16307512 TTATTGGGCCTAATTGATTAAATTAAACAATTAAG
1 TTATTGGGCCTAATTAATTAAATTAAACAATTAAG
16307547 TTAATTGGGC
1 TT-ATTGGGC
16307557 TTCTTAAGGA
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
35 31 0.82
36 7 0.18
ACGTcount: A:0.38, C:0.06, G:0.14, T:0.42
Consensus pattern (35 bp):
TTATTGGGCCTAATTAATTAAATTAAACAATTAAG
Found at i:16309258 original size:19 final size:19
Alignment explanation
Indices: 16309209--16309258 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
16309199 GCTATAAATA
*
16309209 TCTTCTCCTTCCAGCAGCT
1 TCTTCTTCTTCCAGCAGCT
*
16309228 TCTTCAAT-TTCCAGCAGCT
1 TCTTC-TTCTTCCAGCAGCT
16309247 TCTTCTTCTTCC
1 TCTTCTTCTTCC
16309259 TCCTTCCATC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 1 0.04
19 25 0.96
ACGTcount: A:0.12, C:0.38, G:0.08, T:0.42
Consensus pattern (19 bp):
TCTTCTTCTTCCAGCAGCT
Found at i:16310163 original size:38 final size:39
Alignment explanation
Indices: 16310121--16310223 Score: 127
Period size: 38 Copynumber: 2.6 Consensus size: 39
16310111 ATAGTGCCCG
* * *
16310121 TGTGCACGATGTGGGGGGATGCACACGATGGCACTAAC-
1 TGTGCACGATGTGGGGGGATGCACACAATGACACCAACA
* * * *
16310159 TGTGCATGATGTAGGGGGATGCACACAATGACTCCAGCTA
1 TGTGCACGATGTGGGGGGATGCACACAATGACACCAAC-A
16310199 TGTGCACGATGTGGGGGGATGCACA
1 TGTGCACGATGTGGGGGGATGCACA
16310224 TGAGCTGGGT
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
38 31 0.57
40 23 0.43
ACGTcount: A:0.24, C:0.19, G:0.36, T:0.20
Consensus pattern (39 bp):
TGTGCACGATGTGGGGGGATGCACACAATGACACCAACA
Found at i:16311703 original size:14 final size:14
Alignment explanation
Indices: 16311680--16311715 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
16311670 ATTTAGTTAC
*
16311680 ATATACATACATAT
1 ATATATATACATAT
*
16311694 GTATATATACATAT
1 ATATATATACATAT
16311708 ATATATAT
1 ATATATAT
16311716 CTATATTCAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.42
Consensus pattern (14 bp):
ATATATATACATAT
Found at i:16318676 original size:28 final size:28
Alignment explanation
Indices: 16318622--16318676 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
16318612 GACAATTGCT
* *
16318622 GGGGTGAAAAATTTACCGATTTGCCCCC
1 GGGGTGAAAAAATTACCGATTTACCCCC
16318650 GGGGTGAAAAAATTA-CGATTTTACCCC
1 GGGGTGAAAAAATTACCGA-TTTACCCC
16318677 TATACTCCGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 3 0.12
28 21 0.88
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.25
Consensus pattern (28 bp):
GGGGTGAAAAAATTACCGATTTACCCCC
Found at i:16324404 original size:14 final size:15
Alignment explanation
Indices: 16324385--16324416 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
16324375 AATTTTCTAA
16324385 TTCCTGCTT-CCTGG
1 TTCCTGCTTCCCTGG
16324399 TTCCTGCTTCCCTGG
1 TTCCTGCTTCCCTGG
16324414 TTC
1 TTC
16324417 TTGCCATCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.00, C:0.38, G:0.19, T:0.44
Consensus pattern (15 bp):
TTCCTGCTTCCCTGG
Found at i:16326889 original size:18 final size:18
Alignment explanation
Indices: 16326843--16326889 Score: 60
Period size: 17 Copynumber: 2.6 Consensus size: 18
16326833 TTTATGAGAA
*
16326843 AAATATGAATTTATAAAAT
1 AAAT-TGAAATTATAAAAT
*
16326862 AAA-TGGAATTATAAAAT
1 AAATTGAAATTATAAAAT
16326879 AAATTGAAATT
1 AAATTGAAATT
16326890 TTTATAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
17 15 0.62
18 6 0.25
19 3 0.12
ACGTcount: A:0.57, C:0.00, G:0.09, T:0.34
Consensus pattern (18 bp):
AAATTGAAATTATAAAAT
Found at i:16327888 original size:28 final size:27
Alignment explanation
Indices: 16327857--16327910 Score: 81
Period size: 28 Copynumber: 2.0 Consensus size: 27
16327847 ATTTGGAGTA
*
16327857 TAGGGGTAAAATGGTAATTTTGCCACCC
1 TAGGGGCAAAATGGTAATTTT-CCACCC
*
16327885 TAGGGGCAAAATTGTAATTTTCCACC
1 TAGGGGCAAAATGGTAATTTTCCACC
16327911 ACCAGGACAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 5 0.21
28 19 0.79
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.30
Consensus pattern (27 bp):
TAGGGGCAAAATGGTAATTTTCCACCC
Found at i:16334505 original size:19 final size:19
Alignment explanation
Indices: 16334483--16334520 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
16334473 CCATTTGACT
16334483 TATTGGAGTATGATTTGAG
1 TATTGGAGTATGATTTGAG
16334502 TATTGGAGTATGATTTGAG
1 TATTGGAGTATGATTTGAG
16334521 ATTTAGAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.00, G:0.32, T:0.42
Consensus pattern (19 bp):
TATTGGAGTATGATTTGAG
Found at i:16334596 original size:28 final size:28
Alignment explanation
Indices: 16334563--16334637 Score: 123
Period size: 28 Copynumber: 2.7 Consensus size: 28
16334553 ATTTGAAGTA
16334563 TAGGGGTAAAATGGTAATTTTGCCACCC
1 TAGGGGTAAAATGGTAATTTTGCCACCC
16334591 TAGGGGTAAAATGGTAATTTTGCCACCC
1 TAGGGGTAAAATGGTAATTTTGCCACCC
* * *
16334619 CAGGGGCAAAATTGTAATT
1 TAGGGGTAAAATGGTAATT
16334638 GTCCACCACC
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 44 1.00
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.28
Consensus pattern (28 bp):
TAGGGGTAAAATGGTAATTTTGCCACCC
Found at i:16334649 original size:28 final size:28
Alignment explanation
Indices: 16334564--16334650 Score: 122
Period size: 28 Copynumber: 3.1 Consensus size: 28
16334554 TTTGAAGTAT
*
16334564 AGGGGTAAAATGGTAATTTTGCCACCCT
1 AGGGGTAAAATGGTAATTTTGCCACCCC
16334592 AGGGGTAAAATGGTAATTTTGCCACCCC
1 AGGGGTAAAATGGTAATTTTGCCACCCC
* * *
16334620 AGGGGCAAAATTGTAATTGT-CCACCACC
1 AGGGGTAAAATGGTAATTTTGCCACC-CC
16334648 AGG
1 AGG
16334651 ACATTTTTCT
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 5 0.09
28 49 0.91
ACGTcount: A:0.30, C:0.21, G:0.25, T:0.24
Consensus pattern (28 bp):
AGGGGTAAAATGGTAATTTTGCCACCCC
Found at i:16361336 original size:38 final size:40
Alignment explanation
Indices: 16361293--16361395 Score: 120
Period size: 38 Copynumber: 2.6 Consensus size: 40
16361283 ATAGTGCCCG
* *
16361293 TGTGCACGATGTGGGGGGATGTACACAATGGC-ACTGAT-
1 TGTGCATGATGTGGGGGGATGTACACAATGGCGACAGATA
* * ** * *
16361331 TGTGCATGATTTGGGGGGATGCACATGATGGCGCCAGCTA
1 TGTGCATGATGTGGGGGGATGTACACAATGGCGACAGATA
16361371 TGTGCATGATGTGGGGGGATGTACA
1 TGTGCATGATGTGGGGGGATGTACA
16361396 TGAGCCGGGT
Statistics
Matches: 53, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
38 27 0.51
39 3 0.06
40 23 0.43
ACGTcount: A:0.21, C:0.15, G:0.39, T:0.25
Consensus pattern (40 bp):
TGTGCATGATGTGGGGGGATGTACACAATGGCGACAGATA
Found at i:16366127 original size:24 final size:20
Alignment explanation
Indices: 16366074--16366123 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
16366064 TTAACTGGAA
16366074 AAAATAAATAGAGATTAATG
1 AAAATAAATAGAGATTAATG
16366094 AAAATAAATAGAGATTAATG
1 AAAATAAATAGAGATTAATG
16366114 AAAATAAATA
1 AAAATAAATA
16366124 AATAAATAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.64, C:0.00, G:0.12, T:0.24
Consensus pattern (20 bp):
AAAATAAATAGAGATTAATG
Found at i:16374826 original size:40 final size:38
Alignment explanation
Indices: 16374771--16374872 Score: 141
Period size: 38 Copynumber: 2.6 Consensus size: 38
16374761 ATCCAACTCA
*
16374771 TGTGCATCCCCCCACATCGTGCACATAGCTAGAGTCATCG
1 TGTGCATCCCCCCACATCGTGCACA-AGC-AGAGCCATCG
* * *
16374811 TGTGCATCCCCCCACATCATGCACAATCAGTGCCATCG
1 TGTGCATCCCCCCACATCGTGCACAAGCAGAGCCATCG
*
16374849 TGTACATCCCCCCACATCGTGCAC
1 TGTGCATCCCCCCACATCGTGCAC
16374873 CCGAACACTA
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
38 30 0.54
39 2 0.04
40 24 0.43
ACGTcount: A:0.23, C:0.39, G:0.17, T:0.22
Consensus pattern (38 bp):
TGTGCATCCCCCCACATCGTGCACAAGCAGAGCCATCG
Found at i:16377559 original size:37 final size:36
Alignment explanation
Indices: 16377509--16377627 Score: 175
Period size: 37 Copynumber: 3.2 Consensus size: 36
16377499 AATGCGATAT
*
16377509 CATCATCATGTGTGCACTCCTTACTCGCACACTACAA
1 CATCATCATGTGTGCACTCCCTACTCGCACACT-CAA
*
16377546 CATCATCATGTGTGCACTCCCTACTCTCACACTCTAA
1 CATCATCATGTGTGCACTCCCTACTCGCACACTC-AA
* *
16377583 CATTATCATGTGTGTACTCCCTACTCGCACACTTCAA
1 CATCATCATGTGTGCACTCCCTACTCGCACAC-TCAA
16377620 CATCATCA
1 CATCATCA
16377628 CACAACATTA
Statistics
Matches: 74, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
36 1 0.01
37 71 0.96
38 2 0.03
ACGTcount: A:0.26, C:0.35, G:0.09, T:0.29
Consensus pattern (36 bp):
CATCATCATGTGTGCACTCCCTACTCGCACACTCAA
Found at i:16378481 original size:20 final size:20
Alignment explanation
Indices: 16378456--16378493 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
16378446 GAAGAAGAAG
*
16378456 AAGCTGCTGGAGAAATGAAA
1 AAGCTGCTGGAAAAATGAAA
16378476 AAGCTGCTGGAAAAATGA
1 AAGCTGCTGGAAAAATGA
16378494 TACTTATAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.11, G:0.29, T:0.16
Consensus pattern (20 bp):
AAGCTGCTGGAAAAATGAAA
Found at i:16381115 original size:37 final size:36
Alignment explanation
Indices: 16381042--16381115 Score: 94
Period size: 37 Copynumber: 2.0 Consensus size: 36
16381032 TTTGATCAAA
* * *
16381042 ATTCAATATAATGCCTTTTATGGATCAAGCATAACC
1 ATTCAATACAATGCCTTTTATGGATAAAGCACAACC
* *
16381078 ATTCAATACAATGCCTTTTTATGGTTAAAGTACAACC
1 ATTCAATACAATGCC-TTTTATGGATAAAGCACAACC
16381115 A
1 A
16381116 CTCTACTTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
36 14 0.44
37 18 0.56
ACGTcount: A:0.36, C:0.19, G:0.11, T:0.34
Consensus pattern (36 bp):
ATTCAATACAATGCCTTTTATGGATAAAGCACAACC
Found at i:16382209 original size:22 final size:21
Alignment explanation
Indices: 16382183--16382255 Score: 62
Period size: 22 Copynumber: 3.4 Consensus size: 21
16382173 ACTTGTGAAA
16382183 TTTACAGAAAAGTATTGAAACT
1 TTTACA-AAAAGTATTGAAACT
* *
16382205 TTTAC-AAAAGTCTTGATA-T
1 TTTACAAAAAGTATTGAAACT
*
16382224 GTTTTCATAAAAGTATT-AAGACT
1 -TTTACA-AAAAGTATTGAA-ACT
16382247 TTTACAAAA
1 TTTACAAAA
16382256 GTCTCGAGAC
Statistics
Matches: 40, Mismatches: 6, Indels: 11
0.70 0.11 0.19
Matches are distributed among these distances:
19 1 0.03
20 15 0.38
21 4 0.10
22 19 0.47
23 1 0.03
ACGTcount: A:0.42, C:0.10, G:0.11, T:0.37
Consensus pattern (21 bp):
TTTACAAAAAGTATTGAAACT
Found at i:16382213 original size:20 final size:20
Alignment explanation
Indices: 16382190--16382257 Score: 66
Period size: 20 Copynumber: 3.3 Consensus size: 20
16382180 AAATTTACAG
16382190 AAAAGTATTGAAACTTTTAC
1 AAAAGTATTGAAACTTTTAC
* ** *
16382210 AAAAGTCTTGATATGTTTTCAT
1 AAAAGTATTGA-AACTTTT-AC
16382232 AAAAGTATT-AAGACTTTTAC
1 AAAAGTATTGAA-ACTTTTAC
16382252 AAAAGT
1 AAAAGT
16382258 CTCGAGACTT
Statistics
Matches: 37, Mismatches: 8, Indels: 6
0.73 0.16 0.12
Matches are distributed among these distances:
20 18 0.49
21 10 0.27
22 9 0.24
ACGTcount: A:0.43, C:0.09, G:0.12, T:0.37
Consensus pattern (20 bp):
AAAAGTATTGAAACTTTTAC
Found at i:16387095 original size:11 final size:11
Alignment explanation
Indices: 16387079--16387117 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
16387069 AATTTAGCGA
*
16387079 TTTTTTTTTTC
1 TTTTTTTTTCC
16387090 -TTTTTTTTCC
1 TTTTTTTTTCC
*
16387100 TTCTTTTTTCC
1 TTTTTTTTTCC
16387111 TTTTTTT
1 TTTTTTT
16387118 AATAGAAACC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
10 9 0.38
11 15 0.62
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTTTTTTCC
Found at i:16387861 original size:17 final size:18
Alignment explanation
Indices: 16387839--16387877 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
16387829 CGTGCTTTTT
16387839 CTTTTTCTTTCTTC-CTC
1 CTTTTTCTTTCTTCTCTC
*
16387856 CTTTTTTTTTCTTCTCTC
1 CTTTTTCTTTCTTCTCTC
16387874 CTTT
1 CTTT
16387878 GCCCAAAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (18 bp):
CTTTTTCTTTCTTCTCTC
Found at i:16389683 original size:22 final size:21
Alignment explanation
Indices: 16389644--16389684 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
16389634 CCTAGGTGGA
*
16389644 AAAATTCAAGGGAAAAGTGTG
1 AAAATTCAAGGAAAAAGTGTG
*
16389665 AAAATTCACGGAAACAAGTG
1 AAAATTCAAGGAAA-AAGTG
16389685 AAAAAAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.49, C:0.10, G:0.24, T:0.17
Consensus pattern (21 bp):
AAAATTCAAGGAAAAAGTGTG
Found at i:16389689 original size:21 final size:20
Alignment explanation
Indices: 16389642--16389689 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
16389632 ACCCTAGGTG
*
16389642 GAAAAATTCAAGGGAAAAGT
1 GAAAAATTCAAGGAAAAAGT
* *
16389662 GTGAAAATTCACGGAAACAAGT
1 G-AAAAATTCAAGGAAA-AAGT
16389684 GAAAAA
1 GAAAAA
16389690 AAAATAAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
20 1 0.05
21 16 0.73
22 5 0.23
ACGTcount: A:0.54, C:0.08, G:0.23, T:0.15
Consensus pattern (20 bp):
GAAAAATTCAAGGAAAAAGT
Found at i:16392396 original size:21 final size:23
Alignment explanation
Indices: 16392355--16392396 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
16392345 ATCCTTGCAA
*
16392355 TAATACTTGTACTTACTTGATCG
1 TAATACTTGTACTTACATGATCG
16392378 TAATACTT-T-CTTACATGAT
1 TAATACTTGTACTTACATGAT
16392397 TGGCAAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 9 0.50
22 1 0.06
23 8 0.44
ACGTcount: A:0.29, C:0.17, G:0.10, T:0.45
Consensus pattern (23 bp):
TAATACTTGTACTTACATGATCG
Found at i:16394546 original size:35 final size:34
Alignment explanation
Indices: 16394455--16394552 Score: 135
Period size: 34 Copynumber: 2.9 Consensus size: 34
16394445 CATTATGAAA
* * *
16394455 AATACTTTTTCAAA-GCTCAAGCATAACCTTTAC
1 AATACCTTTTCAAAGGATCAAGCACAACCTTTAC
*
16394488 AATGCCTTTTCAAAGGATCAAGCACAACCTTTAC
1 AATACCTTTTCAAAGGATCAAGCACAACCTTTAC
*
16394522 AATACCTTTTCACAAGGATGAAGCACAACCT
1 AATACCTTTTCA-AAGGATCAAGCACAACCT
16394553 CTCTACCGTT
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
33 12 0.21
34 28 0.49
35 17 0.30
ACGTcount: A:0.37, C:0.26, G:0.10, T:0.28
Consensus pattern (34 bp):
AATACCTTTTCAAAGGATCAAGCACAACCTTTAC
Found at i:16397158 original size:19 final size:19
Alignment explanation
Indices: 16397134--16397171 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
16397124 CCATTTGACT
*
16397134 TATTGGAGTATGATTTGAG
1 TATTGGAGTATAATTTGAG
16397153 TATTGGAGTATAATTTGAG
1 TATTGGAGTATAATTTGAG
16397172 GGTTTGGTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.42
Consensus pattern (19 bp):
TATTGGAGTATAATTTGAG
Found at i:16402248 original size:34 final size:33
Alignment explanation
Indices: 16402126--16402248 Score: 79
Period size: 34 Copynumber: 3.5 Consensus size: 33
16402116 TGTGCTTTGT
**
16402126 ATGGGATCAACCATTAAACCTTCACAATGGCCTTTC
1 ATGGG-TCAACCA--AAACCTTCACAATGGTTTTTC
*
16402162 ATAGGAGT-AACCAACAACCCTT-ACAGTGGTTTTTC
1 AT-GG-GTCAACCAA-AA-CCTTCACAATGGTTTTTC
* ** * *
16402197 ACAGACTCAATCGAAACCTTCACAATGGTTTTTC
1 A-TGGGTCAACCAAAACCTTCACAATGGTTTTTC
16402231 ATGGGTTCAACCAAAACC
1 ATGGG-TCAACCAAAACC
16402249 CTTAACAACA
Statistics
Matches: 65, Mismatches: 14, Indels: 18
0.67 0.14 0.19
Matches are distributed among these distances:
33 5 0.08
34 27 0.42
35 18 0.28
36 11 0.17
37 3 0.05
38 1 0.02
ACGTcount: A:0.33, C:0.26, G:0.15, T:0.27
Consensus pattern (33 bp):
ATGGGTCAACCAAAACCTTCACAATGGTTTTTC
Found at i:16405080 original size:73 final size:73
Alignment explanation
Indices: 16405017--16405178 Score: 202
Period size: 73 Copynumber: 2.2 Consensus size: 73
16405007 TGTTAGTGAG
* *
16405017 CAATTAGTCGACTAACTT-CTTTCTTAGTCGATTAAGTTGTTTTTGTCTTGAAGTCCAGATTTCT
1 CAATTAGTCGACTAACTTAC-TTCTTAGTCAATTAAGTTGGTTTTGTCTTGAAGTCCAGATTTCT
16405081 GACAGTAGA
65 GACAGTAGA
** * * *
16405090 CTTTTAGTTGACTAACTTACTTCTTGGTCAATTAAGTTGGTTTTGTCTTGAAGTCCAAATTTCTT
1 CAATTAGTCGACTAACTTACTTCTTAGTCAATTAAGTTGGTTTTGTCTTGAAGTCCAGATTTC-T
16405155 G-CAGTAGA
65 GACAGTAGA
** *
16405163 CTCTTAGTTGACTAAC
1 CAATTAGTCGACTAAC
16405179 CCATTTCTTG
Statistics
Matches: 79, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
73 76 0.96
74 3 0.04
ACGTcount: A:0.24, C:0.17, G:0.17, T:0.42
Consensus pattern (73 bp):
CAATTAGTCGACTAACTTACTTCTTAGTCAATTAAGTTGGTTTTGTCTTGAAGTCCAGATTTCTG
ACAGTAGA
Found at i:16405199 original size:73 final size:73
Alignment explanation
Indices: 16405036--16405199 Score: 231
Period size: 73 Copynumber: 2.2 Consensus size: 73
16405026 GACTAACTTC
* * * *
16405036 TTTCTTAGTCGATTAAGTTGTTTTTGTCTTGAAGTCCAGATTTCTGACAGTAGACTTTTAGTTGA
1 TTTCTTGGTCGATTAAGTTGGTTTTGTCTTGAAGTCCAAATTTCTGACAGTAGACTCTTAGTTGA
**
16405101 CTAACTTA
66 CTAACCCA
* *
16405109 CTTCTTGGTCAATTAAGTTGGTTTTGTCTTGAAGTCCAAATTTCTTG-CAGTAGACTCTTAGTTG
1 TTTCTTGGTCGATTAAGTTGGTTTTGTCTTGAAGTCCAAATTTC-TGACAGTAGACTCTTAGTTG
16405173 ACTAACCCA
65 ACTAACCCA
*
16405182 TTTCTTGGTCGACTAAGT
1 TTTCTTGGTCGATTAAGT
16405200 CTTTTCTATT
Statistics
Matches: 79, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
73 77 0.97
74 2 0.03
ACGTcount: A:0.23, C:0.16, G:0.18, T:0.43
Consensus pattern (73 bp):
TTTCTTGGTCGATTAAGTTGGTTTTGTCTTGAAGTCCAAATTTCTGACAGTAGACTCTTAGTTGA
CTAACCCA
Found at i:16407770 original size:35 final size:36
Alignment explanation
Indices: 16407723--16407858 Score: 127
Period size: 35 Copynumber: 3.9 Consensus size: 36
16407713 CTGAATCCAA
*
16407723 CAGCAAGACTCTTTC-TTTTTCCCTCTCAAAATTGG
1 CAGCAAGTCTCTTTCATTTTTCCCTCTCAAAATTGG
* * * *
16407758 TAGCAAGTCTCTTTC-TTTTTTCGTCTCAAAATTGA
1 CAGCAAGTCTCTTTCATTTTTCCCTCTCAAAATTGG
* ** *
16407793 CAGCAA-TTTCCCTCATTTTTCCCTCTCAAAATCGG
1 CAGCAAGTCTCTTTCATTTTTCCCTCTCAAAATTGG
* * *
16407828 CAACAAGT-TCTCTTCTTTTTTCCCTCACAAA
1 CAGCAAGTCTCT-TTCATTTTTCCCTCTCAAA
16407859 CGAGCAGCCA
Statistics
Matches: 80, Mismatches: 18, Indels: 5
0.78 0.17 0.05
Matches are distributed among these distances:
34 5 0.06
35 58 0.73
36 17 0.21
ACGTcount: A:0.24, C:0.29, G:0.09, T:0.39
Consensus pattern (36 bp):
CAGCAAGTCTCTTTCATTTTTCCCTCTCAAAATTGG
Found at i:16409440 original size:7 final size:7
Alignment explanation
Indices: 16409428--16409453 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
16409418 GATTTAATTC
16409428 TTTTTAT
1 TTTTTAT
16409435 TTTTTAT
1 TTTTTAT
16409442 TTTTTAT
1 TTTTTAT
16409449 TTTTT
1 TTTTT
16409454 TTTCTTAACG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTAT
Found at i:16415543 original size:35 final size:34
Alignment explanation
Indices: 16415471--16415605 Score: 119
Period size: 35 Copynumber: 3.9 Consensus size: 34
16415461 TGAATCTGAC
* *
16415471 AGCAAGACTCTTTCTTTTTCCCTCTCAAAACTAGT
1 AGCAAGTCTCTTTCTTTTTCCCTCTCAAAAC-GGT
16415506 AGCAAGTCTCTTTCTTTTTCCCTCTCAAAATCGGT
1 AGCAAGTCTCTTTCTTTTTCCCTCTCAAAA-CGGT
* ** * * *
16415541 AGCAA-TTTCCCTCATATCTCCCTCTCAAAACCGGC
1 AGCAAGTCTCTTTC-TTTTTCCCTCTCAAAA-CGGT
* * *
16415576 AACAAGTTCTCTTCCTTTTTCCCTCACAAA
1 AGCAAG-TCTCTTTCTTTTTCCCTCTCAAA
16415606 CCAGTAGCCA
Statistics
Matches: 79, Mismatches: 17, Indels: 7
0.77 0.17 0.07
Matches are distributed among these distances:
34 5 0.06
35 57 0.72
36 13 0.16
37 4 0.05
ACGTcount: A:0.24, C:0.33, G:0.08, T:0.35
Consensus pattern (34 bp):
AGCAAGTCTCTTTCTTTTTCCCTCTCAAAACGGT
Found at i:16420940 original size:28 final size:29
Alignment explanation
Indices: 16420899--16420958 Score: 68
Period size: 30 Copynumber: 2.1 Consensus size: 29
16420889 GTCTATGGGC
*
16420899 AATTTTTCAATTTT-TGGGGCAAAAATGT
1 AATTTTTCAATTTTAGGGGGCAAAAATGT
* * *
16420927 AATTTTTGACTTTTACGGGGGCAAAAGTGT
1 AATTTTTCAATTTTA-GGGGGCAAAAATGT
16420957 AA
1 AA
16420959 ATTTCAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 12 0.46
30 14 0.54
ACGTcount: A:0.32, C:0.08, G:0.22, T:0.38
Consensus pattern (29 bp):
AATTTTTCAATTTTAGGGGGCAAAAATGT
Found at i:16435921 original size:45 final size:45
Alignment explanation
Indices: 16435856--16436121 Score: 212
Period size: 45 Copynumber: 5.5 Consensus size: 45
16435846 CATATCATCA
*
16435856 TCATCATCATCATCATGTGCACTCCCTACATCCGCACATAG-TGGGG
1 TCATCATCAGC-TCATGTGCACTCCCTACATCCGCACATAGCT-GGG
* * **
16435902 TCATCATCAGCTCATGTGCACTCTCTACATCCGCACATAGGTAGAA
1 TCATCATCAGCTCATGTGCACTCCCTACATCCGCACATAGCT-GGG
* *
16435948 TCCCCCACCAGTCCTCAGCTCATGTGCACTCCCTACATCTGCACATAGCTGGG
1 T-------CA-TCATCAGCTCATGTGCACTCCCTACATCCGCACATAGCTGGG
* * **
16436001 TCATCATTAGCTCATGTGCACTCCCTATATCCGCACATAGCTAGAA
1 TCATCATCAGCTCATGTGCACTCCCTACATCCGCACATAGCT-GGG
*
16436047 TCCTCGA-CTAGTCCTCAACTTATGTGCACTCCCTACATCCGCACATAGCTGGG
1 TCATC-ATC-AG--CT---C--ATGTGCACTCCCTACATCCGCACATAGCTGGG
*
16436100 TCATCATTAGCTCATGTGCACT
1 TCATCATCAGCTCATGTGCACT
16436122 TCTAGTTACG
Statistics
Matches: 176, Mismatches: 24, Indels: 41
0.73 0.10 0.17
Matches are distributed among these distances:
45 72 0.41
46 20 0.11
47 4 0.02
49 2 0.01
50 2 0.01
52 4 0.02
53 9 0.05
54 63 0.36
ACGTcount: A:0.24, C:0.34, G:0.16, T:0.27
Consensus pattern (45 bp):
TCATCATCAGCTCATGTGCACTCCCTACATCCGCACATAGCTGGG
Found at i:16435986 original size:99 final size:99
Alignment explanation
Indices: 16435868--16436125 Score: 403
Period size: 99 Copynumber: 2.6 Consensus size: 99
16435858 ATCATCATCA
*
16435868 TCATGTGCACTCCCTACATCCGCACATAG-TGGGGTCATCATCAGCTCATGTGCACTCTCTACAT
1 TCATGTGCACTCCCTACATCCGCACATAGCT-GGGTCATCATTAGCTCATGTGCACTCTCTACAT
* *
16435932 CCGCACATAGGTAGAATCCCCCACCAGTCCTCAGC
65 CCGCACATAGCTAGAATCCCCCACCAGTCCTCAAC
* * *
16435967 TCATGTGCACTCCCTACATCTGCACATAGCTGGGTCATCATTAGCTCATGTGCACTCCCTATATC
1 TCATGTGCACTCCCTACATCCGCACATAGCTGGGTCATCATTAGCTCATGTGCACTCTCTACATC
* * *
16436032 CGCACATAGCTAGAATCCTCGACTAGTCCTCAAC
66 CGCACATAGCTAGAATCCCCCACCAGTCCTCAAC
*
16436066 TTATGTGCACTCCCTACATCCGCACATAGCTGGGTCATCATTAGCTCATGTGCACT-TCTA
1 TCATGTGCACTCCCTACATCCGCACATAGCTGGGTCATCATTAGCTCATGTGCACTCTCTA
16436126 GTTACGGGTC
Statistics
Matches: 146, Mismatches: 12, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
98 3 0.02
99 142 0.97
100 1 0.01
ACGTcount: A:0.23, C:0.34, G:0.16, T:0.27
Consensus pattern (99 bp):
TCATGTGCACTCCCTACATCCGCACATAGCTGGGTCATCATTAGCTCATGTGCACTCTCTACATC
CGCACATAGCTAGAATCCCCCACCAGTCCTCAAC
Found at i:16435992 original size:54 final size:53
Alignment explanation
Indices: 16435908--16436096 Score: 205
Period size: 54 Copynumber: 3.7 Consensus size: 53
16435898 GGGGTCATCA
* *
16435908 TCAGCTCATGTGCACTCTCTACATCCGCACATAGGTAGAATCCCCCACCAGTCC
1 TCAGCTCATGTGCACTCCCTACATCCGCACATAGCTAGAAT-CCCCACCAGTCC
* ** *
16435962 TCAGCTCATGTGCACTCCCTACATCTGCACATAGCT-GGGT---CATCA-T--
1 TCAGCTCATGTGCACTCCCTACATCCGCACATAGCTAGAATCCCCACCAGTCC
* * *
16436008 T-AGCTCATGTGCACTCCCTATATCCGCACATAGCTAGAATCCTCGACTAGTCC
1 TCAGCTCATGTGCACTCCCTACATCCGCACATAGCTAGAATCC-CCACCAGTCC
* *
16436061 TCAACTTATGTGCACTCCCTACATCCGCACATAGCT
1 TCAGCTCATGTGCACTCCCTACATCCGCACATAGCT
16436097 GGGTCATCAT
Statistics
Matches: 110, Mismatches: 16, Indels: 18
0.76 0.11 0.12
Matches are distributed among these distances:
45 32 0.29
46 3 0.03
48 1 0.01
49 4 0.04
50 2 0.02
51 1 0.01
53 3 0.03
54 64 0.58
ACGTcount: A:0.24, C:0.35, G:0.15, T:0.26
Consensus pattern (53 bp):
TCAGCTCATGTGCACTCCCTACATCCGCACATAGCTAGAATCCCCACCAGTCC
Found at i:16441535 original size:45 final size:46
Alignment explanation
Indices: 16441462--16441548 Score: 131
Period size: 45 Copynumber: 1.9 Consensus size: 46
16441452 TTCCATATCA
* *
16441462 TCATCATCATCATCATGTGCATTCCCTACATCCACACATAGCGGGG
1 TCATCATCAGCATCATGTGCACTCCCTACATCCACACATAGCGGGG
* *
16441508 TCATCATCAGC-TCATGTGCACTCCCTACATCCGCATATAGC
1 TCATCATCAGCATCATGTGCACTCCCTACATCCACACATAGC
16441549 TAGAATCCCC
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
45 27 0.73
46 10 0.27
ACGTcount: A:0.25, C:0.34, G:0.14, T:0.26
Consensus pattern (46 bp):
TCATCATCAGCATCATGTGCACTCCCTACATCCACACATAGCGGGG
Found at i:16445838 original size:73 final size:73
Alignment explanation
Indices: 16445753--16445908 Score: 176
Period size: 73 Copynumber: 2.2 Consensus size: 73
16445743 TTTTCTGATC
* * *
16445753 CCAG-TTTTTGGTAGT-GAGCAATTAGTCAACTAACTT-CATTCTTAGTCGATTAAG-TTGTTAC
1 CCAGATTTCTGGTAGTAGA-CAATTAGTCAACTAACTTAC-TTCTTAGTCAATTAAGCTGGTT-C
16445814 TGTCTTGAAAT
63 TGTCTTGAAAT
** * *
16445825 CCAGATTTCTGGTAGTAGACTCTTAGTCGACTAACTTACTTCTTGGTCAATTAAGCTGGTTCTGT
1 CCAGATTTCTGGTAGTAGACAATTAGTCAACTAACTTACTTCTTAGTCAATTAAGCTGGTTCTGT
**
16445890 CTTGAGGT
66 CTTGAAAT
16445898 CCAGATTTCTG
1 CCAGATTTCTG
16445909 ACAGTAAACT
Statistics
Matches: 71, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
72 4 0.06
73 60 0.85
74 7 0.10
ACGTcount: A:0.23, C:0.18, G:0.20, T:0.39
Consensus pattern (73 bp):
CCAGATTTCTGGTAGTAGACAATTAGTCAACTAACTTACTTCTTAGTCAATTAAGCTGGTTCTGT
CTTGAAAT
Found at i:16445920 original size:73 final size:73
Alignment explanation
Indices: 16445774--16445932 Score: 205
Period size: 73 Copynumber: 2.2 Consensus size: 73
16445764 TAGTGAGCAA
* * * **
16445774 TTAGTCAACTAACTTCATTCTTAGTCGATTAAGTTGTTACTGTCTTGAAATCCAGATTTCTGGTA
1 TTAGTCGACTAACTTCATTCTTAGTCAATTAAGTGGTTACTGTCTTGAAATCCAGATTTCTGACA
*
16445839 GTAGACTC
66 GTAAACTC
* **
16445847 TTAGTCGACTAACTT-ACTTCTTGGTCAATTAAGCTGGTT-CTGTCTTGAGGTCCAGATTTCTGA
1 TTAGTCGACTAACTTCA-TTCTTAGTCAATTAAG-TGGTTACTGTCTTGAAATCCAGATTTCTGA
16445910 CAGTAAACTC
64 CAGTAAACTC
16445920 TTAGTCGACTAAC
1 TTAGTCGACTAAC
16445933 CCATTTCTTG
Statistics
Matches: 75, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
72 1 0.01
73 70 0.93
74 4 0.05
ACGTcount: A:0.25, C:0.19, G:0.18, T:0.38
Consensus pattern (73 bp):
TTAGTCGACTAACTTCATTCTTAGTCAATTAAGTGGTTACTGTCTTGAAATCCAGATTTCTGACA
GTAAACTC
Found at i:16447101 original size:21 final size:21
Alignment explanation
Indices: 16447075--16447118 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
16447065 TGACCTAATT
16447075 TTGAGTAAATGTAT-TGATACA
1 TTGAGTAAATGTATCT-ATACA
*
16447096 TTGAGTCAATGTATCTATACA
1 TTGAGTAAATGTATCTATACA
16447117 TT
1 TT
16447119 TCAAACAGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 20 0.95
22 1 0.05
ACGTcount: A:0.34, C:0.09, G:0.16, T:0.41
Consensus pattern (21 bp):
TTGAGTAAATGTATCTATACA
Found at i:16459788 original size:43 final size:43
Alignment explanation
Indices: 16459707--16459831 Score: 139
Period size: 43 Copynumber: 2.9 Consensus size: 43
16459697 CATTGACTCG
*
16459707 GCTATGTGCGAGTAGGGAGTGCGCATAGATC-GAG-GATGACCC-
1 GCTATGTGCGAGTAGGGAGTGCGCATA-ACCTG-GTGATGACCCA
* *
16459749 GATTATGTACGAGTAGGGAGTGCGCATAACCTGGTGATGACCCA
1 G-CTATGTGCGAGTAGGGAGTGCGCATAACCTGGTGATGACCCA
* * * *
16459793 GCCATGTGCGAGTAAGGAGTCCGCATAAGCTGGTGATGA
1 GCTATGTGCGAGTAGGGAGTGCGCATAACCTGGTGATGA
16459832 TGATGATGGG
Statistics
Matches: 70, Mismatches: 9, Indels: 7
0.81 0.10 0.08
Matches are distributed among these distances:
42 4 0.06
43 65 0.93
44 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.35, T:0.21
Consensus pattern (43 bp):
GCTATGTGCGAGTAGGGAGTGCGCATAACCTGGTGATGACCCA
Found at i:16460169 original size:22 final size:22
Alignment explanation
Indices: 16460137--16460193 Score: 105
Period size: 22 Copynumber: 2.6 Consensus size: 22
16460127 GGCTGAAAAC
*
16460137 TCGCTGTAGCGAGGATGCATTT
1 TCGCTGCAGCGAGGATGCATTT
16460159 TCGCTGCAGCGAGGATGCATTT
1 TCGCTGCAGCGAGGATGCATTT
16460181 TCGCTGCAGCGAG
1 TCGCTGCAGCGAG
16460194 AATGACACTA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.18, C:0.23, G:0.33, T:0.26
Consensus pattern (22 bp):
TCGCTGCAGCGAGGATGCATTT
Found at i:16467362 original size:22 final size:21
Alignment explanation
Indices: 16467333--16467373 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
16467323 AGACAAGTGT
*
16467333 ATGGTGAAAATTTAGAAATAA
1 ATGGTGAAAATTTAAAAATAA
*
16467354 ATGGATGAAATTTTAAAAAT
1 ATGG-TGAAAATTTAAAAAT
16467374 GGGCCAATGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.51, C:0.00, G:0.17, T:0.32
Consensus pattern (21 bp):
ATGGTGAAAATTTAAAAATAA
Found at i:16472560 original size:54 final size:53
Alignment explanation
Indices: 16472501--16472653 Score: 252
Period size: 54 Copynumber: 2.8 Consensus size: 53
16472491 ATACTGTCCG
*
16472501 GCTATGTGCATGATGTGGTGGGATGCACATGAGTTGGGTGAGATGGGATGTCTA
1 GCTATGTGCATGATGTGGTGGGATGCACATGAGCTGGGTGAGATGGGATGTC-A
* *
16472555 GCTATGTGCACGATGTGGTGGGATGCACATGAGCTGGGTGAGATGGGATGTCC
1 GCTATGTGCATGATGTGGTGGGATGCACATGAGCTGGGTGAGATGGGATGTCA
*
16472608 GACTATGTGCATGATGTGGTCGGATGCACATGAGCTGGGTGAGATG
1 G-CTATGTGCATGATGTGGTGGGATGCACATGAGCTGGGTGAGATG
16472654 CACATGATGA
Statistics
Matches: 93, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
53 1 0.01
54 92 0.99
ACGTcount: A:0.20, C:0.12, G:0.41, T:0.27
Consensus pattern (53 bp):
GCTATGTGCATGATGTGGTGGGATGCACATGAGCTGGGTGAGATGGGATGTCA
Found at i:16480443 original size:18 final size:18
Alignment explanation
Indices: 16480420--16480550 Score: 62
Period size: 18 Copynumber: 7.4 Consensus size: 18
16480410 TGTCTCGGGG
16480420 AGAAGAAAGAGGGAAAAA
1 AGAAGAAAGAGGGAAAAA
*
16480438 AGAAGAAA-A-AG-AAAA
1 AGAAGAAAGAGGGAAAAA
* *
16480453 AGAA-AAAGAAGGAGAGAA
1 AGAAGAAAGAGGGA-AAAA
* * *
16480471 TG-AG-CAGTGGCAGAAGAAA
1 AGAAGAAAGAGG--GAA-AAA
*
16480490 AGAA-AGAGAGGGAAAAA
1 AGAAGAAAGAGGGAAAAA
* *
16480507 AGAAGAAA-AAGAAAAAGA
1 AGAAGAAAGAGGGAAAA-A
16480525 AGAAGAAAGAGAGGAAAAA
1 AGAAGAAAGAG-GGAAAAA
*
16480544 AAAAGAA
1 AGAAGAA
16480551 TAGCTAAATA
Statistics
Matches: 82, Mismatches: 17, Indels: 27
0.65 0.13 0.21
Matches are distributed among these distances:
14 3 0.04
15 9 0.11
16 2 0.02
17 18 0.22
18 27 0.33
19 13 0.16
20 10 0.12
ACGTcount: A:0.67, C:0.02, G:0.30, T:0.02
Consensus pattern (18 bp):
AGAAGAAAGAGGGAAAAA
Found at i:16480521 original size:15 final size:16
Alignment explanation
Indices: 16480503--16480534 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
16480493 AAGAGAGGGA
16480503 AAAAAGAAGAA-AAAG
1 AAAAAGAAGAAGAAAG
16480518 AAAAAGAAGAAGAAAG
1 AAAAAGAAGAAGAAAG
16480534 A
1 A
16480535 GAGGAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (16 bp):
AAAAAGAAGAAGAAAG
Found at i:16480550 original size:22 final size:21
Alignment explanation
Indices: 16480489--16480546 Score: 70
Period size: 18 Copynumber: 3.0 Consensus size: 21
16480479 GGCAGAAGAA
*
16480489 AAGAAAGAGAGG-GAAAAAAG
1 AAGAAAGAGAGGAAAAAAAAG
*
16480509 AAGAAA-A-A-GAAAAAGAAG
1 AAGAAAGAGAGGAAAAAAAAG
16480527 AAGAAAGAGAGGAAAAAAAA
1 AAGAAAGAGAGGAAAAAAAA
16480547 AGAATAGCTA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
17 1 0.03
18 13 0.42
19 2 0.06
20 7 0.23
21 8 0.26
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (21 bp):
AAGAAAGAGAGGAAAAAAAAG
Done.