Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr1
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: 106989029
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3754247 characters in sequence are not A, C, G, or T
File 121 of 322
Found at i:39551152 original size:94 final size:93
Alignment explanation
Indices: 39550997--39551168 Score: 238
Period size: 94 Copynumber: 1.8 Consensus size: 93
39550987 GTATATCGCA
* * *
39550997 AGGCCGATGCATGTCCCAGACATGTCTTACACTAGCTCTCGTCTCAATGCCGATACATGTCCCAT
1 AGGCCGATGCATGTCCCAGACATGTCTTAAACTAGCTCTCATCT-AATGCCGATACATGTCCCAG
39551062 ACATGTCTTACACTGGCTTAAATATCTTG
65 ACATGTCTTACACTGGCTTAAATATCTTG
* * ***
39551091 AGGCCGATGCATGTCCCAGACATGTCTTAAACTGGCTCTCATGCT-ATGGCTGATGTGTGTCCCA
1 AGGCCGATGCATGTCCCAGACATGTCTTAAACTAGCTCTCAT-CTAAT-GCCGATACATGTCCCA
39551155 GACATGTCTTACAC
64 GACATGTCTTACAC
39551169 CACACACATA
Statistics
Matches: 68, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
93 2 0.03
94 64 0.94
95 2 0.03
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.29
Consensus pattern (93 bp):
AGGCCGATGCATGTCCCAGACATGTCTTAAACTAGCTCTCATCTAATGCCGATACATGTCCCAGA
CATGTCTTACACTGGCTTAAATATCTTG
Found at i:39561604 original size:48 final size:47
Alignment explanation
Indices: 39561522--39561740 Score: 119
Period size: 46 Copynumber: 4.6 Consensus size: 47
39561512 TACACCACAA
* * *
39561522 GCTGATGCCATATCCC-GAACAGGTCTTACGCTAGCCTGTATATCGCGAG
1 GCTGATG-CATGTCCCAG-ACATGTCTTACACTAGCCTGTATAT-GCGAG
* * *
39561571 GCTGATGCATGTCCCAGACATGTCTTACACTAGCTCTCGTCTA---AAT
1 GCTGATGCATGTCCCAGACATGTCTTACACTAGC-CT-GTATATGCGAG
* ** * * * **
39561617 GCCGATAAATGTCCCATACATGTCTTACACTGGCTTAAATAT-CTTGAG
1 GCTGATGCATGTCCCAGACATGTCTTACACTAGCCTGTATATGC--GAG
* * * * * *
39561665 GCCGATGCATGTCCCAGACATGTCTTAAACT-GGCTCT-CATGCTATG
1 GCTGATGCATGTCCCAGACATGTCTTACACTAGCCTGTATATGCGA-G
**
39561711 GCTGATGTGTGTCCCAGACATGTCTTACAC
1 GCTGATGCATGTCCCAGACATGTCTTACAC
39561741 CACACACATA
Statistics
Matches: 130, Mismatches: 31, Indels: 21
0.71 0.17 0.12
Matches are distributed among these distances:
44 2 0.02
45 2 0.02
46 59 0.45
47 3 0.02
48 50 0.38
49 10 0.08
50 4 0.03
ACGTcount: A:0.24, C:0.27, G:0.21, T:0.29
Consensus pattern (47 bp):
GCTGATGCATGTCCCAGACATGTCTTACACTAGCCTGTATATGCGAG
Found at i:39561724 original size:94 final size:93
Alignment explanation
Indices: 39561568--39561740 Score: 231
Period size: 94 Copynumber: 1.8 Consensus size: 93
39561558 TGTATATCGC
* * *
39561568 GAGGCTGATGCATGTCCCAGACATGTCTTACACTAGCTCTCGTCTAAATGCCGATAAATGTCCCA
1 GAGGCCGATGCATGTCCCAGACATGTCTTAAACTAGCTCTCATCT-AATGCCGATAAATGTCCCA
*
39561633 TACATGTCTTACACTGGCTTAAATATCTT
65 GACATGTCTTACACTGGCTTAAATATCTT
* * ***
39561662 GAGGCCGATGCATGTCCCAGACATGTCTTAAACTGGCTCTCATGCT-ATGGCTGATGTGTGTCCC
1 GAGGCCGATGCATGTCCCAGACATGTCTTAAACTAGCTCTCAT-CTAAT-GCCGATAAATGTCCC
39561726 AGACATGTCTTACAC
64 AGACATGTCTTACAC
39561741 CACACACATA
Statistics
Matches: 68, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
93 2 0.03
94 64 0.94
95 2 0.03
ACGTcount: A:0.24, C:0.26, G:0.20, T:0.29
Consensus pattern (93 bp):
GAGGCCGATGCATGTCCCAGACATGTCTTAAACTAGCTCTCATCTAATGCCGATAAATGTCCCAG
ACATGTCTTACACTGGCTTAAATATCTT
Found at i:39569125 original size:472 final size:472
Alignment explanation
Indices: 39568241--39569185 Score: 1773
Period size: 472 Copynumber: 2.0 Consensus size: 472
39568231 TTTCTAACGT
39568241 CAGCATCCAATAAGGGGCACACGGCCAAGGCACGCGCCCATGGCCAGAGGCAGTGTCCTCCACAT
1 CAGCATCCAATAAGGGGCACACGGCCAAGGCACGCGCCCATGGCCAGAGGCAGTGTCCTCCACAT
*
39568306 GGCTGAGACACACGGCTGTGTCTCTGCCAGTGTGTTTACTACAATGCAATCTAGCTTGCAAATTT
66 GGCTGAGACACACGGCCGTGTCTCTGCCAGTGTGTTTACTACAATGCAATCTAGCTTGCAAATTT
* *
39568371 TACGTGCAGGGGACACATGGCCGAACGACACGCCCATAGGGCTGACTGTGTGTCACCCATGGTCT
131 TACATGCAGGGGACACATGGCCGAACGACACGCCCATAGGGCTGACCGTGTGTCACCCATGGTCT
* *
39568436 AGACACACGCCGTGTGTCAACCCATGTGGACAATTTAAGGCTATCTACCAAGCCTTTGCCACCCT
196 AGACACACGCCGTGTGTCAACCCATGTGGACAATATAAGGCTATCAACCAAGCCTTTGCCACCCT
39568501 GAAACAAAATCTAACATCAACCAACGCATCAAAGATTATCTTAATATGATTTCTCAACCAAACAA
261 GAAACAAAATCTAACATCAACCAACGCATCAAAGATTATCTTAATATGATTTCTCAACCAAACAA
*
39568566 CCATAGTTAAGACCTATATACATTACATATATTCAACTATGCTAACAATTTCACCTTCATGAAAG
326 CCATAGTTAAGACCTATATACATTACATATATTCAACTATGCCAACAATTTCACCTTCATGAAAG
39568631 GCTAGCTTGCATTCACATAATAACTTTTAATATTAGCCATTTTTGATGGCCTTATTCAAAATGAA
391 GCTAGCTTGCATTCACATAATAACTTTTAATATTAGCCATTTTTGATGGCCTTATTCAAAATGAA
39568696 TCAAATTCTAAAGTAAG
456 TCAAATTCTAAAGTAAG
* *
39568713 CAGCATCCAATAAGGGGCACATGGCCAAGGCACGCGCCCATGGCCAGAGGTAGTGTCCTCCACAT
1 CAGCATCCAATAAGGGGCACACGGCCAAGGCACGCGCCCATGGCCAGAGGCAGTGTCCTCCACAT
* *
39568778 GGCTGAGACACACGGCCGTGTCTCTGCCAGTGTGTTTACTACAATGCATTCTAGCTTGTAAATTT
66 GGCTGAGACACACGGCCGTGTCTCTGCCAGTGTGTTTACTACAATGCAATCTAGCTTGCAAATTT
* *
39568843 TACATGCAGGGGACACATGGCTGAACGACACGCCCATGGGGCTGACCGTGTGTCACCCATGGTCT
131 TACATGCAGGGGACACATGGCCGAACGACACGCCCATAGGGCTGACCGTGTGTCACCCATGGTCT
39568908 AGACACACGCCGTGTGTCAACCCATGTGGACAATATAAGGCTATCAACCAAGCCTTTGCCACCCT
196 AGACACACGCCGTGTGTCAACCCATGTGGACAATATAAGGCTATCAACCAAGCCTTTGCCACCCT
39568973 GAAACAAAATCTAACATCAACCAACGCATCAAAGATTATCTTAATATGATTTCTCAACCAAACAA
261 GAAACAAAATCTAACATCAACCAACGCATCAAAGATTATCTTAATATGATTTCTCAACCAAACAA
39569038 CCATAGTTAAGACCTATATACATTACATATATTCAACTATGCCAACAATTTCACCTTCATGAAAG
326 CCATAGTTAAGACCTATATACATTACATATATTCAACTATGCCAACAATTTCACCTTCATGAAAG
*
39569103 GCTAGCTTGCATTCACATAATAACTTTTAATATTTGCCATTTTTGATGGCCTTATTCAAAATGAA
391 GCTAGCTTGCATTCACATAATAACTTTTAATATTAGCCATTTTTGATGGCCTTATTCAAAATGAA
39569168 TCAAATTCTAAAGTAAG
456 TCAAATTCTAAAGTAAG
39569185 C
1 C
39569186 CAACATATTT
Statistics
Matches: 460, Mismatches: 13, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
472 460 1.00
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.26
Consensus pattern (472 bp):
CAGCATCCAATAAGGGGCACACGGCCAAGGCACGCGCCCATGGCCAGAGGCAGTGTCCTCCACAT
GGCTGAGACACACGGCCGTGTCTCTGCCAGTGTGTTTACTACAATGCAATCTAGCTTGCAAATTT
TACATGCAGGGGACACATGGCCGAACGACACGCCCATAGGGCTGACCGTGTGTCACCCATGGTCT
AGACACACGCCGTGTGTCAACCCATGTGGACAATATAAGGCTATCAACCAAGCCTTTGCCACCCT
GAAACAAAATCTAACATCAACCAACGCATCAAAGATTATCTTAATATGATTTCTCAACCAAACAA
CCATAGTTAAGACCTATATACATTACATATATTCAACTATGCCAACAATTTCACCTTCATGAAAG
GCTAGCTTGCATTCACATAATAACTTTTAATATTAGCCATTTTTGATGGCCTTATTCAAAATGAA
TCAAATTCTAAAGTAAG
Found at i:39569841 original size:48 final size:47
Alignment explanation
Indices: 39569779--39569988 Score: 180
Period size: 46 Copynumber: 4.5 Consensus size: 47
39569769 TGACGCCATA
* * * *
39569779 TCCCAGACAGGTCTTACATTAGTTTGTATATCGCGAGGCTGATGCATG
1 TCCCAGACATGTCTTACACTAGTCT-TATATCTCGAGGCTGATGCATG
* * *
39569827 TCCCAGACATGTCTTACACTAG-CTCTA-GTCTCAATG-TCGATGCATG
1 TCCCAGACATGTCTTACACTAGTCT-TATATCTCGAGGCT-GATGCATG
* * * * *
39569873 TCCTAGACATGCCTTACACT-GGCTTAAATATCTCGTGGCCGATGCATG
1 TCCCAGACATGTCTTACACTAGTCTT--ATATCTCGAGGCTGATGCATG
* * * *
39569921 TCCTAGACATGCCTTACACTAGCTCTCATAT-T-GTGGCTGATGCATG
1 TCCCAGACATGTCTTACACTAG-TCTTATATCTCGAGGCTGATGCATG
39569967 TCCCAGACATGTCTTACACTAG
1 TCCCAGACATGTCTTACACTAG
39569989 CACACATATC
Statistics
Matches: 134, Mismatches: 20, Indels: 18
0.78 0.12 0.10
Matches are distributed among these distances:
45 3 0.02
46 66 0.49
47 5 0.04
48 57 0.43
49 1 0.01
50 2 0.01
ACGTcount: A:0.23, C:0.26, G:0.20, T:0.30
Consensus pattern (47 bp):
TCCCAGACATGTCTTACACTAGTCTTATATCTCGAGGCTGATGCATG
Found at i:39569843 original size:92 final size:94
Alignment explanation
Indices: 39569673--39569846 Score: 248
Period size: 92 Copynumber: 1.9 Consensus size: 94
39569663 GGGTTAAGAT
*
39569673 GCTGACACCATATCCCAGACATGGTCTTACACTGGCTTTCATATAGCGAGGTCGATGCCATGTCC
1 GCTGACACCATATCCCAGACATGGTCTTACACTAGCTTTCATATAGCGAGGTCGATGCCATGTCC
39569738 CAGACAGGTCTTACACTGACACACCACAA
66 CAGACAGGTCTTACACTGACACACCACAA
* * * *
39569767 GCTGACGCCATATCCCAGACA-GGTCTTACATTAG-TTTGTATATCGCGAGG-CTGATG-CATGT
1 GCTGACACCATATCCCAGACATGGTCTTACACTAGCTTT-CATATAGCGAGGTC-GATGCCATGT
*
39569828 CCCAGACATGTCTTACACT
64 CCCAGACAGGTCTTACACT
39569847 AGCTCTAGTC
Statistics
Matches: 72, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
92 27 0.38
93 25 0.35
94 20 0.28
ACGTcount: A:0.26, C:0.29, G:0.20, T:0.25
Consensus pattern (94 bp):
GCTGACACCATATCCCAGACATGGTCTTACACTAGCTTTCATATAGCGAGGTCGATGCCATGTCC
CAGACAGGTCTTACACTGACACACCACAA
Found at i:39569997 original size:46 final size:46
Alignment explanation
Indices: 39569815--39569997 Score: 185
Period size: 46 Copynumber: 3.9 Consensus size: 46
39569805 TATATCGCGA
* *
39569815 GGCTGATGCATGTCCCAGACATGTCTTACACTAGCTCTAGTC-TCAATGT
1 GGCTGATGCATGTCCCAGACATGCCTTACACTAGCTC-A--CAT-ATTGT
* * * *
39569864 --C-GATGCATGTCCTAGACATGCCTTACACTGGCTTAAATATCTCGT
1 GGCTGATGCATGTCCCAGACATGCCTTACACTAGCTCACATAT-T-GT
* * *
39569909 GGCCGATGCATGTCCTAGACATGCCTTACACTAGCTCTCATATTGT
1 GGCTGATGCATGTCCCAGACATGCCTTACACTAGCTCACATATTGT
* *
39569955 GGCTGATGCATGTCCCAGACATGTCTTACACTAGCACACATAT
1 GGCTGATGCATGTCCCAGACATGCCTTACACTAGCTCACATAT
39569998 CACTCATTAT
Statistics
Matches: 113, Mismatches: 15, Indels: 15
0.79 0.10 0.10
Matches are distributed among these distances:
43 1 0.01
44 2 0.02
45 3 0.03
46 69 0.61
47 3 0.03
48 35 0.31
ACGTcount: A:0.24, C:0.27, G:0.19, T:0.30
Consensus pattern (46 bp):
GGCTGATGCATGTCCCAGACATGCCTTACACTAGCTCACATATTGT
Found at i:39569998 original size:94 final size:94
Alignment explanation
Indices: 39569819--39569998 Score: 220
Period size: 94 Copynumber: 1.9 Consensus size: 94
39569809 TCGCGAGGCT
* * * *
39569819 GATGCATGTCCCAGACATGTCTTACACTAGCTCTAGTCTCAATGTCGATGCATGTCCTAGACATG
1 GATGCATGTCCCAGACATGCCTTACACTAGCTCTAGTATCAATGGCGATGCATGTCCCAGACATG
* **
39569884 CCTTACACTGGCTTAAATATCTCGTGGCC
66 CCTTACACTAGCACAAATATCTCGTGGCC
* **
39569913 GATGCATGTCCTAGACATGCCTTACACTAGCTCTCA-TAT-TGTGGCTGATGCATGTCCCAGACA
1 GATGCATGTCCCAGACATGCCTTACACTAGCTCT-AGTATCAATGGC-GATGCATGTCCCAGACA
* *
39569976 TGTCTTACACTAGCACACATATC
64 TGCCTTACACTAGCACAAATATC
39569999 ACTCATTATC
Statistics
Matches: 72, Mismatches: 12, Indels: 4
0.82 0.14 0.05
Matches are distributed among these distances:
93 3 0.04
94 68 0.94
95 1 0.01
ACGTcount: A:0.24, C:0.28, G:0.18, T:0.29
Consensus pattern (94 bp):
GATGCATGTCCCAGACATGCCTTACACTAGCTCTAGTATCAATGGCGATGCATGTCCCAGACATG
CCTTACACTAGCACAAATATCTCGTGGCC
Found at i:39574247 original size:40 final size:40
Alignment explanation
Indices: 39574203--39574394 Score: 228
Period size: 40 Copynumber: 4.8 Consensus size: 40
39574193 TGATATTTGA
*
39574203 TGGAATTGTATCCAGGCTTAAAGACCCGCAGGCTATATGC
1 TGGAATTGTATCCGGGCTTAAAGACCCGCAGGCTATATGC
* * *
39574243 TGGAATTGTTTTCGGGCTTAAAGACCCACAGGCTATATGC
1 TGGAATTGTATCCGGGCTTAAAGACCCGCAGGCTATATGC
** ** *
39574283 TGGAATTGTATTTGGGCTTAAATTCCC-TAGGCTATATGC
1 TGGAATTGTATCCGGGCTTAAAGACCCGCAGGCTATATGC
* *
39574322 TGGAATTGTATCCGGGTTTAAAGACCCGCAGGCT-TCGTGC
1 TGGAATTGTATCCGGGCTTAAAGACCCGCAGGCTAT-ATGC
* * *
39574362 TGGAATGGTATCAGGG-TTAAAGACCCGCGGGCT
1 TGGAATTGTATCCGGGCTTAAAGACCCGCAGGCT
39574395 TGTGCTAGAA
Statistics
Matches: 131, Mismatches: 19, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
39 50 0.38
40 81 0.62
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.29
Consensus pattern (40 bp):
TGGAATTGTATCCGGGCTTAAAGACCCGCAGGCTATATGC
Found at i:39582024 original size:40 final size:40
Alignment explanation
Indices: 39581980--39582172 Score: 228
Period size: 40 Copynumber: 4.8 Consensus size: 40
39581970 TGATATTTGA
39581980 TGGAATTGTATCCGGGCTTAAAGACCCGCAGGCTATATGC
1 TGGAATTGTATCCGGGCTTAAAGACCCGCAGGCTATATGC
* * *
39582020 TGGAATTGTATTCAGGCTTAAAAACCCGCAGGCTATATGC
1 TGGAATTGTATCCGGGCTTAAAGACCCGCAGGCTATATGC
* * * *
39582060 TGGAATAGTATCCAGGCTTAAAGACCCGTAGGCTATATGT
1 TGGAATTGTATCCGGGCTTAAAGACCCGCAGGCTATATGC
* * * * *
39582100 TGGAATTGTATCCGAGTTTAAAGACCGGAAGGCT-TCGTGC
1 TGGAATTGTATCCGGGCTTAAAGACCCGCAGGCTAT-ATGC
* * *
39582140 TGGAATGGTATCAGGG-TTAAAGACCCGCGGGCT
1 TGGAATTGTATCCGGGCTTAAAGACCCGCAGGCT
39582173 TGTGCTAGAA
Statistics
Matches: 130, Mismatches: 22, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
39 15 0.12
40 115 0.88
ACGTcount: A:0.27, C:0.19, G:0.28, T:0.26
Consensus pattern (40 bp):
TGGAATTGTATCCGGGCTTAAAGACCCGCAGGCTATATGC
Found at i:39586021 original size:24 final size:26
Alignment explanation
Indices: 39585981--39586089 Score: 138
Period size: 26 Copynumber: 4.3 Consensus size: 26
39585971 CTGGAGGCCT
39585981 AGCCTCTTTT-AAT-AACTGGGGCA-A
1 AGCC-CTTTTCAATAAACTGGGGCATA
* *
39586005 AGCCCTTTT-GATAAACTGGGGC-CA
1 AGCCCTTTTCAATAAACTGGGGCATA
* *
39586029 AGCCATTTTCAATAAACTGAGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
39586055 AGCCCTTTTCAATAAACTGGGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
39586081 AGCCCTTTT
1 AGCCCTTTT
39586090 AGTCACTTGC
Statistics
Matches: 74, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
23 7 0.09
24 22 0.30
25 11 0.15
26 34 0.46
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.28
Consensus pattern (26 bp):
AGCCCTTTTCAATAAACTGGGGCATA
Found at i:39586922 original size:54 final size:55
Alignment explanation
Indices: 39586846--39586973 Score: 133
Period size: 54 Copynumber: 2.4 Consensus size: 55
39586836 CATCCTACAA
* * **
39586846 GGGTGTTTTGGTAA-ATCTACAAATCAAG-GGTAT-TTCTGTAATTTTGTAAA-TCAG
1 GGGTGTTTTGGTAATTTCTACAAA-CAAGTGGTATGTT-GGTAATTTTACAAACT-AG
* *
39586900 GGGTATTTTGGTAATTTC-ACAAACCAGTGGTATGTTGGTAATTTTACAAACTAG
1 GGGTGTTTTGGTAATTTCTACAAACAAGTGGTATGTTGGTAATTTTACAAACTAG
39586954 GGGTGTTTTGGTAA-TTCTAC
1 GGGTGTTTTGGTAATTTCTAC
39586974 CCTATAGGGG
Statistics
Matches: 62, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
53 6 0.10
54 51 0.82
55 5 0.08
ACGTcount: A:0.27, C:0.10, G:0.23, T:0.39
Consensus pattern (55 bp):
GGGTGTTTTGGTAATTTCTACAAACAAGTGGTATGTTGGTAATTTTACAAACTAG
Found at i:39586931 original size:27 final size:27
Alignment explanation
Indices: 39586897--39586969 Score: 101
Period size: 27 Copynumber: 2.7 Consensus size: 27
39586887 TTTTGTAAAT
39586897 CAGGGGTATTTTGGTAATTTCACAAAC
1 CAGGGGTATTTTGGTAATTTCACAAAC
* * *
39586924 CAGTGGTATGTTGGTAATTTTACAAAC
1 CAGGGGTATTTTGGTAATTTCACAAAC
* *
39586951 TAGGGGTGTTTTGGTAATT
1 CAGGGGTATTTTGGTAATT
39586970 CTACCCTATA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.26, C:0.10, G:0.26, T:0.38
Consensus pattern (27 bp):
CAGGGGTATTTTGGTAATTTCACAAAC
Found at i:39587039 original size:27 final size:27
Alignment explanation
Indices: 39587006--39587085 Score: 115
Period size: 27 Copynumber: 3.0 Consensus size: 27
39586996 TTCACAATTG
* * *
39587006 AGGGTAAAACGGTAATTTTGTAAATCA
1 AGGGTAAAACAGTAATTCTATAAATCA
*
39587033 AGGGTAAAATAGTAATTCTATAAATCA
1 AGGGTAAAACAGTAATTCTATAAATCA
*
39587060 AGGGTAAAACAATAATTCTATAAATC
1 AGGGTAAAACAGTAATTCTATAAATC
39587086 GAGGATACTT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 47 1.00
ACGTcount: A:0.46, C:0.09, G:0.16, T:0.29
Consensus pattern (27 bp):
AGGGTAAAACAGTAATTCTATAAATCA
Found at i:39587283 original size:27 final size:26
Alignment explanation
Indices: 39587017--39587539 Score: 207
Period size: 27 Copynumber: 19.3 Consensus size: 26
39587007 GGGTAAAACG
* * **
39587017 GTAATTTTGTAAATCAAGGGTAAAATA
1 GTAATTTTATAAATCGAGGGT-ATTTA
* * ***
39587044 GTAATTCTATAAATCAAGGGTAAAACA
1 GTAATTTTATAAATCGAGGGT-ATTTA
* * * *
39587071 ATAATTCTATAAATCGAGGATACTTTG
1 GTAATTTTATAAATCGAGGGTA-TTTA
39587098 GTAATTTT-TACAAGTCGAGGGTATTTCA
1 GTAATTTTATA-AA-TCGAGGGTATTT-A
* * *
39587126 ATAATTTTACAAATCAGGGGGTATTTTA
1 GTAATTTTATAAATC-GAGGGTA-TTTA
* *
39587154 GTAATTTTACAAA-CCAGGGATATTTTA
1 GTAATTTTATAAATCGAGGG-TA-TTTA
* * *
39587181 GTAATTTTACAAA-CCAGGGCTATTGTG
1 GTAATTTTATAAATCGAGGG-TATT-TA
** *
39587208 GTAATTTTATTGATCGAGGGTATTTTG
1 GTAATTTTATAAATCGAGGGTA-TTTA
* * * *
39587235 GTAATTTTGTAAACCAAAGGTATTTCA
1 GTAATTTTATAAATCGAGGGTATTT-A
* **
39587262 GTAATTTTGTAAATCGAGGGTAAAATA
1 GTAATTTTATAAATCGAGGGT-ATTTA
* * **
39587289 GTAATTTTGTAAATTGAGGGTA-AGA
1 GTAATTTTATAAATCGAGGGTATTTA
* ** *
39587314 CGGTAATTCTATAAATCGAGGGTAAAATG
1 --GTAATTTTATAAATCGAGGGT-ATTTA
* ** *
39587343 GTAATTCTATAAATCGAGGGTAAAATG
1 GTAATTTTATAAATCGAGGGT-ATTTA
* **
39587370 GTAATTCTATCTTAT--AGGAGTATTTCA
1 GTAATTTTAT-AAATCGAGG-GTATTT-A
*
39587397 GTAATTTTACAAAATCGAGGGTATTTCA
1 GTAATTTTA-TAAATCGAGGGTATTT-A
** * *
39587425 GTAATTTTGCAAA-CTGAGGTTATTTCG
1 GTAATTTTATAAATC-GAGGGTATTT-A
*
39587452 GTAATTTT-TCAAATCGAGGATATTTA
1 GTAATTTTAT-AAATCGAGGGTATTTA
* * *
39587478 GGTAATTTTATAAATTGGGGGTACTTTG
1 -GTAATTTTATAAATCGAGGGTA-TTTA
* *
39587506 GTAATTTTACAAGTCGAGGGTATTTCA
1 GTAATTTTATAAATCGAGGGTATTT-A
39587533 GTAATTT
1 GTAATTT
39587540 GGTAAACTAA
Statistics
Matches: 396, Mismatches: 70, Indels: 60
0.75 0.13 0.11
Matches are distributed among these distances:
25 2 0.01
26 21 0.05
27 296 0.75
28 69 0.17
29 8 0.02
ACGTcount: A:0.34, C:0.08, G:0.20, T:0.37
Consensus pattern (26 bp):
GTAATTTTATAAATCGAGGGTATTTA
Found at i:39594109 original size:46 final size:46
Alignment explanation
Indices: 39594059--39594231 Score: 210
Period size: 46 Copynumber: 3.7 Consensus size: 46
39594049 TGGTTGAGCA
39594059 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
39594105 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--AATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
39594150 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
39594198 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
39594232 GGGGCGGGTT
Statistics
Matches: 107, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 3 0.03
46 61 0.57
47 29 0.27
48 3 0.03
50 3 0.03
51 2 0.02
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:39594215 original size:93 final size:93
Alignment explanation
Indices: 39594056--39594226 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
39594046 GGATGGTTGA
* *
39594056 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
39594121 TGAGTCCGAGTTCGTGAAATGTAACTAG
66 TGAGTCCGAGTTCGTGAAATGTAACTAG
*
39594149 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
39594214 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
39594227 ACTTAGGGGC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAAATGTAACTAG
Found at i:39613480 original size:56 final size:56
Alignment explanation
Indices: 39613420--39613553 Score: 214
Period size: 56 Copynumber: 2.4 Consensus size: 56
39613410 TCCTAGATAG
* ** * *
39613420 GGTCTTACTCACACACATATGTCGGAGTCACATATCGATGCCAACGTATTAAAGGT
1 GGTCTTACTCACACACATATATCAAAGTCACATATAGATGCCAACGTAGTAAAGGT
*
39613476 GGTCTTACTCACACACATATATCAAAGTCACATATAGATGCCAACGTAGTAAATGT
1 GGTCTTACTCACACACATATATCAAAGTCACATATAGATGCCAACGTAGTAAAGGT
39613532 GGTCTTACTCACACACATATAT
1 GGTCTTACTCACACACATATAT
39613554 TGATGCCATG
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
56 72 1.00
ACGTcount: A:0.34, C:0.23, G:0.16, T:0.28
Consensus pattern (56 bp):
GGTCTTACTCACACACATATATCAAAGTCACATATAGATGCCAACGTAGTAAAGGT
Found at i:39623052 original size:5 final size:5
Alignment explanation
Indices: 39623042--39623067 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
39623032 TTAAAATCAA
39623042 CTTTT CTTTT CTTTT CTTTT CTTTT C
1 CTTTT CTTTT CTTTT CTTTT CTTTT C
39623068 GTATAACTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (5 bp):
CTTTT
Found at i:39627771 original size:43 final size:42
Alignment explanation
Indices: 39627701--39627859 Score: 147
Period size: 43 Copynumber: 3.7 Consensus size: 42
39627691 AGCTCGTACA
* * * * *
39627701 ATGCCAACGTCCCAGACGTGGTATTACATGTAATCAAATATGG
1 ATGCCAATGTCCCAGACATGGTCTTACACGTAATCAAATA-CG
* * ** **
39627744 CTGCCACTGTTGCAGACATGGTCTTACACAAAATCAAATACG
1 ATGCCAATGTCCCAGACATGGTCTTACACGTAATCAAATACG
*
39627786 ATGCCAATGTCCCAGACATGGTCTTACACGTAAATCATAATTCG
1 ATGCCAATGTCCCAGACATGGTCTTACACGT-AATCA-AATACG
** **
39627830 ATGCCAACATCCCAGATGTGGTCTTACACG
1 ATGCCAATGTCCCAGACATGGTCTTACACG
39627860 ATAACACATA
Statistics
Matches: 92, Mismatches: 22, Indels: 3
0.79 0.19 0.03
Matches are distributed among these distances:
42 26 0.28
43 35 0.38
44 31 0.34
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.25
Consensus pattern (42 bp):
ATGCCAATGTCCCAGACATGGTCTTACACGTAATCAAATACG
Found at i:39627852 original size:44 final size:43
Alignment explanation
Indices: 39627756--39627860 Score: 140
Period size: 44 Copynumber: 2.4 Consensus size: 43
39627746 GCCACTGTTG
**
39627756 CAGACATGGTCTTACAC-AAAATCAAATACGATGCCAATGTCC
1 CAGACATGGTCTTACACGAAAATCAAATACGATGCCAACATCC
* *
39627798 CAGACATGGTCTTACACGTAAATCATAATTCGATGCCAACATCC
1 CAGACATGGTCTTACACGAAAATCA-AATACGATGCCAACATCC
**
39627842 CAGATGTGGTCTTACACGA
1 CAGACATGGTCTTACACGA
39627861 TAACACATAT
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
42 17 0.31
43 6 0.11
44 31 0.57
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.24
Consensus pattern (43 bp):
CAGACATGGTCTTACACGAAAATCAAATACGATGCCAACATCC
Found at i:39634534 original size:41 final size:40
Alignment explanation
Indices: 39634434--39634614 Score: 172
Period size: 41 Copynumber: 4.5 Consensus size: 40
39634424 AATCAAGCAT
** ** * *
39634434 CTTCGGGGTTTAG-CCGGATATAACCACTCGCAC-AAGGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
* * * *
39634472 CTTCGGGTCTTAACCCGGATATGGTCACTAGCATAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
* *
39634512 CTTTCGGGACTTAGCCCAGATATAGTCGCTAGCACAAATGC
1 C-TTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
* * *
39634553 CTT--GGATCTTAGTCCGGATGTAGTCACTTAGCACAAAAGC
1 CTTCGGGA-CTTAGCCCGGATATAGTCAC-TAGCACAAATGC
39634593 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATAT
39634615 CATTCGAGTA
Statistics
Matches: 114, Mismatches: 22, Indels: 11
0.78 0.15 0.07
Matches are distributed among these distances:
38 13 0.11
39 31 0.27
40 21 0.18
41 46 0.40
42 3 0.03
ACGTcount: A:0.25, C:0.26, G:0.24, T:0.25
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
Found at i:39639146 original size:43 final size:43
Alignment explanation
Indices: 39639041--39639180 Score: 139
Period size: 42 Copynumber: 3.3 Consensus size: 43
39639031 AACGTTCCAG
* *
39639041 ACGTGGTCTTACATGTAAA-CAAATATCGATGCTACTGTCCTAGA
1 ACGTGGTCTTACATGTAAATCAAATA-CGATGCCAATGTCCTA-A
39639085 TA-G-GGTCTTACATG-AAATCAAATACGATGCCAATGTCCTAA
1 -ACGTGGTCTTACATGTAAATCAAATACGATGCCAATGTCCTAA
* * *
39639126 ACGTGGTCTTACACGTAAATCATAAGT-CGATGCCAACGT-CTCAG
1 ACGTGGTCTTACATGTAAATCA-AA-TACGATGCCAATGTCCT-AA
39639170 ACGTGGTCTTA
1 ACGTGGTCTTA
39639181 AATGATAACA
Statistics
Matches: 83, Mismatches: 5, Indels: 15
0.81 0.05 0.15
Matches are distributed among these distances:
40 1 0.01
41 2 0.02
42 27 0.33
43 25 0.30
44 26 0.31
45 2 0.02
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.28
Consensus pattern (43 bp):
ACGTGGTCTTACATGTAAATCAAATACGATGCCAATGTCCTAA
Found at i:39639174 original size:44 final size:42
Alignment explanation
Indices: 39639041--39639180 Score: 112
Period size: 43 Copynumber: 3.3 Consensus size: 42
39639031 AACGTTCCAG
* *
39639041 ACGTGGTCTTACATGTAAA-CAAATATCGATG-CTACTGTCCTAGA
1 ACGTGGTCTTACACG-AAATCAAATA-CGATGCCAAC-GTCCTA-A
* *
39639085 TA-G-GGTCTTACATGAAATCAAATACGATGCCAATGTCCTAA
1 -ACGTGGTCTTACACGAAATCAAATACGATGCCAACGTCCTAA
*
39639126 ACGTGGTCTTACACGTAAATCATAAGT-CGATGCCAACGT-CTCAG
1 ACGTGGTCTTACACG-AAATCA-AA-TACGATGCCAACGTCCT-AA
39639170 ACGTGGTCTTA
1 ACGTGGTCTTA
39639181 AATGATAACA
Statistics
Matches: 82, Mismatches: 5, Indels: 17
0.79 0.05 0.16
Matches are distributed among these distances:
40 1 0.01
41 2 0.02
42 24 0.29
43 27 0.33
44 26 0.32
45 2 0.02
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.28
Consensus pattern (42 bp):
ACGTGGTCTTACACGAAATCAAATACGATGCCAACGTCCTAA
Found at i:39640879 original size:17 final size:17
Alignment explanation
Indices: 39640849--39640885 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
39640839 ATGCACTAAC
* *
39640849 ATGAACATGTAATGACA
1 ATGAAAATGCAATGACA
39640866 ATGAAAATGCAATGACA
1 ATGAAAATGCAATGACA
39640883 ATG
1 ATG
39640886 TATACTTATC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.49, C:0.11, G:0.19, T:0.22
Consensus pattern (17 bp):
ATGAAAATGCAATGACA
Found at i:39641364 original size:24 final size:24
Alignment explanation
Indices: 39641324--39641372 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 24
39641314 TTCTTTTTCT
* *
39641324 TTCTTCTTTTCAGCAACTT-CTTC
1 TTCTTCTTTGCAACAACTTCCTTC
39641347 TTCTTCTTTAGCAACAACTTCCTTC
1 TTCTTCTTT-GCAACAACTTCCTTC
39641372 T
1 T
39641373 CAATAACAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 9 0.41
24 8 0.36
25 5 0.23
ACGTcount: A:0.16, C:0.31, G:0.04, T:0.49
Consensus pattern (24 bp):
TTCTTCTTTGCAACAACTTCCTTC
Found at i:39641367 original size:21 final size:20
Alignment explanation
Indices: 39641324--39641372 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
39641314 TTCTTTTTCT
**
39641324 TTCTTCTTTTCAGCAACTTC
1 TTCTTCTTTTCAGCAACAAC
*
39641344 TTCTTCTTCTTTAGCAACAAC
1 TTCTTCTT-TTCAGCAACAAC
39641365 TTCCTTCT
1 TT-CTTCT
39641373 CAATAACAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 8 0.33
21 11 0.46
22 5 0.21
ACGTcount: A:0.16, C:0.31, G:0.04, T:0.49
Consensus pattern (20 bp):
TTCTTCTTTTCAGCAACAAC
Found at i:39642203 original size:21 final size:20
Alignment explanation
Indices: 39642179--39642217 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
39642169 GAGTACTTTG
39642179 ATGTTTAATGATAGATTATGA
1 ATGTTTAATGATAG-TTATGA
*
39642200 ATGTTTGATGATAGTTAT
1 ATGTTTAATGATAGTTAT
39642218 ACAAGTTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (20 bp):
ATGTTTAATGATAGTTATGA
Found at i:39644172 original size:17 final size:17
Alignment explanation
Indices: 39644142--39644178 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
39644132 ATGCACTAAC
* *
39644142 ATGAACATGTAATGACA
1 ATGAAAATGCAATGACA
39644159 ATGAAAATGCAATGACA
1 ATGAAAATGCAATGACA
39644176 ATG
1 ATG
39644179 TATACTTATC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.49, C:0.11, G:0.19, T:0.22
Consensus pattern (17 bp):
ATGAAAATGCAATGACA
Found at i:39644657 original size:24 final size:24
Alignment explanation
Indices: 39644617--39644665 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 24
39644607 TTCTTTTTCT
* *
39644617 TTCTTCTTTTCAGCAACTT-CTTC
1 TTCTTCTTTGCAACAACTTCCTTC
39644640 TTCTTCTTTAGCAACAACTTCCTTC
1 TTCTTCTTT-GCAACAACTTCCTTC
39644665 T
1 T
39644666 CAATAACAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 9 0.41
24 8 0.36
25 5 0.23
ACGTcount: A:0.16, C:0.31, G:0.04, T:0.49
Consensus pattern (24 bp):
TTCTTCTTTGCAACAACTTCCTTC
Found at i:39644660 original size:21 final size:20
Alignment explanation
Indices: 39644617--39644665 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
39644607 TTCTTTTTCT
**
39644617 TTCTTCTTTTCAGCAACTTC
1 TTCTTCTTTTCAGCAACAAC
*
39644637 TTCTTCTTCTTTAGCAACAAC
1 TTCTTCTT-TTCAGCAACAAC
39644658 TTCCTTCT
1 TT-CTTCT
39644666 CAATAACAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 8 0.33
21 11 0.46
22 5 0.21
ACGTcount: A:0.16, C:0.31, G:0.04, T:0.49
Consensus pattern (20 bp):
TTCTTCTTTTCAGCAACAAC
Found at i:39645496 original size:21 final size:20
Alignment explanation
Indices: 39645472--39645510 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
39645462 GAGTACTTTG
39645472 ATGTTTAATGATAGATTATGA
1 ATGTTTAATGATAG-TTATGA
*
39645493 ATGTTTGATGATAGTTAT
1 ATGTTTAATGATAGTTAT
39645511 ACAAGTTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (20 bp):
ATGTTTAATGATAGTTATGA
Found at i:39651265 original size:28 final size:28
Alignment explanation
Indices: 39651233--39651325 Score: 105
Period size: 28 Copynumber: 3.3 Consensus size: 28
39651223 GCCCCTTTAG
* *
39651233 GCCCAATCTCATTCATATGACCCATCTA
1 GCCCAATCACATTCATATGACCCATCAA
*
39651261 GCCCAATCACATTCATATGGCCCATCAA
1 GCCCAATCACATTCATATGACCCATCAA
* * * * *
39651289 GCCCAATCACTTTTATAAGGCCCGTCAA
1 GCCCAATCACATTCATATGACCCATCAA
*
39651317 GCCTAATCA
1 GCCCAATCA
39651326 AAATCATAGT
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 57 1.00
ACGTcount: A:0.30, C:0.34, G:0.11, T:0.25
Consensus pattern (28 bp):
GCCCAATCACATTCATATGACCCATCAA
Found at i:39651866 original size:21 final size:21
Alignment explanation
Indices: 39651837--39651876 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
39651827 AACTAAACAC
*
39651837 AAGTGACTCGCAAATCATCTT
1 AAGTCACTCGCAAATCATCTT
**
39651858 AAGTCACTCTTAAATCATC
1 AAGTCACTCGCAAATCATC
39651877 CATGACCCCG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.35, C:0.25, G:0.10, T:0.30
Consensus pattern (21 bp):
AAGTCACTCGCAAATCATCTT
Found at i:39654008 original size:27 final size:27
Alignment explanation
Indices: 39653948--39654054 Score: 115
Period size: 27 Copynumber: 4.0 Consensus size: 27
39653938 CCTTAATCGA
* * * *
39653948 TAAAATAACTATTTTTCCCCTATATGG
1 TAAAATGACTGTTTTGCCCCTATGTGG
*
39653975 TAAAATGACTGTTTTGCCCTTATGTGG
1 TAAAATGACTGTTTTGCCCCTATGTGG
* * * *
39654002 TAAAATGATTGTTTTGCCCTTATGAGA
1 TAAAATGACTGTTTTGCCCCTATGTGG
* *
39654029 TAAGATGACTGTTTTACCCCTATGTG
1 TAAAATGACTGTTTTGCCCCTATGTG
39654055 TAGTATATAT
Statistics
Matches: 67, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 67 1.00
ACGTcount: A:0.27, C:0.16, G:0.17, T:0.40
Consensus pattern (27 bp):
TAAAATGACTGTTTTGCCCCTATGTGG
Found at i:39654739 original size:18 final size:17
Alignment explanation
Indices: 39654711--39654744 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
39654701 GACCTTAGCC
39654711 CATTACAGAATAAGAAA
1 CATTACAGAATAAGAAA
*
39654728 CATTATCAGAATTAGAA
1 CATTA-CAGAATAAGAA
39654745 TCAAAATCAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.53, C:0.12, G:0.12, T:0.24
Consensus pattern (17 bp):
CATTACAGAATAAGAAA
Found at i:39654744 original size:6 final size:6
Alignment explanation
Indices: 39654732--39654794 Score: 74
Period size: 6 Copynumber: 10.3 Consensus size: 6
39654722 AAGAAACATT
* * *
39654732 ATCAGA ATTAGA ATCAAA ATCAGA ATCAGA ATCAGA ATCAG- GTGACAGA
1 ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA AT--CAGA
39654781 ATCAGA ATCAGA AT
1 ATCAGA ATCAGA AT
39654795 GTGAATGCAA
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
5 1 0.02
6 43 0.90
7 3 0.06
8 1 0.02
ACGTcount: A:0.49, C:0.14, G:0.17, T:0.19
Consensus pattern (6 bp):
ATCAGA
Found at i:39655392 original size:78 final size:78
Alignment explanation
Indices: 39655254--39655475 Score: 336
Period size: 78 Copynumber: 2.8 Consensus size: 78
39655244 AGCCCACAAT
* * * *
39655254 ATCGATACGAAGCCCACAATAATGGCACACAGCCTTTGGTAACATGATCGGCACTCAGCCATCGA
1 ATCGGTACAAAGCCCACAATAACGGCACACAGCCTTCGGTAACATGATCGGCACTCAGCCATCGA
*
39655319 TAATGGGTCTATA
66 TAACGGGTCTATA
* * *
39655332 ATCGGTACAAAGCCCACAATAACGACACACAGCCTTCGGTAATATGATCGGCACTCAGCCATTGA
1 ATCGGTACAAAGCCCACAATAACGGCACACAGCCTTCGGTAACATGATCGGCACTCAGCCATCGA
39655397 TAACGGGTCTATA
66 TAACGGGTCTATA
* * * *
39655410 ATTGGCACAAAGCCCACAATAGCGGCACACAGCCTTCGGTAACATAATCGGCACTCAGCCATCGA
1 ATCGGTACAAAGCCCACAATAACGGCACACAGCCTTCGGTAACATGATCGGCACTCAGCCATCGA
39655475 T
66 T
39655476 CGGTCAACAG
Statistics
Matches: 129, Mismatches: 15, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
78 129 1.00
ACGTcount: A:0.32, C:0.28, G:0.20, T:0.20
Consensus pattern (78 bp):
ATCGGTACAAAGCCCACAATAACGGCACACAGCCTTCGGTAACATGATCGGCACTCAGCCATCGA
TAACGGGTCTATA
Found at i:39655546 original size:27 final size:26
Alignment explanation
Indices: 39655481--39655563 Score: 96
Period size: 27 Copynumber: 3.1 Consensus size: 26
39655471 TCGATCGGTC
* *
39655481 AACAGATATTGTGACAGAGTCACCAG
1 AACAGATATTGTGGCAGAGCCACCAG
39655507 ATACAGATATTGTGGCAGAGCCACCAG
1 A-ACAGATATTGTGGCAGAGCCACCAG
* *
39655534 AA-ATGATATTTGTGGCATAGCCACAAG
1 AACA-GATA-TTGTGGCAGAGCCACCAG
39655561 AAC
1 AAC
39655564 GCTTCCTCCA
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
25 1 0.02
26 6 0.12
27 42 0.86
ACGTcount: A:0.37, C:0.19, G:0.23, T:0.20
Consensus pattern (26 bp):
AACAGATATTGTGGCAGAGCCACCAG
Found at i:39656202 original size:27 final size:27
Alignment explanation
Indices: 39655787--39656191 Score: 553
Period size: 27 Copynumber: 15.0 Consensus size: 27
39655777 GGGGTAAAAT
* * *
39655787 GGTAATTTTATCCC-ACAAGGGTATCTC
1 GGTAATTCTA-CCCTACAGGGGTATTTC
39655814 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* * *
39655841 AGTAATTCTACCTTACAGGGGTACTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* * *
39655868 GGTAATTCCACCCTATAGAGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
39655895 AGTAATTCTACCCTATAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
39655922 GGTAATTCTACCCTACAGGGGCATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
39655949 AGTAATTCTACCCTACAGGGGTATGTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
39655976 GATAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
39656003 GGTAATTCTTCCCTATAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
39656030 GATAATTCTACCCTACAGGGGTATTTT
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
39656057 AGTAATT-TGACCCTACAGAGGTATTTC
1 GGTAATTCT-ACCCTACAGGGGTATTTC
*
39656084 GGTAATTCTACCATACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
39656111 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
39656138 AGTAATTTTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
39656165 GTTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
39656192 AATATTTCTA
Statistics
Matches: 331, Mismatches: 44, Indels: 6
0.87 0.12 0.02
Matches are distributed among these distances:
26 4 0.01
27 326 0.98
28 1 0.00
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.34
Consensus pattern (27 bp):
GGTAATTCTACCCTACAGGGGTATTTC
Found at i:39656213 original size:27 final size:27
Alignment explanation
Indices: 39656183--39656244 Score: 90
Period size: 27 Copynumber: 2.3 Consensus size: 27
39656173 TACCCTACAG
39656183 GGGTATTTCAAT-ATTTCTACAAATCAA
1 GGGTATTTCAATAATTTC-ACAAATCAA
* *
39656210 GGGTATTTCGATAATTTCACAAATCAG
1 GGGTATTTCAATAATTTCACAAATCAA
39656237 GGGTATTT
1 GGGTATTT
39656245 TGGTAATTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
27 27 0.84
28 5 0.16
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.37
Consensus pattern (27 bp):
GGGTATTTCAATAATTTCACAAATCAA
Found at i:39656238 original size:81 final size:82
Alignment explanation
Indices: 39655805--39656252 Score: 495
Period size: 81 Copynumber: 5.5 Consensus size: 82
39655795 TATCCCACAA
* * * *
39655805 GGGTATCTCG-GTAA-TTCTACCCTACAGGGGTATTTCAGTAATTCTACCTTACAGGGGTACTTC
1 GGGTATTTCGAGTAATTTC-ACCCTACAGGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTC
** * *
39655868 GGTAATTCCACCCTATAG
65 AATAATTCTACCCTACAG
* * *
39655886 AGGTATTTC-AGTAA-TTCTACCCTATAGGGGTATTTCGGTAATTCTACCCTACAGGGGCATTTC
1 GGGTATTTCGAGTAATTTC-ACCCTACAGGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTC
*
39655949 AGTAATTCTACCCTACAG
65 AATAATTCTACCCTACAG
* * *
39655967 GGGTATGTCGA-TAA-TTCTACCCTACAGGGGTATTTCGGTAATTCTTCCCTATAGGGGTATTTC
1 GGGTATTTCGAGTAATTTC-ACCCTACAGGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTC
*
39656030 GATAATTCTACCCTACAG
65 AATAATTCTACCCTACAG
* * * * *
39656048 GGGTATTT-TAGTAATTTGACCCTACAGAGGTATTTCGGTAATTCTACCATACAGGGGTATTTCG
1 GGGTATTTCGAGTAATTTCACCCTACAGGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCA
*
39656112 GTAATTCTACCCTACAG
66 ATAATTCTACCCTACAG
* *
39656129 GGGTATTTC-AGTAATTTTACCCTACAGGGGTATTTCGTTAATTCTACCCTACAGGGGTATTTCA
1 GGGTATTTCGAGTAATTTCACCCTACAGGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCA
* ** *
39656193 ATATTTCTA-CAAATCAA
66 ATAATTCTACCCTA-CAG
** *
39656210 GGGTATTTCGA-TAATTTCA-CAAATCAGGGGTATTTTGGTAATT
1 GGGTATTTCGAGTAATTTCACCCTA-CAGGGGTATTTCGGTAATT
39656253 TTACAAGCCA
Statistics
Matches: 318, Mismatches: 41, Indels: 16
0.85 0.11 0.04
Matches are distributed among these distances:
80 5 0.02
81 309 0.97
82 4 0.01
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.35
Consensus pattern (82 bp):
GGGTATTTCGAGTAATTTCACCCTACAGGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCA
ATAATTCTACCCTACAG
Found at i:39656320 original size:26 final size:27
Alignment explanation
Indices: 39656195--39656338 Score: 191
Period size: 27 Copynumber: 5.3 Consensus size: 27
39656185 GTATTTCAAT
* * * *
39656195 ATTTCTACAAATCAAGGGTATTTCGATA
1 ATTT-TACAAACCAGGGGTATTTTGGTA
* *
39656223 ATTTCACAAATCAGGGGTATTTTGGTA
1 ATTTTACAAACCAGGGGTATTTTGGTA
*
39656250 ATTTTACAAGCCAGGGGTATTTTGGTA
1 ATTTTACAAACCAGGGGTATTTTGGTA
39656277 ATTTTACAAACCAGGGGTATTTTGGTA
1 ATTTTACAAACCAGGGGTATTTTGGTA
* *
39656304 ATTTT-CAAACTATGGGTATTTTGGTA
1 ATTTTACAAACCAGGGGTATTTTGGTA
39656330 ATTTTACAA
1 ATTTTACAA
39656339 GTCGAGAGTA
Statistics
Matches: 105, Mismatches: 10, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
26 24 0.23
27 77 0.73
28 4 0.04
ACGTcount: A:0.31, C:0.11, G:0.19, T:0.39
Consensus pattern (27 bp):
ATTTTACAAACCAGGGGTATTTTGGTA
Found at i:39656368 original size:53 final size:53
Alignment explanation
Indices: 39656210--39656359 Score: 151
Period size: 54 Copynumber: 2.8 Consensus size: 53
39656200 TACAAATCAA
* * * * * * * * *
39656210 GGGTATTTCGATAATTTCACAAATCAGGGGTATTTTGGTAATTTTACAAGCCAG
1 GGGTATTTTGGTAATTTTACAAACCAGGAGTATTTTAGTAATTTT-CAAACTAT
* *
39656264 GGGTATTTTGGTAATTTTACAAACCAGGGGTATTTTGGTAATTTTCAAACTAT
1 GGGTATTTTGGTAATTTTACAAACCAGGAGTATTTTAGTAATTTTCAAACTAT
**
39656317 GGGTATTTTGGTAATTTTACAAGTC-GAGAGTA-TTTAGTAATTT
1 GGGTATTTTGGTAATTTTACAAACCAG-GAGTATTTTAGTAATTT
39656360 GGTAAACTAA
Statistics
Matches: 84, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
52 11 0.13
53 32 0.38
54 41 0.49
ACGTcount: A:0.29, C:0.09, G:0.22, T:0.40
Consensus pattern (53 bp):
GGGTATTTTGGTAATTTTACAAACCAGGAGTATTTTAGTAATTTTCAAACTAT
Found at i:39674345 original size:30 final size:30
Alignment explanation
Indices: 39674311--39674368 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
39674301 CCTTAACTCT
39674311 AACTTTTGAAAAATTACAATTTTGCCCCTA
1 AACTTTTGAAAAATTACAATTTTGCCCCTA
* * * *
39674341 AACTTTTGCATATTTACACTTTTGCCCC
1 AACTTTTGAAAAATTACAATTTTGCCCC
39674369 AAAGCTCAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.29, C:0.24, G:0.07, T:0.40
Consensus pattern (30 bp):
AACTTTTGAAAAATTACAATTTTGCCCCTA
Found at i:39687390 original size:80 final size:79
Alignment explanation
Indices: 39687253--39687514 Score: 276
Period size: 80 Copynumber: 3.3 Consensus size: 79
39687243 TTGAATGCTG
* * * * *
39687253 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATATCCGGACTAAGAT-CCGAAGGCCTT
1 TCCGGGCTAAGTCCCGAAGGCATTGTGC-GAGTTAATAAATCCGGGCTAAG-TCCCGAAGGCCTT
*
39687317 TGTGCGAGATACTAAA
64 TGTGCGAGTTACTAAA
* * * * *
39687333 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGCTAAGTCCCGAAGGCATT-GTGCGAGTTAATAAATCCGGGCTAAGTCCCGAAGGCCTTT
**
39687398 GTGCGAGTTGTTAAA
65 GTGCGAGTTACTAAA
* * * * * * *
39687413 TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGG-CATTG
1 TCCGGGCTAAGTCCCGAAGGCATTGTGCGAGTTAATAAATCCGGGCTAAGTCCCGAAGGCCTTTG
*
39687477 TGTGAGTTACTAAA
66 TGCGAGTTACTAAA
* *
39687491 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
39687515 TGAACGAGGA
Statistics
Matches: 153, Mismatches: 27, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
78 35 0.23
79 31 0.20
80 83 0.54
81 4 0.03
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (79 bp):
TCCGGGCTAAGTCCCGAAGGCATTGTGCGAGTTAATAAATCCGGGCTAAGTCCCGAAGGCCTTTG
TGCGAGTTACTAAA
Found at i:39687457 original size:39 final size:39
Alignment explanation
Indices: 39687306--39687514 Score: 274
Period size: 40 Copynumber: 5.3 Consensus size: 39
39687296 GGACTAAGAT
* * *
39687306 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGG-CATTGTGCGAGTTACTAAATCCGGGTTATGTC
* *
39687346 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
1 CCGAAGGCATT-GTGCGAGTTACTAAATCCGGGTTATGTC
**
39687386 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTATGTC
1 CCGAAGGCATT-GTGCGAGTTACTAAATCCGGGTTATGTC
* * *
39687426 CCGAAGGCATTGTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTGTGCGAGTTACTAAATCCGGGTTATGTC
* * *
39687465 CCGAAGGCATTGTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTGTGCGAGTTACTAAATCCGGGTTATGTC
39687504 CCGAAGGCATT
1 CCGAAGGCATT
39687515 TGAACGAGGA
Statistics
Matches: 158, Mismatches: 10, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
39 76 0.48
40 82 0.52
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.26
Consensus pattern (39 bp):
CCGAAGGCATTGTGCGAGTTACTAAATCCGGGTTATGTC
Found at i:39700235 original size:79 final size:81
Alignment explanation
Indices: 39700099--39700283 Score: 236
Period size: 79 Copynumber: 2.3 Consensus size: 81
39700089 TCGAATGATG
*
39700099 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
39700163 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
39700178 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
39700240 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGATACTATA
* *
39700258 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
39700284 AACGAGTAGC
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 1 0.01
79 58 0.63
80 33 0.36
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGATACTATA
Found at i:39700297 original size:40 final size:40
Alignment explanation
Indices: 39700100--39700283 Score: 216
Period size: 40 Copynumber: 4.6 Consensus size: 40
39700090 CGAATGATGT
* * * *
39700100 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
39700140 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
39700180 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
39700218 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
39700259 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
39700284 AACGAGTAGC
Statistics
Matches: 126, Mismatches: 11, Indels: 14
0.83 0.07 0.09
Matches are distributed among these distances:
39 35 0.28
40 81 0.64
41 10 0.08
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:39700305 original size:79 final size:79
Alignment explanation
Indices: 39700152--39700316 Score: 210
Period size: 79 Copynumber: 2.1 Consensus size: 79
39700142 GGACTAAGAT
* **
39700152 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
39700217 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
39700231 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
39700294 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
39700310 CCGAAGG
1 CCGAAGG
39700317 TACGTGATTT
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
78 2 0.03
79 48 0.64
80 25 0.33
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:39706035 original size:18 final size:19
Alignment explanation
Indices: 39706012--39706054 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
39706002 GAATTTTGGG
39706012 AAATAATAA-AAATTTAA-A
1 AAATAATAAGAAA-TTAAGA
39706030 AAATAA-AAGAAATTAAGA
1 AAATAATAAGAAATTAAGA
39706048 AAATAAT
1 AAATAAT
39706055 CCCAACTCCC
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 6 0.27
18 16 0.73
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (19 bp):
AAATAATAAGAAATTAAGA
Found at i:39715633 original size:46 final size:45
Alignment explanation
Indices: 39715566--39715726 Score: 164
Period size: 46 Copynumber: 3.5 Consensus size: 45
39715556 TGTAACCCGC
* *
39715566 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGC-TTCGCAT
* * * * *
39715612 CCATAGGTGAACTCGGACTCAACTCAATGAGTTCGGATGCCTAG-TT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG--GCTTCGCAT
* * *
39715658 ACATTTCA-CGAACTCGGACTCAACTCAACGAGTTCGGGCATTCGCAT
1 CCA--TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGC-TTCGCAT
39715705 CCATAAGTGAACTCGGACTCAA
1 CCATAAGTGAACTCGGACTCAA
39715727 TGCTCAATCA
Statistics
Matches: 90, Mismatches: 18, Indels: 14
0.74 0.15 0.11
Matches are distributed among these distances:
45 4 0.04
46 51 0.57
47 32 0.36
48 3 0.03
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.22
Consensus pattern (45 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCTTCGCAT
Found at i:39729621 original size:20 final size:21
Alignment explanation
Indices: 39729596--39729638 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
39729586 ATCCCAATCC
39729596 CATGCAT-CAGGT-AATAACAA
1 CATGCATGCA-GTAAATAACAA
39729616 CATGCATGCAGTAAATAACAA
1 CATGCATGCAGTAAATAACAA
39729637 CA
1 CA
39729639 GTCAAACATG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.47, C:0.21, G:0.14, T:0.19
Consensus pattern (21 bp):
CATGCATGCAGTAAATAACAA
Found at i:39731221 original size:26 final size:26
Alignment explanation
Indices: 39731190--39731297 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
39731180 TGAAATGCCC
*
39731190 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
39731216 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
39731242 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
39731268 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
39731294 ATCA
1 ATCA
39731298 ATTTGTACCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:39734522 original size:22 final size:22
Alignment explanation
Indices: 39734497--39734538 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
39734487 AAAGGTGGAG
*
39734497 ATTGTTGACAATTACATGGTAA
1 ATTGTTGAAAATTACATGGTAA
*
39734519 ATTGTTGAAAATTGCATGGT
1 ATTGTTGAAAATTACATGGT
39734539 TTTGCAGCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.07, G:0.21, T:0.38
Consensus pattern (22 bp):
ATTGTTGAAAATTACATGGTAA
Found at i:39741760 original size:15 final size:15
Alignment explanation
Indices: 39741736--39741776 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
39741726 TAAAAAAAAT
*
39741736 TGATAGTAATAGTAA
1 TGATAATAATAGTAA
*
39741751 TGATAATAATATTAA
1 TGATAATAATAGTAA
*
39741766 TGGTAATAATA
1 TGATAATAATA
39741777 AACATAATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.49, C:0.00, G:0.15, T:0.37
Consensus pattern (15 bp):
TGATAATAATAGTAA
Found at i:39741906 original size:3 final size:3
Alignment explanation
Indices: 39741898--39742074 Score: 91
Period size: 3 Copynumber: 58.7 Consensus size: 3
39741888 GGGTAAAAAT
* *
39741898 ATA ATA ATA ATA ATA ATA ATA ATA A-A TATA GTG ATA ATA CATTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA -A-TA ATA
* * * * *
39741945 AAA ATA ATA AGA AT- ATG TTA ATA ATA A-A TTA ATGA ATTA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A A-TA ATA ATA
* * *
39741990 A-A ATGA ATAA ATAA ATA A-A CACA AAA ATA A-A AT- ATA ATT ATA ATA
1 ATA AT-A AT-A AT-A ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * *
39742035 GTA ATA TTA ACA A-A ATA ATA ATA ATA ATA ATA ATG ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
39742075 GTGATAAAAC
Statistics
Matches: 134, Mismatches: 25, Indels: 30
0.71 0.13 0.16
Matches are distributed among these distances:
2 13 0.10
3 100 0.75
4 18 0.13
5 3 0.02
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:39741987 original size:16 final size:17
Alignment explanation
Indices: 39741966--39742008 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
39741956 AATATGTTAA
*
39741966 TAATAAAT-TAATGAAT
1 TAATAAATAAAATGAAT
39741982 TAAT-AATAAAATGAAT
1 TAATAAATAAAATGAAT
*
39741998 AAATAAATAAA
1 TAATAAATAAA
39742009 CACAAAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 3 0.13
16 14 0.61
17 6 0.26
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (17 bp):
TAATAAATAAAATGAAT
Found at i:39742680 original size:10 final size:11
Alignment explanation
Indices: 39742654--39742682 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
39742644 CAAAAGGTAC
39742654 CTTTTTTCTTT
1 CTTTTTTCTTT
39742665 CTTTTTTCTTT
1 CTTTTTTCTTT
39742676 CTTTTTT
1 CTTTTTT
39742683 ATATGTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (11 bp):
CTTTTTTCTTT
Found at i:39755992 original size:21 final size:21
Alignment explanation
Indices: 39755968--39756007 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
39755958 ACCTATATGG
*
39755968 AGGCCACACACGCCCATGTGA
1 AGGCCACACAAGCCCATGTGA
*
39755989 AGGCCCCACAAGCCCATGT
1 AGGCCACACAAGCCCATGT
39756008 AGAGGGGACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.40, G:0.23, T:0.10
Consensus pattern (21 bp):
AGGCCACACAAGCCCATGTGA
Found at i:39763614 original size:26 final size:26
Alignment explanation
Indices: 39763585--39763692 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
39763575 TGGTACAAAT
39763585 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
39763611 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
39763637 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
39763663 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
39763689 TGAT
1 TGAT
39763693 GGGCATTTCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.32, C:0.07, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:39767849 original size:3 final size:3
Alignment explanation
Indices: 39767841--39767865 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
39767831 GTGAGATTAA
39767841 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
39767866 GAAGAAGAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:39768237 original size:2 final size:2
Alignment explanation
Indices: 39768230--39768258 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
39768220 ACCCCTCTTT
39768230 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
39768259 TAATTATCTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:39768553 original size:42 final size:42
Alignment explanation
Indices: 39768500--39768585 Score: 163
Period size: 42 Copynumber: 2.0 Consensus size: 42
39768490 ATTTATACTA
*
39768500 ATAAAAAATTAAATAGTAGGGTGGATTCTAAGATAGTTTATC
1 ATAAAAAATTAAATAGTAGGGAGGATTCTAAGATAGTTTATC
39768542 ATAAAAAATTAAATAGTAGGGAGGATTCTAAGATAGTTTATC
1 ATAAAAAATTAAATAGTAGGGAGGATTCTAAGATAGTTTATC
39768584 AT
1 AT
39768586 TAAATTTAAT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.44, C:0.05, G:0.19, T:0.33
Consensus pattern (42 bp):
ATAAAAAATTAAATAGTAGGGAGGATTCTAAGATAGTTTATC
Found at i:39769716 original size:7 final size:7
Alignment explanation
Indices: 39769704--39769738 Score: 61
Period size: 7 Copynumber: 5.0 Consensus size: 7
39769694 TAAATAAAGC
39769704 CTCTTCA
1 CTCTTCA
39769711 CTCTTCA
1 CTCTTCA
39769718 CTCTTCA
1 CTCTTCA
39769725 CTCTTCA
1 CTCTTCA
*
39769732 CTTTTCA
1 CTCTTCA
39769739 TCTATCTTCT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.14, C:0.40, G:0.00, T:0.46
Consensus pattern (7 bp):
CTCTTCA
Found at i:39776612 original size:21 final size:21
Alignment explanation
Indices: 39776586--39776625 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
39776576 AAAATATTAG
39776586 AATACTTTTATATTTTTAATA
1 AATACTTTTATATTTTTAATA
39776607 AATACTTTTATATTTTTAA
1 AATACTTTTATATTTTTAA
39776626 AATTTTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (21 bp):
AATACTTTTATATTTTTAATA
Found at i:39787132 original size:17 final size:18
Alignment explanation
Indices: 39787110--39787144 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
39787100 GATATGATAC
*
39787110 TAAAAT-TATTAAAAAAT
1 TAAAATATATAAAAAAAT
39787127 TAAAATATATAAAAAAAT
1 TAAAATATATAAAAAAAT
39787145 AGGAAAACAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
TAAAATATATAAAAAAAT
Found at i:39787489 original size:35 final size:37
Alignment explanation
Indices: 39787433--39787523 Score: 150
Period size: 35 Copynumber: 2.5 Consensus size: 37
39787423 AATCATATCC
39787433 TCTAAGATTGCATATCATATCTAAGATTGCA-ATCATA
1 TCTAAGATTG-ATATCATATCTAAGATTGCATATCATA
39787470 TCTAAGATTG-TATCATATCTAAGATTGCATATCATA
1 TCTAAGATTGATATCATATCTAAGATTGCATATCATA
39787506 TCTAAGATTGCATATCAT
1 TCTAAGATTG-ATATCAT
39787524 TGAAGATTAT
Statistics
Matches: 51, Mismatches: 0, Indels: 5
0.91 0.00 0.09
Matches are distributed among these distances:
35 19 0.37
36 16 0.31
37 10 0.20
38 6 0.12
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.37
Consensus pattern (37 bp):
TCTAAGATTGATATCATATCTAAGATTGCATATCATA
Found at i:39787531 original size:17 final size:19
Alignment explanation
Indices: 39787433--39787523 Score: 161
Period size: 19 Copynumber: 4.9 Consensus size: 19
39787423 AATCATATCC
39787433 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
39787452 TCTAAGATTGCA-ATCATA
1 TCTAAGATTGCATATCATA
39787470 TCTAAGATTG--TATCATA
1 TCTAAGATTGCATATCATA
39787487 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
39787506 TCTAAGATTGCATATCAT
1 TCTAAGATTGCATATCAT
39787524 TGAAGATTAT
Statistics
Matches: 69, Mismatches: 0, Indels: 6
0.92 0.00 0.08
Matches are distributed among these distances:
17 16 0.23
18 16 0.23
19 37 0.54
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.37
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:39787931 original size:45 final size:45
Alignment explanation
Indices: 39787876--39788075 Score: 231
Period size: 45 Copynumber: 4.5 Consensus size: 45
39787866 GGAAGGCGAT
* * * *
39787876 ATCTGCTATCTTTGATCTGCTCCCCGTCTAATATAGAGACGTCAA
1 ATCTGTTATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAA
* *
39787921 ATCTGTTATCTTCGATCTTCTCCCCGTCTAATACAGAGACACCAA
1 ATCTGTTATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAA
* * * * *
39787966 ATCTGCT-TCTTCAATCTGCTCCCCGTCTAATACAAAAATGCCAA
1 ATCTGTTATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAA
* * * * *
39788010 ATCTGTTATCTCCGATTTGTTCCCCGTCTAATACAGAGATGGCAA
1 ATCTGTTATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAA
* *
39788055 ATCTGTCATCTTGGATCTGCT
1 ATCTGTTATCTTCGATCTGCT
39788076 TCGATGTAAA
Statistics
Matches: 128, Mismatches: 26, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
44 37 0.29
45 91 0.71
ACGTcount: A:0.25, C:0.28, G:0.14, T:0.33
Consensus pattern (45 bp):
ATCTGTTATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAA
Found at i:39787992 original size:44 final size:45
Alignment explanation
Indices: 39787876--39788149 Score: 225
Period size: 45 Copynumber: 6.1 Consensus size: 45
39787866 GGAAGGCGAT
* * *
39787876 ATCTGCTATCTTTGATCTGCTCCCCGTCTAATATAGAGACGTCAA
1 ATCTGCTATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAA
* * *
39787921 ATCTGTTATCTTCGATCTTCTCCCCGTCTAATACAGAGACACCAA
1 ATCTGCTATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAA
* * * *
39787966 ATCTGCT-TCTTCAATCTGCTCCCCGTCTAATACAAAAATGCCAA
1 ATCTGCTATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAA
* * * * * *
39788010 ATCTGTTATCTCCGATTTGTTCCCCGTCTAATACAGAGATGGCAA
1 ATCTGCTATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAA
* * * * * * *
39788055 ATCTG-TCATCTTGGATCTGCT--TCGATGTAA-ACACATGAAGGTCAG
1 ATCTGCT-ATCTTCGATCTGCTCCCCG-TCTAATACAGA-G-ACGCCAA
* * *
39788100 ATTTGCTATGTCTTCGATCTGCTCCCCGTTTAATACAGAGATGCCAA
1 ATCTGCTA--TCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAA
39788147 ATC
1 ATC
39788150 ATCTTGGATC
Statistics
Matches: 178, Mismatches: 40, Indels: 20
0.75 0.17 0.08
Matches are distributed among these distances:
43 6 0.03
44 43 0.24
45 99 0.56
46 1 0.01
47 18 0.10
48 5 0.03
49 6 0.03
ACGTcount: A:0.26, C:0.27, G:0.15, T:0.32
Consensus pattern (45 bp):
ATCTGCTATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAA
Found at i:39788059 original size:89 final size:90
Alignment explanation
Indices: 39787876--39788048 Score: 242
Period size: 89 Copynumber: 1.9 Consensus size: 90
39787866 GGAAGGCGAT
** * * * * *
39787876 ATCTGCTATCTTTGATCTGCTCCCCGTCTAATATAGAGACGTCAAATCTGTTATCTTCGATCTTC
1 ATCTGCTATCTTCAATCTGCTCCCCGTCTAATACAAAAACGCCAAATCTGTTATCTCCGATCTTC
39787941 TCCCCGTCTAATACAGAGACACCAA
66 TCCCCGTCTAATACAGAGACACCAA
*
39787966 ATCTGCT-TCTTCAATCTGCTCCCCGTCTAATACAAAAATGCCAAATCTGTTATCTCCGAT-TTG
1 ATCTGCTATCTTCAATCTGCTCCCCGTCTAATACAAAAACGCCAAATCTGTTATCTCCGATCTT-
*
39788029 TTCCCCGTCTAATACAGAGA
65 CTCCCCGTCTAATACAGAGA
39788049 TGGCAAATCT
Statistics
Matches: 73, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
88 2 0.03
89 64 0.88
90 7 0.10
ACGTcount: A:0.26, C:0.29, G:0.13, T:0.32
Consensus pattern (90 bp):
ATCTGCTATCTTCAATCTGCTCCCCGTCTAATACAAAAACGCCAAATCTGTTATCTCCGATCTTC
TCCCCGTCTAATACAGAGACACCAA
Found at i:39788221 original size:78 final size:78
Alignment explanation
Indices: 39788110--39789007 Score: 1516
Period size: 78 Copynumber: 11.5 Consensus size: 78
39788100 ATTTGCTATG
* * *
39788110 TCTTCGATCTGCTCCCCGTTTAATACAGAGATGCCAAATCATCTTGGATCTGCTTCAATAAAGGT
1 TCTTTGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGGATCTGCTTCAATGAAGGT
* * *
39788175 -CAGATCTGCTGTG
66 CCA-ATCTGTTATA
* *
39788188 TCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGGATCTGCTTCAATAAAGGT
1 TCTTTGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGGATCTGCTTCAATGAAGGT
* * *
39788253 -CAGATCTGCTGTG
66 CCA-ATCTGTTATA
* *
39788266 TCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGGATCTGCTTCAATAAAGGT
1 TCTTTGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGGATCTGCTTCAATGAAGGT
* * *
39788331 -CAGATCTGCTGTG
66 CCA-ATCTGTTATA
*
39788344 TCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGGATCTGCTTCAATGAAGGT
1 TCTTTGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGGATCTGCTTCAATGAAGGT
39788409 CCAATCTGTTATA
66 CCAATCTGTTATA
39788422 TCTTTGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGGATCTGCTTCAATGAAGGT
1 TCTTTGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGGATCTGCTTCAATGAAGGT
39788487 CCAATCTGTTATA
66 CCAATCTGTTATA
39788500 TCTTTGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGGATCTGCTTCAATGAAGGT
1 TCTTTGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGGATCTGCTTCAATGAAGGT
39788565 CCAATCTGTTATA
66 CCAATCTGTTATA
39788578 TCTTTGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGGATCTGCTTCAATGAAGGT
1 TCTTTGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGGATCTGCTTCAATGAAGGT
39788643 CCAATCTGTTATA
66 CCAATCTGTTATA
39788656 TCTTTGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGGATCTGCTTCAATGAAGGT
1 TCTTTGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGGATCTGCTTCAATGAAGGT
39788721 CCAATCTGTTATA
66 CCAATCTGTTATA
39788734 TCTTTGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGGATCTGCTTCAATGAAGGT
1 TCTTTGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGGATCTGCTTCAATGAAGGT
39788799 CCAATCTGTTATA
66 CCAATCTGTTATA
39788812 TCTTTGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGGATCTGCTTCAATGAAGGT
1 TCTTTGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGGATCTGCTTCAATGAAGGT
39788877 CCAATCTGTTATA
66 CCAATCTGTTATA
39788890 TCTTTGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGGATCTGCTTCAATGAAGGT
1 TCTTTGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGGATCTGCTTCAATGAAGGT
* *
39788955 -CAGATCTGCTATG
66 CCA-ATCTGTTATA
* * * **
39788968 TCTTCGATCTGCTCTCCGTCGAATATGGAGATGCCAAATC
1 TCTTTGATCTGCTCCCCGTCTAATACAGAGATGCCAAATC
39789008 TGTTTCTCCG
Statistics
Matches: 805, Mismatches: 13, Indels: 4
0.98 0.02 0.00
Matches are distributed among these distances:
77 2 0.00
78 801 1.00
79 2 0.00
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (78 bp):
TCTTTGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGGATCTGCTTCAATGAAGGT
CCAATCTGTTATA
Found at i:39789338 original size:220 final size:220
Alignment explanation
Indices: 39788950--39789538 Score: 1047
Period size: 220 Copynumber: 2.7 Consensus size: 220
39788940 TGCTTCAATG
* *
39788950 AAGGTCAGATCTGCTATGTCTTCGATCTGCTCTCCGTCGAATATGGAGATGCCAAATCTGTTTCT
1 AAGGTTAGATCTGTTATGTCTTCGATCTGCTCTCCGTCGAATATGGAGATGCCAAATCTGTTTCT
39789015 CCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATCTGCTTCAGCATAAACACGT
66 CCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATCTGCTTCAGCATAAACACGT
39789080 GAAAGCCAAATCTGCTATGTCTTCGATCTACTCCTTGTAAACGCAAGGATGCCAAATCATCTTGG
131 GAAAGCCAAATCTGCTATGTCTTCGATCTACTCCTTGTAAACGCAAGGATGCCAAATCATCTTGG
39789145 ATCTACTTCAATGTGAAAACATCCT
196 ATCTACTTCAATGTGAAAACATCCT
39789170 AAGGTTAGATCTGTTATGTCTTCGATCTGCTCTCCGTCGAATATGGAGATGCCAAATCTGTTTCT
1 AAGGTTAGATCTGTTATGTCTTCGATCTGCTCTCCGTCGAATATGGAGATGCCAAATCTGTTTCT
39789235 CCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATCTGCTTCAGCATAAACACGT
66 CCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATCTGCTTCAGCATAAACACGT
39789300 GAAAGCCAAATCTGCTATGTCTTCGATCTACTCCTTGTAAACGCAAGGATGCCAAATCATCTTGG
131 GAAAGCCAAATCTGCTATGTCTTCGATCTACTCCTTGTAAACGCAAGGATGCCAAATCATCTTGG
39789365 ATCTACTTCAATGTGAAAACATCCT
196 ATCTACTTCAATGTGAAAACATCCT
*
39789390 AAGGTTAGATCTGTTATGTCTTCGATCTGCTCTCCGTCGAATATGGAGATGCTAAATCTGTTTCT
1 AAGGTTAGATCTGTTATGTCTTCGATCTGCTCTCCGTCGAATATGGAGATGCCAAATCTGTTTCT
* * ** * * *
39789455 TCGATTTGTTCTTTGACAATACAGAGATGTTAAATCATCTTGGATCTACTTCAG-ATTAAACACC
66 CCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATCTGCTTCAGCA-TAAACACG
*
39789519 T-AAAGGTCAAATCTGCTATG
130 TGAAA-GCCAAATCTGCTATG
39789539 CTTTAGCCTG
Statistics
Matches: 356, Mismatches: 11, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
219 4 0.01
220 352 0.99
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.32
Consensus pattern (220 bp):
AAGGTTAGATCTGTTATGTCTTCGATCTGCTCTCCGTCGAATATGGAGATGCCAAATCTGTTTCT
CCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATCTGCTTCAGCATAAACACGT
GAAAGCCAAATCTGCTATGTCTTCGATCTACTCCTTGTAAACGCAAGGATGCCAAATCATCTTGG
ATCTACTTCAATGTGAAAACATCCT
Found at i:39791633 original size:44 final size:44
Alignment explanation
Indices: 39791583--39791671 Score: 169
Period size: 44 Copynumber: 2.0 Consensus size: 44
39791573 CTTCTTCCAA
*
39791583 GATTAACTTAGCTTCCACGGTGTCAACATATCTCAACAGTACTT
1 GATTAACTTAGCTTCCACGGTGTCAACACATCTCAACAGTACTT
39791627 GATTAACTTAGCTTCCACGGTGTCAACACATCTCAACAGTACTT
1 GATTAACTTAGCTTCCACGGTGTCAACACATCTCAACAGTACTT
39791671 G
1 G
39791672 GTCCATTCTT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.30
Consensus pattern (44 bp):
GATTAACTTAGCTTCCACGGTGTCAACACATCTCAACAGTACTT
Found at i:39801103 original size:17 final size:18
Alignment explanation
Indices: 39801081--39801115 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
39801071 GATATGATAC
*
39801081 TAAAAT-TATTAAAAAAT
1 TAAAATATATAAAAAAAT
39801098 TAAAATATATAAAAAAAT
1 TAAAATATATAAAAAAAT
39801116 CAGGGAAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
TAAAATATATAAAAAAAT
Found at i:39801431 original size:19 final size:19
Alignment explanation
Indices: 39801405--39801495 Score: 134
Period size: 19 Copynumber: 4.9 Consensus size: 19
39801395 AATCATATCT
*
39801405 TCTAAGATTGCATATTATA
1 TCTAAGATTGCATATCATA
* *
39801424 TTTAAGATTGTA-ATCATA
1 TCTAAGATTGCATATCATA
39801442 TCTAAGATTG--TATCATA
1 TCTAAGATTGCATATCATA
39801459 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
39801478 TCTAAGATTGCATATCAT
1 TCTAAGATTGCATATCAT
39801496 TGAAGATTAT
Statistics
Matches: 65, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
17 16 0.25
18 14 0.22
19 35 0.54
ACGTcount: A:0.36, C:0.12, G:0.11, T:0.41
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:39804506 original size:30 final size:31
Alignment explanation
Indices: 39804482--39804540 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
39804472 GTAAATACTC
* *
39804482 AAAATTTGAGGGATTAA-AGTGTAAATATAA
1 AAAATTTGAAGGACTAATAGTGTAAATATAA
*
39804512 AAAATTTGAAGGACTAATAGTGAAAATAT
1 AAAATTTGAAGGACTAATAGTGTAAATAT
39804541 TTTAAGGGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 15 0.60
31 10 0.40
ACGTcount: A:0.51, C:0.02, G:0.19, T:0.29
Consensus pattern (31 bp):
AAAATTTGAAGGACTAATAGTGTAAATATAA
Found at i:39809908 original size:29 final size:29
Alignment explanation
Indices: 39809853--39809922 Score: 70
Period size: 29 Copynumber: 2.4 Consensus size: 29
39809843 TAAAAAAAAA
* * **
39809853 TTTTTGAACCCTTAAAAGTTGGTAAAT-T
1 TTTTTAAACCCTTAAAAATTGAAAAATAT
39809881 TTTTTAAACCCTTTAAAAATTGAAAAATAAT
1 TTTTTAAACCC-TTAAAAATTGAAAAAT-AT
*
39809912 ATTTTAAACCC
1 TTTTTAAACCC
39809923 CTTTTAACCT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
28 10 0.29
29 13 0.38
31 11 0.32
ACGTcount: A:0.40, C:0.13, G:0.07, T:0.40
Consensus pattern (29 bp):
TTTTTAAACCCTTAAAAATTGAAAAATAT
Found at i:39813179 original size:93 final size:93
Alignment explanation
Indices: 39813072--39813242 Score: 306
Period size: 93 Copynumber: 1.8 Consensus size: 93
39813062 GCCCCTAAGT
* *
39813072 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
39813137 CGAGTTCGGATGCCTAGTTACATTTCAC
66 CGAGTTCGGATGCCTAGTTACATTTCAC
* *
39813165 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAGGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
39813230 CGAGTTCGGATGC
66 CGAGTTCGGATGC
39813243 TCAACCATCC
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.27, C:0.29, G:0.22, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATTTCAC
Found at i:39813239 original size:46 final size:46
Alignment explanation
Indices: 39813067--39813239 Score: 201
Period size: 46 Copynumber: 3.7 Consensus size: 46
39813057 AACCCGCCCC
* * *
39813067 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
* *
39813113 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT--T
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCATCCA
* *
39813161 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
*
39813206 TAGGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
39813240 TGCTCAACCA
Statistics
Matches: 106, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 1 0.01
45 1 0.01
46 61 0.58
47 29 0.27
48 2 0.02
49 1 0.01
50 3 0.03
51 2 0.02
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
Found at i:39813690 original size:30 final size:30
Alignment explanation
Indices: 39813656--39813715 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
39813646 ATTTAATACG
39813656 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
39813686 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
39813716 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:39819987 original size:28 final size:28
Alignment explanation
Indices: 39819964--39820028 Score: 103
Period size: 28 Copynumber: 2.3 Consensus size: 28
39819954 TCAGTGTACG
*
39819964 AAATATTGAGAATGGCACTTAGTGTGCC
1 AAATATTGAGAATGGCACTTAGTGTGCA
* *
39819992 AGATATTGAGAATGACACTTAGTGTGCA
1 AAATATTGAGAATGGCACTTAGTGTGCA
39820020 AAATATTGA
1 AAATATTGA
39820029 ATGATTCAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.37, C:0.11, G:0.23, T:0.29
Consensus pattern (28 bp):
AAATATTGAGAATGGCACTTAGTGTGCA
Found at i:39820419 original size:11 final size:11
Alignment explanation
Indices: 39820403--39820427 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
39820393 GAGCAAGGGC
39820403 AAAACCATCGT
1 AAAACCATCGT
39820414 AAAACCATCGT
1 AAAACCATCGT
39820425 AAA
1 AAA
39820428 TTATCAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.52, C:0.24, G:0.08, T:0.16
Consensus pattern (11 bp):
AAAACCATCGT
Found at i:39823595 original size:21 final size:21
Alignment explanation
Indices: 39823552--39823595 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
39823542 TACACTATAT
* ** *
39823552 TTTATATTTTTTTACTTAGAG
1 TTTAAATTTTTTTACAAAAAG
39823573 TTTAAATTTTTTTACAAAAAG
1 TTTAAATTTTTTTACAAAAAG
39823594 TT
1 TT
39823596 AACATTTGTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.05, G:0.07, T:0.57
Consensus pattern (21 bp):
TTTAAATTTTTTTACAAAAAG
Found at i:39824167 original size:24 final size:22
Alignment explanation
Indices: 39824125--39824168 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 22
39824115 TTAGTCAAAT
*
39824125 ATTAAAAAATTTAATATAAAAA
1 ATTAAAAAATTTAACATAAAAA
39824147 ATTAAAAAATTTATAACATAAA
1 ATTAAAAAA-TT-TAACATAAA
39824169 TGAGTTAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 9 0.47
23 2 0.11
24 8 0.42
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (22 bp):
ATTAAAAAATTTAACATAAAAA
Found at i:39824676 original size:3 final size:3
Alignment explanation
Indices: 39824668--39824705 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
39824658 TAATTAAAAT
39824668 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
39824706 TGGAGAGTGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:39832936 original size:29 final size:25
Alignment explanation
Indices: 39832875--39832936 Score: 72
Period size: 29 Copynumber: 2.3 Consensus size: 25
39832865 TTCTTATTAT
39832875 TATAATAATAATGATATCAACAAAA
1 TATAATAATAATGATATCAACAAAA
39832900 TATAATAATAGAATGCATAT-AACACATAA
1 TATAATAAT--AATG-ATATCAACA-A-AA
39832929 TATAATAA
1 TATAATAA
39832937 ATCTAAATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
25 9 0.28
27 8 0.25
28 5 0.16
29 10 0.31
ACGTcount: A:0.58, C:0.08, G:0.05, T:0.29
Consensus pattern (25 bp):
TATAATAATAATGATATCAACAAAA
Found at i:39836981 original size:15 final size:15
Alignment explanation
Indices: 39836961--39836993 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
39836951 AGATTTCTTT
39836961 AAAAAAACAAAGGGG
1 AAAAAAACAAAGGGG
39836976 AAAAAAACAAAGGGG
1 AAAAAAACAAAGGGG
39836991 AAA
1 AAA
39836994 TGAAGTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.70, C:0.06, G:0.24, T:0.00
Consensus pattern (15 bp):
AAAAAAACAAAGGGG
Found at i:39837538 original size:11 final size:11
Alignment explanation
Indices: 39837524--39837556 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
39837514 TATAAACTGT
39837524 TTATTTATTTA
1 TTATTTATTTA
39837535 TTATTTATTTA
1 TTATTTATTTA
*
39837546 TTATATATTTA
1 TTATTTATTTA
39837557 AAAATTATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (11 bp):
TTATTTATTTA
Found at i:39837541 original size:15 final size:15
Alignment explanation
Indices: 39837523--39837556 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
39837513 TTATAAACTG
39837523 TTTATTTATT-TATTA
1 TTTATTTATTATA-TA
39837538 TTTATTTATTATATA
1 TTTATTTATTATATA
39837553 TTTA
1 TTTA
39837557 AAAATTATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 16 0.89
16 2 0.11
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTATTTATTATATA
Found at i:39841948 original size:6 final size:7
Alignment explanation
Indices: 39841933--39841957 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
39841923 AATACAACCC
39841933 AAAATAA
1 AAAATAA
39841940 AAAATAA
1 AAAATAA
39841947 AAAATAA
1 AAAATAA
39841954 AAAA
1 AAAA
39841958 ATGAAGAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAATAA
Found at i:39843511 original size:27 final size:27
Alignment explanation
Indices: 39843481--39843630 Score: 140
Period size: 27 Copynumber: 5.5 Consensus size: 27
39843471 ATATTGAGTC
* *
39843481 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* * * *
39843508 CGCACATTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
39843535 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
** ** *
39843563 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
39843590 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
39843617 CGCACACTTAGTGC
1 CGCACACTTAGTGC
39843631 AACAAAGTAG
Statistics
Matches: 102, Mismatches: 19, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
27 79 0.77
28 23 0.23
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:39843574 original size:55 final size:54
Alignment explanation
Indices: 39843481--39843658 Score: 173
Period size: 54 Copynumber: 3.3 Consensus size: 54
39843471 ATATTGAGTC
* * * *
39843481 CGCACACTCAGTGCTATATAATCAACTCGCACATTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCCACATAATCAAAT
* * ** *
39843535 CGCACACTTAGTGCTACATAGTCAAACTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATC-AACTCGCACACTTAGTGCCACATAATCAAAT
* ** *
39843590 CGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACA-AAGT-AGAAT
1 CGCACACTTAGTGCTA-CATAATCAACTCGCACACTTAGTGCCACATAA-TCA-AAT
*
39843644 TGCACACTTAGTGCT
1 CGCACACTTAGTGCT
39843659 GTACAATTTA
Statistics
Matches: 101, Mismatches: 18, Indels: 9
0.79 0.14 0.07
Matches are distributed among these distances:
53 1 0.01
54 55 0.54
55 45 0.45
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.27
Consensus pattern (54 bp):
CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCCACATAATCAAAT
Found at i:39843631 original size:27 final size:27
Alignment explanation
Indices: 39843481--39843657 Score: 137
Period size: 27 Copynumber: 6.5 Consensus size: 27
39843471 ATATTGAGTC
* * *
39843481 CGCACACTCAGTGCTAT-ATAATCAACT
1 CGCACACTTAGTGC-ATCATAGTCAATT
* * * *
39843508 CGCACATTTAGTGCCA-CGTAATCAAAT
1 CGCACACTTAGTG-CATCATAGTCAATT
*
39843535 CGCACACTTAGTGC-TACATAGTCAAACT
1 CGCACACTTAGTGCAT-CATAGTC-AATT
** *
39843563 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCATCATAGTCAATT
* *
39843590 CGCACACTTAGTGCATCATATTCATTT
1 CGCACACTTAGTGCATCATAGTCAATT
* * *
39843617 CGCACACTTAGTGCAACAAAGTAGAATT
1 CGCACACTTAGTGCATCATAGT-CAATT
39843645 -GCACACTTAGTGC
1 CGCACACTTAGTGC
39843658 TGTACAATTT
Statistics
Matches: 122, Mismatches: 21, Indels: 14
0.78 0.13 0.09
Matches are distributed among these distances:
26 1 0.01
27 94 0.77
28 27 0.22
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCATCATAGTCAATT
Found at i:39847679 original size:53 final size:53
Alignment explanation
Indices: 39847598--39847700 Score: 188
Period size: 53 Copynumber: 1.9 Consensus size: 53
39847588 TAGCTTCGTC
*
39847598 ATTGGTGTGGCTATCATCGAGAATCCTTTGACAAATCGTCGGTAATAACCGGG
1 ATTGGTGTGGCTATCATCGAGAAACCTTTGACAAATCGTCGGTAATAACCGGG
*
39847651 ATTGGTGTGGCTATCATCGAGAAACCTTTTACAAATCGTCGGTAATAACC
1 ATTGGTGTGGCTATCATCGAGAAACCTTTGACAAATCGTCGGTAATAACC
39847701 TACGAGCCCC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 48 1.00
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.29
Consensus pattern (53 bp):
ATTGGTGTGGCTATCATCGAGAAACCTTTGACAAATCGTCGGTAATAACCGGG
Found at i:39856365 original size:39 final size:40
Alignment explanation
Indices: 39856320--39856491 Score: 222
Period size: 40 Copynumber: 4.3 Consensus size: 40
39856310 GCTCCTCGTT
* * *
39856320 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
*
39856360 C-AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * *
39856399 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * * *
39856439 CAAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGG-ATTTAGTAACTCGCA
39856479 CAAATGCCTTCGG
1 CAAATGCCTTCGG
39856492 ATCTTAGTCC
Statistics
Matches: 119, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
39 35 0.29
40 80 0.67
41 4 0.03
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
Found at i:39856420 original size:40 final size:39
Alignment explanation
Indices: 39856322--39856544 Score: 216
Period size: 40 Copynumber: 5.6 Consensus size: 39
39856312 TCCTCGTTCA
* * * *
39856322 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* *
39856361 AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
*
39856400 GAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* * *
39856440 AAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCAC
** * * * *
39856480 AAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC
1 -AATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCAC
* *
39856521 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
39856545 CAGCATTCAA
Statistics
Matches: 157, Mismatches: 21, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
39 40 0.25
40 105 0.67
41 12 0.08
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.26
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
Found at i:39856504 original size:80 final size:79
Alignment explanation
Indices: 39856320--39856544 Score: 240
Period size: 80 Copynumber: 2.8 Consensus size: 79
39856310 GCTCCTCGTT
* * * * *
39856320 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACATAACCCGG-
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGT-ACTCGCACAAAGCCTTCGGGACTTAACCCGGA
39856384 ATTTAATAACTCGCA
65 ATTTAATAACTCGCA
* * *
39856399 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTCGGGGCTTAACCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTA-CTCGCACAAA-GCCTTCGGGACTTAACCCGG
* *
39856464 AATTT-GTATCTCGCA
64 AATTTAATAACTCGCA
* * * * *
39856479 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCACAAAGCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGT-AC-TCGCACAAAGCCTTCGGGACTTAACCCG
39856543 GA
63 GA
39856545 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 18, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
78 1 0.01
79 39 0.32
80 69 0.57
81 13 0.11
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (79 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTACTCGCACAAAGCCTTCGGGACTTAACCCGGAA
TTTAATAACTCGCA
Found at i:39856553 original size:41 final size:41
Alignment explanation
Indices: 39856476--39856553 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
39856466 TTTGTATCTC
* * *
39856476 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
39856517 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
39856554 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:39858601 original size:40 final size:40
Alignment explanation
Indices: 39858546--39858776 Score: 324
Period size: 40 Copynumber: 5.8 Consensus size: 40
39858536 CGGATGATAA
* *
39858546 CGAAGGCATTTGTGCTAGTGACTA-ATTCCGGGCTAAGTCC
1 CGAAGGCATTTGTGCGAGTTACTATA-TCCGGGCTAAGTCC
* *
39858586 CGAAGGCATTTGTGCTAGTTACTA-ATTTCGGGCTAAGTCC
1 CGAAGGCATTTGTGCGAGTTACTATA-TCCGGGCTAAGTCC
* *
39858626 CGAAGGAATTTGTGAGAGTTACTATATCCGGGCTAAGTCC
1 CGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCC
*
39858666 CGAAGGCATTTGTGCGAGTTACTATATCCAGGCTAAGTCC
1 CGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCC
* *
39858706 CGAAGGCATTGGTGCGAGCTACTATATCCGGGCTAAGTCC
1 CGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCC
*
39858746 CGAAGGCATTTGAGCGAG-TAGCTATATCCGG
1 CGAAGGCATTTGTGCGAGTTA-CTATATCCGG
39858777 TTAAATCCCA
Statistics
Matches: 175, Mismatches: 14, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
39 2 0.01
40 172 0.98
41 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
CGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCC
Found at i:39864767 original size:143 final size:143
Alignment explanation
Indices: 39864537--39864822 Score: 374
Period size: 143 Copynumber: 2.0 Consensus size: 143
39864527 GGAAGAAGGT
* * * * *
39864537 ACTCAGATTTGGCCGTAAAGGCAAGGTGAGCCCGAGATTCATTGGGCCGTACGAAATTTCCGAAC
1 ACTCAGATTTGGCCGTAAAGGCAAAGTGAGCCCAAGATTCATCGGGCCATACGAAATATCCGAAC
* * * * * **
39864602 AAGTGGGGCCGGTTGCTTATAGATTGATTTTGCCCCCTGAACTTGAAAAGATTCATGACGTCTTT
66 AAGTCGGGCCAGTTGCGTATAGATTGATTTTACCCCCTGAACTTGAAAAGATCCACAACGTCTTT
39864667 CATGTTTCGATGC
131 CATGTTTCGATGC
* * * * * *
39864680 ACTCAGATTTGGGCGTAAGGGCAAATTGAGTCCAAGGTTCATCGGGCCATATGAAATATCCGAAC
1 ACTCAGATTTGGCCGTAAAGGCAAAGTGAGCCCAAGATTCATCGGGCCATACGAAATATCCGAAC
* * * *
39864745 GAGTCGGTCCAGTTGCGTATAGATTGATTTTACCCCCTGAACTTGAAAGGATCCACAACGTTTTT
66 AAGTCGGGCCAGTTGCGTATAGATTGATTTTACCCCCTGAACTTGAAAAGATCCACAACGTCTTT
39864810 CATGTTTCGATGC
131 CATGTTTCGATGC
39864823 TTTGACGCTA
Statistics
Matches: 121, Mismatches: 22, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
143 121 1.00
ACGTcount: A:0.26, C:0.21, G:0.25, T:0.29
Consensus pattern (143 bp):
ACTCAGATTTGGCCGTAAAGGCAAAGTGAGCCCAAGATTCATCGGGCCATACGAAATATCCGAAC
AAGTCGGGCCAGTTGCGTATAGATTGATTTTACCCCCTGAACTTGAAAAGATCCACAACGTCTTT
CATGTTTCGATGC
Found at i:39865273 original size:105 final size:105
Alignment explanation
Indices: 39865088--39865292 Score: 322
Period size: 105 Copynumber: 2.0 Consensus size: 105
39865078 TCTTAAGTGG
* *
39865088 GGGAGAGTTGTGACAGCCCAAAATTGACCCTAGTCGGGAAGTGGTTTCGGGACCGCTAAACCGAG
1 GGGAGAGTTGTGACAGCCCAAAAGTGACCCTAGTCGGAAAGTGGTTTCGGGACCGCTAAACCGAG
* * **
39865153 TCACCGAAAGGTTTGAATGTGATGTTTATTGTCTAGAATT
66 TCACCGAAAGATTTGAATATGATAATTATTGTCTAGAATT
*
39865193 GGGAGAGTTGTGACAGCCCTAAAGTGACCCTAGTCGGAAAGTGGTTTCGGGACCGCTAAACCGAG
1 GGGAGAGTTGTGACAGCCCAAAAGTGACCCTAGTCGGAAAGTGGTTTCGGGACCGCTAAACCGAG
*
39865258 TCACC-AAATTATTTGAATATGATAATTATTGTCTA
66 TCACCGAAA-GATTTGAATATGATAATTATTGTCTA
39865293 AAATATGTGA
Statistics
Matches: 91, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
104 3 0.03
105 88 0.97
ACGTcount: A:0.28, C:0.18, G:0.27, T:0.27
Consensus pattern (105 bp):
GGGAGAGTTGTGACAGCCCAAAAGTGACCCTAGTCGGAAAGTGGTTTCGGGACCGCTAAACCGAG
TCACCGAAAGATTTGAATATGATAATTATTGTCTAGAATT
Found at i:39871004 original size:79 final size:80
Alignment explanation
Indices: 39870906--39871087 Score: 216
Period size: 79 Copynumber: 2.3 Consensus size: 80
39870896 TCCTCGTTCG
* *
39870906 AATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCACAAATGCCTTCGGGA-CTTAACCCG
1 AATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCACAAATGCCTTC-GGATCTTAACCCG
*
39870968 GAT-TTAGTAAC-TCGCAC
63 GATATT-GTAACTTAGCAC
**
39870985 AAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGGA
1 -AATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAACCCGGA
*
39871049 TATTGTCACTTAGCAC
65 TATTGTAACTTAGCAC
39871065 AA-GCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
39871088 CATCATTCAA
Statistics
Matches: 90, Mismatches: 6, Indels: 13
0.83 0.06 0.12
Matches are distributed among these distances:
78 14 0.16
79 56 0.62
80 20 0.22
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.26
Consensus pattern (80 bp):
AATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAACCCGGAT
ATTGTAACTTAGCAC
Found at i:39871021 original size:39 final size:41
Alignment explanation
Indices: 39870906--39871087 Score: 195
Period size: 40 Copynumber: 4.6 Consensus size: 41
39870896 TCCTCGTTCG
* *
39870906 AATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCACA
1 AATGCCTTCGGGACTTAGCCCGGAAT-TAGTAATCTCGCACA
* *
39870946 AATGCCTTCGGGACTTAACCCGGATTTAGTAA-CTCGCACA
1 AATGCCTTCGGGACTTAGCCCGGAATTAGTAATCTCGCACA
39870986 AATGCCTTCGGG-CTTAGCCCGGAATTAGT-ATCTCGCACA
1 AATGCCTTCGGGACTTAGCCCGGAATTAGTAATCTCGCACA
* * *
39871025 AATGCCTTC-GGATCTTAGTCCGGATATT-GTCA-CTTAGCAC-
1 AATGCCTTCGGGA-CTTAGCCCGGA-ATTAGTAATC-TCGCACA
39871065 AA-GCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
39871088 CATCATTCAA
Statistics
Matches: 126, Mismatches: 7, Indels: 19
0.83 0.05 0.12
Matches are distributed among these distances:
38 3 0.02
39 48 0.38
40 64 0.51
41 11 0.09
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.26
Consensus pattern (41 bp):
AATGCCTTCGGGACTTAGCCCGGAATTAGTAATCTCGCACA
Found at i:39872283 original size:51 final size:51
Alignment explanation
Indices: 39872218--39872321 Score: 183
Period size: 51 Copynumber: 2.0 Consensus size: 51
39872208 AGATGAGAAA
39872218 GGATGAACAAAAATTTTCTCCTTTCTTTTCTTTAGCTCACGGCAATGGGGG
1 GGATGAACAAAAATTTTCTCCTTTCTTTTCTTTAGCTCACGGCAATGGGGG
*
39872269 GGATGCAA-AAAAATTTTCTCCTTTTTTTTCTTTAGCTCACGGCAATGGGGG
1 GGATG-AACAAAAATTTTCTCCTTTCTTTTCTTTAGCTCACGGCAATGGGGG
39872320 GG
1 GG
39872322 GGGGGACAAC
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
51 49 0.96
52 2 0.04
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.36
Consensus pattern (51 bp):
GGATGAACAAAAATTTTCTCCTTTCTTTTCTTTAGCTCACGGCAATGGGGG
Found at i:39879330 original size:27 final size:26
Alignment explanation
Indices: 39879300--39879662 Score: 82
Period size: 27 Copynumber: 13.7 Consensus size: 26
39879290 ACTCAACTTG
39879300 TAAAATTACCAAAGTACCCCCGATTTA
1 TAAAATTACCAAA-TACCCCCGATTTA
* * *
39879327 TAAAATTATCCAAATATCCTCGATTTG
1 TAAAATTA-CCAAATACCCCCGATTTA
* *
39879354 TAAAATTACTGAAATA------A--GA
1 TAAAATTAC-CAAATACCCCCGATTTA
* ** *
39879373 TAGAATTACCATTTTACCCTCGATTTA
1 TAAAATTACCA-AATACCCCCGATTTA
* ** ** *
39879400 CAAAATTATTGAAATACCCTTGGTTTA
1 TAAAATTA-CCAAATACCCCCGATTTA
* ** **
39879427 CAAAATTACCCAAATACCATCGATCAA
1 TAAAATTA-CCAAATACCCCCGATTTA
* * *
39879454 TAAAATTACCAAAATACCCCTGGTTTG
1 TAAAATTACC-AAATACCCCCGATTTA
*** *
39879481 TAAAATTACCAAAATACCTTTGGTTTA
1 TAAAATTACC-AAATACCCCCGATTTA
* * *
39879508 TAAAATTACTAAAATA-CCCCTAGTTTG
1 TAAAATTAC-CAAATACCCCCGA-TTTA
* ** * *
39879535 TAAAATTACTAAAATACCCTTTGGTTTG
1 TAAAATTAC-CAAATACCC-CCGATTTA
** *
39879563 TAAAATTACCAAAATA-CCCTTAGTTTG
1 TAAAATTACC-AAATACCCCCGA-TTTA
* * *
39879590 TAAAATTACCAAAATA-TCCCTAGTTTG
1 TAAAATTACC-AAATACCCCCGA-TTTA
* * *
39879617 TAAAATTATCGAAATACCCCTGATTTG
1 TAAAATTA-CCAAATACCCCCGATTTA
*
39879644 TGAAATTACCGAAATACCC
1 TAAAATTACC-AAATACCC
39879663 TTGTAGGGTA
Statistics
Matches: 253, Mismatches: 61, Indels: 44
0.71 0.17 0.12
Matches are distributed among these distances:
18 1 0.00
19 10 0.04
21 1 0.00
25 1 0.00
26 6 0.02
27 204 0.81
28 30 0.12
ACGTcount: A:0.40, C:0.19, G:0.09, T:0.32
Consensus pattern (26 bp):
TAAAATTACCAAATACCCCCGATTTA
Found at i:39879511 original size:54 final size:54
Alignment explanation
Indices: 39879411--39879661 Score: 270
Period size: 54 Copynumber: 4.6 Consensus size: 54
39879401 AAAATTATTG
* ** * * * * **
39879411 AAATACCCTTGGTTTACAAAATTACCCAAATACCATCGATCAATAAAATTACCA
1 AAATACCCCTGGTTTGTAAAATTACCAAAATACCTTTGGTTTATAAAATTACCA
*
39879465 AAATACCCCTGGTTTGTAAAATTACCAAAATACCTTTGGTTTATAAAATTACTA
1 AAATACCCCTGGTTTGTAAAATTACCAAAATACCTTTGGTTTATAAAATTACCA
* * *
39879519 AAATACCCCTAGTTTGTAAAATTACTAAAATACCCTTTGGTTTGTAAAATTACCA
1 AAATACCCCTGGTTTGTAAAATTACCAAAATA-CCTTTGGTTTATAAAATTACCA
* * * * * * *
39879574 AAATACCCTTAGTTTGTAAAATTACCAAAATATCC-CTAGTTTGTAAAATTATCG
1 AAATACCCCTGGTTTGTAAAATTACCAAAATA-CCTTTGGTTTATAAAATTACCA
* * *
39879628 AAATACCCCTGATTTGTGAAATTACCGAAATACC
1 AAATACCCCTGGTTTGTAAAATTACCAAAATACC
39879662 CTTGTAGGGT
Statistics
Matches: 170, Mismatches: 26, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
53 2 0.01
54 116 0.68
55 52 0.31
ACGTcount: A:0.40, C:0.20, G:0.09, T:0.32
Consensus pattern (54 bp):
AAATACCCCTGGTTTGTAAAATTACCAAAATACCTTTGGTTTATAAAATTACCA
Found at i:39879599 original size:109 final size:109
Alignment explanation
Indices: 39879454--39879664 Score: 293
Period size: 109 Copynumber: 1.9 Consensus size: 109
39879444 CATCGATCAA
* * *
39879454 TAAAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAATA-CCTTTGGTTTATAAAATTA-C
1 TAAAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATATCC-CTAGTTTATAAAATTATC
*
39879517 TAAAATACCCCT-AGTTTGTAAAATTACTAAAATACCCTTTGGTTTG
65 -AAAATACCCCTGA-TTTGTAAAATTACCAAAATACCCTTTGGTTTG
* * *
39879563 TAAAATTACCAAAATACCCTTAGTTTGTAAAATTACCAAAATATCCCTAGTTTGTAAAATTATCG
1 TAAAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATATCCCTAGTTTATAAAATTATCA
* *
39879628 AAATACCCCTGATTTGTGAAATTACCGAAATACCCTT
66 AAATACCCCTGATTTGTAAAATTACCAAAATACCCTT
39879665 GTAGGGTAGA
Statistics
Matches: 90, Mismatches: 9, Indels: 6
0.86 0.09 0.06
Matches are distributed among these distances:
109 86 0.96
110 4 0.04
ACGTcount: A:0.39, C:0.18, G:0.09, T:0.34
Consensus pattern (109 bp):
TAAAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATATCCCTAGTTTATAAAATTATCA
AAATACCCCTGATTTGTAAAATTACCAAAATACCCTTTGGTTTG
Found at i:39879677 original size:27 final size:27
Alignment explanation
Indices: 39879647--39879976 Score: 464
Period size: 27 Copynumber: 12.3 Consensus size: 27
39879637 TGATTTGTGA
*
39879647 AATTACCGAAATACCCTTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
39879674 AATTATCGAAATACCCTTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
39879701 AATTACCGGAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
39879728 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
** * *
39879755 AATTATTGCAATACCCCTGTAGGGTAA
1 AATTACCGAAATACCCCTGTAGGGTAG
39879782 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * *
39879809 AATTACCAAAATACTCCTATAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
39879836 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * *
39879863 AATTATCGCAATACCCCTGTAGGGTAA
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
39879890 AATTATCGAAATACCCCTGTAAGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
39879917 AATTACCGAAATACCCCTGTAGGGTGG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * * *
39879944 AATTACCGAGATA-CCTTGTGGGGTAA
1 AATTACCGAAATACCCCTGTAGGGTAG
39879970 AATTACC
1 AATTACC
39879977 ATTTTTCCCC
Statistics
Matches: 270, Mismatches: 33, Indels: 1
0.89 0.11 0.00
Matches are distributed among these distances:
26 16 0.06
27 254 0.94
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.25
Consensus pattern (27 bp):
AATTACCGAAATACCCCTGTAGGGTAG
Found at i:39880455 original size:22 final size:22
Alignment explanation
Indices: 39880403--39880467 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 22
39880393 TTAAAGCCTT
* *
39880403 CTGATTATGGCTTTGTGTCAAC
1 CTGATTATGGCTCTGTGCCAAC
*
39880425 CT-ACATATGGCTCTGTGCCAAC
1 CTGA-TTATGGCTCTGTGCCAAC
* * *
39880447 TTGATTATGGTTGTGTGCCAA
1 CTGATTATGGCTCTGTGCCAA
39880468 ACGTATTTGC
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
21 1 0.03
22 32 0.94
23 1 0.03
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.37
Consensus pattern (22 bp):
CTGATTATGGCTCTGTGCCAAC
Found at i:39885237 original size:26 final size:26
Alignment explanation
Indices: 39885208--39885315 Score: 171
Period size: 26 Copynumber: 4.2 Consensus size: 26
39885198 TCGTACAAAT
*
39885208 TGATAATGGGTTAGATAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
39885234 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
39885260 TGATAATGAGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
39885286 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
39885312 TGAT
1 TGAT
39885316 GGGCATTTAA
Statistics
Matches: 74, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 74 1.00
ACGTcount: A:0.34, C:0.07, G:0.22, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:39886955 original size:27 final size:27
Alignment explanation
Indices: 39886913--39887043 Score: 153
Period size: 27 Copynumber: 4.9 Consensus size: 27
39886903 AGGAAGCATC
*
39886913 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCACAATTATCTGAT
*
39886940 CTGGTGGCTCTACCAC-ATATATCTG-T
1 CTGGTGGCTCTGCCACAAT-TATCTGAT
*
39886966 CCTGGTGGCTATGCCACAATTATCTGAT
1 -CTGGTGGCTCTGCCACAATTATCTGAT
* *
39886994 CTGGTGGCACTGCCAC-ATATATCTGTT
1 CTGGTGGCTCTGCCACAAT-TATCTGAT
*
39887021 CTGGTGGCTCTACCACAA-TATCT
1 CTGGTGGCTCTGCCACAATTATCT
39887044 ATATCTAGTG
Statistics
Matches: 89, Mismatches: 9, Indels: 13
0.80 0.08 0.12
Matches are distributed among these distances:
26 10 0.11
27 75 0.84
28 4 0.04
ACGTcount: A:0.21, C:0.26, G:0.21, T:0.33
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACAATTATCTGAT
Found at i:39886993 original size:54 final size:54
Alignment explanation
Indices: 39886911--39887043 Score: 214
Period size: 54 Copynumber: 2.5 Consensus size: 54
39886901 GGAGGAAGCA
*
39886911 TCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTACCACATATATCTG
1 TCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCACTACCACATATATCTG
*
39886965 TCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCACTGCCACATATATCTG
1 TCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCACTACCACATATATCTG
* * *
39887019 TTCTGGTGGCTCTACCACAA-TATCT
1 TCCTGGTGGCTATGCCACAATTATCT
39887044 ATATCTAGTG
Statistics
Matches: 74, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
53 5 0.07
54 69 0.93
ACGTcount: A:0.20, C:0.26, G:0.20, T:0.33
Consensus pattern (54 bp):
TCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCACTACCACATATATCTG
Found at i:39892348 original size:26 final size:26
Alignment explanation
Indices: 39892319--39892426 Score: 162
Period size: 26 Copynumber: 4.2 Consensus size: 26
39892309 TCGTACAAAT
* *
39892319 TGATAATGGGTTAGTTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* **
39892345 TGATAATGGATTAGGTAAATACTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
39892371 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
39892397 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
39892423 TGAT
1 TGAT
39892427 GGGCATTTCA
Statistics
Matches: 73, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 73 1.00
ACGTcount: A:0.32, C:0.07, G:0.23, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:39894065 original size:27 final size:27
Alignment explanation
Indices: 39894025--39894111 Score: 97
Period size: 27 Copynumber: 3.2 Consensus size: 27
39894015 AGGAAGCGTC
39894025 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTATGCCACAATTATCTGAT
* * *
39894052 CTGGTGGCTCTGCCAC-ATATATTTGTT
1 CTGGTGGCTATGCCACAAT-TATCTGAT
* *
39894079 CTGGTGGCTTTACCACAA-TATCTGTAT
1 CTGGTGGCTATGCCACAATTATCTG-AT
39894106 CTGGTG
1 CTGGTG
39894112 ACTTCGTCAA
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
26 7 0.14
27 42 0.84
28 1 0.02
ACGTcount: A:0.18, C:0.22, G:0.23, T:0.37
Consensus pattern (27 bp):
CTGGTGGCTATGCCACAATTATCTGAT
Found at i:39894324 original size:27 final size:27
Alignment explanation
Indices: 39894282--39894422 Score: 173
Period size: 27 Copynumber: 5.2 Consensus size: 27
39894272 AGGAAGCGTC
*
39894282 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCACAATTATCTGAT
*
39894309 CTGGTGGCTCTACCAC-ATATATCTG-T
1 CTGGTGGCTCTGCCACAAT-TATCTGAT
*
39894335 CCTGGTGGCTATGCCACAATTATCTGAT
1 -CTGGTGGCTCTGCCACAATTATCTGAT
* *
39894363 CTGGTGGCACTGCCAC-ATATATCTGTT
1 CTGGTGGCTCTGCCACAAT-TATCTGAT
39894390 CTGGTGGCTCTGCCACAA-TATCTGTAT
1 CTGGTGGCTCTGCCACAATTATCTG-AT
39894417 CTGGTG
1 CTGGTG
39894423 ACTTCGTCAA
Statistics
Matches: 98, Mismatches: 9, Indels: 14
0.81 0.07 0.12
Matches are distributed among these distances:
26 11 0.11
27 83 0.85
28 4 0.04
ACGTcount: A:0.19, C:0.25, G:0.23, T:0.33
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACAATTATCTGAT
Found at i:39894361 original size:54 final size:54
Alignment explanation
Indices: 39894279--39894422 Score: 236
Period size: 54 Copynumber: 2.7 Consensus size: 54
39894269 TGGAGGAAGC
*
39894279 GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTACCACATATATCT
1 GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCACTACCACATATATCT
*
39894333 GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCACTGCCACATATATCT
1 GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCACTACCACATATATCT
* *
39894387 GTTCTGGTGGCTCTGCCACAA-TATCTGTATCTGGTG
1 GTCCTGGTGGCTATGCCACAATTATCTG-ATCTGGTG
39894423 ACTTCGTCAA
Statistics
Matches: 85, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
53 6 0.07
54 79 0.93
ACGTcount: A:0.19, C:0.25, G:0.23, T:0.33
Consensus pattern (54 bp):
GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCACTACCACATATATCT
Found at i:39894559 original size:84 final size:84
Alignment explanation
Indices: 39894433--39894599 Score: 316
Period size: 84 Copynumber: 2.0 Consensus size: 84
39894423 ACTTCGTCAA
39894433 AATATATGGCAGCCTCGCTGCGATTTCTGTGGTGTGTAGCGGTTGGGTCGATCGAGTAGTCTCCC
1 AATATATGGCAGCCTCGCTGCGATTTCTGTGGTGTGTAGCGGTTGGGTCGATCGAGTAGTCTCCC
39894498 CACATGGTGTAAGGCTGGC
66 CACATGGTGTAAGGCTGGC
* *
39894517 AATATCTGGCAGCCTCGCTGCGATTTCTGTGGTGTGTAGCGGTTGGGTGGATCGAGTAGTCTCCC
1 AATATATGGCAGCCTCGCTGCGATTTCTGTGGTGTGTAGCGGTTGGGTCGATCGAGTAGTCTCCC
39894582 CACATGGTGTAAGGCTGG
66 CACATGGTGTAAGGCTGG
39894600 TATGGGGGTG
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
84 81 1.00
ACGTcount: A:0.16, C:0.21, G:0.34, T:0.29
Consensus pattern (84 bp):
AATATATGGCAGCCTCGCTGCGATTTCTGTGGTGTGTAGCGGTTGGGTCGATCGAGTAGTCTCCC
CACATGGTGTAAGGCTGGC
Found at i:39895251 original size:137 final size:137
Alignment explanation
Indices: 39895042--39895314 Score: 519
Period size: 137 Copynumber: 2.0 Consensus size: 137
39895032 GCTTTAGGGC
*
39895042 GTGTTTTCAAAAACAACAATTGATTTCAAAATAACACGACAACAAGCAAAGCTTCCGCAATAAAA
1 GTGTTTTCAAAAACAACAATAGATTTCAAAATAACACGACAACAAGCAAAGCTTCCGCAATAAAA
39895107 GTATTTTCCAAAATTAATCACTTTTCCTAAAAATGACTTAATCAAATCGGTTTCCTAGAAATATC
66 GTATTTTCCAAAATTAATCACTTTTCCTAAAAATGACTTAATCAAATCGGTTTCCTAGAAATATC
39895172 CATGACT
131 CATGACT
* *
39895179 GTGTTTTCAAAAACAACAATAGATTTCAAACTAACACGACAACAAGCAAAGCTTCCGCAATGAAA
1 GTGTTTTCAAAAACAACAATAGATTTCAAAATAACACGACAACAAGCAAAGCTTCCGCAATAAAA
39895244 GTATTTTCCAAAATTAATCACTTTTCCTAAAAATGACTTAATCAAATCGGTTTCCTAGAAATATC
66 GTATTTTCCAAAATTAATCACTTTTCCTAAAAATGACTTAATCAAATCGGTTTCCTAGAAATATC
39895309 CATGAC
131 CATGAC
39895315 GTTAAGGTGC
Statistics
Matches: 133, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
137 133 1.00
ACGTcount: A:0.41, C:0.20, G:0.10, T:0.29
Consensus pattern (137 bp):
GTGTTTTCAAAAACAACAATAGATTTCAAAATAACACGACAACAAGCAAAGCTTCCGCAATAAAA
GTATTTTCCAAAATTAATCACTTTTCCTAAAAATGACTTAATCAAATCGGTTTCCTAGAAATATC
CATGACT
Done.