Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr13
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: 91551117
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2824764 characters in sequence are not A, C, G, or T
File 126 of 276
Found at i:40671719 original size:46 final size:46
Alignment explanation
Indices: 40671652--40671826 Score: 314
Period size: 46 Copynumber: 3.8 Consensus size: 46
40671642 TGTAACCCGC
* * * *
40671652 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
40671698 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
40671744 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
40671790 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
40671827 TGCTCAACCA
Statistics
Matches: 125, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
46 125 1.00
ACGTcount: A:0.30, C:0.29, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:40682663 original size:15 final size:15
Alignment explanation
Indices: 40682645--40682680 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
40682635 CATGAGTGGG
40682645 TTAATCCTAAGTGCC
1 TTAATCCTAAGTGCC
40682660 TTAATCCTAAGTGCC
1 TTAATCCTAAGTGCC
40682675 TTAATC
1 TTAATC
40682681 ATTTCGACGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.28, C:0.25, G:0.11, T:0.36
Consensus pattern (15 bp):
TTAATCCTAAGTGCC
Found at i:40684387 original size:226 final size:226
Alignment explanation
Indices: 40683993--40684445 Score: 906
Period size: 226 Copynumber: 2.0 Consensus size: 226
40683983 TTGTCAGTTT
40683993 TAGTAGAATGGTTTAGACGATCACCTTCAATTTTTGATGTGGTGCCAGAATTGCGAGCTTGAAGG
1 TAGTAGAATGGTTTAGACGATCACCTTCAATTTTTGATGTGGTGCCAGAATTGCGAGCTTGAAGG
40684058 GTGATTGTTTCGTCTCCCACACGGAGTGTGAGCTCACCTATGCCAACTTCAATAATCATTTTACC
66 GTGATTGTTTCGTCTCCCACACGGAGTGTGAGCTCACCTATGCCAACTTCAATAATCATTTTACC
40684123 AGTTGCTAAAAAGGGCCGTCCCAAAATCAAAGGAGTGTTGCTATCCTCCTCTATGTCTAGAATAA
131 AGTTGCTAAAAAGGGCCGTCCCAAAATCAAAGGAGTGTTGCTATCCTCCTCTATGTCTAGAATAA
40684188 TGAAGTCAATGGGAAATATAAATTTACCGAC
196 TGAAGTCAATGGGAAATATAAATTTACCGAC
40684219 TAGTAGAATGGTTTAGACGATCACCTTCAATTTTTGATGTGGTGCCAGAATTGCGAGCTTGAAGG
1 TAGTAGAATGGTTTAGACGATCACCTTCAATTTTTGATGTGGTGCCAGAATTGCGAGCTTGAAGG
40684284 GTGATTGTTTCGTCTCCCACACGGAGTGTGAGCTCACCTATGCCAACTTCAATAATCATTTTACC
66 GTGATTGTTTCGTCTCCCACACGGAGTGTGAGCTCACCTATGCCAACTTCAATAATCATTTTACC
40684349 AGTTGCTAAAAAGGGCCGTCCCAAAATCAAAGGAGTGTTGCTATCCTCCTCTATGTCTAGAATAA
131 AGTTGCTAAAAAGGGCCGTCCCAAAATCAAAGGAGTGTTGCTATCCTCCTCTATGTCTAGAATAA
40684414 TGAAGTCAATGGGAAATATAAATTTACCGAC
196 TGAAGTCAATGGGAAATATAAATTTACCGAC
40684445 T
1 T
40684446 TTAACTAGCA
Statistics
Matches: 227, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
226 227 1.00
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.30
Consensus pattern (226 bp):
TAGTAGAATGGTTTAGACGATCACCTTCAATTTTTGATGTGGTGCCAGAATTGCGAGCTTGAAGG
GTGATTGTTTCGTCTCCCACACGGAGTGTGAGCTCACCTATGCCAACTTCAATAATCATTTTACC
AGTTGCTAAAAAGGGCCGTCCCAAAATCAAAGGAGTGTTGCTATCCTCCTCTATGTCTAGAATAA
TGAAGTCAATGGGAAATATAAATTTACCGAC
Found at i:40706756 original size:22 final size:23
Alignment explanation
Indices: 40706731--40706817 Score: 92
Period size: 22 Copynumber: 3.9 Consensus size: 23
40706721 TGATGAATAA
40706731 TAAGCTCTACTGAGCTGAAAC-G
1 TAAGCTCTACTGAGCTGAAACAG
40706753 TAAGCTCTA-TCGAGCTG-AACAG
1 TAAGCTCTACT-GAGCTGAAACAG
* *
40706775 TAAGCTCATAC-GAGTTGAAACGG
1 TAAGCTC-TACTGAGCTGAAACAG
* *
40706798 TAAGCTCCAATGAGCTGAAA
1 TAAGCTCTACTGAGCTGAAA
40706818 ATAATAAGCT
Statistics
Matches: 54, Mismatches: 5, Indels: 11
0.77 0.07 0.16
Matches are distributed among these distances:
21 4 0.07
22 29 0.54
23 21 0.39
ACGTcount: A:0.34, C:0.21, G:0.23, T:0.22
Consensus pattern (23 bp):
TAAGCTCTACTGAGCTGAAACAG
Found at i:40706814 original size:45 final size:44
Alignment explanation
Indices: 40706731--40706816 Score: 113
Period size: 45 Copynumber: 1.9 Consensus size: 44
40706721 TGATGAATAA
*
40706731 TAAGCTCTACTGAGCTGAAACGTAAGCTCTATCGAGCTGAACAG
1 TAAGCTCTACTGAGCTGAAACGTAAGCTCAATCGAGCTGAACAG
*
40706775 TAAGCTCATAC-GAGTTGAAACGGTAAGCTCCAAT-GAGCTGAA
1 TAAGCTC-TACTGAGCTGAAAC-GTAAGCT-CAATCGAGCTGAA
40706817 AATAATAAGC
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
44 16 0.43
45 18 0.49
46 3 0.08
ACGTcount: A:0.34, C:0.21, G:0.23, T:0.22
Consensus pattern (44 bp):
TAAGCTCTACTGAGCTGAAACGTAAGCTCAATCGAGCTGAACAG
Found at i:40711224 original size:48 final size:48
Alignment explanation
Indices: 40711168--40711343 Score: 244
Period size: 48 Copynumber: 3.7 Consensus size: 48
40711158 TTAATGAGAT
* *
40711168 CCAGTGTAAGACCATGTTTGGGACATGGCATCGGCATTGATATGTGAG
1 CCAGTGTAAGACCATGTCTGGGACATGGCATCAGCATTGATATGTGAG
* *
40711216 CCAGTGTAAGACCATGTCTGGTACATGGCATCAGCGTTGATATGTGAG
1 CCAGTGTAAGACCATGTCTGGGACATGGCATCAGCATTGATATGTGAG
* * ** *
40711264 CCAGTGTAAGACCATGTCTAGGACATGGCATTAGTTTTGATATGTGTG
1 CCAGTGTAAGACCATGTCTGGGACATGGCATCAGCATTGATATGTGAG
* * *
40711312 CTAGAGTAAGACCATGTTTGGGACATGGCATC
1 CCAGTGTAAGACCATGTCTGGGACATGGCATC
40711344 GGCACTGACA
Statistics
Matches: 113, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
48 113 1.00
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.28
Consensus pattern (48 bp):
CCAGTGTAAGACCATGTCTGGGACATGGCATCAGCATTGATATGTGAG
Found at i:40711370 original size:96 final size:96
Alignment explanation
Indices: 40711161--40711374 Score: 225
Period size: 96 Copynumber: 2.2 Consensus size: 96
40711151 ACCATGGTTA
* * * * * *
40711161 ATGAGATCCAGTGTAAGACCATGTTTGGGACATGGCATCGGCATTGATATGTGAGCCAGTGTAAG
1 ATGAGAGCCAGTATAAGACCATGTCTAGGACATGGCATCAGCATTGATATGTGAGCCAGAGTAAG
* ** *
40711226 ACCATGTCTGGTACATGGCATCAGCGTTGAT
66 ACCATGTCTGGGACATGGCATCAGCACTGAC
* * * ** * *
40711257 ATGTGAGCCAGTGTAAGACCATGTCTAGGACATGGCATTAGTTTTGATATGTGTGCTAGAGTAAG
1 ATGAGAGCCAGTATAAGACCATGTCTAGGACATGGCATCAGCATTGATATGTGAGCCAGAGTAAG
* *
40711322 ACCATGTTTGGGACATGGCATCGGCACTGAC
66 ACCATGTCTGGGACATGGCATCAGCACTGAC
40711353 ATGAGA-CTTC-GTATAAGACCAT
1 ATGAGAGC--CAGTATAAGACCAT
40711375 ATCCAAGATA
Statistics
Matches: 97, Mismatches: 19, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
95 1 0.01
96 95 0.98
97 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (96 bp):
ATGAGAGCCAGTATAAGACCATGTCTAGGACATGGCATCAGCATTGATATGTGAGCCAGAGTAAG
ACCATGTCTGGGACATGGCATCAGCACTGAC
Found at i:40713032 original size:19 final size:19
Alignment explanation
Indices: 40712946--40713031 Score: 154
Period size: 19 Copynumber: 4.5 Consensus size: 19
40712936 GCCTAAGGAC
40712946 ACGGGCGTGTCGAAGGCAT
1 ACGGGCGTGTCGAAGGCAT
40712965 ACGGGCGTGTCGAAGGCAT
1 ACGGGCGTGTCGAAGGCAT
*
40712984 ACAGGCGTGTCGAAGGCAT
1 ACGGGCGTGTCGAAGGCAT
*
40713003 ACGGGCGTGTTGAAGGCAT
1 ACGGGCGTGTCGAAGGCAT
40713022 ACGGGCGTGT
1 ACGGGCGTGT
40713032 TCCCGTGTCC
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 64 1.00
ACGTcount: A:0.21, C:0.20, G:0.42, T:0.17
Consensus pattern (19 bp):
ACGGGCGTGTCGAAGGCAT
Found at i:40714024 original size:28 final size:29
Alignment explanation
Indices: 40713986--40714051 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 29
40713976 TAAAGTGATT
* *
40713986 TTGAGTAAAAGTGCATATT-AGGGATTAAA
1 TTGAG-AAAAGTGCAAATTGAGAGATTAAA
*
40714015 TTGAGAAAAGTGTAAATTGAGAGATTAAA
1 TTGAGAAAAGTGCAAATTGAGAGATTAAA
*
40714044 TTGTGAAA
1 TTGAGAAA
40714052 TAAATGGAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 11 0.34
29 21 0.66
ACGTcount: A:0.44, C:0.02, G:0.24, T:0.30
Consensus pattern (29 bp):
TTGAGAAAAGTGCAAATTGAGAGATTAAA
Found at i:40717529 original size:43 final size:43
Alignment explanation
Indices: 40717468--40717603 Score: 115
Period size: 43 Copynumber: 3.2 Consensus size: 43
40717458 AATTCTAGCA
40717468 TCCCAGAC-GTGGTCTTACATGTAATCCAATATCGATGCCACTG
1 TCCCAGACAG-GGTCTTACATGTAATCCAATATCGATGCCACTG
* * *
40717511 TCCCAGACAGGGTCTTACATGAAAT-TAGATAT-GATGTCGA-TG
1 TCCCAGACAGGGTCTTACATGTAATCCA-ATATCGATG-CCACTG
* *
40717553 TCCC-GAACATGGTCTTACACGTAAATCTCAA-ATCGATGCCAAC-G
1 TCCCAG-ACAGGGTCTTACATGT-AATC-CAATATCGATGCC-ACTG
40717597 TCCCAGA
1 TCCCAGA
40717604 TGTTGTCTTA
Statistics
Matches: 74, Mismatches: 8, Indels: 21
0.72 0.08 0.20
Matches are distributed among these distances:
41 1 0.01
42 24 0.32
43 34 0.46
44 13 0.18
45 2 0.03
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.26
Consensus pattern (43 bp):
TCCCAGACAGGGTCTTACATGTAATCCAATATCGATGCCACTG
Found at i:40720806 original size:26 final size:26
Alignment explanation
Indices: 40720770--40720822 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
40720760 AAGTTTTGAA
40720770 TGCAGTTTTTGGAATGTCTGAATCTT
1 TGCAGTTTTTGGAATGTCTGAATCTT
40720796 TGCAGTTTTTGGAATGTCTGAATCTT
1 TGCAGTTTTTGGAATGTCTGAATCTT
40720822 T
1 T
40720823 TACTCACAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.19, C:0.11, G:0.23, T:0.47
Consensus pattern (26 bp):
TGCAGTTTTTGGAATGTCTGAATCTT
Found at i:40743797 original size:192 final size:192
Alignment explanation
Indices: 40743470--40743853 Score: 768
Period size: 192 Copynumber: 2.0 Consensus size: 192
40743460 ATCTAGGCTA
40743470 AATTTAGATCCTAATCGGATTACTCGTCCGGGCTAAATCCACAATGCACACATATTCTTCAGGAG
1 AATTTAGATCCTAATCGGATTACTCGTCCGGGCTAAATCCACAATGCACACATATTCTTCAGGAG
40743535 GCTCGATCACTCAAGGAACACTCGTCCGGGGTAGATCCTTTCTATATTTGAGATCAACAGATTAC
66 GCTCGATCACTCAAGGAACACTCGTCCGGGGTAGATCCTTTCTATATTTGAGATCAACAGATTAC
40743600 CCGTCTGGGCTAAATCCTTTTCTGCAACAAATGCAGGATCTCGAGTCATGTAAGCCATGGTC
131 CCGTCTGGGCTAAATCCTTTTCTGCAACAAATGCAGGATCTCGAGTCATGTAAGCCATGGTC
40743662 AATTTAGATCCTAATCGGATTACTCGTCCGGGCTAAATCCACAATGCACACATATTCTTCAGGAG
1 AATTTAGATCCTAATCGGATTACTCGTCCGGGCTAAATCCACAATGCACACATATTCTTCAGGAG
40743727 GCTCGATCACTCAAGGAACACTCGTCCGGGGTAGATCCTTTCTATATTTGAGATCAACAGATTAC
66 GCTCGATCACTCAAGGAACACTCGTCCGGGGTAGATCCTTTCTATATTTGAGATCAACAGATTAC
40743792 CCGTCTGGGCTAAATCCTTTTCTGCAACAAATGCAGGATCTCGAGTCATGTAAGCCATGGTC
131 CCGTCTGGGCTAAATCCTTTTCTGCAACAAATGCAGGATCTCGAGTCATGTAAGCCATGGTC
40743854 TATCCATCGA
Statistics
Matches: 192, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
192 192 1.00
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.28
Consensus pattern (192 bp):
AATTTAGATCCTAATCGGATTACTCGTCCGGGCTAAATCCACAATGCACACATATTCTTCAGGAG
GCTCGATCACTCAAGGAACACTCGTCCGGGGTAGATCCTTTCTATATTTGAGATCAACAGATTAC
CCGTCTGGGCTAAATCCTTTTCTGCAACAAATGCAGGATCTCGAGTCATGTAAGCCATGGTC
Found at i:40748667 original size:15 final size:15
Alignment explanation
Indices: 40748647--40748680 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
40748637 TGCTACAAGT
*
40748647 GGTAGTGGTAGTTTA
1 GGTAGTGGCAGTTTA
40748662 GGTAGTGGCAGTTTA
1 GGTAGTGGCAGTTTA
40748677 GGTA
1 GGTA
40748681 CTTTTCAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.21, C:0.03, G:0.41, T:0.35
Consensus pattern (15 bp):
GGTAGTGGCAGTTTA
Found at i:40757144 original size:18 final size:18
Alignment explanation
Indices: 40757121--40757156 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
40757111 GCTTAGTAAG
40757121 CCATATACAAATAAAGTA
1 CCATATACAAATAAAGTA
40757139 CCATATACAAATAAAGTA
1 CCATATACAAATAAAGTA
40757157 ATCACATGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.56, C:0.17, G:0.06, T:0.22
Consensus pattern (18 bp):
CCATATACAAATAAAGTA
Found at i:40759820 original size:43 final size:43
Alignment explanation
Indices: 40759773--40759962 Score: 249
Period size: 43 Copynumber: 4.4 Consensus size: 43
40759763 TATCCTAAAT
* * *
40759773 ATGGTCTTACATGTTATCAC-ATATCGATGCCAATGTCCTAGAC
1 ATGGTCTTACATGTAATCACAATA-CAATGCCAATGTCCCAGAC
* * *
40759816 ATGGTCTTACACGAAATCA-TATAACAATGCCAATGTCCCAGAC
1 ATGGTCTTACATGTAATCACAAT-ACAATGCCAATGTCCCAGAC
*
40759859 ATCGTCTTACATGTAATCACAATACAATGCCAATGTCCCAGAC
1 ATGGTCTTACATGTAATCACAATACAATGCCAATGTCCCAGAC
* * *
40759902 ATGGTCTTAAATGTAAACACAATACAATGCCAATGTCCCAAAC
1 ATGGTCTTACATGTAATCACAATACAATGCCAATGTCCCAGAC
*
40759945 ATGGTCTTATATGTAATC
1 ATGGTCTTACATGTAATC
40759963 GCATCTCGGT
Statistics
Matches: 129, Mismatches: 15, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
43 126 0.98
44 3 0.02
ACGTcount: A:0.35, C:0.24, G:0.14, T:0.28
Consensus pattern (43 bp):
ATGGTCTTACATGTAATCACAATACAATGCCAATGTCCCAGAC
Found at i:40762179 original size:10 final size:10
Alignment explanation
Indices: 40762160--40762198 Score: 60
Period size: 10 Copynumber: 3.8 Consensus size: 10
40762150 TGCTTTTGTA
40762160 CATGATATGC
1 CATGATATGC
*
40762170 CATAATATGC
1 CATGATATGC
40762180 TCATGATATGC
1 -CATGATATGC
40762191 CATGATAT
1 CATGATAT
40762199 ATTCACATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
10 17 0.65
11 9 0.35
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.33
Consensus pattern (10 bp):
CATGATATGC
Found at i:40762283 original size:25 final size:25
Alignment explanation
Indices: 40762245--40762314 Score: 95
Period size: 25 Copynumber: 2.8 Consensus size: 25
40762235 AGGAAGTGCT
* *
40762245 AAAAGGGCTTTGCCCCATTTTACCG
1 AAAAGGGCTTTGCCCCAGTTTACCA
* **
40762270 AAAAGGGCTCTGCCCCAGTTTGTCA
1 AAAAGGGCTTTGCCCCAGTTTACCA
40762295 AAAAGGGCTTTGCCCCAGTT
1 AAAAGGGCTTTGCCCCAGTT
40762315 ATTAAAAGAG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTACCA
Found at i:40767390 original size:17 final size:17
Alignment explanation
Indices: 40767350--40767392 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
40767340 GAGGCTGAAA
*
40767350 TCGGGCACAATGGGCTT
1 TCGGGCCCAATGGGCTT
40767367 TCGGGCCCAATGGGCTT
1 TCGGGCCCAATGGGCTT
40767384 TCGGGCCCA
1 TCGGGCCCA
40767393 TTTGGGTAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.14, C:0.30, G:0.35, T:0.21
Consensus pattern (17 bp):
TCGGGCCCAATGGGCTT
Found at i:40767742 original size:10 final size:10
Alignment explanation
Indices: 40767727--40767765 Score: 60
Period size: 10 Copynumber: 3.8 Consensus size: 10
40767717 TGCTTTTGTA
40767727 CATGATATGC
1 CATGATATGC
*
40767737 CATGATATAC
1 CATGATATGC
40767747 ACATGATATGC
1 -CATGATATGC
40767758 CATGATAT
1 CATGATAT
40767766 ATTCAAATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
10 17 0.65
11 9 0.35
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (10 bp):
CATGATATGC
Found at i:40767751 original size:21 final size:21
Alignment explanation
Indices: 40767726--40767766 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
40767716 CTGCTTTTGT
40767726 ACATGATATGCCATGATATAC
1 ACATGATATGCCATGATATAC
40767747 ACATGATATGCCATGATATA
1 ACATGATATGCCATGATATA
40767767 TTCAAATATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.29
Consensus pattern (21 bp):
ACATGATATGCCATGATATAC
Found at i:40767846 original size:25 final size:25
Alignment explanation
Indices: 40767812--40767881 Score: 95
Period size: 25 Copynumber: 2.8 Consensus size: 25
40767802 AGGAAGTGCT
*
40767812 AAAAGGGCTTTGCCCTAGTTTACCG
1 AAAAGGGCTTTGCCCTAGTTTACCA
* *
40767837 AAAAGGGCTTTGCCTTAGTTTATCA
1 AAAAGGGCTTTGCCCTAGTTTACCA
* *
40767862 AAAACGGCTTTGCCCCAGTT
1 AAAAGGGCTTTGCCCTAGTT
40767882 ATTAAAAGAG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCTAGTTTACCA
Found at i:40767894 original size:24 final size:24
Alignment explanation
Indices: 40767811--40767894 Score: 71
Period size: 25 Copynumber: 3.4 Consensus size: 24
40767801 GAGGAAGTGC
* *
40767811 TAAAAGGGCTTTGCCCTAGTTTACC
1 TAAAAGGGCTTTGCCCCAGTTTA-T
* **
40767836 GAAAAGGGCTTTGCCTTAGTTTAT
1 TAAAAGGGCTTTGCCCCAGTTTAT
* *
40767860 CAAAAACGGCTTTGCCCCAG-TTAT
1 -TAAAAGGGCTTTGCCCCAGTTTAT
40767884 TAAAAGAGGCT
1 TAAAAG-GGCT
40767895 AGGCCTCCAG
Statistics
Matches: 48, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
23 4 0.08
24 8 0.17
25 36 0.75
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.30
Consensus pattern (24 bp):
TAAAAGGGCTTTGCCCCAGTTTAT
Found at i:40771049 original size:60 final size:60
Alignment explanation
Indices: 40770976--40771090 Score: 167
Period size: 60 Copynumber: 1.9 Consensus size: 60
40770966 AATCAGCTTT
* *
40770976 CTTGGAGTAATTCCTTACCCCCTATTCTCCGTCTCTCTTTTCTTCCTCCTCTAGGACTTC
1 CTTGGAGTAATTCCTTACCCCCTATTCTCCGCCTCCCTTTTCTTCCTCCTCTAGGACTTC
* * ** *
40771036 CTTGGAGTAATTCCTTACTCCCTATTTTGTGCCTCCCTTTTCTTCTTCCTCTAGG
1 CTTGGAGTAATTCCTTACCCCCTATTCTCCGCCTCCCTTTTCTTCCTCCTCTAGG
40771091 GTGTATTTAT
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
60 48 1.00
ACGTcount: A:0.11, C:0.34, G:0.11, T:0.43
Consensus pattern (60 bp):
CTTGGAGTAATTCCTTACCCCCTATTCTCCGCCTCCCTTTTCTTCCTCCTCTAGGACTTC
Found at i:40778006 original size:65 final size:65
Alignment explanation
Indices: 40777902--40778032 Score: 253
Period size: 65 Copynumber: 2.0 Consensus size: 65
40777892 ACACGCTGCG
40777902 AACTTACTCTGTATGCATAACAGCCTAATACACCACTCCTTAGGTGTAGCCCTGGCATCGTTCTT
1 AACTTACTCTGTATGCATAACAGCCTAATACACCACTCCTTAGGTGTAGCCCTGGCATCGTTCTT
*
40777967 AACTTGCTCTGTATGCATAACAGCCTAATACACCACTCCTTAGGTGTAGCCCTGGCATCGTTCTT
1 AACTTACTCTGTATGCATAACAGCCTAATACACCACTCCTTAGGTGTAGCCCTGGCATCGTTCTT
40778032 A
1 A
40778033 TTGGCGTAGA
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
65 65 1.00
ACGTcount: A:0.24, C:0.29, G:0.16, T:0.31
Consensus pattern (65 bp):
AACTTACTCTGTATGCATAACAGCCTAATACACCACTCCTTAGGTGTAGCCCTGGCATCGTTCTT
Found at i:40778866 original size:56 final size:56
Alignment explanation
Indices: 40778802--40779027 Score: 293
Period size: 56 Copynumber: 4.0 Consensus size: 56
40778792 TCATGAAACA
40778802 TGTTGTGTTAATGGAAAAATAAAATAAGAAGCATGGGCAATAAACTAAT-AAGAAAT
1 TGTTGTGTTAATGGAAAAATAAAATAAGAAGCATGGGCAA-AAACTAATCAAGAAAT
* * *
40778858 TGTTGTGTTAATGGAAAAATAAAATAAGAAGCATGGGC-AAAAC-ATGTCATGAAACA
1 TGTTGTGTTAATGGAAAAATAAAATAAGAAGCATGGGCAAAAACTA-ATCAAGAAA-T
* * *
40778914 TGTTGTGTTAATGGAAAAATAAAATAAGAAGCATGGGCAAAACATGTCATCAA-ACA-
1 TGTTGTGTTAATGGAAAAATAAAATAAGAAGCATGGGCAAAA-A-CTAATCAAGAAAT
*
40778970 TGTTGTGTTAATGGAAGAATAAAATAAGAAGCATGGGCAATAAACTAAT-AAGAAAT
1 TGTTGTGTTAATGGAAAAATAAAATAAGAAGCATGGGCAA-AAACTAATCAAGAAAT
40779026 TG
1 TG
40779028 AAGGAAGAAA
Statistics
Matches: 148, Mismatches: 12, Indels: 20
0.82 0.07 0.11
Matches are distributed among these distances:
53 1 0.01
54 7 0.05
55 11 0.07
56 118 0.80
57 5 0.03
58 3 0.02
59 3 0.02
ACGTcount: A:0.47, C:0.08, G:0.21, T:0.24
Consensus pattern (56 bp):
TGTTGTGTTAATGGAAAAATAAAATAAGAAGCATGGGCAAAAACTAATCAAGAAAT
Found at i:40778975 original size:112 final size:112
Alignment explanation
Indices: 40778778--40779009 Score: 380
Period size: 112 Copynumber: 2.1 Consensus size: 112
40778768 ACAAGGGATG
40778778 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGCATGGGCAAT
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGCATGGGCAAT
40778843 AAACTAATAAGAAATTGTTGTGTTAATGGAAAAATAAAATAAGAAGC
66 AAACTAATAAGAAATTGTTGTGTTAATGGAAAAATAAAATAAGAAGC
40778890 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGCATGGGCAA-
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGCATGGGCAAT
* * * *
40778954 AACATGTCATCAA-ACA-TGTTGTGTTAATGGAAGAATAAAATAAGAAGC
66 AA-A-CTAAT-AAGAAATTGTTGTGTTAATGGAAAAATAAAATAAGAAGC
40779002 ATGGGCAA
1 ATGGGCAA
40779010 TAAACTAATA
Statistics
Matches: 113, Mismatches: 4, Indels: 6
0.92 0.03 0.05
Matches are distributed among these distances:
111 2 0.02
112 104 0.92
113 5 0.04
114 2 0.02
ACGTcount: A:0.47, C:0.09, G:0.22, T:0.23
Consensus pattern (112 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGCATGGGCAAT
AAACTAATAAGAAATTGTTGTGTTAATGGAAAAATAAAATAAGAAGC
Found at i:40780536 original size:40 final size:39
Alignment explanation
Indices: 40780481--40780664 Score: 215
Period size: 40 Copynumber: 4.6 Consensus size: 39
40780471 ATTTGAATGA
* *
40780481 TATCCGGGCTAAGTCCCGAGGGCATTTATGCTAGTGATTT
1 TATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGA-TT
* *
40780521 TATCCGGGCTAAGTCCCAAAGGCATTTATGCTAGTGAGTT
1 TATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGA-TT
* * *
40780561 TATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATA
1 TATCCGGGCTAAGACCCGAAGGCATTTATGCTAG-TGATT
* * * *
40780601 TATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTA
1 TATCCGGGCTAAGACCCGAAGGCATTTATGCTAG-TGATT
* *
40780641 TACCCGGGTTAAGACCCGAAGGCA
1 TATCCGGGCTAAGACCCGAAGGCA
40780665 ATTGTGCTTG
Statistics
Matches: 132, Mismatches: 11, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
40 129 0.98
41 3 0.02
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (39 bp):
TATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATT
Found at i:40786926 original size:28 final size:27
Alignment explanation
Indices: 40786850--40786964 Score: 117
Period size: 27 Copynumber: 4.3 Consensus size: 27
40786840 CAGCATGGCT
* * *
40786850 ACCAG-AACAGATATTGTGACAAAGTC
1 ACCAGAAACAGATATTGTGGCAGAGCC
* *
40786876 ACCAGATACATATATTGTGGCAGAGCC
1 ACCAGAAACAGATATTGTGGCAGAGCC
*
40786903 ACTAGAAACAGATATTTGTGGCAGAGCC
1 ACCAGAAACAGATA-TTGTGGCAGAGCC
** *
40786931 ACCAG-ATTAGATGTTTGTGGCAGAGCC
1 ACCAGAAACAGAT-ATTGTGGCAGAGCC
40786958 ACCAGAA
1 ACCAGAA
40786965 CGCTTCCTCC
Statistics
Matches: 73, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
26 5 0.07
27 50 0.68
28 18 0.25
ACGTcount: A:0.36, C:0.20, G:0.23, T:0.21
Consensus pattern (27 bp):
ACCAGAAACAGATATTGTGGCAGAGCC
Found at i:40786936 original size:55 final size:54
Alignment explanation
Indices: 40786850--40786964 Score: 144
Period size: 55 Copynumber: 2.1 Consensus size: 54
40786840 CAGCATGGCT
*
40786850 ACCAG-AACAGATATTGTGACAAAGTCACCAGA-TACATATATTGTGGCAGAGCC
1 ACCAGAAACAGATATTGTGACAAAGCCACCAGATTACATAT-TTGTGGCAGAGCC
* * * * *
40786903 ACTAGAAACAGATATTTGTGGCAGAGCCACCAGATTAGATGTTTGTGGCAGAGCC
1 ACCAGAAACAGATA-TTGTGACAAAGCCACCAGATTACATATTTGTGGCAGAGCC
40786958 ACCAGAA
1 ACCAGAA
40786965 CGCTTCCTCC
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
53 4 0.08
54 8 0.15
55 35 0.67
56 5 0.10
ACGTcount: A:0.36, C:0.20, G:0.23, T:0.21
Consensus pattern (54 bp):
ACCAGAAACAGATATTGTGACAAAGCCACCAGATTACATATTTGTGGCAGAGCC
Found at i:40788179 original size:25 final size:22
Alignment explanation
Indices: 40788125--40788179 Score: 56
Period size: 25 Copynumber: 2.3 Consensus size: 22
40788115 TTTCGGCCAG
40788125 AGAAGAAAAGAAGGAGAAAAGA
1 AGAAGAAAAGAAGGAGAAAAGA
* *
40788147 AAATAGAAGAAGAGAGGAGAAGAGA
1 AGA-AGAA-AAGA-AGGAGAAAAGA
40788172 AGGAAGAA
1 A-GAAGAA
40788180 TTCAGCACTC
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
22 2 0.08
23 4 0.15
24 4 0.15
25 15 0.58
26 1 0.04
ACGTcount: A:0.64, C:0.00, G:0.35, T:0.02
Consensus pattern (22 bp):
AGAAGAAAAGAAGGAGAAAAGA
Found at i:40789590 original size:56 final size:56
Alignment explanation
Indices: 40789504--40789628 Score: 189
Period size: 56 Copynumber: 2.2 Consensus size: 56
40789494 CCTACGTTTC
* **
40789504 ACACTTTGCCATAGAT-CAACCATGGTCTTATCTGTCAATTCATCACTGATCACTGA
1 ACACTTTGCCAT-GGTCCAACCATGGTCTTATCCATCAATTCATCACTGATCACTGA
*
40789560 ACACTTTGTCATGGTCCAACCATGGTCTTATCCATCAATTCATCACTGATCACTGA
1 ACACTTTGCCATGGTCCAACCATGGTCTTATCCATCAATTCATCACTGATCACTGA
*
40789616 ACAGTTTGCCATG
1 ACACTTTGCCATG
40789629 TTTAGCACAC
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
55 2 0.03
56 60 0.97
ACGTcount: A:0.27, C:0.27, G:0.14, T:0.32
Consensus pattern (56 bp):
ACACTTTGCCATGGTCCAACCATGGTCTTATCCATCAATTCATCACTGATCACTGA
Found at i:40789650 original size:27 final size:27
Alignment explanation
Indices: 40789620--40789682 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
40789610 CACTGAACAG
**
40789620 TTTGCCATGTTTAGCACACTATATCAC
1 TTTGCCATAATTAGCACACTATATCAC
* *
40789647 TTTGCCATAATTGGCACACTTTATCAC
1 TTTGCCATAATTAGCACACTATATCAC
*
40789674 TTTTCCATA
1 TTTGCCATA
40789683 GTTCAACTAT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.25, C:0.25, G:0.10, T:0.40
Consensus pattern (27 bp):
TTTGCCATAATTAGCACACTATATCAC
Found at i:40789809 original size:31 final size:31
Alignment explanation
Indices: 40789745--40789949 Score: 304
Period size: 31 Copynumber: 6.5 Consensus size: 31
40789735 AGTGTAGCTA
* *
40789745 AAGCTACCACTTATCACTTG-TCACTTGTAGCCG
1 AAGCTACCACTTTTCAC-TGATCA--GGTAGCCG
*
40789778 AAGCTACCACTATTCACTGATCAGGTAGCCG
1 AAGCTACCACTTTTCACTGATCAGGTAGCCG
* *
40789809 AAGCTATCACTTTTCACTGATCAGGTAGCTG
1 AAGCTACCACTTTTCACTGATCAGGTAGCCG
* * *
40789840 GAGGTACCACTTTTCACTGATCTGGTAGCCG
1 AAGCTACCACTTTTCACTGATCAGGTAGCCG
40789871 AAGCTACCACTTTTCACTGATCAGGTAGCCG
1 AAGCTACCACTTTTCACTGATCAGGTAGCCG
40789902 AAGCTACCACTTTTCACTGATCAGGTAGCCG
1 AAGCTACCACTTTTCACTGATCAGGTAGCCG
40789933 AAGCTACCACTTTTCAC
1 AAGCTACCACTTTTCAC
40789950 ATTTTACACA
Statistics
Matches: 157, Mismatches: 14, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
31 137 0.87
32 2 0.01
33 18 0.11
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28
Consensus pattern (31 bp):
AAGCTACCACTTTTCACTGATCAGGTAGCCG
Found at i:40789990 original size:32 final size:33
Alignment explanation
Indices: 40789954--40790054 Score: 109
Period size: 33 Copynumber: 3.1 Consensus size: 33
40789944 TTTCACATTT
* *
40789954 TACACACAAGACGTACATTTCCGTTTCAAG-TG
1 TACACACAAGATGTACATTTCCTTTTCAAGTTG
**
40789986 TACACACAA-AGTGTATGTTTCCTTTTCAAGTTG
1 TACACACAAGA-TGTACATTTCCTTTTCAAGTTG
* *
40790019 TACACACACAG-TGTACATTTCCTTTTCCATTTG
1 TACACACA-AGATGTACATTTCCTTTTCAAGTTG
40790052 TAC
1 TAC
40790055 CATTTAGGTA
Statistics
Matches: 57, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
31 1 0.02
32 24 0.42
33 31 0.54
34 1 0.02
ACGTcount: A:0.28, C:0.24, G:0.13, T:0.36
Consensus pattern (33 bp):
TACACACAAGATGTACATTTCCTTTTCAAGTTG
Found at i:40790026 original size:33 final size:33
Alignment explanation
Indices: 40789966--40790054 Score: 117
Period size: 33 Copynumber: 2.7 Consensus size: 33
40789956 CACACAAGAC
*
40789966 GTACATTTCCGTTTCAAG-TGTACACACAAAGT
1 GTACATTTCCTTTTCAAGTTGTACACACAAAGT
** *
40789998 GTATGTTTCCTTTTCAAGTTGTACACACACAGT
1 GTACATTTCCTTTTCAAGTTGTACACACAAAGT
* *
40790031 GTACATTTCCTTTTCCATTTGTAC
1 GTACATTTCCTTTTCAAGTTGTAC
40790055 CATTTAGGTA
Statistics
Matches: 48, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
32 15 0.31
33 33 0.69
ACGTcount: A:0.25, C:0.22, G:0.13, T:0.39
Consensus pattern (33 bp):
GTACATTTCCTTTTCAAGTTGTACACACAAAGT
Found at i:40792223 original size:18 final size:19
Alignment explanation
Indices: 40792187--40792224 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
40792177 AACTCAAAAT
40792187 TTTTCTTTTTGTCACTTTA
1 TTTTCTTTTTGTCACTTTA
40792206 TTTTCTTATTT-T-ACTTTA
1 TTTTCTT-TTTGTCACTTTA
40792224 T
1 T
40792225 CAAGGATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.39
19 8 0.44
20 3 0.17
ACGTcount: A:0.13, C:0.13, G:0.03, T:0.71
Consensus pattern (19 bp):
TTTTCTTTTTGTCACTTTA
Found at i:40794502 original size:31 final size:31
Alignment explanation
Indices: 40794441--40794515 Score: 73
Period size: 31 Copynumber: 2.4 Consensus size: 31
40794431 CTAAATAAAT
*
40794441 AATATTAAAATAATAATAAATATCTCATTAA
1 AATATTAAAATAATAATAAATATCTAATTAA
** *
40794472 AATATTAATAA-AATAATATTTTTCTAATTAA
1 AATATTAA-AATAATAATAAATATCTAATTAA
40794503 TTAAT-TTAAAATA
1 --AATATTAAAATA
40794516 TCATCAACAT
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
31 26 0.72
32 7 0.19
33 3 0.08
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (31 bp):
AATATTAAAATAATAATAAATATCTAATTAA
Found at i:40803784 original size:37 final size:37
Alignment explanation
Indices: 40803725--40803833 Score: 191
Period size: 37 Copynumber: 2.9 Consensus size: 37
40803715 AGCTCAGACG
* *
40803725 AAATCTCCACACGAAGTTATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
40803762 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
*
40803799 TAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
40803834 ATATATTTCC
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 69 1.00
ACGTcount: A:0.27, C:0.31, G:0.19, T:0.23
Consensus pattern (37 bp):
AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
Found at i:40804030 original size:13 final size:13
Alignment explanation
Indices: 40804012--40804042 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
40804002 GGCTTTACCA
*
40804012 CATATACATATTT
1 CATATAAATATTT
40804025 CATATAAATATTT
1 CATATAAATATTT
40804038 CATAT
1 CATAT
40804043 TGACCATTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.42, C:0.13, G:0.00, T:0.45
Consensus pattern (13 bp):
CATATAAATATTT
Found at i:40804103 original size:48 final size:48
Alignment explanation
Indices: 40803979--40804198 Score: 318
Period size: 50 Copynumber: 4.5 Consensus size: 48
40803969 GCACATCGCC
* *
40803979 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATTTCATA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTC--A
* * *
40804029 TAAATATTTCATATT-GACCATTCGGCTTTACCACATATGCATATCTCA
1 TACATATTTCACATTAG-CCATTCGGCTTTACCACATATACATATCTCA
40804077 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
*
40804125 TACATATATTTCACATT-GACCATTCGGCTTTACCACATATGCATATCTCA
1 TAC--ATATTTCACATTAG-CCATTCGGCTTTACCACATATACATATCTCA
40804175 TACATATTTCACATTAGCCATTCG
1 TACATATTTCACATTAGCCATTCG
40804199 NNNNNNNNNN
Statistics
Matches: 155, Mismatches: 9, Indels: 14
0.87 0.05 0.08
Matches are distributed among these distances:
48 66 0.43
49 4 0.03
50 85 0.55
ACGTcount: A:0.31, C:0.25, G:0.07, T:0.36
Consensus pattern (48 bp):
TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
Found at i:40804106 original size:98 final size:98
Alignment explanation
Indices: 40803979--40804198 Score: 395
Period size: 98 Copynumber: 2.2 Consensus size: 98
40803969 GCACATCGCC
* * * *
40803979 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATATTTCATATAAATATTTCATATT
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACAAATATTTCACATT
40804044 GACCATTCGGCTTTACCACATATGCATATCTCA
66 GACCATTCGGCTTTACCACATATGCATATCTCA
*
40804077 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATATTTCACATT
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACAAATATTTCACATT
40804142 GACCATTCGGCTTTACCACATATGCATATCTCA
66 GACCATTCGGCTTTACCACATATGCATATCTCA
40804175 TACATATTTCACATTAGCCATTCG
1 TACATATTTCACATTAGCCATTCG
40804199 NNNNNNNNNN
Statistics
Matches: 117, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
98 117 1.00
ACGTcount: A:0.31, C:0.25, G:0.07, T:0.36
Consensus pattern (98 bp):
TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACAAATATTTCACATT
GACCATTCGGCTTTACCACATATGCATATCTCA
Found at i:40812365 original size:24 final size:24
Alignment explanation
Indices: 40812338--40812397 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
40812328 AGCTCCCGTT
40812338 ATATGGCTCTTTGTGAACTTCCCG
1 ATATGGCTCTTTGTGAACTTCCCG
* *
40812362 ATATGGTTCTTTGTGAACTTCCTG
1 ATATGGCTCTTTGTGAACTTCCCG
*
40812386 ATTATAGCTCTT
1 A-TATGGCTCTT
40812398 ATGAGCTTCC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
24 23 0.74
25 8 0.26
ACGTcount: A:0.18, C:0.20, G:0.18, T:0.43
Consensus pattern (24 bp):
ATATGGCTCTTTGTGAACTTCCCG
Found at i:40812406 original size:24 final size:24
Alignment explanation
Indices: 40812379--40812455 Score: 93
Period size: 24 Copynumber: 3.2 Consensus size: 24
40812369 TCTTTGTGAA
40812379 CTTCCTGATTATAGCTCTTATGAG
1 CTTCCTGATTATAGCTCTTATGAG
* * * *
40812403 CTTCCCGTTATATAGC-CTGGATAAG
1 CTTCCTGAT-TATAGCTCT-TATGAG
40812428 CTTCCTGATTATAGCTCTTATGAG
1 CTTCCTGATTATAGCTCTTATGAG
40812452 CTTC
1 CTTC
40812456 TCGTTATATA
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
24 23 0.55
25 19 0.45
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.39
Consensus pattern (24 bp):
CTTCCTGATTATAGCTCTTATGAG
Found at i:40812416 original size:25 final size:25
Alignment explanation
Indices: 40812388--40812519 Score: 94
Period size: 25 Copynumber: 5.4 Consensus size: 25
40812378 ACTTCCTGAT
40812388 TATAGCTCTTATGAGCTTCCCGTTA
1 TATAGCTCTTATGAGCTTCCCGTTA
* * * *
40812413 TATAGC-CTGGATAAGCTTCCTGAT-
1 TATAGCTCT-TATGAGCTTCCCGTTA
*
40812437 TATAGCTCTTATGAGCTTCTCGTTA
1 TATAGCTCTTATGAGCTTCCCGTTA
* * *
40812462 TATAGC-CTGGATAAGCTT-CC-TGA
1 TATAGCTCT-TATGAGCTTCCCGTTA
* * *
40812485 TATAACTCTTTGTGAGCTTCCCATTA
1 TATAGCTC-TTATGAGCTTCCCGTTA
*
40812511 TATGGCTCT
1 TATAGCTCT
40812520 AGAGAGAGCT
Statistics
Matches: 79, Mismatches: 20, Indels: 16
0.69 0.17 0.14
Matches are distributed among these distances:
23 7 0.09
24 28 0.35
25 36 0.46
26 8 0.10
ACGTcount: A:0.22, C:0.22, G:0.17, T:0.39
Consensus pattern (25 bp):
TATAGCTCTTATGAGCTTCCCGTTA
Found at i:40812432 original size:49 final size:49
Alignment explanation
Indices: 40812379--40812513 Score: 218
Period size: 49 Copynumber: 2.8 Consensus size: 49
40812369 TCTTTGTGAA
40812379 CTTCCTGATTATAGCTCTTATGAGCTTCCCGTTATATAGCCTGGATAAG
1 CTTCCTGATTATAGCTCTTATGAGCTTCCCGTTATATAGCCTGGATAAG
*
40812428 CTTCCTGATTATAGCTCTTATGAGCTTCTCGTTATATAGCCTGGATAAG
1 CTTCCTGATTATAGCTCTTATGAGCTTCCCGTTATATAGCCTGGATAAG
* * *
40812477 CTTCCTGA-TATAACTCTTTGTGAGCTTCCCATTATAT
1 CTTCCTGATTATAGCTC-TTATGAGCTTCCCGTTATAT
40812514 GGCTCTAGAG
Statistics
Matches: 80, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
48 7 0.09
49 73 0.91
ACGTcount: A:0.22, C:0.22, G:0.16, T:0.39
Consensus pattern (49 bp):
CTTCCTGATTATAGCTCTTATGAGCTTCCCGTTATATAGCCTGGATAAG
Found at i:40822504 original size:27 final size:27
Alignment explanation
Indices: 40822473--40822641 Score: 196
Period size: 27 Copynumber: 6.2 Consensus size: 27
40822463 TAAATTGTAC
40822473 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
40822500 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
40822526 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
40822554 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
40822582 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
40822609 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
40822636 AGCACT
1 AGCACT
40822642 GNNNNNNNNN
Statistics
Matches: 121, Mismatches: 18, Indels: 6
0.83 0.12 0.04
Matches are distributed among these distances:
27 98 0.81
28 23 0.19
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:40822587 original size:82 final size:81
Alignment explanation
Indices: 40822474--40822629 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
40822464 AAATTGTACA
* *
40822474 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
40822538 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
40822555 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
40822620 TGCGAGTTGA
65 TGCGAATTGA
40822630 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:40831684 original size:40 final size:40
Alignment explanation
Indices: 40831601--40831863 Score: 325
Period size: 40 Copynumber: 6.6 Consensus size: 40
40831591 TTGAATGCTG
* * * * * *
40831601 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA
* * * * *
40831641 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA
40831681 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
40831721 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
40831761 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
40831801 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
40831840 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
40831864 TGAACGAGGA
Statistics
Matches: 201, Mismatches: 19, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
39 35 0.17
40 158 0.79
41 8 0.04
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:40831883 original size:79 final size:80
Alignment explanation
Indices: 40831640--40831898 Score: 256
Period size: 80 Copynumber: 3.3 Consensus size: 80
40831630 AAGTGAATAT
* * * * * *
40831640 ATCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCAT
1 ATCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAT
** * *
40831704 TCGTGCGAGTTA-TTAA
65 TCGAACGAG-GAGCTAA
* * *
40831720 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
** ** *
40831785 CGTGCGAGTTGTTAA
66 CGAACGAGGAGCTAA
* * *
40831800 ATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
* *
40831864 TGAACGAGGAGCTAT
66 CGAACGAGGAGCTAA
*
40831879 ATCC-GGTTAAATCCCGAAGG
1 ATCCGGGTTAAGTCCCGAAGG
40831899 TACGTGATTT
Statistics
Matches: 156, Mismatches: 21, Indels: 6
0.85 0.11 0.03
Matches are distributed among these distances:
78 14 0.09
79 48 0.31
80 94 0.60
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (80 bp):
ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
CGAACGAGGAGCTAA
Found at i:40833495 original size:25 final size:25
Alignment explanation
Indices: 40833467--40833581 Score: 124
Period size: 25 Copynumber: 4.6 Consensus size: 25
40833457 CGGGCACACC
*
40833467 ACAGCTTGTATGAGCTTCTCAATTT
1 ACAGCTCGTATGAGCTTCTCAATTT
* * *
40833492 ACAGCTCGTATGAGTTTCCCGATTT
1 ACAGCTCGTATGAGCTTCTCAATTT
* *
40833517 ACAGTTCGTATGAGCTT-TCCAATTC
1 ACAGCTCGTATGAGCTTCT-CAATTT
* * *
40833542 ACAGCTCGTATGAGCTTCCCGATTC
1 ACAGCTCGTATGAGCTTCTCAATTT
*
40833567 ATAGCTCGTATGAGC
1 ACAGCTCGTATGAGC
40833582 ATACAGGAAT
Statistics
Matches: 75, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
25 75 1.00
ACGTcount: A:0.23, C:0.24, G:0.19, T:0.34
Consensus pattern (25 bp):
ACAGCTCGTATGAGCTTCTCAATTT
Found at i:40833549 original size:50 final size:50
Alignment explanation
Indices: 40833466--40833581 Score: 162
Period size: 50 Copynumber: 2.3 Consensus size: 50
40833456 GCGGGCACAC
* * *
40833466 CACAGCTTGTATGAGCTTCTCAATTTACAGCTCGTATGAGTTTCCCGATT
1 CACAGCTCGTATGAGCTTCTCAATTCACAGCTCGTATGAGCTTCCCGATT
* *
40833516 TACAGTTCGTATGAGCTT-TCCAATTCACAGCTCGTATGAGCTTCCCGATT
1 CACAGCTCGTATGAGCTTCT-CAATTCACAGCTCGTATGAGCTTCCCGATT
*
40833566 CATAGCTCGTATGAGC
1 CACAGCTCGTATGAGC
40833582 ATACAGGAAT
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
49 1 0.02
50 56 0.98
ACGTcount: A:0.22, C:0.25, G:0.19, T:0.34
Consensus pattern (50 bp):
CACAGCTCGTATGAGCTTCTCAATTCACAGCTCGTATGAGCTTCCCGATT
Found at i:40838904 original size:49 final size:49
Alignment explanation
Indices: 40838832--40838927 Score: 165
Period size: 49 Copynumber: 2.0 Consensus size: 49
40838822 GCTATTGTGA
* *
40838832 GGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAGTT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGATAGTT
*
40838881 GGTCACATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATAG
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGATAG
40838928 CTTTGGCTAC
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 44 1.00
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.27
Consensus pattern (49 bp):
GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGATAGTT
Found at i:40844194 original size:27 final size:26
Alignment explanation
Indices: 40844146--40844205 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
40844136 GCGAGGCTGC
*
40844146 CAGATATTGTGACGAAGTCACCAGATA
1 CAGATATTGTGACGAAGCCACCAGA-A
* * *
40844173 CAGATATTGTGGCTAGGCCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
40844199 CAGATAT
1 CAGATAT
40844206 ATATATATGT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.22
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:40844218 original size:33 final size:32
Alignment explanation
Indices: 40844167--40844230 Score: 83
Period size: 33 Copynumber: 2.0 Consensus size: 32
40844157 ACGAAGTCAC
* *
40844167 CAGATACAGATATTGTGGCTAGGCCACCAGAA
1 CAGATACAGATATTGTGGCGAAGCCACCAGAA
* *
40844199 CAGATATATATATATGTGGCGAAGCCACCAGA
1 CAGATACAGATAT-TGTGGCGAAGCCACCAGA
40844231 TTGCAGCGAG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
32 11 0.41
33 16 0.59
ACGTcount: A:0.36, C:0.20, G:0.23, T:0.20
Consensus pattern (32 bp):
CAGATACAGATATTGTGGCGAAGCCACCAGAA
Found at i:40844294 original size:27 final size:26
Alignment explanation
Indices: 40844246--40844297 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
40844236 GCGAGGCTGC
*
40844246 CAGATATTGTGACGAAGTCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
* *
40844272 CAGATATATGTGGCGAGGCCACCAGA
1 CAGATAT-TGTGACGAAGCCACCAGA
40844298 TTGCAGCGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.35, C:0.21, G:0.27, T:0.17
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:40844960 original size:27 final size:27
Alignment explanation
Indices: 40844930--40845067 Score: 147
Period size: 27 Copynumber: 5.1 Consensus size: 27
40844920 ATAGTCATTT
*
40844930 TACCCCACAAGGGTATCTT-GGTAATTC
1 TACCCTACAAGGGTAT-TTCGGTAATTC
* * *
40844957 TACCTTACAGGGGTATTTCGGTATTTC
1 TACCCTACAAGGGTATTTCGGTAATTC
*
40844984 TACCCTACAAGGGTATTTTGGTAATTC
1 TACCCTACAAGGGTATTTCGGTAATTC
* **
40845011 TATCCTAC-AGGAGTATTTATGTAATTC
1 TACCCTACAAGG-GTATTTCGGTAATTC
*
40845038 TACCTTAC-AGGGATATTTCGGTAATTC
1 TACCCTACAAGGG-TATTTCGGTAATTC
40845065 TAC
1 TAC
40845068 AACTTATCCA
Statistics
Matches: 93, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
26 6 0.06
27 87 0.94
ACGTcount: A:0.25, C:0.20, G:0.18, T:0.37
Consensus pattern (27 bp):
TACCCTACAAGGGTATTTCGGTAATTC
Found at i:40844995 original size:54 final size:52
Alignment explanation
Indices: 40844926--40845067 Score: 162
Period size: 54 Copynumber: 2.7 Consensus size: 52
40844916 CAAAATAGTC
* * *
40844926 ATTT-TACCCCACAAGGGTATCTTGGTAATTCTACCTTACAGGGGTATTTCGGT
1 ATTTCTACCCTACAAGGGTAT-TTGGTAATTCTACC-TACAGGAGTATTTAGGT
*
40844979 ATTTCTACCCTACAAGGGTATTTTGGTAATTCTATCCTACAGGAGTATTTATGT
1 ATTTCTACCCTACAAGGGTA-TTTGGTAATTCTA-CCTACAGGAGTATTTAGGT
* *
40845033 AATTCTACCTTAC-AGGGATATTTCGGTAATTCTAC
1 ATTTCTACCCTACAAGGG-TATTT-GGTAATTCTAC
40845068 AACTTATCCA
Statistics
Matches: 78, Mismatches: 6, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
53 12 0.15
54 63 0.81
55 3 0.04
ACGTcount: A:0.25, C:0.19, G:0.18, T:0.38
Consensus pattern (52 bp):
ATTTCTACCCTACAAGGGTATTTGGTAATTCTACCTACAGGAGTATTTAGGT
Found at i:40851328 original size:27 final size:26
Alignment explanation
Indices: 40851280--40851339 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
40851270 GCGAGGCTGC
*
40851280 CAGATATTGTGACGAAGTCACCAGATA
1 CAGATATTGTGACGAAGCCACCAGA-A
* * *
40851307 CAGATATTGTGGCTAGGCCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
40851333 CAGATAT
1 CAGATAT
40851340 ATATATGTGG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.22
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:40851384 original size:71 final size:67
Alignment explanation
Indices: 40851307--40851448 Score: 203
Period size: 67 Copynumber: 2.1 Consensus size: 67
40851297 TCACCAGATA
* * *
40851307 CAGATATTGTGGCTAGGCCACCAGAACAGATATATATATGTGGCGAAGCCACCAGATTGCAGCGA
1 CAGATATTGTGACGAAGCCACCAGAACAG----ATATATGTGGCGAAGCCACCAGATTGCAGCGA
40851372 GGCTGC
62 GGCTGC
* *
40851378 CAGATATTGTGACGAAGTCACCAGAACAGATATATGTGGCGAGGCCACCAGATTGCAGCGAGGCT
1 CAGATATTGTGACGAAGCCACCAGAACAGATATATGTGGCGAAGCCACCAGATTGCAGCGAGGCT
40851443 GC
66 GC
40851445 CAGA
1 CAGA
40851449 ACGCTTCCTC
Statistics
Matches: 66, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
67 41 0.62
71 25 0.38
ACGTcount: A:0.30, C:0.23, G:0.29, T:0.18
Consensus pattern (67 bp):
CAGATATTGTGACGAAGCCACCAGAACAGATATATGTGGCGAAGCCACCAGATTGCAGCGAGGCT
GC
Found at i:40851426 original size:27 final size:26
Alignment explanation
Indices: 40851378--40851429 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
40851368 GCGAGGCTGC
*
40851378 CAGATATTGTGACGAAGTCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
* *
40851404 CAGATATATGTGGCGAGGCCACCAGA
1 CAGATAT-TGTGACGAAGCCACCAGA
40851430 TTGCAGCGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.35, C:0.21, G:0.27, T:0.17
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:40852057 original size:26 final size:27
Alignment explanation
Indices: 40852028--40852081 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
40852018 TCACACAAGT
*
40852028 TAGTCATTT-ACGCACGAGGGGCAAAA
1 TAGTCATTTAACACACGAGGGGCAAAA
* *
40852054 TAGTCATTTAACACCCTAGGGGCAAAA
1 TAGTCATTTAACACACGAGGGGCAAAA
40852081 T
1 T
40852082 GGTAATTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 9 0.38
27 15 0.62
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.22
Consensus pattern (27 bp):
TAGTCATTTAACACACGAGGGGCAAAA
Found at i:40852112 original size:27 final size:27
Alignment explanation
Indices: 40852082--40852226 Score: 200
Period size: 27 Copynumber: 5.4 Consensus size: 27
40852072 GGGGCAAAAT
* *
40852082 GGTAATTTTACCCTACAAGGGTATCTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
40852109 GGTAATTCTACCTTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
40852136 GGTATTTCTACCCTACAAGGGTGTTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
40852163 AGTAATTCTATCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
40852190 GGTAATTCTACCTTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
40852217 GGTAATTCTA
1 GGTAATTCTA
40852227 TAACTTATCC
Statistics
Matches: 102, Mismatches: 16, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 102 1.00
ACGTcount: A:0.24, C:0.19, G:0.20, T:0.37
Consensus pattern (27 bp):
GGTAATTCTACCCTACAAGGGTATTTC
Found at i:40863708 original size:46 final size:45
Alignment explanation
Indices: 40863636--40863756 Score: 147
Period size: 46 Copynumber: 2.6 Consensus size: 45
40863626 GTGTTGCCAG
* *
40863636 TGTAAGACATGTCTGGGACATGCATCGGCCT-CGAGATGTAAGTGAA
1 TGTAAGACATGTCTTGGACATGCATCGGCCTACGAGATGT--GTCAA
* *
40863682 TGTAAGAGATGTCTTGGACATACATCGG-CTACGAGATGTGTCAA
1 TGTAAGACATGTCTTGGACATGCATCGGCCTACGAGATGTGTCAA
*
40863726 TGTAAGACCATGTCTTAGACATGGCATCGGC
1 TGTAAGA-CATGTCTTGGACAT-GCATCGGC
40863757 ATGGATATGT
Statistics
Matches: 64, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
44 11 0.17
45 14 0.22
46 39 0.61
ACGTcount: A:0.28, C:0.18, G:0.28, T:0.26
Consensus pattern (45 bp):
TGTAAGACATGTCTTGGACATGCATCGGCCTACGAGATGTGTCAA
Found at i:40866068 original size:14 final size:15
Alignment explanation
Indices: 40866035--40866076 Score: 59
Period size: 14 Copynumber: 2.7 Consensus size: 15
40866025 TTGACACCAA
40866035 AATTCAAATACTTAAAC
1 AATTCAAA-A-TTAAAC
40866052 AATTCAAAATT-AAC
1 AATTCAAAATTAAAC
40866066 AATTCAAAATT
1 AATTCAAAATT
40866077 TAAAGCTATG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
14 14 0.56
15 2 0.08
16 1 0.04
17 8 0.32
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (15 bp):
AATTCAAAATTAAAC
Found at i:40868758 original size:35 final size:35
Alignment explanation
Indices: 40868708--40868777 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 35
40868698 AGAAAGTTTG
*
40868708 AAAGTCATTACGGCTAATTATCGGTGTAATTACCC
1 AAAGTCATTACGGCTAATTATCGATGTAATTACCC
*
40868743 AAAGTCATTATGGCTAATTATCGATGTAATTACCC
1 AAAGTCATTACGGCTAATTATCGATGTAATTACCC
40868778 TAATTCTTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.33
Consensus pattern (35 bp):
AAAGTCATTACGGCTAATTATCGATGTAATTACCC
Found at i:40880679 original size:36 final size:36
Alignment explanation
Indices: 40880632--40880705 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
40880622 TTATTGCTAA
40880632 ATTATTGGTTCCAATTTTAAAAACACATAATTATAC
1 ATTATTGGTTCCAATTTTAAAAACACATAATTATAC
40880668 ATTATTGGTTCCAATTTTAAAAACACATAATTATAC
1 ATTATTGGTTCCAATTTTAAAAACACATAATTATAC
40880704 AT
1 AT
40880706 GCAAATTATT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.42, C:0.14, G:0.05, T:0.39
Consensus pattern (36 bp):
ATTATTGGTTCCAATTTTAAAAACACATAATTATAC
Found at i:40885562 original size:21 final size:22
Alignment explanation
Indices: 40885535--40885584 Score: 68
Period size: 21 Copynumber: 2.3 Consensus size: 22
40885525 AATATAAAAG
*
40885535 TAATTTTAT-ATTAATATTTATA
1 TAATTTTATAATTAA-ATTTAAA
40885557 T-ATTTTATAATTAAATTTAAA
1 TAATTTTATAATTAAATTTAAA
40885578 TAATTTT
1 TAATTTT
40885585 TATCATTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
21 14 0.56
22 11 0.44
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
TAATTTTATAATTAAATTTAAA
Found at i:40887868 original size:196 final size:196
Alignment explanation
Indices: 40887532--40887917 Score: 553
Period size: 196 Copynumber: 2.0 Consensus size: 196
40887522 GTCTTTTGAC
* * * *
40887532 CTCTCATTAAAACTAAATCACCACGAGACACCTTAATGCTGTTTGACTCGATGTTGATTCCACAA
1 CTCTCATCAAAACTAAAGCACCACGAGACACCTTAACGCTATTTGACTCGATGTTGATTCCACAA
**
40887597 CCCTTCAAGTTTAAATTTCCTAAGGAAATGAGGTTTTTCTTTAAATCAGTCACATGTCTAACATC
66 CCCTTCAAGTCCAAATTTCCTAAGGAAATGAGGTTTTTCTTTAAATCAGTCACATGTCTAACATC
* * * * *
40887662 TGACAAAGTTCTAATAATTCTATCC-TGCATTCTGATTTGAATGGTGCCCATACCAATTATTTCA
131 TGAAAAAGTTCTAATAATTCTA-CCATGCATTCTAATCTAAACGGTGCCCATACCAATTATTTCA
40887726 AG
195 AG
* *
40887728 CTCTCATCAAAACTAAAGCACCACGAGATACCTTAACG-TCATTTGACTCGATGTTGATTCTACA
1 CTCTCATCAAAACTAAAGCACCACGAGACACCTTAACGCT-ATTTGACTCGATGTTGATTCCACA
** * * * *
40887792 ACCCTTTGAGTCCAAATTTCCTAGGGAGATGATGTTTTTCTTTAAATCTA-TCACATGTCTGACA
65 ACCCTTCAAGTCCAAATTTCCTAAGGAAATGAGGTTTTTCTTTAAATC-AGTCACATGTCTAACA
40887856 TCTGAAAAAGTTCTAATAATTCTACCATGCATTCTAATCTAAACGGTGCCCATACCAATTAT
129 TCTGAAAAAGTTCTAATAATTCTACCATGCATTCTAATCTAAACGGTGCCCATACCAATTAT
40887918 CTTACAAGGT
Statistics
Matches: 168, Mismatches: 19, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
195 3 0.02
196 164 0.98
197 1 0.01
ACGTcount: A:0.31, C:0.23, G:0.13, T:0.33
Consensus pattern (196 bp):
CTCTCATCAAAACTAAAGCACCACGAGACACCTTAACGCTATTTGACTCGATGTTGATTCCACAA
CCCTTCAAGTCCAAATTTCCTAAGGAAATGAGGTTTTTCTTTAAATCAGTCACATGTCTAACATC
TGAAAAAGTTCTAATAATTCTACCATGCATTCTAATCTAAACGGTGCCCATACCAATTATTTCAA
G
Found at i:40888351 original size:30 final size:30
Alignment explanation
Indices: 40888317--40888414 Score: 90
Period size: 30 Copynumber: 3.3 Consensus size: 30
40888307 AGCTCACTCC
40888317 TAGCTCATATTCAGCTCACGAGCTAAACCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
** * * * * *
40888347 TAGCTCAGCTTCAGCTTAGGAGTTTAATCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
* * *
40888377 CAGCTCA-ACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
40888407 TAGCTCAT
1 TAGCTCAT
40888415 TTTAGTTTAA
Statistics
Matches: 50, Mismatches: 16, Indels: 3
0.72 0.23 0.04
Matches are distributed among these distances:
30 50 1.00
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.30
Consensus pattern (30 bp):
TAGCTCATATTCAGCTCACGAGCTAAACCT
Found at i:40890237 original size:37 final size:37
Alignment explanation
Indices: 40890186--40890256 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
40890176 CATTCTTGTA
40890186 AAGAGAAAACAAAGAAAA-GAAAAGAAAAAGAAAAAGC
1 AAGAGAAAACAAAGAAAATG-AAAGAAAAAGAAAAAGC
*
40890223 AAGAGAAGAA-AAAGAAAATGAAATAAAAAGAAAA
1 AAGAGAA-AACAAAGAAAATGAAAGAAAAAGAAAA
40890257 GAGAGGCAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 28 0.90
38 3 0.10
ACGTcount: A:0.76, C:0.03, G:0.18, T:0.03
Consensus pattern (37 bp):
AAGAGAAAACAAAGAAAATGAAAGAAAAAGAAAAAGC
Found at i:40890256 original size:6 final size:6
Alignment explanation
Indices: 40890196--40890245 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
40890186 AAGAGAAAAC
*
40890196 AAAG-A AAAG-A AAAGAA AAAGAA AAAGCAA GAGAAGAA AAAGAA AATGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAG-AA -A-AAGAA AAAGAA AAAGAA
40890245 A
1 A
40890246 TAAAAAGAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
5 9 0.22
6 22 0.55
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.76, C:0.02, G:0.20, T:0.02
Consensus pattern (6 bp):
AAAGAA
Found at i:40890338 original size:11 final size:12
Alignment explanation
Indices: 40890306--40890336 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
40890296 TTGAGAGAAC
40890306 TTGAAAAAGCCT
1 TTGAAAAAGCCT
40890318 TTGAAAAAGCCT
1 TTGAAAAAGCCT
40890330 TTGAAAA
1 TTGAAAA
40890337 GCAAAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:40892551 original size:30 final size:30
Alignment explanation
Indices: 40892517--40892614 Score: 90
Period size: 30 Copynumber: 3.3 Consensus size: 30
40892507 AGCTCACTCC
40892517 TAGCTCATATTCAGCTCACGAGCTAAACCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
** * * * * *
40892547 TAGCTCAGCTTCAGCTTAGGAGTTTAATCT
1 TAGCTCATATTCAGCTCACGAGCTAAACCT
* * *
40892577 CAGCTCA-ACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
40892607 TAGCTCAT
1 TAGCTCAT
40892615 TTTAGTTTAA
Statistics
Matches: 50, Mismatches: 16, Indels: 3
0.72 0.23 0.04
Matches are distributed among these distances:
30 50 1.00
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.30
Consensus pattern (30 bp):
TAGCTCATATTCAGCTCACGAGCTAAACCT
Found at i:40894364 original size:49 final size:49
Alignment explanation
Indices: 40894288--40894455 Score: 144
Period size: 49 Copynumber: 3.4 Consensus size: 49
40894278 GTTGTGTGTT
* * *
40894288 AGTGTAAGACTTGTCTGGGACATGGCATCAACAC-CGATAGATGAGAGCC
1 AGTGTAAGACCTGTCTGGGACACGGCATCAAC-CTCGATAGATGAAAGCC
** * **
40894337 AGTGTAAGACCTGTCTGGGACACGGCATCGGCCTCGATATATGAAAGTT
1 AGTGTAAGACCTGTCTGGGACACGGCATCAACCTCGATAGATGAAAGCC
* * * * * * **
40894386 AGTGTAAGACCTGTCTAGAACATGCCATCGACTTCGAT-G-TGTTAGCC
1 AGTGTAAGACCTGTCTGGGACACGGCATCAACCTCGATAGATGAAAGCC
*
40894433 AGTGTAAGACCATGTTTGGGACA
1 AGTGTAAGACC-TGTCTGGGACA
40894456 TGGCGTCGGC
Statistics
Matches: 95, Mismatches: 22, Indels: 5
0.78 0.18 0.04
Matches are distributed among these distances:
47 15 0.16
48 9 0.09
49 71 0.75
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.24
Consensus pattern (49 bp):
AGTGTAAGACCTGTCTGGGACACGGCATCAACCTCGATAGATGAAAGCC
Found at i:40904694 original size:19 final size:19
Alignment explanation
Indices: 40904670--40904709 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
40904660 CTTAGGCCAT
*
40904670 TATGGGCCTCGTTGGGC-CG
1 TATGGGCC-CATTGGGCTCG
40904689 TATGGGCCCATTGGGCTCG
1 TATGGGCCCATTGGGCTCG
40904708 TA
1 TA
40904710 GGCCCACACG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.10, C:0.25, G:0.38, T:0.28
Consensus pattern (19 bp):
TATGGGCCCATTGGGCTCG
Found at i:40907571 original size:16 final size:15
Alignment explanation
Indices: 40907550--40907597 Score: 69
Period size: 16 Copynumber: 3.1 Consensus size: 15
40907540 GATGTGAATA
40907550 ATAAAATATATAAAAT
1 ATAAAATAT-TAAAAT
40907566 ATAAAATATTAAAAT
1 ATAAAATATTAAAAT
*
40907581 ATCAAAATATTAGAAT
1 AT-AAAATATTAAAAT
40907597 A
1 A
40907598 ATAATAATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 8 0.27
16 22 0.73
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (15 bp):
ATAAAATATTAAAAT
Found at i:40907580 original size:8 final size:8
Alignment explanation
Indices: 40907546--40907597 Score: 61
Period size: 8 Copynumber: 6.5 Consensus size: 8
40907536 CAATGATGTG
*
40907546 AATAATAA
1 AATATTAA
40907554 AATATATAA
1 AATAT-TAA
40907563 AATA-TAA
1 AATATTAA
40907570 AATATTAA
1 AATATTAA
*
40907578 AATATCAA
1 AATATTAA
*
40907586 AATATTAG
1 AATATTAA
40907594 AATA
1 AATA
40907598 ATAATAATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
7 7 0.18
8 24 0.63
9 7 0.18
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (8 bp):
AATATTAA
Found at i:40907597 original size:24 final size:24
Alignment explanation
Indices: 40907545--40907601 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
40907535 ACAATGATGT
*
40907545 GAATAATAAAATATATAAAATATA
1 GAATAATAAAATATACAAAATATA
* *
40907569 AAATATTAAAATAT-CAAAATATTA
1 GAATAATAAAATATACAAAATA-TA
40907593 GAATAATAA
1 GAATAATAA
40907602 TAATTAATAT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
23 6 0.22
24 21 0.78
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.30
Consensus pattern (24 bp):
GAATAATAAAATATACAAAATATA
Found at i:40909178 original size:14 final size:14
Alignment explanation
Indices: 40909158--40909199 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
40909148 ATGAGTTTTT
40909158 TTTAAAACACAGAAA
1 TTTAAAA-ACAGAAA
*
40909173 -TTAAAAAAAGAGAA
1 TTTAAAAACAGA-AA
40909187 TTTAAAAACAGAA
1 TTTAAAAACAGAA
40909200 TTTGAAAAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
13 4 0.17
14 9 0.39
15 10 0.43
ACGTcount: A:0.64, C:0.07, G:0.10, T:0.19
Consensus pattern (14 bp):
TTTAAAAACAGAAA
Found at i:40909199 original size:102 final size:101
Alignment explanation
Indices: 40909072--40909256 Score: 230
Period size: 102 Copynumber: 1.8 Consensus size: 101
40909062 AATTGACTCT
* * * *
40909072 TTAAAAAAATAGACATTAAAACAGAAATTAAAAATAGCTCAGCACGTGAG-CCAAGGCTCAACTC
1 TTAAAAAAAGAGACATTAAAACAGAAATTAAAAAGACCTCAGCACGTG-GCCCAAGACTCAACTC
40909136 ACCTCTCGCAATATGAGTTTTTTTTAAAACACAGAAA
65 ACCTCTCGCAATATGAGTTTTTTTTAAAACACAGAAA
* * ** ** *
40909173 TTAAAAAAAGAGA-ATTTAAAAACAGAATTTGAAAAGACCTTGGCGTGTGGCCCGAGACTCAACT
1 TTAAAAAAAGAGACA-TT-AAAACAGAAATTAAAAAGACCTCAGCACGTGGCCCAAGACTCAACT
40909237 CACCTCTCGCAATATGAGTT
64 CACCTCTCGCAATATGAGTT
40909257 GATTCTTAAA
Statistics
Matches: 70, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
100 1 0.01
101 15 0.21
102 54 0.77
ACGTcount: A:0.42, C:0.19, G:0.16, T:0.24
Consensus pattern (101 bp):
TTAAAAAAAGAGACATTAAAACAGAAATTAAAAAGACCTCAGCACGTGGCCCAAGACTCAACTCA
CCTCTCGCAATATGAGTTTTTTTTAAAACACAGAAA
Found at i:40909284 original size:14 final size:14
Alignment explanation
Indices: 40909265--40909296 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
40909255 TTGATTCTTA
40909265 AAAAGCATAAATTG
1 AAAAGCATAAATTG
40909279 AAAAGCATAAATTG
1 AAAAGCATAAATTG
40909293 AAAA
1 AAAA
40909297 TACCTCAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.62, C:0.06, G:0.12, T:0.19
Consensus pattern (14 bp):
AAAAGCATAAATTG
Found at i:40909394 original size:192 final size:189
Alignment explanation
Indices: 40909125--40909474 Score: 574
Period size: 192 Copynumber: 1.8 Consensus size: 189
40909115 ACGTGAGCCA
* *
40909125 AGGCTCAACTCACCTCTCGCAATATGAGTTTTTTTTAAAACACAGAAATTAAAAAAAGAGAATTT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTTTTTTTAAAACACAGAAATTAAAAAAACAGAAATT
*
40909190 AAAAACAGAATTTGAAAAGACCTTGGCGTGTGGCCCGAGACTCAACTCACCTCTCGCAATATGAG
66 AAAAACAGAATTTGAAAAGACCTCGGCGTGTGGCCCGAGACTCAACTCACCTCTCGCAATATGAG
*
40909255 TTGATTCTTAAAAAGCATAAATTGAAAAGCATAAATTGAAAATACCTCAATGTGCCCTG
131 TTGATTCTTAAAAAGCAGAAATTGAAAAGCATAAATTGAAAATACCTCAATGTGCCCTG
* * *
40909314 AGGCTCAACTCACCTCTTGCAATATGAGTTGATTTTTTTGAAACACAGAAATTTAAAAAACAGAA
1 AGGCTCAACTCACCTCTCGCAATATGAG-T--TTTTTTTAAAACACAGAAATTAAAAAAACAGAA
*
40909379 ATTAAAGACAGAATTTGAAAAGACCTCGGCGTGTGGCCCGAGACTCAACTCACCTCTCGCAATAT
63 ATTAAAAACAGAATTTGAAAAGACCTCGGCGTGTGGCCCGAGACTCAACTCACCTCTCGCAATAT
* * *
40909444 GAGTTGATTTTTGAAAAGTAGAAATTGAAAA
128 GAGTTGATTCTTAAAAAGCAGAAATTGAAAA
40909475 CGCCTCAGCG
Statistics
Matches: 147, Mismatches: 11, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
189 27 0.18
190 1 0.01
192 119 0.81
ACGTcount: A:0.39, C:0.18, G:0.17, T:0.26
Consensus pattern (189 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTTTTTTTAAAACACAGAAATTAAAAAAACAGAAATT
AAAAACAGAATTTGAAAAGACCTCGGCGTGTGGCCCGAGACTCAACTCACCTCTCGCAATATGAG
TTGATTCTTAAAAAGCAGAAATTGAAAAGCATAAATTGAAAATACCTCAATGTGCCCTG
Found at i:40909516 original size:75 final size:74
Alignment explanation
Indices: 40909388--40909681 Score: 277
Period size: 75 Copynumber: 3.8 Consensus size: 74
40909378 AATTAAAGAC
* * * *
40909388 AGAATTTGAAAAGACCTCGGCGTGTGGCCCGAGACTCAACTCACCTCTCGCAATATGAGTTGA-T
1 AGAAATTGAAAATACCTCAGCGTGT--CCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATT
40909452 TTTTGAAAAGT
64 TTTTGAAAAGT
** * *
40909463 AGAAATTGAAAACGCCTCAGCGTGTGACCCGAGGCTTAACTCACCTCTTGCAATATGAGTTGATT
1 AGAAATTGAAAATACCTCAGCGTGT--CCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATT
*
40909528 CTTTTGAAAAATCT
64 -TTTTG-AAAA-GT
* * * *
40909542 AAAAAAAAAATTGACAATACCTCAGCGTGTCCCGAGGCTCAACTCATCTCTCACAATATGAGTTG
1 -----AGAAATTGAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTG
*
40909607 ATTTTTTG-AAAGAC
61 ATTTTTTGAAAAG-T
* ** * * *
40909621 AGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACTTCTTGCAGTATGAGTTGA
1 AGAAATTGAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
40909682 ATTATGAAAC
Statistics
Matches: 180, Mismatches: 29, Indels: 21
0.78 0.13 0.09
Matches are distributed among these distances:
74 51 0.28
75 55 0.31
76 1 0.01
77 5 0.03
78 4 0.02
79 4 0.02
81 5 0.03
82 34 0.19
84 21 0.12
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.28
Consensus pattern (74 bp):
AGAAATTGAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
TTGAAAAGT
Found at i:40920160 original size:16 final size:15
Alignment explanation
Indices: 40920139--40920186 Score: 69
Period size: 16 Copynumber: 3.1 Consensus size: 15
40920129 GATGTGAATA
40920139 ATAAAATATATAAAAT
1 ATAAAATAT-TAAAAT
40920155 ATAAAATATTAAAAT
1 ATAAAATATTAAAAT
*
40920170 ATCAAAATATTAGAAT
1 AT-AAAATATTAAAAT
40920186 A
1 A
40920187 ATAATAATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 8 0.27
16 22 0.73
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (15 bp):
ATAAAATATTAAAAT
Found at i:40920169 original size:8 final size:8
Alignment explanation
Indices: 40920135--40920186 Score: 61
Period size: 8 Copynumber: 6.5 Consensus size: 8
40920125 CAATGATGTG
*
40920135 AATAATAA
1 AATATTAA
40920143 AATATATAA
1 AATAT-TAA
40920152 AATA-TAA
1 AATATTAA
40920159 AATATTAA
1 AATATTAA
*
40920167 AATATCAA
1 AATATTAA
*
40920175 AATATTAG
1 AATATTAA
40920183 AATA
1 AATA
40920187 ATAATAATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
7 7 0.18
8 24 0.63
9 7 0.18
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (8 bp):
AATATTAA
Found at i:40920186 original size:24 final size:24
Alignment explanation
Indices: 40920134--40920190 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
40920124 ACAATGATGT
*
40920134 GAATAATAAAATATATAAAATATA
1 GAATAATAAAATATACAAAATATA
* *
40920158 AAATATTAAAATAT-CAAAATATTA
1 GAATAATAAAATATACAAAATA-TA
40920182 GAATAATAA
1 GAATAATAA
40920191 TAATTAATAT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
23 6 0.22
24 21 0.78
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.30
Consensus pattern (24 bp):
GAATAATAAAATATACAAAATATA
Found at i:40920404 original size:22 final size:24
Alignment explanation
Indices: 40920341--40920405 Score: 80
Period size: 25 Copynumber: 2.8 Consensus size: 24
40920331 CATGATAATA
*
40920341 TTAAAAATATGTACATAATATAGTG
1 TTAAAAATATATACATAATATAG-G
*
40920366 TTAAAAATACATACATAATATA-G
1 TTAAAAATATATACATAATATAGG
*
40920389 TT-AAGATATATACATAA
1 TTAAAAATATATACATAA
40920406 GATAACATGT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
22 13 0.36
23 3 0.08
25 20 0.56
ACGTcount: A:0.52, C:0.06, G:0.08, T:0.34
Consensus pattern (24 bp):
TTAAAAATATATACATAATATAGG
Found at i:40920460 original size:25 final size:25
Alignment explanation
Indices: 40920426--40920559 Score: 86
Period size: 25 Copynumber: 5.6 Consensus size: 25
40920416 AGAAAAATAT
40920426 ATATATAAATAATATAATATTAAAG
1 ATATATAAATAATATAATATTAAAG
* * * *
40920451 ATATATAAATAAAATAGTATAAAAT
1 ATATATAAATAATATAATATTAAAG
* *
40920476 ATATATATACGTAATATAGA-ATTTAA-
1 ATATATA-A-ATAATATA-ATATTAAAG
** *
40920502 A-ATATACCTAATAT-AT-TAAAAG
1 ATATATAAATAATATAATATTAAAG
*
40920524 A-ATATATATAATATAATATT-AAG
1 ATATATAAATAATATAATATTAAAG
*
40920547 AAATAT-AATAATA
1 ATATATAAATAATA
40920560 ACAAAAAAAG
Statistics
Matches: 84, Mismatches: 17, Indels: 18
0.71 0.14 0.15
Matches are distributed among these distances:
21 4 0.05
22 12 0.14
23 18 0.21
24 5 0.06
25 33 0.39
26 2 0.02
27 10 0.12
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.35
Consensus pattern (25 bp):
ATATATAAATAATATAATATTAAAG
Found at i:40920494 original size:27 final size:27
Alignment explanation
Indices: 40920355--40920494 Score: 94
Period size: 25 Copynumber: 5.3 Consensus size: 27
40920345 AAATATGTAC
* * * *
40920355 ATAATATAGTGTTAAA-A-ATACATAC
1 ATAATATAGTATAAAATATATATATAA
* *
40920380 ATAATATAGT-TAAGATATATACATAA
1 ATAATATAGTATAAAATATATATATAA
* *
40920406 GATAACAT-GTAGAAAAATATATATATAA
1 -ATAATATAGTA-TAAAATATATATATAA
* * *
40920434 ATAATATAATAT-TAA-AGATATATAA
1 ATAATATAGTATAAAATATATATATAA
* *
40920459 ATAAAATAGTATAAAATATATATATAC
1 ATAATATAGTATAAAATATATATATAA
*
40920486 GTAATATAG
1 ATAATATAG
40920495 AATTTAAAAT
Statistics
Matches: 88, Mismatches: 19, Indels: 14
0.73 0.16 0.12
Matches are distributed among these distances:
24 3 0.03
25 30 0.34
26 13 0.15
27 27 0.31
28 15 0.17
ACGTcount: A:0.56, C:0.04, G:0.08, T:0.33
Consensus pattern (27 bp):
ATAATATAGTATAAAATATATATATAA
Found at i:40921080 original size:30 final size:30
Alignment explanation
Indices: 40921044--40921148 Score: 174
Period size: 30 Copynumber: 3.5 Consensus size: 30
40921034 TAGGTACAAG
*
40921044 TGGTGGTGGAGAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
* *
40921074 TGGTGGTGGAAAAAGAGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
*
40921104 TGATGGTGGAAAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
40921134 TGGTGGTGGAAAAGG
1 TGGTGGTGGAAAAGG
40921149 CTAAGATTTA
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 68 1.00
ACGTcount: A:0.23, C:0.03, G:0.50, T:0.25
Consensus pattern (30 bp):
TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
Found at i:40926204 original size:38 final size:38
Alignment explanation
Indices: 40926153--40926443 Score: 213
Period size: 38 Copynumber: 6.9 Consensus size: 38
40926143 ATGGAAAAAA
* *
40926153 GTGGTGCTAAGTGGATATACCATGGTTATACGTGTAAC
1 GTGGTGCTAAGTGGATATACCACGGTTATACATGTAAC
*
40926191 GTGGTGCTAAGTGGATATACCACGATTACACATATTGAAACATGTAAC
1 GTGGTGCTAAGTGGATATACCACG-GT-----TA-T---ACATGTAAC
* * *
40926239 GTGGTGCTAAGTGGATATGCCACAGTTACATATATTGATTCATTAAC
1 GTGGTGCTAAGTGGATATACCACGGTT--ATACA-TG------TAAC
*
40926286 GTGGTGCTAAGTGGATATACCACGGTTAAACATGTAAC
1 GTGGTGCTAAGTGGATATACCACGGTTATACATGTAAC
* *
40926324 GTGGTGCTAAGTGGATATGCCACGGTTACATATATTGATTCATTAAC
1 GTGGTGCTAAGTGGATATACCACGGTT--ATACA-TG------TAAC
* *
40926371 GTGGTGCTAAGTGGATATACCACGATTAAACATGTAAC
1 GTGGTGCTAAGTGGATATACCACGGTTATACATGTAAC
* *
40926409 GTGCTGCTAAGTGGATATGCCACGGTTATACATGT
1 GTGGTGCTAAGTGGATATACCACGGTTATACATGT
40926444 TAATTTAAAA
Statistics
Matches: 203, Mismatches: 22, Indels: 56
0.72 0.08 0.20
Matches are distributed among these distances:
38 88 0.43
39 1 0.00
40 5 0.02
41 4 0.02
42 1 0.00
43 1 0.00
44 7 0.03
45 7 0.03
47 59 0.29
48 30 0.15
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.30
Consensus pattern (38 bp):
GTGGTGCTAAGTGGATATACCACGGTTATACATGTAAC
Found at i:40926291 original size:95 final size:93
Alignment explanation
Indices: 40926187--40926436 Score: 334
Period size: 85 Copynumber: 2.8 Consensus size: 93
40926177 GTTATACGTG
40926187 TAACGTGGTGCTAAGTGGATATACCACGATTACACATATTGAAACATGTAACGTGGTGCTAAGTG
1 TAACGTGGTGCTAAGTGGATATACCACGATTA-ACATATT-AAACATGTAACGTGGTGCTAAGTG
40926252 GATATGCCACAGTTACATATATTGATTCAT
64 GATATGCCACAGTTACATATATTGATTCAT
*
40926282 TAACGTGGTGCTAAGTGGATATACCACG--------GTTAAACATGTAACGTGGTGCTAAGTGGA
1 TAACGTGGTGCTAAGTGGATATACCACGATTAACATATTAAACATGTAACGTGGTGCTAAGTGGA
*
40926339 TATGCCACGGTTACATATATTGATTCAT
66 TATGCCACAGTTACATATATTGATTCAT
*
40926367 TAACGTGGTGCTAAGTGGATATACCACG--------ATTAAACATGTAACGTGCTGCTAAGTGGA
1 TAACGTGGTGCTAAGTGGATATACCACGATTAACATATTAAACATGTAACGTGGTGCTAAGTGGA
*
40926424 TATGCCACGGTTA
66 TATGCCACAGTTA
40926437 TACATGTTAA
Statistics
Matches: 151, Mismatches: 4, Indels: 10
0.92 0.02 0.06
Matches are distributed among these distances:
85 121 0.80
86 2 0.01
95 28 0.19
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.30
Consensus pattern (93 bp):
TAACGTGGTGCTAAGTGGATATACCACGATTAACATATTAAACATGTAACGTGGTGCTAAGTGGA
TATGCCACAGTTACATATATTGATTCAT
Found at i:40926330 original size:85 final size:85
Alignment explanation
Indices: 40926228--40926436 Score: 391
Period size: 85 Copynumber: 2.5 Consensus size: 85
40926218 ACACATATTG
*
40926228 AAACATGTAACGTGGTGCTAAGTGGATATGCCACAGTTACATATATTGATTCATTAACGTGGTGC
1 AAACATGTAACGTGGTGCTAAGTGGATATGCCACGGTTACATATATTGATTCATTAACGTGGTGC
*
40926293 TAAGTGGATATACCACGGTT
66 TAAGTGGATATACCACGATT
40926313 AAACATGTAACGTGGTGCTAAGTGGATATGCCACGGTTACATATATTGATTCATTAACGTGGTGC
1 AAACATGTAACGTGGTGCTAAGTGGATATGCCACGGTTACATATATTGATTCATTAACGTGGTGC
40926378 TAAGTGGATATACCACGATT
66 TAAGTGGATATACCACGATT
*
40926398 AAACATGTAACGTGCTGCTAAGTGGATATGCCACGGTTA
1 AAACATGTAACGTGGTGCTAAGTGGATATGCCACGGTTA
40926437 TACATGTTAA
Statistics
Matches: 121, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
85 121 1.00
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.30
Consensus pattern (85 bp):
AAACATGTAACGTGGTGCTAAGTGGATATGCCACGGTTACATATATTGATTCATTAACGTGGTGC
TAAGTGGATATACCACGATT
Found at i:40928221 original size:21 final size:20
Alignment explanation
Indices: 40928174--40928221 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
40928164 TTTTGATCAT
40928174 ATTATTAAATTAACTTTAAA
1 ATTATTAAATTAACTTTAAA
* *
40928194 ATAATTATAATTTAA-TTTAGA
1 ATTATTA-AA-TTAACTTTAAA
40928215 ATTATTA
1 ATTATTA
40928222 GTTGAAATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 6 0.26
21 13 0.57
22 4 0.17
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (20 bp):
ATTATTAAATTAACTTTAAA
Found at i:40930636 original size:40 final size:40
Alignment explanation
Indices: 40930581--40930804 Score: 315
Period size: 40 Copynumber: 5.5 Consensus size: 40
40930571 TATTCGGATG
*
40930581 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTCCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* *
40930621 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* *
40930661 ATATCCGGGCGAAGTCCCGAAGGCATTTGTGCGAGTAGTTGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGC--G-AGTTACT
* * *
40930704 ATACCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* *
40930744 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
40930784 ATATCC-GGCTAAATCCCGAAG
1 ATATCCGGGCTAAGTCCCGAAG
40930805 ATACTTGGGT
Statistics
Matches: 162, Mismatches: 19, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
39 13 0.08
40 114 0.70
43 35 0.22
ACGTcount: A:0.23, C:0.24, G:0.28, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
Found at i:40930737 original size:83 final size:80
Alignment explanation
Indices: 40930581--40930804 Score: 369
Period size: 83 Copynumber: 2.8 Consensus size: 80
40930571 TATTCGGATG
*
40930581 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTCCTATATCCGGGCTAAGTCCCGAAGGCA
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTGCTATATCCGGGCTAAGTCCCGAAGGCA
40930646 TTTGTGCTAGTGACT
66 TTTGTGCTAGTGACT
* *
40930661 ATATCCGGGCGAAGTCCCGAAGGCATTTGTGCGAGTAGTTGCTATACCCGGGCTAAGTCCCGAAG
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGC--G-AGTTGCTATATCCGGGCTAAGTCCCGAAG
40930726 GCATTTGTGCTAGTGACT
63 GCATTTGTGCTAGTGACT
* *
40930744 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATATCC-GGCTAAATCCCGAAG
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTGCTATATCCGGGCTAAGTCCCGAAG
40930805 ATACTTGGGT
Statistics
Matches: 134, Mismatches: 7, Indels: 7
0.91 0.05 0.05
Matches are distributed among these distances:
79 14 0.10
80 43 0.32
81 1 0.01
82 1 0.01
83 75 0.56
ACGTcount: A:0.23, C:0.24, G:0.28, T:0.25
Consensus pattern (80 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTGCTATATCCGGGCTAAGTCCCGAAGGCA
TTTGTGCTAGTGACT
Found at i:40938159 original size:14 final size:14
Alignment explanation
Indices: 40938130--40938169 Score: 66
Period size: 14 Copynumber: 3.0 Consensus size: 14
40938120 AAATTGAAAG
40938130 TTTTGTTTTTTT--
1 TTTTGTTTTTTTGC
40938142 TTTTGTTTTTTTGC
1 TTTTGTTTTTTTGC
40938156 TTTTGTTTTTTTGC
1 TTTTGTTTTTTTGC
40938170 GAATAGAAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
12 12 0.46
14 14 0.54
ACGTcount: A:0.00, C:0.05, G:0.12, T:0.82
Consensus pattern (14 bp):
TTTTGTTTTTTTGC
Found at i:40938442 original size:92 final size:92
Alignment explanation
Indices: 40938285--40938454 Score: 322
Period size: 92 Copynumber: 1.8 Consensus size: 92
40938275 GACTGCGACG
**
40938285 AAGCCACGACAGCTCCAATGGCTAGTTCCAGCCCCTTTTCGAAGAAAAAAAAGGAAAACAAATTT
1 AAGCCACGACAGCTCCAATGGCTAGACCCAGCCCCTTTTCGAAGAAAAAAAAGGAAAACAAATTT
40938350 TTTTTAAACTGTTGGGAAGTTGAAAAA
66 TTTTTAAACTGTTGGGAAGTTGAAAAA
40938377 AAGCCACGACAGCTCCAATGGCTAGACCCAGCCCCTTTTCGAAGAAAAAAAAGGAAAACAAATTT
1 AAGCCACGACAGCTCCAATGGCTAGACCCAGCCCCTTTTCGAAGAAAAAAAAGGAAAACAAATTT
40938442 TTTTTAAACTGTT
66 TTTTTAAACTGTT
40938455 TCAAATGAAT
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
92 76 1.00
ACGTcount: A:0.39, C:0.21, G:0.17, T:0.24
Consensus pattern (92 bp):
AAGCCACGACAGCTCCAATGGCTAGACCCAGCCCCTTTTCGAAGAAAAAAAAGGAAAACAAATTT
TTTTTAAACTGTTGGGAAGTTGAAAAA
Found at i:40944661 original size:41 final size:41
Alignment explanation
Indices: 40944605--40944956 Score: 297
Period size: 41 Copynumber: 8.7 Consensus size: 41
40944595 AATGCCGCAA
* *
40944605 AAAAAT-GAGAAATAGCGGTGTTTTTATCTAAAACGCCACT
1 AAAAATAGATAAATAGCGGCGTTTTTATCTAAAACGCCACT
* * *
40944645 AAAAATAGATAAATAGCGGTGTTTTTGTCTAAAATGCCACT
1 AAAAATAGATAAATAGCGGCGTTTTTATCTAAAACGCCACT
* * * *
40944686 AAAAACAGATTAATAGCGGTGTTTTTAACT-AAACGCCACT
1 AAAAATAGATAAATAGCGGCGTTTTTATCTAAAACGCCACT
* ** ** *
40944726 AAAAACTGGGGAAATAGCGGCGTTTTTATCCCAAATGCCACT
1 AAAAA-TAGATAAATAGCGGCGTTTTTATCTAAAACGCCACT
* * *
40944768 AAAACTA-ATCAATAGCGGCGTTTTTATCTAAAATGCCA-T
1 AAAAATAGATAAATAGCGGCGTTTTTATCTAAAACGCCACT
* * *
40944807 GAAAAACTAGAGAAATAGCGGCGTTTTTGTC-CAAACGCCACT
1 -AAAAA-TAGATAAATAGCGGCGTTTTTATCTAAAACGCCACT
* * * *
40944849 AAAAACT-GATCAATAGCGACATTTTTATCCAAAACGCCACT
1 AAAAA-TAGATAAATAGCGGCGTTTTTATCTAAAACGCCACT
* * * * * *
40944890 AAAAACTGGAGAAAAAGCGGCGTTTTTGTC-CAAACACCACT
1 AAAAA-TAGATAAATAGCGGCGTTTTTATCTAAAACGCCACT
* * *
40944931 AAAACT-GATCAATAGTGGCGTTTTTA
1 AAAAATAGATAAATAGCGGCGTTTTTA
40944957 GGCCCAAACG
Statistics
Matches: 253, Mismatches: 50, Indels: 19
0.79 0.16 0.06
Matches are distributed among these distances:
39 16 0.06
40 68 0.27
41 121 0.48
42 48 0.19
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.26
Consensus pattern (41 bp):
AAAAATAGATAAATAGCGGCGTTTTTATCTAAAACGCCACT
Found at i:40944849 original size:163 final size:163
Alignment explanation
Indices: 40944615--40944956 Score: 456
Period size: 163 Copynumber: 2.1 Consensus size: 163
40944605 AAAAATGAGA
* * * *
40944615 AATAGCGGTGTTTTTATCTAAAACGCCACTAAAAATAGATAAATAGCGGTGTTTTTGTCTAAAAT
1 AATAGCGGCGTTTTTATCTAAAACGCCACTAAAAATAGAGAAATAGCGGCGTTTTTGTCTAAAAC
* *** * * *
40944680 GCCACTAAAAACAGATTAATAGCGGTGTTTTTA-ACTAAACGCCACTAAAAACTGGGGAAATAGC
66 GCCACTAAAAACAGATCAATAGCGACATTTTTATACAAAACGCCACTAAAAACTGGAGAAAAAGC
**
40944744 GGCGTTTTTATCCCAAATGCCACTAAAACTAATC
131 GGCGTTTTTAT-CCAAACACCACTAAAACTAATC
* *
40944778 AATAGCGGCGTTTTTATCTAAAATGCCA-TGAAAAACTAGAGAAATAGCGGCGTTTTTGTC-CAA
1 AATAGCGGCGTTTTTATCTAAAACGCCACT-AAAAA-TAGAGAAATAGCGGCGTTTTTGTCTAAA
* *
40944841 ACGCCACTAAAAACTGATCAATAGCGACATTTTTATCCAAAACGCCACTAAAAACTGGAGAAAAA
64 ACGCCACTAAAAACAGATCAATAGCGACATTTTTATACAAAACGCCACTAAAAACTGGAGAAAAA
* *
40944906 GCGGCGTTTTTGTCCAAACACCACTAAAACTGATC
129 GCGGCGTTTTTATCCAAACACCACTAAAACTAATC
*
40944941 AATAGTGGCGTTTTTA
1 AATAGCGGCGTTTTTA
40944957 GGCCCAAACG
Statistics
Matches: 156, Mismatches: 20, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
162 1 0.01
163 96 0.62
164 59 0.38
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.27
Consensus pattern (163 bp):
AATAGCGGCGTTTTTATCTAAAACGCCACTAAAAATAGAGAAATAGCGGCGTTTTTGTCTAAAAC
GCCACTAAAAACAGATCAATAGCGACATTTTTATACAAAACGCCACTAAAAACTGGAGAAAAAGC
GGCGTTTTTATCCAAACACCACTAAAACTAATC
Found at i:40944968 original size:82 final size:82
Alignment explanation
Indices: 40944615--40944956 Score: 390
Period size: 82 Copynumber: 4.2 Consensus size: 82
40944605 AAAAATGAGA
* * * * *
40944615 AATAGCGGTGTTTTTATCTAAAACGCCACTAAAAA-TAGATAAATAGCGGTGTTTTTGTCTAAA-
1 AATAGCGGCGTTTTTATCCAAAACGCCACTAAAAACTAGAGAAATAGCGGCGTTTTTGTCCAAAC
* *
40944678 ATGCCACTAAAAACAGATT
66 A--CCACTAAAAACTGATC
* * * * * *
40944697 AATAGCGGTGTTTTTA-ACTAAACGCCACTAAAAACTGGGGAAATAGCGGCGTTTTTATCCCAAA
1 AATAGCGGCGTTTTTATCCAAAACGCCACTAAAAACTAGAGAAATAGCGGCGTTTTTGT-CCAAA
** *
40944761 TGCCACT-AAAACTAATC
65 CACCACTAAAAACTGATC
* *
40944778 AATAGCGGCGTTTTTATCTAAAATGCCA-TGAAAAACTAGAGAAATAGCGGCGTTTTTGTCCAAA
1 AATAGCGGCGTTTTTATCCAAAACGCCACT-AAAAACTAGAGAAATAGCGGCGTTTTTGTCCAAA
*
40944842 CGCCACTAAAAACTGATC
65 CACCACTAAAAACTGATC
* * * *
40944860 AATAGCGACATTTTTATCCAAAACGCCACTAAAAACTGGAGAAAAAGCGGCGTTTTTGTCCAAAC
1 AATAGCGGCGTTTTTATCCAAAACGCCACTAAAAACTAGAGAAATAGCGGCGTTTTTGTCCAAAC
40944925 ACCACT-AAAACTGATC
66 ACCACTAAAAACTGATC
*
40944941 AATAGTGGCGTTTTTA
1 AATAGCGGCGTTTTTA
40944957 GGCCCAAACG
Statistics
Matches: 220, Mismatches: 33, Indels: 15
0.82 0.12 0.06
Matches are distributed among these distances:
81 72 0.33
82 143 0.65
83 5 0.02
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.27
Consensus pattern (82 bp):
AATAGCGGCGTTTTTATCCAAAACGCCACTAAAAACTAGAGAAATAGCGGCGTTTTTGTCCAAAC
ACCACTAAAAACTGATC
Found at i:40945574 original size:15 final size:15
Alignment explanation
Indices: 40945551--40945610 Score: 68
Period size: 15 Copynumber: 3.9 Consensus size: 15
40945541 TTGAAAGTGT
40945551 TTAGGGTTTAGGGTA
1 TTAGGGTTTAGGGTA
* * *
40945566 TTAGTGTTTAAGGTT
1 TTAGGGTTTAGGGTA
40945581 TTAAGGG-TTAGGGTA
1 TT-AGGGTTTAGGGTA
40945596 TTAGGGTTTAAGGGT
1 TTAGGGTTT-AGGGT
40945611 TAGTTGATTA
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
14 4 0.11
15 24 0.67
16 8 0.22
ACGTcount: A:0.22, C:0.00, G:0.37, T:0.42
Consensus pattern (15 bp):
TTAGGGTTTAGGGTA
Found at i:40945591 original size:22 final size:22
Alignment explanation
Indices: 40945546--40945614 Score: 72
Period size: 22 Copynumber: 3.1 Consensus size: 22
40945536 GGTGTTTGAA
40945546 AGTGT-TTAGGGTTT-AGGGTATT
1 AGTGTATTAGGGTTTAAGGG--TT
*
40945568 AGTGT-TTAAGGTTTTAAGGGTT
1 AGTGTATT-AGGGTTTAAGGGTT
*
40945590 AGGGTATTAGGGTTTAAGGGTT
1 AGTGTATTAGGGTTTAAGGGTT
40945612 AGT
1 AGT
40945615 TGATTAAATG
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
22 28 0.70
23 8 0.20
24 4 0.10
ACGTcount: A:0.22, C:0.00, G:0.36, T:0.42
Consensus pattern (22 bp):
AGTGTATTAGGGTTTAAGGGTT
Found at i:40945599 original size:8 final size:7
Alignment explanation
Indices: 40945549--40945611 Score: 56
Period size: 8 Copynumber: 8.4 Consensus size: 7
40945539 GTTTGAAAGT
40945549 GTTTAGG
1 GTTTAGG
40945556 GTTTAGG
1 GTTTAGG
*
40945563 GTATTAGT
1 GT-TTAGG
40945571 GTTTAAGG
1 GTTT-AGG
*
40945579 TTTTAAGG
1 GTTT-AGG
40945587 G-TTAGG
1 GTTTAGG
40945593 GTATTAGG
1 GT-TTAGG
40945601 GTTTAAGG
1 GTTT-AGG
40945609 GTT
1 GTT
40945612 AGTTGATTAA
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
6 4 0.09
7 15 0.32
8 28 0.60
ACGTcount: A:0.21, C:0.00, G:0.37, T:0.43
Consensus pattern (7 bp):
GTTTAGG
Found at i:40949455 original size:120 final size:120
Alignment explanation
Indices: 40949317--40949609 Score: 500
Period size: 120 Copynumber: 2.4 Consensus size: 120
40949307 AATTATTTTA
* * * *
40949317 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTCAAATTT-TCTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT--AATTTATATT
*
40949380 TTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
64 TTACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
*
40949437 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTACTTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
40949502 ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
66 ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
40949557 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
40949610 TAAATATGAT
Statistics
Matches: 165, Mismatches: 6, Indels: 4
0.94 0.03 0.02
Matches are distributed among these distances:
119 4 0.02
120 159 0.96
121 2 0.01
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:40949477 original size:15 final size:15
Alignment explanation
Indices: 40949442--40949483 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
40949432 TTAAGAATTT
*
40949442 TATTAAATTAT-ATA
1 TATTTAATTATAATA
40949456 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
40949470 TATTTAATAATAAT
1 TATTTAATTATAAT
40949484 TATGTTACTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:40949592 original size:16 final size:16
Alignment explanation
Indices: 40949571--40949612 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
40949561 TTATTAAATT
*
40949571 ATATATTTTAATTATA
1 ATATATTTTAATAATA
40949587 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
40949602 AT-TATGTTTAA
1 ATATAT-TTTAA
40949613 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:40949597 original size:15 final size:15
Alignment explanation
Indices: 40949562--40949603 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
40949552 TTAAGAATTT
*
40949562 TATTAAATTAT-ATA
1 TATTTAATTATAATA
40949576 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
40949590 TATTTAATAATAAT
1 TATTTAATTATAAT
40949604 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:40949753 original size:157 final size:157
Alignment explanation
Indices: 40949546--40949862 Score: 564
Period size: 157 Copynumber: 2.0 Consensus size: 157
40949536 ATAAGAATAT
*
40949546 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
* * *
40949611 AAATATGATTAAATTATTTATTATTGATATTAATAATCTTATTAAAATTTAAATAACAATAACAA
66 AAATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
*
40949676 TAATAATTTACCAAAACAAATTTCTGC
131 TAATAATTTACCAAAACAAATTTATGC
40949703 TAATTA-TAAGAATTTTATTAAATTATATATTATTAATTAAAATATATTTAATAATAATTATGTT
1 TAATTATTAAGAATTTTATTAAATTATATATT-TTAATTAAAATATATTTAATAATAATTATGTT
40949767 TAAATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAACA
65 TAAATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAACA
*
40949832 ATAATCATTTACCAAAACAAATTTATGC
130 ATAATAATTTACCAAAACAAATTTATGC
40949860 TAA
1 TAA
40949863 GGGTATTCTA
Statistics
Matches: 153, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
156 25 0.16
157 128 0.84
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (157 bp):
TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
AAATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
TAATAATTTACCAAAACAAATTTATGC
Found at i:40950006 original size:16 final size:16
Alignment explanation
Indices: 40949985--40950053 Score: 129
Period size: 16 Copynumber: 4.2 Consensus size: 16
40949975 GATTTGCTAT
40949985 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
40950001 TACACCTCTAATCCCAA
1 TACACCTCTAAT-CCAA
40950018 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
40950034 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
40950050 TACA
1 TACA
40950054 GCGAACCAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
16 36 0.69
17 16 0.31
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:40950027 original size:33 final size:32
Alignment explanation
Indices: 40949985--40950053 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 32
40949975 GATTTGCTAT
40949985 TACACCTCTAATCCAATACACCTCTAATCCCAA
1 TACACCTCTAATCCAATACACCTCTAAT-CCAA
40950018 TACACCTCTAATCCAATACACCTCTAATCCAA
1 TACACCTCTAATCCAATACACCTCTAATCCAA
40950050 TACA
1 TACA
40950054 GCGAACCAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 8 0.22
33 28 0.78
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.25
Consensus pattern (32 bp):
TACACCTCTAATCCAATACACCTCTAATCCAA
Found at i:40952524 original size:8 final size:8
Alignment explanation
Indices: 40952513--40952539 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
40952503 ATGTTTGGGT
40952513 TTTTGAAA
1 TTTTGAAA
40952521 TTTTGAAA
1 TTTTGAAA
40952529 TTTTGAAA
1 TTTTGAAA
40952537 TTT
1 TTT
40952540 GATTTAGGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.33, C:0.00, G:0.11, T:0.56
Consensus pattern (8 bp):
TTTTGAAA
Found at i:40954469 original size:25 final size:25
Alignment explanation
Indices: 40954441--40954515 Score: 114
Period size: 25 Copynumber: 3.0 Consensus size: 25
40954431 TCCGCATCGT
* *
40954441 CGTTGGCAGCCCTATGCTACATCTC
1 CGTTGGCATCCCTCTGCTACATCTC
40954466 CGTTGGCATCCCTCTGCTACATCTC
1 CGTTGGCATCCCTCTGCTACATCTC
* *
40954491 CGTCGGCATCCCTCTGCTACTTCTC
1 CGTTGGCATCCCTCTGCTACATCTC
40954516 TAGTTTTCTG
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 46 1.00
ACGTcount: A:0.12, C:0.40, G:0.17, T:0.31
Consensus pattern (25 bp):
CGTTGGCATCCCTCTGCTACATCTC
Found at i:40955780 original size:9 final size:9
Alignment explanation
Indices: 40955757--40956074 Score: 95
Period size: 9 Copynumber: 35.1 Consensus size: 9
40955747 TATTATTTAA
40955757 TACATAACT
1 TACATAACT
* *
40955766 TGCATAATT
1 TACATAACT
40955775 TACATAACT
1 TACATAACT
40955784 TACATAA--
1 TACATAACT
40955791 TACATAACT
1 TACATAACT
*
40955800 TACATAATT
1 TACATAACT
* *
40955809 TAAAGATCAAAT
1 T--ACAT-AACT
**
40955821 TTTATAACT
1 TACATAACT
40955830 TACATAA-T
1 TACATAACT
**
40955838 TTTATAACT
1 TACATAACT
40955847 TACATAA--
1 TACATAACT
* * *
40955854 TAAATGAGT
1 TACATAACT
*
40955863 TACATAATT
1 TACATAACT
* *
40955872 TAAATATCAAAT
1 T--ACAT-AACT
* *
40955884 TTCAAAACT
1 TACATAACT
40955893 TACATAA--
1 TACATAACT
40955900 TACATAACT
1 TACATAACT
*
40955909 TACATAATT
1 TACATAACT
* *
40955918 TAAAGATCAAAT
1 T--ACAT-AACT
*
40955930 TTCATAACT
1 TACATAACT
*
40955939 TAGATAA--
1 TACATAACT
40955946 TACATAACT
1 TACATAACT
* *
40955955 TATATAATT
1 TACATAACT
* *
40955964 TAAAGATCAAAT
1 T--ACAT-AACT
*
40955976 TTCATAACT
1 TACATAACT
*
40955985 TACATAATT
1 TACATAACT
* *
40955994 TAAAGATCAAAT
1 T--ACAT-AACT
*
40956006 TTCATAACT
1 TACATAACT
*
40956015 TACATAATT
1 TACATAACT
40956024 TACATAACT
1 TACATAACT
40956033 TACATAA--
1 TACATAACT
* *
40956040 TAAATATCT
1 TACATAACT
40956049 TACATAA--
1 TACATAACT
*
40956056 TACATGACT
1 TACATAACT
40956065 TACATAACT
1 TACATAACT
40956074 T
1 T
40956075 TATTATACTT
Statistics
Matches: 220, Mismatches: 61, Indels: 56
0.65 0.18 0.17
Matches are distributed among these distances:
7 36 0.16
8 6 0.03
9 134 0.61
10 9 0.04
11 15 0.07
12 20 0.09
ACGTcount: A:0.47, C:0.14, G:0.03, T:0.37
Consensus pattern (9 bp):
TACATAACT
Found at i:40955897 original size:46 final size:46
Alignment explanation
Indices: 40955835--40955992 Score: 244
Period size: 46 Copynumber: 3.4 Consensus size: 46
40955825 TAACTTACAT
* * * * *
40955835 AATTTTATAACTTACATAATAAATGAGTTACATAATTTAAATATCA
1 AATTTCATAACTTACATAATACATAACTTACATAATTTAAAGATCA
*
40955881 AATTTCAAAACTTACATAATACATAACTTACATAATTTAAAGATCA
1 AATTTCATAACTTACATAATACATAACTTACATAATTTAAAGATCA
* *
40955927 AATTTCATAACTTAGATAATACATAACTTATATAATTTAAAGATCA
1 AATTTCATAACTTACATAATACATAACTTACATAATTTAAAGATCA
40955973 AATTTCATAACTTACATAAT
1 AATTTCATAACTTACATAAT
40955993 TTAAAGATCA
Statistics
Matches: 102, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 102 1.00
ACGTcount: A:0.48, C:0.12, G:0.03, T:0.37
Consensus pattern (46 bp):
AATTTCATAACTTACATAATACATAACTTACATAATTTAAAGATCA
Found at i:40955898 original size:30 final size:29
Alignment explanation
Indices: 40955796--40955900 Score: 81
Period size: 30 Copynumber: 3.4 Consensus size: 29
40955786 CATAATACAT
* *
40955796 AACTTACATAATTTAAAGATCAAATTTTAT
1 AACTTACATAATTTAAATATCAAA-TTTAA
40955826 AACTTACATAATTTTATAACT-TACATAA--TAA
1 AACTTACATAA-TTTA-AA-TAT-CA-AATTTAA
*
40955857 ATGAGTTACATAATTTAAATATCAAATTTCAA
1 A--ACTTACATAATTTAAATATCAAATTT-AA
40955889 AACTTACATAAT
1 AACTTACATAAT
40955901 ACATAACTTA
Statistics
Matches: 60, Mismatches: 4, Indels: 22
0.70 0.05 0.26
Matches are distributed among these distances:
29 2 0.03
30 24 0.40
31 11 0.18
32 10 0.17
33 11 0.18
34 2 0.03
ACGTcount: A:0.48, C:0.11, G:0.03, T:0.38
Consensus pattern (29 bp):
AACTTACATAATTTAAATATCAAATTTAA
Found at i:40955982 original size:30 final size:30
Alignment explanation
Indices: 40955948--40956025 Score: 147
Period size: 30 Copynumber: 2.6 Consensus size: 30
40955938 TTAGATAATA
*
40955948 CATAACTTATATAATTTAAAGATCAAATTT
1 CATAACTTACATAATTTAAAGATCAAATTT
40955978 CATAACTTACATAATTTAAAGATCAAATTT
1 CATAACTTACATAATTTAAAGATCAAATTT
40956008 CATAACTTACATAATTTA
1 CATAACTTACATAATTTA
40956026 CATAACTTAC
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 47 1.00
ACGTcount: A:0.46, C:0.13, G:0.03, T:0.38
Consensus pattern (30 bp):
CATAACTTACATAATTTAAAGATCAAATTT
Found at i:40965202 original size:43 final size:43
Alignment explanation
Indices: 40965144--40965314 Score: 254
Period size: 43 Copynumber: 4.0 Consensus size: 43
40965134 TATCGAAATG
*
40965144 TGATATACGGGCTTCGGGCCTAGCTGGCTATAATGCCGGTGAAA
1 TGATAT-CGGGCTTCGGGCCTAGCAGGCTATAATGCCGGTGAAA
*
40965188 TGATATCGGGCTTCGGGCCTAGCAGGCTATAATGCCGGTGAGA
1 TGATATCGGGCTTCGGGCCTAGCAGGCTATAATGCCGGTGAAA
* * *
40965231 TAATATCAGGCCTCGGGCCTAGCAGGCTATAATGCCGGTGAAA
1 TGATATCGGGCTTCGGGCCTAGCAGGCTATAATGCCGGTGAAA
** *
40965274 TGATATCGGGCTTCAAGCCTAGCAGGCGA-AATGCCGGTGAA
1 TGATATCGGGCTTCGGGCCTAGCAGGCTATAATGCCGGTGAA
40965315 TGAATTCAGA
Statistics
Matches: 115, Mismatches: 12, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
42 12 0.10
43 97 0.84
44 6 0.05
ACGTcount: A:0.25, C:0.22, G:0.32, T:0.22
Consensus pattern (43 bp):
TGATATCGGGCTTCGGGCCTAGCAGGCTATAATGCCGGTGAAA
Found at i:40965338 original size:42 final size:43
Alignment explanation
Indices: 40965161--40965342 Score: 145
Period size: 43 Copynumber: 4.3 Consensus size: 43
40965151 CGGGCTTCGG
* * * * ***
40965161 GCCTAGCTGGCTATAATGCCGGTGAAATGATATCGGGCTTCGG
1 GCCTAGCAGGCGATAATGCCGGTGAAATGATATCAGACTTAAA
* * * * * ***
40965204 GCCTAGCAGGCTATAATGCCGGTGAGATAATATCAGGCCTCGG
1 GCCTAGCAGGCGATAATGCCGGTGAAATGATATCAGACTTAAA
* * * *
40965247 GCCTAGCAGGCTATAATGCCGGTGAAATGATATCGGGCTTCAA
1 GCCTAGCAGGCGATAATGCCGGTGAAATGATATCAGACTTAAA
40965290 GCCTAGCAGGCGA-AATGCCGGTG-AATGA-ATTCAGACTTAAA
1 GCCTAGCAGGCGATAATGCCGGTGAAATGATA-TCAGACTTAAA
*
40965331 GGTCTAGCAGGC
1 -GCCTAGCAGGC
40965343 TTATGGCCGG
Statistics
Matches: 121, Mismatches: 16, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
40 1 0.01
41 13 0.11
42 20 0.17
43 87 0.72
ACGTcount: A:0.26, C:0.21, G:0.30, T:0.22
Consensus pattern (43 bp):
GCCTAGCAGGCGATAATGCCGGTGAAATGATATCAGACTTAAA
Found at i:40975421 original size:2 final size:2
Alignment explanation
Indices: 40975414--40975445 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
40975404 GAGCTCCTAT
40975414 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
40975446 GTCGATTTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Done.