Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 85040211
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: 85040211
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 160 characters in sequence are not A, C, G, or T
File 55 of 292
Found at i:16181410 original size:40 final size:40
Alignment explanation
Indices: 16181207--16181410 Score: 247
Period size: 40 Copynumber: 5.1 Consensus size: 40
16181197 CAGAATTTAA
** *
16181207 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
16181247 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
16181287 CCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
16181326 CCGGA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
** *
16181366 CCGGATATAGCCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
16181406 CCGGA
1 CCGGA
16181411 CATCATTCGA
Statistics
Matches: 143, Mismatches: 14, Indels: 14
0.84 0.08 0.08
Matches are distributed among these distances:
38 2 0.01
39 34 0.24
40 95 0.66
41 12 0.08
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:16199736 original size:46 final size:45
Alignment explanation
Indices: 16199635--16199723 Score: 144
Period size: 46 Copynumber: 2.0 Consensus size: 45
16199625 TGTAACCTGC
* *
16199635 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA-ATGCCCAT
16199681 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG-ATGCCCA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGAATGCCCA
16199724 AATATCCTAG
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
44 5 0.12
46 36 0.88
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.20
Consensus pattern (45 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGAATGCCCAT
Found at i:16202642 original size:25 final size:25
Alignment explanation
Indices: 16202614--16202693 Score: 115
Period size: 25 Copynumber: 3.2 Consensus size: 25
16202604 TCGTATAACA
* *
16202614 TTACCGTTATTCAACTCAGAGGAGC
1 TTACCGTTATTCAGCTCGGAGGAGC
* *
16202639 TTACCTTTATTTAGCTCGGAGGAGC
1 TTACCGTTATTCAGCTCGGAGGAGC
*
16202664 TTACCGTAATTCAGCTCGGAGGAGC
1 TTACCGTTATTCAGCTCGGAGGAGC
16202689 TTACC
1 TTACC
16202694 ATTTACAGCT
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 48 1.00
ACGTcount: A:0.24, C:0.24, G:0.23, T:0.30
Consensus pattern (25 bp):
TTACCGTTATTCAGCTCGGAGGAGC
Found at i:16204372 original size:38 final size:39
Alignment explanation
Indices: 16204319--16204410 Score: 118
Period size: 38 Copynumber: 2.4 Consensus size: 39
16204309 AGTTTGTGTA
* *
16204319 TTTAATTAT-TCCATAATTTGAACATTATTT-ATATGAG-T
1 TTTAATTATGT-CATAATCTGAACATT-TTTAATAAGAGTT
*
16204357 TTTAATTATGTCATAATCTGAACATTTTTAATAAGGGTT
1 TTTAATTATGTCATAATCTGAACATTTTTAATAAGAGTT
16204396 TTTAATTATGTCATA
1 TTTAATTATGTCATA
16204411 GTTTAGGACA
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
37 3 0.06
38 28 0.58
39 17 0.35
ACGTcount: A:0.34, C:0.08, G:0.10, T:0.49
Consensus pattern (39 bp):
TTTAATTATGTCATAATCTGAACATTTTTAATAAGAGTT
Found at i:16209439 original size:24 final size:25
Alignment explanation
Indices: 16209359--16209439 Score: 67
Period size: 25 Copynumber: 3.3 Consensus size: 25
16209349 TATCAACTTT
** *
16209359 TATGAGCTTACCGA-TACCCAGCTCA
1 TATGAGCTTACC-ATTATGCAGCTCG
* *
16209384 TATGAGCTTACCGTTATTCAGCTCG
1 TATGAGCTTACCATTATGCAGCTCG
* * *
16209409 GAGGAGCTTACCATT-TGCAGCTTG
1 TATGAGCTTACCATTATGCAGCTCG
16209433 TATGAGC
1 TATGAGC
16209440 ATACATGTAC
Statistics
Matches: 44, Mismatches: 11, Indels: 3
0.76 0.19 0.05
Matches are distributed among these distances:
24 12 0.27
25 32 0.73
ACGTcount: A:0.23, C:0.25, G:0.22, T:0.30
Consensus pattern (25 bp):
TATGAGCTTACCATTATGCAGCTCG
Found at i:16211745 original size:14 final size:14
Alignment explanation
Indices: 16211726--16211760 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
16211716 TTGTGTCTTT
16211726 TTTATTTATTTAAC
1 TTTATTTATTTAAC
* *
16211740 TTTATTTATTTTAT
1 TTTATTTATTTAAC
16211754 TTTATTT
1 TTTATTT
16211761 TTATTTTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTATTTATTTAAC
Found at i:16213398 original size:48 final size:48
Alignment explanation
Indices: 16213324--16213933 Score: 639
Period size: 48 Copynumber: 12.6 Consensus size: 48
16213314 TATGTGTGCT
* *
16213324 AGTGTAAGACCATGTCTGTGATATGGCATCGGCCACATTATGAGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCACATTATGAGAGCC
*** * * *
16213372 AGTGTAAGACCATGTCTGGGACATGGCATCGGCGTTGA-TATGTGTGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGC-CACATTATGAGAGCC
* *
16213420 AGTGTAAGACTATGTTTGGGACATGGCATCGGCCACATTATGAGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCACATTATGAGAGCC
* * *
16213468 AGTGCAAGAGCATGTCTGGGACATGGCATCGGCCATATTATATTATGAGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCC-----ACATTATGAGAGCC
*
16213521 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCACATTATTAGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCACATTATGAGAGCC
* * *
16213569 AGTGTAAGACCATGCCTGGGACATGGCATCGGCCACATTATTAGACCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCACATTATGAGAGCC
* *
16213617 AGTGTAAGACCATGTTTGGGACATGGCATCAGCCACATTATGAGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCACATTATGAGAGCC
* * *
16213665 AGTGTAAGACCATGTTTAGGACATGGCATCGG---CATTGA-GACTAGAGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCACATT-ATG---AGAGCC
** * * * *
16213713 AGTGTAAGACCATGTCTGGGACATGAAATTGGCCTCGA-CATGTGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCAC-ATTATGAGAGCC
* * *
16213761 AGTGTAAGACCATGTCTGGGACATGGCATCAGCCATATTCTGAGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCACATTATGAGAGCC
* * *
16213809 AGTGTAAGACCATGTTTAGGACATGGCATCGG---CATTGA-GACTAGAGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCACATT-ATG---AGAGCC
* * * * *
16213857 AGTGTAAGACCATGTCTGGGACATGGAATTGGCCTCGA-CATGTGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCAC-ATTATGAGAGCC
*
16213905 AGTGTAAGACCATGTCTAGGACATGGCAT
1 AGTGTAAGACCATGTCTGGGACATGGCAT
16213934 TGATAATTTA
Statistics
Matches: 469, Mismatches: 67, Indels: 52
0.80 0.11 0.09
Matches are distributed among these distances:
45 9 0.02
46 1 0.00
47 2 0.00
48 403 0.86
49 1 0.00
50 2 0.00
51 4 0.01
52 2 0.00
53 45 0.10
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (48 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGGCCACATTATGAGAGCC
Found at i:16213732 original size:144 final size:144
Alignment explanation
Indices: 16213315--16213933 Score: 748
Period size: 144 Copynumber: 4.3 Consensus size: 144
16213305 TTTGGGTGAT
* * * * *
16213315 ATGTGTGCTAGTGTAAGACCATGTCTGTGATATGGCATCGGCCACATTATGAGAGCCAGTGTAAG
1 ATGTGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCAGCCACATTATGAGAGCCAGTGTAAG
* * * * * * *
16213380 ACCATGTCTGGGACATGGCATCGGCGTTGATA-TGTGTGCTAGTGTAAGACTATGTTTGGGACAT
66 ACCATGTCTAGGACATGGCATCGGCATTGAGACT-AGAGCTAGTGTAAGACCATGTCTGGGACAT
* *
16213444 GGCATCGGCCAC-ATT
130 GGAATCGGCCACGA-C
* * * * *
16213459 ATGAGAGCCAGTGCAAGAGCATGTCTGGGACATGGCATCGGCCATATTATATTATGAGAGCCAGT
1 ATGTGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCAGCC-----ACATTATGAGAGCCAGT
* * * *
16213524 GTAAGACCATGTCTGGGACATGGCATCGGCCACATT---ATTAGAGCCAGTGTAAGACCATGCCT
61 GTAAGACCATGTCTAGGACATGGCATCGG---CATTGAGACTAGAGCTAGTGTAAGACCATGTCT
* *
16213586 GGGACATGGCATCGGCCAC-ATT
123 GGGACATGGAATCGGCCACGA-C
* *
16213608 AT-TAGACCCAGTGTAAGACCATGTTTGGGACATGGCATCAGCCACATTATGAGAGCCAGTGTAA
1 ATGT-GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCAGCCACATTATGAGAGCCAGTGTAA
*
16213672 GACCATGTTTAGGACATGGCATCGGCATTGAGACTAGAGCTAGTGTAAGACCATGTCTGGGACAT
65 GACCATGTCTAGGACATGGCATCGGCATTGAGACTAGAGCTAGTGTAAGACCATGTCTGGGACAT
* * *
16213737 GAAATTGGCCTCGAC
130 GGAATCGGCCACGAC
* *
16213752 ATGTGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCAGCCATATTCTGAGAGCCAGTGTAAG
1 ATGTGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCAGCCACATTATGAGAGCCAGTGTAAG
*
16213817 ACCATGTTTAGGACATGGCATCGGCATTGAGACTAGAGCTAGTGTAAGACCATGTCTGGGACATG
66 ACCATGTCTAGGACATGGCATCGGCATTGAGACTAGAGCTAGTGTAAGACCATGTCTGGGACATG
* *
16213882 GAATTGGCCTCGAC
131 GAATCGGCCACGAC
*
16213896 ATGTGAGCCAGTGTAAGACCATGTCTAGGACATGGCAT
1 ATGTGAGCCAGTGTAAGACCATGTCTGGGACATGGCAT
16213934 TGATAATTTA
Statistics
Matches: 422, Mismatches: 38, Indels: 30
0.86 0.08 0.06
Matches are distributed among these distances:
141 4 0.01
144 291 0.69
145 2 0.00
149 121 0.29
150 1 0.00
152 3 0.01
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (144 bp):
ATGTGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCAGCCACATTATGAGAGCCAGTGTAAG
ACCATGTCTAGGACATGGCATCGGCATTGAGACTAGAGCTAGTGTAAGACCATGTCTGGGACATG
GAATCGGCCACGAC
Found at i:16216626 original size:38 final size:38
Alignment explanation
Indices: 16216584--16216657 Score: 148
Period size: 38 Copynumber: 1.9 Consensus size: 38
16216574 GTGCCTAAAG
16216584 CTCACACCACTTCTATCGCGAGTGTTGGTAGTGCTCGA
1 CTCACACCACTTCTATCGCGAGTGTTGGTAGTGCTCGA
16216622 CTCACACCACTTCTATCGCGAGTGTTGGTAGTGCTC
1 CTCACACCACTTCTATCGCGAGTGTTGGTAGTGCTC
16216658 AACCAAATAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.18, C:0.30, G:0.23, T:0.30
Consensus pattern (38 bp):
CTCACACCACTTCTATCGCGAGTGTTGGTAGTGCTCGA
Found at i:16221231 original size:48 final size:48
Alignment explanation
Indices: 16221117--16221384 Score: 289
Period size: 48 Copynumber: 5.6 Consensus size: 48
16221107 TATGTGTGCT
* * * * * *
16221117 AGTGTAAGACTATGTCTGGGAAATGGCAACAGCCACATTAT-GGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCACATTATAAGAGGC
*
16221164 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCATATTATAAGAGGC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCACATTATAAGAGGC
* * *
16221212 AGTGTAAGACCATGTCTGGGACATGGCATTGG-C-CATTATGAGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCACATTATAAGAGGC
* * * * * *
16221258 AGTGTAAAACCATGTCTAGGACATGGCATTGG---CGTTGATATGTGTGC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCACATT-ATAAGAG-GC
* *
16221305 TAGTGTAAGACCATGTCTGGGACATGGCATCGGCCACAATATGAGA-GC
1 -AGTGTAAGACCATGTCTGGGACATGGCATCGGCCACATTATAAGAGGC
16221353 TAGTGTAAGACCATGTCTGGGACATGGCATCG
1 -AGTGTAAGACCATGTCTGGGACATGGCATCG
16221385 ATAATTTACC
Statistics
Matches: 188, Mismatches: 26, Indels: 13
0.83 0.11 0.06
Matches are distributed among these distances:
45 3 0.02
46 44 0.23
47 38 0.20
48 98 0.52
50 3 0.02
51 2 0.01
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.24
Consensus pattern (48 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGGCCACATTATAAGAGGC
Found at i:16221280 original size:94 final size:95
Alignment explanation
Indices: 16221112--16221384 Score: 347
Period size: 94 Copynumber: 2.9 Consensus size: 95
16221102 GGTGATATGT
* * * *
16221112 GTGCTAGTGTAAGACTATGTCTGGGAAATGGCAACAGCCACATTATG-GAGCCAGTGTAAGACCA
1 GTGCTAGTGTAAGACCATGTCTGGGACATGGC-ATAGGCACATTATGAGAGCCAGTGTAAGACCA
*
16221176 TGTCTGGGACATGGCATCGGCCATATTATAAGA
65 TGTCTGGGACATGGCATCGG-CAT-TGATAAGA
* *
16221209 G-GC-AGTGTAAGACCATGTCTGGGACATGGCATTGGC-CATTATGAGAGCCAGTGTAAAACCAT
1 GTGCTAGTGTAAGACCATGTCTGGGACATGGCATAGGCACATTATGAGAGCCAGTGTAAGACCAT
* * * * *
16221271 GTCTAGGACATGGCATTGGCGTTGATATGT
66 GTCTGGGACATGGCATCGGCATTGATAAGA
* * *
16221301 GTGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCACAATATGAGAGCTAGTGTAAGACCA
1 GTGCTAGTGTAAGACCATGTCTGGGACATGGCATAGG-CACATTATGAGAGCCAGTGTAAGACCA
16221366 TGTCTGGGACATGGCATCG
65 TGTCTGGGACATGGCATCG
16221385 ATAATTTACC
Statistics
Matches: 153, Mismatches: 18, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
92 6 0.04
93 11 0.07
94 68 0.44
95 26 0.17
96 41 0.27
97 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.24
Consensus pattern (95 bp):
GTGCTAGTGTAAGACCATGTCTGGGACATGGCATAGGCACATTATGAGAGCCAGTGTAAGACCAT
GTCTGGGACATGGCATCGGCATTGATAAGA
Found at i:16223711 original size:28 final size:28
Alignment explanation
Indices: 16223669--16223738 Score: 95
Period size: 28 Copynumber: 2.5 Consensus size: 28
16223659 TAATTATATG
** ** *
16223669 TGGCACTTAACGTGCGAAGTATTGGGGA
1 TGGCACTTAGTGTGCGAAGTAACGAGGA
16223697 TGGCACTTAGTGTGCGAAGTAACGAGGA
1 TGGCACTTAGTGTGCGAAGTAACGAGGA
16223725 TGGCACTTAGTGTG
1 TGGCACTTAGTGTG
16223739 TGAAATCCAG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.24, C:0.14, G:0.36, T:0.26
Consensus pattern (28 bp):
TGGCACTTAGTGTGCGAAGTAACGAGGA
Found at i:16223904 original size:32 final size:32
Alignment explanation
Indices: 16223843--16223909 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 32
16223833 TGAGTATGAG
* **
16223843 ATTGGTACGATATGGTACAGGTATCTACGAAA
1 ATTGGTACAATATAATACAGGTATCTACGAAA
* *
16223875 ATTGGTACAATATAATACATGTATGTACGAAA
1 ATTGGTACAATATAATACAGGTATCTACGAAA
16223907 ATT
1 ATT
16223910 CAATTGAGTA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.39, C:0.10, G:0.19, T:0.31
Consensus pattern (32 bp):
ATTGGTACAATATAATACAGGTATCTACGAAA
Found at i:16226518 original size:46 final size:45
Alignment explanation
Indices: 16226468--16226638 Score: 215
Period size: 46 Copynumber: 3.8 Consensus size: 45
16226458 TGGTTGAGCA
16226468 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* * * *
16226514 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGAATGTAACTAG-GCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACT-TATG-GA-T-GCGAAG
16226560 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
*
16226606 -CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
16226639 GGGCGGGTTA
Statistics
Matches: 108, Mismatches: 9, Indels: 17
0.81 0.07 0.13
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 34 0.31
46 64 0.59
47 2 0.02
48 3 0.03
49 1 0.01
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:16231968 original size:40 final size:40
Alignment explanation
Indices: 16231909--16232050 Score: 124
Period size: 40 Copynumber: 3.5 Consensus size: 40
16231899 AAATTGAATA
* * *
16231909 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
* * * ***
16231949 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
* * * ** *
16231989 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTTATT
1 ATATCCGGGCTAAGACCCGAAGACAATT-ATGCTAGAAACT
*
16232029 CTATCCGGGCTAAGACCCGAAG
1 ATATCCGGGCTAAGACCCGAAG
16232051 GCATTTGTGC
Statistics
Matches: 86, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
39 3 0.03
40 83 0.97
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
Found at i:16232051 original size:40 final size:39
Alignment explanation
Indices: 16231948--16232076 Score: 152
Period size: 40 Copynumber: 3.2 Consensus size: 39
16231938 TGCTGGAAAT
* * *
16231948 TATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGC
1 TATATCCGGGCTAAGACCCGAAGGC-ATTGTGCGAGTGAC
* *
16231988 TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTAT
1 TATATCCGGGCTAAGACCCGAAGGCATT-GTGCGAGTGAC
* *
16232028 TCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACGTGAT
1 TATATCCGGGCTAAGACCCGAAGGCA-TTGTGCGA-GTGAC
16232068 TATATCCGG
1 TATATCCGG
16232077 TTATATTCCG
Statistics
Matches: 78, Mismatches: 8, Indels: 6
0.85 0.09 0.07
Matches are distributed among these distances:
39 4 0.05
40 72 0.92
41 2 0.03
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (39 bp):
TATATCCGGGCTAAGACCCGAAGGCATTGTGCGAGTGAC
Found at i:16237264 original size:46 final size:46
Alignment explanation
Indices: 16237214--16237389 Score: 225
Period size: 46 Copynumber: 3.8 Consensus size: 46
16237204 TGGTTGAGCA
16237214 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
16237260 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
16237305 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
16237353 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
16237390 GCGGGTTACA
Statistics
Matches: 112, Mismatches: 9, Indels: 18
0.81 0.06 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.04
45 3 0.03
46 64 0.57
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:16237370 original size:93 final size:93
Alignment explanation
Indices: 16237211--16237381 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
16237201 GGATGGTTGA
* *
16237211 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
16237276 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
16237304 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
16237369 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
16237382 ACTTATGGGC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:16240212 original size:62 final size:62
Alignment explanation
Indices: 16240115--16240239 Score: 241
Period size: 62 Copynumber: 2.0 Consensus size: 62
16240105 TACATATGAG
*
16240115 TCACTTATGTGCAAATTATCCGTGTATCCGAGTTGTATTCCGATGTGTTCAACGTGTGAAAT
1 TCACTTATGTGCAAATTATCCGTGTATCCGAGTTGTATTCCGATGTGTTCAACGGGTGAAAT
16240177 TCACTTATGTGCAAATTATCCGTGTATCCGAGTTGTATTCCGATGTGTTCAACGGGTGAAAT
1 TCACTTATGTGCAAATTATCCGTGTATCCGAGTTGTATTCCGATGTGTTCAACGGGTGAAAT
16240239 T
1 T
16240240 TCTAGTGAAA
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.37
Consensus pattern (62 bp):
TCACTTATGTGCAAATTATCCGTGTATCCGAGTTGTATTCCGATGTGTTCAACGGGTGAAAT
Found at i:16242995 original size:47 final size:47
Alignment explanation
Indices: 16242944--16243038 Score: 190
Period size: 47 Copynumber: 2.0 Consensus size: 47
16242934 GCATTTATCT
16242944 ATTATGATGGATGAGCATAAGATACTTTCTTGTTATCGTACTTATTA
1 ATTATGATGGATGAGCATAAGATACTTTCTTGTTATCGTACTTATTA
16242991 ATTATGATGGATGAGCATAAGATACTTTCTTGTTATCGTACTTATTA
1 ATTATGATGGATGAGCATAAGATACTTTCTTGTTATCGTACTTATTA
16243038 A
1 A
16243039 AGGTGTACAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.31, C:0.11, G:0.17, T:0.42
Consensus pattern (47 bp):
ATTATGATGGATGAGCATAAGATACTTTCTTGTTATCGTACTTATTA
Found at i:16248149 original size:31 final size:31
Alignment explanation
Indices: 16248111--16248174 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
16248101 CCTTTTCATA
16248111 TTTCATATTTCATAATACTGGGCCGAAGCCT
1 TTTCATATTTCATAATACTGGGCCGAAGCCT
*
16248142 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATATTTCATAATACTGGGCCGAAGCCT
16248173 TT
1 TT
16248175 ACTGTAAACG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.23, C:0.22, G:0.16, T:0.39
Consensus pattern (31 bp):
TTTCATATTTCATAATACTGGGCCGAAGCCT
Found at i:16248445 original size:47 final size:47
Alignment explanation
Indices: 16248391--16248484 Score: 161
Period size: 47 Copynumber: 2.0 Consensus size: 47
16248381 GCCTCTTTAA
16248391 ATAACTGGGGCAAAAGCCCTTTCAATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCAAAAGCCCTTTCAATAACTGGGGCATAAGCCCTTTT
* **
16248438 ATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCAAAAGCCCTTTCAATAACTGGGGCATAAGCCCTTTT
16248485 TCACTTCCTC
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 44 1.00
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (47 bp):
ATAACTGGGGCAAAAGCCCTTTCAATAACTGGGGCATAAGCCCTTTT
Found at i:16248484 original size:24 final size:23
Alignment explanation
Indices: 16248365--16248484 Score: 152
Period size: 24 Copynumber: 5.0 Consensus size: 23
16248355 TGCTTTATCA
*
16248365 TATAACTGGAGGCCT-AGCCTCTTT
1 TATAACTGG-GGCATAAGCC-CTTT
* *
16248389 AAATAACTGGGGCAAAAGCCCTTT
1 -TATAACTGGGGCATAAGCCCTTT
*
16248413 CAATAACTGGGGCATAAGCCCTTT
1 -TATAACTGGGGCATAAGCCCTTT
16248437 TATAACTGGGGCATAAGCCCTTT
1 TATAACTGGGGCATAAGCCCTTT
16248460 TGATAACTGGGGCATAAGCCCTTT
1 T-ATAACTGGGGCATAAGCCCTTT
16248484 T
1 T
16248485 TCACTTCCTC
Statistics
Matches: 87, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
23 23 0.26
24 52 0.60
25 12 0.14
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.28
Consensus pattern (23 bp):
TATAACTGGGGCATAAGCCCTTT
Found at i:16248559 original size:20 final size:20
Alignment explanation
Indices: 16248534--16248594 Score: 104
Period size: 20 Copynumber: 3.0 Consensus size: 20
16248524 TTATGATTAC
16248534 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
16248554 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
* *
16248574 GTCATGTGCATCTCATACAT
1 ATCATGTGCATATCATACAT
16248594 A
1 A
16248595 CCACATTTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.33, C:0.21, G:0.11, T:0.34
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:16248669 original size:25 final size:25
Alignment explanation
Indices: 16248637--16248684 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
16248627 ATACATAAAC
* * *
16248637 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
16248662 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
16248685 CATGGTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:16252741 original size:29 final size:29
Alignment explanation
Indices: 16252708--16252830 Score: 167
Period size: 29 Copynumber: 4.2 Consensus size: 29
16252698 GTGACGAGAT
*
16252708 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAAAATA
* *
16252737 TGGCACTAAGTGTGCGTGCTGGAAATATCA
1 TGGCACTAAGTGTGCATGCTGGAAAAAT-A
16252767 -GGCACTAAGTGTGCATGCTGGAAAAATA
1 TGGCACTAAGTGTGCATGCTGGAAAAATA
* * *
16252795 TGACACTATGTGTGCAAGCTGGAAAAATA
1 TGGCACTAAGTGTGCATGCTGGAAAAATA
*
16252824 CGGCACT
1 TGGCACT
16252831 GGGTGTGCGA
Statistics
Matches: 84, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
28 1 0.01
29 82 0.98
30 1 0.01
ACGTcount: A:0.32, C:0.16, G:0.28, T:0.24
Consensus pattern (29 bp):
TGGCACTAAGTGTGCATGCTGGAAAAATA
Found at i:16268283 original size:40 final size:40
Alignment explanation
Indices: 16268228--16268450 Score: 342
Period size: 40 Copynumber: 5.6 Consensus size: 40
16268218 TATTCGAATG
* *
16268228 ATATCCGGGTTAAGTCTCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
16268268 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
*
16268308 ATATCCGGGCTAAGTCCCGAAGGCATTTGAGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
16268348 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCT-AGTGACT
* * *
16268389 ATATCCGGGCTAAGACCCGAAGGTATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGACT
* *
16268429 ATTTCC-GGCTAAATCCCGAAGG
1 ATATCCGGGCTAAGTCCCGAAGG
16268451 TACTTGGGTT
Statistics
Matches: 171, Mismatches: 10, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
39 14 0.08
40 118 0.69
41 39 0.23
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
Found at i:16271463 original size:18 final size:20
Alignment explanation
Indices: 16271436--16271477 Score: 52
Period size: 18 Copynumber: 2.2 Consensus size: 20
16271426 TATAGACTCA
16271436 ATATAAAAC-TAAACAT-AT
1 ATATAAAACTTAAACATCAT
* *
16271454 ATATATAACTTAATCATCAT
1 ATATAAAACTTAAACATCAT
16271474 ATAT
1 ATAT
16271478 GCATGCAAGG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 8 0.40
19 6 0.30
20 6 0.30
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (20 bp):
ATATAAAACTTAAACATCAT
Found at i:16272551 original size:2 final size:2
Alignment explanation
Indices: 16272544--16272575 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
16272534 TGCTTAATTC
*
16272544 AT AT AT AT TT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16272576 CCTTTACATC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:16281188 original size:40 final size:40
Alignment explanation
Indices: 16281129--16281336 Score: 218
Period size: 40 Copynumber: 5.2 Consensus size: 40
16281119 CAATTGAATG
* * * *
16281129 ATATCCGGGCTAAGTCCCGAAGACATTTATGCTAGTAATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * * * *
16281169 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * **
16281209 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * **
16281249 AAATCCGGGCTAATACCCGAAGGCATTTGTGCAAGTCGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * * **
16281289 CTATCCGGGCTAAGACCCGAAGGCATTCGTGCATGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
16281329 ATATCCGG
1 ATATCCGG
16281337 TTGTATTCCG
Statistics
Matches: 142, Mismatches: 26, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 142 1.00
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
Found at i:16281267 original size:80 final size:80
Alignment explanation
Indices: 16281130--16281336 Score: 247
Period size: 80 Copynumber: 2.6 Consensus size: 80
16281120 AATTGAATGA
* * ** * * *
16281130 TATCCGGGCTAAGTCCCGAAGACATTTATGCTAGTAATTATATCCGGGTTAAGACCCGAAGGCAA
1 TATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGGGCTAAGACCCGAAGGCAA
*
16281195 TTGTGCTAGT-G-AC
66 TTGTGCAAGTCGTAC
* * *
16281208 TACATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTTAAATCCGGGCTAATACCCGAAGGC
1 T--ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGGGCTAAGACCCGAAGGC
* *
16281273 ATTTGTGCAAGTCGTTC
64 AATTGTGCAAGTCGTAC
* *
16281290 TATCCGGGCTAAGACCCGAAGGCATTCGTGCATGTGGTTATATCCGG
1 TATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGG
16281337 TTGTATTCCG
Statistics
Matches: 109, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
78 1 0.01
80 105 0.96
81 1 0.01
82 2 0.02
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.26
Consensus pattern (80 bp):
TATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGGGCTAAGACCCGAAGGCAA
TTGTGCAAGTCGTAC
Found at i:16292030 original size:31 final size:31
Alignment explanation
Indices: 16291989--16292052 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
16291979 CCTTTTCATA
*
16291989 TTTCATATTTCATAACACTGGGCCGAAGCCT
1 TTTCAAATTTCATAACACTGGGCCGAAGCCT
**
16292020 TTTCAAATTTCATATTACTGGGCCGAAGCCT
1 TTTCAAATTTCATAACACTGGGCCGAAGCCT
16292051 TT
1 TT
16292053 ACGGTAAACA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (31 bp):
TTTCAAATTTCATAACACTGGGCCGAAGCCT
Found at i:16292298 original size:24 final size:24
Alignment explanation
Indices: 16292246--16292435 Score: 287
Period size: 24 Copynumber: 8.0 Consensus size: 24
16292236 GCTTTATCAT
* *
16292246 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTG
* *
16292271 ATAACTGGGGCAAAAGCCCTTTTT
1 ATAACTGGGGCATAAGCCCTTTTG
16292295 ATAACTGGGGCATAAGCCC-TTTG
1 ATAACTGGGGCATAAGCCCTTTTG
*
16292318 ATAACTGGGGCGTAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTG
16292342 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTG
16292366 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTG
*
16292390 ATAACTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTG
16292413 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
16292436 TCACTTCCTC
Statistics
Matches: 154, Mismatches: 8, Indels: 7
0.91 0.05 0.04
Matches are distributed among these distances:
23 43 0.28
24 99 0.64
25 12 0.08
ACGTcount: A:0.26, C:0.22, G:0.24, T:0.29
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTG
Found at i:16292326 original size:47 final size:48
Alignment explanation
Indices: 16292245--16292436 Score: 282
Period size: 47 Copynumber: 4.0 Consensus size: 48
16292235 TGCTTTATCA
* *
16292245 TATAACTGGAGGCCT-AGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTT
1 TATAACTGG-GGCATAAGCC-CTTTTAATAACTGGGGCATAAGCCCTTTT
* *
16292294 TATAACTGGGGCATAAGCCC-TTTGATAACTGGGGCGTAAGCCCTTTT
1 TATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTT
* *
16292341 GATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTT
1 TATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTT
*
16292389 GATAACTGGGGCATAAGCCC-TTTAATAACTGGGGCATAAGCCCTTTT
1 TATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTT
16292436 T
1 T
16292437 CACTTCCTCC
Statistics
Matches: 133, Mismatches: 8, Indels: 6
0.90 0.05 0.04
Matches are distributed among these distances:
47 69 0.52
48 51 0.38
49 13 0.10
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.30
Consensus pattern (48 bp):
TATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTT
Found at i:16292347 original size:71 final size:72
Alignment explanation
Indices: 16292246--16292436 Score: 298
Period size: 71 Copynumber: 2.7 Consensus size: 72
16292236 GCTTTATCAT
* *
16292246 ATAACTGGAGGCCT-AGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTTTATAACTGGGGCATAA
1 ATAACTGG-GGCATAAGCC-CTTTTAATAACTGGGGCATAAGCCCTTTTTATAACTGGGGCATAA
16292310 GCCC-TTTG
64 GCCCTTTTG
* * *
16292318 ATAACTGGGGCGTAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGC
1 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTTTATAACTGGGGCATAAGC
16292383 CCTTTTG
66 CCTTTTG
16292390 ATAACTGGGGCATAAGCCC-TTTAATAACTGGGGCATAAGCCCTTTTT
1 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTTT
16292437 CACTTCCTCC
Statistics
Matches: 110, Mismatches: 7, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
71 76 0.69
72 34 0.31
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (72 bp):
ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTTTATAACTGGGGCATAAGC
CCTTTTG
Found at i:16292508 original size:9 final size:9
Alignment explanation
Indices: 16292494--16292550 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
16292484 ATCTCGTGTG
16292494 CATATCATA
1 CATATCATA
*
16292503 CATATCATGTG
1 CATATCA--TA
16292514 CATATCATA
1 CATATCATA
* *
16292523 CATGTCATGTG
1 CATATCA--TA
16292534 CATATCATA
1 CATATCATA
16292543 CATATCAT
1 CATATCAT
16292551 GTTTATCAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
9 23 0.61
11 15 0.39
ACGTcount: A:0.35, C:0.21, G:0.09, T:0.35
Consensus pattern (9 bp):
CATATCATA
Found at i:16292513 original size:20 final size:20
Alignment explanation
Indices: 16292490--16292552 Score: 117
Period size: 20 Copynumber: 3.1 Consensus size: 20
16292480 GAACATCTCG
16292490 TGTGCATATCATACATATCA
1 TGTGCATATCATACATATCA
*
16292510 TGTGCATATCATACATGTCA
1 TGTGCATATCATACATATCA
16292530 TGTGCATATCATACATATCA
1 TGTGCATATCATACATATCA
16292550 TGT
1 TGT
16292553 TTATCAAAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.37
Consensus pattern (20 bp):
TGTGCATATCATACATATCA
Found at i:16292635 original size:25 final size:25
Alignment explanation
Indices: 16292589--16292636 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
16292579 ATATATAAAC
* * * *
16292589 CCTAGGGGTATAATGGTTATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
16292614 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
16292637 CATATTATAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:16293826 original size:27 final size:27
Alignment explanation
Indices: 16293796--16293860 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 27
16293786 GGGCATATTC
*
16293796 GTCATTTTACCATACAGGGG-TATCACG
1 GTCACTTTACCATACAGGGGCT-TCACG
* *
16293823 GTCACTTTACCCTACAGGGGCTTTACG
1 GTCACTTTACCATACAGGGGCTTCACG
16293850 GTCACTTTACC
1 GTCACTTTACC
16293861 TAATAGGGGT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
27 33 0.97
28 1 0.03
ACGTcount: A:0.22, C:0.28, G:0.20, T:0.31
Consensus pattern (27 bp):
GTCACTTTACCATACAGGGGCTTCACG
Found at i:16293944 original size:27 final size:27
Alignment explanation
Indices: 16293918--16294170 Score: 127
Period size: 27 Copynumber: 9.3 Consensus size: 27
16293908 ATCTACAAAC
* *
16293918 CAAGGGTATTTCAGTAATTTTGTAAAC
1 CAAGGGTATTTCAGTAATTTTATAAAT
* *
16293945 CAATGGTATTTCTA-TAATTTTTAGAAAGT
1 CAAGGGTATTTC-AGTAA-TTTTATAAA-T
* * *
16293974 CAAGGGTATTTCTGTAACTTTGTAAAT
1 CAAGGGTATTTCAGTAATTTTATAAAT
* ** *
16294001 CAGGGGTATTTTGGTAATTTTACAAAT
1 CAAGGGTATTTCAGTAATTTTATAAAT
** * *
16294028 TGAGGGTATTTC-GATAATTTCACAAA-
1 CAAGGGTATTTCAG-TAATTTTATAAAT
* * * * *
16294054 CCAGTGGTATTT-TGATAATTCTACAAAC
1 CAAG-GGTATTTCAG-TAATTTTATAAAT
* * *
16294082 CAGGGGTATTTTAGTAATTTTGTAAAT
1 CAAGGGTATTTCAGTAATTTTATAAAT
* *** * *
16294109 CGAGGGTAAAACAGTAATTCTGTAAAT
1 CAAGGGTATTTCAGTAATTTTATAAAT
*** *
16294136 CAAGGGTAAAACAGTAATTCTATAAAT
1 CAAGGGTATTTCAGTAATTTTATAAAT
16294163 CAAGGGTA
1 CAAGGGTA
16294171 AAATGGTAAT
Statistics
Matches: 177, Mismatches: 40, Indels: 18
0.75 0.17 0.08
Matches are distributed among these distances:
26 3 0.02
27 143 0.81
28 17 0.10
29 14 0.08
ACGTcount: A:0.35, C:0.10, G:0.19, T:0.36
Consensus pattern (27 bp):
CAAGGGTATTTCAGTAATTTTATAAAT
Found at i:16294100 original size:54 final size:54
Alignment explanation
Indices: 16293865--16294101 Score: 126
Period size: 54 Copynumber: 4.4 Consensus size: 54
16293855 TTTACCTAAT
* ** * * * *
16293865 AGGGGTATTTTAGTCATTTCATCCTACAAG-GGTGTTTTGGTAAATCTACAAACC
1 AGGGGTATTTTAGTAATTTCA-CAAACCAGTGGTATTTTGATAATTCTACAAACC
* * *** * * * *
16293919 AAGGGTATTTCAGTAATTTTGTAAACCAATGGTATTTCT-ATAATTTTTAGAAAGTC
1 AGGGGTATTTTAGTAATTTCACAAACCAGTGGTATTT-TGATAA-TTCTACAAA-CC
* ** * * * * *
16293975 AAGGGTATTTCT-GTAACTTT-GTAAATCAGGGGTATTTTGGTAATTTTACAAA-T
1 AGGGGTATTT-TAGTAA-TTTCACAAACCAGTGGTATTTTGATAATTCTACAAACC
* *
16294028 TGAGGGTA-TTTCGATAATTTCACAAACCAGTGGTATTTTGATAATTCTACAAACC
1 AG-GGGTATTTTAG-TAATTTCACAAACCAGTGGTATTTTGATAATTCTACAAACC
16294083 AGGGGTATTTTAGTAATTT
1 AGGGGTATTTTAGTAATTT
16294102 TGTAAATCGA
Statistics
Matches: 136, Mismatches: 34, Indels: 26
0.69 0.17 0.13
Matches are distributed among these distances:
52 1 0.01
53 9 0.07
54 70 0.51
55 21 0.15
56 32 0.24
57 3 0.02
ACGTcount: A:0.31, C:0.11, G:0.19, T:0.39
Consensus pattern (54 bp):
AGGGGTATTTTAGTAATTTCACAAACCAGTGGTATTTTGATAATTCTACAAACC
Found at i:16294171 original size:27 final size:27
Alignment explanation
Indices: 16294095--16294412 Score: 406
Period size: 27 Copynumber: 11.8 Consensus size: 27
16294085 GGGTATTTTA
* *
16294095 GTAATTTTGTAAATCGAGGGTAAAACA
1 GTAATTCTGTAAATCGAGGGTAAAACG
* *
16294122 GTAATTCTGTAAATCAAGGGTAAAACA
1 GTAATTCTGTAAATCGAGGGTAAAACG
* * *
16294149 GTAATTCTATAAATCAAGGGTAAAATG
1 GTAATTCTGTAAATCGAGGGTAAAACG
16294176 GTAATTCTGTAAATCGAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACG
*
16294203 GTAATTCTATAAATCGAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACG
* * * *
16294230 ATAATTATGTAAATTGGGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACG
* * * *
16294257 GTAATTATGTAAATTGGGGGTAAAACT
1 GTAATTCTGTAAATCGAGGGTAAAACG
* **
16294284 GTAATTCTATAAATCGAGGGTAAAATA
1 GTAATTCTGTAAATCGAGGGTAAAACG
16294311 GTAATTCTGTAAA-CTGAGGGTAAAACG
1 GTAATTCTGTAAATC-GAGGGTAAAACG
16294338 GTAATT-TGTAAATCGAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACG
* **
16294364 GTAATTTTACAAATCGAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACG
*
16294391 GTAATTCTATAAATCGAGGGTA
1 GTAATTCTGTAAATCGAGGGTA
16294413 CTTTGGTAAT
Statistics
Matches: 259, Mismatches: 29, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
26 25 0.10
27 234 0.90
ACGTcount: A:0.40, C:0.08, G:0.23, T:0.28
Consensus pattern (27 bp):
GTAATTCTGTAAATCGAGGGTAAAACG
Found at i:16294434 original size:27 final size:27
Alignment explanation
Indices: 16294363--16294613 Score: 222
Period size: 27 Copynumber: 9.3 Consensus size: 27
16294353 AGGGTAAAAC
****
16294363 GGTAATTTTACAAATCGAGGGTAAAAC
1 GGTAATTTTACAAATCGAGGGTATTTT
* * *
16294390 GGTAATTCTATAAATCGAGGGTACTTT
1 GGTAATTTTACAAATCGAGGGTATTTT
* *
16294417 GGTAATTTTACAAGTCGAGGGTATTTC
1 GGTAATTTTACAAATCGAGGGTATTTT
** ** *
16294444 AATAATTTTACAGGTCGAGGGTATTTC
1 GGTAATTTTACAAATCGAGGGTATTTT
* * *
16294471 AGTAATTTCACAAAT-TAGGGGTATTTT
1 GGTAATTTTACAAATCGA-GGGTATTTT
*
16294498 GGTAATTTTACAAA-CTAGGGGTATTTT
1 GGTAATTTTACAAATCGA-GGGTATTTT
* *
16294525 GATAATTTTACAAA-CTAGGGGTATTTT
1 GGTAATTTTACAAATCGA-GGGTATTTT
* * *
16294552 GGTAATTTTATAAACCAAGGGTATTTT
1 GGTAATTTTACAAATCGAGGGTATTTT
* *
16294579 AGTAATTTTACAAAGC-AGGGTATTTT
1 GGTAATTTTACAAATCGAGGGTATTTT
16294605 GGTAATTTT
1 GGTAATTTT
16294614 GTAAACCAAA
Statistics
Matches: 191, Mismatches: 30, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
26 19 0.10
27 170 0.89
28 2 0.01
ACGTcount: A:0.32, C:0.09, G:0.21, T:0.38
Consensus pattern (27 bp):
GGTAATTTTACAAATCGAGGGTATTTT
Found at i:16294627 original size:26 final size:26
Alignment explanation
Indices: 16294490--16294630 Score: 138
Period size: 27 Copynumber: 5.3 Consensus size: 26
16294480 ACAAATTAGG
* * *
16294490 GGTATTTTGGTAATTTTACAAACTAGG
1 GGTATTTTGGTAATTTTATAAACCA-A
* * * *
16294517 GGTATTTTGATAATTTTACAAACTAGG
1 GGTATTTTGGTAATTTTATAAACCA-A
16294544 GGTATTTTGGTAATTTTATAAACCAA
1 GGTATTTTGGTAATTTTATAAACCAA
* * * *
16294570 GGGTATTTTAGTAATTTTACAAAGCAG
1 -GGTATTTTGGTAATTTTATAAACCAA
*
16294597 GGTATTTTGGTAATTTTGTAAACCAA
1 GGTATTTTGGTAATTTTATAAACCAA
*
16294623 AGTATTTT
1 GGTATTTT
16294631 AAATAGGGAT
Statistics
Matches: 98, Mismatches: 15, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
26 28 0.29
27 70 0.71
ACGTcount: A:0.32, C:0.07, G:0.19, T:0.42
Consensus pattern (26 bp):
GGTATTTTGGTAATTTTATAAACCAA
Found at i:16295238 original size:68 final size:68
Alignment explanation
Indices: 16295091--16295246 Score: 149
Period size: 68 Copynumber: 2.2 Consensus size: 68
16295081 AGCCGATTTG
* * * * *
16295091 TCTCGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATT
1 TCTCGTAGCTCTCTTGTCTACATGGTGTACATCAC-TCGAATCACACATGCGACCTAGCTACATA
*
16295156 TATC
65 TATA
* *
16295160 TCTCACGTAGCTCTCTTGTCTACATGG-GATACATC-C-CGTATCACACATGTGACCTAGCTACT
1 TCT--CGTAGCTCTCTTGTCTACATGGTG-TACATCACTCGAATCACACATGCGACCTAGCTAC-
16295222 ATATAGTA
62 ATATA-TA
16295230 TCTCGTAGC-CTTCTTGT
1 TCTCGTAGCTC-TCTTGT
16295247 ACACATGATG
Statistics
Matches: 73, Mismatches: 8, Indels: 13
0.78 0.09 0.14
Matches are distributed among these distances:
67 1 0.01
68 33 0.45
69 7 0.10
70 6 0.08
71 26 0.36
ACGTcount: A:0.21, C:0.28, G:0.17, T:0.35
Consensus pattern (68 bp):
TCTCGTAGCTCTCTTGTCTACATGGTGTACATCACTCGAATCACACATGCGACCTAGCTACATAT
ATA
Found at i:16298799 original size:30 final size:30
Alignment explanation
Indices: 16298755--16298813 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
16298745 TCTGAGCCTT
16298755 GGGGAAAAAGTGTAAATATGTAAAAGTTTA
1 GGGGAAAAAGTGTAAATATGTAAAAGTTTA
* * *
16298785 GGGGCAAAAA-TGTAATTTTGTCAAAGTTT
1 GGGG-AAAAAGTGTAAATATGTAAAAGTTT
16298814 GGGTCAGAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 20 0.80
31 5 0.20
ACGTcount: A:0.41, C:0.03, G:0.25, T:0.31
Consensus pattern (30 bp):
GGGGAAAAAGTGTAAATATGTAAAAGTTTA
Found at i:16301475 original size:24 final size:24
Alignment explanation
Indices: 16301447--16301498 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
16301437 CCTTCATACC
**
16301447 CATATACACATAAA-CACATCCATA
1 CATATACACA-AAAGCACAGACATA
16301471 CATATACACAAAAGCACAGACATA
1 CATATACACAAAAGCACAGACATA
16301495 CATA
1 CATA
16301499 CCTTCCACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 3 0.12
24 22 0.88
ACGTcount: A:0.52, C:0.27, G:0.04, T:0.17
Consensus pattern (24 bp):
CATATACACAAAAGCACAGACATA
Found at i:16301782 original size:59 final size:59
Alignment explanation
Indices: 16301680--16301851 Score: 263
Period size: 59 Copynumber: 2.9 Consensus size: 59
16301670 CAGATCATGG
* * *
16301680 AATCACATGCCTCTCAACGGGGATACTCAAAAGCACTTAGACCCTAGCATGTATCACAT
1 AATCACATGCCTCTCAACGGGGCTACTCAAAAGCACCTGGACCCTAGCATGTATCACAT
* * * *
16301739 ATTCATATGCCTTTCAACGGGGCTACTCAAAAACACCTGGACCCTAGCATGTATCACAT
1 AATCACATGCCTCTCAACGGGGCTACTCAAAAGCACCTGGACCCTAGCATGTATCACAT
* *
16301798 AATCACATGCCTCTCAACGGGGCTACTCAAAAGCACCCGGACCCTAGCGTGTAT
1 AATCACATGCCTCTCAACGGGGCTACTCAAAAGCACCTGGACCCTAGCATGTAT
16301852 TACGTATCAA
Statistics
Matches: 100, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
59 100 1.00
ACGTcount: A:0.31, C:0.30, G:0.17, T:0.22
Consensus pattern (59 bp):
AATCACATGCCTCTCAACGGGGCTACTCAAAAGCACCTGGACCCTAGCATGTATCACAT
Found at i:16312459 original size:30 final size:29
Alignment explanation
Indices: 16312365--16312466 Score: 109
Period size: 28 Copynumber: 3.5 Consensus size: 29
16312355 TATAGTGAAT
* * *
16312365 CCGCACACTTAGTGCTATATATTTTCAGC
1 CCGCACACTTAGTGCTATAAATTTTAAAC
* *
16312394 TCGCACACTTAGTGCTATAGAA--TCAAAC
1 CCGCACACTTAGTGCTATA-AATTTTAAAC
* *
16312422 TCGCACACTTAGTGCTGTACAATTTTAAAC
1 CCGCACACTTAGTGCTATA-AATTTTAAAC
16312452 CCGCACACTTAGTGC
1 CCGCACACTTAGTGC
16312467 CAATCTTGTC
Statistics
Matches: 61, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
28 23 0.38
29 18 0.30
30 20 0.33
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.29
Consensus pattern (29 bp):
CCGCACACTTAGTGCTATAAATTTTAAAC
Found at i:16320320 original size:30 final size:29
Alignment explanation
Indices: 16320226--16320327 Score: 109
Period size: 28 Copynumber: 3.5 Consensus size: 29
16320216 TATAGTGAAT
* * *
16320226 CCGCACACTTAGTGCTATATATTTTCAGC
1 CCGCACACTTAGTGCTATAAATTTTAAAC
* *
16320255 TCGCACACTTAGTGCTATAGAA--TCAAAC
1 CCGCACACTTAGTGCTATA-AATTTTAAAC
* *
16320283 TCGCACACTTAGTGCTGTACAATTTTAAAC
1 CCGCACACTTAGTGCTATA-AATTTTAAAC
16320313 CCGCACACTTAGTGC
1 CCGCACACTTAGTGC
16320328 CAATCTTGTC
Statistics
Matches: 61, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
28 23 0.38
29 18 0.30
30 20 0.33
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.29
Consensus pattern (29 bp):
CCGCACACTTAGTGCTATAAATTTTAAAC
Found at i:16324735 original size:14 final size:14
Alignment explanation
Indices: 16324718--16324746 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
16324708 CGAAAATAAT
16324718 TTAATTAAAATTAA
1 TTAATTAAAATTAA
16324732 TTAATTAAAATTAA
1 TTAATTAAAATTAA
16324746 T
1 T
16324747 AACATTTTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
TTAATTAAAATTAA
Found at i:16329220 original size:24 final size:24
Alignment explanation
Indices: 16329188--16329235 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
16329178 ATTTCAAGCC
16329188 AAGCTGAATCATTTTTATAACTAT
1 AAGCTGAATCATTTTTATAACTAT
16329212 AAGCTGAATCATTTTTATAACTAT
1 AAGCTGAATCATTTTTATAACTAT
16329236 GGCAGCCTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.12, G:0.08, T:0.42
Consensus pattern (24 bp):
AAGCTGAATCATTTTTATAACTAT
Found at i:16330457 original size:13 final size:13
Alignment explanation
Indices: 16330423--16330458 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
16330413 TGGTTTACCA
**
16330423 ATTTATTTCATTT
1 ATTTATTTTTTTT
16330436 ATTTATTTTTTTT
1 ATTTATTTTTTTT
16330449 ATTTATTTTT
1 ATTTATTTTT
16330459 ATTCCTCTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.78
Consensus pattern (13 bp):
ATTTATTTTTTTT
Found at i:16330829 original size:21 final size:22
Alignment explanation
Indices: 16330805--16330861 Score: 59
Period size: 21 Copynumber: 2.7 Consensus size: 22
16330795 TTGGTTTTTG
16330805 AAAATTATTAAAAATTTTATA-
1 AAAATTATTAAAAATTTTATAC
*
16330826 AAAAATA-TAAAAA--TTATAC
1 AAAATTATTAAAAATTTTATAC
*
16330845 ATAATTATCTAAAAATT
1 AAAATTAT-TAAAAATT
16330862 ATTAAAATGA
Statistics
Matches: 28, Mismatches: 3, Indels: 8
0.72 0.08 0.21
Matches are distributed among these distances:
18 5 0.18
19 5 0.18
20 6 0.21
21 12 0.43
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.37
Consensus pattern (22 bp):
AAAATTATTAAAAATTTTATAC
Found at i:16330863 original size:11 final size:10
Alignment explanation
Indices: 16330805--16330868 Score: 60
Period size: 10 Copynumber: 6.3 Consensus size: 10
16330795 TTGGTTTTTG
16330805 AAAATTATTA
1 AAAATTATTA
*
16330815 AAAATTTTATA
1 AAAATTAT-TA
*
16330826 AAAAATA-TA
1 AAAATTATTA
16330835 AAAATTA-TA
1 AAAATTATTA
*
16330844 CATAATTATCTA
1 -AAAATTAT-TA
16330856 AAAATTATTA
1 AAAATTATTA
16330866 AAA
1 AAA
16330869 TGATAATAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
9 10 0.23
10 18 0.41
11 14 0.32
12 2 0.05
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (10 bp):
AAAATTATTA
Found at i:16340373 original size:62 final size:62
Alignment explanation
Indices: 16340276--16340408 Score: 257
Period size: 62 Copynumber: 2.1 Consensus size: 62
16340266 ATATTTCCCC
16340276 AACACGGGCTACGATAAATTACCACGACTGTGCAACATGGTCGTGGTCAAACCTGCCAAAAT
1 AACACGGGCTACGATAAATTACCACGACTGTGCAACATGGTCGTGGTCAAACCTGCCAAAAT
*
16340338 AACACGGGCTACGATAAATTACCACGACTGTGCAACATGGTCGTGGTCGAACCTGCCAAAAT
1 AACACGGGCTACGATAAATTACCACGACTGTGCAACATGGTCGTGGTCAAACCTGCCAAAAT
16340400 AACACGGGC
1 AACACGGGC
16340409 ATGCAATACG
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
62 70 1.00
ACGTcount: A:0.33, C:0.26, G:0.23, T:0.18
Consensus pattern (62 bp):
AACACGGGCTACGATAAATTACCACGACTGTGCAACATGGTCGTGGTCAAACCTGCCAAAAT
Found at i:16344542 original size:13 final size:13
Alignment explanation
Indices: 16344520--16344560 Score: 64
Period size: 13 Copynumber: 3.2 Consensus size: 13
16344510 AAAGCACGAC
*
16344520 TCACATAGGCGTG
1 TCACACAGGCGTG
16344533 TCACACAGGCGTG
1 TCACACAGGCGTG
*
16344546 TCACACAAGCGTG
1 TCACACAGGCGTG
16344559 TC
1 TC
16344561 CCTGCCGAGC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.24, C:0.29, G:0.27, T:0.20
Consensus pattern (13 bp):
TCACACAGGCGTG
Found at i:16347887 original size:12 final size:12
Alignment explanation
Indices: 16347870--16347894 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
16347860 ATGACATTTT
16347870 GGTGTATTCTAA
1 GGTGTATTCTAA
16347882 GGTGTATTCTAA
1 GGTGTATTCTAA
16347894 G
1 G
16347895 TCTGAGGACG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.08, G:0.28, T:0.40
Consensus pattern (12 bp):
GGTGTATTCTAA
Found at i:16353284 original size:24 final size:24
Alignment explanation
Indices: 16353252--16353297 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
16353242 TTCTCCTCTT
16353252 TTTTCTTC-TCTCTATTTCTTTTCC
1 TTTTCTTCTTCTCTATTT-TTTTCC
* *
16353276 TTTTGTTCTTCTTTATTTTTTT
1 TTTTCTTCTTCTCTATTTTTTT
16353298 AAGAAGTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 11 0.58
25 8 0.42
ACGTcount: A:0.04, C:0.20, G:0.02, T:0.74
Consensus pattern (24 bp):
TTTTCTTCTTCTCTATTTTTTTCC
Found at i:16353292 original size:25 final size:25
Alignment explanation
Indices: 16353249--16353297 Score: 66
Period size: 27 Copynumber: 2.0 Consensus size: 25
16353239 ACGTTCTCCT
16353249 CTTTTTTCTTCTCTCTATTTCTTTTC
1 CTTTTTTCTTCTCTCTATTT-TTTTC
16353275 CTTTTGTTCTTCT-T-TATTTTTTT
1 CTTTT-TTCTTCTCTCTATTTTTTT
16353298 AAGAAGTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 4 0.18
25 5 0.23
26 6 0.27
27 7 0.32
ACGTcount: A:0.04, C:0.20, G:0.02, T:0.73
Consensus pattern (25 bp):
CTTTTTTCTTCTCTCTATTTTTTTC
Found at i:16355080 original size:14 final size:15
Alignment explanation
Indices: 16355043--16355090 Score: 55
Period size: 14 Copynumber: 3.3 Consensus size: 15
16355033 ATGATTAGTC
16355043 TATAATTATAATAAA
1 TATAATTATAATAAA
*
16355058 TATGA-TATAATAAA
1 TATAATTATAATAAA
*
16355072 TA-AATTATAGTAAAA
1 TATAATTATAAT-AAA
16355087 TATA
1 TATA
16355091 CCTGAGATTC
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
13 1 0.04
14 16 0.59
15 9 0.33
16 1 0.04
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (15 bp):
TATAATTATAATAAA
Found at i:16356279 original size:9 final size:9
Alignment explanation
Indices: 16356250--16356341 Score: 60
Period size: 9 Copynumber: 9.6 Consensus size: 9
16356240 ATAATAGTTT
*
16356250 TTTTTGTAA
1 TTTTTATAA
*
16356259 TTTTT-TAT
1 TTTTTATAA
*
16356267 TTTTTATCA
1 TTTTTATAA
*
16356276 TTTTAATAA
1 TTTTTATAA
16356285 TTTTTATATGA
1 TTTTTATA--A
*
16356296 TTATGTATAA
1 TT-TTTATAA
*
16356306 CTTTTTTTATAG
1 ---TTTTTATAA
16356318 TTTTTATAA
1 TTTTTATAA
16356327 TTTTTAATAA
1 TTTTT-ATAA
16356337 TTTTT
1 TTTTT
16356342 CTTTAATTTC
Statistics
Matches: 65, Mismatches: 10, Indels: 15
0.72 0.11 0.17
Matches are distributed among these distances:
8 7 0.11
9 33 0.51
10 10 0.15
11 3 0.05
12 10 0.15
13 2 0.03
ACGTcount: A:0.27, C:0.02, G:0.04, T:0.66
Consensus pattern (9 bp):
TTTTTATAA
Found at i:16356629 original size:30 final size:32
Alignment explanation
Indices: 16356590--16356653 Score: 96
Period size: 30 Copynumber: 2.1 Consensus size: 32
16356580 TAAGTTGTTG
* *
16356590 TAAAGTAATTAAAAA-TTAATTAAGCCC-TCA
1 TAAAATAATTAAAAAGTCAATTAAGCCCTTCA
16356620 TAAAATAATTAAAAAGTCAATTAAGCCCTTCA
1 TAAAATAATTAAAAAGTCAATTAAGCCCTTCA
16356652 TA
1 TA
16356654 CCAATATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 14 0.47
31 11 0.37
32 5 0.17
ACGTcount: A:0.50, C:0.14, G:0.06, T:0.30
Consensus pattern (32 bp):
TAAAATAATTAAAAAGTCAATTAAGCCCTTCA
Found at i:16360918 original size:2 final size:2
Alignment explanation
Indices: 16360911--16360938 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
16360901 CTTACTTATC
16360911 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
16360939 AAATTTTCAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:16361501 original size:2 final size:2
Alignment explanation
Indices: 16361494--16361518 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
16361484 AAGTTTTATG
16361494 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
16361519 TGTTTATCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:16363721 original size:2 final size:2
Alignment explanation
Indices: 16363706--16363752 Score: 78
Period size: 2 Copynumber: 23.5 Consensus size: 2
16363696 ATAAATTAAG
16363706 AT AT AT -T AT GAT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16363748 AT AT A
1 AT AT A
16363753 ACAACTGGTG
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 1 0.02
2 40 0.93
3 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:16368528 original size:230 final size:230
Alignment explanation
Indices: 16368123--16368577 Score: 838
Period size: 230 Copynumber: 2.0 Consensus size: 230
16368113 CATTTAAACA
*
16368123 GTTTCAAACTTTATCTAACACAAAAGAGAAAATATTCCTCTCAACCCTATGATGAAAGAGAAGCA
1 GTTTCAAACTTTATCTAACACAAAAGAGAAAATATTCCTCCCAACCCTATGATGAAAGAGAAGCA
* *
16368188 TACCAAGGTAAACTCCCAAGTCTTCCACTTTAGTGAAACCCAACTTTGCACTTATTTCATTAACT
66 TACCAAGGTAAACTCCCAAGTCCTCCACTCTAGTGAAACCCAACTTTGCACTTATTTCATTAACT
*
16368253 GCTAAATCTGACACATTGCTTGAGAAAAATACCTGCGTCTTTTGTCTATTGACTTTATGACCAGA
131 GCTAAATCTGACACATTACTTGAGAAAAATACCTGCGTCTTTTGTCTATTGACTTTATGACCAGA
*
16368318 GAACCAACAGAAACTCTCCAACACATTTCTGAACG
196 GAACCAACAAAAACTCTCCAACACATTTCTGAACG
*
16368353 GTTTCAAACTTTATCTAACACAAAAGAGAAAGTATTCCTCCCAACCCTATGATGAAAGAGAAGCA
1 GTTTCAAACTTTATCTAACACAAAAGAGAAAATATTCCTCCCAACCCTATGATGAAAGAGAAGCA
*
16368418 TACCAAGGTAAACTCCCAAGTCCTCCACTCTAGTGAAACCCAACTTTGCACTTATTTCATTAGCT
66 TACCAAGGTAAACTCCCAAGTCCTCCACTCTAGTGAAACCCAACTTTGCACTTATTTCATTAACT
*
16368483 GCTAAATCTGACACATTACTTGAGAAAAATACCTGCGTTTTTTGTCTATTGACTTTATGACCAGA
131 GCTAAATCTGACACATTACTTGAGAAAAATACCTGCGTCTTTTGTCTATTGACTTTATGACCAGA
16368548 GAACCAACAAAAACTCTCCAACACATTTCT
196 GAACCAACAAAAACTCTCCAACACATTTCT
16368578 AAGACAATCT
Statistics
Matches: 217, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
230 217 1.00
ACGTcount: A:0.35, C:0.24, G:0.12, T:0.28
Consensus pattern (230 bp):
GTTTCAAACTTTATCTAACACAAAAGAGAAAATATTCCTCCCAACCCTATGATGAAAGAGAAGCA
TACCAAGGTAAACTCCCAAGTCCTCCACTCTAGTGAAACCCAACTTTGCACTTATTTCATTAACT
GCTAAATCTGACACATTACTTGAGAAAAATACCTGCGTCTTTTGTCTATTGACTTTATGACCAGA
GAACCAACAAAAACTCTCCAACACATTTCTGAACG
Found at i:16371366 original size:21 final size:21
Alignment explanation
Indices: 16371333--16371373 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
16371323 GTTTCCTTCT
*
16371333 TCTTACCTTCCTCAAATTGCG
1 TCTTACCTCCCTCAAATTGCG
* *
16371354 TCTTATCTCCCTCAATTTGC
1 TCTTACCTCCCTCAAATTGC
16371374 ACCTGGTTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.17, C:0.34, G:0.07, T:0.41
Consensus pattern (21 bp):
TCTTACCTCCCTCAAATTGCG
Found at i:16381632 original size:159 final size:158
Alignment explanation
Indices: 16381277--16381649 Score: 441
Period size: 158 Copynumber: 2.4 Consensus size: 158
16381267 TAAATAGCTC
* *
16381277 GTTAATGGATATGTTCATTGCAAGCCATGATGATCATTATTCAGACATGTTCTTGAGTCTGCCAT
1 GTTAATGGATAAGTTCATTGCAAGCCATGATGATCATTATTCAGACATGTTCTTTAGTCTGCCAT
* *
16381342 GTAAGGATAAGTTTAGTTAGCTGTAGTGATGGCATTTTAACCATTTTTTATCCTTTAAGGATAAA
66 GTAAGGATAAGTTTAGTTAGATGTAGTGATGACATTTTAACCATTTTTTATCCTTTAAGGATAAA
* * * * *
16381407 TTTAGTCTGCCTTGAAAGGATAAGTTTA
131 TTCAGACTGACGTGAAAGGATAAGTCTA
* * **
16381435 CTTAATGGATAAGTTCATTGCAAGCCATGATGATCATTATGCAGACATGTTCTTTAGTCTGCTTT
1 GTTAATGGATAAGTTCATTGCAAGCCATGATGATCATTATTCAGACATGTTCTTTAGTCTGCCAT
* * ** *
16381500 GTAAGGATAAG-TT-GTTGGATGTAGTGATGACATTTTGACCATTTTTTATCCATTCTTTTGGCT
66 GTAAGGATAAGTTTAGTTAGATGTAGTGATGACATTTTAACCATTTTTTATCC--T-TTAAGGAT
* * * *
16381563 CATAGTTCAGACATGAGGT-AAAGTAT-TG-CTA
128 -A-AATTCAGAC-TGACGTGAAAGGATAAGTCTA
* *
16381594 GTTAATGGATAAGTACATTGCAAGCCATGATGATCATTATTCAGACATGTTTTTTA
1 GTTAATGGATAAGTTCATTGCAAGCCATGATGATCATTATTCAGACATGTTCTTTA
16381650 ACCTGTCATG
Statistics
Matches: 183, Mismatches: 26, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
156 34 0.19
157 2 0.01
158 71 0.39
159 59 0.32
160 2 0.01
161 12 0.07
162 3 0.02
ACGTcount: A:0.28, C:0.13, G:0.20, T:0.39
Consensus pattern (158 bp):
GTTAATGGATAAGTTCATTGCAAGCCATGATGATCATTATTCAGACATGTTCTTTAGTCTGCCAT
GTAAGGATAAGTTTAGTTAGATGTAGTGATGACATTTTAACCATTTTTTATCCTTTAAGGATAAA
TTCAGACTGACGTGAAAGGATAAGTCTA
Found at i:16383741 original size:30 final size:30
Alignment explanation
Indices: 16383697--16383759 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
16383687 ATTTAACAAG
* *
16383697 CAAATGCCTCTAAAATAATAATAAAATTAA
1 CAAATACCTCTAAAATAATAACAAAATTAA
*
16383727 CAAATACCTTTAAAATAATAACAAAATTAA
1 CAAATACCTCTAAAATAATAACAAAATTAA
16383757 CAA
1 CAA
16383760 TAAAATAAGA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.59, C:0.14, G:0.02, T:0.25
Consensus pattern (30 bp):
CAAATACCTCTAAAATAATAACAAAATTAA
Found at i:16391944 original size:16 final size:17
Alignment explanation
Indices: 16391905--16391944 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
16391895 AAATAAATTA
16391905 AACTAAATTGAATAAAC
1 AACTAAATTGAATAAAC
16391922 AGA--AAATTGAA-AAAC
1 A-ACTAAATTGAATAAAC
16391937 AACTAAAT
1 AACTAAAT
16391945 CATAATATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 7
0.74 0.00 0.26
Matches are distributed among these distances:
14 1 0.05
15 5 0.25
16 12 0.60
17 1 0.05
18 1 0.05
ACGTcount: A:0.62, C:0.10, G:0.07, T:0.20
Consensus pattern (17 bp):
AACTAAATTGAATAAAC
Found at i:16396421 original size:15 final size:15
Alignment explanation
Indices: 16396401--16396469 Score: 84
Period size: 15 Copynumber: 4.6 Consensus size: 15
16396391 GTATCTTGGG
16396401 TTTCTTTATCCTGGA
1 TTTCTTTATCCTGGA
* *
16396416 TCTCTTTATTCTGGA
1 TTTCTTTATCCTGGA
* *
16396431 TTTCTTTATTCTGGG
1 TTTCTTTATCCTGGA
* *
16396446 TTTCTCTATCTTGGA
1 TTTCTTTATCCTGGA
16396461 TTTCTTTAT
1 TTTCTTTAT
16396470 TCGGTTTTCT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 45 1.00
ACGTcount: A:0.12, C:0.17, G:0.13, T:0.58
Consensus pattern (15 bp):
TTTCTTTATCCTGGA
Found at i:16396470 original size:30 final size:30
Alignment explanation
Indices: 16396392--16396479 Score: 99
Period size: 30 Copynumber: 3.0 Consensus size: 30
16396382 CATAGTATCG
* * * *
16396392 TATCTTGGGTTTCTTTATCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTCTGGATTTCTC
*
16396422 TAT-TCTGGATTTCTTTATTCTGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCTGGATTTCTC
*
16396452 TATCTTGGATTTCTTTATTC-GGTTTTCT
1 TATCTTGGATTTCTTTATTCTGGATTTCT
16396480 TGTTATCTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
29 8 0.16
30 41 0.82
31 1 0.02
ACGTcount: A:0.10, C:0.17, G:0.16, T:0.57
Consensus pattern (30 bp):
TATCTTGGATTTCTTTATTCTGGATTTCTC
Found at i:16402931 original size:29 final size:29
Alignment explanation
Indices: 16402898--16402970 Score: 146
Period size: 29 Copynumber: 2.5 Consensus size: 29
16402888 GTGATGAGAT
16402898 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
16402927 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
16402956 TGGCACTAAGTGTGC
1 TGGCACTAAGTGTGC
16402971 GAGCTCGAAG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 44 1.00
ACGTcount: A:0.29, C:0.15, G:0.29, T:0.27
Consensus pattern (29 bp):
TGGCACTAAGTGTGCATGCTGGAAATATA
Found at i:16402986 original size:29 final size:30
Alignment explanation
Indices: 16402898--16403030 Score: 141
Period size: 29 Copynumber: 4.6 Consensus size: 30
16402888 GTGATGAGAT
16402898 TGGCACTAAGTGTGC-ATGCTGGAAATATA
1 TGGCACTAAGTGTGCGATGCTGGAAATATA
16402927 TGGCACTAAGTGTGC-ATGCTGGAAATATA
1 TGGCACTAAGTGTGCGATGCTGGAAATATA
* ***
16402956 TGGCACTAAGTGTGCGA-GCTCGAAGGGTA
1 TGGCACTAAGTGTGCGATGCTGGAAATATA
* * * **
16402985 TGGCACTATGTGTGCG-GGCT-TAAATCGCA
1 TGGCACTAAGTGTGCGATGCTGGAAAT-ATA
16403014 TGGCACTAAGTGTGCGA
1 TGGCACTAAGTGTGCGA
16403031 AATCGAGTAT
Statistics
Matches: 90, Mismatches: 10, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
28 2 0.02
29 87 0.97
30 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.32, T:0.26
Consensus pattern (30 bp):
TGGCACTAAGTGTGCGATGCTGGAAATATA
Found at i:16407894 original size:6 final size:6
Alignment explanation
Indices: 16407883--16407907 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
16407873 CATTTCCATG
16407883 TCATTT TCATTT TCATTT TCATTT T
1 TCATTT TCATTT TCATTT TCATTT T
16407908 GGAGAAAACC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.68
Consensus pattern (6 bp):
TCATTT
Found at i:16407956 original size:62 final size:62
Alignment explanation
Indices: 16407884--16408015 Score: 196
Period size: 62 Copynumber: 2.1 Consensus size: 62
16407874 ATTTCCATGT
* *
16407884 CATTTTCATTTTCATTTTC-ATTTTGGAGAAAACCACATTCATTTCCAAATGATTCAT-TTCTC
1 CATTTTCATTTTCA-TTTCAATTGTGGAGAAAACCACAGTCATTTCCAAATG-TTCATATTCTC
* *
16407946 CATTTTCATTTTCATTTCAATTGTGGAGAAAACCATAGTCATTTCCAAATGTTCCTATTCTC
1 CATTTTCATTTTCATTTCAATTGTGGAGAAAACCACAGTCATTTCCAAATGTTCATATTCTC
16408008 CATTTTCA
1 CATTTTCA
16408016 CCATTTCTGT
Statistics
Matches: 64, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
61 8 0.12
62 56 0.88
ACGTcount: A:0.27, C:0.21, G:0.08, T:0.44
Consensus pattern (62 bp):
CATTTTCATTTTCATTTCAATTGTGGAGAAAACCACAGTCATTTCCAAATGTTCATATTCTC
Found at i:16408844 original size:17 final size:17
Alignment explanation
Indices: 16408799--16408873 Score: 59
Period size: 17 Copynumber: 4.5 Consensus size: 17
16408789 ATAATTACTT
16408799 TAATATTAAATT-AATA
1 TAATATTAAATTAAATA
* *
16408815 AAATACT--ATTAAA-A
1 TAATATTAAATTAAATA
*
16408829 TAAGTATTAAATTAAATT
1 TAA-TATTAAATTAAATA
*
16408847 TAATATTAAATTATTAAAA
1 TAATATTAAATTA--AATA
16408866 TAATATTA
1 TAATATTA
16408874 TTTTTGGAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 11
0.71 0.11 0.17
Matches are distributed among these distances:
14 6 0.13
15 5 0.11
16 5 0.11
17 16 0.36
18 3 0.07
19 10 0.22
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.41
Consensus pattern (17 bp):
TAATATTAAATTAAATA
Found at i:16411216 original size:31 final size:31
Alignment explanation
Indices: 16411178--16411272 Score: 172
Period size: 31 Copynumber: 3.1 Consensus size: 31
16411168 CCTTTTCATA
16411178 TTTCATATTTCATAATACTGGGCCGAAGCCT
1 TTTCATATTTCATAATACTGGGCCGAAGCCT
*
16411209 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATATTTCATAATACTGGGCCGAAGCCT
*
16411240 TTTCATATTTCATAGTACTGGGCCGAAGCCT
1 TTTCATATTTCATAATACTGGGCCGAAGCCT
16411271 TT
1 TT
16411273 ACTGTAAACG
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 62 1.00
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (31 bp):
TTTCATATTTCATAATACTGGGCCGAAGCCT
Found at i:16411515 original size:24 final size:24
Alignment explanation
Indices: 16411464--16411582 Score: 161
Period size: 24 Copynumber: 5.0 Consensus size: 24
16411454 GCTTTATCAT
*
16411464 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
* * *
16411489 ATAACTGGGGCAAAACCCCTTTCA
1 ATAACTGGGGCATAAGCCCTTTTA
16411513 ATAACTGGGGCATAAGCCCTTTT-
1 ATAACTGGGGCATAAGCCCTTTTA
*
16411536 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
16411560 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
16411583 TCACTTCCTC
Statistics
Matches: 85, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
23 23 0.27
24 51 0.60
25 11 0.13
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.29
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:16411543 original size:47 final size:48
Alignment explanation
Indices: 16411464--16411582 Score: 161
Period size: 47 Copynumber: 2.5 Consensus size: 48
16411454 GCTTTATCAT
*
16411464 ATAACTGGAGGCCT-AGCCTCTTTTAATAACTGGGGCAAAACCCCTTTCA
1 ATAACTGG-GGCATAAGCC-CTTTTAATAACTGGGGCAAAACCCCTTTCA
* * **
16411513 ATAACTGGGGCATAAGCCCTTTT-ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCAAAACCCCTTTCA
16411560 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
16411583 TCACTTCCTC
Statistics
Matches: 64, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
47 43 0.67
48 9 0.14
49 12 0.19
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.29
Consensus pattern (48 bp):
ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCAAAACCCCTTTCA
Found at i:16411658 original size:20 final size:20
Alignment explanation
Indices: 16411633--16411692 Score: 102
Period size: 20 Copynumber: 3.0 Consensus size: 20
16411623 TATGATTACC
16411633 TCATGTGCATATCATACATA
1 TCATGTGCATATCATACATA
* *
16411653 TCATGTGCATAGCATACATT
1 TCATGTGCATATCATACATA
16411673 TCATGTGCATATCATACATA
1 TCATGTGCATATCATACATA
16411693 CCATATTTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.35
Consensus pattern (20 bp):
TCATGTGCATATCATACATA
Found at i:16411767 original size:25 final size:25
Alignment explanation
Indices: 16411735--16411782 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
16411725 ATACATAAAC
* * *
16411735 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
16411760 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
16411783 CATATTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:16412999 original size:27 final size:27
Alignment explanation
Indices: 16412937--16413001 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 27
16412927 GGGCATATTC
16412937 GTCATTTTACCATACAGGGGTATTACG
1 GTCATTTTACCATACAGGGGTATTACG
* *
16412964 GTCACTTTACCCTACAGGGGCT-TTACG
1 GTCATTTTACCATACAGGGG-TATTACG
*
16412991 GTCTTTTTACC
1 GTCATTTTACC
16413002 TAATAGGGAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
27 32 0.97
28 1 0.03
ACGTcount: A:0.20, C:0.25, G:0.20, T:0.35
Consensus pattern (27 bp):
GTCATTTTACCATACAGGGGTATTACG
Found at i:16413085 original size:27 final size:27
Alignment explanation
Indices: 16413055--16413248 Score: 97
Period size: 27 Copynumber: 7.1 Consensus size: 27
16413045 GTAAATCTAC
16413055 AAACTAAGGGTATTTCAGTAATTTTGT
1 AAACTAAGGGTATTTCAGTAATTTTGT
* * *
16413082 AAACCAATGGTATTTTTA-TAATTTT-T
1 AAACTAAGGGTA-TTTCAGTAATTTTGT
* * *
16413108 AGAAAGTTAAGGGTATTTCTGTAACTTTGT
1 --AAA-CTAAGGGTATTTCAGTAATTTTGT
* * ** **
16413138 AAATTAGGGGTATTTTGGTAATTTTAC
1 AAACTAAGGGTATTTCAGTAATTTTGT
* * * * ***
16413165 AAATTGAGGGTTTTTCGGTAATTTCAC
1 AAACTAAGGGTATTTCAGTAATTTTGT
* *
16413192 AAACCAAGGGTATTTTAGTAATTTTGT
1 AAACTAAGGGTATTTCAGTAATTTTGT
*** *
16413219 AAA-TCAAGGGTAAAACAGTAATTTAGT
1 AAACT-AAGGGTATTTCAGTAATTTTGT
16413246 AAA
1 AAA
16413249 TCGAGGGTAA
Statistics
Matches: 125, Mismatches: 35, Indels: 14
0.72 0.20 0.08
Matches are distributed among these distances:
26 1 0.01
27 98 0.78
28 13 0.10
29 12 0.10
30 1 0.01
ACGTcount: A:0.35, C:0.07, G:0.19, T:0.40
Consensus pattern (27 bp):
AAACTAAGGGTATTTCAGTAATTTTGT
Found at i:16413519 original size:27 final size:27
Alignment explanation
Indices: 16413209--16413526 Score: 342
Period size: 27 Copynumber: 11.8 Consensus size: 27
16413199 GGGTATTTTA
* * * *
16413209 GTAATTTTGTAAATCAAGGGTAAAACA
1 GTAATTATGTAAATTAGGGGTAAAACG
*
16413236 GTAATT-TAGTAAA-TCGAGGGTAAAACG
1 GTAATTAT-GTAAATTAG-GGGTAAAACG
* * *
16413263 GTAATTCTGT-AAGTCGAGGGTAAAACG
1 GTAATTATGTAAATTAG-GGGTAAAACG
* *
16413290 ATAATTATATAAATTA-GGGTAAAACG
1 GTAATTATGTAAATTAGGGGTAAAACG
16413316 GTAATTATGTAAATTAGGGGTAAAACG
1 GTAATTATGTAAATTAGGGGTAAAACG
* * *
16413343 GTAATTTTGT-AAGTCGAGGGTAAAACG
1 GTAATTATGTAAATTAG-GGGTAAAACG
* *
16413370 ATAATTATGTAAATCAGGGGTAAAACG
1 GTAATTATGTAAATTAGGGGTAAAACG
16413397 GTAATTATGTAAATTAGGGGTAAAACG
1 GTAATTATGTAAATTAGGGGTAAAACG
* * *
16413424 GTAATTCTGT-AAGTCGAGGGTAAAACG
1 GTAATTATGTAAATTAG-GGGTAAAACG
* * *
16413451 ATAATTATGTAAATCAGGGGTAAAATG
1 GTAATTATGTAAATTAGGGGTAAAACG
16413478 GTAATTATGTAAATTAGGGGTAAAACG
1 GTAATTATGTAAATTAGGGGTAAAACG
* *
16413505 GTAATTCTGTAAATTGGGGGTA
1 GTAATTATGTAAATTAGGGGTA
16413527 CTTTAGTAAT
Statistics
Matches: 246, Mismatches: 35, Indels: 20
0.82 0.12 0.07
Matches are distributed among these distances:
26 35 0.14
27 201 0.82
28 10 0.04
ACGTcount: A:0.40, C:0.06, G:0.25, T:0.29
Consensus pattern (27 bp):
GTAATTATGTAAATTAGGGGTAAAACG
Found at i:16413537 original size:81 final size:81
Alignment explanation
Indices: 16413210--16413516 Score: 503
Period size: 81 Copynumber: 3.8 Consensus size: 81
16413200 GGTATTTTAG
* * * *
16413210 TAATTTTGTAAATCAAGGGTAAAACAGTAATT-TAGTAAA-TCGAGGGTAAAACGGTAATTCTGT
1 TAATTATGTAAATCAGGGGTAAAACGGTAATTAT-GTAAATTAG-GGGTAAAACGGTAATTCTGT
16413273 AAGTCGAGGGTAAAACGA
64 AAGTCGAGGGTAAAACGA
* * *
16413291 TAATTATATAAATTA-GGGTAAAACGGTAATTATGTAAATTAGGGGTAAAACGGTAATTTTGTAA
1 TAATTATGTAAATCAGGGGTAAAACGGTAATTATGTAAATTAGGGGTAAAACGGTAATTCTGTAA
16413355 GTCGAGGGTAAAACGA
66 GTCGAGGGTAAAACGA
16413371 TAATTATGTAAATCAGGGGTAAAACGGTAATTATGTAAATTAGGGGTAAAACGGTAATTCTGTAA
1 TAATTATGTAAATCAGGGGTAAAACGGTAATTATGTAAATTAGGGGTAAAACGGTAATTCTGTAA
16413436 GTCGAGGGTAAAACGA
66 GTCGAGGGTAAAACGA
*
16413452 TAATTATGTAAATCAGGGGTAAAATGGTAATTATGTAAATTAGGGGTAAAACGGTAATTCTGTAA
1 TAATTATGTAAATCAGGGGTAAAACGGTAATTATGTAAATTAGGGGTAAAACGGTAATTCTGTAA
16413517 ATTGGGGGTA
Statistics
Matches: 213, Mismatches: 10, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
80 70 0.33
81 143 0.67
ACGTcount: A:0.40, C:0.07, G:0.24, T:0.29
Consensus pattern (81 bp):
TAATTATGTAAATCAGGGGTAAAACGGTAATTATGTAAATTAGGGGTAAAACGGTAATTCTGTAA
GTCGAGGGTAAAACGA
Found at i:16413553 original size:27 final size:27
Alignment explanation
Indices: 16413523--16413621 Score: 94
Period size: 27 Copynumber: 3.7 Consensus size: 27
16413513 GTAAATTGGG
*
16413523 GGTACTTT-AGTAATTTTACAAGTCGAA
1 GGTA-TTTCAGTAATTTTACAAATCGAA
* * * *
16413550 GGTATTTCGGTAAATTTGCAAATCGAG
1 GGTATTTCAGTAATTTTACAAATCGAA
* *
16413577 GGTATTTCAGTATTTTTACAAA-CTAA
1 GGTATTTCAGTAATTTTACAAATCGAA
*
16413603 GGGTATTTCGGTAATTTTA
1 -GGTATTTCAGTAATTTTA
16413622 GTAAACTAAA
Statistics
Matches: 57, Mismatches: 13, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
26 5 0.09
27 52 0.91
ACGTcount: A:0.30, C:0.10, G:0.20, T:0.39
Consensus pattern (27 bp):
GGTATTTCAGTAATTTTACAAATCGAA
Found at i:16413561 original size:54 final size:53
Alignment explanation
Indices: 16413503--16413619 Score: 130
Period size: 54 Copynumber: 2.2 Consensus size: 53
16413493 AGGGGTAAAA
* * * *
16413503 CGGTAATTCTGTAAATTGGGGGTACTTT-AGTAATTTTACAAGTCGAA-GGTATTT
1 CGGTAATT-TGCAAATCGAGGGTA-TTTCAGTAATTTTACAA-ACGAAGGGTATTT
* *
16413557 CGGTAAATTTGCAAATCGAGGGTATTTCAGTATTTTTACAAACTAAGGGTATTT
1 CGGT-AATTTGCAAATCGAGGGTATTTCAGTAATTTTACAAACGAAGGGTATTT
16413611 CGGTAATTT
1 CGGTAATTT
16413620 TAGTAAACTA
Statistics
Matches: 54, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
53 11 0.20
54 39 0.72
55 4 0.07
ACGTcount: A:0.29, C:0.10, G:0.22, T:0.38
Consensus pattern (53 bp):
CGGTAATTTGCAAATCGAGGGTATTTCAGTAATTTTACAAACGAAGGGTATTT
Found at i:16413628 original size:28 final size:28
Alignment explanation
Indices: 16413550--16413630 Score: 87
Period size: 27 Copynumber: 3.0 Consensus size: 28
16413540 ACAAGTCGAA
* *
16413550 GGTATTTCGGTAAATTT-GCAAA-TCGAG
1 GGTATTTCGGTAATTTTAGCAAACT-AAG
* *
16413577 GGTATTTCAGTATTTTTA-CAAACTAAG
1 GGTATTTCGGTAATTTTAGCAAACTAAG
*
16413604 GGTATTTCGGTAATTTTAGTAAACTAA
1 GGTATTTCGGTAATTTTAGCAAACTAA
16413631 AGTATTCTAA
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
27 36 0.82
28 8 0.18
ACGTcount: A:0.32, C:0.10, G:0.20, T:0.38
Consensus pattern (28 bp):
GGTATTTCGGTAATTTTAGCAAACTAAG
Found at i:16413635 original size:27 final size:27
Alignment explanation
Indices: 16413578--16413636 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
16413568 CAAATCGAGG
* *
16413578 GTATTTCAGTATTTTTACAAACTAAGG
1 GTATTTCAGTAATTTTACAAACTAAGA
* *
16413605 GTATTTCGGTAATTTTAGTAAACTAA-A
1 GTATTTCAGTAATTTTA-CAAACTAAGA
16413632 GTATT
1 GTATT
16413637 CTAAACAGGG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 20 0.74
28 7 0.26
ACGTcount: A:0.34, C:0.08, G:0.15, T:0.42
Consensus pattern (27 bp):
GTATTTCAGTAATTTTACAAACTAAGA
Found at i:16417475 original size:2 final size:2
Alignment explanation
Indices: 16417468--16417503 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
16417458 ATGAAAGGAA
16417468 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16417504 TTAAAAGAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16419882 original size:38 final size:38
Alignment explanation
Indices: 16419801--16419951 Score: 167
Period size: 38 Copynumber: 3.9 Consensus size: 38
16419791 GAATCCAGTC
* * * *
16419801 ACCAGCACAAAGCCTGCGGAACTTTAAGCCCGGATATAGT
1 ACCAGTACGAAGCCTGCGGGA-TTTAA-CCCGGATATATT
* *
16419841 ACCAGTACTATGCCTGCGGGATTTAACCCGGATATATT
1 ACCAGTACGAAGCCTGCGGGATTTAACCCGGATATATT
* *
16419879 ACCAGCACGAAGCCTGCAGGATTTAACCCGGATATATT
1 ACCAGTACGAAGCCTGCGGGATTTAACCCGGATATATT
* * * * *
16419917 ATCAGTACGAAGCCTACTGGACTTAACTCGGATAT
1 ACCAGTACGAAGCCTGCGGGATTTAACCCGGATAT
16419952 GTATCGAGTG
Statistics
Matches: 96, Mismatches: 15, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
38 74 0.77
39 5 0.05
40 17 0.18
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.23
Consensus pattern (38 bp):
ACCAGTACGAAGCCTGCGGGATTTAACCCGGATATATT
Found at i:16419924 original size:76 final size:78
Alignment explanation
Indices: 16419801--16419951 Score: 191
Period size: 76 Copynumber: 2.0 Consensus size: 78
16419791 GAATCCAGTC
* * * *
16419801 ACCAGCACAAAGCCTGCGGAACTTTAAGCCCGGATATAGTACCAGTACTATGCCTGCGGGATTTA
1 ACCAGCACAAAGCCTGCGGAACTTTAAGCCCGGATATAGTACCAGTACGAAGCCTACGGGACTTA
16419866 ACCCGGATATATT
66 ACCCGGATATATT
* * * *
16419879 ACCAGCACGAAGCCTGCAGG-A-TTTAA-CCCGGATATATTATCAGTACGAAGCCTACTGGACTT
1 ACCAGCACAAAGCCTGC-GGAACTTTAAGCCCGGATATAGTACCAGTACGAAGCCTACGGGACTT
*
16419941 AACTCGGATAT
65 AACCCGGATAT
16419952 GTATCGAGTG
Statistics
Matches: 63, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
76 39 0.62
77 5 0.08
78 17 0.27
79 2 0.03
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.23
Consensus pattern (78 bp):
ACCAGCACAAAGCCTGCGGAACTTTAAGCCCGGATATAGTACCAGTACGAAGCCTACGGGACTTA
ACCCGGATATATT
Found at i:16427097 original size:2 final size:2
Alignment explanation
Indices: 16427090--16427117 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
16427080 TATTGGCCAA
16427090 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16427118 GAATACACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16427570 original size:38 final size:38
Alignment explanation
Indices: 16427430--16427635 Score: 232
Period size: 38 Copynumber: 5.3 Consensus size: 38
16427420 CTAGGTTTAA
* * *
16427430 AACCCGAATCTAGTCACCAGCACAAAGCCTGCGGAACTTT
1 AACCCGGATATAGT-ACCAGCACAAAGCCTGCGGGA-TTT
*
16427470 AAGCCCGGATATAGTACCAGCACAAAGCCTGCGGAACTTT
1 AA-CCCGGATATAGTACCAGCACAAAGCCTGCGGGA-TTT
* * *
16427510 AAGCCCAGATATAGTACTAGCACTAAGCCTGCGGGATTT
1 AA-CCCGGATATAGTACCAGCACAAAGCCTGCGGGATTT
* *
16427549 AACCCGGATATATTACCAGCACAAAGTCTGCGGGATTT
1 AACCCGGATATAGTACCAGCACAAAGCCTGCGGGATTT
* * * * *
16427587 AACCTGGATATATTACCAGCACGAAGCCTGGGGGACTT
1 AACCCGGATATAGTACCAGCACAAAGCCTGCGGGATTT
*
16427625 AACCTGGATAT
1 AACCCGGATAT
16427636 GTATCGAGTG
Statistics
Matches: 149, Mismatches: 16, Indels: 4
0.88 0.09 0.02
Matches are distributed among these distances:
38 75 0.50
39 5 0.03
40 59 0.40
41 10 0.07
ACGTcount: A:0.32, C:0.26, G:0.22, T:0.21
Consensus pattern (38 bp):
AACCCGGATATAGTACCAGCACAAAGCCTGCGGGATTT
Found at i:16430653 original size:30 final size:30
Alignment explanation
Indices: 16430612--16430680 Score: 97
Period size: 30 Copynumber: 2.4 Consensus size: 30
16430602 AAAATCATAT
* * *
16430612 TTTGGCAAAATTATATTTTTGCCCCTAAAC
1 TTTGTCAAAATTACACTTTTGCCCCTAAAC
16430642 TTTGTCAAAATTACACTTTTGCCCCTAAAC
1 TTTGTCAAAATTACACTTTTGCCCCTAAAC
16430672 -TTGT-AAAAT
1 TTTGTCAAAAT
16430681 AGTTTTTATT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
28 5 0.14
29 4 0.11
30 27 0.75
ACGTcount: A:0.32, C:0.20, G:0.09, T:0.39
Consensus pattern (30 bp):
TTTGTCAAAATTACACTTTTGCCCCTAAAC
Found at i:16432594 original size:2 final size:2
Alignment explanation
Indices: 16432587--16432618 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
16432577 GTCATATTTG
16432587 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16432619 GTCGCAAGCT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16433295 original size:12 final size:13
Alignment explanation
Indices: 16433280--16433344 Score: 80
Period size: 13 Copynumber: 5.1 Consensus size: 13
16433270 TTTAAACCAA
16433280 ACTTTTCAAAAG-
1 ACTTTTCAAAAGC
* *
16433292 ACTTCTCAAAAGT
1 ACTTTTCAAAAGC
*
16433305 ACTTTTTC-ACAGC
1 AC-TTTTCAAAAGC
16433318 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
16433331 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
16433344 A
1 A
16433345 TTGCCAAACT
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
12 16 0.36
13 25 0.56
14 4 0.09
ACGTcount: A:0.37, C:0.23, G:0.08, T:0.32
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:16444657 original size:4 final size:4
Alignment explanation
Indices: 16444643--16444731 Score: 64
Period size: 4 Copynumber: 22.8 Consensus size: 4
16444633 ATTTTTCAAT
*
16444643 TTTA TTTTA TTTA TTT- TTATT TTTA TTT- TATTA TTTA -TTA TTTA -TTA
1 TTTA -TTTA TTTA TTTA TT-TA TTTA TTTA T-TTA TTTA TTTA TTTA TTTA
* * *
16444690 TTTA -TTA CTTTA TTTA ATTA TTTA -TTA CTTA ATTA TTTA TTT
1 TTTA TTTA -TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
16444732 TATTATTAAT
Statistics
Matches: 70, Mismatches: 5, Indels: 19
0.74 0.05 0.20
Matches are distributed among these distances:
3 15 0.21
4 45 0.64
5 10 0.14
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (4 bp):
TTTA
Found at i:16444658 original size:14 final size:13
Alignment explanation
Indices: 16444652--16444738 Score: 76
Period size: 12 Copynumber: 6.7 Consensus size: 13
16444642 TTTTATTTTA
16444652 TTTATT-TTTATT
1 TTTATTATTTATT
16444664 TTTA-T-TTTATT
1 TTTATTATTTATT
16444675 ATTTATTATTTATT
1 -TTTATTATTTATT
16444689 ATTTATTACTTTA-T
1 -TTTATTA-TTTATT
*
16444703 TTAATTATTTATT
1 TTTATTATTTATT
*
16444716 ACTTAATTATTTA-T
1 --TTTATTATTTATT
16444730 TTTATTATT
1 TTTATTATT
16444739 AATAAAAATA
Statistics
Matches: 66, Mismatches: 2, Indels: 14
0.80 0.02 0.17
Matches are distributed among these distances:
11 7 0.11
12 20 0.30
13 8 0.12
14 16 0.24
15 15 0.23
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTATTATTTATT
Found at i:16444666 original size:21 final size:21
Alignment explanation
Indices: 16444630--16444692 Score: 83
Period size: 21 Copynumber: 2.9 Consensus size: 21
16444620 AATTTGTATT
*
16444630 TTTATTTTTCAATTTTATTTTA
1 TTTATTTTT-ATTTTTATTTTA
16444652 TTTATTTTTATTTTTATTTTA
1 TTTATTTTTATTTTTATTTTA
16444673 -TTATTTATTATTTATTATTT
1 TTTATTT-TTATTT-TTATTT
16444693 ATTACTTTAT
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
20 6 0.16
21 17 0.45
22 15 0.39
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (21 bp):
TTTATTTTTATTTTTATTTTA
Found at i:16444679 original size:7 final size:7
Alignment explanation
Indices: 16444649--16444738 Score: 88
Period size: 7 Copynumber: 13.7 Consensus size: 7
16444639 CAATTTTATT
16444649 TTATTTA
1 TTATTTA
16444656 TT-TTTA
1 TTATTTA
16444662 TT-TTTA
1 TTATTTA
16444668 -T-TTTA
1 TTATTTA
16444673 TTATTTA
1 TTATTTA
16444680 TTATTTA
1 TTATTTA
16444687 TTATTTA
1 TTATTTA
16444694 TTACTTTA
1 TTA-TTTA
*
16444702 -T-TTAA
1 TTATTTA
16444707 TTATTTA
1 TTATTTA
*
16444714 TTACTTAA
1 TTA-TTTA
16444722 TTATTTA
1 TTATTTA
16444729 -T-TTTA
1 TTATTTA
16444734 TTATT
1 TTATT
16444739 AATAAAAATA
Statistics
Matches: 71, Mismatches: 4, Indels: 16
0.78 0.04 0.18
Matches are distributed among these distances:
5 12 0.17
6 14 0.20
7 35 0.49
8 10 0.14
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (7 bp):
TTATTTA
Found at i:16444683 original size:27 final size:28
Alignment explanation
Indices: 16444626--16444738 Score: 106
Period size: 28 Copynumber: 3.9 Consensus size: 28
16444616 GCCCAATTTG
16444626 TATTTTTATTTTTCAATTTTA-T-TTTATT
1 TATTTTTATTTTT--ATTTTATTATTTATT
16444654 TATTTTTATTTTTATTTTATTATTTA-T
1 TATTTTTATTTTTATTTTATTATTTATT
* *
16444681 TATTTATTATTTATTACTTTATTTAATTATT
1 TATTT-TTATTT-TTATTTTA-TTATTTATT
*
16444712 TATTACTTAATTATTTATTTTATTATT
1 TATT--TTTATT-TTTATTTTATTATT
16444739 AATAAAAATA
Statistics
Matches: 71, Mismatches: 5, Indels: 15
0.78 0.05 0.16
Matches are distributed among these distances:
26 6 0.08
27 7 0.10
28 23 0.32
29 7 0.10
30 6 0.08
31 9 0.13
32 11 0.15
33 2 0.03
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.72
Consensus pattern (28 bp):
TATTTTTATTTTTATTTTATTATTTATT
Found at i:16444691 original size:34 final size:35
Alignment explanation
Indices: 16444621--16444727 Score: 105
Period size: 34 Copynumber: 3.1 Consensus size: 35
16444611 AGGCAGCCCA
* * * *
16444621 ATTTGTATTTTTATTTT-TCAATT-TTATTTTATTT
1 ATTTTTATTTTTATTTTATTATTTATTACTTTA-TT
16444655 ATTTTTATTTTTATTTTATTATTTATTA-TTTATT
1 ATTTTTATTTTTATTTTATTATTTATTACTTTATT
* * *
16444689 ATTTATTA-CTTTATTTAATTATTTATTACTTAATT
1 ATTT-TTATTTTTATTTTATTATTTATTACTTTATT
16444724 ATTT
1 ATTT
16444728 ATTTTATTAT
Statistics
Matches: 63, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
34 40 0.63
35 20 0.32
36 3 0.05
ACGTcount: A:0.25, C:0.03, G:0.01, T:0.71
Consensus pattern (35 bp):
ATTTTTATTTTTATTTTATTATTTATTACTTTATT
Found at i:16444739 original size:15 final size:14
Alignment explanation
Indices: 16444643--16444739 Score: 71
Period size: 15 Copynumber: 6.7 Consensus size: 14
16444633 ATTTTTCAAT
16444643 TTTATT-TTATTTA
1 TTTATTATTATTTA
16444656 TTT-TTATT-TTTA
1 TTTATTATTATTTA
16444668 TTTTATTATT-TATTA
1 -TTTATTATTAT-TTA
16444683 TTTATTATT-TATTA
1 TTTATTATTAT-TTA
16444697 CTTTATTTAATTATTTA
1 -TTTA-TT-ATTATTTA
16444714 -TTACTTAATTATTTA
1 TTTA-TT-ATTATTTA
16444729 TTTTATTATTA
1 -TTTATTATTA
16444740 ATAAAAATAT
Statistics
Matches: 73, Mismatches: 1, Indels: 18
0.79 0.01 0.20
Matches are distributed among these distances:
12 6 0.08
13 8 0.11
14 20 0.27
15 25 0.34
16 4 0.05
17 9 0.12
18 1 0.01
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTATTATTATTTA
Found at i:16450283 original size:10 final size:10
Alignment explanation
Indices: 16450270--16450307 Score: 58
Period size: 10 Copynumber: 3.8 Consensus size: 10
16450260 TTATTTTCAT
16450270 TTATCTTTAA
1 TTATCTTTAA
*
16450280 TTATCTTTAT
1 TTATCTTTAA
*
16450290 TTATCTGTAA
1 TTATCTTTAA
16450300 TTATCTTT
1 TTATCTTT
16450308 TTGAATTTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.24, C:0.11, G:0.03, T:0.63
Consensus pattern (10 bp):
TTATCTTTAA
Found at i:16450291 original size:20 final size:20
Alignment explanation
Indices: 16450268--16450307 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
16450258 ATTTATTTTC
*
16450268 ATTTATCTTTAATTATCTTT
1 ATTTATCTGTAATTATCTTT
16450288 ATTTATCTGTAATTATCTTT
1 ATTTATCTGTAATTATCTTT
16450308 TTGAATTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.25, C:0.10, G:0.03, T:0.62
Consensus pattern (20 bp):
ATTTATCTGTAATTATCTTT
Found at i:16450478 original size:15 final size:15
Alignment explanation
Indices: 16450458--16450494 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
16450448 ATAATAATCC
16450458 TATTTCTATTATATT
1 TATTTCTATTATATT
16450473 TATTTCTATTATATT
1 TATTTCTATTATATT
16450488 TATTTCT
1 TATTTCT
16450495 TTCACAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (15 bp):
TATTTCTATTATATT
Found at i:16454826 original size:79 final size:81
Alignment explanation
Indices: 16454713--16454895 Score: 225
Period size: 79 Copynumber: 2.3 Consensus size: 81
16454703 GCTACTCATT
* * *
16454713 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCATAAATGCCTTCGGGA-CTTAACCCG
1 CAAATGCCTTCGGGACTTAGCCCGATTATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCG
*
16454777 GATTTAGTAACTT-GCA
65 GATATAGTAACTTAGCA
**
16454793 CAAATGCCTTCGGG-CTTAGCCCAGAATT-T-GTAACTCGCACAAATGCCTTCGGATCTTAGTCC
1 CAAATGCCTTCGGGACTTAGCCC-G-ATTATAGTAACTCGCACAAATGCCTTCGGATCTTAACCC
*
16454855 GGATATAGTCACTTAGCA
64 GGATATAGTAACTTAGCA
*
16454873 CAAA-GGCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGACTTAGCCCG
16454896 GACATCATTC
Statistics
Matches: 90, Mismatches: 8, Indels: 11
0.83 0.07 0.10
Matches are distributed among these distances:
78 3 0.03
79 54 0.60
80 31 0.34
81 2 0.02
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.26
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGATTATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGG
ATATAGTAACTTAGCA
Found at i:16454897 original size:40 final size:40
Alignment explanation
Indices: 16454713--16454897 Score: 207
Period size: 40 Copynumber: 4.7 Consensus size: 40
16454703 GCTACTCATT
* *
16454713 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* * * *
16454753 TAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTTGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
16454793 CAAATGCCTTCGGG-CTTAGCCCAGA-ATTTGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA
* * *
16454832 CAAATGCCTTC-GGATCTTAGTCCGGATATAGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA
*
16454873 CAAA-GGCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
16454898 CATCATTCGA
Statistics
Matches: 120, Mismatches: 19, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
38 2 0.02
39 30 0.25
40 76 0.63
41 12 0.10
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:16455616 original size:2 final size:2
Alignment explanation
Indices: 16455609--16455638 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
16455599 TCACGTGCAA
16455609 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16455639 GCAAGAGCCG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16463559 original size:37 final size:37
Alignment explanation
Indices: 16463509--16463583 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
16463499 TAAATGGATC
16463509 AAGTATATTTTCGTCTACCAGAGATGTCTAGAGAGAG
1 AAGTATATTTTCGTCTACCAGAGATGTCTAGAGAGAG
16463546 AAGTATATTTTCGTCTACCAGAGATGTCTAGAGAGAG
1 AAGTATATTTTCGTCTACCAGAGATGTCTAGAGAGAG
16463583 A
1 A
16463584 TAAGAGAATG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.33, C:0.13, G:0.24, T:0.29
Consensus pattern (37 bp):
AAGTATATTTTCGTCTACCAGAGATGTCTAGAGAGAG
Found at i:16463884 original size:22 final size:21
Alignment explanation
Indices: 16463840--16463888 Score: 62
Period size: 22 Copynumber: 2.3 Consensus size: 21
16463830 AATAAATACT
*
16463840 AATTAATTAACTTAATTAATC
1 AATTAATTAAATTAATTAATC
**
16463861 AAATTAATTAAATTAATTTCTC
1 -AATTAATTAAATTAATTAATC
16463883 AATTAA
1 AATTAA
16463889 ATAATTTTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 6 0.25
22 18 0.75
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.43
Consensus pattern (21 bp):
AATTAATTAAATTAATTAATC
Found at i:16463895 original size:16 final size:18
Alignment explanation
Indices: 16463866--16463901 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
16463856 TAATCAAATT
16463866 AATTAAATTAA-TTTCTC
1 AATTAAATTAATTTTCTC
16463883 AATTAAA-TAATTTTCTC
1 AATTAAATTAATTTTCTC
16463900 AA
1 AA
16463902 CTCAATCCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 3 0.17
17 15 0.83
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.44
Consensus pattern (18 bp):
AATTAAATTAATTTTCTC
Found at i:16468807 original size:12 final size:12
Alignment explanation
Indices: 16468790--16468816 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
16468780 AGTTTTCAGG
16468790 GGAAAATTTAGT
1 GGAAAATTTAGT
16468802 GGAAAATTTAGT
1 GGAAAATTTAGT
16468814 GGA
1 GGA
16468817 GAGGAATCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.30, T:0.30
Consensus pattern (12 bp):
GGAAAATTTAGT
Found at i:16483112 original size:23 final size:23
Alignment explanation
Indices: 16483086--16483130 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
16483076 TCTAAAACAA
*
16483086 TTTAAT-TTTTTTCTTTTTATTTC
1 TTTAATATTTTTTC-CTTTATTTC
*
16483109 TTTATTATTTTTTCCTTTATTT
1 TTTAATATTTTTTCCTTTATTT
16483131 TTCTCTCTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.13, C:0.09, G:0.00, T:0.78
Consensus pattern (23 bp):
TTTAATATTTTTTCCTTTATTTC
Found at i:16485621 original size:21 final size:20
Alignment explanation
Indices: 16485597--16485663 Score: 59
Period size: 20 Copynumber: 3.4 Consensus size: 20
16485587 GCCCTTATGT
16485597 TTTTTGGTAATCCGTTACATA
1 TTTTTGGTAATCC-TTACATA
* *
16485618 TTTTT-GTATTTCTT-CATA
1 TTTTTGGTAATCCTTACATA
*
16485636 TTTTATGGTAATCCCTCACA-A
1 TTTT-TGGTAAT-CCTTACATA
16485657 TTTTTGG
1 TTTTTGG
16485664 CATTTGCTCA
Statistics
Matches: 37, Mismatches: 5, Indels: 9
0.73 0.10 0.18
Matches are distributed among these distances:
18 8 0.22
19 3 0.08
20 12 0.32
21 12 0.32
22 2 0.05
ACGTcount: A:0.21, C:0.15, G:0.12, T:0.52
Consensus pattern (20 bp):
TTTTTGGTAATCCTTACATA
Found at i:16486129 original size:40 final size:40
Alignment explanation
Indices: 16486071--16486160 Score: 94
Period size: 40 Copynumber: 2.2 Consensus size: 40
16486061 GCTTATGGTT
* * * *
16486071 TTTTTTGATAAACTCTCATATATTT-TGGTATGT-CCTTATA
1 TTTTTTGGTAAACCCTCATAT-TTTCTAGTA-GTCCCTTACA
* *
16486111 TTTTTTGGTAACCCCTCATGTTTTCTAGTAGTCCCTTACA
1 TTTTTTGGTAAACCCTCATATTTTCTAGTAGTCCCTTACA
16486151 TTTTTTGGTA
1 TTTTTTGGTA
16486161 TTTCTTCATT
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
39 5 0.12
40 37 0.88
ACGTcount: A:0.20, C:0.17, G:0.12, T:0.51
Consensus pattern (40 bp):
TTTTTTGGTAAACCCTCATATTTTCTAGTAGTCCCTTACA
Found at i:16486679 original size:20 final size:20
Alignment explanation
Indices: 16486619--16486681 Score: 72
Period size: 20 Copynumber: 3.1 Consensus size: 20
16486609 TCATCTTTTA
*
16486619 TTTGGTAATTCCTCATAATT
1 TTTGGTAATTCCTCATATTT
* * *
16486639 TTTGGTATTTTCTCATCTTT
1 TTTGGTAATTCCTCATATTT
* *
16486659 TTTGGTAATCCCTCATGTTT
1 TTTGGTAATTCCTCATATTT
16486679 TTT
1 TTT
16486682 TTTGGTAAAA
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.16, C:0.16, G:0.11, T:0.57
Consensus pattern (20 bp):
TTTGGTAATTCCTCATATTT
Done.