Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032254.1 Gossypioides kirkii chromosome KI_12
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: 43711324
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 124 of 135
Found at i:40909833 original size:7 final size:7
Alignment explanation
Indices: 40909821--40909846 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
40909811 TCATCCCATT
40909821 TTCTTTC
1 TTCTTTC
40909828 TTCTTTC
1 TTCTTTC
40909835 TTCTTTC
1 TTCTTTC
40909842 TTCTT
1 TTCTT
40909847 CACACGACAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (7 bp):
TTCTTTC
Found at i:40912581 original size:21 final size:22
Alignment explanation
Indices: 40912544--40912619 Score: 59
Period size: 21 Copynumber: 3.5 Consensus size: 22
40912534 CTGCAACTTT
* *
40912544 TACCGATATAAGC-ATACAAAC
1 TACCGATACATGCAATACAAAC
40912565 TACCGATACAT-CAATACTAATAAC
1 TACCGATACATGCAATAC--A-AAC
* * *
40912589 TACCGATACCTGTAATTC-AAC
1 TACCGATACATGCAATACAAAC
40912610 TACCGATACA
1 TACCGATACA
40912620 ACTCAAGTCA
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
20 1 0.02
21 25 0.57
23 1 0.02
24 13 0.30
25 4 0.09
ACGTcount: A:0.42, C:0.26, G:0.08, T:0.24
Consensus pattern (22 bp):
TACCGATACATGCAATACAAAC
Found at i:40918195 original size:46 final size:46
Alignment explanation
Indices: 40918091--40918369 Score: 368
Period size: 46 Copynumber: 6.1 Consensus size: 46
40918081 ACTTCTGTGA
* * *
40918091 GATGGTAGCTTCAATCTGCCTCTCTTGATTTTAGGGGTAAAAGATTG
1 GATGGTGGCTTCAATCTGCCCCTCTTGA-CTTAGGGGTAAAAGATTG
* * * *
40918138 GATAGTTGCTTCAATCTACCCCTCTTGACTTAGGGGTAAAAGATTA
1 GATGGTGGCTTCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATTG
* *
40918184 GATGGTGGCTTCAATTTGCCCCTCTTGACTTAGGGGTAACAGATTG
1 GATGGTGGCTTCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATTG
**
40918230 GATGGTGGCTTCAATCTGCCTTTCTTGACTTAGGGGTAAAAGATTG
1 GATGGTGGCTTCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATTG
* *
40918276 GA---T-GCTTCAATCTGCCCCTTTTGACTTAGAGGTAAAAGATTG
1 GATGGTGGCTTCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATTG
* * * *
40918318 GATAGTGGCTTCAATCTGCCTCTCTTAACTTAGAGGTAAAAGATTG
1 GATGGTGGCTTCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATTG
40918364 GATGGT
1 GATGGT
40918370 TCAATCTACC
Statistics
Matches: 204, Mismatches: 24, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
42 37 0.18
43 1 0.00
45 1 0.00
46 141 0.69
47 24 0.12
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.34
Consensus pattern (46 bp):
GATGGTGGCTTCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATTG
Found at i:40918326 original size:88 final size:88
Alignment explanation
Indices: 40918098--40918459 Score: 402
Period size: 88 Copynumber: 4.2 Consensus size: 88
40918088 TGAGATGGTA
* * * * *
40918098 GCTTCAATCTGCCTCTCTTGATTTTAGGGGTAAAAGATTGGATAGTTGCTTCAATCTACCCCTCT
1 GCTTCAATCTGCCCCTCTTGA-CTTAGGGGTAAAAGATTGGATAGTGGCTTCAATCTGCCTCTCT
*
40918163 TGACTTAGGGGTAAAAGATTAGATGGT
65 TGACTTAGGGGTAAAAGATT-G--GAT
* * * *
40918190 GGCTTCAATTTGCCCCTCTTGACTTAGGGGTAACAGATTGGATGGTGGCTTCAATCTGCCTTTCT
1 -GCTTCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATTGGATAGTGGCTTCAATCTGCCTCTCT
40918255 TGACTTAGGGGTAAAAGATTGGAT
65 TGACTTAGGGGTAAAAGATTGGAT
* *
40918279 GCTTCAATCTGCCCCTTTTGACTTAGAGGTAAAAGATTGGATAGTGGCTTCAATCTGCCTCTCTT
1 GCTTCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATTGGATAGTGGCTTCAATCTGCCTCTCTT
* *
40918344 AACTTAGAGGTAAAAGATTGGAT
66 GACTTAGGGGTAAAAGATTGGAT
* * * * * * * *
40918367 GGTTCAATCT-ACCC-CATGA--TCGGGGTATAAGATTGG--CGTGTCTTTAATCTGCC-CT-TT
1 GCTTCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATTGGATAGTGGCTTCAATCTGCCTCTCTT
40918424 GA-TTA-GGGTAAAAGATTGGAT
66 GACTTAGGGGTAAAAGATTGGAT
*
40918445 GCTTCAATTTGCCCC
1 GCTTCAATCTGCCCC
40918460 ATGATCGGGG
Statistics
Matches: 235, Mismatches: 33, Indels: 16
0.83 0.12 0.06
Matches are distributed among these distances:
78 23 0.10
79 6 0.03
80 3 0.01
81 2 0.01
82 14 0.06
84 14 0.06
86 3 0.01
87 3 0.01
88 89 0.38
89 2 0.01
91 1 0.00
92 56 0.24
93 19 0.08
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.34
Consensus pattern (88 bp):
GCTTCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATTGGATAGTGGCTTCAATCTGCCTCTCTT
GACTTAGGGGTAAAAGATTGGAT
Found at i:40918343 original size:134 final size:137
Alignment explanation
Indices: 40918091--40918369 Score: 402
Period size: 134 Copynumber: 2.0 Consensus size: 137
40918081 ACTTCTGTGA
*
40918091 GATGGTAGCTTCAATCTGCCTCTCTTGATTTTAGGGGTAAAAGATTGGATAGTTGCTTCAATCTA
1 GATGGTAGCTTCAATCTGCCTCTCTTGATCTTAGGGGTAAAAGATTGGA-AG-TGCTTCAATCTA
* * * * *
40918156 CCCCTCTTGACTTAGGGGTAAAAGATTAGATGGTGGCTTCAATTTGCCCCTCTTGACTTAGGGGT
64 CCCCTCTTGACTTAGAGGTAAAAGATTAGATAGTGGCTTCAATCTGCCCCTCTTAACTTAGAGGT
*
40918221 AACAGATTG
129 AAAAGATTG
* * *
40918230 GATGGTGGCTTCAATCTGCCTTTCTTGA-CTTAGGGGTAAAAGATTGG-A-TGCTTCAATCTGCC
1 GATGGTAGCTTCAATCTGCCTCTCTTGATCTTAGGGGTAAAAGATTGGAAGTGCTTCAATCTACC
* * *
40918292 CCTTTTGACTTAGAGGTAAAAGATTGGATAGTGGCTTCAATCTGCCTCTCTTAACTTAGAGGTAA
66 CCTCTTGACTTAGAGGTAAAAGATTAGATAGTGGCTTCAATCTGCCCCTCTTAACTTAGAGGTAA
40918357 AAGATTG
131 AAGATTG
40918364 GATGGT
1 GATGGT
40918370 TCAATCTACC
Statistics
Matches: 127, Mismatches: 13, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
134 82 0.65
136 1 0.01
138 18 0.14
139 26 0.20
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.34
Consensus pattern (137 bp):
GATGGTAGCTTCAATCTGCCTCTCTTGATCTTAGGGGTAAAAGATTGGAAGTGCTTCAATCTACC
CCTCTTGACTTAGAGGTAAAAGATTAGATAGTGGCTTCAATCTGCCCCTCTTAACTTAGAGGTAA
AAGATTG
Found at i:40918402 original size:38 final size:38
Alignment explanation
Indices: 40918262--40918498 Score: 150
Period size: 38 Copynumber: 5.8 Consensus size: 38
40918252 TCTTGACTTA
* *
40918262 GGGGTAAAAGATTGGATGCTTCAATCTGCCCCTTTTGACTTA
1 GGGGTAAAAGATTGGATGCTTCAATCTGCCCC--ATGA--TC
* * * *
40918304 GAGGTAAAAGATTGGATAGTGGCTTCAATCTGCCTCTCTTAACTTA
1 GGGGTAAAAGATTGG--A-T-GCTTCAATCTGCC-C-CATGA--TC
* * *
40918350 GAGGTAAAAGATTGGATGGTTCAATCTACCCCATGATC
1 GGGGTAAAAGATTGGATGCTTCAATCTGCCCCATGATC
* * * ** *
40918388 GGGGTATAAGATTGGCGTGTCTTTAATCTGCCCTTTGATT
1 GGGGTAAAAGATTGG-ATG-CTTCAATCTGCCCCATGATC
* *
40918428 AGGGTAAAAGATTGGATGCTTCAATTTGCCCCATGATC
1 GGGGTAAAAGATTGGATGCTTCAATCTGCCCCATGATC
** *
40918466 GGGGTATGAGATTGAATGGTCTTCAATCTGCCC
1 GGGGTAAAAGATTGGAT-G-CTTCAATCTGCCC
40918499 TCTTCAGCTT
Statistics
Matches: 156, Mismatches: 29, Indels: 22
0.75 0.14 0.11
Matches are distributed among these distances:
38 42 0.27
39 5 0.03
40 42 0.27
41 1 0.01
42 25 0.16
43 1 0.01
44 2 0.01
45 1 0.01
46 35 0.22
47 1 0.01
48 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (38 bp):
GGGGTAAAAGATTGGATGCTTCAATCTGCCCCATGATC
Found at i:40918451 original size:78 final size:82
Alignment explanation
Indices: 40918124--40918502 Score: 324
Period size: 88 Copynumber: 4.5 Consensus size: 82
40918114 CTTGATTTTA
* * * * *
40918124 GGGGTAAAAGATTGGATAGTTGCTTCAATCTACCCCTCTTGACTTAGGGGTAAAAGATTAGATGG
1 GGGGTATAAGATTGGA-AGTGGCTTCAATCTGCCTCTCTTGACTTA-GGGTAAAAGATT-G--GA
* * *
40918189 TGGCTTCAATTTGCCCCTCTTGACTTA
61 T-GCTTCAATCTG-CCC-CATGA--TC
* *
40918216 GGGGTA-ACAGATTGGATGGTGGCTTCAATCTGCCTTTCTTGACTTAGGGGTAAAAGATTGGATG
1 GGGGTATA-AGATTGGA-AGTGGCTTCAATCTGCCTCTCTTGACTTA-GGGTAAAAGATTGGATG
* *
40918280 CTTCAATCTGCCCCTTTTGACTTA
63 CTTCAATCTGCCCC--ATGA--TC
* * * *
40918304 GAGGTAAAAGATTGGATAGTGGCTTCAATCTGCCTCTCTTAACTTAGAGGTAAAAGATTGGATGG
1 GGGGTATAAGATTGGA-AGTGGCTTCAATCTGCCTCTCTTGACTTAG-GGTAAAAGATTGGATGC
*
40918369 TTCAATCTACCCCATGATC
64 TTCAATCTGCCCCATGATC
* * *
40918388 GGGGTATAAGATTGG-CGTGTCTTTAATCTGCC-CT-TTGA-TTAGGGTAAAAGATTGGATGCTT
1 GGGGTATAAGATTGGAAGTGGCTTCAATCTGCCTCTCTTGACTTAGGGTAAAAGATTGGATGCTT
*
40918449 CAATTTGCCCCATGATC
66 CAATCTGCCCCATGATC
*
40918466 GGGGTATGAGATT-GAA-TGGTCTTCAATCTGCC-CTCTT
1 GGGGTATAAGATTGGAAGTGG-CTTCAATCTGCCTCTCTT
40918503 CAGCTTTAGG
Statistics
Matches: 251, Mismatches: 28, Indels: 29
0.81 0.09 0.09
Matches are distributed among these distances:
77 3 0.01
78 58 0.23
79 6 0.02
80 3 0.01
81 2 0.01
82 14 0.06
84 14 0.06
86 4 0.02
87 4 0.02
88 86 0.34
89 3 0.01
91 2 0.01
92 52 0.21
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (82 bp):
GGGGTATAAGATTGGAAGTGGCTTCAATCTGCCTCTCTTGACTTAGGGTAAAAGATTGGATGCTT
CAATCTGCCCCATGATC
Found at i:40918661 original size:98 final size:96
Alignment explanation
Indices: 40918559--40919170 Score: 560
Period size: 98 Copynumber: 6.4 Consensus size: 96
40918549 TTTACAGGTT
* * *
40918559 TAAGGTATAAGGTTCACCGTTACGGCTTCAACCTTTCCATCCATAACTCCATGGTACAAGATTTG
1 TAAGGTATAAGGTTCACCGTTGCGGCTTCAACCTTTCCCTCCAT--CTCCATGGTACAAGATTCG
** * *
40918624 TCATTGTAGCTTCAATCTTTCACATTATTTTTC
64 TCATTGCGGCTTCAATCTTTCCCATTACTTTTC
* ** * * **
40918657 TAAGGTATAAGGTTCGCCGTTATGGCTTCAACCTTTCCCTCCATATCTTCATGATAGTAGATTCG
1 TAAGGTATAAGGTTCACCGTTGCGGCTTCAACCTTTCCCTCC--ATCTCCATGGTACAAGATTCG
* * * *
40918722 TCATTGCGGTTTCAATCTTTCCCATCACATCTC
64 TCATTGCGGCTTCAATCTTTCCCATTACTTTTC
* * * *
40918755 TAAGGTATAAGGTTCACCGTTGCGACTTTAACCTTTCCCTTCATCTCCATGGTACAAGATTCATC
1 TAAGGTATAAGGTTCACCGTTGCGGCTTCAACCTTTCCCTCCATCTCCATGGTACAAGATTCGTC
* * * *
40918820 GTTGCGACTTGAATCTTTCCCATTAATTTTC
66 ATTGCGGCTTCAATCTTTCCCATTACTTTTC
** * * * *
40918851 -AAGGTATAAGGTTTGCCGTTGCGACTTCAACATTTCCCTCAATCTCTCCATGGTACTAGATTCG
1 TAAGGTATAAGGTTCACCGTTGCGGCTTCAACCTTTCCCTCCA--TCTCCATGGTACAAGATTCG
* * *
40918915 TCATTGCGGCTTCAATCTTTCCCATCACATATC
64 TCATTGCGGCTTCAATCTTTCCCATTACTTTTC
* * ** * * *
40918948 TAGGGTATAAGGTTCACCATTGCAACTTCAACCTTTCCCTTCATCTCCATGGTACTATATTCGTC
1 TAAGGTATAAGGTTCACCGTTGCGGCTTCAACCTTTCCCTCCATCTCCATGGTACAAGATTCGTC
* * * * *
40919013 GTTGTGG-------C--TCCCATCACATCTC
66 ATTGCGGCTTCAATCTTTCCCATTACTTTTC
* *** * **
40919035 TAAGGAATAAGGTTCGTTGTTGCGGCTTCAACCTTTCCCTTCATCTCCATGGTACAAGATTCACC
1 TAAGGTATAAGGTTCACCGTTGCGGCTTCAACCTTTCCCTCCATCTCCATGGTACAAGATTCGTC
* *
40919100 GTTGCGGCTTCAATCTTTCCCATTATTTTTC
66 ATTGCGGCTTCAATCTTTCCCATTACTTTTC
* * * *
40919131 TAAGGTATAATGTTCATCATTGCGGCTTCAATCTTTCCCT
1 TAAGGTATAAGGTTCACCGTTGCGGCTTCAACCTTTCCCT
40919171 TCAAACCTAT
Statistics
Matches: 415, Mismatches: 85, Indels: 30
0.78 0.16 0.06
Matches are distributed among these distances:
87 72 0.17
89 1 0.00
94 1 0.00
95 36 0.09
96 111 0.27
97 44 0.11
98 148 0.36
100 2 0.00
ACGTcount: A:0.22, C:0.26, G:0.15, T:0.37
Consensus pattern (96 bp):
TAAGGTATAAGGTTCACCGTTGCGGCTTCAACCTTTCCCTCCATCTCCATGGTACAAGATTCGTC
ATTGCGGCTTCAATCTTTCCCATTACTTTTC
Found at i:40918778 original size:49 final size:49
Alignment explanation
Indices: 40918732--40918986 Score: 193
Period size: 49 Copynumber: 5.3 Consensus size: 49
40918722 TCATTGCGGT
40918732 TTCAATCTTTCCCATCACATCTCTAAGGTATAAGGTTCACCGTTGCGAC
1 TTCAATCTTTCCCATCACATCTCTAAGGTATAAGGTTCACCGTTGCGAC
* * * * * * * *
40918781 TTTAACCTTTCCC-T-TCATCTCCATGGTACAAGATTCATCGTTGCGAC
1 TTCAATCTTTCCCATCACATCTCTAAGGTATAAGGTTCACCGTTGCGAC
* * * **
40918828 TTGAATCTTTCCCATTA-AT-TTTCAAGGTATAAGGTTTGCCGTTGCGAC
1 TTCAATCTTTCCCATCACATCTCT-AAGGTATAAGGTTCACCGTTGCGAC
* * ** * *
40918876 TTCAA-CATTTCCC-TCA-ATCTCTCCATGGTACT-AGATTCGTCATTGCGGC
1 TTCAATC-TTTCCCATCACATCTCT--AAGGTA-TAAGGTTCACCGTTGCGAC
* * * *
40918925 TTCAATCTTTCCCATCACATATCTAGGGTATAAGGTTCACCATTGCAAC
1 TTCAATCTTTCCCATCACATCTCTAAGGTATAAGGTTCACCGTTGCGAC
*
40918974 TTCAACCTTTCCC
1 TTCAATCTTTCCC
40918987 TTCATCTCCA
Statistics
Matches: 159, Mismatches: 36, Indels: 22
0.73 0.17 0.10
Matches are distributed among these distances:
47 44 0.28
48 36 0.23
49 69 0.43
50 5 0.03
51 5 0.03
ACGTcount: A:0.23, C:0.28, G:0.14, T:0.35
Consensus pattern (49 bp):
TTCAATCTTTCCCATCACATCTCTAAGGTATAAGGTTCACCGTTGCGAC
Found at i:40918824 original size:47 final size:47
Alignment explanation
Indices: 40918749--40919120 Score: 184
Period size: 47 Copynumber: 8.0 Consensus size: 47
40918739 TTTCCCATCA
* * * * *
40918749 CATCTCTAAGGTATAAGGTTCACCGTTGCGACTTTAACCTTTCCCTT
1 CATCTCCATGGTACAAGATTCACCGTTGCGACTTCAACCTTTCCCTT
* * *
40918796 CATCTCCATGGTACAAGATTCATCGTTGCGACTTGAATCTTTCCCATT
1 CATCTCCATGGTACAAGATTCACCGTTGCGACTTCAACCTTTCCC-TT
* * * * * * ** *
40918844 AATTTTCAAGGTATAAGGTTTGCCGTTGCGACTTCAACATTTCCC-T
1 CATCTCCATGGTACAAGATTCACCGTTGCGACTTCAACCTTTCCCTT
* ** * * * *
40918890 CAATCTCTCCATGGTACTAGATTCGTCATTGCGGCTTCAATCTTTCCCATCA
1 C-A--TCTCCATGGTACAAGATTCACCGTTGCGACTTCAACCTTTCCC-T-T
* * * * * * *
40918942 CATATCTAGGGTATAAGGTTCACCATTGCAACTTCAACCTTTCCCTT
1 CATCTCCATGGTACAAGATTCACCGTTGCGACTTCAACCTTTCCCTT
* * ** * * * *
40918989 CATCTCCATGGTACTATATTCGTCGTTGTGGC-TC--CC-AT--C-A
1 CATCTCCATGGTACAAGATTCACCGTTGCGACTTCAACCTTTCCCTT
* * * * * *** *
40919029 CATCTCTAAGGAATAAGGTTCGTTGTTGCGGCTTCAACCTTTCCCTT
1 CATCTCCATGGTACAAGATTCACCGTTGCGACTTCAACCTTTCCCTT
* *
40919076 CATCTCCATGGTACAAGATTCACCGTTGCGGCTTCAATCTTTCCC
1 CATCTCCATGGTACAAGATTCACCGTTGCGACTTCAACCTTTCCC
40919121 ATTATTTTTC
Statistics
Matches: 231, Mismatches: 80, Indels: 28
0.68 0.24 0.08
Matches are distributed among these distances:
40 23 0.10
41 3 0.01
43 3 0.01
44 3 0.01
46 4 0.02
47 94 0.41
48 36 0.16
49 63 0.27
51 1 0.00
52 1 0.00
ACGTcount: A:0.22, C:0.28, G:0.16, T:0.35
Consensus pattern (47 bp):
CATCTCCATGGTACAAGATTCACCGTTGCGACTTCAACCTTTCCCTT
Found at i:40918916 original size:193 final size:194
Alignment explanation
Indices: 40918559--40919016 Score: 614
Period size: 193 Copynumber: 2.4 Consensus size: 194
40918549 TTTACAGGTT
* * * * *
40918559 TAAGGTATAAGGTTCACCGTTACGGCTTCAACCTTTCCATCCATAACTCCATGGTACAAGATTTG
1 TAAGGTATAAGGTTCACCGTTGCGACTTCAACCTTTCCCTTCAT--CTCCATGGTACAAGATTCG
* * * * *
40918624 TCATTGTAGCTTCAATCTTTCACATTATTTTTCTAAGGTATAAGGTTCGCCGTTATGGCTTCAAC
64 TCGTTGGAGCTTCAATCTTTCACATTAATTTTCTAAGGTATAAGGTTCGCCGTTACGACTTCAAC
* * * * * *
40918689 CTTTCCCTCCATATCTTCATGATAGTAGATTCGTCATTGCGGTTTCAATCTTTCCCATCACATCT
129 ATTTCCCTCAATATCTCCATGATACTAGATTCGTCATTGCGGCTTCAATCTTTCCCATCACATAT
40918754 C
194 C
* *
40918755 TAAGGTATAAGGTTCACCGTTGCGACTTTAACCTTTCCCTTCATCTCCATGGTACAAGATTCATC
1 TAAGGTATAAGGTTCACCGTTGCGACTTCAACCTTTCCCTTCATCTCCATGGTACAAGATTCGTC
* * * *
40918820 GTTGCGA-CTTGAATCTTTCCCATTAATTTTC-AAGGTATAAGGTTTGCCGTTGCGACTTCAACA
66 GTTG-GAGCTTCAATCTTTCACATTAATTTTCTAAGGTATAAGGTTCGCCGTTACGACTTCAACA
* *
40918883 TTTCCCTCAATCTCTCCATGGTACTAGATTCGTCATTGCGGCTTCAATCTTTCCCATCACATATC
130 TTTCCCTCAATATCTCCATGATACTAGATTCGTCATTGCGGCTTCAATCTTTCCCATCACATATC
* * * * *
40918948 TAGGGTATAAGGTTCACCATTGCAACTTCAACCTTTCCCTTCATCTCCATGGTACTATATTCGTC
1 TAAGGTATAAGGTTCACCGTTGCGACTTCAACCTTTCCCTTCATCTCCATGGTACAAGATTCGTC
40919013 GTTG
66 GTTG
40919017 TGGCTCCCAT
Statistics
Matches: 230, Mismatches: 31, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
193 147 0.64
194 43 0.19
195 1 0.00
196 39 0.17
ACGTcount: A:0.23, C:0.26, G:0.15, T:0.36
Consensus pattern (194 bp):
TAAGGTATAAGGTTCACCGTTGCGACTTCAACCTTTCCCTTCATCTCCATGGTACAAGATTCGTC
GTTGGAGCTTCAATCTTTCACATTAATTTTCTAAGGTATAAGGTTCGCCGTTACGACTTCAACAT
TTCCCTCAATATCTCCATGATACTAGATTCGTCATTGCGGCTTCAATCTTTCCCATCACATATC
Found at i:40919875 original size:6 final size:6
Alignment explanation
Indices: 40919864--40919949 Score: 63
Period size: 6 Copynumber: 14.0 Consensus size: 6
40919854 TCAACCTCTC
*
40919864 CTTTTT CTTTTTT CTTTTT C--TTT CTTTTT -TTTTC CTTTTTCT CTTTTT
1 CTTTTT C-TTTTT CTTTTT CTTTTT CTTTTT CTTTTT C-TTTT-T CTTTTT
* *
40919912 CTTCTTT -TTTTC CTTTATCT CTTTTT CTTCTT CTTTTT
1 CTT-TTT CTTTTT CTTT-T-T CTTTTT CTTTTT CTTTTT
40919950 TGGTAATTTT
Statistics
Matches: 64, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
4 4 0.06
5 6 0.09
6 30 0.47
7 19 0.30
8 5 0.08
ACGTcount: A:0.01, C:0.21, G:0.00, T:0.78
Consensus pattern (6 bp):
CTTTTT
Found at i:40919889 original size:17 final size:17
Alignment explanation
Indices: 40919867--40919950 Score: 64
Period size: 17 Copynumber: 4.6 Consensus size: 17
40919857 ACCTCTCCTT
40919867 TTTCTTTTTTCTTTTTC
1 TTTCTTTTTTCTTTTTC
40919884 TTTCTTTTTT-TTTCCTT-
1 TTTCTTTTTTCTTT--TTC
*
40919901 TTTCTCTTTTTCTTCTTTT
1 TTTCT-TTTTTCTT-TTTC
*
40919920 TTTCCTTTATCTCTTTTTC
1 TTT-CTTT-TTTCTTTTTC
40919939 TTCTTCTTTTTT
1 -T-TTCTTTTTT
40919951 GGTAATTTTT
Statistics
Matches: 54, Mismatches: 3, Indels: 18
0.72 0.04 0.24
Matches are distributed among these distances:
16 3 0.06
17 15 0.28
18 9 0.17
19 12 0.22
20 13 0.24
21 2 0.04
ACGTcount: A:0.01, C:0.20, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTCTTTTTTCTTTTTC
Found at i:40919894 original size:26 final size:25
Alignment explanation
Indices: 40919865--40919950 Score: 100
Period size: 27 Copynumber: 3.2 Consensus size: 25
40919855 CAACCTCTCC
40919865 TTTTTCTTTTTTCTTTTTCTTTCTTTT
1 TTTTTCTTTTTTCTTTTTC-TTC-TTT
40919892 TTTTTCCTTTTTCTCTTTTTCTTCTTT
1 TTTTT-CTTTTT-TCTTTTTCTTCTTT
* *
40919919 TTTTCCTTTATCTCTTTTTCTTCTTCT
1 TTTTTCTTT-TTTCTTTTTCTTCTT-T
40919946 TTTTT
1 TTTTT
40919951 GGTAATTTTT
Statistics
Matches: 52, Mismatches: 3, Indels: 8
0.83 0.05 0.13
Matches are distributed among these distances:
26 17 0.33
27 18 0.35
28 9 0.17
29 8 0.15
ACGTcount: A:0.01, C:0.20, G:0.00, T:0.79
Consensus pattern (25 bp):
TTTTTCTTTTTTCTTTTTCTTCTTT
Found at i:40919913 original size:29 final size:28
Alignment explanation
Indices: 40919865--40919950 Score: 117
Period size: 26 Copynumber: 3.2 Consensus size: 28
40919855 CAACCTCTCC
40919865 TTTTT-CTTTTT-TCTTTTTCTTTCTTTT
1 TTTTTCCTTTTTCTCTTTTTC-TTCTTTT
40919892 TTTTTCCTTTTTCTCTTTTTCTTC--TT
1 TTTTTCCTTTTTCTCTTTTTCTTCTTTT
* *
40919918 TTTTTCCTTTATCTCTTTTTCTTCTTCT
1 TTTTTCCTTTTTCTCTTTTTCTTCTTTT
40919946 TTTTT
1 TTTTT
40919951 GGTAATTTTT
Statistics
Matches: 53, Mismatches: 2, Indels: 7
0.85 0.03 0.11
Matches are distributed among these distances:
26 25 0.47
27 5 0.09
28 15 0.28
29 8 0.15
ACGTcount: A:0.01, C:0.20, G:0.00, T:0.79
Consensus pattern (28 bp):
TTTTTCCTTTTTCTCTTTTTCTTCTTTT
Found at i:40924808 original size:19 final size:19
Alignment explanation
Indices: 40924784--40924821 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
40924774 CTAAAAAGGT
40924784 ATGTGATTTTTATTTTAAA
1 ATGTGATTTTTATTTTAAA
40924803 ATGTGATTTTTATTTTAAA
1 ATGTGATTTTTATTTTAAA
40924822 CTTCTTGAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.58
Consensus pattern (19 bp):
ATGTGATTTTTATTTTAAA
Found at i:40926389 original size:59 final size:59
Alignment explanation
Indices: 40926307--40926569 Score: 243
Period size: 59 Copynumber: 4.5 Consensus size: 59
40926297 ACGAAAAAGA
** *
40926307 GGTCAAAATCAAAATTTTAGAAAGTTTAGGGGTCAAATGTAATTTTTAGAATA-TTTAAG
1 GGTCAAAATGTAATTTTTAGAAAGTTTAGGGGTCAAATGTAATTTTTAGAA-AGTTTAAG
* *
40926366 GGTCAAAATGTAATTTTTAGAAAGTTTAAGGGTCAAAATGAAATTTTTA-AAAGTTTAAG
1 GGTCAAAATGTAATTTTTAGAAAGTTTAGGGGTC-AAATGTAATTTTTAGAAAGTTTAAG
* * * ** * * *
40926425 GGT-TAAATTTGAATTTTGA-AAAACTTAGGGGTTAGAAAGTAA-TTTTAGAAAGTTTGAG
1 GGTCAAAATGT-AATTTTTAGAAAGTTTAGGGGTCA-AATGTAATTTTTAGAAAGTTTAAG
* * * * *
40926483 GGTTAAAATGTAA-TTTTAGAAAGTTTAAGGGTTAAAATGCAATTTTTAGAAAGTTTGAG
1 GGTCAAAATGTAATTTTTAGAAAGTTT-AGGGGTCAAATGTAATTTTTAGAAAGTTTAAG
* *
40926542 GGTC-AAATTTAAATTTTTGGAAAGTTTA
1 GGTCAAAATGT-AATTTTTAGAAAGTTTA
40926570 AGGGCTAAAA
Statistics
Matches: 166, Mismatches: 27, Indels: 22
0.77 0.13 0.10
Matches are distributed among these distances:
57 10 0.06
58 50 0.30
59 81 0.49
60 25 0.15
ACGTcount: A:0.40, C:0.03, G:0.21, T:0.37
Consensus pattern (59 bp):
GGTCAAAATGTAATTTTTAGAAAGTTTAGGGGTCAAATGTAATTTTTAGAAAGTTTAAG
Found at i:40926587 original size:30 final size:30
Alignment explanation
Indices: 40926321--40926588 Score: 266
Period size: 29 Copynumber: 9.1 Consensus size: 30
40926311 AAAATCAAAA
* *
40926321 TTTTAGAAAGTTT-AGGGGTCAAATGTAAT
1 TTTTAGAAAGTTTAAGGGTTAAAATGTAAT
*
40926350 TTTTAGAATA-TTTAAGGGTCAAAATGTAAT
1 TTTTAGAA-AGTTTAAGGGTTAAAATGTAAT
* *
40926380 TTTTAGAAAGTTTAAGGGTCAAAATGAAAT
1 TTTTAGAAAGTTTAAGGGTTAAAATGTAAT
*
40926410 TTTTA-AAAGTTTAAGGGTT-AAATTTGAAT
1 TTTTAGAAAGTTTAAGGGTTAAAATGT-AAT
* ** *
40926439 TTTGA-AAAACTTAGGGGTTAGAAA-GTAA-
1 TTTTAGAAAGTTTAAGGGTTA-AAATGTAAT
*
40926467 TTTTAGAAAGTTTGAGGGTTAAAATGTAA-
1 TTTTAGAAAGTTTAAGGGTTAAAATGTAAT
*
40926496 TTTTAGAAAGTTTAAGGGTTAAAATGCAAT
1 TTTTAGAAAGTTTAAGGGTTAAAATGTAAT
* * *
40926526 TTTTAGAAAGTTTGAGGG-TCAAATTTAAAT
1 TTTTAGAAAGTTTAAGGGTTAAAATGT-AAT
* * **
40926556 TTTTGGAAAGTTTAAGGGCTAAAACATAAT
1 TTTTAGAAAGTTTAAGGGTTAAAATGTAAT
40926586 TTT
1 TTT
40926589 AAAATAAAAT
Statistics
Matches: 200, Mismatches: 28, Indels: 21
0.80 0.11 0.08
Matches are distributed among these distances:
28 11 0.05
29 92 0.46
30 89 0.44
31 8 0.04
ACGTcount: A:0.39, C:0.03, G:0.21, T:0.38
Consensus pattern (30 bp):
TTTTAGAAAGTTTAAGGGTTAAAATGTAAT
Found at i:40928684 original size:59 final size:57
Alignment explanation
Indices: 40928571--40928922 Score: 492
Period size: 58 Copynumber: 6.1 Consensus size: 57
40928561 TGGATACCTG
* *
40928571 GGGGCAAAATCGTAA-TTTTGGTGAAATCAGGGTT-AAAATGGAATTTTGGAAAGTTC
1 GGGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGAATTTTGG-AAGTTC
* *
40928627 AGGGGTAAAATGGTAATTTTTGATGAAATCATGGTTAAAAATGGAATTTTGGAAAGTTC
1 -GGGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGAATTTTGG-AAGTTC
* ** * *
40928686 GGAGGTTAAATGGTAATTTTTGGTGAAATTGGGGTTAAAAATGGAATTTTAGAAGTTTA
1 GG-GGTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGAATTTTGGAAG-TTC
* * *
40928745 GGGGTAAAATGGTAATTTTTGGTGTAATCGGGGTTAAAAATGGAATTTTGGAAGTTTG
1 GGGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGAATTTTGGAAG-TTC
*
40928803 GGGGTAAAATGGTAATTTTTGGTGAAATTAGGGTTAAAAATGGAATTTTGGAAGTTC
1 GGGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGAATTTTGGAAGTTC
*
40928860 GGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTC
1 -GGGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGAATTTTGG-AAGTTC
40928919 GGGG
1 GGGG
40928923 ACCTATAAAC
Statistics
Matches: 267, Mismatches: 22, Indels: 11
0.89 0.07 0.04
Matches are distributed among these distances:
57 15 0.06
58 177 0.66
59 75 0.28
ACGTcount: A:0.33, C:0.03, G:0.30, T:0.34
Consensus pattern (57 bp):
GGGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGAATTTTGGAAGTTC
Found at i:40928857 original size:116 final size:117
Alignment explanation
Indices: 40928570--40928922 Score: 550
Period size: 116 Copynumber: 3.0 Consensus size: 117
40928560 TTGGATACCT
* * *
40928570 GGGGGCAAAATCGTAA-TTTTGGTGAAATCAGGGTT-AAAATGGAATTTTGGAAAGTTCAGGGGT
1 GGGGGTAAAATGGTAATTTTTGGTGAAATTAGGGTTAAAAATGGAATTTTGG-AAGTTCAGGGGT
* **
40928633 AAAATGGTAATTTTTGATGAAATCATGGTTAAAAATGGAATTTTGGAAAGTTC
65 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTC
* * * * *
40928686 GGAGGTTAAATGGTAATTTTTGGTGAAATTGGGGTTAAAAATGGAATTTTAGAAGTTTAGGGGTA
1 GGGGGTAAAATGGTAATTTTTGGTGAAATTAGGGTTAAAAATGGAATTTTGGAAGTTCAGGGGTA
* *
40928751 AAATGGTAATTTTTGGTGTAATCGGGGTTAAAAATGGAATTTTGG-AAGTTT
66 AAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTC
*
40928802 GGGGGTAAAATGGTAATTTTTGGTGAAATTAGGGTTAAAAATGGAATTTTGGAAGTTCGGGGGTA
1 GGGGGTAAAATGGTAATTTTTGGTGAAATTAGGGTTAAAAATGGAATTTTGGAAGTTCAGGGGTA
40928867 AAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTC
66 AAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTC
40928919 GGGG
1 GGGG
40928923 ACCTATAAAC
Statistics
Matches: 213, Mismatches: 21, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
116 120 0.56
117 79 0.37
118 14 0.07
ACGTcount: A:0.33, C:0.03, G:0.31, T:0.34
Consensus pattern (117 bp):
GGGGGTAAAATGGTAATTTTTGGTGAAATTAGGGTTAAAAATGGAATTTTGGAAGTTCAGGGGTA
AAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTC
Found at i:40929185 original size:162 final size:162
Alignment explanation
Indices: 40929005--40929319 Score: 522
Period size: 162 Copynumber: 1.9 Consensus size: 162
40928995 AATTGTACAT
*
40929005 CTTGAAAAATTCTTGGGCCAATTTTGTAATTAAGTAAAAGTTGATTTAGGGATTAAATAAAAACA
1 CTTGAAAAATTCTTGGGCCAATTTTGTAATTAAATAAAAGTTGATTTAGGGATTAAATAAAAACA
*
40929070 AATTAAAAAAGTCAAGGACTAAATGCACAAATAAGCCAAAAAGCGACACGTGGCAGCCCCTGGTG
66 AATTAAAAAAGTCAAGGACTAAATGCACAAATAAGCCAAAAAACGACACGTGGCAGCCCCTGGTG
*
40929135 CAGTCAAATAATCAAAGGACTAATTTATAAAC
131 CAGTCAAACAATCAAAGGACTAATTTATAAAC
* *
40929167 CTTGAAAAATTGTTGGGCCAATTTTGTAATTAAATAAAAGTTGATTTAGGGATTAAATTAAAACA
1 CTTGAAAAATTCTTGGGCCAATTTTGTAATTAAATAAAAGTTGATTTAGGGATTAAATAAAAACA
* * * * * *
40929232 AATTAAAAATGTCAGGGACTAAATGCATAAATAATCCAAAAAATGACACGTGGCAGCCTCTGGTG
66 AATTAAAAAAGTCAAGGACTAAATGCACAAATAAGCCAAAAAACGACACGTGGCAGCCCCTGGTG
*
40929297 CAGTCAAACAGTCAAAGGACTAA
131 CAGTCAAACAATCAAAGGACTAA
40929320 ATTGAAAACT
Statistics
Matches: 141, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
162 141 1.00
ACGTcount: A:0.43, C:0.14, G:0.18, T:0.25
Consensus pattern (162 bp):
CTTGAAAAATTCTTGGGCCAATTTTGTAATTAAATAAAAGTTGATTTAGGGATTAAATAAAAACA
AATTAAAAAAGTCAAGGACTAAATGCACAAATAAGCCAAAAAACGACACGTGGCAGCCCCTGGTG
CAGTCAAACAATCAAAGGACTAATTTATAAAC
Found at i:40930887 original size:17 final size:17
Alignment explanation
Indices: 40930869--40930924 Score: 80
Period size: 17 Copynumber: 3.4 Consensus size: 17
40930859 TTAATATCAT
40930869 TTTAAA-TTAAATTAAA
1 TTTAAATTTAAATTAAA
40930885 TTTAAATTTAAGA-TAAA
1 TTTAAATTTAA-ATTAAA
*
40930902 TTTAAATTTAAATAAAA
1 TTTAAATTTAAATTAAA
40930919 TTTAAA
1 TTTAAA
40930925 AAAATCAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
16 7 0.19
17 28 0.78
18 1 0.03
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (17 bp):
TTTAAATTTAAATTAAA
Found at i:40930889 original size:11 final size:11
Alignment explanation
Indices: 40930870--40930924 Score: 58
Period size: 11 Copynumber: 5.0 Consensus size: 11
40930860 TAATATCATT
40930870 TTAAA-TTAAA
1 TTAAATTTAAA
40930880 TTAAATTTAAA
1 TTAAATTTAAA
* **
40930891 TTTAAGATAAA
1 TTAAATTTAAA
40930902 TTTAAATTTAAA
1 -TTAAATTTAAA
*
40930914 TAAAATTTAAA
1 TTAAATTTAAA
40930925 AAAATCAAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
10 5 0.14
11 23 0.64
12 8 0.22
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (11 bp):
TTAAATTTAAA
Found at i:40930891 original size:6 final size:6
Alignment explanation
Indices: 40930869--40930924 Score: 59
Period size: 6 Copynumber: 10.0 Consensus size: 6
40930859 TTAATATCAT
40930869 TTTAAA -TTAAA -TTAAA TTTAAA TTTAAGA --TAAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAA-A TTTAAA TTTAAA TTTAAA
*
40930914 -TAAAA TTTAAA
1 TTTAAA TTTAAA
40930925 AAAATCAAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
4 1 0.02
5 17 0.40
6 24 0.56
7 1 0.02
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (6 bp):
TTTAAA
Found at i:40931320 original size:38 final size:38
Alignment explanation
Indices: 40931274--40931400 Score: 109
Period size: 38 Copynumber: 3.3 Consensus size: 38
40931264 TATCCAACTC
40931274 TACTTCAATTTCAAGGGGATAGGCAATGATCTTGCTCT
1 TACTTCAATTTCAAGGGGATAGGCAATGATCTTGCTCT
** * * **
40931312 TACTTCAATTTC-A-GATATAAAGACTTAAT-ACCCAGCT-T
1 TACTTCAATTTCAAGGGGAT--AGGC--AATGATCTTGCTCT
* * *
40931350 TACTTCAATTTCAAGGGGATGGGAAACGATCTTGCTCT
1 TACTTCAATTTCAAGGGGATAGGCAATGATCTTGCTCT
40931388 TACTTCAATTTCA
1 TACTTCAATTTCA
40931401 GAGATAAAGA
Statistics
Matches: 66, Mismatches: 15, Indels: 16
0.68 0.15 0.16
Matches are distributed among these distances:
36 5 0.08
37 6 0.09
38 43 0.65
39 6 0.09
40 6 0.09
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.35
Consensus pattern (38 bp):
TACTTCAATTTCAAGGGGATAGGCAATGATCTTGCTCT
Found at i:40931361 original size:76 final size:76
Alignment explanation
Indices: 40931243--40931979 Score: 1004
Period size: 76 Copynumber: 9.9 Consensus size: 76
40931233 GCTTTACTAA
* * *
40931243 AATTTCA-AGATAAAGGCTTGTTATCCAACTCTACTTCAATTTCAAGGGGATAGGCAATGATCTT
1 AATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGCGGATAGGAAATGATCTT
40931307 GCTCTTACTTC
66 GCTCTTACTTC
* ** * * * * * *
40931318 AATTTCAGATATAAAGACTTAATACCCAGCTTTACTTCAATTTCAAGGGGATGGGAAACGATCTT
1 AATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGCGGATAGGAAATGATCTT
40931383 GCTCTTACTTC
66 GCTCTTACTTC
* *
40931394 AATTTCAGAGATAAAGACTTGTTATCCAATCTTTACTTCAATTTCAA---G--AGG--ATGATGT
1 AATTTCAGAGATAAAGACTTGTTATCCAA-CTCTACTTCAATTTCAAGCGGATAGGAAATGATCT
*
40931452 TGCTCTTACTAC
65 TGCTCTTACTTC
* *** * *
40931464 AATTTCAGAGATAACGACCCATTATCCAACTCTACTTCAATTTCAAGAGGATATGG-CATGATCT
1 AATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGCGGATA-GGAAATGATCT
40931528 TGCTCTTACTTC
65 TGCTCTTACTTC
* * * *
40931540 AATTTCAGAGATAAAGACTCGTTATCCAACTCTACTTCAATTTTAAGTGGATAGGGAATGATCTT
1 AATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGCGGATAGGAAATGATCTT
40931605 GCTCTTACTTC
66 GCTCTTACTTC
* * *
40931616 AATTTTAGAGATAAAGACTTGTTATCCAACTCTACTTCAAATTCAAGCGGATAGGAAAAGATCTT
1 AATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGCGGATAGGAAATGATCTT
40931681 GCTCTTACTTC
66 GCTCTTACTTC
* *
40931692 AATTTCAGAGATAAAGACGTGTTATCCAACTCTACTTCAATTTCAAGCGGATAGGAAAAGATCTT
1 AATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGCGGATAGGAAATGATCTT
40931757 GCTCTTACTTC
66 GCTCTTACTTC
* *
40931768 AATTTCAGAGATAAAGACTTGATATCCAACTCTACTTCAATTTCAAGCGGAT--G--ACG---TT
1 AATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGCGGATAGGAAATGATCTT
40931826 GCTCTTACTTC
66 GCTCTTACTTC
* * *
40931837 AATTTCGGAGATAAAGACGTGTTATCCAACTCTACTTCAATTTCAAGCGGATAGGAAAAGATCTT
1 AATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGCGGATAGGAAATGATCTT
40931902 GCTCTTACTTC
66 GCTCTTACTTC
* *
40931913 AATTTCAGAGATAAAGACGTGTTATCC-ACTCTACTTCAATTTCAAGAGGATAGGAAATGATCTT
1 AATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGCGGATAGGAAATGATCTT
40931977 GCT
66 GCT
40931980 GTGGTCTGAT
Statistics
Matches: 593, Mismatches: 52, Indels: 34
0.87 0.08 0.05
Matches are distributed among these distances:
69 78 0.13
70 41 0.07
71 1 0.00
72 5 0.01
73 2 0.00
74 3 0.01
75 49 0.08
76 397 0.67
77 17 0.03
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.33
Consensus pattern (76 bp):
AATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGCGGATAGGAAATGATCTT
GCTCTTACTTC
Found at i:40931538 original size:38 final size:38
Alignment explanation
Indices: 40931496--40931979 Score: 155
Period size: 38 Copynumber: 12.9 Consensus size: 38
40931486 TATCCAACTC
* *
40931496 TACTTCAATTTCAAGAGGATATGGCATGATCTTGCTCT
1 TACTTCAATTTCAAGAGGATAAGGAATGATCTTGCTCT
* * ***
40931534 TACTTCAATTTC-AGA-GATAAAGACTCGTTATCCAACTC-
1 TACTTCAATTTCAAGAGGATAAGGAAT-G--ATCTTGCTCT
* * *
40931572 TACTTCAATTTTAAGTGGATAGGGAATGATCTTGCTCT
1 TACTTCAATTTCAAGAGGATAAGGAATGATCTTGCTCT
* * * ***
40931610 TACTTCAATTT-TAGA-GATAAAGACTTGTTATCCAACTC-
1 TACTTCAATTTCAAGAGGATAAGGA-ATG--ATCTTGCTCT
* * *
40931648 TACTTCAAATTCAAGCGGAT-AGGAAAAGATCTTGCTCT
1 TACTTCAATTTCAAGAGGATAAGG-AATGATCTTGCTCT
* * ***
40931686 TACTTCAATTTC-AGA-GATAAAGACGTGTTATCCAACTC-
1 TACTTCAATTTCAAGAGGATAAGGA-ATG--ATCTTGCTCT
* *
40931724 TACTTCAATTTCAAGCGGAT-AGGAAAAGATCTTGCTCT
1 TACTTCAATTTCAAGAGGATAAGG-AATGATCTTGCTCT
* * * * *
40931762 TACTTCAATTTC-AGA-GATAAAGACTTGAT-ATCCAACT
1 TACTTCAATTTCAAGAGGATAAGGA-ATGATCTTGC-TCT
* *
40931799 CTACTTCAATTTCAAGCGGAT---G-ACG---TTGCTCT
1 -TACTTCAATTTCAAGAGGATAAGGAATGATCTTGCTCT
* * * ***
40931831 TACTTCAATTTC-GGA-GATAAAGACGTGTTATCCAACTC-
1 TACTTCAATTTCAAGAGGATAAGGA-ATG--ATCTTGCTCT
* *
40931869 TACTTCAATTTCAAGCGGAT-AGGAAAAGATCTTGCTCT
1 TACTTCAATTTCAAGAGGATAAGG-AATGATCTTGCTCT
* * * *
40931907 TACTTCAATTTC-AGA-GATAAAGACGTG-T-TATCCACT
1 TACTTCAATTTCAAGAGGATAAGGA-ATGATCT-TGCTCT
40931943 CTACTTCAATTTCAAGAGGAT-AGGAAATGATCTTGCT
1 -TACTTCAATTTCAAGAGGATAAGG-AATGATCTTGCT
40931980 GTGGTCTGAT
Statistics
Matches: 311, Mismatches: 85, Indels: 99
0.63 0.17 0.20
Matches are distributed among these distances:
29 3 0.01
30 1 0.00
31 12 0.04
32 3 0.01
33 2 0.01
34 1 0.00
35 2 0.01
36 31 0.10
37 64 0.21
38 122 0.39
39 47 0.15
40 23 0.07
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Consensus pattern (38 bp):
TACTTCAATTTCAAGAGGATAAGGAATGATCTTGCTCT
Found at i:40932858 original size:10 final size:9
Alignment explanation
Indices: 40932838--40932863 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
40932828 ACCTCTCCGA
40932838 TTTTTTATT
1 TTTTTTATT
40932847 TTTTTTATT
1 TTTTTTATT
40932856 TTTTTTAT
1 TTTTTTAT
40932864 GTGTAATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (9 bp):
TTTTTTATT
Found at i:40944144 original size:29 final size:29
Alignment explanation
Indices: 40944104--40944323 Score: 197
Period size: 30 Copynumber: 7.6 Consensus size: 29
40944094 TACCCGGGGG
*
40944104 AAAATGGTAATTTTGGTAAAATCAGGGTT
1 AAAATGGTAATTTTGGTAAAATCGGGGTT
*
40944133 AAAAATGG-AATTTTGG-AAAGTTCAGGGG-T
1 -AAAATGGTAATTTTGGTAAA-ATC-GGGGTT
*
40944162 AAAATGGTAATTTTTGGTGAAATCGGGGTT
1 AAAATGGTAA-TTTTGGTAAAATCGGGGTT
** *
40944192 AAAATGG-AATTTTGG-AAGTTCGGGGGT
1 AAAATGGTAATTTTGGTAAAATCGGGGTT
*
40944219 AAAATGGTAATTTTTGGTGAAATCGGGGTT
1 AAAATGGTAA-TTTTGGTAAAATCGGGGTT
*
40944249 AAAAATGG-AATTTTGG-AAAGTTCAGGGG-T
1 -AAAATGGTAATTTTGGTAAA-ATC-GGGGTT
**
40944278 AAAATGGTAATTTTTGGTGTAATCGGGGTT
1 AAAATGGTAA-TTTTGGTAAAATCGGGGTT
40944308 AAAAATGG-AATTTTGG
1 -AAAATGGTAATTTTGG
40944324 AAAGTTCAGG
Statistics
Matches: 156, Mismatches: 17, Indels: 35
0.75 0.08 0.17
Matches are distributed among these distances:
27 15 0.10
28 27 0.17
29 46 0.29
30 51 0.33
31 17 0.11
ACGTcount: A:0.34, C:0.03, G:0.30, T:0.33
Consensus pattern (29 bp):
AAAATGGTAATTTTGGTAAAATCGGGGTT
Found at i:40944191 original size:59 final size:59
Alignment explanation
Indices: 40944099--40944334 Score: 406
Period size: 59 Copynumber: 4.1 Consensus size: 59
40944089 TTGGATACCC
* * *
40944099 GGGGGAAAATGGTAA-TTTTGGTAAAATCAGGGTTAAAAATGGAATTTTGGAAAGTTCA
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCA
*
40944157 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTT-AAAATGGAATTTTGG-AAGTTCG
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCA
40944214 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCA
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCA
*
40944273 GGGGTAAAATGGTAATTTTTGGTGTAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCA
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCA
40944332 GGG
1 GGG
40944335 ACCTATAAAC
Statistics
Matches: 169, Mismatches: 6, Indels: 5
0.94 0.03 0.03
Matches are distributed among these distances:
57 41 0.24
58 44 0.26
59 84 0.50
ACGTcount: A:0.33, C:0.03, G:0.32, T:0.32
Consensus pattern (59 bp):
GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCA
Found at i:40944236 original size:116 final size:116
Alignment explanation
Indices: 40944098--40944330 Score: 407
Period size: 116 Copynumber: 2.0 Consensus size: 116
40944088 TTTGGATACC
40944098 CGGGGGAAAATGGTAATTTTGGTAAAATCAGGGTTAAAAATGGAATTTTGGAAAGTTCAGGGGTA
1 CGGGGGAAAATGGTAATTTTGGTAAAATCAGGGTTAAAAATGGAATTTTGGAAAGTTCAGGGGTA
40944163 AAATGGTAATTTTTGGTGAAATCGGGGTT-AAAATGGAATTTTGG-AAGTT
66 AAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTT
* *
40944212 CGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCAGGGG
1 CGGGGG-AAAATGGTAA-TTTTGGTAAAATCAGGGTTAAAAATGGAATTTTGGAAAGTTCAGGGG
*
40944277 TAAAATGGTAATTTTTGGTGTAATCGGGGTTAAAAATGGAATTTTGGAAAGTT
64 TAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTT
40944330 C
1 C
40944331 AGGGACCTAT
Statistics
Matches: 112, Mismatches: 3, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
114 6 0.05
115 10 0.09
116 75 0.67
117 15 0.13
118 6 0.05
ACGTcount: A:0.33, C:0.04, G:0.31, T:0.32
Consensus pattern (116 bp):
CGGGGGAAAATGGTAATTTTGGTAAAATCAGGGTTAAAAATGGAATTTTGGAAAGTTCAGGGGTA
AAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTT
Found at i:40944663 original size:163 final size:162
Alignment explanation
Indices: 40944393--40944735 Score: 560
Period size: 163 Copynumber: 2.1 Consensus size: 162
40944383 AGGCATTTAG
* * * * *
40944393 CAGTCAAGGGATTAAATTGTAAATCTTGAAAAATTCTTGGGCCAATTTCGTAATTAAGTAAAAGT
1 CAGTCAAAGGACTAAATTATAAACCTTGAAAAATTCTTGGGCCAATTTCGTAATTAAATAAAAGT
40944458 TGATTTAGGGATTAAATTAAAACAAATTAAAAAAGTCAAGGACTAAATGCATAAATAAGCCAAAA
66 TGATTTAGGGATTAAATTAAAACAAATTAAAAAAGTCAAGGACTAAATGCATAAATAAGCC-AAA
40944523 AAACGACACGTGGCAACCCCTGGTGCAGTCAAA
130 AAACGACACGTGGCAACCCCTGGTGCAGTCAAA
* * *
40944556 CAGTCAAAGGACTAATTTATAAACCTTGAAAAATTGTTGGGCCAATTTTGTAATTAAATAAAAGT
1 CAGTCAAAGGACTAAATTATAAACCTTGAAAAATTCTTGGGCCAATTTCGTAATTAAATAAAAGT
* *
40944621 TGATTTAGGGATTAAATTAAAACAAATTAAAAATGTCAAGGACTAAATGCATAAATAATCCAAAA
66 TGATTTAGGGATTAAATTAAAACAAATTAAAAAAGTCAAGGACTAAATGCATAAATAAGCCAAAA
* * *
40944686 AATGACACGTGGCAGCCTCTGGTGCAGTCAAA
131 AACGACACGTGGCAACCCCTGGTGCAGTCAAA
40944718 CAGTCAAAGGACTAAATT
1 CAGTCAAAGGACTAAATT
40944736 GAAAACTAAT
Statistics
Matches: 166, Mismatches: 14, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
162 50 0.30
163 116 0.70
ACGTcount: A:0.43, C:0.14, G:0.17, T:0.26
Consensus pattern (162 bp):
CAGTCAAAGGACTAAATTATAAACCTTGAAAAATTCTTGGGCCAATTTCGTAATTAAATAAAAGT
TGATTTAGGGATTAAATTAAAACAAATTAAAAAAGTCAAGGACTAAATGCATAAATAAGCCAAAA
AACGACACGTGGCAACCCCTGGTGCAGTCAAA
Found at i:40945848 original size:62 final size:60
Alignment explanation
Indices: 40945628--40945841 Score: 212
Period size: 62 Copynumber: 3.6 Consensus size: 60
40945618 AAAAATTTGG
* * * *
40945628 GGTGTTGGCCATGC-AATGGTCGACACCCTCTTTTTGTCAGAAAAAAATTTCAAAATTTTTTT
1 GGTGTTAGCCAT-CAAATGGCCGACACCCCCTTTTTCTCAGAAAAAAA-TTC-AAATTTTTTT
* * * *
40945690 -CTGTTAGTCATCAAATGGCCGACACCCCC-TATT-TCA-AAAAAAATTGC--A-TTTTTG
1 GGTGTTAGCCATCAAATGGCCGACACCCCCTTTTTCTCAGAAAAAAATT-CAAATTTTTTT
40945744 GGTGTTAGCCATCAAATGGCCGACA-CCCCTTATTTCTCGAGAAAAGAAATTCAAATTTTTTT
1 GGTGTTAGCCATCAAATGGCCGACACCCCCTT-TTTCTC-AGAAAA-AAATTCAAATTTTTTT
*
40945806 GGTGTTGGCCATCAAATGGCCGACACCCCCCTTTTT
1 GGTGTTAGCCATCAAATGGCCGACA-CCCCCTTTTT
40945842 TCGAGAATGA
Statistics
Matches: 126, Mismatches: 12, Indels: 27
0.76 0.07 0.16
Matches are distributed among these distances:
54 9 0.07
55 24 0.19
56 2 0.02
57 4 0.03
58 9 0.07
59 8 0.06
60 9 0.07
61 23 0.18
62 29 0.23
63 3 0.02
64 6 0.05
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.33
Consensus pattern (60 bp):
GGTGTTAGCCATCAAATGGCCGACACCCCCTTTTTCTCAGAAAAAAATTCAAATTTTTTT
Found at i:40945855 original size:30 final size:30
Alignment explanation
Indices: 40945821--40945878 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
40945811 TGGCCATCAA
40945821 ATGGCCGACACCCCCCTTTTTTCGAGAATG
1 ATGGCCGACACCCCCCTTTTTTCGAGAATG
40945851 ATGGCCGACACCCCCCTTTTTTCGAGAA
1 ATGGCCGACACCCCCCTTTTTTCGAGAA
40945879 AAAAAATTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.21, C:0.34, G:0.19, T:0.26
Consensus pattern (30 bp):
ATGGCCGACACCCCCCTTTTTTCGAGAATG
Found at i:40947473 original size:30 final size:30
Alignment explanation
Indices: 40947421--40947512 Score: 89
Period size: 30 Copynumber: 3.1 Consensus size: 30
40947411 TCCCTTTACT
*
40947421 TTTTAAATTTAATTTGTAATTTCGTT-TTTA
1 TTTTAAATTTAATTTGTAATTTC-TTGTATA
*
40947451 TTTTAAATTTAATTT-TGGATTTCTTGTATA
1 TTTTAAATTTAATTTGT-AATTTCTTGTATA
* ** * *
40947481 TTTTAATTTTTCTTTCTAATTTCATGTATA
1 TTTTAAATTTAATTTGTAATTTCTTGTATA
40947511 TT
1 TT
40947513 CTAATTATTA
Statistics
Matches: 52, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
29 3 0.06
30 48 0.92
31 1 0.02
ACGTcount: A:0.25, C:0.05, G:0.07, T:0.63
Consensus pattern (30 bp):
TTTTAAATTTAATTTGTAATTTCTTGTATA
Found at i:40948554 original size:62 final size:61
Alignment explanation
Indices: 40948405--40948873 Score: 639
Period size: 62 Copynumber: 7.7 Consensus size: 61
40948395 TTCGAGAAAA
* * *
40948405 ATGGCCAACACCAAAAAAATTT-TAATTTTTTTCTCGAGAAAATGGGGTGCCGGCCATTTG
1 ATGGCCAACACCAAAAAAATTTGAAATTTTTTTCTCGAGAAAAGGGGGTGTCGGCCATTTG
* * *
40948465 ATGGCCAACACCAAAAAAATTTGAAATTTTTTCCTCGAGAACAGGGGGTGTCGACCATTTG
1 ATGGCCAACACCAAAAAAATTTGAAATTTTTTTCTCGAGAAAAGGGGGTGTCGGCCATTTG
* *
40948526 ATGGCCAATACCAAAAAAATTTTGAAATTTTTTTCTTGAGAAAAGGGGGGTGTCGGCCA-TTG
1 ATGGCCAACACCAAAAAAA-TTTGAAATTTTTTTCTCGAGAAAA-GGGGGTGTCGGCCATTTG
* *
40948588 TATGGCCAACACCAAAAAAATTTAAAATTTTTTTCTCAAGAAAAAGGGGGTGTCGGCCA-TTG
1 -ATGGCCAACACCAAAAAAATTTGAAATTTTTTTCTCGAG-AAAAGGGGGTGTCGGCCATTTG
* * *
40948650 CATGGCCAACACCAAAAAAATTTG-AATTTTTTTCTAGAGAAAAGGGGGGTGTCGGCCTTTTA
1 -ATGGCCAACACCAAAAAAATTTGAAATTTTTTTCTCGAGAAAA-GGGGGTGTCGGCCATTTG
* *
40948712 ATGGCCAACACCAAAAAAATTTGAATTTTTTTTCTCGAGAAATAGGGGGTGTCGGTCATTTG
1 ATGGCCAACACCAAAAAAATTTGAAATTTTTTTCTCGAGAAA-AGGGGGTGTCGGCCATTTG
* *
40948774 ATGGCCTACA-CAAAAAAATTTG-AATTTTTTTCTCGAGAAATAGGGGGTGTCGGTCATTTG
1 ATGGCCAACACCAAAAAAATTTGAAATTTTTTTCTCGAGAAA-AGGGGGTGTCGGCCATTTG
**
40948834 ATGATCAACA-CAAAAAAATTT-AAATTTTTTTCTCGAGAAA
1 ATGGCCAACACCAAAAAAATTTGAAATTTTTTTCTCGAGAAA
40948874 TAGAGAATGG
Statistics
Matches: 368, Mismatches: 31, Indels: 20
0.88 0.07 0.05
Matches are distributed among these distances:
60 99 0.27
61 111 0.30
62 122 0.33
63 36 0.10
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.30
Consensus pattern (61 bp):
ATGGCCAACACCAAAAAAATTTGAAATTTTTTTCTCGAGAAAAGGGGGTGTCGGCCATTTG
Found at i:40948716 original size:123 final size:122
Alignment explanation
Indices: 40948405--40948873 Score: 653
Period size: 123 Copynumber: 3.8 Consensus size: 122
40948395 TTCGAGAAAA
* * *
40948405 ATGGCCAACACCAAAAAAATTTTAATTTTTTTCTCGAGAAAATGGGGTGCCGGCCATTTGATGGC
1 ATGGCCAACACCAAAAAAATTTGAATTTTTTTCTCGAGAAAAGGGGGTGTCGGCCATTTGATGGC
* * *
40948470 CAACACCAAAAAAATTTGAAATTTTTTCCTCGAG-AACAGGGGGTGTCGACCATTTG
66 CAACACCAAAAAAATTTGAAATTTTTTTCTCGAGAAAAAGGGGGTGTCGGCCATTTG
* *
40948526 ATGGCCAATACCAAAAAAATTTTGAAATTTTTTTCTTGAGAAAAGGGGGGTGTCGGCCA-TTGTA
1 ATGGCCAACACCAAAAAAA-TTTG-AATTTTTTTCTCGAGAAAA-GGGGGTGTCGGCCATTTG-A
* *
40948590 TGGCCAACACCAAAAAAATTTAAAATTTTTTTCTCAAGAAAAAGGGGGTGTCGGCCA-TTG
62 TGGCCAACACCAAAAAAATTTGAAATTTTTTTCTCGAGAAAAAGGGGGTGTCGGCCATTTG
* * *
40948650 CATGGCCAACACCAAAAAAATTTGAATTTTTTTCTAGAGAAAAGGGGGGTGTCGGCCTTTTAATG
1 -ATGGCCAACACCAAAAAAATTTGAATTTTTTTCTCGAGAAAA-GGGGGTGTCGGCCATTTGATG
* * *
40948715 GCCAACACCAAAAAAATTTGAATTTTTTTTCTCGAGAAATAGGGGGTGTCGGTCATTTG
64 GCCAACACCAAAAAAATTTGAAATTTTTTTCTCGAGAAAAAGGGGGTGTCGGCCATTTG
* * *
40948774 ATGGCCTACA-CAAAAAAATTTGAATTTTTTTCTCGAGAAATAGGGGGTGTCGGTCATTTGATGA
1 ATGGCCAACACCAAAAAAATTTGAATTTTTTTCTCGAGAAA-AGGGGGTGTCGGCCATTTGATGG
*
40948838 TCAACA-CAAAAAAATTT-AAATTTTTTTCTCGAGAAA
65 CCAACACCAAAAAAATTTGAAATTTTTTTCTCGAGAAA
40948874 TAGAGAATGG
Statistics
Matches: 312, Mismatches: 27, Indels: 19
0.87 0.08 0.05
Matches are distributed among these distances:
120 18 0.06
121 29 0.09
122 55 0.18
123 116 0.37
124 60 0.19
125 34 0.11
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.30
Consensus pattern (122 bp):
ATGGCCAACACCAAAAAAATTTGAATTTTTTTCTCGAGAAAAGGGGGTGTCGGCCATTTGATGGC
CAACACCAAAAAAATTTGAAATTTTTTTCTCGAGAAAAAGGGGGTGTCGGCCATTTG
Found at i:40948982 original size:60 final size:58
Alignment explanation
Indices: 40948901--40949015 Score: 149
Period size: 60 Copynumber: 1.9 Consensus size: 58
40948891 CCAAAAATGT
* * * *
40948901 ATTTTTTTTGAAATAGGGGGTGTCGGTCATTTAATGGCCAACACCCCAAAATTTTGAA
1 ATTTTTTTTGAAAAAAGGGGTGTCGATCATTGAATGGCCAACACCCCAAAATTTTGAA
* * *
40948959 ATTTTTTTTGACAAAAAAGGGGTGTCGATCATTGCATGGTCAACACCCCAAATTTTT
1 ATTTTTTTTG--AAAAAAGGGGTGTCGATCATTGAATGGCCAACACCCCAAAATTTT
40949016 TTCATATTCT
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
58 10 0.21
60 38 0.79
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.35
Consensus pattern (58 bp):
ATTTTTTTTGAAAAAAGGGGTGTCGATCATTGAATGGCCAACACCCCAAAATTTTGAA
Found at i:40949855 original size:41 final size:41
Alignment explanation
Indices: 40949801--40949882 Score: 146
Period size: 41 Copynumber: 2.0 Consensus size: 41
40949791 ATACATATTT
* *
40949801 TTTAGGGGTTTAATGTTAGATCTTCCATCACTGTCATTTTC
1 TTTAGGGGATTAATGTTAGATCTTCCATCACTCTCATTTTC
40949842 TTTAGGGGATTAATGTTAGATCTTCCATCACTCTCATTTTC
1 TTTAGGGGATTAATGTTAGATCTTCCATCACTCTCATTTTC
40949883 GTTACTTTGA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.21, C:0.18, G:0.16, T:0.45
Consensus pattern (41 bp):
TTTAGGGGATTAATGTTAGATCTTCCATCACTCTCATTTTC
Found at i:40953014 original size:17 final size:17
Alignment explanation
Indices: 40952988--40953065 Score: 111
Period size: 17 Copynumber: 4.6 Consensus size: 17
40952978 CCAAACAGAC
40952988 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
* *
40953005 ATTAAGTTTATTTTAAA
1 TTTAAATTTATTTTAAA
**
40953022 TTTAAATTTATTGGAAA
1 TTTAAATTTATTTTAAA
*
40953039 TTTAAATTTATTATAAA
1 TTTAAATTTATTTTAAA
40953056 TTTAAATTTA
1 TTTAAATTTA
40953066 AATTTATTTA
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 53 1.00
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:40953025 original size:6 final size:6
Alignment explanation
Indices: 40952988--40953071 Score: 63
Period size: 6 Copynumber: 14.7 Consensus size: 6
40952978 CCAAACAGAC
* * * *
40952988 TTTAAA TTT-AT TTTAAA ATTAAG TTT-AT TTTAAA TTTAAA TTT--A
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
40953032 TTGGAAA TTTAAA TTT--A TTATAAA TTTAAA TTTAAA TTTA
1 TT-TAAA TTTAAA TTTAAA TT-TAAA TTTAAA TTTAAA TTTA
40953072 TTTAAATAAT
Statistics
Matches: 61, Mismatches: 9, Indels: 16
0.71 0.10 0.19
Matches are distributed among these distances:
4 6 0.10
5 9 0.15
6 40 0.66
7 6 0.10
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:40953042 original size:23 final size:21
Alignment explanation
Indices: 40953016--40953078 Score: 71
Period size: 17 Copynumber: 3.0 Consensus size: 21
40953006 TTAAGTTTAT
40953016 TTTAAATTTAAATTTATTGGAAA
1 TTTAAATTTAAATTTATT--AAA
40953039 TTTAAATTT--A-TTA-TAAA
1 TTTAAATTTAAATTTATTAAA
40953056 TTTAAATTTAAATTTATTTAAA
1 TTTAAATTTAAATTTA-TTAAA
40953078 T
1 T
40953079 AATGTCCAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
17 12 0.34
19 2 0.06
20 6 0.17
21 1 0.03
22 5 0.14
23 9 0.26
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.52
Consensus pattern (21 bp):
TTTAAATTTAAATTTATTAAA
Found at i:40953100 original size:13 final size:13
Alignment explanation
Indices: 40953082--40953107 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
40953072 TTTAAATAAT
40953082 GTCCAATTACAAA
1 GTCCAATTACAAA
40953095 GTCCAATTACAAA
1 GTCCAATTACAAA
40953108 TTGGGTCCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.23, G:0.08, T:0.23
Consensus pattern (13 bp):
GTCCAATTACAAA
Found at i:40954280 original size:29 final size:30
Alignment explanation
Indices: 40954237--40954427 Score: 164
Period size: 29 Copynumber: 6.5 Consensus size: 30
40954227 TAGGTTCTCG
* *
40954237 AACTTTTTAAAAATTATA-TTTTTACCCTCA
1 AACTTTTCAAAAATTACATTTTTTA-CCTCA
* * *
40954267 AACTTTTC-AAAATTACATTTTTGACATCG
1 AACTTTTCAAAAATTACATTTTTTACCTCA
* * * *
40954296 AATTTTTCAAAATTTACA-TTTTAACCTTA
1 AACTTTTCAAAAATTACATTTTTTACCTCA
* * *
40954325 AA-TTTTCCAAAAATCACA-CTTTTACCCTTA
1 AACTTTT-CAAAAATTACATTTTTTA-CCTCA
*
40954355 AAC-TTCCAAAAATTACATTTTTTA-CTCA
1 AACTTTTCAAAAATTACATTTTTTACCTCA
*
40954383 AACTTTCCAAAAATTACATTTTTTACCTCA
1 AACTTTTCAAAAATTACATTTTTTACCTCA
40954413 AA-TTTTCTAAAAATT
1 AACTTTTC-AAAAATT
40954428 CCACTTTTGA
Statistics
Matches: 132, Mismatches: 20, Indels: 18
0.78 0.12 0.11
Matches are distributed among these distances:
28 10 0.08
29 75 0.57
30 47 0.36
ACGTcount: A:0.38, C:0.19, G:0.01, T:0.42
Consensus pattern (30 bp):
AACTTTTCAAAAATTACATTTTTTACCTCA
Found at i:40954396 original size:88 final size:88
Alignment explanation
Indices: 40954256--40954444 Score: 217
Period size: 88 Copynumber: 2.1 Consensus size: 88
40954246 AAAATTATAT
* * * *
40954256 TTTTACCCTCAAACTTTTCAAAATTACATTTTTGACATCGAATTTTTCAAAATTTACA-TTTTAA
1 TTTTACCCTCAAACTTTCCAAAATTACATTTTTGACATCAAACTTTCCAAAA-TTACATTTTTAA
*
40954320 CCTTAAATTTTCCAAAAA-TCACAC
65 CCTCAAATTTTCCAAAAATTC-CAC
* * *
40954344 TTTTACCCTTAAAC-TTCCAAAAATTACATTTTTTAC-TCAAACTTTCCAAAAATTACATTTTTT
1 TTTTACCCTCAAACTTTCC-AAAATTACATTTTTGACATCAAACTTTCC-AAAATTACATTTTTA
*
40954407 ACCTCAAATTTTCTAAAAATTCCAC
64 ACCTCAAATTTTCCAAAAATTCCAC
40954432 TTTTGACCC-CAAA
1 TTTT-ACCCTCAAA
40954445 TCCTCCAAAA
Statistics
Matches: 86, Mismatches: 10, Indels: 10
0.81 0.09 0.09
Matches are distributed among these distances:
87 16 0.19
88 64 0.74
89 6 0.07
ACGTcount: A:0.36, C:0.22, G:0.02, T:0.40
Consensus pattern (88 bp):
TTTTACCCTCAAACTTTCCAAAATTACATTTTTGACATCAAACTTTCCAAAATTACATTTTTAAC
CTCAAATTTTCCAAAAATTCCAC
Found at i:40954435 original size:29 final size:29
Alignment explanation
Indices: 40954256--40954529 Score: 122
Period size: 29 Copynumber: 9.4 Consensus size: 29
40954246 AAAATTATAT
* *
40954256 TTTTACCCTCAAACTTTT-C-AAAATTACAT
1 TTTTA-CCTCAAA-TTTTCCAAAAATTCCAC
* * * * *
40954285 TTTTGACATCGAATTTTTCAAAATTTACA-
1 TTTT-ACCTCAAATTTTCCAAAAATTCCAC
*
40954314 TTTTAACCTTAAATTTTCCAAAAA-TCACAC
1 TTTT-ACCTCAAATTTTCCAAAAATTC-CAC
* * * *
40954344 TTTTACCCTTAAA-CTTCCAAAAATTACATT
1 TTTTA-CCTCAAATTTTCCAAAAATTCCA-C
* * *
40954374 TTTTA-CTCAAACTTTCCAAAAATTACATT
1 TTTTACCTCAAATTTTCCAAAAATTCCA-C
*
40954403 TTTTACCTCAAATTTTCTAAAAATTCCAC
1 TTTTACCTCAAATTTTCCAAAAATTCCAC
* ** *
40954432 TTTTGACCCCAAATCCTCCAAAAATACCA-
1 TTTT-ACCTCAAATTTTCCAAAAATTCCAC
* * *
40954461 TTTTACCCCCGAA-TGTCCAAAAATTCCA-
1 TTTTA-CCTCAAATTTTCCAAAAATTCCAC
*
40954489 TTTTGACC-CTAAA-ATTCCAAAAATTACCA-
1 TTTT-ACCTC-AAATTTTCCAAAAATT-CCAC
*
40954518 TTTTACCCCAAA
1 TTTTACCTCAAA
40954530 AAGTCCAAAT
Statistics
Matches: 198, Mismatches: 31, Indels: 33
0.76 0.12 0.13
Matches are distributed among these distances:
27 1 0.01
28 47 0.24
29 86 0.43
30 64 0.32
ACGTcount: A:0.36, C:0.25, G:0.02, T:0.36
Consensus pattern (29 bp):
TTTTACCTCAAATTTTCCAAAAATTCCAC
Found at i:40954445 original size:30 final size:27
Alignment explanation
Indices: 40954328--40954529 Score: 138
Period size: 29 Copynumber: 7.0 Consensus size: 27
40954318 AACCTTAAAT
*
40954328 TTTCCAAAAA-TCACACTTTTACCCTTAAA
1 TTTCCAAAAATTC-CA-TTTTACCC-CAAA
* * *
40954357 CTTCCAAAAATTACATTTTTTA-CTCAAA
1 TTTCCAAAAATTCCA--TTTTACCCCAAA
* *
40954385 CTTTCCAAAAATTACATTTTTTACCTCAAA
1 -TTTCCAAAAATTCCA--TTTTACCCCAAA
*
40954415 TTTTCTAAAAATTCCACTTTTGACCCCAAA
1 -TTTCCAAAAATTCCA-TTTT-ACCCCAAA
* * *
40954445 TCCTCCAAAAATACCATTTTACCCCCGAA
1 T-TTCCAAAAATTCCATTTTA-CCCCAAA
* *
40954474 TGTCCAAAAATTCCATTTTGACCCTAAA
1 TTTCCAAAAATTCCATTTT-ACCCCAAA
*
40954502 ATTCCAAAAATTACCATTTTACCCCAAA
1 TTTCCAAAAATT-CCATTTTACCCCAAA
40954530 AAGTCCAAAT
Statistics
Matches: 142, Mismatches: 22, Indels: 19
0.78 0.12 0.10
Matches are distributed among these distances:
28 42 0.30
29 57 0.40
30 43 0.30
ACGTcount: A:0.37, C:0.27, G:0.02, T:0.34
Consensus pattern (27 bp):
TTTCCAAAAATTCCATTTTACCCCAAA
Found at i:40954479 original size:28 final size:28
Alignment explanation
Indices: 40954403--40954552 Score: 117
Period size: 28 Copynumber: 5.3 Consensus size: 28
40954393 AAATTACATT
* * * * *
40954403 TTTTACCTCAAATTTTCTAAAAATTCCA
1 TTTTACCCCAAAATGTCCAAAAATACCA
*
40954431 CTTTTGACCCC-AAATCCTCCAAAAATACCA
1 -TTTT-ACCCCAAAAT-GTCCAAAAATACCA
** *
40954461 TTTTACCCCCGAATGTCCAAAAATTCCA
1 TTTTACCCCAAAATGTCCAAAAATACCA
*
40954489 TTTTGACCCTAAAAT-TCCAAAAATTACCA
1 TTTT-ACCCCAAAATGTCCAAAAA-TACCA
* * *
40954518 TTTTACCCCAAAAAGTCC-AAATTATCA
1 TTTTACCCCAAAATGTCCAAAAATACCA
40954545 TTTTACCC
1 TTTTACCC
40954553 TCGAGCATAA
Statistics
Matches: 99, Mismatches: 16, Indels: 14
0.77 0.12 0.11
Matches are distributed among these distances:
27 12 0.12
28 40 0.40
29 32 0.32
30 15 0.15
ACGTcount: A:0.36, C:0.29, G:0.03, T:0.32
Consensus pattern (28 bp):
TTTTACCCCAAAATGTCCAAAAATACCA
Found at i:40954536 original size:57 final size:57
Alignment explanation
Indices: 40954421--40954538 Score: 159
Period size: 57 Copynumber: 2.1 Consensus size: 57
40954411 CAAATTTTCT
* ** *
40954421 AAAAATTCCACTTTTGACCCCAAATCCTCCAAAAATACCATTTTACCCCCGAATGTCC
1 AAAAATTCCACTTTTGACCCAAAAT-CTCCAAAAATACCATTTTACCCCAAAAAGTCC
40954479 AAAAATTCCA-TTTTGACCCTAAAAT-TCCAAAAATTACCATTTTACCCCAAAAAGTCC
1 AAAAATTCCACTTTTGACCC-AAAATCTCCAAAAA-TACCATTTTACCCCAAAAAGTCC
40954536 AAA
1 AAA
40954539 TTATCATTTT
Statistics
Matches: 54, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
56 8 0.15
57 32 0.59
58 14 0.26
ACGTcount: A:0.40, C:0.30, G:0.04, T:0.26
Consensus pattern (57 bp):
AAAAATTCCACTTTTGACCCAAAATCTCCAAAAATACCATTTTACCCCAAAAAGTCC
Found at i:40956633 original size:15 final size:15
Alignment explanation
Indices: 40956615--40956655 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
40956605 ATCACATCAG
40956615 TATTAAATTAATAAA
1 TATTAAATTAATAAA
40956630 TATT--ATCTATATAAA
1 TATTAAAT-TA-ATAAA
40956645 TATTAAATTAA
1 TATTAAATTAA
40956656 ATTTAATATC
Statistics
Matches: 22, Mismatches: 0, Indels: 8
0.73 0.00 0.27
Matches are distributed among these distances:
13 2 0.09
14 2 0.09
15 14 0.64
16 2 0.09
17 2 0.09
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
TATTAAATTAATAAA
Found at i:40956649 original size:30 final size:31
Alignment explanation
Indices: 40956615--40956684 Score: 90
Period size: 30 Copynumber: 2.3 Consensus size: 31
40956605 ATCACATCAG
*
40956615 TATTAAATTAATAAATATTATCT-ATA-TAAA
1 TATTAAATTAA-AAATAATATCTCATATTAAA
**
40956645 TATTAAATTAAATTTAATATCTCATATTAAA
1 TATTAAATTAAAAATAATATCTCATATTAAA
40956676 TATTAAATT
1 TATTAAATT
40956685 TAATTTAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
29 8 0.23
30 14 0.40
31 13 0.37
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (31 bp):
TATTAAATTAAAAATAATATCTCATATTAAA
Found at i:40956672 original size:24 final size:22
Alignment explanation
Indices: 40956643--40956701 Score: 73
Period size: 26 Copynumber: 2.5 Consensus size: 22
40956633 TATCTATATA
40956643 AATATTAAATTAAATTTAATATCT
1 AATATTAAATTAAATTTAAT-T-T
*
40956667 CATATTAAATATTAAATTTAATTT
1 AATATT-AA-ATTAAATTTAATTT
40956691 AATATTAAATT
1 AATATTAAATT
40956702 TATTAAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
22 3 0.10
23 2 0.06
24 11 0.35
25 3 0.10
26 12 0.39
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.47
Consensus pattern (22 bp):
AATATTAAATTAAATTTAATTT
Found at i:40956679 original size:31 final size:29
Alignment explanation
Indices: 40956615--40956695 Score: 99
Period size: 31 Copynumber: 2.7 Consensus size: 29
40956605 ATCACATCAG
** *
40956615 TATTAAATTAATAAATATTATCTATATAAA
1 TATTAAATTAA-ATTTAATATCTATATAAA
40956645 TATTAAATTAAATTTAATATCTCATATTAAA
1 TATTAAATTAAATTTAATATCT-ATA-TAAA
*
40956676 TATTAAATTTAATTTAATAT
1 TATTAAATTAAATTTAATAT
40956696 TAAATTTATT
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
29 8 0.18
30 14 0.31
31 23 0.51
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (29 bp):
TATTAAATTAAATTTAATATCTATATAAA
Found at i:40956708 original size:26 final size:26
Alignment explanation
Indices: 40956643--40956700 Score: 79
Period size: 24 Copynumber: 2.4 Consensus size: 26
40956633 TATCTATATA
40956643 AATATT-AA-ATTAAATTTAATATCT
1 AATATTAAATATTAAATTTAATATCT
*
40956667 CATATTAAATATTAAATTTAAT-T-T
1 AATATTAAATATTAAATTTAATATCT
40956691 AATATTAAAT
1 AATATTAAAT
40956701 TTATTAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 15 0.50
25 3 0.10
26 12 0.40
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (26 bp):
AATATTAAATATTAAATTTAATATCT
Found at i:40970651 original size:22 final size:22
Alignment explanation
Indices: 40970602--40970654 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
40970592 GAAATAATTT
* **
40970602 AATAAAAAATATAAATTTTTGA
1 AATAAAAAATACAAATTTTAAA
40970624 AATAAAAAATACAAA-TTTAAA
1 AATAAAAAATACAAATTTTAAA
40970645 AATTAAAAAA
1 AA-TAAAAAA
40970655 ATCAAATAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 6 0.22
22 21 0.78
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.28
Consensus pattern (22 bp):
AATAAAAAATACAAATTTTAAA
Found at i:40970670 original size:21 final size:23
Alignment explanation
Indices: 40970627--40970673 Score: 62
Period size: 21 Copynumber: 2.1 Consensus size: 23
40970617 TTTTTGAAAT
*
40970627 AAAAAATACAAATTTAAAAATTA
1 AAAAAATACAAATTAAAAAATTA
*
40970650 AAAAAAT-CAAA-TAAAAGATTA
1 AAAAAATACAAATTAAAAAATTA
40970671 AAA
1 AAA
40970674 TATTTTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 11 0.50
22 4 0.18
23 7 0.32
ACGTcount: A:0.72, C:0.04, G:0.02, T:0.21
Consensus pattern (23 bp):
AAAAAATACAAATTAAAAAATTA
Found at i:40970777 original size:6 final size:6
Alignment explanation
Indices: 40970766--40970829 Score: 110
Period size: 6 Copynumber: 10.7 Consensus size: 6
40970756 GCAAGAGTGG
40970766 TCGTGA TCGTGA TCGTGA TCGTGA TCGTGA TCGTGA TCGTGA TCGTGA
1 TCGTGA TCGTGA TCGTGA TCGTGA TCGTGA TCGTGA TCGTGA TCGTGA
* *
40970814 TCGTGG TCGTGG TCGT
1 TCGTGA TCGTGA TCGT
40970830 TGTCATCACC
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 57 1.00
ACGTcount: A:0.12, C:0.17, G:0.36, T:0.34
Consensus pattern (6 bp):
TCGTGA
Found at i:40981653 original size:71 final size:72
Alignment explanation
Indices: 40981559--40981710 Score: 281
Period size: 72 Copynumber: 2.1 Consensus size: 72
40981549 TCCATCCCCT
*
40981559 TTTCAAGT-TTTAACAAATATAT-AATCCATCCTTGTATCTTTGCTCTGTATTCAACCCGATCCC
1 TTTCAAGTCTTTAACAAATATATAAATCCATCCTTATATCTTTGCTCTGTATTCAACCCGATCCC
40981622 TAAACTC
66 TAAACTC
40981629 TTTCAAGTCTTTAACAAATATATAAATCCATCCTTATATCTTTGCTCTGTATTCAACCCGATCCC
1 TTTCAAGTCTTTAACAAATATATAAATCCATCCTTATATCTTTGCTCTGTATTCAACCCGATCCC
40981694 TAAACTC
66 TAAACTC
40981701 TTTCAAGTCT
1 TTTCAAGTCT
40981711 GGGCCCGAGC
Statistics
Matches: 79, Mismatches: 1, Indels: 2
0.96 0.01 0.02
Matches are distributed among these distances:
70 8 0.10
71 14 0.18
72 57 0.72
ACGTcount: A:0.29, C:0.26, G:0.07, T:0.39
Consensus pattern (72 bp):
TTTCAAGTCTTTAACAAATATATAAATCCATCCTTATATCTTTGCTCTGTATTCAACCCGATCCC
TAAACTC
Found at i:40984349 original size:24 final size:23
Alignment explanation
Indices: 40984297--40984358 Score: 58
Period size: 24 Copynumber: 2.7 Consensus size: 23
40984287 TATTTATACC
40984297 ATAATTAACATTATTTAATCTTA
1 ATAATTAACATTATTTAATCTTA
40984320 ATTAATTAAC-TTAATTATAAT-TATA
1 A-TAATTAACATT-ATT-TAATCT-TA
*
40984345 ATAATTTA-ATTATT
1 ATAATTAACATTATT
40984359 AATTAAACCA
Statistics
Matches: 33, Mismatches: 1, Indels: 10
0.75 0.02 0.23
Matches are distributed among these distances:
23 6 0.18
24 20 0.61
25 7 0.21
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (23 bp):
ATAATTAACATTATTTAATCTTA
Found at i:40989146 original size:6 final size:6
Alignment explanation
Indices: 40989135--40989225 Score: 64
Period size: 6 Copynumber: 15.7 Consensus size: 6
40989125 TTATTAAGTC
* * *
40989135 TTAAAT TTAAAT ATGAAT TTAAAT TTAAA- TTAAAT CTAAATT TTAAA-
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAA-T TTAAAT
** * * * *
40989182 ACAAAT TTAAAC TTAAA- ATAAAT TTAAAT TCAAA- ATAAAT TTAA
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAA
40989226 TCTTTAAAAT
Statistics
Matches: 63, Mismatches: 17, Indels: 10
0.70 0.19 0.11
Matches are distributed among these distances:
5 15 0.24
6 43 0.68
7 5 0.08
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.40
Consensus pattern (6 bp):
TTAAAT
Found at i:40989175 original size:35 final size:34
Alignment explanation
Indices: 40989136--40989241 Score: 122
Period size: 35 Copynumber: 3.0 Consensus size: 34
40989126 TATTAAGTCT
* *
40989136 TAAATTTAAATATGAATTTAAATTTAAATTAAATC
1 TAAATTTAAA-ATAAATTTAAATTTAAAATAAATC
* * *
40989171 TAAATTTTAAAACAAATTTAAACTTAAAATAAATT
1 TAAA-TTTAAAATAAATTTAAATTTAAAATAAATC
* *
40989206 TAAATTCAAAATAAATTTAATCTTTAAAATAAATC
1 TAAATTTAAAATAAATTTAA-ATTTAAAATAAATC
40989241 T
1 T
40989242 TAAAATGGGT
Statistics
Matches: 59, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
34 14 0.24
35 39 0.66
36 6 0.10
ACGTcount: A:0.54, C:0.06, G:0.01, T:0.40
Consensus pattern (34 bp):
TAAATTTAAAATAAATTTAAATTTAAAATAAATC
Found at i:40989236 original size:18 final size:17
Alignment explanation
Indices: 40989135--40989245 Score: 123
Period size: 17 Copynumber: 6.3 Consensus size: 17
40989125 TTATTAAGTC
*
40989135 TTAAATTTAAATATGAAT
1 TTAAATTTAAA-ATAAAT
*
40989153 TTAAATTTAAATTAAAT
1 TTAAATTTAAAATAAAT
* *
40989170 CTAAATTTTAAAACAAAT
1 TTAAA-TTTAAAATAAAT
*
40989188 TTAAACTTAAAATAAAT
1 TTAAATTTAAAATAAAT
*
40989205 TTAAATTCAAAATAAAT
1 TTAAATTTAAAATAAAT
*
40989222 TTAATCTTTAAAATAAAT
1 TTAA-ATTTAAAATAAAT
40989240 CTTAAA
1 -TTAAA
40989246 ATGGGTTTAA
Statistics
Matches: 77, Mismatches: 13, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
17 37 0.48
18 36 0.47
19 4 0.05
ACGTcount: A:0.54, C:0.05, G:0.01, T:0.40
Consensus pattern (17 bp):
TTAAATTTAAAATAAAT
Found at i:40989921 original size:195 final size:200
Alignment explanation
Indices: 40989575--40989955 Score: 522
Period size: 195 Copynumber: 1.9 Consensus size: 200
40989565 CGTTGACTTT
* * * *
40989575 GACCTGCTTCTTAGAGTCTCATCAGGATGCTGGGTTCGAAGATTTGCTCGCATTGAGCGTTGGTT
1 GACCTGCTTCTCAGAGTCTCATCAGGAAGCTGGGTTCGAAGATTTACTCGCATTGAGC---GGTC
* *
40989640 TGATTTGGTCTTCTTCTCAGTGTCTCATCAAGAAGATGACCACCTCGAATGTTTTAATTCGCTTC
63 TGAGTTGGTCTTCTTCTCA-TG-CTCATCAAGAAGATGACCACCTCGAATGTTTTAATTCACTTC
* * *
40989705 TCTGGATCTCCTCAGGAAGACGAA-TCTGGTCCATTTCTCTGTATCTTATCAGGAAGCTAACCAT
126 TCTGGATCTCCTCAAGAAGACGAATTC-GGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCAT
40989769 TTTATTGCTTC
190 TTTATTGCTTC
* *
40989780 GACCTGCTTCTCAGTGTCTCATCAGGAAGCTTGGTTCGAAGATTTACTCGCATTGAGC-G-CTGA
1 GACCTGCTTCTCAGAGTCTCATCAGGAAGCTGGGTTCGAAGATTTACTCGCATTGAGCGGTCTGA
* * **
40989843 GTTGGTGTTCTTCTC-TG-T-ATCAGGAAGATGACCACCTCGCTTGTTTTAATTCACTTCTCTGG
66 GTTGGTCTTCTTCTCATGCTCATCAAGAAGATGACCACCTCGAATGTTTTAATTCACTTCTCTGG
*
40989905 ATCTCCTCAAGAAGACGAATTCGGTCTACTTCTCTGTATCTCATCAGGAAG
131 ATCTCCTCAAGAAGACGAATTCGGTCCACTTCTCTGTATCTCATCAGGAAG
40989956 ATGACCGTCT
Statistics
Matches: 159, Mismatches: 16, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
195 84 0.53
196 3 0.02
198 2 0.01
200 16 0.10
201 1 0.01
205 53 0.33
ACGTcount: A:0.21, C:0.23, G:0.21, T:0.35
Consensus pattern (200 bp):
GACCTGCTTCTCAGAGTCTCATCAGGAAGCTGGGTTCGAAGATTTACTCGCATTGAGCGGTCTGA
GTTGGTCTTCTTCTCATGCTCATCAAGAAGATGACCACCTCGAATGTTTTAATTCACTTCTCTGG
ATCTCCTCAAGAAGACGAATTCGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATT
GCTTC
Found at i:40989992 original size:86 final size:86
Alignment explanation
Indices: 40989861--40990041 Score: 272
Period size: 86 Copynumber: 2.1 Consensus size: 86
40989851 TCTTCTCTGT
*
40989861 ATCAGGAAGATGACCACCTCGCTTGTTTTAATTCACTTCTCTGGATCTCCTCAAGAAGACGAATT
1 ATCAGGAAGATGACCACCTCGCTTGTTTTAATTCACTTCTCTGGATCTCCTCAAGAAGACAAATT
*
40989926 CGGTCTACTTCTCTGTATCTC
66 CGGTCCACTTCTCTGTATCTC
** * ** *
40989947 ATCAGGAAGATGACCGTCTCGGTTGTTTTAATTTGCTTCTCTGGATCTCCTCAGGAAGACAAATT
1 ATCAGGAAGATGACCACCTCGCTTGTTTTAATTCACTTCTCTGGATCTCCTCAAGAAGACAAATT
* *
40990012 TGGTCCACTTCTCTGTATCTT
66 CGGTCCACTTCTCTGTATCTC
40990033 ATCAGGAAG
1 ATCAGGAAG
40990042 TTGGGGTTCG
Statistics
Matches: 85, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
86 85 1.00
ACGTcount: A:0.23, C:0.24, G:0.19, T:0.34
Consensus pattern (86 bp):
ATCAGGAAGATGACCACCTCGCTTGTTTTAATTCACTTCTCTGGATCTCCTCAAGAAGACAAATT
CGGTCCACTTCTCTGTATCTC
Found at i:40990442 original size:76 final size:76
Alignment explanation
Indices: 40990330--40990892 Score: 919
Period size: 76 Copynumber: 7.4 Consensus size: 76
40990320 TGTCTTGCTC
* * *
40990330 TTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTTACTTCATTTTCAAAGATAAAGACTT
1 TTACTTCAATTTCAAGAGGATAGGAAATGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTT
40990395 GATATCCAGCT
66 GATATCCAGCT
*
40990406 TTACTTCAATTTCAAGAGGATAGGAAATGATCTTGCTCTTACTTAAATTTCAGAGATAAAGACTT
1 TTACTTCAATTTCAAGAGGATAGGAAATGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTT
* *
40990471 GTTATCCAACT
66 GATATCCAGCT
* * *
40990482 CTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTTACTTTAATTTCAGAGATAAAGACTT
1 TTACTTCAATTTCAAGAGGATAGGAAATGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTT
40990547 GATATCCAGCT
66 GATATCCAGCT
* *
40990558 TTACTTCAATTTCAAGAGGATAGGAAATGATCTTGCTCTTACTTCAATTTCAGAAATAGAGACTT
1 TTACTTCAATTTCAAGAGGATAGGAAATGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTT
* *
40990623 GTTATCCAACT
66 GATATCCAGCT
* *
40990634 CTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTT
1 TTACTTCAATTTCAAGAGGATAGGAAATGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTT
40990699 GATATCCAGCT
66 GATATCCAGCT
* *
40990710 TTACTTCAATTTCAAGAGGATAGGAAATGATCTTGCTCTTACTTCAATTTCAGAGATAGAGACTA
1 TTACTTCAATTTCAAGAGGATAGGAAATGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTT
40990775 GATATCCAGCT
66 GATATCCAGCT
* *
40990786 TTACTTCAATTTCAAGAGGATAGGAAATGATCTTGCTCTTACTTCAATTTCAAAGATAGAGACTT
1 TTACTTCAATTTCAAGAGGATAGGAAATGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTT
* *
40990851 GCTATCCAACT
66 GATATCCAGCT
* *
40990862 TTACTTCAATTTCAATAGGATAGGGAATGAT
1 TTACTTCAATTTCAAGAGGATAGGAAATGAT
40990893 GTTTGATTTA
Statistics
Matches: 453, Mismatches: 34, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
76 453 1.00
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (76 bp):
TTACTTCAATTTCAAGAGGATAGGAAATGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTT
GATATCCAGCT
Found at i:40992979 original size:29 final size:30
Alignment explanation
Indices: 40992942--40993262 Score: 161
Period size: 30 Copynumber: 10.8 Consensus size: 30
40992932 GGCAAAAACA
40992942 AGGTCAAAAATGAAATTTTGGAAAG-TTCGG
1 AGGTC-AAAATGAAATTTTGGAAAGTTTCGG
*
40992972 AGGT-AAAATGGTAAGTTTTGGTGAAA---TC-G
1 AGGTCAAAAT-G-AAATTTT-G-GAAAGTTTCGG
* * * *
40993001 AGGTTAAAAATGAGATTTAGGGAAGTTT-GG
1 AGG-TCAAAATGAAATTTTGGAAAGTTTCGG
* * *
40993031 GGGT-AAAATGGTAATTTTTGAAAGTTTC-G
1 AGGTCAAAAT-GAAATTTTGGAAAGTTTCGG
* * *
40993060 AGGCCAAAAT-ATAATTTTAGAAAAGTTTTGG
1 AGGTCAAAATGA-AATTTT-GGAAAGTTTCGG
* *
40993091 -GGTCAAAATGTAATTTTAGAAAGGTTTCGG
1 AGGTCAAAATGAAATTTTGGAAA-GTTTCGG
* *
40993121 -GGTCAAAATGTAATTTTGGAAAAGTTTTGG
1 AGGTCAAAATGAAATTTTGG-AAAGTTTCGG
** *
40993151 -GGTCAAAATTTAATTTTGGTAAAGTTTTGG
1 AGGTCAAAATGAAATTTTGG-AAAGTTTCGG
* * **
40993181 -GGTCAAAATGTAATTTTGAAAAAGTTTTAG
1 AGGTCAAAATGAAATTTTG-GAAAGTTTCGG
* **
40993211 -GGTCAAAATGTAATTTTGGGAAAGTTTTAG
1 AGGTCAAAATGAAATTTT-GGAAAGTTTCGG
* *
40993241 -GGTTAAAATGTAATTTTGGAAA
1 AGGTCAAAATGAAATTTTGGAAA
40993263 AGTTAAAGGG
Statistics
Matches: 239, Mismatches: 31, Indels: 43
0.76 0.10 0.14
Matches are distributed among these distances:
27 3 0.01
28 11 0.05
29 39 0.16
30 171 0.72
31 11 0.05
32 4 0.02
ACGTcount: A:0.36, C:0.04, G:0.26, T:0.35
Consensus pattern (30 bp):
AGGTCAAAATGAAATTTTGGAAAGTTTCGG
Found at i:40993061 original size:59 final size:56
Alignment explanation
Indices: 40992854--40993112 Score: 188
Period size: 59 Copynumber: 4.4 Consensus size: 56
40992844 TGGGTTTTTA
*
40992854 GGGGTAAAATGGTAATTTTTGTGAAATCG-GGGCTAAAAATG-GAATTT-GGAAAGTTTG
1 GGGGTAAAATGGTAA-TTTT-TGAAATCGAGGTC-AAAAATGAG-ATTTAGGAAAGTTTG
* * * * * * *
40992911 GGGAATAAAATGGTAAATTTTGGCAAAAACAAGGTCAAAAATGAAATTTTGGAAAGTTCG
1 GGG-GTAAAATGGT-AATTTTTG--AAATCGAGGTCAAAAATGAGATTTAGGAAAGTTTG
* * *
40992971 GAGGTAAAATGGTAAGTTTTGGTGAAATCGAGGTTAAAAATGAGATTTAGGGAAGTTTG
1 GGGGTAAAATGGTAA-TTTT--TGAAATCGAGGTCAAAAATGAGATTTAGGAAAGTTTG
* * *
40993030 GGGGTAAAATGGTAATTTTTGAAAGTTTCGAGGCCAAAATAT-A-ATTTTAGAAAAGTTTT
1 GGGGTAAAATGGTAATTTTTGAAA---TCGAGGTCAAAA-ATGAGA-TTTAGGAAAGTTTG
*
40993089 GGGGTCAAAAT-GTAATTTTAGAAA
1 GGGGT-AAAATGGTAATTTTTGAAA
40993113 GGTTTCGGGG
Statistics
Matches: 162, Mismatches: 24, Indels: 30
0.75 0.11 0.14
Matches are distributed among these distances:
56 5 0.03
57 4 0.02
58 20 0.12
59 111 0.69
60 21 0.13
61 1 0.01
ACGTcount: A:0.38, C:0.04, G:0.27, T:0.31
Consensus pattern (56 bp):
GGGGTAAAATGGTAATTTTTGAAATCGAGGTCAAAAATGAGATTTAGGAAAGTTTG
Found at i:40993085 original size:30 final size:30
Alignment explanation
Indices: 40993023--40993347 Score: 336
Period size: 30 Copynumber: 10.9 Consensus size: 30
40993013 AGATTTAGGG
* *
40993023 AAGTTTGGGGGT-AAAATGGTAATTTTTG-A
1 AAGTTTTGGGGTCAAAAT-GTAATTTTAGAA
* * * *
40993052 AAGTTTCGAGGCCAAAATATAATTTTAGAA
1 AAGTTTTGGGGTCAAAATGTAATTTTAGAA
40993082 AAGTTTTGGGGTCAAAATGTAATTTTAGAA
1 AAGTTTTGGGGTCAAAATGTAATTTTAGAA
* * *
40993112 AGGTTTCGGGGTCAAAATGTAATTTTGGAA
1 AAGTTTTGGGGTCAAAATGTAATTTTAGAA
* * *
40993142 AAGTTTTGGGGTCAAAATTTAATTTTGGTA
1 AAGTTTTGGGGTCAAAATGTAATTTTAGAA
40993172 AAGTTTTGGGGTCAAAATGTAATTTT-GAAA
1 AAGTTTTGGGGTCAAAATGTAATTTTAG-AA
* * *
40993202 AAGTTTTAGGGTCAAAATGTAATTTTGGGA
1 AAGTTTTGGGGTCAAAATGTAATTTTAGAA
* * *
40993232 AAGTTTTAGGGTTAAAATGTAATTTTGGAA
1 AAGTTTTGGGGTCAAAATGTAATTTTAGAA
*** *
40993262 AAGTTAAAGGGTTAAAATGTAATTTTTAG-A
1 AAGTTTTGGGGTCAAAATGTAA-TTTTAGAA
* * *
40993292 AAGTTTTAGGGTTAAAATATAATTTTCAG-A
1 AAGTTTTGGGGTCAAAATGTAATTTT-AGAA
* *
40993322 AAGTTTTAGGGTCGAAATGTAATTTT
1 AAGTTTTGGGGTCAAAATGTAATTTT
40993348 TGGACAATTT
Statistics
Matches: 259, Mismatches: 31, Indels: 11
0.86 0.10 0.04
Matches are distributed among these distances:
29 22 0.08
30 231 0.89
31 6 0.02
ACGTcount: A:0.36, C:0.03, G:0.23, T:0.38
Consensus pattern (30 bp):
AAGTTTTGGGGTCAAAATGTAATTTTAGAA
Found at i:40995187 original size:17 final size:16
Alignment explanation
Indices: 40995133--40995193 Score: 68
Period size: 17 Copynumber: 3.7 Consensus size: 16
40995123 TTAAAACCAT
*
40995133 TTTAAATTTAATTAAA
1 TTTAAATTTAAATAAA
* *
40995149 TTTAAATTCAAAACAAA
1 TTTAAATT-TAAATAAA
40995166 TTTAAATTTAAATAAA
1 TTTAAATTTAAATAAA
*
40995182 TCTTAAAATTAA
1 T-TTAAATTTAA
40995194 TTCAAACTTA
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
16 15 0.41
17 22 0.59
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (16 bp):
TTTAAATTTAAATAAA
Found at i:40995203 original size:17 final size:17
Alignment explanation
Indices: 40995183--40995216 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
40995173 TTAAATAAAT
*
40995183 CTTAAAATTAATTCAAA
1 CTTAAAATAAATTCAAA
*
40995200 CTTAATATAAATTCAAA
1 CTTAAAATAAATTCAAA
40995217 AATCTCAAGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (17 bp):
CTTAAAATAAATTCAAA
Found at i:40995497 original size:91 final size:91
Alignment explanation
Indices: 40995353--40995898 Score: 896
Period size: 91 Copynumber: 6.0 Consensus size: 91
40995343 AGTAGGGTTT
* * * * * * * *
40995353 GATGTCGGGGTTTTATCTTGCTCTTACTTCAATTTCAGAGAGATAAAGACTTGATATCCATCTTT
1 GATGTCGGTGCTTCATCTTGCTCTTACTTCAACTTCAGAGAGACAAAGGCTTGATATCCAGCTCT
* *
40995418 ACTAT-AACTTCAAAAGGATAGGAAAA
66 ACT-TCAATTTCAAGAGGATAGGAAAA
* *
40995444 GATGTCGGTGCTTCATCTTGTTCTTACTTCAATTTCAGAGAGACAAAGGCTTGATATCCAGCTCT
1 GATGTCGGTGCTTCATCTTGCTCTTACTTCAACTTCAGAGAGACAAAGGCTTGATATCCAGCTCT
40995509 ACTTCAATTTCAAGAGGATAGGAAAA
66 ACTTCAATTTCAAGAGGATAGGAAAA
40995535 GATGTCGGTGCTTCATCTTGCTCTTACTTCAACTTCAGAGAGACAAAGGCTTGATATCCAGCTCT
1 GATGTCGGTGCTTCATCTTGCTCTTACTTCAACTTCAGAGAGACAAAGGCTTGATATCCAGCTCT
40995600 ACTTCAATTTCAAGAGGATAGGAAAA
66 ACTTCAATTTCAAGAGGATAGGAAAA
*
40995626 GATGTCGGTGCTTCATCTTGTTCTTACTTCAACTTCAGAGAGACAAAGGCTTGATATCCAGCTCT
1 GATGTCGGTGCTTCATCTTGCTCTTACTTCAACTTCAGAGAGACAAAGGCTTGATATCCAGCTCT
*
40995691 ACTTCAATTTCAAGAGGATAGGGAAA
66 ACTTCAATTTCAAGAGGATAGGAAAA
40995717 GATGTCGGTGCTTCATCTTGCTCTTACTTCAACTTCAGAGAGACAAAGGCTTGATATCCAGCTCT
1 GATGTCGGTGCTTCATCTTGCTCTTACTTCAACTTCAGAGAGACAAAGGCTTGATATCCAGCTCT
*
40995782 ACTTCAATTTCAAGAGGAATAGGAAAG
66 ACTTCAATTTCAAGAGG-ATAGGAAAA
* *
40995809 GATGTCGGTGCTTCATCTTGCTCTTACTTCAATTTCAGAGAGATAAAGGCTTGATATCCAGCTCT
1 GATGTCGGTGCTTCATCTTGCTCTTACTTCAACTTCAGAGAGACAAAGGCTTGATATCCAGCTCT
* *
40995874 ACTTCAATTTCAAGCGGTTAGGAAA
66 ACTTCAATTTCAAGAGGATAGGAAA
40995899 TAATCTTGCT
Statistics
Matches: 432, Mismatches: 21, Indels: 4
0.95 0.05 0.01
Matches are distributed among these distances:
90 1 0.00
91 345 0.80
92 86 0.20
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.32
Consensus pattern (91 bp):
GATGTCGGTGCTTCATCTTGCTCTTACTTCAACTTCAGAGAGACAAAGGCTTGATATCCAGCTCT
ACTTCAATTTCAAGAGGATAGGAAAA
Found at i:40995953 original size:38 final size:39
Alignment explanation
Indices: 40995911--40996173 Score: 133
Period size: 38 Copynumber: 7.3 Consensus size: 39
40995901 ATCTTGCTCT
40995911 TACTTCAATTTCAGAGATGAATG-CTTGATATCCAACTC
1 TACTTCAATTTCAGAGATGAATGACTTGATATCCAACTC
* * * *
40995949 TACTTCAATTTCA-AG-CGGATGAC--G-T-TGC-TCT-
1 TACTTCAATTTCAGAGATGAATGACTTGATATCCAACTC
* *
40995980 TACTTCAATTTCAGAGAT-AAAGACTTGTTATCCAACTC
1 TACTTCAATTTCAGAGATGAATGACTTGATATCCAACTC
** * ** * ***
40996018 TACTTCAATTTCA-AGCGGATAGGA--AAAGATCTTGCTC
1 TACTTCAATTTCAGAGATGA-ATGACTTGATATCCAACTC
*
40996055 TTACTTCAATTTCAGAGAT-AAAGACTTGATATCCAACTC
1 -TACTTCAATTTCAGAGATGAATGACTTGATATCCAACTC
* *
40996094 TACTTCAATTTCA-AG-CGGATGAC--G-T-T---ACTC
1 TACTTCAATTTCAGAGATGAATGACTTGATATCCAACTC
* * * *
40996124 TTACTTCAATTTTAGAGATTAA-GACGTGTTATCCAACTC
1 -TACTTCAATTTCAGAGATGAATGACTTGATATCCAACTC
40996163 TACTTCAATTT
1 TACTTCAATTT
40996174 TAAGCGGATA
Statistics
Matches: 164, Mismatches: 35, Indels: 52
0.65 0.14 0.21
Matches are distributed among these distances:
30 4 0.02
31 25 0.15
32 13 0.08
33 4 0.02
34 4 0.02
35 4 0.02
36 7 0.04
37 22 0.13
38 65 0.40
39 16 0.10
ACGTcount: A:0.31, C:0.21, G:0.14, T:0.35
Consensus pattern (39 bp):
TACTTCAATTTCAGAGATGAATGACTTGATATCCAACTC
Found at i:40996015 original size:69 final size:72
Alignment explanation
Indices: 40995826--40996263 Score: 532
Period size: 76 Copynumber: 6.0 Consensus size: 72
40995816 GTGCTTCATC
* * *
40995826 TTGCTCTTACTTCAATTTCAGAGAGATAAAGGCTTGATATCCAGCTCTACTTCAATTTCAAGCGG
1 TTGCTCTTACTTCAATTTC--AGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGCGG
* *
40995891 TTAGGAAATAA
64 ATA-GAAA-GA
* *
40995902 TCTTGCTCTTACTTCAATTTCAGAGATGAATG-CTTGATATCCAACTCTACTTCAATTTCAAGCG
1 --TTGCTCTTACTTCAATTTCAGAGAT-AAAGACTTGTTATCCAACTCTACTTCAATTTCAAGCG
*
40995966 GAT-G-ACG-
63 GATAGAAAGA
40995973 TTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGCGGAT
1 TTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGCGGAT
40996038 AGGAAAAGA
66 A-G-AAAGA
*
40996047 TCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTCTACTTCAATTTCAAGCGG
1 --TTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGCGG
*
40996112 AT-G-ACG-
64 ATAGAAAGA
* * * * *
40996118 TTACTCTTACTTCAATTTTAGAGATTAAGACGTGTTATCCAACTCTACTTCAATTTTAAGCGGAT
1 TTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGCGGAT
40996183 AGGAAAAGA
66 A-G-AAAGA
*
40996192 TCTTGCTCCTACTTCAATTTCAGAGATAAAGACTTGTTATCC-ACTCTACTTCAATTTCAAGCGG
1 --TTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGCGG
40996256 ATTAGAAA
64 A-TAGAAA
40996264 TGATCTTGTT
Statistics
Matches: 320, Mismatches: 23, Indels: 38
0.84 0.06 0.10
Matches are distributed among these distances:
68 3 0.01
69 118 0.37
71 2 0.01
72 2 0.01
73 5 0.02
74 5 0.02
75 23 0.07
76 140 0.44
77 3 0.01
78 19 0.06
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.34
Consensus pattern (72 bp):
TTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGCGGAT
AGAAAGA
Found at i:40996091 original size:145 final size:145
Alignment explanation
Indices: 40995826--40996257 Score: 699
Period size: 145 Copynumber: 3.0 Consensus size: 145
40995816 GTGCTTCATC
* * *
40995826 TTGCTCTTACTTCAATTTCAGAGAGATAAAGGCTTGATATCCAGCTCTACTTCAATTTCAAGCGG
1 TTGCTCTTACTTCAATTTC--AGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGCGG
* *
40995891 TTAGGAAATA-ATCTTGCTCTTACTTCAATTTCAGAGATGAATG-CTTGATATCCAACTCTACTT
64 ATAGGAAA-AGATCTTGCTCTTACTTCAATTTCAGAGAT-AAAGACTTGATATCCAACTCTACTT
40995954 CAATTTCAAGCGGATGACG
127 CAATTTCAAGCGGATGACG
40995973 TTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGCGGAT
1 TTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGCGGAT
40996038 AGGAAAAGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTCTACTTCAAT
66 AGGAAAAGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTCTACTTCAAT
40996103 TTCAAGCGGATGACG
131 TTCAAGCGGATGACG
* * * * *
40996118 TTACTCTTACTTCAATTTTAGAGATTAAGACGTGTTATCCAACTCTACTTCAATTTTAAGCGGAT
1 TTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGCGGAT
* *
40996183 AGGAAAAGATCTTGCTCCTACTTCAATTTCAGAGATAAAGACTTGTTATCC-ACTCTACTTCAAT
66 AGGAAAAGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTCTACTTCAAT
40996247 TTCAAGCGGAT
131 TTCAAGCGGAT
40996258 TAGAAATGAT
Statistics
Matches: 271, Mismatches: 12, Indels: 7
0.93 0.04 0.02
Matches are distributed among these distances:
144 28 0.10
145 224 0.83
147 19 0.07
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.34
Consensus pattern (145 bp):
TTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGCGGAT
AGGAAAAGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAACTCTACTTCAAT
TTCAAGCGGATGACG
Found at i:41008194 original size:59 final size:58
Alignment explanation
Indices: 41007994--41008194 Score: 199
Period size: 59 Copynumber: 3.4 Consensus size: 58
41007984 AATTTAGGTT
* *
41007994 TTTAGGGGTAAAATGGTAATTTTT-GTGAAATTGGGGCTAAAAATGGAATTTGGAAAG
1 TTTAGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTGGAAAG
* * ** * ** * *
41008051 TTTAGGGATTAAAATGGTAAATTTTGGCAAAAACAAGGTCAAAAATGAAATTTTGGAAAG
1 TTTAGGG-GTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAA-TTTGGAAAG
* * * * * *
41008111 -TTCGGAGGCAAAACGGTAAGTTTTGGTGAAATCGGGGTTAAAAATGGGATTTAGGGAAG
1 TTTAGG-GGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTT-GGAAAG
41008170 TTTAGGGGTAAAATGGTAATTTTTG
1 TTTAGGGGTAAAATGGTAATTTTTG
41008195 AAAGTTTCGG
Statistics
Matches: 109, Mismatches: 29, Indels: 10
0.74 0.20 0.07
Matches are distributed among these distances:
57 7 0.06
58 18 0.17
59 70 0.64
60 14 0.13
ACGTcount: A:0.36, C:0.04, G:0.29, T:0.31
Consensus pattern (58 bp):
TTTAGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTGGAAAG
Found at i:41008275 original size:60 final size:59
Alignment explanation
Indices: 41008167--41008311 Score: 186
Period size: 60 Copynumber: 2.4 Consensus size: 59
41008157 GGATTTAGGG
* * ***
41008167 AAGTTTAGGGGT-AAAATGGTAATTTTTGAAAGTTTCGGGGTCAAAATATAA-TTTTAGAA
1 AAGTTTTGGGGTCAAAAT-GTAATTTTGGAAAGTTAAAGGGTCAAAATATAATTTTTAG-A
*
41008226 AAGTTTTGGGGTCAAAATGTAATTTTGGAAAAGTTAAAGGGTTAAAATATAATTTTTAGA
1 AAGTTTTGGGGTCAAAATGTAATTTTGG-AAAGTTAAAGGGTCAAAATATAATTTTTAGA
*
41008286 AAGTTTTGGGGTCGAAATGTAATTTT
1 AAGTTTTGGGGTCAAAATGTAATTTT
41008312 TGGACAATTT
Statistics
Matches: 76, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
59 20 0.26
60 50 0.66
61 6 0.08
ACGTcount: A:0.37, C:0.03, G:0.23, T:0.37
Consensus pattern (59 bp):
AAGTTTTGGGGTCAAAATGTAATTTTGGAAAGTTAAAGGGTCAAAATATAATTTTTAGA
Found at i:41008312 original size:30 final size:31
Alignment explanation
Indices: 41008167--41008312 Score: 151
Period size: 30 Copynumber: 4.9 Consensus size: 31
41008157 GGATTTAGGG
41008167 AAGTTTAGGGGT-AAAATGGTAATTTTT-G-A
1 AAGTTTAGGGGTCAAAAT-GTAATTTTTAGAA
* *
41008196 AAGTTTCGGGGTCAAAATATAA-TTTTAGAA
1 AAGTTTAGGGGTCAAAATGTAATTTTTAGAA
* *
41008226 AAGTTTTGGGGTCAAAATGTAA-TTTTGGAA
1 AAGTTTAGGGGTCAAAATGTAATTTTTAGAA
* * * *
41008256 AAGTTAAAGGGTTAAAATATAATTTTTAG-A
1 AAGTTTAGGGGTCAAAATGTAATTTTTAGAA
* *
41008286 AAGTTTTGGGGTCGAAATGTAATTTTT
1 AAGTTTAGGGGTCAAAATGTAATTTTT
41008313 GGACAATTTA
Statistics
Matches: 96, Mismatches: 17, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
28 4 0.04
29 15 0.16
30 72 0.75
31 5 0.05
ACGTcount: A:0.36, C:0.03, G:0.23, T:0.38
Consensus pattern (31 bp):
AAGTTTAGGGGTCAAAATGTAATTTTTAGAA
Found at i:41010137 original size:16 final size:16
Alignment explanation
Indices: 41010116--41010161 Score: 65
Period size: 16 Copynumber: 2.8 Consensus size: 16
41010106 TTAAAACCAT
41010116 TTTAAATTTAATTAAA
1 TTTAAATTTAATTAAA
*
41010132 TTTAAATTTAAATAAA
1 TTTAAATTTAATTAAA
*
41010148 TCTTAAAATTAATT
1 T-TTAAATTTAATT
41010162 CAAAATTAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
16 16 0.62
17 10 0.38
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (16 bp):
TTTAAATTTAATTAAA
Found at i:41010170 original size:17 final size:17
Alignment explanation
Indices: 41010150--41010183 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
41010140 TAAATAAATC
*
41010150 TTAAAATTAATTCAAAA
1 TTAAAATAAATTCAAAA
*
41010167 TTAATATAAATTCAAAA
1 TTAAAATAAATTCAAAA
41010184 ATCTCAAGTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (17 bp):
TTAAAATAAATTCAAAA
Found at i:41010664 original size:29 final size:28
Alignment explanation
Indices: 41010632--41010686 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
41010622 GACCTCTCCT
*
41010632 TTTTATTTTGTTTTTCTTCTTGTTTTTGC
1 TTTTATTTTCTTTTTCTTCTT-TTTTTGC
*
41010661 TTTTCTTTTCTTTTTCTTCTTTTTTT
1 TTTTATTTTCTTTTTCTTCTTTTTTT
41010687 ATTTGTTCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 5 0.21
29 19 0.79
ACGTcount: A:0.02, C:0.13, G:0.05, T:0.80
Consensus pattern (28 bp):
TTTTATTTTCTTTTTCTTCTTTTTTTGC
Found at i:41010695 original size:29 final size:29
Alignment explanation
Indices: 41010632--41010696 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
41010622 GACCTCTCCT
* * *
41010632 TTTTATTTTGTTTTTCTTCTTGTTTTTGC
1 TTTTCTTTTCTTTTTCTTCTTGTTTTTAC
*
41010661 TTTTCTTTTCTTTTTCTTCTT-TTTTTAT
1 TTTTCTTTTCTTTTTCTTCTTGTTTTTAC
41010689 TTGTTCTT
1 TT-TTCTT
41010697 CTTCATTGTA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 7 0.23
29 24 0.77
ACGTcount: A:0.03, C:0.12, G:0.06, T:0.78
Consensus pattern (29 bp):
TTTTCTTTTCTTTTTCTTCTTGTTTTTAC
Found at i:41011526 original size:13 final size:14
Alignment explanation
Indices: 41011508--41011546 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
41011498 CCCTTTTCTC
41011508 TTTTTTTTGTT-TG
1 TTTTTTTTGTTATG
41011521 -TTTTTTTGTTATG
1 TTTTTTTTGTTATG
*
41011534 TTTTTTTCGTTAT
1 TTTTTTTTGTTAT
41011547 AACACGTCGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
12 10 0.43
13 2 0.09
14 11 0.48
ACGTcount: A:0.05, C:0.03, G:0.13, T:0.79
Consensus pattern (14 bp):
TTTTTTTTGTTATG
Found at i:41011545 original size:14 final size:13
Alignment explanation
Indices: 41011509--41011546 Score: 60
Period size: 12 Copynumber: 2.9 Consensus size: 13
41011499 CCTTTTCTCT
41011509 TTTTTTTGTT-TG
1 TTTTTTTGTTATG
41011521 TTTTTTTGTTATG
1 TTTTTTTGTTATG
41011534 TTTTTTTCGTTAT
1 TTTTTTT-GTTAT
41011547 AACACGTCGA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 10 0.42
13 9 0.38
14 5 0.21
ACGTcount: A:0.05, C:0.03, G:0.13, T:0.79
Consensus pattern (13 bp):
TTTTTTTGTTATG
Found at i:41017733 original size:6 final size:6
Alignment explanation
Indices: 41017722--41017812 Score: 64
Period size: 6 Copynumber: 15.7 Consensus size: 6
41017712 TTATTAAGTC
* * *
41017722 TTAAAT TTAAAT ATGAAT TTAAAT TTAAA- TTAAAT CTAAATT TTAAA-
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAA-T TTAAAT
** * * * *
41017769 ACAAAT TTAAAC TTAAA- ATAAAT TTAAAT TCAAA- ATAAAT TTAA
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAA
41017813 TCTTTAAAAT
Statistics
Matches: 63, Mismatches: 17, Indels: 10
0.70 0.19 0.11
Matches are distributed among these distances:
5 15 0.24
6 43 0.68
7 5 0.08
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.40
Consensus pattern (6 bp):
TTAAAT
Found at i:41017762 original size:35 final size:34
Alignment explanation
Indices: 41017723--41017828 Score: 122
Period size: 35 Copynumber: 3.0 Consensus size: 34
41017713 TATTAAGTCT
* *
41017723 TAAATTTAAATATGAATTTAAATTTAAATTAAATC
1 TAAATTTAAA-ATAAATTTAAATTTAAAATAAATC
* * *
41017758 TAAATTTTAAAACAAATTTAAACTTAAAATAAATT
1 TAAA-TTTAAAATAAATTTAAATTTAAAATAAATC
* *
41017793 TAAATTCAAAATAAATTTAATCTTTAAAATAAATC
1 TAAATTTAAAATAAATTTAA-ATTTAAAATAAATC
41017828 T
1 T
41017829 TAAAATGAGT
Statistics
Matches: 59, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
34 14 0.24
35 39 0.66
36 6 0.10
ACGTcount: A:0.54, C:0.06, G:0.01, T:0.40
Consensus pattern (34 bp):
TAAATTTAAAATAAATTTAAATTTAAAATAAATC
Found at i:41017823 original size:18 final size:17
Alignment explanation
Indices: 41017722--41017832 Score: 123
Period size: 17 Copynumber: 6.3 Consensus size: 17
41017712 TTATTAAGTC
*
41017722 TTAAATTTAAATATGAAT
1 TTAAATTTAAA-ATAAAT
*
41017740 TTAAATTTAAATTAAAT
1 TTAAATTTAAAATAAAT
* *
41017757 CTAAATTTTAAAACAAAT
1 TTAAA-TTTAAAATAAAT
*
41017775 TTAAACTTAAAATAAAT
1 TTAAATTTAAAATAAAT
*
41017792 TTAAATTCAAAATAAAT
1 TTAAATTTAAAATAAAT
*
41017809 TTAATCTTTAAAATAAAT
1 TTAA-ATTTAAAATAAAT
41017827 CTTAAA
1 -TTAAA
41017833 ATGAGTTTAA
Statistics
Matches: 77, Mismatches: 13, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
17 37 0.48
18 36 0.47
19 4 0.05
ACGTcount: A:0.54, C:0.05, G:0.01, T:0.40
Consensus pattern (17 bp):
TTAAATTTAAAATAAAT
Found at i:41023055 original size:97 final size:96
Alignment explanation
Indices: 41022888--41023073 Score: 232
Period size: 97 Copynumber: 1.9 Consensus size: 96
41022878 AAAAAGGATG
* * * * *
41022888 TTCGATTATCTCGTTTTGAAAAAAGTCGCACCTAGTAAGTTTAGGTACAAATTTTCAGAATCAGA
1 TTCGATTATCTCGATTTGAAAAAAATCGCACCTAGTAAGTTAAGGCACAAATTTTCAAAATCAGA
* *
41022953 GAT-AAAGAAACATTGCCTCGATTTAATGATA
66 AATAAAAG-AACATTGCATCGATTTAATGATA
* **
41022984 TTCGATTATTTCGATTTGAAAAAAAATCGTGCCTAGTAAGTTAAGGCACAAATTTTCAAAACTC-
1 TTCGATTATCTCGATTTG-AAAAAAATCGCACCTAGTAAGTTAAGGCACAAATTTTCAAAA-TCA
*
41023048 GAAATAAAAGAATATTGCATCGATTT
64 GAAATAAAAGAACATTGCATCGATTT
41023074 TAAAGCTTTT
Statistics
Matches: 76, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
96 16 0.21
97 54 0.71
98 6 0.08
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (96 bp):
TTCGATTATCTCGATTTGAAAAAAATCGCACCTAGTAAGTTAAGGCACAAATTTTCAAAATCAGA
AATAAAAGAACATTGCATCGATTTAATGATA
Found at i:41023467 original size:29 final size:29
Alignment explanation
Indices: 41023435--41023531 Score: 99
Period size: 29 Copynumber: 3.3 Consensus size: 29
41023425 TCAAAAACAA
* *
41023435 AATTTTTGGATGTCTGGGGGTAAAATGGT
1 AATTTTTGGAAGTTTGGGGGTAAAATGGT
* * *
41023464 AATTTTTGAAAGTTTTAGGGTTAAAAATGGT
1 AATTTTTGGAAG-TTTGGGGGT-AAAATGGT
*
41023495 -A-TTTTGGAAAGTTTGAGGGTAAAATGGT
1 AATTTTTGG-AAGTTTGGGGGTAAAATGGT
41023523 AATTTTTGG
1 AATTTTTGG
41023532 TGAAATCGAG
Statistics
Matches: 54, Mismatches: 9, Indels: 9
0.75 0.12 0.12
Matches are distributed among these distances:
28 8 0.15
29 22 0.41
30 16 0.30
31 8 0.15
ACGTcount: A:0.30, C:0.01, G:0.29, T:0.40
Consensus pattern (29 bp):
AATTTTTGGAAGTTTGGGGGTAAAATGGT
Found at i:41023499 original size:30 final size:31
Alignment explanation
Indices: 41023456--41023637 Score: 152
Period size: 30 Copynumber: 6.1 Consensus size: 31
41023446 GTCTGGGGGT
*
41023456 AAAATGGTAATTTTTGAAAGTTTTAGGGTTA
1 AAAATGGTAATTTTTGAAAGTTTGAGGGTTA
*
41023487 AAAATGGT-ATTTTGGAAAGTTTGAGGG-T-
1 AAAATGGTAATTTTTGAAAGTTTGAGGGTTA
* * *
41023515 AAAATGGTAATTTTTGGTGAAA--TCGA-GATCA
1 AAAATGGTAA-TTTT--TGAAAGTTTGAGGGTTA
* * *
41023546 AAAATAG-AATTTTGGAAAG-TT-AGGGGT-
1 AAAATGGTAATTTTTGAAAGTTTGAGGGTTA
*
41023573 AAAATGGTAATTTTTGAAAGTTTTAGGGTTA
1 AAAATGGTAATTTTTGAAAGTTTGAGGGTTA
*
41023604 AAAATGG-AATTTTTAGAAGAGTTTGGGGGTTA
1 AAAATGGTAATTTTT-GAA-AGTTTGAGGGTTA
41023636 AA
1 AA
41023638 TATGATTTTT
Statistics
Matches: 120, Mismatches: 17, Indels: 27
0.73 0.10 0.16
Matches are distributed among these distances:
27 11 0.09
28 21 0.17
29 9 0.08
30 38 0.32
31 24 0.20
32 17 0.14
ACGTcount: A:0.37, C:0.01, G:0.26, T:0.36
Consensus pattern (31 bp):
AAAATGGTAATTTTTGAAAGTTTGAGGGTTA
Found at i:41023518 original size:59 final size:58
Alignment explanation
Indices: 41023451--41023616 Score: 212
Period size: 59 Copynumber: 2.8 Consensus size: 58
41023441 TGGATGTCTG
* *
41023451 GGGGTAAAATGGTAATTTTTGAAAGTTTTAGGGTTAAAAATGGTATTTTGGAAAGTTT
1 GGGGTAAAATGGTAATTTTTGAAAGTTTTAGGGTTAAAAATGGAATTTTGGAAAGTTA
** * * *
41023509 GAGGGTAAAATGGTAATTTTTGGTGAAA--TCGA-GATCAAAAATAGAATTTTGGAAAGTTA
1 G-GGGTAAAATGGTAA-TTTT--TGAAAGTTTTAGGGTTAAAAATGGAATTTTGGAAAGTTA
41023568 GGGGTAAAATGGTAATTTTTGAAAGTTTTAGGGTTAAAAATGGAATTTT
1 GGGGTAAAATGGTAATTTTTGAAAGTTTTAGGGTTAAAAATGGAATTTT
41023617 TAGAAGAGTT
Statistics
Matches: 89, Mismatches: 12, Indels: 14
0.77 0.10 0.12
Matches are distributed among these distances:
55 5 0.06
57 6 0.07
58 30 0.34
59 37 0.42
60 6 0.07
62 5 0.06
ACGTcount: A:0.36, C:0.01, G:0.27, T:0.36
Consensus pattern (58 bp):
GGGGTAAAATGGTAATTTTTGAAAGTTTTAGGGTTAAAAATGGAATTTTGGAAAGTTA
Found at i:41024753 original size:3 final size:3
Alignment explanation
Indices: 41024745--41024848 Score: 66
Period size: 3 Copynumber: 33.3 Consensus size: 3
41024735 TTCCTTCTTT
* * * *
41024745 TTA TTA TTA TTTA TTA TTA ATA ATA ATA TTA TTA TTA ATA TTCA TTAA
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TT-A
** * * * *
41024793 TGC TTA TTA TTA TTGA -TA TTCA TTA TTA GTG TTA TTA GTA ATA TTA
1 TTA TTA TTA TTA TT-A TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA
41024839 TTA TTA TTA T
1 TTA TTA TTA T
41024849 CATTGATGAT
Statistics
Matches: 80, Mismatches: 16, Indels: 10
0.75 0.15 0.09
Matches are distributed among these distances:
2 1 0.01
3 67 0.84
4 12 0.15
ACGTcount: A:0.36, C:0.03, G:0.05, T:0.57
Consensus pattern (3 bp):
TTA
Found at i:41025564 original size:10 final size:11
Alignment explanation
Indices: 41025549--41025598 Score: 50
Period size: 11 Copynumber: 4.6 Consensus size: 11
41025539 ATATCAAGTT
41025549 TTTAAATC-AA
1 TTTAAATCAAA
**
41025559 TTTAAATTTAA
1 TTTAAATCAAA
41025570 -TTAAATTCAAA
1 TTTAAA-TCAAA
*
41025581 TTTAAAGCAAA
1 TTTAAATCAAA
41025592 TTTAAAT
1 TTTAAAT
41025599 TTAAAAGGAT
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
10 12 0.38
11 15 0.47
12 5 0.16
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.42
Consensus pattern (11 bp):
TTTAAATCAAA
Found at i:41025568 original size:6 final size:6
Alignment explanation
Indices: 41025557--41025661 Score: 64
Period size: 6 Copynumber: 18.3 Consensus size: 6
41025547 TTTTTAAATC
* **
41025557 AATTTA AATTT- AA-TTA AATTCA AATTTA AA-GCA AATTTA AATTTAA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTT-A
** * *
41025603 AAGGATA AATTAA AATTTA AGA--TA AATTTA AATTTA AA-ATA AATTTA
1 AA-TTTA AATTTA AATTTA A-ATTTA AATTTA AATTTA AATTTA AATTTA
41025650 AA-TT- AATTTA AA
1 AATTTA AATTTA AA
41025662 CCTAATTTTA
Statistics
Matches: 74, Mismatches: 14, Indels: 22
0.67 0.13 0.20
Matches are distributed among these distances:
4 5 0.07
5 18 0.24
6 43 0.58
7 7 0.09
8 1 0.01
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.39
Consensus pattern (6 bp):
AATTTA
Found at i:41025598 original size:17 final size:17
Alignment explanation
Indices: 41025557--41025653 Score: 99
Period size: 17 Copynumber: 5.6 Consensus size: 17
41025547 TTTTTAAATC
*
41025557 AATTTAAATTT-AATTA
1 AATTTAAATTTAAAGTA
* *
41025573 AATTCAAATTTAAAGCA
1 AATTTAAATTTAAAGTA
41025590 AATTTAAATTTAAAAGGATA
1 AATTTAAATTT-AAA-G-TA
*
41025610 AATTAAAATTT-AAGATA
1 AATTTAAATTTAAAG-TA
*
41025627 AATTTAAATTTAAAATA
1 AATTTAAATTTAAAGTA
41025644 AATTTAAATT
1 AATTTAAATT
41025654 AATTTAAACC
Statistics
Matches: 68, Mismatches: 8, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
16 10 0.15
17 39 0.57
18 7 0.10
19 1 0.01
20 11 0.16
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.39
Consensus pattern (17 bp):
AATTTAAATTTAAAGTA
Found at i:41025621 original size:37 final size:37
Alignment explanation
Indices: 41025571--41025641 Score: 108
Period size: 37 Copynumber: 1.9 Consensus size: 37
41025561 TAAATTTAAT
*
41025571 TAAATTCAAATTTAA-AGCAAATTTAAATTTAAAAGGA
1 TAAATTAAAATTTAAGA-CAAATTTAAATTTAAAAGGA
*
41025608 TAAATTAAAATTTAAGATAAATTTAAATTTAAAA
1 TAAATTAAAATTTAAGACAAATTTAAATTTAAAA
41025642 TAAATTTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
37 30 0.97
38 1 0.03
ACGTcount: A:0.56, C:0.03, G:0.06, T:0.35
Consensus pattern (37 bp):
TAAATTAAAATTTAAGACAAATTTAAATTTAAAAGGA
Found at i:41031912 original size:24 final size:24
Alignment explanation
Indices: 41031880--41031933 Score: 108
Period size: 24 Copynumber: 2.2 Consensus size: 24
41031870 GTTTCTAACA
41031880 GCCTTGCTGATGCTTTTGGGTGTT
1 GCCTTGCTGATGCTTTTGGGTGTT
41031904 GCCTTGCTGATGCTTTTGGGTGTT
1 GCCTTGCTGATGCTTTTGGGTGTT
41031928 GCCTTG
1 GCCTTG
41031934 GCTTGTTCCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.04, C:0.19, G:0.33, T:0.44
Consensus pattern (24 bp):
GCCTTGCTGATGCTTTTGGGTGTT
Found at i:41032851 original size:17 final size:18
Alignment explanation
Indices: 41032816--41032856 Score: 66
Period size: 17 Copynumber: 2.3 Consensus size: 18
41032806 GATCTTTAGG
41032816 TTTAAATTAATTATTAAA
1 TTTAAATTAATTATTAAA
*
41032834 TTTAAATTTATT-TTAAA
1 TTTAAATTAATTATTAAA
41032851 TTTAAA
1 TTTAAA
41032857 AATATTTGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 11 0.50
18 11 0.50
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TTTAAATTAATTATTAAA
Found at i:41032862 original size:17 final size:17
Alignment explanation
Indices: 41032829--41032868 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
41032819 AAATTAATTA
**
41032829 TTAAATTTAAATTTATT
1 TTAAATTTAAAAATATT
41032846 TTAAATTTAAAAATATT
1 TTAAATTTAAAAATATT
*
41032863 TGAAAT
1 TTAAAT
41032869 AAATTTAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (17 bp):
TTAAATTTAAAAATATT
Found at i:41033297 original size:17 final size:18
Alignment explanation
Indices: 41033275--41033315 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
41033265 AAAGGGGGTT
*
41033275 ACAAACCCTATTC-TGAA
1 ACAAACCCAATTCTTGAA
41033292 ACAAACCCAATTCTTGAA
1 ACAAACCCAATTCTTGAA
41033310 ATCAAA
1 A-CAAA
41033316 TTTTCTGGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 12 0.57
18 5 0.24
19 4 0.19
ACGTcount: A:0.46, C:0.27, G:0.05, T:0.22
Consensus pattern (18 bp):
ACAAACCCAATTCTTGAA
Found at i:41033477 original size:22 final size:23
Alignment explanation
Indices: 41033438--41033484 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
41033428 TCAAGTCAAT
*
41033438 ACCAGGTCATTCAAGCATTAATA
1 ACCAGGTCATACAAGCATTAATA
* *
41033461 ACCAGGT-ATACATGCATTCATA
1 ACCAGGTCATACAAGCATTAATA
41033483 AC
1 AC
41033485 TGAAGCTGTC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.26
Consensus pattern (23 bp):
ACCAGGTCATACAAGCATTAATA
Found at i:41033646 original size:3 final size:3
Alignment explanation
Indices: 41033631--41033673 Score: 59
Period size: 3 Copynumber: 14.0 Consensus size: 3
41033621 CTTTGAATGT
* *
41033631 TAA TAA TAT TAA TAA TAA TTA TAA TAA TAAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA
41033674 ATATTTATAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
3 32 0.91
4 3 0.09
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:41033683 original size:13 final size:13
Alignment explanation
Indices: 41033631--41033690 Score: 70
Period size: 13 Copynumber: 4.8 Consensus size: 13
41033621 CTTTGAATGT
41033631 TAAT-AATATTAA
1 TAATAAATATTAA
*
41033643 TAATAATTA-TAA
1 TAATAAATATTAA
*
41033655 TAATAAATAATAA
1 TAATAAATATTAA
*
41033668 TAATAAATATTTA
1 TAATAAATATTAA
*
41033681 TAATTAATAT
1 TAATAAATAT
41033691 CATTATTAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
12 15 0.37
13 26 0.63
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
TAATAAATATTAA
Found at i:41034729 original size:29 final size:28
Alignment explanation
Indices: 41034642--41035036 Score: 197
Period size: 29 Copynumber: 13.5 Consensus size: 28
41034632 AGACTATCCA
*
41034642 AAAATTACCATTTTACCCCCAAACTTTCC
1 AAAATT-CCATTTTACCCCCGAACTTTCC
*
41034671 AAAATTCCATTTTGA-CCTCG-A-TTTCACC
1 AAAATTCCATTTT-ACCCCCGAACTTT--CC
41034699 AAAATTACCATTTTACCCCCGAACTTTCC
1 AAAATT-CCATTTTACCCCCGAACTTTCC
* *
41034728 AAAATTCCATTTTAACCCC--AGTTTCACC
1 AAAATTCCATTTTACCCCCGAACTTT--CC
**
41034756 AAAAATTACCATTTTACCCCTAAACTTTCC
1 -AAAATT-CCATTTTACCCCCGAACTTTCC
* *
41034786 AAAATTCCATTTTTAACCTC-AA-TTTCACC
1 AAAATTCCA-TTTTACCCCCGAACTTT--CC
*
41034815 AAAAATTACCGTTTTACCCCCGAACTTTCC
1 -AAAATT-CCATTTTACCCCCGAACTTTCC
* * *
41034845 TAAATTCCATTTTTAACCTCG-A-TTTCGTC
1 AAAATTCCA-TTTTACCCCCGAACTTTC--C
**
41034874 AAGAATTACCATTTTACCCCTAAACTTTCC
1 AA-AATT-CCATTTTACCCCCGAACTTTCC
* * * *
41034904 AAAATTTCATTTTTAACCCC--AGTTTCATAA
1 AAAATTCCA-TTTTACCCCCGAACTTTC---C
41034934 AAAATTACCATTTTTACCCCCGAACTTTCC
1 AAAATT-CCA-TTTTACCCCCGAACTTTCC
* *
41034964 AAAA-TCCTATTTTTAACCCCG--GTTTCACC
1 AAAATTCC-A-TTTTACCCCCGAACTTT--CC
* * *
41034993 AAAAATCACCATTTTACCCTTCAAACTTTCC
1 -AAAAT-TCCATTTTACCC-CCGAACTTTCC
41035024 AAAATTCCATTTT
1 AAAATTCCATTTT
41035037 TAGCCCCGGT
Statistics
Matches: 283, Mismatches: 40, Indels: 86
0.69 0.10 0.21
Matches are distributed among these distances:
26 7 0.02
27 16 0.06
28 45 0.16
29 97 0.34
30 70 0.25
31 27 0.10
32 13 0.05
33 8 0.03
ACGTcount: A:0.32, C:0.30, G:0.03, T:0.35
Consensus pattern (28 bp):
AAAATTCCATTTTACCCCCGAACTTTCC
Found at i:41034976 original size:60 final size:59
Alignment explanation
Indices: 41034639--41035055 Score: 531
Period size: 59 Copynumber: 7.1 Consensus size: 59
41034629 CCTAGACTAT
* *
41034639 CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCA-TTTTGACCTC-GATTTCA
1 CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCAG-TTTCA
*
41034697 CC-AAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCA-TTTTAACCCCAGTTTCA
1 CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCAGTTTCA
* * *
41034754 CCAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCTCAATTTCA
1 CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCAGTTTCA
* * * * *
41034813 CCAAAAATTACCGTTTTACCCCCGAACTTTCCTAAATTCCATTTTTAACCTC-GATTTCG
1 CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCAG-TTTCA
* * * *
41034872 TCAAGAATTACCATTTTACCCCTAAACTTTCCAAAATTTCATTTTTAACCCCAGTTTCA
1 CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCAGTTTCA
** * *
41034931 TAAAAAATTACCATTTTTACCCCCGAACTTTCCAAAA-TCCTATTTTTAACCCCGGTTTCA
1 CCAAAAATTACCA-TTTTACCCCCAAACTTTCCAAAATTCC-ATTTTTAACCCCAGTTTCA
* * * * *
41034991 CCAAAAATCACCATTTTACCCTTCAAACTTTCCAAAATTCCATTTTTAGCCCCGGTTTCG
1 CCAAAAATTACCATTTTACCC-CCAAACTTTCCAAAATTCCATTTTTAACCCCAGTTTCA
41035051 CCAAA
1 CCAAA
41035056 GTTTCCAAAA
Statistics
Matches: 315, Mismatches: 35, Indels: 16
0.86 0.10 0.04
Matches are distributed among these distances:
57 52 0.17
58 39 0.12
59 136 0.43
60 85 0.27
61 3 0.01
ACGTcount: A:0.32, C:0.30, G:0.04, T:0.34
Consensus pattern (59 bp):
CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCAGTTTCA
Found at i:41035093 original size:38 final size:38
Alignment explanation
Indices: 41035014--41035093 Score: 97
Period size: 38 Copynumber: 2.1 Consensus size: 38
41035004 TTTTACCCTT
* **
41035014 CAAACTTTCCAAAATTCCATTTTTAGCCCCGGTTTCGC
1 CAAACTTTCCAAAATTCCATTTTTAACCCCGGTTTAAC
* * * *
41035052 CAAAGTTTCCAAAATTCTATTTTTAACCTCTGTTTAAC
1 CAAACTTTCCAAAATTCCATTTTTAACCCCGGTTTAAC
41035090 CAAA
1 CAAA
41035094 AATTACCATT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.30, C:0.26, G:0.07, T:0.36
Consensus pattern (38 bp):
CAAACTTTCCAAAATTCCATTTTTAACCCCGGTTTAAC
Found at i:41035151 original size:28 final size:28
Alignment explanation
Indices: 41035089--41035151 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 28
41035079 CTCTGTTTAA
* * *
41035089 CCAAAAATTACCATTTGCCCCTGCACAT
1 CCAAAAATTACCATTTACCCCCGAACAT
*
41035117 CCAAAAATTACCATTTTACCCCCGAATAT
1 CCAAAAATTACCA-TTTACCCCCGAACAT
41035146 CCAAAA
1 CCAAAA
41035152 GTCCCGTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 13 0.43
29 17 0.57
ACGTcount: A:0.38, C:0.33, G:0.05, T:0.24
Consensus pattern (28 bp):
CCAAAAATTACCATTTACCCCCGAACAT
Found at i:41045007 original size:76 final size:76
Alignment explanation
Indices: 41044867--41045644 Score: 1295
Period size: 76 Copynumber: 10.2 Consensus size: 76
41044857 GTAAGAGTGA
* * *
41044867 GAAGAAAGACCAACATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTA
1 GAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTA
41044932 TCTCTGAAATT
66 TCTCTGAAATT
* * * *
41044943 GAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATCGAAGTAGAGTTGGATAACAAGTCTTTA
1 GAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTA
41045008 TCTCTGAAATT
66 TCTCTGAAATT
41045019 GAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTA
1 GAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTA
41045084 TCTCTGAAATT
66 TCTCTGAAATT
* * * * *
41045095 GAAGTAAGGGCAAGATCATTTCCTATCCTCTTGAAATCGAAGTAGAGTTGGATAACAAGTCTTTA
1 GAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTA
41045160 TCTCTGAAATT
66 TCTCTGAAATT
* *
41045171 GAAGTAAGAGCAAGATCATTTCCTATCTTCTTGAAATTGAAGTAAAGCTGGAGATCAAGTCTTTA
1 GAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTA
41045236 TCTCTGAAATT
66 TCTCTGAAATT
* * *
41045247 GAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTA
1 GAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTA
41045312 TCTCTGAAATT
66 TCTCTGAAATT
41045323 GAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTA
1 GAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTA
41045388 TCTCTGAAATT
66 TCTCTGAAATT
41045399 GAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTA
1 GAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTA
* * *
41045464 CCTTTGAATTT
66 TCTCTGAAATT
* *
41045475 GAAGTCAGAGCAAGATCATTTCCTATCTTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTA
1 GAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTA
*
41045540 TCTCTGAATTT
66 TCTCTGAAATT
* * *
41045551 GAAGTAAGAGCAAAATCATTTCCTATCCTCTTGAAATTGAAGTAAAGTTGGATAGCAAGTCTTTA
1 GAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTA
*
41045616 TCTCTCTAAGATT
66 TCTCT-GAA-ATT
41045629 GAAGTAAGAGCAAGAT
1 GAAGTAAGAGCAAGAT
41045645 GAAGCCTCGA
Statistics
Matches: 654, Mismatches: 46, Indels: 2
0.93 0.07 0.00
Matches are distributed among these distances:
76 635 0.97
77 2 0.00
78 17 0.03
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.33
Consensus pattern (76 bp):
GAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTA
TCTCTGAAATT
Found at i:41045947 original size:17 final size:18
Alignment explanation
Indices: 41045912--41045952 Score: 66
Period size: 17 Copynumber: 2.3 Consensus size: 18
41045902 GATCTTTAGG
41045912 TTTAAATTAATTATTAAA
1 TTTAAATTAATTATTAAA
*
41045930 TTTAAATTTATT-TTAAA
1 TTTAAATTAATTATTAAA
41045947 TTTAAA
1 TTTAAA
41045953 AATATTTGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 11 0.50
18 11 0.50
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TTTAAATTAATTATTAAA
Found at i:41045958 original size:17 final size:17
Alignment explanation
Indices: 41045925--41045964 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
41045915 AAATTAATTA
**
41045925 TTAAATTTAAATTTATT
1 TTAAATTTAAAAATATT
41045942 TTAAATTTAAAAATATT
1 TTAAATTTAAAAATATT
*
41045959 TGAAAT
1 TTAAAT
41045965 AAATTTAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (17 bp):
TTAAATTTAAAAATATT
Found at i:41046767 original size:3 final size:3
Alignment explanation
Indices: 41046752--41046797 Score: 56
Period size: 3 Copynumber: 14.7 Consensus size: 3
41046742 CTTTGAATGT
* *
41046752 TAA TAA TAT TAA TAA TAA TTA TAA TAA TAAA TAA TAA TAA TTAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA -TAA TA
41046798 TTTATAATTA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
3 31 0.84
4 6 0.16
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:41047838 original size:59 final size:59
Alignment explanation
Indices: 41047764--41047986 Score: 247
Period size: 59 Copynumber: 3.8 Consensus size: 59
41047754 TCGACTGTCC
* *
41047764 AAAAATTATCATTTTACCCCTAAATTTTCCAAAATTCCATTTTTAACCCC-AGTTTCACT
1 AAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGA-TTTCACT
** * * * * *
41047823 AAAAATTACTGTTTTA-CCCTCGAACTTTCCTAAATTCCGTTTTTAACCTCGATTTCACC
1 AAAAATTACCATTTTACCCCT-AAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACT
* *
41047882 AAGAATTACCATTTTACCCTTTAAA-TTTCCAAAATTCCATTTTTAACCCCGATTTCA-T
1 AAAAATTACCATTTTACCC-CTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACT
* **
41047940 CAAAAATCACCATTTTACCCCCCGAACTTTCCAAAATTCCATTTTTA
1 -AAAAATTACCATTTTA-CCCCTAAACTTTCCAAAATTCCATTTTTA
41047987 GCCTCGGTTT
Statistics
Matches: 134, Mismatches: 23, Indels: 13
0.79 0.14 0.08
Matches are distributed among these distances:
58 4 0.03
59 101 0.75
60 28 0.21
61 1 0.01
ACGTcount: A:0.32, C:0.27, G:0.04, T:0.38
Consensus pattern (59 bp):
AAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACT
Found at i:41047943 original size:29 final size:28
Alignment explanation
Indices: 41047789--41047986 Score: 88
Period size: 30 Copynumber: 6.7 Consensus size: 28
41047779 ACCCCTAAAT
*
41047789 TTTCCAAAATTCCATTTTTAACCCC-AG
1 TTTCCAAAATTCCATTTTTAACCCCGAC
*
41047816 TTTCACTAAAAATTAC-TGTTTT-ACCCTCGAAC
1 TTTC-C--AAAATTCCAT-TTTTAACCC-CG-AC
* * *
41047848 TTTCCTAAATTCCGTTTTTAACCTCGA-
1 TTTCCAAAATTCCATTTTTAACCCCGAC
** *
41047875 TTTCACCAAGAATTACCA-TTTT-ACCCTTTAAA
1 TTT--CCAA-AATT-CCATTTTTAACCC--CGAC
41047907 TTTCCAAAATTCCATTTTTAACCCCGA-
1 TTTCCAAAATTCCATTTTTAACCCCGAC
* *
41047934 TTTCATCAAAAATCACCA-TTTTACCCCCCGAAC
1 TTTC--C-AAAAT-TCCATTTTTA-ACCCCG-AC
41047967 TTTCCAAAATTCCATTTTTA
1 TTTCCAAAATTCCATTTTTA
41047987 GCCTCGGTTT
Statistics
Matches: 130, Mismatches: 15, Indels: 49
0.67 0.08 0.25
Matches are distributed among these distances:
27 11 0.08
28 6 0.05
29 35 0.27
30 52 0.40
31 13 0.10
32 9 0.07
33 4 0.03
ACGTcount: A:0.30, C:0.28, G:0.04, T:0.38
Consensus pattern (28 bp):
TTTCCAAAATTCCATTTTTAACCCCGAC
Found at i:41049562 original size:29 final size:27
Alignment explanation
Indices: 41049509--41049564 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 27
41049499 AAATTTATAA
41049509 ATAAATATTAATAATATTATTTAAATAT
1 ATAAATA-TAATAATATTATTTAAATAT
41049537 ATAAATA-AATAATAATTAATTGTAAATA
1 ATAAATATAATAAT-ATT-ATT-TAAATA
41049565 AATGCTAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
26 6 0.24
27 3 0.12
28 10 0.40
29 6 0.24
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (27 bp):
ATAAATATAATAATATTATTTAAATAT
Found at i:41050158 original size:15 final size:15
Alignment explanation
Indices: 41050123--41050155 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
41050113 TATGAATATA
*
41050123 TTAATTTAATATCGC
1 TTAATTTAATATAGC
41050138 TTAATTTAATA-AGC
1 TTAATTTAATATAGC
41050152 TTAA
1 TTAA
41050156 ATTACCTCAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.39, C:0.09, G:0.06, T:0.45
Consensus pattern (15 bp):
TTAATTTAATATAGC
Found at i:41050426 original size:23 final size:24
Alignment explanation
Indices: 41050383--41050427 Score: 58
Period size: 23 Copynumber: 1.9 Consensus size: 24
41050373 TAATAAAATT
*
41050383 TAAATATTAAATATTTTTTTTTCA
1 TAAATATTAAATATTTATTTTTCA
41050407 TAAA-ATTAAAT-TTTGATTTTT
1 TAAATATTAAATATTT-ATTTTT
41050428 GAAAAATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 3 0.16
23 12 0.63
24 4 0.21
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (24 bp):
TAAATATTAAATATTTATTTTTCA
Found at i:41051015 original size:24 final size:24
Alignment explanation
Indices: 41050988--41051033 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
41050978 TCATTAACAT
41050988 TGTTCATGAACATGTTCGATTATA
1 TGTTCATGAACATGTTCGATTATA
41051012 TGTTCATGAACATGTTCGATTA
1 TGTTCATGAACATGTTCGATTA
41051034 AGTTAAATGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.28, C:0.13, G:0.17, T:0.41
Consensus pattern (24 bp):
TGTTCATGAACATGTTCGATTATA
Found at i:41051026 original size:12 final size:12
Alignment explanation
Indices: 41050978--41051028 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
41050968 TGTTTATTAA
*
41050978 TCATTAACATTGT
1 TCATGAACA-TGT
41050991 TCATGAACATGT
1 TCATGAACATGT
* *
41051003 TCGAT-TATATGT
1 TC-ATGAACATGT
41051015 TCATGAACATGT
1 TCATGAACATGT
41051027 TC
1 TC
41051029 GATTAAGTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
11 2 0.06
12 19 0.61
13 10 0.32
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.41
Consensus pattern (12 bp):
TCATGAACATGT
Found at i:41052361 original size:24 final size:23
Alignment explanation
Indices: 41052316--41052361 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
41052306 TGAATAACAT
*
41052316 AATGCCACGTCTTTTTTCATTGG
1 AATGCCACGTCTTTTTTAATTGG
*
41052339 AATGCCACGTTTTCTTTTAATTG
1 AATGCCACGTCTT-TTTTAATTG
41052362 TAAAATATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.20, C:0.20, G:0.15, T:0.46
Consensus pattern (23 bp):
AATGCCACGTCTTTTTTAATTGG
Found at i:41054209 original size:5 final size:6
Alignment explanation
Indices: 41054194--41054218 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
41054184 AGGCATATAA
41054194 AAAAAC AAAAAC AAAAAC AAAAAC A
1 AAAAAC AAAAAC AAAAAC AAAAAC A
41054219 GTTTTAAAAA
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:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (6 bp):
AAAAAC
Found at i:41055069 original size:60 final size:60
Alignment explanation
Indices: 41055004--41055400 Score: 368
Period size: 60 Copynumber: 6.7 Consensus size: 60
41054994 TAAGCTTCTT
* * * * *
41055004 CAAAATTACATGTTGA-CCCTCAAATTTTTTTAAAATTAAATTTTAACCTCTAAATTTTTC
1 CAAAATTACATTTTGACCCCT-AAACTTTTCTAAAATTACATTTTAACCTCTAAACTTTTC
* * * *
41055064 AAAAATTACA-TTTGACCCCTAAACTTCTCTAAAATTACATTTTGACC-CTTAAAATTTTC
1 CAAAATTACATTTTGACCCCTAAACTTTTCTAAAATTACATTTTAACCTC-TAAACTTTTC
* * *
41055123 CAAAATTACATTTTGACCCTTAAATTTTTCTATAATTACATTTTAACCTCTAAACTTTTC
1 CAAAATTACATTTTGACCCCTAAACTTTTCTAAAATTACATTTTAACCTCTAAACTTTTC
* * * * *
41055183 CAAAATTATATTTTGACCCCTAAACTTTTCCAAAATTGCATTTTAATCTCTAAACTTCTC
1 CAAAATTACATTTTGACCCCTAAACTTTTCTAAAATTACATTTTAACCTCTAAACTTTTC
* * * * * ** *
41055243 TAAAATTATATTTTGA-TCCTAAACTTCTCTAAAATCACATTTT-GTCTCTAAACTTTAC
1 CAAAATTACATTTTGACCCCTAAACTTTTCTAAAATTACATTTTAACCTCTAAACTTTTC
* ** * *
41055301 CAAAATTGCATTTTGACCCC-AAACTTCTTC-AAAATCGCATTTTAA--TGCT-GAGTTTTCC
1 CAAAATTACATTTTGACCCCTAAACTT-TTCTAAAATTACATTTTAACCT-CTAAACTTTT-C
* * *
41055359 CAAAATTACATTTTCA-CCCTAAACTTTTC-AAATTTACGTTTT
1 CAAAATTACATTTTGACCCCTAAACTTTTCTAAAATTACATTTT
41055401 GATCCTGTAT
Statistics
Matches: 279, Mismatches: 48, Indels: 23
0.80 0.14 0.07
Matches are distributed among these distances:
57 20 0.07
58 67 0.24
59 70 0.25
60 121 0.43
61 1 0.00
ACGTcount: A:0.34, C:0.21, G:0.04, T:0.41
Consensus pattern (60 bp):
CAAAATTACATTTTGACCCCTAAACTTTTCTAAAATTACATTTTAACCTCTAAACTTTTC
Done.