Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000851.1 Hibiscus syriacus cultivar Beakdansim tig00001644_pilon, whole genome shotgun sequence
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: 7304151
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 31
Found at i:1578957 original size:86 final size:86
Alignment explanation
Indices: 1578697--1579194 Score: 645
Period size: 85 Copynumber: 5.8 Consensus size: 86
1578687 CAAGGTGAAG
* * * * *
1578697 AGGGCTATCCGTCAGTAAAAAACCTTCGAGTTCGATGACATTCAGCCCAAGGACATATCAAATTT
1 AGGGTTATCTGTCAGCAAAAAACCTTCGAGTTCGATTACATTCAGCTCAAGGACATATCAAATTT
*
1578762 ACA-AATAACTCAAGGCGAGA
66 ACAGCATAACTCAAGGCGAGA
* * *
1578782 ATGGTTATTTGTCAGCAAAAAACCTTCAAGTTCGATTACATTCAGCTCAAGGACATATC-AATTT
1 AGGGTTATCTGTCAGCAAAAAACCTTCGAGTTCGATTACATTCAGCTCAAGGACATATCAAATTT
* *
1578846 ATAGCATAGCTCAAGGCGATG-
66 ACAGCATAACTCAAGGCGA-GA
* *
1578867 AGGGTTATCTGTCAGCAAAAAACCTTTGAGTTTGATTACATTCAGCTCAAGGACATATCAAATTT
1 AGGGTTATCTGTCAGCAAAAAACCTTCGAGTTCGATTACATTCAGCTCAAGGACATATCAAATTT
*
1578932 ATAGCATAACTCAAGGCGAGA
66 ACAGCATAACTCAAGGCGAGA
* * *
1578953 AGGGTTATCTGTCAGCAAAAAACCTTCAAGTTTGATTACATTCAACTCAAGGACATATCAAATTT
1 AGGGTTATCTGTCAGCAAAAAACCTTCGAGTTCGATTACATTCAGCTCAAGGACATATCAAATTT
*
1579018 ACAGTATAACTCAAGGCGA-A
66 ACAGCATAACTCAAGGCGAGA
* * *
1579038 TGGGTTATCTGTCA--ATAAAAACCTTTGAGTTCAATTACATTCAGCTCAAGGGA-ATATCAAAT
1 AGGGTTATCTGTCAGCA-AAAAACCTTCGAGTTCGATTACATTCAGCTCAA-GGACATATCAAAT
* *
1579100 TTACAACATAGA-TTAAGGCGAGA
64 TTACAGCATA-ACTCAAGGCGAGA
* * * * *
1579123 AGGGTTATCTGTCAAC-AAAAACATTCGAGTTCGAATACATTCAGCTCAAGGGCATATTAAATTT
1 AGGGTTATCTGTCAGCAAAAAACCTTCGAGTTCGATTACATTCAGCTCAAGGACATATCAAATTT
1579187 ACAGCATA
66 ACAGCATA
1579195 GCTTAAGTCG
Statistics
Matches: 363, Mismatches: 39, Indels: 22
0.86 0.09 0.05
Matches are distributed among these distances:
83 1 0.00
84 62 0.17
85 197 0.54
86 103 0.28
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.27
Consensus pattern (86 bp):
AGGGTTATCTGTCAGCAAAAAACCTTCGAGTTCGATTACATTCAGCTCAAGGACATATCAAATTT
ACAGCATAACTCAAGGCGAGA
Found at i:1579267 original size:170 final size:170
Alignment explanation
Indices: 1578723--1579267 Score: 613
Period size: 170 Copynumber: 3.2 Consensus size: 170
1578713 AAAAAACCTT
* * *
1578723 CGAGTTCGATGACATTCAGCCCAAGGACATATCAAATTTACAA-ATAACTCAAGGCGAGAATGGT
1 CGAGTTCGATTACATTCAGCTCAAGGACATATCAAATTTACAACATAACTCAAGGCGAGAAGGGT
* * *
1578787 TATTTGTCAGCAAAAAACCTTCAAGTTCGATTACATTCAGCTCAAGGACATA-TCAATTTATAGC
66 TATCTGTCAGCAAAAAACCTTCAAGTTCGATTACATTCAGCTCAAGGACATATTAAATTTACAGC
*
1578851 ATAGCTCAAGGCGATGAGGGTTATCTGTCAGCAAAAA--AC
131 ATAGCTCAAGGCGAT-AGGGTTATCTGTCAACAAAAACTAC
* * *
1578890 CTTTGAGTTTGATTACATTCAGCTCAAGGACATATCAAATTTATAGCATAACTCAAGGCGAGAAG
1 C---GAGTTCGATTACATTCAGCTCAAGGACATATCAAATTTACAACATAACTCAAGGCGAGAAG
* * *
1578955 GGTTATCTGTCAGCAAAAAACCTTCAAGTTTGATTACATTCAACTCAAGGACATATCAAATTTAC
63 GGTTATCTGTCAGCAAAAAACCTTCAAGTTCGATTACATTCAGCTCAAGGACATATTAAATTTAC
* * * *
1579020 AGTATAACTCAAGGCGA-ATGGGTTATCTGTCAATAAAAACCT-T
128 AGCATAGCTCAAGGCGATA-GGGTTATCTGTCAACAAAAA-CTAC
* * *
1579063 TGAGTTCAATTACATTCAGCTCAAGGGA-ATATCAAATTTACAACATAGA-TTAAGGCGAGAAGG
1 CGAGTTCGATTACATTCAGCTCAA-GGACATATCAAATTTACAACATA-ACTCAAGGCGAGAAGG
* * * * *
1579126 GTTATCTGTCAAC-AAAAACATTCGAGTTCGAATACATTCAGCTCAAGGGCATATTAAATTTACA
64 GTTATCTGTCAGCAAAAAACCTTCAAGTTCGATTACATTCAGCTCAAGGACATATTAAATTTACA
* * *** * *
1579190 GCATAGCTTAAGTCGATAAAATCTATTTATCAACAAAAACTAC
129 GCATAGCTCAAGGCGATAGGGT-TATCTGTCAACAAAAACTAC
** * * *
1579233 CGAGTTCGATTTTATTTAGCACAATGACATATCAA
1 CGAGTTCGATTACATTCAGCTCAAGGACATATCAA
1579268 TCGCATGGTA
Statistics
Matches: 314, Mismatches: 49, Indels: 27
0.81 0.13 0.07
Matches are distributed among these distances:
167 1 0.00
169 61 0.19
170 140 0.45
171 91 0.29
172 21 0.07
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.28
Consensus pattern (170 bp):
CGAGTTCGATTACATTCAGCTCAAGGACATATCAAATTTACAACATAACTCAAGGCGAGAAGGGT
TATCTGTCAGCAAAAAACCTTCAAGTTCGATTACATTCAGCTCAAGGACATATTAAATTTACAGC
ATAGCTCAAGGCGATAGGGTTATCTGTCAACAAAAACTAC
Found at i:1580094 original size:40 final size:39
Alignment explanation
Indices: 1580067--1580156 Score: 117
Period size: 40 Copynumber: 2.2 Consensus size: 39
1580057 TAATATATAG
*
1580067 TTTTGAAAACATATATATATAATATATAGTTATTAAAAATA
1 TTTTGAAAA-AAATATATATAATATATAG-TATTAAAAATA
* *
1580108 TTTTGAAAAAAATATATATAATATATAGTTTTGGAAAATA
1 TTTTGAAAAAAATATATATAATATATAGTATT-AAAAATA
1580148 CTTTTGAAA
1 -TTTTGAAA
1580157 GTATATTATA
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
39 3 0.07
40 24 0.55
41 17 0.39
ACGTcount: A:0.49, C:0.02, G:0.08, T:0.41
Consensus pattern (39 bp):
TTTTGAAAAAAATATATATAATATATAGTATTAAAAATA
Found at i:1580104 original size:29 final size:28
Alignment explanation
Indices: 1580050--1580108 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 28
1580040 AAACTTGGAA
1580050 ATATATATAATATATAGTTTTGAAAACAT
1 ATATATATAATATATAGTTTTGAAAA-AT
1580079 ATATATATAATATATAGTTATT-AAAAAT
1 ATATATATAATATATAGTT-TTGAAAAAT
1580107 AT
1 AT
1580109 TTTGAAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
28 4 0.14
29 23 0.79
30 2 0.07
ACGTcount: A:0.51, C:0.02, G:0.05, T:0.42
Consensus pattern (28 bp):
ATATATATAATATATAGTTTTGAAAAAT
Found at i:1580221 original size:36 final size:35
Alignment explanation
Indices: 1580081--1580222 Score: 119
Period size: 36 Copynumber: 3.9 Consensus size: 35
1580071 GAAAACATAT
* *
1580081 ATATATAATATATAGTTATTAAAAATA-TTTTGAAAAAA
1 ATATATATTATATAGTT-TTAGAAATATTTTTG---AAA
* *
1580119 ATATATATAATATATAGTTTTGGAAAATACTTTTG-AA
1 ATATATAT--TATATAGTTTTAG-AAATATTTTTGAAA
* *
1580156 A-GTATATTATATAGTTTTAAAAACTATTTTTGAAA
1 ATATATATTATATAGTTTTAGAAA-TATTTTTGAAA
*
1580191 ATATATATTATATGGTTTTAGAAATGATTTTT
1 ATATATATTATATAGTTTTAGAAAT-ATTTTT
1580223 ATTTTTATTT
Statistics
Matches: 86, Mismatches: 10, Indels: 18
0.75 0.09 0.16
Matches are distributed among these distances:
33 3 0.03
34 18 0.21
35 4 0.05
36 30 0.35
37 3 0.03
38 7 0.08
39 2 0.02
40 14 0.16
41 5 0.06
ACGTcount: A:0.44, C:0.01, G:0.09, T:0.45
Consensus pattern (35 bp):
ATATATATTATATAGTTTTAGAAATATTTTTGAAA
Found at i:1580243 original size:8 final size:8
Alignment explanation
Indices: 1580218--1580252 Score: 52
Period size: 8 Copynumber: 4.1 Consensus size: 8
1580208 TTAGAAATGA
1580218 TTTTTATTT
1 TTTTTA-TT
1580227 TTATTTATT
1 TT-TTTATT
1580236 TTTTTATT
1 TTTTTATT
1580244 TTTTTATT
1 TTTTTATT
1580252 T
1 T
1580253 GGTATTCCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
8 15 0.60
9 6 0.24
10 4 0.16
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (8 bp):
TTTTTATT
Found at i:1584125 original size:24 final size:21
Alignment explanation
Indices: 1584091--1584133 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
1584081 CCCACAAGAC
*
1584091 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGA-AATTCAAAGG
1584113 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
1584134 AGAATGTGTC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAAGG
Found at i:1586774 original size:21 final size:21
Alignment explanation
Indices: 1586748--1586788 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1586738 TTAATAGAAC
**
1586748 AAATTATTCTTAATAAATATT
1 AAATTATAATTAATAAATATT
1586769 AAATTATAATTAATAAATAT
1 AAATTATAATTAATAAATAT
1586789 ATATAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (21 bp):
AAATTATAATTAATAAATATT
Found at i:1587177 original size:27 final size:27
Alignment explanation
Indices: 1587129--1587211 Score: 134
Period size: 27 Copynumber: 3.1 Consensus size: 27
1587119 AAAAAAATAT
1587129 TTTTG-AAA-ATATATATAATATATAG
1 TTTTGAAAACATATATATAATATATAG
* *
1587154 TTTTGAAAACATATAAATATTATATAG
1 TTTTGAAAACATATATATAATATATAG
1587181 TTTTGAAAACATATATATAATATATAG
1 TTTTGAAAACATATATATAATATATAG
1587208 TTTT
1 TTTT
1587212 TAAATAAATT
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
25 5 0.10
26 3 0.06
27 44 0.85
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.45
Consensus pattern (27 bp):
TTTTGAAAACATATATATAATATATAG
Found at i:1587266 original size:43 final size:42
Alignment explanation
Indices: 1587191--1587283 Score: 111
Period size: 43 Copynumber: 2.2 Consensus size: 42
1587181 TTTTGAAAAC
*
1587191 ATATATATAATATATAGTTTTTAAATAAA-TTTTGAAAATAT
1 ATATATATAATATATAGTTTTGAAATAAATTTTTGAAAATAT
* *
1587232 ATATATATATATAATATAGTTTTGGAAA-ATATTTTTGAAAGTAT
1 ATATATATA-AT-ATATAGTTTT-GAAATAAATTTTTGAAAATAT
1587276 AT-TATATA
1 ATATATATA
1587284 GTTTAAAAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
41 9 0.20
42 2 0.04
43 18 0.40
44 16 0.36
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (42 bp):
ATATATATAATATATAGTTTTGAAATAAATTTTTGAAAATAT
Found at i:1587277 original size:36 final size:34
Alignment explanation
Indices: 1587236--1587337 Score: 116
Period size: 34 Copynumber: 2.9 Consensus size: 34
1587226 AAATATATAT
*
1587236 ATATATATAATATAGTTTTGGAAAATATTTTTGAAA
1 ATATATAT-ATATAGTTTT-AAAAATATTTTTGAAA
* *
1587272 GTATAT-TATATAGTTTAAAAAACTATTTTTGAAA
1 ATATATATATATAGTTTTAAAAA-TATTTTTGAAA
*
1587306 ATATATATTATATGGTTTTAAAAATGATTTTT
1 ATATATA-TATATAGTTTTAAAAAT-ATTTTT
1587338 ATTTTTTATT
Statistics
Matches: 56, Mismatches: 6, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
33 4 0.07
34 25 0.45
35 2 0.04
36 25 0.45
ACGTcount: A:0.42, C:0.01, G:0.10, T:0.47
Consensus pattern (34 bp):
ATATATATATATAGTTTTAAAAATATTTTTGAAA
Found at i:1587283 original size:34 final size:35
Alignment explanation
Indices: 1587236--1587337 Score: 118
Period size: 36 Copynumber: 2.9 Consensus size: 35
1587226 AAATATATAT
* *
1587236 ATATATATAATATAGTTTTGGAAAATATTTTTG-AA
1 ATATATATTATATAGTTTT-AAAAATATTTTTGAAA
* *
1587271 A-GTATATTATATAGTTTAAAAAACTATTTTTGAAA
1 ATATATATTATATAGTTTTAAAAA-TATTTTTGAAA
*
1587306 ATATATATTATATGGTTTTAAAAATGATTTTT
1 ATATATATTATATAGTTTTAAAAAT-ATTTTT
1587338 ATTTTTTATT
Statistics
Matches: 56, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
33 4 0.07
34 22 0.39
35 5 0.09
36 25 0.45
ACGTcount: A:0.42, C:0.01, G:0.10, T:0.47
Consensus pattern (35 bp):
ATATATATTATATAGTTTTAAAAATATTTTTGAAA
Found at i:1587379 original size:20 final size:17
Alignment explanation
Indices: 1587332--1587364 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
1587322 TTTAAAAATG
1587332 ATTTTTATTTTTTATTT
1 ATTTTTATTTTTTATTT
1587349 ATTTTTATTTTTTATT
1 ATTTTTATTTTTTATT
1587365 ATTCCTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (17 bp):
ATTTTTATTTTTTATTT
Found at i:1589850 original size:32 final size:31
Alignment explanation
Indices: 1589795--1589883 Score: 78
Period size: 32 Copynumber: 2.8 Consensus size: 31
1589785 AAAGAAACTT
*
1589795 ATTTAATTTTTTTATT-TTAATTTTTTTCTCTTG
1 ATTT-ATTATTTTATTATT-ATTTTTTTCT-TTG
1589828 ATTTATTATTTTATTATTA---TTTTCTTTG
1 ATTTATTATTTTATTATTATTTTTTTCTTTG
*
1589856 ATTTATTTAATATTTAATATTATTTTTT
1 ATTTA-TT-AT-TTTATTATTATTTTTT
1589884 ATTTAACATT
Statistics
Matches: 47, Mismatches: 2, Indels: 13
0.76 0.03 0.21
Matches are distributed among these distances:
28 8 0.17
29 8 0.17
30 2 0.04
31 9 0.19
32 11 0.23
33 6 0.13
34 3 0.06
ACGTcount: A:0.24, C:0.03, G:0.02, T:0.71
Consensus pattern (31 bp):
ATTTATTATTTTATTATTATTTTTTTCTTTG
Found at i:1589857 original size:28 final size:29
Alignment explanation
Indices: 1589800--1589881 Score: 89
Period size: 28 Copynumber: 2.8 Consensus size: 29
1589790 AACTTATTTA
* *
1589800 ATTTTTTTATTTTA-ATTTTTTTCTCTTG
1 ATTTATTTATTTTATATTATTTTCTCTTG
1589828 ATTTA-TTATTTTATTATTATTTTCT-TTG
1 ATTTATTTATTTTA-TATTATTTTCTCTTG
1589856 ATTTATTTAATATTTAATATTATTTT
1 ATTTATTT-AT-TTT-ATATTATTTT
1589882 TTATTTAACA
Statistics
Matches: 46, Mismatches: 2, Indels: 9
0.81 0.04 0.16
Matches are distributed among these distances:
27 8 0.17
28 12 0.26
29 11 0.24
30 2 0.04
31 12 0.26
32 1 0.02
ACGTcount: A:0.23, C:0.04, G:0.02, T:0.71
Consensus pattern (29 bp):
ATTTATTTATTTTATATTATTTTCTCTTG
Found at i:1589886 original size:17 final size:17
Alignment explanation
Indices: 1589839--1589889 Score: 50
Period size: 17 Copynumber: 3.0 Consensus size: 17
1589829 TTTATTATTT
* *
1589839 TATTATTATTTTCTTTGA
1 TATTATT-TTTTATTTAA
**
1589857 T-TTATTTAATATTTAA
1 TATTATTTTTTATTTAA
1589873 TATTATTTTTTATTTAA
1 TATTATTTTTTATTTAA
1589890 CATTTTCGAC
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
16 7 0.27
17 18 0.69
18 1 0.04
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTATTTTTTATTTAA
Found at i:1589973 original size:12 final size:13
Alignment explanation
Indices: 1589951--1589979 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
1589941 GAATAGAATG
1589951 TTTTAAATTTTAA
1 TTTTAAATTTTAA
1589964 TTTT-AATTTTAA
1 TTTTAAATTTTAA
1589976 TTTT
1 TTTT
1589980 CGCAATTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTTAAATTTTAA
Found at i:1590880 original size:16 final size:16
Alignment explanation
Indices: 1590854--1590893 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
1590844 GAATAATAAG
*
1590854 CATGTGGGGTAGATAT
1 CATGCGGGGTAGATAT
*
1590870 TATGCGGGGTAGATAT
1 CATGCGGGGTAGATAT
1590886 CATGCGGG
1 CATGCGGG
1590894 TTAAGACTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.23, C:0.10, G:0.40, T:0.28
Consensus pattern (16 bp):
CATGCGGGGTAGATAT
Found at i:1595345 original size:72 final size:72
Alignment explanation
Indices: 1595136--1595366 Score: 372
Period size: 72 Copynumber: 3.2 Consensus size: 72
1595126 ATATAAATTG
* *
1595136 TGTCTCACTTGAGACTGTTTTACTTGAAAGAGGATTTATTTCCCTCATGATTGTTTTTCTTAAAA
1 TGTCTCACTTGAGACTGTTTTACTTGAAAGAAGATTTATTTCCCTCAAGATTGTTTTTCTTAAAA
* *
1595201 CAGACCT
66 TAGACTT
*
1595208 TGTCTCACTTGAGACTATTTTACTTGAAAGAAGATTTATTTCCCTCAAGATTGTTTTTCTTAAAA
1 TGTCTCACTTGAGACTGTTTTACTTGAAAGAAGATTTATTTCCCTCAAGATTGTTTTTCTTAAAA
1595273 TAGACTT
66 TAGACTT
*
1595280 TGTCTCACTTGAGACTGTTTTACTCGAAAGAAGATTTATTTCCCTCAAGATTGTTTTTCTTAAAA
1 TGTCTCACTTGAGACTGTTTTACTTGAAAGAAGATTTATTTCCCTCAAGATTGTTTTTCTTAAAA
*
1595345 TAAGATTT
66 T-AGACTT
* *
1595353 TATCTCCCTTGAGA
1 TGTCTCACTTGAGA
1595367 TAGTTTCCCT
Statistics
Matches: 148, Mismatches: 10, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
72 131 0.89
73 17 0.11
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.42
Consensus pattern (72 bp):
TGTCTCACTTGAGACTGTTTTACTTGAAAGAAGATTTATTTCCCTCAAGATTGTTTTTCTTAAAA
TAGACTT
Found at i:1595350 original size:36 final size:37
Alignment explanation
Indices: 1595151--1595361 Score: 135
Period size: 36 Copynumber: 5.8 Consensus size: 37
1595141 CACTTGAGAC
* * * * *
1595151 TGTTTTACTTGAAAGAGGA-TTTATTTCCCTCATGAT
1 TGTTTTTCTTAAAAGAAGACTTTATCTCCCTCAAGAT
* * * * ** *
1595187 TGTTTTTCTTAAAA-CAGACCTTGTCTCACTTGAGAC
1 TGTTTTTCTTAAAAGAAGACTTTATCTCCCTCAAGAT
* * * *
1595223 TATTTTACTTGAAAGAAGA-TTTATTTCCCTCAAGAT
1 TGTTTTTCTTAAAAGAAGACTTTATCTCCCTCAAGAT
* * * ** *
1595259 TGTTTTTCTTAAAA-TAGACTTTGTCTCACTTGAGAC
1 TGTTTTTCTTAAAAGAAGACTTTATCTCCCTCAAGAT
* ** *
1595295 TGTTTTACTCGAAAGAAGA-TTTATTTCCCTCAAGAT
1 TGTTTTTCTTAAAAGAAGACTTTATCTCCCTCAAGAT
* *
1595331 TGTTTTTCTTAAAATAAGATTTTATCTCCCT
1 TGTTTTTCTTAAAAGAAGACTTTATCTCCCT
1595362 TGAGATAGTT
Statistics
Matches: 122, Mismatches: 48, Indels: 9
0.68 0.27 0.05
Matches are distributed among these distances:
35 5 0.04
36 101 0.83
37 16 0.13
ACGTcount: A:0.27, C:0.17, G:0.13, T:0.43
Consensus pattern (37 bp):
TGTTTTTCTTAAAAGAAGACTTTATCTCCCTCAAGAT
Found at i:1595505 original size:37 final size:37
Alignment explanation
Indices: 1595437--1595533 Score: 115
Period size: 37 Copynumber: 2.6 Consensus size: 37
1595427 CATTGAAAAC
** * *
1595437 ATTTCCCTTGAAA-TGAATTTTGTCTCTCTTGAGATA
1 ATTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACA
*
1595473 GTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACA
1 ATTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACA
* *
1595510 ATTTCTCTTGAAACATAAACTTTG
1 ATTTCCCTTGAAACA-AAATTTTG
1595534 AAAACGGTTT
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
36 12 0.24
37 32 0.63
38 7 0.14
ACGTcount: A:0.28, C:0.20, G:0.12, T:0.40
Consensus pattern (37 bp):
ATTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACA
Found at i:1595527 original size:102 final size:104
Alignment explanation
Indices: 1595349--1595552 Score: 295
Period size: 102 Copynumber: 2.0 Consensus size: 104
1595339 TTAAAATAAG
* *
1595349 ATTTTATCTCCCTTGAGATAGTTTCCCTCGAAACAGAAAATTTAGTCTCCCTTGAGATAGTTTCA
1 ATTTTATCTCCCTTGAGATAGTTTCCCTCGAAACA-AAAATTTAGTCTCCCTTGAGACAATTTCA
1595414 CTTGAAACATAAACATTGAAAAC-ATTTCCCTTGAAATGA
65 CTTGAAACATAAACATTGAAAACGATTTCCCTTGAAATGA
* * * * *
1595453 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAAC-AAAATTTTGTCTCCCTTGAGACAATTTCTC
1 ATTTTATCTCCCTTGAGATAGTTTCCCTCGAAACAAAAATTTAGTCTCCCTTGAGACAATTTCAC
* * *
1595517 TTGAAACATAAACTTTGAAAACGGTTTCCGTTGAAA
66 TTGAAACATAAACATTGAAAACGATTTCCCTTGAAA
1595553 CAAAATCTTT
Statistics
Matches: 89, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
102 47 0.53
103 11 0.12
104 31 0.35
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (104 bp):
ATTTTATCTCCCTTGAGATAGTTTCCCTCGAAACAAAAATTTAGTCTCCCTTGAGACAATTTCAC
TTGAAACATAAACATTGAAAACGATTTCCCTTGAAATGA
Found at i:1595582 original size:29 final size:28
Alignment explanation
Indices: 1595511--1595585 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 28
1595501 CTTGAGACAA
1595511 TTTCTCTTGAAACATAAACTTTGAAAACGG
1 TTTC-CTTGAAACA-AAACTTTGAAAACGG
* *
1595541 TTTCCGTTGAAACAAAATCTTTG-AATCTGT
1 TTTCC-TTGAAACAAAA-CTTTGAAAAC-GG
1595571 TTTCCTTGAAACAAA
1 TTTCCTTGAAACAAA
1595586 GTTTTGTCTC
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
29 17 0.43
30 23 0.57
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.36
Consensus pattern (28 bp):
TTTCCTTGAAACAAAACTTTGAAAACGG
Found at i:1595629 original size:36 final size:36
Alignment explanation
Indices: 1595571--1595675 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
1595561 TTGAATCTGT
*
1595571 TTTC-CTTGAAACAAAGTTTTGTCTCTCTTGAGACAA
1 TTTCTCTTAAAACAAA-TTTTGTCTCTCTTGAGACAA
*
1595607 TTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACAT
1 TTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACAA
1595643 TTTCTCTTAAAACAAATTTTGTCTCTCTTGAGA
1 TTTCTCTTAAAACAAATTTTGTCTCTCTTGAGA
1595676 TGGTTTCCCT
Statistics
Matches: 66, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
36 56 0.85
37 10 0.15
ACGTcount: A:0.28, C:0.19, G:0.10, T:0.43
Consensus pattern (36 bp):
TTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACAA
Found at i:1595692 original size:36 final size:36
Alignment explanation
Indices: 1595569--1595694 Score: 162
Period size: 36 Copynumber: 3.5 Consensus size: 36
1595559 CTTTGAATCT
* *
1595569 GTTTTCCTTGAAACAAAGTTTTGTCTCTCTTGAGACA
1 GTTTCCCTTAAAACAAA-TTTTGTCTCTCTTGAGACA
* *
1595606 ATTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACA
1 GTTTCCCTTAAAACAAATTTTGTCTCTCTTGAGACA
* * **
1595642 TTTTCTCTTAAAACAAATTTTGTCTCTCTTGAGATG
1 GTTTCCCTTAAAACAAATTTTGTCTCTCTTGAGACA
*
1595678 GTTTCCCTTGAAACAAA
1 GTTTCCCTTAAAACAAA
1595695 ATCTTTGAAT
Statistics
Matches: 79, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
36 66 0.84
37 13 0.16
ACGTcount: A:0.28, C:0.19, G:0.12, T:0.41
Consensus pattern (36 bp):
GTTTCCCTTAAAACAAATTTTGTCTCTCTTGAGACA
Found at i:1595713 original size:138 final size:137
Alignment explanation
Indices: 1595386--1595777 Score: 419
Period size: 138 Copynumber: 2.9 Consensus size: 137
1595376 TCGAAACAGA
* * * * * * *
1595386 AAATTTAGTCTCCCTTGAGATAGTTTCACTTGAAACATAAA-CATTGAAAAC-ATTTCCCTTGAA
1 AAATTT-GTCTCTCTTGAGATGGTTTCCCTTGAAACA-AAATCTTTG-AATCTGTTTTCCTTGAA
** * * * * *
1595449 ATGAA-TTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAATT
63 ACAAAGTTTTGTCTCTCTTGAGACAATTTCTCTTAAAAC-AAATTTTGTCTCTCTTGAGACAATT
*
1595513 TCTCTTGAAAC
127 TCTCTTAAAAC
* * * *
1595524 ATAA------ACT-TTGAAAACGGTTTCCGTTGAAACAAAATCTTTGAATCTGTTTTCCTTGAAA
1 A-AATTTGTCTCTCTTG-AGATGGTTTCCCTTGAAACAAAATCTTTGAATCTGTTTTCCTTGAAA
*
1595582 CAAAGTTTTGTCTCTCTTGAGACAATTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACATTTTC
64 CAAAGTTTTGTCTCTCTTGAGACAATTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACAATTTC
1595647 TCTTAAAAC
129 TCTTAAAAC
1595656 AAATTTTGTCTCTCTTGAGATGGTTTCCCTTGAAACAAAATCTTTGAATCTGTTTTCCTTGAAAC
1 AAA-TTTGTCTCTCTTGAGATGGTTTCCCTTGAAACAAAATCTTTGAATCTGTTTTCCTTGAAAC
* * * *
1595721 AAAGTTTTGTCTCTCTTAAGTC-ATTTACTCTTAAAACAATTTTTTTCTCTCTTGAGA
65 AAAGTTTTGTCTCTCTTGAGACAATTT-CTCTTAAAACAAATTTTGTCTCTCTTGAGA
1595778 TGGTTTCCCT
Statistics
Matches: 212, Mismatches: 28, Indels: 28
0.79 0.10 0.10
Matches are distributed among these distances:
131 11 0.05
132 67 0.32
133 29 0.14
137 4 0.02
138 96 0.45
139 5 0.02
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.40
Consensus pattern (137 bp):
AAATTTGTCTCTCTTGAGATGGTTTCCCTTGAAACAAAATCTTTGAATCTGTTTTCCTTGAAACA
AAGTTTTGTCTCTCTTGAGACAATTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACAATTTCTC
TTAAAAC
Found at i:1595737 original size:102 final size:101
Alignment explanation
Indices: 1595607--1595844 Score: 368
Period size: 102 Copynumber: 2.3 Consensus size: 101
1595597 CTTGAGACAA
* *
1595607 TTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACATTTTCTCTTAAAACAAATTTTGTCTCTCTT
1 TTTC-CTTGAAACAAATTTTGTCTCTCTTGAGACATTTACTCTTAAAACAAATTTTGTCTCTCTT
*
1595672 GAGATGGTTTCCCTTGAAACAAAATCTTTGAATCTGT
65 GAGATGGTTTCCCTTGAAACAAAATCTTTGAATATGT
* * * *
1595709 TTTCCTTGAAACAAAGTTTTGTCTCTCTTAAGTCATTTACTCTTAAAACAATTTTTTTCTCTCTT
1 TTTCCTTGAAACAAA-TTTTGTCTCTCTTGAGACATTTACTCTTAAAACAAATTTTGTCTCTCTT
*
1595774 GAGATGGTTTCCCTTGAAATAAAATCTTTGAATATGT
65 GAGATGGTTTCCCTTGAAACAAAATCTTTGAATATGT
* *
1595811 TTTCCTTGAAACAAATTTCGTCTCCCTTGAGACA
1 TTTCCTTGAAACAAATTTTGTCTCTCTTGAGACA
1595845 ATCTCTTTTG
Statistics
Matches: 123, Mismatches: 12, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
101 25 0.20
102 98 0.80
ACGTcount: A:0.27, C:0.19, G:0.11, T:0.43
Consensus pattern (101 bp):
TTTCCTTGAAACAAATTTTGTCTCTCTTGAGACATTTACTCTTAAAACAAATTTTGTCTCTCTTG
AGATGGTTTCCCTTGAAACAAAATCTTTGAATATGT
Found at i:1595903 original size:36 final size:36
Alignment explanation
Indices: 1595818--1595932 Score: 124
Period size: 36 Copynumber: 3.2 Consensus size: 36
1595808 TGTTTTCCTT
* * * *
1595818 GAAACAAATTTCGTCTCCCTTGAGACAATCTCTTTTG
1 GAAACAAATTTTGTCTCTCTTGAGACAATTTC-TCTG
* * *
1595855 G-AACTAAGTTTTGTATCTCTTGAAACAATTTCTCTG
1 GAAAC-AAATTTTGTCTCTCTTGAGACAATTTCTCTG
* *
1595891 GAAACAAATTTTGTCTCTCTTGAGATAATTTCTCTT
1 GAAACAAATTTTGTCTCTCTTGAGACAATTTCTCTG
1595927 GAAACA
1 GAAACA
1595933 CAAAAAACCC
Statistics
Matches: 64, Mismatches: 12, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
36 39 0.61
37 25 0.39
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (36 bp):
GAAACAAATTTTGTCTCTCTTGAGACAATTTCTCTG
Found at i:1596036 original size:35 final size:35
Alignment explanation
Indices: 1595910--1596039 Score: 178
Period size: 35 Copynumber: 3.8 Consensus size: 35
1595900 TTTGTCTCTC
* * *
1595910 TTGAGATAATTTCTCTTGAAACAC--AAAAAACCC
1 TTGAAATAGTTTCTCTTGAAACACAAAAAAAACCT
*
1595943 TTGAAATAGTTTCTCTTGAAACAAAAAAAAAACCT
1 TTGAAATAGTTTCTCTTGAAACACAAAAAAAACCT
1595978 TTGAAATCA-TTTCTCTTGAAACACAAAAAAAACCT
1 TTGAAAT-AGTTTCTCTTGAAACACAAAAAAAACCT
1596013 TTGAAA-ATGTTTCTCTTGAAACACAAA
1 TTGAAATA-GTTTCTCTTGAAACACAAA
1596040 GACCCTCGAG
Statistics
Matches: 87, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
33 22 0.25
35 64 0.74
36 1 0.01
ACGTcount: A:0.45, C:0.18, G:0.08, T:0.29
Consensus pattern (35 bp):
TTGAAATAGTTTCTCTTGAAACACAAAAAAAACCT
Found at i:1597272 original size:32 final size:31
Alignment explanation
Indices: 1597236--1597312 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
1597226 TGGGGCCGTG
*
1597236 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCGCA
** **
1597268 GGGCCTACCCGAGAATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAAACATCTCAGGGCCGCA
*
1597299 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
1597313 GTCACATTAG
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
31 24 0.65
32 13 0.35
ACGTcount: A:0.27, C:0.31, G:0.27, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCGCA
Found at i:1597295 original size:63 final size:63
Alignment explanation
Indices: 1597189--1597312 Score: 144
Period size: 63 Copynumber: 2.0 Consensus size: 63
1597179 CCCTAAGGGA
* ** ** *
1597189 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTTGGGGCCGTGGGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
* *
1597252 ACATCTTAGGGCC-GCAGGGCCTACCCGAGA-ATGATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAGATA-GATCTCAGGGCCGCAGAGCCTACCTAAGA
1597313 GTCACATTAG
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
62 2 0.04
63 49 0.96
ACGTcount: A:0.26, C:0.28, G:0.28, T:0.18
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:1598236 original size:17 final size:17
Alignment explanation
Indices: 1598214--1598288 Score: 123
Period size: 17 Copynumber: 4.4 Consensus size: 17
1598204 AATGGTCAAC
* *
1598214 GGTCAACGGTCGGGTCA
1 GGTCAACAGTCGGGTCG
*
1598231 GGTCAACGGTCGGGTCG
1 GGTCAACAGTCGGGTCG
1598248 GGTCAACAGTCGGGTCG
1 GGTCAACAGTCGGGTCG
1598265 GGTCAACAGTCGGGTCG
1 GGTCAACAGTCGGGTCG
1598282 GGTCAAC
1 GGTCAAC
1598289 CCGGTTCAGA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 56 1.00
ACGTcount: A:0.17, C:0.24, G:0.41, T:0.17
Consensus pattern (17 bp):
GGTCAACAGTCGGGTCG
Found at i:1598241 original size:7 final size:7
Alignment explanation
Indices: 1598181--1598224 Score: 54
Period size: 7 Copynumber: 6.4 Consensus size: 7
1598171 GTCAAAGAAA
1598181 GTCAACG
1 GTCAACG
1598188 GTCAACG
1 GTCAACG
*
1598195 GTC-ACA
1 GTCAACG
* *
1598201 ATCAATG
1 GTCAACG
1598208 GTCAACG
1 GTCAACG
1598215 GTCAACG
1 GTCAACG
1598222 GTC
1 GTC
1598225 GGGTCAGGTC
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
6 4 0.13
7 26 0.87
ACGTcount: A:0.30, C:0.27, G:0.25, T:0.18
Consensus pattern (7 bp):
GTCAACG
Found at i:1598316 original size:10 final size:10
Alignment explanation
Indices: 1598284--1598333 Score: 50
Period size: 9 Copynumber: 5.1 Consensus size: 10
1598274 TCGGGTCGGG
*
1598284 TCAACCCGGT
1 TCAAACCGGT
*
1598294 TCAGACCGG-
1 TCAAACCGGT
1598303 TCAAACCGGT
1 TCAAACCGGT
*
1598313 TCAAAACTGG-
1 TC-AAACCGGT
1598323 TCAAACCGGT
1 TCAAACCGGT
1598333 T
1 T
1598334 TTCCAGCAGC
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
9 14 0.44
10 12 0.38
11 6 0.19
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.20
Consensus pattern (10 bp):
TCAAACCGGT
Found at i:1598324 original size:20 final size:19
Alignment explanation
Indices: 1598282--1598333 Score: 68
Period size: 20 Copynumber: 2.7 Consensus size: 19
1598272 AGTCGGGTCG
* *
1598282 GGTCAACCCGGTTCAGACC
1 GGTCAAACCGGTTCAAACC
*
1598301 GGTCAAACCGGTTCAAAACT
1 GGTCAAACCGGTTC-AAACC
1598321 GGTCAAACCGGTT
1 GGTCAAACCGGTT
1598334 TTCCAGCAGC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 13 0.45
20 16 0.55
ACGTcount: A:0.27, C:0.29, G:0.25, T:0.19
Consensus pattern (19 bp):
GGTCAAACCGGTTCAAACC
Found at i:1605459 original size:13 final size:13
Alignment explanation
Indices: 1605441--1605465 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1605431 GGTCAAAGAA
1605441 AGTCAACGGTCAC
1 AGTCAACGGTCAC
1605454 AGTCAACGGTCA
1 AGTCAACGGTCA
1605466 ACGGTCGGGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.28, G:0.24, T:0.16
Consensus pattern (13 bp):
AGTCAACGGTCAC
Found at i:1605483 original size:17 final size:17
Alignment explanation
Indices: 1605461--1605540 Score: 106
Period size: 17 Copynumber: 4.4 Consensus size: 17
1605451 CACAGTCAAC
*
1605461 GGTCAACGGTCGGGTCG
1 GGTCAACAGTCGGGTCG
1605478 GGTCAACAGTCCGGTCGGGTCG
1 GGTCAACA-----GTCGGGTCG
1605500 GGTCAACAGTCGGGTCG
1 GGTCAACAGTCGGGTCG
1605517 GGTCAACAGTCGGGTCG
1 GGTCAACAGTCGGGTCG
1605534 GGTCAAC
1 GGTCAAC
1605541 CCGGTTTAGA
Statistics
Matches: 57, Mismatches: 1, Indels: 10
0.84 0.01 0.15
Matches are distributed among these distances:
17 40 0.70
22 17 0.30
ACGTcount: A:0.16, C:0.25, G:0.41, T:0.17
Consensus pattern (17 bp):
GGTCAACAGTCGGGTCG
Found at i:1605505 original size:39 final size:39
Alignment explanation
Indices: 1605461--1605537 Score: 136
Period size: 39 Copynumber: 2.0 Consensus size: 39
1605451 CACAGTCAAC
*
1605461 GGTCAACGGTCGGGTCGGGTCAACAGTCCGGTCGGGTCG
1 GGTCAACAGTCGGGTCGGGTCAACAGTCCGGTCGGGTCG
*
1605500 GGTCAACAGTCGGGTCGGGTCAACAGTCGGGTCGGGTC
1 GGTCAACAGTCGGGTCGGGTCAACAGTCCGGTCGGGTC
1605538 AACCCGGTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.14, C:0.25, G:0.43, T:0.18
Consensus pattern (39 bp):
GGTCAACAGTCGGGTCGGGTCAACAGTCCGGTCGGGTCG
Found at i:1605537 original size:22 final size:22
Alignment explanation
Indices: 1605467--1605520 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
1605457 CAACGGTCAA
1605467 CGGTCGGGTCGGGTCAACAGTC
1 CGGTCGGGTCGGGTCAACAGTC
1605489 CGGTCGGGTCGGGTCAACAGTC
1 CGGTCGGGTCGGGTCAACAGTC
*
1605511 GGGTCGGGTC
1 CGGTCGGGTC
1605521 AACAGTCGGG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.11, C:0.26, G:0.44, T:0.19
Consensus pattern (22 bp):
CGGTCGGGTCGGGTCAACAGTC
Found at i:1605558 original size:19 final size:19
Alignment explanation
Indices: 1605534--1605586 Score: 70
Period size: 19 Copynumber: 2.8 Consensus size: 19
1605524 AGTCGGGTCG
* *
1605534 GGTCAACCCGGTTTAGACC
1 GGTCAAACCGGTTCAGACC
* *
1605553 GGTCAAATCAGTTCAGACC
1 GGTCAAACCGGTTCAGACC
1605572 GGTCAAACCGGTTCA
1 GGTCAAACCGGTTCA
1605587 AAACTGGTTA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.26, C:0.28, G:0.25, T:0.21
Consensus pattern (19 bp):
GGTCAAACCGGTTCAGACC
Found at i:1607247 original size:28 final size:29
Alignment explanation
Indices: 1607192--1607273 Score: 98
Period size: 27 Copynumber: 2.8 Consensus size: 29
1607182 AACTTATTTA
*
1607192 ATTTTTTATTTTA--ATTTTTTTCTCTTG
1 ATTTATTATTTTATTATTTTTTTCTCTTG
1607219 ATTTATTATTTTATTATTTTTTTCT-TTG
1 ATTTATTATTTTATTATTTTTTTCTCTTG
1607247 ATTTATTTAATATTTATTATTATTTTT
1 ATTTA-TT-AT-TTTATTATT-TTTTT
1607274 TACCTAACAT
Statistics
Matches: 48, Mismatches: 1, Indels: 7
0.86 0.02 0.12
Matches are distributed among these distances:
27 12 0.25
28 8 0.17
29 12 0.25
30 2 0.04
31 9 0.19
32 5 0.10
ACGTcount: A:0.21, C:0.04, G:0.02, T:0.73
Consensus pattern (29 bp):
ATTTATTATTTTATTATTTTTTTCTCTTG
Found at i:1609165 original size:15 final size:14
Alignment explanation
Indices: 1609145--1609201 Score: 62
Period size: 15 Copynumber: 3.9 Consensus size: 14
1609135 CACAAATCTC
1609145 ACATTTTCACATAGA
1 ACATTTTCACATA-A
*
1609160 ACA-TTTCATATTAA
1 ACATTTTCACA-TAA
*
1609174 ACATATTCACATATA
1 ACATTTTCACATA-A
1609189 ACATTTTCACATA
1 ACATTTTCACATA
1609202 CCAATAAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
14 12 0.34
15 23 0.66
ACGTcount: A:0.42, C:0.19, G:0.02, T:0.37
Consensus pattern (14 bp):
ACATTTTCACATAA
Found at i:1611105 original size:35 final size:35
Alignment explanation
Indices: 1611053--1611150 Score: 187
Period size: 35 Copynumber: 2.8 Consensus size: 35
1611043 ACCCTGTTTG
1611053 AACTTGTTTTTTGAACTTTCTCATATTTCTTCTTGT
1 AACTTG-TTTTTGAACTTTCTCATATTTCTTCTTGT
1611089 AACTTGTTTTTGAACTTTCTCATATTTCTTCTTGT
1 AACTTGTTTTTGAACTTTCTCATATTTCTTCTTGT
1611124 AACTTGTTTTTGAACTTTCTCATATTT
1 AACTTGTTTTTGAACTTTCTCATATTT
1611151 ATTGTTTCTA
Statistics
Matches: 62, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
35 56 0.90
36 6 0.10
ACGTcount: A:0.18, C:0.16, G:0.08, T:0.57
Consensus pattern (35 bp):
AACTTGTTTTTGAACTTTCTCATATTTCTTCTTGT
Found at i:1611830 original size:99 final size:99
Alignment explanation
Indices: 1611654--1611855 Score: 314
Period size: 99 Copynumber: 2.0 Consensus size: 99
1611644 TTATAATATT
* * **
1611654 ATATGTATACAATAAAGCTTGAGCTGTCCCTCTAGAGCAATTGGTTAAACGCCCCATCTTTATGG
1 ATATCTATACAATAAAGCTTAAGCTGTCCCTCTAGAGCAATTGGTTAAACGCCCCAGATTTATGG
*
1611719 ATAAGATTTAGCTAGCCTGATAAAGGTGATTATA
66 ATAAGATTTAGCTAGCCTGATAAAAGTGATTATA
* * ** *
1611753 ATATCTATACAATAAAGCTTAAGTTGTCCCTCTAGAGCAATTGGTTAAATGCCCTGGATTTATTG
1 ATATCTATACAATAAAGCTTAAGCTGTCCCTCTAGAGCAATTGGTTAAACGCCCCAGATTTATGG
1611818 ATAAGATTTAGCTAGCCTGATAAAAGTGATTATA
66 ATAAGATTTAGCTAGCCTGATAAAAGTGATTATA
1611852 ATAT
1 ATAT
1611856 TAAGTTGTCC
Statistics
Matches: 93, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
99 93 1.00
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Consensus pattern (99 bp):
ATATCTATACAATAAAGCTTAAGCTGTCCCTCTAGAGCAATTGGTTAAACGCCCCAGATTTATGG
ATAAGATTTAGCTAGCCTGATAAAAGTGATTATA
Found at i:1613002 original size:237 final size:238
Alignment explanation
Indices: 1612578--1613050 Score: 750
Period size: 237 Copynumber: 2.0 Consensus size: 238
1612568 AAAGCAATCA
* *
1612578 GTCCGAGTGATCAGATAGAACTTGTAACACTCCCTTGTGACATTGTCAGCAACTCGAGAAGAAAA
1 GTCCGAGTGATCAGATAGAACTTGTAACACTCCCTTGTGACATTGCCAGCAACCCGAGAAGAAAA
* * *
1612643 TGGGGCATGGTTGATTCCAAGGACAAGACCAATAGACAAAAATGAGGCTCCATCCAGGAGACAAA
66 TAGGGCATGGTCGATTCCAAGGACAAGACCAACAGACAAAAATGAGGCTCCATCCAGGAGACAAA
* * * * *
1612708 ACAATAGCTAATTCATGTTGCATACATCTTAGACATATTTAAGAGCATCATATTTATCATTTTTT
131 ACAAGAACTAATTCATGTTACATACATCTTAGACATATTTAAGAACATCACATTTATCATTTTTT
*
1612773 AGCATATATAATTTTTTGTAGCTTTTAGAGTCAAGTTTCAATT
196 AGCATACATAATTTTTTGTAGCTTTTAGAGTCAAGTTTCAATT
* * *
1612816 GTCCGAGTGATCAGATAGAACTTGTAACACTTCTTTGTGACATTGCCAGTAACCCGAGAAGAAAA
1 GTCCGAGTGATCAGATAGAACTTGTAACACTCCCTTGTGACATTGCCAGCAACCCGAGAAGAAAA
* * * * *
1612881 -AGGGCATGGTCGATTCCAAGGACAATACCAGCAGGCAAAAATGAGGCTCTATCTAGGAGACAAA
66 TAGGGCATGGTCGATTCCAAGGACAAGACCAACAGACAAAAATGAGGCTCCATCCAGGAGACAAA
* *
1612945 ATAAGAACTAATTCATGTTACATACATCTTAGACATATTTAAGAACTTCACATTTATCATTTTTT
131 ACAAGAACTAATTCATGTTACATACATCTTAGACATATTTAAGAACATCACATTTATCATTTTTT
1613010 AGCATACATAATTTTTTGTAGCTTTTAGAGTCAAGTTTCAA
196 AGCATACATAATTTTTTGTAGCTTTTAGAGTCAAGTTTCAA
1613051 CTTCAAGATG
Statistics
Matches: 214, Mismatches: 21, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
237 154 0.72
238 60 0.28
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30
Consensus pattern (238 bp):
GTCCGAGTGATCAGATAGAACTTGTAACACTCCCTTGTGACATTGCCAGCAACCCGAGAAGAAAA
TAGGGCATGGTCGATTCCAAGGACAAGACCAACAGACAAAAATGAGGCTCCATCCAGGAGACAAA
ACAAGAACTAATTCATGTTACATACATCTTAGACATATTTAAGAACATCACATTTATCATTTTTT
AGCATACATAATTTTTTGTAGCTTTTAGAGTCAAGTTTCAATT
Found at i:1613599 original size:86 final size:86
Alignment explanation
Indices: 1613443--1613927 Score: 607
Period size: 85 Copynumber: 5.7 Consensus size: 86
1613433 TATATGTCAC
** * *
1613443 AAAAAACCTTCGAGTTCGATGGCATTCAGTTCAAGGACATATCAAATTTTCAGCATAACTCAAGG
1 AAAAAACCTTCGAGTTCGATTACATTCAGCTCAAGGACATATCAAATTTACAGCATAACTCAAGG
*
1613508 CGAGGAGGGTTATCTGTCAGCA
66 CGAGAAGGGTTATCTGTCAG-A
* *
1613530 AAAAAACCTTCGAGTTCGATAACATTCAGCTCAAGGACATATC-AATTTACAGCATAGCTCAAGG
1 AAAAAACCTTCGAGTTCGATTACATTCAGCTCAAGGACATATCAAATTTACAGCATAACTCAAGG
* * *
1613594 CGAGGAGGGCTATCTGTCAGC
66 CGAGAAGGGTTATCTGTCAGA
* * * * *
1613615 AAAAAACCTTCGAGTTCGATTACATTTAGCTCAATGACATATTAAATATACAACATAACTCAAGG
1 AAAAAACCTTCGAGTTCGATTACATTCAGCTCAAGGACATATCAAATTTACAGCATAACTCAAGG
* *
1613680 CGAGAAGAGTTATCTGTCAGT
66 CGAGAAGGGTTATCTGTCAGA
* * * * * *
1613701 AAAAAATCTTCAAGTTTGATTACATTCAGCTCAAGGAAATATCAAATTTACAGCATAACTTAAGA
1 AAAAAACCTTCGAGTTCGATTACATTCAGCTCAAGGACATATCAAATTTACAGCATAACTCAAGG
*
1613766 CGAGAATGGTTATCTGTCA-A
66 CGAGAAGGGTTATCTGTCAGA
* * * * * * *
1613786 TAAAAACCTTCGAGTTCAATTATATTCAGCTCAAGGGCATATCAAATTTACAGTATAGCTTAAGG
1 AAAAAACCTTCGAGTTCGATTACATTCAGCTCAAGGACATATCAAATTTACAGCATAACTCAAGG
*
1613851 CGAGAAGGGCTATCTGTCA-A
66 CGAGAAGGGTTATCTGTCAGA
* * * * *
1613871 CAAAAACCTTCGAGTTCGATTTCATTCAGCTCAAGGGCAAATCAAATTTACATCATA
1 AAAAAACCTTCGAGTTCGATTACATTCAGCTCAAGGACATATCAAATTTACAGCATA
1613928 GCTTAATTCG
Statistics
Matches: 345, Mismatches: 52, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
85 161 0.47
86 144 0.42
87 40 0.12
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.27
Consensus pattern (86 bp):
AAAAAACCTTCGAGTTCGATTACATTCAGCTCAAGGACATATCAAATTTACAGCATAACTCAAGG
CGAGAAGGGTTATCTGTCAGA
Found at i:1613853 original size:171 final size:170
Alignment explanation
Indices: 1613432--1613933 Score: 616
Period size: 171 Copynumber: 2.9 Consensus size: 170
1613422 GCGAGAAAAA
* ** * *
1613432 CTATATGTCACAAAAAACCTTCGAGTTCGATGGCATTCAGTTCAAGGACATATCAAATTTTCAGC
1 CTATCTGTCACAAAAAACCTTCGAGTTCGATTACATTCAGCTCAAGGACATATCAAATTTACAGC
* *
1613497 ATAACTCAAGGCGAGGAGGGTTATCTGTCAGCAAAAAAACCTTCGAGTTCGATAACATTCAGCTC
66 ATAACTCAAGGCGAGAAGGGTTATCTGTCAG--AAAAAACCTTCGAGTTCGATTACATTCAGCTC
* * * *
1613562 AAGGACATATC-AATTTACAGCATAGCTCAAGGCGAGGAGGG
129 AAGGAAATATCAAATTTACAGCATAGCTTAAGACGAGAAGGG
* * * * *
1613603 CTATCTGTCAGCAAAAAACCTTCGAGTTCGATTACATTTAGCTCAATGACATATTAAATATACAA
1 CTATCTGTCA-CAAAAAACCTTCGAGTTCGATTACATTCAGCTCAAGGACATATCAAATTTACAG
* * * *
1613668 CATAACTCAAGGCGAGAAGAGTTATCTGTCAGTAAAAAATCTTCAAGTTTGATTACATTCAGCTC
65 CATAACTCAAGGCGAGAAGGGTTATCTGTCAG-AAAAAACCTTCGAGTTCGATTACATTCAGCTC
* *
1613733 AAGGAAATATCAAATTTACAGCATAACTTAAGACGAGAATGG
129 AAGGAAATATCAAATTTACAGCATAGCTTAAGACGAGAAGGG
* * * *
1613775 TTATCTGTCA-ATAAAAACCTTCGAGTTCAATTATATTCAGCTCAAGGGCATATCAAATTTACAG
1 CTATCTGTCACA-AAAAACCTTCGAGTTCGATTACATTCAGCTCAAGGACATATCAAATTTACAG
* * * * *
1613839 TATAGCTTAAGGCGAGAAGGGCTATCTGTCA-ACAAAAACCTTCGAGTTCGATTTCATTCAGCTC
65 CATAACTCAAGGCGAGAAGGGTTATCTGTCAGA-AAAAACCTTCGAGTTCGATTACATTCAGCTC
* *
1613903 AAGGGCAA-ATCAAATTTACATCATAGCTTAA
129 AA-GGAAATATCAAATTTACAGCATAGCTTAA
1613934 TTCGAGAAAA
Statistics
Matches: 282, Mismatches: 44, Indels: 11
0.84 0.13 0.03
Matches are distributed among these distances:
169 1 0.00
170 51 0.18
171 121 0.43
172 109 0.39
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.27
Consensus pattern (170 bp):
CTATCTGTCACAAAAAACCTTCGAGTTCGATTACATTCAGCTCAAGGACATATCAAATTTACAGC
ATAACTCAAGGCGAGAAGGGTTATCTGTCAGAAAAAACCTTCGAGTTCGATTACATTCAGCTCAA
GGAAATATCAAATTTACAGCATAGCTTAAGACGAGAAGGG
Found at i:1614290 original size:12 final size:11
Alignment explanation
Indices: 1614273--1614316 Score: 58
Period size: 10 Copynumber: 4.2 Consensus size: 11
1614263 CATCATATCT
1614273 TTTATTTAATTA
1 TTTATTT-ATTA
1614285 TTTATTTATT-
1 TTTATTTATTA
1614295 TTTATTT-TTA
1 TTTATTTATTA
1614305 -TTATTTATTA
1 TTTATTTATTA
1614315 TT
1 TT
1614317 CCTTTTTTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
9 8 0.28
10 10 0.34
11 4 0.14
12 7 0.24
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (11 bp):
TTTATTTATTA
Found at i:1614294 original size:16 final size:15
Alignment explanation
Indices: 1614273--1614316 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
1614263 CATCATATCT
1614273 TTTATTTAATTATTTA
1 TTTATTT-ATTATTTA
*
1614289 TTTATTT-TTATTTT
1 TTTATTTATTATTTA
1614303 TATTATTTATTATT
1 T-TTATTTATTATT
1614317 CCTTTTTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
14 7 0.28
15 6 0.24
16 12 0.48
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (15 bp):
TTTATTTATTATTTA
Found at i:1614312 original size:27 final size:27
Alignment explanation
Indices: 1614272--1614333 Score: 67
Period size: 27 Copynumber: 2.3 Consensus size: 27
1614262 ACATCATATC
1614272 TTTTATTTAATTATTTATT-TATTTTTAT
1 TTTTATTTAATTA-TTATTCT-TTTTTAT
*
1614300 TTTTA-TTATTTATTATTCCTTTTTTA-
1 TTTTATTTAATTATTATT-CTTTTTTAT
1614326 TTTTATTT
1 TTTTATTT
1614334 TGGTCCAGGT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
26 10 0.33
27 14 0.47
28 6 0.20
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (27 bp):
TTTTATTTAATTATTATTCTTTTTTAT
Found at i:1614322 original size:19 final size:18
Alignment explanation
Indices: 1614285--1614328 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
1614275 TATTTAATTA
* *
1614285 TTTATTTATTTTTATTTT
1 TTTATTTATTATTACTTT
*
1614303 TATTATTTATTATTCCTTT
1 T-TTATTTATTATTACTTT
1614322 TTTATTT
1 TTTATTT
1614329 TATTTTGGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.77
Consensus pattern (18 bp):
TTTATTTATTATTACTTT
Found at i:1616906 original size:15 final size:15
Alignment explanation
Indices: 1616888--1616945 Score: 80
Period size: 15 Copynumber: 3.9 Consensus size: 15
1616878 TTCAAATCTC
1616888 ACATTTTCACATAAA
1 ACATTTTCACATAAA
*
1616903 ACATTTTCATATAAA
1 ACATTTTCACATAAA
* * *
1616918 TCATATTCACATATA
1 ACATTTTCACATAAA
1616933 ACATTTTCACATA
1 ACATTTTCACATA
1616946 CCAATAAAAT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 36 1.00
ACGTcount: A:0.43, C:0.19, G:0.00, T:0.38
Consensus pattern (15 bp):
ACATTTTCACATAAA
Found at i:1618019 original size:15 final size:15
Alignment explanation
Indices: 1617999--1618056 Score: 89
Period size: 15 Copynumber: 3.9 Consensus size: 15
1617989 GTTCAAATCT
1617999 ACATTTTCACATAAA
1 ACATTTTCACATAAA
*
1618014 ACATTTTCATATAAA
1 ACATTTTCACATAAA
* *
1618029 ACATATTCACATATA
1 ACATTTTCACATAAA
1618044 ACATTTTCACATA
1 ACATTTTCACATA
1618057 CCAATAAAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 38 1.00
ACGTcount: A:0.45, C:0.19, G:0.00, T:0.36
Consensus pattern (15 bp):
ACATTTTCACATAAA
Found at i:1619125 original size:15 final size:15
Alignment explanation
Indices: 1619107--1619164 Score: 82
Period size: 15 Copynumber: 3.9 Consensus size: 15
1619097 TTCAAATCTC
1619107 ACATTTTCACATAAA
1 ACATTTTCACATAAA
*
1619122 ACATTTTCATATAAA
1 ACATTTTCACATAAA
*
1619137 AC-TTATTCACATATA
1 ACATT-TTCACATAAA
1619152 ACATTTTCACATA
1 ACATTTTCACATA
1619165 CCAATAAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
14 2 0.05
15 34 0.89
16 2 0.05
ACGTcount: A:0.43, C:0.19, G:0.00, T:0.38
Consensus pattern (15 bp):
ACATTTTCACATAAA
Found at i:1620234 original size:17 final size:15
Alignment explanation
Indices: 1620216--1620270 Score: 83
Period size: 15 Copynumber: 3.7 Consensus size: 15
1620206 AAATCTCATT
1620216 TTTTCACATAAAACA
1 TTTTCACATAAAACA
*
1620231 TTTTCATATAAAACA
1 TTTTCACATAAAACA
* *
1620246 TATTCACATATAACA
1 TTTTCACATAAAACA
1620261 TTTTCACATA
1 TTTTCACATA
1620271 CCAATAAAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 35 1.00
ACGTcount: A:0.44, C:0.18, G:0.00, T:0.38
Consensus pattern (15 bp):
TTTTCACATAAAACA
Found at i:1621584 original size:509 final size:509
Alignment explanation
Indices: 1620620--1621634 Score: 1527
Period size: 510 Copynumber: 2.0 Consensus size: 509
1620610 AAAGACTTTC
1620620 TTGTTTAATCTGGGATCACTTTGCTTGTTCTGTTATTGTTCTTCAAAGAGAGAGATTTTAGTTTT
1 TTGTTTAATCTGGGATCACTTTGCTTGTTCTGTTATTGTTCTTCAAAGAGAGAGATTTTAGTTTT
*
1620685 AAAGGACACAAAATAAATATCTTTAAGTTTTTTTTTCTATGGAGTTTTGCAAGAGATTGATATTC
66 AAAGGACAAAAAATAAATATCTTTAAG-TTTTTTTTCTATGGAGTTTTGCAAGAGATTGATATTC
** * * ** *
1620750 TTTCACATGTCTTTTCTGTGAAAAATATAGCAATCCAGATTCAAAAACCTGCAAACTTTTCATGT
130 TTTCACATCACTTTTCTATGAAAAATATAGCAATCCAGATTCAAAAACCTACAAAAGTTTCAAGT
*
1620815 AAATAACCTCTTATCATCATTCTAGCAACACTTTAAAAGTAAATATGCTCTTGGTTTTAATTGCA
195 AAATAACCTCTTATCATCATTCTAGCAACACTTTAAAAGTAAATATGATCTTGGTTTTAATTGCA
* *
1620880 AAGGTTTTATCTATCTTAATTGCCAATCATTTTTTTCTGTACTGTTTAATCATCACAAGAGAGAG
260 AAGGTTTTATCTATCTTAATTGCCAATCATTTTTTTCTATACTGTTTAATCATCACAAGAAAGAG
* *
1620945 AGAAAAGGAAAAGGAAGCATTTGCAATAAAAGGGTGTTTTTATGGGAAAACATAAAAGTGTGATA
325 AGAAAAGGAAAAGGAAACATTTGCAATAAAAGAGTGTTTTTATGGGAAAACATAAAAGTGTGATA
* *
1621010 AGAAGAAGAGTTCTTTCTTTCTTGCATTTTTTTCAGTCAAAAAGGCAATAGATTCTTAATTAATG
390 AGAAGAAGAGTTCTTTCTTTCTTGCAGTTTTTTCAGCCAAAAAGGCAATAGATTCTTAATTAATG
* *
1621075 TCCT-AATTTAATGAACTGGTTTCATTTTTTTAGTTATGGTTTCATTTCAATTTT
455 TCCTAAATTTAATGAACTGGTTTCACTTTTTCAGTTATGGTTTCATTTCAATTTT
* * * *
1621129 TTGTTTGATCTGGGTTCTCTTTGCTTGTTCTGTTATTGTTCTTTAAAGAGAGAGATTTTAGTTTT
1 TTGTTTAATCTGGGATCACTTTGCTTGTTCTGTTATTGTTCTTCAAAGAGAGAGATTTTAGTTTT
* *
1621194 AAAGGACAAAAAATAATTATCTTTAAG-TTTTTTTCTATGGAGTTTTGCAAGAGATTGATGTTCT
66 AAAGGACAAAAAATAAATATCTTTAAGTTTTTTTTCTATGGAGTTTTGCAAGAGATTGATATTCT
* *
1621258 TTCCCATCACTTTTCTATGAAAAATATAGCAATTCCA-ATTTCAAAAACCTATAAAAGTTTCAAG
131 TTCACATCACTTTTCTATGAAAAATATAGCAA-TCCAGA-TTCAAAAACCTACAAAAGTTTCAAG
* * * * *
1621322 TAAATAAGCTCTTATCATCTTTCTAGCAGA-ACTTTAGAAGTAAATATTATCTTGGTTTTAATTT
194 TAAATAACCTCTTATCATCATTCTAGCA-ACACTTTAAAAGTAAATATGATCTTGGTTTTAATTG
* * * * * *
1621386 CAAAGGTTTTATCTATGTTATTTGCCAGTCATTTTTTTCTCTATACTGTTTAATCGTCATACGAA
258 CAAAGGTTTTATCTATCTTAATTGCCAATCA-TTTTTT-TCTATACTGTTTAATCATCACAAGAA
* * * *
1621451 AGTGAGAAAAGGAAAAGGAAACATTTGCATTAAAAGAGTGTTTTTATGGGAAAGCATGAAAGTGT
321 AGAGAGAAAAGGAAAAGGAAACATTTGCAATAAAAGAGTGTTTTTATGGGAAAACATAAAAGTGT
* * * * * *
1621516 GATAAGAAGGAGAGTTGTTTCTTTCTTG-GGTTTTTTCTGCCAGAAAGGCAGTAGATTCTTAATT
386 GATAAGAAGAAGAGTTCTTTCTTTCTTGCAGTTTTTTCAGCCAAAAAGGCAATAGATTCTTAATT
1621580 AATGTCCTAAATTTAATGAACTGGTTTCACTTTTTCAGTTATGGTTTCATTTCAA
451 AATGTCCTAAATTTAATGAACTGGTTTCACTTTTTCAGTTATGGTTTCATTTCAA
1621635 CTTCTTTCGT
Statistics
Matches: 454, Mismatches: 46, Indels: 11
0.89 0.09 0.02
Matches are distributed among these distances:
507 65 0.14
508 108 0.24
509 131 0.29
510 150 0.33
ACGTcount: A:0.31, C:0.12, G:0.16, T:0.40
Consensus pattern (509 bp):
TTGTTTAATCTGGGATCACTTTGCTTGTTCTGTTATTGTTCTTCAAAGAGAGAGATTTTAGTTTT
AAAGGACAAAAAATAAATATCTTTAAGTTTTTTTTCTATGGAGTTTTGCAAGAGATTGATATTCT
TTCACATCACTTTTCTATGAAAAATATAGCAATCCAGATTCAAAAACCTACAAAAGTTTCAAGTA
AATAACCTCTTATCATCATTCTAGCAACACTTTAAAAGTAAATATGATCTTGGTTTTAATTGCAA
AGGTTTTATCTATCTTAATTGCCAATCATTTTTTTCTATACTGTTTAATCATCACAAGAAAGAGA
GAAAAGGAAAAGGAAACATTTGCAATAAAAGAGTGTTTTTATGGGAAAACATAAAAGTGTGATAA
GAAGAAGAGTTCTTTCTTTCTTGCAGTTTTTTCAGCCAAAAAGGCAATAGATTCTTAATTAATGT
CCTAAATTTAATGAACTGGTTTCACTTTTTCAGTTATGGTTTCATTTCAATTTT
Found at i:1621876 original size:15 final size:16
Alignment explanation
Indices: 1621839--1621883 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 16
1621829 ACATTTTCGC
1621839 ATAAAACATATTCA-T
1 ATAAAACATATTCACT
1621854 ATAAAACATATTCACT
1 ATAAAACATATTCACT
* *
1621870 -TATAACATTTTCAC
1 ATAAAACATATTCAC
1621884 ATACTAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
15 26 0.96
16 1 0.04
ACGTcount: A:0.47, C:0.18, G:0.00, T:0.36
Consensus pattern (16 bp):
ATAAAACATATTCACT
Found at i:1622886 original size:15 final size:15
Alignment explanation
Indices: 1622863--1622920 Score: 71
Period size: 15 Copynumber: 3.9 Consensus size: 15
1622853 TCAAAATCTC
*
1622863 ACATTTTCACATAAA
1 ACATATTCACATAAA
*
1622878 ACATATTCATATAAA
1 ACATATTCACATAAA
* *
1622893 ACATATTCACTTATA
1 ACATATTCACATAAA
*
1622908 ACATTTTCACATA
1 ACATATTCACATA
1622921 CTAATAAAAT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 36 1.00
ACGTcount: A:0.45, C:0.19, G:0.00, T:0.36
Consensus pattern (15 bp):
ACATATTCACATAAA
Found at i:1623504 original size:15 final size:15
Alignment explanation
Indices: 1623481--1623533 Score: 70
Period size: 15 Copynumber: 3.5 Consensus size: 15
1623471 CTTTCTAATT
1623481 TTCACATAAAACATA
1 TTCACATAAAACATA
*
1623496 TTCATATAAAACATA
1 TTCACATAAAACATA
* * *
1623511 TTCACTTATAACATT
1 TTCACATAAAACATA
1623526 TTCACATA
1 TTCACATA
1623534 CTAATAAAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.45, C:0.19, G:0.00, T:0.36
Consensus pattern (15 bp):
TTCACATAAAACATA
Found at i:1624523 original size:15 final size:16
Alignment explanation
Indices: 1624499--1624547 Score: 59
Period size: 15 Copynumber: 3.2 Consensus size: 16
1624489 GGCTCAAATC
1624499 TCAC-ATAAAACATTT
1 TCACTATAAAACATTT
*
1624514 TCA-TATAAAACATAT
1 TCACTATAAAACATTT
*
1624529 TCACT-TATAACATTT
1 TCACTATAAAACATTT
1624544 TCAC
1 TCAC
1624548 ATACCAATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
15 28 0.97
16 1 0.03
ACGTcount: A:0.43, C:0.20, G:0.00, T:0.37
Consensus pattern (16 bp):
TCACTATAAAACATTT
Found at i:1628435 original size:15 final size:15
Alignment explanation
Indices: 1628417--1628446 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1628407 TTCAAATCTC
1628417 ACATTTTCACATAAA
1 ACATTTTCACATAAA
*
1628432 ACATTTTCATATAAA
1 ACATTTTCACATAAA
1628447 CAGTAAAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.47, C:0.17, G:0.00, T:0.37
Consensus pattern (15 bp):
ACATTTTCACATAAA
Found at i:1629320 original size:15 final size:15
Alignment explanation
Indices: 1629302--1629344 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
1629292 TTCAAATCTC
*
1629302 ACATTTTCATATAAA
1 ACATTTTCACATAAA
* *
1629317 ACATATTCACATATA
1 ACATTTTCACATAAA
*
1629332 ACATTTTAACATA
1 ACATTTTCACATA
1629345 CCAATAAAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.47, C:0.16, G:0.00, T:0.37
Consensus pattern (15 bp):
ACATTTTCACATAAA
Found at i:1630380 original size:15 final size:15
Alignment explanation
Indices: 1630362--1630419 Score: 80
Period size: 15 Copynumber: 3.9 Consensus size: 15
1630352 TTCAAATCTC
1630362 ACATTTTCACATAAA
1 ACATTTTCACATAAA
*
1630377 ACATTTTCATATAAA
1 ACATTTTCACATAAA
* * *
1630392 ACATATTCACTTATA
1 ACATTTTCACATAAA
1630407 ACATTTTCACATA
1 ACATTTTCACATA
1630420 CCAATAAAAT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 36 1.00
ACGTcount: A:0.43, C:0.19, G:0.00, T:0.38
Consensus pattern (15 bp):
ACATTTTCACATAAA
Found at i:1631488 original size:15 final size:15
Alignment explanation
Indices: 1631470--1631542 Score: 101
Period size: 15 Copynumber: 4.9 Consensus size: 15
1631460 TTCAAATCTC
1631470 ACATTTTCACATAAA
1 ACATTTTCACATAAA
*
1631485 ACATTTTCATATAAA
1 ACATTTTCACATAAA
*
1631500 ACATTTTCATATAAA
1 ACATTTTCACATAAA
* * *
1631515 ACATATTCACTTATA
1 ACATTTTCACATAAA
1631530 ACATTTTCACATA
1 ACATTTTCACATA
1631543 CCAATAAAAT
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 51 1.00
ACGTcount: A:0.44, C:0.18, G:0.00, T:0.38
Consensus pattern (15 bp):
ACATTTTCACATAAA
Found at i:1632629 original size:15 final size:15
Alignment explanation
Indices: 1632588--1632630 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
1632578 TTCAAATCTC
* *
1632588 ACATTTTCATAAAAA
1 ACATTTTCACATAAA
* *
1632603 ACATATTCACATATA
1 ACATTTTCACATAAA
1632618 ACATTTTCACATA
1 ACATTTTCACATA
1632631 CCAATAAAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.47, C:0.19, G:0.00, T:0.35
Consensus pattern (15 bp):
ACATTTTCACATAAA
Found at i:1633551 original size:171 final size:171
Alignment explanation
Indices: 1633262--1633603 Score: 652
Period size: 171 Copynumber: 2.0 Consensus size: 171
1633252 TCTTATTTGC
1633262 CAGTCTTTTTTTTCTATGTACTGTTTAATCATCAAGAGAGAGAAAAACTGAAAAGGAAGTGTTTG
1 CAGTCTTTTTTTTCTATGTACTGTTTAATCATCAAGAGAGAGAAAAACTGAAAAGGAAGTGTTTG
1633327 TATTAAAAGGGTGTTTTTATGGGAAAGCATGAAAGTGTGATAAGAAGAAGAATTGTTTCTTTCTT
66 TATTAAAAGGGTGTTTTTATGGGAAAGCATGAAAGTGTGATAAGAAGAAGAATTGTTTCTTTCTT
1633392 TGGTTTTTTTTTCAGCC-AAAAGGCAGTAGATTCTTAATTA
131 TGGTTTTTTTTTCAGCCAAAAAGGCAGTAGATTCTTAATTA
1633432 CAGTC-TTTTTTTCTATGTACTGTTTAATCATCATAAGAGAGAGAAAAACTGAAAAGGAAGTGTT
1 CAGTCTTTTTTTTCTATGTACTGTTTAATCATC--AAGAGAGAGAAAAACTGAAAAGGAAGTGTT
1633496 TGTATTAAAAGGGTGTTTTTATGGGAAAGCATGAAAGTGTGATAAGAAGAAGAATTGTTTCTTTC
64 TGTATTAAAAGGGTGTTTTTATGGGAAAGCATGAAAGTGTGATAAGAAGAAGAATTGTTTCTTTC
1633561 TTTGGTTTTTTTTTCAGCCAAAAAGGCAGTAGATTCTTAATTA
129 TTTGGTTTTTTTTTCAGCCAAAAAGGCAGTAGATTCTTAATTA
1633604 ATGTCCTAAA
Statistics
Matches: 169, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
169 27 0.16
170 5 0.03
171 114 0.67
172 23 0.14
ACGTcount: A:0.33, C:0.09, G:0.21, T:0.37
Consensus pattern (171 bp):
CAGTCTTTTTTTTCTATGTACTGTTTAATCATCAAGAGAGAGAAAAACTGAAAAGGAAGTGTTTG
TATTAAAAGGGTGTTTTTATGGGAAAGCATGAAAGTGTGATAAGAAGAAGAATTGTTTCTTTCTT
TGGTTTTTTTTTCAGCCAAAAAGGCAGTAGATTCTTAATTA
Found at i:1636780 original size:15 final size:15
Alignment explanation
Indices: 1636762--1636815 Score: 72
Period size: 15 Copynumber: 3.6 Consensus size: 15
1636752 TTCAAATCTC
1636762 ACATTTTCACATAAA
1 ACATTTTCACATAAA
*
1636777 ACATTTTCATATAAA
1 ACATTTTCACATAAA
* * *
1636792 AGATATTCACATATA
1 ACATTTTCACATAAA
1636807 ACATTTTCA
1 ACATTTTCA
1636816 AATACCAATA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.44, C:0.17, G:0.02, T:0.37
Consensus pattern (15 bp):
ACATTTTCACATAAA
Found at i:1638795 original size:15 final size:15
Alignment explanation
Indices: 1638775--1638814 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
1638765 AATCTCACAT
1638775 TTTTCACATAAAACA
1 TTTTCACATAAAACA
* *
1638790 TTTTCATATAATACA
1 TTTTCACATAAAACA
*
1638805 TATTCACATA
1 TTTTCACATA
1638815 TAACCTTTAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.42, C:0.17, G:0.00, T:0.40
Consensus pattern (15 bp):
TTTTCACATAAAACA
Found at i:1639854 original size:15 final size:15
Alignment explanation
Indices: 1639834--1639887 Score: 72
Period size: 15 Copynumber: 3.6 Consensus size: 15
1639824 GTTCAATCTC
1639834 ACATTTTCACATAAA
1 ACATTTTCACATAAA
*
1639849 ACATTTTCATATAAA
1 ACATTTTCACATAAA
* * *
1639864 AGATATTCACATATA
1 ACATTTTCACATAAA
1639879 ACATTTTCA
1 ACATTTTCA
1639888 AATACCAATA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.44, C:0.17, G:0.02, T:0.37
Consensus pattern (15 bp):
ACATTTTCACATAAA
Found at i:1640943 original size:15 final size:15
Alignment explanation
Indices: 1640923--1640977 Score: 56
Period size: 15 Copynumber: 3.7 Consensus size: 15
1640913 AATCTCACAT
1640923 TTTTCACATAAAACA
1 TTTTCACATAAAACA
* *
1640938 TTTTCATATAATACA
1 TTTTCACATAAAACA
* * *
1640953 TATTCACATATAACC
1 TTTTCACATAAAACA
*
1640968 TTTTAACATA
1 TTTTCACATA
1640978 CCAATAAAAT
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.42, C:0.18, G:0.00, T:0.40
Consensus pattern (15 bp):
TTTTCACATAAAACA
Found at i:1642049 original size:15 final size:15
Alignment explanation
Indices: 1642029--1642083 Score: 56
Period size: 15 Copynumber: 3.7 Consensus size: 15
1642019 AATCTCACAT
1642029 TTTTCACATAAAACA
1 TTTTCACATAAAACA
* *
1642044 TTTTCATATAATACA
1 TTTTCACATAAAACA
* * *
1642059 TATTCACATATAACC
1 TTTTCACATAAAACA
*
1642074 TTTTAACATA
1 TTTTCACATA
1642084 CCAATAAAAT
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.42, C:0.18, G:0.00, T:0.40
Consensus pattern (15 bp):
TTTTCACATAAAACA
Found at i:1643156 original size:15 final size:15
Alignment explanation
Indices: 1643136--1643190 Score: 56
Period size: 15 Copynumber: 3.7 Consensus size: 15
1643126 AATCTCACAT
1643136 TTTTCACATAAAACA
1 TTTTCACATAAAACA
* *
1643151 TTTTCATATAATACA
1 TTTTCACATAAAACA
* * *
1643166 TATTCACATATAACC
1 TTTTCACATAAAACA
*
1643181 TTTTAACATA
1 TTTTCACATA
1643191 CCAATAAAAT
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.42, C:0.18, G:0.00, T:0.40
Consensus pattern (15 bp):
TTTTCACATAAAACA
Found at i:1644263 original size:15 final size:15
Alignment explanation
Indices: 1644243--1644297 Score: 56
Period size: 15 Copynumber: 3.7 Consensus size: 15
1644233 AATCTCACAT
1644243 TTTTCACATAAAACA
1 TTTTCACATAAAACA
* *
1644258 TTTTCATATAATACA
1 TTTTCACATAAAACA
* * *
1644273 TATTCACATATAACC
1 TTTTCACATAAAACA
*
1644288 TTTTAACATA
1 TTTTCACATA
1644298 CCAATAAAAT
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.42, C:0.18, G:0.00, T:0.40
Consensus pattern (15 bp):
TTTTCACATAAAACA
Found at i:1645366 original size:15 final size:15
Alignment explanation
Indices: 1645348--1645401 Score: 72
Period size: 15 Copynumber: 3.6 Consensus size: 15
1645338 TTCAAATCTC
1645348 ACATTTTCACATAAA
1 ACATTTTCACATAAA
*
1645363 ACATTTTCATATAAA
1 ACATTTTCACATAAA
* * *
1645378 AGATATTCACATATA
1 ACATTTTCACATAAA
1645393 ACATTTTCA
1 ACATTTTCA
1645402 AATACCAATA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.44, C:0.17, G:0.02, T:0.37
Consensus pattern (15 bp):
ACATTTTCACATAAA
Found at i:1646477 original size:15 final size:15
Alignment explanation
Indices: 1646457--1646511 Score: 56
Period size: 15 Copynumber: 3.7 Consensus size: 15
1646447 AATCTCACAT
1646457 TTTTCACATAAAACA
1 TTTTCACATAAAACA
* *
1646472 TTTTCATATAATACA
1 TTTTCACATAAAACA
* * *
1646487 TATTCACATATAACC
1 TTTTCACATAAAACA
*
1646502 TTTTAACATA
1 TTTTCACATA
1646512 CCAATAAAAT
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.42, C:0.18, G:0.00, T:0.40
Consensus pattern (15 bp):
TTTTCACATAAAACA
Found at i:1647579 original size:15 final size:15
Alignment explanation
Indices: 1647561--1647614 Score: 72
Period size: 15 Copynumber: 3.6 Consensus size: 15
1647551 TTCAAATCTC
1647561 ACATTTTCACATAAA
1 ACATTTTCACATAAA
*
1647576 ACATTTTCATATAAA
1 ACATTTTCACATAAA
* * *
1647591 AGATATTCACATATA
1 ACATTTTCACATAAA
1647606 ACATTTTCA
1 ACATTTTCA
1647615 AATACCAATA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.44, C:0.17, G:0.02, T:0.37
Consensus pattern (15 bp):
ACATTTTCACATAAA
Found at i:1648693 original size:15 final size:15
Alignment explanation
Indices: 1648673--1648727 Score: 56
Period size: 15 Copynumber: 3.7 Consensus size: 15
1648663 AATCTCACAT
1648673 TTTTCACATAAAACA
1 TTTTCACATAAAACA
* *
1648688 TTTTCATATAATACA
1 TTTTCACATAAAACA
* * *
1648703 TATTCACATATAACC
1 TTTTCACATAAAACA
*
1648718 TTTTAACATA
1 TTTTCACATA
1648728 CCAATAAAAT
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.42, C:0.18, G:0.00, T:0.40
Consensus pattern (15 bp):
TTTTCACATAAAACA
Found at i:1649796 original size:15 final size:15
Alignment explanation
Indices: 1649776--1649830 Score: 56
Period size: 15 Copynumber: 3.7 Consensus size: 15
1649766 AATCTCACAT
1649776 TTTTCACATAAAACA
1 TTTTCACATAAAACA
* *
1649791 TTTTCATATAATACA
1 TTTTCACATAAAACA
* * *
1649806 TATTCACATATAACC
1 TTTTCACATAAAACA
*
1649821 TTTTAACATA
1 TTTTCACATA
1649831 CCAATAAAAT
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.42, C:0.18, G:0.00, T:0.40
Consensus pattern (15 bp):
TTTTCACATAAAACA
Found at i:1650898 original size:15 final size:15
Alignment explanation
Indices: 1650880--1650937 Score: 80
Period size: 15 Copynumber: 3.9 Consensus size: 15
1650870 TTCAAATCTC
1650880 ACATTTTCACATAAA
1 ACATTTTCACATAAA
*
1650895 ACATTTTCATATAAA
1 ACATTTTCACATAAA
* * *
1650910 ACATATTCACGTATA
1 ACATTTTCACATAAA
1650925 ACATTTTCACATA
1 ACATTTTCACATA
1650938 CCAATAAAAT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 36 1.00
ACGTcount: A:0.43, C:0.19, G:0.02, T:0.36
Consensus pattern (15 bp):
ACATTTTCACATAAA
Found at i:1652005 original size:15 final size:15
Alignment explanation
Indices: 1651987--1652044 Score: 64
Period size: 15 Copynumber: 3.9 Consensus size: 15
1651977 TTCAAATCTC
1651987 ACATTTTCACATAAA
1 ACATTTTCACATAAA
* *
1652002 ACATTTTTATATAAA
1 ACATTTTCACATAAA
* *
1652017 ACATATTT-ACGTATA
1 ACAT-TTTCACATAAA
1652032 ACATTTTCACATA
1 ACATTTTCACATA
1652045 CCAATAAAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
14 3 0.09
15 29 0.83
16 3 0.09
ACGTcount: A:0.43, C:0.16, G:0.02, T:0.40
Consensus pattern (15 bp):
ACATTTTCACATAAA
Found at i:1653125 original size:15 final size:15
Alignment explanation
Indices: 1653107--1653150 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
1653097 ATATTTTGAC
1653107 ATAAAACATTTTCAT
1 ATAAAACATTTTCAT
* *
1653122 ATAAAAGATATTCAT
1 ATAAAACATTTTCAT
*
1653137 ATATAACATTTTCA
1 ATAAAACATTTTCA
1653151 CATACCAATA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.48, C:0.11, G:0.02, T:0.39
Consensus pattern (15 bp):
ATAAAACATTTTCAT
Found at i:1654228 original size:15 final size:15
Alignment explanation
Indices: 1654208--1654262 Score: 65
Period size: 15 Copynumber: 3.7 Consensus size: 15
1654198 AATCTCACAC
1654208 TTTTCACATAAAACA
1 TTTTCACATAAAACA
* *
1654223 TTTTCATATAATACA
1 TTTTCACATAAAACA
* *
1654238 TATTCACATATAACA
1 TTTTCACATAAAACA
*
1654253 TTTTAACATA
1 TTTTCACATA
1654263 CTAATAAAAT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.44, C:0.16, G:0.00, T:0.40
Consensus pattern (15 bp):
TTTTCACATAAAACA
Found at i:1656773 original size:140 final size:140
Alignment explanation
Indices: 1656608--1656882 Score: 430
Period size: 140 Copynumber: 2.0 Consensus size: 140
1656598 ATTAACTACA
* *
1656608 ATTTAATGGAATGATATAATTTAATAGAACAAATAATTCTTAATTTTCAATATATAAATTATTAA
1 ATTTAATGAAATAATATAATTTAATAG-A-AAATAATTCTTAATTTT-AATATATAAATTATTAA
* * *
1656673 TATAA-CTAAT-AAA-AAATAATTCTTAATAAATATTAAATTGTAATTAATAAATATATATAATA
63 TACAATCTAATAAAAGAAATAATTCTTAAGAAATATTAAATTATAATTAATAAATATATATAATA
1656735 TTAAATTATAATC
128 TTAAATTATAATC
*
1656748 ATTTAATGAAATAATATAATTTAATAGAAAATAATTCTTAATTTTAATATATAAATTATTAATGC
1 ATTTAATGAAATAATATAATTTAATAGAAAATAATTCTTAATTTTAATATATAAATTATTAATAC
* *
1656813 AATTTAATAAAAGAAATAATTCTTAAGAAATATTAAATTATAATTAGTAAATATATATAATATTA
66 AATCTAATAAAAGAAATAATTCTTAAGAAATATTAAATTATAATTAATAAATATATATAATATTA
1656878 AATTA
131 AATTA
1656883 ACAAAAAAAT
Statistics
Matches: 124, Mismatches: 8, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
137 20 0.16
138 21 0.17
139 4 0.03
140 79 0.64
ACGTcount: A:0.52, C:0.03, G:0.04, T:0.41
Consensus pattern (140 bp):
ATTTAATGAAATAATATAATTTAATAGAAAATAATTCTTAATTTTAATATATAAATTATTAATAC
AATCTAATAAAAGAAATAATTCTTAAGAAATATTAAATTATAATTAATAAATATATATAATATTA
AATTATAATC
Found at i:1657126 original size:2 final size:2
Alignment explanation
Indices: 1657121--1657176 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
1657111 ACACACACAC
1657121 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1657163 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
1657177 TTTGAAAACA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1657201 original size:36 final size:35
Alignment explanation
Indices: 1657161--1657246 Score: 138
Period size: 34 Copynumber: 2.5 Consensus size: 35
1657151 ATATATATAT
*
1657161 ATATATATATATATATTTTGAAAACATTTTGAAAAC
1 ATATATATATATATATTTTAAAAACATTTT-AAAAC
*
1657197 ATATATATATATAT-TTTTAAAAACATTTTAAAAT
1 ATATATATATATATATTTTAAAAACATTTTAAAAC
1657231 ATATATATATATATAT
1 ATATATATATATATAT
1657247 ATATATATAA
Statistics
Matches: 47, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
34 18 0.38
35 15 0.32
36 14 0.30
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.45
Consensus pattern (35 bp):
ATATATATATATATATTTTAAAAACATTTTAAAAC
Found at i:1657236 original size:2 final size:2
Alignment explanation
Indices: 1657229--1657260 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1657219 ACATTTTAAA
1657229 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1657261 GTTTTGAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1657288 original size:86 final size:88
Alignment explanation
Indices: 1657143--1657329 Score: 244
Period size: 86 Copynumber: 2.2 Consensus size: 88
1657133 ATATATATAT
1657143 ATATATATATATATATATATATATATATATATATTTTGAAAACATTTTGAAAACATATATATATA
1 ATATATATATATATATATATATATATATATATATTTTGAAAACATTTTGAAAACATATAT-TATA
*
1657208 TATTTTTAAAAAC-A-TTTT-AAA
65 TAGTTTTAAAAACTATTTTTGAAA
* *
1657229 ATATATATATATATATATATATATATA-ATATAGTTTTGAAAAATATTTTTG-AAA-GTATATTA
1 ATATATATATATATATATATATATATATATATA-TTTTG-AAAACA-TTTTGAAAACATATATTA
*
1657291 TATAGTTTTCAAAACTATTTTTGAAA
63 TATAGTTTTAAAAACTATTTTTGAAA
*
1657317 GTATATAT-TATAT
1 ATATATATATATAT
1657330 GGTTTTAAAA
Statistics
Matches: 90, Mismatches: 5, Indels: 11
0.85 0.05 0.10
Matches are distributed among these distances:
85 20 0.22
86 38 0.42
87 17 0.19
88 15 0.17
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.47
Consensus pattern (88 bp):
ATATATATATATATATATATATATATATATATATTTTGAAAACATTTTGAAAACATATATTATAT
AGTTTTAAAAACTATTTTTGAAA
Found at i:1657348 original size:36 final size:36
Alignment explanation
Indices: 1657248--1657341 Score: 131
Period size: 34 Copynumber: 2.7 Consensus size: 36
1657238 TATATATATA
* *
1657248 TATATATAATATAGTTTTGAAAAATATTTTTGAAAG
1 TATATATTATATAGTTTTCAAAAATATTTTTGAAAG
*
1657284 --TATATTATATAGTTTTCAAAACTATTTTTGAAAG
1 TATATATTATATAGTTTTCAAAAATATTTTTGAAAG
*
1657318 TATATATTATATGGTTTT-AAAAAT
1 TATATATTATATAGTTTTCAAAAAT
1657342 GGTTTTTTTT
Statistics
Matches: 51, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
34 31 0.61
35 5 0.10
36 15 0.29
ACGTcount: A:0.41, C:0.02, G:0.10, T:0.47
Consensus pattern (36 bp):
TATATATTATATAGTTTTCAAAAATATTTTTGAAAG
Found at i:1661907 original size:98 final size:99
Alignment explanation
Indices: 1661793--1661993 Score: 305
Period size: 98 Copynumber: 2.0 Consensus size: 99
1661783 TTATAATATT
* * * * *
1661793 ATATGTATACAGTAAAGGTAGAGCTGTCCTTCTAGAGCAATTGGTTAAACGCCAAGACTTTATAG
1 ATATATATACAATAAAGCTAGAGCTGTCCCTCTAGAGCAATTGGTTAAACACCAAGACTTTATAG
*
1661858 ATAAGATTCAGCTAGCCTGAT-AAAGTCATTATA
66 ATAAGATTCAGCTAGCCTAATAAAAGTCATTATA
* * *
1661891 ATATATATACAATAAAGCTTGAGCTGTCCCTCTAGAGCAATTGGTTAAACACCACGGCTTTATAG
1 ATATATATACAATAAAGCTAGAGCTGTCCCTCTAGAGCAATTGGTTAAACACCAAGACTTTATAG
*
1661956 ATAAGATTCAGCTAGCCTAATAAAAGTGATTATA
66 ATAAGATTCAGCTAGCCTAATAAAAGTCATTATA
1661990 ATAT
1 ATAT
1661994 TAAGCGGTCC
Statistics
Matches: 92, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
98 77 0.84
99 15 0.16
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.30
Consensus pattern (99 bp):
ATATATATACAATAAAGCTAGAGCTGTCCCTCTAGAGCAATTGGTTAAACACCAAGACTTTATAG
ATAAGATTCAGCTAGCCTAATAAAAGTCATTATA
Found at i:1663435 original size:12 final size:12
Alignment explanation
Indices: 1663418--1663442 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1663408 ACAAAGCACC
1663418 ATTTGGTGCCTA
1 ATTTGGTGCCTA
1663430 ATTTGGTGCCTA
1 ATTTGGTGCCTA
1663442 A
1 A
1663443 ATTATTTAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.20, C:0.16, G:0.24, T:0.40
Consensus pattern (12 bp):
ATTTGGTGCCTA
Found at i:1670923 original size:17 final size:16
Alignment explanation
Indices: 1670902--1670932 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1670892 GCTTCTAAAT
*
1670902 TTTTTTTAGTTCAAGC
1 TTTTTTGAGTTCAAGC
1670918 TTTTTTGAGTTCAAG
1 TTTTTTGAGTTCAAG
1670933 TTTCAATATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.10, G:0.16, T:0.55
Consensus pattern (16 bp):
TTTTTTGAGTTCAAGC
Found at i:1674313 original size:20 final size:19
Alignment explanation
Indices: 1674284--1674321 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
1674274 GATACCCTAG
1674284 AACCAGAGTATTGATACTC
1 AACCAGAGTATTGATACTC
1674303 AACCTAGAGTATTGATACT
1 AACC-AGAGTATTGATACT
1674322 ACCTTATCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.29
Consensus pattern (19 bp):
AACCAGAGTATTGATACTC
Found at i:1674397 original size:20 final size:20
Alignment explanation
Indices: 1674374--1674411 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1674364 AAATAGGTGG
1674374 GTATCGATA-TCAAAGGGTTA
1 GTATCGATACT-AAAGGGTTA
*
1674394 GTATTGATACTAAAGGGT
1 GTATCGATACTAAAGGGT
1674412 CACTATCGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 15 0.94
21 1 0.06
ACGTcount: A:0.34, C:0.08, G:0.26, T:0.32
Consensus pattern (20 bp):
GTATCGATACTAAAGGGTTA
Found at i:1677479 original size:24 final size:24
Alignment explanation
Indices: 1677407--1677479 Score: 66
Period size: 24 Copynumber: 3.2 Consensus size: 24
1677397 CCATTTATTA
1677407 ACCATAAGCTCGTAAGCTTATTTT
1 ACCATAAGCTCGTAAGCTTATTTT
* * *
1677431 ACCA-AA-TTAC-TTA-C-CATTTGT
1 ACCATAAGCT-CGTAAGCTTATTT-T
1677452 ACCATAAGCTCGTAAGCTTATTTT
1 ACCATAAGCTCGTAAGCTTATTTT
1677476 ACCA
1 ACCA
1677480 ATACACTTTC
Statistics
Matches: 36, Mismatches: 6, Indels: 14
0.64 0.11 0.25
Matches are distributed among these distances:
20 4 0.11
21 6 0.17
22 6 0.17
23 6 0.17
24 10 0.28
25 4 0.11
ACGTcount: A:0.32, C:0.23, G:0.10, T:0.36
Consensus pattern (24 bp):
ACCATAAGCTCGTAAGCTTATTTT
Found at i:1677493 original size:45 final size:45
Alignment explanation
Indices: 1677407--1677493 Score: 140
Period size: 45 Copynumber: 1.9 Consensus size: 45
1677397 CCATTTATTA
*
1677407 ACCATAAGCTCGTAAGCTTATTTTACCAAATTACTTACCATTTGT
1 ACCATAAGCTCGTAAGCTTATTTTACCAAATCACTTACCATTTGT
*
1677452 ACCATAAGCTCGTAAGCTTATTTTACC-AATACACTTTCCATT
1 ACCATAAGCTCGTAAGCTTATTTTACCAAAT-CACTTACCATT
1677494 ATTCCATAAC
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
44 3 0.08
45 36 0.92
ACGTcount: A:0.31, C:0.24, G:0.08, T:0.37
Consensus pattern (45 bp):
ACCATAAGCTCGTAAGCTTATTTTACCAAATCACTTACCATTTGT
Found at i:1684615 original size:24 final size:24
Alignment explanation
Indices: 1684543--1684615 Score: 66
Period size: 24 Copynumber: 3.2 Consensus size: 24
1684533 CCATTTATTA
1684543 ACCATAAGCTCGTAAGCTTATTTT
1 ACCATAAGCTCGTAAGCTTATTTT
* * *
1684567 ACCA-AA-TTAC-TTA-C-CATTTGT
1 ACCATAAGCT-CGTAAGCTTATTT-T
1684588 ACCATAAGCTCGTAAGCTTATTTT
1 ACCATAAGCTCGTAAGCTTATTTT
1684612 ACCA
1 ACCA
1684616 ATATAGTTAC
Statistics
Matches: 36, Mismatches: 6, Indels: 14
0.64 0.11 0.25
Matches are distributed among these distances:
20 4 0.11
21 6 0.17
22 6 0.17
23 6 0.17
24 10 0.28
25 4 0.11
ACGTcount: A:0.32, C:0.23, G:0.10, T:0.36
Consensus pattern (24 bp):
ACCATAAGCTCGTAAGCTTATTTT
Found at i:1684662 original size:45 final size:46
Alignment explanation
Indices: 1684543--1684663 Score: 201
Period size: 45 Copynumber: 2.7 Consensus size: 46
1684533 CCATTTATTA
1684543 ACCATAAGCTCGTAAGCTTATTTTACCAA-ATTACTTACCATTTGT
1 ACCATAAGCTCGTAAGCTTATTTTACCAATATTACTTACCATTTGT
*
1684588 ACCATAAGCTCGTAAGCTTATTTTACCAATA-TAGTTACCATTTGT
1 ACCATAAGCTCGTAAGCTTATTTTACCAATATTACTTACCATTTGT
* *
1684633 GCCATAAGCTCGTAATCTTATTTTACCAATA
1 ACCATAAGCTCGTAAGCTTATTTTACCAATA
1684664 CACTTGACAT
Statistics
Matches: 72, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
45 71 0.99
46 1 0.01
ACGTcount: A:0.31, C:0.21, G:0.10, T:0.37
Consensus pattern (46 bp):
ACCATAAGCTCGTAAGCTTATTTTACCAATATTACTTACCATTTGT
Found at i:1684887 original size:60 final size:58
Alignment explanation
Indices: 1684756--1684893 Score: 150
Period size: 60 Copynumber: 2.3 Consensus size: 58
1684746 ATAAGCACCA
* * * *
1684756 TAGTGCTATCCCGAGTATGACACATAAGGTCAAGTCCACCATCTGTACTAGGTATCCTT
1 TAGTG-TATCCCGAATATGACACATAAGGTCAAGCCCACCATATATACTAGGTATCCTT
* ** * **
1684815 AAGTACAGTCCCGAATATGGCACATAAGGTCGTGCCCACCAATATATACTAGGTATCCTT
1 TAGTGTA-TCCCGAATATGACACATAAGGTCAAGCCCACC-ATATATACTAGGTATCCTT
1684875 TAGTGTATTCCCGAATATG
1 TAGTGTA-TCCCGAATATG
1684894 CATCCTGCTG
Statistics
Matches: 63, Mismatches: 14, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
58 1 0.02
59 30 0.48
60 32 0.51
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.28
Consensus pattern (58 bp):
TAGTGTATCCCGAATATGACACATAAGGTCAAGCCCACCATATATACTAGGTATCCTT
Found at i:1685203 original size:15 final size:16
Alignment explanation
Indices: 1685183--1685219 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
1685173 CTTCCTGATG
1685183 ATGTATAA-AACATCC
1 ATGTATAATAACATCC
*
1685198 ATGTATAATAACATGC
1 ATGTATAATAACATCC
1685214 ATGTAT
1 ATGTAT
1685220 TGCACTCACC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (16 bp):
ATGTATAATAACATCC
Found at i:1692062 original size:16 final size:17
Alignment explanation
Indices: 1692041--1692076 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
1692031 GGTTTAAGTT
*
1692041 TTTTGTTTA-TTATTTA
1 TTTTGTTCATTTATTTA
1692057 TTTTGTTCATTTATTTA
1 TTTTGTTCATTTATTTA
1692074 TTT
1 TTT
1692077 ACTTAAGATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.17, C:0.03, G:0.06, T:0.75
Consensus pattern (17 bp):
TTTTGTTCATTTATTTA
Found at i:1700703 original size:54 final size:54
Alignment explanation
Indices: 1700621--1700744 Score: 185
Period size: 54 Copynumber: 2.3 Consensus size: 54
1700611 CTATATGTAC
*
1700621 TATAGGCACTAAGTGTGCAACACACAAAATTCATCATATGTTGATGAACAACAG
1 TATAGGCACTAAGTGTGAAACACACAAAATTCATCATATGTTGATGAACAACAG
* * * *
1700675 TATAGGCACTAAGTGTGAAACTCACAAAATTCATTATATGTTGATGAACGACCG
1 TATAGGCACTAAGTGTGAAACACACAAAATTCATCATATGTTGATGAACAACAG
* *
1700729 TATTGGCACTATGTGT
1 TATAGGCACTAAGTGT
1700745 ACACCCCAGA
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 63 1.00
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.28
Consensus pattern (54 bp):
TATAGGCACTAAGTGTGAAACACACAAAATTCATCATATGTTGATGAACAACAG
Found at i:1706374 original size:54 final size:54
Alignment explanation
Indices: 1706306--1706416 Score: 159
Period size: 54 Copynumber: 2.1 Consensus size: 54
1706296 CTATATGAAC
* * *
1706306 TATAGACACTAAGTGTACAACCCACGAAATTCATTATATGTTGATGAACAACCG
1 TATAGACACAAAGTGTACAACCAACGAAATTCATCATATGTTGATGAACAACCG
* * * *
1706360 TATAGGCACAAAGTGTACAACCAATGGAATTCATCATATGTTGATGAACGACCG
1 TATAGACACAAAGTGTACAACCAACGAAATTCATCATATGTTGATGAACAACCG
1706414 TAT
1 TAT
1706417 CAGCACTACG
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 50 1.00
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.26
Consensus pattern (54 bp):
TATAGACACAAAGTGTACAACCAACGAAATTCATCATATGTTGATGAACAACCG
Found at i:1729337 original size:21 final size:21
Alignment explanation
Indices: 1729311--1729354 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
1729301 TGGTGGGAAA
1729311 GCATTGTAGTTGCTCGCTCAC
1 GCATTGTAGTTGCTCGCTCAC
1729332 GCATTGTAGTTGCTCGCTCAC
1 GCATTGTAGTTGCTCGCTCAC
1729353 GC
1 GC
1729355 CTTAAGTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.14, C:0.30, G:0.25, T:0.32
Consensus pattern (21 bp):
GCATTGTAGTTGCTCGCTCAC
Found at i:1740689 original size:23 final size:23
Alignment explanation
Indices: 1740662--1740705 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
1740652 ATTGACGTTA
*
1740662 TTGGTCAAAGTCAATAGTCAACC
1 TTGGTCAAACTCAATAGTCAACC
*
1740685 TTGGTCAAACTCAATGGTCAA
1 TTGGTCAAACTCAATAGTCAA
1740706 GTCAAAGTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.27
Consensus pattern (23 bp):
TTGGTCAAACTCAATAGTCAACC
Found at i:1754484 original size:20 final size:20
Alignment explanation
Indices: 1754461--1754498 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1754451 CGCCATTCAT
*
1754461 GAATGGTACATGCCATCTAA
1 GAATGGCACATGCCATCTAA
*
1754481 GAATGGCCCATGCCATCT
1 GAATGGCACATGCCATCT
1754499 TCTATATCCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.24
Consensus pattern (20 bp):
GAATGGCACATGCCATCTAA
Found at i:1758196 original size:5 final size:5
Alignment explanation
Indices: 1758186--1758235 Score: 50
Period size: 5 Copynumber: 10.2 Consensus size: 5
1758176 TACAATATAC
** *
1758186 TTATT TTATT TTATT TTA-T TTCCT TCATT TTAATT TTATT TTA-T TTATT
1 TTATT TTATT TTATT TTATT TTATT TTATT TT-ATT TTATT TTATT TTATT
1758235 T
1 T
1758236 AGTTATTTTG
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
4 7 0.19
5 25 0.68
6 5 0.14
ACGTcount: A:0.20, C:0.06, G:0.00, T:0.74
Consensus pattern (5 bp):
TTATT
Found at i:1758201 original size:10 final size:10
Alignment explanation
Indices: 1758186--1758235 Score: 50
Period size: 9 Copynumber: 5.1 Consensus size: 10
1758176 TACAATATAC
1758186 TTATTTTATT
1 TTATTTTATT
1758196 TTATTTTA-T
1 TTATTTTATT
** *
1758205 TTCCTTCATT
1 TTATTTTATT
1758215 TTAATTTTATT
1 TT-ATTTTATT
1758226 TTA-TTTATT
1 TTATTTTATT
1758235 T
1 T
1758236 AGTTATTTTG
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
9 13 0.41
10 12 0.38
11 7 0.22
ACGTcount: A:0.20, C:0.06, G:0.00, T:0.74
Consensus pattern (10 bp):
TTATTTTATT
Found at i:1759902 original size:56 final size:56
Alignment explanation
Indices: 1759815--1760061 Score: 334
Period size: 56 Copynumber: 4.4 Consensus size: 56
1759805 GAAATGAATA
* * * * *
1759815 CACTTAGTATGCATTTCCT-AGTTTTTGCACATATAGTGCCCATATAGAAATTCGTC
1 CACTTAGTATGAATTTCTTAAG-TTTTACACATATAGTGCCCATACAGAAATTCATC
* *
1759871 CACTTAGTATGAATTTCTTAAGTTTTACACATATAGTGCCCATACAAAAATCCATC
1 CACTTAGTATGAATTTCTTAAGTTTTACACATATAGTGCCCATACAGAAATTCATC
** *
1759927 CACTTAGTATGAATTTCTTAAGTTTTACACATATAGTGTGCATACGGAAATTCATC
1 CACTTAGTATGAATTTCTTAAGTTTTACACATATAGTGCCCATACAGAAATTCATC
* * * * *
1759983 CACTCAGTTTGAATTTCTTAAGTTTTACACATACAGCGCCCATACGGAAATTCATC
1 CACTTAGTATGAATTTCTTAAGTTTTACACATATAGTGCCCATACAGAAATTCATC
*
1760039 CACTTAGTATGAATTTATTAAGT
1 CACTTAGTATGAATTTCTTAAGT
1760062 CATTGCACAC
Statistics
Matches: 169, Mismatches: 21, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
56 167 0.99
57 2 0.01
ACGTcount: A:0.32, C:0.20, G:0.13, T:0.36
Consensus pattern (56 bp):
CACTTAGTATGAATTTCTTAAGTTTTACACATATAGTGCCCATACAGAAATTCATC
Found at i:1760514 original size:20 final size:20
Alignment explanation
Indices: 1760489--1760537 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
1760479 TGTTTTGAAT
1760489 GGTATCGATAC-CTTCCCTTC
1 GGTATCGATACTC-TCCCTTC
* *
1760509 GGTATCGATACTCTCTCTTT
1 GGTATCGATACTCTCCCTTC
1760529 GGTATCGAT
1 GGTATCGAT
1760538 GCTGATTGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 25 0.96
21 1 0.04
ACGTcount: A:0.16, C:0.27, G:0.18, T:0.39
Consensus pattern (20 bp):
GGTATCGATACTCTCCCTTC
Found at i:1763499 original size:32 final size:32
Alignment explanation
Indices: 1763458--1763523 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
1763448 AATTTCGCGT
1763458 ACAACTTCTTATCACGAAGTATCTGAAGAACC
1 ACAACTTCTTATCACGAAGTATCTGAAGAACC
1763490 ACAACTTCTTATCACGAAGTATCTGAAGAACC
1 ACAACTTCTTATCACGAAGTATCTGAAGAACC
1763522 AC
1 AC
1763524 TCGAAGATGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.38, C:0.26, G:0.12, T:0.24
Consensus pattern (32 bp):
ACAACTTCTTATCACGAAGTATCTGAAGAACC
Found at i:1764108 original size:53 final size:53
Alignment explanation
Indices: 1764028--1764134 Score: 196
Period size: 53 Copynumber: 2.0 Consensus size: 53
1764018 TAGGATTATG
* *
1764028 TTTTGTCTGATAATATCATAATCTAATGTACGCTCAAGTATTCGGGTCTATCT
1 TTTTGTCTGACAATATCATAATCTAATGTACGCTCAAGTATTCGGGTATATCT
1764081 TTTTGTCTGACAATATCATAATCTAATGTACGCTCAAGTATTCGGGTATATCT
1 TTTTGTCTGACAATATCATAATCTAATGTACGCTCAAGTATTCGGGTATATCT
1764134 T
1 T
1764135 CTATACCAGG
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 52 1.00
ACGTcount: A:0.27, C:0.17, G:0.15, T:0.41
Consensus pattern (53 bp):
TTTTGTCTGACAATATCATAATCTAATGTACGCTCAAGTATTCGGGTATATCT
Found at i:1767082 original size:90 final size:88
Alignment explanation
Indices: 1766968--1767141 Score: 285
Period size: 90 Copynumber: 2.0 Consensus size: 88
1766958 TCCAGAATAT
* *
1766968 TTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTAATATGATTAG
1 TTAAATTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAA-CCCAAATATGATTAG
1767033 GATAACTTAGATATAAAAGGATTA
65 GATAACTTAGATATAAAAGGATTA
1767057 TTAAATTCTAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCAAATATGATTAG
1 TTAAATTC-AATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCAAATATGATTAG
* * *
1767122 GGTAACTTGGCTATAAAAGG
65 GATAACTTAGATATAAAAGG
1767142 GTGTGTTAGG
Statistics
Matches: 79, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
89 38 0.48
90 41 0.52
ACGTcount: A:0.47, C:0.06, G:0.10, T:0.37
Consensus pattern (88 bp):
TTAAATTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCAAATATGATTAGG
ATAACTTAGATATAAAAGGATTA
Found at i:1770328 original size:20 final size:20
Alignment explanation
Indices: 1770299--1770339 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
1770289 AACCAGATTG
1770299 CCCAGAGGGTACAGATACCC
1 CCCAGAGGGTACAGATACCC
*
1770319 CCCAGGGGGTACAGATACCC
1 CCCAGAGGGTACAGATACCC
1770339 C
1 C
1770340 ATGAATGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.27, C:0.37, G:0.27, T:0.10
Consensus pattern (20 bp):
CCCAGAGGGTACAGATACCC
Found at i:1770405 original size:23 final size:23
Alignment explanation
Indices: 1770373--1770417 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1770363 AAACAGAATG
1770373 TCCAGAGGGTACAGATACCCCCC
1 TCCAGAGGGTACAGATACCCCCC
* * *
1770396 TCCAGGGGGTACCGATTCCCCC
1 TCCAGAGGGTACAGATACCCCC
1770418 TTATGTAACA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.40, G:0.24, T:0.16
Consensus pattern (23 bp):
TCCAGAGGGTACAGATACCCCCC
Found at i:1771823 original size:117 final size:118
Alignment explanation
Indices: 1771653--1771868 Score: 269
Period size: 117 Copynumber: 1.8 Consensus size: 118
1771643 ATCATCTTTT
* * * *
1771653 GAAAGCTAAAAAAGATTTAGAAAATCAAAATGAAATGTTGAGAAAGGAGTTAGAGCGTTT-AAAA
1 GAAAGCTAAAAAAGATTTAGAAAATCAAAACGAAATATTGAGAAAGAAGTTAGAAC-TTTCAAAA
* *
1771717 ATGAAATCTGAAAA-ATTTGAAAAAGAAATTTTCGAATTAAACAAACTTCTTCTA
65 ATGAAATCTGAAAATA-TGGAAAAAGAAAATTTCGAATTAAACAAACTTCTTCTA
* * * *
1771771 GAAA-CTAAAAAGGATTTTGAAAATCAAAACGAAATATTGA-AGGAGAATTTAGAACTTTCAAAA
1 GAAAGCTAAAAAAGATTTAGAAAATCAAAACGAAATATTGAGA-AAGAAGTTAGAACTTTCAAAA
* *
1771834 ATGAAATTTGAAAGTATGGAAAAAGAAAATTTCGA
65 ATGAAATCTGAAAATATGGAAAAAGAAAATTTCGA
1771869 TTTGAAAGTT
Statistics
Matches: 83, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
116 4 0.05
117 74 0.89
118 5 0.06
ACGTcount: A:0.51, C:0.07, G:0.17, T:0.25
Consensus pattern (118 bp):
GAAAGCTAAAAAAGATTTAGAAAATCAAAACGAAATATTGAGAAAGAAGTTAGAACTTTCAAAAA
TGAAATCTGAAAATATGGAAAAAGAAAATTTCGAATTAAACAAACTTCTTCTA
Found at i:1786551 original size:11 final size:12
Alignment explanation
Indices: 1786513--1786544 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
1786503 AGGAGTAGTA
1786513 ATTTCAAATTTG
1 ATTTCAAATTTG
1786525 ATTTCAAATTTG
1 ATTTCAAATTTG
1786537 ATTTCAAA
1 ATTTCAAA
1786545 ATGATTTTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.38, C:0.09, G:0.06, T:0.47
Consensus pattern (12 bp):
ATTTCAAATTTG
Found at i:1793402 original size:17 final size:17
Alignment explanation
Indices: 1793370--1793419 Score: 93
Period size: 17 Copynumber: 3.0 Consensus size: 17
1793360 TGACTTGCAT
1793370 GTCTTAGAAT-AAATGG
1 GTCTTAGAATAAAATGG
1793386 GTCTTAGAATAAAATGG
1 GTCTTAGAATAAAATGG
1793403 GTCTTAGAATAAAATGG
1 GTCTTAGAATAAAATGG
1793420 AAATGGCACT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
16 10 0.30
17 23 0.70
ACGTcount: A:0.40, C:0.06, G:0.24, T:0.30
Consensus pattern (17 bp):
GTCTTAGAATAAAATGG
Found at i:1802638 original size:17 final size:17
Alignment explanation
Indices: 1802616--1802656 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
1802606 ATTTAGAAGA
*
1802616 TTTATTATTATTATTAT
1 TTTATTATTATTAATAT
*
1802633 TTTATTTTTATTAATAT
1 TTTATTATTATTAATAT
1802650 TTTATTA
1 TTTATTA
1802657 GTGATTCATG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTATTATTATTAATAT
Found at i:1803255 original size:18 final size:17
Alignment explanation
Indices: 1803228--1803261 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1803218 TATTACATAT
*
1803228 TTATTTCTTTGTATTTAA
1 TTATTACTTTGT-TTTAA
1803246 TTATTACTTTGTTTTA
1 TTATTACTTTGTTTTA
1803262 TCTTGTCTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.21, C:0.06, G:0.06, T:0.68
Consensus pattern (17 bp):
TTATTACTTTGTTTTAA
Found at i:1808153 original size:21 final size:22
Alignment explanation
Indices: 1808129--1808171 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
1808119 AAGACTGTTT
1808129 TCATTTTTCAATTTT-AAAATA
1 TCATTTTTCAATTTTGAAAATA
**
1808150 TCATTTTTGTATTTTGAAAATA
1 TCATTTTTCAATTTTGAAAATA
1808172 GAGGCTTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.35, C:0.07, G:0.05, T:0.53
Consensus pattern (22 bp):
TCATTTTTCAATTTTGAAAATA
Done.