Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007948.1 Hibiscus syriacus cultivar Beakdansim tig00110370_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: 294181
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.33
File 1 of 2
Found at i:1913 original size:33 final size:33
Alignment explanation
Indices: 1871--1936 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
1861 AAAAAGATGG
*
1871 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
***
1904 AGTGGTGAAAGAAGTTTCGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
1937 TATTAGATGG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.29, C:0.02, G:0.45, T:0.24
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:2143 original size:15 final size:14
Alignment explanation
Indices: 2117--2152 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
2107 GAAAAAATAT
2117 GAAGAAAAGAGAGG
1 GAAGAAAAGAGAGG
*
2131 GAAGAAGAAGAGATG
1 GAAGAA-AAGAGAGG
2146 GAAGAAA
1 GAAGAAA
2153 TGAGGAGGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.58, C:0.00, G:0.39, T:0.03
Consensus pattern (14 bp):
GAAGAAAAGAGAGG
Found at i:3737 original size:18 final size:18
Alignment explanation
Indices: 3714--3748 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
3704 CGAGTTAATT
3714 TTTGTATAAGATTTATAA
1 TTTGTATAAGATTTATAA
*
3732 TTTGTATACGATTTATA
1 TTTGTATAAGATTTATA
3749 TTTTTTTATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.34, C:0.03, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGTATAAGATTTATAA
Found at i:4590 original size:197 final size:198
Alignment explanation
Indices: 3834--4632 Score: 1466
Period size: 198 Copynumber: 4.1 Consensus size: 198
3824 TTAAGGGTCA
* *
3834 TGTCGATACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAAC-AGGTGCATC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCACC
3898 AATAAAGTGTCGATCCATATA-AAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
66 AATAAAGTGTCGATCCATATATAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
*
3962 AATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
131 AATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
4027 ATG
196 ATG
*
4030 TGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTCCAGAATGAATT-AAAACAAGGTGCATC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCACC
4093 AATAAAGTGTCGATCCATATATAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
66 AATAAAGTGTCGATCCATATATAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
*
4158 AATCTGTAATTTTTCAATCTAACCGGTACAATTA-ACCGGTTTTATGAGAGAATAAGTCTAAATA
131 AATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
4222 ATG
196 ATG
4225 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCACC
*
4290 CATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 AATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
*
4355 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAG-ATAAGTCTAAAT
130 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
4419 AATG
195 AATG
*
4423 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTTCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCACC
4488 AATAAAGTGTCGATCCATATATAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
66 AATAAAGTGTCGATCCATATATAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
*
4553 AATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATA
131 AATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
4618 ATG
196 ATG
4621 TGTCGACACTAA
1 TGTCGACACTAA
4633 ATACCCCGTT
Statistics
Matches: 585, Mismatches: 11, Indels: 12
0.96 0.02 0.02
Matches are distributed among these distances:
194 5 0.01
195 111 0.19
196 122 0.21
197 128 0.22
198 203 0.35
199 16 0.03
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.32
Consensus pattern (198 bp):
TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCACC
AATAAAGTGTCGATCCATATATAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
AATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
ATG
Found at i:4964 original size:18 final size:18
Alignment explanation
Indices: 4941--5008 Score: 55
Period size: 21 Copynumber: 3.4 Consensus size: 18
4931 ATCGGTCGCA
4941 GAAGATGAAGCTGACGAT
1 GAAGATGAAGCTGACGAT
* *
4959 GAAGATGACGATGATGATGAT
1 GAAGATGA--A-GCTGACGAT
*
4980 GATGACGATGAAGCTGGCGAT
1 GA--A-GATGAAGCTGACGAT
5001 GAAGATGA
1 GAAGATGA
5009 TGACGATGAT
Statistics
Matches: 39, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
18 13 0.33
19 1 0.03
20 1 0.03
21 17 0.44
22 1 0.03
23 1 0.03
24 5 0.13
ACGTcount: A:0.37, C:0.09, G:0.35, T:0.19
Consensus pattern (18 bp):
GAAGATGAAGCTGACGAT
Found at i:4965 original size:6 final size:6
Alignment explanation
Indices: 4941--5036 Score: 57
Period size: 6 Copynumber: 15.3 Consensus size: 6
4931 ATCGGTCGCA
* * * * * *
4941 GAAGAT GAAGCT GACGAT GAAGAT GACGAT GATGAT GATGAT GACGAT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
* ** * *
4989 GAAGCT GGCGAT GAAGAT GATGACGAT GATGAT GGATGAT GAAGAT GA
1 GAAGAT GAAGAT GAAGAT GA--A-GAT GAAGAT -GAAGAT GAAGAT GA
5037 TGATCCAAAC
Statistics
Matches: 70, Mismatches: 16, Indels: 8
0.74 0.17 0.09
Matches are distributed among these distances:
6 58 0.83
7 6 0.09
8 1 0.01
9 5 0.07
ACGTcount: A:0.36, C:0.07, G:0.35, T:0.21
Consensus pattern (6 bp):
GAAGAT
Found at i:4976 original size:3 final size:3
Alignment explanation
Indices: 4956--5040 Score: 71
Period size: 3 Copynumber: 28.0 Consensus size: 3
4946 TGAAGCTGAC
* * * * * ** *
4956 GAT GAA GAT GAC GAT GAT GAT GAT GAT GAC GAT GAA GCT GGC GAT GAA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
* *
5004 GAT GAT GAC GAT GAT GAT GGAT GAT GAA GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT -GAT GAT GAT GAT GAT GAT
5041 CCAAACAAGT
Statistics
Matches: 62, Mismatches: 19, Indels: 2
0.75 0.23 0.02
Matches are distributed among these distances:
3 59 0.95
4 3 0.05
ACGTcount: A:0.35, C:0.06, G:0.35, T:0.24
Consensus pattern (3 bp):
GAT
Found at i:6908 original size:182 final size:183
Alignment explanation
Indices: 6489--7140 Score: 1181
Period size: 182 Copynumber: 3.6 Consensus size: 183
6479 ATAATAAAAC
*
6489 AGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATAGGTCTACAACCTA
1 AGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGAGCGAATAGGTCTACAACCTA
6554 TATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGATAC
66 TATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAG-AAAATGTGTCGATAC
6619 GATTTAAAAAAGTGTCGACATTTTACACATC-GAACCCATAATTATAATGTAAT
130 GATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATAATTATAATGTAAT
* *
6672 AGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCCAATAGGTCTACAACCTA
1 AGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGAGCGAATAGGTCTACAACCTA
*
6737 TATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAATGTGTCGATACA
66 TATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAATGTGTCGATACG
6802 ATTT-AAAAAGTGTCGACATTTTACACATCGGAACCCATAATTATAATGTAAT
131 ATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATAATTATAATGTAAT
*
6854 AGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATAGGTCTACAACCTA
1 AGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGAGCGAATAGGTCTACAACCTA
6919 TATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAATGTGTCGATACG
66 TATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAATGTGTCGATACG
6984 ATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATAA-T-T-ATGTAAT
131 ATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATAATTATAATGTAAT
*
7034 AGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTA
1 AGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGAGCGAATAGGTCTACAACCTA
*
7099 TATCGACACTTTAT-ATATATGTGTCGGTACTTTATGTCCATA
66 TATCGACACTTTTTAATAT-TGTGTCGGTACTTTATGTCCATA
7141 CCATTTAAAA
Statistics
Matches: 455, Mismatches: 11, Indels: 9
0.96 0.02 0.02
Matches are distributed among these distances:
179 4 0.01
180 106 0.23
181 26 0.06
182 172 0.38
183 147 0.32
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (183 bp):
AGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGAGCGAATAGGTCTACAACCTA
TATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAATGTGTCGATACG
ATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATAATTATAATGTAAT
Found at i:9727 original size:23 final size:23
Alignment explanation
Indices: 9696--9755 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
9686 ATAGGTAAAC
*
9696 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
9719 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
9742 ATATAATGTAATAG
1 ATATAATGTAATAG
9756 TAGTGGTTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.37, C:0.07, G:0.18, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:9795 original size:20 final size:20
Alignment explanation
Indices: 9770--9808 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
9760 GGTTATATTG
* *
9770 TAAAGTGTCTATCCTTTTTA
1 TAAAGTGTCCATACTTTTTA
9790 TAAAGTGTCCATACTTTTT
1 TAAAGTGTCCATACTTTTT
9809 TCACTGTGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.15, G:0.10, T:0.49
Consensus pattern (20 bp):
TAAAGTGTCCATACTTTTTA
Found at i:10183 original size:23 final size:23
Alignment explanation
Indices: 10120--10184 Score: 94
Period size: 23 Copynumber: 2.8 Consensus size: 23
10110 ATAGGTAAAC
* *
10120 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTATCCCTT
**
10143 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTATCCCTT
10166 ATATAATGTAATAGGTATC
1 ATATAATGTAATAGGTATC
10185 TATCTCGCAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.35, C:0.08, G:0.18, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTATCCCTT
Found at i:10409 original size:18 final size:18
Alignment explanation
Indices: 10388--10424 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
10378 GTAATTGGAG
10388 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
10406 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
10424 T
1 T
10425 ATATATTCGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:14726 original size:2 final size:2
Alignment explanation
Indices: 14719--14757 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
14709 TATTAAAGAA
*
14719 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
14758 GTACAAAATC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:14843 original size:17 final size:18
Alignment explanation
Indices: 14810--14845 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
14800 ATATATACGT
*
14810 ATAATAATAACATGAATA
1 ATAAAAATAACATGAATA
14828 ATAAAAATAA-ATGAATA
1 ATAAAAATAACATGAATA
14845 A
1 A
14846 AATATTCATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.67, C:0.03, G:0.06, T:0.25
Consensus pattern (18 bp):
ATAAAAATAACATGAATA
Found at i:16210 original size:106 final size:106
Alignment explanation
Indices: 16069--16577 Score: 740
Period size: 106 Copynumber: 4.8 Consensus size: 106
16059 AGTATTGTTA
* *
16069 TGAGTCCAATATCCTCCG-TCGTGAAGTTGAAATTGGCTCTGAAACTAGGAAATTGTTTGTTGAC
1 TGAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGTTTGTTGAC
** * * * *
16133 AGTCGGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCT
65 AACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * *
16175 CGAGTTCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGTTTGTTGACA
* *
16240 ACCAGCCGTCCCTTCGTTGTGAATTTGAACTTGTGTCGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * *
16281 TGAGTCCAATATCCTTCGCTGTGAAGTTAAAATTGGCTCTGAAATTGGGAAATTGTTTGCTGACA
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGTTTGTTGACA
*
16346 ACCAGCCGTCCCTTCGTTGTAAAGTTGAACTTGTGTTGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * * *
16387 TGAGTCCAATAGCCTTCGCTGTGAAGTTGAAATTGACTCTGAAACT-GAAAAGTGGTTTGTTGAC
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAA-TTGTTTGTTGAC
16451 AACCAGCCGTCCC-T--TTGTGAAGTTGAACTTGTGTTGTCT
65 AACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* *
16490 TGAGTTCAATATCCTTTGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGTTTTGTTGAC
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTG-TTTGTTGAC
*
16555 AACCAGTCGTCCCTTCGTTGTGA
65 AACCAGCCGTCCCTTCGTTGTGA
16578 CTCTGAATGA
Statistics
Matches: 361, Mismatches: 35, Indels: 13
0.88 0.09 0.03
Matches are distributed among these distances:
103 68 0.19
104 25 0.07
105 6 0.02
106 255 0.71
107 7 0.02
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.35
Consensus pattern (106 bp):
TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGTTTGTTGACA
ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
Found at i:16694 original size:162 final size:159
Alignment explanation
Indices: 16426--16742 Score: 438
Period size: 162 Copynumber: 2.0 Consensus size: 159
16416 AAATTGACTC
* * * * * *
16426 TGAAACTGAAAAGTGGTTTGTTGACAACCAGCCGTCCCTTTGTGAAGTTGAACTTGTGTTGTCTT
1 TGAAACTGAAAAATGGTTTGTTGACAACCACCCATCCCGTTGTGAAGTTGAACTTGTGTTGCCTC
* * * ** * *
16491 GAGTTCAATATCCTTTGCTGTGAAGTTGAAATTGGCTC-TGAAACTGGGAAATTGTTTTGTTGAC
66 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCATGAAACT-AAAAAGTGGTTTGTTGAC
16555 AACCAGTCGTCCCTTCGTTGTGACTCTGAA
130 AACCAGTCGTCCCTTCGTTGTGACTCTGAA
16585 TGAAACTGAAAAATGGTTTGTTGACAACCACCCATCCATTCGTTGTGAAGTTGAACTTGTGTTGC
1 TGAAACTGAAAAATGGTTTGTTGACAACCACCCATCC---CGTTGTGAAGTTGAACTTGTGTTGC
16650 CTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTAAAAAGTGGTTTG
63 CTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTC---ATGAAACTAAAAAGTGGTTTG
*
16715 TTGACAACCAGTCGTCCTTTCGTTGTGA
125 TTGACAACCAGTCGTCCCTTCGTTGTGA
16743 AGTTGAACTT
Statistics
Matches: 137, Mismatches: 14, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
159 34 0.25
162 60 0.44
165 36 0.26
166 7 0.05
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.34
Consensus pattern (159 bp):
TGAAACTGAAAAATGGTTTGTTGACAACCACCCATCCCGTTGTGAAGTTGAACTTGTGTTGCCTC
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCATGAAACTAAAAAGTGGTTTGTTGACA
ACCAGTCGTCCCTTCGTTGTGACTCTGAA
Found at i:17684 original size:36 final size:37
Alignment explanation
Indices: 17631--17706 Score: 129
Period size: 36 Copynumber: 2.1 Consensus size: 37
17621 GAAACAATTT
17631 CAAAGGTTTTTTCCAAGGGAAACTGTCTCAAGAGAGA
1 CAAAGGTTTTTTCCAAGGGAAACTGTCTCAAGAGAGA
17668 CAAA-GTTTGTTT-CAAGGGAAACTGTCTCAAGAGAGA
1 CAAAGGTTT-TTTCCAAGGGAAACTGTCTCAAGAGAGA
17704 CAA
1 CAA
17707 TGGTGAGCAC
Statistics
Matches: 38, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
36 31 0.82
37 7 0.18
ACGTcount: A:0.37, C:0.16, G:0.24, T:0.24
Consensus pattern (37 bp):
CAAAGGTTTTTTCCAAGGGAAACTGTCTCAAGAGAGA
Found at i:18222 original size:18 final size:18
Alignment explanation
Indices: 18195--18230 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
18185 TGTTGAATCC
*
18195 CCAAAGATGCCCCAATAT
1 CCAAAAATGCCCCAATAT
18213 CCAAAAATGCCCCAATAT
1 CCAAAAATGCCCCAATAT
18231 TTGATGTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.42, C:0.33, G:0.08, T:0.17
Consensus pattern (18 bp):
CCAAAAATGCCCCAATAT
Found at i:19306 original size:21 final size:19
Alignment explanation
Indices: 19289--19346 Score: 75
Period size: 19 Copynumber: 3.1 Consensus size: 19
19279 TTCCTTTTGA
19289 TTTTTGCTTCTTTTCTTTT
1 TTTTTGCTTCTTTTCTTTT
* *
19308 TTGTT-CTTGTTTT-TTTCT
1 TTTTTGCTTCTTTTCTTT-T
19326 TTTTTGCTTCTTTTCTTTT
1 TTTTTGCTTCTTTTCTTTT
19345 TT
1 TT
19347 GTTCTTGATT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
17 3 0.09
18 12 0.38
19 14 0.44
20 3 0.09
ACGTcount: A:0.00, C:0.14, G:0.07, T:0.79
Consensus pattern (19 bp):
TTTTTGCTTCTTTTCTTTT
Found at i:19307 original size:37 final size:36
Alignment explanation
Indices: 19266--19345 Score: 90
Period size: 37 Copynumber: 2.2 Consensus size: 36
19256 TTTGCATGTG
*
19266 CTTTTTGTCCCTT-TTCCTTTTGATTTTTGCTTCTTTT
1 CTTTTTGT-CCTTGTT-CTTTTCATTTTTGCTTCTTTT
* * *
19303 CTTTTTTGTTCTTGTTTTTTTCTTTTTTGCTTCTTTT
1 C-TTTTTGTCCTTGTTCTTTTCATTTTTGCTTCTTTT
19340 CTTTTT
1 CTTTTT
19346 TGTTCTTGAT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
36 5 0.14
37 23 0.62
38 9 0.24
ACGTcount: A:0.01, C:0.17, G:0.07, T:0.74
Consensus pattern (36 bp):
CTTTTTGTCCTTGTTCTTTTCATTTTTGCTTCTTTT
Found at i:19314 original size:15 final size:15
Alignment explanation
Indices: 19301--19352 Score: 61
Period size: 16 Copynumber: 3.3 Consensus size: 15
19291 TTTGCTTCTT
19301 TTCTTTT-TTGTTCTTG
1 TTCTTTTCTT-TT-TTG
*
19317 TTTTTTTCTTTTTTG
1 TTCTTTTCTTTTTTG
19332 CTTCTTTTCTTTTTTG
1 -TTCTTTTCTTTTTTG
19348 TTCTT
1 TTCTT
19353 GATTGAATCT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
15 8 0.25
16 22 0.69
17 2 0.06
ACGTcount: A:0.00, C:0.13, G:0.08, T:0.79
Consensus pattern (15 bp):
TTCTTTTCTTTTTTG
Found at i:19336 original size:11 final size:10
Alignment explanation
Indices: 19301--19339 Score: 51
Period size: 11 Copynumber: 3.7 Consensus size: 10
19291 TTTGCTTCTT
19301 TTCTTTTTTG
1 TTCTTTTTTG
*
19311 TTCTTGTTTTT
1 TTCTT-TTTTG
19322 TTCTTTTTTG
1 TTCTTTTTTG
19332 CTTCTTTT
1 -TTCTTTT
19340 CTTTTTTGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
10 9 0.36
11 16 0.64
ACGTcount: A:0.00, C:0.13, G:0.08, T:0.79
Consensus pattern (10 bp):
TTCTTTTTTG
Found at i:19336 original size:22 final size:22
Alignment explanation
Indices: 19299--19346 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 22
19289 TTTTTGCTTC
19299 TTTTCTTTTTTGTTCTTGT-TT
1 TTTTCTTTTTTGTTCTTGTCTT
*
19320 TTTTCTTTTTTGCTTCTTTTCTT
1 TTTTCTTTTTTG-TTCTTGTCTT
19343 TTTT
1 TTTT
19347 GTTCTTGATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 12 0.50
22 6 0.25
23 6 0.25
ACGTcount: A:0.00, C:0.12, G:0.06, T:0.81
Consensus pattern (22 bp):
TTTTCTTTTTTGTTCTTGTCTT
Found at i:22809 original size:15 final size:15
Alignment explanation
Indices: 22789--22826 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
22779 AACAGTTAGT
22789 AAAATAAAAATAAAA
1 AAAATAAAAATAAAA
*
22804 AAAATAATAATAAAA
1 AAAATAAAAATAAAA
22819 AAAATAAA
1 AAAATAAA
22827 TGGCAAGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (15 bp):
AAAATAAAAATAAAA
Found at i:22812 original size:12 final size:11
Alignment explanation
Indices: 22788--22826 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 11
22778 AAACAGTTAG
*
22788 TAAAATAAAAA
1 TAAAAAAAAAA
22799 TAAAAAAAATAA
1 TAAAAAAAA-AA
22811 TAATAAAAAAAA
1 TAA-AAAAAAAA
22823 TAAA
1 TAAA
22827 TGGCAAGAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
11 9 0.36
12 10 0.40
13 6 0.24
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (11 bp):
TAAAAAAAAAA
Found at i:23953 original size:17 final size:18
Alignment explanation
Indices: 23927--23966 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
23917 ATTATATGGA
23927 TATT-TTATTCAT-TTAT
1 TATTATTATTCATGTTAT
*
23943 TTTTATTATTCATGTTAT
1 TATTATTATTCATGTTAT
23961 TATTAT
1 TATTAT
23967 ACGTATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 3 0.15
17 8 0.40
18 9 0.45
ACGTcount: A:0.25, C:0.05, G:0.03, T:0.68
Consensus pattern (18 bp):
TATTATTATTCATGTTAT
Found at i:24030 original size:2 final size:2
Alignment explanation
Indices: 24025--24051 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
24015 TATATTTTAT
24025 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
24052 TTCTTTAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:24066 original size:53 final size:57
Alignment explanation
Indices: 23970--24094 Score: 136
Period size: 55 Copynumber: 2.3 Consensus size: 57
23960 TTATTATACG
* * * * *
23970 TATATATATATATATATTTTAAATTATTTTCATTTGATTTTTTAC-TAT-ATTTTAT
1 TATATATATATATATATTATAAATTATTTTCATTTAATATTTTACTTATAAGTCTAT
*
24025 TATATATATATATATA-TATATA-TATATTTC-TTTAATATTTTACTTATAAGTCTAT
1 TATATATATATATATATTATAAATTAT-TTTCATTTAATATTTTACTTATAAGTCTAT
24080 TAT-TACTATATATAT
1 TATATA-TATATATAT
24095 TGTAATTATC
Statistics
Matches: 60, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
53 14 0.23
54 13 0.22
55 33 0.55
ACGTcount: A:0.36, C:0.05, G:0.02, T:0.58
Consensus pattern (57 bp):
TATATATATATATATATTATAAATTATTTTCATTTAATATTTTACTTATAAGTCTAT
Found at i:24162 original size:2 final size:2
Alignment explanation
Indices: 24157--24308 Score: 154
Period size: 2 Copynumber: 78.0 Consensus size: 2
24147 CCTATTATTA
24157 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
* * *
24199 AT AT AT AT AT AT AT AT AT AT AT AT A- AT -T AT TT TT AT TT GAT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT
* * * * * * *
24240 -T AT TT CT TT AT TT AC GT AT AT AT CT -T AT A- ACT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT
24279 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
24309 TTTTATTATT
Statistics
Matches: 127, Mismatches: 15, Indels: 16
0.80 0.09 0.10
Matches are distributed among these distances:
1 6 0.05
2 120 0.94
3 1 0.01
ACGTcount: A:0.43, C:0.03, G:0.01, T:0.53
Consensus pattern (2 bp):
AT
Found at i:27021 original size:60 final size:61
Alignment explanation
Indices: 26928--27047 Score: 163
Period size: 60 Copynumber: 2.0 Consensus size: 61
26918 CCGATTCTCG
* *
26928 TCGATTCTGGGATGATCAAGCATAAGGATGATGCAGCCTCATCAAATG-TTTCTTAGCATA
1 TCGATTCCGGGATGATCAAGCATAAGGATGATGCAGCCTCATCAAATGATTCCTTAGCATA
* * * *
26988 TCGATTCCGGGATGATCAATCA-AGCGGATGATGCGGCCTCATCAGATGATTCCTTAGCAT
1 TCGATTCCGGGATGATCAAGCATA-AGGATGATGCAGCCTCATCAAATGATTCCTTAGCAT
27048 TTTCAGATGT
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
59 1 0.02
60 41 0.79
61 10 0.19
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (61 bp):
TCGATTCCGGGATGATCAAGCATAAGGATGATGCAGCCTCATCAAATGATTCCTTAGCATA
Found at i:35657 original size:6 final size:6
Alignment explanation
Indices: 35647--35678 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
35637 CATACTATGT
*
35647 TTCTCT TTCTCC TTCTCC TTCTCC TTCTCC TT
1 TTCTCC TTCTCC TTCTCC TTCTCC TTCTCC TT
35679 TTCCACTTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (6 bp):
TTCTCC
Found at i:50249 original size:15 final size:15
Alignment explanation
Indices: 50223--50261 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
50213 TCCCTGAGCT
* *
50223 TGAAGCTGGGGTTGG
1 TGAAGATGGGGTTGA
*
50238 TGATGATGGGGTTGA
1 TGAAGATGGGGTTGA
50253 TGAAGATGG
1 TGAAGATGG
50262 TTTTGAAGGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.21, C:0.03, G:0.49, T:0.28
Consensus pattern (15 bp):
TGAAGATGGGGTTGA
Found at i:57840 original size:10 final size:10
Alignment explanation
Indices: 57825--57855 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
57815 CTCGGTGGAG
57825 CCAAACCCTT
1 CCAAACCCTT
57835 CCAAACCCTT
1 CCAAACCCTT
57845 CCAAACTCCTT
1 CCAAAC-CCTT
57856 GTAGCCACAC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 16 0.80
11 4 0.20
ACGTcount: A:0.29, C:0.48, G:0.00, T:0.23
Consensus pattern (10 bp):
CCAAACCCTT
Found at i:60715 original size:2 final size:2
Alignment explanation
Indices: 60710--60737 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
60700 CACACACACA
60710 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
60738 TTGATAATAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:62143 original size:15 final size:15
Alignment explanation
Indices: 62123--62151 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
62113 TTTGGAGAAA
62123 AGAGCGACGGTCTTG
1 AGAGCGACGGTCTTG
62138 AGAGCGACGGTCTT
1 AGAGCGACGGTCTT
62152 AAGAAGAACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.21, G:0.38, T:0.21
Consensus pattern (15 bp):
AGAGCGACGGTCTTG
Found at i:62403 original size:3 final size:3
Alignment explanation
Indices: 62395--62441 Score: 60
Period size: 3 Copynumber: 15.7 Consensus size: 3
62385 TCTCCATTTC
* *
62395 TAT TAT TAT TAT TAT TAT T-T TATT TAT TAT TAT TAA AAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT
62440 TA
1 TA
62442 CAAACAGGCT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
2 2 0.05
3 33 0.87
4 3 0.08
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:64214 original size:16 final size:18
Alignment explanation
Indices: 64193--64231 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
64183 TTGGTACATG
64193 TGTGTG-CAC-CTCTATA
1 TGTGTGCCACTCTCTATA
*
64209 TGTGTGCCTCTCTCTATA
1 TGTGTGCCACTCTCTATA
64227 TGTGT
1 TGTGT
64232 TTCCGCTCAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 6 0.30
17 2 0.10
18 12 0.60
ACGTcount: A:0.13, C:0.23, G:0.21, T:0.44
Consensus pattern (18 bp):
TGTGTGCCACTCTCTATA
Found at i:78662 original size:47 final size:47
Alignment explanation
Indices: 78597--78701 Score: 174
Period size: 47 Copynumber: 2.2 Consensus size: 47
78587 ATTGATGGAT
*
78597 GGGATTTGCTTGCATGTCTCTGGTTAAAAGCACAACAGTTTTGATCA
1 GGGATTTGCTTGCATGTCTCTAGTTAAAAGCACAACAGTTTTGATCA
* **
78644 GGGATTTGCTTGCTTGTCTCTAGTTAAAAGCACAATGGTTTTGATCA
1 GGGATTTGCTTGCATGTCTCTAGTTAAAAGCACAACAGTTTTGATCA
78691 GGGATTTGCTT
1 GGGATTTGCTT
78702 TTGTTTATAT
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 54 1.00
ACGTcount: A:0.23, C:0.15, G:0.25, T:0.37
Consensus pattern (47 bp):
GGGATTTGCTTGCATGTCTCTAGTTAAAAGCACAACAGTTTTGATCA
Found at i:79738 original size:32 final size:33
Alignment explanation
Indices: 79701--79764 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
79691 TCGTCTGTTC
79701 CTTTCC-TCCAAATCAGGACAATACAACCCCTT
1 CTTTCCTTCCAAATCAGGACAATACAACCCCTT
79733 CTTTCCTTCCAAATCAGGACAATACAACCCCT
1 CTTTCCTTCCAAATCAGGACAATACAACCCCT
79765 AAAGGATCGT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 6 0.19
33 25 0.81
ACGTcount: A:0.31, C:0.38, G:0.06, T:0.25
Consensus pattern (33 bp):
CTTTCCTTCCAAATCAGGACAATACAACCCCTT
Found at i:96067 original size:17 final size:17
Alignment explanation
Indices: 96036--96069 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
96026 TGGTCTGCTG
96036 GTGGACTGATGTGTTTT
1 GTGGACTGATGTGTTTT
96053 GTGGA-TGATGATGTTTT
1 GTGGACTGATG-TGTTTT
96070 TGAGGTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.15, C:0.03, G:0.35, T:0.47
Consensus pattern (17 bp):
GTGGACTGATGTGTTTT
Found at i:115179 original size:15 final size:15
Alignment explanation
Indices: 115143--115198 Score: 60
Period size: 15 Copynumber: 3.7 Consensus size: 15
115133 CACAGATCAA
*
115143 GATGATCATGAGA-TT
1 GATGATGATGA-ATTT
115158 GATGATGATGAATTT
1 GATGATGATGAATTT
* * *
115173 GATGATGAAGTATTG
1 GATGATGATGAATTT
115188 GATGATGATGA
1 GATGATGATGA
115199 TGAGGGTGGA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
14 1 0.03
15 33 0.97
ACGTcount: A:0.34, C:0.02, G:0.30, T:0.34
Consensus pattern (15 bp):
GATGATGATGAATTT
Found at i:129847 original size:31 final size:31
Alignment explanation
Indices: 129809--129872 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
129799 AAGAGTTAAG
129809 TAAGTTTTTTAGTAGAATTTCTTTGACTATA
1 TAAGTTTTTTAGTAGAATTTCTTTGACTATA
129840 TAAGTTTTTTAGTAGAATTTCTTTGACTATA
1 TAAGTTTTTTAGTAGAATTTCTTTGACTATA
129871 TA
1 TA
129873 TATATAGGGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.30, C:0.06, G:0.12, T:0.52
Consensus pattern (31 bp):
TAAGTTTTTTAGTAGAATTTCTTTGACTATA
Found at i:151693 original size:31 final size:32
Alignment explanation
Indices: 151651--151729 Score: 115
Period size: 31 Copynumber: 2.5 Consensus size: 32
151641 TAGTTATGTC
*
151651 AGGGACCATATTACAAACGGAATAAATG-TGG
1 AGGGACTATATTACAAACGGAATAAATGTTGG
* *
151682 AGGGACTATATTGCAAACGGATTAAATGTTGG
1 AGGGACTATATTACAAACGGAATAAATGTTGG
*
151714 AGGGATTATATTACAA
1 AGGGACTATATTACAA
151730 TTTTTAAAGG
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
31 25 0.60
32 17 0.40
ACGTcount: A:0.39, C:0.10, G:0.25, T:0.25
Consensus pattern (32 bp):
AGGGACTATATTACAAACGGAATAAATGTTGG
Found at i:155607 original size:3 final size:3
Alignment explanation
Indices: 155599--155670 Score: 144
Period size: 3 Copynumber: 24.0 Consensus size: 3
155589 TAACATTCCC
155599 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
155647 TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT
155671 GTTCTTATGA
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 69 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:155798 original size:35 final size:35
Alignment explanation
Indices: 155758--155889 Score: 135
Period size: 35 Copynumber: 3.8 Consensus size: 35
155748 TGATGAACAA
*
155758 TTGAATCGAAAGTG-CGAATGTTTCCTTCTGTTCAC
1 TTGAATCGAAAGTGCCG-ATGCTTCCTTCTGTTCAC
* * * *
155793 TTGAATTGAAAGCGCCGATGCTTCCTTTTGTTCTTC
1 TTGAATCGAAAGTGCCGATGCTTCCTTCTGTTC-AC
** *
155829 TTGAATCGAAAGTGTTGATGCTTCATTTCT-TTCAC
1 TTGAATCGAAAGTGCCGATGCTTC-CTTCTGTTCAC
*
155864 -TGAATCGAAAGTGCTGATGCTTCCTT
1 TTGAATCGAAAGTGCCGATGCTTCCTT
155890 TCGTTCTTCT
Statistics
Matches: 80, Mismatches: 14, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
33 2 0.03
34 22 0.28
35 27 0.34
36 26 0.32
37 3 0.04
ACGTcount: A:0.21, C:0.20, G:0.20, T:0.39
Consensus pattern (35 bp):
TTGAATCGAAAGTGCCGATGCTTCCTTCTGTTCAC
Found at i:155859 original size:29 final size:31
Alignment explanation
Indices: 155823--155896 Score: 85
Period size: 34 Copynumber: 2.2 Consensus size: 31
155813 CTTCCTTTTG
*
155823 TTCTTCTTGAATCGAAAGTGTTGATGCTTCAT
1 TTCTTC-TGAATCGAAAGTGCTGATGCTTCAT
*
155855 TTCTTTCACTGAATCGAAAGTGCTGATGCTTCCT
1 TTC-TT--CTGAATCGAAAGTGCTGATGCTTCAT
155889 TTCGTTCT
1 TTC-TTCT
155897 TCTTATTCAC
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
32 5 0.14
33 2 0.06
34 28 0.78
35 1 0.03
ACGTcount: A:0.19, C:0.20, G:0.18, T:0.43
Consensus pattern (31 bp):
TTCTTCTGAATCGAAAGTGCTGATGCTTCAT
Found at i:155888 original size:70 final size:71
Alignment explanation
Indices: 155758--155900 Score: 184
Period size: 70 Copynumber: 2.0 Consensus size: 71
155748 TGATGAACAA
* * *
155758 TTGAATCGAAAGTGCGAATGTTTCCTTCTGTTCACTTGAATTGAAAGCGCCGATGCTTCCTTTTG
1 TTGAATCGAAAGTGCGAATGCTTCCTTCTGTTCACTTGAATCGAAAGCGCCGATGCTTCCTTTCG
155823 TTCTTC
66 TTCTTC
* * * *
155829 TTGAATCGAAAGTGTTG-ATGCTTCATTTCT-TTCAC-TGAATCGAAAGTGCTGATGCTTCCTTT
1 TTGAATCGAAAGTG-CGAATGCTTC-CTTCTGTTCACTTGAATCGAAAGCGCCGATGCTTCCTTT
155891 CGTTCTTC
64 CGTTCTTC
155899 TT
1 TT
155901 ATTCACCTTC
Statistics
Matches: 63, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
70 33 0.52
71 25 0.40
72 5 0.08
ACGTcount: A:0.20, C:0.20, G:0.19, T:0.41
Consensus pattern (71 bp):
TTGAATCGAAAGTGCGAATGCTTCCTTCTGTTCACTTGAATCGAAAGCGCCGATGCTTCCTTTCG
TTCTTC
Found at i:165828 original size:60 final size:60
Alignment explanation
Indices: 165735--165860 Score: 164
Period size: 60 Copynumber: 2.1 Consensus size: 60
165725 CATTTCAAAA
* * * **
165735 TAGTCCTTAAACTTTTAAATATTACAATTTCATCCTTAAATTAGGGCTCTTATTCTAAAT
1 TAGTCCTTAAACTTTTAAATATTACAATTTCATCATCAAACTAGGAATCTTATTCTAAAT
* *
165795 TAGTCCTTAAACTTTTGAATATT-CTAATTTCATCATCAAACTATGAATCTTATTCTAAAT
1 TAGTCCTTAAACTTTTAAATATTAC-AATTTCATCATCAAACTAGGAATCTTATTCTAAAT
*
165855 TGGTCC
1 TAGTCC
165861 CAAAACCTTT
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
59 1 0.02
60 56 0.98
ACGTcount: A:0.33, C:0.17, G:0.07, T:0.43
Consensus pattern (60 bp):
TAGTCCTTAAACTTTTAAATATTACAATTTCATCATCAAACTAGGAATCTTATTCTAAAT
Found at i:168117 original size:21 final size:20
Alignment explanation
Indices: 168093--168156 Score: 59
Period size: 21 Copynumber: 3.4 Consensus size: 20
168083 AATTTTGAAA
168093 AAATAGTTTTCAAAGTTTGGT
1 AAAT-GTTTTCAAAGTTTGGT
*
168114 AAATG-TTTC----TTT-GA
1 AAATGTTTTCAAAGTTTGGT
168128 AAATGGTTTTCAAAGTTTGGT
1 AAAT-GTTTTCAAAGTTTGGT
168149 AAATGTTT
1 AAATGTTT
168157 CTTTGAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 15
0.67 0.04 0.29
Matches are distributed among these distances:
14 5 0.15
15 4 0.12
16 4 0.12
19 4 0.12
20 8 0.24
21 9 0.26
ACGTcount: A:0.31, C:0.05, G:0.19, T:0.45
Consensus pattern (20 bp):
AAATGTTTTCAAAGTTTGGT
Found at i:168184 original size:37 final size:36
Alignment explanation
Indices: 168086--168203 Score: 186
Period size: 35 Copynumber: 3.3 Consensus size: 36
168076 GGTAACCAAT
168086 TTTGAAAAAATAGTTTTCAAAGTTTGGTAAATGTTTC
1 TTTG-AAAAATAGTTTTCAAAGTTTGGTAAATGTTTC
*
168123 TTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTTC
1 TTTGAAAAATAGTTTTCAAAGTTTGGTAAATGTTTC
*
168158 TTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT-
1 TTTGAAAAATAG-TTTTCAAAGTTTGGTAAATGTTTC
168194 TTTGAAAAAT
1 TTTGAAAAAT
168204 GATAACGGGA
Statistics
Matches: 76, Mismatches: 3, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
35 34 0.45
36 16 0.21
37 26 0.34
ACGTcount: A:0.33, C:0.04, G:0.18, T:0.45
Consensus pattern (36 bp):
TTTGAAAAATAGTTTTCAAAGTTTGGTAAATGTTTC
Found at i:168636 original size:16 final size:16
Alignment explanation
Indices: 168615--168646 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
168605 ACTATTCATA
*
168615 TGAATAGTAAATTTCG
1 TGAATAGTAAAATTCG
168631 TGAATAGTAAAATTCG
1 TGAATAGTAAAATTCG
168647 GTCGGCGATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.06, G:0.19, T:0.34
Consensus pattern (16 bp):
TGAATAGTAAAATTCG
Found at i:172741 original size:21 final size:21
Alignment explanation
Indices: 172717--172777 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
172707 AACTTTGAAA
172717 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
172738 AAAT-GTTTT-----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
*
172752 AAATGATTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
172773 AAATG
1 AAATG
172778 TTTCTTTGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 14
0.64 0.06 0.30
Matches are distributed among these distances:
14 5 0.17
15 7 0.23
20 8 0.27
21 10 0.33
ACGTcount: A:0.33, C:0.03, G:0.20, T:0.44
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:172755 original size:35 final size:36
Alignment explanation
Indices: 172709--172830 Score: 158
Period size: 35 Copynumber: 3.4 Consensus size: 36
172699 TGGTAACCAA
*
172709 CTTTGAAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTG-AAAAATGATTTTCAAAGTTTGGTAAATGTTT
*
172746 TTTTG-AAAATGATTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGATTTTCAAAGTTTGGTAAATGTTT
* * *
172781 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGATT
1 CTTTGAAAAAT-GATTTTCAAAGTTTGGTAAATGTTT
*
172818 -GTTGAAAAATGAT
1 CTTTGAAAAATGAT
172831 AATGGGATAA
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
35 35 0.47
36 14 0.19
37 26 0.35
ACGTcount: A:0.34, C:0.04, G:0.19, T:0.43
Consensus pattern (36 bp):
CTTTGAAAAATGATTTTCAAAGTTTGGTAAATGTTT
Found at i:175700 original size:2 final size:2
Alignment explanation
Indices: 175693--175719 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
175683 TTATAGAATG
175693 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
175720 TATATATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:175724 original size:2 final size:2
Alignment explanation
Indices: 175719--175764 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
175709 ACACACACAC
175719 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
175761 AT AT
1 AT AT
175765 TAAATAGGTG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:176461 original size:18 final size:18
Alignment explanation
Indices: 176438--176473 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
176428 ATAATGTTGA
176438 TAATATTTTCATTTATTG
1 TAATATTTTCATTTATTG
*
176456 TAATATTTTTATTTATTG
1 TAATATTTTCATTTATTG
176474 GTTTTTAGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.28, C:0.03, G:0.06, T:0.64
Consensus pattern (18 bp):
TAATATTTTCATTTATTG
Found at i:178089 original size:10 final size:9
Alignment explanation
Indices: 178076--178120 Score: 54
Period size: 9 Copynumber: 5.0 Consensus size: 9
178066 CAAAACATGT
178076 AAAAAAATA
1 AAAAAAATA
178085 AAAAAAATA
1 AAAAAAATA
*
178094 ATAAAAATA
1 AAAAAAATA
* *
178103 AACAAAATG
1 AAAAAAATA
*
178112 AATAAAATA
1 AAAAAAATA
178121 TTAAAAAAAC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
9 30 1.00
ACGTcount: A:0.80, C:0.02, G:0.02, T:0.16
Consensus pattern (9 bp):
AAAAAAATA
Found at i:178099 original size:18 final size:19
Alignment explanation
Indices: 178058--178129 Score: 76
Period size: 18 Copynumber: 3.7 Consensus size: 19
178048 AGAAAAAATG
*
178058 AAAAATAACAAAACATGTAA-
1 AAAAATAA-AAAAAATG-AAT
178078 AAAAATAAAAAAAAT-AAT
1 AAAAATAAAAAAAATGAAT
*
178096 AAAAATAAACAAAATGAAT
1 AAAAATAAAAAAAATGAAT
178115 AAAATATTAAAAAAA
1 AAAA-A-TAAAAAAA
178130 CAAAGACACA
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
17 2 0.04
18 14 0.31
19 13 0.29
20 9 0.20
21 7 0.16
ACGTcount: A:0.76, C:0.04, G:0.03, T:0.17
Consensus pattern (19 bp):
AAAAATAAAAAAAATGAAT
Found at i:178109 original size:27 final size:26
Alignment explanation
Indices: 178075--178127 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
178065 ACAAAACATG
178075 TAAAAAAATAAAAAAAATAATAAAAA
1 TAAAAAAATAAAAAAAATAATAAAAA
* * *
178101 TAAACAAAATGAATAAAATATTAAAAA
1 TAAA-AAAATAAAAAAAATAATAAAAA
178128 AACAAAGACA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 4 0.17
27 19 0.83
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.19
Consensus pattern (26 bp):
TAAAAAAATAAAAAAAATAATAAAAA
Found at i:178184 original size:18 final size:17
Alignment explanation
Indices: 178162--178210 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 17
178152 ATATTAATGG
178162 AGTAAAAAAAATAAAAA
1 AGTAAAAAAAATAAAAA
*
178179 AGGTAAAAGAAATAAAAA
1 A-GTAAAAAAAATAAAAA
178197 AG-AAATAAAAATAA
1 AGTAAA-AAAAATAA
178211 TATGTACATA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 3 0.11
17 9 0.32
18 16 0.57
ACGTcount: A:0.78, C:0.00, G:0.10, T:0.12
Consensus pattern (17 bp):
AGTAAAAAAAATAAAAA
Found at i:178197 original size:11 final size:11
Alignment explanation
Indices: 178183--178207 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
178173 TAAAAAAGGT
178183 AAAAGAAATAA
1 AAAAGAAATAA
178194 AAAAGAAATAA
1 AAAAGAAATAA
178205 AAA
1 AAA
178208 TAATATGTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.84, C:0.00, G:0.08, T:0.08
Consensus pattern (11 bp):
AAAAGAAATAA
Found at i:178314 original size:37 final size:36
Alignment explanation
Indices: 178237--178329 Score: 87
Period size: 37 Copynumber: 2.5 Consensus size: 36
178227 AGTATTTACT
* * *
178237 AAAACAAATAAAAATAATCAATATATAATACTAAGTA
1 AAAACAAATAAAAA-AAACAATACATAATACTAAGGA
* * *
178274 AAAACAAATAAAAAAAAGATATACATGATATTAAGGA
1 AAAACAAATAAAAAAAACA-ATACATAATACTAAGGA
*
178311 AAAAAATAATAGAAAAAAA
1 AAAACA-AATA-AAAAAAA
178330 TAAAATAAAG
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
36 3 0.07
37 32 0.70
38 4 0.09
39 7 0.15
ACGTcount: A:0.69, C:0.05, G:0.06, T:0.19
Consensus pattern (36 bp):
AAAACAAATAAAAAAAACAATACATAATACTAAGGA
Found at i:178336 original size:18 final size:18
Alignment explanation
Indices: 178313--178350 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
178303 ATTAAGGAAA
178313 AAAATAATAG-AAAAAAAT
1 AAAATAA-AGTAAAAAAAT
*
178331 AAAATAAAGTAAAAATAT
1 AAAATAAAGTAAAAAAAT
178349 AA
1 AA
178351 TATATATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 2 0.11
18 16 0.89
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.18
Consensus pattern (18 bp):
AAAATAAAGTAAAAAAAT
Found at i:178398 original size:49 final size:43
Alignment explanation
Indices: 178314--178402 Score: 106
Period size: 49 Copynumber: 1.9 Consensus size: 43
178304 TTAAGGAAAA
*
178314 AAATAATAGAAAAAAATAAAATAAAGTAAAAATATAATATATAT
1 AAATAATAGAAAAAAATAAAATAAAGAAAAAATAT-ATATATAT
*
178358 AAATAAATAGAAACAAAAATAGAATATTAAGAAAAAATATATATA
1 AAAT-AATAG-AA-AAAAATA-AA-ATAAAGAAAAAATATATATA
178403 AAAACGTATA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
44 4 0.11
45 5 0.13
46 2 0.05
47 7 0.18
48 7 0.18
49 13 0.34
ACGTcount: A:0.70, C:0.01, G:0.06, T:0.24
Consensus pattern (43 bp):
AAATAATAGAAAAAAATAAAATAAAGAAAAAATATATATATAT
Found at i:178401 original size:17 final size:17
Alignment explanation
Indices: 178381--178440 Score: 57
Period size: 17 Copynumber: 3.2 Consensus size: 17
178371 CAAAAATAGA
178381 ATATTAAGAAAAAATAT
1 ATATTAAGAAAAAATAT
* *
178398 ATATAAAAACGTATAAAATAT
1 ATAT--TAA-G-AAAAAATAT
178419 AATATTAAGAAAAAATAT
1 -ATATTAAGAAAAAATAT
178437 ATAT
1 ATAT
178441 ACATAGTAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
17 8 0.24
18 8 0.24
19 3 0.09
20 3 0.09
21 8 0.24
22 4 0.12
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.30
Consensus pattern (17 bp):
ATATTAAGAAAAAATAT
Found at i:178530 original size:20 final size:20
Alignment explanation
Indices: 178497--178534 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
178487 ATGATATAAG
178497 ATATATATATAATAAAAATA
1 ATATATATATAATAAAAATA
178517 ATATA-ATATAAATAAAAA
1 ATATATATAT-AATAAAAA
178535 AGGAATATAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (20 bp):
ATATATATATAATAAAAATA
Found at i:178561 original size:20 final size:20
Alignment explanation
Indices: 178525--178563 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
178515 TAATATAATA
*
178525 TAAATAAAAAAGGAATATAG
1 TAAATAAAAAAGAAATATAG
178545 TAAATAAATAAA-AAATATA
1 TAAATAAA-AAAGAAATATA
178564 ATTAAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.69, C:0.00, G:0.08, T:0.23
Consensus pattern (20 bp):
TAAATAAAAAAGAAATATAG
Found at i:181972 original size:14 final size:14
Alignment explanation
Indices: 181953--181980 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
181943 TTTTAATAAA
181953 TTAAAAAATTAATG
1 TTAAAAAATTAATG
181967 TTAAAAAATTAATG
1 TTAAAAAATTAATG
181981 GGATAATATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (14 bp):
TTAAAAAATTAATG
Found at i:183300 original size:198 final size:199
Alignment explanation
Indices: 182962--183355 Score: 745
Period size: 198 Copynumber: 2.0 Consensus size: 199
182952 TTATATTTCG
182962 AGTTTGAGTTGAACTTGATAATTTTTAACTTGTGAGTTTGAGTCGAGTTGAGCTTACTTTTAAAG
1 AGTTTGAGTTGAACTTGATAATTTTTAACTTGTGAGTTTGAGTCGAGTTGAGCTTACTTTTAAAG
183027 TTTTCAAATTCGACTCGAGCTCAGCAATACTCGAGTTCGACTTGGCTCGTTTAACAAAGTTGTTT
66 TTTTCAAATTCGACTCGAGCTCAGCAATACTCGAGTTCGACTTGGCTCGTTTAACAAAGTTGTTT
183092 GGTTTAATTTTAAAAAAAAAAACAAAATTTCC-GTTTTCTAAAAAATTTTCGGTTTTCAACCGGT
131 GGTTTAATTTTAAAAAAAAAAACAAAATTTCCGGTTTTCTAAAAAATTTTCGGTTTTCAACCGGT
183156 CGGT
196 CGGT
183160 AGTTTGAGTTGAACTTGATAATTTTTAACTTGTGAGTTTGAGTCGAGTTGAGCTTACTTTTAAAG
1 AGTTTGAGTTGAACTTGATAATTTTTAACTTGTGAGTTTGAGTCGAGTTGAGCTTACTTTTAAAG
183225 TTTTCAAATTCGACTCGAGCTCAGCAATACTCGAGTTCGACTTGGCTCGTTTAACAAAGTTGTTT
66 TTTTCAAATTCGACTCGAGCTCAGCAATACTCGAGTTCGACTTGGCTCGTTTAACAAAGTTGTTT
* ** *
183290 GGTTTAATTTTAAAAAAAAAAACAAAATTTCCGGTTTTTTCTAAATTTTTCGGTTTTCAACCGGT
131 GGTTTAATTTTAAAAAAAAAAACAAAATTTCCGGTTTTCTAAAAAATTTTCGGTTTTCAACCGGT
183355 C
196 C
183356 CAGTTCAAAC
Statistics
Matches: 191, Mismatches: 4, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
198 162 0.85
199 29 0.15
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (199 bp):
AGTTTGAGTTGAACTTGATAATTTTTAACTTGTGAGTTTGAGTCGAGTTGAGCTTACTTTTAAAG
TTTTCAAATTCGACTCGAGCTCAGCAATACTCGAGTTCGACTTGGCTCGTTTAACAAAGTTGTTT
GGTTTAATTTTAAAAAAAAAAACAAAATTTCCGGTTTTCTAAAAAATTTTCGGTTTTCAACCGGT
CGGT
Found at i:185336 original size:2 final size:2
Alignment explanation
Indices: 185329--185364 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
185319 AAATTAATCA
185329 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
185365 CTTTTTAGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:185879 original size:21 final size:21
Alignment explanation
Indices: 185850--185902 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
185840 ATTCTGACTA
185850 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
185871 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
*
185892 TCGCAATGCGA
1 TCGCATTGCGA
185903 ATACGTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:185917 original size:20 final size:20
Alignment explanation
Indices: 185892--185985 Score: 143
Period size: 20 Copynumber: 4.7 Consensus size: 20
185882 TTTTCCTAAT
185892 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
185912 TCGCAACGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
185932 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAA-TACGTAAA
185953 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
185973 TCGCAATGCGAAT
1 TCGCAATGCGAAT
185986 CTGACTATCG
Statistics
Matches: 65, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
20 47 0.72
21 18 0.28
ACGTcount: A:0.38, C:0.20, G:0.21, T:0.20
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:185923 original size:41 final size:40
Alignment explanation
Indices: 185892--185985 Score: 143
Period size: 41 Copynumber: 2.3 Consensus size: 40
185882 TTTTCCTAAT
*
185892 TCGCAATGCGAATACGTAAATCGCAACGCGATTACGTAAA
1 TCGCAATGCGAATACGAAAATCGCAACGCGATTACGTAAA
* * *
185932 TCGCAATGCGAATTAGGAAAATCGCAATGCGAATACGTAAA
1 TCGCAATGCGAA-TACGAAAATCGCAACGCGATTACGTAAA
185973 TCGCAATGCGAAT
1 TCGCAATGCGAAT
185986 CTGACTATCG
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
40 13 0.27
41 36 0.73
ACGTcount: A:0.38, C:0.20, G:0.21, T:0.20
Consensus pattern (40 bp):
TCGCAATGCGAATACGAAAATCGCAACGCGATTACGTAAA
Found at i:186545 original size:20 final size:19
Alignment explanation
Indices: 186516--186587 Score: 63
Period size: 20 Copynumber: 3.6 Consensus size: 19
186506 TTATAAACTT
*
186516 AAAATTGCAACATGAAAATG
1 AAAATCGCAACA-GAAAATG
186536 AAAATCGCAACACGAAAATG
1 AAAATCGCAACA-GAAAATG
** *
186556 ACTATCGCAATGAGAGAAATG
1 AAAATCGCAA-CAGA-AAATG
*
186577 AAAATTGCAAC
1 AAAATCGCAAC
186588 GAGAGAATCG
Statistics
Matches: 41, Mismatches: 9, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
20 28 0.68
21 13 0.32
ACGTcount: A:0.51, C:0.15, G:0.17, T:0.17
Consensus pattern (19 bp):
AAAATCGCAACAGAAAATG
Found at i:186636 original size:19 final size:18
Alignment explanation
Indices: 186614--186769 Score: 84
Period size: 20 Copynumber: 8.9 Consensus size: 18
186604 GAAACCAAAA
186614 TCGCATTGCGATTTTCATT
1 TCGC-TTGCGATTTTCATT
*
186633 TCGCGTTGCGA--TTC-TC
1 TCGC-TTGCGATTTTCATT
*
186649 TCG-TTGCGATTTTAATT
1 TCGCTTGCGATTTTCATT
*
186666 TCGCATTGCGA--TTC-TC
1 TCGC-TTGCGATTTTCATT
186682 TCG-TTGCGATTTTCATT
1 TCGCTTGCGATTTTCATT
*
186699 TCGCGTTGCGA--TTC-TC
1 TCGC-TTGCGATTTTCATT
**
186715 TCG-TTGCGATAGTCATT
1 TCGCTTGCGATTTTCATT
*
186732 TCCGCGTTGCGATTTTTATT
1 T-CGC-TTGCGATTTTCATT
*
186752 CTCTCGTTGCGATTTTCA
1 -TCGC-TTGCGATTTTCA
186770 GTTCAACCAA
Statistics
Matches: 105, Mismatches: 15, Indels: 33
0.69 0.10 0.22
Matches are distributed among these distances:
14 18 0.17
16 19 0.18
17 18 0.17
18 2 0.02
19 22 0.21
20 25 0.24
21 1 0.01
ACGTcount: A:0.12, C:0.23, G:0.20, T:0.45
Consensus pattern (18 bp):
TCGCTTGCGATTTTCATT
Found at i:186655 original size:14 final size:14
Alignment explanation
Indices: 186636--186724 Score: 61
Period size: 14 Copynumber: 5.6 Consensus size: 14
186626 TTTCATTTCG
186636 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
* *
186650 CGTTGCGATTTTAATTT
1 CGTTGCGA--TT-CTCT
186667 CGCATTGCGATTCTCT
1 CG--TTGCGATTCTCT
*
186683 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
186702 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
186716 CGTTGCGAT
1 CGTTGCGAT
186725 AGTCATTTCC
Statistics
Matches: 59, Mismatches: 6, Indels: 20
0.69 0.07 0.24
Matches are distributed among these distances:
14 25 0.42
16 9 0.15
17 9 0.15
19 16 0.27
ACGTcount: A:0.11, C:0.24, G:0.21, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:186661 original size:33 final size:33
Alignment explanation
Indices: 186619--186745 Score: 209
Period size: 33 Copynumber: 3.8 Consensus size: 33
186609 CAAAATCGCA
186619 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
186652 TTGCGATTTTAATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
186685 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
**
186718 TTGCGATAGTCATTTCCGCGTTGCGATT
1 TTGCGATTTTCATTT-CGCGTTGCGATT
186746 TTTATTCTCT
Statistics
Matches: 87, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
33 75 0.86
34 12 0.14
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.44
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:188591 original size:36 final size:36
Alignment explanation
Indices: 188544--188617 Score: 139
Period size: 36 Copynumber: 2.1 Consensus size: 36
188534 TTTGGTTGAA
*
188544 GTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACT
1 GTAAATTTATTCAGTTGCTGCCAATTCTGCTAAACT
188580 GTAAATTTATTCAGTTGCTGCCAATTCTGCTAAACT
1 GTAAATTTATTCAGTTGCTGCCAATTCTGCTAAACT
188616 GT
1 GT
188618 GTATTCTTTA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.26, C:0.19, G:0.16, T:0.39
Consensus pattern (36 bp):
GTAAATTTATTCAGTTGCTGCCAATTCTGCTAAACT
Found at i:188650 original size:130 final size:125
Alignment explanation
Indices: 188455--188711 Score: 408
Period size: 130 Copynumber: 2.0 Consensus size: 125
188445 AGATTGCTTA
*
188455 GTAAATTTATTCGTTTCTGCCAATACTGCTAAACTGTTTATTAACATTGTGAAGTTAGTATTTGT
1 GTAAATTTATTCGTTGCTGCCAATACTGCTAAACTGTTTATTAACATTGTGAAGTTAGTATTTGT
*
188520 CTTTTGTTTTGTCTTTTGGTTG-AAGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACT
66 C-TTTGTTTTATCTTTTGGTTGAAAGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACT
* *
188580 GTAAATTTATTCAGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACATTGTGAAGTTAGTA
1 GTAAATTTATTC-GTTGCTGCCAATACTGCTAAAC--TGT-TT-ATTAACATTGTGAAGTTAGTA
*
188645 TTTGTCTTTGTTTTATCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
61 TTTGTCTTTGTTTTATCTTTTGGTTGAAAGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACT
188710 GT
1 GT
188712 GTATTCTTTA
Statistics
Matches: 121, Mismatches: 5, Indels: 7
0.91 0.04 0.05
Matches are distributed among these distances:
125 12 0.10
126 20 0.17
128 3 0.02
129 21 0.17
130 65 0.54
ACGTcount: A:0.23, C:0.14, G:0.18, T:0.46
Consensus pattern (125 bp):
GTAAATTTATTCGTTGCTGCCAATACTGCTAAACTGTTTATTAACATTGTGAAGTTAGTATTTGT
CTTTGTTTTATCTTTTGGTTGAAAGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACT
Found at i:188703 original size:94 final size:94
Alignment explanation
Indices: 188580--188864 Score: 493
Period size: 94 Copynumber: 3.0 Consensus size: 94
188570 CTGCTAAACT
* *
188580 GTAAATTTATTCAGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACATTGTGAAGTTAGTA
1 GTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACATTGTGAAGTTAGTA
188645 TTTGTCTTTGTTTTATCTTTTGGTTGAAA
66 TTTGTCTTTGTTTTATCTTTTGGTTGAAA
*
188674 GTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGTA
1 GTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACATTGTGAAGTTAGTA
188739 TTTGTCTTTGTTTTATCTTTTGGTTGAAA
66 TTTGTCTTTGTTTTATCTTTTGGTTGAAA
* *
188768 GTAAATTTGTTCGTTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAATACTT-TGAAGTTAGT
1 GTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACA-TTGTGAAGTTAGT
*
188832 ATTTGTCTTTGTTTTGTCTTTTGGTTG-AA
65 ATTTGTCTTTGTTTTATCTTTTGGTTGAAA
188861 GTAA
1 GTAA
188865 TGCAATCCAT
Statistics
Matches: 183, Mismatches: 7, Indels: 3
0.95 0.04 0.02
Matches are distributed among these distances:
93 6 0.03
94 176 0.96
95 1 0.01
ACGTcount: A:0.22, C:0.12, G:0.18, T:0.48
Consensus pattern (94 bp):
GTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACATTGTGAAGTTAGTA
TTTGTCTTTGTTTTATCTTTTGGTTGAAA
Found at i:189038 original size:19 final size:19
Alignment explanation
Indices: 189016--189122 Score: 98
Period size: 19 Copynumber: 5.8 Consensus size: 19
189006 GAAACTATAA
189016 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
189035 TCGCATTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
189049 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
189068 TCGCGTTACGATTTTCGTT
1 TCGCGTTGCGATTTTCATT
**
189087 TCGCGTTGCGATAGTCATTTT
1 TCGCGTTGCGATTTTCA--TT
*
189108 TCACGTTGCGATTTT
1 TCGCGTTGCGATTTT
189123 AAGTTCCAGA
Statistics
Matches: 68, Mismatches: 13, Indels: 12
0.73 0.14 0.13
Matches are distributed among these distances:
14 9 0.13
16 3 0.04
17 3 0.04
19 39 0.57
21 14 0.21
ACGTcount: A:0.12, C:0.21, G:0.21, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:191012 original size:14 final size:14
Alignment explanation
Indices: 190993--191028 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
190983 ATTGTTTAAT
190993 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
191007 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
191021 TGATTTGT
1 TGATTTGT
191029 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:191157 original size:19 final size:18
Alignment explanation
Indices: 191135--191225 Score: 58
Period size: 19 Copynumber: 5.4 Consensus size: 18
191125 AAAAATGACT
191135 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
*
191154 ATCGCAA-CG--A-GAGA
1 ATCGCAAGCGAAATGAAA
191168 ATCGCAACGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
*
191187 A-CGCAA-CG--A-CAAA
1 ATCGCAAGCGAAATGAAA
191200 ATCGCAACGCGAAACT-AAA
1 ATCGCAA-GCGAAA-TGAAA
191219 ATCGCAA
1 ATCGCAA
191226 CGCAAAACTA
Statistics
Matches: 57, Mismatches: 3, Indels: 24
0.68 0.04 0.29
Matches are distributed among these distances:
13 4 0.07
14 16 0.28
15 1 0.02
16 6 0.11
17 2 0.04
18 7 0.12
19 21 0.37
ACGTcount: A:0.47, C:0.23, G:0.20, T:0.10
Consensus pattern (18 bp):
ATCGCAAGCGAAATGAAA
Found at i:191203 original size:32 final size:33
Alignment explanation
Indices: 191135--191232 Score: 139
Period size: 32 Copynumber: 3.0 Consensus size: 33
191125 AAAAATGACT
* * *
191135 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
191168 ATCGCAACGCGAAATGAAAA-CGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
191200 ATCGCAACGCGAAACT-AAAATCGCAACG-CAAA
1 ATCGCAACGCGAAA-TGAAAATCGCAACGACAAA
191232 A
1 A
191233 CTAAATTTGC
Statistics
Matches: 60, Mismatches: 3, Indels: 5
0.88 0.04 0.07
Matches are distributed among these distances:
32 33 0.55
33 27 0.45
ACGTcount: A:0.48, C:0.23, G:0.19, T:0.09
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:191226 original size:19 final size:19
Alignment explanation
Indices: 191167--191237 Score: 75
Period size: 19 Copynumber: 4.1 Consensus size: 19
191157 GCAACGAGAG
191167 AATCGCAACGCGAAA-TGAA
1 AATCGCAACGCGAAACT-AA
191186 AA-CGCAA--CG--AC-AA
1 AATCGCAACGCGAAACTAA
191199 AATCGCAACGCGAAACTAA
1 AATCGCAACGCGAAACTAA
*
191218 AATCGCAACGCAAAACTAA
1 AATCGCAACGCGAAACTAA
191237 A
1 A
191238 TTTGCGTTGC
Statistics
Matches: 44, Mismatches: 1, Indels: 14
0.75 0.02 0.24
Matches are distributed among these distances:
13 4 0.09
14 6 0.14
16 4 0.09
18 7 0.16
19 23 0.52
ACGTcount: A:0.51, C:0.25, G:0.15, T:0.08
Consensus pattern (19 bp):
AATCGCAACGCGAAACTAA
Found at i:191283 original size:32 final size:33
Alignment explanation
Indices: 191242--191315 Score: 123
Period size: 33 Copynumber: 2.3 Consensus size: 33
191232 ACTAAATTTG
191242 CGTTGCGATTTTCA-TTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
* *
191274 CGTTGCGATTTTCATTTCGCATTGTGATTTTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
191307 CGTTGCGAT
1 CGTTGCGAT
191316 AGACATTAAG
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
32 14 0.36
33 25 0.64
ACGTcount: A:0.12, C:0.22, G:0.20, T:0.46
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:193624 original size:14 final size:14
Alignment explanation
Indices: 193605--193631 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
193595 TCCCGTGACA
193605 TTTTCTTTGGGGAC
1 TTTTCTTTGGGGAC
193619 TTTTCTTTGGGGA
1 TTTTCTTTGGGGA
193632 TTTCTTCTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.11, G:0.30, T:0.52
Consensus pattern (14 bp):
TTTTCTTTGGGGAC
Found at i:193870 original size:24 final size:24
Alignment explanation
Indices: 193843--193889 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
193833 CAAAATCTGA
193843 GTATTGACCAAGATCAAAGTTCGG
1 GTATTGACCAAGATCAAAGTTCGG
*
193867 GTATTGACCAAGATCAAATTTCG
1 GTATTGACCAAGATCAAAGTTCG
193890 AATACTGACT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (24 bp):
GTATTGACCAAGATCAAAGTTCGG
Found at i:193898 original size:24 final size:24
Alignment explanation
Indices: 193847--193898 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
193837 ATCTGAGTAT
** *
193847 TGACCAAGATCAAAGTTCGGGTAT
1 TGACCAAGATCAAAGTTCGAATAC
*
193871 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTTCGAATAC
193895 TGAC
1 TGAC
193899 TAGTACTCAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (24 bp):
TGACCAAGATCAAAGTTCGAATAC
Found at i:194770 original size:20 final size:21
Alignment explanation
Indices: 194747--194833 Score: 126
Period size: 20 Copynumber: 4.3 Consensus size: 21
194737 CAGAATCTCG
194747 TTGCGATTT-CCTAATTCGCA
1 TTGCGATTTACCTAATTCGCA
*
194767 TTGCGATTTACGTAA-TCGCA
1 TTGCGATTTACCTAATTCGCA
*
194787 TTGCGATTTTCCTAATTCGCA
1 TTGCGATTTACCTAATTCGCA
*
194808 TTGCGATTTACGT-ATTCGCA
1 TTGCGATTTACCTAATTCGCA
194828 TTGCGA
1 TTGCGA
194834 ATTAGGAAAA
Statistics
Matches: 60, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
20 40 0.67
21 20 0.33
ACGTcount: A:0.21, C:0.22, G:0.18, T:0.39
Consensus pattern (21 bp):
TTGCGATTTACCTAATTCGCA
Found at i:194798 original size:41 final size:40
Alignment explanation
Indices: 194747--194833 Score: 156
Period size: 41 Copynumber: 2.1 Consensus size: 40
194737 CAGAATCTCG
194747 TTGCGATTTCCTAATTCGCATTGCGATTTACGTAATCGCA
1 TTGCGATTTCCTAATTCGCATTGCGATTTACGTAATCGCA
*
194787 TTGCGATTTTCCTAATTCGCATTGCGATTTACGTATTCGCA
1 TTGCGA-TTTCCTAATTCGCATTGCGATTTACGTAATCGCA
194828 TTGCGA
1 TTGCGA
194834 ATTAGGAAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
40 6 0.13
41 39 0.87
ACGTcount: A:0.21, C:0.22, G:0.18, T:0.39
Consensus pattern (40 bp):
TTGCGATTTCCTAATTCGCATTGCGATTTACGTAATCGCA
Found at i:194848 original size:41 final size:41
Alignment explanation
Indices: 194762--194848 Score: 111
Period size: 41 Copynumber: 2.1 Consensus size: 41
194752 ATTTCCTAAT
* * * *
194762 TCGCATTGCGATTTACGTAATCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTACGTAATCGCATTGCGAATTACCAAAA
* **
194803 TCGCATTGCGATTTACGTATTCGCATTGCGAATTAGGAAAA
1 TCGCATTGCGATTTACGTAATCGCATTGCGAATTACCAAAA
194844 TCGCA
1 TCGCA
194849 ACGCGAATTT
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.34
Consensus pattern (41 bp):
TCGCATTGCGATTTACGTAATCGCATTGCGAATTACCAAAA
Found at i:194854 original size:21 final size:21
Alignment explanation
Indices: 194830--194875 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
194820 TATTCGCATT
194830 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* * *
194851 GCGAATTTGGGAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
194872 GCGA
1 GCGA
194876 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.17, G:0.28, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:197495 original size:21 final size:20
Alignment explanation
Indices: 197409--197566 Score: 88
Period size: 21 Copynumber: 7.8 Consensus size: 20
197399 AAATGACCAA
**
197409 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
197428 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
197448 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
197468 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
197489 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
197510 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
*
197530 CCAAAATCGCAACGCGAATATT
1 -CAAAATCGCAACGCG-ATTTT
197552 -AAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
197567 ACACATAAAT
Statistics
Matches: 105, Mismatches: 27, Indels: 14
0.72 0.18 0.10
Matches are distributed among these distances:
19 17 0.16
20 40 0.38
21 44 0.42
22 4 0.04
ACGTcount: A:0.39, C:0.25, G:0.16, T:0.20
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:197557 original size:20 final size:20
Alignment explanation
Indices: 197469--197585 Score: 78
Period size: 20 Copynumber: 5.7 Consensus size: 20
197459 ATCAGTTTCC
* *
197469 AAAATCGCAACGCGATTCTT
1 AAAATCGCAACGCGAATATT
* *
197489 GAAAATCGCAATGCG-ATAGT
1 -AAAATCGCAACGCGAATATT
** *
197509 ACAAATTCGCATTGCG-ATTTT
1 A-AAA-TCGCAACGCGAATATT
197530 CCAAAATCGCAACGCGAATATT
1 --AAAATCGCAACGCGAATATT
* *
197552 AAAATCGCAACGCGAACA-C
1 AAAATCGCAACGCGAATATT
197571 ATAAATCGCAACGCG
1 A-AAATCGCAACGCG
197586 TATCCGTAAA
Statistics
Matches: 78, Mismatches: 12, Indels: 13
0.76 0.12 0.13
Matches are distributed among these distances:
19 2 0.03
20 35 0.45
21 33 0.42
22 7 0.09
23 1 0.01
ACGTcount: A:0.38, C:0.24, G:0.17, T:0.21
Consensus pattern (20 bp):
AAAATCGCAACGCGAATATT
Found at i:197595 original size:20 final size:20
Alignment explanation
Indices: 197553--197762 Score: 219
Period size: 20 Copynumber: 10.5 Consensus size: 20
197543 GCGAATATTA
* *
197553 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
197573 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
197593 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
197613 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
197633 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* *
197653 ATATCGCAACGCATATCCGT
1 AAATCGCAACGCGTATCCGT
*
197673 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
197693 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
197713 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
197733 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
197753 AAATCACAAC
1 AAATCGCAAC
197763 ACTGAAATTT
Statistics
Matches: 162, Mismatches: 23, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
19 2 0.01
20 158 0.98
21 2 0.01
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:198482 original size:24 final size:24
Alignment explanation
Indices: 198443--198489 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
198433 AAATTTGGTC
198443 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
198467 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
198490 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:198681 original size:12 final size:12
Alignment explanation
Indices: 198664--198688 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
198654 ATATAATCCT
198664 GAAGAAGAAAAA
1 GAAGAAGAAAAA
198676 GAAGAAGAAAAA
1 GAAGAAGAAAAA
198688 G
1 G
198689 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:201022 original size:33 final size:34
Alignment explanation
Indices: 200971--201201 Score: 197
Period size: 33 Copynumber: 6.7 Consensus size: 34
200961 CGGAAATTAC
* *
200971 AATCGCAACGA-GAGAATCGCAATGCGAAATGAA
1 AATCCCAACGATGAAAATCGCAATGCGAAATGAA
201004 AATCCCAAC-ATGAAAATCGCAATGCGGAAATGAA
1 AATCCCAACGATGAAAATCGCAATGC-GAAATGAA
* *
201038 AATCGCAACGA-GAGAATCGCAATGCGAAATGAA
1 AATCCCAACGATGAAAATCGCAATGCGAAATGAA
* * * *
201071 AATCACAATGCGAAATGAAAATCGCAACGAGAGAATCG-C
1 AATCCCAA--CG--ATGAAAATCGCAATGCGA-AAT-GAA
* *
201110 AATGCGAA--ATGAAAATCGCAATGCGAAATGAA
1 AATCCCAACGATGAAAATCGCAATGCGAAATGAA
* *
201142 AATCGCAACGA-GAGAATCGCAATGCGAAATGAA
1 AATCCCAACGATGAAAATCGCAATGCGAAATGAA
*
201175 AATCGCAATGCGAAATGAAAATCGCAA
1 AATCCCAA--CG--ATGAAAATCGCAA
201202 CGAGAGAATC
Statistics
Matches: 160, Mismatches: 20, Indels: 31
0.76 0.09 0.15
Matches are distributed among these distances:
31 1 0.01
32 9 0.06
33 81 0.51
34 30 0.19
35 5 0.03
37 2 0.01
38 23 0.14
39 8 0.05
40 1 0.01
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.13
Consensus pattern (34 bp):
AATCCCAACGATGAAAATCGCAATGCGAAATGAA
Found at i:201079 original size:19 final size:19
Alignment explanation
Indices: 200985--201201 Score: 240
Period size: 19 Copynumber: 12.4 Consensus size: 19
200975 GCAACGAGAG
200985 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
201004 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
201018 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
201038 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
201052 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
201071 AATCACAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
201090 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
201104 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
201123 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
201142 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
201156 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
201175 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
201194 AATCGCAA
1 AATCGCAA
201202 CGAGAGAATC
Statistics
Matches: 167, Mismatches: 10, Indels: 42
0.76 0.05 0.19
Matches are distributed among these distances:
14 42 0.25
15 3 0.02
16 7 0.04
17 6 0.04
18 4 0.02
19 92 0.55
20 13 0.08
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:201141 original size:71 final size:71
Alignment explanation
Indices: 200985--201201 Score: 227
Period size: 71 Copynumber: 3.1 Consensus size: 71
200975 GCAACGAGAG
* * * *
200985 AATCGCAATGCGAAATGAAAATCCCAAC-ATGAAAATCGCAATGCGGAAATGAAAATCGCAA--C
1 AATCGCAATGCGAAATGAAAATCACAACGA-GAGAATCGAAATGC-GAAACGAAAATCGCAATGC
*
201047 G--A-GAG
64 GAAATGAA
* * *
201052 AATCGCAATGCGAAATGAAAATCACAATGCGA-AAT-GAAAAT-CGCAACGAGAGAATCGCAATG
1 AATCGCAATGCGAAATGAAAATCACAACGAGAGAATCG-AAATGCGAAACGA-A-AATCGCAATG
201114 CGAAATGAA
63 CGAAATGAA
* * *
201123 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCACAACGAGAGAATCGAAATGCGAAACGAAAATCGCAATGCGA
201188 AATGAA
66 AATGAA
201194 AATCGCAA
1 AATCGCAA
201202 CGAGAGAATC
Statistics
Matches: 125, Mismatches: 13, Indels: 20
0.79 0.08 0.13
Matches are distributed among these distances:
64 5 0.04
65 3 0.02
66 14 0.11
67 28 0.22
68 2 0.02
70 1 0.01
71 58 0.46
72 7 0.06
73 7 0.06
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (71 bp):
AATCGCAATGCGAAATGAAAATCACAACGAGAGAATCGAAATGCGAAACGAAAATCGCAATGCGA
AATGAA
Found at i:201212 original size:33 final size:33
Alignment explanation
Indices: 201071--201223 Score: 150
Period size: 33 Copynumber: 4.5 Consensus size: 33
201061 GCGAAATGAA
*
201071 AATCACAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
* *
201104 AATCGCAATGCGAAATGAAAATCGCAATGCGA-
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
* * * *
201136 AAT-GAAAAT-CGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCG-CAATGCGAAATGA-A-AATCGCAA--CG--A-GAG
201175 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
201208 AATCGCAATGCGAAAT
1 AATCGCAATGCGAAAT
201224 TATAAACGCA
Statistics
Matches: 97, Mismatches: 12, Indels: 22
0.74 0.09 0.17
Matches are distributed among these distances:
31 7 0.07
32 7 0.07
33 55 0.57
34 1 0.01
35 1 0.01
36 2 0.02
38 10 0.10
39 7 0.07
40 7 0.07
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAG
Found at i:201239 original size:52 final size:52
Alignment explanation
Indices: 201013--201223 Score: 404
Period size: 52 Copynumber: 4.0 Consensus size: 52
201003 AAATCCCAAC
201013 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
201066 ATGAAAATCACAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
201118 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
201170 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
201222 AT
1 AT
201224 TATAAACGCA
Statistics
Matches: 156, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
52 141 0.90
53 15 0.10
ACGTcount: A:0.46, C:0.17, G:0.23, T:0.14
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:201334 original size:19 final size:19
Alignment explanation
Indices: 201248--201326 Score: 105
Period size: 19 Copynumber: 4.4 Consensus size: 19
201238 GATTCTCTCG
201248 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
201268 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
201287 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
201301 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
201320 TTGCGAT
1 TTGCGAT
201327 AGTCATTTTT
Statistics
Matches: 52, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
14 6 0.12
16 7 0.13
17 7 0.13
19 17 0.33
20 15 0.29
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:201452 original size:14 final size:14
Alignment explanation
Indices: 201433--201469 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
201423 CATCAATTAC
201433 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
201447 ACAAATCATCTTTT
1 ACAAATCAACTTTT
201461 ACAAATCAA
1 ACAAATCAA
201470 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:203466 original size:14 final size:14
Alignment explanation
Indices: 203447--203503 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
203437 GCGAAATGAA
*
203447 AATCGCAACGACAG
1 AATCGCAACGAAAG
203461 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
203478 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
203494 AATCGCAACG
1 AATCGCAACG
203504 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:203474 original size:33 final size:33
Alignment explanation
Indices: 203428--203520 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
203418 GCGAAACCAA
*
203428 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
203461 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
203494 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
203521 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:203485 original size:19 final size:19
Alignment explanation
Indices: 203391--203525 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
203381 TAGTTTACTT
* *
203391 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
203411 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
203430 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
203449 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
203463 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
203482 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
203496 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
203515 TCGCAATGCGA
1 TCGCAACGCGA
203526 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:203543 original size:19 final size:19
Alignment explanation
Indices: 203521--203649 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
203511 AAAATCGCAA
203521 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
203540 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
203554 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
203573 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
203587 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
203606 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
203625 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
203645 TGCGA
1 TGCGA
203650 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:203556 original size:14 final size:14
Alignment explanation
Indices: 203537--203593 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
203527 TTTGGTTTCG
203537 CGTTGCGATTCTGT
1 CGTTGCGATTCTGT
*
203551 CGTTGCGATTTTGGTTT
1 CGTTGCGATTCT-G--T
203568 CGCGTTGCGATTCTGT
1 --CGTTGCGATTCTGT
203584 CGTTGCGATT
1 CGTTGCGATT
203594 TTCATTTCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 21 0.58
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 11 0.31
ACGTcount: A:0.07, C:0.19, G:0.30, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTGT
Found at i:203563 original size:33 final size:33
Alignment explanation
Indices: 203521--203612 Score: 166
Period size: 33 Copynumber: 2.8 Consensus size: 33
203511 AAAATCGCAA
203521 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
203554 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
203587 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
203613 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:203960 original size:93 final size:93
Alignment explanation
Indices: 203697--204071 Score: 709
Period size: 93 Copynumber: 4.1 Consensus size: 93
203687 ATGGATTGCA
*
203697 TTAC-TTCAACCAAAACACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
203761 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
203789 TTACTTTCAACC-AAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
203853 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
203881 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
203946 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
203974 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
* *
204039 TAGCAGAATTGGTAGCAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
204067 TTACT
1 TTACT
204072 AAGCAATCTA
Statistics
Matches: 278, Mismatches: 3, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
92 95 0.34
93 183 0.66
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:205813 original size:19 final size:19
Alignment explanation
Indices: 205789--205872 Score: 97
Period size: 19 Copynumber: 4.7 Consensus size: 19
205779 GCAACGAGAG
*
205789 AATCGCAACGCGAAATGAC
1 AATCGCAACGCGAAATGAA
205808 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
205827 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
*
205841 AATCGCAATGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
205860 AATCGCAATGCGA
1 AATCGCAACGCGA
205873 TTTTGGTTTC
Statistics
Matches: 57, Mismatches: 3, Indels: 10
0.81 0.04 0.14
Matches are distributed among these distances:
14 10 0.18
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 41 0.72
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.12
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:205830 original size:52 final size:52
Alignment explanation
Indices: 205767--205872 Score: 176
Period size: 52 Copynumber: 2.0 Consensus size: 52
205757 TCTTTTGGTT
*
205767 GAAATAAAAATCGCAACGAGAGAATCGCAACGCGAAATGACAATCGCAACGC
1 GAAATAAAAATCGCAACGAGAGAATCGCAACGCGAAATGAAAATCGCAACGC
* * *
205819 GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGC
1 GAAATAAAAATCGCAACGAGAGAATCGCAACGCGAAATGAAAATCGCAACGC
205871 GA
1 GA
205873 TTTTGGTTTC
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.46, C:0.20, G:0.23, T:0.11
Consensus pattern (52 bp):
GAAATAAAAATCGCAACGAGAGAATCGCAACGCGAAATGAAAATCGCAACGC
Found at i:205921 original size:26 final size:25
Alignment explanation
Indices: 205891--205960 Score: 87
Period size: 20 Copynumber: 3.0 Consensus size: 25
205881 TCGCGTTGCG
205891 ATTCTCTCGTTGCGATTTTCATTTC
1 ATTCTCTCGTTGCGATTTTCATTTC
*
205916 ATTTCTCTCGTTGCGA----CA-GTC
1 A-TTCTCTCGTTGCGATTTTCATTTC
205937 ATTCTCTCGTTGCGATTTTCATTT
1 ATTCTCTCGTTGCGATTTTCATTT
205961 ATCTCGTTGC
Statistics
Matches: 37, Mismatches: 2, Indels: 12
0.73 0.04 0.24
Matches are distributed among these distances:
20 14 0.38
21 3 0.08
22 2 0.05
24 2 0.05
25 2 0.05
26 14 0.38
ACGTcount: A:0.13, C:0.24, G:0.14, T:0.49
Consensus pattern (25 bp):
ATTCTCTCGTTGCGATTTTCATTTC
Found at i:205958 original size:20 final size:21
Alignment explanation
Indices: 205912--205974 Score: 83
Period size: 20 Copynumber: 3.0 Consensus size: 21
205902 GCGATTTTCA
205912 TTTCATTTCTCTCGTTGCGAC
1 TTTCATTTCTCTCGTTGCGAC
** *
205933 AGTCA-TTCTCTCGTTGCGAT
1 TTTCATTTCTCTCGTTGCGAC
*
205953 TTTCATTTATCTCGTTGCGAC
1 TTTCATTTCTCTCGTTGCGAC
205974 T
1 T
205975 CTTCTGCAAA
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
20 17 0.50
21 17 0.50
ACGTcount: A:0.13, C:0.25, G:0.16, T:0.46
Consensus pattern (21 bp):
TTTCATTTCTCTCGTTGCGAC
Found at i:206094 original size:33 final size:33
Alignment explanation
Indices: 206052--206122 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
206042 AATACTAACT
*
206052 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
206085 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
206118 TGAAA
1 TGAAA
206123 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:206356 original size:22 final size:22
Alignment explanation
Indices: 206304--206358 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
206294 TGGTTGTGAG
**
206304 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
206326 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
206348 GGATTTCTTCG
1 GGATTTCTTCG
206359 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:206530 original size:20 final size:20
Alignment explanation
Indices: 206505--206678 Score: 217
Period size: 20 Copynumber: 8.7 Consensus size: 20
206495 CTTTAAATAT
206505 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
206525 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
206547 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
206566 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
206586 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
206606 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
206626 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
206646 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
206666 CGCGTTGCGATTT
1 CGCGTTGCGATTT
206679 TCATATTTGC
Statistics
Matches: 132, Mismatches: 18, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
19 2 0.02
20 113 0.86
21 15 0.11
22 2 0.02
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.34
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:206698 original size:60 final size:60
Alignment explanation
Indices: 206505--206678 Score: 249
Period size: 60 Copynumber: 2.9 Consensus size: 60
206495 CTTTAAATAT
**
206505 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
206566 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* *
206626 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTT
206679 TCATATTTGC
Statistics
Matches: 97, Mismatches: 16, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
60 69 0.71
61 28 0.29
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.34
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Done.