Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008364.1 Hibiscus syriacus cultivar Beakdansim tig00111105_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: 5892847
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 24 of 27
Found at i:5354502 original size:183 final size:183
Alignment explanation
Indices: 5354191--5354540 Score: 619
Period size: 183 Copynumber: 1.9 Consensus size: 183
5354181 ATTAAATCCG
5354191 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
** * *
5354256 ATAGATTATGTTCAAACTATGACACTACTCGAACACTTGGCAATTCGGTGTTTGCTTCACTGCTT
66 ATAGATTACATTCAAACCATGACACTACTCGAACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
5354321 TTGTCAGGCCAAAGACTTTGTGATGAGACGAACCCTTCAGTGATTTGTCCCTA
131 TTGTCAGGCCAAAGACTTTGTGATGAGACGAACCCTTCAGTGATTTGTCCCTA
5354374 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
* * *
5354439 ATAGATTACATTCAAACCATGACATTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
66 ATAGATTACATTCAAACCATGACACTACTCGAACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
* *
5354504 TTGTTAGGCCAAAGACTTTGTGATGAGATGAACCCTT
131 TTGTCAGGCCAAAGACTTTGTGATGAGACGAACCCTT
5354541 TAGTTAAACC
Statistics
Matches: 158, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
183 158 1.00
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (183 bp):
TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
ATAGATTACATTCAAACCATGACACTACTCGAACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
TTGTCAGGCCAAAGACTTTGTGATGAGACGAACCCTTCAGTGATTTGTCCCTA
Found at i:5355895 original size:37 final size:37
Alignment explanation
Indices: 5355828--5355914 Score: 122
Period size: 37 Copynumber: 2.4 Consensus size: 37
5355818 ATTGAAAACA
** * *
5355828 TTTCCCTTGAAA-TGAATTTTGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
5355864 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
*
5355901 TTTCTCTTGAAACA
1 TTTCCCTTGAAACA
5355915 TAAACATTGA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
36 12 0.27
37 33 0.73
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.40
Consensus pattern (37 bp):
TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
Found at i:5355917 original size:102 final size:105
Alignment explanation
Indices: 5355733--5355980 Score: 369
Period size: 102 Copynumber: 2.4 Consensus size: 105
5355723 TTTTTCTTAA
* * * *
5355733 AACAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAGAAAGTTTTGTCTCACTTGAGACA
1 AACAAAATTTTGTCTCCCTTGAGATAGTTTCCCTTGAAACAGAAAGTTTTGTCTCACTTGAGACA
*
5355798 GTTTCTCTTTAAACATAAACATTGAAAACATTTCCCTT-G
66 GTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGG
* * *
5355837 AA-ATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACA-AAA-TTTTGTCTCCCTTGAGAC
1 AACA-AAATTTTGTCTCCCTTGAGATAGTTTCCCTTGAAACAGAAAGTTTTGTCTCACTTGAGAC
5355899 AGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGG
65 AGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGG
* *
5355940 AACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
1 AACAAAATTTTGTCTCCCTTGAGATAGTTTCCCTTGAAACA
5355981 TAAACATTGA
Statistics
Matches: 130, Mismatches: 11, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
102 55 0.42
103 40 0.31
104 35 0.27
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.35
Consensus pattern (105 bp):
AACAAAATTTTGTCTCCCTTGAGATAGTTTCCCTTGAAACAGAAAGTTTTGTCTCACTTGAGACA
GTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGG
Found at i:5355970 original size:66 final size:66
Alignment explanation
Indices: 5355864--5356043 Score: 269
Period size: 66 Copynumber: 2.8 Consensus size: 66
5355854 CTTGAGATAG
*
5355864 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
1 TTTCCCTTGGAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
5355929 A
66 A
*
5355930 TTTCCCTTGGAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAGC
1 TTTCCCTTGGAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
5355995 A
66 A
* * * *
5355996 TTTCCCTT-GAA-ATAAA--TTGCCTCTCTTGAGATAGTTTCCCTTGAAACA
1 TTTCCCTTGGAACA-AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
5356044 AAATTTTGTC
Statistics
Matches: 107, Mismatches: 6, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
63 28 0.26
64 1 0.01
65 6 0.06
66 72 0.67
ACGTcount: A:0.32, C:0.22, G:0.12, T:0.34
Consensus pattern (66 bp):
TTTCCCTTGGAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
A
Found at i:5356075 original size:166 final size:169
Alignment explanation
Indices: 5355760--5356145 Score: 613
Period size: 166 Copynumber: 2.3 Consensus size: 169
5355750 CTTGAGATAG
* * *
5355760 TTTCCCTCGAAACAGAAAGTTTTGTCTCACTTGAGACAGTTTCTCTTTAAACATAAACATTGAAA
1 TTTCCCTTGGAACAGAAA-TTTTGTCTCACTTGAGACAGTTTCTCTTGAAACATAAACATTGAAA
* *
5355825 ACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTC
65 ACATTTCCCTTGAAATGAATATTGCCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTC
*
5355890 CCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
130 CCTTGAGACAATTTCTCTTGAAACATAAACATTGAAAACA
* *
5355930 TTTCCCTTGGAACA-AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAG
1 TTTCCCTTGGAACAGAAATTTTGTCTCACTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAA
5355994 CATTTCCCTTGAAAT-AA-ATTGCCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCC
66 CATTTCCCTTGAAATGAATATTGCCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCC
5356057 CTTGAGACAATTTCTCTTGAAACATAAACATTGAAAACA
131 CTTGAGACAATTTCTCTTGAAACATAAACATTGAAAACA
* * *
5356096 TTTCCCTT-GAA-ATG-AATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACA
1 TTTCCCTTGGAACA-GAAATTTTGTCTCACTTGAGACAGTTTCTCTTGAAACA
5356146 AATTTTGTCT
Statistics
Matches: 203, Mismatches: 11, Indels: 9
0.91 0.05 0.04
Matches are distributed among these distances:
164 1 0.00
165 36 0.18
166 90 0.44
167 2 0.01
168 59 0.29
169 3 0.01
170 12 0.06
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.36
Consensus pattern (169 bp):
TTTCCCTTGGAACAGAAATTTTGTCTCACTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAA
CATTTCCCTTGAAATGAATATTGCCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCC
CTTGAGACAATTTCTCTTGAAACATAAACATTGAAAACA
Found at i:5356143 original size:36 final size:36
Alignment explanation
Indices: 5356096--5356181 Score: 111
Period size: 36 Copynumber: 2.4 Consensus size: 36
5356086 ATTGAAAACA
** *
5356096 TTTCCCTTGAAATGAATTTTGTCT-CTCTTGAGATAG
1 TTTCCCTTGAAACAAATTTTGTCTCCT-TTGAGACAG
5356132 TTTCCCTTGAAACAAATTTTGTCTCCTTTGAGACAG
1 TTTCCCTTGAAACAAATTTTGTCTCCTTTGAGACAG
**
5356168 TTTCTATTGAAACA
1 TTTCCCTTGAAACA
5356182 TAAACTTTGA
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
36 42 0.95
37 2 0.05
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.42
Consensus pattern (36 bp):
TTTCCCTTGAAACAAATTTTGTCTCCTTTGAGACAG
Found at i:5356192 original size:101 final size:100
Alignment explanation
Indices: 5355930--5356276 Score: 460
Period size: 100 Copynumber: 3.5 Consensus size: 100
5355920 ATTGAAAACA
* *
5355930 TTTCCCTTGGAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAGC
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
5355995 ATTTCCCTTGAAATAAATTGCCTCTCTTGAGATAG
66 ATTTCCCTTGAAATAAATTGCCTCTCTTGAGATAG
*
5356030 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAATTTCTCTTGAAACATAAACATTGAAAAC
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
* *
5356095 ATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAG
66 ATTTCCCTTGAAAT-AA-ATTGCCTCTCTTGAGATAG
* * *
5356132 TTTCCCTTGAAAC-AAATTTTGTCTCCTTTGAGACAGTTTCTATTGAAACATAAACTTTGAAAAC
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
* *
5356196 AATTTCCCTTGAAACAAA----ATCT-TTGA-ATATG
66 -ATTTCCCTTGAAATAAATTGCCTCTCTTGAGATA-G
* * * *
5356227 TTTTACATT-AAAC-AAATTTCGTCTCTCTTGAGACAGTTTCTCTTGAAACA
1 -TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
5356277 AATTTTGTCT
Statistics
Matches: 224, Mismatches: 18, Indels: 15
0.87 0.07 0.06
Matches are distributed among these distances:
94 3 0.01
95 42 0.19
96 9 0.04
100 76 0.34
101 51 0.23
102 43 0.19
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.37
Consensus pattern (100 bp):
TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
ATTTCCCTTGAAATAAATTGCCTCTCTTGAGATAG
Found at i:5356318 original size:38 final size:36
Alignment explanation
Indices: 5356236--5356350 Score: 167
Period size: 36 Copynumber: 3.1 Consensus size: 36
5356226 GTTTTACATT
*
5356236 AAACAAATTTCGTCTCTCTTGAGACAGTTTCTCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
* * *
5356272 AAACAAATTTTGTCTCTCTTAAGACATGTTTTTCTTA
1 AAACAAATTTTGTCTCTCTTGAGACA-GTTTCTCTTG
*
5356309 AAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTG
1 AAAC-AAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
5356346 AAACA
1 AAACA
5356351 TCAATCCTTG
Statistics
Matches: 69, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
36 25 0.36
37 24 0.35
38 20 0.29
ACGTcount: A:0.30, C:0.20, G:0.11, T:0.39
Consensus pattern (36 bp):
AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
Found at i:5356454 original size:33 final size:33
Alignment explanation
Indices: 5356390--5356504 Score: 153
Period size: 33 Copynumber: 3.5 Consensus size: 33
5356380 CCTTGATACA
*
5356390 GTTTCTCTTGAAACAAAAAAATAAACCTTTGAAATT
1 GTTTCTCTTGAAAC--ACAAA-AAACCTTTGAAATT
*
5356426 GTTTCTCTTGAAACACAAAAAACCTTTGAAAAT
1 GTTTCTCTTGAAACACAAAAAACCTTTGAAATT
*
5356459 GTTTCTCTTGAAACAC--AAAACCTTTGAGATT
1 GTTTCTCTTGAAACACAAAAAACCTTTGAAATT
*
5356490 GTTTCCCTTGAAACA
1 GTTTCTCTTGAAACA
5356505 AATTTCGTCT
Statistics
Matches: 74, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
31 27 0.36
33 29 0.39
34 4 0.05
36 14 0.19
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.33
Consensus pattern (33 bp):
GTTTCTCTTGAAACACAAAAAACCTTTGAAATT
Found at i:5356551 original size:67 final size:67
Alignment explanation
Indices: 5356459--5356645 Score: 239
Period size: 67 Copynumber: 2.7 Consensus size: 67
5356449 CTTTGAAAAT
*
5356459 GTTTCTCTTGAAACACAAAACCTTTGAGATTGTTTCCCTTGAAACAAATTTCGTCTCCCTTGAGA
1 GTTTCTCTTGAAACACAAAATCTTTGAGATTGTTTCCCTTGAAACAAATTTCGTCTCCCTTGAGA
5356524 CA
66 CA
* * * *
5356526 GTTTCTCTTGAAACACAAAATCTTTGAGTTTATTTCCCTTAAAACAAAATTTTGTCTCCCTTGAG
1 GTTTCTCTTGAAACACAAAATCTTTGAGATTGTTTCCCTTGAAAC-AAATTTCGTCTCCCTTGAG
* *
5356591 GCC
65 ACA
* * * * *
5356594 GTTTCTCATGAAACAACATATATCTTTAAGATCGTTTCCCTTGAAACGAATT
1 GTTTCTCTTGAAAC-ACA-AAATCTTTGAGATTGTTTCCCTTGAAACAAATT
5356646 CTGTCTTTTT
Statistics
Matches: 102, Mismatches: 15, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
67 41 0.40
68 32 0.31
69 7 0.07
70 22 0.22
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.36
Consensus pattern (67 bp):
GTTTCTCTTGAAACACAAAATCTTTGAGATTGTTTCCCTTGAAACAAATTTCGTCTCCCTTGAGA
CA
Found at i:5357155 original size:106 final size:107
Alignment explanation
Indices: 5356964--5357196 Score: 317
Period size: 106 Copynumber: 2.2 Consensus size: 107
5356954 GGTTTTAGCT
*
5356964 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAA
1 AGAGCCAATTTCAACTTCACAGCGAAGGACATTGGACTCAAGACAACACAAGTTCAACTTCACAA
** *
5357029 CGAAGGGACGGCTGGTTGTCAAC-AAACAATTTCCCAATTTC
66 CGAAGGGACGGCTGACTGTCAACAAAACAATTTCCCAATTCC
* ** * * *
5357070 GGAGCCAATTTCAACTTCACATTGAA-GAGCATTGGACTCGAGACAGCACAAGTTTAACTTCACA
1 AGAGCCAATTTCAACTTCACAGCGAAGGA-CATTGGACTCAAGACAACACAAGTTCAACTTCACA
* *
5357134 ACGAATGGACGGCTGACTGTCAACAAAACAATTTCCCAGTTCC
65 ACGAAGGGACGGCTGACTGTCAACAAAACAATTTCCCAATTCC
* *
5357177 AGAACCAACTTCAACTTCAC
1 AGAGCCAATTTCAACTTCAC
5357197 GACAGAAGAT
Statistics
Matches: 110, Mismatches: 15, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
105 2 0.02
106 75 0.68
107 33 0.30
ACGTcount: A:0.35, C:0.26, G:0.17, T:0.22
Consensus pattern (107 bp):
AGAGCCAATTTCAACTTCACAGCGAAGGACATTGGACTCAAGACAACACAAGTTCAACTTCACAA
CGAAGGGACGGCTGACTGTCAACAAAACAATTTCCCAATTCC
Found at i:5358756 original size:14 final size:14
Alignment explanation
Indices: 5358724--5358771 Score: 57
Period size: 13 Copynumber: 3.6 Consensus size: 14
5358714 AGTTACTACG
*
5358724 TATATTTTTTGTTA
1 TATATATTTTGTTA
*
5358738 T-TATATTTTGTTC
1 TATATATTTTGTTA
5358751 TATATA-TTT-TTA
1 TATATATTTTGTTA
5358763 TATATATTT
1 TATATATTT
5358772 CTTATTTTTC
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
12 8 0.28
13 16 0.55
14 5 0.17
ACGTcount: A:0.25, C:0.02, G:0.04, T:0.69
Consensus pattern (14 bp):
TATATATTTTGTTA
Found at i:5360368 original size:115 final size:115
Alignment explanation
Indices: 5360166--5360384 Score: 395
Period size: 115 Copynumber: 1.9 Consensus size: 115
5360156 CGATTTGAAG
*
5360166 TATACAATTCGTATCACCTGGTCAGTGGATAGCCCTTACTCAAAACAATTGCGAATCTTTAGTCT
1 TATACAATTCATATCACCTGGTCAGTGGATAGCCCTTACTCAAAACAATTGCGAATCTTTAGTCT
5360231 TATTCGTATGTATTTCAAGAAAACAAAGATGACCATACAGGGGAAAGTTC
66 TATTCGTATGTATTTCAAGAAAACAAAGATGACCATACAGGGGAAAGTTC
*
5360281 TATACAATTCATATCACCTGGTCTGTGGATAGCCCTTACTCAAAACAATTGCGAATCTTTCA-TC
1 TATACAATTCATATCACCTGGTCAGTGGATAGCCCTTACTCAAAACAATTGCGAATCTTT-AGTC
*
5360345 TTATTCGTATGTATTTCAAGAAAACAAAGATGACCGTACA
65 TTATTCGTATGTATTTCAAGAAAACAAAGATGACCATACA
5360385 TGGTATTAGA
Statistics
Matches: 100, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
115 99 0.99
116 1 0.01
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.31
Consensus pattern (115 bp):
TATACAATTCATATCACCTGGTCAGTGGATAGCCCTTACTCAAAACAATTGCGAATCTTTAGTCT
TATTCGTATGTATTTCAAGAAAACAAAGATGACCATACAGGGGAAAGTTC
Found at i:5367077 original size:6 final size:6
Alignment explanation
Indices: 5367066--5367101 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
5367056 TACCGACGAG
*
5367066 GATGAC GATGAC GATGAC GATGAC GATGAA GATGAC
1 GATGAC GATGAC GATGAC GATGAC GATGAC GATGAC
5367102 TGCATGGATG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.36, C:0.14, G:0.33, T:0.17
Consensus pattern (6 bp):
GATGAC
Found at i:5368378 original size:122 final size:122
Alignment explanation
Indices: 5368152--5368379 Score: 257
Period size: 122 Copynumber: 1.9 Consensus size: 122
5368142 AGTATTAAAT
5368152 TTATAAAGACCAAAATGGTGAAAAACAAAAACTTTAAGGATCAAAATAACAAAAATAGAAAGTTA
1 TTATAAAGACCAAAATGGTGAAAAACAAAAACTTTAAGGATCAAAATAACAAAAATAGAAAGTTA
* * ** * *
5368217 AAGTACTAAAATGGCACAAACAAAAACTTAAAGTCCTAAAACAGTAATTATAGAAAC
66 AAGGACCAAAATAACAAAAACAAAAACTTAAAGTACTAAAACAGTAATTATAGAAAC
* * * ** * *
5368274 TTAT-AAGAACCAAAATGGAT-AAAATCCAAAA-TTTAGAGGATTAAAATAGTAAAAATAGAGAT
1 TTATAAAG-ACCAAAATGG-TGAAAAACAAAAACTTTA-AGGATCAAAATAACAAAAATAGAAAG
* *
5368336 TTAAAGGACCAAAATAACAAAAATAGAAAA-TTCAAGTACTAAAA
63 TTAAAGGACCAAAATAACAAAAACA-AAAACTTAAAGTACTAAAA
5368380 TAGTTAAAAT
Statistics
Matches: 87, Mismatches: 15, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
121 7 0.08
122 75 0.86
123 5 0.06
ACGTcount: A:0.57, C:0.11, G:0.12, T:0.21
Consensus pattern (122 bp):
TTATAAAGACCAAAATGGTGAAAAACAAAAACTTTAAGGATCAAAATAACAAAAATAGAAAGTTA
AAGGACCAAAATAACAAAAACAAAAACTTAAAGTACTAAAACAGTAATTATAGAAAC
Found at i:5379657 original size:30 final size:30
Alignment explanation
Indices: 5379621--5379688 Score: 91
Period size: 30 Copynumber: 2.3 Consensus size: 30
5379611 AATATCAAAC
* *
5379621 TTAAAAAACCAGACCCAAACATGGTTTTTT
1 TTAAAAAACCAGACCCAAACACGATTTTTT
* * *
5379651 TTAAAAAATCAGACCCAATCCCGATTTTTT
1 TTAAAAAACCAGACCCAAACACGATTTTTT
5379681 TTAAAAAA
1 TTAAAAAA
5379689 ATCCAACCAT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.43, C:0.19, G:0.07, T:0.31
Consensus pattern (30 bp):
TTAAAAAACCAGACCCAAACACGATTTTTT
Found at i:5382174 original size:20 final size:19
Alignment explanation
Indices: 5382149--5382202 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 19
5382139 GCGAAATAAA
5382149 AATCGCAATGCGATCTCCAG
1 AATCGCAATGCGATC-CCAG
*
5382169 AATCGCAAAT-CAGTTCCCAG
1 AATCGC-AATGC-GATCCCAG
*
5382189 AATCGCAACGCGAT
1 AATCGCAATGCGAT
5382203 AGTACAAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
19 4 0.14
20 18 0.64
21 6 0.21
ACGTcount: A:0.33, C:0.30, G:0.19, T:0.19
Consensus pattern (19 bp):
AATCGCAATGCGATCCCAG
Found at i:5382320 original size:20 final size:20
Alignment explanation
Indices: 5382231--5382441 Score: 201
Period size: 20 Copynumber: 10.5 Consensus size: 20
5382221 GATTTTCCAT
**
5382231 AATCGCAACGCGAAT-ATTAA
1 AATCGCAACGCGAATCCGT-A
* *
5382251 AATCGCAACGCGATTCTG-A
1 AATCGCAACGCGAATCCGTA
* * *
5382270 CTATCGCAACGAGTATCCGTAA
1 -AATCGCAACGCGAATCCGT-A
* *
5382292 AATCACAACGCGTATCCGTA
1 AATCGCAACGCGAATCCGTA
*
5382312 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATCCGTA
* *
5382332 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATCCGTA
* *
5382352 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGAATCCGTA
* *
5382372 AATCGCAATGCGAATACGTA
1 AATCGCAACGCGAATCCGTA
* *
5382392 AATCGCAATGCGAATACGTA
1 AATCGCAACGCGAATCCGTA
* *
5382412 AATCGCAATGCGAATCTGTA
1 AATCGCAACGCGAATCCGTA
5382432 AATCGCAACG
1 AATCGCAACG
5382442 ACATTCTGAC
Statistics
Matches: 163, Mismatches: 24, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
19 1 0.01
20 145 0.89
21 16 0.10
22 1 0.01
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGAATCCGTA
Found at i:5382392 original size:60 final size:60
Alignment explanation
Indices: 5382272--5382441 Score: 232
Period size: 60 Copynumber: 2.8 Consensus size: 60
5382262 GATTCTGACT
* * * * * *
5382272 ATCGCAACGAGTATCCGTAAAATCACAACGCGTATCCGTAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGT-AAATCGCAATGCGTATCCGTAAATCGCAACGCGAATACGTAA
*
5382333 ATCGCAACGAGAATACGTAAATCGCAATGCGTATCCGTAAATCGCAATGCGAATACGTAA
1 ATCGCAACGAGAATACGTAAATCGCAATGCGTATCCGTAAATCGCAACGCGAATACGTAA
* * * *
5382393 ATCGCAATGCGAATACGTAAATCGCAATGCGAATCTGTAAATCGCAACG
1 ATCGCAACGAGAATACGTAAATCGCAATGCGTATCCGTAAATCGCAACG
5382442 ACATTCTGAC
Statistics
Matches: 97, Mismatches: 12, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
60 81 0.84
61 16 0.16
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.20
Consensus pattern (60 bp):
ATCGCAACGAGAATACGTAAATCGCAATGCGTATCCGTAAATCGCAACGCGAATACGTAA
Found at i:5385780 original size:20 final size:20
Alignment explanation
Indices: 5385733--5385781 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
5385723 GACATTCATT
* * *
5385733 TGACTATCGCAATGCGGAAT
1 TGACTATCGCAACGCGAAAA
*
5385753 TGATTATCGCAACGCGAAAA
1 TGACTATCGCAACGCGAAAA
5385773 TGACTATCG
1 TGACTATCG
5385782 TAACTAGAGA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.24
Consensus pattern (20 bp):
TGACTATCGCAACGCGAAAA
Found at i:5385854 original size:20 final size:19
Alignment explanation
Indices: 5385829--5385897 Score: 76
Period size: 20 Copynumber: 3.8 Consensus size: 19
5385819 GCGAAATTAG
*
5385829 TTTCGCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
5385848 TTTTCGCATTGCGA--TTCA
1 -TTTCGCATTGCGATTTTCA
*
5385866 -CTCG--TTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
5385882 TTTCGCATTGCGATTT
1 TTTCGCATTGCGATTT
5385898 GTTCTTTTCC
Statistics
Matches: 41, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
14 6 0.15
16 7 0.17
17 3 0.07
18 4 0.10
19 9 0.22
20 12 0.29
ACGTcount: A:0.13, C:0.22, G:0.19, T:0.46
Consensus pattern (19 bp):
TTTCGCATTGCGATTTTCA
Found at i:5386133 original size:20 final size:21
Alignment explanation
Indices: 5386108--5386162 Score: 87
Period size: 20 Copynumber: 2.7 Consensus size: 21
5386098 AGACATTCAT
*
5386108 TTGACTATCGCAATGCA-AAA
1 TTGACTATCGCAACGCAGAAA
5386128 TTGACTATCGCAACGCAGAAA
1 TTGACTATCGCAACGCAGAAA
5386149 -TGACTATCGCAACG
1 TTGACTATCGCAACG
5386163 AGAGAATCGC
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
20 30 0.91
21 3 0.09
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.22
Consensus pattern (21 bp):
TTGACTATCGCAACGCAGAAA
Found at i:5386184 original size:33 final size:33
Alignment explanation
Indices: 5386134--5386265 Score: 129
Period size: 38 Copynumber: 3.8 Consensus size: 33
5386124 AAAATTGACT
* ** *
5386134 ATCGCAACGCAGAAATGACTATCGCAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAAA
*
5386168 ATCGCAATGTGAAATGAAAATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAAA
* **
5386206 ATCACAATGCGAAATGAAAATCGCAACGAGTTA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
5386239 ATCGCAATGCGAAAATGAAAATCGCAA
1 ATCGCAATGCG-AAATGAAAATCGCAA
5386266 AGATTTTCAT
Statistics
Matches: 82, Mismatches: 10, Indels: 12
0.79 0.10 0.12
Matches are distributed among these distances:
33 26 0.32
34 24 0.29
35 2 0.02
36 2 0.02
37 1 0.01
38 27 0.33
ACGTcount: A:0.45, C:0.18, G:0.20, T:0.16
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
Found at i:5386191 original size:19 final size:19
Alignment explanation
Indices: 5386167--5386265 Score: 118
Period size: 19 Copynumber: 5.4 Consensus size: 19
5386157 GCAACGAGAG
*
5386167 AATCGCAATGTGAAATGAA
1 AATCGCAATGCGAAATGAA
5386186 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
5386205 AATCACAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
**
5386224 AATCGCAA--CG--A-GTT
1 AATCGCAATGCGAAATGAA
5386238 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCG-AAATGAA
5386258 AATCGCAA
1 AATCGCAA
5386266 AGATTTTCAT
Statistics
Matches: 67, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
14 9 0.13
15 1 0.01
16 2 0.03
17 2 0.03
19 44 0.66
20 9 0.13
ACGTcount: A:0.47, C:0.16, G:0.19, T:0.17
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:5386326 original size:20 final size:19
Alignment explanation
Indices: 5386267--5386327 Score: 104
Period size: 19 Copynumber: 3.2 Consensus size: 19
5386257 AAATCGCAAA
5386267 GATTTTCATTTCGCATTGC
1 GATTTTCATTTCGCATTGC
5386286 GATTTTCATTTCGCATTGC
1 GATTTTCATTTCGCATTGC
*
5386305 GATTTTCATTTCCGCGTTGC
1 GATTTTCATTT-CGCATTGC
5386325 GAT
1 GAT
5386328 AATCTGTTTT
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
19 30 0.75
20 10 0.25
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.46
Consensus pattern (19 bp):
GATTTTCATTTCGCATTGC
Found at i:5386463 original size:14 final size:14
Alignment explanation
Indices: 5386427--5386463 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
5386417 ACATCAATTA
*
5386427 ACAAATCAACATTT
1 ACAAATCATCATTT
*
5386441 ACAAATCATCTTTT
1 ACAAATCATCATTT
5386455 ACAAATCAT
1 ACAAATCAT
5386464 TAAACATCAA
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):
ACAAATCATCATTT
Found at i:5386684 original size:96 final size:97
Alignment explanation
Indices: 5386513--5386706 Score: 365
Period size: 96 Copynumber: 2.0 Consensus size: 97
5386503 CATCCATTTC
5386513 ACGCAGCTCACTTCAGGATTAACCTGCAGAAACCAAACATTGAATCAACAATACTTTCTACACAT
1 ACGCAGCTCACTTCAGGATTAACCTGCAGAAACCAAACATTGAATCAACAATACTTTCTACACAT
5386578 CTAAAACTAC-AACAGCAAATTATTGAATTCT
66 CTAAAACTACAAACAGCAAATTATTGAATTCT
5386609 ACGCAGCTCACTTCAGGATTAACCTGCAGAAACCAAACATTGAATCAAC-ATACTTTCTACACAT
1 ACGCAGCTCACTTCAGGATTAACCTGCAGAAACCAAACATTGAATCAACAATACTTTCTACACAT
5386673 CTAAAACCTACAAACAGCAAATTATTGAATTCT
66 CTAAAA-CTACAAACAGCAAATTATTGAATTCT
5386706 A
1 A
5386707 GCTACTTAAC
Statistics
Matches: 96, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
95 21 0.22
96 53 0.55
97 22 0.23
ACGTcount: A:0.41, C:0.25, G:0.09, T:0.25
Consensus pattern (97 bp):
ACGCAGCTCACTTCAGGATTAACCTGCAGAAACCAAACATTGAATCAACAATACTTTCTACACAT
CTAAAACTACAAACAGCAAATTATTGAATTCT
Found at i:5387955 original size:21 final size:21
Alignment explanation
Indices: 5387889--5387955 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
5387879 GTGAATCGGG
*
5387889 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
5387909 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
5387931 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
5387952 CTCT
1 CTCT
5387956 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:5387974 original size:42 final size:41
Alignment explanation
Indices: 5387889--5388011 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
5387879 GTGAATCGGG
* * * *
5387889 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGACAGGGGC
*
5387931 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGACAGGGGC
* * * * *
5387973 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGACAGG
5388012 CGAGTCGGGC
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.06
42 57 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.19, G:0.37, T:0.22
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGACAGGGGC
Found at i:5390003 original size:20 final size:19
Alignment explanation
Indices: 5389978--5390066 Score: 89
Period size: 20 Copynumber: 4.8 Consensus size: 19
5389968 TCTTTTGGTT
5389978 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
5389997 AGAAATGACTATCGCAATGC
1 -GAAATGAAAATCGCAACGC
5390017 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
5390034 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
5390050 GAAATGAAAAATCGCAA
1 GAAATG-AAAATCGCAA
5390067 TTTGTTGCGA
Statistics
Matches: 56, Mismatches: 7, Indels: 12
0.75 0.09 0.16
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 15 0.27
20 25 0.45
ACGTcount: A:0.47, C:0.19, G:0.21, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:5390052 original size:33 final size:37
Alignment explanation
Indices: 5389978--5390066 Score: 114
Period size: 39 Copynumber: 2.4 Consensus size: 37
5389968 TCTTTTGGTT
*
5389978 GAAATGAAAATCGCAACGCAGAAATGACTATCGCAATGC
1 GAAATGAAAATCGCAACGCAG-AATGAC-ATCGCAACGC
5390017 GAAATGAAAATCGCAACG-AG-A-GA-ATCGCAACGC
1 GAAATGAAAATCGCAACGCAGAATGACATCGCAACGC
5390050 GAAATGAAAAATCGCAA
1 GAAATG-AAAATCGCAA
5390067 TTTGTTGCGA
Statistics
Matches: 48, Mismatches: 1, Indels: 7
0.86 0.02 0.12
Matches are distributed among these distances:
33 15 0.31
34 10 0.21
35 2 0.04
36 1 0.02
38 2 0.04
39 18 0.38
ACGTcount: A:0.47, C:0.19, G:0.21, T:0.12
Consensus pattern (37 bp):
GAAATGAAAATCGCAACGCAGAATGACATCGCAACGC
Found at i:5390691 original size:20 final size:20
Alignment explanation
Indices: 5390662--5390917 Score: 191
Period size: 20 Copynumber: 12.7 Consensus size: 20
5390652 CTTTAAAAAT
5390662 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
5390682 CGCATTGCGATTTTACGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
* *
5390704 -TCATTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* * * *
5390723 CACATTGCGA-TTACGTATT
1 CGCGTTGCGATTTACGGATA
* **
5390742 CTCGTTGCGATTTAAAGATA
1 CGCGTTGCGATTTACGGATA
** *
5390762 CGCGTTGCGATTTACATATT
1 CGCGTTGCGATTTACGGATA
*
5390782 CTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
5390802 CGTGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
5390822 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
5390843 CGCGTTGCGATTTTACGGATA
1 CGCGTTGCGA-TTTACGGATA
* * *
5390864 CTCGTTGCGATAGT-CAGA-A
1 CGCGTTGCGAT-TTACGGATA
**
5390883 TCGCGTTGCGATTTATAGA-A
1 -CGCGTTGCGATTTACGGATA
5390903 TCGCGTTGCGATTTA
1 -CGCGTTGCGATTTA
5390918 TATGTTCGCG
Statistics
Matches: 191, Mismatches: 34, Indels: 22
0.77 0.14 0.09
Matches are distributed among these distances:
19 19 0.10
20 119 0.62
21 51 0.27
22 2 0.01
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:5390723 original size:41 final size:41
Alignment explanation
Indices: 5390664--5390955 Score: 296
Period size: 41 Copynumber: 7.2 Consensus size: 41
5390654 TTAAAAATCG
* *
5390664 CGTTGCGATTTACGGATACGCATTGCGATTTTACGTATTAT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* * *
5390705 CATTGCGATTTACGGATACACATTGCGA--TTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
** *
5390744 CGTTGCGATTTAAAGATACGCGTTGCGA-TTTACATATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* *
5390784 CGTTGCGATTTACGGATACGTGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* *
5390825 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATACT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* * * *
5390866 CGTTGCGATAGT-CAGA-ATCGCGTTGCGATTTATA-G-AATCG
1 CGTTGCGAT-TTACGGATA-CGCGTTGCGATTT-TACGTATTCT
** * * *
5390906 CGTTGCGATTTATATG-TTCGCGTTGCGATTTT-CATATTCG
1 CGTTGCGATTTA-CGGATACGCGTTGCGATTTTACGTATTCT
5390946 CGTTGCGATT
1 CGTTGCGATT
5390956 ATGGAAAATC
Statistics
Matches: 212, Mismatches: 29, Indels: 21
0.81 0.11 0.08
Matches are distributed among these distances:
39 35 0.17
40 74 0.35
41 100 0.47
42 3 0.01
ACGTcount: A:0.21, C:0.18, G:0.24, T:0.38
Consensus pattern (41 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
Found at i:5390890 original size:61 final size:58
Alignment explanation
Indices: 5390662--5390917 Score: 194
Period size: 61 Copynumber: 4.2 Consensus size: 58
5390652 CTTTAAAAAT
* * * ** * *
5390662 CGCGTTGCGATTTACGGATACGCATTGCGATTTTACGTATTATCATTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACTCGTTGCGA-TTTA-G-AATCGCGTTGCGATTTACAGATA
* * * * * * *
5390723 CACATTGCGA-TTACGTATTCTCGTTGCGATTTAAAGATACGCGTTGCGATTTACATATT
1 CGCGTTGCGATTTACGGATACTCGTTGCGATTTAGA-AT-CGCGTTGCGATTTACAGATA
* * * *
5390782 CTCGTTGCGATTTACGGATACGT-GTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATAC-TCGTTGCGA-TTTA-GAATCG-CGTTGCGATTTACAGATA
* *
5390843 CGCGTTGCGATTTTACGGATACTCGTTGCGATAGTCAGAATCGCGTTGCGATTTATAGA-A
1 CGCGTTGCGA-TTTACGGATACTCGTTGCGAT--TTAGAATCGCGTTGCGATTTACAGATA
5390903 TCGCGTTGCGATTTA
1 -CGCGTTGCGATTTA
5390918 TATGTTCGCG
Statistics
Matches: 153, Mismatches: 30, Indels: 25
0.74 0.14 0.12
Matches are distributed among these distances:
57 1 0.01
58 1 0.01
59 26 0.17
60 36 0.24
61 65 0.42
62 22 0.14
63 2 0.01
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.36
Consensus pattern (58 bp):
CGCGTTGCGATTTACGGATACTCGTTGCGATTTAGAATCGCGTTGCGATTTACAGATA
Found at i:5390918 original size:20 final size:20
Alignment explanation
Indices: 5390744--5390955 Score: 109
Period size: 20 Copynumber: 10.5 Consensus size: 20
5390734 TACGTATTCT
*
5390744 CGTTGCGATTTAAAG-ATACG
1 CGTTGCGATTTATAGAAT-CG
* * * *
5390764 CGTTGCGATTTACATATTCT
1 CGTTGCGATTTATAGAATCG
* *
5390784 CGTTGCGATTTA-CGGATACG
1 CGTTGCGATTTATAGAAT-CG
* * *
5390804 TGTTGCGATTT-TACGTATTG
1 CGTTGCGATTTATA-GAATCG
* *
5390824 TCGTTGCGATTTA-CGGATACG
1 -CGTTGCGATTTATAGAAT-CG
* *
5390845 CGTTGCGATTT-TACGGATACT
1 CGTTGCGATTTATA-GAAT-CG
5390866 CGTTGCGA--TAGTCAGAATCG
1 CGTTGCGATTTA-T-AGAATCG
5390886 CGTTGCGATTTATAGAATCG
1 CGTTGCGATTTATAGAATCG
*
5390906 CGTTGCGATTTATATG-TTCG
1 CGTTGCGATTTATA-GAATCG
* *
5390926 CGTTGCGATTT-TCATATTCG
1 CGTTGCGATTTAT-AGAATCG
5390946 CGTTGCGATT
1 CGTTGCGATT
5390956 ATGGAAAATC
Statistics
Matches: 152, Mismatches: 23, Indels: 34
0.73 0.11 0.16
Matches are distributed among these distances:
19 3 0.02
20 111 0.73
21 35 0.23
22 3 0.02
ACGTcount: A:0.20, C:0.17, G:0.25, T:0.38
Consensus pattern (20 bp):
CGTTGCGATTTATAGAATCG
Found at i:5394800 original size:7 final size:7
Alignment explanation
Indices: 5394788--5394817 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
5394778 TTACAGCTTC
5394788 GGATCAA
1 GGATCAA
5394795 GGATCAA
1 GGATCAA
5394802 GGATCAA
1 GGATCAA
5394809 GGATCAA
1 GGATCAA
5394816 GG
1 GG
5394818 GAAGTACTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.40, C:0.13, G:0.33, T:0.13
Consensus pattern (7 bp):
GGATCAA
Found at i:5395454 original size:32 final size:32
Alignment explanation
Indices: 5395416--5395540 Score: 142
Period size: 32 Copynumber: 3.7 Consensus size: 32
5395406 TCTAATTCAT
* *
5395416 ATATTCGGGTTGGTTCGGGTTTTTAAAGTGTG
1 ATATTCGGGTTGGGTCGGGTTTTTTAAGTGTG
*
5395448 ATATTCGGGTCAAGTCGGGTCGGATTTTTTTAAGTGTG
1 ATATTCGGGT----T-GGGTCGG-GTTTTTTAAGTGTG
*
5395486 ATATTCGGGTCGGGTCGGGTTTTTTAAGTGTG
1 ATATTCGGGTTGGGTCGGGTTTTTTAAGTGTG
*
5395518 ATATTCGGGTCGGGGTCGGGTTT
1 ATATTCGGGT-TGGGTCGGGTTT
5395541 AGGGTGAAAA
Statistics
Matches: 80, Mismatches: 6, Indels: 13
0.81 0.06 0.13
Matches are distributed among these distances:
32 33 0.41
33 18 0.22
36 1 0.01
37 6 0.08
38 22 0.28
ACGTcount: A:0.14, C:0.10, G:0.36, T:0.40
Consensus pattern (32 bp):
ATATTCGGGTTGGGTCGGGTTTTTTAAGTGTG
Found at i:5395483 original size:38 final size:35
Alignment explanation
Indices: 5395430--5395540 Score: 142
Period size: 33 Copynumber: 3.2 Consensus size: 35
5395420 TCGGGTTGGT
*
5395430 TCGGGTTTTTAAAGTGTGATATTCGGGTCAAGTCGGG
1 TCGGGTTTTTTAAGTGTGATATTCGGGTC--GTCGGG
*
5395467 TCGGATTTTTTTAAGTGTGATATTC-GG--GTCGGG
1 TCGG-GTTTTTTAAGTGTGATATTCGGGTCGTCGGG
5395500 TCGGGTTTTTTAAGTGTGATATTCGGGTCG--GGG
1 TCGGGTTTTTTAAGTGTGATATTCGGGTCGTCGGG
5395533 TCGGGTTT
1 TCGGGTTT
5395541 AGGGTGAAAA
Statistics
Matches: 67, Mismatches: 3, Indels: 12
0.82 0.04 0.15
Matches are distributed among these distances:
32 19 0.28
33 23 0.34
35 1 0.01
37 6 0.09
38 18 0.27
ACGTcount: A:0.14, C:0.10, G:0.36, T:0.40
Consensus pattern (35 bp):
TCGGGTTTTTTAAGTGTGATATTCGGGTCGTCGGG
Found at i:5396032 original size:26 final size:26
Alignment explanation
Indices: 5396003--5396054 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
5395993 CTATCATTTT
5396003 ACATTACTGAAATCAAATTTATCTAA
1 ACATTACTGAAATCAAATTTATCTAA
5396029 ACATTACTGAAATCAAATTTATCTAA
1 ACATTACTGAAATCAAATTTATCTAA
5396055 CATGTCTGCG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.46, C:0.15, G:0.04, T:0.35
Consensus pattern (26 bp):
ACATTACTGAAATCAAATTTATCTAA
Found at i:5397073 original size:15 final size:16
Alignment explanation
Indices: 5397053--5397086 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
5397043 TCGGAGGTGG
*
5397053 GGGATGATA-GGGAGA
1 GGGATGACACGGGAGA
5397068 GGGATGACACGGGAGA
1 GGGATGACACGGGAGA
5397084 GGG
1 GGG
5397087 TTTTAGTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.29, C:0.06, G:0.56, T:0.09
Consensus pattern (16 bp):
GGGATGACACGGGAGA
Found at i:5397783 original size:16 final size:17
Alignment explanation
Indices: 5397762--5397794 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
5397752 CTAAAAGTGC
*
5397762 ATATAT-TTTTTTAAAT
1 ATATATATTTTTGAAAT
5397778 ATATATATTTTTGAAAT
1 ATATATATTTTTGAAAT
5397795 TTTATATGTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (17 bp):
ATATATATTTTTGAAAT
Found at i:5408478 original size:22 final size:22
Alignment explanation
Indices: 5408450--5408528 Score: 67
Period size: 22 Copynumber: 3.7 Consensus size: 22
5408440 TGGCAGCTTC
*
5408450 TTTTCTTCTTCTTTTTGCAGCT
1 TTTTCTTCTTCTTCTTGCAGCT
* *
5408472 TTTTCTTCTTC--GTGGCAGCT
1 TTTTCTTCTTCTTCTTGCAGCT
*
5408492 TCTT-TTCTTCTTCTTGCAG-T
1 TTTTCTTCTTCTTCTTGCAGCT
* *
5408512 TTCTTCTTATTTTTCTT
1 TT-TTCTTCTTCTTCTT
5408529 ATTCTTTTTC
Statistics
Matches: 45, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
19 6 0.13
20 12 0.27
21 7 0.16
22 20 0.44
ACGTcount: A:0.05, C:0.23, G:0.10, T:0.62
Consensus pattern (22 bp):
TTTTCTTCTTCTTCTTGCAGCT
Found at i:5408479 original size:19 final size:19
Alignment explanation
Indices: 5408455--5408525 Score: 63
Period size: 19 Copynumber: 3.6 Consensus size: 19
5408445 GCTTCTTTTC
5408455 TTCTTCTTTTTGCAGCTTT
1 TTCTTCTTTTTGCAGCTTT
* *
5408474 TTCTTCTTCGTGGCAGCTTCTT
1 TTCTTCTT-TTTGCAGC-T-TT
*
5408496 TTCTTCTTCTTGCAG-TTT
1 TTCTTCTTTTTGCAGCTTT
*
5408514 CTTCTTATTTTT
1 -TTCTTCTTTTT
5408526 CTTATTCTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
18 2 0.05
19 18 0.43
20 6 0.14
21 6 0.14
22 10 0.24
ACGTcount: A:0.06, C:0.23, G:0.11, T:0.61
Consensus pattern (19 bp):
TTCTTCTTTTTGCAGCTTT
Found at i:5409170 original size:48 final size:49
Alignment explanation
Indices: 5409094--5409196 Score: 163
Period size: 48 Copynumber: 2.1 Consensus size: 49
5409084 TGATGAGGTT
* * *
5409094 TTGGTTCTTTCAAGCTTCATGTCTAAAGCAAGTCATGTTTGTTTAGAAG
1 TTGGTTCTTTCAAGCTTCATGTCCAAAGCAAGTCAGGTTTGTTAAGAAG
*
5409143 TTGGTT-TTTCAAGCTTCATGTCCAAAGCAAGTTAGGTTTGTTAAGAAG
1 TTGGTTCTTTCAAGCTTCATGTCCAAAGCAAGTCAGGTTTGTTAAGAAG
5409191 TTGGTT
1 TTGGTT
5409197 GTAACATCCC
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
48 44 0.88
49 6 0.12
ACGTcount: A:0.24, C:0.13, G:0.22, T:0.41
Consensus pattern (49 bp):
TTGGTTCTTTCAAGCTTCATGTCCAAAGCAAGTCAGGTTTGTTAAGAAG
Found at i:5411614 original size:3 final size:3
Alignment explanation
Indices: 5411600--5411635 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
5411590 GAGTGTGAGA
*
5411600 AGG AGG ATG AGG AGG AGG AGG AGG AGG AGG AGG AGG
1 AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG
5411636 GAGGGTTAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.33, C:0.00, G:0.64, T:0.03
Consensus pattern (3 bp):
AGG
Found at i:5419566 original size:164 final size:164
Alignment explanation
Indices: 5419295--5419628 Score: 542
Period size: 164 Copynumber: 2.0 Consensus size: 164
5419285 ATTGTGTTCT
* * * * * ** *
5419295 TATGAATTTCAGGATTCTTTGATTCATGCATAAGAAGCTGATATGTATTGTTATGTTCTGCATAG
1 TATGAATCTCAGGAATATTTGATTAATGCATAAGAAACCAATATGTATTGTTATGTTCTGCATAC
*
5419360 CCAATGAAAATGCAATCCACAGTCTTATGACCTATTTTAATTTGCTTTGGTAATGGGGTCATTAC
66 CCAATGAAAATGCAATCCACAGTCTTATGACCTATTTTAATTTGCTTTGGTAATGGGGCCATTAC
*
5419425 CTTAGCAAGACATCATTACATTTTCAAGTGTTTG
131 CTTAGCAAAACATCATTACATTTTCAAGTGTTTG
*
5419459 TATGAATCTCAGGAATATTTGATTAATGCATAAGAAACCAATATGTATTGTTTTGTTCTGCATAC
1 TATGAATCTCAGGAATATTTGATTAATGCATAAGAAACCAATATGTATTGTTATGTTCTGCATAC
*
5419524 CCAATGAAAATGCAATCCACAGTCTTATGACTTATTTTAATTTGCTTTGGTAATGGGGCCATTAC
66 CCAATGAAAATGCAATCCACAGTCTTATGACCTATTTTAATTTGCTTTGGTAATGGGGCCATTAC
* *
5419589 CTTGGCAAAACATCATTACATTTTTAAGTGTTTG
131 CTTAGCAAAACATCATTACATTTTCAAGTGTTTG
5419623 TATGAA
1 TATGAA
5419629 GGTTTTCATT
Statistics
Matches: 156, Mismatches: 14, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
164 156 1.00
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.38
Consensus pattern (164 bp):
TATGAATCTCAGGAATATTTGATTAATGCATAAGAAACCAATATGTATTGTTATGTTCTGCATAC
CCAATGAAAATGCAATCCACAGTCTTATGACCTATTTTAATTTGCTTTGGTAATGGGGCCATTAC
CTTAGCAAAACATCATTACATTTTCAAGTGTTTG
Found at i:5420843 original size:49 final size:49
Alignment explanation
Indices: 5420771--5420875 Score: 201
Period size: 49 Copynumber: 2.1 Consensus size: 49
5420761 AAATCTATTG
*
5420771 TCCTCTTCAATACAAAGTCTGACAATAAGTTCCTCCATGGTCATTTTGT
1 TCCTCTTCAATACAAAGTCTGACAATAAGTTCCTCCATGGTCATTTCGT
5420820 TCCTCTTCAATACAAAGTCTGACAATAAGTTCCTCCATGGTCATTTCGT
1 TCCTCTTCAATACAAAGTCTGACAATAAGTTCCTCCATGGTCATTTCGT
5420869 TCCTCTT
1 TCCTCTT
5420876 ATGCTTCAGG
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 55 1.00
ACGTcount: A:0.25, C:0.27, G:0.11, T:0.37
Consensus pattern (49 bp):
TCCTCTTCAATACAAAGTCTGACAATAAGTTCCTCCATGGTCATTTCGT
Found at i:5422260 original size:118 final size:118
Alignment explanation
Indices: 5422052--5422288 Score: 474
Period size: 118 Copynumber: 2.0 Consensus size: 118
5422042 TACCTATAGT
5422052 GTTTCACAAAGGAGACAAATTGAAAATAATATATATGGGTTATTAATTAGTATCTGAATAAAATC
1 GTTTCACAAAGGAGACAAATTGAAAATAATATATATGGGTTATTAATTAGTATCTGAATAAAATC
5422117 GAAAACAATCAATAATACCGCCTTAAATAAAATTTGACTGTTAATTAGCATCC
66 GAAAACAATCAATAATACCGCCTTAAATAAAATTTGACTGTTAATTAGCATCC
5422170 GTTTCACAAAGGAGACAAATTGAAAATAATATATATGGGTTATTAATTAGTATCTGAATAAAATC
1 GTTTCACAAAGGAGACAAATTGAAAATAATATATATGGGTTATTAATTAGTATCTGAATAAAATC
5422235 GAAAACAATCAATAATACCGCCTTAAATAAAATTTGACTGTTAATTAGCATCC
66 GAAAACAATCAATAATACCGCCTTAAATAAAATTTGACTGTTAATTAGCATCC
5422288 G
1 G
5422289 AATAAAATCA
Statistics
Matches: 119, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
118 119 1.00
ACGTcount: A:0.44, C:0.13, G:0.13, T:0.30
Consensus pattern (118 bp):
GTTTCACAAAGGAGACAAATTGAAAATAATATATATGGGTTATTAATTAGTATCTGAATAAAATC
GAAAACAATCAATAATACCGCCTTAAATAAAATTTGACTGTTAATTAGCATCC
Found at i:5423122 original size:392 final size:393
Alignment explanation
Indices: 5422170--5423253 Score: 1830
Period size: 392 Copynumber: 2.8 Consensus size: 393
5422160 ATTAGCATCC
*
5422170 GTTTCACAAAGGAGACAAATTGAAAATAATATATATGGGTTATTAATTAGTATCTGAATAAAATC
1 GTTTCACAAAGGAGACAAATTGAAAATAATATATATGGGCTATTAATTAGTATCTGAATAAAATC
*
5422235 GAAAACAATCAATAATACCGCCTTAAATAAAATTTGACTGTTAATTAGCATCCGAATAAAATCAG
66 GAAAACAATCAATAATACCACCTTAAATAAAATTTGACTGTTAATTAGCATCCGAATAAAATCAG
* *
5422300 AAATAATCAATTAACACTATATCATATCGAATATATTCGTGAATTGCAAGTCATACCATATTTAA
131 AAATAATCAATTAACACCATATCATATCAAATATATTCGTGAATTGCAAGTCATACCATATTTAA
* *
5422365 TATTTAAATAAAATGAAATCACATAATATCCTTTTTAATTTAGAATATTCAAAAAGATAAGTTTC
196 TATTTAAATAAAAGGAAATCACATAATATCCTTTTTAATTTAGAATATTCAAAAAGATAAGCTTC
* *
5422430 ACTTAAAGGAAAATATTTAATTCGTTTTAGGTAAAATATTTAAATCTTGCTAGAGACTATCACCG
261 ACTT-AAGGAAAATATTTAATTCGTTGTAGGTAAAATATTTAAATCTTGCTACAGACTATCACCG
* * *
5422495 AAAACCAGAGAGGAAGAAGAGAGTTTTTGAACCGTGTTTAACCTAGTAGGTTAGCATTGTATCTA
325 AAAACAAGAGAGGAAGAAGAGAGTTTTTGAACCGTGTTTAACCTAGTAGGTTAACAATGTATCTA
*
5422560 TAGT
390 TAAT
*
5422564 GTTTCACAAAGGAGACGAATTGAAAATAATATATATGGGCTATTAATTAGTATCTGAATAAAATC
1 GTTTCACAAAGGAGACAAATTGAAAATAATATATATGGGCTATTAATTAGTATCTGAATAAAATC
*
5422629 TAAAACAATCAATAATACCACCTTAAATAAAATTTGACTGTTAATTAGCATCCGAATAAAATCAG
66 GAAAACAATCAATAATACCACCTTAAATAAAATTTGACTGTTAATTAGCATCCGAATAAAATCAG
* *
5422694 AAATAATCAATTAACACCATATTATATCAAATATATTCGTGAATTGCAAGTCATACGATATTTAA
131 AAATAATCAATTAACACCATATCATATCAAATATATTCGTGAATTGCAAGTCATACCATATTTAA
*
5422759 TATTTAAATAAAAGGAAATCACATAATATCTTTTTTAATTTAGAATATTCAAAAAGATAAGCTTC
196 TATTTAAATAAAAGGAAATCACATAATATCCTTTTTAATTTAGAATATTCAAAAAGATAAGCTTC
*
5422824 ACTTAAGGAAAATATTTAATTCGTTGTAGGTAAAATATTTAAATCTTGCTACAGACTATCACCTA
261 ACTTAAGGAAAATATTTAATTCGTTGTAGGTAAAATATTTAAATCTTGCTACAGACTATCACCGA
5422889 AAACAAGAGAGGAAGAAGAGAGTTTTTGAACCGTGTTTAACCTAGTAGGTTAACAATGTATCTAT
326 AAACAAGAGAGGAAGAAGAGAGTTTTTGAACCGTGTTTAACCTAGTAGGTTAACAATGTATCTAT
5422954 AAT
391 AAT
* * ** *
5422957 GTTTCACAAAGGAGAC-AATTGAAAATAATAGATTTAAGCTATTAATTAGTACCTGAATAAAATC
1 GTTTCACAAAGGAGACAAATTGAAAATAATATATATGGGCTATTAATTAGTATCTGAATAAAATC
* * * *
5423021 GAAAACAATCAATAATACTACCTTAAATAAAATTTGACTGTTAATTATCATCCGAATAAAATAAA
66 GAAAACAATCAATAATACCACCTTAAATAAAATTTGACTGTTAATTAGCATCCGAATAAAATCAG
* * *
5423086 AAATAATCAATTAACACCGTATCATATCAAATATATTCGTGAATTACAAATCATACCATATTTAA
131 AAATAATCAATTAACACCATATCATATCAAATATATTCGTGAATTGCAAGTCATACCATATTTAA
* *
5423151 TATTTAAATAAAAGGAAATCACATAATATCCTTTTTAATTTAGAATATTAAAAAAGATAAACTTC
196 TATTTAAATAAAAGGAAATCACATAATATCCTTTTTAATTTAGAATATTCAAAAAGATAAGCTTC
* *
5423216 ACTTGAGAAAAATATTTAAATT-GTTGTAGGTAAAATAT
261 ACTTAAGGAAAATATTT-AATTCGTTGTAGGTAAAATAT
5423254 CCACATTCAA
Statistics
Matches: 651, Mismatches: 38, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
392 256 0.39
393 142 0.22
394 253 0.39
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.32
Consensus pattern (393 bp):
GTTTCACAAAGGAGACAAATTGAAAATAATATATATGGGCTATTAATTAGTATCTGAATAAAATC
GAAAACAATCAATAATACCACCTTAAATAAAATTTGACTGTTAATTAGCATCCGAATAAAATCAG
AAATAATCAATTAACACCATATCATATCAAATATATTCGTGAATTGCAAGTCATACCATATTTAA
TATTTAAATAAAAGGAAATCACATAATATCCTTTTTAATTTAGAATATTCAAAAAGATAAGCTTC
ACTTAAGGAAAATATTTAATTCGTTGTAGGTAAAATATTTAAATCTTGCTACAGACTATCACCGA
AAACAAGAGAGGAAGAAGAGAGTTTTTGAACCGTGTTTAACCTAGTAGGTTAACAATGTATCTAT
AAT
Found at i:5423342 original size:20 final size:20
Alignment explanation
Indices: 5423317--5423357 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
5423307 GATCATGGAG
5423317 TTACACCCCTTACACCAACT
1 TTACACCCCTTACACCAACT
5423337 TTACACCCCTTACACCAACT
1 TTACACCCCTTACACCAACT
5423357 T
1 T
5423358 ATGAGGTACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.29, C:0.44, G:0.00, T:0.27
Consensus pattern (20 bp):
TTACACCCCTTACACCAACT
Found at i:5426048 original size:31 final size:32
Alignment explanation
Indices: 5426004--5426066 Score: 78
Period size: 30 Copynumber: 2.0 Consensus size: 32
5425994 ATTTATTTTT
*
5426004 TAAAATATGATATATTTATTTGAATAT-TTTAAA
1 TAAAATATGATATA-TTATGTGAAT-TCTTTAAA
5426037 TAAAA-AT-ATATATTATGTGAATTCTTTAAA
1 TAAAATATGATATATTATGTGAATTCTTTAAA
5426067 ATTCAAATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
29 1 0.04
30 15 0.54
31 5 0.18
32 2 0.07
33 5 0.18
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.46
Consensus pattern (32 bp):
TAAAATATGATATATTATGTGAATTCTTTAAA
Found at i:5426242 original size:37 final size:38
Alignment explanation
Indices: 5426187--5426259 Score: 103
Period size: 37 Copynumber: 1.9 Consensus size: 38
5426177 ACTAAATACA
*
5426187 AATATATTATTTATGAATTTATATTCAATTAAAATATG
1 AATATATTATTTACGAATTTATATTCAATTAAAATATG
* * *
5426225 AATATATTA-TTACGAATTTGTATTCGATTAGAATA
1 AATATATTATTTACGAATTTATATTCAATTAAAATA
5426260 CGATATTATA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
37 22 0.71
38 9 0.29
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.45
Consensus pattern (38 bp):
AATATATTATTTACGAATTTATATTCAATTAAAATATG
Found at i:5428537 original size:22 final size:22
Alignment explanation
Indices: 5428512--5428562 Score: 86
Period size: 22 Copynumber: 2.3 Consensus size: 22
5428502 CTACGGCGGC
5428512 ATCCGTCCCCATCTCCGA-CGAA
1 ATCCGTCCCCATCTCC-ACCGAA
5428534 ATCCGTCCCCATCTCCACCGAA
1 ATCCGTCCCCATCTCCACCGAA
5428556 ATCCGTC
1 ATCCGTC
5428563 TATCTCTATC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 1 0.04
22 27 0.96
ACGTcount: A:0.22, C:0.47, G:0.12, T:0.20
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCACCGAA
Found at i:5429010 original size:20 final size:19
Alignment explanation
Indices: 5428963--5429014 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
5428953 CGATTTTAGT
** *
5428963 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATAGTCAA
*
5428982 TTTGCGTTGCGATAGTCAAA
1 TTCGCGTTGCGATAGTC-AA
5429002 TTCGCGTTGCGAT
1 TTCGCGTTGCGAT
5429015 TTTCATTTTC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 14 0.52
20 13 0.48
ACGTcount: A:0.15, C:0.19, G:0.25, T:0.40
Consensus pattern (19 bp):
TTCGCGTTGCGATAGTCAA
Found at i:5429025 original size:20 final size:20
Alignment explanation
Indices: 5428952--5429037 Score: 104
Period size: 20 Copynumber: 4.4 Consensus size: 20
5428942 AAATCGCAAC
*
5428952 GCGATTTT-AGTTTCGCGTT
1 GCGATTTTCATTTTCGCGTT
5428971 GCGATTTTCATTTT-GCGTT
1 GCGATTTTCATTTTCGCGTT
** **
5428990 GCGATAGTCAAATTCGCGTT
1 GCGATTTTCATTTTCGCGTT
*
5429010 GCGATTTTCATTTTCGTGTT
1 GCGATTTTCATTTTCGCGTT
5429030 GCGATTTT
1 GCGATTTT
5429038 AAGTTTCAGA
Statistics
Matches: 55, Mismatches: 10, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
19 23 0.42
20 32 0.58
ACGTcount: A:0.14, C:0.16, G:0.23, T:0.47
Consensus pattern (20 bp):
GCGATTTTCATTTTCGCGTT
Found at i:5430970 original size:20 final size:20
Alignment explanation
Indices: 5430947--5430995 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
5430937 GAAACTTAAA
5430947 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
5430967 ATCGCAACGCGGAAATGACT
1 ATCGCAACGCGAAAATGACT
5430987 ATCGCAACG
1 ATCGCAACG
5430996 GGATAATCGC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.37, C:0.27, G:0.22, T:0.14
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:5431160 original size:21 final size:20
Alignment explanation
Indices: 5431096--5431165 Score: 86
Period size: 20 Copynumber: 3.5 Consensus size: 20
5431086 GCGATTATCC
**
5431096 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
* * *
5431116 CATTGTGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTTCG
5431136 CGTTGCGATAGTCATTTTTCG
1 CGTTGCGATAGTCA-TTTTCG
5431157 CGTTGCGAT
1 CGTTGCGAT
5431166 TTTAAGTTTC
Statistics
Matches: 41, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
20 27 0.66
21 14 0.34
ACGTcount: A:0.19, C:0.20, G:0.24, T:0.37
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:5431185 original size:20 final size:20
Alignment explanation
Indices: 5431152--5431195 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
5431142 GATAGTCATT
*
5431152 TTTCGCGTTGCGATTTTAAG
1 TTTCGCGTTACGATTTTAAG
*
5431172 TTTCGTGTTACGATTTTAAG
1 TTTCGCGTTACGATTTTAAG
5431192 TTTC
1 TTTC
5431196 AGAAACTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.16, C:0.14, G:0.20, T:0.50
Consensus pattern (20 bp):
TTTCGCGTTACGATTTTAAG
Found at i:5431698 original size:21 final size:21
Alignment explanation
Indices: 5431674--5431786 Score: 95
Period size: 21 Copynumber: 5.4 Consensus size: 21
5431664 CCTGTCATCG
*
5431674 TTCAAGAGGCCTCTCCTATCA
1 TTCAAGAGGCCCCTCCTATCA
*
5431695 TTCAAGAGGCCCCT-ATCATCA
1 TTCAAGAGGCCCCTCCT-ATCA
* *
5431716 TTCAAGAGGCCCCT-ATCATCC
1 TTCAAGAGGCCCCTCCT-ATCA
* * * * *
5431737 CTCAAGAGTCCCCTCCCACCG
1 TTCAAGAGGCCCCTCCTATCA
* *
5431758 TTCAAGAGGCCCCTCCCACCA
1 TTCAAGAGGCCCCTCCTATCA
5431779 TTCAAGAG
1 TTCAAGAG
5431787 CTCGATTCAC
Statistics
Matches: 78, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
20 1 0.01
21 77 0.99
ACGTcount: A:0.25, C:0.39, G:0.15, T:0.21
Consensus pattern (21 bp):
TTCAAGAGGCCCCTCCTATCA
Found at i:5431784 original size:42 final size:42
Alignment explanation
Indices: 5431672--5431786 Score: 115
Period size: 42 Copynumber: 2.7 Consensus size: 42
5431662 CACCTGTCAT
* * * * *
5431672 CGTTCAAGAGGCCTCTCCTATCATTCAAGAGGCCCCTATCAT
1 CGTTCAAGAGGCCCCTCCCACCATTCAAGAGGCCCCTACCAC
* ** * * *
5431714 CATTCAAGAGGCCCCTATCATCC-CTCAAGAGTCCCCTCCCAC
1 CGTTCAAGAGGCCCCTCCCA-CCATTCAAGAGGCCCCTACCAC
5431756 CGTTCAAGAGGCCCCTCCCACCATTCAAGAG
1 CGTTCAAGAGGCCCCTCCCACCATTCAAGAG
5431787 CTCGATTCAC
Statistics
Matches: 56, Mismatches: 15, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
41 2 0.04
42 53 0.95
43 1 0.02
ACGTcount: A:0.24, C:0.39, G:0.16, T:0.21
Consensus pattern (42 bp):
CGTTCAAGAGGCCCCTCCCACCATTCAAGAGGCCCCTACCAC
Found at i:5433223 original size:20 final size:20
Alignment explanation
Indices: 5433153--5433226 Score: 78
Period size: 20 Copynumber: 3.7 Consensus size: 20
5433143 AGGTACACTT
*
5433153 TCGCAACGCTAAA-CTCAAAA
1 TCGCAACGCGAAAGC-CAAAA
* * *
5433173 TCGCAATGCAAAAGTCAAAA
1 TCGCAACGCGAAAGCCAAAA
* *
5433193 TTGCAATGCGAAAGCCAAAA
1 TCGCAACGCGAAAGCCAAAA
5433213 TCGCAACGCGAAAG
1 TCGCAACGCGAAAG
5433227 TCAATTCGCG
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.45, C:0.24, G:0.18, T:0.14
Consensus pattern (20 bp):
TCGCAACGCGAAAGCCAAAA
Found at i:5433294 original size:20 final size:20
Alignment explanation
Indices: 5433269--5433425 Score: 251
Period size: 20 Copynumber: 7.8 Consensus size: 20
5433259 ACAATTTTCT
*
5433269 CGTTGCGATAGTAAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
5433289 CGTTGCGATAGTCAAATTTG
1 CGTTGCGATAGTCAAATTCG
*
5433309 TGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
5433329 TGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
5433349 TGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
5433369 TGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
5433389 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
5433409 CGTTGCGATATTCAAAT
1 CGTTGCGATAGTCAAAT
5433426 GAATGTGTAA
Statistics
Matches: 131, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 131 1.00
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.34
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:5435984 original size:24 final size:24
Alignment explanation
Indices: 5435893--5435970 Score: 138
Period size: 24 Copynumber: 3.2 Consensus size: 24
5435883 CTGAAACATC
* *
5435893 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGGGTATTGACCAAG
5435917 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGGGTATTGACCAAG
5435941 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGGGTATTGACCAAG
5435965 ATCAAA
1 ATCAAA
5435971 TTTCGAATAC
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 52 1.00
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.21
Consensus pattern (24 bp):
ATCAAAGTCCGGGTATTGACCAAG
Found at i:5436816 original size:20 final size:20
Alignment explanation
Indices: 5436791--5436837 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
5436781 AAATTCAGTG
5436791 TTGCGATAGTCAGAATCACA
1 TTGCGATAGTCAGAATCACA
* *
5436811 TTGCGATAGTCAGAATCGCG
1 TTGCGATAGTCAGAATCACA
5436831 TTGCGAT
1 TTGCGAT
5436838 TTACATATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.28
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCACA
Found at i:5436968 original size:19 final size:19
Alignment explanation
Indices: 5436944--5436980 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
5436934 TGCGATACTG
*
5436944 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
*
5436963 GAGATCTCATTGCGATTT
1 GAGATCGCATTGCGATTT
5436981 TGTTGGTCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.22, C:0.16, G:0.27, T:0.35
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:5444038 original size:12 final size:12
Alignment explanation
Indices: 5444009--5444048 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
5443999 TGCGGGAAAA
5444009 TTAAAA-TTA-T
1 TTAAAATTTATT
5444019 TT-AAATTTATT
1 TTAAAATTTATT
5444030 TTAAAATTTATT
1 TTAAAATTTATT
5444042 TTAAAAT
1 TTAAAAT
5444049 ATAGATTGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
9 3 0.11
10 5 0.19
11 3 0.11
12 16 0.59
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
TTAAAATTTATT
Found at i:5444105 original size:66 final size:65
Alignment explanation
Indices: 5444032--5444420 Score: 546
Period size: 66 Copynumber: 5.9 Consensus size: 65
5444022 AATTTATTTT
*
5444032 AAAATTTATTTTAAAATATAGATTGATTTATTTTAAAATATGAATTGATTTATTTTAAAATATAG
1 AAAATTTATTTTAAAATAT-GATTGATTTATTTTAAAATATGAATTGATTTATTTTAAAATATGG
5444097 A
65 A
*** ** *
5444098 TTGATTTATTTTAAAATATGGA-AAATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGG
1 AAAATTTATTTTAAAATAT-GATTGATTTATTTTAAAATATGAATTGATTTATTTTAAAATATGG
5444162 A
65 A
* *
5444163 AAATTTTATTTTAAAATATAGATTGATTTATTTTAAAATATGAATTGATTTATTTTAAAATATGA
1 AAAATTTATTTTAAAATAT-GATTGATTTATTTTAAAATATGAATTGATTTATTTTAAAATATGG
5444228 A
65 A
***
5444229 AAAATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGAAAAAATTTATTTTAAAATATGG
1 AAAATTTATTTTAAAATAT-GATTGATTTATTTTAAAATATGAATTGATTTATTTTAAAATATGG
5444294 A
65 A
*** ***
5444295 TTGATTTATTTTAAAATATGAAAAAATTTATTTTAAAATATGAATTGATTTATTTTAAAATATGG
1 AAAATTTATTTTAAAATATG-ATTGATTTATTTTAAAATATGAATTGATTTATTTTAAAATATGG
5444360 A
65 A
*
5444361 AAAATTTATTTTAAAATATGTATTGATTTATTTTAAAAAATGAATTGATTTATTTTAAAA
1 AAAATTTATTTTAAAATATG-ATTGATTTATTTTAAAATATGAATTGATTTATTTTAAAA
5444421 AATTTATTAT
Statistics
Matches: 281, Mismatches: 40, Indels: 4
0.86 0.12 0.01
Matches are distributed among these distances:
65 57 0.20
66 224 0.80
ACGTcount: A:0.44, C:0.00, G:0.09, T:0.47
Consensus pattern (65 bp):
AAAATTTATTTTAAAATATGATTGATTTATTTTAAAATATGAATTGATTTATTTTAAAATATGGA
Found at i:5444423 original size:22 final size:22
Alignment explanation
Indices: 5444035--5444420 Score: 491
Period size: 22 Copynumber: 17.6 Consensus size: 22
5444025 TTATTTTAAA
5444035 ATTTATTTTAAAATAT-AGATTG
1 ATTTATTTTAAAATATGA-ATTG
5444057 ATTTATTTTAAAATATGAATTG
1 ATTTATTTTAAAATATGAATTG
5444079 ATTTATTTTAAAATAT-AGATTG
1 ATTTATTTTAAAATATGA-ATTG
*
5444101 ATTTATTTTAAAATATGGAA--A
1 ATTTATTTTAAAATAT-GAATTG
*
5444122 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGAATTG
*
5444144 ATTTATTTTAAAATATGGAA--A
1 ATTTATTTTAAAATAT-GAATTG
5444165 ATTTTATTTTAAAATAT-AGATTG
1 A-TTTATTTTAAAATATGA-ATTG
5444188 ATTTATTTTAAAATATGAATTG
1 ATTTATTTTAAAATATGAATTG
***
5444210 ATTTATTTTAAAATATGAAAAA
1 ATTTATTTTAAAATATGAATTG
*
5444232 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGAATTG
***
5444254 ATTTATTTTAAAATATGAAAAA
1 ATTTATTTTAAAATATGAATTG
*
5444276 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGAATTG
***
5444298 ATTTATTTTAAAATATGAAAAA
1 ATTTATTTTAAAATATGAATTG
5444320 ATTTATTTTAAAATATGAATTG
1 ATTTATTTTAAAATATGAATTG
**
5444342 ATTTATTTTAAAATATGGAA-AA
1 ATTTATTTTAAAATAT-GAATTG
*
5444364 ATTTATTTTAAAATATGTATTG
1 ATTTATTTTAAAATATGAATTG
*
5444386 ATTTATTTTAAAAAATGAATTG
1 ATTTATTTTAAAATATGAATTG
5444408 ATTTATTTTAAAA
1 ATTTATTTTAAAA
5444421 AATTTATTAT
Statistics
Matches: 315, Mismatches: 35, Indels: 28
0.83 0.09 0.07
Matches are distributed among these distances:
20 3 0.01
21 21 0.07
22 281 0.89
23 9 0.03
24 1 0.00
ACGTcount: A:0.44, C:0.00, G:0.09, T:0.47
Consensus pattern (22 bp):
ATTTATTTTAAAATATGAATTG
Found at i:5444479 original size:31 final size:31
Alignment explanation
Indices: 5444444--5444502 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
5444434 AGTTGTATAG
5444444 ATTATTTAAATTTCAGTATTATAAAACTAAA
1 ATTATTTAAATTTCAGTATTATAAAACTAAA
*
5444475 ATTATTTAAATTTCAGTATTGTAAAACT
1 ATTATTTAAATTTCAGTATTATAAAACT
5444503 CTTTTAAGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (31 bp):
ATTATTTAAATTTCAGTATTATAAAACTAAA
Found at i:5452212 original size:87 final size:87
Alignment explanation
Indices: 5452116--5452392 Score: 455
Period size: 87 Copynumber: 3.2 Consensus size: 87
5452106 AATAACATAT
* * *
5452116 TAGGTAGCGCTTATATAATAAAATAAGTATTTAACCAGAAATATTATCAACTACAATAACATATT
1 TAGGTAGCGCTTATATAATAAAATAAGTATTTAACCGGAAATATTATTAAGTACAATAACATATT
5452181 AGGTAGCGCTTATATAATGTAA
66 AGGTAGCGCTTATATAATGTAA
5452203 TAGGTAGCGCTTATATAATAAAATAAGTATTTAACCGGAAATATTATTAAGTACAATAACATATT
1 TAGGTAGCGCTTATATAATAAAATAAGTATTTAACCGGAAATATTATTAAGTACAATAACATATT
5452268 AGGTAGCGCTTATATAATGTAA
66 AGGTAGCGCTTATATAATGTAA
* * * * *
5452290 TATGTAGTGCTTATATAATAAAATAGGCATTTAACCGGAAATATTATTAAGTACAATAACATAGT
1 TAGGTAGCGCTTATATAATAAAATAAGTATTTAACCGGAAATATTATTAAGTACAATAACATATT
*
5452355 AGGTATCGCTTATATAATGTAA
66 AGGTAGCGCTTATATAATGTAA
* *
5452377 TATGTAGCGTTTATAT
1 TAGGTAGCGCTTATAT
5452393 TGACTTATTT
Statistics
Matches: 179, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
87 179 1.00
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.34
Consensus pattern (87 bp):
TAGGTAGCGCTTATATAATAAAATAAGTATTTAACCGGAAATATTATTAAGTACAATAACATATT
AGGTAGCGCTTATATAATGTAA
Found at i:5452227 original size:23 final size:23
Alignment explanation
Indices: 5452180--5452227 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
5452170 AATAACATAT
**
5452180 TAGGTAGCGCTTATATAATGTAA
1 TAGGTAGCGCTTATATAATAAAA
5452203 TAGGTAGCGCTTATATAATAAAA
1 TAGGTAGCGCTTATATAATAAAA
5452226 TA
1 TA
5452228 AGTATTTAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.40, C:0.08, G:0.19, T:0.33
Consensus pattern (23 bp):
TAGGTAGCGCTTATATAATAAAA
Found at i:5452314 original size:23 final size:23
Alignment explanation
Indices: 5452270--5452314 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
5452260 AACATATTAG
**
5452270 GTAGCGCTTATATAATGTAATAT
1 GTAGCGCTTATATAATAAAATAT
*
5452293 GTAGTGCTTATATAATAAAATA
1 GTAGCGCTTATATAATAAAATA
5452315 GGCATTTAAC
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:0.40, C:0.07, G:0.16, T:0.38
Consensus pattern (23 bp):
GTAGCGCTTATATAATAAAATAT
Found at i:5452908 original size:30 final size:30
Alignment explanation
Indices: 5452870--5452946 Score: 79
Period size: 30 Copynumber: 2.5 Consensus size: 30
5452860 TTATAATAAA
*
5452870 TAAT-AAATATAAT-TTATAATAATTTTATT
1 TAATAAAATATAATATCATAAT-ATTTTATT
*
5452899 TAATAAAATATAATAATCATAATTTTTTATT
1 TAATAAAATATAAT-ATCATAATATTTTATT
5452930 T-ATAAAATTATAGATAT
1 TAATAAAA-TATA-ATAT
5452947 ATATTTAATA
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
29 4 0.10
30 15 0.37
31 14 0.34
32 8 0.20
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (30 bp):
TAATAAAATATAATATCATAATATTTTATT
Found at i:5452914 original size:42 final size:42
Alignment explanation
Indices: 5452833--5452915 Score: 98
Period size: 42 Copynumber: 2.0 Consensus size: 42
5452823 CTCTCATTAT
* * *
5452833 AATATAATTAATGATATATTATTTTTATTATAATAAATAATA
1 AATATAATTAATAATATATTATTTTTAATAAAATAAATAATA
*
5452875 AATATAATTTATAATA-ATT-TTATTTAATAAAATATAATAAT
1 AATATAATTAATAATATATTATT-TTTAATAAAATA-AATAAT
5452916 CATAATTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
40 2 0.06
41 13 0.37
42 20 0.57
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (42 bp):
AATATAATTAATAATATATTATTTTTAATAAAATAAATAATA
Found at i:5452920 original size:29 final size:31
Alignment explanation
Indices: 5452870--5452937 Score: 81
Period size: 30 Copynumber: 2.3 Consensus size: 31
5452860 TTATAATAAA
*
5452870 TAAT-AAATATAATTTATAATAA-TTTTATT
1 TAATAAAATATAATTAATAATAATTTTTATT
*
5452899 TAATAAAATATAA-TAATCATAATTTTTTATT
1 TAATAAAATATAATTAATAATAA-TTTTTATT
5452930 T-ATAAAAT
1 TAATAAAAT
5452938 TATAGATATA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
29 11 0.32
30 15 0.44
31 8 0.24
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (31 bp):
TAATAAAATATAATTAATAATAATTTTTATT
Found at i:5453012 original size:22 final size:24
Alignment explanation
Indices: 5452945--5453035 Score: 75
Period size: 23 Copynumber: 3.8 Consensus size: 24
5452935 AATTATAGAT
5452945 ATATATTTAAT-AATAATATTGATATA
1 ATAT-TTTAATAAATAATATT-AT-TA
*
5452971 ATAATATTAAATAAAT--TATTA-TA
1 AT-AT-TTTAATAAATAATATTATTA
5452994 ATATTTTAA-AAATAATATTATTA
1 ATATTTTAATAAATAATATTATTA
* *
5453017 TTTTTTTAATAAATAATAT
1 ATATTTTAATAAATAATAT
5453036 CATTTTTTTT
Statistics
Matches: 55, Mismatches: 4, Indels: 14
0.75 0.05 0.19
Matches are distributed among these distances:
20 4 0.07
21 4 0.07
22 7 0.13
23 13 0.24
24 9 0.16
25 1 0.02
26 6 0.11
27 8 0.15
28 3 0.05
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (24 bp):
ATATTTTAATAAATAATATTATTA
Found at i:5453030 original size:24 final size:24
Alignment explanation
Indices: 5452978--5453045 Score: 79
Period size: 24 Copynumber: 2.9 Consensus size: 24
5452968 ATAATAATAT
*
5452978 TAAATAA-ATTATTATAATATTTTAA
1 TAAATAATATTATTAT--TTTTTTAA
5453003 -AAATAATATTATTATTTTTTTAA
1 TAAATAATATTATTATTTTTTTAA
*
5453026 TAAATAATATCATT-TTTTTT
1 TAAATAATATTATTATTTTTT
5453046 ATATTTAATG
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
23 13 0.33
24 18 0.46
25 8 0.21
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.54
Consensus pattern (24 bp):
TAAATAATATTATTATTTTTTTAA
Found at i:5453817 original size:2 final size:2
Alignment explanation
Indices: 5453810--5453852 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
5453800 ATATTGTAAT
5453810 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5453852 T
1 T
5453853 TATTTTTTTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5461391 original size:3 final size:3
Alignment explanation
Indices: 5461383--5461436 Score: 81
Period size: 3 Copynumber: 17.3 Consensus size: 3
5461373 GTTAATTTTC
*
5461383 CTT CTT CTT CTT CTT CTT CCT CTT CCTT CTTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT -CTT C-TT CTT CTT CTT CTT CTT
5461430 CTT CTT C
1 CTT CTT C
5461437 CCACATCTGA
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
3 41 0.87
4 6 0.13
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (3 bp):
CTT
Found at i:5462561 original size:30 final size:30
Alignment explanation
Indices: 5462525--5462586 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
5462515 ACCAAAATAC
5462525 AAACATCCTAAAAGTTTGGATACTATTTAT
1 AAACATCCTAAAAGTTTGGATACTATTTAT
5462555 AAACATCCTAAAAGTTTGGATACTATTTAT
1 AAACATCCTAAAAGTTTGGATACTATTTAT
5462585 AA
1 AA
5462587 GTTTACCCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.42, C:0.13, G:0.10, T:0.35
Consensus pattern (30 bp):
AAACATCCTAAAAGTTTGGATACTATTTAT
Found at i:5463676 original size:26 final size:27
Alignment explanation
Indices: 5463640--5463699 Score: 106
Period size: 27 Copynumber: 2.3 Consensus size: 27
5463630 TGGAACAAAA
5463640 CTAGAATGCTTT-GGATGATTTTGAAG
1 CTAGAATGCTTTGGGATGATTTTGAAG
5463666 CTAGAATGCTTTGGGATGATTTTGAAG
1 CTAGAATGCTTTGGGATGATTTTGAAG
5463693 CTA-AATG
1 CTAGAATG
5463700 AGCTAGAGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
26 16 0.48
27 17 0.52
ACGTcount: A:0.28, C:0.08, G:0.27, T:0.37
Consensus pattern (27 bp):
CTAGAATGCTTTGGGATGATTTTGAAG
Found at i:5463881 original size:21 final size:20
Alignment explanation
Indices: 5463841--5463882 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
5463831 CCAACTTACA
*
5463841 ATGCATTATGAACCATTATT
1 ATGCATTATCAACCATTATT
*
5463861 ATGCATTATACAACTATTATT
1 ATGCATTAT-CAACCATTATT
5463882 A
1 A
5463883 GTTGTATGAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.40
Consensus pattern (20 bp):
ATGCATTATCAACCATTATT
Found at i:5469809 original size:19 final size:18
Alignment explanation
Indices: 5469770--5469811 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 18
5469760 TCACTTATTC
5469770 TTTAAAATGCTAAAATTAT
1 TTTAAAAT-CTAAAATTAT
5469789 TTTAAAAT-TAAAACTTAAT
1 TTTAAAATCTAAAA-TT-AT
5469808 TTTA
1 TTTA
5469812 CACTTTAGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
17 5 0.24
18 2 0.10
19 14 0.67
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (18 bp):
TTTAAAATCTAAAATTAT
Found at i:5472361 original size:21 final size:20
Alignment explanation
Indices: 5472321--5472362 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
5472311 CCAACTTACA
*
5472321 ATGCATTATGAACCATTATT
1 ATGCATTATCAACCATTATT
*
5472341 ATGCATTATACAACTATTATT
1 ATGCATTAT-CAACCATTATT
5472362 A
1 A
5472363 GTTGTATGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.40
Consensus pattern (20 bp):
ATGCATTATCAACCATTATT
Found at i:5475569 original size:19 final size:18
Alignment explanation
Indices: 5475530--5475571 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 18
5475520 TCACTTATTC
5475530 TTTAAAATGCTAAAATTAT
1 TTTAAAAT-CTAAAATTAT
5475549 TTTAAAAT-TAAAACTTAAT
1 TTTAAAATCTAAAA-TT-AT
5475568 TTTA
1 TTTA
5475572 CACTTTAGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
17 5 0.24
18 2 0.10
19 14 0.67
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (18 bp):
TTTAAAATCTAAAATTAT
Found at i:5478575 original size:21 final size:20
Alignment explanation
Indices: 5478535--5478576 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
5478525 CCAACTTACA
*
5478535 ATGCATTATGAACCATTATT
1 ATGCATTATCAACCATTATT
*
5478555 ATGCATTATACAACTATTATT
1 ATGCATTAT-CAACCATTATT
5478576 A
1 A
5478577 GTTGTATGAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.40
Consensus pattern (20 bp):
ATGCATTATCAACCATTATT
Found at i:5483893 original size:17 final size:17
Alignment explanation
Indices: 5483871--5483907 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
5483861 CCGTGTCACT
*
5483871 ATTTAAATTATACTCAA
1 ATTTAAATTAGACTCAA
*
5483888 ATTTAAATTAGATTCAA
1 ATTTAAATTAGACTCAA
5483905 ATT
1 ATT
5483908 CCATTTATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.43
Consensus pattern (17 bp):
ATTTAAATTAGACTCAA
Found at i:5487813 original size:68 final size:68
Alignment explanation
Indices: 5487704--5487858 Score: 238
Period size: 68 Copynumber: 2.3 Consensus size: 68
5487694 AAGCAAATGA
* * * *
5487704 ATCAACAGATGGCATTTAGATTAATTACCAAGTGTCATAAAAAATGAGAGAGAAGACATAAGAGC
1 ATCAACAAATGACATTTAGATTAATTACCAAGTATCATAAAAAATGAGAGAGAAAACATAAGAGC
5487769 ACC
66 ACC
* *
5487772 ATCAACAAATGACATTTAGATTAATTACCATGTATCATAAAAAATGAGAGTGAAAACATAAGAGC
1 ATCAACAAATGACATTTAGATTAATTACCAAGTATCATAAAAAATGAGAGAGAAAACATAAGAGC
5487837 ACC
66 ACC
* *
5487840 ATCAACAACTGATATTTAG
1 ATCAACAAATGACATTTAG
5487859 GTTTAAACTG
Statistics
Matches: 79, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
68 79 1.00
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.23
Consensus pattern (68 bp):
ATCAACAAATGACATTTAGATTAATTACCAAGTATCATAAAAAATGAGAGAGAAAACATAAGAGC
ACC
Found at i:5493440 original size:16 final size:17
Alignment explanation
Indices: 5493412--5493446 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
5493402 CGTATCGCCG
5493412 ACAAAATTTCACTATTC
1 ACAAAATTTCACTATTC
5493429 ACAAAA-TTCACTATTC
1 ACAAAATTTCACTATTC
5493445 AC
1 AC
5493447 CTGAATAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.43, C:0.26, G:0.00, T:0.31
Consensus pattern (17 bp):
ACAAAATTTCACTATTC
Found at i:5498125 original size:18 final size:18
Alignment explanation
Indices: 5498091--5498124 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
5498081 GAAAATAATA
5498091 CAACTCAAACAATAAAAG
1 CAACTCAAACAATAAAAG
*
5498109 CAACT-AAATAATAAAA
1 CAACTCAAACAATAAAA
5498125 ATAATTTGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.65, C:0.18, G:0.03, T:0.15
Consensus pattern (18 bp):
CAACTCAAACAATAAAAG
Found at i:5498199 original size:19 final size:19
Alignment explanation
Indices: 5498161--5498199 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
5498151 ACAAACCAAA
* *
5498161 TAAATAAAAAGTCTATAAT
1 TAAATAAAAACTCTACAAT
*
5498180 TAAATAAAAACTTTACAAT
1 TAAATAAAAACTCTACAAT
5498199 T
1 T
5498200 GCTGGTAAAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.56, C:0.08, G:0.03, T:0.33
Consensus pattern (19 bp):
TAAATAAAAACTCTACAAT
Found at i:5498693 original size:42 final size:42
Alignment explanation
Indices: 5498628--5498707 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 42
5498618 CATAAAACTC
* *
5498628 TGTAGTGGCATCTGACCCAGCTGTAGTGGCATATGAAATGGT
1 TGTAGTGGCATCTGACACAGCTGTAGTGCCATATGAAATGGT
* * * *
5498670 TGTAGTGTCATCTGATACGGCTGTGGTGCCATATGAAA
1 TGTAGTGGCATCTGACACAGCTGTAGTGCCATATGAAA
5498708 CGACTGTGAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 32 1.00
ACGTcount: A:0.24, C:0.16, G:0.30, T:0.30
Consensus pattern (42 bp):
TGTAGTGGCATCTGACACAGCTGTAGTGCCATATGAAATGGT
Found at i:5501988 original size:152 final size:150
Alignment explanation
Indices: 5501781--5502082 Score: 554
Period size: 152 Copynumber: 2.0 Consensus size: 150
5501771 TTCCTAAAAC
5501781 GCACAGTTTTCCCCTCTATCAAACGCTACCGTTTTGGACCTAAATGAAACGACGCCGTTCTGGCG
1 GCACAGTTTTCCCCTCTATCAAACGCTACCGTTTTGGACCTAAATGAAACGACGCCGTTCTGGCG
5501846 TTCTGTTATATAGGTTATTAGGGT-AAATCTGAAACCCTAAATCACTTCAACCCCTCATCCTCC-
66 TTCTGTTATATAGGTTATTAGGGTAAAATCTGAAACCCTAAATCACTTCAACCCCTCATCCTCCA
5501909 AACATACCCACCGCTCTTCT
131 AACATACCCACCGCTCTTCT
5501929 GCACAGTTTTCCCCTCAGCTATCAAAACGCTACCGTTTTGGACCTAAATGAAACGACGCCGTTCT
1 GCACAGTTTTCCCCT---CTATC-AAACGCTACCGTTTTGGACCTAAATGAAACGACGCCGTTCT
5501994 GGCGTTCTGTTATATAGGTTATTAGGGTAAAATCTGAAACCCTAAATCACTTCAACCCCTCATCC
62 GGCGTTCTGTTATATAGGTTATTAGGGTAAAATCTGAAACCCTAAATCACTTCAACCCCTCATCC
5502059 TCCAAACATACCCACCGCTCTTCT
127 TCCAAACATACCCACCGCTCTTCT
5502083 CTGATTTCCT
Statistics
Matches: 148, Mismatches: 0, Indels: 6
0.96 0.00 0.04
Matches are distributed among these distances:
148 15 0.10
151 5 0.03
152 69 0.47
153 39 0.26
154 20 0.14
ACGTcount: A:0.26, C:0.31, G:0.14, T:0.28
Consensus pattern (150 bp):
GCACAGTTTTCCCCTCTATCAAACGCTACCGTTTTGGACCTAAATGAAACGACGCCGTTCTGGCG
TTCTGTTATATAGGTTATTAGGGTAAAATCTGAAACCCTAAATCACTTCAACCCCTCATCCTCCA
AACATACCCACCGCTCTTCT
Found at i:5503646 original size:53 final size:54
Alignment explanation
Indices: 5503482--5503947 Score: 568
Period size: 53 Copynumber: 8.6 Consensus size: 54
5503472 CTCCATAGTC
*
5503482 CTTCAGAGAGTATAAGACTCGAACAATCTTTAACAATCGCGTCTGCCCCCCTATTT
1 CTTCAGAGAGTATAAGACTC-AACAATCTTCAACAATCGCGTCTG-CCCCCTATTT
* * ** * *
5503538 CTTCAGAGAGTATAATACTCGAATAATCTTCAATGATCACGTCTGCCCCCCATTT
1 CTTCAGAGAGTATAAGACTC-AACAATCTTCAACAATCGCGTCTGCCCCCTATTT
*
5503593 CTTCAGAGAGTATAAGACTC-ACAATCTTCATCAATCGCGTCTGCCCCCTATTT
1 CTTCAGAGAGTATAAGACTCAACAATCTTCAACAATCGCGTCTGCCCCCTATTT
* * *
5503646 CGTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCATATTT
1 CTTCAGAGAGTATAAGACTC-AACAATCTTCAACAATCGCGTCTGCCCCCTATTT
* * *
5503701 CTTCAGAGAGTATAAGAC-CCACAATCTTCATCAATCGCGTCTTCCCCCTA-TT
1 CTTCAGAGAGTATAAGACTCAACAATCTTCAACAATCGCGTCTGCCCCCTATTT
* * *
5503753 CTTCAGAGAGTATAAGACCCGAACAATCTTCAACAATCGTGTCCGCCCCCTATTT
1 CTTCAGAGAGTATAAGACTC-AACAATCTTCAACAATCGCGTCTGCCCCCTATTT
* * *
5503808 CTTC--AGAGTATAAGACTCGAACAATCTTCAACGATCACGTCTGCCCTCTATTT
1 CTTCAGAGAGTATAAGACTC-AACAATCTTCAACAATCGCGTCTGCCCCCTATTT
* * * * **
5503861 ATTCAGAGAGTAT--GACCCGAACAATCTTCAGCAATCGTGTCCACCCCCTATTT
1 CTTCAGAGAGTATAAGACTC-AACAATCTTCAACAATCGCGTCTGCCCCCTATTT
*
5503914 CCTCAGAGAGTATAAGACTCGAACAATCTTCAAC
1 CTTCAGAGAGTATAAGACTC-AACAATCTTCAAC
5503948 CCTATTTCTT
Statistics
Matches: 353, Mismatches: 48, Indels: 19
0.84 0.11 0.05
Matches are distributed among these distances:
52 20 0.06
53 162 0.46
54 27 0.08
55 105 0.30
56 39 0.11
ACGTcount: A:0.29, C:0.29, G:0.14, T:0.28
Consensus pattern (54 bp):
CTTCAGAGAGTATAAGACTCAACAATCTTCAACAATCGCGTCTGCCCCCTATTT
Found at i:5503674 original size:108 final size:109
Alignment explanation
Indices: 5503482--5504147 Score: 763
Period size: 108 Copynumber: 6.3 Consensus size: 109
5503472 CTCCATAGTC
*
5503482 CTTCAGAGAGTATAAGACTCGAACAATCTTTAACAATCGCGTCTGCCCCCCTATTTCTTCAGAGA
1 CTTCAGAGAGTATAAGACTC-AACAATCTTCAACAATCGCGTCTG-CCCCCTATTTCTTCAGAGA
* * * * * *
5503547 GTATAATACTCGAATAATCTTCAATGATCACGTCTGCCCCCCATTT
64 GTATAAGACTCGAACAATCTTCAACGATCGCGTCCGCCCCCTATTT
* *
5503593 CTTCAGAGAGTATAAGACTC-ACAATCTTCATCAATCGCGTCTGCCCCCTATTTCGTCAGAGAGT
1 CTTCAGAGAGTATAAGACTCAACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGT
* *
5503657 ATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCATATTT
66 ATAAGACTCGAACAATCTTCAACGATCGCGTCCGCCCCCTATTT
* * *
5503701 CTTCAGAGAGTATAAGAC-CCACAATCTTCATCAATCGCGTCTTCCCCCTA-TTCTTCAGAGAGT
1 CTTCAGAGAGTATAAGACTCAACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGT
* * *
5503764 ATAAGACCCGAACAATCTTCAACAATCGTGTCCGCCCCCTATTT
66 ATAAGACTCGAACAATCTTCAACGATCGCGTCCGCCCCCTATTT
* * * *
5503808 CTTC--AGAGTATAAGACTCGAACAATCTTCAACGATCACGTCTGCCCTCTATTTATTCAGAGAG
1 CTTCAGAGAGTATAAGACTC-AACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAG
* * * * *
5503871 TAT--GACCCGAACAATCTTCAGCAATCGTGTCCACCCCCTATTT
65 TATAAGACTCGAACAATCTTCAACGATCGCGTCCGCCCCCTATTT
*
5503914 CCTCAGAGAGTATAAGACTCGAACAATCTT---CAA-----------CCCTATTTCTTCAGAGAG
1 CTTCAGAGAGTATAAGACTC-AACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAG
* * *
5503965 TATGAGACTTGAACAATCTTCAAACGATCGTGTCCGCCCCCTATTT
65 TATAAGACTCGAACAATCTTC-AACGATCGCGTCCGCCCCCTATTT
* *
5504011 CCTCAGAGAGTATAAGACTCGAACAATCTTCAACTATCGCGTCT-CCCCC--TTTCTTCAGAGAG
1 CTTCAGAGAGTATAAGACTC-AACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAG
* *
5504073 TATAAGACTTGAAC-ATCTTCAACGATCGCGT-CGCCCCCTATTC
65 TATAAGACTCGAACAATCTTCAACGATCGCGTCCGCCCCCTATTT
* *
5504116 CTTCAGAGAGTATGAGACTTGAACAATCTTCA
1 CTTCAGAGAGTATAAGAC-TCAACAATCTTCA
5504148 CGATCGTGGG
Statistics
Matches: 491, Mismatches: 41, Indels: 52
0.84 0.07 0.09
Matches are distributed among these distances:
94 19 0.04
96 14 0.03
97 51 0.10
100 2 0.00
105 52 0.11
106 53 0.11
107 87 0.18
108 169 0.34
109 21 0.04
110 3 0.01
111 20 0.04
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.28
Consensus pattern (109 bp):
CTTCAGAGAGTATAAGACTCAACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGT
ATAAGACTCGAACAATCTTCAACGATCGCGTCCGCCCCCTATTT
Found at i:5503953 original size:41 final size:41
Alignment explanation
Indices: 5503906--5503987 Score: 137
Period size: 41 Copynumber: 2.0 Consensus size: 41
5503896 CGTGTCCACC
5503906 CCCTATTTCCTCAGAGAGTATAAGACTCGAACAATCTTCAA
1 CCCTATTTCCTCAGAGAGTATAAGACTCGAACAATCTTCAA
* * *
5503947 CCCTATTTCTTCAGAGAGTATGAGACTTGAACAATCTTCAA
1 CCCTATTTCCTCAGAGAGTATAAGACTCGAACAATCTTCAA
5503988 ACGATCGTGT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.33, C:0.24, G:0.13, T:0.29
Consensus pattern (41 bp):
CCCTATTTCCTCAGAGAGTATAAGACTCGAACAATCTTCAA
Found at i:5504035 original size:56 final size:54
Alignment explanation
Indices: 5503947--5504153 Score: 280
Period size: 56 Copynumber: 3.9 Consensus size: 54
5503937 CAATCTTCAA
* * *
5503947 CCCTATTTCTTCAGAGAGTATGAGACTTGAACAATCTTCAAACGATCGTGTCCGCC
1 CCCTATTTCCTCAGAGAGTATAAGACTTGAACAATCTTC-AACGATCGCGT-CGCC
* * *
5504003 CCCTATTTCCTCAGAGAGTATAAGACTCGAACAATCTTCAACTATCGCGTCTCC
1 CCCTATTTCCTCAGAGAGTATAAGACTTGAACAATCTTCAACGATCGCGTCGCC
*
5504057 CCC--TTTCTTCAGAGAGTATAAGACTTGAAC-ATCTTCAACGATCGCGTCGCC
1 CCCTATTTCCTCAGAGAGTATAAGACTTGAACAATCTTCAACGATCGCGTCGCC
*
5504108 CCCTA-TTCCTTCAGAGAGTATGAGACTTGAACAATCTTC-ACGATCG
1 CCCTATTTCC-TCAGAGAGTATAAGACTTGAACAATCTTCAACGATCG
5504154 TGGGGAACCT
Statistics
Matches: 135, Mismatches: 12, Indels: 11
0.85 0.08 0.07
Matches are distributed among these distances:
51 22 0.16
52 28 0.21
53 28 0.21
54 12 0.09
55 9 0.07
56 36 0.27
ACGTcount: A:0.27, C:0.29, G:0.16, T:0.28
Consensus pattern (54 bp):
CCCTATTTCCTCAGAGAGTATAAGACTTGAACAATCTTCAACGATCGCGTCGCC
Found at i:5504069 original size:149 final size:145
Alignment explanation
Indices: 5503800--5504095 Score: 380
Period size: 149 Copynumber: 2.0 Consensus size: 145
5503790 CGTGTCCGCC
* * *
5503800 CCCTATTTCTTCAGAGTATAAGACTCGAACAATCTTCAACGATCACGTCTGCCCTCTATTTATTC
1 CCCTATTTCTTCAGAGTATAAGACTCGAACAATCTTCAACGATCACGTCCGCCCCCTATTTACTC
* *
5503865 AGAGAGTATGACCCGAACAATCTTCAGCAATCGTGTCCACCCCCTATTTCCTCAGAGAGTATAAG
66 AGAGAGTATGACCCGAACAATCTTCAACAATCGCGTCCACCCCC-ATTTCCTCAGAGAGTATAAG
5503930 ACTCGAACAATCTTCAA
130 ACTCGAAC-ATCTTCAA
* * ** *
5503947 CCCTATTTCTTCAGAGAGTATGAGACTTGAACAATCTTCAAACGATCGTGTCCGCCCCCTATTTC
1 CCCTATTTCTTC--AGAGTATAAGACTCGAACAATCTTC-AACGATCACGTCCGCCCCCTATTTA
* * * *
5504012 CTCAGAGAGTATAAGACTCGAACAATCTTCAACTATCGCGT-CTCCCCC-TTTCTTCAGAGAGTA
63 CTCAGAGAGTAT--GACCCGAACAATCTTCAACAATCGCGTCCACCCCCATTTCCTCAGAGAGTA
*
5504075 TAAGACTTGAACATCTTCAA
126 TAAGACTCGAACATCTTCAA
5504095 C
1 C
5504096 GATCGCGTCG
Statistics
Matches: 129, Mismatches: 15, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
147 12 0.09
148 9 0.07
149 48 0.37
150 31 0.24
151 6 0.05
152 23 0.18
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.28
Consensus pattern (145 bp):
CCCTATTTCTTCAGAGTATAAGACTCGAACAATCTTCAACGATCACGTCCGCCCCCTATTTACTC
AGAGAGTATGACCCGAACAATCTTCAACAATCGCGTCCACCCCCATTTCCTCAGAGAGTATAAGA
CTCGAACATCTTCAA
Found at i:5504112 original size:202 final size:201
Alignment explanation
Indices: 5503746--5504147 Score: 546
Period size: 202 Copynumber: 2.0 Consensus size: 201
5503736 CGCGTCTTCC
*
5503746 CCCTATTCTTCAGAGAGTATAAGACCCGAACAATCTTCAACAATCGTGTCCGCCCCCTATTTCTT
1 CCCTATTCTTCAGAGAGTATAAGACCCGAACAATCTTCAACAATCGTGTCCGCCCCCTATTTCCT
5503811 CAGAGTATAAGACTCGAACAATCTTCAACGATCACGTCTGCCCTCTATTTATTCAGAGAGTATGA
66 CAGAGTATAAGACTCGAACAATCTTCAACGATCACGTCTGCCCTCTATTTATTCAGAGAGTATGA
* *
5503876 CCCGAACAATCTTCAGCAATCGTGTCCACCCCCTATTTCC-TCAGAGAGTATAAGACTCGAACAA
131 CCCGAACAATCTTCAACAATCGCGTCCACCCCCTA-TTCCTTCAGAGAGTATAAGACTCGAACAA
5503940 TCTTCAA
195 TCTTCAA
* ** *
5503947 CCCTATTTCTTCAGAGAGTATGAGACTTGAACAATCTTCAAACGATCGTGTCCGCCCCCTATTTC
1 CCCTA-TTCTTCAGAGAGTATAAGACCCGAACAATCTTC-AACAATCGTGTCCGCCCCCTATTTC
* * * *
5504012 CTCAGAGAGTATAAGACTCGAACAATCTTCAACTATCGCGTCT-CCC-C-CTTTCTTCAGAGAGT
64 CTC--AGAGTATAAGACTCGAACAATCTTCAACGATCACGTCTGCCCTCTATTTATTCAGAGAGT
** * * * *
5504074 ATAAGACTTGAAC-ATCTTCAACGATCGCGT-CGCCCCCTATTCCTTCAGAGAGTATGAGACTTG
127 AT--GACCCGAACAATCTTCAACAATCGCGTCCACCCCCTATTCCTTCAGAGAGTATAAGACTCG
5504137 AACAATCTTCA
190 AACAATCTTCA
5504148 CGATCGTGGG
Statistics
Matches: 177, Mismatches: 17, Indels: 13
0.86 0.08 0.06
Matches are distributed among these distances:
201 9 0.05
202 81 0.46
203 41 0.23
204 10 0.06
205 36 0.20
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.28
Consensus pattern (201 bp):
CCCTATTCTTCAGAGAGTATAAGACCCGAACAATCTTCAACAATCGTGTCCGCCCCCTATTTCCT
CAGAGTATAAGACTCGAACAATCTTCAACGATCACGTCTGCCCTCTATTTATTCAGAGAGTATGA
CCCGAACAATCTTCAACAATCGCGTCCACCCCCTATTCCTTCAGAGAGTATAAGACTCGAACAAT
CTTCAA
Found at i:5505136 original size:9 final size:8
Alignment explanation
Indices: 5505121--5505186 Score: 55
Period size: 8 Copynumber: 7.9 Consensus size: 8
5505111 TTGAACCCTC
*
5505121 ATTTTTTC
1 ATTTTTTT
5505129 ATTTTTTT
1 ATTTTTTT
5505137 CATTCATTTTTT
1 -ATT---TTTTT
5505149 ATTTTTTT
1 ATTTTTTT
*
5505157 -TTATTTT
1 ATTTTTTT
5505164 -TTTTTTT
1 ATTTTTTT
5505171 ATTTTTTTT
1 A-TTTTTTT
5505180 ATTTTTT
1 ATTTTTT
5505187 CACTTATTTT
Statistics
Matches: 49, Mismatches: 3, Indels: 12
0.77 0.05 0.19
Matches are distributed among these distances:
7 12 0.24
8 18 0.37
9 11 0.22
11 3 0.06
12 5 0.10
ACGTcount: A:0.12, C:0.05, G:0.00, T:0.83
Consensus pattern (8 bp):
ATTTTTTT
Found at i:5505157 original size:21 final size:22
Alignment explanation
Indices: 5505119--5505183 Score: 73
Period size: 21 Copynumber: 3.0 Consensus size: 22
5505109 TCTTGAACCC
5505119 TCATTTTTTCA-TTTTTTTCA-T
1 TCATTTTTT-ATTTTTTTTCATT
*
5505140 TCATTTTTTATTTTTTTTTATT
1 TCATTTTTTATTTTTTTTCATT
**
5505162 TTTTTTTTTATTTTTTTT-ATT
1 TCATTTTTTATTTTTTTTCATT
5505183 T
1 T
5505184 TTTCACTTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
20 1 0.03
21 21 0.54
22 17 0.44
ACGTcount: A:0.12, C:0.06, G:0.00, T:0.82
Consensus pattern (22 bp):
TCATTTTTTATTTTTTTTCATT
Found at i:5505158 original size:12 final size:12
Alignment explanation
Indices: 5505150--5505179 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
5505140 TCATTTTTTA
5505150 TTTTTTTTTATT
1 TTTTTTTTTATT
5505162 TTTTTTTTTATT
1 TTTTTTTTTATT
5505174 TTTTTT
1 TTTTTT
5505180 ATTTTTTCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.07, C:0.00, G:0.00, T:0.93
Consensus pattern (12 bp):
TTTTTTTTTATT
Found at i:5505184 original size:21 final size:22
Alignment explanation
Indices: 5505143--5505209 Score: 82
Period size: 21 Copynumber: 3.0 Consensus size: 22
5505133 TTTTCATTCA
5505143 TTTTTTATTTTTTTTTATTTTT
1 TTTTTTATTTTTTTTTATTTTT
5505165 TTTTTTA-TTTTTTTTATTTTT
1 TTTTTTATTTTTTTTTATTTTT
***
5505186 TCACTTATTTTTCTTCTTATTTTT
1 TTTTTTATTTTT-TT-TTATTTTT
5505210 CTTCAAGCAA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
21 18 0.46
22 11 0.28
23 2 0.05
24 8 0.21
ACGTcount: A:0.10, C:0.06, G:0.00, T:0.84
Consensus pattern (22 bp):
TTTTTTATTTTTTTTTATTTTT
Found at i:5505197 original size:1 final size:1
Alignment explanation
Indices: 5505143--5505186 Score: 52
Period size: 1 Copynumber: 44.0 Consensus size: 1
5505133 TTTTCATTCA
* * * *
5505143 TTTTTTATTTTTTTTTATTTTTTTTTTTATTTTTTTTATTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
5505187 CACTTATTTT
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 35 1.00
ACGTcount: A:0.09, C:0.00, G:0.00, T:0.91
Consensus pattern (1 bp):
T
Found at i:5505213 original size:12 final size:11
Alignment explanation
Indices: 5505143--5505209 Score: 61
Period size: 10 Copynumber: 6.2 Consensus size: 11
5505133 TTTTCATTCA
5505143 TTTT-TTATTT
1 TTTTCTTATTT
5505153 TTTT-TTATTT
1 TTTTCTTATTT
5505163 TTTT-TT-TTAT
1 TTTTCTTATT-T
*
5505173 TTTTTTTATTT
1 TTTTCTTATTT
*
5505184 TTTCACTTATTT
1 TTT-TCTTATTT
5505196 TTCTTCTTATTT
1 TT-TTCTTATTT
5505208 TT
1 TT
5505210 CTTCAAGCAA
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
9 2 0.04
10 21 0.43
11 6 0.12
12 19 0.39
13 1 0.02
ACGTcount: A:0.10, C:0.06, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTCTTATTT
Found at i:5507132 original size:16 final size:16
Alignment explanation
Indices: 5507111--5507144 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
5507101 GGACAATAAG
5507111 ATCTGCCAACGAGCTA
1 ATCTGCCAACGAGCTA
5507127 ATCTGCCAACGAGCTA
1 ATCTGCCAACGAGCTA
5507143 AT
1 AT
5507145 ATTCCAGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.32, C:0.29, G:0.18, T:0.21
Consensus pattern (16 bp):
ATCTGCCAACGAGCTA
Found at i:5527501 original size:23 final size:24
Alignment explanation
Indices: 5527443--5527500 Score: 70
Period size: 22 Copynumber: 2.5 Consensus size: 24
5527433 CGAAATAATA
5527443 AATTTTATTAAAAATTATAACTATT
1 AATTTT-TTAAAAATTATAACTATT
*
5527468 -ATTTTTT-AAAATTTTAA-T-TT
1 AATTTTTTAAAAATTATAACTATT
5527488 AATTTTTTAAAAA
1 AATTTTTTAAAAA
5527501 AAAATTGAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
20 2 0.07
21 8 0.27
22 13 0.43
23 2 0.07
24 5 0.17
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (24 bp):
AATTTTTTAAAAATTATAACTATT
Found at i:5528521 original size:29 final size:31
Alignment explanation
Indices: 5528469--5528526 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 31
5528459 GTTTTTTTGT
** *
5528469 CCAATAGGGCACCCTCCGTAATT-ATTTGAC
1 CCAATAGGGCACCCTAAGAAATTAATTTGAC
5528499 CCAATAGGGCA-CCTAAGAAATTAATTTG
1 CCAATAGGGCACCCTAAGAAATTAATTTG
5528527 GGATCTACGG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 8 0.33
30 16 0.67
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (31 bp):
CCAATAGGGCACCCTAAGAAATTAATTTGAC
Found at i:5532626 original size:347 final size:345
Alignment explanation
Indices: 5531985--5532635 Score: 1036
Period size: 347 Copynumber: 1.9 Consensus size: 345
5531975 TTTTAGCTAC
* * * **
5531985 TTTCTAGTGCTCAATTAATGCACTTTGTCAACTACTTTTTAGAGGTCATTTATTGCAGTAATAAT
1 TTTCCAGTGCTCAATTAATGCACTTTGTCAACTACTTTTCAGAGGTCATTTATTACAACAATAAT
**
5532050 GCAATTGTTGACTTATTTTGTTGGTCATTTACTGCAGAATTCAATCAACTTTTCAAAAAATGGGT
66 GCAATTGTTGACTTATTTTGTTGGTCATTTACTGCAGAATTCAAGAAACTTTTCAAAAAATGGGT
* * *
5532115 TAAATAGTGGTGCATTATCATCTTTAGCAACTTTTCAATGATATGTCAACTCAAATAAAAAAAGT
131 GAAATAGTGGTGCATTATCATCTTCAGCAACTTTTCAATGATATATCAACTCAAATAAAAAAAGT
** * *
5532180 GTTTTTAATCCAGTCAAAATAATGCACCCTTCCAGCTATTGTTTAGTGAAATACGAACTCAAATT
196 GTTTTTAATCCAAACAAAATAATGCACCCTTCCAGCTATTGTTCAGTGAAATACGAACTCAAATC
*
5532245 AGAAAACATTTCAGTGTTGAATTATCACTTCAAATCATAAAAACATGTATTTCAACCAGGCCAAA
261 AGAAAACATTTCAATGTTGAATTATCACTTCAAATCATAAAAACATGTATTTCAACCAGGCCAAA
5532310 TTATTCATTGTTTCAACTAT
326 TTATTCATTGTTTCAACTAT
*
5532330 TTTCCAGTGCTCAATTAATGCACTATT-TCAGCTACTTTTCAGAGGTCATTTATTACAACAATAA
1 TTTCCAGTGCTCAATTAATGCACT-TTGTCAACTACTTTTCAGAGGTCATTTATTACAACAATAA
* * * *
5532394 TGCAATTGTTGGCTTATTTTGTTGGTCATTTATTGTAGAATTCAAGAAACTTTTTTAAAAAATGG
65 TGCAATTGTTGACTTATTTTGTTGGTCATTTACTGCAGAATTCAAGAAAC-TTTTCAAAAAATGG
* * *
5532459 GTGAAATAGTGGTGCATTATCATCTTCATCAACTTTTCAGTGATATATCAACTCAAATCAGAAAA
129 GTGAAATAGTGGTGCATTATCATCTTCAGCAACTTTTCAATGATATATCAACTCAAAT-AAAAAA
*
5532524 TGTGTTTTTAA-CTCAAACAAAATAATGCACCCTTCCAGCTATTGTTCAGTGAAATACGAACTCA
193 AGTGTTTTTAATC-CAAACAAAATAATGCACCCTTCCAGCTATTGTTCAGTGAAATACGAACTCA
5532588 AATCAGAAAACATTTCAATGTTGAATTATCACTTCAAATCATAAAAAC
257 AATCAGAAAACATTTCAATGTTGAATTATCACTTCAAATCATAAAAAC
5532636 GATATGTTTT
Statistics
Matches: 278, Mismatches: 24, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
345 100 0.36
346 69 0.25
347 109 0.39
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.36
Consensus pattern (345 bp):
TTTCCAGTGCTCAATTAATGCACTTTGTCAACTACTTTTCAGAGGTCATTTATTACAACAATAAT
GCAATTGTTGACTTATTTTGTTGGTCATTTACTGCAGAATTCAAGAAACTTTTCAAAAAATGGGT
GAAATAGTGGTGCATTATCATCTTCAGCAACTTTTCAATGATATATCAACTCAAATAAAAAAAGT
GTTTTTAATCCAAACAAAATAATGCACCCTTCCAGCTATTGTTCAGTGAAATACGAACTCAAATC
AGAAAACATTTCAATGTTGAATTATCACTTCAAATCATAAAAACATGTATTTCAACCAGGCCAAA
TTATTCATTGTTTCAACTAT
Found at i:5532661 original size:114 final size:114
Alignment explanation
Indices: 5532526--5532750 Score: 405
Period size: 114 Copynumber: 2.0 Consensus size: 114
5532516 TCAGAAAATG
*
5532526 TGTTTTTAACTCAAACAAAATAATGCACCCTTCCAGCTATTGTTCAGTGAAATACGAACTCAAAT
1 TGTTTTTAACTCAAACAAAATAATGCACCCTTCCAGCTATTGTTCAGTGAAATACAAACTCAAAT
*
5532591 CAGAAAACATTTCAATGTTGAATTATCACTTCAAATCATAAAAACGATA
66 AAGAAAACATTTCAATGTTGAATTATCACTTCAAATCATAAAAACGATA
**
5532640 TGTTTTTAACTCAGGCAAAATAATGCACCCTTCCAGCTATTGTTCAGTGAAATACAAACTCAAAT
1 TGTTTTTAACTCAAACAAAATAATGCACCCTTCCAGCTATTGTTCAGTGAAATACAAACTCAAAT
*
5532705 AAGAAAACATTTCATTGTTGAATTATCACTTCAAATCATAAAAACG
66 AAGAAAACATTTCAATGTTGAATTATCACTTCAAATCATAAAAACG
5532751 TGTATTTCAA
Statistics
Matches: 106, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
114 106 1.00
ACGTcount: A:0.40, C:0.19, G:0.10, T:0.30
Consensus pattern (114 bp):
TGTTTTTAACTCAAACAAAATAATGCACCCTTCCAGCTATTGTTCAGTGAAATACAAACTCAAAT
AAGAAAACATTTCAATGTTGAATTATCACTTCAAATCATAAAAACGATA
Found at i:5533853 original size:29 final size:31
Alignment explanation
Indices: 5533815--5533879 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 31
5533805 GTCGTAGATC
* *
5533815 CCAAATTAATTTATGA-G-GTGTCTTGTTGGG
1 CCAAATTAA-TTATGACGAGTGTCGTATTGGG
5533845 CCAAA-TAATTATGACGAGTGTCGTATTGGG
1 CCAAATTAATTATGACGAGTGTCGTATTGGG
5533875 CCAAA
1 CCAAA
5533880 AAAACCCAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
28 6 0.19
29 4 0.13
30 21 0.68
ACGTcount: A:0.29, C:0.14, G:0.25, T:0.32
Consensus pattern (31 bp):
CCAAATTAATTATGACGAGTGTCGTATTGGG
Found at i:5554235 original size:22 final size:22
Alignment explanation
Indices: 5554208--5554252 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
5554198 CAACGATCAA
5554208 CGGGTCAACGGTCGGGTCGGGT
1 CGGGTCAACGGTCGGGTCGGGT
5554230 CGGGTCAACGGTCGGGTCGGGT
1 CGGGTCAACGGTCGGGTCGGGT
5554252 C
1 C
5554253 AGACCGCTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.09, C:0.24, G:0.49, T:0.18
Consensus pattern (22 bp):
CGGGTCAACGGTCGGGTCGGGT
Found at i:5554306 original size:20 final size:22
Alignment explanation
Indices: 5554281--5554330 Score: 70
Period size: 20 Copynumber: 2.4 Consensus size: 22
5554271 CAGACCGGTC
5554281 AAACCGGTTC-GAACCGATTG-
1 AAACCGGTTCAGAACCGATTGA
*
5554301 AAACCGG-TCAGAACCGGTTGA
1 AAACCGGTTCAGAACCGATTGA
5554322 AAACCGGTT
1 AAACCGGTT
5554331 AAACCGGTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
19 2 0.08
20 16 0.62
21 7 0.27
22 1 0.04
ACGTcount: A:0.32, C:0.24, G:0.26, T:0.18
Consensus pattern (22 bp):
AAACCGGTTCAGAACCGATTGA
Found at i:5554328 original size:11 final size:9
Alignment explanation
Indices: 5554274--5554339 Score: 51
Period size: 10 Copynumber: 6.8 Consensus size: 9
5554264 ACCATTTCAG
*
5554274 ACCGGTCAA
1 ACCGGTTAA
*
5554283 ACCGGTTCGA
1 ACCGGTT-AA
*
5554293 ACCGATTGAA
1 ACCGGTT-AA
*
5554303 ACCGGTCAGA
1 ACCGGTTA-A
5554313 ACCGGTTGAAA
1 ACCGGTT--AA
5554324 ACCGGTTAA
1 ACCGGTTAA
5554333 ACCGGTT
1 ACCGGTT
5554340 TCCAGCAGCC
Statistics
Matches: 45, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
9 16 0.36
10 20 0.44
11 8 0.18
12 1 0.02
ACGTcount: A:0.30, C:0.26, G:0.26, T:0.18
Consensus pattern (9 bp):
ACCGGTTAA
Found at i:5554335 original size:20 final size:19
Alignment explanation
Indices: 5554281--5554339 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 19
5554271 CAGACCGGTC
* *
5554281 AAACCGGTTCGAACCGATTG
1 AAACCGGTT-AAACCGGTTG
*
5554301 AAACCGGTCAGAACCGGTTG
1 AAACCGGTTA-AACCGGTTG
5554321 AAAACCGGTTAAACCGGTT
1 -AAACCGGTTAAACCGGTT
5554340 TCCAGCAGCC
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
20 24 0.73
21 9 0.27
ACGTcount: A:0.32, C:0.24, G:0.25, T:0.19
Consensus pattern (19 bp):
AAACCGGTTAAACCGGTTG
Found at i:5554339 original size:9 final size:10
Alignment explanation
Indices: 5554281--5554339 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
5554271 CAGACCGGTC
5554281 AAACCGGTTCG
1 AAACCGGTT-G
*
5554292 -AACCGATTG
1 AAACCGGTTG
*
5554301 AAACCGG-TC
1 AAACCGGTTG
5554310 AGAACCGGTTG
1 A-AACCGGTTG
5554321 AAAACCGGTT-
1 -AAACCGGTTG
5554331 AAACCGGTT
1 AAACCGGTT
5554340 TCCAGCAGCC
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
9 12 0.30
10 18 0.45
11 9 0.22
12 1 0.03
ACGTcount: A:0.32, C:0.24, G:0.25, T:0.19
Consensus pattern (10 bp):
AAACCGGTTG
Found at i:5561539 original size:17 final size:17
Alignment explanation
Indices: 5561517--5561554 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
5561507 AACGGTCAAC
5561517 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
5561534 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
5561551 GGTC
1 GGTC
5561555 GGGTCAATGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.11, C:0.24, G:0.47, T:0.18
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:5561552 original size:22 final size:22
Alignment explanation
Indices: 5561510--5561573 Score: 92
Period size: 22 Copynumber: 2.8 Consensus size: 22
5561500 GAAAGTCAAC
*
5561510 GGTCAACGGTCAACGGTCGGGTCG
1 GGTCAACGGTC--GGGTCGGGTCG
5561534 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
*
5561556 GGTCAATGGTCGGGTCGG
1 GGTCAACGGTCGGGTCGG
5561574 TTCAGACCGG
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
22 27 0.71
24 11 0.29
ACGTcount: A:0.12, C:0.22, G:0.47, T:0.19
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:5561566 original size:17 final size:17
Alignment explanation
Indices: 5561517--5561573 Score: 60
Period size: 17 Copynumber: 3.1 Consensus size: 17
5561507 AACGGTCAAC
*
5561517 GGTCAACGGTCGGGTCG
1 GGTCAATGGTCGGGTCG
5561534 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAA---T--GGTCGGGTCG
5561556 GGTCAATGGTCGGGTCG
1 GGTCAATGGTCGGGTCG
5561573 G
1 G
5561574 TTCAGACCGG
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
17 17 0.50
19 1 0.03
22 16 0.47
ACGTcount: A:0.11, C:0.21, G:0.49, T:0.19
Consensus pattern (17 bp):
GGTCAATGGTCGGGTCG
Found at i:5563357 original size:20 final size:19
Alignment explanation
Indices: 5563334--5563380 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
5563324 CGATATACCA
5563334 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
5563354 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
5563374 GGTAAAA
1 GGTAAAA
5563381 CGTTACCGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.53, C:0.11, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Done.