Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008319.1 Hibiscus syriacus cultivar Beakdansim tig00111022_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: 4819703
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 21
Found at i:343144 original size:62 final size:62
Alignment explanation
Indices: 343078--343217 Score: 149
Period size: 62 Copynumber: 2.2 Consensus size: 62
343068 CAAAATTAAA
* * *
343078 ATATTATTTATAGTATAAGTATACTTATAAATAATATTAATATATACAAA-AATAT-TATTTAT
1 ATATTATTTATAATACAAATATA-TTATAAATAATATTAATATATACAAATAATATAT-TTTAT
** * * *
343140 ATATTAATACAAAATACAAATATATTATAATTAATATTAATATATATAAATAATATATTTTAT
1 ATATT-ATTTATAATACAAATATATTATAAATAATATTAATATATACAAATAATATATTTTAT
**
343203 ATACGATTTATAATA
1 ATATTATTTATAATA
343218 AAAACTAATT
Statistics
Matches: 62, Mismatches: 13, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
62 36 0.58
63 25 0.40
64 1 0.02
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.44
Consensus pattern (62 bp):
ATATTATTTATAATACAAATATATTATAAATAATATTAATATATACAAATAATATATTTTAT
Found at i:345364 original size:2 final size:2
Alignment explanation
Indices: 345357--345381 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
345347 AAAGGTATGA
345357 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
345382 CCGAAGGAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:347811 original size:3 final size:3
Alignment explanation
Indices: 347796--347883 Score: 64
Period size: 3 Copynumber: 29.3 Consensus size: 3
347786 TTCAAATTTT
347796 TTA TTA CTTA TTA TTA TT- TTA TATA TTA TTA TTA CTTA TTA TT- TT-
1 TTA TTA -TTA TTA TTA TTA TTA T-TA TTA TTA TTA -TTA TTA TTA TTA
347841 TTA -TA TATA TATA TTA TTA TT- TT- TTA TT- TTA TTTA TTTA TTA T
1 TTA TTA T-TA T-TA TTA TTA TTA TTA TTA TTA TTA -TTA -TTA TTA T
347884 ATTCAAGAAT
Statistics
Matches: 75, Mismatches: 0, Indels: 20
0.79 0.00 0.21
Matches are distributed among these distances:
2 14 0.19
3 38 0.51
4 23 0.31
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:347811 original size:10 final size:9
Alignment explanation
Indices: 347796--347883 Score: 64
Period size: 10 Copynumber: 9.8 Consensus size: 9
347786 TTCAAATTTT
347796 TTATTACTTA
1 TTATTA-TTA
347806 TTATTATT-
1 TTATTATTA
347814 TTATATATTA
1 TTAT-TATTA
347824 TTATTACTTA
1 TTATTA-TTA
347834 TTATT-TT-
1 TTATTATTA
347841 TTA-TATATA
1 TTATTAT-TA
347850 TATATTATTA
1 T-TATTATTA
347860 TT-TT-TTA
1 TTATTATTA
347867 TT-TTATTTA
1 TTATTA-TTA
347876 TTTATTAT
1 -TTATTAT
347884 ATTCAAGAAT
Statistics
Matches: 66, Mismatches: 0, Indels: 24
0.73 0.00 0.27
Matches are distributed among these distances:
6 1 0.02
7 11 0.17
8 9 0.14
9 13 0.20
10 26 0.39
11 6 0.09
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (9 bp):
TTATTATTA
Found at i:347833 original size:28 final size:28
Alignment explanation
Indices: 347796--347883 Score: 110
Period size: 28 Copynumber: 3.1 Consensus size: 28
347786 TTCAAATTTT
347796 TTATTACTTATTATTATTTTATATATTA
1 TTATTACTTATTATTATTTTATATATTA
347824 TTATTACTTATTATT-TTTTATATA-TA
1 TTATTACTTATTATTATTTTATATATTA
* *
347850 TATATTA-TTATTTTTTATTTTATTTATTTA
1 T-TATTACTTA-TTATTATTTTATATA-TTA
347880 TTAT
1 TTAT
347884 ATTCAAGAAT
Statistics
Matches: 53, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
26 6 0.11
27 18 0.34
28 23 0.43
29 3 0.06
30 3 0.06
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (28 bp):
TTATTACTTATTATTATTTTATATATTA
Found at i:347834 original size:25 final size:24
Alignment explanation
Indices: 347796--347883 Score: 92
Period size: 25 Copynumber: 3.5 Consensus size: 24
347786 TTCAAATTTT
347796 TTATTACTTATTATTATTTTATATA
1 TTATTA-TTATTATTATTTTATATA
*
347821 TTATTATTACTTATTATTTTTTATA
1 TTATTATTA-TTATTATTTTATATA
347846 TATATATATTATTATT-TTTTAT-T-
1 T-TAT-TATTATTATTATTTTATATA
347869 TTATTTATTTATTAT
1 TTA-TTA-TTATTAT
347884 ATTCAAGAAT
Statistics
Matches: 56, Mismatches: 2, Indels: 12
0.80 0.03 0.17
Matches are distributed among these distances:
22 4 0.07
23 9 0.16
24 4 0.07
25 26 0.46
26 8 0.14
27 5 0.09
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (24 bp):
TTATTATTATTATTATTTTATATA
Found at i:347857 original size:33 final size:32
Alignment explanation
Indices: 347796--347886 Score: 95
Period size: 31 Copynumber: 3.0 Consensus size: 32
347786 TTCAAATTTT
347796 TTATTACTTATTATTATTT-TATATAT-TATTA
1 TTATTACTTATT-TTATTTATATATATATATTA
347827 TTACTTA-TTA-TTT-TTTATATATATATATTA
1 TTA-TTACTTATTTTATTTATATATATATATTA
** *
347857 TTATTTTTTATTTTATTTATTTAT-TATATT
1 TTATTACTTATTTTATTTATATATATATATT
347887 CAAGAATTAA
Statistics
Matches: 52, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
28 3 0.06
29 11 0.21
30 12 0.23
31 15 0.29
32 11 0.21
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (32 bp):
TTATTACTTATTTTATTTATATATATATATTA
Found at i:347883 original size:7 final size:7
Alignment explanation
Indices: 347795--347883 Score: 63
Period size: 7 Copynumber: 12.1 Consensus size: 7
347785 TTTCAAATTT
347795 TTTATTA
1 TTTATTA
*
347802 CTTATTA
1 TTTATTA
*
347809 TTATTTTA
1 TT-TATTA
*
347817 TATATTA
1 TTTATTA
347824 -TTATTA
1 TTTATTA
*
347830 CTTATTA
1 TTTATTA
*
347837 TTTTTTA
1 TTTATTA
*
347844 TATATATA
1 TTTAT-TA
347852 TATTATTA
1 T-TTATTA
*
347860 TTTTTTA
1 TTTATTA
347867 TTTTATTTA
1 -TTTA-TTA
347876 TTTATTA
1 TTTATTA
347883 T
1 T
347884 ATTCAAGAAT
Statistics
Matches: 63, Mismatches: 13, Indels: 12
0.72 0.15 0.14
Matches are distributed among these distances:
6 5 0.08
7 34 0.54
8 18 0.29
9 6 0.10
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (7 bp):
TTTATTA
Found at i:349502 original size:14 final size:14
Alignment explanation
Indices: 349464--349517 Score: 63
Period size: 14 Copynumber: 3.8 Consensus size: 14
349454 ATTTTAAATA
*
349464 ATTTACATTTACAT
1 ATTTACATTTGCAT
*
349478 TTTTACATTTGCAT
1 ATTTACATTTGCAT
349492 ATTTACATTTGGCAT
1 ATTTACATTT-GCAT
* *
349507 CTTTGCATTTG
1 ATTTACATTTG
349518 TATTGCACAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
14 22 0.65
15 12 0.35
ACGTcount: A:0.24, C:0.15, G:0.09, T:0.52
Consensus pattern (14 bp):
ATTTACATTTGCAT
Found at i:352692 original size:6 final size:6
Alignment explanation
Indices: 352667--352712 Score: 56
Period size: 6 Copynumber: 7.3 Consensus size: 6
352657 CTCATCCAGC
* *
352667 AAAGAA AGAAGAA GAAGAA AAAGAA AAAAAA AAAGAA AAAGGAA AA
1 AAAGAA A-AAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAA-GAA AA
352713 TCGAATAAAG
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
6 24 0.71
7 10 0.29
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:355072 original size:83 final size:83
Alignment explanation
Indices: 354933--355196 Score: 442
Period size: 83 Copynumber: 3.2 Consensus size: 83
354923 AATGGAACAA
354933 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACC
1 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACC
354998 AATCATTGAATTTGGAAG
66 AATCATTGAATTTGGAAG
355016 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGC-AAACC
1 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACC
*
355080 AATCATTGAATTTAGAAG
66 AATCATTGAATTTGGAAG
* * * * *
355098 ATGAATTTGTTCATAACATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGG-TTGGACAGAAC
1 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-CAAAAC
355162 CAATCATTGAATTTGGAAG
65 CAATCATTGAATTTGGAAG
*
355181 ATGAATTTGCTCATAG
1 ATGAATGTGCTCATAG
355197 TAGAAATAAA
Statistics
Matches: 170, Mismatches: 9, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
81 4 0.02
82 72 0.42
83 94 0.55
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.37
Consensus pattern (83 bp):
ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACC
AATCATTGAATTTGGAAG
Found at i:357919 original size:22 final size:22
Alignment explanation
Indices: 357890--357944 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
357880 ATCTACACTC
*
357890 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGACAGATTCTCTT
*
357912 TTTAAAGATGACAGATTCTCTT
1 TTCAAAGATGACAGATTCTCTT
357934 TTCAAAGATGA
1 TTCAAAGATGA
357945 AAACTTTATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.38
Consensus pattern (22 bp):
TTCAAAGATGACAGATTCTCTT
Found at i:358544 original size:113 final size:113
Alignment explanation
Indices: 358346--358781 Score: 608
Period size: 113 Copynumber: 3.9 Consensus size: 113
358336 AGCAAAGATA
* **
358346 TGAATTCATCATTCGATGATTCAGCATTACCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAA
1 TGAATTCATCATTCGATGATTCAGCATTACCAGATAAAGTTCATAATGAGAAGAACTCATCTGAA
358411 GAAAAAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCT
66 GAAAAAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCT
* ** *
358459 TGAATTCATCATTCGATGATTCAGCATTACCAGTTCGAGTTCATAATGAGAAGAACTCATTTGAA
1 TGAATTCATCATTCGATGATTCAGCATTACCAGATAAAGTTCATAATGAGAAGAACTCATCTGAA
358524 GAAAAAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCT
66 GAAAAAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCT
* * *
358572 TGAATTCATCATTCGATGATTCAGTATTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAA
1 TGAATTCATCATTCGATGATTCAGCATTACCAGATAAAGTTCATAATGAGAAGAACTCATCTGAA
** * * *
358637 GAAGGAAGAAGAAATTCATAATGAGAAGAATTTTTTCAACCTTTT-GCT
66 GAAAAAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA-CTTTTCGCT
** * * * * *
358685 CAAATCCATC-TCTTGATGGA-TCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTG
1 TGAATTCATCAT-TCGAT-GATTCAGCATTACCAGATAAAGTTCATAATGAGAAGAACTCATCTG
**
358748 AAGAATGAAGAAGAAGTTCATAATGAGAAGAACT
64 AAGAAAAAAGAAGAAGTTCATAATGAGAAGAACT
358782 CATCTGAAGA
Statistics
Matches: 297, Mismatches: 23, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
112 1 0.00
113 289 0.97
114 7 0.02
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (113 bp):
TGAATTCATCATTCGATGATTCAGCATTACCAGATAAAGTTCATAATGAGAAGAACTCATCTGAA
GAAAAAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCT
Found at i:358776 original size:40 final size:40
Alignment explanation
Indices: 358721--358821 Score: 184
Period size: 40 Copynumber: 2.5 Consensus size: 40
358711 TTTCCAGAGA
**
358721 AAGTTCATAATGAGAAGAACTCATCTGAAGAATGAAGAAG
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAAAAAGAAG
358761 AAGTTCATAATGAGAAGAACTCATCTGAAGAAAAAAGAAG
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAAAAAGAAG
358801 AAGTTCATAATGAGAAGAACT
1 AAGTTCATAATGAGAAGAACT
358822 TGTTCAACTT
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 59 1.00
ACGTcount: A:0.50, C:0.10, G:0.21, T:0.20
Consensus pattern (40 bp):
AAGTTCATAATGAGAAGAACTCATCTGAAGAAAAAAGAAG
Found at i:358799 original size:153 final size:153
Alignment explanation
Indices: 358603--358932 Score: 479
Period size: 153 Copynumber: 2.2 Consensus size: 153
358593 CAGTATTTCC
* ** *
358603 AGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAAT
1 AGAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAAAAAGAAGAAATTCATAATGAGAAGAAC
* * *
358668 TTTTTCAACCTTTT-GCTCAAATCCATC-TCTTGATGGA-TCAGCT-TTTCCAGAGAAAGTTCAT
66 TTGTTCAA-CTTTTCGCTCAAATCCATCAT-TCGAT-GATTCAG-TATTTCCAGAAAAAGTTCAT
*
358729 AATGAGAAGAACTCATCTGAAGAATGA
127 AATGAGAAGAACTCATCTGAAGAAGGA
*
358756 AGAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAAAAAGAAGAAGTTCATAATGAGAAGAAC
1 AGAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAAAAAGAAGAAATTCATAATGAGAAGAAC
** *
358821 TTGTTCAACTTTTCGCTTGAATTCATCATTCGATGATTCAGTATTTCCAGAAAAAGTTCATAATG
66 TTGTTCAACTTTTCGCTCAAATCCATCATTCGATGATTCAGTATTTCCAGAAAAAGTTCATAATG
358886 AGAAGAACTCATCTGAAGAAGGA
131 AGAAGAACTCATCTGAAGAAGGA
*
358909 AGAAGAAATTCATAATGAGAAGAA
1 AGAAGAAGTTCATAATGAGAAGAA
358933 TTTGTTCACC
Statistics
Matches: 160, Mismatches: 13, Indels: 8
0.88 0.07 0.04
Matches are distributed among these distances:
152 8 0.05
153 151 0.94
154 1 0.01
ACGTcount: A:0.42, C:0.13, G:0.19, T:0.26
Consensus pattern (153 bp):
AGAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAAAAAGAAGAAATTCATAATGAGAAGAAC
TTGTTCAACTTTTCGCTCAAATCCATCATTCGATGATTCAGTATTTCCAGAAAAAGTTCATAATG
AGAAGAACTCATCTGAAGAAGGA
Found at i:358859 original size:266 final size:264
Alignment explanation
Indices: 358496--359043 Score: 1033
Period size: 266 Copynumber: 2.1 Consensus size: 264
358486 TACCAGTTCG
*
358496 AGTTCATAATGAGAAGAACTCATTTGAAGAAAAAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAAAAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
358561 AACTTTTCGCTTGAATTCATCATTCGATGATTCAGTATTTCCAGAAAAAGTTCATAATGAGAAGA
66 AACTTTTCGCTTGAATTCATCATTCGATGATTCAGTATTTCCAGAAAAAGTTCATAATGAGAAGA
* *
358626 ACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTTTTCAACCTTTTGCTCAAATC
131 ACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC-ACCTTTTGCTCAAATA
* *
358691 CATCTCTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAATGA
195 CATCACTTGATGGATCAGCTTTTCCAGA-AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
358756 AGAAGA
259 AGAAGA
358762 AGTTCATAATGAGAAGAACTCATCTGAAGAAAAAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAAAAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
358827 AACTTTTCGCTTGAATTCATCATTCGATGATTCAGTATTTCCAGAAAAAGTTCATAATGAGAAGA
66 AACTTTTCGCTTGAATTCATCATTCGATGATTCAGTATTTCCAGAAAAAGTTCATAATGAGAAGA
358892 ACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCACCTTTTGCTCAAATAC
131 ACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCACCTTTTGCTCAAATAC
358957 ATCACTTGATGGATCAGCTTTTCCAGAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAG
196 ATCACTTGATGGATCAGCTTTTCCAGAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAG
359022 AAGA
261 AAGA
359026 AGTTCATAATGAGAAGAA
1 AGTTCATAATGAGAAGAA
359044 TTTGTTCAAC
Statistics
Matches: 277, Mismatches: 5, Indels: 2
0.98 0.02 0.01
Matches are distributed among these distances:
264 59 0.21
265 42 0.15
266 176 0.64
ACGTcount: A:0.41, C:0.14, G:0.18, T:0.27
Consensus pattern (264 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAAAAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
AACTTTTCGCTTGAATTCATCATTCGATGATTCAGTATTTCCAGAAAAAGTTCATAATGAGAAGA
ACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCACCTTTTGCTCAAATAC
ATCACTTGATGGATCAGCTTTTCCAGAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAG
AAGA
Found at i:358878 original size:113 final size:112
Alignment explanation
Indices: 358756--359176 Score: 589
Period size: 113 Copynumber: 3.8 Consensus size: 112
358746 TGAAGAATGA
* ** *
358756 AGAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAAAAAGAAGAAGTTCATAATGAGAAGAAC
1 AGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAAC
358821 TTGTTCAACTTTTCGCTTGAATTCATCA-TTCGAT-GATTCAGTATTTCC
66 TTGTTCAACTTTT-GCTTGAATTCATCACTT-GATGGATTCAGT-TTTCC
*
358869 AGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAAT
1 AGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAAC
* ** *
358934 TTGTTCACCTTTTGCTCAAATACATCACTTGATGGA-TCAGCTTTTCC
66 TTGTTCAACTTTTGCTTGAATTCATCACTTGATGGATTCAG-TTTTCC
* *
358981 AG-AAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAT
1 AGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAAC
* * *
359045 TTGTTCAACCTTTTGCCTGAATTCATCACTTGATGGATTAACTTTTCC
66 TTGTTCAA-CTTTTGCTTGAATTCATCACTTGATGGATTCAGTTTTCC
* * * *
359093 AGAGAAAGTTCATAATGAGAAAAACTCATATGAAGAAGGAAGAAGAAATTCATAATGAGAAGAGC
1 AGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAAC
* *
359158 TTGTTCAACCTTTGTTTGA
66 TTGTTCAACTTTTGCTTGA
359177 TGCTATCACA
Statistics
Matches: 276, Mismatches: 26, Indels: 13
0.88 0.08 0.04
Matches are distributed among these distances:
111 68 0.25
112 65 0.24
113 143 0.52
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.28
Consensus pattern (112 bp):
AGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAAC
TTGTTCAACTTTTGCTTGAATTCATCACTTGATGGATTCAGTTTTCC
Found at i:359146 original size:24 final size:23
Alignment explanation
Indices: 359110--359154 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
359100 GTTCATAATG
359110 AGAAAAACTCAT-ATGAAGAAGGA
1 AGAAAAACTCATAATG-AGAAGGA
*
359133 AGAAGAAATTCATAATGAGAAG
1 AGAA-AAACTCATAATGAGAAG
359155 AGCTTGTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 4 0.21
24 12 0.63
25 3 0.16
ACGTcount: A:0.56, C:0.07, G:0.22, T:0.16
Consensus pattern (23 bp):
AGAAAAACTCATAATGAGAAGGA
Found at i:359151 original size:224 final size:226
Alignment explanation
Indices: 358756--359170 Score: 669
Period size: 224 Copynumber: 1.8 Consensus size: 226
358746 TGAAGAATGA
358756 AGAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAAAAAGAAGAAGTTCATAATGAGAAGAAC
1 AGAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAAAAAGAAGAAGTTCATAATGAGAAGAAC
* * *
358821 TTGTTCAACTTTTCGCTTGAATTCATCATTCGATGATTCAGTATTTCCAGAAAAAGTTCATAATG
66 TTGTTCAACTTTTCGCCTGAATTCATCATTCGATGATTAACTATTTCCAGAAAAAGTTCATAATG
* * *
358886 AGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC-ACCTTTTGCT
131 AGAAAAACTCATATGAAGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTGCT
358950 CAAATACATCACTTGATGGATCAGCTTTTCC
196 CAAATACATCACTTGATGGATCAGCTTTTCC
** *
358981 AGAA-AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAT
1 AGAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAAAAAGAAGAAGTTCATAATGAGAAGAAC
*
359045 TTGTTCAACCTTTT-GCCTGAATTCATCACTT-GATGGATTAACT-TTTCCAGAGAAAGTTCATA
66 TTGTTCAA-CTTTTCGCCTGAATTCATCA-TTCGAT-GATTAACTATTTCCAGAAAAAGTTCATA
*
359107 ATGAGAAAAACTCATATGAAGAAGGAAGAAGAAATTCATAATGAGAAGAGCTTGTTCAACCTTT
128 ATGAGAAAAACTCATATGAAGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTT
359171 GTTTGATGCT
Statistics
Matches: 175, Mismatches: 11, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
224 152 0.87
225 23 0.13
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.28
Consensus pattern (226 bp):
AGAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAAAAAGAAGAAGTTCATAATGAGAAGAAC
TTGTTCAACTTTTCGCCTGAATTCATCATTCGATGATTAACTATTTCCAGAAAAAGTTCATAATG
AGAAAAACTCATATGAAGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTGCT
CAAATACATCACTTGATGGATCAGCTTTTCC
Found at i:359284 original size:308 final size:307
Alignment explanation
Indices: 358909--359474 Score: 933
Period size: 308 Copynumber: 1.8 Consensus size: 307
358899 TGAAGAAGGA
*
358909 AGAAGAAATTCATAATGAGAAGAATTTGTTCACCTTTTGCTCAAATACATCACTTGATGGATCAG
1 AGAAGAAATTCATAATGAGAAGAACTTGTTCACCTTTTGCTCAAATACATCACTTGATGGATCAG
*
358974 CTTTTCCAG-AAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
66 CTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGA
* * *
359038 GAAGAATTTGTTCAACCTTTTGC-CTGAATTCATCACTT-GATGGATTAACTTTTCCAGAGAAAG
131 GAAGAATTTGTTCAACCTTTTGCTC-AAATCCATCA-TTCGATGGA-TAACATTTCCAGAGAAAG
*
359101 TTCATAATGAGAAAAACTCATATGAAGAAGGAAGAAGAAATTCATAATGAGAAGAGCTTGTTCAA
193 TTCATAATGAGAAAAACTCATATGAAGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAA
359166 CCTTTGTTTGATGCTATCACAGAAGGAAATAGATCAGTATCAGCATTTCC
258 CCTTTGTTTGATGCTATCACAGAAGGAAATAGATCAGTATCAGCATTTCC
* * *
359216 AGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTCAAATCCATCA-TCTGATGGATC
1 AGAAGAAATTCATAATGAGAAGAACTTGTTC-ACCTTTTGCTCAAATACATCACT-TGATGGATC
359280 AGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAAT
64 AGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAAT
**
359345 GAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTCGATGGATCGCATTTCCAGAGAAAGT
129 GAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTCGATGGATAACATTTCCAGAGAAAGT
* * *
359410 TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAC
194 TCATAATGAGAAAAACTCATATGAAGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAAC
359475 TTTTTGCTTA
Statistics
Matches: 240, Mismatches: 14, Indels: 9
0.91 0.05 0.03
Matches are distributed among these distances:
307 29 0.12
308 119 0.50
309 91 0.38
310 1 0.00
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (307 bp):
AGAAGAAATTCATAATGAGAAGAACTTGTTCACCTTTTGCTCAAATACATCACTTGATGGATCAG
CTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGA
GAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTCGATGGATAACATTTCCAGAGAAAGTTC
ATAATGAGAAAAACTCATATGAAGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCT
TTGTTTGATGCTATCACAGAAGGAAATAGATCAGTATCAGCATTTCC
Found at i:359453 original size:112 final size:113
Alignment explanation
Indices: 359216--360050 Score: 1049
Period size: 112 Copynumber: 7.3 Consensus size: 113
359206 CAGCATTTCC
* * *
359216 AGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTCAAATCCATCA-TCTGATGGATC
1 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCATTC-GATGGATC
* * *
359280 AGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
65 AACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* * * *
359329 AGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTCGATGGATC-
1 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCATTCGATGGATCA
*
359393 GCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
66 ACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* *
359441 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCATTTGATGGATCA
1 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCATTCGATGGATCA
* * ** * *
359506 TCATTACCAGTTAGAGTTCATAATGAGAAGAACTCATTTGAAGAA-GA
66 ACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* * *
359553 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAA-CTTTTCACTTGAATTCATCATTCGATGGATC
1 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTT-GCTTAAATTCATCATTCGATGGATC
* * ** * *
359617 AGCATTGCCAG-GTCGAGTTCATAATGAGAAGAACTTATCTGAAGAA-TA
65 AACATTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* *
359665 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAA-CTTTTCACTTGAATTCATCATTCGATGGATC
1 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTT-GCTTAAATTCATCATTCGATGGATC
* *
359729 AACTTTTCCAGAGAAAGTTCATAATGAGAATAACTCATCTGAAGAAGGA
65 AACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
*
359778 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCATTCGATGGATCA
1 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCATTCGATGGATCA
* * *
359843 ACATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGA
66 ACATTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* * ** * * **
359891 AGAAGAAGTTCATAATAAGAAGAACTTGTTAAACCTTTTGC-TCGACTCTATCCCAGAAGGATAA
1 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTAAATTC-AT--C---A--TTCG
* *
359955 ATCAGCATCAACATTTTCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
58 AT--GGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
*
360013 AGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTT
1 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTT
360051 GTTTGATTCT
Statistics
Matches: 643, Mismatches: 60, Indels: 29
0.88 0.08 0.04
Matches are distributed among these distances:
111 4 0.01
112 305 0.47
113 239 0.37
114 7 0.01
115 1 0.00
118 1 0.00
120 3 0.00
122 82 0.13
123 1 0.00
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (113 bp):
AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTAAATTCATCATTCGATGGATCA
ACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
Found at i:359575 original size:420 final size:420
Alignment explanation
Indices: 358796--359586 Score: 1263
Period size: 420 Copynumber: 1.9 Consensus size: 420
358786 TGAAGAAAAA
** *
358796 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATTCATCATTCGATGATTCA
1 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTCAAATCCATCATTCGATGATTCA
358861 GTATTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATG
66 GTATTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATG
*
358926 AGAAGAATTTGTTCACCTTTTGCTCAAATACATCACTTGATGGATCAGCTTTTCCAGAAAAGTTC
131 AGAAGAATTTGTTCACCTTTTGCTCAAATACATCACTTGATGGATCAGCATTTCCAGAAAAGTTC
*
358991 ATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCT
196 ATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCT
* * * *
359056 TTTGCCTGAATTCATCACTTGATGGATTAACTTTTCCAGAGAAAGTTCATAATGAGAAAAACTCA
261 TTTGCCTAAATTCATCACTTGATGGATCAACATTACCAGAGAAAGTTCATAATGAGAAAAACTCA
*
359121 TATGAAGAAGGAAGAAGAAATTCATAATGAGAAGAGCTTGTTCAACCTTTGTTTGATGCTATCAC
326 TATGAAGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTGTTTGATGCTATCAC
359186 AGAAGGAAATAGATCAGTATCAGCATTTCC
391 AGAAGGAAATAGATCAGTATCAGCATTTCC
*
359216 AGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTT-GCTCAAATCCATCA-TCTGATGGA-
1 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAA-CTTTTCGCTCAAATCCATCATTC-GAT-GAT
359278 TCAGCT-TTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCAT
63 TCAG-TATTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCAT
*
359342 AATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCA-TTCGATGGATC-GCATTTCCAGAG
127 AATGAGAAGAATTTGTTC-ACCTTTTGCTCAAATACATCACTT-GATGGATCAGCATTTCCAGA-
359405 AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
189 AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
* * * * ** *
359470 TCAACTTTTTGCTTAAATTCATCATTTGATGGATCATCATTACCAGTTAGAGTTCATAATGAGAA
254 TCAACCTTTTGCCTAAATTCATCACTTGATGGATCAACATTACCAGAGAAAGTTCATAATGAGAA
* * * *
359535 GAACTCATTTGAAGAA-GAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAAC
319 AAACTCATATGAAGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAAC
359587 TTTTCACTTG
Statistics
Matches: 341, Mismatches: 23, Indels: 14
0.90 0.06 0.04
Matches are distributed among these distances:
419 2 0.01
420 171 0.50
421 168 0.49
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.29
Consensus pattern (420 bp):
AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTCAAATCCATCATTCGATGATTCA
GTATTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATG
AGAAGAATTTGTTCACCTTTTGCTCAAATACATCACTTGATGGATCAGCATTTCCAGAAAAGTTC
ATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCT
TTTGCCTAAATTCATCACTTGATGGATCAACATTACCAGAGAAAGTTCATAATGAGAAAAACTCA
TATGAAGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTGTTTGATGCTATCAC
AGAAGGAAATAGATCAGTATCAGCATTTCC
Found at i:359695 original size:20 final size:20
Alignment explanation
Indices: 359633--359696 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 20
359623 GCCAGGTCGA
359633 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
* * * *
359653 ATCTGAAGAATAAGAAGAA---
1 GT-T-CATAATGAGAAGAACTT
359672 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
359692 GTTCA
1 GTTCA
359697 ACTTTTCACT
Statistics
Matches: 31, Mismatches: 8, Indels: 10
0.63 0.16 0.20
Matches are distributed among these distances:
17 11 0.35
18 1 0.03
19 1 0.03
20 6 0.19
21 1 0.03
22 11 0.35
ACGTcount: A:0.44, C:0.09, G:0.20, T:0.27
Consensus pattern (20 bp):
GTTCATAATGAGAAGAACTT
Found at i:359831 original size:337 final size:338
Alignment explanation
Indices: 359216--360050 Score: 1106
Period size: 337 Copynumber: 2.4 Consensus size: 338
359206 CAGCATTTCC
* *
359216 AGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTCAAATCCATCATCTGATGGATCA
1 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTACTCAAATCCATCATCTGATGGATCA
* *
359281 GCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATG
66 GCATTGCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATG
* * *
359346 AGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTCGATGGATCGCATTTCCAGAGAAAGTT
131 AGAAGAACTTGTTCAACCTTTTACTCAAATCCATCATTCGATGGATCACATTTCCAGAGAAAGTT
*
359411 CATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACT
196 CATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACC
* * *
359476 TTTTGCTTAAATTCATCATTTGATGGATCATCATTACCAGTTAGAGTTCATAATGAGAAGAACTC
261 TTTTGCTTAAATTCATCATTCGATGGATCAACATTACCAGGTAGAGTTCATAATGAGAAGAACTC
*
359541 ATTTGAAG-AAGA
326 ATCTGAAGAAAGA
* ** *
359553 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAA-CTTTTCACTTGAATTCATCAT-TCGATGGAT
1 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTT-ACTCAAATCCATCATCT-GATGGAT
**** * * *
359616 CAGCATTGCCAGGTCGAGTTCATAATGAGAAGAACTTATCTGAAGAA-TAAGAAGAAGTTCATAA
64 CAGCATTGCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAA
** * *
359680 TGAGAAGAACTTGTTCAA-CTTTTCACTTGAATTCATCATTCGATGGATCAACTTTTCCAGAGAA
129 TGAGAAGAACTTGTTCAACCTTTT-ACTCAAATCCATCATTCGATGGATC-ACATTTCCAGAGAA
*
359744 AGTTCATAATGAGAATAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
192 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
* *
359809 AACCTTTTGCTTGAATTCATCATTCGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGA
257 AACCTTTTGCTTAAATTCATCATTCGATGGATCAACATTACCAGGTAGAGTTCATAATGAGAAGA
359874 ACTCATCTGAAGAAAGA
322 ACTCATCTGAAGAAAGA
* * * * * * * * *
359891 AGAAGAAGTTCATAATAAGAAGAACTTGTTAAACCTTTTGCTCGACTCTATC-CCAGAAGGATAA
1 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTACTCAAATCCATCATCTGATGG----
** *
359955 ATCAGCATCAACATTTTCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAA
62 ATCAG------CATTGCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAA
* *
360020 GTTCATAATGAGAAGAGCTTGTTCAACCTTT
121 ATTCATAATGAGAAGAACTTGTTCAACCTTT
360051 GTTTGATTCT
Statistics
Matches: 429, Mismatches: 50, Indels: 26
0.85 0.10 0.05
Matches are distributed among these distances:
335 5 0.01
336 59 0.14
337 239 0.56
338 42 0.10
339 5 0.01
341 5 0.01
347 37 0.09
348 33 0.08
349 4 0.01
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (338 bp):
AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTACTCAAATCCATCATCTGATGGATCA
GCATTGCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATG
AGAAGAACTTGTTCAACCTTTTACTCAAATCCATCATTCGATGGATCACATTTCCAGAGAAAGTT
CATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACC
TTTTGCTTAAATTCATCATTCGATGGATCAACATTACCAGGTAGAGTTCATAATGAGAAGAACTC
ATCTGAAGAAAGA
Found at i:360116 original size:122 final size:122
Alignment explanation
Indices: 359839--360137 Score: 404
Period size: 122 Copynumber: 2.5 Consensus size: 122
359829 CATTCGATGG
* ** * *
359839 ATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCAT
1 ATCAACATTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
*
359904 AATAAGAAGAACTTGTTAAACCTTTTGCTCGACTCTATCCCAGAAGGATAAATCAGC
66 AATAAGAAGAACTTGTTAAACCTTTTGCTCGACTCTATCACAGAAGGATAAATCAGC
* *
359961 ATCAACATTTTCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
1 ATCAACATTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
* * * * * * * *
360026 AATGAGAAGAGCTTGTTCAACC-TTTGTTTGATTCTATCACAGAATGAGATAGATCAGT
66 AATAAGAAGAACTTGTTAAACCTTTTGCTCGACTCTATCACAGAA-G-GATAAATCAGC
* *
360084 ATCAACATTTCCATAAAAAGTTCAT-ATAAGAAGAACTCATCTGAAGAAGGAAGA
1 ATCAACATTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGA
360138 GAATTGTTCA
Statistics
Matches: 156, Mismatches: 19, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
121 18 0.12
122 107 0.69
123 31 0.20
ACGTcount: A:0.41, C:0.15, G:0.19, T:0.25
Consensus pattern (122 bp):
ATCAACATTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
AATAAGAAGAACTTGTTAAACCTTTTGCTCGACTCTATCACAGAAGGATAAATCAGC
Found at i:366189 original size:16 final size:16
Alignment explanation
Indices: 366168--366198 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
366158 AGGGTGCTAA
*
366168 AATATTAGACCCTATG
1 AATATTAAACCCTATG
366184 AATATTAAACCCTAT
1 AATATTAAACCCTAT
366199 TAAAGATAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.19, G:0.06, T:0.32
Consensus pattern (16 bp):
AATATTAAACCCTATG
Found at i:366343 original size:29 final size:30
Alignment explanation
Indices: 366298--366369 Score: 110
Period size: 31 Copynumber: 2.4 Consensus size: 30
366288 TTTTTTCATT
*
366298 TAAGTACCTAAAGTATC-TTTTGGTCAAAA
1 TAAGTACCTAAACTATCTTTTTGGTCAAAA
366327 TAAGTACCTAAACTATCTTTTTTGGTCAAAA
1 TAAGTACCTAAACTATC-TTTTTGGTCAAAA
*
366358 TAGGTACCTAAA
1 TAAGTACCTAAA
366370 GTATTCAATT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
29 16 0.41
31 23 0.59
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (30 bp):
TAAGTACCTAAACTATCTTTTTGGTCAAAA
Found at i:370683 original size:29 final size:30
Alignment explanation
Indices: 370621--370727 Score: 94
Period size: 29 Copynumber: 3.6 Consensus size: 30
370611 CTTATATTAT
* * *
370621 ATAAGTACCTAAAGTATATTATTT-TTC-AT
1 ATAAGTACCTAAAGTATCTT-TTTGGTCAAA
* *
370650 TTAAGTACCTAAAGTGTC-TTTTGGTCAAA
1 ATAAGTACCTAAAGTATCTTTTTGGTCAAA
* *
370679 ATAAGTATCTAAACTATCTTTTTTTGGTCAAA
1 ATAAGTACCTAAAGTATC--TTTTTGGTCAAA
*
370711 ATAGGTACCTAAAGTAT
1 ATAAGTACCTAAAGTAT
370728 TCAATTTTTC
Statistics
Matches: 61, Mismatches: 12, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
27 3 0.05
28 3 0.05
29 30 0.49
32 25 0.41
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.40
Consensus pattern (30 bp):
ATAAGTACCTAAAGTATCTTTTTGGTCAAA
Found at i:370840 original size:27 final size:27
Alignment explanation
Indices: 370808--370901 Score: 89
Period size: 27 Copynumber: 3.3 Consensus size: 27
370798 GAAAAAATTG
*
370808 AATATTCAGGTACTTATTTTGATAAAA
1 AATATTTAGGTACTTATTTTGATAAAA
* * *
370835 AATATTTAGGCACCTATTTTGACCAAAA
1 AATATTTAGGTACTTATTTTGA-TAAAA
* *
370863 AGATAAGTTTAGATACTTATTTTGATCAAA
1 A-AT-A-TTTAGGTACTTATTTTGATAAAA
370893 AATACTTTA
1 AATA-TTTA
370902 AGTAATTCAA
Statistics
Matches: 53, Mismatches: 10, Indels: 7
0.76 0.14 0.10
Matches are distributed among these distances:
27 19 0.36
28 10 0.19
29 4 0.08
30 5 0.09
31 15 0.28
ACGTcount: A:0.40, C:0.11, G:0.11, T:0.38
Consensus pattern (27 bp):
AATATTTAGGTACTTATTTTGATAAAA
Found at i:374157 original size:17 final size:17
Alignment explanation
Indices: 374123--374174 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
374113 ACCGGACAAA
* *
374123 TTTATTATTTTAGAGAG
1 TTTATTAATTTACAGAG
*
374140 TTTATTAATTTACCGAG
1 TTTATTAATTTACAGAG
*
374157 --TATTAATTTAAAGAG
1 TTTATTAATTTACAGAG
374172 TTT
1 TTT
374175 CTACTGTAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
15 13 0.46
17 15 0.54
ACGTcount: A:0.33, C:0.04, G:0.13, T:0.50
Consensus pattern (17 bp):
TTTATTAATTTACAGAG
Found at i:374683 original size:2 final size:2
Alignment explanation
Indices: 374676--374734 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
374666 ATCTATTTGT
374676 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
374718 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
374735 CCCCTATGAA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:376216 original size:84 final size:84
Alignment explanation
Indices: 376094--376263 Score: 331
Period size: 84 Copynumber: 2.0 Consensus size: 84
376084 AATATGCTAT
*
376094 ATCGTCACTTTCGACACATGACACGTGTAGTGTCTGTTGAAAAGATTGGTTAATTCACACATGCA
1 ATCGTCACTTTCGACACATGACACGTGTAGTGTATGTTGAAAAGATTGGTTAATTCACACATGCA
376159 CGGAAAGTGCATGAATATA
66 CGGAAAGTGCATGAATATA
376178 ATCGTCACTTTCGACACATGACACGTGTAGTGTATGTTGAAAAGATTGGTTAATTCACACATGCA
1 ATCGTCACTTTCGACACATGACACGTGTAGTGTATGTTGAAAAGATTGGTTAATTCACACATGCA
376243 CGGAAAGTGCATGAATATA
66 CGGAAAGTGCATGAATATA
376262 AT
1 AT
376264 GGGTCAAAAA
Statistics
Matches: 85, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
84 85 1.00
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (84 bp):
ATCGTCACTTTCGACACATGACACGTGTAGTGTATGTTGAAAAGATTGGTTAATTCACACATGCA
CGGAAAGTGCATGAATATA
Found at i:377032 original size:21 final size:21
Alignment explanation
Indices: 377008--377068 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
376998 CCAACTTTGA
377008 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
377029 AAAT-G-TTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
377043 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
377064 AAATG
1 AAATG
377069 TTTCTTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 4 0.13
16 4 0.13
19 4 0.13
20 4 0.13
21 10 0.32
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.43
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:377041 original size:35 final size:35
Alignment explanation
Indices: 377002--377106 Score: 176
Period size: 35 Copynumber: 3.0 Consensus size: 35
376992 TGGCAACCAA
377002 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
377037 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
**
377072 CTTTGAAAAATATTTTTCAAAGTTTGGTAAA-GTTT
1 CTTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
377107 GGTAGATAAT
Statistics
Matches: 67, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
35 44 0.66
36 23 0.34
ACGTcount: A:0.30, C:0.06, G:0.18, T:0.46
Consensus pattern (35 bp):
CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:381664 original size:21 final size:21
Alignment explanation
Indices: 381640--381700 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
381630 CCAACTTTGA
381640 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
381661 AAAT-G-TTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
381675 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
381696 AAATG
1 AAATG
381701 TTTCTTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 4 0.13
16 4 0.13
19 4 0.13
20 4 0.13
21 10 0.32
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.43
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:381721 original size:36 final size:35
Alignment explanation
Indices: 381634--381738 Score: 185
Period size: 35 Copynumber: 3.0 Consensus size: 35
381624 TGGCAACCAA
381634 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
381669 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
*
381704 CTTTGAAAAATGTTTTTCAAAGTTTGGTAAA-GTTT
1 CTTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
381739 GGTAGATGTT
Statistics
Matches: 68, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
35 44 0.65
36 24 0.35
ACGTcount: A:0.30, C:0.06, G:0.19, T:0.46
Consensus pattern (35 bp):
CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:385798 original size:19 final size:19
Alignment explanation
Indices: 385774--385811 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
385764 TTAAAATATA
385774 AAATATAATA-AATTATAAT
1 AAATAT-ATACAATTATAAT
*
385793 AAATATTTACAATTATAAT
1 AAATATATACAATTATAAT
385812 CATATATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 2 0.12
19 15 0.88
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (19 bp):
AAATATATACAATTATAAT
Found at i:387880 original size:36 final size:36
Alignment explanation
Indices: 387804--388055 Score: 391
Period size: 36 Copynumber: 7.0 Consensus size: 36
387794 ACACTAGAAC
*
387804 CGGAAGTGTCGATGCTT-CCTCCCGTTC-ACTTGAAT
1 CGGAAGTGCCGATGCTTCCCT-CCGTTCGACTTGAAT
* * * *
387839 CGGAAGTGCCGATGCTTTCTTTCGTTCGATTTGAAT
1 CGGAAGTGCCGATGCTTCCCTCCGTTCGACTTGAAT
* *
387875 CGGAAGTGCTGATGCTTCCCTCCGTTCGATTTGAAT
1 CGGAAGTGCCGATGCTTCCCTCCGTTCGACTTGAAT
387911 CGGAAGTGCCGATGCTTCCCTCCGTTCGACTTGAAT
1 CGGAAGTGCCGATGCTTCCCTCCGTTCGACTTGAAT
*
387947 CGGAAGTGCCGATGCTTCCCTCCGTTCGATTTGAAT
1 CGGAAGTGCCGATGCTTCCCTCCGTTCGACTTGAAT
*
387983 CGGAAGTGCCGATGCTTTCCTCCGTTCGACTTGAAT
1 CGGAAGTGCCGATGCTTCCCTCCGTTCGACTTGAAT
*
388019 CGGAAGTGCCGATGCTTACCTCCGTTCGACTTGAAT
1 CGGAAGTGCCGATGCTTCCCTCCGTTCGACTTGAAT
388055 C
1 C
388056 AATGCAAACT
Statistics
Matches: 201, Mismatches: 14, Indels: 3
0.92 0.06 0.01
Matches are distributed among these distances:
35 21 0.10
36 180 0.90
ACGTcount: A:0.17, C:0.27, G:0.25, T:0.31
Consensus pattern (36 bp):
CGGAAGTGCCGATGCTTCCCTCCGTTCGACTTGAAT
Found at i:396630 original size:2 final size:2
Alignment explanation
Indices: 396623--396674 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
396613 TGTAGCGAGA
396623 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
396665 AT AT AT AT AT
1 AT AT AT AT AT
396675 TAAAATAAGG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:398871 original size:19 final size:18
Alignment explanation
Indices: 398844--398881 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
398834 CAAAATTATA
398844 AAATTTTAA-AGAAAAAAT
1 AAATTTTAATA-AAAAAAT
398862 AAATTCTTAATAAAAAAAT
1 AAATT-TTAATAAAAAAAT
398881 A
1 A
398882 TAAAATATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.28
19 12 0.67
20 1 0.06
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.29
Consensus pattern (18 bp):
AAATTTTAATAAAAAAAT
Found at i:399411 original size:5 final size:5
Alignment explanation
Indices: 399401--399425 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
399391 GGGAGTTTGA
399401 TTTAT TTTAT TTTAT TTTAT TTTAT
1 TTTAT TTTAT TTTAT TTTAT TTTAT
399426 ATATTAGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTAT
Found at i:401345 original size:85 final size:85
Alignment explanation
Indices: 401202--401369 Score: 336
Period size: 85 Copynumber: 2.0 Consensus size: 85
401192 AATGTATGTA
401202 ACTCGAAATACACGACCAAATTATGAACGTGATCGTTAGGGTCGATAGTTAGGGTCGGAGTCCTA
1 ACTCGAAATACACGACCAAATTATGAACGTGATCGTTAGGGTCGATAGTTAGGGTCGGAGTCCTA
401267 TCGACCCTTGTCTTGGCCTT
66 TCGACCCTTGTCTTGGCCTT
401287 ACTCGAAATACACGACCAAATTATGAACGTGATCGTTAGGGTCGATAGTTAGGGTCGGAGTCCTA
1 ACTCGAAATACACGACCAAATTATGAACGTGATCGTTAGGGTCGATAGTTAGGGTCGGAGTCCTA
401352 TCGACCCTTGTCTTGGCC
66 TCGACCCTTGTCTTGGCC
401370 CTCGGATCTA
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
85 83 1.00
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.27
Consensus pattern (85 bp):
ACTCGAAATACACGACCAAATTATGAACGTGATCGTTAGGGTCGATAGTTAGGGTCGGAGTCCTA
TCGACCCTTGTCTTGGCCTT
Found at i:406640 original size:38 final size:38
Alignment explanation
Indices: 406589--406666 Score: 138
Period size: 38 Copynumber: 2.1 Consensus size: 38
406579 TTTTTGCCAA
406589 CACGCATTACCATTTCAGCAAAACCAATATCCGCCGCC
1 CACGCATTACCATTTCAGCAAAACCAATATCCGCCGCC
* *
406627 CACGCCTTACCATTTCAGCAAAACCACTATCCGCCGCC
1 CACGCATTACCATTTCAGCAAAACCAATATCCGCCGCC
406665 CA
1 CA
406667 ATGAGTGAAC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.29, C:0.42, G:0.10, T:0.18
Consensus pattern (38 bp):
CACGCATTACCATTTCAGCAAAACCAATATCCGCCGCC
Found at i:408357 original size:7 final size:7
Alignment explanation
Indices: 408347--408467 Score: 233
Period size: 7 Copynumber: 17.3 Consensus size: 7
408337 TACACTTCAC
*
408347 ACTTAAT
1 ACTTGAT
408354 ACTTGAT
1 ACTTGAT
408361 ACTTGAT
1 ACTTGAT
408368 ACTTGAT
1 ACTTGAT
408375 ACTTGAT
1 ACTTGAT
408382 ACTTGAT
1 ACTTGAT
408389 ACTTGAT
1 ACTTGAT
408396 ACTTGAT
1 ACTTGAT
408403 ACTTGAT
1 ACTTGAT
408410 ACTTGAT
1 ACTTGAT
408417 ACTTGAT
1 ACTTGAT
408424 ACTTGAT
1 ACTTGAT
408431 ACTTGAT
1 ACTTGAT
408438 ACTTGAT
1 ACTTGAT
408445 ACTTGAT
1 ACTTGAT
408452 ACTTGAT
1 ACTTGAT
408459 ACTTGAT
1 ACTTGAT
408466 AC
1 AC
408468 ATATGCTTAC
Statistics
Matches: 113, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
7 113 1.00
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.42
Consensus pattern (7 bp):
ACTTGAT
Found at i:419331 original size:37 final size:37
Alignment explanation
Indices: 419289--419363 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 37
419279 TTCATTAAAC
* *
419289 ATTTTTAT-ATTTTCAATTTTGTAAAAAAAATTATATA
1 ATTTTTATGAATTTAAATTTTGTAAAAAAAA-TATATA
* *
419326 ATTTTTATGAATTTAAATTTTTTAAAGAAAATATATA
1 ATTTTTATGAATTTAAATTTTGTAAAAAAAATATATA
419363 A
1 A
419364 ATATTTTTCA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
37 15 0.45
38 18 0.55
ACGTcount: A:0.45, C:0.01, G:0.04, T:0.49
Consensus pattern (37 bp):
ATTTTTATGAATTTAAATTTTGTAAAAAAAATATATA
Found at i:419850 original size:21 final size:21
Alignment explanation
Indices: 419824--419876 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
419814 ATTCTGACTA
419824 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
*
419845 TCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCAAAT
*
419866 TCGCAATGCGA
1 TCGCATTGCGA
419877 ATACGTAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:419910 original size:31 final size:31
Alignment explanation
Indices: 419872--419931 Score: 120
Period size: 31 Copynumber: 1.9 Consensus size: 31
419862 TAATTCGCAA
419872 TGCGAATACGTAAATCGCAATGCGAATTTAT
1 TGCGAATACGTAAATCGCAATGCGAATTTAT
419903 TGCGAATACGTAAATCGCAATGCGAATTT
1 TGCGAATACGTAAATCGCAATGCGAATTT
419932 GGAAAATCGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28
Consensus pattern (31 bp):
TGCGAATACGTAAATCGCAATGCGAATTTAT
Found at i:420008 original size:20 final size:20
Alignment explanation
Indices: 419866--419990 Score: 142
Period size: 20 Copynumber: 6.7 Consensus size: 20
419856 TTTTCCTAAT
419866 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
419886 TCGCAATGCGAAT---T---
1 TCGCAATGCGAATACGTAAA
*
419900 T---ATTGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
** *
419917 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAA-TACGTAAA
419938 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
419958 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
419978 TCGCAATGCGAAT
1 TCGCAATGCGAAT
419991 CTGACTATCG
Statistics
Matches: 87, Mismatches: 8, Indels: 20
0.76 0.07 0.17
Matches are distributed among these distances:
11 8 0.09
14 2 0.02
17 2 0.02
20 58 0.67
21 17 0.20
ACGTcount: A:0.38, C:0.18, G:0.21, T:0.23
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:420008 original size:40 final size:41
Alignment explanation
Indices: 419903--419990 Score: 142
Period size: 41 Copynumber: 2.2 Consensus size: 41
419893 GCGAATTTAT
**
419903 TGCGAATACGTAAATCGCAATGCGAATTTGGAAAATCGCAA
1 TGCGAATACGTAAATCGCAATGCGAATTACGAAAATCGCAA
*
419944 TGCGAATACGTAAATCGCAATGCGAA-TACGTAAATCGCAA
1 TGCGAATACGTAAATCGCAATGCGAATTACGAAAATCGCAA
419984 TGCGAAT
1 TGCGAAT
419991 CTGACTATCG
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
40 18 0.41
41 26 0.59
ACGTcount: A:0.39, C:0.18, G:0.22, T:0.22
Consensus pattern (41 bp):
TGCGAATACGTAAATCGCAATGCGAATTACGAAAATCGCAA
Found at i:420203 original size:22 final size:22
Alignment explanation
Indices: 420178--420253 Score: 98
Period size: 22 Copynumber: 3.5 Consensus size: 22
420168 CACTCTCTAA
* * *
420178 GACGACATCTGTCCCCATCTCT
1 GACGAAATCAGTCCCCATCTCC
420200 GACGAAATCAGTCCCCATCTCC
1 GACGAAATCAGTCCCCATCTCC
* *
420222 GACGATATCAGTCTCCATCTCC
1 GACGAAATCAGTCCCCATCTCC
*
420244 GGCGAAATCA
1 GACGAAATCA
420254 TTCACGGTCA
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.25, C:0.37, G:0.16, T:0.22
Consensus pattern (22 bp):
GACGAAATCAGTCCCCATCTCC
Found at i:420666 original size:20 final size:20
Alignment explanation
Indices: 420590--420659 Score: 106
Period size: 20 Copynumber: 3.5 Consensus size: 20
420580 CGATTCTGTC
*
420590 GTTGCGATTTTCA-TTTCGC
1 GTTGCGATTTTCATTTTCGT
**
420609 GTTGCGATAGTCATTTTCGT
1 GTTGCGATTTTCATTTTCGT
420629 GTTGCGATTTTCATTTTCGT
1 GTTGCGATTTTCATTTTCGT
420649 GTTGCGATTTT
1 GTTGCGATTTT
420660 AAGTTTCAGA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
19 11 0.24
20 34 0.76
ACGTcount: A:0.11, C:0.16, G:0.23, T:0.50
Consensus pattern (20 bp):
GTTGCGATTTTCATTTTCGT
Found at i:422563 original size:20 final size:20
Alignment explanation
Indices: 422538--422734 Score: 233
Period size: 20 Copynumber: 10.5 Consensus size: 20
422528 AGAATAGTTT
422538 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
* *
422558 ACTATCGCAACGCGAAAATT
1 ACTATCGCAATGCGAAAATG
*
422578 ACTATCGCAA--CG-AGA-G
1 ACTATCGCAATGCGAAAATG
422594 A--ATCGCAATGCG-AAATG
1 ACTATCGCAATGCGAAAATG
**
422611 AAAATCGCAA--C-AACAA--
1 ACTATCGCAATGCGAA-AATG
*
422627 A--ATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
422645 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
422665 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
422685 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
422705 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
422725 ACTATCGCAA
1 ACTATCGCAA
422735 CGAAAGAATC
Statistics
Matches: 157, Mismatches: 6, Indels: 28
0.82 0.03 0.15
Matches are distributed among these distances:
14 14 0.09
16 9 0.06
17 8 0.05
18 5 0.03
19 7 0.04
20 114 0.73
ACGTcount: A:0.42, C:0.22, G:0.19, T:0.17
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:422827 original size:20 final size:20
Alignment explanation
Indices: 422804--422856 Score: 106
Period size: 20 Copynumber: 2.6 Consensus size: 20
422794 ATTCGCATTG
422804 CGATAGTCATTTTTGCAAAA
1 CGATAGTCATTTTTGCAAAA
422824 CGATAGTCATTTTTGCAAAA
1 CGATAGTCATTTTTGCAAAA
422844 CGATAGTCATTTT
1 CGATAGTCATTTT
422857 CGCGTTGCGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (20 bp):
CGATAGTCATTTTTGCAAAA
Found at i:422867 original size:20 final size:20
Alignment explanation
Indices: 422785--422887 Score: 98
Period size: 20 Copynumber: 5.2 Consensus size: 20
422775 CTCTCGTTGT
**
422785 GATAGTCAAATTCGCATTGC
1 GATAGTCATTTTCGCATTGC
* ***
422805 GATAGTCATTTTTGCAAAAC
1 GATAGTCATTTTCGCATTGC
* ***
422825 GATAGTCATTTTTGCAAAAC
1 GATAGTCATTTTCGCATTGC
*
422845 GATAGTCATTTTCGCGTTGC
1 GATAGTCATTTTCGCATTGC
*
422865 GATAGTCATTTTCGCGTTGC
1 GATAGTCATTTTCGCATTGC
422885 GAT
1 GAT
422888 TTTAAGTTTC
Statistics
Matches: 72, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 72 1.00
ACGTcount: A:0.26, C:0.17, G:0.20, T:0.36
Consensus pattern (20 bp):
GATAGTCATTTTCGCATTGC
Found at i:422897 original size:20 final size:20
Alignment explanation
Indices: 422844--422897 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 20
422834 TTTTGCAAAA
* *
422844 CGATAGTCATTTTCGCGTTG
1 CGATAGTAAGTTTCGCGTTG
* *
422864 CGATAGTCATTTTCGCGTTG
1 CGATAGTAAGTTTCGCGTTG
**
422884 CGATTTTAAGTTTC
1 CGATAGTAAGTTTC
422898 AGATTCTATT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.17, C:0.19, G:0.22, T:0.43
Consensus pattern (20 bp):
CGATAGTAAGTTTCGCGTTG
Found at i:423733 original size:21 final size:21
Alignment explanation
Indices: 423707--423748 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
423697 CCAGAATGGG
423707 GGGAATCGGTACCCCTTCATA
1 GGGAATCGGTACCCCTTCATA
423728 GGGAATCGGTACCCCTTCATA
1 GGGAATCGGTACCCCTTCATA
423749 ATATTCAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.29, G:0.24, T:0.24
Consensus pattern (21 bp):
GGGAATCGGTACCCCTTCATA
Found at i:423894 original size:19 final size:19
Alignment explanation
Indices: 423853--423900 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
423843 GAGCCTCGGG
* *
423853 TTACTGTTCAAACAGTGAT
1 TTACTGTTCAAACAGTAAA
*
423872 TTACTGTTCAAATAGTAAA
1 TTACTGTTCAAACAGTAAA
*
423891 TTACTATTCA
1 TTACTGTTCA
423901 TAAAAACATT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (19 bp):
TTACTGTTCAAACAGTAAA
Found at i:424012 original size:30 final size:31
Alignment explanation
Indices: 423965--424055 Score: 168
Period size: 31 Copynumber: 3.0 Consensus size: 31
423955 AAATTTTGAA
423965 TAAATTCAATT-AAGTCCAAAAA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
423994 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
424025 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
424056 CCTTAAATTG
Statistics
Matches: 60, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
29 11 0.18
30 11 0.18
31 38 0.63
ACGTcount: A:0.43, C:0.18, G:0.07, T:0.33
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:424242 original size:23 final size:23
Alignment explanation
Indices: 424215--424262 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
424205 AAGCTCCCCC
424215 TTTTTCATTAAGAAATTGAATTT
1 TTTTTCATTAAGAAATTGAATTT
*
424238 TTTTTTATTAAGAAATTGAATTT
1 TTTTTCATTAAGAAATTGAATTT
424261 TT
1 TT
424263 CAAACTAAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.33, C:0.02, G:0.08, T:0.56
Consensus pattern (23 bp):
TTTTTCATTAAGAAATTGAATTT
Found at i:426287 original size:34 final size:32
Alignment explanation
Indices: 426234--426303 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
426224 CCTTACAAAC
*
426234 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
*
426266 TCCCTAGCTTTTACACGGGCTAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGCTAAACTAGAACCTT
426300 TCCC
1 TCCC
426304 CTTTACAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 22 0.65
ACGTcount: A:0.21, C:0.31, G:0.16, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
Found at i:426612 original size:21 final size:21
Alignment explanation
Indices: 426586--426627 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
426576 CCAGAATGGG
*
426586 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
426607 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
426628 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:426773 original size:19 final size:19
Alignment explanation
Indices: 426732--426779 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
426722 GAGCCTCGGG
* *
426732 TTACTGTTCAAACAGTGAT
1 TTACTGTTCAAACAGTAAA
*
426751 TTACTGTTCAAATAGTAAA
1 TTACTGTTCAAACAGTAAA
*
426770 TTACTATTCA
1 TTACTGTTCA
426780 TAAAAATATT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (19 bp):
TTACTGTTCAAACAGTAAA
Found at i:426891 original size:30 final size:31
Alignment explanation
Indices: 426844--426934 Score: 168
Period size: 31 Copynumber: 3.0 Consensus size: 31
426834 AAATTTTGAA
426844 TAAATTCAATT-AAGTCCAAAAA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
426873 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
426904 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
426935 CCTTAAATTG
Statistics
Matches: 60, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
29 11 0.18
30 11 0.18
31 38 0.63
ACGTcount: A:0.43, C:0.18, G:0.07, T:0.33
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:427296 original size:21 final size:21
Alignment explanation
Indices: 427223--427308 Score: 59
Period size: 21 Copynumber: 4.1 Consensus size: 21
427213 CCTGACTCAC
*
427223 CTGTCATCGTTCAAGAGGCCC
1 CTGTCATCGTTCAAGAGGCCA
* ** * *
427244 CTATCATCCCTCAAGA-GACT
1 CTGTCATCGTTCAAGAGGCCA
*
427264 CT-TCCCACCGTTCAAGAGGCCA
1 CTGT--CATCGTTCAAGAGGCCA
* *
427286 CTGTCATCGTTGAAGAGGTCA
1 CTGTCATCGTTCAAGAGGCCA
427307 CT
1 CT
427309 CCTAACATTC
Statistics
Matches: 48, Mismatches: 13, Indels: 8
0.70 0.19 0.12
Matches are distributed among these distances:
19 1 0.02
20 4 0.08
21 38 0.79
22 4 0.08
23 1 0.02
ACGTcount: A:0.23, C:0.33, G:0.20, T:0.24
Consensus pattern (21 bp):
CTGTCATCGTTCAAGAGGCCA
Found at i:428721 original size:14 final size:14
Alignment explanation
Indices: 428689--428723 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
428679 GATTGTTTAA
428689 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
* *
428703 ATGATTTGTAAATG
1 TTGATTTGTAAAAG
428717 TTGATTT
1 TTGATTT
428724 ATTTAATTGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.20, T:0.49
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:428870 original size:14 final size:14
Alignment explanation
Indices: 428851--428904 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
428841 GGAAATGACT
428851 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
428865 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAGA
428884 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
428898 ATCGCAA
1 ATCGCAA
428905 TGCGAAAATG
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 17 0.52
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.30
ACGTcount: A:0.44, C:0.20, G:0.24, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:428881 original size:33 final size:33
Alignment explanation
Indices: 428831--428919 Score: 133
Period size: 33 Copynumber: 2.6 Consensus size: 33
428821 AAAACAGACT
* **
428831 ATCGCAACGCGGAAATGACTATCGCAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
428865 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
428898 ATCGCAATGCGAAAATGAAAAT
1 ATCGCAATGCG-AAATGAAAAT
428920 TTGCAATTTT
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
33 32 0.63
34 19 0.37
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:428975 original size:33 final size:33
Alignment explanation
Indices: 428920--429002 Score: 121
Period size: 33 Copynumber: 2.5 Consensus size: 33
428910 AAATGAAAAT
*
428920 TTGCAATTTTCATTTTCGCATTGCGATTCACTCG
1 TTGCGATTTTCA-TTTCGCATTGCGATTCACTCG
*
428954 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCACTCG
**
428987 TTGCGATAGTCATTTC
1 TTGCGATTTTCATTTC
429003 CGCGTTACGA
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 34 0.76
34 11 0.24
ACGTcount: A:0.16, C:0.23, G:0.17, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCACTCG
Found at i:429013 original size:20 final size:20
Alignment explanation
Indices: 428985--429073 Score: 117
Period size: 20 Copynumber: 4.5 Consensus size: 20
428975 GCGATTCTCT
428985 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
* *
429005 CGTTACGATAGTCAATTCCG
1 CGTTGCGATAGTCATTTCCG
429025 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
* **
429045 TGTTGTAATAGTCATATT-CG
1 CGTTGCGATAGTCAT-TTCCG
429065 CGTTGCGAT
1 CGTTGCGAT
429074 TTCCGCGTTA
Statistics
Matches: 58, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
20 56 0.97
21 2 0.03
ACGTcount: A:0.19, C:0.21, G:0.24, T:0.36
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:431525 original size:24 final size:24
Alignment explanation
Indices: 431498--431544 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
431488 CAAAATCCGA
*
431498 GTATTGACCAATATCAAAGTTCGG
1 GTATTGACCAAGATCAAAGTTCGG
*
431522 GTATTGACCAAGATCAAATTTCG
1 GTATTGACCAAGATCAAAGTTCG
431545 AATACCGACT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (24 bp):
GTATTGACCAAGATCAAAGTTCGG
Found at i:432406 original size:20 final size:20
Alignment explanation
Indices: 432381--432447 Score: 82
Period size: 20 Copynumber: 3.4 Consensus size: 20
432371 AAATTCAGTA
*
432381 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCGCG
*
432401 TTGCGATAGTCAGATTCGCG
1 TTGCGATAGTCAGAATCGCG
* *
432421 TTGCGAT-TTACAGATTCGCG
1 TTGCGATAGT-CAGAATCGCG
432441 TTGCGAT
1 TTGCGAT
432448 TTACGTATTC
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
19 1 0.02
20 42 0.98
ACGTcount: A:0.21, C:0.19, G:0.27, T:0.33
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCGCG
Found at i:432448 original size:20 final size:20
Alignment explanation
Indices: 432414--432607 Score: 300
Period size: 20 Copynumber: 9.7 Consensus size: 20
432404 CGATAGTCAG
432414 ATTCGCGTTGCGATTTACAG-
1 ATTCGCGTTGCGATTTAC-GT
432434 ATTCGCGTTGCGATTTACGT
1 ATTCGCGTTGCGATTTACGT
432454 ATTCGCGTTGCGATTTACGT
1 ATTCGCGTTGCGATTTACGT
432474 ATTCGCGTTGCGATTTACGT
1 ATTCGCGTTGCGATTTACGT
432494 ATTCGCGTTGCGATTTACGT
1 ATTCGCGTTGCGATTTACGT
*
432514 ATTCGCGTTGCGATTTACTT
1 ATTCGCGTTGCGATTTACGT
432534 ATTCGCGTTGCGATTTACGT
1 ATTCGCGTTGCGATTTACGT
* * * **
432554 AATCGCATTGCGATTTTCCAA
1 ATTCGCGTTGCGA-TTTACGT
432575 ATTCGCGTTGCGATTTACGT
1 ATTCGCGTTGCGATTTACGT
*
432595 ATTCGCATTGCGA
1 ATTCGCGTTGCGA
432608 ATTAGGAAAA
Statistics
Matches: 159, Mismatches: 13, Indels: 4
0.90 0.07 0.02
Matches are distributed among these distances:
19 1 0.01
20 143 0.90
21 15 0.09
ACGTcount: A:0.18, C:0.21, G:0.23, T:0.39
Consensus pattern (20 bp):
ATTCGCGTTGCGATTTACGT
Found at i:432629 original size:21 final size:21
Alignment explanation
Indices: 432605--432644 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
432595 ATTCGCATTG
432605 CGAATTAGGAAAATCGCAACA
1 CGAATTAGGAAAATCGCAACA
*
432626 CGAATTTGGAAAATCGCAA
1 CGAATTAGGAAAATCGCAA
432645 TGCGATAGTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.45, C:0.17, G:0.20, T:0.17
Consensus pattern (21 bp):
CGAATTAGGAAAATCGCAACA
Found at i:440860 original size:2 final size:2
Alignment explanation
Indices: 440853--440899 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
440843 ATACTATTAC
440853 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
440895 AT AT A
1 AT AT A
440900 AATAGATAAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:446074 original size:29 final size:31
Alignment explanation
Indices: 446013--446076 Score: 78
Period size: 29 Copynumber: 2.1 Consensus size: 31
446003 TAAAATTATA
* * *
446013 TATATAATTAAATTAAAATCAAAATTTTATG
1 TATATAATTAAATCAAAATCAAAAGTTCATG
*
446044 TATATAATTATA-CAAAATC-AAAGTTCATG
1 TATATAATTAAATCAAAATCAAAAGTTCATG
446073 TATA
1 TATA
446077 ATTAGATATT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 12 0.41
30 6 0.21
31 11 0.38
ACGTcount: A:0.50, C:0.06, G:0.05, T:0.39
Consensus pattern (31 bp):
TATATAATTAAATCAAAATCAAAAGTTCATG
Found at i:446304 original size:2 final size:2
Alignment explanation
Indices: 446297--446321 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
446287 TCTTAACAGC
446297 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
446322 TGTCCGATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:447629 original size:25 final size:24
Alignment explanation
Indices: 447584--447638 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 24
447574 ATAATAATAT
*
447584 ATTTTCTTCTTTAAAATTTTAT-A
1 ATTTACTTCTTTAAAATTTTATGA
*
447607 AGTTTACTTCTCTTCAAATTTTATGA
1 A-TTTACTTCT-TTAAAATTTTATGA
447633 ATTTAC
1 ATTTAC
447639 CTCCTAACAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 1 0.04
24 8 0.30
25 16 0.59
26 2 0.07
ACGTcount: A:0.29, C:0.13, G:0.04, T:0.55
Consensus pattern (24 bp):
ATTTACTTCTTTAAAATTTTATGA
Found at i:450798 original size:15 final size:16
Alignment explanation
Indices: 450778--450807 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
450768 TAACTTTAAT
450778 TTATTATT-ATAAAAG
1 TTATTATTAATAAAAG
450793 TTATTATTAATAAAA
1 TTATTATTAATAAAA
450808 ATATATTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
TTATTATTAATAAAAG
Found at i:457350 original size:34 final size:30
Alignment explanation
Indices: 457322--457380 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 30
457312 AATTTAAGGT
*
457322 AAAATGGTTTTTGGACTTGAATTGAATTT-AC
1 AAAAT-GTATTTGGACTT-AATTGAATTTAAC
457353 AAAATGTATTTGGACTTAATTGAATTTA
1 AAAATGTATTTGGACTTAATTGAATTTA
457381 TTCAAAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 10 0.38
30 11 0.42
31 5 0.19
ACGTcount: A:0.36, C:0.05, G:0.17, T:0.42
Consensus pattern (30 bp):
AAAATGTATTTGGACTTAATTGAATTTAAC
Found at i:457388 original size:31 final size:31
Alignment explanation
Indices: 457322--457380 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 31
457312 AATTTAAGGT
*
457322 AAAATGGTTTTTGGACTTGAATTGAATTTAC
1 AAAATGGTATTTGGACTTGAATTGAATTTAC
457353 AAAAT-GTATTTGGACTT-AATTGAATTTA
1 AAAATGGTATTTGGACTTGAATTGAATTTA
457381 TTCAAAATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 11 0.41
30 11 0.41
31 5 0.19
ACGTcount: A:0.36, C:0.05, G:0.17, T:0.42
Consensus pattern (31 bp):
AAAATGGTATTTGGACTTGAATTGAATTTAC
Found at i:457503 original size:21 final size:21
Alignment explanation
Indices: 457474--457530 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
457464 GTATGTAAAA
*
457474 GGGGAACCGATTCCCCCCAAG
1 GGGGTACCGATTCCCCCCAAG
457495 GGGGTACCGATTCCCCCCAAG
1 GGGGTACCGATTCCCCCCAAG
*
457516 AGGGTACCGATTCCC
1 GGGGTACCGATTCCC
457531 TTACTGTTCA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.21, C:0.37, G:0.28, T:0.14
Consensus pattern (21 bp):
GGGGTACCGATTCCCCCCAAG
Found at i:457596 original size:21 final size:21
Alignment explanation
Indices: 457570--457611 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
457560 ATTTGAATAT
457570 TATGAAGGGGTA-TCGATTCCC
1 TATGAAGGGGTACT-GATTCCC
457591 TATGAAGGGGTACTGATTCCC
1 TATGAAGGGGTACTGATTCCC
457612 CCCATTCTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 19 0.95
22 1 0.05
ACGTcount: A:0.24, C:0.19, G:0.29, T:0.29
Consensus pattern (21 bp):
TATGAAGGGGTACTGATTCCC
Found at i:457674 original size:21 final size:21
Alignment explanation
Indices: 457641--457680 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
457631 TTTTTGCAGA
*
457641 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
457663 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
457681 AGATATGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:479572 original size:11 final size:11
Alignment explanation
Indices: 479556--479592 Score: 65
Period size: 11 Copynumber: 3.3 Consensus size: 11
479546 AGCAGCCCCC
479556 CCCCTTAGCAG
1 CCCCTTAGCAG
479567 CCCCTTAGCAG
1 CCCCTTAGCAG
479578 CCCCCTTAGCAG
1 -CCCCTTAGCAG
479590 CCC
1 CCC
479593 ATGTGTTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 14 0.56
12 11 0.44
ACGTcount: A:0.16, C:0.51, G:0.16, T:0.16
Consensus pattern (11 bp):
CCCCTTAGCAG
Found at i:479582 original size:12 final size:12
Alignment explanation
Indices: 479555--479592 Score: 69
Period size: 12 Copynumber: 3.2 Consensus size: 12
479545 CAGCAGCCCC
479555 CCCCCTTAGCAG
1 CCCCCTTAGCAG
479567 -CCCCTTAGCAG
1 CCCCCTTAGCAG
479578 CCCCCTTAGCAG
1 CCCCCTTAGCAG
479590 CCC
1 CCC
479593 ATGTGTTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 11 0.44
12 14 0.56
ACGTcount: A:0.16, C:0.53, G:0.16, T:0.16
Consensus pattern (12 bp):
CCCCCTTAGCAG
Found at i:482797 original size:15 final size:16
Alignment explanation
Indices: 482769--482800 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
482759 AAAATCTTTC
482769 TTTCCCGTTCTGGATT
1 TTTCCCGTTCTGGATT
482785 TTTCCCG-TCTGGATT
1 TTTCCCGTTCTGGATT
482800 T
1 T
482801 GGATCTGCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.06, C:0.25, G:0.19, T:0.50
Consensus pattern (16 bp):
TTTCCCGTTCTGGATT
Found at i:483991 original size:12 final size:12
Alignment explanation
Indices: 483974--484013 Score: 71
Period size: 12 Copynumber: 3.2 Consensus size: 12
483964 ACAGCAGCCC
483974 CCCCCTTAGCAG
1 CCCCCTTAGCAG
483986 CCCCCTTAGCAG
1 CCCCCTTAGCAG
483998 CCCCCCTTAGCAG
1 -CCCCCTTAGCAG
484011 CCC
1 CCC
484014 ATGTGTTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
12 15 0.56
13 12 0.44
ACGTcount: A:0.15, C:0.55, G:0.15, T:0.15
Consensus pattern (12 bp):
CCCCCTTAGCAG
Found at i:484002 original size:13 final size:13
Alignment explanation
Indices: 483973--484013 Score: 75
Period size: 13 Copynumber: 3.2 Consensus size: 13
483963 TACAGCAGCC
483973 CCCCCCTTAGCAG
1 CCCCCCTTAGCAG
483986 -CCCCCTTAGCAG
1 CCCCCCTTAGCAG
483998 CCCCCCTTAGCAG
1 CCCCCCTTAGCAG
484011 CCC
1 CCC
484014 ATGTGTTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
12 12 0.44
13 15 0.56
ACGTcount: A:0.15, C:0.56, G:0.15, T:0.15
Consensus pattern (13 bp):
CCCCCCTTAGCAG
Found at i:484142 original size:28 final size:28
Alignment explanation
Indices: 484105--484160 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
484095 TTTCATTTTA
484105 AATTTAATCACTGAATTATAAAAAGTTT
1 AATTTAATCACTGAATTATAAAAAGTTT
484133 AATTTAATCACTGAATTATAAAAAGTTT
1 AATTTAATCACTGAATTATAAAAAGTTT
484161 TCTTCATAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.39
Consensus pattern (28 bp):
AATTTAATCACTGAATTATAAAAAGTTT
Found at i:486490 original size:16 final size:16
Alignment explanation
Indices: 486453--486499 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
486443 TTGTTAGTAT
*
486453 TTTATTTAACTATTTAA
1 TTTATTTAA-TATTTTA
*
486470 ATTATTTAATATTTTA
1 TTTATTTAATATTTTA
486486 TTTATTTAAT-TTTT
1 TTTATTTAATATTTT
486500 TTGCAGATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
15 4 0.15
16 15 0.56
17 8 0.30
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (16 bp):
TTTATTTAATATTTTA
Found at i:488828 original size:25 final size:25
Alignment explanation
Indices: 488780--488843 Score: 69
Period size: 25 Copynumber: 2.6 Consensus size: 25
488770 TATTTTGTTA
* * *
488780 ATTTGGTTAGATTTTTTTTAAATTT
1 ATTTTGTTAGATTTTTGTTAAATTG
488805 ATTTTGTTAGACTTTTTGTT-AATTG
1 ATTTTGTTAGA-TTTTTGTTAAATTG
*
488830 ATTTTGATA-ATTTT
1 ATTTTGTTAGATTTT
488844 GTTTATTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
23 4 0.12
24 1 0.03
25 22 0.65
26 7 0.21
ACGTcount: A:0.23, C:0.02, G:0.12, T:0.62
Consensus pattern (25 bp):
ATTTTGTTAGATTTTTGTTAAATTG
Found at i:488931 original size:35 final size:37
Alignment explanation
Indices: 488870--488940 Score: 101
Period size: 38 Copynumber: 1.9 Consensus size: 37
488860 TATCAATTAA
*
488870 ATTATTTATCATTTAATATAAGTTATTGTAA-TTTGATT
1 ATTATTTAGCATTTAATAT-A-TTATTGTAAGTTTGATT
488908 ATTATTTAGCATTTAATAT-TTATTGTAAGTTTG
1 ATTATTTAGCATTTAATATATTATTGTAAGTTTG
488941 TTGTATTTAG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
35 9 0.29
36 4 0.13
38 18 0.58
ACGTcount: A:0.32, C:0.03, G:0.10, T:0.55
Consensus pattern (37 bp):
ATTATTTAGCATTTAATATATTATTGTAAGTTTGATT
Found at i:491205 original size:24 final size:24
Alignment explanation
Indices: 491173--491220 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
491163 TCTCAAGTTT
491173 CTCTTGAATAATATTTTAACATAA
1 CTCTTGAATAATATTTTAACATAA
*
491197 CTCTTGAATGATATTTTAACATAA
1 CTCTTGAATAATATTTTAACATAA
491221 TCATTTAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.40, C:0.12, G:0.06, T:0.42
Consensus pattern (24 bp):
CTCTTGAATAATATTTTAACATAA
Found at i:491428 original size:24 final size:23
Alignment explanation
Indices: 491399--491449 Score: 77
Period size: 22 Copynumber: 2.2 Consensus size: 23
491389 TAACACAATA
491399 AATTTTATACACATAAACGTAAAT
1 AATTTT-TACACATAAACGTAAAT
*
491423 CA-TTTTACACATAAACGTAAAT
1 AATTTTTACACATAAACGTAAAT
491445 AATTT
1 AATTT
491450 AAATGATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 18 0.75
23 5 0.21
24 1 0.04
ACGTcount: A:0.47, C:0.14, G:0.04, T:0.35
Consensus pattern (23 bp):
AATTTTTACACATAAACGTAAAT
Found at i:491433 original size:22 final size:22
Alignment explanation
Indices: 491406--491449 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
491396 ATAAATTTTA
*
491406 TACACATAAACGTAAATCATTT
1 TACACATAAACGTAAATAATTT
491428 TACACATAAACGTAAATAATTT
1 TACACATAAACGTAAATAATTT
491450 AAATGATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.48, C:0.16, G:0.05, T:0.32
Consensus pattern (22 bp):
TACACATAAACGTAAATAATTT
Found at i:491845 original size:15 final size:15
Alignment explanation
Indices: 491825--491853 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
491815 CGCTATAGCC
491825 CTACGTGGCGTAAGG
1 CTACGTGGCGTAAGG
491840 CTACGTGGCGTAAG
1 CTACGTGGCGTAAG
491854 ACGCGCCTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.21, G:0.38, T:0.21
Consensus pattern (15 bp):
CTACGTGGCGTAAGG
Found at i:492305 original size:2 final size:2
Alignment explanation
Indices: 492298--492334 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
492288 TGGATGGTCA
*
492298 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AG AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
492335 GATCTGCAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:497149 original size:20 final size:20
Alignment explanation
Indices: 497094--497173 Score: 90
Period size: 20 Copynumber: 4.0 Consensus size: 20
497084 AATCGCATTA
* * *
497094 CGATTTTCAAATTCGTAACA
1 CGATTTTCGAATTCGCAACT
* *
497114 CTGAATTTCAAATTCGCAACT
1 C-GATTTTCGAATTCGCAACT
497135 CGA-TTTCTGAATTCGCAACT
1 CGATTTTC-GAATTCGCAACT
497155 CGATTTTCGAATTCGCAAC
1 CGATTTTCGAATTCGCAAC
497174 ATGAATTTTA
Statistics
Matches: 53, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
19 4 0.08
20 28 0.53
21 21 0.40
ACGTcount: A:0.30, C:0.24, G:0.12, T:0.34
Consensus pattern (20 bp):
CGATTTTCGAATTCGCAACT
Found at i:497348 original size:22 final size:22
Alignment explanation
Indices: 497304--497349 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
497294 TATCACTCTT
* *
497304 TCCAGCGACATCCATTCCTATA
1 TCCAACGACATCCATTCCCATA
497326 TCCAACGACATCC-TTCCCCATA
1 TCCAACGACATCCATT-CCCATA
497348 TC
1 TC
497350 TATTTTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 2 0.10
22 19 0.90
ACGTcount: A:0.26, C:0.41, G:0.07, T:0.26
Consensus pattern (22 bp):
TCCAACGACATCCATTCCCATA
Found at i:498001 original size:12 final size:12
Alignment explanation
Indices: 497980--498013 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
497970 ACCACATTTC
*
497980 CAATACCAAACA
1 CAATATCAAACA
497992 CAATATCAAACA
1 CAATATCAAACA
*
498004 CAATCTCAAA
1 CAATATCAAA
498014 ACCCACAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:500689 original size:29 final size:29
Alignment explanation
Indices: 500656--500711 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
500646 AGATTTTTTG
**
500656 TTGCGATTATTGCGAAAGTCAAATTCGCA
1 TTGCGATTACCGCGAAAGTCAAATTCGCA
*
500685 TTGCGATTGCCGCGAAAGTCAAATTCG
1 TTGCGATTACCGCGAAAGTCAAATTCG
500712 AAACACGAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.29
Consensus pattern (29 bp):
TTGCGATTACCGCGAAAGTCAAATTCGCA
Found at i:500792 original size:20 final size:20
Alignment explanation
Indices: 500733--500794 Score: 106
Period size: 20 Copynumber: 3.1 Consensus size: 20
500723 TCGCAACACA
*
500733 AATTTGACTTTCGCGTTGCA
1 AATTTGACTTTCGCGTTGCG
*
500753 AATTTGACTTTCACGTTGCG
1 AATTTGACTTTCGCGTTGCG
500773 AATTTGACTTTCGCGTTGCG
1 AATTTGACTTTCGCGTTGCG
500793 AA
1 AA
500795 AGTGTACCTT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.39
Consensus pattern (20 bp):
AATTTGACTTTCGCGTTGCG
Found at i:501685 original size:20 final size:20
Alignment explanation
Indices: 501644--501685 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
501634 GCGCCGGAGA
* * *
501644 TCGTGTTGCGATTTTCATTT
1 TCGTGTTGCGAATTTAAGTT
501664 TCGTGTTGCGAATTTAAGTT
1 TCGTGTTGCGAATTTAAGTT
501684 TC
1 TC
501686 AAATAGTCTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.14, C:0.14, G:0.21, T:0.50
Consensus pattern (20 bp):
TCGTGTTGCGAATTTAAGTT
Found at i:502240 original size:20 final size:20
Alignment explanation
Indices: 502217--502286 Score: 104
Period size: 20 Copynumber: 3.5 Consensus size: 20
502207 TGACTTATGT
*
502217 GTTGCGAATTACAGATTCGC
1 GTTGCGAATTATAGATTCGC
*
502237 GTTGCGATTTATAGATTCGC
1 GTTGCGAATTATAGATTCGC
*
502257 GTTGCGATTTATAGATTCGC
1 GTTGCGAATTATAGATTCGC
*
502277 GTTACGAATT
1 GTTGCGAATT
502287 TGAAAATCGC
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.23, C:0.16, G:0.24, T:0.37
Consensus pattern (20 bp):
GTTGCGAATTATAGATTCGC
Found at i:502842 original size:4 final size:4
Alignment explanation
Indices: 502833--502887 Score: 110
Period size: 4 Copynumber: 13.8 Consensus size: 4
502823 GAGAAACATG
502833 CAAT CAAT CAAT CAAT CAAT CAAT CAAT CAAT CAAT CAAT CAAT CAAT
1 CAAT CAAT CAAT CAAT CAAT CAAT CAAT CAAT CAAT CAAT CAAT CAAT
502881 CAAT CAA
1 CAAT CAA
502888 AGTACAACAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 51 1.00
ACGTcount: A:0.51, C:0.25, G:0.00, T:0.24
Consensus pattern (4 bp):
CAAT
Found at i:503770 original size:2 final size:2
Alignment explanation
Indices: 503763--503803 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
503753 TTTGTTGATT
* *
503763 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TG TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
503804 TGTATTGTTG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (2 bp):
TA
Found at i:504358 original size:13 final size:13
Alignment explanation
Indices: 504340--504366 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
504330 TTTTCTGATC
504340 GATACTCAACCTA
1 GATACTCAACCTA
504353 GATACTCAACCTA
1 GATACTCAACCTA
504366 G
1 G
504367 TCAATTGACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.30, G:0.11, T:0.22
Consensus pattern (13 bp):
GATACTCAACCTA
Found at i:504665 original size:43 final size:43
Alignment explanation
Indices: 504604--504694 Score: 164
Period size: 43 Copynumber: 2.1 Consensus size: 43
504594 AGTTCGATAA
*
504604 ATTTGCTGTTTGTATGTTATGAATTTGCTATTTGATGTTATGT
1 ATTTGCTGTTTGTATGTTATGAATTTGCTATTTGATGTTATAT
*
504647 ATTTGCTGTTTGTATGTTATGAATTTGCTGTTTGATGTTATAT
1 ATTTGCTGTTTGTATGTTATGAATTTGCTATTTGATGTTATAT
504690 ATTTG
1 ATTTG
504695 TTGTGTATGC
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 46 1.00
ACGTcount: A:0.19, C:0.04, G:0.21, T:0.56
Consensus pattern (43 bp):
ATTTGCTGTTTGTATGTTATGAATTTGCTATTTGATGTTATAT
Found at i:504694 original size:21 final size:22
Alignment explanation
Indices: 504603--504687 Score: 138
Period size: 22 Copynumber: 4.0 Consensus size: 22
504593 TAGTTCGATA
504603 AATTTGCTGTTTGTATGTTATG
1 AATTTGCTGTTTGTATGTTATG
*
504625 AATTTGCTATTTG-ATGTTATG
1 AATTTGCTGTTTGTATGTTATG
*
504646 TATTTGCTGTTTGTATGTTATG
1 AATTTGCTGTTTGTATGTTATG
504668 AATTTGCTGTTTG-ATGTTAT
1 AATTTGCTGTTTGTATGTTAT
504688 ATATTTGTTG
Statistics
Matches: 58, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
21 26 0.45
22 32 0.55
ACGTcount: A:0.19, C:0.05, G:0.21, T:0.55
Consensus pattern (22 bp):
AATTTGCTGTTTGTATGTTATG
Found at i:505794 original size:30 final size:30
Alignment explanation
Indices: 505760--505928 Score: 203
Period size: 30 Copynumber: 5.9 Consensus size: 30
505750 TCTTTTTGAT
*
505760 TATGTAAGAAATATTATATGGTTTGTGGTC
1 TATGTTAGAAATATTATATGGTTTGTGGTC
505790 TATGTTAGAAATATTATATGGTTT-T--T-
1 TATGTTAGAAATATTATATGGTTTGTGGTC
* * *
505816 GATGTTCA-AAACATTATATGGTTTGTGGTT
1 TATGTT-AGAAATATTATATGGTTTGTGGTC
*
505846 TATGTTAGAAATATTATATTG-TT-T-GTC
1 TATGTTAGAAATATTATATGGTTTGTGGTC
*
505873 GATGTTCA-AAATATTATATGGTTTGTGGTC
1 TATGTT-AGAAATATTATATGGTTTGTGGTC
505903 TATGTTAGAAATATTATATGGTTTGT
1 TATGTTAGAAATATTATATGGTTTGT
505929 ATTAAAGTTA
Statistics
Matches: 118, Mismatches: 10, Indels: 22
0.79 0.07 0.15
Matches are distributed among these distances:
26 20 0.17
27 22 0.19
28 4 0.03
29 7 0.06
30 65 0.55
ACGTcount: A:0.29, C:0.04, G:0.20, T:0.47
Consensus pattern (30 bp):
TATGTTAGAAATATTATATGGTTTGTGGTC
Found at i:505900 original size:57 final size:57
Alignment explanation
Indices: 505768--505928 Score: 279
Period size: 57 Copynumber: 2.8 Consensus size: 57
505758 ATTATGTAAG
*
505768 AAATATTATATGGTTTGTGGTCTATGTTAGAAATATTATATGGTTT-TTGATGTTCA
1 AAATATTATATGGTTTGTGGTCTATGTTAGAAATATTATATGGTTTGTCGATGTTCA
* * *
505824 AAACATTATATGGTTTGTGGTTTATGTTAGAAATATTATATTGTTTGTCGATGTTCA
1 AAATATTATATGGTTTGTGGTCTATGTTAGAAATATTATATGGTTTGTCGATGTTCA
505881 AAATATTATATGGTTTGTGGTCTATGTTAGAAATATTATATGGTTTGT
1 AAATATTATATGGTTTGTGGTCTATGTTAGAAATATTATATGGTTTGT
505929 ATTAAAGTTA
Statistics
Matches: 97, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
56 43 0.44
57 54 0.56
ACGTcount: A:0.29, C:0.04, G:0.20, T:0.48
Consensus pattern (57 bp):
AAATATTATATGGTTTGTGGTCTATGTTAGAAATATTATATGGTTTGTCGATGTTCA
Found at i:507269 original size:31 final size:31
Alignment explanation
Indices: 507231--507289 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
507221 AATTGTATGG
*
507231 ATTATTTAAATTTCAATATTGTAAAACTAAA
1 ATTATTTAAATTTCAATATTGCAAAACTAAA
*
507262 ATTATTTAAATTTCAGTATTGCAAAACT
1 ATTATTTAAATTTCAATATTGCAAAACT
507290 CTTTTAAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.44, C:0.08, G:0.05, T:0.42
Consensus pattern (31 bp):
ATTATTTAAATTTCAATATTGCAAAACTAAA
Found at i:508089 original size:40 final size:39
Alignment explanation
Indices: 508045--508123 Score: 104
Period size: 40 Copynumber: 2.0 Consensus size: 39
508035 ACCTGAGATG
*
508045 TTATATGCTTGGTAAAACTTCAGGTTGCAAACCGAAAATA
1 TTATATACTTGGTAAAACTTCAGGTTGC-AACCGAAAATA
* * * *
508085 TTATATATTTGGTAACATTTCAGGTTGCAACCTAAAATA
1 TTATATACTTGGTAAAACTTCAGGTTGCAACCGAAAATA
508124 CTCTTAATAT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
39 10 0.29
40 24 0.71
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.34
Consensus pattern (39 bp):
TTATATACTTGGTAAAACTTCAGGTTGCAACCGAAAATA
Found at i:508650 original size:22 final size:22
Alignment explanation
Indices: 508618--508663 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
508608 TCAATACTTC
508618 AAAGTTAAAGGACTAAATTTAT
1 AAAGTTAAAGGACTAAATTTAT
*
508640 AAAGTTGAAGGACTAAATTTAT
1 AAAGTTAAAGGACTAAATTTAT
508662 AA
1 AA
508664 TTAAACAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.50, C:0.04, G:0.15, T:0.30
Consensus pattern (22 bp):
AAAGTTAAAGGACTAAATTTAT
Found at i:508970 original size:30 final size:30
Alignment explanation
Indices: 508936--509043 Score: 105
Period size: 30 Copynumber: 3.6 Consensus size: 30
508926 TACCCCTATA
*
508936 TTTG-TTTCTTTGTTTTTGTTGTGATGGGCT
1 TTTGTTTTCTTTG-TTTTGTTGTGATGGGTT
* *
508966 TTTGTTTTCTTTGCTTCTGCTGTGA-GGGTT
1 TTTGTTTTCTTTG-TTTTGTTGTGATGGGTT
* *
508996 TTTGTTTTCTTTGGTTTGTTGTGGTGGGTT
1 TTTGTTTTCTTTGTTTTGTTGTGATGGGTT
* *
509026 TCTT-CTTTCTTTGGTTTG
1 T-TTGTTTTCTTTGTTTTG
509044 CTTTCATGGG
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
29 7 0.11
30 40 0.61
31 19 0.29
ACGTcount: A:0.02, C:0.09, G:0.27, T:0.62
Consensus pattern (30 bp):
TTTGTTTTCTTTGTTTTGTTGTGATGGGTT
Found at i:510116 original size:36 final size:36
Alignment explanation
Indices: 510076--510152 Score: 109
Period size: 36 Copynumber: 2.1 Consensus size: 36
510066 TGAAGGTGAA
* *
510076 CAAGTAGAATGAAAGGAAGCATCGACACTTTCGATT
1 CAAGTAGAACGAAAGGAAGCATCAACACTTTCGATT
* * *
510112 CAAGTCGAACGGAAGGAGGCATCAACACTTTCGATT
1 CAAGTAGAACGAAAGGAAGCATCAACACTTTCGATT
510148 CAAGT
1 CAAGT
510153 GTTCATCTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.36, C:0.19, G:0.23, T:0.21
Consensus pattern (36 bp):
CAAGTAGAACGAAAGGAAGCATCAACACTTTCGATT
Found at i:511999 original size:37 final size:37
Alignment explanation
Indices: 511958--512048 Score: 148
Period size: 37 Copynumber: 2.5 Consensus size: 37
511948 GGACAGGTTG
*
511958 CAATCGAAAATGTTATATTTTTCATAATATTCAGTTA
1 CAATCGAAAATGTTATATTTTTCATAATATTCAATTA
*
511995 CAATCGAAAATGTTATATTTTTTATAATATTCAATTA
1 CAATCGAAAATGTTATATTTTTCATAATATTCAATTA
512032 CAA-CTGAAAATGTTATA
1 CAATC-GAAAATGTTATA
512049 AATTTGTATA
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
36 1 0.02
37 50 0.98
ACGTcount: A:0.41, C:0.10, G:0.08, T:0.42
Consensus pattern (37 bp):
CAATCGAAAATGTTATATTTTTCATAATATTCAATTA
Found at i:512649 original size:18 final size:17
Alignment explanation
Indices: 512622--512660 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 17
512612 AAATGTTATT
*
512622 ATTCATAGAAGTCTTAA
1 ATTCATAGAAGTATTAA
512639 ATTCAATAGAAGTATTAA
1 ATTC-ATAGAAGTATTAA
512657 ATTC
1 ATTC
512661 GAGCAACTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.36
Consensus pattern (17 bp):
ATTCATAGAAGTATTAA
Found at i:517827 original size:22 final size:22
Alignment explanation
Indices: 517796--517850 Score: 96
Period size: 22 Copynumber: 2.6 Consensus size: 22
517786 TGCTGTGCAA
517796 AGTC-TTAGTTTTTATTTTAGG
1 AGTCTTTAGTTTTTATTTTAGG
517817 AGTCTTTAGTTTTTATTTTAGG
1 AGTCTTTAGTTTTTATTTTAGG
517839 AGTCTTTA-TTTT
1 AGTCTTTAGTTTT
517851 GACCATAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 8 0.24
22 25 0.76
ACGTcount: A:0.18, C:0.05, G:0.16, T:0.60
Consensus pattern (22 bp):
AGTCTTTAGTTTTTATTTTAGG
Found at i:526385 original size:113 final size:112
Alignment explanation
Indices: 526204--526519 Score: 447
Period size: 113 Copynumber: 2.8 Consensus size: 112
526194 AGGCCCCCAA
* * ** *
526204 AAAAATATATATATATAGTGGCATTTTTCCAATAAACGTCACTATAGATTGACCTATTGCGACGT
1 AAAAA-ATATATATATAGTGAC-GTTTTCCAATAAACACCACTATAGATGGACCTATTGCGACGT
*
526269 TTTTTTCCAAAAAAACGCCACTATTATTGTGCAGGCCCCAAAAAAAAGCCC
64 TTTTTT-CAAAAAAACGCCACTATTATTGCGCAGG-CCCAAAAAAAAGCCC
* *
526320 -AAAAATATATATATAGTGACGTTTTCCAATAAACACCACTATAGATGGACCTAATGCGATGTTT
1 AAAAAATATATATATAGTGACGTTTTCCAATAAACACCACTATAGATGGACCTATTGCGACGTTT
* *
526384 TTTTC-AAAAAACACCACTATTATTGCGCAGGCCCAAAAAAATGCCC
66 TTTTCAAAAAAACGCCACTATTATTGCGCAGGCCCAAAAAAAAGCCC
* *
526430 AAAAAAAAATATATATAGTGACGTTTTTCCAATAAACACCACTATAGATGGACCTATTACGACGT
1 -AAAAAATATATATATAGTGACG-TTTTCCAATAAACACCACTATAGATGGACCTATTGCGACG-
526495 TTTTTTTCAAAAAAACGCCACTATT
63 TTTTTTTCAAAAAAACGCCACTATT
526520 GTTACCCAAA
Statistics
Matches: 180, Mismatches: 15, Indels: 11
0.87 0.07 0.05
Matches are distributed among these distances:
110 14 0.08
111 24 0.13
112 21 0.12
113 79 0.44
114 23 0.13
115 19 0.11
ACGTcount: A:0.39, C:0.20, G:0.12, T:0.29
Consensus pattern (112 bp):
AAAAAATATATATATAGTGACGTTTTCCAATAAACACCACTATAGATGGACCTATTGCGACGTTT
TTTTCAAAAAAACGCCACTATTATTGCGCAGGCCCAAAAAAAAGCCC
Done.