Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008174.1 Hibiscus syriacus cultivar Beakdansim tig00110769_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: 210847
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:8712 original size:35 final size:35
Alignment explanation
Indices: 8665--8778 Score: 138
Period size: 35 Copynumber: 3.3 Consensus size: 35
8655 AAAATAGTCC
* * * *
8665 TCAATTTCATTCTAAACCCCAATTTTTAAAGTAAT
1 TCAATTTAATTCTAAACCCCAAATTCTAAAATAAT
* * *
8700 TCAATTTTATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTAATTCTAAACCCCAAATTCTAAAATAAT
* * *
8735 TCAATTAAATTTTAAACCCCAAATTCTAAAATACT
1 TCAATTTAATTCTAAACCCCAAATTCTAAAATAAT
8770 TCAATTTAA
1 TCAATTTAA
8779 GGTTTAGAAT
Statistics
Matches: 66, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 66 1.00
ACGTcount: A:0.42, C:0.19, G:0.01, T:0.38
Consensus pattern (35 bp):
TCAATTTAATTCTAAACCCCAAATTCTAAAATAAT
Found at i:11191 original size:22 final size:22
Alignment explanation
Indices: 11163--11204 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
11153 AAAATATCTT
*
11163 AAAAATAACAAAATCGATAGAA
1 AAAAATAACAAAATAGATAGAA
11185 AAAAATAACAAAATAGATAG
1 AAAAATAACAAAATAGATAG
11205 TGCATTTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.69, C:0.07, G:0.10, T:0.14
Consensus pattern (22 bp):
AAAAATAACAAAATAGATAGAA
Found at i:12224 original size:26 final size:25
Alignment explanation
Indices: 12195--12250 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 25
12185 CTTCTCATAT
*
12195 TTTAAAATTTAAAATTTAATCTTTA
1 TTTAAAATGTAAAATTTAATCTTTA
* * *
12220 GTTTAAAATGTAAACTTTTATTTTTA
1 -TTTAAAATGTAAAATTTAATCTTTA
12246 TTTAA
1 TTTAA
12251 TTTAGTTCTA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
25 5 0.19
26 21 0.81
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.54
Consensus pattern (25 bp):
TTTAAAATGTAAAATTTAATCTTTA
Found at i:12450 original size:23 final size:23
Alignment explanation
Indices: 12424--12479 Score: 60
Period size: 23 Copynumber: 2.3 Consensus size: 23
12414 TAACATTTGA
12424 TTAATTAACATTGTTT-TTGGATT
1 TTAATTAACATTGTTTATTGG-TT
* *
12447 TTAATTTACTTTGTTTGATTGGTT
1 TTAATTAACATTGTTT-ATTGGTT
12471 TTAAATTAA
1 TT-AATTAA
12480 AAGAGAGACA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 14 0.52
24 4 0.15
25 9 0.33
ACGTcount: A:0.27, C:0.04, G:0.12, T:0.57
Consensus pattern (23 bp):
TTAATTAACATTGTTTATTGGTT
Found at i:29582 original size:28 final size:28
Alignment explanation
Indices: 29550--29608 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
29540 AGTGGATTAA
29550 CAGTCATTATTTTTGAAGATGAAGAGAG
1 CAGTCATTATTTTTGAAGATGAAGAGAG
29578 CAGTCATTATTTTTGAAGATGAAGAGAG
1 CAGTCATTATTTTTGAAGATGAAGAGAG
29606 CAG
1 CAG
29609 GGATAGGGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.36, C:0.08, G:0.25, T:0.31
Consensus pattern (28 bp):
CAGTCATTATTTTTGAAGATGAAGAGAG
Found at i:33247 original size:6 final size:6
Alignment explanation
Indices: 33236--33265 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
33226 ATAGAAGAAG
33236 ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA
1 ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA
33266 TTGGTAGACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (6 bp):
ATTAAA
Found at i:48452 original size:37 final size:37
Alignment explanation
Indices: 48411--48486 Score: 152
Period size: 37 Copynumber: 2.1 Consensus size: 37
48401 TAACATGACA
48411 CTGTTAAATGATGAATTTCAGAGTATATAAACATTTT
1 CTGTTAAATGATGAATTTCAGAGTATATAAACATTTT
48448 CTGTTAAATGATGAATTTCAGAGTATATAAACATTTT
1 CTGTTAAATGATGAATTTCAGAGTATATAAACATTTT
48485 CT
1 CT
48487 AGGCTCATAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.37, C:0.09, G:0.13, T:0.41
Consensus pattern (37 bp):
CTGTTAAATGATGAATTTCAGAGTATATAAACATTTT
Found at i:50455 original size:23 final size:22
Alignment explanation
Indices: 50383--50460 Score: 90
Period size: 23 Copynumber: 3.6 Consensus size: 22
50373 TGAAATTTTA
* * *
50383 ATTATTTTAAAATT-TTTAATT
1 ATTATTTTAATATTATCTAAAT
50404 ATT-TTTTAAT-TTATCTAAAT
1 ATTATTTTAATATTATCTAAAT
*
50424 AATATTTTAATATTAATCTAAAT
1 ATTATTTTAATATT-ATCTAAAT
50447 ATTATTTTAATATT
1 ATTATTTTAATATT
50461 TTTAACTTAT
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
19 2 0.04
20 13 0.27
21 10 0.21
22 2 0.04
23 21 0.44
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.58
Consensus pattern (22 bp):
ATTATTTTAATATTATCTAAAT
Found at i:50460 original size:11 final size:11
Alignment explanation
Indices: 50383--50460 Score: 56
Period size: 11 Copynumber: 7.3 Consensus size: 11
50373 TGAAATTTTA
50383 ATTATTTTAA-
1 ATTATTTTAAT
*
50393 AAT-TTTTAATT
1 ATTATTTTAA-T
50404 ATT-TTTTAAT
1 ATTATTTTAAT
* *
50414 -TTATCTAAAT
1 ATTATTTTAAT
*
50424 AATATTTTAAT
1 ATTATTTTAAT
* *
50435 ATTAATCTAAAT
1 ATT-ATTTTAAT
50447 ATTATTTTAAT
1 ATTATTTTAAT
50458 ATT
1 ATT
50461 TTTAACTTAT
Statistics
Matches: 51, Mismatches: 12, Indels: 9
0.71 0.17 0.12
Matches are distributed among these distances:
9 8 0.16
10 8 0.16
11 26 0.51
12 9 0.18
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.58
Consensus pattern (11 bp):
ATTATTTTAAT
Found at i:64615 original size:5 final size:5
Alignment explanation
Indices: 64605--64631 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
64595 CAACACACAA
64605 GATTG GATTG GATTG GATTG GATTG GA
1 GATTG GATTG GATTG GATTG GATTG GA
64632 CGAGAGGGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.22, C:0.00, G:0.41, T:0.37
Consensus pattern (5 bp):
GATTG
Found at i:66255 original size:34 final size:34
Alignment explanation
Indices: 66202--66290 Score: 126
Period size: 34 Copynumber: 2.6 Consensus size: 34
66192 CCTCTCGCAA
* *
66202 ATCGCCTACGGAGTCCTATATTTCTAATATGCAG
1 ATCGCCTACAGAGTTCTATATTTCTAATATGCAG
*
66236 ATCGCCTACAGAGTTCTATATTTCTAATATGCAT
1 ATCGCCTACAGAGTTCTATATTTCTAATATGCAG
*
66270 ATTGCCT-CTAGAGTTCTATAT
1 ATCGCCTAC-AGAGTTCTATAT
66291 CCTTAACCTG
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
33 1 0.02
34 49 0.98
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.37
Consensus pattern (34 bp):
ATCGCCTACAGAGTTCTATATTTCTAATATGCAG
Found at i:82358 original size:2 final size:2
Alignment explanation
Indices: 82353--82392 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
82343 TCTCTCTCTC
82353 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
82393 TTTTTTTCCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:83961 original size:7 final size:7
Alignment explanation
Indices: 83949--83976 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
83939 ACTCTTCTTC
83949 TTCAAGG
1 TTCAAGG
83956 TTCAAGG
1 TTCAAGG
83963 TTCAAGG
1 TTCAAGG
83970 TTCAAGG
1 TTCAAGG
83977 ATGTTTAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.29, C:0.14, G:0.29, T:0.29
Consensus pattern (7 bp):
TTCAAGG
Found at i:91270 original size:12 final size:12
Alignment explanation
Indices: 91246--91279 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
91236 ATAATAATTC
91246 TTTATAT-TTTA
1 TTTATATATTTA
*
91257 TTTATTTATTTA
1 TTTATATATTTA
91269 TTTATATATTT
1 TTTATATATTT
91280 TCCCCTTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 6 0.30
12 14 0.70
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTATATATTTA
Found at i:96374 original size:84 final size:83
Alignment explanation
Indices: 96208--97609 Score: 1263
Period size: 84 Copynumber: 17.1 Consensus size: 83
96198 TAAAAGATAG
* * * * * * * *
96208 CATTTACAGCATAACTCAAGGCTATAAGGGTTATCTGCCAGCAAAGACCTTCGAGTTCGACCACG
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAACAAAGACCTTCGAGTTCGACTACG
96273 CTCAGCTCCAA-GGCACAT
66 CTCAGCT-CAAGGGCACAT
** * * * * *
96291 CATTTGCAATATAACTCAAGGCAAGAAGGGCTATTTGCCAACAAAAGACCTTTGAGTTCGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAAC-AAAGACCTTCGAGTTCGACTAC
* * *
96356 GCTCAACTCAACGACACAT
65 GCTCAGCTCAAGGGCACAT
** * * * * *
96375 CATTTGCAATATAACTCAAGGCAAGAAGGGCTATTTGCCAACAAAAGACCTTTGAGTTCGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAAC-AAAGACCTTCGAGTTCGACTAC
* * *
96440 GCTCAACTCAACGACACAT
65 GCTCAGCTCAAGGGCACAT
* * ** * *
96459 CATTTGTAGCATAGCTTAAGTCGAGAAGGGCTATCTGCC--C-AAGACCCCCGAGTTCGATTACA
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAACAAAGACCTTCGAGTTCGACTACG
*
96521 CTCAGCTTCGAGGGCACAT
66 CTCAGC-TCAAGGGCACAT
* *
96540 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGTCAACCAAAGACCTTCGAGTTCGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAA-CAAAGACCTTCGAGTTCGACTAC
96605 GCTCAGCTCCAA-GGCACAT
65 GCTCAGCT-CAAGGGCACAT
* * * ** * *
96624 CATTTGCTGTATAGCTTAAGTCGAGAAGGGCTATCTG-C--CAAAGACCCCCGAGTTCGATTACA
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAACAAAGACCTTCGAGTTCGACTACG
*
96686 CTCAGCTTCGAGGGCACAT
66 CTCAGC-TCAAGGGCACAT
* * * *
96705 CATTTGCAGCATAACTTAAGTCAAGAAGGGTTATCTACCAACCAAAGACCTTTGAGTTCGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAA-CAAAGACCTTCGAGTTCGACTAC
* *
96770 GCTCAGCTCAACGACACAT
65 GCTCAGCTCAAGGGCACAT
* * * ** * *
96789 CATTTGCAGTATAGCTTAAGTCGAAAAGGGCTATCTG-C--CAAAGACCCCCGAGTTCGATTACA
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAACAAAGACCTTCGAGTTCGACTACG
* *
96851 CTCAGCTTCGAGGGCATAT
66 CTCAGC-TCAAGGGCACAT
* * * * * ** *
96870 CATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAAC-AAAGACCTTCGAGTTCGACTAC
96935 GCTCAGCTCTAA-GGCACAT
65 GCTCAGCTC-AAGGGCACAT
* ** * * * *
96954 CATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG-C--CAAAGACCCCCCAGTTTGATTACA
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAACAAAGACCTTCGAGTTCGACTACG
*
97016 CTCAGCTTCGAGGGCACAT
66 CTCAGC-TCAAGGGCACAT
** * * *
97035 CATTTGCAATATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTAT
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAA-CAAAGACCTTCGAGTTCGACTAC
*
97100 GCTCAGCTCAACGGCACAT
65 GCTCAGCTCAAGGGCACAT
* * * *
97119 CATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCT-CC--C-----CC--CGAGTTCGATTACA
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAACAAAGACCTTCGAGTTCGACTACG
*
97174 CTCAGCTTCGAGGGCACAT
66 CTCAGC-TCAAGGGCACAT
* * * * * * * *
97193 CATTTACAGCATAACTCAAGGCTAGAAGGGTTATATG-TAACCAAAGATCTTCGAGTTCGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAA-CAAAGACCTTCGAGTTCGACTAC
97257 GCTCAGCTCCAA-GGCACAT
65 GCTCAGCT-CAAGGGCACAT
* * * * * *
97276 CATTTGCAGCATAGCTTAAGTCGATAAGGGCTATCTG-C--CAAAGACCCTCGAGTTCAATTACA
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAACAAAGACCTTCGAGTTCGACTACG
*
97338 CTCAGCTTCGAGGGCACAT
66 CTCAGC-TCAAGGGCACAT
* * *
97357 CATTTGCAGCATAACTTAAATCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAA-CAAAGACCTTCGAGTTCGACTAC
* *
97422 GCTCAACTCTAA-GGCATAT
65 GCTCAGCTC-AAGGGCACAT
** * *
97441 CATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTG-C--CAAAGACCCCCGAGTTCGATTACA
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAACAAAGACCTTCGAGTTCGACTACG
*
97503 CTCAGCTTCGAGGGCACAT
66 CTCAGC-TCAAGGGCACAT
* * * * * * * * * *
97522 TATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTTGACTACG
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAACAAAGACCTTCGAGTTCGACTACG
*
97587 CTCAGCTCCAA-GGCATAT
66 CTCAGCT-CAAGGGCACAT
97605 CATTT
1 CATTT
97610 ACAACATAGC
Statistics
Matches: 1074, Mismatches: 193, Indels: 104
0.78 0.14 0.08
Matches are distributed among these distances:
73 16 0.01
74 38 0.04
75 2 0.00
77 1 0.00
80 152 0.14
81 242 0.23
82 6 0.01
83 90 0.08
84 403 0.38
85 124 0.12
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (83 bp):
CATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAACAAAGACCTTCGAGTTCGACTACG
CTCAGCTCAAGGGCACAT
Found at i:96601 original size:165 final size:164
Alignment explanation
Indices: 96208--97624 Score: 1877
Period size: 165 Copynumber: 8.6 Consensus size: 164
96198 TAAAAGATAG
* * * *
96208 CATTTACAGCATAACTCAAGGCTATAAGGGTTATCTGCC-AGCAAAGACCTTCGAGTTCGACCAC
1 CATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
** * * * * *
96272 GCTCAGCTCCAAGGCACATCATTTGCAATATAACTCAAGGCAAGAAGGGCTATTTGCCAACAAAA
66 GCTCAGCT-CAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG-C--C-AAA
*** * * * * * *
96337 GACCTTTGAGTTCGACTACGCTCAAC-TCAACGACACAT
126 GACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACAT
** * * * * *
96375 CATTTGCAATATAACTCAAGGCAAGAAGGGCTATTTGCCAACAAAAGACCTTTGAGTTCGACTAC
1 CATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
* * * *
96440 GCTCAACTCAACGACACATCATTTGTAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCCAAGACC
66 GCTCAGCTCAA-GGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
96505 CCCGAGTTCGATTACACTCAGCTTCGAGGGCACAT
130 CCCGAGTTCGATTACACTCAGCTTCGAGGGCACAT
* * * *
96540 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGTCAACCAAAGACCTTCGAGTTCGACTAC
1 CATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
* *
96605 GCTCAGCTCCAAGGCACATCATTTGCTGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
66 GCTCAGCT-CAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
96670 CCCGAGTTCGATTACACTCAGCTTCGAGGGCACAT
130 CCCGAGTTCGATTACACTCAGCTTCGAGGGCACAT
* * * * *
96705 CATTTGCAGCATAACTTAAGTCAAGAAGGGTTATCTACCAACCAAAGACCTTTGAGTTCGACTAC
1 CATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
* * *
96770 GCTCAGCTCAACGACACATCATTTGCAGTATAGCTTAAGTCGAAAAGGGCTATCTGCCAAAGACC
66 GCTCAGCTCAA-GGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
*
96835 CCCGAGTTCGATTACACTCAGCTTCGAGGGCATAT
130 CCCGAGTTCGATTACACTCAGCTTCGAGGGCACAT
* **
96870 CATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTG-TGACCAAAAGACCTTCGAGTTCGACTA
1 CATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACC-AAAGACCTTCGAGTTCGACTA
96934 CGCTCAGCTCTAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGAC
65 CGCTCAGCTC-AAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGAC
* *
96999 CCCCCAGTTTGATTACACTCAGCTTCGAGGGCACAT
129 CCCCGAGTTCGATTACACTCAGCTTCGAGGGCACAT
** * * * * *
97035 CATTTGCAATATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTAT
1 CATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
*
97100 GCTCAGCTCAACGGCACATCATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCT--C-----CC
66 GCTCAGCTCAA-GGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
97158 CCCGAGTTCGATTACACTCAGCTTCGAGGGCACAT
130 CCCGAGTTCGATTACACTCAGCTTCGAGGGCACAT
* * * *
97193 CATTTACAGCATAACTCAAGGCTAGAAGGGTTATATG-TAACCAAAGATCTTCGAGTTCGACTAC
1 CATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
*
97257 GCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGATAAGGGCTATCTGCCAAAGACC
66 GCTCAGCT-CAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
* *
97322 CTCGAGTTCAATTACACTCAGCTTCGAGGGCACAT
130 CCCGAGTTCGATTACACTCAGCTTCGAGGGCACAT
* ** * *
97357 CATTTGCAGCATAACTTAAATCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTAC
1 CATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
* * *
97422 GCTCAACTCTAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
66 GCTCAGCTC-AAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
97487 CCCGAGTTCGATTACACTCAGCTTCGAGGGCACAT
130 CCCGAGTTCGATTACACTCAGCTTCGAGGGCACAT
* * * * *
97522 TATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGTC-ACCAAAGACCTTCGAGTTTGACTAC
1 CATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
* * * *
97586 GCTCAGCTCCAAGGCATATCATTTACAACATAGCCTAAG
66 GCTCAGCT-CAAGGCACATCATTTGCAGCATAGCTTAAG
97625 GAATAAGGTT
Statistics
Matches: 1103, Mismatches: 127, Indels: 43
0.87 0.10 0.03
Matches are distributed among these distances:
157 72 0.07
158 68 0.06
159 1 0.00
163 1 0.00
164 152 0.14
165 702 0.64
166 8 0.01
167 36 0.03
168 63 0.06
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (164 bp):
CATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
GCTCAGCTCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCC
CCGAGTTCGATTACACTCAGCTTCGAGGGCACAT
Found at i:96853 original size:330 final size:330
Alignment explanation
Indices: 96208--97624 Score: 2077
Period size: 330 Copynumber: 4.3 Consensus size: 330
96198 TAAAAGATAG
* * * *
96208 CATTTACAGCATAACTCAAGGCTATAAGGGTTATCTG-CCAGCAAAGACCTTCGAGTTCGACCAC
1 CATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAACCAAAGACCTTCGAGTTCGACTAC
** * * * * *
96272 GCTCAGCTCCAAGGCACATCATTTGCAATATAACTCAAGGCAAGAAGGGCTATTTGCCAACAAAA
66 GCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG-C--C-AAA
*** * * * * * * * * *
96337 GACCTTTGAGTTCGACTACGCTCAAC-TCAACGACACATCATTTGCAATATAACTCAAGGCAAGA
127 GACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAACATAACTTAAGTCAAGA
* * * *
96401 AGGGCTATTTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAACTCAACGACACATCATTTGT
192 AGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACGCTCAACTCAACGACACATCATTTGC
*
96466 AGCATAGCTTAAGTCGAGAAGGGCTATCTGCCCAAGACCCCCGAGTTCGATTACACTCAGCTTCG
257 AGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCG
96531 AGGGCACAT
322 AGGGCACAT
* * * *
96540 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGTCAACCAAAGACCTTCGAGTTCGACTAC
1 CATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAACCAAAGACCTTCGAGTTCGACTAC
* *
96605 GCTCAGCTCCAAGGCACATCATTTGCTGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
66 GCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
*
96670 CCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCAAGAAGGG
131 CCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAACATAACTTAAGTCAAGAAGGG
* * *
96735 TTATCTACCAACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCAACGACACATCATTTGCAGTA
196 TTATCTGCCAACCAAAGACCTTTGAGTTCGACTACGCTCAACTCAACGACACATCATTTGCAGCA
*
96800 TAGCTTAAGTCGAAAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGG
261 TAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGG
*
96865 CATAT
326 CACAT
*
96870 CATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGT-GACCAAAAGACCTTCGAGTTCGACTA
1 CATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAACC-AAAGACCTTCGAGTTCGACTA
*
96934 CGCTCAGCTCTAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGAC
65 CGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGAC
* * * *
96999 CCCCCAGTTTGATTACACTCAGCTTCGAGGGCACATCATTTGCAATATAACTTAAGTCGAGAAGG
130 CCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAACATAACTTAAGTCAAGAAGG
* * * *
97064 GTTATCTGCCAACCAAAGACCTTTGAGTTCGACTATGCTCAGCTCAACGGCACATCATTTGCAGT
195 GTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACGCTCAACTCAACGACACATCATTTGCAGC
97129 ATAGCTTAAGTCGAGAAGGGCTATCT--C-----CCCCCGAGTTCGATTACACTCAGCTTCGAGG
260 ATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGG
97187 GCACAT
325 GCACAT
* *
97193 CATTTACAGCATAACTCAAGGCTAGAAGGGTTATATGT-AACCAAAGATCTTCGAGTTCGACTAC
1 CATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAACCAAAGACCTTCGAGTTCGACTAC
*
97257 GCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGATAAGGGCTATCTGCCAAAGACC
66 GCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
* * * * *
97322 CTCGAGTTCAATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAATCGAGAAGGG
131 CCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAACATAACTTAAGTCAAGAAGGG
* *
97387 TTATCTGCCAACCAAAGACCTTTGAGTTCGACTACGCTCAACTCTAA-GGCATATCATTTGCAGC
196 TTATCTGCCAACCAAAGACCTTTGAGTTCGACTACGCTCAACTC-AACGACACATCATTTGCAGC
*
97451 ATAACTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGG
260 ATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGG
97516 GCACAT
325 GCACAT
* * *
97522 TATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGTC-ACCAAAGACCTTCGAGTTTGACTAC
1 CATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAACCAAAGACCTTCGAGTTCGACTAC
* * * *
97586 GCTCAGCTCCAAGGCATATCATTTACAACATAGCCTAAG
66 GCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAG
97625 GAATAAGGTT
Statistics
Matches: 991, Mismatches: 82, Indels: 27
0.90 0.07 0.02
Matches are distributed among these distances:
322 224 0.23
323 78 0.08
324 1 0.00
328 1 0.00
329 156 0.16
330 425 0.43
332 33 0.03
333 73 0.07
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (330 bp):
CATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAACCAAAGACCTTCGAGTTCGACTAC
GCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
CCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAACATAACTTAAGTCAAGAAGGG
TTATCTGCCAACCAAAGACCTTTGAGTTCGACTACGCTCAACTCAACGACACATCATTTGCAGCA
TAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGG
CACAT
Found at i:98024 original size:2 final size:2
Alignment explanation
Indices: 98017--98060 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
98007 TTACATGTGT
98017 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
98059 TA
1 TA
98061 AATAATCATA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:100924 original size:2 final size:2
Alignment explanation
Indices: 100917--100946 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
100907 TTGGTATTAT
100917 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
100947 ACAAATCAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:102220 original size:26 final size:26
Alignment explanation
Indices: 102190--102252 Score: 76
Period size: 26 Copynumber: 2.4 Consensus size: 26
102180 TCCACAAGAG
102190 AAACAACAAGAGACACAGAGAGAGC-A-
1 AAACAACAAGA-ACACAG-GAGAGCAAC
* *
102216 AAACAACAAGAACATAGGAGGGCAAC
1 AAACAACAAGAACACAGGAGAGCAAC
102242 AAACAACAAGA
1 AAACAACAAGA
102253 CAATAGCGAG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
24 5 0.15
25 6 0.18
26 22 0.67
ACGTcount: A:0.59, C:0.19, G:0.21, T:0.02
Consensus pattern (26 bp):
AAACAACAAGAACACAGGAGAGCAAC
Found at i:107578 original size:188 final size:189
Alignment explanation
Indices: 107246--107627 Score: 732
Period size: 188 Copynumber: 2.0 Consensus size: 189
107236 ATTAAGCGTA
107246 TCATTCCTATATTATATGTAGTTGCAGCTAGGGTGGTAAATGAATTGGGCTTGAACGAATAAGTT
1 TCATTCCTATATTATATGTAGTTGCAGCTAGGGTGGTAAATGAATTGGGCTTGAACGAATAAGTT
107311 TGTCTTCATATTCGTTTGTTTATTTTTTAATGTGTTTATGTTCGGTTCATGTTGTTTAAATTTTA
66 TGTCTTCATATTCGTTTGTTTATTTTTTAATGTGTTTATGTTCGGTTCATGTTGTTTAAATTTTA
107376 ATATTGTGTTTGGTTTGTTCAGCGTTTGCATACATGTATTTCAGCATTCCTCAACATG-
131 ATATTGTGTTTGGTTTGTTCAGCGTTTGCATACATGTATTTCAGCATTCCTCAACATGT
107434 TCATTCCTATATTATATGTAGTTGCAGCTAGGGTGGTAAATGAATTGGGCTTGAACGAATAAGTT
1 TCATTCCTATATTATATGTAGTTGCAGCTAGGGTGGTAAATGAATTGGGCTTGAACGAATAAGTT
107499 TGTCTTCATATTCGTTTGTTTATTTTTTAATGTGTTTATGTTCGGTTCATGTTTGTTTAAATTTT
66 TGTCTTCATATTCGTTTGTTTATTTTTTAATGTGTTTATGTTCGGTTCATG-TTGTTTAAATTTT
*
107564 AATATTGT-TTTGGTTTGTTCAGCGTTTGCATGCATGTATTTCAGCATTCCTCAACATGT
130 AATATTGTGTTTGGTTTGTTCAGCGTTTGCATACATGTATTTCAGCATTCCTCAACATGT
107623 TCATT
1 TCATT
107628 TTTATGTCCA
Statistics
Matches: 191, Mismatches: 1, Indels: 3
0.98 0.01 0.02
Matches are distributed among these distances:
188 165 0.86
189 26 0.14
ACGTcount: A:0.22, C:0.12, G:0.19, T:0.47
Consensus pattern (189 bp):
TCATTCCTATATTATATGTAGTTGCAGCTAGGGTGGTAAATGAATTGGGCTTGAACGAATAAGTT
TGTCTTCATATTCGTTTGTTTATTTTTTAATGTGTTTATGTTCGGTTCATGTTGTTTAAATTTTA
ATATTGTGTTTGGTTTGTTCAGCGTTTGCATACATGTATTTCAGCATTCCTCAACATGT
Found at i:114468 original size:19 final size:20
Alignment explanation
Indices: 114435--114473 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
114425 ACTAGCCTTA
114435 TTGAATTAAACCAAA-GAAG
1 TTGAATTAAACCAAATGAAG
**
114454 TTGAATTAATGCAAATGAAG
1 TTGAATTAAACCAAATGAAG
114474 AAAAGAGCCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.49, C:0.08, G:0.18, T:0.26
Consensus pattern (20 bp):
TTGAATTAAACCAAATGAAG
Found at i:115824 original size:15 final size:14
Alignment explanation
Indices: 115804--115846 Score: 52
Period size: 15 Copynumber: 3.0 Consensus size: 14
115794 ATTTATATAT
115804 TTTAATAATTAAAAA
1 TTTAATAA-TAAAAA
*
115819 TTTAATAAAAAATAA
1 TTTAATAATAAA-AA
115834 TTT-ATAATAAAAA
1 TTTAATAATAAAAA
115847 AATCATTATG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
13 2 0.08
14 10 0.40
15 13 0.52
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
TTTAATAATAAAAA
Found at i:116190 original size:8 final size:8
Alignment explanation
Indices: 116177--116202 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
116167 ATTATATGAT
116177 TGTTTAAA
1 TGTTTAAA
116185 TGTTTAAA
1 TGTTTAAA
116193 TGTTTAAA
1 TGTTTAAA
116201 TG
1 TG
116203 ATATATTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50
Consensus pattern (8 bp):
TGTTTAAA
Found at i:117562 original size:18 final size:19
Alignment explanation
Indices: 117526--117568 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
117516 GCTTACTCAT
117526 TAATTTGTGAAAATAAAAA
1 TAATTTGTGAAAATAAAAA
* * *
117545 -AATTTGTTAAATTTAAAA
1 TAATTTGTGAAAATAAAAA
117563 TAATTT
1 TAATTT
117569 AAAATAACGT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.42
Consensus pattern (19 bp):
TAATTTGTGAAAATAAAAA
Found at i:122917 original size:75 final size:75
Alignment explanation
Indices: 122838--123006 Score: 186
Period size: 75 Copynumber: 2.3 Consensus size: 75
122828 ACTATTTAAG
* * *
122838 AATTTATATTCAATTAGAATTTG-AAA-TGTTATCTACGAATTTATA-TTATATTGAAATAATAA
1 AATTTATATTCGATTAGAA-TTGCAAAGTGTTATCTACGAATTTATATTTA-ATTAAAATAAGAA
*
122900 TATATTTTTTATA
64 TATA-TTATTATA
* * * * *
122913 AATTTATATTTGATTA-AA-TGCAAATGTGTTATTTATGAATTTTTATTTAATTAAAATACGAAT
1 AATTTATATTCGATTAGAATTGCAAA-GTGTTATCTACGAATTTATATTTAATTAAAATAAGAAT
122976 ATATTATTATA
65 ATATTATTATA
122987 AATTTATATTCGATTAGAAT
1 AATTTATATTCGATTAGAAT
123007 ACAATATTAT
Statistics
Matches: 78, Mismatches: 10, Indels: 11
0.79 0.10 0.11
Matches are distributed among these distances:
72 2 0.03
73 3 0.04
74 24 0.31
75 46 0.59
76 3 0.04
ACGTcount: A:0.41, C:0.04, G:0.08, T:0.48
Consensus pattern (75 bp):
AATTTATATTCGATTAGAATTGCAAAGTGTTATCTACGAATTTATATTTAATTAAAATAAGAATA
TATTATTATA
Found at i:122954 original size:37 final size:37
Alignment explanation
Indices: 122875--123010 Score: 125
Period size: 37 Copynumber: 3.6 Consensus size: 37
122865 GTTATCTACG
*
122875 AATTTATATTAT-ATTGAAATA-ATAATATATTTTTTATA
1 AATTTATATT-TGATT-AAATACA-AATATATTATTTATA
* * * *
122913 AATTTATATTTGATTAAATGCAAATGTGTTATTTATG
1 AATTTATATTTGATTAAATACAAATATATTATTTATA
* * *
122950 AATTTTTATTTAATTAAAATACGAATATATTA-TTATA
1 AATTTATATTTGATT-AAATACAAATATATTATTTATA
*
122987 AATTTATATTCGATTAGAATACAA
1 AATTTATATTTGATTA-AATACAA
123011 TATTATAGTT
Statistics
Matches: 78, Mismatches: 16, Indels: 9
0.76 0.16 0.09
Matches are distributed among these distances:
36 1 0.01
37 51 0.65
38 26 0.33
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.48
Consensus pattern (37 bp):
AATTTATATTTGATTAAATACAAATATATTATTTATA
Found at i:127801 original size:12 final size:12
Alignment explanation
Indices: 127784--127811 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
127774 TTTGAAGAAT
127784 TGCATGATCATG
1 TGCATGATCATG
127796 TGCATGATCATG
1 TGCATGATCATG
127808 TGCA
1 TGCA
127812 AAGGAGGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (12 bp):
TGCATGATCATG
Found at i:133565 original size:18 final size:19
Alignment explanation
Indices: 133527--133565 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
133517 GTATGATTTT
*
133527 AAAAAAATAATGATAATTA
1 AAAAAAATAATGATAAATA
*
133546 AAAAAAATTATGA-AAATA
1 AAAAAAATAATGATAAATA
133564 AA
1 AA
133566 TGCATCACTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (19 bp):
AAAAAAATAATGATAAATA
Found at i:137881 original size:20 final size:21
Alignment explanation
Indices: 137856--137902 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
137846 ATAAGGGATC
137856 AAAAATTAAAT-TAACCCTTA
1 AAAAATTAAATATAACCCTTA
* * *
137876 AAAAATTACATATCACCTTTA
1 AAAAATTAAATATAACCCTTA
137897 AAAAAT
1 AAAAAT
137903 GTGCCAAGTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 10 0.43
21 13 0.57
ACGTcount: A:0.55, C:0.15, G:0.00, T:0.30
Consensus pattern (21 bp):
AAAAATTAAATATAACCCTTA
Found at i:143778 original size:24 final size:24
Alignment explanation
Indices: 143746--143799 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
143736 GAATAGAAAA
143746 CTTAGAAGTAACAGGATCAACAAC
1 CTTAGAAGTAACAGGATCAACAAC
*
143770 CTTAGAAGTAACAGGATCAGCAAC
1 CTTAGAAGTAACAGGATCAACAAC
143794 CTTAGA
1 CTTAGA
143800 GGACAGTAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.43, C:0.20, G:0.19, T:0.19
Consensus pattern (24 bp):
CTTAGAAGTAACAGGATCAACAAC
Found at i:150146 original size:50 final size:49
Alignment explanation
Indices: 150024--150147 Score: 133
Period size: 50 Copynumber: 2.5 Consensus size: 49
150014 GCAGTAAAGT
* * * *
150024 GCGCCCTCTGAACCGCGCTATACGTTGATTTGGCGCCAAGTGGGTATAAC
1 GCGCCCCCTG-ACCGCGCTATACGGTGATCTGGCGCCAAGTGGGTACAAC
* * *
150074 GCGCCCCCTG-CCTTGCGATATACGGTGATCTGGCGCCATGTGGGTACAGC
1 GCGCCCCCTGACC--GCGCTATACGGTGATCTGGCGCCAAGTGGGTACAAC
*
150124 GCGTCCCCTGATCCGCGCTATACG
1 GCGCCCCCTGA-CCGCGCTATACG
150148 TCACGTAGGG
Statistics
Matches: 61, Mismatches: 9, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
48 2 0.03
50 57 0.93
52 2 0.03
ACGTcount: A:0.16, C:0.32, G:0.29, T:0.23
Consensus pattern (49 bp):
GCGCCCCCTGACCGCGCTATACGGTGATCTGGCGCCAAGTGGGTACAAC
Found at i:154398 original size:18 final size:18
Alignment explanation
Indices: 154375--154414 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
154365 AAAGACGATG
154375 GCGGCATCATATATGGCT
1 GCGGCATCATATATGGCT
*
154393 GCGGCATCATATATGGTT
1 GCGGCATCATATATGGCT
154411 GCGG
1 GCGG
154415 TGGCTACTGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.20, C:0.20, G:0.33, T:0.28
Consensus pattern (18 bp):
GCGGCATCATATATGGCT
Found at i:156115 original size:111 final size:111
Alignment explanation
Indices: 155921--156253 Score: 621
Period size: 111 Copynumber: 3.0 Consensus size: 111
155911 ATTGCAAAAA
*
155921 TTAATTCTTACTCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
*
155986 AATTAAAACGTTAAAATGTTATCGTATCAGCAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
156032 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
156097 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
* *
156143 TTAATTTTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
*
156208 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
156254 ATGATTTCTA
Statistics
Matches: 217, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
111 217 1.00
ACGTcount: A:0.44, C:0.11, G:0.08, T:0.36
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
Found at i:156704 original size:35 final size:35
Alignment explanation
Indices: 156657--156742 Score: 100
Period size: 35 Copynumber: 2.5 Consensus size: 35
156647 AAAACAGTCA
* * *
156657 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
* * * *
156692 TCAATTTTATTCTAAACCCTAAATTCTAAAATACT
1 TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
*
156727 TCAATTAAATTCTAAA
1 TCAATTTAATTCTAAA
156743 ATACTTCAAT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.41, C:0.21, G:0.01, T:0.37
Consensus pattern (35 bp):
TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
Found at i:156736 original size:21 final size:21
Alignment explanation
Indices: 156711--156753 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
156701 TTCTAAACCC
156711 TAAATTCTAAAATACTTCAAT
1 TAAATTCTAAAATACTTCAAT
156732 TAAATTCTAAAATACTTCAAT
1 TAAATTCTAAAATACTTCAAT
156753 T
1 T
156754 TAAGGTAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.47, C:0.14, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATTCTAAAATACTTCAAT
Found at i:156906 original size:16 final size:18
Alignment explanation
Indices: 156874--156907 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
156864 TATTAATGTA
156874 TGAATCATTTATATTTTT
1 TGAATCATTTATATTTTT
156892 TGAAT-ATTT-TATTTTT
1 TGAATCATTTATATTTTT
156908 AATAAGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (18 bp):
TGAATCATTTATATTTTT
Found at i:157563 original size:23 final size:23
Alignment explanation
Indices: 157533--157592 Score: 104
Period size: 23 Copynumber: 2.7 Consensus size: 23
157523 GTCACCAATG
157533 ACACGTGTCATGATCATGTGCTA
1 ACACGTGTCATGATCATGTGCTA
157556 ACACGTGTCATGATCATGTGCTA
1 ACACGTGTCATGATCATGTGCTA
*
157579 ACACATGTCA-GATC
1 ACACGTGTCATGATC
157593 CTAATTAAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
22 4 0.11
23 32 0.89
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.28
Consensus pattern (23 bp):
ACACGTGTCATGATCATGTGCTA
Found at i:158657 original size:376 final size:376
Alignment explanation
Indices: 157964--158716 Score: 1461
Period size: 376 Copynumber: 2.0 Consensus size: 376
157954 AATTATACTA
157964 TTATATTTATATAAAAAATACGTATCACATGAAATAAGATGAAATCAAATAATAATAACTTTGAC
1 TTATATTTATATAAAAAATACGTATCACATGAAATAAGATGAAATCAAATAATAATAACTTTGAC
158029 ATAATTGAATTTAATTTAAGTATTTTGGAATTTAGGGTTTAGAATAAAATTGAATTACTTTGGAA
66 ATAATTGAATTTAATTTAAGTATTTTGGAATTTAGGGTTTAGAATAAAATTGAATTACTTTGGAA
158094 ATTGGGGTTTAGAATGAAATTGATGATTGTTTTGCAAGTTTTAAAAGTTGGGGGACCTAAATTAA
131 ATTGGGGTTTAGAATGAAATTGATGATTGTTTTGCAAGTTTTAAAAGTTGGGGGACCTAAATTAA
158159 AGTGACTGAAAAGTTCAATGACCATTTATATAATTTATCCTAATTTTCTAACTGTGGTTTAAGTT
196 AGTGACTGAAAAGTTCAATGACCATTTATATAATTTATCCTAATTTTCTAACTGTGGTTTAAGTT
*
158224 GGGGGACCATATTGCAAACGGAATAAATGTTGGGGGACTGTATTGCAAGTTTTAAATGTTGGGGG
261 GGGGGACCATATTGCAAACAGAATAAATGTTGGGGGACTGTATTGCAAGTTTTAAATGTTGGGGG
158289 ACCTAAATGCAAGCTTCTGAAATGTTCAGTGACCATTACTATACTTTACCC
326 ACCTAAATGCAAGCTTCTGAAATGTTCAGTGACCATTACTATACTTTACCC
*
158340 TTATATTTATATAAAAAATACGTATCACATGAAATAAGATGAAATTAAATAATAATAACTTTGAC
1 TTATATTTATATAAAAAATACGTATCACATGAAATAAGATGAAATCAAATAATAATAACTTTGAC
158405 ATAATTGAATTTAATTTAAGTATTTTGGAATTTAGGGTTTAGAATAAAATTGAATTACTTTGGAA
66 ATAATTGAATTTAATTTAAGTATTTTGGAATTTAGGGTTTAGAATAAAATTGAATTACTTTGGAA
*
158470 ATTGGGGTTTAGAATGAAATTGATGATTGTTTTGCAAGTTTTAAAAGTTGGGGGACCTAAATTCA
131 ATTGGGGTTTAGAATGAAATTGATGATTGTTTTGCAAGTTTTAAAAGTTGGGGGACCTAAATTAA
*
158535 AGTGACTGAAAAGTTCAATGACCATTTTTATAATTTATCCTAATTTTCTAACTGTGGTTTAAGTT
196 AGTGACTGAAAAGTTCAATGACCATTTATATAATTTATCCTAATTTTCTAACTGTGGTTTAAGTT
158600 GGGGGACCATATTGCAAACAGAATAAATGTTGGGGGACTGTATTGCAAGTTTTAAATGTTGGGGG
261 GGGGGACCATATTGCAAACAGAATAAATGTTGGGGGACTGTATTGCAAGTTTTAAATGTTGGGGG
*
158665 ACGTAAATGCAAGCTTCTGAAATGTTCAGTGACCATTACTATACTTTACCC
326 ACCTAAATGCAAGCTTCTGAAATGTTCAGTGACCATTACTATACTTTACCC
158716 T
1 T
158717 AAAAGTAATT
Statistics
Matches: 372, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
376 372 1.00
ACGTcount: A:0.35, C:0.10, G:0.19, T:0.36
Consensus pattern (376 bp):
TTATATTTATATAAAAAATACGTATCACATGAAATAAGATGAAATCAAATAATAATAACTTTGAC
ATAATTGAATTTAATTTAAGTATTTTGGAATTTAGGGTTTAGAATAAAATTGAATTACTTTGGAA
ATTGGGGTTTAGAATGAAATTGATGATTGTTTTGCAAGTTTTAAAAGTTGGGGGACCTAAATTAA
AGTGACTGAAAAGTTCAATGACCATTTATATAATTTATCCTAATTTTCTAACTGTGGTTTAAGTT
GGGGGACCATATTGCAAACAGAATAAATGTTGGGGGACTGTATTGCAAGTTTTAAATGTTGGGGG
ACCTAAATGCAAGCTTCTGAAATGTTCAGTGACCATTACTATACTTTACCC
Found at i:160925 original size:51 final size:52
Alignment explanation
Indices: 160847--160949 Score: 154
Period size: 51 Copynumber: 2.0 Consensus size: 52
160837 AGTTCTCATG
** * *
160847 CAATAACCTTCAATTAGTGTGTGTGATTGGCCA-CTTGTGAATGAAAACTAT
1 CAATAACCAGCAATTAGTGGGTCTGATTGGCCATCTTGTGAATGAAAACTAT
*
160898 CAATAACCAGCAATTAGTGGGTCTGATTGGCCATTTTGTGAATGAAAACTAT
1 CAATAACCAGCAATTAGTGGGTCTGATTGGCCATCTTGTGAATGAAAACTAT
160950 GCTTTCTTAT
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
51 29 0.63
52 17 0.37
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (52 bp):
CAATAACCAGCAATTAGTGGGTCTGATTGGCCATCTTGTGAATGAAAACTAT
Found at i:171270 original size:33 final size:34
Alignment explanation
Indices: 171224--171296 Score: 96
Period size: 33 Copynumber: 2.2 Consensus size: 34
171214 CCATAGATTA
* *
171224 TAATTTCACGAGCCTGTCTATCTT-C-TAGTTTAG
1 TAATTTCAAGAGCCTGCCTAT-TTACTTAGTTTAG
*
171257 TAATTTCAAGAGCCTGCCTATTTACTTATTTTAG
1 TAATTTCAAGAGCCTGCCTATTTACTTAGTTTAG
171291 TAATTT
1 TAATTT
171297 ATTACTGTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
32 2 0.06
33 20 0.57
34 13 0.37
ACGTcount: A:0.25, C:0.18, G:0.12, T:0.45
Consensus pattern (34 bp):
TAATTTCAAGAGCCTGCCTATTTACTTAGTTTAG
Found at i:186805 original size:20 final size:20
Alignment explanation
Indices: 186776--186867 Score: 74
Period size: 20 Copynumber: 5.0 Consensus size: 20
186766 AGCAACAAAA
* *
186776 TAAAAATGATTCTATCTAAT
1 TAAAACTGATCCTATCTAAT
186796 TAAAACTGATCCTATCTAA-
1 TAAAACTGATCCTATCTAAT
* *
186815 T--AACT-A-AC-A--GAAT
1 TAAAACTGATCCTATCTAAT
* *
186828 AAAAACTGATTCTATCTAAT
1 TAAAACTGATCCTATCTAAT
186848 TAAAACTGATCCTATCTAAT
1 TAAAACTGATCCTATCTAAT
186868 AACTAACATA
Statistics
Matches: 55, Mismatches: 9, Indels: 16
0.69 0.11 0.20
Matches are distributed among these distances:
12 2 0.04
14 1 0.02
15 5 0.09
16 2 0.04
17 5 0.09
18 1 0.02
19 1 0.02
20 38 0.69
ACGTcount: A:0.45, C:0.16, G:0.05, T:0.34
Consensus pattern (20 bp):
TAAAACTGATCCTATCTAAT
Found at i:186841 original size:52 final size:51
Alignment explanation
Indices: 186769--186883 Score: 203
Period size: 52 Copynumber: 2.2 Consensus size: 51
186759 TAAAATTAGC
186769 AACAAAATAAAAATGATTCTATCTAATTAAAACTGATCCTATCTAATAACT
1 AACAAAATAAAAATGATTCTATCTAATTAAAACTGATCCTATCTAATAACT
*
186820 AACAGAATAAAAACTGATTCTATCTAATTAAAACTGATCCTATCTAATAACT
1 AACAAAATAAAAA-TGATTCTATCTAATTAAAACTGATCCTATCTAATAACT
*
186872 AACATAATAAAA
1 AACAAAATAAAA
186884 TATCTAGTTA
Statistics
Matches: 61, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
51 12 0.20
52 49 0.80
ACGTcount: A:0.50, C:0.16, G:0.04, T:0.30
Consensus pattern (51 bp):
AACAAAATAAAAATGATTCTATCTAATTAAAACTGATCCTATCTAATAACT
Found at i:193149 original size:17 final size:16
Alignment explanation
Indices: 193123--193154 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
193113 TTGCCTGCTG
193123 GCCGCTGCCGCCGCCC
1 GCCGCTGCCGCCGCCC
193139 GCCGTCTGCCGCCGCC
1 GCCG-CTGCCGCCGCC
193155 GTCAGCCGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.00, C:0.59, G:0.31, T:0.09
Consensus pattern (16 bp):
GCCGCTGCCGCCGCCC
Found at i:193154 original size:20 final size:20
Alignment explanation
Indices: 193124--193171 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
193114 TGCCTGCTGG
* *
193124 CCGCTGCCGCCGCCCGCCGT
1 CCGCCGCCGCCGCCAGCCGT
* *
193144 CTGCCGCCGCCGTCAGCCGT
1 CCGCCGCCGCCGCCAGCCGT
193164 CCGCCGCC
1 CCGCCGCC
193172 ACACTCTGAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.02, C:0.58, G:0.29, T:0.10
Consensus pattern (20 bp):
CCGCCGCCGCCGCCAGCCGT
Found at i:207041 original size:29 final size:29
Alignment explanation
Indices: 207008--207094 Score: 174
Period size: 29 Copynumber: 3.0 Consensus size: 29
206998 AAACTTATGA
207008 ATGTCTATGAATCATATTGAATAGCATAC
1 ATGTCTATGAATCATATTGAATAGCATAC
207037 ATGTCTATGAATCATATTGAATAGCATAC
1 ATGTCTATGAATCATATTGAATAGCATAC
207066 ATGTCTATGAATCATATTGAATAGCATAC
1 ATGTCTATGAATCATATTGAATAGCATAC
207095 GTGCTCAGAT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 58 1.00
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.34
Consensus pattern (29 bp):
ATGTCTATGAATCATATTGAATAGCATAC
Done.