Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008981.1 Hibiscus syriacus cultivar Beakdansim tig00112343_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: 1473337
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
File 2 of 7
Found at i:179298 original size:84 final size:83
Alignment explanation
Indices: 178797--179298 Score: 481
Period size: 84 Copynumber: 6.0 Consensus size: 83
178787 ACAAATTTAT
* * * * * * * * **
178797 TGACAGATAACCCTTCTTGCCTTGAGCTATGCTGTAAATTTGGTTTGCCTCTGAGCTGAATGTAA
1 TGACAGATAACCCTTCTCGACTTAAGTTATGCTGCAAA--TGATGTGCCTCGGAGCTGAGCGTAA
* *
178862 TCGAACTCGAAGGCCTTCGG
64 TCGAACTCGAAGGTCTTTGG
* * * *
178882 TTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGT
1 -TGACAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTCGGAGCTGAGCGTAAT
178947 CGAACTCGAAGGTCTTTGG
65 CGAACTCGAAGGTCTTTGG
* * * * * * **
178966 TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAACCTGAGTATAAT
1 TGACAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG-CCTCGGAGCTGAGCGTAAT
*
179031 CGAACTCGAGGGTCTTT-G
65 CGAACTCGAAGGTCTTTGG
* * * * * *
179049 -G-CAGATAGCCCTTTTCGACTTAAGTTATACTGCAAATGATGTGCCTTGGAGTTGAGCGTAGTC
1 TGACAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTCGGAGCTGAGCGTAATC
*
179112 GAACTCGAAGGTATTTGG
66 GAACTCGAAGGTCTTTGG
* * *
179130 TTGGA-AGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAG
1 -T-GACAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTCGGAGCTGAGCGTAA
*
179194 TCAAACTCGAAGGTCTTTTGG
64 TCGAACTCGAAGGTC-TTTGG
* * * * * * * ** *
179215 TGACAGATAACCCTTCTAGCCTTGAGTTGTGCTGTAAATGATGTACCCTCGAAGCCAAGTGTAAT
1 TGACAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT-GCCTCGGAGCTGAGCGTAAT
*
179280 CGAACTCGAGGGTCTTTGG
65 CGAACTCGAAGGTCTTTGG
179299 CAGATAACCG
Statistics
Matches: 342, Mismatches: 65, Indels: 20
0.80 0.15 0.05
Matches are distributed among these distances:
80 27 0.08
81 36 0.11
82 1 0.00
83 42 0.12
84 173 0.51
85 30 0.09
86 33 0.10
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (83 bp):
TGACAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTCGGAGCTGAGCGTAATC
GAACTCGAAGGTCTTTGG
Found at i:179435 original size:34 final size:35
Alignment explanation
Indices: 179357--179445 Score: 153
Period size: 35 Copynumber: 2.6 Consensus size: 35
179347 AACTCGAAGG
*
179357 TTTTGTGTTTCGAGAGAAACAATTTCAAAGGGTTT
1 TTTTGTGTTTCAAGAGAAACAATTTCAAAGGGTTT
179392 TTTTGTGTTTCAAGAGAAACAATTTCAAA-GGTTT
1 TTTTGTGTTTCAAGAGAAACAATTTCAAAGGGTTT
*
179426 TTTTATGTTTCAAGAGAAAC
1 TTTTGTGTTTCAAGAGAAAC
179446 TGTCTCAAGA
Statistics
Matches: 52, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
34 24 0.46
35 28 0.54
ACGTcount: A:0.31, C:0.09, G:0.19, T:0.40
Consensus pattern (35 bp):
TTTTGTGTTTCAAGAGAAACAATTTCAAAGGGTTT
Found at i:179578 original size:36 final size:36
Alignment explanation
Indices: 179531--179646 Score: 187
Period size: 36 Copynumber: 3.2 Consensus size: 36
179521 GTTCAAAGAT
*
179531 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGATAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
179567 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* **
179603 TATGTTTCAAGAAAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
179639 CTTTGTTT
1 -TTTGTTT
179647 TGAGTAAATT
Statistics
Matches: 74, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
36 68 0.92
37 6 0.08
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.28
Consensus pattern (36 bp):
TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
Found at i:180392 original size:43 final size:43
Alignment explanation
Indices: 180323--180446 Score: 203
Period size: 43 Copynumber: 2.9 Consensus size: 43
180313 TGTGTAGATG
* * *
180323 GGCACGATATCCTTCGCCGTGAAGTTGAAATCGTGGATTTGTA
1 GGCACGATATCCTCCGTCGTGGAGTTGAAATCGTGGATTTGTA
* *
180366 GGCATGATATCCTCCGTCGTGGAGTTGAAATCATGGATTTGTA
1 GGCACGATATCCTCCGTCGTGGAGTTGAAATCGTGGATTTGTA
180409 GGCACGATATCCTCCGTCGTGGAGTTGAAATCGTGGAT
1 GGCACGATATCCTCCGTCGTGGAGTTGAAATCGTGGAT
180447 GGCCATTTCA
Statistics
Matches: 74, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 74 1.00
ACGTcount: A:0.23, C:0.19, G:0.29, T:0.30
Consensus pattern (43 bp):
GGCACGATATCCTCCGTCGTGGAGTTGAAATCGTGGATTTGTA
Found at i:181741 original size:95 final size:95
Alignment explanation
Indices: 181552--181787 Score: 307
Period size: 95 Copynumber: 2.5 Consensus size: 95
181542 GCATTTAGCC
* *
181552 AATTGCTCTAGAGGGACAACTCAA--TATTATTGTATAAATATAATTATCACATTTATCAGGTTA
1 AATTGCTTTAGAGGGACAACTCAAGCT-TTATTGTAT--ATAT-A-TATCACATTTATCAGGCTA
* *
181615 GCTGAATATTATCCATAAAGTCAGGGTGTTTAACA
61 GCTGAATATTATCCATAAAGCCAGGGAGTTTAACA
*
181650 AATTGCTTTAGAGGGACAACTCAAGCTTTATTGTATAGTATA-ATCACCTTTATCAGGCTAGCTG
1 AATTGCTTTAGAGGGACAACTCAAGCTTTATTGTATA-TATATATCACATTTATCAGGCTAGCTG
* * *
181714 ACTCTTATCCATAAAGCCGGGGAGTTTAACA
65 AATATTATCCATAAAGCCAGGGAGTTTAACA
* *
181745 AATTGCTTTAGAGGGACAGCTCAAGCTTTATTATATATATATA
1 AATTGCTTTAGAGGGACAACTCAAGCTTTATTGTATATATATA
181788 ATATTATAAT
Statistics
Matches: 124, Mismatches: 10, Indels: 11
0.86 0.07 0.08
Matches are distributed among these distances:
94 4 0.03
95 82 0.66
97 2 0.02
98 26 0.21
99 9 0.07
100 1 0.01
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Consensus pattern (95 bp):
AATTGCTTTAGAGGGACAACTCAAGCTTTATTGTATATATATATCACATTTATCAGGCTAGCTGA
ATATTATCCATAAAGCCAGGGAGTTTAACA
Found at i:184090 original size:96 final size:95
Alignment explanation
Indices: 183911--184148 Score: 291
Period size: 95 Copynumber: 2.6 Consensus size: 95
183901 ATTATATATG
* *
183911 TATACAATAAAGCTTGATTTGTCCCTCTAAAGCAATTGGTTAAACGCCCTGGCTTTATAGATAAG
1 TATAAAATAAAGCTTGATTTGTCCCTCTAAAGCAATTGGTTAAACGCCCCGGCTTTATAGATAAG
*
183976 ATTCAGCTAGCCTGATAAATGTGATTATAC
66 ATTCAGCTAGCCTAATAAATGTGATTATAC
* *
184006 TATAAAATAAAGCTTGATTTGTCCCTCTAGAGCAATTGGTTAAAACGCCCCGGCTTTATGGATAA
1 TATAAAATAAAGCTTGATTTGTCCCTCTAAAGCAATTGGTT-AAACGCCCCGGCTTTATAGATAA
* *
184071 TATTCAGTTAGCCTAATAAA-G-G--T-T-C
65 GATTCAGCTAGCCTAATAAATGTGATTATAC
* * * *
184096 T-TATAAT--A--TTGAGTTGTCCCTCTAAAGCAAATGGTTAAACACCCCGGCTTTAT
1 TATAAAATAAAGCTTGATTTGTCCCTCTAAAGCAATTGGTTAAACGCCCCGGCTTTAT
184149 GGATTCAGCT
Statistics
Matches: 130, Mismatches: 12, Indels: 13
0.84 0.08 0.08
Matches are distributed among these distances:
84 16 0.12
85 25 0.19
87 1 0.01
89 5 0.04
90 2 0.02
91 1 0.01
92 1 0.01
94 1 0.01
95 40 0.31
96 38 0.29
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (95 bp):
TATAAAATAAAGCTTGATTTGTCCCTCTAAAGCAATTGGTTAAACGCCCCGGCTTTATAGATAAG
ATTCAGCTAGCCTAATAAATGTGATTATAC
Found at i:185719 original size:84 final size:84
Alignment explanation
Indices: 185318--186060 Score: 599
Period size: 84 Copynumber: 8.9 Consensus size: 84
185308 TATTTGCCAA
* * * *
185318 CAAAAGACCTTCGAGTTTGACT-CGCTCAACTCA-AAGGCACATAATTTGCAGCATAGCTTAAGT
1 CAAAAGACCTTCGAGTTCGACTACGCTCAGCT-ATAAGGCACATCATTTGCAGCATAACTTAAGT
* * *
185381 CAAGAAGGGTTATTTGCCAC
65 CGAGAAGGGTTATCTGTCAC
* * * * ** ** * *
185401 CAAAAGACCTTCGTGTTTGACTACGTTTAGCTCCAAGGCACATCATTTATAGCATAACTCAAGGC
1 CAAAAGACCTTCGAGTTCGACTACGCTCAGCTATAAGGCACATCATTTGCAGCATAACTTAAGTC
*
185466 TAGAAGGGTTATC--T-AC
66 GAGAAGGGTTATCTGTCAC
* * * *
185482 CAAAAAACACTTTCGAGTTCGACTATGCTCAGCTCA-AAGGCAAATCATTTGCAGCATAGCTTAA
1 CAAAAGAC-C-TTCGAGTTCGACTACGCTCAGCT-ATAAGGCACATCATTTGCAGCATAACTTAA
*
185546 GTCGAGAAGGGCTATCTG---C
63 GTCGAGAAGGGTTATCTGTCAC
* * ** * * *
185565 C-AAAGACCCTT-GAGTTTGATTAAACTCAGCT-TCGAGGGCACATCATTTACAGCATAACTCAA
1 CAAAAGA-CCTTCGAGTTCGACTACGCTCAGCTAT--AAGGCACATCATTTGCAGCATAACTTAA
* * *
185627 GGCTAGAAGGGTTATATGTCAC
63 GTCGAGAAGGGTTATCTGTCAC
* * * * *
185649 CAAAAGACCTTCGAGTTTGACTACGCTCAGCTATAAGCCATATCATTTGTAGTATAACTTAAGTC
1 CAAAAGACCTTCGAGTTCGACTACGCTCAGCTATAAGGCACATCATTTGCAGCATAACTTAAGTC
185714 GAGAAGGGTTATCT-TCCAAC
66 GAGAAGGGTTATCTGT-C-AC
* ** * *
185734 C-AAAGACCTTCGAGTTCGACTATGCTCAGCTCCAAGGCACATTATTTGCAGTATAACTTAAGTC
1 CAAAAGACCTTCGAGTTCGACTACGCTCAGCTATAAGGCACATCATTTGCAGCATAACTTAAGTC
*
185798 GAGAAGGGCTATCTG---C
66 GAGAAGGGTTATCTGTCAC
* * * * * * * * *
185814 C-AAAGA-CTCTCGAGTTCAAATACACTCAGCTTTGAGGGTAGATCATTTACAGCATAACTCAAG
1 CAAAAGACCT-TCGAGTTCGACTACGCTCAGCTAT-AAGGCACATCATTTGCAGCATAACTTAAG
* *
185877 GCTAGAAGGGTTATCTGTCAC
64 TCGAGAAGGGTTATCTGTCAC
* * * * * *
185898 CAAAAGACCTTCGAGTTCGACTATGCTCATCTCTAAGGCATATTATTTGCAACATAACTTAAGTC
1 CAAAAGACCTTCGAGTTCGACTACGCTCAGCTATAAGGCACATCATTTGCAGCATAACTTAAGTC
*
185963 GAGAAGGGTTATCTGCCAAC
66 GAGAAGGGTTATCTGTC-AC
* ** * * * *
185983 C-AAACACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAGCTCAAGGC
1 CAAAAGACCTTCGAGTTCGACTACGCTCAGCTATAAGGCACATCATTTGCAGCATAACTTAAGTC
* *
186047 AAGAAGGGCTATCT
66 GAGAAGGGTTATCT
186061 ATCAATAAAA
Statistics
Matches: 522, Mismatches: 110, Indels: 55
0.76 0.16 0.08
Matches are distributed among these distances:
79 2 0.00
80 41 0.08
81 84 0.16
82 6 0.01
83 79 0.15
84 256 0.49
85 51 0.10
86 3 0.01
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.26
Consensus pattern (84 bp):
CAAAAGACCTTCGAGTTCGACTACGCTCAGCTATAAGGCACATCATTTGCAGCATAACTTAAGTC
GAGAAGGGTTATCTGTCAC
Found at i:185721 original size:165 final size:164
Alignment explanation
Indices: 185327--186060 Score: 432
Period size: 165 Copynumber: 4.4 Consensus size: 164
185317 ACAAAAGACC
* * * * * * * *
185327 TTCGAGTTTGACT-CGCTCAACTCAAAGGCACATAATTTGCAGCATAGCTTAAGTCAAGAAGGGT
1 TTCGAGTTCGACTACGCTCAGCTCAAAGCCAAATCATTTGCAGCATAACTTAAGTCGAGAAGGGC
* * * *** * * * *
185391 TATTTGCCACCAAAAGA-CCTTCGTGTTTGACTACGTTTAGC-TCCAAGGCACATCATTTATAGC
66 TATCTG---CC-AAAGACCCTT-GAGTTTGATTAAACTCAGCTTCGAGGGCACATCATTTACAGC
185454 ATAACTCAAGGCTAGAAGGGTTATCTACCAAAAAACACT
126 ATAACTCAAGGCTAGAAGGGTTATCTACCAAAAAACACT
* * *
185493 TTCGAGTTCGACTATGCTCAGCTCAAAGGCAAATCATTTGCAGCATAGCTTAAGTCGAGAAGGGC
1 TTCGAGTTCGACTACGCTCAGCTCAAAGCCAAATCATTTGCAGCATAACTTAAGTCGAGAAGGGC
185558 TATCTGCCAAAGACCCTTGAGTTTGATTAAACTCAGCTTCGAGGGCACATCATTTACAGCATAAC
66 TATCTGCCAAAGACCCTTGAGTTTGATTAAACTCAGCTTCGAGGGCACATCATTTACAGCATAAC
* *
185623 TCAAGGCTAGAAGGGTTATATGTCACCAAAAGAC-C-
131 TCAAGGCTAGAAGGG-T-TATCT-ACCAAAAAACACT
* * * *
185658 TTCGAGTTTGACTACGCTCAGCT-ATAAGCCATATCATTTGTAGTATAACTTAAGTCGAGAAGGG
1 TTCGAGTTCGACTACGCTCAGCTCA-AAGCCAAATCATTTGCAGCATAACTTAAGTCGAGAAGGG
* * * * ** * * * *
185722 TTATCTTCCAACCAAAGA-CCTTCGAGTTCGACTATGCTCAGC-TCCAAGGCACATTATTTGCAG
65 CTATC-T---GCCAAAGACCCTT-GAGTTTGATTAAACTCAGCTTCGAGGGCACATCATTTACAG
* * * * * * *
185785 TATAACTTAAGTCGAGAAGGGCTATCTGCC---AAAGACT
125 CATAACTCAAGGCTAGAAGGGTTATCTACCAAAAAACACT
* * * * ** * ** * * * * *
185822 CTCGAGTTCAAATACACTCAGCTTTGAGGGTAGATCATTTACAGCATAACTCAAGGCTAGAAGGG
1 TTCGAGTTCGACTACGCTCAGC-TCAAAGCCAAATCATTTGCAGCATAACTTAAGTCGAGAAGGG
* * * ** * * * * * * *
185887 TTATCTGTCACCAAAAGA-CCTTCGAGTTCGACTATGCTCATC-TCTAAGGCATATTATTTGCAA
65 CTATCTG---CC-AAAGACCCTT-GAGTTTGATTAAACTCAGCTTCGAGGGCACATCATTTACAG
* * * * * *
185950 CATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAACACC
125 CATAACTCAAGGCTAGAAGGGTTATCTACCAA-AAAACACT
* * * * * * * *
185991 TTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAGCTCAAGGCAAGAAGGGC
1 TTCGAGTTCGACTACGCTCAGCTCAAAGCCAAATCATTTGCAGCATAACTTAAGTCGAGAAGGGC
186056 TATCT
66 TATCT
186061 ATCAATAAAA
Statistics
Matches: 462, Mismatches: 82, Indels: 46
0.78 0.14 0.08
Matches are distributed among these distances:
162 2 0.00
163 19 0.04
164 66 0.14
165 171 0.37
166 22 0.05
167 59 0.13
168 78 0.17
169 45 0.10
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.26
Consensus pattern (164 bp):
TTCGAGTTCGACTACGCTCAGCTCAAAGCCAAATCATTTGCAGCATAACTTAAGTCGAGAAGGGC
TATCTGCCAAAGACCCTTGAGTTTGATTAAACTCAGCTTCGAGGGCACATCATTTACAGCATAAC
TCAAGGCTAGAAGGGTTATCTACCAAAAAACACT
Found at i:185845 original size:249 final size:249
Alignment explanation
Indices: 185353--186060 Score: 950
Period size: 249 Copynumber: 2.8 Consensus size: 249
185343 TCAACTCAAA
* * * * * * * * *
185353 GGCACATAATTTGCAGCATAGCTTAAGTCAAGAAGGGTTATTTGCCACCAAAAGACCTTCGTGTT
1 GGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATATGTCACCAAAAGACCTTCGAGTT
* * * * * * * *
185418 TGACTACGTTTAGCTCCAAGGCACATCATTTATAGCATAACTCAAGGCTAGAAGGGTTATCTACC
66 TGACTACGCTCAGCTCTAAGGCATATCATTTGTAGCATAACTTAAGTCGAGAAGGGTTATCTACC
* * * *
185483 AA-AAAACACTTTCGAGTTCGACTATGCTCAGCTCAAAGGCAAATCATTTGCAGCATAGCTTAAG
131 AACCAAACACCTTCGAGTTCGACTATGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAG
* ** *
185547 TCGAGAAGGGCTATCTGCCAAAGACCCTTGAGTTTGATTAAACTCAGCTTCGAG
196 TCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCAAATAAACTCAGCTTCGAG
185601 GGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATATGTCACCAAAAGACCTTCGAGTT
1 GGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATATGTCACCAAAAGACCTTCGAGTT
* * * *
185666 TGACTACGCTCAGCTATAAGCCATATCATTTGTAGTATAACTTAAGTCGAGAAGGGTTATCTTCC
66 TGACTACGCTCAGCTCTAAGGCATATCATTTGTAGCATAACTTAAGTCGAGAAGGGTTATCTACC
* * * *
185731 AACCAAAGACCTTCGAGTTCGACTATGCTCAGCTCCAAGGCACATTATTTGCAGTATAACTTAAG
131 AACCAAACACCTTCGAGTTCGACTATGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAG
* * *
185796 TCGAGAAGGGCTATCTGCCAAAGACTCTCGAGTTCAAATACACTCAGCTTTGAG
196 TCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCAAATAAACTCAGCTTCGAG
* * *
185850 GGTAGATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTT
1 GGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATATGTCACCAAAAGACCTTCGAGTT
* * * * * * *
185915 CGACTATGCTCATCTCTAAGGCATATTATTTGCAACATAACTTAAGTCGAGAAGGGTTATCTGCC
66 TGACTACGCTCAGCTCTAAGGCATATCATTTGTAGCATAACTTAAGTCGAGAAGGGTTATCTACC
* * *
185980 AACCAAACACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAGCTCAAG
131 AACCAAACACCTTCGAGTTCGACTATGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAG
* *
186045 GCAAGAAGGGCTATCT
196 TCGAGAAGGGCTATCT
186061 ATCAATAAAA
Statistics
Matches: 401, Mismatches: 58, Indels: 1
0.87 0.13 0.00
Matches are distributed among these distances:
248 111 0.28
249 290 0.72
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.26
Consensus pattern (249 bp):
GGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATATGTCACCAAAAGACCTTCGAGTT
TGACTACGCTCAGCTCTAAGGCATATCATTTGTAGCATAACTTAAGTCGAGAAGGGTTATCTACC
AACCAAACACCTTCGAGTTCGACTATGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAG
TCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCAAATAAACTCAGCTTCGAG
Found at i:186930 original size:37 final size:35
Alignment explanation
Indices: 186883--186975 Score: 98
Period size: 36 Copynumber: 2.6 Consensus size: 35
186873 ATAAGGGGTC
* *
186883 GTCTCGCTTGAGACTAATTTACTC-AAAACTAAGTTTT
1 GTCTCTCTTGAGAC-AATTT-CTCTAAAAC-AAATTTT
* * *
186920 GTCTTTCTTGAGACAGTTTCTCTTGAAACAAATTTT
1 GTCTCTCTTGAGACAATTTCTC-TAAAACAAATTTT
186956 GTCTCTCTTGAGACAATTTC
1 GTCTCTCTTGAGACAATTTC
186976 CCTTGAAACA
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
35 3 0.06
36 28 0.60
37 16 0.34
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.41
Consensus pattern (35 bp):
GTCTCTCTTGAGACAATTTCTCTAAAACAAATTTT
Found at i:186959 original size:36 final size:36
Alignment explanation
Indices: 186916--187240 Score: 321
Period size: 36 Copynumber: 9.1 Consensus size: 36
186906 CAAAACTAAG
*
186916 TTTTGTCTTTCTTGAGACAGTTTCTCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAA
* *
186952 TTTTGTCTCTCTTGAGACAATTTCCCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAA
* * *
186988 ------ATCT-TTGA-ATATGTTT-TCCTTTAAACAAA
1 TTTTGTCTCTCTTGAGACA-GTTTCT-CTTGAAACAAA
* * * *
187017 TTTTGTCTCTCTAGAGACAGTTTCTTTTGGAACTAAG
1 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC-AAA
* * * *
187054 TTTTGTGTATCTTAAGATAGTTTCTCTTGAAA-ACAA
1 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACA-AA
* * *
187090 TTTTCTCTCTCTTGAAACAGTTTCCCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAA
*
187126 TTTTGTCTCTCTTGAGACAG-TTCTCTTAAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAA
*
187161 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAA
* *
187197 TTTTTTCTCTCTTGAGACAGTTTTCCCTTGAAACAGAA
1 TTTTGTCTCTCTTGAGACAG-TTTCTCTTGAAACA-AA
187235 TCTTTG
1 T-TTTG
187241 AATATGTTTT
Statistics
Matches: 233, Mismatches: 38, Indels: 33
0.77 0.12 0.11
Matches are distributed among these distances:
28 2 0.01
29 17 0.07
30 3 0.01
35 37 0.16
36 123 0.53
37 45 0.19
38 3 0.01
39 3 0.01
ACGTcount: A:0.26, C:0.19, G:0.13, T:0.42
Consensus pattern (36 bp):
TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAA
Found at i:187170 original size:71 final size:72
Alignment explanation
Indices: 187010--187218 Score: 278
Period size: 71 Copynumber: 2.9 Consensus size: 72
187000 GTTTTCCTTT
* ** * * * * * *
187010 AAACAAATTTTGTCTCTCTAGAGACAGTTTCTTTTGGAACTAAGTTTTGTGTATCTTAAGATAGT
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAATTTTGTCTCTCTTGAGACAG-
187075 TTCTCTTGA
64 TTCTCTTGA
* *
187084 AAAC-AATTTTCTCTCTCTTGAAACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTT
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTT
187148 CTCTT-A
66 CTCTTGA
*
187154 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTTTCTCTCTTGAGACAGTT
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTT
187219 TTCCCTTGAA
Statistics
Matches: 120, Mismatches: 14, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
70 5 0.04
71 64 0.53
72 18 0.15
73 29 0.24
74 4 0.03
ACGTcount: A:0.27, C:0.19, G:0.13, T:0.41
Consensus pattern (72 bp):
AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTT
CTCTTGA
Found at i:187210 original size:21 final size:21
Alignment explanation
Indices: 187147--187211 Score: 52
Period size: 21 Copynumber: 3.4 Consensus size: 21
187137 TTGAGACAGT
* *
187147 TCTCTTAAAACAAATTTTGTC
1 TCTCTTGAAACAAATTTTTTC
* *
187168 TCTCTTGAGAC--A--GTTTC
1 TCTCTTGAAACAAATTTTTTC
187185 -C-CTTGAAACAAATTTTTTC
1 TCTCTTGAAACAAATTTTTTC
187204 TCTCTTGA
1 TCTCTTGA
187212 GACAGTTTTC
Statistics
Matches: 32, Mismatches: 6, Indels: 12
0.64 0.12 0.24
Matches are distributed among these distances:
15 7 0.22
16 1 0.03
17 4 0.12
19 5 0.16
20 1 0.03
21 14 0.44
ACGTcount: A:0.26, C:0.22, G:0.09, T:0.43
Consensus pattern (21 bp):
TCTCTTGAAACAAATTTTTTC
Found at i:187321 original size:138 final size:136
Alignment explanation
Indices: 187109--187368 Score: 360
Period size: 138 Copynumber: 1.9 Consensus size: 136
187099 TCTTGAAACA
* * *
187109 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTCTCTTAAAACAAATTTTGTCTCTCTT
1 GTTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAGTTATCTTAAAACAAATTTTGCCTCTCTT
* * *
187174 GAGACAGTTTCCCTTGAAACAAATTTTTTCTCTCTTGAGACAGTTTTCCCTTGAAACAGAATCTT
66 GAGACAGTTTCCCTTGAAACAAATTTTGTCTATCTTGAGACA-ATTTCCCTTGAAACAGAATCTT
187239 TGAATAT
130 TGAATAT
* * ** *
187246 GTTTTCCTTGAAACAAATTTCGTCTC-CTTGAGACAGTTTATTTTGGAACTAAGTTTTGCCTCTC
1 GTTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG-TTATCTTAAAAC-AAATTTTGCCTCTC
* * *
187310 TTGAGATAGTTTCTCTTGAAATAAATTTTGTCTATCTTGAGACAATTTCCCTTGAAACA
64 TTGAGACAGTTTCCCTTGAAACAAATTTTGTCTATCTTGAGACAATTTCCCTTGAAACA
187369 AAGTTTTGTC
Statistics
Matches: 107, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
136 10 0.09
137 46 0.43
138 51 0.48
ACGTcount: A:0.27, C:0.19, G:0.13, T:0.41
Consensus pattern (136 bp):
GTTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAGTTATCTTAAAACAAATTTTGCCTCTCTT
GAGACAGTTTCCCTTGAAACAAATTTTGTCTATCTTGAGACAATTTCCCTTGAAACAGAATCTTT
GAATAT
Found at i:187361 original size:245 final size:247
Alignment explanation
Indices: 186907--187405 Score: 772
Period size: 245 Copynumber: 2.0 Consensus size: 247
186897 TAATTTACTC
* * *
186907 AAAACTAAGTTTTGTCTTTCTTGAGACAGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAA
1 AAAAC-AAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAA
* *
186972 TTTCCCTTGAAACAAAATCTTTGAATATGTTTTCCTTTAAACAAATTTTGTCTCTCTAGAGACAG
65 TTTCCCTTGAAACAAAATCTTTGAATATGTTTTCCTTGAAACAAATTTCGTCTCTCTAGAGACAG
* ** *
187037 TTTCTTTTGGAACTAAGTTTTGTGTATCTTAAGATAGTTTCTCTTGAAAACAATTTTCTCTCTCT
130 TTTATTTTGGAACTAAGTTTTGCCTATCTTAAGATAGTTTCTCTTGAAAACAATTTTCTCTATCT
*
187102 TGAAACAGTTTCCCTTGAAACAAA-TTTTGTCTCTCTTGAGACAG-TTCTCTT
195 TGAAACAATTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTT
* *
187153 AAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTTTCTCTCTTGAGACAGT
1 AAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA-A
* *
187218 TTTCCCTTGAAACAGAATCTTTGAATATGTTTTCCTTGAAACAAATTTCGTCTC-CTTGAGACAG
65 TTTCCCTTGAAACAAAATCTTTGAATATGTTTTCCTTGAAACAAATTTCGTCTCTCTAGAGACAG
* * *
187282 TTTATTTTGGAACTAAGTTTTGCCTCTCTTGAGATAGTTTCTCTTGAAATA-AATTTTGTCTATC
130 TTTATTTTGGAACTAAGTTTTGCCTATCTTAAGATAGTTTCTCTTGAAA-ACAATTTTCTCTATC
*
187346 TTGAGACAATTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTT
194 TTGAAACAATTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTT
*
187400 GAAACA
1 AAAACA
187406 CAAAAAAACC
Statistics
Matches: 230, Mismatches: 19, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
245 141 0.61
246 77 0.33
247 12 0.05
ACGTcount: A:0.27, C:0.18, G:0.13, T:0.41
Consensus pattern (247 bp):
AAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAAT
TTCCCTTGAAACAAAATCTTTGAATATGTTTTCCTTGAAACAAATTTCGTCTCTCTAGAGACAGT
TTATTTTGGAACTAAGTTTTGCCTATCTTAAGATAGTTTCTCTTGAAAACAATTTTCTCTATCTT
GAAACAATTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTT
Found at i:187364 original size:36 final size:37
Alignment explanation
Indices: 187248--187405 Score: 189
Period size: 37 Copynumber: 4.4 Consensus size: 37
187238 TTGAATATGT
*
187248 TTTC-CTTGAAACAAA-TTTCGTCTC-CTTGAGACAG
1 TTTCTCTTGAAACAAAGTTTTGTCTCTCTTGAGACAG
* * * * * *
187282 TTTATTTTGGAACTAAGTTTTGCCTCTCTTGAGATAG
1 TTTCTCTTGAAACAAAGTTTTGTCTCTCTTGAGACAG
* * *
187319 TTTCTCTTGAAATAAA-TTTTGTCTATCTTGAGACAA
1 TTTCTCTTGAAACAAAGTTTTGTCTCTCTTGAGACAG
*
187355 TTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAG
1 TTTCTCTTGAAACAAAGTTTTGTCTCTCTTGAGACAG
187392 TTTCTCTTGAAACA
1 TTTCTCTTGAAACA
187406 CAAAAAAACC
Statistics
Matches: 99, Mismatches: 21, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
34 3 0.03
35 8 0.08
36 37 0.37
37 51 0.52
ACGTcount: A:0.26, C:0.18, G:0.15, T:0.41
Consensus pattern (37 bp):
TTTCTCTTGAAACAAAGTTTTGTCTCTCTTGAGACAG
Found at i:187373 original size:73 final size:72
Alignment explanation
Indices: 187248--187405 Score: 201
Period size: 73 Copynumber: 2.2 Consensus size: 72
187238 TTGAATATGT
* ** * *
187248 TTTC-CTTGAAACAAATTTCGTCTCCTTGAGACAGTTTATTTTGGAACTAAGTTTTGCCTCTCTT
1 TTTCTCTTGAAACAAATTTCGTCTCCTTGAGACAATTTACCTTGAAACAAAGTTTTGCCTCTCTT
*
187312 GAGATAG
66 GAGACAG
* * * * *
187319 TTTCTCTTGAAATAAATTTTGTCTATCTTGAGACAATTTCCCTTGAAACAAAGTTTTGTCTCTCT
1 TTTCTCTTGAAACAAATTTCGTCT-CCTTGAGACAATTTACCTTGAAACAAAGTTTTGCCTCTCT
187384 TGAGACAG
65 TGAGACAG
187392 TTTCTCTTGAAACA
1 TTTCTCTTGAAACA
187406 CAAAAAAACC
Statistics
Matches: 73, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
71 4 0.05
72 17 0.23
73 52 0.71
ACGTcount: A:0.26, C:0.18, G:0.15, T:0.41
Consensus pattern (72 bp):
TTTCTCTTGAAACAAATTTCGTCTCCTTGAGACAATTTACCTTGAAACAAAGTTTTGCCTCTCTT
GAGACAG
Found at i:187784 original size:12 final size:13
Alignment explanation
Indices: 187738--187789 Score: 51
Period size: 12 Copynumber: 4.2 Consensus size: 13
187728 CATATATACG
187738 TATTATATA-TA-
1 TATTATATATTAT
187749 TATATATATATTA-
1 TAT-TATATATTAT
187762 TATGTA-ATATTAT
1 TAT-TATATATTAT
187775 TATTAT-TATTAT
1 TATTATATATTAT
187787 TAT
1 TAT
187790 AACATATATT
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
11 3 0.08
12 23 0.64
13 10 0.28
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (13 bp):
TATTATATATTAT
Found at i:189018 original size:11 final size:11
Alignment explanation
Indices: 188970--189037 Score: 61
Period size: 11 Copynumber: 6.3 Consensus size: 11
188960 TTTAAATATG
*
188970 TTATATATTT-
1 TTATTTATTTA
*
188980 TTATTTTTTCTA
1 TTATTTATT-TA
188992 TTATTT-TTTCA
1 TTATTTATTT-A
*
189003 CTATTTATTTA
1 TTATTTATTTA
189014 TTATTTATTT-
1 TTATTTATTTA
*
189024 TTATTTTTTTA
1 TTATTTATTTA
189035 TTA
1 TTA
189038 ATTACTATAT
Statistics
Matches: 48, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
10 17 0.35
11 22 0.46
12 9 0.19
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.74
Consensus pattern (11 bp):
TTATTTATTTA
Found at i:189055 original size:2 final size:2
Alignment explanation
Indices: 189043--189071 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
189033 TATTAATTAC
189043 TA TA T- 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
189072 CCTAACCTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:189497 original size:24 final size:24
Alignment explanation
Indices: 189406--189499 Score: 66
Period size: 24 Copynumber: 3.7 Consensus size: 24
189396 AAATACTATT
* * *
189406 TTTATTTTCATTTTTTACTTGTTTG
1 TTTATTTT-ATTTTTTATTTATTTA
* *
189431 TTTATTCTCTGTTTTTTA--TAATTA
1 TTTATT-T-TATTTTTTATTTATTTA
189455 TTTATTTTACCTATCTTTTATTTATTTA
1 TTTATTTTA--T-T-TTTTATTTATTTA
189483 TTTATTTTATTTTTTAT
1 TTTATTTTATTTTTTAT
189500 CTAATACTTT
Statistics
Matches: 55, Mismatches: 6, Indels: 17
0.71 0.08 0.22
Matches are distributed among these distances:
22 1 0.02
23 1 0.02
24 16 0.29
25 8 0.15
26 14 0.25
27 1 0.02
28 14 0.25
ACGTcount: A:0.18, C:0.07, G:0.03, T:0.71
Consensus pattern (24 bp):
TTTATTTTATTTTTTATTTATTTA
Found at i:189950 original size:15 final size:15
Alignment explanation
Indices: 189932--190045 Score: 72
Period size: 15 Copynumber: 7.6 Consensus size: 15
189922 TGTAATTTTA
*
189932 GTATTGTATTTTTTG
1 GTATTGTATTTTATG
* *
189947 GTATTTTAATTTATG
1 GTATTGTATTTTATG
189962 GTATTGTATTTTATG
1 GTATTGTATTTTATG
* * *
189977 TTGTTTTAATTTT-TG
1 GTATTGT-ATTTTATG
* *
189992 AT-TTGGTGTTTTATG
1 GTATT-GTATTTTATG
* *
190007 TTATTTTAATTTT-TG
1 GTATTGT-ATTTTATG
*
190022 ATATTGTATTTTATG
1 GTATTGTATTTTATG
*
190037 CTATTGTAT
1 GTATTGTAT
190046 AATAGTCTTC
Statistics
Matches: 76, Mismatches: 17, Indels: 12
0.72 0.16 0.11
Matches are distributed among these distances:
14 11 0.14
15 54 0.71
16 11 0.14
ACGTcount: A:0.19, C:0.01, G:0.16, T:0.64
Consensus pattern (15 bp):
GTATTGTATTTTATG
Found at i:189967 original size:30 final size:30
Alignment explanation
Indices: 189924--190041 Score: 141
Period size: 30 Copynumber: 4.0 Consensus size: 30
189914 CATAATTATG
* * *
189924 TAATTTTAG-TATTGTATTTTTTGGTATTT
1 TAATTTTTGATATTGTATTTTATGTTATTT
* * *
189953 TAATTTATGGTATTGTATTTTATGTTGTTT
1 TAATTTTTGATATTGTATTTTATGTTATTT
*
189983 TAATTTTTGAT-TTGGTGTTTTATGTTATTT
1 TAATTTTTGATATT-GTATTTTATGTTATTT
*
190013 TAATTTTTGATATTGTATTTTATGCTATT
1 TAATTTTTGATATTGTATTTTATGTTATT
190042 GTATAATAGT
Statistics
Matches: 75, Mismatches: 11, Indels: 5
0.82 0.12 0.05
Matches are distributed among these distances:
29 9 0.12
30 64 0.85
31 2 0.03
ACGTcount: A:0.20, C:0.01, G:0.14, T:0.64
Consensus pattern (30 bp):
TAATTTTTGATATTGTATTTTATGTTATTT
Found at i:195077 original size:19 final size:19
Alignment explanation
Indices: 195050--195099 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
195040 TCATTGTAGT
195050 TGTTATTTGCTATGATCCA
1 TGTTATTTGCTATGATCCA
* *
195069 TGTTTTTTGCCATGATCCA
1 TGTTATTTGCTATGATCCA
195088 TGTTATTTGCTA
1 TGTTATTTGCTA
195100 ACCATTTCTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.18, C:0.16, G:0.16, T:0.50
Consensus pattern (19 bp):
TGTTATTTGCTATGATCCA
Found at i:199679 original size:171 final size:172
Alignment explanation
Indices: 199390--199744 Score: 511
Period size: 171 Copynumber: 2.0 Consensus size: 172
199380 ATAAAAATTA
*
199390 AATATTTTTTAATTCAAAAAAAGTTTATAATTAATTTAAATAATATATAAATAAAATTTTCAAAT
1 AATATTTTTTAATTCAAAAAAAGTTTACAATTAATTTAAATAATATATAAATAAAA--TT--AAT
199455 AAACTTTTTAATTAATTAATATTGATTTAGGTTTAAAAATTATTAGATCTTAAATTATTAATTGA
62 AAACTTTTTAATTAATTAATATTGATTTAGGTTTAAAAATTATTAGATCTTAAATTATTAATTGA
*** *
199520 ATTTTAAATGGTTTGGGTTGAGCTTATATGTTATATATAATATA-T
127 ATTTTAAATGGTTTGAACTGAGCTCATATGTTATATATAATATATT
* *
199565 AATATTTTTTAATT-AAAAAACATTTTACATTTAATTTAAATAATATATAATTATAAAA-T-ATA
1 AATATTTTTTAATTCAAAAAA-AGTTTACAATTAATTTAAATAATATATAA--ATAAAATTAATA
* * * *
199627 AATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTGGATCTTAAATTATTAATTGGA
63 AACTTTTTAATTAATTAATATTGATTTAGGTTTAAAAATTATTAGATCTTAAATTATTAATTGAA
199692 TTTTAAATGGTTTGAACTGAGCTCATATGTTATATATAATATATTT
128 TTTTAAATGGTTTGAACTGAGCTCATATGTTATATATAATATA-TT
199738 AATATTT
1 AATATTT
199745 AAAATTTAAT
Statistics
Matches: 164, Mismatches: 11, Indels: 12
0.88 0.06 0.06
Matches are distributed among these distances:
171 103 0.63
173 8 0.05
174 7 0.04
175 40 0.24
177 6 0.04
ACGTcount: A:0.42, C:0.03, G:0.08, T:0.47
Consensus pattern (172 bp):
AATATTTTTTAATTCAAAAAAAGTTTACAATTAATTTAAATAATATATAAATAAAATTAATAAAC
TTTTTAATTAATTAATATTGATTTAGGTTTAAAAATTATTAGATCTTAAATTATTAATTGAATTT
TAAATGGTTTGAACTGAGCTCATATGTTATATATAATATATT
Found at i:228771 original size:21 final size:21
Alignment explanation
Indices: 228747--228786 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
228737 TTTATTTTAT
228747 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
228768 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
228787 AACTTGAAGT
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:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
AACTTTATTTCAATTATCGTA
Found at i:228822 original size:32 final size:33
Alignment explanation
Indices: 228781--228879 Score: 155
Period size: 33 Copynumber: 3.0 Consensus size: 33
228771 TTTGTTTCAA
228781 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTAGAAGTTTTTAAGTATTTGAAT
*
228813 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTAGAAGTTTTTAAGTATTTGAAT
* * *
228846 TTATCAAACTTAGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTAGAAGTTTTTAAGTATTTGAAT
228879 T
1 T
228880 ATGTTGAGTT
Statistics
Matches: 62, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
32 11 0.18
33 51 0.82
ACGTcount: A:0.33, C:0.07, G:0.14, T:0.45
Consensus pattern (33 bp):
TTATCGAACTTAGAAGTTTTTAAGTATTTGAAT
Found at i:228908 original size:13 final size:13
Alignment explanation
Indices: 228865--228919 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
228855 TTAGAAGTAT
228865 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
228878 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
228892 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
228905 TTAAGTATTTGAA
1 TTAAGTATTTCAA
228918 TT
1 TT
228920 TATCGAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:229138 original size:21 final size:21
Alignment explanation
Indices: 229113--229169 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
229103 CGGAGCTTAG
*
229113 GGGAATCGATACCCTCTCATA
1 GGGAATCGATTCCCTCTCATA
* * *
229134 GGGAATCGGTTTCTTCTCATA
1 GGGAATCGATTCCCTCTCATA
229155 GGGAATCGATTCCCT
1 GGGAATCGATTCCCT
229170 AAGTGTAAAA
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.23, C:0.25, G:0.23, T:0.30
Consensus pattern (21 bp):
GGGAATCGATTCCCTCTCATA
Found at i:229373 original size:17 final size:18
Alignment explanation
Indices: 229353--229386 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
229343 ATTTTTTTAT
229353 AACC-GATTTTTTAAAAA
1 AACCGGATTTTTTAAAAA
*
229370 AACCGGTTTTTTTAAAA
1 AACCGGATTTTTTAAAA
229387 CTGAAACCGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.41, C:0.12, G:0.09, T:0.38
Consensus pattern (18 bp):
AACCGGATTTTTTAAAAA
Found at i:230234 original size:22 final size:22
Alignment explanation
Indices: 230181--230242 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 22
230171 GATAAAAACA
*
230181 TACAAATAATTAAAAAAATAAAG
1 TACAAA-AATGAAAAAAATAAAG
*
230204 TACACAAAATGAAAAATATAAAGG
1 TACA-AAAATGAAAAAAATAAA-G
*
230228 T-CAAAAAGGAAAAAA
1 TACAAAAATGAAAAAA
230243 GAAATGCATG
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
22 10 0.30
23 19 0.58
24 4 0.12
ACGTcount: A:0.68, C:0.06, G:0.10, T:0.16
Consensus pattern (22 bp):
TACAAAAATGAAAAAAATAAAG
Found at i:232090 original size:36 final size:36
Alignment explanation
Indices: 232050--232124 Score: 150
Period size: 36 Copynumber: 2.1 Consensus size: 36
232040 GCCTTTTTTT
232050 TGTTAGATTAAAATTGTTAATACCATAAATAGTATA
1 TGTTAGATTAAAATTGTTAATACCATAAATAGTATA
232086 TGTTAGATTAAAATTGTTAATACCATAAATAGTATA
1 TGTTAGATTAAAATTGTTAATACCATAAATAGTATA
232122 TGT
1 TGT
232125 ATATAATTTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.43, C:0.05, G:0.12, T:0.40
Consensus pattern (36 bp):
TGTTAGATTAAAATTGTTAATACCATAAATAGTATA
Found at i:232854 original size:53 final size:53
Alignment explanation
Indices: 232762--232968 Score: 238
Period size: 53 Copynumber: 3.9 Consensus size: 53
232752 TTTTATGTAT
232762 TAAGATATTGAGAGATATACATACTTACACTGGTGTAAGTATGTGTTAATTGC
1 TAAGATATTGAGAGATATACATACTTACACTGGTGTAAGTATGTGTTAATTGC
* * ** *
232815 CAATG-TATTGAGAGATATACATACTTACATCT-GTATAAGTATGCATTAATTTC
1 TAA-GATATTGAGAGATATACATACTTACA-CTGGTGTAAGTATGTGTTAATTGC
* * ** *
232868 TAAGATATTGAGAGATGTACATAATTACACTGGTGTAAGTACATGTTAATTGT
1 TAAGATATTGAGAGATATACATACTTACACTGGTGTAAGTATGTGTTAATTGC
* * * * * *
232921 TAAGATATTTAGAGATGTACATACTTATACCGGTGTAAATAAGTGTTA
1 TAAGATATTGAGAGATATACATACTTACACTGGTGTAAGTATGTGTTA
232969 GTTGATATAT
Statistics
Matches: 128, Mismatches: 22, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
52 3 0.02
53 122 0.95
54 3 0.02
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.36
Consensus pattern (53 bp):
TAAGATATTGAGAGATATACATACTTACACTGGTGTAAGTATGTGTTAATTGC
Found at i:235668 original size:12 final size:13
Alignment explanation
Indices: 235652--235684 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
235642 ATTATTATCT
235652 AAAAATAATTTTA
1 AAAAATAATTTTA
235665 AAAAATAA-TTTA
1 AAAAATAATTTTA
235677 AATAAATA
1 AA-AAATA
235685 TATTAAACTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 6 0.32
13 13 0.68
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (13 bp):
AAAAATAATTTTA
Found at i:235757 original size:16 final size:17
Alignment explanation
Indices: 235728--235760 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
235718 CTCTAAATAA
235728 TTTTAATATGATTTTAT
1 TTTTAATATGATTTTAT
235745 TTTTAATAT-ATTTTAT
1 TTTTAATATGATTTTAT
235761 ATATTTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (17 bp):
TTTTAATATGATTTTAT
Found at i:235779 original size:27 final size:26
Alignment explanation
Indices: 235721--235780 Score: 79
Period size: 26 Copynumber: 2.3 Consensus size: 26
235711 TTGAATTCTC
235721 TAAATAATTTTAATATGATTTTATTTT
1 TAAATAATTTTAATAT-ATTTTATTTT
235748 T-AATATATTTT-ATATATTTTTATTTT
1 TAAATA-ATTTTAATATA-TTTTATTTT
235774 TAAATAA
1 TAAATAA
235781 AAATGGTAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
25 1 0.03
26 19 0.63
27 10 0.33
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (26 bp):
TAAATAATTTTAATATATTTTATTTT
Found at i:236638 original size:2 final size:2
Alignment explanation
Indices: 236631--236659 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
236621 TATTTAATGA
236631 AT AT 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 AT AT A
236660 ATTATGATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:242586 original size:35 final size:35
Alignment explanation
Indices: 242540--242615 Score: 134
Period size: 35 Copynumber: 2.2 Consensus size: 35
242530 TTAGATTCAT
* *
242540 TTCAACTTTATCTTGGAAATCACTCTCTTGTTAAC
1 TTCAACTTTATCTTGAAAACCACTCTCTTGTTAAC
242575 TTCAACTTTATCTTGAAAACCACTCTCTTGTTAAC
1 TTCAACTTTATCTTGAAAACCACTCTCTTGTTAAC
242610 TTCAAC
1 TTCAAC
242616 CTAGAACCAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.28, C:0.25, G:0.07, T:0.41
Consensus pattern (35 bp):
TTCAACTTTATCTTGAAAACCACTCTCTTGTTAAC
Found at i:247006 original size:26 final size:27
Alignment explanation
Indices: 246958--247013 Score: 96
Period size: 26 Copynumber: 2.1 Consensus size: 27
246948 AAACCCCTAG
*
246958 AAATATGTTTAGGGGTTTTTCCTATTT
1 AAATAGGTTTAGGGGTTTTTCCTATTT
246985 AAATAGGTTTA-GGGTTTTTCCTATTT
1 AAATAGGTTTAGGGGTTTTTCCTATTT
247011 AAA
1 AAA
247014 GTTCTTTACA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
26 18 0.64
27 10 0.36
ACGTcount: A:0.27, C:0.07, G:0.18, T:0.48
Consensus pattern (27 bp):
AAATAGGTTTAGGGGTTTTTCCTATTT
Found at i:248308 original size:22 final size:22
Alignment explanation
Indices: 248291--248356 Score: 132
Period size: 22 Copynumber: 3.0 Consensus size: 22
248281 CTCGTATAAA
248291 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
248313 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
248335 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
248357 GATGTCCATA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 44 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.18
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:248616 original size:30 final size:30
Alignment explanation
Indices: 248571--248629 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
248561 ATCGCGTAGT
* *
248571 CATATTATTTCCATACCTTTATCACATAGA
1 CATATCATTTACATACCTTTATCACATAGA
248601 CATATCATTTACATACCTTTATCACATAG
1 CATATCATTTACATACCTTTATCACATAG
248630 CTCATATAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.34, C:0.24, G:0.03, T:0.39
Consensus pattern (30 bp):
CATATCATTTACATACCTTTATCACATAGA
Found at i:248699 original size:29 final size:29
Alignment explanation
Indices: 248654--248709 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
248644 TTTTCTGCAT
248654 ATTCATGTCATGCAATACATATAATATGA
1 ATTCATGTCATGCAATACATATAATATGA
* *
248683 ATTCATGTCATGTAATACATTTAATAT
1 ATTCATGTCATGCAATACATATAATAT
248710 AATATGGAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.39, C:0.12, G:0.09, T:0.39
Consensus pattern (29 bp):
ATTCATGTCATGCAATACATATAATATGA
Found at i:249154 original size:67 final size:68
Alignment explanation
Indices: 249009--249160 Score: 225
Period size: 68 Copynumber: 2.2 Consensus size: 68
248999 TTTTCTCATG
* *
249009 GGGGAATCGGTTCCCCCCCCTGGGGGTATCGATTCCCCTCAAGCATTCTGGAATTTCATATACGA
1 GGGGTATCGG-TCCCCCCCCTGGGGGTATCGATTCCCCTCAAGCATTCTGGAATATCATATACGA
*
249074 TGAG
65 TGAA
* * *
249078 GGGGTATCGGTCCCCCCCCTGGGGGTATCGATTCCCCTCTAGCATTCTGGAA-ATCATATTCGTT
1 GGGGTATCGGTCCCCCCCCTGGGGGTATCGATTCCCCTCAAGCATTCTGGAATATCATATACGAT
249142 GAA
66 GAA
*
249145 GGGGTATCGGTTCCCC
1 GGGGTATCGGTCCCCC
249161 TTGAATGGGT
Statistics
Matches: 76, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
67 26 0.34
68 41 0.54
69 9 0.12
ACGTcount: A:0.18, C:0.28, G:0.27, T:0.27
Consensus pattern (68 bp):
GGGGTATCGGTCCCCCCCCTGGGGGTATCGATTCCCCTCAAGCATTCTGGAATATCATATACGAT
GAA
Found at i:249170 original size:21 final size:21
Alignment explanation
Indices: 249140--249182 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
249130 ATCATATTCG
* *
249140 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
249161 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
249182 T
1 T
249183 AGCCCGAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:255237 original size:22 final size:22
Alignment explanation
Indices: 255220--255285 Score: 132
Period size: 22 Copynumber: 3.0 Consensus size: 22
255210 CTCGTATAAA
255220 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
255242 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
255264 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
255286 GATGTCCATA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 44 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.18
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:255545 original size:30 final size:30
Alignment explanation
Indices: 255500--255558 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
255490 ATCGCGTAGT
* *
255500 CATATTATTTCCATACCTTTATCACATAGA
1 CATATCATTTACATACCTTTATCACATAGA
255530 CATATCATTTACATACCTTTATCACATAG
1 CATATCATTTACATACCTTTATCACATAG
255559 CTCATATAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.34, C:0.24, G:0.03, T:0.39
Consensus pattern (30 bp):
CATATCATTTACATACCTTTATCACATAGA
Found at i:255628 original size:29 final size:29
Alignment explanation
Indices: 255583--255638 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
255573 TTTTCTGCAT
255583 ATTCATGTCATGCAATACATATAATATGA
1 ATTCATGTCATGCAATACATATAATATGA
* *
255612 ATTCATGTCATGTAATACATTTAATAT
1 ATTCATGTCATGCAATACATATAATAT
255639 AATATGGAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.39, C:0.12, G:0.09, T:0.39
Consensus pattern (29 bp):
ATTCATGTCATGCAATACATATAATATGA
Found at i:256051 original size:68 final size:66
Alignment explanation
Indices: 255937--256087 Score: 214
Period size: 68 Copynumber: 2.3 Consensus size: 66
255927 TTTTTCTCAT
* *
255937 GGGGGAATCGGTTCCCCCCCCTGGGGGTATCGATTCCCCTCAAGCATTCTGGAATTTCATATACG
1 GGGGGTATCGG-TCCCCCCCCTGGGGGTATCGATTCCCCTCAAGCATTCTGGAA-ATCATATACG
256002 ATGA
64 -TGA
* *
256006 GGGGGTATCGGTCCCCCCCCTGGGGGTATCGATTCCCCTCTAGCATTCTGGAAATCATATTCGTG
1 GGGGGTATCGGTCCCCCCCCTGGGGGTATCGATTCCCCTCAAGCATTCTGGAAATCATATACGTG
256071 A
66 A
* *
256072 -AGGGTATCGGTTCCCC
1 GGGGGTATCGGTCCCCC
256088 TTGAATGGGT
Statistics
Matches: 76, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
65 14 0.18
66 3 0.04
67 8 0.11
68 41 0.54
69 10 0.13
ACGTcount: A:0.18, C:0.28, G:0.27, T:0.26
Consensus pattern (66 bp):
GGGGGTATCGGTCCCCCCCCTGGGGGTATCGATTCCCCTCAAGCATTCTGGAAATCATATACGTG
A
Found at i:256097 original size:21 final size:20
Alignment explanation
Indices: 256069--256109 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
256059 ATCATATTCG
* *
256069 TGAAGGGTATCGGTTCCCCT
1 TGAAGGGTACCGATTCCCCT
256089 TGAATGGGTACCGATTCCCCT
1 TGAA-GGGTACCGATTCCCCT
256110 AGCCCGAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.17, C:0.27, G:0.27, T:0.29
Consensus pattern (20 bp):
TGAAGGGTACCGATTCCCCT
Found at i:258723 original size:21 final size:21
Alignment explanation
Indices: 258699--258841 Score: 146
Period size: 21 Copynumber: 6.7 Consensus size: 21
258689 TGTTCTGAAT
258699 GACCACATATATGTCCCGAAA-
1 GACCACATATATGTCCC-AAAG
*
258720 GACCACATAGAATTGTCCCTAAA-
1 GACCACATA-TA-TGTCCC-AAAG
*
258743 GACCACATATATGTTCCAAAG
1 GACCACATATATGTCCCAAAG
*
258764 GATCACATATATGTCCCAAAG
1 GACCACATATATGTCCCAAAG
** *
258785 GACTGCATATATGTTCCAAAG
1 GACCACATATATGTCCCAAAG
* * *
258806 GATCGCATATATGTTCCAAAG
1 GACCACATATATGTCCCAAAG
*
258827 GATCACATATATGTC
1 GACCACATATATGTC
258842 TTGAATAACC
Statistics
Matches: 105, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
20 3 0.03
21 82 0.78
22 2 0.02
23 18 0.17
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.25
Consensus pattern (21 bp):
GACCACATATATGTCCCAAAG
Found at i:258743 original size:23 final size:22
Alignment explanation
Indices: 258676--258751 Score: 75
Period size: 23 Copynumber: 3.4 Consensus size: 22
258666 TATCCTGAAG
* *
258676 GACCACATAGAAATGT-TCTGAAT
1 GACCACATAG-AATGTCCCT-AAA
* *
258699 GACCACATA-TATGTCCCGAAA
1 GACCACATAGAATGTCCCTAAA
258720 GACCACATAGAATTGTCCCTAAA
1 GACCACATAGAA-TGTCCCTAAA
258743 GACCACATA
1 GACCACATA
258752 TATGTTCCAA
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
21 15 0.34
22 2 0.05
23 27 0.61
ACGTcount: A:0.39, C:0.25, G:0.14, T:0.21
Consensus pattern (22 bp):
GACCACATAGAATGTCCCTAAA
Found at i:258771 original size:44 final size:43
Alignment explanation
Indices: 258673--258807 Score: 134
Period size: 44 Copynumber: 3.1 Consensus size: 43
258663 AATTATCCTG
* * *
258673 AAGGACCACATAGAAATGT-TCTGAATGACCACATATATGTCCCGA
1 AAGGACCACATAG-AATGTCCCT-AAAGACCACATATATGTTCC-A
258718 AA-GACCACATAGAATTGTCCCTAAAGACCACATATATGTTCCA
1 AAGGACCACATAGAA-TGTCCCTAAAGACCACATATATGTTCCA
* * **
258761 AAGGATCACATA-TATGTCCC-AAAGGACTGCATATATGTTCCA
1 AAGGACCACATAGAATGTCCCTAAA-GACCACATATATGTTCCA
258803 AAGGA
1 AAGGA
258808 TCGCATATAT
Statistics
Matches: 79, Mismatches: 7, Indels: 11
0.81 0.07 0.11
Matches are distributed among these distances:
41 3 0.04
42 27 0.34
43 6 0.08
44 39 0.49
45 4 0.05
ACGTcount: A:0.39, C:0.22, G:0.16, T:0.23
Consensus pattern (43 bp):
AAGGACCACATAGAATGTCCCTAAAGACCACATATATGTTCCA
Found at i:260750 original size:2 final size:2
Alignment explanation
Indices: 260743--260768 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
260733 ATGCTTTCTA
260743 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
260769 TGGTTTGTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:261256 original size:36 final size:36
Alignment explanation
Indices: 261184--261256 Score: 85
Period size: 36 Copynumber: 2.0 Consensus size: 36
261174 TACAATAATT
**
261184 AATTTATATATTTTTTAAAAAAAATTAAATTCATAA
1 AATTTATATATTTTTTAAAAAAAATTAAAAACATAA
* * *
261220 AATTTATATAATTTTTT-TACAAAATTAAAAAGATAA
1 AATTTATAT-ATTTTTTAAAAAAAATTAAAAACATAA
261256 A
1 A
261257 TAGGTTTAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
36 24 0.77
37 7 0.23
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.42
Consensus pattern (36 bp):
AATTTATATATTTTTTAAAAAAAATTAAAAACATAA
Found at i:261442 original size:14 final size:13
Alignment explanation
Indices: 261410--261441 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
261400 GAAGAATGAT
261410 ATTTTTGAAAGAA
1 ATTTTTGAAAGAA
261423 ATTTTTGAAAGAA
1 ATTTTTGAAAGAA
261436 ATTTTT
1 ATTTTT
261442 TTAAGGGCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (13 bp):
ATTTTTGAAAGAA
Found at i:267990 original size:2 final size:2
Alignment explanation
Indices: 267985--268014 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
267975 TTAAAATTAA
267985 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
268015 TAAAGAAAAA
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):
AT
Found at i:269453 original size:14 final size:14
Alignment explanation
Indices: 269434--269465 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
269424 TATATTGAAA
269434 TCATTTAAATAGTT
1 TCATTTAAATAGTT
269448 TCATTTAAATAGTT
1 TCATTTAAATAGTT
269462 TCAT
1 TCAT
269466 AATCATATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.34, C:0.09, G:0.06, T:0.50
Consensus pattern (14 bp):
TCATTTAAATAGTT
Found at i:271330 original size:16 final size:17
Alignment explanation
Indices: 271309--271348 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
271299 TGTCACGTTT
271309 ATATTTTCTTTAAA-AA
1 ATATTTTCTTTAAATAA
* *
271325 ATATTTTTTTTAAATAT
1 ATATTTTCTTTAAATAA
271342 ATATTTT
1 ATATTTT
271349 AAAAAAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 13 0.62
17 8 0.38
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (17 bp):
ATATTTTCTTTAAATAA
Found at i:274580 original size:22 final size:22
Alignment explanation
Indices: 274539--274606 Score: 127
Period size: 22 Copynumber: 3.0 Consensus size: 22
274529 CTCGTATAAA
274539 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
274562 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
274584 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
274606 T
1 T
274607 ATGTCCATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
22 33 0.73
23 12 0.27
ACGTcount: A:0.26, C:0.28, G:0.26, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:275265 original size:21 final size:21
Alignment explanation
Indices: 275239--275278 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
275229 CTTTTTCTCA
*
275239 TGGGGGAATCGGTTCCCCCTC
1 TGGGGGAATCGATTCCCCCTC
*
275260 TGGGGGTATCGATTCCCCC
1 TGGGGGAATCGATTCCCCC
275279 CAAGCAATCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.33, G:0.33, T:0.25
Consensus pattern (21 bp):
TGGGGGAATCGATTCCCCCTC
Found at i:275357 original size:67 final size:66
Alignment explanation
Indices: 275240--275412 Score: 213
Period size: 67 Copynumber: 2.6 Consensus size: 66
275230 TTTTTCTCAT
* * * *
275240 GGGGGAATCGGTTCCCCCTCTGGGGGTATCGATTCCCCCCAAGCAATCTGGAATTTCATATACGA
1 GGGGGTATCGGTTCCCCC-CTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCAT-TACGA
275305 TGA
64 TGA
* * * *
275308 GGGGGTATCGGTTCCCCCCTGGGGGTACCGATTCCCCTCTAGCATTCTGGAAATTCATTTCGTTG
1 GGGGGTATCGGTTCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATTACGATG
275373 A
66 A
* *
275374 GGGGGTATCGGTT-CCCCTTGAATGGGTACCGATTCCCCT
1 GGGGGTATCGGTTCCCCCCTG--GGGGTACCGATTCCCCT
275413 AACCCAGAAA
Statistics
Matches: 93, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
65 6 0.06
66 19 0.20
67 51 0.55
68 17 0.18
ACGTcount: A:0.17, C:0.27, G:0.28, T:0.28
Consensus pattern (66 bp):
GGGGGTATCGGTTCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATTACGATG
A
Found at i:293843 original size:3 final size:3
Alignment explanation
Indices: 293835--293917 Score: 139
Period size: 3 Copynumber: 27.7 Consensus size: 3
293825 TTTTTATCCA
* *
293835 TAT TAT TAT TAT TAG TAT TAT TAT TAT TAT TAT TAT TAC TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
293883 TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
293918 AATATATATT
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
3 74 1.00
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:294420 original size:6 final size:6
Alignment explanation
Indices: 294397--294432 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
294387 AAAAAAAGGG
*
294397 AGAGAC AGAAACC AGAGAC AGAGAC AGAGAC AGAGA
1 AGAGAC AGAGA-C AGAGAC AGAGAC AGAGAC AGAGA
294433 ACGAAAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
6 22 0.81
7 5 0.19
ACGTcount: A:0.53, C:0.17, G:0.31, T:0.00
Consensus pattern (6 bp):
AGAGAC
Found at i:295329 original size:19 final size:19
Alignment explanation
Indices: 295291--295326 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
295281 TAATTTAGTC
295291 ATTTATTTTATATGTTTTA
1 ATTTATTTTATATGTTTTA
295310 ATTTATTTTAT-TGTTTT
1 ATTTATTTTATATGTTTT
295327 TAAATATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.22, C:0.00, G:0.06, T:0.72
Consensus pattern (19 bp):
ATTTATTTTATATGTTTTA
Found at i:295394 original size:22 final size:21
Alignment explanation
Indices: 295355--295397 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
295345 AGAATTTTTC
**
295355 TTTTATTATATTGTTAAATAT
1 TTTTATTATATTCATAAATAT
295376 TTTTATATATATTCATAAATAT
1 TTTTAT-TATATTCATAAATAT
295398 ATATAATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.58
Consensus pattern (21 bp):
TTTTATTATATTCATAAATAT
Found at i:296107 original size:28 final size:27
Alignment explanation
Indices: 296076--296129 Score: 63
Period size: 28 Copynumber: 2.0 Consensus size: 27
296066 AATTCTTTTT
* *
296076 TTTTTAAAATTTTTATATATATTTATTA
1 TTTTCAAAATATTTATATAT-TTTATTA
* *
296104 TTTTCATAATATTTATATGTTTTATT
1 TTTTCAAAATATTTATATATTTTATT
296130 TGCAAGTATT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
27 6 0.27
28 16 0.73
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (27 bp):
TTTTCAAAATATTTATATATTTTATTA
Found at i:296115 original size:18 final size:19
Alignment explanation
Indices: 296084--296119 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
296074 TTTTTTTAAA
*
296084 ATTTTTATATATATTTATT
1 ATTTTCATATATATTTATT
296103 ATTTTCATA-ATATTTAT
1 ATTTTCATATATATTTAT
296120 ATGTTTTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (19 bp):
ATTTTCATATATATTTATT
Found at i:296120 original size:24 final size:23
Alignment explanation
Indices: 296093--296153 Score: 63
Period size: 24 Copynumber: 2.6 Consensus size: 23
296083 AATTTTTATA
*
296093 TATATTTATTATTTTCATAATATT
1 TATATTTATTATTTGCA-AATATT
*
296117 TATATGTT-TTATTTGCAAGTATT
1 TATAT-TTATTATTTGCAAATATT
296140 T-TATTTCATTATTT
1 TATATTT-ATTATTT
296154 ATTTTTCTGT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
21 2 0.06
22 3 0.09
23 12 0.38
24 13 0.41
25 2 0.06
ACGTcount: A:0.28, C:0.05, G:0.05, T:0.62
Consensus pattern (23 bp):
TATATTTATTATTTGCAAATATT
Found at i:303538 original size:114 final size:114
Alignment explanation
Indices: 303330--303542 Score: 336
Period size: 114 Copynumber: 1.9 Consensus size: 114
303320 AAGTGCCACG
* *
303330 TGCTCATAGTAGAAATAAGAAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGAAAGTGTTCTTTGAGTTATCTGATC
* * *
303395 TGGTTTGGTAAGAACTACAAAACCAATCATTGGATTTAAAAAATGAATT
66 TGATTCGGTAAGAACCACAAAACCAATCATTGGATTTAAAAAATGAATT
*
303444 TGCTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGAAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGAAAGTGTTCTTTGAGTTATCTGATC
* * * *
303509 TGATTCGGTAGGAACCCCAGAACCGATCATTGGA
66 TGATTCGGTAAGAACCACAAAACCAATCATTGGA
303543 ATTGAAAGAT
Statistics
Matches: 89, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
114 89 1.00
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Consensus pattern (114 bp):
TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGAAAGTGTTCTTTGAGTTATCTGATC
TGATTCGGTAAGAACCACAAAACCAATCATTGGATTTAAAAAATGAATT
Found at i:305742 original size:40 final size:40
Alignment explanation
Indices: 305687--305766 Score: 142
Period size: 40 Copynumber: 2.0 Consensus size: 40
305677 TAAGCAGAGT
305687 CCACAGAAAAGGATGAATGCGTTGTCAAATGTTTTACATC
1 CCACAGAAAAGGATGAATGCGTTGTCAAATGTTTTACATC
* *
305727 CCACAGAAAAGGATGAATGTGTTGTCAAGTGTTTTACATC
1 CCACAGAAAAGGATGAATGCGTTGTCAAATGTTTTACATC
305767 TAAGCTGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.29
Consensus pattern (40 bp):
CCACAGAAAAGGATGAATGCGTTGTCAAATGTTTTACATC
Found at i:306190 original size:22 final size:22
Alignment explanation
Indices: 306159--306213 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
306149 ATCTACACTC
**
306159 TTCAAAGATGGTAGATTC-CTTT
1 TTCAAAGATGACAGATTCTC-TT
*
306181 TTTAAAGATGACAGATTCTCTT
1 TTCAAAGATGACAGATTCTCTT
306203 TTCAAAGATGA
1 TTCAAAGATGA
306214 AAGCTTTATC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 27 0.96
23 1 0.04
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.38
Consensus pattern (22 bp):
TTCAAAGATGACAGATTCTCTT
Found at i:307399 original size:117 final size:114
Alignment explanation
Indices: 306650--307955 Score: 1658
Period size: 117 Copynumber: 11.4 Consensus size: 114
306640 ATTTCCAGAG
306650 AGAGTTCATAATGAGAAGAA--CTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTT
1 AGAGTTCATAATGAGAAGAACTCTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTT
* * * * *
306713 GTTCAACTTTTTGTTC-AAATCCATCA-TCTGATGGATCATCATTGCCAG-
66 GTTCAACCTTTT-TTCTGAATTCATCAGT-TGATGGATTATCTTTGCCAGT
* *
306761 AGAAGGTTCATAATGAGAAGAA--CTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAAT
1 AG-A-GTTCATAATGAGAAGAACTCTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAC
* *
306824 TTGTTCAACCTTTTGTT-TGAATTCATCACTTGATGGATTATCATTGCCAG-
64 TTGTTCAACCTTTT-TTCTGAATTCATCAGTTGATGGATTATCTTTGCCAGT
* *
306874 AGAAGGTTCATAATGAGAAGAA--CTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAAT
1 AG-A-GTTCATAATGAGAAGAACTCTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAC
* * *
306937 TTGTTCAACCTTTTGTT-TGAATTCATCACTTGATGGATTATCATTGCC-GG
64 TTGTTCAACCTTTT-TTCTGAATTCATCAGTTGATGGATTATCTTTGCCAGT
*
306987 AGAAGGTTCATAATGAGAAGAA--CTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAT
1 AG-A-GTTCATAATGAGAAGAACTCTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAC
** * * *
307050 TTGTTCAACCTTTTACCGGAATTCATCAAATTGATGGATTATCTTTTCCAG-
64 TTGTTCAACCTTTTTTCTGAATTCATC-AGTTGATGGATTATCTTTGCCAGT
* *
307101 AGAAGGTTCATAATGAGAAGAA--CTCATTTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAT
1 AG-A-GTTCATAATGAGAAGAACTCTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAC
* ** * * * * *
307164 TTGTTCAATCTTTTACCCGAATCCATCATTTGATGGATCAGTCTTTTCCAG-
64 TTGTTCAACCTTTTTTCTGAATTCATCAGTTGATGGATTA-TCTTTGCCAGT
307215 AGAAAGTTCATAATGAGAAGAACT-T-ATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAC
1 AG--AGTTCATAATGAGAAGAACTCTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAC
*
307278 TTGTTCAACCTTTTTTCTGAATTCATCAAGTTGATGGATTATCTTTGACATGT
64 TTGTTCAACCTTTTTTCTGAATTCATC-AGTTGATGGATTATCTTTGCCA-GT
307331 AGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACT
1 AGAGTTCATAATGAGAAGAACTC-TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACT
*
307396 TGTTCAACCTTTTTTCAGAATTCATCAAGTTGATGGATTATCTTTGCCATGT
65 TGTTCAACCTTTTTTCTGAATTCATC-AGTTGATGGATTATCTTTGCCA-GT
307448 AGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACT
1 AGAGTTCATAATGAGAAGAACTC-TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACT
307513 TGTTCAACCTTTTTTCTGAATTCATCAAGTTGATGGATTATCTTTGCCATGT
65 TGTTCAACCTTTTTTCTGAATTCATC-AGTTGATGGATTATCTTTGCCA-GT
307565 AGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACT
1 AGAGTTCATAATGAGAAGAACTC-TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACT
* **
307630 TGTTCAATCTTTTGCCTGAATTCATCAAGTTGATGGATTATCTTTGCCAAGT
65 TGTTCAACCTTTTTTCTGAATTCATC-AGTTGATGGATTATCTTTGCC-AGT
307682 AGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACT
1 AGAGTTCATAATGAGAAGAACTC-TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACT
* * * * * *
307747 TGTTCAATC-TTTTGCTTGAATTCATCATTTGATGGATCAACATTG-CAGGT
65 TGTTCAACCTTTTTTC-TGAATTCATCAGTTGATGGATTATCTTTGCCA-GT
*
307797 AGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGAAAGAAGAAGTTCATAATGAGAAGAACT
1 AGAGTTCATAATGAGAAGAACTC-TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACT
* * * * * ** *
307862 TGTTCAATC-TTTTGCTTGAATTCATCATTTGATGGATCATCATCCCCAGC
65 TGTTCAACCTTTTTTC-TGAATTCATCAGTTGATGGATTATCTTTGCCAGT
*
307912 AGAAAGTTCATAATGAGAAGAA--CTCATCTGAAGAAAG-AGAAGAA
1 AG--AGTTCATAATGAGAAGAACTCTCATCTGAAGAAGGAAGAAGAA
307956 TTTATTCAAT
Statistics
Matches: 1122, Mismatches: 49, Indels: 46
0.92 0.04 0.04
Matches are distributed among these distances:
111 2 0.00
112 2 0.00
113 313 0.28
114 232 0.21
115 129 0.11
116 24 0.02
117 419 0.37
118 1 0.00
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.29
Consensus pattern (114 bp):
AGAGTTCATAATGAGAAGAACTCTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTT
GTTCAACCTTTTTTCTGAATTCATCAGTTGATGGATTATCTTTGCCAGT
Found at i:308088 original size:3 final size:3
Alignment explanation
Indices: 308080--308175 Score: 156
Period size: 3 Copynumber: 31.7 Consensus size: 3
308070 TTTTTATCCA
* *
308080 TAT TAT TAT TAT TAG TAT TAT TAT TAT TAT TAT TAT TAT TAT TAC TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
308128 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAA TAT ATAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT
308174 TA
1 TA
308176 AACATATATA
Statistics
Matches: 86, Mismatches: 6, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
3 83 0.97
4 3 0.03
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:309569 original size:19 final size:19
Alignment explanation
Indices: 309531--309566 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
309521 TAATTTAGTC
309531 ATTTATTTTATATGTTTTA
1 ATTTATTTTATATGTTTTA
309550 ATTTATTTTAT-TGTTTT
1 ATTTATTTTATATGTTTT
309567 TAAATATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.22, C:0.00, G:0.06, T:0.72
Consensus pattern (19 bp):
ATTTATTTTATATGTTTTA
Found at i:309633 original size:22 final size:21
Alignment explanation
Indices: 309594--309636 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
309584 TAGAATTTTC
**
309594 TTTTATTATATTGTTAAATAT
1 TTTTATTATATTCATAAATAT
309615 TTTTATATATATTCATAAATAT
1 TTTTAT-TATATTCATAAATAT
309637 ATATAATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.58
Consensus pattern (21 bp):
TTTTATTATATTCATAAATAT
Found at i:310538 original size:25 final size:26
Alignment explanation
Indices: 310510--310560 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
310500 ATGTCTGATA
*
310510 ATAAATGAGTTATTTAA-AAAAATAT
1 ATAAATGACTTATTTAATAAAAATAT
* *
310535 ATAAATTACTTATTTAATTAAAATAT
1 ATAAATGACTTATTTAATAAAAATAT
310561 TATTATAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 15 0.68
26 7 0.32
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.41
Consensus pattern (26 bp):
ATAAATGACTTATTTAATAAAAATAT
Found at i:313176 original size:21 final size:20
Alignment explanation
Indices: 313152--313206 Score: 51
Period size: 20 Copynumber: 2.6 Consensus size: 20
313142 ATTAAATATC
313152 TTATACATAAACTTA-ACTAAT
1 TTATACATAAACTTACAC--AT
*
313173 TTATAAGATAAAC-TACACAT
1 TTAT-ACATAAACTTACACAT
313193 TTAATACATAAACT
1 TT-ATACATAAACT
313207 ATTAGTTTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
20 11 0.39
21 8 0.29
22 9 0.32
ACGTcount: A:0.49, C:0.15, G:0.02, T:0.35
Consensus pattern (20 bp):
TTATACATAAACTTACACAT
Found at i:315869 original size:14 final size:17
Alignment explanation
Indices: 315838--315869 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
315828 ATCCTAGATT
315838 ATATTATTAATAGAAAA
1 ATATTATTAATAGAAAA
315855 ATATT-TTAAT-GAAAA
1 ATATTATTAATAGAAAA
315870 CGTATAATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 5 0.33
16 5 0.33
17 5 0.33
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (17 bp):
ATATTATTAATAGAAAA
Found at i:328512 original size:81 final size:82
Alignment explanation
Indices: 328283--328513 Score: 286
Period size: 84 Copynumber: 2.8 Consensus size: 82
328273 CACAAAGACC
*
328283 TTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCT
1 TTCGATTACACTCAGCTCCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCT
*
328348 GCCAACCAAAGACCTTTGAG
66 G---ACCAAAGACCTTCGAG
* * * * *
328368 TTCGACTACGCTCAGCTCC-AAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCT
1 TTCGATTACACTCAGCTCCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCT
*
328432 G-CCAAAGACCTTCGGG
66 GACCAAAGACCTTCGAG
* * * * * * *
328448 TTCGATTATACTCATCTCCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGAGTTATCT
1 TTCGATTACACTCAGCTCCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCT
328513 G
66 G
328514 TCAACAAAAA
Statistics
Matches: 125, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
80 28 0.22
81 38 0.30
84 43 0.34
85 16 0.13
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.26
Consensus pattern (82 bp):
TTCGATTACACTCAGCTCCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCT
GACCAAAGACCTTCGAG
Found at i:328564 original size:21 final size:21
Alignment explanation
Indices: 328538--328591 Score: 108
Period size: 21 Copynumber: 2.6 Consensus size: 21
328528 TGAGATTGTT
328538 TCCCTTGAGACAATTTTCGTC
1 TCCCTTGAGACAATTTTCGTC
328559 TCCCTTGAGACAATTTTCGTC
1 TCCCTTGAGACAATTTTCGTC
328580 TCCCTTGAGACA
1 TCCCTTGAGACA
328592 GTTTCCCTTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.20, C:0.30, G:0.15, T:0.35
Consensus pattern (21 bp):
TCCCTTGAGACAATTTTCGTC
Found at i:328599 original size:36 final size:36
Alignment explanation
Indices: 328559--328751 Score: 264
Period size: 36 Copynumber: 5.3 Consensus size: 36
328549 AATTTTCGTC
* *
328559 TCCCTTGAGACAATTTTCGTCTCCCTTGAGACAGTT
1 TCCCTTGAAACAATTTTCGTCTCTCTTGAGACAGTT
* *
328595 TCCCTTGAAAGAAATTTCGTCTCTCTTGAGACAGTT
1 TCCCTTGAAACAATTTTCGTCTCTCTTGAGACAGTT
328631 TCCCTTGAAACATATTTT-GTCTCTCTTGAGACAGTT
1 TCCCTTGAAACA-ATTTTCGTCTCTCTTGAGACAGTT
** *
328667 TCCCTTGAAACAAAATTCGTCTCCCTTGAGACAGTT
1 TCCCTTGAAACAATTTTCGTCTCTCTTGAGACAGTT
*
328703 TCCCTTGAAACAAATTGGT-GTCTCTCTTGAGACAGTT
1 TCCCTTGAAAC-AATT-TTCGTCTCTCTTGAGACAGTT
*
328740 TCTCTTGAAACA
1 TCCCTTGAAACA
328752 CCAAACCCTT
Statistics
Matches: 139, Mismatches: 14, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
35 3 0.02
36 102 0.73
37 33 0.24
38 1 0.01
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.36
Consensus pattern (36 bp):
TCCCTTGAAACAATTTTCGTCTCTCTTGAGACAGTT
Found at i:328664 original size:72 final size:72
Alignment explanation
Indices: 328559--329047 Score: 303
Period size: 72 Copynumber: 6.7 Consensus size: 72
328549 AATTTTCGTC
* * * *
328559 TCCCTTGAGAC-AATTTTCGTCTCCCTTGAGACAGTTTCCCTTGAAAGAAATTTCGTCTCTCTTG
1 TCCCTTGAAACAAATTTT-GTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTCGTCTCTCTTG
328623 AGACAGTT
65 AGACAGTT
* *
328631 TCCCTTGAAACATATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTCGTCTCCCTTGA
1 TCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTCGTCTCTCTTGA
328696 GACAGTT
66 GACAGTT
* * *
328703 TCCCTTGAAACAAATTGGTGTCTCTCTTGAGACAGTTTCTCTTGAAACACCAAACCCTT-GATTT
1 TCCCTTGAAACAAATT-TTGTCTCTCTTGAGACAGTTTCCCTTGAAACA--AAA---TTCG-TCT
** * *
328767 CGATT-ACACTCAGCT
59 CTCTTGAGA--CAGTT
*** ** * * ** ** * ****** **** ***
328782 T-CGAGGGCACATCATTTACAG-CATAACTCAAGGCTAGAAGAGTTATCTGTCAACAA--AAAC-
1 TCCCTTGAAACA-AATTT--TGTC-TCTCTTGAGAC-AGTTTCCCT-TGAAACAA-AATTCGTCT
**
328842 CT-TTGAGATTGTT
59 CTCTTGAGACAGTT
* * * * * *
328855 TCCCTTGAGACAAATTTCGTCTCCCTTGAGACAGTTTCCCTTGAAAGAAATTTCGTCTCTATTGA
1 TCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTCGTCTCTCTTGA
328920 GACAGTT
66 GACAGTT
* *
328927 TCCCTTGAAACATATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTCGTCTCCCTTGA
1 TCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTCGTCTCTCTTGA
328992 GACAGTT
66 GACAGTT
* *
328999 TCCCTTGAAACAAATTGGTGTCTCTCTTGAGACAGTTTCTCTTGAAACA
1 TCCCTTGAAACAAATT-TTGTCTCTCTTGAGACAGTTTCCCTTGAAACA
329048 CCAAACCCTT
Statistics
Matches: 306, Mismatches: 85, Indels: 51
0.69 0.19 0.12
Matches are distributed among these distances:
68 1 0.00
69 3 0.01
70 4 0.01
71 9 0.03
72 164 0.54
73 72 0.24
74 7 0.02
75 6 0.02
77 3 0.01
78 12 0.04
79 9 0.03
80 8 0.03
81 5 0.02
82 3 0.01
ACGTcount: A:0.26, C:0.24, G:0.16, T:0.34
Consensus pattern (72 bp):
TCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTCGTCTCTCTTGA
GACAGTT
Found at i:328892 original size:36 final size:36
Alignment explanation
Indices: 328852--329047 Score: 286
Period size: 36 Copynumber: 5.4 Consensus size: 36
328842 CTTTGAGATT
* *
328852 GTTTCCCTTGAGACAAATTTCGTCTCCCTTGAGACA
1 GTTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACA
* *
328888 GTTTCCCTTGAAAGAAATTTCGTCTCTATTGAGACA
1 GTTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACA
* *
328924 GTTTCCCTTGAAACATATTTTGTCTCTCTTGAGACA
1 GTTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACA
* *
328960 GTTTCCCTTGAAACAAAATTCGTCTCCCTTGAGACA
1 GTTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACA
328996 GTTTCCCTTGAAACAAATTGGT-GTCTCTCTTGAGACA
1 GTTTCCCTTGAAACAAATT--TCGTCTCTCTTGAGACA
*
329033 GTTTCTCTTGAAACA
1 GTTTCCCTTGAAACA
329048 CCAAACCCTT
Statistics
Matches: 143, Mismatches: 15, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
36 114 0.80
37 28 0.20
38 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (36 bp):
GTTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACA
Found at i:329093 original size:296 final size:296
Alignment explanation
Indices: 328559--329130 Score: 1099
Period size: 296 Copynumber: 1.9 Consensus size: 296
328549 AATTTTCGTC
* *
328559 TCCCTTGAGACAATTTTCGTCTCCCTTGAGACAGTTTCCCTTGAAAGAAATTTCGTCTCTCTTGA
1 TCCCTTGAGACAAATTTCGTCTCCCTTGAGACAGTTTCCCTTGAAAGAAATTTCGTCTCTATTGA
328624 GACAGTTTCCCTTGAAACATATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTCGTCT
66 GACAGTTTCCCTTGAAACATATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTCGTCT
328689 CCCTTGAGACAGTTTCCCTTGAAACAAATTGGTGTCTCTCTTGAGACAGTTTCTCTTGAAACACC
131 CCCTTGAGACAGTTTCCCTTGAAACAAATTGGTGTCTCTCTTGAGACAGTTTCTCTTGAAACACC
*
328754 AAACCCTTGATTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAG
196 AAACCCTTGATTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCAAG
*
328819 AAGAGTTATCTGTCAACAAAAACCTTTGAGATTGTT
261 AAGAGCTATCTGTCAACAAAAACCTTTGAGATTGTT
328855 TCCCTTGAGACAAATTTCGTCTCCCTTGAGACAGTTTCCCTTGAAAGAAATTTCGTCTCTATTGA
1 TCCCTTGAGACAAATTTCGTCTCCCTTGAGACAGTTTCCCTTGAAAGAAATTTCGTCTCTATTGA
328920 GACAGTTTCCCTTGAAACATATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTCGTCT
66 GACAGTTTCCCTTGAAACATATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTCGTCT
328985 CCCTTGAGACAGTTTCCCTTGAAACAAATTGGTGTCTCTCTTGAGACAGTTTCTCTTGAAACACC
131 CCCTTGAGACAGTTTCCCTTGAAACAAATTGGTGTCTCTCTTGAGACAGTTTCTCTTGAAACACC
329050 AAACCCTTGATTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCAAG
196 AAACCCTTGATTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCAAG
*
329115 AAGGGCTATCTGTCAA
261 AAGAGCTATCTGTCAA
329131 TAAGATTGTC
Statistics
Matches: 271, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
296 271 1.00
ACGTcount: A:0.27, C:0.24, G:0.16, T:0.33
Consensus pattern (296 bp):
TCCCTTGAGACAAATTTCGTCTCCCTTGAGACAGTTTCCCTTGAAAGAAATTTCGTCTCTATTGA
GACAGTTTCCCTTGAAACATATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTCGTCT
CCCTTGAGACAGTTTCCCTTGAAACAAATTGGTGTCTCTCTTGAGACAGTTTCTCTTGAAACACC
AAACCCTTGATTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCAAG
AAGAGCTATCTGTCAACAAAAACCTTTGAGATTGTT
Found at i:330876 original size:106 final size:106
Alignment explanation
Indices: 329480--330859 Score: 2283
Period size: 106 Copynumber: 13.0 Consensus size: 106
329470 GGCCTCAAGA
* * *
329480 TGGACTCCAGACAACGTAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAACTT
1 TGGACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTT
* * *
329545 CCCAATTTCAGAGCCAATTTCAACTTCACAGCAAAGGATAT
66 CTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATAT
* *
329586 TGGACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACTGCTGGTTGTCAACAAACAATTT
1 TGGACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTT
* *
329651 CCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATAT
66 CTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATAT
* * * *
329692 TGGACTCCACACAACGTAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAACTT
1 TGGACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTT
329757 CTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATAT
66 CTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATAT
* * *
329798 TGGACTCGAGACAACGCAAGTTCAACTTCATGACGAAGGGACCGTTGATTGTCAACAAACAACTT
1 TGGACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTT
*
329863 CTCAATTTCAGAGCCAATTTCAACTTCACAAAGAAGGATAT
66 CTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATAT
* *
329904 TGGACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTATCAACAAACAATTT
1 TGGACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTT
* * *
329969 CCCAATTTCGGAGACAATTTCAACTTCACAACGAAGGATAT
66 CTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATAT
* *
330010 TGGACTCGAGACAACGCAAGTTCAACTTCATGACGAAGGGATCGCTGGTTGTCAACAAACAACTT
1 TGGACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTT
330075 CTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATAT
66 CTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATAT
* *
330116 TGGACTCGAGACAACGCAAGTTCAACTTCATGACGAAGGGACCGCTGATTGTCAACAAACAACTT
1 TGGACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTT
330181 CTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATAT
66 CTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATAT
* *
330222 TGGACTCGAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTT
1 TGGACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTT
* * *
330287 CCCAATTTCGGAGCCAATTTCAACTTCACAGCGAAGGATAT
66 CTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATAT
* * *
330328 TGGACTCCAGACAACGTAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAACTT
1 TGGACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTT
330393 CTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATAT
66 CTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATAT
*
330434 TGGACTCGAGACAACGCAAGTTCAACTTCATGACGAAGGGACCGCTGGTTGTCAACAAACAACTT
1 TGGACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTT
330499 CTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATAT
66 CTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATAT
* * * *
330540 TGGACTCCAGACAACGTAAGTTCAACTTCACGATGAAGGGACCGCTGGTTGTCAATAAACAACTT
1 TGGACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTT
*
330605 CTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGAATAT
66 CTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATAT
* * *
330646 TGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTT
1 TGGACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTT
*
330711 CTCAATTTCAGAGCCAATTTTAACTTCACAACGAAGGATAT
66 CTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATAT
* *
330752 TGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTT
1 TGGACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTT
** * ** *
330817 CTCAATTTCAGTTCCAATTTCAATTTCACGTCGAAAGATAT
66 CTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATAT
330858 TG
1 TG
330860 ACCTCATAAT
Statistics
Matches: 1198, Mismatches: 76, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
106 1198 1.00
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.23
Consensus pattern (106 bp):
TGGACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTT
CTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATAT
Found at i:331123 original size:3 final size:3
Alignment explanation
Indices: 331104--331147 Score: 52
Period size: 3 Copynumber: 14.0 Consensus size: 3
331094 ATATATATAC
* *
331104 ATT ATTT ATT GTT ATT ATT AATT ATT ATT ATT ATT ATT AAT ATT
1 ATT A-TT ATT ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT
331148 TTTAATTTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
3 29 0.83
4 6 0.17
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:331128 original size:16 final size:16
Alignment explanation
Indices: 331104--331139 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
331094 ATATATATAC
* *
331104 ATTATTTATTGTTATT
1 ATTAATTATTATTATT
331120 ATTAATTATTATTATT
1 ATTAATTATTATTATT
331136 ATTA
1 ATTA
331140 TTAATATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (16 bp):
ATTAATTATTATTATT
Found at i:331152 original size:9 final size:9
Alignment explanation
Indices: 331116--331159 Score: 52
Period size: 9 Copynumber: 4.8 Consensus size: 9
331106 TATTTATTGT
331116 TATTATTAA
1 TATTATTAA
*
331125 TTATTATTAT
1 -TATTATTAA
331135 TATTATTAA
1 TATTATTAA
*
331144 TATTTTTAA
1 TATTATTAA
*
331153 TTTTATT
1 TATTATT
331160 TTTTTGCAAG
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
9 21 0.72
10 8 0.28
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (9 bp):
TATTATTAA
Found at i:333146 original size:21 final size:20
Alignment explanation
Indices: 333122--333176 Score: 51
Period size: 20 Copynumber: 2.6 Consensus size: 20
333112 ATTAAATATC
333122 TTATACATAAACTTA-ACTAAT
1 TTATACATAAACTTACAC--AT
*
333143 TTATAAGATAAAC-TACACAT
1 TTAT-ACATAAACTTACACAT
333163 TTAATACATAAACT
1 TT-ATACATAAACT
333177 ATTAGTTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
20 11 0.39
21 8 0.29
22 9 0.32
ACGTcount: A:0.49, C:0.15, G:0.02, T:0.35
Consensus pattern (20 bp):
TTATACATAAACTTACACAT
Found at i:334338 original size:34 final size:35
Alignment explanation
Indices: 334246--334345 Score: 109
Period size: 34 Copynumber: 2.9 Consensus size: 35
334236 TTTAGCTTGG
*
334246 AAATAAATATGTTCCCGAA-AGCTAAATGAAT-ATT
1 AAATAAATATGTTCCCGAACA-CTAAACGAATGATT
* * * *
334280 AAATAAATTTGTT-TCGGACCCTAAACGAATGATT
1 AAATAAATATGTTCCCGAACACTAAACGAATGATT
*
334314 -AATGAATATGTTCCCGAACACTAAACGAATGA
1 AAATAAATATGTTCCCGAACACTAAACGAATGA
334346 ATATAAACTC
Statistics
Matches: 53, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
33 22 0.42
34 31 0.58
ACGTcount: A:0.43, C:0.15, G:0.14, T:0.28
Consensus pattern (35 bp):
AAATAAATATGTTCCCGAACACTAAACGAATGATT
Found at i:345397 original size:13 final size:14
Alignment explanation
Indices: 345369--345397 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
345359 ATATTTTATA
345369 ATATTTTTACTATT
1 ATATTTTTACTATT
345383 ATATTTTTACT-TT
1 ATATTTTTACTATT
345396 AT
1 AT
345398 TTAATATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.27
14 11 0.73
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.66
Consensus pattern (14 bp):
ATATTTTTACTATT
Found at i:349301 original size:51 final size:51
Alignment explanation
Indices: 349225--349349 Score: 223
Period size: 51 Copynumber: 2.5 Consensus size: 51
349215 TTATACAAAA
*
349225 CGCGGTAACTGCCCCGCGCTATATAAAATTATGTCAGGAGTAAAGGTATGT
1 CGCGGTACCTGCCCCGCGCTATATAAAATTATGTCAGGAGTAAAGGTATGT
*
349276 CGCGGTACCTGCCCCGCGCTATATAAAGTTATGTCAGGAGTAAAGGTATGT
1 CGCGGTACCTGCCCCGCGCTATATAAAATTATGTCAGGAGTAAAGGTATGT
*
349327 CGTGGTACCTGCCCCGCGCTATA
1 CGCGGTACCTGCCCCGCGCTATA
349350 CCCCCTACGT
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 71 1.00
ACGTcount: A:0.25, C:0.24, G:0.26, T:0.25
Consensus pattern (51 bp):
CGCGGTACCTGCCCCGCGCTATATAAAATTATGTCAGGAGTAAAGGTATGT
Found at i:349443 original size:51 final size:51
Alignment explanation
Indices: 349364--349490 Score: 139
Period size: 51 Copynumber: 2.5 Consensus size: 51
349354 CTACGTGGCG
* * * * * * *
349364 TATAGCGCGCTGCAGGGGTCACGCTATA-CCCACGCGTATGCCAGATCACCA
1 TATAGCGCGGTGCAGGGGGCGCGCTATACCCCACGTG-ACGCCAAAACACCA
* * * *
349415 TATAGCGCGGTGCAGGGGGCGCGTTATACCCCACGTGGCGCCAAAACATCG
1 TATAGCGCGGTGCAGGGGGCGCGCTATACCCCACGTGACGCCAAAACACCA
349466 TATAGCGCGGTGCAGGGGGCGCGCT
1 TATAGCGCGGTGCAGGGGGCGCGCT
349491 TTACTGCTAA
Statistics
Matches: 63, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
51 56 0.89
52 7 0.11
ACGTcount: A:0.20, C:0.30, G:0.33, T:0.17
Consensus pattern (51 bp):
TATAGCGCGGTGCAGGGGGCGCGCTATACCCCACGTGACGCCAAAACACCA
Found at i:349796 original size:31 final size:31
Alignment explanation
Indices: 349760--349823 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
349750 AAAACATAAT
*
349760 ATATAATCACTTTTATTTTTATTTAGTTAAG
1 ATATAATCACTTTTATTTTTATTTAATTAAG
*
349791 ATATAATCACTTTTGTTTTTATTTAATTAAG
1 ATATAATCACTTTTATTTTTATTTAATTAAG
349822 AT
1 AT
349824 GTGATCATCA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.33, C:0.06, G:0.06, T:0.55
Consensus pattern (31 bp):
ATATAATCACTTTTATTTTTATTTAATTAAG
Found at i:350922 original size:29 final size:30
Alignment explanation
Indices: 350879--350938 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 30
350869 ATATATCTAA
* **
350879 AAAAATTAGTTTTTAAAACTTTTTTTTGTT
1 AAAAATAAGTTTTTAAAAAGTTTTTTTGTT
350909 AAAAATAAG-TTTTAAAAAGTTTTTTTGTT
1 AAAAATAAGTTTTTAAAAAGTTTTTTTGTT
350938 A
1 A
350939 TATTTTTAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 19 0.70
30 8 0.30
ACGTcount: A:0.38, C:0.02, G:0.08, T:0.52
Consensus pattern (30 bp):
AAAAATAAGTTTTTAAAAAGTTTTTTTGTT
Found at i:351602 original size:10 final size:10
Alignment explanation
Indices: 351587--351616 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
351577 CTTTTTATTT
351587 TTTATTTTAC
1 TTTATTTTAC
*
351597 TTTATTTTAG
1 TTTATTTTAC
351607 TTTATTTTAC
1 TTTATTTTAC
351617 AACTTACATG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.20, C:0.07, G:0.03, T:0.70
Consensus pattern (10 bp):
TTTATTTTAC
Found at i:352096 original size:38 final size:39
Alignment explanation
Indices: 352030--352118 Score: 130
Period size: 38 Copynumber: 2.4 Consensus size: 39
352020 TTTTCACCCT
352030 AAACCCGAACCCGACCCGACCCGAATATCACACTTAAAA
1 AAACCCGAACCCGACCCGACCCGAATATCACACTTAAAA
* * *
352069 AAACCCG-ACCTGACTCGACTCGAATATCACACTT-AAA
1 AAACCCGAACCCGACCCGACCCGAATATCACACTTAAAA
352106 AAACCC-AACCCGA
1 AAACCCGAACCCGA
352119 ACAAAATAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
37 14 0.31
38 24 0.53
39 7 0.16
ACGTcount: A:0.40, C:0.37, G:0.10, T:0.12
Consensus pattern (39 bp):
AAACCCGAACCCGACCCGACCCGAATATCACACTTAAAA
Found at i:352444 original size:205 final size:205
Alignment explanation
Indices: 352076--352592 Score: 746
Period size: 205 Copynumber: 2.5 Consensus size: 205
352066 AAAAAACCCG
* * * *
352076 ACCTGACTCGACTCGAATATCACACTTAAAAAACCCAACCCGAACAAAATAAAGTTTCATCCGAC
1 ACCTGAATCGACCCAAATATCACACTTAAAAAACCCGACCCGAACAAAATAAAGTTTCATCCGAC
**
352141 CCGAATATATGAATTAGAAATATGACCCGACCCGACCCGAAATAATAAAAAAGTATTTTTATTTA
66 CCGAATATATGAATTAGAAATCCGACCCGACCCGACCCGAAATAATAAAAAAGTATTTTTATTTA
* *
352206 ATAAAAACAATGACTTAATCCGACCCGACCTGAATTATATATATTTTCGGGTCGGTCCGGTTTTT
131 ATAAAAACAATGACTTAATCCAACCCAACCTGAATTATATATATTTTCGGGTCGGTCCGGTTTTT
*
352271 TTCACTCTAA
196 TTCACCCTAA
352281 ACCTGAATCGACCCAAATATCACACTTAAAAAACCCGACCCGAACAAAATAAAGTTTCATCCGAC
1 ACCTGAATCGACCCAAATATCACACTTAAAAAACCCGACCCGAACAAAATAAAGTTTCATCCGAC
* * *
352346 CCTAATATATGAATTAGAAATCCAACCCGACCCGACCCGAAATAATAAAAAATTATTTTTATTTA
66 CCGAATATATGAATTAGAAATCCGACCCGACCCGACCCGAAATAATAAAAAAGTATTTTTATTTA
* *
352411 ATAAAAACAATGACTTAATCCAACCCAACCTGAATTATATATATTTTTGGGTCGGTTCGGTTTTT
131 ATAAAAACAATGACTTAATCCAACCCAACCTGAATTATATATATTTTCGGGTCGGTCCGGTTTTT
352476 TTCACCCTAA
196 TTCACCCTAA
* * * *
352486 ACCCGAACCCGACCCGACCCAAATATCACACTTAAAAAAATCCGATCCGACTCGACCAAAATAAA
1 ACCTG-A----A-TCGACCCAAATATCACACTT-AAAAAA--C---CCGACCCGAACAAAATAAA
* *
352551 GTTTCACCCGACCCGAATATATGAATTAGAAACCCGACCCGA
54 GTTTCATCCGACCCGAATATATGAATTAGAAATCCGACCCGA
352593 AATAATAAAA
Statistics
Matches: 278, Mismatches: 22, Indels: 12
0.89 0.07 0.04
Matches are distributed among these distances:
205 195 0.70
206 1 0.00
210 1 0.00
211 19 0.07
212 6 0.02
214 1 0.00
217 55 0.20
ACGTcount: A:0.38, C:0.25, G:0.11, T:0.25
Consensus pattern (205 bp):
ACCTGAATCGACCCAAATATCACACTTAAAAAACCCGACCCGAACAAAATAAAGTTTCATCCGAC
CCGAATATATGAATTAGAAATCCGACCCGACCCGACCCGAAATAATAAAAAAGTATTTTTATTTA
ATAAAAACAATGACTTAATCCAACCCAACCTGAATTATATATATTTTCGGGTCGGTCCGGTTTTT
TTCACCCTAA
Found at i:353130 original size:23 final size:23
Alignment explanation
Indices: 353097--353142 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
353087 GGAAATCTTT
353097 AAAATAAAA-TTAAAATAATAAAA
1 AAAATAAAATTTAAAA-AATAAAA
*
353120 AAAATAGAATTTAAAAAATAAAA
1 AAAATAAAATTTAAAAAATAAAA
353143 CAAGAGATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 15 0.71
24 6 0.29
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (23 bp):
AAAATAAAATTTAAAAAATAAAA
Found at i:359500 original size:41 final size:41
Alignment explanation
Indices: 359461--359543 Score: 112
Period size: 41 Copynumber: 2.0 Consensus size: 41
359451 TACGTAAAAA
359461 AAAATTATTGAAGATTCATCTATTAAAATCAGATATAAAACAG
1 AAAATTATT--AGATTCATCTATTAAAATCAGATATAAAACAG
** * *
359504 GGATTTATTTGATTCATCTATTAAAATCAGATATAAAACA
1 AAAATTATTAGATTCATCTATTAAAATCAGATATAAAACA
359544 TGGATTTATT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
41 30 0.83
43 6 0.17
ACGTcount: A:0.47, C:0.10, G:0.10, T:0.34
Consensus pattern (41 bp):
AAAATTATTAGATTCATCTATTAAAATCAGATATAAAACAG
Found at i:359549 original size:41 final size:41
Alignment explanation
Indices: 359473--359555 Score: 157
Period size: 41 Copynumber: 2.0 Consensus size: 41
359463 AATTATTGAA
359473 GATTCATCTATTAAAATCAGATATAAAACAGGGATTTATTT
1 GATTCATCTATTAAAATCAGATATAAAACAGGGATTTATTT
*
359514 GATTCATCTATTAAAATCAGATATAAAACATGGATTTATTT
1 GATTCATCTATTAAAATCAGATATAAAACAGGGATTTATTT
359555 G
1 G
359556 GACTGGTTAA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.41, C:0.10, G:0.12, T:0.37
Consensus pattern (41 bp):
GATTCATCTATTAAAATCAGATATAAAACAGGGATTTATTT
Found at i:362128 original size:31 final size:31
Alignment explanation
Indices: 362093--362162 Score: 106
Period size: 31 Copynumber: 2.3 Consensus size: 31
362083 CATCAGGTTG
362093 ATATCTTAAATAAATAAAAAC-AAATATGATC
1 ATATCTTAAATAAATAAAAACGAAA-ATGATC
* *
362124 ATATCTTAATTAAATAAAAACGAAAGTGATC
1 ATATCTTAAATAAATAAAAACGAAAATGATC
362155 ATATCTTA
1 ATATCTTA
362163 TATATTTTGA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
31 33 0.92
32 3 0.08
ACGTcount: A:0.53, C:0.10, G:0.06, T:0.31
Consensus pattern (31 bp):
ATATCTTAAATAAATAAAAACGAAAATGATC
Found at i:363922 original size:15 final size:15
Alignment explanation
Indices: 363899--363929 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
363889 CGGCCTTCCA
*
363899 GGCGGCTTCACGCTC
1 GGCGACTTCACGCTC
363914 GGCGACTTCACGCTC
1 GGCGACTTCACGCTC
363929 G
1 G
363930 CGTTCCTCGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.10, C:0.39, G:0.32, T:0.19
Consensus pattern (15 bp):
GGCGACTTCACGCTC
Found at i:367398 original size:19 final size:19
Alignment explanation
Indices: 367365--367420 Score: 87
Period size: 19 Copynumber: 3.0 Consensus size: 19
367355 TTTCTCATTA
* *
367365 TGACTT-TGATCAAGGCTT
1 TGACTTCTGATGAAGGATT
367383 TGACTTCTGATGAAGGATT
1 TGACTTCTGATGAAGGATT
367402 TGACTTCTGATGAAGGATT
1 TGACTTCTGATGAAGGATT
367421 CCATCTATGC
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
18 6 0.17
19 29 0.83
ACGTcount: A:0.25, C:0.12, G:0.25, T:0.38
Consensus pattern (19 bp):
TGACTTCTGATGAAGGATT
Found at i:380155 original size:2 final size:2
Alignment explanation
Indices: 380148--380172 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
380138 AATCAATTTA
380148 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
380173 CACATCAAAC
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:380442 original size:28 final size:26
Alignment explanation
Indices: 380394--380455 Score: 72
Period size: 26 Copynumber: 2.3 Consensus size: 26
380384 ATAACAAAAT
380394 ATTTTATTTAAAAAATCATTTGAATTAA
1 ATTTTATTTAAAAAATCATTT--ATTAA
*
380422 ATTTTAATTTATAAAAT-ATTTATTAA
1 ATTTT-ATTTAAAAAATCATTTATTAA
380448 ATTATTAT
1 ATT-TTAT
380456 GAAATGGTCA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
26 10 0.32
27 2 0.06
28 9 0.29
29 10 0.32
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (26 bp):
ATTTTATTTAAAAAATCATTTATTAA
Found at i:383213 original size:31 final size:32
Alignment explanation
Indices: 383164--383225 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 32
383154 AATTTTTACA
*
383164 AATAATTTGATTAAATTTATTAACCATTTTGT
1 AATAATTTGATTAAATTTAATAACCATTTTGT
*
383196 AATAATTTGA-TAAATTTAATGACCATTTTG
1 AATAATTTGATTAAATTTAATAACCATTTTG
383226 ATAACATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
31 18 0.64
32 10 0.36
ACGTcount: A:0.39, C:0.06, G:0.08, T:0.47
Consensus pattern (32 bp):
AATAATTTGATTAAATTTAATAACCATTTTGT
Found at i:385365 original size:75 final size:75
Alignment explanation
Indices: 385278--385610 Score: 398
Period size: 75 Copynumber: 4.4 Consensus size: 75
385268 CTTAACCGGT
* * * * *
385278 TAAAATAAAATAGACACTACTTATTATGTTAAACTACCTACCGGTTTGTTTAAATGTTACTAATA
1 TAAAATAAAATAGGCGCTACCTATTACGTTAAACTACCTACCGGTTTGTTTAAAGGTTACTAATA
*
385343 ATGTAAATGA
66 ATGTAAACGA
* * * * * * *
385353 TAAAATAAAATAGGTGTTACCTATTACGTTAAAATACTTATCAGTTTGTTTAAAGATTACTAATA
1 TAAAATAAAATAGGCGCTACCTATTACGTTAAACTACCTACCGGTTTGTTTAAAGGTTACTAATA
385418 ATGTAAA-GA
66 ATGTAAACGA
* * * *
385427 GTAAAATAAAATAGACACTACCTATTACGTTAAATTATCTACCGGTTTGTTTAAAGGTTACTAAT
1 -TAAAATAAAATAGGCGCTACCTATTACGTTAAACTACCTACCGGTTTGTTTAAAGGTTACTAAT
*
385492 AATGTAAACGG
65 AATGTAAACGA
* * * * *
385503 TAAAATAAAACAGGCGTTACCTATTACGTTAAACTAGCTACCGGTTTGTTTAAAGGTTAATTATA
1 TAAAATAAAATAGGCGCTACCTATTACGTTAAACTACCTACCGGTTTGTTTAAAGGTTACTAATA
* *
385568 AGGTAAACGG
66 ATGTAAACGA
* * *
385578 TAAAATAAAATAGGTGCTACATATTATGTTAAA
1 TAAAATAAAATAGGCGCTACCTATTACGTTAAA
385611 TAGGCGCTAC
Statistics
Matches: 219, Mismatches: 37, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
74 2 0.01
75 216 0.99
76 1 0.00
ACGTcount: A:0.41, C:0.11, G:0.14, T:0.34
Consensus pattern (75 bp):
TAAAATAAAATAGGCGCTACCTATTACGTTAAACTACCTACCGGTTTGTTTAAAGGTTACTAATA
ATGTAAACGA
Found at i:385603 original size:150 final size:150
Alignment explanation
Indices: 385278--385611 Score: 456
Period size: 150 Copynumber: 2.2 Consensus size: 150
385268 CTTAACCGGT
* * *
385278 TAAAATAAAATAGACACTACTTATTATGTTAAACTACCTACCGGTTTGTTTAAATGTTACTAATA
1 TAAAATAAAATAGACACTACATATTATGTTAAATTACCTACCGGTTTGTTTAAAGGTTACTAATA
* * * *
385343 ATGTAAATGATAAAATAAAATAGGTGTTACCTATTACGTTAAAATACTTATCAGTTTGTTTAAAG
66 ATGTAAACGATAAAATAAAACAGGCGTTACCTATTACGTTAAAATACTTACCAGTTTGTTTAAAG
* *
385408 ATTACTAATAATGTAAAGAG
131 ATTAATAATAAGGTAAAGAG
* * *
385428 TAAAATAAAATAGACACTACCTATTACGTTAAATTATCTACCGGTTTGTTTAAAGGTTACTAATA
1 TAAAATAAAATAGACACTACATATTATGTTAAATTACCTACCGGTTTGTTTAAAGGTTACTAATA
* * *
385493 ATGTAAACGGTAAAATAAAACAGGCGTTACCTATTACGTTAAACTAGC-TACCGGTTTGTTTAAA
66 ATGTAAACGATAAAATAAAACAGGCGTTACCTATTACGTTAAAATA-CTTACCAGTTTGTTTAAA
* *
385557 GGTTAATTATAAGGTAAACG-G
130 GATTAATAATAAGGTAAA-GAG
***
385578 TAAAATAAAATAGGTGCTACATATTATGTTAAAT
1 TAAAATAAAATAGACACTACATATTATGTTAAAT
385612 AGGCGCTACA
Statistics
Matches: 161, Mismatches: 21, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
150 159 0.99
151 2 0.01
ACGTcount: A:0.41, C:0.11, G:0.14, T:0.34
Consensus pattern (150 bp):
TAAAATAAAATAGACACTACATATTATGTTAAATTACCTACCGGTTTGTTTAAAGGTTACTAATA
ATGTAAACGATAAAATAAAACAGGCGTTACCTATTACGTTAAAATACTTACCAGTTTGTTTAAAG
ATTAATAATAAGGTAAAGAG
Found at i:385611 original size:23 final size:23
Alignment explanation
Indices: 385585--385649 Score: 103
Period size: 23 Copynumber: 2.8 Consensus size: 23
385575 CGGTAAAATA
*
385585 AAATAGGTGCTACATATTATGTT
1 AAATAGGCGCTACATATTATGTT
385608 AAATAGGCGCTACATATTATGTT
1 AAATAGGCGCTACATATTATGTT
* *
385631 AAATAAGCGCTACCTATTA
1 AAATAGGCGCTACATATTA
385650 CATTAAACTA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.34
Consensus pattern (23 bp):
AAATAGGCGCTACATATTATGTT
Found at i:385655 original size:23 final size:23
Alignment explanation
Indices: 385593--385656 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 23
385583 TAAAATAGGT
** *
385593 GCTACATATTATGTTAAATAGGC
1 GCTACATATTACATTAAATAAGC
**
385616 GCTACATATTATGTTAAATAAGC
1 GCTACATATTACATTAAATAAGC
*
385639 GCTACCTATTACATTAAA
1 GCTACATATTACATTAAA
385657 CTAGCTACCT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.34
Consensus pattern (23 bp):
GCTACATATTACATTAAATAAGC
Found at i:385732 original size:22 final size:23
Alignment explanation
Indices: 385706--385753 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
385696 CGGTAAAATA
*
385706 AAATAAGCG-TACCTATTACTTT
1 AAATAAGCGCTACCTATTACGTT
385728 AAATAAGCGCTACCTATTACGTT
1 AAATAAGCGCTACCTATTACGTT
385751 AAA
1 AAA
385754 CTAGCTACCG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 9 0.38
23 15 0.62
ACGTcount: A:0.40, C:0.19, G:0.10, T:0.31
Consensus pattern (23 bp):
AAATAAGCGCTACCTATTACGTT
Found at i:385736 original size:97 final size:98
Alignment explanation
Indices: 385608--385851 Score: 341
Period size: 97 Copynumber: 2.5 Consensus size: 98
385598 ATATTATGTT
* * *
385608 AAATAGGCGCTACATATTATGTTAAATAAGCGCTACCTATTACATTAAACTAGCTACCTATTTGT
1 AAATAGACGCTACCTATTATGTTAAATAAGCGCTACCTATTACATTAAACTAGCTACCGATTTGT
*
385673 TTAAAGATTAATAATGATGTAAACGGTAAAATA
66 TTAAAGATTAATAATAATGTAAACGGTAAAATA
*
385706 AAATA-A-GCGTACCTATTACT-TTAAATAAGCGCTACCTATTACGTTAAACTAGCTACCGATTT
1 AAATAGACGC-TACCTATTA-TGTTAAATAAGCGCTACCTATTACATTAAACTAGCTACCGATTT
* * *
385768 GTTTAAAGGTTAATAATAATGTAAATGGTTAAATA
64 GTTTAAAGATTAATAATAATGTAAACGGTAAAATA
* * **
385803 AAATAGACGCTACTTATTATGTTAAATAGGTACTACCTATTACATTAAA
1 AAATAGACGCTACCTATTATGTTAAATAAGCGCTACCTATTACATTAAA
385852 TAACCACTAC
Statistics
Matches: 128, Mismatches: 13, Indels: 10
0.85 0.09 0.07
Matches are distributed among these distances:
96 2 0.02
97 85 0.66
98 39 0.30
99 2 0.02
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.34
Consensus pattern (98 bp):
AAATAGACGCTACCTATTATGTTAAATAAGCGCTACCTATTACATTAAACTAGCTACCGATTTGT
TTAAAGATTAATAATAATGTAAACGGTAAAATA
Found at i:385771 original size:218 final size:219
Alignment explanation
Indices: 385520--385972 Score: 658
Period size: 218 Copynumber: 2.1 Consensus size: 219
385510 AAACAGGCGT
* *
385520 TACCTATTACGTTAAACTAGCTACCGGTTTGTTTAAAGGTTAATTATAAGGTAAACGGTAAAATA
1 TACCTATTACGTTAAACTAGCTACCGATTTGTTTAAAGGTTAATAATAAGGTAAACGGTAAAATA
** * ** * *
385585 AAATAGGTGCTACATATTATGTTAAATAGGCGCTACATATTATGTTAAATAAGCGCTACCTATTA
66 AAATAGACGCTACATATTATGTTAAATAGGCACTACATATTACATTAAATAACCACTACCTATTA
* * *
385650 CATTAAACTAGCTACCTATTTGTTTAAAGATTAATAATGATGTAAACGGTAAAATAAAATA-A-G
131 CATTAAACTAACTACCGATTTGTTTAAAGATTAATAATAATGTAAACGGTAAAATAAAATAGACG
*
385713 CGTACCTATTACTTTAAATAAGCGC
196 C-TACCTATTACGTTAAATAAGCGC
* * *
385738 TACCTATTACGTTAAACTAGCTACCGATTTGTTTAAAGGTTAATAATAATGTAAATGGTTAAATA
1 TACCTATTACGTTAAACTAGCTACCGATTTGTTTAAAGGTTAATAATAAGGTAAACGGTAAAATA
* * *
385803 AAATAGACGCTACTTATTATGTTAAATAGGTACTACCTATTACATTAAATAACCACTACCTATTA
66 AAATAGACGCTACATATTATGTTAAATAGGCACTACATATTACATTAAATAACCACTACCTATTA
** * *
385868 TGTTAAACTAACTACCGATTTGTTTAAAGGTTAATAATAATGTAAATGGTAAAATAAAATAGACG
131 CATTAAACTAACTACCGATTTGTTTAAAGATTAATAATAATGTAAACGGTAAAATAAAATAGACG
385933 CTACCTATTACGTTAAATAAGCGC
196 CTACCTATTACGTTAAATAAGCGC
**
385957 TATTTATTACGTTAAA
1 TACCTATTACGTTAAA
385973 TAAGCGCTAC
Statistics
Matches: 208, Mismatches: 25, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
218 169 0.81
219 37 0.18
220 2 0.01
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.34
Consensus pattern (219 bp):
TACCTATTACGTTAAACTAGCTACCGATTTGTTTAAAGGTTAATAATAAGGTAAACGGTAAAATA
AAATAGACGCTACATATTATGTTAAATAGGCACTACATATTACATTAAATAACCACTACCTATTA
CATTAAACTAACTACCGATTTGTTTAAAGATTAATAATAATGTAAACGGTAAAATAAAATAGACG
CTACCTATTACGTTAAATAAGCGC
Found at i:385838 original size:23 final size:23
Alignment explanation
Indices: 385812--385879 Score: 73
Period size: 23 Copynumber: 2.9 Consensus size: 23
385802 AAAATAGACG
* ***
385812 CTACTTATTATGTTAAATAGGTA
1 CTACCTATTATGTTAAATAACCA
**
385835 CTACCTATTACATTAAATAACCA
1 CTACCTATTATGTTAAATAACCA
385858 CTACCTATTATGTTAAACTAAC
1 CTACCTATTATGTTAAA-TAAC
385880 TACCGATTTG
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
23 32 0.89
24 4 0.11
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
CTACCTATTATGTTAAATAACCA
Found at i:385862 original size:121 final size:121
Alignment explanation
Indices: 385706--385995 Score: 429
Period size: 121 Copynumber: 2.4 Consensus size: 121
385696 CGGTAAAATA
* * *
385706 AAATAAGC-GTACCTATTACTTTAAATAAGCGCTACCTATTACGTTAAACTAGCTACCGATTTGT
1 AAATAAGCACTACCTATTACATTAAATAAGCGCTACCTATTACGTTAAACTAACTACCGATTTGT
* * *
385770 TTAAAGGTTAATAATAATGTAAATGGTTAAATAAAATAGACGCTACTTATTATGTT
66 TTAAAGGTTAATAATAATGTAAATGGTAAAATAAAATAGACGCTACCTATTACGTT
* * * * *
385826 AAATAGGTACTACCTATTACATTAAATAACCACTACCTATTATGTTAAACTAACTACCGATTTGT
1 AAATAAGCACTACCTATTACATTAAATAAGCGCTACCTATTACGTTAAACTAACTACCGATTTGT
385891 TTAAAGGTTAATAATAATGTAAATGGTAAAATAAAATAGACGCTACCTATTACGTT
66 TTAAAGGTTAATAATAATGTAAATGGTAAAATAAAATAGACGCTACCTATTACGTT
* ** * *
385947 AAATAAGCGCTATTTATTACGTTAAATAAGCGCTACCTATTGCGTTAAA
1 AAATAAGCACTACCTATTACATTAAATAAGCGCTACCTATTACGTTAAA
385996 TAAGCGCTAC
Statistics
Matches: 148, Mismatches: 21, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
120 6 0.04
121 142 0.96
ACGTcount: A:0.39, C:0.14, G:0.12, T:0.34
Consensus pattern (121 bp):
AAATAAGCACTACCTATTACATTAAATAAGCGCTACCTATTACGTTAAACTAACTACCGATTTGT
TTAAAGGTTAATAATAATGTAAATGGTAAAATAAAATAGACGCTACCTATTACGTT
Found at i:385950 original size:23 final size:23
Alignment explanation
Indices: 385931--386018 Score: 149
Period size: 23 Copynumber: 3.8 Consensus size: 23
385921 ATAAAATAGA
385931 CGCTACCTATTACGTTAAATAAG
1 CGCTACCTATTACGTTAAATAAG
**
385954 CGCTATTTATTACGTTAAATAAG
1 CGCTACCTATTACGTTAAATAAG
*
385977 CGCTACCTATTGCGTTAAATAAG
1 CGCTACCTATTACGTTAAATAAG
386000 CGCTACCTATTACGTTAAA
1 CGCTACCTATTACGTTAAA
386019 CTAACTACCG
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 59 1.00
ACGTcount: A:0.33, C:0.20, G:0.14, T:0.33
Consensus pattern (23 bp):
CGCTACCTATTACGTTAAATAAG
Found at i:388153 original size:20 final size:20
Alignment explanation
Indices: 388117--388154 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
388107 ATCATATTCC
**
388117 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
388137 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
388155 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:395239 original size:29 final size:29
Alignment explanation
Indices: 395203--395266 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 29
395193 TGAAAGTTAT
395203 AATTTAAGGATAAAATTAAAATAATTAAA
1 AATTTAAGGATAAAATTAAAATAATTAAA
* * * *
395232 AATTTAAGGATTAATTTAAAATAATTCAT
1 AATTTAAGGATAAAATTAAAATAATTAAA
395261 AATTTA
1 AATTTA
395267 GGGAATATGA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.55, C:0.02, G:0.06, T:0.38
Consensus pattern (29 bp):
AATTTAAGGATAAAATTAAAATAATTAAA
Found at i:401964 original size:2 final size:2
Alignment explanation
Indices: 401957--401981 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
401947 TCTGTATCCC
401957 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
401982 GAAAACTTTA
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
Done.