Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008356.1 Hibiscus syriacus cultivar Beakdansim tig00111095_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: 12862612
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 16 of 56
Found at i:3156498 original size:150 final size:149
Alignment explanation
Indices: 3156220--3156496 Score: 348
Period size: 149 Copynumber: 1.9 Consensus size: 149
3156210 CACTCATTCG
* * * ** *
3156220 AAAACACTGAAACTGATAATTATTATGAAATAGGTCAATTTCCAATATAACTTGTGAAATATACC
1 AAAACACTGAAACCGATAATTATAATGAAATAGGTCAATTTACAATATAACCGGTGAAATATAAC
* *
3156285 GGTTAATTAGAAAATAGGTCTACATCACGTATCGACACTTGTGGAATTTGTTTCGATACTTTTGC
66 GGTTAATTAGAAAATAGGTCTACATCACGTATCGACACTTGTGGAAATTGTGTCGATACTTTTGC
3156350 CTAAATAGTATCGATCCCA
131 CTAAATAGTATCGATCCCA
* *
3156369 AAAACA-TCGAAACCGATAATTATAATGTAATAGGT-AACTTTACAATGTAACCGGTAGAAATAT
1 AAAACACT-GAAACCGATAATTATAATGAAATAGGTCAA-TTTACAATATAACCGGT-GAAATAT
* * **
3156432 AATGGTTAATTCGAAAATAGGTCTACAT-A-GTATATCGACACTT-TTTAAATTGTGTCGATACT
63 AACGGTTAATTAGAAAATAGGTCTACATCACG--TATCGACACTTGTGGAAATTGTGTCGATACT
3156494 TTT
126 TTT
3156497 TGTCCAGAAT
Statistics
Matches: 109, Mismatches: 14, Indels: 10
0.82 0.11 0.08
Matches are distributed among these distances:
148 4 0.04
149 62 0.57
150 43 0.39
ACGTcount: A:0.38, C:0.14, G:0.15, T:0.33
Consensus pattern (149 bp):
AAAACACTGAAACCGATAATTATAATGAAATAGGTCAATTTACAATATAACCGGTGAAATATAAC
GGTTAATTAGAAAATAGGTCTACATCACGTATCGACACTTGTGGAAATTGTGTCGATACTTTTGC
CTAAATAGTATCGATCCCA
Found at i:3156626 original size:199 final size:199
Alignment explanation
Indices: 3156351--3157074 Score: 867
Period size: 199 Copynumber: 3.7 Consensus size: 199
3156341 TACTTTTGCC
* **
3156351 TAAATAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAGGT-AACTTTACAAT
1 TAAAAAGTATCGATCCCAAAAACATCGAAACAAATAATTATAATGTAATAGGTCAA-TTTACAAT
*
3156415 GTAACCGGTAGAAATATAATGGTTAATTCGAAAATAGGTCTACATAGTATATCGACACTTTTTAA
65 GTAACCGGTAGAAATATAATGGTTAATTCGAAAATAGGTCTACATAGTGTATCGACACTTTTTAA
* * *
3156480 ATTGTGTCGATACTTTTTGTCCAGAATGAATGACTAACCGGGGTGCACGAATAAAGTGTCGAGAC
130 ATTGTGTCGATACTTTTTGTCCAGAATGAATGACCAACCGGGGTGCACAAATAAAGTGTCGATAC
3156545 ATTTA
195 ATTTA
* * * *
3156550 TAAAAAATATCGATCCCATAAACATTGAATA-AAATAATTATAATGTAATAGGTCAATTTCCAAT
1 TAAAAAGTATCGATCCCAAAAACATCGAA-ACAAATAATTATAATGTAATAGGTCAATTTACAAT
**
3156614 GTAACCGGTAG-AA-AT-A----TAA--CG------GGTCTACATCA-TGTATCGACACTTGTGG
65 GTAACCGGTAGAAATATAATGGTTAATTCGAAAATAGGTCTACAT-AGTGTATCGACACTT-TTT
* ** ** **
3156663 AATTTGTGTCGATACTTTTTGTCCAGAATGAATTCCCAA-AAGGGTGCACTCATAAAGTGTCGAT
128 AAATTGTGTCGATACTTTTTGTCCAGAATGAATGACCAACCGGGGTGCACAAATAAAGTGTCGAT
3156727 ACATTTA
193 ACATTTA
** * *
3156734 TAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATATGTAAATTTACAATG
1 TAAAAAGTATCGATCCCAAAAACATCGAAACAAATAATTATAATGTAATAGGTCAATTTACAATG
* ** * *
3156799 TAACTGGTAGAAATATACCGGTTAATTCGAAAATAGGCCTACATAATGTATCGACACTTTTTAAA
66 TAACCGGTAGAAATATAATGGTTAATTCGAAAATAGGTCTACATAGTGTATCGACACTTTTTAAA
*
3156864 TTGTGTCGATACTTTTTGTTCAGAATGAATGACCAACCGGGGTGCACAAATAAAGTGTCGATACA
131 TTGTGTCGATACTTTTTGTCCAGAATGAATGACCAACCGGGGTGCACAAATAAAGTGTCGATACA
3156929 TTTA
196 TTTA
* * * * *
3156933 TAAAAAGTATTGATCCCATAAACATCGAATA-ATATAATTATAATGTAATAGTTCAATTTCCAAT
1 TAAAAAGTATCGATCCCAAAAACATCGAA-ACAAATAATTATAATGTAATAGGTCAATTTACAAT
** * * ** * *
3156997 GTAACCTTTAGAAATATACTAGTTAATTAAAAAATAGGTCTTCATAGTGTATCAACACTTTTTAA
65 GTAACCGGTAGAAATATAATGGTTAATTCGAAAATAGGTCTACATAGTGTATCGACACTTTTTAA
3157062 AGTTGTGTCGATA
130 A-TTGTGTCGATA
3157075 TATTTTTAAA
Statistics
Matches: 442, Mismatches: 59, Indels: 47
0.81 0.11 0.09
Matches are distributed among these distances:
183 1 0.00
184 112 0.25
185 39 0.09
186 2 0.00
190 2 0.00
191 3 0.01
192 3 0.01
193 2 0.00
196 1 0.00
197 2 0.00
198 39 0.09
199 221 0.50
200 15 0.03
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (199 bp):
TAAAAAGTATCGATCCCAAAAACATCGAAACAAATAATTATAATGTAATAGGTCAATTTACAATG
TAACCGGTAGAAATATAATGGTTAATTCGAAAATAGGTCTACATAGTGTATCGACACTTTTTAAA
TTGTGTCGATACTTTTTGTCCAGAATGAATGACCAACCGGGGTGCACAAATAAAGTGTCGATACA
TTTA
Found at i:3156773 original size:184 final size:185
Alignment explanation
Indices: 3156450--3157014 Score: 679
Period size: 184 Copynumber: 3.0 Consensus size: 185
3156440 ATTCGAAAAT
* *
3156450 AGGTCTACATAGTATATCGACACTTTTTAAATTGTGTCGATACTTTTTGTCCAGAATGAATGACT
1 AGGTCTACATA-TGTATCGACACTTTTTAAATTGTGTCGATACTTTTTGTCCAGAATGAATGACC
* * * *
3156515 AACCGGGGTGCACGAATAAAGTGTCGAGACATTTATAAAAAATATCGATCCCATAAACATTGAAT
65 AACCGGGGTGCACAAATAAAGTGTCGATACATTTATAAAAAGTATCGATCCCATAAACATCGAAT
3156580 AAAATAATTATAATGTAATAGGTCAATTTCCAATGTAACCGGTAGAAATATAA-CG
130 AAAATAATTATAATGTAATAGGTCAATTTCCAATGTAACCGGTAGAAATATAATCG
** * **
3156635 -GGTCTACATCATGTATCGACACTTGTGGAATTTGTGTCGATACTTTTTGTCCAGAATGAATTCC
1 AGGTCTACAT-ATGTATCGACACTT-TTTAAATTGTGTCGATACTTTTTGTCCAGAATGAATGAC
** ** *
3156699 CAA-AAGGGTGCACTCATAAAGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAA
64 CAACCGGGGTGCACAAATAAAGTGTCGATACATTTATAAAAAGTATCGATCCCATAAACATCGAA
** * * * *
3156763 -ACCCATAATTATAATGTAATATGTAAATTTACAATGTAACTGGTAGAAATATACCGGTTAATTC
129 TA-AAATAATTATAATGTAATAGGTCAATTTCCAATGTAACCGGTAG-AA-ATA-----TAA-TC
3156827 G
185 G
* *
3156828 AAAATAGGCCTACATAATGTATCGACACTTTTTAAATTGTGTCGATACTTTTTGTTCAGAATGAA
1 -----AGGTCTACAT-ATGTATCGACACTTTTTAAATTGTGTCGATACTTTTTGTCCAGAATGAA
*
3156893 TGACCAACCGGGGTGCACAAATAAAGTGTCGATACATTTATAAAAAGTATTGATCCCATAAACAT
60 TGACCAACCGGGGTGCACAAATAAAGTGTCGATACATTTATAAAAAGTATCGATCCCATAAACAT
* * **
3156958 CGAATAATATAATTATAATGTAATAGTTCAATTTCCAATGTAACCTTTAGAAATATA
125 CGAATAAAATAATTATAATGTAATAGGTCAATTTCCAATGTAACCGGTAGAAATATA
3157015 CTAGTTAATT
Statistics
Matches: 316, Mismatches: 44, Indels: 33
0.80 0.11 0.08
Matches are distributed among these distances:
183 1 0.00
184 112 0.35
185 39 0.12
186 3 0.01
191 3 0.01
192 2 0.01
193 2 0.01
197 3 0.01
198 38 0.12
199 112 0.35
200 1 0.00
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.31
Consensus pattern (185 bp):
AGGTCTACATATGTATCGACACTTTTTAAATTGTGTCGATACTTTTTGTCCAGAATGAATGACCA
ACCGGGGTGCACAAATAAAGTGTCGATACATTTATAAAAAGTATCGATCCCATAAACATCGAATA
AAATAATTATAATGTAATAGGTCAATTTCCAATGTAACCGGTAGAAATATAATCG
Found at i:3158728 original size:19 final size:19
Alignment explanation
Indices: 3158704--3158751 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
3158694 ATGTAGGGGA
3158704 AATTTTGTATACGATTCAT
1 AATTTTGTATACGATTCAT
*
3158723 AATTTTGTATACGATTTAT
1 AATTTTGTATACGATTCAT
3158742 AATTTTGTAT
1 AATTTTGTAT
3158752 GTGAATGTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.31, C:0.06, G:0.10, T:0.52
Consensus pattern (19 bp):
AATTTTGTATACGATTCAT
Found at i:3161693 original size:191 final size:191
Alignment explanation
Indices: 3161222--3161908 Score: 792
Period size: 191 Copynumber: 3.5 Consensus size: 191
3161212 AACTACATAA
* * *
3161222 ATAAA-TGTCGGTACATTTATAAAAAGTATCGATCCCAAAAACATCTAAACCCATAACTATAATG
1 ATAAAGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATG
* * *
3161286 TAATAGGTAAATTTACAATGTAACCAGTATAAATTTACTGGTTTTATGAGAAAATAGGTCTACAT
66 TAATAGGTAAATTTACAATGTAACCGGTAGAAATTTACCGGTTTTATGAGAAAATAGGTCTACAT
* * *
3161351 AATGTATCGACACTTGTGGAACTTGTGTCGATACTTGTTGTCCAGAATGAATGCCCAAA-AGGTT
131 AATGTATCG--AC-------ACTTGTGTCGATACTTTTTGTCCAGAATGAATG-CCAAACGGGGT
3161415 GCACGA-
186 GCAC-AC
*
3161421 ATAAAGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTGTAATG
1 ATAAAGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATG
* * * * *
3161486 CAATATGTAAATTTACAATGTAACCGGTAGAAATTTACCGATTTTATGAAAAAATAGGTATA-AT
66 TAATAGGTAAATTTACAATGTAACCGGTAGAAATTTACCGGTTTTATGAGAAAATAGGTCTACA-
*
3161550 TAATGTATCGACACTTGTGTCGATACTTTTTGTCCAGAATTAATGCCAAACGGGGTGCACAC
130 TAATGTATCGACACTTGTGTCGATACTTTTTGTCCAGAATGAATGCCAAACGGGGTGCACAC
* * *
3161612 ATAAAGTGTCGATGCATTTATTAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATG
1 ATAAAGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATG
* * * * * **
3161677 TAATAGGTATATTTACAATGTACCCGATCGAAATATACCGGTTTTATGAGAAAATAATTCTACAT
66 TAATAGGTAAATTTACAATGTAACCGGTAGAAATTTACCGGTTTTATGAGAAAATAGGTCTACAT
* * *
3161742 AATGTATCAACACTTTTTAAGTTTGCGTCGATACTTTTT-TCCAGAATGAATGCCCAACGAGGTG
131 AATGTATCGACAC---TT--G--T--GTCGATACTTTTTGTCCAGAATGAATGCCAAACGGGGTG
**
3161806 CATGC
187 CACAC
* ** * *
3161811 ATAAAGTGCCGATACATTTA-AAATTGTATCGATCCCAAAAATATCGAAACCGATAATTATAATG
1 ATAAAGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATG
* * *
3161875 TAATAGGTAAATTTGCAATGTTACCGGTACAAAT
66 TAATAGGTAAATTTACAATGTAACCGGTAGAAAT
3161909 AAACCAATTT
Statistics
Matches: 423, Mismatches: 51, Indels: 29
0.84 0.10 0.06
Matches are distributed among these distances:
190 6 0.01
191 162 0.38
192 1 0.00
194 2 0.00
196 1 0.00
198 70 0.17
199 49 0.12
200 132 0.31
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (191 bp):
ATAAAGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATG
TAATAGGTAAATTTACAATGTAACCGGTAGAAATTTACCGGTTTTATGAGAAAATAGGTCTACAT
AATGTATCGACACTTGTGTCGATACTTTTTGTCCAGAATGAATGCCAAACGGGGTGCACAC
Found at i:3163943 original size:17 final size:17
Alignment explanation
Indices: 3163923--3163955 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
3163913 TAAAACATAT
3163923 TAAATAA-TAAATATAAC
1 TAAATAACTAAA-ATAAC
3163940 TAAATAACTAAAATAA
1 TAAATAACTAAAATAA
3163956 ATAATCAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (17 bp):
TAAATAACTAAAATAAC
Found at i:3164444 original size:22 final size:21
Alignment explanation
Indices: 3164397--3164452 Score: 51
Period size: 21 Copynumber: 2.6 Consensus size: 21
3164387 GAGACGAATT
* *
3164397 AAAATTTTTAAAAAAACGAAA
1 AAAATTATTAAAAAAAAGAAA
* *
3164418 TAAATTATTAATAAAAAATAAA
1 AAAATTATTAA-AAAAAAGAAA
3164440 AAAA-TATATAAAA
1 AAAATTAT-TAAAA
3164453 TATATGATAA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
21 14 0.50
22 14 0.50
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.27
Consensus pattern (21 bp):
AAAATTATTAAAAAAAAGAAA
Found at i:3165073 original size:49 final size:49
Alignment explanation
Indices: 3165001--3165097 Score: 185
Period size: 49 Copynumber: 2.0 Consensus size: 49
3164991 TGCTTGCAGA
3165001 TTGAATAATCACCATATTTACAATTCAATCATCATATTTCTAAATCATT
1 TTGAATAATCACCATATTTACAATTCAATCATCATATTTCTAAATCATT
*
3165050 TTGAATAATCCCCATATTTACAATTCAATCATCATATTTCTAAATCAT
1 TTGAATAATCACCATATTTACAATTCAATCATCATATTTCTAAATCAT
3165098 CATACTTTTG
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.38, C:0.20, G:0.02, T:0.40
Consensus pattern (49 bp):
TTGAATAATCACCATATTTACAATTCAATCATCATATTTCTAAATCATT
Found at i:3167400 original size:20 final size:20
Alignment explanation
Indices: 3167371--3167416 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
3167361 AAGAAAAACT
3167371 GAAA-ATGGGTGAAGAGATA
1 GAAATATGGGTGAAGAGATA
* *
3167390 GAAATATGGGTGGAGAGATG
1 GAAATATGGGTGAAGAGATA
3167410 GAAATAT
1 GAAATAT
3167417 ATTTCTGGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 4 0.17
20 20 0.83
ACGTcount: A:0.43, C:0.00, G:0.37, T:0.20
Consensus pattern (20 bp):
GAAATATGGGTGAAGAGATA
Found at i:3171771 original size:22 final size:22
Alignment explanation
Indices: 3171746--3171804 Score: 75
Period size: 22 Copynumber: 2.6 Consensus size: 22
3171736 TAGTTTTATA
3171746 AAGTTATTATTTTTATTTT-TTC
1 AAGTT-TTATTTTTATTTTATTC
* *
3171768 AAGTTTTCGTTTTTATTTTATTT
1 AAGTTTT-ATTTTTATTTTATTC
3171791 AAGTTTTATTTTTA
1 AAGTTTTATTTTTA
3171805 AACATGTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
21 2 0.06
22 21 0.66
23 9 0.28
ACGTcount: A:0.22, C:0.03, G:0.07, T:0.68
Consensus pattern (22 bp):
AAGTTTTATTTTTATTTTATTC
Found at i:3179133 original size:134 final size:133
Alignment explanation
Indices: 3178894--3179332 Score: 437
Period size: 134 Copynumber: 3.3 Consensus size: 133
3178884 TCGAGAAACG
* * * * * * * *
3178894 TTGACTCATTCCACTGTT-CTTCAAGGAAGATTGAATCAAGGTAAACTTGTTCCACTGTAACTC-
1 TTGATTCATTCCACTGTTACTT-AGGGAAGATTGAATCTAGGCACACTCGTTCCACTATTACTCA
* * * * *
3178957 AGGTAATATCAAATGTTGAACA-AGATGGATTTGTTTCTCTTCTTCTTGAGGGAAAATCAGATAT
65 AGG-AATATCAAATCTTGAA-AGAGATAGATTTATTTCGCTTCTTCTTGAGGGAAAATCAGATCT
3179021 GAGGACT
128 G-GGACT
* * * * * *
3179028 TTGATTCGTTCAATTGTTACTTAGGGAAGATTGAAT-TGAGTCAGACTCGTTCCACTATTACTTA
1 TTGATTCATTCCACTGTTACTTAGGGAAGATTGAATCT-AGGCACACTCGTTCCACTATTACTCA
* *
3179092 TA-GAATATCAAATCTTGAAAGAGATAGATTTATTTCGCTTCTTCTTGAGAGAAAATTAGATCTG
65 -AGGAATATCAAATCTTGAAAGAGATAGATTTATTTCGCTTCTTCTTGAGGGAAAATCAGATCT-
3179156 GGGA-T
128 GGGACT
* ** *
3179161 GTTGATTCATTCCACCGTT-CTTCAATGAAGATTGAATCTAGGCACACTTGTTCCACTATTACTC
1 -TTGATTCATTCCACTGTTACTT-AGGGAAGATTGAATCTAGGCACACTCGTTCCACTATTACTC
* **
3179225 AAGGAATATCAAATCTTGAAAGAGAGAGA--TATGTTCTGCTTCTTAATGAGGGAAAATCAGATC
64 AAGGAATATCAAATCTTGAAAGAGATAGATTTAT-TTC-GCTTCTTCTTGAGGGAAAATCAGATC
*
3179288 TGGAGACA
127 TGG-GACT
*
3179296 TTGATTCATTCCACTGTTACTCAGGGAAGATTGAATC
1 TTGATTCATTCCACTGTTACTTAGGGAAGATTGAATC
3179333 AAGTTTGATT
Statistics
Matches: 250, Mismatches: 40, Indels: 30
0.78 0.12 0.09
Matches are distributed among these distances:
132 3 0.01
133 11 0.04
134 227 0.91
135 8 0.03
136 1 0.00
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (133 bp):
TTGATTCATTCCACTGTTACTTAGGGAAGATTGAATCTAGGCACACTCGTTCCACTATTACTCAA
GGAATATCAAATCTTGAAAGAGATAGATTTATTTCGCTTCTTCTTGAGGGAAAATCAGATCTGGG
ACT
Found at i:3179946 original size:111 final size:110
Alignment explanation
Indices: 3179809--3180029 Score: 397
Period size: 111 Copynumber: 2.0 Consensus size: 110
3179799 TACTAGGTAA
*
3179809 GAAACTTTTCTTACTTTTCAAAAAAAATCAATTTTCATATTTAAATGAGAAACTTTTCTCATTTT
1 GAAACTTTTCTTACTTTTCAAAAAAAATCAATTTTCAGATTTAAATGAGAAACTTTTCTCATTTT
*
3179874 TCGAAAAACATGTAAAAAAGATCCTGCCCGAAGGTCTTATGGACGG
66 TCGAAAAACATGT-AAAAAGATCATGCCCGAAGGTCTTATGGACGG
3179920 GAAACTTTTCTTACTTTTCAAAAAAAATCAATTTTCAGATTTAAATGAGAAACTTTTCTCATTTT
1 GAAACTTTTCTTACTTTTCAAAAAAAATCAATTTTCAGATTTAAATGAGAAACTTTTCTCATTTT
* *
3179985 TCGAGAAACATGTAAAAATATCATGCCCGAAGGTCTTATGGACGG
66 TCGAAAAACATGTAAAAAGATCATGCCCGAAGGTCTTATGGACGG
3180030 CCCGAATGAC
Statistics
Matches: 106, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
110 30 0.28
111 76 0.72
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.34
Consensus pattern (110 bp):
GAAACTTTTCTTACTTTTCAAAAAAAATCAATTTTCAGATTTAAATGAGAAACTTTTCTCATTTT
TCGAAAAACATGTAAAAAGATCATGCCCGAAGGTCTTATGGACGG
Found at i:3180277 original size:20 final size:20
Alignment explanation
Indices: 3180244--3180359 Score: 56
Period size: 20 Copynumber: 5.7 Consensus size: 20
3180234 AAACATCCTG
**
3180244 CCCGAAGGTTTTATAGATGA
1 CCCGAAGGACTTATAGATGA
**
3180264 CCCGAAGGACTTATCATCTTG-
1 CCCGAAGGACTTAT-A-GATGA
* * *
3180285 CTCGAAAGACTTAAAGATGA
1 CCCGAAGGACTTATAGATGA
* *
3180305 CCCGAAGGATTTA-AGAATCA
1 CCCGAAGGACTTATAG-ATGA
* * * *
3180325 TGCTCGAAAGACTTATTGATGG
1 --CCCGAAGGACTTATAGATGA
3180347 CCCGAAGGACTTA
1 CCCGAAGGACTTA
3180360 CTAATTTTGG
Statistics
Matches: 68, Mismatches: 21, Indels: 14
0.66 0.20 0.14
Matches are distributed among these distances:
19 4 0.06
20 37 0.54
21 12 0.18
22 14 0.21
23 1 0.01
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.25
Consensus pattern (20 bp):
CCCGAAGGACTTATAGATGA
Found at i:3180333 original size:234 final size:234
Alignment explanation
Indices: 3179920--3180593 Score: 929
Period size: 234 Copynumber: 2.9 Consensus size: 234
3179910 TTATGGACGG
**
3179920 GAAACTTTTCTTACTTTTCAAAAAAAATCAATTTTCAGATTTAAATGAGAAACTTTTCTCATTTT
1 GAAACTTTTCTTACTTTTCAAAAAATTTCAATTTTCAGATTTAAATGAGAAACTTTTCTCATTTT
* * * * * * * *
3179985 TCGAGAAACATGTAAAAATATCATGCCCGAAGGTCTTATGGACGGCCCGAATGACTTATTATCTT
66 TCGAAAAACATGTGAAAACATCCTGCCCGAAGGTCTTATAGATGGCCCGAAGGACTTATCATCTT
* * *
3180050 TCTCAAAAGACTTATAGATGACTCGAAGGATTTAA-ACATCATGCTCGAAAGACTTACTGATGAC
131 GCTCGAAAGACTTATAGATGACCCGAAGGATTTAAGA-ATCATGCTCGAAAGACTTACTGATGAC
* *
3180114 CTGAAGGACTTACCAATTTTTGAAATAATTTACTAGGTAA
195 CCGAAGGACTTACCAATTTTGGAAATAATTTACTAGGTAA
* * * * *
3180154 GAATCTTTTCTTACTTTTCAAAAAATTTCACTTTTCCGATTTAAATGAGAAACTTTCCTGATTTT
1 GAAACTTTTCTTACTTTTCAAAAAATTTCAATTTTCAGATTTAAATGAGAAACTTTTCTCATTTT
* * * * *
3180219 TTGAAAAATATATGAAAACATCCTGCCCGAAGGTTTTATAGATGACCCGAAGGACTTATCATCTT
66 TCGAAAAACATGTGAAAACATCCTGCCCGAAGGTCTTATAGATGGCCCGAAGGACTTATCATCTT
* * *
3180284 GCTCGAAAGACTTAAAGATGACCCGAAGGATTTAAGAATCATGCTCGAAAGACTTATTGATGGCC
131 GCTCGAAAGACTTATAGATGACCCGAAGGATTTAAGAATCATGCTCGAAAGACTTACTGATGACC
* * *
3180349 CGAAGGACTTACTAATTTTGGAAATAGTTTACTATGTAA
196 CGAAGGACTTACCAATTTTGGAAATAATTTACTAGGTAA
** *
3180388 GAAAAATTTCTTACTTTTC-AAAAATTTTAATTTTCAGATTTAAATGAGAAACTTTTCTCATTTT
1 GAAACTTTTCTTACTTTTCAAAAAATTTCAATTTTCAGATTTAAATGAGAAACTTTTCTCATTTT
* * * * * *
3180452 TCGAAAAACATGTGAAAACATCCTACCTGAAGGTCTTATAGATGGCTCAAAGAACTTATCATCCT
66 TCGAAAAACATGTGAAAACATCCTGCCCGAAGGTCTTATAGATGGCCCGAAGGACTTATCATCTT
* * *
3180517 GCTCGAAAGACTTATAGATGACCCGAAGGATTTAAGCATCATGCTTGAAATACTTACTGATGACC
131 GCTCGAAAGACTTATAGATGACCCGAAGGATTTAAGAATCATGCTCGAAAGACTTACTGATGACC
*
3180582 CGAATGACTTAC
196 CGAAGGACTTAC
3180594 TAAGTAATAA
Statistics
Matches: 382, Mismatches: 57, Indels: 3
0.86 0.13 0.01
Matches are distributed among these distances:
233 164 0.43
234 217 0.57
235 1 0.00
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (234 bp):
GAAACTTTTCTTACTTTTCAAAAAATTTCAATTTTCAGATTTAAATGAGAAACTTTTCTCATTTT
TCGAAAAACATGTGAAAACATCCTGCCCGAAGGTCTTATAGATGGCCCGAAGGACTTATCATCTT
GCTCGAAAGACTTATAGATGACCCGAAGGATTTAAGAATCATGCTCGAAAGACTTACTGATGACC
CGAAGGACTTACCAATTTTGGAAATAATTTACTAGGTAA
Found at i:3180339 original size:42 final size:41
Alignment explanation
Indices: 3180258--3180359 Score: 132
Period size: 42 Copynumber: 2.5 Consensus size: 41
3180248 AAGGTTTTAT
** *
3180258 AGATGACCCGAAGGACTTATCATCTTGCTCGAAAGACTTAA
1 AGATGACCCGAAGGACTTAGAATCATGCTCGAAAGACTTAA
* *
3180299 AGATGACCCGAAGGATTTAAGAATCATGCTCGAAAGACTTAT
1 AGATGACCCGAAGGACTT-AGAATCATGCTCGAAAGACTTAA
* *
3180341 TGATGGCCCGAAGGACTTA
1 AGATGACCCGAAGGACTTA
3180360 CTAATTTTGG
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
41 18 0.35
42 34 0.65
ACGTcount: A:0.34, C:0.20, G:0.23, T:0.24
Consensus pattern (41 bp):
AGATGACCCGAAGGACTTAGAATCATGCTCGAAAGACTTAA
Found at i:3190103 original size:2 final size:2
Alignment explanation
Indices: 3190096--3190178 Score: 166
Period size: 2 Copynumber: 41.5 Consensus size: 2
3190086 ACATAAAATG
3190096 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3190138 AT AT AT AT AT AT 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 AT AT AT AT AT AT A
3190179 ACCATTGGAC
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 81 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3191082 original size:12 final size:12
Alignment explanation
Indices: 3191065--3191128 Score: 51
Period size: 12 Copynumber: 5.3 Consensus size: 12
3191055 AAGGCGAGAA
3191065 CTTTCTTATTTT
1 CTTTCTTATTTT
*
3191077 CTTTCTTTTTTT
1 CTTTCTTATTTT
*
3191089 CTCTCATT-TTTT
1 CTTTC-TTATTTT
* *
3191101 -TTCCTGATTTTT
1 CTTTCTTA-TTTT
*
3191113 CTTTCTTTTTTT
1 CTTTCTTATTTT
3191125 CTTT
1 CTTT
3191129 TGGTGTTCGA
Statistics
Matches: 40, Mismatches: 8, Indels: 8
0.71 0.14 0.14
Matches are distributed among these distances:
10 1 0.03
11 2 0.05
12 31 0.77
13 6 0.15
ACGTcount: A:0.05, C:0.19, G:0.02, T:0.75
Consensus pattern (12 bp):
CTTTCTTATTTT
Found at i:3194379 original size:21 final size:21
Alignment explanation
Indices: 3194340--3194379 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3194330 GATCACTGTT
*
3194340 ATAATTTACCCTTTGTTTTAA
1 ATAATTTACCCTTTATTTTAA
3194361 ATAATTTA-CCTTTAATTTT
1 ATAATTTACCCTTT-ATTTT
3194380 TTAATTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.30, C:0.12, G:0.03, T:0.55
Consensus pattern (21 bp):
ATAATTTACCCTTTATTTTAA
Found at i:3196158 original size:23 final size:23
Alignment explanation
Indices: 3196114--3196158 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
3196104 TGTTAGGAAA
* *
3196114 AAATAATAAAATGAAATAAAAAT
1 AAATAATAAAAGGAAAGAAAAAT
* *
3196137 AAATAATAAAGGGAAAGGAAAA
1 AAATAATAAAAGGAAAGAAAAA
3196159 GGAAAAGGAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.71, C:0.00, G:0.13, T:0.16
Consensus pattern (23 bp):
AAATAATAAAAGGAAAGAAAAAT
Found at i:3196288 original size:7 final size:7
Alignment explanation
Indices: 3196276--3196331 Score: 51
Period size: 7 Copynumber: 7.6 Consensus size: 7
3196266 GAAAATCAAT
3196276 AAATAAA
1 AAATAAA
3196283 AAATAAA
1 AAATAAA
3196290 AAGATAAA
1 AA-ATAAA
*
3196298 AGATAAA
1 AAATAAA
*
3196305 ATAAGAAA
1 A-AATAAA
3196313 AAACTAAA
1 AAA-TAAA
3196321 AAGA-AAA
1 AA-ATAAA
3196328 AAAT
1 AAAT
3196332 GTTAGATTCT
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
6 1 0.03
7 22 0.55
8 16 0.40
9 1 0.03
ACGTcount: A:0.79, C:0.02, G:0.07, T:0.12
Consensus pattern (7 bp):
AAATAAA
Found at i:3196296 original size:15 final size:14
Alignment explanation
Indices: 3196280--3196331 Score: 59
Period size: 14 Copynumber: 3.5 Consensus size: 14
3196270 ATCAATAAAT
3196280 AAAAAATAAAAAGA
1 AAAAAATAAAAAGA
*
3196294 TAAAAGATAAAATAAGA
1 -AAAAAAT-AAA-AAGA
*
3196311 AAAAACTAAAAAGA
1 AAAAAATAAAAAGA
3196325 AAAAAAT
1 AAAAAAT
3196332 GTTAGATTCT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
14 10 0.32
15 9 0.29
16 8 0.26
17 4 0.13
ACGTcount: A:0.79, C:0.02, G:0.08, T:0.12
Consensus pattern (14 bp):
AAAAAATAAAAAGA
Found at i:3196375 original size:9 final size:9
Alignment explanation
Indices: 3196371--3196413 Score: 59
Period size: 9 Copynumber: 4.8 Consensus size: 9
3196361 AAAATAAGTA
3196371 AAATAAAAT
1 AAATAAAAT
*
3196380 AAGTAAAAT
1 AAATAAAAT
3196389 AAATAAAAT
1 AAATAAAAT
**
3196398 AACCAAAAT
1 AAATAAAAT
3196407 AAATAAA
1 AAATAAA
3196414 CAAAAGTGTG
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.74, C:0.05, G:0.02, T:0.19
Consensus pattern (9 bp):
AAATAAAAT
Found at i:3196380 original size:14 final size:14
Alignment explanation
Indices: 3196361--3196391 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
3196351 TAAATTTCGA
3196361 AAAATAAGTAAAAT
1 AAAATAAGTAAAAT
3196375 AAAATAAGTAAAAT
1 AAAATAAGTAAAAT
3196389 AAA
1 AAA
3196392 TAAAATAACC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.19
Consensus pattern (14 bp):
AAAATAAGTAAAAT
Found at i:3196394 original size:18 final size:18
Alignment explanation
Indices: 3196371--3196413 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
3196361 AAAATAAGTA
**
3196371 AAATAAAATAAGTAAAAT
1 AAATAAAATAACCAAAAT
3196389 AAATAAAATAACCAAAAT
1 AAATAAAATAACCAAAAT
3196407 AAATAAA
1 AAATAAA
3196414 CAAAAGTGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.74, C:0.05, G:0.02, T:0.19
Consensus pattern (18 bp):
AAATAAAATAACCAAAAT
Found at i:3197464 original size:12 final size:12
Alignment explanation
Indices: 3197449--3197474 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3197439 TATATATAAG
3197449 TAATAAAAAAAA
1 TAATAAAAAAAA
3197461 TAATAAAAAAAA
1 TAATAAAAAAAA
3197473 TA
1 TA
3197475 TTTTTTAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (12 bp):
TAATAAAAAAAA
Found at i:3197605 original size:34 final size:31
Alignment explanation
Indices: 3197531--3197632 Score: 109
Period size: 31 Copynumber: 3.2 Consensus size: 31
3197521 AAAAATATTA
* *
3197531 TATATAAATTTTC-AAAAATATTTTTTTAAAG
1 TATAT-AATTTTCAAAAAATGTTTTTTTAAAC
3197562 TATATAATTTTCAAAAAATGTTTTTTCTGAAAAC
1 TATATAATTTTCAAAAAATGTTTTTT-T--AAAC
* *
3197596 TATATAATTTT-ACAAAATGTTTTTTTTAAAT
1 TATATAATTTTCAAAAAATG-TTTTTTTAAAC
3197627 TATATA
1 TATATA
3197633 TTATATTAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
30 7 0.11
31 26 0.42
32 1 0.02
33 8 0.13
34 20 0.32
ACGTcount: A:0.42, C:0.05, G:0.04, T:0.49
Consensus pattern (31 bp):
TATATAATTTTCAAAAAATGTTTTTTTAAAC
Found at i:3197633 original size:33 final size:31
Alignment explanation
Indices: 3197530--3197632 Score: 102
Period size: 33 Copynumber: 3.2 Consensus size: 31
3197520 AAAAAATATT
*
3197530 ATATATAAATTTT-CAAAAAT-ATTTTTTTAAA
1 ATATAT-AATTTTAC-AAAATGTTTTTTTTAAA
* * *
3197561 GTATATAATTTTCAAAAAATGTTTTTTCTGAAA
1 ATATATAATTTT-ACAAAATGTTTTTT-TTAAA
3197594 ACTATATAATTTTACAAAATGTTTTTTTTAAA
1 A-TATATAATTTTACAAAATGTTTTTTTTAAA
*
3197626 TTATATA
1 ATATATA
3197633 TTATATTAAA
Statistics
Matches: 59, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
30 6 0.10
31 16 0.27
32 9 0.15
33 17 0.29
34 11 0.19
ACGTcount: A:0.43, C:0.05, G:0.04, T:0.49
Consensus pattern (31 bp):
ATATATAATTTTACAAAATGTTTTTTTTAAA
Found at i:3197695 original size:37 final size:36
Alignment explanation
Indices: 3197627--3197788 Score: 211
Period size: 37 Copynumber: 4.4 Consensus size: 36
3197617 TTTTTTAAAT
*
3197627 TATATATTATATTAAATTTTCAAAATGATTTTAAAAAC
1 TATATATTATA-TATATTTTCAAAAT-ATTTTAAAAAC
3197665 TATATATTATATATATTTTCTAAAATATTTTAAAAAC
1 TATATATTATATATATTTTC-AAAATATTTTAAAAAC
* *
3197702 TATATATTATATAGT-TTTT-AAAAGTGTTTTAAAATC
1 TATATATTATATA-TATTTTCAAAA-TATTTTAAAAAC
* *
3197738 TATATATTATATAGATTTTCAAAATATTTTTAGAAAC
1 TATATATTATATATATTTTCAAAATA-TTTTAAAAAC
3197775 TATATATTATATAT
1 TATATATTATATAT
3197789 GTATCTTTAA
Statistics
Matches: 110, Mismatches: 8, Indels: 13
0.84 0.06 0.10
Matches are distributed among these distances:
35 4 0.04
36 28 0.25
37 61 0.55
38 17 0.15
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.48
Consensus pattern (36 bp):
TATATATTATATATATTTTCAAAATATTTTAAAAAC
Found at i:3197706 original size:73 final size:74
Alignment explanation
Indices: 3197596--3197787 Score: 207
Period size: 73 Copynumber: 2.6 Consensus size: 74
3197586 TTCTGAAAAC
* ** *
3197596 TATATA-ATTTTACAAAATGTTTTTTTTAAATTATA-TATTATATTAAATTTTCAAAA-TGATTT
1 TATATAGATTTT-CAAAAT-ATTTTTAAAAACTATATTATTATA-T-AATTTTCAAAAGTG-TTT
3197658 TAAAAACTATATAT
61 TAAAAACTATATAT
* * *
3197672 TATATATATTTTCTAAAATA-TTTTAAAAACTATA-TATTATATAGTTTTTAAAAGTGTTTTAAA
1 TATATAGATTTTC-AAAATATTTTTAAAAACTATATTATTATATAATTTTCAAAAGTGTTTTAAA
*
3197735 ATCTATATAT
65 AACTATATAT
*
3197745 TATATAGATTTTCAAAATATTTTTAGAAACTATA-TATTATATA
1 TATATAGATTTTCAAAATATTTTTAAAAACTATATTATTATATA
3197788 TGTATCTTTA
Statistics
Matches: 103, Mismatches: 9, Indels: 11
0.84 0.07 0.09
Matches are distributed among these distances:
72 6 0.06
73 59 0.57
74 3 0.03
75 18 0.17
76 7 0.07
77 10 0.10
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.49
Consensus pattern (74 bp):
TATATAGATTTTCAAAATATTTTTAAAAACTATATTATTATATAATTTTCAAAAGTGTTTTAAAA
ACTATATAT
Found at i:3200067 original size:16 final size:17
Alignment explanation
Indices: 3200021--3200056 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
3200011 AGTCACATAA
*
3200021 ATTATAATA-AAAAAAT
1 ATTATAATATTAAAAAT
3200037 ATTATAATATTAAAAAT
1 ATTATAATATTAAAAAT
3200054 ATT
1 ATT
3200057 TACAATTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
ATTATAATATTAAAAAT
Found at i:3200853 original size:22 final size:22
Alignment explanation
Indices: 3200828--3200883 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 22
3200818 TTAAAACTAT
*
3200828 AAAAAAAAGTTG-TT-AAATTA
1 AAAAAAAAATTGTTTCAAATTA
*
3200848 TCAAAAATAAATTGTTTCAAATTA
1 --AAAAAAAAATTGTTTCAAATTA
3200872 AAAAAAAAATTG
1 AAAAAAAAATTG
3200884 AAACTTTAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
22 21 0.72
23 2 0.07
24 6 0.21
ACGTcount: A:0.59, C:0.04, G:0.07, T:0.30
Consensus pattern (22 bp):
AAAAAAAAATTGTTTCAAATTA
Found at i:3202211 original size:60 final size:61
Alignment explanation
Indices: 3202091--3202216 Score: 146
Period size: 60 Copynumber: 2.1 Consensus size: 61
3202081 ATTTTGTGAT
* * *
3202091 CATTTTATAACTTCTAAGAGTTGAGGGACTCAAAAAAAATAATGCCTTATAGTTGTGGGAC
1 CATTTTATAAATTCTAAGAGTTGAGGGACTCAAAAAAAATAATGCCTTATAGTCGAGGGAC
* * * * * * **
3202152 CATTTTATAAATTTTAATAGTTGATGGATTC-AACAAAATAGTGTTTTATAGTCGAGGGAC
1 CATTTTATAAATTCTAAGAGTTGAGGGACTCAAAAAAAATAATGCCTTATAGTCGAGGGAC
3202212 CATTT
1 CATTT
3202217 GTATTGTAAC
Statistics
Matches: 54, Mismatches: 11, Indels: 1
0.82 0.17 0.02
Matches are distributed among these distances:
60 28 0.52
61 26 0.48
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.36
Consensus pattern (61 bp):
CATTTTATAAATTCTAAGAGTTGAGGGACTCAAAAAAAATAATGCCTTATAGTCGAGGGAC
Found at i:3204111 original size:16 final size:16
Alignment explanation
Indices: 3204090--3204124 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
3204080 ATACTGCCAA
3204090 AAAGGATGAAAATAAC
1 AAAGGATGAAAATAAC
3204106 AAAGGATGAAAATAAC
1 AAAGGATGAAAATAAC
3204122 AAA
1 AAA
3204125 TAATGAAGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.66, C:0.06, G:0.17, T:0.11
Consensus pattern (16 bp):
AAAGGATGAAAATAAC
Found at i:3204130 original size:16 final size:16
Alignment explanation
Indices: 3204090--3204131 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
3204080 ATACTGCCAA
*
3204090 AAAGGATGAAAATAAC
1 AAAGAATGAAAATAAC
*
3204106 AAAGGATGAAAATAAC
1 AAAGAATGAAAATAAC
*
3204122 AAATAATGAA
1 AAAGAATGAA
3204132 GTCAGGCTAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.64, C:0.05, G:0.17, T:0.14
Consensus pattern (16 bp):
AAAGAATGAAAATAAC
Found at i:3213990 original size:14 final size:14
Alignment explanation
Indices: 3213971--3213997 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3213961 TACATTTTCA
3213971 TTCTTCATTCTTTG
1 TTCTTCATTCTTTG
3213985 TTCTTCATTCTTT
1 TTCTTCATTCTTT
3213998 ACATTCATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.22, G:0.04, T:0.67
Consensus pattern (14 bp):
TTCTTCATTCTTTG
Found at i:3217551 original size:8 final size:8
Alignment explanation
Indices: 3217538--3217647 Score: 115
Period size: 8 Copynumber: 14.0 Consensus size: 8
3217528 AAAGAGAATG
3217538 AATGAAAA
1 AATGAAAA
3217546 AATGAAAA
1 AATGAAAA
*
3217554 AGTG--AA
1 AATGAAAA
3217560 AATGAAAA
1 AATGAAAA
3217568 AATGAAAAA
1 AATG-AAAA
3217577 AATGAAAA
1 AATGAAAA
3217585 AATGAAAA
1 AATGAAAA
3217593 AATGAAAA
1 AATGAAAA
3217601 AA--AAGAA
1 AATGAA-AA
3217608 AA--AAAA
1 AATGAAAA
*
3217614 AAGGAAAAA
1 AATG-AAAA
*
3217623 AAGGAAAA
1 AATGAAAA
3217631 AATGAAAAA
1 AATG-AAAA
3217640 AATGAAAA
1 AATGAAAA
3217648 GAAAAAAGAA
Statistics
Matches: 91, Mismatches: 3, Indels: 16
0.83 0.03 0.15
Matches are distributed among these distances:
6 11 0.12
7 6 0.07
8 50 0.55
9 24 0.26
ACGTcount: A:0.76, C:0.00, G:0.15, T:0.09
Consensus pattern (8 bp):
AATGAAAA
Found at i:3217563 original size:14 final size:14
Alignment explanation
Indices: 3217544--3217659 Score: 68
Period size: 17 Copynumber: 8.3 Consensus size: 14
3217534 AATGAATGAA
*
3217544 AAAATGAAAAAGTG
1 AAAATGAAAAAATG
3217558 AAAATGAAAAAATG
1 AAAATGAAAAAATG
3217572 AAAAAAATGAAAAAATG
1 ---AAAATGAAAAAATG
*
3217589 AAAAAATGAAAAAAAAG
1 --AAAATG-AAAAAATG
*
3217606 AAAA--AAAAAAGG
1 AAAATGAAAAAATG
*
3217618 AAAA--AAAGGAA--
1 AAAATGAAA-AAATG
3217629 AAAATGAAAAAAATG
1 AAAATG-AAAAAATG
3217644 AAAA-GAAAAAA-G
1 AAAATGAAAAAATG
3217656 AAAA
1 AAAA
3217660 AGGAGGGTTC
Statistics
Matches: 87, Mismatches: 5, Indels: 22
0.76 0.04 0.19
Matches are distributed among these distances:
11 4 0.05
12 19 0.22
13 10 0.11
14 17 0.20
15 8 0.09
16 8 0.09
17 21 0.24
ACGTcount: A:0.78, C:0.00, G:0.15, T:0.08
Consensus pattern (14 bp):
AAAATGAAAAAATG
Found at i:3217578 original size:9 final size:9
Alignment explanation
Indices: 3217558--3217647 Score: 98
Period size: 9 Copynumber: 10.1 Consensus size: 9
3217548 TGAAAAAGTG
3217558 AAAATG-AA
1 AAAATGAAA
3217566 AAAATGAAA
1 AAAATGAAA
3217575 AAAATG-AA
1 AAAATGAAA
3217583 AAAATG-AA
1 AAAATGAAA
3217591 AAAATGAAA
1 AAAATGAAA
*
3217600 AAAAAGAAAAAA
1 AAAATG---AAA
*
3217612 AAAAGGAAA
1 AAAATGAAA
*
3217621 AAAA-GGAA
1 AAAATGAAA
3217629 AAAATGAAA
1 AAAATGAAA
3217638 AAAATGAAA
1 AAAATGAAA
3217647 A
1 A
3217648 GAAAAAAGAA
Statistics
Matches: 72, Mismatches: 4, Indels: 11
0.83 0.05 0.13
Matches are distributed among these distances:
8 29 0.40
9 35 0.49
12 8 0.11
ACGTcount: A:0.79, C:0.00, G:0.13, T:0.08
Consensus pattern (9 bp):
AAAATGAAA
Found at i:3217592 original size:47 final size:45
Alignment explanation
Indices: 3217524--3217663 Score: 156
Period size: 46 Copynumber: 3.0 Consensus size: 45
3217514 CTATGCTTGA
** ** *
3217524 AAAAAAAGAGAATGAATGAAAAAATGAAAAAGTGAAAATGAAAAAATG
1 AAAAAAAG-GAAAAAATGAAAAAATGAAAAAAAGAAAA--AAAAAAGG
*
3217572 AAAAAAATGAAAAAATGAAAAAATGAAAAAAAAGAAAAAAAAAAGG
1 AAAAAAAGGAAAAAATGAAAAAATG-AAAAAAAGAAAAAAAAAAGG
* *
3217618 AAAAAAAGGAAAAAATGAAAAAAATGAAAAGAA-AAAAGAAAAAGG
1 AAAAAAAGGAAAAAATG-AAAAAATGAAAAAAAGAAAAAAAAAAGG
3217663 A
1 A
3217664 GGGTTCGAGA
Statistics
Matches: 81, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
45 12 0.15
46 29 0.36
47 23 0.28
48 17 0.21
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (45 bp):
AAAAAAAGGAAAAAATGAAAAAATGAAAAAAAGAAAAAAAAAAGG
Found at i:3217660 original size:8 final size:8
Alignment explanation
Indices: 3217558--3217661 Score: 70
Period size: 8 Copynumber: 12.8 Consensus size: 8
3217548 TGAAAAAGTG
*
3217558 AAAATGAA
1 AAAAAGAA
*
3217566 AAAATGAA
1 AAAAAGAA
3217574 AAAAATGAA
1 AAAAA-GAA
*
3217583 AAAATGAA
1 AAAAAGAA
*
3217591 AAAATG-A
1 AAAAAGAA
3217598 AAAAA-AA
1 AAAAAGAA
*
3217605 GAAAA-AA
1 AAAAAGAA
*
3217612 AAAAGGAA
1 AAAAAGAA
3217620 AAAAAGGAA
1 AAAAA-GAA
*
3217629 AAAATGAA
1 AAAAAGAA
3217637 AAAAATGAA
1 AAAAA-GAA
*
3217646 AAGAAAAAA
1 AA-AAAGAA
3217655 GAAAAAG
1 -AAAAAG
3217662 GAGGGTTCGA
Statistics
Matches: 78, Mismatches: 11, Indels: 13
0.76 0.11 0.13
Matches are distributed among these distances:
7 15 0.19
8 34 0.44
9 24 0.31
10 5 0.06
ACGTcount: A:0.79, C:0.00, G:0.14, T:0.07
Consensus pattern (8 bp):
AAAAAGAA
Found at i:3218752 original size:105 final size:105
Alignment explanation
Indices: 3218570--3219403 Score: 1425
Period size: 105 Copynumber: 7.9 Consensus size: 105
3218560 TCAACAACAA
* *
3218570 TCAAATCCACCACAGAAGGAGGTGACCCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
1 TCAAATCCACCGCAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
3218635 CCTAAAGGAGAAGGTTCGTAATGAGAAGAGCATGTTCCTT
66 CCTAAAGGAGAAGGTTCGTAATGAGAAGAGCATGTTCCTT
*
3218675 TCAAATCCACCGCAGAAGTAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
1 TCAAATCCACCGCAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
*
3218740 CCTAAAGGAGAAGGTTCGTAATGAGAAGAGCCTGTTCCTT
66 CCTAAAGGAGAAGGTTCGTAATGAGAAGAGCATGTTCCTT
*
3218780 TCAAATCCACCGCAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATTAGAAGAACTCGT
1 TCAAATCCACCGCAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
*
3218845 CCTAAAGGAGAAGGTTCGTAATGAGAAGAGCCTGTTCCTT
66 CCTAAAGGAGAAGGTTCGTAATGAGAAGAGCATGTTCCTT
* *
3218885 TCAAATCTACCGCAGAAGGAGGTGAACCAATATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
1 TCAAATCCACCGCAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
3218950 CCTAAAGGAGAAGGTTCGTAATGAGAAGAGCATGTTCCTT
66 CCTAAAGGAGAAGGTTCGTAATGAGAAGAGCATGTTCCTT
*
3218990 TCAAATCCACCGAAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
1 TCAAATCCACCGCAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
3219055 CCTAAAGGAGAAGGTTCGTAATGAGAAGAGCATGTTCCTT
66 CCTAAAGGAGAAGGTTCGTAATGAGAAGAGCATGTTCCTT
*
3219095 TCAAATCCACCGCAGAAGGAGGTGAACCAATATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
1 TCAAATCCACCGCAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
* *
3219160 CTTAAAGGAGAAGGTTCGTAATGAGAAGAGTATGTTCCTT
66 CCTAAAGGAGAAGGTTCGTAATGAGAAGAGCATGTTCCTT
*
3219200 TCAAATCCACCACAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
1 TCAAATCCACCGCAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
* *
3219265 CTTAAAGGAGAAGGTTCGTAATGAGAAGAGCTTGTTCCTT
66 CCTAAAGGAGAAGGTTCGTAATGAGAAGAGCATGTTCCTT
* * * * *
3219305 TCAAATTCACCCCAGAAGGAGGTGAATCGACATTTCCAGAAGAGTTCATAATGAGAAGAACTCAT
1 TCAAATCCACCGCAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
* *
3219370 CCGATAAAAGAAGAAGAAGTTCATAATGAGAAGA
66 CC--T-AAAGGAGAAG--GTTCGTAATGAGAAGA
3219404 ACTTGTTCAA
Statistics
Matches: 695, Mismatches: 29, Indels: 5
0.95 0.04 0.01
Matches are distributed among these distances:
105 670 0.96
107 1 0.00
108 9 0.01
110 15 0.02
ACGTcount: A:0.37, C:0.18, G:0.23, T:0.22
Consensus pattern (105 bp):
TCAAATCCACCGCAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
CCTAAAGGAGAAGGTTCGTAATGAGAAGAGCATGTTCCTT
Found at i:3219411 original size:20 final size:20
Alignment explanation
Indices: 3219347--3219412 Score: 55
Period size: 20 Copynumber: 3.3 Consensus size: 20
3219337 TTTCCAGAAG
3219347 AGTTCATAATGAGAAGAACT
1 AGTTCATAATGAGAAGAACT
* * **
3219367 CA-TCCGATAA-AAGAAGAAGA
1 -AGTTC-ATAATGAGAAGAACT
3219387 AGTTCATAATGAGAAGAACT
1 AGTTCATAATGAGAAGAACT
*
3219407 TGTTCA
1 AGTTCA
3219413 ACCTTAGCTC
Statistics
Matches: 33, Mismatches: 9, Indels: 7
0.67 0.18 0.14
Matches are distributed among these distances:
19 5 0.15
20 23 0.70
21 5 0.15
ACGTcount: A:0.45, C:0.12, G:0.20, T:0.23
Consensus pattern (20 bp):
AGTTCATAATGAGAAGAACT
Found at i:3222413 original size:44 final size:44
Alignment explanation
Indices: 3222363--3222450 Score: 167
Period size: 44 Copynumber: 2.0 Consensus size: 44
3222353 ATATAATATA
*
3222363 AAGTAAAAAAACTAAACCTAATTTCTTTTGCTTTTTACTTTTCC
1 AAGTAAAAAAACTAAACCTAATTTCATTTGCTTTTTACTTTTCC
3222407 AAGTAAAAAAACTAAACCTAATTTCATTTGCTTTTTACTTTTCC
1 AAGTAAAAAAACTAAACCTAATTTCATTTGCTTTTTACTTTTCC
3222451 TTAAAAGTAT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.35, C:0.18, G:0.05, T:0.42
Consensus pattern (44 bp):
AAGTAAAAAAACTAAACCTAATTTCATTTGCTTTTTACTTTTCC
Found at i:3223452 original size:3 final size:3
Alignment explanation
Indices: 3223444--3223480 Score: 56
Period size: 3 Copynumber: 11.7 Consensus size: 3
3223434 TAATTTGTAT
3223444 TAA TAA TAA TAA TAA TAA TAA TAA TATA TAA TTAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA -TAA TA
3223481 TTTATAATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
3 26 0.81
4 6 0.19
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:3223578 original size:22 final size:22
Alignment explanation
Indices: 3223547--3223628 Score: 94
Period size: 22 Copynumber: 3.7 Consensus size: 22
3223537 CAATTCATGG
* * *
3223547 AAGTGTCTTAGCATTGGTACTA
1 AAGTGCCTTAGCACTGATACTA
*
3223569 AAGTGCCTTAGCACTGATACGA
1 AAGTGCCTTAGCACTGATACTA
* *
3223591 AAGTACATTTA-CACTGATACTA
1 AAGTGC-CTTAGCACTGATACTA
3223613 AAGTGCCTTAGCACTG
1 AAGTGCCTTAGCACTG
3223629 CTGGTATATA
Statistics
Matches: 49, Mismatches: 9, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
21 3 0.06
22 43 0.88
23 3 0.06
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.29
Consensus pattern (22 bp):
AAGTGCCTTAGCACTGATACTA
Found at i:3226856 original size:83 final size:83
Alignment explanation
Indices: 3226758--3226925 Score: 300
Period size: 83 Copynumber: 2.0 Consensus size: 83
3226748 CTGATTATTC
*
3226758 ATTTTTTTCTAGGATATCTGATTTGAACTATTCAAAAATTAAGAAATAAATTAGATATTTAAATT
1 ATTTTTTTCTAGGATATCTAATTTGAACTATTCAAAAATTAAGAAATAAATTAGATATTTAAATT
*
3226823 TTCAGATACAATTAACGG
66 TTCAGATACAATGAACGG
*
3226841 ATTTTTTTCTCGGATATCTAATTTGAACTATTCAAAAATTAAGAAATAAATTAGATATTTAAATT
1 ATTTTTTTCTAGGATATCTAATTTGAACTATTCAAAAATTAAGAAATAAATTAGATATTTAAATT
*
3226906 TTCAGATGCAATGAACGG
66 TTCAGATACAATGAACGG
3226924 AT
1 AT
3226926 GTGATGAATG
Statistics
Matches: 81, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
83 81 1.00
ACGTcount: A:0.40, C:0.09, G:0.11, T:0.39
Consensus pattern (83 bp):
ATTTTTTTCTAGGATATCTAATTTGAACTATTCAAAAATTAAGAAATAAATTAGATATTTAAATT
TTCAGATACAATGAACGG
Found at i:3226947 original size:83 final size:83
Alignment explanation
Indices: 3226778--3226947 Score: 227
Period size: 83 Copynumber: 2.0 Consensus size: 83
3226768 AGGATATCTG
*
3226778 ATTTGAACTATTCAAAAATTAAGAAATAAATTAGATATTTAAATTTTCAGATACAATTAACGGAT
1 ATTTGAACTATTCAAAAATTAAGAAATAAATTAGATATTTAAATTTTCAGATACAATGAACGGAT
** *** **
3226843 TTTTTTCTCGGATATCTA
66 TGATGAATCGGATATAGA
*
3226861 ATTTGAACTATTCAAAAATTAAGAAATAAATTAGATATTTAAATTTTCAGATGCAATGAACGGAT
1 ATTTGAACTATTCAAAAATTAAGAAATAAATTAGATATTTAAATTTTCAGATACAATGAACGGAT
3226926 GTGATGAAT-GGA-ATAAGA
66 -TGATGAATCGGATAT-AGA
3226944 ATTT
1 ATTT
3226948 TTTCCACAGC
Statistics
Matches: 76, Mismatches: 9, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
82 2 0.03
83 71 0.93
84 3 0.04
ACGTcount: A:0.43, C:0.08, G:0.13, T:0.36
Consensus pattern (83 bp):
ATTTGAACTATTCAAAAATTAAGAAATAAATTAGATATTTAAATTTTCAGATACAATGAACGGAT
TGATGAATCGGATATAGA
Found at i:3227508 original size:2 final size:2
Alignment explanation
Indices: 3227501--3227544 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
3227491 AGAAACATCA
*
3227501 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3227543 AT
1 AT
3227545 GTATGTATGT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3233827 original size:19 final size:19
Alignment explanation
Indices: 3233803--3233840 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
3233793 AGATTATGCA
3233803 GGGGGTA-CAGATTCCCCCT
1 GGGGGTATC-GATTCCCCCT
3233822 GGGGGTATCGATTCCCCCT
1 GGGGGTATCGATTCCCCCT
3233841 AAAGAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 17 0.94
20 1 0.06
ACGTcount: A:0.13, C:0.32, G:0.32, T:0.24
Consensus pattern (19 bp):
GGGGGTATCGATTCCCCCT
Found at i:3234713 original size:31 final size:32
Alignment explanation
Indices: 3234654--3234714 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
3234644 ACTTATGTTC
*
3234654 TTCGGGATATATGGACAATATTACCTATGTCT
1 TTCGGGACATATGGACAATATTACCTATGTCT
* *
3234686 TTCGGGACATATGGATAGTA-TACCTATGT
1 TTCGGGACATATGGACAATATTACCTATGT
3234715 TCTAAGAAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 9 0.35
32 17 0.65
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.36
Consensus pattern (32 bp):
TTCGGGACATATGGACAATATTACCTATGTCT
Found at i:3234761 original size:31 final size:31
Alignment explanation
Indices: 3234640--3234767 Score: 132
Period size: 31 Copynumber: 4.1 Consensus size: 31
3234630 AGAGTCGAGG
* *
3234640 GTTTACTTATGTTCTTCGGGATATATGGACA
1 GTTTACCTATGTTCTTCGGGACATATGGACA
* *
3234671 ATATTACCTATG-TCTTTCGGGACATATGGATA
1 GT-TTACCTATGTTC-TTCGGGACATATGGACA
* ** **
3234703 GTATACCTATGTTCTAAGAAACATATGGACA
1 GTTTACCTATGTTCTTCGGGACATATGGACA
* *
3234734 GTTTACCTAGGTTCTTCGGGACCTATGGACA
1 GTTTACCTATGTTCTTCGGGACATATGGACA
3234765 GTT
1 GTT
3234768 GTCGAGGTTC
Statistics
Matches: 76, Mismatches: 18, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
31 50 0.66
32 26 0.34
ACGTcount: A:0.27, C:0.16, G:0.21, T:0.36
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACA
Found at i:3239676 original size:88 final size:88
Alignment explanation
Indices: 3239530--3239692 Score: 220
Period size: 88 Copynumber: 1.9 Consensus size: 88
3239520 AGGCTAGAAT
* * **
3239530 GGTGTATGTCTCTGAGATGTATCGAAACCCTTTGGTCACACCATGATATATACCCTTGTTCATGT
1 GGTGTATGTCTCTGAGATGCATCGAAACCCTTCGACCACACCATGATATATACCCTTGTTCATGT
3239595 GTTTGATGTTGGTAGACTAGAGG
66 GTTTGATGTTGGTAGACTAGAGG
* * * * * *
3239618 GGTGTATGTCTTTGAGATGCAGT-GAAACCCTTCGACCATACCATGATGTCTACTCTTGTTTATG
1 GGTGTATGTCTCTGAGATGCA-TCGAAACCCTTCGACCACACCATGATATATACCCTTGTTCATG
3239682 TGTTTGATGTT
65 TGTTTGATGTT
3239693 TGCTTGTCGC
Statistics
Matches: 64, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
88 63 0.98
89 1 0.02
ACGTcount: A:0.21, C:0.17, G:0.24, T:0.37
Consensus pattern (88 bp):
GGTGTATGTCTCTGAGATGCATCGAAACCCTTCGACCACACCATGATATATACCCTTGTTCATGT
GTTTGATGTTGGTAGACTAGAGG
Found at i:3241740 original size:21 final size:21
Alignment explanation
Indices: 3241715--3241790 Score: 71
Period size: 21 Copynumber: 3.6 Consensus size: 21
3241705 CCCTTAAGGG
*
3241715 AAGGGATCGATCATTTTCATC
1 AAGGGATCGATCCTTTTCATC
* * ** *
3241736 GAGGGATCAATCCTTTTGGTA
1 AAGGGATCGATCCTTTTCATC
* *
3241757 AAGAGATCGATCCTTTTCCTC
1 AAGGGATCGATCCTTTTCATC
*
3241778 TAGGGATCGATCC
1 AAGGGATCGATCC
3241791 CAAACTCACT
Statistics
Matches: 41, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.32
Consensus pattern (21 bp):
AAGGGATCGATCCTTTTCATC
Found at i:3250234 original size:17 final size:16
Alignment explanation
Indices: 3250212--3250245 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
3250202 TAAAAACAGT
3250212 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
3250229 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
3250245 A
1 A
3250246 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:3252795 original size:24 final size:24
Alignment explanation
Indices: 3252750--3252830 Score: 64
Period size: 24 Copynumber: 3.5 Consensus size: 24
3252740 AAACTTAACA
*
3252750 GTGCATCGATGCATCTCTTTGAAT
1 GTGCATCGATGCATCTCGTTGAAT
*
3252774 GTGCATCGATTCATCAT-GTTG-A-
1 GTGCATCGATGCATC-TCGTTGAAT
* * * *
3252796 -TGCACCGATGCA-CGCCTTGAGT
1 GTGCATCGATGCATCTCGTTGAAT
3252818 GTGCATCGATGCA
1 GTGCATCGATGCA
3252831 CGGGGTTTTG
Statistics
Matches: 44, Mismatches: 8, Indels: 11
0.70 0.13 0.17
Matches are distributed among these distances:
20 4 0.09
21 10 0.23
23 12 0.27
24 17 0.39
25 1 0.02
ACGTcount: A:0.21, C:0.23, G:0.25, T:0.31
Consensus pattern (24 bp):
GTGCATCGATGCATCTCGTTGAAT
Found at i:3254396 original size:21 final size:21
Alignment explanation
Indices: 3254354--3254397 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
3254344 ACCCCGGGAG
*
3254354 CTAGCTCTTCACGAGCTGCTC
1 CTAGCTCTTCACGAGCTCCTC
* *
3254375 CTAGCTCTTCTCGTGCTCCTC
1 CTAGCTCTTCACGAGCTCCTC
3254396 CT
1 CT
3254398 CCGGCACCAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.09, C:0.41, G:0.16, T:0.34
Consensus pattern (21 bp):
CTAGCTCTTCACGAGCTCCTC
Found at i:3255050 original size:2 final size:2
Alignment explanation
Indices: 3255043--3255070 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3255033 CAGCTTAAGC
3255043 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3255071 CTCAATTGGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3255546 original size:20 final size:20
Alignment explanation
Indices: 3255517--3255554 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
3255507 TTTCAAAGTG
3255517 ATGCACCGATGCACCAATCC
1 ATGCACCGATGCACCAATCC
*
3255537 ATGCATCGATGCACCAAT
1 ATGCACCGATGCACCAAT
3255555 TAATTTTTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.34, G:0.16, T:0.18
Consensus pattern (20 bp):
ATGCACCGATGCACCAATCC
Found at i:3255604 original size:26 final size:26
Alignment explanation
Indices: 3255574--3255625 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
3255564 AAACATCGAA
*
3255574 TGCATTTTATGCATCGATGCACTCAG
1 TGCATTTGATGCATCGATGCACTCAG
3255600 TGCATTTGATGCATCGATGCACTCAG
1 TGCATTTGATGCATCGATGCACTCAG
3255626 GCTTTTTCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.33
Consensus pattern (26 bp):
TGCATTTGATGCATCGATGCACTCAG
Found at i:3258099 original size:22 final size:21
Alignment explanation
Indices: 3258051--3258107 Score: 57
Period size: 21 Copynumber: 2.7 Consensus size: 21
3258041 ACCATTGCAA
3258051 GAAAGGGATTGATCTTTTAAGG
1 GAAAGGGATTGATCTTTT-AGG
3258073 G-AAGGGATTGATCCTTTT-GG
1 GAAAGGGATTGAT-CTTTTAGG
*
3258093 TGAAA-GGATCGATCT
1 -GAAAGGGATTGATCT
3258108 CAAACTCATT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
20 4 0.13
21 19 0.61
22 8 0.26
ACGTcount: A:0.28, C:0.09, G:0.32, T:0.32
Consensus pattern (21 bp):
GAAAGGGATTGATCTTTTAGG
Found at i:3258166 original size:21 final size:20
Alignment explanation
Indices: 3258124--3258202 Score: 70
Period size: 20 Copynumber: 3.9 Consensus size: 20
3258114 CATTGGAATC
* **
3258124 CAAGGGATCGAT-CTTTTAT
1 CAAGGGATTGATCCTTTGGT
3258143 CAAGGGGATTGATCCTTTGGT
1 CAA-GGGATTGATCCTTTGGT
* *
3258164 CAAAGGGATCGATCCTTTTGT
1 C-AAGGGATTGATCCTTTGGT
* *
3258185 TAAAGGATTGATCCTTTG
1 CAAGGGATTGATCCTTTG
3258203 AGCAAAAAAT
Statistics
Matches: 48, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
19 3 0.06
20 22 0.46
21 21 0.44
22 2 0.04
ACGTcount: A:0.24, C:0.15, G:0.25, T:0.35
Consensus pattern (20 bp):
CAAGGGATTGATCCTTTGGT
Found at i:3258193 original size:41 final size:41
Alignment explanation
Indices: 3258125--3258202 Score: 113
Period size: 41 Copynumber: 1.9 Consensus size: 41
3258115 ATTGGAATCC
*
3258125 AAGGGATCGATCTTTTATCAAGGGGATTGATCCTTTGGTCA
1 AAGGGATCGATCTTTTATCAAGAGGATTGATCCTTTGGTCA
* *
3258166 AAGGGATCGATCCTTTTGTTAA-AGGATTGATCCTTTG
1 AAGGGATCGAT-CTTTTATCAAGAGGATTGATCCTTTG
3258203 AGCAAAAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
41 25 0.76
42 8 0.24
ACGTcount: A:0.24, C:0.14, G:0.26, T:0.36
Consensus pattern (41 bp):
AAGGGATCGATCTTTTATCAAGAGGATTGATCCTTTGGTCA
Found at i:3258197 original size:20 final size:21
Alignment explanation
Indices: 3258125--3258202 Score: 79
Period size: 21 Copynumber: 3.8 Consensus size: 21
3258115 ATTGGAATCC
* **
3258125 AAGGGATCGAT-CTTTTATCA
1 AAGGGATTGATCCTTTGGTCA
*
3258145 AGGGGATTGATCCTTTGGTCA
1 AAGGGATTGATCCTTTGGTCA
* * *
3258166 AAGGGATCGATCCTTTTGTTA
1 AAGGGATTGATCCTTTGGTCA
3258187 AA-GGATTGATCCTTTG
1 AAGGGATTGATCCTTTG
3258203 AGCAAAAAAT
Statistics
Matches: 47, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 21 0.45
21 26 0.55
ACGTcount: A:0.24, C:0.14, G:0.26, T:0.36
Consensus pattern (21 bp):
AAGGGATTGATCCTTTGGTCA
Found at i:3258338 original size:11 final size:11
Alignment explanation
Indices: 3258324--3258359 Score: 63
Period size: 11 Copynumber: 3.3 Consensus size: 11
3258314 ACTTTGAATT
*
3258324 ATTTTTGATAA
1 ATTTTTGACAA
3258335 ATTTTTGACAA
1 ATTTTTGACAA
3258346 ATTTTTGACAA
1 ATTTTTGACAA
3258357 ATT
1 ATT
3258360 CAATTAAGTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.36, C:0.06, G:0.08, T:0.50
Consensus pattern (11 bp):
ATTTTTGACAA
Found at i:3264909 original size:32 final size:32
Alignment explanation
Indices: 3264836--3264909 Score: 76
Period size: 32 Copynumber: 2.3 Consensus size: 32
3264826 TTTTGGTATT
* **
3264836 GTGGTATATAATATATTATTATTTTGGGTGAA
1 GTGGTATATGATATATTATTATTTTCAGTGAA
* *** *
3264868 ATAACATATGATATATTATTATTTTCAGTGAC
1 GTGGTATATGATATATTATTATTTTCAGTGAA
3264900 GTGGTATATG
1 GTGGTATATG
3264910 TCACATCATT
Statistics
Matches: 30, Mismatches: 12, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.32, C:0.04, G:0.19, T:0.45
Consensus pattern (32 bp):
GTGGTATATGATATATTATTATTTTCAGTGAA
Found at i:3269154 original size:34 final size:35
Alignment explanation
Indices: 3269111--3269184 Score: 105
Period size: 39 Copynumber: 2.0 Consensus size: 35
3269101 GTCTGTTTAG
3269111 TATAGAGATGGGTTC-AATCCAATCCTCTTATTAT
1 TATAGAGATGGGTTCAAATCCAATCCTCTTATTAT
3269145 TATAGAGATGGGTTCAAATTAATCCAATCCTCTTATTAT
1 TATAGAGATGGGTTC--A--AATCCAATCCTCTTATTAT
3269184 T
1 T
3269185 TGTCAAAAAC
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
34 15 0.43
39 20 0.57
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (35 bp):
TATAGAGATGGGTTCAAATCCAATCCTCTTATTAT
Found at i:3269566 original size:118 final size:118
Alignment explanation
Indices: 3269424--3269640 Score: 353
Period size: 118 Copynumber: 1.8 Consensus size: 118
3269414 TTTGTGATAG
* * * * *
3269424 AATTTTCACTTCTTTTCCTAGATTTGTGATAGAATTTTCATAGTTCCATGCGAGTATTATTTTGA
1 AATTTTCACTTATTTTCCTAGATTTGTGATAGAATTTTCATAATTCCATACGAGTATTAATTTAA
3269489 AAGAGAATTCGTTGTTTTTGTTGAAATTTATTGAAATTTCATCCAGAAGGTAA
66 AAGAGAATTCGTTGTTTTTGTTGAAATTTATTGAAATTTCATCCAGAAGGTAA
* *
3269542 AATTTTCACTTATTTTCCTGGATTTGTGATAGAATTTTCATAATTCCATACTAGTATTAATTTAA
1 AATTTTCACTTATTTTCCTAGATTTGTGATAGAATTTTCATAATTCCATACGAGTATTAATTTAA
* *
3269607 AAGGGAATTCGTTGTTTTTGTTGAAATTTGTTGA
66 AAGAGAATTCGTTGTTTTTGTTGAAATTTATTGA
3269641 TCCACATAAT
Statistics
Matches: 90, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
118 90 1.00
ACGTcount: A:0.29, C:0.10, G:0.16, T:0.46
Consensus pattern (118 bp):
AATTTTCACTTATTTTCCTAGATTTGTGATAGAATTTTCATAATTCCATACGAGTATTAATTTAA
AAGAGAATTCGTTGTTTTTGTTGAAATTTATTGAAATTTCATCCAGAAGGTAA
Found at i:3275698 original size:24 final size:24
Alignment explanation
Indices: 3275671--3275759 Score: 90
Period size: 24 Copynumber: 3.7 Consensus size: 24
3275661 TATATCAAAA
*
3275671 ATCAAAACATAATTCAAGTCAAGT
1 ATCAAAACAGAATTCAAGTCAAGT
* * * *
3275695 ATCATATCAGAATCCAGGTCAAGT
1 ATCAAAACAGAATTCAAGTCAAGT
* *
3275719 ATCAAATCAGAA-TCTATGTCAAGT
1 ATCAAAACAGAATTC-AAGTCAAGT
*
3275743 ATCATAACAGAATTCAA
1 ATCAAAACAGAATTCAA
3275760 ATCGGAAATC
Statistics
Matches: 52, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
23 1 0.02
24 49 0.94
25 2 0.04
ACGTcount: A:0.45, C:0.18, G:0.11, T:0.26
Consensus pattern (24 bp):
ATCAAAACAGAATTCAAGTCAAGT
Found at i:3280446 original size:57 final size:57
Alignment explanation
Indices: 3280348--3280468 Score: 134
Period size: 57 Copynumber: 2.1 Consensus size: 57
3280338 TCTGCAGCAA
* * *
3280348 CTTCATCTCAGCCAGTAATAATTTCATCTCAACCTCTAAGAAGGATGCACCCTCCAT
1 CTTCATCTCAGCCAGTAATAATTTCATATCAACCTCGAAGAAGGATGCAACCTCCAT
* * ** * * * *
3280405 CTTCATCTCATCCTGTAATTGTTTCATATCAACTTGGAAGAATGATGCAACCTTCAT
1 CTTCATCTCAGCCAGTAATAATTTCATATCAACCTCGAAGAAGGATGCAACCTCCAT
*
3280462 TTTCATC
1 CTTCATC
3280469 ACAACCTCCA
Statistics
Matches: 52, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
57 52 1.00
ACGTcount: A:0.28, C:0.27, G:0.11, T:0.34
Consensus pattern (57 bp):
CTTCATCTCAGCCAGTAATAATTTCATATCAACCTCGAAGAAGGATGCAACCTCCAT
Found at i:3283946 original size:2 final size:2
Alignment explanation
Indices: 3283939--3283964 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3283929 ATGCCCATCC
3283939 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
3283965 TAATCAATCA
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:3289066 original size:21 final size:21
Alignment explanation
Indices: 3289040--3289079 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3289030 CAGAACCCCA
*
3289040 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
3289061 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
3289080 TCAAAGGGGG
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:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:3289110 original size:22 final size:23
Alignment explanation
Indices: 3289061--3289120 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
3289051 ATTCCCCTGT
3289061 GGGGGGAATCGGTTCCCCTTCAA
1 GGGGGGAATCGGTTCCCCTTCAA
*
3289084 AGGGGGAATCGGTT-CCCTT--A
1 GGGGGGAATCGGTTCCCCTTCAA
* *
3289104 GGGGGGGATCGATTCCC
1 GGGGGGAATCGGTTCCC
3289121 TCTGCACCAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
20 12 0.38
21 2 0.06
22 5 0.16
23 13 0.41
ACGTcount: A:0.17, C:0.23, G:0.38, T:0.22
Consensus pattern (23 bp):
GGGGGGAATCGGTTCCCCTTCAA
Found at i:3297462 original size:15 final size:15
Alignment explanation
Indices: 3297439--3297477 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
3297429 TTATTATATG
*
3297439 TGAATATGTTTTATA
1 TGAAAATGTTTTATA
*
3297454 TGAAAATGTTTTATG
1 TGAAAATGTTTTATA
3297469 TGAAAATGT
1 TGAAAATGT
3297478 GCTAATTGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (15 bp):
TGAAAATGTTTTATA
Found at i:3297671 original size:24 final size:24
Alignment explanation
Indices: 3297635--3297705 Score: 99
Period size: 24 Copynumber: 3.0 Consensus size: 24
3297625 AGAGTCAAGG
3297635 ATTCTACGCGGTCCTTTGGGA-AA
1 ATTCTACGCGGTCCTTTGGGACAA
*
3297658 ACTTCTACGTGGTCCTTTGGGACAA
1 A-TTCTACGCGGTCCTTTGGGACAA
* *
3297683 ATTCTATGCGGTCCTTCGGGACA
1 ATTCTACGCGGTCCTTTGGGACA
3297706 TATATGTGGC
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
23 1 0.02
24 38 0.90
25 3 0.07
ACGTcount: A:0.20, C:0.24, G:0.25, T:0.31
Consensus pattern (24 bp):
ATTCTACGCGGTCCTTTGGGACAA
Found at i:3302893 original size:17 final size:17
Alignment explanation
Indices: 3302866--3302908 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
3302856 ATTTATTCAA
*
3302866 TAAAGCTAGTTTACTAAT
1 TAAA-CTAGTTCACTAAT
*
3302884 TAAACTAGTTCATTAAT
1 TAAACTAGTTCACTAAT
3302901 TAAACTAG
1 TAAACTAG
3302909 CTCCTTTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 19 0.83
18 4 0.17
ACGTcount: A:0.42, C:0.12, G:0.09, T:0.37
Consensus pattern (17 bp):
TAAACTAGTTCACTAAT
Found at i:3304646 original size:21 final size:21
Alignment explanation
Indices: 3304622--3304749 Score: 145
Period size: 21 Copynumber: 6.1 Consensus size: 21
3304612 TTTGCAACGT
*
3304622 GAACTTTGACTATCGCAATGC
1 GAACTTGGACTATCGCAATGC
*
3304643 GAACTTGGACTATCGCAATAC
1 GAACTTGGACTATCGCAATGC
*
3304664 GAACTTGGACTATCGCAATGA
1 GAACTTGGACTATCGCAATGC
* *
3304685 GAA-TATGTA-AATCGCAATGC
1 GAACT-TGGACTATCGCAATGC
* * *
3304705 GATA-GTCGACTATCGCAACGC
1 GA-ACTTGGACTATCGCAATGC
3304726 GAACTTGGACTATCGCAATGC
1 GAACTTGGACTATCGCAATGC
3304747 GAA
1 GAA
3304750 TATGTAAATC
Statistics
Matches: 88, Mismatches: 15, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
20 15 0.17
21 73 0.83
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.23
Consensus pattern (21 bp):
GAACTTGGACTATCGCAATGC
Found at i:3304762 original size:20 final size:21
Alignment explanation
Indices: 3304633--3304768 Score: 88
Period size: 21 Copynumber: 6.6 Consensus size: 21
3304623 AACTTTGACT
* *
3304633 ATCGCAATGCGAACT-TGGACT
1 ATCGCAATGCGAA-TATGTACA
* * *
3304654 ATCGCAATACGAACT-TGGACT
1 ATCGCAATGCGAA-TATGTACA
*
3304675 ATCGCAATGAGAATATGTA-A
1 ATCGCAATGCGAATATGTACA
*
3304695 ATCGCAATGCG-ATA-GTCGACT
1 ATCGCAATGCGAATATGT--ACA
* * *
3304716 ATCGCAACGCGAACT-TGGACT
1 ATCGCAATGCGAA-TATGTACA
3304737 ATCGCAATGCGAATATGTA-A
1 ATCGCAATGCGAATATGTACA
3304757 ATCGCAATGCGA
1 ATCGCAATGCGA
3304769 TAGTCGAAGT
Statistics
Matches: 95, Mismatches: 12, Indels: 17
0.77 0.10 0.14
Matches are distributed among these distances:
18 2 0.02
19 3 0.03
20 25 0.26
21 62 0.65
22 1 0.01
23 2 0.02
ACGTcount: A:0.34, C:0.21, G:0.22, T:0.23
Consensus pattern (21 bp):
ATCGCAATGCGAATATGTACA
Found at i:3304783 original size:62 final size:62
Alignment explanation
Indices: 3304633--3304775 Score: 225
Period size: 62 Copynumber: 2.3 Consensus size: 62
3304623 AACTTTGACT
* * **
3304633 ATCGCAATGCGA-ACTTGGACTATCGCAATACGAACTTGGACTATCGCAATGAGAATATGTAA
1 ATCGCAATGCGATA-GTCGACTATCGCAACGCGAACTTGGACTATCGCAATGAGAATATGTAA
*
3304695 ATCGCAATGCGATAGTCGACTATCGCAACGCGAACTTGGACTATCGCAATGCGAATATGTAA
1 ATCGCAATGCGATAGTCGACTATCGCAACGCGAACTTGGACTATCGCAATGAGAATATGTAA
3304757 ATCGCAATGCGATAGTCGA
1 ATCGCAATGCGATAGTCGA
3304776 AGTTCGCATT
Statistics
Matches: 75, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
62 74 0.99
63 1 0.01
ACGTcount: A:0.34, C:0.21, G:0.22, T:0.23
Consensus pattern (62 bp):
ATCGCAATGCGATAGTCGACTATCGCAACGCGAACTTGGACTATCGCAATGAGAATATGTAA
Found at i:3304792 original size:21 final size:21
Alignment explanation
Indices: 3304758--3304915 Score: 180
Period size: 21 Copynumber: 7.6 Consensus size: 21
3304748 AATATGTAAA
*
3304758 TCGCAATGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCGAAGT
* *
3304779 TCGCATTGCAATAGTCCAAGT
1 TCGCATTGCGATAGTCGAAGT
3304800 TCGCATTGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCGAAGT
* *
3304821 TCGCGTTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCGAAGT
*
3304842 TCGCATTGCGATAGTCG-ACT
1 TCGCATTGCGATAGTCGAAGT
*
3304862 ATCGCATTGCGAT-TTAC-ATA-T
1 -TCGCATTGCGATAGT-CGA-AGT
*
3304883 TCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCGAAGT
*
3304904 TCGCGTTGCGAT
1 TCGCATTGCGAT
3304916 TTATTCCAAA
Statistics
Matches: 117, Mismatches: 13, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
20 17 0.15
21 99 0.85
22 1 0.01
ACGTcount: A:0.23, C:0.22, G:0.25, T:0.30
Consensus pattern (21 bp):
TCGCATTGCGATAGTCGAAGT
Found at i:3304804 original size:62 final size:60
Alignment explanation
Indices: 3304675--3304857 Score: 147
Period size: 62 Copynumber: 3.0 Consensus size: 60
3304665 AACTTGGACT
* * ** * ** *
3304675 ATCGCAATGAGAATATGTAAATCGCAATGCGATAGTCG-ACTATCGCAACGCGAACTTGGACT
1 ATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGAAGT-TCGCATTGC-AA-TAGTCCA
3304737 ATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGAAGTTCGCATTGCAATAGTCCA
1 ATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGAAGTTCGCATTGCAATAGTCCA
* * ** * *
3304797 AGTTCGCATTGCG-ATA-GTCGAAGTTCGCGTTGCGATAGTCCAAGTTCGCATTGCGATAGTC
1 A--TCGCAATGCGAATATGT--AA-ATCGCAATGCGATAGTCGAAGTTCGCATTGCAATAGTC
3304858 GACTATCGCA
Statistics
Matches: 101, Mismatches: 14, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
60 6 0.06
61 5 0.05
62 55 0.54
63 35 0.35
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.26
Consensus pattern (60 bp):
ATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGAAGTTCGCATTGCAATAGTCCA
Found at i:3304810 original size:42 final size:42
Alignment explanation
Indices: 3304758--3304940 Score: 205
Period size: 42 Copynumber: 4.4 Consensus size: 42
3304748 AATATGTAAA
* *
3304758 TCGCAATGCGATAGTCGAAGTTCGCATTGCAATAGTCCAAGT
1 TCGCATTGCGATAGTCGAAGTTCGCATTGCGATAGTCCAAGT
*
3304800 TCGCATTGCGATAGTCGAAGTTCGCGTTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCGAAGTTCGCATTGCGATAGTCCAAGT
* * *
3304842 TCGCATTGCGATAGTCG-ACTATCGCATTGCGAT-TTACATA-T
1 TCGCATTGCGATAGTCGAAGT-TCGCATTGCGATAGTCCA-AGT
* * * *
3304883 TCGCATTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAAT
1 TCGCATTGCGATAGTCGAAGTTCGCATTGCGA--TAGTCCAAGT
3304927 TCG--TTGCGATAGTC
1 TCGCATTGCGATAGTC
3304941 CAAAATCGCA
Statistics
Matches: 123, Mismatches: 11, Indels: 14
0.83 0.07 0.09
Matches are distributed among these distances:
41 32 0.26
42 81 0.66
43 2 0.02
44 8 0.07
ACGTcount: A:0.23, C:0.22, G:0.23, T:0.31
Consensus pattern (42 bp):
TCGCATTGCGATAGTCGAAGTTCGCATTGCGATAGTCCAAGT
Found at i:3304929 original size:23 final size:22
Alignment explanation
Indices: 3304764--3304949 Score: 99
Period size: 21 Copynumber: 8.9 Consensus size: 22
3304754 TAAATCGCAA
* * *
3304764 TGCGA-TAGTCGAAGTTCGCAT
1 TGCGATTAGTCCAAATTCGCGT
* * *
3304785 TGC-AATAGTCCAAGTTCGCAT
1 TGCGATTAGTCCAAATTCGCGT
* *
3304806 TGCGA-TAGTCGAAGTTCGCGT
1 TGCGATTAGTCCAAATTCGCGT
* *
3304827 TGCGA-TAGTCCAAGTTCGCAT
1 TGCGATTAGTCCAAATTCGCGT
* * *
3304848 TGCGA-TAGT-CGACTATCGCAT
1 TGCGATTAGTCCAAAT-TCGCGT
* * *
3304869 TGCGATT--TACATATTCGCAT
1 TGCGATTAGTCCAAATTCGCGT
*
3304889 TGCGA-TAGTCCAAGTTCGCGT
1 TGCGATTAGTCCAAATTCGCGT
*
3304910 TGCGATTTATTCCAAATT--CGT
1 TGCGA-TTAGTCCAAATTCGCGT
*
3304931 TGCGA-TAGTCCAAAATCGC
1 TGCGATTAGTCCAAATTCGC
3304950 AACGACTGGT
Statistics
Matches: 136, Mismatches: 18, Indels: 22
0.77 0.10 0.12
Matches are distributed among these distances:
19 10 0.07
20 16 0.12
21 99 0.73
22 2 0.01
23 9 0.07
ACGTcount: A:0.24, C:0.22, G:0.23, T:0.31
Consensus pattern (22 bp):
TGCGATTAGTCCAAATTCGCGT
Found at i:3305044 original size:6 final size:6
Alignment explanation
Indices: 3305033--3305063 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
3305023 GACACGTATT
3305033 ACCACG ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG A
3305064 GACGAGAAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.35, C:0.48, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:3305607 original size:6 final size:6
Alignment explanation
Indices: 3305562--3305610 Score: 66
Period size: 6 Copynumber: 8.5 Consensus size: 6
3305552 TCTCGTCTCG
* *
3305562 GGTCG- GGTCG- GGTCGG GGTCGG GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
3305608 GGT
1 GGT
3305611 TATACGTGTC
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
5 10 0.24
6 32 0.76
ACGTcount: A:0.00, C:0.16, G:0.57, T:0.27
Consensus pattern (6 bp):
GGTCGT
Found at i:3305755 original size:21 final size:21
Alignment explanation
Indices: 3305731--3305888 Score: 180
Period size: 21 Copynumber: 7.6 Consensus size: 21
3305721 TTTGGAATAA
* *
3305731 ATCGCAGTGCGAACTTGGACT
1 ATCGCAATGCGAACTTCGACT
* *
3305752 ATCGCAATGTGAA-TAT-GTA-A
1 ATCGCAATGCGAACT-TCG-ACT
*
3305772 ATCGCAATGCGATA-GTCGACT
1 ATCGCAATGCGA-ACTTCGACT
*
3305793 ATCGCAATGCGAACTTGGACT
1 ATCGCAATGCGAACTTCGACT
*
3305814 ATCGCAACGCGAACTTCGACT
1 ATCGCAATGCGAACTTCGACT
3305835 ATCGCAATGCGAACTTCGACT
1 ATCGCAATGCGAACTTCGACT
*
3305856 ATCGCATTGCGAACTTCGACT
1 ATCGCAATGCGAACTTCGACT
*
3305877 ATCGCATTGCGA
1 ATCGCAATGCGA
3305889 TTTACATATT
Statistics
Matches: 119, Mismatches: 12, Indels: 12
0.83 0.08 0.08
Matches are distributed among these distances:
20 16 0.13
21 103 0.87
ACGTcount: A:0.28, C:0.25, G:0.22, T:0.25
Consensus pattern (21 bp):
ATCGCAATGCGAACTTCGACT
Found at i:3305833 original size:42 final size:42
Alignment explanation
Indices: 3305706--3305888 Score: 187
Period size: 42 Copynumber: 4.4 Consensus size: 42
3305696 TGCGATTTTG
* * * *
3305706 GACTATCGCAA--CGAATTTGGAATAAATCGCAGTGCGAACTTG
1 GACTATCGCAATGCGAACTTGGACT--ATCGCAATGCGAACTTC
* * * *
3305748 GACTATCGCAATGTGAA-TATGTA-AATCGCAATGCGATA-GTC
1 GACTATCGCAATGCGAACT-TGGACTATCGCAATGCGA-ACTTC
*
3305789 GACTATCGCAATGCGAACTTGGACTATCGCAACGCGAACTTC
1 GACTATCGCAATGCGAACTTGGACTATCGCAATGCGAACTTC
* *
3305831 GACTATCGCAATGCGAACTTCGACTATCGCATTGCGAACTTC
1 GACTATCGCAATGCGAACTTGGACTATCGCAATGCGAACTTC
*
3305873 GACTATCGCATTGCGA
1 GACTATCGCAATGCGA
3305889 TTTACATATT
Statistics
Matches: 119, Mismatches: 15, Indels: 14
0.80 0.10 0.09
Matches are distributed among these distances:
41 32 0.27
42 80 0.67
43 1 0.01
44 6 0.05
ACGTcount: A:0.30, C:0.23, G:0.22, T:0.25
Consensus pattern (42 bp):
GACTATCGCAATGCGAACTTGGACTATCGCAATGCGAACTTC
Found at i:3305903 original size:20 final size:20
Alignment explanation
Indices: 3305878--3305929 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
3305868 ACTTCGACTA
3305878 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
3305898 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
3305918 TCGCATTGCGAT
1 TCGCATTGCGAT
3305930 AGTCCAAGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.23, C:0.21, G:0.17, T:0.38
Consensus pattern (20 bp):
TCGCATTGCGATTTACATAT
Found at i:3305943 original size:21 final size:21
Alignment explanation
Indices: 3305917--3306116 Score: 228
Period size: 21 Copynumber: 9.6 Consensus size: 21
3305907 GATTTACATA
3305917 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
3305938 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
3305959 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
* * *
3305980 TTTGCATTACAATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
* *
3306001 TTCGCATTGCGATAGT-CGAC
1 TTCGCATTGCGATAGTCCAAG
* *
3306021 TATCGCATTGCGAT-TTACATA-
1 T-TCGCATTGCGATAGTCCA-AG
* * *
3306042 TTCGTATTGCGATAGT-CGAC
1 TTCGCATTGCGATAGTCCAAG
*
3306062 TATCGCATTGCTATAGTCCAAG
1 T-TCGCATTGCGATAGTCCAAG
*
3306084 TTCGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCCAAG
*
3306105 TTCGCGTTGCGA
1 TTCGCATTGCGA
3306117 ATCTGGAAAC
Statistics
Matches: 152, Mismatches: 20, Indels: 14
0.82 0.11 0.08
Matches are distributed among these distances:
19 1 0.01
20 17 0.11
21 130 0.86
22 4 0.03
ACGTcount: A:0.24, C:0.22, G:0.23, T:0.32
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCCAAG
Found at i:3306648 original size:22 final size:22
Alignment explanation
Indices: 3306623--3306700 Score: 79
Period size: 22 Copynumber: 3.5 Consensus size: 22
3306613 ATAAATATTT
*
3306623 TATTAGTAATAAAATTTTATCA
1 TATTAGTATTAAAATTTTATCA
* *
3306645 TATTAGTATTAGATCATTTAATC-
1 TATTAGTATTA-A-AATTTTATCA
3306668 -ATTAGTACTTAAAATTTTATCA
1 TATTAGTA-TTAAAATTTTATCA
*
3306690 TATTAATATTA
1 TATTAGTATTA
3306701 GATATTTTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
21 7 0.16
22 21 0.47
23 10 0.22
24 7 0.16
ACGTcount: A:0.41, C:0.06, G:0.05, T:0.47
Consensus pattern (22 bp):
TATTAGTATTAAAATTTTATCA
Found at i:3306681 original size:45 final size:43
Alignment explanation
Indices: 3306624--3306707 Score: 132
Period size: 45 Copynumber: 1.9 Consensus size: 43
3306614 TAAATATTTT
*
3306624 ATTAGTAATAAAATTTTATCATATTAGTATTAGATCATTTAATC
1 ATTAGTAATAAAATTTTATCATATTAATATTAGAT-ATTTAATC
*
3306668 ATTAGTACTTAAAATTTTATCATATTAATATTAGATATTT
1 ATTAGTA-ATAAAATTTTATCATATTAATATTAGATATTT
3306708 TTTTAATAGA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
44 11 0.30
45 26 0.70
ACGTcount: A:0.40, C:0.06, G:0.06, T:0.48
Consensus pattern (43 bp):
ATTAGTAATAAAATTTTATCATATTAATATTAGATATTTAATC
Found at i:3309809 original size:185 final size:184
Alignment explanation
Indices: 3309491--3309858 Score: 619
Period size: 185 Copynumber: 2.0 Consensus size: 184
3309481 TCAAAAATAA
*
3309491 TTAGTTGACTAGCTGCCAAAGCATATTGTTGATGTGTCATTCTCACGAGTTTAATTATTGATGTG
1 TTAGTCGACTAGCTGCCAAAGCATATTGTTGATGTGTCATTCTCACGAGTTTAATTATTGATGTG
* *
3309556 ACATATATAATGTTACTAAAGTGATGACATGGCATGTATCACATCCCAAGATAGAAACACACAAA
66 ACATATATAATATTACTAAAGTGATGACATGGCATGTACCACATCCCAAGATAGAAACACACAAA
3309621 ACAACCGGTGCATGGATAGCAACATCGTCAAACAATCACAAAATAGGAAACATAG
131 ACAA-CGGTGCATGGATAGCAACATCGTCAAACAATCACAAAATAGGAAACATAG
* * *
3309676 TTAGTCGACTAGCTGTCAACGCATATTGTTGATGTGTCATTCTCACGTGTTTAATTATTGATGTG
1 TTAGTCGACTAGCTGCCAAAGCATATTGTTGATGTGTCATTCTCACGAGTTTAATTATTGATGTG
* * *
3309741 ACATATATAATATTACTAAAGTGATGACGTGGCATGTACCACATTCCAATATAGAAACACACAAA
66 ACATATATAATATTACTAAAGTGATGACATGGCATGTACCACATCCCAAGATAGAAACACACAAA
* * *
3309806 ACAACTGTGCATGGATAGCAACATCGTCTAACAGTCACAAAATAGGAAACATA
131 ACAACGGTGCATGGATAGCAACATCGTCAAACAATCACAAAATAGGAAACATA
3309859 TTACTATAGA
Statistics
Matches: 171, Mismatches: 12, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
184 46 0.27
185 125 0.73
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.28
Consensus pattern (184 bp):
TTAGTCGACTAGCTGCCAAAGCATATTGTTGATGTGTCATTCTCACGAGTTTAATTATTGATGTG
ACATATATAATATTACTAAAGTGATGACATGGCATGTACCACATCCCAAGATAGAAACACACAAA
ACAACGGTGCATGGATAGCAACATCGTCAAACAATCACAAAATAGGAAACATAG
Found at i:3316325 original size:19 final size:19
Alignment explanation
Indices: 3316301--3316363 Score: 78
Period size: 17 Copynumber: 3.4 Consensus size: 19
3316291 TTCTATCATA
3316301 ATTTTATTTAAAAAAAATT
1 ATTTTATTTAAAAAAAATT
*
3316320 ATTTTATTT-AAAAATA-T
1 ATTTTATTTAAAAAAAATT
3316337 ATTTTA-TTAAAAAAAACTT
1 ATTTTATTTAAAAAAAA-TT
3316356 AATTTTAT
1 -ATTTTAT
3316364 ATGTATTTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
16 2 0.05
17 13 0.35
18 6 0.16
19 10 0.27
20 6 0.16
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (19 bp):
ATTTTATTTAAAAAAAATT
Found at i:3316644 original size:2 final size:2
Alignment explanation
Indices: 3316631--3316706 Score: 143
Period size: 2 Copynumber: 38.0 Consensus size: 2
3316621 TTATCATTAA
*
3316631 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3316673 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3316707 GGATAAATTT
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 72 1.00
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3317191 original size:2 final size:2
Alignment explanation
Indices: 3317184--3317221 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
3317174 TTATCATTAA
3317184 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3317222 GAATAAATAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3319672 original size:57 final size:57
Alignment explanation
Indices: 3319556--3319699 Score: 156
Period size: 57 Copynumber: 2.6 Consensus size: 57
3319546 ATTTGTAAGA
** * *
3319556 AAAATAAATTGTT-AATTT-TTT-TTA-GAATCTTGAATGATCCTATCTTTTAAAAAT
1 AAAATAAATTGTTGAATTTATTTCTTAGGAATCTCAAACGAT-CTATATTTTAAAAAT
*
3319610 -AAATAAATTGTTGAATTTATTTCTTAGGAATCTCAAACGAT-TATATTTTATTAAAT
1 AAAATAAATTGTTGAATTTATTTCTTAGGAATCTCAAACGATCTATATTTTA-AAAAT
* * *
3319666 AAAATAAAATGTTGAACTTATTTCTTGGGAATCT
1 AAAATAAATTGTTGAATTTATTTCTTAGGAATCT
3319700 TGAATAATTT
Statistics
Matches: 76, Mismatches: 8, Indels: 9
0.82 0.09 0.10
Matches are distributed among these distances:
53 12 0.16
54 5 0.07
55 11 0.14
56 7 0.09
57 41 0.54
ACGTcount: A:0.39, C:0.08, G:0.10, T:0.44
Consensus pattern (57 bp):
AAAATAAATTGTTGAATTTATTTCTTAGGAATCTCAAACGATCTATATTTTAAAAAT
Found at i:3319777 original size:58 final size:57
Alignment explanation
Indices: 3319666--3319789 Score: 142
Period size: 58 Copynumber: 2.2 Consensus size: 57
3319656 TTTATTAAAT
* * * *
3319666 AAAATAAAATGTTGAACTTATTTCTTGGGAATCTTGAATAATTTTAACTTGTAAAAG
1 AAAATAAATTATTGAACTTATTTCTTGAGAATCTTGAATAATTCTAACTTGTAAAAG
* * * *
3319723 AAAATAAATTATTGAATTTATTTTCTTGATAATTTTGAATAATTCT-ATTATGTAAAAG
1 AAAATAAATTATTGAACTTA-TTTCTTGAGAATCTTGAATAATTCTAACT-TGTAAAAG
*
3319781 GAAATAAAT
1 AAAATAAAT
3319790 AGTTTGTCGG
Statistics
Matches: 56, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
57 19 0.34
58 37 0.66
ACGTcount: A:0.43, C:0.05, G:0.11, T:0.41
Consensus pattern (57 bp):
AAAATAAATTATTGAACTTATTTCTTGAGAATCTTGAATAATTCTAACTTGTAAAAG
Found at i:3322164 original size:15 final size:15
Alignment explanation
Indices: 3322144--3322182 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
3322134 TATTGTCCTT
3322144 ATGGTATCGGTACCC
1 ATGGTATCGGTACCC
*
3322159 ATGGTATCAGTACCC
1 ATGGTATCGGTACCC
*
3322174 TTGGTATCG
1 ATGGTATCG
3322183 ATACTACCTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.21, C:0.23, G:0.26, T:0.31
Consensus pattern (15 bp):
ATGGTATCGGTACCC
Found at i:3327713 original size:28 final size:28
Alignment explanation
Indices: 3327677--3327780 Score: 102
Period size: 29 Copynumber: 3.6 Consensus size: 28
3327667 AAAAAAGTTG
* *
3327677 AATACTTTAGTACCTATTTTGACCAAAA
1 AATAATTTAGTACTTATTTTGACCAAAA
*
3327705 AATAATTTAGGTACTTATTTTGAGCAAAA
1 AATAATTTA-GTACTTATTTTGACCAAAA
* *
3327734 AGACAACTTTAAGTACTTATTTTGATC-AAA
1 A-ATAA-TTT-AGTACTTATTTTGACCAAAA
*
3327764 AATACTTTAGGTACTTA
1 AATAATTTA-GTACTTA
3327781 AAAGAATAAA
Statistics
Matches: 64, Mismatches: 7, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
27 1 0.02
28 18 0.28
29 20 0.31
30 7 0.11
31 17 0.27
32 1 0.02
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.38
Consensus pattern (28 bp):
AATAATTTAGTACTTATTTTGACCAAAA
Found at i:3327753 original size:31 final size:30
Alignment explanation
Indices: 3327680--3327765 Score: 104
Period size: 31 Copynumber: 2.9 Consensus size: 30
3327670 AAAGTTGAAT
* *
3327680 ACTTT-AGTACCTATTTTGACCAAAAAATA
1 ACTTTAAGTACTTATTTTGACCAAAAAACA
* *
3327709 A-TTTAGGTACTTATTTTGAGCAAAAAGACA
1 ACTTTAAGTACTTATTTTGACCAAAAA-ACA
*
3327739 ACTTTAAGTACTTATTTTGATCAAAAA
1 ACTTTAAGTACTTATTTTGACCAAAAA
3327766 TACTTTAGGT
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
28 3 0.06
29 19 0.40
30 3 0.06
31 23 0.48
ACGTcount: A:0.41, C:0.13, G:0.10, T:0.36
Consensus pattern (30 bp):
ACTTTAAGTACTTATTTTGACCAAAAAACA
Found at i:3332461 original size:23 final size:23
Alignment explanation
Indices: 3332435--3332498 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 23
3332425 CAGCTCATAT
*
3332435 AATTGCACCTAAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
* *
3332458 AATTGCACCGGAGTGCCGCGTAG
1 AATTGCACCGAAGTGCCACGTAG
* *
3332481 AATTGCATCGTAGTGCCA
1 AATTGCACCGAAGTGCCA
3332499 TATAATAATG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.27, C:0.25, G:0.27, T:0.22
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACGTAG
Found at i:3332717 original size:97 final size:97
Alignment explanation
Indices: 3332514--3332818 Score: 506
Period size: 97 Copynumber: 3.1 Consensus size: 97
3332504 TAATGTCCAT
3332514 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATC--ATACATA--CCAAGGATCAAGTATGTGTCTCACCA
3332579 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
62 GACTT--CACATGTTCCAAAGAATACATATATGTCCCG
*
3332617 AAGGACCACATATCATTCCTTAAGAATCATGCATACCAAGGATCAAGTATGTGTCTCACCAGACT
1 AAGGACCACATATCATTCCTTAAGAATCATACATACCAAGGATCAAGTATGTGTCTCACCAGACT
3332682 TCACATGTTCCAAAGAATACATATATGTCCCG
66 TCACATGTTCCAAAGAATACATATATGTCCCG
3332714 AAGGACCAC--ATCATTCCTTAAGAATCATACATATACCAAGGATCAAGTATGTGTCTCACCAGA
1 AAGGACCACATATCATTCCTTAAGAATCATAC--ATACCAAGGATCAAGTATGTGTCTCACCAGA
*
3332777 CCTCACATGTTCCAAAGAATACATATATGTCCCG
64 CTTCACATGTTCCAAAGAATACATATATGTCCCG
3332811 AAGGACCA
1 AAGGACCA
3332819 TAGACCCTCT
Statistics
Matches: 197, Mismatches: 3, Indels: 10
0.94 0.01 0.05
Matches are distributed among these distances:
95 20 0.10
97 112 0.57
99 31 0.16
101 6 0.03
103 28 0.14
ACGTcount: A:0.36, C:0.25, G:0.14, T:0.25
Consensus pattern (97 bp):
AAGGACCACATATCATTCCTTAAGAATCATACATACCAAGGATCAAGTATGTGTCTCACCAGACT
TCACATGTTCCAAAGAATACATATATGTCCCG
Found at i:3333342 original size:20 final size:21
Alignment explanation
Indices: 3333301--3333341 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
3333291 TTTTTTATTA
*
3333301 TGGGGGAATCGGTTCCCCCCC
1 TGGGGGAATCGATTCCCCCCC
*
3333322 TGGGGGTATCGATTCCCCCC
1 TGGGGGAATCGATTCCCCCC
3333342 TAGCGTTCTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.10, C:0.37, G:0.32, T:0.22
Consensus pattern (21 bp):
TGGGGGAATCGATTCCCCCCC
Found at i:3333391 original size:21 final size:21
Alignment explanation
Indices: 3333367--3333407 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
3333357 TCATATTCGT
*
3333367 TTGAGGGGGTATCGATTCCCC
1 TTGAAGGGGTATCGATTCCCC
*
3333388 TTGAATGGGTATCGATTCCC
1 TTGAAGGGGTATCGATTCCC
3333408 ATAGCCCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.22, G:0.29, T:0.32
Consensus pattern (21 bp):
TTGAAGGGGTATCGATTCCCC
Found at i:3342422 original size:21 final size:21
Alignment explanation
Indices: 3342396--3342435 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3342386 CAGAACCCCA
*
3342396 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
3342417 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
3342436 TCAAAGGGGA
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:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:3342466 original size:22 final size:24
Alignment explanation
Indices: 3342416--3342467 Score: 58
Period size: 22 Copynumber: 2.3 Consensus size: 24
3342406 GATTCCCCTG
3342416 TGGGGGG-AATCGGTTCCCCTTCA
1 TGGGGGGAAATCGGTTCCCCTTCA
**
3342439 -AAGGGGAAATCGGTT-CCC-TCA
1 TGGGGGGAAATCGGTTCCCCTTCA
3342460 TGGGGGGA
1 TGGGGGGA
3342468 TCGATTCCCT
Statistics
Matches: 23, Mismatches: 4, Indels: 5
0.72 0.12 0.16
Matches are distributed among these distances:
21 3 0.13
22 12 0.52
23 8 0.35
ACGTcount: A:0.19, C:0.21, G:0.38, T:0.21
Consensus pattern (24 bp):
TGGGGGGAAATCGGTTCCCCTTCA
Found at i:3348984 original size:23 final size:22
Alignment explanation
Indices: 3348953--3349016 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 22
3348943 CAGCTCATAT
*
3348953 AATTTCACCTAAGTGCCACGTAG
1 AATTGCACCT-AGTGCCACGTAG
* *
3348976 AATTGCACCGGAGTGCCGCGTAG
1 AATTGCACC-TAGTGCCACGTAG
3348999 AATTGCACCGTAGTGCCA
1 AATTGCACC-TAGTGCCA
3349017 TATAATAATG
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.27, C:0.27, G:0.25, T:0.22
Consensus pattern (22 bp):
AATTGCACCTAGTGCCACGTAG
Found at i:3349157 original size:103 final size:103
Alignment explanation
Indices: 3349032--3349352 Score: 597
Period size: 103 Copynumber: 3.1 Consensus size: 103
3349022 TAATGTCCAT
* *
3349032 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAATGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
3349097 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
3349135 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
3349200 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* *
3349238 AAGGACCACATATCATTCCTTAAGAATTATATAAATATACCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
*
3349303 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
3349341 AAGGACCACATA
1 AAGGACCACATA
3349353 GACCCTCTAC
Statistics
Matches: 213, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
103 213 1.00
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:3349922 original size:21 final size:21
Alignment explanation
Indices: 3349898--3349940 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
3349888 TCATATTCGT
* *
3349898 TTGAGGGGGTATCGATTCCCC
1 TTGAAGGGGTATCAATTCCCC
*
3349919 TTGAATGGGTATCAATTCCCC
1 TTGAAGGGGTATCAATTCCCC
3349940 T
1 T
3349941 AGCCCAGAAA
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:0.19, C:0.23, G:0.26, T:0.33
Consensus pattern (21 bp):
TTGAAGGGGTATCAATTCCCC
Found at i:3358889 original size:39 final size:38
Alignment explanation
Indices: 3358756--3358892 Score: 159
Period size: 39 Copynumber: 3.5 Consensus size: 38
3358746 CAAGATTCCC
* * *
3358756 AAAAAAAAATCTAATGATTTATTTCCATTTACAAAACAG
1 AAAAATAAATCAAACGATTTATTTCC-TTTACAAAACAG
* * *
3358795 AAAAATAAATCATATGATTTATTTCTTTTTACAAAACAG
1 AAAAATAAATCAAACGATTTATTTC-CTTTACAAAACAG
*
3358834 AAAAATAAATCCAACGATTTATTTCCTTTCACAAAACATG
1 AAAAATAAATCAAACGATTTATTTCCTTT-ACAAAACA-G
*
3358874 -AAAATAAAGCAAACGATTT
1 AAAAATAAATCAAACGATTT
3358893 GTTTTGATTT
Statistics
Matches: 85, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
38 3 0.04
39 81 0.95
40 1 0.01
ACGTcount: A:0.49, C:0.14, G:0.06, T:0.31
Consensus pattern (38 bp):
AAAAATAAATCAAACGATTTATTTCCTTTACAAAACAG
Found at i:3358964 original size:40 final size:39
Alignment explanation
Indices: 3358910--3359073 Score: 163
Period size: 40 Copynumber: 4.2 Consensus size: 39
3358900 TTTTTTTTTT
* *
3358910 CTTTTATAAAATAGGAAACTAAACCCAACGATTTATTTAC
1 CTTTTACAACATAGGAAACTAAACCCAACGATTTATTT-C
* * *
3358950 TTTTTACAACATAGGAAAATAAATCCAACGATTTATTTC
1 CTTTTACAACATAGGAAACTAAACCCAACGATTTATTTC
** **
3358989 CTTTTACAAACA-AGGAAACTAAA-TTATATAATTTATTTC
1 CTTTTAC-AACATAGGAAACTAAACCCA-ACGATTTATTTC
* * **
3359028 CTTTT-CAAAATAGGAAATTAATTCCAACGATTTATTTC
1 CTTTTACAACATAGGAAACTAAACCCAACGATTTATTTC
3359066 CTTTTACA
1 CTTTTACA
3359074 TATTAGAATC
Statistics
Matches: 101, Mismatches: 18, Indels: 11
0.78 0.14 0.08
Matches are distributed among these distances:
37 3 0.03
38 26 0.26
39 35 0.35
40 37 0.37
ACGTcount: A:0.40, C:0.16, G:0.07, T:0.37
Consensus pattern (39 bp):
CTTTTACAACATAGGAAACTAAACCCAACGATTTATTTC
Found at i:3359005 original size:39 final size:40
Alignment explanation
Indices: 3358910--3359073 Score: 187
Period size: 39 Copynumber: 4.2 Consensus size: 40
3358900 TTTTTTTTTT
* *
3358910 CTTTTATAAA-ATAGGAAACTAAACCCAACGATTTATTTAC
1 CTTTTACAAACATAGGAAACTAAATCCAACGATTTATTT-C
* *
3358950 TTTTTAC-AACATAGGAAAATAAATCCAACGATTTATTTC
1 CTTTTACAAACATAGGAAACTAAATCCAACGATTTATTTC
* **
3358989 CTTTTACAAACA-AGGAAACTAAAT-TATATAATTTATTTC
1 CTTTTACAAACATAGGAAACTAAATCCA-ACGATTTATTTC
* *
3359028 CTTTT-CAAA-ATAGGAAATTAATTCCAACGATTTATTTC
1 CTTTTACAAACATAGGAAACTAAATCCAACGATTTATTTC
3359066 CTTTTACA
1 CTTTTACA
3359074 TATTAGAATC
Statistics
Matches: 104, Mismatches: 14, Indels: 13
0.79 0.11 0.10
Matches are distributed among these distances:
37 1 0.01
38 30 0.29
39 38 0.37
40 35 0.34
ACGTcount: A:0.40, C:0.16, G:0.07, T:0.37
Consensus pattern (40 bp):
CTTTTACAAACATAGGAAACTAAATCCAACGATTTATTTC
Found at i:3359143 original size:38 final size:38
Alignment explanation
Indices: 3359100--3359210 Score: 143
Period size: 39 Copynumber: 2.9 Consensus size: 38
3359090 GATTCTTAAG
*
3359100 AAAATAAATTTACTGATTTATTTCCTTTT-CAAAATAGA
1 AAAATAAATTTAC-AATTTATTTCCTTTTACAAAATAGA
* * *
3359138 AAAATAAATTTAACAATTTTTTTCCTTTTACAAACTAGG
1 AAAATAAATTT-ACAATTTATTTCCTTTTACAAAATAGA
*
3359177 AAAATAAATTCAACAATTTATTTCCTTTTACAAA
1 AAAATAAATT-TACAATTTATTTCCTTTTACAAA
3359211 CTAGGAACAT
Statistics
Matches: 64, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
38 24 0.38
39 40 0.62
ACGTcount: A:0.43, C:0.13, G:0.04, T:0.41
Consensus pattern (38 bp):
AAAATAAATTTACAATTTATTTCCTTTTACAAAATAGA
Found at i:3359192 original size:39 final size:39
Alignment explanation
Indices: 3359115--3359217 Score: 163
Period size: 39 Copynumber: 2.7 Consensus size: 39
3359105 AAATTTACTG
* * *
3359115 ATTTATTTCCTTTT-CAAAATAGAAAAATAAATTTAACA
1 ATTTATTTCCTTTTACAAACTAGGAAAATAAATTCAACA
*
3359153 ATTTTTTTCCTTTTACAAACTAGGAAAATAAATTCAACA
1 ATTTATTTCCTTTTACAAACTAGGAAAATAAATTCAACA
3359192 ATTTATTTCCTTTTACAAACTAGGAA
1 ATTTATTTCCTTTTACAAACTAGGAA
3359218 CATGATCAAA
Statistics
Matches: 59, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
38 13 0.22
39 46 0.78
ACGTcount: A:0.42, C:0.14, G:0.05, T:0.40
Consensus pattern (39 bp):
ATTTATTTCCTTTTACAAACTAGGAAAATAAATTCAACA
Found at i:3359484 original size:117 final size:117
Alignment explanation
Indices: 3359263--3359578 Score: 302
Period size: 117 Copynumber: 2.7 Consensus size: 117
3359253 AATAAAATTC
** * * * * * *
3359263 ATTTTCCTTAACAAA-ATAGAATCATTTAAGATTATCAAGAAAATAAATTTAATAATTTATTAAC
1 ATTTTCCTT-ACAAAGATAGAATCATCCAAGATTCTGAAGAAAATAAATTCAACAATCTATT--T
* * * *
3359327 TT-TTACAAA-ATAGAATCATTTAAGATTCTCAAGAAAATAAATTTAACAATTT-
63 TTCTTACAAAGTTAAAATCATATAAGATTCTCAAGAAAATAAATTCAACAATTTA
** ** * * * *
3359379 ATTTCTTTTTTTAATGATAGAATCATCCACGATTCTGAAGAAAATAAATTCGACAATTTATTTTT
1 ATTT-TCCTTACAAAGATAGAATCATCCAAGATTCTGAAGAAAATAAATTCAACAATCTATTTTT
3359444 CTTACAAAGTTAAAATCATATAAGATT-TCCAATG-AAATAAATTCAACAATTTA
65 CTTACAAAGTTAAAATCATATAAGATTCT-CAA-GAAAATAAATTCAACAATTTA
* ** * *
3359497 ATTTTCCTTACAAAGTTAGAATCATTTAAGATTCTTAAGGAAATAAATTCAACAATCTATTTTTC
1 ATTTTCCTTACAAAGATAGAATCATCCAAGATTCTGAAGAAAATAAATTCAACAATCTATTTTTC
*
3359562 TTACAAAGTTAGAATCA
66 TTACAAAGTTAAAATCA
3359579 ATGCAAGATT
Statistics
Matches: 161, Mismatches: 32, Indels: 13
0.78 0.16 0.06
Matches are distributed among these distances:
115 2 0.01
116 14 0.09
117 140 0.87
118 5 0.03
ACGTcount: A:0.44, C:0.12, G:0.07, T:0.38
Consensus pattern (117 bp):
ATTTTCCTTACAAAGATAGAATCATCCAAGATTCTGAAGAAAATAAATTCAACAATCTATTTTTC
TTACAAAGTTAAAATCATATAAGATTCTCAAGAAAATAAATTCAACAATTTA
Found at i:3359487 original size:58 final size:58
Alignment explanation
Indices: 3359279--3359578 Score: 291
Period size: 58 Copynumber: 5.1 Consensus size: 58
3359269 CTTAACAAAA
* * * * * * *
3359279 TAGAATCATTTAAGATTATCAAGAAAATAAATTTAATAATTTATTAACTT-TTACAAA-A
1 TAGAATCATATAAGATTCTCAAGGAAATAAATTCAACAATTTATT--TTTCTTACAAAGT
* * * * ** * *
3359337 TAGAATCATTTAAGATTCTCAAGAAAATAAATTTAACAATTTATTTCTTTTTTTAATGA
1 TAGAATCATATAAGATTCTCAAGGAAATAAATTCAACAATTTATTT-TTCTTACAAAGT
** * * * *
3359396 TAGAATCATCCACGATTCTGAAGAAAATAAATTCGACAATTTATTTTTCTTACAAAGT
1 TAGAATCATATAAGATTCTCAAGGAAATAAATTCAACAATTTATTTTTCTTACAAAGT
* * *
3359454 TAAAATCATATAAGATT-TCCAATGAAATAAATTCAACAATTTAATTTTCCTTACAAAGT
1 TAGAATCATATAAGATTCT-CAAGGAAATAAATTCAACAATTT-ATTTTTCTTACAAAGT
* * *
3359513 TAGAATCATTTAAGATTCTTAAGGAAATAAATTCAACAATCTATTTTTCTTACAAAGT
1 TAGAATCATATAAGATTCTCAAGGAAATAAATTCAACAATTTATTTTTCTTACAAAGT
3359571 TAGAATCA
1 TAGAATCA
3359579 ATGCAAGATT
Statistics
Matches: 204, Mismatches: 32, Indels: 12
0.82 0.13 0.05
Matches are distributed among these distances:
57 3 0.01
58 109 0.53
59 91 0.45
60 1 0.00
ACGTcount: A:0.44, C:0.11, G:0.07, T:0.38
Consensus pattern (58 bp):
TAGAATCATATAAGATTCTCAAGGAAATAAATTCAACAATTTATTTTTCTTACAAAGT
Found at i:3359765 original size:39 final size:40
Alignment explanation
Indices: 3359709--3359822 Score: 140
Period size: 45 Copynumber: 2.8 Consensus size: 40
3359699 ACAAACAAAA
* *
3359709 AATCAAAAGGAATTAATCCTTTAATTTTAC-CAACCCAAT
1 AATCAAAAGGAATTAATCCTTTGATTTTACGCAACCCAAC
* *
3359748 AATCAAAAGGAACTAATCCTTTGATTTTAATTTTCGCAATCCAAC
1 AATCAAAAGGAATTAATCCTTTGATTTT-A----CGCAACCCAAC
3359793 AATCAAAAGGAATTAATCCTTTGATTTTAC
1 AATCAAAAGGAATTAATCCTTTGATTTTAC
3359823 TTTTGATAAT
Statistics
Matches: 64, Mismatches: 5, Indels: 11
0.80 0.06 0.14
Matches are distributed among these distances:
39 26 0.41
40 2 0.03
44 2 0.03
45 34 0.53
ACGTcount: A:0.40, C:0.18, G:0.08, T:0.33
Consensus pattern (40 bp):
AATCAAAAGGAATTAATCCTTTGATTTTACGCAACCCAAC
Found at i:3359779 original size:45 final size:45
Alignment explanation
Indices: 3359728--3359846 Score: 161
Period size: 45 Copynumber: 2.6 Consensus size: 45
3359718 GAATTAATCC
*
3359728 TTTAATTTTACCAACCCAATAATCAAAAGGAACTAATCCTTTGAT
1 TTTAATTTTACCAATCCAATAATCAAAAGGAACTAATCCTTTGAT
* *
3359773 TTTAATTTT-CGCAATCCAACAATCAAAAGGAATTAATCCTTTGAT
1 TTTAATTTTAC-CAATCCAATAATCAAAAGGAACTAATCCTTTGAT
* *
3359818 TTTACTTTTGA-TAATCCAATAATCAAAAG
1 TTTAATTTT-ACCAATCCAATAATCAAAAG
3359847 CCTTGGATTA
Statistics
Matches: 65, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
44 1 0.02
45 64 0.98
ACGTcount: A:0.39, C:0.18, G:0.08, T:0.35
Consensus pattern (45 bp):
TTTAATTTTACCAATCCAATAATCAAAAGGAACTAATCCTTTGAT
Found at i:3360064 original size:14 final size:15
Alignment explanation
Indices: 3360045--3360077 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
3360035 GTTATATGGT
3360045 AATAATACCAT-AAC
1 AATAATACCATGAAC
*
3360059 AATAATATCATGAAC
1 AATAATACCATGAAC
3360074 AATA
1 AATA
3360078 TCATGATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.58, C:0.15, G:0.03, T:0.24
Consensus pattern (15 bp):
AATAATACCATGAAC
Found at i:3362137 original size:20 final size:20
Alignment explanation
Indices: 3362112--3362151 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
3362102 AGTTTGATGG
3362112 TCAAAGTATAAATTTAGAAA
1 TCAAAGTATAAATTTAGAAA
*
3362132 TCAAAGTATAAATTTGGAAA
1 TCAAAGTATAAATTTAGAAA
3362152 AGTTTAAGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.53, C:0.05, G:0.12, T:0.30
Consensus pattern (20 bp):
TCAAAGTATAAATTTAGAAA
Found at i:3367077 original size:21 final size:21
Alignment explanation
Indices: 3367051--3367096 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
3367041 TGTGAAAGAC
*
3367051 TAAGACTTCCCCGGATGGTGA
1 TAAGACTTCCCCAGATGGTGA
3367072 TAAGACTTCCCCAGATGGTGA
1 TAAGACTTCCCCAGATGGTGA
3367093 -AAGA
1 TAAGA
3367097 TAACCCAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 4 0.17
21 20 0.83
ACGTcount: A:0.30, C:0.22, G:0.26, T:0.22
Consensus pattern (21 bp):
TAAGACTTCCCCAGATGGTGA
Done.