Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003626.1 Hibiscus syriacus cultivar Beakdansim tig00007672_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: 55488
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Found at i:1660 original size:3 final size:3
Alignment explanation
Indices: 1652--1686 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
1642 TGTTAGGATA
1652 AAT AAT AAT AAT AAT AAT AA- AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1687 GGATGAATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2869 original size:226 final size:222
Alignment explanation
Indices: 2466--2906 Score: 717
Period size: 226 Copynumber: 2.0 Consensus size: 222
2456 GTAAATTATC
* * *
2466 TATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTAATCTTTAGTTA
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTAATATTTAGTTA
*
2531 ATATTGTTAAATTTAAAATCTAAATAATATTTTATAAATATCAAAACAATCAAATAATTTTTGTG
66 ATATTGTTAAATTTAAAATCTAAATAATATTTTATAAATATCAAAACAATCAAATAAATTTTGTG
*
2596 TAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAAC
131 TAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAAAAAATTGAAA-
2661 ATAAATTACATAACTTTCAAAAAAGTATA
195 ATAAATTACATAACTTT-AAAAAAGTATA
*
2690 TATCATTTTTATAAAAGTGTCCATAC-T-TTTCACTGTTGAAAACATATTTATTATTATATTTGG
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTATTA--ATATTTAG
*
2753 TTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATC-AAACAATCAAATAAAATT
63 TTAATATTGTTAAATTTAAAATCTAAATAATATTTTAT-AAATATCAAAACAATCAAAT-AAATT
* *
2817 TTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAATAAATT
126 TTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAAAAAATT
2882 GAAAATAAATTACATAACTTTAAAA
191 GAAAATAAATTACATAACTTTAAAA
2907 GCAGTTTTAA
Statistics
Matches: 203, Mismatches: 9, Indels: 10
0.91 0.04 0.05
Matches are distributed among these distances:
222 8 0.04
223 17 0.08
224 29 0.14
225 72 0.35
226 77 0.38
ACGTcount: A:0.46, C:0.08, G:0.07, T:0.39
Consensus pattern (222 bp):
TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTAATATTTAGTTA
ATATTGTTAAATTTAAAATCTAAATAATATTTTATAAATATCAAAACAATCAAATAAATTTTGTG
TAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAAAAAATTGAAAA
TAAATTACATAACTTTAAAAAAGTATA
Found at i:3157 original size:20 final size:18
Alignment explanation
Indices: 3134--3179 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 18
3124 CGATATAACA
3134 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAA-C
*
3154 GGTATCAAAATGATAAAAC
1 GGTA-AAAAATGATAAAAC
3173 GGTAAAA
1 GGTAAAA
3180 TGATACCGGA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
18 2 0.09
19 5 0.22
20 13 0.57
21 3 0.13
ACGTcount: A:0.54, C:0.09, G:0.17, T:0.20
Consensus pattern (18 bp):
GGTAAAAAATGATAAAAC
Found at i:5506 original size:33 final size:33
Alignment explanation
Indices: 5464--5529 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
5454 AAATAGAAGG
*
5464 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
***
5497 AGTGGTGAAAGAAGTTTCGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
5530 TATTAGATGG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.29, C:0.02, G:0.45, T:0.24
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:7357 original size:19 final size:19
Alignment explanation
Indices: 7313--7356 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
7303 AATGTCGAGT
7313 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
7332 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
7351 T-ATTTT
1 TAATTTT
7357 TTATGTGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 5 0.21
19 19 0.79
ACGTcount: A:0.32, C:0.02, G:0.09, T:0.57
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:8001 original size:198 final size:199
Alignment explanation
Indices: 7436--8649 Score: 2248
Period size: 197 Copynumber: 6.1 Consensus size: 199
7426 TTAAGGGTCA
*
7436 TGTCGATACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATT-AAAACAAGGTGCATC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCATC
7500 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
7565 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
7630 AATG
196 AATG
7634 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCATC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCATC
7699 AATAAAGTGTCGATCC--ATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
7762 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
7827 AATG
196 AATG
*
7831 TGTCGACACTAATATACTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCATC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCATC
7896 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCC-AAAGTATAATG
66 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
* * *
7960 TAATATGTAATTTTTCAATCTAACCGGTACAATAATACCGGTTTTATGAGAGAATATGTCTAAAT
131 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
8025 AATG
196 AATG
8029 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCATC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCATC
8094 AATAAAGTGTCGATCC--ATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
8157 TAATATGTAA-TTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
8221 AATG
196 AATG
*
8225 TGTCGACACTAATATAGTTTGTGTCGATATTTTCTTTCCAGAATGAATTAAAAACAAGGTGCATC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCATC
8290 AATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
8354 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGG-TTTATGAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
8418 AATG
196 AATG
* *
8422 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCATC
*
8487 CATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
* * *
8552 TAATATGTAATTTTTCAATCTAACCGGTACAATAATACCGGTTTTATGAGAGAATATGTCTAAAT
131 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
8617 AATG
196 AATG
*
8621 TGTCGACACTAATATATTTTGTGTCGATA
1 TGTCGACACTAATATAGTTTGTGTCGATA
8650 CTAATTTAAA
Statistics
Matches: 989, Mismatches: 18, Indels: 17
0.97 0.02 0.02
Matches are distributed among these distances:
196 170 0.17
197 379 0.38
198 320 0.32
199 120 0.12
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (199 bp):
TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCATC
AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
AATG
Found at i:8511 original size:395 final size:395
Alignment explanation
Indices: 7436--8649 Score: 2256
Period size: 395 Copynumber: 3.1 Consensus size: 395
7426 TTAAGGGTCA
*
7436 TGTCGATACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATT-AAAACAAGGTGCATC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCATC
7500 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
7565 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
7630 AATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTG
196 AATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTG
7695 CATCAATAAAGTGTCGATCCATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAA
261 CATCAATAAAGTGTCGATCCATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAA
7760 TGTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAA
326 TGTAATATGTAA-TTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAA
7825 ATAATG
390 ATAATG
*
7831 TGTCGACACTAATATACTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCATC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCATC
7896 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCC-AAAGTATAATG
66 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
* * *
7960 TAATATGTAATTTTTCAATCTAACCGGTACAATAATACCGGTTTTATGAGAGAATATGTCTAAAT
131 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
8025 AATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTG
196 AATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTG
8090 CATCAATAAAGTGTCGATCCATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAA
261 CATCAATAAAGTGTCGATCCATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAA
8155 TGTAATATGTAATTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
326 TGTAATATGTAATTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
8220 TAATG
391 TAATG
*
8225 TGTCGACACTAATATAGTTTGTGTCGATATTTTCTTTCCAGAATGAATTAAAAACAAGGTGCATC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCATC
8290 AATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
8354 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGG-TTTATGAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
*
8418 AATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTG
196 AATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTG
* *
8483 CACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTAT
261 CATCAATAAAGTGTCGATCC--ATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTAT
* *
8548 AATGTAATATGTAATTTTTCAATCTAACCGGTACAATAATACCGGTTTTATGAGAGAATATGTCT
324 AATGTAATATGTAATTTTT-AATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCT
8613 AAATAATG
388 AAATAATG
*
8621 TGTCGACACTAATATATTTTGTGTCGATA
1 TGTCGACACTAATATAGTTTGTGTCGATA
8650 CTAATTTAAA
Statistics
Matches: 798, Mismatches: 16, Indels: 9
0.97 0.02 0.01
Matches are distributed among these distances:
393 134 0.17
394 193 0.24
395 324 0.41
396 147 0.18
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (395 bp):
TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCATC
AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
AATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTG
CATCAATAAAGTGTCGATCCATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAA
TGTAATATGTAATTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
TAATG
Found at i:10134 original size:18 final size:18
Alignment explanation
Indices: 10111--10178 Score: 55
Period size: 21 Copynumber: 3.4 Consensus size: 18
10101 ATCGGTCGCA
10111 GAAGATGAAGCTGACGAT
1 GAAGATGAAGCTGACGAT
* *
10129 GAAGATGACGATGATGATGAT
1 GAAGATGA--A-GCTGACGAT
*
10150 GATGACGATGAAGCTGGCGAT
1 GA--A-GATGAAGCTGACGAT
10171 GAAGATGA
1 GAAGATGA
10179 TGACGATGAT
Statistics
Matches: 39, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
18 13 0.33
19 1 0.03
20 1 0.03
21 17 0.44
22 1 0.03
23 1 0.03
24 5 0.13
ACGTcount: A:0.37, C:0.09, G:0.35, T:0.19
Consensus pattern (18 bp):
GAAGATGAAGCTGACGAT
Found at i:10135 original size:6 final size:6
Alignment explanation
Indices: 10111--10208 Score: 70
Period size: 6 Copynumber: 16.3 Consensus size: 6
10101 ATCGGTCGCA
* * * * * *
10111 GAAGAT GAAGCT GACGAT GAAGAT GACGAT GATGAT GATGAT GACGAT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
* ** * * * * *
10159 GAAGCT GGCGAT GAAGAT GATGAC GATGAT GATGAT GATGAT GAAGAT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
10207 GA
1 GA
10209 TGATCCAAAC
Statistics
Matches: 74, Mismatches: 18, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
6 74 1.00
ACGTcount: A:0.37, C:0.07, G:0.35, T:0.21
Consensus pattern (6 bp):
GAAGAT
Found at i:10146 original size:3 final size:3
Alignment explanation
Indices: 10126--10212 Score: 84
Period size: 3 Copynumber: 29.0 Consensus size: 3
10116 TGAAGCTGAC
* * * * * ** *
10126 GAT GAA GAT GAC GAT GAT GAT GAT GAT GAC GAT GAA GCT GGC GAT GAA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
* *
10174 GAT GAT GAC GAT GAT GAT GAT GAT GAT GAA GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
10213 CCAAACAAGT
Statistics
Matches: 65, Mismatches: 19, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.36, C:0.06, G:0.34, T:0.24
Consensus pattern (3 bp):
GAT
Found at i:10161 original size:42 final size:42
Alignment explanation
Indices: 10114--10204 Score: 146
Period size: 42 Copynumber: 2.2 Consensus size: 42
10104 GGTCGCAGAA
*
10114 GATGAAGCTGACGATGAAGATGACGATGATGATGATGATGAC
1 GATGAAGCTGACGATGAAGATGACGACGATGATGATGATGAC
* * *
10156 GATGAAGCTGGCGATGAAGATGATGACGATGATGATGATGAT
1 GATGAAGCTGACGATGAAGATGACGACGATGATGATGATGAC
10198 GATGAAG
1 GATGAAG
10205 ATGATGATCC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.35, C:0.08, G:0.35, T:0.22
Consensus pattern (42 bp):
GATGAAGCTGACGATGAAGATGACGACGATGATGATGATGAC
Found at i:10212 original size:18 final size:18
Alignment explanation
Indices: 10111--10208 Score: 88
Period size: 18 Copynumber: 5.4 Consensus size: 18
10101 ATCGGTCGCA
* *
10111 GAAGATGAAGCTGACGAT
1 GAAGATGAAGATGATGAT
*
10129 GAAGATGACGATGATGAT
1 GAAGATGAAGATGATGAT
* * * *
10147 GATGATGACGATGAAGCT
1 GAAGATGAAGATGATGAT
** *
10165 GGCGATGAAGATGATGAC
1 GAAGATGAAGATGATGAT
* *
10183 GATGATGATGATGATGAT
1 GAAGATGAAGATGATGAT
10201 GAAGATGA
1 GAAGATGA
10209 TGATCCAAAC
Statistics
Matches: 63, Mismatches: 17, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 63 1.00
ACGTcount: A:0.37, C:0.07, G:0.35, T:0.21
Consensus pattern (18 bp):
GAAGATGAAGATGATGAT
Found at i:12009 original size:184 final size:182
Alignment explanation
Indices: 11677--12026 Score: 664
Period size: 184 Copynumber: 1.9 Consensus size: 182
11667 CTTTCAACAT
11677 ATTATAATAAATAGATATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATAGG
1 ATTATAATAAATAGATATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATAGG
11742 TCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAA
66 TCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAA
11807 TGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
131 TGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
*
11859 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAAT-AAATAGAT-ATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
11924 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
64 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
*
11989 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTA
129 AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTA
12027 AGATATTAAT
Statistics
Matches: 164, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
182 8 0.05
183 7 0.04
184 149 0.91
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (182 bp):
ATTATAATAAATAGATATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATAGG
TCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAA
TGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
Found at i:12327 original size:23 final size:23
Alignment explanation
Indices: 12296--12358 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
12286 ATAGGTAAAC
*
12296 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
12319 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
12342 ATATAATGTAATAGGTA
1 ATATAATGTAATAGGTA
12359 ATGGTTATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.37, C:0.06, G:0.19, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:12366 original size:23 final size:23
Alignment explanation
Indices: 12296--12368 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
12286 ATAGGTAAAC
* * **
12296 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTATCGGTT
*
12319 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTATCGGTT
12342 ATATAATGTAATAGGTAAT-GGTT
1 ATATAATGTAATAGGT-ATCGGTT
12365 ATAT
1 ATAT
12369 TGTAAAGTGT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
23 42 0.95
24 2 0.05
ACGTcount: A:0.36, C:0.05, G:0.19, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTATCGGTT
Found at i:12785 original size:23 final size:23
Alignment explanation
Indices: 12722--12786 Score: 94
Period size: 23 Copynumber: 2.8 Consensus size: 23
12712 ATAGGTAAAC
* *
12722 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTATCCCTT
**
12745 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTATCCCTT
12768 ATATAATGTAATAGGTATC
1 ATATAATGTAATAGGTATC
12787 TATCTCGCAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.35, C:0.08, G:0.18, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTATCCCTT
Found at i:13010 original size:18 final size:18
Alignment explanation
Indices: 12989--13025 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
12979 GTAATTGGAG
12989 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
13007 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
13025 T
1 T
13026 ATATATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:13033 original size:24 final size:24
Alignment explanation
Indices: 12981--13027 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
12971 TTTCATATGT
* *
12981 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATC
*
13005 AATTTGAGTTTGAATTTCAATAT
1 AATTTGAGTTTGAATTTAAATAT
13028 ATATTTCGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATC
Found at i:19297 original size:18 final size:18
Alignment explanation
Indices: 19274--19313 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
19264 TAAAAATAAG
19274 AATAATTCCAATGTTGTC
1 AATAATTCCAATGTTGTC
19292 AATAATTCCAATGTTGTC
1 AATAATTCCAATGTTGTC
19310 AATA
1 AATA
19314 CTATAGATTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.38
Consensus pattern (18 bp):
AATAATTCCAATGTTGTC
Found at i:23070 original size:21 final size:20
Alignment explanation
Indices: 23032--23070 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
23022 TAATTAGGTT
*
23032 AATTAACTGATTTCGAACCA
1 AATTAACTGATATCGAACCA
23052 AATTAACTGATAATCGAAC
1 AATTAACTGAT-ATCGAAC
23071 TTTGAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.44, C:0.18, G:0.10, T:0.28
Consensus pattern (20 bp):
AATTAACTGATATCGAACCA
Found at i:29718 original size:814 final size:814
Alignment explanation
Indices: 28150--30600 Score: 4811
Period size: 814 Copynumber: 3.0 Consensus size: 814
28140 AAATTGAAGA
28150 CAAAATATGAGTATCATATGAAACTAAAAGAAATGGTGACAAACACAATCTCATGATAAAAATTT
1 CAAAATATGAGTATCATATGAAACTAAAAGAAATGGTGACAAACACAATCTCATGATAAAAATTT
28215 GTAACTTCAAACGAATAACACCAACACATACTGGAAGGAATTTTGATGATTTCTTCATAAAAGCT
66 GTAACTTCAAACGAATAACACCAACACATACTGGAAGGAATTTTGATGATTTCTTCATAAAAGCT
*
28280 AATGTACTACCAAGACAACCTGATCGCTGTCAAGAGCAAATGTAATTGTATCTTAGCCCAGAAAG
131 AATGTACTGCCAAGACAACCTGATCGCTGTCAAGAGCAAATGTAATTGTATCTTAGCCCAGAAAG
28345 CATTTTAAGAGAGAAAAACAAAGTTAAAGTGCCAGGTAGAAAATTCCGAGCACAACCAAATATGT
196 CATTTTAAGAGAGAAAAACAAAGTTAAAGTGCCAGGTAGAAAATTCCGAGCACAACCAAATATGT
28410 TTTAGAATGGATGTTTCAACAGTATGTAAAATGTTCTGAGTTGGAATACATTAATTACAGACCTG
261 TTTAGAATGGATGTTTCAACAGTATGTAAAATGTTCTGAGTTGGAATACATTAATTACAGACCTG
28475 AGCCAAAACCCATCCAACTAACCAATCGATATCACTTTTGTGATTGGATAAGACAAGGGCATGTT
326 AGCCAAAACCCATCCAACTAACCAATCGATATCACTTTTGTGATTGGATAAGACAAGGGCATGTT
28540 CCTTACCTGAAAAAAATCAACAATATCAGATGGAAAGTAAATGATTCAAAAGATTTAGGATAGAA
391 CCTTACCTGAAAAAAATCAACAATATCAGATGGAAAGTAAATGATTCAAAAGATTTAGGATAGAA
28605 CAATAGCCATTATCCATGTAACTCTAAGCCTAAGACCTAAGTTTCTTAGTAGAGGAAATTGACGT
456 CAATAGCCATTATCCATGTAACTCTAAGCCTAAGACCTAAGTTTCTTAGTAGAGGAAATTGACGT
28670 CACCCATAAAACTGAAGCTTTCATGGTCAGCAAAAACTTTAATCTGCAAATAAAATGTATCAAAG
521 CACCCATAAAACTGAAGCTTTCATGGTCAGCAAAAACTTTAATCTGCAAATAAAATGTATCAAAG
28735 ATCTAAAGTTAATTTTCAGGAGACAACTAAAGAAATGGCATTCATGGTACCGGTTCTTTTTCCAC
586 ATCTAAAGTTAATTTTCAGGAGACAACTAAAGAAATGGCATTCATGGTACCGGTTCTTTTTCCAC
28800 ATTAAAAAAGGTTGGCTCAATAAAAGTAAATAATTAACAACTTATTCATATAACACCTATCAGCC
651 ATTAAAAAAGGTTGGCTCAATAAAAGTAAATAATTAACAACTTATTCATATAACACCTATCAGCC
28865 CTTAGAGAAGATAGGAAACTTCACAACAACTGTTCAAATCATTATTTGCCTAAAATCTAGATGAA
716 CTTAGAGAAGATAGGAAACTTCACAACAACTGTTCAAATCATTATTTGCCTAAAATCTAGATGAA
28930 TTGACAATGCACCGATCTTTATGCCTCTGGACAC
781 TTGACAATGCACCGATCTTTATGCCTCTGGACAC
28964 CAAAATATGAGTATCATATGAAACTAAAAGAAATGGTGACAAACACAATCTCATGATAAAAATTT
1 CAAAATATGAGTATCATATGAAACTAAAAGAAATGGTGACAAACACAATCTCATGATAAAAATTT
29029 GTAACTTCAAACGAATAACACCAACACATACTGGAAGGAATTTTGATGATTTCTTCATAAAAGCT
66 GTAACTTCAAACGAATAACACCAACACATACTGGAAGGAATTTTGATGATTTCTTCATAAAAGCT
*
29094 AATGTACTGCCAAGACAACCTGATCGCTGTCAAGAGCATATGTAATTGTATCTTAGCCCAGAAAG
131 AATGTACTGCCAAGACAACCTGATCGCTGTCAAGAGCAAATGTAATTGTATCTTAGCCCAGAAAG
29159 CATTTTAAGAGAGAAAAACAAAGTTAAAGTGCCAGGTAGAAAATTCCGAGCACAACCAAATATGT
196 CATTTTAAGAGAGAAAAACAAAGTTAAAGTGCCAGGTAGAAAATTCCGAGCACAACCAAATATGT
29224 TTTAGAATGGATGTTTCAACAGTATGTAAAATGTTCTGAGTTGGAATACATTAATTACAGACCTG
261 TTTAGAATGGATGTTTCAACAGTATGTAAAATGTTCTGAGTTGGAATACATTAATTACAGACCTG
29289 AGCCAAAACCCATCCAACTAACCAATCGATATCACTTTTGTGATTGGATAAGACAAGGGCATGTT
326 AGCCAAAACCCATCCAACTAACCAATCGATATCACTTTTGTGATTGGATAAGACAAGGGCATGTT
29354 CCTTACCTGAAAAAAATCAACAATATCAGATGGAAAGTAAATGATTCAAAAGATTTAGGATAGAA
391 CCTTACCTGAAAAAAATCAACAATATCAGATGGAAAGTAAATGATTCAAAAGATTTAGGATAGAA
29419 CAATAGCCATTATCCATGTAACTCTAAGCCTAAGACCTAAGTTTCTTAGTAGAGGAAATTGACGT
456 CAATAGCCATTATCCATGTAACTCTAAGCCTAAGACCTAAGTTTCTTAGTAGAGGAAATTGACGT
29484 CACCCATAAAACTGAAGCTTTCATGGTCAGCAAAAACTTTAATCTGCAAATAAAATGTATCAAAG
521 CACCCATAAAACTGAAGCTTTCATGGTCAGCAAAAACTTTAATCTGCAAATAAAATGTATCAAAG
29549 ATCTAAAGTTAATTTTCAGGAGACAACTAAAGAAATGGCATTCATGGTACCGGTTCTTTTTCCAC
586 ATCTAAAGTTAATTTTCAGGAGACAACTAAAGAAATGGCATTCATGGTACCGGTTCTTTTTCCAC
29614 ATTAAAAAAGGTTGGCTCAATAAAAGTAAATAATTAACAACTTATTCATATAACACCTATCAGCC
651 ATTAAAAAAGGTTGGCTCAATAAAAGTAAATAATTAACAACTTATTCATATAACACCTATCAGCC
29679 CTTAGAGAAGATAGGAAACTTCACAACAACTGTTCAAATCATTA----CCTAAAATCTAGATGAA
716 CTTAGAGAAGATAGGAAACTTCACAACAACTGTTCAAATCATTATTTGCCTAAAATCTAGATGAA
29740 TTGACAATGCACCGATCTTTATGCCTCTGGACAC
781 TTGACAATGCACCGATCTTTATGCCTCTGGACAC
*
29774 CAAAATATGAGTATCATATGAAACTAAAAGAAATGGTGACAAACACAATCTCATGGTAAAAATTT
1 CAAAATATGAGTATCATATGAAACTAAAAGAAATGGTGACAAACACAATCTCATGATAAAAATTT
29839 GTAACTTCAAACGAATAACACCAACACATACTGGAAGGAATTTTGATGATTTCTTCATAAAAGCT
66 GTAACTTCAAACGAATAACACCAACACATACTGGAAGGAATTTTGATGATTTCTTCATAAAAGCT
29904 AATGTACTGCCAAGACAACCTGATCGCTGTCAAGAGCAAATGTAATTGTATCTTAGCCCAGAAAG
131 AATGTACTGCCAAGACAACCTGATCGCTGTCAAGAGCAAATGTAATTGTATCTTAGCCCAGAAAG
*
29969 CATTTTAAGAGAGAAAAACAAAGTTAAAGTGCCAGGTAGAAAATTCCGAGCACAACTAAATATGT
196 CATTTTAAGAGAGAAAAACAAAGTTAAAGTGCCAGGTAGAAAATTCCGAGCACAACCAAATATGT
30034 TTTAGAATGGATGTTTCAACAGTATGTAAAATGTTCTGAGTTGGAATACATTAATTACAGACCTG
261 TTTAGAATGGATGTTTCAACAGTATGTAAAATGTTCTGAGTTGGAATACATTAATTACAGACCTG
*
30099 AGCCAAAACCCATCCAACTAACCAATCAATATCACTTTTGTGATTGGATAAGACAAGGGCATGTT
326 AGCCAAAACCCATCCAACTAACCAATCGATATCACTTTTGTGATTGGATAAGACAAGGGCATGTT
30164 CCTTACCTGAAAAAAATCAACAATATCAGATGGAAAGTAAATGATTCAAAAGATTTAGGATAGAA
391 CCTTACCTGAAAAAAATCAACAATATCAGATGGAAAGTAAATGATTCAAAAGATTTAGGATAGAA
30229 CAATAGCCATTATCCATGTAACTCTAAGCCTAAGACCTAAGTTTCTTAGTAGAGGAAATTGACGT
456 CAATAGCCATTATCCATGTAACTCTAAGCCTAAGACCTAAGTTTCTTAGTAGAGGAAATTGACGT
30294 CACCCATAAAACTGAAGCTTTCATGGTCAGCAAAAACTTTAATCTGCAAATAAAATGTATCAAAG
521 CACCCATAAAACTGAAGCTTTCATGGTCAGCAAAAACTTTAATCTGCAAATAAAATGTATCAAAG
30359 ATCTAAAGTTAATTTTCAGGAGACAACTAAAGAAATGGCATTCATGGTACCGGTTCTTTTTCCAC
586 ATCTAAAGTTAATTTTCAGGAGACAACTAAAGAAATGGCATTCATGGTACCGGTTCTTTTTCCAC
*
30424 ATTAAAAAAGGTTGGCTCAATAAAAGTCAATAATTAACAACTTATTCATATAACACCTATCAGCC
651 ATTAAAAAAGGTTGGCTCAATAAAAGTAAATAATTAACAACTTATTCATATAACACCTATCAGCC
30489 CTTAGAGAAGATAGGAAACTTCACAACAACTGTTCAAATCATTATTTGCCTAAAATCTAGATGAA
716 CTTAGAGAAGATAGGAAACTTCACAACAACTGTTCAAATCATTATTTGCCTAAAATCTAGATGAA
30554 TTGACAATGCACCGATCTTTATGCCTCTGGACAC
781 TTGACAATGCACCGATCTTTATGCCTCTGGACAC
30588 CAAAAATATGAGT
1 C-AAAATATGAGT
30601 TGGGCAAACA
Statistics
Matches: 1625, Mismatches: 7, Indels: 9
0.99 0.00 0.01
Matches are distributed among these distances:
810 805 0.50
814 809 0.50
815 11 0.01
ACGTcount: A:0.40, C:0.18, G:0.16, T:0.27
Consensus pattern (814 bp):
CAAAATATGAGTATCATATGAAACTAAAAGAAATGGTGACAAACACAATCTCATGATAAAAATTT
GTAACTTCAAACGAATAACACCAACACATACTGGAAGGAATTTTGATGATTTCTTCATAAAAGCT
AATGTACTGCCAAGACAACCTGATCGCTGTCAAGAGCAAATGTAATTGTATCTTAGCCCAGAAAG
CATTTTAAGAGAGAAAAACAAAGTTAAAGTGCCAGGTAGAAAATTCCGAGCACAACCAAATATGT
TTTAGAATGGATGTTTCAACAGTATGTAAAATGTTCTGAGTTGGAATACATTAATTACAGACCTG
AGCCAAAACCCATCCAACTAACCAATCGATATCACTTTTGTGATTGGATAAGACAAGGGCATGTT
CCTTACCTGAAAAAAATCAACAATATCAGATGGAAAGTAAATGATTCAAAAGATTTAGGATAGAA
CAATAGCCATTATCCATGTAACTCTAAGCCTAAGACCTAAGTTTCTTAGTAGAGGAAATTGACGT
CACCCATAAAACTGAAGCTTTCATGGTCAGCAAAAACTTTAATCTGCAAATAAAATGTATCAAAG
ATCTAAAGTTAATTTTCAGGAGACAACTAAAGAAATGGCATTCATGGTACCGGTTCTTTTTCCAC
ATTAAAAAAGGTTGGCTCAATAAAAGTAAATAATTAACAACTTATTCATATAACACCTATCAGCC
CTTAGAGAAGATAGGAAACTTCACAACAACTGTTCAAATCATTATTTGCCTAAAATCTAGATGAA
TTGACAATGCACCGATCTTTATGCCTCTGGACAC
Found at i:31833 original size:2 final size:2
Alignment explanation
Indices: 31828--31857 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
31818 TATGCATTGT
31828 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
31858 GGGAGAAATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:32353 original size:10 final size:10
Alignment explanation
Indices: 32340--32365 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
32330 AAATTATATA
32340 AAATTAATGC
1 AAATTAATGC
32350 AAATTAATGC
1 AAATTAATGC
32360 AAATTA
1 AAATTA
32366 GTATTGACAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.54, C:0.08, G:0.08, T:0.31
Consensus pattern (10 bp):
AAATTAATGC
Found at i:34985 original size:23 final size:23
Alignment explanation
Indices: 34955--35001 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
34945 GATTTGGCTC
34955 AGAAATCCTGAAAAAAATGCTAA
1 AGAAATCCTGAAAAAAATGCTAA
34978 AGAAATCCTGAAAAAAATGCTAA
1 AGAAATCCTGAAAAAAATGCTAA
35001 A
1 A
35002 ACGGTCAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.57, C:0.13, G:0.13, T:0.17
Consensus pattern (23 bp):
AGAAATCCTGAAAAAAATGCTAA
Found at i:35612 original size:12 final size:11
Alignment explanation
Indices: 35536--35696 Score: 67
Period size: 10 Copynumber: 14.8 Consensus size: 11
35526 CAATTCGTGT
35536 TTTATTATTTTA
1 TTTATTA-TTTA
*
35548 ATT-TTATTTA
1 TTTATTATTTA
35558 TTTATTTATTTA
1 TTTA-TTATTTA
*
35570 TTTTAGTATTTAA
1 -TTTATTATTT-A
* *
35583 TATATTATGT-
1 TTTATTATTTA
35593 TTTATTATTTA
1 TTTATTATTTA
35604 TTGTATTATTTTA
1 TT-TATTA-TTTA
*
35617 TGGTA-TA-TTA
1 T-TTATTATTTA
* *
35627 TATA-TATATA
1 TTTATTATTTA
*
35637 TTCTATT-CTTA
1 TT-TATTATTTA
*
35648 -TTATTATTGA
1 TTTATTATTTA
35658 TTT-TT-TTTCA
1 TTTATTATTT-A
35668 TTT-TTCATTTA
1 TTTATT-ATTTA
35679 TTTATTA-TTA
1 TTTATTATTTA
35689 -TTATTATT
1 TTTATTATT
35697 ATTACTTTTT
Statistics
Matches: 114, Mismatches: 17, Indels: 38
0.67 0.10 0.22
Matches are distributed among these distances:
9 16 0.14
10 36 0.32
11 16 0.14
12 34 0.30
13 12 0.11
ACGTcount: A:0.27, C:0.02, G:0.04, T:0.67
Consensus pattern (11 bp):
TTTATTATTTA
Found at i:35996 original size:3 final size:3
Alignment explanation
Indices: 35988--36039 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
35978 TTACTTCCTT
35988 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
36036 TTA T
1 TTA T
36040 CTTTTAACAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:37043 original size:21 final size:22
Alignment explanation
Indices: 36998--37043 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
36988 ATCAATCCTT
*
36998 AACTTAAATAAAAATACATTCA
1 AACTGAAATAAAAATACATTCA
*
37020 AACTGAAATAAAAATA-ATTGA
1 AACTGAAATAAAAATACATTCA
37041 AAC
1 AAC
37044 AATTCTTAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 7 0.32
22 15 0.68
ACGTcount: A:0.61, C:0.11, G:0.04, T:0.24
Consensus pattern (22 bp):
AACTGAAATAAAAATACATTCA
Found at i:37245 original size:31 final size:32
Alignment explanation
Indices: 37207--37266 Score: 113
Period size: 31 Copynumber: 1.9 Consensus size: 32
37197 GAATTTTATA
37207 AGATAACAGTGTTGTGTCTATTTT-TAATGAT
1 AGATAACAGTGTTGTGTCTATTTTGTAATGAT
37238 AGATAACAGTGTTGTGTCTATTTTGTAAT
1 AGATAACAGTGTTGTGTCTATTTTGTAAT
37267 AAAATCTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 24 0.86
32 4 0.14
ACGTcount: A:0.28, C:0.07, G:0.20, T:0.45
Consensus pattern (32 bp):
AGATAACAGTGTTGTGTCTATTTTGTAATGAT
Found at i:40426 original size:21 final size:22
Alignment explanation
Indices: 40392--40434 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
40382 CATGCACAAA
*
40392 ATTGGATAAAAAACCGATCCGG
1 ATTGGATAAAAAACCGAACCGG
40414 ATTGGAT-AAAAACCGAACCGG
1 ATTGGATAAAAAACCGAACCGG
40435 TTTTTTCACT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.42, C:0.19, G:0.23, T:0.16
Consensus pattern (22 bp):
ATTGGATAAAAAACCGAACCGG
Found at i:40557 original size:17 final size:18
Alignment explanation
Indices: 40535--40576 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
40525 TTTTGGTTTG
*
40535 AAAAAAAA-CTAGTTTTT
1 AAAAAAAACCAAGTTTTT
*
40552 AAAAAAAACCAATTTTTT
1 AAAAAAAACCAAGTTTTT
40570 AAAAAAA
1 AAAAAAA
40577 TCGGATAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.62, C:0.07, G:0.02, T:0.29
Consensus pattern (18 bp):
AAAAAAAACCAAGTTTTT
Found at i:43334 original size:64 final size:66
Alignment explanation
Indices: 43220--43382 Score: 167
Period size: 64 Copynumber: 2.5 Consensus size: 66
43210 ATTGTTCAAG
* * * * *
43220 GTGTATCGATGCACATGAAGTGCATCGATGCA-CTCCTTTAAAATAAAAACATCGAAT-GCCA-T
1 GTGTATCGATGTACAAGTAGTGCATCGATGCACCCCCCTTAAAATAAAAACATCGAATAG-CATT
43282 CA
65 CA
* ** * *
43284 GTGTATCGATGTACAAGTAGTGCGTCGATGCACCCCCCTT-AAATGCAAACATCGAATAGGATTT
1 GTGTATCGATGTACAAGTAGTGCATCGATGCACCCCCCTTAAAATAAAAACATCGAATAGCATTC
43348 A
66 A
*
43349 -TGTATCGATGTA-TAGATAGTGCATCGATGCACCC
1 GTGTATCGATGTACAAG-TAGTGCATCGATGCACCC
43383 GTTAAGGGAT
Statistics
Matches: 83, Mismatches: 12, Indels: 8
0.81 0.12 0.08
Matches are distributed among these distances:
63 2 0.02
64 73 0.88
65 8 0.10
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.26
Consensus pattern (66 bp):
GTGTATCGATGTACAAGTAGTGCATCGATGCACCCCCCTTAAAATAAAAACATCGAATAGCATTC
A
Done.