Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007147.1 Hibiscus syriacus cultivar Beakdansim tig00018692_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: 109208
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:12238 original size:20 final size:20
Alignment explanation
Indices: 12201--12239 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
12191 AAGAGATTAA
*
12201 ATTGTAAAAATGGTAAATTT
1 ATTGTAAAAATAGTAAATTT
12221 ATTGTTAAAAATAG-AAATT
1 ATTG-TAAAAATAGTAAATT
12240 GGAGTTACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.49, C:0.00, G:0.13, T:0.38
Consensus pattern (20 bp):
ATTGTAAAAATAGTAAATTT
Found at i:17586 original size:60 final size:59
Alignment explanation
Indices: 17498--17609 Score: 154
Period size: 60 Copynumber: 1.9 Consensus size: 59
17488 TAGGACGAGG
* *
17498 GTCGTAGTTTTGGATAAAACTAGAATGTTTAAAAGTTTAGAAATTAATTTAAATTGAGA
1 GTCGTAGTTTGGGATAAAACTAGAATGTTTAAAACTTTAGAAATTAATTTAAATTGAGA
* * *
17557 GTCGTAGTTTGGAGATGAAACTCA-AATGTTTAAAACTTTGGAGATTAATTTAA
1 GTCGTAGTTTGG-GATAAAACT-AGAATGTTTAAAACTTTAGAAATTAATTTAA
17610 GATGAAGGTT
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
59 11 0.24
60 34 0.74
61 1 0.02
ACGTcount: A:0.38, C:0.05, G:0.20, T:0.37
Consensus pattern (59 bp):
GTCGTAGTTTGGGATAAAACTAGAATGTTTAAAACTTTAGAAATTAATTTAAATTGAGA
Found at i:17625 original size:60 final size:57
Alignment explanation
Indices: 17444--17627 Score: 142
Period size: 60 Copynumber: 3.1 Consensus size: 57
17434 GTATATATTG
* * * * * * *
17444 ATAGTTTAGAGATGAAATTGAAATGTTTAAAATTTG-GATCACTTTAGGACGAGGGTC
1 ATAGTTTGGAGATGAAACT-AAATGTTTAAAATTTGAGATTAATTTAAGATGAAGGTC
* * * *
17501 GTAGTTTTG-GATAAAACTAGAATGTTTAAAAGTTTAGAAATTAATTTAA-ATTG-AGAGTC
1 ATAGTTTGGAGATGAAACTA-AATGTTTAAAA-TTT-GAGATTAATTTAAGA-TGAAG-GTC
* *
17560 GTAGTTTGGAGATGAAACTCAAATGTTTAAAACTTTGGAGATTAATTTAAGATGAAGGTT
1 ATAGTTTGGAGATGAAACT-AAATGTTTAAAA-TTT-GAGATTAATTTAAGATGAAGGTC
17620 ATAGTTTG
1 ATAGTTTG
17628 AAAATCTGTG
Statistics
Matches: 100, Mismatches: 17, Indels: 17
0.75 0.13 0.13
Matches are distributed among these distances:
55 1 0.01
56 18 0.18
57 10 0.10
58 3 0.03
59 19 0.19
60 45 0.45
61 4 0.04
ACGTcount: A:0.37, C:0.05, G:0.22, T:0.36
Consensus pattern (57 bp):
ATAGTTTGGAGATGAAACTAAATGTTTAAAATTTGAGATTAATTTAAGATGAAGGTC
Found at i:20096 original size:2 final size:2
Alignment explanation
Indices: 20089--20119 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
20079 AAGAAAGAAG
20089 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
20120 TACAAGATCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:27232 original size:47 final size:48
Alignment explanation
Indices: 27173--27267 Score: 147
Period size: 48 Copynumber: 2.0 Consensus size: 48
27163 AAAAAAAGTC
* *
27173 ATATCATTGATATGTTTA-TTTTAGTTGATGAAATCTTAATTCGATTA
1 ATATCATTGATATGTTTACTTCTAATTGATGAAATCTTAATTCGATTA
* *
27220 ATATTATTGATATGTTTACTTCTAATTGATGGAATCTTAATTCGATTA
1 ATATCATTGATATGTTTACTTCTAATTGATGAAATCTTAATTCGATTA
27268 TTTTAGTTCG
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
47 17 0.40
48 26 0.60
ACGTcount: A:0.32, C:0.07, G:0.13, T:0.48
Consensus pattern (48 bp):
ATATCATTGATATGTTTACTTCTAATTGATGAAATCTTAATTCGATTA
Found at i:27711 original size:25 final size:25
Alignment explanation
Indices: 27663--27726 Score: 114
Period size: 25 Copynumber: 2.6 Consensus size: 25
27653 AAAAGTATGT
27663 ATGTAGGTATGTA-G-GCATGATGC
1 ATGTAGGTATGTAGGCGCATGATGC
27686 ATGTAGGTATGTAGGCGCATGATGC
1 ATGTAGGTATGTAGGCGCATGATGC
27711 ATGTAGGTATGTAGGC
1 ATGTAGGTATGTAGGC
27727 ATGAGATGTT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
23 13 0.33
24 1 0.03
25 25 0.64
ACGTcount: A:0.25, C:0.09, G:0.36, T:0.30
Consensus pattern (25 bp):
ATGTAGGTATGTAGGCGCATGATGC
Found at i:27734 original size:25 final size:25
Alignment explanation
Indices: 27663--27734 Score: 98
Period size: 25 Copynumber: 3.0 Consensus size: 25
27653 AAAAGTATGT
27663 ATGTAGGTATGTAGGCAT--GATGC
1 ATGTAGGTATGTAGGCATGAGATGC
27686 ATGTAGGTATGTAGGC--GCATGATGC
1 ATGTAGGTATGTAGGCATG-A-GATGC
27711 ATGTAGGTATGTAGGCATGAGATG
1 ATGTAGGTATGTAGGCATGAGATG
27735 TTATGAACCC
Statistics
Matches: 43, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
23 16 0.37
25 25 0.58
26 1 0.02
27 1 0.02
ACGTcount: A:0.26, C:0.08, G:0.36, T:0.29
Consensus pattern (25 bp):
ATGTAGGTATGTAGGCATGAGATGC
Found at i:40891 original size:38 final size:38
Alignment explanation
Indices: 40828--40905 Score: 113
Period size: 38 Copynumber: 2.1 Consensus size: 38
40818 TTTTCACCCT
40828 AAACCCGACCCGACCTGACCCGAATATCACACTTAAAA
1 AAACCCGACCCGACCTGACCCGAATATCACACTTAAAA
* * *
40866 AAACCCGACCTGA-CTCGACCTGAATATCGCACTTAAAA
1 AAACCCGACCCGACCT-GACCCGAATATCACACTTAAAA
40904 AA
1 AA
40906 TCTGACCCGA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 2 0.06
38 34 0.94
ACGTcount: A:0.40, C:0.33, G:0.12, T:0.15
Consensus pattern (38 bp):
AAACCCGACCCGACCTGACCCGAATATCACACTTAAAA
Found at i:41362 original size:196 final size:182
Alignment explanation
Indices: 40938--41385 Score: 458
Period size: 196 Copynumber: 2.4 Consensus size: 182
40928 AAAGTTTCAT
* *
40938 CCGACCTGACCCGAATATATGAATTAGAA--ATCCGACCCAAAATAATAAACAATTATTTTTATT
1 CCGACCTGACCCGAATATATGAATTAGAACCATCCGACCCGAAATAATAAAAAATTATTTTTATT
* * *
41001 TAAT-AAAATAGTGACTTAATCTGACCCGAATTATATATATTTTCGGGTCGATCCGATTTTTTTA
66 TAATAAAAACAGTGACTTAATCCGACCCGAATTATATATATTTTCGGGTCGATCCGATTTTTTCA
* *
41065 ACCCTAAACCCAAACCCGACCCTACCCAAATATCACACTTAAAAAACCCGAC
131 ACCATAAACCCAAACCCGACCCGACCCAAATATCACACTTAAAAAACCCGAC
* * * ** * ** *
41117 CCGTCCCGAACAAAATAAAGTTTCATCT-GAACCAACCCGACCCGAAATAATAAAAAATTATTTT
1 CCGACCTGACCCGAATATA--TGAAT-TAGAACC-ATCCGACCCGAAATAATAAAAAATTATTTT
41181 TATTTAATAAAAACAGTGACTTAATCCGACTCAACCTGAATTATATATATTTTCGGGTC-AGTCC
62 TATTTAATAAAAACAGTGACTTAATCCGA--C--CC-GAATTATATATATTTTCGGGTCGA-TCC
* * * * * *
41245 GGTTTTTTCCACCATAAACCCGACCCTGACCTGACCCGGCCCGAATATCACACTTAAAAAAACCC
121 GATTTTTTCAACCATAAACCC-A----AACCCGACCCGACCCAAATATCACACTT-AAAAAACCC
41310 GAC
180 GAC
*
41313 CCGAACTGACCCGAATATATGAATTAGAAACTCGATCCGACCCGAAATAATAAAAACA-TATTTT
1 CCGACCTGACCCGAATATATGAATTAG-AAC-C-ATCCGACCCGAAATAATAAAAA-ATTATTTT
*
41377 TATTCAATA
62 TATTTAATA
41386 TATGAATAAG
Statistics
Matches: 212, Mismatches: 34, Indels: 29
0.77 0.12 0.11
Matches are distributed among these distances:
179 13 0.06
181 6 0.03
182 1 0.00
184 35 0.17
185 18 0.08
187 1 0.00
189 3 0.01
190 42 0.20
191 1 0.00
193 1 0.00
194 4 0.02
195 26 0.12
196 60 0.28
197 1 0.00
ACGTcount: A:0.38, C:0.25, G:0.11, T:0.27
Consensus pattern (182 bp):
CCGACCTGACCCGAATATATGAATTAGAACCATCCGACCCGAAATAATAAAAAATTATTTTTATT
TAATAAAAACAGTGACTTAATCCGACCCGAATTATATATATTTTCGGGTCGATCCGATTTTTTCA
ACCATAAACCCAAACCCGACCCGACCCAAATATCACACTTAAAAAACCCGAC
Found at i:42347 original size:224 final size:225
Alignment explanation
Indices: 41949--42386 Score: 749
Period size: 224 Copynumber: 2.0 Consensus size: 225
41939 TATCTATCCT
* *
41949 TTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTAGTTAATAT
1 TTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGTTAATAT
**
42014 TGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGTA
66 TGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTTTGTGTA
42079 AATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACAT
131 AATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACAT
42144 AAATTACATAACTTTCAAAAAATATATATCA
196 AAATTACATAACTTT-AAAAAATATATATCA
* *
42175 TTTTATAAAAGTGTTCATACTTATTTCACTGTTGAAAACATA-TTATTATTATATTTGGTTAATA
1 TTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTATTATTATATTTAGTTAATA
42239 TTGTTAAATTT-AAATGCTAAATAATA-TTT-TAAAATATCAAAACAATCAAATAAAATTTTGTG
65 TTGTTAAATTTAAAAT-CTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTTTGTG
* *
42301 TAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAATTGAAAC
129 TAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAAC
42366 ATAAATTACATAACTTTAAAA
194 ATAAATTACATAACTTTAAAA
42387 GCAGTTTTAA
Statistics
Matches: 202, Mismatches: 8, Indels: 7
0.93 0.04 0.03
Matches are distributed among these distances:
223 4 0.02
224 111 0.55
225 7 0.03
226 71 0.35
227 9 0.04
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.39
Consensus pattern (225 bp):
TTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGTTAATAT
TGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTTTGTGTA
AATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACAT
AAATTACATAACTTTAAAAAATATATATCA
Found at i:42640 original size:19 final size:18
Alignment explanation
Indices: 42618--42663 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 18
42608 CGATATAACA
42618 GGTAAAATATGATAAAACC
1 GGTAAAATATGAT-AAACC
42637 GGTATCAAA-ATGATAAACC
1 GGTA--AAATATGATAAACC
42656 GGTAAAAT
1 GGTAAAAT
42664 GATACCGGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
17 3 0.12
19 13 0.54
20 5 0.21
21 3 0.12
ACGTcount: A:0.50, C:0.11, G:0.17, T:0.22
Consensus pattern (18 bp):
GGTAAAATATGATAAACC
Found at i:45007 original size:33 final size:33
Alignment explanation
Indices: 44965--45030 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
44955 AAATAGATGG
*
44965 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
***
44998 AGTGGTGAAAGAAGTTTCGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
45031 TATTAAGATG
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:46842 original size:19 final size:19
Alignment explanation
Indices: 46818--46866 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
46808 AATGTCGAGT
46818 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
46837 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
*
46856 TATTTTTGTAT
1 TAATTTTGTAT
46867 GTTAATATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.57
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:47734 original size:199 final size:198
Alignment explanation
Indices: 46985--48544 Score: 2855
Period size: 198 Copynumber: 7.9 Consensus size: 198
46975 CAATATGGCC
* * *
46985 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCAATCCCAAAAACATCGAAA
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCG-AA
*
47050 ACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAG
64 CCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAG
*
47115 AGGATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAA
129 AGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAA
**
47180 TTAAA
194 TGGAA
47185 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
47250 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
47315 AATATGTCTAAATAA--TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTT-CCAGAATGAAT
47378 GGAA
195 GGAA
47382 AACAAGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
*
47446 C-AAAGTATAATGTAATATGTAATTTTTCAATGTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
47510 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTCCAGAATGAAT
**
47575 TAAA
195 GGAA
47579 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
47644 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
*
47709 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTTTGTCGATATTTTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTT-CCAGAATGAAT
47774 GGAA
195 GGAA
47778 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
*
47843 CAAAAGTATAATGTAATATGTAATTTTTCAATGTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
*
47908 GATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATG
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATG
47973 GAA
196 GAA
*
47976 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
48041 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
*
48106 GATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATG
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATG
48171 GAA
196 GAA
*
48174 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
48239 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
*
48304 GATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATG
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATG
48369 G-A
196 GAA
*
48371 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
*
48436 CAAAAGTATAATGTAATATGTAATTTTTCAATGTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
48501 AATATGTCTAAATAA--TGTCGACACTAATATAGTTTGTGTCGATA
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA
48545 CTAATTTAAA
Statistics
Matches: 1332, Mismatches: 21, Indels: 19
0.97 0.02 0.01
Matches are distributed among these distances:
195 106 0.08
196 66 0.05
197 269 0.20
198 533 0.40
199 324 0.24
200 34 0.03
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (198 bp):
AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATG
GAA
Found at i:50017 original size:18 final size:18
Alignment explanation
Indices: 49996--50063 Score: 55
Period size: 21 Copynumber: 3.4 Consensus size: 18
49986 AGCGGTCGCA
49996 GAAGATGAAGCTGACGAT
1 GAAGATGAAGCTGACGAT
* *
50014 GAAGATGACGATGATGATGAT
1 GAAGATGA--A-GCTGACGAT
*
50035 GATGACGATGAAGCTGGCGAT
1 GA--A-GATGAAGCTGACGAT
50056 GAAGATGA
1 GAAGATGA
50064 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:50020 original size:6 final size:6
Alignment explanation
Indices: 49996--50093 Score: 70
Period size: 6 Copynumber: 16.3 Consensus size: 6
49986 AGCGGTCGCA
* * * * * *
49996 GAAGAT GAAGCT GACGAT GAAGAT GACGAT GATGAT GATGAT GACGAT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
* ** * * * * *
50044 GAAGCT GGCGAT GAAGAT GATGAC GATGAT GATGAT GATGAT GAAGAT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
50092 GA
1 GA
50094 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:50031 original size:3 final size:3
Alignment explanation
Indices: 50011--50097 Score: 84
Period size: 3 Copynumber: 29.0 Consensus size: 3
50001 TGAAGCTGAC
* * * * * ** *
50011 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
* *
50059 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
50098 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:50046 original size:42 final size:42
Alignment explanation
Indices: 49999--50089 Score: 146
Period size: 42 Copynumber: 2.2 Consensus size: 42
49989 GGTCGCAGAA
*
49999 GATGAAGCTGACGATGAAGATGACGATGATGATGATGATGAC
1 GATGAAGCTGACGATGAAGATGACGACGATGATGATGATGAC
* * *
50041 GATGAAGCTGGCGATGAAGATGATGACGATGATGATGATGAT
1 GATGAAGCTGACGATGAAGATGACGACGATGATGATGATGAC
50083 GATGAAG
1 GATGAAG
50090 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:50097 original size:18 final size:18
Alignment explanation
Indices: 49996--50093 Score: 88
Period size: 18 Copynumber: 5.4 Consensus size: 18
49986 AGCGGTCGCA
* *
49996 GAAGATGAAGCTGACGAT
1 GAAGATGAAGATGATGAT
*
50014 GAAGATGACGATGATGAT
1 GAAGATGAAGATGATGAT
* * * *
50032 GATGATGACGATGAAGCT
1 GAAGATGAAGATGATGAT
** *
50050 GGCGATGAAGATGATGAC
1 GAAGATGAAGATGATGAT
* *
50068 GATGATGATGATGATGAT
1 GAAGATGAAGATGATGAT
50086 GAAGATGA
1 GAAGATGA
50094 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:52214 original size:182 final size:183
Alignment explanation
Indices: 51577--52271 Score: 1265
Period size: 183 Copynumber: 3.8 Consensus size: 183
51567 ATTATAATAA
* * * * *
51577 AATAGGTAAATTTGCAATATAACCGGTATAAATATACC-GTCTTATGCGCGAATAGGTCTACAAC
1 AATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAAC
*
51641 CTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGA
66 CTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGA
51706 TACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATAAT-T-ATGT
131 TACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATAATATAATGT
51757 AATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAAC
1 AATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAAC
51822 CTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGA
66 CTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGA
51887 TACGATTT-AAAAAGTGTCGACATTTTACACATCGGAACCCATAATTATAATGT
131 TACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATAA-TATAATGT
51940 AATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAAC
1 AATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAAC
*
52005 CTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGA
66 CTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGA
52070 TACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATAATATAATGT
131 TACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATAATATAATGT
52123 AATAGATAA-TTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAAC
1 AATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAAC
*
52187 CTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCATATTGGAATAAAAATGTGTCGA
66 CTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGA
*
52252 TACCATTTAAAAAAGTGTCG
131 TACGATTTAAAAAAGTGTCG
52272 GTAATTTGAA
Statistics
Matches: 500, Mismatches: 10, Indels: 8
0.97 0.02 0.02
Matches are distributed among these distances:
180 71 0.14
181 97 0.19
182 138 0.28
183 158 0.32
184 36 0.07
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.34
Consensus pattern (183 bp):
AATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAAC
CTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGA
TACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATAATATAATGT
Found at i:54871 original size:23 final size:23
Alignment explanation
Indices: 54840--54903 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
54830 ATAGGTAAAC
*
54840 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
54863 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
54886 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
54904 TGGTTATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:54910 original size:23 final size:23
Alignment explanation
Indices: 54840--54912 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
54830 ATAGGTAAAC
* **
54840 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
*
54863 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
54886 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
54909 ATAT
1 ATAT
54913 TGTAAAGTGT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
23 42 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:55290 original size:23 final size:23
Alignment explanation
Indices: 55264--55327 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
55254 AATAGGTAAC
*
55264 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
55287 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
55310 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
55328 TGGTTATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:55334 original size:23 final size:23
Alignment explanation
Indices: 55264--55336 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
55254 AATAGGTAAC
* **
55264 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
*
55287 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
55310 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
55333 ATAT
1 ATAT
55337 TGTAAAGTGT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
23 42 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:55638 original size:25 final size:25
Alignment explanation
Indices: 55604--55654 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
55594 ACAACAAATC
*
55604 AATTAAACATTGTTGTGGGTACATT
1 AATTAAACATTGTTATGGGTACATT
*
55629 AATTGAACATTGTTATGGGTACATT
1 AATTAAACATTGTTATGGGTACATT
55654 A
1 A
55655 TTTGGATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.39
Consensus pattern (25 bp):
AATTAAACATTGTTATGGGTACATT
Found at i:55924 original size:18 final size:18
Alignment explanation
Indices: 55903--55937 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
55893 GTAATTGGAG
55903 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
55921 TTTGAGTTTGAATTTCA
1 TTTGAATTTAAATTTCA
55938 TATATATTTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.06, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:56240 original size:39 final size:39
Alignment explanation
Indices: 56197--56283 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 39
56187 TCCGATGCTC
*
56197 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
*
56236 ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
56275 ATCAAAATC
1 ATCAAAATC
56284 TACAACTTGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.48, C:0.21, G:0.14, T:0.17
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
Found at i:61551 original size:15 final size:15
Alignment explanation
Indices: 61531--61563 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
61521 TCCGTGATGC
61531 TGTCATTATAAATCT
1 TGTCATTATAAATCT
61546 TGTCATTATAAATCT
1 TGTCATTATAAATCT
61561 TGT
1 TGT
61564 AGCAGTAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.30, C:0.12, G:0.09, T:0.48
Consensus pattern (15 bp):
TGTCATTATAAATCT
Found at i:61986 original size:29 final size:29
Alignment explanation
Indices: 61935--62002 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 29
61925 TGTTGAGTCT
* * *
61935 TTCGAGTATTGAAAGTTATAAAATGATCA
1 TTCGAGTATTAAAAATTACAAAATGATCA
* *
61964 TTCGACTATTAAAAATTACAAAATGGTCA
1 TTCGAGTATTAAAAATTACAAAATGATCA
61993 TTCGAGTATT
1 TTCGAGTATT
62003 CATATGTTTC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (29 bp):
TTCGAGTATTAAAAATTACAAAATGATCA
Found at i:69589 original size:10 final size:10
Alignment explanation
Indices: 69574--69648 Score: 52
Period size: 10 Copynumber: 7.7 Consensus size: 10
69564 CATTTAATAA
69574 ATAAACGAAC
1 ATAAACGAAC
69584 ATAAACGAAC
1 ATAAACGAAC
*
69594 ----ACAAAC
1 ATAAACGAAC
69600 ATAAACGAAC
1 ATAAACGAAC
** *
69610 ACGAAC-ATAA
1 ATAAACGA-AC
69620 ATGAACACGAAC
1 AT-AA-ACGAAC
69632 ATAAACGAAC
1 ATAAACGAAC
69642 ATAAACG
1 ATAAACG
69649 TTGGAGACCC
Statistics
Matches: 49, Mismatches: 8, Indels: 16
0.67 0.11 0.22
Matches are distributed among these distances:
6 5 0.10
9 1 0.02
10 34 0.69
11 3 0.06
12 5 0.10
13 1 0.02
ACGTcount: A:0.59, C:0.21, G:0.11, T:0.09
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:69602 original size:16 final size:16
Alignment explanation
Indices: 69581--69647 Score: 98
Period size: 16 Copynumber: 4.2 Consensus size: 16
69571 TAAATAAACG
69581 AACATAAACGAACACA
1 AACATAAACGAACACA
*
69597 AACATAAACGAACACG
1 AACATAAACGAACACA
* *
69613 AACATAAATGAACACG
1 AACATAAACGAACACA
*
69629 AACATAAACGAACATA
1 AACATAAACGAACACA
69645 AAC
1 AAC
69648 GTTGGAGACC
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 46 1.00
ACGTcount: A:0.60, C:0.22, G:0.09, T:0.09
Consensus pattern (16 bp):
AACATAAACGAACACA
Found at i:69614 original size:32 final size:32
Alignment explanation
Indices: 69578--69642 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
69568 TAATAAATAA
69578 ACGAACATAAACGAACACAAACATAAACGAAC
1 ACGAACATAAACGAACACAAACATAAACGAAC
* *
69610 ACGAACATAAATGAACACGAACATAAACGAAC
1 ACGAACATAAACGAACACAAACATAAACGAAC
69642 A
1 A
69643 TAAACGTTGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.58, C:0.23, G:0.11, T:0.08
Consensus pattern (32 bp):
ACGAACATAAACGAACACAAACATAAACGAAC
Found at i:71196 original size:24 final size:24
Alignment explanation
Indices: 71159--71213 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 24
71149 TATTAGGTTA
*
71159 AACATAAATGAACGCACATAAACG
1 AACATAAATAAACGCACATAAACG
* *
71183 AACATAACTAAACGCATATAAACG
1 AACATAAATAAACGCACATAAACG
71207 AACATAA
1 AACATAA
71214 TCGAACGTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.56, C:0.20, G:0.09, T:0.15
Consensus pattern (24 bp):
AACATAAATAAACGCACATAAACG
Found at i:71220 original size:24 final size:24
Alignment explanation
Indices: 71159--71220 Score: 74
Period size: 24 Copynumber: 2.6 Consensus size: 24
71149 TATTAGGTTA
71159 AACATAAAT-GAACGCACATAAACG
1 AACAT-AATCGAACGCACATAAACG
* *
71183 AACATAA-CTAAACGCATATAAACG
1 AACATAATC-GAACGCACATAAACG
71207 AACATAATCGAACG
1 AACATAATCGAACG
71221 TTCACGAACG
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
23 2 0.06
24 29 0.91
25 1 0.03
ACGTcount: A:0.53, C:0.21, G:0.11, T:0.15
Consensus pattern (24 bp):
AACATAATCGAACGCACATAAACG
Found at i:71749 original size:9 final size:9
Alignment explanation
Indices: 71735--71759 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
71725 GCTCTCCGAA
71735 TGCGGCGGT
1 TGCGGCGGT
71744 TGCGGCGGT
1 TGCGGCGGT
71753 TGCGGCG
1 TGCGGCG
71760 CCCCGGAGCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.00, C:0.24, G:0.56, T:0.20
Consensus pattern (9 bp):
TGCGGCGGT
Found at i:76463 original size:179 final size:179
Alignment explanation
Indices: 76156--76519 Score: 613
Period size: 179 Copynumber: 2.0 Consensus size: 179
76146 AAAAATCATA
* *
76156 AAATGATCTTCGATCATAGGAAGTTGCTTTGTTGAGTCAATCGATTATAAGAAGTTACAAAATGG
1 AAATGATCTTCGATCATAGGAAGTTACTTTGTTGAGTCAATCAATTATAAGAAGTTACAAAATGG
* *
76221 TCACTCAACTATTTATTAGGTTCAAAACTCATTATTTTTCGTTAAAAAAATTAAAATAATCTGAA
66 TCACCCAACTATTTATTAGGTTCAAAACTCATTATTTTTCGTTAAAAAAATTAAAACAATCTGAA
* * *
76286 CTGTACATTAACGTGTTGACTGAGATATGATAAAATCTAATCTCATAAC
131 CTGGACATTAACATGTTGACTGAGATATGATAAAATCTAATCGCATAAC
*
76335 AAATGATCTTCGATCATAGGAAGTTACTTTGTTGAGTCCATCAATTATAAGAAGTTACAAAATGG
1 AAATGATCTTCGATCATAGGAAGTTACTTTGTTGAGTCAATCAATTATAAGAAGTTACAAAATGG
*
76400 TCACCCAACTATTTATTATGTTCAAAACTCATTATTTTTCGTT-AAAAAATTAAAAACAATCTGA
66 TCACCCAACTATTTATTAGGTTCAAAACTCATTATTTTTCGTTAAAAAAATT-AAAACAATCTGA
* *
76464 GCTGGACATTAACATGTTGGCTGAGATATGATAAAATCTAATCGCATAAC
130 ACTGGACATTAACATGTTGACTGAGATATGATAAAATCTAATCGCATAAC
76514 AAATGA
1 AAATGA
76520 CTATCATATC
Statistics
Matches: 173, Mismatches: 11, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
178 8 0.05
179 165 0.95
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.34
Consensus pattern (179 bp):
AAATGATCTTCGATCATAGGAAGTTACTTTGTTGAGTCAATCAATTATAAGAAGTTACAAAATGG
TCACCCAACTATTTATTAGGTTCAAAACTCATTATTTTTCGTTAAAAAAATTAAAACAATCTGAA
CTGGACATTAACATGTTGACTGAGATATGATAAAATCTAATCGCATAAC
Found at i:76646 original size:29 final size:29
Alignment explanation
Indices: 76604--76670 Score: 134
Period size: 29 Copynumber: 2.3 Consensus size: 29
76594 TAGAATATAA
76604 TTAATAGTCGAGTTAACATTTTGTAACTT
1 TTAATAGTCGAGTTAACATTTTGTAACTT
76633 TTAATAGTCGAGTTAACATTTTGTAACTT
1 TTAATAGTCGAGTTAACATTTTGTAACTT
76662 TTAATAGTC
1 TTAATAGTC
76671 AAGTGACTCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.31, C:0.10, G:0.13, T:0.45
Consensus pattern (29 bp):
TTAATAGTCGAGTTAACATTTTGTAACTT
Found at i:80560 original size:3 final size:3
Alignment explanation
Indices: 80554--80581 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
80544 CTATAATAAC
80554 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
80582 GCAGCGTAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:82487 original size:3 final size:3
Alignment explanation
Indices: 82479--82524 Score: 83
Period size: 3 Copynumber: 15.3 Consensus size: 3
82469 TATAGTACAT
*
82479 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA GTA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
82525 AAGACACACA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:87582 original size:22 final size:21
Alignment explanation
Indices: 87557--87601 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 21
87547 ATAATCACTA
87557 AATTTATCA-AACGGTTAAAAAT
1 AATTTATCACAA--GTTAAAAAT
87579 AA-TTATCACAAGTTAAAAAT
1 AATTTATCACAAGTTAAAAAT
87599 AAT
1 AAT
87602 AATATAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
20 11 0.52
21 6 0.29
22 4 0.19
ACGTcount: A:0.53, C:0.09, G:0.07, T:0.31
Consensus pattern (21 bp):
AATTTATCACAAGTTAAAAAT
Found at i:87705 original size:20 final size:22
Alignment explanation
Indices: 87680--87720 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
87670 TTAAAGTTTT
87680 AATAATA-AA-AAGTATTTTAA
1 AATAATATAATAAGTATTTTAA
*
87700 AATAATATAATAATTATTTTA
1 AATAATATAATAAGTATTTTA
87721 TCCTTCAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
21 2 0.11
22 9 0.50
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.41
Consensus pattern (22 bp):
AATAATATAATAAGTATTTTAA
Found at i:94272 original size:21 final size:22
Alignment explanation
Indices: 94237--94316 Score: 85
Period size: 21 Copynumber: 3.7 Consensus size: 22
94227 TTGGTGCAGA
94237 GGGAATCGA-TCCCCCCATGA-
1 GGGAATCGATTCCCCCCATGAG
**
94257 GGGAATCGATTCCCCCTTTGAAG
1 GGGAATCGATTCCCCCCATG-AG
* *
94280 GGGAACCGATTCCCCCCA-CAG
1 GGGAATCGATTCCCCCCATGAG
*
94301 GGGAATCGATGCCCCC
1 GGGAATCGATTCCCCC
94317 TGGGGTTCTG
Statistics
Matches: 49, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
20 9 0.18
21 24 0.49
22 1 0.02
23 15 0.31
ACGTcount: A:0.23, C:0.35, G:0.26, T:0.16
Consensus pattern (22 bp):
GGGAATCGATTCCCCCCATGAG
Found at i:98676 original size:2 final size:2
Alignment explanation
Indices: 98669--98710 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
98659 GAACACCAAA
98669 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
98711 TAAAATCTAG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:104703 original size:17 final size:16
Alignment explanation
Indices: 104660--104713 Score: 56
Period size: 17 Copynumber: 3.3 Consensus size: 16
104650 ATCTGCCATG
*
104660 TAATAATACAAACACAA
1 TAATAATA-AAATACAA
104677 TAATAATAAAAGTACAA
1 TAATAATAAAA-TACAA
**
104694 TAATCGTAAAATA-AA
1 TAATAATAAAATACAA
104709 TAATA
1 TAATA
104714 TATATATAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
15 6 0.19
16 5 0.16
17 21 0.66
ACGTcount: A:0.63, C:0.09, G:0.04, T:0.24
Consensus pattern (16 bp):
TAATAATAAAATACAA
Found at i:107133 original size:49 final size:51
Alignment explanation
Indices: 107062--107161 Score: 161
Period size: 49 Copynumber: 2.0 Consensus size: 51
107052 TAGGGCGGAT
107062 CAGGTACCGCGCTATACCTTTACTCCT-A-ATAATTTTATATAGCGCGGGG
1 CAGGTACCGCGCTATACCTTTACTCCTGACATAATTTTATATAGCGCGGGG
*
107111 CAGGTACCGCGAC-ATACTTTTACTCCTGACATAATTTTATATAGCGCGGGG
1 CAGGTACCGCG-CTATACCTTTACTCCTGACATAATTTTATATAGCGCGGGG
107162 TAAGTACCAC
Statistics
Matches: 47, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
49 24 0.51
50 2 0.04
51 21 0.45
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.30
Consensus pattern (51 bp):
CAGGTACCGCGCTATACCTTTACTCCTGACATAATTTTATATAGCGCGGGG
Found at i:107169 original size:51 final size:49
Alignment explanation
Indices: 107065--107169 Score: 149
Period size: 51 Copynumber: 2.1 Consensus size: 49
107055 GGCGGATCAG
*
107065 GTACCGCGCTATACCTTTACTCCTAATAATTTTATATAGCGCGGGGCAG
1 GTACCGCGCTATACCTTTACTCCTAATAATTTTATATAGCGCGGGGCAA
* *
107114 GTACCGCGAC-ATACTTTTACTCCTGACATAATTTTATATAGCGCGGGGTAA
1 GTACCGCG-CTATACCTTTACTCCT-A-ATAATTTTATATAGCGCGGGGCAA
107165 GTACC
1 GTACC
107170 ACGTTTTGTA
Statistics
Matches: 50, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
49 21 0.42
50 2 0.04
51 27 0.54
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (49 bp):
GTACCGCGCTATACCTTTACTCCTAATAATTTTATATAGCGCGGGGCAA
Found at i:108043 original size:10 final size:10
Alignment explanation
Indices: 108024--108053 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
108014 ACCTTAAAAA
*
108024 GAGAGTATTT
1 GAGAGAATTT
108034 GAGAGAATTT
1 GAGAGAATTT
108044 GAGAGAATTT
1 GAGAGAATTT
108054 AGTGTGATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.37, C:0.00, G:0.30, T:0.33
Consensus pattern (10 bp):
GAGAGAATTT
Found at i:108270 original size:51 final size:50
Alignment explanation
Indices: 108167--108391 Score: 213
Period size: 51 Copynumber: 4.5 Consensus size: 50
108157 GATATATAGA
* * * * *
108167 TATAGCGCGCTGCAGGGGCCGCGCTATACCCACGTGGCGCCGACTCACCG
1 TATAGCGCGGTGCAGGGGGCACGCTATACCCACGTGGCGCCAAATCACCG
* * * *
108217 TATAACGCGGTGCAGGGGACACGCTATATCCCACGTGGCGTCAAATCATCG
1 TATAGCGCGGTGCAGGGGGCACGCTATA-CCCACGTGGCGCCAAATCACCG
* * * * * ** * **
108268 TATAGTGCGATGTAGGGGGCGCGCTTTACTGA--TAAG-GCCAGCTCACCG
1 TATAGCGCGGTGCAGGGGGCACGCTATACCCACGT-GGCGCCAAATCACCG
*
108316 TATAGCGCGGTGCAGGGGGCACGCTATACCCCACGTGGCGCCAAATCATCG
1 TATAGCGCGGTGCAGGGGGCACGCTATA-CCCACGTGGCGCCAAATCACCG
*
108367 TATAGTGCGGTGCAGGGGGCACGCT
1 TATAGCGCGGTGCAGGGGGCACGCT
108392 TTACTGATAA
Statistics
Matches: 135, Mismatches: 34, Indels: 11
0.75 0.19 0.06
Matches are distributed among these distances:
48 32 0.24
49 3 0.02
50 27 0.20
51 73 0.54
ACGTcount: A:0.20, C:0.29, G:0.32, T:0.18
Consensus pattern (50 bp):
TATAGCGCGGTGCAGGGGGCACGCTATACCCACGTGGCGCCAAATCACCG
Found at i:108325 original size:99 final size:99
Alignment explanation
Indices: 108210--108403 Score: 325
Period size: 99 Copynumber: 2.0 Consensus size: 99
108200 GTGGCGCCGA
* *
108210 CTCACCGTATAACGCGGTGCAGGGGACACGCTATATCCCACGTGGCGTCAAATCATCGTATAGTG
1 CTCACCGTATAACGCGGTGCAGGGGACACGCTATACCCCACGTGGCGCCAAATCATCGTATAGTG
* *
108275 CGATGTAGGGGGCGCGCTTTACTGATAAGGCCAG
66 CGATGCAGGGGGCACGCTTTACTGATAAGGCCAG
* *
108309 CTCACCGTATAGCGCGGTGCAGGGGGCACGCTATACCCCACGTGGCGCCAAATCATCGTATAGTG
1 CTCACCGTATAACGCGGTGCAGGGGACACGCTATACCCCACGTGGCGCCAAATCATCGTATAGTG
*
108374 CGGTGCAGGGGGCACGCTTTACTGATAAGG
66 CGATGCAGGGGGCACGCTTTACTGATAAGG
108404 GTGTTAGATC
Statistics
Matches: 88, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
99 88 1.00
ACGTcount: A:0.22, C:0.26, G:0.31, T:0.20
Consensus pattern (99 bp):
CTCACCGTATAACGCGGTGCAGGGGACACGCTATACCCCACGTGGCGCCAAATCATCGTATAGTG
CGATGCAGGGGGCACGCTTTACTGATAAGGCCAG
Found at i:108577 original size:25 final size:27
Alignment explanation
Indices: 108545--108603 Score: 86
Period size: 27 Copynumber: 2.3 Consensus size: 27
108535 TTAATTAATT
108545 ATTTTATTAATAAT-AT-TCACTTAAA
1 ATTTTATTAATAATCATCTCACTTAAA
* *
108570 ATTTTATTAATATTCATCTCATTTAAA
1 ATTTTATTAATAATCATCTCACTTAAA
108597 ATTTTAT
1 ATTTTAT
108604 ACTATTAACC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 13 0.43
26 2 0.07
27 15 0.50
ACGTcount: A:0.39, C:0.08, G:0.00, T:0.53
Consensus pattern (27 bp):
ATTTTATTAATAATCATCTCACTTAAA
Found at i:108817 original size:10 final size:9
Alignment explanation
Indices: 108775--108815 Score: 50
Period size: 9 Copynumber: 4.8 Consensus size: 9
108765 GTTTTCTAAT
108775 TTTTTTTAA
1 TTTTTTTAA
108784 TTTTTTT-A
1 TTTTTTTAA
**
108792 -TAGTTTAA
1 TTTTTTTAA
108800 TTTTTTTAA
1 TTTTTTTAA
108809 TTTTTTT
1 TTTTTTT
108816 TATTGATAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
7 4 0.15
8 2 0.08
9 20 0.77
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (9 bp):
TTTTTTTAA
Done.