Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001027.1 Hibiscus syriacus cultivar Beakdansim tig00002046_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: 79076
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:6500 original size:30 final size:30
Alignment explanation
Indices: 6464--6520 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
6454 ATCTTACTTG
6464 CACTTCCATTTACCACATTC-AGGTTGCCTA
1 CACTTCCATTTACCACA-TCAAGGTTGCCTA
6494 CACTTCCATTTACCACATCAAGGTTGC
1 CACTTCCATTTACCACATCAAGGTTGC
6521 TTATGGCAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 2 0.08
30 24 0.92
ACGTcount: A:0.25, C:0.33, G:0.11, T:0.32
Consensus pattern (30 bp):
CACTTCCATTTACCACATCAAGGTTGCCTA
Found at i:17578 original size:227 final size:227
Alignment explanation
Indices: 17178--17624 Score: 790
Period size: 227 Copynumber: 2.0 Consensus size: 227
17168 GTAAATTATC
* * *
17178 TATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTAGT
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
**
17243 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
66 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTT
17308 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAA-AAATTG
131 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAATTG
17372 AAACATAAATTACATAACTTTCAAAAAAGTATA
196 AAACATAAATTACATAACTTT-AAAAAAGTATA
*
17405 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTATTATATTTGG
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTATTATTATATTTAG
*
17470 TTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATC-AAACAATCAAATAAAATT
65 TTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATT
*
17534 TTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAATT
130 TTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAATT
17599 GAAACATAAATTACATAACTTTAAAA
195 GAAACATAAATTACATAACTTTAAAA
17625 GCAGTTTTAA
Statistics
Matches: 210, Mismatches: 8, Indels: 4
0.95 0.04 0.02
Matches are distributed among these distances:
227 114 0.54
228 96 0.46
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.40
Consensus pattern (227 bp):
TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTT
TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAATTG
AAACATAAATTACATAACTTTAAAAAAGTATA
Found at i:20257 original size:33 final size:33
Alignment explanation
Indices: 20202--20267 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
20192 AAATAGATGG
*
20202 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
*** *
20235 AGTGGTGAAAGAAGTTTCGGTGTTAATGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
20268 TATTAAGATG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.29, C:0.02, G:0.44, T:0.26
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:22091 original size:18 final size:19
Alignment explanation
Indices: 22048--22095 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
22038 AATGTCGAGT
22048 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
22067 TAATTTTGTATACGA-TTA
1 TAATTTTGTATAAGATTTA
*
22085 TATTTTTGTAT
1 TAATTTTGTAT
22096 GTGAATATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 13 0.48
19 14 0.52
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.56
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:22791 original size:199 final size:199
Alignment explanation
Indices: 22214--23614 Score: 2502
Period size: 198 Copynumber: 7.1 Consensus size: 199
22204 CAATATGGCC
* * *
22214 AACAGGGTGCACCCATAAAGTGTCGATCCATATA-AAAAAGTGTCAATCCCAAAA-CATCGAAAA
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG-AAC
*
22277 CCAAAAGTAT-ATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTACGAGA
65 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
*
22341 GGATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTCCAGAATGAA
130 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAA
**
22405 TGGAA
195 TTAAA
*
22410 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
22475 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
*
22540 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTTCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
22605 TAAA
196 TAAA
22609 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCC-AAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
22673 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
22738 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
22803 TAAA
196 TAAA
*
22807 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAAAA
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG-AAC
22872 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
65 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
*
22937 GGATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTCCAGAATGAA
130 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAA
**
23001 TGGAA
195 TTAAA
*
23006 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
23071 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
23136 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTTGTGTCGATATTTTTTTTCCAGAATGAA
131 AATATGTCTAAATAATGTGTCGACACTAATATAG-TTTGTGTCGATATTTTTTTTCCAGAATGAA
23201 TTAAA
195 TTAAA
*
23206 AACAAGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCGAAAA
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG-AAC
23270 CC-AAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
65 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
*
23334 GGATATGTCTAAATAA-GTGTCGACACT-A-ATAGTTTGTGTCGATA-TTTTTTTCCAGAATGAA
130 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAA
**
23395 TGGAA
195 TTAAA
*
23400 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
*
23465 CAAAAGTATAATGTAATATGTAAATTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
23530 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
23595 TAAA
196 TAAA
23599 AACAAGGTGCACCCAT
1 AACAAGGTGCACCCAT
23615 CTGTTGAAGA
Statistics
Matches: 1160, Mismatches: 30, Indels: 27
0.95 0.02 0.02
Matches are distributed among these distances:
194 58 0.05
195 113 0.10
196 49 0.04
197 33 0.03
198 429 0.37
199 307 0.26
200 171 0.15
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (199 bp):
AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
TAAA
Found at i:24109 original size:18 final size:18
Alignment explanation
Indices: 24088--24155 Score: 55
Period size: 21 Copynumber: 3.4 Consensus size: 18
24078 AGCGGTCGCA
24088 GAAGATGAAGCTGACGAT
1 GAAGATGAAGCTGACGAT
* *
24106 GAAGATGACGATGATGATGAT
1 GAAGATGA--A-GCTGACGAT
*
24127 GATGACGATGAAGCTGGCGAT
1 GA--A-GATGAAGCTGACGAT
24148 GAAGATGA
1 GAAGATGA
24156 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:24112 original size:6 final size:6
Alignment explanation
Indices: 24088--24185 Score: 70
Period size: 6 Copynumber: 16.3 Consensus size: 6
24078 AGCGGTCGCA
* * * * * *
24088 GAAGAT GAAGCT GACGAT GAAGAT GACGAT GATGAT GATGAT GACGAT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
* ** * * * * *
24136 GAAGCT GGCGAT GAAGAT GATGAC GATGAT GATGAT GATGAT GAAGAT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
24184 GA
1 GA
24186 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:24123 original size:3 final size:3
Alignment explanation
Indices: 24103--24189 Score: 84
Period size: 3 Copynumber: 29.0 Consensus size: 3
24093 TGAAGCTGAC
* * * * * ** *
24103 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
* *
24151 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
24190 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:24138 original size:42 final size:42
Alignment explanation
Indices: 24091--24181 Score: 146
Period size: 42 Copynumber: 2.2 Consensus size: 42
24081 GGTCGCAGAA
*
24091 GATGAAGCTGACGATGAAGATGACGATGATGATGATGATGAC
1 GATGAAGCTGACGATGAAGATGACGACGATGATGATGATGAC
* * *
24133 GATGAAGCTGGCGATGAAGATGATGACGATGATGATGATGAT
1 GATGAAGCTGACGATGAAGATGACGACGATGATGATGATGAC
24175 GATGAAG
1 GATGAAG
24182 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:24189 original size:18 final size:18
Alignment explanation
Indices: 24088--24185 Score: 88
Period size: 18 Copynumber: 5.4 Consensus size: 18
24078 AGCGGTCGCA
* *
24088 GAAGATGAAGCTGACGAT
1 GAAGATGAAGATGATGAT
*
24106 GAAGATGACGATGATGAT
1 GAAGATGAAGATGATGAT
* * * *
24124 GATGATGACGATGAAGCT
1 GAAGATGAAGATGATGAT
** *
24142 GGCGATGAAGATGATGAC
1 GAAGATGAAGATGATGAT
* *
24160 GATGATGATGATGATGAT
1 GAAGATGAAGATGATGAT
24178 GAAGATGA
1 GAAGATGA
24186 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:25958 original size:184 final size:184
Alignment explanation
Indices: 25649--25992 Score: 589
Period size: 184 Copynumber: 1.9 Consensus size: 184
25639 CTTTCAACAT
* *
25649 ATTATAATAAAATAGGTAAATTTGCAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATAAAATAGATAAATTTGCAATATAACCGGTATAAATATACCGGTCTTATGAGCGAATA
* *
25714 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAA
*
25779 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
131 AATGTGTCGATACCATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
** * * *
25833 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATA
1 ATTATAATAAAATAGATAAATTTGCAATATAACCGGTATAAATATACCGGTCTTATGAGCGAATA
*
25898 GGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCAGATTGGAATAAA
66 GGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAA
25963 AATGTGTCGATACCATTTAAAAAAGTGTCG
131 AATGTGTCGATACCATTTAAAAAAGTGTCG
25993 GTAATTTGAA
Statistics
Matches: 149, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
184 149 1.00
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (184 bp):
ATTATAATAAAATAGATAAATTTGCAATATAACCGGTATAAATATACCGGTCTTATGAGCGAATA
GGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAA
AATGTGTCGATACCATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
Found at i:28618 original size:22 final size:23
Alignment explanation
Indices: 28562--28624 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 23
28552 ATAGGTAAAC
*
28562 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
28585 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
28608 ATAT-ATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
28625 TGGTTATATT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
22 12 0.34
23 23 0.66
ACGTcount: A:0.35, C:0.06, G:0.21, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:28631 original size:22 final size:23
Alignment explanation
Indices: 28562--28633 Score: 76
Period size: 23 Copynumber: 3.2 Consensus size: 23
28552 ATAGGTAAAC
* **
28562 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
*
28585 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
28608 ATAT-ATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
28630 ATAT
1 ATAT
28634 TGTAAAGTGT
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
22 19 0.45
23 23 0.55
ACGTcount: A:0.33, C:0.06, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:29019 original size:23 final size:24
Alignment explanation
Indices: 28988--29059 Score: 89
Period size: 23 Copynumber: 3.2 Consensus size: 24
28978 ATAGGTAAAC
*
28988 ATATGATGTAATAGGTAGTC-CTT
1 ATATAATGTAATAGGTAGTCGCTT
*
29011 ATATAATGTAATAGGT--TCGTTT
1 ATATAATGTAATAGGTAGTCGCTT
*
29033 ATATAATGTAATAGGTAGT-GGTT
1 ATATAATGTAATAGGTAGTCGCTT
29056 ATAT
1 ATAT
29060 TGTAAAGTGT
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
21 2 0.05
22 18 0.42
23 22 0.51
24 1 0.02
ACGTcount: A:0.33, C:0.04, G:0.21, T:0.42
Consensus pattern (24 bp):
ATATAATGTAATAGGTAGTCGCTT
Found at i:29361 original size:25 final size:25
Alignment explanation
Indices: 29327--29377 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
29317 ACAACAAATC
*
29327 AATTAAACATTGTTGTGGGTACATT
1 AATTAAACATTGTTATGGGTACATT
*
29352 AATTGAACATTGTTATGGGTACATT
1 AATTAAACATTGTTATGGGTACATT
29377 A
1 A
29378 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:29647 original size:18 final size:18
Alignment explanation
Indices: 29626--29662 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
29616 GTAATTGGAG
29626 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
29644 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
29662 T
1 T
29663 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:29670 original size:24 final size:24
Alignment explanation
Indices: 29618--29664 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
29608 TTTCATATGT
* *
29618 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATC
*
29642 AATTTGAGTTTGAATTTCAATAT
1 AATTTGAGTTTGAATTTAAATAT
29665 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:29963 original size:39 final size:39
Alignment explanation
Indices: 29920--30003 Score: 150
Period size: 39 Copynumber: 2.2 Consensus size: 39
29910 TCCGATGCTC
*
29920 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
*
29959 ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
29998 ATCAAA
1 ATCAAA
30004 TCTACAACTT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.49, C:0.20, G:0.14, T:0.17
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
Found at i:30434 original size:23 final size:23
Alignment explanation
Indices: 30403--30466 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
30393 ATAGGTAAAC
*
30403 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
30426 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
30449 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
30467 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:30473 original size:23 final size:23
Alignment explanation
Indices: 30403--30475 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
30393 ATAGGTAAAC
* **
30403 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
*
30426 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
30449 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
30472 ATAT
1 ATAT
30476 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:33866 original size:14 final size:15
Alignment explanation
Indices: 33838--33867 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
33828 TTGACGAAAC
*
33838 GATTTAATTTAAAAA
1 GATTAAATTTAAAAA
33853 GATTAAATTTAAAAA
1 GATTAAATTTAAAAA
33868 AAAATGGATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.37
Consensus pattern (15 bp):
GATTAAATTTAAAAA
Found at i:39934 original size:17 final size:19
Alignment explanation
Indices: 39905--39943 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
39895 TTAAATATAA
39905 TAAATATAATTTATTT-TT
1 TAAATATAATTTATTTATT
39923 TAAATA-AATTTATTTATT
1 TAAATATAATTTATTTATT
39941 TAA
1 TAA
39944 TAGTTGATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TAAATATAATTTATTTATT
Found at i:41379 original size:7 final size:7
Alignment explanation
Indices: 41367--41448 Score: 51
Period size: 7 Copynumber: 10.7 Consensus size: 7
41357 AAGGAAAAAT
41367 AAAATAA
1 AAAATAA
41374 AAAATAA
1 AAAATAA
41381 AAAATAA
1 AAAATAA
41388 AAAA-AA
1 AAAATAA
41394 TATTAAATAA
1 -A--AAATAA
41404 ATAATATTAA
1 A-AA-A-TAA
41414 ATAAATCAA
1 A-AAAT-AA
* *
41423 AAGGAGAA
1 AA-AATAA
41431 AAAAT-A
1 AAAATAA
41437 AAAATAA
1 AAAATAA
41444 AAAAT
1 AAAAT
41449 GTTAACTTTT
Statistics
Matches: 62, Mismatches: 4, Indels: 18
0.74 0.05 0.21
Matches are distributed among these distances:
6 8 0.13
7 26 0.42
8 9 0.15
9 10 0.16
10 9 0.15
ACGTcount: A:0.76, C:0.01, G:0.04, T:0.20
Consensus pattern (7 bp):
AAAATAA
Found at i:41401 original size:23 final size:23
Alignment explanation
Indices: 41325--41409 Score: 62
Period size: 23 Copynumber: 3.4 Consensus size: 23
41315 AAAGTGTTAG
* *
41325 ATAAGAAATAAGAAATAATATTAA
1 ATAAAAAATAA-AAAAAATATTAA
* **
41349 ATAAATCAAAGGAAAAATAAAATAAAAA
1 ATAAA--AAA--TAAAA-AAAATATTAA
41377 ATAAAAAATAAAAAAAATATTAA
1 ATAAAAAATAAAAAAAATATTAA
*
41400 ATAAATAATA
1 ATAAAAAATA
41410 TTAAATAAAT
Statistics
Matches: 47, Mismatches: 9, Indels: 11
0.70 0.13 0.16
Matches are distributed among these distances:
23 17 0.36
24 8 0.17
26 6 0.13
27 2 0.04
28 14 0.30
ACGTcount: A:0.73, C:0.01, G:0.05, T:0.21
Consensus pattern (23 bp):
ATAAAAAATAAAAAAAATATTAA
Found at i:41404 original size:30 final size:28
Alignment explanation
Indices: 41361--41448 Score: 72
Period size: 30 Copynumber: 2.9 Consensus size: 28
41351 AAATCAAAGG
41361 AAAAATAAAATAAAAAATAAAAAATAAA
1 AAAAATAAAATAAAAAATAAAAAATAAA
41389 AAAAATATTAAATAAATAATATTAAATAAATCAAA
1 AAAAATA--AAATAAA-AA-A-TAAA-AAAT-AAA
*
41424 AGGAGAA-AAAAT-AAAAATAAAAAAT
1 A--AAAATAAAATAAAAAATAAAAAAT
41449 GTTAACTTTT
Statistics
Matches: 50, Mismatches: 1, Indels: 17
0.74 0.01 0.25
Matches are distributed among these distances:
28 7 0.14
29 4 0.08
30 11 0.22
31 3 0.06
32 3 0.06
33 6 0.12
34 8 0.16
35 4 0.08
36 1 0.02
37 3 0.06
ACGTcount: A:0.76, C:0.01, G:0.03, T:0.19
Consensus pattern (28 bp):
AAAAATAAAATAAAAAATAAAAAATAAA
Found at i:41500 original size:22 final size:19
Alignment explanation
Indices: 41466--41516 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 19
41456 TTTAAAAGTG
*
41466 GTAAAATAAAAATAATAAGAA
1 GTAAAAAAAAAATAA-AA-AA
41487 GTAAAAAAACAAATAAAAAA
1 GTAAAAAAA-AAATAAAAAA
*
41507 TTAAAAAAAA
1 GTAAAAAAAA
41517 TGCTAAAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 1 0.04
20 10 0.37
21 10 0.37
22 6 0.22
ACGTcount: A:0.76, C:0.02, G:0.06, T:0.16
Consensus pattern (19 bp):
GTAAAAAAAAAATAAAAAA
Found at i:41602 original size:23 final size:24
Alignment explanation
Indices: 41533--41604 Score: 62
Period size: 23 Copynumber: 3.0 Consensus size: 24
41523 AATTAAAAGG
*
41533 AGAAGAAAAAATGAATAACTAAAA
1 AGAAGAAAAAATGAACAACTAAAA
* *
41557 A-AATAAAAAAT--ACTAAAGTTAAAA
1 AGAAGAAAAAATGAAC--AA-CTAAAA
41581 AGAA-AAAAAATGAACAACTAAAA
1 AGAAGAAAAAATGAACAACTAAAA
41604 A
1 A
41605 TTTAAAGGAC
Statistics
Matches: 38, Mismatches: 4, Indels: 13
0.69 0.07 0.24
Matches are distributed among these distances:
21 1 0.03
23 17 0.45
24 16 0.42
25 2 0.05
26 2 0.05
ACGTcount: A:0.72, C:0.06, G:0.08, T:0.14
Consensus pattern (24 bp):
AGAAGAAAAAATGAACAACTAAAA
Found at i:41603 original size:47 final size:49
Alignment explanation
Indices: 41511--41604 Score: 138
Period size: 47 Copynumber: 1.9 Consensus size: 49
41501 AAAAAATTAA
* *
41511 AAAAAATGCTAAAATTAAAAGGAGAAGAAAAAATGAATAACTAAAAAAAT
1 AAAAAATACTAAAATTAAAA-GAGAAGAAAAAATGAACAACTAAAAAAAT
*
41561 AAAAAATACTAAAGTTAAAA-AGAA-AAAAAATGAACAACTAAAAA
1 AAAAAATACTAAAATTAAAAGAGAAGAAAAAATGAACAACTAAAAA
41605 TTTAAAGGAC
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
47 19 0.46
48 4 0.10
50 18 0.44
ACGTcount: A:0.70, C:0.05, G:0.10, T:0.15
Consensus pattern (49 bp):
AAAAAATACTAAAATTAAAAGAGAAGAAAAAATGAACAACTAAAAAAAT
Found at i:42777 original size:39 final size:39
Alignment explanation
Indices: 42701--42782 Score: 130
Period size: 39 Copynumber: 2.1 Consensus size: 39
42691 ATAAATAAAA
*
42701 AAAATGTTTTCAAAAACTATATATTATATATATGTTTTC
1 AAAATGTTTTCAAAAACTATATATTATATATACGTTTTC
*
42740 AAAATGTTTTCAAAAAACTATATATTATATA-CCGTTTTC
1 AAAATGTTTTC-AAAAACTATATATTATATATACGTTTTC
42779 AAAA
1 AAAA
42783 CTATATAATA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
39 21 0.52
40 19 0.47
ACGTcount: A:0.44, C:0.10, G:0.05, T:0.41
Consensus pattern (39 bp):
AAAATGTTTTCAAAAACTATATATTATATATACGTTTTC
Found at i:42806 original size:24 final size:24
Alignment explanation
Indices: 42753--42806 Score: 65
Period size: 26 Copynumber: 2.2 Consensus size: 24
42743 ATGTTTTCAA
*
42753 AAAACTATATATTATATACCGTTTTC
1 AAAACTATATAATATATA-C-TTTTC
42779 AAAACTATATAATATATA-TTTTC
1 AAAACTATATAATATATACTTTTC
42802 GAAAA
1 -AAAA
42807 TCAATTTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
23 5 0.19
24 4 0.15
26 17 0.65
ACGTcount: A:0.46, C:0.11, G:0.04, T:0.39
Consensus pattern (24 bp):
AAAACTATATAATATATACTTTTC
Found at i:43322 original size:22 final size:22
Alignment explanation
Indices: 43282--43323 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
43272 TACAAAATTA
**
43282 AAAATATAAAAAAGGTTTAATG
1 AAAATATAAAAAAAATTTAATG
*
43304 AAAATGTAAAAAAAATTTAA
1 AAAATATAAAAAAAATTTAA
43324 CCCCTAAACT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.64, C:0.00, G:0.10, T:0.26
Consensus pattern (22 bp):
AAAATATAAAAAAAATTTAATG
Found at i:43727 original size:2 final size:2
Alignment explanation
Indices: 43720--43756 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
43710 AGCCCTTACC
43720 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 A
43757 ACATATTTAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:52386 original size:5 final size:5
Alignment explanation
Indices: 52376--52579 Score: 300
Period size: 5 Copynumber: 40.8 Consensus size: 5
52366 AGGTTGTGTA
52376 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
52426 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
* *
52476 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TGTAT TGTAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
* * * * * * * * * *
52526 TGTAT TGTAT TGTAT TGTAT TGTAT TGTAT TGTAT TGTAT TGTAT TGTAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
52576 TATA
1 TATA
52580 CAGATAACAA
Statistics
Matches: 197, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
5 197 1.00
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (5 bp):
TATAT
Found at i:62678 original size:10 final size:10
Alignment explanation
Indices: 62663--62693 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
62653 AAATAATACC
62663 TCTTGTTCAG
1 TCTTGTTCAG
62673 TCTTGTTCAG
1 TCTTGTTCAG
62683 TCTTGTTCAG
1 TCTTGTTCAG
62693 T
1 T
62694 GCCATGAGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.10, C:0.19, G:0.19, T:0.52
Consensus pattern (10 bp):
TCTTGTTCAG
Found at i:65207 original size:20 final size:20
Alignment explanation
Indices: 65182--65243 Score: 53
Period size: 20 Copynumber: 3.3 Consensus size: 20
65172 TATTTTAAAC
65182 CATTAATGTCATATGAATAA
1 CATTAATGTCATATGAATAA
*
65202 CATTAACT-T-AT-T-AAT-C
1 CATTAA-TGTCATATGAATAA
* *
65218 CATTAATGCCATATGAGTAA
1 CATTAATGTCATATGAATAA
65238 CATTAA
1 CATTAA
65244 AATTATTAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 12
0.67 0.08 0.25
Matches are distributed among these distances:
15 1 0.03
16 6 0.19
17 5 0.16
18 2 0.06
19 4 0.12
20 13 0.41
21 1 0.03
ACGTcount: A:0.42, C:0.15, G:0.08, T:0.35
Consensus pattern (20 bp):
CATTAATGTCATATGAATAA
Found at i:65231 original size:36 final size:37
Alignment explanation
Indices: 65176--65252 Score: 111
Period size: 36 Copynumber: 2.1 Consensus size: 37
65166 TTCACATATT
* *
65176 TTAAACCATTAATGTCATATGAATAACATT-AACTTA
1 TTAAACCATTAATGCCATATGAATAACATTAAAATTA
* *
65212 TTAATCCATTAATGCCATATGAGTAACATTAAAATTA
1 TTAAACCATTAATGCCATATGAATAACATTAAAATTA
65249 TTAA
1 TTAA
65253 CCTATTAGGA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
36 27 0.75
37 9 0.25
ACGTcount: A:0.44, C:0.13, G:0.06, T:0.36
Consensus pattern (37 bp):
TTAAACCATTAATGCCATATGAATAACATTAAAATTA
Found at i:76591 original size:218 final size:219
Alignment explanation
Indices: 76210--76650 Score: 866
Period size: 218 Copynumber: 2.0 Consensus size: 219
76200 TTCATCCAAC
76210 CCACTGCTAACTTACTATCACTTTCCACAATGAGCCTTCCCTTTGATACCCAATCTGAAGAGAGA
1 CCACTGCTAACTTACTATCACTTTCCACAATGAGCCTTCCCTTTGATACCCAATCTGAAGAGAGA
76275 AAGATGTTTATGCCTTTTTTTATAGCTTTCAACTCTGCTAGAATGATAGGAGTAGGACCAACATT
66 AAGATGTTTATGCCTTTTTTTATAGCTTTCAACTCTGCTAGAATGATAGGAGTAGGACCAACATT
76340 TTCTGAAAAAGAAAGAAGCTTATTCTGATTCCAATCTCTCAGAATACCCCCAATTCCAGTAATCA
131 TTCTGAAAAAGAAAGAAGCTTATTCTGATTCCAATCTCTCAGAATACCCCCAATTCCAGTAATCA
76405 TACCCACACTACTAACAGCTCCAT
196 TACCCACACTACTAACAGCTCCAT
*
76429 CCACTGCTAACTTACTATCACTTTCCACAATGAGCCTTTCCTTTGATACCCAATCTGAAGAGAGA
1 CCACTGCTAACTTACTATCACTTTCCACAATGAGCCTTCCCTTTGATACCCAATCTGAAGAGAGA
76494 AAGATGTTTATGCC-TTTTTTATAGCTTTCAACTCTGCTAGAATGATAGGAGTAGGACCAACATT
66 AAGATGTTTATGCCTTTTTTTATAGCTTTCAACTCTGCTAGAATGATAGGAGTAGGACCAACATT
76558 TTCTGAAAAAGAAAGAAGCTTATTCTGATTCCAATCTCTCAGAATACCCCCAATTCCAGTAATCA
131 TTCTGAAAAAGAAAGAAGCTTATTCTGATTCCAATCTCTCAGAATACCCCCAATTCCAGTAATCA
76623 TACCCACACTACTAACAGCTCCAT
196 TACCCACACTACTAACAGCTCCAT
76647 CCAC
1 CCAC
76651 ATTCATCTTA
Statistics
Matches: 221, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
218 143 0.65
219 78 0.35
ACGTcount: A:0.32, C:0.26, G:0.13, T:0.29
Consensus pattern (219 bp):
CCACTGCTAACTTACTATCACTTTCCACAATGAGCCTTCCCTTTGATACCCAATCTGAAGAGAGA
AAGATGTTTATGCCTTTTTTTATAGCTTTCAACTCTGCTAGAATGATAGGAGTAGGACCAACATT
TTCTGAAAAAGAAAGAAGCTTATTCTGATTCCAATCTCTCAGAATACCCCCAATTCCAGTAATCA
TACCCACACTACTAACAGCTCCAT
Done.