Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001947.1 Hibiscus syriacus cultivar Beakdansim tig00003941_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: 22409
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:8744 original size:65 final size:65
Alignment explanation
Indices: 8660--8792 Score: 205
Period size: 65 Copynumber: 2.0 Consensus size: 65
8650 ATACAAAAAT
*
8660 TAATTAATAAAACAAATGATTATTCAACTCATGAAAATTACCATGACA-TAATACAAAAATTATA
1 TAATTAATAAAACAAATGATTATTCAAATCATGAAAATTACCATGACATTAATACAAAAATTATA
* *
8724 TAATTAAATAAAATAAATGATTATTTAAATCATGAAAATTACCATGACATTCTAATACAAAAATT
1 TAATT-AATAAAACAAATGATTATTCAAATCATGAAAATTACCATGACA-T-TAATACAAAAATT
8789 ATA
63 ATA
8792 T
1 T
8793 GCATTATTTA
Statistics
Matches: 62, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
64 5 0.08
65 40 0.65
68 17 0.27
ACGTcount: A:0.53, C:0.11, G:0.05, T:0.32
Consensus pattern (65 bp):
TAATTAATAAAACAAATGATTATTCAAATCATGAAAATTACCATGACATTAATACAAAAATTATA
Found at i:9136 original size:2 final size:2
Alignment explanation
Indices: 9131--9193 Score: 119
Period size: 2 Copynumber: 32.0 Consensus size: 2
9121 CACTAATTTA
9131 AT AT AT AT AT AT AT AT AT -T 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
9172 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
9194 CCAACTAAAC
Statistics
Matches: 60, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 59 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:9240 original size:46 final size:46
Alignment explanation
Indices: 9180--9268 Score: 169
Period size: 46 Copynumber: 1.9 Consensus size: 46
9170 ATATATATAT
9180 ATATATATATATATCCAACTAAACTATACGTTAAACAAATAAAATA
1 ATATATATATATATCCAACTAAACTATACGTTAAACAAATAAAATA
*
9226 ATATATATATATATCCAACTAAGCTATACGTTAAACAAATAAA
1 ATATATATATATATCCAACTAAACTATACGTTAAACAAATAAA
9269 TATGGCTATT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 42 1.00
ACGTcount: A:0.53, C:0.13, G:0.03, T:0.30
Consensus pattern (46 bp):
ATATATATATATATCCAACTAAACTATACGTTAAACAAATAAAATA
Found at i:10424 original size:3 final size:3
Alignment explanation
Indices: 10410--10443 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
10400 CTTAATATAC
*
10410 TAA TAC TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
10444 TTAATTATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:13239 original size:15 final size:17
Alignment explanation
Indices: 13206--13246 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
13196 CTTTTTTTAT
*
13206 TATTTAATAA-AAAATA
1 TATTTAAAAATAAAATA
13222 TA-TTAAAAATAAAA-A
1 TATTTAAAAATAAAATA
13237 TATTTAAAAA
1 TATTTAAAAA
13247 ATATAAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 9 0.41
16 13 0.59
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
TATTTAAAAATAAAATA
Found at i:13255 original size:17 final size:17
Alignment explanation
Indices: 13215--13246 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
13205 TTATTTAATA
13215 AAAAATATATTAAAAAT
1 AAAAATATATTAAAAAT
13232 AAAAATAT-TTAAAAA
1 AAAAATATATTAAAAA
13247 ATATAAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (17 bp):
AAAAATATATTAAAAAT
Found at i:14264 original size:228 final size:223
Alignment explanation
Indices: 13866--14309 Score: 746
Period size: 228 Copynumber: 2.0 Consensus size: 223
13856 GTAAATTATC
* * * *
13866 TATCCTTTTTATAAAGTGTCTATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTAGTT
1 TATCATTTTTATAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGTT
*
13931 AATATTGTTAAATTTAAAATCTAAATAATTTTATAAATATCAAAACAATCAAATAATTTTTTGTG
66 AATATTGTTAAATTTAAAATCTAAATAATTTTATAAATATCAAAACAATCAAATAATATTTTGTG
13996 TAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAAC
131 TAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAAC
14061 ATAAATTACATAACTTTCAAAAAAGTATA
196 ATAAATTACATAACTTT-AAAAAAGTATA
*
14090 TATCATTTTTATAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTATTATATTTGGT
1 TATCATTTTTATAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTATTATTATATTTAGT
*
14155 TAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAAT-ATAATT
65 TAATATTGTTAAATTTAAAATCTAAAT-A-ATTTTAT-AAATATCAAAACAATCAAATAAT-ATT
* *
14219 TTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAATT
126 TTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATT
14284 GAAACATAAATTACATAACTTTAAAA
191 GAAACATAAATTACATAACTTTAAAA
14310 GCAGTTTTAA
Statistics
Matches: 206, Mismatches: 9, Indels: 7
0.93 0.04 0.03
Matches are distributed among these distances:
224 34 0.17
225 51 0.25
226 1 0.00
227 13 0.06
228 107 0.52
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.40
Consensus pattern (223 bp):
TATCATTTTTATAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGTT
AATATTGTTAAATTTAAAATCTAAATAATTTTATAAATATCAAAACAATCAAATAATATTTTGTG
TAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAAC
ATAAATTACATAACTTTAAAAAAGTATA
Found at i:14415 original size:21 final size:20
Alignment explanation
Indices: 14375--14421 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 20
14365 CGATATACCA
14375 GGTAAAAATATGATAAAACC
1 GGTAAAAATATGATAAAACC
14395 GGTAACAAA-ATGATAAAAACC
1 GGTAA-AAATATGAT-AAAACC
14416 GGTAAA
1 GGTAAA
14422 TTTAAAAGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 11 0.44
21 14 0.56
ACGTcount: A:0.55, C:0.11, G:0.17, T:0.17
Consensus pattern (20 bp):
GGTAAAAATATGATAAAACC
Found at i:14565 original size:20 final size:19
Alignment explanation
Indices: 14542--14588 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 19
14532 CGATATAACA
14542 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
14562 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
14582 GGTAAAA
1 GGTAAAA
14589 TGATACGGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.55, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:14590 original size:17 final size:18
Alignment explanation
Indices: 14546--14593 Score: 62
Period size: 20 Copynumber: 2.6 Consensus size: 18
14536 ATAACAGGTA
14546 AAAATATGATAAAACCGGT
1 AAAA-ATGATAAAACCGGT
14565 AACAAAATGATAAAACCGGT
1 -A-AAAATGATAAAACCGGT
14585 -AAAATGATA
1 AAAAATGATA
14594 CGGATATATT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
17 9 0.33
20 15 0.56
21 3 0.11
ACGTcount: A:0.56, C:0.10, G:0.15, T:0.19
Consensus pattern (18 bp):
AAAAATGATAAAACCGGT
Found at i:18751 original size:19 final size:19
Alignment explanation
Indices: 18729--18777 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
18719 AAAGTCGAGT
18729 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
18748 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
*
18767 TATTTTTGTAT
1 TAATTTTGTAT
18778 GTGAATATAA
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:20018 original size:193 final size:199
Alignment explanation
Indices: 18903--20431 Score: 2697
Period size: 192 Copynumber: 7.9 Consensus size: 199
18893 GCCAACAGGA
*
18903 TGCACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCAATCCC-AAATCATCGAACCCAAAAG
1 TGCACCCATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAG
18967 TA-AATGTAATATGTAA--TTTCAATCTAACCGGTACAAATTATACCGGTTTTATGAGAGAATAT
65 TATAATGTAATATGTAATTTTTCAATCTAACCGGTAC-AATTATACCGGTTTTATGAGAGAATAT
19029 GTCTAAATAATGTGTCGACACTAAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGGAA
129 GTCTAAATAATGTGTCGACACT-AATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGGAA
19094 AACAAGG
193 AACAAGG
19101 TGCACCCATAAAGTGTCGATCCATATATAAAAA--GTCGATCCCAAAATCATCGAA-CCAAAAG-
1 TGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGT
19162 -T-ATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTAT--GAGAATATGT
66 ATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGT
19223 CTAAA-AATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGG-AAAC
131 CTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGGAAAAC
19286 AAGG
196 AAGG
19290 TGCA-CCATAAAGTGTCGATCC-TATATAAAAA-TGTCGATCCCAAAATCATCGAACCCAAAAGT
1 TGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGT
*
19352 ATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATT-TACCGGTTTTATAAGAGAATATGT
66 ATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGT
19416 CTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGGAAAAC
131 CTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGGAAAAC
19481 AAGG
196 AAGG
19485 TGCACCCATAAAGTGTCGATCCA-ATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGT
1 TGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGT
19549 ATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGT
66 ATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGT
19614 CCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCCAGAATGAATGGAAA
131 -CTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTT-CCCAGAATGAATGGAAA
19679 AC-AGG
194 ACAAGG
19684 TGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGT
1 TGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGT
19749 ATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATA-CGGTTTTATGAGAGAATATGT
66 ATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGT
*
19813 TTAAAT-ATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT-G-AAAC
131 CTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGGAAAAC
19875 -AGG
196 AAGG
19878 TGCA-CCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCC-AAATCATCGAACCCAAAAGT
1 TGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGT
19941 ATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATA-CGGTTTTATGAGAGAATATGT
66 ATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGT
20005 CTAAATAATGTGTCGACACTAATATA-TTTGTGTCGATACTTTTTT-CCAGAATGAATGG-AAAC
131 CTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGGAAAAC
20067 AAGG
196 AAGG
20071 TGCACCCATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGT
1 TGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGT
*
20135 ATAATGT-A-ATGTATTTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGT
66 ATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGT
20198 CTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTT-CCAGAATGAATGGAAAAC
131 CTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGGAAAAC
20262 AAGG
196 AAGG
20266 TGCACCCATAAAGTGTCGATCCATATATAAAAA-TGTCGATCCCAAAATCATCGAACCCAAAAGT
1 TGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGT
20330 ATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACC-GTTTTAT--GAGAATATGT
66 ATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGT
20392 C-AAATAATGTGTCGACACTAATATAGTTTGTGTCGATACT
131 CTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACT
20432 AATTTAAATA
Statistics
Matches: 1294, Mismatches: 6, Indels: 67
0.95 0.00 0.05
Matches are distributed among these distances:
187 10 0.01
188 38 0.03
189 19 0.01
190 40 0.03
191 38 0.03
192 197 0.15
193 195 0.15
194 175 0.14
195 120 0.09
196 61 0.05
197 149 0.12
198 56 0.04
199 93 0.07
200 103 0.08
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.31
Consensus pattern (199 bp):
TGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGT
ATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGT
CTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGGAAAAC
AAGG
Found at i:21899 original size:3 final size:3
Alignment explanation
Indices: 21891--21959 Score: 66
Period size: 3 Copynumber: 23.0 Consensus size: 3
21881 TGAAGCTGAC
* * * ** * *
21891 GAT GAT GAT GAT GAT GAC GAT GAA GCT GGC GAT GAA GAT GAC GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
*
21939 GAT GAT GAT GAA GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT
21960 CCAAACAAGT
Statistics
Matches: 51, Mismatches: 15, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.35, C:0.06, G:0.35, T:0.25
Consensus pattern (3 bp):
GAT
Found at i:21900 original size:18 final size:18
Alignment explanation
Indices: 21879--21959 Score: 72
Period size: 18 Copynumber: 4.2 Consensus size: 18
21869 GGTCGCAGAA
*
21879 GATGAAGCTGACGATGAT
1 GATGAAGATGACGATGAT
*
21897 GATGATGATGACGATGAAGCT
1 GATGAAGATGACGATG-A--T
21918 GGCGATGAAGATGACGATGAT
1 ---GATGAAGATGACGATGAT
* *
21939 GATGATGATGAAGATGAT
1 GATGAAGATGACGATGAT
21957 GAT
1 GAT
21960 CCAAACAAGT
Statistics
Matches: 52, Mismatches: 5, Indels: 12
0.75 0.07 0.17
Matches are distributed among these distances:
18 33 0.63
19 1 0.02
21 2 0.04
23 1 0.02
24 15 0.29
ACGTcount: A:0.35, C:0.07, G:0.35, T:0.23
Consensus pattern (18 bp):
GATGAAGATGACGATGAT
Found at i:21959 original size:12 final size:12
Alignment explanation
Indices: 21876--21955 Score: 79
Period size: 12 Copynumber: 6.7 Consensus size: 12
21866 AGCGGTCGCA
* *
21876 GAAGATGAAGCT
1 GAAGATGACGAT
* *
21888 GACGATGATGAT
1 GAAGATGACGAT
*
21900 GATGATGACGAT
1 GAAGATGACGAT
* *
21912 GAAGCTGGCGAT
1 GAAGATGACGAT
21924 GAAGATGACGAT
1 GAAGATGACGAT
* *
21936 GATGATGATGAT
1 GAAGATGACGAT
21948 GAAGATGA
1 GAAGATGA
21956 TGATCCAAAC
Statistics
Matches: 55, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 55 1.00
ACGTcount: A:0.36, C:0.07, G:0.35, T:0.21
Consensus pattern (12 bp):
GAAGATGACGAT
Done.