Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008852.1 Hibiscus syriacus cultivar Beakdansim tig00112068_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: 47187
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:904 original size:41 final size:42
Alignment explanation
Indices: 808--905 Score: 112
Period size: 42 Copynumber: 2.4 Consensus size: 42
798 TTTCTTACTT
* *
808 CTAAGTCCTTCGGGCCATTAGTAAGTCTTTCGAGAATGATGC
1 CTAAGTCCTTCGGGTCATTAGTAAGCCTTTCGAGAATGATGC
* *
850 CTAAATCCTTCGGGTCATCTA-TAAGCCTTTTGAGCAA-GATG-
1 CTAAGTCCTTCGGGTCAT-TAGTAAGCCTTTCGAG-AATGATGC
*
891 GTAAGTCCTTCGGGT
1 CTAAGTCCTTCGGGT
906 AGGATGTTTT
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
41 13 0.27
42 31 0.65
43 4 0.08
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.32
Consensus pattern (42 bp):
CTAAGTCCTTCGGGTCATTAGTAAGCCTTTCGAGAATGATGC
Found at i:1093 original size:220 final size:217
Alignment explanation
Indices: 691--1110 Score: 612
Period size: 220 Copynumber: 1.9 Consensus size: 217
681 CCTTCGGCAA
* * ** *
691 GATGTTTTCATATGATTCTCAAAAATGAGAAAGATTTTCCAAAGTTTCTCATTAAATCTTTTCTG
1 GATGTTTTCACATGATTCTCAAAAATGAGAAAAAGATTCCAAAGTTTCTCATTAAATCATTTCTG
* * *
756 AAAATTGATTTTTTTTAAAAAAGTAAGAAAAGATTTCCAAAGTTTCTTACTTCTAAGTCCTTCGG
66 AAAATTGAATTATTTTAAAAAAGTAAGAAAACATTTCCAAAGTTTCTTACTTCTAAGTCCTTCGG
* * **
821 GCCATTAGTAAGTCTTTCGAGAATGATGCCTAAATCCTTCGGGTCATCTATAAGCCTTTTGAGCA
131 GCCATCAGTAAGTCTTTCAAGAATGATGCCTAAATCCTTCGGGTCATCTATAAGCCTTTAAAGCA
886 AGATGGTAAGTCCTTCGGGTAG
196 AGATGGTAAGTCCTTCGGGTAG
*
908 GATGTTTTTCACATGATTTTCAAAAAAATGAGAAAAAGATTCCAAAGTTTCTCATTTAAATCATT
1 GATG-TTTTCACATGATTCTC--AAAAATGAGAAAAAGATTCCAAAGTTTCTCA-TTAAATCATT
* * *
973 TCTTAAAATT-AATTATTTT-GAAAAGTAAGAAAATCATTTCCAAAGTTTCTTACTTAGTAAGTC
62 TCTGAAAATTGAATTATTTTAAAAAAGTAAGAAAA-CATTTCCAAAGTTTCTTACTT-CTAAGTC
*
1036 CTTCGGGCCATCAGTAAGTCTTTCAAGCATGATGCCTAAATCCTTC-GGTCATCTATAAGCCTTT
125 CTTCGGGCCATCAGTAAGTCTTTCAAGAATGATGCCTAAATCCTTCGGGTCATCTATAAGCCTTT
1100 AAAGCAAGATG
190 AAAGCAAGATG
1111 ATAGTTCTTC
Statistics
Matches: 180, Mismatches: 17, Indels: 9
0.87 0.08 0.04
Matches are distributed among these distances:
217 4 0.02
218 14 0.08
219 13 0.07
220 82 0.46
221 67 0.37
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Consensus pattern (217 bp):
GATGTTTTCACATGATTCTCAAAAATGAGAAAAAGATTCCAAAGTTTCTCATTAAATCATTTCTG
AAAATTGAATTATTTTAAAAAAGTAAGAAAACATTTCCAAAGTTTCTTACTTCTAAGTCCTTCGG
GCCATCAGTAAGTCTTTCAAGAATGATGCCTAAATCCTTCGGGTCATCTATAAGCCTTTAAAGCA
AGATGGTAAGTCCTTCGGGTAG
Found at i:1842 original size:24 final size:24
Alignment explanation
Indices: 1741--1847 Score: 132
Period size: 24 Copynumber: 4.6 Consensus size: 24
1731 CCATTTTCCA
1741 ATTATTATTA-TA-TATT-ATATT
1 ATTATTATTATTACTATTAATATT
*
1762 ATTATTATTATTACTATTATTATT
1 ATTATTATTATTACTATTAATATT
*
1786 ATTATTATTATTACTATTACTATT
1 ATTATTATTATTACTATTAATATT
* * *
1810 ATTATTATTATTATTATTATAAAAT
1 ATTATTATTATTACTATTA-ATATT
1835 ATTA-TATTATTAC
1 ATTATTATTATTAC
1848 AACCCCATTT
Statistics
Matches: 75, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
21 10 0.13
22 2 0.03
23 4 0.05
24 53 0.71
25 6 0.08
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (24 bp):
ATTATTATTATTACTATTAATATT
Found at i:1846 original size:3 final size:3
Alignment explanation
Indices: 1741--1829 Score: 135
Period size: 3 Copynumber: 29.7 Consensus size: 3
1731 CCATTTTCCA
*
1741 ATT ATT ATT ATAT ATT A-T ATT ATT ATT ATT ATT ACT ATT ATT ATT
1 ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* *
1786 ATT ATT ATT ATT ACT ATT ACT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1830 AAAATATTAT
Statistics
Matches: 78, Mismatches: 6, Indels: 4
0.89 0.07 0.05
Matches are distributed among these distances:
2 2 0.03
3 73 0.94
4 3 0.04
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:8899 original size:14 final size:14
Alignment explanation
Indices: 8880--8908 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
8870 AATAAACTTT
8880 TATGTAATATTTCA
1 TATGTAATATTTCA
8894 TATGTAATATTTCA
1 TATGTAATATTTCA
8908 T
1 T
8909 GGGTCTAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.07, G:0.07, T:0.52
Consensus pattern (14 bp):
TATGTAATATTTCA
Found at i:10826 original size:12 final size:12
Alignment explanation
Indices: 10795--10828 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
10785 AACAAAATTT
*
10795 ATTGAACCCATA
1 ATTGAACTCATA
10807 ATTGAACTCATA
1 ATTGAACTCATA
10819 ATTGAACTCA
1 ATTGAACTCA
10829 ATGATAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.41, C:0.21, G:0.09, T:0.29
Consensus pattern (12 bp):
ATTGAACTCATA
Found at i:16535 original size:2 final size:2
Alignment explanation
Indices: 16528--16576 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
16518 ACATTCTTCA
16528 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
16570 AT AT AT A
1 AT AT AT A
16577 CACGTCTACT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:17507 original size:54 final size:54
Alignment explanation
Indices: 17118--17562 Score: 439
Period size: 55 Copynumber: 8.1 Consensus size: 54
17108 TACCAATATG
* * * * * * * * * *
17118 GAAATTCAAAAACTCATTTTGAAATCCTTGGGGTGCACATATAGTGTCGATACG
1 GAAATTCATAAACTCATTATGAATTTCTTAGGTTGCACACATAGTGCCAATACA
** * * *** **
17172 GTCATTCACAAACTCATTGTGAATTAAGTAGGTTATACACATAGTGCCAATAC-
1 GAAATTCATAAACTCATTATGAATTTCTTAGGTTGCACACATAGTGCCAATACA
* * *
17225 GATAATTCACAAACTCATTATTTATGAGTTACTTAGGTTGCACACATAGTGCCAATACA
1 GA-AATTCATAAACTC---A-TTATGAATTTCTTAGGTTGCACACATAGTGCCAATACA
* **
17284 GAAATTTATAAACTCATTATGAATTTCGTGGGGTTGCACACATAGTGCCAATAC-
1 GAAATTCATAAACTCATTATGAATTTC-TTAGGTTGCACACATAGTGCCAATACA
* * *
17338 GAAAATTCATAAACTCATTATGAATTTCATGGGATTGCACACATAGTTCCAATAC-
1 G-AAATTCATAAACTCATTATGAATTTCTTAGG-TTGCACACATAGTGCCAATACA
* *
17393 GAAAATTCATAAACTCATTATGAATTT-TGTGGGGTTGCACACATAGTGCCAATACG
1 G-AAATTCATAAACTCATTATGAATTTCT-T-AGGTTGCACACATAGTGCCAATACA
** * *
17449 GAAATTCATAAACAAATTATGAATTTCTTAGGTTGCACACACAGTACCAATACA
1 GAAATTCATAAACTCATTATGAATTTCTTAGGTTGCACACATAGTGCCAATACA
* *
17503 GAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACATAGTGCCAATACA
1 GAAATTCATAAACTCATTATGAATTTCTTAGGTTGCACACATAGTGCCAATACA
17557 GAAATT
1 GAAATT
17563 TCAACATATA
Statistics
Matches: 332, Mismatches: 46, Indels: 26
0.82 0.11 0.06
Matches are distributed among these distances:
53 1 0.00
54 139 0.42
55 142 0.43
56 5 0.02
57 1 0.00
58 42 0.13
59 2 0.01
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.31
Consensus pattern (54 bp):
GAAATTCATAAACTCATTATGAATTTCTTAGGTTGCACACATAGTGCCAATACA
Found at i:19701 original size:55 final size:56
Alignment explanation
Indices: 19630--19773 Score: 197
Period size: 55 Copynumber: 2.6 Consensus size: 56
19620 TAAGTGTACA
* *
19630 AAAACTTAAGAAATTCATACTAAGTGTATGAATTTCT-ATATGGGCACTTTGTGTGC
1 AAAAC-TAAGAAATTCATACTAAGTGTATGAATTTCTCATATGGGCACTATGTATGC
*
19686 AAAACTAAGAAATTCATACTAAGTGTATGAATTT-TCGTATGGGCACTATGTATGC
1 AAAACTAAGAAATTCATACTAAGTGTATGAATTTCTCATATGGGCACTATGTATGC
* * *
19741 GAAA-TAA-AAATTCATGCCAAGTGTATGAATTTC
1 AAAACTAAGAAATTCATACTAAGTGTATGAATTTC
19774 AGTATAGGAA
Statistics
Matches: 80, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
53 23 0.29
54 4 0.05
55 48 0.60
56 5 0.06
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.33
Consensus pattern (56 bp):
AAAACTAAGAAATTCATACTAAGTGTATGAATTTCTCATATGGGCACTATGTATGC
Found at i:20042 original size:68 final size:68
Alignment explanation
Indices: 19957--20348 Score: 556
Period size: 68 Copynumber: 5.8 Consensus size: 68
19947 AAAGATTAAT
* *
19957 AGGCTTAACTGTGCATTTGACAAAAATGTGTCATTTATGCCAGTTAGATGGAAGGCTAAGTGCCT
1 AGGCCTAACTGTGCATTTGACAAAAATGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
20022 TTG
66 TTG
*
20025 AGGCCTAACTGTGCATTTGACAGAAAA-GTGTCATTTATGCCAGTCAGATGAAAGGCTAAGTGCC
1 AGGCCTAACTGTGCATTTGACA-AAAATGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCC
20089 TTTG
65 TTTG
* * * *
20093 AGGTCTAACTGTGCATTTGACAGAAAGAT-T-TCATTTATGTCAGTTAGATAAAAGGCTAACTGC
1 AGGCCTAACTGTGCATTTGACA-AAA-ATGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGC
20156 CTTTG
64 CTTTG
* ** * * * *
20161 AGACCTATTTGTGTATTTGATAGAAATGTGTCATTTATGCCAGTTAGATAAAAGGCTAAGTGCCT
1 AGGCCTAACTGTGCATTTGACAAAAATGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
20226 TTG
66 TTG
* *
20229 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
1 AGGCCTAACTGTGCATTTGACAAAAATGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
*
20294 TCG
66 TTG
* * *
20297 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGTCAGTTAGATGAA
1 AGGCCTAACTGTGCATTTGACAAAAATGTGTCATTTATGCCAGTTAGATGAA
20349 CGGTTAAACA
Statistics
Matches: 293, Mismatches: 26, Indels: 10
0.89 0.08 0.03
Matches are distributed among these distances:
66 2 0.01
67 3 0.01
68 282 0.96
69 6 0.02
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.32
Consensus pattern (68 bp):
AGGCCTAACTGTGCATTTGACAAAAATGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
TTG
Found at i:20333 original size:204 final size:204
Alignment explanation
Indices: 19966--20345 Score: 661
Period size: 204 Copynumber: 1.9 Consensus size: 204
19956 TAGGCTTAAC
**
19966 TGTGCATTTGACAAAAATGTGTCATTTATGCCAGTTAGATGGAAGGCTAAGTGCCTTTGAGGCCT
1 TGTGCATTTGACAAAAATGTGTCATTTATGCCAGTTAGATAAAAGGCTAAGTGCCTTTGAGGCCT
*
20031 AACTGTGCATTTGACAGAAAAGTGTCATTTATGCCAGTCAGATGAAAGGCTAAGTGCCTTTGAGG
66 AACTGTGCATTTGACAGAAAAGTGTCATTTATGCCAGTCAGATGAAAGGCTAAGTGCCTTCGAGG
* *
20096 TCTAACTGTGCATTTGACAGAAAGATTTCATTTATGTCAGTTAGATAAAAGGCTAACTGCCTTTG
131 CCTAACTGTGCATTTGACAGAAAGATGTCATTTATGTCAGTTAGATAAAAGGCTAACTGCCTTTG
20161 AGACCTATT
196 AGACCTATT
* * *
20170 TGTGTATTTGATAGAAATGTGTCATTTATGCCAGTTAGATAAAAGGCTAAGTGCCTTTGAGGCCT
1 TGTGCATTTGACAAAAATGTGTCATTTATGCCAGTTAGATAAAAGGCTAAGTGCCTTTGAGGCCT
* *
20235 AACTGTGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCTTCGAGG
66 AACTGTGCATTTGACAGAAAAGTGTCATTTATGCCAGTCAGATGAAAGGCTAAGTGCCTTCGAGG
*
20300 CCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGTCAGTTAGAT
131 CCTAACTGTGCATTTGACAGAAAGATGTCATTTATGTCAGTTAGAT
20346 GAACGGTTAA
Statistics
Matches: 165, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
204 165 1.00
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.32
Consensus pattern (204 bp):
TGTGCATTTGACAAAAATGTGTCATTTATGCCAGTTAGATAAAAGGCTAAGTGCCTTTGAGGCCT
AACTGTGCATTTGACAGAAAAGTGTCATTTATGCCAGTCAGATGAAAGGCTAAGTGCCTTCGAGG
CCTAACTGTGCATTTGACAGAAAGATGTCATTTATGTCAGTTAGATAAAAGGCTAACTGCCTTTG
AGACCTATT
Found at i:20386 original size:29 final size:29
Alignment explanation
Indices: 20344--20400 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
20334 TGTCAGTTAG
20344 ATGAACGGTTAAACACTGTTGAGTAAAAT
1 ATGAACGGTTAAACACTGTTGAGTAAAAT
20373 ATGAACGGTTAAACACTGTTGAGTAAAA
1 ATGAACGGTTAAACACTGTTGAGTAAAA
20401 GAATAATAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.42, C:0.11, G:0.21, T:0.26
Consensus pattern (29 bp):
ATGAACGGTTAAACACTGTTGAGTAAAAT
Found at i:28466 original size:7 final size:8
Alignment explanation
Indices: 28448--28478 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
28438 TTTTATTTCG
28448 AAAATTTA
1 AAAATTTA
28456 AAAATTTA
1 AAAATTTA
28464 AAAATTTGA
1 AAAATTT-A
28473 AAAATT
1 AAAATT
28479 CTTGTGTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 15 0.68
9 7 0.32
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.35
Consensus pattern (8 bp):
AAAATTTA
Found at i:28856 original size:21 final size:21
Alignment explanation
Indices: 28830--28869 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
28820 CAGAACCCCA
*
28830 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
28851 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
28870 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:28904 original size:20 final size:21
Alignment explanation
Indices: 28850--28912 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 21
28840 GATTCCCCTG
28850 TGGGGGGAATCGGTTCCCCTTCAA
1 TGGGGGG-ATCGGTT-CCC-TCAA
* *
28874 AGGGGGAATCGGTTCCCTC-A
1 TGGGGGGATCGGTTCCCTCAA
*
28894 TGGGGGGATCGATTCCCTC
1 TGGGGGGATCGGTTCCCTC
28913 TGCACAAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 17 0.50
21 2 0.06
22 3 0.09
23 7 0.21
24 5 0.15
ACGTcount: A:0.16, C:0.25, G:0.35, T:0.24
Consensus pattern (21 bp):
TGGGGGGATCGGTTCCCTCAA
Found at i:36377 original size:55 final size:55
Alignment explanation
Indices: 36293--36437 Score: 213
Period size: 55 Copynumber: 2.6 Consensus size: 55
36283 TACAAAGGGA
*
36293 GGTACCAATACACTCTTGGATGTATCGATACACCCCCAACATCGAATGTAATTTG
1 GGTACCGATACACTCTTGGATGTATCGATACACCCCCAACATCGAATGTAATTTG
* *
36348 GGTACCGATACACTCTTGGATGTATCGATACACCCCCTACATCGAATGTATTTTG
1 GGTACCGATACACTCTTGGATGTATCGATACACCCCCAACATCGAATGTAATTTG
* *
36403 TGTATCGATACACTGGC-T-GATGTATCGATACACCC
1 GGTACCGATACACT--CTTGGATGTATCGATACACCC
36438 TTGGCTCCAA
Statistics
Matches: 83, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
55 81 0.98
56 1 0.01
57 1 0.01
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.29
Consensus pattern (55 bp):
GGTACCGATACACTCTTGGATGTATCGATACACCCCCAACATCGAATGTAATTTG
Found at i:44856 original size:15 final size:15
Alignment explanation
Indices: 44824--44862 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
44814 TTCTTATATC
44824 TTATTTCATCTTCCGT
1 TTATTT-ATCTTCCGT
**
44840 TTATTTATCTTTTGT
1 TTATTTATCTTCCGT
44855 TTATTTAT
1 TTATTTAT
44863 TCTAATCTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 15 0.71
16 6 0.29
ACGTcount: A:0.15, C:0.13, G:0.05, T:0.67
Consensus pattern (15 bp):
TTATTTATCTTCCGT
Found at i:45258 original size:10 final size:10
Alignment explanation
Indices: 45206--45258 Score: 56
Period size: 10 Copynumber: 5.5 Consensus size: 10
45196 TATTTTTTTT
45206 CAAAAAAA-C
1 CAAAAAAAGC
* *
45215 AAAAAAAAGG
1 CAAAAAAAGC
*
45225 CAAAAAAAGG
1 CAAAAAAAGC
45235 CAAAAAAA-C
1 CAAAAAAAGC
*
45244 AAAAAAAAGC
1 CAAAAAAAGC
45254 CAAAA
1 CAAAA
45259 TTTCAAAAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
9 14 0.39
10 22 0.61
ACGTcount: A:0.77, C:0.13, G:0.09, T:0.00
Consensus pattern (10 bp):
CAAAAAAAGC
Done.