Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006910.1 Hibiscus syriacus cultivar Beakdansim tig00017688_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: 74097
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Found at i:226 original size:13 final size:14
Alignment explanation
Indices: 195--228 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
185 AGGGGGAGTA
195 ATTTTCAAAAATTG
1 ATTTTCAAAAATTG
209 A-TTTCAAAAA-TG
1 ATTTTCAAAAATTG
221 ATTTTCAA
1 ATTTTCAA
229 TAAGAAAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 3 0.16
13 15 0.79
14 1 0.05
ACGTcount: A:0.44, C:0.09, G:0.06, T:0.41
Consensus pattern (14 bp):
ATTTTCAAAAATTG
Found at i:11860 original size:7 final size:7
Alignment explanation
Indices: 11848--11875 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
11838 GAATTTGTTC
11848 GATGATG
1 GATGATG
11855 GATGATG
1 GATGATG
11862 GATGATG
1 GATGATG
11869 GATGATG
1 GATGATG
11876 AATTAAGGGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.29, C:0.00, G:0.43, T:0.29
Consensus pattern (7 bp):
GATGATG
Found at i:17463 original size:111 final size:111
Alignment explanation
Indices: 17337--17555 Score: 420
Period size: 111 Copynumber: 2.0 Consensus size: 111
17327 TCTATTAATC
17337 CAATAAAAATACTTTGTATGATTGTTATGATATGTCTACATATTAAATGTATATACTACGTAAAA
1 CAATAAAAATACTTTGTATGATTGTTATGATATGTCTACATATTAAATGTATATACTACGTAAAA
17402 TATATTTTTAAATTTTTTAATAATTTATAAGTTATCATTTTATGAT
66 TATATTTTTAAATTTTTTAATAATTTATAAGTTATCATTTTATGAT
*
17448 CAATAAAAATACTTTGTATGATTGTTATGATATGTCTACATATTATATGTATATACTACGTAAAA
1 CAATAAAAATACTTTGTATGATTGTTATGATATGTCTACATATTAAATGTATATACTACGTAAAA
*
17513 TATATTTTTAAATTTTTTAATAATTTATAAGTTATTATTTTAT
66 TATATTTTTAAATTTTTTAATAATTTATAAGTTATCATTTTAT
17556 AACTATATAT
Statistics
Matches: 106, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
111 106 1.00
ACGTcount: A:0.38, C:0.06, G:0.08, T:0.48
Consensus pattern (111 bp):
CAATAAAAATACTTTGTATGATTGTTATGATATGTCTACATATTAAATGTATATACTACGTAAAA
TATATTTTTAAATTTTTTAATAATTTATAAGTTATCATTTTATGAT
Found at i:17667 original size:16 final size:17
Alignment explanation
Indices: 17636--17677 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
17626 AATTTTTAAT
* *
17636 AATATTTTATTATTTTT
1 AATATTTAATTATTTTA
*
17653 TATATTTAATT-TTTTA
1 AATATTTAATTATTTTA
17669 AATATTTAA
1 AATATTTAA
17678 AATTTAAAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 12 0.57
17 9 0.43
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
AATATTTAATTATTTTA
Found at i:20401 original size:29 final size:30
Alignment explanation
Indices: 20369--20428 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 30
20359 ATTTCGTCAA
20369 TAAAT-ATTTCTTATAAATT-TTATTGTGAC
1 TAAATAATTTCTTAT-AATTCTTATTGTGAC
20398 TAAATAAATTTCTTATAATTCGTTATTGTGA
1 TAAAT-AATTTCTTATAATTC-TTATTGTGA
20429 AAGAATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
29 5 0.19
30 4 0.15
31 9 0.33
32 9 0.33
ACGTcount: A:0.35, C:0.07, G:0.08, T:0.50
Consensus pattern (30 bp):
TAAATAATTTCTTATAATTCTTATTGTGAC
Found at i:20904 original size:145 final size:144
Alignment explanation
Indices: 20675--20957 Score: 394
Period size: 145 Copynumber: 2.0 Consensus size: 144
20665 AATATTTGTT
* * * *
20675 ATTGTTATTTTGACTAAGTAAATTTTTCATCATTTATTATTTTGAGAAAAATAGTGTGACTAAAT
1 ATTGTTATTATGACTAAGTAAAATTTTCATCAATTATTATTTTAAGAAAAATAGTGTGACTAAAT
20740 AAATTTGACATAATTTCTTATTTTGACTAAATTTAATATATTATTAT-AATTAAATAAATTTGTC
66 AAATTTGACATAATTTCTTATTTTGACTAAATTTAATAT-TT-TTATGAA-TAAATAAATTTGTC
20804 ACAATTAGTTACAAATA
128 ACAATTAGTTACAAATA
* *
20821 ATTGTTATTATGATTATA-TAAAATTTTCAT-AATTAGTTATTTTAAG-AAAATATTGTGACTAA
1 ATTGTTATTATGACTA-AGTAAAATTTTCATCAATTA-TTATTTTAAGAAAAATAGTGTGACTAA
* * * *
20883 ATAAATTTGACATAATTTCTTATTTTGATTACATTTAATATTTTTATGAATAAATAGATTTGTTA
64 ATAAATTTGACATAATTTCTTATTTTGACTAAATTTAATATTTTTATGAATAAATAAATTTGTCA
*
20948 CAATTTGTTA
129 CAATTAGTTA
20958 TTTTAATGTG
Statistics
Matches: 123, Mismatches: 11, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
143 26 0.21
144 4 0.03
145 58 0.47
146 34 0.28
147 1 0.01
ACGTcount: A:0.39, C:0.06, G:0.08, T:0.47
Consensus pattern (144 bp):
ATTGTTATTATGACTAAGTAAAATTTTCATCAATTATTATTTTAAGAAAAATAGTGTGACTAAAT
AAATTTGACATAATTTCTTATTTTGACTAAATTTAATATTTTTATGAATAAATAAATTTGTCACA
ATTAGTTACAAATA
Found at i:21029 original size:145 final size:145
Alignment explanation
Indices: 20675--21011 Score: 362
Period size: 145 Copynumber: 2.3 Consensus size: 145
20665 AATATTTGTT
* * * * * * * *
20675 ATTGTTATTTTGACTAAGTAAATTTTTCATCATTTA-TTATTTTGAGAAAAATAGTGTGACTAAA
1 ATTGTTATTATGACTAAATAAAATTTTCAT-AATTAGTTA-TGTAAAAAAAATATTGTGACTAAA
20739 TAAATTTGACATAATTTCTTATTTTGACTAAATTTAATATATTATTATAATTAAATAAATTTGTC
64 TAAATTTGACATAATTTCTTATTTTGACTAAATTTAATATATTATTATAATTAAATAAATTTGTC
20804 ACAATTAGTTACAAATA
129 ACAATTAGTTACAAATA
* * * * *
20821 ATTGTTATTATGATTATATAAAATTTTCATAATTAGTTATTTTAAGAAAATATTGTGACTAAATA
1 ATTGTTATTATGACTAAATAAAATTTTCATAATTAGTTATGTAAAAAAAATATTGTGACTAAATA
* * * *
20886 AATTTGACATAATTTCTTATTTTGATTACATTTAATAT-TT-TTATGAA-TAAATAGATTTGTTA
66 AATTTGACATAATTTCTTATTTTGACTAAATTTAATATATTATTAT-AATTAAATAAATTTGTCA
* ***
20948 CAATTTGTTA-TTTTA
130 CAATTAGTTACAAATA
* * * *
20963 ATGTGTTGTTATGACTAAATAGATTTTTCATAATT-TTTATAGTAAAAAA
1 AT-TGTTATTATGACTAAATAAAATTTTCATAATTAGTTAT-GTAAAAAA
21012 TTAATATTTT
Statistics
Matches: 160, Mismatches: 27, Indels: 11
0.81 0.14 0.06
Matches are distributed among these distances:
142 8 0.05
143 58 0.36
144 4 0.03
145 62 0.39
146 28 0.17
ACGTcount: A:0.39, C:0.05, G:0.09, T:0.47
Consensus pattern (145 bp):
ATTGTTATTATGACTAAATAAAATTTTCATAATTAGTTATGTAAAAAAAATATTGTGACTAAATA
AATTTGACATAATTTCTTATTTTGACTAAATTTAATATATTATTATAATTAAATAAATTTGTCAC
AATTAGTTACAAATA
Found at i:21050 original size:33 final size:33
Alignment explanation
Indices: 20985--21081 Score: 97
Period size: 37 Copynumber: 2.8 Consensus size: 33
20975 GACTAAATAG
* * * * *
20985 ATTTTTCATAATTTTTATAGTAA-AAAATTAAT
1 ATTTTTTATAAATCTTATAATAATAAAACTAAT
21017 ATTTTTTATAAATCTTATAATAATAAAACTAAT
1 ATTTTTTATAAATCTTATAATAATAAAACTAAT
*
21050 ATTAAATATTTATAAATCTTATAATAGTAAAA
1 ATT---T-TTTATAAATCTTATAATAATAAAA
21082 ATAACATTAA
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
32 19 0.35
33 11 0.20
36 1 0.02
37 23 0.43
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.45
Consensus pattern (33 bp):
ATTTTTTATAAATCTTATAATAATAAAACTAAT
Found at i:21064 original size:37 final size:37
Alignment explanation
Indices: 21021--21094 Score: 121
Period size: 37 Copynumber: 2.0 Consensus size: 37
21011 ATTAATATTT
* *
21021 TTTATAAATCTTATAATAATAAAACTAATATTAAATA
1 TTTATAAATCTTATAATAATAAAAATAACATTAAATA
*
21058 TTTATAAATCTTATAATAGTAAAAATAACATTAAATA
1 TTTATAAATCTTATAATAATAAAAATAACATTAAATA
21095 GCATTAAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.54, C:0.05, G:0.01, T:0.39
Consensus pattern (37 bp):
TTTATAAATCTTATAATAATAAAAATAACATTAAATA
Found at i:25996 original size:22 final size:21
Alignment explanation
Indices: 25971--26021 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 21
25961 TTTAATTAGA
* *
25971 TTATTTTTATTTTATTTTGATT
1 TTATTTTTAATTT-TTTGGATT
25993 TTATATTTTAATTTTTTGGATT
1 TTAT-TTTTAATTTTTTGGATT
26015 TTATTTT
1 TTATTTT
26022 AACAAAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 3 0.12
22 15 0.58
23 8 0.31
ACGTcount: A:0.20, C:0.00, G:0.06, T:0.75
Consensus pattern (21 bp):
TTATTTTTAATTTTTTGGATT
Found at i:26001 original size:18 final size:18
Alignment explanation
Indices: 25973--26007 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
25963 TAATTAGATT
25973 ATTTTTATTTT-ATTTTG
1 ATTTTTATTTTAATTTTG
25990 ATTTTATATTTTAATTTT
1 ATTTT-TATTTTAATTTT
26008 TTGGATTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 6 0.38
19 5 0.31
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (18 bp):
ATTTTTATTTTAATTTTG
Found at i:26118 original size:19 final size:20
Alignment explanation
Indices: 26085--26124 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
26075 TATTTAAGTA
26085 AAAAAAAGTATTTTTTATTT
1 AAAAAAAGTATTTTTTATTT
*
26105 AAAATAAGTATTTTTT-TTT
1 AAAAAAAGTATTTTTTATTT
26124 A
1 A
26125 CTTATGAACC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (20 bp):
AAAAAAAGTATTTTTTATTT
Found at i:27385 original size:16 final size:16
Alignment explanation
Indices: 27364--27396 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
27354 GTAACTCTTG
27364 ACTATAGCTGATATTT
1 ACTATAGCTGATATTT
27380 ACTATAGCTGATATTT
1 ACTATAGCTGATATTT
27396 A
1 A
27397 AGCTCTAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.42
Consensus pattern (16 bp):
ACTATAGCTGATATTT
Found at i:30707 original size:16 final size:18
Alignment explanation
Indices: 30682--30715 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
30672 GAAAATTATA
30682 TTTATACTTA-TTTATTT
1 TTTATACTTATTTTATTT
30699 TTTAT-CTTATTTTATTT
1 TTTATACTTATTTTATTT
30716 ATTTCACACT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTATACTTATTTTATTT
Found at i:32220 original size:28 final size:28
Alignment explanation
Indices: 32171--32247 Score: 73
Period size: 29 Copynumber: 2.7 Consensus size: 28
32161 GATTTCTCTT
* * **
32171 TTGATTGAAAATTATAAAAATATTTGTCC
1 TTGATTGTAATTTAT-AAAATAAATGTCC
*
32200 TTGATTGTAATTTATAAAATAAATGTTC
1 TTGATTGTAATTTATAAAATAAATGTCC
* *
32228 TTCTATTATAATTTATAAAA
1 TT-GATTGTAATTTATAAAA
32248 AGATTTACCC
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
28 12 0.30
29 28 0.70
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.45
Consensus pattern (28 bp):
TTGATTGTAATTTATAAAATAAATGTCC
Found at i:32264 original size:29 final size:29
Alignment explanation
Indices: 32232--32307 Score: 125
Period size: 29 Copynumber: 2.6 Consensus size: 29
32222 ATGTTCTTCT
*
32232 ATTATAATTTATAAAAAGATTTACCCTAC
1 ATTATAATTTACAAAAAGATTTACCCTAC
*
32261 ATTATAATTTACAAAAAGATTTATCCTAC
1 ATTATAATTTACAAAAAGATTTACCCTAC
*
32290 ATTATAATTCACAAAAAG
1 ATTATAATTTACAAAAAG
32308 GATTGTCCTT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 44 1.00
ACGTcount: A:0.47, C:0.13, G:0.04, T:0.36
Consensus pattern (29 bp):
ATTATAATTTACAAAAAGATTTACCCTAC
Found at i:61491 original size:28 final size:27
Alignment explanation
Indices: 61460--61520 Score: 79
Period size: 28 Copynumber: 2.3 Consensus size: 27
61450 AAAATCTTTA
*
61460 TTATAAACCAAATACAATGAATAATATT
1 TTATAAACAAAATACAAT-AATAATATT
* *
61488 TTATTAACAAAATACAATAATATTATT
1 TTATAAACAAAATACAATAATAATATT
61515 TT-TAAA
1 TTATAAA
61521 ATATTAGAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 3 0.10
27 10 0.34
28 16 0.55
ACGTcount: A:0.52, C:0.08, G:0.02, T:0.38
Consensus pattern (27 bp):
TTATAAACAAAATACAATAATAATATT
Found at i:61558 original size:15 final size:14
Alignment explanation
Indices: 61532--61561 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
61522 TATTAGAATA
61532 ATTTATTTAATATT
1 ATTTATTTAATATT
61546 ATTTATGTTAATATT
1 ATTTAT-TTAATATT
61561 A
1 A
61562 CTATTAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (14 bp):
ATTTATTTAATATT
Found at i:63439 original size:54 final size:54
Alignment explanation
Indices: 63375--63477 Score: 134
Period size: 54 Copynumber: 1.9 Consensus size: 54
63365 CATTTATAAC
*
63375 AAAATATAATTTGACCAACAAAAATATTTAGAATAAATTATAATTGTAATTATA
1 AAAATATAATTTGACCAACAAAAATATTTAGAATAAATTATAATAGTAATTATA
** ** * * *
63429 AAAATATAATTTGGTCAGTAAATATATTTAGAGTAAATTGTAATAGTAA
1 AAAATATAATTTGACCAACAAAAATATTTAGAATAAATTATAATAGTAA
63478 GTAAATTAAT
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
54 41 1.00
ACGTcount: A:0.50, C:0.04, G:0.10, T:0.36
Consensus pattern (54 bp):
AAAATATAATTTGACCAACAAAAATATTTAGAATAAATTATAATAGTAATTATA
Found at i:63767 original size:31 final size:35
Alignment explanation
Indices: 63732--63806 Score: 86
Period size: 35 Copynumber: 2.3 Consensus size: 35
63722 ACTAACTTTT
* *
63732 TTTTAAATAA-AATTGAAAGGA-TTT-ATT-AGAA
1 TTTTAAAAAACAATGGAAAGGAGTTTAATTAAGAA
*
63763 TTTTAAAAAACAATGGAAGGGAGTTTAATTAAGAA
1 TTTTAAAAAACAATGGAAAGGAGTTTAATTAAGAA
*
63798 TTTTTAAAA
1 TTTTAAAAA
63807 TTTTTAAAGT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
31 9 0.25
32 9 0.25
33 3 0.08
34 3 0.08
35 12 0.33
ACGTcount: A:0.48, C:0.01, G:0.15, T:0.36
Consensus pattern (35 bp):
TTTTAAAAAACAATGGAAAGGAGTTTAATTAAGAA
Found at i:71514 original size:16 final size:16
Alignment explanation
Indices: 71483--71525 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
71473 ATTGAGGTAC
71483 ATTTACATAT-AACAT
1 ATTTACATATAAACAT
*
71498 ATTTGCATATAAACAT
1 ATTTACATATAAACAT
*
71514 A-TTCCATATAAA
1 ATTTACATATAAA
71526 TTCGAGAACT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 19 0.76
16 6 0.24
ACGTcount: A:0.47, C:0.14, G:0.02, T:0.37
Consensus pattern (16 bp):
ATTTACATATAAACAT
Found at i:71785 original size:31 final size:31
Alignment explanation
Indices: 71747--71808 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
71737 GGAACATAAG
71747 AAAGAAGAAATGGAGAGGCTTGTGTTCTTCA
1 AAAGAAGAAATGGAGAGGCTTGTGTTCTTCA
*
71778 AAAGAAGAAATGGAGAGGTTTGTGTTCTTCA
1 AAAGAAGAAATGGAGAGGCTTGTGTTCTTCA
71809 CATGGCAGCA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.35, C:0.08, G:0.29, T:0.27
Consensus pattern (31 bp):
AAAGAAGAAATGGAGAGGCTTGTGTTCTTCA
Done.