Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008766.1 Hibiscus syriacus cultivar Beakdansim tig00111863_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: 59032
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:10560 original size:35 final size:34
Alignment explanation
Indices: 10509--10578 Score: 104
Period size: 35 Copynumber: 2.0 Consensus size: 34
10499 TCATTAAACT
*
10509 TTTTATATTTTAAATTTTGTAAAAAAAATATAAA
1 TTTTATAATTTAAATTTTGTAAAAAAAATATAAA
* *
10543 TTTTATGAATTTAAATTTTTTAAAAAATATATAAA
1 TTTTAT-AATTTAAATTTTGTAAAAAAAATATAAA
10578 T
1 T
10579 ATTTTTCAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
34 6 0.19
35 26 0.81
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (34 bp):
TTTTATAATTTAAATTTTGTAAAAAAAATATAAA
Found at i:10590 original size:36 final size:35
Alignment explanation
Indices: 10509--10590 Score: 103
Period size: 35 Copynumber: 2.3 Consensus size: 35
10499 TCATTAAACT
*
10509 TTTTAT-ATTTTAAATTTTGTAAAAAAAATATAAA
1 TTTTATCAATTTAAATTTTGTAAAAAAAATATAAA
* * *
10543 TTTTATGAATTTAAATTTTTTAAAAAATATATAAA
1 TTTTATCAATTTAAATTTTGTAAAAAAAATATAAA
*
10578 TATTTTTCAATTT
1 T-TTTATCAATTT
10591 GTTAAAAAAC
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
34 6 0.15
35 26 0.63
36 9 0.22
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.51
Consensus pattern (35 bp):
TTTTATCAATTTAAATTTTGTAAAAAAAATATAAA
Found at i:12214 original size:26 final size:27
Alignment explanation
Indices: 12185--12240 Score: 69
Period size: 26 Copynumber: 2.1 Consensus size: 27
12175 TTCATAGAAA
* *
12185 ATATATTATTGTATT-ATTTTCAATTT
1 ATATATTATTGTATTAAATTTAAATTT
* *
12211 ATATATTTTTTTATTAAATTTAAATTT
1 ATATATTATTGTATTAAATTTAAATTT
12238 ATA
1 ATA
12241 AAATTTATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
26 13 0.52
27 12 0.48
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (27 bp):
ATATATTATTGTATTAAATTTAAATTT
Found at i:12369 original size:14 final size:14
Alignment explanation
Indices: 12346--12384 Score: 62
Period size: 13 Copynumber: 2.9 Consensus size: 14
12336 AAGTTATGAT
12346 AATTTGTGAAAATA
1 AATTTGTGAAAATA
*
12360 AATTTTTG-AAATA
1 AATTTGTGAAAATA
12373 AATTTGTGAAAA
1 AATTTGTGAAAA
12385 CAAAAGATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 12 0.55
14 10 0.45
ACGTcount: A:0.49, C:0.00, G:0.13, T:0.38
Consensus pattern (14 bp):
AATTTGTGAAAATA
Found at i:13203 original size:3 final size:3
Alignment explanation
Indices: 13195--13235 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
13185 TAATGTCAAA
13195 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
13236 AAAAGTAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:19512 original size:2 final size:2
Alignment explanation
Indices: 19505--19552 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
19495 AAGACACGTG
19505 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19547 TA TA TA
1 TA TA TA
19553 ATTACCAATT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:21477 original size:15 final size:15
Alignment explanation
Indices: 21457--21487 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
21447 ACATTGATAT
21457 AATATATAAATATTA
1 AATATATAAATATTA
21472 AATATATAAATATTA
1 AATATATAAATATTA
21487 A
1 A
21488 GGATTAAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
AATATATAAATATTA
Found at i:21481 original size:8 final size:8
Alignment explanation
Indices: 21453--21484 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
21443 GATTACATTG
21453 ATAT-AAT
1 ATATAAAT
21460 ATATAAAT
1 ATATAAAT
21468 AT-TAAAT
1 ATATAAAT
21475 ATATAAAT
1 ATATAAAT
21483 AT
1 AT
21485 TAAGGATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
7 11 0.48
8 12 0.52
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (8 bp):
ATATAAAT
Found at i:21606 original size:22 final size:20
Alignment explanation
Indices: 21581--21630 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 20
21571 ATAATTAAAT
*
21581 AATTAAATGATCTAATTGATAA
1 AATTAAAAGATC-AA-TGATAA
*
21603 AATTAAAAGATCGATGATAA
1 AATTAAAAGATCAATGATAA
21623 AATTAAAA
1 AATTAAAA
21631 TAATTAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 14 0.54
21 1 0.04
22 11 0.42
ACGTcount: A:0.56, C:0.04, G:0.10, T:0.30
Consensus pattern (20 bp):
AATTAAAAGATCAATGATAA
Found at i:42353 original size:19 final size:20
Alignment explanation
Indices: 42313--42350 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
42303 CGGTTATACT
* *
42313 ATCCGGTTTTAAAATATCCG
1 ATCCGGTTTAAAAAAATCCG
42333 ATCCGGTTTAAAAAAATC
1 ATCCGGTTTAAAAAAATC
42351 GATTTTTCCC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.32
Consensus pattern (20 bp):
ATCCGGTTTAAAAAAATCCG
Found at i:44110 original size:37 final size:38
Alignment explanation
Indices: 44025--44110 Score: 106
Period size: 37 Copynumber: 2.3 Consensus size: 38
44015 ATTAAACATT
*
44025 TTTTATATTTTTAATTTTATAAAAAAAATTATATAAATA
1 TTTTATA-ATTTAATTTTATAAAAAAAATTATATAAATA
* *
44064 --TTATGAATTTAATTTTTTAAAGAAAA-TATATAAATA
1 TTTTAT-AATTTAATTTTATAAAAAAAATTATATAAATA
44100 TTTTATAATTT
1 TTTTATAATTT
44111 GTAATATTAT
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
36 10 0.24
37 26 0.63
38 5 0.12
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (38 bp):
TTTTATAATTTAATTTTATAAAAAAAATTATATAAATA
Found at i:47913 original size:21 final size:21
Alignment explanation
Indices: 47888--47935 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
47878 TCTAAATTCG
47888 TGCGATAGTCCAAGTTCACGT
1 TGCGATAGTCCAAGTTCACGT
*
47909 TGCGATAGTCGAAGTTCACGT
1 TGCGATAGTCCAAGTTCACGT
47930 TGCGAT
1 TGCGAT
47936 TTTCCACGAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.29
Consensus pattern (21 bp):
TGCGATAGTCCAAGTTCACGT
Found at i:48210 original size:18 final size:18
Alignment explanation
Indices: 48176--48210 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
48166 TATTTTGGAT
*
48176 TTTTCACTATCGTAACAC
1 TTTTCACTATCGCAACAC
*
48194 TTTTCACTATTGCAACA
1 TTTTCACTATCGCAACA
48211 ACACGTTTTT
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:0.29, C:0.26, G:0.06, T:0.40
Consensus pattern (18 bp):
TTTTCACTATCGCAACAC
Found at i:52040 original size:196 final size:199
Alignment explanation
Indices: 51679--52075 Score: 585
Period size: 197 Copynumber: 2.0 Consensus size: 199
51669 GTTTTAGTAT
* * * *
51679 TTAAACTTTTAATTTTTCAAAACCATACCTAATGTTTAGTTTTCGTTTTATCTTAGTATCCCTCC
1 TTAAACTTTTAATTTTTCAAAACCATACCTAATGTTTAGTTTTCGTTTCATCTTAATACCCCACC
*
51744 GTTACAAACTTAACACGTTTAGTACCTAACTATAAGTATTGGTCCGTTTTAGTACCTAACGTTAA
66 GTTACAAAATTAACACGTTTAGTACCTAACTATAAGTATTGGTCCGTTTTAGTACCTAACGTTAA
* *
51809 ATTTTGAACCGGGTAAAAAATGAAATCAAAACTAAACTTTAGGTATGGTTTT-GAAAAAAAATTA
131 ATTTTGAACCGAGTAAAAAATGAAATCAAAACTAAAATTTAGGTATGGTTTTAGAAAAAAAATTA
51873 AAAG
196 AAAG
51877 TTAAACTTTTAATTTTTTTCAAAACCATACCTAATG-TTAGTTTTCGTTTCAT-TTAATACCCCA
1 TTAAACTTTTAA--TTTTTCAAAACCATACCTAATGTTTAGTTTTCGTTTCATCTTAATACCCCA
51940 CCGTTA-AAAATTAACACGTTTAGTACCTAACTATAAGTATTGGTCCG-TTTAGTACCTAACGTT
64 CCGTTACAAAATTAACACGTTTAGTACCTAACTATAAGTATTGGTCCGTTTTAGTACCTAACGTT
* * ** *
52003 AAA-TTTGAA-CGAAGTACTAAAATGAAA-CTAAAACTAAAATTTATGTATTTTTTTATAAAAAA
129 AAATTTTGAACCG-AGTA-AAAAATGAAATC-AAAACTAAAATTTAGGTATGGTTTTAGAAAAAA
52065 AATTAAAAG
191 AATTAAAAG
52074 TT
1 TT
52076 TAGGTACTAA
Statistics
Matches: 181, Mismatches: 12, Indels: 13
0.88 0.06 0.06
Matches are distributed among these distances:
194 2 0.01
195 10 0.06
196 49 0.27
197 57 0.31
198 26 0.14
199 15 0.08
200 22 0.12
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.38
Consensus pattern (199 bp):
TTAAACTTTTAATTTTTCAAAACCATACCTAATGTTTAGTTTTCGTTTCATCTTAATACCCCACC
GTTACAAAATTAACACGTTTAGTACCTAACTATAAGTATTGGTCCGTTTTAGTACCTAACGTTAA
ATTTTGAACCGAGTAAAAAATGAAATCAAAACTAAAATTTAGGTATGGTTTTAGAAAAAAAATTA
AAAG
Found at i:55434 original size:19 final size:20
Alignment explanation
Indices: 55410--55450 Score: 75
Period size: 19 Copynumber: 2.1 Consensus size: 20
55400 GGTCAGGTGG
55410 TCAACTCTTTATC-TTGTTC
1 TCAACTCTTTATCTTTGTTC
55429 TCAACTCTTTATCTTTGTTC
1 TCAACTCTTTATCTTTGTTC
55449 TC
1 TC
55451 TCATATCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.15, C:0.27, G:0.05, T:0.54
Consensus pattern (20 bp):
TCAACTCTTTATCTTTGTTC
Found at i:56638 original size:2 final size:2
Alignment explanation
Indices: 56631--56683 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
56621 AGATGGTGGG
56631 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
56673 T- TA TA TA TA TA
1 TA TA TA TA TA TA
56684 ATTGTTTTCT
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 49 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:57016 original size:22 final size:21
Alignment explanation
Indices: 56983--57023 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
56973 TTATGTATCT
*
56983 TTCAATTTTTATAAAATAATA
1 TTCAATTATTATAAAATAATA
*
57004 TTCATATTATTATGAAATAA
1 TTCA-ATTATTATAAAATAA
57024 AAGAATTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.46
Consensus pattern (21 bp):
TTCAATTATTATAAAATAATA
Done.