Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004023.1 Hibiscus syriacus cultivar Beakdansim tig00008784_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: 54933
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:2902 original size:20 final size:20
Alignment explanation
Indices: 2877--2915 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
2867 ACATTATCCC
2877 CATCCGAACATTAGAAGGTT
1 CATCCGAACATTAGAAGGTT
2897 CATCCGAACATTAGAAGGT
1 CATCCGAACATTAGAAGGT
2916 ATAGGTTCCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.23
Consensus pattern (20 bp):
CATCCGAACATTAGAAGGTT
Found at i:3628 original size:23 final size:23
Alignment explanation
Indices: 3602--3659 Score: 107
Period size: 23 Copynumber: 2.5 Consensus size: 23
3592 ATGAAAATAT
3602 AATCCAAATTAATTATATAATCA
1 AATCCAAATTAATTATATAATCA
3625 AATCCAAATTAATTATATAATCA
1 AATCCAAATTAATTATATAATCA
*
3648 AATCCCAATTAA
1 AATCCAAATTAA
3660 ATAAGCAGGA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.33
Consensus pattern (23 bp):
AATCCAAATTAATTATATAATCA
Found at i:16033 original size:14 final size:14
Alignment explanation
Indices: 16014--16058 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
16004 CATTCGGTAA
16014 TTCATTCGTTTATG
1 TTCATTCGTTTATG
**
16028 TTCATTTATTTATG
1 TTCATTCGTTTATG
* *
16042 TACGTTCGTTTATG
1 TTCATTCGTTTATG
16056 TTC
1 TTC
16059 TTCAGACCCA
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.16, C:0.13, G:0.13, T:0.58
Consensus pattern (14 bp):
TTCATTCGTTTATG
Found at i:16274 original size:24 final size:24
Alignment explanation
Indices: 16241--16294 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
16231 CTCAATTAAT
* *
16241 TTTATGTTCGTTCTTTTATGTTCA
1 TTTATCTTCGTTCATTTATGTTCA
* *
16265 TTTATCTTCGTTCATTTGTGTTCG
1 TTTATCTTCGTTCATTTATGTTCA
16289 TTTATC
1 TTTATC
16295 ATTTTAACGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.11, C:0.15, G:0.13, T:0.61
Consensus pattern (24 bp):
TTTATCTTCGTTCATTTATGTTCA
Found at i:17086 original size:13 final size:14
Alignment explanation
Indices: 17067--17105 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
17057 ATATAAATTT
17067 TAATTAATTTTAAA
1 TAATTAATTTTAAA
17081 -AATTAA-TTTAAA
1 TAATTAATTTTAAA
17093 TAATTACATTTTA
1 TAATTA-ATTTTA
17106 TTTTGAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 6 0.27
13 11 0.50
14 1 0.05
15 4 0.18
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (14 bp):
TAATTAATTTTAAA
Found at i:17088 original size:23 final size:24
Alignment explanation
Indices: 17052--17097 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 24
17042 ATTAAATATA
*
17052 TAAAAATATAAATTTTAATTAATTT
1 TAAAAATATAAA-TTTAAATAATTT
17077 TAAAAAT-T-AATTTAAATAATT
1 TAAAAATATAAATTTAAATAATT
17098 ACATTTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 10 0.50
23 2 0.10
24 1 0.05
25 7 0.35
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (24 bp):
TAAAAATATAAATTTAAATAATTT
Found at i:20023 original size:23 final size:23
Alignment explanation
Indices: 19997--20057 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
19987 CTCATATAAA
*
19997 TGCACCGAAGTGCCACATAGAAT
1 TGCACCGTAGTGCCACATAGAAT
* * *
20020 TGCACCGTAGCGCCGCGTAGAAT
1 TGCACCGTAGTGCCACATAGAAT
20043 TGCACCGTAGTGCCA
1 TGCACCGTAGTGCCA
20058 TATAATAATG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.26, C:0.30, G:0.26, T:0.18
Consensus pattern (23 bp):
TGCACCGTAGTGCCACATAGAAT
Found at i:20244 original size:103 final size:103
Alignment explanation
Indices: 20073--20393 Score: 597
Period size: 103 Copynumber: 3.1 Consensus size: 103
20063 TAATGTCCAT
* * * *
20073 AAGGACTACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
20138 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
20176 AAGAACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
20241 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
20279 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
20344 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
20382 AAGGACCACATA
1 AAGGACCACATA
20394 GACCCTCGAC
Statistics
Matches: 212, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 212 1.00
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:28791 original size:20 final size:20
Alignment explanation
Indices: 28736--28791 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
28726 ATGCGATCTT
*
28736 AAATTCGCGTTGCGATTTTC
1 AAATTCGCGTTGTGATTTTC
* * *
28756 CATTTCGCGTTATGATTTTC
1 AAATTCGCGTTGTGATTTTC
*
28776 AAATTCGTGTTGTGAT
1 AAATTCGCGTTGTGAT
28792 AGTCCAACAG
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.20, C:0.16, G:0.20, T:0.45
Consensus pattern (20 bp):
AAATTCGCGTTGTGATTTTC
Found at i:29875 original size:6 final size:6
Alignment explanation
Indices: 29855--29919 Score: 116
Period size: 6 Copynumber: 11.2 Consensus size: 6
29845 CTGTCTCGTC
29855 TCGT-G TCGT-G TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
29901 TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG T
29920 AATACGTGTC
Statistics
Matches: 59, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 9 0.15
6 50 0.85
ACGTcount: A:0.00, C:0.17, G:0.48, T:0.35
Consensus pattern (6 bp):
TCGTGG
Found at i:32726 original size:26 final size:26
Alignment explanation
Indices: 32690--32740 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
32680 ATTAAACCTA
32690 TAAATTTTACCTCTTTCCTCACTGGC
1 TAAATTTTACCTCTTTCCTCACTGGC
32716 TAAATTTTACCTCTTTCCTCACTGG
1 TAAATTTTACCTCTTTCCTCACTGG
32741 GTTCTTTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.20, C:0.29, G:0.08, T:0.43
Consensus pattern (26 bp):
TAAATTTTACCTCTTTCCTCACTGGC
Found at i:34205 original size:14 final size:14
Alignment explanation
Indices: 34186--34218 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
34176 TTGGTAGGTT
34186 GCATGAGTTATGAA
1 GCATGAGTTATGAA
34200 GCATGAGTTATGAA
1 GCATGAGTTATGAA
34214 GCATG
1 GCATG
34219 TTCATGATAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.33, C:0.09, G:0.30, T:0.27
Consensus pattern (14 bp):
GCATGAGTTATGAA
Found at i:34335 original size:3 final size:3
Alignment explanation
Indices: 34322--34356 Score: 61
Period size: 3 Copynumber: 11.3 Consensus size: 3
34312 CATGATTTTA
34322 ATT ATTT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
34357 ATGGTAGCAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:37610 original size:20 final size:21
Alignment explanation
Indices: 37585--37625 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
37575 ATAACTATTA
37585 AAATATTATT-TAT-TTTTAAT
1 AAATATT-TTATATATTTTAAT
37605 AAATATTTTATATATTTTAAT
1 AAATATTTTATATATTTTAAT
37626 TATAATTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 2 0.11
20 10 0.53
21 7 0.37
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
AAATATTTTATATATTTTAAT
Found at i:44893 original size:15 final size:15
Alignment explanation
Indices: 44875--44913 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 15
44865 TTATTAAGAT
44875 TTTAAA-AACTATCTG
1 TTTAAAGAA-TATCTG
44890 TTTAAAGTAATATCTG
1 TTTAAAG-AATATCTG
44906 TTTAAAGA
1 TTTAAAGA
44914 TAACTCTCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 7 0.32
16 13 0.59
17 2 0.09
ACGTcount: A:0.41, C:0.08, G:0.10, T:0.41
Consensus pattern (15 bp):
TTTAAAGAATATCTG
Done.