Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008768.1 Hibiscus syriacus cultivar Beakdansim tig00111867_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: 74387
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:962 original size:40 final size:39
Alignment explanation
Indices: 874--999 Score: 177
Period size: 40 Copynumber: 3.3 Consensus size: 39
864 GCAAATGTTG
874 ATAT-CTATTTGTCA-TACTATTCTCAAACAAATGCTCTC
1 ATATACTA-TTGTCATTACTATTCTCAAACAAATGCTCTC
**
912 ATATACTATTGTCATTACTATTCTCAAACACAATATTCTC
1 ATATACTATTGTCATTACTATTCTCAAACA-AATGCTCTC
* *
952 ATATACTATTGTCATTACTAATCTC-AACAAATGCTGTC
1 ATATACTATTGTCATTACTATTCTCAAACAAATGCTCTC
990 ATATACTATT
1 ATATACTATT
1000 ATCAAATAGA
Statistics
Matches: 79, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
38 26 0.33
39 22 0.28
40 31 0.39
ACGTcount: A:0.34, C:0.21, G:0.05, T:0.40
Consensus pattern (39 bp):
ATATACTATTGTCATTACTATTCTCAAACAAATGCTCTC
Found at i:966 original size:13 final size:13
Alignment explanation
Indices: 908--977 Score: 63
Period size: 12 Copynumber: 5.4 Consensus size: 13
898 AAACAAATGC
908 TCTCATATACTAT
1 TCTCATATACTAT
*
921 TGTCAT-TACTAT
1 TCTCATATACTAT
* *
933 TCTCAAACACAATAT
1 TCTCATATAC--TAT
948 TCTCATATACTAT
1 TCTCATATACTAT
* *
961 TGTCAT-TACTAA
1 TCTCATATACTAT
973 TCTCA
1 TCTCA
978 ACAAATGCTG
Statistics
Matches: 45, Mismatches: 9, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
12 19 0.42
13 15 0.33
15 11 0.24
ACGTcount: A:0.33, C:0.23, G:0.03, T:0.41
Consensus pattern (13 bp):
TCTCATATACTAT
Found at i:1801 original size:12 final size:12
Alignment explanation
Indices: 1784--1808 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1774 ATCTCTTTAT
1784 TTTCTTTCATTA
1 TTTCTTTCATTA
1796 TTTCTTTCATTA
1 TTTCTTTCATTA
1808 T
1 T
1809 GCTAAGTATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTCTTTCATTA
Found at i:8799 original size:23 final size:23
Alignment explanation
Indices: 8724--8799 Score: 89
Period size: 23 Copynumber: 3.3 Consensus size: 23
8714 CAGCCCATAT
8724 AAATGCACCGAAGTGCCACGTAG
1 AAATGCACCGAAGTGCCACGTAG
* * * *
8747 AATTACACCGAAGTGGCACATAG
1 AAATGCACCGAAGTGCCACGTAG
* * *
8770 AATTGCACCGTAGTGCCGCGTAG
1 AAATGCACCGAAGTGCCACGTAG
8793 AAATGCA
1 AAATGCA
8800 TTAGAGTGCC
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 43 1.00
ACGTcount: A:0.34, C:0.24, G:0.25, T:0.17
Consensus pattern (23 bp):
AAATGCACCGAAGTGCCACGTAG
Found at i:9961 original size:64 final size:63
Alignment explanation
Indices: 9851--9992 Score: 155
Period size: 64 Copynumber: 2.2 Consensus size: 63
9841 CCCTTGAAGC
* *
9851 GCATCGATGCACTACCCATGCATCGATACACAAATCACCTTCGATGTTTTCA-TTTTAAGGAGGT
1 GCATCGATGCACTACCCATGCATCGATACACAAATCA-CTTCGATGTATCCATTTTTAAGG-GGT
* * * * *
9915 GCATCGATGCACT-CCTTATGCATCGATGCACTAACTGCA-TTTGATGTATCCATTTTTAATGGG
1 GCATCGATGCACTACC-CATGCATCGATACAC-AAAT-CACTTCGATGTATCCATTTTTAAGGGG
9978 T
63 T
9979 GCATCGATGCACTA
1 GCATCGATGCACTA
9993 ACTGCATTCG
Statistics
Matches: 66, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
63 2 0.03
64 52 0.79
65 10 0.15
66 2 0.03
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (63 bp):
GCATCGATGCACTACCCATGCATCGATACACAAATCACTTCGATGTATCCATTTTTAAGGGGT
Found at i:9983 original size:45 final size:45
Alignment explanation
Indices: 9933--10036 Score: 190
Period size: 45 Copynumber: 2.3 Consensus size: 45
9923 GCACTCCTTA
*
9933 TGCATCGATGCACTAACTGCATTTGATGTATCCATTTTTAATGGG
1 TGCATCGATGCACTAACTGCATTCGATGTATCCATTTTTAATGGG
*
9978 TGCATCGATGCACTAACTGCATTCGATGTTTCCATTTTTAATGGG
1 TGCATCGATGCACTAACTGCATTCGATGTATCCATTTTTAATGGG
10023 TGCATCGATGCACT
1 TGCATCGATGCACT
10037 TCCTGTGCAT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
45 57 1.00
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.37
Consensus pattern (45 bp):
TGCATCGATGCACTAACTGCATTCGATGTATCCATTTTTAATGGG
Found at i:25839 original size:149 final size:149
Alignment explanation
Indices: 25569--25883 Score: 551
Period size: 149 Copynumber: 2.1 Consensus size: 149
25559 GGGTAGAGGG
* *
25569 TCTACGCGGTCCTTCGGGACAAATGTATATTCTTTGGAACATTTATGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACAAATATATATTCTTTGGAACATGTATGAAGTCTTGAAAGACACAT
* *
25634 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGTATATGTATATGATCCTTAAGGAATTATATGTGGTCCTTATGGACATCATTA
25699 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
* * *
25718 TCTACGCGGTCCTTCGGGATATATATATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACAAATATATATTCTTTGGAACATGTATGAAGTCTTGAAAGACACAT
25783 ACTTGATCCCTAGTATATGTATATGATCCTTAAGGAATTATATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGTATATGTATATGATCCTTAAGGAATTATATGTGGTCCTTATGGACATCATTA
25848 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
25867 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
25884 TGCATTTATA
Statistics
Matches: 158, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
148 1 0.01
149 157 0.99
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.34
Consensus pattern (149 bp):
TCTACGCGGTCCTTCGGGACAAATATATATTCTTTGGAACATGTATGAAGTCTTGAAAGACACAT
ACTTGATCCCTAGTATATGTATATGATCCTTAAGGAATTATATGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTGCAAT
Found at i:25895 original size:23 final size:23
Alignment explanation
Indices: 25851--25895 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
25841 ATCATTATAT
*
25851 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
* *
25874 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
25896 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:32884 original size:149 final size:149
Alignment explanation
Indices: 32609--32923 Score: 551
Period size: 149 Copynumber: 2.1 Consensus size: 149
32599 GGGTAGAGGG
* *
32609 TCTATGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTATGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATATATATTCTTTGGAACATGTATGAAGTCTTGAAAGACACAT
* * *
32674 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGTATATGTATATGATCCTTAAGGAATTATAGGTGGTCCTTATGGACATCATTA
32739 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
* *
32758 TCTACGCGGTCCTTCGGGATATATATATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATATATATTCTTTGGAACATGTATGAAGTCTTGAAAGACACAT
32823 ACTTGATCCCTAGTATATGTATATGATCCTTAAGGAATTATAGGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGTATATGTATATGATCCTTAAGGAATTATAGGTGGTCCTTATGGACATCATTA
32888 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
32907 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
32924 TGCATTTATA
Statistics
Matches: 158, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
148 1 0.01
149 157 0.99
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (149 bp):
TCTACGCGGTCCTTCGGGACATATATATATTCTTTGGAACATGTATGAAGTCTTGAAAGACACAT
ACTTGATCCCTAGTATATGTATATGATCCTTAAGGAATTATAGGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTGCAAT
Found at i:32935 original size:23 final size:23
Alignment explanation
Indices: 32891--32935 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
32881 ATCATTATAT
*
32891 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
* *
32914 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
32936 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Done.