Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006547.1 Hibiscus syriacus cultivar Beakdansim tig00015979_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: 61406
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:2748 original size:19 final size:20
Alignment explanation
Indices: 2726--2772 Score: 69
Period size: 21 Copynumber: 2.4 Consensus size: 20
2716 AAATTTTGGA
2726 TTTTTTG-CTTTTTTTTTTG
1 TTTTTTGCCTTTTTTTTTTG
*
2745 TTTTTTGCCCTTTTTTTTTTT
1 TTTTTTG-CCTTTTTTTTTTG
2766 TTTTTTG
1 TTTTTTG
2773 AAAAAAATAG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 7 0.28
21 18 0.72
ACGTcount: A:0.00, C:0.09, G:0.09, T:0.83
Consensus pattern (20 bp):
TTTTTTGCCTTTTTTTTTTG
Found at i:5675 original size:19 final size:20
Alignment explanation
Indices: 5638--5676 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
5628 CTTCAACTTC
*
5638 TTTTCTTTCTTTTCTTTGCT
1 TTTTCTTTCTTTTCATTGCT
*
5658 TTTTC-TTCTTTTGATTGCT
1 TTTTCTTTCTTTTCATTGCT
5677 GGATTTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.03, C:0.18, G:0.08, T:0.72
Consensus pattern (20 bp):
TTTTCTTTCTTTTCATTGCT
Found at i:6639 original size:91 final size:91
Alignment explanation
Indices: 6484--6666 Score: 269
Period size: 91 Copynumber: 2.0 Consensus size: 91
6474 GGTAGTTGAT
*
6484 GCTTGGTCGAATAGGGAGAGAACCCTTCATCTTGGCGCCTAAATGAACCACATGCAAGGAACATG
1 GCTTGGTCGAATAGGGAGAGAACCCTTCATCTTGGCGCCTAAATGAACCAAATGCAAGGAACATG
*
6549 GGGGCTGATCACATGCAAAACACATG
66 GAGGCTGATCACATGCAAAACACATG
* * *
6575 GCTTGG-CTGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATGATCCAAATGCAAGGCACAT
1 GCTTGGTC-GAATAGGGAGAGAACCCTTCATCTTGGCGCCTAAATGAACCAAATGCAAGGAACAT
* * **
6639 GGAGGCTGGTCATATGCAAGGCACATG
65 GGAGGCTGATCACATGCAAAACACATG
6666 G
1 G
6667 GTGTTCTAGG
Statistics
Matches: 82, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
90 1 0.01
91 81 0.99
ACGTcount: A:0.30, C:0.22, G:0.28, T:0.20
Consensus pattern (91 bp):
GCTTGGTCGAATAGGGAGAGAACCCTTCATCTTGGCGCCTAAATGAACCAAATGCAAGGAACATG
GAGGCTGATCACATGCAAAACACATG
Found at i:7795 original size:10 final size:10
Alignment explanation
Indices: 7770--7808 Score: 51
Period size: 11 Copynumber: 3.7 Consensus size: 10
7760 CCAACACTTG
*
7770 GGAGCTACATT
1 GGAGCTA-AAT
7781 GGAGCTAAAT
1 GGAGCTAAAT
7791 GGAGCTAAATT
1 GGAGCTAAA-T
7802 GGAGCTA
1 GGAGCTA
7809 TACCATCATC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
10 11 0.42
11 15 0.58
ACGTcount: A:0.33, C:0.13, G:0.31, T:0.23
Consensus pattern (10 bp):
GGAGCTAAAT
Found at i:8726 original size:22 final size:21
Alignment explanation
Indices: 8688--8728 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
8678 CCATCTCCAT
8688 TTCATCATCAAAGCCATCATC
1 TTCATCATCAAAGCCATCATC
8709 TTCATCCATC-AAGACCATCA
1 TTCAT-CATCAAAG-CCATCA
8729 ATTTTCGCAG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.34, C:0.34, G:0.05, T:0.27
Consensus pattern (21 bp):
TTCATCATCAAAGCCATCATC
Found at i:11577 original size:18 final size:18
Alignment explanation
Indices: 11549--11583 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
11539 CGTGACTTAT
11549 GAGTACATCACCATTTCAA
1 GAGTACATCACC-TTTCAA
11568 GAGT-CATCACCTTTCA
1 GAGTACATCACCTTTCA
11584 TGAATCAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 7 0.44
19 4 0.25
ACGTcount: A:0.31, C:0.29, G:0.11, T:0.29
Consensus pattern (18 bp):
GAGTACATCACCTTTCAA
Found at i:13252 original size:22 final size:21
Alignment explanation
Indices: 13220--13260 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
13210 CCATCTCCAT
13220 TTCATCATCAAAACCATCATC
1 TTCATCATCAAAACCATCATC
*
13241 TTCATCCATCAAGACCATCA
1 TTCAT-CATCAAAACCATCA
13261 ATTTTCACAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.37, C:0.34, G:0.02, T:0.27
Consensus pattern (21 bp):
TTCATCATCAAAACCATCATC
Found at i:13878 original size:17 final size:17
Alignment explanation
Indices: 13848--13948 Score: 76
Period size: 17 Copynumber: 5.9 Consensus size: 17
13838 AATTAAGAGT
* *
13848 TAGTCTAATAAATGAAC
1 TAGTTTAATGAATGAAC
*
13865 TAGTTTGATGAATGAAC
1 TAGTTTAATGAATGAAC
*
13882 TAGTTTAATTAATGAAC
1 TAGTTTAATGAATGAAC
* * *
13899 TAACTTTATTCAATGAAC
1 T-AGTTTAATGAATGAAC
* ** *
13917 TAGATGCATGAATGAAG
1 TAGTTTAATGAATGAAC
* *
13934 TAGCTTACTGAATGA
1 TAGTTTAATGAATGA
13949 TCTAAATATG
Statistics
Matches: 64, Mismatches: 19, Indels: 2
0.75 0.22 0.02
Matches are distributed among these distances:
17 50 0.78
18 14 0.22
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.34
Consensus pattern (17 bp):
TAGTTTAATGAATGAAC
Found at i:41967 original size:46 final size:47
Alignment explanation
Indices: 41885--41974 Score: 123
Period size: 47 Copynumber: 1.9 Consensus size: 47
41875 TGAGAGCCTT
*
41885 TGGCGCCAAGCATGAAGAGACACACACTATTCGGCCAAAGGGAGAAAA
1 TGGCGCCAAGCATGAACAGACACACACTATTCGGCC-AAGGGAGAAAA
*
41933 TGGCGCCAAG-ATGAACCA-ACATACA-TATTCGGCCAAGGGAGA
1 TGGCGCCAAGCATGAA-CAGACACACACTATTCGGCCAAGGGAGA
41975 TGTCTTTCCA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
45 8 0.21
46 9 0.23
47 11 0.28
48 11 0.28
ACGTcount: A:0.38, C:0.23, G:0.27, T:0.12
Consensus pattern (47 bp):
TGGCGCCAAGCATGAACAGACACACACTATTCGGCCAAGGGAGAAAA
Found at i:42817 original size:11 final size:11
Alignment explanation
Indices: 42809--42843 Score: 54
Period size: 12 Copynumber: 3.2 Consensus size: 11
42799 GAAAAAGACA
42809 AAAAGAAGAAG
1 AAAAGAAGAAG
42820 AAAAGAAGAAAG
1 AAAAGAAG-AAG
42832 AAAAGAA-AAG
1 AAAAGAAGAAG
42842 AA
1 AA
42844 TTCAAAAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 5 0.22
11 8 0.35
12 10 0.43
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (11 bp):
AAAAGAAGAAG
Found at i:42837 original size:17 final size:17
Alignment explanation
Indices: 42790--42843 Score: 65
Period size: 18 Copynumber: 3.1 Consensus size: 17
42780 ATTGGAGTGC
42790 AAAAAG-AAAGAAAAAGA
1 AAAAAGAAAAG-AAAAGA
42807 CAAAAAGAAGAAGAAAAGA
1 -AAAAAGAA-AAGAAAAGA
*
42826 AGAAAGAAAAGAAAAGA
1 AAAAAGAAAAGAAAAGA
42843 A
1 A
42844 TTCAAAAAGA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
17 10 0.30
18 13 0.39
19 7 0.21
20 3 0.09
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (17 bp):
AAAAAGAAAAGAAAAGA
Found at i:48784 original size:17 final size:17
Alignment explanation
Indices: 48759--48798 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
48749 GTATGTTGTT
*
48759 CATTAAAGCATGCATTG
1 CATTTAAGCATGCATTG
* *
48776 CATTTAAGCATGTATTT
1 CATTTAAGCATGCATTG
48793 CATTTA
1 CATTTA
48799 GGGAAGTAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (17 bp):
CATTTAAGCATGCATTG
Found at i:48881 original size:18 final size:18
Alignment explanation
Indices: 48858--48901 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
48848 ATGCATTTAG
48858 TTCATTAAATAAAGTTAT
1 TTCATTAAATAAAGTTAT
* *
48876 TTCATTGAATAATGTTAT
1 TTCATTAAATAAAGTTAT
48894 TTCATTAA
1 TTCATTAA
48902 TCAAACTAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.48
Consensus pattern (18 bp):
TTCATTAAATAAAGTTAT
Done.