Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007179.1 Hibiscus syriacus cultivar Beakdansim tig00018855_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: 69243
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:9364 original size:2 final size:2
Alignment explanation
Indices: 9359--9384 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
9349 AGAACATGGT
9359 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
9385 AGATCGTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:9877 original size:20 final size:20
Alignment explanation
Indices: 9852--9897 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
9842 TAATAAGAAA
* *
9852 ATTTTTAGTGTAAAACCTCG
1 ATTTTTAATCTAAAACCTCG
* *
9872 ATTTTTAATCTAAAATCTTG
1 ATTTTTAATCTAAAACCTCG
9892 ATTTTT
1 ATTTTT
9898 TTTTCATTTG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.11, G:0.09, T:0.50
Consensus pattern (20 bp):
ATTTTTAATCTAAAACCTCG
Found at i:11722 original size:15 final size:14
Alignment explanation
Indices: 11702--11736 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
11692 GAACCCATGG
11702 TTTCTTTTCTTCTCT
1 TTTCTTTTC-TCTCT
11717 TTTCTTTTCTCTCT
1 TTTCTTTTCTCTCT
11731 TCTTCT
1 T-TTCT
11737 GTGCACGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTCTTTTCTCTCT
Found at i:12593 original size:16 final size:17
Alignment explanation
Indices: 12572--12606 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
12562 CTGGTTTGGT
*
12572 TTTTAACAT-ATTATTA
1 TTTTAAAATCATTATTA
12588 TTTTAAAATCATTATTA
1 TTTTAAAATCATTATTA
12605 TT
1 TT
12607 ATTAGTTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (17 bp):
TTTTAAAATCATTATTA
Found at i:12610 original size:23 final size:23
Alignment explanation
Indices: 12580--12625 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
12570 GTTTTTAACA
*
12580 TATTATTATTTTAAAATCATTAT
1 TATTATTAGTTTAAAATCATTAT
* *
12603 TATTATTAGTTTGAAATTATTAT
1 TATTATTAGTTTAAAATCATTAT
12626 CACAATCAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (23 bp):
TATTATTAGTTTAAAATCATTAT
Found at i:13260 original size:21 final size:21
Alignment explanation
Indices: 13234--13278 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
13224 AAACTACATA
13234 TTTAGTACCTAAACTATCAAT
1 TTTAGTACCTAAACTATCAAT
* * *
13255 TTTAGTACTTAAACTTTTAAT
1 TTTAGTACCTAAACTATCAAT
13276 TTT
1 TTT
13279 TCAAAACCAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.13, G:0.04, T:0.49
Consensus pattern (21 bp):
TTTAGTACCTAAACTATCAAT
Found at i:16791 original size:15 final size:15
Alignment explanation
Indices: 16771--16800 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
16761 GAAGAATTAA
16771 CTCTTCCAAAGGATG
1 CTCTTCCAAAGGATG
16786 CTCTTCCAAAGGATG
1 CTCTTCCAAAGGATG
16801 TGGTTGAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.27
Consensus pattern (15 bp):
CTCTTCCAAAGGATG
Found at i:25533 original size:18 final size:19
Alignment explanation
Indices: 25496--25533 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
25486 TTACTGGCTT
*
25496 ATGTTTGAAACTCGTACTTG
1 ATGTTTGAAAATC-TACTTG
25516 ATGTTTGAAAAT-TACTTG
1 ATGTTTGAAAATCTACTTG
25534 GCATATATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
20 11 0.65
ACGTcount: A:0.29, C:0.11, G:0.18, T:0.42
Consensus pattern (19 bp):
ATGTTTGAAAATCTACTTG
Found at i:37335 original size:22 final size:22
Alignment explanation
Indices: 37310--37351 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
37300 CAATTCATTT
37310 ATCTT-TTCTTTATCTTGTTTTA
1 ATCTTATT-TTTATCTTGTTTTA
37332 ATCTTATTTTTATCTTGTTT
1 ATCTTATTTTTATCTTGTTT
37352 CCAGCACCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.14, C:0.12, G:0.05, T:0.69
Consensus pattern (22 bp):
ATCTTATTTTTATCTTGTTTTA
Found at i:38850 original size:22 final size:22
Alignment explanation
Indices: 38818--38878 Score: 113
Period size: 22 Copynumber: 2.8 Consensus size: 22
38808 CGGATACTCA
*
38818 ACCTTGGCCAACAAGTTAGTAT
1 ACCTTGACCAACAAGTTAGTAT
38840 ACCTTGACCAACAAGTTAGTAT
1 ACCTTGACCAACAAGTTAGTAT
38862 ACCTTGACCAACAAGTT
1 ACCTTGACCAACAAGTT
38879 TCACTATCGT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.34, C:0.25, G:0.15, T:0.26
Consensus pattern (22 bp):
ACCTTGACCAACAAGTTAGTAT
Found at i:57922 original size:264 final size:264
Alignment explanation
Indices: 57452--57980 Score: 1031
Period size: 264 Copynumber: 2.0 Consensus size: 264
57442 CGAGTCCTTC
57452 TCAAAGAGCATAATCCTCGGTACTTTTTCCTAGATGATAAGTAAACAAAAACTTGATATAATCAA
1 TCAAAGAGCATAATCCTCGGTACTTTTTCCTAGATGATAAGTAAACAAAAACTTGATATAATCAA
57517 GTTGAATATTGCAAATCCATGCTCTTGATGAGTCATTTGCTGAAAATAATAAGAATGAGTTCAAG
66 GTTGAATATTGCAAATCCATGCTCTTGATGAGTCATTTGCTGAAAATAATAAGAATGAGTTCAAG
57582 TCATCTATATTGTAATATGTGATAGTTATCAATTGTAGCAGCGTTACTTACCTTTGAAAAACGAA
131 TCATCTATATTGTAATATGTGATAGTTATCAATTGTAGCAGCGTTACTTACCTTTGAAAAACGAA
57647 ATCTATGTCATCAGCCCTTAGTTCTATTAGGAGGTTTGTGCTAAGAACTTCCGTCACTCCTATAG
196 ATCTATGTCATCAGCCCTTAGTTCTATTAGGAGGTTTGTGCTAAGAACTTCCGTCACTCCTATAG
57712 AGAA
261 AGAA
*
57716 TCAAAGAGCATAATCCTCGGTACTTTTTCCTAGATGATAAGTAAACAAAGACTTGATATAATCAA
1 TCAAAGAGCATAATCCTCGGTACTTTTTCCTAGATGATAAGTAAACAAAAACTTGATATAATCAA
*
57781 GTTTAATATTGCAAATCCATGCTCTTGATGAGTCATTTGCTGAAAATAATAAGAATGAGTTCAAG
66 GTTGAATATTGCAAATCCATGCTCTTGATGAGTCATTTGCTGAAAATAATAAGAATGAGTTCAAG
*
57846 TCGTCTATATTGTAATATGTGATAGTTATCAATTGTAGCAGCGTTACTTACCTTTGAAAAACGAA
131 TCATCTATATTGTAATATGTGATAGTTATCAATTGTAGCAGCGTTACTTACCTTTGAAAAACGAA
57911 ATCTATGTCATCAGCCCTTAGTTCTATTAGGAGGTTTGTGCTAAGAACTTCCGTCACTCCTATAG
196 ATCTATGTCATCAGCCCTTAGTTCTATTAGGAGGTTTGTGCTAAGAACTTCCGTCACTCCTATAG
57976 AGAA
261 AGAA
57980 T
1 T
57981 GAATGAGAAA
Statistics
Matches: 262, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
264 262 1.00
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Consensus pattern (264 bp):
TCAAAGAGCATAATCCTCGGTACTTTTTCCTAGATGATAAGTAAACAAAAACTTGATATAATCAA
GTTGAATATTGCAAATCCATGCTCTTGATGAGTCATTTGCTGAAAATAATAAGAATGAGTTCAAG
TCATCTATATTGTAATATGTGATAGTTATCAATTGTAGCAGCGTTACTTACCTTTGAAAAACGAA
ATCTATGTCATCAGCCCTTAGTTCTATTAGGAGGTTTGTGCTAAGAACTTCCGTCACTCCTATAG
AGAA
Found at i:61618 original size:35 final size:35
Alignment explanation
Indices: 61579--61647 Score: 86
Period size: 36 Copynumber: 1.9 Consensus size: 35
61569 ACTTAACAAT
61579 AAATTTTGAACG-GGATACTAAAATAAAACAAAATC
1 AAATTTTGAACGAGG-TACTAAAATAAAACAAAATC
* **
61614 AAATTTTTAACGACGGTACTAAAATGTAACAAAA
1 AAATTTTGAACGA-GGTACTAAAATAAAACAAAA
61648 ACTAAAGTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
35 11 0.38
36 16 0.55
37 2 0.07
ACGTcount: A:0.52, C:0.12, G:0.12, T:0.25
Consensus pattern (35 bp):
AAATTTTGAACGAGGTACTAAAATAAAACAAAATC
Found at i:62781 original size:15 final size:16
Alignment explanation
Indices: 62756--62791 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
62746 TAAAATGTGT
*
62756 AATTATATTAATTTAA
1 AATTATATTAAATTAA
62772 AATT-TATTAAATTAA
1 AATTATATTAAATTAA
62787 AATTA
1 AATTA
62792 ATTGATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AATTATATTAAATTAA
Found at i:67811 original size:17 final size:17
Alignment explanation
Indices: 67789--67822 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
67779 CTGTTTCCTT
67789 GTGAAAAGAGATCCAAG
1 GTGAAAAGAGATCCAAG
67806 GTGAAAAGAGATCCAAG
1 GTGAAAAGAGATCCAAG
67823 CAATAAGTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.12, G:0.29, T:0.12
Consensus pattern (17 bp):
GTGAAAAGAGATCCAAG
Done.