Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001510.1 Hibiscus syriacus cultivar Beakdansim tig00002956_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: 52994
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.32
Found at i:5952 original size:13 final size:13
Alignment explanation
Indices: 5936--5985 Score: 50
Period size: 13 Copynumber: 4.0 Consensus size: 13
5926 TTTTATTTAA
*
5936 ATAAATTAAAATT
1 ATAAATAAAAATT
*
5949 ATAAATCAAAA-T
1 ATAAATAAAAATT
*
5961 A-AAAAAAAAATT
1 ATAAATAAAAATT
*
5973 AAAAATAAAAATT
1 ATAAATAAAAATT
5986 GTAATTTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
11 7 0.23
12 4 0.13
13 20 0.65
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (13 bp):
ATAAATAAAAATT
Found at i:6407 original size:17 final size:16
Alignment explanation
Indices: 6371--6409 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
6361 ATAATCACAA
6371 TTTTATTTTATTTCAT
1 TTTTATTTTATTTCAT
6387 TTTTATTTTAATTAT-AT
1 TTTTATTTT-ATT-TCAT
6404 TTTTAT
1 TTTTAT
6410 ATTTTATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 9 0.43
17 11 0.52
18 1 0.05
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTTATTTTATTTCAT
Found at i:9353 original size:2 final size:2
Alignment explanation
Indices: 9346--9375 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
9336 GGATCGGGAC
9346 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
9376 ATTCTCATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:14471 original size:22 final size:22
Alignment explanation
Indices: 14441--14562 Score: 163
Period size: 22 Copynumber: 5.5 Consensus size: 22
14431 GGCATGTGAA
* *
14441 ATATATCCCGAAGGACCTCTGT
1 ATATGTCCCGAAAGACCTCTGT
14463 ATATGTCCCGAAAGACCTCTGT
1 ATATGTCCCGAAAGACCTCTGT
* * *
14485 ATATATCCCGAAGGACCTATGT
1 ATATGTCCCGAAAGACCTCTGT
*
14507 ATATGTCCCGAATGACCTCTGT
1 ATATGTCCCGAAAGACCTCTGT
* *
14529 ATATGTCCTGAAAGACCTATGT
1 ATATGTCCCGAAAGACCTCTGT
*
14551 ATATGTCTCGAA
1 ATATGTCCCGAA
14563 TGACTTATGT
Statistics
Matches: 87, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 87 1.00
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.30
Consensus pattern (22 bp):
ATATGTCCCGAAAGACCTCTGT
Found at i:14508 original size:44 final size:44
Alignment explanation
Indices: 14441--14562 Score: 190
Period size: 44 Copynumber: 2.8 Consensus size: 44
14431 GGCATGTGAA
*
14441 ATATATCCCGAAGGACCTCTGTATATGTCCCGAAAGACCTCTGT
1 ATATATCCCGAAGGACCTATGTATATGTCCCGAAAGACCTCTGT
*
14485 ATATATCCCGAAGGACCTATGTATATGTCCCGAATGACCTCTGT
1 ATATATCCCGAAGGACCTATGTATATGTCCCGAAAGACCTCTGT
* * * *
14529 ATATGTCCTGAAAGACCTATGTATATGTCTCGAA
1 ATATATCCCGAAGGACCTATGTATATGTCCCGAA
14563 TGACTTATGT
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
44 72 1.00
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.30
Consensus pattern (44 bp):
ATATATCCCGAAGGACCTATGTATATGTCCCGAAAGACCTCTGT
Found at i:14524 original size:66 final size:66
Alignment explanation
Indices: 14441--14573 Score: 194
Period size: 66 Copynumber: 2.0 Consensus size: 66
14431 GGCATGTGAA
*
14441 ATATATCCCGAAGGACCTCTGTATATGTCCCGAAAGACCTCTGTATATATCCCGAAGGACCTATG
1 ATATATCCCGAAGGACCTCTGTATATGTCCCGAAAGACCTATGTATATATCCCGAAGGACCTATG
14506 T
66 T
* * * * * * *
14507 ATATGTCCCGAATGACCTCTGTATATGTCCTGAAAGACCTATGTATATGTCTCGAATGACTTATG
1 ATATATCCCGAAGGACCTCTGTATATGTCCCGAAAGACCTATGTATATATCCCGAAGGACCTATG
14572 T
66 T
14573 A
1 A
14574 ACTCTCGACT
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
66 59 1.00
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.31
Consensus pattern (66 bp):
ATATATCCCGAAGGACCTCTGTATATGTCCCGAAAGACCTATGTATATATCCCGAAGGACCTATG
T
Found at i:17549 original size:54 final size:54
Alignment explanation
Indices: 17491--17881 Score: 566
Period size: 54 Copynumber: 7.2 Consensus size: 54
17481 GATGCACATG
* * * *
17491 TAGTGCCTATACGGTCGTTCATCAACACATGATGAATTCCGTGGGTTGCACACA
1 TAGTGCATGTACGGTTGTTCATCAACTCATGATGAATTCCGTGGGTTGCACACA
* * *
17545 TAGTGCCTATACGGTTGTTCATCAACTCATGATAAATTCCGTGGGTTGCACACA
1 TAGTGCATGTACGGTTGTTCATCAACTCATGATGAATTCCGTGGGTTGCACACA
* * * *
17599 TAGTGCTTGTATGGTTGTTCATCAACTCATGATGAATTTCATGGGTTTGCACACA
1 TAGTGCATGTACGGTTGTTCATCAACTCATGATGAATTCCGTGGG-TTGCACACA
* * * *
17654 TAGTACTTGTACGGTTGTTCATCAACTCATGATGAATTCCATGGTTTGCACACA
1 TAGTGCATGTACGGTTGTTCATCAACTCATGATGAATTCCGTGGGTTGCACACA
* *
17708 TAGTGCATGTACGATTGTTCATCAACTCATGATGAATTTCGTGGGTTTGCACACA
1 TAGTGCATGTACGGTTGTTCATCAACTCATGATGAATTCCGTGGG-TTGCACACA
*
17763 TAGTGCATGTACGGTTGTTCATCAACTCATGATGAATTCCGTGGTTTGCACACA
1 TAGTGCATGTACGGTTGTTCATCAACTCATGATGAATTCCGTGGGTTGCACACA
* *
17817 TAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCTGTGGGTTGCACACA
1 TAGTGCATGTACGGTTGTTCATCAACTCATGATGAATTCCGTGGGTTGCACACA
* *
17871 TAATGCCTGTA
1 TAGTGCATGTA
17882 GTACACATAA
Statistics
Matches: 308, Mismatches: 27, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
54 207 0.67
55 101 0.33
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.34
Consensus pattern (54 bp):
TAGTGCATGTACGGTTGTTCATCAACTCATGATGAATTCCGTGGGTTGCACACA
Found at i:17692 original size:109 final size:109
Alignment explanation
Indices: 17491--17881 Score: 581
Period size: 109 Copynumber: 3.6 Consensus size: 109
17481 GATGCACATG
* * * * * * *
17491 TAGTGCCTATACGGTCGTTCATCAACACATGATGAATTCCGTGGG-TTGCACACATAGTGCCTAT
1 TAGTGCATGTACGGTTGTTCATCAACTCATGATGAATTTCGTGGGTTTGCACACATAGTGCATGT
* *
17555 ACGGTTGTTCATCAACTCATGATAAATTCCGTGGGTTGCACACA
66 ACGGTTGTTCATCAACTCATGATGAATTCCGTGGTTTGCACACA
* * * * *
17599 TAGTGCTTGTATGGTTGTTCATCAACTCATGATGAATTTCATGGGTTTGCACACATAGTACTTGT
1 TAGTGCATGTACGGTTGTTCATCAACTCATGATGAATTTCGTGGGTTTGCACACATAGTGCATGT
*
17664 ACGGTTGTTCATCAACTCATGATGAATTCCATGGTTTGCACACA
66 ACGGTTGTTCATCAACTCATGATGAATTCCGTGGTTTGCACACA
*
17708 TAGTGCATGTACGATTGTTCATCAACTCATGATGAATTTCGTGGGTTTGCACACATAGTGCATGT
1 TAGTGCATGTACGGTTGTTCATCAACTCATGATGAATTTCGTGGGTTTGCACACATAGTGCATGT
17773 ACGGTTGTTCATCAACTCATGATGAATTCCGTGGTTTGCACACA
66 ACGGTTGTTCATCAACTCATGATGAATTCCGTGGTTTGCACACA
* * *
17817 TAGTGCATGTACGGTTATTCATCAACTCATGATGAA-TTCTGTGGG-TTGCACACATAATGCCTG
1 TAGTGCATGTACGGTTGTTCATCAACTCATGATGAATTTC-GTGGGTTTGCACACATAGTGCATG
17880 TA
65 TA
17882 GTACACATAA
Statistics
Matches: 257, Mismatches: 24, Indels: 4
0.90 0.08 0.01
Matches are distributed among these distances:
108 59 0.23
109 198 0.77
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.34
Consensus pattern (109 bp):
TAGTGCATGTACGGTTGTTCATCAACTCATGATGAATTTCGTGGGTTTGCACACATAGTGCATGT
ACGGTTGTTCATCAACTCATGATGAATTCCGTGGTTTGCACACA
Found at i:17811 original size:163 final size:163
Alignment explanation
Indices: 17500--17881 Score: 586
Period size: 163 Copynumber: 2.3 Consensus size: 163
17490 GTAGTGCCTA
* * * *
17500 TACGGTCGTTCATCAACACATGATGAATTCCGTGGGTTGCACACATAGTGCCTATACGGTTGTTC
1 TACGGTTGTTCATCAACTCATGATGAATTCCGTGGGTTGCACACATAGTGCCTGTACGATTGTTC
* *
17565 ATCAACTCATGATAAATTCCGTGGGTTGCACACATAGTGCTTGTATGGTTGTTCATCAACTCATG
66 ATCAACTCATGATAAATTCCGTGGGTTGCACACATAGTGCATGTACGGTTGTTCATCAACTCATG
* *
17630 ATGAATTTCATGGGTTTGCACACATAGTACTTG
131 ATGAATTCCATGGGTTTGCACACATAGTACATG
* * *
17663 TACGGTTGTTCATCAACTCATGATGAATTCCATGGTTTGCACACATAGTGCATGTACGATTGTTC
1 TACGGTTGTTCATCAACTCATGATGAATTCCGTGGGTTGCACACATAGTGCCTGTACGATTGTTC
* *
17728 ATCAACTCATGATGAATTTCGTGGGTTTGCACACATAGTGCATGTACGGTTGTTCATCAACTCAT
66 ATCAACTCATGATAAATTCCGTGGG-TTGCACACATAGTGCATGTACGGTTGTTCATCAACTCAT
* *
17793 GATGAATTCCGT-GGTTTGCACACATAGTGCATG
130 GATGAATTCCATGGGTTTGCACACATAGTACATG
* * *
17826 TACGGTTATTCATCAACTCATGATGAATTCTGTGGGTTGCACACATAATGCCTGTA
1 TACGGTTGTTCATCAACTCATGATGAATTCCGTGGGTTGCACACATAGTGCCTGTA
17882 GTACACATAA
Statistics
Matches: 197, Mismatches: 21, Indels: 2
0.90 0.10 0.01
Matches are distributed among these distances:
163 150 0.76
164 47 0.24
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.34
Consensus pattern (163 bp):
TACGGTTGTTCATCAACTCATGATGAATTCCGTGGGTTGCACACATAGTGCCTGTACGATTGTTC
ATCAACTCATGATAAATTCCGTGGGTTGCACACATAGTGCATGTACGGTTGTTCATCAACTCATG
ATGAATTCCATGGGTTTGCACACATAGTACATG
Found at i:19742 original size:21 final size:21
Alignment explanation
Indices: 19661--19742 Score: 92
Period size: 21 Copynumber: 3.9 Consensus size: 21
19651 ATAAAATTTG
* **
19661 TCCCGAAGAACCTCATGCATA
1 TCCCGAAGGACCTCATATATA
* * *
19682 TCCCGAAAGACCTCGTGTATA
1 TCCCGAAGGACCTCATATATA
* *
19703 TCCTGAAGGACCTCGTATATA
1 TCCCGAAGGACCTCATATATA
19724 TCCCGAAGGACCTCATATA
1 TCCCGAAGGACCTCATATA
19743 ACCCTCGACT
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 52 1.00
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.23
Consensus pattern (21 bp):
TCCCGAAGGACCTCATATATA
Found at i:20472 original size:24 final size:24
Alignment explanation
Indices: 20440--20517 Score: 74
Period size: 24 Copynumber: 3.4 Consensus size: 24
20430 CCATGATCGT
20440 TATCGATACTACTTTACATAGTAG
1 TATCGATACTACTTTACATAGTAG
* **
20464 TATCGATACT-CCTTGGAT-G-A-
1 TATCGATACTACTTTACATAGTAG
* **
20484 TTTCGATACTACTACACATAGTAG
1 TATCGATACTACTTTACATAGTAG
20508 TATCGATACT
1 TATCGATACT
20518 CCTTGAGAGG
Statistics
Matches: 40, Mismatches: 10, Indels: 8
0.69 0.17 0.14
Matches are distributed among these distances:
20 9 0.22
21 4 0.10
22 2 0.05
23 6 0.15
24 19 0.47
ACGTcount: A:0.31, C:0.19, G:0.14, T:0.36
Consensus pattern (24 bp):
TATCGATACTACTTTACATAGTAG
Found at i:20534 original size:44 final size:44
Alignment explanation
Indices: 20440--20537 Score: 144
Period size: 44 Copynumber: 2.2 Consensus size: 44
20430 CCATGATCGT
**
20440 TATCGATACTACTTTACATAGTAGTATCGATACTCCTTGGATGA
1 TATCGATACTACTACACATAGTAGTATCGATACTCCTTGGATGA
* *
20484 TTTCGATACTACTACACATAGTAGTATCGATACTCCTTGAGA-GG
1 TATCGATACTACTACACATAGTAGTATCGATACTCCTTG-GATGA
20528 TATCGATACT
1 TATCGATACT
20538 GTTGGGTTGC
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
44 46 0.96
45 2 0.04
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35
Consensus pattern (44 bp):
TATCGATACTACTACACATAGTAGTATCGATACTCCTTGGATGA
Found at i:34399 original size:12 final size:12
Alignment explanation
Indices: 34382--34406 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
34372 AATGAATTTT
34382 AAGATTTTCCAA
1 AAGATTTTCCAA
34394 AAGATTTTCCAA
1 AAGATTTTCCAA
34406 A
1 A
34407 GTATATTCGA
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:0.44, C:0.16, G:0.08, T:0.32
Consensus pattern (12 bp):
AAGATTTTCCAA
Found at i:42084 original size:17 final size:18
Alignment explanation
Indices: 42048--42087 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
42038 AGAACAACAC
42048 GAGGAACAAGCTCCACCA
1 GAGGAACAAGCTCCACCA
*
42066 GAGGAACAAGC-CGACCA
1 GAGGAACAAGCTCCACCA
42083 GAGGA
1 GAGGA
42088 TCAAATGCCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 10 0.48
18 11 0.52
ACGTcount: A:0.40, C:0.28, G:0.30, T:0.03
Consensus pattern (18 bp):
GAGGAACAAGCTCCACCA
Found at i:48602 original size:18 final size:18
Alignment explanation
Indices: 48571--48605 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
48561 ACTGAAAATT
* *
48571 TGTCCTGAATGACCACTA
1 TGTCCCGAAGGACCACTA
48589 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
48606 TATAATCTGT
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:0.26, C:0.31, G:0.20, T:0.23
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:50320 original size:15 final size:16
Alignment explanation
Indices: 50295--50348 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 16
50285 TCGATACTTG
50295 CCTTATGGTATCGATAC
1 CCTT-TGGTATCGATAC
50312 CC-TTGGTATCGAATCTAC
1 CCTTTGGTATCG-A--TAC
50330 CCTTTAGGTATCGATAC
1 CCTTT-GGTATCGATAC
50347 CC
1 CC
50349 CTTGAATAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
15 8 0.25
16 2 0.06
17 7 0.22
18 5 0.16
19 3 0.09
20 7 0.22
ACGTcount: A:0.22, C:0.28, G:0.17, T:0.33
Consensus pattern (16 bp):
CCTTTGGTATCGATAC
Done.