Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008453.1 Hibiscus syriacus cultivar Beakdansim tig00111261_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: 61766
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:13485 original size:18 final size:18
Alignment explanation
Indices: 13459--13500 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
13449 CCAATGGAAA
* *
13459 CTATACTCAAATACGAAT
1 CTATCCTCAAATAAGAAT
13477 CTATCCTCAAATAAGAAT
1 CTATCCTCAAATAAGAAT
13495 CTATCC
1 CTATCC
13501 ATATAAAGCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.40, C:0.26, G:0.05, T:0.29
Consensus pattern (18 bp):
CTATCCTCAAATAAGAAT
Found at i:16348 original size:26 final size:26
Alignment explanation
Indices: 16328--16389 Score: 79
Period size: 26 Copynumber: 2.4 Consensus size: 26
16318 AAAAAACCGT
**
16328 CCCGACCCGACCAAAATAAAATTTCA
1 CCCGACCCGACCAAAATAAAATACCA
* **
16354 CCCGACCCGACCAAAATAAAGTTTCA
1 CCCGACCCGACCAAAATAAAATACCA
16380 CCCGACCCGA
1 CCCGACCCGA
16390 ATATATGAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.37, C:0.39, G:0.11, T:0.13
Consensus pattern (26 bp):
CCCGACCCGACCAAAATAAAATACCA
Found at i:20450 original size:13 final size:13
Alignment explanation
Indices: 20432--20457 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
20422 GTACAGACGC
20432 GCATATGAAGACT
1 GCATATGAAGACT
20445 GCATATGAAGACT
1 GCATATGAAGACT
20458 ATTAACCCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.23
Consensus pattern (13 bp):
GCATATGAAGACT
Found at i:30618 original size:20 final size:20
Alignment explanation
Indices: 30595--30643 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
30585 CTCAAAATCA
*
30595 TTTTTCAAAA-CTTCATTTTG
1 TTTTTCAAAATC-TAATTTTG
*
30615 TTTTCCAAAATCTAATTTTG
1 TTTTTCAAAATCTAATTTTG
30635 -TTTTCAAAA
1 TTTTTCAAAA
30644 GAAAATCAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 8 0.32
20 16 0.64
21 1 0.04
ACGTcount: A:0.31, C:0.14, G:0.04, T:0.51
Consensus pattern (20 bp):
TTTTTCAAAATCTAATTTTG
Found at i:40289 original size:23 final size:24
Alignment explanation
Indices: 40240--40301 Score: 76
Period size: 23 Copynumber: 2.7 Consensus size: 24
40230 TTTTGTGTAG
*
40240 AGGGAATCGA-T-ACCCTCTTGAA
1 AGGGAATCGATTCCCCCTCTTGAA
* *
40262 GGGGAATCGTTTCCCCCT-TTGAA
1 AGGGAATCGATTCCCCCTCTTGAA
40285 AGGGAATCGATTCCCCC
1 AGGGAATCGATTCCCCC
40302 CCCCCCACAG
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
22 8 0.24
23 21 0.64
24 4 0.12
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.24
Consensus pattern (24 bp):
AGGGAATCGATTCCCCCTCTTGAA
Found at i:41935 original size:18 final size:18
Alignment explanation
Indices: 41898--41936 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
41888 AGAACAACAC
* *
41898 GAGGAACAAGCACGAGCA
1 GAGGAACAAGCACAACCA
41916 GAGGAACAAGCACAACCA
1 GAGGAACAAGCACAACCA
41934 GAG
1 GAG
41937 AATCAAATGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.46, C:0.23, G:0.31, T:0.00
Consensus pattern (18 bp):
GAGGAACAAGCACAACCA
Found at i:44719 original size:3 final size:3
Alignment explanation
Indices: 44713--44758 Score: 58
Period size: 3 Copynumber: 15.7 Consensus size: 3
44703 TTTTTATATA
** *
44713 TAT TAT TAT TAT CGT TA- TAT TAT TAT TAT TAC TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
44759 ATTTACAAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
2 2 0.06
3 34 0.94
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:44881 original size:25 final size:25
Alignment explanation
Indices: 44852--44925 Score: 114
Period size: 25 Copynumber: 3.0 Consensus size: 25
44842 GAACCAACCC
44852 ATCAGATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
44877 ATCAGATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
* * *
44902 AACAAATTAGGGTTT-TAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
44926 TCCCCTAATG
Statistics
Matches: 46, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
24 8 0.17
25 38 0.83
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.28
Consensus pattern (25 bp):
ATCAGATTAGGGTTTCAAACCCTAA
Found at i:59294 original size:88 final size:89
Alignment explanation
Indices: 59146--59387 Score: 316
Period size: 90 Copynumber: 2.7 Consensus size: 89
59136 CAGACCAGAT
* *
59146 CTCTTCATCACGTATGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGT
1 CTCTTCATCACGTAAGAGCCGTGTCAACC-T-GATAACCAGTCGTCCTCATCACGTAGGAACCGT
**
59211 GTTATCA-CCTTTAGATGGCCAAGAA
64 GTTATCACCCTAAAGATGGCCAAGAA
59236 CTCTTCATCACGTAAGAGCCGTGTCAACCTGATAACCAGTCGTCCTCATCACGTAGGAACCGTGT
1 CTCTTCATCACGTAAGAGCCGTGTCAACCTGATAACCAGTCGTCCTCATCACGTAGGAACCGTGT
59301 TATCATCCCTAAAGATGGCCAAGAA
66 TATCA-CCCTAAAGATGGCCAAGAA
* * * * *
59326 TTCTTCATCATGTAGGAG-CGTGTCATCCCTG---ACCAGATC-TCCTCATCACGTAGGAGCCGT
1 CTCTTCATCACGTAAGAGCCGTGTCA-ACCTGATAACCAG-TCGTCCTCATCACGTAGGAACCGT
59386 GT
64 GT
59388 CACCCTTAGA
Statistics
Matches: 139, Mismatches: 9, Indels: 11
0.87 0.06 0.07
Matches are distributed among these distances:
87 27 0.19
88 41 0.29
89 8 0.06
90 63 0.45
ACGTcount: A:0.26, C:0.29, G:0.20, T:0.25
Consensus pattern (89 bp):
CTCTTCATCACGTAAGAGCCGTGTCAACCTGATAACCAGTCGTCCTCATCACGTAGGAACCGTGT
TATCACCCTAAAGATGGCCAAGAA
Found at i:59589 original size:3 final size:3
Alignment explanation
Indices: 59583--59624 Score: 63
Period size: 3 Copynumber: 15.0 Consensus size: 3
59573 CCGGGTTTTT
59583 TTA TTA TTA -TA TTA TT- TTA TTA TTA TTA TTA -TA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
59625 ATTTACAATA
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
2 6 0.17
3 30 0.83
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:59597 original size:8 final size:8
Alignment explanation
Indices: 59584--59622 Score: 55
Period size: 8 Copynumber: 5.1 Consensus size: 8
59574 CGGGTTTTTT
59584 TATTATTA
1 TATTATTA
*
59592 TATTATTT
1 TATTATTA
59600 TATTA-T-
1 TATTATTA
59606 TATTATTA
1 TATTATTA
59614 TATTATTA
1 TATTATTA
59622 T
1 T
59623 TAATTTACAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
6 5 0.18
7 2 0.07
8 21 0.75
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (8 bp):
TATTATTA
Found at i:59597 original size:11 final size:11
Alignment explanation
Indices: 59583--59624 Score: 68
Period size: 11 Copynumber: 3.8 Consensus size: 11
59573 CCGGGTTTTT
59583 TTATTATTATA
1 TTATTATTATA
59594 TTATT-TTATTA
1 TTATTATTA-TA
59605 TTATTATTATA
1 TTATTATTATA
59616 TTATTATTA
1 TTATTATTA
59625 ATTTACAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
10 3 0.10
11 23 0.79
12 3 0.10
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
TTATTATTATA
Found at i:59803 original size:24 final size:25
Alignment explanation
Indices: 59716--59813 Score: 164
Period size: 25 Copynumber: 4.0 Consensus size: 25
59706 GAACCAACCC
59716 ATCAGATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
59741 ATCAGATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
59766 ATCAGATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
* *
59791 AACA-ATTAGGGTTT-TAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
59814 TCCCTAATGG
Statistics
Matches: 71, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
23 8 0.11
24 10 0.14
25 53 0.75
ACGTcount: A:0.37, C:0.19, G:0.15, T:0.29
Consensus pattern (25 bp):
ATCAGATTAGGGTTTCAAACCCTAA
Done.