Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008997.1 Hibiscus syriacus cultivar Beakdansim tig00112373_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: 39321
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:1296 original size:17 final size:17
Alignment explanation
Indices: 1276--1317 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
1266 ACTACTTCCC
1276 TAAATGAAATACATGCT
1 TAAATGAAATACATGCT
* *
1293 TAAATGCAATGCATGCT
1 TAAATGAAATACATGCT
*
1310 TTAATGAA
1 TAAATGAA
1318 CAACATACTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.31
Consensus pattern (17 bp):
TAAATGAAATACATGCT
Found at i:2296 original size:15 final size:16
Alignment explanation
Indices: 2278--2310 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
2268 TTTCCAACCC
2278 TTCACTTTCAT-TTCT
1 TTCACTTTCATGTTCT
2293 TTCACTTTCATGTTCT
1 TTCACTTTCATGTTCT
2309 TT
1 TT
2311 TGAACTATCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.12, C:0.24, G:0.03, T:0.61
Consensus pattern (16 bp):
TTCACTTTCATGTTCT
Found at i:10646 original size:14 final size:14
Alignment explanation
Indices: 10627--10660 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
10617 GTGCTTCAAC
10627 TTCTTT-CTTTTCTT
1 TTCTTTGCTTTT-TT
10641 TTCTTTGCTTTTTT
1 TTCTTTGCTTTTTT
10655 TTCTTT
1 TTCTTT
10661 TTGAGTACTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 14 0.74
15 5 0.26
ACGTcount: A:0.00, C:0.18, G:0.03, T:0.79
Consensus pattern (14 bp):
TTCTTTGCTTTTTT
Found at i:15798 original size:20 final size:19
Alignment explanation
Indices: 15769--15810 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
15759 AAACTCCTTC
*
15769 GAAAACACATGATTTTTAAT
1 GAAAACACAT-AATTTTAAT
*
15789 GAAAATACATAATTTTAAT
1 GAAAACACATAATTTTAAT
15808 GAA
1 GAA
15811 GATAAATGCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.50, C:0.07, G:0.10, T:0.33
Consensus pattern (19 bp):
GAAAACACATAATTTTAAT
Found at i:20034 original size:13 final size:13
Alignment explanation
Indices: 20012--20041 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
20002 ACTAAACACC
20012 TTTC-ACATACCT
1 TTTCAACATACCT
20024 TTTCAACATACCT
1 TTTCAACATACCT
20037 TTTCA
1 TTTCA
20042 TCTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:23209 original size:36 final size:35
Alignment explanation
Indices: 23157--23275 Score: 148
Period size: 35 Copynumber: 3.4 Consensus size: 35
23147 ATCACCATTT
*
23157 TTTCACGCCTACAACATCACCATCTTCCATCACCA
1 TTTCACGCCTATAACATCACCATCTTCCATCACCA
* *
23192 TATTCACGTCTATAACATCACCATCTTCCATCATCA
1 T-TTCACGCCTATAACATCACCATCTTCCATCACCA
* * * *
23228 TTGCACGCCTATATCATCACCAACTTCTATCACCA
1 TTTCACGCCTATAACATCACCATCTTCCATCACCA
* *
23263 TTTTATGCCTATA
1 TTTCACGCCTATA
23276 TAACCAACAA
Statistics
Matches: 71, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
35 39 0.55
36 32 0.45
ACGTcount: A:0.29, C:0.35, G:0.04, T:0.32
Consensus pattern (35 bp):
TTTCACGCCTATAACATCACCATCTTCCATCACCA
Found at i:27742 original size:38 final size:38
Alignment explanation
Indices: 27691--27830 Score: 182
Period size: 36 Copynumber: 3.8 Consensus size: 38
27681 TAAGATACTA
**
27691 CCTATAACATCACCATCTTCCATCACCATTTTTTCATT
1 CCTATAACATCACCATCTTCCATCACCATTTTTTCACG
27729 CCTATAACATCACCATCTTCCATCACCA--TTTTCACG
1 CCTATAACATCACCATCTTCCATCACCATTTTTTCACG
* *
27765 CCTATAACATCACCATATTCCATCACCA---TTGCACG
1 CCTATAACATCACCATCTTCCATCACCATTTTTTCACG
* * *
27800 CCTATATCATCACCAACTTCTATCACCATTT
1 CCTATAACATCACCATCTTCCATCACCATTT
27831 AACGCCTATA
Statistics
Matches: 91, Mismatches: 8, Indels: 6
0.87 0.08 0.06
Matches are distributed among these distances:
35 30 0.33
36 33 0.36
38 28 0.31
ACGTcount: A:0.29, C:0.36, G:0.02, T:0.33
Consensus pattern (38 bp):
CCTATAACATCACCATCTTCCATCACCATTTTTTCACG
Found at i:27790 original size:13 final size:13
Alignment explanation
Indices: 27736--27793 Score: 50
Period size: 13 Copynumber: 4.7 Consensus size: 13
27726 ATTCCTATAA
*
27736 CATCACCATCTTC
1 CATCACCATATTC
*
27749 CATCACCAT-TTT
1 CATCACCATATTC
* **
27761 CA-CGCC-TATAA
1 CATCACCATATTC
27772 CATCACCATATTC
1 CATCACCATATTC
27785 CATCACCAT
1 CATCACCAT
27794 TGCACGCCTA
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
10 1 0.03
11 6 0.17
12 7 0.20
13 21 0.60
ACGTcount: A:0.29, C:0.40, G:0.02, T:0.29
Consensus pattern (13 bp):
CATCACCATATTC
Found at i:27811 original size:35 final size:36
Alignment explanation
Indices: 27691--27840 Score: 180
Period size: 35 Copynumber: 4.2 Consensus size: 36
27681 TAAGATACTA
* **
27691 CCTATAACATCACCATCTTCCATCACCATTTTTTCATT
1 CCTATAACATCACCATATTCCATCACCA--TTTTCACG
*
27729 CCTATAACATCACCATCTTCCATCACCATTTTCACG
1 CCTATAACATCACCATATTCCATCACCATTTTCACG
*
27765 CCTATAACATCACCATATTCCATCACCA-TTGCACG
1 CCTATAACATCACCATATTCCATCACCATTTTCACG
* * *
27800 CCTATATCATCACCA-ACTTCTATCACCA-TTTAACG
1 CCTATAACATCACCATA-TTCCATCACCATTTTCACG
27835 CCTATA
1 CCTATA
27841 TAACCAGTAA
Statistics
Matches: 103, Mismatches: 8, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
34 1 0.01
35 41 0.40
36 33 0.32
38 28 0.27
ACGTcount: A:0.29, C:0.36, G:0.03, T:0.32
Consensus pattern (36 bp):
CCTATAACATCACCATATTCCATCACCATTTTCACG
Found at i:37105 original size:9 final size:9
Alignment explanation
Indices: 37091--37122 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
37081 GTGCTTTAAC
37091 TTTCTTTCT
1 TTTCTTTCT
37100 TTTCTTTCT
1 TTTCTTTCT
37109 TTTCTTT-T
1 TTTCTTTCT
37117 TTTCTT
1 TTTCTT
37123 CCTCTTTGGG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 7 0.30
9 16 0.70
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTCTTTCT
Found at i:37108 original size:13 final size:13
Alignment explanation
Indices: 37090--37122 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
37080 AGTGCTTTAA
37090 CTTTCTTTCTTTT
1 CTTTCTTTCTTTT
37103 CTTTCTTTTCTTTT
1 CTTTC-TTTCTTTT
37117 -TTTCTT
1 CTTTCTT
37123 CCTCTTTGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 2 0.11
13 9 0.47
14 8 0.42
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (13 bp):
CTTTCTTTCTTTT
Found at i:37159 original size:22 final size:22
Alignment explanation
Indices: 37125--37169 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
37115 TTTTTCTTCC
* *
37125 TCTTTGGGTGCTTTCAATTTCT
1 TCTTTGAGAGCTTTCAATTTCT
* *
37147 TCTTTGAGAGCTTTGATTTTCT
1 TCTTTGAGAGCTTTCAATTTCT
37169 T
1 T
37170 TGCTGAATTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.11, C:0.16, G:0.18, T:0.56
Consensus pattern (22 bp):
TCTTTGAGAGCTTTCAATTTCT
Found at i:39182 original size:18 final size:19
Alignment explanation
Indices: 39151--39188 Score: 69
Period size: 18 Copynumber: 2.1 Consensus size: 19
39141 ACCACGTCAC
39151 AAAGGACGTTCATCATTGT
1 AAAGGACGTTCATCATTGT
39170 AAAGGAC-TTCATCATTGT
1 AAAGGACGTTCATCATTGT
39188 A
1 A
39189 TCTCCCAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (19 bp):
AAAGGACGTTCATCATTGT
Done.