Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007332.1 Hibiscus syriacus cultivar Beakdansim tig00019613_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: 50857
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Found at i:7598 original size:16 final size:16
Alignment explanation
Indices: 7577--7607 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
7567 GTTATGACCC
*
7577 AAGAGAATCGGAGAAG
1 AAGAGAATCGAAGAAG
7593 AAGAGAATCGAAGAA
1 AAGAGAATCGAAGAA
7608 ATAGAAATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.06, G:0.32, T:0.06
Consensus pattern (16 bp):
AAGAGAATCGAAGAAG
Found at i:11331 original size:16 final size:16
Alignment explanation
Indices: 11310--11340 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
11300 GTTATGACCC
*
11310 AAGAGAATCGGAGAAG
1 AAGAGAATCGAAGAAG
11326 AAGAGAATCGAAGAA
1 AAGAGAATCGAAGAA
11341 ATAGAAATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.06, G:0.32, T:0.06
Consensus pattern (16 bp):
AAGAGAATCGAAGAAG
Found at i:13190 original size:21 final size:21
Alignment explanation
Indices: 13151--13194 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
13141 TTTAATTGAG
* * *
13151 TATATATATATTTTTTTAAAA
1 TATATATATAATCTCTTAAAA
13172 TATATATATAATCTCTTAAAA
1 TATATATATAATCTCTTAAAA
13193 TA
1 TA
13195 AACTTAATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (21 bp):
TATATATATAATCTCTTAAAA
Found at i:20035 original size:7 final size:7
Alignment explanation
Indices: 20022--20065 Score: 54
Period size: 7 Copynumber: 6.4 Consensus size: 7
20012 GTCAAAGGAA
20022 GTCAACG
1 GTCAACG
*
20029 ATCAACG
1 GTCAACG
20036 GTC-ACG
1 GTCAACG
20042 GTCAACG
1 GTCAACG
20049 GTCAACG
1 GTCAACG
* *
20056 ATCAGCG
1 GTCAACG
20063 GTC
1 GTC
20066 GGGTCGGGTC
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
6 6 0.19
7 25 0.81
ACGTcount: A:0.27, C:0.30, G:0.27, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:20047 original size:20 final size:21
Alignment explanation
Indices: 20022--20065 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
20012 GTCAAAGGAA
*
20022 GTCAACGATCAACGGTCA-CG
1 GTCAACGATCAACGATCAGCG
*
20042 GTCAACGGTCAACGATCAGCG
1 GTCAACGATCAACGATCAGCG
20063 GTC
1 GTC
20066 GGGTCGGGTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 16 0.76
21 5 0.24
ACGTcount: A:0.27, C:0.30, G:0.27, T:0.16
Consensus pattern (21 bp):
GTCAACGATCAACGATCAGCG
Found at i:20080 original size:14 final size:14
Alignment explanation
Indices: 20063--20096 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
20053 ACGATCAGCG
20063 GTCGGGTCGGGTCA
1 GTCGGGTCGGGTCA
*
20077 GTCGGGTTGGGTCA
1 GTCGGGTCGGGTCA
20091 GATCGG
1 G-TCGG
20097 TCAAACCGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.09, C:0.18, G:0.50, T:0.24
Consensus pattern (14 bp):
GTCGGGTCGGGTCA
Found at i:20115 original size:10 final size:10
Alignment explanation
Indices: 20100--20147 Score: 64
Period size: 10 Copynumber: 4.8 Consensus size: 10
20090 AGATCGGTCA
20100 AACCGGTTCG
1 AACCGGTTCG
20110 AACCGGTTCG
1 AACCGGTTCG
20120 AACCGG-TCG
1 AACCGGTTCG
20129 AAACCGG-TCAG
1 -AACCGGTTC-G
20140 AACCGGTT
1 AACCGGTT
20148 GAAAGTCAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
9 3 0.09
10 30 0.86
11 2 0.06
ACGTcount: A:0.25, C:0.29, G:0.29, T:0.17
Consensus pattern (10 bp):
AACCGGTTCG
Found at i:20125 original size:20 final size:21
Alignment explanation
Indices: 20094--20151 Score: 72
Period size: 20 Copynumber: 3.0 Consensus size: 21
20084 TGGGTCAGAT
20094 CGGTCA-AACCGGTTCG-AAC
1 CGGTCAGAACCGGTTCGAAAC
20113 CGGTTC-GAACCGG-TCGAAAC
1 CGG-TCAGAACCGGTTCGAAAC
20133 CGGTCAGAACCGGTT-GAAA
1 CGGTCAGAACCGGTTCGAAA
20152 GTCAAACCGG
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
19 8 0.24
20 25 0.74
21 1 0.03
ACGTcount: A:0.28, C:0.28, G:0.29, T:0.16
Consensus pattern (21 bp):
CGGTCAGAACCGGTTCGAAAC
Found at i:26569 original size:19 final size:19
Alignment explanation
Indices: 26545--26603 Score: 84
Period size: 19 Copynumber: 3.1 Consensus size: 19
26535 GTCGGGTCGG
26545 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
*
26564 TCAGACAGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
26583 TC-GAACCGGTCAGAACCGGT
1 TCAG-ACCGGTCA-AACCGGT
26603 T
1 T
26604 TCCAGCCCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
18 1 0.03
19 27 0.75
20 8 0.22
ACGTcount: A:0.27, C:0.29, G:0.27, T:0.17
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGT
Found at i:26591 original size:10 final size:11
Alignment explanation
Indices: 26545--26603 Score: 53
Period size: 10 Copynumber: 6.1 Consensus size: 11
26535 GTCGGGTCGG
26545 TCAG-ACCGG-
1 TCAGAACCGGT
26554 TCA-AACCGGT
1 TCAGAACCGGT
*
26564 TCAG-ACAGG-
1 TCAGAACCGGT
26573 TCA-AACCGGT
1 TCAGAACCGGT
26583 TC-GAACCGG-
1 TCAGAACCGGT
26592 TCAGAACCGGT
1 TCAGAACCGGT
26603 T
1 T
26604 TCCAGCCCTC
Statistics
Matches: 40, Mismatches: 2, Indels: 14
0.71 0.04 0.25
Matches are distributed among these distances:
9 17 0.43
10 22 0.55
11 1 0.03
ACGTcount: A:0.27, C:0.29, G:0.27, T:0.17
Consensus pattern (11 bp):
TCAGAACCGGT
Found at i:43518 original size:18 final size:18
Alignment explanation
Indices: 43495--43561 Score: 98
Period size: 18 Copynumber: 3.7 Consensus size: 18
43485 AGACAAGCGA
43495 AGCCAAGTGATGTTTGTC
1 AGCCAAGTGATGTTTGTC
*
43513 AGCCAAGTGACGTTTGTC
1 AGCCAAGTGATGTTTGTC
* *
43531 AGCCAAGTGATGTATCTC
1 AGCCAAGTGATGTTTGTC
*
43549 AGCCGAGTGATGT
1 AGCCAAGTGATGT
43562 ATCTCATCCA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 44 1.00
ACGTcount: A:0.24, C:0.19, G:0.28, T:0.28
Consensus pattern (18 bp):
AGCCAAGTGATGTTTGTC
Found at i:43562 original size:18 final size:18
Alignment explanation
Indices: 43495--43572 Score: 93
Period size: 18 Copynumber: 4.3 Consensus size: 18
43485 AGACAAGCGA
* *
43495 AGCCAAGTGATGTTTGTC
1 AGCCAAGTGATGTATCTC
* * *
43513 AGCCAAGTGACGTTTGTC
1 AGCCAAGTGATGTATCTC
43531 AGCCAAGTGATGTATCTC
1 AGCCAAGTGATGTATCTC
*
43549 AGCCGAGTGATGTATCTC
1 AGCCAAGTGATGTATCTC
*
43567 ATCCAA
1 AGCCAA
43573 TCCCTCCTAG
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 53 1.00
ACGTcount: A:0.26, C:0.22, G:0.24, T:0.28
Consensus pattern (18 bp):
AGCCAAGTGATGTATCTC
Found at i:43727 original size:42 final size:42
Alignment explanation
Indices: 43681--43886 Score: 211
Period size: 42 Copynumber: 4.9 Consensus size: 42
43671 TCATCCTCAC
* * *
43681 CCTCACCCTCACCGCCACCTCCTCCTCCACCTTCACTATCAT
1 CCTCACCCTCGCCGCCACCTCCTCCTCCACCTCCACCATCAT
* * **
43723 CCTCACCCTCGCCGCCACCTCCTCATTCACCTCCGTCATCAT
1 CCTCACCCTCGCCGCCACCTCCTCCTCCACCTCCACCATCAT
* * * *
43765 CCTCACACTCGCCACCACTTCCTACTCCACCTCCACCATCAT
1 CCTCACCCTCGCCGCCACCTCCTCCTCCACCTCCACCATCAT
* * *
43807 CCTCA-CCTCACC-CTCACCTCCACCTTCTCCACCTCCACCACCAT
1 CCTCACCCTCGCCGC-CACCT---CCTCCTCCACCTCCACCATCAT
**
43851 -CTCACCCTCGCCGCCACCTCCTCCTCTGCCTCCACC
1 CCTCACCCTCGCCGCCACCTCCTCCTCCACCTCCACC
43887 TCGACCTCCA
Statistics
Matches: 134, Mismatches: 24, Indels: 13
0.78 0.14 0.08
Matches are distributed among these distances:
40 1 0.01
41 23 0.17
42 74 0.55
43 4 0.03
44 31 0.23
45 1 0.01
ACGTcount: A:0.16, C:0.58, G:0.04, T:0.22
Consensus pattern (42 bp):
CCTCACCCTCGCCGCCACCTCCTCCTCCACCTCCACCATCAT
Found at i:44321 original size:39 final size:39
Alignment explanation
Indices: 44275--44360 Score: 136
Period size: 39 Copynumber: 2.2 Consensus size: 39
44265 TTTTCCACGT
*
44275 TCCCCATCAACACCTTGCAATTTTAGTCATCCTCTTCCC
1 TCCCCATCAAAACCTTGCAATTTTAGTCATCCTCTTCCC
* * *
44314 TCTCCATCAAAACCTTGTAATTTTAGTCATCCTTTTCCC
1 TCCCCATCAAAACCTTGCAATTTTAGTCATCCTCTTCCC
44353 TCCCCATC
1 TCCCCATC
44361 GAAAGAACGT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.21, C:0.38, G:0.05, T:0.36
Consensus pattern (39 bp):
TCCCCATCAAAACCTTGCAATTTTAGTCATCCTCTTCCC
Found at i:44824 original size:36 final size:36
Alignment explanation
Indices: 44751--44880 Score: 172
Period size: 36 Copynumber: 3.6 Consensus size: 36
44741 TCCGATGCTG
** * *
44751 CTCCACCTCCAACGTGTAATGCT-CCCCACCCGCTC
1 CTCCACCTCCAACGTCCAATGCTGCTCCACCCCCTC
* *
44786 CTCCACCTCCAACGTCCGATGCTGCTTCACCCCCTC
1 CTCCACCTCCAACGTCCAATGCTGCTCCACCCCCTC
*
44822 CTCCACCTCCAACTTCCAATGCTGCTCCACCCCCTC
1 CTCCACCTCCAACGTCCAATGCTGCTCCACCCCCTC
* *
44858 CTCCACGTCCAACGTCAAATGCT
1 CTCCACCTCCAACGTCCAATGCT
44881 CCTTCTCCAC
Statistics
Matches: 82, Mismatches: 12, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
35 20 0.24
36 62 0.76
ACGTcount: A:0.18, C:0.51, G:0.10, T:0.22
Consensus pattern (36 bp):
CTCCACCTCCAACGTCCAATGCTGCTCCACCCCCTC
Found at i:45012 original size:42 final size:41
Alignment explanation
Indices: 44932--45016 Score: 143
Period size: 42 Copynumber: 2.0 Consensus size: 41
44922 ATCTGGAGCA
* *
44932 CCACCACCACCTCCTGGTGGAGAGCTCCTGGAGCACCACCT
1 CCACCACCACCTCCAGCTGGAGAGCTCCTGGAGCACCACCT
44973 CCACCACCACCTCCAGCTGGAGGAGCTCCTGGAGCACCACCT
1 CCACCACCACCTCCAGCTGGA-GAGCTCCTGGAGCACCACCT
45015 CC
1 CC
45017 TGGAGGTCGA
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
41 19 0.46
42 22 0.54
ACGTcount: A:0.20, C:0.46, G:0.21, T:0.13
Consensus pattern (41 bp):
CCACCACCACCTCCAGCTGGAGAGCTCCTGGAGCACCACCT
Found at i:45069 original size:27 final size:28
Alignment explanation
Indices: 45025--45102 Score: 83
Period size: 27 Copynumber: 2.8 Consensus size: 28
45015 CCTGGAGGTC
*
45025 GAGCTCTTGGTCCCCCACCTCCA-C-CTG
1 GAGCTCCTGG-CCCCCACCTCCACCACTG
45052 GAGCTCCTGGCCCTCCACCTCCACCAGCTG
1 GAGCTCCTGGCCC-CCACCTCCACCA-CTG
*
45082 GAGCTCGTGG--CCCACCTCCAC
1 GAGCTCCTGGCCCCCACCTCCAC
45103 TAGGTGCCAA
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
26 3 0.07
27 28 0.62
28 2 0.04
30 12 0.27
ACGTcount: A:0.13, C:0.49, G:0.21, T:0.18
Consensus pattern (28 bp):
GAGCTCCTGGCCCCCACCTCCACCACTG
Done.