Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002741.1 Hibiscus syriacus cultivar Beakdansim tig00005651_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: 66528
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1998 original size:22 final size:22
Alignment explanation
Indices: 1973--2014 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1963 AAAGAACAGT
*
1973 TAAAA-AAATATAACATATAAAA
1 TAAAATAAACATAA-ATATAAAA
1995 TAAAATAAACATAAATATAA
1 TAAAATAAACATAAATATAA
2015 GGACCTAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (22 bp):
TAAAATAAACATAAATATAAAA
Found at i:5719 original size:18 final size:16
Alignment explanation
Indices: 5679--5713 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
5669 ATATTTCTTT
* *
5679 AATTGATTGAGTTTAA
1 AATTAATTGAATTTAA
5695 AATTAATTGAATTTAA
1 AATTAATTGAATTTAA
5711 AAT
1 AAT
5714 ATTAATGGGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.11, T:0.43
Consensus pattern (16 bp):
AATTAATTGAATTTAA
Found at i:5799 original size:14 final size:14
Alignment explanation
Indices: 5780--5806 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5770 AACATAACCT
5780 AACATAAATGAACG
1 AACATAAATGAACG
5794 AACATAAATGAAC
1 AACATAAATGAAC
5807 ATAAACAAGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.15, G:0.11, T:0.15
Consensus pattern (14 bp):
AACATAAATGAACG
Found at i:7610 original size:5 final size:5
Alignment explanation
Indices: 7600--7628 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
7590 CATCATAATA
7600 ACTAT ACTAT ACTAT ACTAT ACTAT ACTA
1 ACTAT ACTAT ACTAT ACTAT ACTAT ACTA
7629 CATTGATTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.41, C:0.21, G:0.00, T:0.38
Consensus pattern (5 bp):
ACTAT
Found at i:10064 original size:21 final size:22
Alignment explanation
Indices: 10024--10064 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
10014 ATTTTAGTAC
* *
10024 AAGCTCAAATAGATAGAAAATA
1 AAGCACAAAGAGATAGAAAATA
10046 AAGCACAAAGAGA-AGAAAA
1 AAGCACAAAGAGATAGAAAA
10065 AAATCCCAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.63, C:0.10, G:0.17, T:0.10
Consensus pattern (22 bp):
AAGCACAAAGAGATAGAAAATA
Found at i:26771 original size:54 final size:54
Alignment explanation
Indices: 26688--27054 Score: 225
Period size: 54 Copynumber: 6.7 Consensus size: 54
26678 TAACGTGATT
* * * *
26688 TACTCCTCTATAAAAAAAGGAACACTAGAGCTCGCTTGGTCATAAAAATTTGCTC
1 TACTCCTCCAT-AACAAAGGAACACTAGAGCTCACTCGGTCATAAAAATTTGCTC
* * * * * **
26743 TACTCCTCCATAACGAAGGAACAATAGAGTTTACTCGGTCTTGGAAATTTGCTC
1 TACTCCTCCATAACAAAGGAACACTAGAGCTCACTCGGTCATAAAAATTTGCTC
* * * * * * * *
26797 TACTCCTCCATGACAAAGGAACGCTAGAGCTTACTCAGTCTTGGAAAA-TGGTTC
1 TACTCCTCCATAACAAAGGAACACTAGAGCTCACTCGGTCAT-AAAAATTTGCTC
* * * * * * ** *
26851 TACTTCTCGATAACAAAGGAACGCTAGAGCTTACTCTGTCTTGGAAATATGCTC
1 TACTCCTCCATAACAAAGGAACACTAGAGCTCACTCGGTCATAAAAATTTGCTC
* * * * * * ** *
26905 TACTCCACTATAACAAAGGAACGCTAGAGCTTAGTCGGTCTTGGAAGTTTGCTC
1 TACTCCTCCATAACAAAGGAACACTAGAGCTCACTCGGTCATAAAAATTTGCTC
** * * * * * *
26959 TACTCCTCCATAACAAA-GAGATGCTAAAGCTTACTTGGTCTTAAAAAAGTATGGGTC
1 TACTCCTCCATAACAAAGGA-ACACTAGAGCTCACTCGGTCAT-AAAAA-T-TTGCTC
* * * *
27016 CACTCCTCAATAATAAAGGAACACTAGAGCTTACTCGGT
1 TACTCCTCCATAACAAAGGAACACTAGAGCTCACTCGGT
27055 ATCTAAAATG
Statistics
Matches: 252, Mismatches: 53, Indels: 12
0.79 0.17 0.04
Matches are distributed among these distances:
53 6 0.02
54 194 0.77
55 16 0.06
56 1 0.00
57 33 0.13
58 2 0.01
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.28
Consensus pattern (54 bp):
TACTCCTCCATAACAAAGGAACACTAGAGCTCACTCGGTCATAAAAATTTGCTC
Found at i:26990 original size:108 final size:106
Alignment explanation
Indices: 26733--27051 Score: 323
Period size: 108 Copynumber: 2.9 Consensus size: 106
26723 TTGGTCATAA
* * * *
26733 AAATTTGCTCTACTCCTCCATAACGAAGGAACAATAGAGTTTACTCGGTCTTGGAAATTTGCTCT
1 AAATTTGCTCTACTCCTCCATAACAAAGGAGC--TAGAGCTTACTCGGTCTTGGAAATATGCTCT
* *
26798 ACTCCTCCATGACAAAGGAACGCTAGAGCTTACTCAGTCTTGG
64 ACTCCACCATAACAAAGGAACGCTAGAGCTTACTCAGTCTTGG
* * * * * *
26841 AAAATGGTTCTACTTCTCGATAACAAAGGAACGCTAGAGCTTACTCTGTCTTGGAAATATGCTCT
1 AAATTTGCTCTACTCCTCCATAACAAAGG-A-GCTAGAGCTTACTCGGTCTTGGAAATATGCTCT
* * *
26906 ACTCCACTATAACAAAGGAACGCTAGAGCTTAGTCGGTCTTGG
64 ACTCCACCATAACAAAGGAACGCTAGAGCTTACTCAGTCTTGG
* * * ** *
26949 AAGTTTGCTCTACTCCTCCATAACAAAGAGATGCTAAAGCTTACTTGGTCTTAAAAAAGTATGGG
1 AAATTTGCTCTACTCCTCCATAACAAAG-GA-GCTAGAGCTTACTCGGTCTT-GGAAA-TAT-GC
* * * * *
27014 TCCACTCCTCAATAATAAAGGAACACTAGAGCTTACTC
61 TCTACTCCACCATAACAAAGGAACGCTAGAGCTTACTC
27052 GGTATCTAAA
Statistics
Matches: 171, Mismatches: 34, Indels: 9
0.80 0.16 0.04
Matches are distributed among these distances:
108 129 0.75
109 5 0.03
110 4 0.02
111 33 0.19
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (106 bp):
AAATTTGCTCTACTCCTCCATAACAAAGGAGCTAGAGCTTACTCGGTCTTGGAAATATGCTCTAC
TCCACCATAACAAAGGAACGCTAGAGCTTACTCAGTCTTGG
Found at i:30645 original size:116 final size:116
Alignment explanation
Indices: 30351--30721 Score: 465
Period size: 116 Copynumber: 3.2 Consensus size: 116
30341 CAATGTACCT
* * * * *
30351 AATAAGCACCTAAGTGGCACAATGATGTATAGGTTCTGTAGTATACAACAATAATATATACTAAC
1 AATAAGAACCTAAGTGCCACAATGATGTATAGGTACTGTAGTATACAACGA-AA-CTATACTAAC
*
30416 AATTATGGAGTGGTAATTCATTATGAATACCATCCTTGCACACAAAAGTGCACT
64 AATTATGGAGTGGTAATTCATTATGAATACCATCCTTGCACAC-AAAGTGCACG
* * * * *
30470 AATAAGCACCTAAGTACCACAATGACGT-TGAGGTACTGTAGTATACAATGATACTATACTAACA
1 AATAAGAACCTAAGTGCCACAATGATGTAT-AGGTACTGTAGTATACAACGAAACTATACTAACA
**** * *
30534 ATTCCAAAGTGATAATTCATTATGAATACCAACCTTGCACACAAAGTGCACG
65 ATTATGGAGTGGTAATTCATTATGAATACCATCCTTGCACACAAAGTGCACG
* * * * *
30586 AATAAGAACTTGAGTGCCACAATGATGTATATGTACTGTAGTATATAACGACACTATACTAACAA
1 AATAAGAACCTAAGTGCCACAATGATGTATAGGTACTGTAGTATACAACGAAACTATACTAACAA
* *
30651 TTATGGAGTGGTAATTCATTATGAATACCATCCTTTCACACAAAGTGCACCC
66 TTATGGAGTGGTAATTCATTATGAATACCATCCTTGCACACAAAGTGCA-CG
*
30703 AATAAGCACCTAAGTGCCA
1 AATAAGAACCTAAGTGCCA
30722 TAGTACAACA
Statistics
Matches: 214, Mismatches: 35, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
116 105 0.49
117 64 0.30
118 2 0.01
119 43 0.20
ACGTcount: A:0.39, C:0.19, G:0.15, T:0.27
Consensus pattern (116 bp):
AATAAGAACCTAAGTGCCACAATGATGTATAGGTACTGTAGTATACAACGAAACTATACTAACAA
TTATGGAGTGGTAATTCATTATGAATACCATCCTTGCACACAAAGTGCACG
Found at i:34209 original size:145 final size:145
Alignment explanation
Indices: 33998--34285 Score: 567
Period size: 145 Copynumber: 2.0 Consensus size: 145
33988 CTAGAGTTGG
33998 TTCTATCATCCTCAACCAGTCATGTACATTCTATCCTAGCCATCAAAATCATCATCATCATCGGG
1 TTCTATCATCCTCAACCAGTCATGTACATTCTATCCTAGCCATCAAAATCATCATCATCATCGGG
34063 TATCCTTAACTAATTCCAAAAACTATTCAAACATTTACTAATGTCATGGCATATTTATTTCACCA
66 TATCCTTAACTAATTCCAAAAACTATTCAAACATTTACTAATGTCATGGCATATTTATTTCACCA
34128 CTACTATCATGTACA
131 CTACTATCATGTACA
34143 TTCTATCATCCTCAACCAGTCATGTACATTCTATCCTAGCCATCAAAATCATCATCATCATCGGG
1 TTCTATCATCCTCAACCAGTCATGTACATTCTATCCTAGCCATCAAAATCATCATCATCATCGGG
*
34208 TATCCTTAACTAATTCCAAAAACTATTCAAACATTTACTAATGTCATGGCATATTTATTTCACTA
66 TATCCTTAACTAATTCCAAAAACTATTCAAACATTTACTAATGTCATGGCATATTTATTTCACCA
34273 CTACTATCATGTA
131 CTACTATCATGTA
34286 GTGATGCGAG
Statistics
Matches: 142, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
145 142 1.00
ACGTcount: A:0.33, C:0.26, G:0.07, T:0.34
Consensus pattern (145 bp):
TTCTATCATCCTCAACCAGTCATGTACATTCTATCCTAGCCATCAAAATCATCATCATCATCGGG
TATCCTTAACTAATTCCAAAAACTATTCAAACATTTACTAATGTCATGGCATATTTATTTCACCA
CTACTATCATGTACA
Found at i:43795 original size:19 final size:20
Alignment explanation
Indices: 43771--43810 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
43761 ATGGTTACAA
43771 TTGAAT-ATGTCATGGCAAG
1 TTGAATAATGTCATGGCAAG
43790 TTGAATGAAATGTCATGGCAA
1 TTGAAT--AATGTCATGGCAA
43811 ATTCAATTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.33
22 12 0.67
ACGTcount: A:0.35, C:0.10, G:0.25, T:0.30
Consensus pattern (20 bp):
TTGAATAATGTCATGGCAAG
Found at i:64235 original size:12 final size:12
Alignment explanation
Indices: 64218--64243 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
64208 TGAAGTGGAT
64218 GAAGATGAAGAA
1 GAAGATGAAGAA
64230 GAAGATGAAGAA
1 GAAGATGAAGAA
64242 GA
1 GA
64244 GATTGCCAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.58, C:0.00, G:0.35, T:0.08
Consensus pattern (12 bp):
GAAGATGAAGAA
Found at i:65684 original size:20 final size:20
Alignment explanation
Indices: 65661--65728 Score: 59
Period size: 20 Copynumber: 3.4 Consensus size: 20
65651 ATTCTTACAG
65661 TATCGATACTGCATGAACAA
1 TATCGATACTGCATGAACAA
* * *
65681 TATCGATATTGTTC-T-TACAG
1 TATCGATACTG--CATGAACAA
* *
65701 TTTCAATACTGCATGAACAA
1 TATCGATACTGCATGAACAA
65721 TATCGATA
1 TATCGATA
65729 TTGTTCACGT
Statistics
Matches: 34, Mismatches: 10, Indels: 8
0.65 0.19 0.15
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.88
21 1 0.03
22 1 0.03
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.34
Consensus pattern (20 bp):
TATCGATACTGCATGAACAA
Found at i:65696 original size:40 final size:40
Alignment explanation
Indices: 65641--65734 Score: 161
Period size: 40 Copynumber: 2.4 Consensus size: 40
65631 GGGTACATAG
* *
65641 TATCGATATTATTCTTACAGTATCGATACTGCATGAACAA
1 TATCGATATTGTTCTTACAGTATCAATACTGCATGAACAA
*
65681 TATCGATATTGTTCTTACAGTTTCAATACTGCATGAACAA
1 TATCGATATTGTTCTTACAGTATCAATACTGCATGAACAA
65721 TATCGATATTGTTC
1 TATCGATATTGTTC
65735 ACGTAGTACA
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 51 1.00
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.38
Consensus pattern (40 bp):
TATCGATATTGTTCTTACAGTATCAATACTGCATGAACAA
Done.