Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003832.1 Hibiscus syriacus cultivar Beakdansim tig00008218_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: 67265
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Found at i:2167 original size:38 final size:38
Alignment explanation
Indices: 2096--2169 Score: 96
Period size: 38 Copynumber: 1.9 Consensus size: 38
2086 GCGTTATTTT
*** *
2096 ATTAAATGAACGAACATGAACAATTTTTTGTTCGTTTA
1 ATTAAATGAACGAACATGAACAATGCCTCGTTCGTTTA
2134 ATTAAATGAACGAACATGAAC-ATAGCCTCGTTCGTT
1 ATTAAATGAACGAACATGAACAAT-GCCTCGTTCGTT
2170 CATTTATGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
37 2 0.06
38 29 0.94
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (38 bp):
ATTAAATGAACGAACATGAACAATGCCTCGTTCGTTTA
Found at i:2207 original size:14 final size:14
Alignment explanation
Indices: 2188--2223 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
2178 TTCGTGAACG
2188 TCGGTTATGTTCGT
1 TCGGTTATGTTCGT
2202 TCGGTTATGTTCGT
1 TCGGTTATGTTCGT
*
2216 TCAGTTAT
1 TCGGTTAT
2224 TCGTTTATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.11, C:0.14, G:0.25, T:0.50
Consensus pattern (14 bp):
TCGGTTATGTTCGT
Found at i:2231 original size:22 final size:22
Alignment explanation
Indices: 2201--2245 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
2191 GTTATGTTCG
2201 TTCGGTTATGTTCGTTCAGTTA
1 TTCGGTTATGTTCGTTCAGTTA
* * *
2223 TTCGTTTATGTTCTTTCATTTA
1 TTCGGTTATGTTCGTTCAGTTA
2245 T
1 T
2246 GTTTAACCCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.13, C:0.13, G:0.16, T:0.58
Consensus pattern (22 bp):
TTCGGTTATGTTCGTTCAGTTA
Found at i:3005 original size:16 final size:15
Alignment explanation
Indices: 2967--3010 Score: 61
Period size: 16 Copynumber: 2.9 Consensus size: 15
2957 AGGGTCTCCA
2967 CGTTTATGTTCGTAT
1 CGTTTATGTTCGTAT
* *
2982 CATTTATGTTCGTGTT
1 CGTTTATGTTCGT-AT
2998 CGTTTATGTTCGT
1 CGTTTATGTTCGT
3011 TTATTTATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
15 12 0.48
16 13 0.52
ACGTcount: A:0.11, C:0.14, G:0.20, T:0.55
Consensus pattern (15 bp):
CGTTTATGTTCGTAT
Found at i:9042 original size:29 final size:29
Alignment explanation
Indices: 9010--9078 Score: 104
Period size: 29 Copynumber: 2.4 Consensus size: 29
9000 AATTAATTAC
*
9010 AAAACTAACACCC-TTTTAACAATATTTTA
1 AAAACTAACACCCTTTTTAA-AATATTTAA
*
9039 AAAACTAACACCCTTTTTTAAATATTTAA
1 AAAACTAACACCCTTTTTAAAATATTTAA
9068 AAAACTAACAC
1 AAAACTAACAC
9079 TCAGTCAACG
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
29 32 0.86
30 5 0.14
ACGTcount: A:0.48, C:0.20, G:0.00, T:0.32
Consensus pattern (29 bp):
AAAACTAACACCCTTTTTAAAATATTTAA
Found at i:15814 original size:29 final size:29
Alignment explanation
Indices: 15775--15856 Score: 123
Period size: 29 Copynumber: 2.8 Consensus size: 29
15765 ATCCTAATAG
*
15775 AAATTAATTACAAAACTAACACCC-TTTT
1 AAATTATTTACAAAACTAACACCCTTTTT
15803 AACATTATTTACAAAACTAACACCCTTTTTT
1 AA-ATTATTTACAAAACTAACACCC-TTTTT
15834 AAA-TATTTACAAAACTAACACCC
1 AAATTATTTACAAAACTAACACCC
15857 GGTCAACGGT
Statistics
Matches: 50, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
28 2 0.04
29 41 0.82
30 1 0.02
31 6 0.12
ACGTcount: A:0.45, C:0.23, G:0.00, T:0.32
Consensus pattern (29 bp):
AAATTATTTACAAAACTAACACCCTTTTT
Found at i:20597 original size:3 final size:3
Alignment explanation
Indices: 20589--20641 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
20579 TTTTTACCCA
20589 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
20637 TAT TA
1 TAT TA
20642 AATATATATT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:22824 original size:17 final size:17
Alignment explanation
Indices: 22795--22838 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
22785 TTTAATTTTT
*
22795 AATTTTT-TCTTTTCAA
1 AATTTTTATATTTTCAA
*
22811 AATTTTTATATTTTCAT
1 AATTTTTATATTTTCAA
*
22828 AATATTTATAT
1 AATTTTTATAT
22839 GTTTTTATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 7 0.29
17 17 0.71
ACGTcount: A:0.32, C:0.07, G:0.00, T:0.61
Consensus pattern (17 bp):
AATTTTTATATTTTCAA
Found at i:22875 original size:13 final size:15
Alignment explanation
Indices: 22844--22880 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
22834 TATATGTTTT
22844 TATTTTATTTGCAAG
1 TATTTTATTTGCAAG
22859 TATTTTATTT-C-AG
1 TATTTTATTTGCAAG
22872 TA-TTTATTT
1 TATTTTATTT
22881 TTCTGTCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 7 0.32
13 4 0.18
14 1 0.05
15 10 0.45
ACGTcount: A:0.24, C:0.05, G:0.08, T:0.62
Consensus pattern (15 bp):
TATTTTATTTGCAAG
Found at i:32170 original size:24 final size:24
Alignment explanation
Indices: 32150--32204 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 24
32140 TATGTTCGTG
32150 AATGTTCGATTATGTTCGTTCGGT
1 AATGTTCGATTATGTTCGTTCGGT
* *
32174 TATGTTCGGTTATGTTCGTTCGGT
1 AATGTTCGATTATGTTCGTTCGGT
*
32198 TATGTTC
1 AATGTTC
32205 TTTCATTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.13, C:0.13, G:0.25, T:0.49
Consensus pattern (24 bp):
AATGTTCGATTATGTTCGTTCGGT
Found at i:32176 original size:14 final size:14
Alignment explanation
Indices: 32153--32204 Score: 67
Period size: 14 Copynumber: 4.0 Consensus size: 14
32143 GTTCGTGAAT
*
32153 GTTCGATTATGTTC
1 GTTCGGTTATGTTC
32167 GTTCGGTTA---T-
1 GTTCGGTTATGTTC
32177 GTTCGGTTATGTTC
1 GTTCGGTTATGTTC
32191 GTTCGGTTATGTTC
1 GTTCGGTTATGTTC
32205 TTTCATTTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
10 9 0.27
11 1 0.03
13 1 0.03
14 22 0.67
ACGTcount: A:0.10, C:0.13, G:0.27, T:0.50
Consensus pattern (14 bp):
GTTCGGTTATGTTC
Found at i:32204 original size:10 final size:10
Alignment explanation
Indices: 32167--32191 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
32157 GATTATGTTC
32167 GTTCGGTTAT
1 GTTCGGTTAT
32177 GTTCGGTTAT
1 GTTCGGTTAT
32187 GTTCG
1 GTTCG
32192 TTCGGTTATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.08, C:0.12, G:0.32, T:0.48
Consensus pattern (10 bp):
GTTCGGTTAT
Found at i:32214 original size:14 final size:14
Alignment explanation
Indices: 32159--32217 Score: 54
Period size: 14 Copynumber: 4.5 Consensus size: 14
32149 GAATGTTCGA
*
32159 TTATGTTCGTTCGG
1 TTATGTTCGTTCAG
32173 TTATGTTCG----G
1 TTATGTTCGTTCAG
*
32183 TTATGTTCGTTCGG
1 TTATGTTCGTTCAG
* *
32197 TTATGTTCTTTCAT
1 TTATGTTCGTTCAG
32211 TTATGTT
1 TTATGTT
32218 TAACTCAATC
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
10 10 0.26
14 28 0.74
ACGTcount: A:0.10, C:0.12, G:0.22, T:0.56
Consensus pattern (14 bp):
TTATGTTCGTTCAG
Found at i:32967 original size:10 final size:10
Alignment explanation
Indices: 32952--32994 Score: 59
Period size: 10 Copynumber: 4.1 Consensus size: 10
32942 GTCTCCAACA
32952 TTTATGTTCG
1 TTTATGTTCG
32962 TTTATGTTCG
1 TTTATGTTCG
*
32972 TGTTCGTGTTCG
1 T-TT-ATGTTCG
32984 TTTATGTTCG
1 TTTATGTTCG
32994 T
1 T
32995 GTTCGTTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
10 18 0.62
11 4 0.14
12 7 0.24
ACGTcount: A:0.07, C:0.12, G:0.23, T:0.58
Consensus pattern (10 bp):
TTTATGTTCG
Found at i:32977 original size:16 final size:16
Alignment explanation
Indices: 32972--33004 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
32962 TTTATGTTCG
32972 TGTTCGTGTTCGTTTA
1 TGTTCGTGTTCGTTTA
32988 TGTTCGTGTTCGTTTA
1 TGTTCGTGTTCGTTTA
33004 T
1 T
33005 TTATTAAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTGTTCGTTTA
Found at i:32984 original size:22 final size:22
Alignment explanation
Indices: 32956--33000 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
32946 CCAACATTTA
32956 TGTTCGTTTATGTTCGTGTTCG
1 TGTTCGTTTATGTTCGTGTTCG
32978 TGTTCGTTTATGTTCGTGTTCG
1 TGTTCGTTTATGTTCGTGTTCG
33000 T
1 T
33001 TTATTTATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.04, C:0.13, G:0.27, T:0.56
Consensus pattern (22 bp):
TGTTCGTTTATGTTCGTGTTCG
Found at i:36256 original size:2 final size:2
Alignment explanation
Indices: 36249--36300 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
36239 ATTAGAGATA
36249 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
36291 AT AT AT AT AT
1 AT AT AT AT AT
36301 GGGTGGATAG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:37839 original size:39 final size:40
Alignment explanation
Indices: 37767--37844 Score: 104
Period size: 39 Copynumber: 2.0 Consensus size: 40
37757 CTTTAAAGAG
* * * *
37767 TGGTAACTATTTTTTTATTACCCTTTAATTTTTATTTGTA
1 TGGTAACTATTTTCTTATTACCCCTTAAATTTTACTTGTA
*
37807 TGGTAATTA-TTTCTTATTACCCCTTAAATTTTACTTGT
1 TGGTAACTATTTTCTTATTACCCCTTAAATTTTACTTGT
37845 TTCACCTAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
39 25 0.76
40 8 0.24
ACGTcount: A:0.23, C:0.13, G:0.08, T:0.56
Consensus pattern (40 bp):
TGGTAACTATTTTCTTATTACCCCTTAAATTTTACTTGTA
Found at i:40090 original size:14 final size:14
Alignment explanation
Indices: 40071--40116 Score: 83
Period size: 14 Copynumber: 3.3 Consensus size: 14
40061 TGTTCGTGAA
40071 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
40085 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
*
40099 CGTTCAGTTATGTT
1 CGTTCGGTTATGTT
40113 CGTT
1 CGTT
40117 TATGTTCTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
14 31 1.00
ACGTcount: A:0.09, C:0.15, G:0.26, T:0.50
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:40113 original size:24 final size:24
Alignment explanation
Indices: 40086--40136 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
40076 GGTTATGTTC
40086 GTTCGGTTATGTTCGTTCAGTTAT
1 GTTCGGTTATGTTCGTTCAGTTAT
* * *
40110 GTTCGTTTATGTTCTTTCATTTAT
1 GTTCGGTTATGTTCGTTCAGTTAT
40134 GTT
1 GTT
40137 TAACCCAATC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.12, C:0.12, G:0.20, T:0.57
Consensus pattern (24 bp):
GTTCGGTTATGTTCGTTCAGTTAT
Found at i:40884 original size:16 final size:15
Alignment explanation
Indices: 40863--40913 Score: 68
Period size: 16 Copynumber: 3.3 Consensus size: 15
40853 GTCTCCAACG
40863 TTTATGTTCGTATTCA
1 TTTATGTTCGT-TTCA
*
40879 TTTATGTTCGTGTTCG
1 TTTATGTTCGT-TTCA
40895 TTTATGTTCGTTT-A
1 TTTATGTTCGTTTCA
40909 TTTAT
1 TTTAT
40914 TAAATGAACG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
14 5 0.16
15 2 0.06
16 25 0.78
ACGTcount: A:0.14, C:0.10, G:0.16, T:0.61
Consensus pattern (15 bp):
TTTATGTTCGTTTCA
Found at i:46991 original size:29 final size:29
Alignment explanation
Indices: 46957--47025 Score: 104
Period size: 29 Copynumber: 2.4 Consensus size: 29
46947 AATTAATTAC
*
46957 AAAACTAACACCC-TTTTAACAATATTTTA
1 AAAACTAACACCCTTTTTAA-AATATTTAA
*
46986 AAAACTAACACCCTTTTTTAAATATTTAA
1 AAAACTAACACCCTTTTTAAAATATTTAA
47015 AAAACTAACAC
1 AAAACTAACAC
47026 TCAGTCAACG
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
29 32 0.86
30 5 0.14
ACGTcount: A:0.48, C:0.20, G:0.00, T:0.32
Consensus pattern (29 bp):
AAAACTAACACCCTTTTTAAAATATTTAA
Found at i:53757 original size:29 final size:29
Alignment explanation
Indices: 53718--53799 Score: 123
Period size: 29 Copynumber: 2.8 Consensus size: 29
53708 ATCCTAATAG
*
53718 AAATTAATTACAAAACTAACACCC-TTTT
1 AAATTATTTACAAAACTAACACCCTTTTT
53746 AACATTATTTACAAAACTAACACCCTTTTTT
1 AA-ATTATTTACAAAACTAACACCC-TTTTT
53777 AAA-TATTTACAAAACTAACACCC
1 AAATTATTTACAAAACTAACACCC
53800 GGTCAACGGT
Statistics
Matches: 50, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
28 2 0.04
29 41 0.82
30 1 0.02
31 6 0.12
ACGTcount: A:0.45, C:0.23, G:0.00, T:0.32
Consensus pattern (29 bp):
AAATTATTTACAAAACTAACACCCTTTTT
Found at i:58523 original size:3 final size:3
Alignment explanation
Indices: 58515--58568 Score: 63
Period size: 3 Copynumber: 16.7 Consensus size: 3
58505 TTTTTACCCA
*
58515 TAT TAT TAT TAT TATT TAT TAT TAT TAT TAT ATAT ATAT TAT TAA TAT
1 TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT -TAT -TAT TAT TAT TAT
58563 ATAT TA
1 -TAT TA
58569 AATACATATA
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
3 33 0.72
4 13 0.28
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:58562 original size:13 final size:13
Alignment explanation
Indices: 58515--58568 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
58505 TTTTTACCCA
*
58515 TATTATTAT-TAT
1 TATTAATATATAT
*
58527 TATTTAT-TATTAT
1 TATTAATATA-TAT
58540 TATTATATATATAT
1 TATTA-ATATATAT
58554 TATTAATATATAT
1 TATTAATATATAT
58567 TA
1 TA
58569 AATACATATA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
11 1 0.03
12 5 0.14
13 17 0.49
14 10 0.29
15 2 0.06
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (13 bp):
TATTAATATATAT
Found at i:60698 original size:17 final size:17
Alignment explanation
Indices: 60669--60712 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
60659 TTTAATTTTT
*
60669 AATTTTT-TCTTTTCAA
1 AATTTTTATATTTTCAA
*
60685 AATTTTTATATTTTCAT
1 AATTTTTATATTTTCAA
*
60702 AATATTTATAT
1 AATTTTTATAT
60713 GTTTTATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 7 0.29
17 17 0.71
ACGTcount: A:0.32, C:0.07, G:0.00, T:0.61
Consensus pattern (17 bp):
AATTTTTATATTTTCAA
Found at i:60757 original size:14 final size:15
Alignment explanation
Indices: 60720--60757 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
60710 TATGTTTTAT
60720 TTTATTTTTCAAGTA
1 TTTATTTTTCAAGTA
*
60735 TTT-TATTTC-AGTA
1 TTTATTTTTCAAGTA
60748 TTTATTTTTC
1 TTTATTTTTC
60758 TGTCAAAGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
13 7 0.35
14 10 0.50
15 3 0.15
ACGTcount: A:0.21, C:0.08, G:0.05, T:0.66
Consensus pattern (15 bp):
TTTATTTTTCAAGTA
Done.