Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003426.1 Hibiscus syriacus cultivar Beakdansim tig00007219_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: 40503
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.34
Found at i:907 original size:138 final size:136
Alignment explanation
Indices: 416--924 Score: 525
Period size: 137 Copynumber: 3.7 Consensus size: 136
406 TCGTTTTCAA
* *
416 AGTGTAATCCTCAGACAATCAAGAACTTCCTCAATGCGAAGGAACCG-G--GTCTCCAAATTATC
1 AGTGTCATCCTCAGACAATCAA-AA-TTCCTAAATGCGAAGGAACCGTGTTGTCTCCAAATTATC
* *** * * * * * *
478 CAAAAATGA-ATTTGTCCTCACCAAGAAGGAA-AATGTTGTGCACCGACCATATCTCCTCAACAC
64 CAAAAACGATAGACGTCCTCAACACGAAGGAACAATGTCGTCCACTGACCAGATCTCCTCAACAC
541 GAA-GAGC
129 GAAGGAGC
* * * * * * * *
548 AGTGTCATCCTCAAACAATCAGATTTCCTCAACGTGAAGGAACCGTGTTATATCCAAATTATCCA
1 AGTGTCATCCTCAGACAATCAAAATTCCTAAATGCGAAGGAACCGTGTTGTCTCCAAATTATCCA
* * * *
613 AAAAGGGATATACGT-CTGCAACACGAAGGAACAATGTCGTCCACTGATCAGATCTCCTCAACGC
66 AAAA-CGATAGACGTCCT-CAACACGAAGGAACAATGTCGTCCACTGACCAGATCTCCTCAACAC
* *
677 GAAGAAGA
129 GAAGGAGC
* * *
685 AATGTCATCCTCAGACAATCAGACTTCCTAAA--CGAAGGAACCGTGTTGTCTCCAAATTATCAC
1 AGTGTCATCCTCAGACAATCAAAATTCCTAAATGCGAAGGAACCGTGTTGTCTCCAAATTAT--C
* * *
748 CAAATACGGATAGACGACCTCAGCACGAAGGAACAATGTCGTCCACTGACCAGATCTCCTC-ACA
64 CAAAAAC-GATAGACGTCCTCAACACGAAGGAACAATGTCGTCCACTGACCAGATCTCCTCAACA
*
812 CGAAGGATC
128 CGAAGGAGC
*
821 AGTGTCATCCTCAGACAATCAAAATTCCTAAATGCGAAGGAACCGTGTTGTCTCTAAATTATCTC
1 AGTGTCATCCTCAGACAATCAAAATTCCTAAATGCGAAGGAACCGTGTTGTCTCCAAATTA--TC
* * *
886 CAAATACGACTAGATGTCCTCAACACGAAGGAAAAATGT
64 CAAAAACGA-TAGACGTCCTCAACACGAAGGAACAATGT
925 AACCAACTAG
Statistics
Matches: 314, Mismatches: 46, Indels: 28
0.81 0.12 0.07
Matches are distributed among these distances:
130 19 0.06
131 2 0.01
132 19 0.06
133 18 0.06
134 4 0.01
135 40 0.13
136 66 0.21
137 84 0.27
138 61 0.19
140 1 0.00
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.22
Consensus pattern (136 bp):
AGTGTCATCCTCAGACAATCAAAATTCCTAAATGCGAAGGAACCGTGTTGTCTCCAAATTATCCA
AAAACGATAGACGTCCTCAACACGAAGGAACAATGTCGTCCACTGACCAGATCTCCTCAACACGA
AGGAGC
Found at i:1474 original size:102 final size:102
Alignment explanation
Indices: 1151--1485 Score: 367
Period size: 102 Copynumber: 3.3 Consensus size: 102
1141 TCATCTTCAT
* * *
1151 ATTGACCCGATTTCCTCAATGAGAAGGAACAACATCATATGAAAGCGACCA-AGACTCTTCACAT
1 ATTGACTCGATTTCCTCAACGAGAAGGAACAATATCATATGAAAGCGACCAGA-ACTCTTCACAT
* * *
1215 GGATGAGTAGTGTCGTTTTCAACACCATATTATCTCTAT
65 GGATGAGCAGTGTC-ATTTCAACACCATATTATCTCTAA
* * *
1254 ATTGACTCGACTTT-CTCAATGAGAAGGAA-AATGTCATATGAAA-CGACCAAGAACACTTCAAC
1 ATTGACTCGA-TTTCCTCAACGAGAAGGAACAATATCATATGAAAGCGACC-AGAACTCTTC-AC
* * **
1316 ATGGGTGAGCAGTGTTATTTCAACACCATA-TATCTCTGG
63 ATGGATGAGCAGTGTCATTTCAACACCATATTATCTCTAA
* * * * *
1355 ATTGACCCGATTTCCTCAACGAGAATGAACAATATCATATAAAAGCGGCCAGAACTTTTCACATG
1 ATTGACTCGATTTCCTCAACGAGAAGGAACAATATCATATGAAAGCGACCAGAACTCTTCACATG
* * * * *
1420 GATGAGCAGTGTCACTTGAACAACAAATTATCTCCAA
66 GATGAGCAGTGTCATTTCAACACCATATTATCTCTAA
1457 ATTGA-TCGATTTTCCTCAACGAGAAGGAA
1 ATTGACTCGA-TTTCCTCAACGAGAAGGAA
1486 TAGTGTCTCT
Statistics
Matches: 194, Mismatches: 29, Indels: 19
0.80 0.12 0.08
Matches are distributed among these distances:
100 3 0.02
101 63 0.32
102 81 0.42
103 44 0.23
104 3 0.02
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (102 bp):
ATTGACTCGATTTCCTCAACGAGAAGGAACAATATCATATGAAAGCGACCAGAACTCTTCACATG
GATGAGCAGTGTCATTTCAACACCATATTATCTCTAA
Found at i:1671 original size:3 final size:3
Alignment explanation
Indices: 1663--1697 Score: 61
Period size: 3 Copynumber: 11.3 Consensus size: 3
1653 TTTTATCGGG
1663 ATT ATT ATT ATT ATTT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT A
1698 ATAATATTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:5375 original size:153 final size:152
Alignment explanation
Indices: 5139--5428 Score: 449
Period size: 153 Copynumber: 1.9 Consensus size: 152
5129 CGATCACCAT
5139 TCCGAACGGTCAAAAGTTGCGCAAGACCATCACGAACAACATACTGAAAATTCAGGACGATCAGA
1 TCCGAACGGTCAAAAGTTGCGCAAGACCATCACGAACAACATACTGAAAATTCAGGACGATCAGA
* ** * * *
5204 CGATGACGGCGGTGGATCGGAGAAAATAAGTT-GAACGGTTTTTGGCCTCTTGCCTGCGATCGGG
66 CGATGACGACGGCAGATCGGAGAAAATAA-TTCGAACGGTTTTTAGCCTCTTG-CGGCGATCAGG
5268 ATCTCCGATTAACATTCCGAATGG
129 ATCTCCGATTAACATTCCGAATGG
*
5292 TCCGAACGGTCAAAAGTTGCGCGAGACCATCACGAACAACATACTG-AAATTCAGGACGATCAGA
1 TCCGAACGGTCAAAAGTTGCGCAAGACCATCACGAACAACATACTGAAAATTCAGGACGATCAGA
* * *
5356 TGGTGGACGACGGCAGATCGGAGAAAATAATTCGAACGGTTTTTAGCCTTTTGCGGCGATCAGGA
66 CGAT-GACGACGGCAGATCGGAGAAAATAATTCGAACGGTTTTTAGCCTCTTGCGGCGATCAGGA
5421 TCTCCGAT
130 TCTCCGAT
5429 CAATGTTCAA
Statistics
Matches: 125, Mismatches: 10, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
152 40 0.32
153 85 0.68
ACGTcount: A:0.30, C:0.22, G:0.26, T:0.21
Consensus pattern (152 bp):
TCCGAACGGTCAAAAGTTGCGCAAGACCATCACGAACAACATACTGAAAATTCAGGACGATCAGA
CGATGACGACGGCAGATCGGAGAAAATAATTCGAACGGTTTTTAGCCTCTTGCGGCGATCAGGAT
CTCCGATTAACATTCCGAATGG
Found at i:6293 original size:2 final size:2
Alignment explanation
Indices: 6193--6275 Score: 145
Period size: 2 Copynumber: 43.0 Consensus size: 2
6183 TTTCGTACAT
6193 TA TA TA T- TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6233 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6274 TA
1 TA
6276 AAAGTTATAA
Statistics
Matches: 78, Mismatches: 0, Indels: 6
0.93 0.00 0.07
Matches are distributed among these distances:
1 3 0.04
2 75 0.96
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:13274 original size:38 final size:38
Alignment explanation
Indices: 13223--13300 Score: 120
Period size: 38 Copynumber: 2.1 Consensus size: 38
13213 TCTTTTCGAT
* **
13223 TTCATTTGGGTATTTTGATGAATTTATTTCTAGGGTTC
1 TTCATTTGGGTATTTTCACAAATTTATTTCTAGGGTTC
*
13261 TTCATTTGGGTATTTTCACAAATTTGTTTCTAGGGTTC
1 TTCATTTGGGTATTTTCACAAATTTATTTCTAGGGTTC
13299 TT
1 TT
13301 TTCGATTTGT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.18, C:0.10, G:0.19, T:0.53
Consensus pattern (38 bp):
TTCATTTGGGTATTTTCACAAATTTATTTCTAGGGTTC
Found at i:13309 original size:23 final size:21
Alignment explanation
Indices: 13282--13335 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 21
13272 ATTTTCACAA
13282 ATTTGTTTCTAGGGTTCTT-TTC
1 ATTTGTTT-TA-GGTTCTTGTTC
*
13304 GATTTGTATTTAGGTTTTTGTTC
1 -ATTTGT-TTTAGGTTCTTGTTC
13327 ATTTGTTTT
1 ATTTGTTTT
13336 GAACTTGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
21 3 0.11
22 12 0.43
23 11 0.39
24 2 0.07
ACGTcount: A:0.11, C:0.07, G:0.19, T:0.63
Consensus pattern (21 bp):
ATTTGTTTTAGGTTCTTGTTC
Found at i:14241 original size:8 final size:8
Alignment explanation
Indices: 14228--14261 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
14218 AGATAAAGAC
14228 AAATAATA
1 AAATAATA
14236 AAATAATA
1 AAATAATA
*
14244 AATAAAATA
1 AA-ATAATA
14253 AAATAATA
1 AAATAATA
14261 A
1 A
14262 TTTGAGTTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
AAATAATA
Found at i:14770 original size:18 final size:18
Alignment explanation
Indices: 14747--14782 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
14737 TTAACTGGCT
14747 TACAATTCTCACGTTTGG
1 TACAATTCTCACGTTTGG
14765 TACAATTCTCACGTTTGG
1 TACAATTCTCACGTTTGG
14783 AATTGAGCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.22, G:0.17, T:0.39
Consensus pattern (18 bp):
TACAATTCTCACGTTTGG
Found at i:15069 original size:19 final size:21
Alignment explanation
Indices: 15032--15070 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 21
15022 AAACAATGTA
15032 AAGATAAATCCTAAATTAAAG
1 AAGATAAATCCTAAATTAAAG
15053 AAGA-AAATCCT-AATTAAA
1 AAGATAAATCCTAAATTAAA
15071 ATACTTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 7 0.39
20 7 0.39
21 4 0.22
ACGTcount: A:0.59, C:0.10, G:0.08, T:0.23
Consensus pattern (21 bp):
AAGATAAATCCTAAATTAAAG
Found at i:15728 original size:22 final size:22
Alignment explanation
Indices: 15703--15759 Score: 96
Period size: 22 Copynumber: 2.6 Consensus size: 22
15693 AGTTTGCTAA
*
15703 AAAATAAAATGAATTTAAAAAT
1 AAAATAAAATGAATTTAAAAAG
*
15725 AAAATAAAACGAATTTAAAAAG
1 AAAATAAAATGAATTTAAAAAG
15747 AAAATAAAATGAA
1 AAAATAAAATGAA
15760 ATGGGTTGCC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.70, C:0.02, G:0.07, T:0.21
Consensus pattern (22 bp):
AAAATAAAATGAATTTAAAAAG
Found at i:17590 original size:21 final size:21
Alignment explanation
Indices: 17548--17590 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
17538 TTTCTGGGCT
* *
17548 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
* *
17569 AGGGGAATCGATTCCCCCTCA
1 AGGGGAATCGATACCCACTCA
17590 A
1 A
17591 ACGAATATGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.19
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:18603 original size:30 final size:30
Alignment explanation
Indices: 18567--18743 Score: 354
Period size: 30 Copynumber: 5.9 Consensus size: 30
18557 TATGGATAGT
18567 TTACCGAGGATCTTTATGACCTCTGGACAG
1 TTACCGAGGATCTTTATGACCTCTGGACAG
18597 TTACCGAGGATCTTTATGACCTCTGGACAG
1 TTACCGAGGATCTTTATGACCTCTGGACAG
18627 TTACCGAGGATCTTTATGACCTCTGGACAG
1 TTACCGAGGATCTTTATGACCTCTGGACAG
18657 TTACCGAGGATCTTTATGACCTCTGGACAG
1 TTACCGAGGATCTTTATGACCTCTGGACAG
18687 TTACCGAGGATCTTTATGACCTCTGGACAG
1 TTACCGAGGATCTTTATGACCTCTGGACAG
18717 TTACCGAGGATCTTTATGACCTCTGGA
1 TTACCGAGGATCTTTATGACCTCTGGA
18744 TAGGTTCTTC
Statistics
Matches: 147, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 147 1.00
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.31
Consensus pattern (30 bp):
TTACCGAGGATCTTTATGACCTCTGGACAG
Found at i:22105 original size:21 final size:21
Alignment explanation
Indices: 22063--22105 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
22053 TTTCTGGGCT
* *
22063 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
* *
22084 AGGGGAATCGATTCCCCCTCA
1 AGGGGAATCGATACCCACTCA
22105 A
1 A
22106 ACGAATATGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.19
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:23115 original size:30 final size:30
Alignment explanation
Indices: 23079--23255 Score: 354
Period size: 30 Copynumber: 5.9 Consensus size: 30
23069 TATGGATAGT
23079 TTACCGAGGATCTTTATGACCTCTGGACAG
1 TTACCGAGGATCTTTATGACCTCTGGACAG
23109 TTACCGAGGATCTTTATGACCTCTGGACAG
1 TTACCGAGGATCTTTATGACCTCTGGACAG
23139 TTACCGAGGATCTTTATGACCTCTGGACAG
1 TTACCGAGGATCTTTATGACCTCTGGACAG
23169 TTACCGAGGATCTTTATGACCTCTGGACAG
1 TTACCGAGGATCTTTATGACCTCTGGACAG
23199 TTACCGAGGATCTTTATGACCTCTGGACAG
1 TTACCGAGGATCTTTATGACCTCTGGACAG
23229 TTACCGAGGATCTTTATGACCTCTGGA
1 TTACCGAGGATCTTTATGACCTCTGGA
23256 TAGGTTCTTC
Statistics
Matches: 147, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 147 1.00
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.31
Consensus pattern (30 bp):
TTACCGAGGATCTTTATGACCTCTGGACAG
Found at i:24281 original size:72 final size:72
Alignment explanation
Indices: 24162--24305 Score: 218
Period size: 72 Copynumber: 2.0 Consensus size: 72
24152 TGTGGAAAGA
* * * *
24162 TCTCATTTTCAACCTAAATTGAAATTTAAAAAACATGTAAAAACAAAATATTAGTGCACATTAAA
1 TCTCATTTTCAACCT-AATTGAAATTAAAAAAACATGTAAAAACAAAATATCAATACACATTAAA
24227 TAGAGAGG
65 TAGAGAGG
*
24235 TCTCATTTTCAACCT-ATTGAAATTAAAAAAAACATGTAAAAACAAAATATCAATACACATTTAA
1 TCTCATTTTCAACCTAATTGAAATT-AAAAAAACATGTAAAAACAAAATATCAATACACATTAAA
24299 TAGAGAG
65 TAGAGAG
24306 AATTACTGGC
Statistics
Matches: 65, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
71 9 0.14
72 41 0.63
73 15 0.23
ACGTcount: A:0.49, C:0.13, G:0.09, T:0.28
Consensus pattern (72 bp):
TCTCATTTTCAACCTAATTGAAATTAAAAAAACATGTAAAAACAAAATATCAATACACATTAAAT
AGAGAGG
Found at i:28724 original size:25 final size:24
Alignment explanation
Indices: 28678--28727 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
28668 TATATATATT
**
28678 ATTAAAATTTTATTTATTAAAAAA
1 ATTAAAATTTTATTTAAGAAAAAA
*
28702 ATTAAAATATTTTTTTAAGAAAAAA
1 ATTAAAAT-TTTATTTAAGAAAAAA
28727 A
1 A
28728 ATCTTCCCCA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 8 0.36
25 14 0.64
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (24 bp):
ATTAAAATTTTATTTAAGAAAAAA
Found at i:29639 original size:2 final size:2
Alignment explanation
Indices: 29632--29681 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
29622 AATTCGGTGC
29632 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
29674 TA TA TA TA
1 TA TA TA TA
29682 AGAACCGACA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.