Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002690.1 Hibiscus syriacus cultivar Beakdansim tig00005555_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: 169424
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
File 2 of 2
Found at i:159732 original size:19 final size:19
Alignment explanation
Indices: 159708--159744 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
159698 ATGACCAACA
*
159708 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
159727 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
159745 CAGTATCGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:159797 original size:20 final size:20
Alignment explanation
Indices: 159770--159897 Score: 150
Period size: 20 Copynumber: 6.3 Consensus size: 20
159760 GTTTCCAGAT
*
159770 TCGCAACGCGATTTTGACTA
1 TCGCAACGCGATTCTGACTA
* ** *
159790 TTGCAACGCGATAAT-ACAAAA
1 TCGCAACGCGATTCTGAC--TA
* *
159811 TCACAACGTGATTCTGACTA
1 TCGCAACGCGATTCTGACTA
* *
159831 TCGTAACGAGATTCTGACTA
1 TCGCAACGCGATTCTGACTA
159851 TCGCAACGCGATTCTGACTA
1 TCGCAACGCGATTCTGACTA
159871 TCGCAACGCGATTCTGACTA
1 TCGCAACGCGATTCTGACTA
159891 TCGCAAC
1 TCGCAAC
159898 ACTGAATTTC
Statistics
Matches: 90, Mismatches: 15, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
19 2 0.02
20 75 0.83
21 11 0.12
22 2 0.02
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (20 bp):
TCGCAACGCGATTCTGACTA
Found at i:160080 original size:18 final size:17
Alignment explanation
Indices: 160047--160080 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
160037 CATCCGTTTC
*
160047 TATATCCAACGACATCA
1 TATATCCAAAGACATCA
160064 TATATCCAAAAGACATC
1 TATATCC-AAAGACATC
160081 CTTCCCCATC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.44, C:0.26, G:0.06, T:0.24
Consensus pattern (17 bp):
TATATCCAAAGACATCA
Found at i:163030 original size:12 final size:12
Alignment explanation
Indices: 163013--163051 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
163003 AAGCAAAAGG
163013 CAATCAAAATCA
1 CAATCAAAATCA
163025 CAATCAAAATCA
1 CAATCAAAATCA
* **
163037 AAATCCTAATCA
1 CAATCAAAATCA
163049 CAA
1 CAA
163052 CCGGCTTCAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.56, C:0.26, G:0.00, T:0.18
Consensus pattern (12 bp):
CAATCAAAATCA
Found at i:163262 original size:20 final size:20
Alignment explanation
Indices: 163216--163263 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
163206 TTACACATTC
*
163216 ATTTGAATATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
163236 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
163256 ATTTGACT
1 ATTTGACT
163264 TTCGGGTTGC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:164860 original size:21 final size:21
Alignment explanation
Indices: 164830--164899 Score: 70
Period size: 21 Copynumber: 3.3 Consensus size: 21
164820 GTGAATTGGG
164830 CTCTTGAATGGTGGGAGGGAC
1 CTCTTGAATGGTGGGAGGGAC
* * ** *
164851 CTCTTCAATGATGACAGGGGC
1 CTCTTGAATGGTGGGAGGGAC
*
164872 CTCTTGAACGGTGGGAGGGGA-
1 CTCTTGAATGGTGGGA-GGGAC
164893 CTCTTGA
1 CTCTTGA
164900 GGGATGATAG
Statistics
Matches: 37, Mismatches: 11, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
21 34 0.92
22 3 0.08
ACGTcount: A:0.20, C:0.19, G:0.37, T:0.24
Consensus pattern (21 bp):
CTCTTGAATGGTGGGAGGGAC
Found at i:164906 original size:42 final size:42
Alignment explanation
Indices: 164830--164913 Score: 107
Period size: 42 Copynumber: 2.0 Consensus size: 42
164820 GTGAATTGGG
* *
164830 CTCTTGAATGGTGGGAGGGACCTCTTCAATGATGACAGGGGC
1 CTCTTGAACGGTGGGAGGGACCTCTTCAAGGATGACAGGGGC
* * *
164872 CTCTTGAACGGTGGGAGGGGA-CTCTTGAGGGATGATAGGGGC
1 CTCTTGAACGGTGGGA-GGGACCTCTTCAAGGATGACAGGGGC
164914 ATATTGAATG
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
42 32 0.89
43 4 0.11
ACGTcount: A:0.20, C:0.17, G:0.40, T:0.23
Consensus pattern (42 bp):
CTCTTGAACGGTGGGAGGGACCTCTTCAAGGATGACAGGGGC
Found at i:164921 original size:42 final size:42
Alignment explanation
Indices: 164833--164952 Score: 100
Period size: 42 Copynumber: 2.9 Consensus size: 42
164823 AATTGGGCTC
* * * *
164833 TTGAATGGTGGGAGGGACCTCTTCAATGATGACAGGGGCCTC
1 TTGAACGGTGGGAGGGACCTCTTCAAGGATGACAGGGGCATA
* * *
164875 TTGAACGGTGGGAGGGGA-CTCTTGAGGGATGATAGGGGCATA
1 TTGAACGGTGGGA-GGGACCTCTTCAAGGATGACAGGGGCATA
* * * * *
164917 TTGAATGATAGGAGAGG-CCTCTTGAACGATGACAGG
1 TTGAACGGTGGGAG-GGACCTCTTCAAGGATGACAGG
164953 TGAGTCGGGC
Statistics
Matches: 62, Mismatches: 13, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
41 1 0.02
42 57 0.92
43 4 0.06
ACGTcount: A:0.25, C:0.14, G:0.38, T:0.23
Consensus pattern (42 bp):
TTGAACGGTGGGAGGGACCTCTTCAAGGATGACAGGGGCATA
Found at i:165453 original size:20 final size:20
Alignment explanation
Indices: 165428--165471 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
165418 AATGGTTTAT
165428 GAAACTTAAAATCGCAACAC
1 GAAACTTAAAATCGCAACAC
*
165448 GAAACTTAAAATCGCAACGC
1 GAAACTTAAAATCGCAACAC
165468 GAAA
1 GAAA
165472 ATGACTATCG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.50, C:0.23, G:0.14, T:0.14
Consensus pattern (20 bp):
GAAACTTAAAATCGCAACAC
Found at i:165481 original size:20 final size:20
Alignment explanation
Indices: 165458--165546 Score: 115
Period size: 20 Copynumber: 4.5 Consensus size: 20
165448 GAAACTTAAA
165458 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
165478 ATCGCAACGCGGAAATGACT
1 ATCGCAACGCGAAAATGACT
* **
165498 ATCGCAACCCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
* **
165518 ATCACAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
165538 ATCGCAACG
1 ATCGCAACG
165547 GGATAATCGC
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 61 1.00
ACGTcount: A:0.35, C:0.27, G:0.19, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:165574 original size:18 final size:19
Alignment explanation
Indices: 165551--165588 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
165541 GCAACGGGAT
*
165551 AATCGCAATGCGAAA-TAA
1 AATCGCAACGCGAAACTAA
165569 AATCGCAACGCGAAACTAA
1 AATCGCAACGCGAAACTAA
165588 A
1 A
165589 TTTGCGTTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (19 bp):
AATCGCAACGCGAAACTAA
Found at i:165622 original size:20 final size:20
Alignment explanation
Indices: 165589--165629 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
165579 CGAAACTAAA
*
165589 TTTGCGTTGCGATTTTCATT
1 TTTGCATTGCGATTTTCATT
* *
165609 TTTGCATTGTGATTTTTATT
1 TTTGCATTGCGATTTTCATT
165629 T
1 T
165630 CGCATTACGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.12, C:0.10, G:0.17, T:0.61
Consensus pattern (20 bp):
TTTGCATTGCGATTTTCATT
Found at i:165671 original size:20 final size:20
Alignment explanation
Indices: 165646--165694 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
165636 ACGATTATCC
165646 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
**
165666 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
165686 CGTTGCGAT
1 CGTTGCGAT
165695 TTTAAGTTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.18, C:0.20, G:0.27, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:165704 original size:20 final size:20
Alignment explanation
Indices: 165646--165713 Score: 66
Period size: 20 Copynumber: 3.4 Consensus size: 20
165636 ACGATTATCC
*
165646 CGTTGCGATAGTCAA-ATTCG
1 CGTTGCGATAGT-AAGTTTCG
* *
165666 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTAAGTTTCG
**
165686 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATAGTAAGTTTCG
*
165706 TGTTGCGA
1 CGTTGCGA
165714 CTATTCTTCT
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
19 1 0.03
20 39 0.98
ACGTcount: A:0.18, C:0.18, G:0.26, T:0.38
Consensus pattern (20 bp):
CGTTGCGATAGTAAGTTTCG
Found at i:167559 original size:20 final size:20
Alignment explanation
Indices: 167513--167586 Score: 76
Period size: 20 Copynumber: 3.7 Consensus size: 20
167503 GAAACTTAAA
* **
167513 ATCGTAACACGAAAATGAAA
1 ATCGCAACACGAAAATGACT
167533 ATCGCAACACGAAAATGACT
1 ATCGCAACACGAAAATGACT
* * **
167553 ATTGCAACGCGAATTTGACT
1 ATCGCAACACGAAAATGACT
*
167573 ATCGCAACGCGAAA
1 ATCGCAACACGAAA
167587 CTAAAATCGA
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.43, C:0.22, G:0.18, T:0.18
Consensus pattern (20 bp):
ATCGCAACACGAAAATGACT
Found at i:168008 original size:22 final size:22
Alignment explanation
Indices: 167982--168030 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
167972 GATCGAGATA
167982 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
168004 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
168026 G-CGGA
1 GACGGA
168031 GTCGCCGTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 4 0.15
22 23 0.85
ACGTcount: A:0.18, C:0.14, G:0.47, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGTCGGAGATGGG
Found at i:168247 original size:21 final size:21
Alignment explanation
Indices: 168223--168269 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
168213 TATTCGCATT
*
168223 GCGATTTTCTAAAATCGCAAC
1 GCGATTTTCGAAAATCGCAAC
* * *
168244 GCGAATTTGGAAAATCGCAAT
1 GCGATTTTCGAAAATCGCAAC
168265 GCGAT
1 GCGAT
168270 AGTCAAAATC
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26
Consensus pattern (21 bp):
GCGATTTTCGAAAATCGCAAC
Found at i:168279 original size:20 final size:20
Alignment explanation
Indices: 168172--168288 Score: 83
Period size: 20 Copynumber: 5.8 Consensus size: 20
168162 TAGCGCTTTG
*
168172 AAAATCGCATTGCGATAGTC
1 AAAATCGCATTGCGATATTC
* * *
168192 AGAATCGCGTTGCGATTTTC
1 AAAATCGCATTGCGATATTC
* * *
168212 ATATTCGCATTGCGATTTTC
1 AAAATCGCATTGCGATATTC
** *
168232 TAAAATCGCAACGCGA-ATTTGG
1 -AAAATCGCATTGCGATA-TT-C
* *
168254 AAAATCGCAATGCGATAGTC
1 AAAATCGCATTGCGATATTC
*
168274 AAAATCGCGTTGCGA
1 AAAATCGCATTGCGA
168289 ATCTGGAAAC
Statistics
Matches: 75, Mismatches: 18, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
20 46 0.61
21 28 0.37
22 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (20 bp):
AAAATCGCATTGCGATATTC
Done.