Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002489.1 Hibiscus syriacus cultivar Beakdansim tig00005075_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: 44479
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:2503 original size:15 final size:16
Alignment explanation
Indices: 2483--2518 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
2473 AAAAATTAAG
2483 AAATT-ATAAAATGGA
1 AAATTAATAAAATGGA
*
2498 AAATTAATAAAATGTA
1 AAATTAATAAAATGGA
2514 AAATT
1 AAATT
2519 TTATTTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.26
16 14 0.74
ACGTcount: A:0.61, C:0.00, G:0.08, T:0.31
Consensus pattern (16 bp):
AAATTAATAAAATGGA
Found at i:2515 original size:23 final size:23
Alignment explanation
Indices: 2474--2517 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
2464 TTTCTTTAAA
*
2474 AAAATTAAGAAATTATAAAATGG
1 AAAATTAAGAAAATATAAAATGG
* *
2497 AAAATTAATAAAATGTAAAAT
1 AAAATTAAGAAAATATAAAAT
2518 TTTATTTAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.64, C:0.00, G:0.09, T:0.27
Consensus pattern (23 bp):
AAAATTAAGAAAATATAAAATGG
Found at i:9521 original size:14 final size:15
Alignment explanation
Indices: 9502--9531 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
9492 TCTCCTATAT
9502 TTTAATTTAA-TCAA
1 TTTAATTTAATTCAA
9516 TTTAATTTAATTCAA
1 TTTAATTTAATTCAA
9531 T
1 T
9532 GACTTCAGGC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (15 bp):
TTTAATTTAATTCAA
Found at i:11963 original size:20 final size:20
Alignment explanation
Indices: 11940--11977 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
11930 CAATGCGAAC
*
11940 TCCAATTTCGCAACACAGTT
1 TCCAAATTCGCAACACAGTT
11960 TCCAAATTCGCAACACAG
1 TCCAAATTCGCAACACAG
11978 AAGTCAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.11, T:0.24
Consensus pattern (20 bp):
TCCAAATTCGCAACACAGTT
Found at i:12036 original size:19 final size:20
Alignment explanation
Indices: 11986--12028 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
11976 AGAAGTCAAA
* *
11986 TTCGCAAAGCGCA-TTTATT
1 TTCGCAACGCGAATTTTATT
12005 TTCGCAACGCGAATTTTATT
1 TTCGCAACGCGAATTTTATT
12025 TTCG
1 TTCG
12029 AATTCGAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.23, C:0.21, G:0.16, T:0.40
Consensus pattern (20 bp):
TTCGCAACGCGAATTTTATT
Found at i:12529 original size:20 final size:20
Alignment explanation
Indices: 12506--12550 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
12496 GAAAATGAAA
12506 TTCGCAACACGATTTTCATT
1 TTCGCAACACGATTTTCATT
****
12526 TTCGCGTTGCGATTTTCATT
1 TTCGCAACACGATTTTCATT
12546 TTCGC
1 TTCGC
12551 GTTGTGAATT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.16, T:0.44
Consensus pattern (20 bp):
TTCGCAACACGATTTTCATT
Found at i:12551 original size:20 final size:20
Alignment explanation
Indices: 12515--12554 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
12505 ATTCGCAACA
12515 CGATTTTCATTTTCGCGTTG
1 CGATTTTCATTTTCGCGTTG
12535 CGATTTTCATTTTCGCGTTG
1 CGATTTTCATTTTCGCGTTG
12555 TGAATTTAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.10, C:0.20, G:0.20, T:0.50
Consensus pattern (20 bp):
CGATTTTCATTTTCGCGTTG
Found at i:12568 original size:20 final size:20
Alignment explanation
Indices: 12525--12568 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
12515 CGATTTTCAT
* * *
12525 TTTCGCGTTGCGATTTTCAT
1 TTTCGCGTTGCGAATTTAAG
*
12545 TTTCGCGTTGTGAATTTAAG
1 TTTCGCGTTGCGAATTTAAG
12565 TTTC
1 TTTC
12569 AGAAACTACT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.14, C:0.16, G:0.20, T:0.50
Consensus pattern (20 bp):
TTTCGCGTTGCGAATTTAAG
Found at i:14090 original size:21 final size:21
Alignment explanation
Indices: 14047--14095 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
14037 GTTAGGGGAG
14047 TTACGTGATGAGGTCAGTGCT
1 TTACGTGATGAGGTCAGTGCT
* *
14068 TTGCGTGATGAGGTACGGT-CT
1 TTACGTGATGAGGT-CAGTGCT
14089 TTACGTG
1 TTACGTG
14096 GCGAGGTAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 21 0.88
22 3 0.12
ACGTcount: A:0.16, C:0.14, G:0.35, T:0.35
Consensus pattern (21 bp):
TTACGTGATGAGGTCAGTGCT
Found at i:14153 original size:21 final size:21
Alignment explanation
Indices: 14129--14187 Score: 91
Period size: 21 Copynumber: 2.8 Consensus size: 21
14119 GACAATGGTG
14129 CTTTACGTGGTGAGGTATCTA
1 CTTTACGTGGTGAGGTATCTA
*
14150 CTTTATGTGGTGAGGTATCTA
1 CTTTACGTGGTGAGGTATCTA
* *
14171 CTTTACATGATGAGGTA
1 CTTTACGTGGTGAGGTA
14188 GCCGCTCTAC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.22, C:0.12, G:0.27, T:0.39
Consensus pattern (21 bp):
CTTTACGTGGTGAGGTATCTA
Found at i:14538 original size:21 final size:21
Alignment explanation
Indices: 14479--14539 Score: 88
Period size: 21 Copynumber: 2.9 Consensus size: 21
14469 GCCTGATTCA
*
14479 CCTGTCATCGTTCAAGAAGCC
1 CCTGTCATCGTTCAAGAGGCC
*
14500 CCT-TCTATCATTCAAGAGGCC
1 CCTGTC-ATCGTTCAAGAGGCC
14521 CCTGTCATCGTTCAAGAGG
1 CCTGTCATCGTTCAAGAGG
14540 TACCTCCCAC
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
20 2 0.06
21 31 0.89
22 2 0.06
ACGTcount: A:0.23, C:0.31, G:0.20, T:0.26
Consensus pattern (21 bp):
CCTGTCATCGTTCAAGAGGCC
Found at i:14554 original size:42 final size:42
Alignment explanation
Indices: 14479--14559 Score: 108
Period size: 42 Copynumber: 1.9 Consensus size: 42
14469 GCCTGATTCA
* * * *
14479 CCTGTCATCGTTCAAGAAGCCCCTTCTATCATTCAAGAGGCC
1 CCTGTCATCGTTCAAGAAGCACCTCCCACCATTCAAGAGGCC
* *
14521 CCTGTCATCGTTCAAGAGGTACCTCCCACCATTCAAGAG
1 CCTGTCATCGTTCAAGAAGCACCTCCCACCATTCAAGAG
14560 CCTGATTCAC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 33 1.00
ACGTcount: A:0.25, C:0.33, G:0.17, T:0.25
Consensus pattern (42 bp):
CCTGTCATCGTTCAAGAAGCACCTCCCACCATTCAAGAGGCC
Found at i:16024 original size:207 final size:206
Alignment explanation
Indices: 15669--16066 Score: 656
Period size: 207 Copynumber: 1.9 Consensus size: 206
15659 AAAAGTATGT
*
15669 ATAAACAACCATTTGTTATTGGTAAGTTTGAGCAAGTGTTGTTAACATATATACTCTTTGTTGGT
1 ATAAACAACCAGTTGTTATTGGTAAGTTTGAGCAAGTGTTGTTAACATATATAC-CTTTGTTGGT
* *
15734 TTGAAATTGTTTGGTTAAGTACCTAGAATTCAATAATTTGTTGTTTGTTGGTTTTAGATATGTAG
65 TTGAAAGTGTTTGGTTAAGTACCTAGAATTCAATAATTTGCTGTTTGTTGGTTTTAGATATGTAG
* * *
15799 AAAGTGTTGTTTGAGCAAATGTTTGGTTTGTGCAGGTTAATCCTGAAGTGAGCTGCGTGAAATTG
130 AAAGTGTTGTTCGAGCAAATGTTTGGTTTCTGCAAGTTAATCCTGAAGTGAGCTGCGTGAAATTG
15864 ATGTATTTGTGC
195 ATGTATTTGTGC
* *
15876 ATAAACAACCAGTTGTTATTGGTAAGTTTGTGCAAGTGTTGTTAACTGTTATATA-C-TTGTTGG
1 ATAAACAACCAGTTGTTATTGGTAAGTTTGAGCAAGTGTTGTTAAC--ATATATACCTTTGTTGG
* *
15939 TTTGAAAGTGTTTGGTTTAAGTACCTATAATTCAATAATTTGCTGTTTGTTGGTTTTAGATGTGT
64 TTTGAAAGTGTTTGG-TTAAGTACCTAGAATTCAATAATTTGCTGTTTGTTGGTTTTAGATATGT
16004 AGAAAGTGTTGTTCGAGCAAATGTTTGGTTTCTGCAAGTTAATCCTGAAGTGAGCTGCGTGAA
128 AGAAAGTGTTGTTCGAGCAAATGTTTGGTTTCTGCAAGTTAATCCTGAAGTGAGCTGCGTGAA
16067 TATATTTGGA
Statistics
Matches: 178, Mismatches: 10, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
206 21 0.12
207 151 0.85
209 6 0.03
ACGTcount: A:0.26, C:0.09, G:0.24, T:0.41
Consensus pattern (206 bp):
ATAAACAACCAGTTGTTATTGGTAAGTTTGAGCAAGTGTTGTTAACATATATACCTTTGTTGGTT
TGAAAGTGTTTGGTTAAGTACCTAGAATTCAATAATTTGCTGTTTGTTGGTTTTAGATATGTAGA
AAGTGTTGTTCGAGCAAATGTTTGGTTTCTGCAAGTTAATCCTGAAGTGAGCTGCGTGAAATTGA
TGTATTTGTGC
Found at i:27992 original size:17 final size:17
Alignment explanation
Indices: 27970--28004 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
27960 CACGTGAGGA
*
27970 TTATTTTTCTTCTTATT
1 TTATTTATCTTCTTATT
*
27987 TTATTTATCTTTTTATT
1 TTATTTATCTTCTTATT
28004 T
1 T
28005 ACTGTTTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.14, C:0.09, G:0.00, T:0.77
Consensus pattern (17 bp):
TTATTTATCTTCTTATT
Found at i:28652 original size:24 final size:24
Alignment explanation
Indices: 28620--28683 Score: 101
Period size: 24 Copynumber: 2.7 Consensus size: 24
28610 AAATATGAGG
*
28620 CCAAGATCAAATTTCGGGTATTGA
1 CCAAGATCAAATTTCAGGTATTGA
*
28644 CCAAGATCAAATTCCAGGTATTGA
1 CCAAGATCAAATTTCAGGTATTGA
*
28668 CTAAGATCAAATTTCA
1 CCAAGATCAAATTTCA
28684 AATACTGACT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.16, T:0.28
Consensus pattern (24 bp):
CCAAGATCAAATTTCAGGTATTGA
Found at i:29640 original size:20 final size:20
Alignment explanation
Indices: 29615--29710 Score: 74
Period size: 20 Copynumber: 4.8 Consensus size: 20
29605 TAAAACCTAG
*
29615 TGCGAAATTAAAATTCGTGT
1 TGCGAAATTAAAATTCGAGT
29635 TGCG-AATTCGAAAA-TCGAGT
1 TGCGAAATT--AAAATTCGAGT
** *
29655 TGCGAAAACAAAATTCGCGT
1 TGCGAAATTAAAATTCGAGT
29675 TGCG-AATTCAGAAA-TCGAGT
1 TGCGAAATT-A-AAATTCGAGT
* *
29695 TGCGAATTTGAAATTC
1 TGCGAAATTAAAATTC
29711 AGTATTGCGA
Statistics
Matches: 59, Mismatches: 9, Indels: 16
0.70 0.11 0.19
Matches are distributed among these distances:
19 13 0.22
20 34 0.58
21 12 0.20
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (20 bp):
TGCGAAATTAAAATTCGAGT
Found at i:29709 original size:40 final size:40
Alignment explanation
Indices: 29615--29710 Score: 131
Period size: 40 Copynumber: 2.4 Consensus size: 40
29605 TAAAACCTAG
*
29615 TGCGAAATTAAAATTCGTGTTGCGAATTCGAAAATCGAGT
1 TGCGAAATTAAAATTCGCGTTGCGAATTCGAAAATCGAGT
**
29655 TGCGAAAACAAAATTCGCGTTGCGAATTC-AGAAATCGAGT
1 TGCGAAATTAAAATTCGCGTTGCGAATTCGA-AAATCGAGT
* *
29695 TGCGAATTTGAAATTC
1 TGCGAAATTAAAATTC
29711 AGTATTGCGA
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
39 1 0.02
40 47 0.98
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (40 bp):
TGCGAAATTAAAATTCGCGTTGCGAATTCGAAAATCGAGT
Found at i:30691 original size:25 final size:26
Alignment explanation
Indices: 30641--30691 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
30631 TTGGTTTTTT
* *
30641 AATTTTTTTAATTTAAATATTTAATA
1 AATTATTTTAATTTAAATATTAAATA
*
30667 AATTATTTTATTTTAAA-ATTAAATA
1 AATTATTTTAATTTAAATATTAAATA
30692 TTTTAACTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 7 0.32
26 15 0.68
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (26 bp):
AATTATTTTAATTTAAATATTAAATA
Found at i:40810 original size:20 final size:21
Alignment explanation
Indices: 40765--40824 Score: 77
Period size: 20 Copynumber: 2.8 Consensus size: 21
40755 TCCCCTGTGA
40765 GGGGAATCGGTTCCCCTTCAAAG
1 GGGGAATCGGTT-CCC-TCAAAG
40788 GGGGAATCGGTTCCCTC-AAG
1 GGGGAATCGGTTCCCTCAAAG
* *
40808 GGGGGATCGATTCCCTC
1 GGGGAATCGGTTCCCTC
40825 TGCACCAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
20 18 0.51
21 2 0.06
22 3 0.09
23 12 0.34
ACGTcount: A:0.18, C:0.27, G:0.33, T:0.22
Consensus pattern (21 bp):
GGGGAATCGGTTCCCTCAAAG
Done.