Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009310.1 Hibiscus syriacus cultivar Beakdansim tig00113047_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: 43508
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:29 original size:14 final size:14
Alignment explanation
Indices: 10--47 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
1 ATGCTCTCA
10 ATGGCCTCGGTCGG
1 ATGGCCTCGGTCGG
*
24 ATGGCCTCAGTCGG
1 ATGGCCTCGGTCGG
38 ATGGCCTCGG
1 ATGGCCTCGG
48 ATGCCAGCGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.11, C:0.29, G:0.39, T:0.21
Consensus pattern (14 bp):
ATGGCCTCGGTCGG
Found at i:125 original size:29 final size:29
Alignment explanation
Indices: 88--145 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
78 GCAATCTCTT
*
88 GTAGCTCGCCGGGAAGACATGGCGACCTA
1 GTAGCTCGCCCGGAAGACATGGCGACCTA
* *
117 GTAGGTCGCCCGGAAGGCATGGCGACCTA
1 GTAGCTCGCCCGGAAGACATGGCGACCTA
146 CGGCCAACAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.22, C:0.28, G:0.36, T:0.14
Consensus pattern (29 bp):
GTAGCTCGCCCGGAAGACATGGCGACCTA
Found at i:1891 original size:2 final size:2
Alignment explanation
Indices: 1884--1908 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1874 CTTTAAAATG
1884 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1909 TATCATTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3444 original size:2 final size:2
Alignment explanation
Indices: 3437--3470 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
3427 TTACCTATAT
*
3437 GA GA GA GA GA GA GA GA GA GA GG GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
3471 TCCATATTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (2 bp):
GA
Found at i:14399 original size:35 final size:34
Alignment explanation
Indices: 14318--14404 Score: 106
Period size: 35 Copynumber: 2.5 Consensus size: 34
14308 ATTTGGTATT
*
14318 TAAATACAACAAACTTACAATAAGAATTAAATGG
1 TAAATACAACAAAATTACAATAAGAATTAAATGG
*
14352 TAAATGATAACAAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--GA-ATTAAATGG
14390 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
14405 ACTGAAATAT
Statistics
Matches: 47, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
34 5 0.11
35 26 0.55
36 1 0.02
37 5 0.11
38 10 0.21
ACGTcount: A:0.56, C:0.09, G:0.08, T:0.26
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGAATTAAATGG
Found at i:14521 original size:48 final size:51
Alignment explanation
Indices: 14417--14525 Score: 122
Period size: 48 Copynumber: 2.3 Consensus size: 51
14407 TGAAATATTT
* * ** *
14417 TAAAAAAAATCTAACAAATTTAACAAAATAAAGTAAGTATTAAATGAGAAA
1 TAAAAAAAATCTAACAAATTAAACAAAATAAAGTAAATACAAAATAAGAAA
*
14468 TAAAAAAAAT-T-AC-AATTAAACAAAATAAAGTAAATAC-AAAT-A-TAA
1 TAAAAAAAATCTAACAAATTAAACAAAATAAAGTAAATACAAAATAAGAAA
14513 TAAAAAAAATCTA
1 TAAAAAAAATCTA
14526 TCGATGCCTA
Statistics
Matches: 52, Mismatches: 4, Indels: 8
0.81 0.06 0.12
Matches are distributed among these distances:
45 12 0.23
46 2 0.04
47 4 0.08
48 21 0.40
49 2 0.04
50 1 0.02
51 10 0.19
ACGTcount: A:0.66, C:0.06, G:0.05, T:0.23
Consensus pattern (51 bp):
TAAAAAAAATCTAACAAATTAAACAAAATAAAGTAAATACAAAATAAGAAA
Found at i:14642 original size:18 final size:18
Alignment explanation
Indices: 14616--14654 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
14606 ACTCCTCGCT
* *
14616 GTCATCATCGTCGTCGTC
1 GTCACCATCGTCATCGTC
14634 GTCACCATCGTCATCGTC
1 GTCACCATCGTCATCGTC
14652 GTC
1 GTC
14655 GTCGTCCTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.13, C:0.36, G:0.21, T:0.31
Consensus pattern (18 bp):
GTCACCATCGTCATCGTC
Found at i:14963 original size:18 final size:18
Alignment explanation
Indices: 14940--14976 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
14930 GTGGTTGAGA
14940 CATCATATATGGCCGCGG
1 CATCATATATGGCCGCGG
*
14958 CATCATATATGGCTGCGG
1 CATCATATATGGCCGCGG
14976 C
1 C
14977 GGCTGCTGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.27, G:0.27, T:0.24
Consensus pattern (18 bp):
CATCATATATGGCCGCGG
Found at i:16620 original size:111 final size:111
Alignment explanation
Indices: 16483--16704 Score: 408
Period size: 111 Copynumber: 2.0 Consensus size: 111
16473 ATTACAAAAA
*
16483 TTAATTCTTAATCTAATAATCATGCATTAAATAAATAAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATAAACTAAATATTACTAATAATTTAAATTA
* *
16548 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAACAAAGTGTAGAGATAT
*
16594 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATAAACTAAATATTACTAATAATTTAAATTA
16659 AATTAAAACGTTAAAATGTTACCGTATCAACAAAGTGTAGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAACAAAGTGTAGAGATAT
16705 ATGATTTCCA
Statistics
Matches: 107, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
111 107 1.00
ACGTcount: A:0.46, C:0.11, G:0.08, T:0.36
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAATCATGCATTAAATAAATAAACTAAATATTACTAATAATTTAAATTA
AATTAAAACGTTAAAATGTTACCGTATCAACAAAGTGTAGAGATAT
Found at i:18342 original size:11 final size:11
Alignment explanation
Indices: 18326--18350 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
18316 TTTACTCCAA
18326 AATAATTTAAT
1 AATAATTTAAT
18337 AATAATTTAAT
1 AATAATTTAAT
18348 AAT
1 AAT
18351 TTTTAAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
AATAATTTAAT
Found at i:24426 original size:20 final size:20
Alignment explanation
Indices: 24401--24452 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
24391 TATTCTCTGA
*
24401 TAATCTTACATTTCCACTGG
1 TAATCTTACATTACCACTGG
24421 TAATCTTACATTACCACTGG
1 TAATCTTACATTACCACTGG
24441 TAATCTTACATT
1 TAATCTTACATT
24453 CCGTGAACCA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.29, C:0.23, G:0.08, T:0.40
Consensus pattern (20 bp):
TAATCTTACATTACCACTGG
Found at i:28545 original size:35 final size:35
Alignment explanation
Indices: 28499--28585 Score: 104
Period size: 36 Copynumber: 2.5 Consensus size: 35
28489 CTGTTAAAAG
*
28499 TTTCAAAGTTTGGTAA-CCAACTTTGGAAAATGTTT
1 TTTCAAAGTTTGGTAATCCAACTTTGAAAAATG-TT
****
28534 TTTCAAAGTTTGGTAAATGTTTCTTTGAAAAATGTT
1 TTTCAAAGTTTGGT-AATCCAACTTTGAAAAATGTT
28570 TTTCAAAGTTTGGTAA
1 TTTCAAAGTTTGGTAA
28586 AATTTTGGTA
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
35 16 0.36
36 18 0.40
37 11 0.24
ACGTcount: A:0.31, C:0.08, G:0.17, T:0.44
Consensus pattern (35 bp):
TTTCAAAGTTTGGTAATCCAACTTTGAAAAATGTT
Found at i:29039 original size:16 final size:16
Alignment explanation
Indices: 29018--29051 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
29008 TTACTATTCA
*
29018 CGTGAATAGTGAATTT
1 CGTGAATAGTGAAATT
29034 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
29050 CG
1 CG
29052 GTCGGCGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.32
Consensus pattern (16 bp):
CGTGAATAGTGAAATT
Found at i:29819 original size:15 final size:16
Alignment explanation
Indices: 29801--29833 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
29791 GTGGCAGATC
29801 AAAATCCAG-ACGGGA
1 AAAATCCAGAACGGGA
*
29816 AAAATCTAGAACGGGA
1 AAAATCCAGAACGGGA
29832 AA
1 AA
29834 GAAAGATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.52, C:0.15, G:0.24, T:0.09
Consensus pattern (16 bp):
AAAATCCAGAACGGGA
Found at i:33121 original size:35 final size:35
Alignment explanation
Indices: 33075--33161 Score: 104
Period size: 36 Copynumber: 2.5 Consensus size: 35
33065 TTGTTAAAAG
*
33075 TTTCAAAGTTTGGTAA-CCAACTTTGGAAAATGTTT
1 TTTCAAAGTTTGGTAATCCAACTTTGAAAAATG-TT
****
33110 TTTCAAAGTTTGGTAAATGTTTCTTTGAAAAATGTT
1 TTTCAAAGTTTGGT-AATCCAACTTTGAAAAATGTT
33146 TTTCAAAGTTTGGTAA
1 TTTCAAAGTTTGGTAA
33162 AATTTTGGTA
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
35 16 0.36
36 18 0.40
37 11 0.24
ACGTcount: A:0.31, C:0.08, G:0.17, T:0.44
Consensus pattern (35 bp):
TTTCAAAGTTTGGTAATCCAACTTTGAAAAATGTT
Found at i:37981 original size:21 final size:21
Alignment explanation
Indices: 37939--37981 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
37929 TTTCTGGGTT
* * *
37939 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
37960 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
37981 A
1 A
37982 TGAAATGAAT
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:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:38042 original size:66 final size:68
Alignment explanation
Indices: 37961--38112 Score: 211
Period size: 67 Copynumber: 2.2 Consensus size: 68
37951 ACCCATTCAA
* *
37961 GGGGAACCGATACCCCCTCAAT-G-AAATGAATTTCCAGAATGCTAGAGGGGAATCGGTACCCC-
1 GGGGAACCGATACCCCCTC-ATCGTAAATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCA
38023 AGGG
65 AGGG
* * *
38027 GGGGAACCGATACCCCCTCATCGTATATGAAATTCCAGATTGCTTGAGGGGAATCGATACCCCTA
1 GGGGAACCGATACCCCCTCATCGTAAATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCC-A
38092 AGGG
65 AGGG
*
38096 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
38113 ATGAGAAAAG
Statistics
Matches: 76, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
65 2 0.03
66 20 0.26
67 34 0.45
69 20 0.26
ACGTcount: A:0.28, C:0.26, G:0.28, T:0.18
Consensus pattern (68 bp):
GGGGAACCGATACCCCCTCATCGTAAATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCAA
GGG
Found at i:38531 original size:28 final size:30
Alignment explanation
Indices: 38468--38525 Score: 84
Period size: 28 Copynumber: 2.0 Consensus size: 30
38458 AGAAAAAGTT
*
38468 ATATGCACTATGTGATAAAGGTATGTAAATG
1 ATATGCACTATGT-ATAAAGGTATGGAAATG
38499 ATATGC-CTATGT-TAAAGGTATGGAAAT
1 ATATGCACTATGTATAAAGGTATGGAAAT
38526 ACTATGTCTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 14 0.54
30 6 0.23
31 6 0.23
ACGTcount: A:0.38, C:0.07, G:0.22, T:0.33
Consensus pattern (30 bp):
ATATGCACTATGTATAAAGGTATGGAAATG
Found at i:38819 original size:22 final size:22
Alignment explanation
Indices: 38745--38811 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
38735 TTATGGACAT
38745 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
38767 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
38789 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
38811 A
1 A
38812 TTTATACGAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (22 bp):
AATTCTACGGGCACTTCGGTGC
Done.