Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001837.1 Hibiscus syriacus cultivar Beakdansim tig00003716_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: 77361
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:4484 original size:31 final size:32
Alignment explanation
Indices: 4435--4516 Score: 91
Period size: 31 Copynumber: 2.6 Consensus size: 32
4425 CTTTTTCATT
*
4435 TAAGTACTTAAAGTATTTTTTT-GG-TCAAAA
1 TAAGTACTAAAAGTATTTTTTTGGGATCAAAA
*
4465 TAAGTATCTAAAATTATTTTTTTGGGATCAAAA
1 TAAGTA-CTAAAAGTATTTTTTTGGGATCAAAA
4498 T-AGATAC-ATAAAGTATTTT
1 TAAG-TACTA-AAAGTATTTT
4517 ATGTCAAACA
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
30 6 0.14
31 15 0.34
32 14 0.32
33 9 0.20
ACGTcount: A:0.39, C:0.06, G:0.12, T:0.43
Consensus pattern (32 bp):
TAAGTACTAAAAGTATTTTTTTGGGATCAAAA
Found at i:7375 original size:43 final size:43
Alignment explanation
Indices: 7328--7419 Score: 157
Period size: 43 Copynumber: 2.1 Consensus size: 43
7318 TCTTATTACC
* * *
7328 ATTAAAGTCTTTATTAAAGTAAAATTCTCTAATTGATTATTTT
1 ATTAAAGTCTTTATTAAAGTAAAATTCTCTAATCGATCACTTT
7371 ATTAAAGTCTTTATTAAAGTAAAATTCTCTAATCGATCACTTT
1 ATTAAAGTCTTTATTAAAGTAAAATTCTCTAATCGATCACTTT
7414 ATTAAA
1 ATTAAA
7420 TTAACTAATT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 46 1.00
ACGTcount: A:0.39, C:0.10, G:0.07, T:0.45
Consensus pattern (43 bp):
ATTAAAGTCTTTATTAAAGTAAAATTCTCTAATCGATCACTTT
Found at i:17858 original size:11 final size:12
Alignment explanation
Indices: 17818--17861 Score: 63
Period size: 12 Copynumber: 3.8 Consensus size: 12
17808 TATTTAAACG
*
17818 GGTATTGGGCCA
1 GGTATTGGGTCA
*
17830 GGTATTGGGTCG
1 GGTATTGGGTCA
17842 GGTATTGGGTC-
1 GGTATTGGGTCA
17853 GGTATTGGG
1 GGTATTGGG
17862 CTGGGAATCG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
11 9 0.30
12 21 0.70
ACGTcount: A:0.11, C:0.09, G:0.48, T:0.32
Consensus pattern (12 bp):
GGTATTGGGTCA
Found at i:17860 original size:23 final size:24
Alignment explanation
Indices: 17816--17861 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
17806 ATTATTTAAA
17816 CGGGTATTGGGCCAGGTATTGGGT
1 CGGGTATTGGGCCAGGTATTGGGT
*
17840 CGGGTATTGGGTC-GGTATTGGG
1 CGGGTATTGGGCCAGGTATTGGG
17862 CTGGGAATCG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.11, C:0.11, G:0.48, T:0.30
Consensus pattern (24 bp):
CGGGTATTGGGCCAGGTATTGGGT
Found at i:17972 original size:15 final size:14
Alignment explanation
Indices: 17923--17973 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
17913 ATATTTTTTA
*
17923 TTTAA-ATTAAATT
1 TTTAATATTATATT
17936 TATTAATATTATATT
1 T-TTAATATTATATT
*
17951 TAT-ATATATATATT
1 TTTAATAT-TATATT
17965 TTTAATATT
1 TTTAATATT
17974 TATCGGGTCG
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
13 5 0.16
14 14 0.45
15 12 0.39
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TTTAATATTATATT
Found at i:18005 original size:13 final size:12
Alignment explanation
Indices: 17974--18010 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
17964 TTTTAATATT
*
17974 TATCGGGTCGGG
1 TATCGGGGCGGG
17986 TATCGGGGCGGG
1 TATCGGGGCGGG
17998 TAATCGGGGCGGG
1 T-ATCGGGGCGGG
18011 GATTACCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 12 0.52
13 11 0.48
ACGTcount: A:0.11, C:0.16, G:0.54, T:0.19
Consensus pattern (12 bp):
TATCGGGGCGGG
Found at i:20687 original size:1 final size:1
Alignment explanation
Indices: 20681--20707 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
20671 TCTAAACCGC
20681 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
20708 CTAAACTGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:21228 original size:12 final size:11
Alignment explanation
Indices: 21211--21245 Score: 61
Period size: 11 Copynumber: 3.1 Consensus size: 11
21201 CTACATATAA
21211 TAAAAATATATT
1 TAAAAAT-TATT
21223 TAAAAATTATT
1 TAAAAATTATT
21234 TAAAAATTATT
1 TAAAAATTATT
21245 T
1 T
21246 TTGATGATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 16 0.70
12 7 0.30
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
TAAAAATTATT
Found at i:24027 original size:26 final size:26
Alignment explanation
Indices: 23997--24058 Score: 74
Period size: 26 Copynumber: 2.4 Consensus size: 26
23987 CTTAATCGTC
23997 ATTTTAAATATATTTAAA-AATATCAT
1 ATTTTAAATATATTTAAATAA-ATCAT
* *
24023 ATTTTAAATAATTTTTAAATAAATTAT
1 ATTTTAAAT-ATATTTAAATAAATCAT
24050 A-TTTAAATA
1 ATTTTAAATA
24059 AGAAATTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
25 1 0.03
26 16 0.50
27 13 0.41
28 2 0.06
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (26 bp):
ATTTTAAATATATTTAAATAAATCAT
Found at i:26425 original size:22 final size:23
Alignment explanation
Indices: 26385--26427 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
26375 GATGATGTTG
* *
26385 TATTTTTTAAATTACTTTTATAT
1 TATTATTTAAATTAATTTTATAT
26408 TATTATTT-AATTAATTTTAT
1 TATTATTTAAATTAATTTTAT
26428 TCAACTAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (23 bp):
TATTATTTAAATTAATTTTATAT
Found at i:26723 original size:15 final size:17
Alignment explanation
Indices: 26703--26735 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
26693 AATTATATGT
26703 ATTT-AATTA-TTTAAA
1 ATTTAAATTATTTTAAA
26718 ATTTAAATTATTTTAAA
1 ATTTAAATTATTTTAAA
26735 A
1 A
26736 AATATGGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 5 0.31
17 7 0.44
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
ATTTAAATTATTTTAAA
Found at i:27835 original size:23 final size:24
Alignment explanation
Indices: 27804--27849 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
27794 TTATATTATA
* *
27804 TATATATATATATATAA-TAAAAT
1 TATAGATATATATAGAATTAAAAT
*
27827 TATAGATATTTATAGAATTAAAA
1 TATAGATATATATAGAATTAAAA
27850 AATATTTTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.41
Consensus pattern (24 bp):
TATAGATATATATAGAATTAAAAT
Found at i:33679 original size:16 final size:16
Alignment explanation
Indices: 33655--33688 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
33645 TATCGCCGAC
*
33655 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
33671 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
33687 CG
1 CG
33689 TGAATAGTAA
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:0.26, G:0.09, T:0.32
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:34399 original size:2 final size:2
Alignment explanation
Indices: 34392--34423 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
34382 AATTTTTAAA
34392 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
34424 GAATTATAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:34718 original size:22 final size:22
Alignment explanation
Indices: 34676--34716 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
34666 TTTATTAGAT
34676 TATAAAAATATTAAAATTATAC
1 TATAAAAATATTAAAATTATAC
*
34698 TATAATAAT-TT-AAATTATA
1 TATAAAAATATTAAAATTATA
34717 TATTCTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
21 2 0.11
22 8 0.44
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (22 bp):
TATAAAAATATTAAAATTATAC
Found at i:51807 original size:15 final size:15
Alignment explanation
Indices: 51787--51823 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
51777 CCCCTATGTT
51787 TTTGGTCTAACCGAC
1 TTTGGTCTAACCGAC
51802 TTTGGTCTAACCGAC
1 TTTGGTCTAACCGAC
51817 TTTGGTC
1 TTTGGTC
51824 ACCAATTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.16, C:0.24, G:0.22, T:0.38
Consensus pattern (15 bp):
TTTGGTCTAACCGAC
Found at i:61263 original size:36 final size:35
Alignment explanation
Indices: 61218--61328 Score: 134
Period size: 35 Copynumber: 3.2 Consensus size: 35
61208 TAAGATACTA
* *
61218 CCTA-AACATCACCATCTTCTATCACCGTTTTTACG
1 CCTATAACATCACCATCTTCTATCACC-ATTTCACG
* * *
61253 CCTATAACATCACCATCTTCCATTACCATTGCACG
1 CCTATAACATCACCATCTTCTATCACCATTTCACG
* * *
61288 CCTATATCCTTACCATCTTCTATCACCATTTCACG
1 CCTATAACATCACCATCTTCTATCACCATTTCACG
61323 CCTATA
1 CCTATA
61329 TAACCACCAA
Statistics
Matches: 64, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
35 44 0.69
36 20 0.31
ACGTcount: A:0.26, C:0.36, G:0.05, T:0.33
Consensus pattern (35 bp):
CCTATAACATCACCATCTTCTATCACCATTTCACG
Found at i:69869 original size:2 final size:2
Alignment explanation
Indices: 69862--69888 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
69852 ACTACCAAAA
69862 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
69889 CATACCCTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:72347 original size:60 final size:60
Alignment explanation
Indices: 72266--72385 Score: 170
Period size: 60 Copynumber: 2.0 Consensus size: 60
72256 GTCCTCCAAT
* *
72266 TATGACCCTCATTTTAAATTAGTCCTTAAACTTTTTAACA-TTCTAATTTCAACCCCAAAC
1 TATGACCCTCATTCTAAATTAGTCCTTAAACTTTTGAACATTTC-AATTTCAACCCCAAAC
* * **
72326 TATGACTCTTATTCTAAATTAGTCCTTAAACTTTTGAACATTTCAATTTCATTCCCAAAC
1 TATGACCCTCATTCTAAATTAGTCCTTAAACTTTTGAACATTTCAATTTCAACCCCAAAC
72386 CCTCATTTAA
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
60 50 0.94
61 3 0.06
ACGTcount: A:0.33, C:0.23, G:0.04, T:0.40
Consensus pattern (60 bp):
TATGACCCTCATTCTAAATTAGTCCTTAAACTTTTGAACATTTCAATTTCAACCCCAAAC
Found at i:72716 original size:60 final size:59
Alignment explanation
Indices: 72571--72749 Score: 198
Period size: 60 Copynumber: 3.0 Consensus size: 59
72561 ACATAGTTTG
* * * * **
72571 GGATGAAATTAAAATGTTCAAAAGTTTAGGTACTAATTTAGAATG-AGGTCATAGTTTGG
1 GGATGAAATTAAAATGTTTAAAAGTTTAGG-ACTAATTTAAAATGAAGATCATAATTTAA
* * * *
72630 GGATGGAATTGAAATGTTTAAAAGTTTAAGGACTAATTTAAAATGAAAATAATAATTTAA
1 GGATGAAATTAAAATGTTTAAAAGTTT-AGGACTAATTTAAAATGAAGATCATAATTTAA
* * * *
72690 GGATGAAATTTAAATTTTTAAAAGTTTGGGGACTAATTTAATATGAAGATCATAATTTAA
1 GGATGAAATTAAAATGTTTAAAAGTTT-AGGACTAATTTAAAATGAAGATCATAATTTAA
72750 AGACACATGA
Statistics
Matches: 100, Mismatches: 18, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
59 37 0.37
60 63 0.63
ACGTcount: A:0.42, C:0.03, G:0.19, T:0.35
Consensus pattern (59 bp):
GGATGAAATTAAAATGTTTAAAAGTTTAGGACTAATTTAAAATGAAGATCATAATTTAA
Done.