Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002982.1 Hibiscus syriacus cultivar Beakdansim tig00006171_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: 51838
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Found at i:485 original size:11 final size:11
Alignment explanation
Indices: 469--498 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
459 CAATAAAGAT
469 ATAATTATTCA
1 ATAATTATTCA
480 ATAATTATTCA
1 ATAATTATTCA
491 A-AATTATT
1 ATAATTATT
499 GATATAAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 7 0.37
11 12 0.63
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (11 bp):
ATAATTATTCA
Found at i:597 original size:19 final size:20
Alignment explanation
Indices: 583--629 Score: 64
Period size: 18 Copynumber: 2.5 Consensus size: 20
573 TTTTAATATT
583 AAAAATAAATTTTAAAAATA
1 AAAAATAAATTTTAAAAATA
603 AAAAATAAA--TT-AAAATGA
1 AAAAATAAATTTTAAAAAT-A
621 AAAAATAAA
1 AAAAATAAA
630 CGTTTTAATG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.19
18 12 0.46
20 9 0.35
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.23
Consensus pattern (20 bp):
AAAAATAAATTTTAAAAATA
Found at i:1081 original size:18 final size:18
Alignment explanation
Indices: 1050--1086 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1040 CATAAATAGC
1050 AATTACAAATAAAAAATA
1 AATTACAAATAAAAAATA
1068 AATTA-AAATGAAAAAATA
1 AATTACAAAT-AAAAAATA
1086 A
1 A
1087 TCGATTAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.73, C:0.03, G:0.03, T:0.22
Consensus pattern (18 bp):
AATTACAAATAAAAAATA
Found at i:5534 original size:28 final size:26
Alignment explanation
Indices: 5483--5534 Score: 68
Period size: 28 Copynumber: 1.9 Consensus size: 26
5473 TTGTAAGTTG
*
5483 AATTTATAAAATTTTAAAGTACGATA
1 AATTTATAAAATTTTAAAGAACGATA
*
5509 AATTTATAAAAAGTTTTAGAGAACGA
1 AATTTAT-AAAA-TTTTAAAGAACGA
5535 AGATAAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 7 0.32
27 4 0.18
28 11 0.50
ACGTcount: A:0.50, C:0.04, G:0.12, T:0.35
Consensus pattern (26 bp):
AATTTATAAAATTTTAAAGAACGATA
Found at i:9078 original size:16 final size:16
Alignment explanation
Indices: 9044--9084 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
9034 GATTACTTCA
* *
9044 GAATGATT-AAGTTCT
1 GAATGATTCAAATGCT
9059 GAATGATTCAAATGCT
1 GAATGATTCAAATGCT
9075 GAATGATTCA
1 GAATGATTCA
9085 GAGGCTCTGG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.37, C:0.10, G:0.20, T:0.34
Consensus pattern (16 bp):
GAATGATTCAAATGCT
Found at i:10845 original size:37 final size:38
Alignment explanation
Indices: 10771--10846 Score: 127
Period size: 37 Copynumber: 2.0 Consensus size: 38
10761 ATACTCATCA
10771 AGAAATCAAAGAAAATTTGAATTATAAAATTATTTCAT
1 AGAAATCAAAGAAAATTTGAATTATAAAATTATTTCAT
* *
10809 AGAAATCAAAGAAAATTT-AATTTTAAAATTGTTTCAT
1 AGAAATCAAAGAAAATTTGAATTATAAAATTATTTCAT
10846 A
1 A
10847 TCTTTTTAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
37 18 0.50
38 18 0.50
ACGTcount: A:0.51, C:0.05, G:0.08, T:0.36
Consensus pattern (38 bp):
AGAAATCAAAGAAAATTTGAATTATAAAATTATTTCAT
Found at i:13213 original size:27 final size:28
Alignment explanation
Indices: 13161--13215 Score: 94
Period size: 27 Copynumber: 2.0 Consensus size: 28
13151 TTTTGTATCA
13161 TATTTCTCTTTTATTTTTTATTTAGTCG
1 TATTTCTCTTTTATTTTTTATTTAGTCG
*
13189 TATTTTTCTTTTA-TTTTTATTTAGTCG
1 TATTTCTCTTTTATTTTTTATTTAGTCG
13216 GCGACGACAC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 14 0.54
28 12 0.46
ACGTcount: A:0.15, C:0.09, G:0.07, T:0.69
Consensus pattern (28 bp):
TATTTCTCTTTTATTTTTTATTTAGTCG
Found at i:18420 original size:15 final size:15
Alignment explanation
Indices: 18400--18436 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
18390 AGACATGTAG
18400 TTTACCCTAATTATT
1 TTTACCCTAATTATT
18415 TTTACCCTAATTATT
1 TTTACCCTAATTATT
18430 TTTACCC
1 TTTACCC
18437 GTCATTTGCG
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:0.24, C:0.24, G:0.00, T:0.51
Consensus pattern (15 bp):
TTTACCCTAATTATT
Found at i:19371 original size:4 final size:4
Alignment explanation
Indices: 19362--19397 Score: 72
Period size: 4 Copynumber: 9.0 Consensus size: 4
19352 GTGAAGTTGA
19362 TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG
19398 CTACAAATAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:23314 original size:56 final size:57
Alignment explanation
Indices: 23233--23346 Score: 203
Period size: 56 Copynumber: 2.0 Consensus size: 57
23223 GTATTTTGCG
*
23233 TGTGATGATTTTTACTTTTAGGTAAAAAGT-AAAACCGGAGTAAGGGGTATTTGACA
1 TGTGATGATTTTTACTTTTAAGTAAAAAGTAAAAACCGGAGTAAGGGGTATTTGACA
*
23289 TGTGATGATTTTTACTTTTAAGTAAAAAGTAAAAATCGGAGTAAGGGGTATTTGACA
1 TGTGATGATTTTTACTTTTAAGTAAAAAGTAAAAACCGGAGTAAGGGGTATTTGACA
23346 T
1 T
23347 CTTACCTATT
Statistics
Matches: 55, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
56 29 0.53
57 26 0.47
ACGTcount: A:0.35, C:0.06, G:0.24, T:0.35
Consensus pattern (57 bp):
TGTGATGATTTTTACTTTTAAGTAAAAAGTAAAAACCGGAGTAAGGGGTATTTGACA
Found at i:29602 original size:2 final size:2
Alignment explanation
Indices: 29597--29638 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
29587 GCGCGCACAC
29597 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
29639 CTACTTGTAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:31782 original size:60 final size:60
Alignment explanation
Indices: 31628--31786 Score: 237
Period size: 60 Copynumber: 2.6 Consensus size: 60
31618 ACACGTTGGG
* ** *
31628 CTAAGTAACAAATATTACCTACATCGGTAATTAGACTTTCATGCGATTACCTAAATTTTC
1 CTAAGTAACAAAGATTACCTACATCGGTAATTAGGTTTTCATGCGATTACCTAAATTTCC
*
31688 CTAAGTAACAATGATTACCTACATCGGTAATTAGGTTTTCATGCGATTACCTAAATTTCC
1 CTAAGTAACAAAGATTACCTACATCGGTAATTAGGTTTTCATGCGATTACCTAAATTTCC
* * **
31748 CTAAGTAACAACGATTACCTACACCGGTCTTTAGGTTTT
1 CTAAGTAACAAAGATTACCTACATCGGTAATTAGGTTTT
31787 TTAACTACGT
Statistics
Matches: 90, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
60 90 1.00
ACGTcount: A:0.32, C:0.21, G:0.13, T:0.35
Consensus pattern (60 bp):
CTAAGTAACAAAGATTACCTACATCGGTAATTAGGTTTTCATGCGATTACCTAAATTTCC
Found at i:41409 original size:51 final size:51
Alignment explanation
Indices: 41350--41455 Score: 203
Period size: 51 Copynumber: 2.1 Consensus size: 51
41340 GACTTCGTCC
*
41350 GTCGATAGCAATATATGTTATGTTCGTATCGTGTTCGTGTTATCTTTTTAT
1 GTCGATAGCAATATATGTTATGTTCGTATCGTGTTCGTGTTATCTCTTTAT
41401 GTCGATAGCAATATATGTTATGTTCGTATCGTGTTCGTGTTATCTCTTTAT
1 GTCGATAGCAATATATGTTATGTTCGTATCGTGTTCGTGTTATCTCTTTAT
41452 GTCG
1 GTCG
41456 TATTCGATCG
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 54 1.00
ACGTcount: A:0.19, C:0.13, G:0.21, T:0.47
Consensus pattern (51 bp):
GTCGATAGCAATATATGTTATGTTCGTATCGTGTTCGTGTTATCTCTTTAT
Found at i:43768 original size:22 final size:22
Alignment explanation
Indices: 43743--43787 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
43733 TTCTCTCCGT
*
43743 TGCACACACAGTAGTTCTATTG
1 TGCACACACAGTAGTTATATTG
*
43765 TGCACACACATTAGTTATATTG
1 TGCACACACAGTAGTTATATTG
43787 T
1 T
43788 ACGCTAGTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.36
Consensus pattern (22 bp):
TGCACACACAGTAGTTATATTG
Done.