Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006934.1 Hibiscus syriacus cultivar Beakdansim tig00017798_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: 49111
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:3625 original size:10 final size:11
Alignment explanation
Indices: 3610--3642 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
3600 TTTCAATTCC
3610 TTTATCTT-TT
1 TTTATCTTGTT
3620 TTTATCTTGTT
1 TTTATCTTGTT
*
3631 TTAATCTTGTT
1 TTTATCTTGTT
3642 T
1 T
3643 CTTACATTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
10 8 0.38
11 13 0.62
ACGTcount: A:0.12, C:0.09, G:0.06, T:0.73
Consensus pattern (11 bp):
TTTATCTTGTT
Found at i:22182 original size:54 final size:54
Alignment explanation
Indices: 22118--22227 Score: 211
Period size: 54 Copynumber: 2.0 Consensus size: 54
22108 ACGACGTAGG
22118 TAAGATGTGTATGCATTATCAATAGATTAATAAAGTTCTGAACATATATAATCT
1 TAAGATGTGTATGCATTATCAATAGATTAATAAAGTTCTGAACATATATAATCT
*
22172 TAAGATGTGTATGCGTTATCAATAGATTAATAAAGTTCTGAACATATATAATCT
1 TAAGATGTGTATGCATTATCAATAGATTAATAAAGTTCTGAACATATATAATCT
22226 TA
1 TA
22228 TAATTATTAA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 55 1.00
ACGTcount: A:0.40, C:0.09, G:0.14, T:0.37
Consensus pattern (54 bp):
TAAGATGTGTATGCATTATCAATAGATTAATAAAGTTCTGAACATATATAATCT
Found at i:28257 original size:2 final size:2
Alignment explanation
Indices: 28252--28300 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
28242 ATAAAAAAGA
28252 AT AT AT AT AT 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 AT AT AT AT AT
28294 AT AT AT A
1 AT AT AT A
28301 AAAATGTTAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:30765 original size:22 final size:22
Alignment explanation
Indices: 30738--30802 Score: 112
Period size: 22 Copynumber: 3.0 Consensus size: 22
30728 CTGTTAGACA
*
30738 GGGGGGAATCGGTACCCCCTGG
1 GGGGGGAATCTGTACCCCCTGG
*
30760 GGGGGGAATCTGTATCCCCTGG
1 GGGGGGAATCTGTACCCCCTGG
30782 GGGGGGAATCTGTACCCCCTG
1 GGGGGGAATCTGTACCCCCTG
30803 AATAATCTGA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.14, C:0.26, G:0.42, T:0.18
Consensus pattern (22 bp):
GGGGGGAATCTGTACCCCCTGG
Found at i:32750 original size:3 final size:3
Alignment explanation
Indices: 32742--32783 Score: 59
Period size: 3 Copynumber: 14.3 Consensus size: 3
32732 TACGTCCTCA
* *
32742 TTC TTC TTC TTC TAC TTC TTC TTC TTC TTC TTG TT- TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
32784 ATTACCTTTC
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.02, C:0.29, G:0.02, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:33847 original size:34 final size:32
Alignment explanation
Indices: 33778--33840 Score: 90
Period size: 34 Copynumber: 1.9 Consensus size: 32
33768 CCTTACAAAC
*
33778 TCCCTAGTTTTTCCGGGCTAAACTAGAACAGT
1 TCCCTAGTTTTACCGGGCTAAACTAGAACAGT
*
33810 TCCCTAGATTTTACACGGGCTAAGCTAGAAC
1 TCCCTAG-TTTTAC-CGGGCTAAACTAGAAC
33841 TTTTCCCCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
32 7 0.26
33 5 0.19
34 15 0.56
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGCTAAACTAGAACAGT
Found at i:34234 original size:20 final size:19
Alignment explanation
Indices: 34203--34274 Score: 90
Period size: 20 Copynumber: 3.6 Consensus size: 19
34193 GACATGGGAT
*
34203 AATCGGTACCCCTGGGAGGG
1 AATCTGTACCCCTGGG-GGG
*
34223 AATCTGTTCCCCCTGGGGGG
1 AATCTG-TACCCCTGGGGGG
*
34243 AATCGGTACCCCCTGGGGGG
1 AATCTGTA-CCCCTGGGGGG
34263 AATCTGTACCCC
1 AATCTGTACCCC
34275 ATGAACAATT
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
19 5 0.11
20 31 0.69
21 9 0.20
ACGTcount: A:0.17, C:0.31, G:0.33, T:0.19
Consensus pattern (19 bp):
AATCTGTACCCCTGGGGGG
Found at i:34788 original size:53 final size:48
Alignment explanation
Indices: 34670--34796 Score: 137
Period size: 48 Copynumber: 2.5 Consensus size: 48
34660 CTTTGAATTT
* **
34670 GATATCCTTCGTCGTGAAGTTGAAATCCAATCTTGTGTAAGTGGGCAC
1 GATATCATTCGTCGTGAAGTTGAAATCCAATCTTGTGTAAGTGGAAAC
* * *
34718 AATATCATTCGTCGTGAAGTTAAAATCCAATCTTGTATGTTGCTAGTGGAAAC
1 GATATCATTCGTCGTGAAGTTGAAATCCAATCTTG--TG-T--AAGTGGAAAC
* *
34771 GATATCTTTCGTTGTGAAGTTGAAAT
1 GATATCATTCGTCGTGAAGTTGAAAT
34797 AATGGATGGC
Statistics
Matches: 64, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
48 32 0.50
50 2 0.03
51 1 0.02
53 29 0.45
ACGTcount: A:0.28, C:0.15, G:0.22, T:0.35
Consensus pattern (48 bp):
GATATCATTCGTCGTGAAGTTGAAATCCAATCTTGTGTAAGTGGAAAC
Found at i:46539 original size:55 final size:52
Alignment explanation
Indices: 46480--46599 Score: 129
Period size: 55 Copynumber: 2.2 Consensus size: 52
46470 TAGCAATAAT
46480 AATAAATAAAAAAGAAATATATATATATATA-TAATATATAAT-GTTAAATTAAGTA
1 AATAAATAAAAAAGAAA-ATATATATA-ATAGTAATA-ATAATGGTTAAATT-AG-A
*
46535 AAT-AATAAAAGAAAGAAAATATGTATAATAGTAATAATAATGGGTTAAATTAGA
1 AATAAAT-AAA-AAAGAAAATATATATAATAGTAATAATAAT-GGTTAAATTAGA
*
46589 AAGAAATAAAA
1 AATAAATAAAA
46600 TAGGAGGTAA
Statistics
Matches: 57, Mismatches: 2, Indels: 14
0.78 0.03 0.19
Matches are distributed among these distances:
53 1 0.02
54 17 0.30
55 24 0.42
56 15 0.26
ACGTcount: A:0.61, C:0.00, G:0.10, T:0.29
Consensus pattern (52 bp):
AATAAATAAAAAAGAAAATATATATAATAGTAATAATAATGGTTAAATTAGA
Done.