Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006506.1 Hibiscus syriacus cultivar Beakdansim tig00015836_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: 245942
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:234826 original size:34 final size:35
Alignment explanation
Indices: 234783--234852 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 35
234773 TTTCATTTAT
234783 GGGGAATCGATA-CCCCCAGGGGGAATCTGTTCCC
1 GGGGAATCGATACCCCCCAGGGGGAATCTGTTCCC
234817 GGGGAATCGATACCCCCCCAGGGGGAATCTGTTCCC
1 GGGGAATCGATA-CCCCCCAGGGGGAATCTGTTCCC
234853 CCTGTACATA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
34 12 0.35
36 22 0.65
ACGTcount: A:0.20, C:0.31, G:0.31, T:0.17
Consensus pattern (35 bp):
GGGGAATCGATACCCCCCAGGGGGAATCTGTTCCC
Found at i:237701 original size:2 final size:2
Alignment explanation
Indices: 237694--237734 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
237684 TGCCTTAATC
237694 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT A
237735 GGATCCAAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:238196 original size:2 final size:2
Alignment explanation
Indices: 238189--238269 Score: 162
Period size: 2 Copynumber: 40.5 Consensus size: 2
238179 AATCAAATTT
238189 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
238231 TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA T
238270 CCAATGATAT
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 79 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:240301 original size:38 final size:39
Alignment explanation
Indices: 240249--240344 Score: 108
Period size: 38 Copynumber: 2.5 Consensus size: 39
240239 CTCGTATAAA
*
240249 TGTCCC-AAAGGACCTATCATCCCGAAGGATGTCATCTG
1 TGTCCCGAAAGGACCTATCATCCCGAAGGATGTAATCTG
* * * *
240287 TGTCCCGAAA-GACCTGTCATCTCGAATGATGTAATTTG
1 TGTCCCGAAAGGACCTATCATCCCGAAGGATGTAATCTG
* *
240325 TGTCCCG-TAGGACCTGTCAT
1 TGTCCCGAAAGGACCTATCAT
240345 ATGTCTTATA
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
37 1 0.02
38 46 0.92
39 3 0.06
ACGTcount: A:0.24, C:0.26, G:0.22, T:0.28
Consensus pattern (39 bp):
TGTCCCGAAAGGACCTATCATCCCGAAGGATGTAATCTG
Found at i:240549 original size:46 final size:46
Alignment explanation
Indices: 240493--240605 Score: 171
Period size: 46 Copynumber: 2.5 Consensus size: 46
240483 ATGTGTAACC
240493 ATGT-ATTTCATATCATATCACATGTATCA-AGTATTACATATTCAT
1 ATGTCATTTCATATCATATCACATGTATCACA-TATTACATATTCAT
*
240538 ATGTCATTTCATATCATATCACATGTATCACATATTGCATATTCAT
1 ATGTCATTTCATATCATATCACATGTATCACATATTACATATTCAT
*
240584 ATATCATTTCATAT-A-ATCACAT
1 ATGTCATTTCATATCATATCACAT
240606 AGCTTATCTC
Statistics
Matches: 64, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
44 7 0.11
45 5 0.08
46 51 0.80
47 1 0.02
ACGTcount: A:0.35, C:0.18, G:0.05, T:0.42
Consensus pattern (46 bp):
ATGTCATTTCATATCATATCACATGTATCACATATTACATATTCAT
Found at i:241048 original size:21 final size:21
Alignment explanation
Indices: 240991--241039 Score: 77
Period size: 18 Copynumber: 2.5 Consensus size: 21
240981 TTTTTCATTT
240991 AGGGGGAATCGATA---CCCC
1 AGGGGGAATCGATACCCCCCC
241009 AGGGGGAATCGATACCCCCCC
1 AGGGGGAATCGATACCCCCCC
241030 AGGGGGAATC
1 AGGGGGAATC
241040 TGTTCCCCCT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
18 14 0.50
21 14 0.50
ACGTcount: A:0.27, C:0.29, G:0.35, T:0.10
Consensus pattern (21 bp):
AGGGGGAATCGATACCCCCCC
Found at i:241961 original size:2 final size:2
Alignment explanation
Indices: 241954--241991 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
241944 TCATATAGTC
241954 TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
241992 CATAACTCCA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:242825 original size:63 final size:64
Alignment explanation
Indices: 242748--242909 Score: 197
Period size: 63 Copynumber: 2.5 Consensus size: 64
242738 ATCCCTTGAC
* *
242748 GGGTGCATCGATGCACTATCTATGCATCGATACA-TAAATCCCATTCGATGTTTGTA-TTTAAGG
1 GGGTGCATCGATGCACTATCTGTGCATCGATACACT-AATCCCATTCGATGTTTGTATTTTAAAG
* * ** *
242811 GGGTGCATAGATGCACTA-CTCGTGCATCGATACACTGATGGCATTCGATGTTTTTATTTTAAAG
1 GGGTGCATCGATGCACTATCT-GTGCATCGATACACTAATCCCATTCGATGTTTGTATTTTAAAG
*
242875 GAGTGCATCGATGCACT-TCATGTGCATCGATACAC
1 GGGTGCATCGATGCACTATC-TGTGCATCGATACAC
242910 CTTGAACAAT
Statistics
Matches: 85, Mismatches: 9, Indels: 9
0.83 0.09 0.09
Matches are distributed among these distances:
62 2 0.02
63 45 0.53
64 37 0.44
65 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.32
Consensus pattern (64 bp):
GGGTGCATCGATGCACTATCTGTGCATCGATACACTAATCCCATTCGATGTTTGTATTTTAAAG
Done.