Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003889.1 Hibiscus syriacus cultivar Beakdansim tig00008401_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: 63254
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.33
Found at i:6417 original size:23 final size:23
Alignment explanation
Indices: 6303--6409 Score: 178
Period size: 23 Copynumber: 4.7 Consensus size: 23
6293 ACATCTTATA
* *
6303 TGGCACTACGGTGTAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
*
6326 GGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
*
6349 TGGCACTTCAGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
6372 TGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
6395 TGGCACTTCGGTGCA
1 TGGCACTTCGGTGCA
6410 TTTATACGAG
Statistics
Matches: 78, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 78 1.00
ACGTcount: A:0.19, C:0.25, G:0.27, T:0.29
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:17347 original size:22 final size:22
Alignment explanation
Indices: 17287--17347 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 22
17277 ATAAGGGAGA
* * *
17287 GGGAATCGATACCCCCTTGAAG
1 GGGAACCGATTCCCCTTTGAAG
*
17309 GGGAACCTATTTCCCCTTTGAAG
1 GGGAACCGA-TTCCCCTTTGAAG
17332 GGGAACCGATTCCCCT
1 GGGAACCGATTCCCCT
17348 AGGGGAATCA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
22 14 0.42
23 19 0.58
ACGTcount: A:0.23, C:0.30, G:0.25, T:0.23
Consensus pattern (22 bp):
GGGAACCGATTCCCCTTTGAAG
Found at i:21117 original size:2 final size:2
Alignment explanation
Indices: 21079--21107 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
21069 TGATAATCAT
21079 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 T
21108 TAACATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:21559 original size:15 final size:13
Alignment explanation
Indices: 21513--21559 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
21503 CATTACACAT
21513 TCACATA-TTCATA
1 TCACATAGTTC-TA
*
21526 TCACATAGTTCTT
1 TCACATAGTTCTA
21539 TCACATAGCTCTCTA
1 TCACATAG-T-TCTA
21554 TCACAT
1 TCACAT
21560 TTCATATGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
13 16 0.55
14 4 0.14
15 9 0.31
ACGTcount: A:0.30, C:0.28, G:0.04, T:0.38
Consensus pattern (13 bp):
TCACATAGTTCTA
Found at i:29756 original size:2 final size:2
Alignment explanation
Indices: 29749--29779 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
29739 AGATAAGATT
29749 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
29780 ATATATATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:29784 original size:2 final size:2
Alignment explanation
Indices: 29779--29805 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
29769 TCTCTCTCTC
29779 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 T
29806 CACAAATGTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:61054 original size:22 final size:22
Alignment explanation
Indices: 61013--61079 Score: 116
Period size: 22 Copynumber: 3.0 Consensus size: 22
61003 CTCGTATAAA
61013 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
61036 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
*
61058 TGCACCGTAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
61080 GATGTCCATA
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
22 31 0.72
23 12 0.28
ACGTcount: A:0.25, C:0.28, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:61729 original size:2 final size:2
Alignment explanation
Indices: 61722--61775 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
61712 TCTCTTAAAC
61722 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
61764 AT AT AT AT AT AT
1 AT AT AT AT AT AT
61776 TCACATGTTC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:62806 original size:21 final size:21
Alignment explanation
Indices: 62782--62826 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
62772 TCTTGTTCGT
* *
62782 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
62803 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
62824 TTG
1 TTG
62827 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Done.