Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008654.1 Hibiscus syriacus cultivar Beakdansim tig00111648_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: 3533819
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 18 of 18
Found at i:3519401 original size:17 final size:17
Alignment explanation
Indices: 3519379--3519414 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
3519369 AATCATTCTA
3519379 TTTTAATTTAGTATAAT
1 TTTTAATTTAGTATAAT
3519396 TTTTAATTTAGTATAAT
1 TTTTAATTTAGTATAAT
3519413 TT
1 TT
3519415 GACATTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (17 bp):
TTTTAATTTAGTATAAT
Found at i:3523173 original size:2 final size:2
Alignment explanation
Indices: 3523162--3523223 Score: 117
Period size: 2 Copynumber: 31.5 Consensus size: 2
3523152 TAGAAACTTC
3523162 TA TA -A 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
3523203 TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
3523224 GAGAAAAATG
Statistics
Matches: 59, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 58 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3526513 original size:21 final size:21
Alignment explanation
Indices: 3526438--3526535 Score: 103
Period size: 21 Copynumber: 4.7 Consensus size: 21
3526428 GGTGTTTGAG
*
3526438 TGCATGGATGCACTGCATGG-
1 TGCATGGATGCACTGCAGGGA
*
3526458 TGCATCGATGCACTAGTGCA-GG-
1 TGCATGGATGCAC---TGCAGGGA
*
3526480 TGAATGGATGCACTGCAGGGA
1 TGCATGGATGCACTGCAGGGA
* *
3526501 TGCATGTATGCACTGCAGGGG
1 TGCATGGATGCACTGCAGGGA
3526522 TGCATGGATGCACT
1 TGCATGGATGCACT
3526536 TTGACACCCT
Statistics
Matches: 66, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
19 4 0.06
20 14 0.21
21 31 0.47
22 13 0.20
23 4 0.06
ACGTcount: A:0.22, C:0.19, G:0.35, T:0.23
Consensus pattern (21 bp):
TGCATGGATGCACTGCAGGGA
Found at i:3526529 original size:42 final size:41
Alignment explanation
Indices: 3526437--3526535 Score: 114
Period size: 42 Copynumber: 2.4 Consensus size: 41
3526427 CGGTGTTTGA
*
3526437 GTGCATGGATGCACTGCATGGTGCATCGATGCACTAGTGCAG
1 GTGCATGGATGCACTGCAGGGTGCATCGATGCACTAGTG-AG
*
3526479 GTGAATGGATGCACTGCAGGGATGCAT-GTATGCACTGCAG-G-G
1 GTGCATGGATGCACTGCAGGG-TGCATCG-ATGCACT--AGTGAG
3526521 GTGCATGGATGCACT
1 GTGCATGGATGCACT
3526536 TTGACACCCT
Statistics
Matches: 50, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
42 35 0.70
43 12 0.24
44 1 0.02
45 2 0.04
ACGTcount: A:0.22, C:0.19, G:0.35, T:0.23
Consensus pattern (41 bp):
GTGCATGGATGCACTGCAGGGTGCATCGATGCACTAGTGAG
Found at i:3530049 original size:21 final size:21
Alignment explanation
Indices: 3529974--3530112 Score: 142
Period size: 21 Copynumber: 6.7 Consensus size: 21
3529964 GGTGTTTGAG
* *
3529974 TGCATGGATGCACTACATGG-
1 TGCATGGATGCACTGCAGGGA
*
3529994 TGCATCGATGCACTAGTGCA-GG-
1 TGCATGGATGCAC---TGCAGGGA
* *
3530016 TGTATGGATGCACCGCAGGGA
1 TGCATGGATGCACTGCAGGGA
* *
3530037 TGCATGTATGCACTGCATGGA
1 TGCATGGATGCACTGCAGGGA
* *
3530058 TGCATGTATGCACTGCAGGGG
1 TGCATGGATGCACTGCAGGGA
3530079 TGCATGGATGCACTGCAGGG-
1 TGCATGGATGCACTGCAGGGA
3530099 TGCATGGATGCACT
1 TGCATGGATGCACT
3530113 TGACACCCTT
Statistics
Matches: 102, Mismatches: 12, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
19 3 0.03
20 28 0.27
21 55 0.54
22 13 0.13
23 3 0.03
ACGTcount: A:0.22, C:0.20, G:0.34, T:0.24
Consensus pattern (21 bp):
TGCATGGATGCACTGCAGGGA
Found at i:3530056 original size:63 final size:61
Alignment explanation
Indices: 3529973--3530112 Score: 169
Period size: 63 Copynumber: 2.2 Consensus size: 61
3529963 CGGTGTTTGA
*
3529973 GTGCATGGATGCACTACATGG-TGCATCG-ATGCACTAGTGCA-GGTGTATGGATGCACCGCAGG
1 GTGCATGGATGCACTACATGGATGCAT-GTATGCAC---TGCAGGGTGCATGGATGCACCGCAGG
* * *
3530035 GATGCATGTATGCACTGCATGGATGCATGTATGCACTGCAGGGGTGCATGGATGCACTGCAGG
1 G-TGCATGGATGCACTACATGGATGCATGTATGCACTGCA-GGGTGCATGGATGCACCGCAGG
3530098 GTGCATGGATGCACT
1 GTGCATGGATGCACT
3530113 TGACACCCTT
Statistics
Matches: 68, Mismatches: 5, Indels: 10
0.82 0.06 0.12
Matches are distributed among these distances:
61 4 0.06
62 14 0.21
63 39 0.57
64 11 0.16
ACGTcount: A:0.22, C:0.20, G:0.34, T:0.24
Consensus pattern (61 bp):
GTGCATGGATGCACTACATGGATGCATGTATGCACTGCAGGGTGCATGGATGCACCGCAGG
Found at i:3530620 original size:16 final size:16
Alignment explanation
Indices: 3530599--3530637 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
3530589 AACATTAGGA
3530599 ACTTCAAGTATTCAAG
1 ACTTCAAGTATTCAAG
3530615 ACTTCAAGTATTCAAG
1 ACTTCAAGTATTCAAG
3530631 ACTTCAA
1 ACTTCAA
3530638 CAATCATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.38, C:0.21, G:0.10, T:0.31
Consensus pattern (16 bp):
ACTTCAAGTATTCAAG
Found at i:3530636 original size:8 final size:9
Alignment explanation
Indices: 3530599--3530637 Score: 50
Period size: 8 Copynumber: 4.8 Consensus size: 9
3530589 AACATTAGGA
3530599 ACTTCAAGT
1 ACTTCAAGT
3530608 A-TTCAAG-
1 ACTTCAAGT
3530615 ACTTCAAGT
1 ACTTCAAGT
3530624 A-TTCAAG-
1 ACTTCAAGT
3530631 ACTTCAA
1 ACTTCAA
3530638 CAATCATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
7 2 0.07
8 23 0.85
9 2 0.07
ACGTcount: A:0.38, C:0.21, G:0.10, T:0.31
Consensus pattern (9 bp):
ACTTCAAGT
Found at i:3530853 original size:3 final size:3
Alignment explanation
Indices: 3530847--3530889 Score: 59
Period size: 3 Copynumber: 14.3 Consensus size: 3
3530837 ATACTAATAA
* * *
3530847 TAT TAT TAT TAT TAT TAT TAT TAC TAT TGT TAT TAT TTT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
3530890 TACATGTTAC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:3531669 original size:22 final size:22
Alignment explanation
Indices: 3531613--3531695 Score: 91
Period size: 23 Copynumber: 3.8 Consensus size: 22
3531603 TCGTAATTTT
*
3531613 CACCGAAGTGCCACATA-ATTG
1 CACCGAAGTGCCACATAGGTTG
*
3531634 TC-TCGAAG-GACCACATAGGTTG
1 -CACCGAAGTG-CCACATAGGTTG
3531656 CACCGAAGTGCCACATAGGTTTG
1 CACCGAAGTGCCACATAGG-TTG
*
3531679 CACCAAAGTGCCACATA
1 CACCGAAGTGCCACATA
3531696 TTTGTCCCAA
Statistics
Matches: 52, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
20 1 0.02
21 13 0.25
22 18 0.35
23 20 0.38
ACGTcount: A:0.31, C:0.28, G:0.22, T:0.19
Consensus pattern (22 bp):
CACCGAAGTGCCACATAGGTTG
Found at i:3531705 original size:21 final size:22
Alignment explanation
Indices: 3531644--3531716 Score: 80
Period size: 23 Copynumber: 3.3 Consensus size: 22
3531634 TCTCGAAGGA
* *
3531644 CCACATAGGTTGCACCGAAGTG
1 CCACATAGTTTGCACCAAAGTG
3531666 CCACATAGGTTTGCACCAAAGTG
1 CCACATA-GTTTGCACCAAAGTG
3531689 CCACATA-TTTGTC-CCAAAG-G
1 CCACATAGTTTG-CACCAAAGTG
3531709 ACCACATA
1 -CCACATA
3531717 ATTATCTCAA
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
20 1 0.02
21 17 0.37
22 8 0.17
23 20 0.43
ACGTcount: A:0.32, C:0.29, G:0.19, T:0.21
Consensus pattern (22 bp):
CCACATAGTTTGCACCAAAGTG
Found at i:3531727 original size:21 final size:21
Alignment explanation
Indices: 3531681--3531737 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
3531671 TAGGTTTGCA
* *
3531681 CCAAAGTG-CCACATATTTGTC
1 CCAAAG-GACCACATAATTATC
3531702 CCAAAGGACCACATAATTATC
1 CCAAAGGACCACATAATTATC
*
3531723 TCAAAGGA-CACATAA
1 CCAAAGGACCACATAA
3531738 GACCCTCGAC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 8 0.25
21 24 0.75
ACGTcount: A:0.40, C:0.26, G:0.12, T:0.21
Consensus pattern (21 bp):
CCAAAGGACCACATAATTATC
Done.