Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006683.1 Hibiscus syriacus cultivar Beakdansim tig00016580_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: 55405
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:16057 original size:16 final size:17
Alignment explanation
Indices: 16036--16071 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 17
16026 TTTGAAACAA
16036 GTACATATAT-GTGTGT
1 GTACATATATAGTGTGT
16052 GTACATATATACGTGTGT
1 GTACATATATA-GTGTGT
16070 GT
1 GT
16072 GTGTGTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 10 0.56
18 8 0.44
ACGTcount: A:0.25, C:0.08, G:0.25, T:0.42
Consensus pattern (17 bp):
GTACATATATAGTGTGT
Found at i:16161 original size:15 final size:15
Alignment explanation
Indices: 16141--16171 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
16131 GCAGTCACAT
16141 TGGTCATGCATTCAA
1 TGGTCATGCATTCAA
16156 TGGTCATGCATTCAA
1 TGGTCATGCATTCAA
16171 T
1 T
16172 AAGTTGTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.35
Consensus pattern (15 bp):
TGGTCATGCATTCAA
Found at i:22073 original size:19 final size:19
Alignment explanation
Indices: 22049--22086 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
22039 ACACAACATC
22049 ATTAATTCTTCTATATAGG
1 ATTAATTCTTCTATATAGG
22068 ATTAATTCTTCTATATAGG
1 ATTAATTCTTCTATATAGG
22087 TCCATCAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.47
Consensus pattern (19 bp):
ATTAATTCTTCTATATAGG
Found at i:27030 original size:18 final size:18
Alignment explanation
Indices: 27004--27039 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
26994 CACTCGATAC
* *
27004 CACTTCCCTTTTACTTTT
1 CACTACCCTTATACTTTT
27022 CACTACCCTTATACTTTT
1 CACTACCCTTATACTTTT
27040 TTCAGTCTCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.33, G:0.00, T:0.50
Consensus pattern (18 bp):
CACTACCCTTATACTTTT
Found at i:28794 original size:15 final size:15
Alignment explanation
Indices: 28771--28803 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
28761 ACATTACCCA
*
28771 CCCCGCATCCGCCCG
1 CCCCACATCCGCCCG
28786 CCCCACATCCGCCCG
1 CCCCACATCCGCCCG
28801 CCC
1 CCC
28804 AGCTAAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.09, C:0.70, G:0.15, T:0.06
Consensus pattern (15 bp):
CCCCACATCCGCCCG
Found at i:29966 original size:2 final size:2
Alignment explanation
Indices: 29959--29983 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
29949 ATGATATACA
29959 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 A
29984 CACGATTTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:33055 original size:3 final size:3
Alignment explanation
Indices: 33047--33092 Score: 56
Period size: 3 Copynumber: 15.3 Consensus size: 3
33037 CGAAATAACT
* * * *
33047 ATA ATA ATA ATA ATA ATA TTA TTA TTA TTA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
33093 AATGCTACAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (3 bp):
ATA
Found at i:35771 original size:100 final size:100
Alignment explanation
Indices: 35594--35781 Score: 281
Period size: 100 Copynumber: 1.9 Consensus size: 100
35584 ATATGATTTT
*
35594 GAAAAAATAAAAATTTAAGTACTGAAATAGAAACAAATCCTAGAGATGTAATTAAGGATGGGCAT
1 GAAAAAATAAAAATTTAAGTACTGAAACAGAAACAAATCCTAGAGATGTAATTAAGGATGGGCAT
* *
35659 GAGACCCGAACCCGACGAGTTCCAACCCGACCCGG
66 GAGACCCAAACCCAACGAGTTCCAACCCGACCCGG
* *
35694 GAAAAAATAAAAATTTAAGTA-TCGAAAC-GGACCAAAATCCTAGAGATGTAATTAAGGATGGGC
1 GAAAAAATAAAAATTTAAGTACT-GAAACAGAAAC-AAATCCTAGAGATGTAATTAAGGATGGGC
* *
35757 ATGGGAGCCAAACCCAACGAGTTCC
64 ATGAGACCCAAACCCAACGAGTTCC
35782 GACCGGGTCG
Statistics
Matches: 79, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
99 4 0.05
100 75 0.95
ACGTcount: A:0.43, C:0.19, G:0.21, T:0.18
Consensus pattern (100 bp):
GAAAAAATAAAAATTTAAGTACTGAAACAGAAACAAATCCTAGAGATGTAATTAAGGATGGGCAT
GAGACCCAAACCCAACGAGTTCCAACCCGACCCGG
Found at i:38751 original size:14 final size:15
Alignment explanation
Indices: 38710--38751 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 15
38700 AAGATATTTG
38710 AACAAACTATTAATAC
1 AACAAA-TATTAATAC
*
38726 ACACATATATTAATA-
1 A-ACAAATATTAATAC
38741 AACAAATATTA
1 AACAAATATTA
38752 CTTCAATGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 9 0.39
15 1 0.04
16 9 0.39
17 4 0.17
ACGTcount: A:0.57, C:0.14, G:0.00, T:0.29
Consensus pattern (15 bp):
AACAAATATTAATAC
Found at i:41852 original size:2 final size:2
Alignment explanation
Indices: 41845--41871 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
41835 AATGTTCTTC
41845 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 A
41872 AAATAACGTT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:48370 original size:22 final size:24
Alignment explanation
Indices: 48345--48395 Score: 61
Period size: 22 Copynumber: 2.2 Consensus size: 24
48335 AAATATTCAA
*
48345 AATAATATTATTTTA-TAT-ATTT
1 AATAATAATATTTTAGTATAATTT
*
48367 AATATTAATATTTTAGTATCAATTT
1 AATAATAATATTTTAGTAT-AATTT
48392 AATA
1 AATA
48396 TAAAAAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 13 0.54
23 3 0.12
25 8 0.33
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (24 bp):
AATAATAATATTTTAGTATAATTT
Found at i:48433 original size:51 final size:53
Alignment explanation
Indices: 48353--48453 Score: 154
Period size: 51 Copynumber: 1.9 Consensus size: 53
48343 AAAATAATAT
* *
48353 TATTTTATATATTTAATATTAATATTTTAGTATCAATTTAATATAAAAAATTAA
1 TATTTTATATATTTAAGATTAATATTTTAGTACCAATTTAATA-AAAAAATTAA
48407 TATTTTA-ATA-TTAAGA-TAATATTTTAGTACCAATTTAATAAAAAAAT
1 TATTTTATATATTTAAGATTAATATTTTAGTACCAATTTAATAAAAAAAT
48454 AATTATTAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
50 7 0.16
51 23 0.51
52 5 0.11
53 3 0.07
54 7 0.16
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.47
Consensus pattern (53 bp):
TATTTTATATATTTAAGATTAATATTTTAGTACCAATTTAATAAAAAAATTAA
Found at i:48478 original size:51 final size:50
Alignment explanation
Indices: 48369--48484 Score: 128
Period size: 51 Copynumber: 2.3 Consensus size: 50
48359 ATATATTTAA
* **
48369 TATTAATATTTTAGTATCAATTTAATATAAAAAATTAATATTTTAATATT
1 TATTAATATTTTAGTACCAATTTAATATAAAAAATTAATATTAAAATATT
* *
48419 AAGATAATATTTTAGTACCAATTTAATA-AAAAAA-TAATTATTAAAATATATT
1 TA-TTAATATTTTAGTACCAATTTAATATAAAAAATTAA-TATT-AAA-ATATT
48471 TATTAATAATTTTA
1 TATTAAT-ATTTTA
48485 ATAATATAAT
Statistics
Matches: 54, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
49 3 0.06
50 11 0.20
51 28 0.52
52 12 0.22
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (50 bp):
TATTAATATTTTAGTACCAATTTAATATAAAAAATTAATATTAAAATATT
Found at i:51465 original size:17 final size:18
Alignment explanation
Indices: 51439--51474 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
51429 TTAAAATATT
*
51439 TATAATAATTAT-TTATA
1 TATAAAAATTATATTATA
51456 TATAAAAATTATATTATA
1 TATAAAAATTATATTATA
51474 T
1 T
51475 GAATTCTGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TATAAAAATTATATTATA
Found at i:54304 original size:40 final size:42
Alignment explanation
Indices: 54235--54340 Score: 180
Period size: 41 Copynumber: 2.5 Consensus size: 42
54225 TGATTAATGG
54235 ATTGTGTGATTATGTTTTCAATGTAATGATT-CCAGTGTTATT
1 ATTGTGTGATTATG-TTTCAATGTAATGATTCCCAGTGTTATT
54277 A-TGTGTGATTATGTTTCAATGTAATGATTCCCAGTGTTATT
1 ATTGTGTGATTATGTTTCAATGTAATGATTCCCAGTGTTATT
*
54318 ATTGTGTGATTATGTTTGAATGT
1 ATTGTGTGATTATGTTTCAATGT
54341 CAATTTAAGA
Statistics
Matches: 61, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
40 16 0.26
41 24 0.39
42 21 0.34
ACGTcount: A:0.24, C:0.07, G:0.21, T:0.49
Consensus pattern (42 bp):
ATTGTGTGATTATGTTTCAATGTAATGATTCCCAGTGTTATT
Found at i:55386 original size:7 final size:7
Alignment explanation
Indices: 55374--55405 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
55364 TATAATACTT
55374 TAAATAA
1 TAAATAA
55381 TAAATAA
1 TAAATAA
55388 TAATATAA
1 TAA-ATAA
55396 TAAATAA
1 TAAATAA
55403 TAA
1 TAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (7 bp):
TAAATAA
Found at i:55395 original size:15 final size:15
Alignment explanation
Indices: 55377--55405 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
55367 AATACTTTAA
55377 ATAATAAATAATAAT
1 ATAATAAATAATAAT
55392 ATAATAAATAATAA
1 ATAATAAATAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
ATAATAAATAATAAT
Done.