Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007715.1 Hibiscus syriacus cultivar Beakdansim tig00109943_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: 43308
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Found at i:16563 original size:19 final size:20
Alignment explanation
Indices: 16541--16586 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
16531 AATTTTTATC
16541 AAAAACATT-ATTTTTCAAA-
1 AAAAA-ATTAATTTTTCAAAT
*
16560 AAAAAATTAATTTTTGAAAT
1 AAAAAATTAATTTTTCAAAT
16580 AAAAAAT
1 AAAAAAT
16587 GTTTTTGATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 3 0.12
19 14 0.58
20 7 0.29
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (20 bp):
AAAAAATTAATTTTTCAAAT
Found at i:16679 original size:12 final size:13
Alignment explanation
Indices: 16652--16684 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
16642 ATATTATAAT
*
16652 TTTTCAAACTTAG
1 TTTTCAAACATAG
16665 TTTTCAAA-ATAG
1 TTTTCAAACATAG
16677 TTTTCAAA
1 TTTTCAAA
16685 TTTGCCCATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.36, C:0.12, G:0.06, T:0.45
Consensus pattern (13 bp):
TTTTCAAACATAG
Found at i:22558 original size:2 final size:2
Alignment explanation
Indices: 22553--22601 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
22543 AAAAAATAGC
22553 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
22595 AT AT AT A
1 AT AT AT A
22602 ATTTTATTCA
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:27071 original size:2 final size:2
Alignment explanation
Indices: 27064--27105 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
27054 TGTAACACAT
27064 TA TA TA TA TA TA TA TA -A 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
27105 T
1 T
27106 TCGTATTCGT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:29758 original size:3 final size:3
Alignment explanation
Indices: 29752--29875 Score: 189
Period size: 3 Copynumber: 41.7 Consensus size: 3
29742 TTTTTATCCA
*
29752 TAT TAT TAT TAT TAA TAT TAT TAT TAT TAT TAT TAT TAT TACT TA-
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT
*
29797 TAT TAT TAT TAT TAT TAT TAT TAC TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
29845 TAT TAT TAT TAT CAT TAT TAC TA- TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
29876 AATATATTAA
Statistics
Matches: 111, Mismatches: 7, Indels: 6
0.90 0.06 0.05
Matches are distributed among these distances:
2 4 0.04
3 104 0.94
4 3 0.03
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:30385 original size:22 final size:24
Alignment explanation
Indices: 30357--30405 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
30347 AGAACGAGAC
* *
30357 AGAGAGACA-A-AAAAAAGAATAG
1 AGAGAGACATAGAAAAAAAAACAG
30379 AGAGAGACATAGAAAAAAAAACAG
1 AGAGAGACATAGAAAAAAAAACAG
30403 AGA
1 AGA
30406 AAATACAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 9 0.39
23 1 0.04
24 13 0.57
ACGTcount: A:0.67, C:0.06, G:0.22, T:0.04
Consensus pattern (24 bp):
AGAGAGACATAGAAAAAAAAACAG
Found at i:31211 original size:18 final size:17
Alignment explanation
Indices: 31186--31232 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 17
31176 TAGATTTTTA
*
31186 ATTTTATTTTTTCGTTT
1 ATTTTATTTTTTCATTT
31203 A-TTTATATTTTTCATTT
1 ATTTTAT-TTTTTCATTT
31220 ATTTTATTGTTTT
1 ATTTTATT-TTTT
31233 TAAATATATT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 5 0.19
17 12 0.46
18 9 0.35
ACGTcount: A:0.17, C:0.04, G:0.04, T:0.74
Consensus pattern (17 bp):
ATTTTATTTTTTCATTT
Found at i:31287 original size:12 final size:12
Alignment explanation
Indices: 31272--31305 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
31262 TTTTATTATA
31272 TTATTAAATATT
1 TTATTAAATATT
31284 TTATTAAATATT
1 TTATTAAATATT
31296 TTA-TAAATAT
1 TTATTAAATAT
31306 ATAATAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 7 0.32
12 15 0.68
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
TTATTAAATATT
Found at i:31304 original size:11 final size:11
Alignment explanation
Indices: 31276--31315 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
31266 ATTATATTAT
31276 TAAATATTTTA
1 TAAATATTTTA
31287 TTAAATATTTTA
1 -TAAATATTTTA
* *
31299 TAAATATATAA
1 TAAATATTTTA
31310 TAAATA
1 TAAATA
31316 GTATTTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
11 15 0.58
12 11 0.42
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
TAAATATTTTA
Found at i:32011 original size:17 final size:16
Alignment explanation
Indices: 31989--32036 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 16
31979 CTTTTCAAAT
31989 TTTTTATTTATTTATTA
1 TTTTTATTTATTTA-TA
*
32006 TTTTTATAATATTTATA
1 TTTTTAT-TTATTTATA
*
32023 TGTTTTTTTTATTT
1 T-TTTTATTTATTT
32037 GCAAGTATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 15 0.58
18 11 0.42
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.75
Consensus pattern (16 bp):
TTTTTATTTATTTATA
Found at i:42628 original size:19 final size:19
Alignment explanation
Indices: 42585--42636 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 19
42575 TATTATGCTT
42585 GAAGAGAATAGAAAAAAAAA
1 GAAGA-AATAGAAAAAAAAA
*
42605 -TAGAAAT-GAAAAAAAAGA
1 GAAGAAATAGAAAAAAAA-A
*
42623 GAAGAAAAAGAAAA
1 GAAGAAATAGAAAA
42637 GGGGGTCAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
17 9 0.35
18 4 0.15
19 8 0.31
20 5 0.19
ACGTcount: A:0.75, C:0.00, G:0.19, T:0.06
Consensus pattern (19 bp):
GAAGAAATAGAAAAAAAAA
Done.