Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002455.1 Hibiscus syriacus cultivar Beakdansim tig00005028_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: 79067
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:5339 original size:6 final size:6
Alignment explanation
Indices: 5328--5353 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
5318 GAAGGGAGAA
5328 GAAGGG GAAGGG GAAGGG GAAGGG GA
1 GAAGGG GAAGGG GAAGGG GAAGGG GA
5354 CAGCCTTGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.65, T:0.00
Consensus pattern (6 bp):
GAAGGG
Found at i:10369 original size:30 final size:30
Alignment explanation
Indices: 10328--10394 Score: 116
Period size: 30 Copynumber: 2.2 Consensus size: 30
10318 CATTCTTTTG
10328 TGTATAATAAGATTTAATATATTAGGTTTAA
1 TGTA-AATAAGATTTAATATATTAGGTTTAA
*
10359 TGTAAATAAGATTTGATATATTAGGTTTAA
1 TGTAAATAAGATTTAATATATTAGGTTTAA
10389 TGTAAA
1 TGTAAA
10395 AATATGAGTT
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
30 31 0.89
31 4 0.11
ACGTcount: A:0.42, C:0.00, G:0.15, T:0.43
Consensus pattern (30 bp):
TGTAAATAAGATTTAATATATTAGGTTTAA
Found at i:10765 original size:22 final size:23
Alignment explanation
Indices: 10725--10767 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
10715 TATTTTTACA
10725 TTAAACTAATATATTATAATATT
1 TTAAACTAATATATTATAATATT
10748 TTAAA-TAAT-TATTAATAATA
1 TTAAACTAATATATT-ATAATA
10768 AAATTTTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 4 0.21
22 10 0.53
23 5 0.26
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (23 bp):
TTAAACTAATATATTATAATATT
Found at i:15375 original size:3 final size:3
Alignment explanation
Indices: 15367--15429 Score: 108
Period size: 3 Copynumber: 21.0 Consensus size: 3
15357 TTTCTCTATC
*
15367 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
15415 TAT CAT TAT TAT TAT
1 TAT TAT TAT TAT TAT
15430 GCTAGAACAT
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:18173 original size:26 final size:26
Alignment explanation
Indices: 18137--18198 Score: 124
Period size: 26 Copynumber: 2.4 Consensus size: 26
18127 CATACTCGTT
18137 CTCCATTTCCAATTATGATAATCAGA
1 CTCCATTTCCAATTATGATAATCAGA
18163 CTCCATTTCCAATTATGATAATCAGA
1 CTCCATTTCCAATTATGATAATCAGA
18189 CTCCATTTCC
1 CTCCATTTCC
18199 TGTCACCAGC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.31, C:0.27, G:0.06, T:0.35
Consensus pattern (26 bp):
CTCCATTTCCAATTATGATAATCAGA
Found at i:28055 original size:3 final size:3
Alignment explanation
Indices: 28047--28078 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
28037 CCTCAGATTT
28047 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
28079 TGTTTGCATC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:35267 original size:20 final size:17
Alignment explanation
Indices: 35225--35263 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
35215 TTTTCAGTAG
35225 GGTTGGTGGTCTATTGA
1 GGTTGGTGGTCTATTGA
35242 GGTTGGTGGTCTATTGA
1 GGTTGGTGGTCTATTGA
35259 GGTTG
1 GGTTG
35264 TTGGGGCTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.10, C:0.05, G:0.44, T:0.41
Consensus pattern (17 bp):
GGTTGGTGGTCTATTGA
Found at i:43167 original size:20 final size:21
Alignment explanation
Indices: 43119--43176 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 21
43109 CTTAGTTTCC
* *
43119 AAAATCACAGCGTGAATAGTA
1 AAAATCGCAACGTGAATAGTA
43140 AAAATCGCAACGTGAATAGT-
1 AAAATCGCAACGTGAATAGTA
*
43160 ATAATCGCAACGTGAAT
1 AAAATCGCAACGTGAAT
43177 TTAGAAAATC
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
20 16 0.47
21 18 0.53
ACGTcount: A:0.45, C:0.16, G:0.19, T:0.21
Consensus pattern (21 bp):
AAAATCGCAACGTGAATAGTA
Found at i:43593 original size:21 final size:20
Alignment explanation
Indices: 43539--43632 Score: 100
Period size: 20 Copynumber: 4.7 Consensus size: 20
43529 CATATAGATT
*
43539 CGTTGCGATTTTATTATTCA
1 CGTTGCGATTTTACTATTCA
*
43559 CGTTGCGCTTTTACTATTCA
1 CGTTGCGATTTTACTATTCA
*
43579 CGTTGCAGTTTTTACTATTCA
1 CGTTGC-GATTTTACTATTCA
* * *
43600 TGTTGCGAATTTGACTA-TCG
1 CGTTGCG-ATTTTACTATTCA
*
43620 CGTTGCGAATTTA
1 CGTTGCGATTTTA
43633 ACTTCTGTGT
Statistics
Matches: 62, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
19 4 0.06
20 33 0.53
21 25 0.40
ACGTcount: A:0.19, C:0.18, G:0.18, T:0.45
Consensus pattern (20 bp):
CGTTGCGATTTTACTATTCA
Found at i:43624 original size:41 final size:40
Alignment explanation
Indices: 43539--43632 Score: 100
Period size: 41 Copynumber: 2.3 Consensus size: 40
43529 CATATAGATT
* * *
43539 CGTTGCGATTTTATTATTCACGTTGCGCTTTTACTATTCA
1 CGTTGCGATTTTACTATTCACGTTGCGATTTGACTATTCA
* * *
43579 CGTTGCAGTTTTTACTATTCATGTTGCGAATTTGACTA-TCG
1 CGTTGC-GATTTTACTATTCACGTTGCG-ATTTGACTATTCA
*
43620 CGTTGCGAATTTA
1 CGTTGCGATTTTA
43633 ACTTCTGTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
40 11 0.25
41 26 0.59
42 7 0.16
ACGTcount: A:0.19, C:0.18, G:0.18, T:0.45
Consensus pattern (40 bp):
CGTTGCGATTTTACTATTCACGTTGCGATTTGACTATTCA
Found at i:43644 original size:20 final size:20
Alignment explanation
Indices: 43600--43651 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
43590 TTACTATTCA
*
43600 TGTTGCGAATTTGACTATCG
1 TGTTGCGAATTTAACTATCG
*
43620 CGTTGCGAATTTAACT-TCTG
1 TGTTGCGAATTTAACTATC-G
43640 TGTTGCG-ATTTA
1 TGTTGCGAATTTA
43652 CAAATTCACG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 7 0.25
20 21 0.75
ACGTcount: A:0.19, C:0.15, G:0.23, T:0.42
Consensus pattern (20 bp):
TGTTGCGAATTTAACTATCG
Found at i:54656 original size:12 final size:12
Alignment explanation
Indices: 54639--54663 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
54629 TTCGGTAAAA
54639 AAATAATATTTT
1 AAATAATATTTT
54651 AAATAATATTTT
1 AAATAATATTTT
54663 A
1 A
54664 CCAAAAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
AAATAATATTTT
Found at i:54710 original size:14 final size:12
Alignment explanation
Indices: 54680--54705 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
54670 AAATTAAAAA
54680 TTAATAATATTT
1 TTAATAATATTT
54692 TTAATAATATTT
1 TTAATAATATTT
54704 TT
1 TT
54706 TTAATCGTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
TTAATAATATTT
Done.