Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003787.1 Hibiscus syriacus cultivar Beakdansim tig00008105_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: 60496
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:2925 original size:21 final size:21
Alignment explanation
Indices: 2899--2945 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
2889 TTAATATTCT
2899 GGTAGAAAAAATAACATTTTA
1 GGTAGAAAAAATAACATTTTA
2920 GGTAGAAAAAATAACATTTTA
1 GGTAGAAAAAATAACATTTTA
2941 GGTAG
1 GGTAG
2946 CGCTTTACTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.49, C:0.04, G:0.19, T:0.28
Consensus pattern (21 bp):
GGTAGAAAAAATAACATTTTA
Found at i:6471 original size:32 final size:32
Alignment explanation
Indices: 6405--6471 Score: 75
Period size: 32 Copynumber: 2.1 Consensus size: 32
6395 ACCCAAATCG
* **
6405 AAAATCAATCGATCTGATGTTGATCCGATTCA
1 AAAATCAATCGATCTGATATTGATCCGACCCA
6437 AAAATCAA-CTGATCTGATATTG-TCCGGACCCA
1 AAAATCAATC-GATCTGATATTGATCC-GACCCA
6469 AAA
1 AAA
6472 TCTAAACGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
31 4 0.13
32 26 0.87
ACGTcount: A:0.37, C:0.21, G:0.15, T:0.27
Consensus pattern (32 bp):
AAAATCAATCGATCTGATATTGATCCGACCCA
Found at i:7163 original size:14 final size:16
Alignment explanation
Indices: 7139--7175 Score: 60
Period size: 15 Copynumber: 2.4 Consensus size: 16
7129 TTTTTAATAA
7139 TAAAAATGA-TTTTTT
1 TAAAAATGATTTTTTT
7154 TAAAAA-GATTTTTTT
1 TAAAAATGATTTTTTT
7169 TAAAAAT
1 TAAAAAT
7176 CAAAGCTCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 2 0.10
15 18 0.90
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (16 bp):
TAAAAATGATTTTTTT
Found at i:13068 original size:15 final size:15
Alignment explanation
Indices: 13048--13123 Score: 61
Period size: 15 Copynumber: 5.3 Consensus size: 15
13038 CTATGATATG
13048 AATTTTTATATAAAT
1 AATTTTTATATAAAT
*
13063 AATTTTTATTTAAAT
1 AATTTTTATATAAAT
* *
13078 -A--TAT-TATCAAT
1 AATTTTTATATAAAT
*
13089 GATTTTTTATATAAAT
1 -AATTTTTATATAAAT
* *
13105 GATTTTTATTTAAAT
1 AATTTTTATATAAAT
13120 AATT
1 AATT
13124 AGAATTTCAC
Statistics
Matches: 45, Mismatches: 11, Indels: 10
0.68 0.17 0.15
Matches are distributed among these distances:
11 5 0.11
12 2 0.04
14 1 0.02
15 31 0.69
16 6 0.13
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (15 bp):
AATTTTTATATAAAT
Found at i:13098 original size:42 final size:41
Alignment explanation
Indices: 13045--13124 Score: 133
Period size: 42 Copynumber: 1.9 Consensus size: 41
13035 CAACTATGAT
13045 ATGAATTTTTATATAAATAATTTTTATTTAAATATATTATCA
1 ATGAATTTTTATATAAATAATTTTTATTTAAATA-ATTATCA
* *
13087 ATGATTTTTTATATAAATGATTTTTATTTAAATAATTA
1 ATGAATTTTTATATAAATAATTTTTATTTAAATAATTA
13125 GAATTTCACT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
41 4 0.11
42 32 0.89
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.54
Consensus pattern (41 bp):
ATGAATTTTTATATAAATAATTTTTATTTAAATAATTATCA
Found at i:16198 original size:15 final size:14
Alignment explanation
Indices: 16181--16252 Score: 60
Period size: 14 Copynumber: 5.1 Consensus size: 14
16171 ATCGATAAAT
16181 TTTTATATAAATAA
1 TTTTATATAAATAA
* *
16195 TTTTATTTGAAT-A
1 TTTTATATAAATAA
*
16208 TATTATCGATAAAT--
1 TTTTAT--ATAAATAA
16222 TTTTATATAAATAA
1 TTTTATATAAATAA
*
16236 TTTTTATTTAAATAA
1 -TTTTATATAAATAA
16251 TT
1 TT
16253 AAAATTTCAC
Statistics
Matches: 46, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
12 6 0.13
13 6 0.13
14 17 0.37
15 17 0.37
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (14 bp):
TTTTATATAAATAA
Found at i:16211 original size:41 final size:42
Alignment explanation
Indices: 16161--16253 Score: 154
Period size: 41 Copynumber: 2.2 Consensus size: 42
16151 TTAAATAATA
16161 AAATAATATTATCGATAAATTTTTATATAAATAA-TTTTATTT
1 AAAT-ATATTATCGATAAATTTTTATATAAATAATTTTTATTT
*
16203 GAATATATTATCGATAAATTTTTATATAAATAATTTTTATTT
1 AAATATATTATCGATAAATTTTTATATAAATAATTTTTATTT
16245 AAATA-ATTA
1 AAATATATTA
16254 AAATTTCACT
Statistics
Matches: 48, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
41 33 0.69
42 15 0.31
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.49
Consensus pattern (42 bp):
AAATATATTATCGATAAATTTTTATATAAATAATTTTTATTT
Found at i:18342 original size:60 final size:60
Alignment explanation
Indices: 18205--18347 Score: 166
Period size: 60 Copynumber: 2.4 Consensus size: 60
18195 AATATAATGA
18205 ATAGTCGG-GTGACCATTTTGTAACTTTTAATAGTCGAGGGGCTCAACAAAGAAACACCTT
1 ATAGTCGGAG-GACCATTTTGTAACTTTTAATAGTCGAGGGGCTCAACAAAGAAACACCTT
* * * * * * *
18265 GTAGTCGAATGATCATTTTGTAACTTTTAATAGTC-AGGGGACTCAATAAAGTAATATCC-T
1 ATAGTCGGAGGACCATTTTGTAACTTTTAATAGTCGAGGGG-CTCAACAAAGAAACA-CCTT
18325 ATAGTCGGAGGACCATTTGTGTA
1 ATAGTCGGAGGACCATTT-TGTA
18348 TTTTAACCAT
Statistics
Matches: 68, Mismatches: 11, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
59 5 0.07
60 57 0.84
61 6 0.09
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.31
Consensus pattern (60 bp):
ATAGTCGGAGGACCATTTTGTAACTTTTAATAGTCGAGGGGCTCAACAAAGAAACACCTT
Found at i:21112 original size:2 final size:2
Alignment explanation
Indices: 21105--21130 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
21095 TTTGATTTAC
21105 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
21131 CACTTTTTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:27103 original size:61 final size:61
Alignment explanation
Indices: 27012--27136 Score: 196
Period size: 61 Copynumber: 2.0 Consensus size: 61
27002 TCTGTCTTGA
*
27012 TTTCTTTTAAATTTCAATTTGGAAATATGTTAACGAGGCAATCTGCACTGCATTTATTTTC
1 TTTCTTTTAAATTTCAATTTAGAAATATGTTAACGAGGCAATCTGCACTGCATTTATTTTC
* ** * *
27073 TTTCTTTTAACTTTTGATTTAGAAATATGTTCACGAGGCATTCTGCACTGCATTTATTTTC
1 TTTCTTTTAAATTTCAATTTAGAAATATGTTAACGAGGCAATCTGCACTGCATTTATTTTC
27134 TTT
1 TTT
27137 TACCTATTCT
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
61 58 1.00
ACGTcount: A:0.25, C:0.15, G:0.13, T:0.47
Consensus pattern (61 bp):
TTTCTTTTAAATTTCAATTTAGAAATATGTTAACGAGGCAATCTGCACTGCATTTATTTTC
Found at i:30284 original size:16 final size:16
Alignment explanation
Indices: 30263--30296 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
30253 TGCCCTTGAG
*
30263 ATTTGTCTAATCTCAA
1 ATTTGTCTAATCTAAA
30279 ATTTGTCTAATCTAAA
1 ATTTGTCTAATCTAAA
30295 AT
1 AT
30297 ACTATAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.35, C:0.15, G:0.06, T:0.44
Consensus pattern (16 bp):
ATTTGTCTAATCTAAA
Found at i:31106 original size:30 final size:31
Alignment explanation
Indices: 31072--31129 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
31062 CCGGATATCA
*
31072 TATCCGAAA-TTTCGGATATCCAAAAATAAT
1 TATCCAAAATTTTCGGATATCCAAAAATAAT
*
31102 TATCCAAAATTTTCGGATATCCGAAAAT
1 TATCCAAAATTTTCGGATATCCAAAAAT
31130 TAGAATTAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 8 0.32
31 17 0.68
ACGTcount: A:0.41, C:0.17, G:0.10, T:0.31
Consensus pattern (31 bp):
TATCCAAAATTTTCGGATATCCAAAAATAAT
Found at i:31486 original size:36 final size:36
Alignment explanation
Indices: 31453--31520 Score: 104
Period size: 35 Copynumber: 1.9 Consensus size: 36
31443 TACAAATTGT
31453 AAAATATTTATAT-ATTTTCTTTA-AAAATTAAATTC
1 AAAATATTTATATAATTTT-TTTACAAAATTAAATTC
*
31488 ATAATATTTATATAATTTTTTTACAAAATTAAA
1 AAAATATTTATATAATTTTTTTACAAAATTAAA
31521 AATATAAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
35 16 0.53
36 14 0.47
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (36 bp):
AAAATATTTATATAATTTTTTTACAAAATTAAATTC
Found at i:53899 original size:24 final size:23
Alignment explanation
Indices: 53829--53901 Score: 78
Period size: 23 Copynumber: 3.1 Consensus size: 23
53819 AAAAACTGGA
53829 AAAACGTGCCACAAAGGTAAAGAT
1 AAAACGTGCCACAAA-GTAAAGAT
*
53853 -AAACGTGCCACAAA-AACAGAGAT
1 AAAACGTGCCACAAAGTA-A-AGAT
*
53876 AAAACGTGCAACACAAGTAAAGAT
1 AAAACGTGCCACA-AAGTAAAGAT
53900 AA
1 AA
53902 GTGTGCAACA
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
21 1 0.02
22 1 0.02
23 18 0.44
24 17 0.41
25 3 0.07
26 1 0.02
ACGTcount: A:0.53, C:0.18, G:0.18, T:0.11
Consensus pattern (23 bp):
AAAACGTGCCACAAAGTAAAGAT
Done.