Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006771.1 Hibiscus syriacus cultivar Beakdansim tig00017107_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: 50176
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Found at i:11228 original size:21 final size:21
Alignment explanation
Indices: 11202--11244 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
11192 ACTTTCTAGG
11202 AGTTTCGAAACTATGACCCAA
1 AGTTTCGAAACTATGACCCAA
* * *
11223 AGTTTCGATACTCTTACCCAA
1 AGTTTCGAAACTATGACCCAA
11244 A
1 A
11245 AACTCACGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.35, C:0.26, G:0.12, T:0.28
Consensus pattern (21 bp):
AGTTTCGAAACTATGACCCAA
Found at i:16967 original size:159 final size:157
Alignment explanation
Indices: 16606--17309 Score: 1022
Period size: 158 Copynumber: 4.5 Consensus size: 157
16596 TTATATTCAT
* *
16606 TTTTTTTACTAAATTTGAACCACATGCTCCTAAACCATCGTAGAATACATATGTACTTTCAATTC
1 TTTTTTTACCAAATTTGAACCACATGCTCCTAAACCATCATAGAATACATATGTACTTTCAATTC
* * * *
16671 TTCTTTTTAATAACAAATTGTCTATTTTTCAATTTAGTCTCTCAAATTTTTATAATTTCCTTATT
66 TTCTTTTTGATAACAAATTGTCTATTTTTCAATTTAGCCCCTCAATTTTTTATAATTTCCTTATT
16736 TCTTAAATTCATCCTTTAGTTTAAGTC
131 TCTTAAATTCATCCTTTAGTTTAAGTC
* * *
16763 GTTTTTTTACCAAATTTGAACCACATGCTCCTAGATCATCCTAGAATACATATGTACTTTCAATT
1 -TTTTTTTACCAAATTTGAACCACATGCTCCTAAACCATCATAGAATACATATGTACTTTCAATT
16828 CTTCTTTTTGATAACAAATTGTCTATTTTTCAATTTAGCCCCTCAATGTTTTTATAATTTCCTTA
65 CTTCTTTTTGATAACAAATTGTCTATTTTTCAATTTAGCCCCTCAAT-TTTTTATAATTTCCTTA
*
16893 TTTCTTAAATTCA-CCATTTAATTTAAGTC
129 TTTCTTAAATTCATCC-TTTAGTTTAAGTC
* *
16922 TATTTTTTACTAAATTTAAACCACATGCTCCTAAACCATCATAGAATACATATGTACTTTCAATT
1 T-TTTTTTACCAAATTTGAACCACATGCTCCTAAACCATCATAGAATACATATGTACTTTCAATT
* *
16987 CTTCTTTTTGATAACAAATTGTCTAATTTTCAATTTAGCCCCTCAATTTTTTATAATTTTCTTAT
65 CTTCTTTTTGATAACAAATTGTCTATTTTTCAATTTAGCCCCTCAATTTTTTATAATTTCCTTAT
17052 TTCTTAAATTCATCCTTTAGTTTAAGTCC
130 TTCTTAAATTCATCCTTTAGTTTAAGT-C
* * *
17081 TTTTTTTACCAAATTTGAACCACATGCTCTTAAACTATCGTAGAATACATATGTACTTTCAATTC
1 TTTTTTTACCAAATTTGAACCACATGCTCCTAAACCATCATAGAATACATATGTACTTTCAATTC
* * * * *
17146 CTCTTTTT-ATAACAAATTATCTATTTTTCAATTTAGTCCCTTAATTTTTCATAATTTCCTTATT
66 TTCTTTTTGATAACAAATTGTCTATTTTTCAATTTAGCCCCTCAATTTTTTATAATTTCCTTATT
* *
17210 TCTTCAATTCATCC-TTATTTTAAGTC
131 TCTTAAATTCATCCTTTAGTTTAAGTC
* * * ** * *
17236 TGTTTTTACCAAATTTAAACCACATGCTCATGTACCA-CAATAGAATACCTATATAAC-TTCAAT
1 TTTTTTTACCAAATTTGAACCACATGCTCCTAAACCATC-ATAGAATACATATGT-ACTTTCAAT
17299 TCTTACTTTTT
64 TCTT-CTTTTT
17310 TACTAAAAAT
Statistics
Matches: 497, Mismatches: 41, Indels: 18
0.89 0.07 0.03
Matches are distributed among these distances:
154 1 0.00
155 53 0.11
156 18 0.04
157 63 0.13
158 212 0.43
159 150 0.30
ACGTcount: A:0.30, C:0.19, G:0.06, T:0.46
Consensus pattern (157 bp):
TTTTTTTACCAAATTTGAACCACATGCTCCTAAACCATCATAGAATACATATGTACTTTCAATTC
TTCTTTTTGATAACAAATTGTCTATTTTTCAATTTAGCCCCTCAATTTTTTATAATTTCCTTATT
TCTTAAATTCATCCTTTAGTTTAAGTC
Found at i:23433 original size:7 final size:7
Alignment explanation
Indices: 23421--23468 Score: 51
Period size: 7 Copynumber: 6.7 Consensus size: 7
23411 AATATAATTT
23421 TTTTTAA
1 TTTTTAA
23428 TTTTTAA
1 TTTTTAA
23435 TTTTTAA
1 TTTTTAA
*
23442 TTTTATTA
1 TTTT-TAA
*
23450 TTTTTTA
1 TTTTTAA
* *
23457 TATTTAG
1 TTTTTAA
23464 TTTTT
1 TTTTT
23469 TAATATTTGA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
7 29 0.83
8 6 0.17
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.75
Consensus pattern (7 bp):
TTTTTAA
Found at i:23474 original size:15 final size:14
Alignment explanation
Indices: 23420--23476 Score: 53
Period size: 15 Copynumber: 3.9 Consensus size: 14
23410 AAATATAATT
*
23420 TTTTTTAATTTTTA
1 TTTTTTAATATTTA
*
23434 ATTTTTAAT-TTTA
1 TTTTTTAATATTTA
*
23447 TTATTTTTTATATTTA
1 -T-TTTTTAATATTTA
23463 GTTTTTTAATATTT
1 -TTTTTTAATATTT
23477 GAGTAATTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
13 4 0.11
14 8 0.23
15 18 0.51
16 5 0.14
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.74
Consensus pattern (14 bp):
TTTTTTAATATTTA
Found at i:23706 original size:31 final size:29
Alignment explanation
Indices: 23671--23728 Score: 89
Period size: 31 Copynumber: 1.9 Consensus size: 29
23661 CGTTGGTCAA
*
23671 AGGGCCACATTGAGTTTGTTTTATAAGTTGG
1 AGGGCCACATTGA-TTT-TTTTAAAAGTTGG
23702 AGGGCCACATTGATTTTTTTAAAAGTT
1 AGGGCCACATTGATTTTTTTAAAAGTT
23729 CAAGGACCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 10 0.38
30 3 0.12
31 13 0.50
ACGTcount: A:0.26, C:0.10, G:0.24, T:0.40
Consensus pattern (29 bp):
AGGGCCACATTGATTTTTTTAAAAGTTGG
Found at i:24868 original size:14 final size:14
Alignment explanation
Indices: 24851--24877 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
24841 AATCTTATAA
24851 TAATAAAATTAAAT
1 TAATAAAATTAAAT
24865 TAATAAAATTAAA
1 TAATAAAATTAAA
24878 AGATACAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
TAATAAAATTAAAT
Found at i:25041 original size:14 final size:14
Alignment explanation
Indices: 25024--25051 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
25014 TTCAGGAAAT
25024 ATAATTTATTTTTC
1 ATAATTTATTTTTC
25038 ATAATTTATTTTTC
1 ATAATTTATTTTTC
25052 GGAAACGGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.07, G:0.00, T:0.64
Consensus pattern (14 bp):
ATAATTTATTTTTC
Found at i:25685 original size:25 final size:23
Alignment explanation
Indices: 25645--25724 Score: 69
Period size: 25 Copynumber: 3.3 Consensus size: 23
25635 ACATTTTATA
25645 TATT-TTAACTTAAAAACCAT-TTT
1 TATTATTAACTTAAAAA--ATATTT
25668 TA-TATTAACTTATTAAAAATATTT
1 TATTATTAACTTA--AAAAATATTT
25692 TATTATTAACTTAATTTAAAATATTT
1 TATTATTAACTTAA---AAAATATTT
25718 TA-TATTA
1 TATTATTA
25725 TTTTTATTTA
Statistics
Matches: 49, Mismatches: 0, Indels: 14
0.78 0.00 0.22
Matches are distributed among these distances:
22 1 0.02
23 13 0.27
24 5 0.10
25 19 0.39
26 11 0.22
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.51
Consensus pattern (23 bp):
TATTATTAACTTAAAAAATATTT
Found at i:25718 original size:26 final size:24
Alignment explanation
Indices: 25665--25724 Score: 93
Period size: 25 Copynumber: 2.4 Consensus size: 24
25655 TAAAAACCAT
25665 TTTTATATTAACTTATTAAAAATA
1 TTTTATATTAACTTATTAAAAATA
*
25689 TTTTATTATTAACTTAATTTAAAATA
1 TTTTA-TATTAACTT-ATTAAAAATA
25715 TTTTATATTA
1 TTTTATATTA
25725 TTTTTATTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
24 5 0.15
25 14 0.42
26 14 0.42
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (24 bp):
TTTTATATTAACTTATTAAAAATA
Found at i:25738 original size:26 final size:26
Alignment explanation
Indices: 25637--25741 Score: 92
Period size: 26 Copynumber: 4.1 Consensus size: 26
25627 AATTCATAAC
* *
25637 ATTTTATA-TATTTTAACTTAAAAACC
1 ATTTTATATTATTTTAATTTAAAAA-T
**
25663 ATTTTTATATTAACTT-A-TTAAAAAT
1 A-TTTTATATTATTTTAATTTAAAAAT
**
25688 ATTTTATTATTAACTTAATTT-AAAAT
1 ATTTTA-TATTATTTTAATTTAAAAAT
*
25714 ATTTTATATTATTTTTATTTAAAAAT
1 ATTTTATATTATTTTAATTTAAAAAT
25740 AT
1 AT
25742 ATACTTTATG
Statistics
Matches: 67, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
24 5 0.07
25 21 0.31
26 27 0.40
27 10 0.15
28 4 0.06
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (26 bp):
ATTTTATATTATTTTAATTTAAAAAT
Found at i:25742 original size:21 final size:21
Alignment explanation
Indices: 25718--25763 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
25708 TAAAATATTT
*
25718 TATATTATTTTTAT-TTAAAAA
1 TATATTA-CTTTATGTTAAAAA
25739 TATA-TACTTTATGTTAAAAA
1 TATATTACTTTATGTTAAAAA
25759 T-TATT
1 TATATT
25764 TAAAAATATG
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
19 7 0.32
20 11 0.50
21 4 0.18
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.54
Consensus pattern (21 bp):
TATATTACTTTATGTTAAAAA
Found at i:26630 original size:3 final size:3
Alignment explanation
Indices: 26617--26650 Score: 59
Period size: 3 Copynumber: 11.0 Consensus size: 3
26607 CCTTCATCCA
26617 TTC TATC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC T-TC TTC TTC TTC TTC TTC TTC TTC TTC TTC
26651 CTCTGCACGT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.03, C:0.32, G:0.00, T:0.65
Consensus pattern (3 bp):
TTC
Found at i:42071 original size:32 final size:32
Alignment explanation
Indices: 42035--42268 Score: 360
Period size: 32 Copynumber: 7.3 Consensus size: 32
42025 AATCATGTGT
* * ** *
42035 ATTATCTGAATGCAACCCTAACTCTATTGTGC
1 ATTATCTGAATGCAACACTGACTCTGCTATGC
*
42067 ATTATCTGAATGCAACACTGACTCTACTATGC
1 ATTATCTGAATGCAACACTGACTCTGCTATGC
42099 ATTATCTGAATGCAACACTGACTCTGCTATGC
1 ATTATCTGAATGCAACACTGACTCTGCTATGC
42131 ATTATCTGAATGCAACACTGACTCTGCTATGC
1 ATTATCTGAATGCAACACTGACTCTGCTATGC
*
42163 ATTATCTGAATGCAACACTGACTATGCTATGC
1 ATTATCTGAATGCAACACTGACTCTGCTATGC
* *
42195 ATTATCTGATTGCAACACTGACTCTGCTATAC
1 ATTATCTGAATGCAACACTGACTCTGCTATGC
* *
42227 ATTATCTGATTGCAACACTAACTCTGCTATGC
1 ATTATCTGAATGCAACACTGACTCTGCTATGC
*
42259 ATTATTTGAA
1 ATTATCTGAA
42269 AGTAATATTG
Statistics
Matches: 189, Mismatches: 13, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 189 1.00
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.33
Consensus pattern (32 bp):
ATTATCTGAATGCAACACTGACTCTGCTATGC
Found at i:44187 original size:15 final size:15
Alignment explanation
Indices: 44167--44197 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
44157 CAAATAACTA
44167 TTATATTTAAACAAT
1 TTATATTTAAACAAT
*
44182 TTATATTTAAGCAAT
1 TTATATTTAAACAAT
44197 T
1 T
44198 ATTTAATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.06, G:0.03, T:0.48
Consensus pattern (15 bp):
TTATATTTAAACAAT
Found at i:45010 original size:34 final size:30
Alignment explanation
Indices: 44935--45003 Score: 138
Period size: 30 Copynumber: 2.3 Consensus size: 30
44925 AATCATTAAT
44935 CGTTTTTTCCTTATAGTTTTATTTATTTTC
1 CGTTTTTTCCTTATAGTTTTATTTATTTTC
44965 CGTTTTTTCCTTATAGTTTTATTTATTTTC
1 CGTTTTTTCCTTATAGTTTTATTTATTTTC
44995 CGTTTTTTC
1 CGTTTTTTC
45004 GTTCCTTCTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.12, C:0.14, G:0.07, T:0.67
Consensus pattern (30 bp):
CGTTTTTTCCTTATAGTTTTATTTATTTTC
Done.