Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006583.1 Hibiscus syriacus cultivar Beakdansim tig00016135_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: 50007
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:2629 original size:16 final size:16
Alignment explanation
Indices: 2588--2667 Score: 56
Period size: 15 Copynumber: 4.8 Consensus size: 16
2578 ATAATTTCTA
*
2588 ATATTTTAAAAATATT
1 ATATTTTAATAATATT
*
2604 ATA-ATTAATAATATT
1 ATATTTTAATAATATT
*
2619 CTATTTTAATAAATAATT
1 ATATTTTAAT-AAT-ATT
2637 AATATAATTT-ATAATAGTT
1 -ATAT--TTTAATAATA-TT
*
2656 TTATTTTAATAA
1 ATATTTTAATAA
2668 ATATAATAAT
Statistics
Matches: 50, Mismatches: 6, Indels: 15
0.70 0.08 0.21
Matches are distributed among these distances:
15 12 0.24
16 11 0.22
17 7 0.14
18 7 0.14
19 8 0.16
20 2 0.04
21 3 0.06
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (16 bp):
ATATTTTAATAATATT
Found at i:2815 original size:26 final size:25
Alignment explanation
Indices: 2745--2818 Score: 73
Period size: 26 Copynumber: 3.0 Consensus size: 25
2735 AAAATAATAT
* *
2745 AAATAA-ATAATTA-TAATATTTAA
1 AAATAATATTATTATTAGTATTTAA
* *
2768 AAATATTATTATTATTATTATTTAA
1 AAATAATATTATTATTAGTATTTAA
2793 TAAATAATATTATTTATT-GTATTTAA
1 -AAATAATATTA-TTATTAGTATTTAA
2819 CGTTTATAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
23 5 0.12
24 6 0.14
25 9 0.21
26 17 0.40
27 5 0.12
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (25 bp):
AAATAATATTATTATTAGTATTTAA
Found at i:2815 original size:29 final size:25
Alignment explanation
Indices: 2745--2806 Score: 74
Period size: 26 Copynumber: 2.5 Consensus size: 25
2735 AAAATAATAT
* *
2745 AAATAA-ATAATTA-TAATATTTAA
1 AAATAATATTATTATTATTATTTAA
*
2768 AAATATTATTATTATTATTATTTAA
1 AAATAATATTATTATTATTATTTAA
2793 TAAATAATATTATT
1 -AAATAATATTATT
2807 TATTGTATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
23 5 0.16
24 6 0.19
25 9 0.28
26 12 0.38
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (25 bp):
AAATAATATTATTATTATTATTTAA
Found at i:11537 original size:27 final size:27
Alignment explanation
Indices: 11499--11552 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
11489 CCGAAGGTGC
*
11499 AACTTTGATGATCAAGATCTTTCCTTT
1 AACTTTAATGATCAAGATCTTTCCTTT
*
11526 AACTTTAATGATTAAGATCTTTCCTTT
1 AACTTTAATGATCAAGATCTTTCCTTT
11553 TACGTAGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.28, C:0.17, G:0.09, T:0.46
Consensus pattern (27 bp):
AACTTTAATGATCAAGATCTTTCCTTT
Found at i:13812 original size:30 final size:29
Alignment explanation
Indices: 13777--13835 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 29
13767 TAATTCTAAT
13777 AACTTAAATATAACTCAAATTTAAAAAAAA
1 AACTTAAATATAACTCAAA-TTAAAAAAAA
*
13807 AACTTAAATTTAACTCAAATTAAAAAAAA
1 AACTTAAATATAACTCAAATTAAAAAAAA
13836 TGTTTGTGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 10 0.36
30 18 0.64
ACGTcount: A:0.63, C:0.10, G:0.00, T:0.27
Consensus pattern (29 bp):
AACTTAAATATAACTCAAATTAAAAAAAA
Found at i:22752 original size:21 final size:21
Alignment explanation
Indices: 22728--22778 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
22718 ATGCACAATA
22728 GATCGATCCTTTATTAAAAGG
1 GATCGATCCTTTATTAAAAGG
*
22749 GATCGATTCTTTATTAAAAGG
1 GATCGATCCTTTATTAAAAGG
22770 GATCGATCC
1 GATCGATCC
22779 CAAACTCATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (21 bp):
GATCGATCCTTTATTAAAAGG
Found at i:25819 original size:19 final size:19
Alignment explanation
Indices: 25791--25828 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
25781 AATTAGAAAC
25791 AAATTAATCA-ATATTTAAT
1 AAATTAATCATA-ATTTAAT
*
25810 AAATTGATCATAATTTAAT
1 AAATTAATCATAATTTAAT
25829 TTTCTATTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 16 0.94
20 1 0.06
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (19 bp):
AAATTAATCATAATTTAAT
Found at i:26058 original size:19 final size:19
Alignment explanation
Indices: 26034--26071 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
26024 AAATGATCTC
26034 CCACATAAATACAAACATG
1 CCACATAAATACAAACATG
* *
26053 CCACATAAGTACAGACATG
1 CCACATAAATACAAACATG
26072 TCAGCGTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.47, C:0.26, G:0.11, T:0.16
Consensus pattern (19 bp):
CCACATAAATACAAACATG
Found at i:26103 original size:65 final size:62
Alignment explanation
Indices: 25987--26115 Score: 168
Period size: 65 Copynumber: 2.0 Consensus size: 62
25977 GAAAATGATT
* * *
25987 TGCCAATAAGTACAGACATGTCAACGTGAGAATGTGCAAATGATCTCCCACATAAATACAAACA
1 TGCCAATAAGTACAGACATGTCAACGTAAAAATGTGCAAATGACCTCCCAC--AAATACAAACA
* * * *
26051 TGCCACATAAGTACAGACATGTCAGCGTAAAAATGTGCAAATGGCCTTCCACAAGTACAAACA
1 TGCCA-ATAAGTACAGACATGTCAACGTAAAAATGTGCAAATGACCTCCCACAAATACAAACA
26114 TG
1 TG
26116 TTCCAAAACG
Statistics
Matches: 57, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
63 12 0.21
64 5 0.09
65 40 0.70
ACGTcount: A:0.40, C:0.22, G:0.17, T:0.20
Consensus pattern (62 bp):
TGCCAATAAGTACAGACATGTCAACGTAAAAATGTGCAAATGACCTCCCACAAATACAAACA
Found at i:26947 original size:2 final size:2
Alignment explanation
Indices: 26940--26998 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
26930 CTTGTTTGAG
26940 TA TA TA TA TA TA TA TA TA 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
26982 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
26999 TATTGTTTAA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:30847 original size:22 final size:22
Alignment explanation
Indices: 30804--30847 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
30794 TTTTACTTTT
* *
30804 AATTTATATAATTTATATATAA
1 AATTTAAATAATTTATAGATAA
30826 AATTTAAAT-ATTTATGAGATAA
1 AATTTAAATAATTTAT-AGATAA
30848 TTATGAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (22 bp):
AATTTAAATAATTTATAGATAA
Found at i:32778 original size:21 final size:22
Alignment explanation
Indices: 32744--32786 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
32734 GTCATAAAAT
32744 CCTGTGGTGATGGCATC-GAAA
1 CCTGTGGTGATGGCATCTGAAA
* *
32765 CCTGTTGTGGTGGCATCTGAAA
1 CCTGTGGTGATGGCATCTGAAA
32787 TAGAGGTGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.21, C:0.19, G:0.33, T:0.28
Consensus pattern (22 bp):
CCTGTGGTGATGGCATCTGAAA
Found at i:32816 original size:21 final size:21
Alignment explanation
Indices: 32754--32828 Score: 62
Period size: 21 Copynumber: 3.6 Consensus size: 21
32744 CCTGTGGTGA
*
32754 TGGCATC-GAAACCTGTTGTGG
1 TGGCATCTGAAA-CAGTTGTGG
* **
32775 TGGCATCTGAAATAGAGGTGG
1 TGGCATCTGAAACAGTTGTGG
* *
32796 TGGCGTTTGAAACAGTTGTGG
1 TGGCATCTGAAACAGTTGTGG
* *
32817 AGCCATCTGAAA
1 TGGCATCTGAAA
32829 TGGTTGCATC
Statistics
Matches: 40, Mismatches: 13, Indels: 2
0.73 0.24 0.04
Matches are distributed among these distances:
21 36 0.90
22 4 0.10
ACGTcount: A:0.25, C:0.15, G:0.33, T:0.27
Consensus pattern (21 bp):
TGGCATCTGAAACAGTTGTGG
Found at i:33972 original size:79 final size:79
Alignment explanation
Indices: 33841--33998 Score: 289
Period size: 79 Copynumber: 2.0 Consensus size: 79
33831 TCGGCGAGGT
*
33841 GACACAACCACATACAATGAACTTGGTTGCGAGATTTATCGGGCATCAAGATCCCTCATATGAGT
1 GACACAACCACATACAATGAACTTAGTTGCGAGATTTATCGGGCATCAAGATCCCTCATATGAGT
33906 CGTAATATGCAAGC
66 CGTAATATGCAAGC
* *
33920 GACACAACCACATATAATGAACTTAGTTGCGAGATTTATCGGGCATCAAGATCCCTCCTATGAGT
1 GACACAACCACATACAATGAACTTAGTTGCGAGATTTATCGGGCATCAAGATCCCTCATATGAGT
33985 CGTAATATGCAAGC
66 CGTAATATGCAAGC
33999 CCGGACAAAT
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
79 76 1.00
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.25
Consensus pattern (79 bp):
GACACAACCACATACAATGAACTTAGTTGCGAGATTTATCGGGCATCAAGATCCCTCATATGAGT
CGTAATATGCAAGC
Found at i:36287 original size:2 final size:2
Alignment explanation
Indices: 36280--36316 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
36270 CTTGTTTGAG
36280 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
36317 TATTGTTTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:41614 original size:30 final size:28
Alignment explanation
Indices: 41557--41616 Score: 75
Period size: 30 Copynumber: 2.1 Consensus size: 28
41547 TACAATGATG
*
41557 AGACTTAAACTAAAATCCTAAAATTTAA
1 AGACCTAAACTAAAATCCTAAAATTTAA
* *
41585 AGACCTAAACATATAAATCTTAAAGTTTAA
1 AGACCTAAAC-TA-AAATCCTAAAATTTAA
41615 AG
1 AG
41617 TATTAATTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 9 0.33
29 2 0.07
30 16 0.59
ACGTcount: A:0.52, C:0.13, G:0.07, T:0.28
Consensus pattern (28 bp):
AGACCTAAACTAAAATCCTAAAATTTAA
Found at i:41707 original size:27 final size:29
Alignment explanation
Indices: 41665--41728 Score: 87
Period size: 28 Copynumber: 2.3 Consensus size: 29
41655 GCGATGAACT
*
41665 AAATTAAAATAATTAAAAAAACAA-CAAA
1 AAATAAAAATAATTAAAAAAACAACCAAA
* *
41693 TAATAAAAAT-ATTAAGAAAACAACCAAA
1 AAATAAAAATAATTAAAAAAACAACCAAA
41721 AAATAAAA
1 AAATAAAA
41729 TAAAATAAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 12 0.39
28 19 0.61
ACGTcount: A:0.73, C:0.08, G:0.02, T:0.17
Consensus pattern (29 bp):
AAATAAAAATAATTAAAAAAACAACCAAA
Found at i:41729 original size:27 final size:26
Alignment explanation
Indices: 41669--41730 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 26
41659 TGAACTAAAT
*
41669 TAAAATAATTAAAAAAACAACAAATAA
1 TAAAAT-ATTAAAAAAACAACAAAAAA
*
41696 TAAAAATATTAAGAAAACAACCAAAAAA
1 T-AAAATATTAAAAAAACAA-CAAAAAA
41724 TAAAATA
1 TAAAATA
41731 AAATAAGTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
27 19 0.61
28 12 0.39
ACGTcount: A:0.73, C:0.08, G:0.02, T:0.18
Consensus pattern (26 bp):
TAAAATATTAAAAAAACAACAAAAAA
Found at i:42481 original size:2 final size:2
Alignment explanation
Indices: 42474--42510 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
42464 CAAAGCTCAA
42474 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
42511 TCGAAACCCA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:42864 original size:30 final size:30
Alignment explanation
Indices: 42790--42873 Score: 91
Period size: 30 Copynumber: 2.8 Consensus size: 30
42780 GGGAACAAGG
* *
42790 GATGATG-GAATTGGTGTTGAAAAAAATGT
1 GATGATGTGTATTGGTGTTGAAAAAAATGA
*
42819 GATGGTGTGTATTGGTGTTGAAAAAAATGA
1 GATGATGTGTATTGGTGTTGAAAAAAATGA
* * *
42849 GGTGATAG-GTGTTGGTATTGAAAAA
1 GATGAT-GTGTATTGGTGTTGAAAAA
42874 TTGTGTTTAC
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
29 6 0.13
30 39 0.85
31 1 0.02
ACGTcount: A:0.35, C:0.00, G:0.33, T:0.32
Consensus pattern (30 bp):
GATGATGTGTATTGGTGTTGAAAAAAATGA
Found at i:43535 original size:21 final size:19
Alignment explanation
Indices: 43496--43537 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 19
43486 AATGTAAAAT
*
43496 GTGTATCGATACTGTTACA
1 GTGTATCGATACTGCTACA
43515 GTGTATCGATACACTGCTACA
1 GTGTATCGAT--ACTGCTACA
43536 GT
1 GT
43538 AATTTCAGCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 10 0.50
21 10 0.50
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.33
Consensus pattern (19 bp):
GTGTATCGATACTGCTACA
Found at i:44625 original size:15 final size:16
Alignment explanation
Indices: 44607--44636 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
44597 CCACTATTAA
44607 AAATAA-AAAATTATC
1 AAATAATAAAATTATC
44622 AAATAATAAAATTAT
1 AAATAATAAAATTAT
44637 TGGTAAACCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (16 bp):
AAATAATAAAATTATC
Found at i:49547 original size:83 final size:83
Alignment explanation
Indices: 49407--49575 Score: 302
Period size: 83 Copynumber: 2.0 Consensus size: 83
49397 TGAGGTGATT
*
49407 AAAGTGTAGTTGAACCTATAAAAAATGATACTTGATGTTAATTCTAATTCGAATTGATCGAAACC
1 AAAGTGTAGTTGAACCTATAAAAAATGATACTTGATGTTAATTCTAATTCGAATTGATCAAAACC
49472 AGACACAGATTAGCCTGG
66 AGACACAGATTAGCCTGG
* *
49490 AAAGTGTAGTTGAGCCTATAAAAAATGATACTTGATGTTAATTCTAATTCGAGTTGATCAAAACC
1 AAAGTGTAGTTGAACCTATAAAAAATGATACTTGATGTTAATTCTAATTCGAATTGATCAAAACC
*
49555 AGACACAGATTCGCCTGG
66 AGACACAGATTAGCCTGG
49573 AAA
1 AAA
49576 CAAGCAGCCA
Statistics
Matches: 82, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
83 82 1.00
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.28
Consensus pattern (83 bp):
AAAGTGTAGTTGAACCTATAAAAAATGATACTTGATGTTAATTCTAATTCGAATTGATCAAAACC
AGACACAGATTAGCCTGG
Done.