Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001646.1 Hibiscus syriacus cultivar Beakdansim tig00003295_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: 64219
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:1476 original size:21 final size:21
Alignment explanation
Indices: 1452--1511 Score: 93
Period size: 21 Copynumber: 2.8 Consensus size: 21
1442 GAAGGGGTAT
1452 CGATACCCTGCTACAGTGCAC
1 CGATACCCTGCTACAGTGCAC
* *
1473 CGATACCCTTCTACAGTGTAC
1 CGATACCCTGCTACAGTGCAC
1494 CGATACCCTTGCTACAGT
1 CGATACCC-TGCTACAGT
1512 AACTTTGGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
21 27 0.77
22 8 0.23
ACGTcount: A:0.23, C:0.35, G:0.17, T:0.25
Consensus pattern (21 bp):
CGATACCCTGCTACAGTGCAC
Found at i:3427 original size:31 final size:31
Alignment explanation
Indices: 3392--3462 Score: 94
Period size: 30 Copynumber: 2.4 Consensus size: 31
3382 TACAATCATT
3392 CACAACTTTTCCAAAAATTACA-AATTGGTCC
1 CACAACTTTTCCAAAAATTACATAA-TGGTCC
*
3423 CACAACTTTT-CAAAATTTACATAATGGTCC
1 CACAACTTTTCCAAAAATTACATAATGGTCC
*
3453 C-CAAATTTTC
1 CACAACTTTTC
3463 TAAAGCTTGT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
29 7 0.19
30 17 0.47
31 12 0.33
ACGTcount: A:0.37, C:0.25, G:0.06, T:0.32
Consensus pattern (31 bp):
CACAACTTTTCCAAAAATTACATAATGGTCC
Found at i:8120 original size:23 final size:23
Alignment explanation
Indices: 8094--8162 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
8084 CACCACAACT
*
8094 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* * *
8117 CGTAGAATTGCACTGGAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
*
8140 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
8163 TATAATAATG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.26, C:0.25, G:0.28, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:11363 original size:101 final size:101
Alignment explanation
Indices: 11188--11390 Score: 406
Period size: 101 Copynumber: 2.0 Consensus size: 101
11178 CACATGGAGA
11188 GCATTTCATAATTTGGAGGTCTCTTACTGAAGCTGCTCTTAACCTAGTGTTGGGGGCAGTCTACT
1 GCATTTCATAATTTGGAGGTCTCTTACTGAAGCTGCTCTTAACCTAGTGTTGGGGGCAGTCTACT
11253 ATCTTACCTCCCCCTTACCCCATTACATATGGGAAC
66 ATCTTACCTCCCCCTTACCCCATTACATATGGGAAC
11289 GCATTTCATAATTTGGAGGTCTCTTACTGAAGCTGCTCTTAACCTAGTGTTGGGGGCAGTCTACT
1 GCATTTCATAATTTGGAGGTCTCTTACTGAAGCTGCTCTTAACCTAGTGTTGGGGGCAGTCTACT
11354 ATCTTACCTCCCCCTTACCCCATTACATATGGGAAC
66 ATCTTACCTCCCCCTTACCCCATTACATATGGGAAC
11390 G
1 G
11391 AGGGACAACC
Statistics
Matches: 102, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
101 102 1.00
ACGTcount: A:0.22, C:0.27, G:0.19, T:0.33
Consensus pattern (101 bp):
GCATTTCATAATTTGGAGGTCTCTTACTGAAGCTGCTCTTAACCTAGTGTTGGGGGCAGTCTACT
ATCTTACCTCCCCCTTACCCCATTACATATGGGAAC
Found at i:15845 original size:21 final size:21
Alignment explanation
Indices: 15820--15862 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
15810 AAAATATTAA
*
15820 AAAAATATTAATATTTTAAAT
1 AAAAATAATAATATTTTAAAT
15841 AAAAATAATAATATTTTAAAT
1 AAAAATAATAATATTTTAAAT
15862 A
1 A
15863 TATTTTACCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
AAAAATAATAATATTTTAAAT
Found at i:27850 original size:5 final size:5
Alignment explanation
Indices: 27836--27984 Score: 291
Period size: 5 Copynumber: 30.0 Consensus size: 5
27826 TTGTGACTGT
27836 TATT- TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
27885 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
27935 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
27985 ACATGTATAT
Statistics
Matches: 144, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
4 4 0.03
5 140 0.97
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATTA
Found at i:38689 original size:18 final size:16
Alignment explanation
Indices: 38651--38687 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
38641 GTATTTCTTT
38651 TATATGTATGTGTATA
1 TATATGTATGTGTATA
* *
38667 TATATGTGTGTGTTTA
1 TATATGTATGTGTATA
38683 TATAT
1 TATAT
38688 ATATATATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.19, T:0.54
Consensus pattern (16 bp):
TATATGTATGTGTATA
Found at i:38833 original size:81 final size:81
Alignment explanation
Indices: 38692--38945 Score: 292
Period size: 81 Copynumber: 3.0 Consensus size: 81
38682 ATATATATAT
* * *
38692 ATATATATAAAGATAAGTGACCCGTTTTCTCCCGCATTCATATTAAGTAGTGACAAATCTAGAAA
1 ATATATAT-AAGATAGGTGACCC-TTTTTTCCC-CATTCATGTTAAGTAGTGACAAATCTAGAAA
38757 TATATTTTAAGGTGGAAAC
63 TATATTTTAAGGTGGAAAC
* * * * *
38776 ATATATATAAGATAGGTGACCCTTTTTTTCCCATTCGTGTTAAGTAATAACATATCTAGAAATAT
1 ATATATATAAGATAGGTGACCCTTTTTTCCCCATTCATGTTAAGTAGTGACAAATCTAGAAATAT
*
38841 ATTTTAGGGTGGACACAC
66 ATTTTAAGGTGGA-A-AC
* ** * *
38859 ATTATTATATAGGATAGGTGATCGGTTTTCTCCCCCTATTCATGTTAAGTAGTGACAGATCTAGA
1 A-TA-TATATAAGATAGGTGA-CCCTTTT-TTCCCC-ATTCATGTTAAGTAGTGACAAATCTAGA
38924 AATATATTTTAAGGTGGAAAC
61 AATATATTTTAAGGTGGAAAC
38945 A
1 A
38946 CACACACACA
Statistics
Matches: 144, Mismatches: 19, Indels: 12
0.82 0.11 0.07
Matches are distributed among these distances:
81 41 0.28
82 8 0.06
83 16 0.11
84 10 0.07
85 15 0.10
86 8 0.06
87 5 0.03
88 41 0.28
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.35
Consensus pattern (81 bp):
ATATATATAAGATAGGTGACCCTTTTTTCCCCATTCATGTTAAGTAGTGACAAATCTAGAAATAT
ATTTTAAGGTGGAAAC
Found at i:38925 original size:88 final size:83
Alignment explanation
Indices: 38692--39001 Score: 304
Period size: 88 Copynumber: 3.6 Consensus size: 83
38682 ATATATATAT
* * *
38692 ATATATATAAAGATAAGTGACCCGTTTTCTCCCGCATTCATATTAAGTAGTGACAAATCTAGAAA
1 ATATATAT-AAGATAGGTGA-CCGTTTTCTCCCCCATTCATGTTAAGTAGTGACAAATCTAGAAA
38757 TATATTTTAAGGTGGAA-AC
64 TATATTTTAAGGTGGAACAC
* ** * * * *
38776 ATATATATAAGATAGGTGACCCTTTT-TTTCCCATTCGTGTTAAGTAATAACATATCTAGAAATA
1 ATATATATAAGATAGGTGACCGTTTTCTCCCCCATTCATGTTAAGTAGTGACAAATCTAGAAATA
*
38840 TATTTTAGGGTGGACACAC
66 TATTTTAAGGTGGA-ACAC
* * *
38859 ATTATTATATAGGATAGGTGATCGGTTTTCTCCCCCTATTCATGTTAAGTAGTGACAGATCTAGA
1 A-TA-TATATAAGATAGGTGA-CCGTTTTCTCCCCC-ATTCATGTTAAGTAGTGACAAATCTAGA
38924 AATATATTTTAAGGTGGAAACACACACAC
62 AATATATTTTAAGGTGG------A-ACAC
* * * *
38953 ACATATATAAGATAGATGACCG-GTT-TCCCCCATTCGTGTTAAGTAGTGA
1 ATATATATAAGATAGGTGACCGTTTTCTCCCCCATTCATGTTAAGTAGTGA
39002 TGGATCGATT
Statistics
Matches: 186, Mismatches: 27, Indels: 22
0.79 0.11 0.09
Matches are distributed among these distances:
81 43 0.23
82 7 0.04
83 13 0.07
84 10 0.05
85 15 0.08
86 5 0.03
87 4 0.02
88 57 0.31
89 6 0.03
90 2 0.01
91 2 0.01
92 14 0.08
93 1 0.01
94 7 0.04
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.33
Consensus pattern (83 bp):
ATATATATAAGATAGGTGACCGTTTTCTCCCCCATTCATGTTAAGTAGTGACAAATCTAGAAATA
TATTTTAAGGTGGAACAC
Found at i:49873 original size:18 final size:18
Alignment explanation
Indices: 49850--49892 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
49840 TAAATATATT
49850 ATTATTGAACTACAATG-A
1 ATTATT-AACTACAATGAA
* *
49868 ATTATTTATTACAATGAA
1 ATTATTAACTACAATGAA
49886 ATTATTA
1 ATTATTA
49893 CCTTAATGCA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.42
Consensus pattern (18 bp):
ATTATTAACTACAATGAA
Found at i:56883 original size:4 final size:4
Alignment explanation
Indices: 56876--56900 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
56866 TATATATATA
56876 TATG TATG TATG TATG TATG TATG T
1 TATG TATG TATG TATG TATG TATG T
56901 GAAGAGAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:57609 original size:2 final size:2
Alignment explanation
Indices: 57602--57627 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
57592 CCATCACCTT
57602 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
57628 CCCCCCCCCC
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:60679 original size:31 final size:30
Alignment explanation
Indices: 60626--60688 Score: 72
Period size: 31 Copynumber: 2.1 Consensus size: 30
60616 TCGTTAAAAA
* *
60626 TTAATGCATTTAGTACCCAAACTATCAGTT
1 TTAATCCATTTAGTACCCAAACTATCAATT
* * *
60656 TTAATCCATTTTAGTATCTAAACTTTCAATT
1 TTAATCCA-TTTAGTACCCAAACTATCAATT
60687 TT
1 TT
60689 TCAAAATTTA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
30 7 0.26
31 20 0.74
ACGTcount: A:0.32, C:0.17, G:0.06, T:0.44
Consensus pattern (30 bp):
TTAATCCATTTAGTACCCAAACTATCAATT
Found at i:61111 original size:21 final size:21
Alignment explanation
Indices: 61060--61112 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
61050 ATTATGACTA
61060 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
61081 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
61102 TCGCAATGCGA
1 TCGCAATGCGA
61113 ATAAGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:61166 original size:41 final size:41
Alignment explanation
Indices: 61139--61216 Score: 129
Period size: 41 Copynumber: 1.9 Consensus size: 41
61129 GCGAATTGGG
*
61139 AAAAACGCAATGCGATACTGACTATCGCAACGCGATAATAC
1 AAAAACGCAACGCGATACTGACTATCGCAACGCGATAATAC
* *
61180 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATA
1 AAAAACGCAACGCGATACTGACTATCGCAACGCGATA
61217 CTGACTTTCG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.38, C:0.26, G:0.18, T:0.18
Consensus pattern (41 bp):
AAAAACGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:61173 original size:20 final size:20
Alignment explanation
Indices: 61144--61236 Score: 107
Period size: 20 Copynumber: 4.6 Consensus size: 20
61134 TTGGGAAAAA
*
61144 CGCAATGCGATACTGACTAT
1 CGCAACGCGATACTGACTAT
* *
61164 CGCAACGCGATAAT-ACAAAAT
1 CGCAACGCGATACTGAC--TAT
*
61185 CGCAACGCGATACTGACTTT
1 CGCAACGCGATACTGACTAT
*
61205 CGCAACGCGATACTGACTTT
1 CGCAACGCGATACTGACTAT
*
61225 CGCAACGAGATA
1 CGCAACGCGATA
61237 ATACATAATC
Statistics
Matches: 63, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
19 2 0.03
20 44 0.70
21 15 0.24
22 2 0.03
ACGTcount: A:0.33, C:0.27, G:0.19, T:0.20
Consensus pattern (20 bp):
CGCAACGCGATACTGACTAT
Found at i:61250 original size:21 final size:20
Alignment explanation
Indices: 61144--61256 Score: 95
Period size: 20 Copynumber: 5.5 Consensus size: 20
61134 TTGGGAAAAA
* *
61144 CGCAATGCGATACTGACTAT
1 CGCAACGCGATAATGACTAT
*
61164 CGCAACGCGATAAT-ACAAAAT
1 CGCAACGCGATAATGAC--TAT
* *
61185 CGCAACGCGATACTGACTTT
1 CGCAACGCGATAATGACTAT
* *
61205 CGCAACGCGATACTGACTTT
1 CGCAACGCGATAATGACTAT
*
61225 CGCAACGAGATAAT-ACATAAT
1 CGCAACGCGATAATGAC-T-AT
*
61246 CGCAATGCGAT
1 CGCAACGCGAT
61257 TTTCAAAGCG
Statistics
Matches: 77, Mismatches: 11, Indels: 9
0.79 0.11 0.09
Matches are distributed among these distances:
19 4 0.05
20 46 0.60
21 25 0.32
22 2 0.03
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.21
Consensus pattern (20 bp):
CGCAACGCGATAATGACTAT
Found at i:61451 original size:22 final size:20
Alignment explanation
Indices: 61426--61470 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 20
61416 TCTCACCATA
*
61426 TCCGACGAAATCCATCCCTATC
1 TCCGACAAAATCCAT--CTATC
*
61448 TCCGGCAAAATCCATCTATC
1 TCCGACAAAATCCATCTATC
61468 TCC
1 TCC
61471 ATCTCAGAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 8 0.38
22 13 0.62
ACGTcount: A:0.27, C:0.40, G:0.09, T:0.24
Consensus pattern (20 bp):
TCCGACAAAATCCATCTATC
Found at i:61731 original size:20 final size:20
Alignment explanation
Indices: 61702--61745 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
61692 GCGATTTTAG
61702 TTTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGTCAT
* **
61722 TTTCGTGTTGCGATTTTCAT
1 TTTCGCGTTGCGATAGTCAT
61742 TTTC
1 TTTC
61746 AGAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.11, C:0.18, G:0.20, T:0.50
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGTCAT
Found at i:63658 original size:20 final size:21
Alignment explanation
Indices: 63635--63690 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 21
63625 GGCAACACGA
63635 AAATGACTATCGCAACGTG-G
1 AAATGACTATCGCAACGTGCG
*
63655 AAATGGCTATCGCAA--TGCG
1 AAATGACTATCGCAACGTGCG
**
63674 AAATGAAAATCGCAACG
1 AAATGACTATCGCAACG
63691 ACAAAATCGC
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
18 2 0.07
19 13 0.45
20 14 0.48
ACGTcount: A:0.39, C:0.20, G:0.23, T:0.18
Consensus pattern (21 bp):
AAATGACTATCGCAACGTGCG
Found at i:63798 original size:20 final size:20
Alignment explanation
Indices: 63752--63819 Score: 77
Period size: 20 Copynumber: 3.5 Consensus size: 20
63742 GCGATTTTGT
**
63752 CGTTGCGATTTTCATTT-CG
1 CGTTGCGATAGTCATTTCCG
*
63771 CATTGCGATAG-CTATTTCCG
1 CGTTGCGATAGTC-ATTTCCG
*
63791 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTCCG
63811 CGTTGCGAT
1 CGTTGCGAT
63820 TTTAAGTTTC
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
18 1 0.02
19 12 0.29
20 27 0.66
21 1 0.02
ACGTcount: A:0.15, C:0.22, G:0.24, T:0.40
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Done.