Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003271.1 Hibiscus syriacus cultivar Beakdansim tig00006876_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: 67717
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:3196 original size:19 final size:19
Alignment explanation
Indices: 3172--3208 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
3162 CTTGATTCGA
3172 TATAAATTATTAATTTAAG
1 TATAAATTATTAATTTAAG
3191 TATAAATTATTAATTTAA
1 TATAAATTATTAATTTAA
3209 CCTTTTATAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (19 bp):
TATAAATTATTAATTTAAG
Found at i:3305 original size:22 final size:19
Alignment explanation
Indices: 3279--3333 Score: 101
Period size: 19 Copynumber: 2.8 Consensus size: 19
3269 TATATTATAT
3279 AATTATTAAAAATATAATA
1 AATTATTAAAAATATAATA
3298 AATTATTAAAAATATAATA
1 AATTATTAAAAATATAATA
3317 AATTATTATAAAATATA
1 AATTATTA-AAAATATA
3334 TTATTTTAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 27 0.77
20 8 0.23
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
AATTATTAAAAATATAATA
Found at i:12270 original size:22 final size:22
Alignment explanation
Indices: 12243--12288 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
12233 ATGAATGACA
*
12243 ACAATTCAATCGAATGAGGAAG
1 ACAATTCAATCGAAGGAGGAAG
* *
12265 ACAATTTAATCGTAGGAGGAAG
1 ACAATTCAATCGAAGGAGGAAG
12287 AC
1 AC
12289 GAAACAGAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.43, C:0.13, G:0.24, T:0.20
Consensus pattern (22 bp):
ACAATTCAATCGAAGGAGGAAG
Found at i:25525 original size:21 final size:21
Alignment explanation
Indices: 25499--25543 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
25489 TGTATTTACC
25499 ATAGATTTGTCAAAAAAATCA
1 ATAGATTTGTCAAAAAAATCA
25520 ATAGATTTGTCAAAAAAATCA
1 ATAGATTTGTCAAAAAAATCA
25541 ATA
1 ATA
25544 ATTAGTTAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.53, C:0.09, G:0.09, T:0.29
Consensus pattern (21 bp):
ATAGATTTGTCAAAAAAATCA
Found at i:29037 original size:18 final size:18
Alignment explanation
Indices: 29014--29049 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
29004 TGAGGGCACA
*
29014 TGTACTTATCTTGAAATT
1 TGTACTTATCTTAAAATT
*
29032 TGTACTTGTCTTAAAATT
1 TGTACTTATCTTAAAATT
29050 CAAATTTTCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.28, C:0.11, G:0.11, T:0.50
Consensus pattern (18 bp):
TGTACTTATCTTAAAATT
Found at i:30051 original size:6 final size:6
Alignment explanation
Indices: 30040--30064 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
30030 GAAGACACGT
30040 ATTACC ATTACC ATTACC ATTACC A
1 ATTACC ATTACC ATTACC ATTACC A
30065 CGATCACGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.32, G:0.00, T:0.32
Consensus pattern (6 bp):
ATTACC
Found at i:30072 original size:6 final size:6
Alignment explanation
Indices: 30061--30141 Score: 153
Period size: 6 Copynumber: 13.5 Consensus size: 6
30051 CATTACCATT
*
30061 ACCACG ATCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
30109 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
30142 CGAGACGAGA
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 73 1.00
ACGTcount: A:0.33, C:0.49, G:0.16, T:0.01
Consensus pattern (6 bp):
ACCACG
Found at i:30152 original size:5 final size:5
Alignment explanation
Indices: 30142--30173 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
30132 GACCACGACC
30142 CGAGA CGAGA CGAGA CGAGA CGAGA CGAGA CG
1 CGAGA CGAGA CGAGA CGAGA CGAGA CGAGA CG
30174 GCGGCGGCGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.38, C:0.22, G:0.41, T:0.00
Consensus pattern (5 bp):
CGAGA
Found at i:36334 original size:34 final size:32
Alignment explanation
Indices: 36267--36336 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 32
36257 ACCTTACAAC
* * *
36267 TCCCTAGTTTTTCCGGGTTAAACTAGGACCTT
1 TCCCTAGTTTTTACGGGCTAAACTAGAACCTT
*
36299 TCCCTAGCTTTTATACGGGCTAAGCTAGAACCTT
1 TCCCTAG-TTTT-TACGGGCTAAACTAGAACCTT
36333 TCCC
1 TCCC
36337 CTTTACAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 7 0.22
33 4 0.12
34 21 0.66
ACGTcount: A:0.20, C:0.29, G:0.17, T:0.34
Consensus pattern (32 bp):
TCCCTAGTTTTTACGGGCTAAACTAGAACCTT
Found at i:36645 original size:21 final size:21
Alignment explanation
Indices: 36619--36660 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
36609 CCAGAATGGG
*
36619 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
36640 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
36661 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:36782 original size:20 final size:21
Alignment explanation
Indices: 36745--36803 Score: 84
Period size: 21 Copynumber: 2.8 Consensus size: 21
36735 CTTTAGACAG
36745 GGGGGAATC-GATACCCCCTGA
1 GGGGGAATCTG-TACCCCCTGA
* *
36766 GGGGGTATCTGTACCCCCTGG
1 GGGGGAATCTGTACCCCCTGA
36787 GGGGGAATCTGTACCCC
1 GGGGGAATCTGTACCCC
36804 ATAGGCAATC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
21 33 0.97
22 1 0.03
ACGTcount: A:0.17, C:0.29, G:0.36, T:0.19
Consensus pattern (21 bp):
GGGGGAATCTGTACCCCCTGA
Found at i:38740 original size:3 final size:3
Alignment explanation
Indices: 38732--38781 Score: 50
Period size: 3 Copynumber: 17.0 Consensus size: 3
38722 TACGTCCTCA
* *
38732 TTC TTC TTC TTC TTC TTC TTG TTT TTC TTC -TC TTC -TC TTTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC -TTC TTC
*
38776 ATC TTC
1 TTC TTC
38782 CTTCACCATC
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
2 4 0.10
3 33 0.85
4 2 0.05
ACGTcount: A:0.02, C:0.30, G:0.02, T:0.66
Consensus pattern (3 bp):
TTC
Found at i:39819 original size:34 final size:32
Alignment explanation
Indices: 39757--39826 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
39747 ACCTTACAAC
* *
39757 TCCCTAGTTTTTCCGGGTTAAACTAGAACCTT
1 TCCCTAGTTTTTACGGGCTAAACTAGAACCTT
*
39789 TCCCTAGCTTTTATACGGGCTAAGCTAGAACCTT
1 TCCCTAG-TTTT-TACGGGCTAAACTAGAACCTT
39823 TCCC
1 TCCC
39827 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 4 0.12
34 22 0.67
ACGTcount: A:0.21, C:0.29, G:0.16, T:0.34
Consensus pattern (32 bp):
TCCCTAGTTTTTACGGGCTAAACTAGAACCTT
Found at i:40066 original size:20 final size:22
Alignment explanation
Indices: 40041--40080 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
40031 AGTCGTATAT
40041 AGCCG-TTGGGGATG-TTTTAG
1 AGCCGTTTGGGGATGATTTTAG
40061 AGCCGTTTGGGGATGATTTT
1 AGCCGTTTGGGGATGATTTT
40081 TATACTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.15, C:0.10, G:0.38, T:0.38
Consensus pattern (22 bp):
AGCCGTTTGGGGATGATTTTAG
Found at i:40135 original size:21 final size:21
Alignment explanation
Indices: 40109--40150 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
40099 CCAGAATGGG
*
40109 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
40130 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
40151 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:40212 original size:21 final size:21
Alignment explanation
Indices: 40186--40228 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
40176 CTGTTGAACA
40186 GGGGGGAATCGGTACCCCCTG
1 GGGGGGAATCGGTACCCCCTG
40207 GGGGGGAATCGGTACCCCCTG
1 GGGGGGAATCGGTACCCCCTG
40228 G
1 G
40229 ACATTTTGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.14, C:0.28, G:0.44, T:0.14
Consensus pattern (21 bp):
GGGGGGAATCGGTACCCCCTG
Found at i:40280 original size:21 final size:21
Alignment explanation
Indices: 40254--40316 Score: 108
Period size: 21 Copynumber: 3.0 Consensus size: 21
40244 GCTTTAGACA
*
40254 GGGGGGAATCGGTACCCCCTG
1 GGGGGGAATCTGTACCCCCTG
*
40275 GGGGGGTATCTGTACCCCCTG
1 GGGGGGAATCTGTACCCCCTG
40296 GGGGGGAATCTGTACCCCCTG
1 GGGGGGAATCTGTACCCCCTG
40317 TGCAATCTTG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.13, C:0.29, G:0.40, T:0.19
Consensus pattern (21 bp):
GGGGGGAATCTGTACCCCCTG
Found at i:43544 original size:66 final size:66
Alignment explanation
Indices: 43438--43571 Score: 268
Period size: 66 Copynumber: 2.0 Consensus size: 66
43428 TGCACAACGG
43438 TTCATTAAGTTTTTAACGGAGGGGAAATTAAAGTTTTAAACAAATAATACTTAAATAATTTATAT
1 TTCATTAAGTTTTTAACGGAGGGGAAATTAAAGTTTTAAACAAATAATACTTAAATAATTTATAT
43503 A
66 A
43504 TTCATTAAGTTTTTAACGGAGGGGAAATTAAAGTTTTAAACAAATAATACTTAAATAATTTATAT
1 TTCATTAAGTTTTTAACGGAGGGGAAATTAAAGTTTTAAACAAATAATACTTAAATAATTTATAT
43569 A
66 A
43570 TT
1 TT
43572 TATAAAGTGT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 68 1.00
ACGTcount: A:0.43, C:0.06, G:0.12, T:0.39
Consensus pattern (66 bp):
TTCATTAAGTTTTTAACGGAGGGGAAATTAAAGTTTTAAACAAATAATACTTAAATAATTTATAT
A
Found at i:46773 original size:24 final size:25
Alignment explanation
Indices: 46716--46783 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 25
46706 AATGTAATCC
46716 TTGAATTATTTTTTAATAATTTAATTT
1 TTGAA-TA-TTTTTAATAATTTAATTT
46743 TAT-AATATTTTT-AT-ATTTAATTT
1 T-TGAATATTTTTAATAATTTAATTT
*
46766 ATTGAATA-TCTTAATAAT
1 -TTGAATATTTTTAATAAT
46784 CATTTATATT
Statistics
Matches: 35, Mismatches: 1, Indels: 12
0.73 0.02 0.25
Matches are distributed among these distances:
23 13 0.37
24 9 0.26
25 7 0.20
26 2 0.06
27 3 0.09
28 1 0.03
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.59
Consensus pattern (25 bp):
TTGAATATTTTTAATAATTTAATTT
Found at i:47235 original size:20 final size:20
Alignment explanation
Indices: 47210--47253 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
47200 TTTTTAATAA
*
47210 TTATTATCTAATTTAATTAT
1 TTATTAACTAATTTAATTAT
* *
47230 TTATTAACTATTTTATTTAT
1 TTATTAACTAATTTAATTAT
47250 TTAT
1 TTAT
47254 AGTTTAAAAA
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:0.32, C:0.05, G:0.00, T:0.64
Consensus pattern (20 bp):
TTATTAACTAATTTAATTAT
Found at i:50374 original size:164 final size:161
Alignment explanation
Indices: 50170--50496 Score: 602
Period size: 164 Copynumber: 2.0 Consensus size: 161
50160 AAAATTCGGT
*
50170 CTAAATCGGATTAAATTGACTCCTAAACAATCGAAATATTACCATAAATAGTAAAAACTAACTAA
1 CTAAATCGGATTAAATTGACTCCTAAACAATCGAAATATTACCATAAATAGTAAAAAATAACTAA
50235 ATCTAGTGATTCGGAGGGGAAACGGCAGAATTTGAGGTTG-AAAAAAGGCCACATGGAGCGTAGC
66 ATCTAGTGATTCGGAGGGGAAACGGCAGAATTTGAGGTTGAAAAAAAGGCCACATGGAGCGTAGC
50299 TCAATGTGGAGAGCGTGCGCGTCGAAAAGAG
131 TCAATGTGGAGAGCGTGCGCGTCGAAAAGAG
50330 CTAAATCGGATTTAAATTGACTCCTAATTAACAATCGAAATATTACCATAAATAGTAAAAAATAA
1 CTAAATCGGA-TTAAATTGACTCCT-A--AACAATCGAAATATTACCATAAATAGTAAAAAATAA
50395 CTAAATCTAGTGATTCGGAGGGGAAACGGCAGAATTTGAGGTTGAAAAAAAGGCCACATGGAGCG
62 CTAAATCTAGTGATTCGGAGGGGAAACGGCAGAATTTGAGGTTGAAAAAAAGGCCACATGGAGCG
50460 TAGCTCAATGTGGAGAGCGTGCGCGTCGAAAAGAG
127 TAGCTCAATGTGGAGAGCGTGCGCGTCGAAAAGAG
50495 CT
1 CT
50497 TTCCGGATTG
Statistics
Matches: 161, Mismatches: 1, Indels: 5
0.96 0.01 0.03
Matches are distributed among these distances:
160 10 0.06
161 14 0.09
162 1 0.01
164 79 0.49
165 57 0.35
ACGTcount: A:0.39, C:0.15, G:0.24, T:0.22
Consensus pattern (161 bp):
CTAAATCGGATTAAATTGACTCCTAAACAATCGAAATATTACCATAAATAGTAAAAAATAACTAA
ATCTAGTGATTCGGAGGGGAAACGGCAGAATTTGAGGTTGAAAAAAAGGCCACATGGAGCGTAGC
TCAATGTGGAGAGCGTGCGCGTCGAAAAGAG
Found at i:59039 original size:19 final size:18
Alignment explanation
Indices: 59017--59077 Score: 56
Period size: 18 Copynumber: 3.4 Consensus size: 18
59007 TGAAATATGA
59017 ATATATTATTTATAAATGT
1 ATATATTATTTATAAAT-T
*
59036 ATAT-TTGATTAAATAAA-T
1 ATATATT-ATT-TATAAATT
*
59054 ATATATTATTTATGAATT
1 ATATATTATTTATAAATT
59072 -TATATT
1 ATATATT
59078 CAATTAAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
17 10 0.29
18 11 0.31
19 9 0.26
20 5 0.14
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (18 bp):
ATATATTATTTATAAATT
Found at i:59040 original size:17 final size:17
Alignment explanation
Indices: 59017--59077 Score: 59
Period size: 17 Copynumber: 3.4 Consensus size: 17
59007 TGAAATATGA
59017 ATATATTATTTATAAAT
1 ATATATTATTTATAAAT
* *
59034 GTATATTTGATTAAATAAAT
1 ATATA-TT-ATT-TATAAAT
*
59054 ATATATTATTTATGAAT
1 ATATATTATTTATAAAT
*
59071 TTATATT
1 ATATATT
59078 CAATTAAAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
17 15 0.43
18 5 0.14
19 5 0.14
20 10 0.29
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (17 bp):
ATATATTATTTATAAAT
Found at i:59059 original size:37 final size:37
Alignment explanation
Indices: 58980--59097 Score: 125
Period size: 37 Copynumber: 3.2 Consensus size: 37
58970 ATTTAATGTG
* *
58980 AATATATTA-TTACAAATTATATTCGATTGAAATATG
1 AATATATTATTTATAAATTATATTCGATTGAAATATA
*
59016 AATATATTATTTATAAATGTATATTTGATT-AAATA-A
1 AATATATTATTTATAAAT-TATATTCGATTGAAATATA
* * * *
59052 ATATATATTATTTATGAATTTATATTCAATTAAAATACA
1 A-ATATATTATTTAT-AAATTATATTCGATTGAAATATA
59091 AATATAT
1 AATATAT
59098 GTTACAAGTT
Statistics
Matches: 70, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
36 10 0.14
37 34 0.49
38 24 0.34
39 2 0.03
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (37 bp):
AATATATTATTTATAAATTATATTCGATTGAAATATA
Found at i:66936 original size:18 final size:17
Alignment explanation
Indices: 66910--66951 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
66900 TTTTCATTAT
* *
66910 AAAAAATTATAAATGAA
1 AAAAAATTACAAATCAA
66927 AAAGAAATTACAAATCAA
1 AAA-AAATTACAAATCAA
66945 AAAAAAT
1 AAAAAAT
66952 ATTATTAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.71, C:0.05, G:0.05, T:0.19
Consensus pattern (17 bp):
AAAAAATTACAAATCAA
Done.