Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001784.1 Hibiscus syriacus cultivar Beakdansim tig00003603_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: 60808
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.33
Found at i:2184 original size:31 final size:31
Alignment explanation
Indices: 2146--2300 Score: 208
Period size: 31 Copynumber: 5.1 Consensus size: 31
2136 ACTCGTATAA
*
2146 TAATCTGTTCATATGTCCCGAAGAACATAGG
1 TAATCTGTCCATATGTCCCGAAGAACATAGG
2177 TAATCTGTCCATATGTCCCGAAGAACATAGG
1 TAATCTGTCCATATGTCCCGAAGAACATAGG
* ** *
2208 TATTCTGTCCATATGTCCAAAATAACATAGG
1 TAATCTGTCCATATGTCCCGAAGAACATAGG
*
2239 TAAAT-TGTCCATATGTCCAG-A-AACATAGG
1 T-AATCTGTCCATATGTCCCGAAGAACATAGG
* *
2268 TAAACTTTCCATATGTCCCGAAGAACATAGG
1 TAATCTGTCCATATGTCCCGAAGAACATAGG
2299 TA
1 TA
2301 TCCCTCGACT
Statistics
Matches: 110, Mismatches: 10, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
28 2 0.02
29 22 0.20
30 2 0.02
31 82 0.75
32 2 0.02
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (31 bp):
TAATCTGTCCATATGTCCCGAAGAACATAGG
Found at i:4184 original size:30 final size:29
Alignment explanation
Indices: 4120--4205 Score: 77
Period size: 29 Copynumber: 2.9 Consensus size: 29
4110 ACCCATTTGT
* * * *
4120 AACTTTTTAAAATTACATTTTGATC-CCTA
1 AACTTTATAAATTTACAATTTGGTCACC-A
* *
4149 AACTTT-TCAAAGTTTATACTTTGGTCACCA
1 AACTTTAT-AAA-TTTACAATTTGGTCACCA
4179 AACTTTATAAATTTACAATTTGGTCAC
1 AACTTTATAAATTTACAATTTGGTCAC
4206 TCACTATAAT
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
28 1 0.02
29 23 0.49
30 20 0.43
31 3 0.06
ACGTcount: A:0.34, C:0.17, G:0.07, T:0.42
Consensus pattern (29 bp):
AACTTTATAAATTTACAATTTGGTCACCA
Found at i:4200 original size:29 final size:29
Alignment explanation
Indices: 4124--4205 Score: 78
Period size: 30 Copynumber: 2.8 Consensus size: 29
4114 ATTTGTAACT
* * *
4124 TTTTAAAATTACATTTTGATC-CCTAAAC
1 TTTTAAATTTACAATTTGGTCACCTAAAC
* *
4152 TTTTCAAAGTTTATACTTTGGTCACC-AAAC
1 TTTT-AAA-TTTACAATTTGGTCACCTAAAC
4182 TTTATAAATTTACAATTTGGTCAC
1 TTT-TAAATTTACAATTTGGTCAC
4206 TCACTATAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
28 4 0.09
29 17 0.39
30 20 0.45
31 3 0.07
ACGTcount: A:0.33, C:0.17, G:0.07, T:0.43
Consensus pattern (29 bp):
TTTTAAATTTACAATTTGGTCACCTAAAC
Found at i:9585 original size:31 final size:31
Alignment explanation
Indices: 9532--9596 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
9522 GCTCGTATAA
*
9532 TAATATGTTCATATGTTCCGAAGAACATAGG
1 TAATATGTCCATATGTTCCGAAGAACATAGG
*
9563 TAATCTGTCCATATGTAT-CGAAGAACATAGG
1 TAATATGTCCATATGT-TCCGAAGAACATAGG
9594 TAA
1 TAA
9597 CCATCGACTC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
31 30 0.97
32 1 0.03
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.31
Consensus pattern (31 bp):
TAATATGTCCATATGTTCCGAAGAACATAGG
Found at i:11479 original size:29 final size:29
Alignment explanation
Indices: 11446--11510 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
11436 GACCCATTTG
* *
11446 TAACTTTTTAAA-ATTATATTTTGGTCAA
1 TAACTTTTCAAAGATTATACTTTGGTCAA
* *
11474 TAAACTTTTCAAAGTTTATACTTTGGTCAC
1 T-AACTTTTCAAAGATTATACTTTGGTCAA
11504 TAACTTT
1 TAACTTT
11511 ATAATTTTAC
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
28 1 0.03
29 16 0.52
30 14 0.45
ACGTcount: A:0.32, C:0.12, G:0.08, T:0.48
Consensus pattern (29 bp):
TAACTTTTCAAAGATTATACTTTGGTCAA
Found at i:11869 original size:22 final size:22
Alignment explanation
Indices: 11810--11869 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
11800 TTAACATTAG
* *
11810 TACTAAAGTGCCTCAACACTGA
1 TACTAAAGTGCCTTAGCACTGA
* * *
11832 TACGAAAGCGCATTAGCACTGA
1 TACTAAAGTGCCTTAGCACTGA
*
11854 TACTAAAATGCCTTAG
1 TACTAAAGTGCCTTAG
11870 ATGTATTTCA
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.37, C:0.23, G:0.17, T:0.23
Consensus pattern (22 bp):
TACTAAAGTGCCTTAGCACTGA
Found at i:17542 original size:55 final size:55
Alignment explanation
Indices: 17471--17856 Score: 508
Period size: 55 Copynumber: 7.1 Consensus size: 55
17461 TATATGTTGC
* * * *
17471 AATTTTCGTATTGGCACTATGTGTGCAACTTCATGAAATTCGTAATGAGTTTATG
1 AATTTCCGTATTGGCACTATGTGTGCAACCTCACGAAATTCATAATGAGTTTATG
* * *
17526 AATTTCTGTATTGGCACTATGTGTGCAACTTCATGAAATTCATAATGAGTTTATG
1 AATTTCCGTATTGGCACTATGTGTGCAACCTCACGAAATTCATAATGAGTTTATG
*
17581 AATTTCCGTATTGGCACTATGTGTGCAACCTTACGAAATTCATAATGAGTTTATG
1 AATTTCCGTATTGGCACTATGTGTGCAACCTCACGAAATTCATAATGAGTTTATG
* * * *
17636 AATTTCCGTATTGGAACTATGTGTGCAACCCCACGAAATTTATAATGAGTTTATA
1 AATTTCCGTATTGGCACTATGTGTGCAACCTCACGAAATTCATAATGAGTTTATG
* * * * * *
17691 AATTTTCGTATTAGCACTATGTATGCAACCCCACAAAATTCATAATGAGTTTTTG
1 AATTTCCGTATTGGCACTATGTGTGCAACCTCACGAAATTCATAATGAGTTTATG
* * * *
17746 AATTTCCATATTGGCACTATGTGTGCAACCT-AAGTAATTCATAATGAGTTTGTG
1 AATTTCCGTATTGGCACTATGTGTGCAACCTCACGAAATTCATAATGAGTTTATG
* * * *
17800 AATTAT-CGTATTGGCACTATGTGAGCAACCT-ACGTAATTCACAATGAGTTTGTG
1 AATT-TCCGTATTGGCACTATGTGTGCAACCTCACGAAATTCATAATGAGTTTATG
17854 AAT
1 AAT
17857 GACCATATCA
Statistics
Matches: 297, Mismatches: 33, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
54 70 0.24
55 227 0.76
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.37
Consensus pattern (55 bp):
AATTTCCGTATTGGCACTATGTGTGCAACCTCACGAAATTCATAATGAGTTTATG
Found at i:25549 original size:31 final size:29
Alignment explanation
Indices: 25465--25565 Score: 96
Period size: 30 Copynumber: 3.3 Consensus size: 29
25455 ACATTTTCAT
* *
25465 ATAAGTACCTAAAGTGTTTTTTTTGTCAAA
1 ATAAGTACTTAAAAT-TTTTTTTTGTCAAA
*
25495 ATAAGCA-TTAAAATTTATATTTTTGTTCAAA
1 ATAAGTACTTAAAATTT-T-TTTTTG-TCAAA
* *
25526 ATAGGTACTTAAAATATTTTTTTTATCAAA
1 ATAAGTACTTAAAAT-TTTTTTTTGTCAAA
*
25556 ATATGTACTT
1 ATAAGTACTT
25566 TAAGTATTCA
Statistics
Matches: 59, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
28 2 0.03
29 6 0.10
30 26 0.44
31 15 0.25
32 8 0.14
33 2 0.03
ACGTcount: A:0.38, C:0.08, G:0.09, T:0.46
Consensus pattern (29 bp):
ATAAGTACTTAAAATTTTTTTTTGTCAAA
Found at i:27378 original size:33 final size:32
Alignment explanation
Indices: 27333--27404 Score: 110
Period size: 33 Copynumber: 2.2 Consensus size: 32
27323 CCAACTTTTC
*
27333 TTTCC-TTTACATTTTCATTTCCCTGGTAGATT
1 TTTCCTTTTACATTTTCATTTCCCTGATAGA-T
*
27365 TTTCCTTTTACATTTTCATTTCCCTGATATAT
1 TTTCCTTTTACATTTTCATTTCCCTGATAGAT
27397 TTTCCTTT
1 TTTCCTTT
27405 CTTATTACAA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
32 14 0.38
33 23 0.62
ACGTcount: A:0.15, C:0.22, G:0.06, T:0.57
Consensus pattern (32 bp):
TTTCCTTTTACATTTTCATTTCCCTGATAGAT
Found at i:37221 original size:14 final size:14
Alignment explanation
Indices: 37202--37229 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
37192 ATGATGACAT
37202 GTTATAATTTTTCA
1 GTTATAATTTTTCA
37216 GTTATAATTTTTCA
1 GTTATAATTTTTCA
37230 TATACCGATT
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:0.07, T:0.57
Consensus pattern (14 bp):
GTTATAATTTTTCA
Found at i:38945 original size:19 final size:18
Alignment explanation
Indices: 38921--38972 Score: 70
Period size: 18 Copynumber: 2.8 Consensus size: 18
38911 TAACAGACTT
38921 GTCTGTTTTCTACAATACA
1 GTCTGTTTTCTAC-ATACA
*
38940 GTCTGTTTTCTTTC-TACA
1 GTCTGTTTTC-TACATACA
38958 GTCTGTTTTCTACAT
1 GTCTGTTTTCTACAT
38973 GGTATCAGGT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
17 2 0.07
18 15 0.52
19 10 0.34
20 2 0.07
ACGTcount: A:0.17, C:0.21, G:0.12, T:0.50
Consensus pattern (18 bp):
GTCTGTTTTCTACATACA
Found at i:42972 original size:19 final size:18
Alignment explanation
Indices: 42948--42998 Score: 68
Period size: 18 Copynumber: 2.8 Consensus size: 18
42938 TAACAGACTT
42948 GTCTGTTTTCTACAATACA
1 GTCTGTTTTCTAC-ATACA
*
42967 GTCTGTTTTCTTTC-TACA
1 GTCTGTTTTC-TACATACA
42985 GTCTGTTTTCTACA
1 GTCTGTTTTCTACA
42999 CTTGTACTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
17 2 0.07
18 14 0.50
19 10 0.36
20 2 0.07
ACGTcount: A:0.18, C:0.22, G:0.12, T:0.49
Consensus pattern (18 bp):
GTCTGTTTTCTACATACA
Found at i:56541 original size:18 final size:19
Alignment explanation
Indices: 56506--56542 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
56496 CACGGAATGT
56506 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
56526 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
56543 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:57869 original size:27 final size:27
Alignment explanation
Indices: 57835--57900 Score: 114
Period size: 27 Copynumber: 2.4 Consensus size: 27
57825 GATAATGACT
*
57835 CTGAATCATTCAGAATGTACTTCTGTG
1 CTGAATCATTCAGAACGTACTTCTGTG
*
57862 CTGAATCATTCAGAACGTACTTTTGTG
1 CTGAATCATTCAGAACGTACTTCTGTG
57889 CTGAATCATTCA
1 CTGAATCATTCA
57901 ACACTGTTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.36
Consensus pattern (27 bp):
CTGAATCATTCAGAACGTACTTCTGTG
Found at i:57914 original size:23 final size:24
Alignment explanation
Indices: 57858--57929 Score: 76
Period size: 23 Copynumber: 2.9 Consensus size: 24
57848 AATGTACTTC
57858 TGTGCTGAATCATTCAGAACGTACT-TT
1 TGTGCTGAATCATTC--AAC--ACTGTT
57885 TGTGCTGAATCATTCAACACTGTT
1 TGTGCTGAATCATTCAACACTGTT
* *
57909 T-TGCTGAATCAGTCAATACTG
1 TGTGCTGAATCATTCAACACTG
57930 AATCATAAGT
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
23 21 0.50
24 3 0.07
25 3 0.07
27 15 0.36
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.36
Consensus pattern (24 bp):
TGTGCTGAATCATTCAACACTGTT
Found at i:59332 original size:22 final size:22
Alignment explanation
Indices: 59279--59333 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
59269 ATCCGCCCTA
59279 ACTA-ATATTATATTATATAAT
1 ACTATATATTATATTATATAAT
* * *
59300 ACTGTAAATTATGTTATAT-AT
1 ACTATATATTATATTATATAAT
59321 ACATATATATTAT
1 AC-TATATATTAT
59334 CATTTATTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
21 7 0.26
22 20 0.74
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.47
Consensus pattern (22 bp):
ACTATATATTATATTATATAAT
Found at i:60423 original size:19 final size:19
Alignment explanation
Indices: 60399--60437 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
60389 ACATATGTTA
*
60399 TGATTTTCTTTATTTTATC
1 TGATTTACTTTATTTTATC
60418 TGATTTACTTTATTTTATC
1 TGATTTACTTTATTTTATC
60437 T
1 T
60438 ATTATATATG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.18, C:0.10, G:0.05, T:0.67
Consensus pattern (19 bp):
TGATTTACTTTATTTTATC
Found at i:60499 original size:2 final size:2
Alignment explanation
Indices: 60492--60529 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
60482 TCCTTTTTAT
* *
60492 TA TA TA TA GA TA TA T- TA TA TA TA TA TA TA TA TA AA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
60530 TTTTCTTAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:60509 original size:15 final size:15
Alignment explanation
Indices: 60489--60521 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
60479 TTATCCTTTT
60489 TATTATATATAGATA
1 TATTATATATAGATA
*
60504 TATTATATATATATA
1 TATTATATATAGATA
60519 TAT
1 TAT
60522 ATAAATATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (15 bp):
TATTATATATAGATA
Done.