Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007074.1 Hibiscus syriacus cultivar Beakdansim tig00018456_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: 62110
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Found at i:2112 original size:16 final size:15
Alignment explanation
Indices: 2091--2127 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
2081 AGGTTAAATG
2091 ATGTATTTTAATTTTA
1 ATGTATTTTAA-TTTA
2107 ATGTA-TTTAATTTA
1 ATGTATTTTAATTTA
2121 AT-TATTT
1 ATGTATTT
2128 ATCTTCCAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
13 2 0.10
14 8 0.40
15 5 0.25
16 5 0.25
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.62
Consensus pattern (15 bp):
ATGTATTTTAATTTA
Found at i:2843 original size:34 final size:35
Alignment explanation
Indices: 2791--2858 Score: 86
Period size: 34 Copynumber: 2.0 Consensus size: 35
2781 ACCTAACACT
2791 AATTTTATACAATATTAAAAGA-AAATTAA-ATTTA
1 AATTTTATACAATATTAAAA-ATAAATTAATATTTA
* * *
2825 AATTTTATATATTTTTAAAAATAAATTAATATTT
1 AATTTTATACAATATTAAAAATAAATTAATATTT
2859 TCTTTTTCAC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
33 1 0.03
34 24 0.83
35 4 0.14
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (35 bp):
AATTTTATACAATATTAAAAATAAATTAATATTTA
Found at i:3106 original size:2 final size:2
Alignment explanation
Indices: 3099--3128 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3089 CTACTTTGTA
3099 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3129 TATGTTTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11414 original size:35 final size:35
Alignment explanation
Indices: 11368--11440 Score: 137
Period size: 35 Copynumber: 2.1 Consensus size: 35
11358 TCAAAGTAAA
11368 ACTTCAAGATAACTGTGATCAAGGAACTCATTTGC
1 ACTTCAAGATAACTGTGATCAAGGAACTCATTTGC
*
11403 ACTTCAAGATAACTGTGATCAAGGAACTCCTTTGC
1 ACTTCAAGATAACTGTGATCAAGGAACTCATTTGC
11438 ACT
1 ACT
11441 GTCAGTACCA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29
Consensus pattern (35 bp):
ACTTCAAGATAACTGTGATCAAGGAACTCATTTGC
Found at i:11481 original size:29 final size:29
Alignment explanation
Indices: 11449--11541 Score: 71
Period size: 29 Copynumber: 3.1 Consensus size: 29
11439 CTGTCAGTAC
11449 CATACAATGTTAAGTTGCAAAGTTAGCAT
1 CATACAATGTTAAGTTGCAAAGTTAGCAT
* *** ** * * *
11478 CATATCACT-TACTCCTTTGCACTGTCAGTAC
1 CATA-CAATGT--TAAGTTGCAAAGTTAGCAT
11509 CATACAATGTTAAGTTGCAAAGTTAGCAT
1 CATACAATGTTAAGTTGCAAAGTTAGCAT
11538 CATA
1 CATA
11542 TCACTTATCA
Statistics
Matches: 42, Mismatches: 18, Indels: 8
0.62 0.26 0.12
Matches are distributed among these distances:
29 20 0.48
30 6 0.14
31 16 0.38
ACGTcount: A:0.33, C:0.20, G:0.14, T:0.32
Consensus pattern (29 bp):
CATACAATGTTAAGTTGCAAAGTTAGCAT
Found at i:11496 original size:60 final size:60
Alignment explanation
Indices: 11428--11548 Score: 242
Period size: 60 Copynumber: 2.0 Consensus size: 60
11418 TGATCAAGGA
11428 ACTCCTTTGCACTGTCAGTACCATACAATGTTAAGTTGCAAAGTTAGCATCATATCACTT
1 ACTCCTTTGCACTGTCAGTACCATACAATGTTAAGTTGCAAAGTTAGCATCATATCACTT
11488 ACTCCTTTGCACTGTCAGTACCATACAATGTTAAGTTGCAAAGTTAGCATCATATCACTT
1 ACTCCTTTGCACTGTCAGTACCATACAATGTTAAGTTGCAAAGTTAGCATCATATCACTT
11548 A
1 A
11549 TCAATCCCAA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 61 1.00
ACGTcount: A:0.31, C:0.23, G:0.13, T:0.33
Consensus pattern (60 bp):
ACTCCTTTGCACTGTCAGTACCATACAATGTTAAGTTGCAAAGTTAGCATCATATCACTT
Found at i:18568 original size:72 final size:72
Alignment explanation
Indices: 18483--18686 Score: 270
Period size: 72 Copynumber: 2.8 Consensus size: 72
18473 TTAATGCATC
* * *
18483 TAAATTCCCAATCTCTTGGGGAATAGAACC-AGTTAATAGGTTTGAATGAAGATCCAAGT-GGCT
1 TAAATTCCCAATCTCTTGGGGAATAGAACCTTG-TAATAGATTTGAATGAAGATCCAAGTAAG-T
*
18546 CAAGTTGGA
64 CAACTTGGA
* ***
18555 TAAATTCCCAATCTGTCT-GGGAATAGAACCTTGTAATAGATTTGAATGAAGCGACAAGTAAGTC
1 TAAATTCCCAATCTCT-TGGGGAATAGAACCTTGTAATAGATTTGAATGAAGATCCAAGTAAGTC
18619 AACTTGGA
65 AACTTGGA
* *
18627 TAAGTTCCCAATCTCTTGGGGAATAGAACCTTGTAATCGATTTGAATGAAGATCCAAGTA
1 TAAATTCCCAATCTCTTGGGGAATAGAACCTTGTAATAGATTTGAATGAAGATCCAAGTA
18687 TCCCAAGAGA
Statistics
Matches: 114, Mismatches: 14, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
71 1 0.01
72 110 0.96
73 3 0.03
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.28
Consensus pattern (72 bp):
TAAATTCCCAATCTCTTGGGGAATAGAACCTTGTAATAGATTTGAATGAAGATCCAAGTAAGTCA
ACTTGGA
Found at i:26783 original size:29 final size:28
Alignment explanation
Indices: 26745--26847 Score: 120
Period size: 29 Copynumber: 3.6 Consensus size: 28
26735 CCCTTTCATT
*
26745 TAAGCACCTAAAGTATTTGTTAGTCAAAA
1 TAAGTACCTAAAGTATTT-TTAGTCAAAA
* *
26774 TAAGTACCTAAAATTATTTTTTGTCAAAA
1 TAAGTACCT-AAAGTATTTTTAGTCAAAA
26803 TAAGTACCTAAAGTA-TTTTATGTCAAAA
1 TAAGTACCTAAAGTATTTTTA-GTCAAAA
*
26831 T-AGATACCTAAACTATT
1 TAAG-TACCTAAAGTATT
26848 CACACTTTTT
Statistics
Matches: 64, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
27 6 0.09
28 23 0.36
29 27 0.42
30 8 0.12
ACGTcount: A:0.42, C:0.13, G:0.10, T:0.36
Consensus pattern (28 bp):
TAAGTACCTAAAGTATTTTTAGTCAAAA
Found at i:26828 original size:28 final size:27
Alignment explanation
Indices: 26745--26847 Score: 118
Period size: 28 Copynumber: 3.6 Consensus size: 27
26735 CCCTTTCATT
*
26745 TAAGCACCTAAAGTATTTGTTAGTCAAAA
1 TAAGTACCTAAAGTATTT-TT-GTCAAAA
*
26774 TAAGTACCTAAAATTATTTTTTGTCAAAA
1 TAAGTACCT-AAAGTA-TTTTTGTCAAAA
26803 TAAGTACCTAAAGTATTTTATGTCAAAA
1 TAAGTACCTAAAGTATTTT-TGTCAAAA
*
26831 T-AGATACCTAAACTATT
1 TAAG-TACCTAAAGTATT
26848 CACACTTTTT
Statistics
Matches: 66, Mismatches: 4, Indels: 9
0.84 0.05 0.11
Matches are distributed among these distances:
27 6 0.09
28 26 0.39
29 24 0.36
30 7 0.11
31 3 0.05
ACGTcount: A:0.42, C:0.13, G:0.10, T:0.36
Consensus pattern (27 bp):
TAAGTACCTAAAGTATTTTTGTCAAAA
Found at i:29228 original size:19 final size:19
Alignment explanation
Indices: 29190--29228 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
29180 ATTGATTAAC
* **
29190 AAAATTAATATTTTCGGTA
1 AAAAATAATATTTTAAGTA
29209 AAAAATAATATTTTAAGTA
1 AAAAATAATATTTTAAGTA
29228 A
1 A
29229 TATTTTATCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.51, C:0.03, G:0.08, T:0.38
Consensus pattern (19 bp):
AAAAATAATATTTTAAGTA
Found at i:29541 original size:30 final size:30
Alignment explanation
Indices: 29506--29610 Score: 95
Period size: 32 Copynumber: 3.4 Consensus size: 30
29496 CGAGAATATT
29506 ATAATAAATAAATTTATAAGATTATTA-AAA
1 ATAATAAATAAATTTATAA-ATTATTACAAA
* * * *
29536 ATAATAATTAAATTTATTAATTTGTTATAAA
1 ATAATAAATAAATTTA-TAAATTATTACAAA
* *
29567 ATAATCATTAAATTTTAATAAATTATTACAAA
1 ATAATAAATAAA-TTT-ATAAATTATTACAAA
* *
29599 ATGATTAATAAA
1 ATAATAAATAAA
29611 GTCACCGACT
Statistics
Matches: 61, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
30 20 0.33
31 17 0.28
32 23 0.38
33 1 0.02
ACGTcount: A:0.54, C:0.02, G:0.03, T:0.41
Consensus pattern (30 bp):
ATAATAAATAAATTTATAAATTATTACAAA
Found at i:29571 original size:31 final size:30
Alignment explanation
Indices: 29506--29600 Score: 95
Period size: 30 Copynumber: 3.1 Consensus size: 30
29496 CGAGAATATT
*
29506 ATAATAAATAAATTTATAAGATTATTAAAA
1 ATAATAATTAAATTTATAAGATTATTAAAA
* *
29536 ATAATAATTAAATTTATTAA-TTTGTTATAAA
1 ATAATAATTAAATTTA-TAAGATTATTA-AAA
*
29567 ATAATCATTAAATTTTAATAA-ATTATTACAAA
1 ATAATAATTAAA-TTT-ATAAGATTATTA-AAA
29599 AT
1 AT
29601 GATTAATAAA
Statistics
Matches: 54, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
30 20 0.37
31 17 0.31
32 16 0.30
33 1 0.02
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (30 bp):
ATAATAATTAAATTTATAAGATTATTAAAA
Found at i:30436 original size:176 final size:176
Alignment explanation
Indices: 30142--30491 Score: 691
Period size: 176 Copynumber: 2.0 Consensus size: 176
30132 AAGGGAATCA
30142 AATGTTCCAATGGTCGTAGACGCGGTATGTAATCAGTAACTACAAGTATGCTACACTGTCGGGTG
1 AATGTTCCAATGGTCGTAGACGCGGTATGTAATCAGTAACTACAAGTATGCTACACTGTCGGGTG
30207 AAGATTCATGCTCGAAATACCAGTTGCTATCCTTCTTTGGGAGGGAGATCGGGTGTGGGGATAAT
66 AAGATTCATGCTCGAAATACCAGTTGCTATCCTTCTTTGGGAGGGAGATCGGGTGTGGGGATAAT
30272 GTTTATGAATTTGCTGCTGATTTTCCTATTGTTACCATAACCTCCT
131 GTTTATGAATTTGCTGCTGATTTTCCTATTGTTACCATAACCTCCT
30318 AATGTTCCAATGGTCGTAGACGCGGTATGTAATCAGTAACTACAAGTATGCTACACTGTCGGGTG
1 AATGTTCCAATGGTCGTAGACGCGGTATGTAATCAGTAACTACAAGTATGCTACACTGTCGGGTG
*
30383 AAGATTCATGCTCGAAATACCAGTTGCTATCCTTCTTTGGGTGGGAGATCGGGTGTGGGGATAAT
66 AAGATTCATGCTCGAAATACCAGTTGCTATCCTTCTTTGGGAGGGAGATCGGGTGTGGGGATAAT
30448 GTTTATGAATTTGCTGCTGATTTTCCTATTGTTACCATAACCTC
131 GTTTATGAATTTGCTGCTGATTTTCCTATTGTTACCATAACCTC
30492 ATAGGACGGA
Statistics
Matches: 173, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
176 173 1.00
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (176 bp):
AATGTTCCAATGGTCGTAGACGCGGTATGTAATCAGTAACTACAAGTATGCTACACTGTCGGGTG
AAGATTCATGCTCGAAATACCAGTTGCTATCCTTCTTTGGGAGGGAGATCGGGTGTGGGGATAAT
GTTTATGAATTTGCTGCTGATTTTCCTATTGTTACCATAACCTCCT
Found at i:30922 original size:2 final size:2
Alignment explanation
Indices: 30915--30948 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
30905 TTGAGTGTAT
30915 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
30949 CACACACATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:43312 original size:19 final size:19
Alignment explanation
Indices: 43288--43325 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
43278 AGTCTGTTTT
43288 GGCAAGAATTAATGAAGCA
1 GGCAAGAATTAATGAAGCA
43307 GGCAAGAATTAATGAAGCA
1 GGCAAGAATTAATGAAGCA
43326 ATTGGGTTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.47, C:0.11, G:0.26, T:0.16
Consensus pattern (19 bp):
GGCAAGAATTAATGAAGCA
Found at i:54540 original size:60 final size:59
Alignment explanation
Indices: 54433--54605 Score: 181
Period size: 60 Copynumber: 2.9 Consensus size: 59
54423 AGTATATAAC
* * * * *
54433 TATAGCTT-GGGATGAAATTAGAATGTTCAAAAAGCTTGGGATCAATTTAGAATGA-AGGT
1 TATAGTTTAGGGATGAAATTAAAATATTCAAAAA-TTTGGGATCAATTTAAAATGATA-GT
*
54492 TATAGTTTAGGGATAAAATTAAAATATTCAAAAATTTGAGGA-CTAATTTAAAATGATAGT
1 TATAGTTTAGGGATGAAATTAAAATATTCAAAAATTTG-GGATC-AATTTAAAATGATAGT
* * * * *
54552 CATAGTTTAGGGATGATATTAAAATATTTAAAAATTTAGGGGTTAATTTAAAAT
1 TATAGTTTAGGGATGAAATTAAAATATTCAAAAATTT-GGGATCAATTTAAAAT
54606 AAAGGACATA
Statistics
Matches: 96, Mismatches: 12, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
59 11 0.11
60 83 0.86
61 2 0.02
ACGTcount: A:0.42, C:0.04, G:0.19, T:0.35
Consensus pattern (59 bp):
TATAGTTTAGGGATGAAATTAAAATATTCAAAAATTTGGGATCAATTTAAAATGATAGT
Found at i:55593 original size:30 final size:30
Alignment explanation
Indices: 55532--55629 Score: 108
Period size: 30 Copynumber: 3.1 Consensus size: 30
55522 AAAAAAATTG
*
55532 AATACTTTAGGTATCTATTTTGATCAAAAA
1 AATACTTTAGGTACCTATTTTGATCAAAAA
55562 AATACTTTAGGTACCTATTTTGA-CAAAAAAAAA
1 AATACTTTAGGTACCTATTTTGATC----AAAAA
* *
55595 AGATAACTTTAGATACTTATTTTGATCAAAAA
1 A-AT-ACTTTAGGTACCTATTTTGATCAAAAA
55627 AAT
1 AAT
55630 TTATATACTT
Statistics
Matches: 58, Mismatches: 3, Indels: 13
0.78 0.04 0.18
Matches are distributed among these distances:
29 1 0.02
30 22 0.38
31 2 0.03
32 6 0.10
33 6 0.10
34 2 0.03
35 18 0.31
36 1 0.02
ACGTcount: A:0.45, C:0.10, G:0.09, T:0.36
Consensus pattern (30 bp):
AATACTTTAGGTACCTATTTTGATCAAAAA
Found at i:55595 original size:34 final size:36
Alignment explanation
Indices: 55557--55628 Score: 103
Period size: 35 Copynumber: 2.1 Consensus size: 36
55547 TATTTTGATC
*
55557 AAAAAAAT-ACTTTAGGTACCTATTTTGA-CAAAAA
1 AAAAAAATAACTTTAGATACCTATTTTGATCAAAAA
* *
55591 AAAAAGATAACTTTAGATACTTATTTTGATCAAAAA
1 AAAAAAATAACTTTAGATACCTATTTTGATCAAAAA
55627 AA
1 AA
55629 TTTATATACT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
34 7 0.21
35 18 0.55
36 8 0.24
ACGTcount: A:0.51, C:0.10, G:0.08, T:0.31
Consensus pattern (36 bp):
AAAAAAATAACTTTAGATACCTATTTTGATCAAAAA
Found at i:57773 original size:59 final size:60
Alignment explanation
Indices: 57710--57823 Score: 135
Period size: 60 Copynumber: 1.9 Consensus size: 60
57700 GATGAAATCA
*
57710 AAATGATCAAAAAATTAGAG-ACCAATTTAG-ATGA-AGGTCATAGTTTGAGGATGAAAATG
1 AAATGATC-AAAAATTAGAGAACCAATTTAGAATGATA-GTCATAGTTTAAGGATGAAAATG
* * * * *
57769 AAATGCTCAAAAGTTTGAGAACTAATTTAGAATGATATTCATAGTTTAAGGATGA
1 AAATGATCAAAAATTAGAGAACCAATTTAGAATGATAGTCATAGTTTAAGGATGA
57824 CATTAGAATG
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
58 9 0.20
59 16 0.35
60 20 0.43
61 1 0.02
ACGTcount: A:0.44, C:0.07, G:0.20, T:0.29
Consensus pattern (60 bp):
AAATGATCAAAAATTAGAGAACCAATTTAGAATGATAGTCATAGTTTAAGGATGAAAATG
Found at i:59656 original size:14 final size:14
Alignment explanation
Indices: 59637--59673 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
59627 TTCTGCATAA
59637 GGACAGCTGGCACT
1 GGACAGCTGGCACT
59651 GGACAGCTGGCACT
1 GGACAGCTGGCACT
59665 GGACAGCTG
1 GGACAGCTG
59674 TCTCTGCACG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.22, C:0.27, G:0.38, T:0.14
Consensus pattern (14 bp):
GGACAGCTGGCACT
Done.