Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002976.1 Hibiscus syriacus cultivar Beakdansim tig00006155_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: 73464
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:8233 original size:20 final size:20
Alignment explanation
Indices: 8196--8233 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
8186 TTCCTAGATT
*
8196 AATTATTTTTTTATAAAAAC
1 AATTATTTTATTATAAAAAC
8216 AATTAATTTTATTA-AAAA
1 AATT-ATTTTATTATAAAA
8234 TAAAAAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (20 bp):
AATTATTTTATTATAAAAAC
Found at i:16994 original size:2 final size:2
Alignment explanation
Indices: 16987--17020 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
16977 GAACGATTTA
16987 AT AT 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 AT AT
17021 GTGGAAGTTT
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):
AT
Found at i:17553 original size:38 final size:36
Alignment explanation
Indices: 17473--17553 Score: 90
Period size: 38 Copynumber: 2.2 Consensus size: 36
17463 TAACAAGTTG
* * *
17473 AAAAATATTTATATATTTTCTTAAAAAATTTAAATT
1 AAAAAAATTTATATATTTTCTTAAAAAATTGAAAAT
* *
17509 AAAAAAATTTATATAATTTTTTTTACAAAATTGAAAAT
1 AAAAAAATTTATAT-A-TTTTCTTAAAAAATTGAAAAT
*
17547 ATAAAAA
1 AAAAAAA
17554 GGTTTAATGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
36 13 0.35
37 1 0.03
38 23 0.62
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.42
Consensus pattern (36 bp):
AAAAAAATTTATATATTTTCTTAAAAAATTGAAAAT
Found at i:18969 original size:51 final size:50
Alignment explanation
Indices: 18864--18973 Score: 130
Period size: 51 Copynumber: 2.2 Consensus size: 50
18854 TTTACATCGG
* * ***
18864 TGTAAGTATTTATTAAGTAATACATTATTTATTTTATTTACTTACACTGG
1 TGTAAGTATTTATTAAGTAATACATTATTTATTTTATTAAATTACACCAA
* ** *
18914 TGTAAGTATTTATTAAGTGATATGTTTTTTTATTTTATTAAATTACACCAA
1 TGTAAGTATTTATTAAGTAATA-CATTATTTATTTTATTAAATTACACCAA
18965 TGTAAGTAT
1 TGTAAGTAT
18974 ATGTTATGTG
Statistics
Matches: 50, Mismatches: 9, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
50 21 0.42
51 29 0.58
ACGTcount: A:0.33, C:0.06, G:0.11, T:0.50
Consensus pattern (50 bp):
TGTAAGTATTTATTAAGTAATACATTATTTATTTTATTAAATTACACCAA
Found at i:19690 original size:18 final size:19
Alignment explanation
Indices: 19652--19701 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
19642 AATTTAGACT
19652 ATAACAAAAATATAAAAATA
1 ATAA-AAAAATATAAAAATA
**
19672 A-AAAAAAATATAATTATA
1 ATAAAAAAATATAAAAATA
*
19690 ATAAAAACATAT
1 ATAAAAAAATAT
19702 TATATATAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
18 14 0.54
19 11 0.42
20 1 0.04
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.24
Consensus pattern (19 bp):
ATAAAAAAATATAAAAATA
Found at i:19695 original size:17 final size:17
Alignment explanation
Indices: 19651--19710 Score: 50
Period size: 17 Copynumber: 3.5 Consensus size: 17
19641 CAATTTAGAC
* *
19651 TATAACAAAAATATAAA
1 TATAATAAAAATATAAT
* *
19668 AATAAAAAAAAATATAAT
1 TAT-AATAAAAATATAAT
*
19686 TATAATAAAAACAT-AT
1 TATAATAAAAATATAAT
19702 TATATATAA
1 TATA-ATAA
19711 CTCACTATTA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
16 6 0.17
17 15 0.43
18 14 0.40
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.28
Consensus pattern (17 bp):
TATAATAAAAATATAAT
Found at i:24279 original size:6 final size:6
Alignment explanation
Indices: 24268--24293 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
24258 CTATATTGTT
24268 TTTAAA TTTAAA TTTAAA TTTAAA TT
1 TTTAAA TTTAAA TTTAAA TTTAAA TT
24294 AATTATATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:29412 original size:64 final size:63
Alignment explanation
Indices: 29330--29486 Score: 174
Period size: 64 Copynumber: 2.5 Consensus size: 63
29320 TTCAGTGTGT
* *
29330 ATCGATGCACAGGAAGTGCATCGATGCACCCATTAAAAAT-AGAAACATCGAATGCAATTAGTGC
1 ATCGATGCATAGGAAGTGCATCGATGCACCCATT-AAAATGA-AAACATCGAAGGCAATTAGTGC
* * ** * *
29394 ATCGATGCATAAGG-AGTGCATTGATGCACCCCCTTAAAATGAAAACATCGAAGGTGATTTGTGT
1 ATCGATGCAT-AGGAAGTGCATCGATGCA-CCCATTAAAATGAAAACATCGAAGGCAATTAGTGC
* *
29458 ATCGATGCATGGGTAGTGCATCGATGCAC
1 ATCGATGCATAGGAAGTGCATCGATGCAC
29487 TTCAAAGGAA
Statistics
Matches: 79, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
63 3 0.04
64 67 0.85
65 9 0.11
ACGTcount: A:0.34, C:0.19, G:0.24, T:0.24
Consensus pattern (63 bp):
ATCGATGCATAGGAAGTGCATCGATGCACCCATTAAAATGAAAACATCGAAGGCAATTAGTGC
Found at i:30394 original size:2 final size:2
Alignment explanation
Indices: 30387--30424 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
30377 GAACATGTGA
30387 AT AT AT AT 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 AT AT AT AT
30425 GATAAGACAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30839 original size:23 final size:23
Alignment explanation
Indices: 30804--30866 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
30794 AACCTTATAT
*
30804 GGCACTTCAGTGCATTTCTACGC
1 GGCACTTCGGTGCATTTCTACGC
* * *
30827 GGCACTACGGTGCAATTCTACGT
1 GGCACTTCGGTGCATTTCTACGC
30850 GGCACTTCGGTGCATTT
1 GGCACTTCGGTGCATTT
30867 ATATGAACTG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.17, C:0.27, G:0.25, T:0.30
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACGC
Found at i:38396 original size:77 final size:78
Alignment explanation
Indices: 38251--38396 Score: 190
Period size: 77 Copynumber: 1.9 Consensus size: 78
38241 AGGGGTAATT
* *
38251 CATTTTATTAATAAAAAATATTAACATTTCAGATCGCAACCTATTTCTTAATGAATCATGATAAT
1 CATTTTATTAATAAAAAATATTAACATTTAAGATCGCAACCTATTTCTTAATGAATCATGACAAT
38316 TTTAGGTATAACC
66 TTTAGGTATAACC
* * * *
38329 CATTTTATTAAT-AAAAATATTAACATTCTAAGA-CGTAACTTATTTTTTAGTGAA-CTATGACA
1 CATTTTATTAATAAAAAATATTAACATT-TAAGATCGCAACCTATTTCTTAATGAATC-ATGACA
*
38391 TTTTTA
64 ATTTTA
38397 ACCTATTATG
Statistics
Matches: 59, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
76 1 0.02
77 42 0.71
78 16 0.27
ACGTcount: A:0.39, C:0.12, G:0.08, T:0.41
Consensus pattern (78 bp):
CATTTTATTAATAAAAAATATTAACATTTAAGATCGCAACCTATTTCTTAATGAATCATGACAAT
TTTAGGTATAACC
Found at i:43141 original size:22 final size:21
Alignment explanation
Indices: 43116--43178 Score: 83
Period size: 22 Copynumber: 3.0 Consensus size: 21
43106 ACAAATCACA
*
43116 ATTTGATAATTTTAAAAAATTT
1 ATTT-ATAATTTTAAAAAAATT
*
43138 ATTTAAAATTTTAAAAAAAATT
1 ATTTATAATTTT-AAAAAAATT
43160 ATTTAT-ATTTTAAAAAAAT
1 ATTTATAATTTTAAAAAAAT
43179 ATAAAATTCT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 8 0.22
21 12 0.32
22 17 0.46
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (21 bp):
ATTTATAATTTTAAAAAAATT
Found at i:43148 original size:21 final size:20
Alignment explanation
Indices: 43123--43178 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 20
43113 ACAATTTGAT
*
43123 AATTTTAAAAAATTTATTTAA
1 AATTTTAAAAAAATTATTT-A
43144 AATTTTAAAAAAAATTATTTA
1 AATTTT-AAAAAAATTATTTA
*
43165 TATTTTAAAAAAAT
1 AATTTTAAAAAAAT
43179 ATAAAATTCT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
20 8 0.25
21 12 0.38
22 12 0.38
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
AATTTTAAAAAAATTATTTA
Found at i:46646 original size:36 final size:36
Alignment explanation
Indices: 46600--46702 Score: 161
Period size: 36 Copynumber: 2.9 Consensus size: 36
46590 AGTTGAGTAT
* *
46600 TATCAACTTTGATACATTCATGTATCAATGTTATCA
1 TATCAACTTTGGTACATTCGTGTATCAATGTTATCA
* * *
46636 TATTAGCTTTGGTACATTCGTATATCAATGTTATCA
1 TATCAACTTTGGTACATTCGTGTATCAATGTTATCA
46672 TATCAACTTTGGTACATTCGTGTATCAATGT
1 TATCAACTTTGGTACATTCGTGTATCAATGT
46703 CTAGCACTTT
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 59 1.00
ACGTcount: A:0.29, C:0.16, G:0.13, T:0.43
Consensus pattern (36 bp):
TATCAACTTTGGTACATTCGTGTATCAATGTTATCA
Found at i:54407 original size:18 final size:18
Alignment explanation
Indices: 54386--54427 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
54376 ATATTCATTA
54386 AGATTAAGCCATTCTATT
1 AGATTAAGCCATTCTATT
54404 AGATTAAGCCATTCTATT
1 AGATTAAGCCATTCTATT
54422 AGATTA
1 AGATTA
54428 TGAGAAATCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (18 bp):
AGATTAAGCCATTCTATT
Found at i:55718 original size:27 final size:27
Alignment explanation
Indices: 55680--55736 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
55670 AGGTGGAACA
55680 TCTTCTCAAAAGCATCTGCTTGTAAGC
1 TCTTCTCAAAAGCATCTGCTTGTAAGC
55707 TCTTCTCAAAAGCATCTGCTTGTAAGC
1 TCTTCTCAAAAGCATCTGCTTGTAAGC
55734 TCT
1 TCT
55737 CGGATAAACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.25, C:0.26, G:0.14, T:0.35
Consensus pattern (27 bp):
TCTTCTCAAAAGCATCTGCTTGTAAGC
Found at i:70977 original size:34 final size:34
Alignment explanation
Indices: 70929--70998 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 34
70919 TAAAAGTAAA
* * *
70929 AAATATCCAGAATTATAATAAAGAATTACAGTAT
1 AAATATCCAAAATTACAATAAAGAATTACAATAT
*
70963 AAATATCCAAAATTACAATAAAGATTTACAATAT
1 AAATATCCAAAATTACAATAAAGAATTACAATAT
70997 AA
1 AA
70999 TTTAAATGTA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.56, C:0.10, G:0.06, T:0.29
Consensus pattern (34 bp):
AAATATCCAAAATTACAATAAAGAATTACAATAT
Done.