Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004696.1 Hibiscus syriacus cultivar Beakdansim tig00010543_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: 59790
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:6210 original size:8 final size:8
Alignment explanation
Indices: 6194--6226 Score: 57
Period size: 8 Copynumber: 4.1 Consensus size: 8
6184 AACTTTGAAC
*
6194 GAAGTGAA
1 GAAGAGAA
6202 GAAGAGAA
1 GAAGAGAA
6210 GAAGAGAA
1 GAAGAGAA
6218 GAAGAGAA
1 GAAGAGAA
6226 G
1 G
6227 TGAGAGACAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.58, C:0.00, G:0.39, T:0.03
Consensus pattern (8 bp):
GAAGAGAA
Found at i:6899 original size:12 final size:12
Alignment explanation
Indices: 6882--6906 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
6872 TTAATTTGAA
6882 TATTTTTTTTTT
1 TATTTTTTTTTT
6894 TATTTTTTTTTT
1 TATTTTTTTTTT
6906 T
1 T
6907 TTAATTAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (12 bp):
TATTTTTTTTTT
Found at i:12496 original size:13 final size:13
Alignment explanation
Indices: 12478--12531 Score: 51
Period size: 13 Copynumber: 4.4 Consensus size: 13
12468 ATGAACGAAC
12478 ATAAACAAACACA
1 ATAAACAAACACA
*
12491 ATAAAC-GA-AC-
1 ATAAACAAACACA
* *
12501 GTAAACATACACA
1 ATAAACAAACACA
*
12514 ACAAACAAACACA
1 ATAAACAAACACA
12527 ATAAA
1 ATAAA
12532 TGTACATAAA
Statistics
Matches: 31, Mismatches: 7, Indels: 6
0.70 0.16 0.14
Matches are distributed among these distances:
10 5 0.16
11 3 0.10
12 3 0.10
13 20 0.65
ACGTcount: A:0.65, C:0.22, G:0.04, T:0.09
Consensus pattern (13 bp):
ATAAACAAACACA
Found at i:12505 original size:23 final size:23
Alignment explanation
Indices: 12461--12524 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 23
12451 ATGATAAAAG
*
12461 AACACAAATGAACGAACATAAACA
1 AACAC-AATAAACGAACATAAACA
*
12485 AACACAATAAACGAACGTAAACA
1 AACACAATAAACGAACATAAACA
* * *
12508 TACACAACAAACAAACA
1 AACACAATAAACGAACA
12525 CAATAAATGT
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
23 29 0.85
24 5 0.15
ACGTcount: A:0.62, C:0.23, G:0.06, T:0.08
Consensus pattern (23 bp):
AACACAATAAACGAACATAAACA
Found at i:13713 original size:18 final size:18
Alignment explanation
Indices: 13690--13731 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
13680 TTATATATAC
13690 TTAAAAAAATAAAAAAAA
1 TTAAAAAAATAAAAAAAA
* * *
13708 TTAAAAAATTAAAACATA
1 TTAAAAAAATAAAAAAAA
13726 TTAAAA
1 TTAAAA
13732 TTAATTGTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (18 bp):
TTAAAAAAATAAAAAAAA
Found at i:25932 original size:14 final size:14
Alignment explanation
Indices: 25911--25943 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
25901 TATATCCTAC
*
25911 CCCTAATTTA-AAA
1 CCCTAAATTATAAA
25924 CCCTAAATTATAAA
1 CCCTAAATTATAAA
25938 CCCTAA
1 CCCTAA
25944 GTTGAGTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.45, C:0.27, G:0.00, T:0.27
Consensus pattern (14 bp):
CCCTAAATTATAAA
Found at i:29773 original size:2 final size:2
Alignment explanation
Indices: 29766--29815 Score: 50
Period size: 2 Copynumber: 26.0 Consensus size: 2
29756 ACCGGGCCGA
* * * *
29766 AT AT AT AT AT AT TT AA AT -T AA AT AT AT AA AT AT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29806 AT AT AT AT AT
1 AT AT AT AT AT
29816 TAATTTAAAT
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
1 2 0.05
2 36 0.95
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:29806 original size:36 final size:37
Alignment explanation
Indices: 29766--29850 Score: 106
Period size: 36 Copynumber: 2.4 Consensus size: 37
29756 ACCGGGCCGA
29766 ATATATATATAT-TTAAATTAAATATATAA-ATATT-AT
1 ATATATATATATATTAAATTAAAT-TA-AATATATTAAT
* *
29802 ATATATATATATATTAATTTAAATTAAATTTATTAAT
1 ATATATATATATATTAAATTAAATTAAATATATTAAT
29839 AT-TATATATATA
1 ATATATATATATA
29851 ATAATTATTT
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
35 2 0.05
36 28 0.64
37 14 0.32
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (37 bp):
ATATATATATATATTAAATTAAATTAAATATATTAAT
Found at i:29807 original size:17 final size:17
Alignment explanation
Indices: 29767--29817 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
29757 CCGGGCCGAA
*
29767 TATATATATATTTAA-AT
1 TATATATATA-TAAATAT
29784 TA-A-ATATATAAATAT
1 TATATATATATAAATAT
*
29799 TATATATATATATATAT
1 TATATATATATAAATAT
29816 TA
1 TA
29818 ATTTAAATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
14 3 0.10
15 9 0.31
16 2 0.07
17 15 0.52
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TATATATATATAAATAT
Found at i:29822 original size:42 final size:42
Alignment explanation
Indices: 29766--29857 Score: 138
Period size: 42 Copynumber: 2.3 Consensus size: 42
29756 ACCGGGCCGA
29766 ATATATATA-T-ATTTAAATTAAATATATAAATATTATATAT
1 ATATATATATTAATTTAAATTAAATATATAAATATTATATAT
* *
29806 ATATATATATTAATTTAAATTAAATTTATTAATATTATATAT
1 ATATATATATTAATTTAAATTAAATATATAAATATTATATAT
29848 ATA-ATA-ATTA
1 ATATATATATTA
29858 TTTTTAATAT
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
40 13 0.27
41 4 0.08
42 31 0.65
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (42 bp):
ATATATATATTAATTTAAATTAAATATATAAATATTATATAT
Found at i:41042 original size:3 final size:3
Alignment explanation
Indices: 41034--41066 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
41024 TATCCTTGGA
41034 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
41067 TCGTTGAATC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:41802 original size:51 final size:51
Alignment explanation
Indices: 41726--42130 Score: 500
Period size: 51 Copynumber: 8.0 Consensus size: 51
41716 GGCGCAGACT
** * *
41726 CAGCAAGGTGGAAACA-CAGAGTCCCAAACATATACTCAACTACCTCAACAG
1 CAGCAAGGTGGAAACATTGGA-TCCCAAACATATACTCAGCTACCACAACAG
* * *
41777 CAGCAAGGTGGAAACTTTGGATCCCAAACATATACTCAGCTACCGCATCAG
1 CAGCAAGGTGGAAACATTGGATCCCAAACATATACTCAGCTACCACAACAG
* * *
41828 CGGCAAGGTGGAAACATTGGATCCCAAACATATACTCATCTACCAGAACAG
1 CAGCAAGGTGGAAACATTGGATCCCAAACATATACTCAGCTACCACAACAG
**
41879 CAGCAAGGTGGAAACATT-GATTCCCAAACATATACTGTGCTACCACAACAG
1 CAGCAAGGTGGAAACATTGGA-TCCCAAACATATACTCAGCTACCACAACAG
* * *
41930 CAGCAAGGTGGAAACATT-GATTCCCAAACATATACTCTGCTAGCACATCAG
1 CAGCAAGGTGGAAACATTGGA-TCCCAAACATATACTCAGCTACCACAACAG
* * * *
41981 CAGCAAGGTGGAAACAATGGAACCCAAACATATGCTCAGTTACCACAACAG
1 CAGCAAGGTGGAAACATTGGATCCCAAACATATACTCAGCTACCACAACAG
* * **
42032 CAGCAAGGTGGAAACATT-GATTCCCAGACATTTACTTTGCTA-C-C-ACAG
1 CAGCAAGGTGGAAACATTGGA-TCCCAAACATATACTCAGCTACCACAACAG
* *
42080 CAGCAAGGTGGAAAAATTGGTTCCCAAACATATACTCAGCTACCACAACAG
1 CAGCAAGGTGGAAACATTGGATCCCAAACATATACTCAGCTACCACAACAG
42131 ATCTTAATGT
Statistics
Matches: 305, Mismatches: 41, Indels: 16
0.84 0.11 0.04
Matches are distributed among these distances:
48 38 0.12
49 3 0.01
50 6 0.02
51 254 0.83
52 4 0.01
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.19
Consensus pattern (51 bp):
CAGCAAGGTGGAAACATTGGATCCCAAACATATACTCAGCTACCACAACAG
Found at i:42007 original size:153 final size:152
Alignment explanation
Indices: 41726--42126 Score: 558
Period size: 153 Copynumber: 2.6 Consensus size: 152
41716 GGCGCAGACT
** * **
41726 CAGCAAGGTGGAAACACAGAGTCCCAAACATATACTCAACTACCTCAACAGCAGCAAGGTGGAAA
1 CAGCAAGGTGGAAACATTGATTCCCAAACATATACTCTGCTACC-CAACAGCAGCAAGGTGGAAA
* * * * *
41791 CTTTGGA-TCCCAAACATATACTCAGCTACCGCATCAGCGGCAAGGTGGAAACATTGGATCCCAA
65 CATT-GATTCCCAAACATATACTCAGCTACCACATCAGCAGCAAGGTGGAAACAATGGAACCCAA
*
41855 ACATATACTCA-TCTACCAGAACAG
129 ACATATACTCAGT-TACCACAACAG
*
41879 CAGCAAGGTGGAAACATTGATTCCCAAACATATACTGTGCTACCACAACAGCAGCAAGGTGGAAA
1 CAGCAAGGTGGAAACATTGATTCCCAAACATATACTCTGCTACC-CAACAGCAGCAAGGTGGAAA
* *
41944 CATTGATTCCCAAACATATACTCTGCTAGCACATCAGCAGCAAGGTGGAAACAATGGAACCCAAA
65 CATTGATTCCCAAACATATACTCAGCTACCACATCAGCAGCAAGGTGGAAACAATGGAACCCAAA
*
42009 CATATGCTCAGTTACCACAACAG
130 CATATACTCAGTTACCACAACAG
* * * *
42032 CAGCAAGGTGGAAACATTGATTCCCAGACATTTACTTTGCTA-CC-ACAGCAGCAAGGTGGAAAA
1 CAGCAAGGTGGAAACATTGATTCCCAAACATATACTCTGCTACCCAACAGCAGCAAGGTGGAAAC
*
42095 ATTGGTTCCCAAACATATACTCAGCTACCACA
66 ATTGATTCCCAAACATATACTCAGCTACCACA
42127 ACAGATCTTA
Statistics
Matches: 223, Mismatches: 23, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
150 47 0.21
151 1 0.00
152 3 0.01
153 171 0.77
154 1 0.00
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.19
Consensus pattern (152 bp):
CAGCAAGGTGGAAACATTGATTCCCAAACATATACTCTGCTACCCAACAGCAGCAAGGTGGAAAC
ATTGATTCCCAAACATATACTCAGCTACCACATCAGCAGCAAGGTGGAAACAATGGAACCCAAAC
ATATACTCAGTTACCACAACAG
Found at i:54202 original size:25 final size:24
Alignment explanation
Indices: 54167--54227 Score: 61
Period size: 25 Copynumber: 2.5 Consensus size: 24
54157 TAAAATGGTT
* *
54167 CGGTTTGATTTGGTTTGGTTTTAAA
1 CGGTTTAATTTGGTTCGG-TTTAAA
54192 CGGTTTAATTTTTGGTTCGGTTTAAA
1 CGGTTTAA--TTTGGTTCGGTTTAAA
*
54218 -GGTTTCATTT
1 CGGTTTAATTT
54228 TTTTGATTCG
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
23 3 0.10
25 13 0.42
26 6 0.19
27 9 0.29
ACGTcount: A:0.16, C:0.07, G:0.25, T:0.52
Consensus pattern (24 bp):
CGGTTTAATTTGGTTCGGTTTAAA
Found at i:54228 original size:25 final size:27
Alignment explanation
Indices: 54175--54229 Score: 78
Period size: 25 Copynumber: 2.1 Consensus size: 27
54165 TTCGGTTTGA
*
54175 TTTGGTTTGGTTTTAAACGGTTTAATT
1 TTTGGTTCGGTTTTAAACGGTTTAATT
*
54202 TTTGGTTCGG-TTTAAA-GGTTTCATT
1 TTTGGTTCGGTTTTAAACGGTTTAATT
54227 TTT
1 TTT
54230 TTGATTCGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 11 0.42
26 6 0.23
27 9 0.35
ACGTcount: A:0.16, C:0.05, G:0.22, T:0.56
Consensus pattern (27 bp):
TTTGGTTCGGTTTTAAACGGTTTAATT
Found at i:54229 original size:26 final size:27
Alignment explanation
Indices: 54175--54240 Score: 73
Period size: 27 Copynumber: 2.4 Consensus size: 27
54165 TTCGGTTTGA
*
54175 TTTGGTTTGGTTTTAAACGGTTTA-ATT
1 TTTGGTTCGG-TTTAAACGGTTTATATT
*
54202 TTTGGTTCGGTTTAAA-GGTTTCATTTT
1 TTTGGTTCGGTTTAAACGGTTT-ATATT
*
54229 TTTGATTCGGTT
1 TTTGGTTCGGTT
54241 CGATTCAAGT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
25 5 0.15
26 7 0.21
27 22 0.65
ACGTcount: A:0.15, C:0.06, G:0.23, T:0.56
Consensus pattern (27 bp):
TTTGGTTCGGTTTAAACGGTTTATATT
Found at i:55386 original size:2 final size:2
Alignment explanation
Indices: 55379--55403 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
55369 TTTTGAGTTT
55379 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
55404 TTAGGGTGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.