Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003830.1 Hibiscus syriacus cultivar Beakdansim tig00008210_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: 87000
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:1997 original size:41 final size:41
Alignment explanation
Indices: 1972--2152 Score: 224
Period size: 41 Copynumber: 4.4 Consensus size: 41
1962 CTAAAAGTCG
* *
1972 TACTTTAGTTGCATTTATTTGACAAACGCCGCTAAATA-CTCA
1 TACTTTAGTGGCATTT-TTTGACAAACGCCGCTAAA-ACCTAA
*
2014 TACTTTAGTGGCATTTTTAGACAAAC-CCGCTAAAACCTAA
1 TACTTTAGTGGCATTTTTTGACAAACGCCGCTAAAACCTAA
* * *
2054 TACTTTAGTGGCGTTTTTTGTA-AAACGCCACTAAAACCTAG
1 TACTTTAGTGGCATTTTTTG-ACAAACGCCGCTAAAACCTAA
* * *
2095 TACTCTAGTGGCATTTTTTGACAAACGCTGCTAAAACCTAG
1 TACTTTAGTGGCATTTTTTGACAAACGCCGCTAAAACCTAA
*
2136 CACTTTAGTGGCATTTT
1 TACTTTAGTGGCATTTT
2153 AAGAAAAAAA
Statistics
Matches: 122, Mismatches: 13, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
39 1 0.01
40 34 0.28
41 72 0.59
42 15 0.12
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.34
Consensus pattern (41 bp):
TACTTTAGTGGCATTTTTTGACAAACGCCGCTAAAACCTAA
Found at i:2058 original size:82 final size:82
Alignment explanation
Indices: 1972--2187 Score: 249
Period size: 82 Copynumber: 2.6 Consensus size: 82
1962 CTAAAAGTCG
* * *
1972 TACTTTAGTTGCATTTATTTGACAAACGCCGCTAAATACTCATACTTTAGTGGCATTTTTAGACA
1 TACTTTAGTGGCATTT-TTTGAAAAACGCCACTAAATACTCATACTTTAGTGGCATTTTTAGACA
2037 AAC-CCGCTAAAACCTAA
65 AACGCCGCTAAAACCTAA
* * * *
2054 TACTTTAGTGGCGTTTTTTGTAAAACGCCACTAAA-AC-CTAGTACTCTAGTGGCATTTTTTGAC
1 TACTTTAGTGGCATTTTTTGAAAAACGCCACTAAATACTC-A-TACTTTAGTGGCATTTTTAGAC
* *
2117 AAACGCTGCTAAAACCTAG
64 AAACGCCGCTAAAACCTAA
* ** **
2136 CACTTTAGTGGCATTTTAAGAAAAAAAACCACTAAATACTCATACTTTAGTG
1 TACTTTAGTGGCATTTTTTG-AAAAACGCCACTAAATACTCATACTTTAGTG
2188 ACGTTTGTAT
Statistics
Matches: 111, Mismatches: 17, Indels: 11
0.80 0.12 0.08
Matches are distributed among these distances:
79 1 0.01
80 3 0.03
81 40 0.36
82 42 0.38
83 21 0.19
84 3 0.03
85 1 0.01
ACGTcount: A:0.33, C:0.20, G:0.14, T:0.32
Consensus pattern (82 bp):
TACTTTAGTGGCATTTTTTGAAAAACGCCACTAAATACTCATACTTTAGTGGCATTTTTAGACAA
ACGCCGCTAAAACCTAA
Found at i:13358 original size:7 final size:7
Alignment explanation
Indices: 13346--13375 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
13336 GACCCGACCC
13346 GACCGTT
1 GACCGTT
13353 GACCGTT
1 GACCGTT
13360 -ACCGTT
1 GACCGTT
13366 GACCGTT
1 GACCGTT
13373 GAC
1 GAC
13376 TTTCTTTGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.17, C:0.30, G:0.27, T:0.27
Consensus pattern (7 bp):
GACCGTT
Found at i:13365 original size:13 final size:13
Alignment explanation
Indices: 13347--13372 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
13337 ACCCGACCCG
13347 ACCGTTGACCGTT
1 ACCGTTGACCGTT
13360 ACCGTTGACCGTT
1 ACCGTTGACCGTT
13373 GACTTTCTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.31, G:0.23, T:0.31
Consensus pattern (13 bp):
ACCGTTGACCGTT
Found at i:17328 original size:24 final size:24
Alignment explanation
Indices: 17296--17364 Score: 67
Period size: 24 Copynumber: 3.0 Consensus size: 24
17286 TAGTGCATCG
17296 ATGTATAAGGAGTGCATCGATGCAC
1 ATGT-TAAGGAGTGCATCGATGCAC
*
17321 ATGTTAAGG-GATGCATCGATACAC
1 ATGTTAAGGAG-TGCATCGATGCAC
*
17345 -TG-T-A-GAATGCATCGATGCAC
1 ATGTTAAGGAGTGCATCGATGCAC
17365 TTCAAGGGGA
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
20 13 0.33
21 1 0.03
22 1 0.03
23 3 0.08
24 17 0.44
25 4 0.10
ACGTcount: A:0.32, C:0.17, G:0.26, T:0.25
Consensus pattern (24 bp):
ATGTTAAGGAGTGCATCGATGCAC
Found at i:21043 original size:13 final size:13
Alignment explanation
Indices: 21025--21050 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
21015 CTTTTACGTG
21025 AAGAAGAAGAAGA
1 AAGAAGAAGAAGA
21038 AAGAAGAAGAAGA
1 AAGAAGAAGAAGA
21051 GAACTCTGGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (13 bp):
AAGAAGAAGAAGA
Found at i:21538 original size:21 final size:21
Alignment explanation
Indices: 21514--21584 Score: 106
Period size: 21 Copynumber: 3.4 Consensus size: 21
21504 GTAAACTTTG
*
21514 GTTTATTATTATGGATTTCAA
1 GTTTATTGTTATGGATTTCAA
*
21535 GTTTCTTGTTATGGATTTCAA
1 GTTTATTGTTATGGATTTCAA
* *
21556 GTTTGTTGTTATGGATGTCAA
1 GTTTATTGTTATGGATTTCAA
21577 GTTTATTG
1 GTTTATTG
21585 GATAATGCTA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 45 1.00
ACGTcount: A:0.21, C:0.06, G:0.21, T:0.52
Consensus pattern (21 bp):
GTTTATTGTTATGGATTTCAA
Found at i:25802 original size:16 final size:17
Alignment explanation
Indices: 25778--25810 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
25768 ATTGAGTTTT
25778 TTTTATCACTAG-GTCG
1 TTTTATCACTAGCGTCG
*
25794 TTTTCTCACTAGCGTCG
1 TTTTATCACTAGCGTCG
25811 ATATAAATGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.42
Consensus pattern (17 bp):
TTTTATCACTAGCGTCG
Found at i:36181 original size:21 final size:21
Alignment explanation
Indices: 36151--36191 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
36141 AAATGTTAAA
* *
36151 AAATATTAATGTTTTAGGTAG
1 AAATAATAATGTTTAAGGTAG
36172 AAATAATAATGTTTAAGGTA
1 AAATAATAATGTTTAAGGTA
36192 CTTTTTACCG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.17, T:0.39
Consensus pattern (21 bp):
AAATAATAATGTTTAAGGTAG
Found at i:41481 original size:28 final size:28
Alignment explanation
Indices: 41441--41505 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 28
41431 TTTAAATCTA
*
41441 TAAATTTTTAAAACTTTT-AAGTACTCCC
1 TAAATTTTAAAAACTTTTAAAGTAC-CCC
* *
41469 TAAATTTTAAAAATTTTTAAATTACCCC
1 TAAATTTTAAAAACTTTTAAAGTACCCC
*
41497 TAAACTTTA
1 TAAATTTTA
41506 TCACCATATC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 27 0.84
29 5 0.16
ACGTcount: A:0.40, C:0.15, G:0.02, T:0.43
Consensus pattern (28 bp):
TAAATTTTAAAAACTTTTAAAGTACCCC
Found at i:46689 original size:39 final size:39
Alignment explanation
Indices: 46635--46714 Score: 160
Period size: 39 Copynumber: 2.1 Consensus size: 39
46625 GAAGTTACAT
46635 TGAACAGGATGAAGCACTTGGTCAGTGTATGGTTGGATA
1 TGAACAGGATGAAGCACTTGGTCAGTGTATGGTTGGATA
46674 TGAACAGGATGAAGCACTTGGTCAGTGTATGGTTGGATA
1 TGAACAGGATGAAGCACTTGGTCAGTGTATGGTTGGATA
46713 TG
1 TG
46715 CTGATTTCGA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.28, C:0.10, G:0.34, T:0.29
Consensus pattern (39 bp):
TGAACAGGATGAAGCACTTGGTCAGTGTATGGTTGGATA
Found at i:53018 original size:23 final size:23
Alignment explanation
Indices: 52990--53042 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
52980 ATCATTTTGG
*
52990 TTTTATGTCACA-TTTTCTTCTGT
1 TTTTATGACACATTTTTC-TCTGT
*
53013 TTTTATGACACGTTTTTCTCTGT
1 TTTTATGACACATTTTTCTCTGT
*
53036 CTTTATG
1 TTTTATG
53043 GTATATTTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 21 0.81
24 5 0.19
ACGTcount: A:0.13, C:0.17, G:0.11, T:0.58
Consensus pattern (23 bp):
TTTTATGACACATTTTTCTCTGT
Found at i:53701 original size:27 final size:28
Alignment explanation
Indices: 53658--53711 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 28
53648 CATTTGATCC
*
53658 TCATAATTTATATATTCTATCATATTAG
1 TCATAATTTATACATTCTATCATATTAG
53686 TCATAA-TTATACATTCTATCATATTA
1 TCATAATTTATACATTCTATCATATTA
53712 CTTGTGCAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 19 0.76
28 6 0.24
ACGTcount: A:0.37, C:0.13, G:0.02, T:0.48
Consensus pattern (28 bp):
TCATAATTTATACATTCTATCATATTAG
Found at i:54306 original size:19 final size:21
Alignment explanation
Indices: 54282--54322 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
54272 AATATTAAAT
54282 TAATTT-A-TATTTAAAAAAA
1 TAATTTAATTATTTAAAAAAA
*
54301 TAATTTAATTTTTTAAAAAAA
1 TAATTTAATTATTTAAAAAAA
54322 T
1 T
54323 TCAAACTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 6 0.32
20 1 0.05
21 12 0.63
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
TAATTTAATTATTTAAAAAAA
Found at i:54707 original size:60 final size:57
Alignment explanation
Indices: 54640--54775 Score: 139
Period size: 60 Copynumber: 2.3 Consensus size: 57
54630 ATGCATCACT
** * * ** *
54640 AAACTTTTGAACATTTTAATTTCATCCTTAAACTATGATTCTCATTCTAAATTGATCCCC
1 AAACTTTTGAACATTCCAAATTCATCCTCAAACTATGACCCTCAGTCTAAATT-A--CCC
** *
54700 AAACTTTT-AACAATTCCAAATTCATCCTCAAGTTATGACCCTTAGTCTAAATTACCC
1 AAACTTTTGAAC-ATTCCAAATTCATCCTCAAACTATGACCCTCAGTCTAAATTACCC
54757 AAACTTTTGAACATTCCAA
1 AAACTTTTGAACATTCCAA
54776 TAATATCCCC
Statistics
Matches: 64, Mismatches: 10, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
57 18 0.28
58 3 0.05
59 4 0.06
60 39 0.61
ACGTcount: A:0.35, C:0.24, G:0.05, T:0.37
Consensus pattern (57 bp):
AAACTTTTGAACATTCCAAATTCATCCTCAAACTATGACCCTCAGTCTAAATTACCC
Found at i:54911 original size:59 final size:60
Alignment explanation
Indices: 54810--54922 Score: 149
Period size: 59 Copynumber: 1.9 Consensus size: 60
54800 ATTTCAAAGT
* * *
54810 TGAAATTAGAATATTTAAAAGTTTGGGGATCAAATTAGAATGAA-AGCATAATTTGAGGA
1 TGAAATTAGAATATTCAAAAGTTTGGGCATCAAATTAAAATGAAGAGCATAATTTGAGGA
* * *
54869 TGAAATTAGGATATTCAAAAGTTTAGGGCCT-AATTTAAAATGAAGAGCATAATT
1 TGAAATTAGAATATTCAAAAGTTT-GGGCATCAAATTAAAATGAAGAGCATAATT
54923 CAAGGACATA
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
59 33 0.72
60 13 0.28
ACGTcount: A:0.43, C:0.05, G:0.20, T:0.31
Consensus pattern (60 bp):
TGAAATTAGAATATTCAAAAGTTTGGGCATCAAATTAAAATGAAGAGCATAATTTGAGGA
Found at i:66769 original size:21 final size:21
Alignment explanation
Indices: 66743--66807 Score: 64
Period size: 21 Copynumber: 3.1 Consensus size: 21
66733 GTTTTAAGTT
66743 AGAGTTTAGGGTTTAGAATTA
1 AGAGTTTAGGGTTTAGAATTA
* *
66764 AGAG-TTATGGTTTAAGATTTA
1 AGAGTTTAGGGTTT-AGAATTA
*
66785 ATA-TTTAGGGTTTTA-AATTA
1 AGAGTTTAGGG-TTTAGAATTA
66805 AGA
1 AGA
66808 TTAAAGTATA
Statistics
Matches: 35, Mismatches: 6, Indels: 7
0.73 0.12 0.15
Matches are distributed among these distances:
20 14 0.40
21 18 0.51
22 3 0.09
ACGTcount: A:0.35, C:0.00, G:0.23, T:0.42
Consensus pattern (21 bp):
AGAGTTTAGGGTTTAGAATTA
Found at i:69409 original size:51 final size:51
Alignment explanation
Indices: 69343--69461 Score: 148
Period size: 51 Copynumber: 2.3 Consensus size: 51
69333 TGATTTTAAA
* * *
69343 TTAAAGTGGTATAGGGTTCGATAAGGTGAAAATGGTGAAGGATTTTGTAGG
1 TTAAAGTGGTTTAGGGTTCGATAAGGTGAAAATGGTCAAGGATTGTGTAGG
* *** * * *
69394 TTAAAGTAGTTTAGGGTTTTTTAAGGTGAGAGTGGTCAAGGGTTGTGTAGG
1 TTAAAGTGGTTTAGGGTTCGATAAGGTGAAAATGGTCAAGGATTGTGTAGG
69445 TTAAAGTGGTTTAGGGT
1 TTAAAGTGGTTTAGGGT
69462 AAGGTTCGAT
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
51 57 1.00
ACGTcount: A:0.27, C:0.02, G:0.36, T:0.35
Consensus pattern (51 bp):
TTAAAGTGGTTTAGGGTTCGATAAGGTGAAAATGGTCAAGGATTGTGTAGG
Found at i:69413 original size:25 final size:25
Alignment explanation
Indices: 69385--69461 Score: 82
Period size: 25 Copynumber: 3.0 Consensus size: 25
69375 TGGTGAAGGA
*
69385 TTTTGTAGGTTAAAGTAGTTTAGGG
1 TTTTGTAGGTTAAAGTGGTTTAGGG
* * * **
69410 TTTTTTAAGGTGAGAGTGGTCAAGGG
1 TTTTGT-AGGTTAAAGTGGTTTAGGG
*
69436 TTGTGTAGGTTAAAGTGGTTTAGGG
1 TTTTGTAGGTTAAAGTGGTTTAGGG
69461 T
1 T
69462 AAGGTTCGAT
Statistics
Matches: 39, Mismatches: 12, Indels: 2
0.74 0.23 0.04
Matches are distributed among these distances:
25 21 0.54
26 18 0.46
ACGTcount: A:0.22, C:0.01, G:0.36, T:0.40
Consensus pattern (25 bp):
TTTTGTAGGTTAAAGTGGTTTAGGG
Found at i:72994 original size:21 final size:21
Alignment explanation
Indices: 72970--73009 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
72960 GAATCAGTCA
72970 TTCAAATATATTAATTATTCT
1 TTCAAATATATTAATTATTCT
72991 TTCAAATATATTAATTATT
1 TTCAAATATATTAATTATT
73010 ATTTAAGGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (21 bp):
TTCAAATATATTAATTATTCT
Found at i:73805 original size:21 final size:21
Alignment explanation
Indices: 73781--73833 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
73771 AAAACCCTGT
*
73781 GGGCTAGGAATATAACATTGC
1 GGGCTAGGAATATAACACTGC
* *
73802 GGGCT-GGATATATACCACTGT
1 GGGCTAGGA-ATATAACACTGC
73823 GGGCTAGGAAT
1 GGGCTAGGAAT
73834 GCAAGCATGC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 3 0.11
21 21 0.78
22 3 0.11
ACGTcount: A:0.28, C:0.15, G:0.32, T:0.25
Consensus pattern (21 bp):
GGGCTAGGAATATAACACTGC
Done.