Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005703.1 Hibiscus syriacus cultivar Beakdansim tig00013337_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: 73275
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.32
Found at i:12311 original size:27 final size:27
Alignment explanation
Indices: 12268--12335 Score: 77
Period size: 27 Copynumber: 2.6 Consensus size: 27
12258 AGTTAGAATT
* *
12268 TCAAGTAA--CCATAGAAAACAGTGCG
1 TCAAGTAATGCCATGGAAAACAGGGCG
* *
12293 TCAAGTAATGCCATGGAAATCAGGGTG
1 TCAAGTAATGCCATGGAAAACAGGGCG
*
12320 TCAAGTGATGCCATGG
1 TCAAGTAATGCCATGG
12336 TATAATAGAT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
25 8 0.22
27 28 0.78
ACGTcount: A:0.35, C:0.18, G:0.26, T:0.21
Consensus pattern (27 bp):
TCAAGTAATGCCATGGAAAACAGGGCG
Found at i:30930 original size:24 final size:24
Alignment explanation
Indices: 30902--30950 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
30892 AAATCTAGGA
*
30902 TGCAGCTTATATTA-CATAATCTTC
1 TGCAGCTCA-ATTACCATAATCTTC
*
30926 TGCAGCTCAATTACCATATTCTTC
1 TGCAGCTCAATTACCATAATCTTC
30950 T
1 T
30951 CTAGTTTCTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 4 0.18
24 18 0.82
ACGTcount: A:0.27, C:0.24, G:0.08, T:0.41
Consensus pattern (24 bp):
TGCAGCTCAATTACCATAATCTTC
Found at i:34144 original size:65 final size:65
Alignment explanation
Indices: 34067--34223 Score: 210
Period size: 65 Copynumber: 2.4 Consensus size: 65
34057 TACACCCATT
* *
34067 TCGAATGCATTTTGTGTACCGATGCACA-AGGCATGCATCGATGCACTCTTGAATATTTTGAAAC
1 TCGAATGCATTTTGTGTACCGATGCACAGA-CCATGCATCGATGCACTCCTGAATATTTTGAAAC
34131 A
65 A
* ** *
34132 TTGAATGCATTTTGTGTACCGATGCACAGACCATGCATCGATGCACTCCTGGCTCTTTTGAAACA
1 TCGAATGCATTTTGTGTACCGATGCACAGACCATGCATCGATGCACTCCTGAATATTTTGAAACA
* *
34197 TCGAATGTAATTAT-TGTACCGATGCAC
1 TCGAATG-CATTTTGTGTACCGATGCAC
34224 CCCTAGTGTA
Statistics
Matches: 81, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
65 76 0.94
66 5 0.06
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (65 bp):
TCGAATGCATTTTGTGTACCGATGCACAGACCATGCATCGATGCACTCCTGAATATTTTGAAACA
Found at i:38317 original size:15 final size:15
Alignment explanation
Indices: 38297--38327 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
38287 GAGAAGTAAA
38297 GTATGAACATTAGTT
1 GTATGAACATTAGTT
38312 GTATGAACATTAGTT
1 GTATGAACATTAGTT
38327 G
1 G
38328 AAAGACCTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.06, G:0.23, T:0.39
Consensus pattern (15 bp):
GTATGAACATTAGTT
Found at i:40060 original size:21 final size:22
Alignment explanation
Indices: 40013--40092 Score: 99
Period size: 23 Copynumber: 3.6 Consensus size: 22
40003 ACACTAGACA
40013 GTGCATCGATGCATCCCTTGAAT
1 GTGCATCGATGCAT-CCTTGAAT
* * *
40036 GTGCATCGATACAT-CATGAAG
1 GTGCATCGATGCATCCTTGAAT
*
40057 GTGCACCGATGCATTCCTTGAAT
1 GTGCATCGATGCA-TCCTTGAAT
40080 GTGCATCGATGCA
1 GTGCATCGATGCA
40093 CTCTGCTGTG
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
21 16 0.34
22 1 0.02
23 30 0.64
ACGTcount: A:0.25, C:0.24, G:0.24, T:0.28
Consensus pattern (22 bp):
GTGCATCGATGCATCCTTGAAT
Found at i:40508 original size:2 final size:2
Alignment explanation
Indices: 40501--40528 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
40491 TTTTGAAATA
40501 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
40529 TCAAAAATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:42040 original size:16 final size:15
Alignment explanation
Indices: 42014--42043 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
42004 ACTTAGGTTT
42014 TATGTTTTGGATTGA
1 TATGTTTTGGATTGA
42029 TATGTGTTTGGATTG
1 TATGT-TTTGGATTG
42044 TTTTATTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.17, C:0.00, G:0.30, T:0.53
Consensus pattern (15 bp):
TATGTTTTGGATTGA
Found at i:42867 original size:46 final size:46
Alignment explanation
Indices: 42817--42915 Score: 135
Period size: 46 Copynumber: 2.2 Consensus size: 46
42807 GCCATGCATT
* * *
42817 GATGCACTCTTGAATATTTTGAAACATCGAATGCATTTTGTGTACC
1 GATGCACTCCTGAATATTTTGAAACATCGAATGCAATTAGTGTACC
** * *
42863 GATGCACTCCTGGCTCTTTTGAAACATCGAATGTAATTAGTGTACC
1 GATGCACTCCTGAATATTTTGAAACATCGAATGCAATTAGTGTACC
42909 GATGCAC
1 GATGCAC
42916 CCCTAGTGTA
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.33
Consensus pattern (46 bp):
GATGCACTCCTGAATATTTTGAAACATCGAATGCAATTAGTGTACC
Found at i:43677 original size:21 final size:22
Alignment explanation
Indices: 43638--43682 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
43628 ATTTTTTTCA
* *
43638 ATGATGACATGATATTATC-TT
1 ATGATAACATGATAATATCATT
*
43659 ATGATAACATGTTAATATCATT
1 ATGATAACATGATAATATCATT
43681 AT
1 AT
43683 TATTTTTTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.38, C:0.09, G:0.11, T:0.42
Consensus pattern (22 bp):
ATGATAACATGATAATATCATT
Found at i:45611 original size:15 final size:16
Alignment explanation
Indices: 45588--45621 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
45578 TAAATAAACA
45588 TAAAGTTTAAAAAA-T
1 TAAAGTTTAAAAAAGT
*
45603 TAAATTTTAAAAAAGT
1 TAAAGTTTAAAAAAGT
45619 TAA
1 TAA
45622 TAAGAGACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (16 bp):
TAAAGTTTAAAAAAGT
Found at i:49558 original size:33 final size:34
Alignment explanation
Indices: 49513--49577 Score: 96
Period size: 33 Copynumber: 1.9 Consensus size: 34
49503 CTTTACAAAC
*
49513 TCCCTAGTTTTTCAC-GGGATAAGCTAGAACCTT
1 TCCCTAGCTTTTCACGGGGATAAGCTAGAACCTT
* *
49546 TCCCTAGCTTTTCACGGGGCTCAGCTAGAACC
1 TCCCTAGCTTTTCACGGGGATAAGCTAGAACC
49578 AAAACCCCTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 14 0.50
34 14 0.50
ACGTcount: A:0.22, C:0.29, G:0.20, T:0.29
Consensus pattern (34 bp):
TCCCTAGCTTTTCACGGGGATAAGCTAGAACCTT
Found at i:49967 original size:20 final size:20
Alignment explanation
Indices: 49942--49982 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
49932 TTGATTTTAC
*
49942 TGTAGCAGTATTGGTACCCA
1 TGTAGCAGTATTGATACCCA
49962 TGTAGCAGTATTGATACCCA
1 TGTAGCAGTATTGATACCCA
49982 T
1 T
49983 TTTTTCATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.32
Consensus pattern (20 bp):
TGTAGCAGTATTGATACCCA
Found at i:51033 original size:22 final size:22
Alignment explanation
Indices: 50987--51043 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 22
50977 AGTGCAAATA
*
50987 CACTTTCGTATTAGTGATGATG
1 CACTTTAGTATTAGTGATGATG
*
51009 CACTTTAGTATTAGTGTTG-TGG
1 CACTTTAGTATTAGTGATGAT-G
51031 CACTTTAGATATT
1 CACTTTAG-TATT
51044 TGATGGCAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
21 1 0.03
22 26 0.84
23 4 0.13
ACGTcount: A:0.23, C:0.12, G:0.21, T:0.44
Consensus pattern (22 bp):
CACTTTAGTATTAGTGATGATG
Found at i:51640 original size:17 final size:19
Alignment explanation
Indices: 51608--51647 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
51598 TGCCTTAATG
51608 TATAAGATTGCAT-AAAAC
1 TATAAGATTGCATAAAAAC
*
51626 TATAATATT-CATAAAAAC
1 TATAAGATTGCATAAAAAC
51644 TATA
1 TATA
51648 TAATGTCAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 3 0.15
18 17 0.85
ACGTcount: A:0.53, C:0.10, G:0.05, T:0.33
Consensus pattern (19 bp):
TATAAGATTGCATAAAAAC
Found at i:57744 original size:23 final size:23
Alignment explanation
Indices: 57696--57799 Score: 162
Period size: 23 Copynumber: 4.7 Consensus size: 23
57686 TTAGTGCAGA
*
57696 GGGAATCGA-TCCCCC-TTG-A-
1 GGGAACCGATTCCCCCTTTGAAG
*
57715 GGGAACCGATTCCCCCTCTGAAG
1 GGGAACCGATTCCCCCTTTGAAG
57738 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCCTTTGAAG
57761 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCCTTTGAAG
57784 GGGAACCGATTCCCCC
1 GGGAACCGATTCCCCC
57800 CCACAGGGGA
Statistics
Matches: 78, Mismatches: 3, Indels: 4
0.92 0.04 0.05
Matches are distributed among these distances:
19 8 0.10
20 6 0.08
21 2 0.03
22 1 0.01
23 61 0.78
ACGTcount: A:0.21, C:0.34, G:0.26, T:0.19
Consensus pattern (23 bp):
GGGAACCGATTCCCCCTTTGAAG
Found at i:57807 original size:22 final size:22
Alignment explanation
Indices: 57715--57822 Score: 128
Period size: 23 Copynumber: 4.8 Consensus size: 22
57705 TCCCCCTTGA
57715 GGGAACCGATTCCCCCTCTGAAG
1 GGGAACCGATTCCCCCTC-GAAG
*
57738 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCC-TCGAAG
*
57761 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCC-TCGAAG
*
57784 GGGAACCGATTCCCCC-CCACAG
1 GGGAACCGATTCCCCCTCGA-AG
* *
57806 GGGAATCGATACCCCCT
1 GGGAACCGATTCCCCCT
57823 AGGGTTCTAG
Statistics
Matches: 77, Mismatches: 5, Indels: 6
0.88 0.06 0.07
Matches are distributed among these distances:
21 1 0.01
22 16 0.21
23 59 0.77
24 1 0.01
ACGTcount: A:0.22, C:0.35, G:0.25, T:0.18
Consensus pattern (22 bp):
GGGAACCGATTCCCCCTCGAAG
Found at i:62003 original size:2 final size:2
Alignment explanation
Indices: 61998--62042 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
61988 GAAAAAACAG
61998 TA TA TA TA 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 TA TA TA TA
62040 TA T
1 TA T
62043 CATTCCCAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:67755 original size:21 final size:21
Alignment explanation
Indices: 67699--67755 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 21
67689 GCTAAAACTC
* *
67699 TTCTTCTTCATTTTTTATTCCT
1 TTCTTCTTGA-TTTTTACTCCT
* * * *
67721 TTGTTATTGGTTTTTACTCTT
1 TTCTTCTTGATTTTTACTCCT
67742 TTCTTCTTGATTTT
1 TTCTTCTTGATTTT
67756 CTCTCTTCAA
Statistics
Matches: 26, Mismatches: 9, Indels: 1
0.72 0.25 0.03
Matches are distributed among these distances:
21 20 0.77
22 6 0.23
ACGTcount: A:0.09, C:0.16, G:0.07, T:0.68
Consensus pattern (21 bp):
TTCTTCTTGATTTTTACTCCT
Found at i:69100 original size:34 final size:34
Alignment explanation
Indices: 69057--69167 Score: 118
Period size: 34 Copynumber: 3.3 Consensus size: 34
69047 TAAGTGTGAA
*
69057 TATGTGTGGATAAGTGGAGTTATCTCGCTGTCTT
1 TATGTGTGGATAAGTGGAGTTATCTCGATGTCTT
** ** * *
69091 TATGTGTGGACGAGTGGAGTTATCTCTTTATCCT
1 TATGTGTGGATAAGTGGAGTTATCTCGATGTCTT
*
69125 TATGTGTGGACTAA-TGGAGTTATCTTGATGT-TCT
1 TATGTGTGGA-TAAGTGGAGTTATCTCGATGTCT-T
69159 TATGTGTGG
1 TATGTGTGG
69168 TTGATCACGA
Statistics
Matches: 62, Mismatches: 13, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
34 61 0.98
35 1 0.02
ACGTcount: A:0.18, C:0.11, G:0.29, T:0.42
Consensus pattern (34 bp):
TATGTGTGGATAAGTGGAGTTATCTCGATGTCTT
Found at i:70847 original size:20 final size:21
Alignment explanation
Indices: 70810--70849 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
70800 AAATTAAGTT
70810 AAATGAATTTTAAGATTTTAC
1 AAATGAATTTTAAGATTTTAC
70831 AAATG-ATTTTACA-ATTTTA
1 AAATGAATTTTA-AGATTTTA
70850 TATTCGATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.45
Consensus pattern (21 bp):
AAATGAATTTTAAGATTTTAC
Found at i:71147 original size:63 final size:64
Alignment explanation
Indices: 71091--71213 Score: 203
Period size: 64 Copynumber: 1.9 Consensus size: 64
71081 GATGCATTCT
* *
71091 CCATGCATCGATGCACT-TGAATATTTTCAAACATCGAATGCATTTGATGCATCGATGCACAAG
1 CCATGCATCGATGCACTCAGAATATTTTCAAACATCGAATGCATTTCATGCATCGATGCACAAG
**
71154 CCATGCATCGATGCACTCAGGCTATTTTCAAACATCGAATGCATTTCATGCATCGATGCA
1 CCATGCATCGATGCACTCAGAATATTTTCAAACATCGAATGCATTTCATGCATCGATGCA
71214 ACTTGGTGCA
Statistics
Matches: 55, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
63 17 0.31
64 38 0.69
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.28
Consensus pattern (64 bp):
CCATGCATCGATGCACTCAGAATATTTTCAAACATCGAATGCATTTCATGCATCGATGCACAAG
Done.