Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004956.1 Hibiscus syriacus cultivar Beakdansim tig00011143_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: 61897
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:3895 original size:14 final size:13
Alignment explanation
Indices: 3870--3904 Score: 61
Period size: 14 Copynumber: 2.6 Consensus size: 13
3860 TAACTTTTTG
3870 GTCAACGGTCAAA
1 GTCAACGGTCAAA
3883 GTCAACTGGTCAAA
1 GTCAAC-GGTCAAA
3897 GTCAACGG
1 GTCAACGG
3905 GTTGACTCAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 8 0.38
14 13 0.62
ACGTcount: A:0.34, C:0.23, G:0.26, T:0.17
Consensus pattern (13 bp):
GTCAACGGTCAAA
Found at i:5848 original size:20 final size:20
Alignment explanation
Indices: 5823--5861 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
5813 AGTATTTTGA
5823 CATGCACCGATGCACCAATC
1 CATGCACCGATGCACCAATC
* *
5843 CATGCATCGATGCATCAAT
1 CATGCACCGATGCACCAAT
5862 TAATTTCTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.31, C:0.33, G:0.15, T:0.21
Consensus pattern (20 bp):
CATGCACCGATGCACCAATC
Found at i:14652 original size:45 final size:46
Alignment explanation
Indices: 14603--14693 Score: 130
Period size: 46 Copynumber: 2.0 Consensus size: 46
14593 GAACATCGAA
* * *
14603 TGCATTTTATGCATTGATGCAC-ATACCATGCATCGATGCACTCAG
1 TGCATTTGATGCATCGATGCACAAAACCATGCATCGATGCACTCAG
* *
14648 TGCATTTGATTCATCGATGCACAAAACTATGCATCGATGCACTCAG
1 TGCATTTGATGCATCGATGCACAAAACCATGCATCGATGCACTCAG
14694 ACTTTTTCAA
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
45 19 0.47
46 21 0.52
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.30
Consensus pattern (46 bp):
TGCATTTGATGCATCGATGCACAAAACCATGCATCGATGCACTCAG
Found at i:19710 original size:24 final size:24
Alignment explanation
Indices: 19683--19729 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
19673 CCGATTATGA
19683 TTCTCATCTTAAAATAAAAGGGGG
1 TTCTCATCTTAAAATAAAAGGGGG
19707 TTCTCATCTTAAAATAAAAGGGG
1 TTCTCATCTTAAAATAAAAGGGG
19730 TAAACCGTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (24 bp):
TTCTCATCTTAAAATAAAAGGGGG
Found at i:20309 original size:27 final size:27
Alignment explanation
Indices: 20271--20335 Score: 121
Period size: 27 Copynumber: 2.4 Consensus size: 27
20261 GTGCATGTTA
*
20271 ATTTCTGCTTCTTTGTTGTCTGCTATC
1 ATTTCAGCTTCTTTGTTGTCTGCTATC
20298 ATTTCAGCTTCTTTGTTGTCTGCTATC
1 ATTTCAGCTTCTTTGTTGTCTGCTATC
20325 ATTTCAGCTTC
1 ATTTCAGCTTC
20336 ATGGAAAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.11, C:0.23, G:0.14, T:0.52
Consensus pattern (27 bp):
ATTTCAGCTTCTTTGTTGTCTGCTATC
Found at i:24941 original size:76 final size:72
Alignment explanation
Indices: 24809--24954 Score: 238
Period size: 76 Copynumber: 2.0 Consensus size: 72
24799 AATAGCTGGA
*
24809 AAAGGAAAACTTGTATTCTTCATTATTTAAATTATATATTACAGGATCCTTGGAGGGGTCGACCC
1 AAAGGAAAACTTGTATTCTTCATTATTTAAATTATATATTACAAGATCCTTGGAGGGGTCGACCC
24874 AATAACT
66 AATAACT
*
24881 AAAGGAAAACTTGTATTCTTCATTATTTATTTAAATTATATATTACAAGATCTTTGGAGGGGTCG
1 AAAGGAAAACTTGTATTCTTC---A-TTATTTAAATTATATATTACAAGATCCTTGGAGGGGTCG
24946 ACCCAATAA
62 ACCCAATAA
24955 TTAAGAGAAA
Statistics
Matches: 68, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
72 21 0.31
75 1 0.01
76 46 0.68
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.35
Consensus pattern (72 bp):
AAAGGAAAACTTGTATTCTTCATTATTTAAATTATATATTACAAGATCCTTGGAGGGGTCGACCC
AATAACT
Found at i:33330 original size:3 final size:3
Alignment explanation
Indices: 33324--33368 Score: 67
Period size: 3 Copynumber: 15.7 Consensus size: 3
33314 TATTTGCTTA
*
33324 TAT TAT TAT TAT TAT TAT TAT TA- TGT TA- TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
33369 AATAATTAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
2 3 0.08
3 35 0.92
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:33352 original size:28 final size:28
Alignment explanation
Indices: 33313--33368 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
33303 GTTTTTTTTC
33313 TTATTTGCTTATATTATTATTATTATTA
1 TTATTTGCTTATATTATTATTATTATTA
33341 TTATTATG-TTATATTATTATTATTATTA
1 TTATT-TGCTTATATTATTATTATTATTA
33369 AATAATTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 25 0.93
29 2 0.07
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.64
Consensus pattern (28 bp):
TTATTTGCTTATATTATTATTATTATTA
Found at i:38408 original size:15 final size:15
Alignment explanation
Indices: 38388--38421 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
38378 GGGATCAATA
38388 CATTTTGCATACATG
1 CATTTTGCATACATG
*
38403 CATTTTGCATACATT
1 CATTTTGCATACATG
38418 CATT
1 CATT
38422 ATTCATTGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.26, C:0.21, G:0.09, T:0.44
Consensus pattern (15 bp):
CATTTTGCATACATG
Found at i:46209 original size:20 final size:19
Alignment explanation
Indices: 46130--46214 Score: 84
Period size: 20 Copynumber: 4.2 Consensus size: 19
46120 ATTTATTAAT
46130 AAATTCTAAGTTTATTTTCTCT-
1 AAATTC-AA-TTTATTTT-T-TG
46152 AAATTCAATTTA-TTTTTG
1 AAATTCAATTTATTTTTTG
*
46170 AAATTTAATTTATTTTTTTG
1 AAATTCAATTTA-TTTTTTG
46190 AAATTCAATTTATTCTTTTG
1 AAATTCAATTTATT-TTTTG
46210 TAAAT
1 -AAAT
46215 GGATTAACAT
Statistics
Matches: 56, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
17 1 0.02
18 12 0.21
19 5 0.09
20 26 0.46
21 6 0.11
22 6 0.11
ACGTcount: A:0.32, C:0.07, G:0.05, T:0.56
Consensus pattern (19 bp):
AAATTCAATTTATTTTTTG
Found at i:47555 original size:113 final size:113
Alignment explanation
Indices: 47340--47631 Score: 401
Period size: 113 Copynumber: 2.6 Consensus size: 113
47330 TAGCAAAGAT
* * *
47340 TCAAATCCATCAC--AATGGATCAACATTTCCAGA-AAGAGTTCATAATGAGAAGAACTCATCTA
1 TCAAATCCATCACTTGATGGATCAGCATTTCCAGAGAA-AGTTCATAATGAGAAGAACTCATCTG
* * *
47402 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
65 AAGAAGGAAGAAGAAATTCATAATGAGAAGAACTTATTCAACCTTTTGC
* *
47451 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAAAACTCATCTGA
1 TCAAATCCATCACTTGATGGATCAGCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
* * * *
47516 AGAAGGAAGAATAAATTCATAATGAGAAGAATTTATTCAACTTTTTGT
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAACTTATTCAACCTTTTGC
** * * *
47564 TTGAATTCATCATTTGATGGATCAGCATTACCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCACTTGATGGATCAGCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
47629 AGA
66 AGA
47632 GAAGAGTTTG
Statistics
Matches: 159, Mismatches: 19, Indels: 4
0.87 0.10 0.02
Matches are distributed among these distances:
111 13 0.08
113 144 0.91
114 2 0.01
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.27
Consensus pattern (113 bp):
TCAAATCCATCACTTGATGGATCAGCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
AGAAGGAAGAAGAAATTCATAATGAGAAGAACTTATTCAACCTTTTGC
Found at i:47765 original size:20 final size:20
Alignment explanation
Indices: 47703--47766 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
47693 TTTTCAGAAG
47703 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
* ***
47723 -ATC-TGAA-GAGGAAGAAGAA
1 GTTCAT-AATGA-GAAGAACTT
47742 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
47762 GTTCA
1 GTTCA
47767 ACTTTTTGTA
Statistics
Matches: 31, Mismatches: 8, Indels: 10
0.63 0.16 0.20
Matches are distributed among these distances:
18 3 0.10
19 10 0.32
20 15 0.48
21 3 0.10
ACGTcount: A:0.42, C:0.09, G:0.23, T:0.25
Consensus pattern (20 bp):
GTTCATAATGAGAAGAACTT
Found at i:49964 original size:98 final size:96
Alignment explanation
Indices: 49762--49965 Score: 204
Period size: 98 Copynumber: 2.1 Consensus size: 96
49752 TATAAGCATG
*
49762 TTTTAATTTAATATTAAAGAAAAAGACTATCTTAAAGCACCTAGAAGTCCGTTTTCTGATTTTTT
1 TTTT-ATTTAATATTAAAGAAAAAGACTATCTTAAAGCACCTAGAAGTCCGTTTTCTGATTTTCT
* **
49827 TACTCTATAAAATATATACTAATTTTTTATTAATA
65 TA--C-ATAAAAAATATACTAATTTTAAATTAATA
* *
49862 -TTTATTTAATA-TAGAAG-AAAAGAGCTGTCTTAAGGCACCTAGAAGTCC-TTTTCTGATATTT
1 TTTTATTTAATATTA-AAGAAAAAGA-CTATCTTAAAGCACCTAGAAGTCCGTTTTCTGAT-TTT
*
49923 CTTA-ATAAATAAATAT-CTTATTTATAAATTAATAGA
63 CTTACATAAA-AAATATACTAATTT-TAAATTAAT--A
49959 TTTTATT
1 TTTTATT
49966 AAAGATACTA
Statistics
Matches: 89, Mismatches: 7, Indels: 18
0.78 0.06 0.16
Matches are distributed among these distances:
94 11 0.12
95 12 0.13
97 18 0.20
98 45 0.51
99 3 0.03
ACGTcount: A:0.38, C:0.10, G:0.09, T:0.43
Consensus pattern (96 bp):
TTTTATTTAATATTAAAGAAAAAGACTATCTTAAAGCACCTAGAAGTCCGTTTTCTGATTTTCTT
ACATAAAAAATATACTAATTTTAAATTAATA
Found at i:58743 original size:29 final size:29
Alignment explanation
Indices: 58711--58806 Score: 72
Period size: 29 Copynumber: 3.2 Consensus size: 29
58701 AAATTGGTCC
58711 CTAAACTTTTAAATATTTTAATTTTATCT
1 CTAAACTTTTAAATATTTTAATTTTATCT
* * *
58740 CTAAAC-TATGAATATCGTTCTAA-ATTAGTC-
1 CTAAACTTTTAAATAT--TT-TAATTTTA-TCT
* *
58770 CTTAAACTTTTAAATATTTCAATTTCATCT
1 C-TAAACTTTTAAATATTTTAATTTTATCT
*
58800 CCAAACT
1 CTAAACT
58807 ATGGTCTTCA
Statistics
Matches: 50, Mismatches: 9, Indels: 16
0.67 0.12 0.21
Matches are distributed among these distances:
28 7 0.14
29 15 0.30
30 11 0.22
31 10 0.20
32 7 0.14
ACGTcount: A:0.35, C:0.17, G:0.03, T:0.45
Consensus pattern (29 bp):
CTAAACTTTTAAATATTTTAATTTTATCT
Found at i:58821 original size:60 final size:60
Alignment explanation
Indices: 58701--58840 Score: 174
Period size: 60 Copynumber: 2.3 Consensus size: 60
58691 TCTTAATTTC
* * * *
58701 AAATTGGTCCCTAAACTTTTAAATATTTTAATTTTATCTCTAAACTATGAATATCGTTCT
1 AAATTGGTCCCTAAACTTTTAAATATTTCAATTTCATCTCCAAACTATGAATATCATTCT
* * * *
58761 AAATTAGTCCTTAAACTTTTAAATATTTCAATTTCATCTCCAAACTATG-GTCTTCATTCT
1 AAATTGGTCCCTAAACTTTTAAATATTTCAATTTCATCTCCAAACTATGAAT-ATCATTCT
* *
58821 AAGTTGGTCCCCAAACTTTT
1 AAATTGGTCCCTAAACTTTT
58841 TGAACATTCC
Statistics
Matches: 67, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
59 1 0.01
60 66 0.99
ACGTcount: A:0.31, C:0.19, G:0.07, T:0.43
Consensus pattern (60 bp):
AAATTGGTCCCTAAACTTTTAAATATTTCAATTTCATCTCCAAACTATGAATATCATTCT
Found at i:59065 original size:60 final size:59
Alignment explanation
Indices: 58988--59135 Score: 158
Period size: 60 Copynumber: 2.5 Consensus size: 59
58978 GATGAATTTG
* * *
58988 AGGATGAAATT-TGAATATTTAAAAGTTTAGAGAATAATTTAGAAAAAGTGTCATAGTTT
1 AGGATGAAATTAT-AATATTTAAAAGTTTAAAGAATAAGTTAGAAAAAGAGTCATAGTTT
* * ** *
59047 AAGGATGAAATTATAATATTCAAAAGTTTAAAGATTAAGTTAGAACGAGAGTTATAGTTT
1 -AGGATGAAATTATAATATTTAAAAGTTTAAAGAATAAGTTAGAAAAAGAGTCATAGTTT
* *
59107 AGGGTAAAATTGA-AATATTTAAAA-TTTAA
1 AGGATGAAATT-ATAATATTTAAAAGTTTAA
59136 GGATCAATTT
Statistics
Matches: 75, Mismatches: 11, Indels: 6
0.82 0.12 0.07
Matches are distributed among these distances:
58 5 0.07
59 19 0.25
60 50 0.67
61 1 0.01
ACGTcount: A:0.46, C:0.02, G:0.18, T:0.34
Consensus pattern (59 bp):
AGGATGAAATTATAATATTTAAAAGTTTAAAGAATAAGTTAGAAAAAGAGTCATAGTTT
Found at i:59737 original size:18 final size:20
Alignment explanation
Indices: 59699--59738 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
59689 CACGGAATGT
59699 AAGATTACCAGTGGAAATAA
1 AAGATTACCAGTGGAAATAA
59719 AAGATTACCAG-GG-AATAA
1 AAGATTACCAGTGGAAATAA
59737 AA
1 AA
59739 TTACTGGGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 7 0.35
19 2 0.10
20 11 0.55
ACGTcount: A:0.53, C:0.10, G:0.20, T:0.17
Consensus pattern (20 bp):
AAGATTACCAGTGGAAATAA
Found at i:61786 original size:22 final size:24
Alignment explanation
Indices: 61745--61798 Score: 76
Period size: 23 Copynumber: 2.3 Consensus size: 24
61735 GACCATGAGG
*
61745 AGTATCGATACTACTATG-AAAAT
1 AGTATCTATACTACTATGAAAAAT
*
61768 AGTATCTATA-TATTATGAAAAAT
1 AGTATCTATACTACTATGAAAAAT
61791 AGTATCTA
1 AGTATCTA
61799 CTATTATACT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 6 0.21
23 22 0.79
ACGTcount: A:0.44, C:0.09, G:0.11, T:0.35
Consensus pattern (24 bp):
AGTATCTATACTACTATGAAAAAT
Found at i:61803 original size:22 final size:21
Alignment explanation
Indices: 61753--61805 Score: 70
Period size: 23 Copynumber: 2.4 Consensus size: 21
61743 GGAGTATCGA
*
61753 TACTACTATGAAAATAGTATC
1 TACTATTATGAAAATAGTATC
*
61774 TATATATTATGAAAAATAGTATC
1 TA-CTATTATG-AAAATAGTATC
61797 TACTATTAT
1 TACTATTAT
61806 ACTTAAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 2 0.07
22 12 0.44
23 13 0.48
ACGTcount: A:0.43, C:0.09, G:0.08, T:0.40
Consensus pattern (21 bp):
TACTATTATGAAAATAGTATC
Done.