Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007308.1 Hibiscus syriacus cultivar Beakdansim tig00019470_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: 72929
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:99 original size:5 final size:5
Alignment explanation
Indices: 89--152 Score: 60
Period size: 5 Copynumber: 12.6 Consensus size: 5
79 ATCAAAGATA
* * *
89 AAAAT AAAAT AAAAAT ACAAT GAGAT AAAAT AAAAT AAAAT AACAA- ATAAA-
1 AAAAT AAAAT -AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AA-AAT A-AAAT
140 AAAAT AAAAT AAA
1 AAAAT AAAAT AAA
153 GAAGACTATC
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
4 3 0.06
5 38 0.78
6 8 0.16
ACGTcount: A:0.77, C:0.03, G:0.03, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:122 original size:26 final size:27
Alignment explanation
Indices: 84--152 Score: 83
Period size: 25 Copynumber: 2.6 Consensus size: 27
74 TTTATATCAA
84 AGATAAAAATAAAATAAAAAT-AC-AAT
1 AGAT-AAAATAAAATAAAAATAACAAAT
110 GAGATAAAATAAAAT-AAAATAACAAAT
1 -AGATAAAATAAAATAAAAATAACAAAT
*
137 A-AAAAAATAAAATAAA
1 AGATAAAATAAAATAAA
153 GAAGACTATC
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
25 16 0.42
26 15 0.39
27 7 0.18
ACGTcount: A:0.75, C:0.03, G:0.04, T:0.17
Consensus pattern (27 bp):
AGATAAAATAAAATAAAAATAACAAAT
Found at i:627 original size:14 final size:14
Alignment explanation
Indices: 608--658 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
598 ACTCAAATGA
608 AAATTAAATGCTGG
1 AAATTAAATGCTGG
*
622 AAATTAAAAGGACT-G
1 AAATT-AAATG-CTGG
* *
637 AAATAAAATGCAGG
1 AAATTAAATGCTGG
651 AAATTAAA
1 AAATTAAA
659 GGGTAGAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
13 1 0.03
14 17 0.59
15 9 0.31
16 2 0.07
ACGTcount: A:0.55, C:0.06, G:0.18, T:0.22
Consensus pattern (14 bp):
AAATTAAATGCTGG
Found at i:898 original size:34 final size:33
Alignment explanation
Indices: 846--956 Score: 120
Period size: 34 Copynumber: 3.4 Consensus size: 33
836 TTAGTTTGTG
*
846 CAATAAAATAAAATGTTAGTAAGTTAGTAAGAA
1 CAATAAAATAAAAAGTTAGTAAGTTAGTAAGAA
* *
879 CAATAAAAATAAAAAGTTAGTAGGTTAGTATGAA
1 CAAT-AAAATAAAAAGTTAGTAAGTTAGTAAGAA
**
913 CAA-ATAAAT-AAAAGTTAG-AATGTTAGTTCGAA
1 CAATA-AAATAAAAAGTTAGTAA-GTTAGTAAGAA
*
945 CGATAAAATAAA
1 CAATAAAATAAA
957 TGTTAGAATG
Statistics
Matches: 66, Mismatches: 7, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
31 1 0.02
32 25 0.38
33 11 0.17
34 29 0.44
ACGTcount: A:0.54, C:0.05, G:0.15, T:0.26
Consensus pattern (33 bp):
CAATAAAATAAAAAGTTAGTAAGTTAGTAAGAA
Found at i:938 original size:32 final size:32
Alignment explanation
Indices: 851--969 Score: 109
Period size: 32 Copynumber: 3.6 Consensus size: 32
841 TTGTGCAATA
* *
851 AAATAAAATGTTAGTAA-GTTAGTAAGAACAATAA
1 AAATAAAA-GTTAG-AATGTTAGTATGAACAA-AT
* *
885 AAATAAAAAGTTAGTAGGTTAGTATGAACAAAT
1 AAAT-AAAAGTTAGAATGTTAGTATGAACAAAT
*
918 AAATAAAAGTTAGAATGTTAGT-TCGAAC-GAT
1 AAATAAAAGTTAGAATGTTAGTAT-GAACAAAT
*
949 AAAATAAATGTTAGAATGTTA
1 -AAATAAAAGTTAGAATGTTA
970 TTAAGTTAGT
Statistics
Matches: 74, Mismatches: 7, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
31 3 0.04
32 39 0.53
33 6 0.08
34 22 0.30
35 4 0.05
ACGTcount: A:0.51, C:0.03, G:0.17, T:0.29
Consensus pattern (32 bp):
AAATAAAAGTTAGAATGTTAGTATGAACAAAT
Found at i:7883 original size:14 final size:14
Alignment explanation
Indices: 7864--7898 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
7854 GGTTTGAAAC
*
7864 GAGTCAACTCGCCT
1 GAGTCAACTCACCT
7878 GAGTCAACTCACCT
1 GAGTCAACTCACCT
*
7892 TAGTCAA
1 GAGTCAA
7899 ATCGTTGACT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.23
Consensus pattern (14 bp):
GAGTCAACTCACCT
Found at i:14843 original size:23 final size:24
Alignment explanation
Indices: 14817--14861 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 24
14807 TTGTTGTTCA
14817 CGAACATATTCGTTTA-ATGTTTG
1 CGAACATATTCGTTTATATGTTTG
** *
14840 CGAATGTGTTCGTTTATATGTT
1 CGAACATATTCGTTTATATGTT
14862 CATGGACGTA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 13 0.72
24 5 0.28
ACGTcount: A:0.22, C:0.11, G:0.20, T:0.47
Consensus pattern (24 bp):
CGAACATATTCGTTTATATGTTTG
Found at i:14929 original size:35 final size:35
Alignment explanation
Indices: 14847--14933 Score: 95
Period size: 35 Copynumber: 2.5 Consensus size: 35
14837 TTGCGAATGT
*
14847 GTTCGTTTATATGTTCATGGACGTATTCATTTAGC
1 GTTCGTTTATATGTTCATGGAAGTATTCATTTAGC
* ** * * *
14882 GTTCATGAATATGTTCTAT-TAAGTGTTCATTTATC
1 GTTCGTTTATATGTTC-ATGGAAGTATTCATTTAGC
14917 GTTCGTTTATATGTTCA
1 GTTCGTTTATATGTTCA
14934 AATTTTAGTT
Statistics
Matches: 41, Mismatches: 10, Indels: 3
0.76 0.19 0.06
Matches are distributed among these distances:
34 1 0.02
35 38 0.93
36 2 0.05
ACGTcount: A:0.22, C:0.13, G:0.17, T:0.48
Consensus pattern (35 bp):
GTTCGTTTATATGTTCATGGAAGTATTCATTTAGC
Found at i:25221 original size:16 final size:16
Alignment explanation
Indices: 25195--25233 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
25185 TCGTCAAGAC
25195 ATGATTACTAGTTCACT
1 ATGA-TACTAGTTCACT
25212 ATGATACTAGTTCACT
1 ATGATACTAGTTCACT
25228 ATGATA
1 ATGATA
25234 TGTATTAATC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 18 0.82
17 4 0.18
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.38
Consensus pattern (16 bp):
ATGATACTAGTTCACT
Found at i:35535 original size:30 final size:30
Alignment explanation
Indices: 35501--35561 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 30
35491 CAATCGTTTG
35501 GAAAATCTTAAAATTAC-TTTAACTTAATTT
1 GAAAATCTTAAAA-TACATTTAACTTAATTT
*
35531 GAAAATCTTAAAATCCATTTAACTTAATTT
1 GAAAATCTTAAAATACATTTAACTTAATTT
35561 G
1 G
35562 TTATATCGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 2 0.07
30 27 0.93
ACGTcount: A:0.43, C:0.11, G:0.05, T:0.41
Consensus pattern (30 bp):
GAAAATCTTAAAATACATTTAACTTAATTT
Found at i:38028 original size:20 final size:20
Alignment explanation
Indices: 37956--38040 Score: 80
Period size: 20 Copynumber: 4.0 Consensus size: 20
37946 AACAGAACCC
*
37956 CAGGGGGGTATCGATTCCCCT
1 CAGGGGGGAATCGATT-CCCT
** *
37977 GTGGGGGGAATCGGTTCCCATT
1 CAGGGGGGAATCGATTCCC--T
* *
37999 CAAAGGGGGAATCGGTTCCCT
1 C-AGGGGGGAATCGATTCCCT
38020 CAGGGGGGAATCGATTCCCT
1 CAGGGGGGAATCGATTCCCT
38040 C
1 C
38041 TGCACCAAAA
Statistics
Matches: 52, Mismatches: 9, Indels: 7
0.76 0.13 0.10
Matches are distributed among these distances:
20 21 0.40
21 14 0.27
22 1 0.02
23 16 0.31
ACGTcount: A:0.18, C:0.25, G:0.35, T:0.22
Consensus pattern (20 bp):
CAGGGGGGAATCGATTCCCT
Found at i:41888 original size:22 final size:21
Alignment explanation
Indices: 41846--41885 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
41836 GAGTTTGTTT
*
41846 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
41867 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
41886 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:44138 original size:30 final size:30
Alignment explanation
Indices: 44104--44164 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 30
44094 CAATCGTTTG
44104 GAAAATCTTAAAATTAC-TTTAACTTAATTT
1 GAAAATCTTAAAA-TACATTTAACTTAATTT
*
44134 GAAAATCTTAAAATCCATTTAACTTAATTT
1 GAAAATCTTAAAATACATTTAACTTAATTT
44164 G
1 G
44165 TTATATCGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 2 0.07
30 27 0.93
ACGTcount: A:0.43, C:0.11, G:0.05, T:0.41
Consensus pattern (30 bp):
GAAAATCTTAAAATACATTTAACTTAATTT
Found at i:48463 original size:29 final size:29
Alignment explanation
Indices: 48416--48471 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
48406 TCTCACTTCT
* *
48416 ATTTAATCACTAGAGTTTTAATTTTTTTA
1 ATTTAATCACTAAAGTTTTAAATTTTTTA
*
48445 ATTTAATCACTAAATTTTTAAATTTTT
1 ATTTAATCACTAAAGTTTTAAATTTTT
48472 CTTATTTTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.34, C:0.07, G:0.04, T:0.55
Consensus pattern (29 bp):
ATTTAATCACTAAAGTTTTAAATTTTTTA
Found at i:51760 original size:74 final size:74
Alignment explanation
Indices: 51671--51817 Score: 294
Period size: 74 Copynumber: 2.0 Consensus size: 74
51661 CGTCCATGAT
51671 GTACCCCCTATTGTGTATCTTTGTCCGTGCATCCTAGATTTTAACACGTTATTGTGATGCCAATA
1 GTACCCCCTATTGTGTATCTTTGTCCGTGCATCCTAGATTTTAACACGTTATTGTGATGCCAATA
51736 ACTTTAGAC
66 ACTTTAGAC
51745 GTACCCCCTATTGTGTATCTTTGTCCGTGCATCCTAGATTTTAACACGTTATTGTGATGCCAATA
1 GTACCCCCTATTGTGTATCTTTGTCCGTGCATCCTAGATTTTAACACGTTATTGTGATGCCAATA
51810 ACTTTAGA
66 ACTTTAGA
51818 TGTAAATGCA
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 73 1.00
ACGTcount: A:0.23, C:0.22, G:0.16, T:0.38
Consensus pattern (74 bp):
GTACCCCCTATTGTGTATCTTTGTCCGTGCATCCTAGATTTTAACACGTTATTGTGATGCCAATA
ACTTTAGAC
Found at i:64990 original size:20 final size:21
Alignment explanation
Indices: 64967--65016 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
64957 TATGTAAACA
64967 AAAATAAAA-AA-TCTTTAATT
1 AAAATAAAATAACT-TTTAATT
*
64987 AAAA-AAAATAACTTTTAGTT
1 AAAATAAAATAACTTTTAATT
65007 AAAATAAAAT
1 AAAATAAAAT
65017 TTAATTAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 4 0.15
20 16 0.62
21 6 0.23
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.32
Consensus pattern (21 bp):
AAAATAAAATAACTTTTAATT
Found at i:66393 original size:14 final size:14
Alignment explanation
Indices: 66368--66405 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
66358 TAGTGGAAAT
66368 AATACA-AGTTAAA
1 AATACATAGTTAAA
66381 AATACATAGTTAAA
1 AATACATAGTTAAA
*
66395 AA-ACCTAGTTA
1 AATACATAGTTA
66406 CATTACATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 14 0.61
14 9 0.39
ACGTcount: A:0.55, C:0.11, G:0.08, T:0.26
Consensus pattern (14 bp):
AATACATAGTTAAA
Found at i:68789 original size:263 final size:263
Alignment explanation
Indices: 68322--68846 Score: 890
Period size: 263 Copynumber: 2.0 Consensus size: 263
68312 GTGGTTTTTG
* ** *
68322 TTGAGTTAATTGATCGATGGAATCGGCCAAGAGGGGGTGAATTGGCAATAAATATTTTGGTGGAA
1 TTGAGTTAATCGATCGACAGAATCGGCCAAGAGGGGGTGAATTGGCAATAAAAATTTTGGTGGAA
* * *
68387 ACTTTTGCAGAAAATTAAAAATATTTTCGCAGTGATTTAGAGTGGTTCGAATTTCTCAACCAAAG
66 ACTTTTGCAGAAAATGAAAAATATTTGCGCAGCGATTTAGAGTGGTTCGAATTTCTCAACCAAAG
*
68452 TCTACGTCCACTACCTTAGCTATCCACACTAAGGATTTTCTACAAATTCACTAATTTGTCTTTCT
131 TCTACGTCCACTACCTTAGCTATCCACACTAAGGATTTTCCACAAATTCACTAATTTGTCTTTCT
*
68517 TTTGAGGACAAAGAGTAACCTTAAAAATCCCTCAAGAATTATAACCCAAATTCTTGAGAACACTC
196 TTTGAGGACAAAGAGTAACCTTAAAAATCCCACAAGAATTATAACCCAAATTCTTGAGAACACTC
68582 TCA
261 TCA
*
68585 TTGAGTTAATCGATTGACAGAATCGGCCAAGAGGGGGTGAATTGGCAATAAAAATTTTGGT-GAA
1 TTGAGTTAATCGATCGACAGAATCGGCCAAGAGGGGGTGAATTGGCAATAAAAATTTTGGTGGAA
* * *
68649 GCTTTTGTAGAAAATGAAAAATATTTGCGCAGCGATTTAGAGTGGTTCGACTTTCTCAACCAAAG
66 ACTTTTGCAGAAAATGAAAAATATTTGCGCAGCGATTTAGAGTGGTTCGAATTTCTCAACCAAAG
*
68714 TCTAATGTCCACTACCTTAGCTATCCACACTAAGGATTTTCCACAAATTCACTAATTTGTCTTTC
131 TCT-ACGTCCACTACCTTAGCTATCCACACTAAGGATTTTCCACAAATTCACTAATTTGTCTTTC
* *
68779 TTTTGAGGACAAAGAGTAACCTTACAAATCCCACAAGAATTATACCCCAAATTCTTGAGAACACT
195 TTTTGAGGACAAAGAGTAACCTTAAAAATCCCACAAGAATTATAACCCAAATTCTTGAGAACACT
68844 CTC
260 CTC
68847 TCCAAATAGA
Statistics
Matches: 245, Mismatches: 16, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
262 65 0.27
263 180 0.73
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (263 bp):
TTGAGTTAATCGATCGACAGAATCGGCCAAGAGGGGGTGAATTGGCAATAAAAATTTTGGTGGAA
ACTTTTGCAGAAAATGAAAAATATTTGCGCAGCGATTTAGAGTGGTTCGAATTTCTCAACCAAAG
TCTACGTCCACTACCTTAGCTATCCACACTAAGGATTTTCCACAAATTCACTAATTTGTCTTTCT
TTTGAGGACAAAGAGTAACCTTAAAAATCCCACAAGAATTATAACCCAAATTCTTGAGAACACTC
TCA
Found at i:69425 original size:65 final size:65
Alignment explanation
Indices: 69292--69480 Score: 206
Period size: 64 Copynumber: 2.9 Consensus size: 65
69282 TGCACTTAGG
* * * *
69292 GTGCATCGGTACACTAATTTGC-TTCGATGTTTCAAAATAGATT-GG-GTGTATCGATGCATGGC
1 GTGCATCGGTGCACTAA-ATACATTCGATGTTTCAAAATA-ATTAGGAGTGCATCGATGCATGGC
69354 TT
64 TT
* * *
69356 GTGCATTGGTGCACTAAATACATTTGATGTTTCAAAATATTTAGGAGTGCATCGATGCATGGCTT
1 GTGCATCGGTGCACTAAATACATTCGATGTTTCAAAATAATTAGGAGTGCATCGATGCATGGCTT
* * ** ** *
69421 GTGCATCGGTGCATTAAATGCATTCGA-AATTCAATTTAATTAGGAGTGCATCAATGCATG
1 GTGCATCGGTGCACTAAATACATTCGATGTTTCAAAATAATTAGGAGTGCATCGATGCATG
69481 AACTAGTTCA
Statistics
Matches: 105, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
63 4 0.04
64 60 0.57
65 41 0.39
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.34
Consensus pattern (65 bp):
GTGCATCGGTGCACTAAATACATTCGATGTTTCAAAATAATTAGGAGTGCATCGATGCATGGCTT
Found at i:72019 original size:23 final size:23
Alignment explanation
Indices: 71989--72116 Score: 138
Period size: 23 Copynumber: 5.7 Consensus size: 23
71979 ATGCACAATA
71989 GAGTGCATCGATGCACATTCAAG
1 GAGTGCATCGATGCACATTCAAG
72012 GAGTGCATC-AGTGCACATTCAAG
1 GAGTGCATCGA-TGCACATTCAAG
*
72035 GAGTGCATCGGTGCACATTCAAG
1 GAGTGCATCGATGCACATTCAAG
* * * *
72058 AAGTGCATCGGTGCACCTTC-AT
1 GAGTGCATCGATGCACATTCAAG
* *
72080 G-GTGAATCGATACACATTCAAG
1 GAGTGCATCGATGCACATTCAAG
*
72102 G-GATACATCGATGCA
1 GAG-TGCATCGATGCA
72117 TTGTCTAGTG
Statistics
Matches: 88, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
21 14 0.16
22 5 0.06
23 69 0.78
ACGTcount: A:0.30, C:0.22, G:0.26, T:0.23
Consensus pattern (23 bp):
GAGTGCATCGATGCACATTCAAG
Done.