Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003166.1 Hibiscus syriacus cultivar Beakdansim tig00006661_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: 52124
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:107 original size:22 final size:22
Alignment explanation
Indices: 79--129 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
69 AGTCGAGGGT
*
79 TTCATAGGTCCTTCGGGACATA
1 TTCATAGGTCCTTCGGGACAAA
101 TTCATAGGTCCTTCGGGACAAA
1 TTCATAGGTCCTTCGGGACAAA
123 TCTCATA
1 T-TCATA
130 TGCCACTCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
22 22 0.81
23 5 0.19
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.31
Consensus pattern (22 bp):
TTCATAGGTCCTTCGGGACAAA
Found at i:4117 original size:64 final size:64
Alignment explanation
Indices: 4036--4172 Score: 145
Period size: 64 Copynumber: 2.2 Consensus size: 64
4026 ATTCAATGTG
* * *
4036 ATCGATGCA-CTCTTTAAACAAG-AAACATCGAATACAATTAGTGCATCGATGCATAAGG-AGTG
1 ATCGATGCACCCCCTTAAA-AAGAAAACATCGAAGACAATTAGTGCATCGATGCAT-AGGTAGTG
4098 C
64 C
* *** * * *
4099 ATCGATGCACCCCCTTAAAATGAAAACATCGAAGGTGATTGGTGTATCGATGCATGGGTAGTGC
1 ATCGATGCACCCCCTTAAAAAGAAAACATCGAAGACAATTAGTGCATCGATGCATAGGTAGTGC
4163 ATCGATGCAC
1 ATCGATGCAC
4173 ATTTTAAAGA
Statistics
Matches: 61, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
63 13 0.21
64 48 0.79
ACGTcount: A:0.34, C:0.20, G:0.23, T:0.24
Consensus pattern (64 bp):
ATCGATGCACCCCCTTAAAAAGAAAACATCGAAGACAATTAGTGCATCGATGCATAGGTAGTGC
Found at i:4205 original size:20 final size:20
Alignment explanation
Indices: 4180--4217 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
4170 CACATTTTAA
4180 AGAATGCATCGATGCACTGT
1 AGAATGCATCGATGCACTGT
*
4200 AGAATGTATCGATGCACT
1 AGAATGCATCGATGCACT
4218 TCAAAGGGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (20 bp):
AGAATGCATCGATGCACTGT
Found at i:10151 original size:17 final size:17
Alignment explanation
Indices: 10101--10152 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 17
10091 GGTTATAAGG
*
10101 AATATATGAAATTGAATT
1 AATATAT-AAATTAAATT
* *
10119 AAGTAAATAGATTAAATT
1 AA-TATATAAATTAAATT
10137 AATATATAAATTAAAT
1 AATATATAAATTAAAT
10153 ACTATTAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
17 12 0.43
18 12 0.43
19 4 0.14
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.37
Consensus pattern (17 bp):
AATATATAAATTAAATT
Found at i:10825 original size:23 final size:23
Alignment explanation
Indices: 10795--10864 Score: 95
Period size: 23 Copynumber: 3.0 Consensus size: 23
10785 CATTTTATAT
10795 GGCACTTCGGTGCAATTCTACGA
1 GGCACTTCGGTGCAATTCTACGA
* * *
10818 GGCACTTCGATGTAATTCTACGT
1 GGCACTTCGGTGCAATTCTACGA
* *
10841 GGCACTTCGGTGCATTTATACGA
1 GGCACTTCGGTGCAATTCTACGA
10864 G
1 G
10865 ATGTGGTGAC
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.21, C:0.23, G:0.26, T:0.30
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGA
Found at i:16233 original size:60 final size:60
Alignment explanation
Indices: 16116--16240 Score: 155
Period size: 60 Copynumber: 2.1 Consensus size: 60
16106 GTCGAGCGAT
* **
16116 CATTTTATAACTTTTAATAATCAAATGACTCAATAAAATAGAACCCTATAGTTAGAGGAC
1 CATTTTATAACTTTTAATAATCAAATGACTCAATAAAATAGAACCATATAGACAGAGGAC
* * * *
16176 TATTTTATAACTTTTAATAATC-AATAGACTTAATAAAATA-ATACTATATTGACAGAGGAC
1 CATTTTATAACTTTTAATAATCAAAT-GACTCAATAAAATAGA-ACCATATAGACAGAGGAC
16236 CATTT
1 CATTT
16241 GTATTATTTA
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
59 4 0.07
60 51 0.93
ACGTcount: A:0.43, C:0.13, G:0.09, T:0.35
Consensus pattern (60 bp):
CATTTTATAACTTTTAATAATCAAATGACTCAATAAAATAGAACCATATAGACAGAGGAC
Found at i:29557 original size:18 final size:18
Alignment explanation
Indices: 29534--29568 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
29524 ACTGGATAAT
29534 TGTCCCGAAA-GACCACTA
1 TGTCCC-AAAGGACCACTA
29552 TGTCCCAAAGGACCACT
1 TGTCCCAAAGGACCACT
29569 TTAGTCCCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 13 0.81
ACGTcount: A:0.31, C:0.34, G:0.17, T:0.17
Consensus pattern (18 bp):
TGTCCCAAAGGACCACTA
Found at i:36332 original size:18 final size:18
Alignment explanation
Indices: 36309--36345 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
36299 ACTGGATAAT
*
36309 TGTCCCGAATGACCACTA
1 TGTCCCGAAGGACCACTA
36327 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
36345 T
1 T
36346 AATCCCTCGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.27, C:0.32, G:0.19, T:0.22
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:36796 original size:18 final size:18
Alignment explanation
Indices: 36773--36810 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
36763 GCTCTAAATC
36773 TACATA-ATAATACATTGA
1 TACATATATAATA-ATTGA
*
36791 TACATATATACTAATTGA
1 TACATATATAATAATTGA
36809 TA
1 TA
36811 TATTTTAATC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.47, C:0.11, G:0.05, T:0.37
Consensus pattern (18 bp):
TACATATATAATAATTGA
Found at i:45047 original size:24 final size:22
Alignment explanation
Indices: 44991--45048 Score: 55
Period size: 24 Copynumber: 2.5 Consensus size: 22
44981 TATCTCTTAT
44991 ATCACTTTTCATATAAACACATA
1 ATCA-TTTTCATATAAACACATA
* *
45014 ATTCA-CTTCATATGCATACACATA
1 A-TCATTTTCATAT--AAACACATA
45038 ATCATTTTCAT
1 ATCATTTTCAT
45049 TATTTCACAT
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
22 7 0.25
23 4 0.14
24 17 0.61
ACGTcount: A:0.38, C:0.22, G:0.02, T:0.38
Consensus pattern (22 bp):
ATCATTTTCATATAAACACATA
Found at i:45344 original size:18 final size:18
Alignment explanation
Indices: 45321--45358 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
45311 GCTCTAAATC
45321 TACATA-ATAATACATTGA
1 TACATATATAATA-ATTGA
*
45339 TACATATATACTAATTGA
1 TACATATATAATAATTGA
45357 TA
1 TA
45359 TATTTTAATC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.47, C:0.11, G:0.05, T:0.37
Consensus pattern (18 bp):
TACATATATAATAATTGA
Found at i:45572 original size:18 final size:19
Alignment explanation
Indices: 45529--45572 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
45519 TAAGGGGTGT
*
45529 ATCGATGCACTTACTGTGC
1 ATCGATGCACTTACTGTAC
45548 ATCGATGCACTTA-T-TAC
1 ATCGATGCACTTACTGTAC
45565 ATTCGATG
1 A-TCGATG
45573 TTTTTATTCC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 3 0.13
18 7 0.30
19 13 0.57
ACGTcount: A:0.25, C:0.23, G:0.18, T:0.34
Consensus pattern (19 bp):
ATCGATGCACTTACTGTAC
Found at i:45779 original size:21 final size:22
Alignment explanation
Indices: 45734--45777 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 22
45724 CTTACACTCA
45734 TTAATACTCAATAATCACTTCT
1 TTAATACTCAATAATCACTTCT
45756 TTAA-ACTCAA-AATC-CTATCT
1 TTAATACTCAATAATCACT-TCT
45776 TT
1 TT
45778 TATCTGGTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
19 2 0.10
20 9 0.43
21 6 0.29
22 4 0.19
ACGTcount: A:0.36, C:0.23, G:0.00, T:0.41
Consensus pattern (22 bp):
TTAATACTCAATAATCACTTCT
Found at i:45806 original size:13 final size:13
Alignment explanation
Indices: 45788--45823 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
45778 TATCTGGTAT
45788 TCAAAAATCATAC
1 TCAAAAATCATAC
45801 TCAAAAATCATAC
1 TCAAAAATCATAC
*
45814 TCAAATATCA
1 TCAAAAATCA
45824 ATATGTTCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.53, C:0.22, G:0.00, T:0.25
Consensus pattern (13 bp):
TCAAAAATCATAC
Found at i:50315 original size:34 final size:34
Alignment explanation
Indices: 50270--50336 Score: 84
Period size: 34 Copynumber: 1.9 Consensus size: 34
50260 AATAGGAATT
*
50270 ACAACTTCTCTC-GATCTAACAAGGAGAAAACAATA
1 ACAACTTCTCTCTGA--TAAAAAGGAGAAAACAATA
50305 ACAA-TTCTCTCTTGATAAAAAGGAGAAAACAA
1 ACAACTTCTCTC-TGATAAAAAGGAGAAAACAA
50337 CTCTCAAGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
34 23 0.79
35 4 0.14
36 2 0.07
ACGTcount: A:0.48, C:0.19, G:0.12, T:0.21
Consensus pattern (34 bp):
ACAACTTCTCTCTGATAAAAAGGAGAAAACAATA
Found at i:50555 original size:23 final size:23
Alignment explanation
Indices: 50502--50556 Score: 83
Period size: 23 Copynumber: 2.4 Consensus size: 23
50492 CTATGTCACT
50502 TTTCAACCATTATTGGTGCCAAC
1 TTTCAACCATTATTGGTGCCAAC
* * *
50525 TATGAACCATTATTGTTGCCAAC
1 TTTCAACCATTATTGGTGCCAAC
50548 TTTCAACCA
1 TTTCAACCA
50557 CCTAAAGTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.29, C:0.25, G:0.11, T:0.35
Consensus pattern (23 bp):
TTTCAACCATTATTGGTGCCAAC
Done.