Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004133.1 Hibiscus syriacus cultivar Beakdansim tig00009039_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: 82729
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:6162 original size:12 final size:12
Alignment explanation
Indices: 6145--6169 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
6135 TTCTTACGAT
6145 AATTAGTATCAA
1 AATTAGTATCAA
6157 AATTAGTATCAA
1 AATTAGTATCAA
6169 A
1 A
6170 GTATCAGGTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.08, G:0.08, T:0.32
Consensus pattern (12 bp):
AATTAGTATCAA
Found at i:29254 original size:59 final size:59
Alignment explanation
Indices: 29159--29278 Score: 170
Period size: 59 Copynumber: 2.0 Consensus size: 59
29149 AATAGATGGA
* * * *
29159 TAAGTATCCTATCGAACTCTCCTAGTCGCGATGAAAA-GACAAACTCGATAATATGACTC
1 TAAGTATCCTATCAAACCCTCCTAGTCGCAACGAAAAGGA-AAACTCGATAATATGACTC
* *
29218 TAAGTGTCCTATCAAACCCTCCTAGTCGCAACGAAAAGGAAAACTCGATAATATGGCTC
1 TAAGTATCCTATCAAACCCTCCTAGTCGCAACGAAAAGGAAAACTCGATAATATGACTC
29277 TA
1 TA
29279 CCCAACCCTC
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
59 52 0.96
60 2 0.04
ACGTcount: A:0.36, C:0.24, G:0.16, T:0.24
Consensus pattern (59 bp):
TAAGTATCCTATCAAACCCTCCTAGTCGCAACGAAAAGGAAAACTCGATAATATGACTC
Found at i:32651 original size:18 final size:19
Alignment explanation
Indices: 32616--32652 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
32606 CACGGAATGT
32616 AAGATTACCAGGGGGAATAA
1 AAGATTACCA-GGGGAATAA
32636 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
32653 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.27, T:0.16
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:34164 original size:59 final size:59
Alignment explanation
Indices: 34066--34182 Score: 200
Period size: 59 Copynumber: 2.0 Consensus size: 59
34056 GATGGATAAT
*
34066 TGTCCTATCGAACCCTCCTAGTCGCAATGAAAAGACAAACTCGATAATATGACTCTAAG
1 TGTCCTATCGAACCATCCTAGTCGCAATGAAAAGACAAACTCGATAATATGACTCTAAG
*
34125 TGTCCTATCGAACCATCCTAGTCGCAATGAAAATG-CAAACTCGATAATATGGCTCTAA
1 TGTCCTATCGAACCATCCTAGTCGCAATGAAAA-GACAAACTCGATAATATGACTCTAA
34183 CCAACCCTAA
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
59 54 0.98
60 1 0.02
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.25
Consensus pattern (59 bp):
TGTCCTATCGAACCATCCTAGTCGCAATGAAAAGACAAACTCGATAATATGACTCTAAG
Found at i:34620 original size:59 final size:59
Alignment explanation
Indices: 34522--34638 Score: 164
Period size: 59 Copynumber: 2.0 Consensus size: 59
34512 GATGAATAAT
* * * * *
34522 TGTCCTATTGAACCCTCATAGTCGCAATGAAAAGACAAACTTGATAATATGACTCTAAG
1 TGTCCTATCGAACCATCATAATCGCAATGAAAAGACAAACTCGATAATATAACTCTAAG
*
34581 TGTCCTATCGAACCATCCTAATCGCAATGAAAATG-CAAACTCGATAATATAACTCTAA
1 TGTCCTATCGAACCATCATAATCGCAATGAAAA-GACAAACTCGATAATATAACTCTAA
34639 CCAACCCTCC
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
59 50 0.98
60 1 0.02
ACGTcount: A:0.38, C:0.22, G:0.13, T:0.26
Consensus pattern (59 bp):
TGTCCTATCGAACCATCATAATCGCAATGAAAAGACAAACTCGATAATATAACTCTAAG
Found at i:38193 original size:14 final size:14
Alignment explanation
Indices: 38174--38243 Score: 104
Period size: 14 Copynumber: 5.0 Consensus size: 14
38164 AACAGACTTG
38174 TCTGTTTTCTACAT
1 TCTGTTTTCTACAT
* *
38188 TCTGTTTTATACAG
1 TCTGTTTTCTACAT
38202 TCTGTTTTCTACAT
1 TCTGTTTTCTACAT
* *
38216 TCTGTTTTATACAG
1 TCTGTTTTCTACAT
38230 TCTGTTTTCTACAT
1 TCTGTTTTCTACAT
38244 GGTATCAGGT
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 48 1.00
ACGTcount: A:0.17, C:0.19, G:0.10, T:0.54
Consensus pattern (14 bp):
TCTGTTTTCTACAT
Found at i:38213 original size:28 final size:28
Alignment explanation
Indices: 38173--38243 Score: 142
Period size: 28 Copynumber: 2.5 Consensus size: 28
38163 TAACAGACTT
38173 GTCTGTTTTCTACATTCTGTTTTATACA
1 GTCTGTTTTCTACATTCTGTTTTATACA
38201 GTCTGTTTTCTACATTCTGTTTTATACA
1 GTCTGTTTTCTACATTCTGTTTTATACA
38229 GTCTGTTTTCTACAT
1 GTCTGTTTTCTACAT
38244 GGTATCAGGT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.17, C:0.18, G:0.11, T:0.54
Consensus pattern (28 bp):
GTCTGTTTTCTACATTCTGTTTTATACA
Found at i:42925 original size:14 final size:14
Alignment explanation
Indices: 42906--42990 Score: 89
Period size: 14 Copynumber: 5.9 Consensus size: 14
42896 AACAGACTTG
42906 TCTGTTTTCTACAT
1 TCTGTTTTCTACAT
* *
42920 TCTGTTTTATACAG
1 TCTGTTTTCTACAT
42934 TCTGTTTTCTACAT
1 TCTGTTTTCTACAT
*
42948 CAGTCTGTTTTTTACAT
1 ---TCTGTTTTCTACAT
* * *
42965 TTTGTTTTATACAG
1 TCTGTTTTCTACAT
42979 TCTGTTTTCTAC
1 TCTGTTTTCTAC
42991 CTCTTTCCAC
Statistics
Matches: 58, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
14 45 0.78
17 13 0.22
ACGTcount: A:0.16, C:0.18, G:0.11, T:0.55
Consensus pattern (14 bp):
TCTGTTTTCTACAT
Found at i:42955 original size:45 final size:45
Alignment explanation
Indices: 42905--42990 Score: 154
Period size: 45 Copynumber: 1.9 Consensus size: 45
42895 TAACAGACTT
42905 GTCTGTTTTCTACATTCTGTTTTATACAGTCTGTTTTCTACATCA
1 GTCTGTTTTCTACATTCTGTTTTATACAGTCTGTTTTCTACATCA
* *
42950 GTCTGTTTTTTACATTTTGTTTTATACAGTCTGTTTTCTAC
1 GTCTGTTTTCTACATTCTGTTTTATACAGTCTGTTTTCTAC
42991 CTCTTTCCAC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.16, C:0.17, G:0.12, T:0.55
Consensus pattern (45 bp):
GTCTGTTTTCTACATTCTGTTTTATACAGTCTGTTTTCTACATCA
Found at i:44377 original size:81 final size:81
Alignment explanation
Indices: 44239--44396 Score: 271
Period size: 81 Copynumber: 2.0 Consensus size: 81
44229 AGGCAACTGG
* * *
44239 TTACTAATCGGTGTGGCTGGAAGGTTAAGAAGTGGTTGGATAAGGAATAGATATTTGTCCTTATC
1 TTACTAATCGGTGTGGCTAGAAGGTCAAGAAGTGGCTGGATAAGGAATAGATATTTGTCCTTATC
44304 TTCTTTGAATGAAATC
66 TTCTTTGAATGAAATC
* *
44320 TTACTAATTGGTGTGGCTAGAAGGTCAAGAAGTGGCTGGATAAGGAATAGATCTTTGTCCTTATC
1 TTACTAATCGGTGTGGCTAGAAGGTCAAGAAGTGGCTGGATAAGGAATAGATATTTGTCCTTATC
44385 TTCTTTGAATGA
66 TTCTTTGAATGA
44397 GATTTCCCCC
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
81 72 1.00
ACGTcount: A:0.28, C:0.11, G:0.26, T:0.35
Consensus pattern (81 bp):
TTACTAATCGGTGTGGCTAGAAGGTCAAGAAGTGGCTGGATAAGGAATAGATATTTGTCCTTATC
TTCTTTGAATGAAATC
Found at i:44937 original size:2 final size:2
Alignment explanation
Indices: 44930--44960 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
44920 AAGCCAAATA
44930 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
44961 TAAATATTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:52580 original size:17 final size:18
Alignment explanation
Indices: 52558--52594 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
52548 TTTTAACTCA
52558 AAATTATTT-AAAAATTT
1 AAATTATTTGAAAAATTT
*
52575 AAATTATTTGATAAATTT
1 AAATTATTTGAAAAATTT
52593 AA
1 AA
52595 CAATAATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (18 bp):
AAATTATTTGAAAAATTT
Found at i:66323 original size:36 final size:36
Alignment explanation
Indices: 66274--66342 Score: 129
Period size: 36 Copynumber: 1.9 Consensus size: 36
66264 ATCCCCTAGG
66274 CAAGTCAACCAATTTCCAAGTATGATTAGACATAGA
1 CAAGTCAACCAATTTCCAAGTATGATTAGACATAGA
*
66310 CAAGTCAATCAATTTCCAAGTATGATTAGACAT
1 CAAGTCAACCAATTTCCAAGTATGATTAGACAT
66343 TATCGATTCT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.41, C:0.19, G:0.13, T:0.28
Consensus pattern (36 bp):
CAAGTCAACCAATTTCCAAGTATGATTAGACATAGA
Found at i:67168 original size:17 final size:17
Alignment explanation
Indices: 67146--67188 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
67136 TCTAAGTCAT
67146 TTGATTCTCCTATCTAA
1 TTGATTCTCCTATCTAA
*
67163 TTGATTATCCTATCTAA
1 TTGATTCTCCTATCTAA
67180 TTGATTCTC
1 TTGATTCTC
67189 AACTTCTGCC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.23, C:0.21, G:0.07, T:0.49
Consensus pattern (17 bp):
TTGATTCTCCTATCTAA
Found at i:72774 original size:14 final size:14
Alignment explanation
Indices: 72755--72784 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
72745 TTAAATGATA
72755 AACGAACACAAATG
1 AACGAACACAAATG
*
72769 AACGAACATAAATG
1 AACGAACACAAATG
72783 AA
1 AA
72785 AGGATGTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.60, C:0.17, G:0.13, T:0.10
Consensus pattern (14 bp):
AACGAACACAAATG
Found at i:72822 original size:13 final size:13
Alignment explanation
Indices: 72800--72860 Score: 56
Period size: 13 Copynumber: 4.8 Consensus size: 13
72790 GTAAATTAAC
*
72800 ATAAAAGAACACA
1 ATAAACGAACACA
72813 ATAAACGAAC-C-
1 ATAAACGAACACA
*
72824 -TAAATGAACACA
1 ATAAACGAACACA
*
72836 CGTAAACGAACACA
1 -ATAAACGAACACA
*
72850 ATAAATGAACA
1 ATAAACGAACA
72861 TAAACGAACA
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
10 8 0.21
11 1 0.03
12 1 0.03
13 18 0.46
14 11 0.28
ACGTcount: A:0.59, C:0.20, G:0.10, T:0.11
Consensus pattern (13 bp):
ATAAACGAACACA
Found at i:72827 original size:23 final size:24
Alignment explanation
Indices: 72801--72846 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
72791 TAAATTAACA
72801 TAAAAGAACACA-ATAAACGAACC
1 TAAAAGAACACACATAAACGAACC
* *
72824 TAAATGAACACACGTAAACGAAC
1 TAAAAGAACACACATAAACGAAC
72847 ACAATAAATG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.57, C:0.22, G:0.11, T:0.11
Consensus pattern (24 bp):
TAAAAGAACACACATAAACGAACC
Found at i:72869 original size:10 final size:10
Alignment explanation
Indices: 72850--72884 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
72840 AACGAACACA
*
72850 ATAAATGAAC
1 ATAAACGAAC
72860 ATAAACGAAC
1 ATAAACGAAC
*
72870 AAAAACGAAC
1 ATAAACGAAC
72880 ATAAA
1 ATAAA
72885 TCAACTTCCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.66, C:0.14, G:0.09, T:0.11
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:76483 original size:23 final size:23
Alignment explanation
Indices: 76457--76525 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
76447 CACCACAGCT
* *
76457 CGTATAATTACACCGAAGTGCTA
1 CGTAGAATTACACCGAAGTGCCA
* * *
76480 CGTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTACACCGAAGTGCCA
*
76503 CGTAGAATTACACCGTAGTGCCA
1 CGTAGAATTACACCGAAGTGCCA
76526 TATAATAATG
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.29, C:0.25, G:0.25, T:0.22
Consensus pattern (23 bp):
CGTAGAATTACACCGAAGTGCCA
Found at i:76831 original size:29 final size:29
Alignment explanation
Indices: 76798--76865 Score: 136
Period size: 29 Copynumber: 2.3 Consensus size: 29
76788 TTTCTTGCAT
76798 ATTCATGTCACATAATGCATATGGTATGA
1 ATTCATGTCACATAATGCATATGGTATGA
76827 ATTCATGTCACATAATGCATATGGTATGA
1 ATTCATGTCACATAATGCATATGGTATGA
76856 ATTCATGTCA
1 ATTCATGTCA
76866 TGTATCATAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (29 bp):
ATTCATGTCACATAATGCATATGGTATGA
Found at i:76875 original size:34 final size:33
Alignment explanation
Indices: 76800--76876 Score: 108
Period size: 29 Copynumber: 2.4 Consensus size: 33
76790 TCTTGCATAT
76800 TCATGTCACATAATGCATATGGTATGAATTCATG
1 TCATGT-ACATAATGCATATGGTATGAATTCATG
76834 TC----ACATAATGCATATGGTATGAATTCATG
1 TCATGTACATAATGCATATGGTATGAATTCATG
76863 TCATGTATCATAAT
1 TCATGTA-CATAAT
76877 ATGAAATGCG
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
29 29 0.76
33 1 0.03
34 8 0.21
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (33 bp):
TCATGTACATAATGCATATGGTATGAATTCATG
Found at i:82549 original size:27 final size:29
Alignment explanation
Indices: 82508--82591 Score: 84
Period size: 32 Copynumber: 2.9 Consensus size: 29
82498 ATTATACAAA
*
82508 TAGTCACTCAA-CTGTATTGT-TTT-ATTT
1 TAGTCAC-CAAGCTGTATTCTCTTTAATTT
*
82535 TAGTCACCAAGCTGTTTTCTCTTTACAAATTT
1 TAGTCACCAAGCTGTATTCTCTTT---AATTT
*
82567 TAGTCACCAAGCTGTTTTCTCTTTA
1 TAGTCACCAAGCTGTATTCTCTTTA
82592 CAAATTTAGT
Statistics
Matches: 49, Mismatches: 2, Indels: 10
0.80 0.03 0.16
Matches are distributed among these distances:
26 3 0.06
27 14 0.29
28 3 0.06
29 1 0.02
32 28 0.57
ACGTcount: A:0.23, C:0.20, G:0.11, T:0.46
Consensus pattern (29 bp):
TAGTCACCAAGCTGTATTCTCTTTAATTT
Found at i:82567 original size:32 final size:32
Alignment explanation
Indices: 82531--82598 Score: 136
Period size: 32 Copynumber: 2.1 Consensus size: 32
82521 GTATTGTTTT
82531 ATTTTAGTCACCAAGCTGTTTTCTCTTTACAA
1 ATTTTAGTCACCAAGCTGTTTTCTCTTTACAA
82563 ATTTTAGTCACCAAGCTGTTTTCTCTTTACAA
1 ATTTTAGTCACCAAGCTGTTTTCTCTTTACAA
82595 ATTT
1 ATTT
82599 AGTAACAAAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.25, C:0.21, G:0.09, T:0.46
Consensus pattern (32 bp):
ATTTTAGTCACCAAGCTGTTTTCTCTTTACAA
Done.