Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003760.1 Hibiscus syriacus cultivar Beakdansim tig00008059_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: 65825
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:4030 original size:29 final size:28
Alignment explanation
Indices: 3988--4092 Score: 160
Period size: 29 Copynumber: 3.7 Consensus size: 28
3978 CGGTGACCGA
3988 TATATTTCCTGATCTAACACCGGTCAGAT
1 TATATTTCC-GATCTAACACCGGTCAGAT
*
4017 TATATTTCTCGATCTAACACCAGT--GAT
1 TATATTTC-CGATCTAACACCGGTCAGAT
4044 TATATTTCCGATCTAACACCGGTCAGAT
1 TATATTTCCGATCTAACACCGGTCAGAT
4072 TATATTTCCCGATCTAACACC
1 TATATTT-CCGATCTAACACC
4093 CGTAACAGTA
Statistics
Matches: 70, Mismatches: 2, Indels: 8
0.88 0.03 0.10
Matches are distributed among these distances:
26 14 0.20
27 11 0.16
28 10 0.14
29 34 0.49
30 1 0.01
ACGTcount: A:0.29, C:0.26, G:0.11, T:0.34
Consensus pattern (28 bp):
TATATTTCCGATCTAACACCGGTCAGAT
Found at i:4073 original size:55 final size:56
Alignment explanation
Indices: 3988--4092 Score: 194
Period size: 55 Copynumber: 1.9 Consensus size: 56
3978 CGGTGACCGA
*
3988 TATATTTCCTGATCTAACACCGGTCAGATTATATTTCTCGATCTAACACCAGTGAT
1 TATATTTCCTGATCTAACACCGGTCAGATTATATTTCCCGATCTAACACCAGTGAT
4044 TATATTTCC-GATCTAACACCGGTCAGATTATATTTCCCGATCTAACACC
1 TATATTTCCTGATCTAACACCGGTCAGATTATATTTCCCGATCTAACACC
4093 CGTAACAGTA
Statistics
Matches: 48, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
55 39 0.81
56 9 0.19
ACGTcount: A:0.29, C:0.26, G:0.11, T:0.34
Consensus pattern (56 bp):
TATATTTCCTGATCTAACACCGGTCAGATTATATTTCCCGATCTAACACCAGTGAT
Found at i:7871 original size:35 final size:34
Alignment explanation
Indices: 7786--7872 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 34
7776 ATTTGGTATC
7786 TAAATACAACAAAATTACAATAAGAATTAAATGG
1 TAAATACAACAAAATTACAATAAGAATTAAATGG
* * *
7820 TAAATGATAACCAAATTATAATAACTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--GA-ATTAAATGG
7858 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
7873 ACTAAAATAT
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.53
36 1 0.02
37 5 0.11
38 10 0.22
ACGTcount: A:0.56, C:0.08, G:0.08, T:0.28
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGAATTAAATGG
Found at i:8110 original size:15 final size:15
Alignment explanation
Indices: 8090--8121 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
8080 ATCGCTGTCA
8090 TCATCGTCGTCGTCG
1 TCATCGTCGTCGTCG
8105 TCATCGTCGTCGTCG
1 TCATCGTCGTCGTCG
8120 TC
1 TC
8122 CTGAGCAGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.06, C:0.34, G:0.25, T:0.34
Consensus pattern (15 bp):
TCATCGTCGTCGTCG
Found at i:10173 original size:16 final size:17
Alignment explanation
Indices: 10154--10187 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
10144 AAATTATATT
10154 AGTAAAATA-TTAAATA
1 AGTAAAATACTTAAATA
10170 AGTAAAATACTTAAATA
1 AGTAAAATACTTAAATA
10187 A
1 A
10188 ATTAAATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.62, C:0.03, G:0.06, T:0.29
Consensus pattern (17 bp):
AGTAAAATACTTAAATA
Found at i:10194 original size:17 final size:16
Alignment explanation
Indices: 10156--10196 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 16
10146 ATTATATTAG
*
10156 TAAAATATTAAATAAG
1 TAAAATATTAAATAAA
10172 TAAAATACTTAAATAAA
1 TAAAATA-TTAAATAAA
*
10189 TTAAATAT
1 TAAAATAT
10197 ATAATATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 8 0.36
17 14 0.64
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.34
Consensus pattern (16 bp):
TAAAATATTAAATAAA
Found at i:10616 original size:29 final size:28
Alignment explanation
Indices: 10560--10643 Score: 98
Period size: 29 Copynumber: 2.9 Consensus size: 28
10550 GCTTTACTGC
10560 TACTAGTGTTAATCTAAAAATATAATCT
1 TACTAGTGTTAATCTAAAAATATAATCT
*
10588 TACTAGTGTTAAATTTAAAAATATAATCT
1 TACTAGTGTT-AATCTAAAAATATAATCT
* * *
10617 GA-TCAGTGTTAGATCGATAAATATAAT
1 TACT-AGTGTTA-ATCTAAAAATATAAT
10644 ATCACTGGTA
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
28 12 0.25
29 36 0.75
ACGTcount: A:0.43, C:0.08, G:0.11, T:0.38
Consensus pattern (28 bp):
TACTAGTGTTAATCTAAAAATATAATCT
Found at i:39312 original size:15 final size:15
Alignment explanation
Indices: 39292--39321 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
39282 TGTTCCTTTT
39292 CGCTATTGCATAGAA
1 CGCTATTGCATAGAA
39307 CGCTATTGCATAGAA
1 CGCTATTGCATAGAA
39322 GGTTCTGGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (15 bp):
CGCTATTGCATAGAA
Found at i:46115 original size:15 final size:16
Alignment explanation
Indices: 46089--46118 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
46079 GAAAATACAC
46089 TATGTATTGCTGAAGG
1 TATGTATTGCTGAAGG
46105 TATGT-TTGCTGAAG
1 TATGTATTGCTGAAG
46119 ATCATCTGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.23, C:0.07, G:0.30, T:0.40
Consensus pattern (16 bp):
TATGTATTGCTGAAGG
Found at i:53420 original size:15 final size:16
Alignment explanation
Indices: 53393--53423 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
53383 ATATTTTGAA
53393 TTATAATTAATATTTT
1 TTATAATTAATATTTT
53409 TTATAA-TAATATTTT
1 TTATAATTAATATTTT
53424 CTCTTTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTATAATTAATATTTT
Found at i:57694 original size:34 final size:35
Alignment explanation
Indices: 57655--57749 Score: 102
Period size: 35 Copynumber: 2.7 Consensus size: 35
57645 AACACAGTCA
*
57655 TCAATTACATTTTAAACCCCAAA-TCCAAAATGGT
1 TCAATTACATTCTAAACCCCAAATTCCAAAATGGT
* * **
57689 TCAATTATATTCTAAACCTCAAATTCCAAAATACT
1 TCAATTACATTCTAAACCCCAAATTCCAAAATGGT
* * **
57724 TAAATTACATGCCCAACCCCAAATTC
1 TCAATTACATTCTAAACCCCAAATTC
57750 ATAACACATT
Statistics
Matches: 49, Mismatches: 11, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
34 20 0.41
35 29 0.59
ACGTcount: A:0.41, C:0.26, G:0.03, T:0.29
Consensus pattern (35 bp):
TCAATTACATTCTAAACCCCAAATTCCAAAATGGT
Found at i:58098 original size:145 final size:146
Alignment explanation
Indices: 57911--58194 Score: 448
Period size: 146 Copynumber: 1.9 Consensus size: 146
57901 CTCAATTCGG
*
57911 TTTATAAATAGTTTACTCGAAATTTTTTCGATTTGAGTTTATAAAATTTAAATCAAGTCGAATTG
1 TTTATAAATAGTTGACTC-AAATTTTTTCGATTTGAGTTTATAAAATTTAAATCAAGTCGAATTG
** * *
57976 AA-TGAATTTTCAAGTTTCTGTTTAAATTTAATTATAAATATTTATCATATTATAATATTATTTG
65 AATTGAATTTTCAAGTTTCCATTTAAATTTAATTATAAATATTTATAATACTATAATATTATTTG
*
58040 ATTCTAATTCAGTTCAA
130 ATTATAATTCAGTTCAA
58057 TTTATAAAATAGTTGACTC-AATTTTTTC-AGTTTGAGTTTATAAAATTTAAATCAAGTCGAATT
1 TTTAT-AAATAGTTGACTCAAATTTTTTCGA-TTTGAGTTTATAAAATTTAAATCAAGTCGAATT
* *
58120 GAATTTAATTTTCGAGTTTCCATTTAAATTTAATTATAAATATTTATAATACTATAATATTATTT
64 GAATTGAATTTTCAAGTTTCCATTTAAATTTAATTATAAATATTTATAATACTATAATATTATTT
58185 GATTATAATT
129 GATTATAATT
58195 TAAATAGTTT
Statistics
Matches: 127, Mismatches: 8, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
144 1 0.01
145 45 0.35
146 69 0.54
147 12 0.09
ACGTcount: A:0.37, C:0.07, G:0.08, T:0.48
Consensus pattern (146 bp):
TTTATAAATAGTTGACTCAAATTTTTTCGATTTGAGTTTATAAAATTTAAATCAAGTCGAATTGA
ATTGAATTTTCAAGTTTCCATTTAAATTTAATTATAAATATTTATAATACTATAATATTATTTGA
TTATAATTCAGTTCAA
Found at i:58760 original size:35 final size:35
Alignment explanation
Indices: 58681--58760 Score: 97
Period size: 35 Copynumber: 2.3 Consensus size: 35
58671 GGGGTTGGGT
** *
58681 ATATAATTGAAGTATTTTGGAATTTGAGATTTAGA
1 ATATAATTGAAACATTTTAGAATTTGAGATTTAGA
* * *
58716 ATGTAATTGAAACATTTTAGAATTTGGGGTTTAGA
1 ATATAATTGAAACATTTTAGAATTTGAGATTTAGA
*
58751 ATATCATTGA
1 ATATAATTGA
58761 TGAATGTGTT
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.36, C:0.03, G:0.20, T:0.41
Consensus pattern (35 bp):
ATATAATTGAAACATTTTAGAATTTGAGATTTAGA
Found at i:64508 original size:36 final size:36
Alignment explanation
Indices: 64459--64553 Score: 156
Period size: 36 Copynumber: 2.7 Consensus size: 36
64449 AGCTGATAAC
* *
64459 GGTGATGGTGAGGAAGGGGATGGCATGGATGGTGAT
1 GGTGAAGGCGAGGAAGGGGATGGCATGGATGGTGAT
64495 GGTGAAGGCGAGGAAGGGGATGGCATGGATGGTGAT
1 GGTGAAGGCGAGGAAGGGGATGGCATGGATGGTGAT
*
64531 GGTGAAGGCGAGG-AGAGGATGGC
1 GGTGAAGGCGAGGAAGGGGATGGC
64554 GGGGTTGCTG
Statistics
Matches: 56, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
35 9 0.16
36 47 0.84
ACGTcount: A:0.24, C:0.05, G:0.54, T:0.17
Consensus pattern (36 bp):
GGTGAAGGCGAGGAAGGGGATGGCATGGATGGTGAT
Done.