Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005331.1 Hibiscus syriacus cultivar Beakdansim tig00012075_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: 67832
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:5310 original size:21 final size:20
Alignment explanation
Indices: 5276--5314 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
5266 CAATCATAAA
*
5276 ATATGAAATATATTAATTTT
1 ATATAAAATATATTAATTTT
5296 ATATAAAATTATATTAATT
1 ATATAAAA-TATATTAATT
5315 GAGTTTGAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (20 bp):
ATATAAAATATATTAATTTT
Found at i:19135 original size:4 final size:4
Alignment explanation
Indices: 19126--19167 Score: 84
Period size: 4 Copynumber: 10.5 Consensus size: 4
19116 TTATTTTATT
19126 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AA
19168 AGATGATATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 38 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:20377 original size:30 final size:31
Alignment explanation
Indices: 20341--20402 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
20331 TACCTTCTTA
20341 CATCGGTCCATAGA-TTTTCGAGTTAACCCT
1 CATCGGTCCATAGATTTTTCGAGTTAACCCT
20371 CATCGGTCCATAGATTTTTCGAGTTAACCCT
1 CATCGGTCCATAGATTTTTCGAGTTAACCCT
20402 C
1 C
20403 GTACATTGAC
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 14 0.45
31 17 0.55
ACGTcount: A:0.23, C:0.27, G:0.16, T:0.34
Consensus pattern (31 bp):
CATCGGTCCATAGATTTTTCGAGTTAACCCT
Found at i:21985 original size:18 final size:19
Alignment explanation
Indices: 21956--22002 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 19
21946 GGGATCTTCC
21956 TCTTCTTCTTCCTCCTCTT
1 TCTTCTTCTTCCTCCTCTT
*
21975 TCTTC-TCTTCCTCTTC-T
1 TCTTCTTCTTCCTCCTCTT
*
21992 TCATCTTCTTC
1 TCTTCTTCTTC
22003 TGGGGGGATC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 5 0.20
18 15 0.60
19 5 0.20
ACGTcount: A:0.02, C:0.40, G:0.00, T:0.57
Consensus pattern (19 bp):
TCTTCTTCTTCCTCCTCTT
Found at i:28645 original size:14 final size:14
Alignment explanation
Indices: 28626--28653 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
28616 AATATTCACT
28626 TATTACCCTACAAG
1 TATTACCCTACAAG
28640 TATTACCCTACAAG
1 TATTACCCTACAAG
28654 ACAAGTATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.29, G:0.07, T:0.29
Consensus pattern (14 bp):
TATTACCCTACAAG
Found at i:39223 original size:64 final size:63
Alignment explanation
Indices: 39128--39268 Score: 169
Period size: 64 Copynumber: 2.2 Consensus size: 63
39118 CACATTGAAT
* *
39128 GTGCATCGATGCACTCTTTAAAGAAGAAACATCGAATGCAAATGGTACATCGATGCATAAGG-A
1 GTGCATCGATGCACCCTTTAAAGAAGAAACATCGAAGGCAAATGGTACATCGATGCAT-AGGTA
* * * * **
39191 GTGCATCGATGCATCCCTTTAAA-ATGAAAACATCGAAGGTAATTTGTGTATCGATGCATAGGTA
1 GTGCATCGATGCA-CCCTTTAAAGAAG-AAACATCGAAGGCAAATGGTACATCGATGCATAGGTA
39255 GTGCATCGATGCAC
1 GTGCATCGATGCAC
39269 ATGTTAAAGA
Statistics
Matches: 67, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
63 19 0.28
64 48 0.72
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.26
Consensus pattern (63 bp):
GTGCATCGATGCACCCTTTAAAGAAGAAACATCGAAGGCAAATGGTACATCGATGCATAGGTA
Found at i:40079 original size:30 final size:30
Alignment explanation
Indices: 40045--40114 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
40035 GGTTCTTCGG
* * * *
40045 GACCTATGGACAATTGCTGAGGTTCTTTAT
1 GACCTCTGGACAATTACCGAGGATCTTTAT
* *
40075 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGACAATTACCGAGGATCTTTAT
40105 GACCTCTGGA
1 GACCTCTGGA
40115 TAGGTCATTC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.33
Consensus pattern (30 bp):
GACCTCTGGACAATTACCGAGGATCTTTAT
Found at i:44113 original size:15 final size:13
Alignment explanation
Indices: 44081--44115 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 13
44071 ACATATTATA
44081 TATTAATAATTTT
1 TATTAATAATTTT
44094 TATTATATAATTTT
1 TATTA-ATAATTTT
44108 TAATTAAT
1 T-ATTAAT
44116 CATTGATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 5 0.25
14 11 0.55
15 4 0.20
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TATTAATAATTTT
Found at i:60168 original size:23 final size:23
Alignment explanation
Indices: 60135--60183 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
60125 ATAAGAACTC
60135 CAACATGGAATAAATGAATAATA
1 CAACATGGAATAAATGAATAATA
* *
60158 CAACATTGAATAATTGAATAATA
1 CAACATGGAATAAATGAATAATA
60181 CAA
1 CAA
60184 TAATATGATA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.55, C:0.10, G:0.10, T:0.24
Consensus pattern (23 bp):
CAACATGGAATAAATGAATAATA
Found at i:62755 original size:59 final size:60
Alignment explanation
Indices: 62645--62787 Score: 216
Period size: 59 Copynumber: 2.4 Consensus size: 60
62635 TTAGGCATTG
* * *
62645 ACTATTAAAAGTTATAAAATAGTCCCCTAACTATAGGGAGTTACTTTGTTGAGTCCCTCA
1 ACTATTAAAAGTTACAAAATGGTCCCCTAACTATAGGGAATTACTTTGTTGAGTCCCTCA
* * *
62705 ACTTTTAAAAATTACAAAATGGTCCCCTAA-TATAGGGAATTACTTTGTTGAGTCTCTCA
1 ACTATTAAAAGTTACAAAATGGTCCCCTAACTATAGGGAATTACTTTGTTGAGTCCCTCA
*
62764 ACTACTAAAAGTTACAAAATGGTC
1 ACTATTAAAAGTTACAAAATGGTC
62788 ACATGATAAT
Statistics
Matches: 74, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
59 48 0.65
60 26 0.35
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (60 bp):
ACTATTAAAAGTTACAAAATGGTCCCCTAACTATAGGGAATTACTTTGTTGAGTCCCTCA
Found at i:64559 original size:22 final size:22
Alignment explanation
Indices: 64518--64559 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
64508 CTAAATCACT
*
64518 ATTTTATTATTAATTTTAATTA
1 ATTTTATTATTAATTATAATTA
64540 ATTTTATTAATTAA-TATAAT
1 ATTTTATT-ATTAATTATAAT
64560 GGTAACACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
ATTTTATTATTAATTATAATTA
Found at i:65092 original size:20 final size:20
Alignment explanation
Indices: 65067--65217 Score: 230
Period size: 20 Copynumber: 7.5 Consensus size: 20
65057 AAATGACCAA
*
65067 CAAATTCGCAACACAGATGT
1 CAAATTCGCAACACAGAAGT
65087 CAAATTCGCAACACAGAAGT
1 CAAATTCGCAACACAGAAGT
* *
65107 CAAATTCGTAACACAAAAGT
1 CAAATTCGCAACACAGAAGT
*
65127 CAAATTCGCAACATAGAAGT
1 CAAATTCGCAACACAGAAGT
*
65147 CAAATTCGCAACACATAAGT
1 CAAATTCGCAACACAGAAGT
* *
65167 CAAATTTGCAACACAAAAGT
1 CAAATTCGCAACACAGAAGT
*
65187 CAAATTCGCAACACATAAGT
1 CAAATTCGCAACACAGAAGT
65207 CAAATTCGCAA
1 CAAATTCGCAA
65218 AGCGCGTTTA
Statistics
Matches: 119, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 119 1.00
ACGTcount: A:0.46, C:0.23, G:0.12, T:0.19
Consensus pattern (20 bp):
CAAATTCGCAACACAGAAGT
Found at i:65283 original size:19 final size:19
Alignment explanation
Indices: 65259--65305 Score: 94
Period size: 19 Copynumber: 2.5 Consensus size: 19
65249 TTTCGAATTC
65259 GAAACACAATATTAATTGA
1 GAAACACAATATTAATTGA
65278 GAAACACAATATTAATTGA
1 GAAACACAATATTAATTGA
65297 GAAACACAA
1 GAAACACAA
65306 ATGTAAACAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.55, C:0.13, G:0.11, T:0.21
Consensus pattern (19 bp):
GAAACACAATATTAATTGA
Found at i:65446 original size:20 final size:21
Alignment explanation
Indices: 65398--65446 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
65388 ACATCCGTCC
*
65398 CCATCTCCGATGAAATCCGTT
1 CCATCTCCGACGAAATCCGTT
65419 CCATCTCCGACGAAATCCG-T
1 CCATCTCCGACGAAATCCGTT
*
65439 CTATCTCC
1 CCATCTCC
65447 ATCTCTCATA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 8 0.31
21 18 0.69
ACGTcount: A:0.22, C:0.39, G:0.12, T:0.27
Consensus pattern (21 bp):
CCATCTCCGACGAAATCCGTT
Found at i:66730 original size:20 final size:20
Alignment explanation
Indices: 66702--66739 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
66692 TTTTCTCGTT
*
66702 GCGATAGTCAAATTCGCAAC
1 GCGAAAGTCAAATTCGCAAC
66722 GCGAAAGTCAAATTCGCA
1 GCGAAAGTCAAATTCGCA
66740 TTGCGGTTTT
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:0.37, C:0.24, G:0.21, T:0.18
Consensus pattern (20 bp):
GCGAAAGTCAAATTCGCAAC
Done.