Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006451.1 Hibiscus syriacus cultivar Beakdansim tig00015627_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: 58902
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:25130 original size:26 final size:26
Alignment explanation
Indices: 25098--25175 Score: 81
Period size: 26 Copynumber: 3.0 Consensus size: 26
25088 AAAAACTATT
25098 TAAATAAATAATAATATTATTAATAA
1 TAAATAAATAATAATATTATTAATAA
* * *
25124 TAAATAAAT-CTAATATAAGATAATAA
1 TAAATAAATAATAATATTA-TTAATAA
25150 T-AAT-AATAATAATACATTATTAATAA
1 TAAATAAATAATAAT--ATTATTAATAA
25176 ACAATATGTG
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
24 3 0.07
25 14 0.33
26 22 0.52
27 3 0.07
ACGTcount: A:0.60, C:0.03, G:0.01, T:0.36
Consensus pattern (26 bp):
TAAATAAATAATAATATTATTAATAA
Found at i:25316 original size:21 final size:21
Alignment explanation
Indices: 25292--25332 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
25282 GTGATTTAAA
25292 TAAATCTAATGA-AAAATATTT
1 TAAATCTAAT-ACAAAATATTT
25313 TAAATCTAATACAAAATATT
1 TAAATCTAATACAAAATATT
25333 ATTTAAATAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.05
21 18 0.95
ACGTcount: A:0.54, C:0.07, G:0.02, T:0.37
Consensus pattern (21 bp):
TAAATCTAATACAAAATATTT
Found at i:26219 original size:20 final size:20
Alignment explanation
Indices: 26190--26262 Score: 92
Period size: 20 Copynumber: 3.6 Consensus size: 20
26180 TCTGTCTAGT
26190 AAAGGATCGATCCCTTTTCA
1 AAAGGATCGATCCCTTTTCA
* ***
26210 AAATGATCGATCCCTTAAGA
1 AAAGGATCGATCCCTTTTCA
*
26230 GAAAGGATCGATCCCTTTTTA
1 -AAAGGATCGATCCCTTTTCA
26251 AAAGGATCGATC
1 AAAGGATCGATC
26263 TCTTGGAGAA
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (20 bp):
AAAGGATCGATCCCTTTTCA
Found at i:39656 original size:90 final size:89
Alignment explanation
Indices: 39541--39717 Score: 284
Period size: 90 Copynumber: 2.0 Consensus size: 89
39531 TCCCGAATAT
* * *
39541 TTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAA-AAAAATCCCTGATATGATTA
1 TTAAATTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAA-CCCTAATATGACTA
39605 GGGTAACTTGGATATAAAAGGATTA
65 GGGTAACTTGGATATAAAAGGATTA
39630 TTAAATTCTAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGACTA
1 TTAAATTC-AATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGACTA
* *
39695 GGGTGACTTGGCTATAAAAGGAT
65 GGGTAACTTGGATATAAAAGGAT
39718 GTGTTAGGTC
Statistics
Matches: 81, Mismatches: 5, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
89 7 0.09
90 69 0.85
91 5 0.06
ACGTcount: A:0.45, C:0.07, G:0.12, T:0.36
Consensus pattern (89 bp):
TTAAATTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGACTAG
GGTAACTTGGATATAAAAGGATTA
Found at i:42516 original size:2 final size:2
Alignment explanation
Indices: 42509--42549 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
42499 TCAAAACAAT
42509 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
42550 GAGGTAAGTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:44392 original size:47 final size:45
Alignment explanation
Indices: 44324--44448 Score: 155
Period size: 47 Copynumber: 2.8 Consensus size: 45
44314 ATAAAATCTC
* * *
44324 TTACCATTTATCCCATAAGCTCTTAAGCTTATTTTACCAAAATAT
1 TTACCATTTATTCCATAAGCTCATAAGCTTATTTTACCAAAATAA
* * *
44369 TTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTATCAATATAA
1 TTACCATTT--ATTCCATAAGCTCATAAGCTTATTTTACCAAAATAA
*
44416 TTGCCA-TTATT-CATAAGCTCATAAGCTTATTTT
1 TTACCATTTATTCCATAAGCTCATAAGCTTATTTT
44449 CATACTTACC
Statistics
Matches: 71, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
43 21 0.30
44 3 0.04
45 9 0.13
46 2 0.03
47 36 0.51
ACGTcount: A:0.33, C:0.19, G:0.06, T:0.42
Consensus pattern (45 bp):
TTACCATTTATTCCATAAGCTCATAAGCTTATTTTACCAAAATAA
Found at i:49024 original size:143 final size:140
Alignment explanation
Indices: 48796--49163 Score: 498
Period size: 134 Copynumber: 2.6 Consensus size: 140
48786 TTACAGTTCT
* *
48796 TCAGGGAAGATTGAATC-TGGGTAGACTTGTTCTGCTGTTACTCAGGGAATATCAAATCTTGAAA
1 TCAGAGAAGATTGAATCAT-GGTAGACTTGTTCTGCTGTCACTCAGGGAATATCAAATCTTGAAA
* * *
48860 GAGAGTGATTTGTTCCGCTTCTTCTGATTCTTCTGAAGGGAATATCAGATCTGGATGAGTTGATC
65 GAGAGTGATATGTTCCACTTCTTCTGA-T-TT-TGAAGGGAATATCAGATATGGATGAGTTGATC
* *
48925 AATTCCGCTGTCAC
127 AATTCCGCTATCAA
* *
48939 TTAGAGAAGATTGAATCATGGTAGACTTGTTCTGCTGTCACTAAGGGAATATCAAATCTTGAAAG
1 TCAGAGAAGATTGAATCATGGTAGACTTGTTCTGCTGTCACTCAGGGAATATCAAATCTTGAAAG
* * * *
49004 AGAGTGATCTATTCCA---CTTC---TTTTGAAGGGAATATCATATATGGATGAGTTGATCCATT
66 AGAGTGATATGTTCCACTTCTTCTGATTTTGAAGGGAATATCAGATATGGATGAGTTGATCAATT
49063 CCGCTATCAA
131 CCGCTATCAA
* * * *
49073 TCAGGGAAGATTGAATCATGGTAGACTTGTTCCGTTGTCACTCAGGGAATATCAAATCTTGAAAT
1 TCAGAGAAGATTGAATCATGGTAGACTTGTTCTGCTGTCACTCAGGGAATATCAAATCTTGAAAG
49138 AGAGTGATATGTTCCACTTCTTCTGA
66 AGAGTGATATGTTCCACTTCTTCTGA
49164 AGGGAATAAC
Statistics
Matches: 198, Mismatches: 20, Indels: 17
0.84 0.09 0.07
Matches are distributed among these distances:
134 114 0.58
135 2 0.01
136 1 0.01
137 4 0.02
140 4 0.02
143 72 0.36
144 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.33
Consensus pattern (140 bp):
TCAGAGAAGATTGAATCATGGTAGACTTGTTCTGCTGTCACTCAGGGAATATCAAATCTTGAAAG
AGAGTGATATGTTCCACTTCTTCTGATTTTGAAGGGAATATCAGATATGGATGAGTTGATCAATT
CCGCTATCAA
Found at i:49127 original size:134 final size:134
Alignment explanation
Indices: 48887--49217 Score: 482
Period size: 134 Copynumber: 2.5 Consensus size: 134
48877 CTTCTTCTGA
* * * *
48887 TTCTTCTGAAGGGAATATCAGATCTGGATGAGTTGATCAATTCCGCTGTCACTTAGAGAAGATTG
1 TTCTTCTGAAGGGAATATCAGATCTGGATGAGTTGATCCATTCCGCTGTCAATCAGGGAAGATTG
* *
48952 AATCATGGTAGACTTGTTCTGCTGTCACTAAGGGAATATCAAATCTTGAAAGAGAGTGATCTATT
66 AATCATGGTAGACTTGTTCCGCTGTCACTAAGGGAATATCAAATCTTGAAAGAGAGTGATATATT
49017 CCAC
131 CCAC
* * * *
49021 TTCTTTTGAAGGGAATATCATATATGGATGAGTTGATCCATTCCGCTATCAATCAGGGAAGATTG
1 TTCTTCTGAAGGGAATATCAGATCTGGATGAGTTGATCCATTCCGCTGTCAATCAGGGAAGATTG
* * * *
49086 AATCATGGTAGACTTGTTCCGTTGTCACTCAGGGAATATCAAATCTTGAAATAGAGTGATATGTT
66 AATCATGGTAGACTTGTTCCGCTGTCACTAAGGGAATATCAAATCTTGAAAGAGAGTGATATATT
49151 CCAC
131 CCAC
* ** * * *
49155 TTCTTCTGAAGGGAATAACAGATCTTTATGAATTGATCCATTCCGCTGTTATTCAGGGAAGAT
1 TTCTTCTGAAGGGAATATCAGATCTGGATGAGTTGATCCATTCCGCTGTCAATCAGGGAAGAT
49218 CAAATCTTGA
Statistics
Matches: 173, Mismatches: 24, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
134 173 1.00
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.33
Consensus pattern (134 bp):
TTCTTCTGAAGGGAATATCAGATCTGGATGAGTTGATCCATTCCGCTGTCAATCAGGGAAGATTG
AATCATGGTAGACTTGTTCCGCTGTCACTAAGGGAATATCAAATCTTGAAAGAGAGTGATATATT
CCAC
Found at i:49168 original size:48 final size:48
Alignment explanation
Indices: 49116--49267 Score: 132
Period size: 48 Copynumber: 3.2 Consensus size: 48
49106 GTTGTCACTC
* *
49116 AGGGAATATCAAATCTTGAAATAGAGTGATATGTTCCACTTCTTCTGA
1 AGGGAATATCAAATCTTGAAATAGAATGATATGTTCCGCTTCTTCTGA
* * * *** * * **
49164 AGGGAATAACAGATCTT--TAT-GAATTGATCCATTCCGC-TGTTATTC
1 AGGGAATATCAAATCTTGAAATAGAA-TGATATGTTCCGCTTCTTCTGA
* * *
49209 AGGGAAGATCAAATCTTGAAAGAGAATGATTTGTTCCGCTTCTTCTGA
1 AGGGAATATCAAATCTTGAAATAGAATGATATGTTCCGCTTCTTCTGA
49257 AGGGAATATCA
1 AGGGAATATCA
49268 GATTTTTCAA
Statistics
Matches: 74, Mismatches: 25, Indels: 10
0.68 0.23 0.09
Matches are distributed among these distances:
45 20 0.27
46 11 0.15
47 11 0.15
48 32 0.43
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.32
Consensus pattern (48 bp):
AGGGAATATCAAATCTTGAAATAGAATGATATGTTCCGCTTCTTCTGA
Found at i:49755 original size:192 final size:191
Alignment explanation
Indices: 49401--49797 Score: 618
Period size: 192 Copynumber: 2.1 Consensus size: 191
49391 AAGGCTTACA
* ** * * *
49401 GATGACCCGATGGATTT-AAAAATCATGCTCGAAAGACTTACTGATGGCCCGAATGACTTATGAA
1 GATGACCCGAAGGATTTGAGCAA-CATGCTCGAAAGACTTACTGATGACCCGAAGGACTTATAAA
*
49465 TTTTGGAAATAGTTTATTGGTAAGAAAGCTTTCTTACTTTTCAAAATTTCAAATTTCAGATTTAA
65 TTTTGGAAATAGTTTATTGGTAAGAAACCTTTCTTACTTTTCAAAATTTCAAATTTCAGATTTAA
**
49530 TATGAGAAACATTTCTCATATTTGAAAAGACATGTGAAAACATCCTGCCTGAAGGTCTTATG
130 TATGAGAAACATTTCTCATATTTGAAAAGACATGTGAAAACATCCTGCCCAAAGGTCTTATG
* *
49592 GATGGCCCGAAGGATTTGAGCAACATGCTCGAAAGACTTACTGATGACCCGAAGGATTTATAAAT
1 GATGACCCGAAGGATTTGAGCAACATGCTCGAAAGACTTACTGATGACCCGAAGGACTTATAAAT
*
49657 TTTGGAAATAGTTTATTGGGTAAGAAACCTTTCTTACTTTTCAAAATTTCAATTTTCAGATTTAA
66 TTTGGAAATAGTTTATT-GGTAAGAAACCTTTCTTACTTTTCAAAATTTCAAATTTCAGATTTAA
* *
49722 TATGAGAAACCTTTCTCATATTTTG-ATAGACATGTGAAAACATCCTGCCCAAAGGTCTTATG
130 TATGAGAAACATTTCTCATA-TTTGAAAAGACATGTGAAAACATCCTGCCCAAAGGTCTTATG
*
49784 GATGACCCGGAGGA
1 GATGACCCGAAGGA
49798 CTTATAAATT
Statistics
Matches: 187, Mismatches: 16, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
191 70 0.37
192 113 0.60
193 4 0.02
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (191 bp):
GATGACCCGAAGGATTTGAGCAACATGCTCGAAAGACTTACTGATGACCCGAAGGACTTATAAAT
TTTGGAAATAGTTTATTGGTAAGAAACCTTTCTTACTTTTCAAAATTTCAAATTTCAGATTTAAT
ATGAGAAACATTTCTCATATTTGAAAAGACATGTGAAAACATCCTGCCCAAAGGTCTTATG
Done.