Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008606.1 Hibiscus syriacus cultivar Beakdansim tig00111562_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: 365242
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
File 2 of 2
Found at i:311308 original size:6 final size:6
Alignment explanation
Indices: 311297--311554 Score: 509
Period size: 6 Copynumber: 43.2 Consensus size: 6
311287 TTGTTACAAA
311297 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
311345 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
311393 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
311441 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
311489 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
311537 TATATG TATATG -ATATG T
1 TATATG TATATG TATATG T
311555 CATCACAAAG
Statistics
Matches: 251, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
5 5 0.02
6 246 0.98
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (6 bp):
TATATG
Found at i:320861 original size:30 final size:30
Alignment explanation
Indices: 320825--320883 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
320815 CTGCACCCAA
320825 ATTCAAGAAAAACATATTAATCATTAACTT
1 ATTCAAGAAAAACATATTAATCATTAACTT
*
320855 ATTCAAGAAAAACATATTAATCGTTAACT
1 ATTCAAGAAAAACATATTAATCATTAACT
320884 GATGGTTTAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.49, C:0.14, G:0.05, T:0.32
Consensus pattern (30 bp):
ATTCAAGAAAAACATATTAATCATTAACTT
Found at i:325245 original size:49 final size:49
Alignment explanation
Indices: 325187--325284 Score: 169
Period size: 49 Copynumber: 2.0 Consensus size: 49
325177 TGCTATACTA
*
325187 GCTATGATATCGAATTTAGTTTAAGCACATGATAACTAGTCAAGATAGG
1 GCTATGATATAGAATTTAGTTTAAGCACATGATAACTAGTCAAGATAGG
* *
325236 GCTATGATATAGAATTTAGTTTAAGCACATGATACCTAGTCAGGATAGG
1 GCTATGATATAGAATTTAGTTTAAGCACATGATAACTAGTCAAGATAGG
325285 AATATTCAAC
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 46 1.00
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.31
Consensus pattern (49 bp):
GCTATGATATAGAATTTAGTTTAAGCACATGATAACTAGTCAAGATAGG
Found at i:327547 original size:20 final size:20
Alignment explanation
Indices: 327524--327564 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
327514 CTTATTTTTC
327524 AAATAAAT-TTATAATATTTA
1 AAATAAATGTT-TAATATTTA
*
327544 AAATTAATGTTTAATATTTA
1 AAATAAATGTTTAATATTTA
327564 A
1 A
327565 TGAATAGTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 17 0.89
21 2 0.11
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (20 bp):
AAATAAATGTTTAATATTTA
Found at i:335607 original size:21 final size:23
Alignment explanation
Indices: 335564--335613 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
335554 AATGATTTTA
335564 GAATTT-A-TATTTTCTTTAATT
1 GAATTTAAGTATTTTCTTTAATT
*
335585 G-ATTTAAGTATTTT-TTTATTT
1 GAATTTAAGTATTTTCTTTAATT
335606 GAATTTAA
1 GAATTTAA
335614 AATTAATTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 4 0.16
21 9 0.36
22 12 0.48
ACGTcount: A:0.30, C:0.02, G:0.08, T:0.60
Consensus pattern (23 bp):
GAATTTAAGTATTTTCTTTAATT
Found at i:338643 original size:15 final size:15
Alignment explanation
Indices: 338623--338652 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
338613 CAAATTATAT
338623 CTCTAAATTAGGAAA
1 CTCTAAATTAGGAAA
*
338638 CTCTAAGTTAGGAAA
1 CTCTAAATTAGGAAA
338653 GATACTAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.27
Consensus pattern (15 bp):
CTCTAAATTAGGAAA
Found at i:342436 original size:6 final size:6
Alignment explanation
Indices: 342425--342456 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
342415 GGATGGATTG
342425 GGGGAA GGGGAA GGGGAA GGGGAA GGGGAA GG
1 GGGGAA GGGGAA GGGGAA GGGGAA GGGGAA GG
342457 TAGTCGTCCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.69, T:0.00
Consensus pattern (6 bp):
GGGGAA
Found at i:343456 original size:27 final size:27
Alignment explanation
Indices: 343426--343500 Score: 150
Period size: 27 Copynumber: 2.8 Consensus size: 27
343416 ACAATCATAT
343426 AATTATTTATAAGTAGATTATCAAATG
1 AATTATTTATAAGTAGATTATCAAATG
343453 AATTATTTATAAGTAGATTATCAAATG
1 AATTATTTATAAGTAGATTATCAAATG
343480 AATTATTTATAAGTAGATTAT
1 AATTATTTATAAGTAGATTAT
343501 ATGTAAAGGC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 48 1.00
ACGTcount: A:0.44, C:0.03, G:0.11, T:0.43
Consensus pattern (27 bp):
AATTATTTATAAGTAGATTATCAAATG
Found at i:352629 original size:69 final size:69
Alignment explanation
Indices: 352518--352652 Score: 243
Period size: 69 Copynumber: 2.0 Consensus size: 69
352508 TGAATCCCGC
* * *
352518 CCAGCCTGAAGTGTAGGCACCCAGCTCACCCCAACTTTGTGAAGCAACAGCTGCAGCCACCTCCC
1 CCAGCCCGAAGTGTAGGCACCCAACTCACCCCAACATTGTGAAGCAACAGCTGCAGCCACCTCCC
352583 AGCA
66 AGCA
352587 CCAGCCCGAAGTGTAGGCACCCAACTCACCCCAACATTGTGAAGCAACAGCTGCAGCCACCTCCC
1 CCAGCCCGAAGTGTAGGCACCCAACTCACCCCAACATTGTGAAGCAACAGCTGCAGCCACCTCCC
352652 A
66 A
352653 TGGTTTGTTA
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
69 63 1.00
ACGTcount: A:0.27, C:0.40, G:0.19, T:0.13
Consensus pattern (69 bp):
CCAGCCCGAAGTGTAGGCACCCAACTCACCCCAACATTGTGAAGCAACAGCTGCAGCCACCTCCC
AGCA
Found at i:352939 original size:29 final size:30
Alignment explanation
Indices: 352893--352975 Score: 71
Period size: 29 Copynumber: 2.8 Consensus size: 30
352883 CAAATTTTGG
* **
352893 TTAGTGATCAAAACATAAATTTTG-AAAGT
1 TTAGTGACCAAAGTATAAATTTTGAAAAGT
* *
352922 TTAGTGACCAAAGTATAAGTTTAGAAAAGT
1 TTAGTGACCAAAGTATAAATTTTGAAAAGT
* *
352952 TCAAG-GACCAAAGTGATAATTTTT
1 T-TAGTGACCAAAGT-ATAAATTTT
352976 CCGAAAAAGA
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
29 19 0.44
30 15 0.35
31 9 0.21
ACGTcount: A:0.42, C:0.08, G:0.17, T:0.33
Consensus pattern (30 bp):
TTAGTGACCAAAGTATAAATTTTGAAAAGT
Found at i:358899 original size:54 final size:55
Alignment explanation
Indices: 358835--358941 Score: 162
Period size: 54 Copynumber: 2.0 Consensus size: 55
358825 GGCTTCAGAT
* *
358835 GATTCATGAAGAAGAACATTCGACGAATGAAG-AATTTGAACCTGACTGAAGAAC
1 GATTCATGAAGAAGAACATCCGACGAATGAAGAAATTTGAAACTGACTGAAGAAC
* * *
358889 GATTCATGAAGAAGGACATCCGATGAATGAAGAAATTTGAAACTGATTGAAGA
1 GATTCATGAAGAAGAACATCCGACGAATGAAGAAATTTGAAACTGACTGAAGA
358942 CTGATCCACA
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
54 29 0.62
55 18 0.38
ACGTcount: A:0.43, C:0.12, G:0.23, T:0.21
Consensus pattern (55 bp):
GATTCATGAAGAAGAACATCCGACGAATGAAGAAATTTGAAACTGACTGAAGAAC
Found at i:358956 original size:55 final size:54
Alignment explanation
Indices: 358843--358964 Score: 138
Period size: 55 Copynumber: 2.2 Consensus size: 54
358833 ATGATTCATG
* * * * **
358843 AAGAAGAACATTCGACGAATGAAGAATTTGAACCTGACTGAAGAACGATTCATG
1 AAGAAGGACATCCGACGAATGAAGAATTTGAAACTGACTGAAGAACGATCCACA
* *
358897 AAGAAGGACATCCGATGAATGAAGAAATTTGAAACTGATTGAAG-ACTGATCCACA
1 AAGAAGGACATCCGACGAATGAAG-AATTTGAAACTGACTGAAGAAC-GATCCACA
*
358952 AAGAAAGACATCC
1 AAGAAGGACATCC
358965 TAAAGATGTT
Statistics
Matches: 57, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
54 23 0.40
55 34 0.60
ACGTcount: A:0.44, C:0.16, G:0.21, T:0.19
Consensus pattern (54 bp):
AAGAAGGACATCCGACGAATGAAGAATTTGAAACTGACTGAAGAACGATCCACA
Found at i:359747 original size:67 final size:70
Alignment explanation
Indices: 359617--359759 Score: 222
Period size: 67 Copynumber: 2.1 Consensus size: 70
359607 CCCTATTATA
359617 CAAGAAAATATGAAGACTTCGGTGAGAATCTGAATGTTAGTGGTGCAACCAATGTGATGATAGCA
1 CAAGAAAATATGAAGACTTCGGTGAGAATCTGAATGTTA-TGGTGCAACCAATGTGATGATAGCA
359682 A-TGAT
65 ACTGAT
* *
359687 CAAGAACA-ATGAAGACTTCGAGTGAGAATCTGAATG-T-TGGTGCAGCCAATGTGATGATAGCA
1 CAAGAAAATATGAAGACTTCG-GTGAGAATCTGAATGTTATGGTGCAACCAATGTGATGATAGCA
359749 ACTGAT
65 ACTGAT
359755 CAAGA
1 CAAGA
359760 CCTGTTAGGG
Statistics
Matches: 69, Mismatches: 2, Indels: 6
0.90 0.03 0.08
Matches are distributed among these distances:
67 25 0.36
68 9 0.13
69 13 0.19
70 22 0.32
ACGTcount: A:0.37, C:0.13, G:0.26, T:0.24
Consensus pattern (70 bp):
CAAGAAAATATGAAGACTTCGGTGAGAATCTGAATGTTATGGTGCAACCAATGTGATGATAGCAA
CTGAT
Found at i:364515 original size:36 final size:36
Alignment explanation
Indices: 364475--364571 Score: 103
Period size: 33 Copynumber: 2.8 Consensus size: 36
364465 AAAGCCAAGT
* *
364475 CTTCACCAAAGAGTAATGAAGCAAATCCA-ATTGAGC
1 CTTCACC-AAGAGTAGTGAAGCAAATCCATATTAAGC
* *
364511 CTTCACCAA-AGTAGTGAAG-TAA-CCATCTTAAGC
1 CTTCACCAAGAGTAGTGAAGCAAATCCATATTAAGC
*
364544 CTTCACCGAAGAGTAGTGAAGCATATCC
1 CTTCACC-AAGAGTAGTGAAGCAAATCC
364572 TTTTTAATCC
Statistics
Matches: 50, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
32 3 0.06
33 14 0.28
34 11 0.22
35 12 0.24
36 8 0.16
37 2 0.04
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.22
Consensus pattern (36 bp):
CTTCACCAAGAGTAGTGAAGCAAATCCATATTAAGC
Found at i:365107 original size:54 final size:54
Alignment explanation
Indices: 364960--365198 Score: 362
Period size: 54 Copynumber: 4.5 Consensus size: 54
364950 TAAAGTGGTA
364960 AAGAAGAAGATGTTCGAGTTCCATACTCCCTAGAG-AA-AGGGAGCGAACCCGT
1 AAGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGT
365012 AAGAAGAAGATGTTCG-GTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGT
1 AAGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGT
* * * * *
365065 AAAAAGAAGATGCTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCAAATCCAT
1 AAGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGT
*
365119 AAGAAGAAGATGTTCGAGTTCCATAC-CCCTAGA-TAAGAGGGAGCGAACCCGT
1 AAGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGT
* * *
365171 AAGAAGAAGACGTTTGATTTCCATACTC
1 AAGAAGAAGATGTTCGAGTTCCATACTC
365199 TCTGAAGCAA
Statistics
Matches: 169, Mismatches: 14, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
51 18 0.11
52 56 0.33
53 37 0.22
54 58 0.34
ACGTcount: A:0.36, C:0.21, G:0.25, T:0.18
Consensus pattern (54 bp):
AAGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGT
Done.