Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008336.1 Hibiscus syriacus cultivar Beakdansim tig00111053_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: 846240
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
File 4 of 4
Found at i:810588 original size:21 final size:21
Alignment explanation
Indices: 810564--810603 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
810554 CAATATAAGA
* *
810564 ACAATATCAATACTTACACGT
1 ACAATATCAACACTGACACGT
810585 ACAATATCAACACTGACAC
1 ACAATATCAACACTGACAC
810604 CCGAAAATGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.45, C:0.28, G:0.05, T:0.23
Consensus pattern (21 bp):
ACAATATCAACACTGACACGT
Found at i:811242 original size:3 final size:3
Alignment explanation
Indices: 811220--811273 Score: 83
Period size: 3 Copynumber: 17.7 Consensus size: 3
811210 CAAAAACATT
811220 TTA TTA -TA TTA TATA TTTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA T-TA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
811266 TTA TTA TT
1 TTA TTA TT
811274 TTTGTAGGCC
Statistics
Matches: 48, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.04
3 41 0.85
4 4 0.08
5 1 0.02
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:811360 original size:33 final size:33
Alignment explanation
Indices: 811323--811391 Score: 113
Period size: 33 Copynumber: 2.1 Consensus size: 33
811313 TTCAGAAAAT
811323 AAACCAACGTATTTAAGT-CTCATTGAAACACTA
1 AAACCAACGTATTTAAGTCCT-ATTGAAACACTA
*
811356 AAACCAACGTATTTGAGTCCTATTGAAACACTA
1 AAACCAACGTATTTAAGTCCTATTGAAACACTA
811389 AAA
1 AAA
811392 TCGAAGCATT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
33 32 0.94
34 2 0.06
ACGTcount: A:0.43, C:0.20, G:0.10, T:0.26
Consensus pattern (33 bp):
AAACCAACGTATTTAAGTCCTATTGAAACACTA
Found at i:811771 original size:2 final size:2
Alignment explanation
Indices: 811766--811792 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
811756 TTTTCATTGT
811766 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 T
811793 TTCATTTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:825003 original size:12 final size:12
Alignment explanation
Indices: 824978--825015 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
824968 CATAATGTCA
824978 AAATTAATTTTTT
1 AAATT-ATTTTTT
824991 AAA-TATTTATTT
1 AAATTATTT-TTT
825003 AAATTATTTTTT
1 AAATTATTTTTT
825015 A
1 A
825016 CTTTATAGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
11 4 0.17
12 11 0.48
13 8 0.35
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (12 bp):
AAATTATTTTTT
Found at i:829209 original size:24 final size:24
Alignment explanation
Indices: 829182--829242 Score: 113
Period size: 24 Copynumber: 2.5 Consensus size: 24
829172 TTTTCTTTCA
829182 CTTCAATCAAGCTCGAATTTTAGG
1 CTTCAATCAAGCTCGAATTTTAGG
829206 CTTCAATCAAGCTCGAATTTTAGG
1 CTTCAATCAAGCTCGAATTTTAGG
*
829230 CTTCAATCGAGCT
1 CTTCAATCAAGCT
829243 TCTAAATTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.33
Consensus pattern (24 bp):
CTTCAATCAAGCTCGAATTTTAGG
Found at i:830787 original size:31 final size:32
Alignment explanation
Indices: 830752--830811 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
830742 AAAGATATTT
830752 GGACCAATTT-GTAATTTTGAAAAAGTTAGGG
1 GGACCAATTTGGTAATTTTGAAAAAGTTAGGG
*
830783 GGACCTATTTGGTAATTTTGAAAAAGTTA
1 GGACCAATTTGGTAATTTTGAAAAAGTTA
830812 TGGGTTTGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
31 9 0.33
32 18 0.67
ACGTcount: A:0.35, C:0.07, G:0.23, T:0.35
Consensus pattern (32 bp):
GGACCAATTTGGTAATTTTGAAAAAGTTAGGG
Found at i:832458 original size:20 final size:19
Alignment explanation
Indices: 832429--832501 Score: 65
Period size: 20 Copynumber: 3.6 Consensus size: 19
832419 AATGTATTTT
*
832429 GTGCACCGATGCACAAGTAA
1 GTGCATCGATGCAC-AGTAA
*
832449 GTGCATCGATGCACCGTTAA
1 GTGCATCGATGCACAG-TAA
* *
832469 GGATGCATCGATACACTGTATA
1 -G-TGCATCGATGCACAGTA-A
832491 GTGCATCGATG
1 GTGCATCGATG
832502 AATACCTTCA
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
19 1 0.02
20 25 0.57
21 4 0.09
22 14 0.32
ACGTcount: A:0.29, C:0.22, G:0.26, T:0.23
Consensus pattern (19 bp):
GTGCATCGATGCACAGTAA
Found at i:833286 original size:30 final size:30
Alignment explanation
Indices: 833252--833324 Score: 119
Period size: 30 Copynumber: 2.4 Consensus size: 30
833242 GGTTCTTCGG
* *
833252 GACCTATGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAAGATCTTTAT
*
833282 GACCTCTAGATAGTTACCGAAGATCTTTAT
1 GACCTCTGGATAGTTACCGAAGATCTTTAT
833312 GACCTCTGGATAG
1 GACCTCTGGATAG
833325 GTCCTTCGGG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.32
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAAGATCTTTAT
Found at i:837805 original size:64 final size:66
Alignment explanation
Indices: 837691--837835 Score: 172
Period size: 64 Copynumber: 2.3 Consensus size: 66
837681 TGCACATTCA
* * * *
837691 AAGTGCATCGATGCA--CCCTTTAAAGAAGAAACATCGAATGCAATTAGTGCATCGATGCATAAG
1 AAGTGCATCGATGCACTCCCTTGAAACAAGAAACATCGAATGCAATTAGTGCACCGATGCACAAG
837754 -
66 T
** * * * *
837754 GCGTGCATCGATGCACTCCCTTGATACAA-AAACATCGAATGTATTTTGTGCACCGATGCACAAG
1 AAGTGCATCGATGCACTCCCTTGAAACAAGAAACATCGAATGCAATTAGTGCACCGATGCACAAG
837818 T
66 T
837819 AAGTGCATCGATGCACT
1 AAGTGCATCGATGCACT
837836 GTTAAGGATG
Statistics
Matches: 67, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
63 13 0.19
64 30 0.45
65 24 0.36
ACGTcount: A:0.33, C:0.22, G:0.21, T:0.24
Consensus pattern (66 bp):
AAGTGCATCGATGCACTCCCTTGAAACAAGAAACATCGAATGCAATTAGTGCACCGATGCACAAG
T
Found at i:837830 original size:20 final size:19
Alignment explanation
Indices: 837801--837875 Score: 78
Period size: 20 Copynumber: 3.7 Consensus size: 19
837791 AATGTATTTT
* *
837801 GTGCACCGATGCACAAGTAA
1 GTGCATCGATGCAC-TGTAA
837821 GTGCATCGATGCACTGTTAA
1 GTGCATCGATGCACTG-TAA
*
837841 GGATGCATCGATACACTGTATA
1 -G-TGCATCGATGCACTGTA-A
837863 GTGCATCGATGCA
1 GTGCATCGATGCA
837876 TACCTTCATT
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
19 1 0.02
20 27 0.57
21 4 0.09
22 15 0.32
ACGTcount: A:0.29, C:0.21, G:0.25, T:0.24
Consensus pattern (19 bp):
GTGCATCGATGCACTGTAA
Found at i:838660 original size:30 final size:30
Alignment explanation
Indices: 838626--838728 Score: 170
Period size: 30 Copynumber: 3.4 Consensus size: 30
838616 GGTTCTTCGG
* *
838626 GACCTATGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
*
838656 GACCTCTAGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
*
838686 GACCTCTGGATAGTTATCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
838716 GACCTCTGGATAG
1 GACCTCTGGATAG
838729 GTCCTTCGAG
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 68 1.00
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.32
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCTTTAT
Found at i:840684 original size:28 final size:28
Alignment explanation
Indices: 840660--840799 Score: 97
Period size: 28 Copynumber: 4.9 Consensus size: 28
840650 ATTATATATG
*
840660 ATATTGTTTATTATGGCTTTGATATGAC
1 ATATTGTTTATAATGGCTTTGATATGAC
* *
840688 ATATTGTTTATAATGGTTTTGATAAAATCATGAG
1 ATATTGTTTATAATGGCTTTG-----AT-ATGAC
* * * * *
840722 ATAATGATTT-TAAAGTCCTTG--ATGAG
1 ATATTG-TTTATAATGGCTTTGATATGAC
*
840748 ATATTGTTTATTATGGCTTTGATATGAC
1 ATATTGTTTATAATGGCTTTGATATGAC
* *
840776 ATATTGTTTATCATGGTTTTGATA
1 ATATTGTTTATAATGGCTTTGATA
840800 AAATCATGAG
Statistics
Matches: 86, Mismatches: 16, Indels: 20
0.70 0.13 0.16
Matches are distributed among these distances:
25 3 0.03
26 17 0.20
28 45 0.52
33 2 0.02
34 16 0.19
35 3 0.03
ACGTcount: A:0.29, C:0.06, G:0.18, T:0.47
Consensus pattern (28 bp):
ATATTGTTTATAATGGCTTTGATATGAC
Found at i:840808 original size:88 final size:88
Alignment explanation
Indices: 840659--840835 Score: 327
Period size: 88 Copynumber: 2.0 Consensus size: 88
840649 TATTATATAT
840659 GATATTGTTTATTATGGCTTTGATATGACATATTGTTTATAATGGTTTTGATAAAATCATGAGAT
1 GATATTGTTTATTATGGCTTTGATATGACATATTGTTTATAATGGTTTTGATAAAATCATGAGAT
840724 AATGATTTTAAAGTCCTTGATGA
66 AATGATTTTAAAGTCCTTGATGA
*
840747 GATATTGTTTATTATGGCTTTGATATGACATATTGTTTATCATGGTTTTGATAAAATCATGAGAT
1 GATATTGTTTATTATGGCTTTGATATGACATATTGTTTATAATGGTTTTGATAAAATCATGAGAT
**
840812 GGTGATTTTAAAGTCCTTGATGA
66 AATGATTTTAAAGTCCTTGATGA
840835 G
1 G
840836 GTAAAATGGA
Statistics
Matches: 86, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
88 86 1.00
ACGTcount: A:0.30, C:0.06, G:0.20, T:0.44
Consensus pattern (88 bp):
GATATTGTTTATTATGGCTTTGATATGACATATTGTTTATAATGGTTTTGATAAAATCATGAGAT
AATGATTTTAAAGTCCTTGATGA
Found at i:840868 original size:88 final size:88
Alignment explanation
Indices: 840680--840858 Score: 214
Period size: 88 Copynumber: 2.0 Consensus size: 88
840670 TTATGGCTTT
840680 GATATGACATATTGTTTATAATGGTTTTGATAAAATCATGAGATAATGATTTTAAAGTCCTTGAT
1 GATATGACATATTGTTTATAATGGTTTTGATAAAATCATGAGATAATGATTTTAAAGTCCTTGAT
*** ** *** **
840745 GAGATATTGTTTATTATGGCTTT
66 GAGATAAAATGGATTATAAATCG
* **
840768 GATATGACATATTGTTTATCATGGTTTTGATAAAATCATGAGATGGTGATTTTAAAGTCCTTGAT
1 GATATGACATATTGTTTATAATGGTTTTGATAAAATCATGAGATAATGATTTTAAAGTCCTTGAT
*
840833 GAGGTAAAATGGATTAAGTAAATCG
66 GAGATAAAATGGATT-A-TAAATCG
840858 G
1 G
840859 GTTGGATATT
Statistics
Matches: 75, Mismatches: 14, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
88 71 0.95
89 1 0.01
90 3 0.04
ACGTcount: A:0.33, C:0.06, G:0.21, T:0.40
Consensus pattern (88 bp):
GATATGACATATTGTTTATAATGGTTTTGATAAAATCATGAGATAATGATTTTAAAGTCCTTGAT
GAGATAAAATGGATTATAAATCG
Found at i:840943 original size:12 final size:12
Alignment explanation
Indices: 840926--840955 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
840916 TTATTAAGTT
840926 TTATTTTATATA
1 TTATTTTATATA
840938 TTATTTTATATA
1 TTATTTTATATA
840950 TTATTT
1 TTATTT
840956 GCCTGTCAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (12 bp):
TTATTTTATATA
Found at i:842676 original size:21 final size:19
Alignment explanation
Indices: 842638--842683 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
842628 AATTAATCCT
842638 ACTAAGTATTAAAGCTAAGA
1 ACTAA-TATTAAAGCTAAGA
842658 ACTAATATTAAGGAGCTAAGA
1 ACTAATATTAA--AGCTAAGA
842679 A-TAAT
1 ACTAAT
842684 GATTCAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.50, C:0.09, G:0.15, T:0.26
Consensus pattern (19 bp):
ACTAATATTAAAGCTAAGA
Found at i:845574 original size:12 final size:12
Alignment explanation
Indices: 845540--845578 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
845530 GGGTTGCCAA
845540 TGGTGGTACATC
1 TGGTGGTACATC
845552 -GGTAGGTACATC
1 TGGT-GGTACATC
*
845564 TGGTGGAACATC
1 TGGTGGTACATC
845576 TGG
1 TGG
845579 AGGGACATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
11 3 0.12
12 18 0.75
13 3 0.12
ACGTcount: A:0.21, C:0.15, G:0.36, T:0.28
Consensus pattern (12 bp):
TGGTGGTACATC
Found at i:845586 original size:24 final size:24
Alignment explanation
Indices: 845540--845586 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
845530 GGGTTGCCAA
* *
845540 TGGTGGTACATCGGTAGGTACATC
1 TGGTGGAACATCGGTAGGGACATC
845564 TGGTGGAACATCTGG-AGGGACAT
1 TGGTGGAACATC-GGTAGGGACAT
845587 AAGATGTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 18 0.90
25 2 0.10
ACGTcount: A:0.23, C:0.15, G:0.36, T:0.26
Consensus pattern (24 bp):
TGGTGGAACATCGGTAGGGACATC
Done.