Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009605.1 Hibiscus syriacus cultivar Beakdansim tig00116989_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: 9158330
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 35 of 35
Found at i:9136299 original size:90 final size:89
Alignment explanation
Indices: 9136146--9136317 Score: 299
Period size: 90 Copynumber: 1.9 Consensus size: 89
9136136 TAACACACCC
9136146 TTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATT
1 TTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATT
*
9136211 TAATTAATAGAATTTAATAATCCT
66 TAATTAATAGAAATTAATAATCCT
* *
9136235 TTTTATATCCAAGTTATCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTATAT
1 TTTTATAGCCAAGTTACCCTAATCATATTAGGG-TTTTATTATTTCAAATTAATTAAATCTATAT
*
9136300 TTAATTAATTGAAATTAA
65 TTAATTAATAGAAATTAA
9136318 ATATTCAGGA
Statistics
Matches: 78, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
89 31 0.40
90 47 0.60
ACGTcount: A:0.38, C:0.10, G:0.06, T:0.46
Consensus pattern (89 bp):
TTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATT
TAATTAATAGAAATTAATAATCCT
Found at i:9154834 original size:3 final size:3
Alignment explanation
Indices: 9154826--9154850 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
9154816 AGAACAAGTC
9154826 GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA G
9154851 GGAAACTCAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:9155287 original size:20 final size:20
Alignment explanation
Indices: 9155259--9155301 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
9155249 TGCCCCACCA
9155259 TTTTTCTTTCATTTTC-CTT
1 TTTTTCTTTCATTTTCTCTT
**
9155278 TTTTTCCTTTTTTTTTCTCTT
1 TTTTT-CTTTCATTTTCTCTT
9155299 TTT
1 TTT
9155302 GCTTAACTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 5 0.25
20 9 0.45
21 6 0.30
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (20 bp):
TTTTTCTTTCATTTTCTCTT
Found at i:9155893 original size:18 final size:18
Alignment explanation
Indices: 9155866--9155958 Score: 82
Period size: 18 Copynumber: 5.1 Consensus size: 18
9155856 TACTTTTTAA
9155866 AATT-TAATTTTTATATT
1 AATTATAATTTTTATATT
*
9155883 AATTATAATTTGTATATTATA
1 AATTATAATTT-T-TA-TATT
*
9155904 AATT-TAGTTTTTATATT
1 AATTATAATTTTTATATT
* *
9155921 ATTTACAATTCTTTATATT
1 AATTATAATT-TTTATATT
* *
9155940 ATTTATAATTCTTATATT
1 AATTATAATTTTTATATT
9155958 A
1 A
9155959 TAAATTTTAT
Statistics
Matches: 62, Mismatches: 8, Indels: 11
0.77 0.10 0.14
Matches are distributed among these distances:
17 10 0.16
18 19 0.31
19 19 0.31
20 7 0.11
21 7 0.11
ACGTcount: A:0.35, C:0.03, G:0.02, T:0.59
Consensus pattern (18 bp):
AATTATAATTTTTATATT
Found at i:9155908 original size:38 final size:39
Alignment explanation
Indices: 9155865--9155941 Score: 111
Period size: 38 Copynumber: 2.0 Consensus size: 39
9155855 ATACTTTTTA
*
9155865 AAATTTAATTTTTATATTAATTATAATT-TGTATATTAT
1 AAATTTAATTTTTATATTAATTACAATTCTGTATATTAT
* * *
9155903 AAATTTAGTTTTTATATTATTTACAATTCTTTATATTAT
1 AAATTTAATTTTTATATTAATTACAATTCTGTATATTAT
9155942 TTATAATTCT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
38 25 0.74
39 9 0.26
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.58
Consensus pattern (39 bp):
AAATTTAATTTTTATATTAATTACAATTCTGTATATTAT
Found at i:9155920 original size:20 final size:20
Alignment explanation
Indices: 9155865--9155922 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
9155855 ATACTTTTTA
9155865 AAATTTAATTTTTATA-T-T
1 AAATTTAATTTTTATATTAT
*
9155883 -AATTATAATTTGTATATTAT
1 AAATT-TAATTTTTATATTAT
*
9155903 AAATTTAGTTTTTATATTAT
1 AAATTTAATTTTTATATTAT
9155923 TTACAATTCT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
17 4 0.12
18 10 0.30
19 1 0.03
20 14 0.42
21 4 0.12
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (20 bp):
AAATTTAATTTTTATATTAT
Found at i:9155937 original size:19 final size:19
Alignment explanation
Indices: 9155913--9155959 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
9155903 AAATTTAGTT
9155913 TTTATATTATTTACAATTC
1 TTTATATTATTTACAATTC
*
9155932 TTTATATTATTTATAATTC
1 TTTATATTATTTACAATTC
9155951 -TTATATTAT
1 TTTATATTAT
9155960 AAATTTTATT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
18 9 0.33
19 18 0.67
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTATATTATTTACAATTC
Found at i:9155972 original size:13 final size:14
Alignment explanation
Indices: 9155938--9155974 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
9155928 ATTCTTTATA
9155938 TTATTTAT-AATTC
1 TTATTTATAAATTC
9155951 TTATATTATAAATT-
1 TTAT-TTATAAATTC
9155965 TTATTTATAA
1 TTATTTATAA
9155975 TAACTAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 10 0.45
14 8 0.36
15 4 0.18
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (14 bp):
TTATTTATAAATTC
Found at i:9156557 original size:23 final size:23
Alignment explanation
Indices: 9156527--9156588 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
9156517 CAGTGGCAAC
*
9156527 CAGCAAGCATCACTGTACCAATT
1 CAGCAAGCATCACTGCACCAATT
* *
9156550 CAGCAAGCATCATTGCATCAATT
1 CAGCAAGCATCACTGCACCAATT
9156573 CAGCAAGCATCA-TGCA
1 CAGCAAGCATCACTGCA
9156589 TTAAGAAAGC
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
22 4 0.11
23 32 0.89
ACGTcount: A:0.35, C:0.29, G:0.15, T:0.21
Consensus pattern (23 bp):
CAGCAAGCATCACTGCACCAATT
Found at i:9156701 original size:20 final size:20
Alignment explanation
Indices: 9156676--9156720 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
9156666 AACCCTTACA
* * *
9156676 AATATCAAGTAGAAGCAAGC
1 AATATCAAATAGAAACAAAC
9156696 AATATCAAATAGAAACAAAC
1 AATATCAAATAGAAACAAAC
9156716 AATAT
1 AATAT
9156721 AAAGCATAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.58, C:0.13, G:0.11, T:0.18
Consensus pattern (20 bp):
AATATCAAATAGAAACAAAC
Done.