Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002996.1 Hibiscus syriacus cultivar Beakdansim tig00006197_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: 55964
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:2824 original size:22 final size:21
Alignment explanation
Indices: 2782--2821 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2772 GAGTTTATTT
*
2782 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
2803 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
2822 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:9052 original size:90 final size:89
Alignment explanation
Indices: 8939--9111 Score: 292
Period size: 90 Copynumber: 1.9 Consensus size: 89
8929 TAATCCCGAA
* * *
8939 TATTTAATTTTAATTAATTAAATATATATTTAATTAATTTAAAATAATAAAATCCCTAATATGAT
1 TATTAAATTTTAATTAATCAAATATAGATTTAATTAATTTAAAATAATAAAA-CCCTAATATGAT
9004 TAGGGTAACTTGGATATAAGAGGAT
65 TAGGGTAACTTGGATATAAGAGGAT
*
9029 TATTAAATTTTAATTAATCAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATT
1 TATTAAATTTTAATTAATCAAATATAGATTTAATTAATTTAAAATAATAAAACCCTAATATGATT
*
9094 AGGGTAACTTGGCTATAA
66 AGGGTAACTTGGATATAA
9112 AAGGGTGTGT
Statistics
Matches: 78, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
89 30 0.38
90 48 0.62
ACGTcount: A:0.45, C:0.06, G:0.10, T:0.40
Consensus pattern (89 bp):
TATTAAATTTTAATTAATCAAATATAGATTTAATTAATTTAAAATAATAAAACCCTAATATGATT
AGGGTAACTTGGATATAAGAGGAT
Found at i:9524 original size:21 final size:21
Alignment explanation
Indices: 9495--9534 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
9485 TTTGAGCAGA
9495 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCC-AACGGCTCC
*
9517 AAAA-CATCCTCAACGGCT
1 AAAATCATCCCCAACGGCT
9535 ATATACGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
21 6 0.35
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:11366 original size:16 final size:16
Alignment explanation
Indices: 11345--11377 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
11335 ACATATATAT
11345 ATATATATTAACATTC
1 ATATATATTAACATTC
11361 ATATATATTAACATTC
1 ATATATATTAACATTC
11377 A
1 A
11378 CGTTGCCTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.45, C:0.12, G:0.00, T:0.42
Consensus pattern (16 bp):
ATATATATTAACATTC
Found at i:16229 original size:25 final size:25
Alignment explanation
Indices: 16201--16268 Score: 109
Period size: 25 Copynumber: 2.7 Consensus size: 25
16191 TAAATTACAC
16201 TTTTAAAAATTCTTTTTTACAACAT
1 TTTTAAAAATTCTTTTTTACAACAT
* *
16226 TTTTAAAAATACTTTTCTACAACAT
1 TTTTAAAAATTCTTTTTTACAACAT
*
16251 TTTTAAAAGTTCTTTTTT
1 TTTTAAAAATTCTTTTTT
16269 CTTAAGTTTA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.34, C:0.12, G:0.01, T:0.53
Consensus pattern (25 bp):
TTTTAAAAATTCTTTTTTACAACAT
Found at i:19144 original size:12 final size:12
Alignment explanation
Indices: 19127--19159 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
19117 TTTAGATTCA
19127 TGAACAGTGTTG
1 TGAACAGTGTTG
19139 TGAACAGTGTTG
1 TGAACAGTGTTG
19151 TGAACAGTG
1 TGAACAGTG
19160 CAAAATAGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.27, C:0.09, G:0.33, T:0.30
Consensus pattern (12 bp):
TGAACAGTGTTG
Found at i:22774 original size:6 final size:6
Alignment explanation
Indices: 22763--22801 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
22753 GCCAAAAGAT
22763 TCACAC TCACAC TCACAC TCACAC TCACAC TCACAC TCA
1 TCACAC TCACAC TCACAC TCACAC TCACAC TCACAC TCA
22802 ACTATGTTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.33, C:0.49, G:0.00, T:0.18
Consensus pattern (6 bp):
TCACAC
Found at i:31842 original size:16 final size:17
Alignment explanation
Indices: 31810--31842 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
31800 TATGTTACAT
*
31810 GTGTCATAGGTATTAAA
1 GTGTCATAGGAATTAAA
31827 GTGTCAT-GGAATTAAA
1 GTGTCATAGGAATTAAA
31843 ATATAAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.36, C:0.06, G:0.24, T:0.33
Consensus pattern (17 bp):
GTGTCATAGGAATTAAA
Found at i:32749 original size:19 final size:16
Alignment explanation
Indices: 32715--32745 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
32705 TACAAAATCT
32715 AATAATTCATAATATA
1 AATAATTCATAATATA
*
32731 AATAATTCATTATAT
1 AATAATTCATAATAT
32746 TATAGTCAGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (16 bp):
AATAATTCATAATATA
Found at i:33245 original size:13 final size:14
Alignment explanation
Indices: 33227--33255 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
33217 GGGTCGACGA
33227 GTCAAC-GGGTCGG
1 GTCAACTGGGTCGG
33240 GTCAACTGGGTCGG
1 GTCAACTGGGTCGG
33254 GT
1 GT
33256 AGTTTTGCAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.14, C:0.21, G:0.45, T:0.21
Consensus pattern (14 bp):
GTCAACTGGGTCGG
Found at i:37535 original size:35 final size:35
Alignment explanation
Indices: 37481--37548 Score: 109
Period size: 35 Copynumber: 1.9 Consensus size: 35
37471 AACACATTCA
*
37481 TCAATTTCATTCTAAACCCCAAATTCTAAAATAAT
1 TCAATTGCATTCTAAACCCCAAATTCTAAAATAAT
* *
37516 TCAATTGCATTTTAGACCCCAAATTCTAAAATA
1 TCAATTGCATTCTAAACCCCAAATTCTAAAATA
37549 CTTTAATTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.41, C:0.22, G:0.03, T:0.34
Consensus pattern (35 bp):
TCAATTGCATTCTAAACCCCAAATTCTAAAATAAT
Found at i:37585 original size:27 final size:27
Alignment explanation
Indices: 37554--37611 Score: 116
Period size: 27 Copynumber: 2.1 Consensus size: 27
37544 AAATACTTTA
37554 ATTTAGGGTTTAGAATATAATTAAAGT
1 ATTTAGGGTTTAGAATATAATTAAAGT
37581 ATTTAGGGTTTAGAATATAATTAAAGT
1 ATTTAGGGTTTAGAATATAATTAAAGT
37608 ATTT
1 ATTT
37612 TAGAATTTGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.40, C:0.00, G:0.17, T:0.43
Consensus pattern (27 bp):
ATTTAGGGTTTAGAATATAATTAAAGT
Found at i:37625 original size:35 final size:35
Alignment explanation
Indices: 37581--37654 Score: 121
Period size: 35 Copynumber: 2.1 Consensus size: 35
37571 TAATTAAAGT
37581 ATTTAGGGTTTAGAATATAATTAAAGTATTTTAGA
1 ATTTAGGGTTTAGAATATAATTAAAGTATTTTAGA
* * *
37616 ATTTGGGGTTTAGAATATAATTAAAGTGTTTTGGA
1 ATTTAGGGTTTAGAATATAATTAAAGTATTTTAGA
37651 ATTT
1 ATTT
37655 TGAACATTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.35, C:0.00, G:0.20, T:0.45
Consensus pattern (35 bp):
ATTTAGGGTTTAGAATATAATTAAAGTATTTTAGA
Found at i:46705 original size:19 final size:20
Alignment explanation
Indices: 46670--46707 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
46660 TTTTTATTTG
46670 ATTTTTTTCATTGTGCATTA
1 ATTTTTTTCATTGTGCATTA
*
46690 ATTTTTTTC-TTTTGCATT
1 ATTTTTTTCATTGTGCATT
46708 GAACTGCAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.16, C:0.11, G:0.08, T:0.66
Consensus pattern (20 bp):
ATTTTTTTCATTGTGCATTA
Done.