Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005241.1 Hibiscus syriacus cultivar Beakdansim tig00011863_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: 56588
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:10055 original size:25 final size:23
Alignment explanation
Indices: 10027--10084 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 23
10017 AATAAATAAT
*
10027 ATTATTTATAATAAAACTTAATATA
1 ATTATTTATAA-AAAA-TTAAAATA
* *
10052 ATTATTTTTAAAATATTAAAATA
1 ATTATTTATAAAAAATTAAAATA
10075 ATTTATTTAT
1 A-TTATTTAT
10085 TATTAAATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
23 8 0.29
24 10 0.36
25 10 0.36
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (23 bp):
ATTATTTATAAAAAATTAAAATA
Found at i:10092 original size:27 final size:27
Alignment explanation
Indices: 10006--10096 Score: 77
Period size: 27 Copynumber: 3.4 Consensus size: 27
9996 TTATTGCAAA
*
10006 TATTAAAATATAATAAATAATATTATTTA-
1 TATT-AAATATTA-AAATAAT-TTATTTAT
* *
10035 TAATAAA-ACTTAATATAA-TTATTT-T
1 TATTAAATA-TTAAAATAATTTATTTAT
10060 TA--AAATATTAAAATAATTTATTTAT
1 TATTAAATATTAAAATAATTTATTTAT
10085 TATTAAATATTA
1 TATTAAATATTA
10097 TTTTTATAAT
Statistics
Matches: 51, Mismatches: 4, Indels: 16
0.72 0.06 0.23
Matches are distributed among these distances:
23 11 0.22
24 7 0.14
25 11 0.22
27 14 0.27
28 5 0.10
29 3 0.06
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (27 bp):
TATTAAATATTAAAATAATTTATTTAT
Found at i:10217 original size:19 final size:19
Alignment explanation
Indices: 10149--10217 Score: 63
Period size: 19 Copynumber: 3.6 Consensus size: 19
10139 TTAAATATCT
10149 TTATTAA-AATATTATTAGA
1 TTATTAATAATATTATTA-A
10168 TTATTATATTAATATTA--AA
1 TTATTA-A-TAATATTATTAA
* *
10187 TATATAAATAATATTATTCA
1 T-TATTAATAATATTATTAA
10207 TTATTAATAAT
1 TTATTAATAAT
10218 TTAATAATAC
Statistics
Matches: 41, Mismatches: 3, Indels: 12
0.73 0.05 0.21
Matches are distributed among these distances:
18 8 0.20
19 18 0.44
20 8 0.20
22 7 0.17
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (19 bp):
TTATTAATAATATTATTAA
Found at i:21666 original size:216 final size:216
Alignment explanation
Indices: 21162--21812 Score: 1277
Period size: 216 Copynumber: 3.0 Consensus size: 216
21152 TTGGTAATTA
21162 AAAATTTGGTGGAAGCTTTTGCAGAAAATTGAAAATATTTGCACAGCGATTTAGAGTGGTTCGAC
1 AAAATTTGGTGGAAGCTTTTGCAGAAAATTGAAAATATTTGCACAGCGATTTAGAGTGGTTCGAC
21227 TCTCTTAACCAAAGTCTACGTCCACTACCTTAGCTATCTACACTAAGGATTTTTCAACAAATTCA
66 TCTCTTAACCAAAGTCTACGTCCACTACCTTAGCTATCTACACTAAGGATTTTTCAACAAATTCA
21292 CTAATTTGTTC-TTTTTTTAGGACAAAGAGTAACCTTACAACTCCCTCAAGAATTATATCCCAAA
131 CTAATTTGTTCTTTTTTTTAGGACAAAGAGTAACCTTACAACTCCCTCAAGAATTATATCCCAAA
21356 TTCTTGAGCACACTCTCTCCC
196 TTCTTGAGCACACTCTCTCCC
21377 AAAATTTGGTGGAAGCTTTTGCAGAAAATTGAAAATATTTGCACAGCGATTTAGAGTGGTTCGAC
1 AAAATTTGGTGGAAGCTTTTGCAGAAAATTGAAAATATTTGCACAGCGATTTAGAGTGGTTCGAC
21442 TCTCTTAACCAAAGTCTACGTCCACTACCTTAGCTATCTACACTAAGGATTTTTCAACAAATTCA
66 TCTCTTAACCAAAGTCTACGTCCACTACCTTAGCTATCTACACTAAGGATTTTTCAACAAATTCA
21507 CTAATTTGTTCTTTTTTTTAGGACAAAGAGTAACCTTACAACTCCCTCAAGAATTATATCCCAAA
131 CTAATTTGTTCTTTTTTTTAGGACAAAGAGTAACCTTACAACTCCCTCAAGAATTATATCCCAAA
21572 TTCTTGAGCACACTCTCTCCC
196 TTCTTGAGCACACTCTCTCCC
21593 AAAATTTGGTGGAAGCTTTTGCAGAAAATTGAAAATATTTGCACAGCGATTTAGAGTGGTTCGAC
1 AAAATTTGGTGGAAGCTTTTGCAGAAAATTGAAAATATTTGCACAGCGATTTAGAGTGGTTCGAC
21658 TCTCTTAACCAAAGTCTACGTCCACTACCTTAGCTATCTACACTAAGGATTTTTCAACAAATTCA
66 TCTCTTAACCAAAGTCTACGTCCACTACCTTAGCTATCTACACTAAGGATTTTTCAACAAATTCA
21723 CTAATTTGTTCTTTTTTTTTAGGACAAAGAGTAACCTTACAACTCCCTCAAGAATTATATCCCAA
131 CTAATTTGTTC-TTTTTTTTAGGACAAAGAGTAACCTTACAACTCCCTCAAGAATTATATCCCAA
*
21788 ATTCTTGAGCACACTTTCTCCC
195 ATTCTTGAGCACACTCTCTCCC
21810 AAA
1 AAA
21813 GAGAAATACA
Statistics
Matches: 433, Mismatches: 1, Indels: 2
0.99 0.00 0.00
Matches are distributed among these distances:
215 141 0.33
216 215 0.50
217 77 0.18
ACGTcount: A:0.32, C:0.22, G:0.13, T:0.33
Consensus pattern (216 bp):
AAAATTTGGTGGAAGCTTTTGCAGAAAATTGAAAATATTTGCACAGCGATTTAGAGTGGTTCGAC
TCTCTTAACCAAAGTCTACGTCCACTACCTTAGCTATCTACACTAAGGATTTTTCAACAAATTCA
CTAATTTGTTCTTTTTTTTAGGACAAAGAGTAACCTTACAACTCCCTCAAGAATTATATCCCAAA
TTCTTGAGCACACTCTCTCCC
Found at i:25102 original size:23 final size:23
Alignment explanation
Indices: 25059--25105 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
25049 ATGCACAACA
*
25059 GAGTGCATTGATGCACATTCAAG
1 GAGTGCATTGATACACATTCAAG
*
25082 GAGTGCATTGGTACATC-TTCAAG
1 GAGTGCATTGATACA-CATTCAAG
25105 G
1 G
25106 TGTATCGATG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 20 0.95
24 1 0.05
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.28
Consensus pattern (23 bp):
GAGTGCATTGATACACATTCAAG
Found at i:31000 original size:64 final size:65
Alignment explanation
Indices: 30868--31069 Score: 189
Period size: 64 Copynumber: 3.1 Consensus size: 65
30858 TACACTTGGG
** * ** **
30868 GTGCATCGATGCATAAAACACATTCGATGCTTCAAATAAGCCT-GGAGTGCATCGATGCA-TGGT
1 GTGCATCGATGCATAAAATGCATTCGATG-TTCAAATTA-TTTAGGAGTGCATCGATGCATTCCT
30931 AT
64 AT
*
30933 GTGCATCGATGCATAAAATGCATTCGATGTTCAAATTATTTAGGAGTGAATCGATGCATTCCT-T
1 GTGCATCGATGCATAAAATGCATTCGATGTTCAAATTATTTAGGAGTGCATCGATGCATTCCTAT
* * * ** * * *
30997 GTGCATCGGTACACAAAATGCATTCGAAATTCAATTTATTCAAGG-GTGCATCGATGCATT-ATA
1 GTGCATCGATGCATAAAATGCATTCGATGTTCAAATTATT-TAGGAGTGCATCGATGCATTCCTA
31060 T
65 T
31061 AGTGCATCG
1 -GTGCATCG
31070 GTACACTACT
Statistics
Matches: 115, Mismatches: 17, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
63 2 0.02
64 73 0.63
65 40 0.35
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.30
Consensus pattern (65 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTCAAATTATTTAGGAGTGCATCGATGCATTCCTAT
Found at i:40544 original size:2 final size:2
Alignment explanation
Indices: 40537--40566 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
40527 TTTCATCACC
40537 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
40567 TCAATTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40964 original size:30 final size:28
Alignment explanation
Indices: 40911--40976 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 28
40901 TTGGACTGGT
* *
40911 GACTAGAATGTAAATTTTAAAAGTTTAGG
1 GACTA-AATGTAAATTATAAAAGTTTAAG
40940 GACTAAAGTGTAAAGTTATAAAAGTTTAAG
1 GACTAAA-TGTAAA-TTATAAAAGTTTAAG
*
40970 GATTAAA
1 GACTAAA
40977 AGTATAAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 2 0.06
29 11 0.34
30 19 0.59
ACGTcount: A:0.45, C:0.03, G:0.20, T:0.32
Consensus pattern (28 bp):
GACTAAATGTAAATTATAAAAGTTTAAG
Found at i:40994 original size:31 final size:29
Alignment explanation
Indices: 40921--40996 Score: 89
Period size: 30 Copynumber: 2.5 Consensus size: 29
40911 GACTAGAATG
* *
40921 TAAATTTTAAAAGTTTAGGGACTAAAGTG
1 TAAATTTTAAAAGTTTAAGGACTAAAGTA
* *
40950 TAAAGTTATAAAAGTTTAAGGATTAAAAGTA
1 TAAA-TTTTAAAAGTTTAAGGACT-AAAGTA
40981 TAAATTTTCAAAAGTT
1 TAAATTTT-AAAAGTT
40997 CAATTTTGGA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
29 4 0.10
30 19 0.49
31 16 0.41
ACGTcount: A:0.46, C:0.03, G:0.16, T:0.36
Consensus pattern (29 bp):
TAAATTTTAAAAGTTTAAGGACTAAAGTA
Found at i:53780 original size:2 final size:2
Alignment explanation
Indices: 53775--53813 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
53765 GTTAATTCCA
53775 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
53814 GTTTCAATGG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:53930 original size:30 final size:32
Alignment explanation
Indices: 53870--53944 Score: 118
Period size: 30 Copynumber: 2.4 Consensus size: 32
53860 AGTATTGCTG
* *
53870 AGCTCGGCTCGAACTCTAAAACTATATGAACA
1 AGCTCGACTCGAACTCGAAAACTATATGAACA
53902 AGCTCGACTCGAACTCGAAAA-T-TATGAACA
1 AGCTCGACTCGAACTCGAAAACTATATGAACA
53932 AGCTCGACTCGAA
1 AGCTCGACTCGAA
53945 AACTCGCAAG
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
30 21 0.51
31 1 0.02
32 19 0.46
ACGTcount: A:0.37, C:0.25, G:0.17, T:0.20
Consensus pattern (32 bp):
AGCTCGACTCGAACTCGAAAACTATATGAACA
Found at i:54112 original size:11 final size:11
Alignment explanation
Indices: 54094--54207 Score: 147
Period size: 11 Copynumber: 10.3 Consensus size: 11
54084 ATTTTAAACC
54094 CGATTCAAGCT
1 CGATTCAAGCT
*
54105 CAATTCAAGCT
1 CGATTCAAGCT
* * *
54116 CAATTTTAAACT
1 CGA-TTCAAGCT
54128 CGATTCAAGCT
1 CGATTCAAGCT
*
54139 CGATTCAAACT
1 CGATTCAAGCT
*
54150 CGATTTAAGCT
1 CGATTCAAGCT
*
54161 CGATTCAAACT
1 CGATTCAAGCT
54172 CGATTCAAGCT
1 CGATTCAAGCT
*
54183 CGATTCAAACT
1 CGATTCAAGCT
54194 CGATTCAAGCT
1 CGATTCAAGCT
54205 CGA
1 CGA
54208 CGGATTTTAA
Statistics
Matches: 88, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
11 80 0.91
12 8 0.09
ACGTcount: A:0.32, C:0.25, G:0.13, T:0.29
Consensus pattern (11 bp):
CGATTCAAGCT
Found at i:54151 original size:22 final size:22
Alignment explanation
Indices: 54094--54207 Score: 174
Period size: 22 Copynumber: 5.1 Consensus size: 22
54084 ATTTTAAACC
* *
54094 CGATTCAAGCTCAATTCAAGCT
1 CGATTCAAACTCGATTCAAGCT
* *
54116 CAATTTTAAACTCGATTCAAGCT
1 CGA-TTCAAACTCGATTCAAGCT
*
54139 CGATTCAAACTCGATTTAAGCT
1 CGATTCAAACTCGATTCAAGCT
54161 CGATTCAAACTCGATTCAAGCT
1 CGATTCAAACTCGATTCAAGCT
54183 CGATTCAAACTCGATTCAAGCT
1 CGATTCAAACTCGATTCAAGCT
54205 CGA
1 CGA
54208 CGGATTTTAA
Statistics
Matches: 83, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
22 65 0.78
23 18 0.22
ACGTcount: A:0.32, C:0.25, G:0.13, T:0.29
Consensus pattern (22 bp):
CGATTCAAACTCGATTCAAGCT
Found at i:54163 original size:33 final size:34
Alignment explanation
Indices: 54077--54207 Score: 185
Period size: 33 Copynumber: 3.9 Consensus size: 34
54067 AACTCGACTG
* *
54077 AAGCTCGATTTTAAACCCGATTCAAGCTCAATTC
1 AAGCTCGATTTTAAACTCGATTCAAGCTCGATTC
*
54111 AAGCTCAATTTTAAACTCGATTCAAGCTCGATTC
1 AAGCTCGATTTTAAACTCGATTCAAGCTCGATTC
* * *
54145 AAACTCGA-TTTAAGCTCGATTCAAACTCGATTC
1 AAGCTCGATTTTAAACTCGATTCAAGCTCGATTC
*
54178 AAGCTCGA-TTCAAACTCGATTCAAGCTCGA
1 AAGCTCGATTTTAAACTCGATTCAAGCTCGA
54208 CGGATTTTAA
Statistics
Matches: 86, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
33 49 0.57
34 37 0.43
ACGTcount: A:0.33, C:0.25, G:0.13, T:0.29
Consensus pattern (34 bp):
AAGCTCGATTTTAAACTCGATTCAAGCTCGATTC
Done.