Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006194.1 Hibiscus syriacus cultivar Beakdansim tig00014739_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: 63365
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Found at i:12480 original size:15 final size:16
Alignment explanation
Indices: 12462--12502 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
12452 TTTTTGAAGT
12462 TTTTTTTTTTTTTG-C
1 TTTTTTTTTTTTTGAC
*
12477 TTTTTTATTTTTTGACC
1 TTTTTTTTTTTTTGA-C
12494 TTTTTTTTT
1 TTTTTTTTT
12503 ATTAAAACAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 13 0.59
17 9 0.41
ACGTcount: A:0.05, C:0.07, G:0.05, T:0.83
Consensus pattern (16 bp):
TTTTTTTTTTTTTGAC
Found at i:20285 original size:16 final size:16
Alignment explanation
Indices: 20252--20290 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
20242 GTTTACTTCA
*
20252 GAATGA-TTAAGTGCT
1 GAATGATTTAAATGCT
*
20267 GAATGATTTAAATGTT
1 GAATGATTTAAATGCT
20283 GAATGATT
1 GAATGATT
20291 CAGATGCTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 6 0.29
16 15 0.71
ACGTcount: A:0.36, C:0.03, G:0.23, T:0.38
Consensus pattern (16 bp):
GAATGATTTAAATGCT
Found at i:20854 original size:29 final size:29
Alignment explanation
Indices: 20822--20877 Score: 96
Period size: 29 Copynumber: 1.9 Consensus size: 29
20812 TAGGGTGGTC
20822 TTTTGT-AGCACATAATAATTGTTTTTTTT
1 TTTTGTAAG-ACATAATAATTGTTTTTTTT
20851 TTTTGTAAGACATAATAATTGTTTTTT
1 TTTTGTAAGACATAATAATTGTTTTTT
20878 CTTGAATGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 24 0.92
30 2 0.08
ACGTcount: A:0.27, C:0.05, G:0.11, T:0.57
Consensus pattern (29 bp):
TTTTGTAAGACATAATAATTGTTTTTTTT
Found at i:24034 original size:28 final size:28
Alignment explanation
Indices: 24002--24103 Score: 100
Period size: 28 Copynumber: 3.6 Consensus size: 28
23992 AAGGGTAGGC
24002 TAATCAGTTTATTGTCTATTGTTTCTGT
1 TAATCAGTTTATTGTCTATTGTTTCTGT
**
24030 TAATCAGTTTATTGTTTCTCAATAATTT-TGT
1 TAATCAGTTTATTG--TCT--ATTGTTTCTGT
** * *
24061 TAAGGA-TATAGTGTCTATTGTTTCTGT
1 TAATCAGTTTATTGTCTATTGTTTCTGT
24088 TAATCAGTTTATTGTC
1 TAATCAGTTTATTGTC
24104 AGGTGGATTC
Statistics
Matches: 56, Mismatches: 12, Indels: 12
0.70 0.15 0.15
Matches are distributed among these distances:
26 5 0.09
27 7 0.12
28 24 0.43
30 8 0.14
31 7 0.12
32 5 0.09
ACGTcount: A:0.23, C:0.10, G:0.15, T:0.53
Consensus pattern (28 bp):
TAATCAGTTTATTGTCTATTGTTTCTGT
Found at i:29230 original size:2 final size:2
Alignment explanation
Indices: 29174--29217 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
29164 TACGGACACT
29174 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
29216 TA
1 TA
29218 AAATAAAATA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:29865 original size:16 final size:17
Alignment explanation
Indices: 29834--29867 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
29824 AATGAGTTAT
29834 ATTTATATTCAAATGGA
1 ATTTATATTCAAATGGA
*
29851 ATTTAT-TTTAAATGGA
1 ATTTATATTCAAATGGA
29867 A
1 A
29868 ACTAGATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.41, C:0.03, G:0.12, T:0.44
Consensus pattern (17 bp):
ATTTATATTCAAATGGA
Found at i:41828 original size:3 final size:3
Alignment explanation
Indices: 41820--41939 Score: 152
Period size: 3 Copynumber: 39.0 Consensus size: 3
41810 GGCCCGTTTG
* * *
41820 TAA TAA TAA TTAA TAA TAA TAT TAG TAA TAAA TAA TAA -AA TTAG TAA
1 TAA TAA TAA -TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA -TAA TAA
* *
41867 TTA TAA TTA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
41915 TAAA TAA TAA TAA TAA TAA TAA TAA
1 T-AA TAA TAA TAA TAA TAA TAA TAA
41940 AATTTAAATG
Statistics
Matches: 103, Mismatches: 9, Indels: 10
0.84 0.07 0.08
Matches are distributed among these distances:
2 2 0.02
3 91 0.88
4 10 0.10
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:45005 original size:60 final size:60
Alignment explanation
Indices: 44939--45082 Score: 189
Period size: 60 Copynumber: 2.4 Consensus size: 60
44929 TATTACCTGG
* * * *
44939 TAATGATTTTTTCCGTGAACCAAACATTAAAATACAATTCCAGATGATCATTCTCCTTGA
1 TAATGATATTTTCCGTGAACCAAACATGAAAATACAATTCCAGAAGATCATTCCCCTTGA
* * * * * *
44999 TAATGATCTTTTCTGTGAACTAAACATGAGAGTACAATTCCGGAAGATCATTCCCCTTGA
1 TAATGATATTTTCCGTGAACCAAACATGAAAATACAATTCCAGAAGATCATTCCCCTTGA
*
45059 TAATGATATTTTCCGCGAACCAAA
1 TAATGATATTTTCCGTGAACCAAA
45083 TGCCCTTAGA
Statistics
Matches: 71, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
60 71 1.00
ACGTcount: A:0.34, C:0.20, G:0.13, T:0.33
Consensus pattern (60 bp):
TAATGATATTTTCCGTGAACCAAACATGAAAATACAATTCCAGAAGATCATTCCCCTTGA
Found at i:47591 original size:55 final size:55
Alignment explanation
Indices: 47495--47599 Score: 138
Period size: 55 Copynumber: 1.9 Consensus size: 55
47485 ACATGTGACA
* * * * * *
47495 ATGACGTGGCATTTCCATGTCACTATTTTATGTTGATGTGGAATTTACACAAATG
1 ATGACGTGGCATGTCCACGTCACTAATATATGCTGACGTGGAATTTACACAAATG
* *
47550 ATGATGTGGCATGTCCACGTCACTAATATGTGCTGACGTGGAATTTACAC
1 ATGACGTGGCATGTCCACGTCACTAATATATGCTGACGTGGAATTTACAC
47600 GTCAGTTTTT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
55 42 1.00
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.34
Consensus pattern (55 bp):
ATGACGTGGCATGTCCACGTCACTAATATATGCTGACGTGGAATTTACACAAATG
Found at i:48766 original size:195 final size:195
Alignment explanation
Indices: 48434--48801 Score: 612
Period size: 195 Copynumber: 1.9 Consensus size: 195
48424 TGGCTGCCGA
* * *
48434 TCTTCGGCAACCTCTTCGATCTTGGCGATAAACCCCACAGGTCATTGGCTAAGCTTGCTCATGTT
1 TCTTCGGCAACCTCTTCGATATTGGCGATAAACCCCACAGGTCATTGGCTAAGCTCGCTCAGGTT
* * *
48499 CAAGGCCCCGTTATGGGTCTCCAACTCGACAGCTTATTCACCGCCGTCGTTTCATCGGAAACAAC
66 CAAGGCCCCGTTATGCGTCTCCAACTCGACAGCTTATTCACCACCGTCGTTTCATCGAAAACAAC
* *
48564 CGCGAAAGAAGTCTTGAAAGAACAGGACCTCGTCTTCTGTAACCGTACCGTTGTCGATGTCGTCC
131 CGCGAAAGAAGTCTTGAAAGAACAAGACCTCGTATTCTGTAACCGTACCGTTGTCGATGTCGTCC
*
48629 TCTTCGGCAACCTCTTCGATATTGGCGATAAACCCCACAGGTTATTGGCTAAGCTCGCTCAGGTT
1 TCTTCGGCAACCTCTTCGATATTGGCGATAAACCCCACAGGTCATTGGCTAAGCTCGCTCAGGTT
* * *
48694 CACGGCGCCGTTATGCGTCTCCAACTCTG-CAGCTTATTCACCATCGTCGTTTCATCGAAAACAA
66 CAAGGCCCCGTTATGCGTCTCCAACTC-GACAGCTTATTCACCACCGTCGTTTCATCGAAAACAA
48758 CCGCGAAAGAAGTCTTGAAAGAACAAGACCTCGTATTCTGTAAC
130 CCGCGAAAGAAGTCTTGAAAGAACAAGACCTCGTATTCTGTAAC
48802 TGAACTATCG
Statistics
Matches: 160, Mismatches: 12, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
195 159 0.99
196 1 0.01
ACGTcount: A:0.24, C:0.29, G:0.21, T:0.26
Consensus pattern (195 bp):
TCTTCGGCAACCTCTTCGATATTGGCGATAAACCCCACAGGTCATTGGCTAAGCTCGCTCAGGTT
CAAGGCCCCGTTATGCGTCTCCAACTCGACAGCTTATTCACCACCGTCGTTTCATCGAAAACAAC
CGCGAAAGAAGTCTTGAAAGAACAAGACCTCGTATTCTGTAACCGTACCGTTGTCGATGTCGTCC
Found at i:54135 original size:106 final size:108
Alignment explanation
Indices: 54009--54288 Score: 252
Period size: 106 Copynumber: 2.6 Consensus size: 108
53999 CTCCCTTTTG
* * * * *
54009 CTTCAGGGAGTATAAAACTCAAACAATCTTCATAAAACAAGTCTGTTCTCTATTCCTTCAGAGAG
1 CTTCAGAGAGTATAAGACTCAAACAATCTTCATAAAACAAGTCCGCTCCCTATT-CTTCAGAGAG
* *
54074 TATAGGAC-T-A-AATCTTCAACAAATGTGTCCGCTCCCCATTC
65 TATAGGACTTAACAACCTTCAACAAACGTGTCCGCTCCCCATTC
* * ** *
54115 CTTCAGAGAGTATAGGACT----CAATCTTCAATCAAACGTGTCCGCTCCCTATTTTTCAGAGAG
1 CTTCAGAGAGTATAAGACTCAAACAATCTTC-ATAAAACAAGTCCGCTCCCTATTCTTCAGAGAG
* * * *
54176 TATATGACTTGAACAACCTTCAACAAACGTTTCTGCTCCCTATTC
65 TATAGGACTT-AACAACCTTCAACAAACGTGTCCGCTCCCCATTC
* * ** ** *
54221 CTTCAGAGAGTATAAGACTCAAATAATTTTCA-ACATTCGTGTCTGCTCCCTATTTCTTCAGAGA
1 CTTCAGAGAGTATAAGACTCAAACAATCTTCATA-AAACAAGTCCGCTCCCTA-TTCTTCAGAGA
54285 GTAT
64 GTAT
54289 TAGACTCGAA
Statistics
Matches: 139, Mismatches: 24, Indels: 18
0.77 0.13 0.10
Matches are distributed among these distances:
102 24 0.17
103 18 0.13
105 1 0.01
106 60 0.43
109 16 0.12
110 20 0.14
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.31
Consensus pattern (108 bp):
CTTCAGAGAGTATAAGACTCAAACAATCTTCATAAAACAAGTCCGCTCCCTATTCTTCAGAGAGT
ATAGGACTTAACAACCTTCAACAAACGTGTCCGCTCCCCATTC
Found at i:54232 original size:55 final size:55
Alignment explanation
Indices: 53997--54417 Score: 376
Period size: 55 Copynumber: 7.8 Consensus size: 55
53987 CCACTGGGTT
* * * * ** **
53997 TGCTCCCTTTTGCTTCAGGGAGTATAAAACTCAAACAATCTTCATA-AAACAAGTC
1 TGCTCCCTATTCCTTCAGAGAGTATAAGACTTGAACAATCTTCA-ACAAACGTGTC
* * * *
54052 TGTTCTCTATTCCTTCAGAGAGTATAGGAC-T--A-AATCTTCAACAAATGTGTC
1 TGCTCCCTATTCCTTCAGAGAGTATAAGACTTGAACAATCTTCAACAAACGTGTC
* * *
54103 CGCTCCCCATTCCTTCAGAGAGTATAGGAC-T---CAATCTTCAATCAAACGTGTC
1 TGCTCCCTATTCCTTCAGAGAGTATAAGACTTGAACAATCTTCAA-CAAACGTGTC
* * * * *
54155 CGCTCCCTATT-TTTCAGAGAGTATATGACTTGAACAACCTTCAACAAACGTTTC
1 TGCTCCCTATTCCTTCAGAGAGTATAAGACTTGAACAATCTTCAACAAACGTGTC
** * * **
54209 TGCTCCCTATTCCTTCAGAGAGTATAAGACTCAAATAATTTTCAACATTCGTGTC
1 TGCTCCCTATTCCTTCAGAGAGTATAAGACTTGAACAATCTTCAACAAACGTGTC
* * * * * ** *
54264 TGCTCCCTATTTCTTCAGAGAGTATTAGACTCGAACAATTTTCAATATTCATGTC
1 TGCTCCCTATTCCTTCAGAGAGTATAAGACTTGAACAATCTTCAACAAACGTGTC
* * * *
54319 TGCTCCCTATTGCTTAAGAGAGTATGAGACTTGAACAATCTTCAACAATCGTGTC
1 TGCTCCCTATTCCTTCAGAGAGTATAAGACTTGAACAATCTTCAACAAACGTGTC
* ** *
54374 TGCTCTCTATTTGTTCAGAGAGTATAAGACTCGAACAATCTTCA
1 TGCTCCCTATTCCTTCAGAGAGTATAAGACTTGAACAATCTTCA
54418 TTTGCTTCAC
Statistics
Matches: 306, Mismatches: 52, Indels: 16
0.82 0.14 0.04
Matches are distributed among these distances:
50 1 0.00
51 66 0.22
52 21 0.07
54 19 0.06
55 199 0.65
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.33
Consensus pattern (55 bp):
TGCTCCCTATTCCTTCAGAGAGTATAAGACTTGAACAATCTTCAACAAACGTGTC
Done.