Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004525.1 Hibiscus syriacus cultivar Beakdansim tig00009985_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: 53049
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:12622 original size:3 final size:3
Alignment explanation
Indices: 12614--12676 Score: 126
Period size: 3 Copynumber: 21.0 Consensus size: 3
12604 TCAGAAACCA
12614 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
12662 TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT
12677 GGGGCATTTC
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:20321 original size:23 final size:23
Alignment explanation
Indices: 20291--20373 Score: 109
Period size: 23 Copynumber: 3.7 Consensus size: 23
20281 GTCGAGGGTT
20291 CTATGTGGTCATTCGGGACAAAA
1 CTATGTGGTCATTCGGGACAAAA
* * *
20314 CTATGTGGTCCTTCAGGATAAAA
1 CTATGTGGTCATTCGGGACAAAA
20337 CTATGTGGTCATTCGGGAC-AAA
1 CTATGTGGTCATTCGGGACAAAA
20359 -TATGTGG-CACTTCGG
1 CTATGTGGTCA-TTCGG
20374 TGCAAATTAT
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
20 2 0.04
21 12 0.23
22 3 0.06
23 36 0.68
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.29
Consensus pattern (23 bp):
CTATGTGGTCATTCGGGACAAAA
Found at i:20364 original size:21 final size:22
Alignment explanation
Indices: 20291--20386 Score: 99
Period size: 23 Copynumber: 4.3 Consensus size: 22
20281 GTCGAGGGTT
20291 CTATGTGGTCATTCGGGACAAAA
1 CTATGTGGTCATTCGGGAC-AAA
* * *
20314 CTATGTGGTCCTTCAGGATAAAA
1 CTATGTGGTCATTCGGGA-CAAA
20337 CTATGTGGTCATTCGGGACAAA
1 CTATGTGGTCATTCGGGACAAA
20359 -TATGTGG-CACTTCGGTG-CAAA
1 CTATGTGGTCA-TTCGG-GACAAA
*
20380 TTATGTG
1 CTATGTG
20387 AGTTGTGGTG
Statistics
Matches: 63, Mismatches: 6, Indels: 9
0.81 0.08 0.12
Matches are distributed among these distances:
20 2 0.03
21 16 0.25
22 10 0.16
23 35 0.56
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (22 bp):
CTATGTGGTCATTCGGGACAAA
Found at i:27728 original size:15 final size:15
Alignment explanation
Indices: 27693--27722 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
27683 GGTCAATAAA
*
27693 TCAGAAAGCATGGTG
1 TCAGAAAGCACGGTG
27708 TCAGAAAGCACGGTG
1 TCAGAAAGCACGGTG
27723 ATAGAACCCC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.17, G:0.33, T:0.17
Consensus pattern (15 bp):
TCAGAAAGCACGGTG
Found at i:30000 original size:36 final size:33
Alignment explanation
Indices: 29930--29996 Score: 118
Period size: 33 Copynumber: 2.1 Consensus size: 33
29920 TTACAAGTAG
29930 ATAATCATATTTCAAGAAATAATAATTTATTTT
1 ATAATCATATTTCAAGAAATAATAATTTATTTT
*
29963 ATAATCATATTTCAAGAAGTAATAA-TTATTTT
1 ATAATCATATTTCAAGAAATAATAATTTATTTT
29995 AT
1 AT
29997 TTATGATTGT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 9 0.27
33 24 0.73
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (33 bp):
ATAATCATATTTCAAGAAATAATAATTTATTTT
Found at i:30982 original size:59 final size:57
Alignment explanation
Indices: 30853--30983 Score: 158
Period size: 59 Copynumber: 2.3 Consensus size: 57
30843 TTTTTTAGGG
* *
30853 TAAAG-TATATAAATGGTCATCAATTATAAGATGTTATTTGTTGAGTCATCTAACTAT
1 TAAAGTTATA-AAATGATCATCAACTATAAGATGTTATTTGTTGAGTCATCTAACTAT
* * * *
30910 TAAAGTTACAAAATGATCTATCAACTATATGATGTTATTTTGTTGGGTCATC-GACTAT
1 TAAAGTTATAAAATGATC-ATCAACTATAAGATGTTA-TTTGTTGAGTCATCTAACTAT
30968 TAAAAGTTATAAAATG
1 T-AAAGTTATAAAATG
30984 GTCACCTAAT
Statistics
Matches: 63, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
57 12 0.19
58 25 0.40
59 26 0.41
ACGTcount: A:0.37, C:0.09, G:0.15, T:0.39
Consensus pattern (57 bp):
TAAAGTTATAAAATGATCATCAACTATAAGATGTTATTTGTTGAGTCATCTAACTAT
Found at i:36420 original size:31 final size:31
Alignment explanation
Indices: 36385--36473 Score: 97
Period size: 31 Copynumber: 2.9 Consensus size: 31
36375 TTAACGATCG
*
36385 AGTGACCAATTTGTTATAAATCGATAATATT
1 AGTGACCAATTTGTTATAAATCAATAATATT
* * * *
36416 AGTGATCGATTTTTTCTAAATCAATAATATT
1 AGTGACCAATTTGTTATAAATCAATAATATT
* * * *
36447 AGTGATCGATTTTTTCTAAATCAATAA
1 AGTGACCAATTTGTTATAAATCAATAA
36474 CATTCGTAAT
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 53 1.00
ACGTcount: A:0.37, C:0.10, G:0.11, T:0.42
Consensus pattern (31 bp):
AGTGACCAATTTGTTATAAATCAATAATATT
Done.