Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008888.1 Hibiscus syriacus cultivar Beakdansim tig00112153_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: 1025554
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 5
Found at i:1009563 original size:29 final size:29
Alignment explanation
Indices: 1009521--1009598 Score: 106
Period size: 29 Copynumber: 2.7 Consensus size: 29
1009511 ATGTATTCAT
1009521 TATTTTAGTCCCTTATA-TTTCAATTTTTG-
1 TATTTTAGTCCCTTA-AGTTTCAA-TTTTGC
* *
1009550 TTTTTTAGTCCCTTAAGTTTCTATTTTGC
1 TATTTTAGTCCCTTAAGTTTCAATTTTGC
1009579 TATTTTAGTCCCTTAAGTTT
1 TATTTTAGTCCCTTAAGTTT
1009599 TTATTTTTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
28 6 0.14
29 38 0.86
ACGTcount: A:0.18, C:0.15, G:0.09, T:0.58
Consensus pattern (29 bp):
TATTTTAGTCCCTTAAGTTTCAATTTTGC
Found at i:1013014 original size:4 final size:4
Alignment explanation
Indices: 1013005--1013035 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
1012995 ATTGCTAATT
*
1013005 TTTA TTTA TTTA TTTA CTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1013036 TATGTTCGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:1013238 original size:14 final size:14
Alignment explanation
Indices: 1013192--1013243 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
1013182 AATTCATGCC
1013192 CTTTACATTTTATTTA
1 CTTTA-ATTTTA-TTA
* *
1013208 -TTTAATTTTAGTC
1 CTTTAATTTTATTA
1013221 CTTTAATTTTATTA
1 CTTTAATTTTATTA
*
1013235 CTTTTATTT
1 CTTTAATTT
1013244 ACTGTTTTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
13 1 0.03
14 25 0.83
15 4 0.13
ACGTcount: A:0.23, C:0.10, G:0.02, T:0.65
Consensus pattern (14 bp):
CTTTAATTTTATTA
Found at i:1015623 original size:2 final size:2
Alignment explanation
Indices: 1015616--1015688 Score: 146
Period size: 2 Copynumber: 36.5 Consensus size: 2
1015606 GTACATACAT
1015616 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
1015658 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1015689 TGAGACAGTG
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 71 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1017018 original size:29 final size:31
Alignment explanation
Indices: 1016980--1017038 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 31
1016970 CATGTCCGTT
1016980 TTTTCAATTTAATAACTAACGTTT-ATTTTA
1 TTTTCAATTTAATAACTAACGTTTGATTTTA
* *
1017010 TTTT-AATTTTATATCTAACGTTTGATTTT
1 TTTTCAATTTAATAACTAACGTTTGATTTT
1017039 GTCACTTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 17 0.65
30 9 0.35
ACGTcount: A:0.29, C:0.08, G:0.05, T:0.58
Consensus pattern (31 bp):
TTTTCAATTTAATAACTAACGTTTGATTTTA
Found at i:1017727 original size:5 final size:5
Alignment explanation
Indices: 1017717--1017744 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
1017707 TAGAGTGAGA
1017717 GGGAG GGGAG GGGAG GGGAG GGGAG GGG
1 GGGAG GGGAG GGGAG GGGAG GGGAG GGG
1017745 GGTTGGGTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.82, T:0.00
Consensus pattern (5 bp):
GGGAG
Found at i:1017786 original size:18 final size:18
Alignment explanation
Indices: 1017755--1017796 Score: 59
Period size: 17 Copynumber: 2.3 Consensus size: 18
1017745 GGTTGGGTGT
*
1017755 TTTTTTGAATATATATATA
1 TTTTTTCAATATATA-ATA
1017774 TTTTTTCAA-ATATAATA
1 TTTTTTCAATATATAATA
1017791 TTTTTT
1 TTTTTT
1017797 TAATGGGTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 9 0.41
18 5 0.23
19 8 0.36
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (18 bp):
TTTTTTCAATATATAATA
Found at i:1023067 original size:9 final size:9
Alignment explanation
Indices: 1023053--1023079 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
1023043 AACACAAAAA
1023053 AAAAATAAT
1 AAAAATAAT
1023062 AAAAATAAT
1 AAAAATAAT
1023071 AAAAATAAT
1 AAAAATAAT
1023080 TTGAAAACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (9 bp):
AAAAATAAT
Done.