Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004253.1 Hibiscus syriacus cultivar Beakdansim tig00009324_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: 37608
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:8299 original size:12 final size:14
Alignment explanation
Indices: 8282--8314 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
8272 TAAAATTCAT
8282 AAATAATT-A-TTA
1 AAATAATTAATTTA
8294 AAATAATTAATTTA
1 AAATAATTAATTTA
8308 AAATAAT
1 AAATAAT
8315 CTTTTAGATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 8 0.42
13 1 0.05
14 10 0.53
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
AAATAATTAATTTA
Found at i:13652 original size:21 final size:21
Alignment explanation
Indices: 13628--13667 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
13618 TGATCAAATG
13628 ATAT-TATTTTAGTAATTTTAT
1 ATATATATTTT-GTAATTTTAT
*
13649 ATATATATTTTGTGATTTT
1 ATATATATTTTGTAATTTT
13668 TAGGTAGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.62
Consensus pattern (21 bp):
ATATATATTTTGTAATTTTAT
Found at i:14086 original size:18 final size:17
Alignment explanation
Indices: 14063--14098 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
14053 AACAAAAAGT
*
14063 AATTTTAATGGCTTCAAA
1 AATTTTAAGGGCTT-AAA
14081 AATTTTAAGGGCTTAAA
1 AATTTTAAGGGCTTAAA
14098 A
1 A
14099 TACAATTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.42, C:0.08, G:0.14, T:0.36
Consensus pattern (17 bp):
AATTTTAAGGGCTTAAA
Found at i:14963 original size:2 final size:2
Alignment explanation
Indices: 14958--14989 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
14948 TTTTCGCTCA
14958 AT 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 AT
14990 TTTAAACTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:15202 original size:24 final size:25
Alignment explanation
Indices: 15158--15209 Score: 63
Period size: 24 Copynumber: 2.1 Consensus size: 25
15148 TAAGTTTTAT
*
15158 ATTTTTAAATATTTTATATTTTC-C
1 ATTTTTAAATATTTTAAATTTTCAC
*
15182 ATTTTTTAAT-TTTTAAAATTTTCAC
1 ATTTTTAAATATTTT-AAATTTTCAC
15207 ATT
1 ATT
15210 CATAAAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 4 0.17
24 16 0.67
25 4 0.17
ACGTcount: A:0.31, C:0.08, G:0.00, T:0.62
Consensus pattern (25 bp):
ATTTTTAAATATTTTAAATTTTCAC
Found at i:16224 original size:58 final size:60
Alignment explanation
Indices: 16150--16291 Score: 207
Period size: 58 Copynumber: 2.4 Consensus size: 60
16140 TTAAATTTTT
* ** *
16150 CGACTATTAAAAGTTACAAAATGATC-ATTTGACAATAGGGAGTTGTTTTGTTGAGT-CC
1 CGACTATTAAAAGTTACAAAATGATCTATTTAACAATAACGAGTTGTTTTGTCGAGTCCC
* *
16208 CGACTATTAAAAGTTACAAAATAATCTTTTTAACAATAACGAGTTGTTTTGTCGAGTCCC
1 CGACTATTAAAAGTTACAAAATGATCTATTTAACAATAACGAGTTGTTTTGTCGAGTCCC
16268 CTGACTATTAAAAGTTACAAAATG
1 C-GACTATTAAAAGTTACAAAATG
16292 TCACCCGACT
Statistics
Matches: 74, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
58 25 0.34
59 25 0.34
60 3 0.04
61 21 0.28
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (60 bp):
CGACTATTAAAAGTTACAAAATGATCTATTTAACAATAACGAGTTGTTTTGTCGAGTCCC
Found at i:16693 original size:3 final size:3
Alignment explanation
Indices: 16667--16711 Score: 56
Period size: 3 Copynumber: 15.0 Consensus size: 3
16657 TTTTGCCCAT
* *
16667 TTA TTT TTA TTTA TGA TT- TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
16712 AATTTATATT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
2 2 0.06
3 31 0.86
4 3 0.08
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:19053 original size:63 final size:64
Alignment explanation
Indices: 18974--19110 Score: 188
Period size: 64 Copynumber: 2.2 Consensus size: 64
18964 TACAAAGTAT
* * * *
18974 ATCGATGCACAGGGAGTGCATCGATGCA-CCCA-TATTAATGGAAACATCGAATGTAATTGGTGC
1 ATCGATGCACAAGGAGTGCATCGATGCATCCCATTA-AAATGAAAACATCGAAGGTAATTGGTGC
* * *
19037 ATCGATGCATAAGGAGTGCATCGATGCATCCCCTTAAAATGAAAACATCGAAGGTGATTGGTGC
1 ATCGATGCACAAGGAGTGCATCGATGCATCCCATTAAAATGAAAACATCGAAGGTAATTGGTGC
19101 ATCGATGCAC
1 ATCGATGCAC
19111 TGTTGAATGA
Statistics
Matches: 64, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
63 26 0.41
64 36 0.56
65 2 0.03
ACGTcount: A:0.32, C:0.20, G:0.25, T:0.23
Consensus pattern (64 bp):
ATCGATGCACAAGGAGTGCATCGATGCATCCCATTAAAATGAAAACATCGAAGGTAATTGGTGC
Found at i:22799 original size:63 final size:64
Alignment explanation
Indices: 22722--22858 Score: 197
Period size: 64 Copynumber: 2.2 Consensus size: 64
22712 TACAGAGTGT
* * *
22722 ATCGATGCACAAGGAGTGCATCGATGCA-CCCA-TATTAATGGAAACATCGAATGTAATTGGTGC
1 ATCGATGCACAAGGAGTGCATCGATGCATCCCATTA-AAATGAAAACATCGAAGGTAATTGGTGC
* * *
22785 ATCGATGCATAAGGAGTGCATCGATGCATCCCCTTAAAATGAAAACATCGAAGGTGATTGGTGC
1 ATCGATGCACAAGGAGTGCATCGATGCATCCCATTAAAATGAAAACATCGAAGGTAATTGGTGC
22849 ATCGATGCAC
1 ATCGATGCAC
22859 TGTTGAATAC
Statistics
Matches: 65, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
63 27 0.42
64 36 0.55
65 2 0.03
ACGTcount: A:0.33, C:0.20, G:0.24, T:0.23
Consensus pattern (64 bp):
ATCGATGCACAAGGAGTGCATCGATGCATCCCATTAAAATGAAAACATCGAAGGTAATTGGTGC
Found at i:24378 original size:2 final size:2
Alignment explanation
Indices: 24366--24412 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
24356 ATATCATGCT
*
24366 TA TA AA 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
24408 TA TA T
1 TA TA T
24413 TTACTTTAGT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:27266 original size:19 final size:19
Alignment explanation
Indices: 27242--27299 Score: 63
Period size: 17 Copynumber: 3.2 Consensus size: 19
27232 ACCGAAACCA
27242 GTTTTTTCGGTTCGGTTCG
1 GTTTTTTCGGTTCGGTTCG
27261 GTTTTTTAACGGTTC-G---G
1 GTTTTTT--CGGTTCGGTTCG
27278 GTTTTTT-GGTTCGGTTCG
1 GTTTTTTCGGTTCGGTTCG
27296 GTTT
1 GTTT
27300 ATCGGTTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 13
0.72 0.00 0.28
Matches are distributed among these distances:
14 5 0.15
15 1 0.03
17 8 0.24
18 5 0.15
19 7 0.21
20 1 0.03
21 6 0.18
ACGTcount: A:0.03, C:0.12, G:0.31, T:0.53
Consensus pattern (19 bp):
GTTTTTTCGGTTCGGTTCG
Found at i:29255 original size:25 final size:25
Alignment explanation
Indices: 29226--29278 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
29216 AGATAAATTC
29226 GGAGAAAATTGAGTGAAATAGAAAA
1 GGAGAAAATTGAGTGAAATAGAAAA
29251 GGAGAAAATTGAGTGAAATAGAAAA
1 GGAGAAAATTGAGTGAAATAGAAAA
29276 GGA
1 GGA
29279 TAAATGAGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.55, C:0.00, G:0.30, T:0.15
Consensus pattern (25 bp):
GGAGAAAATTGAGTGAAATAGAAAA
Found at i:30883 original size:20 final size:19
Alignment explanation
Indices: 30839--30887 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
30829 TTAATAAATA
*
30839 AAATTATTATTATATTATG
1 AAATTATTATTAAATTATG
*
30858 ACAATTATTATTAAACTTATT
1 A-AATTATTATTAAA-TTATG
30879 AAATTATTA
1 AAATTATTA
30888 CAAACTTGTC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 1 0.04
20 20 0.77
21 5 0.19
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (19 bp):
AAATTATTATTAAATTATG
Found at i:34357 original size:2 final size:2
Alignment explanation
Indices: 34350--34408 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
34340 AAAATGCATC
34350 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
34392 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
34409 GTTTCTATAA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.