Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005795.1 Hibiscus syriacus cultivar Beakdansim tig00013584_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: 59457
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:7534 original size:18 final size:18
Alignment explanation
Indices: 7479--7535 Score: 87
Period size: 18 Copynumber: 3.2 Consensus size: 18
7469 CGACCCGTTT
*
7479 ACCCGTTGACCCGACCCG
1 ACCCGTTTACCCGACCCG
* *
7497 AACAGTTTACCCGACCCG
1 ACCCGTTTACCCGACCCG
7515 ACCCGTTTACCCGACCCG
1 ACCCGTTTACCCGACCCG
7533 ACC
1 ACC
7536 TATTGACTCG
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.21, C:0.47, G:0.18, T:0.14
Consensus pattern (18 bp):
ACCCGTTTACCCGACCCG
Found at i:9691 original size:24 final size:24
Alignment explanation
Indices: 9664--9777 Score: 151
Period size: 24 Copynumber: 4.8 Consensus size: 24
9654 ATTTGAATTA
9664 TGATCTGATACTTGACATGGATTC
1 TGATCTGATACTTGACATGGATTC
* *
9688 TGATATGATA-TCTGACATGGATTT
1 TGATCTGATACT-TGACATGGATTC
*
9712 TGATCTGATACTTGACTTGGATTC
1 TGATCTGATACTTGACATGGATTC
*
9736 TGATCTGATACTTGACCTGGATT-
1 TGATCTGATACTTGACATGGATTC
* *
9759 TTATATGATACTTGACATG
1 TGATCTGATACTTGACATG
9778 AATTATGTTT
Statistics
Matches: 79, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
23 17 0.22
24 61 0.77
25 1 0.01
ACGTcount: A:0.25, C:0.14, G:0.20, T:0.40
Consensus pattern (24 bp):
TGATCTGATACTTGACATGGATTC
Found at i:9719 original size:48 final size:48
Alignment explanation
Indices: 9664--9777 Score: 169
Period size: 48 Copynumber: 2.4 Consensus size: 48
9654 ATTTGAATTA
9664 TGATCTGATACTTGACATGGATTCTGATATGATA-TCTGACATGGATTT
1 TGATCTGATACTTGACATGGATTCTGATATGATACT-TGACATGGATTT
* * *
9712 TGATCTGATACTTGACTTGGATTCTGATCTGATACTTGACCTGGATTT
1 TGATCTGATACTTGACATGGATTCTGATATGATACTTGACATGGATTT
*
9760 T-ATATGATACTTGACATG
1 TGATCTGATACTTGACATG
9778 AATTATGTTT
Statistics
Matches: 60, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
47 15 0.25
48 44 0.73
49 1 0.02
ACGTcount: A:0.25, C:0.14, G:0.20, T:0.40
Consensus pattern (48 bp):
TGATCTGATACTTGACATGGATTCTGATATGATACTTGACATGGATTT
Found at i:13175 original size:19 final size:19
Alignment explanation
Indices: 13122--13176 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
13112 TTTTTAAAAT
*
13122 AAAAAA-CTTACAATTATAA
1 AAAAAATCTTA-AATTTTAA
*
13141 AAAAAATCTCAAATTTTAA
1 AAAAAATCTTAAATTTTAA
13160 AAAAAATCTTAAATTTT
1 AAAAAATCTTAAATTTT
13177 TGAAAACCTG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
19 29 0.91
20 3 0.09
ACGTcount: A:0.58, C:0.09, G:0.00, T:0.33
Consensus pattern (19 bp):
AAAAAATCTTAAATTTTAA
Found at i:15907 original size:2 final size:2
Alignment explanation
Indices: 15900--15925 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
15890 TACGATAAAC
15900 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
15926 CAGAAAACCG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16765 original size:13 final size:13
Alignment explanation
Indices: 16747--16773 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
16737 GTTGAAAATA
16747 GTCTAAATATTCT
1 GTCTAAATATTCT
16760 GTCTAAATATTCT
1 GTCTAAATATTCT
16773 G
1 G
16774 ATAGGGAAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.11, T:0.44
Consensus pattern (13 bp):
GTCTAAATATTCT
Found at i:23724 original size:28 final size:27
Alignment explanation
Indices: 23639--23727 Score: 85
Period size: 28 Copynumber: 3.3 Consensus size: 27
23629 AACGAAATCG
*
23639 TTTTAATGAATAAACTATTTTAATCTTT
1 TTTTAATGAATAAACTATTTT-ATTTTT
* * *
23667 TTTTAAT--ATAAA-AAATTGATTTATT
1 TTTTAATGAATAAACTATTTTATTT-TT
23692 GTTTTAATGAATAAACTATTTTACTTTTT
1 -TTTTAATGAATAAACTATTTTA-TTTTT
23721 TTTTAAT
1 TTTTAAT
23728 ATAAAATGCA
Statistics
Matches: 48, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
24 3 0.06
25 5 0.10
26 12 0.25
28 19 0.40
29 6 0.12
30 3 0.06
ACGTcount: A:0.36, C:0.04, G:0.04, T:0.55
Consensus pattern (27 bp):
TTTTAATGAATAAACTATTTTATTTTT
Found at i:24112 original size:41 final size:42
Alignment explanation
Indices: 24058--24138 Score: 128
Period size: 41 Copynumber: 2.0 Consensus size: 42
24048 TAAAATTTTG
*
24058 AAAGTAAACCTATTTTTAGAATTTGAAG-GGACGAAATTAAT
1 AAAGTAAACCTATTTATAGAATTTGAAGAGGACGAAATTAAT
* *
24099 AAAGTAAATCTATTTATAGAATTTGAAGAGGGCGAAATTA
1 AAAGTAAACCTATTTATAGAATTTGAAGAGGACGAAATTA
24139 GTTTTTTGAT
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
41 26 0.72
42 10 0.28
ACGTcount: A:0.44, C:0.06, G:0.19, T:0.31
Consensus pattern (42 bp):
AAAGTAAACCTATTTATAGAATTTGAAGAGGACGAAATTAAT
Found at i:25419 original size:20 final size:22
Alignment explanation
Indices: 25394--25433 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
25384 CTCTATGTAA
25394 TTTCTCA-A-TTTGGATTAACC
1 TTTCTCATATTTTGGATTAACC
25414 TTTCTCATATTTTGGATTAA
1 TTTCTCATATTTTGGATTAA
25434 ACTTGATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 1 0.06
22 10 0.56
ACGTcount: A:0.25, C:0.15, G:0.10, T:0.50
Consensus pattern (22 bp):
TTTCTCATATTTTGGATTAACC
Found at i:34886 original size:18 final size:18
Alignment explanation
Indices: 34845--34882 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
34835 TTATTTTTAC
*
34845 TTTAATTGCTTTTACTTA
1 TTTAATCGCTTTTACTTA
34863 TTTAATCGCTTTTA-TTA
1 TTTAATCGCTTTTACTTA
34880 TTT
1 TTT
34883 TAATATTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.21, C:0.11, G:0.05, T:0.63
Consensus pattern (18 bp):
TTTAATCGCTTTTACTTA
Found at i:38643 original size:53 final size:53
Alignment explanation
Indices: 38563--38669 Score: 178
Period size: 53 Copynumber: 2.0 Consensus size: 53
38553 TTAAAGAATT
* *
38563 ATATCCTACATAGACATGAATATTGAACGCAAATGCTCCAAGAAATAAAATGA
1 ATATCCTACATAGACATGAATATTGAACACAAATACTCCAAGAAATAAAATGA
* *
38616 ATATCCTATATAGACATGAATATTGAACACAAATACTTCAAGAAATAAAATGA
1 ATATCCTACATAGACATGAATATTGAACACAAATACTCCAAGAAATAAAATGA
38669 A
1 A
38670 GACTCGAAAG
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
53 50 1.00
ACGTcount: A:0.50, C:0.15, G:0.11, T:0.24
Consensus pattern (53 bp):
ATATCCTACATAGACATGAATATTGAACACAAATACTCCAAGAAATAAAATGA
Found at i:47561 original size:33 final size:33
Alignment explanation
Indices: 47524--47595 Score: 108
Period size: 33 Copynumber: 2.2 Consensus size: 33
47514 ATGGTTCTCC
* *
47524 TCAAGGACCAAAAGCTATGTTACATGGACTAAT
1 TCAAGGAACAAAAGCTATGTTACATGAACTAAT
* *
47557 TCAAGTAACAAAAGCTATGTTACTTGAACTAAT
1 TCAAGGAACAAAAGCTATGTTACATGAACTAAT
47590 TCAAGG
1 TCAAGG
47596 GTGGGTGTCA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.26
Consensus pattern (33 bp):
TCAAGGAACAAAAGCTATGTTACATGAACTAAT
Found at i:48750 original size:10 final size:10
Alignment explanation
Indices: 48737--48770 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
48727 CCTCGCTGCG
48737 CCTAGGTGCA
1 CCTAGGTGCA
48747 CCTAGGTGCA
1 CCTAGGTGCA
*
48757 CCTAGGTGCG
1 CCTAGGTGCA
48767 CCTA
1 CCTA
48771 AGCTACGTGC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.18, C:0.32, G:0.29, T:0.21
Consensus pattern (10 bp):
CCTAGGTGCA
Found at i:55068 original size:16 final size:17
Alignment explanation
Indices: 55043--55074 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
55033 TCGCCGACCG
55043 AATTTCACTATTCACGA
1 AATTTCACTATTCACGA
55060 AATTT-ACTATTCACG
1 AATTTCACTATTCACG
55075 TGAATAGTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.34, C:0.22, G:0.06, T:0.38
Consensus pattern (17 bp):
AATTTCACTATTCACGA
Found at i:56112 original size:15 final size:15
Alignment explanation
Indices: 56092--56121 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
56082 CTCGCCTAAT
56092 CTTCCTTCCGGATCC
1 CTTCCTTCCGGATCC
56107 CTTCCTTCCGGATCC
1 CTTCCTTCCGGATCC
56122 ATCGATCACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.07, C:0.47, G:0.13, T:0.33
Consensus pattern (15 bp):
CTTCCTTCCGGATCC
Done.