Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001852.1 Hibiscus syriacus cultivar Beakdansim tig00003750_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: 71880
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:6877 original size:23 final size:23
Alignment explanation
Indices: 6850--6901 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
6840 TTGATTTAAT
6850 TTAAAA-AAACAAAAGTTTAAG-GA
1 TTAAAATAAA-AAAAGTTT-AGTGA
*
6873 TTAAAATTAAAAAAGTTTAGTGA
1 TTAAAATAAAAAAAGTTTAGTGA
6896 TTAAAA
1 TTAAAA
6902 CATTTTAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
22 2 0.08
23 22 0.85
24 2 0.08
ACGTcount: A:0.58, C:0.02, G:0.12, T:0.29
Consensus pattern (23 bp):
TTAAAATAAAAAAAGTTTAGTGA
Found at i:12409 original size:16 final size:17
Alignment explanation
Indices: 12390--12430 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
12380 AGAAACGAGA
12390 AAAAAATATT-TAAAAT
1 AAAAAATATTCTAAAAT
*
12406 AAAAAA-ATTCTGAAAT
1 AAAAAATATTCTAAAAT
*
12422 AAAATATAT
1 AAAAAATAT
12431 ACTGAAACAC
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 3 0.14
16 16 0.76
17 2 0.10
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.29
Consensus pattern (17 bp):
AAAAAATATTCTAAAAT
Found at i:25502 original size:26 final size:26
Alignment explanation
Indices: 25466--25519 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
25456 GTATTTGCCG
25466 TTCGGATGAAATTTAGATTAAAAAAC
1 TTCGGATGAAATTTAGATTAAAAAAC
25492 TTCGGATGAAATTTAGATTAAAAAAC
1 TTCGGATGAAATTTAGATTAAAAAAC
25518 TT
1 TT
25520 ATTATATTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.44, C:0.07, G:0.15, T:0.33
Consensus pattern (26 bp):
TTCGGATGAAATTTAGATTAAAAAAC
Found at i:31767 original size:17 final size:17
Alignment explanation
Indices: 31711--31776 Score: 59
Period size: 17 Copynumber: 4.0 Consensus size: 17
31701 CTAATTTTTC
31711 ATTATAT-TATT-TTA-
1 ATTATATATATTATTAT
*
31725 ATTAT-TATTATTATTAA
1 ATTATATA-TATTATTAT
* *
31742 ATAAAATATATTATTAT
1 ATTATATATATTATTAT
31759 ATTATATATATATATTAT
1 ATTATATATAT-TATTAT
31777 TATCATTAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
13 1 0.02
14 5 0.12
15 4 0.10
16 3 0.07
17 20 0.49
18 8 0.20
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTATATATATTATTAT
Found at i:33107 original size:12 final size:12
Alignment explanation
Indices: 33077--33114 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
33067 ATTACTTTTA
33077 TATTTTAATTAT
1 TATTTTAATTAT
**
33089 TGCTTTAATTAT
1 TATTTTAATTAT
33101 TATTTT-ATTAT
1 TATTTTAATTAT
33112 TAT
1 TAT
33115 CTTAGTCATA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
11 8 0.36
12 14 0.64
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.66
Consensus pattern (12 bp):
TATTTTAATTAT
Found at i:33137 original size:10 final size:10
Alignment explanation
Indices: 33122--33146 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
33112 TATCTTAGTC
33122 ATATAAATAT
1 ATATAAATAT
33132 ATATAAATAT
1 ATATAAATAT
33142 ATATA
1 ATATA
33147 TTATTTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (10 bp):
ATATAAATAT
Found at i:36984 original size:23 final size:23
Alignment explanation
Indices: 36928--36986 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
36918 GGGAGAGACA
* *
36928 AAATAAGATT-AAAAAATAATTT
1 AAATAAAATTAAAAAAATAATTC
*
36950 AATTTAAAATTAAAAAAATAATTC
1 AA-ATAAAATTAAAAAAATAATTC
*
36974 AAATAATATTAAA
1 AAATAAAATTAAA
36987 TCTTTTATAT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
22 2 0.07
23 15 0.50
24 13 0.43
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (23 bp):
AAATAAAATTAAAAAAATAATTC
Found at i:41513 original size:13 final size:13
Alignment explanation
Indices: 41495--41522 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
41485 GACAACATAG
41495 AAAAATAAGAAAA
1 AAAAATAAGAAAA
41508 AAAAATAAGAAAA
1 AAAAATAAGAAAA
41521 AA
1 AA
41523 CAGCTAAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.86, C:0.00, G:0.07, T:0.07
Consensus pattern (13 bp):
AAAAATAAGAAAA
Found at i:41843 original size:14 final size:14
Alignment explanation
Indices: 41807--41850 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
41797 TTTTGTAATG
41807 AACCCTAAACCATA
1 AACCCTAAACCATA
* * *
41821 AATCATAAATCATA
1 AACCCTAAACCATA
*
41835 AACCCTAAACCCTA
1 AACCCTAAACCATA
41849 AA
1 AA
41851 TATAATTATA
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.52, C:0.30, G:0.00, T:0.18
Consensus pattern (14 bp):
AACCCTAAACCATA
Found at i:41850 original size:21 final size:20
Alignment explanation
Indices: 41812--41855 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
41802 TAATGAACCC
*
41812 TAAACCATAAATCATAAATCA
1 TAAACCATAAACCATAAAT-A
* *
41833 TAAACCCTAAACCCTAAATA
1 TAAACCATAAACCATAAATA
41853 TAA
1 TAA
41856 TTATATGATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.55, C:0.23, G:0.00, T:0.23
Consensus pattern (20 bp):
TAAACCATAAACCATAAATA
Found at i:44926 original size:12 final size:12
Alignment explanation
Indices: 44911--44954 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
44901 TTAAAGCTTG
44911 AATCGAGCTCAA
1 AATCGAGCTCAA
44923 AATCGAGCTTC--
1 AATCGAGC-TCAA
*
44934 AATCAAGCTCAA
1 AATCGAGCTCAA
44946 AATCGAGCT
1 AATCGAGCT
44955 GCTTAGCTCG
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
10 2 0.07
11 7 0.26
12 16 0.59
13 2 0.07
ACGTcount: A:0.39, C:0.25, G:0.16, T:0.20
Consensus pattern (12 bp):
AATCGAGCTCAA
Found at i:44931 original size:23 final size:23
Alignment explanation
Indices: 44905--44954 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
44895 TTTGAGTTAA
* *
44905 AGCTTGAATCGAGCTCAAAATCG
1 AGCTTCAATCAAGCTCAAAATCG
44928 AGCTTCAATCAAGCTCAAAATCG
1 AGCTTCAATCAAGCTCAAAATCG
44951 AGCT
1 AGCT
44955 GCTTAGCTCG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.22
Consensus pattern (23 bp):
AGCTTCAATCAAGCTCAAAATCG
Found at i:52180 original size:41 final size:41
Alignment explanation
Indices: 52123--52204 Score: 155
Period size: 41 Copynumber: 2.0 Consensus size: 41
52113 GCAGAAGCAG
*
52123 ATGATTGCAGACGAGGGACAACCGCATGCAAAAATGATCCC
1 ATGATTGCAGACGAGGGACAACCGCATACAAAAATGATCCC
52164 ATGATTGCAGACGAGGGACAACCGCATACAAAAATGATCCC
1 ATGATTGCAGACGAGGGACAACCGCATACAAAAATGATCCC
52205 TGCAAAGCTC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.38, C:0.24, G:0.23, T:0.15
Consensus pattern (41 bp):
ATGATTGCAGACGAGGGACAACCGCATACAAAAATGATCCC
Found at i:60558 original size:29 final size:27
Alignment explanation
Indices: 60510--60563 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
60500 TTAGGAGTAG
60510 ATAAATTTATAAAAAAATAAAGAAAAAA
1 ATAAATTTATAAAAAAATAAA-AAAAAA
* *
60538 ATAAATTT-TAATAAAATATAAAAAAA
1 ATAAATTTATAAAAAAATAAAAAAAAA
60564 TTTAAATGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 6 0.25
27 10 0.42
28 8 0.33
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (27 bp):
ATAAATTTATAAAAAAATAAAAAAAAA
Found at i:60577 original size:28 final size:27
Alignment explanation
Indices: 60510--60579 Score: 70
Period size: 27 Copynumber: 2.5 Consensus size: 27
60500 TTAGGAGTAG
*
60510 ATAAATTTATAAAAAAATAAAGAAAAAA
1 ATAAA-TTATAATAAAATAAAGAAAAAA
* *
60538 ATAAATTTTAATAAAATATAA-AAAAAT
1 ATAAATTATAATAAAATA-AAGAAAAAA
*
60565 TTAAATGTATAATAA
1 ATAAAT-TATAATAA
60580 TTTTAAATTT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
27 21 0.60
28 14 0.40
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (27 bp):
ATAAATTATAATAAAATAAAGAAAAAA
Found at i:60698 original size:2 final size:2
Alignment explanation
Indices: 60691--60722 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
60681 TCTCCTTTGA
60691 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
60723 GGATTCCTCT
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:60930 original size:24 final size:25
Alignment explanation
Indices: 60897--60945 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
60887 ACTATAATAA
*
60897 AATTATAATATTAATTT-TGTATTTT
1 AATTATAATA-TAATTTATCTATTTT
60922 AATT-TAATATAATTTATCTATTTT
1 AATTATAATATAATTTATCTATTTT
60946 TTAATCTCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 6 0.27
24 12 0.55
25 4 0.18
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (25 bp):
AATTATAATATAATTTATCTATTTT
Found at i:71250 original size:26 final size:27
Alignment explanation
Indices: 71198--71250 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
71188 GCCTTAGTTG
71198 AACTTCTGACATATTCTGACAAGGCAC
1 AACTTCTGACATATTCTGACAAGGCAC
71225 AACTTCTGACATATT-TGACAAGGCAC
1 AACTTCTGACATATTCTGACAAGGCAC
71251 GAATCGTCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 11 0.42
27 15 0.58
ACGTcount: A:0.34, C:0.25, G:0.15, T:0.26
Consensus pattern (27 bp):
AACTTCTGACATATTCTGACAAGGCAC
Done.