Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006980.1 Hibiscus syriacus cultivar Beakdansim tig00017981_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: 99316
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:3053 original size:20 final size:21
Alignment explanation
Indices: 3017--3067 Score: 54
Period size: 20 Copynumber: 2.5 Consensus size: 21
3007 CGTTACACTT
* *
3017 TGTTGGAAATT-ACTGTTTGAG
1 TGTT-GAAATTGACTGTTAGAA
3038 TGTTGAAATTGA-TGTTAGAA
1 TGTTGAAATTGACTGTTAGAA
3058 TG-TGAAATTG
1 TGTTGAAATTG
3068 GATCAATTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 8 0.30
20 14 0.52
21 5 0.19
ACGTcount: A:0.29, C:0.02, G:0.27, T:0.41
Consensus pattern (21 bp):
TGTTGAAATTGACTGTTAGAA
Found at i:9152 original size:21 final size:19
Alignment explanation
Indices: 9124--9169 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
9114 TCATTGATTC
9124 ATTA-TTCTTAGCTCCTTAAT
1 ATTAGTTCTTAGCT--TTAAT
9144 ATTAGTTCTTAGCTTTAAT
1 ATTAGTTCTTAGCTTTAAT
9163 ACTTAGT
1 A-TTAGT
9170 AGGATTAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.26, C:0.15, G:0.09, T:0.50
Consensus pattern (19 bp):
ATTAGTTCTTAGCTTTAAT
Found at i:25139 original size:17 final size:18
Alignment explanation
Indices: 25106--25140 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
25096 CAAAAAACAC
*
25106 AAAAAACTATAACTATAA
1 AAAAAACTATAAATATAA
25124 AAAAAACTA-AAATATAA
1 AAAAAACTATAAATATAA
25141 GAAAGGGAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.71, C:0.09, G:0.00, T:0.20
Consensus pattern (18 bp):
AAAAAACTATAAATATAA
Found at i:31976 original size:18 final size:17
Alignment explanation
Indices: 31922--31970 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
31912 TTGGACTCAT
* *
31922 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TGA
31940 GAGTGCATCGATGCATGA
1 -AGTGCATCGATGCATGA
31958 AGTGCATTCGATG
1 AGTGCA-TCGATG
31971 TTTGAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.18, G:0.31, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATGA
Found at i:32054 original size:64 final size:64
Alignment explanation
Indices: 31942--32151 Score: 194
Period size: 64 Copynumber: 3.2 Consensus size: 64
31932 TGCACTAAGA
* *
31942 GTGCATCGATGCATGAAGTGCATTCGATGTTTGAA--AAAT-AGCCTAGTGCATCGATGCATGGA
1 GTGCATCGATGCATGAAATGCATTCGATGTTTCAATTAAATCAG---AGTGCATCGATGCATGGA
32004 TT
63 TT
* * * * **
32006 GTGCATCGATGCATCAAATGCATTCGATGTTTTAATTGAATCAGAGTGCATTGATGCATGGAGA
1 GTGCATCGATGCATGAAATGCATTCGATGTTTCAATTAAATCAGAGTGCATCGATGCATGGATT
* * * * * *
32070 GTCCATCGGTGCATGGAATGCATTAGATGTTTCAATTTATTCATTGA-TGCATCGATGCATGGTA
1 GTGCATCGATGCATGAAATGCATTCGATGTTTCAATTAAATCA--GAGTGCATCGATGCATGG-A
32134 TT
63 TT
*
32136 GATGCATCGGTGCATG
1 G-TGCATCGATGCATG
32152 CCTTTGAAAA
Statistics
Matches: 120, Mismatches: 19, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
64 84 0.70
65 14 0.12
66 7 0.06
67 15 0.12
ACGTcount: A:0.27, C:0.15, G:0.26, T:0.32
Consensus pattern (64 bp):
GTGCATCGATGCATGAAATGCATTCGATGTTTCAATTAAATCAGAGTGCATCGATGCATGGATT
Found at i:32136 original size:21 final size:21
Alignment explanation
Indices: 32112--32151 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
32102 CAATTTATTC
32112 ATTGATGCATCGATGCATGGT
1 ATTGATGCATCGATGCATGGT
*
32133 ATTGATGCATCGGTGCATG
1 ATTGATGCATCGATGCATG
32152 CCTTTGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.15, G:0.30, T:0.33
Consensus pattern (21 bp):
ATTGATGCATCGATGCATGGT
Found at i:33195 original size:21 final size:21
Alignment explanation
Indices: 33152--33195 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
33142 TCAAAGGAGG
* * *
33152 AGGAGGAGCACGAGAGGAGCT
1 AGGAGCAGCACGAGAAGAACT
*
33173 AGGAGCAGCTCGAGAAGAACT
1 AGGAGCAGCACGAGAAGAACT
33194 AG
1 AG
33196 CTCCCGGAGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.16, G:0.41, T:0.07
Consensus pattern (21 bp):
AGGAGCAGCACGAGAAGAACT
Found at i:38969 original size:18 final size:17
Alignment explanation
Indices: 38915--38963 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
38905 TTAGACTCCT
* *
38915 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TGA
38933 GAGTGCATCGATGCATGA
1 -AGTGCATCGATGCATGA
38951 AGTGCATTCGATG
1 AGTGCA-TCGATG
38964 TTTGAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.18, G:0.31, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATGA
Found at i:39047 original size:64 final size:64
Alignment explanation
Indices: 38935--39137 Score: 207
Period size: 64 Copynumber: 3.1 Consensus size: 64
38925 TGCACTAAGA
* *
38935 GTGCATCGATGCATGAAGTGCATTCGATGTTTGAA--AAAT-AGCCTAGTGCATCGATGCATGGA
1 GTGCATCGATGCATGAAATGCATTCGATGTTTCAATTAAATCAG---AGTGCATCGATGCATGGA
38997 TT
63 TT
* * * **
38999 GTGCATCGATGCATCAAATGCATTCGATGTTTTAATTGAATCAGAGTGCATCGATGCATGGAGA
1 GTGCATCGATGCATGAAATGCATTCGATGTTTCAATTAAATCAGAGTGCATCGATGCATGGATT
* * * * *
39063 ATGCATCGGTGCATGGAATGCATTCGATGTTTCAATTTATTCATTGA-TGCATCGATGCATGGAA
1 GTGCATCGATGCATGAAATGCATTCGATGTTTCAATTAAATCA--GAGTGCATCGATGCATGG-A
39127 TT
63 TT
39129 GATGCATCG
1 G-TGCATCG
39138 GCAATGAATA
Statistics
Matches: 116, Mismatches: 16, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
64 86 0.74
65 15 0.13
66 6 0.05
67 9 0.08
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.32
Consensus pattern (64 bp):
GTGCATCGATGCATGAAATGCATTCGATGTTTCAATTAAATCAGAGTGCATCGATGCATGGATT
Found at i:39083 original size:17 final size:19
Alignment explanation
Indices: 39045--39091 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
39035 TGAATCAGAG
39045 TGCATCGATGCATGGAGAA
1 TGCATCGATGCATGGAGAA
*
39064 TGCATCGGTGCAT-G-GAA
1 TGCATCGATGCATGGAGAA
39081 TGCATTCGATG
1 TGCA-TCGATG
39092 TTTCAATTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 7 0.28
18 6 0.24
19 12 0.48
ACGTcount: A:0.26, C:0.17, G:0.32, T:0.26
Consensus pattern (19 bp):
TGCATCGATGCATGGAGAA
Found at i:44131 original size:28 final size:29
Alignment explanation
Indices: 44074--44132 Score: 86
Period size: 28 Copynumber: 2.1 Consensus size: 29
44064 ATTGTTTCCT
*
44074 TTATTACTTATTTATCTCTTTGTCTTTAA
1 TTATTACTTATTTATATCTTTGTCTTTAA
44103 TTATTACCTTATTT-TATC-TTGTCTTTAA
1 TTATTA-CTTATTTATATCTTTGTCTTTAA
44131 TT
1 TT
44133 CTCTTAGTCT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
28 12 0.43
29 9 0.32
30 7 0.25
ACGTcount: A:0.20, C:0.14, G:0.03, T:0.63
Consensus pattern (29 bp):
TTATTACTTATTTATATCTTTGTCTTTAA
Found at i:56581 original size:20 final size:21
Alignment explanation
Indices: 56545--56595 Score: 54
Period size: 20 Copynumber: 2.5 Consensus size: 21
56535 TGTTAAACTT
* *
56545 TGTTGGAAATT-ATTGTTTGAG
1 TGTT-GAAATTGATTGTTAGAA
56566 TGTTGAAATTGA-TGTTAGAA
1 TGTTGAAATTGATTGTTAGAA
56586 TG-TGAAATTG
1 TGTTGAAATTG
56596 GATCAATATG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 8 0.30
20 14 0.52
21 5 0.19
ACGTcount: A:0.29, C:0.00, G:0.27, T:0.43
Consensus pattern (21 bp):
TGTTGAAATTGATTGTTAGAA
Found at i:65793 original size:21 final size:19
Alignment explanation
Indices: 65765--65810 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
65755 TCATCGAATC
65765 ATTA-TTCTTAGCTCCTTAAT
1 ATTAGTTCTTAGCT--TTAAT
65785 ATTAGTTCTTAGCTTTAAT
1 ATTAGTTCTTAGCTTTAAT
65804 ACTTAGT
1 A-TTAGT
65811 AGGATTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.26, C:0.15, G:0.09, T:0.50
Consensus pattern (19 bp):
ATTAGTTCTTAGCTTTAAT
Found at i:71392 original size:12 final size:12
Alignment explanation
Indices: 71375--71399 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
71365 AACAAAAACC
71375 ACAAAAACTAAA
1 ACAAAAACTAAA
71387 ACAAAAACTAAA
1 ACAAAAACTAAA
71399 A
1 A
71400 TATAAGAAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.16, G:0.00, T:0.08
Consensus pattern (12 bp):
ACAAAAACTAAA
Found at i:83026 original size:35 final size:35
Alignment explanation
Indices: 82961--83030 Score: 97
Period size: 34 Copynumber: 2.0 Consensus size: 35
82951 TTTGCTGCAC
* * *
82961 TTTTCTTTCTCTTTTTTTTCTTTTCTTGATTCACT
1 TTTTCTTTCTCTTTATTTTCTTTGCATGATTCACT
82996 TTTTC-TTCTCTTTATTTTCTTTGCAATGATTCACT
1 TTTTCTTTCTCTTTATTTTCTTTGC-ATGATTCACT
83031 CTGGTGATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
34 17 0.55
35 14 0.45
ACGTcount: A:0.10, C:0.20, G:0.04, T:0.66
Consensus pattern (35 bp):
TTTTCTTTCTCTTTATTTTCTTTGCATGATTCACT
Done.