Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002332.1 Hibiscus syriacus cultivar Beakdansim tig00004766_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: 63162
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:1275 original size:64 final size:62
Alignment explanation
Indices: 1159--1323 Score: 154
Period size: 64 Copynumber: 2.6 Consensus size: 62
1149 TTTCAGGTAA
* * * * *
1159 GTGTACCGATGCATAAATCAATGCATCGATGCACCCTTGTTTTAATTGAACATCAAATAGCTTTT
1 GTGTACCGATGCA-CAAGCCATGCATCGATGCACCCATGTTTTAA-T-AACATCAAATAGATTTT
* *
1224 GTGTACCGATGCACATA-CCATGCATCGATGCACTCCATGTATATTAA-AACATCGAATTGATTT
1 GTGTACCGATGCACA-AGCCATGCATCGATGCAC-CCATGT-T-TTAATAACATCAAATAGATTT
1287 T
62 T
* * * *
1288 ATGCACTGATGCACAAGCCATGCATCGATGTACCCA
1 GTGTACCGATGCACAAGCCATGCATCGATGCACCCA
1324 GGCTTTTTCA
Statistics
Matches: 85, Mismatches: 10, Indels: 12
0.79 0.09 0.11
Matches are distributed among these distances:
63 4 0.05
64 57 0.67
65 19 0.22
66 1 0.01
67 4 0.05
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.30
Consensus pattern (62 bp):
GTGTACCGATGCACAAGCCATGCATCGATGCACCCATGTTTTAATAACATCAAATAGATTTT
Found at i:1337 original size:64 final size:64
Alignment explanation
Indices: 1231--1365 Score: 154
Period size: 64 Copynumber: 2.1 Consensus size: 64
1221 TTTGTGTACC
*
1231 GATGCACATACCATGCATCGATGCACTCCATGTATATTAAAACATCGAATTG-AT-TTTATGCAC
1 GATGCACATACCATGCATCGATGCACTCCAGGTATATTAAAACATCGAA--GCATATTTATGCAC
1294 T
64 T
* *
1295 GATGCACA-AGCCATGCATCGATGTAC-CCAGGCT-TTTTCAAAACATCGAAGCATATTTATGCA
1 GATGCACATA-CCATGCATCGATGCACTCCAGG-TATATT-AAAACATCGAAGCATATTTATGCA
*
1357 TT
63 CT
1359 GATGCAC
1 GATGCAC
1366 CCTCAGTGTA
Statistics
Matches: 62, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
62 1 0.02
63 10 0.16
64 51 0.82
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.29
Consensus pattern (64 bp):
GATGCACATACCATGCATCGATGCACTCCAGGTATATTAAAACATCGAAGCATATTTATGCACT
Found at i:9029 original size:21 final size:22
Alignment explanation
Indices: 8987--9029 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
8977 CATTTTGAAT
* *
8987 GTTGTTGGATTGTTTTACTTTG
1 GTTGTTGGATTGTTTGAATTTG
9009 GTTGTTGGA-TGTTTGAATTTG
1 GTTGTTGGATTGTTTGAATTTG
9030 TTTAATGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.12, C:0.02, G:0.30, T:0.56
Consensus pattern (22 bp):
GTTGTTGGATTGTTTGAATTTG
Found at i:9775 original size:65 final size:64
Alignment explanation
Indices: 9658--9820 Score: 168
Period size: 65 Copynumber: 2.5 Consensus size: 64
9648 TTTCAGGTAA
* * * * * * * *
9658 GTGTACCGATGCATAAATCAATGCATTGATGCACCCTTGTTTTAATTGAACATCAAATAGCTTTT
1 GTGTACCGATGCA-CAAGCCATGCATCGATGCACCCATGTATTAATTAAACATCAAATAGATTTT
* *
9723 GTGTACCGATGCACATA-CCATGCATCGATGCACTCCATGTATT-ATTAAAACATCGAATTGATT
1 GTGTACCGATGCACA-AGCCATGCATCGATGCAC-CCATGTATTAATT-AAACATCAAATAGATT
9786 TT
63 TT
* *
9788 ATGCACCGATGCACAAGCCATGCATCGATGCAC
1 GTGTACCGATGCACAAGCCATGCATCGATGCAC
9821 ACAGGCTTTT
Statistics
Matches: 83, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
64 19 0.23
65 64 0.77
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.30
Consensus pattern (64 bp):
GTGTACCGATGCACAAGCCATGCATCGATGCACCCATGTATTAATTAAACATCAAATAGATTTT
Found at i:12085 original size:18 final size:18
Alignment explanation
Indices: 12059--12094 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
12049 AATTAGCATG
12059 CACAACCTTGTTCATAAT
1 CACAACCTTGTTCATAAT
* *
12077 CACATCCTTGTTCTTAAT
1 CACAACCTTGTTCATAAT
12095 TCTATCAGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.28, C:0.28, G:0.06, T:0.39
Consensus pattern (18 bp):
CACAACCTTGTTCATAAT
Found at i:16866 original size:2 final size:2
Alignment explanation
Indices: 16859--16889 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
16849 AGTTAATTAT
16859 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
16890 TATGATTATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:17877 original size:16 final size:16
Alignment explanation
Indices: 17852--17882 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
17842 GCATGAGTAA
*
17852 AATTTGGGATATTTTT
1 AATTTAGGATATTTTT
17868 AATTTAGGATATTTT
1 AATTTAGGATATTTT
17883 AGGTAAAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.16, T:0.55
Consensus pattern (16 bp):
AATTTAGGATATTTTT
Found at i:18844 original size:39 final size:39
Alignment explanation
Indices: 18788--18869 Score: 155
Period size: 39 Copynumber: 2.1 Consensus size: 39
18778 TAAGACATCC
18788 TTCATACAAATAGGATGATTAATAATTAAAGTGTTATGG
1 TTCATACAAATAGGATGATTAATAATTAAAGTGTTATGG
*
18827 TTCATACAAATATGATGATTAATAATTAAAGTGTTATGG
1 TTCATACAAATAGGATGATTAATAATTAAAGTGTTATGG
18866 TTCA
1 TTCA
18870 ATAGAATTTT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.40, C:0.06, G:0.16, T:0.38
Consensus pattern (39 bp):
TTCATACAAATAGGATGATTAATAATTAAAGTGTTATGG
Found at i:21644 original size:6 final size:6
Alignment explanation
Indices: 21628--21660 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
21618 GAGTCTCAAA
*
21628 ATTTTT A-TTTT ATTTTT ATTTTT AATTTT ATTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTT
21661 ACTTTCGCCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
5 5 0.21
6 19 0.79
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (6 bp):
ATTTTT
Found at i:25885 original size:12 final size:12
Alignment explanation
Indices: 25868--25895 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
25858 CGAGTCTCAA
25868 ATTTTTTATTTT
1 ATTTTTTATTTT
25880 ATTTTTTATTTT
1 ATTTTTTATTTT
25892 ATTT
1 ATTT
25896 ACTTTCGTCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (12 bp):
ATTTTTTATTTT
Found at i:26159 original size:2 final size:2
Alignment explanation
Indices: 26152--26182 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
26142 ATCATAATTA
*
26152 AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
26183 ATAATTAACT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:27439 original size:39 final size:39
Alignment explanation
Indices: 27385--27544 Score: 284
Period size: 39 Copynumber: 4.1 Consensus size: 39
27375 TAAGACATCC
*
27385 TTCATACAAATAGGATGATTAATAGTTAAAGTGTTATGG
1 TTCATACAAATAGGATGATTAATAATTAAAGTGTTATGG
*
27424 TTCATACAAATAGGATGATTAATAGTTAAAGTGTTATGG
1 TTCATACAAATAGGATGATTAATAATTAAAGTGTTATGG
27463 TTCATACAAATAGGATGATTAATAATTAAAGTGTTATGG
1 TTCATACAAATAGGATGATTAATAATTAAAGTGTTATGG
* *
27502 TTCATACAAATAGGATGATTTATAATTAAAGTGTTACGG
1 TTCATACAAATAGGATGATTAATAATTAAAGTGTTATGG
27541 TTCA
1 TTCA
27545 ATAGAATTTT
Statistics
Matches: 118, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 118 1.00
ACGTcount: A:0.39, C:0.06, G:0.19, T:0.36
Consensus pattern (39 bp):
TTCATACAAATAGGATGATTAATAATTAAAGTGTTATGG
Found at i:29265 original size:31 final size:31
Alignment explanation
Indices: 29224--29298 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 31
29214 CGGTCCATCT
* * *
29224 GATTTAAGTCCCTAATATTATCAGTCCGTCC
1 GATTTAAGTCCCTAACAGTATCAATCCGTCC
* * *
29255 GATTTCAGTCCCTAACAGTATCAATTCGTTC
1 GATTTAAGTCCCTAACAGTATCAATCCGTCC
*
29286 GATTTTAGTCCCT
1 GATTTAAGTCCCT
29299 CAGTCATGTT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.24, C:0.25, G:0.13, T:0.37
Consensus pattern (31 bp):
GATTTAAGTCCCTAACAGTATCAATCCGTCC
Found at i:35104 original size:36 final size:37
Alignment explanation
Indices: 35035--35107 Score: 130
Period size: 37 Copynumber: 2.0 Consensus size: 37
35025 CTTTTTTTTG
*
35035 GACTTTTAGCTATTAAATTAGATAACATATATGCTAA
1 GACTTTTAACTATTAAATTAGATAACATATATGCTAA
35072 GACTTTTAACTATTAAATTAG-TAACATATATGCTAA
1 GACTTTTAACTATTAAATTAGATAACATATATGCTAA
35108 ATTATGTCAA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
36 15 0.43
37 20 0.57
ACGTcount: A:0.41, C:0.11, G:0.10, T:0.38
Consensus pattern (37 bp):
GACTTTTAACTATTAAATTAGATAACATATATGCTAA
Found at i:39481 original size:3 final size:3
Alignment explanation
Indices: 39473--39498 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
39463 ACACCGATCT
39473 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
39499 TCACATCTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:41711 original size:21 final size:22
Alignment explanation
Indices: 41671--41712 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
41661 TTAACTGATC
41671 GAATTATTATAAAATAATTATT
1 GAATTATTATAAAATAATTATT
41693 GAATT-TTATTAAAAT-ATTAT
1 GAATTATTA-TAAAATAATTAT
41713 AAAATAATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (22 bp):
GAATTATTATAAAATAATTATT
Found at i:41739 original size:32 final size:32
Alignment explanation
Indices: 41675--41739 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 32
41665 CTGATCGAAT
* * *
41675 TATTATAAAATAATTATTGAATTTTATTAAAA
1 TATTATAAAATAATCATTGAAATTTATAAAAA
41707 TATTATAAAATAATCATT-AAATTTATCAAAAA
1 TATTATAAAATAATCATTGAAATTTAT-AAAAA
41739 T
1 T
41740 TTAGTATTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 7 0.24
32 22 0.76
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (32 bp):
TATTATAAAATAATCATTGAAATTTATAAAAA
Found at i:46504 original size:21 final size:21
Alignment explanation
Indices: 46458--46505 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
46448 GGTGTAGAGA
*
46458 GAACTGGCGGTGGTGTTAAAC
1 GAACTGGCGATGGTGTTAAAC
* *
46479 AAACTGGCGATGGTAG-TAAGC
1 GAACTGGCGATGGT-GTTAAAC
46500 GAACTG
1 GAACTG
46506 ATGGTGATGT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 21 0.95
22 1 0.05
ACGTcount: A:0.29, C:0.15, G:0.35, T:0.21
Consensus pattern (21 bp):
GAACTGGCGATGGTGTTAAAC
Found at i:62098 original size:66 final size:66
Alignment explanation
Indices: 61992--62116 Score: 223
Period size: 66 Copynumber: 1.9 Consensus size: 66
61982 GATGAAATCG
* * *
61992 CCTCTTGCGAGGTCAAAACATGTAAGTTGCTTAGCAAACAAGTGTTGGATGGAACTACCTTCATC
1 CCTCTTGCGAGGCCAAAACATGTAAGTTGCTTAGCAAACAAATGTCGGATGGAACTACCTTCATC
62057 A
66 A
62058 CCTCTTGCGAGGCCAAAACATGTAAGTTGCTTAGCAAACAAATGTCGGATGGAACTACC
1 CCTCTTGCGAGGCCAAAACATGTAAGTTGCTTAGCAAACAAATGTCGGATGGAACTACC
62117 GGGCCAATCG
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 56 1.00
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.25
Consensus pattern (66 bp):
CCTCTTGCGAGGCCAAAACATGTAAGTTGCTTAGCAAACAAATGTCGGATGGAACTACCTTCATC
A
Done.