Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008218.1 Hibiscus syriacus cultivar Beakdansim tig00110848_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: 63309
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.34
Found at i:924 original size:18 final size:18
Alignment explanation
Indices: 894--939 Score: 58
Period size: 20 Copynumber: 2.5 Consensus size: 18
884 ACCAAATAAA
*
894 ATAA-ATAATATATATATA
1 ATAATATAATATATATA-G
912 ATTAATATAATATATATAG
1 A-TAATATAATATATATAG
931 ATAATATAA
1 ATAATATAA
940 ATGTGTAAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 9 0.36
19 4 0.16
20 12 0.48
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (18 bp):
ATAATATAATATATATAG
Found at i:1846 original size:60 final size:63
Alignment explanation
Indices: 1753--1919 Score: 207
Period size: 65 Copynumber: 2.7 Consensus size: 63
1743 GTGAAGTTGA
* * *
1753 GCTTTGAATTAGATATCATTCATTGTGAAGTTGAAATCCAAGTATTG-T-TT-CACAAAATTG
1 GCTTTGAGTTGGATATCATTCGTTGTGAAGTTGAAATCCAAGTATTGATATTCCACAAAATTG
* * **
1813 GCTTTGAGTTGGATATCATTCGTTGTGAAGTTGAAGTCCAA-TCTTGTATAAATTCCACCTAATT
1 GCTTTGAGTTGGATATCATTCGTTGTGAAGTTGAAATCCAAGTATTG-AT--ATTCCACAAAATT
1877 G
63 G
*
1878 GCTTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAAG
1 GCTTTGAGTTGGATATCATTCGTTGTGAAGTTGAAATCCAAG
1920 CATGTGTAAG
Statistics
Matches: 91, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
59 4 0.04
60 37 0.41
61 1 0.01
64 2 0.02
65 47 0.52
ACGTcount: A:0.28, C:0.14, G:0.20, T:0.38
Consensus pattern (63 bp):
GCTTTGAGTTGGATATCATTCGTTGTGAAGTTGAAATCCAAGTATTGATATTCCACAAAATTG
Found at i:2786 original size:17 final size:17
Alignment explanation
Indices: 2753--2791 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
2743 TGGACCCACC
*
2753 TTATTTTCTTCTCTTTT
1 TTATTTTCTTATCTTTT
2770 TTATTTTCTTAT-TTTT
1 TTATTTTCTTATCTTTT
*
2786 TAATTT
1 TTATTT
2792 AGGGACCCCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 9 0.45
17 11 0.55
ACGTcount: A:0.13, C:0.10, G:0.00, T:0.77
Consensus pattern (17 bp):
TTATTTTCTTATCTTTT
Found at i:2840 original size:12 final size:11
Alignment explanation
Indices: 2823--2858 Score: 54
Period size: 12 Copynumber: 3.1 Consensus size: 11
2813 ACCCTAAACA
2823 TTTTTTCTTTT
1 TTTTTTCTTTT
2834 CTTTTTTCTTTT
1 -TTTTTTCTTTT
2846 TTCTTTTCTTTT
1 TT-TTTTCTTTT
2858 T
1 T
2859 CTTCTTCGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 2 0.09
12 21 0.91
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (11 bp):
TTTTTTCTTTT
Found at i:19205 original size:12 final size:12
Alignment explanation
Indices: 19184--19213 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
19174 GAAAGTACGC
19184 GAAAAATAGAGA
1 GAAAAATAGAGA
*
19196 GAAAACTAGAGA
1 GAAAAATAGAGA
19208 GAAAAA
1 GAAAAA
19214 GAAGATTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.67, C:0.03, G:0.23, T:0.07
Consensus pattern (12 bp):
GAAAAATAGAGA
Found at i:19402 original size:19 final size:19
Alignment explanation
Indices: 19374--19484 Score: 61
Period size: 19 Copynumber: 5.8 Consensus size: 19
19364 ATATAATATT
*
19374 CTAAATCCTAATTAAAATA
1 CTAAAACCTAATTAAAATA
* *
19393 CTAAAACCTATTTAAACTA
1 CTAAAACCTAATTAAAATA
*
19412 --AAATACCTAA-AACAAATA
1 CTAAA-ACCTAATTA-AAATA
** *
19430 -TAAAATATAA-AAATAATA
1 CTAAAACCTAATTAA-AATA
*
19448 TCCTAAAACTTAATTAAAATA
1 --CTAAAACCTAATTAAAATA
*
19469 CTAAAACCTATTTAAA
1 CTAAAACCTAATTAAA
19485 CTAAAATACA
Statistics
Matches: 71, Mismatches: 13, Indels: 16
0.71 0.13 0.16
Matches are distributed among these distances:
17 5 0.07
18 19 0.27
19 33 0.46
21 12 0.17
22 2 0.03
ACGTcount: A:0.57, C:0.14, G:0.00, T:0.29
Consensus pattern (19 bp):
CTAAAACCTAATTAAAATA
Found at i:19413 original size:24 final size:24
Alignment explanation
Indices: 19386--19493 Score: 76
Period size: 24 Copynumber: 4.3 Consensus size: 24
19376 AAATCCTAAT
19386 TAAAATACTAAAACCTATTTAAAC
1 TAAAATACTAAAACCTATTTAAAC
** * *
19410 TAAAATACCTAAAACAAATATAAAA
1 TAAAATA-CTAAAACCTATTTAAAC
* * * *
19435 TATAAA-AATAATATCCTAAAACTT-AAT
1 TA-AAATACTAA-AACCT---ATTTAAAC
19462 TAAAATACTAAAACCTATTTAAAC
1 TAAAATACTAAAACCTATTTAAAC
19486 TAAAATAC
1 TAAAATAC
19494 AAAGATAAAA
Statistics
Matches: 61, Mismatches: 15, Indels: 16
0.66 0.16 0.17
Matches are distributed among these distances:
23 3 0.05
24 20 0.33
25 18 0.30
26 10 0.16
27 8 0.13
28 2 0.03
ACGTcount: A:0.58, C:0.14, G:0.00, T:0.28
Consensus pattern (24 bp):
TAAAATACTAAAACCTATTTAAAC
Found at i:19433 original size:25 final size:24
Alignment explanation
Indices: 19386--19433 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
19376 AAATCCTAAT
** *
19386 TAAAATACTAAAACCTATTTAAAC
1 TAAAATACTAAAACAAATATAAAC
19410 TAAAATACCTAAAACAAATATAAA
1 TAAAATA-CTAAAACAAATATAAA
19434 ATATAAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.60, C:0.15, G:0.00, T:0.25
Consensus pattern (24 bp):
TAAAATACTAAAACAAATATAAAC
Found at i:19437 original size:65 final size:65
Alignment explanation
Indices: 19310--19437 Score: 188
Period size: 65 Copynumber: 2.0 Consensus size: 65
19300 TAAAACATCT
* *
19310 TAAATCCTAATTAAAACACTTAAAACTATTTAAAATAAAATACCTAAAAGAATAATATAATATTC
1 TAAATCCTAATTAAAACACTTAAAACTATTTAAAATAAAATACCTAAAAAAATAATAAAATATTC
* *
19375 TAAATCCTAATTAAAATAC-TAAAACCTATTTAAACTAAAATACCTAAAACAAAT-ATAAAATAT
1 TAAATCCTAATTAAAACACTTAAAA-CTATTTAAAATAAAATACCTAAAA-AAATAATAAAATAT
19438 AAAAATAATA
Statistics
Matches: 57, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
64 5 0.09
65 49 0.86
66 3 0.05
ACGTcount: A:0.56, C:0.13, G:0.01, T:0.30
Consensus pattern (65 bp):
TAAATCCTAATTAAAACACTTAAAACTATTTAAAATAAAATACCTAAAAAAATAATAAAATATTC
Found at i:19454 original size:32 final size:32
Alignment explanation
Indices: 19413--19474 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 32
19403 TTTAAACTAA
19413 AATACCTAAAAC-AAATATAAAATA-TAAAAAT
1 AATACCTAAAACTAAAT-TAAAATACTAAAAAT
*
19444 AATATCCTAAAACTTAATTAAAATACTAAAA
1 AATA-CCTAAAACTAAATTAAAATACTAAAA
19475 CCTATTTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
31 4 0.15
32 15 0.56
33 8 0.30
ACGTcount: A:0.63, C:0.11, G:0.00, T:0.26
Consensus pattern (32 bp):
AATACCTAAAACTAAATTAAAATACTAAAAAT
Found at i:19517 original size:76 final size:75
Alignment explanation
Indices: 19361--19529 Score: 216
Period size: 76 Copynumber: 2.2 Consensus size: 75
19351 ACCTAAAAGA
* * * *
19361 ATAATATAATATTCTAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACA
1 ATAAAATAATATCCTAAAACCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAAAA
19426 AATATAAAAT
66 AATATAAAAT
*
19436 ATAAAAATAATATCCTAAAACTTAATTAAAATACTAAAACCTATTTAAACTAAAATA-C-AAAGA
1 AT-AAAATAATATCCTAAAACCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAA-A
**
19499 TAAAATATAACGT
64 -AAAATATAAAAT
* *
19512 TTAAAATATTATCCTAAA
1 ATAAAATAATATCCTAAA
19530 CTTGAGTTTA
Statistics
Matches: 82, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
74 3 0.04
75 19 0.23
76 60 0.73
ACGTcount: A:0.56, C:0.12, G:0.01, T:0.30
Consensus pattern (75 bp):
ATAAAATAATATCCTAAAACCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAAAA
AATATAAAAT
Found at i:23634 original size:19 final size:19
Alignment explanation
Indices: 23612--23651 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
23602 AATAATATTC
23612 AAAA-TAAAAGATAATTCCT
1 AAAATTAAAA-ATAATTCCT
*
23631 AAAATTAAAAATAATTTCT
1 AAAATTAAAAATAATTCCT
23650 AA
1 AA
23652 TTTAAATTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.60, C:0.07, G:0.03, T:0.30
Consensus pattern (19 bp):
AAAATTAAAAATAATTCCT
Found at i:24795 original size:40 final size:40
Alignment explanation
Indices: 24750--24837 Score: 176
Period size: 40 Copynumber: 2.2 Consensus size: 40
24740 TAAATCAAAA
24750 TAGGCTCAGGTATAAAAATATAGTGAACAAGGAAAATGAT
1 TAGGCTCAGGTATAAAAATATAGTGAACAAGGAAAATGAT
24790 TAGGCTCAGGTATAAAAATATAGTGAACAAGGAAAATGAT
1 TAGGCTCAGGTATAAAAATATAGTGAACAAGGAAAATGAT
24830 TAGGCTCA
1 TAGGCTCA
24838 AAATGGTTCA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 48 1.00
ACGTcount: A:0.45, C:0.09, G:0.23, T:0.23
Consensus pattern (40 bp):
TAGGCTCAGGTATAAAAATATAGTGAACAAGGAAAATGAT
Found at i:41346 original size:19 final size:19
Alignment explanation
Indices: 41322--41361 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
41312 GTGTTTTAAG
41322 TGTGTTTTAAAATGATAAA
1 TGTGTTTTAAAATGATAAA
41341 TGTGTTTTAAAATGATAAA
1 TGTGTTTTAAAATGATAAA
41360 TG
1 TG
41362 GGAGAAGTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.40, C:0.00, G:0.17, T:0.42
Consensus pattern (19 bp):
TGTGTTTTAAAATGATAAA
Found at i:43805 original size:29 final size:30
Alignment explanation
Indices: 43758--43823 Score: 89
Period size: 29 Copynumber: 2.2 Consensus size: 30
43748 CCCGAAGGAC
* *
43758 CTATCCAGAGGTCACAAAG-ACCCCGGTAA
1 CTATCCAGAGATCACAAAGAACCCCGGCAA
* *
43787 CTATCCAGAGATCATAAAGAACCTCGGCAA
1 CTATCCAGAGATCACAAAGAACCCCGGCAA
43817 CTATCCA
1 CTATCCA
43824 TAGGTCCCGA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 17 0.53
30 15 0.47
ACGTcount: A:0.36, C:0.30, G:0.17, T:0.17
Consensus pattern (30 bp):
CTATCCAGAGATCACAAAGAACCCCGGCAA
Found at i:47824 original size:18 final size:18
Alignment explanation
Indices: 47801--47838 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
47791 TAACCGAATG
47801 CGATACTAAGAACTACAC
1 CGATACTAAGAACTACAC
47819 CGATACTAAGAACTACAC
1 CGATACTAAGAACTACAC
47837 CG
1 CG
47839 TAATAAATGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.42, C:0.29, G:0.13, T:0.16
Consensus pattern (18 bp):
CGATACTAAGAACTACAC
Found at i:55806 original size:17 final size:17
Alignment explanation
Indices: 55784--55817 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
55774 ATTATCAATA
55784 CTCAACCTTGGGTATCG
1 CTCAACCTTGGGTATCG
55801 CTCAACCTTGGGTATCG
1 CTCAACCTTGGGTATCG
55818 ATGCTAACGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.18, C:0.29, G:0.24, T:0.29
Consensus pattern (17 bp):
CTCAACCTTGGGTATCG
Found at i:61118 original size:64 final size:64
Alignment explanation
Indices: 61044--61201 Score: 180
Period size: 64 Copynumber: 2.5 Consensus size: 64
61034 CCCTTAACAT
* * *
61044 GTGCATCGATGCACTACTCATGCATCGGTACACCAATCACATTCGATGTTTTCATTTT-AAGGGG
1 GTGCATCGATGCACTACTCATGCATCGATACACCAAGCACATTCGATGTTTCCATTTTGAA-GGG
* * * * ** *
61108 GTGCATCGATGCACTCCTTATGCATCGATGCACTAAGGGCATTCGATGTTTCCATTTTGAATGG
1 GTGCATCGATGCACTACTCATGCATCGATACACCAAGCACATTCGATGTTTCCATTTTGAAGGG
*
61172 GTGCATCGATGCACT--T-GTGCATCGATACAC
1 GTGCATCGATGCACTACTCATGCATCGATACAC
61202 ACTGAACAAT
Statistics
Matches: 81, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
61 12 0.15
62 1 0.01
64 66 0.81
65 2 0.02
ACGTcount: A:0.23, C:0.23, G:0.22, T:0.31
Consensus pattern (64 bp):
GTGCATCGATGCACTACTCATGCATCGATACACCAAGCACATTCGATGTTTCCATTTTGAAGGG
Done.