Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004522.1 Hibiscus syriacus cultivar Beakdansim tig00009978_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: 57766
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:21153 original size:19 final size:19
Alignment explanation
Indices: 21131--21169 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
21121 ATTTTAATCT
21131 ATAATTATATTCTTAAATA
1 ATAATTATATTCTTAAATA
21150 ATAATTATATTCTTAAATA
1 ATAATTATATTCTTAAATA
21169 A
1 A
21170 AAGGCTAGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (19 bp):
ATAATTATATTCTTAAATA
Found at i:22370 original size:27 final size:27
Alignment explanation
Indices: 22339--22473 Score: 135
Period size: 27 Copynumber: 5.3 Consensus size: 27
22329 AATGAATCCT
22339 TTCATGCATTTTCAATTATGGCATCTG
1 TTCATGCATTTTCAATTATGGCATCTG
*
22366 TTCATG--TCTT--A--AT-GCATCCT-
1 TTCATGCATTTTCAATTATGGCAT-CTG
22386 TTCATGCATTTTCAATTATGGCATCCT-
1 TTCATGCATTTTCAATTATGGCAT-CTG
* * *
22413 TTCATGAATTTTCAATTATGACATCCG
1 TTCATGCATTTTCAATTATGGCATCTG
* *
22440 TTCATGCATTTTCAATTATGACATCCG
1 TTCATGCATTTTCAATTATGGCATCTG
22467 TTCATGC
1 TTCATGC
22474 CTTAATGCAT
Statistics
Matches: 93, Mismatches: 6, Indels: 18
0.79 0.05 0.15
Matches are distributed among these distances:
20 10 0.11
21 4 0.04
22 3 0.03
23 1 0.01
24 1 0.01
25 3 0.03
26 3 0.03
27 68 0.73
ACGTcount: A:0.24, C:0.21, G:0.12, T:0.43
Consensus pattern (27 bp):
TTCATGCATTTTCAATTATGGCATCTG
Found at i:22370 original size:47 final size:46
Alignment explanation
Indices: 22284--22552 Score: 299
Period size: 47 Copynumber: 5.6 Consensus size: 46
22274 CGTATTAACA
*
22284 CATCCATTT-ATGCATTTTAATATATATGGCATCCTTTCATGCCTTAATG
1 CATCC-TTTCATGCATTTTCA-AT-TATGGCAT-CTTTCATGCCTTAATG
* *
22333 AATCCTTTCATGCATTTTCAATTATGGCATCTGTTCATGTCTTAATG
1 CATCCTTTCATGCATTTTCAATTATGGCATCT-TTCATGCCTTAATG
**
22380 CATCCTTTCATGCATTTTCAATTATGGCATCCTTTCATGAATTTTCAATTATG
1 CATCCTTTCATGCATTTTCAATTATGGCAT-CTTTCATG--CCTT--A--ATG
* * *
22433 ACATCCGTTCATGCATTTTCAATTATGACATCCGTTCATGCCTTAATG
1 -CATCCTTTCATGCATTTTCAATTATGGCAT-CTTTCATGCCTTAATG
* *
22481 CATCCTTTCAT-CATTTTCAATTATGGTATCTTTTCTTGCCTTAATG
1 CATCCTTTCATGCATTTTCAATTATGGCATC-TTTCATGCCTTAATG
22527 CATCCTTTCATGCATTTTCAATTATG
1 CATCCTTTCATGCATTTTCAATTATG
22553 AATTTGATTT
Statistics
Matches: 193, Mismatches: 15, Indels: 26
0.82 0.06 0.11
Matches are distributed among these distances:
45 1 0.01
46 42 0.22
47 80 0.41
48 10 0.05
49 17 0.09
50 1 0.01
51 1 0.01
52 2 0.01
53 3 0.02
54 36 0.19
ACGTcount: A:0.24, C:0.22, G:0.10, T:0.44
Consensus pattern (46 bp):
CATCCTTTCATGCATTTTCAATTATGGCATCTTTCATGCCTTAATG
Found at i:22389 original size:20 final size:20
Alignment explanation
Indices: 22312--22391 Score: 54
Period size: 20 Copynumber: 3.6 Consensus size: 20
22302 AATATATATG
*
22312 GCATCCTTTCATGCCTTAAT
1 GCATCCTTTCATGTCTTAAT
* *
22332 GAATCCTTTCATGCATTTTCAATTAT
1 GCATCCTTTCATG--TCTT--A--AT
22358 GGCAT-CTGTTCATGTCTTAAT
1 -GCATCCT-TTCATGTCTTAAT
22379 GCATCCTTTCATG
1 GCATCCTTTCATG
22392 CATTTTCAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 18
0.67 0.07 0.26
Matches are distributed among these distances:
20 22 0.48
21 4 0.09
22 2 0.04
23 1 0.02
24 1 0.02
25 3 0.07
26 4 0.09
27 9 0.20
ACGTcount: A:0.21, C:0.24, G:0.12, T:0.42
Consensus pattern (20 bp):
GCATCCTTTCATGTCTTAAT
Found at i:22456 original size:101 final size:99
Alignment explanation
Indices: 22330--22515 Score: 300
Period size: 101 Copynumber: 1.9 Consensus size: 99
22320 TCATGCCTTA
* * * *
22330 ATGAATCCTTTCATGCATTTTCAATTATGGCATCTGTTCATGTCTTAATGCATCCTTTCATGCAT
1 ATGAATCCGTTCATGCATTTTCAATTATGACATCCGTTCATGCCTTAATGCATCCTTTCAT-CAT
22395 TTTCAATTATGGCATCCTTTCATGAATTTTCAATT
65 TTTCAATTATGGCATCCTTTCATGAATTTTCAATT
22430 ATGACATCCGTTCATGCATTTTCAATTATGACATCCGTTCATGCCTTAATGCATCCTTTCATCAT
1 ATGA-ATCCGTTCATGCATTTTCAATTATGACATCCGTTCATGCCTTAATGCATCCTTTCATCAT
* *
22495 TTTCAATTATGGTATCTTTTC
65 TTTCAATTATGGCATCCTTTC
22516 TTGCCTTAAT
Statistics
Matches: 79, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
100 26 0.33
101 53 0.67
ACGTcount: A:0.24, C:0.22, G:0.11, T:0.44
Consensus pattern (99 bp):
ATGAATCCGTTCATGCATTTTCAATTATGACATCCGTTCATGCCTTAATGCATCCTTTCATCATT
TTCAATTATGGCATCCTTTCATGAATTTTCAATT
Found at i:22502 original size:46 final size:47
Alignment explanation
Indices: 22434--22553 Score: 179
Period size: 46 Copynumber: 2.6 Consensus size: 47
22424 TCAATTATGA
*
22434 CATCCGTTCATGCATTTTCAATTATGACATCCGTTCATGCCTTAATG
1 CATCCTTTCATGCATTTTCAATTATGACATCCGTTCATGCCTTAATG
** ** *
22481 CATCCTTTCAT-CATTTTCAATTATGGTATCTTTTCTTGCCTTAATG
1 CATCCTTTCATGCATTTTCAATTATGACATCCGTTCATGCCTTAATG
22527 CATCCTTTCATGCATTTTCAATTATGA
1 CATCCTTTCATGCATTTTCAATTATGA
22554 ATTTGATTTA
Statistics
Matches: 65, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
46 41 0.63
47 24 0.37
ACGTcount: A:0.23, C:0.23, G:0.10, T:0.44
Consensus pattern (47 bp):
CATCCTTTCATGCATTTTCAATTATGACATCCGTTCATGCCTTAATG
Found at i:24035 original size:76 final size:75
Alignment explanation
Indices: 23875--24086 Score: 254
Period size: 76 Copynumber: 2.9 Consensus size: 75
23865 TAAAACATCT
* * * * * * * *
23875 TAAATCCTAATGAAAACACTTAAAACTATTTAAACTAAAATCCCT-AAA-AAA-TAATAT-TTAA
1 TAAAACCTAATTAAAATACTAAAAATTATTTAAACTAAAATACCTAAAACAAAGTAAAATATAAA
*
23936 AATAATATTC
66 AATAATATCC
*
23946 TAAATCCTAATTAAAATACT-AAAATATATTTAAACTAAAATACCTAAAACAAAGCTAAAATATA
1 TAAAACCTAATTAAAATACTAAAAAT-TATTTAAACTAAAATACCTAAAACAAAG-TAAAATATA
24010 AAAATAATATCC
64 AAAATAATATCC
* *
24022 TAAAACTTAATTAAAATACTAAAAATTATTTAAAATAAAATACCTAAAACAAAGATAAAATATAA
1 TAAAACCTAATTAAAATACTAAAAATTATTTAAACTAAAATACCTAAAACAAAG-TAAAATATAA
24087 TGTTTAAAAT
Statistics
Matches: 123, Mismatches: 11, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
70 4 0.03
71 36 0.29
72 3 0.02
73 3 0.02
75 5 0.04
76 67 0.54
77 5 0.04
ACGTcount: A:0.58, C:0.12, G:0.01, T:0.29
Consensus pattern (75 bp):
TAAAACCTAATTAAAATACTAAAAATTATTTAAACTAAAATACCTAAAACAAAGTAAAATATAAA
AATAATATCC
Found at i:24045 original size:19 final size:19
Alignment explanation
Indices: 24021--24058 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
24011 AAATAATATC
*
24021 CTAAAACTTAATTAAAATA
1 CTAAAAATTAATTAAAATA
*
24040 CTAAAAATTATTTAAAATA
1 CTAAAAATTAATTAAAATA
24059 AAATACCTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.34
Consensus pattern (19 bp):
CTAAAAATTAATTAAAATA
Found at i:25813 original size:5 final size:5
Alignment explanation
Indices: 25796--25924 Score: 102
Period size: 5 Copynumber: 24.8 Consensus size: 5
25786 CTGTTTAAAG
* * * *
25796 AAAACT AAAAT TAAAT TAATT AAAAT AAAAT AAAAT AAAAT -AAAT AGAAT
1 AAAA-T AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
* **
25846 GAAAAT AAAGTTT GCTAA- AAAAT AAAAT AAAAAT AAAA- ATAAAT AAAAAT
1 -AAAAT AAA--AT -AAAAT AAAAT AAAAT -AAAAT AAAAT A-AAAT -AAAAT
25896 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
25925 AATAGAACAA
Statistics
Matches: 101, Mismatches: 12, Indels: 21
0.75 0.09 0.16
Matches are distributed among these distances:
4 7 0.07
5 74 0.73
6 17 0.17
7 2 0.02
8 1 0.01
ACGTcount: A:0.73, C:0.02, G:0.03, T:0.22
Consensus pattern (5 bp):
AAAAT
Found at i:32193 original size:73 final size:76
Alignment explanation
Indices: 32107--32319 Score: 301
Period size: 76 Copynumber: 2.8 Consensus size: 76
32097 TAAAACATCT
* * * *
32107 TAAATCCTAATTAAAACACTTAAAA-CTATTTAAACTAAAATAACTAAAA-ATA-ATAATAT-TT
1 TAAATCCTAATTAAAACAC-TAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATA
*
32168 AAAATAATATTC
65 AAAATAATATCC
*
32180 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAA
1 TAAATCCTAATTAAAACACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAA
32245 AAATAATATCC
66 AAATAATATCC
* *
32256 TAAAACTTAATT-AAACTACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATA
1 TAAATCCTAATTAAAAC-ACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATA
32320 GTGTTTAAAA
Statistics
Matches: 126, Mismatches: 9, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
72 5 0.04
73 41 0.33
74 2 0.02
75 9 0.07
76 69 0.55
ACGTcount: A:0.57, C:0.13, G:0.01, T:0.29
Consensus pattern (76 bp):
TAAATCCTAATTAAAACACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAA
AAATAATATCC
Found at i:32279 original size:19 final size:19
Alignment explanation
Indices: 32255--32292 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
32245 AAATAATATC
*
32255 CTAAAACTTAATTAAACTA
1 CTAAAACCTAATTAAACTA
*
32274 CTAAAACCTATTTAAACTA
1 CTAAAACCTAATTAAACTA
32293 AAATACCTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.50, C:0.18, G:0.00, T:0.32
Consensus pattern (19 bp):
CTAAAACCTAATTAAACTA
Found at i:32729 original size:20 final size:21
Alignment explanation
Indices: 32704--32759 Score: 69
Period size: 22 Copynumber: 2.7 Consensus size: 21
32694 CGAAGTTGCC
32704 TGGTATCGATACCCT-TACCA
1 TGGTATCGATACCCTATACCA
* *
32724 TGGTATCGATACTGCTATACTA
1 TGGTATCGATAC-CCTATACCA
*
32746 TGGTACCGATACCC
1 TGGTATCGATACCC
32760 CCTACGGTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 12 0.40
21 3 0.10
22 15 0.50
ACGTcount: A:0.25, C:0.27, G:0.18, T:0.30
Consensus pattern (21 bp):
TGGTATCGATACCCTATACCA
Found at i:32815 original size:95 final size:95
Alignment explanation
Indices: 32652--32830 Score: 261
Period size: 95 Copynumber: 1.9 Consensus size: 95
32642 GCACTTATCA
* * * *
32652 GGTACAGATACCCCCTTCCGGTATCGATACCGAAATTAGCTTCGAAGTTGCCTGGTATCGATACC
1 GGTACAGATACCCCCTTACGGTATCGATACCAAAATTAGATTCGAAGTTGCCTGGTATCGATAAC
*
32717 CTTACCATGGTATCGATACTGCTATACTAT
66 CTTACAATGGTATCGATACTGCTATACTAT
* * * *
32747 GGTACCGATACCCCC-TACGGTATCGTTACCAAAATTAGATTCGATGTTTGCTTGGTATCGATAA
1 GGTACAGATACCCCCTTACGGTATCGATACCAAAATTAGATTCGAAG-TTGCCTGGTATCGATAA
32811 CCTTACAATGGTATCGATAC
65 CCTTACAATGGTATCGATAC
32831 CCTTACAATG
Statistics
Matches: 74, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
94 26 0.35
95 48 0.65
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.30
Consensus pattern (95 bp):
GGTACAGATACCCCCTTACGGTATCGATACCAAAATTAGATTCGAAGTTGCCTGGTATCGATAAC
CTTACAATGGTATCGATACTGCTATACTAT
Found at i:32850 original size:20 final size:20
Alignment explanation
Indices: 32799--32850 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
32789 GATGTTTGCT
*
32799 TGGTATCGATAACCTTACAA
1 TGGTATCGATACCCTTACAA
32819 TGGTATCGATACCCTTACAA
1 TGGTATCGATACCCTTACAA
*
32839 TGGTATCAATAC
1 TGGTATCGATAC
32851 TGATTGAATC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.31
Consensus pattern (20 bp):
TGGTATCGATACCCTTACAA
Found at i:39014 original size:20 final size:20
Alignment explanation
Indices: 38989--39110 Score: 82
Period size: 20 Copynumber: 5.4 Consensus size: 20
38979 ATATGACATT
38989 CTTTCATGCCTTAATGCATC
1 CTTTCATGCCTTAATGCATC
*
39009 CTTTCATGCATTTTCAATTATGGCATC
1 CTTTCATGC--CTT--A--AT-GCATC
* *
39036 CGTTCATGCCTTAATACATC
1 CTTTCATGCCTTAATGCATC
*
39056 CTTTCATGCATTTTCAATTATGACATC
1 CTTTCATGC--CTT--A--ATG-CATC
39083 CTTTCATGCCTTAATGCATC
1 CTTTCATGCCTTAATGCATC
39103 CTTTCATG
1 CTTTCATG
39111 TATTTTTAAT
Statistics
Matches: 80, Mismatches: 8, Indels: 28
0.69 0.07 0.24
Matches are distributed among these distances:
20 33 0.41
21 5 0.06
22 4 0.05
23 2 0.03
24 2 0.03
25 4 0.05
26 4 0.05
27 26 0.32
ACGTcount: A:0.22, C:0.26, G:0.10, T:0.42
Consensus pattern (20 bp):
CTTTCATGCCTTAATGCATC
Found at i:39035 original size:27 final size:27
Alignment explanation
Indices: 39004--39091 Score: 100
Period size: 27 Copynumber: 3.5 Consensus size: 27
38994 ATGCCTTAAT
39004 GCATCCTTTCATGCATTTTCAATTATG
1 GCATCCTTTCATGCATTTTCAATTATG
* *
39031 GCATCCGTTCATGC--CTT-AA-TA--
1 GCATCCTTTCATGCATTTTCAATTATG
39052 -CATCCTTTCATGCATTTTCAATTATG
1 GCATCCTTTCATGCATTTTCAATTATG
*
39078 ACATCCTTTCATGC
1 GCATCCTTTCATGC
39092 CTTAATGCAT
Statistics
Matches: 50, Mismatches: 4, Indels: 14
0.74 0.06 0.21
Matches are distributed among these distances:
20 12 0.24
22 2 0.04
23 4 0.08
24 4 0.08
25 2 0.04
27 26 0.52
ACGTcount: A:0.23, C:0.26, G:0.10, T:0.41
Consensus pattern (27 bp):
GCATCCTTTCATGCATTTTCAATTATG
Found at i:39060 original size:47 final size:47
Alignment explanation
Indices: 38907--39170 Score: 327
Period size: 47 Copynumber: 5.5 Consensus size: 47
38897 CGTATTAACA
* * * *
38907 CATCCATTT-ATGCATTTTAATATGTATGGAATTCTTTCATTCCTTAATG
1 CATCC-TTTCATGCATTTTCA-AT-TATGGCATCCTTTCATGCCTTAATG
* * *
38956 CATCCTTTCATGCATTTTAATATATATGACATTCTTTCATGCCTTAATG
1 CATCCTTTCATGCATTTTCA-AT-TATGGCATCCTTTCATGCCTTAATG
* *
39005 CATCCTTTCATGCATTTTCAATTATGGCATCCGTTCATGCCTTAATA
1 CATCCTTTCATGCATTTTCAATTATGGCATCCTTTCATGCCTTAATG
*
39052 CATCCTTTCATGCATTTTCAATTATGACATCCTTTCATGCCTTAATG
1 CATCCTTTCATGCATTTTCAATTATGGCATCCTTTCATGCCTTAATG
* *
39099 CATCCTTTCATGTATTTTTAATTATGG-AGT-CTGTTCATGCCTTAATG
1 CATCCTTTCATGCATTTTCAATTATGGCA-TCCT-TTCATGCCTTAATG
*
39146 CATCCTTTCATGCATTGTCAATTAT
1 CATCCTTTCATGCATTTTCAATTAT
39171 AAATTTGATT
Statistics
Matches: 194, Mismatches: 18, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
46 3 0.02
47 126 0.65
48 5 0.03
49 60 0.31
ACGTcount: A:0.24, C:0.21, G:0.10, T:0.44
Consensus pattern (47 bp):
CATCCTTTCATGCATTTTCAATTATGGCATCCTTTCATGCCTTAATG
Found at i:39681 original size:20 final size:20
Alignment explanation
Indices: 39656--39716 Score: 59
Period size: 22 Copynumber: 2.9 Consensus size: 20
39646 CAATGTTGCC
39656 TGGTATCCATACCCTTACCA
1 TGGTATCCATACCCTTACCA
* * *
39676 TGGTATTCATACTACTATACTA
1 TGGTATCCATAC-CCT-TACCA
*
39698 TGGTATCGATACCCCTTAC
1 TGGTATCCATA-CCCTTAC
39717 GGTATCGATA
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
20 11 0.34
21 5 0.16
22 15 0.47
23 1 0.03
ACGTcount: A:0.26, C:0.28, G:0.11, T:0.34
Consensus pattern (20 bp):
TGGTATCCATACCCTTACCA
Found at i:52012 original size:21 final size:21
Alignment explanation
Indices: 51987--52027 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
51977 CCATGAATAG
*
51987 TGCTACAGTGTACCGATGCAT
1 TGCTACAGTGTACCAATGCAT
52008 TGCTACAGTGTACCAATGCA
1 TGCTACAGTGTACCAATGCA
52028 CAAAAACATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.27
Consensus pattern (21 bp):
TGCTACAGTGTACCAATGCAT
Found at i:52809 original size:23 final size:23
Alignment explanation
Indices: 52776--52819 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
52766 AATACATATA
*
52776 TGTCCCAAAGGTCCACGTAGAAT
1 TGTCCCAAAGGACCACGTAGAAT
* *
52799 TGTCCCGAAGGACCGCGTAGA
1 TGTCCCAAAGGACCACGTAGA
52820 CCCTGTACTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.18
Consensus pattern (23 bp):
TGTCCCAAAGGACCACGTAGAAT
Done.