Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007171.1 Hibiscus syriacus cultivar Beakdansim tig00018808_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: 71190
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:1099 original size:42 final size:42
Alignment explanation
Indices: 1051--1156 Score: 158
Period size: 42 Copynumber: 2.5 Consensus size: 42
1041 AATCATCTAT
* *
1051 AAGATCCGGGTGTTCGATGAAAGCACATAACATCATCTGTAG
1 AAGATCCGGGTGTACGACGAAAGCACATAACATCATCTGTAG
** *
1093 AAGATCCGGGTGTACGACGAAAGCACATAACATCATCTACAA
1 AAGATCCGGGTGTACGACGAAAGCACATAACATCATCTGTAG
*
1135 AAGATACGGGTGTACGACGAAA
1 AAGATCCGGGTGTACGACGAAA
1157 AGAACATATA
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 58 1.00
ACGTcount: A:0.38, C:0.20, G:0.24, T:0.19
Consensus pattern (42 bp):
AAGATCCGGGTGTACGACGAAAGCACATAACATCATCTGTAG
Found at i:11929 original size:23 final size:22
Alignment explanation
Indices: 11903--11969 Score: 80
Period size: 23 Copynumber: 2.9 Consensus size: 22
11893 AAAATAATTT
*
11903 CAGAATCGAAAAACACTGTTTAC
1 CAGAA-CGAAAAACTCTGTTTAC
* *
11926 CAGAACTGAAAAACTTTATTTAC
1 CAGAAC-GAAAAACTCTGTTTAC
11949 CAGAACCGAAAAACTCTGTTT
1 CAGAA-CGAAAAACTCTGTTT
11970 CTATATGGTA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
22 1 0.03
23 35 0.95
24 1 0.03
ACGTcount: A:0.42, C:0.21, G:0.12, T:0.25
Consensus pattern (22 bp):
CAGAACGAAAAACTCTGTTTAC
Found at i:14860 original size:27 final size:27
Alignment explanation
Indices: 14805--14860 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
14795 TTCGTGCCCA
*
14805 AAATCATATATAAAAAAATCTTTTAAT
1 AAATCATATATAAAAAAATATTTTAAT
* *
14832 AAATCA-ATATAAAAATATATATTTCAT
1 AAATCATATATAAAAAAATAT-TTTAAT
14859 AA
1 AA
14861 CATAATTCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 12 0.48
27 13 0.52
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (27 bp):
AAATCATATATAAAAAAATATTTTAAT
Found at i:17725 original size:17 final size:17
Alignment explanation
Indices: 17705--17738 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
17695 TTTATTAAAA
17705 TTTTAAGTTTAATTTAG
1 TTTTAAGTTTAATTTAG
* *
17722 TTTTTATTTTAATTTAG
1 TTTTAAGTTTAATTTAG
17739 AGTGAAATTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.26, C:0.00, G:0.09, T:0.65
Consensus pattern (17 bp):
TTTTAAGTTTAATTTAG
Found at i:18552 original size:17 final size:18
Alignment explanation
Indices: 18511--18561 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 18
18501 TTTAATAAGA
* * *
18511 TTAATTTTTATTAAAATT
1 TTAATTTTAATTTAGATT
18529 TTAATTTTAATTTAGATT
1 TTAATTTTAATTTAGATT
18547 TT-ATTTTAATTTAGA
1 TTAATTTTAATTTAGA
18562 GTGAAATTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
17 13 0.43
18 17 0.57
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (18 bp):
TTAATTTTAATTTAGATT
Found at i:21677 original size:37 final size:37
Alignment explanation
Indices: 21601--21677 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 37
21591 TTTTTATATT
*
21601 TTTAATTTTATAAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTATAAAAAAAATTATATAAATATTATCAA
* * *
21638 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTATAAAAAAAATTATATAAATATTAT-CAA
21675 TTT
1 TTT
21678 GTAATATTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 13 0.37
37 22 0.63
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.47
Consensus pattern (37 bp):
TTTAATTTTATAAAAAAAATTATATAAATATTATCAA
Found at i:24130 original size:14 final size:15
Alignment explanation
Indices: 24093--24132 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
24083 TAACGAAAAG
24093 AATA-ATTTTA-ATA
1 AATATATTTTATATA
24106 AATATATTTTTATATA
1 AATATA-TTTTATATA
24122 AA-ATATTTTAT
1 AATATATTTTAT
24133 TTTCTTACGT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 4 0.17
14 7 0.29
15 8 0.33
16 5 0.21
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
AATATATTTTATATA
Found at i:25102 original size:26 final size:26
Alignment explanation
Indices: 25047--25103 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
25037 CAATTTTAGT
**
25047 ATTGTGAATGGAATAAACTAAATTGT
1 ATTGTGAATGGAATAAACTAAATTAA
* *
25073 ATTGTGAATGGGATAAACTAGATTAA
1 ATTGTGAATGGAATAAACTAAATTAA
25099 ATTGT
1 ATTGT
25104 CCATAATAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.40, C:0.04, G:0.21, T:0.35
Consensus pattern (26 bp):
ATTGTGAATGGAATAAACTAAATTAA
Found at i:26100 original size:16 final size:16
Alignment explanation
Indices: 26081--26112 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
26071 AATTTAATAT
26081 CAATTGACTTTACTAA
1 CAATTGACTTTACTAA
26097 CAATTGACTTTACTAA
1 CAATTGACTTTACTAA
26113 ATAAAATGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.38
Consensus pattern (16 bp):
CAATTGACTTTACTAA
Found at i:28395 original size:16 final size:17
Alignment explanation
Indices: 28355--28408 Score: 55
Period size: 17 Copynumber: 3.5 Consensus size: 17
28345 CACGAAATAT
*
28355 AATATTAT-TT-TTTAA
1 AATATTATATTATTCAA
28370 AATA--ATATTA-TCAA
1 AATATTATATTATTCAA
*
28384 AATATTATATTATTTAA
1 AATATTATATTATTCAA
28401 AATATTAT
1 AATATTAT
28409 TGGTAATGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
13 2 0.06
14 9 0.28
15 4 0.12
16 6 0.19
17 11 0.34
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (17 bp):
AATATTATATTATTCAA
Found at i:28727 original size:50 final size:50
Alignment explanation
Indices: 28666--28801 Score: 157
Period size: 50 Copynumber: 2.7 Consensus size: 50
28656 TATTTTATGG
* * *
28666 GAGATGTACATACTTACAATGGTATAAGTATGTGTTTATTTTTAGGTTGA
1 GAGATGTACATACTTACAACGGTATAAATATGTGTTTATTTTTAAGTTGA
* * * *
28716 GAGATTTACATACTTACACCGGTGTAAATGTGTGTTTATTTTTAAGTTG-
1 GAGATGTACATACTTACAACGGTATAAATATGTGTTTATTTTTAAGTTGA
* * * *
28765 GAAGATGTGCATAATTACACCAGTATAAATATGTGTT
1 G-AGATGTACATACTTACAACGGTATAAATATGTGTT
28802 AATTGTTATA
Statistics
Matches: 72, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
49 1 0.01
50 71 0.99
ACGTcount: A:0.31, C:0.09, G:0.21, T:0.40
Consensus pattern (50 bp):
GAGATGTACATACTTACAACGGTATAAATATGTGTTTATTTTTAAGTTGA
Found at i:36284 original size:27 final size:28
Alignment explanation
Indices: 36226--36286 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 28
36216 TTTCTGTTTT
*
36226 TTTTGCTGGTTCTCCTTTCTTTTTCTGT
1 TTTTGCTGGTTCTCCTTTCTTTTTCTGA
* * * *
36254 TTTTGCTGGTTGT-TTTTTTTTTTTTGA
1 TTTTGCTGGTTCTCCTTTCTTTTTCTGA
36281 TTTTGC
1 TTTTGC
36287 AGATTTGGTG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
27 16 0.57
28 12 0.43
ACGTcount: A:0.02, C:0.13, G:0.16, T:0.69
Consensus pattern (28 bp):
TTTTGCTGGTTCTCCTTTCTTTTTCTGA
Found at i:46576 original size:34 final size:34
Alignment explanation
Indices: 46538--46605 Score: 100
Period size: 34 Copynumber: 2.0 Consensus size: 34
46528 CGATTATAAT
46538 ATATTATTTTATCAAGTTAATTAACTATTAAAAG
1 ATATTATTTTATCAAGTTAATTAACTATTAAAAG
* * * *
46572 ATATTATTTTATCGAGTTTATTGACTGTTAAAAG
1 ATATTATTTTATCAAGTTAATTAACTATTAAAAG
46606 TTATAAAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.38, C:0.06, G:0.10, T:0.46
Consensus pattern (34 bp):
ATATTATTTTATCAAGTTAATTAACTATTAAAAG
Found at i:48444 original size:3 final size:3
Alignment explanation
Indices: 48438--48495 Score: 107
Period size: 3 Copynumber: 19.3 Consensus size: 3
48428 TACAAATTTG
*
48438 ATA ATA ATA ATA GTA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
48486 ATA ATA ATA A
1 ATA ATA ATA A
48496 ATGGTACCAC
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:51379 original size:19 final size:20
Alignment explanation
Indices: 51352--51392 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
51342 ATTAAATTTG
51352 ATTAAATTAAAAT-TAAAAT
1 ATTAAATTAAAATATAAAAT
* *
51371 ATTACATTAATATATAAAAT
1 ATTAAATTAAAATATAAAAT
51391 AT
1 AT
51393 ATTTTAAGGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (20 bp):
ATTAAATTAAAATATAAAAT
Found at i:65682 original size:29 final size:29
Alignment explanation
Indices: 65640--65710 Score: 124
Period size: 29 Copynumber: 2.4 Consensus size: 29
65630 TTTAACGAAC
*
65640 GAACATAAACAAATATGAACAAGCTGAAT
1 GAACATAAACAAATATGAACAAGCTAAAT
65669 GAACATAAACAAATATGAACAAGCTAAAT
1 GAACATAAACAAATATGAACAAGCTAAAT
*
65698 GAACATGAACAAA
1 GAACATAAACAAA
65711 AAATTCCGTT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.58, C:0.14, G:0.13, T:0.15
Consensus pattern (29 bp):
GAACATAAACAAATATGAACAAGCTAAAT
Found at i:65688 original size:16 final size:16
Alignment explanation
Indices: 65640--65689 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 16
65630 TTTAACGAAC
65640 GAACATAAACAAATAT
1 GAACATAAACAAATAT
* **
65656 GAAC--AAGCTGA-AT
1 GAACATAAACAAATAT
65669 GAACATAAACAAATAT
1 GAACATAAACAAATAT
65685 GAACA
1 GAACA
65690 AGCTAAATGA
Statistics
Matches: 25, Mismatches: 6, Indels: 6
0.68 0.16 0.16
Matches are distributed among these distances:
13 6 0.24
14 4 0.16
15 4 0.16
16 11 0.44
ACGTcount: A:0.58, C:0.14, G:0.12, T:0.16
Consensus pattern (16 bp):
GAACATAAACAAATAT
Found at i:66467 original size:9 final size:9
Alignment explanation
Indices: 66453--66496 Score: 58
Period size: 9 Copynumber: 5.2 Consensus size: 9
66443 TATTTAAATC
66453 TATTATTAA
1 TATTATTAA
*
66462 TATTATT-T
1 TATTATTAA
66470 TATTA-T-A
1 TATTATTAA
66477 TATTATTAA
1 TATTATTAA
66486 TATTATTAA
1 TATTATTAA
66495 TA
1 TA
66497 ATTTTTTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
7 6 0.19
8 6 0.19
9 19 0.61
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (9 bp):
TATTATTAA
Found at i:68095 original size:35 final size:36
Alignment explanation
Indices: 68014--68095 Score: 103
Period size: 36 Copynumber: 2.3 Consensus size: 36
68004 TTTTAGTACG
* ** * *
68014 TTAATTTTTATTTTTTTTTAATATCATTTTTAAAGT
1 TTAATTTTTATTTTATTTTAATATCAAGTTCAAAAT
68050 TTAATTTTTATTTTATTTTAATAT-AAGTTCAAAAT
1 TTAATTTTTATTTTATTTTAATATCAAGTTCAAAAT
*
68085 TTAAATTTTAT
1 TTAATTTTTAT
68096 AAAAATTAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
35 17 0.43
36 23 0.57
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (36 bp):
TTAATTTTTATTTTATTTTAATATCAAGTTCAAAAT
Found at i:69750 original size:2 final size:2
Alignment explanation
Indices: 69732--69780 Score: 82
Period size: 2 Copynumber: 24.5 Consensus size: 2
69722 ATTCTTTAAG
69732 TA TA TA T- TA TA TCA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA
69774 TA TA TA T
1 TA TA TA T
69781 TTCGATGCTA
Statistics
Matches: 45, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 1 0.02
2 42 0.93
3 2 0.04
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:70044 original size:43 final size:44
Alignment explanation
Indices: 69982--70064 Score: 114
Period size: 43 Copynumber: 1.9 Consensus size: 44
69972 TACCTAGGGA
* *
69982 TATGAGTCGCCATGTTGTTTCTGGTCCGTTCAATTTGATCTGGC
1 TATGAGTCGCCATGTTGTTTCTCGTCCATTCAATTTGATCTGGC
* * *
70026 TATGAGTCG-GATGTTGTTTTTCGTCCATTCATTTTGATC
1 TATGAGTCGCCATGTTGTTTCTCGTCCATTCAATTTGATC
70065 CGATAAATAT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
43 25 0.74
44 9 0.26
ACGTcount: A:0.14, C:0.18, G:0.23, T:0.45
Consensus pattern (44 bp):
TATGAGTCGCCATGTTGTTTCTCGTCCATTCAATTTGATCTGGC
Found at i:71138 original size:36 final size:34
Alignment explanation
Indices: 71096--71177 Score: 101
Period size: 36 Copynumber: 2.3 Consensus size: 34
71086 AATCGATTAA
71096 ACGGGGACGGAAAAAAATCGTTTATGCTAAACGGGG
1 ACGGGGACGG-AAAAAAT-GTTTATGCTAAACGGGG
* * *
71132 ACGGGGACAGGGAAAAATGTTTATGTTAAATGGGG
1 ACGGGGAC-GGAAAAAATGTTTATGCTAAACGGGG
71167 ACAGGGGACGG
1 AC-GGGGACGG
71178 GGTTGGGTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
35 19 0.46
36 20 0.49
37 2 0.05
ACGTcount: A:0.34, C:0.11, G:0.38, T:0.17
Consensus pattern (34 bp):
ACGGGGACGGAAAAAATGTTTATGCTAAACGGGG
Done.