Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007431.1 Hibiscus syriacus cultivar Beakdansim tig00020146_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: 57026
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.33
Found at i:3595 original size:276 final size:274
Alignment explanation
Indices: 3074--3601 Score: 758
Period size: 276 Copynumber: 1.9 Consensus size: 274
3064 ATAGTTAAAG
*
3074 AAATTATCTTTTCTGAACCCATGAATGCAATGATCAGTACAAAACATAAATTAACTAGAACCAAG
1 AAATTATCTATTCTGAACCCATGAATGCAATGATCAGTACAAAACATAAATTAACTAGAACCAAG
* * *
3139 AACTAATTTCCTGCATACACCTCCACCAACAAATTAAGCTTCAACACATCTATTTAATTGGTCAT
66 AACTAATTCCCTGCATACACCTCCACCAACAAATTAAGATTCAACACATCTATTTAATTGATCAT
*
3204 ATATGCTCAAGGGGTAAAAACACTTGAACATTAAAACAAAGCTGCACCACAGAAGCAAACACCAA
131 ATATGCTCAAGGGGCAAAAACACTTGAACATTAAAACAAAGCTGCACCACAGAAGCAAACACCAA
** * *
3269 GAAAAGTGCTAAGATGAACATATACAACAATTCCTTATGAAAGCTTTTCTAAACTTTTTTTCACC
196 GAAAAGTGAGAAGATGAACACATACAACAATTCCTTATGAAAGATTTTCTAAACTTTTTTTCACC
3334 ATTTTGAGTCAACA
261 ATTTTGAGTCAACA
* *
3348 AAATTATCATATTCTGAACCCATGAATGCAGTGATCAGTACGAGACACA-AAATTAACTAGAACC
1 AAATTATC-TATTCTGAACCCATGAATGCAATGATCAGTAC-A-AAACATAAATTAACTAGAACC
* *** * *
3412 AAGAACTAATTCCCTGCATACACTTCCACCAGTGAA-TAGGATTCAACACATCTATATTATTTGA
63 AAGAACTAATTCCCTGCATACACCTCCACCAACAAATTAAGATTCAACACATCTAT-TTAATTGA
* *
3476 TCATATATGCTCAAGGGGCAAAAACACTTGAATATTTAAACAAAAGCTGCACCACAGAAGCAAA-
127 TCATATATGCTCAAGGGGCAAAAACACTTGAACATTAAAAC-AAAGCTGCACCACAGAAGCAAAC
* * * * *
3540 AGCCCAGAAAAGTGAGAAGATGCAGACATACGACATTTCCTTATG-AAGATTTTCTAAACTTT
191 A-CCAAGAAAAGTGAGAAGATGAACACATACAACAATTCCTTATGAAAGATTTTCTAAACTTT
3602 AAATATTTTC
Statistics
Matches: 224, Mismatches: 24, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
274 8 0.04
275 47 0.21
276 108 0.48
277 61 0.27
ACGTcount: A:0.41, C:0.21, G:0.13, T:0.26
Consensus pattern (274 bp):
AAATTATCTATTCTGAACCCATGAATGCAATGATCAGTACAAAACATAAATTAACTAGAACCAAG
AACTAATTCCCTGCATACACCTCCACCAACAAATTAAGATTCAACACATCTATTTAATTGATCAT
ATATGCTCAAGGGGCAAAAACACTTGAACATTAAAACAAAGCTGCACCACAGAAGCAAACACCAA
GAAAAGTGAGAAGATGAACACATACAACAATTCCTTATGAAAGATTTTCTAAACTTTTTTTCACC
ATTTTGAGTCAACA
Found at i:9847 original size:2 final size:2
Alignment explanation
Indices: 9791--9835 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
9781 TTATCTTCAT
9791 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
9833 TA T
1 TA T
9836 CATTCGTATA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:10021 original size:34 final size:34
Alignment explanation
Indices: 9940--10025 Score: 88
Period size: 34 Copynumber: 2.5 Consensus size: 34
9930 TAATTAAACT
* *
9940 TGTATCGTTCCTTATTATATACTTACTCTTTTTCC
1 TGTATCGTTCCTT-TCATATACTTACTATTTTTCC
*
9975 TGTA-C-TAATCCTTTCACTATA-TTATTATTTTTCC
1 TGTATCGT--TCCTTTCA-TATACTTACTATTTTTCC
10009 TGTATCGTTCCTTTCAT
1 TGTATCGTTCCTTTCAT
10026 TGTACTGTTA
Statistics
Matches: 43, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
33 2 0.05
34 26 0.60
35 14 0.33
36 1 0.02
ACGTcount: A:0.19, C:0.22, G:0.06, T:0.53
Consensus pattern (34 bp):
TGTATCGTTCCTTTCATATACTTACTATTTTTCC
Found at i:10347 original size:65 final size:65
Alignment explanation
Indices: 10243--10508 Score: 372
Period size: 65 Copynumber: 4.1 Consensus size: 65
10233 GATCTTTGTA
* * * * * *
10243 GTATTCAATTATCATTCCACCTCACGCACCACAAAGGTACATGAGTCATATGACTAATATGTACT
1 GTATTCAATTATCACTCCACCCCATGCACCACAAAGGTACATGAGTCATATGAGTGATATGTATT
* *
10308 GTATTTAATTATCACTCCACCCCATGCACCACAAAGGTACATGAGTCATATGAGTGATGTGTATT
1 GTATTCAATTATCACTCCACCCCATGCACCACAAAGGTACATGAGTCATATGAGTGATATGTATT
* * * * *
10373 GTATTCAATTATCACTCCACCCCATGCACCACAGAGATACATGAGTCGTATTAGTGATTTGTATT
1 GTATTCAATTATCACTCCACCCCATGCACCACAAAGGTACATGAGTCATATGAGTGATATGTATT
* ** *
10438 GTATTCAATTATCATTCCACCTTATGCACCACAAAGGTACATGAGTCATATGAATGATATGTATT
1 GTATTCAATTATCACTCCACCCCATGCACCACAAAGGTACATGAGTCATATGAGTGATATGTATT
10503 -TATTCA
1 GTATTCA
10509 CTCTACATCT
Statistics
Matches: 178, Mismatches: 23, Indels: 1
0.88 0.11 0.00
Matches are distributed among these distances:
64 6 0.03
65 172 0.97
ACGTcount: A:0.32, C:0.22, G:0.14, T:0.32
Consensus pattern (65 bp):
GTATTCAATTATCACTCCACCCCATGCACCACAAAGGTACATGAGTCATATGAGTGATATGTATT
Found at i:12242 original size:23 final size:23
Alignment explanation
Indices: 12216--12260 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
12206 CACCACAGCT
*
12216 CGTATAAATGCACCGAAGTGCCC
1 CGTAGAAATGCACCGAAGTGCCC
* *
12239 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
12261 ATATAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.29, G:0.24, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCC
Found at i:12542 original size:149 final size:149
Alignment explanation
Indices: 12239--12535 Score: 585
Period size: 149 Copynumber: 2.0 Consensus size: 149
12229 CGAAGTGCCC
*
12239 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
12304 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
12369 CATATGTCCCGAAGAACCA
131 CATATGTCCCGAAGAACCA
12388 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
12453 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
12518 CATATGTCCCGAAGAACC
131 CATATGTCCCGAAGAACC
12536 GTGTAGACCC
Statistics
Matches: 147, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 147 1.00
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.28
Consensus pattern (149 bp):
CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
CATATGTCCCGAAGAACCA
Found at i:13439 original size:18 final size:18
Alignment explanation
Indices: 13418--13452 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
13408 TCCCATCTAG
13418 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
13436 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
13453 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:14059 original size:20 final size:21
Alignment explanation
Indices: 14030--14072 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
14020 ATTTTGTCGT
*
14030 TTGAAGGGGTATCG-TTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
14050 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
14071 TT
1 TT
14073 TCCCAGAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.16, C:0.26, G:0.26, T:0.33
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:17369 original size:23 final size:23
Alignment explanation
Indices: 17343--17387 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
17333 CACCACAGCT
*
17343 CGTATAAATGCACCGAAGTGCCC
1 CGTAGAAATGCACCGAAGTGCCC
* *
17366 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
17388 ATATAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.29, G:0.24, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCC
Found at i:17622 original size:146 final size:148
Alignment explanation
Indices: 17366--17666 Score: 561
Period size: 146 Copynumber: 2.0 Consensus size: 148
17356 CGAAGTGCCC
17366 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAA-GATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
17431 CATATACATATGCTAGGGATCAAGTATGTGTATTTCCAGACTTCACACATGTTCCAAAGAATATA
65 CATATACATATGCTAGGGATCAAGTATGTGTATTTCCAGACTTCACACATGTTCCAAAGAATATA
17496 CATATGTCCCGAAGAACCA
130 CATATGTCCCGAAGAACCA
17515 CGTAGAATTGCACCGTAGTGCCATAT-A-ATGTCCATAAGGACCACATAGAATTCTTTAAGAATC
1 CGTAGAATTGCACCGTAGTGCCATATAAGATGTCCATAAGGACCACATAGAATTCTTTAAGAATC
*
17578 ATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATAC
66 ATATACATATGCTAGGGATCAAGTATGTGTATTTCCAGACTTCACACATGTTCCAAAGAATATAC
*
17643 ATATGTCCCGAAGAACCG
131 ATATGTCCCGAAGAACCA
17661 CGTAGA
1 CGTAGA
17667 CCCTCGACTC
Statistics
Matches: 150, Mismatches: 2, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
146 123 0.82
148 1 0.01
149 26 0.17
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (148 bp):
CGTAGAATTGCACCGTAGTGCCATATAAGATGTCCATAAGGACCACATAGAATTCTTTAAGAATC
ATATACATATGCTAGGGATCAAGTATGTGTATTTCCAGACTTCACACATGTTCCAAAGAATATAC
ATATGTCCCGAAGAACCA
Found at i:18564 original size:18 final size:18
Alignment explanation
Indices: 18543--18577 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
18533 TCCCATCTAG
18543 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
18561 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
18578 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:19187 original size:21 final size:21
Alignment explanation
Indices: 19157--19201 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
19147 ATTTTGTCGT
* *
19157 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
19178 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
19199 TTG
1 TTG
19202 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:23922 original size:32 final size:31
Alignment explanation
Indices: 23834--23923 Score: 99
Period size: 32 Copynumber: 2.8 Consensus size: 31
23824 AAAAAGTAAT
* *
23834 AATTTAATGATTATTTTATGAAAATTATATAA
1 AATTTAATGATTATTTTAT-AATATTTTATAA
* ** * *
23866 AATTTAGTGAGCATTTCATTATATTTTGATAA
1 AATTTAATGATTATTTTATAATATTTT-ATAA
23898 AATTTAATGATTATTTTATAATATTT
1 AATTTAATGATTATTTTATAATATTT
23924 AAAAAAATAA
Statistics
Matches: 45, Mismatches: 12, Indels: 2
0.76 0.20 0.03
Matches are distributed among these distances:
31 5 0.11
32 40 0.89
ACGTcount: A:0.40, C:0.02, G:0.08, T:0.50
Consensus pattern (31 bp):
AATTTAATGATTATTTTATAATATTTTATAA
Found at i:26757 original size:77 final size:77
Alignment explanation
Indices: 26628--26787 Score: 259
Period size: 77 Copynumber: 2.1 Consensus size: 77
26618 TGCGCAAGCA
* * *
26628 GTGCTTCGGGTCACAAGTGTTGCTCGTGAAGGCCACGTAATCTGTTCTTAACAGTGAGTTTCTAT
1 GTGCTCCGGGTCACAAGTGTTGCTCGTGAAGGCCACGTAATCGGTTCCTAACAGTGAGTTTCTAT
*
26693 ATAAAACCTTAC
66 ATAAAACCATAC
*
26705 GTGCTCCGGGTCACACGTGTTG-TACGTGAAGGCCACGTAATCGGTTCCTAACAGTGAGTTTCTA
1 GTGCTCCGGGTCACAAGTGTTGCT-CGTGAAGGCCACGTAATCGGTTCCTAACAGTGAGTTTCTA
26769 TATAAAACCATAC
65 TATAAAACCATAC
26782 GTGCTC
1 GTGCTC
26788 GTATCAAGTA
Statistics
Matches: 77, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
76 1 0.01
77 76 0.99
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.30
Consensus pattern (77 bp):
GTGCTCCGGGTCACAAGTGTTGCTCGTGAAGGCCACGTAATCGGTTCCTAACAGTGAGTTTCTAT
ATAAAACCATAC
Found at i:28398 original size:13 final size:13
Alignment explanation
Indices: 28380--28405 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
28370 AAAAAAAATG
28380 TCTCATTATTTTA
1 TCTCATTATTTTA
28393 TCTCATTATTTTA
1 TCTCATTATTTTA
28406 ACTATGACTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.15, G:0.00, T:0.62
Consensus pattern (13 bp):
TCTCATTATTTTA
Found at i:36017 original size:32 final size:33
Alignment explanation
Indices: 35979--36046 Score: 95
Period size: 32 Copynumber: 2.1 Consensus size: 33
35969 CAACTTAAGA
*
35979 GGGGCAAAGTATAATTAA-TCATA-AAATATGAG
1 GGGGCAAAGTATAATTAACCCATAGAAA-ATGAG
*
36011 GGGGCAAGGTATAATTAACCCATAGAAAATGAG
1 GGGGCAAAGTATAATTAACCCATAGAAAATGAG
36044 GGG
1 GGG
36047 TTAAAATCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
32 17 0.53
33 12 0.38
34 3 0.09
ACGTcount: A:0.43, C:0.09, G:0.28, T:0.21
Consensus pattern (33 bp):
GGGGCAAAGTATAATTAACCCATAGAAAATGAG
Found at i:43227 original size:29 final size:30
Alignment explanation
Indices: 43183--43247 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 30
43173 CAGATCAGTG
*
43183 TATAATTGAAACAAAAACT-AAAGTTTAATGT
1 TATAATT-AAAC-AAAACTGAAAGTTTAATGA
*
43214 TATAATT-AACAAAATTGAAAGTTTAATGA
1 TATAATTAAACAAAACTGAAAGTTTAATGA
43243 TATAA
1 TATAA
43248 ACGATACAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
28 5 0.16
29 19 0.61
31 7 0.23
ACGTcount: A:0.52, C:0.05, G:0.09, T:0.34
Consensus pattern (30 bp):
TATAATTAAACAAAACTGAAAGTTTAATGA
Done.