Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002299.1 Hibiscus syriacus cultivar Beakdansim tig00004678_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: 77905
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:2056 original size:45 final size:45
Alignment explanation
Indices: 2006--2257 Score: 398
Period size: 45 Copynumber: 5.6 Consensus size: 45
1996 TTATGCTGGA
* * *
2006 AATGCACCCATATGCATTTTTGC-TATGACATCCTTTCATGCCAAT
1 AATGCACCCATATGCATTATT-CTTTTGGCATCCTTTCATGCCAAT
* *
2051 AATGCACCTATATGCATTATTCTTTTGGCATCCTTTCATTCCAAT
1 AATGCACCCATATGCATTATTCTTTTGGCATCCTTTCATGCCAAT
2096 AATGCACCCATATGCATTATTCTTTTGGCATCCTTTCATGCCAAT
1 AATGCACCCATATGCATTATTCTTTTGGCATCCTTTCATGCCAAT
**
2141 AATAAACCCATATGCATTATTCTTTTGGCATCCTTTCATGCCAAT
1 AATGCACCCATATGCATTATTCTTTTGGCATCCTTTCATGCCAAT
* * *
2186 AATGCTCTCATATGCAATATTCTTTTGGCATCCTTTCATGCCAAT
1 AATGCACCCATATGCATTATTCTTTTGGCATCCTTTCATGCCAAT
2231 AATGCACCCATATGCATTATTCTTTTG
1 AATGCACCCATATGCATTATTCTTTTG
2258 TTTATTCGTT
Statistics
Matches: 189, Mismatches: 17, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
44 1 0.01
45 188 0.99
ACGTcount: A:0.26, C:0.25, G:0.10, T:0.39
Consensus pattern (45 bp):
AATGCACCCATATGCATTATTCTTTTGGCATCCTTTCATGCCAAT
Found at i:2704 original size:20 final size:20
Alignment explanation
Indices: 2663--2730 Score: 79
Period size: 19 Copynumber: 3.5 Consensus size: 20
2653 TGGCTCCTCA
*
2663 GTATCGATAC-CCTACCATG
1 GTATCGATACACCTACTATG
2682 GTATCGATACTACC-ACTATG
1 GTATCGATAC-ACCTACTATG
* *
2702 GTACCGATA-ACCTATTATG
1 GTATCGATACACCTACTATG
2721 GTATCGATAC
1 GTATCGATAC
2731 CATTTTGCAT
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
18 3 0.07
19 23 0.56
20 13 0.32
21 2 0.05
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.29
Consensus pattern (20 bp):
GTATCGATACACCTACTATG
Found at i:3248 original size:16 final size:16
Alignment explanation
Indices: 3227--3259 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
3217 TTAATCCCAT
3227 CTAATCCTTCCTTAAG
1 CTAATCCTTCCTTAAG
3243 CTAATCCTTCCTTAAG
1 CTAATCCTTCCTTAAG
3259 C
1 C
3260 ATATATATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.33, G:0.06, T:0.36
Consensus pattern (16 bp):
CTAATCCTTCCTTAAG
Found at i:14946 original size:26 final size:26
Alignment explanation
Indices: 14917--14995 Score: 140
Period size: 26 Copynumber: 3.0 Consensus size: 26
14907 TGGTAAAGTG
*
14917 AGTTTTAAAGAGTACAATATCGGCTT
1 AGTTTTAAAGAGTACAAGATCGGCTT
14943 AGTTTTAAAGAGTACAAGATCGGCTT
1 AGTTTTAAAGAGTACAAGATCGGCTT
*
14969 AGTTTTAAAGAGTACAAGATCGACTT
1 AGTTTTAAAGAGTACAAGATCGGCTT
14995 A
1 A
14996 CTTGCCTCTC
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 51 1.00
ACGTcount: A:0.37, C:0.11, G:0.20, T:0.32
Consensus pattern (26 bp):
AGTTTTAAAGAGTACAAGATCGGCTT
Found at i:20828 original size:90 final size:88
Alignment explanation
Indices: 20726--21016 Score: 379
Period size: 90 Copynumber: 3.2 Consensus size: 88
20716 TTATGTTGAA
20726 AATGCACCCATATGCATTTCAGCTATGGCATCCTTTCATGCCAATAATGCACCCATATGCATTAT
1 AATGCACCCATATGCATTTCAGCTATGGCATCCTTTCATGCCAATAATGCA-CCATATGCATTAT
20791 TCTTTTAGCATCCTTTTATGCAAAT
65 TCTTTT-GCATCCTTTTATGCAAAT
* * *
20816 AATGCACCCATATACATTTCAGCTATGGCATCCTTTCATGCACATAAGAATGTCA-TATTATGCA
1 AATGCACCCATATGCATTTCAGCTATGGCATCCTTTCATGC-C--AATAATG-CACCA-TATGCA
*
20880 TTATTCTTTTGGCATCCTTTTATGTAAAT
61 TTATTCTTTT-GCATCCTTTTATGCAAAT
* * *
20909 AATGCACCCATATGCATTATTA-TTTTGGCATCCTTTCATGCCAATAATGCACTCATATGCATTA
1 AATGCACCCATATGCATT-TCAGCTATGGCATCCTTTCATGCCAATAATGCAC-CATATGCATTA
* *
20973 TTCTTTTGTCATCCTTTCATGCCAAT
64 TTCTTTTG-CATCCTTTTATGCAAAT
*
20999 AATGAACCCATATGCATT
1 AATGCACCCATATGCATT
21017 ATTCTTTTGT
Statistics
Matches: 177, Mismatches: 15, Indels: 18
0.84 0.07 0.09
Matches are distributed among these distances:
89 3 0.02
90 93 0.53
91 2 0.01
92 2 0.01
93 73 0.41
94 4 0.02
ACGTcount: A:0.28, C:0.23, G:0.11, T:0.37
Consensus pattern (88 bp):
AATGCACCCATATGCATTTCAGCTATGGCATCCTTTCATGCCAATAATGCACCATATGCATTATT
CTTTTGCATCCTTTTATGCAAAT
Found at i:21011 original size:138 final size:134
Alignment explanation
Indices: 20751--21025 Score: 331
Period size: 138 Copynumber: 2.0 Consensus size: 134
20741 ATTTCAGCTA
* * *
20751 TGGCATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTTAGCATCCTTTTATGCAAAT
1 TGGCATCCTTTCATGCAAATAATGCACCCATATGCATTATTATTTTAGCATCCTTTCATGCAAAT
**
20816 AATGCACCCATATACATTTCAGCTATGGCATCCTTTCATGCACATAAGAATGTCATATTATGCAT
66 AATGCACCCATATACATTTCA-CTATGGCATCCTTTCATGCACATAAGAA--TCCCA-TATGCAT
20881 TATTCTTT
127 TATTCTTT
* * * *
20889 TGGCATCCTTTTATGTAAATAATGCACCCATATGCATTATTATTTTGGCATCCTTTCATGCCAAT
1 TGGCATCCTTTCATGCAAATAATGCACCCATATGCATTATTATTTTAGCATCCTTTCATGCAAAT
* * * * *
20954 AATGCACTCATATGCATTATTC-TTTTGTCATCCTTTCATGC-CAATAATGAA-CCCATATGCAT
66 AATGCACCCATATACA-T-TTCACTATGGCATCCTTTCATGCAC-ATAA-GAATCCCATATGCAT
21016 TATTCTTT
127 TATTCTTT
21024 TG
1 TG
21026 TTCATTCGTT
Statistics
Matches: 119, Mismatches: 14, Indels: 11
0.83 0.10 0.08
Matches are distributed among these distances:
135 17 0.14
136 2 0.02
137 1 0.01
138 92 0.77
139 4 0.03
140 3 0.03
ACGTcount: A:0.27, C:0.23, G:0.11, T:0.39
Consensus pattern (134 bp):
TGGCATCCTTTCATGCAAATAATGCACCCATATGCATTATTATTTTAGCATCCTTTCATGCAAAT
AATGCACCCATATACATTTCACTATGGCATCCTTTCATGCACATAAGAATCCCATATGCATTATT
CTTT
Found at i:21026 original size:45 final size:45
Alignment explanation
Indices: 20726--21025 Score: 324
Period size: 45 Copynumber: 6.6 Consensus size: 45
20716 TTATGTTGAA
* *
20726 AATGCACCCATATGCA-T-TTCAGCTATGGCATCCTTTCATGCCAAT
1 AATGCACCCATATGCATTATTC--TTTTGGCATCCTTTCATGCCAAT
* * *
20771 AATGCACCCATATGCATTATTCTTTTAGCATCCTTTTATGCAAAT
1 AATGCACCCATATGCATTATTCTTTTGGCATCCTTTCATGCCAAT
* * * *
20816 AATGCACCCATATACA-T-TTCAGCTATGGCATCCTTTCATGCACATAAG
1 AATGCACCCATATGCATTATTC--TTTTGGCATCCTTTCATGC-C--AAT
* * **
20864 AATGTCA--TATTATGCATTATTCTTTTGGCATCCTTTTATGTAAAT
1 AATG-CACCCA-TATGCATTATTCTTTTGGCATCCTTTCATGCCAAT
*
20909 AATGCACCCATATGCATTATTATTTTGGCATCCTTTCATGCCAAT
1 AATGCACCCATATGCATTATTCTTTTGGCATCCTTTCATGCCAAT
* *
20954 AATGCACTCATATGCATTATTCTTTTGTCATCCTTTCATGCCAAT
1 AATGCACCCATATGCATTATTCTTTTGGCATCCTTTCATGCCAAT
*
20999 AATGAACCCATATGCATTATTCTTTTG
1 AATGCACCCATATGCATTATTCTTTTG
21026 TTCATTCGTT
Statistics
Matches: 212, Mismatches: 30, Indels: 26
0.79 0.11 0.10
Matches are distributed among these distances:
43 3 0.01
44 3 0.01
45 168 0.79
46 2 0.01
47 4 0.02
48 26 0.12
49 3 0.01
50 3 0.01
ACGTcount: A:0.28, C:0.23, G:0.11, T:0.38
Consensus pattern (45 bp):
AATGCACCCATATGCATTATTCTTTTGGCATCCTTTCATGCCAAT
Found at i:21503 original size:19 final size:19
Alignment explanation
Indices: 21463--21506 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
21453 GTATCGATAC
*
21463 TACCATATTATGGTACCGA
1 TACCATATTATGGTACCAA
* *
21482 TACCCTATTATGGTATCAA
1 TACCATATTATGGTACCAA
21501 TACCAT
1 TACCAT
21507 TTTTGCATTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.32, C:0.23, G:0.11, T:0.34
Consensus pattern (19 bp):
TACCATATTATGGTACCAA
Found at i:64003 original size:21 final size:21
Alignment explanation
Indices: 63979--64018 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
63969 TTTTCAAAGG
*
63979 CATGCA-CTGATGTATCAATAC
1 CATGCATC-GATGCATCAATAC
64000 CATGCATCGATGCATCAAT
1 CATGCATCGATGCATCAAT
64019 GAATAAATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 16 0.94
22 1 0.06
ACGTcount: A:0.33, C:0.25, G:0.15, T:0.28
Consensus pattern (21 bp):
CATGCATCGATGCATCAATAC
Found at i:64068 original size:19 final size:19
Alignment explanation
Indices: 64044--64080 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
64034 TCGAATGCAT
64044 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
64063 TCCATGCATCGATGCACT
1 TCCATGCACCGATGCACT
64081 ATGATTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.38, G:0.16, T:0.24
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:64107 original size:64 final size:63
Alignment explanation
Indices: 63999--64209 Score: 212
Period size: 64 Copynumber: 3.3 Consensus size: 63
63989 TGTATCAATA
* * * * *
63999 CCATGCATCGATGCATCAATGAATAAATTGAAACATCGAATGCATTCCATGCACCGATGCACTCT
1 CCATGCATCGATGCA-CTATGATTTAATTAAAACATCGAATGCATT-CATGCATCGATGCACTCT
* **
64064 CCATGCATCGATGCACTATGATTTAATTAAAACATCGAATGCATTTGATGCATCGATGCACAAT
1 CCATGCATCGATGCACTATGATTTAATTAAAACATCGAATGCA-TTCATGCATCGATGCACTCT
* * * *
64128 CCATGCATCGATGCACCAGGCTATTT--TTCAAACATCGAATGCACTTCATGCATCGGTGCACTC
1 CCATGCATCGATGCACTATG--ATTTAATTAAAACATCGAATGCA-TTCATGCATCGATGCACTC
64191 T
63 T
* *
64192 -TAGTGCACCGATGCACTA
1 CCA-TGCATCGATGCACTA
64210 GGAGTCCAAC
Statistics
Matches: 123, Mismatches: 19, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
63 1 0.01
64 101 0.82
65 17 0.14
66 4 0.03
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.27
Consensus pattern (63 bp):
CCATGCATCGATGCACTATGATTTAATTAAAACATCGAATGCATTCATGCATCGATGCACTCT
Found at i:70021 original size:24 final size:23
Alignment explanation
Indices: 69993--70072 Score: 85
Period size: 24 Copynumber: 3.5 Consensus size: 23
69983 CACTTAACAA
*
69993 TGCATCGATGCATCCCTTTGAATG
1 TGCATCGATGCATACC-TTGAATG
*
70017 TGCATCGATGCA-ACC--GCATG
1 TGCATCGATGCATACCTTGAATG
* *
70037 ATGCACCGATGCATGCCTTGAATG
1 -TGCATCGATGCATACCTTGAATG
70061 TGCATCGATGCA
1 TGCATCGATGCA
70073 CAAGATCATG
Statistics
Matches: 46, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
20 4 0.09
21 11 0.24
22 2 0.04
23 13 0.28
24 16 0.35
ACGTcount: A:0.24, C:0.26, G:0.24, T:0.26
Consensus pattern (23 bp):
TGCATCGATGCATACCTTGAATG
Found at i:72713 original size:64 final size:64
Alignment explanation
Indices: 72586--72749 Score: 220
Period size: 64 Copynumber: 2.5 Consensus size: 64
72576 TTTTCAAAGG
* *
72586 CATGCACCGATGCATAATACCATGCATCGATGCATCAATGAATAAATTGAAACATCGAATGCATT
1 CATGCACCGATGCACAAT-CCATGCATCGATGCA-CAATGAATAAATTAAAACATCGAATGCATT
72651 T
64 T
* ** * * *
72652 CATTCACCGATGCACTCTCCATGCATCGATGCACTATGATTTAATTAAAACATCGAATGCATTT
1 CATGCACCGATGCACAATCCATGCATCGATGCACAATGAATAAATTAAAACATCGAATGCATTT
* *
72716 GATGCATCGATGCACAATCCATGCATCGATGCAC
1 CATGCACCGATGCACAATCCATGCATCGATGCAC
72750 CAGGCTATTT
Statistics
Matches: 85, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
64 56 0.66
65 15 0.18
66 14 0.16
ACGTcount: A:0.34, C:0.24, G:0.15, T:0.27
Consensus pattern (64 bp):
CATGCACCGATGCACAATCCATGCATCGATGCACAATGAATAAATTAAAACATCGAATGCATTT
Found at i:72767 original size:64 final size:63
Alignment explanation
Indices: 72586--72793 Score: 195
Period size: 64 Copynumber: 3.2 Consensus size: 63
72576 TTTTCAAAGG
* * * * ** *
72586 CATGCACCGATGCATAATACCATGCATCGATGCATCAATGAATAAATTGAAACATCGAATGCATT
1 CATGCATCGATGCACAAT-CCATGCATCGATGCA-CCA-GGATTTATTAAAACATCGAATGCATT
72651 T
63 T
* * ** * *
72652 CATTCACCGATGCACTCTCCATGCATCGATGCACTATGATTTAATTAAAACATCGAATGCATTT
1 CATGCATCGATGCACAATCCATGCATCGATGCACCAGGATTT-ATTAAAACATCGAATGCATTT
* * *
72716 GATGCATCGATGCACAATCCATGCATCGATGCACCAGGCTATTT-TTCAAACATC-AATGCACTT
1 CATGCATCGATGCACAATCCATGCATCGATGCACCAGG--ATTTATTAAAACATCGAATGCATTT
*
72779 CATGCATCGTTGCAC
1 CATGCATCGATGCAC
72794 TCTTAGTGCA
Statistics
Matches: 118, Mismatches: 21, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
63 23 0.19
64 62 0.53
65 15 0.13
66 18 0.15
ACGTcount: A:0.32, C:0.25, G:0.15, T:0.28
Consensus pattern (63 bp):
CATGCATCGATGCACAATCCATGCATCGATGCACCAGGATTTATTAAAACATCGAATGCATTT
Found at i:75671 original size:21 final size:21
Alignment explanation
Indices: 75647--75686 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
75637 TTTTCAAAGG
75647 CATGCA-CAGATGCATCAATAC
1 CATGCATC-GATGCATCAATAC
75668 CATGCATCGATGCATCAAT
1 CATGCATCGATGCATCAAT
75687 GAATAAATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.35, C:0.28, G:0.15, T:0.23
Consensus pattern (21 bp):
CATGCATCGATGCATCAATAC
Found at i:75726 original size:17 final size:17
Alignment explanation
Indices: 75706--75746 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
75696 GAAACATCGA
*
75706 ATGCATTCCATGCACCG
1 ATGCACTCCATGCACCG
*
75723 ATGCACTCCATGCATCG
1 ATGCACTCCATGCACCG
75740 ATGCACT
1 ATGCACT
75747 ATGATTTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.24, C:0.34, G:0.17, T:0.24
Consensus pattern (17 bp):
ATGCACTCCATGCACCG
Found at i:75774 original size:62 final size:63
Alignment explanation
Indices: 75647--75809 Score: 193
Period size: 62 Copynumber: 2.5 Consensus size: 63
75637 TTTTCAAAGG
* *
75647 CATGCACAGATGCATCAATACCATGCATCGATGCATCAATGAATAAATTGAAACATCGAATGCAT
1 CATGCACCGATGCA-C-AT-CCATGCATCGATGCA-CAATGAATAAATTAAAACATCGAATGCAT
75712 TC
62 TC
* * * * *
75714 CATGCACCGATGCAC-TCCATGCATCGATGCACTATGATTTAATTAAAACATTGAATGCATTT
1 CATGCACCGATGCACATCCATGCATCGATGCACAATGAATAAATTAAAACATCGAATGCATTC
* *
75776 GATGCATCGATGCACAATCCATGCATCGATGCAC
1 CATGCACCGATGCAC-ATCCATGCATCGATGCAC
75810 CAGGCTATTT
Statistics
Matches: 85, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
62 38 0.45
63 15 0.18
64 18 0.21
66 1 0.01
67 13 0.15
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.26
Consensus pattern (63 bp):
CATGCACCGATGCACATCCATGCATCGATGCACAATGAATAAATTAAAACATCGAATGCATTC
Found at i:75827 original size:64 final size:61
Alignment explanation
Indices: 75697--75856 Score: 187
Period size: 64 Copynumber: 2.6 Consensus size: 61
75687 GAATAAATTG
* * * *
75697 AAACATCGAATGCATTCCATGCACCGATGCACTCCATGCATCGATGCACTATGATTTAATTA
1 AAACATCGAATGCATTTCATGCATCGATGCACTCCATGCATCGATGCACCAGGATTT-ATTA
* * *
75759 AAACATTGAATGCATTTGATGCATCGATGCACAATCCATGCATCGATGCACCAGGCTATTT-TTC
1 AAACATCGAATGCATTTCATGCATCGATGCAC--TCCATGCATCGATGCACCAGG--ATTTATTA
* *
75823 AAACATCGAATGCACTTCATTCATCGATGCACTC
1 AAACATCGAATGCATTTCATGCATCGATGCACTC
75857 TTAGTTTACC
Statistics
Matches: 83, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
62 30 0.36
64 49 0.59
66 4 0.05
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.28
Consensus pattern (61 bp):
AAACATCGAATGCATTTCATGCATCGATGCACTCCATGCATCGATGCACCAGGATTTATTA
Done.