Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007235.1 Hibiscus syriacus cultivar Beakdansim tig00019155_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: 60025
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:3706 original size:3 final size:3
Alignment explanation
Indices: 3698--3747 Score: 72
Period size: 3 Copynumber: 18.0 Consensus size: 3
3688 TTTAAATGCT
3698 TTA TTA TTA TTA -TA TTA TTA TTA TTA TT- TTA TTA TTA TTA TT- TT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3742 TTA TTA
1 TTA TTA
3748 AGTTTAGGTG
Statistics
Matches: 44, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
2 8 0.18
3 36 0.82
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:3717 original size:14 final size:13
Alignment explanation
Indices: 3697--3747 Score: 75
Period size: 14 Copynumber: 3.8 Consensus size: 13
3687 CTTTAAATGC
3697 TTTATTATTATTA
1 TTTATTATTATTA
3710 TATTATTATTATTA
1 T-TTATTATTATTA
3724 TTTTATTATTATTA
1 -TTTATTATTATTA
*
3738 TTTTTTATTA
1 TTTATTATTA
3748 AGTTTAGGTG
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
13 10 0.29
14 24 0.69
15 1 0.03
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTATTATTATTA
Found at i:3720 original size:17 final size:17
Alignment explanation
Indices: 3698--3739 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
3688 TTTAAATGCT
3698 TTATTATTATTATATTA
1 TTATTATTATTATATTA
*
3715 TTATTATTATTTTATTA
1 TTATTATTATTATATTA
3732 TTATTATT
1 TTATTATT
3740 TTTTATTAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
TTATTATTATTATATTA
Found at i:3940 original size:52 final size:53
Alignment explanation
Indices: 3804--3961 Score: 225
Period size: 52 Copynumber: 3.1 Consensus size: 53
3794 TTTAACAATG
* *
3804 AACGCTCAATCACT-CTACTGCAGTCGTTGGTGTTC-AATTTGCAACCG-AAT
1 AACGCCCAATCACTCCTACTGCAGTCGTTGGTGTTCGAATTTGTAACCGAAAT
* *
3854 ACCGCCCAATCACTCCTACTGCAGTCGTTAGTGTTCGAA-TTGTAACCGAAAT
1 AACGCCCAATCACTCCTACTGCAGTCGTTGGTGTTCGAATTTGTAACCGAAAT
* * *
3906 AACGCCCAATCACTCCTACTACAATCATTGGTGTTCGAATTTGTAACCGAAAT
1 AACGCCCAATCACTCCTACTGCAGTCGTTGGTGTTCGAATTTGTAACCGAAAT
3959 AAC
1 AAC
3962 ACCATTCTTT
Statistics
Matches: 95, Mismatches: 9, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
50 12 0.13
51 28 0.29
52 39 0.41
53 16 0.17
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.28
Consensus pattern (53 bp):
AACGCCCAATCACTCCTACTGCAGTCGTTGGTGTTCGAATTTGTAACCGAAAT
Found at i:4743 original size:2 final size:2
Alignment explanation
Indices: 4730--4766 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
4720 GTGGAAATTT
*
4730 TA TA TC TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4767 CCCACAATCA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:17271 original size:2 final size:2
Alignment explanation
Indices: 17264--17296 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
17254 AACCATTCAA
17264 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
17297 ATTGCATAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:17865 original size:233 final size:233
Alignment explanation
Indices: 17458--17924 Score: 934
Period size: 233 Copynumber: 2.0 Consensus size: 233
17448 ATTTAACGTC
17458 ATAAAATGAGGCATACTAATTTAAAGAATAAAATGTAATTAATAATGGAAAATAAGGAAGTAACA
1 ATAAAATGAGGCATACTAATTTAAAGAATAAAATGTAATTAATAATGGAAAATAAGGAAGTAACA
17523 ACAACAATAAAACCCTATTCCTATATGCAATGGGGTAAGGGGAGATAGGGTAGTAGGATGCCCCC
66 ACAACAATAAAACCCTATTCCTATATGCAATGGGGTAAGGGGAGATAGGGTAGTAGGATGCCCCC
17588 AATGCTAGGTTGATAGTAGCTTCCGTGAAAGACCTCCGGAAGTCAGAAAATTAAAAAATAAAGAT
131 AATGCTAGGTTGATAGTAGCTTCCGTGAAAGACCTCCGGAAGTCAGAAAATTAAAAAATAAAGAT
17653 AAAATACAATGCATGTATAAATAAATAAATAAATACAT
196 AAAATACAATGCATGTATAAATAAATAAATAAATACAT
17691 ATAAAATGAGGCATACTAATTTAAAGAATAAAATGTAATTAATAATGGAAAATAAGGAAGTAACA
1 ATAAAATGAGGCATACTAATTTAAAGAATAAAATGTAATTAATAATGGAAAATAAGGAAGTAACA
17756 ACAACAATAAAACCCTATTCCTATATGCAATGGGGTAAGGGGAGATAGGGTAGTAGGATGCCCCC
66 ACAACAATAAAACCCTATTCCTATATGCAATGGGGTAAGGGGAGATAGGGTAGTAGGATGCCCCC
17821 AATGCTAGGTTGATAGTAGCTTCCGTGAAAGACCTCCGGAAGTCAGAAAATTAAAAAATAAAGAT
131 AATGCTAGGTTGATAGTAGCTTCCGTGAAAGACCTCCGGAAGTCAGAAAATTAAAAAATAAAGAT
17886 AAAATACAATGCATGTATAAATAAATAAATAAATACAT
196 AAAATACAATGCATGTATAAATAAATAAATAAATACAT
17924 A
1 A
17925 ATTGAACAGT
Statistics
Matches: 234, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
233 234 1.00
ACGTcount: A:0.46, C:0.12, G:0.18, T:0.23
Consensus pattern (233 bp):
ATAAAATGAGGCATACTAATTTAAAGAATAAAATGTAATTAATAATGGAAAATAAGGAAGTAACA
ACAACAATAAAACCCTATTCCTATATGCAATGGGGTAAGGGGAGATAGGGTAGTAGGATGCCCCC
AATGCTAGGTTGATAGTAGCTTCCGTGAAAGACCTCCGGAAGTCAGAAAATTAAAAAATAAAGAT
AAAATACAATGCATGTATAAATAAATAAATAAATACAT
Found at i:29659 original size:19 final size:20
Alignment explanation
Indices: 29595--29661 Score: 70
Period size: 19 Copynumber: 3.5 Consensus size: 20
29585 ACGGTTAAAT
* *
29595 TAATATATTATATAATTTATA
1 TAATATTTTA-ATAATTAATA
29616 T-AT-TTTTAATAATTAATA
1 TAATATTTTAATAATTAATA
29634 TAATATTTTAATAATATAA-A
1 TAATATTTTAATAAT-TAATA
29654 -AATATTTT
1 TAATATTTT
29662 TTTAAATATT
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
18 10 0.24
19 14 0.34
20 13 0.32
21 4 0.10
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
TAATATTTTAATAATTAATA
Found at i:29662 original size:20 final size:21
Alignment explanation
Indices: 29615--29662 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
29605 TATAATTTAT
29615 ATATTTTTAATAATTAATATA
1 ATATTTTTAATAATTAATATA
29636 ATA-TTTTAATAATATAA-A-A
1 ATATTTTTAATAAT-TAATATA
29655 ATATTTTT
1 ATATTTTT
29663 TTAAATATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
19 4 0.16
20 15 0.60
21 6 0.24
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
ATATTTTTAATAATTAATATA
Found at i:29687 original size:2 final size:2
Alignment explanation
Indices: 29675--29704 Score: 51
Period size: 2 Copynumber: 14.5 Consensus size: 2
29665 AAATATTAAT
29675 TA TA GTA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA T
29705 TAACTGGGGC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 25 0.93
3 2 0.07
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:35645 original size:38 final size:38
Alignment explanation
Indices: 35587--35694 Score: 132
Period size: 38 Copynumber: 2.8 Consensus size: 38
35577 CGGCCCGATA
*
35587 AATATTAA-AAATAATT-ATTTATATATATATATATATAT
1 AATATTAATAAAT--TTAATTTAAATATATATATATATAT
*
35625 AATATTAATAAATTTAATTTAAAT-TAAAATATATATAT
1 AATATTAATAAATTTAATTTAAATAT-ATATATATATAT
* *
35663 AATATTTATATATTTAATTTAAATATATATAT
1 AATATTAATAAATTTAATTTAAATATATATAT
35695 CCGGCTCGAT
Statistics
Matches: 61, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
37 3 0.05
38 53 0.87
39 5 0.08
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (38 bp):
AATATTAATAAATTTAATTTAAATATATATATATATAT
Found at i:35674 original size:15 final size:15
Alignment explanation
Indices: 35614--35693 Score: 50
Period size: 13 Copynumber: 5.8 Consensus size: 15
35604 TTTATATATA
35614 TATATATATATAATAT
1 TATATATATATAAT-T
* *
35630 TA-ATAAATTTAATT
1 TATATATATATAATT
* *
35644 TA-A-AT-TAAAATA
1 TATATATATATAATT
35656 TATATATA-AT-ATT
1 TATATATATATAATT
35669 TATATAT-T-TAATT
1 TATATATATATAATT
*
35682 TAAATATATATA
1 TATATATATATA
35694 TCCGGCTCGA
Statistics
Matches: 48, Mismatches: 9, Indels: 15
0.67 0.12 0.21
Matches are distributed among these distances:
12 7 0.15
13 20 0.42
14 8 0.17
15 11 0.23
16 2 0.04
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
TATATATATATAATT
Found at i:35851 original size:25 final size:25
Alignment explanation
Indices: 35811--35862 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
35801 AAATTCCTGC
** *
35811 GGTTTTTTAAGTGGGGACGGGTACG
1 GGTTTTTTAAACGGGGACGGGGACG
*
35836 GGTTTTTTAAACGGGGATGGGGACG
1 GGTTTTTTAAACGGGGACGGGGACG
35861 GG
1 GG
35863 GGACCAATAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.17, C:0.08, G:0.46, T:0.29
Consensus pattern (25 bp):
GGTTTTTTAAACGGGGACGGGGACG
Found at i:36161 original size:16 final size:15
Alignment explanation
Indices: 36135--36168 Score: 59
Period size: 16 Copynumber: 2.2 Consensus size: 15
36125 GCTACAATCT
36135 AACAAACTATTCTAG
1 AACAAACTATTCTAG
36150 AACAACACTATTCTAG
1 AACAA-ACTATTCTAG
36166 AAC
1 AAC
36169 TCACAACATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.47, C:0.24, G:0.06, T:0.24
Consensus pattern (15 bp):
AACAAACTATTCTAG
Found at i:38873 original size:30 final size:30
Alignment explanation
Indices: 38839--38906 Score: 118
Period size: 30 Copynumber: 2.3 Consensus size: 30
38829 TGGCAGATGT
*
38839 GTTGATGGAGCAGGTACTGGTGGAACACAC
1 GTTGATGGAGCAGGCACTGGTGGAACACAC
*
38869 GTTGATGGAGCAGGCACTGGTGGAACGCAC
1 GTTGATGGAGCAGGCACTGGTGGAACACAC
38899 GTTGATGG
1 GTTGATGG
38907 GACTTGCAGT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.24, C:0.16, G:0.40, T:0.21
Consensus pattern (30 bp):
GTTGATGGAGCAGGCACTGGTGGAACACAC
Found at i:41793 original size:16 final size:15
Alignment explanation
Indices: 41767--41800 Score: 59
Period size: 16 Copynumber: 2.2 Consensus size: 15
41757 GCTACAATCT
41767 AACAAACTATTCTAG
1 AACAAACTATTCTAG
41782 AACAACACTATTCTAG
1 AACAA-ACTATTCTAG
41798 AAC
1 AAC
41801 TCACAACATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.47, C:0.24, G:0.06, T:0.24
Consensus pattern (15 bp):
AACAAACTATTCTAG
Found at i:47002 original size:89 final size:89
Alignment explanation
Indices: 46888--47088 Score: 348
Period size: 89 Copynumber: 2.2 Consensus size: 89
46878 ACTTTTGAAT
* *
46888 ATTCTAGTTTCATCCTCAAACTATACTTTCATTTTAAATTAGTACCCAAACTTTTGAACATATCA
1 ATTCTA-TATCATCCTCAAACTATACTTTCATTTTAAATTAGTACCCAAACTTTTAAACATATCA
46953 TATTCATCCCCAAACTATAACCCTC
65 TATTCATCCCCAAACTATAACCCTC
46978 ATTCTATATCATCCTCAAACTATACTTTCATTTTAAATTAGTACCCAAACTTTTAAACATATCAT
1 ATTCTATATCATCCTCAAACTATACTTTCATTTTAAATTAGTACCCAAACTTTTAAACATATCAT
*
47043 ATTCATCCCCAAACTATAACTCTC
66 ATTCATCCCCAAACTATAACCCTC
*
47067 ATTCTATATTGATCCTCAAACT
1 ATTCTATA-TCATCCTCAAACT
47089 TTTAAATATT
Statistics
Matches: 106, Mismatches: 4, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
89 88 0.83
90 18 0.17
ACGTcount: A:0.34, C:0.26, G:0.02, T:0.37
Consensus pattern (89 bp):
ATTCTATATCATCCTCAAACTATACTTTCATTTTAAATTAGTACCCAAACTTTTAAACATATCAT
ATTCATCCCCAAACTATAACCCTC
Found at i:47304 original size:60 final size:59
Alignment explanation
Indices: 47146--47310 Score: 154
Period size: 60 Copynumber: 2.8 Consensus size: 59
47136 ATATTACTGG
* * * * * **
47146 AATGATCAAATGTTTGGGGACCAATTTAAAATAAGGGT-ACTAGTTTGAGGCTGAATTTGG
1 AATGTTCAAATGTTTGAGGACCAATTTAAAATAAGAGTCA-TAG-TTGAGGATGAAATTAA
* * * ***
47206 AATGTTCAGAA-GTTTGTGGATCAATTTAGAACGGGAGTCATAGTTGAAGGATGAAATTAA
1 AATGTTCA-AATGTTTGAGGACCAATTTAAAATAAGAGTCATAGTTG-AGGATGAAATTAA
*
47266 AATGTTCAAATGTTTAAGGACCAATTTAAAATAAGAGTCATAGTT
1 AATGTTCAAATGTTTGAGGACCAATTTAAAATAAGAGTCATAGTT
47311 TGGAAATGTA
Statistics
Matches: 82, Mismatches: 19, Indels: 8
0.75 0.17 0.07
Matches are distributed among these distances:
59 5 0.06
60 74 0.90
61 3 0.04
ACGTcount: A:0.37, C:0.08, G:0.24, T:0.32
Consensus pattern (59 bp):
AATGTTCAAATGTTTGAGGACCAATTTAAAATAAGAGTCATAGTTGAGGATGAAATTAA
Found at i:48999 original size:2 final size:2
Alignment explanation
Indices: 48992--49017 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
48982 TTATTTATGC
48992 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
49018 GAGCATGATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:49396 original size:2 final size:2
Alignment explanation
Indices: 49389--49417 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
49379 GTTTTACGTT
49389 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
49418 TATTTACCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:56300 original size:36 final size:36
Alignment explanation
Indices: 56185--56300 Score: 173
Period size: 35 Copynumber: 3.2 Consensus size: 36
56175 CCATTACAAT
* * *
56185 TTTTC-AACAAACATCTACCAAACTTTGAAAAATCA
1 TTTTCAAAGAAACATTTACCAAACTTTGAAAAACCA
*
56220 TTTTTCAAATAAACATTTACCAAACTTTG-AAAACCA
1 -TTTTCAAAGAAACATTTACCAAACTTTGAAAAACCA
56256 TTTTCAAAGAAACATTTACCAAACTTTGAAAAACCA
1 TTTTCAAAGAAACATTTACCAAACTTTGAAAAACCA
56292 TTTTCAAAG
1 TTTTCAAAG
56301 TTGGTTGCCA
Statistics
Matches: 74, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
35 27 0.36
36 27 0.36
37 20 0.27
ACGTcount: A:0.45, C:0.20, G:0.04, T:0.31
Consensus pattern (36 bp):
TTTTCAAAGAAACATTTACCAAACTTTGAAAAACCA
Found at i:57866 original size:18 final size:20
Alignment explanation
Indices: 57839--57889 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 20
57829 ATTATATATA
*
57839 TCCCGTAGGACCA-T-TACG
1 TCCCGAAGGACCACTATACG
57857 TCCCGAAGGACCACTGTATACG
1 TCCCGAAGGACCAC--TATACG
57879 TCCCGAAGGAC
1 TCCCGAAGGAC
57890 TACGTCCCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 12 0.43
21 1 0.04
22 15 0.54
ACGTcount: A:0.25, C:0.33, G:0.24, T:0.18
Consensus pattern (20 bp):
TCCCGAAGGACCACTATACG
Found at i:57895 original size:15 final size:15
Alignment explanation
Indices: 57875--57907 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
57865 GACCACTGTA
*
57875 TACGTCCCGAAGGAC
1 TACGTCCCAAAGGAC
57890 TACGTCCCAAAGGAC
1 TACGTCCCAAAGGAC
57905 TAC
1 TAC
57908 AATACCCTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.30, C:0.33, G:0.21, T:0.15
Consensus pattern (15 bp):
TACGTCCCAAAGGAC
Found at i:58439 original size:16 final size:17
Alignment explanation
Indices: 58411--58442 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
58401 TTTCATTTAG
58411 GGGGAATCGATACCCCA
1 GGGGAATCGATACCCCA
58428 GGGGAA-CGATACCCC
1 GGGGAATCGATACCCC
58443 TGGACATTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.28, C:0.31, G:0.31, T:0.09
Consensus pattern (17 bp):
GGGGAATCGATACCCCA
Done.