Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005709.1 Hibiscus syriacus cultivar Beakdansim tig00013350_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: 65936
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:1758 original size:2 final size:2
Alignment explanation
Indices: 1751--1791 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1741 CAAAATTCAA
1751 AT AT AT AT 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 AT AT AT AT A
1792 AATTATACAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:11861 original size:2 final size:2
Alignment explanation
Indices: 11856--11882 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
11846 TACGCAGTGT
11856 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 T
11883 TTGAATGAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:21160 original size:125 final size:124
Alignment explanation
Indices: 21028--21268 Score: 315
Period size: 125 Copynumber: 1.9 Consensus size: 124
21018 TAATAAATTA
* * ** *
21028 TTATCTTATAATCCGAGAACTAATTGTATA-TTTTACCTTATAATTTTTTTAAAAAT-AAATTAA
1 TTATCTTATAATCCAAGAACTAATTATATATTTTTACCTTATAA-AATTTTAAAAATAAAATAAA
* * * *
21091 ATTATAAATAAAAAATATAAAAAAATCTTAAAATATATGATTATTTAAAATTTATGAAAATG
65 ATAATAAAT-AAAAATATAAAAAAAT-TTAAAATAAACGATAATTTAAAATTTATGAAAATG
* * * *
21153 TTATCTTATAATCTAATAACTATTTATATATTTTTACCTTTTAAAATTTTAAAAATAAAATAAAA
1 TTATCTTATAATCCAAGAACTAATTATATATTTTTACCTTATAAAATTTTAAAAATAAAATAAAA
*
21218 TAATAAATAAAAATTTAAAAAAATTTAAAATAAACGATAATTTAAAATTTA
66 TAATAAATAAAAATATAAAAAAATTTAAAATAAACGATAATTTAAAATTTA
21269 CAAGATTAAT
Statistics
Matches: 100, Mismatches: 14, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
124 24 0.24
125 50 0.50
126 26 0.26
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (124 bp):
TTATCTTATAATCCAAGAACTAATTATATATTTTTACCTTATAAAATTTTAAAAATAAAATAAAA
TAATAAATAAAAATATAAAAAAATTTAAAATAAACGATAATTTAAAATTTATGAAAATG
Found at i:22942 original size:39 final size:39
Alignment explanation
Indices: 22899--22981 Score: 130
Period size: 39 Copynumber: 2.1 Consensus size: 39
22889 AAAACTAGGG
* *
22899 ATTGATTGGGGCACGTTAAAGAAGGGTTCATTTTCTAGC
1 ATTGATTGGGACACGTTAAAGAAGGGTTCATTTTATAGC
* *
22938 ATTGATTGGGACACGTTGAAGAAGGGTTCATTTTATAGG
1 ATTGATTGGGACACGTTAAAGAAGGGTTCATTTTATAGC
22977 ATTGA
1 ATTGA
22982 AAAATAAAGT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.28, C:0.10, G:0.29, T:0.34
Consensus pattern (39 bp):
ATTGATTGGGACACGTTAAAGAAGGGTTCATTTTATAGC
Found at i:25602 original size:28 final size:28
Alignment explanation
Indices: 25553--25606 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
25543 ATATTTACTT
* ** *
25553 AAAAAAACTCTAATTTCTCTTAAAATAC
1 AAAAAAACTCAAAAATCCCTTAAAATAC
25581 AAAAAAACTCAAAAATCCCTTAAAAT
1 AAAAAAACTCAAAAATCCCTTAAAAT
25607 TATTTTAGAG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.56, C:0.19, G:0.00, T:0.26
Consensus pattern (28 bp):
AAAAAAACTCAAAAATCCCTTAAAATAC
Found at i:27205 original size:40 final size:38
Alignment explanation
Indices: 27121--27206 Score: 109
Period size: 40 Copynumber: 2.2 Consensus size: 38
27111 AAAAACTAGG
* *
27121 GATTGATTGGGACACGTTAAAAAAGGGTTCATCTTCTA
1 GATTGAATGGGACACGTTAAAAAAGGGTTCATCTTATA
* *
27159 GCATTGAATGGGACACGTTGAAGAAAGGGTTCATTTTATAA
1 G-ATTGAATGGGACACGTT-AAAAAAGGGTTCATCTTAT-A
27200 GATTGAA
1 GATTGAA
27207 AAAATAGAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
38 1 0.02
39 16 0.39
40 22 0.54
41 2 0.05
ACGTcount: A:0.34, C:0.10, G:0.26, T:0.30
Consensus pattern (38 bp):
GATTGAATGGGACACGTTAAAAAAGGGTTCATCTTATA
Found at i:27593 original size:21 final size:22
Alignment explanation
Indices: 27560--27617 Score: 57
Period size: 21 Copynumber: 2.7 Consensus size: 22
27550 ATATGTACTA
* *
27560 CCACGTCATCACCGTAG-ATTG
1 CCACGTGAGCACCGTAGAATTG
* *
27581 TCACGTTAGCACCGT-GAATTG
1 CCACGTGAGCACCGTAGAATTG
*
27602 CCATGTGAGCACCGTA
1 CCACGTGAGCACCGTA
27618 TCGATCAACG
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
20 1 0.03
21 28 0.97
ACGTcount: A:0.24, C:0.29, G:0.22, T:0.24
Consensus pattern (22 bp):
CCACGTGAGCACCGTAGAATTG
Found at i:28002 original size:18 final size:19
Alignment explanation
Indices: 27981--28025 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
27971 ATTATTAATT
*
27981 TTATTTTAATTTT-ATTAA
1 TTATTTAAATTTTGATTAA
* *
27999 TTATTAAAATTTTGATTGA
1 TTATTTAAATTTTGATTAA
28018 TTATTTAA
1 TTATTTAA
28026 CAAATTAAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (19 bp):
TTATTTAAATTTTGATTAA
Found at i:29081 original size:29 final size:28
Alignment explanation
Indices: 29028--29085 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 28
29018 TTTCAACGTC
29028 AAATTGAAAGAAATTAAATTTGAATTTT
1 AAATTGAAAGAAATTAAATTTGAATTTT
*
29056 AAATTGAAATTGAAA-TGAATTTGAATTTT
1 AAATTGAAA--GAAATTAAATTTGAATTTT
29085 A
1 A
29086 GCTTTCACAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 9 0.33
29 14 0.52
30 4 0.15
ACGTcount: A:0.48, C:0.00, G:0.12, T:0.40
Consensus pattern (28 bp):
AAATTGAAAGAAATTAAATTTGAATTTT
Found at i:29579 original size:36 final size:35
Alignment explanation
Indices: 29538--29609 Score: 101
Period size: 36 Copynumber: 2.0 Consensus size: 35
29528 CCATTCCCAT
*
29538 CTTTTCTTCACTTTTTTTCTTCTTTC-TTTCTCTTCA
1 CTTTTCTTCACTTTCTTTC-TC-TTCATTTCTCTTCA
*
29574 CTTTTCTTCACTTTCTTTCTCTTCATTTTTCTTCA
1 CTTTTCTTCACTTTCTTTCTCTTCATTTCTCTTCA
29609 C
1 C
29610 GTATCTGAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
34 3 0.09
35 12 0.36
36 18 0.55
ACGTcount: A:0.07, C:0.29, G:0.00, T:0.64
Consensus pattern (35 bp):
CTTTTCTTCACTTTCTTTCTCTTCATTTCTCTTCA
Found at i:29608 original size:25 final size:25
Alignment explanation
Indices: 29537--29609 Score: 96
Period size: 25 Copynumber: 2.9 Consensus size: 25
29527 CCCATTCCCA
*
29537 TCTTT-TCTTCACTTTTT-TTCTTCTT
1 TCTTTCTCTTCA-TTTTTCTTC-ACTT
*
29562 TCTTTCTCTTCACTTTTCTTCACTT
1 TCTTTCTCTTCATTTTTCTTCACTT
29587 TCTTTCTCTTCATTTTTCTTCAC
1 TCTTTCTCTTCATTTTTCTTCAC
29610 GTATCTGAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
25 34 0.79
26 9 0.21
ACGTcount: A:0.07, C:0.29, G:0.00, T:0.64
Consensus pattern (25 bp):
TCTTTCTCTTCATTTTTCTTCACTT
Found at i:32716 original size:20 final size:22
Alignment explanation
Indices: 32691--32748 Score: 84
Period size: 20 Copynumber: 2.6 Consensus size: 22
32681 TTCCCCTTGA
32691 AGTGCATCGATGCATTC-T-AC
1 AGTGCATCGATGCATTCTTAAC
32711 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC-TTAAC
32734 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
32749 CTACCCATGT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 17 0.50
22 1 0.03
23 3 0.09
24 13 0.38
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (22 bp):
AGTGCATCGATGCATTCTTAAC
Found at i:32845 original size:64 final size:63
Alignment explanation
Indices: 32736--32876 Score: 151
Period size: 64 Copynumber: 2.2 Consensus size: 63
32726 TCTTTAACAT
* * * *
32736 GTGCATCGATGCACTACCCATGTATCGATACACAAATTACCTTCGACGTTTTCAT-TTTAAGGG
1 GTGCATCGATGCACTACCCATGCATCGATACACAAATTACATTCGACG-TTTCATCTTTAAAGA
* * * * * *
32799 GATGCATCGATGCACT-CCTTATGCATCGATGCACCAATTGCATTCGATGTTTCTTCTTTAAAGA
1 G-TGCATCGATGCACTACC-CATGCATCGATACACAAATTACATTCGACGTTTCATCTTTAAAGA
32863 GTGCATCGATGCAC
1 GTGCATCGATGCAC
32877 ATTGAATATG
Statistics
Matches: 65, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
63 21 0.32
64 44 0.68
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (63 bp):
GTGCATCGATGCACTACCCATGCATCGATACACAAATTACATTCGACGTTTCATCTTTAAAGA
Found at i:36920 original size:20 final size:22
Alignment explanation
Indices: 36895--36952 Score: 84
Period size: 20 Copynumber: 2.6 Consensus size: 22
36885 TTCCCCTTGA
36895 AGTGCATCGATGCATTC-T-AC
1 AGTGCATCGATGCATTCTTAAC
36915 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC-TTAAC
36938 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
36953 CTACCCATGC
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 17 0.50
22 1 0.03
23 3 0.09
24 13 0.38
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (22 bp):
AGTGCATCGATGCATTCTTAAC
Found at i:37030 original size:45 final size:45
Alignment explanation
Indices: 36959--37062 Score: 122
Period size: 45 Copynumber: 2.3 Consensus size: 45
36949 TGCACTACCC
* * * *
36959 ATGCATCGATACACAAATTACCTTCGATGTTTTCAT-TTTAAGGGG
1 ATGCATCGATGCACAAATTACATTCGATG-TTTCATCTTTAAAGAG
* * *
37004 ATGCATCGATGCACTAATTGCATTCGATGTTTCTTCTTTAAAGAG
1 ATGCATCGATGCACAAATTACATTCGATGTTTCATCTTTAAAGAG
37049 -TGCATCGATGCACA
1 ATGCATCGATGCACA
37063 TTGAATATGC
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
44 18 0.36
45 32 0.64
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (45 bp):
ATGCATCGATGCACAAATTACATTCGATGTTTCATCTTTAAAGAG
Found at i:39439 original size:2 final size:2
Alignment explanation
Indices: 39432--39473 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
39422 ACTAATCCAT
39432 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
39474 ATCATCATTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:41147 original size:21 final size:22
Alignment explanation
Indices: 41111--41155 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
41101 TTTTCTTTTT
*
41111 TTTTAAATATAATTTTTTTAAA
1 TTTTAAATATAATTTTTTAAAA
*
41133 TTTTATATA-AATTTTTTAAAA
1 TTTTAAATATAATTTTTTAAAA
41154 TT
1 TT
41156 ACTATATTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
TTTTAAATATAATTTTTTAAAA
Found at i:41161 original size:20 final size:20
Alignment explanation
Indices: 41117--41161 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
41107 TTTTTTTTAA
* *
41117 ATATAATTTTTTTAAATTTT
1 ATATAAATTTTTTAAATATT
41137 ATATAAATTTTTTAAA-ATT
1 ATATAAATTTTTTAAATATT
41156 ACTATA
1 A-TATA
41162 TTGTGGCTCG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 3 0.14
20 19 0.86
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (20 bp):
ATATAAATTTTTTAAATATT
Found at i:41161 original size:22 final size:20
Alignment explanation
Indices: 41117--41162 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
41107 TTTTTTTTAA
* *
41117 ATATAATTTTTTTAAATTTT
1 ATATAATTTTTTAAAATTCT
41137 ATATAAATTTTTTAAAATTACT
1 ATAT-AATTTTTTAAAATT-CT
41159 ATAT
1 ATAT
41163 TGTGGCTCGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 4 0.18
21 13 0.59
22 5 0.23
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (20 bp):
ATATAATTTTTTAAAATTCT
Found at i:41823 original size:60 final size:59
Alignment explanation
Indices: 41746--41882 Score: 157
Period size: 60 Copynumber: 2.3 Consensus size: 59
41736 TAAAGTACGC
** * *
41746 AAATAGTCTCCGACTATATGGTATTACTTTATTAAGTATATTGACTATTAAAAGTTACA
1 AAATAGTCTCCGACTATAAAGTATTACTTTATTAAGTACATCGACTATTAAAAGTTACA
* * * * *
41805 AAATAGTTCTCCGACTATAAAGTGTTGCTTTATTGAGTCCCTCGACTATTAAAAGTTACA
1 AAATAG-TCTCCGACTATAAAGTATTACTTTATTAAGTACATCGACTATTAAAAGTTACA
* *
41865 AAATGGTCACTCGACTAT
1 AAATAGTCTC-CGACTAT
41883 TCATTATGTT
Statistics
Matches: 65, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
59 9 0.14
60 56 0.86
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (59 bp):
AAATAGTCTCCGACTATAAAGTATTACTTTATTAAGTACATCGACTATTAAAAGTTACA
Found at i:43307 original size:30 final size:30
Alignment explanation
Indices: 43258--43318 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
43248 CTATTTTATT
*
43258 TAAATATTTAAAGTATATTTTT-ATCAAAA
1 TAAATATTAAAAGTATATTTTTGATCAAAA
* *
43287 TAAATACTTAAAATTATATTTTTGGTCAAAA
1 TAAATA-TTAAAAGTATATTTTTGATCAAAA
43318 T
1 T
43319 GGGTACTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 6 0.22
30 14 0.52
31 7 0.26
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (30 bp):
TAAATATTAAAAGTATATTTTTGATCAAAA
Found at i:53622 original size:41 final size:41
Alignment explanation
Indices: 53577--53657 Score: 119
Period size: 41 Copynumber: 2.0 Consensus size: 41
53567 TTTTGATATC
**
53577 ATATATTTTATTTAAAG-TGTAAGGTTTAGGATTTAAAATTT
1 ATATATTTTATTTAAAGCT-TAAAATTTAGGATTTAAAATTT
*
53618 ATATATTTTGTTTAAAGCTTAAAATTTAGGATTTAAAATT
1 ATATATTTTATTTAAAGCTTAAAATTTAGGATTTAAAATT
53658 ATTTAAATAT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
41 35 0.97
42 1 0.03
ACGTcount: A:0.38, C:0.01, G:0.12, T:0.48
Consensus pattern (41 bp):
ATATATTTTATTTAAAGCTTAAAATTTAGGATTTAAAATTT
Found at i:58033 original size:30 final size:27
Alignment explanation
Indices: 57999--58055 Score: 69
Period size: 30 Copynumber: 2.0 Consensus size: 27
57989 AAATTAAATA
57999 ATTATAAAATTATCATTAGATTTTCATAAT
1 ATTATAAAATT-T-ATTAG-TTTTCATAAT
* *
58029 ATTATTAAATTTATTAGTTTTTATAAT
1 ATTATAAAATTTATTAGTTTTCATAAT
58056 TGTCCTAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 9 0.36
28 5 0.20
29 1 0.04
30 10 0.40
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.53
Consensus pattern (27 bp):
ATTATAAAATTTATTAGTTTTCATAAT
Found at i:59273 original size:10 final size:10
Alignment explanation
Indices: 59258--59288 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
59248 TTCTGCGAGG
59258 TTACTATTCA
1 TTACTATTCA
59268 TTACTATTCA
1 TTACTATTCA
59278 TTACTATTCA
1 TTACTATTCA
59288 T
1 T
59289 GTGAATAGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.29, C:0.19, G:0.00, T:0.52
Consensus pattern (10 bp):
TTACTATTCA
Found at i:64643 original size:5 final size:5
Alignment explanation
Indices: 64633--64657 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
64623 TAATTCAATG
64633 GATTC GATTC GATTC GATTC GATTC
1 GATTC GATTC GATTC GATTC GATTC
64658 AGCAGTGTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.40
Consensus pattern (5 bp):
GATTC
Done.