Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006389.1 Hibiscus syriacus cultivar Beakdansim tig00015390_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: 56468
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:412 original size:26 final size:25
Alignment explanation
Indices: 361--413 Score: 61
Period size: 26 Copynumber: 2.1 Consensus size: 25
351 AAAATATATT
* * *
361 TTAAAAATAAATTATAATTATTTTA
1 TTAAAAATAAATTAGAATGATCTTA
*
386 TTAAAAATAATATTAGAGTGATCTTA
1 TTAAAAATAA-ATTAGAATGATCTTA
412 TT
1 TT
414 CAAGCAATAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
25 10 0.43
26 13 0.57
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (25 bp):
TTAAAAATAAATTAGAATGATCTTA
Found at i:14105 original size:20 final size:20
Alignment explanation
Indices: 14076--14115 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
14066 AATAATCACG
*
14076 TAAAACCATAATGTAATATT
1 TAAAAACATAATGTAATATT
*
14096 TAAAAACATAATTTAATATT
1 TAAAAACATAATGTAATATT
14116 ATGGTATCCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.53, C:0.07, G:0.03, T:0.38
Consensus pattern (20 bp):
TAAAAACATAATGTAATATT
Found at i:15697 original size:13 final size:14
Alignment explanation
Indices: 15668--15698 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
15658 AACTATGCAA
15668 GTGATATGAACTAT
1 GTGATATGAACTAT
15682 GTGATATGAA-TAT
1 GTGATATGAACTAT
15695 GTGA
1 GTGA
15699 AATATGATAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.41
14 10 0.59
ACGTcount: A:0.35, C:0.03, G:0.26, T:0.35
Consensus pattern (14 bp):
GTGATATGAACTAT
Found at i:17355 original size:18 final size:19
Alignment explanation
Indices: 17332--17377 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
17322 CGATTTCCCG
17332 ATATATATAAT-TTCAAAC
1 ATATATATAATATTCAAAC
*
17350 ATATAT-TAATATTCATAC
1 ATATATATAATATTCAAAC
17368 -TA-ATATAATA
1 ATATATATAATA
17378 AATTCTAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 2 0.08
17 11 0.44
18 12 0.48
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (19 bp):
ATATATATAATATTCAAAC
Found at i:19151 original size:377 final size:377
Alignment explanation
Indices: 18408--19409 Score: 1844
Period size: 377 Copynumber: 2.7 Consensus size: 377
18398 TACTTCCATG
*
18408 ACACTCCTAAAATCGAAATATTATCTTATTTCAGCTAAATATAACTTTATATTCAACCACCATAA
1 ACACTCCTAAAATCGAAATATTATCTTATTTCAACTAAATATAACTTTATATTCAACCACCATAA
*
18473 ATACCCATTTCACCATTTAAGCACGAAACAATTAAATACCTATATAAATTTGTAGAGAATTAAGT
66 ATACCCATTTCACCATTTAAGCAAGAAACAATTAAATACCTATATAAATTTGTAGAGAATTAAGT
* *
18538 GTAGATCATTTTATTATTTCATACTTTAGTCCAAATTCTCATTAAAATGTACC-AAAAATAAAAA
131 GTAGATCGTTTTATTATTTCATACTTTAGTCCAAATTCTCACTAAAATGTACCAAAAAATAAAAA
*
18602 ATAAAACCTTGCTCACCTTGGCTATGGAGTCACGACAGGTTGTTGGAGAAGAGAAGAGTTCTCTT
196 AGAAAACCTTGCTCACCTTGGCTATGGAGTCACGACAGGTTGTTGGAGAAGAGAAGAGTTCTCTT
* *
18667 GAAATTTCTTACAAAATATCTCCTTAAAAGTCCAATTTAAAATGAATTAAAATTTATTTTAGCCC
261 GAAATGTCTTACAAAATATCTCCTTAAAAGTCCAATTTAAAATGAATTAAAATTCATTTTAGCCC
*
18732 AAAAGTCAAAATTACCCTTAATGGATCCTAATTTTTACCAATATGCCATCCT
326 AAAAGTCAAAATTACCCTTAATGAATCCTAATTTTTACCAATATGCCATCCT
18784 ACACTCCTAAAATCGAAATATTATCTTATTTCAACTAAATATAACTTTATATTCAACCACCATAA
1 ACACTCCTAAAATCGAAATATTATCTTATTTCAACTAAATATAACTTTATATTCAACCACCATAA
*
18849 ATACCCATTTCACCATTTAAGCATGAAACAATTAAATACCTATATAAATTTGTAGAGAATTAAGT
66 ATACCCATTTCACCATTTAAGCAAGAAACAATTAAATACCTATATAAATTTGTAGAGAATTAAGT
* *
18914 GTAGAACGTTTTATTATTTCATACTTTAGTCCAAATTTTCACTAAAATGTACCAAAAAATAAAAA
131 GTAGATCGTTTTATTATTTCATACTTTAGTCCAAATTCTCACTAAAATGTACCAAAAAATAAAAA
* *
18979 AGAAAACCTTGCTCACCTTGGCTATGGAATCACGACAGGTTGTTGGAGAAGATAAGAGTTCTCTT
196 AGAAAACCTTGCTCACCTTGGCTATGGAGTCACGACAGGTTGTTGGAGAAGAGAAGAGTTCTCTT
19044 GAAATGTCTTACAAAATATCTCCTTAAAAGTCCAATTTAAAATGAATTAAAATTCATTTTAGCCC
261 GAAATGTCTTACAAAATATCTCCTTAAAAGTCCAATTTAAAATGAATTAAAATTCATTTTAGCCC
19109 AAAAGTCAAAATTACCCTTAATGAATCCTAATTTTTACCAATATGCCATCCT
326 AAAAGTCAAAATTACCCTTAATGAATCCTAATTTTTACCAATATGCCATCCT
*
19161 ACACTCCTAAAATCGAAATATTATCTTAGTTCAACTAAATATAACTTTATATTCAACCACCATAA
1 ACACTCCTAAAATCGAAATATTATCTTATTTCAACTAAATATAACTTTATATTCAACCACCATAA
*
19226 ATACCAATTTCACCATTTAAGCAAGAAACAATTAAATACCTATATAAATTTGTAGAGAATTAAGT
66 ATACCCATTTCACCATTTAAGCAAGAAACAATTAAATACCTATATAAATTTGTAGAGAATTAAGT
*
19291 GTAGATTGTTTTATTATTTCATACTTTAGTCCAAATTCTCACTAAAATGTACCAAAAAATAAAAA
131 GTAGATCGTTTTATTATTTCATACTTTAGTCCAAATTCTCACTAAAATGTACCAAAAAATAAAAA
*
19356 AGAAAACCTTGCTCACCTTGGCTATGGAGTCACGACATGTTGTTGGAGAAGAGA
196 AGAAAACCTTGCTCACCTTGGCTATGGAGTCACGACAGGTTGTTGGAGAAGAGA
19410 TGTAACACCC
Statistics
Matches: 604, Mismatches: 21, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
376 177 0.29
377 427 0.71
ACGTcount: A:0.40, C:0.18, G:0.10, T:0.33
Consensus pattern (377 bp):
ACACTCCTAAAATCGAAATATTATCTTATTTCAACTAAATATAACTTTATATTCAACCACCATAA
ATACCCATTTCACCATTTAAGCAAGAAACAATTAAATACCTATATAAATTTGTAGAGAATTAAGT
GTAGATCGTTTTATTATTTCATACTTTAGTCCAAATTCTCACTAAAATGTACCAAAAAATAAAAA
AGAAAACCTTGCTCACCTTGGCTATGGAGTCACGACAGGTTGTTGGAGAAGAGAAGAGTTCTCTT
GAAATGTCTTACAAAATATCTCCTTAAAAGTCCAATTTAAAATGAATTAAAATTCATTTTAGCCC
AAAAGTCAAAATTACCCTTAATGAATCCTAATTTTTACCAATATGCCATCCT
Found at i:20307 original size:31 final size:31
Alignment explanation
Indices: 20269--20453 Score: 318
Period size: 31 Copynumber: 6.0 Consensus size: 31
20259 CCCAAAGGAC
* * *
20269 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
20300 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
20331 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
20362 CAATCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
20393 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
20424 CAGTCCATATGTCCCGAAGAACATAGGTAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAA
20454 CCCTCGACCC
Statistics
Matches: 148, Mismatches: 5, Indels: 2
0.95 0.03 0.01
Matches are distributed among these distances:
31 147 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:21670 original size:2 final size:2
Alignment explanation
Indices: 21663--21694 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
21653 ATCCTTATCC
21663 AT AT AT 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 AT AT AT
21695 CATTTAATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:23066 original size:22 final size:22
Alignment explanation
Indices: 23034--23078 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 22
23024 GCGGGTTGGA
*
23034 ATTTTTCAAAAAATAATGTTTTT
1 ATTTTTC-AAAAATAAAGTTTTT
23057 ATTTTT-AAAAATAAAGTTTTT
1 ATTTTTCAAAAATAAAGTTTTT
23078 A
1 A
23079 AAATTACATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 15 0.71
23 6 0.29
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.51
Consensus pattern (22 bp):
ATTTTTCAAAAATAAAGTTTTT
Found at i:27363 original size:19 final size:17
Alignment explanation
Indices: 27333--27385 Score: 54
Period size: 19 Copynumber: 3.1 Consensus size: 17
27323 TAGTACTTTA
27333 ATTTTTTTTAAATTTTT
1 ATTTTTTTTAAATTTTT
*
27350 ATTTTTTTAGTAAATTTTC
1 ATTTTTTT--TAAATTTTT
* *
27369 AATTATTTT-AATTTTT
1 ATTTTTTTTAAATTTTT
27385 A
1 A
27386 AGTTATTATT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
16 7 0.23
17 9 0.30
19 14 0.47
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.68
Consensus pattern (17 bp):
ATTTTTTTTAAATTTTT
Found at i:32074 original size:25 final size:26
Alignment explanation
Indices: 32046--32095 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 26
32036 AAACACAATA
32046 ATTT-GAAAA-TTAACATTTTTTTTTT
1 ATTTCGAAAATTTAA-ATTTTTTTTTT
32071 ATTTCGAAAATTTTAAATTTTTTTT
1 ATTTCGAAAA-TTTAAATTTTTTTT
32096 GGAAAATTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 4 0.18
26 5 0.23
27 9 0.41
28 4 0.18
ACGTcount: A:0.32, C:0.04, G:0.04, T:0.60
Consensus pattern (26 bp):
ATTTCGAAAATTTAAATTTTTTTTTT
Found at i:39967 original size:16 final size:16
Alignment explanation
Indices: 39946--39977 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
39936 TAGAAAATAC
39946 ATATAAAAAAATTTAA
1 ATATAAAAAAATTTAA
*
39962 ATATAAAAGAATTTAA
1 ATATAAAAAAATTTAA
39978 TTTTAGATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (16 bp):
ATATAAAAAAATTTAA
Found at i:44544 original size:15 final size:15
Alignment explanation
Indices: 44524--44565 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
44514 TTGTAGGAGT
*
44524 TTTTGGTTTGTTTTA
1 TTTTGGCTTGTTTTA
44539 TTTTGGCTTGTTTTA
1 TTTTGGCTTGTTTTA
44554 TTTTGGCGTTGT
1 TTTTGGC-TTGT
44566 CATGTGAACT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 21 0.84
16 4 0.16
ACGTcount: A:0.05, C:0.05, G:0.24, T:0.67
Consensus pattern (15 bp):
TTTTGGCTTGTTTTA
Found at i:44687 original size:2 final size:2
Alignment explanation
Indices: 44680--44777 Score: 196
Period size: 2 Copynumber: 49.0 Consensus size: 2
44670 ATGTTTCCTT
44680 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
44722 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
44764 TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
44778 ATGTGAGTGC
Statistics
Matches: 96, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 96 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:50560 original size:11 final size:11
Alignment explanation
Indices: 50546--50570 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
50536 ATTTGAAGTA
50546 TTGTGGAAGGG
1 TTGTGGAAGGG
50557 TTGTGGAAGGG
1 TTGTGGAAGGG
50568 TTG
1 TTG
50571 ATGTCTTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.00, G:0.52, T:0.32
Consensus pattern (11 bp):
TTGTGGAAGGG
Done.