Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005822.1 Hibiscus syriacus cultivar Beakdansim tig00013642_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: 39411
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:15397 original size:7 final size:7
Alignment explanation
Indices: 15382--15470 Score: 79
Period size: 7 Copynumber: 12.7 Consensus size: 7
15372 AATAAGATTA
15382 AGGGTTT
1 AGGGTTT
*
15389 AGGGCTT
1 AGGGTTT
15396 AGGGTTT
1 AGGGTTT
15403 AGGGTTT
1 AGGGTTT
*
15410 AGGATTT
1 AGGGTTT
**
15417 AGGGCAT
1 AGGGTTT
*
15424 AAGGTTT
1 AGGGTTT
15431 AGGGTTT
1 AGGGTTT
* *
15438 AAGATTT
1 AGGGTTT
*
15445 AGAGTTT
1 AGGGTTT
*
15452 ATGGTTT
1 AGGGTTT
**
15459 ATAGTTT
1 AGGGTTT
15466 AGGGT
1 AGGGT
15471 ATATTCTAAC
Statistics
Matches: 62, Mismatches: 20, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
7 62 1.00
ACGTcount: A:0.22, C:0.02, G:0.35, T:0.40
Consensus pattern (7 bp):
AGGGTTT
Found at i:15429 original size:28 final size:28
Alignment explanation
Indices: 15386--15446 Score: 95
Period size: 28 Copynumber: 2.2 Consensus size: 28
15376 AGATTAAGGG
* * *
15386 TTTAGGGCTTAGGGTTTAGGGTTTAGGA
1 TTTAGGGCATAAGGTTTAGGGTTTAAGA
15414 TTTAGGGCATAAGGTTTAGGGTTTAAGA
1 TTTAGGGCATAAGGTTTAGGGTTTAAGA
15442 TTTAG
1 TTTAG
15447 AGTTTATGGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.23, C:0.03, G:0.34, T:0.39
Consensus pattern (28 bp):
TTTAGGGCATAAGGTTTAGGGTTTAAGA
Found at i:16458 original size:30 final size:28
Alignment explanation
Indices: 16422--16526 Score: 113
Period size: 29 Copynumber: 3.6 Consensus size: 28
16412 TTAATACATA
*
16422 AACTATCACTTTTGTTTCATTTTAGTACCT
1 AACTATCA-TTTT-TTTCGTTTTAGTACCT
*
16452 AACTATCATTTTTTCCCGTTTTAGTACCT
1 AACTATCATTTTTT-TCGTTTTAGTACCT
*
16481 AACTATCATTTTTTTTCCGTTTTAGTACTT
1 AACTATCA-TTTTTTT-CGTTTTAGTACCT
*
16511 AAGCTA-GATTTTTTTC
1 AA-CTATCATTTTTTTC
16527 AAAACTATAC
Statistics
Matches: 66, Mismatches: 5, Indels: 10
0.81 0.06 0.12
Matches are distributed among these distances:
28 3 0.05
29 31 0.47
30 29 0.44
31 3 0.05
ACGTcount: A:0.22, C:0.19, G:0.08, T:0.51
Consensus pattern (28 bp):
AACTATCATTTTTTTCGTTTTAGTACCT
Found at i:16473 original size:29 final size:30
Alignment explanation
Indices: 16441--16526 Score: 122
Period size: 30 Copynumber: 2.9 Consensus size: 30
16431 TTTTGTTTCA
16441 TTTTAGTACCTAACTATCA-TTTTTTCCCG
1 TTTTAGTACCTAACTATCATTTTTTTCCCG
*
16470 TTTTAGTACCTAACTATCATTTTTTTTCCG
1 TTTTAGTACCTAACTATCATTTTTTTCCCG
* *
16500 TTTTAGTACTTAAGCTA-GATTTTTTTC
1 TTTTAGTACCTAA-CTATCATTTTTTTC
16527 AAAACTATAC
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
29 19 0.37
30 29 0.57
31 3 0.06
ACGTcount: A:0.21, C:0.19, G:0.08, T:0.52
Consensus pattern (30 bp):
TTTTAGTACCTAACTATCATTTTTTTCCCG
Found at i:18367 original size:64 final size:64
Alignment explanation
Indices: 18299--18455 Score: 176
Period size: 64 Copynumber: 2.5 Consensus size: 64
18289 TTGAAGGTGT
** * *
18299 ATCGATGCATTGGTAATGCATCGATGCA-CTCTTTTAA-AATAGAAACATCGAATGCA-ATTAGT
1 ATCGATGCATAAGTAATGCATCGATGCATC-CCTATAATAATA-AAACATCGAATGCATATTA-T
18361 GC
63 GC
* * *
18363 ATCGATGCATAAGTCATGCATCGATGCATCCCTATAATAATACAACATCGAATGCATTTTATGC
1 ATCGATGCATAAGTAATGCATCGATGCATCCCTATAATAATAAAACATCGAATGCATATTATGC
* * *
18427 ACCGATGCATCAGTAGTGCATCGATGCAT
1 ATCGATGCATAAGTAATGCATCGATGCAT
18456 ACCTTCATTA
Statistics
Matches: 79, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
64 71 0.90
65 8 0.10
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (64 bp):
ATCGATGCATAAGTAATGCATCGATGCATCCCTATAATAATAAAACATCGAATGCATATTATGC
Found at i:18810 original size:18 final size:18
Alignment explanation
Indices: 18775--18810 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
18765 AAAATGGGTA
* *
18775 CATATGTTATATGTATTG
1 CATATGTTACATGAATTG
18793 CATATGTTACATGAATTG
1 CATATGTTACATGAATTG
18811 AATGAATATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.08, G:0.17, T:0.44
Consensus pattern (18 bp):
CATATGTTACATGAATTG
Found at i:19962 original size:22 final size:18
Alignment explanation
Indices: 19920--19989 Score: 86
Period size: 18 Copynumber: 3.7 Consensus size: 18
19910 TTAAGGAGTA
*
19920 GTCCTTCGGGACATAGTG
1 GTCCTACGGGACATAGTG
19938 GTCCTACGGGACATATACAGTG
1 GTCCTACGGGAC--AT--AGTG
*
19960 GTCCTTCGGGACATAGTG
1 GTCCTACGGGACATAGTG
19978 GTCCTACGGGAC
1 GTCCTACGGGAC
19990 GAATACTGAA
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
18 26 0.58
20 4 0.09
22 15 0.33
ACGTcount: A:0.20, C:0.24, G:0.31, T:0.24
Consensus pattern (18 bp):
GTCCTACGGGACATAGTG
Found at i:21863 original size:16 final size:16
Alignment explanation
Indices: 21842--21872 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
21832 AATATTGAAA
21842 CTTGAACTCAAAAAGG
1 CTTGAACTCAAAAAGG
21858 CTTGAACTCAAAAAG
1 CTTGAACTCAAAAAG
21873 AAATTAGAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.45, C:0.19, G:0.16, T:0.19
Consensus pattern (16 bp):
CTTGAACTCAAAAAGG
Found at i:24947 original size:29 final size:29
Alignment explanation
Indices: 24880--24996 Score: 135
Period size: 29 Copynumber: 4.0 Consensus size: 29
24870 CACATTCAAA
* *
24880 AATTACAAAAATATCACCTTTATTAAAAAT
1 AATTACCAAAATATCACCGTT-TTAAAAAT
*
24910 AATTACCAAAATATCACCGTTTTACAAAT
1 AATTACCAAAATATCACCGTTTTAAAAAT
* * *
24939 AATTCCCAAAATATCATCGTTTTAAAAAC
1 AATTACCAAAATATCACCGTTTTAAAAAT
* * *
24968 AATTACCAGAATGTCACTGTTTGTAAAAA
1 AATTACCAAAATATCACCGTTT-TAAAAA
24997 ATCCAAAAAT
Statistics
Matches: 74, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
29 49 0.66
30 25 0.34
ACGTcount: A:0.46, C:0.17, G:0.05, T:0.32
Consensus pattern (29 bp):
AATTACCAAAATATCACCGTTTTAAAAAT
Found at i:32432 original size:30 final size:29
Alignment explanation
Indices: 32398--32588 Score: 140
Period size: 29 Copynumber: 6.6 Consensus size: 29
32388 CACATTCGAA
* *
32398 AATTACAAAAATATCACTTTTATTAAAAAT
1 AATTACCAAAATATCACTGTT-TTAAAAAT
* *
32428 AATTACCAAAATATCACCGTTTTATAAAT
1 AATTACCAAAATATCACTGTTTTAAAAAT
* *
32457 AATTCCCAAAATGTCA-TCGTTTTAAAAAT
1 AATTACCAAAATATCACT-GTTTTAAAAAT
* ** *
32486 AATTACCAGAATGCCACTGTTTTTAAAA-
1 AATTACCAAAATATCACTGTTTTAAAAAT
* * ** *
32514 AATT-CCCAAATGTCACAATTTTCAAAAT
1 AATTACCAAAATATCACTGTTTTAAAAAT
* * *
32542 AATTCCCAAAATAACACCT-TTTTCAAAAT
1 AATTACCAAAATATCA-CTGTTTTAAAAAT
*
32571 AATT-CTCAAAATGTCACT
1 AATTAC-CAAAATATCACT
32589 TGGTCGGGTC
Statistics
Matches: 131, Mismatches: 24, Indels: 14
0.78 0.14 0.08
Matches are distributed among these distances:
27 17 0.13
28 11 0.08
29 83 0.63
30 20 0.15
ACGTcount: A:0.44, C:0.18, G:0.04, T:0.34
Consensus pattern (29 bp):
AATTACCAAAATATCACTGTTTTAAAAAT
Found at i:32465 original size:29 final size:28
Alignment explanation
Indices: 32423--32587 Score: 154
Period size: 29 Copynumber: 5.8 Consensus size: 28
32413 ACTTTTATTA
* *
32423 AAAATAATTACCAAAATATCACCGTTTT
1 AAAATAATTCCCAAAATGTCACCGTTTT
*
32451 ATAAATAATTCCCAAAATGTCATCGTTTT
1 A-AAATAATTCCCAAAATGTCACCGTTTT
* * * *
32480 AAAAATAATTACCAGAATGCCACTGTTTTT
1 -AAAATAATTCCCAAAATGTCACCG-TTTT
**
32510 AAAA-AATTCCC-AAATGTCACAATTTT
1 AAAATAATTCCCAAAATGTCACCGTTTT
** *
32536 CAAAATAATTCCCAAAATAACACCTTTTT
1 -AAAATAATTCCCAAAATGTCACCGTTTT
*
32565 CAAAATAATTCTCAAAATGTCAC
1 -AAAATAATTCCCAAAATGTCAC
32588 TTGGTCGGGT
Statistics
Matches: 111, Mismatches: 20, Indels: 11
0.78 0.14 0.08
Matches are distributed among these distances:
26 4 0.04
27 11 0.10
28 14 0.13
29 77 0.69
30 5 0.05
ACGTcount: A:0.44, C:0.19, G:0.05, T:0.32
Consensus pattern (28 bp):
AAAATAATTCCCAAAATGTCACCGTTTT
Found at i:33916 original size:26 final size:26
Alignment explanation
Indices: 33887--33938 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
33877 CGTAATAAAG
33887 AAAACAATTTACAAGTAATATTTTTT
1 AAAACAATTTACAAGTAATATTTTTT
*
33913 AAAACAATTTACAAGTAGTATTTTTT
1 AAAACAATTTACAAGTAATATTTTTT
33939 CTTTTCACTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.44, C:0.08, G:0.06, T:0.42
Consensus pattern (26 bp):
AAAACAATTTACAAGTAATATTTTTT
Found at i:37332 original size:12 final size:12
Alignment explanation
Indices: 37294--37349 Score: 78
Period size: 12 Copynumber: 4.7 Consensus size: 12
37284 ATATACAAAT
37294 ACCTAACTC-TC
1 ACCTAACTCTTC
37305 ACCTAACTCTTTC
1 ACCTAACTC-TTC
*
37318 ACCTAATTCTTC
1 ACCTAACTCTTC
*
37330 ACCTAACTCTTT
1 ACCTAACTCTTC
37342 ACCTAACT
1 ACCTAACT
37350 AAATTGATGT
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
11 9 0.22
12 21 0.52
13 10 0.25
ACGTcount: A:0.27, C:0.38, G:0.00, T:0.36
Consensus pattern (12 bp):
ACCTAACTCTTC
Found at i:37345 original size:24 final size:23
Alignment explanation
Indices: 37293--37349 Score: 87
Period size: 24 Copynumber: 2.4 Consensus size: 23
37283 AATATACAAA
37293 TACCTAACTCTCACCTAACTCTT
1 TACCTAACTCTCACCTAACTCTT
*
37316 TCACCTAATTCTTCACCTAACTCTT
1 T-ACCTAACTC-TCACCTAACTCTT
37341 TACCTAACT
1 TACCTAACT
37350 AAATTGATGT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
23 1 0.03
24 15 0.50
25 14 0.47
ACGTcount: A:0.26, C:0.37, G:0.00, T:0.37
Consensus pattern (23 bp):
TACCTAACTCTCACCTAACTCTT
Done.