Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003060.1 Hibiscus syriacus cultivar Beakdansim tig00006377_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: 59567
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Found at i:17463 original size:19 final size:20
Alignment explanation
Indices: 17435--17480 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
17425 TTTAATAAGA
*
17435 AAATTGATCTAAA-AAAATT
1 AAATTTATCTAAAGAAAATT
* *
17454 AAATTTATCTAAAGTAATTT
1 AAATTTATCTAAAGAAAATT
17474 AAATTTA
1 AAATTTA
17481 AATCAAATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 12 0.52
20 11 0.48
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.39
Consensus pattern (20 bp):
AAATTTATCTAAAGAAAATT
Found at i:18351 original size:16 final size:15
Alignment explanation
Indices: 18322--18359 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
18312 AAAATATTTT
18322 TAATTATTTAAAATAA
1 TAATTATTTAAAAT-A
18338 TAATATATTT-AAATA
1 TAAT-TATTTAAAATA
18353 TAATTAT
1 TAATTAT
18360 CATAATATCT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
14 3 0.14
15 5 0.24
16 8 0.38
17 5 0.24
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TAATTATTTAAAATA
Found at i:19145 original size:21 final size:21
Alignment explanation
Indices: 19120--19162 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
19110 GAAAATATTA
* *
19120 AAAAATATTGATATTTTAAAT
1 AAAAATAATAATATTTTAAAT
19141 AAAAATAATAATATTTTAAAT
1 AAAAATAATAATATTTTAAAT
19162 A
1 A
19163 TTTTTTACTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (21 bp):
AAAAATAATAATATTTTAAAT
Found at i:25591 original size:27 final size:27
Alignment explanation
Indices: 25553--25617 Score: 103
Period size: 27 Copynumber: 2.4 Consensus size: 27
25543 AATGCTATGT
25553 TATTTGGACTCGAATGAGAATATCAGA
1 TATTTGGACTCGAATGAGAATATCAGA
* *
25580 TATTTGGACTCGAATGAGAGTATCGGA
1 TATTTGGACTCGAATGAGAATATCAGA
*
25607 TATTTGTACTC
1 TATTTGGACTC
25618 AAATTGTCGA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.31, C:0.12, G:0.23, T:0.34
Consensus pattern (27 bp):
TATTTGGACTCGAATGAGAATATCAGA
Found at i:27473 original size:26 final size:27
Alignment explanation
Indices: 27433--27491 Score: 84
Period size: 26 Copynumber: 2.2 Consensus size: 27
27423 ATATGTCCCC
*
27433 TAAAATTTTATAAGTCCGATCATTCT-
1 TAAAATTTTAAAAGTCCGATCATTCTA
* *
27459 TAAAATTTTAAAAGTCCGTTCATTGTA
1 TAAAATTTTAAAAGTCCGATCATTCTA
27486 TAAAAT
1 TAAAAT
27492 CTTACATCCG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
26 23 0.79
27 6 0.21
ACGTcount: A:0.39, C:0.12, G:0.08, T:0.41
Consensus pattern (27 bp):
TAAAATTTTAAAAGTCCGATCATTCTA
Found at i:32574 original size:10 final size:10
Alignment explanation
Indices: 32559--32590 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
32549 CAAGGATTGA
32559 AATTTTAAAT
1 AATTTTAAAT
32569 AATTTT-AA-
1 AATTTTAAAT
32577 AATTTTAAAT
1 AATTTTAAAT
32587 AATT
1 AATT
32591 ATTGAAGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
8 6 0.30
9 4 0.20
10 10 0.50
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (10 bp):
AATTTTAAAT
Found at i:34360 original size:13 final size:13
Alignment explanation
Indices: 34324--34368 Score: 54
Period size: 13 Copynumber: 3.2 Consensus size: 13
34314 ATAAATTAAA
34324 TGATATTGAAGTATG
1 TGATA-TGAA-TATG
34339 TGAATATGAATATG
1 TG-ATATGAATATG
*
34353 TGATATGAATGTG
1 TGATATGAATATG
34366 TGA
1 TGA
34369 AGCATATGAG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
13 13 0.46
14 6 0.21
15 6 0.21
16 3 0.11
ACGTcount: A:0.36, C:0.00, G:0.27, T:0.38
Consensus pattern (13 bp):
TGATATGAATATG
Found at i:36584 original size:64 final size:64
Alignment explanation
Indices: 36515--36670 Score: 176
Period size: 64 Copynumber: 2.4 Consensus size: 64
36505 TTGAAGGTGT
** *
36515 ATCGATGCACAGGTAGTGCATCGATGCA-CTCTTTTAA-AATAAAAAGATCGAATGCA-ATTAGT
1 ATCGATGCACAGGTAGTGCATCGATGCATC-CCATTAATAAT-AAAACATCGAATGCATATTA-T
36577 GC
63 GC
* * *
36579 ATCGATGCATAAGGCA-TGCATCGATGCATCCCATTAATAATAAAACATCGAATGCATTTTATGC
1 ATCGATGCA-CAGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCATATTATGC
* *
36643 ACCGATGCACAAGTAGTGCATCGATGCA
1 ATCGATGCACAGGTAGTGCATCGATGCA
36671 AACCTTTATT
Statistics
Matches: 77, Mismatches: 10, Indels: 10
0.79 0.10 0.10
Matches are distributed among these distances:
63 3 0.04
64 63 0.82
65 11 0.14
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.26
Consensus pattern (64 bp):
ATCGATGCACAGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCATATTATGC
Found at i:37068 original size:29 final size:29
Alignment explanation
Indices: 37035--37165 Score: 237
Period size: 29 Copynumber: 4.6 Consensus size: 29
37025 ACATGTGATA
37035 GACATGAGCTACATGATCACAAGAGAAAT
1 GACATGAGCTACATGATCACAAGAGAAAT
37064 GACATGAGCTACATGATCACAAGAGAAAT
1 GACATGAGCTACATGATCACAAGAGAAAT
37093 GACATGAGCTACATGATCACAAGAGAAAT
1 GACATGAGCTACATGATCACAAGAGAAAT
* *
37122 GACATGAACAACATGATCACAAGAGAAAT
1 GACATGAGCTACATGATCACAAGAGAAAT
37151 GACATGAG-TACATGA
1 GACATGAGCTACATGA
37166 ACATATAAAA
Statistics
Matches: 98, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
28 6 0.06
29 92 0.94
ACGTcount: A:0.46, C:0.17, G:0.21, T:0.17
Consensus pattern (29 bp):
GACATGAGCTACATGATCACAAGAGAAAT
Found at i:37268 original size:15 final size:15
Alignment explanation
Indices: 37250--37283 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
37240 GAGGGTATAA
37250 TAGTCCTTCGGGACG
1 TAGTCCTTCGGGACG
*
37265 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGACG
37280 TAGT
1 TAGT
37284 GATCCTACGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.15, C:0.21, G:0.32, T:0.32
Consensus pattern (15 bp):
TAGTCCTTCGGGACG
Found at i:42796 original size:14 final size:14
Alignment explanation
Indices: 42777--42807 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
42767 TTATTCTATC
42777 ATTAAATAATAAAA
1 ATTAAATAATAAAA
42791 ATTAAATAATAAAA
1 ATTAAATAATAAAA
42805 ATT
1 ATT
42808 TTACGAATGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (14 bp):
ATTAAATAATAAAA
Found at i:43188 original size:20 final size:20
Alignment explanation
Indices: 43163--43234 Score: 117
Period size: 20 Copynumber: 3.6 Consensus size: 20
43153 TATTCTCTGA
*
43163 TAATCTTACATTCCCGCTGG
1 TAATCTTACATTCCCGTTGG
*
43183 TAATCTTATATTCCCGTTGG
1 TAATCTTACATTCCCGTTGG
*
43203 TAATCTTACATTCTCGTTGG
1 TAATCTTACATTCCCGTTGG
43223 TAATCTTACATT
1 TAATCTTACATT
43235 TCGTGAAACA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.22, C:0.22, G:0.12, T:0.43
Consensus pattern (20 bp):
TAATCTTACATTCCCGTTGG
Found at i:54276 original size:20 final size:20
Alignment explanation
Indices: 54251--54403 Score: 95
Period size: 20 Copynumber: 7.5 Consensus size: 20
54241 AAATAACCAA
54251 TAAATTCGCAACACAGAAGT
1 TAAATTCGCAACACAGAAGT
*
54271 TAAATTCGCAACGC-GATAGT
1 TAAATTCGCAACACAGA-AGT
* * *
54291 CAAATTCGCAACGC-GAATCT
1 TAAATTCGCAACACAGAA-GT
* *
54311 GTAAA-TCGCAACGC-GAATTT
1 -TAAATTCGCAACACAGAA-GT
54331 GTAAA-TCGCAACACAGAAGT
1 -TAAATTCGCAACACAGAAGT
*
54351 CAAATTCGCAACACTA-AA-T
1 TAAATTCGCAACAC-AGAAGT
*
54370 TCCAAATTCGCAACACAAAAAGT
1 T--AAATTCGCAACAC-AGAAGT
*
54393 CAAATTCGCAA
1 TAAATTCGCAA
54404 AGCGCGTTTA
Statistics
Matches: 112, Mismatches: 11, Indels: 19
0.79 0.08 0.13
Matches are distributed among these distances:
19 7 0.06
20 71 0.63
21 31 0.28
22 2 0.02
23 1 0.01
ACGTcount: A:0.42, C:0.24, G:0.14, T:0.20
Consensus pattern (20 bp):
TAAATTCGCAACACAGAAGT
Found at i:54360 original size:40 final size:40
Alignment explanation
Indices: 54251--54403 Score: 136
Period size: 40 Copynumber: 3.8 Consensus size: 40
54241 AAATAACCAA
* *
54251 TAAATTCGCAACACAGAAGTTAAATTCGCAACGCG-ATAG
1 TAAATTCGCAACACAGAAGTCAAATTCGCAACGCGAATTG
*
54290 TCAAATTCGCAACGC-GAA-TCTGTAAA-TCGCAACGCGAATTTG
1 T-AAATTCGCAACACAGAAGTC---AAATTCGCAACGCGAA-TTG
* * *
54332 TAAA-TCGCAACACAGAAGTCAAATTCGCAACACTAAATTC
1 TAAATTCGCAACACAGAAGTCAAATTCGCAACGC-GAATTG
* *
54372 CAAATTCGCAACACAAAAAGTCAAATTCGCAA
1 TAAATTCGCAACAC-AGAAGTCAAATTCGCAA
54404 AGCGCGTTTA
Statistics
Matches: 93, Mismatches: 9, Indels: 21
0.76 0.07 0.17
Matches are distributed among these distances:
38 1 0.01
39 7 0.08
40 43 0.46
41 21 0.23
42 21 0.23
ACGTcount: A:0.42, C:0.24, G:0.14, T:0.20
Consensus pattern (40 bp):
TAAATTCGCAACACAGAAGTCAAATTCGCAACGCGAATTG
Found at i:54377 original size:21 final size:21
Alignment explanation
Indices: 54336--54403 Score: 86
Period size: 21 Copynumber: 3.3 Consensus size: 21
54326 AATTTGTAAA
*
54336 TCGCAACAC-AGAAGTCAAAT
1 TCGCAACACAAAAAGTCAAAT
* *
54356 TCGCAACAC-TAAATTCCAAAT
1 TCGCAACACAAAAAGT-CAAAT
54377 TCGCAACACAAAAAGTCAAAT
1 TCGCAACACAAAAAGTCAAAT
54398 TCGCAA
1 TCGCAA
54404 AGCGCGTTTA
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
20 12 0.29
21 25 0.61
22 4 0.10
ACGTcount: A:0.46, C:0.26, G:0.10, T:0.18
Consensus pattern (21 bp):
TCGCAACACAAAAAGTCAAAT
Found at i:54602 original size:22 final size:22
Alignment explanation
Indices: 54554--54608 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
54544 CTCTTTACGG
* *
54554 CGAAATCCGTCCCCATCTGCGA
1 CGAAATCTGTCCCCATCTCCGA
*
54576 CGAAATCTGTCCCCATCTCCGG
1 CGAAATCTGTCCCCATCTCCGA
*
54598 TGAAATCTGTC
1 CGAAATCTGTC
54609 TATCTCAATC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.22, C:0.36, G:0.18, T:0.24
Consensus pattern (22 bp):
CGAAATCTGTCCCCATCTCCGA
Found at i:55000 original size:20 final size:20
Alignment explanation
Indices: 54953--55002 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
54943 AAACTTAAAT
*
54953 TCGCAACACGAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
54973 TCGCAACGCGAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
54993 TCGCAACGCG
1 TCGCAACGCG
55003 GTTTTAGTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.46, C:0.24, G:0.20, T:0.10
Consensus pattern (20 bp):
TCGCAACGCGAAAATGAAAA
Found at i:57212 original size:18 final size:19
Alignment explanation
Indices: 57168--57221 Score: 67
Period size: 21 Copynumber: 2.8 Consensus size: 19
57158 GATTCACCTG
*
57168 TCATCGTTTAAGAGGCGTC
1 TCATCGTTCAAGAGGCGTC
57187 TCTTATCGTTCAAGAGGC-TC
1 TC--ATCGTTCAAGAGGCGTC
57207 TCATCGTTC-AGAGGC
1 TCATCGTTCAAGAGGC
57222 CCCTCCCACC
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
17 6 0.19
18 7 0.22
19 2 0.06
20 4 0.12
21 13 0.41
ACGTcount: A:0.20, C:0.24, G:0.24, T:0.31
Consensus pattern (19 bp):
TCATCGTTCAAGAGGCGTC
Found at i:57242 original size:21 final size:21
Alignment explanation
Indices: 57211--57281 Score: 67
Period size: 21 Copynumber: 3.5 Consensus size: 21
57201 AGGCTCTCAT
57211 CGTTC-AGAGGCCCCTCCCAC
1 CGTTCAAGAGGCCCCTCCCAC
** *
57231 CGTTCAAGAGGCCCCTGTCAT
1 CGTTCAAGAGGCCCCTCCCAC
* *
57252 CGTTCAATG-GG-TCTTCCCAC
1 CGTTCAA-GAGGCCCCTCCCAC
57272 CGTTCAAGAG
1 CGTTCAAGAG
57282 CCCGATTCAA
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
19 1 0.03
20 17 0.43
21 21 0.52
22 1 0.03
ACGTcount: A:0.18, C:0.37, G:0.23, T:0.23
Consensus pattern (21 bp):
CGTTCAAGAGGCCCCTCCCAC
Found at i:58708 original size:65 final size:64
Alignment explanation
Indices: 58579--58738 Score: 207
Period size: 65 Copynumber: 2.4 Consensus size: 64
58569 GTGGTACACT
* *
58579 TTTTTTGCTTGTTTAACTGAATTT-TACATTGAAGTTGATTTGTTAATTGATGAGGAAATAAGAA
1 TTTTTTGCTTGTTTAATTG-ATTTGTA-A--AAAGTTGATTTGTTAATTGATGAGGAAATAAGAA
58643 TTA
62 TTA
* * *
58646 TTTTTTGCTTGTTTAATTGA-TTGTAAAAAGTTGATTTATTTAATTTGATGTGTAAATAAGAATT
1 TTTTTTGCTTGTTTAATTGATTTGTAAAAAGTTGATTT-GTTAA-TTGATGAGGAAATAAGAATT
58710 A
64 A
58711 TTTTTTGCTTGTTTAATTGATTTGTAAA
1 TTTTTTGCTTGTTTAATTGATTTGTAAA
58739 GTGATTTGTG
Statistics
Matches: 84, Mismatches: 5, Indels: 9
0.86 0.05 0.09
Matches are distributed among these distances:
63 10 0.12
64 4 0.05
65 42 0.50
66 10 0.12
67 18 0.21
ACGTcount: A:0.30, C:0.03, G:0.16, T:0.51
Consensus pattern (64 bp):
TTTTTTGCTTGTTTAATTGATTTGTAAAAAGTTGATTTGTTAATTGATGAGGAAATAAGAATTA
Found at i:58833 original size:20 final size:20
Alignment explanation
Indices: 58810--58873 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 20
58800 AAATTCGTAA
58810 TGCGAAAGTCAAATTCGCGT
1 TGCGAAAGTCAAATTCGCGT
* * **
58830 TGCGATAGTCAAA-TCACAA
1 TGCGAAAGTCAAATTCGCGT
* *
58849 CGCAAAAGTCAAATTCGCGT
1 TGCGAAAGTCAAATTCGCGT
58869 TGCGA
1 TGCGA
58874 TTTTCGATTT
Statistics
Matches: 31, Mismatches: 12, Indels: 2
0.69 0.27 0.04
Matches are distributed among these distances:
19 13 0.42
20 18 0.58
ACGTcount: A:0.34, C:0.22, G:0.22, T:0.22
Consensus pattern (20 bp):
TGCGAAAGTCAAATTCGCGT
Done.