Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007261.1 Hibiscus syriacus cultivar Beakdansim tig00019246_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: 50462
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.31
Found at i:3495 original size:14 final size:15
Alignment explanation
Indices: 3460--3503 Score: 72
Period size: 14 Copynumber: 2.9 Consensus size: 15
3450 TCTGGATTTT
3460 TGTAGAAAACAGACTG
1 TGTAGAAAACAGAC-G
3476 TGTAGAAAACAGAC-
1 TGTAGAAAACAGACG
3490 TGTAGAAAACAGAC
1 TGTAGAAAACAGAC
3504 AAGTCTGTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 14 0.50
16 14 0.50
ACGTcount: A:0.48, C:0.14, G:0.23, T:0.16
Consensus pattern (15 bp):
TGTAGAAAACAGACG
Found at i:4250 original size:206 final size:205
Alignment explanation
Indices: 3891--4302 Score: 657
Period size: 206 Copynumber: 2.0 Consensus size: 205
3881 TGCTGGATGA
* * *
3891 GCTTAATACAATGACTGGAAAGAAGTCGTAACCCTACCAGAGGGAAGATTGAATATAAGCAGCTG
1 GCTTAATACAAAGACTGGAAAGAAGTCGTAACCCTACCAGAGGGAAGATGGAATACAAGCAGCTG
* *
3956 ATCACACGTGCAAGCGTTAGCCGGCAAATATTTCGTTACTTTTTCCAAGGCACAAAACCAGGTAA
66 ATCACACGCGCAAGCGTTAGCCGGCAAATATTTAGTTACTTTTTCCAAGGCACAAAACCAGGTAA
* * *
4021 GATACAAAGTACAATCTTTTTCGATAAGAAATCCTAATAAACTAGGAGTACCTGATTTCTCAACT
131 GATACAAAGTACAATCCTTTTCGATAAGAAATCCTAATAAACTAAGAGAACCTGATTTCTCAACT
4086 ATTCATTTGG
196 ATTCATTTGG
*
4096 GCTTAATACAAAGACTGGAAAGAAGTCGTAACCCTACGAGAGGGAAGATGGAATACAAGCAGAC-
1 GCTTAATACAAAGACTGGAAAGAAGTCGTAACCCTACCAGAGGGAAGATGGAATACAAGCAG-CT
* * * **
4160 GATCATACGAGCGCAAG-GTTTGCTGGCAAATATTTAGTTACTTTTTCCATTGCACAAAACCAGG
65 GATCACAC--GCGCAAGCGTTAGCCGGCAAATATTTAGTTACTTTTTCCAAGGCACAAAACCAGG
4224 TAAGATACAAAGTACAATCCTTTTCGATAAGAAATCCTAATAAACTAAGAGAACCTGATTTCTCA
128 TAAGATACAAAGTACAATCCTTTTCGATAAGAAATCCTAATAAACTAAGAGAACCTGATTTCTCA
4289 ACTATTCATTTGG
193 ACTATTCATTTGG
4302 G
1 G
4303 ATTATTTCAA
Statistics
Matches: 190, Mismatches: 14, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
205 65 0.34
206 119 0.63
207 6 0.03
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26
Consensus pattern (205 bp):
GCTTAATACAAAGACTGGAAAGAAGTCGTAACCCTACCAGAGGGAAGATGGAATACAAGCAGCTG
ATCACACGCGCAAGCGTTAGCCGGCAAATATTTAGTTACTTTTTCCAAGGCACAAAACCAGGTAA
GATACAAAGTACAATCCTTTTCGATAAGAAATCCTAATAAACTAAGAGAACCTGATTTCTCAACT
ATTCATTTGG
Found at i:6218 original size:21 final size:21
Alignment explanation
Indices: 6185--6229 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
6175 AAATTATGTG
* * *
6185 TTTAGTATTTAAACTATCAGT
1 TTTAATATCTAAACTATCAAT
*
6206 TTTAATATCTAAACTTTCAAT
1 TTTAATATCTAAACTATCAAT
6227 TTT
1 TTT
6230 TTCAAAATCA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.11, G:0.04, T:0.51
Consensus pattern (21 bp):
TTTAATATCTAAACTATCAAT
Found at i:6710 original size:22 final size:23
Alignment explanation
Indices: 6685--6728 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
6675 AATTAAGTTT
6685 TAATCTTA-AAACAATTTCAAAA
1 TAATCTTACAAACAATTTCAAAA
* **
6707 TAATTTTACAAAGTATTTCAAA
1 TAATCTTACAAACAATTTCAAA
6729 CCATTTCAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.50, C:0.11, G:0.02, T:0.36
Consensus pattern (23 bp):
TAATCTTACAAACAATTTCAAAA
Found at i:10924 original size:17 final size:17
Alignment explanation
Indices: 10902--10939 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
10892 CTATGCAAGA
10902 AGAGTTAAATCAATTTG
1 AGAGTTAAATCAATTTG
10919 AGAGTTAAATCAATTTG
1 AGAGTTAAATCAATTTG
10936 AGAG
1 AGAG
10940 AAGTAAAGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.42, C:0.05, G:0.21, T:0.32
Consensus pattern (17 bp):
AGAGTTAAATCAATTTG
Found at i:12700 original size:23 final size:20
Alignment explanation
Indices: 12650--12709 Score: 77
Period size: 23 Copynumber: 2.9 Consensus size: 20
12640 TTTTGGTGCA
*
12650 GAGGGAATCGA-TCCCCCTT
1 GAGGGAACCGATTCCCCCTT
12669 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCC-TT
12690 GAAAGGGAACCGATTCCCCC
1 G--AGGGAACCGATTCCCCC
12710 CACACAGGGG
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
19 10 0.28
20 6 0.17
21 3 0.08
23 17 0.47
ACGTcount: A:0.23, C:0.33, G:0.25, T:0.18
Consensus pattern (20 bp):
GAGGGAACCGATTCCCCCTT
Found at i:17846 original size:20 final size:20
Alignment explanation
Indices: 17795--17849 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 20
17785 TTATTGAAAT
17795 CTCAGTCTCGATACCAAGCCC
1 CTCAGTCTCGATACCAA-CCC
*
17816 CTCGGTCTCGATACCTAA-CC
1 CTCAGTCTCGATACC-AACCC
*
17836 CTCAGTATCGATAC
1 CTCAGTCTCGATAC
17850 TCCTATAAGG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
20 14 0.47
21 14 0.47
22 2 0.07
ACGTcount: A:0.24, C:0.38, G:0.15, T:0.24
Consensus pattern (20 bp):
CTCAGTCTCGATACCAACCC
Found at i:21320 original size:24 final size:24
Alignment explanation
Indices: 21293--21342 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
21283 GTAAAGAACC
*
21293 AAAATAAACTT-AAATATACCATTA
1 AAAATAAACTTCAAACA-ACCATTA
*
21317 AAAATAAAGTTCAAACAACCATTA
1 AAAATAAACTTCAAACAACCATTA
21341 AA
1 AA
21343 TCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.60, C:0.14, G:0.02, T:0.24
Consensus pattern (24 bp):
AAAATAAACTTCAAACAACCATTA
Found at i:30486 original size:12 final size:12
Alignment explanation
Indices: 30469--30497 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
30459 TTCTAATCTG
30469 ATAAACCTGAAA
1 ATAAACCTGAAA
30481 ATAAACCTGAAA
1 ATAAACCTGAAA
30493 ATAAA
1 ATAAA
30498 ACAAAAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.62, C:0.14, G:0.07, T:0.17
Consensus pattern (12 bp):
ATAAACCTGAAA
Found at i:33208 original size:30 final size:30
Alignment explanation
Indices: 33174--33506 Score: 220
Period size: 30 Copynumber: 11.4 Consensus size: 30
33164 CATATTCGAT
* * *
33174 TTAAATGACTTAAATAGCAAAAACATAAAC
1 TTAAAGGACTAAAATAGCAAAAACAGAAAC
** * *
33204 TTAAAGGGTTAAAATAGCAAAAATAGAAAT
1 TTAAAGGACTAAAATAGCAAAAACAGAAAC
* * *
33234 TTAAGGGACTAAAATAGAAAAAATAGAAAC
1 TTAAAGGACTAAAATAGCAAAAACAGAAAC
* *
33264 TTAAAGCACT--AACA-CAACAAA-A-AAA-
1 TTAAAGGACTAAAATAGCAA-AAACAGAAAC
* * *
33289 TTAAAGGAATAAAATGGCAAAAACATAAAC
1 TTAAAGGACTAAAATAGCAAAAACAGAAAC
* * * *
33319 TTAAAGGGCTAAAATAGTAAAAATC-TAAAT
1 TTAAAGGACTAAAATAGCAAAAA-CAGAAAC
** * *
33349 TTAAAAAACTAAAATGGC-AAAATAGAAAC
1 TTAAAGGACTAAAATAGCAAAAACAGAAAC
* * *
33378 TTAAAGGGC-AAAATAGTAAAAACATAAAC
1 TTAAAGGACTAAAATAGCAAAAACAGAAAC
* * * * *
33407 TTAAGGGTCT-AAATAGTAAATACA-AACAT
1 TTAAAGGACTAAAATAGCAAAAACAGAA-AC
* * * *
33436 TTAAAGGACTAAAATAACAAAAATAGACAT
1 TTAAAGGACTAAAATAGCAAAAACAGAAAC
* *
33466 TTAAAGGACTAAAATATCAAAAACAAAAAC
1 TTAAAGGACTAAAATAGCAAAAACAGAAAC
*
33496 TTAAGGGACTA
1 TTAAAGGACTA
33507 TAATGCTATT
Statistics
Matches: 232, Mismatches: 57, Indels: 28
0.73 0.18 0.09
Matches are distributed among these distances:
25 8 0.03
26 3 0.01
27 8 0.03
28 18 0.08
29 54 0.23
30 139 0.60
31 2 0.01
ACGTcount: A:0.58, C:0.10, G:0.12, T:0.20
Consensus pattern (30 bp):
TTAAAGGACTAAAATAGCAAAAACAGAAAC
Found at i:33360 original size:85 final size:85
Alignment explanation
Indices: 33204--33360 Score: 190
Period size: 85 Copynumber: 1.8 Consensus size: 85
33194 AAACATAAAC
** * *
33204 TTAAAGGGTTAAAATAGCAAAAATAGAAATTTAAGGGACTAAAATAGAAAAAATAGAAACTTAAA
1 TTAAAGGAATAAAATAGCAAAAACAGAAATTAAAGGGACTAAAATAGAAAAAATAGAAACTTAAA
**
33269 GCACTAACACAACAAAAAAA
66 AAACTAACACAACAAAAAAA
* * * ** *
33289 TTAAAGGAATAAAATGGCAAAAACATAAACTTAAAGGG-CTAAAATAGTAAAAATCTAAATTTAA
1 TTAAAGGAATAAAATAGCAAAAACAGAAA-TTAAAGGGACTAAAATAGAAAAAATAGAAACTTAA
33353 AAAACTAA
65 AAAACTAA
33361 AATGGCAAAA
Statistics
Matches: 59, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
85 52 0.88
86 7 0.12
ACGTcount: A:0.59, C:0.09, G:0.12, T:0.20
Consensus pattern (85 bp):
TTAAAGGAATAAAATAGCAAAAACAGAAATTAAAGGGACTAAAATAGAAAAAATAGAAACTTAAA
AAACTAACACAACAAAAAAA
Found at i:33387 original size:20 final size:20
Alignment explanation
Indices: 33354--33393 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
33344 TAAATTTAAA
*
33354 AAACTAAAATGGCAAAATAG
1 AAACTAAAAGGGCAAAATAG
*
33374 AAACTTAAAGGGCAAAATAG
1 AAACTAAAAGGGCAAAATAG
33394 TAAAAACATA
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:0.57, C:0.10, G:0.17, T:0.15
Consensus pattern (20 bp):
AAACTAAAAGGGCAAAATAG
Found at i:33506 original size:60 final size:60
Alignment explanation
Indices: 33289--33499 Score: 176
Period size: 59 Copynumber: 3.6 Consensus size: 60
33279 AACAAAAAAA
* * * * **
33289 TTAAAGGAATAAAATGGCAAAAACATAAACTTAAAGGGCTAAAATAGTAAAAATCTAAAT
1 TTAAAGGACTAAAATAGCAAAAACAAAAACTTAAAGGGCTAAAATAGCAAAAATAGAAAT
** * * * * * * *
33349 TTAAAAAACTAAAATGGC-AAAATAGAAACTTAAAGGGC-AAAATAGTAAAAACATAAAC
1 TTAAAGGACTAAAATAGCAAAAACAAAAACTTAAAGGGCTAAAATAGCAAAAATAGAAAT
* * * * * * * * *
33407 TTAAGGGTCT-AAATAGTAAATACAAACATTTAAAGGACTAAAATAACAAAAATAGACAT
1 TTAAAGGACTAAAATAGCAAAAACAAAAACTTAAAGGGCTAAAATAGCAAAAATAGAAAT
*
33466 TTAAAGGACTAAAATATCAAAAACAAAAACTTAA
1 TTAAAGGACTAAAATAGCAAAAACAAAAACTTAA
33500 GGGACTATAA
Statistics
Matches: 115, Mismatches: 33, Indels: 6
0.75 0.21 0.04
Matches are distributed among these distances:
57 5 0.04
58 37 0.32
59 40 0.35
60 33 0.29
ACGTcount: A:0.58, C:0.10, G:0.11, T:0.21
Consensus pattern (60 bp):
TTAAAGGACTAAAATAGCAAAAACAAAAACTTAAAGGGCTAAAATAGCAAAAATAGAAAT
Found at i:34001 original size:3 final size:3
Alignment explanation
Indices: 33995--34052 Score: 68
Period size: 3 Copynumber: 19.7 Consensus size: 3
33985 GATATGTAAT
*
33995 TAA TAA TAA TTAA TAA CAA TAA TAA TAA T-A TAA TAA TAA TAA TAA
1 TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
34040 -ATA TAA -AA TAA TA
1 TA-A TAA TAA TAA TA
34053 TTTGTTGGTA
Statistics
Matches: 48, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
2 5 0.10
3 39 0.81
4 4 0.08
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:34049 original size:20 final size:19
Alignment explanation
Indices: 33995--34052 Score: 68
Period size: 17 Copynumber: 3.1 Consensus size: 19
33985 GATATGTAAT
*
33995 TAATAATAAT-TAATAACAA
1 TAATAATAATATAA-AATAA
34014 TAATAATAATAT--AATAA
1 TAATAATAATATAAAATAA
34031 TAATAATAAATATAAAATAA
1 TAATAAT-AATATAAAATAA
34051 TA
1 TA
34053 TTTGTTGGTA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
17 11 0.32
18 5 0.15
19 10 0.29
20 8 0.24
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
TAATAATAATATAAAATAA
Found at i:35782 original size:20 final size:20
Alignment explanation
Indices: 35753--35795 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
35743 AATTCATAGT
35753 TTTATAATTA-TTCAATAAA
1 TTTATAATTATTTCAATAAA
*
35772 TTTAGTAATTATTTTAATAAA
1 TTTA-TAATTATTTCAATAAA
35793 TTT
1 TTT
35796 TAAAATTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.19
20 6 0.29
21 11 0.52
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (20 bp):
TTTATAATTATTTCAATAAA
Found at i:35802 original size:21 final size:20
Alignment explanation
Indices: 35752--35802 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
35742 AAATTCATAG
35752 TTTTATAATTATTCAATAAA
1 TTTTATAATTATTCAATAAA
*
35772 -TTTAGTAATTATTTTAATAAA
1 TTTTA-TAATTA-TTCAATAAA
*
35793 TTTTAAAATT
1 TTTTATAATT
35803 TAATAATCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 4 0.15
20 6 0.23
21 12 0.46
22 4 0.15
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (20 bp):
TTTTATAATTATTCAATAAA
Found at i:42514 original size:2 final size:2
Alignment explanation
Indices: 42509--42537 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
42499 AGCAGCATGA
42509 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 A
42538 ATCTCAAGCT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:42870 original size:16 final size:16
Alignment explanation
Indices: 42849--42903 Score: 83
Period size: 16 Copynumber: 3.4 Consensus size: 16
42839 TTCATGTTCG
*
42849 ACATAAATGAGCACGA
1 ACATAAATGAACACGA
*
42865 ACATAAACGAACACGA
1 ACATAAATGAACACGA
*
42881 ATATAAATGAACACGA
1 ACATAAATGAACACGA
42897 ACATAAA
1 ACATAAA
42904 CGTTAGAGAT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.56, C:0.18, G:0.13, T:0.13
Consensus pattern (16 bp):
ACATAAATGAACACGA
Found at i:43907 original size:14 final size:14
Alignment explanation
Indices: 43890--43921 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
43880 AATGAACATA
*
43890 AACGAACATAACCT
1 AACGAACATAACCG
43904 AACGAACATAACCG
1 AACGAACATAACCG
43918 AACG
1 AACG
43922 TTCACGAACG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.50, C:0.28, G:0.12, T:0.09
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:45595 original size:2 final size:2
Alignment explanation
Indices: 45588--45619 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
45578 TTTGAGTTAA
45588 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
45620 GAAATTATTA
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:47243 original size:34 final size:32
Alignment explanation
Indices: 47179--47244 Score: 78
Period size: 32 Copynumber: 2.0 Consensus size: 32
47169 CCGTGTTAAA
* * *
47179 TACACAGTGGAAAAGAGATGCAATCGTATACG
1 TACACAGTGCAAAAGAGATGCAAGCATATACG
*
47211 TACACATTGCAAAAGAGAAATGCAAGCATATACG
1 TACACAGTGCAAAAGAG--ATGCAAGCATATACG
47245 ATTTATACGT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
32 15 0.54
34 13 0.46
ACGTcount: A:0.44, C:0.17, G:0.21, T:0.18
Consensus pattern (32 bp):
TACACAGTGCAAAAGAGATGCAAGCATATACG
Found at i:49420 original size:21 final size:19
Alignment explanation
Indices: 49389--49430 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 19
49379 TTTTAATGAA
49389 AATTTTTTTTAAAAAAACTT
1 AATTTTTTTT-AAAAAACTT
49409 AATTTATTTTTAAAAAACTT
1 AATTT-TTTTTAAAAAACTT
49429 AA
1 AA
49431 ACTTTTATGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 16 0.76
21 5 0.24
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (19 bp):
AATTTTTTTTAAAAAACTT
Done.