Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002901.1 Hibiscus syriacus cultivar Beakdansim tig00005992_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: 50576
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:35 original size:14 final size:15
Alignment explanation
Indices: 11--40 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
1 AAAACACACT
11 TAAAGCACACACTTC
1 TAAAGCACACACTTC
26 TAAA-CACACACTTC
1 TAAAGCACACACTTC
40 T
1 T
41 CCCCCTTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.40, C:0.33, G:0.03, T:0.23
Consensus pattern (15 bp):
TAAAGCACACACTTC
Found at i:13400 original size:20 final size:20
Alignment explanation
Indices: 13375--13412 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
13365 TTTATCACGA
13375 ATTTGTAAATCCTTCGAGTC
1 ATTTGTAAATCCTTCGAGTC
* *
13395 ATTTGTAAGTCTTTCGAG
1 ATTTGTAAATCCTTCGAG
13413 CATGATGCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.16, G:0.18, T:0.42
Consensus pattern (20 bp):
ATTTGTAAATCCTTCGAGTC
Found at i:13448 original size:42 final size:42
Alignment explanation
Indices: 13380--13461 Score: 128
Period size: 42 Copynumber: 2.0 Consensus size: 42
13370 CACGAATTTG
* *
13380 TAAATCCTTCGAGTCATTTGTAAGTCTTTCGAGCATGATGCT
1 TAAATCCTTCGAGTCATCTGTAAGTCTTTCGAGCAAGATGCT
* *
13422 TAAATCCTTCGGGTCATCTGTTAGTCTTTCGAGCAAGATG
1 TAAATCCTTCGAGTCATCTGTAAGTCTTTCGAGCAAGATG
13462 ATAAGTCCTT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.37
Consensus pattern (42 bp):
TAAATCCTTCGAGTCATCTGTAAGTCTTTCGAGCAAGATGCT
Found at i:13734 original size:3 final size:3
Alignment explanation
Indices: 13676--13718 Score: 61
Period size: 3 Copynumber: 14.0 Consensus size: 3
13666 ATAATAATAG
13676 TAT TAT TAAT TA- TAT ATAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT T-AT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT
13719 CTTACATATT
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
2 2 0.05
3 29 0.78
4 6 0.16
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:13736 original size:9 final size:10
Alignment explanation
Indices: 13679--13766 Score: 62
Period size: 9 Copynumber: 9.1 Consensus size: 10
13669 ATAATAGTAT
13679 TATTAATTATA
1 TATT-ATTATA
13690 TA-TATTAT-
1 TATTATTATA
13698 TATTATTAT-
1 TATTATTATA
13707 TATTATTAT-
1 TATTATTATA
* *
13716 TA-TCTTACA
1 TATTATTATA
13725 TATTTATTATA
1 TA-TTATTATA
**
13736 TAAAATATATA
1 TATTAT-TATA
*
13747 AATTA-TATA
1 TATTATTATA
13756 TATTATTATA
1 TATTATTATA
13766 T
1 T
13767 TTACAAATAT
Statistics
Matches: 61, Mismatches: 10, Indels: 13
0.73 0.12 0.15
Matches are distributed among these distances:
8 6 0.10
9 32 0.52
10 8 0.13
11 15 0.25
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (10 bp):
TATTATTATA
Found at i:20532 original size:95 final size:96
Alignment explanation
Indices: 20315--20539 Score: 276
Period size: 96 Copynumber: 2.4 Consensus size: 96
20305 GTACTGATGA
* * * * * * *
20315 GGTAGTATCGATACTATGATAAGGGTATCGATACCAGGTAACATCGAACCTAATTTTGGTATCGA
1 GGTAATATCGATACCATGGTAGGGGTATCGATACCAAGCAACATCGAACCTAATTTTGGTATCAA
* *
20380 TACCAGATGAGGGCTATCGATACCATAGTAT
66 TACCAGAAGAGGGCTATCGATACCATAGTAG
* * * *
20411 AGTAATATCGATACCATGGT-GAGGGTATTGATACCAAGCCACATCGAAGCTAATTTTGGTATCA
1 GGTAATATCGATACCATGGTAG-GGGTATCGATACCAAGCAACATCGAACCTAATTTTGGTATCA
* *
20475 ATA-CTGTAAG-GGGGTATCGATACCATAGTAG
65 ATACCAG-AAGAGGGCTATCGATACCATAGTAG
20506 GGTAATATCGATACCATGGTAGGGGTATCGATAC
1 GGTAATATCGATACCATGGTAGGGGTATCGATAC
20540 TGAAGGGCTA
Statistics
Matches: 109, Mismatches: 17, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
95 51 0.47
96 58 0.53
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.28
Consensus pattern (96 bp):
GGTAATATCGATACCATGGTAGGGGTATCGATACCAAGCAACATCGAACCTAATTTTGGTATCAA
TACCAGAAGAGGGCTATCGATACCATAGTAG
Found at i:20536 original size:20 final size:20
Alignment explanation
Indices: 20485--20539 Score: 74
Period size: 22 Copynumber: 2.6 Consensus size: 20
20475 ATACTGTAAG
20485 GGGGTATCGATACCATAGTA
1 GGGGTATCGATACCATAGTA
* *
20505 GGGTAATATCGATACCATGGTA
1 GGG--GTATCGATACCATAGTA
20527 GGGGTATCGATAC
1 GGGGTATCGATAC
20540 TGAAGGGCTA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 12 0.40
22 18 0.60
ACGTcount: A:0.29, C:0.15, G:0.31, T:0.25
Consensus pattern (20 bp):
GGGGTATCGATACCATAGTA
Found at i:26622 original size:30 final size:31
Alignment explanation
Indices: 26588--26654 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 31
26578 GAATGACCTA
* *
26588 TCCATAGGTCATAAAGAACCTCGAT-AACTG
1 TCCATAGGTCACAAAGAACCTAGATAAACTG
* * *
26618 TCCATAGGTCCCGAAGAACCTAGGTAAACTG
1 TCCATAGGTCACAAAGAACCTAGATAAACTG
26649 TCCATA
1 TCCATA
26655 TGTTCTTTAG
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
30 20 0.65
31 11 0.35
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.22
Consensus pattern (31 bp):
TCCATAGGTCACAAAGAACCTAGATAAACTG
Found at i:26733 original size:32 final size:32
Alignment explanation
Indices: 26614--26738 Score: 114
Period size: 31 Copynumber: 4.0 Consensus size: 32
26604 AACCTCGATA
* * *
26614 ACTGTCCATAGGTCCCGA-AGAACCTAGGTAA-
1 ACTGTCCATATGTTCC-ATAGAACATAGGTAAT
**
26645 ACTGTCCATATGTTCTTTAGAACATAGGT-AT
1 ACTGTCCATATGTTCCATAGAACATAGGTAAT
* * *
26676 ACTGTCCATATGCCTCGAAAG-ACATAGGTAAT
1 ACTGTCCATATG-TTCCATAGAACATAGGTAAT
**
26708 TTTGTCCATATGTTCCATAGAACATAGGTAA
1 ACTGTCCATATGTTCCATAGAACATAGGTAA
26739 ACCCTCGACT
Statistics
Matches: 75, Mismatches: 14, Indels: 9
0.77 0.14 0.09
Matches are distributed among these distances:
30 1 0.01
31 48 0.64
32 26 0.35
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (32 bp):
ACTGTCCATATGTTCCATAGAACATAGGTAAT
Found at i:27762 original size:64 final size:62
Alignment explanation
Indices: 27677--27815 Score: 145
Period size: 64 Copynumber: 2.2 Consensus size: 62
27667 TTAACATGTA
* * * * *
27677 CATCGATGCACTACCCATGCATCGATATA-CAAATCACCTTCGATGTTTTCATTTTAAGGGGGTG
1 CATCGATGCACTAACCATGCATCGATACACCAAAGCA--TTCGATGTTTTCATTTTAA-AGAGTG
** * *
27741 CATCGATGCACTAACTGTGCATCGGTACACTCAAGGCATTCGATGTTTTCATTTTAAAGAGTG
1 CATCGATGCACTAACCATGCATCGATACAC-CAAAGCATTCGATGTTTTCATTTTAAAGAGTG
*
27804 CATCGATACACT
1 CATCGATGCACT
27816 TTGTCCAGAA
Statistics
Matches: 63, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
63 15 0.24
64 43 0.68
66 5 0.08
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (62 bp):
CATCGATGCACTAACCATGCATCGATACACCAAAGCATTCGATGTTTTCATTTTAAAGAGTG
Found at i:28598 original size:54 final size:54
Alignment explanation
Indices: 28529--28779 Score: 342
Period size: 54 Copynumber: 4.6 Consensus size: 54
28519 CAATTTCGGT
* * **
28529 ACTAAGTGTGTATTTCACGGAATTCATCCTATCTGGATGAATAATCGTTTTGAT
1 ACTAAGTGTGCATTTCACGGAATTCATCCTATATGGATGAATAATCGTTTTGGC
* * ** *
28583 AATAAGTGTGCATTTCACGGAATTCATCTTATATGGGCGAATAA-CTGTTTCGGC
1 ACTAAGTGTGCATTTCACGGAATTCATCCTATATGGATGAATAATC-GTTTTGGC
*
28637 ACTAAGTGTGCATTTCACGGAATTCATCCTATTTGGATGAATAATCGTTTTGGC
1 ACTAAGTGTGCATTTCACGGAATTCATCCTATATGGATGAATAATCGTTTTGGC
* * * * * *
28691 ACTAAGAGTGCATTTCACGAAATTTATCCTATGTGGATGAATAACCATTTTGGC
1 ACTAAGTGTGCATTTCACGGAATTCATCCTATATGGATGAATAATCGTTTTGGC
28745 ACTAAGTGTGCATTTCACGGAATTCATCCTATATG
1 ACTAAGTGTGCATTTCACGGAATTCATCCTATATG
28780 AATAACCGTT
Statistics
Matches: 170, Mismatches: 25, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
53 1 0.01
54 168 0.99
55 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (54 bp):
ACTAAGTGTGCATTTCACGGAATTCATCCTATATGGATGAATAATCGTTTTGGC
Found at i:34082 original size:21 final size:21
Alignment explanation
Indices: 34056--34100 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
34046 GATTTCTGGG
* *
34056 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
34077 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
34098 CAA
1 CAA
34101 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:35810 original size:13 final size:13
Alignment explanation
Indices: 35792--35854 Score: 52
Period size: 13 Copynumber: 5.5 Consensus size: 13
35782 TTATATGGCA
35792 CTACGGTGCAATT
1 CTACGGTGCAATT
35805 CTACGG-GC-A--
1 CTACGGTGCAATT
*
35814 CTTCGGTGCAATT
1 CTACGGTGCAATT
35827 CTACGG-GC-A--
1 CTACGGTGCAATT
*
35836 CTTCGGTGCAATT
1 CTACGGTGCAATT
35849 CTACGG
1 CTACGG
35855 GGCACTTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 16
0.66 0.07 0.28
Matches are distributed among these distances:
9 10 0.26
10 4 0.11
11 4 0.11
12 4 0.11
13 16 0.42
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (13 bp):
CTACGGTGCAATT
Found at i:35820 original size:22 final size:22
Alignment explanation
Indices: 35788--35868 Score: 144
Period size: 22 Copynumber: 3.6 Consensus size: 22
35778 ATCATTATAT
*
35788 GGCACTACGGTGCAATTCTACG
1 GGCACTTCGGTGCAATTCTACG
35810 GGCACTTCGGTGCAATTCTACG
1 GGCACTTCGGTGCAATTCTACG
35832 GGCACTTCGGTGCAATTCTACGG
1 GGCACTTCGGTGCAATTCTAC-G
35855 GGCACTTCGGTGCA
1 GGCACTTCGGTGCA
35869 TTTATACGAG
Statistics
Matches: 57, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
22 42 0.74
23 15 0.26
ACGTcount: A:0.19, C:0.27, G:0.30, T:0.25
Consensus pattern (22 bp):
GGCACTTCGGTGCAATTCTACG
Found at i:37153 original size:61 final size:61
Alignment explanation
Indices: 37062--37183 Score: 199
Period size: 61 Copynumber: 2.0 Consensus size: 61
37052 GATGATTAGG
* * *
37062 AGGTACAGATCAGATCCCTCGGATGTTATCACTCCTGAAGAAATGGAGATCAAACCAGATT
1 AGGTAAAGATAAGATCCCTCGGATGTTATCACTCCTGAAGAAATAGAGATCAAACCAGATT
* *
37123 AGGTAAAGATAAGATCCCTCGGATGTTATCACTCCTGAAGAAATATAGATCCAACCAGATT
1 AGGTAAAGATAAGATCCCTCGGATGTTATCACTCCTGAAGAAATAGAGATCAAACCAGATT
37184 TGACTTATAA
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
61 56 1.00
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.24
Consensus pattern (61 bp):
AGGTAAAGATAAGATCCCTCGGATGTTATCACTCCTGAAGAAATAGAGATCAAACCAGATT
Found at i:43369 original size:95 final size:95
Alignment explanation
Indices: 43270--43492 Score: 270
Period size: 95 Copynumber: 2.3 Consensus size: 95
43260 TACTGATGAG
* * * * *
43270 GTAGTATCGATACTATGATAATGGTATCGATACCAGGTAACATCAAACCTAATTTTGGTATCGAT
1 GTAGTATCGATACCATGGTAAGGGTATCGATACCAAGCAACATCAAACCTAATTTTGGTATCGAT
* *
43335 ACCAG-AGGGGAGTATCGGTACCATAGCATA
66 ACCAGAAGGGG-GTATCGATACCATAGCAGA
* * * *
43365 GTAGTATCGATACCATGGTGAGGGTATC-AGTACCAAGCCACATCGAAGCTAATTTTGGTATCGA
1 GTAGTATCGATACCATGGTAAGGGTATCGA-TACCAAGCAACATCAAACCTAATTTTGGTATCGA
** * *
43429 TACTGGAAGGGGGTATCGATACCATAGTAGG
65 TACCAGAAGGGGGTATCGATACCATAGCAGA
*
43460 GTAGTATCGATACCATGGTAGGGGTATCGATAC
1 GTAGTATCGATACCATGGTAAGGGTATCGATAC
43493 TGAAGGGCTA
Statistics
Matches: 108, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
94 1 0.01
95 101 0.94
96 6 0.06
ACGTcount: A:0.31, C:0.17, G:0.26, T:0.26
Consensus pattern (95 bp):
GTAGTATCGATACCATGGTAAGGGTATCGATACCAAGCAACATCAAACCTAATTTTGGTATCGAT
ACCAGAAGGGGGTATCGATACCATAGCAGA
Found at i:43469 original size:22 final size:20
Alignment explanation
Indices: 43438--43492 Score: 83
Period size: 22 Copynumber: 2.6 Consensus size: 20
43428 ATACTGGAAG
43438 GGGGTATCGATACCATAGTA
1 GGGGTATCGATACCATAGTA
*
43458 GGGTAGTATCGATACCATGGTA
1 GGG--GTATCGATACCATAGTA
43480 GGGGTATCGATAC
1 GGGGTATCGATAC
43493 TGAAGGGCTA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 13 0.41
22 19 0.59
ACGTcount: A:0.27, C:0.15, G:0.33, T:0.25
Consensus pattern (20 bp):
GGGGTATCGATACCATAGTA
Found at i:44278 original size:54 final size:54
Alignment explanation
Indices: 43820--44253 Score: 555
Period size: 54 Copynumber: 8.0 Consensus size: 54
43810 CCAATTTGGA
* * * * *
43820 ACTAATTGTGTATTTCACGGAATTCATCCTATATGGATGAATAACCATTTTGGC
1 ACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGGC
* * *
43874 ACTAAGTGTGAATTTCACGGAATTCATCCTATGTGGATGAATAACAGTTTCAGC
1 ACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGGC
* * * * ** * * *
43928 ACTAAGTGTGTATTTCATGAAATTCATCATAACTGGATGAATAACAGTTTCAGA
1 ACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGGC
* *
43982 ACTAAGTGTGCATTTTACGGAATTCATCCTATGTGGATGAATAACCGTTTTGGC
1 ACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGGC
* * * * *
44036 ACTAAGTGTGCATTTCACGGAATTCATTCTATGTGAATGAATAATCATTTCGGA
1 ACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGGC
* * *
44090 ACTAAGTGTGTATTTCACAGG-ATTCATCCTATGTGGATGAATAATCGTTTCAGC
1 ACTAAGTGTGCATTTCAC-GGAATTCATCCTATGTGGATGAATAACCGTTTCGGC
* * * * * *
44144 ACTAAGTATGCATTTCACGAAATTTATCTTATGTAGATGAATAACTGTTTCGGC
1 ACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGGC
44198 ACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGGC
1 ACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGGC
44252 AC
1 AC
44254 CATGAGTGCA
Statistics
Matches: 325, Mismatches: 53, Indels: 4
0.85 0.14 0.01
Matches are distributed among these distances:
53 1 0.00
54 322 0.99
55 2 0.01
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.34
Consensus pattern (54 bp):
ACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGGC
Found at i:44307 original size:108 final size:108
Alignment explanation
Indices: 43831--44309 Score: 527
Period size: 108 Copynumber: 4.4 Consensus size: 108
43821 CTAATTGTGT
* * * *
43831 ATTTCACGGAATTCATCCTATATGGATGAATAACCATTTTGGCACTAAGTGTGAATTTCACGGAA
1 ATTTCACGAAATTCATCATATATGGATGAATAACCATTTCGGCACTAAGTGTGCATTTCACGGAA
* * *
43896 TTCATCCTATGTGGATGAATAACAGTTTCAGCACTAAGTGTGT
66 TTCATCCTATGTGGATGAATAACCGTTTCAGCACTAAGAGTGC
* * * *
43939 ATTTCATGAAATTCATCATA-ACTGGATGAATAA-CAGTTTCAGAACTAAGTGTGCATTTTACGG
1 ATTTCACGAAATTCATCATATA-TGGATGAATAACCA-TTTCGGCACTAAGTGTGCATTTCACGG
** *
44002 AATTCATCCTATGTGGATGAATAACCGTTTTGGCACTAAGTGTGC
64 AATTCATCCTATGTGGATGAATAACCGTTTCAGCACTAAGAGTGC
* * * * * *
44047 ATTTCACGGAATTCATTC-TATGTGAATGAATAATCATTTCGGAACTAAGTGTGTATTTCACAGG
1 ATTTCACGAAATTCA-TCATATATGGATGAATAACCATTTCGGCACTAAGTGTGCATTTCAC-GG
*
44111 -ATTCATCCTATGTGGATGAATAATCGTTTCAGCACTAAGTA-TGC
64 AATTCATCCTATGTGGATGAATAACCGTTTCAGCACTAAG-AGTGC
* * * * **
44155 ATTTCACGAAATTTATCTTATGTAGATGAATAACTGTTTCGGCACTAAGTGTGCATTTCACGGAA
1 ATTTCACGAAATTCATCATATATGGATGAATAACCATTTCGGCACTAAGTGTGCATTTCACGGAA
* * *
44220 TTCATCCTATGTGGATGAATAACCGTTTCGGCACCATGAGTGC
66 TTCATCCTATGTGGATGAATAACCGTTTCAGCACTAAGAGTGC
*** * ** * * *
44263 AAAACACGAAATTCATAATATATTTATGAATGACCATATGGGCACTA
1 ATTTCACGAAATTCATCATATATGGATGAATAACCATTTCGGCACTA
44310 TATATTCACT
Statistics
Matches: 311, Mismatches: 50, Indels: 20
0.82 0.13 0.05
Matches are distributed among these distances:
107 8 0.03
108 297 0.95
109 6 0.02
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Consensus pattern (108 bp):
ATTTCACGAAATTCATCATATATGGATGAATAACCATTTCGGCACTAAGTGTGCATTTCACGGAA
TTCATCCTATGTGGATGAATAACCGTTTCAGCACTAAGAGTGC
Done.