Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008861.1 Hibiscus syriacus cultivar Beakdansim tig00112085_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: 51468
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.32
Found at i:2970 original size:24 final size:24
Alignment explanation
Indices: 2941--2994 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
2931 AATGGTTCAG
*
2941 GGCGCATAAATCTTTATTGCCTCA
1 GGCGCATAAACCTTTATTGCCTCA
2965 GGCGCATAAACCTTTATTGCCTCA
1 GGCGCATAAACCTTTATTGCCTCA
2989 GGCGCA
1 GGCGCA
2995 AGGCACAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.28
Consensus pattern (24 bp):
GGCGCATAAACCTTTATTGCCTCA
Found at i:6322 original size:16 final size:16
Alignment explanation
Indices: 6294--6330 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
6284 CACTGTTTTG
6294 TCATTTAAATATCTATT
1 TCATTTAAATATCTA-T
6311 TCATTT-AATATCTAT
1 TCATTTAAATATCTAT
6326 TCATT
1 TCATT
6331 GATGAAATGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 6 0.30
16 8 0.40
17 6 0.30
ACGTcount: A:0.32, C:0.14, G:0.00, T:0.54
Consensus pattern (16 bp):
TCATTTAAATATCTAT
Found at i:26728 original size:16 final size:16
Alignment explanation
Indices: 26707--26765 Score: 100
Period size: 16 Copynumber: 3.7 Consensus size: 16
26697 TAATAAATAA
*
26707 ACGAACATAAACGAAT
1 ACGAACATAAACGAAC
26723 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
26739 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
26755 ACGAACATAAA
1 ACGAACATAAA
26766 TGTTGGAGAC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 41 1.00
ACGTcount: A:0.58, C:0.20, G:0.12, T:0.10
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:26766 original size:16 final size:16
Alignment explanation
Indices: 26699--26767 Score: 97
Period size: 16 Copynumber: 4.4 Consensus size: 16
26689 CGTTCATTTA
26699 ATAAAT-AA-ACGAAC
1 ATAAATGAACACGAAC
* *
26713 ATAAACGAATACGAAC
1 ATAAATGAACACGAAC
*
26729 ATAAACGAACACGAAC
1 ATAAATGAACACGAAC
26745 ATAAATGAACACGAAC
1 ATAAATGAACACGAAC
26761 ATAAATG
1 ATAAATG
26768 TTGGAGACCC
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
14 5 0.10
15 2 0.04
16 43 0.86
ACGTcount: A:0.58, C:0.17, G:0.12, T:0.13
Consensus pattern (16 bp):
ATAAATGAACACGAAC
Found at i:27023 original size:11 final size:11
Alignment explanation
Indices: 26987--27110 Score: 83
Period size: 11 Copynumber: 11.0 Consensus size: 11
26977 AAATTTCATC
* *
26987 AGCTCGAATAA
1 AGCTCGATTGA
*
26998 AGCTCGACTCG-
1 AGCTCGA-TTGA
27009 AGCTCGATTGA
1 AGCTCGATTGA
* *
27020 AGCTCAATTTTA
1 AGCTCGA-TTGA
* *
27032 AGTTCGATTCA
1 AGCTCGATTGA
27043 AGCTCGATTTTG-
1 AGCTCGA--TTGA
*
27055 AGCTCGATTCA
1 AGCTCGATTGA
27066 AGCTCGATTTTG-
1 AGCTCGA--TTGA
*
27078 AGCTCGATTCA
1 AGCTCGATTGA
*
27089 AGCTCGATTCA
1 AGCTCGATTGA
27100 AGCTCGATTGA
1 AGCTCGATTGA
27111 CCCAGTCCAA
Statistics
Matches: 89, Mismatches: 15, Indels: 18
0.73 0.12 0.15
Matches are distributed among these distances:
10 6 0.07
11 57 0.64
12 22 0.25
13 4 0.04
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.31
Consensus pattern (11 bp):
AGCTCGATTGA
Found at i:27040 original size:23 final size:23
Alignment explanation
Indices: 27009--27108 Score: 139
Period size: 23 Copynumber: 4.4 Consensus size: 23
26999 GCTCGACTCG
* *
27009 AGCTCGATTGAAGCTCAATTTTA
1 AGCTCGATTCAAGCTCGATTTTA
* *
27032 AGTTCGATTCAAGCTCGATTTTG
1 AGCTCGATTCAAGCTCGATTTTA
*
27055 AGCTCGATTCAAGCTCGATTTTG
1 AGCTCGATTCAAGCTCGATTTTA
*
27078 AGCTCGATTCAAGCTCGA-TTCA
1 AGCTCGATTCAAGCTCGATTTTA
27100 AGCTCGATT
1 AGCTCGATT
27109 GACCCAGTCC
Statistics
Matches: 70, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
22 11 0.16
23 59 0.84
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.34
Consensus pattern (23 bp):
AGCTCGATTCAAGCTCGATTTTA
Found at i:27060 original size:12 final size:12
Alignment explanation
Indices: 27043--27086 Score: 63
Period size: 12 Copynumber: 3.8 Consensus size: 12
27033 GTTCGATTCA
27043 AGCTCGATTTTG
1 AGCTCGATTTTG
**
27055 AGCTCGA-TTCA
1 AGCTCGATTTTG
27066 AGCTCGATTTTG
1 AGCTCGATTTTG
27078 AGCTCGATT
1 AGCTCGATT
27087 CAAGCTCGAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
11 9 0.33
12 18 0.67
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.36
Consensus pattern (12 bp):
AGCTCGATTTTG
Found at i:27073 original size:34 final size:33
Alignment explanation
Indices: 26987--27108 Score: 109
Period size: 34 Copynumber: 3.6 Consensus size: 33
26977 AAATTTCATC
* * * * *
26987 AGCTCGAATAAAGCTCGACTCGAGCTCGATTGA
1 AGCTCGATTCAAGCTCGATTCAAGCTCGATTCA
* * * **
27020 AGCTCAATTTTAAGTTCGATTCAAGCTCGATTTTG
1 AGCTCGA-TTCAAGCTCGATTCAAGCTCGA-TTCA
**
27055 AGCTCGATTCAAGCTCGATTTTGAGCTCGATTCA
1 AGCTCGATTCAAGCTCGA-TTCAAGCTCGATTCA
27089 AGCTCGATTCAAGCTCGATT
1 AGCTCGATTCAAGCTCGATT
27109 GACCCAGTCC
Statistics
Matches: 71, Mismatches: 15, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
33 8 0.11
34 46 0.65
35 17 0.24
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.31
Consensus pattern (33 bp):
AGCTCGATTCAAGCTCGATTCAAGCTCGATTCA
Found at i:41117 original size:15 final size:15
Alignment explanation
Indices: 41087--41143 Score: 62
Period size: 15 Copynumber: 3.7 Consensus size: 15
41077 CTTCGTCCTT
*
41087 TCCTCTCTCTTTCTCC
1 TCCTC-CTCTTCCTCC
41103 TCC-CCATCTTCCTCC
1 TCCTCC-TCTTCCTCC
*
41118 TCCTCCTCCTCCTCC
1 TCCTCCTCTTCCTCC
*
41133 TCCTCGTCTTC
1 TCCTCCTCTTC
41144 ATCCATATCG
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
14 1 0.03
15 29 0.83
16 5 0.14
ACGTcount: A:0.02, C:0.56, G:0.02, T:0.40
Consensus pattern (15 bp):
TCCTCCTCTTCCTCC
Found at i:41118 original size:3 final size:3
Alignment explanation
Indices: 41099--41137 Score: 53
Period size: 3 Copynumber: 13.0 Consensus size: 3
41089 CTCTCTCTTT
*
41099 CTC CTC C-C CATC TTC CTC CTC CTC CTC CTC CTC CTC CTC
1 CTC CTC CTC C-TC CTC CTC CTC CTC CTC CTC CTC CTC CTC
41138 GTCTTCATCC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 2 0.06
3 29 0.91
4 1 0.03
ACGTcount: A:0.03, C:0.64, G:0.00, T:0.33
Consensus pattern (3 bp):
CTC
Found at i:43576 original size:21 final size:21
Alignment explanation
Indices: 43550--43602 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
43540 TTTTCCAGAT
43550 TCGCAACGCGAACATCGACTA
1 TCGCAACGCGAACATCGACTA
*
43571 TCGCAACGCGAACTTCGACTA
1 TCGCAACGCGAACATCGACTA
*
43592 TCGCAATGCGA
1 TCGCAACGCGA
43603 TTTTCCAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.30, C:0.32, G:0.21, T:0.17
Consensus pattern (21 bp):
TCGCAACGCGAACATCGACTA
Found at i:43659 original size:21 final size:20
Alignment explanation
Indices: 43614--43769 Score: 122
Period size: 21 Copynumber: 7.5 Consensus size: 20
43604 TTTCCAAATT
43614 CGTTGCGATAGTCCAAGTT--
1 CGTTGCGATAG-CCAAGTTCG
43633 CGTTGCGATAGCCGAAGTTCG
1 CGTTGCGATAGCC-AAGTTCG
* *
43654 CGTTGCGATTTATTCTAAGTTCG
1 CGTTGCGA--TA-GCCAAGTTCG
*
43677 CGTTGCGATATTCCAAGTTCG
1 CGTTGCGATA-GCCAAGTTCG
*
43698 CGTTGCGATAGTCGAAGTTCG
1 CGTTGCGATAG-CCAAGTTCG
*
43719 CGTTGCGATTTATTCCAAGTT--
1 CGTTGCGA--TA-GCCAAGTTCG
*
43740 CGTTGCGATAGTCGAAGTTCG
1 CGTTGCGATAG-CCAAGTTCG
*
43761 CTTTGCGAT
1 CGTTGCGAT
43770 TTATTCCAAA
Statistics
Matches: 114, Mismatches: 10, Indels: 24
0.77 0.07 0.16
Matches are distributed among these distances:
18 2 0.02
19 24 0.21
21 62 0.54
23 25 0.22
24 1 0.01
ACGTcount: A:0.19, C:0.21, G:0.27, T:0.34
Consensus pattern (20 bp):
CGTTGCGATAGCCAAGTTCG
Found at i:43693 original size:63 final size:61
Alignment explanation
Indices: 43598--43769 Score: 231
Period size: 63 Copynumber: 2.8 Consensus size: 61
43588 ACTATCGCAA
*
43598 TGCGA-TT-TTCCAAATTCGTTGCGATAGTCCAAGTTCGTTGCGATAGCCGAAGTTCGCGT
1 TGCGATTTATTCCAAGTTCGTTGCGATAGTCCAAGTTCGTTGCGATAGCCGAAGTTCGCGT
* * *
43657 TGCGATTTATTCTAAGTTCGCGTTGCGATATTCCAAGTTCGCGTTGCGATAGTCGAAGTTCGCGT
1 TGCGATTTATTCCAAGTT--CGTTGCGATAGTCCAAGTT--CGTTGCGATAGCCGAAGTTCGCGT
*
43722 TGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCTTTGCGAT
1 TGCGATTTATTCCAAGTTCGTTGCGATAGTCCAAGTTCG--TTGCGAT
43770 TTATTCCAAA
Statistics
Matches: 98, Mismatches: 7, Indels: 12
0.84 0.06 0.10
Matches are distributed among these distances:
59 5 0.05
60 2 0.02
61 9 0.09
63 42 0.43
65 40 0.41
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (61 bp):
TGCGATTTATTCCAAGTTCGTTGCGATAGTCCAAGTTCGTTGCGATAGCCGAAGTTCGCGT
Found at i:43716 original size:42 final size:40
Alignment explanation
Indices: 43598--43794 Score: 202
Period size: 42 Copynumber: 4.7 Consensus size: 40
43588 ACTATCGCAA
* * *
43598 TGCGATTTTCCAAATTCGTTGCGATAGTCCAAGTT--CGT
1 TGCGATATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGT
* * *
43636 TGCGATA-GCCGAAGTTCGCGTTGCGATTTATTCTAAGTTCGCGT
1 TGCGATATTCC-AAGTT--CGTTGCGA--TAGTCGAAGTTCGCGT
43680 TGCGATATTCCAAGTTCGCGTTGCGATAGTCGAAGTTCGCGT
1 TGCGATATTCCAAGTT--CGTTGCGATAGTCGAAGTTCGCGT
*
43722 TGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCTT
1 TGCGA--TATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGT
*
43764 TGCGATTTATTCCAAATTCGTTGCGATAGTC
1 TGCGA--TATTCCAAGTTCGTTGCGATAGTC
43795 CAAAATCGTA
Statistics
Matches: 139, Mismatches: 10, Indels: 16
0.84 0.06 0.10
Matches are distributed among these distances:
37 2 0.01
38 10 0.07
40 8 0.06
42 81 0.58
44 36 0.26
45 2 0.01
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.36
Consensus pattern (40 bp):
TGCGATATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGT
Found at i:43787 original size:21 final size:21
Alignment explanation
Indices: 43598--43790 Score: 115
Period size: 21 Copynumber: 9.3 Consensus size: 21
43588 ACTATCGCAA
*
43598 TGCGA-TT-TTCCAAATTCGT
1 TGCGATTTATTCCAAGTTCGT
*
43617 TGCGA--TAGTCCAAGTTCGT
1 TGCGATTTATTCCAAGTTCGT
*
43636 TGCGA--TA-GCCGAAGTTCGCGT
1 TGCGATTTATTCC-AAGTT--CGT
*
43657 TGCGATTTATTCTAAGTTCGCGT
1 TGCGATTTATTCCAAGTT--CGT
43680 TGCGA--TATTCCAAGTTCGCGT
1 TGCGATTTATTCCAAGTT--CGT
* *
43701 TGCGA--TAGTCGAAGTTCGCGT
1 TGCGATTTATTCCAAGTT--CGT
43722 TGCGATTTATTCCAAGTTCGT
1 TGCGATTTATTCCAAGTTCGT
* *
43743 TGCGA--TAGTCGAAGTTCGCTT
1 TGCGATTTATTCCAAGTTCG--T
*
43764 TGCGATTTATTCCAAATTCGT
1 TGCGATTTATTCCAAGTTCGT
43785 TGCGAT
1 TGCGAT
43791 AGTCCAAAAT
Statistics
Matches: 146, Mismatches: 15, Indels: 24
0.79 0.08 0.13
Matches are distributed among these distances:
18 3 0.02
19 38 0.26
21 68 0.47
23 36 0.25
24 1 0.01
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.36
Consensus pattern (21 bp):
TGCGATTTATTCCAAGTTCGT
Found at i:43898 original size:6 final size:6
Alignment explanation
Indices: 43887--43919 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
43877 GACACGTATA
43887 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
43920 CGAGACAAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.33, C:0.52, G:0.15, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:44752 original size:40 final size:42
Alignment explanation
Indices: 44674--44766 Score: 138
Period size: 40 Copynumber: 2.3 Consensus size: 42
44664 TGCGATTTTG
*
44674 GACTATCGCAATGAATTTGGAATAAATCGCAACGCGAACTTA
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTA
*
44716 GACTGTCGCAACGAATTTGG-A-AAATCGCAACGCGAACTTCA
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTT-A
44757 -ACTATCGCAA
1 GACTATCGCAA
44767 TGTGAATATG
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
40 27 0.57
41 2 0.04
42 18 0.38
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.22
Consensus pattern (42 bp):
GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTA
Found at i:49699 original size:57 final size:58
Alignment explanation
Indices: 49591--49701 Score: 163
Period size: 57 Copynumber: 1.9 Consensus size: 58
49581 ATGACCTGCC
*
49591 TTCTCTCATATTTCCTTTTCAGGTCAGTATACATGCCATTGGTTTATGCTGTTTACTA
1 TTCTCTCATATTTCCTTTTCAGGTCAGCATACATGCCATTGGTTTATGCTGTTTACTA
* * *
49649 TTCTCTCATATTTCCTTTT-AGGTCGGCATACCTGTCATTGG-TTATTGCTGTTT
1 TTCTCTCATATTTCCTTTTCAGGTCAGCATACATGCCATTGGTTTA-TGCTGTTT
49702 TTTACTATCT
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
56 3 0.06
57 26 0.54
58 19 0.40
ACGTcount: A:0.16, C:0.21, G:0.15, T:0.48
Consensus pattern (58 bp):
TTCTCTCATATTTCCTTTTCAGGTCAGCATACATGCCATTGGTTTATGCTGTTTACTA
Done.