Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001254.1 Hibiscus syriacus cultivar Beakdansim tig00002464_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: 78058
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:8856 original size:11 final size:11
Alignment explanation
Indices: 8840--8875 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
8830 TAGAATTATT
8840 AATTTAAATTA
1 AATTTAAATTA
*
8851 AATTTAAATTT
1 AATTTAAATTA
*
8862 AATTTAATTTA
1 AATTTAAATTA
8873 AAT
1 AAT
8876 AGTAATATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
AATTTAAATTA
Found at i:8857 original size:6 final size:6
Alignment explanation
Indices: 8840--8875 Score: 51
Period size: 5 Copynumber: 6.5 Consensus size: 6
8830 TAGAATTATT
8840 AATTTA AA-TTA AATTTA AATTT- AATTT- AATTTA AAT
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AAT
8876 AGTAATATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 15 0.54
6 13 0.46
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
AATTTA
Found at i:24123 original size:2 final size:2
Alignment explanation
Indices: 24116--24151 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
24106 CCAATACAAT
24116 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
24152 AAGTAAAATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:25811 original size:50 final size:51
Alignment explanation
Indices: 25701--25817 Score: 191
Period size: 51 Copynumber: 2.3 Consensus size: 51
25691 GTGCGCCTCA
* *
25701 TGCACCGCGCTATACGATGATTTGGCGCCACTTGAGGTATAGCGCGCCCCC
1 TGCACCGCGCTATACGATGAGTTGGCGCCACGTGAGGTATAGCGCGCCCCC
*
25752 TGCACCGCGCTATACGATGAGTTGGCGCCACGTG-GGTATAGCGCGGCCCC
1 TGCACCGCGCTATACGATGAGTTGGCGCCACGTGAGGTATAGCGCGCCCCC
*
25802 TGCAGCGCGCTATACG
1 TGCACCGCGCTATACG
25818 CCACGTAGGG
Statistics
Matches: 62, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
50 30 0.48
51 32 0.52
ACGTcount: A:0.17, C:0.32, G:0.31, T:0.20
Consensus pattern (51 bp):
TGCACCGCGCTATACGATGAGTTGGCGCCACGTGAGGTATAGCGCGCCCCC
Found at i:25836 original size:25 final size:25
Alignment explanation
Indices: 25808--25861 Score: 99
Period size: 25 Copynumber: 2.2 Consensus size: 25
25798 CCCCTGCAGC
*
25808 GCGCTATACGCCACGTAGGGGTATA
1 GCGCTATACGACACGTAGGGGTATA
25833 GCGCTATACGACACGTAGGGGTATA
1 GCGCTATACGACACGTAGGGGTATA
25858 GCGC
1 GCGC
25862 GGATCAGGTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.24, C:0.24, G:0.33, T:0.19
Consensus pattern (25 bp):
GCGCTATACGACACGTAGGGGTATA
Found at i:25964 original size:47 final size:48
Alignment explanation
Indices: 25854--25972 Score: 179
Period size: 49 Copynumber: 2.5 Consensus size: 48
25844 CACGTAGGGG
**
25854 TATAGCGCGGATCAGGTACCGCGCTATACCTTTACTCCTAATAATTTTA
1 TATAGCGCGGGGCAGGTACCGCGCTATACCTTTACTCC-AATAATTTTA
*
25903 TATAGCGCGAGGCAGGTACCGCGAC-ATACCTTTACTCC-ATAATTTTA
1 TATAGCGCGGGGCAGGTACCGCG-CTATACCTTTACTCCAATAATTTTA
25950 TATAGCGCGGGGCAGGTACCGCG
1 TATAGCGCGGGGCAGGTACCGCG
25973 TTTTGTATAA
Statistics
Matches: 65, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
47 31 0.48
49 33 0.51
50 1 0.02
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.27
Consensus pattern (48 bp):
TATAGCGCGGGGCAGGTACCGCGCTATACCTTTACTCCAATAATTTTA
Found at i:31590 original size:110 final size:111
Alignment explanation
Indices: 31396--31622 Score: 366
Period size: 110 Copynumber: 2.1 Consensus size: 111
31386 ATTACAAAAA
* * * *
31396 TTAATTCTTAATCTAATAATCATGCATTAAATGAATCAACTAATTATTAATAATAATTTAAATTA
1 TTAATTATTAATATAATAATCATGCATTAAATAAATCAACTAAATATTAATAATAATTTAAATTA
*
31461 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
* *
31507 TTAATTATTAATATAATAATCATGTATTAAATAAAT-AACTAAATATTACTAATAATTTAAATTA
1 TTAATTATTAATATAATAATCATGCATTAAATAAATCAACTAAATATTAATAATAATTTAAATTA
*
31571 AATTAAAACGTTAAAATGTTACCGTATGAGCAAAGTGTAGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
*
31617 ATAATT
1 TTAATT
31623 TCCATCCGAG
Statistics
Matches: 107, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
110 75 0.70
111 32 0.30
ACGTcount: A:0.46, C:0.08, G:0.09, T:0.37
Consensus pattern (111 bp):
TTAATTATTAATATAATAATCATGCATTAAATAAATCAACTAAATATTAATAATAATTTAAATTA
AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
Found at i:31743 original size:12 final size:10
Alignment explanation
Indices: 31729--31769 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
31719 ACCTTAAAAA
*
31729 GAGAGTATTT
1 GAGAGAATTT
31739 GAGAGAAATTT
1 GAGAG-AATTT
31750 -AGAGAATTT
1 GAGAGAATTT
31759 GAGAGAATTT
1 GAGAGAATTT
31769 G
1 G
31770 GTGTGATAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 5 0.18
10 19 0.68
11 4 0.14
ACGTcount: A:0.39, C:0.00, G:0.29, T:0.32
Consensus pattern (10 bp):
GAGAGAATTT
Found at i:31904 original size:50 final size:51
Alignment explanation
Indices: 31849--31967 Score: 131
Period size: 50 Copynumber: 2.4 Consensus size: 51
31839 GCCCCTTGCA
*
31849 CCGCGCTATACCCCACGTGT-CAGATA-T-ACAGGTATAGCGCGCTGCAGGGG
1 CCGCGCTATACCCCACGTGTGC-GATACTCAC-CGTATAGCGCGCTGCAGGGG
* *
31899 CCGCGCTATA-CCCACGT-TGCGCTAGCTCACCGTATAGCGCGGTGCAGGGG
1 CCGCGCTATACCCCACGTGTGCGATA-CTCACCGTATAGCGCGCTGCAGGGG
**
31949 GTGCGCTATACCCCACGTG
1 CCGCGCTATACCCCACGTG
31968 ACGCCAAATC
Statistics
Matches: 58, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
48 4 0.07
49 8 0.14
50 37 0.64
51 9 0.16
ACGTcount: A:0.18, C:0.33, G:0.30, T:0.18
Consensus pattern (51 bp):
CCGCGCTATACCCCACGTGTGCGATACTCACCGTATAGCGCGCTGCAGGGG
Found at i:31988 original size:51 final size:50
Alignment explanation
Indices: 31880--32006 Score: 157
Period size: 51 Copynumber: 2.5 Consensus size: 50
31870 AGATATACAG
* * * ** *
31880 GTATAGCGCGCTGCAGGGGCCGCGCTATACCCACGTTGCGCTAGCTCACC
1 GTATAGCGCGGTGCAGGGGGCGCGCTATACCCACGTTGCGCCAAATCACA
* *
31930 GTATAGCGCGGTGCAGGGGGTGCGCTATACCCCACG-TGACGCCAAATCATA
1 GTATAGCGCGGTGCAGGGGGCGCGCTATA-CCCACGTTG-CGCCAAATCACA
31981 GTATAGCGCGGTGCAGGGGGCGCGCT
1 GTATAGCGCGGTGCAGGGGGCGCGCT
32007 TTACTGCTAA
Statistics
Matches: 66, Mismatches: 9, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
50 28 0.42
51 38 0.58
ACGTcount: A:0.18, C:0.30, G:0.35, T:0.17
Consensus pattern (50 bp):
GTATAGCGCGGTGCAGGGGGCGCGCTATACCCACGTTGCGCCAAATCACA
Found at i:33378 original size:14 final size:15
Alignment explanation
Indices: 33359--33391 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
33349 CTAAATTGGT
33359 GTTGCAGCTGCGG-A
1 GTTGCAGCTGCGGAA
*
33373 GTTGCAGTTGCGGAA
1 GTTGCAGCTGCGGAA
33388 GTTG
1 GTTG
33392 TAGATGTTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.15, C:0.15, G:0.42, T:0.27
Consensus pattern (15 bp):
GTTGCAGCTGCGGAA
Found at i:35553 original size:16 final size:16
Alignment explanation
Indices: 35532--35565 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
35522 TTACTATTCA
*
35532 CGTGAATAGTGAATTT
1 CGTGAATAGTGAAATT
35548 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
35564 CG
1 CG
35566 GTCGGCGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.32
Consensus pattern (16 bp):
CGTGAATAGTGAAATT
Found at i:36333 original size:15 final size:16
Alignment explanation
Indices: 36315--36347 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
36305 GTGGCAGATC
36315 AAAATCCAG-ACGGGA
1 AAAATCCAGAACGGGA
*
36330 AAAATCTAGAACGGGA
1 AAAATCCAGAACGGGA
36346 AA
1 AA
36348 GAAAGATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.52, C:0.15, G:0.24, T:0.09
Consensus pattern (16 bp):
AAAATCCAGAACGGGA
Found at i:40821 original size:24 final size:25
Alignment explanation
Indices: 40793--40839 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
40783 TCGGGCCGGA
40793 TATATATATATTTAAATT-AAATAT
1 TATATATATATTTAAATTGAAATAT
* *
40817 TATATATATTTTTTAATTGAAAT
1 TATATATATATTTAAATTGAAAT
40840 TAAATTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (25 bp):
TATATATATATTTAAATTGAAATAT
Found at i:46631 original size:17 final size:17
Alignment explanation
Indices: 46609--46644 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
46599 AGTTATTAAC
* *
46609 AACTGTTTAAATCTATT
1 AACTGTTAAAATCAATT
46626 AACTGTTAAAATCAATT
1 AACTGTTAAAATCAATT
46643 AA
1 AA
46645 TGACTTCTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.44, C:0.11, G:0.06, T:0.39
Consensus pattern (17 bp):
AACTGTTAAAATCAATT
Found at i:49038 original size:19 final size:19
Alignment explanation
Indices: 49014--49058 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
49004 GTTTTGTAGG
49014 GGGAATGTGAGATTCCCAT
1 GGGAATGTGAGATTCCCAT
49033 GGGAATGTGAGATTCCCAT
1 GGGAATGTGAGATTCCCAT
49052 GGGAATG
1 GGGAATG
49059 GAATCCACAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.27, C:0.13, G:0.36, T:0.24
Consensus pattern (19 bp):
GGGAATGTGAGATTCCCAT
Found at i:49630 original size:18 final size:19
Alignment explanation
Indices: 49607--49650 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
49597 TCCATAATCC
*
49607 TATTCC-CTGATAATCTTT
1 TATTCCACTGATAATCTTA
*
49625 TATTCCCACTGGTAATCTTA
1 TATT-CCACTGATAATCTTA
49645 TATTCC
1 TATTCC
49651 GTGAACCAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 4 0.18
19 4 0.18
20 14 0.64
ACGTcount: A:0.23, C:0.25, G:0.07, T:0.45
Consensus pattern (19 bp):
TATTCCACTGATAATCTTA
Found at i:50519 original size:30 final size:29
Alignment explanation
Indices: 50466--50541 Score: 84
Period size: 30 Copynumber: 2.7 Consensus size: 29
50456 TCTGCATAAA
* *
50466 ATATGTATATCACATAT--AAAAAAATTT
1 ATATGGATATCACATATGGAAAAAAATAT
50493 ATATGGATATCACATATGGAAAAAAAATAT
1 ATATGGATATCACATATGG-AAAAAAATAT
* * *
50523 ACATAGATATCATATATGG
1 ATATGGATATCACATATGG
50542 TTACAGGAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
27 16 0.39
30 25 0.61
ACGTcount: A:0.50, C:0.08, G:0.11, T:0.32
Consensus pattern (29 bp):
ATATGGATATCACATATGGAAAAAAATAT
Found at i:56739 original size:41 final size:41
Alignment explanation
Indices: 56682--56761 Score: 142
Period size: 41 Copynumber: 2.0 Consensus size: 41
56672 AATTCATGAC
56682 CGAGTCAAACTACCGGGGATCGAAAACCAATCAAGACTGAT
1 CGAGTCAAACTACCGGGGATCGAAAACCAATCAAGACTGAT
* *
56723 CGAGTCTAACTACCGGGGATCGAAAACCAATCGAGACTG
1 CGAGTCAAACTACCGGGGATCGAAAACCAATCAAGACTG
56762 TCACGATCTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.36, C:0.25, G:0.24, T:0.15
Consensus pattern (41 bp):
CGAGTCAAACTACCGGGGATCGAAAACCAATCAAGACTGAT
Done.