Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000079.1 Hibiscus syriacus cultivar Beakdansim tig00000143_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: 36690
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:7266 original size:21 final size:21
Alignment explanation
Indices: 7231--7289 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 21
7221 CGGGCTAAGG
* *
7231 GTTTAGGAATAAGGGTTTAT-
1 GTTTAGGATTTAGGGTTTATA
7251 GATTTAAGG-TTTAGGGTTTATA
1 G-TTT-AGGATTTAGGGTTTATA
7273 GTTTAGGATTTAGGGTT
1 GTTTAGGATTTAGGGTT
7290 CATTGTAAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
20 4 0.12
21 25 0.76
22 4 0.12
ACGTcount: A:0.25, C:0.00, G:0.31, T:0.44
Consensus pattern (21 bp):
GTTTAGGATTTAGGGTTTATA
Found at i:7270 original size:14 final size:14
Alignment explanation
Indices: 7230--7289 Score: 52
Period size: 14 Copynumber: 4.3 Consensus size: 14
7220 TCGGGCTAAG
*
7230 GGTTTAGGA-ATAA
1 GGTTTAGGATTTAA
*
7243 GGGTTTATGATTTAA
1 -GGTTTAGGATTTAA
*
7258 GGTTTAGGGTTTATA
1 GGTTTAGGATTTA-A
*
7273 -GTTTAGGATTTAG
1 GGTTTAGGATTTAA
7286 GGTT
1 GGTT
7290 CATTGTAAAG
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
14 33 0.89
15 4 0.11
ACGTcount: A:0.25, C:0.00, G:0.32, T:0.43
Consensus pattern (14 bp):
GGTTTAGGATTTAA
Found at i:7471 original size:11 final size:11
Alignment explanation
Indices: 7455--7517 Score: 60
Period size: 11 Copynumber: 5.9 Consensus size: 11
7445 GTATTATAAA
7455 ATTTTTAATAT
1 ATTTTTAATAT
7466 ATTTTTAA-A-
1 ATTTTTAATAT
7475 ATTTTATAAT-T
1 ATTTT-TAATAT
** * *
7486 ATTAATAGTGT
1 ATTTTTAATAT
7497 ATTTTTAATAT
1 ATTTTTAATAT
7508 ATTTTTAATA
1 ATTTTTAATA
7518 ATGTAATTTT
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
9 5 0.12
10 7 0.17
11 29 0.71
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (11 bp):
ATTTTTAATAT
Found at i:7476 original size:20 final size:20
Alignment explanation
Indices: 7451--7488 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
7441 AGTTGTATTA
7451 TAAAATTTT-TAATATATTTT
1 TAAAATTTTATAAT-TATTTT
7471 TAAAATTTTATAATTATT
1 TAAAATTTTATAATTATT
7489 AATAGTGTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
TAAAATTTTATAATTATTTT
Found at i:8793 original size:12 final size:12
Alignment explanation
Indices: 8776--8801 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
8766 TTTTAATATT
8776 TATCGGGCCGGA
1 TATCGGGCCGGA
8788 TATCGGGCCGGA
1 TATCGGGCCGGA
8800 TA
1 TA
8802 ATTGGGTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.19, C:0.23, G:0.38, T:0.19
Consensus pattern (12 bp):
TATCGGGCCGGA
Found at i:8870 original size:28 final size:29
Alignment explanation
Indices: 8838--8893 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 29
8828 AAACTCGTTC
8838 CCGTCCCCGTTTAACATAAAC-ATTTTTA
1 CCGTCCCCGTTTAACATAAACGATTTTTA
8866 CCGTCCCCGTTTAACATAAACGATTTTT
1 CCGTCCCCGTTTAACATAAACGATTTTT
8894 TCTCATCCCG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
28 21 0.78
29 6 0.22
ACGTcount: A:0.27, C:0.29, G:0.09, T:0.36
Consensus pattern (29 bp):
CCGTCCCCGTTTAACATAAACGATTTTTA
Found at i:8903 original size:29 final size:28
Alignment explanation
Indices: 8841--8908 Score: 93
Period size: 28 Copynumber: 2.4 Consensus size: 28
8831 CTCGTTCCCG
*
8841 TCCCCGTTTAACATAAACATTTTTACCG
1 TCCCCGTTTAACATAAACATTTTTACCA
*
8869 TCCCCGTTTAACATAAACGATTTTTTCTCA
1 TCCCCGTTTAACATAAAC-ATTTTTAC-CA
8899 T-CCCGTTTAA
1 TCCCCGTTTAA
8909 TTCGATTTTC
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
28 18 0.50
29 16 0.44
30 2 0.06
ACGTcount: A:0.26, C:0.28, G:0.07, T:0.38
Consensus pattern (28 bp):
TCCCCGTTTAACATAAACATTTTTACCA
Found at i:19814 original size:20 final size:20
Alignment explanation
Indices: 19789--19828 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
19779 AACACGTATA
19789 GCTTGACAAAACTTGATTTC
1 GCTTGACAAAACTTGATTTC
19809 GCTTGACAAAACTTGATTTC
1 GCTTGACAAAACTTGATTTC
19829 TCAAAGACTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (20 bp):
GCTTGACAAAACTTGATTTC
Found at i:24094 original size:30 final size:30
Alignment explanation
Indices: 24060--24122 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
24050 CCTTTAATAA
*
24060 ATTGGCATAATAATAAATTTGGTCCTTAAT
1 ATTGGCATAATAATAAATTTAGTCCTTAAT
* *
24090 ATTGGCATAATTATATATTTAGTCCTTAAT
1 ATTGGCATAATAATAAATTTAGTCCTTAAT
24120 ATT
1 ATT
24123 TACATATTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.35, C:0.10, G:0.11, T:0.44
Consensus pattern (30 bp):
ATTGGCATAATAATAAATTTAGTCCTTAAT
Found at i:24144 original size:31 final size:29
Alignment explanation
Indices: 24060--24144 Score: 80
Period size: 30 Copynumber: 2.8 Consensus size: 29
24050 CCTTTAATAA
* * *
24060 ATTGGCATAATAATAAATTTGGTCCTTAAT
1 ATTGACATAATTAT-AATTTAGTCCTTAAT
*
24090 ATTGGCATAATTATATATTTAGTCCTTAAT
1 ATTGACATAATTATA-ATTTAGTCCTTAAT
* *
24120 ATTTACATATTTTATCAATTTAGTC
1 ATTGACATA-ATTAT-AATTTAGTC
24145 ACTATTTTAG
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
29 1 0.02
30 33 0.70
31 12 0.26
32 1 0.02
ACGTcount: A:0.34, C:0.11, G:0.09, T:0.46
Consensus pattern (29 bp):
ATTGACATAATTATAATTTAGTCCTTAAT
Found at i:24685 original size:94 final size:93
Alignment explanation
Indices: 24552--24955 Score: 539
Period size: 94 Copynumber: 4.5 Consensus size: 93
24542 AATTATTTTA
* * * * *
24552 TTCGATTAATAATTTTTAAATAAATTTCGATTAGATTAACGGCCAAATAATTTCGGTTCGATTAA
1 TTCGGTTAATAATTTTCAAATAAATTTCGGTTCGATTAACGGTCAAATAATTTCGGTTCGATTAA
*
24617 TGGTTAAAGAAAAAAATCGGTTGATTTGG
66 T-GTTAAAGAAAAAAATCGGTTAATTTGG
* *
24646 TTCGGTTAATAATTTTCAAATAAATTTGGGTTCGATTAACGGTCAAATAATTTTGGTTCGATTAA
1 TTCGGTTAATAATTTTCAAATAAATTTCGGTTCGATTAACGGTCAAATAATTTCGGTTCGATTAA
24711 TGGTTAAAG--AAAAA------AA-----
66 T-GTTAAAGAAAAAAATCGGTTAATTTGG
*
24727 TTCGGTTAATAATTTTCAAATAAATTTCGGTTCGATTAACGGTCAAATAATTTCGGTTCAATTAA
1 TTCGGTTAATAATTTTCAAATAAATTTCGGTTCGATTAACGGTCAAATAATTTCGGTTCGATTAA
*
24792 TGTTAAAGAAAAAAATTTGGTTAATTTGG
66 TGTTAAAGAAAAAAA-TCGGTTAATTTGG
** * *
24821 TTCAATTAATAATTTTCAAATAAATTTCGGTTTGATTAACGGTCAAATAATTTCAGTTCGATTAA
1 TTCGGTTAATAATTTTCAAATAAATTTCGGTTCGATTAACGGTCAAATAATTTCGGTTCGATTAA
*
24886 TGTTAAAGAAAAAATTCGGTTAATTTGG
66 TGTTAAAGAAAAAAATCGGTTAATTTGG
*
24914 TTCGGTTAATAATTTT-AAATAAATTTTGGTTCGATTAACGGT
1 TTCGGTTAATAATTTTCAAATAAATTTCGGTTCGATTAACGGT
24956 TAAAGAAAAA
Statistics
Matches: 274, Mismatches: 22, Indels: 30
0.84 0.07 0.09
Matches are distributed among these distances:
80 7 0.03
81 63 0.23
82 5 0.02
86 1 0.00
89 2 0.01
92 29 0.11
93 26 0.09
94 141 0.51
ACGTcount: A:0.37, C:0.08, G:0.16, T:0.39
Consensus pattern (93 bp):
TTCGGTTAATAATTTTCAAATAAATTTCGGTTCGATTAACGGTCAAATAATTTCGGTTCGATTAA
TGTTAAAGAAAAAAATCGGTTAATTTGG
Found at i:24693 original size:27 final size:27
Alignment explanation
Indices: 24661--24791 Score: 108
Period size: 26 Copynumber: 4.9 Consensus size: 27
24651 TTAATAATTT
*
24661 TCAAATAAATTTGGGTTCGATTAACGG
1 TCAAATAAATTTCGGTTCGATTAACGG
* *
24688 TCAAAT-AATTTTGGTTCGATTAATGG
1 TCAAATAAATTTCGGTTCGATTAACGG
* * * * ***
24714 TTAAAGAAAAAAATTCGGTT--AATAATTT
1 -T-CA-AATAAATTTCGGTTCGATTAACGG
24742 TCAAATAAATTTCGGTTCGATTAACGG
1 TCAAATAAATTTCGGTTCGATTAACGG
*
24769 TCAAAT-AATTTCGGTTCAATTAA
1 TCAAATAAATTTCGGTTCGATTAA
24792 TGTTAAAGAA
Statistics
Matches: 81, Mismatches: 17, Indels: 13
0.73 0.15 0.12
Matches are distributed among these distances:
25 12 0.15
26 35 0.43
27 18 0.22
28 6 0.07
29 2 0.02
30 8 0.10
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.37
Consensus pattern (27 bp):
TCAAATAAATTTCGGTTCGATTAACGG
Found at i:24785 original size:81 final size:80
Alignment explanation
Indices: 24646--24816 Score: 297
Period size: 81 Copynumber: 2.1 Consensus size: 80
24636 GTTGATTTGG
* * *
24646 TTCGGTTAATAATTTTCAAATAAATTTGGGTTCGATTAACGGTCAAATAATTTTGGTTCGATTAA
1 TTCGGTTAATAATTTTCAAATAAATTTCGGTTCGATTAACGGTCAAATAATTTCGGTTCAATTAA
24711 TGGTTAAAGAAAAAAA
66 T-GTTAAAGAAAAAAA
24727 TTCGGTTAATAATTTTCAAATAAATTTCGGTTCGATTAACGGTCAAATAATTTCGGTTCAATTAA
1 TTCGGTTAATAATTTTCAAATAAATTTCGGTTCGATTAACGGTCAAATAATTTCGGTTCAATTAA
24792 TGTTAAAGAAAAAAA
66 TGTTAAAGAAAAAAA
*
24807 TTTGGTTAAT
1 TTCGGTTAAT
24817 TTGGTTCAAT
Statistics
Matches: 86, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
80 23 0.27
81 63 0.73
ACGTcount: A:0.38, C:0.08, G:0.16, T:0.38
Consensus pattern (80 bp):
TTCGGTTAATAATTTTCAAATAAATTTCGGTTCGATTAACGGTCAAATAATTTCGGTTCAATTAA
TGTTAAAGAAAAAAA
Found at i:24860 original size:175 final size:173
Alignment explanation
Indices: 24551--24909 Score: 558
Period size: 175 Copynumber: 2.1 Consensus size: 173
24541 AAATTATTTT
* * *
24551 ATTCGATTAATAATTTTTAAATAAATTTCGATTAGATTAACGGCCAAATAATTTCGGTTCGATTA
1 ATTCGGTTAATAATTTTCAAATAAATTTCGATTAGATTAACGGCCAAATAATTTCGGTTCAATTA
* ** *
24616 ATGGTTAAAGAAAAAAATCGGTTGATTTGGTTCGGTTAATAATTTTCAAATAAATTTGGGTTCGA
66 ATGGTTAAAGAAAAAAATCGGTTAATTTGGTTCAATTAATAATTTTCAAATAAATTTCGGTTCGA
**
24681 TTAACGGTCAAATAATTTTGGTTCGATTAATGGTTAAAGAAAAAA
131 TTAACGGTCAAATAATTTCAGTTCGATTAAT-GTTAAAG-AAAAA
* * *
24726 ATTCGGTTAATAATTTTCAAATAAATTTCGGTTCGATTAACGGTCAAATAATTTCGGTTCAATTA
1 ATTCGGTTAATAATTTTCAAATAAATTTCGATTAGATTAACGGCCAAATAATTTCGGTTCAATTA
* *
24791 AT-GTTAAAGAAAAAAATTTGGTTAATTTGGTTCAATTAATAATTTTCAAATAAATTTCGGTTTG
66 ATGGTTAAAGAAAAAAA-TCGGTTAATTTGGTTCAATTAATAATTTTCAAATAAATTTCGGTTCG
24855 ATTAACGGTCAAATAATTTCAGTTCGATTAATGTTAAAGAAAAA
130 ATTAACGGTCAAATAATTTCAGTTCGATTAATGTTAAAGAAAAA
24899 ATTCGGTTAAT
1 ATTCGGTTAAT
24910 TTGGTTCGGT
Statistics
Matches: 169, Mismatches: 14, Indels: 4
0.90 0.07 0.02
Matches are distributed among these distances:
173 16 0.09
174 21 0.12
175 132 0.78
ACGTcount: A:0.38, C:0.08, G:0.16, T:0.38
Consensus pattern (173 bp):
ATTCGGTTAATAATTTTCAAATAAATTTCGATTAGATTAACGGCCAAATAATTTCGGTTCAATTA
ATGGTTAAAGAAAAAAATCGGTTAATTTGGTTCAATTAATAATTTTCAAATAAATTTCGGTTCGA
TTAACGGTCAAATAATTTCAGTTCGATTAATGTTAAAGAAAAA
Found at i:25044 original size:64 final size:62
Alignment explanation
Indices: 24863--25047 Score: 194
Period size: 64 Copynumber: 2.9 Consensus size: 62
24853 TGATTAACGG
*
24863 TCAAAT-AATTTCAGTTCGATTAAT-GTTAAAGAAAAAATTCGGTTAATTTGGTTCGGTTAATAA
1 TCAAATAAATTTCGGTTCGATTAATGGTTAAAGAAAAAATTCGGTTAA-----TTCGGTTAATAA
24926 TT
61 TT
* * * *** *
24928 TTAAATAAATTTTGGTTCGATTAACGGTTAAAGAAAAAAATTTATTTTATTCGGTTAATAATT
1 TCAAATAAATTTCGGTTCGATTAATGGTTAAAG-AAAAAATTCGGTTAATTCGGTTAATAATT
* *
24991 TCCAAATAAATTTCGGTTTGATTAATGGTTAAATGGAAAAATTCGGTTAATTCGGTT
1 T-CAAATAAATTTCGGTTCGATTAATGGTTAAA-GAAAAAATTCGGTTAATTCGGTT
25048 CGGTTAATAA
Statistics
Matches: 98, Mismatches: 17, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
63 15 0.15
64 44 0.45
65 6 0.06
66 15 0.15
67 7 0.07
68 11 0.11
ACGTcount: A:0.37, C:0.07, G:0.16, T:0.41
Consensus pattern (62 bp):
TCAAATAAATTTCGGTTCGATTAATGGTTAAAGAAAAAATTCGGTTAATTCGGTTAATAATT
Done.