Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001091.1 Hibiscus syriacus cultivar Beakdansim tig00002157_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: 65805
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Found at i:554 original size:13 final size:13
Alignment explanation
Indices: 536--560 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
526 TTTATTGCAT
536 TATATATATATAA
1 TATATATATATAA
549 TATATATATATA
1 TATATATATATA
561 TATTTATTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TATATATATATAA
Found at i:1862 original size:31 final size:31
Alignment explanation
Indices: 1793--1870 Score: 95
Period size: 31 Copynumber: 2.5 Consensus size: 31
1783 GTCACTGAAC
* *
1793 TTGTAATTTGAT-CCTAGAATTTCTTTTTAA
1 TTGTAATTTGATCCCTAGAATTTATTTGTAA
* * *
1823 ATGCAATTTGATCCCTGGAATTTATTTGTAA
1 TTGTAATTTGATCCCTAGAATTTATTTGTAA
*
1854 TTGTAATTTAATCCCTA
1 TTGTAATTTGATCCCTA
1871 ATTCCTTGTT
Statistics
Matches: 38, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
30 10 0.26
31 28 0.74
ACGTcount: A:0.28, C:0.13, G:0.12, T:0.47
Consensus pattern (31 bp):
TTGTAATTTGATCCCTAGAATTTATTTGTAA
Found at i:16612 original size:34 final size:30
Alignment explanation
Indices: 16573--16641 Score: 86
Period size: 30 Copynumber: 2.2 Consensus size: 30
16563 GGATATAACA
*
16573 AATTTAAGGCAAAATGGTTTTTGGACTTGAATTG
1 AATTTAA--CAAAAT-GTTTTTAGACTT-AATTG
16607 AATTT-ACAAAATGTTTTTAGACTTAATTG
1 AATTTAACAAAATGTTTTTAGACTTAATTG
16636 AATTTA
1 AATTTA
16642 TTCAAAGTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
29 10 0.30
30 11 0.33
31 6 0.18
33 1 0.03
34 5 0.15
ACGTcount: A:0.36, C:0.06, G:0.16, T:0.42
Consensus pattern (30 bp):
AATTTAACAAAATGTTTTTAGACTTAATTG
Found at i:16652 original size:29 final size:30
Alignment explanation
Indices: 16582--16641 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 30
16572 AAATTTAAGG
*
16582 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTAGACTTGAATTGAATTTA
16613 CAAAATGTTTTTAGACTT-AATTGAATTTA
1 CAAAATGTTTTTAGACTTGAATTGAATTTA
16642 TTCAAAGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.35, C:0.07, G:0.15, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTAGACTTGAATTGAATTTA
Found at i:16747 original size:21 final size:21
Alignment explanation
Indices: 16721--16799 Score: 149
Period size: 21 Copynumber: 3.8 Consensus size: 21
16711 AGGGTGTCAA
16721 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACCCCTGC
16742 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACCCCTGC
*
16763 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCACCCCTGC
16784 AGTGCATCCATGCACC
1 AGTGCATCCATGCACC
16800 TGCACTAGTG
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 56 1.00
ACGTcount: A:0.20, C:0.41, G:0.19, T:0.20
Consensus pattern (21 bp):
AGTGCATCCATGCACCCCTGC
Found at i:16782 original size:42 final size:43
Alignment explanation
Indices: 16721--16840 Score: 158
Period size: 42 Copynumber: 2.8 Consensus size: 43
16711 AGGGTGTCAA
*
16721 AGTGCATCCATGCACCCCTGCAGTGCATCCATGCACCCCTG-C-
1 AGTGCATCCATGCATCCCTGCAGTGCATCCATGCA-CCCTGACT
16763 AGTGCATCCATGCATCCCTGCAGTGCATCCATGCA-CCTGCACT
1 AGTGCATCCATGCATCCCTGCAGTGCATCCATGCACCCTG-ACT
* * *
16806 AGTGCATCGATGCAT-CATACAGTGCATCCATGCAC
1 AGTGCATCCATGCATCCCTGCAGTGCATCCATGCAC
16841 TCAAACACCG
Statistics
Matches: 70, Mismatches: 4, Indels: 7
0.86 0.05 0.09
Matches are distributed among these distances:
40 4 0.06
42 52 0.74
43 14 0.20
ACGTcount: A:0.23, C:0.37, G:0.19, T:0.22
Consensus pattern (43 bp):
AGTGCATCCATGCATCCCTGCAGTGCATCCATGCACCCTGACT
Found at i:16889 original size:20 final size:20
Alignment explanation
Indices: 16861--16928 Score: 91
Period size: 20 Copynumber: 3.4 Consensus size: 20
16851 AATGCAATTA
*
16861 GTGCATCGATGCATCCTTCT
1 GTGCATCGATGCATCCTGCT
* **
16881 GTTCATCGATGCATCAAGGCT
1 GTGCATCGATGCATC-CTGCT
16902 GTGCATCGATGCATCCTGCT
1 GTGCATCGATGCATCCTGCT
16922 GTGCATC
1 GTGCATC
16929 CATACACGAA
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 24 0.60
21 16 0.40
ACGTcount: A:0.18, C:0.28, G:0.24, T:0.31
Consensus pattern (20 bp):
GTGCATCGATGCATCCTGCT
Found at i:16941 original size:41 final size:41
Alignment explanation
Indices: 16861--16943 Score: 114
Period size: 41 Copynumber: 2.0 Consensus size: 41
16851 AATGCAATTA
* * * *
16861 GTGCATCGATGCATCCTTCTGTTCATCGATGCATCAAGGCT
1 GTGCATCGATGCATCCTGCTGTGCATCCATACATCAAGGCT
16902 GTGCATCGATGCATCCTGCTGTGCATCCATACA-CGAAGGCT
1 GTGCATCGATGCATCCTGCTGTGCATCCATACATC-AAGGCT
16943 G
1 G
16944 CAACGACTAG
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
40 1 0.03
41 36 0.97
ACGTcount: A:0.20, C:0.28, G:0.24, T:0.28
Consensus pattern (41 bp):
GTGCATCGATGCATCCTGCTGTGCATCCATACATCAAGGCT
Found at i:17064 original size:20 final size:22
Alignment explanation
Indices: 17026--17065 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
17016 TTTGAGTAGA
17026 AAAATCATCCCCAAACGGCTCT
1 AAAATCATCCCCAAACGGCTCT
17048 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
17066 ATATACAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCT
Found at i:17737 original size:63 final size:63
Alignment explanation
Indices: 17663--17792 Score: 260
Period size: 63 Copynumber: 2.1 Consensus size: 63
17653 ACCAATTCCC
17663 GACACAACTGAGAAGATGGCTTCCACCTCCGGCTCGTTCCACATGGAAGACTCCCTACCAACG
1 GACACAACTGAGAAGATGGCTTCCACCTCCGGCTCGTTCCACATGGAAGACTCCCTACCAACG
17726 GACACAACTGAGAAGATGGCTTCCACCTCCGGCTCGTTCCACATGGAAGACTCCCTACCAACG
1 GACACAACTGAGAAGATGGCTTCCACCTCCGGCTCGTTCCACATGGAAGACTCCCTACCAACG
17789 GACA
1 GACA
17793 AGCCTCCATA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 67 1.00
ACGTcount: A:0.28, C:0.35, G:0.21, T:0.17
Consensus pattern (63 bp):
GACACAACTGAGAAGATGGCTTCCACCTCCGGCTCGTTCCACATGGAAGACTCCCTACCAACG
Found at i:19603 original size:34 final size:30
Alignment explanation
Indices: 19564--19632 Score: 95
Period size: 30 Copynumber: 2.2 Consensus size: 30
19554 GGATATAACA
19564 AATTTAAGGCAAAATGATTTTTGGACTTGAATTG
1 AATTTAA--CAAAATG-TTTTTGGACTT-AATTG
19598 AATTT-ACAAAATGTTTTTGGACTTAATTG
1 AATTTAACAAAATGTTTTTGGACTTAATTG
19627 AATTTA
1 AATTTA
19633 TTCAAAGTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
29 10 0.29
30 11 0.32
31 7 0.21
33 1 0.03
34 5 0.15
ACGTcount: A:0.36, C:0.06, G:0.16, T:0.42
Consensus pattern (30 bp):
AATTTAACAAAATGTTTTTGGACTTAATTG
Found at i:19643 original size:29 final size:30
Alignment explanation
Indices: 19573--19632 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 30
19563 AAATTTAAGG
19573 CAAAATGATTTTTGGACTTGAATTGAATTTA
1 CAAAATG-TTTTTGGACTTGAATTGAATTTA
19604 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
19633 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.35, C:0.07, G:0.15, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:19780 original size:20 final size:20
Alignment explanation
Indices: 19712--19882 Score: 81
Period size: 20 Copynumber: 8.7 Consensus size: 20
19702 AGGGTGTCAA
*
19712 AGTGCATCCATGCATCCCTGC
1 AGTGCATCGATGCAT-CCTGC
*
19733 AGTGCATCCATGCA-CCTGCAC
1 AGTGCATCGATGCATCCTG--C
*
19754 TAGTGCATCGATGCATCATGC
1 -AGTGCATCGATGCATCCTGC
*
19775 AGTGCATCCATGCA--CT-C
1 AGTGCATCGATGCATCCTGC
** * *
19792 A-AACACCGAATACAAT--T--
1 AGTGCATCG-ATGC-ATCCTGC
* *
19809 AGTGCGTCGATGCATCCTTC
1 AGTGCATCGATGCATCCTGC
* **
19829 TGTGCATCGATGCATCAAGC
1 AGTGCATCGATGCATCCTGC
*
19849 TGTGCATCGATGCATCCTGC
1 AGTGCATCGATGCATCCTGC
* *
19869 TGTGCATCCATGCA
1 AGTGCATCGATGCA
19883 CGAAGGCTGC
Statistics
Matches: 116, Mismatches: 22, Indels: 25
0.71 0.13 0.15
Matches are distributed among these distances:
16 5 0.04
17 9 0.08
18 7 0.06
19 4 0.03
20 59 0.51
21 16 0.14
22 13 0.11
23 3 0.03
ACGTcount: A:0.24, C:0.30, G:0.20, T:0.25
Consensus pattern (20 bp):
AGTGCATCGATGCATCCTGC
Found at i:24664 original size:3 final size:3
Alignment explanation
Indices: 24643--24681 Score: 53
Period size: 3 Copynumber: 12.7 Consensus size: 3
24633 AAGAAAAGAA
24643 AAT AATT AA- AAT AAAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AA-T AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AA
24682 AGAGTTAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
2 2 0.06
3 25 0.76
4 6 0.18
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:34222 original size:20 final size:20
Alignment explanation
Indices: 34199--34292 Score: 75
Period size: 20 Copynumber: 4.4 Consensus size: 20
34189 TGTCTGATCC
34199 TAATATATTTTGAAAATATA
1 TAATATATTTTGAAAATATA
34219 TAATATACTTTTGAAACATATGCA
1 TAATATA-TTTTGAAA-ATAT--A
*
34243 TAATATATAATTTTGAAAACATA
1 T-A-ATAT-ATTTTGAAAATATA
* *
34266 T-GTAT-TTTTGAATATATA
1 TAATATATTTTGAAAATATA
34284 TATATATAT
1 TA-ATATAT
34293 ATATAATTTT
Statistics
Matches: 59, Mismatches: 5, Indels: 19
0.71 0.06 0.23
Matches are distributed among these distances:
18 12 0.20
20 13 0.22
21 9 0.15
22 4 0.07
23 2 0.03
24 2 0.03
25 4 0.07
26 12 0.20
27 1 0.02
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (20 bp):
TAATATATTTTGAAAATATA
Found at i:34275 original size:44 final size:48
Alignment explanation
Indices: 34201--34354 Score: 142
Period size: 46 Copynumber: 3.3 Consensus size: 48
34191 TCTGATCCTA
* *
34201 ATAT-ATTTTGAAAATATATAATATACTTTTGAA-ACATATGCATA-AT
1 ATATAATTTTGAAAACATATAATATA-TTTTGAATACATATACATATAT
* * *
34247 ATATAATTTTGAAAACATAT-GTAT-TTTTGAATATATATATATATAT
1 ATATAATTTTGAAAACATATAATATATTTTGAATACATATACATATAT
* * * *
34293 ATATAATTTTGAAAACATATATTAATTTTTTAAAAACATAT--ATAGTAT
1 ATATAATTTTGAAAACATATAAT-ATATTTTGAATACATATACATA-TAT
*
34341 ATATAGTTTTGAAA
1 ATATAATTTTGAAA
34355 TTATAATATA
Statistics
Matches: 91, Mismatches: 10, Indels: 12
0.81 0.09 0.11
Matches are distributed among these distances:
44 7 0.08
45 8 0.09
46 29 0.32
47 18 0.20
48 18 0.20
49 11 0.12
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.44
Consensus pattern (48 bp):
ATATAATTTTGAAAACATATAATATATTTTGAATACATATACATATAT
Found at i:34304 original size:46 final size:48
Alignment explanation
Indices: 34245--34354 Score: 145
Period size: 48 Copynumber: 2.3 Consensus size: 48
34235 CATATGCATA
* *
34245 ATATATAATTTTGAAAACATAT-GT-ATTTTTGAATATATATATATA-T
1 ATATATAATTTTGAAAACATATAGTAATTTTTGAA-AAACATATATAGT
* *
34291 ATATATAATTTTGAAAACATATATTAATTTTTTAAAAACATATATAGT
1 ATATATAATTTTGAAAACATATAGTAATTTTTGAAAAACATATATAGT
*
34339 ATATATAGTTTTGAAA
1 ATATATAATTTTGAAA
34355 TTATAATATA
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
46 22 0.39
47 10 0.18
48 24 0.43
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.45
Consensus pattern (48 bp):
ATATATAATTTTGAAAACATATAGTAATTTTTGAAAAACATATATAGT
Found at i:34342 original size:48 final size:46
Alignment explanation
Indices: 34232--34354 Score: 142
Period size: 48 Copynumber: 2.6 Consensus size: 46
34222 TATACTTTTG
34232 AAACATATGCATA-ATATATAATTTTGAAAACATATGTATTTTTGAAT
1 AAACATAT--ATATATATATAATTTTGAAAACATATGTATTTTTGAAT
* * * *
34279 ATATATATATATATATATAATTTTGAAAACATATATTAATTTTTTAA-
1 AAACATATATATATATATAATTTTGAAAACATAT-GT-ATTTTTGAAT
*
34326 AAACATATATAGTATATATAGTTTTGAAA
1 AAACATATATA-TATATATAATTTTGAAA
34355 TTATAATATA
Statistics
Matches: 65, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
45 3 0.05
46 22 0.34
47 16 0.25
48 24 0.37
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.43
Consensus pattern (46 bp):
AAACATATATATATATATAATTTTGAAAACATATGTATTTTTGAAT
Found at i:34396 original size:43 final size:43
Alignment explanation
Indices: 34340--34462 Score: 153
Period size: 43 Copynumber: 2.8 Consensus size: 43
34330 ATATATAGTA
** *
34340 TATATAGTTTTGAAATTATA-ATAT-A-ATAATTTTGAAATTAT
1 TATATAGTTTTGAAAACATATATATAATATAATTTTGAAAGT-T
34381 AGTATATAGTTTTGAAAACATATATATAATATAATTTTGAAAGTT
1 --TATATAGTTTTGAAAACATATATATAATATAATTTTGAAAGTT
*
34426 TATATAGTTTTGAAAACATATATATATATATTATTTT
1 TATATAGTTTTGAAAACATATATATA-ATATAATTTT
34463 ATTTTCCAGT
Statistics
Matches: 72, Mismatches: 4, Indels: 7
0.87 0.05 0.08
Matches are distributed among these distances:
43 44 0.61
44 13 0.18
45 2 0.03
46 13 0.18
ACGTcount: A:0.43, C:0.02, G:0.08, T:0.47
Consensus pattern (43 bp):
TATATAGTTTTGAAAACATATATATAATATAATTTTGAAAGTT
Found at i:37021 original size:15 final size:15
Alignment explanation
Indices: 36979--37023 Score: 54
Period size: 17 Copynumber: 2.9 Consensus size: 15
36969 TTCTTTCTCT
*
36979 TTTTTTTTATAATGA
1 TTTTTTTTATTATGA
36994 TATTTGTTTTATTATGA
1 T-TTT-TTTTATTATGA
*
37011 TTTTTTATATTAT
1 TTTTTTTTATTAT
37024 TCTTGGAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
15 9 0.35
16 6 0.23
17 11 0.42
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69
Consensus pattern (15 bp):
TTTTTTTTATTATGA
Found at i:58548 original size:12 final size:12
Alignment explanation
Indices: 58531--58555 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
58521 ATTTTCCTTA
58531 GATAAAGTTCTT
1 GATAAAGTTCTT
58543 GATAAAGTTCTT
1 GATAAAGTTCTT
58555 G
1 G
58556 TTACTTTATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.08, G:0.20, T:0.40
Consensus pattern (12 bp):
GATAAAGTTCTT
Done.