Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004594.1 Hibiscus syriacus cultivar Beakdansim tig00010266_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: 49733
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:265 original size:64 final size:62
Alignment explanation
Indices: 197--341 Score: 182
Period size: 62 Copynumber: 2.3 Consensus size: 62
187 TACACTAAGA
* * * * * *
197 GTGCACCGATGCATGAAGTGCATTCAATGTTTCAAACAAGCCAGAGTGCATCGATGCATGGCCT
1 GTGCATCGATGCATAAAATACATTCAAT-TTTCAAA-AACCCAGAGTGCATCGATGCATGGCAT
* * * *
261 GTGCATCGATGCATAAAATACATTCGATTTTCATAAACCCTGAGTGCATCGATGCATGGTAT
1 GTGCATCGATGCATAAAATACATTCAATTTTCAAAAACCCAGAGTGCATCGATGCATGGCAT
323 GTGCATCGATGCATAAAAT
1 GTGCATCGATGCATAAAAT
342 GAATTCGATG
Statistics
Matches: 71, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
62 42 0.59
63 6 0.08
64 23 0.32
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (62 bp):
GTGCATCGATGCATAAAATACATTCAATTTTCAAAAACCCAGAGTGCATCGATGCATGGCAT
Found at i:8833 original size:64 final size:63
Alignment explanation
Indices: 8746--8903 Score: 226
Period size: 64 Copynumber: 2.5 Consensus size: 63
8736 TCTTAGTGCA
* * * * * *
8746 TGCACCGATGCATGAAGTGCATTCAATGTTTCAAACAAGCCAGAGTGCATCGATGCATGGTCTG
1 TGCATCGATGCATAAAATGCATTCGATGTTTCAAA-AACCCAGAGTGCATCGATGCATGGTATG
* *
8810 TGCATCGATGCATAAAATGCATTCGATGTTTTCATAAACCCTGAGTGCATCGATGCATGGTATG
1 TGCATCGATGCATAAAATGCATTCGATG-TTTCAAAAACCCAGAGTGCATCGATGCATGGTATG
8874 TGCATCGATGCATAAAATGCATTCGATGTT
1 TGCATCGATGCATAAAATGCATTCGATGTT
8904 CAATTTATTC
Statistics
Matches: 85, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
63 2 0.02
64 77 0.91
65 6 0.07
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.29
Consensus pattern (63 bp):
TGCATCGATGCATAAAATGCATTCGATGTTTCAAAAACCCAGAGTGCATCGATGCATGGTATG
Found at i:12286 original size:17 final size:17
Alignment explanation
Indices: 12264--12303 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
12254 ACATACATAT
12264 ATTTAGGTTAATTATAC
1 ATTTAGGTTAATTATAC
12281 ATTTAGGTTAATTATAC
1 ATTTAGGTTAATTATAC
12298 ATTTAG
1 ATTTAG
12304 TCCCTAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.35, C:0.05, G:0.12, T:0.47
Consensus pattern (17 bp):
ATTTAGGTTAATTATAC
Found at i:13615 original size:46 final size:46
Alignment explanation
Indices: 13540--13631 Score: 116
Period size: 46 Copynumber: 2.0 Consensus size: 46
13530 TTATATTATT
* * *
13540 TTATTTTTTGAATAAATGCATGCGAACTAGAAATCATGCGGTTAGG
1 TTATTTTTTGAACAAATGCATGCGAACTAGAAAGCATGAGGTTAGG
*
13586 TTATTTTTCCTGAACAAA-GCATG-GGACTAGAAAGCATGAGGTTAGG
1 TTATTTTT--TGAACAAATGCATGCGAACTAGAAAGCATGAGGTTAGG
13632 ATATGATTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
46 28 0.70
47 5 0.12
48 7 0.17
ACGTcount: A:0.33, C:0.12, G:0.24, T:0.32
Consensus pattern (46 bp):
TTATTTTTTGAACAAATGCATGCGAACTAGAAAGCATGAGGTTAGG
Found at i:25793 original size:1 final size:1
Alignment explanation
Indices: 25789--25862 Score: 67
Period size: 1 Copynumber: 74.0 Consensus size: 1
25779 TTTTTGGCTC
* ** *** * *
25789 TTTTTTGTTTTTTTGCTTTTTTTTTTTTTTTTTTTTTTTTTTTGCCTTTTTTTGTTTTTGTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
*
25854 TATTTTTTT
1 TTTTTTTTT
25863 GAAAAAAAAA
Statistics
Matches: 59, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 59 1.00
ACGTcount: A:0.01, C:0.04, G:0.07, T:0.88
Consensus pattern (1 bp):
T
Found at i:25807 original size:16 final size:15
Alignment explanation
Indices: 25788--25863 Score: 93
Period size: 16 Copynumber: 5.0 Consensus size: 15
25778 CTTTTTGGCT
25788 CTTTTTTGTTTTTTTG
1 CTTTTTT-TTTTTTTG
25804 CTTTTTTTTTTTTT-
1 CTTTTTTTTTTTTTG
*
25818 TTTTTTTTTTTTTTG
1 CTTTTTTTTTTTTTG
*
25833 CCTTTTTTTGTTTTTG
1 -CTTTTTTTTTTTTTG
25849 -TTTTTTATTTTTTTG
1 CTTTTTT-TTTTTTTG
25864 AAAAAAAAAT
Statistics
Matches: 53, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
14 19 0.36
15 14 0.26
16 20 0.38
ACGTcount: A:0.01, C:0.05, G:0.08, T:0.86
Consensus pattern (15 bp):
CTTTTTTTTTTTTTG
Found at i:25810 original size:18 final size:17
Alignment explanation
Indices: 25779--25831 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 17
25769 GAAATTTGGC
* *
25779 TTTTTGGCTCTTTTTTGT
1 TTTTTTGCT-TTTTTTTT
25797 TTTTTTGCTTTTTTTTT
1 TTTTTTGCTTTTTTTTT
25814 TTTTTT--TTTTTTTTT
1 TTTTTTGCTTTTTTTTT
25829 TTT
1 TTT
25832 GCCTTTTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
15 12 0.36
17 13 0.39
18 8 0.24
ACGTcount: A:0.00, C:0.06, G:0.08, T:0.87
Consensus pattern (17 bp):
TTTTTTGCTTTTTTTTT
Found at i:25821 original size:29 final size:31
Alignment explanation
Indices: 25789--25863 Score: 109
Period size: 31 Copynumber: 2.5 Consensus size: 31
25779 TTTTTGGCTC
* *
25789 TTTTTTGTTTTTTTG-CTTTTTTT-TTTTTT
1 TTTTTTATTTTTTTGCCTTTTTTTGTTTTTG
*
25818 TTTTTTTTTTTTTTGCCTTTTTTTGTTTTTG
1 TTTTTTATTTTTTTGCCTTTTTTTGTTTTTG
25849 TTTTTTATTTTTTTG
1 TTTTTTATTTTTTTG
25864 AAAAAAAAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
29 14 0.34
30 8 0.20
31 19 0.46
ACGTcount: A:0.01, C:0.04, G:0.08, T:0.87
Consensus pattern (31 bp):
TTTTTTATTTTTTTGCCTTTTTTTGTTTTTG
Found at i:28431 original size:20 final size:20
Alignment explanation
Indices: 28406--28443 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
28396 TTTTGGTGCA
*
28406 GAGGGAATCGATACCCCCAT
1 GAGGGAACCGATACCCCCAT
28426 GAGGGAACCGATACCCCC
1 GAGGGAACCGATACCCCC
28444 GTCGGGTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.34, G:0.26, T:0.11
Consensus pattern (20 bp):
GAGGGAACCGATACCCCCAT
Found at i:32076 original size:23 final size:23
Alignment explanation
Indices: 32050--32098 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 23
32040 TACATTTTGC
* *
32050 AAGAATGATAGATTGTCTTTTTA
1 AAGAATGATAGATTCTCTTTTCA
32073 AAG-ATGATAGATTCTCTTTTCA
1 AAGAATGATAGATTCTCTTTTCA
32095 AAGA
1 AAGA
32099 CAAAAGCTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 20 0.87
23 3 0.13
ACGTcount: A:0.37, C:0.08, G:0.16, T:0.39
Consensus pattern (23 bp):
AAGAATGATAGATTCTCTTTTCA
Found at i:35105 original size:38 final size:38
Alignment explanation
Indices: 35062--35169 Score: 89
Period size: 38 Copynumber: 3.2 Consensus size: 38
35052 CATAATTTGA
35062 TAATATAATTTCAATATTAAATGCTATAATAAGATTAT
1 TAATATAATTTCAATATTAAATGCTATAATAAGATTAT
* * *
35100 T-A-AT-A--TCTACA-T-AATAC-ATAAT----TTGA-
1 TAATATAATTTCAATATTAAATGCTATAATAAGATT-AT
35126 TAATATAATTTCAATATTAAATGCTATAATAAGATTAT
1 TAATATAATTTCAATATTAAATGCTATAATAAGATTAT
35164 TAATAT
1 TAATAT
35170 CTATGTTAAT
Statistics
Matches: 50, Mismatches: 6, Indels: 28
0.60 0.07 0.33
Matches are distributed among these distances:
26 3 0.06
27 2 0.04
28 2 0.04
29 1 0.02
30 5 0.10
31 8 0.16
32 2 0.04
33 8 0.16
34 5 0.10
35 1 0.02
36 2 0.04
37 2 0.04
38 9 0.18
ACGTcount: A:0.47, C:0.06, G:0.05, T:0.42
Consensus pattern (38 bp):
TAATATAATTTCAATATTAAATGCTATAATAAGATTAT
Found at i:35117 original size:64 final size:64
Alignment explanation
Indices: 35043--35172 Score: 260
Period size: 64 Copynumber: 2.0 Consensus size: 64
35033 TTTATTGTTA
35043 TACATAATACATAATTTGATAATATAATTTCAATATTAAATGCTATAATAAGATTATTAATATC
1 TACATAATACATAATTTGATAATATAATTTCAATATTAAATGCTATAATAAGATTATTAATATC
35107 TACATAATACATAATTTGATAATATAATTTCAATATTAAATGCTATAATAAGATTATTAATATC
1 TACATAATACATAATTTGATAATATAATTTCAATATTAAATGCTATAATAAGATTATTAATATC
35171 TA
1 TA
35173 TGTTAATATA
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 66 1.00
ACGTcount: A:0.47, C:0.08, G:0.05, T:0.41
Consensus pattern (64 bp):
TACATAATACATAATTTGATAATATAATTTCAATATTAAATGCTATAATAAGATTATTAATATC
Found at i:35893 original size:18 final size:18
Alignment explanation
Indices: 35872--35910 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 18
35862 AATTATTAGG
35872 AAATAA-AAAAAGTTCAAA
1 AAATAAGAAAAA-TTCAAA
35890 AAATAAGTAAAAATTCAAA
1 AAATAAG-AAAAATTCAAA
35909 AA
1 AA
35911 TATCAAAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.32
19 8 0.42
20 5 0.26
ACGTcount: A:0.72, C:0.05, G:0.05, T:0.18
Consensus pattern (18 bp):
AAATAAGAAAAATTCAAA
Found at i:39582 original size:22 final size:22
Alignment explanation
Indices: 39507--39582 Score: 80
Period size: 22 Copynumber: 3.5 Consensus size: 22
39497 ACGGAGATGA
*
39507 CTTAGCACTCATACTAAAGTGC
1 CTTAGCACTGATACTAAAGTGC
* * * *
39529 CTCAGCACTAATACGAAGGTGC
1 CTTAGCACTGATACTAAAGTGC
* * *
39551 ATTCGCACTGATACTAAAGTTC
1 CTTAGCACTGATACTAAAGTGC
39573 CTTAGCACTG
1 CTTAGCACTG
39583 CTGGTATATA
Statistics
Matches: 41, Mismatches: 13, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.26
Consensus pattern (22 bp):
CTTAGCACTGATACTAAAGTGC
Found at i:43863 original size:19 final size:18
Alignment explanation
Indices: 43834--43881 Score: 78
Period size: 19 Copynumber: 2.6 Consensus size: 18
43824 TTTGTTACCT
43834 GCTGCTTTATTCGTGACA
1 GCTGCTTTATTCGTGACA
43852 GCTGCTTTTATTCGTGACA
1 GCTGC-TTTATTCGTGACA
*
43871 GCTGGTTTATT
1 GCTGCTTTATT
43882 TGTTGTTCCT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
18 11 0.39
19 17 0.61
ACGTcount: A:0.15, C:0.19, G:0.23, T:0.44
Consensus pattern (18 bp):
GCTGCTTTATTCGTGACA
Found at i:48277 original size:38 final size:39
Alignment explanation
Indices: 48235--48332 Score: 144
Period size: 40 Copynumber: 2.5 Consensus size: 39
48225 GCGAAGTTGA
* *
48235 CATCTTTGGTTGGTGGCTAACTTGTAC-ATTGGAAAATT
1 CATCTTTGGTAGGTGGCCAACTTGTACAATTGGAAAATT
* *
48273 CATCTTTGGTAGGTGACCAACTTGTACATATTTGAAAATT
1 CATCTTTGGTAGGTGGCCAACTTGTACA-ATTGGAAAATT
48313 CATCTTTGGTAGGTGGCCAA
1 CATCTTTGGTAGGTGGCCAA
48333 ACTTTTGCAC
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
38 24 0.45
40 29 0.55
ACGTcount: A:0.26, C:0.15, G:0.22, T:0.37
Consensus pattern (39 bp):
CATCTTTGGTAGGTGGCCAACTTGTACAATTGGAAAATT
Found at i:49190 original size:20 final size:20
Alignment explanation
Indices: 49167--49429 Score: 80
Period size: 20 Copynumber: 11.7 Consensus size: 20
49157 TTTAGTTATG
*
49167 GCATCCTTTCATGCGTTAAT
1 GCATCCTTTCATGCCTTAAT
* *
49187 GCATCCCTTCATGCATTTTAGTTAT
1 GCATCCTTTCATGC--CTTA---AT
49212 GGCATCCTTTCATGCCTTAAT
1 -GCATCCTTTCATGCCTTAAT
* *
49233 GCATCCGTTTCTTGCATTTTAGTTAT
1 GCATCC-TTTCATGC--CTTA---AT
*
49259 GACATCCTTTCATTCCTTAAT
1 G-CATCCTTTCATGCCTTAAT
* * *
49280 GCATTCGTTCATGCATTTTAAATTAT
1 GCATCCTTTCATGC--CTT--A--AT
*
49306 GACATCCTTTCATTCCTTAAT
1 G-CATCCTTTCATGCCTTAAT
* *
49327 GCATCC-GTCATGCATTTTAGTTAT
1 GCATCCTTTCATGC--CTTA---AT
49351 GGCATCCTTTCATGCCTT-AT
1 -GCATCCTTTCATGCCTTAAT
* * *
49371 CCATCCTTTCATACATTTTAGTTAT
1 GCATCCTTTCATGC--CTTA---AT
*
49396 GGCATCCTTTCATGTCTTAAT
1 -GCATCCTTTCATGCCTTAAT
49417 GCATCCTTTCATG
1 GCATCCTTTCATG
49430 TATTTTAATT
Statistics
Matches: 180, Mismatches: 29, Indels: 68
0.65 0.10 0.25
Matches are distributed among these distances:
19 17 0.09
20 49 0.27
21 22 0.12
22 5 0.03
23 4 0.02
24 14 0.08
25 12 0.07
26 42 0.23
27 15 0.08
ACGTcount: A:0.21, C:0.24, G:0.12, T:0.43
Consensus pattern (20 bp):
GCATCCTTTCATGCCTTAAT
Found at i:49217 original size:26 final size:26
Alignment explanation
Indices: 49141--49409 Score: 125
Period size: 26 Copynumber: 11.5 Consensus size: 26
49131 CGAAACTTCT
**
49141 GCATCCTTTCATATATTTTAGTTATG
1 GCATCCTTTCATGCATTTTAGTTATG
*
49167 GCATCCTTTCATGC--GTTA---AT-
1 GCATCCTTTCATGCATTTTAGTTATG
*
49187 GCATCCCTTCATGCATTTTAGTTATG
1 GCATCCTTTCATGCATTTTAGTTATG
*
49213 GCATCCTTTCATGC--CTTA---AT-
1 GCATCCTTTCATGCATTTTAGTTATG
*
49233 GCATCCGTTTCTTGCATTTTAGTTATG
1 GCATCC-TTTCATGCATTTTAGTTATG
* * *
49260 ACATCCTTTCATTC--CTTA---AT-
1 GCATCCTTTCATGCATTTTAGTTATG
* * *
49280 GCATTCGTTCATGCATTTTAAATTATG
1 GCATCCTTTCATGCATTTT-AGTTATG
* * *
49307 ACATCCTTTCATTC--CTTA---AT-
1 GCATCCTTTCATGCATTTTAGTTATG
*
49327 GCATCC-GTCATGCATTTTAGTTATG
1 GCATCCTTTCATGCATTTTAGTTATG
*
49352 GCATCCTTTCATGC------CTTAT-
1 GCATCCTTTCATGCATTTTAGTTATG
* *
49371 CCATCCTTTCATACATTTTAGTTATG
1 GCATCCTTTCATGCATTTTAGTTATG
49397 GCATCCTTTCATG
1 GCATCCTTTCATG
49410 TCTTAATGCA
Statistics
Matches: 175, Mismatches: 34, Indels: 68
0.63 0.12 0.25
Matches are distributed among these distances:
19 17 0.10
20 38 0.22
21 18 0.10
22 5 0.03
23 4 0.02
24 12 0.07
25 14 0.08
26 52 0.30
27 15 0.09
ACGTcount: A:0.21, C:0.23, G:0.12, T:0.44
Consensus pattern (26 bp):
GCATCCTTTCATGCATTTTAGTTATG
Found at i:49267 original size:47 final size:46
Alignment explanation
Indices: 49140--49443 Score: 414
Period size: 46 Copynumber: 6.6 Consensus size: 46
49130 ACGAAACTTC
** *
49140 TGCATCCTTTCATATATTTTAGTTATGGCATCCTTTCATGCGTTAA
1 TGCATCCTTTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAA
*
49186 TGCATCCCTTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAA
1 TGCATCCTTTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAA
* * *
49232 TGCATCCGTTTCTTGCATTTTAGTTATGACATCCTTTCATTCCTTAA
1 TGCATCC-TTTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAA
* * * * *
49279 TGCATTCGTTCATGCATTTTAAATTATGACATCCTTTCATTCCTTAA
1 TGCATCCTTTCATGCATTTT-AGTTATGGCATCCTTTCATGCCTTAA
*
49326 TGCATCC-GTCATGCATTTTAGTTATGGCATCCTTTCATGCCTT-A
1 TGCATCCTTTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAA
* * *
49370 TCCATCCTTTCATACATTTTAGTTATGGCATCCTTTCATGTCTTAA
1 TGCATCCTTTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAA
* *
49416 TGCATCCTTTCATGTATTTTAATTATGG
1 TGCATCCTTTCATGCATTTTAGTTATGG
49444 ATTCGGTTTG
Statistics
Matches: 229, Mismatches: 25, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
44 7 0.03
45 54 0.24
46 96 0.42
47 72 0.31
ACGTcount: A:0.21, C:0.22, G:0.12, T:0.45
Consensus pattern (46 bp):
TGCATCCTTTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAA
Done.