Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004942.1 Hibiscus syriacus cultivar Beakdansim tig00011112_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: 57673
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:3885 original size:23 final size:23
Alignment explanation
Indices: 3844--3904 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 23
3834 AATATTAATA
*
3844 AATATGTTCGCGAATGTTAAATG
1 AATATGTTCGCGAACGTTAAATG
* * *
3867 AATATGTTTGTGAACGTTAAAAG
1 AATATGTTCGCGAACGTTAAATG
*
3890 -ATCATGTTCACGAAC
1 AAT-ATGTTCGCGAAC
3905 ACGAACACCT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
22 2 0.07
23 28 0.93
ACGTcount: A:0.36, C:0.11, G:0.20, T:0.33
Consensus pattern (23 bp):
AATATGTTCGCGAACGTTAAATG
Found at i:10645 original size:2 final size:2
Alignment explanation
Indices: 10638--10669 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
10628 TAAAAAGATT
10638 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
10670 ATTCAACCGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:11225 original size:20 final size:22
Alignment explanation
Indices: 11201--11255 Score: 60
Period size: 20 Copynumber: 2.6 Consensus size: 22
11191 TAAATATTTT
* *
11201 TTTCGCAACACAGTTTTTA-AA
1 TTTCGCAACACAATTTTAACAA
* *
11222 -TTCGAAACTCAATTTTAACAA
1 TTTCGCAACACAATTTTAACAA
11243 TTTCGCAACACAA
1 TTTCGCAACACAA
11256 ATTTCTTTTT
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
20 14 0.54
21 2 0.08
22 10 0.38
ACGTcount: A:0.38, C:0.22, G:0.07, T:0.33
Consensus pattern (22 bp):
TTTCGCAACACAATTTTAACAA
Found at i:11265 original size:62 final size:60
Alignment explanation
Indices: 11153--11332 Score: 152
Period size: 62 Copynumber: 2.9 Consensus size: 60
11143 TAATAGAGAA
* ** *
11153 TTTAGAATTCGCAACTTGATTTTGACAATTTCGCAATATAAATATT-TTTTTCGCAACACAGT-T
1 TTTA-AATTCGAAACTCAATTTT-ACAATTTCGCAACA-AAAT-TTCTTTTTCGCAACACA-TAT
*
11216 TTTAAATTCGAAACTCAATTTTAACAATTTCGCAACACAAATTTCTTTTTAGCAACA-ATAT
1 TTTAAATTCGAAACTCAATTTT-ACAATTTCGCAACA-AAATTTCTTTTTCGCAACACATAT
* * * ** * *
11277 TTTTAATTTGTAACTCAATTTTTGAA-TTCGCAACTAGATTTTCTTTTTCGCAACAC
1 TTTAAATTCGAAACTCAATTTTACAATTTCGCAAC-AAAATTTCTTTTTCGCAACAC
11333 GAATTTATTT
Statistics
Matches: 98, Mismatches: 15, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
59 24 0.24
60 4 0.04
61 23 0.23
62 43 0.44
63 4 0.04
ACGTcount: A:0.33, C:0.17, G:0.08, T:0.42
Consensus pattern (60 bp):
TTTAAATTCGAAACTCAATTTTACAATTTCGCAACAAAATTTCTTTTTCGCAACACATAT
Found at i:11379 original size:20 final size:20
Alignment explanation
Indices: 11314--11381 Score: 93
Period size: 20 Copynumber: 3.4 Consensus size: 20
11304 TCGCAACTAG
11314 ATTTTCTTTTTCGCAACACGA
1 ATTTT-TTTTTCGCAACACGA
* *
11335 ATTTATTTTTT-GCTATACGA
1 ATTT-TTTTTTCGCAACACGA
11355 ATTTTTTTTTCGCAACACGA
1 ATTTTTTTTTCGCAACACGA
11375 ATTTTTT
1 ATTTTTT
11382 GGGTATATAA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
19 6 0.15
20 25 0.61
21 9 0.22
22 1 0.02
ACGTcount: A:0.24, C:0.16, G:0.09, T:0.51
Consensus pattern (20 bp):
ATTTTTTTTTCGCAACACGA
Found at i:11545 original size:16 final size:15
Alignment explanation
Indices: 11510--11548 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
11500 TCCCCATCTC
*
11510 TAATTTTTTTTTACA
1 TAATTTTTTTCTACA
*
11525 TAATTTTATTTCTATA
1 TAATTTT-TTTCTACA
11541 TAATTTTT
1 TAATTTTT
11549 CAATAAGTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (15 bp):
TAATTTTTTTCTACA
Found at i:12152 original size:12 final size:12
Alignment explanation
Indices: 12131--12164 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
12121 ACCACATTTC
*
12131 CAATACCAAACA
1 CAATATCAAACA
12143 CAATATCAAACA
1 CAATATCAAACA
*
12155 CAATCTCAAA
1 CAATATCAAA
12165 ATCCATAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:12341 original size:24 final size:24
Alignment explanation
Indices: 12288--12343 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
12278 TAGTATTCGA
*
12288 AATTTGATATTGCTCAATACCCTG
1 AATTTGATATTGCTCAATACCCGG
* * *
12312 AATTTGATCTTGGTCAATACTCGG
1 AATTTGATATTGCTCAATACCCGG
*
12336 ATTTTGAT
1 AATTTGAT
12344 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.41
Consensus pattern (24 bp):
AATTTGATATTGCTCAATACCCGG
Found at i:13762 original size:31 final size:31
Alignment explanation
Indices: 13727--13979 Score: 425
Period size: 31 Copynumber: 8.2 Consensus size: 31
13717 GGTCACAATA
13727 TAAACTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
* *
13758 TAAACTGTTCATATGTGGCTTTAAACATATA
1 TAAACTGTTCATATGTGCCTTTAAACATATG
*
13789 CAAACTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
* *
13820 TAGACTGTTCATATGTGCCTTTAAACATATA
1 TAAACTGTTCATATGTGCCTTTAAACATATG
* *
13851 CAAACTGTTCATATGTTCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
*
13882 TAGACTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
13913 TAAACTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
*
13944 TAAACTGTTCATATGTGCCTTTAAACATATA
1 TAAACTGTTCATATGTGCCTTTAAACATATG
13975 TAAAC
1 TAAAC
13980 CCTCGACTCT
Statistics
Matches: 205, Mismatches: 17, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 205 1.00
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (31 bp):
TAAACTGTTCATATGTGCCTTTAAACATATG
Found at i:13896 original size:15 final size:15
Alignment explanation
Indices: 13876--13959 Score: 50
Period size: 15 Copynumber: 5.5 Consensus size: 15
13866 TTCCTTTAAA
13876 CATATGTAGACTGTT
1 CATATGTAGACTGTT
*
13891 CATATGT-GCCT-TT
1 CATATGTAGACTGTT
*
13904 AAACATATGTAAACTGTT
1 ---CATATGTAGACTGTT
*
13922 CATATGT-GCCT-TT
1 CATATGTAGACTGTT
*
13935 AAACATATGTAAACTGTT
1 ---CATATGTAGACTGTT
13953 CATATGT
1 CATATGT
13960 GCCTTTAAAC
Statistics
Matches: 52, Mismatches: 7, Indels: 20
0.66 0.09 0.25
Matches are distributed among these distances:
13 4 0.08
14 5 0.10
15 21 0.40
16 14 0.27
17 4 0.08
18 4 0.08
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.39
Consensus pattern (15 bp):
CATATGTAGACTGTT
Found at i:14601 original size:64 final size:63
Alignment explanation
Indices: 14489--14650 Score: 159
Period size: 64 Copynumber: 2.5 Consensus size: 63
14479 TAATAAAGGT
* * * * ** *
14489 ATGCATCGATGCACT-ATTGATGCATCGGTGCATAAAATGTATTTGATGTTGT-ATTATTGCTAG
1 ATGCATCGATGCACTCCTT-ATGCATCGGTGCACAAAATGCATTCGATGTT-TCATTATT-AAAA
14552 G
63 G
* * *
14553 ATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAAAAG
1 ATGCATCGATGCACTCCTTATGCATCGGTGCACAAAATGCATTCGATGTTTCATTATTAAAAG
*
14616 AGTGCATCGATGCACTACC-AATGCATCGGTGCACA
1 A-TGCATCGATGCACT-CCTTATGCATCGGTGCACA
14651 TTCAAACAAT
Statistics
Matches: 81, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
63 4 0.05
64 73 0.90
65 4 0.05
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (63 bp):
ATGCATCGATGCACTCCTTATGCATCGGTGCACAAAATGCATTCGATGTTTCATTATTAAAAG
Found at i:16898 original size:18 final size:17
Alignment explanation
Indices: 16875--16924 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
16865 AAGCAAAAAG
16875 AAATCAAAATCGTAATCA
1 AAATCAAAAT-GTAATCA
* *
16893 AAATCAAAATTGCAATTA
1 AAATCAAAA-TGTAATCA
*
16911 AAATGAAAATGTAA
1 AAATCAAAATGTAA
16925 ATCCCAATCA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 4 0.15
18 22 0.81
19 1 0.04
ACGTcount: A:0.58, C:0.10, G:0.08, T:0.24
Consensus pattern (17 bp):
AAATCAAAATGTAATCA
Found at i:17320 original size:20 final size:20
Alignment explanation
Indices: 17224--17318 Score: 109
Period size: 20 Copynumber: 4.8 Consensus size: 20
17214 TTAACAACTC
*
17224 AAATTCGCAACACGATAATA
1 AAATTCGCAACTCGATAATA
* *
17244 GAATTCGCAACTCGATATTA
1 AAATTCGCAACTCGATAATA
** *
17264 AAATTCATAACTCGATATTA
1 AAATTCGCAACTCGATAATA
* *
17284 AAATTCGTAACTCGAAAATA
1 AAATTCGCAACTCGATAATA
*
17304 TAATTCGCAACTCGA
1 AAATTCGCAACTCGA
17319 AATCGATTTC
Statistics
Matches: 64, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 64 1.00
ACGTcount: A:0.43, C:0.19, G:0.11, T:0.27
Consensus pattern (20 bp):
AAATTCGCAACTCGATAATA
Found at i:17441 original size:20 final size:20
Alignment explanation
Indices: 17370--17467 Score: 90
Period size: 20 Copynumber: 5.0 Consensus size: 20
17360 TCGAGTTGCA
17370 ATTTTCGTGTTGCGAATTTG
1 ATTTTCGTGTTGCGAATTTG
* *** ***
17390 ATTTTTGAAATGCGAAACCG
1 ATTTTCGTGTTGCGAATTTG
* *
17410 ATTTTTGCGTTGCGAATTTG
1 ATTTTCGTGTTGCGAATTTG
17430 ATTTTCGTGTTGCGAATTTG
1 ATTTTCGTGTTGCGAATTTG
* *
17450 AATATCGTGTTGC-AATTT
1 ATTTTCGTGTTGCGAATTT
17468 TCGCATTACA
Statistics
Matches: 61, Mismatches: 17, Indels: 1
0.77 0.22 0.01
Matches are distributed among these distances:
19 5 0.08
20 56 0.92
ACGTcount: A:0.21, C:0.11, G:0.22, T:0.45
Consensus pattern (20 bp):
ATTTTCGTGTTGCGAATTTG
Found at i:19042 original size:21 final size:21
Alignment explanation
Indices: 19025--19136 Score: 118
Period size: 21 Copynumber: 5.3 Consensus size: 21
19015 AGTATGGAAT
*
19025 GTGGATCCTGAACGATGGGAG
1 GTGGATCCTGAACAATGGGAG
* *
19046 GTGGATCCCGAACGATGGGAG
1 GTGGATCCTGAACAATGGGAG
* * * *
19067 AG-GCATCTTGAACAATGAGAT
1 -GTGGATCCTGAACAATGGGAG
**
19088 GTAAATCCTGAACAATGGGAG
1 GTGGATCCTGAACAATGGGAG
*
19109 GTGGATCCTGAACAATGGTAG
1 GTGGATCCTGAACAATGGGAG
19130 GTGGATC
1 GTGGATC
19137 AGTTTTCTTC
Statistics
Matches: 74, Mismatches: 15, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
20 1 0.01
21 72 0.97
22 1 0.01
ACGTcount: A:0.29, C:0.15, G:0.35, T:0.21
Consensus pattern (21 bp):
GTGGATCCTGAACAATGGGAG
Found at i:19565 original size:21 final size:21
Alignment explanation
Indices: 19541--19595 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
19531 TTCACCATTG
19541 TCATCACGTAAAGCACAGACC
1 TCATCACGTAAAGCACAGACC
*
19562 TCATCACGTAAAGCACTGACC
1 TCATCACGTAAAGCACAGACC
19583 TCATCACGTAAAG
1 TCATCACGTAAAG
19596 GACATAACTC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.36, C:0.31, G:0.15, T:0.18
Consensus pattern (21 bp):
TCATCACGTAAAGCACAGACC
Found at i:19606 original size:21 final size:21
Alignment explanation
Indices: 19541--19608 Score: 93
Period size: 21 Copynumber: 3.2 Consensus size: 21
19531 TTCACCATTG
*
19541 TCATCACGTAAAGCACAGACC
1 TCATCACGTAAAGCACATACC
19562 TCATCACGTAAAGCAC-TGACC
1 TCATCACGTAAAGCACAT-ACC
* *
19583 TCATCACGTAAAGGACATAAC
1 TCATCACGTAAAGCACATACC
19604 TCATC
1 TCATC
19609 CTGTGGAGGT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
21 41 0.98
22 1 0.02
ACGTcount: A:0.37, C:0.31, G:0.13, T:0.19
Consensus pattern (21 bp):
TCATCACGTAAAGCACATACC
Found at i:19820 original size:42 final size:42
Alignment explanation
Indices: 19774--19871 Score: 108
Period size: 42 Copynumber: 2.3 Consensus size: 42
19764 GTCGAGTTGT
* *
19774 AGAATCGACACGATCAGGTGATGGATCTCGATATCGAAGTGG
1 AGAATCGACACGATCAGGTGATGGATCTCGATATCGAACTGA
* * * * *
19816 AGAATTGACTATG-TGAGGTGATGGATCTCGGTGTCGAACTGA
1 AGAATCGAC-ACGATCAGGTGATGGATCTCGATATCGAACTGA
*
19858 AGAATCGACTCGAT
1 AGAATCGACACGAT
19872 GAAAAAGTAA
Statistics
Matches: 44, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
41 1 0.02
42 41 0.93
43 2 0.05
ACGTcount: A:0.30, C:0.15, G:0.31, T:0.24
Consensus pattern (42 bp):
AGAATCGACACGATCAGGTGATGGATCTCGATATCGAACTGA
Found at i:21407 original size:20 final size:20
Alignment explanation
Indices: 21370--21408 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
21360 ATTGAAACTT
* *
21370 AAATTCGCAACACGAAAATG
1 AAATTCACAACAAGAAAATG
*
21390 AAATTCACAACAATAAAAT
1 AAATTCACAACAAGAAAAT
21409 CGCAACGCGA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.56, C:0.18, G:0.08, T:0.18
Consensus pattern (20 bp):
AAATTCACAACAAGAAAATG
Found at i:21483 original size:20 final size:20
Alignment explanation
Indices: 21446--21483 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
21436 CGAAATCTGT
* *
21446 GTTGCGAATTTCATTTTCGA
1 GTTGCGAATTTAAGTTTCGA
21466 GTTGCGAATTTAAGTTTC
1 GTTGCGAATTTAAGTTTC
21484 AAGAATAAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.13, G:0.21, T:0.45
Consensus pattern (20 bp):
GTTGCGAATTTAAGTTTCGA
Found at i:24846 original size:17 final size:18
Alignment explanation
Indices: 24824--24857 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
24814 ATAACTTTAC
24824 AAGTTT-ATTTTCAAATA
1 AAGTTTAATTTTCAAATA
24841 AAGTTTAATTTTCAAAT
1 AAGTTTAATTTTCAAAT
24858 TTGAAAGTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.47
Consensus pattern (18 bp):
AAGTTTAATTTTCAAATA
Found at i:30338 original size:9 final size:9
Alignment explanation
Indices: 30326--30377 Score: 56
Period size: 9 Copynumber: 6.1 Consensus size: 9
30316 TAATATTTTA
30326 TATTTAATT
1 TATTTAATT
*
30335 TATTTAA-G
1 TATTTAATT
30343 TATTTAATT
1 TATTTAATT
30352 TATTTAA--
1 TATTTAATT
*
30359 TATTTTATT
1 TATTTAATT
*
30368 TAATTAATT
1 TATTTAATT
30377 T
1 T
30378 TTTGCAGATA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
7 6 0.17
8 7 0.20
9 22 0.63
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (9 bp):
TATTTAATT
Found at i:30348 original size:17 final size:16
Alignment explanation
Indices: 30319--30375 Score: 78
Period size: 16 Copynumber: 3.5 Consensus size: 16
30309 ATATTTTTAA
*
30319 TATTTTATATTTAATT
1 TATTTAATATTTAATT
30335 TATTTAAGTATTTAATT
1 TATTTAA-TATTTAATT
*
30352 TATTTAATATTTTATT
1 TATTTAATATTTAATT
*
30368 TAATTAAT
1 TATTTAAT
30376 TTTTTGCAGA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
16 21 0.57
17 16 0.43
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (16 bp):
TATTTAATATTTAATT
Found at i:32614 original size:21 final size:20
Alignment explanation
Indices: 32560--32615 Score: 53
Period size: 21 Copynumber: 2.8 Consensus size: 20
32550 ATAGATTTTG
*
32560 TTTTTTTATTATAT-TTGTA
1 TTTTTTTATTATTTATTGTA
**
32579 TTTAGTTACTT-TTTATTGTAA
1 TTTTTTTA-TTATTTATTGT-A
32600 TTTTTTTATTATTTAT
1 TTTTTTTATTATTTAT
32616 CATTTAATAC
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
19 8 0.29
20 8 0.29
21 12 0.43
ACGTcount: A:0.21, C:0.02, G:0.05, T:0.71
Consensus pattern (20 bp):
TTTTTTTATTATTTATTGTA
Done.