Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000606.1 Hibiscus syriacus cultivar Beakdansim tig00001178_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: 77263
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:8128 original size:3 final size:3
Alignment explanation
Indices: 8120--8172 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
8110 TCAAACATTG
8120 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
8168 AAT AA
1 AAT AA
8173 CCCATTGACT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:9099 original size:34 final size:34
Alignment explanation
Indices: 9056--9123 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
9046 TAATATTGAA
9056 GTGTAAATGAGAAAAACAGAAACTAAAATTAAGC
1 GTGTAAATGAGAAAAACAGAAACTAAAATTAAGC
9090 GTGTAAATGAGAAAAACAGAAACTAAAATTAAGC
1 GTGTAAATGAGAAAAACAGAAACTAAAATTAAGC
9124 CCTTTTGGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.56, C:0.09, G:0.18, T:0.18
Consensus pattern (34 bp):
GTGTAAATGAGAAAAACAGAAACTAAAATTAAGC
Found at i:21563 original size:20 final size:20
Alignment explanation
Indices: 21534--21576 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
21524 ATTTCACCAC
*
21534 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCCTAA
*
21554 ATGCATCTATATGATCCTAA
1 ATGCAACTATATGATCCTAA
21574 ATG
1 ATG
21577 AGCTTTTAGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.35, C:0.21, G:0.12, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:23309 original size:14 final size:15
Alignment explanation
Indices: 23290--23327 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
23280 TCCCCATCTC
23290 TAATTTTTTT-TACA
1 TAATTTTTTTCTACA
*
23304 TAATTTTATTTCTATA
1 TAATTTT-TTTCTACA
23320 TAATTTTT
1 TAATTTTT
23328 CAATGATTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (15 bp):
TAATTTTTTTCTACA
Found at i:26278 original size:18 final size:18
Alignment explanation
Indices: 26255--26290 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
26245 AAGCAAAAGG
26255 AAATCAAAATCGCAATCA
1 AAATCAAAATCGCAATCA
26273 AAATCAAAATCGCAATCA
1 AAATCAAAATCGCAATCA
26291 CAACCGGCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.56, C:0.22, G:0.06, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCGCAATCA
Found at i:26669 original size:13 final size:15
Alignment explanation
Indices: 26648--26683 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
26638 GCCAAATTCG
26648 AAACGCG-AAATCGC
1 AAACGCGAAAATCGC
26662 AAAC-CGAAAATCGC
1 AAACGCGAAAATCGC
26676 -AACGCGAA
1 AAACGCGAA
26684 TTTGACTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
13 5 0.25
14 15 0.75
ACGTcount: A:0.47, C:0.28, G:0.19, T:0.06
Consensus pattern (15 bp):
AAACGCGAAAATCGC
Found at i:28248 original size:21 final size:20
Alignment explanation
Indices: 28222--28319 Score: 117
Period size: 21 Copynumber: 4.7 Consensus size: 20
28212 GTGAATCGGG
* *
28222 CTCTTGAACGGTGGGAGGGAC
1 CTCTTGAACGATGAGAGGG-C
*
28243 CTCTTGAACGATGACATGGGC
1 CTCTTGAACGATGAGA-GGGC
28264 CTCTTGAACGATGAGAGGGGC
1 CTCTTGAACGATGAGA-GGGC
28285 CTCTTGAACGAT-AGGAGGCGC
1 CTCTTGAACGATGA-GAGG-GC
28306 CTCTTGAACGATGA
1 CTCTTGAACGATGA
28320 CAGGTGCATC
Statistics
Matches: 68, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
20 3 0.04
21 61 0.90
22 4 0.06
ACGTcount: A:0.23, C:0.21, G:0.34, T:0.21
Consensus pattern (20 bp):
CTCTTGAACGATGAGAGGGC
Found at i:28634 original size:21 final size:21
Alignment explanation
Indices: 28610--28666 Score: 80
Period size: 21 Copynumber: 2.7 Consensus size: 21
28600 GTAGAGCGGC
28610 TACCTCATCACGTAAAG-TAG
1 TACCTCATCACGTAAAGATAG
* *
28630 ATACCTCACCACGTAAAGATCG
1 -TACCTCATCACGTAAAGATAG
28652 TACCTCATCACGTAA
1 TACCTCATCACGTAA
28667 CGCACCATTG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.35, C:0.30, G:0.12, T:0.23
Consensus pattern (21 bp):
TACCTCATCACGTAAAGATAG
Found at i:30506 original size:20 final size:20
Alignment explanation
Indices: 30463--30506 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
30453 CCGTTGCGAT
* * *
30463 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGAATTTAAG
30483 TTTCGTGTTGCGAATTTAAG
1 TTTCGTGTTGCGAATTTAAG
30503 TTTC
1 TTTC
30507 AAAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.14, C:0.14, G:0.20, T:0.52
Consensus pattern (20 bp):
TTTCGTGTTGCGAATTTAAG
Found at i:32106 original size:6 final size:6
Alignment explanation
Indices: 32095--32455 Score: 676
Period size: 6 Copynumber: 60.8 Consensus size: 6
32085 ATTTCATATT
*
32095 TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGCA
1 TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA
*
32143 TATGCA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA
1 TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA
32191 TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATG-- TATGTA
1 TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA
32237 TATGTA TATGTA TATGTA TATGTA TATG-- TATGTA TATGTA TATGTA
1 TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA
32283 TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA
1 TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA
32331 TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA
1 TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA
32379 TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA
1 TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA
32427 TATGTA TATGTA TATGTA TATGTA TATGT
1 TATGTA TATGTA TATGTA TATGTA TATGT
32456 TCAGCACTTA
Statistics
Matches: 349, Mismatches: 2, Indels: 8
0.97 0.01 0.02
Matches are distributed among these distances:
4 8 0.02
6 341 0.98
ACGTcount: A:0.33, C:0.01, G:0.17, T:0.50
Consensus pattern (6 bp):
TATGTA
Found at i:33038 original size:18 final size:19
Alignment explanation
Indices: 33003--33039 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
32993 CACGGAATGT
33003 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
33023 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
33040 TGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:33221 original size:38 final size:37
Alignment explanation
Indices: 33186--33256 Score: 97
Period size: 37 Copynumber: 1.9 Consensus size: 37
33176 TACAAATTGT
*
33186 AAAATATTTATATATTTTCTTTAAAAAAATTAAATTC
1 AAAATATTTATATAATTTCTTTAAAAAAATTAAATTC
* * * *
33223 ATAATATTTATATAATTTGTTTTACAAAATTAAA
1 AAAATATTTATATAATTTCTTTAAAAAAATTAAA
33257 AATATAAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 29 1.00
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.46
Consensus pattern (37 bp):
AAAATATTTATATAATTTCTTTAAAAAAATTAAATTC
Found at i:36812 original size:37 final size:37
Alignment explanation
Indices: 36753--36865 Score: 162
Period size: 35 Copynumber: 3.2 Consensus size: 37
36743 ATCCCATTAT
*
36753 CATTTTTC-AACAAACATCTACCAAACTTTGAAAAAC
1 CATTTTTCAAACAAACATTTACCAAACTTTGAAAAAC
* *
36789 TATTTTTCAAAGAAACATTTACCAAACTTTG-AAAAC
1 CATTTTTCAAACAAACATTTACCAAACTTTGAAAAAC
*
36825 CA-TTTTCAAATAAACATTTACCAAACTTTG-AAAAC
1 CATTTTTCAAACAAACATTTACCAAACTTTGAAAAAC
36860 CATTTT
1 CATTTT
36866 AATAATTTCA
Statistics
Matches: 70, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
35 34 0.49
36 16 0.23
37 20 0.29
ACGTcount: A:0.43, C:0.20, G:0.04, T:0.33
Consensus pattern (37 bp):
CATTTTTCAAACAAACATTTACCAAACTTTGAAAAAC
Found at i:36828 original size:21 final size:21
Alignment explanation
Indices: 36804--36864 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
36794 TTCAAAGAAA
36804 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
*
36825 CATTT-TCAAA---T--AAA-
1 CATTTACCAAACTTTGAAAAC
36839 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
36860 CATTT
1 CATTT
36865 TAATAATTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 7 0.23
17 1 0.03
18 1 0.03
20 7 0.23
21 10 0.32
ACGTcount: A:0.43, C:0.21, G:0.03, T:0.33
Consensus pattern (21 bp):
CATTTACCAAACTTTGAAAAC
Found at i:41441 original size:35 final size:35
Alignment explanation
Indices: 41346--41455 Score: 123
Period size: 35 Copynumber: 3.1 Consensus size: 35
41336 TCATTATCAT
* * *
41346 TTTTC-AACAAACATCTACCAAACTTTAAAAAACTA
1 TTTTCAAAAAAACATTTACCAAACTTT-AAAAACCA
* * *
41381 TTTTTTAAAGAAATATTTACCAAACTTTAAAAACCA
1 -TTTTCAAAAAAACATTTACCAAACTTTAAAAACCA
* *
41417 TTTTCAAAAAAACATTTATCAAACTTTGAAAACCA
1 TTTTCAAAAAAACATTTACCAAACTTTAAAAACCA
41452 TTTT
1 TTTT
41456 AATACTTTCA
Statistics
Matches: 63, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
35 34 0.54
36 11 0.17
37 18 0.29
ACGTcount: A:0.46, C:0.17, G:0.02, T:0.35
Consensus pattern (35 bp):
TTTTCAAAAAAACATTTACCAAACTTTAAAAACCA
Found at i:57694 original size:31 final size:31
Alignment explanation
Indices: 57659--57771 Score: 109
Period size: 31 Copynumber: 3.6 Consensus size: 31
57649 TGAGAGATTT
* * *
57659 TGATAAGTTTAAAGATCATTTTGTAATAGTC
1 TGATAAATTTAATGATCATTTTATAATAGTC
** * * *
57690 TGATACGTTTAACGATCTTTTTATAATAGTT
1 TGATAAATTTAATGATCATTTTATAATAGTC
* * *
57721 TGATAAAATTTAATTACCATTTTATAATTGTC
1 TGAT-AAATTTAATGATCATTTTATAATAGTC
*
57753 TGGTAAATTTAATGATCAT
1 TGATAAATTTAATGATCAT
57772 CCTATAATTT
Statistics
Matches: 65, Mismatches: 16, Indels: 2
0.78 0.19 0.02
Matches are distributed among these distances:
31 43 0.66
32 22 0.34
ACGTcount: A:0.35, C:0.08, G:0.12, T:0.45
Consensus pattern (31 bp):
TGATAAATTTAATGATCATTTTATAATAGTC
Done.