Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003602.1 Hibiscus syriacus cultivar Beakdansim tig00007617_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: 60207
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Found at i:2465 original size:2 final size:2
Alignment explanation
Indices: 2458--2503 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
2448 CGCTAGTATG
2458 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2500 TA TA
1 TA TA
2504 CATAGATAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2601 original size:21 final size:21
Alignment explanation
Indices: 2575--2614 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2565 TTAACTATGG
2575 AAAAGG-TATATAAATAAGTAT
1 AAAAGGATAT-TAAATAAGTAT
*
2596 AAAAGGATATTAGATAAGT
1 AAAAGGATATTAAATAAGT
2615 TGTGTAGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.55, C:0.00, G:0.17, T:0.28
Consensus pattern (21 bp):
AAAAGGATATTAAATAAGTAT
Found at i:7458 original size:21 final size:21
Alignment explanation
Indices: 7429--7482 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
7419 TTTGTTGAAT
*
7429 GTTGAGAAGATGGTGTGGTGGG
1 GTTG-GAAGATGGTGTAGTGGG
**
7451 GTTGGAAGATTTTGTAGTGGG
1 GTTGGAAGATGGTGTAGTGGG
*
7472 GTGGGAAGATG
1 GTTGGAAGATG
7483 CAGAAGGTTG
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.20, C:0.00, G:0.50, T:0.30
Consensus pattern (21 bp):
GTTGGAAGATGGTGTAGTGGG
Found at i:10152 original size:26 final size:27
Alignment explanation
Indices: 10112--10170 Score: 84
Period size: 26 Copynumber: 2.2 Consensus size: 27
10102 CACATCGCTA
10112 ACTTTATAAACATAAACAAATCCACAT
1 ACTTTATAAACATAAACAAATCCACAT
* *
10139 ACTTT-TAACCATAAACAAATGCACAT
1 ACTTTATAAACATAAACAAATCCACAT
*
10165 TCTTTA
1 ACTTTA
10171 GACAGGAGGA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 23 0.82
27 5 0.18
ACGTcount: A:0.46, C:0.22, G:0.02, T:0.31
Consensus pattern (27 bp):
ACTTTATAAACATAAACAAATCCACAT
Found at i:10523 original size:18 final size:18
Alignment explanation
Indices: 10500--10540 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
10490 CTTTTTGAAC
10500 AACCTATTATAATAGGAA
1 AACCTATTATAATAGGAA
10518 AACCTATTATAATAGGAA
1 AACCTATTATAATAGGAA
10536 AACCT
1 AACCT
10541 TAATATCTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.49, C:0.15, G:0.10, T:0.27
Consensus pattern (18 bp):
AACCTATTATAATAGGAA
Found at i:11175 original size:28 final size:28
Alignment explanation
Indices: 11143--11221 Score: 142
Period size: 28 Copynumber: 2.9 Consensus size: 28
11133 CATTCTTTAG
11143 ACATAAACAAATCCACATAACTTTATAA
1 ACATAAACAAATCCACATAACTTTATAA
11171 ACATAAACAAATCCACATAACTTTATAA
1 ACATAAACAAATCCACATAACTTTATAA
*
11199 ACATAAACAAAACCACAT-ACTTT
1 ACATAAACAAATCCACATAACTTT
11222 TCCTAGTGTT
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
27 5 0.10
28 45 0.90
ACGTcount: A:0.53, C:0.23, G:0.00, T:0.24
Consensus pattern (28 bp):
ACATAAACAAATCCACATAACTTTATAA
Found at i:23524 original size:63 final size:63
Alignment explanation
Indices: 23446--23568 Score: 169
Period size: 63 Copynumber: 2.0 Consensus size: 63
23436 TAATAATATC
* * *
23446 TTTTAATTTGAAATATTCAAAA-TATATAAACTCAT-TTTACTATTCAAACTTAAATATATATTA
1 TTTTAATTTAAAATATCCAAAACTATAT-AA-TCATCTTTAATATTCAAACTTAAATATATATTA
* *
23509 TTTTAATTTAAAATATCCAAAACTATATAATTATCTTTAATATTCAAAGTTAAATATATA
1 TTTTAATTTAAAATATCCAAAACTATATAATCATCTTTAATATTCAAACTTAAATATATA
23569 ATAAATACAT
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
62 3 0.06
63 45 0.85
64 5 0.09
ACGTcount: A:0.46, C:0.09, G:0.02, T:0.44
Consensus pattern (63 bp):
TTTTAATTTAAAATATCCAAAACTATATAATCATCTTTAATATTCAAACTTAAATATATATTA
Found at i:29383 original size:23 final size:21
Alignment explanation
Indices: 29352--29404 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 21
29342 AATTTTCATT
29352 AAATATATATAATTTAATTAAA
1 AAAT-TATATAATTTAATTAAA
**
29374 AATATGTATA-AATTTTGTTAAA
1 AA-AT-TATATAATTTAATTAAA
29396 AAATTATAT
1 AAATTATAT
29405 TGATTAGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
20 4 0.15
21 2 0.08
22 14 0.54
23 6 0.23
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (21 bp):
AAATTATATAATTTAATTAAA
Found at i:29396 original size:21 final size:21
Alignment explanation
Indices: 29333--29396 Score: 69
Period size: 21 Copynumber: 3.0 Consensus size: 21
29323 AATGTCAAAT
29333 ATATATATAAATTTTCATT-AA
1 ATATATATAAATTTT-ATTAAA
*
29354 ATATATAT-AATTTAATTAAAA
1 ATATATATAAATTTTATT-AAA
* *
29375 ATATGTATAAATTTTGTTAAA
1 ATATATATAAATTTTATTAAA
29396 A
1 A
29397 AATTATATTG
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
19 3 0.08
20 5 0.14
21 21 0.58
22 7 0.19
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (21 bp):
ATATATATAAATTTTATTAAA
Found at i:31206 original size:13 final size:13
Alignment explanation
Indices: 31190--31214 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31180 AAGATTAGTA
31190 AAAAAGAAAAAAG
1 AAAAAGAAAAAAG
31203 AAAAAGAAAAAA
1 AAAAAGAAAAAA
31215 TCCCCCGCCG
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:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (13 bp):
AAAAAGAAAAAAG
Found at i:31509 original size:6 final size:6
Alignment explanation
Indices: 31498--31530 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
31488 TGTCTTCATA
31498 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTT
31531 CTCTGCATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTAT
Found at i:41255 original size:18 final size:18
Alignment explanation
Indices: 41235--41271 Score: 65
Period size: 18 Copynumber: 2.0 Consensus size: 18
41225 TTTTTTTTTT
41235 AAATATTAATATTTTAATA
1 AAATA-TAATATTTTAATA
41254 AAATATAATATTTTAATA
1 AAATATAATATTTTAATA
41272 TTAAAAAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
AAATATAATATTTTAATA
Found at i:45412 original size:40 final size:40
Alignment explanation
Indices: 45366--45446 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
45356 CGCACTAGTC
45366 TATATGTGCCAATGATTTGTATATTTTTTTTTTCATTCTT
1 TATATGTGCCAATGATTTGTATATTTTTTTTTTCATTCTT
45406 TATATGTGCCAATGATTTGTATATTTTTTTTTTCATTCTT
1 TATATGTGCCAATGATTTGTATATTTTTTTTTTCATTCTT
45446 T
1 T
45447 CTATAAAATG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.20, C:0.10, G:0.10, T:0.60
Consensus pattern (40 bp):
TATATGTGCCAATGATTTGTATATTTTTTTTTTCATTCTT
Found at i:49640 original size:35 final size:35
Alignment explanation
Indices: 49594--49661 Score: 136
Period size: 35 Copynumber: 1.9 Consensus size: 35
49584 GACATCTTAT
49594 AGACGGTCACTAGTAAAACCACGTGTTTGCACATA
1 AGACGGTCACTAGTAAAACCACGTGTTTGCACATA
49629 AGACGGTCACTAGTAAAACCACGTGTTTGCACA
1 AGACGGTCACTAGTAAAACCACGTGTTTGCACA
49662 CGTGATTATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.34, C:0.24, G:0.21, T:0.22
Consensus pattern (35 bp):
AGACGGTCACTAGTAAAACCACGTGTTTGCACATA
Found at i:49913 original size:16 final size:17
Alignment explanation
Indices: 49890--49932 Score: 86
Period size: 17 Copynumber: 2.5 Consensus size: 17
49880 TATATTATTT
49890 TAAAAAAAACTTTTTTC
1 TAAAAAAAACTTTTTTC
49907 TAAAAAAAACTTTTTTC
1 TAAAAAAAACTTTTTTC
49924 TAAAAAAAA
1 TAAAAAAAA
49933 ATTCAACCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.35
Consensus pattern (17 bp):
TAAAAAAAACTTTTTTC
Found at i:49973 original size:14 final size:14
Alignment explanation
Indices: 49954--49980 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
49944 CCCCTTCCCG
49954 TCCCCTTCTCCTTT
1 TCCCCTTCTCCTTT
49968 TCCCCTTCTCCTT
1 TCCCCTTCTCCTT
49981 CCACAACAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (14 bp):
TCCCCTTCTCCTTT
Found at i:50182 original size:24 final size:24
Alignment explanation
Indices: 50154--50207 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 24
50144 CCGATCGTTG
*
50154 TAAATCAC-AACTCCATTGCAAAGT
1 TAAATCACTAAATCCATTGCAAA-T
*
50178 TAAAT-ACTAAATCCTTTGCAAAT
1 TAAATCACTAAATCCATTGCAAAT
50201 TCAAATC
1 T-AAATC
50208 TTTGCACCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 4 0.16
24 21 0.84
ACGTcount: A:0.43, C:0.22, G:0.06, T:0.30
Consensus pattern (24 bp):
TAAATCACTAAATCCATTGCAAAT
Found at i:51799 original size:14 final size:14
Alignment explanation
Indices: 51780--51806 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
51770 ATTTTCCTAG
51780 CTAAATTCATTCTC
1 CTAAATTCATTCTC
51794 CTAAATTCATTCT
1 CTAAATTCATTCT
51807 ATTTTCATTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.26, G:0.00, T:0.44
Consensus pattern (14 bp):
CTAAATTCATTCTC
Found at i:59464 original size:20 final size:19
Alignment explanation
Indices: 59439--59478 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
59429 TCCAGATTGT
59439 CCAAGGGAACCGATTCCCCC
1 CCAA-GGAACCGATTCCCCC
*
59459 CCAAGGTACCGATTCCCCC
1 CCAAGGAACCGATTCCCCC
59478 C
1 C
59479 TGAATGGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.23, C:0.47, G:0.17, T:0.12
Consensus pattern (19 bp):
CCAAGGAACCGATTCCCCC
Done.