Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009116.1 Hibiscus syriacus cultivar Beakdansim tig00112601_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: 56433
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1358 original size:16 final size:16
Alignment explanation
Indices: 1334--1380 Score: 85
Period size: 16 Copynumber: 2.9 Consensus size: 16
1324 CCTACCCTTG
1334 TCATAACCATTTCTAT
1 TCATAACCATTTCTAT
*
1350 TCCTAACCATTTCTAT
1 TCATAACCATTTCTAT
1366 TCATAACCATTTCTA
1 TCATAACCATTTCTA
1381 ATAGGCTTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.30, C:0.28, G:0.00, T:0.43
Consensus pattern (16 bp):
TCATAACCATTTCTAT
Found at i:2455 original size:26 final size:26
Alignment explanation
Indices: 2416--2483 Score: 109
Period size: 26 Copynumber: 2.6 Consensus size: 26
2406 CCCTAGAACA
* *
2416 CCCATGTGCTTTGCATATGATCAGCC
1 CCCATGTGCCTTGCATATGACCAGCC
*
2442 CCCATGTGCCTTGCATATGACCAGGC
1 CCCATGTGCCTTGCATATGACCAGCC
2468 CCCATGTGCCTTGCAT
1 CCCATGTGCCTTGCAT
2484 GTAGGTTCAT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.18, C:0.34, G:0.21, T:0.28
Consensus pattern (26 bp):
CCCATGTGCCTTGCATATGACCAGCC
Found at i:10851 original size:17 final size:17
Alignment explanation
Indices: 10825--10858 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
10815 CTCCTCTCGT
*
10825 ATTCTCTTTGCATTCCA
1 ATTCTCTTTGAATTCCA
*
10842 ATTCTTTTTGAATTCCA
1 ATTCTCTTTGAATTCCA
10859 CTCTCACACT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.24, G:0.06, T:0.50
Consensus pattern (17 bp):
ATTCTCTTTGAATTCCA
Found at i:13543 original size:13 final size:12
Alignment explanation
Indices: 13524--13584 Score: 56
Period size: 13 Copynumber: 5.0 Consensus size: 12
13514 TTATTGGCGT
13524 GATATGGTGATG
1 GATATGGTGATG
13536 GAATATGGTGAT-
1 G-ATATGGTGATG
*
13548 GATATAGGCG-T-
1 GATAT-GGTGATG
13559 GATAATGGTGATG
1 GAT-ATGGTGATG
13572 GAATATGGTGATG
1 G-ATATGGTGATG
13585 AAAATAGTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
11 11 0.27
12 8 0.20
13 20 0.49
14 2 0.05
ACGTcount: A:0.30, C:0.02, G:0.38, T:0.31
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:17518 original size:33 final size:33
Alignment explanation
Indices: 17476--17544 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
17466 GTTGATGAAT
*
17476 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGG-CATGAAATGGTAATG
* * *
17509 GAAGGATGATGTTATTGGCATGATATGGTGATG
1 GAAGGATGATGTTAATGGCATGAAATGGTAATG
17542 GAA
1 GAA
17545 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 25 0.81
34 6 0.19
ACGTcount: A:0.33, C:0.01, G:0.35, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCATGAAATGGTAATG
Found at i:17549 original size:13 final size:12
Alignment explanation
Indices: 17530--17590 Score: 56
Period size: 13 Copynumber: 5.0 Consensus size: 12
17520 TTATTGGCAT
17530 GATATGGTGATG
1 GATATGGTGATG
17542 GAATATGGTGAT-
1 G-ATATGGTGATG
*
17554 GATATAGGCG-T-
1 GATAT-GGTGATG
17565 GATAATGGTGATG
1 GAT-ATGGTGATG
17578 GACTATGGTGATG
1 GA-TATGGTGATG
17591 AAAATAGTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
11 11 0.27
12 8 0.20
13 21 0.51
14 1 0.02
ACGTcount: A:0.28, C:0.03, G:0.38, T:0.31
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:17578 original size:36 final size:35
Alignment explanation
Indices: 17515--17591 Score: 109
Period size: 36 Copynumber: 2.2 Consensus size: 35
17505 AATGGAAGGA
* *
17515 TGATGTTATTGGCATGATATGGTGATGGAATATGG
1 TGATGATATAGGCATGATATGGTGATGGAATATGG
* *
17550 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
1 TGATGATATAGGCATGAT-ATGGTGATGGAATATGG
17586 TGATGA
1 TGATGA
17592 AAATAGTATC
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
35 15 0.41
36 22 0.59
ACGTcount: A:0.27, C:0.04, G:0.35, T:0.34
Consensus pattern (35 bp):
TGATGATATAGGCATGATATGGTGATGGAATATGG
Found at i:17977 original size:19 final size:20
Alignment explanation
Indices: 17930--17980 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
17920 GAAATCCCTT
**
17930 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
17950 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
17969 TGAAGATACATG
1 TGAAAATACATG
17981 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:19866 original size:22 final size:20
Alignment explanation
Indices: 19841--19880 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
19831 ATGTTTGTTT
19841 ATGGTAATGGGAGCTAAGTATG
1 ATGGTAAT--GAGCTAAGTATG
*
19863 ATGGTCATGAGCTAAGTA
1 ATGGTAATGAGCTAAGTA
19881 CATCATCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
22 7 0.41
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.28
Consensus pattern (20 bp):
ATGGTAATGAGCTAAGTATG
Found at i:21234 original size:13 final size:13
Alignment explanation
Indices: 21212--21241 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
21202 ACTAAACACC
21212 TTTC-ACATACCT
1 TTTCAACATACCT
21224 TTTCAACATACCT
1 TTTCAACATACCT
21237 TTTCA
1 TTTCA
21242 TCTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:25418 original size:22 final size:20
Alignment explanation
Indices: 25393--25432 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
25383 ATGTTTGTTT
25393 ATGGTAATGGGAGCTAAGTATG
1 ATGGTAAT--GAGCTAAGTATG
*
25415 ATGGTCATGAGCTAAGTA
1 ATGGTAATGAGCTAAGTA
25433 CATCATCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
22 7 0.41
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.28
Consensus pattern (20 bp):
ATGGTAATGAGCTAAGTATG
Found at i:28275 original size:24 final size:21
Alignment explanation
Indices: 28241--28283 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
28231 TGCACAAGAT
*
28241 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGA-AATTCAAAGG
28263 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
28284 AGAATGAGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAAGG
Found at i:50324 original size:18 final size:20
Alignment explanation
Indices: 50301--50351 Score: 70
Period size: 21 Copynumber: 2.6 Consensus size: 20
50291 CGGCCAAGAG
*
50301 CATGTATCTTCA-TT-AAGT
1 CATGTATTTTCATTTAAAGT
50319 CATGTATTTTCATTTAAAAGT
1 CATGTATTTTCATTT-AAAGT
50340 CATGTATTTTCA
1 CATGTATTTTCA
50352 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 11 0.38
19 2 0.07
21 16 0.55
ACGTcount: A:0.29, C:0.14, G:0.10, T:0.47
Consensus pattern (20 bp):
CATGTATTTTCATTTAAAGT
Found at i:54156 original size:19 final size:21
Alignment explanation
Indices: 54132--54183 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
54122 CGGCCAAGAG
*
54132 CATGTATCTTCA-TTAAAA-T
1 CATGTATTTTCATTTAAAAGT
54151 CATGTATTTTCATTTAAAAGT
1 CATGTATTTTCATTTAAAAGT
54172 CATGTATTTTCA
1 CATGTATTTTCA
54184 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 6 0.20
21 13 0.43
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAGT
Done.