Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008486.1 Hibiscus syriacus cultivar Beakdansim tig00111327_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: 56252
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.32
Found at i:4498 original size:22 final size:20
Alignment explanation
Indices: 4473--4512 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
4463 ATGTTTGTTT
4473 ATGGTAATGGGAGCTAAGTATG
1 ATGGTAAT--GAGCTAAGTATG
*
4495 ATGGTCATGAGCTAAGTA
1 ATGGTAATGAGCTAAGTA
4513 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:13165 original size:36 final size:36
Alignment explanation
Indices: 13090--13187 Score: 162
Period size: 36 Copynumber: 2.8 Consensus size: 36
13080 TATAAGTTGG
* *
13090 TGATAATATAGGCGTGAT-ATGGTGATGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGC
*
13125 TGATGATATAGGCGTGATAATGGTGATGGACTATGC
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGC
13161 TGATGATATAGGCGTGATAATGGTGAT
1 TGATGATATAGGCGTGATAATGGTGAT
13188 AGACAGATTG
Statistics
Matches: 59, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
35 17 0.29
36 42 0.71
ACGTcount: A:0.30, C:0.05, G:0.34, T:0.32
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGAATATGC
Found at i:17258 original size:11 final size:11
Alignment explanation
Indices: 17242--17266 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
17232 TTGGCATTGA
17242 TGGACTTGATT
1 TGGACTTGATT
17253 TGGACTTGATT
1 TGGACTTGATT
17264 TGG
1 TGG
17267 GCACATTGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.08, G:0.32, T:0.44
Consensus pattern (11 bp):
TGGACTTGATT
Found at i:20294 original size:15 final size:15
Alignment explanation
Indices: 20259--20287 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
20249 GTGCTTCAAC
20259 TTCTTT-CTTTTCTT
1 TTCTTTGCTTTTCTT
20273 TTCTTTGCTTTTCTT
1 TTCTTTGCTTTTCTT
20288 CTTTTTGAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.00, C:0.21, G:0.03, T:0.76
Consensus pattern (15 bp):
TTCTTTGCTTTTCTT
Found at i:20310 original size:27 final size:29
Alignment explanation
Indices: 20280--20340 Score: 74
Period size: 27 Copynumber: 2.2 Consensus size: 29
20270 CTTTTCTTTG
*
20280 CTTTTC-TTCTTTTTGAATGC-TAAATTT
1 CTTTTCTTTCTTTTGGAATGCTTAAATTT
* *
20307 C-TTTCTTTCTTTTGGAGTGCTTCAATTT
1 CTTTTCTTTCTTTTGGAATGCTTAAATTT
20335 CTTTTC
1 CTTTTC
20341 CGATTTTCTT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
26 4 0.14
27 13 0.46
28 7 0.25
29 4 0.14
ACGTcount: A:0.13, C:0.18, G:0.10, T:0.59
Consensus pattern (29 bp):
CTTTTCTTTCTTTTGGAATGCTTAAATTT
Found at i:31496 original size:11 final size:11
Alignment explanation
Indices: 31482--31531 Score: 50
Period size: 10 Copynumber: 4.6 Consensus size: 11
31472 AAATTTTGGC
31482 TTTTTTGGC-T
1 TTTTTTGGCTT
*
31492 TTTTTT-GTTT
1 TTTTTTGGCTT
*
31502 TTTTTTGTTCTT
1 TTTTTTG-GCTT
*
31514 TTTTTTGCCTT
1 TTTTTTGGCTT
31525 TTTTTTG
1 TTTTTTG
31532 AAAAAAAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
9 1 0.03
10 13 0.39
11 10 0.30
12 9 0.27
ACGTcount: A:0.00, C:0.08, G:0.12, T:0.80
Consensus pattern (11 bp):
TTTTTTGGCTT
Found at i:35966 original size:11 final size:11
Alignment explanation
Indices: 35946--35978 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
35936 AAAGTAGTAT
35946 CTCAAAGAAGA
1 CTCAAAGAAGA
*
35957 CTCAACGAAGA
1 CTCAAAGAAGA
35968 CTCAAAGAAGA
1 CTCAAAGAAGA
35979 ACCAATGTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.52, C:0.21, G:0.18, T:0.09
Consensus pattern (11 bp):
CTCAAAGAAGA
Found at i:43259 original size:33 final size:33
Alignment explanation
Indices: 43195--43295 Score: 82
Period size: 33 Copynumber: 3.0 Consensus size: 33
43185 CTTGTTGATG
* * *
43195 AATG-AAGGATGAT-TTAATGGTGATGAAATGGT
1 AATGAAAGGATGATGTTATTGGCG-TGATATGGT
43227 AATGAAAGGATGATGTTATTGGCGTGATATGGT
1 AATGAAAGGATGATGTTATTGGCGTGATATGGT
* * *
43260 GATGGAATATGG-TGATGATATAGGCGTGATAATGGT
1 AAT-GAA-A-GGATGATGTTATTGGCGTGAT-ATGGT
43296 GATGGACAGA
Statistics
Matches: 57, Mismatches: 6, Indels: 8
0.80 0.08 0.11
Matches are distributed among these distances:
32 4 0.07
33 19 0.33
34 10 0.18
35 17 0.30
36 7 0.12
ACGTcount: A:0.33, C:0.02, G:0.34, T:0.32
Consensus pattern (33 bp):
AATGAAAGGATGATGTTATTGGCGTGATATGGT
Found at i:47017 original size:11 final size:11
Alignment explanation
Indices: 47001--47026 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
46991 TGTAGGAGTC
47001 TTTTCTTTTCT
1 TTTTCTTTTCT
47012 TTTTCTTTTCT
1 TTTTCTTTTCT
47023 TTTT
1 TTTT
47027 TTCTCGTTGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTCTTTTCT
Found at i:47441 original size:33 final size:33
Alignment explanation
Indices: 47377--47477 Score: 82
Period size: 33 Copynumber: 3.0 Consensus size: 33
47367 CTTGTTGATG
* * *
47377 AATG-AAGGATGAT-TTAATGGTGATGAAATGGT
1 AATGAAAGGATGATGTTATTGGCG-TGATATGGT
47409 AATGAAAGGATGATGTTATTGGCGTGATATGGT
1 AATGAAAGGATGATGTTATTGGCGTGATATGGT
* * *
47442 GATGGAATATGG-TGATGATATAGGCGTGATAATGGT
1 AAT-GAA-A-GGATGATGTTATTGGCGTGAT-ATGGT
47478 GATGGACAGA
Statistics
Matches: 57, Mismatches: 6, Indels: 8
0.80 0.08 0.11
Matches are distributed among these distances:
32 4 0.07
33 19 0.33
34 10 0.18
35 17 0.30
36 7 0.12
ACGTcount: A:0.33, C:0.02, G:0.34, T:0.32
Consensus pattern (33 bp):
AATGAAAGGATGATGTTATTGGCGTGATATGGT
Found at i:49955 original size:19 final size:20
Alignment explanation
Indices: 49914--49964 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
49904 GAAACCCCTT
* *
49914 TGAAAATACATGATTTTTGA
1 TGAAAATACATGAGTTTTAA
49934 TGAAAATACATG-GTTTTAA
1 TGAAAATACATGAGTTTTAA
*
49953 TGAAGATACATG
1 TGAAAATACATG
49965 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.41, C:0.06, G:0.18, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGAGTTTTAA
Found at i:54127 original size:19 final size:20
Alignment explanation
Indices: 54086--54136 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
54076 GAAACCCCTT
*
54086 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
54106 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
54125 TGAAGATACATG
1 TGAAAATACATG
54137 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Done.