Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008698.1 Hibiscus syriacus cultivar Beakdansim tig00111730_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: 66933
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:3958 original size:15 final size:14
Alignment explanation
Indices: 3932--3962 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
3922 GTGCTTCAAC
3932 TTCTTTCTTTTCTT
1 TTCTTTCTTTTCTT
3946 TTCTTTGCTTTTCTT
1 TTCTTT-CTTTTCTT
3961 TT
1 TT
3963 TGAGTGTCGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.00, C:0.19, G:0.03, T:0.77
Consensus pattern (14 bp):
TTCTTTCTTTTCTT
Found at i:5993 original size:13 final size:13
Alignment explanation
Indices: 5969--6001 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
5959 ATACTAAACA
5969 CTTTTC-ACATAC
1 CTTTTCAACATAC
5981 CTTTTCAACATAC
1 CTTTTCAACATAC
5994 CTTTTCAA
1 CTTTTCAA
6002 TTTTGGCTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 6 0.30
13 14 0.70
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.42
Consensus pattern (13 bp):
CTTTTCAACATAC
Found at i:11008 original size:19 final size:20
Alignment explanation
Indices: 10984--11034 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
10974 CGGCCAAGAG
* *
10984 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
11003 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
11023 CATGTATTTTCA
1 CATGTATTTTCA
11035 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:11725 original size:14 final size:14
Alignment explanation
Indices: 11692--11738 Score: 58
Period size: 16 Copynumber: 3.1 Consensus size: 14
11682 AAAGAAATTC
11692 AAAAGAGAAAAATCAG
1 AAAAGAGAAAAA--AG
11708 AAAAGAGAAAAAAG
1 AAAAGAGAAAAAAG
*
11722 AAAAGAAAAGAAAAG
1 AAAAGAGAA-AAAAG
11737 AA
1 AA
11739 TTCAAAAAGA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
14 10 0.34
15 7 0.24
16 12 0.41
ACGTcount: A:0.77, C:0.02, G:0.19, T:0.02
Consensus pattern (14 bp):
AAAAGAGAAAAAAG
Found at i:11727 original size:5 final size:5
Alignment explanation
Indices: 11706--11738 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
11696 GAGAAAAATC
*
11706 AGAAA AGAGA A-AAA AGAAA AGAAA AGAAA AGAA
1 AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA AGAA
11739 TTCAAAAAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
4 3 0.12
5 22 0.88
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (5 bp):
AGAAA
Found at i:15114 original size:19 final size:20
Alignment explanation
Indices: 15090--15140 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
15080 CGGCCAAGAG
* *
15090 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
15109 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
15129 CATGTATTTTCA
1 CATGTATTTTCA
15141 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:19246 original size:19 final size:20
Alignment explanation
Indices: 19222--19272 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
19212 CGGCCAAGAG
* *
19222 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
19241 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
19261 CATGTATTTTCA
1 CATGTATTTTCA
19273 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:23384 original size:19 final size:20
Alignment explanation
Indices: 23360--23410 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
23350 CGGCCAAGAG
* *
23360 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
23379 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
23399 CATGTATTTTCA
1 CATGTATTTTCA
23411 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:24102 original size:18 final size:18
Alignment explanation
Indices: 24081--24140 Score: 63
Period size: 18 Copynumber: 3.4 Consensus size: 18
24071 AAGAAATTCA
24081 AAAAGAAGAAAAAATCAG
1 AAAAGAAGAAAAAATCAG
*
24099 AAAAGAAGAAAAGAA-AAG
1 AAAAGAAGAAAA-AATCAG
*
24117 AAAAGAA-AAAGAATTCA-
1 AAAAGAAGAAA-AAATCAG
24134 AAAAGAA
1 AAAAGAA
24141 AGCAAAGCCA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
17 11 0.31
18 23 0.64
19 2 0.06
ACGTcount: A:0.75, C:0.03, G:0.17, T:0.05
Consensus pattern (18 bp):
AAAAGAAGAAAAAATCAG
Found at i:27528 original size:19 final size:19
Alignment explanation
Indices: 27504--27553 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
27494 CGGCCAAGAG
* *
27504 CATGTATCTTCATTAAAAT
1 CATGTATTTTCATCAAAAT
27523 CATGTATTTTCATCAAAAT
1 CATGTATTTTCATCAAAAT
27542 CATGTATTTTCA
1 CATGTATTTTCA
27554 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.34, C:0.16, G:0.06, T:0.44
Consensus pattern (19 bp):
CATGTATTTTCATCAAAAT
Found at i:31665 original size:19 final size:20
Alignment explanation
Indices: 31641--31691 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
31631 CGGCCAAGAG
* *
31641 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
31660 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
31680 CATGTATTTTCA
1 CATGTATTTTCA
31692 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:35804 original size:19 final size:19
Alignment explanation
Indices: 35780--35829 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
35770 CGGCCAAGAG
* *
35780 CATGTATCTTCATTAAAAT
1 CATGTATTTTCATCAAAAT
35799 CATGTATTTTCATCAAAAT
1 CATGTATTTTCATCAAAAT
35818 CATGTATTTTCA
1 CATGTATTTTCA
35830 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.34, C:0.16, G:0.06, T:0.44
Consensus pattern (19 bp):
CATGTATTTTCATCAAAAT
Found at i:36523 original size:17 final size:17
Alignment explanation
Indices: 36496--36552 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
36486 AAAGAAATTC
36496 AAAAG-AGAAAAATCAG
1 AAAAGAAGAAAAATCAG
*
36512 AAAAGAAGAAAAGA-AAG
1 AAAAGAAGAAAA-ATCAG
36529 AAAAGAA-AAAGAATTCA-
1 AAAAGAAGAAA-AA-TCAG
36546 AAAAGAA
1 AAAAGAA
36553 AGCAAAGCCA
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
16 9 0.26
17 23 0.68
18 2 0.06
ACGTcount: A:0.74, C:0.04, G:0.18, T:0.05
Consensus pattern (17 bp):
AAAAGAAGAAAAATCAG
Found at i:39115 original size:12 final size:13
Alignment explanation
Indices: 39092--39116 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39082 ACGTACAACG
39092 AAAATACAAAAAA
1 AAAATACAAAAAA
39105 AAAATACAAAAA
1 AAAATACAAAAA
39117 GAAGTTCAAG
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:0.84, C:0.08, G:0.00, T:0.08
Consensus pattern (13 bp):
AAAATACAAAAAA
Found at i:45297 original size:19 final size:20
Alignment explanation
Indices: 45273--45323 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
45263 CGGTCAAGAG
* *
45273 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
45292 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
45312 CATGTATTTTCA
1 CATGTATTTTCA
45324 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:48484 original size:30 final size:30
Alignment explanation
Indices: 48430--48486 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
48420 TTTACTTAGC
**
48430 TTTATTATGTTTACATATGTTTTAGATTAA
1 TTTATTATGTTTACATATCATTTAGATTAA
* *
48460 TTTATTATGTTTTCATTTCATTTAGAT
1 TTTATTATGTTTACATATCATTTAGAT
48487 ATCATGGCAG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.26, C:0.05, G:0.09, T:0.60
Consensus pattern (30 bp):
TTTATTATGTTTACATATCATTTAGATTAA
Found at i:49425 original size:19 final size:20
Alignment explanation
Indices: 49401--49451 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
49391 CGGCCAAGAG
* *
49401 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
49420 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
49440 CATGTATTTTCA
1 CATGTATTTTCA
49452 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:60063 original size:8 final size:8
Alignment explanation
Indices: 60050--60080 Score: 62
Period size: 8 Copynumber: 3.9 Consensus size: 8
60040 CTTTGAATGT
60050 ACTTTGCA
1 ACTTTGCA
60058 ACTTTGCA
1 ACTTTGCA
60066 ACTTTGCA
1 ACTTTGCA
60074 ACTTTGC
1 ACTTTGC
60081 TTCACTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.23, C:0.26, G:0.13, T:0.39
Consensus pattern (8 bp):
ACTTTGCA
Found at i:60172 original size:13 final size:12
Alignment explanation
Indices: 60149--60183 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
60139 TGTAGGAGTC
60149 TTTCTCTTTTCTT
1 TTTCTC-TTTCTT
60162 TTTCTTCTTTCTT
1 TTTC-TCTTTCTT
60175 TTTCTCTTT
1 TTTCTCTTT
60184 TGTTGCTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 5 0.24
13 14 0.67
14 2 0.10
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTCTCTTTCTT
Found at i:64037 original size:22 final size:22
Alignment explanation
Indices: 63981--64038 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
63971 TGCAAAAGTG
63981 AAAGAAAAA-AAAGCACTCAAA
1 AAAGAAAAAGAAAGCACTCAAA
** **
64002 AGAAGAAATTGAAAGCACTTGAA
1 A-AAGAAAAAGAAAGCACTCAAA
64025 AAAGAAAAAGAAAG
1 AAAGAAAAAGAAAG
64039 AAAGATTGTG
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
21 1 0.03
22 17 0.59
23 11 0.38
ACGTcount: A:0.66, C:0.09, G:0.17, T:0.09
Consensus pattern (22 bp):
AAAGAAAAAGAAAGCACTCAAA
Done.