Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005410.1 Hibiscus syriacus cultivar Beakdansim tig00012405_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: 65403
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:636 original size:22 final size:22
Alignment explanation
Indices: 602--646 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
592 TTTATTTCTC
* *
602 TTTTTTCATTTTTTTCATTTTT
1 TTTTTTCACTTTTTCCATTTTT
*
624 TTTTTTCCCTTTTTCCATTTTT
1 TTTTTTCACTTTTTCCATTTTT
646 T
1 T
647 CTTCTTTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.07, C:0.16, G:0.00, T:0.78
Consensus pattern (22 bp):
TTTTTTCACTTTTTCCATTTTT
Found at i:687 original size:34 final size:32
Alignment explanation
Indices: 612--689 Score: 84
Period size: 34 Copynumber: 2.3 Consensus size: 32
602 TTTTTTCATT
* **
612 TTTTTCATTTTTTTTTTTCCCTTTTTCCATTT
1 TTTTTCTTTTTTTTTTTTCCCTTTTTCCATCA
**
644 TTTCTTCTTTTTTTTCTTTTCGTTTTTTTCCATCA
1 TTT-TTCTTTTTTTT-TTTTC-CCTTTTTCCATCA
679 TTTTTCTTTTT
1 TTTTTCTTTTT
690 CTCATTTTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
32 3 0.08
33 10 0.26
34 13 0.34
35 12 0.32
ACGTcount: A:0.05, C:0.18, G:0.01, T:0.76
Consensus pattern (32 bp):
TTTTTCTTTTTTTTTTTTCCCTTTTTCCATCA
Found at i:720 original size:9 final size:8
Alignment explanation
Indices: 590--721 Score: 72
Period size: 9 Copynumber: 15.4 Consensus size: 8
580 CTTGAACCTC
590 CTTTTATTT
1 CTTTT-TTT
599 CTCTTTTTT
1 CT-TTTTTT
608 CATTTTTTT
1 C-TTTTTTT
*
617 C-ATTTTT
1 CTTTTTTT
*
624 -TTTTTTC
1 CTTTTTTT
* *
631 CCTTTTTC
1 CTTTTTTT
*
639 CATTTTTT
1 CTTTTTTT
647 CTTCTTTTT
1 CTT-TTTTT
656 -TTTCTTTT
1 CTTT-TTTT
664 CGTTTTTTT
1 C-TTTTTTT
*
673 CCATCATTTTT
1 -C-T-TTTTTT
*
684 CTTTTTCT
1 CTTTTTTT
692 CATTTTTTT
1 C-TTTTTTT
701 CATTTTTTT
1 C-TTTTTTT
710 CTTTTATTT
1 CTTTT-TTT
719 CTT
1 CTT
722 CTTCAAGCAA
Statistics
Matches: 99, Mismatches: 12, Indels: 24
0.73 0.09 0.18
Matches are distributed among these distances:
7 10 0.10
8 29 0.29
9 45 0.45
10 10 0.10
11 5 0.05
ACGTcount: A:0.07, C:0.17, G:0.01, T:0.75
Consensus pattern (8 bp):
CTTTTTTT
Found at i:10370 original size:45 final size:48
Alignment explanation
Indices: 10303--10401 Score: 141
Period size: 45 Copynumber: 2.1 Consensus size: 48
10293 TATTATCCAC
*
10303 AAAAAGAAATCCTAACCTCATGATATCTAATTCGCATG-TTTATTC-A
1 AAAAAGAAATCCTAACCGCATGATATCTAATTCGCATGATTTATTCGA
* *
10349 AAAAATAAA-CCTAACCGCATGATATCTAGTTCGCATGCATTTATTCGA
1 AAAAAGAAATCCTAACCGCATGATATCTAATTCGCATG-ATTTATTCGA
10397 AAAAA
1 AAAAA
10402 ACGAAAATAA
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
45 26 0.55
46 8 0.17
47 7 0.15
48 6 0.13
ACGTcount: A:0.41, C:0.19, G:0.10, T:0.29
Consensus pattern (48 bp):
AAAAAGAAATCCTAACCGCATGATATCTAATTCGCATGATTTATTCGA
Found at i:17320 original size:17 final size:18
Alignment explanation
Indices: 17269--17337 Score: 79
Period size: 18 Copynumber: 3.9 Consensus size: 18
17259 GATGAATTCT
17269 AAATG-TTTACAATTATC
1 AAATGATTTACAATTATC
*
17286 AAATGATTTTCAATTATC
1 AAATGATTTACAATTATC
* *
17304 AGAT-ATTTACAAATATC
1 AAATGATTTACAATTATC
* *
17321 ATATGTTTTACAATTAT
1 AAATGATTTACAATTAT
17338 AAGACACAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
17 19 0.44
18 24 0.56
ACGTcount: A:0.41, C:0.10, G:0.06, T:0.43
Consensus pattern (18 bp):
AAATGATTTACAATTATC
Found at i:23382 original size:13 final size:13
Alignment explanation
Indices: 23364--23397 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
23354 AATGGATAAT
23364 TTTGAAAACTAA-G
1 TTTGAAAAC-AAGG
23377 TTTGAAAACAAGG
1 TTTGAAAACAAGG
23390 TTTGAAAA
1 TTTGAAAA
23398 TCAATATACG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 2 0.10
13 18 0.90
ACGTcount: A:0.47, C:0.06, G:0.18, T:0.29
Consensus pattern (13 bp):
TTTGAAAACAAGG
Found at i:23904 original size:22 final size:22
Alignment explanation
Indices: 23879--23933 Score: 92
Period size: 23 Copynumber: 2.5 Consensus size: 22
23869 TATCGGTTCC
23879 CTCAAGGGGGAATCGGTACCCA
1 CTCAAGGGGGAATCGGTACCCA
23901 CTCAAAGGGGGAATCGGTACCCA
1 CTC-AAGGGGGAATCGGTACCCA
*
23924 TTCAAGGGGG
1 CTCAAGGGGG
23934 GTATCGATTC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
22 10 0.32
23 21 0.68
ACGTcount: A:0.27, C:0.24, G:0.35, T:0.15
Consensus pattern (22 bp):
CTCAAGGGGGAATCGGTACCCA
Found at i:23912 original size:23 final size:23
Alignment explanation
Indices: 23882--23939 Score: 89
Period size: 23 Copynumber: 2.5 Consensus size: 23
23872 CGGTTCCCTC
23882 AAGGGGGAATCGGTACCCACTCA
1 AAGGGGGAATCGGTACCCACTCA
*
23905 AAGGGGGAATCGGTACCCATTCA
1 AAGGGGGAATCGGTACCCACTCA
* *
23928 AGGGGGGTATCG
1 AAGGGGGAATCG
23940 ATTCCTAGCA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.28, C:0.21, G:0.36, T:0.16
Consensus pattern (23 bp):
AAGGGGGAATCGGTACCCACTCA
Found at i:29631 original size:21 final size:21
Alignment explanation
Indices: 29579--29631 Score: 81
Period size: 21 Copynumber: 2.5 Consensus size: 21
29569 TAGAGCGTGG
*
29579 GGGGAATCGGAAACCCCTCAT
1 GGGGAATCGGTAACCCCTCAT
29600 GGGGAATCGGTAACCCCTCAAT
1 GGGGAATCGGTAACCCCTC-AT
29622 -GGGAATCGGT
1 GGGGAATCGGT
29632 TCCTGTAGTG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 28 0.93
22 2 0.07
ACGTcount: A:0.26, C:0.25, G:0.32, T:0.17
Consensus pattern (21 bp):
GGGGAATCGGTAACCCCTCAT
Found at i:31537 original size:15 final size:16
Alignment explanation
Indices: 31519--31548 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
31509 TTTTACTTTG
31519 AGATATTTT-AATGGA
1 AGATATTTTCAATGGA
31534 AGATATTTTCAATGG
1 AGATATTTTCAATGG
31549 CAAGTGGTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.37, C:0.03, G:0.20, T:0.40
Consensus pattern (16 bp):
AGATATTTTCAATGGA
Found at i:38011 original size:6 final size:6
Alignment explanation
Indices: 38000--38030 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
37990 GACACGTATT
38000 ACCACG ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG A
38031 TCCGAGCCGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.35, C:0.48, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:38042 original size:5 final size:5
Alignment explanation
Indices: 38032--38061 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
38022 CGACCACGAT
*
38032 CCGAG CCGAG CCGAG CCGAG CCGAG ACGAG
1 CCGAG CCGAG CCGAG CCGAG CCGAG CCGAG
38062 ACGGACGGAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.23, C:0.37, G:0.40, T:0.00
Consensus pattern (5 bp):
CCGAG
Found at i:38052 original size:15 final size:15
Alignment explanation
Indices: 38027--38061 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
38017 GACCACGACC
*
38027 ACGATCCGAGCCGAG
1 ACGAGCCGAGCCGAG
*
38042 CCGAGCCGAGCCGAG
1 ACGAGCCGAGCCGAG
38057 ACGAG
1 ACGAG
38062 ACGGACGGAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.26, C:0.34, G:0.37, T:0.03
Consensus pattern (15 bp):
ACGAGCCGAGCCGAG
Found at i:45707 original size:193 final size:193
Alignment explanation
Indices: 45378--45770 Score: 723
Period size: 193 Copynumber: 2.0 Consensus size: 193
45368 CAGGTACCAC
45378 TATGAATAATAACATTACTAGCTTTAATCAGCTGGTAACTGATCTGATGAATATGGACGTGACTT
1 TATGAATAATAACATTACTAGCTTTAATCAGCTGGTAACTGATCTGATGAATATGGACGTGACTT
*
45443 TTGAAGATGAAGATCTGGCTCTGATGTTGATGGGATCACTTCCTGATGAGTTTGAGTATCTTAAA
66 TTGAAGATGAAGATCTGGCTCTGATGTTGATGGGATCACTTCCTAATGAGTTTGAGTATCTTAAA
*
45508 ACTACTCTACTTCATGGGAAAGTTGATGTGTCTCTCAGTGAAGTAACTGCTGCCTTGTATAGT
131 ACTACTCTACTTCATGGGAAAGTTGATGTGTCTCTCAGTGAAGTAACTACTGCCTTGTATAGT
* *
45571 TATGAATGATCACATTACTAGCTTTAATCAGCTGGTAACTGATCTGATGAATATGGACGTGACTT
1 TATGAATAATAACATTACTAGCTTTAATCAGCTGGTAACTGATCTGATGAATATGGACGTGACTT
*
45636 TTGAAGATGAAGATCTGGCTCTGATGTTGATGGGATCACTTCCTAATGAGTTTGAGTATCTTGAA
66 TTGAAGATGAAGATCTGGCTCTGATGTTGATGGGATCACTTCCTAATGAGTTTGAGTATCTTAAA
* *
45701 ACTACTCTACTTCATGGGAAAGTTGATGTGTCTCTCAGTGAAGTGACTACTGCCTTGTATTGT
131 ACTACTCTACTTCATGGGAAAGTTGATGTGTCTCTCAGTGAAGTAACTACTGCCTTGTATAGT
45764 TATGAAT
1 TATGAAT
45771 TAAGAAATAA
Statistics
Matches: 193, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
193 193 1.00
ACGTcount: A:0.27, C:0.15, G:0.22, T:0.35
Consensus pattern (193 bp):
TATGAATAATAACATTACTAGCTTTAATCAGCTGGTAACTGATCTGATGAATATGGACGTGACTT
TTGAAGATGAAGATCTGGCTCTGATGTTGATGGGATCACTTCCTAATGAGTTTGAGTATCTTAAA
ACTACTCTACTTCATGGGAAAGTTGATGTGTCTCTCAGTGAAGTAACTACTGCCTTGTATAGT
Found at i:61976 original size:18 final size:18
Alignment explanation
Indices: 61953--61995 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
61943 GTTGTTTTTA
* *
61953 AAATAAAATATAAGAATT
1 AAATAAAAGAAAAGAATT
*
61971 AAATAAAAGAAAATAATT
1 AAATAAAAGAAAAGAATT
61989 AAATAAA
1 AAATAAA
61996 TAATTTAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (18 bp):
AAATAAAAGAAAAGAATT
Found at i:63972 original size:60 final size:60
Alignment explanation
Indices: 63879--63994 Score: 214
Period size: 60 Copynumber: 1.9 Consensus size: 60
63869 AATCGAATGA
*
63879 ACAAAAATAAAATTTTCTAACCCCCTGATTTCCTCATTGTAGTCTTCTAACTCCCTTATG
1 ACAAAAATAAAATTTTCTAACCCCCTAATTTCCTCATTGTAGTCTTCTAACTCCCTTATG
*
63939 ACAAAAATAAAATTTTCTAACCCTCTAATTTCCTCATTGTAGTCTTCTAACTCCCT
1 ACAAAAATAAAATTTTCTAACCCCCTAATTTCCTCATTGTAGTCTTCTAACTCCCT
63995 GCATATATCA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
60 54 1.00
ACGTcount: A:0.31, C:0.27, G:0.05, T:0.37
Consensus pattern (60 bp):
ACAAAAATAAAATTTTCTAACCCCCTAATTTCCTCATTGTAGTCTTCTAACTCCCTTATG
Done.