Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008699.1 Hibiscus syriacus cultivar Beakdansim tig00111731_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: 63812
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.31
Found at i:3052 original size:19 final size:19
Alignment explanation
Indices: 3028--3070 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
3018 CGGCCAAGAG
*
3028 CATGTATCTTCATTAAAAT
1 CATGTATCTTCATCAAAAT
*
3047 CATGTATTTTCATCAAAAT
1 CATGTATCTTCATCAAAAT
3066 CATGT
1 CATGT
3071 TTTCAAAGGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.35, C:0.16, G:0.07, T:0.42
Consensus pattern (19 bp):
CATGTATCTTCATCAAAAT
Found at i:3075 original size:17 final size:18
Alignment explanation
Indices: 3036--3075 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
3026 AGCATGTATC
*
3036 TTCATTAAAATCATGTATT
1 TTCATCAAAATCATG-ATT
3055 TTCATCAAAATCATG-TT
1 TTCATCAAAATCATGATT
3072 TTCA
1 TTCA
3076 AAGGGGTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 6 0.30
19 14 0.70
ACGTcount: A:0.35, C:0.15, G:0.05, T:0.45
Consensus pattern (18 bp):
TTCATCAAAATCATGATT
Found at i:7173 original size:19 final size:20
Alignment explanation
Indices: 7149--7199 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
7139 CGGCCAAGAG
* *
7149 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
7168 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
7188 CATGTATTTTCA
1 CATGTATTTTCA
7200 AAGGGTTTCA
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:11305 original size:19 final size:20
Alignment explanation
Indices: 11281--11331 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
11271 CGGCCAAGAG
* *
11281 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
11300 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
11320 CATGTATTTTCA
1 CATGTATTTTCA
11332 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:14616 original size:12 final size:13
Alignment explanation
Indices: 14593--14617 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
14583 ACGTACAACG
14593 AAAATACAAAAAA
1 AAAATACAAAAAA
14606 AAAATACAAAAA
1 AAAATACAAAAA
14618 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:20806 original size:19 final size:20
Alignment explanation
Indices: 20782--20832 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
20772 CGGTCAAGAG
* *
20782 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
20801 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
20821 CATGTATTTTCA
1 CATGTATTTTCA
20833 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:24946 original size:19 final size:20
Alignment explanation
Indices: 24922--24972 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
24912 CGGCCAAGAG
* *
24922 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
24941 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
24961 CATGTATTTTCA
1 CATGTATTTTCA
24973 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:27541 original size:60 final size:60
Alignment explanation
Indices: 27431--27543 Score: 154
Period size: 60 Copynumber: 1.9 Consensus size: 60
27421 TGGACCATAC
* ** * *
27431 CACACGTTGGGATAGTTTGGTGGAGCATTTTGAAGACATATACAGGTCACAAACAGATGA
1 CACACGTTGGGACAACTTGGTGGAGCATTTGGAAGACATATACAGCTCACAAACAGATGA
* **
27491 CACACGTTGGGACAACTTGGTGGAGCATTTGGGAGACATATATTGCTCACAAA
1 CACACGTTGGGACAACTTGGTGGAGCATTTGGAAGACATATACAGCTCACAAA
27544 TAGCTCACAA
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
60 45 1.00
ACGTcount: A:0.32, C:0.17, G:0.27, T:0.25
Consensus pattern (60 bp):
CACACGTTGGGACAACTTGGTGGAGCATTTGGAAGACATATACAGCTCACAAACAGATGA
Found at i:35641 original size:8 final size:8
Alignment explanation
Indices: 35628--35658 Score: 62
Period size: 8 Copynumber: 3.9 Consensus size: 8
35618 CTTTGAATGT
35628 ACTTTGCA
1 ACTTTGCA
35636 ACTTTGCA
1 ACTTTGCA
35644 ACTTTGCA
1 ACTTTGCA
35652 ACTTTGC
1 ACTTTGC
35659 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:35752 original size:13 final size:12
Alignment explanation
Indices: 35729--35763 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
35719 TGTAGGAGTC
35729 TTTCTCTTTTCTT
1 TTTCTC-TTTCTT
35742 TTTCTTCTTTCTT
1 TTTC-TCTTTCTT
35755 TTTCTCTTT
1 TTTCTCTTT
35764 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:39656 original size:22 final size:22
Alignment explanation
Indices: 39600--39657 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
39590 TGCAAAAGTG
39600 AAAGAAAAA-AAAGCACTCAAA
1 AAAGAAAAAGAAAGCACTCAAA
** **
39621 AGAAGAAATTGAAAGCACTTGAA
1 A-AAGAAAAAGAAAGCACTCAAA
39644 AAAGAAAAAGAAAG
1 AAAGAAAAAGAAAG
39658 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
Found at i:43397 original size:19 final size:21
Alignment explanation
Indices: 43373--43424 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
43363 CGGCCAAGAG
* *
43373 CATGTATCTTCA-TTACAA-T
1 CATGTATTTTCATTTAAAAGT
43392 CATGTATTTTCATTTAAAAGT
1 CATGTATTTTCATTTAAAAGT
43413 CATGTATTTTCA
1 CATGTATTTTCA
43425 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 11 0.38
20 5 0.17
21 13 0.45
ACGTcount: A:0.31, C:0.15, G:0.08, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAGT
Found at i:52670 original size:23 final size:24
Alignment explanation
Indices: 52638--52690 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
52628 TTATCTTTTC
*
52638 TTTTTTAA-TTTTCAAAATT-TGT
1 TTTTTTAATTTTTCAAAATTCTAT
*
52660 TTTTTTAAATTTTTCAGAATTCTAT
1 TTTTTT-AATTTTTCAAAATTCTAT
52685 TTTTTT
1 TTTTTT
52691 CAAGATGAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 6 0.23
23 2 0.08
24 10 0.38
25 8 0.31
ACGTcount: A:0.25, C:0.06, G:0.04, T:0.66
Consensus pattern (24 bp):
TTTTTTAATTTTTCAAAATTCTAT
Found at i:53977 original size:28 final size:28
Alignment explanation
Indices: 53945--54079 Score: 118
Period size: 28 Copynumber: 4.9 Consensus size: 28
53935 TGAATTAACT
*
53945 AAACAAATGATGAATATGCTGTTATGCA
1 AAACAAATGATGAACATGCTGTTATGCA
53973 AAACAAATGATGAACATGCTGTTATG--
1 AAACAAATGATGAACATGCTGTTATGCA
** ** * * * *
53999 TGAC-TGTGAGTGTACGTGAAT-TTA-ACA
1 AAACAAATGA-TGAACATG-CTGTTATGCA
* *
54026 AAACAAATGATAAATATGCTGTTATGCA
1 AAACAAATGATGAACATGCTGTTATGCA
54054 AAACAAATGATGAACATGCTGTTATG
1 AAACAAATGATGAACATGCTGTTATG
54080 AACCCCACGA
Statistics
Matches: 79, Mismatches: 21, Indels: 14
0.69 0.18 0.12
Matches are distributed among these distances:
25 3 0.04
26 12 0.15
27 10 0.13
28 54 0.68
ACGTcount: A:0.41, C:0.11, G:0.19, T:0.29
Consensus pattern (28 bp):
AAACAAATGATGAACATGCTGTTATGCA
Found at i:57337 original size:38 final size:39
Alignment explanation
Indices: 57286--57363 Score: 149
Period size: 38 Copynumber: 2.0 Consensus size: 39
57276 GAAAAGATTA
57286 AGGCAATACAAGAATGGCCAAAGCC-GTCAATGTCAGCC
1 AGGCAATACAAGAATGGCCAAAGCCGGTCAATGTCAGCC
57324 AGGCAATACAAGAATGGCCAAAGCCGGTCAATGTCAGCC
1 AGGCAATACAAGAATGGCCAAAGCCGGTCAATGTCAGCC
57363 A
1 A
57364 AGTCTGGAGT
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
38 25 0.64
39 14 0.36
ACGTcount: A:0.37, C:0.26, G:0.24, T:0.13
Consensus pattern (39 bp):
AGGCAATACAAGAATGGCCAAAGCCGGTCAATGTCAGCC
Found at i:58224 original size:11 final size:13
Alignment explanation
Indices: 58192--58221 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
58182 TGGCCAAAGA
58192 TGAAAAGGTATGT
1 TGAAAAGGTATGT
58205 TGAAAAGGTATG-
1 TGAAAAGGTATGT
58217 TGAAA
1 TGAAA
58222 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:61611 original size:21 final size:21
Alignment explanation
Indices: 61587--61639 Score: 106
Period size: 21 Copynumber: 2.5 Consensus size: 21
61577 CATCCTTATT
61587 TCATTTCATTTCTTATCTTTA
1 TCATTTCATTTCTTATCTTTA
61608 TCATTTCATTTCTTATCTTTA
1 TCATTTCATTTCTTATCTTTA
61629 TCATTTCATTT
1 TCATTTCATTT
61640 AATCTTTTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.19, C:0.19, G:0.00, T:0.62
Consensus pattern (21 bp):
TCATTTCATTTCTTATCTTTA
Found at i:62654 original size:18 final size:20
Alignment explanation
Indices: 62613--62654 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
62603 ATGGATCCTT
62613 TGAAAATACATGATTTTAAA
1 TGAAAATACATGATTTTAAA
62633 TGAAAATAC-TGATTTT-AA
1 TGAAAATACATGATTTTAAA
62651 TGAA
1 TGAA
62655 GACATGCTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 6 0.27
19 7 0.32
20 9 0.41
ACGTcount: A:0.48, C:0.05, G:0.12, T:0.36
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Done.