Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003176.1 Hibiscus syriacus cultivar Beakdansim tig00006685_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: 56067
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.34
Found at i:3670 original size:39 final size:39
Alignment explanation
Indices: 3601--3682 Score: 103
Period size: 39 Copynumber: 2.1 Consensus size: 39
3591 ATCTTTATGA
* * * *
3601 AAATGAAGAAGACTCCACAACTACATGATATCTTCAGAT
1 AAATGAAGAAGACTCCAAAAATACACGATATCTTCAGAG
*
3640 AAATGAAGAAGAC-CCTAAAAATACACGATATTTTCAGAG
1 AAATGAAGAAGACTCC-AAAAATACACGATATCTTCAGAG
3679 AAAT
1 AAAT
3683 AAATTAACTT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
38 2 0.05
39 35 0.95
ACGTcount: A:0.48, C:0.17, G:0.13, T:0.22
Consensus pattern (39 bp):
AAATGAAGAAGACTCCAAAAATACACGATATCTTCAGAG
Found at i:22498 original size:12 final size:12
Alignment explanation
Indices: 22467--22505 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
22457 TTTTTATTAA
* *
22467 TATATATATATA
1 TATATATGTATG
22479 TATATATGTATG
1 TATATATGTATG
22491 TATATATGTATG
1 TATATATGTATG
22503 TAT
1 TAT
22506 GTACTTACTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.51
Consensus pattern (12 bp):
TATATATGTATG
Found at i:25655 original size:2 final size:2
Alignment explanation
Indices: 25648--25673 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
25638 AACGTGCATA
25648 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
25674 GAATTCATCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:26814 original size:15 final size:15
Alignment explanation
Indices: 26794--26822 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
26784 TCACCGACTA
26794 AACCGAATTAACCAT
1 AACCGAATTAACCAT
26809 AACCGAATTAACCA
1 AACCGAATTAACCA
26823 AATTTTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.28, G:0.07, T:0.17
Consensus pattern (15 bp):
AACCGAATTAACCAT
Found at i:26970 original size:30 final size:30
Alignment explanation
Indices: 26934--27001 Score: 109
Period size: 30 Copynumber: 2.3 Consensus size: 30
26924 TCCCCGACCG
* *
26934 AACTAATTCGGTGGCCGACCGAATTAACCA
1 AACTAATTCGATGGCCAACCGAATTAACCA
*
26964 AACTAATTCGATGGCCAACCGAATTAATCA
1 AACTAATTCGATGGCCAACCGAATTAACCA
26994 AACTAATT
1 AACTAATT
27002 TTATTTGGTC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.38, C:0.24, G:0.15, T:0.24
Consensus pattern (30 bp):
AACTAATTCGATGGCCAACCGAATTAACCA
Found at i:29661 original size:18 final size:19
Alignment explanation
Indices: 29629--29670 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
29619 AATCTTTACC
* *
29629 CTTTTTTTTACTTTAATTG
1 CTTTTATTTACTTTAATCG
29648 CTTTTATTTA-TTTAATCG
1 CTTTTATTTACTTTAATCG
29666 CTTTT
1 CTTTT
29671 TACTATTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 12 0.57
19 9 0.43
ACGTcount: A:0.17, C:0.12, G:0.05, T:0.67
Consensus pattern (19 bp):
CTTTTATTTACTTTAATCG
Found at i:30604 original size:173 final size:173
Alignment explanation
Indices: 30311--30657 Score: 658
Period size: 173 Copynumber: 2.0 Consensus size: 173
30301 GTATCATTAA
30311 TTTTCTATCATCAGATATAATTTTTTAATTACACCATATAAAATATCTCATCAATGTTACCATTG
1 TTTTCTATCATCAGATATAATTTTTTAATTACACCATATAAAATATCTCATCAATGTTACCATTG
*
30376 AGAAACATAATTTTGAAATACAATTTATGTAACTCTAGATAAAAACAATTATCATGATTATCCTA
66 AGAAACATAATTTTGAAATACAATTTATGTAACTCTAGATAAAAACAAGTATCATGATTATCCTA
*
30441 AAAGAGTCTTTCAATGAAACCAAAGAGGAAGTCTCTACAAAAT
131 AAAGAGTCTTTCAATGAAACCAAAGAAGAAGTCTCTACAAAAT
*
30484 TTTTCTATCATCAGATATAATTTTTTAATTACACCATATAAAATATCTCATCAATGTTATCATTG
1 TTTTCTATCATCAGATATAATTTTTTAATTACACCATATAAAATATCTCATCAATGTTACCATTG
30549 AGAAACATAATTTTGAAATACAATTTATGTAACTCTAGATAAAAACAAGTATCATGATTATCCTA
66 AGAAACATAATTTTGAAATACAATTTATGTAACTCTAGATAAAAACAAGTATCATGATTATCCTA
*
30614 AAAGAGTCTTTTAATGAAACCAAAGAAGAAGTCTCTACAAAAT
131 AAAGAGTCTTTCAATGAAACCAAAGAAGAAGTCTCTACAAAAT
30657 T
1 T
30658 AATGTCTTTT
Statistics
Matches: 170, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
173 170 1.00
ACGTcount: A:0.42, C:0.14, G:0.09, T:0.35
Consensus pattern (173 bp):
TTTTCTATCATCAGATATAATTTTTTAATTACACCATATAAAATATCTCATCAATGTTACCATTG
AGAAACATAATTTTGAAATACAATTTATGTAACTCTAGATAAAAACAAGTATCATGATTATCCTA
AAAGAGTCTTTCAATGAAACCAAAGAAGAAGTCTCTACAAAAT
Found at i:40524 original size:21 final size:21
Alignment explanation
Indices: 40487--40526 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
40477 CCCCCTTTGA
*
40487 AGGGGAACTGATTCCCCCCAC
1 AGGGGAACTGATACCCCCCAC
40508 AGGGGAA-TCGATACCCCCC
1 AGGGGAACT-GATACCCCCC
40527 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.25, C:0.38, G:0.25, T:0.12
Consensus pattern (21 bp):
AGGGGAACTGATACCCCCCAC
Found at i:47760 original size:55 final size:55
Alignment explanation
Indices: 47686--48107 Score: 470
Period size: 55 Copynumber: 7.8 Consensus size: 55
47676 CGACCATCGG
* * * ** * *
47686 GTTCGCTCCCTCTTGCTTCAGGGAGTATAAAACTAAAACAATCTTCATA-AAACAT
1 GTTCGCTCCCTATTCCTTCAGAGAGTATAGGACTTAAACAATCTTCA-ACAAACGT
* * *
47741 GTTTGTTCCCTATTCCTTCAGAGAGTATAGGAC-T---CGATCTTCAACAAACGT
1 GTTCGCTCCCTATTCCTTCAGAGAGTATAGGACTTAAACAATCTTCAACAAACGT
** * *
47792 GTTCGCTCCCTATTTTTTCAGAGAGTATAGGACTTGAACAACCTTCAACAAACGT
1 GTTCGCTCCCTATTCCTTCAGAGAGTATAGGACTTAAACAATCTTCAACAAACGT
*
47847 GTAT-GCTCCCTATTCCTTTAGAGAGTATAGGAC-T---CAATCTTCAACAAACGT
1 GT-TCGCTCCCTATTCCTTCAGAGAGTATAGGACTTAAACAATCTTCAACAAACGT
* * * *
47898 GTTCGCTCCCTATTTCTTCAGAGAGTATATGACTTGAACAACCTTCAACAAACGT
1 GTTCGCTCCCTATTCCTTCAGAGAGTATAGGACTTAAACAATCTTCAACAAACGT
* * *
47953 GTCCACTCCCTATTCCTTCAGAGAGTATAGGACTTGAACAATCTTCAACAAACGT
1 GTTCGCTCCCTATTCCTTCAGAGAGTATAGGACTTAAACAATCTTCAACAAACGT
* * * **
48008 GTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTCAAACAATCTTCAACAATTGT
1 GTTCGCTCCCTATTCCTTCAGAGAGTATAGGACTTAAACAATCTTCAACAAACGT
* * *
48063 G-TCTGCTCCATATTCCTTCAGAGAGTATAAGACTCAAACAATCTT
1 GTTC-GCTCCCTATTCCTTCAGAGAGTATAGGACTTAAACAATCTT
48108 AATGTTTCAA
Statistics
Matches: 318, Mismatches: 37, Indels: 24
0.84 0.10 0.06
Matches are distributed among these distances:
50 2 0.01
51 86 0.27
52 2 0.01
54 2 0.01
55 225 0.71
56 1 0.00
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.30
Consensus pattern (55 bp):
GTTCGCTCCCTATTCCTTCAGAGAGTATAGGACTTAAACAATCTTCAACAAACGT
Found at i:47832 original size:106 final size:106
Alignment explanation
Indices: 47686--48099 Score: 524
Period size: 106 Copynumber: 3.9 Consensus size: 106
47676 CGACCATCGG
* * * * * * * *
47686 GTTCGCTCCCTCTTGCTTCAGGGAGTATAAAACTAAAACAATCTTCATA-AAACATGTTTGTTCC
1 GTTCGCTCCCTATTTCTTCAGAGAGTATAAGACTTAAACAACCTTCA-ACAAACGTGTTTGCTCC
*
47750 CTATTCCTTCAGAGAGTATAGGACTCGATCTTCAACAAACGT
65 CTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACAAACGT
* * * *
47792 GTTCGCTCCCTATTTTTTCAGAGAGTATAGGACTTGAACAACCTTCAACAAACGTGTATGCTCCC
1 GTTCGCTCCCTATTTCTTCAGAGAGTATAAGACTTAAACAACCTTCAACAAACGTGTTTGCTCCC
*
47857 TATTCCTTTAGAGAGTATAGGACTCAATCTTCAACAAACGT
66 TATTCCTTCAGAGAGTATAGGACTCAATCTTCAACAAACGT
* * ***
47898 GTTCGCTCCCTATTTCTTCAGAGAGTATATGACTTGAACAACCTTCAACAAACGTGTCCACTCCC
1 GTTCGCTCCCTATTTCTTCAGAGAGTATAAGACTTAAACAACCTTCAACAAACGTGTTTGCTCCC
47963 TATTCCTTCAGAGAGTATAGGACTTGAACAATCTTCAACAAACGT
66 TATTCCTTCAGAGAGTATAGGAC-T---CAATCTTCAACAAACGT
* * * * ** * *
48008 GTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTCAAACAATCTTCAACAATTGTGTCTGCTCCA
1 GTTCGCTCCCTATTTCTTCAGAGAGTATAAGACTTAAACAACCTTCAACAAACGTGTTTGCTCCC
*
48073 TATTCCTTCAGAGAGTATAAGACTCAA
66 TATTCCTTCAGAGAGTATAGGACTCAA
48100 ACAATCTTAA
Statistics
Matches: 271, Mismatches: 32, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
105 1 0.00
106 175 0.65
107 1 0.00
109 1 0.00
110 93 0.34
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.30
Consensus pattern (106 bp):
GTTCGCTCCCTATTTCTTCAGAGAGTATAAGACTTAAACAACCTTCAACAAACGTGTTTGCTCCC
TATTCCTTCAGAGAGTATAGGACTCAATCTTCAACAAACGT
Found at i:49161 original size:9 final size:9
Alignment explanation
Indices: 49149--49199 Score: 59
Period size: 10 Copynumber: 5.6 Consensus size: 9
49139 CTTTTATTCG
49149 TTTTTTTCA
1 TTTTTTTCA
*
49158 TTTTTTTTA
1 TTTTTTTCA
*
49167 TTTTTTTTTA
1 -TTTTTTTCA
49177 TTTTTTTTCA
1 -TTTTTTTCA
49187 -TTTTTTCA
1 TTTTTTTCA
49195 TTTTT
1 TTTTT
49200 ATCTTCAAGC
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
8 8 0.21
9 12 0.32
10 18 0.47
ACGTcount: A:0.10, C:0.06, G:0.00, T:0.84
Consensus pattern (9 bp):
TTTTTTTCA
Found at i:49162 original size:10 final size:10
Alignment explanation
Indices: 49149--49192 Score: 72
Period size: 10 Copynumber: 4.5 Consensus size: 10
49139 CTTTTATTCG
49149 TTTTTTTCAT
1 TTTTTTTCAT
49159 TTTTTTT-AT
1 TTTTTTTCAT
*
49168 TTTTTTTTAT
1 TTTTTTTCAT
49178 TTTTTTTCAT
1 TTTTTTTCAT
49188 TTTTT
1 TTTTT
49193 CATTTTTATC
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
9 9 0.28
10 23 0.72
ACGTcount: A:0.09, C:0.05, G:0.00, T:0.86
Consensus pattern (10 bp):
TTTTTTTCAT
Done.