Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005742.1 Hibiscus syriacus cultivar Beakdansim tig00013429_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: 70378
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:9606 original size:22 final size:22
Alignment explanation
Indices: 9568--9609 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
9558 TCATGGCAAG
9568 AAAAAATGCAAGAGTAAAAAGT
1 AAAAAATGCAAGAGTAAAAAGT
*
9590 AAAAATTGCTAAG-GTAAAAA
1 AAAAAATGC-AAGAGTAAAAA
9610 TTAATTGCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.62, C:0.05, G:0.17, T:0.17
Consensus pattern (22 bp):
AAAAAATGCAAGAGTAAAAAGT
Found at i:22919 original size:19 final size:17
Alignment explanation
Indices: 22884--22918 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
22874 AATGAGGTTT
22884 TTTTCTATCATAATATA
1 TTTTCTATCATAATATA
*
22901 TTTTCTATCATAACATA
1 TTTTCTATCATAATATA
22918 T
1 T
22919 AGTGAGTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.34, C:0.14, G:0.00, T:0.51
Consensus pattern (17 bp):
TTTTCTATCATAATATA
Found at i:25149 original size:28 final size:28
Alignment explanation
Indices: 25096--25152 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 28
25086 ATTATATATA
25096 TATATATATAATTCTAAAATTTAAAGTTT
1 TATATATATAATTCTAAAA-TTAAAGTTT
25125 TATACTATATAATTC-ACAAA-TAAAGTTT
1 TATA-TATATAATTCTA-AAATTAAAGTTT
25153 AAAAATTCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
28 8 0.31
29 5 0.19
30 13 0.50
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.44
Consensus pattern (28 bp):
TATATATATAATTCTAAAATTAAAGTTT
Found at i:26746 original size:19 final size:19
Alignment explanation
Indices: 26722--26766 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
26712 TTCGTCTTTG
26722 TGGGAAGTAAGGAGCCATC
1 TGGGAAGTAAGGAGCCATC
*
26741 TGGGAAGTAAGGAGCCGTC
1 TGGGAAGTAAGGAGCCATC
26760 TGGGAAG
1 TGGGAAG
26767 GTATATCCCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.29, C:0.13, G:0.42, T:0.16
Consensus pattern (19 bp):
TGGGAAGTAAGGAGCCATC
Found at i:38092 original size:26 final size:26
Alignment explanation
Indices: 38050--38103 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
38040 ACTAAATGCA
*
38050 TATGGTGGACACGACCTTATGTGTAT
1 TATGGTGGACACAACCTTATGTGTAT
38076 TATGGTGGGACA-AACCTTATGTGTAT
1 TATGGT-GGACACAACCTTATGTGTAT
38102 TA
1 TA
38104 GCACTTCGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 21 0.81
27 5 0.19
ACGTcount: A:0.26, C:0.13, G:0.26, T:0.35
Consensus pattern (26 bp):
TATGGTGGACACAACCTTATGTGTAT
Found at i:62460 original size:2 final size:2
Alignment explanation
Indices: 62443--62484 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
62433 TCATAATAAC
*
62443 TA TA GA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
62484 T
1 T
62485 GAAAATAACT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:64840 original size:23 final size:23
Alignment explanation
Indices: 64796--64840 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
64786 GTTTGAGATA
* **
64796 CAACATCACCACCATCTTCCATT
1 CAACATCAACACCATCAACCATT
*
64819 CAACATCAACATCATCAACCAT
1 CAACATCAACACCATCAACCAT
64841 CTTCCATCAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.38, C:0.40, G:0.00, T:0.22
Consensus pattern (23 bp):
CAACATCAACACCATCAACCATT
Found at i:69740 original size:17 final size:17
Alignment explanation
Indices: 69707--69824 Score: 84
Period size: 17 Copynumber: 6.9 Consensus size: 17
69697 TTTTTGCTTG
*
69707 AAGAAGAAAA-GAAAAA
1 AAGAAAAAAATGAAAAA
*
69723 AAGGGAAAAAAGTG-AAAA
1 AA--GAAAAAAATGAAAAA
*
69741 AAGAAAAAAAAGAAAAA
1 AAGAAAAAAATGAAAAA
* *
69758 AAGAAAAAATTGGAAAA
1 AAGAAAAAAATGAAAAA
* *
69775 ATG-GAAAAATGTAAAAA
1 AAGAAAAAAATG-AAAAA
*
69792 ATGAAAAAAATGAAAGAA
1 AAGAAAAAAATGAAA-AA
69810 AA-AATAAAAA-GAAAA
1 AAGAA-AAAAATGAAAA
69825 TAAAATTGGT
Statistics
Matches: 81, Mismatches: 13, Indels: 16
0.74 0.12 0.15
Matches are distributed among these distances:
16 17 0.21
17 36 0.44
18 27 0.33
19 1 0.01
ACGTcount: A:0.75, C:0.00, G:0.17, T:0.08
Consensus pattern (17 bp):
AAGAAAAAAATGAAAAA
Found at i:69749 original size:9 final size:8
Alignment explanation
Indices: 69707--69824 Score: 76
Period size: 8 Copynumber: 13.9 Consensus size: 8
69697 TTTTTGCTTG
*
69707 AAGAAGAA
1 AAGAAAAA
69715 AAGAAAAA
1 AAGAAAAA
*
69723 AAGGGAAAA
1 AA-GAAAAA
*
69732 AAGTGAAAA
1 AAG-AAAAA
69741 AAGAAAAAA
1 AAG-AAAAA
69750 AAGAAAAA
1 AAGAAAAA
69758 AAGAAAAA
1 AAGAAAAA
* *
69766 ATTGGAAAA
1 A-AGAAAAA
* *
69775 ATGGAAAA
1 AAGAAAAA
*
69783 ATGTAAAAA
1 AAG-AAAAA
*
69792 ATGAAAAA
1 AAGAAAAA
69800 AATGAAAGAA
1 AA-GAAA-AA
69810 AA-AATAAA
1 AAGAA-AAA
69818 AAGAAAA
1 AAGAAAA
69825 TAAAATTGGT
Statistics
Matches: 94, Mismatches: 8, Indels: 16
0.80 0.07 0.14
Matches are distributed among these distances:
8 48 0.51
9 42 0.45
10 4 0.04
ACGTcount: A:0.75, C:0.00, G:0.17, T:0.08
Consensus pattern (8 bp):
AAGAAAAA
Found at i:69773 original size:43 final size:42
Alignment explanation
Indices: 69707--69811 Score: 120
Period size: 43 Copynumber: 2.4 Consensus size: 42
69697 TTTTTGCTTG
*
69707 AAGAAGAAAAGAAAAAAAGGGAAAAAAGTGAAAAAAGAAAAAA
1 AAGAAAAAAAGAAAAAAAGGGAAAAAAG-GAAAAAAGAAAAAA
** * * *
69750 AAGAAAAAAAGAAAAAATTGGAAAAATGGAAAAATGTAAAAA
1 AAGAAAAAAAGAAAAAAAGGGAAAAAAGGAAAAAAGAAAAAA
*
69792 ATGAAAAAAATGAAAGAAAA
1 AAGAAAAAAA-GAAA-AAAA
69812 AATAAAAAGA
Statistics
Matches: 52, Mismatches: 8, Indels: 3
0.83 0.13 0.05
Matches are distributed among these distances:
42 21 0.40
43 28 0.54
44 3 0.06
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (42 bp):
AAGAAAAAAAGAAAAAAAGGGAAAAAAGGAAAAAAGAAAAAA
Found at i:69802 original size:26 final size:25
Alignment explanation
Indices: 69713--69824 Score: 88
Period size: 26 Copynumber: 4.4 Consensus size: 25
69703 CTTGAAGAAG
*
69713 AAAAGAAAAAAAGGGAAAAAAGTGAA
1 AAAAGAAAAAAATGGAAAAAAGT-AA
* *
69739 AAAAGAAAAAAAAGAAAAAAAG-AA
1 AAAAGAAAAAAATGGAAAAAAGTAA
* *
69763 AAAATTG-GAAAAATGGAAAAATGTAA
1 AAAA--GAAAAAAATGGAAAAAAGTAA
69789 AAAATGAAAAAAATGAAAGAAAAAA-T-A
1 AAAA-GAAAAAAATG---GAAAAAAGTAA
69816 AAAAGAAAA
1 AAAAGAAAA
69825 TAAAATTGGT
Statistics
Matches: 71, Mismatches: 8, Indels: 14
0.76 0.09 0.15
Matches are distributed among these distances:
24 6 0.08
25 14 0.20
26 39 0.55
27 5 0.07
28 1 0.01
29 6 0.08
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (25 bp):
AAAAGAAAAAAATGGAAAAAAGTAA
Done.