Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001267.1 Hibiscus syriacus cultivar Beakdansim tig00002486_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: 64073
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Found at i:2933 original size:24 final size:24
Alignment explanation
Indices: 2906--3013 Score: 137
Period size: 24 Copynumber: 4.5 Consensus size: 24
2896 ACTGGCGAAC
* *
2906 GAGATCTACGATGTAAAGGTGATG
1 GAGATCTACGATGCATAGGTGATG
* * *
2930 GAGATCTATGACGTATAGGTGATG
1 GAGATCTACGATGCATAGGTGATG
*
2954 GAGATCTACGACT-CATAGGTGAAG
1 GAGATCTACGA-TGCATAGGTGATG
*
2978 GAGATCTACGACGCATAGGTGATG
1 GAGATCTACGATGCATAGGTGATG
3002 GAGATCTACGAT
1 GAGATCTACGAT
3014 ATCGAACAGG
Statistics
Matches: 72, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
24 72 1.00
ACGTcount: A:0.31, C:0.13, G:0.31, T:0.24
Consensus pattern (24 bp):
GAGATCTACGATGCATAGGTGATG
Found at i:2958 original size:48 final size:47
Alignment explanation
Indices: 2906--3013 Score: 153
Period size: 48 Copynumber: 2.3 Consensus size: 47
2896 ACTGGCGAAC
* * * *
2906 GAGATCTACGATGTAAAGGTGATGGAGATCTATGACGTATAGGTGATG
1 GAGATCTACGAT-CAAAGGTGAAGGAGATCTACGACGCATAGGTGATG
*
2954 GAGATCTACGACTCATAGGTGAAGGAGATCTACGACGCATAGGTGATG
1 GAGATCTACGA-TCAAAGGTGAAGGAGATCTACGACGCATAGGTGATG
3002 GAGATCTACGAT
1 GAGATCTACGAT
3014 ATCGAACAGG
Statistics
Matches: 54, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
47 1 0.02
48 52 0.96
49 1 0.02
ACGTcount: A:0.31, C:0.13, G:0.31, T:0.24
Consensus pattern (47 bp):
GAGATCTACGATCAAAGGTGAAGGAGATCTACGACGCATAGGTGATG
Found at i:10179 original size:3 final size:3
Alignment explanation
Indices: 10173--10201 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
10163 ACAAACCAAA
10173 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
10202 AACTAATTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:21900 original size:38 final size:38
Alignment explanation
Indices: 21844--21919 Score: 118
Period size: 38 Copynumber: 2.0 Consensus size: 38
21834 TTTCACCCTG
*
21844 AACCCGAACCTGACCGACCCAAATATCACACTTAAAAA
1 AACCCGAACCCGACCGACCCAAATATCACACTTAAAAA
*
21882 AACCCG-ACCCGACTCGACCCGAATATCACACTTAAAAA
1 AACCCGAACCCGAC-CGACCCAAATATCACACTTAAAAA
21920 CCCGACTCGA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
37 6 0.17
38 29 0.83
ACGTcount: A:0.42, C:0.36, G:0.09, T:0.13
Consensus pattern (38 bp):
AACCCGAACCCGACCGACCCAAATATCACACTTAAAAA
Found at i:28482 original size:30 final size:30
Alignment explanation
Indices: 28448--28514 Score: 134
Period size: 30 Copynumber: 2.2 Consensus size: 30
28438 CTATCTCTTG
28448 TAAAAATATGGATTTTTATAGTATATGTAT
1 TAAAAATATGGATTTTTATAGTATATGTAT
28478 TAAAAATATGGATTTTTATAGTATATGTAT
1 TAAAAATATGGATTTTTATAGTATATGTAT
28508 TAAAAAT
1 TAAAAAT
28515 CATGTTATAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.43, C:0.00, G:0.12, T:0.45
Consensus pattern (30 bp):
TAAAAATATGGATTTTTATAGTATATGTAT
Found at i:40596 original size:64 final size:62
Alignment explanation
Indices: 40507--40686 Score: 195
Period size: 64 Copynumber: 2.8 Consensus size: 62
40497 TTGGACTCCT
* *
40507 AGTGCATCGGTGCACT-AAGAGTGCATCGATGCATGAAGTGCATTCGATGTTTAA-AAAAT-AG
1 AGTGCATCGATGCA-TGGAGAGTGCATCGATGCATGAA-TGCATTCGATGTTTAATAAAATCAG
* ** * *
40568 CCTGGTGCATCGATGCATGGATTGTGCATCGATGCATCAAATGCATTCGATGTTTTAATTAAATC
1 ---AGTGCATCGATGCATGGAGAGTGCATCGATGCAT-GAATGCATTCGATG-TTTAATAAAATC
40633 AG
61 AG
*
40635 AGTGCATCGATGCATGGAGAGTGCATCGGTGCATGGAATGCATTCGATGTTT
1 AGTGCATCGATGCATGGAGAGTGCATCGATGCAT-GAATGCATTCGATGTTT
40687 CAATTTATTC
Statistics
Matches: 98, Mismatches: 13, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
63 4 0.04
64 81 0.83
65 7 0.07
66 4 0.04
67 2 0.02
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.29
Consensus pattern (62 bp):
AGTGCATCGATGCATGGAGAGTGCATCGATGCATGAATGCATTCGATGTTTAATAAAATCAG
Found at i:40657 original size:19 final size:19
Alignment explanation
Indices: 40633--40683 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
40623 TAATTAAATC
40633 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
40652 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
40671 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
40684 TTTCAATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:40721 original size:21 final size:21
Alignment explanation
Indices: 40697--40736 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
40687 CAATTTATTC
40697 ATTGATGCATC-GATGCATGGT
1 ATTGATGCATCAG-TGCATGGT
40718 ATTGATGCATCAGTGCATG
1 ATTGATGCATCAGTGCATG
40737 CCTTTGAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.25, C:0.15, G:0.28, T:0.33
Consensus pattern (21 bp):
ATTGATGCATCAGTGCATGGT
Found at i:43358 original size:24 final size:22
Alignment explanation
Indices: 43287--43366 Score: 83
Period size: 24 Copynumber: 3.5 Consensus size: 22
43277 CATGGTCTTG
43287 TGCATCGATGCACATTCAAGGCA
1 TGCATCGATGCACATTCAAGG-A
* *
43310 TGCATCGGTGCATCATGC--GGA
1 TGCATCGATGCA-CATTCAAGGA
43331 TGCATCGATGCACATTCAAAGAGA
1 TGCATCGATGCACATTC-AAG-GA
*
43355 TGCATTGATGCA
1 TGCATCGATGCA
43367 TTGTTAAGTG
Statistics
Matches: 47, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
20 4 0.09
21 12 0.26
22 2 0.04
23 12 0.26
24 17 0.36
ACGTcount: A:0.29, C:0.23, G:0.25, T:0.24
Consensus pattern (22 bp):
TGCATCGATGCACATTCAAGGA
Found at i:49199 original size:18 final size:17
Alignment explanation
Indices: 49145--49193 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
49135 TTGGACTCCT
* *
49145 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TGA
49163 GAGTGCATCGATGCATGA
1 -AGTGCATCGATGCATGA
49181 AGTGCATTCGATG
1 AGTGCA-TCGATG
49194 TTTGAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.18, G:0.31, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATGA
Found at i:53104 original size:18 final size:18
Alignment explanation
Indices: 53083--53121 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
53073 GGTCAACGCC
*
53083 GGTCAACGGGTCGGGTCG
1 GGTCAACAGGTCGGGTCG
53101 GGTCAACAGGTCGGGTCG
1 GGTCAACAGGTCGGGTCG
53119 GGT
1 GGT
53122 TGTGACCGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.13, C:0.21, G:0.49, T:0.18
Consensus pattern (18 bp):
GGTCAACAGGTCGGGTCG
Done.