Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007664.1 Hibiscus syriacus cultivar Beakdansim tig00026155_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: 47157
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Found at i:9840 original size:18 final size:17
Alignment explanation
Indices: 9817--9863 Score: 67
Period size: 18 Copynumber: 2.7 Consensus size: 17
9807 TGTTTCTGAG
9817 GGAATTGGAATCTGTGAA
1 GGAATTGGAATCTGT-AA
* *
9835 GGAATTAGAATCTGTCA
1 GGAATTGGAATCTGTAA
9852 GGAATTGGAATC
1 GGAATTGGAATC
9864 CAATTCCATA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 12 0.46
18 14 0.54
ACGTcount: A:0.34, C:0.09, G:0.30, T:0.28
Consensus pattern (17 bp):
GGAATTGGAATCTGTAA
Found at i:10245 original size:37 final size:37
Alignment explanation
Indices: 10188--10279 Score: 159
Period size: 37 Copynumber: 2.5 Consensus size: 37
10178 TTTACACCCT
*
10188 AAACCCGAACCCGACCCGACCCGAATATCACACTTAAA
1 AAACCCG-ACCCGACTCGACCCGAATATCACACTTAAA
10226 AAACCCGACCCGACTCGACCCGAATATCACACTTAAA
1 AAACCCGACCCGACTCGACCCGAATATCACACTTAAA
10263 AAACCCGA-CCGACTCGA
1 AAACCCGACCCGACTCGA
10280 ACAAAATAAA
Statistics
Matches: 53, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
36 9 0.17
37 37 0.70
38 7 0.13
ACGTcount: A:0.38, C:0.39, G:0.12, T:0.11
Consensus pattern (37 bp):
AAACCCGACCCGACTCGACCCGAATATCACACTTAAA
Found at i:12156 original size:18 final size:18
Alignment explanation
Indices: 12133--12169 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
12123 GGTTTTTTTT
*
12133 TGGTAAAATGAGAGTAAA
1 TGGTAAAAAGAGAGTAAA
*
12151 TGGTAAAAAGAGATTAAA
1 TGGTAAAAAGAGAGTAAA
12169 T
1 T
12170 AAATAAAAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.00, G:0.24, T:0.24
Consensus pattern (18 bp):
TGGTAAAAAGAGAGTAAA
Found at i:12176 original size:19 final size:20
Alignment explanation
Indices: 12154--12206 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 20
12144 GAGTAAATGG
12154 TAAAAAGAGATTAAA-TAAA
1 TAAAAAGAGATTAAAGTAAA
*
12173 TAAAAACA-ATTAAAGTAAA
1 TAAAAAGAGATTAAAGTAAA
* *
12192 -AATAAGAGAATAAAG
1 TAAAAAGAGATTAAAG
12207 ATTGAAAATG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
18 11 0.39
19 17 0.61
ACGTcount: A:0.68, C:0.02, G:0.11, T:0.19
Consensus pattern (20 bp):
TAAAAAGAGATTAAAGTAAA
Found at i:13072 original size:26 final size:26
Alignment explanation
Indices: 13043--13095 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
13033 CCAGCAGGCG
* * *
13043 CGCTGACTAGATCTTTTAGAAAATGT
1 CGCTGACTAAACCTTGTAGAAAATGT
*
13069 CGCTGACTAAACCTTGTAGAAACTGT
1 CGCTGACTAAACCTTGTAGAAAATGT
13095 C
1 C
13096 ACAACAGACC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (26 bp):
CGCTGACTAAACCTTGTAGAAAATGT
Found at i:19696 original size:18 final size:18
Alignment explanation
Indices: 19673--19708 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
19663 GGCGTTTTTG
*
19673 GTAAAATGAGAGTAAATA
1 GTAAAAAGAGAGTAAATA
*
19691 GTAAAAAGAGATTAAATA
1 GTAAAAAGAGAGTAAATA
19709 AATAAAAGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.58, C:0.00, G:0.19, T:0.22
Consensus pattern (18 bp):
GTAAAAAGAGAGTAAATA
Found at i:19715 original size:18 final size:18
Alignment explanation
Indices: 19693--19744 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 18
19683 AGTAAATAGT
19693 AAAAAGAGATTAAA-TAA
1 AAAAAGAGATTAAAGTAA
19710 ATAAAAGCA-ATTAAAGTAA
1 A-AAAAG-AGATTAAAGTAA
*
19729 AAATAAGAGAATAAAG
1 AAA-AAGAGATTAAAG
19745 ATTGAAAATG
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
17 1 0.03
18 14 0.48
19 14 0.48
ACGTcount: A:0.67, C:0.02, G:0.13, T:0.17
Consensus pattern (18 bp):
AAAAAGAGATTAAAGTAA
Found at i:22378 original size:49 final size:49
Alignment explanation
Indices: 22325--22423 Score: 189
Period size: 49 Copynumber: 2.0 Consensus size: 49
22315 TACGTTCGCA
*
22325 CACCCGTAGGTTCGTGGAACTAGAGGTTCAAAGGTAGTAACACTTGTCC
1 CACCCGGAGGTTCGTGGAACTAGAGGTTCAAAGGTAGTAACACTTGTCC
22374 CACCCGGAGGTTCGTGGAACTAGAGGTTCAAAGGTAGTAACACTTGTCC
1 CACCCGGAGGTTCGTGGAACTAGAGGTTCAAAGGTAGTAACACTTGTCC
22423 C
1 C
22424 TAGGTGAGTG
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.23
Consensus pattern (49 bp):
CACCCGGAGGTTCGTGGAACTAGAGGTTCAAAGGTAGTAACACTTGTCC
Found at i:26672 original size:18 final size:17
Alignment explanation
Indices: 26649--26695 Score: 67
Period size: 18 Copynumber: 2.7 Consensus size: 17
26639 TGTTTCTGAG
26649 GGAATTGGAATCTGTGAA
1 GGAATTGGAATCTGT-AA
* *
26667 GGAATTAGAATCTGTCA
1 GGAATTGGAATCTGTAA
26684 GGAATTGGAATC
1 GGAATTGGAATC
26696 CAATTCCATA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 12 0.46
18 14 0.54
ACGTcount: A:0.34, C:0.09, G:0.30, T:0.28
Consensus pattern (17 bp):
GGAATTGGAATCTGTAA
Found at i:27117 original size:36 final size:38
Alignment explanation
Indices: 27029--27121 Score: 154
Period size: 38 Copynumber: 2.5 Consensus size: 38
27019 TTTACACCCT
*
27029 AAACCCGAACCCGACCCGACCCGAATATCACACTTAAAA
1 AAACCCG-ACCCGACTCGACCCGAATATCACACTTAAAA
27068 AAACCCGACCCGACTCGACCCGAATATCACACTT-AAA
1 AAACCCGACCCGACTCGACCCGAATATCACACTTAAAA
27105 AAACCCGA-CCGACTCGA
1 AAACCCGACCCGACTCGA
27122 ACAAAATAAA
Statistics
Matches: 53, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
36 9 0.17
37 11 0.21
38 26 0.49
39 7 0.13
ACGTcount: A:0.39, C:0.39, G:0.12, T:0.11
Consensus pattern (38 bp):
AAACCCGACCCGACTCGACCCGAATATCACACTTAAAA
Found at i:28996 original size:18 final size:18
Alignment explanation
Indices: 28973--29009 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
28963 GGGTTTTTTT
*
28973 TGGTAAAATGAGAGTAAA
1 TGGTAAAAAGAGAGTAAA
*
28991 TGGTAAAAAGAGATTAAA
1 TGGTAAAAAGAGAGTAAA
29009 T
1 T
29010 AAATAAAAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.00, G:0.24, T:0.24
Consensus pattern (18 bp):
TGGTAAAAAGAGAGTAAA
Found at i:29016 original size:19 final size:20
Alignment explanation
Indices: 28994--29046 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 20
28984 GAGTAAATGG
28994 TAAAAAGAGATTAAA-TAAA
1 TAAAAAGAGATTAAAGTAAA
*
29013 TAAAAACA-ATTAAAGTAAA
1 TAAAAAGAGATTAAAGTAAA
* *
29032 -AATAAGAGAATAAAG
1 TAAAAAGAGATTAAAG
29047 ATTGAAAATG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
18 11 0.39
19 17 0.61
ACGTcount: A:0.68, C:0.02, G:0.11, T:0.19
Consensus pattern (20 bp):
TAAAAAGAGATTAAAGTAAA
Found at i:29913 original size:26 final size:26
Alignment explanation
Indices: 29884--29936 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
29874 CCAGCAGGCG
* * *
29884 CGCTGACTAGATCTTTTAGAAAATGT
1 CGCTGACTAAACCTTGTAGAAAATGT
*
29910 CGCTGACTAAACCTTGTAGAAACTGT
1 CGCTGACTAAACCTTGTAGAAAATGT
29936 C
1 C
29937 ACATCAGACC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (26 bp):
CGCTGACTAAACCTTGTAGAAAATGT
Found at i:36541 original size:18 final size:18
Alignment explanation
Indices: 36518--36553 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
36508 GGCGTTTTTG
*
36518 GTAAAATGAGAGTAAATA
1 GTAAAAAGAGAGTAAATA
*
36536 GTAAAAAGAGATTAAATA
1 GTAAAAAGAGAGTAAATA
36554 AATAAAAGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.58, C:0.00, G:0.19, T:0.22
Consensus pattern (18 bp):
GTAAAAAGAGAGTAAATA
Found at i:36560 original size:18 final size:18
Alignment explanation
Indices: 36538--36589 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 18
36528 AGTAAATAGT
36538 AAAAAGAGATTAAA-TAA
1 AAAAAGAGATTAAAGTAA
36555 ATAAAAGCA-ATTAAAGTAA
1 A-AAAAG-AGATTAAAGTAA
*
36574 AAATAAGAGAATAAAG
1 AAA-AAGAGATTAAAG
36590 ATTGAAAATG
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
17 1 0.03
18 14 0.48
19 14 0.48
ACGTcount: A:0.67, C:0.02, G:0.13, T:0.17
Consensus pattern (18 bp):
AAAAAGAGATTAAAGTAA
Found at i:39190 original size:33 final size:33
Alignment explanation
Indices: 39148--39213 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
39138 ACACCCGTGG
39148 AACTAGAGGTTCAAAGGTAGTAACACTTGTCCC
1 AACTAGAGGTTCAAAGGTAGTAACACTTGTCCC
39181 AACTAGAGGTTCAAAGGTAGTAACACTTGTCCC
1 AACTAGAGGTTCAAAGGTAGTAACACTTGTCCC
39214 TAGGTGAGTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.24
Consensus pattern (33 bp):
AACTAGAGGTTCAAAGGTAGTAACACTTGTCCC
Found at i:43476 original size:17 final size:18
Alignment explanation
Indices: 43437--43483 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
43427 TGTTTCTGAG
*
43437 GGAATTGGAATTTGTGAA
1 GGAATTGGAATCTGTGAA
*
43455 GGAATTGGAATCTGT-CA
1 GGAATTGGAATCTGTGAA
43472 GGAATTGGAATC
1 GGAATTGGAATC
43484 CAATTCCATA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 13 0.48
18 14 0.52
ACGTcount: A:0.32, C:0.06, G:0.32, T:0.30
Consensus pattern (18 bp):
GGAATTGGAATCTGTGAA
Found at i:43879 original size:38 final size:37
Alignment explanation
Indices: 43818--43903 Score: 136
Period size: 38 Copynumber: 2.3 Consensus size: 37
43808 TTTTCACCCT
*
43818 AAACCCGAACCCGACCCGACCCGAATATCACACTTAAAA
1 AAACCCG-ACCCAACCCGACCCGAATATCACACTT-AAA
*
43857 AAACCCGACCCAACTCGACCCGAATATCACACTTAAA
1 AAACCCGACCCAACCCGACCCGAATATCACACTTAAA
43894 AAACCCGACC
1 AAACCCGACC
43904 GACTCGAACA
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
37 13 0.29
38 25 0.56
39 7 0.16
ACGTcount: A:0.41, C:0.40, G:0.09, T:0.10
Consensus pattern (37 bp):
AAACCCGACCCAACCCGACCCGAATATCACACTTAAA
Found at i:44678 original size:2 final size:2
Alignment explanation
Indices: 44673--44709 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
44663 AAATTAATGT
44673 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
44710 TAAAAAAACT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:45804 original size:19 final size:20
Alignment explanation
Indices: 45782--45834 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 20
45772 GAGTAAATGG
45782 TAAAAAGAGATTAAA-TAAA
1 TAAAAAGAGATTAAAGTAAA
*
45801 TAAAAACA-ATTAAAGTAAA
1 TAAAAAGAGATTAAAGTAAA
* *
45820 -AATAAGAGAATAAAG
1 TAAAAAGAGATTAAAG
45835 ATTGAAATGA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
18 11 0.39
19 17 0.61
ACGTcount: A:0.68, C:0.02, G:0.11, T:0.19
Consensus pattern (20 bp):
TAAAAAGAGATTAAAGTAAA
Done.