Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003331.1 Hibiscus syriacus cultivar Beakdansim tig00007012_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: 52211
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:2082 original size:16 final size:16
Alignment explanation
Indices: 2061--2091 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
2051 TTCCCTTCAG
2061 ATTATGATTCCAAAAT
1 ATTATGATTCCAAAAT
2077 ATTATGATTCCAAAA
1 ATTATGATTCCAAAA
2092 CCTTGTCTGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.45, C:0.13, G:0.06, T:0.35
Consensus pattern (16 bp):
ATTATGATTCCAAAAT
Found at i:14810 original size:38 final size:38
Alignment explanation
Indices: 14763--14876 Score: 101
Period size: 38 Copynumber: 3.1 Consensus size: 38
14753 ATGTAAAATG
* *
14763 TATAGTTTTTAAAAAAATAGTTTTAAAAACATATAGTA
1 TATAATTTTTAAAAAAATAGTTTTAAAAACATATAATA
* * * *
14801 TATAATTTTT---AAGATAATTTTAAAAGCTTATAATA
1 TATAATTTTTAAAAAAATAGTTTTAAAAACATATAATA
* * * *
14836 TAGAA-TTTTAAAAAAAAATGTTTTGAAAATATATAATA
1 TATAATTTTTAAAAAAATA-GTTTTAAAAACATATAATA
14874 TAT
1 TAT
14877 TTTTTCAAAA
Statistics
Matches: 57, Mismatches: 15, Indels: 8
0.71 0.19 0.10
Matches are distributed among these distances:
34 4 0.07
35 24 0.42
37 4 0.07
38 25 0.44
ACGTcount: A:0.50, C:0.02, G:0.07, T:0.41
Consensus pattern (38 bp):
TATAATTTTTAAAAAAATAGTTTTAAAAACATATAATA
Found at i:20687 original size:33 final size:34
Alignment explanation
Indices: 20612--20678 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 34
20602 GTAATAAACA
* *
20612 AAATTAAACAAAATAATTTAACAAAAACTCCAAC
1 AAATTTAACAAAATAAATTAACAAAAACTCCAAC
20646 AAATTTAACAAAATAAATTAA-AATAAA-TCCAAC
1 AAATTTAACAAAATAAATTAACAA-AAACTCCAAC
20679 TATATTAACG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
33 8 0.27
34 22 0.73
ACGTcount: A:0.63, C:0.15, G:0.00, T:0.22
Consensus pattern (34 bp):
AAATTTAACAAAATAAATTAACAAAAACTCCAAC
Found at i:20895 original size:6 final size:6
Alignment explanation
Indices: 20886--20928 Score: 68
Period size: 6 Copynumber: 7.2 Consensus size: 6
20876 ATCATCATCA
* *
20886 TCGTCC TCGTCC TCGTCC TCGTCC TCGTCA TTGTCC TCGTCC T
1 TCGTCC TCGTCC TCGTCC TCGTCC TCGTCC TCGTCC TCGTCC T
20929 GAGTAGCTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.02, C:0.44, G:0.16, T:0.37
Consensus pattern (6 bp):
TCGTCC
Found at i:21282 original size:27 final size:27
Alignment explanation
Indices: 21245--21308 Score: 83
Period size: 27 Copynumber: 2.4 Consensus size: 27
21235 CAGGTAATGG
* * *
21245 TGGCGGCGGCGGCATCGGGTATGGGAA
1 TGGCGGTGGCGACATCGGGTAAGGGAA
* *
21272 TTGTGGTGGCGACATCGGGTAAGGGAA
1 TGGCGGTGGCGACATCGGGTAAGGGAA
21299 TGGCGGTGGC
1 TGGCGGTGGC
21309 TGCTGTGAAG
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.16, C:0.16, G:0.50, T:0.19
Consensus pattern (27 bp):
TGGCGGTGGCGACATCGGGTAAGGGAA
Found at i:22987 original size:9 final size:9
Alignment explanation
Indices: 22957--23008 Score: 56
Period size: 8 Copynumber: 6.1 Consensus size: 9
22947 ATCTGCAGAA
22957 AAATTAAAT
1 AAATTAAAT
*
22966 -AAGTAAA-
1 AAATTAAAT
*
22973 ATATTAAAT
1 AAATTAAAT
22982 AAATTAAAT
1 AAATTAAAT
*
22991 -ACTTAAAT
1 AAATTAAAT
22999 AAATTAAAT
1 AAATTAAAT
23008 A
1 A
23009 TAAAATATTA
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
8 18 0.53
9 16 0.47
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (9 bp):
AAATTAAAT
Found at i:22996 original size:17 final size:16
Alignment explanation
Indices: 22959--23015 Score: 78
Period size: 16 Copynumber: 3.5 Consensus size: 16
22949 CTGCAGAAAA
* *
22959 ATTAAATAAGTAAAAT
1 ATTAAATAAATTAAAT
22975 ATTAAATAAATTAAAT
1 ATTAAATAAATTAAAT
22991 ACTTAAATAAATTAAAT
1 A-TTAAATAAATTAAAT
*
23008 ATAAAATA
1 ATTAAATA
23016 TTAAAAATAT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
16 21 0.57
17 16 0.43
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (16 bp):
ATTAAATAAATTAAAT
Found at i:23080 original size:10 final size:10
Alignment explanation
Indices: 23054--23083 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
23044 GAGATATTAT
*
23054 AGAGAAGTTG
1 AGAGAATTTG
23064 AGAGAATTTG
1 AGAGAATTTG
23074 AGAGAATTTG
1 AGAGAATTTG
23084 GTGTGATGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.40, C:0.00, G:0.33, T:0.27
Consensus pattern (10 bp):
AGAGAATTTG
Found at i:27256 original size:2 final size:2
Alignment explanation
Indices: 27245--27276 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
27235 TAGGTAAAAG
27245 TA TA -A 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 T
27277 GAATTTTGTC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:27513 original size:59 final size:59
Alignment explanation
Indices: 27421--27541 Score: 233
Period size: 59 Copynumber: 2.1 Consensus size: 59
27411 AAATGTTTAA
*
27421 AAGGTTATATTCAAACACTTGAATAAAAAATCACATATATAAATAATATGTTATTTGAG
1 AAGGTTATACTCAAACACTTGAATAAAAAATCACATATATAAATAATATGTTATTTGAG
27480 AAGGTTATACTCAAACACTTGAATAAAAAATCACATATATAAATAATATGTTATTTGAG
1 AAGGTTATACTCAAACACTTGAATAAAAAATCACATATATAAATAATATGTTATTTGAG
27539 AAG
1 AAG
27542 CTCATGACTA
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 61 1.00
ACGTcount: A:0.48, C:0.09, G:0.11, T:0.32
Consensus pattern (59 bp):
AAGGTTATACTCAAACACTTGAATAAAAAATCACATATATAAATAATATGTTATTTGAG
Found at i:27555 original size:59 final size:59
Alignment explanation
Indices: 27431--27555 Score: 216
Period size: 59 Copynumber: 2.1 Consensus size: 59
27421 AAGGTTATAT
* *
27431 TCAAACACTTGAATAAAAAATCACATATATAAATAATATGTTATTTGAGAAGGTTATAC
1 TCAAACACTTGAATAAAAAATCACATATATAAATAATATGTTATTTGAGAAGCTCATAC
27490 TCAAACACTTGAATAAAAAATCACATATATAAATAATATGTTATTTGAGAAGCTCATGAC
1 TCAAACACTTGAATAAAAAATCACATATATAAATAATATGTTATTTGAGAAGCTCAT-AC
27550 T-AAACA
1 TCAAACA
27556 TGTTAATTTT
Statistics
Matches: 63, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
59 60 0.95
60 3 0.05
ACGTcount: A:0.48, C:0.12, G:0.10, T:0.30
Consensus pattern (59 bp):
TCAAACACTTGAATAAAAAATCACATATATAAATAATATGTTATTTGAGAAGCTCATAC
Found at i:38368 original size:21 final size:21
Alignment explanation
Indices: 38331--38370 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
38321 CCCCCTTTGA
*
38331 AGGGGAACTGATTCCCCCCAC
1 AGGGGAACTGATACCCCCCAC
38352 AGGGGAA-TCGATACCCCCC
1 AGGGGAACT-GATACCCCCC
38371 TGGGGTACTG
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:40916 original size:22 final size:23
Alignment explanation
Indices: 40891--40934 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
40881 AATTAAGTTT
40891 TAATCTTA-AAACAATTTCAAAA
1 TAATCTTACAAACAATTTCAAAA
* **
40913 TAATTTTACAAAGTATTTCAAA
1 TAATCTTACAAACAATTTCAAA
40935 CCATTTCAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.50, C:0.11, G:0.02, T:0.36
Consensus pattern (23 bp):
TAATCTTACAAACAATTTCAAAA
Found at i:42990 original size:2 final size:2
Alignment explanation
Indices: 42983--43012 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
42973 TACATAAACC
42983 AT AT 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 AT AT
43013 GAAGGAAAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:49929 original size:28 final size:28
Alignment explanation
Indices: 49877--49930 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
49867 CTAAATTGAT
**
49877 TTTTGGTTTTGTTACAGGGCCAACTTAA
1 TTTTGGTTTTGTTACAGGGAAAACTTAA
49905 TTTTGGTTTTGTT-CTAGGGAAAACTT
1 TTTTGGTTTTGTTAC-AGGGAAAACTT
49931 TTTTTAAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 1 0.04
28 22 0.96
ACGTcount: A:0.20, C:0.11, G:0.22, T:0.46
Consensus pattern (28 bp):
TTTTGGTTTTGTTACAGGGAAAACTTAA
Found at i:50036 original size:22 final size:22
Alignment explanation
Indices: 50009--50066 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
49999 TAGATATTCA
50009 AAAAATTAAATATAAAAATACT
1 AAAAATTAAATATAAAAATACT
* * *
50031 AAAAA-TAAAAATTAAATTACT
1 AAAAATTAAATATAAAAATACT
*
50052 AAAATATTGAATATA
1 AAAA-ATTAAATATA
50067 CATATTAAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
21 17 0.61
22 6 0.21
23 5 0.18
ACGTcount: A:0.66, C:0.03, G:0.02, T:0.29
Consensus pattern (22 bp):
AAAAATTAAATATAAAAATACT
Found at i:50849 original size:23 final size:22
Alignment explanation
Indices: 50795--50863 Score: 63
Period size: 23 Copynumber: 3.1 Consensus size: 22
50785 TAAAAATATT
* *
50795 TTTTATTTTTAGTATTT-TTATA
1 TTTTATTTTTAATATTTAATA-A
*
50817 TTTAATTTTTTAATATTTGAATAA
1 TTTTA-TTTTTAATATTT-AATAA
50841 TTTTATTTTT-ATATTTAA-AA
1 TTTTATTTTTAATATTTAATAA
50861 TTT
1 TTT
50864 AAAATAAATT
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
20 5 0.12
21 2 0.05
22 10 0.25
23 16 0.40
24 5 0.12
25 2 0.05
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (22 bp):
TTTTATTTTTAATATTTAATAA
Found at i:51573 original size:176 final size:180
Alignment explanation
Indices: 51254--51603 Score: 441
Period size: 178 Copynumber: 2.0 Consensus size: 180
51244 ATTCATAGTT
* * *
51254 CTTTGACTATTGCAAATTAAAAGATAATTTTATTTGAATATTAATAGGTAATTACTCTTTAATGA
1 CTTTGACCATTGCAAATTAAAAGATAATTTAATTTGAATATTAATAGGTAATTACTCTTGAATGA
* *
51319 GTCAATTTAAAAATGTATTTGTTATCTTTTAATTTTGAATATTAAAATAAATTAATACTTTTGTA
66 GTCAATTTAAAAA-GTATTTGTTATCTTTTAACTTTAAATATTAAAATAAATTAATACTTTTGTA
* *
51384 TATTTCAAATTAAAATAATA-TGTTTATGTTTGAATAGTAAAATGATTTAC
130 TATTTCAAATTAAAATAATACTATTTAAGTTTGAATAGTAAAATGATTTAC
* * *
51434 CTTTGACCATTGCAAATT-AAATATTA-TTAATTTGAATATTAGTAGGATAA-TACTCTGTGAAT
1 CTTTGACCATTGCAAATTAAAAGATAATTTAATTTGAATATTAATAGG-TAATTACTCT-TGAAT
*
51496 -ATGTCAA-TTAAAAA-TA-TTGTTATCTTTTTAACTTTAAATA-TAAAGAT-AATTATATATTT
64 GA-GTCAATTTAAAAAGTATTTGTTATC-TTTTAACTTTAAATATTAAA-ATAAATTA-ATACTT
* *
51555 TTGTATATTTTAAATTAAAATAATATCTATTTAAGTTTGAATGGTAAAA
125 TTGTATATTTCAAATTAAAATAATA-CTATTTAAGTTTGAATAGTAAAA
51604 GGGGTTTATC
Statistics
Matches: 149, Mismatches: 13, Indels: 18
0.83 0.07 0.10
Matches are distributed among these distances:
175 17 0.11
176 46 0.31
178 51 0.34
179 18 0.12
180 17 0.11
ACGTcount: A:0.40, C:0.06, G:0.09, T:0.45
Consensus pattern (180 bp):
CTTTGACCATTGCAAATTAAAAGATAATTTAATTTGAATATTAATAGGTAATTACTCTTGAATGA
GTCAATTTAAAAAGTATTTGTTATCTTTTAACTTTAAATATTAAAATAAATTAATACTTTTGTAT
ATTTCAAATTAAAATAATACTATTTAAGTTTGAATAGTAAAATGATTTAC
Done.