Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009029.1 Hibiscus syriacus cultivar Beakdansim tig00112429_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: 496945
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
File 3 of 3
Found at i:479940 original size:2 final size:2
Alignment explanation
Indices: 479933--479960 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
479923 TTTGTCCTAT
479933 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
479961 GTTTGAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:480023 original size:37 final size:39
Alignment explanation
Indices: 479935--480024 Score: 121
Period size: 37 Copynumber: 2.3 Consensus size: 39
479925 TGTCCTATTA
*
479935 TATATATATATATATATATATATATAGTTTGAAAAATATT
1 TATATAT-TATATATATATATATATAGTTTGAAAAACATT
* * *
479975 TTTAAAATATATATATA-ATATATAGTTTG-AAAACATT
1 TATATATTATATATATATATATATAGTTTGAAAAACATT
480012 TATATATTATATA
1 TATATATTATATA
480025 GTTTTTAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
37 17 0.40
38 12 0.28
39 10 0.23
40 4 0.09
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47
Consensus pattern (39 bp):
TATATATTATATATATATATATATAGTTTGAAAAACATT
Found at i:480047 original size:65 final size:65
Alignment explanation
Indices: 479947--480143 Score: 249
Period size: 65 Copynumber: 3.0 Consensus size: 65
479937 TATATATATA
** * *
479947 TATATATATATATAGTTTGAAAAATATTTTTAAAATATATATATAATATATAG-TTTGAAAACAT
1 TATATATATATATAGTTTTTAAAACATTTTGAAAATATATATAT-ATATATAGTTTTGAAAACAT
480011 T
65 T
*
480012 TATATAT-TATATAGTTTTTAAAACACTTTTGAAAATATATATAT-TATATAGTTTTTAAAACAT
1 TATATATATATATAGTTTTTAAAACA-TTTTGAAAATATATATATATATATAGTTTTGAAAACAT
480075 T
65 T
* * *
480076 T-TGAAAATATATATAGTTTTTAAAACATTTTGAAAACATATATATATTATATAGTTTTGAAATC
1 TAT--ATATATATATAGTTTTTAAAACATTTTGAAAATATATATATA-TATATAGTTTTGAAAAC
480140 ATT
63 ATT
480143 T
1 T
480144 TGAAAACTTA
Statistics
Matches: 116, Mismatches: 9, Indels: 12
0.85 0.07 0.09
Matches are distributed among these distances:
63 8 0.07
64 27 0.23
65 44 0.38
66 18 0.16
67 19 0.16
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (65 bp):
TATATATATATATAGTTTTTAAAACATTTTGAAAATATATATATATATATAGTTTTGAAAACATT
Found at i:480053 original size:37 final size:36
Alignment explanation
Indices: 480012--480193 Score: 209
Period size: 37 Copynumber: 5.1 Consensus size: 36
480002 TGAAAACATT
480012 TATATATTATATAGTTTTTAAAACACTTTTGAAAATA
1 TATATATTATATAGTTTTTAAAACA-TTTTGAAAATA
480049 TATATATTATATAGTTTTTAAAACATTTTG---A-A
1 TATATATTATATAGTTTTTAAAACATTTTGAAAATA
480081 -A-ATA-TATATAGTTTTTAAAACATTTTGAAAACATA
1 TATATATTATATAGTTTTTAAAACATTTTG-AAA-ATA
* *
480116 TATATATTATATAGTTTTGAAATCATTTTGAAAACT-
1 TATATATTATATAGTTTTTAAAACATTTTGAAAA-TA
* * *
480152 TATATAATATATAGTTTTAAAAATATTTTTGAAAACTA
1 TATATATTATATAGTTTTTAAAACA-TTTTGAAAA-TA
480190 TATA
1 TATA
480194 ATTTTGAAAA
Statistics
Matches: 127, Mismatches: 6, Indels: 23
0.81 0.04 0.15
Matches are distributed among these distances:
29 23 0.18
30 3 0.02
31 1 0.01
32 1 0.01
33 1 0.01
34 1 0.01
35 1 0.01
36 28 0.22
37 43 0.34
38 25 0.20
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (36 bp):
TATATATTATATAGTTTTTAAAACATTTTGAAAATA
Found at i:480090 original size:29 final size:29
Alignment explanation
Indices: 480056--480119 Score: 119
Period size: 29 Copynumber: 2.2 Consensus size: 29
480046 ATATATATAT
*
480056 TATATAGTTTTTAAAACATTTTGAAAATA
1 TATATAGTTTTTAAAACATTTTGAAAACA
480085 TATATAGTTTTTAAAACATTTTGAAAACA
1 TATATAGTTTTTAAAACATTTTGAAAACA
480114 TATATA
1 TATATA
480120 TATTATATAG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.45, C:0.05, G:0.06, T:0.44
Consensus pattern (29 bp):
TATATAGTTTTTAAAACATTTTGAAAACA
Found at i:480127 original size:38 final size:37
Alignment explanation
Indices: 480084--480193 Score: 150
Period size: 38 Copynumber: 2.9 Consensus size: 37
480074 TTTTGAAAAT
*
480084 ATATATAGTTTTTAAAACATTTTGAAAACATATATATA
1 ATATATAGTTTTAAAAACATTTTGAAAAC-TATATATA
* * *
480122 TTATATAGTTTTGAAATCATTTTGAAAACT-TATATA
1 ATATATAGTTTTAAAAACATTTTGAAAACTATATATA
*
480158 ATATATAGTTTTAAAAATATTTTTGAAAACTATATA
1 ATATATAGTTTTAAAAACA-TTTTGAAAACTATATA
480194 ATTTTGAAAA
Statistics
Matches: 63, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
36 21 0.33
37 12 0.19
38 30 0.48
ACGTcount: A:0.45, C:0.05, G:0.06, T:0.45
Consensus pattern (37 bp):
ATATATAGTTTTAAAAACATTTTGAAAACTATATATA
Found at i:480194 original size:36 final size:36
Alignment explanation
Indices: 480084--480284 Score: 147
Period size: 38 Copynumber: 5.6 Consensus size: 36
480074 TTTTGAAAAT
* *
480084 ATATATAGTTTTTAAAACA-TTTTGAAAACATATATA
1 ATATATAGTTTTAAAAATATTTTTGAAAAC-TATATA
*
480120 TATTATATAGTTTT-GAAATCA-TTTTGAAAACTTATATA
1 -A-TATATAGTTTTAAAAAT-ATTTTTGAAAAC-TATATA
480158 ATATATAGTTTTAAAAATATTTTTGAAAAC--TAT-
1 ATATATAGTTTTAAAAATATTTTTGAAAACTATATA
* * *
480191 ATA-AT--TTTGAAAACATTTTTTTTAAAA-TATATA
1 ATATATAGTTTTAAAA-ATATTTTTGAAAACTATATA
* *
480224 ATATATAATTTT-AAAATACTTTTGAAAA-TATATA
1 ATATATAGTTTTAAAAATATTTTTGAAAACTATATA
*
480258 TTATATAGGTTTTTGGAAAAATATTTT
1 ATATATA-G-TTTT--AAAAATATTTT
480285 ATATATATAT
Statistics
Matches: 134, Mismatches: 14, Indels: 30
0.75 0.08 0.17
Matches are distributed among these distances:
30 7 0.05
31 11 0.08
32 5 0.04
33 6 0.04
34 27 0.20
35 3 0.02
36 19 0.14
37 19 0.14
38 28 0.21
39 9 0.07
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.46
Consensus pattern (36 bp):
ATATATAGTTTTAAAAATATTTTTGAAAACTATATA
Found at i:480222 original size:30 final size:28
Alignment explanation
Indices: 480157--480225 Score: 84
Period size: 30 Copynumber: 2.4 Consensus size: 28
480147 AAACTTATAT
*
480157 AATATATAGTTTTAAAAATATTTTTGAA
1 AATATATAATTTTAAAAATATTTTTGAA
* *
480185 AACTATATAATTTTGAAAACATTTTTTTTAA
1 AA-TATATAATTTT-AAAA-ATATTTTTGAA
480216 AATATATAAT
1 AATATATAAT
480226 ATATAATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
28 2 0.06
29 10 0.29
30 12 0.34
31 11 0.31
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.46
Consensus pattern (28 bp):
AATATATAATTTTAAAAATATTTTTGAA
Found at i:480264 original size:102 final size:101
Alignment explanation
Indices: 479944--480264 Score: 291
Period size: 102 Copynumber: 3.1 Consensus size: 101
479934 ATATATATAT
* * * ** * * *
479944 ATATATATATATATATAGTTTGAAAAATATTTTTAAAATATATATA-TAAT--ATATAGTTTGAA
1 ATATATAT-TATATATAGTTTTAAAAACATTTTGAAAATATATATAGTTTTGAAAACATTTTGAA
* * *
480006 AACATTTATATATTATATAGTTTTTAAAACACTTTTGAAA
65 AACA--TATATAATATATA-ATTTTAAAATACTTTTGAAA
* *
480046 ATATATA-TATTATATAGTTTTTAAAACATTTTGAAAATATATATAGTTTTTAAAACATTTTGAA
1 ATATATATTA-TATATAGTTTTAAAAACATTTTGAAAATATATATAGTTTTGAAAACATTTTGAA
* *
480110 AACATATATATATTATATAGTTTTGAAAT-CATTTTGAAA
65 AACATATATA-A-TATATAATTTTAAAATAC-TTTTGAAA
* *
480149 ACT-TATATAATATATAGTTTTAAAAATATTTTTGAAAACTATATA-A-TTTTGAAAACATTTTT
1 A-TATATATTATATATAGTTTTAAAAACA-TTTTGAAAA-TATATATAGTTTTGAAAACA--TTT
**
480211 TTTAAA-ATATATAATATATAATTTTAAAATACTTTTGAAA
61 TGAAAACATATATAATATATAATTTTAAAATACTTTTGAAA
480251 ATATATATTATATA
1 ATATATATTATATA
480265 GGTTTTTGGA
Statistics
Matches: 182, Mismatches: 22, Indels: 30
0.78 0.09 0.13
Matches are distributed among these distances:
100 2 0.01
101 32 0.18
102 49 0.27
103 48 0.26
104 38 0.21
105 13 0.07
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.46
Consensus pattern (101 bp):
ATATATATTATATATAGTTTTAAAAACATTTTGAAAATATATATAGTTTTGAAAACATTTTGAAA
ACATATATAATATATAATTTTAAAATACTTTTGAAA
Found at i:480294 original size:102 final size:98
Alignment explanation
Indices: 480000--480297 Score: 264
Period size: 102 Copynumber: 2.9 Consensus size: 98
479990 TAATATATAG
* * *
480000 TTTGAAAACATTTATATATTATATAGTTTTTAAAACACTTTTGAAAATATATATATTATATAGTT
1 TTTGAAAACA--TATATAATATATA-ATTTTAAAATACTTTTG-AAA-ATATATATTATATAGTT
* * * *
480065 TTTAAAACAT-TTTGAAAATATATATAGTTTTTAAAACAT
61 TTTAAAA-ATATTT-TATATATATATAATTTTGAAAACAT
* * *
480104 TTTGAAAACATATATATATTATATAGTTTTGAAAT-CATTTTGAAAACTTATATAATATATAG-T
1 TTTGAAAACATATATA-A-TATATAATTTTAAAATAC-TTTTGAAAA--TATATATTATATAGTT
*
480167 TTTAAAAATATTTT-TGAAAACTATATAATTTTGAAAACATTT
61 TTTAAAAATATTTTAT--ATA-TATATAATTTTGAAAACA--T
**
480209 TTTTTAAA-ATATATAATATATAATTTTAAAATACTTTTGAAAATATATATTATATAGGTTTTTG
1 TTTGAAAACATATATAATATATAATTTTAAAATACTTTTGAAAATATATATTATATA-GTTTTT-
480273 GAAAAATATTTTATATATATATAAT
64 -AAAAATATTTTATATATATATAAT
480298 ATTATTATTA
Statistics
Matches: 161, Mismatches: 16, Indels: 36
0.76 0.08 0.17
Matches are distributed among these distances:
100 12 0.07
101 4 0.02
102 58 0.36
103 45 0.28
104 34 0.21
105 8 0.05
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (98 bp):
TTTGAAAACATATATAATATATAATTTTAAAATACTTTTGAAAATATATATTATATAGTTTTTAA
AAATATTTTATATATATATAATTTTGAAAACAT
Found at i:483056 original size:34 final size:36
Alignment explanation
Indices: 483011--483104 Score: 149
Period size: 36 Copynumber: 2.7 Consensus size: 36
483001 ACCCGACCCG
483011 AAATAT-TAAAATATTATATATATAATT-A-ATATA
1 AAATATATAAAATATTATATATATAATTAATATATA
483044 AAATATATAAAATATTATATATATAATTAATATATA
1 AAATATATAAAATATTATATATATAATTAATATATA
* *
483080 AAAAATAAAAAATATTATATATATA
1 AAATATATAAAATATTATATATATA
483105 TATATAATCG
Statistics
Matches: 56, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
33 6 0.11
34 21 0.38
35 1 0.02
36 28 0.50
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (36 bp):
AAATATATAAAATATTATATATATAATTAATATATA
Found at i:484544 original size:17 final size:17
Alignment explanation
Indices: 484522--484599 Score: 120
Period size: 17 Copynumber: 4.6 Consensus size: 17
484512 TTGGGTGGCT
* *
484522 TGGGTGTAGAAGATGAA
1 TGGGTGTTGAAGATGAG
484539 TGGGTGTTGAAGATGAG
1 TGGGTGTTGAAGATGAG
*
484556 TGGTTGTTGAAGATGAG
1 TGGGTGTTGAAGATGAG
*
484573 TGGGTGTTGGAGATGAG
1 TGGGTGTTGAAGATGAG
484590 TGGGTGTTGA
1 TGGGTGTTGA
484600 TGGATAATAA
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 55 1.00
ACGTcount: A:0.23, C:0.00, G:0.46, T:0.31
Consensus pattern (17 bp):
TGGGTGTTGAAGATGAG
Done.