Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007177.1 Hibiscus syriacus cultivar Beakdansim tig00018836_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: 66277
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:15374 original size:32 final size:32
Alignment explanation
Indices: 15325--15404 Score: 83
Period size: 32 Copynumber: 2.5 Consensus size: 32
15315 ATCCTTGATA
*
15325 TTTTTTGTGATTT-TTCTTGCTATTTCGAATG-
1 TTTTTT-TGCTTTGTTCTTGCTATTTCGAATGC
* * *
15356 TTTTTTCTGCTTTGTTCTTGTTGTTTCGATTGC
1 TTTTTT-TGCTTTGTTCTTGCTATTTCGAATGC
15389 TTGTTTTTGCTTTGTT
1 TT-TTTTTGCTTTGTT
15405 TGCTTGGTTG
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
31 11 0.27
32 15 0.37
33 11 0.27
34 4 0.10
ACGTcount: A:0.06, C:0.11, G:0.17, T:0.65
Consensus pattern (32 bp):
TTTTTTTGCTTTGTTCTTGCTATTTCGAATGC
Found at i:15855 original size:17 final size:18
Alignment explanation
Indices: 15835--15935 Score: 84
Period size: 17 Copynumber: 5.6 Consensus size: 18
15825 ATAATATTAG
*
15835 TATAATAATA-AATAGAA
1 TATAATAATACAATATAA
15852 TATAACT-ATAACTAATATAA
1 TATAA-TAAT-AC-AATATAA
* *
15872 TATAATACTATAATATTAA
1 TATAATAATACAATA-TAA
*
15891 TATAAT-ATACAATATAC
1 TATAATAATACAATATAA
*
15908 TATAAT-ATATAATATAA
1 TATAATAATACAATATAA
15925 GTATAATAATA
1 -TATAATAATA
15936 TACTTTAATA
Statistics
Matches: 68, Mismatches: 8, Indels: 14
0.76 0.09 0.16
Matches are distributed among these distances:
17 24 0.35
18 18 0.26
19 14 0.21
20 12 0.18
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.37
Consensus pattern (18 bp):
TATAATAATACAATATAA
Found at i:15872 original size:5 final size:5
Alignment explanation
Indices: 15839--16098 Score: 77
Period size: 5 Copynumber: 51.6 Consensus size: 5
15829 TATTAGTATA
* * *
15839 ATAAT A-AAT AGAAT ATAACT ATAA- CTAAT ATAAT AT-A- ATACT ATAAT
1 ATAAT ATAAT ATAAT ATAA-T ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
*
15886 ATTAAT ATAAT ATACAAT ATACT ATAATAT ATAAT ATAAGT AT-A- ATAAT
1 A-TAAT ATAAT AT--AAT ATAAT AT-A-AT ATAAT ATAA-T ATAAT ATAAT
* * * * *
15935 ATACT TTAAT AT-GT ACT-AT GTAAT AT-AT ATAAT A-AGT ATAAT AT-AT
1 ATAAT ATAAT ATAAT A-TAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
** * ** *
15981 ATTTT ATAAT GT-AT ATGCT AT-AT A-ACAT ATAAT AT-AT AGTATAC
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATA-AT ATAAT ATAAT A-TA-AT
* *
16025 ATAAT ACTACT ATAAT AT-AT ATAAT ATGGAAT ATAATAT ATAAT ACTACT
1 ATAAT A-TAAT ATAAT ATAAT ATAAT AT--AAT AT-A-AT ATAAT A-TAAT
16075 ATAAT ATAAT A-ATAT ATAAAT ATA
1 ATAAT ATAAT ATA-AT AT-AAT ATA
16099 TACTATCGGA
Statistics
Matches: 190, Mismatches: 31, Indels: 68
0.66 0.11 0.24
Matches are distributed among these distances:
3 4 0.02
4 36 0.19
5 98 0.52
6 32 0.17
7 20 0.11
ACGTcount: A:0.52, C:0.05, G:0.04, T:0.39
Consensus pattern (5 bp):
ATAAT
Found at i:15884 original size:22 final size:19
Alignment explanation
Indices: 15825--15946 Score: 82
Period size: 17 Copynumber: 6.7 Consensus size: 19
15815 AATTGAAAAA
* *
15825 ATAATATTAGTATAATAAT
1 ATAATATTAATATAATACT
*
15844 A-AATA-GAATAT-A-ACT
1 ATAATATTAATATAATACT
15859 ATAACTAATATAATATAATACT
1 ATAA-T-AT-TAATATAATACT
15881 ATAATATTAATATAATA-T
1 ATAATATTAATATAATACT
* *
15899 ACAATA-TACTATAATA-T
1 ATAATATTAATATAATACT
*
15916 ATAATA-TAAGTATAATAAT
1 ATAATATTAA-TATAATACT
*
15935 ATACT-TTAATAT
1 ATAATATTAATAT
15947 GTACTATGTA
Statistics
Matches: 84, Mismatches: 9, Indels: 21
0.74 0.08 0.18
Matches are distributed among these distances:
15 3 0.04
16 3 0.04
17 22 0.26
18 21 0.25
19 19 0.23
20 7 0.08
21 2 0.02
22 7 0.08
ACGTcount: A:0.54, C:0.05, G:0.02, T:0.39
Consensus pattern (19 bp):
ATAATATTAATATAATACT
Found at i:15891 original size:24 final size:24
Alignment explanation
Indices: 15864--15946 Score: 87
Period size: 24 Copynumber: 3.2 Consensus size: 24
15854 TAACTATAAC
15864 TAATATAATATAATACTATAATAT
1 TAATATAATATAATACTATAATAT
15888 TAATATAATATACAATATACTATAATAT
1 TAATATAATAT---A-ATACTATAATAT
* *
15916 ATAATATAAGTATAATAATATACT-T
1 -TAATATAA-TATAATACTATAATAT
15941 TAATAT
1 TAATAT
15947 GTACTATGTA
Statistics
Matches: 51, Mismatches: 2, Indels: 12
0.78 0.03 0.18
Matches are distributed among these distances:
24 17 0.33
25 1 0.02
26 8 0.16
27 2 0.04
28 12 0.24
29 8 0.16
30 3 0.06
ACGTcount: A:0.53, C:0.05, G:0.01, T:0.41
Consensus pattern (24 bp):
TAATATAATATAATACTATAATAT
Found at i:15918 original size:7 final size:7
Alignment explanation
Indices: 15871--16100 Score: 77
Period size: 7 Copynumber: 31.7 Consensus size: 7
15861 AACTAATATA
15871 ATATAAT
1 ATATAAT
15878 ACTATAAT
1 A-TATAAT
15886 AT-T-A-
1 ATATAAT
15890 ATATAAT
1 ATATAAT
*
15897 ATACAATAT
1 ATA-TA-AT
15906 ACTATAAT
1 A-TATAAT
15914 ATATAAT
1 ATATAAT
*
15921 ATA-AGT
1 ATATAAT
15927 ATAATAAT
1 AT-ATAAT
15935 ATACTTTAAT
1 ATA---TAAT
* *
15945 ATGTACT
1 ATATAAT
*
15952 ATGTAAT
1 ATATAAT
15959 ATAT-AT
1 ATATAAT
15965 A-ATAA-
1 ATATAAT
*
15970 GTATAAT
1 ATATAAT
*
15977 ATATATT
1 ATATAAT
*
15984 TTATAATGT
1 ATATAA--T
**
15993 ATATGCT
1 ATATAAT
*
16000 ATATAAC
1 ATATAAT
16007 ATATAAT
1 ATATAAT
16014 ATATAGTAT
1 ATATA--AT
*
16023 ACATAAT
1 ATATAAT
16030 ACTACT-AT
1 A-TA-TAAT
16038 A-AT-AT
1 ATATAAT
16043 ATATAAT
1 ATATAAT
**
16050 ATGGAAT
1 ATATAAT
16057 ATA-ATAT
1 ATATA-AT
*
16064 ATAATACT
1 AT-ATAAT
16072 ACTATAAT
1 A-TATAAT
16080 ATAATAAT
1 AT-ATAAT
16088 ATATAAAT
1 ATAT-AAT
16096 ATATA
1 ATATA
16101 CTATCGGACA
Statistics
Matches: 167, Mismatches: 27, Indels: 58
0.66 0.11 0.23
Matches are distributed among these distances:
4 2 0.01
5 8 0.05
6 18 0.11
7 73 0.44
8 41 0.25
9 17 0.10
10 8 0.05
ACGTcount: A:0.50, C:0.05, G:0.04, T:0.40
Consensus pattern (7 bp):
ATATAAT
Found at i:16085 original size:28 final size:25
Alignment explanation
Indices: 16002--16100 Score: 78
Period size: 26 Copynumber: 3.8 Consensus size: 25
15992 TATATGCTAT
* *
16002 ATAACATATAATATATAGTATACAT-A
1 ATAATATATAATATATA-TA-ATATGA
*
16028 ATACTACTATAATATATATAATATGGAA
1 ATAATA-TATAATATATATAATAT-G-A
16056 TATAATATATAATACTACTATAATAT-A
1 -ATAATATATAATA-TA-TATAATATGA
16083 ATAATATATAA-ATATATA
1 ATAATATATAATATATATA
16101 CTATCGGACA
Statistics
Matches: 62, Mismatches: 4, Indels: 17
0.75 0.05 0.20
Matches are distributed among these distances:
23 4 0.06
24 2 0.03
25 4 0.06
26 17 0.27
27 12 0.19
28 8 0.13
29 7 0.11
30 8 0.13
ACGTcount: A:0.54, C:0.06, G:0.03, T:0.37
Consensus pattern (25 bp):
ATAATATATAATATATATAATATGA
Found at i:16096 original size:16 final size:16
Alignment explanation
Indices: 16055--16098 Score: 54
Period size: 16 Copynumber: 2.7 Consensus size: 16
16045 ATAATATGGA
*
16055 ATATAATATATAATACT
1 ATATAA-ATATAATAAT
16072 ACTAT-AATATAATAAT
1 A-TATAAATATAATAAT
16088 ATATAAATATA
1 ATATAAATATA
16099 TACTATCGGA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
15 3 0.12
16 16 0.67
17 2 0.08
18 3 0.12
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.39
Consensus pattern (16 bp):
ATATAAATATAATAAT
Found at i:16097 original size:39 final size:41
Alignment explanation
Indices: 15999--16098 Score: 125
Period size: 39 Copynumber: 2.5 Consensus size: 41
15989 ATGTATATGC
*
15999 TATATAACATATAATATATAGTATACATAATACTACTATAATA
1 TATATAATATATAA-ATATAG-ATACATAATACTACTATAATA
** *
16042 TATATAATAT-GGAATATA-ATATATAATACTACTATAATA
1 TATATAATATATAAATATAGATACATAATACTACTATAATA
16081 TA-ATAATATATAAATATA
1 TATATAATATATAAATATA
16099 TACTATCGGA
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
38 7 0.14
39 28 0.56
41 5 0.10
42 1 0.02
43 9 0.18
ACGTcount: A:0.53, C:0.06, G:0.03, T:0.38
Consensus pattern (41 bp):
TATATAATATATAAATATAGATACATAATACTACTATAATA
Found at i:21557 original size:12 final size:12
Alignment explanation
Indices: 21540--21570 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
21530 TTCTCCTCTT
21540 TCATCCCCTTTC
1 TCATCCCCTTTC
21552 TCATCCCCTTTC
1 TCATCCCCTTTC
21564 TCATCCC
1 TCATCCC
21571 ATCTAAGTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.10, C:0.52, G:0.00, T:0.39
Consensus pattern (12 bp):
TCATCCCCTTTC
Found at i:28321 original size:2 final size:2
Alignment explanation
Indices: 28316--28343 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
28306 ATACACACAC
28316 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
28344 GATTAAGTTT
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):
AT
Found at i:42130 original size:43 final size:44
Alignment explanation
Indices: 42069--42155 Score: 167
Period size: 43 Copynumber: 2.0 Consensus size: 44
42059 TGTCATTACG
42069 GGTAAACTCGAAACCAAGACTCACCATCTTCCGTTACTAGGCTA
1 GGTAAACTCGAAACCAAGACTCACCATCTTCCGTTACTAGGCTA
42113 GGTAAACTC-AAACCAAGACTCACCATCTTCCGTTACTAGGCTA
1 GGTAAACTCGAAACCAAGACTCACCATCTTCCGTTACTAGGCTA
42156 CGGGCTGGTA
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
43 34 0.79
44 9 0.21
ACGTcount: A:0.32, C:0.30, G:0.15, T:0.23
Consensus pattern (44 bp):
GGTAAACTCGAAACCAAGACTCACCATCTTCCGTTACTAGGCTA
Found at i:48654 original size:13 final size:13
Alignment explanation
Indices: 48636--48660 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
48626 CAAAGAGTTG
48636 AAATCTGAATTAT
1 AAATCTGAATTAT
48649 AAATCTGAATTA
1 AAATCTGAATTA
48661 AATTTAAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.08, T:0.36
Consensus pattern (13 bp):
AAATCTGAATTAT
Found at i:49960 original size:21 final size:22
Alignment explanation
Indices: 49919--49960 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
49909 AAAAAATTAT
*
49919 TTTTATATTAATTTATACAATA
1 TTTTATATTAATTAATACAATA
49941 TTTTAT-TTAAATTAAT-CAAT
1 TTTTATATT-AATTAATACAAT
49961 TGATATATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (22 bp):
TTTTATATTAATTAATACAATA
Found at i:54350 original size:30 final size:30
Alignment explanation
Indices: 54310--54369 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
54300 TTAAGATCAC
* *
54310 GTAACGACCATATAATAAAAGATTAAAAAT
1 GTAACAACCATATAAGAAAAGATTAAAAAT
54340 GTAACAACCATATAAGAAAAGATTAAAAAT
1 GTAACAACCATATAAGAAAAGATTAAAAAT
54370 CTAATTAAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.58, C:0.10, G:0.10, T:0.22
Consensus pattern (30 bp):
GTAACAACCATATAAGAAAAGATTAAAAAT
Found at i:61519 original size:2 final size:2
Alignment explanation
Indices: 61512--61536 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
61502 TTTATAAGTT
61512 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 T
61537 TTTTAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.