Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002516.1 Hibiscus syriacus cultivar Beakdansim tig00005118_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: 59600
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:7875 original size:15 final size:15
Alignment explanation
Indices: 7852--7881 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
7842 GAATATACAC
7852 ACTCAATAAATTAAT
1 ACTCAATAAATTAAT
*
7867 ACTCGATAAATTAAT
1 ACTCAATAAATTAAT
7882 TTTTTTCTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.13, G:0.03, T:0.33
Consensus pattern (15 bp):
ACTCAATAAATTAAT
Found at i:8554 original size:44 final size:44
Alignment explanation
Indices: 8404--8554 Score: 123
Period size: 44 Copynumber: 3.5 Consensus size: 44
8394 ATTGAGGTCC
** * *
8404 TAATATTACTCAATCTCACTATTATCTTTATAATTGAAG-TCTT
1 TAATATTTTTCAATCTCACTTTTAACTTTATAATTGAAGCTCTT
** * * **
8447 TAATATTTTGTCAATCAT-TTTTTTTACTTTTTAATTGAAGC-CCC
1 TAATATTTT-TCAATC-TCACTTTTAACTTTATAATTGAAGCTCTT
* * * *
8491 TAAT-TTTGT-AATTTCACTTTTAACTTTATAATTGAGGCTTTT
1 TAATATTTTTCAATCTCACTTTTAACTTTATAATTGAAGCTCTT
8533 TAATATTTTTCAATCTCACTTT
1 TAATATTTTTCAATCTCACTTT
8555 CTATCTTTTC
Statistics
Matches: 79, Mismatches: 22, Indels: 13
0.69 0.19 0.11
Matches are distributed among these distances:
40 1 0.01
41 21 0.27
42 5 0.06
43 14 0.18
44 37 0.47
45 1 0.01
ACGTcount: A:0.28, C:0.15, G:0.06, T:0.52
Consensus pattern (44 bp):
TAATATTTTTCAATCTCACTTTTAACTTTATAATTGAAGCTCTT
Found at i:8578 original size:85 final size:86
Alignment explanation
Indices: 8393--8578 Score: 191
Period size: 85 Copynumber: 2.2 Consensus size: 86
8383 ATAATCGACT
*
8393 AATTGAGGTCCTAATATTACTCAATCTCACTATTATCTTTATAATTGAAGTCTTTAATATTTTGT
1 AATTGAGGTCCTAATATTACTCAATCTCACTATTAACTTTATAATTGAAGTCTTTAATATTTTGT
* * * *
8458 CAATCATTTTTTTTACTTTTT
66 CAATCACTTTCTATACTTTTC
** ** * * * *
8479 AATTGAAGCCCCTAAT-TTTGT-AATTTCACTTTTAACTTTATAATTGAGGCTTTTTAATATTTT
1 AATTG-AGGTCCTAATATTACTCAATCTCACTATTAACTTTATAATTGAAG-TCTTTAATATTTT
8542 -TCAATCTCACTTTCTAT-CTTTTC
64 GTCAA--TCACTTTCTATACTTTTC
8565 AATTGAGGTCCTAA
1 AATTGAGGTCCTAA
8579 GACTTTTCAA
Statistics
Matches: 81, Mismatches: 15, Indels: 9
0.77 0.14 0.09
Matches are distributed among these distances:
85 35 0.43
86 30 0.37
87 16 0.20
ACGTcount: A:0.27, C:0.16, G:0.08, T:0.49
Consensus pattern (86 bp):
AATTGAGGTCCTAATATTACTCAATCTCACTATTAACTTTATAATTGAAGTCTTTAATATTTTGT
CAATCACTTTCTATACTTTTC
Found at i:8698 original size:43 final size:44
Alignment explanation
Indices: 8472--8804 Score: 146
Period size: 43 Copynumber: 7.8 Consensus size: 44
8462 CATTTTTTTT
* *
8472 ACTTTTTAATTGA-AGCCCCTAA--TTTTGTAATTTCACTTT-TA
1 ACTTTATAATTGAGA-CCCCTAAGTTTTTTTAATTTCACTTTCTA
* *** * *
8513 ACTTTATAATTGAGGCTTTTTAA-TATTTTTCAATCTCACTTTCTA
1 ACTTTATAATTGAGAC-CCCTAAGT-TTTTTTAATTTCACTTTCTA
* ** ** * * * *
8558 TCTTT-TCAATTGAG-GTCCTAAGACTTTTCAATCTCAATTTCTG
1 ACTTTAT-AATTGAGACCCCTAAGTTTTTTTAATTTCACTTTCTA
* * *
8601 TCTTTATAATAGAGACCCCTAA---TTTTTAATTTCACTTTTTA
1 ACTTTATAATTGAGACCCCTAAGTTTTTTTAATTTCACTTTCTA
*
8642 ACTTTATAATTGAGACCCTTAAGTTTTTTTAA-TTCACTTTCTA
1 ACTTTATAATTGAGACCCCTAAGTTTTTTTAATTTCACTTTCTA
* * * * * * * *
8685 ATTTTCTATTTGAGGCCCCTAAG-TTTTTCAATCTCA-ATTAT-
1 ACTTTATAATTGAGACCCCTAAGTTTTTTTAATTTCACTTTCTA
* * *
8726 ACATTTAT-ATTAAGGCCCCT-A-TTTTTTTAATCTCGA-TTTCTA
1 AC-TTTATAATTGAGACCCCTAAGTTTTTTTAATTTC-ACTTTCTA
* * * *
8768 CCTTTATAATTAAGGCCTCTAA-TTTTTTATAATTTCA
1 ACTTTATAATTGAGACCCCTAAGTTTTTT-TAATTTCA
8805 TAAAATTCTC
Statistics
Matches: 225, Mismatches: 47, Indels: 38
0.73 0.15 0.12
Matches are distributed among these distances:
40 12 0.05
41 66 0.29
42 29 0.13
43 71 0.32
44 34 0.15
45 13 0.06
ACGTcount: A:0.27, C:0.18, G:0.08, T:0.48
Consensus pattern (44 bp):
ACTTTATAATTGAGACCCCTAAGTTTTTTTAATTTCACTTTCTA
Found at i:8722 original size:127 final size:129
Alignment explanation
Indices: 8487--8723 Score: 324
Period size: 127 Copynumber: 1.9 Consensus size: 129
8477 TTAATTGAAG
* **
8487 CCCCTAATTTTGTAATTTCACTTTTAACTTTATAATTGAGGCTTTTTAATATTTTTCAATCTCAC
1 CCCCTAATTTTGTAATTTCACTTTTAACTTTATAATTGAGACTCCTTAATATTTTTCAATCTCAC
* *
8552 TTTCTATCTTTTCAATTGAGGTCCTAAGACTTTTCAATCTCAATTTCTGTCTTTATAATAGAGA
66 TTTCTATATTTTCAATTGAGGCCCTAAGACTTTTCAATCTCAATTTCTGTCTTTATAATAGAGA
*
8616 CCCCTAATTTT-TAATTTCACTTTTTAACTTTATAATTGAGAC-CCTTAAGT-TTTTTTAAT-TC
1 CCCCTAATTTTGTAATTTCAC-TTTTAACTTTATAATTGAGACTCCTTAA-TATTTTTCAATCTC
* *
8677 ACTTTCTA-ATTTTCTATTTGAGGCCCCTAAG-TTTTTCAATCTCAATT
64 ACTTTCTATATTTTC-AATTGAGG-CCCTAAGACTTTTCAATCTCAATT
8724 ATACATTTAT
Statistics
Matches: 96, Mismatches: 8, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
126 5 0.05
127 32 0.33
128 27 0.28
129 32 0.33
ACGTcount: A:0.26, C:0.19, G:0.08, T:0.48
Consensus pattern (129 bp):
CCCCTAATTTTGTAATTTCACTTTTAACTTTATAATTGAGACTCCTTAATATTTTTCAATCTCAC
TTTCTATATTTTCAATTGAGGCCCTAAGACTTTTCAATCTCAATTTCTGTCTTTATAATAGAGA
Found at i:8742 original size:41 final size:43
Alignment explanation
Indices: 8697--8795 Score: 123
Period size: 41 Copynumber: 2.4 Consensus size: 43
8687 TTTCTATTTG
*
8697 AGGCCCCTAAGTTTTTCAATCTC-AATTATACATTTAT-ATTA
1 AGGCCCCTAATTTTTTCAATCTCGAATTATACATTTATAATTA
* * * *
8738 AGGCCCCT-ATTTTTTTAATCTCGATTTCTACCTTTATAATTA
1 AGGCCCCTAATTTTTTCAATCTCGAATTATACATTTATAATTA
*
8780 AGGCCTCTAATTTTTT
1 AGGCCCCTAATTTTTT
8796 ATAATTTCAT
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
40 12 0.24
41 19 0.39
42 11 0.22
43 7 0.14
ACGTcount: A:0.26, C:0.20, G:0.08, T:0.45
Consensus pattern (43 bp):
AGGCCCCTAATTTTTTCAATCTCGAATTATACATTTATAATTA
Found at i:17160 original size:32 final size:31
Alignment explanation
Indices: 17084--17160 Score: 109
Period size: 33 Copynumber: 2.4 Consensus size: 31
17074 TTTTAAACTT
* *
17084 TATTTCAATTATCGAACTTGAAGTTTTTAAG
1 TATTTCAATTATCAAACTTGAAGTATTTAAG
*
17115 TATTTGAATTTATCAAACTTGGAAGTATTTAAG
1 TATTTCAA-TTATCAAACTT-GAAGTATTTAAG
17148 TATTTCAATTATC
1 TATTTCAATTATC
17161 GTAAACTTTG
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
31 7 0.17
32 15 0.38
33 18 0.45
ACGTcount: A:0.34, C:0.09, G:0.12, T:0.45
Consensus pattern (31 bp):
TATTTCAATTATCAAACTTGAAGTATTTAAG
Found at i:23038 original size:31 final size:31
Alignment explanation
Indices: 22995--23053 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
22985 GATAATATAA
* *
22995 TAATTATTTTATAGTATTTAAATAAATTTAT
1 TAATAATTTTATAATATTTAAATAAATTTAT
* *
23026 TAATAATTTTATAATCTTTTAATAAATT
1 TAATAATTTTATAATATTTAAATAAATT
23054 AGATAATATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (31 bp):
TAATAATTTTATAATATTTAAATAAATTTAT
Found at i:23061 original size:31 final size:31
Alignment explanation
Indices: 22992--23061 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 31
22982 TTTGATAATA
* *
22992 TAATAATTATTTTATAGTATTTAAATAAATT
1 TAATAATAATTTTATAATATTTAAATAAATT
* * *
23023 TATTAATAATTTTATAATCTTTTAATAAA-T
1 TAATAATAATTTTATAATATTTAAATAAATT
23053 TAGATAATA
1 TA-ATAATA
23062 TAAGTTTAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
30 3 0.09
31 29 0.91
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.50
Consensus pattern (31 bp):
TAATAATAATTTTATAATATTTAAATAAATT
Found at i:23134 original size:73 final size:73
Alignment explanation
Indices: 22957--23167 Score: 220
Period size: 73 Copynumber: 2.9 Consensus size: 73
22947 AATAATCACT
* * * * *
22957 ATAATGTTGTAATAAATTATAAAAGTTTGATAATATAA---TAATTATTTTATAGTATTTAAATA
1 ATAATGTTGTAATAAATTATAAAAGTTTGATAATATAAGTTTAATTATATAATA-TTTTTTACTA
* *
23019 AATTTATTA
65 AGTTGATTA
* * * *
23028 ATAAT-TT-T-ATAATCTTTTAATAAATTAGATAATATAAGTTTAATTATATAATATTTTTTACT
1 ATAATGTTGTAATAA-ATTATAA-AAGTTTGATAATATAAGTTTAATTATATAATATTTTTTACT
23090 AAGTTCGA-TA
64 AAGTT-GATTA
* *
23100 ATAATGTTGTAATAAATTATAAAAGTTTGATAATACAAGTTTAATTGTATAATATTTTTTACTAA
1 ATAATGTTGTAATAAATTATAAAAGTTTGATAATATAAGTTTAATTATATAATATTTTTTACTAA
23165 GTT
66 GTT
23168 TAATATATTT
Statistics
Matches: 114, Mismatches: 17, Indels: 16
0.78 0.12 0.11
Matches are distributed among these distances:
68 4 0.04
69 6 0.05
70 16 0.14
71 5 0.04
72 17 0.15
73 56 0.49
74 6 0.05
75 4 0.04
ACGTcount: A:0.43, C:0.02, G:0.08, T:0.47
Consensus pattern (73 bp):
ATAATGTTGTAATAAATTATAAAAGTTTGATAATATAAGTTTAATTATATAATATTTTTTACTAA
GTTGATTA
Found at i:23301 original size:32 final size:30
Alignment explanation
Indices: 23243--23310 Score: 84
Period size: 32 Copynumber: 2.2 Consensus size: 30
23233 TCAATAAAGT
*
23243 TTAAAAGTTATAAAATACTTATTAAATTTA
1 TTAAAAGTTATAAAATACTTAATAAATTTA
23273 TTAAAAGATTATAAAAATTA-TTAATAAATTTA
1 TTAAAAG-TTAT-AAAA-TACTTAATAAATTTA
23305 TCTAAA
1 T-TAAA
23311 TACTATAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
30 7 0.21
31 4 0.12
32 16 0.48
33 6 0.18
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.41
Consensus pattern (30 bp):
TTAAAAGTTATAAAATACTTAATAAATTTA
Found at i:23318 original size:32 final size:34
Alignment explanation
Indices: 23265--23329 Score: 82
Period size: 32 Copynumber: 2.0 Consensus size: 34
23255 AAATACTTAT
*
23265 TAAATTTATTAAAAGATTAT-AAA-AATTATTAA
1 TAAATTTATTAAAAGACTATAAAATAATTATTAA
*
23297 TAAATTTATCT-AAATACTATAAAATAATTATTA
1 TAAATTTAT-TAAAAGACTATAAAATAATTATTA
23330 TATTATCGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
32 16 0.57
33 4 0.14
34 8 0.29
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.42
Consensus pattern (34 bp):
TAAATTTATTAAAAGACTATAAAATAATTATTAA
Found at i:24563 original size:29 final size:29
Alignment explanation
Indices: 24530--24591 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
24520 TTAATTTATC
* *
24530 TTTTTTTTATCAAAATAGATACATAAAATA
1 TTTTTTGT-TCAAAACAGATACATAAAATA
* *
24560 TTTTTTGTTCAAAACAGATACCTAAAGTA
1 TTTTTTGTTCAAAACAGATACATAAAATA
24589 TTT
1 TTT
24592 AATTTTTTCT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 21 0.75
30 7 0.25
ACGTcount: A:0.40, C:0.10, G:0.06, T:0.44
Consensus pattern (29 bp):
TTTTTTGTTCAAAACAGATACATAAAATA
Found at i:36598 original size:28 final size:28
Alignment explanation
Indices: 36563--36616 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
36553 CCATTTAAGT
36563 AAAAATGATTAAGAAAACTAAGTATTTC
1 AAAAATGATTAAGAAAACTAAGTATTTC
36591 AAAAATGATTAAGAAAACTAAGTATT
1 AAAAATGATTAAGAAAACTAAGTATT
36617 CCTAAGCATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.56, C:0.06, G:0.11, T:0.28
Consensus pattern (28 bp):
AAAAATGATTAAGAAAACTAAGTATTTC
Found at i:53029 original size:28 final size:28
Alignment explanation
Indices: 52989--53042 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
52979 TGTCATGTTA
52989 ACATTATTATTTTTTTAACGGTAGGTTG
1 ACATTATTATTTTTTTAACGGTAGGTTG
53017 ACATTATTATTTTTTTAACGGTAGGT
1 ACATTATTATTTTTTTAACGGTAGGT
53043 GATCAAAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.26, C:0.07, G:0.17, T:0.50
Consensus pattern (28 bp):
ACATTATTATTTTTTTAACGGTAGGTTG
Found at i:53623 original size:30 final size:30
Alignment explanation
Indices: 53587--53664 Score: 93
Period size: 31 Copynumber: 2.5 Consensus size: 30
53577 CCCAAAAGCC
* *
53587 TAACAAATGGTCACTAATGTGATCGATTTG
1 TAACAAATAGTCACTAATATGATCGATTTG
* *
53617 TAACAAATTAGTCATTAATATTATCGATTTG
1 TAACAAA-TAGTCACTAATATGATCGATTTG
*
53648 TAACAAATTAATCACTA
1 TAACAAA-TAGTCACTA
53665 GATGTTAATA
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
30 7 0.17
31 34 0.83
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.36
Consensus pattern (30 bp):
TAACAAATAGTCACTAATATGATCGATTTG
Found at i:54791 original size:31 final size:31
Alignment explanation
Indices: 54753--54817 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
54743 CAACGGCGAG
*
54753 TGACTAATTTGTTACAAATCGATAATATTAA
1 TGACTAATTTGTTACAAATCGATAACATTAA
*
54784 TGACTAATTTGTTACGAATCGATAACATTAA
1 TGACTAATTTGTTACAAATCGATAACATTAA
54815 TGA
1 TGA
54818 TCATTGTTAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.40, C:0.11, G:0.12, T:0.37
Consensus pattern (31 bp):
TGACTAATTTGTTACAAATCGATAACATTAA
Found at i:58912 original size:29 final size:29
Alignment explanation
Indices: 58870--58940 Score: 142
Period size: 29 Copynumber: 2.4 Consensus size: 29
58860 AAATTCTAAA
58870 ATATTTGTATTAACTATCATCTACATTAG
1 ATATTTGTATTAACTATCATCTACATTAG
58899 ATATTTGTATTAACTATCATCTACATTAG
1 ATATTTGTATTAACTATCATCTACATTAG
58928 ATATTTGTATTAA
1 ATATTTGTATTAA
58941 TAAATGTTGG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.35, C:0.11, G:0.07, T:0.46
Consensus pattern (29 bp):
ATATTTGTATTAACTATCATCTACATTAG
Done.