Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007844.1 Hibiscus syriacus cultivar Beakdansim tig00110198_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: 2094103
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 7
Found at i:2089052 original size:6 final size:6
Alignment explanation
Indices: 2089041--2089078 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
2089031 GACACGTATT
2089041 ACCACG ACCACG ACCACG ACCACG ACCACG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
2089079 CGAGACGGCG
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.16
6 27 0.84
ACGTcount: A:0.32, C:0.53, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:2089834 original size:6 final size:6
Alignment explanation
Indices: 2089823--2089861 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
2089813 TCTCGTCTCG
2089823 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
2089862 AATACGTGTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.00, C:0.15, G:0.51, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:2089997 original size:20 final size:20
Alignment explanation
Indices: 2089972--2090101 Score: 129
Period size: 20 Copynumber: 6.4 Consensus size: 20
2089962 TTTTGCCGTT
2089972 TTGCGATTCTTGGAATCGCG
1 TTGCGATTCTTGGAATCGCG
** *
2089992 TTGCGATT-TTCTCAATCGCA
1 TTGCGATTCTT-GGAATCGCG
*
2090012 TTGCGATTCCTGGAATCGCG
1 TTGCGATTCTTGGAATCGCG
**
2090032 TTGCGATT-TTCTCAATCGCG
1 TTGCGATTCTT-GGAATCGCG
* *
2090052 TTGCGATTCTTTGAATCGCA
1 TTGCGATTCTTGGAATCGCG
*
2090072 TTGCGATTCTTGGAAGATTGCG
1 TTGCGATTCTTGG-A-ATCGCG
2090094 TTGCGATT
1 TTGCGATT
2090102 TTCTTTTGAC
Statistics
Matches: 89, Mismatches: 15, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
19 3 0.03
20 70 0.79
21 4 0.04
22 12 0.13
ACGTcount: A:0.17, C:0.21, G:0.25, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTTGGAATCGCG
Found at i:2090019 original size:40 final size:40
Alignment explanation
Indices: 2089972--2090079 Score: 180
Period size: 40 Copynumber: 2.7 Consensus size: 40
2089962 TTTTGCCGTT
2089972 TTGCGATTCTTGGAATCGCGTTGCGATTTTCTCAATCGCA
1 TTGCGATTCTTGGAATCGCGTTGCGATTTTCTCAATCGCA
* *
2090012 TTGCGATTCCTGGAATCGCGTTGCGATTTTCTCAATCGCG
1 TTGCGATTCTTGGAATCGCGTTGCGATTTTCTCAATCGCA
* *
2090052 TTGCGATTCTTTGAATCGCATTGCGATT
1 TTGCGATTCTTGGAATCGCGTTGCGATT
2090080 CTTGGAAGAT
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 63 1.00
ACGTcount: A:0.17, C:0.22, G:0.23, T:0.38
Consensus pattern (40 bp):
TTGCGATTCTTGGAATCGCGTTGCGATTTTCTCAATCGCA
Found at i:2090069 original size:60 final size:62
Alignment explanation
Indices: 2089985--2090105 Score: 185
Period size: 60 Copynumber: 2.0 Consensus size: 62
2089975 CGATTCTTGG
2089985 AATCGCGTTGCGATTTTCTCAATCGCATTGCGATTCCTGG-A-ATCGCGTTGCGATTTTCTC
1 AATCGCGTTGCGATTTTCTCAATCGCATTGCGATTCCTGGAAGATCGCGTTGCGATTTTCTC
* * *
2090045 AATCGCGTTGCGATTCTT-TGAATCGCATTGCGATTCTTGGAAGATTGCGTTGCGATTTTCT
1 AATCGCGTTGCGATT-TTCTCAATCGCATTGCGATTCCTGGAAGATCGCGTTGCGATTTTCT
2090106 TTTGACCGTT
Statistics
Matches: 55, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
60 35 0.64
61 3 0.05
62 17 0.31
ACGTcount: A:0.17, C:0.21, G:0.23, T:0.38
Consensus pattern (62 bp):
AATCGCGTTGCGATTTTCTCAATCGCATTGCGATTCCTGGAAGATCGCGTTGCGATTTTCTC
Found at i:2090157 original size:20 final size:19
Alignment explanation
Indices: 2089985--2090163 Score: 112
Period size: 20 Copynumber: 8.9 Consensus size: 19
2089975 CGATTCTTGG
2089985 AATCGCGTTGCGATTTTCT
1 AATCGCGTTGCGATTTTCT
* *
2090004 CAATCGCATTGCGA-TTCCT
1 -AATCGCGTTGCGATTTTCT
2090023 GGAATCGCGTTGCGATTTTCT
1 --AATCGCGTTGCGATTTTCT
2090044 CAATCGCGTTGCGATTCTT-T
1 -AATCGCGTTGCGATT-TTCT
* **
2090064 GAATCGCATTGCGATTCTTGGA
1 -AATCGCGTTGCGATT-TT-CT
*
2090086 AGATTGCGTTGCGATTTTCT
1 A-ATCGCGTTGCGATTTTCT
* *
2090106 -TTTGACCGTTGCGATTTTCT
1 AATCG--CGTTGCGATTTTCT
** * *
2090126 TTTCAACATTGCGATTTTCT
1 AATC-GCGTTGCGATTTTCT
2090146 AAATCGCGTTGCGATTTT
1 -AATCGCGTTGCGATTTT
2090164 TGTTTCGCAT
Statistics
Matches: 127, Mismatches: 21, Indels: 22
0.75 0.12 0.13
Matches are distributed among these distances:
18 3 0.02
19 4 0.03
20 95 0.75
21 13 0.10
22 12 0.09
ACGTcount: A:0.17, C:0.21, G:0.21, T:0.41
Consensus pattern (19 bp):
AATCGCGTTGCGATTTTCT
Found at i:2090922 original size:29 final size:29
Alignment explanation
Indices: 2090880--2090938 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
2090870 TCACGTTGCG
2090880 ATTTATTACAAATTCGTTGCCATAGTCCA
1 ATTTATTACAAATTCGTTGCCATAGTCCA
* *
2090909 ATTTATTCCAAATTCGTTGCGATAGTCCA
1 ATTTATTACAAATTCGTTGCCATAGTCCA
2090938 A
1 A
2090939 AATCGTGTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.37
Consensus pattern (29 bp):
ATTTATTACAAATTCGTTGCCATAGTCCA
Found at i:2090985 original size:21 final size:21
Alignment explanation
Indices: 2090915--2090986 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 21
2090905 TCCAATTTAT
2090915 TCCAAATT--CGTTGCGATAG
1 TCCAAATTCGCGTTGCGATAG
* *
2090934 TCCAAAATCGTGTTGCGATAG
1 TCCAAATTCGCGTTGCGATAG
* * **
2090955 TCGAAGTTCGCGTTGCGATTT
1 TCCAAATTCGCGTTGCGATAG
2090976 TCCAAATTCGC
1 TCCAAATTCGC
2090987 AACGACTGGT
Statistics
Matches: 41, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
19 7 0.17
21 34 0.83
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.32
Consensus pattern (21 bp):
TCCAAATTCGCGTTGCGATAG
Found at i:2091076 original size:6 final size:6
Alignment explanation
Indices: 2091060--2091089 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
2091050 TTGTCGAAGA
2091060 CACGTAC CACGAC CACGAC CACGAC CACGA
1 CACG-AC CACGAC CACGAC CACGAC CACGA
2091090 GACGACGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 19 0.83
7 4 0.17
ACGTcount: A:0.33, C:0.47, G:0.17, T:0.03
Consensus pattern (6 bp):
CACGAC
Found at i:2091841 original size:21 final size:21
Alignment explanation
Indices: 2091812--2091925 Score: 101
Period size: 21 Copynumber: 5.4 Consensus size: 21
2091802 TTTGGAATAA
2091812 ATCGCAACGCGAACTTGGACT
1 ATCGCAACGCGAACTTGGACT
* * *
2091833 ATCGTAA--CGAATTTGGAAT
1 ATCGCAACGCGAACTTGGACT
*
2091852 AAATCGCAACGCGAACTTCGACT
1 --ATCGCAACGCGAACTTGGACT
* *
2091875 ATCGCAA--CGAATTTGGAAT
1 ATCGCAACGCGAACTTGGACT
*
2091894 AAATTGCAACGCGAACTTGGACT
1 --ATCGCAACGCGAACTTGGACT
2091917 ATCGCAACG
1 ATCGCAACG
2091926 AATTTGGAAA
Statistics
Matches: 71, Mismatches: 14, Indels: 16
0.70 0.14 0.16
Matches are distributed among these distances:
19 19 0.27
21 33 0.46
23 19 0.27
ACGTcount: A:0.34, C:0.23, G:0.21, T:0.22
Consensus pattern (21 bp):
ATCGCAACGCGAACTTGGACT
Found at i:2091857 original size:42 final size:42
Alignment explanation
Indices: 2091798--2091934 Score: 247
Period size: 42 Copynumber: 3.3 Consensus size: 42
2091788 CCAGTCGTTG
*
2091798 CGAATTTGGAATAAATCGCAACGCGAACTTGGACTATCGTAA
1 CGAATTTGGAATAAATCGCAACGCGAACTTGGACTATCGCAA
*
2091840 CGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAA
1 CGAATTTGGAATAAATCGCAACGCGAACTTGGACTATCGCAA
*
2091882 CGAATTTGGAATAAATTGCAACGCGAACTTGGACTATCGCAA
1 CGAATTTGGAATAAATCGCAACGCGAACTTGGACTATCGCAA
2091924 CGAATTTGGAA
1 CGAATTTGGAA
2091935 AATCACATTG
Statistics
Matches: 91, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 91 1.00
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.23
Consensus pattern (42 bp):
CGAATTTGGAATAAATCGCAACGCGAACTTGGACTATCGCAA
Found at i:2091970 original size:84 final size:86
Alignment explanation
Indices: 2091793--2091976 Score: 218
Period size: 84 Copynumber: 2.2 Consensus size: 86
2091783 TACCACCAGT
* *
2091793 CGTTGCGAATTTGGAATAAATCGCAACGCGAACTTGGACTATCGTAACGAATTTGGAATAAATCG
1 CGTTGCGAATTTGGAATAAATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAATAAATCA
*
2091858 CAACGCGAACTTCGACTATCG
66 CAACGCGAACGTCGACTATCG
** *
2091879 C--AACGAATTTGGAATAAATTGCAACGCGAACTTGGACTATCGCAACGAATTTGG-A-AAATCA
1 CGTTGCGAATTTGGAATAAATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAATAAATCA
** *
2091940 CATTGCGATA-GTCGAAGT-TCG
66 CAACGCGA-ACGTCG-ACTATCG
*
2091961 CGTTGCGAATCTGGAA
1 CGTTGCGAATTTGGAA
2091977 GCTGATTTGC
Statistics
Matches: 82, Mismatches: 12, Indels: 10
0.79 0.12 0.10
Matches are distributed among these distances:
82 18 0.22
83 4 0.05
84 59 0.72
86 1 0.01
ACGTcount: A:0.33, C:0.20, G:0.23, T:0.24
Consensus pattern (86 bp):
CGTTGCGAATTTGGAATAAATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAATAAATCA
CAACGCGAACGTCGACTATCG
Done.