Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003364.1 Hibiscus syriacus cultivar Beakdansim tig00007076_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: 82568
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:20224 original size:27 final size:27
Alignment explanation
Indices: 20164--20240 Score: 86
Period size: 27 Copynumber: 2.9 Consensus size: 27
20154 GCTTAGGGCC
* * *
20164 CCTAATTTCTATATTTATAATTAAGGCT
1 CCTAATTTCTTTATTTATAATT-GGGAT
*
20192 CC-AATTTCTTTACTTATAATTGGGAT
1 CCTAATTTCTTTATTTATAATTGGGAT
20218 CCTAATTT-TTATATTTATAATTG
1 CCTAATTTCTT-TATTTATAATTG
20241 ATGACCTTTC
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
26 7 0.17
27 33 0.79
28 2 0.05
ACGTcount: A:0.30, C:0.13, G:0.08, T:0.49
Consensus pattern (27 bp):
CCTAATTTCTTTATTTATAATTGGGAT
Found at i:30140 original size:29 final size:29
Alignment explanation
Indices: 30098--30187 Score: 171
Period size: 29 Copynumber: 3.1 Consensus size: 29
30088 TATATTTATA
*
30098 GAACTAAGTATGAGATTGATAAGTTGAAT
1 GAACCAAGTATGAGATTGATAAGTTGAAT
30127 GAACCAAGTATGAGATTGATAAGTTGAAT
1 GAACCAAGTATGAGATTGATAAGTTGAAT
30156 GAACCAAGTATGAGATTGATAAGTTGAAT
1 GAACCAAGTATGAGATTGATAAGTTGAAT
30185 GAA
1 GAA
30188 AATAATGGTT
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 60 1.00
ACGTcount: A:0.42, C:0.06, G:0.24, T:0.28
Consensus pattern (29 bp):
GAACCAAGTATGAGATTGATAAGTTGAAT
Found at i:31330 original size:18 final size:17
Alignment explanation
Indices: 31307--31353 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 17
31297 TTTCTCTCTC
31307 TTCCCTTTCACGTACCGT
1 TTCCCTTTC-CGTACCGT
31325 TTCCCTTCTCCGTACCGT
1 TTCCCTT-TCCGTACCGT
*
31343 TTCCGTTTCCG
1 TTCCCTTTCCG
31354 ACTCTCCCGT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 4 0.15
18 21 0.78
19 2 0.07
ACGTcount: A:0.06, C:0.40, G:0.13, T:0.40
Consensus pattern (17 bp):
TTCCCTTTCCGTACCGT
Found at i:34136 original size:10 final size:10
Alignment explanation
Indices: 34121--34145 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
34111 ACTCTTGTGT
34121 TTTTTTTTTC
1 TTTTTTTTTC
34131 TTTTTTTTTC
1 TTTTTTTTTC
34141 TTTTT
1 TTTTT
34146 AAGGCCTGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:35253 original size:298 final size:299
Alignment explanation
Indices: 34707--35289 Score: 1105
Period size: 298 Copynumber: 2.0 Consensus size: 299
34697 TTGTGTAGTA
*
34707 TTTTAAGTTCTCTACACTTGGTATCATATAGTATGATTGGCTGAAGGGGAAAAAAATCAAATTCA
1 TTTTAAGTTCTCTACACTTGGTATCATATAGTATGATTGGCTGAAGGGGAAAAAAATAAAATTCA
*
34772 TGACTAAGGATTTTGTTAGTGATATTTTAATATATAAGTAAAAAGAGATTGTTGTGTATAACTTG
66 TGACTAAGGATTTTGTTAGTGATATTTTAATATACAAGTAAAAAGAGATTGTTGTGTATAACTTG
34837 GGCTGTAAGGTTAGAGTTTTAATGTTGCAAGAAAAATCTCCTTGTTAAAAGAAAAAAATGGAGCT
131 GGCTGTAAGGTTAGAGTTTTAATGTTGCAAGAAAAATCTCCTTGTTAAAAGAAAAAAATGGAGCT
*
34902 TTTGCTCAAATAAATGGAGAACCTGCTCTTAAGCTGAAAATGTTTTTGCCCTTTTTTCTTCTAAT
196 TTTGCTCAAATAAATGGAGAACCTGCTCTTAAGCTGAAAATGTTTTAGCCCTTTTTTCTTCTAAT
34967 CAGTGTAACGTATTTTTATTCTAAAAAGAAAGTATTTTC
261 CAGTGTAACGTATTTTTATTCTAAAAAGAAAGTATTTTC
35006 TTTTAAGTTCTCTACACTTGGTATCATATAGTATGATTGGCTGAA-GGGAAAAAAATAAAATTCA
1 TTTTAAGTTCTCTACACTTGGTATCATATAGTATGATTGGCTGAAGGGGAAAAAAATAAAATTCA
35070 TGACTAAGGATTTTGTTAGTGATATTTTAATATACAAGTAAAAAGAGATTGTTGTGTATAACTTG
66 TGACTAAGGATTTTGTTAGTGATATTTTAATATACAAGTAAAAAGAGATTGTTGTGTATAACTTG
35135 GGCTGTAAGGTTAGAGTTTTAATGTTGCAAGAAAAATCTCCTTGTTAAAAGAAAAAAATGGAGCT
131 GGCTGTAAGGTTAGAGTTTTAATGTTGCAAGAAAAATCTCCTTGTTAAAAGAAAAAAATGGAGCT
* *
35200 TTTGCTCAAATAAATGGAGAACCTGCTCTTAAGCTGAAATTGTTTTAGCCCTTTTTTGTTCTAAT
196 TTTGCTCAAATAAATGGAGAACCTGCTCTTAAGCTGAAAATGTTTTAGCCCTTTTTTCTTCTAAT
*
35265 CAGTTTAACGTATTTTTATTCTAAA
261 CAGTGTAACGTATTTTTATTCTAAA
35290 CAAATGAAAC
Statistics
Matches: 278, Mismatches: 6, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
298 233 0.84
299 45 0.16
ACGTcount: A:0.34, C:0.11, G:0.18, T:0.37
Consensus pattern (299 bp):
TTTTAAGTTCTCTACACTTGGTATCATATAGTATGATTGGCTGAAGGGGAAAAAAATAAAATTCA
TGACTAAGGATTTTGTTAGTGATATTTTAATATACAAGTAAAAAGAGATTGTTGTGTATAACTTG
GGCTGTAAGGTTAGAGTTTTAATGTTGCAAGAAAAATCTCCTTGTTAAAAGAAAAAAATGGAGCT
TTTGCTCAAATAAATGGAGAACCTGCTCTTAAGCTGAAAATGTTTTAGCCCTTTTTTCTTCTAAT
CAGTGTAACGTATTTTTATTCTAAAAAGAAAGTATTTTC
Found at i:48399 original size:21 final size:21
Alignment explanation
Indices: 48359--48402 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
48349 ATGGATTTAA
* *
48359 TAATATCAATCGAGTTAAATT
1 TAATATCAATCGAATAAAATT
*
48380 TAATATCAATTGAATAAAATT
1 TAATATCAATCGAATAAAATT
48401 TA
1 TA
48403 GTATTTATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.39
Consensus pattern (21 bp):
TAATATCAATCGAATAAAATT
Found at i:48545 original size:14 final size:14
Alignment explanation
Indices: 48517--48559 Score: 59
Period size: 14 Copynumber: 3.0 Consensus size: 14
48507 ATATTTGCCT
48517 TAATTATATAAAATA
1 TAATTATA-AAAATA
* *
48532 TATTTTTAAAAATA
1 TAATTATAAAAATA
48546 TAATTATAAAAATA
1 TAATTATAAAAATA
48560 AAAATATGAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
14 18 0.75
15 6 0.25
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
TAATTATAAAAATA
Found at i:59758 original size:2 final size:2
Alignment explanation
Indices: 59751--59785 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
59741 AAGCTAAATA
59751 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
59786 ATAATTTCAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:60904 original size:12 final size:12
Alignment explanation
Indices: 60887--60916 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
60877 GTACATGATC
60887 ATTTTGTCTCGT
1 ATTTTGTCTCGT
*
60899 ATTTTGTTTCGT
1 ATTTTGTCTCGT
60911 ATTTTG
1 ATTTTG
60917 AATTTTAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.10, C:0.10, G:0.17, T:0.63
Consensus pattern (12 bp):
ATTTTGTCTCGT
Found at i:62936 original size:16 final size:16
Alignment explanation
Indices: 62911--62955 Score: 72
Period size: 16 Copynumber: 2.8 Consensus size: 16
62901 ACAGAGTCTC
*
62911 TGAATTATTCAACATT
1 TGAATCATTCAACATT
62927 TGAATCATTCAACATT
1 TGAATCATTCAACATT
*
62943 TAAATCATTCAAC
1 TGAATCATTCAAC
62956 GCTTAATCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.40, C:0.18, G:0.04, T:0.38
Consensus pattern (16 bp):
TGAATCATTCAACATT
Found at i:62965 original size:15 final size:16
Alignment explanation
Indices: 62917--62967 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
62907 TCTCTGAATT
* *
62917 ATTCAACATTTGAATC
1 ATTCAACACTTAAATC
*
62933 ATTCAACATTTAAATC
1 ATTCAACACTTAAATC
*
62949 ATTCAACGCTT-AATC
1 ATTCAACACTTAAATC
62964 ATTC
1 ATTC
62968 TAAAGTAAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
15 8 0.25
16 24 0.75
ACGTcount: A:0.37, C:0.22, G:0.04, T:0.37
Consensus pattern (16 bp):
ATTCAACACTTAAATC
Found at i:77357 original size:35 final size:34
Alignment explanation
Indices: 77272--77358 Score: 90
Period size: 35 Copynumber: 2.5 Consensus size: 34
77262 ATTTGGTATT
*
77272 TAAATACAACAAACTTACAATAAGAATTAAATGG
1 TAAATACAACAAAATTACAATAAGAATTAAATGG
*
77306 TAAATGATAATC-AAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAA-CAAAATTACAATAA--GA-ATTAAATGG
77344 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
77359 ACTAAAATAT
Statistics
Matches: 45, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
34 6 0.13
35 22 0.49
36 2 0.04
37 5 0.11
38 10 0.22
ACGTcount: A:0.55, C:0.09, G:0.08, T:0.28
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGAATTAAATGG
Found at i:77608 original size:27 final size:27
Alignment explanation
Indices: 77573--77624 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
77563 TCCTCATTGT
*
77573 CATCATCATCGTCGTCGTCGTCGTCAC
1 CATCATCATCGTCATCGTCGTCGTCAC
* * *
77600 CATCGTCATTGTCATTGTCGTCGTC
1 CATCATCATCGTCATCGTCGTCGTC
77625 TTGAGCAGGT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.13, C:0.33, G:0.19, T:0.35
Consensus pattern (27 bp):
CATCATCATCGTCATCGTCGTCGTCAC
Found at i:79749 original size:108 final size:108
Alignment explanation
Indices: 79443--79766 Score: 555
Period size: 109 Copynumber: 3.0 Consensus size: 108
79433 ATTACAATAA
*
79443 TTAATTCTTAATTTAATAAT-CATTAAATAAATCAACTAATTATTACTAATAATTTAAATTAAAT
1 TTAATTCTTAATTTAATAATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTAAAT
*
79507 TTAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
66 TAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
*
79550 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACT-AAT-TTACTAATAATTTAAATTA
1 TTAATTCTTAAT-T--TAATAATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
*
79613 AATTAAAACGTTAAAATATTACCGTATCAGCAAAGTGTCGAGATAT
63 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
79659 TTAATTCTTAATTTAATAATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTAAAT
1 TTAATTCTTAATTTAATAATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTAAAT
*
79724 TAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
66 TAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
79767 ATGATTTTCA
Statistics
Matches: 204, Mismatches: 7, Indels: 11
0.92 0.03 0.05
Matches are distributed among these distances:
106 24 0.12
107 15 0.07
108 65 0.32
109 75 0.37
110 8 0.04
111 17 0.08
ACGTcount: A:0.45, C:0.10, G:0.08, T:0.37
Consensus pattern (108 bp):
TTAATTCTTAATTTAATAATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTAAAT
TAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
Found at i:79928 original size:10 final size:10
Alignment explanation
Indices: 79892--79929 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
79882 TTAAAGAGAT
*
79892 AGAGTATTTG
1 AGAGAATTTG
79902 AGAGAAATTT-
1 AGAG-AATTTG
79912 AGAGAATTTG
1 AGAGAATTTG
79922 AGAGAATT
1 AGAGAATT
79930 AGGTGTGATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 5 0.20
10 16 0.64
11 4 0.16
ACGTcount: A:0.42, C:0.00, G:0.26, T:0.32
Consensus pattern (10 bp):
AGAGAATTTG
Found at i:80364 original size:2 final size:2
Alignment explanation
Indices: 80357--80383 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
80347 ATAATATTAT
80357 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 T
80384 TTTTGTTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:81051 original size:4 final size:4
Alignment explanation
Indices: 81042--81076 Score: 61
Period size: 4 Copynumber: 8.8 Consensus size: 4
81032 TTCACCAGTT
*
81042 ATGC ATGC ATGC ATGT ATGC ATGC ATGC ATGC ATG
1 ATGC ATGC ATGC ATGC ATGC ATGC ATGC ATGC ATG
81077 TATATATGCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.29
Consensus pattern (4 bp):
ATGC
Found at i:81090 original size:12 final size:12
Alignment explanation
Indices: 81046--81088 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
81036 CCAGTTATGC
81046 ATGCATGCATGT
1 ATGCATGCATGT
*
81058 ATGCATGCATGC
1 ATGCATGCATGT
* *
81070 ATGCATGTATAT
1 ATGCATGCATGT
81082 ATGCATG
1 ATGCATG
81089 TAAACGGTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.33
Consensus pattern (12 bp):
ATGCATGCATGT
Done.