Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003461.1 Hibiscus syriacus cultivar Beakdansim tig00007311_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: 71504
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.33
Found at i:10106 original size:77 final size:79
Alignment explanation
Indices: 10014--10167 Score: 183
Period size: 77 Copynumber: 2.0 Consensus size: 79
10004 AATTAATAAA
*
10014 TAAAATACTATTTAATTAATT-CAAATTAAATAT-ACATT-AAAGACTTATAATATGAATTACAA
1 TAAAATACTATTTAATT-ATTCCAAATTAAATATCA-ATTAAAAGACTTATAATATAAATTACAA
10076 TC-TTTAATGTTTATT
64 TCTTTTAATGTTTATT
* * * * * *
10091 TAAAA-ACTTATTTAATTATTCCGAATTATATATCAATTAAAAGAGTTGTAATCTAAATTACATT
1 TAAAATAC-TATTTAATTATTCCAAATTAAATATCAATTAAAAGACTTATAATATAAATTACAAT
10155 CTTTTAATGTTTA
65 CTTTTAATGTTTA
10168 CTTACTATAT
Statistics
Matches: 65, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
76 5 0.08
77 27 0.42
78 22 0.34
79 11 0.17
ACGTcount: A:0.43, C:0.08, G:0.05, T:0.44
Consensus pattern (79 bp):
TAAAATACTATTTAATTATTCCAAATTAAATATCAATTAAAAGACTTATAATATAAATTACAATC
TTTTAATGTTTATT
Found at i:16297 original size:2 final size:2
Alignment explanation
Indices: 16290--16320 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
16280 TCTGATCCAA
16290 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 A
16321 ACATCTTTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:16633 original size:48 final size:48
Alignment explanation
Indices: 16580--16675 Score: 167
Period size: 48 Copynumber: 2.0 Consensus size: 48
16570 CAACACTGAC
16580 TTCCTTTTTTAATATTTTATTCG-TTTATACTTTTATATTTCAATCGAA
1 TTCCTTTTTTAATATTTTATT-GTTTTATACTTTTATATTTCAATCGAA
*
16628 TTCCTTTTTTAATATTTTATTGTTTTATTCTTTTATATTTCAATCGAA
1 TTCCTTTTTTAATATTTTATTGTTTTATACTTTTATATTTCAATCGAA
16676 CTATTTGCAC
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
47 1 0.02
48 45 0.98
ACGTcount: A:0.24, C:0.11, G:0.04, T:0.60
Consensus pattern (48 bp):
TTCCTTTTTTAATATTTTATTGTTTTATACTTTTATATTTCAATCGAA
Found at i:16716 original size:58 final size:58
Alignment explanation
Indices: 16647--16764 Score: 236
Period size: 58 Copynumber: 2.0 Consensus size: 58
16637 TAATATTTTA
16647 TTGTTTTATTCTTTTATATTTCAATCGAACTATTTGCACCATTTTGAAACTGAACAAC
1 TTGTTTTATTCTTTTATATTTCAATCGAACTATTTGCACCATTTTGAAACTGAACAAC
16705 TTGTTTTATTCTTTTATATTTCAATCGAACTATTTGCACCATTTTGAAACTGAACAAC
1 TTGTTTTATTCTTTTATATTTCAATCGAACTATTTGCACCATTTTGAAACTGAACAAC
16763 TT
1 TT
16765 CTTGCTCGAT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 60 1.00
ACGTcount: A:0.29, C:0.17, G:0.08, T:0.46
Consensus pattern (58 bp):
TTGTTTTATTCTTTTATATTTCAATCGAACTATTTGCACCATTTTGAAACTGAACAAC
Found at i:32016 original size:19 final size:18
Alignment explanation
Indices: 31992--32040 Score: 64
Period size: 19 Copynumber: 2.7 Consensus size: 18
31982 AAATATTCAG
31992 AGTGCATCGATGCATGGA
1 AGTGCATCGATGCATGGA
*
32010 TAGTGCATCGGTGCATGGA
1 -AGTGCATCGATGCATGGA
32029 A-TGCATTCGATG
1 AGTGCA-TCGATG
32041 TTCAATTAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 4 0.15
18 6 0.22
19 17 0.63
ACGTcount: A:0.24, C:0.16, G:0.33, T:0.27
Consensus pattern (18 bp):
AGTGCATCGATGCATGGA
Found at i:32016 original size:65 final size:65
Alignment explanation
Indices: 31883--32042 Score: 225
Period size: 65 Copynumber: 2.5 Consensus size: 65
31873 TGCACCAAGT
* * *
31883 GTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAAATAGCCTGGTGCATCGATGCATGGCTT
1 GTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGGTGCATCGATGCATGGATA
* **
31947 GTGCATCGATGCATCAAATGCATTCGATGTTTTG-AAAATATTCAGAGTGCATCGATGCATGGAT
1 GTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAG-GTGCATCGATGCATGGAT
32011 A
65 A
* *
32012 GTGCATCGGTGCATGGAATGCATTCGATGTT
1 GTGCATCGATGCATGAAATGCATTCGATGTT
32043 CAATTAATTC
Statistics
Matches: 85, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
64 36 0.42
65 49 0.58
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.31
Consensus pattern (65 bp):
GTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGGTGCATCGATGCATGGATA
Found at i:32082 original size:65 final size:65
Alignment explanation
Indices: 31884--32091 Score: 207
Period size: 65 Copynumber: 3.2 Consensus size: 65
31874 GCACCAAGTG
* * ** *
31884 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCCTG-GTGCATCGATGCATGG-CTT
1 TGCATCGGTGCATGAAATGCATTCGATGTTT-CAAAATATTCAGAGTGCATCGATGCATGGAC-T
31947 G-
64 GA
* * *
31948 TGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGCATGGA-T-
1 TGCATCGGTGCATGAAATGCATTCGATG-TTTCAAAATATTCAGAGTGCATCGATGCATGGACTG
32011 A
65 A
* *
32012 GTGCATCGGTGCATGGAATGCATTCGATG-TTC-AATTAATTCATCGA-TGCATCGATGCATGGA
1 -TGCATCGGTGCATGAAATGCATTCGATGTTTCAAAAT-ATTCA--GAGTGCATCGATGCATGGA
32074 CTGA
62 CTGA
32078 TGCATCGGTGCATG
1 TGCATCGGTGCATG
32092 CCTTTGAATA
Statistics
Matches: 124, Mismatches: 10, Indels: 19
0.81 0.07 0.12
Matches are distributed among these distances:
62 3 0.02
63 7 0.06
64 52 0.42
65 61 0.49
66 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.30
Consensus pattern (65 bp):
TGCATCGGTGCATGAAATGCATTCGATGTTTCAAAATATTCAGAGTGCATCGATGCATGGACTGA
Found at i:39219 original size:64 final size:66
Alignment explanation
Indices: 39116--39276 Score: 220
Period size: 65 Copynumber: 2.5 Consensus size: 66
39106 GTGCACCAAG
* *
39116 TGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAAATAGCCTG-GTGCATCGATGCATGGC
1 TGTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGAGTGCATCGATGCATGGA
39179 T
66 T
* **
39180 TGTGCATCGATGCATCAAATGCATTCGATGTTTTG-AAAATATTCAGAGTGCATCGATGCATGGA
1 TGTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGAGTGCATCGATGCATGGA
39244 T
66 T
** * *
39245 AATGCATCGGTGCATGGAATGCATTCGATGTT
1 TGTGCATCGATGCATGAAATGCATTCGATGTT
39277 CAATTAATTC
Statistics
Matches: 85, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
64 37 0.44
65 48 0.56
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.31
Consensus pattern (66 bp):
TGTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGAGTGCATCGATGCATGGA
T
Found at i:39252 original size:19 final size:17
Alignment explanation
Indices: 39228--39274 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 17
39218 ATATTCAGAG
39228 TGCATCGATGCATGGATAA
1 TGCATCGATGCATGG--AA
*
39247 TGCATCGGTGCATGGAA
1 TGCATCGATGCATGGAA
39264 TGCATTCGATG
1 TGCA-TCGATG
39275 TTCAATTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 6 0.24
18 5 0.20
19 14 0.56
ACGTcount: A:0.26, C:0.17, G:0.30, T:0.28
Consensus pattern (17 bp):
TGCATCGATGCATGGAA
Found at i:39315 original size:65 final size:65
Alignment explanation
Indices: 39118--39325 Score: 214
Period size: 65 Copynumber: 3.2 Consensus size: 65
39108 GCACCAAGTG
* * ** *
39118 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCCTG-GTGCATCGATGCATGG-CTT
1 TGCATCGGTGCATGAAATGCATTCGATGTTT-CAAAATATTCAGAGTGCATCGATGCATGGAC-T
39181 G-
64 GA
* * * *
39182 TGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGCATGGA-TA
1 TGCATCGGTGCATGAAATGCATTCGATG-TTTCAAAATATTCAGAGTGCATCGATGCATGGACTG
39246 A
65 A
* *
39247 TGCATCGGTGCATGGAATGCATTCGATG-TTC-AATTAATTCATCGA-TGCATCGATGCATGGAC
1 TGCATCGGTGCATGAAATGCATTCGATGTTTCAAAAT-ATTCA--GAGTGCATCGATGCATGGAC
39309 TGA
63 TGA
39312 TGCATCGGTGCATG
1 TGCATCGGTGCATG
39326 CCTTTGAATA
Statistics
Matches: 124, Mismatches: 12, Indels: 15
0.82 0.08 0.10
Matches are distributed among these distances:
62 3 0.02
63 7 0.06
64 52 0.42
65 62 0.50
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.30
Consensus pattern (65 bp):
TGCATCGGTGCATGAAATGCATTCGATGTTTCAAAATATTCAGAGTGCATCGATGCATGGACTGA
Found at i:54661 original size:2 final size:2
Alignment explanation
Indices: 54654--54685 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
54644 AAACGGTTGA
54654 AT AT 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 AT AT
54686 CTAAAGCACT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:55802 original size:19 final size:20
Alignment explanation
Indices: 55778--55815 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
55768 GAAGTTTCAG
55778 AGTGAAACAG-ATCCAAGAA
1 AGTGAAACAGAATCCAAGAA
*
55797 AGTGAATCAGAATCCAAGA
1 AGTGAAACAGAATCCAAGA
55816 GATGGAGGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.50, C:0.16, G:0.21, T:0.13
Consensus pattern (20 bp):
AGTGAAACAGAATCCAAGAA
Found at i:65704 original size:22 final size:21
Alignment explanation
Indices: 65665--65705 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
65655 GAATTCAAAG
65665 ATATGAATTAAAATAATTCGA
1 ATATGAATTAAAATAATTCGA
65686 ATATGGAATTTAAAA-AATTC
1 ATAT-GAA-TTAAAATAATTC
65706 TAATTCAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 4 0.22
22 8 0.44
23 6 0.33
ACGTcount: A:0.51, C:0.05, G:0.10, T:0.34
Consensus pattern (21 bp):
ATATGAATTAAAATAATTCGA
Done.