Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001463.1 Hibiscus syriacus cultivar Beakdansim tig00002827_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: 62782
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:516 original size:2 final size:2
Alignment explanation
Indices: 509--554 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
499 CTATGCTAGT
509 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
551 TA TA
1 TA TA
555 AGCACACACG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6083 original size:31 final size:31
Alignment explanation
Indices: 6046--6109 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
6036 ACCGGTTACA
* *
6046 ACCCGACGC-GACCCATTGACTCGACCCGTTG
1 ACCCGAC-CTGACCCATTGACACGAACCGTTG
6077 ACCCGACCTGACCCATTGACACGAACCGTTG
1 ACCCGACCTGACCCATTGACACGAACCGTTG
6108 AC
1 AC
6110 TAGTGTTGAC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 1 0.03
31 29 0.97
ACGTcount: A:0.23, C:0.41, G:0.20, T:0.16
Consensus pattern (31 bp):
ACCCGACCTGACCCATTGACACGAACCGTTG
Found at i:8601 original size:24 final size:24
Alignment explanation
Indices: 8470--8584 Score: 160
Period size: 24 Copynumber: 4.8 Consensus size: 24
8460 TCGAATTGAT
8470 TTCTGATATGATACTTGACATGGA
1 TTCTGATATGATACTTGACATGGA
8494 TTCTGATATGATA-TCTGACATGGA
1 TTCTGATATGATACT-TGACATGGA
* *
8518 TTCTGATCTGATACTTGACTTGGA
1 TTCTGATATGATACTTGACATGGA
* * *
8542 TTCTGATCTGATATTTGACTTGGA
1 TTCTGATATGATACTTGACATGGA
*
8566 TTTTGATATGATACTTGAC
1 TTCTGATATGATACTTGAC
8585 GTGAATTATG
Statistics
Matches: 83, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
23 1 0.01
24 81 0.98
25 1 0.01
ACGTcount: A:0.25, C:0.13, G:0.20, T:0.42
Consensus pattern (24 bp):
TTCTGATATGATACTTGACATGGA
Found at i:8607 original size:48 final size:48
Alignment explanation
Indices: 8467--8607 Score: 174
Period size: 48 Copynumber: 2.9 Consensus size: 48
8457 TTTTCGAATT
* *
8467 GATTTCTGATATGATACTTGACATGGATTCTGATATGATATCTGACATG
1 GATTT-TGATATGATACTTGACATGGATTCTGATATGATATTTGACTTG
* * * *
8516 GATTCTGATCTGATACTTGACTTGGATTCTGATCTGATATTTGACTTG
1 GATTTTGATATGATACTTGACATGGATTCTGATATGATATTTGACTTG
* * * * *
8564 GATTTTGATATGATACTTGACGTGAATTATGATTTGATTTTTGA
1 GATTTTGATATGATACTTGACATGGATTCTGATATGATATTTGA
8608 TATATACATT
Statistics
Matches: 79, Mismatches: 13, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
48 75 0.95
49 4 0.05
ACGTcount: A:0.26, C:0.11, G:0.21, T:0.43
Consensus pattern (48 bp):
GATTTTGATATGATACTTGACATGGATTCTGATATGATATTTGACTTG
Found at i:13131 original size:24 final size:24
Alignment explanation
Indices: 13104--13212 Score: 121
Period size: 24 Copynumber: 4.5 Consensus size: 24
13094 ATTTGATTTA
* *
13104 TGATCTGATACTTGACAAGGATTC
1 TGATATGATACTTGACATGGATTC
13128 TGATATGATA-TCTGACATGGATTC
1 TGATATGATACT-TGACATGGATTC
** *
13152 TGATCCGATACTTGACTTGGATTC
1 TGATATGATACTTGACATGGATTC
* * * *
13176 TTATATGATATTTGACTTGGATTT
1 TGATATGATACTTGACATGGATTC
13200 TGATATGATACTT
1 TGATATGATACTT
13213 AACGTGAATT
Statistics
Matches: 71, Mismatches: 12, Indels: 4
0.82 0.14 0.05
Matches are distributed among these distances:
23 1 0.01
24 69 0.97
25 1 0.01
ACGTcount: A:0.27, C:0.13, G:0.19, T:0.41
Consensus pattern (24 bp):
TGATATGATACTTGACATGGATTC
Found at i:13163 original size:48 final size:48
Alignment explanation
Indices: 13104--13212 Score: 146
Period size: 48 Copynumber: 2.3 Consensus size: 48
13094 ATTTGATTTA
13104 TGATCTGATACTTGACAAGGATTCTGATATGATATCTGACATGGATTC
1 TGATCTGATACTTGACAAGGATTCTGATATGATATCTGACATGGATTC
* ** * * * *
13152 TGATCCGATACTTGACTTGGATTCTTATATGATATTTGACTTGGATTT
1 TGATCTGATACTTGACAAGGATTCTGATATGATATCTGACATGGATTC
*
13200 TGATATGATACTT
1 TGATCTGATACTT
13213 AACGTGAATT
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
48 52 1.00
ACGTcount: A:0.27, C:0.13, G:0.19, T:0.41
Consensus pattern (48 bp):
TGATCTGATACTTGACAAGGATTCTGATATGATATCTGACATGGATTC
Found at i:15770 original size:21 final size:22
Alignment explanation
Indices: 15709--15771 Score: 67
Period size: 21 Copynumber: 2.8 Consensus size: 22
15699 AGTGAGGGAG
*
15709 GCAGAGAGAGAAGCAGC-GAAA
1 GCAGAGAGAGAAGCAACAGAAA
15730 GCAGAGAGAGTAGTAGCAACAG-AA
1 GCAGAGAGAG-A--AGCAACAGAAA
*
15754 GTAGAGAGAGAAGCAACA
1 GCAGAGAGAGAAGCAACA
15772 TATCAGTAGA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
21 17 0.47
22 1 0.03
23 1 0.03
24 16 0.44
25 1 0.03
ACGTcount: A:0.48, C:0.13, G:0.35, T:0.05
Consensus pattern (22 bp):
GCAGAGAGAGAAGCAACAGAAA
Found at i:16217 original size:40 final size:40
Alignment explanation
Indices: 16171--16250 Score: 99
Period size: 41 Copynumber: 2.0 Consensus size: 40
16161 CTTCTCTATA
**
16171 AAAAATGCTTCTATA-TATCAGACCTTTTGCGGCATTTGTT
1 AAAAATGCCACTATAGTAT-AGACCTTTTGCGGCATTTGTT
* *
16211 AAAAATGCCACTATAGTTATAGAGCTTTTGCGGCGTTTGT
1 AAAAATGCCACTATAG-TATAGACCTTTTGCGGCATTTGT
16251 ATCCAAAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
40 13 0.38
41 18 0.53
42 3 0.09
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.38
Consensus pattern (40 bp):
AAAAATGCCACTATAGTATAGACCTTTTGCGGCATTTGTT
Found at i:32114 original size:24 final size:25
Alignment explanation
Indices: 32086--32134 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
32076 ATAAATTAAA
32086 AAAG-ATTTAATTT-CTCTTTTATTC
1 AAAGAATTT-ATTTCCTCTTTTATTC
32110 AAAGACATTTATTTCCTCTTTTATT
1 AAAGA-ATTTATTTCCTCTTTTATT
32135 AGAATATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 4 0.18
25 4 0.18
26 14 0.64
ACGTcount: A:0.29, C:0.14, G:0.04, T:0.53
Consensus pattern (25 bp):
AAAGAATTTATTTCCTCTTTTATTC
Found at i:32154 original size:26 final size:26
Alignment explanation
Indices: 32099--32156 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
32089 GATTTAATTT
*
32099 CTCTTTTATTCAAAGACATTTATTTC
1 CTCTTTTATTCAAAGACATTTATTAC
* * *
32125 CTCTTTTATT-AGAATATATTTATTAG
1 CTCTTTTATTCA-AAGACATTTATTAC
32151 CTCTTT
1 CTCTTT
32157 CAGTCCAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 1 0.04
26 26 0.96
ACGTcount: A:0.26, C:0.16, G:0.05, T:0.53
Consensus pattern (26 bp):
CTCTTTTATTCAAAGACATTTATTAC
Found at i:36163 original size:20 final size:19
Alignment explanation
Indices: 36121--36172 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 19
36111 ATTTTTTCCT
36121 TTTATTTTAATTTTTTATA
1 TTTATTTTAATTTTTTATA
*
36140 TTTATTTTAGTCTTTATT-TA
1 TTTATTTTAAT-TTT-TTATA
*
36160 TTTAATTTAATTT
1 TTTATTTTAATTT
36173 AACTTGTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
19 12 0.43
20 14 0.50
21 2 0.07
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.71
Consensus pattern (19 bp):
TTTATTTTAATTTTTTATA
Found at i:50236 original size:21 final size:21
Alignment explanation
Indices: 50212--50263 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
50202 TTCAAAGGGT
*
50212 AGTATCGATACATATTTGTAG
1 AGTATCGATACATATTCGTAG
50233 AGTATCGATACATATTCGTAG
1 AGTATCGATACATATTCGTAG
*
50254 AATATCGATA
1 AGTATCGATA
50264 TTCGGGTCTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.35
Consensus pattern (21 bp):
AGTATCGATACATATTCGTAG
Done.