Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005088.1 Hibiscus syriacus cultivar Beakdansim tig00011434_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: 201410
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:187471 original size:40 final size:40
Alignment explanation
Indices: 187365--187638 Score: 293
Period size: 40 Copynumber: 6.8 Consensus size: 40
187355 CTTTAAAAAT
* * *
187365 CGCGTTGCGATTTACGGATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATA
*
187405 CGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATA
1 CGCGTTGCGA-TTTACGTATTCTCGTTGCGATTTACGGATA
*
187446 CG-GATTGCGATTTACGTATTCTCGTTGCGATTTACAGATA
1 CGCG-TTGCGATTTACGTATTCTCGTTGCGATTTACGGATA
187486 CGCGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATA
* * * *
187526 CGCGTTGCGATTTTACGGATACTCGTTGCGATAGT-CAGA-A
1 CGCGTTGCGA-TTTACGTATTCTCGTTGCGAT-TTACGGATA
* ** * * * ** *
187566 TCGCGTTACGATTTATATGTTCGCGTTGCGATTTTCATATT
1 -CGCGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATA
* * *
187607 CGCGTTGCGATTTTCATATTCGCGTTGCGATT
1 CGCGTTGCGATTTACGTATTCTCGTTGCGATT
187639 CTGGAAAATC
Statistics
Matches: 201, Mismatches: 25, Indels: 16
0.83 0.10 0.07
Matches are distributed among these distances:
39 1 0.00
40 133 0.66
41 66 0.33
42 1 0.00
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.37
Consensus pattern (40 bp):
CGCGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATA
Found at i:187579 original size:121 final size:121
Alignment explanation
Indices: 187365--187638 Score: 338
Period size: 121 Copynumber: 2.3 Consensus size: 121
187355 CTTTAAAAAT
* * * **
187365 CGCGTTGCGATTTACGGATACGCGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCG
1 CGCGTTGCGATTTACGTATTCGCGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATACTCG
* * * * *
187430 TTGCGATTTACGGATACGGATTGCGATTTACGTATTCTCGTTGCGATTTACAGATA
66 TTGCGATTCACGAATACGGATTACGATTTACATATTCGCGTTGCGATTTACAGATA
*
187486 CGCGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATACTCG
1 CGCGTTGCGATTTACGTATTCGCGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATACTCG
* * * * *
187551 TTGCGATAGTCA-GAAT-CGCG-TTACGATTTATATGTTCGCGTTGCGATTTTCATATT
66 TTGCGAT--TCACGAATACG-GATTACGATTTACATATTCGCGTTGCGATTTACAGATA
* *
187607 CGCGTTGCGATTTTCATATTCGCGTTGCGATT
1 CGCGTTGCGATTTACGTATTCGCGTTGCGATT
187639 CTGGAAAATC
Statistics
Matches: 131, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
121 125 0.95
122 4 0.03
123 2 0.02
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.37
Consensus pattern (121 bp):
CGCGTTGCGATTTACGTATTCGCGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATACTCG
TTGCGATTCACGAATACGGATTACGATTTACATATTCGCGTTGCGATTTACAGATA
Found at i:187589 original size:20 final size:20
Alignment explanation
Indices: 187566--187638 Score: 112
Period size: 20 Copynumber: 3.6 Consensus size: 20
187556 ATAGTCAGAA
* *
187566 TCGCGTTACGATTTAT-ATGT
1 TCGCGTTGCGATTT-TCATAT
187586 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCATAT
187606 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCATAT
187626 TCGCGTTGCGATT
1 TCGCGTTGCGATT
187639 CTGGAAAATC
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
19 1 0.02
20 49 0.98
ACGTcount: A:0.15, C:0.19, G:0.22, T:0.44
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCATAT
Found at i:187699 original size:42 final size:42
Alignment explanation
Indices: 187564--187699 Score: 122
Period size: 42 Copynumber: 3.3 Consensus size: 42
187554 CGATAGTCAG
* *
187564 AATCGCGTTACG-ATTTAT-ATGTTCGCGTTGCGATT-TTCAT
1 AATCGCGTTGCGAATTT-TCATATTCGCGTTGCGATTCTTCAT
* ** *
187604 ATTCGCGTTGCG-ATTTTCATATTCGCGTTGCGATTCTGGAA
1 AATCGCGTTGCGAATTTTCATATTCGCGTTGCGATTCTTCAT
** *
187645 AATCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTCTTCAT
1 AATCGCGTTGCGAATTT-TCA-TATTCGCGTTGCGATTCTTCAT
187687 AATCGCGTTGCGA
1 AATCGCGTTGCGA
187700 TTCTGGGAAC
Statistics
Matches: 76, Mismatches: 15, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
39 1 0.01
40 30 0.39
41 11 0.14
42 31 0.41
43 3 0.04
ACGTcount: A:0.21, C:0.20, G:0.21, T:0.38
Consensus pattern (42 bp):
AATCGCGTTGCGAATTTTCATATTCGCGTTGCGATTCTTCAT
Found at i:187703 original size:21 final size:20
Alignment explanation
Indices: 187468--187701 Score: 106
Period size: 20 Copynumber: 11.5 Consensus size: 20
187458 TACGTATTCT
* *
187468 CGTTGCGATTTACA-GATACG
1 CGTTGCGATTTTCATAAT-CG
* * * *
187488 CGTTGCGATTTACGTATTCT
1 CGTTGCGATTTTCATAATCG
*
187508 CGTTGCGATTTACGGAT-A-CG
1 CGTTGCGATTTTC--ATAATCG
*
187528 CGTTGCGATTTTACGGAT-A-CT
1 CGTTGCGATTTT-C--ATAATCG
** *
187549 CGTTGCGATAGTCAGAATCG
1 CGTTGCGATTTTCATAATCG
* **
187569 CGTTACGATTTAT-ATGTTCG
1 CGTTGCGATTT-TCATAATCG
*
187589 CGTTGCGATTTTCATATTCG
1 CGTTGCGATTTTCATAATCG
*
187609 CGTTGCGATTTTCATATTCG
1 CGTTGCGATTTTCATAATCG
** *
187629 CGTTGCGATTCTGGAAAATCG
1 CGTTGCGATT-TTCATAATCG
**
187650 CAATGCGAATTTGT-ACT-ATCG
1 CGTTGCG-ATTT-TCA-TAATCG
*
187671 CATTGCGATTCTTCATAATCG
1 CGTTGCGATT-TTCATAATCG
187692 CGTTGCGATT
1 CGTTGCGATT
187702 CTGGGAACTG
Statistics
Matches: 168, Mismatches: 31, Indels: 29
0.74 0.14 0.13
Matches are distributed among these distances:
18 1 0.01
19 2 0.01
20 104 0.62
21 57 0.34
22 4 0.02
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.37
Consensus pattern (20 bp):
CGTTGCGATTTTCATAATCG
Found at i:188510 original size:35 final size:34
Alignment explanation
Indices: 188428--188541 Score: 165
Period size: 35 Copynumber: 3.2 Consensus size: 34
188418 AAAACAATCC
188428 TCAATTTCATTCTAAACCACAAATTCCAAAATTAAT
1 TCAATTTCATTCTAAACC-CAAATTCCAAAA-TAAT
188464 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCC-AAATTCCAAAATAAT
* * *
188499 TCAATTACATTCTAAAACCCAAATTCTAAAATACT
1 TCAATTTCATTCT-AAACCCAAATTCCAAAATAAT
188534 TCAATTTC
1 TCAATTTC
188542 TGTCTTTTTT
Statistics
Matches: 72, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
35 37 0.51
36 35 0.49
ACGTcount: A:0.43, C:0.23, G:0.00, T:0.34
Consensus pattern (34 bp):
TCAATTTCATTCTAAACCCAAATTCCAAAATAAT
Found at i:189597 original size:35 final size:34
Alignment explanation
Indices: 189549--189660 Score: 161
Period size: 35 Copynumber: 3.2 Consensus size: 34
189539 ATTCCTCCTT
* *
189549 AAATTGAAATATTTTAGAATTTGGGTTTTAGAATG
1 AAATTGAATTATTTTGGAATTTGGG-TTTAGAATG
*
189584 TAATTGAATTATTTTGGAATTTAGGGTTTAGAATG
1 AAATTGAATTATTTTGGAATTT-GGGTTTAGAATG
*
189619 AAATTGAATTACTTTGGAATTTGGGGTTTAGAATG
1 AAATTGAATTATTTTGGAATTT-GGGTTTAGAATG
189654 AAATTGA
1 AAATTGA
189661 GGAATGTTTT
Statistics
Matches: 70, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
35 67 0.96
36 3 0.04
ACGTcount: A:0.35, C:0.01, G:0.22, T:0.42
Consensus pattern (34 bp):
AAATTGAATTATTTTGGAATTTGGGTTTAGAATG
Found at i:191083 original size:37 final size:38
Alignment explanation
Indices: 191016--191100 Score: 136
Period size: 37 Copynumber: 2.2 Consensus size: 38
191006 CCAGAACGTG
191016 ACGCTCCAATTCTTGTCTCTGATTTGTTTGGTAATAGTA
1 ACGCTCCAATTCTTG-CTCTGATTTGTTTGGTAATAGTA
* *
191055 TCGCTCCAATTCTTG-TCTGATTTGTTTGGTAATGGTA
1 ACGCTCCAATTCTTGCTCTGATTTGTTTGGTAATAGTA
191092 ACGCTCCAA
1 ACGCTCCAA
191101 ATCTAGATAT
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
37 29 0.67
39 14 0.33
ACGTcount: A:0.20, C:0.20, G:0.19, T:0.41
Consensus pattern (38 bp):
ACGCTCCAATTCTTGCTCTGATTTGTTTGGTAATAGTA
Found at i:199283 original size:24 final size:22
Alignment explanation
Indices: 199230--199293 Score: 87
Period size: 22 Copynumber: 3.0 Consensus size: 22
199220 TCTACTAGTG
199230 TTCCAAATATATCGTCAGTGTT
1 TTCCAAATATATCGTCAGTGTT
*
199252 TTCCAAATATATCGTTAGTGTT
1 TTCCAAATATATCGTCAGTGTT
*
199274 TTCCTAAA-ATATAGT-AGTGT
1 TTCC-AAATATATCGTCAGTGT
199294 ATGTTTCCTC
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
21 5 0.13
22 31 0.79
23 3 0.08
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (22 bp):
TTCCAAATATATCGTCAGTGTT
Done.