Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002064.1 Hibiscus syriacus cultivar Beakdansim tig00004208_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: 55006
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:2304 original size:29 final size:29
Alignment explanation
Indices: 2219--2304 Score: 88
Period size: 29 Copynumber: 3.0 Consensus size: 29
2209 ATAATCATGT
*
2219 AATTATTTTATAATTTTTAATAATA-AAA
1 AATTATTTTATAATTTTTAATAATAGATA
*** *
2247 ATATTAACAATATAA-TTTT-ATAATTGATA
1 A-ATT-ATTTTATAATTTTTAATAATAGATA
2276 AATTATTTTATAATTTTTAATAATAGATA
1 AATTATTTTATAATTTTTAATAATAGATA
2305 CTCAATAAAT
Statistics
Matches: 44, Mismatches: 9, Indels: 9
0.71 0.15 0.15
Matches are distributed among these distances:
27 6 0.14
28 13 0.30
29 19 0.43
30 6 0.14
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.49
Consensus pattern (29 bp):
AATTATTTTATAATTTTTAATAATAGATA
Found at i:2941 original size:6 final size:6
Alignment explanation
Indices: 2932--2996 Score: 78
Period size: 6 Copynumber: 10.7 Consensus size: 6
2922 GAAGAAGGCT
* * *
2932 GGGAAG GGGAAG GGGACG GGGACG GGGACG GGGACGG GGGAC- GGGAAG
1 GGGACG GGGACG GGGACG GGGACG GGGACG GGGAC-G GGGACG GGGACG
2980 GGGACG GGGACG AGGGA
1 GGGACG GGGACG -GGGA
2997 GAGGGAAAGA
Statistics
Matches: 53, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
5 4 0.08
6 39 0.74
7 10 0.19
ACGTcount: A:0.23, C:0.11, G:0.66, T:0.00
Consensus pattern (6 bp):
GGGACG
Found at i:5066 original size:2 final size:2
Alignment explanation
Indices: 5061--5088 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5051 AGTTTTTTAA
5061 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
5089 TATCTAATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6496 original size:10 final size:11
Alignment explanation
Indices: 6471--6499 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
6461 ATTATATCTT
6471 TAAAATAAATA
1 TAAAATAAATA
6482 TAAAATAAA-A
1 TAAAATAAATA
6492 TAAAATAA
1 TAAAATAA
6500 TACAAACATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 9 0.50
11 9 0.50
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (11 bp):
TAAAATAAATA
Found at i:11409 original size:33 final size:33
Alignment explanation
Indices: 11353--11435 Score: 103
Period size: 33 Copynumber: 2.5 Consensus size: 33
11343 TTCGATGTTG
* **
11353 TTGGAGTTGGAGAATTCTTCGGAATCAATGTCA
1 TTGGAGTTGGAGCATTCACCGGAATCAATGTCA
* *
11386 TTGGAGTTAGAGCATTCACCGGAATCGATGTCA
1 TTGGAGTTGGAGCATTCACCGGAATCAATGTCA
* *
11419 TTGAACTTGGAGCATTC
1 TTGGAGTTGGAGCATTC
11436 GTGTTCATCA
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.31
Consensus pattern (33 bp):
TTGGAGTTGGAGCATTCACCGGAATCAATGTCA
Found at i:17789 original size:19 final size:20
Alignment explanation
Indices: 17765--17814 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
17755 GATAAATTTA
*
17765 TTAATAATTTTATAA-TCTT
1 TTAATAATTTTATAAGTATT
*
17784 TTAATAAATTTAATAAGTATT
1 TTAAT-AATTTTATAAGTATT
17805 TT-ATAATTTT
1 TTAATAATTTT
17815 TTAAATTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 10 0.38
20 11 0.42
21 5 0.19
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (20 bp):
TTAATAATTTTATAAGTATT
Found at i:17810 original size:11 final size:10
Alignment explanation
Indices: 17734--17825 Score: 52
Period size: 11 Copynumber: 9.2 Consensus size: 10
17724 CGATAATATA
17734 ATAATTATTTT
1 ATAA-TATTTT
* *
17745 ATAGTATTTAG
1 ATAATATTT-T
17756 ATAA-A-TTT
1 ATAATATTTT
17764 ATTAATAATTTT
1 A-TAAT-ATTTT
*
17776 ATAATCTTTT
1 ATAATATTTT
*
17786 AATAA-ATTTA
1 -ATAATATTTT
17796 ATAAGTATTTT
1 ATAA-TATTTT
17807 ATAAT-TTTT
1 ATAATATTTT
17816 -TAA-ATTTT
1 ATAATATTTT
17824 AT
1 AT
17826 TGAAAAATGA
Statistics
Matches: 63, Mismatches: 8, Indels: 22
0.68 0.09 0.24
Matches are distributed among these distances:
8 8 0.13
9 14 0.22
10 14 0.22
11 23 0.37
12 4 0.06
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.55
Consensus pattern (10 bp):
ATAATATTTT
Found at i:17817 original size:31 final size:30
Alignment explanation
Indices: 17732--17818 Score: 95
Period size: 31 Copynumber: 2.8 Consensus size: 30
17722 TTCGATAATA
* *
17732 TAATAATTATTTTAT-AGTATTTAGATAAATT
1 TAATAA-TATTTTATAATTTTTTA-ATAAATT
* *
17763 TATTAATAATTTTATAATCTTTTAATAAATT
1 TAATAAT-ATTTTATAATTTTTTAATAAATT
17794 TAATAAGTATTTTATAATTTTTTAA
1 TAATAA-TATTTTATAATTTTTTAA
17819 ATTTTATTGA
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
30 1 0.02
31 40 0.85
32 6 0.13
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.54
Consensus pattern (30 bp):
TAATAATATTTTATAATTTTTTAATAAATT
Found at i:18565 original size:19 final size:19
Alignment explanation
Indices: 18543--18630 Score: 63
Period size: 20 Copynumber: 4.4 Consensus size: 19
18533 AAAGTTTAAA
18543 AAATTATAAAATATTTATT
1 AAATTATAAAATATTTATT
* *
18562 AAATTTATTAAAAGA-TTATA
1 AAA-TTA-TAAAATATTTATT
18582 AAATTATTAATAA-ATTTATCT
1 AAATTA-TAA-AATATTTAT-T
*
18603 AAATACTATAAAATAATTATT
1 AAAT--TATAAAATATTTATT
*
18624 ATATTAT
1 AAATTAT
18631 CAAACTTTTA
Statistics
Matches: 56, Mismatches: 5, Indels: 16
0.73 0.06 0.21
Matches are distributed among these distances:
19 14 0.25
20 16 0.29
21 16 0.29
22 8 0.14
23 2 0.04
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.44
Consensus pattern (19 bp):
AAATTATAAAATATTTATT
Found at i:18573 original size:31 final size:31
Alignment explanation
Indices: 18538--18624 Score: 97
Period size: 31 Copynumber: 2.8 Consensus size: 31
18528 TGAATAAAGT
18538 TTAAAAAATTATAAAATATTTATTAAATTTA
1 TTAAAAAATTATAAAATATTTATTAAATTTA
* *
18569 TTAAAAGATTATAAAAT-TATTAATAAATTTA
1 TTAAAAAATTATAAAATAT-TTATTAAATTTA
* * *
18600 TCT-AAATACTATAAAATAATTATTA
1 T-TAAAAAATTATAAAATATTTATTA
18625 TATTATCAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
30 1 0.02
31 45 0.96
32 1 0.02
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.43
Consensus pattern (31 bp):
TTAAAAAATTATAAAATATTTATTAAATTTA
Found at i:18600 original size:20 final size:20
Alignment explanation
Indices: 18533--18600 Score: 63
Period size: 19 Copynumber: 3.5 Consensus size: 20
18523 TTTAGTGAAT
*
18533 AAAG-TTTAAAAAATTA-TA
1 AAAGATTTATAAAATTATTA
* *
18551 AAATATTTATTAAATTTATTA
1 AAAGATTTA-TAAAATTATTA
18572 AAAGA-TTATAAAATTATTA
1 AAAGATTTATAAAATTATTA
18591 ATAA-ATTTAT
1 A-AAGATTTAT
18601 CTAAATACTA
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
18 3 0.08
19 16 0.40
20 15 0.38
21 6 0.15
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (20 bp):
AAAGATTTATAAAATTATTA
Found at i:21316 original size:27 final size:30
Alignment explanation
Indices: 21184--21319 Score: 145
Period size: 30 Copynumber: 4.6 Consensus size: 30
21174 CACCTCACCT
* * *
21184 TCATCACCATCC-CCACCACCACCCCAAAGC
1 TCATCACCA-CCGCCACCAACACCCAAAATC
* * *
21214 TCGTCATCACCGCCACCAGCACCCAAAATC
1 TCATCACCACCGCCACCAACACCCAAAATC
21244 TCATCACCACCGCCACCAACACCCAAAATC
1 TCATCACCACCGCCACCAACACCCAAAATC
* *
21274 TCATCACCACAGCCACCATCA-CCAAAATC
1 TCATCACCACCGCCACCAACACCCAAAATC
* *
21303 -C-TCTCCACCTCCACCAA
1 TCATCACCACCGCCACCAA
21320 AACAATTGTC
Statistics
Matches: 91, Mismatches: 14, Indels: 5
0.83 0.13 0.05
Matches are distributed among these distances:
27 12 0.13
28 1 0.01
29 10 0.11
30 68 0.75
ACGTcount: A:0.32, C:0.51, G:0.04, T:0.12
Consensus pattern (30 bp):
TCATCACCACCGCCACCAACACCCAAAATC
Found at i:29370 original size:2 final size:2
Alignment explanation
Indices: 29358--29394 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
29348 TGACTTTACA
29358 AT AT A- 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 AT AT AT
29395 TTGATTAAAC
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:35400 original size:31 final size:32
Alignment explanation
Indices: 35297--35401 Score: 142
Period size: 31 Copynumber: 3.3 Consensus size: 32
35287 GATGAGCAAA
* **
35297 ACTCGATTCGACTTGAAAATTTGATTTTTT-G
1 ACTCGACTCGACTTGAAAATCCGATTTTTTCG
* *
35328 ACTCCACTCCACTTGAAAATCCGATTTTTTCG
1 ACTCGACTCGACTTGAAAATCCGATTTTTTCG
*
35360 ACTCAACTCGACTTGAAAA-CCGATTTTTTCG
1 ACTCGACTCGACTTGAAAATCCGATTTTTTCG
35391 ACTCGACTCGA
1 ACTCGACTCGA
35402 AAAAACTTGA
Statistics
Matches: 65, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
31 47 0.72
32 18 0.28
ACGTcount: A:0.27, C:0.25, G:0.13, T:0.35
Consensus pattern (32 bp):
ACTCGACTCGACTTGAAAATCCGATTTTTTCG
Found at i:43342 original size:22 final size:22
Alignment explanation
Indices: 43314--43364 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
43304 ATTTTTTTGA
43314 CGTCTTGCTTGGGATCTCCCGG
1 CGTCTTGCTTGGGATCTCCCGG
*
43336 CGTCTTGTTTGGGATCTCCCGG
1 CGTCTTGCTTGGGATCTCCCGG
43358 CGTCTTG
1 CGTCTTG
43365 AGGGTGTTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.04, C:0.29, G:0.31, T:0.35
Consensus pattern (22 bp):
CGTCTTGCTTGGGATCTCCCGG
Found at i:44294 original size:32 final size:32
Alignment explanation
Indices: 44233--44294 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
44223 CAACATCCTC
*
44233 AAGACGCCGGGAGATCCCAAATAAGACGCCTG
1 AAGACGCCGGGAGATCCCAAACAAGACGCCTG
* *
44265 AAGACGCCGGGAGATCCCAAGCAATACGCC
1 AAGACGCCGGGAGATCCCAAACAAGACGCC
44295 AAAAAAATCT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.34, C:0.31, G:0.27, T:0.08
Consensus pattern (32 bp):
AAGACGCCGGGAGATCCCAAACAAGACGCCTG
Found at i:51113 original size:19 final size:19
Alignment explanation
Indices: 51089--51153 Score: 58
Period size: 19 Copynumber: 3.2 Consensus size: 19
51079 CCTTAATAAA
51089 ATTCATGATACACATTAAT
1 ATTCATGATACACATTAAT
** * *
51108 ATTCATGAATTTTTATAGTTAAA
1 ATTCATG-A--TACACA-TTAAT
51131 ATTCATGATACACATTAAT
1 ATTCATGATACACATTAAT
51150 ATTC
1 ATTC
51154 TGTTACCGTA
Statistics
Matches: 34, Mismatches: 8, Indels: 8
0.68 0.16 0.16
Matches are distributed among these distances:
19 15 0.44
20 4 0.12
22 4 0.12
23 11 0.32
ACGTcount: A:0.40, C:0.12, G:0.06, T:0.42
Consensus pattern (19 bp):
ATTCATGATACACATTAAT
Found at i:53937 original size:21 final size:20
Alignment explanation
Indices: 53901--53943 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
53891 AGAGTATATA
53901 TTTTTAATTTTAGTCTCAAAT
1 TTTTTAATTTTAGTCT-AAAT
53922 TTTTATAATTTT-GTCTAAAT
1 TTTT-TAATTTTAGTCTAAAT
53942 TT
1 TT
53944 CAAAAACGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 6 0.29
21 8 0.38
22 7 0.33
ACGTcount: A:0.28, C:0.07, G:0.05, T:0.60
Consensus pattern (20 bp):
TTTTTAATTTTAGTCTAAAT
Done.