Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006885.1 Hibiscus syriacus cultivar Beakdansim tig00017551_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: 105096
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:2203 original size:5 final size:5
Alignment explanation
Indices: 2193--2232 Score: 53
Period size: 5 Copynumber: 8.0 Consensus size: 5
2183 ACCACAACCA
* * *
2193 CGAGC CGAGC CGAGC CTAGC CGAGC CGTGC CGTGC CGAGC
1 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC
2233 TGAGACGAGA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.15, C:0.40, G:0.38, T:0.07
Consensus pattern (5 bp):
CGAGC
Found at i:8111 original size:5 final size:5
Alignment explanation
Indices: 8097--8137 Score: 55
Period size: 5 Copynumber: 8.2 Consensus size: 5
8087 CCACGACAAT
* * *
8097 GAGCT GAGCC AAGCC GAGCC GAGCC GAGCT GAGCC GAGCC G
1 GAGCC GAGCC GAGCC GAGCC GAGCC GAGCC GAGCC GAGCC G
8138 TGCTGTGTCG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.22, C:0.34, G:0.39, T:0.05
Consensus pattern (5 bp):
GAGCC
Found at i:8149 original size:15 final size:15
Alignment explanation
Indices: 8096--8142 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
8086 ACCACGACAA
* *
8096 TGAGCTGAGCCAAGC
1 TGAGCCGAGCCGAGC
*
8111 CGAGCCGAGCCGAGC
1 TGAGCCGAGCCGAGC
*
8126 TGAGCCGAGCCGTGC
1 TGAGCCGAGCCGAGC
8141 TG
1 TG
8143 TGTCGAGACG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.19, C:0.32, G:0.38, T:0.11
Consensus pattern (15 bp):
TGAGCCGAGCCGAGC
Found at i:14035 original size:10 final size:10
Alignment explanation
Indices: 14017--14050 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
14007 ACCACGTCCA
14017 CGAGCCGTGC
1 CGAGCCGTGC
*
14027 CGTGCCGTGC
1 CGAGCCGTGC
*
14037 CGAGCCGAGC
1 CGAGCCGTGC
14047 CGAG
1 CGAG
14051 AAGAGACGGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.12, C:0.38, G:0.41, T:0.09
Consensus pattern (10 bp):
CGAGCCGTGC
Found at i:17574 original size:23 final size:23
Alignment explanation
Indices: 17547--17602 Score: 94
Period size: 23 Copynumber: 2.4 Consensus size: 23
17537 TTTTATAAGG
17547 TTGAATCGAAGTAGATTTCATGC
1 TTGAATCGAAGTAGATTTCATGC
* *
17570 TTGAATCGAAGTTGATTTCATGT
1 TTGAATCGAAGTAGATTTCATGC
17593 TTGAATCGAA
1 TTGAATCGAA
17603 TCAAAATTGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.30, C:0.11, G:0.21, T:0.38
Consensus pattern (23 bp):
TTGAATCGAAGTAGATTTCATGC
Found at i:22040 original size:47 final size:47
Alignment explanation
Indices: 21946--22168 Score: 327
Period size: 45 Copynumber: 4.9 Consensus size: 47
21936 GTAACCATGC
* * *
21946 AAATAAGCTTATGAGCTTACGGAA--T-AATGGCAAGTATATTGGAA
1 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATATTGGAA
*
21990 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATATTAGAA
1 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATATTGGAA
*
22037 AAATAAGCTTACGAGATTATGGAATTTAAATGGTAAG--TATTGGAA
1 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATATTGGAA
*
22082 AAATAAGCTTACGAGCTTGTGGAATTTAAATGGTAAGTAT-TT-GAA
1 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATATTGGAA
*
22127 AAATAAGATTACGAGCTTATGGAATTTAAATGGTAAG-ATATT
1 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATATT
22169 TTATATTATT
Statistics
Matches: 163, Mismatches: 10, Indels: 11
0.89 0.05 0.06
Matches are distributed among these distances:
44 24 0.15
45 82 0.50
46 3 0.02
47 54 0.33
ACGTcount: A:0.41, C:0.06, G:0.21, T:0.31
Consensus pattern (47 bp):
AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATATTGGAA
Found at i:22090 original size:92 final size:91
Alignment explanation
Indices: 21971--22168 Score: 326
Period size: 92 Copynumber: 2.2 Consensus size: 91
21961 CTTACGGAAT
*
21971 AATGGCAAGTATATTGGAAAAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATATTAGA
1 AATGGTAAG-ATATTGGAAAAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTAT-TT-GA
*
22036 AAAATAAGCTTACGAGATTATGGAATTTA
63 AAAATAAGATTACGAGATTATGGAATTTA
*
22065 AATGGTAAG-TATTGGAAAAATAAGCTTACGAGCTTGTGGAATTTAAATGGTAAGTATTTGAAAA
1 AATGGTAAGATATTGGAAAAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATTTGAAAA
*
22129 ATAAGATTACGAGCTTATGGAATTTA
66 ATAAGATTACGAGATTATGGAATTTA
22155 AATGGTAAGATATT
1 AATGGTAAGATATT
22169 TTATATTATT
Statistics
Matches: 99, Mismatches: 4, Indels: 5
0.92 0.04 0.05
Matches are distributed among these distances:
90 38 0.38
91 6 0.06
92 47 0.47
94 8 0.08
ACGTcount: A:0.41, C:0.06, G:0.21, T:0.32
Consensus pattern (91 bp):
AATGGTAAGATATTGGAAAAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATTTGAAAA
ATAAGATTACGAGATTATGGAATTTA
Found at i:30352 original size:30 final size:30
Alignment explanation
Indices: 30317--30379 Score: 126
Period size: 30 Copynumber: 2.1 Consensus size: 30
30307 AACCCTTTGA
30317 CAAGTATCATATAACACATGGGAAGCAAGG
1 CAAGTATCATATAACACATGGGAAGCAAGG
30347 CAAGTATCATATAACACATGGGAAGCAAGG
1 CAAGTATCATATAACACATGGGAAGCAAGG
30377 CAA
1 CAA
30380 ATGGTGTGCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.44, C:0.17, G:0.22, T:0.16
Consensus pattern (30 bp):
CAAGTATCATATAACACATGGGAAGCAAGG
Found at i:36656 original size:30 final size:30
Alignment explanation
Indices: 36621--36683 Score: 126
Period size: 30 Copynumber: 2.1 Consensus size: 30
36611 AACCCTTTGA
36621 CAAGTATCATATAACACATGGGAAGCAAGG
1 CAAGTATCATATAACACATGGGAAGCAAGG
36651 CAAGTATCATATAACACATGGGAAGCAAGG
1 CAAGTATCATATAACACATGGGAAGCAAGG
36681 CAA
1 CAA
36684 ATGGTGTGCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.44, C:0.17, G:0.22, T:0.16
Consensus pattern (30 bp):
CAAGTATCATATAACACATGGGAAGCAAGG
Found at i:40356 original size:726 final size:721
Alignment explanation
Indices: 38982--40397 Score: 1542
Period size: 726 Copynumber: 2.0 Consensus size: 721
38972 ATTAAAAAGA
* * * *
38982 GCAAATAAATAAATAAATTTCTTTTGTAGAAAAGGTGGTGATTGTCATCGAGAAGATACTTTGAA
1 GCAAATAAATAAATAAATTTCTTTTGTAGAAAAGGAGGTGATTATCATCAAGAAGAAACTTTGAA
* * * ***** * *
39047 ATATATATAATAATTTCATTTATCATTCTTTAAAAGAATAATTATTGTTACAAAATATATTTAAT
66 ATATATACAATAATTTAATTTATCATTATTTAAAAGAATAATTACCAACACAAAACATATTTAAC
** * *
39112 TAAAATACTAATACATCTTCTTTAATAGTTTACTTTAAATTTATTTCATGTGTTTTGCTAGAAAA
131 TAAAATACTAATACATAGTCTTTAATAGTTTACTTTAAATTTAATTCACGTGTTTTGCTAGAAAA
* * * * * * *
39177 TATATGAGTACTTGCATTTATTATTTTAATTTAAAGTTGTCAAAAGCTGATTTCAAAACAAAATT
196 TATATGAGCACTTCCATTCATGATTATAATTTAAAGTTGTCAAAAGCTGATTTAAAAACAAAATA
* * * ** * *
39242 TTCAATTAAATGTTTGATTCTAAGAAAACATAAAAATCGAATACATAATTATTAACGAATATATC
261 TCCAATTAAATGTTTAACTCTAAGAAAACATAAAAATCGAATACATAACCATTAACGAATACAAC
* ** * * * *
39307 CTTGGAAAGAATCTAATATGGAGATGCGGGGTGTCAATCCTCGTACTTCTTGCATGCAGAGGGAG
326 CTT-GAAAGAATCTAATATGGAGATGCAGGGAATCAATCCTCGCACTTCTCGCATGCAAAGCGAG
* * ** * *
39372 CGCTCTACCATTTGAGCTACATCCTCTCACTCTTTTCAACATTCACGCTTAACGTTAAAATAGCT
390 CGCTCTACCATTTGAGCTACATCCCCTAACTCTACTAAACATTCACGCTTAACGTTAAAATAACT
* *
39437 TAATCATTTTTATTTTACTGCAACATTATTTTTTATATTTACTTAAAACAACATTTATTATTATT
455 TAATCATTTTTATTTTACTGCAACA-CATTTTTTATATCTACTTAAAACAACATTTATTATTATT
*** ** * * * *
39502 TTTTAAAAAAGTTTGTTTTTTAGAAGAATTGAAAACTTAATACTTTTTTTCTCACTTCATATTCA
519 CCGTAAAAAAGTTAATTTTTTAGAAGAAGTGAAAACTTAATACTATTTATCTCACTTCATATTAA
** * *
39567 AGTTATGATAAATGGAGATGTAGGGTATATATCTGGCATTCTAAGAGAGCGCTCTATCATTTGAG
584 AGTTATGATAAATGGAGATGTAGGGTATATATCTGGCACGCTAAGAGAGCACTCTACCATTTGAG
*
39632 CTACATCCCCTCACATTAATATGATTTCATGATTGACACTAAAATGTCTATGCTATATAAATACA
649 CTACATCCCCTCACATT-ATATGATTTCATGATTAACACTAAAATGTCTATGCTATATAAATACA
39697 AGAAAAGTT
713 AGAAAAGTT
* *
39706 GCAAATAATTAAATAAATTTCTTTTGTTAGAAATA-GAGGTGATTATTATCAAGAAGAAACTTTT
1 GCAAATAAATAAATAAATTTCTTTTG-TAGAAA-AGGAGGTGATTATCATCAAGAAGAAAC-TTT
* *
39770 GAAATATATACAATAATTTAATTTA-CAATTATATT-AAAGATTAGTTACCAACACAAAACATAT
63 GAAATATATACAATAATTTAATTTATC-ATTAT-TTAAAAGAATAATTACCAACACAAAACATAT
* * * *
39833 TTAACTAATATACTAATATATAGTCTTTAATAGTTTA-TATTAATTTTAATTCACGTGTTTTGGT
126 TTAACTAAAATACTAATACATAGTCTTTAATAGTTTACT-TTAAATTTAATTCACGTGTTTTGCT
* * * *
39897 AGAAAA-ATATGAGCACTTCCATTCATGATTATAATTTTAAGTTTTCAAATG-TATATTTAAAAA
190 AGAAAATATATGAGCACTTCCATTCATGATTATAATTTAAAGTTGTCAAAAGCT-GATTTAAAAA
* * *
39960 CAAAATATCCAATTAAATGTTTAACTCTAAGTAAACATAAAAAT-TAACTACATAACCATTGAC-
254 CAAAATATCCAATTAAATGTTTAACTCTAAGAAAACATAAAAATCGAA-TACATAACCATTAACG
* * * *
40023 AATACAACC-T-CAA-AATCTAATATGGAGGTGCAGGGAATCGATCCT-GCAGTTCTCGCATGCA
318 AATACAACCTTGAAAGAATCTAATATGGAGATGCAGGGAATCAATCCTCGCACTTCTCGCATGCA
** *
40084 AAGCGAGCGCTCTACCATTTGAGCTA-ATCCCCTAA-TCCTACTAAATTTTCATGCTTAACGTTA
383 AAGCGAGCGCTCTACCATTTGAGCTACATCCCCTAACT-CTACTAAACATTCACGCTTAACGTTA
* * *
40147 ATATAATTTAATCATTTTTATTTTACTGCAAC-CATTTTTTATATCTATTTAAAA-AA-ATGATT
447 AAATAACTTAATCATTTTTATTTTACTGCAACACATTTTTTATATCTACTTAAAACAACAT--TT
* * *
40209 ATTATTATTCCGT-AAAAAGTTCAATTTTTTGAGAATAAGTGATAA-TGTATTA-TATTTATCTC
510 ATTATTATTCCGTAAAAAAGTT-AATTTTTT-AGAAGAAGTGAAAACT-TAATACTATTTATCTC
* * * **
40271 ACTTGATTTTAAAGTTATTATAAATGGAGATGT-GGGATATCAATCCCCATACCTCTTTCACGCT
572 ACTTCATATTAAAGTTATGATAAATGGAGATGTAGGG---T--AT----ATA--TCTGGCACGCT
* * * * *
40335 AAGTGAGCACTCTACCATTTGAGTTACATCCCCTCACATTTTATGGTTTCATGTTTAACACTA
626 AAGAGAGCACTCTACCATTTGAGCTACATCCCCTCACATTATATGATTTCATGATTAACACTA
40398 GAATATTGTT
Statistics
Matches: 568, Mismatches: 99, Indels: 49
0.79 0.14 0.07
Matches are distributed among these distances:
714 2 0.00
715 13 0.02
716 75 0.13
717 16 0.03
718 57 0.10
719 37 0.07
720 29 0.05
721 2 0.00
723 1 0.00
724 38 0.07
725 143 0.25
726 153 0.27
727 2 0.00
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.38
Consensus pattern (721 bp):
GCAAATAAATAAATAAATTTCTTTTGTAGAAAAGGAGGTGATTATCATCAAGAAGAAACTTTGAA
ATATATACAATAATTTAATTTATCATTATTTAAAAGAATAATTACCAACACAAAACATATTTAAC
TAAAATACTAATACATAGTCTTTAATAGTTTACTTTAAATTTAATTCACGTGTTTTGCTAGAAAA
TATATGAGCACTTCCATTCATGATTATAATTTAAAGTTGTCAAAAGCTGATTTAAAAACAAAATA
TCCAATTAAATGTTTAACTCTAAGAAAACATAAAAATCGAATACATAACCATTAACGAATACAAC
CTTGAAAGAATCTAATATGGAGATGCAGGGAATCAATCCTCGCACTTCTCGCATGCAAAGCGAGC
GCTCTACCATTTGAGCTACATCCCCTAACTCTACTAAACATTCACGCTTAACGTTAAAATAACTT
AATCATTTTTATTTTACTGCAACACATTTTTTATATCTACTTAAAACAACATTTATTATTATTCC
GTAAAAAAGTTAATTTTTTAGAAGAAGTGAAAACTTAATACTATTTATCTCACTTCATATTAAAG
TTATGATAAATGGAGATGTAGGGTATATATCTGGCACGCTAAGAGAGCACTCTACCATTTGAGCT
ACATCCCCTCACATTATATGATTTCATGATTAACACTAAAATGTCTATGCTATATAAATACAAGA
AAAGTT
Found at i:42489 original size:24 final size:22
Alignment explanation
Indices: 42446--42489 Score: 52
Period size: 22 Copynumber: 1.9 Consensus size: 22
42436 TAGCTTAATC
*
42446 ATTTTTATTTTACTACAACATT
1 ATTTTTATTTTACTAAAACATT
*
42468 ATTTTTATATTTATTTAAAACA
1 ATTTTTAT-TTTA-CTAAAACA
42490 ACATTTATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 8 0.44
23 4 0.22
24 6 0.33
ACGTcount: A:0.36, C:0.09, G:0.00, T:0.55
Consensus pattern (22 bp):
ATTTTTATTTTACTAAAACATT
Found at i:42524 original size:22 final size:22
Alignment explanation
Indices: 42478--42523 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
42468 ATTTTTATAT
*
42478 TTATTTAAAACAACATTTATTA
1 TTATTTAAAACAAAATTTATTA
42500 TTATTTAAAA-AAAA-TTATT-
1 TTATTTAAAACAAAATTTATTA
42519 TTATT
1 TTATT
42524 AAGAAGAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 5 0.22
20 5 0.22
21 3 0.13
22 10 0.43
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (22 bp):
TTATTTAAAACAAAATTTATTA
Found at i:82908 original size:17 final size:17
Alignment explanation
Indices: 82886--82926 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
82876 TGCTTGTATG
*
82886 AGTGCATGAGGCATGTA
1 AGTGCATGAAGCATGTA
82903 AGTGCATGAAGCATGTA
1 AGTGCATGAAGCATGTA
82920 AGTGCAT
1 AGTGCAT
82927 TTTTGGTGTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.32, C:0.12, G:0.32, T:0.24
Consensus pattern (17 bp):
AGTGCATGAAGCATGTA
Found at i:86869 original size:14 final size:14
Alignment explanation
Indices: 86850--86885 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
86840 GTAAAAAGAT
*
86850 AATAAAAGTGATTA
1 AATAAAAGTAATTA
86864 AATAAAAGTAATTA
1 AATAAAAGTAATTA
86878 AAGTAAAA
1 AA-TAAAA
86886 ATAAGAAGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 15 0.75
15 5 0.25
ACGTcount: A:0.64, C:0.00, G:0.11, T:0.25
Consensus pattern (14 bp):
AATAAAAGTAATTA
Found at i:92430 original size:14 final size:14
Alignment explanation
Indices: 92411--92440 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
92401 GTAAAAAGAT
*
92411 AATAAAAGTGATTA
1 AATAAAAGTAATTA
92425 AATAAAAGTAATTA
1 AATAAAAGTAATTA
92439 AA
1 AA
92441 GCAAAAATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.63, C:0.00, G:0.10, T:0.27
Consensus pattern (14 bp):
AATAAAAGTAATTA
Found at i:98408 original size:13 final size:13
Alignment explanation
Indices: 98376--98413 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
98366 TCTTAACTCT
*
98376 AATTCAAA-TTCA
1 AATTCAAATTTTA
*
98388 ATTTCAAATTTTA
1 AATTCAAATTTTA
98401 AATTCAAATTTTA
1 AATTCAAATTTTA
98414 TTTTTACGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
12 7 0.32
13 15 0.68
ACGTcount: A:0.45, C:0.11, G:0.00, T:0.45
Consensus pattern (13 bp):
AATTCAAATTTTA
Found at i:98560 original size:16 final size:15
Alignment explanation
Indices: 98535--98573 Score: 51
Period size: 18 Copynumber: 2.4 Consensus size: 15
98525 TATAAATACT
98535 AAATATATAATATTAAA
1 AAATATA-AATA-TAAA
98552 TAAATATAAATATAAA
1 -AAATATAAATATAAA
98568 AAATAT
1 AAATAT
98574 TAATGTTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.29
16 4 0.19
17 4 0.19
18 7 0.33
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
AAATATAAATATAAA
Found at i:98562 original size:6 final size:6
Alignment explanation
Indices: 98524--98567 Score: 54
Period size: 6 Copynumber: 7.2 Consensus size: 6
98514 AATTTTAATT
*
98524 ATATAA ATACTAA ATATATA ATATTA A-ATAA ATATAA ATATAA A
1 ATATAA ATA-TAA ATATA-A ATATAA ATATAA ATATAA ATATAA A
98568 AAATATTAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
5 4 0.12
6 18 0.55
7 11 0.33
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (6 bp):
ATATAA
Done.