Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006694.1 Hibiscus syriacus cultivar Beakdansim tig00016653_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: 36498
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:1824 original size:53 final size:53
Alignment explanation
Indices: 1748--1863 Score: 191
Period size: 53 Copynumber: 2.2 Consensus size: 53
1738 TAAAATTAGC
* *
1748 AACAGAAT--AAAATTGATTCTATCTAATTAAAACTGATCATATCTAATAACT
1 AACAGAATAAAAAATTGATTATATCTAATTAAAACGGATCATATCTAATAACT
*
1799 AACAGAATAAAAAATTGATTATATCTAATTAAAACGGATCCTATCTAATAACT
1 AACAGAATAAAAAATTGATTATATCTAATTAAAACGGATCATATCTAATAACT
1852 AACAGAATAAAA
1 AACAGAATAAAA
1864 TATCTACTTA
Statistics
Matches: 60, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
51 8 0.13
53 52 0.87
ACGTcount: A:0.51, C:0.13, G:0.07, T:0.29
Consensus pattern (53 bp):
AACAGAATAAAAAATTGATTATATCTAATTAAAACGGATCATATCTAATAACT
Found at i:4753 original size:42 final size:44
Alignment explanation
Indices: 4667--4753 Score: 133
Period size: 44 Copynumber: 2.0 Consensus size: 44
4657 AGACATATTT
*
4667 AATATTCAAATTTAAATAGATAATAATATCTTTTAGTATCTTTA
1 AATATTCAAATTTAAACAGATAATAATATCTTTTAGTATCTTTA
* *
4711 AATATTCAAATTTAAACATATAAT-A-ATCTTTTATTATCTTTA
1 AATATTCAAATTTAAACAGATAATAATATCTTTTAGTATCTTTA
4753 A
1 A
4754 TTTTAAAATA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
42 17 0.43
43 1 0.03
44 22 0.55
ACGTcount: A:0.44, C:0.08, G:0.02, T:0.46
Consensus pattern (44 bp):
AATATTCAAATTTAAACAGATAATAATATCTTTTAGTATCTTTA
Found at i:5405 original size:2 final size:2
Alignment explanation
Indices: 5383--5561 Score: 149
Period size: 2 Copynumber: 96.0 Consensus size: 2
5373 AATAATACAA
*
5383 AT AT A- AT AT AT AA ACT A- AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
5424 AT AT AT AT AA AT AT AC AT AT AT AT AT AT AT -T GT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
5464 AT A- AT AT AT AT AC A- AT AT AT A- AT A- AT A- AT A- AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5499 A- AT A- AT AT AT ACT AT AT A- AT AT AT A- AT AT AT A- AT AT AT
1 AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
5537 TT AT AT A- AT AT ACT AT ACT AT AT AT
1 AT AT AT AT AT AT A-T AT A-T AT AT AT
5562 GCATATAAAA
Statistics
Matches: 146, Mismatches: 10, Indels: 42
0.74 0.05 0.21
Matches are distributed among these distances:
1 17 0.12
2 122 0.84
3 7 0.05
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (2 bp):
AT
Found at i:13591 original size:24 final size:24
Alignment explanation
Indices: 13536--13592 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 24
13526 TACAAAGGCA
*
13536 TGTGCTTTTGCAGCAGACGAAACC
1 TGTGCTTTTACAGCAGACGAAACC
* * * *
13560 TATTCTTTTACAGCAGATGAAACT
1 TGTGCTTTTACAGCAGACGAAACC
13584 TGTGCTTTT
1 TGTGCTTTT
13593 GCAACTGATG
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.37
Consensus pattern (24 bp):
TGTGCTTTTACAGCAGACGAAACC
Found at i:17548 original size:23 final size:23
Alignment explanation
Indices: 17522--17603 Score: 137
Period size: 23 Copynumber: 3.6 Consensus size: 23
17512 TAGGCCCCCA
* *
17522 TAGGATATCGGTACCTCCATAGC
1 TAGGGTATCGATACCTCCATAGC
*
17545 TAGGTTATCGATACCTCCATAGC
1 TAGGGTATCGATACCTCCATAGC
17568 TAGGGTATCGATACCTCCATAGC
1 TAGGGTATCGATACCTCCATAGC
17591 TAGGGTATCGATA
1 TAGGGTATCGATA
17604 TTCATATTGC
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 56 1.00
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.28
Consensus pattern (23 bp):
TAGGGTATCGATACCTCCATAGC
Found at i:19421 original size:18 final size:16
Alignment explanation
Indices: 19407--19439 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
19397 TAAATATTCA
19407 TACCCCACATGATATT
1 TACCCCACATGATATT
19423 TACCCCACATGAT-TT
1 TACCCCACATGATATT
19438 TA
1 TA
19440 TTCCTACCCG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.30, C:0.30, G:0.06, T:0.33
Consensus pattern (16 bp):
TACCCCACATGATATT
Found at i:20464 original size:19 final size:20
Alignment explanation
Indices: 20425--20466 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
20415 TTAGATTGTA
* *
20425 AAATAAGATAAATGAATATT
1 AAATAAGATAAAAGAAAATT
20445 AAATAA-ATAAAAGAAAATT
1 AAATAAGATAAAAGAAAATT
20464 AAA
1 AAA
20467 AATATTAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.69, C:0.00, G:0.07, T:0.24
Consensus pattern (20 bp):
AAATAAGATAAAAGAAAATT
Found at i:21570 original size:7 final size:7
Alignment explanation
Indices: 21558--21791 Score: 195
Period size: 7 Copynumber: 33.4 Consensus size: 7
21548 AATAATACAA
21558 ATATAAT
1 ATATAAT
21565 ATATAA-
1 ATATAAT
*
21571 A-CTAAT
1 ATATAAT
21577 ATATATAT
1 ATATA-AT
21585 ATATAAT
1 ATATAAT
*
21592 AAATATAAC
1 --ATATAAT
21601 ATATAAAT
1 ATAT-AAT
21609 ATATAAT
1 ATATAAT
21616 A-ATAAT
1 ATATAAT
*
21622 ATATATT
1 ATATAAT
*
21629 ATATATT
1 ATATAAT
21636 ATAT-A-
1 ATATAAT
21641 ATAT-AT
1 ATATAAT
*
21647 ATACAAT
1 ATATAAT
21654 ATATAA-
1 ATATAAT
21660 ATATAAT
1 ATATAAT
21667 ATAT-AT
1 ATATAAT
21673 ATAT-AT
1 ATATAAT
*
21679 ATATACCAA
1 ATATA--AT
21688 ATAT-AT
1 ATATAAT
*
21694 ATATACT
1 ATATAAT
21701 ATATAAT
1 ATATAAT
21708 ATATAA-
1 ATATAAT
21714 ATATAATAT
1 ATAT-A-AT
21723 ATATAAT
1 ATATAAT
21730 ATAATAAT
1 AT-ATAAT
*
21738 ATATACT
1 ATATAAT
*
21745 ATATACT
1 ATATAAT
21752 ATATATAT
1 ATATA-AT
21760 ATATAAT
1 ATATAAT
21767 ATCAT-AT
1 AT-ATAAT
21774 AATATAAT
1 -ATATAAT
21782 ATATAAT
1 ATATAAT
21789 ATA
1 ATA
21792 CTATATTATA
Statistics
Matches: 191, Mismatches: 14, Indels: 44
0.77 0.06 0.18
Matches are distributed among these distances:
5 8 0.04
6 38 0.20
7 96 0.50
8 34 0.18
9 15 0.08
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (7 bp):
ATATAAT
Found at i:21580 original size:2 final size:2
Alignment explanation
Indices: 21558--21810 Score: 199
Period size: 2 Copynumber: 133.5 Consensus size: 2
21548 AATAATACAA
* *
21558 AT AT A- AT AT AT AA ACT A- AT AT AT AT AT AT AT A- AT AA AT AT
1 AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
21598 A- AC AT AT AA AT AT AT A- AT A- AT A- AT AT AT AT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
21635 -T AT AT A- AT AT AT AT AC A- AT AT AT AA AT AT A- AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
21673 AT AT AT AT AT ACC AA AT AT AT AT AT ACT AT AT A- AT AT AT AA AT
1 AT AT AT AT AT A-T AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT
21716 AT A- AT AT AT AT A- AT AT A- AT A- AT AT AT ACT AT AT ACT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT A-T AT AT
21756 AT AT AT AT A- AT AT CAT AT A- AT AT A- AT AT AT A- AT AT ACT AT
1 AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT A-T AT
21796 AT -T AT ACT AT AT AT A
1 AT AT AT A-T AT AT AT A
21811 CATAAAAAAG
Statistics
Matches: 206, Mismatches: 15, Indels: 60
0.73 0.05 0.21
Matches are distributed among these distances:
1 22 0.11
2 170 0.83
3 14 0.07
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (2 bp):
AT
Found at i:21797 original size:7 final size:6
Alignment explanation
Indices: 21558--21810 Score: 199
Period size: 5 Copynumber: 44.5 Consensus size: 6
21548 AATAATACAA
* * *
21558 ATATA- ATATAT AAACTA- ATATAT ATATAT ATA-AT AAATAT A-ACAT
1 ATATAT ATATAT ATA-TAT ATATAT ATATAT ATATAT ATATAT ATATAT
*
21603 ATAAAT ATATA- ATA-AT A-ATAT ATAT-T ATATAT -TATAT A-ATAT
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT
* * * *
21645 ATATAC A-ATAT ATAAAT ATA-AT ATATAT ATATAT ATATACC AAATAT
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATA-T ATATAT
*
21692 ATATAT ACTATAT A-ATAT ATAAAT ATA-AT ATATAT A-ATAT A-ATA-
1 ATATAT A-TATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT
21736 ATATAT ACTATAT ACTATAT ATATAT ATA-AT ATCATAT A-ATAT A-ATAT
1 ATATAT A-TATAT A-TATAT ATATAT ATATAT AT-ATAT ATATAT ATATAT
21784 ATA-AT ATACTAT AT-TAT ACTATAT ATA
1 ATATAT ATA-TAT ATATAT A-TATAT ATA
21811 CATAAAAAAG
Statistics
Matches: 207, Mismatches: 14, Indels: 53
0.76 0.05 0.19
Matches are distributed among these distances:
4 3 0.01
5 90 0.43
6 78 0.38
7 36 0.17
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (6 bp):
ATATAT
Found at i:21807 original size:66 final size:60
Alignment explanation
Indices: 21575--21808 Score: 211
Period size: 59 Copynumber: 3.9 Consensus size: 60
21565 ATATAAACTA
* * * * **
21575 ATATATATATATATAATAAATATAACATATAA-ATATATAATAATAATATATATTATATAT
1 ATATATATATATATCATAAATATAATATATAATATATAT-ATTATACTATATACAATATAT
*
21635 -TATATA-ATATAT-ATACAATATATAAATATAATATATATA-TATA-TATATACCAAATATAT
1 ATATATATATATATCATA-AATATA-ATATATAATATATATATTATACTATATA-C-AATATAT
21694 ATATACTATATAATAT-ATAAATATAATATAT-ATAATATAATAATATATACTATATAC--TATA
1 ATATA-TATAT-ATATCATAAATATAATATATAAT-ATAT-AT-AT-TATACTATATACAATATA
21755 T
60 T
21756 ATATATATA-ATATCATATAATATAATATATAATATACTATATTATACTATATA
1 ATATATATATATATCATA-AATATAATATATAATATA-TATATTATACTATATA
21809 TACATAAAAA
Statistics
Matches: 150, Mismatches: 5, Indels: 39
0.77 0.03 0.20
Matches are distributed among these distances:
57 9 0.06
58 15 0.10
59 35 0.23
60 17 0.11
61 32 0.21
62 23 0.15
63 8 0.05
65 5 0.03
66 6 0.04
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (60 bp):
ATATATATATATATCATAAATATAATATATAATATATATATTATACTATATACAATATAT
Found at i:26533 original size:21 final size:21
Alignment explanation
Indices: 26509--26548 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
26499 TTTATTTTAT
26509 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
26530 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
26549 AACTTGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
AACTTTATTTCAATTATCGTA
Found at i:26585 original size:33 final size:32
Alignment explanation
Indices: 26543--26686 Score: 165
Period size: 33 Copynumber: 4.6 Consensus size: 32
26533 TTTGTTTCAA
26543 TTATCGAACTTGAAGTTTTTAAGTATTTTGAAT
1 TTATCGAACTTGAAGTTTTTAAGTA-TTTGAAT
26576 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
* * *
26609 TTATCAAACTTGGAAGTATTTAAGTATTTCAA-
1 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
*
26641 TTAT-G---TTG-AGTTAATTAAGTATTTGAAT
1 TTATCGAACTTGAAGTT-TTTAAGTATTTGAAT
*
26669 TTATCGAACTTGAGGTTT
1 TTATCGAACTTGAAGTTT
26687 GATGCTTTCT
Statistics
Matches: 94, Mismatches: 9, Indels: 17
0.78 0.08 0.14
Matches are distributed among these distances:
26 3 0.03
27 13 0.14
28 6 0.06
29 1 0.01
32 7 0.07
33 50 0.53
34 14 0.15
ACGTcount: A:0.31, C:0.06, G:0.17, T:0.46
Consensus pattern (32 bp):
TTATCGAACTTGAAGTTTTTAAGTATTTGAAT
Found at i:26893 original size:21 final size:21
Alignment explanation
Indices: 26868--26921 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
26858 AGCGTGGGGA
*
26868 AATCGGTACCCTCTCATAGGG
1 AATCGGTTCCCTCTCATAGGG
*
26889 AATCGGTTTCCTCTCATAGGG
1 AATCGGTTCCCTCTCATAGGG
26910 AATCGGTTCCCT
1 AATCGGTTCCCT
26922 AAGTGTAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.20, C:0.28, G:0.22, T:0.30
Consensus pattern (21 bp):
AATCGGTTCCCTCTCATAGGG
Found at i:27154 original size:22 final size:19
Alignment explanation
Indices: 27107--27142 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
27097 GTTTGTTTAT
27107 AACCGG-TTTTTTTAAAAA
1 AACCGGTTTTTTTTAAAAA
27125 AACCGGTTTTTTTTAAAA
1 AACCGGTTTTTTTTAAAA
27143 TCGAAACCGG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.42
Consensus pattern (19 bp):
AACCGGTTTTTTTTAAAAA
Found at i:33134 original size:17 final size:17
Alignment explanation
Indices: 33112--33146 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
33102 ATCGGATAAG
33112 TAACCTTCTTATAATAC
1 TAACCTTCTTATAATAC
33129 TAACCTTCTTATAATAC
1 TAACCTTCTTATAATAC
33146 T
1 T
33147 CCCAAGGCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.34, C:0.23, G:0.00, T:0.43
Consensus pattern (17 bp):
TAACCTTCTTATAATAC
Found at i:35701 original size:32 final size:30
Alignment explanation
Indices: 35648--35706 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 30
35638 GACTAAAATT
35648 AAAAAATATAATATTAATGATAATTTTATA
1 AAAAAATATAATATTAATGATAATTTTATA
35678 AAAAAATAT-ATAGTTCAATTGATAATTTT
1 AAAAAATATAATA-TT-AA-TGATAATTTT
35707 GTTTTGGTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
29 3 0.12
30 11 0.42
31 2 0.08
32 10 0.38
ACGTcount: A:0.53, C:0.02, G:0.05, T:0.41
Consensus pattern (30 bp):
AAAAAATATAATATTAATGATAATTTTATA
Done.