Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002730.1 Hibiscus syriacus cultivar Beakdansim tig00005627_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: 72040
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:527 original size:264 final size:263
Alignment explanation
Indices: 13--555 Score: 911
Period size: 264 Copynumber: 2.0 Consensus size: 263
3 CGATATTCAT
*
13 TGAATTGTATA-TCGTTTAGATATCGATCGAAGACAAGTCCAAGATGGTTTGAAGTTATAAGAGT
1 TGAATTGTATATTCGTGTAGATATCGAT---A-ACAAGTCCAAGATGGTTTGAAGTTATAAGAGT
77 GTATAAGAGTTGTACGTATAGAATGGCTAGTGAGGTCTAGGTGAGGCATATAGTTGATATATGAT
62 GTATAAGAGTTGTACGTATAGAATGGCTAGTGAGGTCTAGGTGAGGCATATAGTTGATATATGAT
142 GTTTAATGGAAATAATACTTGCGATGAGTCTATTTCCTATATTATAATGCAGAATTCATGAATGT
127 GTTTAATGGAAATAATACTTGCGATGAGTCTATTTCCTATATTATAATGC--AATTCATGAATGT
207 AGGCATGTGTTTGATATGAGTATATGTGTTATGTTACATGATCCATGGGAATATATGTTGTCTGA
190 AGGCATGTGTTTGATATGAGTATATGTGTTATGTTACATGATCCATGGGAATATATGTTGTCTGA
272 TAAACCATG
255 TAAACCATG
281 TGAATTGTATATTCGTGTAGATATCGAT-ACAAGTCCAAGATGGTTTGAAGTTATAAGAGTGTAT
1 TGAATTGTATATTCGTGTAGATATCGATAACAAGTCCAAGATGGTTTGAAGTTATAAGAGTGTAT
345 AAGAGTTGTACGTATAGGAATGGCTAGTGAGGTCTAGGTGAGTGCATACTAGTTTGATATATGAT
66 AAGAGTTGTACGTATA-GAATGGCTAGTGAGGTCTAGGTGAG-GCATA-TAG-TTGATATATGAT
410 GTTTAATGG-AATAATACTTGCGATGAGTCTATTTCCTATATTAT-ATGC-ATTCATGAATGTAG
127 GTTTAATGGAAATAATACTTGCGATGAGTCTATTTCCTATATTATAATGCAATTCATGAATGTAG
*
472 GCATGTGTTTGATATGAGTATATGTGTTATATGTTACATGATCCATGGG-ATATATGTTGTTTGA
192 GCATGTGTTTGATATGAGTATATGTG-T-TATGTTACATGATCCATGGGAATATATGTTGTCTGA
536 TAAACCATG
255 TAAACCATG
545 TGAATTG-ATAT
1 TGAATTGTATAT
556 GATATATATG
Statistics
Matches: 266, Mismatches: 2, Indels: 19
0.93 0.01 0.07
Matches are distributed among these distances:
263 44 0.17
264 83 0.31
265 45 0.17
266 9 0.03
267 38 0.14
268 32 0.12
269 15 0.06
ACGTcount: A:0.31, C:0.09, G:0.24, T:0.37
Consensus pattern (263 bp):
TGAATTGTATATTCGTGTAGATATCGATAACAAGTCCAAGATGGTTTGAAGTTATAAGAGTGTAT
AAGAGTTGTACGTATAGAATGGCTAGTGAGGTCTAGGTGAGGCATATAGTTGATATATGATGTTT
AATGGAAATAATACTTGCGATGAGTCTATTTCCTATATTATAATGCAATTCATGAATGTAGGCAT
GTGTTTGATATGAGTATATGTGTTATGTTACATGATCCATGGGAATATATGTTGTCTGATAAACC
ATG
Found at i:904 original size:21 final size:22
Alignment explanation
Indices: 871--911 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
861 AATCGAGGGT
871 TACATAGGTCCTTCAGGACATA
1 TACATAGGTCCTTCAGGACATA
*
893 TACATA-GTCCTTCGGGACA
1 TACATAGGTCCTTCAGGACA
912 AATTTCATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (22 bp):
TACATAGGTCCTTCAGGACATA
Found at i:4460 original size:29 final size:30
Alignment explanation
Indices: 4418--4491 Score: 132
Period size: 29 Copynumber: 2.5 Consensus size: 30
4408 GTAATTAAAG
4418 AAGGAATTAAAGAATCAACCATTCATCC-A
1 AAGGAATTAAAGAATCAACCATTCATCCAA
4447 AAGGAATTAAAGAATCAACCATTCATCCAA
1 AAGGAATTAAAGAATCAACCATTCATCCAA
4477 AATGGAATTAAAGAA
1 AA-GGAATTAAAGAA
4492 GGAATTAACA
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
29 28 0.65
30 3 0.07
31 12 0.28
ACGTcount: A:0.51, C:0.16, G:0.12, T:0.20
Consensus pattern (30 bp):
AAGGAATTAAAGAATCAACCATTCATCCAA
Found at i:14767 original size:54 final size:54
Alignment explanation
Indices: 14699--15266 Score: 795
Period size: 54 Copynumber: 10.5 Consensus size: 54
14689 ACATTATAAG
* * * *
14699 TTCTCTGGGGTGCACACGTAGTGCCAATACGGTTGTTCATCAACATATGATGAA
1 TTCTGTGGGTTGCACACTTAGTGCCTATACGGTTGTTCATCAACATATGATGAA
* * * ** **
14753 TTATGTTGGTTGCACACTTAGTGCATATATAGTCATTCATCAACATATGATGAA
1 TTCTGTGGGTTGCACACTTAGTGCCTATACGGTTGTTCATCAACATATGATGAA
* * *
14807 TT-TCGTCGGTTGCACACTTAGTGCCTATAAGGTTATTCATCAACATATGATGAA
1 TTCT-GTGGGTTGCACACTTAGTGCCTATACGGTTGTTCATCAACATATGATGAA
* *
14861 TTCTTTGGGTTGCACACTTAGTGCCTATACGGTTGTCCATCAACATATGATGAA
1 TTCTGTGGGTTGCACACTTAGTGCCTATACGGTTGTTCATCAACATATGATGAA
*
14915 TTCTTTGGGTTGCACACTTAGTGCCTATACGGTTGTTCATCAACATATGATGAA
1 TTCTGTGGGTTGCACACTTAGTGCCTATACGGTTGTTCATCAACATATGATGAA
* **
14969 TTCTGTGGGTTGCACACTTAGTGCCTATACAGTCATTCATCAACATATGATGAA
1 TTCTGTGGGTTGCACACTTAGTGCCTATACGGTTGTTCATCAACATATGATGAA
*
15023 TTCCGTGGGTTGCACACTTAGTGCCTATACGGTTGTTCATCAACATATGATGAA
1 TTCTGTGGGTTGCACACTTAGTGCCTATACGGTTGTTCATCAACATATGATGAA
* * * * *
15077 TTTTGT-TGTTGCACACATAGTGCTTATAAGGTTGTTCATCAACATATGATGAA
1 TTCTGTGGGTTGCACACTTAGTGCCTATACGGTTGTTCATCAACATATGATGAA
*
15130 TTAC-ATGGGTTGCACACTTAGTGCCTATACGGTTGTTCATCAACATATGATGAA
1 TT-CTGTGGGTTGCACACTTAGTGCCTATACGGTTGTTCATCAACATATGATGAA
* *
15184 TT-TCGTGGGTTGCACACTTAGTGCCTATACGGTTGTTCATAAATATATGATGAA
1 TTCT-GTGGGTTGCACACTTAGTGCCTATACGGTTGTTCATCAACATATGATGAA
*
15238 TT-TCGTGGGTTGCACACTTAGTGCTTATA
1 TTCT-GTGGGTTGCACACTTAGTGCCTATA
15267 GTACACATAG
Statistics
Matches: 462, Mismatches: 46, Indels: 12
0.89 0.09 0.02
Matches are distributed among these distances:
53 47 0.10
54 414 0.90
55 1 0.00
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.35
Consensus pattern (54 bp):
TTCTGTGGGTTGCACACTTAGTGCCTATACGGTTGTTCATCAACATATGATGAA
Found at i:20297 original size:54 final size:54
Alignment explanation
Indices: 20213--20479 Score: 403
Period size: 54 Copynumber: 4.9 Consensus size: 54
20203 GTCGATACAA
* * *
20213 TTGTTCATTAACATATGATGAATTCAGTGGGTTGCACACTTAGTGCATATACGG
1 TTGTTCATCAACATATGATGAATTCTGTGGGTTGCACACTTAGTGCTTATACGG
**
20267 TCATTCATCAACATATGATGAATTCTGTGGGTTGCACACTTAGTGCTTATACGG
1 TTGTTCATCAACATATGATGAATTCTGTGGGTTGCACACTTAGTGCTTATACGG
* * * ** *
20321 TTGTTCATCAACATATGATGAATTTTGTGGGTTGCAAACTTAGTCCCGATACTG
1 TTGTTCATCAACATATGATGAATTCTGTGGGTTGCACACTTAGTGCTTATACGG
20375 TTGTTCATCAACATATGATGAATT-TCGTGGGTTGCACACTTAGTG-TCTATACGG
1 TTGTTCATCAACATATGATGAATTCT-GTGGGTTGCACACTTAGTGCT-TATACGG
20429 TTGTTCATCAACATATGATGAATTCTGTGGGTTGCACACTTAGTGCTTATA
1 TTGTTCATCAACATATGATGAATTCTGTGGGTTGCACACTTAGTGCTTATA
20480 GTATACACAA
Statistics
Matches: 191, Mismatches: 18, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
53 1 0.01
54 188 0.98
55 2 0.01
ACGTcount: A:0.26, C:0.16, G:0.21, T:0.37
Consensus pattern (54 bp):
TTGTTCATCAACATATGATGAATTCTGTGGGTTGCACACTTAGTGCTTATACGG
Found at i:28691 original size:21 final size:20
Alignment explanation
Indices: 28663--28701 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
28653 CATTGCAGGA
*
28663 ATTTATGGCCTCGACAAAAG
1 ATTTATGGCCTCAACAAAAG
*
28683 ATTTCATGGCTTCAACAAA
1 ATTT-ATGGCCTCAACAAA
28702 GATCTTGATA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.28
Consensus pattern (20 bp):
ATTTATGGCCTCAACAAAAG
Found at i:29659 original size:24 final size:24
Alignment explanation
Indices: 29630--29705 Score: 72
Period size: 24 Copynumber: 3.3 Consensus size: 24
29620 TTACCATTTA
29630 TTTACCATAAGCTCGTAAGCTTAT
1 TTTACCATAAGCTCGTAAGCTTAT
* * *
29654 TTTACCA-AA-ATAC-TTA-C-CAT
1 TTTACCATAAGCT-CGTAAGCTTAT
29674 TTGTACCATAAGCTCGTAAGCTTAT
1 TT-TACCATAAGCTCGTAAGCTTAT
29699 TTTACCA
1 TTTACCA
29706 ATACACTTGC
Statistics
Matches: 39, Mismatches: 6, Indels: 14
0.66 0.10 0.24
Matches are distributed among these distances:
20 4 0.10
21 6 0.15
22 6 0.15
23 6 0.15
24 13 0.33
25 4 0.10
ACGTcount: A:0.32, C:0.22, G:0.09, T:0.37
Consensus pattern (24 bp):
TTTACCATAAGCTCGTAAGCTTAT
Found at i:29719 original size:45 final size:45
Alignment explanation
Indices: 29632--29719 Score: 149
Period size: 45 Copynumber: 2.0 Consensus size: 45
29622 ACCATTTATT
*
29632 TACCATAAGCTCGTAAGCTTATTTTACCAAAATACTTACCATTTG
1 TACCATAAGCTCGTAAGCTTATTTTACCAAAACACTTACCATTTG
* *
29677 TACCATAAGCTCGTAAGCTTATTTTACCAATACACTTGCCATT
1 TACCATAAGCTCGTAAGCTTATTTTACCAAAACACTTACCATT
29720 ATTCCATAAC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.32, C:0.24, G:0.09, T:0.35
Consensus pattern (45 bp):
TACCATAAGCTCGTAAGCTTATTTTACCAAAACACTTACCATTTG
Found at i:48837 original size:6 final size:6
Alignment explanation
Indices: 48815--48858 Score: 52
Period size: 6 Copynumber: 7.2 Consensus size: 6
48805 CAGGAAAAAG
* * *
48815 AAATAAA AAATAA AAATAA AAATAA AGATGA CAATAA AAATAA A
1 AAAT-AA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA A
48859 TTCATTATTT
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
6 27 0.87
7 4 0.13
ACGTcount: A:0.77, C:0.02, G:0.05, T:0.16
Consensus pattern (6 bp):
AAATAA
Found at i:51007 original size:18 final size:19
Alignment explanation
Indices: 50984--51026 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
50974 GAAAATATTC
*
50984 TTTTTATTTTA-TTCCTTT
1 TTTTTATTTTATTTCCTTA
51002 TTTTTATTTTATTTCCTTA
1 TTTTTATTTTATTTCCTTA
51021 TTTTTA
1 TTTTTA
51027 CTTCTCACTC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 11 0.48
19 12 0.52
ACGTcount: A:0.14, C:0.09, G:0.00, T:0.77
Consensus pattern (19 bp):
TTTTTATTTTATTTCCTTA
Found at i:56460 original size:12 final size:12
Alignment explanation
Indices: 56428--56467 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
56418 TCAAATAACA
56428 TTAAAA-TTA-T
1 TTAAAATTTATT
*
56438 TT-AAATCTATT
1 TTAAAATTTATT
56449 TTAAAATTTATT
1 TTAAAATTTATT
56461 TTAAAAT
1 TTAAAAT
56468 ATGGATTGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
9 3 0.12
10 4 0.16
11 3 0.12
12 15 0.60
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (12 bp):
TTAAAATTTATT
Found at i:56479 original size:22 final size:22
Alignment explanation
Indices: 56454--56951 Score: 755
Period size: 22 Copynumber: 22.6 Consensus size: 22
56444 CTATTTTAAA
56454 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
56476 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
*
56498 ATTTATTTTAAAATATTGATTG
1 ATTTATTTTAAAATATGGATTG
*
56520 ATTTATTTTAAAATATGGATTA
1 ATTTATTTTAAAATATGGATTG
*
56542 ATTTATTTTAAAATATGAATTG
1 ATTTATTTTAAAATATGGATTG
***
56564 ATTTATTTTAAAATATGGAAAA
1 ATTTATTTTAAAATATGGATTG
56586 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
56608 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
56630 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
56652 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
**
56674 ATTTATTTTAAAATATGGA-AA
1 ATTTATTTTAAAATATGGATTG
* *
56695 ATTTTATTTTTAAATTTGGATTG
1 A-TTTATTTTAAAATATGGATTG
* *
56718 ATTTATTTTAAAATATTGATGG
1 ATTTATTTTAAAATATGGATTG
56740 ATTTATTTTTAAAATATGGATTG
1 ATTTA-TTTTAAAATATGGATTG
56763 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
***
56785 ATTTATTTTAAAATATGGAAAA
1 ATTTATTTTAAAATATGGATTG
* * * *
56807 AGTTATTTTTAAATTTGAATTG
1 ATTTATTTTAAAATATGGATTG
* *
56829 ATTTATTTTAAAATTTTGATTG
1 ATTTATTTTAAAATATGGATTG
*
56851 ATTTATTTTAAAATATGGATTA
1 ATTTATTTTAAAATATGGATTG
56873 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
56895 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
* *
56917 ATTTATTTTAAAGTTTGGATTG
1 ATTTATTTTAAAATATGGATTG
56939 ATTTATTTTAAAA
1 ATTTATTTTAAAA
56952 AAATTATTAT
Statistics
Matches: 428, Mismatches: 45, Indels: 6
0.89 0.09 0.01
Matches are distributed among these distances:
21 1 0.00
22 406 0.95
23 21 0.05
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.51
Consensus pattern (22 bp):
ATTTATTTTAAAATATGGATTG
Found at i:57032 original size:31 final size:31
Alignment explanation
Indices: 56975--57033 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
56965 AGTTGTATGG
*
56975 ATTATTTAAATTTCAGTATTATAAAACTAAA
1 ATTATTTAAATTTCAGTATTACAAAACTAAA
* *
57006 ATTATTTCAATTTCAGTATTGCAAAACT
1 ATTATTTAAATTTCAGTATTACAAAACT
57034 CTTTTAAGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.42, C:0.10, G:0.05, T:0.42
Consensus pattern (31 bp):
ATTATTTAAATTTCAGTATTACAAAACTAAA
Done.