Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001710.1 Hibiscus syriacus cultivar Beakdansim tig00003439_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: 42261
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.35
Found at i:17583 original size:38 final size:36
Alignment explanation
Indices: 17532--17655 Score: 117
Period size: 37 Copynumber: 3.3 Consensus size: 36
17522 CCAGAGTCAG
17532 TTCCCTTTGAAACATCAAATTTGTATCTTTTGAGATTGT
1 TTCCC-TTGAAACATCAAATTT-T-TCTTTTGAGATTGT
* ** *
17571 TTCCCTTAAAACATC-AATTTATCTCCCTTGAGATAGT
1 TTCCCTTGAAACATCAAATTT-T-TCTTTTGAGATTGT
*
17608 TTCCCTTGAAACACCAAATTTTTCTTTCTTGAGACTT-T
1 TTCCCTTGAAACATCAAATTTTTC-TT-TTGAGA-TTGT
17646 TTCCCTTGAA
1 TTCCCTTGAA
17656 GCAATAGTTT
Statistics
Matches: 70, Mismatches: 11, Indels: 9
0.78 0.12 0.10
Matches are distributed among these distances:
36 2 0.03
37 31 0.44
38 31 0.44
39 6 0.09
ACGTcount: A:0.26, C:0.22, G:0.10, T:0.43
Consensus pattern (36 bp):
TTCCCTTGAAACATCAAATTTTTCTTTTGAGATTGT
Found at i:17602 original size:37 final size:38
Alignment explanation
Indices: 17441--17628 Score: 138
Period size: 37 Copynumber: 5.0 Consensus size: 38
17431 TATCATTTTA
* * **
17441 TCTCCCTTGAGATTA-TTTCCCATGAAACATC-AGCTTG
1 TCTCCCTTGAGA-TAGTTTCCCTTAAAACATCAAATTTG
* *
17478 TCTCCCTTGAGATAATTT-CCTTCAAAACATCGAATTTTG
1 TCTCCCTTGAGATAGTTTCCCTT-AAAACATC-AAATTTG
* *
17517 TCTCACC-AGAG-TCAG-TTCCCTTTGAAACATCAAATTTG
1 TCTC-CCTTGAGAT-AGTTTCCC-TTAAAACATCAAATTTG
* ** * *
17555 TATCTTTTGAGATTGTTTCCCTTAAAACATC-AATTTA
1 TCTCCCTTGAGATAGTTTCCCTTAAAACATCAAATTTG
* *
17592 TCTCCCTTGAGATAGTTTCCCTTGAAACACCAAATTT
1 TCTCCCTTGAGATAGTTTCCCTTAAAACATCAAATTT
17629 TTCTTTCTTG
Statistics
Matches: 118, Mismatches: 21, Indels: 23
0.73 0.13 0.14
Matches are distributed among these distances:
36 5 0.04
37 52 0.44
38 30 0.25
39 27 0.23
40 4 0.03
ACGTcount: A:0.28, C:0.24, G:0.11, T:0.37
Consensus pattern (38 bp):
TCTCCCTTGAGATAGTTTCCCTTAAAACATCAAATTTG
Found at i:18452 original size:119 final size:118
Alignment explanation
Indices: 18280--18500 Score: 327
Period size: 119 Copynumber: 1.9 Consensus size: 118
18270 TATGAAAAAG
* * *
18280 TGATCAAGAAAGAATAAGTTCATATATGAGAGCTTCTTCGACCTCAACATGACCTTTATGGGAGA
1 TGATCAAGAAAGAAGAAATTCATATATGAGAGCTTCTTCGACCTCAACATGACCTTTATGGGAAA
*
18345 ATATGTG-GTTTATATAGGAGAGCTCATCTACTCTTTCCAAAGATAGGAGGAAA
66 ATATG-GAGCTTATATAGGAGAGCTCATCTACTCTTTCCAAAGATAGGAGGAAA
* * * *
18398 TGATCAGGAAAGAAGAGAATTCATATATGAGAGCTTGTTCTACCTCAATATGACCTTTATGGGAA
1 TGATCAAGAAAGAAGA-AATTCATATATGAGAGCTTCTTCGACCTCAACATGACCTTTATGGGAA
**
18463 AATATGGAGCTTATATAGGAGAGCTTGTCTACTCTTTC
65 AATATGGAGCTTATATAGGAGAGCTCATCTACTCTTTC
18501 GAGACAAGAT
Statistics
Matches: 91, Mismatches: 10, Indels: 3
0.88 0.10 0.03
Matches are distributed among these distances:
118 15 0.16
119 76 0.84
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.30
Consensus pattern (118 bp):
TGATCAAGAAAGAAGAAATTCATATATGAGAGCTTCTTCGACCTCAACATGACCTTTATGGGAAA
ATATGGAGCTTATATAGGAGAGCTCATCTACTCTTTCCAAAGATAGGAGGAAA
Found at i:18886 original size:43 final size:46
Alignment explanation
Indices: 18815--18899 Score: 131
Period size: 43 Copynumber: 1.9 Consensus size: 46
18805 GAAAAATGAA
18815 AAAAATGAAATATTTAAAAAATAAAGAGAAAAT-AAGAAATATGGG
1 AAAAATGAAATATTTAAAAAATAAAGAGAAAATGAAGAAATATGGG
* *
18860 AAAAA-GAAA-ATTTTAAAAATAGAGAGAAAATGAAGAAATA
1 AAAAATGAAATATTTAAAAAATAAAGAGAAAATGAAGAAATA
18900 AGAAAAAAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
43 20 0.54
44 12 0.32
45 5 0.14
ACGTcount: A:0.66, C:0.00, G:0.15, T:0.19
Consensus pattern (46 bp):
AAAAATGAAATATTTAAAAAATAAAGAGAAAATGAAGAAATATGGG
Found at i:18908 original size:44 final size:45
Alignment explanation
Indices: 18812--18914 Score: 131
Period size: 44 Copynumber: 2.3 Consensus size: 45
18802 ATTGAAAAAT
*
18812 GAAAAAAATGAAATATTTAAAAAATAAAGAGAAAATAAGAAATAT
1 GAAAAAAATGAAATATTTAAAAAATAAAGAGAAAATAAGAAATAA
** * *
18857 GGGAAAAA-GAAA-ATTTTAAAAATAGAGAGAAAATGAAGAAATAA
1 GAAAAAAATGAAATATTTAAAAAATAAAGAGAAAAT-AAGAAATAA
18901 GAAAAAAAT-AAATA
1 GAAAAAAATGAAATA
18915 ATGGAAATAA
Statistics
Matches: 48, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
43 20 0.42
44 21 0.44
45 7 0.15
ACGTcount: A:0.68, C:0.00, G:0.15, T:0.17
Consensus pattern (45 bp):
GAAAAAAATGAAATATTTAAAAAATAAAGAGAAAATAAGAAATAA
Found at i:24498 original size:22 final size:22
Alignment explanation
Indices: 24451--24498 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
24441 ATTAAGTCGT
* * *
24451 TGGGCCTAATTGGGATAAAATT
1 TGGGCCCAATTGGCATAAAATA
24473 TGGGCCCAATTGGACATAAAA-A
1 TGGGCCCAATTGG-CATAAAATA
24495 TGGG
1 TGGG
24499 ATTTTGAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.33, C:0.12, G:0.29, T:0.25
Consensus pattern (22 bp):
TGGGCCCAATTGGCATAAAATA
Found at i:27524 original size:3 final size:3
Alignment explanation
Indices: 27518--27554 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
27508 GTTATTGTTG
27518 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
27555 ACAAAAACAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:28823 original size:20 final size:20
Alignment explanation
Indices: 28798--28864 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
28788 ATCGATAAGA
*
28798 GTATCGATACTCTACCCTTG
1 GTATCGACACTCTACCCTTG
28818 GTATCGACACTCTACCCTTG
1 GTATCGACACTCTACCCTTG
*
28838 GTATCGACAATCTACCCTTG
1 GTATCGACACTCTACCCTTG
28858 GTATCGA
1 GTATCGA
28865 TACTTCCATG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.22, C:0.30, G:0.16, T:0.31
Consensus pattern (20 bp):
GTATCGACACTCTACCCTTG
Found at i:36368 original size:17 final size:17
Alignment explanation
Indices: 36342--36374 Score: 50
Period size: 16 Copynumber: 1.9 Consensus size: 17
36332 CCACCAATAG
36342 AAAAAGTTCCCTTTTTAT
1 AAAAAGTT-CCTTTTTAT
36360 AAAAA-TTCCTTTTTA
1 AAAAAGTTCCTTTTTA
36375 AATTCAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 8 0.53
17 2 0.13
18 5 0.33
ACGTcount: A:0.36, C:0.15, G:0.03, T:0.45
Consensus pattern (17 bp):
AAAAAGTTCCTTTTTAT
Found at i:40435 original size:24 final size:24
Alignment explanation
Indices: 40405--40450 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
40395 TAGTTATTAC
*
40405 ATATATGATTTTTATCATGAATAT
1 ATATATGATGTTTATCATGAATAT
*
40429 ATATATGATGTTTATTATGAAT
1 ATATATGATGTTTATCATGAAT
40451 GTTACTTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.37, C:0.02, G:0.11, T:0.50
Consensus pattern (24 bp):
ATATATGATGTTTATCATGAATAT
Found at i:40751 original size:61 final size:61
Alignment explanation
Indices: 40600--40738 Score: 170
Period size: 61 Copynumber: 2.2 Consensus size: 61
40590 GCAGGTTTAT
* *
40600 ATTAGCACTAGTGTGTAAGGACACTAAATGCAGGTGGAGGGCACAACCTTATGTGTCATATCCAG
1 ATTAGCACTAGAGTGTAA--AC-CT-AGTGCAGGTGGAGGGCACAACCTTATGTGTCATATCCAG
* * ** **
40665 ATTAGCACTAGAGTGTAAACCTAGTGTAGGTGGTGGGCATGACCTTATGTGTCATATCTGG
1 ATTAGCACTAGAGTGTAAACCTAGTGCAGGTGGAGGGCACAACCTTATGTGTCATATCCAG
40726 ATTAGCACTAGAG
1 ATTAGCACTAGAG
40739 CTTAAGTTTA
Statistics
Matches: 66, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
61 45 0.68
62 2 0.03
63 2 0.03
65 17 0.26
ACGTcount: A:0.29, C:0.17, G:0.27, T:0.27
Consensus pattern (61 bp):
ATTAGCACTAGAGTGTAAACCTAGTGCAGGTGGAGGGCACAACCTTATGTGTCATATCCAG
Done.