Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000543.1 Hibiscus syriacus cultivar Beakdansim tig00001053_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: 66850
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Found at i:1941 original size:41 final size:41
Alignment explanation
Indices: 1895--1973 Score: 149
Period size: 41 Copynumber: 1.9 Consensus size: 41
1885 TGTTTCATCA
1895 ATAATATAATTTAAATAATAATGAATCAAAGTTAAAAAATC
1 ATAATATAATTTAAATAATAATGAATCAAAGTTAAAAAATC
*
1936 ATAATATAATTTAAATAATAATGAGTCAAAGTTAAAAA
1 ATAATATAATTTAAATAATAATGAATCAAAGTTAAAAA
1974 TCTGAAAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.58, C:0.04, G:0.06, T:0.32
Consensus pattern (41 bp):
ATAATATAATTTAAATAATAATGAATCAAAGTTAAAAAATC
Found at i:3486 original size:17 final size:17
Alignment explanation
Indices: 3464--3500 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
3454 ATATCAAGTC
*
3464 AAAAATATAAGATGCAT
1 AAAAATATAAGATCCAT
*
3481 AAAAATATAATATCCAT
1 AAAAATATAAGATCCAT
3498 AAA
1 AAA
3501 TATCCAACAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.62, C:0.08, G:0.05, T:0.24
Consensus pattern (17 bp):
AAAAATATAAGATCCAT
Found at i:5200 original size:14 final size:15
Alignment explanation
Indices: 5181--5210 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
5171 TACAAGGAAA
5181 AAAATAAT-GTATAT
1 AAAATAATAGTATAT
5195 AAAATAATAGTATAT
1 AAAATAATAGTATAT
5210 A
1 A
5211 TATATACACA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (15 bp):
AAAATAATAGTATAT
Found at i:5368 original size:4 final size:4
Alignment explanation
Indices: 5359--5402 Score: 52
Period size: 4 Copynumber: 11.0 Consensus size: 4
5349 TGCGCGCATG
* * * *
5359 TATA TATA TATA TATA TATA TATA TGTA TTTA TGTA TATG TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
5403 AACATGGATC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (4 bp):
TATA
Found at i:5370 original size:6 final size:6
Alignment explanation
Indices: 5359--5402 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
5349 TGCGCGCATG
* * * *
5359 TATATA TATATA TATATA TATATA TGTATT TATGTA TATGTA TA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TA
5403 AACATGGATC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (6 bp):
TATATA
Found at i:8084 original size:39 final size:39
Alignment explanation
Indices: 8024--8141 Score: 182
Period size: 39 Copynumber: 3.0 Consensus size: 39
8014 GATACCATTT
* *
8024 CAACCCAATATCTAGTATTGTCAAAACTCCTTGGGAAGA
1 CAACCCAATATCTAGTCTTGTCAAAATTCCTTGGGAAGA
* *
8063 CAACCCAATATATAGTCTTGTCAAAATTCCTTGGGAATA
1 CAACCCAATATCTAGTCTTGTCAAAATTCCTTGGGAAGA
* *
8102 GAACGCAATATCTAGTCTTGTCAAAATTCCTTGGGAAGA
1 CAACCCAATATCTAGTCTTGTCAAAATTCCTTGGGAAGA
8141 C
1 C
8142 CACTTGATGT
Statistics
Matches: 70, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 70 1.00
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.28
Consensus pattern (39 bp):
CAACCCAATATCTAGTCTTGTCAAAATTCCTTGGGAAGA
Found at i:8164 original size:78 final size:78
Alignment explanation
Indices: 8029--8174 Score: 186
Period size: 78 Copynumber: 1.9 Consensus size: 78
8019 CATTTCAACC
*
8029 CAATATCTAGTATTGTCAAAACTCCTTGGGAAGACAACCCAATATATAGTCTTGTCAAAAT-TCC
1 CAATATCTAGTATTGTCAAAACTCCTTGGGAAGACAACCCAATATATAGTCTGGTC-AAATCTCC
8093 TTGGGAATAGAACG
65 TTGGGAATAGAACG
* * * *** * * *
8107 CAATATCTAGTCTTGTCAAAATTCCTTGGGAAGACCACTTGATGTTTATTCTGGTCAAATCTCCT
1 CAATATCTAGTATTGTCAAAACTCCTTGGGAAGACAACCCAATATATAGTCTGGTCAAATCTCCT
8172 TGG
66 TGG
8175 TTTCTTCCTC
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
77 4 0.07
78 53 0.93
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Consensus pattern (78 bp):
CAATATCTAGTATTGTCAAAACTCCTTGGGAAGACAACCCAATATATAGTCTGGTCAAATCTCCT
TGGGAATAGAACG
Found at i:19809 original size:32 final size:31
Alignment explanation
Indices: 19773--19846 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 31
19763 GGTCACGGGA
* *
19773 CCTACCTAAGAACACATCTTATGGCCGTAGGG
1 CCTACCTAAGAA-ACATCTTAAGGCCGTAGAG
* ** *
19805 CCTACCCAAGAATGATCTTAAGGCTGTAGAG
1 CCTACCTAAGAAACATCTTAAGGCCGTAGAG
19836 CCTACCTAAGA
1 CCTACCTAAGA
19847 GTCACATTAG
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
31 24 0.69
32 11 0.31
ACGTcount: A:0.31, C:0.27, G:0.20, T:0.22
Consensus pattern (31 bp):
CCTACCTAAGAAACATCTTAAGGCCGTAGAG
Found at i:20568 original size:18 final size:18
Alignment explanation
Indices: 20545--20591 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
20535 AAAGTTAACG
20545 GTCAACGGGTC-AGTTCGA
1 GTCAACGGGTCAAGTT-GA
* * *
20563 GTCAACAGATCAAGTTGT
1 GTCAACGGGTCAAGTTGA
20581 GTCAACGGGTC
1 GTCAACGGGTC
20592 GAATTAGGTC
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
18 19 0.83
19 4 0.17
ACGTcount: A:0.26, C:0.21, G:0.30, T:0.23
Consensus pattern (18 bp):
GTCAACGGGTCAAGTTGA
Found at i:25305 original size:24 final size:24
Alignment explanation
Indices: 25261--25306 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
25251 CATATAAATT
** *
25261 TGCACCGAAGTGCTGCGTAGAATA
1 TGCACCGAAGTGCCACATAGAATA
25285 TGCACCGAAGTGCCACATAGAA
1 TGCACCGAAGTGCCACATAGAA
25307 ATGTCAAGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.33, C:0.24, G:0.26, T:0.17
Consensus pattern (24 bp):
TGCACCGAAGTGCCACATAGAATA
Found at i:25372 original size:23 final size:23
Alignment explanation
Indices: 25297--25399 Score: 75
Period size: 23 Copynumber: 4.5 Consensus size: 23
25287 CACCGAAGTG
* **
25297 CCACATAGAAATGTCAAGAAGGA
1 CCACGTAGAAATGTCTCGAAGGA
** * * *
25320 CCAAATAGATATGTCCCAAAGGA
1 CCACGTAGAAATGTCTCGAAGGA
25343 -CAGCGTAGAAATGTCTCGAAGGA
1 CCA-CGTAGAAATGTCTCGAAGGA
* * *
25366 CCACGTATAACTGTCAT-GAATGA
1 CCACGTAGAAATGTC-TCGAAGGA
25389 CCACGTAGAAA
1 CCACGTAGAAA
25400 CCTTGACTCT
Statistics
Matches: 62, Mismatches: 15, Indels: 6
0.75 0.18 0.07
Matches are distributed among these distances:
22 2 0.03
23 57 0.92
24 3 0.05
ACGTcount: A:0.41, C:0.20, G:0.21, T:0.17
Consensus pattern (23 bp):
CCACGTAGAAATGTCTCGAAGGA
Found at i:28666 original size:17 final size:18
Alignment explanation
Indices: 28644--28677 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
28634 TTTTGAAAAA
28644 GTTTTGA-AAAAAATATG
1 GTTTTGAGAAAAAATATG
*
28661 GTTTTGAGAAACAATAT
1 GTTTTGAGAAAAAATAT
28678 ATGTATAGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.44, C:0.03, G:0.18, T:0.35
Consensus pattern (18 bp):
GTTTTGAGAAAAAATATG
Found at i:29160 original size:20 final size:19
Alignment explanation
Indices: 29128--29206 Score: 54
Period size: 20 Copynumber: 3.9 Consensus size: 19
29118 AGAACCCCAA
*
29128 GGGGGTATC-GTTCCCTGTG
1 GGGGGAATCGGTTCCCT-TG
*
29147 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCCTT---G
29170 GGGGGAATCGGTTCCCTCATG
1 GGGGGAATCGGTTCCCT--TG
*
29191 GGGGG-ATCGATTCCCT
1 GGGGGAATCGGTTCCCT
29207 CTGCACCAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
19 8 0.16
20 14 0.29
21 9 0.18
22 4 0.08
23 13 0.27
24 1 0.02
ACGTcount: A:0.14, C:0.24, G:0.37, T:0.25
Consensus pattern (19 bp):
GGGGGAATCGGTTCCCTTG
Found at i:29207 original size:20 final size:20
Alignment explanation
Indices: 29147--29207 Score: 59
Period size: 20 Copynumber: 2.9 Consensus size: 20
29137 GTTCCCTGTG
* *
29147 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGATT-CCC-TC-AT
*
29170 GGGGGAATCGGTTCCCTCAT
1 GGGGGAATCGATTCCCTCAT
*
29190 GGGGGGATCGATTCCCTC
1 GGGGGAATCGATTCCCTC
29208 TGCACCAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
20 17 0.49
21 2 0.06
22 3 0.09
23 13 0.37
ACGTcount: A:0.16, C:0.26, G:0.34, T:0.23
Consensus pattern (20 bp):
GGGGGAATCGATTCCCTCAT
Found at i:41946 original size:23 final size:23
Alignment explanation
Indices: 41825--41949 Score: 85
Period size: 23 Copynumber: 5.4 Consensus size: 23
41815 CCAAAGTGTT
41825 GCGTAGAATATG-CACCAAAGTG-CC
1 GCGTAGAA-ATGTC-CCAAAG-GACC
* *
41849 ACGTAGAAATG-CCCTAGAGGACC
1 GCGTAGAAATGTCCC-AAAGGACC
* * * *
41872 ACATAGATATATCCCAAAGGACC
1 GCGTAGAAATGTCCCAAAGGACC
*
41895 GCATAGAAATGTCCCAAAGGACC
1 GCGTAGAAATGTCCCAAAGGACC
** * * *
41918 ATGTAGAATTGTCCCGAATGACC
1 GCGTAGAAATGTCCCAAAGGACC
41941 GCGTAGAAA
1 GCGTAGAAA
41950 CCTTGACTCT
Statistics
Matches: 80, Mismatches: 18, Indels: 7
0.76 0.17 0.07
Matches are distributed among these distances:
22 3 0.04
23 67 0.84
24 10 0.12
ACGTcount: A:0.37, C:0.24, G:0.22, T:0.17
Consensus pattern (23 bp):
GCGTAGAAATGTCCCAAAGGACC
Found at i:45190 original size:2 final size:2
Alignment explanation
Indices: 45183--45214 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
45173 ATCTTATGTT
45183 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
45215 TATATATATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:45219 original size:2 final size:2
Alignment explanation
Indices: 45214--45251 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
45204 ACACACACAC
45214 AT AT AT 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
45252 CAATGATTCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:51274 original size:21 final size:21
Alignment explanation
Indices: 51220--51268 Score: 98
Period size: 21 Copynumber: 2.3 Consensus size: 21
51210 TTTGGGAGTT
51220 CATCGATACACATTGAAGATG
1 CATCGATACACATTGAAGATG
51241 CATCGATACACATTGAAGATG
1 CATCGATACACATTGAAGATG
51262 CATCGAT
1 CATCGAT
51269 GGACATAACC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.24
Consensus pattern (21 bp):
CATCGATACACATTGAAGATG
Found at i:56247 original size:17 final size:17
Alignment explanation
Indices: 56222--56257 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
56212 ACGGTTAGGG
56222 TTAGAGATTTGAGATTT
1 TTAGAGATTTGAGATTT
* *
56239 TTAGGGATTTGTGATTT
1 TTAGAGATTTGAGATTT
56256 TT
1 TT
56258 TGTAATTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.22, C:0.00, G:0.25, T:0.53
Consensus pattern (17 bp):
TTAGAGATTTGAGATTT
Found at i:56293 original size:13 final size:13
Alignment explanation
Indices: 56271--56319 Score: 57
Period size: 13 Copynumber: 3.8 Consensus size: 13
56261 AATTTTAGAA
*
56271 AAATAGTTTTTAT
1 AAATATTTTTTAT
56284 AAATATTTTTT-T
1 AAATATTTTTTAT
*
56296 AAA-ATTTCTTTAA
1 AAATATTT-TTTAT
56309 AAATATTTTTT
1 AAATATTTTTT
56320 TAATTACCAG
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
11 4 0.13
12 7 0.23
13 16 0.52
14 4 0.13
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (13 bp):
AAATATTTTTTAT
Found at i:57664 original size:6 final size:6
Alignment explanation
Indices: 57653--57677 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
57643 CCACGTGTAC
57653 GGATTT GGATTT GGATTT GGATTT G
1 GGATTT GGATTT GGATTT GGATTT G
57678 AGTGTTTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.36, T:0.48
Consensus pattern (6 bp):
GGATTT
Found at i:60041 original size:113 final size:112
Alignment explanation
Indices: 59697--60261 Score: 780
Period size: 113 Copynumber: 5.1 Consensus size: 112
59687 GTGTTAATAC
* *
59697 TTATAAAAGTATCGACACTATCAACATATCCGGTAGCTCTTTACCTGTTTTGTCATTTATAGACC
1 TTAT-AAAGTATCGACACTTTCAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACC
* * * *
59762 GATTTTAT-ATTTTTTTACCTGTTTTA-T-TTATGGATCGATACATTT
65 GGTTTTGTCATTTTTTTACTTGTTATATTGTTATGGATCGATACATTT
* *
59807 TTATAAAGTATCGATA-TTATC-ACATATCCGGTAGCGCTTTACTTGTTTTGTCATTTATAGACC
1 TTATAAAGTATCGACACTT-TCAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACC
* *
59870 AGTTTTGTCA-TTTTTTACCTGTTATATTGTTATGGATCGATACATTT
65 GGTTTTGTCATTTTTTTACTTGTTATATTGTTATGGATCGATACATTT
* * *
59917 TTATAAAGTATCGACACTTTCAATATATTCGGTAACGCTTTACCTGTTTTGTCATTTATAGACCG
1 TTATAAAGTATCGACACTTTCAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCG
* *
59982 GTTTTATCATTTTTTTTACTTGTTATATTATTATGGATCGATACATTT
66 GTTTTGTCA-TTTTTTTACTTGTTATATTGTTATGGATCGATACATTT
* * *
60030 TTATAAAGTATCGACATTTTCAATATATCCGGTAGCGCTTTACCTGTTATGTCATTTATAGACCG
1 TTATAAAGTATCGACACTTTCAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCG
* * * *
60095 GTTTTGTTA-TTTTTT--TTGTTATATTGTTACGGATAGATACGTTT
66 GTTTTGTCATTTTTTTACTTGTTATATTGTTATGGATCGATACATTT
60139 TTAT-AAGT-T-GACACTTTCAA-ATATCCGGTAGCGCTTTA-CTGTTTTGTCATTTATAGACCG
1 TTATAAAGTATCGACACTTTCAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCG
* * *
60199 ATTTTGTCATTTTTTTACTTGTTATATTGTTATGGATCAATATATTT
66 GTTTTGTCATTTTTTTACTTGTTATATTGTTATGGATCGATACATTT
60246 TTATAAAGTATCGACA
1 TTATAAAGTATCGACA
60262 TAAACCGACA
Statistics
Matches: 405, Mismatches: 36, Indels: 28
0.86 0.08 0.06
Matches are distributed among these distances:
104 28 0.07
105 24 0.06
106 10 0.02
107 29 0.07
108 69 0.17
109 45 0.11
110 43 0.11
111 54 0.13
113 103 0.25
ACGTcount: A:0.25, C:0.14, G:0.14, T:0.47
Consensus pattern (112 bp):
TTATAAAGTATCGACACTTTCAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCG
GTTTTGTCATTTTTTTACTTGTTATATTGTTATGGATCGATACATTT
Done.