Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005952.1 Hibiscus syriacus cultivar Beakdansim tig00013983_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: 56313
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:4822 original size:59 final size:58
Alignment explanation
Indices: 4663--4825 Score: 202
Period size: 59 Copynumber: 2.8 Consensus size: 58
4653 TTTGGATGTC
* * ** * *
4663 TGGGATGAAAGTGAAATATTCAAAAGTTTGGGGAACAATTTAGAATAATGTCATAGTT
1 TGGGATGAAATTGGAATATTCAAAAGTTTAAGGAACAATTTATAATAAAGTCATAGTT
* * *
4721 TGGGGATGATATTGG-ATATTCAAAATTTTAAGGAAAAATTTATAATAAAAGTCATAGTT
1 T-GGGATGAAATTGGAATATTCAAAAGTTTAAGGAACAATTTATAAT-AAAGTCATAGTT
* *
4780 TGGGATGAAATTGGAATATTCAAAAGTTTAAGGACCACTTTATAAT
1 TGGGATGAAATTGGAATATTCAAAAGTTTAAGGAACAATTTATAAT
4826 GAGGATCATA
Statistics
Matches: 88, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
58 39 0.44
59 49 0.56
ACGTcount: A:0.40, C:0.06, G:0.21, T:0.33
Consensus pattern (58 bp):
TGGGATGAAATTGGAATATTCAAAAGTTTAAGGAACAATTTATAATAAAGTCATAGTT
Found at i:6486 original size:20 final size:20
Alignment explanation
Indices: 6439--6479 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
6429 TTGTAAGGTT
6439 TATGAAATTGAGTGGCTTGG
1 TATGAAATTGAGTGGCTTGG
6459 TATGAAATTGAGTGGCTTGG
1 TATGAAATTGAGTGGCTTGG
6479 T
1 T
6480 GAGAAATATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.24, C:0.05, G:0.34, T:0.37
Consensus pattern (20 bp):
TATGAAATTGAGTGGCTTGG
Found at i:10542 original size:32 final size:29
Alignment explanation
Indices: 10500--10560 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 29
10490 TTCTGGTGAG
*
10500 CTTAACGAGCAACCAGTCGAGCAACAAATTTT
1 CTTAACGAGC-ACCAATCGAG-AA-AAATTTT
*
10532 CTTAATGAGCACCAATCGAGAAAAATTTT
1 CTTAACGAGCACCAATCGAGAAAAATTTT
10561 AAAGAACTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
29 7 0.26
30 2 0.07
31 9 0.33
32 9 0.33
ACGTcount: A:0.39, C:0.21, G:0.15, T:0.25
Consensus pattern (29 bp):
CTTAACGAGCACCAATCGAGAAAAATTTT
Found at i:10585 original size:67 final size:67
Alignment explanation
Indices: 10509--10638 Score: 181
Period size: 67 Copynumber: 1.9 Consensus size: 67
10499 GCTTAACGAG
*
10509 CAACCAGTCGAGCAACAAATTTTCTTAATGAGCACCAATCGAG-AAAAATTTTAAAGAACTTAAA
1 CAACCAGTCGAGCAACAAATTTTCTTAAGGAGCACCAATCG-GTAAAAATTTTAAAGAACTTAAA
10573 AAT
65 AAT
* * * * * *
10576 CAACTAGTCGAGCAATAAATTTTCTTAAGGAGCACTAATCGGTCAAAATTTTAACGAGCTTAA
1 CAACCAGTCGAGCAACAAATTTTCTTAAGGAGCACCAATCGGTAAAAATTTTAAAGAACTTAA
10639 CAAGTAACAA
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
66 1 0.02
67 54 0.98
ACGTcount: A:0.42, C:0.18, G:0.14, T:0.26
Consensus pattern (67 bp):
CAACCAGTCGAGCAACAAATTTTCTTAAGGAGCACCAATCGGTAAAAATTTTAAAGAACTTAAAA
AT
Found at i:16934 original size:44 final size:45
Alignment explanation
Indices: 16831--16967 Score: 179
Period size: 45 Copynumber: 3.0 Consensus size: 45
16821 ATAAAATTTC
* * *
16831 TTATTAATATATTTATCATTTATCCCATAAGCTCGTAAGCTTATT
1 TTATCAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATT
* *
16876 TTA-CAAGTATACTTACCATTTATCCCATAAGCTTG-AAGTTTATT
1 TTATCAA-TATACTTACCATTTATCCCATAAGCTCGTAAGCTTATT
* *
16920 TTATCAATATACTTACAATTTAATCTCATAAGCTCGTAAGCTTATT
1 TTATCAATATACTTACCATTT-ATCCCATAAGCTCGTAAGCTTATT
16966 TT
1 TT
16968 TTTGTTTATC
Statistics
Matches: 79, Mismatches: 9, Indels: 7
0.83 0.09 0.07
Matches are distributed among these distances:
44 26 0.33
45 43 0.54
46 10 0.13
ACGTcount: A:0.32, C:0.17, G:0.07, T:0.44
Consensus pattern (45 bp):
TTATCAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATT
Found at i:19102 original size:20 final size:20
Alignment explanation
Indices: 19072--19117 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
19062 CTAAACTTTT
*
19072 CAAAGTTTATACTTTGGTCAC
1 CAAA-TTTATAATTTGGTCAC
19093 CAAATTTATAATTTGGTCAC
1 CAAATTTATAATTTGGTCAC
*
19113 TAAAT
1 CAAAT
19118 AAATCCATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 19 0.83
21 4 0.17
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.39
Consensus pattern (20 bp):
CAAATTTATAATTTGGTCAC
Found at i:23823 original size:45 final size:46
Alignment explanation
Indices: 23759--23937 Score: 274
Period size: 46 Copynumber: 4.0 Consensus size: 46
23749 ATTTCTTAAT
* *
23759 CAATATATTTACTATTT-ATCCCATAAGCTCGTAAGCTTATTTTAC
1 CAATATACTTACCATTTAATCCCATAAGCTCGTAAGCTTATTTTAC
*
23804 CAGTATACTTACCATTT-ATCCCATAAGCTCG-AAGCTTATTTTAC
1 CAATATACTTACCATTTAATCCCATAAGCTCGTAAGCTTATTTTAC
* **
23848 AAATATACTTATAATTTAATCCCATAAGCTCGTAAGCTTATTTTAC
1 CAATATACTTACCATTTAATCCCATAAGCTCGTAAGCTTATTTTAC
*
23894 CAATATACTTACCATTTAATCCCATAAGCTCGTAAGCTTTTTTT
1 CAATATACTTACCATTTAATCCCATAAGCTCGTAAGCTTATTTT
23938 TATGTTTATC
Statistics
Matches: 121, Mismatches: 11, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
44 26 0.21
45 42 0.35
46 53 0.44
ACGTcount: A:0.32, C:0.21, G:0.07, T:0.40
Consensus pattern (46 bp):
CAATATACTTACCATTTAATCCCATAAGCTCGTAAGCTTATTTTAC
Found at i:23877 original size:90 final size:91
Alignment explanation
Indices: 23772--23937 Score: 291
Period size: 90 Copynumber: 1.8 Consensus size: 91
23762 TATATTTACT
*
23772 ATTTATCCCATAAGCTCGTAAGCTTATTTTACCAGTATACTTACCATTT-ATCCCATAAGCTCG-
1 ATTTATCCCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTAATCCCATAAGCTCGT
23835 AAGCTTATTTTACAAATATACTTATA
66 AAGCTTATTTTACAAATATACTTATA
23861 ATTTAATCCCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTAATCCCATAAGCTCG
1 ATTT-ATCCCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTAATCCCATAAGCTCG
*
23926 TAAGCTTTTTTT
65 TAAGCTTATTTT
23938 TATGTTTATC
Statistics
Matches: 72, Mismatches: 2, Indels: 3
0.94 0.03 0.04
Matches are distributed among these distances:
89 4 0.06
90 44 0.61
91 14 0.19
92 10 0.14
ACGTcount: A:0.31, C:0.22, G:0.08, T:0.39
Consensus pattern (91 bp):
ATTTATCCCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTAATCCCATAAGCTCGT
AAGCTTATTTTACAAATATACTTATA
Found at i:29239 original size:70 final size:70
Alignment explanation
Indices: 29126--29266 Score: 282
Period size: 70 Copynumber: 2.0 Consensus size: 70
29116 GCTGTAATAG
29126 AAAATTCTCTTAAGTTACATAGGAACAAAGAGCTTATATCAATCGAAGTAAAGCACAACACATTT
1 AAAATTCTCTTAAGTTACATAGGAACAAAGAGCTTATATCAATCGAAGTAAAGCACAACACATTT
29191 CGAAA
66 CGAAA
29196 AAAATTCTCTTAAGTTACATAGGAACAAAGAGCTTATATCAATCGAAGTAAAGCACAACACATTT
1 AAAATTCTCTTAAGTTACATAGGAACAAAGAGCTTATATCAATCGAAGTAAAGCACAACACATTT
29261 CGAAA
66 CGAAA
29266 A
1 A
29267 TACCTTCAGT
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 71 1.00
ACGTcount: A:0.46, C:0.17, G:0.13, T:0.24
Consensus pattern (70 bp):
AAAATTCTCTTAAGTTACATAGGAACAAAGAGCTTATATCAATCGAAGTAAAGCACAACACATTT
CGAAA
Found at i:32175 original size:18 final size:18
Alignment explanation
Indices: 32152--32192 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
32142 TTCATCTAAC
*
32152 GGAGAACGACGAAGATTG
1 GGAGAACGACGAAGATCG
32170 GGAGAACGACGAAGATCG
1 GGAGAACGACGAAGATCG
32188 GGAGA
1 GGAGA
32193 TGAAACCCGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.39, C:0.12, G:0.41, T:0.07
Consensus pattern (18 bp):
GGAGAACGACGAAGATCG
Found at i:40491 original size:29 final size:31
Alignment explanation
Indices: 40423--40492 Score: 74
Period size: 29 Copynumber: 2.3 Consensus size: 31
40413 TTAACGGCTC
* *
40423 AGTAGTATAATTGAAACGAAAATCAAATTTT
1 AGTAGTATAATTGAAACGAAAATAAAAGTTT
* *
40454 AGT-GTTATAATTG-AA-TAAATTAAAAGTTT
1 AGTAG-TATAATTGAAACGAAAATAAAAGTTT
40483 AGTAGTATAA
1 AGTAGTATAA
40493 GCGATACAAC
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
29 18 0.55
30 4 0.12
31 11 0.33
ACGTcount: A:0.47, C:0.03, G:0.14, T:0.36
Consensus pattern (31 bp):
AGTAGTATAATTGAAACGAAAATAAAAGTTT
Found at i:41343 original size:8 final size:8
Alignment explanation
Indices: 41330--41360 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
41320 TGGAACAAAA
41330 AATATTAT
1 AATATTAT
41338 AATATTAT
1 AATATTAT
41346 AATATTAT
1 AATATTAT
41354 AAATATT
1 -AATATT
41361 TAGAGTTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 16 0.73
9 6 0.27
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (8 bp):
AATATTAT
Found at i:46839 original size:23 final size:23
Alignment explanation
Indices: 46813--46881 Score: 111
Period size: 23 Copynumber: 3.0 Consensus size: 23
46803 CACCACAGCT
*
46813 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
*
46836 CGTAGAATTGCACCGGAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
*
46859 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
46882 TATAATAATG
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 43 1.00
ACGTcount: A:0.28, C:0.26, G:0.26, T:0.20
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:47206 original size:25 final size:25
Alignment explanation
Indices: 47177--47234 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
47167 ATGCATATGG
*
47177 TATGAATTCATG-TCATGTATCATAA
1 TATGAATTCA-GATCATGTATCAAAA
* *
47202 TATGAAATGAGATCATGTATCAAAA
1 TATGAATTCAGATCATGTATCAAAA
47227 TATTGAAT
1 TA-TGAAT
47235 CTAGACTTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
24 1 0.04
25 22 0.81
26 4 0.15
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.36
Consensus pattern (25 bp):
TATGAATTCAGATCATGTATCAAAA
Done.