Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002622.1 Hibiscus syriacus cultivar Beakdansim tig00005337_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: 50416
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.34
Found at i:7385 original size:185 final size:185
Alignment explanation
Indices: 7067--7456 Score: 651
Period size: 185 Copynumber: 2.1 Consensus size: 185
7057 ATTAAATTTT
* * * *
7067 AAATATTAAATATTTTATATATAACATATGGGTTCAGCCCAAACCATTTAAAATCCAATTAATAA
1 AAATATTAAATATTTTATATATAACATATGGGCTAAGCCCAAACCACTTAAAACCCAATTAATAA
7132 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATAAATTTT
66 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATAAATTTT
*
7197 TTATTTTATAATTATATATTATTTAAATTAATTGTAAACTGTTTTTTT-AATTAAA
131 TTATTTTATAATTATATATTATTTAAATTAATTATAAACT-TTTTTTTGAATTAAA
*
7252 AAATATTAAATATATTATATATAACATATGGGCTAAGCCCAAACCACTTAAAACCCAATTAATAA
1 AAATATTAAATATTTTATATATAACATATGGGCTAAGCCCAAACCACTTAAAACCCAATTAATAA
* *
7317 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATCTGAAA-TT
66 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATAT-AAATTT
7381 TTTATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTTGAATTAAA
130 TTTATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTTGAATTAAA
* *
7437 AAACATTTAAT-TTTTATATA
1 AAATATTAAATATTTTATATA
7457 AATTAGAAAA
Statistics
Matches: 192, Mismatches: 11, Indels: 5
0.92 0.05 0.02
Matches are distributed among these distances:
184 15 0.08
185 174 0.91
186 3 0.02
ACGTcount: A:0.45, C:0.09, G:0.04, T:0.42
Consensus pattern (185 bp):
AAATATTAAATATTTTATATATAACATATGGGCTAAGCCCAAACCACTTAAAACCCAATTAATAA
TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATAAATTTT
TTATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTTGAATTAAA
Found at i:13341 original size:23 final size:23
Alignment explanation
Indices: 13315--13359 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
13305 CACCACAGCT
*
13315 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
*
13338 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
13360 TTATAATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.27, C:0.27, G:0.24, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:13577 original size:149 final size:149
Alignment explanation
Indices: 13338--13641 Score: 572
Period size: 149 Copynumber: 2.0 Consensus size: 149
13328 CGAAGTGCCA
*
13338 CGTAGAATTGCACCGTAGTGCCTTATAATAATATCCATAAGGACCACATATTATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATATCCATAAGGACCACATATTATTCCTTAAGAAT
13403 CATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
66 CATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
13468 TATATATCCCGAAGGACCC
131 TATATATCCCGAAGGACCC
* *
13487 CGTAGAATTGCACCGTAGTGTCATATAATAATTTCCATAAGGACCACATATTATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATATCCATAAGGACCACATATTATTCCTTAAGAAT
13552 CATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
66 CATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
*
13617 TATATATCCCGAAGGACCG
131 TATATATCCCGAAGGACCC
13636 CGTAGA
1 CGTAGA
13642 CCCTCTACCC
Statistics
Matches: 151, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
149 151 1.00
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.29
Consensus pattern (149 bp):
CGTAGAATTGCACCGTAGTGCCATATAATAATATCCATAAGGACCACATATTATTCCTTAAGAAT
CATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
TATATATCCCGAAGGACCC
Found at i:18742 original size:23 final size:23
Alignment explanation
Indices: 18716--18761 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
18706 CACCACAGCT
*
18716 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
*
18739 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
18762 TATAATAATG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.28, C:0.26, G:0.24, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:18998 original size:149 final size:149
Alignment explanation
Indices: 18739--19042 Score: 590
Period size: 149 Copynumber: 2.0 Consensus size: 149
18729 CGAAGTGCCA
18739 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAAT
* *
18804 CATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCTACATAATATA
66 CATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
18869 TATATATCCCGAAGGACCG
131 TATATATCCCGAAGGACCG
18888 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAAT
18953 CATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
66 CATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
19018 TATATATCCCGAAGGACCG
131 TATATATCCCGAAGGACCG
19037 CGTAGA
1 CGTAGA
19043 CCCTCTACCC
Statistics
Matches: 153, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 153 1.00
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.29
Consensus pattern (149 bp):
CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAAT
CATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
TATATATCCCGAAGGACCG
Found at i:19627 original size:63 final size:63
Alignment explanation
Indices: 19498--19637 Score: 183
Period size: 63 Copynumber: 2.2 Consensus size: 63
19488 TAATGGAGGC
* * * *
19498 ATGCATCGATGCACTTCTGATGCATCGATGCACTGAGGGCATTCGATGTTCATTTTATTAGAA
1 ATGCATCGATGCACTCCTGATGCATCGATGCACTGACGACATTCGATGTTCATTTTATAAGAA
* ** **
19561 ATGCATCGATGCACTCCTTATGCATCGATGCACTGACGACATTCGATGTTTGTATTTA-AATTA
1 ATGCATCGATGCACTCCTGATGCATCGATGCACTGACGACATTCGATGTTCAT-TTTATAAGAA
19624 ATGCATCGATGCAC
1 ATGCATCGATGCAC
19638 CTTCAACAAA
Statistics
Matches: 67, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
63 63 0.94
64 4 0.06
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.33
Consensus pattern (63 bp):
ATGCATCGATGCACTCCTGATGCATCGATGCACTGACGACATTCGATGTTCATTTTATAAGAA
Found at i:22618 original size:2 final size:2
Alignment explanation
Indices: 22611--22637 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
22601 TTTTAAAAAC
22611 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
22638 ATAAAGAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:26986 original size:17 final size:17
Alignment explanation
Indices: 26961--26993 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
26951 TTAAACTTAT
26961 TTTTCCTTT-TTTTTAA
1 TTTTCCTTTATTTTTAA
26977 TTTTCACTTTATTTTTA
1 TTTTC-CTTTATTTTTA
26994 GTACTAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 4 0.27
18 6 0.40
ACGTcount: A:0.15, C:0.12, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTTCCTTTATTTTTAA
Found at i:31251 original size:25 final size:25
Alignment explanation
Indices: 31217--31270 Score: 108
Period size: 25 Copynumber: 2.2 Consensus size: 25
31207 CTTCAGTTTT
31217 AGGCGAGATGATTATAGTTTCTGCA
1 AGGCGAGATGATTATAGTTTCTGCA
31242 AGGCGAGATGATTATAGTTTCTGCA
1 AGGCGAGATGATTATAGTTTCTGCA
31267 AGGC
1 AGGC
31271 TCGAGAAGGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.28, C:0.13, G:0.30, T:0.30
Consensus pattern (25 bp):
AGGCGAGATGATTATAGTTTCTGCA
Found at i:32867 original size:20 final size:20
Alignment explanation
Indices: 32842--32879 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
32832 AAGCTTGTGT
32842 ATATTTTCTTTAAATATTGC
1 ATATTTTCTTTAAATATTGC
* *
32862 ATATTTTTTTTGAATATT
1 ATATTTTCTTTAAATATT
32880 CTTAATTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.29, C:0.05, G:0.05, T:0.61
Consensus pattern (20 bp):
ATATTTTCTTTAAATATTGC
Done.