Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004841.1 Hibiscus syriacus cultivar Beakdansim tig00010914_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: 50880
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:8860 original size:16 final size:16
Alignment explanation
Indices: 8813--8862 Score: 57
Period size: 17 Copynumber: 3.0 Consensus size: 16
8803 CCTACTAATG
*
8813 TTAATTTTAAAC-CTA
1 TTAATTTTAAACTCAA
8828 TTGATATTTTAAAACTCAA
1 TT-A-ATTTT-AAACTCAA
8847 TTAATTTTAAACTCAA
1 TTAATTTTAAACTCAA
8863 ATAAAAAGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
15 2 0.07
16 9 0.30
17 10 0.33
18 5 0.17
19 4 0.13
ACGTcount: A:0.42, C:0.12, G:0.02, T:0.44
Consensus pattern (16 bp):
TTAATTTTAAACTCAA
Found at i:9140 original size:22 final size:22
Alignment explanation
Indices: 9115--9156 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
9105 TTAATTTTAA
**
9115 AATATATATAATTTTATATAAT
1 AATATATATAAAATTATATAAT
*
9137 AATATTTATAAAATTATATA
1 AATATATATAAAATTATATA
9157 TTTTCTAAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
AATATATATAAAATTATATAAT
Found at i:9445 original size:17 final size:16
Alignment explanation
Indices: 9421--9464 Score: 61
Period size: 17 Copynumber: 2.7 Consensus size: 16
9411 TAATAGAAAC
*
9421 AAAAATTAAATTTAAT
1 AAAAATTAAATTAAAT
*
9437 AATAAATTAAAATAAAT
1 AA-AAATTAAATTAAAT
9454 AAAAATTAAAT
1 AAAAATTAAAT
9465 GATATAAACA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 10 0.42
17 14 0.58
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
AAAAATTAAATTAAAT
Found at i:9471 original size:16 final size:15
Alignment explanation
Indices: 9421--9472 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 15
9411 TAATAGAAAC
*
9421 AAAAATTAAATTTAAT
1 AAAAATTAAATAT-AT
*
9437 AATAAATTAAAATAAAT
1 AA-AAATT-AAATATAT
9454 AAAAATTAAATGATAT
1 AAAAATTAAAT-ATAT
9470 AAA
1 AAA
9473 CAATAATCAC
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
15 4 0.13
16 13 0.43
17 9 0.30
18 4 0.13
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (15 bp):
AAAAATTAAATATAT
Found at i:19626 original size:16 final size:16
Alignment explanation
Indices: 19601--19631 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
19591 CTGTCAATTA
19601 ATTTTATTTAAAAAAT
1 ATTTTATTTAAAAAAT
*
19617 ATTTTTTTTAAAAAA
1 ATTTTATTTAAAAAA
19632 AAATCTAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
ATTTTATTTAAAAAAT
Found at i:22356 original size:19 final size:18
Alignment explanation
Indices: 22328--22366 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
22318 TCATCATTTT
22328 AATTTTGAATAATTATTA
1 AATTTTGAATAATTATTA
*
22346 AATTATTGAATCATTATTA
1 AATT-TTGAATAATTATTA
22365 AA
1 AA
22367 CCCTAAACCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (18 bp):
AATTTTGAATAATTATTA
Found at i:26049 original size:178 final size:178
Alignment explanation
Indices: 25750--26087 Score: 534
Period size: 178 Copynumber: 1.9 Consensus size: 178
25740 TATATAAGGC
* * *
25750 TTTAGAGCGATAGTGACAAATCGTATGGTGTTACTGTTTTTCTTTTATAACGTCGTCTGGGATTT
1 TTTAGAGCGATAGTAACAAATCGTATAGTGTTACTGTTTTTCTTTTATAACATCGTCTGGGATTT
* *
25815 AAACTCTAATGAAGTATCGCATTGTTCCTCTTAATTAACAGAATATTATTAAGTTACTTAAGCTG
66 AAACTCTAACGAAGTATCACATTGTTCCTCTTAATTAACAGAATATTATTAAGTTACTTAAGCTG
25880 AAATCTAACAATTTGTTTTCACCGTTAGAGGCTTACCATTTCGTCATA
131 AAATCTAACAATTTGTTTTCACCGTTAGAGGCTTACCATTTCGTCATA
*
25928 TTTAGAGGGATAGTAACAAATCGTATAGTGTTACTGTTTTT-TCTTTATAACATCGTCTGGGATT
1 TTTAGAGCGATAGTAACAAATCGTATAGTGTTACTGTTTTTCT-TTTATAACATCGTCTGGGATT
* * * * *
25992 TAAGCTTTAACGAAGTATCACATTGTTCTTCTTAATTAATAGAATATTATTAAGTTACTTAATCT
65 TAAACTCTAACGAAGTATCACATTGTTCCTCTTAATTAACAGAATATTATTAAGTTACTTAAGCT
* * *
26057 GAGATTTAACAATTTGTTTTCATCGTTAGAG
130 GAAATCTAACAATTTGTTTTCACCGTTAGAG
26088 ACTTGTTATT
Statistics
Matches: 145, Mismatches: 14, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
177 1 0.01
178 144 0.99
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.41
Consensus pattern (178 bp):
TTTAGAGCGATAGTAACAAATCGTATAGTGTTACTGTTTTTCTTTTATAACATCGTCTGGGATTT
AAACTCTAACGAAGTATCACATTGTTCCTCTTAATTAACAGAATATTATTAAGTTACTTAAGCTG
AAATCTAACAATTTGTTTTCACCGTTAGAGGCTTACCATTTCGTCATA
Found at i:31350 original size:2 final size:2
Alignment explanation
Indices: 31345--31370 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
31335 ACGCGCGCAC
31345 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
31371 GTGAATTTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:36583 original size:32 final size:33
Alignment explanation
Indices: 36537--36599 Score: 110
Period size: 32 Copynumber: 1.9 Consensus size: 33
36527 ATGCATGTTA
*
36537 CCGATTAAATAACTTAGTTGTAAAT-ATACGAC
1 CCGATTAAAGAACTTAGTTGTAAATGATACGAC
36569 CCGATTAAAGAACTTAGTTGTAAATGATACG
1 CCGATTAAAGAACTTAGTTGTAAATGATACG
36600 CATATTTTGT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 24 0.83
33 5 0.17
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.30
Consensus pattern (33 bp):
CCGATTAAAGAACTTAGTTGTAAATGATACGAC
Found at i:42848 original size:23 final size:23
Alignment explanation
Indices: 42788--42848 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 23
42778 CACCACAGCT
* *
42788 CGTATAATTGCACCAAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* * *
42811 CGTAGAATTACACCGGAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
42834 CGTAGAATTGCACCG
1 CGTAGAATTGCACCG
42849 TATACTATAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.30, C:0.26, G:0.25, T:0.20
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:43194 original size:16 final size:16
Alignment explanation
Indices: 43169--43199 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
43159 TACGCGTAGA
*
43169 ACATATTCATATAATC
1 ACATAGTCATATAATC
43185 ACATAGTCATATAAT
1 ACATAGTCATATAAT
43200 ATTTCATATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.16, G:0.03, T:0.35
Consensus pattern (16 bp):
ACATAGTCATATAATC
Found at i:44396 original size:20 final size:21
Alignment explanation
Indices: 44341--44400 Score: 95
Period size: 22 Copynumber: 2.9 Consensus size: 21
44331 TTCGCTTGAG
*
44341 GGGTATCGATTCCCCATTGAAT
1 GGGTACCGATTCCCC-TTGAAT
44363 GGGTACCGATTCCCCTTGAAT
1 GGGTACCGATTCCCCTTGAAT
44384 GGGTACC-ATTCCCCTTG
1 GGGTACCGATTCCCCTTG
44401 CCCAGAAATC
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
20 10 0.27
21 13 0.35
22 14 0.38
ACGTcount: A:0.18, C:0.28, G:0.23, T:0.30
Consensus pattern (21 bp):
GGGTACCGATTCCCCTTGAAT
Found at i:48414 original size:2 final size:2
Alignment explanation
Indices: 48407--48437 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
48397 TCATAACCAA
48407 AT AT 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 AT AT A
48438 AAAAGCCAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.