Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006918.1 Hibiscus syriacus cultivar Beakdansim tig00017734_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: 58741
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:12271 original size:27 final size:27
Alignment explanation
Indices: 12224--12276 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
12214 ATTAAAAATG
* *
12224 AAAAAGAAAAGGAAAGAAAAATGAGGA
1 AAAAAGAAAAAGAAAGAAAAAAGAGGA
*
12251 AAAAAGAAAAATAAA-ATAAAAAGAGG
1 AAAAAGAAAAAGAAAGA-AAAAAGAGG
12277 GTTTAAGATG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 1 0.05
27 21 0.95
ACGTcount: A:0.74, C:0.00, G:0.21, T:0.06
Consensus pattern (27 bp):
AAAAAGAAAAAGAAAGAAAAAAGAGGA
Found at i:13708 original size:111 final size:111
Alignment explanation
Indices: 13503--13821 Score: 444
Period size: 111 Copynumber: 2.9 Consensus size: 111
13493 GTGACAGCGG
* *
13503 AATGAATCAACTCCTCCAGATCTGATATTCCCTTAGAAGAAGTGAAACAGATCAC-CATATTCCA
1 AATGGATCAACTCCTCCAGATCTGATATTCCCTTAGAAGAAGTGGAACAGATCACTC-TATTCCA
* *
13567 AGATTTGATATTCCCTGAGTAACAGCAGAACAAGTCTACCCCGATTC
65 AGATTTGATATTCCCTGAGTGACAGTAGAACAAGTCTACCCCGATTC
** *
13614 AATGGATTGACTCCTCCAGATCTGATATTCCCTTAGAAGAAGTGGAACATATCACTCTATTCCAA
1 AATGGATCAACTCCTCCAGATCTGATATTCCCTTAGAAGAAGTGGAACAGATCACTCTATTCCAA
*
13679 GATTTGATATTCCCTGAGTGACAGTAGAACAAGTCTACCCTGATTC
66 GATTTGATATTCCCTGAGTGACAGTAGAACAAGTCTACCCCGATTC
* * * * * *
13725 AATGGATCAACTCCCCCAAATATGATATTCCCTTTAGAAGAAGCGGAACAGATCCCTCTCATCCC
1 AATGGATCAACTCCTCCAGATCTGATATTCCC-TTAGAAGAAGTGGAACAGATCACTCT-ATTCC
* *
13790 CAGATTTGATA-TCCCTTGAGTGACAGTGGAAC
64 AAGATTTGATATTCCC-TGAGTGACAGTAGAAC
13822 TGATCATTTA
Statistics
Matches: 185, Mismatches: 19, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
111 128 0.69
112 28 0.15
113 29 0.16
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.27
Consensus pattern (111 bp):
AATGGATCAACTCCTCCAGATCTGATATTCCCTTAGAAGAAGTGGAACAGATCACTCTATTCCAA
GATTTGATATTCCCTGAGTGACAGTAGAACAAGTCTACCCCGATTC
Found at i:13954 original size:3 final size:3
Alignment explanation
Indices: 13946--13994 Score: 80
Period size: 3 Copynumber: 15.7 Consensus size: 3
13936 TTTCGTCCCG
13946 TTA TTA TTAA GTTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TT-A -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
13993 TT
1 TT
13995 TAAGATTACT
Statistics
Matches: 44, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
3 40 0.91
4 2 0.05
5 2 0.05
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:14563 original size:2 final size:2
Alignment explanation
Indices: 14556--14587 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
14546 TTTGCATACA
14556 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
14588 GCGAGTCTAA
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:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:15501 original size:2 final size:2
Alignment explanation
Indices: 15494--15780 Score: 214
Period size: 2 Copynumber: 150.5 Consensus size: 2
15484 TTTTGTAAGG
* *
15494 AT AT AT AT AT AT AT AT AT -T AT A- AT AT TT A- AGT GT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT
15533 AT AT 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 AT AT
* * * * *
15575 AT AT AT AT AT AGT AT GT AG A- AT GT AT AT TT AT -T TT AT -T AT
1 AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
** * * *
15615 CC AT AT -T AT GT A- AT AT AT AT A- AT AT AGC AT AT AT A- AC AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT
** * * * * *
15654 GC GT A- AC ACT -T AT AT GT AT AT AT -T AT A- AT -T AT TT TT AT
1 AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
15692 -T A- AT TT AC AT AA 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 AT AT
15732 AT AT 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 AT AT
15774 AT AT AT A
1 AT AT AT A
15781 AAATTTATGC
Statistics
Matches: 227, Mismatches: 36, Indels: 44
0.74 0.12 0.14
Matches are distributed among these distances:
1 18 0.08
2 206 0.91
3 3 0.01
ACGTcount: A:0.45, C:0.03, G:0.04, T:0.48
Consensus pattern (2 bp):
AT
Found at i:17637 original size:13 final size:13
Alignment explanation
Indices: 17621--17652 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
17611 CAAAAAAAAA
17621 ACAAAAAAGGCAC
1 ACAAAAAAGGCAC
17634 ACAAAAAAGGCAC
1 ACAAAAAAGGCAC
17647 A-AAAAA
1 ACAAAAA
17653 CAAAAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 5 0.26
13 14 0.74
ACGTcount: A:0.69, C:0.19, G:0.12, T:0.00
Consensus pattern (13 bp):
ACAAAAAAGGCAC
Found at i:25505 original size:24 final size:20
Alignment explanation
Indices: 25456--25513 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 20
25446 TTCCCATTGA
*
25456 AGTGCATCGGTGCATTCTAC
1 AGTGCATCGATGCATTCTAC
25476 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC--T-AC
25499 AGGTGCATCGATGCA
1 A-GTGCATCGATGCA
25514 CTACCATGCA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 16 0.48
22 1 0.03
23 3 0.09
24 13 0.39
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.29
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:27626 original size:15 final size:15
Alignment explanation
Indices: 27603--27678 Score: 59
Period size: 15 Copynumber: 5.1 Consensus size: 15
27593 ATGATTATGC
*
27603 ATAACGTCACCATAT
1 ATAATGTCACCATAT
27618 ATAATGTCACCA-AT
1 ATAATGTCACCATAT
* * **
27632 ATAGTGGCAAAACTA-
1 ATAATGTCACCA-TAT
*
27647 AAAATTGTCACCATAT
1 ATAA-TGTCACCATAT
27663 ATAATGTCACCA-AT
1 ATAATGTCACCATAT
27677 AT
1 AT
27679 CGTTTTGTTC
Statistics
Matches: 46, Mismatches: 11, Indels: 9
0.70 0.17 0.14
Matches are distributed among these distances:
14 14 0.30
15 23 0.50
16 9 0.20
ACGTcount: A:0.43, C:0.20, G:0.09, T:0.28
Consensus pattern (15 bp):
ATAATGTCACCATAT
Found at i:34831 original size:7 final size:7
Alignment explanation
Indices: 34819--34848 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
34809 GCTTTAAGTT
34819 TGCCGTG
1 TGCCGTG
34826 TGCCGTG
1 TGCCGTG
34833 TGCCGTG
1 TGCCGTG
*
34840 TGCCATG
1 TGCCGTG
34847 TG
1 TG
34849 TCTATGCAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.03, C:0.27, G:0.40, T:0.30
Consensus pattern (7 bp):
TGCCGTG
Found at i:49223 original size:27 final size:27
Alignment explanation
Indices: 49185--49238 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
49175 TTTGATTGTG
** *
49185 AATGACATTGTCGTGGCAAGTAGAGTT
1 AATGACATTGTCGCAGCAAGTAAAGTT
49212 AATGACATTGTCGCAGCAAGTAAAGTT
1 AATGACATTGTCGCAGCAAGTAAAGTT
49239 GCCAAGACAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (27 bp):
AATGACATTGTCGCAGCAAGTAAAGTT
Found at i:52116 original size:19 final size:19
Alignment explanation
Indices: 52094--52148 Score: 65
Period size: 19 Copynumber: 2.9 Consensus size: 19
52084 CTAATTAACC
* *
52094 TGACTTAACCCATTGACTT
1 TGACCTAACCCGTTGACTT
* *
52113 TGACCCAACTCGTTGACTT
1 TGACCTAACCCGTTGACTT
*
52132 TGACCTGACCCGTTGAC
1 TGACCTAACCCGTTGAC
52149 CGTTGACTTA
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.22, C:0.31, G:0.16, T:0.31
Consensus pattern (19 bp):
TGACCTAACCCGTTGACTT
Found at i:53351 original size:15 final size:16
Alignment explanation
Indices: 53321--53351 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
53311 GTTCATAAGC
53321 CAGTAAATCAATAAAT
1 CAGTAAATCAATAAAT
53337 CAGTAAATC-ATAAAT
1 CAGTAAATCAATAAAT
53352 TTTTGTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.55, C:0.13, G:0.06, T:0.26
Consensus pattern (16 bp):
CAGTAAATCAATAAAT
Found at i:53523 original size:4 final size:4
Alignment explanation
Indices: 53509--53549 Score: 55
Period size: 4 Copynumber: 10.2 Consensus size: 4
53499 ATTTAGAGTG
* * *
53509 TGTA CGTA TGTA TGTA TGTA TGTA TGTA TGAA TGCA TGTA T
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA T
53550 CAAGTTTAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.27, C:0.05, G:0.24, T:0.44
Consensus pattern (4 bp):
TGTA
Done.