Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003748.1 Hibiscus syriacus cultivar Beakdansim tig00008024_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: 73290
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:4000 original size:20 final size:20
Alignment explanation
Indices: 3940--4000 Score: 50
Period size: 20 Copynumber: 3.0 Consensus size: 20
3930 TAGAATTAGG
* *
3940 GTTTATGGTTCATAGATTATAT
1 GTTTATGATTTATA-ATT-TAT
* ***
3962 GGTTATGATTTAGGGTTTAT
1 GTTTATGATTTATAATTTAT
3982 GTTTATGATTTATAATTTA
1 GTTTATGATTTATAATTTA
4001 GGGTTTTAAG
Statistics
Matches: 29, Mismatches: 10, Indels: 2
0.71 0.24 0.05
Matches are distributed among these distances:
20 18 0.62
21 2 0.07
22 9 0.31
ACGTcount: A:0.26, C:0.02, G:0.20, T:0.52
Consensus pattern (20 bp):
GTTTATGATTTATAATTTAT
Found at i:15529 original size:3 final size:3
Alignment explanation
Indices: 15521--15581 Score: 122
Period size: 3 Copynumber: 20.3 Consensus size: 3
15511 ATGTGGACTG
15521 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
15569 ATA ATA ATA ATA A
1 ATA ATA ATA ATA A
15582 GGGTGAACTA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:16012 original size:48 final size:48
Alignment explanation
Indices: 15917--16013 Score: 131
Period size: 48 Copynumber: 2.0 Consensus size: 48
15907 ATATCGGTCG
* * * * *
15917 CCTCCTGTTGTCTTGGTCTGTTGCTGAACCACTTGGCGGCTGTTGCTT
1 CCTCATGTTGTCTTGGTCTATTGCTGAACCACTTGGAGACTGCTGCTT
* *
15965 CCTCATGTTGTCTTGGTCTATTGCTGAACTACTTGGAGATTGCTGCTT
1 CCTCATGTTGTCTTGGTCTATTGCTGAACCACTTGGAGACTGCTGCTT
16013 C
1 C
16014 TTGGCCTTGG
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
48 42 1.00
ACGTcount: A:0.10, C:0.25, G:0.25, T:0.40
Consensus pattern (48 bp):
CCTCATGTTGTCTTGGTCTATTGCTGAACCACTTGGAGACTGCTGCTT
Found at i:22303 original size:3 final size:3
Alignment explanation
Indices: 22290--22328 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
22280 GGATTATGAG
* *
22290 AGA ATA AGA AGA AGA AGA AGA AGA AGAA AGA AGG AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AG-A AGA AGA AGA AG
22329 GGTCAACGGG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.64, C:0.00, G:0.33, T:0.03
Consensus pattern (3 bp):
AGA
Found at i:25773 original size:60 final size:60
Alignment explanation
Indices: 25702--25829 Score: 148
Period size: 60 Copynumber: 2.1 Consensus size: 60
25692 TATATAATGA
* * * * * * * *
25702 ATAATCGAGTGACCATTTTATAATTTTTAATAGTTAAGAGATTCAATAAAGTAATATTCT
1 ATAATCAAGTGACAATTTTATAACTTTTAATAATCAAGAAATTCAATAAAATAATATTAT
* * *
25762 ATAATCAAGTGATAATTTTATAACTTTTAATAATCAATAAATTTAATAAAATAATATTAT
1 ATAATCAAGTGACAATTTTATAACTTTTAATAATCAAGAAATTCAATAAAATAATATTAT
*
25822 ATAGTCAA
1 ATAATCAA
25830 AGGGTTATTT
Statistics
Matches: 56, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
60 56 1.00
ACGTcount: A:0.45, C:0.07, G:0.08, T:0.40
Consensus pattern (60 bp):
ATAATCAAGTGACAATTTTATAACTTTTAATAATCAAGAAATTCAATAAAATAATATTAT
Found at i:26859 original size:13 final size:13
Alignment explanation
Indices: 26841--26866 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
26831 TAAACTCTAA
26841 ATTAGGGTTTATG
1 ATTAGGGTTTATG
26854 ATTAGGGTTTATG
1 ATTAGGGTTTATG
26867 GTCTAGATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.00, G:0.31, T:0.46
Consensus pattern (13 bp):
ATTAGGGTTTATG
Found at i:27359 original size:2 final size:2
Alignment explanation
Indices: 27352--27394 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
27342 ATTATTCTTT
27352 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
27394 T
1 T
27395 TAATTTGACA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:28507 original size:18 final size:16
Alignment explanation
Indices: 28485--28534 Score: 66
Period size: 18 Copynumber: 3.1 Consensus size: 16
28475 TCACGGAATG
28485 TAAGATTACCTGGGAA
1 TAAGATTACCTGGGAA
*
28501 TAAAAGATTACCAGGGAA
1 T--AAGATTACCTGGGAA
28519 TAAGATTA-CTGGGAA
1 TAAGATTACCTGGGAA
28534 T
1 T
28535 GTTGTATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
15 7 0.23
16 8 0.27
18 15 0.50
ACGTcount: A:0.42, C:0.10, G:0.24, T:0.24
Consensus pattern (16 bp):
TAAGATTACCTGGGAA
Found at i:30421 original size:18 final size:18
Alignment explanation
Indices: 30398--30433 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
30388 CAATTTTTTT
30398 TATAAAAATTAAGAAAAA
1 TATAAAAATTAAGAAAAA
*
30416 TATAAATATTAAGAAAAA
1 TATAAAAATTAAGAAAAA
30434 GGAAAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.25
Consensus pattern (18 bp):
TATAAAAATTAAGAAAAA
Found at i:47006 original size:2 final size:2
Alignment explanation
Indices: 47001--47060 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
46991 CTCTCAAATA
47001 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
47043 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
47061 TAATAACTCA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:51186 original size:18 final size:18
Alignment explanation
Indices: 51163--51199 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
51153 ACAGTGATGC
51163 TGATATTTGACTTTTATA
1 TGATATTTGACTTTTATA
51181 TGATATTTGACTTTTATA
1 TGATATTTGACTTTTATA
51199 T
1 T
51200 ACCAATAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.27, C:0.05, G:0.11, T:0.57
Consensus pattern (18 bp):
TGATATTTGACTTTTATA
Found at i:59689 original size:2 final size:2
Alignment explanation
Indices: 59682--59706 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
59672 CATCATCATC
59682 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 A
59707 GAGAGAGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:59711 original size:2 final size:2
Alignment explanation
Indices: 59706--59734 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
59696 ATATATATAT
59706 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
59735 ATTAAAATCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:61731 original size:4 final size:4
Alignment explanation
Indices: 61724--61753 Score: 51
Period size: 4 Copynumber: 7.2 Consensus size: 4
61714 GTGAGAGAGA
61724 ACAT ACAT ACAT ACAT ACAT ACAT AACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT -ACAT A
61754 TATATATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 21 0.84
5 4 0.16
ACGTcount: A:0.53, C:0.23, G:0.00, T:0.23
Consensus pattern (4 bp):
ACAT
Found at i:66522 original size:26 final size:26
Alignment explanation
Indices: 66486--66538 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
66476 ATATATTCAA
66486 TATATGTTCTAAATACCCTCAACTAT
1 TATATGTTCTAAATACCCTCAACTAT
66512 TATATGTTCTAAATACCCTCAACTAT
1 TATATGTTCTAAATACCCTCAACTAT
66538 T
1 T
66539 TGACAATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.34, C:0.23, G:0.04, T:0.40
Consensus pattern (26 bp):
TATATGTTCTAAATACCCTCAACTAT
Found at i:72099 original size:28 final size:28
Alignment explanation
Indices: 72059--72114 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
72049 AGTGTTGGGC
72059 GTAGGTCGCCATGC-CTTCCGGGCGACCT
1 GTAGGTCGCCATGCAC-TCCGGGCGACCT
72087 GTAGGTCGCCATGCACTCCGGGCGACCT
1 GTAGGTCGCCATGCACTCCGGGCGACCT
72115 ACCCTTGCTC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 26 0.96
29 1 0.04
ACGTcount: A:0.12, C:0.36, G:0.32, T:0.20
Consensus pattern (28 bp):
GTAGGTCGCCATGCACTCCGGGCGACCT
Done.