Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003909.1 Hibiscus syriacus cultivar Beakdansim tig00008455_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: 45937
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:1730 original size:39 final size:39
Alignment explanation
Indices: 1687--1764 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
1677 AAGTTAAAAT
*
1687 AATTTACTGCAGTTTATCCTAGGAAGTTGATCTTTCTTA
1 AATTTACTGCAGTTTATCCTAGGAAGTGGATCTTTCTTA
1726 AATTTACTGCAGTTTATCCTAGGAAGTGGATCTTTCTTA
1 AATTTACTGCAGTTTATCCTAGGAAGTGGATCTTTCTTA
1765 CCATGCAAGG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.26, C:0.15, G:0.17, T:0.42
Consensus pattern (39 bp):
AATTTACTGCAGTTTATCCTAGGAAGTGGATCTTTCTTA
Found at i:5970 original size:28 final size:28
Alignment explanation
Indices: 5939--5992 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
5929 CTGTAATCGA
5939 TGTAAACTCTTCATTCGTTTTGAATTTG
1 TGTAAACTCTTCATTCGTTTTGAATTTG
5967 TGTAAACTCTTCATTCGTTTTGAATT
1 TGTAAACTCTTCATTCGTTTTGAATT
5993 CATGTATGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.22, C:0.15, G:0.13, T:0.50
Consensus pattern (28 bp):
TGTAAACTCTTCATTCGTTTTGAATTTG
Found at i:5998 original size:28 final size:28
Alignment explanation
Indices: 5938--5998 Score: 104
Period size: 28 Copynumber: 2.2 Consensus size: 28
5928 CCTGTAATCG
*
5938 ATGTAAACTCTTCATTCGTTTTGAATTT
1 ATGTAAACTCTTCATTCGTTTTGAATTC
*
5966 GTGTAAACTCTTCATTCGTTTTGAATTC
1 ATGTAAACTCTTCATTCGTTTTGAATTC
5994 ATGTA
1 ATGTA
5999 TGAACTAGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.13, T:0.48
Consensus pattern (28 bp):
ATGTAAACTCTTCATTCGTTTTGAATTC
Found at i:13350 original size:40 final size:41
Alignment explanation
Indices: 13257--13350 Score: 97
Period size: 40 Copynumber: 2.3 Consensus size: 41
13247 CGATGTTAAA
* * * *
13257 ATTATATTATAAATAAATTGAAATGAAATTATTATTATATT
1 ATTATATTTTAAGTAAATTAAAATGAAATTATAATTATATT
13298 ATT-TACTTTTAAGT-AATTAAAAT-AAATTATCAATTA-ATT
1 ATTATA-TTTTAAGTAAATTAAAATGAAATTAT-AATTATATT
13337 GATTATATTTTAAG
1 -ATTATATTTTAAG
13351 AATGTTAATA
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
39 10 0.22
40 24 0.53
41 11 0.24
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.47
Consensus pattern (41 bp):
ATTATATTTTAAGTAAATTAAAATGAAATTATAATTATATT
Found at i:14164 original size:3 final size:3
Alignment explanation
Indices: 14120--14152 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
14110 ATGTACATTT
14120 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
14153 GTTACTAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:16133 original size:20 final size:20
Alignment explanation
Indices: 16106--16144 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
16096 ATTTTAGAAT
*
16106 AAAAATT-ATAATTTAAAAA
1 AAAAATTAAAAATTTAAAAA
16125 AAAATATTAAAAATTTAAAA
1 AAAA-ATTAAAAATTTAAAA
16145 TAAACAACGC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 3 0.18
21 10 0.59
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (20 bp):
AAAAATTAAAAATTTAAAAA
Found at i:24346 original size:14 final size:14
Alignment explanation
Indices: 24329--24373 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 14
24319 AGATTAAAAC
24329 AAAAAGATAAACAA
1 AAAAAGATAAACAA
*
24343 AAAAAGATTAAAAAA
1 AAAAAGA-TAAACAA
24358 AATAAAGATAAGACAA
1 AA-AAAGATAA-ACAA
24374 TTAAGCCAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
14 7 0.27
15 11 0.42
16 8 0.31
ACGTcount: A:0.76, C:0.04, G:0.09, T:0.11
Consensus pattern (14 bp):
AAAAAGATAAACAA
Found at i:30810 original size:15 final size:15
Alignment explanation
Indices: 30766--30810 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
30756 GGTTAGCCTT
30766 ATAATTATTAATTAA
1 ATAATTATTAATTAA
*
30781 AT-ACTA-TAA--AA
1 ATAATTATTAATTAA
30792 ATAATTATTAATTAA
1 ATAATTATTAATTAA
30807 ATAA
1 ATAA
30811 CTAATTAATC
Statistics
Matches: 24, Mismatches: 2, Indels: 8
0.71 0.06 0.24
Matches are distributed among these distances:
11 4 0.17
12 3 0.12
13 6 0.25
14 3 0.12
15 8 0.33
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (15 bp):
ATAATTATTAATTAA
Found at i:32639 original size:3 final size:3
Alignment explanation
Indices: 32631--32659 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
32621 CATAATCAAC
32631 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
32660 ACTGCGAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:39957 original size:21 final size:20
Alignment explanation
Indices: 39911--39957 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
39901 TAAGTGTAAA
*
39911 TATAATTTAAATGCTATGTT
1 TATAATTTAAATGCTATGTC
*
39931 TTTAATTTAGAATG-TAATGTC
1 TATAATTTA-AATGCT-ATGTC
39952 TATAAT
1 TATAAT
39958 AGACATTATA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 9 0.41
21 13 0.59
ACGTcount: A:0.36, C:0.04, G:0.11, T:0.49
Consensus pattern (20 bp):
TATAATTTAAATGCTATGTC
Found at i:40057 original size:13 final size:13
Alignment explanation
Indices: 40041--40065 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40031 TTTTATACAA
40041 CACTTTTCAAAAT
1 CACTTTTCAAAAT
40054 CACTTTTCAAAA
1 CACTTTTCAAAA
40066 AGTGCGCTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.24, G:0.00, T:0.36
Consensus pattern (13 bp):
CACTTTTCAAAAT
Found at i:40488 original size:18 final size:19
Alignment explanation
Indices: 40467--40507 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
40457 TATCTTAACC
*
40467 TAAATTCACATATTAA-AT
1 TAAATTAACATATTAACAT
*
40485 TAAATTAACATCTTAACAT
1 TAAATTAACATATTAACAT
40504 TAAA
1 TAAA
40508 CTATATATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATTAACATATTAACAT
Found at i:40551 original size:28 final size:28
Alignment explanation
Indices: 40510--40621 Score: 95
Period size: 28 Copynumber: 4.0 Consensus size: 28
40500 ACATTAAACT
40510 ATATATTTTATTCTTATCATAACTTAAAA
1 ATATA-TTTATTCTTATCATAACTTAAAA
** *
40539 ATATATTTATTCTTATTTTAACCTAAAA
1 ATATATTTATTCTTATCATAACTTAAAA
* * *
40567 ATATATATATT-TT-TTATTAATTTTAAAA
1 ATATATTTATTCTTATCA-TAA-CTTAAAA
* *
40595 A-ATAATTTATTCTTACCTTAACTTAAA
1 ATAT-ATTTATTCTTATCATAACTTAAA
40622 TATTTATATT
Statistics
Matches: 66, Mismatches: 12, Indels: 11
0.74 0.13 0.12
Matches are distributed among these distances:
26 2 0.03
27 7 0.11
28 47 0.71
29 10 0.15
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (28 bp):
ATATATTTATTCTTATCATAACTTAAAA
Found at i:40764 original size:32 final size:31
Alignment explanation
Indices: 40645--40766 Score: 124
Period size: 31 Copynumber: 4.0 Consensus size: 31
40635 TTCCTATAAT
* * * *
40645 ATATTAAAATTAAGATAAAAATAAAACATA-
1 ATATTTAAATAAAAATAAAAATAAAATATAC
*
40675 AT-TTTAAAT-TAAATCAAAAATAAAATATAC
1 ATATTTAAATAAAAAT-AAAAATAAAATATAC
* *
40705 ATTTTTAAATAAAAATAAAAATGAAATATAC
1 ATATTTAAATAAAAATAAAAATAAAATATAC
* *
40736 ATATTTAATTTAAAAATAAGAATAAAATATA
1 ATATTTAA-ATAAAAATAAAAATAAAATATA
40767 TATTTCACGT
Statistics
Matches: 77, Mismatches: 10, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
28 3 0.04
29 19 0.25
30 4 0.05
31 28 0.36
32 23 0.30
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.32
Consensus pattern (31 bp):
ATATTTAAATAAAAATAAAAATAAAATATAC
Found at i:40989 original size:29 final size:29
Alignment explanation
Indices: 40654--41009 Score: 176
Period size: 30 Copynumber: 11.8 Consensus size: 29
40644 TATATTAAAA
* * *
40654 TTAAGATAAAAATAAAACATAATTTTAAA
1 TTAAGATAAAAATAAAATATATTTTTAAG
*
40683 TTAA-ATCAAAAATAAAATATACATTTTTAAA
1 TTAAGAT-AAAAATAAAATAT--ATTTTTAAG
* * * * *
40714 TAAAAATAAAAATGAAATATACATATTTAAT
1 TTAAGATAAAAAT-AAA-ATATATTTTTAAG
* * * *
40745 TTAAAAATAAGAATAAAATATATATTTCACG
1 TT-AAGATAAAAATAAAATATAT-TTTTAAG
* ** * * *
40776 TTAAAATAAGGATAAATTATATTTAATAAT
1 TTAAGATAAAAATAAAATATATTT-TTAAG
* ** * * *
40806 TTAAGGTATGACTATAATATATTTAATAAG
1 TTAAGATAAAAATAAAATATATTT-TTAAG
* ***
40836 TTAAGTTAAGAACATAATAATATATGTAACAAG
1 TTAAGATAA-AA-ATAA-AATATAT-TTTTAAG
* * * *
40869 TTAAAATAAAAATAAGATATACTTTTCAAAT
1 TTAAGATAAAAATAAAATATA-TTTT-TAAG
40900 TTAAGATAAAAATAAAATATATTTTTAAG
1 TTAAGATAAAAATAAAATATATTTTTAAG
* * * *
40929 TTAGGATAAGATTAGAATATA-TTTTAAG
1 TTAAGATAAAAATAAAATATATTTTTAAG
* * *
40957 TTAAAATAAAAATAAAATGTATTTTTAAC
1 TTAAGATAAAAATAAAATATATTTTTAAG
* * *
40986 TTAAGACAAGAATAAAATAGATTT
1 TTAAGATAAAAATAAAATATATTT
41010 AATAATTCAA
Statistics
Matches: 250, Mismatches: 61, Indels: 32
0.73 0.18 0.09
Matches are distributed among these distances:
28 24 0.10
29 62 0.25
30 63 0.25
31 60 0.24
32 19 0.08
33 21 0.08
34 1 0.00
ACGTcount: A:0.54, C:0.04, G:0.07, T:0.35
Consensus pattern (29 bp):
TTAAGATAAAAATAAAATATATTTTTAAG
Done.