Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008635.1 Hibiscus syriacus cultivar Beakdansim tig00111608_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: 48809
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Found at i:1679 original size:21 final size:21
Alignment explanation
Indices: 1649--1697 Score: 64
Period size: 23 Copynumber: 2.3 Consensus size: 21
1639 GAGGAATCTA
1649 TCCCCCTTG-AGGGAACCGAT
1 TCCCCCTTGAAGGGAACCGAT
*
1669 TCCCCCTTTGAAAGGGAATCGAT
1 TCCCCC-TTG-AAGGGAACCGAT
1692 TCCCCC
1 TCCCCC
1698 CACAGGGGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 6 0.24
21 3 0.12
23 16 0.64
ACGTcount: A:0.20, C:0.37, G:0.20, T:0.22
Consensus pattern (21 bp):
TCCCCCTTGAAGGGAACCGAT
Found at i:6028 original size:93 final size:91
Alignment explanation
Indices: 5870--6038 Score: 250
Period size: 93 Copynumber: 1.8 Consensus size: 91
5860 ACATATAGCC
* *
5870 TTTTTCCTTATGATTCTAGTAAGTGTACTAAAAAAGACCCAACATTTTTCATAGAATGTGGCTAA
1 TTTTTCCTCATGATTCTAGTAAGTGTACTAAAAAAGACCCAACATTTTTCATAGAATGTGACTAA
5935 TCCTTCTCACTTATATATACATATCA
66 TCCTTCTCACTTATATATACATATCA
** **
5961 TTTTTCCTCATGATTCTAGTAAGTGTACTACAAAAATGGTCCATTATTTTTCATAGAA-GATGAC
1 TTTTTCCTCATGATTCTAGTAAGTGTACTA-AAAAA-GACCCAACATTTTTCATAGAATG-TGAC
6025 TAATCCTTCTCACT
63 TAATCCTTCTCACT
6039 CATGTAGATT
Statistics
Matches: 69, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
91 29 0.42
92 6 0.09
93 34 0.49
ACGTcount: A:0.31, C:0.19, G:0.11, T:0.39
Consensus pattern (91 bp):
TTTTTCCTCATGATTCTAGTAAGTGTACTAAAAAAGACCCAACATTTTTCATAGAATGTGACTAA
TCCTTCTCACTTATATATACATATCA
Found at i:11388 original size:23 final size:23
Alignment explanation
Indices: 11356--11399 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
11346 ATGGTAGCAA
*
11356 ATGGATATGTCGTGGCAAATTGG
1 ATGGAAATGTCGTGGCAAATTGG
*
11379 ATGGAAATGTCTTGGCAAATT
1 ATGGAAATGTCGTGGCAAATT
11400 AAATTGTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.30, C:0.09, G:0.30, T:0.32
Consensus pattern (23 bp):
ATGGAAATGTCGTGGCAAATTGG
Found at i:12928 original size:19 final size:20
Alignment explanation
Indices: 12889--12930 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
12879 ATTTTACCAC
*
12889 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGCGCCTAA
*
12909 ATGCATCTATATG-GCCTAA
1 ATGCAACTATATGCGCCTAA
12928 ATG
1 ATG
12931 AGCTCTTAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.33, C:0.21, G:0.14, T:0.31
Consensus pattern (20 bp):
ATGCAACTATATGCGCCTAA
Found at i:13940 original size:18 final size:18
Alignment explanation
Indices: 13917--13966 Score: 91
Period size: 18 Copynumber: 2.8 Consensus size: 18
13907 CACTATGAAG
13917 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
13935 TGTCCCGAAGGACCACTG
1 TGTCCCGAAGGACCACTA
13953 TGTCCCGAAGGACC
1 TGTCCCGAAGGACC
13967 GCGTAGACCC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.24, C:0.34, G:0.26, T:0.16
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:14766 original size:24 final size:20
Alignment explanation
Indices: 14713--14770 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 20
14703 TTCCTCTTGA
*
14713 AGTGCATCGATACATTCTAC
1 AGTGCATCGATGCATTCTAC
14733 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC--T-AC
14756 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
14771 CTACCCATGC
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:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:14845 original size:64 final size:63
Alignment explanation
Indices: 14758--14918 Score: 184
Period size: 64 Copynumber: 2.5 Consensus size: 63
14748 TCTTTAACAT
* *
14758 GTGCATCGATGCACTACCCATGCATCGATACACCAATCAT-ATTCGATGTTTTCATTT-TAAGGG
1 GTGCATCGATGCACT-CCTATGCATCGATACACCAA-CATCATTCGATGTTTCCATTTCTAAGGG
* * * *
14821 GATGCATCGATGCACTCCTTATGCATCGATGCA-CTACCTGCATTCGATGTTTCCATTTCTAATG
1 G-TGCATCGATGCACTCC-TATGCATCGATACACCAACAT-CATTCGATGTTTCCATTTCTAAGG
14885 G
63 G
*
14886 GTGCATCGATGCACTTCCTGTGCATCGATACAC
1 GTGCATCGATGCAC-TCCTATGCATCGATACAC
14919 ACTGAACAAT
Statistics
Matches: 83, Mismatches: 8, Indels: 12
0.81 0.08 0.12
Matches are distributed among these distances:
62 2 0.02
63 5 0.06
64 67 0.81
65 9 0.11
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.32
Consensus pattern (63 bp):
GTGCATCGATGCACTCCTATGCATCGATACACCAACATCATTCGATGTTTCCATTTCTAAGGG
Found at i:16340 original size:55 final size:55
Alignment explanation
Indices: 16275--16474 Score: 346
Period size: 55 Copynumber: 3.6 Consensus size: 55
16265 CATGCTTGGG
* * * * *
16275 GGGTATCGATACACTCCTCAGTGTACCAATATACAAATAGCACTCGATGTTTTGA
1 GGGTATCGATACACTCCTCAGTGTACCGATACACAAATGGAATTCGATGTTTTGA
16330 GGGTATCGATACACTCCTCAGTGTACCGATACACAAATGGAATTCGATGTTTTGA
1 GGGTATCGATACACTCCTCAGTGTACCGATACACAAATGGAATTCGATGTTTTGA
16385 GGGTATCGATACACTCCTCAGTGTACCGATACACAAATGGAATTCGATGTTTTGA
1 GGGTATCGATACACTCCTCAGTGTACCGATACACAAATGGAATTCGATGTTTTGA
*
16440 GGATATCGATACACTCCTCAGTGTACCGATACACA
1 GGGTATCGATACACTCCTCAGTGTACCGATACACA
16475 CTCAAACAAT
Statistics
Matches: 139, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 139 1.00
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.28
Consensus pattern (55 bp):
GGGTATCGATACACTCCTCAGTGTACCGATACACAAATGGAATTCGATGTTTTGA
Found at i:21940 original size:13 final size:13
Alignment explanation
Indices: 21922--21951 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
21912 AATTACAAAA
21922 TTAAAGAATCAAG
1 TTAAAGAATCAAG
*
21935 TTAAAGAATCAAT
1 TTAAAGAATCAAG
21948 TTAA
1 TTAA
21952 TTAAAAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.53, C:0.07, G:0.10, T:0.30
Consensus pattern (13 bp):
TTAAAGAATCAAG
Found at i:32513 original size:19 final size:19
Alignment explanation
Indices: 32474--32514 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
32464 ACGATAGAAT
*
32474 AAAGTAAAATCTTATTACG
1 AAAGTAAAATCTTATAACG
32493 AAAGTAAAAT-TTATAATCG
1 AAAGTAAAATCTTATAA-CG
32512 AAA
1 AAA
32515 CTTTTATTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.54, C:0.07, G:0.10, T:0.29
Consensus pattern (19 bp):
AAAGTAAAATCTTATAACG
Found at i:40076 original size:178 final size:178
Alignment explanation
Indices: 39777--40311 Score: 1043
Period size: 178 Copynumber: 3.0 Consensus size: 178
39767 AATGTTAAAA
*
39777 ACTTATCCAAGAAATTCGAACAAAAAATCGGTACGAACAGATCTGACTGCACCGGTAAACGAACC
1 ACTTATCCAAGAAACTCGAACAAAAAATCGGTACGAACAGATCTGACTGCACCGGTAAACGAACC
*
39842 ATAACATGGGATGAAATTATTGAAAGACCACCGACAATTGCAAATTAGAATCAAATTTCGTGAGA
66 ATAACATGGGATGAAATTATTGAAAGACCACCGACAATTGCAAATTATAATCAAATTTCGTGAGA
39907 CAATTATCTTCAAATTTAAAACACGTGTTCAAATCCGATAGGAGCAGG
131 CAATTATCTTCAAATTTAAAACACGTGTTCAAATCCGATAGGAGCAGG
39955 ACTTATCCAAGAAACTCGAACAAAAAATCGGTACGAACAGATCTGACTGCACCGGTAAACGAACC
1 ACTTATCCAAGAAACTCGAACAAAAAATCGGTACGAACAGATCTGACTGCACCGGTAAACGAACC
40020 ATAACATGGGATGAAATTATTGAAAGACCACCGACAATTGCAAATTATAATCAAATTTCGTGAGA
66 ATAACATGGGATGAAATTATTGAAAGACCACCGACAATTGCAAATTATAATCAAATTTCGTGAGA
40085 CAATTATCTTCAAATTTAAAACACGTGTTCAAATCCGATAGGAGCAGG
131 CAATTATCTTCAAATTTAAAACACGTGTTCAAATCCGATAGGAGCAGG
*
40133 ACTTATCCAAGAAACTCGAACAAAAAATCGGTACGAACAGATCTGACTGTACCGGTAAACGAACC
1 ACTTATCCAAGAAACTCGAACAAAAAATCGGTACGAACAGATCTGACTGCACCGGTAAACGAACC
40198 ATAACATGGGATGAAATTATTGAAAGACCACCGACAATTGCAAATTATAATCAAATTTCGTGAGA
66 ATAACATGGGATGAAATTATTGAAAGACCACCGACAATTGCAAATTATAATCAAATTTCGTGAGA
40263 CAATTATCTTCAAATTTAAAACACGTGTTCAAATCCGATAGGAGCAGG
131 CAATTATCTTCAAATTTAAAACACGTGTTCAAATCCGATAGGAGCAGG
40311 A
1 A
40312 TAAATCAACA
Statistics
Matches: 354, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
178 354 1.00
ACGTcount: A:0.41, C:0.19, G:0.17, T:0.23
Consensus pattern (178 bp):
ACTTATCCAAGAAACTCGAACAAAAAATCGGTACGAACAGATCTGACTGCACCGGTAAACGAACC
ATAACATGGGATGAAATTATTGAAAGACCACCGACAATTGCAAATTATAATCAAATTTCGTGAGA
CAATTATCTTCAAATTTAAAACACGTGTTCAAATCCGATAGGAGCAGG
Found at i:43354 original size:2 final size:2
Alignment explanation
Indices: 43290--43336 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
43280 TGTCAAAAAT
43290 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
43332 TA TA T
1 TA TA T
43337 CCACCTTCAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:48280 original size:18 final size:18
Alignment explanation
Indices: 48257--48295 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
48247 GAAAATTTTT
48257 ATAGAAAATATC-ATAGTG
1 ATAG-AAATATCAATAGTG
48275 ATAGAAATATCAATAGTG
1 ATAGAAATATCAATAGTG
48293 ATA
1 ATA
48296 TTTTTATCGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.51, C:0.05, G:0.15, T:0.28
Consensus pattern (18 bp):
ATAGAAATATCAATAGTG
Done.