Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000728.1 Hibiscus syriacus cultivar Beakdansim tig00001415_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: 61486
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:854 original size:34 final size:35
Alignment explanation
Indices: 811--877 Score: 118
Period size: 34 Copynumber: 1.9 Consensus size: 35
801 TAAAATATAC
*
811 AGTTTAATCTTATAAACACA-ATCTCATCTATAAT
1 AGTTTAATCTTATAAAAACACATCTCATCTATAAT
845 AGTTTAATCTTATAAAAACACATCTCATCTATA
1 AGTTTAATCTTATAAAAACACATCTCATCTATA
878 TACAAGTGTG
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 19 0.61
35 12 0.39
ACGTcount: A:0.42, C:0.18, G:0.03, T:0.37
Consensus pattern (35 bp):
AGTTTAATCTTATAAAAACACATCTCATCTATAAT
Found at i:8577 original size:51 final size:51
Alignment explanation
Indices: 8522--8636 Score: 142
Period size: 51 Copynumber: 2.3 Consensus size: 51
8512 GCTCCCTGCC
* ** * *
8522 CCGCGCTATATGCTGATTTGGC-GCCACGTGGGGTATAGCGCGTCCCCTGTA
1 CCGCGCTATACGCTGACATGGCTGACACGT-GGGTATAGCGCGCCCCCTGTA
* *
8573 CCGCGCTATACGCTGACATGGCTTACACGTGGGTATAGCGCGCCCCCTGTT
1 CCGCGCTATACGCTGACATGGCTGACACGTGGGTATAGCGCGCCCCCTGTA
*
8624 CCGCGTTATACGC
1 CCGCGCTATACGC
8637 CACGTAGGGG
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
51 50 0.91
52 5 0.09
ACGTcount: A:0.15, C:0.32, G:0.29, T:0.24
Consensus pattern (51 bp):
CCGCGCTATACGCTGACATGGCTGACACGTGGGTATAGCGCGCCCCCTGTA
Found at i:8877 original size:12 final size:13
Alignment explanation
Indices: 8857--8885 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
8847 TTCGTGCGAT
8857 TTTTCGTTATAAA
1 TTTTCGTTATAAA
8870 TTTT-GTTATAAA
1 TTTTCGTTATAAA
8882 TTTT
1 TTTT
8886 TTTTATTACA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.28, C:0.03, G:0.07, T:0.62
Consensus pattern (13 bp):
TTTTCGTTATAAA
Found at i:11767 original size:35 final size:34
Alignment explanation
Indices: 11686--11772 Score: 106
Period size: 35 Copynumber: 2.5 Consensus size: 34
11676 ATTTGGTATT
*
11686 TAAATACAACAAACTTACAATAAGAATTAAATGG
1 TAAATACAACAAAATTACAATAAGAATTAAATGG
*
11720 TAAATGATAACAAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--GA-ATTAAATGG
11758 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
11773 ACTGAAATAC
Statistics
Matches: 47, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
34 5 0.11
35 26 0.55
36 1 0.02
37 5 0.11
38 10 0.21
ACGTcount: A:0.56, C:0.09, G:0.08, T:0.26
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGAATTAAATGG
Found at i:12383 original size:18 final size:18
Alignment explanation
Indices: 12360--12412 Score: 88
Period size: 18 Copynumber: 2.9 Consensus size: 18
12350 TGGTAATGGA
12360 AAGGCTGCGACATCATAT
1 AAGGCTGCGACATCATAT
12378 AAGGCTGCGACATCATAT
1 AAGGCTGCGACATCATAT
* *
12396 ATGGCTGCGGCATCATA
1 AAGGCTGCGACATCATA
12413 AATGGTTGCG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.30, C:0.23, G:0.25, T:0.23
Consensus pattern (18 bp):
AAGGCTGCGACATCATAT
Found at i:12423 original size:18 final size:18
Alignment explanation
Indices: 12362--12422 Score: 79
Period size: 18 Copynumber: 3.4 Consensus size: 18
12352 GTAATGGAAA
12362 GGCTGCGACATCATATAA-
1 GGCTGCGACATCATA-AAT
*
12380 GGCTGCGACATCATATAT
1 GGCTGCGACATCATAAAT
*
12398 GGCTGCGGCATCATAAAT
1 GGCTGCGACATCATAAAT
*
12416 GGTTGCG
1 GGCTGCG
12423 GTGGCTGCTG
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
17 1 0.03
18 37 0.97
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (18 bp):
GGCTGCGACATCATAAAT
Found at i:25487 original size:29 final size:30
Alignment explanation
Indices: 25433--25511 Score: 108
Period size: 29 Copynumber: 2.6 Consensus size: 30
25423 GTGATCAAAA
25433 TAAAAATAATTTTAAAGTTTAGTGAATAAAT
1 TAAAAATAA-TTTAAAGTTTAGTGAATAAAT
25464 TAAAAA-AATTTAAAGTTT-GATGAATAAAT
1 TAAAAATAATTTAAAGTTTAG-TGAATAAAT
*
25493 TAAGAAATAAGTTAAAGTT
1 TAA-AAATAATTTAAAGTT
25512 CAATGAGAAA
Statistics
Matches: 44, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
28 1 0.02
29 22 0.50
30 5 0.11
31 16 0.36
ACGTcount: A:0.53, C:0.00, G:0.11, T:0.35
Consensus pattern (30 bp):
TAAAAATAATTTAAAGTTTAGTGAATAAAT
Found at i:25717 original size:15 final size:13
Alignment explanation
Indices: 25695--25731 Score: 74
Period size: 13 Copynumber: 2.8 Consensus size: 13
25685 TCCTCTGAGT
25695 TTTCTCTCTCCTC
1 TTTCTCTCTCCTC
25708 TTTCTCTCTCCTC
1 TTTCTCTCTCCTC
25721 TTTCTCTCTCC
1 TTTCTCTCTCC
25732 AGAAAGGGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54
Consensus pattern (13 bp):
TTTCTCTCTCCTC
Found at i:29807 original size:27 final size:27
Alignment explanation
Indices: 29757--29825 Score: 104
Period size: 27 Copynumber: 2.6 Consensus size: 27
29747 TTATTATAGT
*
29757 TGTTGAACGATA-TACATTTCACTTAA
1 TGTTGAACTATATTACATTTCACTTAA
*
29783 TGTTGAACTATATTACATTTGACTTAA
1 TGTTGAACTATATTACATTTCACTTAA
*
29810 TGTTGAACTACATTAC
1 TGTTGAACTATATTAC
29826 TTGAATGGTT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
26 11 0.28
27 28 0.72
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.41
Consensus pattern (27 bp):
TGTTGAACTATATTACATTTCACTTAA
Found at i:30063 original size:33 final size:33
Alignment explanation
Indices: 30019--30085 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
30009 ATTTGCGGCG
* * * * *
30019 TTTATATAAAAAATGTCGTTAAATATCATAACC
1 TTTATAGAAAAAACGCCGCTAAATATAATAACC
30052 TTTATAGAAAAAACGCCGCTAAATATAATAACC
1 TTTATAGAAAAAACGCCGCTAAATATAATAACC
30085 T
1 T
30086 ATTGCAGCGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.46, C:0.15, G:0.07, T:0.31
Consensus pattern (33 bp):
TTTATAGAAAAAACGCCGCTAAATATAATAACC
Found at i:45132 original size:17 final size:18
Alignment explanation
Indices: 45093--45139 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
45083 TGTTTTTGAG
*
45093 GGAATTGGAATCTGTGAA
1 GGAATTGAAATCTGTGAA
*
45111 GGAATTGAAATCTGT-CA
1 GGAATTGAAATCTGTGAA
*
45128 GGAATTTAAATC
1 GGAATTGAAATC
45140 AAATTCCATA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 12 0.46
18 14 0.54
ACGTcount: A:0.36, C:0.09, G:0.26, T:0.30
Consensus pattern (18 bp):
GGAATTGAAATCTGTGAA
Found at i:45793 original size:32 final size:33
Alignment explanation
Indices: 45717--45795 Score: 99
Period size: 32 Copynumber: 2.5 Consensus size: 33
45707 CCTAAACCCG
* *
45717 AACCCGACTCGACCCGAATATCACACTTAAAAA
1 AACCCGACCCGACCCAAATATCACACTTAAAAA
* *
45750 AACTCGA-CCGACCCAAATATCACACTT-TAAA
1 AACCCGACCCGACCCAAATATCACACTTAAAAA
*
45781 AACCCAACCCGACCC
1 AACCCGACCCGACCC
45796 GAACAAAATA
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
31 8 0.21
32 25 0.64
33 6 0.15
ACGTcount: A:0.41, C:0.38, G:0.08, T:0.14
Consensus pattern (33 bp):
AACCCGACCCGACCCAAATATCACACTTAAAAA
Found at i:46715 original size:42 final size:42
Alignment explanation
Indices: 46647--46758 Score: 179
Period size: 42 Copynumber: 2.7 Consensus size: 42
46637 CCTGAATTCT
* *
46647 CGTGTTTGTTTCACGTGATTCGTTTTCCGGAAAATGTTTTCC
1 CGTGTTTGTTTCACGTAATTCATTTTCCGGAAAATGTTTTCC
*
46689 CGTGTTTGTTTCACGTAATTCATTTTCTGGAAAATGTTTTCC
1 CGTGTTTGTTTCACGTAATTCATTTTCCGGAAAATGTTTTCC
* *
46731 AGTGTTTGTTTCACGTAATTGATTTTCC
1 CGTGTTTGTTTCACGTAATTCATTTTCC
46759 TGAACGTAAT
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 64 1.00
ACGTcount: A:0.17, C:0.17, G:0.19, T:0.47
Consensus pattern (42 bp):
CGTGTTTGTTTCACGTAATTCATTTTCCGGAAAATGTTTTCC
Found at i:46980 original size:31 final size:31
Alignment explanation
Indices: 46945--47058 Score: 89
Period size: 31 Copynumber: 3.8 Consensus size: 31
46935 AAATATTATT
46945 TATTA-ATTTATTAATATT-TATAATAATATAA
1 TATTATATTT-TTAATATTATATAA-AATATAA
*
46976 TATTATATTTTTAATATTATATAAAATAATCA
1 TATTATATTTTTAATATTATATAAAAT-ATAA
* * *
47008 -ATTATA-TTATAATA--ATATAAGATATTA
1 TATTATATTTTTAATATTATATAAAATATAA
* *
47035 TATT-TTTATTTTAATAATATATAA
1 TATTATAT-TTTTAATATTATATAA
47059 TAATTTTTTT
Statistics
Matches: 69, Mismatches: 6, Indels: 16
0.76 0.07 0.18
Matches are distributed among these distances:
27 4 0.06
28 11 0.16
29 7 0.10
30 7 0.10
31 28 0.41
32 12 0.17
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (31 bp):
TATTATATTTTTAATATTATATAAAATATAA
Found at i:46983 original size:22 final size:23
Alignment explanation
Indices: 46953--46996 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
46943 TTTATTAATT
46953 TATTAATATTTATAATAATATAA
1 TATTAATATTTATAATAATATAA
* *
46976 TATT-ATATTTTTAATATTATA
1 TATTAATATTTATAATAATATA
46997 TAAAATAATC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
TATTAATATTTATAATAATATAA
Found at i:47254 original size:31 final size:32
Alignment explanation
Indices: 47201--47263 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 32
47191 ATAATATTTA
47201 TAATATTTTTATTTCAATAAAATATACAAAAAT
1 TAATATTTTTATTTCAATAAAAT-TACAAAAAT
*
47234 TAATATTTTTA-TT-AATAAAATTATAAAAAT
1 TAATATTTTTATTTCAATAAAATTACAAAAAT
47264 ACTATTTAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 8 0.28
31 8 0.28
32 2 0.07
33 11 0.38
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.44
Consensus pattern (32 bp):
TAATATTTTTATTTCAATAAAATTACAAAAAT
Found at i:47307 original size:17 final size:19
Alignment explanation
Indices: 47268--47308 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
47258 AAAAATACTA
*
47268 TTTAATAATAATAAATTATT
1 TTTAATAATAATAAA-TAGT
47288 TTTAATAATAA-AAA-AGT
1 TTTAATAATAATAAATAGT
47305 TTTA
1 TTTA
47309 TGATAAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 6 0.30
19 3 0.15
20 11 0.55
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (19 bp):
TTTAATAATAATAAATAGT
Found at i:47529 original size:15 final size:15
Alignment explanation
Indices: 47509--47550 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
47499 CATTTTCCAA
47509 AATTCAAATTCCAGT
1 AATTCAAATTCCAGT
** *
47524 AATTCATTTTTCAGT
1 AATTCAAATTCCAGT
47539 AATTCAAATTCC
1 AATTCAAATTCC
47551 GAAAAACCAA
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.36, C:0.19, G:0.05, T:0.40
Consensus pattern (15 bp):
AATTCAAATTCCAGT
Found at i:47543 original size:30 final size:29
Alignment explanation
Indices: 47494--47550 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
47484 TCCAGAAATA
47494 TAATTCATTTTCCAAAATTCAAATTCCAG
1 TAATTCATTTTCCAAAATTCAAATTCCAG
* *
47523 TAATTCATTTTTCAGTAATTCAAATTCC
1 TAATTCATTTTCCA-AAATTCAAATTCC
47551 GAAAAACCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 13 0.52
30 12 0.48
ACGTcount: A:0.35, C:0.19, G:0.04, T:0.42
Consensus pattern (29 bp):
TAATTCATTTTCCAAAATTCAAATTCCAG
Found at i:49989 original size:95 final size:95
Alignment explanation
Indices: 49816--50018 Score: 370
Period size: 95 Copynumber: 2.1 Consensus size: 95
49806 TCATGTATGA
49816 AAAGTTGGTGTTAAAAAATTATTAGTTCTGATATGCTAAATGCATCTGCTTAACCCAAATACCTT
1 AAAG-TGGT-TTAAAAAATTATTAGTTCTGATATGCTAAATGCATCTGCTTAACCCAAATACCTT
49881 TATTTTTGTTTTGATCTTATCCTAATTAGGCC
64 TATTTTTGTTTTGATCTTATCCTAATTAGGCC
*
49913 AAAGTGGTTTAAAAAATTATTAGTTCTGATATGCTAAATGCATCTGCTTAATCCAAATACCTTTA
1 AAAGTGGTTTAAAAAATTATTAGTTCTGATATGCTAAATGCATCTGCTTAACCCAAATACCTTTA
49978 TTTTTGTTTTGATCTTATCCTAATTAGGCC
66 TTTTTGTTTTGATCTTATCCTAATTAGGCC
*
50008 AAAGTGATTTA
1 AAAGTGGTTTA
50019 TTATTATTAA
Statistics
Matches: 104, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
95 96 0.92
96 4 0.04
97 4 0.04
ACGTcount: A:0.31, C:0.14, G:0.13, T:0.41
Consensus pattern (95 bp):
AAAGTGGTTTAAAAAATTATTAGTTCTGATATGCTAAATGCATCTGCTTAACCCAAATACCTTTA
TTTTTGTTTTGATCTTATCCTAATTAGGCC
Done.