Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001417.1 Hibiscus syriacus cultivar Beakdansim tig00002754_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: 68089
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Found at i:3237 original size:14 final size:14
Alignment explanation
Indices: 3218--3247 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3208 CAAAAAAATA
*
3218 AAAATTAAATTTTT
1 AAAATTAAATTATT
3232 AAAATTAAATTATT
1 AAAATTAAATTATT
3246 AA
1 AA
3248 TAATATTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
AAAATTAAATTATT
Found at i:11112 original size:2 final size:2
Alignment explanation
Indices: 11105--11133 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
11095 ATTCTACCTC
11105 AT AT 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 AT AT A
11134 CAGACACACA
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:11850 original size:185 final size:186
Alignment explanation
Indices: 11488--11878 Score: 583
Period size: 185 Copynumber: 2.1 Consensus size: 186
11478 ATTAAATTTT
** **
11488 AAATATTAAATATATTATATATAACATATGGACTCGGCCCAAAACATTTAAAATTCAATTAATAA
1 AAATATTAAATATATTATATATAACATATGGACTAAGCCCAAAACATTTAAAACCCAATTAATAA
*
11553 TTTAAGATATAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATAAAATTT
66 TTTAAGATACAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATAAAATTT
*
11618 TTATTTTATAATTATATATTATTTAAATTAATTGTAAACTGTTTTTTT-AATTAAA
131 TTATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTTTGAATTAAA
* * *
11673 AAATATTAAATATATTATATATAACATATGGGCTAAGTCCAAACCATTTAAAACCCAATTAATAA
1 AAATATTAAATATATTATATATAACATATGGACTAAGCCCAAAACATTTAAAACCCAATTAATAA
* * * * *
11738 TTTAAGATCCAATAA-TTTTAAAACCTATATCAATATTAATTAATTAAAAAACTTTATCTGAAAT
66 TTTAAGATACAATAACTTTT-AAACCTAAATCAATATTAATTAATTAAAAAA-ATTATATAAAAT
11802 TTTTATTTTATAATTATATATTATTTAAATTAATTATAAACT-TTTTTTTGAATTAAA
129 TTTTATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTTTGAATTAAA
* * *
11859 AAACATTTAAT-TTTTATATA
1 AAATATTAAATATATTATATA
11879 AATTATAAAA
Statistics
Matches: 186, Mismatches: 17, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
184 4 0.02
185 116 0.62
186 66 0.35
ACGTcount: A:0.46, C:0.08, G:0.04, T:0.42
Consensus pattern (186 bp):
AAATATTAAATATATTATATATAACATATGGACTAAGCCCAAAACATTTAAAACCCAATTAATAA
TTTAAGATACAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATAAAATTT
TTATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTTTGAATTAAA
Found at i:19141 original size:2 final size:2
Alignment explanation
Indices: 19134--19209 Score: 145
Period size: 2 Copynumber: 38.5 Consensus size: 2
19124 GACTACCAAA
19134 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
19176 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
19210 ATTAAAATCA
Statistics
Matches: 73, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 72 0.99
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:23785 original size:89 final size:89
Alignment explanation
Indices: 23629--23805 Score: 250
Period size: 89 Copynumber: 2.0 Consensus size: 89
23619 ATTATAAATA
*
23629 TGTTACATAATTTTAGATGATATTTGATTTACTAAAAATAATATAAATTACACTTACGCACATAA
1 TGTTACATAATTTTAGAGGATATTTGATTTACTAAAAATAATATAAATTACACTTAC-CACATAA
*
23694 AAAAATGAA-ATATATATATATATC
65 AAAAATGAAGAAATATATATATATC
* ** * *
23718 TGTTACATAATTTTAGAGGATATTTGATTTACTAAATAATAGTATAAATTTTATTTA-CATATAA
1 TGTTACATAATTTTAGAGGATATTTGATTTACTAAA-AATAATATAAATTACACTTACCACATAA
*
23782 AAAAATGAAGAAATATATGTATAT
65 AAAAATGAAGAAATATATATATAT
23806 GAACGGTCAT
Statistics
Matches: 78, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
88 15 0.19
89 47 0.60
90 16 0.21
ACGTcount: A:0.46, C:0.06, G:0.08, T:0.39
Consensus pattern (89 bp):
TGTTACATAATTTTAGAGGATATTTGATTTACTAAAAATAATATAAATTACACTTACCACATAAA
AAAATGAAGAAATATATATATATC
Found at i:30134 original size:22 final size:21
Alignment explanation
Indices: 30109--30161 Score: 79
Period size: 22 Copynumber: 2.5 Consensus size: 21
30099 ATTTTCAATA
30109 ATTATAAAATGATAATTAAAC
1 ATTATAAAATGATAATTAAAC
* *
30130 TATTATAAAATGATCATTATAC
1 -ATTATAAAATGATAATTAAAC
30152 ATTATAAAAT
1 ATTATAAAAT
30162 AGTGATAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
21 10 0.34
22 19 0.66
ACGTcount: A:0.53, C:0.06, G:0.04, T:0.38
Consensus pattern (21 bp):
ATTATAAAATGATAATTAAAC
Found at i:31478 original size:19 final size:18
Alignment explanation
Indices: 31454--31494 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
31444 TTGATTTACA
* *
31454 GAATGTAAGATTATCAGTG
1 GAATGTAAAATTACCAG-G
31473 GAATGTAAAATTACCAGG
1 GAATGTAAAATTACCAGG
31491 GAAT
1 GAAT
31495 AGGATTACTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.41, C:0.07, G:0.24, T:0.27
Consensus pattern (18 bp):
GAATGTAAAATTACCAGG
Found at i:33666 original size:24 final size:26
Alignment explanation
Indices: 33619--33675 Score: 75
Period size: 25 Copynumber: 2.3 Consensus size: 26
33609 TTTGTAATTT
*
33619 TAAAAATTTTATTTAAAAATAAAA-A
1 TAAAAATTATATTTAAAAATAAAACA
*
33644 TAAAAATTATATTTTAAAA-AAAACA
1 TAAAAATTATATTTAAAAATAAAACA
33669 -AAAAATT
1 TAAAAATT
33676 TGAAATAGCC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 11 0.38
25 18 0.62
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (26 bp):
TAAAAATTATATTTAAAAATAAAACA
Found at i:34905 original size:12 final size:12
Alignment explanation
Indices: 34890--34944 Score: 74
Period size: 12 Copynumber: 4.6 Consensus size: 12
34880 GTTATTTAAA
34890 CGGGTATTGGGC
1 CGGGTATTGGGC
*
34902 CGGGTATTGGGT
1 CGGGTATTGGGC
34914 CGGGTATTGGGC
1 CGGGTATTGGGC
* * *
34926 CGAGAATCGGGC
1 CGGGTATTGGGC
34938 CGGGTAT
1 CGGGTAT
34945 ATATATATTT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 36 1.00
ACGTcount: A:0.13, C:0.16, G:0.47, T:0.24
Consensus pattern (12 bp):
CGGGTATTGGGC
Found at i:35079 original size:13 final size:13
Alignment explanation
Indices: 35049--35100 Score: 53
Period size: 13 Copynumber: 4.5 Consensus size: 13
35039 TTTAATATTT
*
35049 ATCGGGTCGGGT-
1 ATCGGGGCGGGTA
35061 ATCGGGGCGGGTA
1 ATCGGGGCGGGTA
35074 AT-----CGGGTA
1 ATCGGGGCGGGTA
35082 ATCGGGGCGGGTA
1 ATCGGGGCGGGTA
35095 ATCGGG
1 ATCGGG
35101 TAATTGGGGC
Statistics
Matches: 33, Mismatches: 1, Indels: 11
0.73 0.02 0.24
Matches are distributed among these distances:
8 8 0.24
12 11 0.33
13 14 0.42
ACGTcount: A:0.15, C:0.15, G:0.50, T:0.19
Consensus pattern (13 bp):
ATCGGGGCGGGTA
Found at i:35087 original size:21 final size:21
Alignment explanation
Indices: 35055--35113 Score: 102
Period size: 21 Copynumber: 2.9 Consensus size: 21
35045 ATTTATCGGG
35055 TCGGGT-ATCGGGGCGGGTAA
1 TCGGGTAATCGGGGCGGGTAA
35075 TCGGGTAATCGGGGCGGGTAA
1 TCGGGTAATCGGGGCGGGTAA
*
35096 TCGGGTAATTGGGGCGGG
1 TCGGGTAATCGGGGCGGG
35114 GATTACCAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
20 6 0.16
21 31 0.84
ACGTcount: A:0.15, C:0.14, G:0.51, T:0.20
Consensus pattern (21 bp):
TCGGGTAATCGGGGCGGGTAA
Found at i:36311 original size:26 final size:28
Alignment explanation
Indices: 36250--36311 Score: 65
Period size: 31 Copynumber: 2.2 Consensus size: 28
36240 GAGTATTGCT
* *
36250 GAGCTCGACTCGACTCGAAAACTTTGAAAT
1 GAGCTCGACTCGACTCGAAAACTTCG--AC
36280 GAAGCTCGACTCGACTCGAAAAC-TCG-C
1 G-AGCTCGACTCGACTCGAAAACTTCGAC
36307 GAGCT
1 GAGCT
36312 TAAAATTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
26 4 0.14
27 1 0.03
30 3 0.10
31 21 0.72
ACGTcount: A:0.31, C:0.27, G:0.23, T:0.19
Consensus pattern (28 bp):
GAGCTCGACTCGACTCGAAAACTTCGAC
Found at i:40186 original size:60 final size:60
Alignment explanation
Indices: 40122--40235 Score: 149
Period size: 60 Copynumber: 1.9 Consensus size: 60
40112 CTATGGCTAT
* * * *
40122 CATTCCAAATTAGTCCTC-AAGTTTTTGAACATTTTAATTTCATCACCAAACTATGAAACC
1 CATTCCAAATTAATCCCCAAACTTTTTGAACATTTCAATTTCATC-CCAAACTATGAAACC
* * *
40182 CATTCTAGATTAATCCCCAAACTTTTTGAATATTTCAATTTCATCCCAAACTAT
1 CATTCCAAATTAATCCCCAAACTTTTTGAACATTTCAATTTCATCCCAAACTAT
40236 ATTTATATAC
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
60 23 0.50
61 23 0.50
ACGTcount: A:0.34, C:0.24, G:0.05, T:0.37
Consensus pattern (60 bp):
CATTCCAAATTAATCCCCAAACTTTTTGAACATTTCAATTTCATCCCAAACTATGAAACC
Found at i:41495 original size:22 final size:18
Alignment explanation
Indices: 41443--41501 Score: 73
Period size: 18 Copynumber: 3.1 Consensus size: 18
41433 GACCCGAATT
41443 AATATATTTATTAAAAAA
1 AATATATTTATTAAAAAA
*
41461 AATATTTTTATTAAATAAA
1 AATATATTTATTAAA-AAA
41480 AATATGAATTTAATTAAAAAA
1 AATAT--ATTT-ATTAAAAAA
41501 A
1 A
41502 TAACATATAG
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
18 14 0.40
19 8 0.23
21 7 0.20
22 6 0.17
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (18 bp):
AATATATTTATTAAAAAA
Found at i:45201 original size:37 final size:36
Alignment explanation
Indices: 45126--45201 Score: 91
Period size: 36 Copynumber: 2.1 Consensus size: 36
45116 TTTTTATATT
*
45126 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
* * *
45162 TTTATTTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAAATTATATAAATATTAT-CAA
45199 TTT
1 TTT
45202 GTAATATTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
36 25 0.74
37 9 0.26
ACGTcount: A:0.46, C:0.01, G:0.04, T:0.49
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:53541 original size:32 final size:32
Alignment explanation
Indices: 53500--53564 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
53490 GGAGAAGAGA
* *
53500 AGGAAAAAGGGTAAATTACACCATGAGTTATT
1 AGGAAAAAGGGTAAATTACACCATCAGTCATT
53532 AGGAAAAAGGGTAAATTACACCATCAGTCATT
1 AGGAAAAAGGGTAAATTACACCATCAGTCATT
53564 A
1 A
53565 AACTTTACTC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.45, C:0.12, G:0.20, T:0.23
Consensus pattern (32 bp):
AGGAAAAAGGGTAAATTACACCATCAGTCATT
Done.