Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001247.1 Hibiscus syriacus cultivar Beakdansim tig00002449_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: 42253
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:1329 original size:22 final size:23
Alignment explanation
Indices: 1303--1347 Score: 83
Period size: 22 Copynumber: 2.0 Consensus size: 23
1293 ACTAGAAGGG
1303 GTATCGATACCATAGTA-GGGTA
1 GTATCGATACCATAGTATGGGTA
1325 GTATCGATACCATAGTATGGGTA
1 GTATCGATACCATAGTATGGGTA
1348 TTGATACTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.31, C:0.13, G:0.27, T:0.29
Consensus pattern (23 bp):
GTATCGATACCATAGTATGGGTA
Found at i:1886 original size:78 final size:78
Alignment explanation
Indices: 1754--1902 Score: 255
Period size: 78 Copynumber: 1.9 Consensus size: 78
1744 AAAACGAATG
* *
1754 TAAAAGAATAATGCATATGGGTGCATATTGGCATGAAAGGATGCCATAGCTGAAATGTATATGGG
1 TAAAAGAATAATGCATATGGGTGCATATTGGCATGAAAGGATGCCAGAGCTGAAATGGATATGGG
1819 TACATTGTCAGCA
66 TACATTGTCAGCA
1832 TAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCAGAG-TGAAATGGATATGG
1 TAAAAGAATAATGCATATGGGTGCA-TATTGGCATGAAAGGATGCCAGAGCTGAAATGGATATGG
*
1896 GTGCATT
65 GTACATT
1903 ATCAACAGAA
Statistics
Matches: 67, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
78 44 0.66
79 23 0.34
ACGTcount: A:0.36, C:0.10, G:0.28, T:0.27
Consensus pattern (78 bp):
TAAAAGAATAATGCATATGGGTGCATATTGGCATGAAAGGATGCCAGAGCTGAAATGGATATGGG
TACATTGTCAGCA
Found at i:1948 original size:45 final size:45
Alignment explanation
Indices: 1841--2091 Score: 253
Period size: 45 Copynumber: 5.6 Consensus size: 45
1831 ATAAAAGAAT
* *** * *
1841 AATGCATATGGGTGCATTATTGGCATG-AAAGGATGCCAGAG-TGA
1 AATGCATATGGGTACATTATCAACA-GAAAAGTATGCTAGAGTTGA
* *
1885 AATGGATATGGGTGCATTATCAACAGAAAAGTATGCTAGAGTTGA
1 AATGCATATGGGTACATTATCAACAGAAAAGTATGCTAGAGTTGA
*
1930 AATGCATATGGGTACATTATCAACAGAAAAGTATGTTAGAGTTGA
1 AATGCATATGGGTACATTATCAACAGAAAAGTATGCTAGAGTTGA
* * * *
1975 AATG-TTATGGGTACATTATCAACAAAAAAAATATACTATG-GTTGA
1 AATGCATATGGGTACATTATCAAC-AGAAAAGTATGCTA-GAGTTGA
* * * * * *
2020 GATGTATATGAGTACATTATCAACATAAAA-TATACTATAG-TGA
1 AATGCATATGGGTACATTATCAACAGAAAAGTATGCTAGAGTTGA
*
2063 AATGCATATGGGTGCATTATCAACAGAAA
1 AATGCATATGGGTACATTATCAACAGAAA
2092 TATGTTATAG
Statistics
Matches: 177, Mismatches: 24, Indels: 13
0.83 0.11 0.06
Matches are distributed among these distances:
43 28 0.16
44 59 0.33
45 72 0.41
46 18 0.10
ACGTcount: A:0.40, C:0.10, G:0.22, T:0.28
Consensus pattern (45 bp):
AATGCATATGGGTACATTATCAACAGAAAAGTATGCTAGAGTTGA
Found at i:2807 original size:15 final size:16
Alignment explanation
Indices: 2770--2814 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 16
2760 AATGAAATTC
*
2770 TGGAAATTTAAAGGAT
1 TGGAAATTAAAAGGAT
* *
2786 TGAAAATTAAAATGA-
1 TGGAAATTAAAAGGAT
2801 TGGAAATTAAAAGG
1 TGGAAATTAAAAGG
2815 GAAAAAATTT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
15 12 0.50
16 12 0.50
ACGTcount: A:0.51, C:0.00, G:0.22, T:0.27
Consensus pattern (16 bp):
TGGAAATTAAAAGGAT
Found at i:14276 original size:22 final size:22
Alignment explanation
Indices: 14245--14287 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
14235 TCTATATTGA
*
14245 GGGTTCGGTATCAAGACCAAGG
1 GGGTTCGGTATCAAAACCAAGG
*
14267 GGGTTTGGTATCAAAACCAAG
1 GGGTTCGGTATCAAAACCAAG
14288 ATTTCATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.30, C:0.16, G:0.33, T:0.21
Consensus pattern (22 bp):
GGGTTCGGTATCAAAACCAAGG
Found at i:14450 original size:20 final size:20
Alignment explanation
Indices: 14427--14475 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
14417 TTGAGGAGAG
* *
14427 AGTATTGATGCTATAAGGTC
1 AGTATCGATGCTATAAGGCC
* *
14447 AGTATCGATGTTGTAAGGCC
1 AGTATCGATGCTATAAGGCC
14467 AGTATCGAT
1 AGTATCGAT
14476 ACCAAGGTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.29, C:0.12, G:0.27, T:0.33
Consensus pattern (20 bp):
AGTATCGATGCTATAAGGCC
Found at i:16110 original size:21 final size:21
Alignment explanation
Indices: 16084--16132 Score: 98
Period size: 21 Copynumber: 2.3 Consensus size: 21
16074 GAAGATGTTC
16084 AATTTTTTTGTTAATTGTTGT
1 AATTTTTTTGTTAATTGTTGT
16105 AATTTTTTTGTTAATTGTTGT
1 AATTTTTTTGTTAATTGTTGT
16126 AATTTTT
1 AATTTTT
16133 AAGACATTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.20, C:0.00, G:0.12, T:0.67
Consensus pattern (21 bp):
AATTTTTTTGTTAATTGTTGT
Found at i:28054 original size:15 final size:16
Alignment explanation
Indices: 28022--28054 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
28012 AATCTAAGCG
*
28022 TAGATATAAAATTCGA
1 TAGAAATAAAATTCGA
28038 TAGAAATAAAA-TCGA
1 TAGAAATAAAATTCGA
28053 TA
1 TA
28055 CTTAAATCGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.55, C:0.06, G:0.12, T:0.27
Consensus pattern (16 bp):
TAGAAATAAAATTCGA
Found at i:31144 original size:46 final size:45
Alignment explanation
Indices: 31094--31182 Score: 142
Period size: 46 Copynumber: 2.0 Consensus size: 45
31084 TTTGAAAAAC
* * *
31094 CTGAGTGCATCGATGCATGGTCTTGTGTATCGATGCATCAAATGTA
1 CTGAGTGCATCGATGCATGGT-ATGTGCATCGATGCATAAAATGTA
31140 CTGAGTGCATCGATGCATGGTATGTGCATCGATGCATAAAATG
1 CTGAGTGCATCGATGCATGGTATGTGCATCGATGCATAAAATG
31183 CATTCGATGT
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
45 19 0.47
46 21 0.52
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.30
Consensus pattern (45 bp):
CTGAGTGCATCGATGCATGGTATGTGCATCGATGCATAAAATGTA
Found at i:40948 original size:41 final size:41
Alignment explanation
Indices: 40891--40972 Score: 155
Period size: 41 Copynumber: 2.0 Consensus size: 41
40881 TGTTTATTTT
*
40891 TTGGGGATGGGAATTAACCGAAACCGTAGGGATCCGTAAGG
1 TTGGGGATAGGAATTAACCGAAACCGTAGGGATCCGTAAGG
40932 TTGGGGATAGGAATTAACCGAAACCGTAGGGATCCGTAAGG
1 TTGGGGATAGGAATTAACCGAAACCGTAGGGATCCGTAAGG
40973 GATGATATGG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.30, C:0.15, G:0.35, T:0.20
Consensus pattern (41 bp):
TTGGGGATAGGAATTAACCGAAACCGTAGGGATCCGTAAGG
Found at i:41837 original size:20 final size:21
Alignment explanation
Indices: 41797--41838 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
41787 TTAGAATAAT
* *
41797 TTATTTATTATTATTAAAATA
1 TTATTTATTATAATAAAAATA
41818 TTATTTA-TATAATAAAAATA
1 TTATTTATTATAATAAAAATA
41838 T
1 T
41839 AAGATTACTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
TTATTTATTATAATAAAAATA
Found at i:42025 original size:19 final size:19
Alignment explanation
Indices: 41985--42031 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
41975 TGAATACATA
*
41985 ATAATATTATTAATAATTT
1 ATAATATTATTAATAATAT
*
42004 ATAATATTATTTATGAA-AT
1 ATAATATTATTAAT-AATAT
42023 ATAA-ATTAT
1 ATAATATTAT
42032 ATAAATTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 5 0.20
19 18 0.72
20 2 0.08
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (19 bp):
ATAATATTATTAATAATAT
Done.