Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007883.1 Hibiscus syriacus cultivar Beakdansim tig00110263_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: 1590433
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 9
Found at i:1562542 original size:27 final size:27
Alignment explanation
Indices: 1562512--1562606 Score: 154
Period size: 27 Copynumber: 3.5 Consensus size: 27
1562502 GAGATGAGAC
* **
1562512 TGAGTTGTGATTTAAAGTTTTAGGTTA
1 TGAGTTGCGATTTAGGGTTTTAGGTTA
*
1562539 TGAGTTACGATTTAGGGTTTTAGGTTA
1 TGAGTTGCGATTTAGGGTTTTAGGTTA
1562566 TGAGTTGCGATTTAGGGTTTTAGGTTA
1 TGAGTTGCGATTTAGGGTTTTAGGTTA
1562593 TGAGTTGCGATTTA
1 TGAGTTGCGATTTA
1562607 CGGGATATAC
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 63 1.00
ACGTcount: A:0.22, C:0.03, G:0.29, T:0.45
Consensus pattern (27 bp):
TGAGTTGCGATTTAGGGTTTTAGGTTA
Found at i:1567055 original size:3 final size:3
Alignment explanation
Indices: 1567049--1567096 Score: 87
Period size: 3 Copynumber: 16.0 Consensus size: 3
1567039 TTTTTTAACT
*
1567049 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA CTA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1567097 GAAGTATTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1572293 original size:20 final size:22
Alignment explanation
Indices: 1572268--1572321 Score: 67
Period size: 24 Copynumber: 2.5 Consensus size: 22
1572258 AGGCAACCCA
1572268 TATTTAATTT-G-ATTCATTTT
1 TATTTAATTTAGTATTCATTTT
*
1572288 TATTTAATTTTAGTTATTCTTTTT
1 TATTTAA-TTTAG-TATTCATTTT
1572312 TATTTAATTT
1 TATTTAATTT
1572322 CTTTTGATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
20 7 0.24
21 3 0.10
22 1 0.03
23 3 0.10
24 15 0.52
ACGTcount: A:0.24, C:0.04, G:0.04, T:0.69
Consensus pattern (22 bp):
TATTTAATTTAGTATTCATTTT
Found at i:1573474 original size:23 final size:24
Alignment explanation
Indices: 1573406--1573496 Score: 132
Period size: 24 Copynumber: 3.9 Consensus size: 24
1573396 CACCGAACTG
*
1573406 CCACATAGAATTTTTCCCGAAGGA
1 CCACATAGAATTTGTCCCGAAGGA
* *
1573430 CCGCATAGAATTTGTCCTGAAGGA
1 CCACATAGAATTTGTCCCGAAGGA
*
1573454 CCACATAGAA-ATGTCCCGAAGGA
1 CCACATAGAATTTGTCCCGAAGGA
1573477 CCACATAG-ATTTGTCCCGAA
1 CCACATAGAATTTGTCCCGAA
1573497 AGACGCGTAG
Statistics
Matches: 59, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
22 1 0.02
23 28 0.47
24 30 0.51
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.22
Consensus pattern (24 bp):
CCACATAGAATTTGTCCCGAAGGA
Found at i:1574282 original size:13 final size:13
Alignment explanation
Indices: 1574264--1574304 Score: 73
Period size: 13 Copynumber: 3.2 Consensus size: 13
1574254 TAATGTTCTT
*
1574264 CCAGTACCAATAC
1 CCAGTACCGATAC
1574277 CCAGTACCGATAC
1 CCAGTACCGATAC
1574290 CCAGTACCGATAC
1 CCAGTACCGATAC
1574303 CC
1 CC
1574305 TTGCCAGATT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.32, C:0.41, G:0.12, T:0.15
Consensus pattern (13 bp):
CCAGTACCGATAC
Found at i:1578401 original size:150 final size:150
Alignment explanation
Indices: 1578121--1578445 Score: 573
Period size: 150 Copynumber: 2.2 Consensus size: 150
1578111 CCACAGCTCG
*
1578121 TATAAATCACCGAAGTG-CCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGAC
1 TATATATC-CCGAAG-GACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGAC
*
1578185 CACATAGAATTCCTTAAGAATCATATATATATACTAGGGATCAAGTATGTGTCTTTCCAAGACTT
64 CACATAGAATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCCAAGACTT
*
1578250 CACACATGTTCCACAGAATATA
129 CACACATGTTCCAAAGAATATA
1578272 TATATATCCCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCA
1 TATATATCCCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCA
1578337 CATAGAATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCCAAGACTTCA
66 CATAGAATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCCAAGACTTCA
1578402 CACATGTTCCAAAGAATATA
131 CACATGTTCCAAAGAATATA
* *
1578422 CATATGT-CCGAAGGACCGCGTAGA
1 TATATATCCCGAAGGACCGCGTAGA
1578446 CCCTCTACCC
Statistics
Matches: 168, Mismatches: 5, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
149 18 0.11
150 143 0.85
151 7 0.04
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.27
Consensus pattern (150 bp):
TATATATCCCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCA
CATAGAATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCCAAGACTTCA
CACATGTTCCAAAGAATATA
Found at i:1579033 original size:64 final size:63
Alignment explanation
Indices: 1578900--1579056 Score: 158
Period size: 64 Copynumber: 2.4 Consensus size: 63
1578890 TAATGAAGGT
* * * ** *
1578900 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAATGCATTCGATGTTGTATTATTACTGGG
1 ATGCATCGATGCA-TACTAATGCATCGATGCATAAAATGCATTCGATGTTCTATTATTAAAGAG
* *
1578964 ATGCATCGATGCATGACTTATGCATCGATGCACT-AATTGCATTCGATGTTTCTATT-TTAAA-A
1 ATGCATCGATGCAT-ACTAATGCATCGATGCA-TAAAATGCATTCGATG-TTCTATTATTAAAGA
1579026 G
63 G
*
1579027 AGTGCATCGATGCATTACCAATGCATCGAT
1 A-TGCATCGATGCA-TACTAATGCATCGAT
1579057 ACACCTTCAA
Statistics
Matches: 79, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
63 3 0.04
64 68 0.86
65 8 0.10
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.33
Consensus pattern (63 bp):
ATGCATCGATGCATACTAATGCATCGATGCATAAAATGCATTCGATGTTCTATTATTAAAGAG
Found at i:1579115 original size:21 final size:21
Alignment explanation
Indices: 1579089--1579128 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
1579079 TTTTAAACTT
1579089 TATGCATCGATGCACTATGAA
1 TATGCATCGATGCACTATGAA
1579110 TATGCATCGATGCACTATG
1 TATGCATCGATGCACTATG
1579129 CCCAGAATCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (21 bp):
TATGCATCGATGCACTATGAA
Found at i:1582059 original size:46 final size:47
Alignment explanation
Indices: 1581979--1582067 Score: 135
Period size: 46 Copynumber: 1.9 Consensus size: 47
1581969 AAGTAGAATT
* * *
1581979 TGTCCCGAAGGACCGCGTAGAATTTGTCCCGAAGGACCACGTAAAAA
1 TGTCCCGAAGGACCACATAGAATTTATCCCGAAGGACCACGTAAAAA
*
1582026 TGTCCCGAATGACCACATAG-ATTTATCCCGAAGGACCACGTA
1 TGTCCCGAAGGACCACATAGAATTTATCCCGAAGGACCACGTA
1582068 GAACCCTCGA
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
46 21 0.55
47 17 0.45
ACGTcount: A:0.31, C:0.27, G:0.22, T:0.19
Consensus pattern (47 bp):
TGTCCCGAAGGACCACATAGAATTTATCCCGAAGGACCACGTAAAAA
Found at i:1582069 original size:23 final size:23
Alignment explanation
Indices: 1581971--1582069 Score: 117
Period size: 23 Copynumber: 4.2 Consensus size: 23
1581961 GAAGTGCCAA
*
1581971 GTAGAATTTGTCCCGAAGGACCGC
1 GTAG-ATTTGTCCCGAAGGACCAC
1581995 GTAGAATTTGTCCCGAAGGACCAC
1 GTAG-ATTTGTCCCGAAGGACCAC
* ** *
1582019 GTAAAAATGTCCCGAATGACCAC
1 GTAGATTTGTCCCGAAGGACCAC
* *
1582042 ATAGATTTATCCCGAAGGACCAC
1 GTAGATTTGTCCCGAAGGACCAC
1582065 GTAGA
1 GTAGA
1582070 ACCCTCGACT
Statistics
Matches: 63, Mismatches: 12, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
23 37 0.59
24 26 0.41
ACGTcount: A:0.32, C:0.24, G:0.23, T:0.20
Consensus pattern (23 bp):
GTAGATTTGTCCCGAAGGACCAC
Done.