Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002119.1 Hibiscus syriacus cultivar Beakdansim tig00004344_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: 57908
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.32
Found at i:15326 original size:20 final size:20
Alignment explanation
Indices: 15287--15326 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
15277 ATTTTTTAGG
*
15287 GTGTATTATCGCTAGGCACT
1 GTGTATTATCGCTAGACACT
*
15307 GTGTATTATCGCTCGACACT
1 GTGTATTATCGCTAGACACT
15327 CTTTTTGTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.20, C:0.23, G:0.23, T:0.35
Consensus pattern (20 bp):
GTGTATTATCGCTAGACACT
Found at i:18384 original size:2 final size:2
Alignment explanation
Indices: 18377--18424 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
18367 CAAAATTGTA
18377 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
18419 AT AT AT
1 AT AT AT
18425 TAATAAAAAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18443 original size:8 final size:9
Alignment explanation
Indices: 18375--18445 Score: 70
Period size: 8 Copynumber: 8.8 Consensus size: 9
18365 ATCAAAATTG
18375 TAATATATA
1 TAATATATA
18384 T-ATATATA
1 TAATATATA
18392 T-ATATATA
1 TAATATATA
18400 T-ATATATA
1 TAATATATA
18408 T-ATATATA
1 TAATATATA
18416 T-ATATATA
1 TAATATATA
18424 TTAATA-A-A
1 -TAATATATA
18432 -AATAT-TA
1 TAATATATA
18439 TAATATA
1 TAATATA
18446 CTATTTGTCA
Statistics
Matches: 56, Mismatches: 0, Indels: 12
0.82 0.00 0.18
Matches are distributed among these distances:
6 4 0.07
7 1 0.02
8 45 0.80
9 3 0.05
10 3 0.05
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (9 bp):
TAATATATA
Found at i:25303 original size:23 final size:23
Alignment explanation
Indices: 25277--25320 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
25267 CATATTAAAT
*
25277 TAAAAATATTTTTAAAATTTACA
1 TAAAAATATATTTAAAATTTACA
25300 TAAAAATATATTTAAAATTTA
1 TAAAAATATATTTAAAATTTA
25321 TAAATTCTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (23 bp):
TAAAAATATATTTAAAATTTACA
Found at i:30577 original size:87 final size:86
Alignment explanation
Indices: 30328--30579 Score: 292
Period size: 86 Copynumber: 2.9 Consensus size: 86
30318 AAGCGATCGG
* *
30328 ACAAACTATAGTATTCTTCATAGTTAGAATGAATAGATGATTGAAGAATCAAACCTAAATACTAT
1 ACAAACTATAGTGTTCTTCATAGTTAGAATGAATAGATGATCGAAGAATCAAACCTAAATACTAT
* * *
30393 AATAGTGAA-AGCGACAACCAA
66 AACAAT-AATAGCAACAACCAA
* * * * * *
30414 ACGAACTATAGTGTTCTTCATGGGTAGAATGAATAGATGATGGAAGAATCAAACCCATATACTAT
1 ACAAACTATAGTGTTCTTCATAGTTAGAATGAATAGATGATCGAAGAATCAAACCTAAATACTAT
* *
30479 AACAATGATAGCAACAATCAA
66 AACAATAATAGCAACAACCAA
* ** * *
30500 ACAATACTATAATGTTCTTCATAGTTAGAACCAATAAATGATCGAAGAACCAAACCTAAATAAC-
1 ACAA-ACTATAGTGTTCTTCATAGTTAGAATGAATAGATGATCGAAGAATCAAACCTAAAT-ACT
*
30564 ATAGCAATAATAGCAA
64 ATAACAATAATAGCAA
30580 TGACTGAAAC
Statistics
Matches: 138, Mismatches: 25, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
85 1 0.01
86 75 0.54
87 60 0.43
88 2 0.01
ACGTcount: A:0.46, C:0.15, G:0.14, T:0.25
Consensus pattern (86 bp):
ACAAACTATAGTGTTCTTCATAGTTAGAATGAATAGATGATCGAAGAATCAAACCTAAATACTAT
AACAATAATAGCAACAACCAA
Found at i:56169 original size:15 final size:14
Alignment explanation
Indices: 56137--56166 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
56127 AATGGGAAGT
*
56137 AATCCTTGCAAAAA
1 AATCCCTGCAAAAA
56151 AATCCCTGCAAAAA
1 AATCCCTGCAAAAA
56165 AA
1 AA
56167 ATCTTTGCAT
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:0.53, C:0.23, G:0.07, T:0.17
Consensus pattern (14 bp):
AATCCCTGCAAAAA
Found at i:56175 original size:15 final size:15
Alignment explanation
Indices: 56137--56175 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
56127 AATGGGAAGT
56137 AATCCTTGC-AAAAA
1 AATCCTTGCAAAAAA
*
56151 AATCCCTGCAAAAAA
1 AATCCTTGCAAAAAA
*
56166 AATCTTTGCA
1 AATCCTTGCA
56176 TATAGACAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.46, C:0.23, G:0.08, T:0.23
Consensus pattern (15 bp):
AATCCTTGCAAAAAA
Done.