Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008722.1 Hibiscus syriacus cultivar Beakdansim tig00111780_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: 447499
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 3
Found at i:405860 original size:18 final size:18
Alignment explanation
Indices: 405839--405873 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
405829 TCCCATCTAG
405839 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
405857 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
405874 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:406480 original size:21 final size:21
Alignment explanation
Indices: 406456--406500 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
406446 TTTTGTTCGG
406456 TTGAAGGGGTATCAG-TTCCCC
1 TTGAAGGGGTA-CAGATTCCCC
* *
406477 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACAGATTCCCC
406498 TTG
1 TTG
406501 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.18, C:0.24, G:0.27, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACAGATTCCCC
Found at i:408713 original size:14 final size:14
Alignment explanation
Indices: 408705--408775 Score: 78
Period size: 14 Copynumber: 5.4 Consensus size: 14
408695 AAACATAAAT
*
408705 GAACGAACATAAAC
1 GAACGAACATAACC
408719 GAAC--A--TAACC
1 GAACGAACATAACC
408729 GAACGAACATAACC
1 GAACGAACATAACC
*
408743 AAACGAACATAACC
1 GAACGAACATAACC
* *
408757 AAACGAACATAACT
1 GAACGAACATAACC
408771 GAACG
1 GAACG
408776 TTCACGAACG
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
10 8 0.16
12 2 0.04
14 39 0.80
ACGTcount: A:0.54, C:0.25, G:0.13, T:0.08
Consensus pattern (14 bp):
GAACGAACATAACC
Found at i:408732 original size:24 final size:24
Alignment explanation
Indices: 408696--408768 Score: 83
Period size: 28 Copynumber: 2.9 Consensus size: 24
408686 GATTGGGTTA
**
408696 AACATAAATGAACGAACATAAACG
1 AACATAACCGAACGAACATAAACG
408720 AACATAACCGAACGAACATAACCAAACG
1 AACATAACCGAACGAACAT----AAACG
*
408748 AACATAACCAAACGAACATAA
1 AACATAACCGAACGAACATAA
408769 CTGAACGTTC
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
24 19 0.45
28 23 0.55
ACGTcount: A:0.58, C:0.23, G:0.10, T:0.10
Consensus pattern (24 bp):
AACATAACCGAACGAACATAAACG
Found at i:408775 original size:28 final size:28
Alignment explanation
Indices: 408715--408769 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
408705 GAACGAACAT
*
408715 AAACGAACATAACCGAACGAACATAACC
1 AAACGAACATAACCAAACGAACATAACC
408743 AAACGAACATAACCAAACGAACATAAC
1 AAACGAACATAACCAAACGAACATAAC
408770 TGAACGTTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.56, C:0.27, G:0.09, T:0.07
Consensus pattern (28 bp):
AAACGAACATAACCAAACGAACATAACC
Found at i:409782 original size:21 final size:21
Alignment explanation
Indices: 409726--409775 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
409716 TTAACGGCTG
* *
409726 CATCATAGCGTTTTTTAAGGT
1 CATCATAGCATTTTTCAAGGT
409747 CATCATAGCATTTTTCAAGGT
1 CATCATAGCATTTTTCAAGGT
409768 CATCATAG
1 CATCATAG
409776 TTATTTTTGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.28, C:0.18, G:0.16, T:0.38
Consensus pattern (21 bp):
CATCATAGCATTTTTCAAGGT
Found at i:416406 original size:3 final size:3
Alignment explanation
Indices: 416393--416440 Score: 55
Period size: 3 Copynumber: 16.7 Consensus size: 3
416383 AAACTAGCAC
* * *
416393 TTA TT- TTA TTA TTA TTA TTA TTA TTA TAA TAA ATA TT- TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
416439 TT
1 TT
416441 CTATTAATAG
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
2 4 0.10
3 35 0.90
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:416454 original size:29 final size:31
Alignment explanation
Indices: 416394--416468 Score: 82
Period size: 29 Copynumber: 2.5 Consensus size: 31
416384 AACTAGCACT
*
416394 TATTTTATTATTATTATTATTATTATAATAAA
1 TATTTTATTATTATTACTATTA-TATAATAAA
*
416426 TATTTTATTATTATT-CTATTA-ATAGTAAA
1 TATTTTATTATTATTACTATTATATAATAAA
* * *
416455 AACTTCATTATTAT
1 TATTTTATTATTAT
416469 GCATGGAAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
29 18 0.47
31 5 0.13
32 15 0.39
ACGTcount: A:0.39, C:0.04, G:0.01, T:0.56
Consensus pattern (31 bp):
TATTTTATTATTATTACTATTATATAATAAA
Found at i:419295 original size:63 final size:64
Alignment explanation
Indices: 419136--419298 Score: 170
Period size: 63 Copynumber: 2.6 Consensus size: 64
419126 GTATGCTTAT
* * * * * *
419136 TATACACGCAGGCATGGCACAAACTGATG-TGTGATTTGTGTCTACGTGTAATCCGGTGATGTAA
1 TATACATGCATGCATGGCACAAACTGATGATGTGA-CTGTATCTACGTGTAATCCGATGATATAA
* ** * * * *
419200 GATACATTTATGCATGGCGCAAACCGAT-ATGTGACTGTATCTATGTGTAATCCGATGGTATAA
1 TATACATGCATGCATGGCACAAACTGATGATGTGACTGTATCTACGTGTAATCCGATGATATAA
*
419263 TATACATGCATGCATGTCACAAACTG-TGATGTGACT
1 TATACATGCATGCATGGCACAAACTGATGATGTGACT
419299 TGTGTCTGTG
Statistics
Matches: 78, Mismatches: 19, Indels: 5
0.76 0.19 0.05
Matches are distributed among these distances:
62 1 0.01
63 51 0.65
64 26 0.33
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (64 bp):
TATACATGCATGCATGGCACAAACTGATGATGTGACTGTATCTACGTGTAATCCGATGATATAA
Found at i:422640 original size:60 final size:60
Alignment explanation
Indices: 422575--422687 Score: 160
Period size: 60 Copynumber: 1.9 Consensus size: 60
422565 ATGACTATCC
* *
422575 TTCTAAATTAATTC-TCAAAC-TTTTGAACATTTCAACTTT-ATCCCCAAACTATAACCTTTA
1 TTCTAAATTAATCCAT-AAACTTTTTGAACA-TTCAAATTTCAT-CCCAAACTATAACCTTTA
422635 TTCTAAATTAATCCATAAACTTTTTGAACATTCAAATTTCATCCCAAACTATA
1 TTCTAAATTAATCCATAAACTTTTTGAACATTCAAATTTCATCCCAAACTATA
422688 TGTATATACT
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
60 36 0.75
61 12 0.25
ACGTcount: A:0.37, C:0.22, G:0.02, T:0.39
Consensus pattern (60 bp):
TTCTAAATTAATCCATAAACTTTTTGAACATTCAAATTTCATCCCAAACTATAACCTTTA
Found at i:422931 original size:61 final size:61
Alignment explanation
Indices: 422866--422998 Score: 146
Period size: 60 Copynumber: 2.2 Consensus size: 61
422856 GAAAGAGAGA
* * ** *
422866 CATAGTTTAG-GGATGAAATTAAAATGTTCAAAAAGTTTAGGGA-CTAATTTAAAATTAGAAT
1 CATAGTTTAGAGGATGAAAATAAAAT-ATCAAAAAGTTTAAAGATC-AATTTAAAATAAGAAT
* * *
422927 CATAGTTT-GAGGATGAAAATAGAATATCCAAAAGTTTAAAGATCAATTTAAAATAAGAGT
1 CATAGTTTAGAGGATGAAAATAAAATATCAAAAAGTTTAAAGATCAATTTAAAATAAGAAT
*
422987 TATAGTTTAGAG
1 CATAGTTTAGAG
422999 ACATATGATG
Statistics
Matches: 60, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
60 35 0.58
61 25 0.42
ACGTcount: A:0.45, C:0.05, G:0.18, T:0.32
Consensus pattern (61 bp):
CATAGTTTAGAGGATGAAAATAAAATATCAAAAAGTTTAAAGATCAATTTAAAATAAGAAT
Found at i:434983 original size:18 final size:19
Alignment explanation
Indices: 434943--434984 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
434933 ACTTCGTAAT
* *
434943 TAATATATATTAGTATAAGA
1 TAATATATATTA-TAAAAAA
434963 TAATATATATT-TAAAAAA
1 TAATATATATTATAAAAAA
434981 TAAT
1 TAAT
434985 TTTTATTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 9 0.45
20 11 0.55
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (19 bp):
TAATATATATTATAAAAAA
Found at i:440032 original size:24 final size:23
Alignment explanation
Indices: 439995--440040 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
439985 TCCAATAATA
439995 TTATATTTTAAAATTATATAAAAAT
1 TTATATTTTAAAATT-TA-AAAAAT
440020 TTATA-TTTAAAATTTAAAAAA
1 TTATATTTTAAAATTTAAAAAA
440041 CTTAGTAGAC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 5 0.24
23 2 0.10
24 9 0.43
25 5 0.24
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (23 bp):
TTATATTTTAAAATTTAAAAAAT
Found at i:440034 original size:13 final size:13
Alignment explanation
Indices: 439995--440035 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
439985 TCCAATAATA
439995 TTATATTTTAAAA-
1 TTATA-TTTAAAAT
*
440008 TTATA-TAAAAAT
1 TTATATTTAAAAT
440020 TTATATTTAAAAT
1 TTATATTTAAAAT
440033 TTA
1 TTA
440036 AAAAACTTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 5 0.21
12 5 0.21
13 14 0.58
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (13 bp):
TTATATTTAAAAT
Done.