Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009586.1 Hibiscus syriacus cultivar Beakdansim tig00116964_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: 3773412
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 19 of 19
Found at i:3761339 original size:25 final size:25
Alignment explanation
Indices: 3761293--3761345 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 25
3761283 ATTCGTATTT
3761293 TTTTCATTACATTTGCATTTTTATA
1 TTTTCATTACATTTGCATTTTTATA
* *
3761318 TTTTCATTTTCATTTTCA-TTTTATA
1 TTTTCA-TTACATTTGCATTTTTATA
3761343 TTT
1 TTT
3761346 GCATCTTTGC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 16 0.64
26 9 0.36
ACGTcount: A:0.21, C:0.11, G:0.02, T:0.66
Consensus pattern (25 bp):
TTTTCATTACATTTGCATTTTTATA
Found at i:3763544 original size:72 final size:72
Alignment explanation
Indices: 3763412--3763546 Score: 191
Period size: 72 Copynumber: 1.9 Consensus size: 72
3763402 TACAATAAAG
*
3763412 CTTGAGTTATCCCCCTAAAGCAATTGGTTAATAGCCCCGATTTTATGGATAATATCCAGCTAGTC
1 CTTGAGTTATCCCCCTAAAGCAATTGGTTAATAGCCCCGACTTTATGGATAATATCCAGCTAGTC
3763477 TGTTATA
66 TGTTATA
* * * * * *
3763484 CTTGGGTTGTCCCTCTAAAGCAATTGGTTAATTA-CCCTGGCTTTATGGATAATATTCAGCTAG
1 CTTGAGTTATCCCCCTAAAGCAATTGGTTAA-TAGCCCCGACTTTATGGATAATATCCAGCTAG
3763547 CCTATTAATA
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
72 53 0.96
73 2 0.04
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.36
Consensus pattern (72 bp):
CTTGAGTTATCCCCCTAAAGCAATTGGTTAATAGCCCCGACTTTATGGATAATATCCAGCTAGTC
TGTTATA
Found at i:3764940 original size:42 final size:41
Alignment explanation
Indices: 3764893--3765024 Score: 123
Period size: 42 Copynumber: 3.3 Consensus size: 41
3764883 AATGTTGAGA
3764893 CATTTTGAAGGCCCATTTTAGACATAAATGATCCACGTGGGG
1 CATTTTGAAGGCCCATTTTAGACATAAATGATCCA-GTGGGG
* ** * * * *
3764935 CATTTTGAAGGCTCACATTAG-TATGAAA-G-T---TTGAGA
1 CATTTTGAAGGCCCATTTTAGACAT-AAATGATCCAGTGGGG
*
3764971 CATTTTGAAGGCCCATTTTAGACAAAAATGATCCATGTGGGG
1 CATTTTGAAGGCCCATTTTAGACATAAATGATCCA-GTGGGG
3765013 CATTTTGAAGGC
1 CATTTTGAAGGC
3765025 TCACATTAAC
Statistics
Matches: 67, Mismatches: 15, Indels: 16
0.68 0.15 0.16
Matches are distributed among these distances:
36 24 0.36
37 2 0.03
38 1 0.01
40 1 0.01
41 3 0.04
42 36 0.54
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.30
Consensus pattern (41 bp):
CATTTTGAAGGCCCATTTTAGACATAAATGATCCAGTGGGG
Found at i:3764976 original size:78 final size:78
Alignment explanation
Indices: 3764887--3765032 Score: 274
Period size: 78 Copynumber: 1.9 Consensus size: 78
3764877 AAATAGAATG
*
3764887 TTGAGACATTTTGAAGGCCCATTTTAGACATAAATGATCCACGTGGGGCATTTTGAAGGCTCACA
1 TTGAGACATTTTGAAGGCCCATTTTAGACAAAAATGATCCACGTGGGGCATTTTGAAGGCTCACA
3764952 TTAGTATGAAAGT
66 TTAGTATGAAAGT
*
3764965 TTGAGACATTTTGAAGGCCCATTTTAGACAAAAATGATCCATGTGGGGCATTTTGAAGGCTCACA
1 TTGAGACATTTTGAAGGCCCATTTTAGACAAAAATGATCCACGTGGGGCATTTTGAAGGCTCACA
3765030 TTA
66 TTA
3765033 ACAAGAAGCA
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
78 66 1.00
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.31
Consensus pattern (78 bp):
TTGAGACATTTTGAAGGCCCATTTTAGACAAAAATGATCCACGTGGGGCATTTTGAAGGCTCACA
TTAGTATGAAAGT
Found at i:3765920 original size:22 final size:22
Alignment explanation
Indices: 3765868--3765924 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
3765858 ACATATACAT
*
3765868 TCTTTAAAAATGATAGATTCTC
1 TCTTTAAAGATGATAGATTCTC
3765890 TCTTTAAAGATGATAGATTCTC
1 TCTTTAAAGATGATAGATTCTC
3765912 T-TTTCAAAGATGA
1 TCTTT-AAAGATGA
3765925 AAATTTTATT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
21 3 0.09
22 30 0.91
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.40
Consensus pattern (22 bp):
TCTTTAAAGATGATAGATTCTC
Found at i:3766665 original size:48 final size:47
Alignment explanation
Indices: 3766557--3766962 Score: 499
Period size: 45 Copynumber: 8.7 Consensus size: 47
3766547 CTATTTCCTA
*
3766557 CATCCATAAGACCTACAGTGTAGGATGTTATT-AAAAAGCCTTCGGGT
1 CATCCATAAGACCTACAGTGCAGGATGTT-TTCAAAAAGCCTTCGGGT
* * *
3766604 CATCCATAGGACCTTCAGTGCAGGATGTTATCAAAAAAGCCTTCGGGT
1 CATCCATAAGACCTACAGTGCAGGATGTTTTC-AAAAAGCCTTCGGGT
* * *
3766652 CATCCATAAGACCTTCAATGCAGGATGTTATCAAAAAAGCCTTCGGGT
1 CATCCATAAGACCTACAGTGCAGGATGTTTTC-AAAAAGCCTTCGGGT
* * * * *
3766700 CATCCATAGGACCTTCAGTGCATGATGTTATCAAAAAAGCCTTCTGGT
1 CATCCATAAGACCTACAGTGCAGGATGTTTTC-AAAAAGCCTTCGGGT
* *
3766748 CATCTATAAGACCTACAGTGTAGGATGTTTTC-AAAA-CCTTCGGGT
1 CATCCATAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGT
* * * *
3766793 CATCCATAAGACCTACAGTGTATGATGTTTTC--AAAGCCTTTGAGT
1 CATCCATAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGT
*
3766838 CATCCATAAGACCTACAGTGCATGATGTTTTC-AAAA-CCTTCGGGT
1 CATCCATAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGT
3766883 CATCCATAAGACCTACAGTGCAGGATGTTTTC-AAAA-CCTTCGGGT
1 CATCCATAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGT
** *
3766928 CATCTGTAAGACC-ATCAGTGCATGATGTTTTCAAA
1 CATCCATAAGACCTA-CAGTGCAGGATGTTTTCAAA
3766963 TGAGATTTTA
Statistics
Matches: 325, Mismatches: 28, Indels: 13
0.89 0.08 0.04
Matches are distributed among these distances:
44 4 0.01
45 154 0.47
46 10 0.03
47 26 0.08
48 131 0.40
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Consensus pattern (47 bp):
CATCCATAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGT
Found at i:3767315 original size:14 final size:14
Alignment explanation
Indices: 3767298--3767337 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
3767288 TGTCCATTCG
3767298 TTTTATT-TTATTAT
1 TTTTATTATTATT-T
*
3767312 TTTTATTACTATTT
1 TTTTATTATTATTT
3767326 TTTTATTATTAT
1 TTTTATTATTAT
3767338 AATTATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 19 0.83
15 4 0.17
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.75
Consensus pattern (14 bp):
TTTTATTATTATTT
Found at i:3767346 original size:2 final size:2
Alignment explanation
Indices: 3767341--3767365 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3767331 TTATTATAAT
3767341 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
3767366 TATTAAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3768646 original size:14 final size:15
Alignment explanation
Indices: 3768610--3768653 Score: 72
Period size: 15 Copynumber: 3.0 Consensus size: 15
3768600 TATTCTTATA
3768610 GTTTTAATTTCATTT
1 GTTTTAATTTCATTT
3768625 GTTTTAATTTCATTT
1 GTTTTAATTTCATTT
*
3768640 G-TTTAATTACATTT
1 GTTTTAATTTCATTT
3768654 TAATTTAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
14 12 0.43
15 16 0.57
ACGTcount: A:0.23, C:0.07, G:0.07, T:0.64
Consensus pattern (15 bp):
GTTTTAATTTCATTT
Found at i:3768664 original size:25 final size:27
Alignment explanation
Indices: 3768626--3768702 Score: 81
Period size: 25 Copynumber: 2.9 Consensus size: 27
3768616 ATTTCATTTG
*
3768626 TTTTAATTTCATTTGTT-TAATTA-CA
1 TTTTAATTTAATTTGTTATAATTATCA
*
3768651 TTTTAATTTAATTT-TTATTATTATCA
1 TTTTAATTTAATTTGTTATAATTATCA
*
3768677 TTTTAATTTCAATATGTTCA-AATTAT
1 TTTTAATTT-AATTTGTT-ATAATTAT
3768703 TAATTATTAT
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
24 2 0.05
25 18 0.42
26 11 0.26
27 4 0.09
28 7 0.16
29 1 0.02
ACGTcount: A:0.31, C:0.06, G:0.03, T:0.60
Consensus pattern (27 bp):
TTTTAATTTAATTTGTTATAATTATCA
Done.