Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000212.1 Hibiscus syriacus cultivar Beakdansim tig00000375_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: 42353
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Found at i:5200 original size:102 final size:101
Alignment explanation
Indices: 5056--5259 Score: 318
Period size: 102 Copynumber: 2.0 Consensus size: 101
5046 TCACATGATG
* *
5056 ACTCTACCTGACTAGCTCGGGGTGGAAGGTATGCTCCATTTCACTTAGAATGTGTGATGGTAGTG
1 ACTCTACCTGACTAGCTCGGGGTAGAAGGTATGCTCCATTTCACTTAGAATGTGGGATGGTAGTG
*
5121 TGATGAGTTGACACCCCTTAAAGTATGCTTAAAAAA
66 TGATGAGATGACACCCCTTAAAGTATGCTTAAAAAA
* * * * *
5157 ACTCTACTTGACTAGCTTGGGAGTAGAAGGTATGCTCCCTTTCATTTAGAGTGTGGGATGGTAGT
1 ACTCTACCTGACTAGCTCGGG-GTAGAAGGTATGCTCCATTTCACTTAGAATGTGGGATGGTAGT
*
5222 GTGATGAGATGACTCCCCTTAAAGTATGCTTAAAAAA
65 GTGATGAGATGACACCCCTTAAAGTATGCTTAAAAAA
5259 A
1 A
5260 GTTGAAGTTA
Statistics
Matches: 93, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
101 19 0.20
102 74 0.80
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (101 bp):
ACTCTACCTGACTAGCTCGGGGTAGAAGGTATGCTCCATTTCACTTAGAATGTGGGATGGTAGTG
TGATGAGATGACACCCCTTAAAGTATGCTTAAAAAA
Found at i:12443 original size:36 final size:36
Alignment explanation
Indices: 12396--12620 Score: 317
Period size: 36 Copynumber: 6.3 Consensus size: 36
12386 AAGTTTGCAT
*
12396 CGATTCAAGTCGAACGGAGGGAAGCATCGGCACTTC
1 CGATTCAAGTCGAACGGAAGGAAGCATCGGCACTTC
* *
12432 CGATTCAAGTCGAACGGAGGGAAGCATTGGCACTTC
1 CGATTCAAGTCGAACGGAAGGAAGCATCGGCACTTC
* * *
12468 CGATTCAAATCGAACGAAAGGAAGCATCGGTACTTC
1 CGATTCAAGTCGAACGGAAGGAAGCATCGGCACTTC
* *
12504 CGATTCAAGTCAAACGGAAGGAAGCATCGACACTTC
1 CGATTCAAGTCGAACGGAAGGAAGCATCGGCACTTC
* *
12540 CGATTCAAGT-GAACGGAAGGAAGCATCGACATTTC
1 CGATTCAAGTCGAACGGAAGGAAGCATCGGCACTTC
* * * *
12575 TGATTCAAATCGAACGGAAGGAAGCATAGGCACTTT
1 CGATTCAAGTCGAACGGAAGGAAGCATCGGCACTTC
12611 CGATTCAAGT
1 CGATTCAAGT
12621 GTTTATTTTT
Statistics
Matches: 167, Mismatches: 21, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
35 31 0.19
36 136 0.81
ACGTcount: A:0.33, C:0.22, G:0.26, T:0.20
Consensus pattern (36 bp):
CGATTCAAGTCGAACGGAAGGAAGCATCGGCACTTC
Found at i:19318 original size:22 final size:22
Alignment explanation
Indices: 19293--19350 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
19283 ATTAAATTAA
19293 TAATA-AAATATATTTAATAAGT
1 TAATATAAATATATTT-ATAAGT
* *
19315 TAATATAAAAATATTTTTAAGT
1 TAATATAAATATATTTATAAGT
*
19337 TAATATATATATAT
1 TAATATAAATATAT
19351 ACATACAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
22 22 0.71
23 9 0.29
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (22 bp):
TAATATAAATATATTTATAAGT
Found at i:19325 original size:25 final size:23
Alignment explanation
Indices: 19284--19345 Score: 74
Period size: 25 Copynumber: 2.7 Consensus size: 23
19274 TTTTTTAAAA
*
19284 TTAAATTAATA-ATAAAATATATT
1 TTAAGTTAATATATAAAATAT-TT
19307 TAATAAGTTAATATA-AAAATATTT
1 T--TAAGTTAATATATAAAATATTT
19331 TTAAGTTAATATATA
1 TTAAGTTAATATATA
19346 TATATACATA
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
22 12 0.35
23 2 0.06
24 3 0.09
25 16 0.47
26 1 0.03
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (23 bp):
TTAAGTTAATATATAAAATATTT
Found at i:22631 original size:33 final size:32
Alignment explanation
Indices: 22584--22648 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 32
22574 AACTGATCCA
22584 ATCATTAAACTGATTCTAAAGTAGCCTTGAGT
1 ATCATTAAACTGATTCTAAAGTAGCCTTGAGT
22616 ATCATTAAAACTGATTCTAAAGTAGCCTTGAGT
1 ATCATT-AAACTGATTCTAAAGTAGCCTTGAGT
22649 TGGATCTTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 6 0.19
33 26 0.81
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Consensus pattern (32 bp):
ATCATTAAACTGATTCTAAAGTAGCCTTGAGT
Found at i:30195 original size:23 final size:21
Alignment explanation
Indices: 30164--30217 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 21
30154 TTTTTTAAAA
*
30164 TTAAATTAATAATAAAATATT
1 TTAAGTTAATAATAAAATATT
30185 TAATAAGTTAAT-ATAAAATATT
1 T--TAAGTTAATAATAAAATATT
30207 TTAAGTTAATA
1 TTAAGTTAATA
30218 TATATATACA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
20 9 0.31
21 1 0.03
22 11 0.38
23 8 0.28
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.43
Consensus pattern (21 bp):
TTAAGTTAATAATAAAATATT
Found at i:30218 original size:20 final size:20
Alignment explanation
Indices: 30164--30219 Score: 76
Period size: 20 Copynumber: 2.6 Consensus size: 20
30154 TTTTTTAAAA
*
30164 TTAAATTAATAATAAAATATT
1 TTAAGTTAAT-ATAAAATATT
30185 TAATAAGTTAATATAAAATATT
1 T--TAAGTTAATATAAAATATT
30207 TTAAGTTAATATA
1 TTAAGTTAATATA
30220 TATATACATA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
20 12 0.38
21 1 0.03
22 11 0.34
23 8 0.25
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.43
Consensus pattern (20 bp):
TTAAGTTAATATAAAATATT
Found at i:33416 original size:33 final size:32
Alignment explanation
Indices: 33369--33433 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 32
33359 AACTGATCCA
33369 ATCATTAAACTGATTCTAAAGTAGCCTTGAGT
1 ATCATTAAACTGATTCTAAAGTAGCCTTGAGT
33401 ATCATTAAAACTGATTCTAAAGTAGCCTTGAGT
1 ATCATT-AAACTGATTCTAAAGTAGCCTTGAGT
33434 TGGATCTTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 6 0.19
33 26 0.81
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Consensus pattern (32 bp):
ATCATTAAACTGATTCTAAAGTAGCCTTGAGT
Found at i:41882 original size:28 final size:27
Alignment explanation
Indices: 41802--41882 Score: 72
Period size: 28 Copynumber: 2.9 Consensus size: 27
41792 ACATTTTTGT
*
41802 CCTTTTAATTTCATTCCTTTAATTTCC
1 CCTTTTAATTTCAGTCCTTTAATTTCC
* * ** * *
41829 CCTTTTATTTTTCTGTGTTTTTATTTCTG
1 CCTTTTA-ATTTCAGTCCTTTAATTTC-C
*
41858 GCTTTTAATTTCAGTCCTTTAATTT
1 CCTTTTAATTTCAGTCCTTTAATTT
41883 ATACCCTTTT
Statistics
Matches: 39, Mismatches: 13, Indels: 3
0.71 0.24 0.05
Matches are distributed among these distances:
27 7 0.18
28 26 0.67
29 6 0.15
ACGTcount: A:0.15, C:0.19, G:0.06, T:0.60
Consensus pattern (27 bp):
CCTTTTAATTTCAGTCCTTTAATTTCC
Done.