Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007604.1 Hibiscus syriacus cultivar Beakdansim tig00022304_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: 89696
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Found at i:1445 original size:28 final size:24
Alignment explanation
Indices: 1390--1455 Score: 114
Period size: 24 Copynumber: 2.8 Consensus size: 24
1380 TACTCGTTGC
*
1390 TGAATGACGTACCTTTCCCTACGA
1 TGAATGAAGTACCTTTCCCTACGA
1414 TGAATGAAGTACCTTTCCCTACGA
1 TGAATGAAGTACCTTTCCCTACGA
*
1438 TGAATGAAGTCCCTTTCC
1 TGAATGAAGTACCTTTCC
1456 TCTAGCTGGA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.26, C:0.27, G:0.17, T:0.30
Consensus pattern (24 bp):
TGAATGAAGTACCTTTCCCTACGA
Found at i:1809 original size:14 final size:14
Alignment explanation
Indices: 1790--1818 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1780 CGAACGCGAC
1790 TAACGCTTTCCTGG
1 TAACGCTTTCCTGG
1804 TAACGCTTTCCTGG
1 TAACGCTTTCCTGG
1818 T
1 T
1819 TTTGTAAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.28, G:0.21, T:0.38
Consensus pattern (14 bp):
TAACGCTTTCCTGG
Found at i:20606 original size:18 final size:18
Alignment explanation
Indices: 20591--20636 Score: 92
Period size: 18 Copynumber: 2.6 Consensus size: 18
20581 TATTTGATAG
20591 GCTTTTGTGGTTTGATTC
1 GCTTTTGTGGTTTGATTC
20609 GCTTTTGTGGTTTGATTC
1 GCTTTTGTGGTTTGATTC
20627 GCTTTTGTGG
1 GCTTTTGTGG
20637 AAGGTGATGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.04, C:0.11, G:0.30, T:0.54
Consensus pattern (18 bp):
GCTTTTGTGGTTTGATTC
Found at i:27935 original size:32 final size:32
Alignment explanation
Indices: 27894--27955 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
27884 CATCTATTTT
27894 CATTGTTCAACTCTTTGACAACACGAAAAATC
1 CATTGTTCAACTCTTTGACAACACGAAAAATC
*
27926 CATTGTTCAACTCTTTGACAACATGAAAAA
1 CATTGTTCAACTCTTTGACAACACGAAAAA
27956 ACCAAAAGCT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.39, C:0.23, G:0.10, T:0.29
Consensus pattern (32 bp):
CATTGTTCAACTCTTTGACAACACGAAAAATC
Found at i:28590 original size:16 final size:17
Alignment explanation
Indices: 28558--28603 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 17
28548 CATCCCTTGG
28558 GGTTAGTTCATTCTCTT
1 GGTTAGTTCATTCTCTT
*
28575 GGTTAGTTGA-TCTCTT
1 GGTTAGTTCATTCTCTT
* *
28591 GCTTAGTTTATTC
1 GGTTAGTTCATTC
28604 CATTTACTGC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 14 0.56
17 11 0.44
ACGTcount: A:0.13, C:0.15, G:0.20, T:0.52
Consensus pattern (17 bp):
GGTTAGTTCATTCTCTT
Found at i:42209 original size:7 final size:7
Alignment explanation
Indices: 42194--42224 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
42184 TTCTTGCCTC
*
42194 CCTCTCT
1 CCTCCCT
42201 CCTCCCT
1 CCTCCCT
42208 CCTCCCT
1 CCTCCCT
42215 CCTCCCT
1 CCTCCCT
42222 CCT
1 CCT
42225 TGGAGCTCGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.00, C:0.68, G:0.00, T:0.32
Consensus pattern (7 bp):
CCTCCCT
Found at i:47067 original size:17 final size:17
Alignment explanation
Indices: 47045--47078 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
47035 GAGCTTTCCT
47045 CGTACGATGCGATGGTC
1 CGTACGATGCGATGGTC
47062 CGTACGATGCGATGGTC
1 CGTACGATGCGATGGTC
47079 GTCAGTTTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.18, C:0.24, G:0.35, T:0.24
Consensus pattern (17 bp):
CGTACGATGCGATGGTC
Found at i:48651 original size:16 final size:17
Alignment explanation
Indices: 48625--48658 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
48615 GTAGTGTACT
48625 TTTACGATATGGTAGTA
1 TTTACGATATGGTAGTA
48642 TTTA-GATATGGTAGTA
1 TTTACGATATGGTAGTA
48658 T
1 T
48659 AGTGGCCCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.29, C:0.03, G:0.24, T:0.44
Consensus pattern (17 bp):
TTTACGATATGGTAGTA
Found at i:49240 original size:27 final size:27
Alignment explanation
Indices: 49202--49255 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
49192 TCAAAAGTAA
49202 GAACAATAATACAACTAAACACTTTCC
1 GAACAATAATACAACTAAACACTTTCC
*
49229 GAACAATAATACAACTAAAGACTTTCC
1 GAACAATAATACAACTAAACACTTTCC
49256 TTCTAGTAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.48, C:0.24, G:0.06, T:0.22
Consensus pattern (27 bp):
GAACAATAATACAACTAAACACTTTCC
Found at i:49311 original size:28 final size:28
Alignment explanation
Indices: 49271--49327 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
49261 GTAGTGTACC
49271 TTCGCATACGCATCGCATCTCTCTTATA
1 TTCGCATACGCATCGCATCTCTCTTATA
49299 TTCGCATACGCATCGCATCTCTCTTATA
1 TTCGCATACGCATCGCATCTCTCTTATA
49327 T
1 T
49328 AAGATAAAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.21, C:0.32, G:0.11, T:0.37
Consensus pattern (28 bp):
TTCGCATACGCATCGCATCTCTCTTATA
Found at i:52532 original size:31 final size:31
Alignment explanation
Indices: 52494--52588 Score: 190
Period size: 31 Copynumber: 3.1 Consensus size: 31
52484 GCATGAATTC
52494 TTGGGCTATATAAAAAATGTAATAAAGTCAA
1 TTGGGCTATATAAAAAATGTAATAAAGTCAA
52525 TTGGGCTATATAAAAAATGTAATAAAGTCAA
1 TTGGGCTATATAAAAAATGTAATAAAGTCAA
52556 TTGGGCTATATAAAAAATGTAATAAAGTCAA
1 TTGGGCTATATAAAAAATGTAATAAAGTCAA
52587 TT
1 TT
52589 CAATGAATAG
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 64 1.00
ACGTcount: A:0.47, C:0.06, G:0.16, T:0.31
Consensus pattern (31 bp):
TTGGGCTATATAAAAAATGTAATAAAGTCAA
Found at i:59045 original size:28 final size:24
Alignment explanation
Indices: 58990--59055 Score: 114
Period size: 24 Copynumber: 2.8 Consensus size: 24
58980 TACTCGTTGC
*
58990 TGAATGACGTACCTTTCCCTACGA
1 TGAATGAAGTACCTTTCCCTACGA
59014 TGAATGAAGTACCTTTCCCTACGA
1 TGAATGAAGTACCTTTCCCTACGA
*
59038 TGAATGAAGTCCCTTTCC
1 TGAATGAAGTACCTTTCC
59056 TCTAGCTGGA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.26, C:0.27, G:0.17, T:0.30
Consensus pattern (24 bp):
TGAATGAAGTACCTTTCCCTACGA
Found at i:59409 original size:14 final size:14
Alignment explanation
Indices: 59390--59418 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
59380 CGAACGCGAC
59390 TAACGCTTTCCTGG
1 TAACGCTTTCCTGG
59404 TAACGCTTTCCTGG
1 TAACGCTTTCCTGG
59418 T
1 T
59419 TTTGTAAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.28, G:0.21, T:0.38
Consensus pattern (14 bp):
TAACGCTTTCCTGG
Found at i:78207 original size:18 final size:18
Alignment explanation
Indices: 78192--78237 Score: 92
Period size: 18 Copynumber: 2.6 Consensus size: 18
78182 TATTTGATAG
78192 GCTTTTGTGGTTTGATTC
1 GCTTTTGTGGTTTGATTC
78210 GCTTTTGTGGTTTGATTC
1 GCTTTTGTGGTTTGATTC
78228 GCTTTTGTGG
1 GCTTTTGTGG
78238 AAGGTGATGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.04, C:0.11, G:0.30, T:0.54
Consensus pattern (18 bp):
GCTTTTGTGGTTTGATTC
Found at i:85529 original size:32 final size:32
Alignment explanation
Indices: 85488--85549 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
85478 CATCTATTTT
85488 CATTGTTCAACTCTTTGACAACACGAAAAATC
1 CATTGTTCAACTCTTTGACAACACGAAAAATC
*
85520 CATTGTTCAACTCTTTGACAACATGAAAAA
1 CATTGTTCAACTCTTTGACAACACGAAAAA
85550 CCAAAAGCTC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.39, C:0.23, G:0.10, T:0.29
Consensus pattern (32 bp):
CATTGTTCAACTCTTTGACAACACGAAAAATC
Found at i:86183 original size:16 final size:17
Alignment explanation
Indices: 86151--86196 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 17
86141 CATCCCTTGG
86151 GGTTAGTTCATTCTCTT
1 GGTTAGTTCATTCTCTT
*
86168 GGTTAGTTGA-TCTCTT
1 GGTTAGTTCATTCTCTT
* *
86184 GCTTAGTTTATTC
1 GGTTAGTTCATTC
86197 CATTTACTCT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 14 0.56
17 11 0.44
ACGTcount: A:0.13, C:0.15, G:0.20, T:0.52
Consensus pattern (17 bp):
GGTTAGTTCATTCTCTT
Done.