Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004614.1 Hibiscus syriacus cultivar Beakdansim tig00010320_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: 491648
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
File 2 of 2
Found at i:441168 original size:19 final size:19
Alignment explanation
Indices: 441144--441180 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
441134 TGACTTATTA
441144 AAGGGAGATGAATGCATTC
1 AAGGGAGATGAATGCATTC
*
441163 AAGGGAGATGGATGCATT
1 AAGGGAGATGAATGCATT
441181 ATTTTCAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.35, C:0.08, G:0.35, T:0.22
Consensus pattern (19 bp):
AAGGGAGATGAATGCATTC
Found at i:444121 original size:13 final size:13
Alignment explanation
Indices: 444099--444128 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
444089 ACTAAACACC
444099 TTTC-ACATACCT
1 TTTCAACATACCT
444111 TTTCAACATACCT
1 TTTCAACATACCT
444124 TTTCA
1 TTTCA
444129 TCTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:452975 original size:8 final size:8
Alignment explanation
Indices: 452964--453021 Score: 73
Period size: 8 Copynumber: 7.0 Consensus size: 8
452954 AAAGAAGAGA
452964 AAAAGAAG
1 AAAAGAAG
*
452972 AAAAGAAT
1 AAAAGAAG
452980 AAAAGAAG
1 AAAAGAAG
452988 AAAAGAAG
1 AAAAGAAG
452996 AAAAGAAAAG
1 AAAAG--AAG
453006 AAAAGAA-
1 AAAAGAAG
453013 AAAGAGAAG
1 AAA-AGAAG
453022 TTCAAAAAGA
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
7 3 0.07
8 33 0.75
10 8 0.18
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (8 bp):
AAAAGAAG
Found at i:452977 original size:5 final size:5
Alignment explanation
Indices: 452953--453014 Score: 60
Period size: 5 Copynumber: 12.8 Consensus size: 5
452943 TTGGAGTGCA
* *
452953 AAAAG AAGAG AAAA- AGAAG AAAAG AATAA- AAGAAG AAAAG --AAG AAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG AA-AAG AA-AAG AAAAG AAAAG AAAAG
453001 AAAAG AAAAG AAAA
1 AAAAG AAAAG AAAA
453015 AGAGAAGTTC
Statistics
Matches: 47, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
3 3 0.06
4 3 0.06
5 37 0.79
6 4 0.09
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (5 bp):
AAAAG
Found at i:461752 original size:11 final size:11
Alignment explanation
Indices: 461736--461785 Score: 59
Period size: 11 Copynumber: 4.6 Consensus size: 11
461726 ATTGGAGTGC
*
461736 AAAAAGAAGAG
1 AAAAAGAAAAG
461747 AAAAAGAAGAA-
1 AAAAAGAA-AAG
*
461758 AAGAAGAAAAG
1 AAAAAGAAAAG
461769 -AAAAGAAAAG
1 AAAAAGAAAAG
461779 AAAAAGA
1 AAAAAGA
461786 GAAGTTCAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
10 11 0.33
11 21 0.64
12 1 0.03
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:461759 original size:8 final size:8
Alignment explanation
Indices: 461748--461789 Score: 50
Period size: 8 Copynumber: 5.0 Consensus size: 8
461738 AAAGAAGAGA
461748 AAAAGAAG
1 AAAAGAAG
461756 AAAAGAAG
1 AAAAGAAG
461764 AAAAGAAAAG
1 AAAAG--AAG
461774 AAAAGAA-
1 AAAAGAAG
461781 AAAGAGAAG
1 AAA-AGAAG
461790 TTCAAAAAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
7 3 0.10
8 19 0.63
10 8 0.27
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (8 bp):
AAAAGAAG
Found at i:461761 original size:5 final size:5
Alignment explanation
Indices: 461737--461782 Score: 53
Period size: 5 Copynumber: 9.8 Consensus size: 5
461727 TTGGAGTGCA
* *
461737 AAAAG AAGAG AAAA- AGAAG AAAAG --AAG AAAAG AAAAG AAAAG AAAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
461783 AGAGAAGTTC
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
3 3 0.09
4 3 0.09
5 28 0.82
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:461788 original size:18 final size:18
Alignment explanation
Indices: 461737--461780 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
461727 TTGGAGTGCA
461737 AAAAGAAGAGAAA-AAGAAG
1 AAAAGAAGA-AAAGAA-AAG
461756 AAAAGAAGAAAAGAAAAG
1 AAAAGAAGAAAAGAAAAG
461774 AAAAGAA
1 AAAAGAA
461781 AAAGAGAAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 13 0.54
19 11 0.46
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (18 bp):
AAAAGAAGAAAAGAAAAG
Found at i:463893 original size:16 final size:16
Alignment explanation
Indices: 463869--463900 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
463859 TAGTTAGCTC
*
463869 ATTTTCATTCTAACAT
1 ATTTGCATTCTAACAT
463885 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
463901 TGGTGGAAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.31, C:0.19, G:0.03, T:0.47
Consensus pattern (16 bp):
ATTTGCATTCTAACAT
Found at i:465321 original size:29 final size:29
Alignment explanation
Indices: 465285--465343 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
465275 AATCATCCAC
465285 AATGAAAGAAAATTCATTTTGACTCCATT
1 AATGAAAGAAAATTCATTTTGACTCCATT
465314 AATGAAAGAAAATTCATTTTGACTCCATT
1 AATGAAAGAAAATTCATTTTGACTCCATT
465343 A
1 A
465344 TCTCCTAGCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.42, C:0.14, G:0.10, T:0.34
Consensus pattern (29 bp):
AATGAAAGAAAATTCATTTTGACTCCATT
Found at i:473786 original size:24 final size:21
Alignment explanation
Indices: 473751--473793 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
473741 GGCTCATTCT
*
473751 TTTGAATTTCAAGAGGTACATCC
1 TTTGAATGTCAA-AGG-ACATCC
473774 TTTGAAATGTCAAAGGACAT
1 TTTG-AATGTCAAAGGACAT
473794 ATCTTGTGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 7 0.39
24 7 0.39
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (21 bp):
TTTGAATGTCAAAGGACATCC
Found at i:477096 original size:20 final size:21
Alignment explanation
Indices: 477059--477097 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
477049 GATGGTCTTG
*
477059 ATGAAGGATGTTGATGATGAA
1 ATGAAGGATGGTGATGATGAA
*
477080 ATGAA-GATGGTGGTGATG
1 ATGAAGGATGGTGATGATG
477098 TTGTATCTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.33, C:0.00, G:0.38, T:0.28
Consensus pattern (21 bp):
ATGAAGGATGGTGATGATGAA
Found at i:485240 original size:8 final size:8
Alignment explanation
Indices: 485227--485290 Score: 51
Period size: 8 Copynumber: 7.5 Consensus size: 8
485217 GAACTTCTCT
485227 TTTTCTT-
1 TTTTCTTC
485234 TTCTTCTTC
1 TT-TTCTTC
485243 TTTTCTTC
1 TTTTCTTC
*
485251 TTTTCTGATT
1 TTTTCT--TC
485261 TTTCTCTTC
1 TTT-TCTTC
485270 TTTT-TGTC
1 TTTTCT-TC
485278 TTTTCTTTC
1 TTTTC-TTC
485287 TTTT
1 TTTT
485291 TGCACTCCAA
Statistics
Matches: 47, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
7 3 0.06
8 24 0.51
9 12 0.26
10 5 0.11
11 3 0.06
ACGTcount: A:0.02, C:0.20, G:0.03, T:0.75
Consensus pattern (8 bp):
TTTTCTTC
Found at i:485242 original size:19 final size:19
Alignment explanation
Indices: 485220--485256 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
485210 TCTTTTTGAA
485220 CTTCTCTTT-TTCTTTTCTT
1 CTTCT-TTTCTTCTTTTCTT
485239 CTTCTTTTCTTCTTTTCT
1 CTTCTTTTCTTCTTTTCT
485257 GATTTTTCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 3 0.18
19 14 0.82
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (19 bp):
CTTCTTTTCTTCTTTTCTT
Found at i:485289 original size:17 final size:18
Alignment explanation
Indices: 485241--485292 Score: 65
Period size: 17 Copynumber: 2.9 Consensus size: 18
485231 CTTTTCTTCT
485241 TCTTTTC-TTCTTTTCTGA
1 TCTTTTCTTTCTTTT-TGA
485259 T-TTTTCTCTTCTTTTTG-
1 TCTTTTCT-TTCTTTTTGA
485276 TCTTTTCTTTCTTTTTG
1 TCTTTTCTTTCTTTTTG
485293 CACTCCAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
17 15 0.48
18 9 0.29
19 7 0.23
ACGTcount: A:0.02, C:0.19, G:0.06, T:0.73
Consensus pattern (18 bp):
TCTTTTCTTTCTTTTTGA
Found at i:485290 original size:27 final size:28
Alignment explanation
Indices: 485220--485290 Score: 78
Period size: 27 Copynumber: 2.6 Consensus size: 28
485210 TCTTTTTGAA
*
485220 CTTCTCTT-TTTCTTTTCTTCTTCTTTT
1 CTTCTTTTCTTTCTTTTCTTCTTCTTTT
*
485247 CTTCTTTTCTGAT-TTTTC-TCTTCTTTT
1 CTTCTTTTCT-TTCTTTTCTTCTTCTTTT
485274 -TGTCTTTTCTTTCTTTT
1 CT-TCTTTTCTTTCTTTT
485291 TGCACTCCAA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
26 2 0.05
27 28 0.76
28 6 0.16
29 1 0.03
ACGTcount: A:0.01, C:0.23, G:0.03, T:0.73
Consensus pattern (28 bp):
CTTCTTTTCTTTCTTTTCTTCTTCTTTT
Found at i:487929 original size:19 final size:21
Alignment explanation
Indices: 487886--487937 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
487876 GAAACCCCTT
487886 TGAAGATACATGACTTTTAAA
1 TGAAGATACATGACTTTTAAA
*
487907 TGAAAATACATGA-TTTT-AA
1 TGAAGATACATGACTTTTAAA
487926 TGAAGATACATG
1 TGAAGATACATG
487938 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 13 0.45
20 4 0.14
21 12 0.41
ACGTcount: A:0.44, C:0.08, G:0.15, T:0.33
Consensus pattern (21 bp):
TGAAGATACATGACTTTTAAA
Found at i:488860 original size:23 final size:24
Alignment explanation
Indices: 488830--488883 Score: 92
Period size: 24 Copynumber: 2.3 Consensus size: 24
488820 ATATTATAAC
488830 TGATGTATGGC-TCTGATACCACT
1 TGATGTATGGCTTCTGATACCACT
*
488853 TGATGTATGGCTTCTGATGCCACT
1 TGATGTATGGCTTCTGATACCACT
488877 TGATGTA
1 TGATGTA
488884 AGGTAATTCT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 11 0.38
24 18 0.62
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.37
Consensus pattern (24 bp):
TGATGTATGGCTTCTGATACCACT
Found at i:489661 original size:90 final size:91
Alignment explanation
Indices: 489545--489717 Score: 269
Period size: 90 Copynumber: 1.9 Consensus size: 91
489535 GGGAAATGAT
* *
489545 GCTTGGCCGAATAGGGAGAGAGCTCTTCATCTTGGCGCCTAAATAAAT-CACATGCAAGGCACAT
1 GCTTGGCCAAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAAT-AATCCACATGCAAGGCACAT
*
489609 -GGGGCTGTTCACATGCAAAACACGTG
65 GGGGGCTGGTCACATGCAAAACACGTG
* *
489635 GCTTGGCCAAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATGATCCTCATGCAAGGCACATG
1 GCTTGGCCAAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATAATCCACATGCAAGGCACATG
*
489700 GGGGCTGGTCATATGCAA
66 GGGGCTGGTCACATGCAA
489718 GGCACATGGG
Statistics
Matches: 75, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
89 2 0.03
90 57 0.76
91 16 0.21
ACGTcount: A:0.28, C:0.23, G:0.27, T:0.22
Consensus pattern (91 bp):
GCTTGGCCAAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATAATCCACATGCAAGGCACATG
GGGGCTGGTCACATGCAAAACACGTG
Done.