Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000614.1 Hibiscus syriacus cultivar Beakdansim tig00001191_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: 71745
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:1445 original size:2 final size:2
Alignment explanation
Indices: 1440--1468 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1430 TTCATAAAAA
1440 AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1469 TAAAAATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:3789 original size:21 final size:20
Alignment explanation
Indices: 3759--3820 Score: 74
Period size: 19 Copynumber: 3.1 Consensus size: 20
3749 ATGTATTTAT
3759 TAATA-ATTTTAATAATAATA
1 TAATATATTTTAATAAT-ATA
*
3779 TAATATATTTTAATATTATA
1 TAATATATTTTAATAATATA
**
3799 TTCT-TATTTTAATAATATA
1 TAATATATTTTAATAATATA
3818 TAA
1 TAA
3821 ATTAATAATA
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
19 15 0.43
20 10 0.29
21 10 0.29
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (20 bp):
TAATATATTTTAATAATATA
Found at i:3838 original size:21 final size:19
Alignment explanation
Indices: 3814--3859 Score: 60
Period size: 18 Copynumber: 2.4 Consensus size: 19
3804 ATTTTAATAA
3814 TATATAAATTAATAATAAAAT
1 TATATAAA-T-ATAATAAAAT
3835 TATAT-AATATAATAAAAT
1 TATATAAATATAATAAAAT
3853 TA-ATAAA
1 TATATAAA
3860 ATTTATTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 2 0.08
18 14 0.58
19 1 0.04
20 2 0.08
21 5 0.21
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
TATATAAATATAATAAAAT
Found at i:3862 original size:27 final size:27
Alignment explanation
Indices: 3826--3879 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
3816 TATAAATTAA
3826 TAATAAAA-TTATATAATATAATAAAAT
1 TAATAAAATTTAT-TAATATAATAAAAT
* *
3853 TAATAAAATTTATTAATTTTATAAAAT
1 TAATAAAATTTATTAATATAATAAAAT
3880 ATTATTATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 20 0.83
28 4 0.17
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (27 bp):
TAATAAAATTTATTAATATAATAAAAT
Found at i:11329 original size:15 final size:15
Alignment explanation
Indices: 11309--11377 Score: 86
Period size: 15 Copynumber: 4.4 Consensus size: 15
11299 TCCATTATAG
*
11309 AGAAAAAAAGAGAAA
1 AGAAAAAAAGAAAAA
11324 AGAAAATAAAAGAAAAAA
1 AG-AAA-AAAAG-AAAAA
11342 AGAAAAAAAGAAAAA
1 AGAAAAAAAGAAAAA
11357 A-AGAAAAAAGAAAAA
1 AGA-AAAAAAGAAAAA
11372 AGAAAA
1 AGAAAA
11378 GAAATTAAAT
Statistics
Matches: 48, Mismatches: 1, Indels: 10
0.81 0.02 0.17
Matches are distributed among these distances:
14 1 0.02
15 24 0.50
16 9 0.19
17 8 0.17
18 6 0.12
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.01
Consensus pattern (15 bp):
AGAAAAAAAGAAAAA
Found at i:11342 original size:8 final size:8
Alignment explanation
Indices: 11309--11377 Score: 90
Period size: 8 Copynumber: 8.8 Consensus size: 8
11299 TCCATTATAG
11309 AGAAAAAA
1 AGAAAAAA
11317 AGAGAAAAGA
1 AGA-AAAA-A
*
11327 A-AATAAA
1 AGAAAAAA
11334 AGAAAAAA
1 AGAAAAAA
11342 AGAAAAAA
1 AGAAAAAA
11350 AGAAAAAA
1 AGAAAAAA
11358 AG-AAAAA
1 AGAAAAAA
11365 AG-AAAAA
1 AGAAAAAA
11372 AGAAAA
1 AGAAAA
11378 GAAATTAAAT
Statistics
Matches: 55, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
7 16 0.29
8 32 0.58
9 5 0.09
10 2 0.04
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.01
Consensus pattern (8 bp):
AGAAAAAA
Found at i:13677 original size:149 final size:150
Alignment explanation
Indices: 13352--13743 Score: 599
Period size: 149 Copynumber: 2.6 Consensus size: 150
13342 AAAAAATGAA
* *
13352 ATGATAAAGGTTTCTCATTCCAATTTGAAAAATTGAAATTTTTGAAAAGTAAGAAAGGTTTCTTA
1 ATGATAAAGGTTTCTTATTCAAATTTGAAAAATTGAAATTTTTGAAAAGTAAGAAAGGTTTCTTA
13417 CCTAGTAAAATATTTCCAAAATTTATAAGTCATTCGGACCATCCATAAGACCTTTGGGCAGGATG
66 CCTAGTAAAATATTTCCAAAATTTAT-AGTCATTCGGACCATCCATAAGACCTTTGGGCAGGATG
13482 ATTTCAAATGTCTATAAAAAT
130 ATTTCAAATGTCTATAAAAAT
**
13503 ATGATAAAGGTTTCTTATTCAAATTTGAAATTTTGAAATTTTTGAAAAGTAAGAAAGGTTTCTTA
1 ATGATAAAGGTTTCTTATTCAAATTTGAAAAATTGAAATTTTTGAAAAGTAAGAAAGGTTTCTTA
* * * *
13568 CCTAGTAAAGTATTTCCAAAATTTAT-GTCCTTCGGTCCATCCATAAGACCTTTGGGCAGTATG-
66 CCTAGTAAAATATTTCCAAAATTTATAGTCATTCGGACCATCCATAAGACCTTTGGGCAGGATGA
* * *
13631 TTTTATATTGTCTATCAAAAT
131 TTTCA-AATGTCTATAAAAAT
* * * * *
13652 ATGAGAAAGGTTTATTATTCGAATTTGAAAAATTGAAATTTTTAAAAAGTAAGAAATGTTTCTTA
1 ATGATAAAGGTTTCTTATTCAAATTTGAAAAATTGAAATTTTTGAAAAGTAAGAAAGGTTTCTTA
*
13717 CCTAGTAAACTATTTCCAAAATTTATA
66 CCTAGTAAAATATTTCCAAAATTTATA
13744 AGTCCTTTGG
Statistics
Matches: 220, Mismatches: 19, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
148 4 0.02
149 130 0.59
151 86 0.39
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.37
Consensus pattern (150 bp):
ATGATAAAGGTTTCTTATTCAAATTTGAAAAATTGAAATTTTTGAAAAGTAAGAAAGGTTTCTTA
CCTAGTAAAATATTTCCAAAATTTATAGTCATTCGGACCATCCATAAGACCTTTGGGCAGGATGA
TTTCAAATGTCTATAAAAAT
Found at i:13838 original size:41 final size:41
Alignment explanation
Indices: 13739--13854 Score: 126
Period size: 42 Copynumber: 2.8 Consensus size: 41
13729 TTTCCAAAAT
* * * * * *
13739 TTATAAGTCCTTTGGGCCATCAGTAAGTCTTTCGAGCATGA
1 TTATAAGTCCTTCGGGTCATCTGTAAGCCTTTCAAGCAAGA
*
13780 TGCT-TAAATCCTTCGGGTCATCTGTAAGCCTTTCAAGCAAGA
1 T--TATAAGTCCTTCGGGTCATCTGTAAGCCTTTCAAGCAAGA
*
13822 TTATAAGTCCTTCGGGTCATCTATAAGACCTTT
1 TTATAAGTCCTTCGGGTCATCTGTAAG-CCTTT
13855 GGCCAGGATG
Statistics
Matches: 62, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
40 1 0.02
41 23 0.37
42 37 0.60
43 1 0.02
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.34
Consensus pattern (41 bp):
TTATAAGTCCTTCGGGTCATCTGTAAGCCTTTCAAGCAAGA
Found at i:14066 original size:42 final size:42
Alignment explanation
Indices: 13973--14069 Score: 108
Period size: 42 Copynumber: 2.3 Consensus size: 42
13963 TCCAAAATTT
* * * *
13973 ATAAGTCCTTCGGTTCATCAGTAAGTCTTTCGAGCACGATGG
1 ATAAGTCCTTCGGCTCATCAGTAAGCCTTTAGAGCAAGATGG
* *
14015 TTAAATCCTTCGGCTCATCTA-TAAAGCCTTTAGAGCAAGAT-G
1 ATAAGTCCTTCGGCTCATC-AGT-AAGCCTTTAGAGCAAGATGG
14057 ATAAGTCCTTCGG
1 ATAAGTCCTTCGG
14070 GTTATTCATA
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
42 29 0.64
43 16 0.36
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.31
Consensus pattern (42 bp):
ATAAGTCCTTCGGCTCATCAGTAAGCCTTTAGAGCAAGATGG
Found at i:14341 original size:235 final size:233
Alignment explanation
Indices: 13594--14400 Score: 1151
Period size: 235 Copynumber: 3.5 Consensus size: 233
13584 CAAAATTTAT
* * **
13594 GTCCTTC-GGTCCATCCATAAGACCTTTGGGC-AGTATGTTTT-ATATTGTCTATCAAAATATGA
1 GTCCTTCGGGT-CATCCATAAGACCTTTGGGCAAG-ATGTTTTCACA-TGTCTTTTGAAATATGA
* * * * *
13656 GAAAGGTTTAT--TATTCGAATTTGAAAAATTGAAATTTTTAAAAAGTAAGAAATGTTTCTTACC
63 GAAAGGTTTCTCATATT-AAATCTG-AAAATTGAAA-TTTTGAAAAGTAAGAAAGGTTTCTTACC
** *
13719 TAGTAAACTATTTCCAAAATTTATAAGTCCTTTGGGCCATCAGTAAGTCTTTCGAGCATGATGCT
125 TAGTAAACTATTTCCAAAATTTATAAGTCCTTTGGTTCATCAGTAAGTCTTTCGAGCACGATGCT
* *
13784 TAAATCCTTCGGGTCATCTGTAAGCCTTTCAAGCAAGATTATAA
190 TAAATCCTTCGGGTCATCTGTAAGCCTTTCGAGCAAGATGATAA
* * *
13828 GTCCTTCGGGTCATCTATAAGACCTTTGGCCAGGATGTTTTCACATGTCTTTTGAAATATGAGAA
1 GTCCTTCGGGTCATCCATAAGACCTTTGGGCAAGATGTTTTCACATGTCTTTTGAAATATGAGAA
**
13893 AGG-TTCTCATATTAAATCTGAAAATTGAAATTTTGAAAAGTACTAAAGGTTTCTTACCTAGTAA
66 AGGTTTCTCATATTAAATCTGAAAATTGAAATTTTGAAAAGTAAGAAAGGTTTCTTACCTAGTAA
* *
13957 ACTATTTCCAAAATTTATAAGTCCTTCGGTTCATCAGTAAGTCTTTCGAGCACGATGGTTAAATC
131 ACTATTTCCAAAATTTATAAGTCCTTTGGTTCATCAGTAAGTCTTTCGAGCACGATGCTTAAATC
* * *
14022 CTTCGGCTCATCTATAAAGCCTTTAGAGCAAGATGATAA
196 CTTCGGGTCATCTGT-AAGCCTTTCGAGCAAGATGATAA
* * * * *
14061 GTCCTTCGGGTTATTCATAAGACCTTCGGGCAGGATGTTTTCACATGCCTTTTGAAATATGAGAA
1 GTCCTTCGGGTCATCCATAAGACCTTTGGGCAAGATGTTTTCACATGTCTTTTGAAATATGAGAA
14126 AGGTTTCTCATATTAAATCTGAAAATTGAAATTTTGAAAAGTAAGAAAGGTTTCTTACCTAGTAA
66 AGGTTTCTCATATTAAATCTGAAAATTGAAATTTTGAAAAGTAAGAAAGGTTTCTTACCTAGTAA
* *
14191 GA-TAATTTCCAAAATTTTATAAGTCATTTGGTTCATCAGTAAGTCTTTCAAGCACGATGCTTAA
131 -ACT-ATTTCCAAAA-TTTATAAGTCCTTTGGTTCATCAGTAAGTCTTTCGAGCACGATGCTTAA
*
14255 ATTCTTCGGGTCATCTGTAAGCCTTTCGAGCAAGATGATAA
193 ATCCTTCGGGTCATCTGTAAGCCTTTCGAGCAAGATGATAA
* *
14296 GTCTTTCGGGTCATCCATAAGACCTTTGGGCAAGATGTCTTCACATGTCTTTTGAAATATGAGAA
1 GTCCTTCGGGTCATCCATAAGACCTTTGGGCAAGATGTTTTCACATGTCTTTTGAAATATGAGAA
* *
14361 AGTTTTCTCATATTAAATTTGAAAATTGAAATTTTGAAAA
66 AGGTTTCTCATATTAAATCTGAAAATTGAAATTTTGAAAA
14401 ATCTAATATT
Statistics
Matches: 514, Mismatches: 49, Indels: 19
0.88 0.08 0.03
Matches are distributed among these distances:
232 103 0.20
233 95 0.18
234 117 0.23
235 139 0.27
236 60 0.12
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Consensus pattern (233 bp):
GTCCTTCGGGTCATCCATAAGACCTTTGGGCAAGATGTTTTCACATGTCTTTTGAAATATGAGAA
AGGTTTCTCATATTAAATCTGAAAATTGAAATTTTGAAAAGTAAGAAAGGTTTCTTACCTAGTAA
ACTATTTCCAAAATTTATAAGTCCTTTGGTTCATCAGTAAGTCTTTCGAGCACGATGCTTAAATC
CTTCGGGTCATCTGTAAGCCTTTCGAGCAAGATGATAA
Found at i:14853 original size:15 final size:14
Alignment explanation
Indices: 14833--14867 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
14823 TTTCATTATA
14833 ATTATTATTAATATT
1 ATTATTATTAA-ATT
14848 ATTATTATTAAATT
1 ATTATTATTAAATT
*
14862 TTTATT
1 ATTATT
14868 TTATTTTGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.42
15 11 0.58
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
ATTATTATTAAATT
Found at i:25285 original size:15 final size:15
Alignment explanation
Indices: 25267--25317 Score: 61
Period size: 15 Copynumber: 3.4 Consensus size: 15
25257 TTTCATTTTC
25267 TTTCATCCTTTCTTA
1 TTTCATCCTTTCTTA
*
25282 TTTCATTACC-TT-TTC
1 TTTCA-T-CCTTTCTTA
25297 TTTCATCCTTTCTTA
1 TTTCATCCTTTCTTA
25312 TTTCAT
1 TTTCAT
25318 TACCTTATCT
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
13 2 0.07
14 3 0.10
15 20 0.67
16 3 0.10
17 2 0.07
ACGTcount: A:0.14, C:0.25, G:0.00, T:0.61
Consensus pattern (15 bp):
TTTCATCCTTTCTTA
Found at i:25296 original size:18 final size:18
Alignment explanation
Indices: 25275--25328 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 18
25265 TCTTTCATCC
25275 TTTCTTATTTCATTACCT
1 TTTCTTATTTCATTACCT
25293 TTTC---TTTCA-T-CC-
1 TTTCTTATTTCATTACCT
25305 TTTCTTATTTCATTACCT
1 TTTCTTATTTCATTACCT
*
25323 TATCTT
1 TTTCTT
25329 TTCTTAACCA
Statistics
Matches: 29, Mismatches: 1, Indels: 12
0.69 0.02 0.29
Matches are distributed among these distances:
12 4 0.14
13 2 0.07
14 1 0.03
15 10 0.34
16 1 0.03
17 2 0.07
18 9 0.31
ACGTcount: A:0.15, C:0.24, G:0.00, T:0.61
Consensus pattern (18 bp):
TTTCTTATTTCATTACCT
Found at i:25333 original size:35 final size:30
Alignment explanation
Indices: 25250--25329 Score: 133
Period size: 30 Copynumber: 2.7 Consensus size: 30
25240 TTTTTCTCTC
* *
25250 TATTTCATTTCATTTTCTTTCATCCTTTCT
1 TATTTCATTACCTTTTCTTTCATCCTTTCT
25280 TATTTCATTACCTTTTCTTTCATCCTTTCT
1 TATTTCATTACCTTTTCTTTCATCCTTTCT
*
25310 TATTTCATTACCTTATCTTT
1 TATTTCATTACCTTTTCTTT
25330 TCTTAACCAT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 47 1.00
ACGTcount: A:0.15, C:0.24, G:0.00, T:0.61
Consensus pattern (30 bp):
TATTTCATTACCTTTTCTTTCATCCTTTCT
Found at i:43074 original size:28 final size:28
Alignment explanation
Indices: 43042--43176 Score: 109
Period size: 28 Copynumber: 4.9 Consensus size: 28
43032 TGAATTAACT
*
43042 AAACAAATGATGAATATGCTGTTATGCA
1 AAACAAATGATGAACATGCTGTTATGCA
*
43070 AAACAAATGATGAACATGTTGTTATG--
1 AAACAAATGATGAACATGCTGTTATGCA
** ** * * * *
43096 TGA-ATGTGAGTGCACGTGAAT-TTA-ACA
1 AAACAAATGA-TGAACATG-CTGTTATGCA
* *
43123 AAACAAATGATAAATATGCTGTTATGCA
1 AAACAAATGATGAACATGCTGTTATGCA
43151 AAACAAATGATGAACATGCTGTTATG
1 AAACAAATGATGAACATGCTGTTATG
43177 AACCCCACGA
Statistics
Matches: 78, Mismatches: 22, Indels: 14
0.68 0.19 0.12
Matches are distributed among these distances:
25 4 0.05
26 11 0.14
27 9 0.12
28 54 0.69
ACGTcount: A:0.41, C:0.10, G:0.19, T:0.29
Consensus pattern (28 bp):
AAACAAATGATGAACATGCTGTTATGCA
Found at i:43153 original size:81 final size:80
Alignment explanation
Indices: 43002--43176 Score: 278
Period size: 81 Copynumber: 2.2 Consensus size: 80
42992 GATAATGAAA
* * * * *
43002 AACATGTTGTAAAGTGAATGCGGGTGCACGTGAATTAACTAAACAAATGATGAATATGCTGTTAT
1 AACATGTTGTTATGTGAATGCGAGTGCACGTGAATTAACAAAACAAATGATAAATATGCTGTTAT
43067 GCAAAACAAATGATG
66 GCAAAACAAATGATG
*
43082 AACATGTTGTTATGTGAATGTGAGTGCACGTGAATTTAACAAAACAAATGATAAATATGCTGTTA
1 AACATGTTGTTATGTGAATGCGAGTGCACGTGAA-TTAACAAAACAAATGATAAATATGCTGTTA
43147 TGCAAAACAAATGATG
65 TGCAAAACAAATGATG
*
43163 AACATGCTGTTATG
1 AACATGTTGTTATG
43177 AACCCCACGA
Statistics
Matches: 87, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
80 30 0.34
81 57 0.66
ACGTcount: A:0.39, C:0.11, G:0.21, T:0.29
Consensus pattern (80 bp):
AACATGTTGTTATGTGAATGCGAGTGCACGTGAATTAACAAAACAAATGATAAATATGCTGTTAT
GCAAAACAAATGATG
Found at i:44443 original size:13 final size:13
Alignment explanation
Indices: 44421--44450 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
44411 ACTAGACACC
44421 TTTC-ACATACCT
1 TTTCAACATACCT
44433 TTTCAACATACCT
1 TTTCAACATACCT
44446 TTTCA
1 TTTCA
44451 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:48362 original size:23 final size:24
Alignment explanation
Indices: 48308--48362 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
48298 TTTTCTTTTC
*
48308 TTTTCTTTTTTTAATTTTCAGAAT
1 TTTTTTTTTTTTAATTTTCAGAAT
**
48332 TTGGTTTTTTTTAATTTTCAG-AT
1 TTTTTTTTTTTTAATTTTCAGAAT
48355 TTTTTTTT
1 TTTTTTTT
48363 CAAAATGAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
23 8 0.31
24 18 0.69
ACGTcount: A:0.16, C:0.05, G:0.07, T:0.71
Consensus pattern (24 bp):
TTTTTTTTTTTTAATTTTCAGAAT
Found at i:49656 original size:28 final size:28
Alignment explanation
Indices: 49624--49677 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
49614 TGAATTAACT
*
49624 AAACAAATGATGAATATGCTGTTATGCA
1 AAACAAATGATGAACATGCTGTTATGCA
*
49652 AAACAAATGATGAACATGTTGTTATG
1 AAACAAATGATGAACATGCTGTTATG
49678 TGAGTGTGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.43, C:0.09, G:0.19, T:0.30
Consensus pattern (28 bp):
AAACAAATGATGAACATGCTGTTATGCA
Found at i:49728 original size:81 final size:80
Alignment explanation
Indices: 49584--49758 Score: 269
Period size: 81 Copynumber: 2.2 Consensus size: 80
49574 GATAATGAAA
* * * * * *
49584 AACATGTTGTAAAGTGAATGTGGGTGCACGTGAATTAACTAAACAAATGATGAATATGCTGTTAT
1 AACATGTTGTTATGTGAATGTGAGTACACGTGAATTAACAAAACAAATGATAAATATGCTGTTAT
49649 GCAAAACAAATGATG
66 GCAAAACAAATGATG
* *
49664 AACATGTTGTTATGTGAGTGTGAGTACACGTGAATTTAACAAAACAAATGATAAATATGTTGTTA
1 AACATGTTGTTATGTGAATGTGAGTACACGTGAA-TTAACAAAACAAATGATAAATATGCTGTTA
49729 TGCAAAACAAATGATG
65 TGCAAAACAAATGATG
49745 AACATGTTGTTATG
1 AACATGTTGTTATG
49759 AACCCCACGA
Statistics
Matches: 86, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
80 29 0.34
81 57 0.66
ACGTcount: A:0.39, C:0.09, G:0.21, T:0.30
Consensus pattern (80 bp):
AACATGTTGTTATGTGAATGTGAGTACACGTGAATTAACAAAACAAATGATAAATATGCTGTTAT
GCAAAACAAATGATG
Found at i:49743 original size:28 final size:28
Alignment explanation
Indices: 49703--49758 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
49693 GTGAATTTAA
*
49703 CAAAACAAATGATAAATATGTTGTTATG
1 CAAAACAAATGATAAACATGTTGTTATG
*
49731 CAAAACAAATGATGAACATGTTGTTATG
1 CAAAACAAATGATAAACATGTTGTTATG
49759 AACCCCACGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.45, C:0.09, G:0.16, T:0.30
Consensus pattern (28 bp):
CAAAACAAATGATAAACATGTTGTTATG
Found at i:51295 original size:15 final size:15
Alignment explanation
Indices: 51272--51306 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
51262 CTGGTCATGA
*
51272 GGCACTCACATGGGC
1 GGCATTCACATGGGC
51287 GGCATTCACATGGGC
1 GGCATTCACATGGGC
51302 GGCAT
1 GGCAT
51307 AGGGAGTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.20, C:0.29, G:0.34, T:0.17
Consensus pattern (15 bp):
GGCATTCACATGGGC
Found at i:55745 original size:17 final size:16
Alignment explanation
Indices: 55724--55779 Score: 60
Period size: 17 Copynumber: 3.4 Consensus size: 16
55714 AGGATAAAGT
55724 AATGAAAAATAAGAAA
1 AATGAAAAATAAGAAA
*
55740 AGATGAATGAATAAG-AA
1 A-ATGAA-AAATAAGAAA
*
55757 AATGAAATAGTAAGAAA
1 AATGAAA-AATAAGAAA
55774 AATGAA
1 AATGAA
55780 GATAACTTAC
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
16 11 0.33
17 16 0.48
18 6 0.18
ACGTcount: A:0.66, C:0.00, G:0.18, T:0.16
Consensus pattern (16 bp):
AATGAAAAATAAGAAA
Found at i:55992 original size:6 final size:6
Alignment explanation
Indices: 55981--56024 Score: 63
Period size: 6 Copynumber: 7.2 Consensus size: 6
55971 GATGTATGAG
55981 TCTTTT TC-TTT TCTTTT TCTTTT TCTTCTT TCTTTT TCTCTTT T
1 TCTTTT TCTTTT TCTTTT TCTTTT TCTT-TT TCTTTT TCT-TTT T
56025 TGTTGCTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
5 5 0.14
6 20 0.57
7 10 0.29
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (6 bp):
TCTTTT
Found at i:56004 original size:12 final size:12
Alignment explanation
Indices: 55981--56024 Score: 63
Period size: 13 Copynumber: 3.6 Consensus size: 12
55971 GATGTATGAG
55981 TCTTTTTC-TTT
1 TCTTTTTCTTTT
55992 TCTTTTTCTTTT
1 TCTTTTTCTTTT
56004 TCTTCTTTCTTTT
1 TCTT-TTTCTTTT
56017 TCTCTTTT
1 TCT-TTTT
56025 TGTTGCTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
11 8 0.27
12 7 0.23
13 14 0.47
14 1 0.03
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (12 bp):
TCTTTTTCTTTT
Found at i:56014 original size:19 final size:17
Alignment explanation
Indices: 55981--56024 Score: 61
Period size: 19 Copynumber: 2.4 Consensus size: 17
55971 GATGTATGAG
55981 TCTTTTTCTTTTCTTTT
1 TCTTTTTCTTTTCTTTT
55998 TCTTTTTCTTCTTTCTTTT
1 TCTTTTTC-T-TTTCTTTT
56017 TCTCTTTT
1 TCT-TTTT
56025 TGTTGCTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.33
18 1 0.04
19 11 0.46
20 4 0.17
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (17 bp):
TCTTTTTCTTTTCTTTT
Found at i:64919 original size:36 final size:36
Alignment explanation
Indices: 64846--64950 Score: 158
Period size: 36 Copynumber: 2.9 Consensus size: 36
64836 ATTTATAAGT
* * * *
64846 TGGTGATAATATGGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCATGATAATGGTGATGGACTA
*
64881 TGGTGATGATATAGGCCTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCATGATAATGGTGATGGACTA
64917 TGGTGATGATATAGGCATGATAATGGTGATGGAC
1 TGGTGATGATATAGGCATGATAATGGTGATGGAC
64951 AGATTGTATC
Statistics
Matches: 64, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
35 18 0.28
36 46 0.72
ACGTcount: A:0.29, C:0.06, G:0.35, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCATGATAATGGTGATGGACTA
Found at i:69047 original size:22 final size:23
Alignment explanation
Indices: 69019--69070 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 23
69009 AATTATAAGT
*
69019 TGGTGATAATATGGGCATGAT-A
1 TGGTGATAATATAGGCATGATAA
* *
69041 TGGTGATGATATAGGCGTGATAA
1 TGGTGATAATATAGGCATGATAA
69064 TGGTGAT
1 TGGTGAT
69071 GGACTATGGT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 18 0.69
23 8 0.31
ACGTcount: A:0.29, C:0.04, G:0.35, T:0.33
Consensus pattern (23 bp):
TGGTGATAATATAGGCATGATAA
Found at i:69062 original size:36 final size:38
Alignment explanation
Indices: 69021--69110 Score: 122
Period size: 36 Copynumber: 2.5 Consensus size: 38
69011 TTATAAGTTG
69021 GTGATAATATGG-GCAT-GA-TATGGTGATGATATAGGC
1 GTGATAATATGGTG-ATGGACTATGGTGATGATATAGGC
69057 GTGAT-A-ATGGTGATGGACTATGGTGATGATATAGGC
1 GTGATAATATGGTGATGGACTATGGTGATGATATAGGC
69093 GTGAT-A-ATGGTGATGGAC
1 GTGATAATATGGTGATGGAC
69111 AGCTTGTATC
Statistics
Matches: 51, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
34 6 0.12
35 4 0.08
36 41 0.80
ACGTcount: A:0.29, C:0.06, G:0.36, T:0.30
Consensus pattern (38 bp):
GTGATAATATGGTGATGGACTATGGTGATGATATAGGC
Done.