Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002175.1 Hibiscus syriacus cultivar Beakdansim tig00004433_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: 90297
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:1904 original size:29 final size:29
Alignment explanation
Indices: 1869--1949 Score: 108
Period size: 29 Copynumber: 2.8 Consensus size: 29
1859 AAACTAAATT
* * *
1869 GATGTCATTACTTACATAATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAAGTAAA
* *
1898 GATGTCATTGCTTACCTCATTTAAGTAAT
1 GATGTCATTGCTTACATCATTTAAGTAAA
*
1927 GATGTCATTGCTTATATCATTTA
1 GATGTCATTGCTTACATCATTTA
1950 GTTAGGTGAG
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 45 1.00
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAAGTAAA
Found at i:4994 original size:59 final size:59
Alignment explanation
Indices: 4867--4995 Score: 145
Period size: 59 Copynumber: 2.2 Consensus size: 59
4857 TAGTGACATT
* * *
4867 ATTGAAATGTTCAAAAGTTTAGGGACCAATACAGAATGAGAATCATAGTTTGGGGGTGA
1 ATTGAAATGTTCAAAAGTTTAGGGACCAATACAGAATGAGAATCATAGTTTGAGGATAA
* * ** *
4926 ATATAAAATGTTCAAAAGTTT-GGGATCAATTTAGAATG-GAAGTCATGGTTTGAGGATAAA
1 AT-TGAAATGTTCAAAAGTTTAGGGACCAATACAGAATGAGAA-TCATAGTTTGAGGAT-AA
4986 ATTGAAATGT
1 ATTGAAATGT
4996 AAAAGAAATT
Statistics
Matches: 58, Mismatches: 9, Indels: 6
0.79 0.12 0.08
Matches are distributed among these distances:
58 3 0.05
59 35 0.60
60 20 0.34
ACGTcount: A:0.39, C:0.06, G:0.25, T:0.30
Consensus pattern (59 bp):
ATTGAAATGTTCAAAAGTTTAGGGACCAATACAGAATGAGAATCATAGTTTGAGGATAA
Found at i:7418 original size:3 final size:3
Alignment explanation
Indices: 7410--7497 Score: 176
Period size: 3 Copynumber: 29.3 Consensus size: 3
7400 ACCGTTTGAC
7410 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
7458 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
7498 TAAATCCACT
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 85 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:16346 original size:4 final size:4
Alignment explanation
Indices: 16337--16363 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
16327 TAAACACCCA
16337 TATT TATT TATT TATT TATT TATT TAT
1 TATT TATT TATT TATT TATT TATT TAT
16364 ATATATCTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:23869 original size:23 final size:23
Alignment explanation
Indices: 23843--23890 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
23833 ATAAAGTACA
*
23843 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
23866 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
23889 AT
1 AT
23891 TTACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:24341 original size:23 final size:23
Alignment explanation
Indices: 24315--24377 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
24305 ATATAACCAC
24315 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
24338 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
24361 TACCTATTACATCATAT
1 TACCTATTACATTATAT
24378 TTTTACCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:24777 original size:21 final size:23
Alignment explanation
Indices: 24746--24806 Score: 90
Period size: 21 Copynumber: 2.7 Consensus size: 23
24736 ATATAACCAC
24746 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
*
24769 TA-CTA-TACATTATATAAACGC
1 TACCTATTACATTATATAAACGA
*
24790 TACCTATTACATCATAT
1 TACCTATTACATTATAT
24807 GTTTACCTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
21 17 0.50
22 6 0.18
23 11 0.32
ACGTcount: A:0.41, C:0.20, G:0.03, T:0.36
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:24800 original size:23 final size:23
Alignment explanation
Indices: 24736--24806 Score: 92
Period size: 23 Copynumber: 3.2 Consensus size: 23
24726 ACACTTTACA
* *
24736 ATATAACCACTACCTATTACATT
1 ATATAAACGCTACCTATTACATT
*
24759 ATATAAACGATA-CTA-TACATT
1 ATATAAACGCTACCTATTACATT
*
24780 ATATAAACGCTACCTATTACATC
1 ATATAAACGCTACCTATTACATT
24803 ATAT
1 ATAT
24807 GTTTACCTAT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
21 17 0.41
22 6 0.15
23 18 0.44
ACGTcount: A:0.42, C:0.21, G:0.03, T:0.34
Consensus pattern (23 bp):
ATATAAACGCTACCTATTACATT
Found at i:24819 original size:429 final size:430
Alignment explanation
Indices: 23957--25006 Score: 1918
Period size: 431 Copynumber: 2.5 Consensus size: 430
23947 TATTACATTA
*
23957 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTT-AAAGTTATGTAA
1 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAAGTTATGTAA
*
24021 TTTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
66 TTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
24086 ATTTGCACAAAAAATTATTTGA-TTTTTTGATATTTTATAAAATATTATTTAAAATTTTTAATTT
131 ATTTGCACAAAAAATTATTTGATTTTTTTGATATTTTATAAAATATTATTTAAAATTTTTAATTT
24150 AATAATAATATATATCGTAACGTAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATC
196 AATAATAATATATATCGTAACGTAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATC
24215 TTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTT
261 TTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTT
24280 TTATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTAT
326 TTATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTAT
* *
24345 TACATTATATAAGCGCTACCTATTACATCATATTTTTACC
391 TACATTATATAAACGCTACCTATTACATCATATGTTTACC
24385 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAAGTTATGTAA
1 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAAGTTATGTAA
24450 TTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
66 TTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
*
24515 ATTTGCACAAAAAATTATTTGATTTTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTT
131 ATTTGCACAAAAAATTATTTGATTTTTTTGATATTTTATAAAATATTATTTAAAATTTTTAATTT
24580 AATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATAT
196 AATAATAATATATATCGTAACGT-AAAAATAAATCATTAGACGCCTATAATTACTAAATTAATAT
* *
24645 CTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCTACAGTGAAAAAAGTATGGACATT
260 CTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACT
24710 TTTATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATATAAACGATA-CTA
325 TTTATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTA
24774 -TACATTATATAAACGCTACCTATTACATCATATGTTTACC
390 TTACATTATATAAACGCTACCTATTACATCATATGTTTACC
*
24814 TATTATA-TGAAAGTGTTCATACTTTTTAT-AAAAGGATCGATACTTTTTTTAAAAGTTATGTAA
1 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAAGTTATGTAA
24877 TTTATGTTTCAATTTTTTTAACAGTGTTTCATG-TTTCCACCTACAATATTAATTTAATAATTTC
66 TTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
* * * * *
24941 ATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTATAA-TTTAAATTT
131 ATTTGCACAAAAAATTATTTGATTTTTTTGATATTTTATAAAATATTATTTAAAATTTTTAATTT
25005 AA
196 AA
25007 CAACATTAAC
Statistics
Matches: 606, Mismatches: 13, Indels: 9
0.96 0.02 0.01
Matches are distributed among these distances:
425 10 0.02
426 82 0.14
427 67 0.11
428 72 0.12
429 143 0.24
430 67 0.11
431 165 0.27
ACGTcount: A:0.39, C:0.12, G:0.08, T:0.42
Consensus pattern (430 bp):
TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAAGTTATGTAA
TTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
ATTTGCACAAAAAATTATTTGATTTTTTTGATATTTTATAAAATATTATTTAAAATTTTTAATTT
AATAATAATATATATCGTAACGTAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATC
TTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTT
TTATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTAT
TACATTATATAAACGCTACCTATTACATCATATGTTTACC
Found at i:24847 original size:21 final size:22
Alignment explanation
Indices: 24823--24869 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
24813 CTATTATATG
*
24823 AAAGTGTTC-ATACTTTTTATA
1 AAAGTGATCGATACTTTTTATA
*
24844 AAAG-GATCGATACTTTTTTTA
1 AAAGTGATCGATACTTTTTATA
24865 AAAGT
1 AAAGT
24870 TATGTAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 3 0.14
21 19 0.86
ACGTcount: A:0.36, C:0.09, G:0.13, T:0.43
Consensus pattern (22 bp):
AAAGTGATCGATACTTTTTATA
Found at i:25211 original size:25 final size:24
Alignment explanation
Indices: 25149--25213 Score: 85
Period size: 24 Copynumber: 2.7 Consensus size: 24
25139 CACTCAAAAG
*
25149 ATGTATATACCTAAATATGTAGTT
1 ATGTACATACCTAAATATGTAGTT
***
25173 AACAACATACCTAAATATGTAGTT
1 ATGTACATACCTAAATATGTAGTT
25197 ATTGTACATACCTAAAT
1 A-TGTACATACCTAAAT
25214 TTAATGATAA
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
24 21 0.64
25 12 0.36
ACGTcount: A:0.42, C:0.14, G:0.09, T:0.35
Consensus pattern (24 bp):
ATGTACATACCTAAATATGTAGTT
Found at i:28010 original size:183 final size:183
Alignment explanation
Indices: 27673--28010 Score: 534
Period size: 183 Copynumber: 1.8 Consensus size: 183
27663 AATTACCGAC
* *
27673 ACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAATATTA
1 ACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAATATTA
* * * * *
27738 TAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCGGTTATAT
66 AAAAGTGTCGATATAGGTTGTAGACCTATTCACGCATAAAACCGGTATATTTATACCGGATACAT
*
27803 TACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATGTCGAT
131 TACAAAATTACCTATTACATTATAAATCTGGGTTCCGATGTGTAAATGTCGAT
27856 ACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAATATTA
1 ACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAATATTA
*
27921 AAAAGTGTCGATATAGGTTGTAGACCTATTCACGCATAAAATCGGTATATTTATACC-GATAGCA
66 AAAAGTGTCGATATAGGTTGTAGACCTATTCACGCATAAAACCGGTATATTTATACCGGATA-CA
* * * **
27985 TTGCTAATTTACCTATTTTATTATAA
130 TTACAAAATTACCTATTACATTATAA
28011 TATGTTGAAA
Statistics
Matches: 140, Mismatches: 14, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
182 3 0.02
183 137 0.98
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.36
Consensus pattern (183 bp):
ACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAATATTA
AAAAGTGTCGATATAGGTTGTAGACCTATTCACGCATAAAACCGGTATATTTATACCGGATACAT
TACAAAATTACCTATTACATTATAAATCTGGGTTCCGATGTGTAAATGTCGAT
Found at i:30467 original size:199 final size:199
Alignment explanation
Indices: 29857--31016 Score: 2015
Period size: 199 Copynumber: 5.9 Consensus size: 199
29847 TTTAAATTAG
29857 TATCGACACAAACTATA--ACGTGTCGACACATTA-TTAGACATATTATCTCATAAAACCGGTAT
1 TATCGACACAAACTATATTA-GTGTCGACACATTATTTAGACATATTATCTCATAAAACCGGTAT
*
29919 ACTTGTACCGGTTAGATTGAAAAATT--ATA-TACATTATACTTTTGGGTTCGATGA-TTTGGGA
65 AATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGA
29980 TCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAA
130 TCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAA
30045 AAAAA
195 AAAAA
* *
30050 TATTGACACAAACTATATTAGTGTCGACACATTATTTATACATATTATCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTATCTCATAAAACCGGTATA
30115 ATTGTACCGGTTAGATTG-AAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
30179 CGACAC-TTTT-TATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
30242 AAAA
196 AAAA
* * * *
30246 TATCGACACAAACTATATTAGTGTCGACACATTATTTATATATATTATCTGATAAAACAGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTATCTCATAAAACCGGTATA
30311 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
30376 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
30441 AAAA
196 AAAA
*
30445 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTATCTCATAAAACCGGTATA
30510 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* *
30575 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTACATTCATTCTGGACAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
30640 AAAA
196 AAAA
*
30644 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTATCTCATAAAACCGGTATA
30709 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* * *
30774 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCATGTTTTACATTCATTCTGGACAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
*
30839 AACA
196 AAAA
* *
30843 TATCGACACAAACTATATTAGTGTCGACACATTA-TTAGACATATTCTCTCATAAAAACCGGTAG
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTATCTCAT-AAAACCGGTAT
* * *
30907 ACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGG
65 AATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGG-GTTCGATGATTTTGGG
30972 AT-GACAC-TTTT-TATATGGATCGACACTTTATGGGTGCACCCTGTT
129 ATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTT
31017 GGCCATATTG
Statistics
Matches: 934, Mismatches: 21, Indels: 20
0.96 0.02 0.02
Matches are distributed among these distances:
193 16 0.02
194 20 0.02
195 47 0.05
196 139 0.15
197 114 0.12
198 40 0.04
199 542 0.58
200 16 0.02
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (199 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTATCTCATAAAACCGGTATA
ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
AAAA
Found at i:31179 original size:19 final size:19
Alignment explanation
Indices: 31133--31181 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
31123 TTATATTCAC
*
31133 ATACAAAAATATAAATCGT
1 ATACAAAATTATAAATCGT
*
31152 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
31171 ATACAAAATTA
1 ATACAAAATTA
31182 ACCCTACATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.57, C:0.10, G:0.02, T:0.31
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:33099 original size:21 final size:21
Alignment explanation
Indices: 33075--33123 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
33065 ACTGTATCTT
* *
33075 CGACTCTCTCGAGTTTCTCTA
1 CGACTCTATCAAGTTTCTCTA
* *
33096 CGACTCGATCAAGTTTCTCTT
1 CGACTCTATCAAGTTTCTCTA
33117 CGACTCT
1 CGACTCT
33124 TGATTGTCTT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.16, C:0.33, G:0.14, T:0.37
Consensus pattern (21 bp):
CGACTCTATCAAGTTTCTCTA
Found at i:35367 original size:17 final size:18
Alignment explanation
Indices: 35345--35387 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
35335 ATATATCCGG
35345 TATCATTT-TACCGGTTT
1 TATCATTTATACCGGTTT
35362 TATCATTTTGATACCGGTTT
1 TATCA-TTT-ATACCGGTTT
35382 TATCAT
1 TATCAT
35388 ATTTTAACTG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.22
18 3 0.13
19 1 0.04
20 14 0.61
ACGTcount: A:0.21, C:0.16, G:0.12, T:0.51
Consensus pattern (18 bp):
TATCATTTATACCGGTTT
Found at i:35542 original size:20 final size:20
Alignment explanation
Indices: 35516--35561 Score: 76
Period size: 20 Copynumber: 2.3 Consensus size: 20
35506 CACTTTTAAA
35516 TTTACCGGTTTTATCAT-TT
1 TTTACCGGTTTTATCATATT
35535 TGTTACCGGTTTTATCATATT
1 T-TTACCGGTTTTATCATATT
35556 TTTACC
1 TTTACC
35562 TGGTATATCG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.54
Consensus pattern (20 bp):
TTTACCGGTTTTATCATATT
Found at i:37343 original size:14 final size:14
Alignment explanation
Indices: 37324--37351 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
37314 ATCATAACAA
37324 AATTATATAACTAT
1 AATTATATAACTAT
37338 AATTATATAACTAT
1 AATTATATAACTAT
37352 TCTTTCACTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
AATTATATAACTAT
Found at i:38053 original size:19 final size:19
Alignment explanation
Indices: 38028--38081 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
38018 AATCTATTTG
38028 ATTAAAATAATATAAATTA
1 ATTAAAATAATATAAATTA
* * ***
38047 TTTAAAATACTATTGTTTA
1 ATTAAAATAATATAAATTA
38066 ATTAAAATAATATAAA
1 ATTAAAATAATATAAA
38082 AATTATTAAA
Statistics
Matches: 25, Mismatches: 10, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (19 bp):
ATTAAAATAATATAAATTA
Found at i:38796 original size:23 final size:21
Alignment explanation
Indices: 38761--38839 Score: 67
Period size: 23 Copynumber: 3.8 Consensus size: 21
38751 AAAAAACCAG
* *
38761 TTTTTTAAAAAAAAACCGAAAT
1 TTTTTTGATAAAAAACC-AAAT
*
38783 TTTTTTGGATAAAAATCC-AA-
1 TTTTTT-GATAAAAAACCAAAT
38803 TTTTTT--TAAAAAACCAAATTT
1 TTTTTTGATAAAAAACCAAA--T
38824 TTTTTTGATAAAAAAC
1 TTTTTTGATAAAAAAC
38840 AAAAACCGAT
Statistics
Matches: 46, Mismatches: 4, Indels: 13
0.73 0.06 0.21
Matches are distributed among these distances:
17 8 0.17
18 2 0.04
20 6 0.13
21 8 0.17
22 6 0.13
23 16 0.35
ACGTcount: A:0.46, C:0.09, G:0.05, T:0.41
Consensus pattern (21 bp):
TTTTTTGATAAAAAACCAAAT
Found at i:38814 original size:18 final size:18
Alignment explanation
Indices: 38770--38827 Score: 64
Period size: 18 Copynumber: 3.0 Consensus size: 18
38760 GTTTTTTAAA
38770 AAAAAACCGAAATTTTTTT
1 AAAAAACC-AAATTTTTTT
38789 GGATAAAAATCC-AATTTTTTT
1 --A-AAAAA-CCAAATTTTTTT
38810 AAAAAACCAAATTTTTTT
1 AAAAAACCAAATTTTTTT
38828 TTGATAAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
17 2 0.06
18 14 0.41
19 1 0.03
21 10 0.29
22 5 0.15
23 2 0.06
ACGTcount: A:0.45, C:0.10, G:0.05, T:0.40
Consensus pattern (18 bp):
AAAAAACCAAATTTTTTT
Found at i:40921 original size:18 final size:18
Alignment explanation
Indices: 40898--40932 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
40888 GGAGTAATTC
*
40898 TGGTATACAGCATGCCTT
1 TGGTATACAGCAGGCCTT
*
40916 TGGTATAGAGCAGGCCT
1 TGGTATACAGCAGGCCT
40933 ACAGAAAGAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.23, C:0.20, G:0.29, T:0.29
Consensus pattern (18 bp):
TGGTATACAGCAGGCCTT
Found at i:49751 original size:16 final size:16
Alignment explanation
Indices: 49730--49767 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
49720 AATCCTTACC
49730 TTTGCTTCCCACCGCA
1 TTTGCTTCCCACCGCA
49746 TTTGCTTCCCACCGCA
1 TTTGCTTCCCACCGCA
49762 TTTGCT
1 TTTGCT
49768 GCGACGATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.11, C:0.39, G:0.13, T:0.37
Consensus pattern (16 bp):
TTTGCTTCCCACCGCA
Found at i:67561 original size:18 final size:18
Alignment explanation
Indices: 67530--67575 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
67520 TTAATTTCCG
67530 ATCGAAT-ATCTAAAAAAA
1 ATCGAATAAT-TAAAAAAA
*
67548 ATTGAATAATTAAAAAAA
1 ATCGAATAATTAAAAAAA
67566 ATCGAATAAT
1 ATCGAATAAT
67576 CGAATTGGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 23 0.92
19 2 0.08
ACGTcount: A:0.61, C:0.07, G:0.07, T:0.26
Consensus pattern (18 bp):
ATCGAATAATTAAAAAAA
Found at i:71078 original size:2 final size:2
Alignment explanation
Indices: 71071--71120 Score: 54
Period size: 2 Copynumber: 26.5 Consensus size: 2
71061 ATCATAAAAT
*
71071 TA TA TA TA -A TA TA CT- TA AA TA -A TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA
71111 TA TA T- TA TA T
1 TA TA TA TA TA T
71121 TGAAATACTT
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
1 4 0.10
2 36 0.88
3 1 0.02
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:79606 original size:22 final size:22
Alignment explanation
Indices: 79556--79622 Score: 59
Period size: 22 Copynumber: 3.0 Consensus size: 22
79546 TATTAAATTT
*
79556 AATATATAAT-TAAAATATAAT-A
1 AATATATAATAT-ATATA-AATAA
*
79578 AACATATAATATATATAAATAA
1 AATATATAATATATATAAATAA
*
79600 AATATAT-ATATATTAAAAATAA
1 AATATATAATATA-TATAAATAA
79622 A
1 A
79623 GCCGGTTAAC
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
21 8 0.21
22 29 0.76
23 1 0.03
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.34
Consensus pattern (22 bp):
AATATATAATATATATAAATAA
Found at i:79620 original size:17 final size:15
Alignment explanation
Indices: 79557--79609 Score: 63
Period size: 15 Copynumber: 3.5 Consensus size: 15
79547 ATTAAATTTA
*
79557 ATATATAATTAAAAT
1 ATATATAAATAAAAT
*
79572 ATA-ATAAACATATAAT
1 ATATAT-AA-ATAAAAT
79588 ATATATAAATAAAAT
1 ATATATAAATAAAAT
79603 ATATATA
1 ATATATA
79610 TATTAAAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
14 2 0.06
15 18 0.56
16 10 0.31
17 2 0.06
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (15 bp):
ATATATAAATAAAAT
Found at i:80525 original size:39 final size:39
Alignment explanation
Indices: 80471--80668 Score: 317
Period size: 39 Copynumber: 5.1 Consensus size: 39
80461 GTCACTAAAC
* * *
80471 CTGAGGGAGTGGTTAATGTTGCAA-TCAATTCTTCAAAAT
1 CTGAGGGAGAGGTTAATGTGGCAACT-GATTCTTCAAAAT
*
80510 CTGAGGGAGAGGTTAATGTGGCAACTGATTCTACAAAAT
1 CTGAGGGAGAGGTTAATGTGGCAACTGATTCTTCAAAAT
* *
80549 CTGAGGGAGAGGTTAATGTTGCAACTGATTCTACAAAAT
1 CTGAGGGAGAGGTTAATGTGGCAACTGATTCTTCAAAAT
80588 CTGAGGGAGAGGTTAATGTGGCAACTGATTCTTCAAAAT
1 CTGAGGGAGAGGTTAATGTGGCAACTGATTCTTCAAAAT
*
80627 CTGAGGGAGAGGTTAATGTGGCAACTGATTCTTCAAAGT
1 CTGAGGGAGAGGTTAATGTGGCAACTGATTCTTCAAAAT
80666 CTG
1 CTG
80669 CTGTTATTGA
Statistics
Matches: 150, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
39 149 0.99
40 1 0.01
ACGTcount: A:0.31, C:0.13, G:0.27, T:0.29
Consensus pattern (39 bp):
CTGAGGGAGAGGTTAATGTGGCAACTGATTCTTCAAAAT
Done.