Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002675.1 Hibiscus syriacus cultivar Beakdansim tig00005510_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: 64728
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:2986 original size:19 final size:19
Alignment explanation
Indices: 2962--3010 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
2952 AATGTAGGGT
2962 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
2981 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
3000 TAATTTTGTAT
1 TAATTTTGTAT
3011 GTGAATATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.33, C:0.02, G:0.10, T:0.55
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:3882 original size:200 final size:182
Alignment explanation
Indices: 3567--4664 Score: 1359
Period size: 200 Copynumber: 5.8 Consensus size: 182
3557 CCATATATAA
*
3567 AAAGTGTCGATCC-C-A-AAAACATCGAAAACCAAAAGTATAATGTAATATGTAATTTTTCAATC
1 AAAGTGTCGATCCACGATCAAACATCGAAAACCAAAAGTATAATGTAATATGTAATTTTTCAATC
* * * * *
3629 TAACCGGTACAAGTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGTCGACACTTTTTTA
66 TAACCGGTACAAATATACCAGTTTTATGAGAGAATAAGTCTAAATAATGTGTCGAAACTTTTGTA
* *
3694 GTTTGTGTCGATATTTTTGGTCCAGAATTAATGGCAAACAGGGTGCAACCGT
131 GTTTGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGGTGCAACCAT
*
3746 AAAGTGTCGATCC-CG-T-AAACATCGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATC
1 AAAGTGTCGATCCACGATCAAACATCGAAAACCAAAAGTATAATGTAATATGTAATTTTTCAATC
*
3808 TAACCAGTACAAATATACCAGTTTTATGAGAGAATAAGTCTAAATAATGTGTCGAAACTTTTGTA
66 TAACCGGTACAAATATACCAGTTTTATGAGAGAATAAGTCTAAATAATGTGTCGAAACTTTTGTA
*
3873 GTTTGTGTCGATATTTTTGGTCCATAATGAATGGCAAACAGGGTGCAACCAT
131 GTTTGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGGTGCAACCAT
3925 AAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAACCAAAAGTATAATGTA
1 AAAGTGTCGATCC----------A----CGAT--C--AAACATCGAAAACCAAAAGTATAATGTA
* * *
3990 ATATGTAATTTTTCAATCTAACCGATACAAGTATACCAGTTTTATGAGAGAATATGTCTAAATAA
48 ATATGTAATTTTTCAATCTAACCGGTACAAATATACCAGTTTTATGAGAGAATAAGTCTAAATAA
** *
4055 TGTGTCGGCACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGGTGCA
113 TGTGTCGAAACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGGTGCA
4120 ACCAT
178 ACCAT
4125 AAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAGAAACATCGAAAACCAAAAGTATAATGTA
1 AAAGTGTCGATCC----------A----CGAT--C--AAACATCGAAAACCAAAAGTATAATGTA
* * *
4190 ATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATATGTCTAAATAA
48 ATATGTAATTTTTCAATCTAACCGGTACAAATATACCAGTTTTATGAGAGAATAAGTCTAAATAA
* * *
4255 TGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATTAATGGCAAACAGGGTGCA
113 TGTGTCGAAACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGGTGCA
*
4320 ACCGT
178 ACCAT
*
4325 AAAGTGTCGATCC-CG-T-AAACATCGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATC
1 AAAGTGTCGATCCACGATCAAACATCGAAAACCAAAAGTATAATGTAATATGTAATTTTTCAATC
*
4387 TAACCGGTACAAATATACCGGTTTTATGAGAGAATAAGTCTAAATAATGTGTCGAAACTTTTGTA
66 TAACCGGTACAAATATACCAGTTTTATGAGAGAATAAGTCTAAATAATGTGTCGAAACTTTTGTA
*
4452 GTTTGTGTCGATATTTTTGGTCCATAATGAATGGCAAACAGGGTGCAACCAT
131 GTTTGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGGTGCAACCAT
4504 AAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAACCAAAAGTATAATGTA
1 AAAGTGTCGATCC----------A----CGAT--C--AAACATCGAAAACCAAAAGTATAATGTA
* * *
4569 ATATGTAATTTTTCAATCTAACCGATACAAGTATACCAGTTTTATGAGAGAATAGGTCTAAATAA
48 ATATGTAATTTTTCAATCTAACCGGTACAAATATACCAGTTTTATGAGAGAATAAGTCTAAATAA
* *
4634 TGTGTCGACACTTTTTTAGTTTGTGTCGATA
113 TGTGTCGAAACTTTTGTAGTTTGTGTCGATA
4665 CTAATTTAAA
Statistics
Matches: 835, Mismatches: 40, Indels: 67
0.89 0.04 0.07
Matches are distributed among these distances:
179 348 0.42
184 1 0.00
185 2 0.00
194 4 0.00
195 2 0.00
200 478 0.57
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (182 bp):
AAAGTGTCGATCCACGATCAAACATCGAAAACCAAAAGTATAATGTAATATGTAATTTTTCAATC
TAACCGGTACAAATATACCAGTTTTATGAGAGAATAAGTCTAAATAATGTGTCGAAACTTTTGTA
GTTTGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGGTGCAACCAT
Found at i:3930 original size:379 final size:382
Alignment explanation
Indices: 3366--4664 Score: 1833
Period size: 379 Copynumber: 3.4 Consensus size: 382
3356 CCATATATAA
*
3366 AAAGTGTCGATCC-C-A-AAAACATCGAAAACCAAAAGTATAATGTAATATGTAATTTTTCAATC
1 AAAGTGTCGATCCACGATCAAACATCGAAAACCAAAAGTATAATGTAATATGTAATTTTTCAATC
* *
3428 TAACCGGTACAAAGTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGTCGGCACTTTTTT
66 TAACCGGTACAAA-TATACCAGTTTTATGAGAGAATATGTCTAAATAATGTGTCGACACTTTTTT
3493 AGTTTGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGGTGCAACCATAAAGTGTCGATC
130 AGTTTGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGGTGCAACCATAAAGTGTCGATC
3558 CATATATAAAAAGTGTCGATCCCAAAAACATCGAAAACCAAAAGTATAATGTAATATGTAATTTT
195 CATATATAAAAAGTGTCGATCCCAAAAACATCGAAAACCAAAAGTATAATGTAATATGTAATTTT
3623 TCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGTCGACACT
260 TCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGTCGACACT
* *
3688 TTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATTAATGGCAAACAGGGTGCAACCGT
325 TTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGGTGCAACCAT
*
3746 AAAGTGTCGATCC-CG-T-AAACATCGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATC
1 AAAGTGTCGATCCACGATCAAACATCGAAAACCAAAAGTATAATGTAATATGTAATTTTTCAATC
* * * *
3808 TAACCAGTACAAATATACCAGTTTTATGAGAGAATAAGTCTAAATAATGTGTCGAAACTTTTGTA
66 TAACCGGTACAAATATACCAGTTTTATGAGAGAATATGTCTAAATAATGTGTCGACACTTTTTTA
*
3873 GTTTGTGTCGATATTTTTGGTCCATAATGAATGGCAAACAGGGTGCAACCATAAAGTGTCGATCC
131 GTTTGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGGTGCAACCATAAAGTGTCGATCC
3938 ATATATAAAAAGTGTCGATCCCAAAAACATCGAAAACCAAAAGTATAATGTAATATGTAATTTTT
196 ATATATAAAAAGTGTCGATCCCAAAAACATCGAAAACCAAAAGTATAATGTAATATGTAATTTTT
* * *
4003 CAATCTAACCGATACAAGTATACCAGTTTTATGAGAGAATATGTCTAAATAATGTGTCGGCACTT
261 CAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGTCGACACTT
4068 TTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGGTGCAACCAT
326 TTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGGTGCAACCAT
4125 AAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAGAAACATCGAAAACCAAAAGTATAATGTA
1 AAAGTGTCGATCC----------A----CGAT--C--AAACATCGAAAACCAAAAGTATAATGTA
* *
4190 ATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATATGTCTAAATAA
48 ATATGTAATTTTTCAATCTAACCGGTACAAATATACCAGTTTTATGAGAGAATATGTCTAAATAA
*
4255 TGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATTAATGGCAAACAGGGTGCA
113 TGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGGTGCA
* *
4320 ACCGTAAAGTGTCGATCC---------------CG-T-----AAACATCGAAACCCAAAAGTATA
178 ACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAACCAAAAGTATA
* *
4364 ATGTAATATGTAATTTTTCAATCTAACCGGTACAAATATACCGGTTTTATGAGAGAATAAGTCTA
243 ATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATATGTCTA
* * *
4429 AATAATGTGTCGAAACTTTTGTAGTTTGTGTCGATATTTTTGGTCCATAATGAATGGCAAACAGG
308 AATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGG
4494 GTGCAACCAT
373 GTGCAACCAT
4504 AAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAACCAAAAGTATAATGTA
1 AAAGTGTCGATCC----------A----CGAT--C--AAACATCGAAAACCAAAAGTATAATGTA
* * *
4569 ATATGTAATTTTTCAATCTAACCGATACAAGTATACCAGTTTTATGAGAGAATAGGTCTAAATAA
48 ATATGTAATTTTTCAATCTAACCGGTACAAATATACCAGTTTTATGAGAGAATATGTCTAAATAA
4634 TGTGTCGACACTTTTTTAGTTTGTGTCGATA
113 TGTGTCGACACTTTTTTAGTTTGTGTCGATA
4665 CTAATTTAAA
Statistics
Matches: 860, Mismatches: 36, Indels: 47
0.91 0.04 0.05
Matches are distributed among these distances:
379 617 0.72
380 71 0.08
384 1 0.00
385 2 0.00
394 2 0.00
395 1 0.00
400 166 0.19
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (382 bp):
AAAGTGTCGATCCACGATCAAACATCGAAAACCAAAAGTATAATGTAATATGTAATTTTTCAATC
TAACCGGTACAAATATACCAGTTTTATGAGAGAATATGTCTAAATAATGTGTCGACACTTTTTTA
GTTTGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGGTGCAACCATAAAGTGTCGATCC
ATATATAAAAAGTGTCGATCCCAAAAACATCGAAAACCAAAAGTATAATGTAATATGTAATTTTT
CAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGTCGACACTT
TTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGGTGCAACCAT
Found at i:4265 original size:579 final size:579
Alignment explanation
Indices: 3166--4664 Score: 2854
Period size: 579 Copynumber: 2.6 Consensus size: 579
3156 CCATATATAA
** *
3166 AAAGTGTCGATCCCAAAAACATCGAAAACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAA
1 AAAGTGTCGATCCCGTAAACATCGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAA
* * * *
3231 CCGGTACAAGTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGTCGACACTTTTTTAGTT
66 CCGGTACAAATATACCGGTTTTATGAGAGAATAAGTCTAAATAATGTGTCGAAACTTTTGTAGTT
*
3296 TGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATA
131 TGTGTCGATATTTTTGGTCCATAATGAATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATA
3361 TATAAAAAGTGTCGATCCCAAAAACATCGAAAACCAAAAGTATAATGTAATATGTAATTTTTCAA
196 TATAAAAAGTGTCGATCCCAAAAACATCGAAAACCAAAAGTATAATGTAATATGTAATTTTTCAA
* *
3426 TCTAACCGGTACAAAGTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGTCGGCACTTTT
261 TCTAACCGATAC-AAGTATACCAGTTTTATGAGAGAATATGTCTAAATAATGTGTCGGCACTTTT
3491 TTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGGTGCAACCATAAAGTGTCGA
325 TTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGGTGCAACCATAAAGTGTCGA
3556 TCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAACCAAAAGTATAATGTAATATGTAATT
390 TCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAACCAAAAGTATAATGTAATATGTAATT
3621 TTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGTCGACA
455 TTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGTCGACA
3686 CTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATTAATGGCAAACAGGGTGCAACCGT
520 CTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATTAATGGCAAACAGGGTGCAACCGT
3746 AAAGTGTCGATCCCGTAAACATCGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAA
1 AAAGTGTCGATCCCGTAAACATCGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAA
* *
3811 CCAGTACAAATATACCAGTTTTATGAGAGAATAAGTCTAAATAATGTGTCGAAACTTTTGTAGTT
66 CCGGTACAAATATACCGGTTTTATGAGAGAATAAGTCTAAATAATGTGTCGAAACTTTTGTAGTT
3876 TGTGTCGATATTTTTGGTCCATAATGAATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATA
131 TGTGTCGATATTTTTGGTCCATAATGAATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATA
3941 TATAAAAAGTGTCGATCCCAAAAACATCGAAAACCAAAAGTATAATGTAATATGTAATTTTTCAA
196 TATAAAAAGTGTCGATCCCAAAAACATCGAAAACCAAAAGTATAATGTAATATGTAATTTTTCAA
4006 TCTAACCGATACAAGTATACCAGTTTTATGAGAGAATATGTCTAAATAATGTGTCGGCACTTTTT
261 TCTAACCGATACAAGTATACCAGTTTTATGAGAGAATATGTCTAAATAATGTGTCGGCACTTTTT
4071 TAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGGTGCAACCATAAAGTGTCGAT
326 TAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGGTGCAACCATAAAGTGTCGAT
*
4136 CCATATATAAAAAGTGTCGATCCCAGAAACATCGAAAACCAAAAGTATAATGTAATATGTAATTT
391 CCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAACCAAAAGTATAATGTAATATGTAATTT
4201 TTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGTCGACAC
456 TTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGTCGACAC
4266 TTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATTAATGGCAAACAGGGTGCAACCGT
521 TTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATTAATGGCAAACAGGGTGCAACCGT
4325 AAAGTGTCGATCCCGTAAACATCGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAA
1 AAAGTGTCGATCCCGTAAACATCGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAA
4390 CCGGTACAAATATACCGGTTTTATGAGAGAATAAGTCTAAATAATGTGTCGAAACTTTTGTAGTT
66 CCGGTACAAATATACCGGTTTTATGAGAGAATAAGTCTAAATAATGTGTCGAAACTTTTGTAGTT
4455 TGTGTCGATATTTTTGGTCCATAATGAATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATA
131 TGTGTCGATATTTTTGGTCCATAATGAATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATA
4520 TATAAAAAGTGTCGATCCCAAAAACATCGAAAACCAAAAGTATAATGTAATATGTAATTTTTCAA
196 TATAAAAAGTGTCGATCCCAAAAACATCGAAAACCAAAAGTATAATGTAATATGTAATTTTTCAA
* *
4585 TCTAACCGATACAAGTATACCAGTTTTATGAGAGAATAGGTCTAAATAATGTGTCGACACTTTTT
261 TCTAACCGATACAAGTATACCAGTTTTATGAGAGAATATGTCTAAATAATGTGTCGGCACTTTTT
4650 TAGTTTGTGTCGATA
326 TAGTTTGTGTCGATA
4665 CTAATTTAAA
Statistics
Matches: 902, Mismatches: 17, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
579 641 0.71
580 261 0.29
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (579 bp):
AAAGTGTCGATCCCGTAAACATCGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAA
CCGGTACAAATATACCGGTTTTATGAGAGAATAAGTCTAAATAATGTGTCGAAACTTTTGTAGTT
TGTGTCGATATTTTTGGTCCATAATGAATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATA
TATAAAAAGTGTCGATCCCAAAAACATCGAAAACCAAAAGTATAATGTAATATGTAATTTTTCAA
TCTAACCGATACAAGTATACCAGTTTTATGAGAGAATATGTCTAAATAATGTGTCGGCACTTTTT
TAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGGTGCAACCATAAAGTGTCGAT
CCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAACCAAAAGTATAATGTAATATGTAATTT
TTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGTCGACAC
TTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATTAATGGCAAACAGGGTGCAACCGT
Found at i:6159 original size:6 final size:6
Alignment explanation
Indices: 6148--6253 Score: 86
Period size: 6 Copynumber: 17.7 Consensus size: 6
6138 CAACCGATCA
* * * * *
6148 ATGAAG ATGAAG CTGACG ATGAAG ATGACG ATGATG ATGATG ATGAAG
1 ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG
* * * * * * * *
6196 CTGACG ATGAAG ATGACG ATGAAG ATGATG ACGATG ATGACG ATGATG
1 ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG
*
6244 ATGATG ATGA
1 ATGAAG ATGA
6254 TCCAAACAAG
Statistics
Matches: 82, Mismatches: 18, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
6 82 1.00
ACGTcount: A:0.38, C:0.08, G:0.33, T:0.22
Consensus pattern (6 bp):
ATGAAG
Found at i:6197 original size:36 final size:36
Alignment explanation
Indices: 6148--6254 Score: 151
Period size: 36 Copynumber: 3.0 Consensus size: 36
6138 CAACCGATCA
*
6148 ATGAAGATGAAGCTGACGATGAAGATGACGATGATG
1 ATGATGATGAAGCTGACGATGAAGATGACGATGATG
*
6184 ATGATGATGAAGCTGACGATGAAGATGACGATGAAG
1 ATGATGATGAAGCTGACGATGAAGATGACGATGATG
* * * * *
6220 ATGATGACGATGATGACGATGATGATGATGATGAT
1 ATGATGATGAAGCTGACGATGAAGATGACGATGAT
6255 CCAAACAAGT
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 63 1.00
ACGTcount: A:0.37, C:0.07, G:0.33, T:0.22
Consensus pattern (36 bp):
ATGATGATGAAGCTGACGATGAAGATGACGATGATG
Found at i:6254 original size:6 final size:6
Alignment explanation
Indices: 6165--6254 Score: 90
Period size: 6 Copynumber: 15.0 Consensus size: 6
6155 TGAAGCTGAC
* * * * * * *
6165 GATGAA GATGAC GATGAT GATGAT GATGAA GCTGAC GATGAA GATGAC
1 GATGAT GATGAT GATGAT GATGAT GATGAT GATGAT GATGAT GATGAT
* * *
6213 GATGAA GATGAT GACGAT GATGAC GATGAT GATGAT GATGAT
1 GATGAT GATGAT GATGAT GATGAT GATGAT GATGAT GATGAT
6255 CCAAACAAGT
Statistics
Matches: 70, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
6 70 1.00
ACGTcount: A:0.37, C:0.07, G:0.33, T:0.23
Consensus pattern (6 bp):
GATGAT
Found at i:6254 original size:12 final size:12
Alignment explanation
Indices: 6148--6253 Score: 122
Period size: 12 Copynumber: 8.8 Consensus size: 12
6138 CAACCGATCA
*
6148 ATGAAGATGAAG
1 ATGACGATGAAG
*
6160 CTGACGATGAAG
1 ATGACGATGAAG
*
6172 ATGACGATGATG
1 ATGACGATGAAG
*
6184 ATGATGATGAAG
1 ATGACGATGAAG
*
6196 CTGACGATGAAG
1 ATGACGATGAAG
6208 ATGACGATGAAG
1 ATGACGATGAAG
* * *
6220 ATGATGACGATG
1 ATGACGATGAAG
*
6232 ATGACGATGATG
1 ATGACGATGAAG
*
6244 ATGATGATGA
1 ATGACGATGA
6254 TCCAAACAAG
Statistics
Matches: 79, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 79 1.00
ACGTcount: A:0.38, C:0.08, G:0.33, T:0.22
Consensus pattern (12 bp):
ATGACGATGAAG
Found at i:7771 original size:183 final size:183
Alignment explanation
Indices: 7463--8224 Score: 1355
Period size: 183 Copynumber: 4.2 Consensus size: 183
7453 ACAAAGTTTT
** *
7463 GACACTTTTTAATATTGTGTATGTACTTTATGTCTAGAATGGAAGAAAAATGTGTCGATACCTTG
1 GACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTG
7528 TCAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATA
66 TCAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATA
* *
7593 TAACCGGTATAAATATACCATTTTTATGAGAGAATAGGTCTACAACCTATATC
131 TAACCGGTATAAATATACCAGTTTTATGAGCGAATAGGTCTACAACCTATATC
**
7646 GACACTTTTTAATATTGTGTATGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTG
1 GACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTG
* *
7711 TCAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTGTAATGTAATAAATAATTTTGTAATA
66 TCAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATA
*
7776 TAACCGGTATAAATATACC-GATTTTATGAGTGAATAGGTCTACAACCTATATC
131 TAACCGGTATAAATATACCAG-TTTTATGAGCGAATAGGTCTACAACCTATATC
* *
7829 GACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATATGTCGATACCTTG
1 GACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTG
7894 TCAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATA
66 TCAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATA
* *
7959 TAACCGATATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATC
131 TAACCGGTATAAATATACCAGTTTTATGAGCGAATAGGTCTACAACCTATATC
*
8012 GACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCTTG
1 GACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTG
8077 TCAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATA
66 TCAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATA
* *
8142 TAACCTGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATC
131 TAACCGGTATAAATATACCAGTTTTATGAGCGAATAGGTCTACAACCTATATC
8195 GACACTTTTTAATATTGTGTCGGTACTTTA
1 GACACTTTTTAATATTGTGTCGGTACTTTA
8225 CAATAGGAGT
Statistics
Matches: 561, Mismatches: 16, Indels: 4
0.97 0.03 0.01
Matches are distributed among these distances:
183 560 1.00
184 1 0.00
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (183 bp):
GACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTG
TCAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATA
TAACCGGTATAAATATACCAGTTTTATGAGCGAATAGGTCTACAACCTATATC
Found at i:11048 original size:23 final size:23
Alignment explanation
Indices: 11017--11066 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
11007 ATAGGTAAAA
*
11017 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
*
11040 ATATAATGTAATAGGTAGTGCTT
1 ATATAATGTAATAGGTAGCGCTT
11063 ATAT
1 ATAT
11067 TGTAAAGTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.34, C:0.06, G:0.22, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:11463 original size:23 final size:23
Alignment explanation
Indices: 11432--11481 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
11422 ATAGGTAAAA
*
11432 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
*
11455 ATATAATGTAATAGGTAGTGCTT
1 ATATAATGTAATAGGTAGCGCTT
11478 ATAT
1 ATAT
11482 TGTAAAGTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.34, C:0.06, G:0.22, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:11521 original size:415 final size:415
Alignment explanation
Indices: 10755--12659 Score: 3584
Period size: 415 Copynumber: 4.6 Consensus size: 415
10745 ATATTATTAT
*
10755 TAAATTAAAAACGATAAACATATATATTACATATTTATTATTATCTTTGGTTAATATTGTTAAAT
1 TAAATTAAAAACAATAAACATATATATTACATATTTATTATTATCTTTGGTTAATATTGTTAAAT
*
10820 TTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAAATTTTTGTGCAAATGAAAT
66 TTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAATGAAAT
10885 TATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACATAAATTAC
131 TATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACATAAATTAC
10950 ATAACTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAA
196 ATAACTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAA
11015 AAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTAGTGCTTATATTGTAAAGTATCTA
261 AAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTAGTGCTTATATTGTAAAGTATCTA
*
11080 TCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAATATTAATTTAAGGTTATCTTTTG
326 TCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTG
*
11145 AGTGAGTTTTAAGATATTAATTTAT
391 AGTGAGTTTTAAGATATTAATTTAG
11170 TAAATTAAAAACAATAAACATATATATTACATATTTATTATTATCTTTGGTTAATATTGTTAAAT
1 TAAATTAAAAACAATAAACATATATATTACATATTTATTATTATCTTTGGTTAATATTGTTAAAT
11235 TTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAATGAAAT
66 TTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAATGAAAT
*
11300 TATTAAATTAATATTATAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACATAAATTAC
131 TATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACATAAATTAC
*
11365 ATAACTTTAAAAAAAGTATCGATCTTTTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAA
196 ATAACTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAA
*
11430 AAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTAGTGCTTATATTGTAAAGTATTTA
261 AAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTAGTGCTTATATTGTAAAGTATCTA
*
11495 TCCTTTTTATAAAAGTGTTCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTG
326 TCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTG
11560 AGTGAGTTTTAAGATATTAATTTAG
391 AGTGAGTTTTAAGATATTAATTTAG
11585 TAAATTAAAAACAATAAACATATATATTACATATTTATTATTATCTTTGGTTAATATTGTTAAAT
1 TAAATTAAAAACAATAAACATATATATTACATATTTATTATTATCTTTGGTTAATATTGTTAAAT
11650 TTAAATTCTAAATATTATTTTATAAAATATC-AAACAATCAAATAATTTTTTGTGCAAATGAAAT
66 TTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAATGAAAT
*
11714 TATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATT-AAAAAAATTGAAACATAAATTAT
131 TATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACATAAATTAC
*
11778 ATAACTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGAACACTTTCAATATAATAGGTAA
196 ATAACTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAA
*
11843 AAATATGATGTAATAGGTAGCGTTTATATAATGTAATAGGTAGTGCTTATATTGTAAAGTATCTA
261 AAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTAGTGCTTATATTGTAAAGTATCTA
11908 TCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTG
326 TCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTG
11973 AGTGAGTTTTAAGATATTAATTTAG
391 AGTGAGTTTTAAGATATTAATTTAG
11998 TAAATTAAAAACAATAAACATATATATTACATATTTATTATTATCTTTGGTTAATATTGTTAAAT
1 TAAATTAAAAACAATAAACATATATATTACATATTTATTATTATCTTTGGTTAATATTGTTAAAT
*
12063 TTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATATTTTTTTGTGCAAATGAAAT
66 TTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAATGAAAT
* *
12128 TATTAAATTAATATTATAGGTGGAAAACATGAAACACTATTAAAAAATATTGAAACATAAATTAC
131 TATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACATAAATTAC
12193 ATAACTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAA
196 ATAACTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAA
12258 AAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTAGTGCTTATATTGTAAAGTATCTA
261 AAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTAGTGCTTATATTGTAAAGTATCTA
* *
12323 TCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTGAAAAACATTAATTTAAGATTATCTTTTG
326 TCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTG
12388 AGTGAGTTTTAAGATATTAATTTAG
391 AGTGAGTTTTAAGATATTAATTTAG
*
12413 TAAATTAAAAACAATAAACATATATATTATATATTTATTATTATCTTTGGTTAATATTGTTAAAT
1 TAAATTAAAAACAATAAACATATATATTACATATTTATTATTATCTTTGGTTAATATTGTTAAAT
12478 TTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAATGAAAT
66 TTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAATGAAAT
*
12543 TATTAAATTAATATTGTAGGTGGAAAACATTAAACACTATT--AAAAAATTGAAACATAAATTAC
131 TATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACATAAATTAC
* * *
12606 ATAACTTTAAAAAAAATATCGATCTTTTTTATAAAAAAGTATAGACACTTTCAA
196 ATAACTTTAAAAAAAGTATCGATCCTTTTTAT-AAAAAGTATGGACACTTTCAA
12660 CATATTATAA
Statistics
Matches: 1456, Mismatches: 31, Indels: 7
0.97 0.02 0.00
Matches are distributed among these distances:
413 384 0.26
414 165 0.11
415 907 0.62
ACGTcount: A:0.43, C:0.08, G:0.10, T:0.39
Consensus pattern (415 bp):
TAAATTAAAAACAATAAACATATATATTACATATTTATTATTATCTTTGGTTAATATTGTTAAAT
TTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAATGAAAT
TATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACATAAATTAC
ATAACTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAA
AAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTAGTGCTTATATTGTAAAGTATCTA
TCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTG
AGTGAGTTTTAAGATATTAATTTAG
Found at i:11827 original size:22 final size:22
Alignment explanation
Indices: 11783--11827 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
11773 ATTATATAAC
*
11783 TTTAAAAAAAGTATCGATCCTT
1 TTTAAAAAAAGTATCGAACCTT
*
11805 TTTATAAAAAGTAT-GAACACTT
1 TTTAAAAAAAGTATCGAAC-CTT
11827 T
1 T
11828 CAATATAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 3 0.15
22 17 0.85
ACGTcount: A:0.42, C:0.11, G:0.09, T:0.38
Consensus pattern (22 bp):
TTTAAAAAAAGTATCGAACCTT
Found at i:11876 original size:23 final size:23
Alignment explanation
Indices: 11845--11894 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
11835 ATAGGTAAAA
* *
11845 ATATGATGTAATAGGTAGCGTTT
1 ATATAATGTAATAGGTAGCGCTT
*
11868 ATATAATGTAATAGGTAGTGCTT
1 ATATAATGTAATAGGTAGCGCTT
11891 ATAT
1 ATAT
11895 TGTAAAGTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:12291 original size:23 final size:23
Alignment explanation
Indices: 12260--12309 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
12250 ATAGGTAAAA
*
12260 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
*
12283 ATATAATGTAATAGGTAGTGCTT
1 ATATAATGTAATAGGTAGCGCTT
12306 ATAT
1 ATAT
12310 TGTAAAGTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.34, C:0.06, G:0.22, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:12461 original size:828 final size:829
Alignment explanation
Indices: 10755--12659 Score: 3600
Period size: 828 Copynumber: 2.3 Consensus size: 829
10745 ATATTATTAT
*
10755 TAAATTAAAAACGATAAACATATATATTACATATTTATTATTATCTTTGGTTAATATTGTTAAAT
1 TAAATTAAAAACAATAAACATATATATTACATATTTATTATTATCTTTGGTTAATATTGTTAAAT
*
10820 TTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAAATTTTTGTGCAAATGAAAT
66 TTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAATGAAAT
10885 TATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACATAAATTAC
131 TATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATT-AAAAAAATTGAAACATAAATTAC
*
10950 ATAACTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAA
195 ATAACTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGAACACTTTCAATATAATAGGTAA
11015 AAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTAGTGCTTATATTGTAAAGTATCTA
260 AAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTAGTGCTTATATTGTAAAGTATCTA
*
11080 TCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAATATTAATTTAAGGTTATCTTTTG
325 TCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTG
*
11145 AGTGAGTTTTAAGATATTAATTTATTAAATTAAAAACAATAAACATATATATTACATATTTATTA
390 AGTGAGTTTTAAGATATTAATTTAGTAAATTAAAAACAATAAACATATATATTACATATTTATTA
11210 TTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAATATCAAAACAATC
455 TTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAATATCAAAACAATC
11275 AAATAATTTTTTGTGCAAATGAAATTATTAAATTAATATTATAGGTGGAAAACATGAAACACTAT
520 AAATAATTTTTTGTGCAAATGAAATTATTAAATTAATATTATAGGTGGAAAACATGAAACACTAT
*
11340 TAAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCTTTTTTATAAAAAGTA
585 TAAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTA
11405 TGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGG
650 TGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGG
* * *
11470 TAGTGCTTATATTGTAAAGTATTTATCCTTTTTATAAAAGTGTTCATACTTTTTTCACTGTGGAA
715 TAGTGCTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTGAAA
*
11535 AACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAG
780 AACATTAATTTAAGATTATCTTTTGAGTGAGTTTTAAGATATTAATTTAG
11585 TAAATTAAAAACAATAAACATATATATTACATATTTATTATTATCTTTGGTTAATATTGTTAAAT
1 TAAATTAAAAACAATAAACATATATATTACATATTTATTATTATCTTTGGTTAATATTGTTAAAT
11650 TTAAATTCTAAATATTATTTTATAAAATATC-AAACAATCAAATAATTTTTTGTGCAAATGAAAT
66 TTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAATGAAAT
*
11714 TATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATAAATTATA
131 TATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATAAATTACA
11779 TAACTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGAACACTTTCAATATAATAGGTAAA
196 TAACTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGAACACTTTCAATATAATAGGTAAA
*
11844 AATATGATGTAATAGGTAGCGTTTATATAATGTAATAGGTAGTGCTTATATTGTAAAGTATCTAT
261 AATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTAGTGCTTATATTGTAAAGTATCTAT
11909 CCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGA
326 CCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGA
11974 GTGAGTTTTAAGATATTAATTTAGTAAATTAAAAACAATAAACATATATATTACATATTTATTAT
391 GTGAGTTTTAAGATATTAATTTAGTAAATTAAAAACAATAAACATATATATTACATATTTATTAT
12039 TATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCA
456 TATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCA
*
12104 AATATTTTTTTGTGCAAATGAAATTATTAAATTAATATTATAGGTGGAAAACATGAAACACTATT
521 AATAATTTTTTGTGCAAATGAAATTATTAAATTAATATTATAGGTGGAAAACATGAAACACTATT
*
12169 AAAAAATATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTAT
586 AAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTAT
12234 GGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGT
651 GGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGT
12299 AGTGCTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTGAAAA
716 AGTGCTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTGAAAA
12364 ACATTAATTTAAGATTATCTTTTGAGTGAGTTTTAAGATATTAATTTAG
781 ACATTAATTTAAGATTATCTTTTGAGTGAGTTTTAAGATATTAATTTAG
*
12413 TAAATTAAAAACAATAAACATATATATTATATATTTATTATTATCTTTGGTTAATATTGTTAAAT
1 TAAATTAAAAACAATAAACATATATATTACATATTTATTATTATCTTTGGTTAATATTGTTAAAT
12478 TTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAATGAAAT
66 TTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAATGAAAT
*
12543 TATTAAATTAATATTGTAGGTGGAAAACATTAAACACTATT-AAAAAATTGAAACATAAATTACA
131 TATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATAAATTACA
* *
12607 TAACTTTAAAAAAAATATCGATCTTTTTTATAAAAAAGTAT-AGACACTTTCAA
196 TAACTTTAAAAAAAGTATCGATCCTTTTTAT-AAAAAGTATGA-ACACTTTCAA
12660 CATATTATAA
Statistics
Matches: 1053, Mismatches: 19, Indels: 7
0.98 0.02 0.01
Matches are distributed among these distances:
828 793 0.75
829 165 0.16
830 95 0.09
ACGTcount: A:0.43, C:0.08, G:0.10, T:0.39
Consensus pattern (829 bp):
TAAATTAAAAACAATAAACATATATATTACATATTTATTATTATCTTTGGTTAATATTGTTAAAT
TTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAATGAAAT
TATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATAAATTACA
TAACTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGAACACTTTCAATATAATAGGTAAA
AATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTAGTGCTTATATTGTAAAGTATCTAT
CCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGA
GTGAGTTTTAAGATATTAATTTAGTAAATTAAAAACAATAAACATATATATTACATATTTATTAT
TATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCA
AATAATTTTTTGTGCAAATGAAATTATTAAATTAATATTATAGGTGGAAAACATGAAACACTATT
AAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTAT
GGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGT
AGTGCTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTGAAAA
ACATTAATTTAAGATTATCTTTTGAGTGAGTTTTAAGATATTAATTTAG
Found at i:13399 original size:16 final size:17
Alignment explanation
Indices: 13367--13401 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
13357 ACTTATAAAA
13367 TTTTAAGAATAATATAT
1 TTTTAAGAATAATATAT
*
13384 TTTTAAAGAAAAATATAT
1 TTTT-AAGAATAATATAT
13402 AGGAAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (17 bp):
TTTTAAGAATAATATAT
Found at i:18006 original size:15 final size:15
Alignment explanation
Indices: 17986--18014 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
17976 CATTTCCATG
17986 AAAATATTAATTATT
1 AAAATATTAATTATT
18001 AAAATATTAATTAT
1 AAAATATTAATTAT
18015 ATATATATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
AAAATATTAATTATT
Found at i:18022 original size:15 final size:15
Alignment explanation
Indices: 17989--18101 Score: 50
Period size: 15 Copynumber: 7.9 Consensus size: 15
17979 TTCCATGAAA
*
17989 ATATTAATTAT-TAAA
1 ATATTAATTATAT-AT
18004 ATATTAATTATATAT
1 ATATTAATTATATAT
18019 ATA-T-A-TATATAT
1 ATATTAATTATATAT
*
18031 ATA-TAATTTTA-AT
1 ATATTAATTATATAT
*
18044 AATATTATACTT-TTTA-
1 -ATATTA-A-TTATATAT
18060 ATATTATATTA-ATAT
1 ATATTA-ATTATATAT
*
18075 ATACTAAGTTATAT-T
1 ATATTAA-TTATATAT
*
18090 ATAATAA-TATAT
1 ATATTAATTATAT
18102 GAATATTATA
Statistics
Matches: 80, Mismatches: 6, Indels: 26
0.71 0.05 0.23
Matches are distributed among these distances:
12 11 0.14
13 9 0.11
14 12 0.15
15 40 0.50
16 5 0.06
17 3 0.04
ACGTcount: A:0.47, C:0.02, G:0.01, T:0.50
Consensus pattern (15 bp):
ATATTAATTATATAT
Found at i:18032 original size:25 final size:25
Alignment explanation
Indices: 18004--18101 Score: 63
Period size: 23 Copynumber: 4.2 Consensus size: 25
17994 AATTATTAAA
18004 ATATTAATTATATATATATATATAT
1 ATATTAATTATATATATATATATAT
*
18029 ATATATAATTTTA-ATA-ATAT-TAT
1 ATAT-TAATTATATATATATATATAT
*
18052 ACTTTTTAA-TAT-TATAT-TA-ATAT
1 A--TATTAATTATATATATATATATAT
*
18075 ATACTAAGTTATAT-TATA-ATA-AT
1 ATATTAA-TTATATATATATATATAT
18098 ATAT
1 ATAT
18102 GAATATTATA
Statistics
Matches: 56, Mismatches: 6, Indels: 24
0.65 0.07 0.28
Matches are distributed among these distances:
21 4 0.07
23 27 0.48
24 9 0.16
25 9 0.16
26 7 0.12
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.51
Consensus pattern (25 bp):
ATATTAATTATATATATATATATAT
Found at i:18048 original size:18 final size:18
Alignment explanation
Indices: 18027--18072 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
18017 ATATATATAT
18027 ATATATATAATTTTAATA
1 ATATATATAATTTTAATA
*
18045 ATAT-TATACTTTTTAATA
1 ATATATATA-ATTTTAATA
*
18063 TTATAT-TAAT
1 ATATATATAAT
18073 ATATACTAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 5
0.74 0.10 0.16
Matches are distributed among these distances:
17 5 0.22
18 17 0.74
19 1 0.04
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.54
Consensus pattern (18 bp):
ATATATATAATTTTAATA
Found at i:18063 original size:56 final size:59
Alignment explanation
Indices: 18003--18133 Score: 159
Period size: 59 Copynumber: 2.3 Consensus size: 59
17993 TAATTATTAA
**
18003 AATATTAATTATATATATA-T-A-TATATATATATAATTTTA-AT-AATATTATACTTTTT
1 AATATTAATTATATATATACTAAGT-TATAT-TATAATAATATATGAATATTATACTTTTT
18059 AATATTATATTA-ATATATACTAAGTTATATTATAATAATATATGAATATTATACTTTTT
1 AATATTA-ATTATATATATACTAAGTTATATTATAATAATATATGAATATTATACTTTTT
*
18118 AAT-TTAATAATATATA
1 AATATTAATTATATATA
18134 ATAAAATATT
Statistics
Matches: 65, Mismatches: 3, Indels: 12
0.81 0.04 0.15
Matches are distributed among these distances:
56 14 0.22
57 16 0.25
58 16 0.25
59 19 0.29
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (59 bp):
AATATTAATTATATATATACTAAGTTATATTATAATAATATATGAATATTATACTTTTT
Found at i:18129 original size:31 final size:31
Alignment explanation
Indices: 18056--18136 Score: 85
Period size: 33 Copynumber: 2.5 Consensus size: 31
18046 TATTATACTT
*
18056 TTTAATATTATATTAATATATACTAAGTTATA
1 TTTAATAATATA-TAATATATACTAAGTTATA
**
18088 TTATAATAATATATGAATATTATACT-TTTTA-A
1 TT-TAATAATATAT-AATA-TATACTAAGTTATA
18120 TTTAATAATATATAATA
1 TTTAATAATATATAATA
18137 AAATATTAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
30 4 0.09
31 11 0.26
32 6 0.14
33 16 0.37
34 6 0.14
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.49
Consensus pattern (31 bp):
TTTAATAATATATAATATATACTAAGTTATA
Found at i:20195 original size:19 final size:16
Alignment explanation
Indices: 20171--20209 Score: 51
Period size: 19 Copynumber: 2.2 Consensus size: 16
20161 TTACTATGTC
20171 AAATAAAAAGATAATATAA
1 AAATAAAAA-AT-AT-TAA
20190 AAATAAAAAATATTAA
1 AAATAAAAAATATTAA
20206 AAAT
1 AAAT
20210 TTGAAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 7 0.35
17 2 0.10
18 2 0.10
19 9 0.45
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (16 bp):
AAATAAAAAATATTAA
Found at i:23522 original size:31 final size:31
Alignment explanation
Indices: 23466--23560 Score: 88
Period size: 31 Copynumber: 3.0 Consensus size: 31
23456 ATATAAATTT
* *
23466 AAGGACTAAATTG-AATACATATAAAAGTGA
1 AAGGATTAAATTGAAATAAATATAAAAGTGA
* *
23496 AA-GACTTAAAATTGAAATAAAT-TAAAAAATAA
1 AAGGA-TT-AAATTGAAATAAATAT-AAAAGTGA
*
23528 AAGGATTAAATTGAAATAAATGTAAAATGTGA
1 AAGGATTAAATTGAAATAAATATAAAA-GTGA
23560 A
1 A
23561 TAAATAATGA
Statistics
Matches: 52, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
29 2 0.04
30 3 0.06
31 25 0.48
32 20 0.38
33 2 0.04
ACGTcount: A:0.58, C:0.03, G:0.14, T:0.25
Consensus pattern (31 bp):
AAGGATTAAATTGAAATAAATATAAAAGTGA
Found at i:23696 original size:18 final size:18
Alignment explanation
Indices: 23658--23707 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
23648 AAATTATAAA
23658 TATAAACTATAT-TTATGT
1 TATAAACTATATATTA-GT
23676 TATAAACTATATAATTA-T
1 TATAAACTATAT-ATTAGT
*
23694 TATAAGCTATATAT
1 TATAAACTATATAT
23708 ATAAATTATG
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
17 2 0.07
18 24 0.83
20 3 0.10
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (18 bp):
TATAAACTATATATTAGT
Found at i:23738 original size:15 final size:15
Alignment explanation
Indices: 23620--23750 Score: 56
Period size: 17 Copynumber: 8.3 Consensus size: 15
23610 ATAATATATA
23620 TATATATATATATAA-
1 TATATATATATA-AAC
*
23635 TATAAGTTTATATAAA-
1 TAT-A-TATATATAAAC
*
23651 T-TATAAATATAAAC
1 TATATATATATAAAC
*
23665 TATATTTATGTTATAAAC
1 TATA--TAT-ATATAAAC
*
23683 TATATAATTATTATAAGC
1 TATAT-A-TA-TATAAAC
*
23701 --TATATATATAAAT
1 TATATATATATAAAC
* * *
23714 TATGTTTATATGAAC
1 TATATATATATAAAC
23729 TATATATATATATAAAC
1 --TATATATATATAAAC
23746 TATAT
1 TATAT
23751 CTGTAAACTA
Statistics
Matches: 86, Mismatches: 16, Indels: 28
0.66 0.12 0.22
Matches are distributed among these distances:
13 13 0.15
14 4 0.05
15 21 0.24
16 8 0.09
17 22 0.26
18 18 0.21
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (15 bp):
TATATATATATAAAC
Found at i:23944 original size:17 final size:17
Alignment explanation
Indices: 23945--24000 Score: 85
Period size: 17 Copynumber: 3.2 Consensus size: 17
23935 GAAATTGAGA
23945 AAATTTGAGAATATAGGG
1 AAAT-TGAGAATATAGGG
23963 AAATTGAGAATATAGGG
1 AAATTGAGAATATAGGG
*
23980 AAATTGAGAATTTAGAGG
1 AAATTGAGAATATAG-GG
23998 AAA
1 AAA
24001 ATTGGGAAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
17 27 0.75
18 9 0.25
ACGTcount: A:0.48, C:0.00, G:0.27, T:0.25
Consensus pattern (17 bp):
AAATTGAGAATATAGGG
Found at i:23944 original size:27 final size:27
Alignment explanation
Indices: 23891--23972 Score: 128
Period size: 27 Copynumber: 3.0 Consensus size: 27
23881 ATTTGATTTT
* *
23891 ATTTGGGAATTTAGAGGAAAATTGAGAAA
1 ATTTGAGAATATAG-GG-AAATTGAGAAA
23920 ATTTGAGAATATAGGGAAATTGAGAAA
1 ATTTGAGAATATAGGGAAATTGAGAAA
23947 ATTTGAGAATATAGGGAAATTGAGAA
1 ATTTGAGAATATAGGGAAATTGAGAA
23973 TATAGGGAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
27 37 0.73
28 2 0.04
29 12 0.24
ACGTcount: A:0.46, C:0.00, G:0.27, T:0.27
Consensus pattern (27 bp):
ATTTGAGAATATAGGGAAATTGAGAAA
Found at i:24008 original size:44 final size:44
Alignment explanation
Indices: 23897--24011 Score: 153
Period size: 44 Copynumber: 2.6 Consensus size: 44
23887 TTTTATTTGG
*
23897 GAATTTAGAGGAAAATTGAGAAAATTTGAGAATATAGGGAAATTGA
1 GAATTTAGAGGAAAATTG-GGAAA-TTGAGAATATAGGGAAATTGA
* *
23943 GAAAATTT-GA-GAATATAGGGAAATTGAGAATATAGGGAAATTGA
1 G--AATTTAGAGGAAAATTGGGAAATTGAGAATATAGGGAAATTGA
23987 GAATTTAGAGGAAAATTGGGAAATT
1 GAATTTAGAGGAAAATTGGGAAATT
24012 TAGAGGGAAT
Statistics
Matches: 60, Mismatches: 5, Indels: 10
0.80 0.07 0.13
Matches are distributed among these distances:
42 5 0.08
43 2 0.03
44 35 0.58
45 4 0.07
46 7 0.12
47 2 0.03
48 5 0.08
ACGTcount: A:0.47, C:0.00, G:0.27, T:0.26
Consensus pattern (44 bp):
GAATTTAGAGGAAAATTGGGAAATTGAGAATATAGGGAAATTGA
Found at i:24239 original size:2 final size:2
Alignment explanation
Indices: 24232--24369 Score: 98
Period size: 2 Copynumber: 72.0 Consensus size: 2
24222 TTTAATTTTC
* * * *
24232 TA TA TA TA TA -A AA TA TA TA GTT TA TA AA T- TA TA -A TT TA TA
1 TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA
* * *
24272 T- TA -A TA TA GTA TA TA TA TA TA TA TG TA TG TC TA -A CTA -A TA
1 TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
*
24312 TA -A GTA -A TT TA TA T- TA TA TA TA 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
24352 TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
24370 GAAACACTAT
Statistics
Matches: 108, Mismatches: 14, Indels: 28
0.72 0.09 0.19
Matches are distributed among these distances:
1 10 0.09
2 93 0.86
3 5 0.05
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.48
Consensus pattern (2 bp):
TA
Found at i:24435 original size:7 final size:7
Alignment explanation
Indices: 24423--24501 Score: 68
Period size: 7 Copynumber: 11.3 Consensus size: 7
24413 TTATTAAAAA
24423 AAACCCT
1 AAACCCT
24430 AAACCCT
1 AAACCCT
*
24437 AAACCTT
1 AAACCCT
* *
24444 AAAACAT
1 AAACCCT
24451 AAACCCT
1 AAACCCT
*
24458 AAACCAT
1 AAACCCT
* **
24465 TAACTTT
1 AAACCCT
*
24472 AAACCAT
1 AAACCCT
**
24479 AAACTAT
1 AAACCCT
24486 AAACCCT
1 AAACCCT
24493 AAACCCT
1 AAACCCT
24500 AA
1 AA
24502 TATAAATAGA
Statistics
Matches: 57, Mismatches: 15, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
7 57 1.00
ACGTcount: A:0.49, C:0.30, G:0.00, T:0.20
Consensus pattern (7 bp):
AAACCCT
Found at i:24456 original size:28 final size:28
Alignment explanation
Indices: 24416--24497 Score: 96
Period size: 28 Copynumber: 3.0 Consensus size: 28
24406 ATATAGATTA
24416 TTAAAA-A-AAACCCTAAACCCTAAACC
1 TTAAAACATAAACCCTAAACCCTAAACC
* * *
24442 TTAAAACATAAACCCTAAACCATTAACT
1 TTAAAACATAAACCCTAAACCCTAAACC
* **
24470 TTAAACCATAAACTATAAACCCTAAACC
1 TTAAAACATAAACCCTAAACCCTAAACC
24498 CTAATATAAA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
26 6 0.13
27 1 0.02
28 38 0.84
ACGTcount: A:0.51, C:0.28, G:0.00, T:0.21
Consensus pattern (28 bp):
TTAAAACATAAACCCTAAACCCTAAACC
Found at i:24977 original size:13 final size:13
Alignment explanation
Indices: 24959--24983 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
24949 AGTAATATAT
24959 ATATATATATAAC
1 ATATATATATAAC
24972 ATATATATATAA
1 ATATATATATAA
24984 ACTATATAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (13 bp):
ATATATATATAAC
Found at i:24989 original size:13 final size:15
Alignment explanation
Indices: 24957--24991 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
24947 ATAGTAATAT
24957 ATATATATATATAAC
1 ATATATATATATAAC
24972 ATATATATATA-AAC
1 ATATATATATATAAC
24986 -TATATA
1 ATATATA
24992 AAGTAAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 6 0.30
14 3 0.15
15 11 0.55
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (15 bp):
ATATATATATATAAC
Found at i:25343 original size:13 final size:13
Alignment explanation
Indices: 25311--25337 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
25301 TATTATACAT
25311 TTAAATAATTTTA
1 TTAAATAATTTTA
25324 TTAAATAATTTTA
1 TTAAATAATTTTA
25337 T
1 T
25338 ATAATATGTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TTAAATAATTTTA
Found at i:25524 original size:16 final size:16
Alignment explanation
Indices: 25505--25558 Score: 81
Period size: 16 Copynumber: 3.4 Consensus size: 16
25495 AAATATCAGA
25505 TCAGGTTAAAAACATG
1 TCAGGTTAAAAACATG
* *
25521 TCAGATTAAAAACAGG
1 TCAGGTTAAAAACATG
*
25537 TCAGGTTGAAAACATG
1 TCAGGTTAAAAACATG
25553 TCAGGT
1 TCAGGT
25559 AATACCAGTT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.41, C:0.13, G:0.22, T:0.24
Consensus pattern (16 bp):
TCAGGTTAAAAACATG
Found at i:34263 original size:25 final size:25
Alignment explanation
Indices: 34229--34287 Score: 100
Period size: 25 Copynumber: 2.4 Consensus size: 25
34219 ACTAAGTTAC
34229 AGAATGAAACGTTAGACACCAAACT
1 AGAATGAAACGTTAGACACCAAACT
*
34254 AGAATGAAACGTTAGACAGCAAACT
1 AGAATGAAACGTTAGACACCAAACT
*
34279 AGAACGAAA
1 AGAATGAAA
34288 TAAACGTTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.51, C:0.17, G:0.19, T:0.14
Consensus pattern (25 bp):
AGAATGAAACGTTAGACACCAAACT
Found at i:35418 original size:76 final size:76
Alignment explanation
Indices: 35333--35492 Score: 304
Period size: 76 Copynumber: 2.1 Consensus size: 76
35323 TCAAAAGATT
35333 TTTTTAATAATTTTAATTTATAGTTAAACTATTTATATCATGGATTTGGATACTTTATCATTTAT
1 TTTTTAATAATTTTAATTTATAGTTAAACTATTTATATCATGGATTTGGATACTTTATCATTTAT
*
35398 ATTAATATTCA
66 ATAAATATTCA
35409 TTTTTAATAATTTTAATTTATAGTTAAACTATTTATATCATGGATTTGGATACTTTATCATTTAT
1 TTTTTAATAATTTTAATTTATAGTTAAACTATTTATATCATGGATTTGGATACTTTATCATTTAT
35474 ATAAATATTCA
66 ATAAATATTCA
35485 -TTTTAATA
1 TTTTTAATA
35493 TTAATTTTTA
Statistics
Matches: 83, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
75 8 0.10
76 75 0.90
ACGTcount: A:0.35, C:0.06, G:0.06, T:0.53
Consensus pattern (76 bp):
TTTTTAATAATTTTAATTTATAGTTAAACTATTTATATCATGGATTTGGATACTTTATCATTTAT
ATAAATATTCA
Found at i:35761 original size:32 final size:32
Alignment explanation
Indices: 35720--35806 Score: 138
Period size: 32 Copynumber: 2.7 Consensus size: 32
35710 TCTATGAAAA
35720 TTCAATTCAGGTCAAAATTGGATTGGTTGCTT
1 TTCAATTCAGGTCAAAATTGGATTGGTTGCTT
*
35752 TTCAATTCAGGTCAAAATTGGATTGGTTGGTT
1 TTCAATTCAGGTCAAAATTGGATTGGTTGCTT
* * *
35784 TCCAAGTCATGTCAAAATTGGAT
1 TTCAATTCAGGTCAAAATTGGAT
35807 CGATTGACTT
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 51 1.00
ACGTcount: A:0.28, C:0.13, G:0.22, T:0.38
Consensus pattern (32 bp):
TTCAATTCAGGTCAAAATTGGATTGGTTGCTT
Found at i:45276 original size:30 final size:30
Alignment explanation
Indices: 45241--45314 Score: 94
Period size: 30 Copynumber: 2.5 Consensus size: 30
45231 TCAAAATACA
45241 TAAGATATGGTCACTTACATTTTATTTAAT
1 TAAGATATGGTCACTTACATTTTATTTAAT
* ***
45271 TAAGATAGGGTCACTTTTGTTTTATTTAAT
1 TAAGATATGGTCACTTACATTTTATTTAAT
* *
45301 TAAAATGTGGTCAC
1 TAAGATATGGTCAC
45315 CCCGAGTTAA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.31, C:0.09, G:0.15, T:0.45
Consensus pattern (30 bp):
TAAGATATGGTCACTTACATTTTATTTAAT
Found at i:45910 original size:22 final size:22
Alignment explanation
Indices: 45864--45909 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
45854 ATTATATTTC
*
45864 TTTATTTTGAATTTTAATAAAT
1 TTTATTTTGAATTATAATAAAT
*
45886 TTTATTTT-AATTATAATTAAT
1 TTTATTTTGAATTATAATAAAT
45907 TTT
1 TTT
45910 TTGAATTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 14 0.64
22 8 0.36
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (22 bp):
TTTATTTTGAATTATAATAAAT
Found at i:46477 original size:3 final size:3
Alignment explanation
Indices: 46471--46553 Score: 157
Period size: 3 Copynumber: 27.3 Consensus size: 3
46461 TATTATTATT
46471 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATAA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA
46517 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
46554 AGTGAAAATT
Statistics
Matches: 79, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
3 76 0.96
4 3 0.04
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:47928 original size:20 final size:21
Alignment explanation
Indices: 47903--47954 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
47893 TTTTTCCAAT
*
47903 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
47923 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
47944 TCGCAATGCGA
1 TCGCAATGCGA
47955 TACTAACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:47967 original size:41 final size:41
Alignment explanation
Indices: 47940--48057 Score: 182
Period size: 41 Copynumber: 2.9 Consensus size: 41
47930 GCGAATTGGG
* * * *
47940 AAAATCGCAATGCGATACTAACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATAC
*
47981 AAAATCGCAACGAGATACTGACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATAC
*
48022 AAAATCGCAACGAGATACTGACTTTCGCAACGCGAT
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGAT
48058 TCTGACTTTC
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 72 1.00
ACGTcount: A:0.40, C:0.23, G:0.17, T:0.20
Consensus pattern (41 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATAC
Found at i:47968 original size:20 final size:20
Alignment explanation
Indices: 47943--48078 Score: 101
Period size: 20 Copynumber: 6.7 Consensus size: 20
47933 AATTGGGAAA
*
47943 ATCGCAATGCGATACTAACT
1 ATCGCAACGCGATACTAACT
* * **
47963 ATCGCAATGCGATAATACAAA
1 ATCGCAACGCGATACTA-ACT
* *
47984 ATCGCAACGAGATACTGACT
1 ATCGCAACGCGATACTAACT
* * **
48004 ATCGCAATGCGATAATACAAA
1 ATCGCAACGCGATACTA-ACT
* *
48025 ATCGCAACGAGATACTGACT
1 ATCGCAACGCGATACTAACT
* * *
48045 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTAACT
*
48065 TTCGCAACGCGATA
1 ATCGCAACGCGATA
48079 ATACATAATC
Statistics
Matches: 89, Mismatches: 25, Indels: 4
0.75 0.21 0.03
Matches are distributed among these distances:
20 61 0.69
21 28 0.31
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.22
Consensus pattern (20 bp):
ATCGCAACGCGATACTAACT
Found at i:48038 original size:21 final size:21
Alignment explanation
Indices: 47963--48038 Score: 75
Period size: 21 Copynumber: 3.7 Consensus size: 21
47953 GATACTAACT
* *
47963 ATCGCAATGCGATAATACAAA
1 ATCGCAACGAGATAATACAAA
* *
47984 ATCGCAACGAGATACTGAC--T
1 ATCGCAACGAGATAAT-ACAAA
* *
48004 ATCGCAATGCGATAATACAAA
1 ATCGCAACGAGATAATACAAA
48025 ATCGCAACGAGATA
1 ATCGCAACGAGATA
48039 CTGACTTTCG
Statistics
Matches: 42, Mismatches: 10, Indels: 6
0.72 0.17 0.10
Matches are distributed among these distances:
19 2 0.05
20 13 0.31
21 25 0.60
22 2 0.05
ACGTcount: A:0.43, C:0.21, G:0.17, T:0.18
Consensus pattern (21 bp):
ATCGCAACGAGATAATACAAA
Found at i:48284 original size:22 final size:22
Alignment explanation
Indices: 48256--48299 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
48246 CCATCTCTCA
48256 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
48278 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
48300 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:48612 original size:20 final size:20
Alignment explanation
Indices: 48558--48616 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
48548 GCGATTCTCT
**
48558 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
48578 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* **
48598 TGTTGCGATTTTCATTTTC
1 CGTTGCGATAGTCATTTTC
48617 AGAAACTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.17, C:0.19, G:0.22, T:0.42
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:48807 original size:25 final size:26
Alignment explanation
Indices: 48746--48807 Score: 60
Period size: 25 Copynumber: 2.4 Consensus size: 26
48736 CTCTTTATGT
*
48746 TTATTATTGTTTTTGGTATATCTTCAC
1 TTATTA-TGTTTTTGGTATATCTTAAC
48773 --AGTGTA-GTTTTTGGTATATC-TAAC
1 TTA-T-TATGTTTTTGGTATATCTTAAC
48797 TTATTATGTTT
1 TTATTATGTTT
48808 ATTGTTTTTG
Statistics
Matches: 29, Mismatches: 1, Indels: 12
0.69 0.02 0.29
Matches are distributed among these distances:
24 5 0.17
25 20 0.69
26 2 0.07
27 2 0.07
ACGTcount: A:0.21, C:0.08, G:0.15, T:0.56
Consensus pattern (26 bp):
TTATTATGTTTTTGGTATATCTTAAC
Found at i:49952 original size:18 final size:18
Alignment explanation
Indices: 49931--49975 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
49921 TCTACTTCGG
*
49931 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
49949 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
49967 GAGCCATCA
1 GAGCCATCA
49976 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:50508 original size:19 final size:20
Alignment explanation
Indices: 50454--50520 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
50444 ATAGTTACTT
* *
50454 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
50474 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
50494 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
50513 TCGCAACG
1 TCGCAACG
50521 ACAAAATCAC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:50539 original size:33 final size:33
Alignment explanation
Indices: 50497--50584 Score: 149
Period size: 33 Copynumber: 2.7 Consensus size: 33
50487 ATGGCTATCG
50497 CAATGCGAAATGAAAATCGCAACGACAAAATCA
1 CAATGCGAAATGAAAATCGCAACGACAAAATCA
* *
50530 CAATGCGAAATGAAAATCGCAACGATAAAATCG
1 CAATGCGAAATGAAAATCGCAACGACAAAATCA
*
50563 CAACGCGAAATGAAAATCGCAA
1 CAATGCGAAATGAAAATCGCAA
50585 TGCGATTTGT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 52 1.00
ACGTcount: A:0.50, C:0.20, G:0.17, T:0.12
Consensus pattern (33 bp):
CAATGCGAAATGAAAATCGCAACGACAAAATCA
Found at i:50547 original size:19 final size:19
Alignment explanation
Indices: 50493--50589 Score: 97
Period size: 19 Copynumber: 5.6 Consensus size: 19
50483 GGAAATGGCT
50493 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
50512 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
*
50526 ATCACAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
50545 ATCGCAA--CG--AT-AAA
1 ATCGCAATGCGAAATGAAA
*
50559 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
50578 ATCGCAATGCGA
1 ATCGCAATGCGA
50590 TTTGTGTTTC
Statistics
Matches: 63, Mismatches: 5, Indels: 20
0.72 0.06 0.23
Matches are distributed among these distances:
14 19 0.30
15 3 0.05
16 4 0.06
17 4 0.06
18 3 0.05
19 30 0.48
ACGTcount: A:0.47, C:0.21, G:0.19, T:0.13
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:50620 original size:14 final size:14
Alignment explanation
Indices: 50601--50691 Score: 83
Period size: 14 Copynumber: 5.9 Consensus size: 14
50591 TTGTGTTTCG
50601 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
50615 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
50631 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
*
50647 CGTTGCGATTTTCATTT
1 CGTTGCGA-TTT--TGT
50664 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
50680 CGTTGCGATTTT
1 CGTTGCGATTTT
50692 CATTTCGCAT
Statistics
Matches: 64, Mismatches: 4, Indels: 18
0.74 0.05 0.21
Matches are distributed among these distances:
14 27 0.42
15 3 0.05
16 12 0.19
17 4 0.06
18 12 0.19
19 6 0.09
ACGTcount: A:0.11, C:0.18, G:0.23, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:50665 original size:33 final size:33
Alignment explanation
Indices: 50596--50707 Score: 208
Period size: 33 Copynumber: 3.4 Consensus size: 33
50586 GCGATTTGTG
*
50596 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
50628 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
50661 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
50694 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
50708 AGGCATTTCC
Statistics
Matches: 78, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
32 26 0.33
33 52 0.67
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (33 bp):
TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
Found at i:50726 original size:20 final size:19
Alignment explanation
Indices: 50692--50747 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
50682 TTGCGATTTT
*
50692 CATTTCGCATTGCGATAGG
1 CATTTCGCGTTGCGATAGG
*
50711 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGG
50731 CATTTTCGCGTTGCGAT
1 CA-TTTCGCGTTGCGAT
50748 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 5 0.15
20 25 0.76
21 3 0.09
ACGTcount: A:0.16, C:0.23, G:0.25, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGG
Found at i:52849 original size:20 final size:20
Alignment explanation
Indices: 52832--52900 Score: 120
Period size: 20 Copynumber: 3.5 Consensus size: 20
52822 CGTTTTCTCA
* *
52832 TTGCGATAGCGATTTTCTCG
1 TTGCGATAGCCATTTTCGCG
52852 TTGCGATAGCCATTTTCGCG
1 TTGCGATAGCCATTTTCGCG
52872 TTGCGATAGCCATTTTCGCG
1 TTGCGATAGCCATTTTCGCG
52892 TTGCGATAG
1 TTGCGATAG
52901 TCAAATGAAT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.16, C:0.22, G:0.26, T:0.36
Consensus pattern (20 bp):
TTGCGATAGCCATTTTCGCG
Found at i:55373 original size:23 final size:23
Alignment explanation
Indices: 55324--55376 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
55314 TCTAAACATC
*
55324 ATCAAATCCGAGTATTGACTAAT
1 ATCAAATCCGAGTATTGACTAAG
* *
55347 ATCAAAGTCCGGGTATTGAC-CAG
1 ATCAAA-TCCGAGTATTGACTAAG
55370 ATCAAAT
1 ATCAAAT
55377 TTCGAATACT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
22 1 0.04
23 13 0.50
24 12 0.46
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.26
Consensus pattern (23 bp):
ATCAAATCCGAGTATTGACTAAG
Found at i:56136 original size:40 final size:40
Alignment explanation
Indices: 56085--56198 Score: 124
Period size: 40 Copynumber: 2.9 Consensus size: 40
56075 GAACTTTGAA
* *
56085 AATCGCATTGCGATTATGTATTATCTCGTTGCGAAGTCAG
1 AATCGCGTTGCGATTATGTATTATCGCGTTGCGAAGTCAG
* * * *
56125 AATCGCGTTGCGA--AAGTCAGTATCGCGTTACGAAATTCAG
1 AATCGCGTTGCGATTATGT-ATTATCGCGTTGCG-AAGTCAG
* *
56165 TATCGCGTTGCGATTTTGTATTATCGCGTTGCGA
1 AATCGCGTTGCGATTATGTATTATCGCGTTGCGA
56199 TTTTCCCAAT
Statistics
Matches: 59, Mismatches: 11, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
38 3 0.05
39 11 0.19
40 31 0.53
41 12 0.20
42 2 0.03
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (40 bp):
AATCGCGTTGCGATTATGTATTATCGCGTTGCGAAGTCAG
Found at i:56143 original size:20 final size:20
Alignment explanation
Indices: 56106--56177 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
56096 GATTATGTAT
*
56106 TATCTCGTTGCG-AAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
56125 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
* *
56145 TATCGCGTTACGAAATTCAG
1 TATCGCGTTGCGAAAGTCAG
56165 TATCGCGTTGCGA
1 TATCGCGTTGCGA
56178 TTTTGTATTA
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
19 10 0.22
20 36 0.78
ACGTcount: A:0.25, C:0.21, G:0.26, T:0.28
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:56232 original size:20 final size:19
Alignment explanation
Indices: 56167--56239 Score: 58
Period size: 21 Copynumber: 3.6 Consensus size: 19
56157 AAATTCAGTA
56167 TCGCGTTGCGATTT-TGTATT
1 TCGCGTTGCGATTTCT-TA-T
**
56187 ATCGCGTTGCGATTTTCCCAAT
1 -TCGCGTTGCGA-TTT-CTTAT
56209 TCGCGTTGCGATTTACTTAT
1 TCGCGTTGCGATTT-CTTAT
*
56229 TCGCATTGCGA
1 TCGCGTTGCGA
56240 ATTGGGAAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
20 16 0.37
21 22 0.51
22 4 0.09
23 1 0.02
ACGTcount: A:0.15, C:0.22, G:0.22, T:0.41
Consensus pattern (19 bp):
TCGCGTTGCGATTTCTTAT
Found at i:56310 original size:21 final size:21
Alignment explanation
Indices: 56270--56310 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
56260 ACTGTAGACC
**
56270 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
56291 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
56311 GCAAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:56730 original size:15 final size:15
Alignment explanation
Indices: 56710--56744 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
56700 GACCCGAATT
*
56710 TAACCAAACTGAAAG
1 TAACCAAACCGAAAG
*
56725 TAACCAAACCGAAAT
1 TAACCAAACCGAAAG
56740 TAACC
1 TAACC
56745 CAAATTAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.51, C:0.26, G:0.09, T:0.14
Consensus pattern (15 bp):
TAACCAAACCGAAAG
Found at i:57021 original size:48 final size:48
Alignment explanation
Indices: 56965--57061 Score: 151
Period size: 48 Copynumber: 2.0 Consensus size: 48
56955 GTTACCTGAA
*
56965 CCGACCCGACTTACTATAGGCACGAATAAAACCAAAACCCT-AAATGAC
1 CCGACCCGACTTACTATAGACACGAATAAAACCAAAA-CCTAAAATGAC
* *
57013 CCGACCCGACTTACTATAGACCCGAATAAAACCGAAACCTAAAATGAC
1 CCGACCCGACTTACTATAGACACGAATAAAACCAAAACCTAAAATGAC
57061 C
1 C
57062 TGAACCGAAC
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
47 3 0.07
48 42 0.93
ACGTcount: A:0.41, C:0.32, G:0.12, T:0.14
Consensus pattern (48 bp):
CCGACCCGACTTACTATAGACACGAATAAAACCAAAACCTAAAATGAC
Found at i:59442 original size:32 final size:32
Alignment explanation
Indices: 59406--59468 Score: 126
Period size: 32 Copynumber: 2.0 Consensus size: 32
59396 CATTATCATG
59406 TTAGTTTTCTTCCGAAGCTGCTCGCATTCCAA
1 TTAGTTTTCTTCCGAAGCTGCTCGCATTCCAA
59438 TTAGTTTTCTTCCGAAGCTGCTCGCATTCCA
1 TTAGTTTTCTTCCGAAGCTGCTCGCATTCCA
59469 TTTCCACGGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.17, C:0.29, G:0.16, T:0.38
Consensus pattern (32 bp):
TTAGTTTTCTTCCGAAGCTGCTCGCATTCCAA
Found at i:60076 original size:13 final size:13
Alignment explanation
Indices: 60058--60089 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
60048 TTCTTGCGTT
60058 TTGCGCGTTATAA
1 TTGCGCGTTATAA
60071 TTGCGCGTTATAA
1 TTGCGCGTTATAA
60084 TTGCGC
1 TTGCGC
60090 CTATCCTACG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.38
Consensus pattern (13 bp):
TTGCGCGTTATAA
Found at i:60760 original size:39 final size:38
Alignment explanation
Indices: 60713--60787 Score: 100
Period size: 39 Copynumber: 1.9 Consensus size: 38
60703 TTATTAAATT
60713 TTTCTTAAATT-TTTACACCA-TAACTTTCTAAATTATTAA
1 TTTCTTAAATTATTT-CA-CATTAACTTTCT-AATTATTAA
*
60752 TTTCTTAAATTATTTCACATTAATTTTCTAATTATT
1 TTTCTTAAATTATTTCACATTAACTTTCTAATTATT
60788 TTTTAAATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
38 9 0.27
39 21 0.64
40 3 0.09
ACGTcount: A:0.33, C:0.13, G:0.00, T:0.53
Consensus pattern (38 bp):
TTTCTTAAATTATTTCACATTAACTTTCTAATTATTAA
Found at i:61049 original size:23 final size:23
Alignment explanation
Indices: 61023--61068 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
61013 TATATATGAC
61023 TTAAATATTTTTA-TATTAACTTA
1 TTAAATA-TTTTACTATTAACTTA
61046 TTAAATATTTTACTATTAACTTA
1 TTAAATATTTTACTATTAACTTA
61069 ACTTAATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 5 0.23
23 17 0.77
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.54
Consensus pattern (23 bp):
TTAAATATTTTACTATTAACTTA
Done.