Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008425.1 Hibiscus syriacus cultivar Beakdansim tig00111208_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: 2340112
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 12
Found at i:188163 original size:19 final size:19
Alignment explanation
Indices: 188141--188179 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
188131 GTTTGTCTCT
188141 AGGTACTTAGTGTGTCAGC
1 AGGTACTTAGTGTGTCAGC
188160 AGGTACTTAGTGTGTCAGC
1 AGGTACTTAGTGTGTCAGC
188179 A
1 A
188180 AGTTAAGGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.23, C:0.15, G:0.31, T:0.31
Consensus pattern (19 bp):
AGGTACTTAGTGTGTCAGC
Found at i:190779 original size:30 final size:26
Alignment explanation
Indices: 190694--190759 Score: 78
Period size: 26 Copynumber: 2.3 Consensus size: 26
190684 TTGTATATCT
*
190694 TAAATATATCTTTATTCTTATTTTAACTTAT
1 TAAATATAT-TTTATT-TTATTTTAA--T-G
190725 TAAATATATTTTATTTTATTTTAATG
1 TAAATATATTTTATTTTATTTTAATG
190751 TAAATATAT
1 TAAATATAT
190760 ATATTATCTT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
26 9 0.26
27 1 0.03
29 9 0.26
30 6 0.18
31 9 0.26
ACGTcount: A:0.36, C:0.05, G:0.02, T:0.58
Consensus pattern (26 bp):
TAAATATATTTTATTTTATTTTAATG
Found at i:190964 original size:30 final size:30
Alignment explanation
Indices: 190928--190985 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
190918 AGTTGGTTCA
190928 TGCATATATTTTATCTTTATCATCACTTTG
1 TGCATATATTTTATCTTTATCATCACTTTG
*
190958 TGCATATATTTTATCTTTATTATCACTT
1 TGCATATATTTTATCTTTATCATCACTT
190986 AAAAATATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.24, C:0.16, G:0.05, T:0.55
Consensus pattern (30 bp):
TGCATATATTTTATCTTTATCATCACTTTG
Found at i:195445 original size:18 final size:20
Alignment explanation
Indices: 195422--195469 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
195412 TATGCAATTA
*
195422 GTATCGATACT-GA-TGTAG
1 GTATCGATACTAGATTGAAG
*
195440 GTATCGATACTATATTGAAG
1 GTATCGATACTAGATTGAAG
195460 GTATCGATAC
1 GTATCGATAC
195470 CATGGATTCC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 11 0.42
19 1 0.04
20 14 0.54
ACGTcount: A:0.31, C:0.12, G:0.23, T:0.33
Consensus pattern (20 bp):
GTATCGATACTAGATTGAAG
Found at i:196363 original size:54 final size:54
Alignment explanation
Indices: 195886--196352 Score: 575
Period size: 54 Copynumber: 8.6 Consensus size: 54
195876 CTATGTGTAC
* *
195886 TATATGCACTAAGTGTGCAACCCACAAAATTCATCATATGTTGATGAACGACCT
1 TATAGGCACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAACGACCT
* * *
195940 TATAGGCACTAAGTGTTCAACCCACAGAATTCATCATATGTTGATGAATGACCG
1 TATAGGCACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAACGACCT
* * *
195994 TATAGGCACTAAGTGTGTAACCCACGGAATTCATCATATGTTGATGAACGACCG
1 TATAGGCACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAACGACCT
* * *
196048 TATAGGCACTAAGTGTGCAACCCACAAAATTCATCATATGTTAATGGACGA-CT
1 TATAGGCACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAACGACCT
* * * * *
196101 GTATAGGCACTAAGTGGGTAACCCACAAAATTCATCATATATTGATGAACGAACT
1 -TATAGGCACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAACGACCT
*
196156 GTATAGGCACTAAGTGTGCAACCCAC-GAAATTCATCATATGTTGATGAACGATCT
1 -TATAGGCACTAAGTGTGCAACCCACAG-AATTCATCATATGTTGATGAACGACCT
* * * *
196211 TATAGGCACTAAATGTGCAACCCA-TGAAATTCATCATATGTTGATCAACGACCG
1 TATAGGCACTAAGTGTGCAACCCACAG-AATTCATCATATGTTGATGAACGACCT
* * * * * *
196265 TATAGGCACTCAGTGTGCAAACCA-AGGAATTCATAATGTGTTTATGAATGACCT
1 TATAGGCACTAAGTGTGCAACCCACA-GAATTCATCATATGTTGATGAACGACCT
* **
196319 TATCA-GCACTAAGTGTGCAATCCATTGAATTCAT
1 TAT-AGGCACTAAGTGTGCAACCCACAGAATTCAT
196353 AATTTGTTTA
Statistics
Matches: 364, Mismatches: 42, Indels: 14
0.87 0.10 0.03
Matches are distributed among these distances:
53 1 0.00
54 310 0.85
55 53 0.15
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.27
Consensus pattern (54 bp):
TATAGGCACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAACGACCT
Found at i:201312 original size:54 final size:54
Alignment explanation
Indices: 201230--201638 Score: 444
Period size: 54 Copynumber: 7.6 Consensus size: 54
201220 TAGATGTATA
* * * * *
201230 TTGATGAACGACCATATAGGAACCAAGTGAGCAACCCATGGAATTCATCATATG
1 TTGATGAACGACCGTATAGGCACTAAGTGTGCAACCCACGGAATTCATCATATG
* ** *
201284 TTGATGAACGACTGTATAGGCACTAAGTGTGCAACCCACAAAATTCATCATATA
1 TTGATGAACGACCGTATAGGCACTAAGTGTGCAACCCACGGAATTCATCATATG
* * * *
201338 TTGATGGATGACCGTATAGGCACTAAGTGGGCAACCCACGAAATTCATCATATG
1 TTGATGAACGACCGTATAGGCACTAAGTGTGCAACCCACGGAATTCATCATATG
* *
201392 TTGATGAACGATCGTATAGGCACTAAGTGTGCAACCCATGGAATTCATCATATG
1 TTGATGAACGACCGTATAGGCACTAAGTGTGCAACCCACGGAATTCATCATATG
** *
201446 TTGATGAACGACCGTATATTCACTAAATGTGCAACCCACGGAATTCATCATATG
1 TTGATGAACGACCGTATAGGCACTAAGTGTGCAACCCACGGAATTCATCATATG
* * * ** *
201500 TTGATGAACGACCGTGTAGGCACTAAGTGTGCAAACCAC-AAATTCAAAATGTG
1 TTGATGAACGACCGTATAGGCACTAAGTGTGCAACCCACGGAATTCATCATATG
* * * * * * * *** * *
201553 TTTATGAAGGATCGTAT-GGCACCAAGTTTTCAATCCATATAATTCATAATGTG
1 TTGATGAACGACCGTATAGGCACTAAGTGTGCAACCCACGGAATTCATCATATG
* * * *
201606 TTTATGAATGACCGTATCGGCACTACGTGTGCA
1 TTGATGAACGACCGTATAGGCACTAAGTGTGCA
201639 CCCTAGAGAA
Statistics
Matches: 301, Mismatches: 52, Indels: 4
0.84 0.15 0.01
Matches are distributed among these distances:
52 16 0.05
53 50 0.17
54 235 0.78
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (54 bp):
TTGATGAACGACCGTATAGGCACTAAGTGTGCAACCCACGGAATTCATCATATG
Found at i:201497 original size:162 final size:161
Alignment explanation
Indices: 201230--201630 Score: 498
Period size: 162 Copynumber: 2.5 Consensus size: 161
201220 TAGATGTATA
* * * *
201230 TTGATGAACGACCATATAGGAACCAAGTGAGCAACCCATGGAATTCATCATATGTTGATGAACGA
1 TTGATGAACGATCGTATAGGCACCAAGTGTGCAACCCATGGAATTCATCATATGTTGATGAACGA
* * * *
201295 CTGTATAGGCACTAAGTGTGCAACCCACAAAATTCATCATATATTGATGGATGACCGTATAGGCA
66 CCGTATAGGCACTAAATGTGCAACCCACAAAATTCATCATATATTGATGAACGACCGTATAGGCA
* **
201360 CTAAGTGGGCAACCCACGAAATTCATCATATG
131 CTAAGTGGGCAAACCAC-AAATTCAAAATATG
*
201392 TTGATGAACGATCGTATAGGCACTAAGTGTGCAACCCATGGAATTCATCATATGTTGATGAACGA
1 TTGATGAACGATCGTATAGGCACCAAGTGTGCAACCCATGGAATTCATCATATGTTGATGAACGA
** ** * *
201457 CCGTATATTCACTAAATGTGCAACCCACGGAATTCATCATATGTTGATGAACGACCGTGTAGGCA
66 CCGTATAGGCACTAAATGTGCAACCCACAAAATTCATCATATATTGATGAACGACCGTATAGGCA
* *
201522 CTAAGTGTGCAAACCACAAATTCAAAATGTG
131 CTAAGTGGGCAAACCACAAATTCAAAATATG
* * * * * ** * * * *
201553 TTTATGAAGGATCGTAT-GGCACCAAGTTTTCAATCCATATAATTCATAATGTGTTTATGAATGA
1 TTGATGAACGATCGTATAGGCACCAAGTGTGCAACCCATGGAATTCATCATATGTTGATGAACGA
*
201617 CCGTATCGGCACTA
66 CCGTATAGGCACTA
201631 CGTGTGCACC
Statistics
Matches: 204, Mismatches: 35, Indels: 2
0.85 0.15 0.01
Matches are distributed among these distances:
160 48 0.24
161 26 0.13
162 130 0.64
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27
Consensus pattern (161 bp):
TTGATGAACGATCGTATAGGCACCAAGTGTGCAACCCATGGAATTCATCATATGTTGATGAACGA
CCGTATAGGCACTAAATGTGCAACCCACAAAATTCATCATATATTGATGAACGACCGTATAGGCA
CTAAGTGGGCAAACCACAAATTCAAAATATG
Found at i:203031 original size:12 final size:12
Alignment explanation
Indices: 203014--203038 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
203004 GAATGAATGG
203014 TAGGGATTGATT
1 TAGGGATTGATT
203026 TAGGGATTGATT
1 TAGGGATTGATT
203038 T
1 T
203039 TAAATATGGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.00, G:0.32, T:0.44
Consensus pattern (12 bp):
TAGGGATTGATT
Found at i:205496 original size:31 final size:31
Alignment explanation
Indices: 205458--205582 Score: 198
Period size: 31 Copynumber: 4.0 Consensus size: 31
205448 CCCGAAGGAC
* * *
205458 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
205489 CAGTCCATATGTCCCGAAGAACATAAGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
205520 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
205551 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
205582 C
1 C
205583 CCTCGACCCT
Statistics
Matches: 88, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
31 87 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:207796 original size:3 final size:3
Alignment explanation
Indices: 207788--207854 Score: 134
Period size: 3 Copynumber: 22.3 Consensus size: 3
207778 GTAAAAGCAA
207788 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
207836 AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT A
207855 GTAGTAGTAG
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 64 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:210313 original size:29 final size:28
Alignment explanation
Indices: 210281--210356 Score: 107
Period size: 29 Copynumber: 2.6 Consensus size: 28
210271 GTATCTATTA
**
210281 TAATTTATAAAAGGTTTTATCTTTAATTT
1 TAATTTATAAAA-GTTTTATCCCTAATTT
210310 TAATTTATAAAAAGTTTTATCCCTAATTT
1 TAATTTAT-AAAAGTTTTATCCCTAATTT
210339 TAATTTATATAAAGTTTT
1 TAATTTATA-AAAGTTTT
210357 GTCCTTTTAC
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
28 1 0.02
29 38 0.88
30 4 0.09
ACGTcount: A:0.37, C:0.05, G:0.05, T:0.53
Consensus pattern (28 bp):
TAATTTATAAAAGTTTTATCCCTAATTT
Found at i:210343 original size:58 final size:56
Alignment explanation
Indices: 210244--210356 Score: 133
Period size: 58 Copynumber: 2.0 Consensus size: 56
210234 AACCTTTCTC
210244 CTTTAATGTAATTTATAAAAAGTTGTGGTATCTATTATAATTTATA-AAAGGTTTTAT
1 CTTTAATGTAATTTATAAAAAGTTGT-GTATCTATTATAATTTATATAAA-GTTTTAT
* *
210301 CTTTAATTTTAATTTATAAAAAGTT-T-TATCCCTAATTTTAATTTATATAAAGTTTT
1 CTTTAA-TGTAATTTATAAAAAGTTGTGTAT--CT-ATTATAATTTATATAAAGTTTT
210357 GTCCTTTTAC
Statistics
Matches: 49, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
55 3 0.06
57 9 0.18
58 34 0.69
59 3 0.06
ACGTcount: A:0.36, C:0.05, G:0.08, T:0.50
Consensus pattern (56 bp):
CTTTAATGTAATTTATAAAAAGTTGTGTATCTATTATAATTTATATAAAGTTTTAT
Found at i:210406 original size:26 final size:26
Alignment explanation
Indices: 210376--210426 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
210366 CTAAAATGTT
* *
210376 TTGTCCTTTAGTGTAATTTATAAAAG
1 TTGTCCTTAAATGTAATTTATAAAAG
*
210402 TTGTCCTTAAATGTGATTTATAAAA
1 TTGTCCTTAAATGTAATTTATAAAA
210427 AAGTTGTGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.33, C:0.08, G:0.14, T:0.45
Consensus pattern (26 bp):
TTGTCCTTAAATGTAATTTATAAAAG
Found at i:212812 original size:678 final size:684
Alignment explanation
Indices: 210905--213679 Score: 4716
Period size: 705 Copynumber: 4.0 Consensus size: 684
210895 AGACCTTGGC
*
210905 CATAGTCAACCGCAAAAGTACCTTGCACACTTGCTTTAGGTGTTCTTGGATATCCTATACCACTA
1 CATAGTCAACCGCAAAAGTACCTTGCACACTTGCTTTAGGTGTTCTCGGATATCCTATACCACTA
210970 GATGATCTTCAGCGCCTGAACTGGACTGATGCGACTATACATGCATACCTAAGGCCCAGAGGCCA
66 GATGATCTTCAGCGCCTGAACTGGACTGATGCGACTATACATGCATACCTAAGGCCCAGAGGCCA
*
211035 TACGACACTGACATCGTTACCCAGCTCCTCATGAGTGTTTGAGCCTCACGCCTTAACTAGCTCCT
131 TACGACACTGACATCGTTACCCAACTCCTCATGAGTGTTTGAGCCTCACGCCTTAACTAGCTCCT
*
211100 GAAGTGTGTTGTATACTGAAAATGTCCTACTAGGGAAACTAAGGTAACTTGGGTATACCCTAACA
196 GAAGTGTGTTGTATACTGAAAATGTCCTACTAGGGAAACTAAGGTAACTTGGGTATACCCTAGCA
211165 CAATTAGACTCATTAAGGTGAGTTCATCCTCTCACAAGCTTCTATCTCACTCGTTCTCTCATCTA
261 CAATTAGACTCATTAAGGTGAGTTCATCCTCTCACAAGCTTCTATCTCACTCGTTCTCTCATCTA
*
211230 GAATGTTATGCGAAAGATTATTAGTCTATTACTACTATTATCTATTAGGATGATCTATTATGGTC
326 GAATGTTATGCGAAGGATTATTAGTCTATTACTACTATTATCTATTAGGATGATCTATTATGGTC
211295 GTTCGTTACTTAAGGGTATTTTAGTTATTCTCTACCTCTAGGAAATTCTTTATGTTATTCACTGG
391 GTTCGTTACTTAAGGGTATTTTAGTTATTCTCTACCTCTAGGAAATTCTTTATGTTATTCACTGG
*
211360 TTGTACTATTCACTAGCCCGATATCTGACTCAGGGTCAACACTGGGTAACGACACTCTGATCGCT
456 TTGTACTATTCACTAGCCCGATATCTGACTCAGGGTCAACACTGGGTAGCGACACTCTGATCGCT
211425 CTTATTGAACTTCTTTTCAATACCCCTCGAATTGAAAGGACAACTTACACCTCCTAGGTTCATTG
521 CTTATTGAACTTCTTTTCAATACCCCTCGAATTGAAAGGACAACTTACACCTCC-----T-A-TG
*
211490 ACGTTCTTGAAGGCCACGTTTTCTGCTATTTCTAAATCTGAATTGCTTATTGTACCACTGGTCAG
579 -TG-T-TT----G-CA----TTC--CTATTTCTAAATCTGAATTGCTTATTGTACCACTGGTCAG
211555 TACATTCCCCTACAACGATCCTTGTTCTCAACTATCTTGACTAAAGATATTTCGA
630 TACATTCCCCTACAACGATCCTTGTTCTCAACTATCTTGACTAAAGATATTTCGA
211610 CATAGTCAACCGCAAAAGTACCTTGCACACTTGCTTTAGGTGTTCTCGGATATCCTATACCACTA
1 CATAGTCAACCGCAAAAGTACCTTGCACACTTGCTTTAGGTGTTCTCGGATATCCTATACCACTA
*
211675 GATGATCTTCAGCGCCTAAACTGGACTGATGCGACTATACATGCATACCTAAGGCCCAGAGGCCA
66 GATGATCTTCAGCGCCTGAACTGGACTGATGCGACTATACATGCATACCTAAGGCCCAGAGGCCA
211740 TACGACACTGACATCGTTACCCAACTCCTCATGAGTGTTTGAGCCTCACGCCTTAACTAGCTCCT
131 TACGACACTGACATCGTTACCCAACTCCTCATGAGTGTTTGAGCCTCACGCCTTAACTAGCTCCT
211805 GAAGTGTGTTGTATACTGAAAATGTCCTACTAGGGAAACTAAGGTAACTTGGGTATACCCTAGCA
196 GAAGTGTGTTGTATACTGAAAATGTCCTACTAGGGAAACTAAGGTAACTTGGGTATACCCTAGCA
211870 CAATTAGACTCATTAAGGTGAGTTCATCCTCTCACAAGCTTCTATCTCACTCGTTCTCTCATCTA
261 CAATTAGACTCATTAAGGTGAGTTCATCCTCTCACAAGCTTCTATCTCACTCGTTCTCTCATCTA
211935 GAATGTTATGCGAAGGATTATTAGTCTATTACTACTATTATCTATTAGGATGATCTATTATGGTC
326 GAATGTTATGCGAAGGATTATTAGTCTATTACTACTATTATCTATTAGGATGATCTATTATGGTC
212000 GTTCGTTACTTAAGGGTATTTTAGTTATTCTCTACCTCTAGGAAATTCTTTATGTTATTCACTGG
391 GTTCGTTACTTAAGGGTATTTTAGTTATTCTCTACCTCTAGGAAATTCTTTATGTTATTCACTGG
* * *
212065 TTGTATTATTTACTAGCCTGATATCTGACTCAGGGTCAACACTGGGTAGCGACACTCTGATCGCT
456 TTGTACTATTCACTAGCCCGATATCTGACTCAGGGTCAACACTGGGTAGCGACACTCTGATCGCT
212130 CTTATTGAACTTCTTTTCAATACCCCTCGAATTGAAAGGACAACTTACACCTCCTA-G-G-TT-C
521 CTTATTGAACTTCTTTTCAATACCCCTCGAATTGAAAGGACAACTTACACCTCCTATGTGTTTGC
212191 A-T-CTATTTCTAAATCTGAATTGCTTATTGTACCACTGGTCAGTACATTCCCCTACAACGATCC
586 ATTCCTATTTCTAAATCTGAATTGCTTATTGTACCACTGGTCAGTACATTCCCCTACAACGATCC
212254 TTGTTCTCAACTATCTTGACTAAAGATATTTCGA
651 TTGTTCTCAACTATCTTGACTAAAGATATTTCGA
* *
212288 CATAGTCAACCGCAAAAGTACCTTGCACACTTGCTTTATGTGTTCTCAGATATCCTATACCACTA
1 CATAGTCAACCGCAAAAGTACCTTGCACACTTGCTTTAGGTGTTCTCGGATATCCTATACCACTA
212353 GATGATCTTCAGCGCCTGAACTGGACTGATGCGACTATACATGCATACCTAAGGCCCAGAGGCCA
66 GATGATCTTCAGCGCCTGAACTGGACTGATGCGACTATACATGCATACCTAAGGCCCAGAGGCCA
*
212418 TACGACACTGACATCGTTACCCAACTCCTCACGAGTGTTTGAGCCTCACGCCTTAACTAGCTCCT
131 TACGACACTGACATCGTTACCCAACTCCTCATGAGTGTTTGAGCCTCACGCCTTAACTAGCTCCT
212483 GAAGTGTGTTGTATACTGAAAATGTCCTACTAGGGAAACTAAGGTAACTTGGGTATACCCTAGCA
196 GAAGTGTGTTGTATACTGAAAATGTCCTACTAGGGAAACTAAGGTAACTTGGGTATACCCTAGCA
212548 CAATTAGACTCATTAAGGTGAGTTCATCCTCTCACAAGCTTCTATCTCACTCGTTCTCTCATCTA
261 CAATTAGACTCATTAAGGTGAGTTCATCCTCTCACAAGCTTCTATCTCACTCGTTCTCTCATCTA
212613 GAATGTTATGCGAAGGATTATTAGTCTATTACTACTATTATCTATTAGGATGATCTATTATGGTC
326 GAATGTTATGCGAAGGATTATTAGTCTATTACTACTATTATCTATTAGGATGATCTATTATGGTC
*
212678 GTTCGTTACTTAAGGGTATTTTAGTTATTCTCTACCTCTAGAAAATTCTTTATGTTATTCACTGG
391 GTTCGTTACTTAAGGGTATTTTAGTTATTCTCTACCTCTAGGAAATTCTTTATGTTATTCACTGG
* *
212743 TTGTACTATTTACTAGCCCGAAATCTGACTCAGGGTCAACACTGGGTAGCGACACTCTGATCGCT
456 TTGTACTATTCACTAGCCCGATATCTGACTCAGGGTCAACACTGGGTAGCGACACTCTGATCGCT
* *
212808 CTTATTGAACTTGTTTTCAATACCCCTCGAATTGAAAGGACAACTTACACCTCCTAGGTTCATTG
521 CTTATTGAACTTCTTTTCAATACCCCTCGAATTGAAAGGACAACTTACACCTCCTA---T--GTG
212873 ACATTCTCGAAGGCCACGTTTTCCGCTATTTCTAAATCTGAATTGCTTATTGTACCACTGGTCAG
581 ---TT-T-----G-CA----TT-C-CTATTTCTAAATCTGAATTGCTTATTGTACCACTGGTCAG
212938 TACATTCCCCTACAACGATCCTTGTTCTCAACTATCTTGACTAAAGATATTTCGA
630 TACATTCCCCTACAACGATCCTTGTTCTCAACTATCTTGACTAAAGATATTTCGA
*
212993 CATAGTCAACCGCAAAAGTACCTTGCACACTTGCTTTATGTGTTCTCGGATATCCTATACCACTA
1 CATAGTCAACCGCAAAAGTACCTTGCACACTTGCTTTAGGTGTTCTCGGATATCCTATACCACTA
213058 GATGATCTTCAGCGCCTGAACTGGACTGATGCGACTATACATGCATACCTAAGGCCCAGAGGCCA
66 GATGATCTTCAGCGCCTGAACTGGACTGATGCGACTATACATGCATACCTAAGGCCCAGAGGCCA
213123 TACGACACTGACATCGTTACCCAACTCCTCATGAGTGTTTGAGCCTCACGCCTTAACTAGCTCCT
131 TACGACACTGACATCGTTACCCAACTCCTCATGAGTGTTTGAGCCTCACGCCTTAACTAGCTCCT
213188 GAAGTGTGTTGTATACTGAAAATGTCCTACTAGGGAAACTAAGGTAACTTGGGTATACCCTAGCA
196 GAAGTGTGTTGTATACTGAAAATGTCCTACTAGGGAAACTAAGGTAACTTGGGTATACCCTAGCA
*
213253 CAATTAGACTCATTAAGGTGAGTTCATCCTCTCACAAGCTTCTATCTCACTCGTTCTCTCATCCA
261 CAATTAGACTCATTAAGGTGAGTTCATCCTCTCACAAGCTTCTATCTCACTCGTTCTCTCATCTA
*
213318 GAATGTTATGCGAAGGATTATTAGTCTATTACTACTATTATCTATTAGGATGATCTATTCTGGTC
326 GAATGTTATGCGAAGGATTATTAGTCTATTACTACTATTATCTATTAGGATGATCTATTATGGTC
213383 GTTCGTTACTTAAGGGTATTTTAGTTATTCTCTACCTCTAGGAAATTCTTTATGTTATTCACTGG
391 GTTCGTTACTTAAGGGTATTTTAGTTATTCTCTACCTCTAGGAAATTCTTTATGTTATTCACTGG
*
213448 TTGTACTATTCGCTAGCCCGATATCTGACTCAGGGTCAACACTGGGTAGCGACACTCTGATCGCT
456 TTGTACTATTCACTAGCCCGATATCTGACTCAGGGTCAACACTGGGTAGCGACACTCTGATCGCT
213513 CTTATTGAACTTCTTTTCAATACCCCTCGAATTGAAAGGACAACTTACACCTCCTAGGTTCATTG
521 CTTATTGAACTTCTTTTCAATACCCCTCGAATTGAAAGGACAACTTACACCTCC-----T-A-TG
* *
213578 ACGTTCTCGAAGGCCACGTTTTTCGCTTTTTCTAAATCTGAATTGCTTATTGTACCACTGGTCAG
579 -TGTT-T-----G-CA-----TTC-CTATTTCTAAATCTGAATTGCTTATTGTACCACTGGTCAG
*
213643 TACATTCCCCTACAAAGATCCTTGTTCTCAACTATCT
630 TACATTCCCCTACAACGATCCTTGTTCTCAACTATCT
213680 GTACACGTTC
Statistics
Matches: 2001, Mismatches: 34, Indels: 70
0.95 0.02 0.03
Matches are distributed among these distances:
678 662 0.33
681 1 0.00
685 1 0.00
686 2 0.00
689 1 0.00
690 1 0.00
692 2 0.00
695 1 0.00
697 3 0.00
699 1 0.00
700 1 0.00
702 1 0.00
705 1315 0.66
706 4 0.00
708 1 0.00
709 2 0.00
710 1 0.00
711 1 0.00
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.33
Consensus pattern (684 bp):
CATAGTCAACCGCAAAAGTACCTTGCACACTTGCTTTAGGTGTTCTCGGATATCCTATACCACTA
GATGATCTTCAGCGCCTGAACTGGACTGATGCGACTATACATGCATACCTAAGGCCCAGAGGCCA
TACGACACTGACATCGTTACCCAACTCCTCATGAGTGTTTGAGCCTCACGCCTTAACTAGCTCCT
GAAGTGTGTTGTATACTGAAAATGTCCTACTAGGGAAACTAAGGTAACTTGGGTATACCCTAGCA
CAATTAGACTCATTAAGGTGAGTTCATCCTCTCACAAGCTTCTATCTCACTCGTTCTCTCATCTA
GAATGTTATGCGAAGGATTATTAGTCTATTACTACTATTATCTATTAGGATGATCTATTATGGTC
GTTCGTTACTTAAGGGTATTTTAGTTATTCTCTACCTCTAGGAAATTCTTTATGTTATTCACTGG
TTGTACTATTCACTAGCCCGATATCTGACTCAGGGTCAACACTGGGTAGCGACACTCTGATCGCT
CTTATTGAACTTCTTTTCAATACCCCTCGAATTGAAAGGACAACTTACACCTCCTATGTGTTTGC
ATTCCTATTTCTAAATCTGAATTGCTTATTGTACCACTGGTCAGTACATTCCCCTACAACGATCC
TTGTTCTCAACTATCTTGACTAAAGATATTTCGA
Found at i:219309 original size:27 final size:26
Alignment explanation
Indices: 219244--219310 Score: 75
Period size: 27 Copynumber: 2.6 Consensus size: 26
219234 TAAATAATAT
*
219244 TAATTAAATT-AAAATTTTAAAATTA
1 TAATTAAATTAAAAATTTCAAAATTA
**
219269 T-ATTGAAACAAAAAATTTCCAAAATTA
1 TAATT-AAATTAAAAATTT-CAAAATTA
219296 TAATTAAATTAAAAA
1 TAATTAAATTAAAAA
219311 ATATTCTTTC
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
24 3 0.09
25 4 0.12
26 7 0.21
27 16 0.48
28 3 0.09
ACGTcount: A:0.58, C:0.04, G:0.01, T:0.36
Consensus pattern (26 bp):
TAATTAAATTAAAAATTTCAAAATTA
Found at i:223178 original size:62 final size:61
Alignment explanation
Indices: 223068--223327 Score: 345
Period size: 62 Copynumber: 4.3 Consensus size: 61
223058 AATGACCAAC
* * * * *
223068 AAAATCGCAACGCGATAT-CAA-AACCGCAACGCGATTTAA-AAAAGCGCAACGTTGA-AAAG
1 AAAATCGCAACGCGATTTCCAAGAATCGCAACGCGA-TTAAGAAAATCGCAACG-CGATTAAG
* *
223127 AAGATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTCAGAAAATCGCAACGCGATTCCAAG
1 AAAATCGCAACGCGAT-TTCCAAGAATCGCAACGCGATTAAGAAAATCGCAACGCGATT--AAG
223191 --AATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAGAAAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGAT-TTCCAAGAATCGCAACGCGATTAAGAAAATCGCAACGCGATTAAG
*
223251 AAAATCGCAACGCGA-TTCCAAGAATCGCAACGCGATTAAGATAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTTCCAAGAATCGCAACGCGATTAAGAAAATCGCAACGCGATTAAG
223311 AAAATCGCAACGCGATT
1 AAAATCGCAACGCGATT
223328 CAGAAAATGA
Statistics
Matches: 181, Mismatches: 10, Indels: 18
0.87 0.05 0.09
Matches are distributed among these distances:
59 15 0.08
60 63 0.35
61 9 0.05
62 91 0.50
64 3 0.02
ACGTcount: A:0.40, C:0.25, G:0.20, T:0.16
Consensus pattern (61 bp):
AAAATCGCAACGCGATTTCCAAGAATCGCAACGCGATTAAGAAAATCGCAACGCGATTAAG
Found at i:223332 original size:20 final size:20
Alignment explanation
Indices: 223068--223335 Score: 244
Period size: 20 Copynumber: 13.2 Consensus size: 20
223058 AATGACCAAC
223068 AAAATCGCAACGCGATATC--
1 AAAATCGCAACGCGAT-TCAG
* * *
223087 AAAACCGCAACGCGATTTAA
1 AAAATCGCAACGCGATTCAG
* * **
223107 AAAAGCGCAACGTTGA-AAAG
1 AAAATCGCAACG-CGATTCAG
*
223127 AAGATCGCAACGCGATCTTCCA-
1 AAAATCGCAACGCGA--TT-CAG
*
223149 AGAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCAG
223169 AAAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATT-CAG
*
223189 AGAATCGCAACGCGATCTTCCA-
1 AAAATCGCAACGCGA--TT-CAG
* *
223211 AGAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTCAG
*
223231 AAAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTCAG
223251 AAAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATT-CAG
* *
223271 AGAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTCAG
* *
223291 ATAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTCAG
223311 AAAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCAG
223331 AAAAT
1 AAAAT
223336 GAGTAAATTC
Statistics
Matches: 211, Mismatches: 24, Indels: 27
0.81 0.09 0.10
Matches are distributed among these distances:
18 1 0.00
19 21 0.10
20 150 0.71
21 5 0.02
22 33 0.16
23 1 0.00
ACGTcount: A:0.41, C:0.24, G:0.19, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATTCAG
Found at i:223442 original size:6 final size:6
Alignment explanation
Indices: 223431--223497 Score: 111
Period size: 6 Copynumber: 11.5 Consensus size: 6
223421 GACACGTATT
223431 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
*
223479 ACCCCG ACC-CG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACC
223498 CGAGACGAGA
Statistics
Matches: 60, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
5 10 0.17
6 50 0.83
ACGTcount: A:0.30, C:0.54, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:225183 original size:58 final size:57
Alignment explanation
Indices: 225120--225319 Score: 242
Period size: 58 Copynumber: 3.5 Consensus size: 57
225110 TCAAGAAAAT
* *
225120 AACAATTTATTTTCCTTACAAAGTTAAAATAATTCAAGATTTCTATGGAAATAAATTC
1 AACAATCTATTTTCCTTACAAAGTTAAAATAATTTAAGA-TTCTATGGAAATAAATTC
* * *
225178 AACAATTTA-TTTCCTTTACAAAGTTAAAATTATTTAAGATTCTCAAGGAAATAAATTC
1 AACAATCTATTTTCC-TTACAAAGTTAAAATAATTTAAGATTCT-ATGGAAATAAATTC
* * * * *
225236 AACAATCTATTTTCCTTACAAATTTAGAATCATTTTAGAGTCT-TAGAGAAATAAATTC
1 AACAATCTATTTTCCTTACAAAGTTAAAATAATTTAAGATTCTAT-G-GAAATAAATTC
*
225294 AACAATCTATCTTCCTTACAAAGTTA
1 AACAATCTATTTTCCTTACAAAGTTA
225320 GAATCAACGC
Statistics
Matches: 125, Mismatches: 12, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
57 10 0.08
58 110 0.88
59 5 0.04
ACGTcount: A:0.41, C:0.14, G:0.07, T:0.38
Consensus pattern (57 bp):
AACAATCTATTTTCCTTACAAAGTTAAAATAATTTAAGATTCTATGGAAATAAATTC
Found at i:225555 original size:45 final size:46
Alignment explanation
Indices: 225507--225654 Score: 162
Period size: 45 Copynumber: 3.3 Consensus size: 46
225497 TTTAGCTACC
**
225507 CAATAATCAAAAGGAATTAATAATTTGATTTTAATTTTCG-CAATC-
1 CAATAATCAAAAGGAATTAATCCTTTGATTTTAATTTTCGACAA-CA
* * * *
225552 CAATATTCAAAAGGAACTAATCCTTTTATTTTACTTTT-GACAACA
1 CAATAATCAAAAGGAATTAATCCTTTGATTTTAATTTTCGACAACA
* * *
225597 CAATAATCAAAA-GAATTTAATCCTTTGATTTT-ACTTTCGACGACT
1 CAATAATCAAAAGGAA-TTAATCCTTTGATTTTAATTTTCGACAACA
225642 CAATAATCAAAAG
1 CAATAATCAAAAG
225655 TCTTGGATTA
Statistics
Matches: 85, Mismatches: 13, Indels: 9
0.79 0.12 0.08
Matches are distributed among these distances:
44 8 0.09
45 77 0.91
ACGTcount: A:0.41, C:0.16, G:0.08, T:0.36
Consensus pattern (46 bp):
CAATAATCAAAAGGAATTAATCCTTTGATTTTAATTTTCGACAACA
Found at i:231524 original size:36 final size:35
Alignment explanation
Indices: 231478--231551 Score: 130
Period size: 36 Copynumber: 2.1 Consensus size: 35
231468 GGTATGTGGT
231478 TCATCCGACACTGCTCGCAACGAAATTGAGAAAGC
1 TCATCCGACACTGCTCGCAACGAAATTGAGAAAGC
*
231513 TCATCCCGACACTGCTTGCAACGAAATTGAGAAAGC
1 TCAT-CCGACACTGCTCGCAACGAAATTGAGAAAGC
231549 TCA
1 TCA
231552 GGGTAAGGAT
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
35 4 0.11
36 33 0.89
ACGTcount: A:0.34, C:0.28, G:0.19, T:0.19
Consensus pattern (35 bp):
TCATCCGACACTGCTCGCAACGAAATTGAGAAAGC
Found at i:232819 original size:7 final size:7
Alignment explanation
Indices: 232807--232872 Score: 68
Period size: 7 Copynumber: 10.0 Consensus size: 7
232797 GTTGGACGCC
232807 ATTTGCA
1 ATTTGCA
232814 ATTTGCA
1 ATTTGCA
232821 ATTTGCA
1 ATTTGCA
232828 ATTTGCA
1 ATTTGCA
* *
232835 AGTTGGA
1 ATTTGCA
232842 A--TGCA
1 ATTTGCA
232847 ATTTGCA
1 ATTTGCA
* *
232854 AGTTGGA
1 ATTTGCA
232861 A--TGCA
1 ATTTGCA
232866 ATTTGCA
1 ATTTGCA
232873 GATGCAATGG
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
5 8 0.16
7 41 0.84
ACGTcount: A:0.30, C:0.12, G:0.21, T:0.36
Consensus pattern (7 bp):
ATTTGCA
Found at i:232848 original size:19 final size:19
Alignment explanation
Indices: 232824--232872 Score: 98
Period size: 19 Copynumber: 2.6 Consensus size: 19
232814 ATTTGCAATT
232824 TGCAATTTGCAAGTTGGAA
1 TGCAATTTGCAAGTTGGAA
232843 TGCAATTTGCAAGTTGGAA
1 TGCAATTTGCAAGTTGGAA
232862 TGCAATTTGCA
1 TGCAATTTGCA
232873 GATGCAATGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.31, C:0.12, G:0.24, T:0.33
Consensus pattern (19 bp):
TGCAATTTGCAAGTTGGAA
Found at i:242538 original size:98 final size:99
Alignment explanation
Indices: 242369--242570 Score: 325
Period size: 98 Copynumber: 2.1 Consensus size: 99
242359 TGAAAATAAT
* *
242369 ATATTCAGGCTATTAATAAGTGTCCAAATAAAATCAGAAATAACCATTTAACACTATCATATTGA
1 ATATTCAGGCTATTAATAAGTATCCAAATAAAATCAAAAATAACCATTTAACACTATCATATTGA
242434 ATATATTCATGAATTGCAAGTCATACCA-TTTTA
66 ATATATTCATGAATTGCAAGTCATACCATTTTTA
* * * *
242467 ATATTCGGGCTATTAATAAGTATCCGAATAAAATCAAAAATAATCATTTAACATTATCATATTGA
1 ATATTCAGGCTATTAATAAGTATCCAAATAAAATCAAAAATAACCATTTAACACTATCATATTGA
* *
242532 ATATATTCGTGAATTGCAAGTCATATCATTTTTA
66 ATATATTCATGAATTGCAAGTCATACCATTTTTA
242566 ATATT
1 ATATT
242571 TAAATTAAAA
Statistics
Matches: 95, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
98 85 0.89
99 10 0.11
ACGTcount: A:0.41, C:0.13, G:0.09, T:0.36
Consensus pattern (99 bp):
ATATTCAGGCTATTAATAAGTATCCAAATAAAATCAAAAATAACCATTTAACACTATCATATTGA
ATATATTCATGAATTGCAAGTCATACCATTTTTA
Found at i:248623 original size:27 final size:27
Alignment explanation
Indices: 248584--248637 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
248574 TCGGTGCCGG
* *
248584 AGGAGGAGGAGGAGCACGAGAAGAACT
1 AGGAGCAGAAGGAGCACGAGAAGAACT
* *
248611 AGGAGCAGAAGGAGCTCGTGAAGAACT
1 AGGAGCAGAAGGAGCACGAGAAGAACT
248638 GACTCCCGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.39, C:0.13, G:0.41, T:0.07
Consensus pattern (27 bp):
AGGAGCAGAAGGAGCACGAGAAGAACT
Found at i:256601 original size:19 final size:19
Alignment explanation
Indices: 256559--256614 Score: 85
Period size: 19 Copynumber: 2.9 Consensus size: 19
256549 TAGACCTTTG
* *
256559 GTATCGATACCCACATGTTT
1 GTATCGATACCC-TATGATT
256579 GTATCGATACCCTATGATT
1 GTATCGATACCCTATGATT
256598 GTATCGATACCCTATGA
1 GTATCGATACCCTATGA
256615 CTGACTAAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
19 22 0.65
20 12 0.35
ACGTcount: A:0.27, C:0.23, G:0.16, T:0.34
Consensus pattern (19 bp):
GTATCGATACCCTATGATT
Found at i:256703 original size:18 final size:21
Alignment explanation
Indices: 256657--256709 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 21
256647 TACTCTAACC
256657 TGAGTATCGATACTCTGGTAT
1 TGAGTATCGATACTCTGGTAT
256678 TGGAGTATCGATA-T-TGG-AT
1 T-GAGTATCGATACTCTGGTAT
256697 TGAGTATCGATAC
1 TGAGTATCGATAC
256710 CAAAATTGGT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
18 11 0.37
19 3 0.10
20 3 0.10
21 2 0.07
22 11 0.37
ACGTcount: A:0.26, C:0.11, G:0.26, T:0.36
Consensus pattern (21 bp):
TGAGTATCGATACTCTGGTAT
Found at i:256768 original size:21 final size:21
Alignment explanation
Indices: 256742--256839 Score: 180
Period size: 21 Copynumber: 4.7 Consensus size: 21
256732 AAATACCCCA
*
256742 AGTATCGATACCCCTATTGGG
1 AGTATCGATACCCCTACTGGG
256763 AGTATCGATA-CCCTACTGGG
1 AGTATCGATACCCCTACTGGG
256783 AGTATCGATACCCCTACTGGG
1 AGTATCGATACCCCTACTGGG
256804 AGTATCGATACCCCTACTGGG
1 AGTATCGATACCCCTACTGGG
256825 AGTATCGATACCCCT
1 AGTATCGATACCCCT
256840 GCCCTGGTAG
Statistics
Matches: 75, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
20 19 0.25
21 56 0.75
ACGTcount: A:0.24, C:0.28, G:0.22, T:0.26
Consensus pattern (21 bp):
AGTATCGATACCCCTACTGGG
Found at i:256796 original size:41 final size:42
Alignment explanation
Indices: 256742--256839 Score: 180
Period size: 41 Copynumber: 2.4 Consensus size: 42
256732 AAATACCCCA
*
256742 AGTATCGATACCCCTATTGGGAGTATCGATA-CCCTACTGGG
1 AGTATCGATACCCCTACTGGGAGTATCGATACCCCTACTGGG
256783 AGTATCGATACCCCTACTGGGAGTATCGATACCCCTACTGGG
1 AGTATCGATACCCCTACTGGGAGTATCGATACCCCTACTGGG
256825 AGTATCGATACCCCT
1 AGTATCGATACCCCT
256840 GCCCTGGTAG
Statistics
Matches: 55, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
41 30 0.55
42 25 0.45
ACGTcount: A:0.24, C:0.28, G:0.22, T:0.26
Consensus pattern (42 bp):
AGTATCGATACCCCTACTGGGAGTATCGATACCCCTACTGGG
Found at i:264174 original size:15 final size:15
Alignment explanation
Indices: 264154--264182 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
264144 AGCTGATTTT
264154 ATTTTATTTTTTTAC
1 ATTTTATTTTTTTAC
264169 ATTTTATTTTTTTA
1 ATTTTATTTTTTTA
264183 GGATAGAACA
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:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (15 bp):
ATTTTATTTTTTTAC
Found at i:266623 original size:60 final size:60
Alignment explanation
Indices: 266530--266674 Score: 168
Period size: 60 Copynumber: 2.4 Consensus size: 60
266520 TGGACCTAGA
* * * * * * *
266530 GGCACTCCCCTCAAGTGGCTCATTT-TCTTTGTGCATTGGGTAAGTCCTTATAAACTTGAG
1 GGCACTCTCCTCAGGTGACTCCTTTGT-TTTGTGCATTAGGTAAGTCCATATAAACCTGAG
* *
266590 GGCACTC-CTCTCAGGTTACTCCTTTGTTTTGTGCATTAGGTAAGTCCATATGAACCTGAG
1 GGCACTCTC-CTCAGGTGACTCCTTTGTTTTGTGCATTAGGTAAGTCCATATAAACCTGAG
*
266650 GGCACTCTCCTCAGGTGGCTCCTTT
1 GGCACTCTCCTCAGGTGACTCCTTT
266675 TATGTGGCTC
Statistics
Matches: 72, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
59 1 0.01
60 69 0.96
61 2 0.03
ACGTcount: A:0.18, C:0.26, G:0.22, T:0.34
Consensus pattern (60 bp):
GGCACTCTCCTCAGGTGACTCCTTTGTTTTGTGCATTAGGTAAGTCCATATAAACCTGAG
Found at i:267385 original size:23 final size:23
Alignment explanation
Indices: 267343--267386 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
267333 AATATTTAAT
*
267343 TAAATAATATGAATATAAAACCA
1 TAAATAATATGAATAAAAAACCA
267366 TAAAT-ATATGAATAGAAAAAC
1 TAAATAATATGAATA-AAAAAC
267387 GTTGATGCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.61, C:0.07, G:0.07, T:0.25
Consensus pattern (23 bp):
TAAATAATATGAATAAAAAACCA
Found at i:269992 original size:39 final size:39
Alignment explanation
Indices: 269948--270034 Score: 106
Period size: 39 Copynumber: 2.2 Consensus size: 39
269938 CAATCTAATA
* *
269948 ATTTATTTTATTTTAC-AAATCA-GAAAAATAAATCCAACG
1 ATTTATTTCATTTTACAAAAT-ATG-AAAATAAATCAAACG
* *
269987 ATTTATTTCCTTTTACAAAATATGAAAATAAATCAAACT
1 ATTTATTTCATTTTACAAAATATGAAAATAAATCAAACG
270026 ATTTATTTC
1 ATTTATTTC
270035 CTCTAACATA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
39 37 0.88
40 5 0.12
ACGTcount: A:0.44, C:0.13, G:0.03, T:0.40
Consensus pattern (39 bp):
ATTTATTTCATTTTACAAAATATGAAAATAAATCAAACG
Found at i:270152 original size:39 final size:39
Alignment explanation
Indices: 270068--270191 Score: 142
Period size: 39 Copynumber: 3.2 Consensus size: 39
270058 AGATTATTAA
* * * *
270068 GAAAATAAATT-TAATGATTTATTTTCTTTTACAAACTAG
1 GAAAATAAATTCT-ATGATTTATTTCCTTTCATAAAATAG
* *
270107 GGAAATAAATTCTATGATTTATTTCCTTCCATAAAATAG
1 GAAAATAAATTCTATGATTTATTTCCTTTCATAAAATAG
* * * *
270146 GAAAATAAACTCAACGATTTATTTCCTTTCATAAAACAG
1 GAAAATAAATTCTATGATTTATTTCCTTTCATAAAATAG
270185 GAAAATA
1 GAAAATA
270192 GATCCAACTA
Statistics
Matches: 72, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
39 71 0.99
40 1 0.01
ACGTcount: A:0.43, C:0.12, G:0.09, T:0.36
Consensus pattern (39 bp):
GAAAATAAATTCTATGATTTATTTCCTTTCATAAAATAG
Found at i:270209 original size:39 final size:39
Alignment explanation
Indices: 270122--270213 Score: 114
Period size: 39 Copynumber: 2.4 Consensus size: 39
270112 TAAATTCTAT
* * *
270122 GATTTATTTCCTTCCATAAAATAGGAAAATAAACTCAAC
1 GATTCATTTCCTTTCATAAAACAGGAAAATAAACTCAAC
* *
270161 GATTTATTTCCTTTCATAAAACAGGAAAATAGA-TCCAAC
1 GATTCATTTCCTTTCATAAAACAGGAAAATAAACT-CAAC
*
270200 TATTCATTTCCTTT
1 GATTCATTTCCTTT
270214 TACAAATCAG
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
38 1 0.02
39 46 0.98
ACGTcount: A:0.38, C:0.18, G:0.08, T:0.36
Consensus pattern (39 bp):
GATTCATTTCCTTTCATAAAACAGGAAAATAAACTCAAC
Found at i:270249 original size:175 final size:171
Alignment explanation
Indices: 269969--270342 Score: 451
Period size: 175 Copynumber: 2.2 Consensus size: 171
269959 TTTACAAATC
* * * *
269969 AGAAAAATAAATCCAACGATTTATTTCCTTTTACAAAATATGAAAATAAATCAAACTATTTATTT
1 AGAAAAATAAAT-CAACGATTTATTTCCTTTCACAAAACAGGAAAATAAATCAAACTATTCATTT
* * *
270034 CCTCTAACATATCAGAATCATATAAGATTATTAAGAAAATAAATTTAATGATTTATTTTCTTTTA
65 CCTCTAACAAATCAGAATCATATAAGATTATCAAGAAAATAAATTCAATGATTTATTTTCTTTTA
* * * * * *
270099 CAAACTAGGGAAATAAATTCTATGATTTATTTCCTTCCATAAAAT
130 AAAAATAGGAAAATAAATTCAACGATTTATTT--TTCCA-AAAAA
* * * *
270144 AGGAAAATAAACTCAACGATTTATTTCCTTTCATAAAACAGGAAAATAGATCCAACTATTCATTT
1 AGAAAAATAAA-TCAACGATTTATTTCCTTTCACAAAACAGGAAAATAAATCAAACTATTCATTT
* * * * * * * *
270209 CCTTTTACAAATCAGAATTATGTGAGGTTCTCAGGAAAATAAATTCAATGATTTATTTTCTTTTA
65 CCTCTAACAAATCAGAATCATATAAGATTATCAAGAAAATAAATTCAATGATTTATTTTCTTTTA
**
270274 AAAAATAGGAAAATAAATTCAACGATTTATTTTTTTAAAAAA
130 AAAAATAGGAAAATAAATTCAACGATTTATTTTTCCAAAAAA
270316 AGAAAAATAAATTCAACGATTTATTTC
1 AGAAAAATAAA-TCAACGATTTATTTC
270343 ATTTTAACAA
Statistics
Matches: 169, Mismatches: 29, Indels: 5
0.83 0.14 0.02
Matches are distributed among these distances:
172 29 0.17
173 3 0.02
175 136 0.80
176 1 0.01
ACGTcount: A:0.43, C:0.12, G:0.08, T:0.36
Consensus pattern (171 bp):
AGAAAAATAAATCAACGATTTATTTCCTTTCACAAAACAGGAAAATAAATCAAACTATTCATTTC
CTCTAACAAATCAGAATCATATAAGATTATCAAGAAAATAAATTCAATGATTTATTTTCTTTTAA
AAAATAGGAAAATAAATTCAACGATTTATTTTTCCAAAAAA
Found at i:270295 original size:39 final size:37
Alignment explanation
Indices: 270241--270349 Score: 166
Period size: 36 Copynumber: 2.9 Consensus size: 37
270231 TGAGGTTCTC
*
270241 AGGAAAATAAATTCAATGATTTATTTTCTTTTAAAAAA
1 AGGAAAATAAATTCAACGATTTA-TTTCTTTTAAAAAA
270279 TAGGAAAATAAATTCAACGATTTATTT-TTTTAAAAAA
1 -AGGAAAATAAATTCAACGATTTATTTCTTTTAAAAAA
*
270316 AGAAAAATAAATTCAACGATTTATTTCATTTTAA
1 AGGAAAATAAATTCAACGATTTATTTC-TTTTAA
270350 CAATATAATT
Statistics
Matches: 66, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
36 25 0.38
37 10 0.15
38 9 0.14
39 22 0.33
ACGTcount: A:0.48, C:0.06, G:0.07, T:0.39
Consensus pattern (37 bp):
AGGAAAATAAATTCAACGATTTATTTCTTTTAAAAAA
Found at i:270510 original size:58 final size:58
Alignment explanation
Indices: 270408--270552 Score: 188
Period size: 58 Copynumber: 2.5 Consensus size: 58
270398 AAGTTTCACG
** * *
270408 AGAAAATAAATTTAACAATTTATTTCTTTTAACCAAATATAATCATTTAAGATTCTCA
1 AGAAAATAAATTTAACAATTTATTAATTTTAACCAAATAGAATCATTTAAGAATCTCA
*
270466 AGAAAATAAATTTAATAATTTATTAAATTTT-A-CACAATAGAATCATTTAAGAATCTCA
1 AGAAAATAAATTTAACAATTTATT-AATTTTAACCA-AATAGAATCATTTAAGAATCTCA
* *
270524 A-AAACTAAATTTAACAATTTATTTATTTT
1 AGAAAATAAATTTAACAATTTATTAATTTT
270553 TAAAGGATAT
Statistics
Matches: 77, Mismatches: 8, Indels: 6
0.85 0.09 0.07
Matches are distributed among these distances:
56 5 0.06
57 22 0.29
58 46 0.60
59 4 0.05
ACGTcount: A:0.47, C:0.10, G:0.03, T:0.40
Consensus pattern (58 bp):
AGAAAATAAATTTAACAATTTATTAATTTTAACCAAATAGAATCATTTAAGAATCTCA
Found at i:270567 original size:57 final size:55
Alignment explanation
Indices: 270410--270568 Score: 176
Period size: 58 Copynumber: 2.8 Consensus size: 55
270400 GTTTCACGAG
* *
270410 AAAATAAATTTAACAATTTATTT-CTTTTAACCAAATATAATCATTTAAGATTCTCAA
1 AAAATAAATTTAACAATTTATTTAATTTTAA--AAATATAATCATTTAAGAATCTC-A
* * * *
270467 GAAAATAAATTTAATAATTTATTAAATTTTACACAATAGAATCATTTAAGAATCTCA
1 -AAAATAAATTTAACAATTTATTTAATTTTA-AAAATATAATCATTTAAGAATCTCA
* *
270524 AAAACTAAATTTAACAATTTATTTATTTTTAAAGGATATAATCAT
1 AAAA-TAAATTTAACAATTTATTTAATTTTAAA-AATATAATCAT
270569 CCACGATTAT
Statistics
Matches: 85, Mismatches: 12, Indels: 9
0.80 0.11 0.08
Matches are distributed among these distances:
56 5 0.06
57 33 0.39
58 41 0.48
59 5 0.06
60 1 0.01
ACGTcount: A:0.47, C:0.09, G:0.04, T:0.40
Consensus pattern (55 bp):
AAAATAAATTTAACAATTTATTTAATTTTAAAAATATAATCATTTAAGAATCTCA
Found at i:270654 original size:58 final size:57
Alignment explanation
Indices: 270595--270791 Score: 243
Period size: 58 Copynumber: 3.4 Consensus size: 57
270585 AATAATAATT
* * * *
270595 TATTTTCCTTACAAAGTTAAAATAATTCAAGATT-TCTATGGAAATAAATTTAACAATT
1 TATTTTCCTTACAAAGTTAGAATAATTTAAGATTCTC-A-GGAAATAAATTCAACAATC
* *
270653 TATTTCCCTTACAAAGTTAGAATTATTTAAGATTCTCAAGGAAATAAATTCAACAATC
1 TATTTTCCTTACAAAGTTAGAATAATTTAAGATTCTC-AGGAAATAAATTCAACAATC
* * * *
270711 TATTTTTCTTACAAAGTTAGAATCATTTTAGAGTCTCAGAGAAATAAATTCAACAATC
1 TATTTTCCTTACAAAGTTAGAATAATTTAAGATTCTCAG-GAAATAAATTCAACAATC
* *
270769 TGTCTTCCTTACAAAGTTAGAAT
1 TATTTTCCTTACAAAGTTAGAAT
270792 CAGCGCAAGA
Statistics
Matches: 122, Mismatches: 15, Indels: 4
0.87 0.11 0.03
Matches are distributed among these distances:
57 2 0.02
58 117 0.96
59 3 0.02
ACGTcount: A:0.40, C:0.14, G:0.09, T:0.37
Consensus pattern (57 bp):
TATTTTCCTTACAAAGTTAGAATAATTTAAGATTCTCAGGAAATAAATTCAACAATC
Found at i:275772 original size:143 final size:143
Alignment explanation
Indices: 275579--275839 Score: 368
Period size: 143 Copynumber: 1.8 Consensus size: 143
275569 AAAATAATCA
* * *
275579 TATTTTAATATTTATTTTTTAATATTAAGAAATGGGCTGTCTTAAAGCACCTAGAAGTCCTTTTC
1 TATTTTAATATTTA--TTTTAATATTAAGAAAAGAGCTGTCTTAAAGCACCTAGAAGTCATTTTC
* *
275644 TGATA-TTCTTAAATAAATAAATATCATATT-TTTATAAAT-TATATATATATTAATTTATTTTA
64 TGACATTTC-TAAATAAATAAATAT--T-TTATTTATAAATATATATATAAATTAATTTATTTTA
275706 ATTATTTTTAGAAAGATGT
125 ATTATTTTTAGAAAGATGT
* * *
275725 TATTTTAATATTTA-TTTACTTTTAAGAAAAGAGCTGTCTTAAGGCACCTAGAAGTCATTTTCTG
1 TATTTTAATATTTATTTTAATATTAAGAAAAGAGCTGTCTTAAAGCACCTAGAAGTCATTTTCTG
275789 ACATTTCTAAATAAATAAATATTTTATTTATAAATATATATATAAATTAAT
66 ACATTTCTAAATAAATAAATATTTTATTTATAAATATATATATAAATTAAT
275840 AGATTTTCTT
Statistics
Matches: 104, Mismatches: 8, Indels: 10
0.85 0.07 0.08
Matches are distributed among these distances:
140 2 0.02
141 10 0.10
142 14 0.13
143 61 0.59
144 3 0.03
146 14 0.13
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (143 bp):
TATTTTAATATTTATTTTAATATTAAGAAAAGAGCTGTCTTAAAGCACCTAGAAGTCATTTTCTG
ACATTTCTAAATAAATAAATATTTTATTTATAAATATATATATAAATTAATTTATTTTAATTATT
TTTAGAAAGATGT
Found at i:277914 original size:8 final size:7
Alignment explanation
Indices: 277894--277932 Score: 51
Period size: 7 Copynumber: 5.3 Consensus size: 7
277884 CATACATACA
277894 TTTGCAT
1 TTTGCAT
277901 TTTGCAT
1 TTTGCAT
277908 CTTTGCAT
1 -TTTGCAT
*
277916 TTTTCATT
1 TTTGCA-T
277924 TTTGCAT
1 TTTGCAT
277931 TT
1 TT
277933 ATACTTTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
7 15 0.54
8 13 0.46
ACGTcount: A:0.13, C:0.15, G:0.10, T:0.62
Consensus pattern (7 bp):
TTTGCAT
Found at i:277914 original size:15 final size:15
Alignment explanation
Indices: 277894--277932 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
277884 CATACATACA
277894 TTTGCATTTTGCATC
1 TTTGCATTTTGCATC
* *
277909 TTTGCATTTTTCATT
1 TTTGCATTTTGCATC
277924 TTTGCATTT
1 TTTGCATTT
277933 ATACTTTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.13, C:0.15, G:0.10, T:0.62
Consensus pattern (15 bp):
TTTGCATTTTGCATC
Found at i:278008 original size:12 final size:12
Alignment explanation
Indices: 277991--278045 Score: 56
Period size: 12 Copynumber: 4.3 Consensus size: 12
277981 ACATTCACAT
277991 ATTTACATTTGC
1 ATTTACATTTGC
*
278003 ATTTACATTTGT
1 ATTTACATTTGC
*
278015 ATTTTTTACATTTGT
1 A---TTTACATTTGC
*
278030 ATTTACATTTTC
1 ATTTACATTTGC
278042 ATTT
1 ATTT
278046 TTACATAATT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
12 25 0.68
15 12 0.32
ACGTcount: A:0.24, C:0.11, G:0.05, T:0.60
Consensus pattern (12 bp):
ATTTACATTTGC
Found at i:278024 original size:15 final size:15
Alignment explanation
Indices: 278004--278033 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
277994 TACATTTGCA
278004 TTTACATTTGTATTT
1 TTTACATTTGTATTT
278019 TTTACATTTGTATTT
1 TTTACATTTGTATTT
278034 ACATTTTCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.07, G:0.07, T:0.67
Consensus pattern (15 bp):
TTTACATTTGTATTT
Found at i:278025 original size:27 final size:26
Alignment explanation
Indices: 277992--278051 Score: 86
Period size: 27 Copynumber: 2.3 Consensus size: 26
277982 CATTCACATA
277992 TTTACATTTGCATTTACATTTGT-ATTT
1 TTTACATTTGCATTTACATTT-TCA-TT
*
278019 TTTACATTTGTATTTACATTTTCATT
1 TTTACATTTGCATTTACATTTTCATT
278045 TTTACAT
1 TTTACAT
278052 AATTACATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
26 10 0.32
27 21 0.68
ACGTcount: A:0.23, C:0.12, G:0.05, T:0.60
Consensus pattern (26 bp):
TTTACATTTGCATTTACATTTTCATT
Found at i:280475 original size:21 final size:22
Alignment explanation
Indices: 280445--280507 Score: 74
Period size: 21 Copynumber: 2.8 Consensus size: 22
280435 AGAAGAAGGA
* *
280445 AAAAAGAAAAAGGGAAAAAAAG
1 AAAAAGAAAAAAGAAAAAAAAG
280467 AAAAA-AAAAAAGAAAAAAAAG
1 AAAAAGAAAAAAGAAAAAAAAG
*
280488 AAAAAGGGAAAAAAGGAAAA
1 AAAAA--GAAAAAAGAAAAA
280508 TTGAATCAAG
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
21 19 0.54
22 5 0.14
24 11 0.31
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (22 bp):
AAAAAGAAAAAAGAAAAAAAAG
Found at i:280476 original size:12 final size:12
Alignment explanation
Indices: 280459--280486 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
280449 AGAAAAAGGG
280459 AAAAAAAGAAAA
1 AAAAAAAGAAAA
280471 AAAAAAAGAAAA
1 AAAAAAAGAAAA
280483 AAAA
1 AAAA
280487 GAAAAAGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (12 bp):
AAAAAAAGAAAA
Found at i:280500 original size:9 final size:8
Alignment explanation
Indices: 280440--280507 Score: 63
Period size: 8 Copynumber: 9.0 Consensus size: 8
280430 AAGAAAGAAG
280440 AAGGAAAA
1 AAGGAAAA
280448 AA-GAAAA
1 AAGGAAAA
*
280455 AGGGAAAA
1 AAGGAAAA
*
280463 AAAG-AAA
1 AAGGAAAA
280470 AA--AAAA
1 AAGGAAAA
*
280476 AAGAAAAA
1 AAGGAAAA
*
280484 AAAGAAAA
1 AAGGAAAA
*
280492 AGGGAAAA
1 AAGGAAAA
280500 AAGGAAAA
1 AAGGAAAA
280508 TTGAATCAAG
Statistics
Matches: 48, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
6 5 0.10
7 11 0.23
8 32 0.67
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (8 bp):
AAGGAAAA
Found at i:282965 original size:114 final size:114
Alignment explanation
Indices: 282764--282983 Score: 352
Period size: 114 Copynumber: 1.9 Consensus size: 114
282754 CATGTTCTCG
* * *
282764 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGGTCTGATTT
1 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTATTTGAGTTATCTGATCTGATTC
* * *
282829 GGTATGAACCCCAAAATCAATCATTGGATTTGAAAGATGAATTTGCTCA
66 GGTAGGAACCCCAAAATCAATCATTGGAATTAAAAGATGAATTTGCTCA
*
282878 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTATTTGAGTTATCTGATCTGGTTC
1 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTATTTGAGTTATCTGATCTGATTC
*
282943 GGTAGGAACCCCAGAA-CAAATCATTGGAATTAAAAGATGAA
66 GGTAGGAACCCCAAAATC-AATCATTGGAATTAAAAGATGAA
282984 CTGCATGATC
Statistics
Matches: 97, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
113 1 0.01
114 96 0.99
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.30
Consensus pattern (114 bp):
TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTATTTGAGTTATCTGATCTGATTC
GGTAGGAACCCCAAAATCAATCATTGGAATTAAAAGATGAATTTGCTCA
Found at i:285530 original size:22 final size:22
Alignment explanation
Indices: 285504--285555 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
285494 TACACTCTTA
*
285504 AAAGATGATAGATTCTCTTTTT
1 AAAGATGATAGATTCTCTTTTC
*
285526 AAAGATGATAGATTTTCTTTTC
1 AAAGATGATAGATTCTCTTTTC
285548 AAAGATGA
1 AAAGATGA
285556 AAGCTTTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.37, C:0.08, G:0.15, T:0.40
Consensus pattern (22 bp):
AAAGATGATAGATTCTCTTTTC
Found at i:286518 original size:76 final size:76
Alignment explanation
Indices: 286392--286622 Score: 399
Period size: 76 Copynumber: 3.0 Consensus size: 76
286382 TATTTCCCAT
* *
286392 ATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTAATGTTTTCAAA
1 ATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
286457 GCCTTAGGGTC
66 GCCTTAGGGTC
286468 ATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
1 ATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
286533 GCCTTAGGGTC
66 GCCTTAGGGTC
* *
286544 ATCTGTAAGTCGTACAGTGCATGATATTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
1 ATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
** *
286609 ATCTTCGGGTC
66 GCCTTAGGGTC
286620 ATC
1 ATC
286623 AGCATTACCA
Statistics
Matches: 148, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
76 148 1.00
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.35
Consensus pattern (76 bp):
ATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
GCCTTAGGGTC
Found at i:286768 original size:113 final size:113
Alignment explanation
Indices: 286636--287229 Score: 734
Period size: 113 Copynumber: 5.2 Consensus size: 113
286626 ATTACCAGGT
*
286636 AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGT
1 AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
* * *
286701 TCAACCTTTTGCTCAAATCCATCACTTGATGGACCAACATTTCCAGAG
66 TCAACCTTTTGCTCGAATTCATCACTTGATGGATCAACATTTCCAGAG
* * * *
286749 AAAGTTCATAATGAGAAGAACTTATCTGAAGAA-GAATAAGAAGTTCATAATGAGAAGAGCTTGT
1 AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
* * * * * *
286813 TCAACCTTTTGCTCG-ACTCTATCGCAGAAAGAGATAGATCAGCATCAATATTTCTAGA-
66 TCAACCTTTTGCTCGAATTC-AT--C------A-CTTGAT--GGATCAACATTTCCAGAG
*
286871 AGGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAATAAGTTCATAATGAGAAGAACTTG
1 A-GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTG
* * * *
286936 TTCAACTTTTTGCTCGAATTCATCATTTGATGGATCAGCATTGCCAG-G
65 TTCAACCTTTTGCTCGAATTCATCACTTGATGGATCAACATTTCCAGAG
* *
286984 TAGAGTTCATAATAAGAAGAACTCATCTGAA-AGAGGAAGAATAAGTTCATAATGAGAAGAACTT
1 -AGAGTTCATAATGAGAAGAACTCATCTGAAGA-AGGAAGAAGAAGTTCATAATGAGAAGAACTT
* * *
287048 ATTCAACTTTTTGCTCGAATTCATCA-TTCGATGGATCAACATTACCAG-G
64 GTTCAACCTTTTGCTCGAATTCATCACTT-GATGGATCAACATTTCCAGAG
*
287097 TAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAAAAGAAGTTCATAATGAGAAGAACTTG
1 -AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTG
* *
287162 TTCAACCTTTTGCTCGAATTCATCACTTGATGGATCAACATTTTCAGAA
65 TTCAACCTTTTGCTCGAATTCATCACTTGATGGATCAACATTTCCAGAG
*
287211 AAAGTTCATAATGAGAAGA
1 AGAGTTCATAATGAGAAGA
287230 GCTTGTTCAA
Statistics
Matches: 420, Mismatches: 39, Indels: 44
0.83 0.08 0.09
Matches are distributed among these distances:
111 2 0.00
112 49 0.12
113 262 0.62
114 5 0.01
115 4 0.01
116 1 0.00
120 1 0.00
121 4 0.01
122 2 0.00
123 43 0.10
124 44 0.10
125 3 0.01
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.27
Consensus pattern (113 bp):
AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
TCAACCTTTTGCTCGAATTCATCACTTGATGGATCAACATTTCCAGAG
Found at i:287383 original size:124 final size:122
Alignment explanation
Indices: 287207--287489 Score: 404
Period size: 124 Copynumber: 2.3 Consensus size: 122
287197 CAACATTTTC
*
287207 AGAAAAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATA
1 AGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATA
** ** * *
287272 GATCAGCATCAATTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
66 GATCAAAATCAACATTTCCAGA-AAAGTTCATAATGAGAAGAACTCATCAGAAAAAGG
** * *
287330 AAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGTTTGACTTTATCACAGAAGTAGAT
1 -AGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGAT
*
287395 AGATCAAAATCAACATTTCCAGAAATGTTCATAATGAGAAGAACTCATCAGAAAAAGG
65 AGATCAAAATCAACATTTCCAGAAAAGTTCATAATGAGAAGAACTCATCAGAAAAAGG
* * **
287453 AGAAGAAATTTATAATGAGAAGAATTTGTTCAACCTT
1 AGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTT
287490 GCCTTAATTT
Statistics
Matches: 143, Mismatches: 16, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
122 33 0.23
123 32 0.22
124 78 0.55
ACGTcount: A:0.41, C:0.14, G:0.19, T:0.27
Consensus pattern (122 bp):
AGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATA
GATCAAAATCAACATTTCCAGAAAAGTTCATAATGAGAAGAACTCATCAGAAAAAGG
Found at i:287760 original size:39 final size:39
Alignment explanation
Indices: 287674--287811 Score: 170
Period size: 39 Copynumber: 3.5 Consensus size: 39
287664 CCAGTGGAAG
* *
287674 AGTTCATAATGAGAAA-AACTCATCTGAAGAAGGAATAAGA
1 AGTTCATAATGA-AAAGAACTCATCTAAAGAA-GAATAATA
*
287714 AATTCATAATGAAAAGAACTCATCTAAAGAAGAATAATA
1 AGTTCATAATGAAAAGAACTCATCTAAAGAAGAATAATA
* ** * *
287753 AGTTCATAATGAGAAGAACTCATCTTGAGAGGAAGAATA
1 AGTTCATAATGAAAAGAACTCATCTAAAGAAGAATAATA
*
287792 AGTTCATAATGAGAAGAACT
1 AGTTCATAATGAAAAGAACT
287812 TGTTCGGCCT
Statistics
Matches: 88, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
39 63 0.72
40 25 0.28
ACGTcount: A:0.49, C:0.10, G:0.18, T:0.22
Consensus pattern (39 bp):
AGTTCATAATGAAAAGAACTCATCTAAAGAAGAATAATA
Found at i:287903 original size:17 final size:17
Alignment explanation
Indices: 287881--287937 Score: 73
Period size: 17 Copynumber: 3.4 Consensus size: 17
287871 CAGCATTTCT
287881 AGAAGAAGTTCATAATG
1 AGAAGAAGTTCATAATG
* *
287898 AGAAGAA-CTCAT-CTG
1 AGAAGAAGTTCATAATG
287913 AAGAAGAAGTTCATAATG
1 -AGAAGAAGTTCATAATG
287931 AGAAGAA
1 AGAAGAA
287938 CTCATCTGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
15 2 0.06
16 11 0.33
17 18 0.55
18 2 0.06
ACGTcount: A:0.49, C:0.09, G:0.23, T:0.19
Consensus pattern (17 bp):
AGAAGAAGTTCATAATG
Found at i:287917 original size:16 final size:16
Alignment explanation
Indices: 287898--287953 Score: 69
Period size: 16 Copynumber: 3.4 Consensus size: 16
287888 GTTCATAATG
287898 AGAAGAACTCATCTGA
1 AGAAGAACTCATCTGA
* *
287914 AGAAGAAGTTCATAATG-
1 AGAAGAA-CTCAT-CTGA
287931 AGAAGAACTCATCTGA
1 AGAAGAACTCATCTGA
287947 AGAAGAA
1 AGAAGAA
287954 GAAGAAGTGC
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
15 2 0.06
16 18 0.55
17 11 0.33
18 2 0.06
ACGTcount: A:0.48, C:0.12, G:0.21, T:0.18
Consensus pattern (16 bp):
AGAAGAACTCATCTGA
Found at i:287978 original size:39 final size:33
Alignment explanation
Indices: 287881--287954 Score: 148
Period size: 33 Copynumber: 2.2 Consensus size: 33
287871 CAGCATTTCT
287881 AGAAGAAGTTCATAATGAGAAGAACTCATCTGA
1 AGAAGAAGTTCATAATGAGAAGAACTCATCTGA
287914 AGAAGAAGTTCATAATGAGAAGAACTCATCTGA
1 AGAAGAAGTTCATAATGAGAAGAACTCATCTGA
287947 AGAAGAAG
1 AGAAGAAG
287955 AAGAAGTGCA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.47, C:0.11, G:0.23, T:0.19
Consensus pattern (33 bp):
AGAAGAAGTTCATAATGAGAAGAACTCATCTGA
Found at i:289560 original size:143 final size:144
Alignment explanation
Indices: 289367--289627 Score: 379
Period size: 143 Copynumber: 1.8 Consensus size: 144
289357 AAAATAATCA
* * * *
289367 TATTTTAATATTTATTTTTTAATATTAAGAAATGGGCTGTCTTAAAGCACCTAGAATTCCTTTTC
1 TATTTTAATATTTATTTATT-ATATTAAGAAAAGAGCTGTCTTAAAGCACCTAGAAGTCCTTTTC
* *
289432 TGATA-TTCTTAAATAAATAAATATCATATT-TTTATAAAT-TATATATATATTAATTTATTTTA
65 TAATATTTC-TAAATAAATAAATAT--T-TTATTTATAAATATATATATAAATTAATTTATTTTA
289494 ATTATTTTTAGAAAGATGT
126 ATTATTTTTAGAAAGATGT
*
289513 TATTTTAATATTTATTTATT-T-TTAAGAAAAGAGCTGTCTTAAGGCACCTAGAAGTCCTTTTCT
1 TATTTTAATATTTATTTATTATATTAAGAAAAGAGCTGTCTTAAAGCACCTAGAAGTCCTTTTCT
289576 AATATTTCTAAATAAATAAATATTTTATTTATAAATATATATATAAATTAAT
66 AATATTTCTAAATAAATAAATATTTTATTTATAAATATATATATAAATTAAT
289628 AGATTTTCTT
Statistics
Matches: 105, Mismatches: 7, Indels: 10
0.86 0.06 0.08
Matches are distributed among these distances:
140 2 0.02
141 10 0.10
142 14 0.13
143 56 0.53
144 4 0.04
146 19 0.18
ACGTcount: A:0.38, C:0.07, G:0.07, T:0.47
Consensus pattern (144 bp):
TATTTTAATATTTATTTATTATATTAAGAAAAGAGCTGTCTTAAAGCACCTAGAAGTCCTTTTCT
AATATTTCTAAATAAATAAATATTTTATTTATAAATATATATATAAATTAATTTATTTTAATTAT
TTTTAGAAAGATGT
Found at i:292432 original size:36 final size:35
Alignment explanation
Indices: 292386--292459 Score: 130
Period size: 36 Copynumber: 2.1 Consensus size: 35
292376 GGTATGTGGT
292386 TCATCCGACACTGCTCGCAACGAAATTGAGAAAGC
1 TCATCCGACACTGCTCGCAACGAAATTGAGAAAGC
*
292421 TCATCCCGACACTGCTTGCAACGAAATTGAGAAAGC
1 TCAT-CCGACACTGCTCGCAACGAAATTGAGAAAGC
292457 TCA
1 TCA
292460 GGGTAAGGAT
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
35 4 0.11
36 33 0.89
ACGTcount: A:0.34, C:0.28, G:0.19, T:0.19
Consensus pattern (35 bp):
TCATCCGACACTGCTCGCAACGAAATTGAGAAAGC
Found at i:298096 original size:98 final size:99
Alignment explanation
Indices: 297927--298128 Score: 343
Period size: 98 Copynumber: 2.1 Consensus size: 99
297917 TGAAAATAAT
*
297927 ATATTCAGGCTATTAATAAGTATCCAAATAAAATCAGAAATAACCATTTAACACTATCATATTGA
1 ATATTCAGGCTATTAATAAGTATCCAAATAAAATCAAAAATAACCATTTAACACTATCATATTGA
297992 ATATATTCATGAATTGCAAGTCATACCA-TTTTA
66 ATATATTCATGAATTGCAAGTCATACCATTTTTA
* * *
298025 ATATTCGGGCTATTAATAAGTATCCGAATAAAATCAAAAATAATCATTTAACACTATCATATTGA
1 ATATTCAGGCTATTAATAAGTATCCAAATAAAATCAAAAATAACCATTTAACACTATCATATTGA
* *
298090 ATATATTCGTGAATTGCAAGTCATATCATTTTTA
66 ATATATTCATGAATTGCAAGTCATACCATTTTTA
298124 ATATT
1 ATATT
298129 TAAATTAAAA
Statistics
Matches: 97, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
98 87 0.90
99 10 0.10
ACGTcount: A:0.42, C:0.14, G:0.09, T:0.36
Consensus pattern (99 bp):
ATATTCAGGCTATTAATAAGTATCCAAATAAAATCAAAAATAACCATTTAACACTATCATATTGA
ATATATTCATGAATTGCAAGTCATACCATTTTTA
Found at i:298912 original size:34 final size:34
Alignment explanation
Indices: 298867--298933 Score: 84
Period size: 34 Copynumber: 1.9 Consensus size: 34
298857 AATAGGAATT
*
298867 ACAACTTCTCTC-GATCCAACAAGGAGAAAACAATG
1 ACAACTTCTCTCTGAT--AAAAAGGAGAAAACAATG
298902 ACAA-TTCTCTCTTGATAAAAAGGAGAAAACAA
1 ACAACTTCTCTC-TGATAAAAAGGAGAAAACAA
298934 CTCTCAAGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
34 22 0.76
35 4 0.14
36 3 0.10
ACGTcount: A:0.46, C:0.21, G:0.13, T:0.19
Consensus pattern (34 bp):
ACAACTTCTCTCTGATAAAAAGGAGAAAACAATG
Found at i:303157 original size:65 final size:64
Alignment explanation
Indices: 303088--303248 Score: 180
Period size: 65 Copynumber: 2.5 Consensus size: 64
303078 ATAGTCGGGC
* * * ** * * *
303088 TGCATCGATGCATGGCTTGTGCATCGGTGCATTAAATGCATTCGATGTTTCTATTT-GTTCAAGA
1 TGCATCGATGCATGGCTAGTGCATCGGTACACTAAATGCATTCGAAATAT-AATTTAATT-AAGA
303152 G
64 G
* ** *
303153 TGCATCGATGCATAGAGAGTGCATCGGTACACTAAATGCATTCGAAATATAATTTAATTGAGAG
1 TGCATCGATGCATGGCTAGTGCATCGGTACACTAAATGCATTCGAAATATAATTTAATTAAGAG
303217 TGCATCGATGCATGGACTAGTGCATCGGTACA
1 TGCATCGATGCATGG-CTAGTGCATCGGTACA
303249 TCTCTTTGAA
Statistics
Matches: 79, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
64 22 0.28
65 57 0.72
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (64 bp):
TGCATCGATGCATGGCTAGTGCATCGGTACACTAAATGCATTCGAAATATAATTTAATTAAGAG
Found at i:304289 original size:27 final size:27
Alignment explanation
Indices: 304250--304303 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
304240 TCGGTGCTGG
* *
304250 AGGAGGAGGAGGAGCACGAGAAGAACT
1 AGGAGCAGAAGGAGCACGAGAAGAACT
* *
304277 AGGAGCAGAAGGAGCTCGTGAAGAACT
1 AGGAGCAGAAGGAGCACGAGAAGAACT
304304 GGCTCCCGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.39, C:0.13, G:0.41, T:0.07
Consensus pattern (27 bp):
AGGAGCAGAAGGAGCACGAGAAGAACT
Found at i:313266 original size:23 final size:23
Alignment explanation
Indices: 313240--313286 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
313230 ATCTCTATTA
* *
313240 ATGAAAAATATTTAAGTCTTTTC
1 ATGAAAAATAGTTAAGTCATTTC
*
313263 ATGAAAAATAGTTAATTCATTTC
1 ATGAAAAATAGTTAAGTCATTTC
313286 A
1 A
313287 CCCAAAAAGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.43, C:0.09, G:0.09, T:0.40
Consensus pattern (23 bp):
ATGAAAAATAGTTAAGTCATTTC
Found at i:318774 original size:3 final size:3
Alignment explanation
Indices: 318761--318803 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
318751 TCTCCTCCTC
*
318761 CTT CTT TTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
318804 ATCTGCATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:323020 original size:24 final size:24
Alignment explanation
Indices: 322991--323062 Score: 85
Period size: 22 Copynumber: 3.0 Consensus size: 24
322981 ATGTTCATTT
322991 TACATAACTTAGAAAGAAAAAAAA
1 TACATAACTTAGAAAGAAAAAAAA
* * * *
323015 TGCATAAC-TACAAA-TATAAAAA
1 TACATAACTTAGAAAGAAAAAAAA
323037 TACATAACTTAGAAAGAAAGAAAAA
1 TACATAACTTAGAAAGAAA-AAAAA
323062 T
1 T
323063 TATATTGTAG
Statistics
Matches: 37, Mismatches: 8, Indels: 5
0.74 0.16 0.10
Matches are distributed among these distances:
22 13 0.35
23 10 0.27
24 8 0.22
25 6 0.16
ACGTcount: A:0.62, C:0.10, G:0.08, T:0.19
Consensus pattern (24 bp):
TACATAACTTAGAAAGAAAAAAAA
Found at i:324437 original size:16 final size:16
Alignment explanation
Indices: 324410--324455 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
324400 GATATGAGAA
324410 AAATTCAATTTAAATTT
1 AAATT-AATTTAAATTT
*
324427 AAATTAATTTAATTTT
1 AAATTAATTTAAATTT
*
324443 AAAATAATGTTAA
1 AAATTAAT-TTAA
324456 TAAATAATCT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
16 17 0.65
17 9 0.35
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (16 bp):
AAATTAATTTAAATTT
Found at i:324628 original size:30 final size:30
Alignment explanation
Indices: 324592--324648 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
324582 ATATTTCAGA
**
324592 TAATTTAAAGTTTGTTGCGGCGTTACGGTG
1 TAATTTAAAGCGTGTTGCGGCGTTACGGTG
* *
324622 TAATTTATAGCGTGTTGCGGTGTTACG
1 TAATTTAAAGCGTGTTGCGGCGTTACG
324649 TAACGGTGTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.19, C:0.11, G:0.30, T:0.40
Consensus pattern (30 bp):
TAATTTAAAGCGTGTTGCGGCGTTACGGTG
Found at i:325758 original size:92 final size:90
Alignment explanation
Indices: 325616--325798 Score: 296
Period size: 92 Copynumber: 2.0 Consensus size: 90
325606 ATCATTAAAG
325616 TTGCCTTGTTAGAGGCAGAATGCTCATGCTTACAGGGTTTGCCTCTCAGGGCCCTGCTTTGTACT
1 TTGCCTTGTTAGAGGCAGAATGCTCATGCTTACAGGGTTTGCCTCTCAGGGCCCTGCTTTGTACT
* *
325681 CTTTTCAGCTTATTGAGTAAAACTT
66 CTTTTCAGCTTACTGAATAAAACTT
* *
325706 TTGCCTTGTTAGAGGAAGCAGCATGCTCATTCTTACA-GGTTTGCCTCTCAGGGCCCTGCTTTGT
1 TTGCCTTGTTAGA-G--GCAGAATGCTCATGCTTACAGGGTTTGCCTCTCAGGGCCCTGCTTTGT
325770 ACTCTTTTCAGCTTACTGAATAAAACTT
63 ACTCTTTTCAGCTTACTGAATAAAACTT
325798 T
1 T
325799 GTGGTTAATT
Statistics
Matches: 86, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
90 13 0.15
91 1 0.01
92 54 0.63
93 18 0.21
ACGTcount: A:0.20, C:0.23, G:0.21, T:0.37
Consensus pattern (90 bp):
TTGCCTTGTTAGAGGCAGAATGCTCATGCTTACAGGGTTTGCCTCTCAGGGCCCTGCTTTGTACT
CTTTTCAGCTTACTGAATAAAACTT
Found at i:326172 original size:21 final size:21
Alignment explanation
Indices: 326148--326188 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
326138 AACAAATCTT
* *
326148 TTCATCAAATGGTCTTAACTC
1 TTCATCAAAAGGTCATAACTC
326169 TTCATCAAAAGGTCATAACT
1 TTCATCAAAAGGTCATAACT
326189 TTTTTATTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.34, C:0.22, G:0.10, T:0.34
Consensus pattern (21 bp):
TTCATCAAAAGGTCATAACTC
Found at i:333862 original size:24 final size:25
Alignment explanation
Indices: 333835--333885 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 25
333825 TAGCCTATTT
333835 AAAAAACAAAACTT-AAAATAAAAG
1 AAAAAACAAAACTTAAAAATAAAAG
**
333859 AAAAATGAAAACTTAAAAAATAAAAG
1 AAAAAACAAAACTT-AAAAATAAAAG
333885 A
1 A
333886 GAGAACGTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 12 0.52
26 11 0.48
ACGTcount: A:0.75, C:0.06, G:0.06, T:0.14
Consensus pattern (25 bp):
AAAAAACAAAACTTAAAAATAAAAG
Found at i:334741 original size:23 final size:24
Alignment explanation
Indices: 334691--334767 Score: 72
Period size: 24 Copynumber: 3.3 Consensus size: 24
334681 CAATTAAGGG
* *
334691 AATTACCTTTTACAATTTATTAGT
1 AATTATCTTTTACAATTTATTAGA
334715 AATTATCTTTTATC-ATTT-TTAGA
1 AATTATCTTTTA-CAATTTATTAGA
* * *
334738 AATTAT-ATTTGC-ATTTATTAGG
1 AATTATCTTTTACAATTTATTAGA
334760 AATTATCT
1 AATTATCT
334768 CTTAGGTTTT
Statistics
Matches: 44, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
21 5 0.11
22 13 0.30
23 10 0.23
24 15 0.34
25 1 0.02
ACGTcount: A:0.32, C:0.09, G:0.06, T:0.52
Consensus pattern (24 bp):
AATTATCTTTTACAATTTATTAGA
Found at i:338542 original size:21 final size:20
Alignment explanation
Indices: 338505--338543 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
338495 GTGGAAGCTT
*
338505 TTGCAGAAAATTGAAAGTAA
1 TTGCACAAAATTGAAAGTAA
*
338525 TTGCACAACAATTTAAAGT
1 TTGCACAA-AATTGAAAGT
338544 GGTTAGACTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.46, C:0.10, G:0.15, T:0.28
Consensus pattern (20 bp):
TTGCACAAAATTGAAAGTAA
Found at i:341374 original size:22 final size:22
Alignment explanation
Indices: 341349--341457 Score: 103
Period size: 23 Copynumber: 4.9 Consensus size: 22
341339 AACAGAACCC
* *
341349 CAGGGGGGTATCGATTCCCCTA
1 CAGGGGGGAATCGATTCCCCTT
* *
341371 CAGGGGGAAATCGGTTCCCCTT
1 CAGGGGGGAATCGATTCCCCTT
*
341393 CAAGGGGGAAATC-AGTTCCCCTT
1 C-AGGGGGGAATCGA-TTCCCCTT
* *
341416 CAAAGGGGGAATCGGTTCCCCTT
1 C-AGGGGGGAATCGATTCCCCTT
* *
341439 CAAGGGGGTATCGATTCCC
1 CAGGGGGGAATCGATTCCC
341458 TCTGCACCAA
Statistics
Matches: 74, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
22 35 0.47
23 39 0.53
ACGTcount: A:0.21, C:0.27, G:0.30, T:0.22
Consensus pattern (22 bp):
CAGGGGGGAATCGATTCCCCTT
Found at i:341398 original size:23 final size:23
Alignment explanation
Indices: 341358--341446 Score: 128
Period size: 23 Copynumber: 3.9 Consensus size: 23
341348 CCAGGGGGGT
* *
341358 ATCGATTCCCCTAC-AGGGGGAA
1 ATCGGTTCCCCTTCAAGGGGGAA
341380 ATCGGTTCCCCTTCAAGGGGGAA
1 ATCGGTTCCCCTTCAAGGGGGAA
*
341403 ATCAGTTCCCCTTCAAAGGGGG-A
1 ATCGGTTCCCCTTC-AAGGGGGAA
341426 ATCGGTTCCCCTTCAAGGGGG
1 ATCGGTTCCCCTTCAAGGGGG
341447 TATCGATTCC
Statistics
Matches: 61, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
22 19 0.31
23 35 0.57
24 7 0.11
ACGTcount: A:0.22, C:0.27, G:0.29, T:0.21
Consensus pattern (23 bp):
ATCGGTTCCCCTTCAAGGGGGAA
Found at i:345309 original size:22 final size:21
Alignment explanation
Indices: 345267--345306 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
345257 GAGTTTATTT
345267 TCATTTTTCAATTTTAAAACA
1 TCATTTTTCAATTTTAAAACA
345288 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
345307 ACAATTTCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:348426 original size:12 final size:12
Alignment explanation
Indices: 348409--348433 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
348399 GATAAGAATA
348409 AAATAATTAAAT
1 AAATAATTAAAT
348421 AAATAATTAAAT
1 AAATAATTAAAT
348433 A
1 A
348434 TAAATCGTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AAATAATTAAAT
Found at i:349480 original size:5 final size:5
Alignment explanation
Indices: 349467--349568 Score: 62
Period size: 5 Copynumber: 19.8 Consensus size: 5
349457 TCTGATATAT
* ** * **
349467 TTTTG TTTTA TTTTA TTACA TTTTTA TTTTTA TTTTA TTTTCA ATGAA
1 TTTTA TTTTA TTTTA TTTTA -TTTTA -TTTTA TTTTA TTTT-A TTTTA
* * * * *
349515 CTTTA TTTTCA -TTAA ATTGA TTTTA TTTTA ATTTA TTTTA TTTTA TTTTA
1 TTTTA TTTT-A TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
349565 TTTT
1 TTTT
349569 TCTCTGAACA
Statistics
Matches: 75, Mismatches: 18, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
4 1 0.01
5 62 0.83
6 12 0.16
ACGTcount: A:0.24, C:0.04, G:0.03, T:0.70
Consensus pattern (5 bp):
TTTTA
Found at i:352473 original size:17 final size:18
Alignment explanation
Indices: 352447--352488 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
352437 CTTTAAATTA
*
352447 TTTATGTAATTATT-TCT
1 TTTATTTAATTATTATCT
*
352464 TTTATTTAATTCTTATCT
1 TTTATTTAATTATTATCT
352482 TTTATTT
1 TTTATTT
352489 TAAAAACAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 12 0.55
18 10 0.45
ACGTcount: A:0.21, C:0.07, G:0.02, T:0.69
Consensus pattern (18 bp):
TTTATTTAATTATTATCT
Found at i:352569 original size:19 final size:19
Alignment explanation
Indices: 352530--352578 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
352520 TTTACTACTA
* *
352530 TTATTTATTATTTTCCCTT
1 TTATTTATTATTATCCATT
*
352549 TTATTTATTATTATCTATT
1 TTATTTATTATTATCCATT
352568 TTATTTTATTA
1 TTA-TTTATTA
352579 AATCTTTTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 19 0.73
20 7 0.27
ACGTcount: A:0.22, C:0.08, G:0.00, T:0.69
Consensus pattern (19 bp):
TTATTTATTATTATCCATT
Found at i:364343 original size:20 final size:20
Alignment explanation
Indices: 364306--364344 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
364296 GAGGTCTTCG
* **
364306 AGAAAAGGTCAATGGTCAAT
1 AGAAAAAGTCAACAGTCAAT
364326 AGAAAAAGTCAACAGTCAA
1 AGAAAAAGTCAACAGTCAA
364345 AGTCAATGAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.51, C:0.13, G:0.21, T:0.15
Consensus pattern (20 bp):
AGAAAAAGTCAACAGTCAAT
Found at i:366114 original size:20 final size:20
Alignment explanation
Indices: 366089--366129 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
366079 TTCAATATTT
*
366089 TTTATACTTACTTTTATAAA
1 TTTATACTTACTTTTAGAAA
* *
366109 TTTATATTTATTTTTAGAAA
1 TTTATACTTACTTTTAGAAA
366129 T
1 T
366130 ATAAATATGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.34, C:0.05, G:0.02, T:0.59
Consensus pattern (20 bp):
TTTATACTTACTTTTAGAAA
Found at i:380035 original size:15 final size:14
Alignment explanation
Indices: 380010--380042 Score: 57
Period size: 15 Copynumber: 2.3 Consensus size: 14
380000 TTCAATTTAG
380010 AAATATAAAAATAA
1 AAATATAAAAATAA
380024 AAATATTAAAAATAA
1 AAATA-TAAAAATAA
380039 AAAT
1 AAAT
380043 TATTGAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (14 bp):
AAATATAAAAATAA
Found at i:383841 original size:3 final size:3
Alignment explanation
Indices: 383822--383870 Score: 52
Period size: 3 Copynumber: 17.3 Consensus size: 3
383812 TTTGGCCTGC
*
383822 ATA A-A ATA ATA AAA ATA AT- ATA A-A TATA A-A ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA
383864 ATA ATA A
1 ATA ATA A
383871 AACGGGTCTC
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
2 7 0.18
3 31 0.79
4 1 0.03
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:383850 original size:11 final size:10
Alignment explanation
Indices: 383822--383863 Score: 50
Period size: 11 Copynumber: 4.1 Consensus size: 10
383812 TTTGGCCTGC
383822 ATAAAATAAT
1 ATAAAATAAT
383832 A-AAAATAAT
1 ATAAAATAAT
*
383841 ATAAATATAAA
1 ATAAA-ATAAT
383852 ATAATAATAAT
1 ATAA-AATAAT
383863 A
1 A
383864 ATAATAAAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
9 9 0.33
10 4 0.15
11 13 0.48
12 1 0.04
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (10 bp):
ATAAAATAAT
Found at i:383850 original size:25 final size:26
Alignment explanation
Indices: 383822--383871 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 26
383812 TTTGGCCTGC
383822 ATAAAATAATAAAAATAAT-ATAAAT
1 ATAAAATAATAAAAATAATAATAAAT
*
383847 ATAAAATAATAATAATAATAATAAA
1 ATAAAATAATAAAAATAATAATAAA
383872 ACGGGTCTCC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 18 0.78
26 5 0.22
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (26 bp):
ATAAAATAATAAAAATAATAATAAAT
Found at i:384799 original size:38 final size:38
Alignment explanation
Indices: 384302--384965 Score: 522
Period size: 38 Copynumber: 16.8 Consensus size: 38
384292 TACAACACTG
** * * * *
384302 AAAGATTGAC-TCATCTTTGCGAGAAAGTTAAGAAGAAA
1 AAAGATTGACTTC-TCTTCACGAGGAAGTCAAGAATAAC
* *
384340 AAAGATAGACTTCTCTTCACGAGGAAGTCAATG-ACAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAA-GAATAAC
384378 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* * * * * * *
384416 AAAGATTGACTTCTTTTCGCGAGGGATTCAAAAACAAA
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* * * * * * * *
384454 AAAGATTAACTTCTCTTCGCGAGGGATTTAAAAACAAA
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
*
384492 AAAGATTAACTTCTCTTCACGAGGAAGTCAAGAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* *
384530 AAAGATTGATTTCTCTTCACGAGGAAGTCAATAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* * *
384568 AAATATTGACTTCTCTTCACGAGAAAGTCAATAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* * * *
384606 AAAGATTGATTGACTCCTCTTCACGAGGGAGTCAGGAACAAC
1 -AA-A--GATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
384648 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* ** * * * *
384686 AAAGATTAACTGACTCCTCTTTGCGAGGGAGTCAGGAACAAA
1 AAAGA-T---TGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* * * *
384728 AAAGATTGACTACTCTTCACAAGGACGTCAAGAATTAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* *
384766 AAATATTGACTTCTCTTCACGAGAAAGTCAAGAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* ** * * *
384804 ATTGAAATATTGACTTCTCTTCGTGAGGAAATCAATAATGACATTG
1 ----AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAAT-A-A--C
* *
384850 AAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
** * * *
384888 ATTGAAAGATTGACTTCTCTTCGTGAGGAAATCAATAATGACATTG
1 ----AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAAT-A-A--C
* * *
384934 AAAGATTGACTCCTCTTCGCGAGGGAGTCAAG
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAG
384966 TTGAAGCTTC
Statistics
Matches: 507, Mismatches: 92, Indels: 50
0.78 0.14 0.08
Matches are distributed among these distances:
37 1 0.00
38 317 0.63
39 6 0.01
40 3 0.01
41 4 0.01
42 172 0.34
43 2 0.00
44 2 0.00
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.25
Consensus pattern (38 bp):
AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
Found at i:384872 original size:84 final size:84
Alignment explanation
Indices: 384770--384965 Score: 347
Period size: 84 Copynumber: 2.3 Consensus size: 84
384760 AATTACAAAT
* *
384770 ATTGACTTCTCTTCACGAGAAAGTCAAGAATAACATTGAAATATTGACTTCTCTTCGTGAGGAAA
1 ATTGACTCCTCTTCACGAGAAAGTCAAGAATAACATTGAAAGATTGACTTCTCTTCGTGAGGAAA
384835 TCAATAATGACATTGAAAG
66 TCAATAATGACATTGAAAG
384854 ATTGACTCCTCTTCACGAGAAAGTCAAGAATAACATTGAAAGATTGACTTCTCTTCGTGAGGAAA
1 ATTGACTCCTCTTCACGAGAAAGTCAAGAATAACATTGAAAGATTGACTTCTCTTCGTGAGGAAA
384919 TCAATAATGACATTGAAAG
66 TCAATAATGACATTGAAAG
* **
384938 ATTGACTCCTCTTCGCGAGGGAGTCAAG
1 ATTGACTCCTCTTCACGAGAAAGTCAAG
384966 TTGAAGCTTC
Statistics
Matches: 107, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
84 107 1.00
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.28
Consensus pattern (84 bp):
ATTGACTCCTCTTCACGAGAAAGTCAAGAATAACATTGAAAGATTGACTTCTCTTCGTGAGGAAA
TCAATAATGACATTGAAAG
Found at i:384950 original size:126 final size:122
Alignment explanation
Indices: 384378--384957 Score: 397
Period size: 118 Copynumber: 4.9 Consensus size: 122
384368 CAATGACAAC
* * * * * ** *
384378 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAGATTGACTTCTTTTCGCGAGGGAT
1 AAAGATTGACTACTCTTCACAAGAAAGTCAAGAATAACAAAGATTGACTTCTCTTCACGAGAAAG
** * * * * * **
384443 TC-A-AA-AACA-AAAAAGATTAACTTCTCTTCGCGAGGGATTTAA-AA--ACA-AA
66 TCAAGAATAACATTGAAAGATTGACTCCTCTTCGCGAGGAAATCAATAATGACATTG
* * * * * *
384492 AAAGATTAACTTCTCTTCACGAGGAAGTCAAGAATAACAAAGATTGATTTCTCTTCACGAGGAAG
1 AAAGATTGACTACTCTTCACAAGAAAGTCAAGAATAACAAAGATTGACTTCTCTTCACGAGAAAG
* * * * * **
384557 TCAATAATAAC----AAATATTGACTTCTCTTCACGA-GAAAGTCAATAATAACAAAG
66 TCAAGAATAACATTGAAAGATTGACTCCTCTTCGCGAGGAAA-TCAATAATGACATTG
** * * ** * * *
384610 ATTGATTGACTCCTCTTCACGAGGGAGTCAGGAACAACAAAGATTGACTTCTCTTCACGAGGAAG
1 AAAGATTGACTACTCTTCACAAGAAAGTCAAGAATAACAAAGATTGACTTCTCTTCACGAGAAAG
** * * * * * ** **
384675 TCAAGAATAACAAAGATTA-ACTGACTCCTCTTTGCGAGGGAGTC-AGGA--ACA-AA
66 TCAAGAATAACATTGA-AAGATTGACTCCTCTTCGCGAGGAAATCAATAATGACATTG
* * * *
384728 AAAGATTGACTACTCTTCACAAGGACGTCAAGAATTACAAATATTGACTTCTCTTCACGAGAAAG
1 AAAGATTGACTACTCTTCACAAGAAAGTCAAGAATAACAAAGATTGACTTCTCTTCACGAGAAAG
* * *
384793 TCAAGAATAACATTGAAATATTGACTTCTCTTCGTGAGGAAATCAATAATGACATTG
66 TCAAGAATAACATTGAAAGATTGACTCCTCTTCGCGAGGAAATCAATAATGACATTG
* * **
384850 AAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATAACATTGAAAGATTGACTTCTCTTCGTGAG
1 AAAGATTGACTACTCTTCACAAGAAAGTCAAGAATAAC----AAAGATTGACTTCTCTTCACGA-
* *
384915 GAAA-TCAATAATGACATTGAAAGATTGACTCCTCTTCGCGAGG
61 GAAAGTCAAGAATAACATTGAAAGATTGACTCCTCTTCGCGAGG
384958 GAGTCAAGTT
Statistics
Matches: 373, Mismatches: 69, Indels: 36
0.78 0.14 0.08
Matches are distributed among these distances:
113 2 0.01
114 83 0.22
115 3 0.01
116 2 0.01
117 7 0.02
118 156 0.42
119 5 0.01
121 5 0.01
122 50 0.13
123 3 0.01
126 53 0.14
127 4 0.01
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.26
Consensus pattern (122 bp):
AAAGATTGACTACTCTTCACAAGAAAGTCAAGAATAACAAAGATTGACTTCTCTTCACGAGAAAG
TCAAGAATAACATTGAAAGATTGACTCCTCTTCGCGAGGAAATCAATAATGACATTG
Found at i:391103 original size:21 final size:23
Alignment explanation
Indices: 391077--391123 Score: 80
Period size: 22 Copynumber: 2.1 Consensus size: 23
391067 GTTTTTCTAC
391077 TTTCGAAT-GGAAAATAATAG-T
1 TTTCGAATAGGAAAATAATAGCT
391098 TTTCGAATAGGAAAATAATAGCT
1 TTTCGAATAGGAAAATAATAGCT
391121 TTT
1 TTT
391124 GAAAACATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 8 0.33
22 12 0.50
23 4 0.17
ACGTcount: A:0.40, C:0.06, G:0.17, T:0.36
Consensus pattern (23 bp):
TTTCGAATAGGAAAATAATAGCT
Found at i:392255 original size:41 final size:40
Alignment explanation
Indices: 392201--392436 Score: 117
Period size: 41 Copynumber: 5.8 Consensus size: 40
392191 GAATAGTACT
* *
392201 TTAGCGGCGTTTTTATACAAACGCCGCAATAAGTGTAATA
1 TTAGTGGCATTTTTATACAAACGCCGCAATAAGTGTAATA
** *
392241 TATAGTGGCATTTTTCA-ACAAACGCCGCAACATATTTGTACT-
1 T-TAGTGGCATTTTT-ATACAAACGCCGC-A-ATAAGTGTAATA
* * * * * *
392283 TTAGTGGCGTTTTTAAACACAAACACCGCAA-AAGATTTGGACA
1 TTAGTGGCATTTTT--ATACAAACGCCGCAATAAG-TGT-AATA
* * * * **
392326 GTAGTGGCGTTTATA-ACAAACGCCG-ATATAGAATAGT-ACG
1 TTAGTGGCATTTTTATACAAACGCCGCA-ATA-AGT-GTAATA
* * * *
392366 TTAGCGACATTTTTATACAAACGCAGCAATAGGTGTAATA
1 TTAGTGGCATTTTTATACAAACGCCGCAATAAGTGTAATA
*
392406 TATAGTGACATTTTTATA-AAACGCCGCAATA
1 T-TAGTGGCATTTTTATACAAACGCCGCAATA
392437 TATTTGTACT
Statistics
Matches: 147, Mismatches: 32, Indels: 34
0.69 0.15 0.16
Matches are distributed among these distances:
39 3 0.02
40 39 0.27
41 67 0.46
42 8 0.05
43 30 0.20
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.29
Consensus pattern (40 bp):
TTAGTGGCATTTTTATACAAACGCCGCAATAAGTGTAATA
Found at i:392381 original size:165 final size:164
Alignment explanation
Indices: 392162--392507 Score: 525
Period size: 165 Copynumber: 2.1 Consensus size: 164
392152 GGTTAACATA
* * * * *
392162 TAGTGGCGTTTATAAAAAACGCCGCTACTGAATAGTACTTTAGCGGCGTTTTTATACAAACGCCG
1 TAGTGGCGTTTATAAAAAACGCCGATACTGAATAGTACGTTAGCGACATTTTTATACAAACGCAG
*
392227 CAATAAGTGTAATATATAGTGGCATTTTTCA-ACAAACGCCGCAACATATTTGTACTTTAGTGGC
66 CAATAAGTGTAATATATAGTGACATTTTT-ATA-AAACGCCGCAACATATTTGTACTTTAGTGGC
*
392291 GTTTTTAAACACAAACACCGCAAAAGATTTGGACAG
129 GTTTTTAAACACAAACACCGCAAAAGATATGGACAG
*
392327 TAGTGGCGTTTATAACAAACGCCGATA-TAGAATAGTACGTTAGCGACATTTTTATACAAACGCA
1 TAGTGGCGTTTATAAAAAACGCCGATACT-GAATAGTACGTTAGCGACATTTTTATACAAACGCA
* * *
392391 GCAATAGGTGTAATATATAGTGACATTTTTATAAAACGCCGCAATATATTTGTACTTTTGTGGCG
65 GCAATAAGTGTAATATATAGTGACATTTTTATAAAACGCCGCAACATATTTGTACTTTAGTGGCG
* * *
392456 TTTTTAAACACAAACGCTGCAAAATATATGGACAG
130 TTTTTAAACACAAACACCGCAAAAGATATGGACAG
392491 TAGTGGCGTTTATAAAA
1 TAGTGGCGTTTATAAAA
392508 GACGTCGCGA
Statistics
Matches: 164, Mismatches: 15, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
164 79 0.48
165 85 0.52
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.30
Consensus pattern (164 bp):
TAGTGGCGTTTATAAAAAACGCCGATACTGAATAGTACGTTAGCGACATTTTTATACAAACGCAG
CAATAAGTGTAATATATAGTGACATTTTTATAAAACGCCGCAACATATTTGTACTTTAGTGGCGT
TTTTAAACACAAACACCGCAAAAGATATGGACAG
Found at i:392495 original size:83 final size:83
Alignment explanation
Indices: 392243--392497 Score: 218
Period size: 81 Copynumber: 3.1 Consensus size: 83
392233 GTGTAATATA
* *
392243 TAGTGGCATTTTTCAACAAACGCCGCAACATATTTGTACTTTAGTGGCGTTTTTAAACACAAACA
1 TAGTGGCATTTTT-AACAAACGCCGCAATATATTTGTACTTTAGTGGCGTTTTTAAACACAAACG
* * *
392308 CCGCAAAAGATTTGGACAG
65 CAGCAAAATATATGGACAG
* * * * * * * * * *
392327 TAGTGGCGTTTATAACAAACGCCG-ATATAGAATAGTACGTTAGCGACATTTTT--ATACAAACG
1 TAGTGGCATTTTTAACAAACGCCGCA-ATATATTTGTACTTTAGTGGCGTTTTTAAACACAAACG
* * *
392389 CAGCAATAGGTGTAAT--ATA-
65 CAGCAA-A-ATAT-ATGGACAG
* *
392408 TAGTGACATTTTTATA-AAACGCCGCAATATATTTGTACTTTTGTGGCGTTTTTAAACACAAACG
1 TAGTGGCATTTTTA-ACAAACGCCGCAATATATTTGTACTTTAGTGGCGTTTTTAAACACAAACG
*
392472 CTGCAAAATATATGGACAG
65 CAGCAAAATATATGGACAG
392491 TAGTGGC
1 TAGTGGC
392498 GTTTATAAAA
Statistics
Matches: 125, Mismatches: 35, Indels: 23
0.68 0.19 0.13
Matches are distributed among these distances:
80 2 0.02
81 52 0.42
82 9 0.07
83 50 0.40
84 12 0.10
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (83 bp):
TAGTGGCATTTTTAACAAACGCCGCAATATATTTGTACTTTAGTGGCGTTTTTAAACACAAACGC
AGCAAAATATATGGACAG
Found at i:392552 original size:165 final size:162
Alignment explanation
Indices: 392162--392559 Score: 482
Period size: 164 Copynumber: 2.4 Consensus size: 162
392152 GGTTAACATA
* *
392162 TAGTGGCGTTTATAAAAAACGC-CGCTACTGAATAGT-ACTTTAGCGGCGTTTTTATACAAACGC
1 TAGTGGCGTTTAT-AAAAACGCGCGATA--GAGTA-TAAC-TTAGCGGCGTTTTTATACAAACGC
*
392225 CGCAATAAGTGTAATATATAGTGGCATTTTTCAACAAACGCCGCAACATATTTGTACTTTAGTGG
61 CGCAATAAGTGTAATATATAGTGACATTTTTCAACAAACGCCGCAACATATTTGTACTTTAGTGG
*
392290 CGTTTTTAAACACAAACACCGCAAAAGATTTGGACAG
126 CGTTTTTAAACACAAACACCGCAAAAGATATGGACAG
* * * * *
392327 TAGTGGCGTTTATAACAAACGC-CGATATAGAATAGTACGTTAGCGACATTTTTATACAAACGCA
1 TAGTGGCGTTTATAA-AAACGCGCGATAGAGTATA--AC-TTAGCGGCGTTTTTATACAAACGCC
* * *
392391 GCAATAGGTGTAATATATAGTGACATTTTT-ATA-AAACGCCGCAATATATTTGTACTTTTGTGG
62 GCAATAAGTGTAATATATAGTGACATTTTTCA-ACAAACGCCGCAACATATTTGTACTTTAGTGG
* * *
392454 CGTTTTTAAACACAAACGCTGCAAAATATATGGACAG
126 CGTTTTTAAACACAAACACCGCAAAAGATATGGACAG
**
392491 TAGTGGCGTTTATAAAAGACGTCGCGATAGAGTATAACTATAGCGGCGTTTGGATTACAAACGCC
1 TAGTGGCGTTTATAAAA-ACG-CGCGATAGAGTATAACT-TAGCGGCGTTTTTA-TACAAACGCC
392556 GCAA
62 GCAA
392560 ATTTCTATAA
Statistics
Matches: 200, Mismatches: 23, Indels: 20
0.82 0.09 0.08
Matches are distributed among these distances:
162 1 0.00
163 5 0.03
164 94 0.47
165 90 0.45
166 10 0.05
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (162 bp):
TAGTGGCGTTTATAAAAACGCGCGATAGAGTATAACTTAGCGGCGTTTTTATACAAACGCCGCAA
TAAGTGTAATATATAGTGACATTTTTCAACAAACGCCGCAACATATTTGTACTTTAGTGGCGTTT
TTAAACACAAACACCGCAAAAGATATGGACAG
Found at i:400638 original size:21 final size:20
Alignment explanation
Indices: 400609--400671 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 20
400599 TGAAGCAAGG
*
400609 GAAGAAGAGAGAGCAACAGCA
1 GAAGCAGAGAGAG-AACAGCA
*
400630 GAAGCAGAGAGAGAAGCAACA
1 GAAGCAGAGAGAGAA-CAGCA
* *
400651 GCAGCACAGAGAGAAACAGCA
1 GAAGCAGAGAGAG-AACAGCA
400672 TATCAGTAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
20 2 0.06
21 31 0.89
22 2 0.06
ACGTcount: A:0.51, C:0.17, G:0.32, T:0.00
Consensus pattern (20 bp):
GAAGCAGAGAGAGAACAGCA
Found at i:400660 original size:23 final size:23
Alignment explanation
Indices: 400614--400664 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 23
400604 CAAGGGAAGA
400614 AGAGAGAGCAACAGCAGAAGCAG
1 AGAGAGAGCAACAGCAGAAGCAG
*
400637 AGAGAGAAGCAACAGCAGCA-CAG
1 AGAGAG-AGCAACAGCAGAAGCAG
400660 AGAGA
1 AGAGA
400665 AACAGCATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 14 0.54
24 12 0.46
ACGTcount: A:0.49, C:0.18, G:0.33, T:0.00
Consensus pattern (23 bp):
AGAGAGAGCAACAGCAGAAGCAG
Found at i:400671 original size:24 final size:24
Alignment explanation
Indices: 400620--400671 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
400610 AAGAAGAGAG
*
400620 AGCAACAGCAGAAGCAGAGAGAGA
1 AGCAACAGCAGAAGCAGAGAGAAA
*
400644 AGCAACAGCAGCA-CAGAGAGAAA
1 AGCAACAGCAGAAGCAGAGAGAAA
400667 CAGCA
1 -AGCA
400672 TATCAGTAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 9 0.36
24 16 0.64
ACGTcount: A:0.50, C:0.21, G:0.29, T:0.00
Consensus pattern (24 bp):
AGCAACAGCAGAAGCAGAGAGAAA
Found at i:401067 original size:44 final size:43
Alignment explanation
Indices: 401007--401105 Score: 119
Period size: 43 Copynumber: 2.3 Consensus size: 43
400997 TTTGTAACAA
* * * *
401007 AAAAAATGCCGCTATATACCATATATTTTA-CGGCGTTTGTATCC
1 AAAAAACGCCGCTATATACC-GA-ACTTTAGCGGCATTTGTATCC
* *
401051 TAAAAACGCCGCTATATACCGACCTTTAGCGGCATTTGTATCC
1 AAAAAACGCCGCTATATACCGAACTTTAGCGGCATTTGTATCC
401094 AAAAAACGCCGC
1 AAAAAACGCCGC
401106 AAAATATCTT
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
42 4 0.09
43 25 0.53
44 18 0.38
ACGTcount: A:0.32, C:0.25, G:0.15, T:0.27
Consensus pattern (43 bp):
AAAAAACGCCGCTATATACCGAACTTTAGCGGCATTTGTATCC
Found at i:401215 original size:43 final size:42
Alignment explanation
Indices: 401167--401345 Score: 198
Period size: 43 Copynumber: 4.2 Consensus size: 42
401157 GCATTTTACG
* *
401167 GCGTTTGTGGGGAAAACGCCGCTAAATCTCAACACCTATTGC
1 GCGTTTGTGAGAAAAACGCCGCTAAATCTCAACACCTATTGC
** *
401209 GACGTTTGTGAGAAAAATACCGCTAAATCTCAAAACCTATTGC
1 G-CGTTTGTGAGAAAAACGCCGCTAAATCTCAACACCTATTGC
*
401252 GTCGTTTGTGAGAAAAACGCTGCTAAATCTCAACACCTATTGC
1 G-CGTTTGTGAGAAAAACGCCGCTAAATCTCAACACCTATTGC
** * * * *
401295 GCGCGTGCATG-GGAAAACGCCACTAAACCTCAACACCAATTGC
1 GCGTTTG--TGAGAAAAACGCCGCTAAATCTCAACACCTATTGC
401338 GGCGTTTG
1 -GCGTTTG
401346 ATATCAACAC
Statistics
Matches: 114, Mismatches: 19, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
42 5 0.04
43 102 0.89
44 7 0.06
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.23
Consensus pattern (42 bp):
GCGTTTGTGAGAAAAACGCCGCTAAATCTCAACACCTATTGC
Found at i:401471 original size:12 final size:14
Alignment explanation
Indices: 401435--401471 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
401425 CGCCACAAAC
401435 TTTAGCGGCGCTAT
1 TTTAGCGGCGCTAT
401449 TTTCAGCGGCGCT-T
1 TTT-AGCGGCGCTAT
401463 TTT-GCGGCG
1 TTTAGCGGCG
401472 TTTATCATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 6 0.27
14 7 0.32
15 9 0.41
ACGTcount: A:0.08, C:0.24, G:0.32, T:0.35
Consensus pattern (14 bp):
TTTAGCGGCGCTAT
Found at i:401921 original size:13 final size:13
Alignment explanation
Indices: 401905--401929 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
401895 GGTGGTCAGC
401905 GGTGGTAGACAGT
1 GGTGGTAGACAGT
401918 GGTGGTAGACAG
1 GGTGGTAGACAG
401930 CGACCATGGT
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:0.24, C:0.08, G:0.48, T:0.20
Consensus pattern (13 bp):
GGTGGTAGACAGT
Found at i:414890 original size:15 final size:15
Alignment explanation
Indices: 414870--414898 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
414860 AAGACTAACT
414870 TTATTTTAATTTAAG
1 TTATTTTAATTTAAG
414885 TTATTTTAATTTAA
1 TTATTTTAATTTAA
414899 CAAAGCAAAG
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:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (15 bp):
TTATTTTAATTTAAG
Found at i:414943 original size:15 final size:15
Alignment explanation
Indices: 414920--414954 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
414910 AAATTGGTGG
*
414920 AAAAT-AAATATATT
1 AAAATAAAATAAATT
414934 AAAATAAAATAAATT
1 AAAATAAAATAAATT
414949 AAAATA
1 AAAATA
414955 GTCTTTCAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
AAAATAAAATAAATT
Found at i:415185 original size:23 final size:24
Alignment explanation
Indices: 415159--415205 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
415149 TAACCCGTGG
415159 TGATCACATCTTAAATAAA-AAAA
1 TGATCACATCTTAAATAAATAAAA
* * *
415182 TGATCATATTTTAATTAAATAAAA
1 TGATCACATCTTAAATAAATAAAA
415206 ATGAAGGTGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 16 0.80
24 4 0.20
ACGTcount: A:0.53, C:0.09, G:0.04, T:0.34
Consensus pattern (24 bp):
TGATCACATCTTAAATAAATAAAA
Found at i:415839 original size:22 final size:22
Alignment explanation
Indices: 415813--416372 Score: 577
Period size: 22 Copynumber: 25.5 Consensus size: 22
415803 ATAATAATTT
*
415813 TTTTAAAATAAATAAATTCATA
1 TTTTAAAATAAATCAATTCATA
*
415835 TTTTAAAATAAATCAATACATA
1 TTTTAAAATAAATCAATTCATA
*
415857 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTCATA
* *
415879 TTTTAATATAAATCAATCCATA
1 TTTTAAAATAAATCAATTCATA
***
415901 TTTTAAAAT-AATTTTTTCCATA
1 TTTTAAAATAAATCAATT-CATA
* *
415923 TTTTAAAATAAGTCAATCCATA
1 TTTTAAAATAAATCAATTCATA
* *
415945 TTTTAGAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTCATA
* ***
415967 TTTTAAAATAATTTTTTTCCATA
1 TTTTAAAATAAATCAATT-CATA
* *
415990 TTTTAAAATAAATAAATCCATA
1 TTTTAAAATAAATCAATTCATA
* *
416012 TTTTAAAATAAACCAATCCATA
1 TTTTAAAATAAATCAATTCATA
*
416034 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTCATA
*
416056 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTCATA
*
416078 TTTTAAAATAAATC-TTTCCATA
1 TTTTAAAATAAATCAATT-CATA
416100 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATTCATA
**
416122 TTTTAAAATAAAAT-TTTTCATA
1 TTTTAAAAT-AAATCAATTCATA
416144 TTTTAAAATAAATCAA-TCAATA
1 TTTTAAAATAAATCAATTC-ATA
416166 TTTTAAAATAAATCAA-TCAATA
1 TTTTAAAATAAATCAATTC-ATA
**
416188 TTTTAAAATAAAT-TTTTCTATA
1 TTTTAAAATAAATCAATTC-ATA
*
416210 TTTTAAAATAAAT-GATTCATA
1 TTTTAAAATAAATCAATTCATA
*
416231 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTCATA
* *
416253 ATTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTCATA
** * ** *
416275 AATTAATCCATATTTTAA--CATA
1 TTTTAA--AATAAATCAATTCATA
*
416297 TTTTAAAATAAATCGA-TCTATA
1 TTTTAAAATAAATCAATTC-ATA
*
416319 TTTTAAAATAAATTAA-TCTATA
1 TTTTAAAATAAATCAATTC-ATA
416341 TTTTAAAATAAATCAA-TCTATA
1 TTTTAAAATAAATCAATTC-ATA
416363 TTTTAAAATA
1 TTTTAAAATA
416373 GATTTTAAAA
Statistics
Matches: 464, Mismatches: 60, Indels: 28
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.01
21 28 0.06
22 399 0.86
23 26 0.06
24 6 0.01
ACGTcount: A:0.48, C:0.10, G:0.01, T:0.41
Consensus pattern (22 bp):
TTTTAAAATAAATCAATTCATA
Found at i:415883 original size:66 final size:66
Alignment explanation
Indices: 415813--416372 Score: 648
Period size: 66 Copynumber: 8.5 Consensus size: 66
415803 ATAATAATTT
* *
415813 TTTTAAAATAAATAAATTCATATTTTAAAATAAATCAATACATATTTTAAAATAAATCAATCCAT
1 TTTTAAAATAAATCAATTCATATTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCAT
415878 A
66 A
* * * *** *
415879 TTTTAATATAAATCAATCCATATTTTAAAATAATTTTTTCCATATTTTAAAATAAGTCAATCCAT
1 TTTTAAAATAAATCAATTCATATTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCAT
415944 A
66 A
* * * *** *
415945 TTTTAGAATAAATCAATCCATATTTTAAAATAATTTTTTTCCATATTTTAAAATAAATAAATCCA
1 TTTTAAAATAAATCAATTCATATTTTAAAATAA-ATCAATCCATATTTTAAAATAAATCAATCCA
416010 TA
65 TA
* *
416012 TTTTAAAATAAACCAATCCATATTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCAT
1 TTTTAAAATAAATCAATTCATATTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCAT
416077 A
66 A
* * ** *
416078 TTTTAAAATAAATC-TTTCCATATTTTAAAATAAATCAATTCATATTTTAAAATAAAAT-TTTTC
1 TTTTAAAATAAATCAATT-CATATTTTAAAATAAATCAATCCATATTTTAAAAT-AAATCAATCC
416141 ATA
64 ATA
* *** *
416144 TTTTAAAATAAATCAA-TCAATATTTTAAAATAAATCAATCAATATTTTAAAATAAATTTTTCTA
1 TTTTAAAATAAATCAATTC-ATATTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCA
416208 TA
65 TA
* *
416210 TTTTAAAATAAAT-GATTCATATTTTAAAATAAATCAATCCATAATTTAAAATAAATCAATCCAT
1 TTTTAAAATAAATCAATTCATATTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCAT
416274 A
66 A
** * ** * * * * *
416275 AATTAATCCATATTTTAA--CATATTTTAAAATAAATCGATCTATATTTTAAAATAAATTAATCT
1 TTTTAA--AATAAATCAATTCATATTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCC
416338 ATA
64 ATA
416341 TTTTAAAATAAATCAA-TCTATATTTTAAAATA
1 TTTTAAAATAAATCAATTC-ATATTTTAAAATA
416373 GATTTTAAAA
Statistics
Matches: 426, Mismatches: 56, Indels: 24
0.84 0.11 0.05
Matches are distributed among these distances:
64 6 0.01
65 53 0.12
66 296 0.69
67 70 0.16
68 1 0.00
ACGTcount: A:0.48, C:0.10, G:0.01, T:0.41
Consensus pattern (66 bp):
TTTTAAAATAAATCAATTCATATTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCAT
A
Found at i:416392 original size:11 final size:12
Alignment explanation
Indices: 416362--416401 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
416352 ATCAATCTAT
416362 ATTTTAAAATAG
1 ATTTTAAAATAG
416374 ATTTTAAAATAG
1 ATTTTAAAATAG
416386 A-TTT-AAAT-G
1 ATTTTAAAATAG
416395 ATTTTAA
1 ATTTTAA
416402 TTTTCCCGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
9 2 0.08
10 7 0.27
11 4 0.15
12 13 0.50
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.45
Consensus pattern (12 bp):
ATTTTAAAATAG
Found at i:422536 original size:23 final size:24
Alignment explanation
Indices: 422510--422628 Score: 94
Period size: 23 Copynumber: 5.2 Consensus size: 24
422500 TGTTGTTGTG
*
422510 GTTTATGTTCGTTTA-TTGTGTTT
1 GTTTATGTTCGTTTACTTGTGTTC
*
422533 GTTTTTGTTCGTTTACGTTCGT-TT-
1 GTTTATGTTCGTTTAC-TT-GTGTTC
422557 G-TT-TG-T-GTTTACTTGTGTTC
1 GTTTATGTTCGTTTACTTGTGTTC
* **
422577 ATTTACATTCGTTTA-TTGTGTTC
1 GTTTATGTTCGTTTACTTGTGTTC
* *
422600 GTTTAT-TTCGTTCATTTGTGTTC
1 GTTTATGTTCGTTTACTTGTGTTC
422623 GTTTAT
1 GTTTAT
422629 CATTTAGATG
Statistics
Matches: 79, Mismatches: 7, Indels: 20
0.75 0.07 0.19
Matches are distributed among these distances:
18 2 0.03
19 4 0.05
20 6 0.08
21 3 0.04
22 9 0.11
23 43 0.54
24 6 0.08
25 4 0.05
26 2 0.03
ACGTcount: A:0.09, C:0.10, G:0.19, T:0.61
Consensus pattern (24 bp):
GTTTATGTTCGTTTACTTGTGTTC
Found at i:422576 original size:34 final size:33
Alignment explanation
Indices: 422510--422598 Score: 106
Period size: 34 Copynumber: 2.7 Consensus size: 33
422500 TGTTGTTGTG
* ** *
422510 GTTTATGTTCGTTTATTGTGTTTGTTTTTGTTC
1 GTTTACGTTCGTTTATTGTGTTTACTTGTGTTC
*
422543 GTTTACGTTCGTTTGTTTGTGTTTACTTGTGTTC
1 GTTTACGTTCGTTT-ATTGTGTTTACTTGTGTTC
* *
422577 ATTTACATTCGTTTATTGTGTT
1 GTTTACGTTCGTTTATTGTGTT
422599 CGTTTATTTC
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
33 20 0.43
34 27 0.57
ACGTcount: A:0.09, C:0.09, G:0.20, T:0.62
Consensus pattern (33 bp):
GTTTACGTTCGTTTATTGTGTTTACTTGTGTTC
Found at i:424203 original size:20 final size:21
Alignment explanation
Indices: 424178--424219 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
424168 CGTTACACAG
424178 GGGGGAATCGGTACCC-CCTA
1 GGGGGAATCGGTACCCTCCTA
*
424198 GGGGGAATCGGTTCCCTCCTA
1 GGGGGAATCGGTACCCTCCTA
424219 G
1 G
424220 CATACTGGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.17, C:0.29, G:0.36, T:0.19
Consensus pattern (21 bp):
GGGGGAATCGGTACCCTCCTA
Found at i:424910 original size:16 final size:15
Alignment explanation
Indices: 424874--424926 Score: 52
Period size: 17 Copynumber: 3.3 Consensus size: 15
424864 AAGTTCTCAT
*
424874 AAATCCAAACAAATTCA
1 AAAT-CAAAC-AATCCA
424891 AAATCAAACAATCCA
1 AAATCAAACAATCCA
*
424906 CAAATTCAAACATTCCA
1 -AAA-TCAAACAATCCA
424923 AAAT
1 AAAT
424927 ATTCAAAATG
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
15 6 0.19
16 11 0.34
17 15 0.47
ACGTcount: A:0.57, C:0.25, G:0.00, T:0.19
Consensus pattern (15 bp):
AAATCAAACAATCCA
Found at i:426956 original size:20 final size:20
Alignment explanation
Indices: 426927--426964 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
426917 CCCCTTCAAA
*
426927 GGGGGAATCGGTTCCCTCAT
1 GGGGGAATCGATTCCCTCAT
*
426947 GGGGGTATCGATTCCCTC
1 GGGGGAATCGATTCCCTC
426965 TGCACTAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.26, G:0.34, T:0.26
Consensus pattern (20 bp):
GGGGGAATCGATTCCCTCAT
Found at i:437057 original size:2 final size:2
Alignment explanation
Indices: 437050--437105 Score: 105
Period size: 2 Copynumber: 28.5 Consensus size: 2
437040 CGACCTGACC
437050 TA TA TA TA TA TA TA TA 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
437092 TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA T
437106 TTTAAGAAAT
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 52 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:438450 original size:25 final size:25
Alignment explanation
Indices: 438422--438476 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
438412 TATATATATA
* *
438422 ATATTTTTTATTTTTTATATTAATT
1 ATATTTATAATTTTTTATATTAATT
* **
438447 ATATATATAATTTTTTATATTTTTT
1 ATATTTATAATTTTTTATATTAATT
438472 ATATT
1 ATATT
438477 AATTATATAT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (25 bp):
ATATTTATAATTTTTTATATTAATT
Found at i:438451 original size:34 final size:35
Alignment explanation
Indices: 438412--438496 Score: 147
Period size: 34 Copynumber: 2.5 Consensus size: 35
438402 CGATTATATA
438412 TATATATATAATATTTTT-TATTTTTTATATTAAT
1 TATATATATAATATTTTTATATTTTTTATATTAAT
438446 TATATATATAAT-TTTTTATATTTTTTATATTAAT
1 TATATATATAATATTTTTATATTTTTTATATTAAT
*
438480 TATATATAAAATATTTT
1 TATATATATAATATTTT
438497 CGGGTTCGGG
Statistics
Matches: 48, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
33 5 0.10
34 39 0.81
35 4 0.08
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (35 bp):
TATATATATAATATTTTTATATTTTTTATATTAAT
Found at i:441269 original size:2 final size:2
Alignment explanation
Indices: 441262--441291 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
441252 CCTGCAAAGG
441262 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
441292 GCTGAATTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:442541 original size:60 final size:60
Alignment explanation
Indices: 442473--442636 Score: 154
Period size: 60 Copynumber: 2.7 Consensus size: 60
442463 TATAATTTTT
* ** *
442473 ATTTTAAATTGAT-CTCTAAAATTTTAAATATTTTAATTTC-TCCCATAAACTATGAC-TATC
1 ATTTTAAATTGATCCT-TAAAATTTTAAACATTCCAATTTCATCCC-CAAACTATGACAT-TC
* * *
442533 ATTTTAAATTAATCCTTAAACTTTTGAACATTCCAATTTCATCCCCAAACTATGACATTC
1 ATTTTAAATTGATCCTTAAAATTTTAAACATTCCAATTTCATCCCCAAACTATGACATTC
* ** ** *
442593 ATTATAAATTGGCCCCCAAACATTTTGAACATTCCAATTTCATC
1 ATTTTAAATTGATCCTTAAA-ATTTTAAACATTCCAATTTCATC
442637 ACTTACTATA
Statistics
Matches: 86, Mismatches: 14, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
60 57 0.66
61 29 0.34
ACGTcount: A:0.35, C:0.21, G:0.04, T:0.40
Consensus pattern (60 bp):
ATTTTAAATTGATCCTTAAAATTTTAAACATTCCAATTTCATCCCCAAACTATGACATTC
Found at i:442884 original size:31 final size:29
Alignment explanation
Indices: 442835--442926 Score: 87
Period size: 29 Copynumber: 3.1 Consensus size: 29
442825 AGGGATGAAA
* *
442835 TTAGAATGTTCAAAAGTTTAAGGACTAAT
1 TTAGAATATTCAATAGTTTAAGGACTAAT
* * * *
442864 TTAGACTGAGTGTC-ATAGTTTAGGGATTAAA
1 TTAGAAT-A-T-TCAATAGTTTAAGGACTAAT
*
442895 TTAGAATATTCAATAGTTTAAGGACCAAT
1 TTAGAATATTCAATAGTTTAAGGACTAAT
442924 TTA
1 TTA
442927 AAAATAGAAT
Statistics
Matches: 48, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
28 2 0.04
29 23 0.48
30 1 0.02
31 20 0.42
32 2 0.04
ACGTcount: A:0.38, C:0.08, G:0.18, T:0.36
Consensus pattern (29 bp):
TTAGAATATTCAATAGTTTAAGGACTAAT
Found at i:442925 original size:60 final size:60
Alignment explanation
Indices: 442766--442926 Score: 205
Period size: 60 Copynumber: 2.7 Consensus size: 60
442756 GATGAATTTG
* ** * *
442766 GGGATAAAATTGGAATATTCAAAAGTTTGGGGACTAATATAGAAAGAGGGTCCTAGTTTA
1 GGGATAAAATTAGAATATTCAAAAGTTTAAGGACTAATTTAGAAAGAGGGTCATAGTTTA
* * ** *
442826 GGGATGAAATTAGAATGTTCAAAAGTTTAAGGACTAATTTAGACTGAGTGTCATAGTTTA
1 GGGATAAAATTAGAATATTCAAAAGTTTAAGGACTAATTTAGAAAGAGGGTCATAGTTTA
* * *
442886 GGGATTAAATTAGAATATTCAATAGTTTAAGGACCAATTTA
1 GGGATAAAATTAGAATATTCAAAAGTTTAAGGACTAATTTA
442927 AAAATAGAAT
Statistics
Matches: 87, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
60 87 1.00
ACGTcount: A:0.39, C:0.07, G:0.23, T:0.32
Consensus pattern (60 bp):
GGGATAAAATTAGAATATTCAAAAGTTTAAGGACTAATTTAGAAAGAGGGTCATAGTTTA
Done.