Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 113035596
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: 113035596
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 271 characters in sequence are not A, C, G, or T
File 78 of 378
Found at i:20988750 original size:13 final size:14
Alignment explanation
Indices: 20988733--20988765 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
20988723 GCCCAATACC
*
20988733 TAAAATAAAATAAA
1 TAAAATAAAAGAAA
20988747 -AAAATAAAAGAAA
1 TAAAATAAAAGAAA
20988760 TAAAAT
1 TAAAAT
20988766 CCAAATATCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (14 bp):
TAAAATAAAAGAAA
Found at i:20988830 original size:9 final size:9
Alignment explanation
Indices: 20988818--20988845 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
20988808 CACTCTACTA
20988818 AATCACTCC
1 AATCACTCC
20988827 AATCACTCC
1 AATCACTCC
20988836 AATCACTCC
1 AATCACTCC
20988845 A
1 A
20988846 CTAAATCACC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.36, C:0.43, G:0.00, T:0.21
Consensus pattern (9 bp):
AATCACTCC
Found at i:20988851 original size:31 final size:31
Alignment explanation
Indices: 20988778--20988854 Score: 102
Period size: 31 Copynumber: 2.5 Consensus size: 31
20988768 AAATATCTTT
* *
20988778 ACTCCACTAAACCACTCCAACTACTCTAACC
1 ACTCCACTAAATCACTCCAACTACTCCAACC
* *
20988809 ACTCTACTAAATCACTCCAA-TCACTCCAATC
1 ACTCCACTAAATCACTCCAACT-ACTCCAACC
20988840 ACTCCACTAAATCAC
1 ACTCCACTAAATCAC
20988855 CTCAACCATC
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
30 1 0.03
31 39 0.98
ACGTcount: A:0.36, C:0.42, G:0.00, T:0.22
Consensus pattern (31 bp):
ACTCCACTAAATCACTCCAACTACTCCAACC
Found at i:20989308 original size:3 final size:3
Alignment explanation
Indices: 20989297--20989379 Score: 59
Period size: 3 Copynumber: 27.3 Consensus size: 3
20989287 TTTTATTTTT
* *
20989297 TTA TT- TTA TTA TTT TTA CTA TTA TT- TATA TTA TTA TTA TTA TT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA
20989340 TCTCA TGTA TATA TTA TTA TT- TATA TTA TTA TTA -TA TTA T
1 T-T-A T-TA T-TA TTA TTA TTA T-TA TTA TTA TTA TTA TTA T
20989380 ATATACCCTC
Statistics
Matches: 65, Mismatches: 6, Indels: 18
0.73 0.07 0.20
Matches are distributed among these distances:
2 7 0.11
3 49 0.75
4 7 0.11
5 2 0.03
ACGTcount: A:0.30, C:0.04, G:0.01, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:20989354 original size:21 final size:18
Alignment explanation
Indices: 20989301--20989383 Score: 87
Period size: 18 Copynumber: 4.4 Consensus size: 18
20989291 ATTTTTTTAT
* *
20989301 TTTATTATTTTTACTATTA
1 TTTA-TATTATTATTATTA
20989320 TTTATATTATTATTATTA
1 TTTATATTATTATTATTA
*
20989338 TTTCTCATGTATATATTATTA
1 TTTAT-AT-TAT-TATTATTA
20989359 TTTATATTATTATTA-TA
1 TTTATATTATTATTATTA
20989376 TTATATAT
1 TT-TATAT
20989384 ACCCTCTCCA
Statistics
Matches: 56, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
17 4 0.07
18 26 0.46
19 9 0.16
20 5 0.09
21 12 0.21
ACGTcount: A:0.31, C:0.04, G:0.01, T:0.64
Consensus pattern (18 bp):
TTTATATTATTATTATTA
Found at i:20989501 original size:12 final size:13
Alignment explanation
Indices: 20989454--20989506 Score: 53
Period size: 12 Copynumber: 4.5 Consensus size: 13
20989444 TTCTGACTAC
*
20989454 TATTATTATATA-
1 TATTATTATGTAT
20989466 TA-TA-TATGTAT
1 TATTATTATGTAT
*
20989477 TATTGTT-TGTAT
1 TATTATTATGTAT
20989489 TATTATTAT-TAT
1 TATTATTATGTAT
20989501 TATTAT
1 TATTAT
20989507 CACCCCTATT
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
10 5 0.15
11 4 0.12
12 23 0.68
13 2 0.06
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (13 bp):
TATTATTATGTAT
Found at i:20989746 original size:120 final size:123
Alignment explanation
Indices: 20989586--20989806 Score: 308
Period size: 120 Copynumber: 1.8 Consensus size: 123
20989576 TTTGCTATTA
* * *
20989586 TTATTATTATTATTATATATTAGTGTATATTTTATGTATAT-ATATATATTTA-TATATAGTATT
1 TTATTATTATTATTATATAGTAGTGTATATTTTATGTATATAATATATATATATTATATA-TATA
* *
20989649 GT-TTTTTA-TTACTTTAATTTAATATTTTTATTATATTTGCTTTTTGTATTTCTATAT
65 GTATTATTATTTACTTTAATTTAATATTATTATTATATTTGCTTTTTGTATTTCTATAT
* *
20989706 TTATTATTATTATTATATAGTAGTGTGTATTTCTAT-TATATACATATATATATATTTTATATAT
1 TTATTATTATTATTATATAGTAGTGTATATTT-TATGTATATA-ATATATATATATTATATATAT
*
20989770 AGTATTATTATTTACTTTACTTTAATATTATTATTAT
64 AGTATTATTATTTACTTTAATTTAATATTATTATTAT
20989807 TATCATTATA
Statistics
Matches: 87, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
120 35 0.40
121 3 0.03
122 15 0.17
123 10 0.11
124 24 0.28
ACGTcount: A:0.31, C:0.03, G:0.05, T:0.60
Consensus pattern (123 bp):
TTATTATTATTATTATATAGTAGTGTATATTTTATGTATATAATATATATATATTATATATATAG
TATTATTATTTACTTTAATTTAATATTATTATTATATTTGCTTTTTGTATTTCTATAT
Found at i:20992239 original size:19 final size:19
Alignment explanation
Indices: 20992225--20992263 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
20992215 CTTTTGCGTT
20992225 CATTCCATACATTTGCATTA
1 CATTCCA-ACATTTGCATTA
*
20992245 CATTGCAACATTTGCATTA
1 CATTCCAACATTTGCATTA
20992264 AACTTTCACT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (19 bp):
CATTCCAACATTTGCATTA
Found at i:20995958 original size:53 final size:52
Alignment explanation
Indices: 20995855--20995958 Score: 136
Period size: 53 Copynumber: 2.0 Consensus size: 52
20995845 GTCCAAATAA
* * * * *
20995855 ATTTTCTTCTTATTGCATTGCTATCTTTGATTAAATCATTCGTTTTGAGTTG
1 ATTTCCTTCTTATTGCATTGCAATCTTTGATTAAATCATCCATTTCGAGTTG
* *
20995907 ATTTCCTTCTTATTGCATTTGCAATCTTTGATTAATTTATCCATTTCGAGTT
1 ATTTCCTTCTTATTGCA-TTGCAATCTTTGATTAAATCATCCATTTCGAGTT
20995959 ATGCTCCTAA
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
52 16 0.36
53 28 0.64
ACGTcount: A:0.20, C:0.15, G:0.12, T:0.53
Consensus pattern (52 bp):
ATTTCCTTCTTATTGCATTGCAATCTTTGATTAAATCATCCATTTCGAGTTG
Found at i:20997347 original size:205 final size:203
Alignment explanation
Indices: 20996922--20997402 Score: 784
Period size: 205 Copynumber: 2.4 Consensus size: 203
20996912 CGGAGAGTAG
20996922 ATCGAAGACATAGCTGATTTAGG-TTTCACGTGTTTACGTTGAAGCAAATCTAAGATGATTTGGC
1 ATCGAAGACATAGCTGATTT-GGCTTTCACGTGTTTACGTTGAAGCAAATCTAAGATGATTTGGC
*
20996986 ATTTCTGTATTGTCAGAGAACAAATCGAAGTCTAGCATCTCACTTCGACGGAAGGTAGACACATA
65 ATCTCTGTATTGTCAGAGAACAAATCGAAGTCTAGCATCTCACTTCGACGGAAGGTAGACACATA
* * * * *
20997051 GCAGATCAACCTTCAGATGTTTATACTGAAGTAGATCCAAGATGGTTTGGCATCCTTCTGCTTAC
130 GCAGATCAACCTTCAAATGTTTATACTGAAGCAGATCCAAGATGGTTTGCCATCCTTATACTTAC
20997116 AAGGAGCAA
195 AAGGAGCAA
* *
20997125 ATCGAAGACATAGCTGATTTGGCTTTCACGTGCTTACGTTAAAGCAAATCTAAGATGATTTGGCA
1 ATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAGCAAATCTAAGATGATTTGGCA
* * * * *
20997190 TCTCTGTATTGTCAGAGAACAAATTGAAGTCTGGTATCTCCACTTCGATGGAGGGTAGACACATA
66 TCTCTGTATTGTCAGAGAACAAATCGAAGTCTAGCATCT-CACTTCGACGGAAGGTAGACACATA
20997255 GCAGATCCAACCTTCAAATGTTTATACTGAAGCAGATCCAAGATGGTTTGCCATCCTTATACTTA
130 GCAGAT-CAACCTTCAAATGTTTATACTGAAGCAGATCCAAGATGGTTTGCCATCCTTATACTTA
20997320 CAAGGAGCAA
194 CAAGGAGCAA
* * *
20997330 ATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAGCAAATCCAAGATAATTTGGCG
1 ATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAGCAAATCTAAGATGATTTGGCA
20997395 TCTCTGTA
66 TCTCTGTA
20997403 GCGGCGAAGA
Statistics
Matches: 257, Mismatches: 18, Indels: 4
0.92 0.06 0.01
Matches are distributed among these distances:
202 2 0.01
203 95 0.37
204 29 0.11
205 131 0.51
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.30
Consensus pattern (203 bp):
ATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAGCAAATCTAAGATGATTTGGCA
TCTCTGTATTGTCAGAGAACAAATCGAAGTCTAGCATCTCACTTCGACGGAAGGTAGACACATAG
CAGATCAACCTTCAAATGTTTATACTGAAGCAGATCCAAGATGGTTTGCCATCCTTATACTTACA
AGGAGCAA
Found at i:20997462 original size:44 final size:44
Alignment explanation
Indices: 20997414--20998787 Score: 1099
Period size: 44 Copynumber: 31.2 Consensus size: 44
20997404 CGGCGAAGAG
* *
20997414 CAGATCGAAGATTGCAGATTTGGCATCCCTGTGTTTATAGGGAA
1 CAGATCGAAGATAGCAGATTTGGCATCCCTGTGCTTATAGGGAA
* * * * * * *
20997458 CAGATTGAAGATAGTAGATCTGACATTCCTGTGCTTACAGTGAA
1 CAGATCGAAGATAGCAGATTTGGCATCCCTGTGCTTATAGGGAA
**
20997502 GCAGATCGAAGATTTCAGCA--TGGCATCCCTGTGCTTATAGGGAA
1 -CAGATCGAAGATAGCAG-ATTTGGCATCCCTGTGCTTATAGGGAA
* * *
20997546 CA-AGTTGAAAACAGCAGATTTGGCATCCCTGTGCTTATAGGGAA
1 CAGA-TCGAAGATAGCAGATTTGGCATCCCTGTGCTTATAGGGAA
* ** * * * * *
20997590 TAGATCGAAGATAATAGATCTGACATTCCTGTGCTTACAGTGAA
1 CAGATCGAAGATAGCAGATTTGGCATCCCTGTGCTTATAGGGAA
** *
20997634 GCAGATCGAAGATTTCAGCA--TGGTATCCCTGTGCTTATAGGGAA
1 -CAGATCGAAGATAGCAG-ATTTGGCATCCCTGTGCTTATAGGGAA
* * * *
20997678 CA-AGTTGAAAACAGCAGATTTGGCATCCCCGTGCTTATAGGGAA
1 CAGA-TCGAAGATAGCAGATTTGGCATCCCTGTGCTTATAGGGAA
* * * * * *
20997722 CAGATCAAAGATAGCAGATCTGACATTCCTGTGCTTACAGTGAA
1 CAGATCGAAGATAGCAGATTTGGCATCCCTGTGCTTATAGGGAA
* * ** * *
20997766 GCATATCAAAGATTTCAGCA--TGGTATCCCTGTGCTTATAAGGAA
1 -CAGATCGAAGATAGCAG-ATTTGGCATCCCTGTGCTTATAGGGAA
* *
20997810 CA-AGTTGAAAATAGCAGATTTGGCATCCCTGTGCTTATAGGGAA
1 CAGA-TCGAAGATAGCAGATTTGGCATCCCTGTGCTTATAGGGAA
* * *
20997854 CAGATCGAAGATAGCAGATCTGGCATCCCTGTGCTTACAGTGAA
1 CAGATCGAAGATAGCAGATTTGGCATCCCTGTGCTTATAGGGAA
* **
20997898 GTAGATCGAAGATTTCAGCA--TGGCATCCCTGTGCTTATAGGGAA
1 -CAGATCGAAGATAGCAG-ATTTGGCATCCCTGTGCTTATAGGGAA
* * *
20997942 CA-AGTTGAAAACAGCAGATTTGGCATCCCTGTGCTTATAGGGAA
1 CAGA-TCGAAGATAGCAGATTTGGCATCCCTGTGCTTATAGGGAA
* **
20997986 CAGAT-TACAGATTTCAGCA--TGGCATCCCTGTGCTTATAGGGAA
1 CAGATCGA-AGATAGCAG-ATTTGGCATCCCTGTGCTTATAGGGAA
* * * * *
20998029 CA-AGTTGAAAACAGTAGATTTGACATCCCTGTGCTTATAGGGAA
1 CAGA-TCGAAGATAGCAGATTTGGCATCCCTGTGCTTATAGGGAA
* ** * *
20998073 CAGATCGAAGATAGCAGATCTAACATTCCTGTGCTTA-CGGTGAA
1 CAGATCGAAGATAGCAGATTTGGCATCCCTGTGCTTATAGG-GAA
** *
20998117 GCAGATCGAAGATTTCAGCA--TGGTATCCCTGTGCTTATAGGGAA
1 -CAGATCGAAGATAGCAG-ATTTGGCATCCCTGTGCTTATAGGGAA
* * * *
20998161 CA-AGTTGAAAACAGTAGATTTGGCATCCCTGTGCTTATAGGGAA
1 CAGA-TCGAAGATAGCAGATTTGGCATCCCTGTGCTTATAGGGAA
* * * *
20998205 CAGATCGAAGATAGCAGATCTGACATTCCTGTGCTTA-CGGTGAA
1 CAGATCGAAGATAGCAGATTTGGCATCCCTGTGCTTATAGG-GAA
** *
20998249 GCAGATCGAAGATTTCAGCA--TGGCATCCATGTGCTTATAGGGAA
1 -CAGATCGAAGATAGCAG-ATTTGGCATCCCTGTGCTTATAGGGAA
* * * * *
20998293 CA-AGTTGAAAACAGTAGATTTGGCATTCCTGTGCTTATAGGGAA
1 CAGA-TCGAAGATAGCAGATTTGGCATCCCTGTGCTTATAGGGAA
* * * *
20998337 CAGATCGAAGATAGCAGATCTGACATTCCTGTGCTTA-CGGTGAAA
1 CAGATCGAAGATAGCAGATTTGGCATCCCTGTGCTTATAGG-G-AA
** *
20998382 CAGATCGAAGATTTCAGCA--TGACATCCCTGTGCTTATAGGGAA
1 CAGATCGAAGATAGCAG-ATTTGGCATCCCTGTGCTTATAGGGAA
* *
20998425 CA-AGTTGAAGATAACAGATTTGGCATCCCTGTGCTTATAGGGAA
1 CAGA-TCGAAGATAGCAGATTTGGCATCCCTGTGCTTATAGGGAA
* * * * * *
20998469 CAGATCGAAGATAGCAGATCTGACATTCCTGTGGTTACAGTGAA
1 CAGATCGAAGATAGCAGATTTGGCATCCCTGTGCTTATAGGGAA
*** *
20998513 GCAGATCGAAGATTTTAGCA--TGGTATCCCTGTGCTTATAGGGAA
1 -CAGATCGAAGATAGCAG-ATTTGGCATCCCTGTGCTTATAGGGAA
* * * *
20998557 CA-AGTTGAAAACAGCAGATTTGGCATCCATGTGCTTATAGGGAA
1 CAGA-TCGAAGATAGCAGATTTGGCATCCCTGTGCTTATAGGGAA
* * * * *
20998601 CAGATCGAAGATAGCAGATCTGACATTCCTGTGCTTACAGTGAA
1 CAGATCGAAGATAGCAGATTTGGCATCCCTGTGCTTATAGGGAA
** *
20998645 GCAGATCGAAGATTTCAGCA--TGGAATCCCTGTGCTTATAGGGAA
1 -CAGATCGAAGATAGCAG-ATTTGGCATCCCTGTGCTTATAGGGAA
* *
20998689 CA-AGTTGAAGATAGCAGATTTGGCATCCCTGTGTTTATAGGGAA
1 CAGA-TCGAAGATAGCAGATTTGGCATCCCTGTGCTTATAGGGAA
* * * * *
20998733 GA-AGTTGAAGACAGCAGATTTGGCATCCCTGTGTTTATGGGGAA
1 CAGA-TCGAAGATAGCAGATTTGGCATCCCTGTGCTTATAGGGAA
20998777 CAGATCGAAGA
1 CAGATCGAAGA
20998788 AGTAGATCAA
Statistics
Matches: 1050, Mismatches: 213, Indels: 134
0.75 0.15 0.10
Matches are distributed among these distances:
42 20 0.02
43 130 0.12
44 744 0.71
45 147 0.14
46 9 0.01
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.26
Consensus pattern (44 bp):
CAGATCGAAGATAGCAGATTTGGCATCCCTGTGCTTATAGGGAA
Found at i:20998124 original size:264 final size:261
Alignment explanation
Indices: 20997522--20998787 Score: 1359
Period size: 264 Copynumber: 4.8 Consensus size: 261
20997512 GATTTCAGCA
* * * * * * *
20997522 TGGCATCCCTGTGCTTATAGGGAACA-AGTTGAAAACAGCAGATTTGGCATCCCTGTGCTTATAG
1 TGGCATCCCTGTGCTTATAGGGAACAGA-TCGAAGATAGCAGATCTGACATTCCTGTGCTTA-CG
* * * * * * *
20997586 G-GAATAGATCGAAGATAAT-AG-ATCTGACATTCCTGTGCTTACAGTGAAGC-AGATCGAAGAT
64 GTGAACAGATCGAAGAT-TTCAGCA--TGGCATCCCTGTGCTTATAGGGAA-CAAG-TTGAAGAT
* * * *
20997647 TTCAGCA-TGGTATCCCTGTGCTTATAGGGAACAAGTTGAAAACAGCAGATTTGGCATCCCCGTG
124 ATCAG-ATTGGCATCCCTGTGCTTATAGGGAACAAGTTGAAGACAGCAGATTTGGCATCCCTGTG
* ** * * * * *
20997711 CTTATAGGGAACAGATCAAAGATAGCAG-ATCTGACATTCCTGTGCTTACAGTGAAGC-A-TATC
188 CTTATAGGGAACAGATCGAAGATTTCAGCA--TGGCATCCCTGTGCTTATAGGGAA-CAAGT-TG
**
20997773 AAAGA-TTTCAGCA--
249 AAA-ACAGT-AG-ATT
* * * * * * * *
20997786 TGGTATCCCTGTGCTTATAAGGAACA-AGTTGAAAATAGCAGATTTGGCATCCCTGTGCTTATAG
1 TGGCATCCCTGTGCTTATAGGGAACAGA-TCGAAGATAGCAGATCTGACATTCCTGTGCTTA-CG
** * * ** * *
20997850 G-GAACAGATCGAAGATAGCAG-ATCTGGCATCCCTGTGCTTACAGTGAAGTAGATCGAAGATTT
64 GTGAACAGATCGAAGATTTCAGCA--TGGCATCCCTGTGCTTATAGGGAACAAG-TTGAAGATAT
*
20997913 CAGCA-TGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAACAGCAGATTTGGCATCCCTGTGCT
126 CAG-ATTGGCATCCCTGTGCTTATAGGGAACAAGTTGAAGACAGCAGATTTGGCATCCCTGTGCT
*
20997977 TATAGGGAACAGAT-TACAGATTTCAGCATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAAC
190 TATAGGGAACAGATCGA-AGATTTCAGCATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAAC
20998041 AGTAGATT
254 AGTAGATT
* *
20998049 TGACATCCCTGTGCTTATAGGGAACAGATCGAAGATAGCAGATCTAACATTCCTGTGCTTACGGT
1 TGGCATCCCTGTGCTTATAGGGAACAGATCGAAGATAGCAGATCTGACATTCCTGTGCTTACGGT
* * *
20998114 GAAGCAGATCGAAGATTTCAGCATGGTATCCCTGTGCTTATAGGGAACAAGTTGAAAACAGT-AG
66 GAA-CAGATCGAAGATTTCAGCATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAGATA-TCAG
* * * * *
20998178 ATTTGGCATCCCTGTGCTTATAGGGAAC-AGATCGAAGATAGCAGATCTGACATTCCTGTGCTTA
129 A-TTGGCATCCCTGTGCTTATAGGGAACAAG-TTGAAGACAGCAGATTTGGCATCCCTGTGCTTA
* *
20998242 -CGGTGAAGCAGATCGAAGATTTCAGCATGGCATCCATGTGCTTATAGGGAACAAGTTGAAAACA
192 TAGG-GAA-CAGATCGAAGATTTCAGCATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAACA
20998306 GTAGATT
255 GTAGATT
*
20998313 TGGCATTCCTGTGCTTATAGGGAACAGATCGAAGATAGCAGATCTGACATTCCTGTGCTTACGGT
1 TGGCATCCCTGTGCTTATAGGGAACAGATCGAAGATAGCAGATCTGACATTCCTGTGCTTACGGT
* *
20998378 GAAACAGATCGAAGATTTCAGCATGACATCCCTGTGCTTATAGGGAACAAGTTGAAGATAACAGA
66 G-AACAGATCGAAGATTTCAGCATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAGATATCAGA
* * * * * * *
20998443 TTTGGCATCCCTGTGCTTATAGGGAAC-AGATCGAAGATAGCAGATCTGACATTCCTGTGGTTAC
130 -TTGGCATCCCTGTGCTTATAGGGAACAAG-TTGAAGACAGCAGATTTGGCATCCCTGTGCTTAT
* * * *
20998507 AGTGAAGCAGATCGAAGATTTTAGCATGGTATCCCTGTGCTTATAGGGAACAAGTTGAAAACAGC
193 AGGGAA-CAGATCGAAGATTTCAGCATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAACAGT
20998572 AGATT
257 AGATT
* *
20998577 TGGCATCCATGTGCTTATAGGGAACAGATCGAAGATAGCAGATCTGACATTCCTGTGCTTACAGT
1 TGGCATCCCTGTGCTTATAGGGAACAGATCGAAGATAGCAGATCTGACATTCCTGTGCTTACGGT
* *
20998642 GAAGCAGATCGAAGATTTCAGCATGGAATCCCTGTGCTTATAGGGAACAAGTTGAAGATAGCAGA
66 GAA-CAGATCGAAGATTTCAGCATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAGATATCAGA
* * * *
20998707 TTTGGCATCCCTGTGTTTATAGGGAAGAAGTTGAAGACAGCAGATTTGGCATCCCTGTGTTTATG
130 -TTGGCATCCCTGTGCTTATAGGGAACAAGTTGAAGACAGCAGATTTGGCATCCCTGTGCTTATA
20998772 GGGAACAGATCGAAGA
194 GGGAACAGATCGAAGA
20998788 AGTAGATCAA
Statistics
Matches: 895, Mismatches: 82, Indels: 51
0.87 0.08 0.05
Matches are distributed among these distances:
261 2 0.00
262 17 0.02
263 173 0.19
264 695 0.78
265 8 0.01
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.26
Consensus pattern (261 bp):
TGGCATCCCTGTGCTTATAGGGAACAGATCGAAGATAGCAGATCTGACATTCCTGTGCTTACGGT
GAACAGATCGAAGATTTCAGCATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAGATATCAGAT
TGGCATCCCTGTGCTTATAGGGAACAAGTTGAAGACAGCAGATTTGGCATCCCTGTGCTTATAGG
GAACAGATCGAAGATTTCAGCATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAACAGTAGAT
T
Found at i:20998161 original size:132 final size:132
Alignment explanation
Indices: 20997918--20998787 Score: 1302
Period size: 132 Copynumber: 6.6 Consensus size: 132
20997908 GATTTCAGCA
* * * * * * *
20997918 TGGCATCCCTGTGCTTATAGGGAACA-AGTTGAAAACAGCAGATTTGGCATCCCTGTGCTTATAG
1 TGGCATCCCTGTGCTTATAGGGAACAGA-TCGAAGATAGCAGATCTGACATTCCTGTGCTTA-CG
* *
20997982 G-GAA-CAGAT-TACAGATTTCAGCATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAACAGT
64 GTGAAGCAGATCGA-AGATTTCAGCATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAACAGC
20998044 AGATT
128 AGATT
* *
20998049 TGACATCCCTGTGCTTATAGGGAACAGATCGAAGATAGCAGATCTAACATTCCTGTGCTTACGGT
1 TGGCATCCCTGTGCTTATAGGGAACAGATCGAAGATAGCAGATCTGACATTCCTGTGCTTACGGT
* *
20998114 GAAGCAGATCGAAGATTTCAGCATGGTATCCCTGTGCTTATAGGGAACAAGTTGAAAACAGTAGA
66 GAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAACAGCAGA
20998179 TT
131 TT
20998181 TGGCATCCCTGTGCTTATAGGGAACAGATCGAAGATAGCAGATCTGACATTCCTGTGCTTACGGT
1 TGGCATCCCTGTGCTTATAGGGAACAGATCGAAGATAGCAGATCTGACATTCCTGTGCTTACGGT
* *
20998246 GAAGCAGATCGAAGATTTCAGCATGGCATCCATGTGCTTATAGGGAACAAGTTGAAAACAGTAGA
66 GAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAACAGCAGA
20998311 TT
131 TT
*
20998313 TGGCATTCCTGTGCTTATAGGGAACAGATCGAAGATAGCAGATCTGACATTCCTGTGCTTACGGT
1 TGGCATCCCTGTGCTTATAGGGAACAGATCGAAGATAGCAGATCTGACATTCCTGTGCTTACGGT
* * * * *
20998378 GAAACAGATCGAAGATTTCAGCATGACATCCCTGTGCTTATAGGGAACAAGTTGAAGATAACAGA
66 GAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAACAGCAGA
20998443 TT
131 TT
* *
20998445 TGGCATCCCTGTGCTTATAGGGAACAGATCGAAGATAGCAGATCTGACATTCCTGTGGTTACAGT
1 TGGCATCCCTGTGCTTATAGGGAACAGATCGAAGATAGCAGATCTGACATTCCTGTGCTTACGGT
* *
20998510 GAAGCAGATCGAAGATTTTAGCATGGTATCCCTGTGCTTATAGGGAACAAGTTGAAAACAGCAGA
66 GAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAACAGCAGA
20998575 TT
131 TT
* *
20998577 TGGCATCCATGTGCTTATAGGGAACAGATCGAAGATAGCAGATCTGACATTCCTGTGCTTACAGT
1 TGGCATCCCTGTGCTTATAGGGAACAGATCGAAGATAGCAGATCTGACATTCCTGTGCTTACGGT
* * *
20998642 GAAGCAGATCGAAGATTTCAGCATGGAATCCCTGTGCTTATAGGGAACAAGTTGAAGATAGCAGA
66 GAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAACAGCAGA
20998707 TT
131 TT
* * * * * * * * *
20998709 TGGCATCCCTGTGTTTATAGGGAAGA-AGTTGAAGACAGCAGATTTGGCATCCCTGTGTTTATGG
1 TGGCATCCCTGTGCTTATAGGGAACAGA-TCGAAGATAGCAGATCTGACATTCCTGTGCTTACGG
*
20998773 GGAA-CAGATCGAAGA
65 TGAAGCAGATCGAAGA
20998788 AGTAGATCAA
Statistics
Matches: 683, Mismatches: 51, Indels: 10
0.92 0.07 0.01
Matches are distributed among these distances:
130 2 0.00
131 66 0.10
132 614 0.90
133 1 0.00
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26
Consensus pattern (132 bp):
TGGCATCCCTGTGCTTATAGGGAACAGATCGAAGATAGCAGATCTGACATTCCTGTGCTTACGGT
GAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAACAGCAGA
TT
Found at i:20998417 original size:483 final size:483
Alignment explanation
Indices: 20997414--20998480 Score: 1735
Period size: 483 Copynumber: 2.2 Consensus size: 483
20997404 CGGCGAAGAG
* * *
20997414 CAGATCGAAGATTGCAG-ATTTGGCATCCCTGTGTTTATAGGGAAC-AGATTGAAGATAGTAGAT
1 CAGATCGAAGATTTCAGCA--TGGCATCCCTGTGCTTATAGGGAACAAG-TTGAAGATAGCAGAT
* * * * *
20997477 CTGACATTCCTGTGCTTACAGTGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGCTTATAG
63 TTGGCATCCCTGTGCTTATAGGGAA-CAGATCGAAGATTTCAGCATGGCATCCCTGTGCTTATAG
* * *
20997542 GGAACAAGTTGAAAACAGCAGATTTGGCATCCCTGTGCTTATAGGGAATAGATCGAAGATAATAG
127 GGAACAAGTTGAAAACAGCAGATTTGACATCCCTGTGCTTATAGGGAACAGATCGAAGATAACAG
*
20997607 ATCTGACATTCCTGTGCTTACAGTGAAGCAGATCGAAGATTTCAGCATGGTATCCCTGTGCTTAT
192 ATCTAACATTCCTGTGCTTACAGTGAAGCAGATCGAAGATTTCAGCATGGTATCCCTGTGCTTAT
20997672 AGGGAACAAGTTGAAAACAGCAGATTTGGCATCCCCGTGCTTATAGGGAACAGATCAAAGATAGC
257 AGGGAACAAGTTGAAAACAGCAGATTTGGCATCCCCGTGCTTATAGGGAACAGATCAAAGATAGC
* * *
20997737 AGATCTGACATTCCTGTGCTTACAGTGAAGCATATCAAAGATTTCAGCATGGTATCCCTGTGCTT
322 AGATCTGACATTCCTGTGCTTACAGTGAAGCAGATCAAAGATTTCAGCATGGCATCCATGTGCTT
*
20997802 ATAAGGAACAAGTTGAAAATAGCAGATTTGGCATCCCTGTGCTTATAGGGAACAGATCGAAGATA
387 ATAAGGAACAAGTTGAAAACAGCAGATTTGGCATCCCTGTGCTTATAGGGAACAGATCGAAGATA
* *
20997867 GCAGATCTGGCATCCCTGTGCTTACAGTGAAG
452 GCAGATCTGACATCCCTGTGCTTACAGTGAAA
* * *
20997899 TAGATCGAAGATTTCAGCATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAACAGCAGATTTG
1 CAGATCGAAGATTTCAGCATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAGATAGCAGATTTG
*
20997964 GCATCCCTGTGCTTATAGGGAACAGAT-TACAGATTTCAGCATGGCATCCCTGTGCTTATAGGGA
66 GCATCCCTGTGCTTATAGGGAACAGATCGA-AGATTTCAGCATGGCATCCCTGTGCTTATAGGGA
* *
20998028 ACAAGTTGAAAACAGTAGATTTGACATCCCTGTGCTTATAGGGAACAGATCGAAGATAGCAGATC
130 ACAAGTTGAAAACAGCAGATTTGACATCCCTGTGCTTATAGGGAACAGATCGAAGATAACAGATC
*
20998093 TAACATTCCTGTGCTTACGGTGAAGCAGATCGAAGATTTCAGCATGGTATCCCTGTGCTTATAGG
195 TAACATTCCTGTGCTTACAGTGAAGCAGATCGAAGATTTCAGCATGGTATCCCTGTGCTTATAGG
* * *
20998158 GAACAAGTTGAAAACAGTAGATTTGGCATCCCTGTGCTTATAGGGAACAGATCGAAGATAGCAGA
260 GAACAAGTTGAAAACAGCAGATTTGGCATCCCCGTGCTTATAGGGAACAGATCAAAGATAGCAGA
* *
20998223 TCTGACATTCCTGTGCTTACGGTGAAGCAGATCGAAGATTTCAGCATGGCATCCATGTGCTTATA
325 TCTGACATTCCTGTGCTTACAGTGAAGCAGATCAAAGATTTCAGCATGGCATCCATGTGCTTATA
* * *
20998288 GGGAACAAGTTGAAAACAGTAGATTTGGCATTCCTGTGCTTATAGGGAACAGATCGAAGATAGCA
390 AGGAACAAGTTGAAAACAGCAGATTTGGCATCCCTGTGCTTATAGGGAACAGATCGAAGATAGCA
* *
20998353 GATCTGACATTCCTGTGCTTACGGTGAAA
455 GATCTGACATCCCTGTGCTTACAGTGAAA
* *
20998382 CAGATCGAAGATTTCAGCATGACATCCCTGTGCTTATAGGGAACAAGTTGAAGATAACAGATTTG
1 CAGATCGAAGATTTCAGCATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAGATAGCAGATTTG
20998447 GCATCCCTGTGCTTATAGGGAACAGATCGAAGAT
66 GCATCCCTGTGCTTATAGGGAACAGATCGAAGAT
20998481 AGCAGATCTG
Statistics
Matches: 537, Mismatches: 41, Indels: 10
0.91 0.07 0.02
Matches are distributed among these distances:
482 1 0.00
483 461 0.86
484 57 0.11
485 17 0.03
486 1 0.00
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.26
Consensus pattern (483 bp):
CAGATCGAAGATTTCAGCATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAGATAGCAGATTTG
GCATCCCTGTGCTTATAGGGAACAGATCGAAGATTTCAGCATGGCATCCCTGTGCTTATAGGGAA
CAAGTTGAAAACAGCAGATTTGACATCCCTGTGCTTATAGGGAACAGATCGAAGATAACAGATCT
AACATTCCTGTGCTTACAGTGAAGCAGATCGAAGATTTCAGCATGGTATCCCTGTGCTTATAGGG
AACAAGTTGAAAACAGCAGATTTGGCATCCCCGTGCTTATAGGGAACAGATCAAAGATAGCAGAT
CTGACATTCCTGTGCTTACAGTGAAGCAGATCAAAGATTTCAGCATGGCATCCATGTGCTTATAA
GGAACAAGTTGAAAACAGCAGATTTGGCATCCCTGTGCTTATAGGGAACAGATCGAAGATAGCAG
ATCTGACATCCCTGTGCTTACAGTGAAA
Found at i:20998599 original size:615 final size:615
Alignment explanation
Indices: 20997429--20998605 Score: 2048
Period size: 615 Copynumber: 1.9 Consensus size: 615
20997419 CGAAGATTGC
* * * * *
20997429 AGATTTGGCATCCCTGTGTTTATAGGGAACAGATTGAAGATAGTAGATCTGACATTCCTGTGCTT
1 AGATTTGACATCCCTGTGCTTATAGGGAACAGATCGAAGATAGCAGATCTAACATTCCTGTGCTT
20997494 ACAGTGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAACA
66 ACAGTGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAACA
* *
20997559 GCAGATTTGGCATCCCTGTGCTTATAGGGAATAGATCGAAGATAATAGATCTGACATTCCTGTGC
131 GCAGATTTGGCATCCCTGTGCTTATAGGGAACAGATCGAAGATAACAGATCTGACATTCCTGTGC
* *
20997624 TTACAGTGAAGCAGATCGAAGATTTCAGCATGGTATCCCTGTGCTTATAGGGAACAAGTTGAAAA
196 TTACAGTGAAGCAGATCGAAGATTTCAGCATGGCATCCATGTGCTTATAGGGAACAAGTTGAAAA
20997689 CAGCAGATTTGGCATCCCCGTGCTTATAGGGAACAGATCAAAGATAGCAGATCTGACATTCCTGT
261 CAGCAGATTTGGCATCCCCGTGCTTATAGGGAACAGATCAAAGATAGCAGATCTGACATTCCTGT
* * **
20997754 GCTTACAGTGAAGCATATCAAAGATTTCAGCATGGTATCCCTGTGCTTATAAGGAACAAGTTGAA
326 GCTTACAGTGAAACAGATCAAAGATTTCAGCATGACATCCCTGTGCTTATAAGGAACAAGTTGAA
* *
20997819 AATAGCAGATTTGGCATCCCTGTGCTTATAGGGAACAGATCGAAGATAGCAGATCTGGCATCCCT
391 AATAACAGATTTGGCATCCCTGTGCTTATAGGGAACAGATCGAAGATAGCAGATCTGACATCCCT
*
20997884 GTGCTTACAGTGAAGTAGATCGAAGATTTCAGCATGGCATCCCTGTGCTTATAGGGAACAAGTTG
456 GTGCTTACAGTGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGCTTATAGGGAACAAGTTG
*
20997949 AAAACAGCAGATTTGGCATCCCTGTGCTTATAGGGAACAGATTACAGATTTCAGCATGGCATCCC
521 AAAACAGCAGATTTGGCATCCATGTGCTTATAGGGAACAGATTACAGATTTCAGCATGGCATCCC
20998014 TGTGCTTATAGGGAACAAGTTGAAAACAGT
586 TGTGCTTATAGGGAACAAGTTGAAAACAGT
20998044 AGATTTGACATCCCTGTGCTTATAGGGAACAGATCGAAGATAGCAGATCTAACATTCCTGTGCTT
1 AGATTTGACATCCCTGTGCTTATAGGGAACAGATCGAAGATAGCAGATCTAACATTCCTGTGCTT
* *
20998109 ACGGTGAAGCAGATCGAAGATTTCAGCATGGTATCCCTGTGCTTATAGGGAACAAGTTGAAAACA
66 ACAGTGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAACA
* *
20998174 GTAGATTTGGCATCCCTGTGCTTATAGGGAACAGATCGAAGATAGCAGATCTGACATTCCTGTGC
131 GCAGATTTGGCATCCCTGTGCTTATAGGGAACAGATCGAAGATAACAGATCTGACATTCCTGTGC
*
20998239 TTACGGTGAAGCAGATCGAAGATTTCAGCATGGCATCCATGTGCTTATAGGGAACAAGTTGAAAA
196 TTACAGTGAAGCAGATCGAAGATTTCAGCATGGCATCCATGTGCTTATAGGGAACAAGTTGAAAA
* * * *
20998304 CAGTAGATTTGGCATTCCTGTGCTTATAGGGAACAGATCGAAGATAGCAGATCTGACATTCCTGT
261 CAGCAGATTTGGCATCCCCGTGCTTATAGGGAACAGATCAAAGATAGCAGATCTGACATTCCTGT
* * *
20998369 GCTTACGGTGAAACAGATCGAAGATTTCAGCATGACATCCCTGTGCTTATAGGGAACAAGTTGAA
326 GCTTACAGTGAAACAGATCAAAGATTTCAGCATGACATCCCTGTGCTTATAAGGAACAAGTTGAA
* *
20998434 GATAACAGATTTGGCATCCCTGTGCTTATAGGGAACAGATCGAAGATAGCAGATCTGACATTCCT
391 AATAACAGATTTGGCATCCCTGTGCTTATAGGGAACAGATCGAAGATAGCAGATCTGACATCCCT
* * *
20998499 GTGGTTACAGTGAAGCAGATCGAAGATTTTAGCATGGTATCCCTGTGCTTATAGGGAACAAGTTG
456 GTGCTTACAGTGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGCTTATAGGGAACAAGTTG
20998564 AAAACAGCAGATTTGGCATCCATGTGCTTATAGGGAACAGAT
521 AAAACAGCAGATTTGGCATCCATGTGCTTATAGGGAACAGAT
20998606 CGAAGATAGC
Statistics
Matches: 528, Mismatches: 34, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
615 528 1.00
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.27
Consensus pattern (615 bp):
AGATTTGACATCCCTGTGCTTATAGGGAACAGATCGAAGATAGCAGATCTAACATTCCTGTGCTT
ACAGTGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAACA
GCAGATTTGGCATCCCTGTGCTTATAGGGAACAGATCGAAGATAACAGATCTGACATTCCTGTGC
TTACAGTGAAGCAGATCGAAGATTTCAGCATGGCATCCATGTGCTTATAGGGAACAAGTTGAAAA
CAGCAGATTTGGCATCCCCGTGCTTATAGGGAACAGATCAAAGATAGCAGATCTGACATTCCTGT
GCTTACAGTGAAACAGATCAAAGATTTCAGCATGACATCCCTGTGCTTATAAGGAACAAGTTGAA
AATAACAGATTTGGCATCCCTGTGCTTATAGGGAACAGATCGAAGATAGCAGATCTGACATCCCT
GTGCTTACAGTGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGCTTATAGGGAACAAGTTG
AAAACAGCAGATTTGGCATCCATGTGCTTATAGGGAACAGATTACAGATTTCAGCATGGCATCCC
TGTGCTTATAGGGAACAAGTTGAAAACAGT
Found at i:20999078 original size:22 final size:22
Alignment explanation
Indices: 20999053--20999196 Score: 96
Period size: 22 Copynumber: 6.4 Consensus size: 22
20999043 AAATATCTTT
*
20999053 ACTCCACTAAACCATTCCAACC
1 ACTCCACTAAACCACTCCAACC
20999075 ACTCCACTAAACCACTCCAACC
1 ACTCCACTAAACCACTCCAACC
* ** *
20999097 ACTCCAACCAGTCCACT-AAACC
1 ACTCC-ACTAAACCACTCCAACC
* * *
20999119 ACTACACTAACCCACTCC-ACT
1 ACTCCACTAAACCACTCCAACC
** *
20999140 AAACCACCCT-AACCACCCTACTAAACC
1 ACTCCA--CTAAACCA--CT-C-CAACC
*
20999167 ACTCCACTAAACCACCCCAACC
1 ACTCCACTAAACCACTCCAACC
20999189 ACTCCACT
1 ACTCCACT
20999197 TGCCTACAAA
Statistics
Matches: 91, Mismatches: 21, Indels: 20
0.69 0.16 0.15
Matches are distributed among these distances:
21 13 0.14
22 50 0.55
23 11 0.12
24 3 0.03
25 3 0.03
26 5 0.05
27 6 0.07
ACGTcount: A:0.36, C:0.49, G:0.01, T:0.15
Consensus pattern (22 bp):
ACTCCACTAAACCACTCCAACC
Found at i:20999087 original size:13 final size:13
Alignment explanation
Indices: 20999071--20999196 Score: 99
Period size: 13 Copynumber: 9.9 Consensus size: 13
20999061 AAACCATTCC
20999071 AACCACTCCACTA
1 AACCACTCCACTA
*
20999084 AACCACTCCAACCACTCC
1 AACCACT----CCACT-A
*
20999102 AACCAGTCCACTA
1 AACCACTCCACTA
*
20999115 AACCACTACACTA
1 AACCACTCCACTA
*
20999128 ACCCACTCCACTA
1 AACCACTCCACTA
20999141 AACCA--CC-CT-
1 AACCACTCCACTA
20999150 AACCAC-CCTACTA
1 AACCACTCC-ACTA
20999163 AACCACTCCACTA
1 AACCACTCCACTA
20999176 AACCAC-CC-C--
1 AACCACTCCACTA
20999185 AACCACTCCACT
1 AACCACTCCACT
20999197 TGCCTACAAA
Statistics
Matches: 92, Mismatches: 8, Indels: 27
0.72 0.06 0.21
Matches are distributed among these distances:
9 11 0.12
10 6 0.07
11 4 0.04
12 4 0.04
13 49 0.53
14 7 0.08
17 5 0.05
18 6 0.07
ACGTcount: A:0.37, C:0.49, G:0.01, T:0.13
Consensus pattern (13 bp):
AACCACTCCACTA
Found at i:20999154 original size:35 final size:35
Alignment explanation
Indices: 20999115--20999196 Score: 121
Period size: 35 Copynumber: 2.3 Consensus size: 35
20999105 CAGTCCACTA
* * *
20999115 AACCACTACACTAACCCACTCCACTAAACCACCCT
1 AACCACTCCACTAAACCACTCCACTAAACCACCCC
20999150 AACCAC-CCTACTAAACCACTCCACTAAACCACCCC
1 AACCACTCC-ACTAAACCACTCCACTAAACCACCCC
20999185 AACCACTCCACT
1 AACCACTCCACT
20999197 TGCCTACAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
34 1 0.02
35 39 0.93
36 2 0.05
ACGTcount: A:0.37, C:0.50, G:0.00, T:0.13
Consensus pattern (35 bp):
AACCACTCCACTAAACCACTCCACTAAACCACCCC
Found at i:21000406 original size:22 final size:21
Alignment explanation
Indices: 21000385--21000483 Score: 71
Period size: 22 Copynumber: 4.7 Consensus size: 21
21000375 ATCTTTACTC
21000385 CACTAAACCACTCCAACCACT
1 CACTAAACCACTCCAACCACT
* *
21000406 --CT-AACCACTCC-ACTAAAT
1 CACTAAACCACTCCAAC-CACT
* *
21000424 CACTCCAATCACTCCAACCACTT
1 CACT-AAACCACTCCAACCAC-T
* *
21000447 CACTAAACCACCCCAACCACC
1 CACTAAACCACTCCAACCACT
*
21000468 CTACTAAACTACTCCA
1 C-ACTAAACCACTCCA
21000484 CTAAACCACC
Statistics
Matches: 59, Mismatches: 11, Indels: 15
0.69 0.13 0.18
Matches are distributed among these distances:
17 2 0.03
18 11 0.19
19 2 0.03
20 2 0.03
21 1 0.02
22 34 0.58
23 7 0.12
ACGTcount: A:0.36, C:0.46, G:0.00, T:0.17
Consensus pattern (21 bp):
CACTAAACCACTCCAACCACT
Found at i:21000416 original size:31 final size:31
Alignment explanation
Indices: 21000381--21000501 Score: 145
Period size: 31 Copynumber: 3.8 Consensus size: 31
21000371 AAATATCTTT
21000381 ACTCCACTAAACCACTCCAACCACTCTAACC
1 ACTCCACTAAACCACTCCAACCACTCTAACC
* * *
21000412 ACTCCACTAAATCACTCCAATCACTCCAACC
1 ACTCCACTAAACCACTCCAACCACTCTAACC
* * *
21000443 ACTTCACTAAACCACCCCAACCACCCTACTAAACT
1 ACTCCACTAAACCACTCCAACCA--CT-CT-AACC
21000478 ACTCCACTAAACCAC-CCAACCACT
1 ACTCCACTAAACCACTCCAACCACT
21000502 TCACTTGCCT
Statistics
Matches: 76, Mismatches: 10, Indels: 7
0.82 0.11 0.08
Matches are distributed among these distances:
31 47 0.62
32 2 0.03
33 2 0.03
34 8 0.11
35 17 0.22
ACGTcount: A:0.36, C:0.47, G:0.00, T:0.17
Consensus pattern (31 bp):
ACTCCACTAAACCACTCCAACCACTCTAACC
Found at i:21000911 original size:3 final size:3
Alignment explanation
Indices: 21000892--21000982 Score: 66
Period size: 3 Copynumber: 30.3 Consensus size: 3
21000882 GAGCTTTGTT
* *
21000892 TTA TT- TTA TTA TT- TTA TTA TTT TTA CTA TTA TT- TATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA
* *
21000935 TTA TTA TGTC TCA TGTA TATA TTA TTA TT- TATA TTA TTA TTA -TA TTA
1 TTA TTA T-TA TTA T-TA T-TA TTA TTA TTA T-TA TTA TTA TTA TTA TTA
21000982 T
1 T
21000983 ATATGCCCTC
Statistics
Matches: 70, Mismatches: 9, Indels: 18
0.72 0.09 0.19
Matches are distributed among these distances:
2 8 0.11
3 53 0.76
4 9 0.13
ACGTcount: A:0.30, C:0.03, G:0.02, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:21001104 original size:12 final size:13
Alignment explanation
Indices: 21001057--21001109 Score: 53
Period size: 12 Copynumber: 4.5 Consensus size: 13
21001047 TTCTGACTAC
*
21001057 TATTATTATATA-
1 TATTATTATGTAT
21001069 TA-TA-TATGTAT
1 TATTATTATGTAT
*
21001080 TATTGTT-TGTAT
1 TATTATTATGTAT
21001092 TATTATTAT-TAT
1 TATTATTATGTAT
21001104 TATTAT
1 TATTAT
21001110 CACCCCTATT
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
10 5 0.15
11 4 0.12
12 23 0.68
13 2 0.06
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (13 bp):
TATTATTATGTAT
Found at i:21002385 original size:35 final size:35
Alignment explanation
Indices: 21002346--21002415 Score: 113
Period size: 35 Copynumber: 2.0 Consensus size: 35
21002336 TGCCTCGAAA
* * *
21002346 CCTTTTTAGTTGAACTCCTTATCATTAATATTTTG
1 CCTTTTTAATTGAACACCTTATCATGAATATTTTG
21002381 CCTTTTTAATTGAACACCTTATCATGAATATTTTG
1 CCTTTTTAATTGAACACCTTATCATGAATATTTTG
21002416 GAATTTATCT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.26, C:0.17, G:0.09, T:0.49
Consensus pattern (35 bp):
CCTTTTTAATTGAACACCTTATCATGAATATTTTG
Found at i:21004494 original size:20 final size:20
Alignment explanation
Indices: 21004471--21004517 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
21004461 GTATAATTAA
21004471 TATGTGTTTAATTTAATATG
1 TATGTGTTTAATTTAATATG
21004491 TATGTGTTTAATTTAATATG
1 TATGTGTTTAATTTAATATG
21004511 TATGTGT
1 TATGTGT
21004518 GGTAAGTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.28, C:0.00, G:0.17, T:0.55
Consensus pattern (20 bp):
TATGTGTTTAATTTAATATG
Found at i:21004954 original size:45 final size:45
Alignment explanation
Indices: 21004904--21005016 Score: 181
Period size: 45 Copynumber: 2.5 Consensus size: 45
21004894 CGACTACTGT
* *
21004904 TACTGTTGCCGTTACTGTTACTGATTCGACACTTTGTGTGTCGAA
1 TACTGTTACCGTTACTGTTACTGATTCAACACTTTGTGTGTCGAA
* *
21004949 TACTGTTACCGTTACTGTTACAGATTCAACACTTTGTGTGTTGAA
1 TACTGTTACCGTTACTGTTACTGATTCAACACTTTGTGTGTCGAA
*
21004994 TACTGTTACTGTTACTGTTACTG
1 TACTGTTACCGTTACTGTTACTG
21005017 CTACCGTTAC
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 62 1.00
ACGTcount: A:0.20, C:0.19, G:0.19, T:0.42
Consensus pattern (45 bp):
TACTGTTACCGTTACTGTTACTGATTCAACACTTTGTGTGTCGAA
Found at i:21005005 original size:6 final size:6
Alignment explanation
Indices: 21004994--21005037 Score: 61
Period size: 6 Copynumber: 7.2 Consensus size: 6
21004984 GTGTGTTGAA
* *
21004994 TACTGT TACTGT TACTGT TACTGC TACCGT TACTGAT TACTGT T
1 TACTGT TACTGT TACTGT TACTGT TACTGT TACTG-T TACTGT T
21005038 TAGGTACTGT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
6 27 0.82
7 6 0.18
ACGTcount: A:0.18, C:0.20, G:0.16, T:0.45
Consensus pattern (6 bp):
TACTGT
Found at i:21007110 original size:12 final size:13
Alignment explanation
Indices: 21007082--21007114 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
21007072 TTATTTCTTT
21007082 TTCTCCATCTACC
1 TTCTCCATCTACC
*
21007095 TTCTCC-TCTTCC
1 TTCTCCATCTACC
21007107 TTCTCCAT
1 TTCTCCAT
21007115 AGCCGAACCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.09, C:0.45, G:0.00, T:0.45
Consensus pattern (13 bp):
TTCTCCATCTACC
Found at i:21008212 original size:28 final size:28
Alignment explanation
Indices: 21008180--21008244 Score: 112
Period size: 28 Copynumber: 2.3 Consensus size: 28
21008170 ATTTACTAGA
*
21008180 ATACCCCTATGTATGCAAAATTACCATT
1 ATACCCCTATGTATGCAAAATGACCATT
*
21008208 ATACCCCTATGTATGCAAAATGACCTTT
1 ATACCCCTATGTATGCAAAATGACCATT
21008236 ATACCCCTA
1 ATACCCCTA
21008245 GGGTTAATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.34, C:0.28, G:0.08, T:0.31
Consensus pattern (28 bp):
ATACCCCTATGTATGCAAAATGACCATT
Found at i:21008408 original size:27 final size:28
Alignment explanation
Indices: 21008350--21008439 Score: 112
Period size: 27 Copynumber: 3.2 Consensus size: 28
21008340 AGGAAGCGTC
*
21008350 CTGGTGGCTA-TGCCACAAATTATCTGTT
1 CTGGTGGC-ACTGCCACAAAATATCTGTT
* **
21008378 CTGGTGGCCCTGCCAC-GTATATCTGTT
1 CTGGTGGCACTGCCACAAAATATCTGTT
21008405 CTGGTGGCACTGCCACAAAATATCTGTAT
1 CTGGTGGCACTGCCACAAAATATCTGT-T
21008434 CTGGTG
1 CTGGTG
21008440 ACTCTGTCAC
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
27 23 0.44
28 22 0.42
29 7 0.13
ACGTcount: A:0.19, C:0.24, G:0.24, T:0.32
Consensus pattern (28 bp):
CTGGTGGCACTGCCACAAAATATCTGTT
Found at i:21008450 original size:29 final size:28
Alignment explanation
Indices: 21008360--21008450 Score: 94
Period size: 27 Copynumber: 3.2 Consensus size: 28
21008350 CTGGTGGCTA
* * *
21008360 TGCCACAAATTATCTGTTCTGGTGGCCC
1 TGCCACAAAATATCTGTTCTGGTGACAC
** *
21008388 TGCCAC-GTATATCTGTTCTGGTGGCAC
1 TGCCACAAAATATCTGTTCTGGTGACAC
*
21008415 TGCCACAAAATATCTGTATCTGGTGACTC
1 TGCCACAAAATATCTGT-TCTGGTGACAC
*
21008444 TGTCACA
1 TGCCACA
21008451 TTTTCTGTAT
Statistics
Matches: 52, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
27 23 0.44
28 14 0.27
29 15 0.29
ACGTcount: A:0.21, C:0.26, G:0.21, T:0.32
Consensus pattern (28 bp):
TGCCACAAAATATCTGTTCTGGTGACAC
Found at i:21008458 original size:55 final size:56
Alignment explanation
Indices: 21008350--21008464 Score: 137
Period size: 55 Copynumber: 2.1 Consensus size: 56
21008340 AGGAAGCGTC
* * *
21008350 CTGGTGGCTATGCCACAAATTATCTGTTCTGGTGGCCCTGCCACGTATATCTGT-T
1 CTGGTGGCTATGCCACAAAATATCTGTTCTGGTGACCCTGCCACATATATCTGTAT
* * *
21008405 CTGGTGGC-ACTGCCACAAAATATCTGTATCTGGTGACTCTGTCACAT-TTTCTGTAT
1 CTGGTGGCTA-TGCCACAAAATATCTGT-TCTGGTGACCCTGCCACATATATCTGTAT
21008461 CTGG
1 CTGG
21008465 CAGCCATGCT
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
54 1 0.02
55 30 0.59
56 20 0.39
ACGTcount: A:0.18, C:0.24, G:0.23, T:0.35
Consensus pattern (56 bp):
CTGGTGGCTATGCCACAAAATATCTGTTCTGGTGACCCTGCCACATATATCTGTAT
Found at i:21016035 original size:28 final size:28
Alignment explanation
Indices: 21016003--21016095 Score: 150
Period size: 28 Copynumber: 3.3 Consensus size: 28
21015993 ATTTACTAGA
21016003 ATACCCCTATGTATGCAAAATTACCATT
1 ATACCCCTATGTATGCAAAATTACCATT
*
21016031 ATACCCCTATGTATACAAAATTACCATT
1 ATACCCCTATGTATGCAAAATTACCATT
* * *
21016059 ATACCCTTATGTATGCAAAATGACCTTT
1 ATACCCCTATGTATGCAAAATTACCATT
21016087 ATACCCCTA
1 ATACCCCTA
21016096 GGGTTAATTT
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 59 1.00
ACGTcount: A:0.35, C:0.26, G:0.06, T:0.32
Consensus pattern (28 bp):
ATACCCCTATGTATGCAAAATTACCATT
Found at i:21016301 original size:29 final size:28
Alignment explanation
Indices: 21016211--21016301 Score: 85
Period size: 27 Copynumber: 3.2 Consensus size: 28
21016201 CTGGTGGCTA
* * *
21016211 TGCCACAAATTATCTGTTCTGGTGGCCC
1 TGCCACAAAATATCTGTTCTGGTGACAC
* ** *
21016239 TGCTAC-GTATATCTGTTCTGGTGGCAC
1 TGCCACAAAATATCTGTTCTGGTGACAC
*
21016266 TGCCACAAAATATCTGTATCTGGTGACTC
1 TGCCACAAAATATCTGT-TCTGGTGACAC
*
21016295 TGTCACA
1 TGCCACA
21016302 TTTTCTGTAT
Statistics
Matches: 50, Mismatches: 11, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
27 22 0.44
28 13 0.26
29 15 0.30
ACGTcount: A:0.21, C:0.25, G:0.21, T:0.33
Consensus pattern (28 bp):
TGCCACAAAATATCTGTTCTGGTGACAC
Found at i:21016309 original size:55 final size:56
Alignment explanation
Indices: 21016201--21016315 Score: 130
Period size: 55 Copynumber: 2.1 Consensus size: 56
21016191 AGGAAGCGTC
* * *
21016201 CTGGTGGCTATGCCACAAATTATCTGTTCTGGTGGCCCTGCTACGTATATCTGT-T
1 CTGGTGGCTATGCCACAAAATATCTGTTCTGGTGACCCTGCTACATATATCTGTAT
* *
21016256 CTGGTGGC-ACTGCCACAAAATATCTGTATCTGGTGACTCTG-TCACAT-TTTCTGTAT
1 CTGGTGGCTA-TGCCACAAAATATCTGT-TCTGGTGACCCTGCT-ACATATATCTGTAT
21016312 CTGG
1 CTGG
21016316 AAGCCATGCT
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
54 1 0.02
55 31 0.61
56 19 0.37
ACGTcount: A:0.18, C:0.23, G:0.23, T:0.36
Consensus pattern (56 bp):
CTGGTGGCTATGCCACAAAATATCTGTTCTGGTGACCCTGCTACATATATCTGTAT
Found at i:21019699 original size:32 final size:33
Alignment explanation
Indices: 21019630--21019710 Score: 92
Period size: 32 Copynumber: 2.4 Consensus size: 33
21019620 ACATTGTCAG
*
21019630 TCCAACCAAACACACTAGATGCTCACACGAGCCAA
1 TCCAACC-AACACACTA-ATGCTCACAAGAGCCAA
** * *
21019665 TCCCTCCAACACACT-ATGCTCATAAGAGCTAA
1 TCCAACCAACACACTAATGCTCACAAGAGCCAA
21019697 TCCAACCAACACAC
1 TCCAACCAACACAC
21019711 CAAACAGAGT
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
32 26 0.67
34 8 0.21
35 5 0.13
ACGTcount: A:0.38, C:0.38, G:0.09, T:0.15
Consensus pattern (33 bp):
TCCAACCAACACACTAATGCTCACAAGAGCCAA
Found at i:21023559 original size:22 final size:24
Alignment explanation
Indices: 21023534--21023577 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
21023524 TTTTAAATTT
21023534 AAAT-TTAATTATAAAA-ATATAG
1 AAATATTAATTATAAAACATATAG
*
21023556 AAATATTAGTTATAAAACATAT
1 AAATATTAATTATAAAACATAT
21023578 TTTTATTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 4 0.21
23 11 0.58
24 4 0.21
ACGTcount: A:0.57, C:0.02, G:0.05, T:0.36
Consensus pattern (24 bp):
AAATATTAATTATAAAACATATAG
Found at i:21038394 original size:9 final size:9
Alignment explanation
Indices: 21038367--21038403 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
21038357 TGAGTTTTTG
21038367 AATTCGAAT
1 AATTCGAAT
* *
21038376 AACTCAAAT
1 AATTCGAAT
21038385 AATTCGAAT
1 AATTCGAAT
21038394 AATTCGAAT
1 AATTCGAAT
21038403 A
1 A
21038404 TTAAACTATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.49, C:0.14, G:0.08, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:21039766 original size:18 final size:18
Alignment explanation
Indices: 21039743--21039779 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
21039733 TATAGTTTGA
* *
21039743 TATTCGGTTTATTTGAAT
1 TATTCGGGTTATTCGAAT
21039761 TATTCGGGTTATTCGAAT
1 TATTCGGGTTATTCGAAT
21039779 T
1 T
21039780 CAAAAACCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.22, C:0.08, G:0.19, T:0.51
Consensus pattern (18 bp):
TATTCGGGTTATTCGAAT
Found at i:21042837 original size:14 final size:14
Alignment explanation
Indices: 21042810--21042845 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
21042800 ATACATAAAA
*
21042810 TAGTCATTTCATATT
1 TAGT-ATTTAATATT
21042825 TAGTATTTAATATT
1 TAGTATTTAATATT
21042839 TAGTATT
1 TAGTATT
21042846 ATGTATATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 16 0.80
15 4 0.20
ACGTcount: A:0.31, C:0.06, G:0.08, T:0.56
Consensus pattern (14 bp):
TAGTATTTAATATT
Found at i:21043754 original size:21 final size:21
Alignment explanation
Indices: 21043730--21043772 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
21043720 AACCAGAGCT
* *
21043730 ACAACTCCTGCCGGAGCAACC
1 ACAACCCCCGCCGGAGCAACC
*
21043751 ACAACCCCCGCTGGAGCAACC
1 ACAACCCCCGCCGGAGCAACC
21043772 A
1 A
21043773 TTGAGGAATC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.44, G:0.19, T:0.07
Consensus pattern (21 bp):
ACAACCCCCGCCGGAGCAACC
Found at i:21047237 original size:126 final size:126
Alignment explanation
Indices: 21047009--21047259 Score: 376
Period size: 126 Copynumber: 2.0 Consensus size: 126
21046999 GGCCGATCAT
* * * * *
21047009 GAATTATTGTAGAAAAAGAGCGTCTACGTGAGAGTTTTTTTCAGAAATTTTGCTGACAATGCATC
1 GAATTACTGTAGAAAAACAGCGTCCACATGAGAGCTTTTTTCAGAAATTTTGCTGACAATGCATC
* * *
21047074 CTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACGTCTTCTCAAAATTATTTTTTCAA
66 CTGCTTGAAGCGTTTTTGACACTATTTATTCAAAAACGTCTTATCAAAATTATTTTTTCAA
* * * *
21047135 GAATTACTGTAGAAAAACAGCGTCCACATGGGAGCTTTTTTCTGTAATTTTGCTGACAGTGCATC
1 GAATTACTGTAGAAAAACAGCGTCCACATGAGAGCTTTTTTCAGAAATTTTGCTGACAATGCATC
* *
21047200 TTGCTTGAAGCGTTTTTGACACTATTTATTCAAAAACGTTTTATCAAAATTATTTTTTCA
66 CTGCTTGAAGCGTTTTTGACACTATTTATTCAAAAACGTCTTATCAAAATTATTTTTTCA
21047260 CGGTACAAAA
Statistics
Matches: 111, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
126 111 1.00
ACGTcount: A:0.29, C:0.16, G:0.17, T:0.39
Consensus pattern (126 bp):
GAATTACTGTAGAAAAACAGCGTCCACATGAGAGCTTTTTTCAGAAATTTTGCTGACAATGCATC
CTGCTTGAAGCGTTTTTGACACTATTTATTCAAAAACGTCTTATCAAAATTATTTTTTCAA
Found at i:21047365 original size:30 final size:29
Alignment explanation
Indices: 21047331--21047416 Score: 91
Period size: 34 Copynumber: 2.8 Consensus size: 29
21047321 AACCTTTCAC
*
21047331 CCTAATTTAATTTATTTAAAACCCTAGAAT
1 CCTAATTTAATTTATTTAAAACCATA-AAT
*
21047361 CCTAATTTACTTAATTTATCTAAAAACCATAAAT
1 CCTAA--T--TTAATTTAT-TTAAAACCATAAAT
*
21047395 CCTAATTTAACTTATTTAAAAC
1 CCTAATTTAATTTATTTAAAAC
21047417 AACAATTTAT
Statistics
Matches: 47, Mismatches: 4, Indels: 11
0.76 0.06 0.18
Matches are distributed among these distances:
29 6 0.13
30 13 0.28
32 2 0.04
34 17 0.36
35 9 0.19
ACGTcount: A:0.42, C:0.17, G:0.01, T:0.40
Consensus pattern (29 bp):
CCTAATTTAATTTATTTAAAACCATAAAT
Found at i:21047375 original size:34 final size:35
Alignment explanation
Indices: 21047337--21047412 Score: 104
Period size: 34 Copynumber: 2.2 Consensus size: 35
21047327 TCACCCTAAT
* *
21047337 TTAATTTAT-TTAAAACCCTAGAATCCTAATTT-AC
1 TTAATTTATCTAAAAACCATA-AATCCTAATTTAAC
21047371 TTAATTTATCTAAAAACCATAAATCCTAATTTAAC
1 TTAATTTATCTAAAAACCATAAATCCTAATTTAAC
21047406 TT-ATTTA
1 TTAATTTA
21047413 AAACAACAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
34 25 0.66
35 13 0.34
ACGTcount: A:0.41, C:0.16, G:0.01, T:0.42
Consensus pattern (35 bp):
TTAATTTATCTAAAAACCATAAATCCTAATTTAAC
Found at i:21047469 original size:17 final size:18
Alignment explanation
Indices: 21047443--21047479 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
21047433 ACCCTAAACC
21047443 TAAAACCCTAATTT-ATT
1 TAAAACCCTAATTTAATT
*
21047460 TAAAATCCTAATTTAATT
1 TAAAACCCTAATTTAATT
21047478 TA
1 TA
21047480 TTTAAAACCC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.43, C:0.14, G:0.00, T:0.43
Consensus pattern (18 bp):
TAAAACCCTAATTTAATT
Found at i:21047477 original size:22 final size:22
Alignment explanation
Indices: 21047451--21047492 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
21047441 CCTAAAACCC
*
21047451 TAATTTATTTAAAATCCTAATT
1 TAATTTATTTAAAACCCTAATT
21047473 TAATTTATTTAAAACCCTAA
1 TAATTTATTTAAAACCCTAA
21047493 AAAATCATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.43, C:0.12, G:0.00, T:0.45
Consensus pattern (22 bp):
TAATTTATTTAAAACCCTAATT
Found at i:21047661 original size:34 final size:34
Alignment explanation
Indices: 21047591--21047661 Score: 81
Period size: 34 Copynumber: 2.1 Consensus size: 34
21047581 TCTACACCTA
** * *
21047591 AAACCCTAATTTACTTAATTTATTTAACAACTCT
1 AAACCCTAATTTAAATAATTTATTAAACAACACT
*
21047625 AAACCCTAATTTAAATAATTT-TTAAAATAACACT
1 AAACCCTAATTTAAATAATTTATT-AAACAACACT
21047659 AAA
1 AAA
21047662 TCCTTTTTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
33 2 0.06
34 29 0.94
ACGTcount: A:0.46, C:0.17, G:0.00, T:0.37
Consensus pattern (34 bp):
AAACCCTAATTTAAATAATTTATTAAACAACACT
Found at i:21048922 original size:16 final size:16
Alignment explanation
Indices: 21048901--21048933 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
21048891 AACTATCAGT
21048901 AAAGCTAATTCTAAAG
1 AAAGCTAATTCTAAAG
21048917 AAAGCTAATTCTAAAG
1 AAAGCTAATTCTAAAG
21048933 A
1 A
21048934 TTGGACCTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.52, C:0.12, G:0.12, T:0.24
Consensus pattern (16 bp):
AAAGCTAATTCTAAAG
Found at i:21052434 original size:12 final size:12
Alignment explanation
Indices: 21052417--21052448 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
21052407 GAATGTGATA
21052417 TTTTTACTCTAT
1 TTTTTACTCTAT
21052429 TTTTTACTCTAT
1 TTTTTACTCTAT
21052441 TTTTTACT
1 TTTTTACT
21052449 TACTTATTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.69
Consensus pattern (12 bp):
TTTTTACTCTAT
Found at i:21058491 original size:15 final size:15
Alignment explanation
Indices: 21058473--21058520 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
21058463 TTTAGTTTTG
21058473 TTAATTAAGGTTTAA
1 TTAATTAAGGTTTAA
* * *
21058488 TTAAATAAAGTATAA
1 TTAATTAAGGTTTAA
*
21058503 TTAATT-AGTTTTAA
1 TTAATTAAGGTTTAA
21058517 TTAA
1 TTAA
21058521 GGTATAAAAG
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
14 9 0.35
15 17 0.65
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (15 bp):
TTAATTAAGGTTTAA
Found at i:21059112 original size:44 final size:44
Alignment explanation
Indices: 21059062--21059147 Score: 172
Period size: 44 Copynumber: 2.0 Consensus size: 44
21059052 ATTCATGCAG
21059062 TTAGTAGGATGTTATAATTTGAATTGAATTATTATATAGATCTA
1 TTAGTAGGATGTTATAATTTGAATTGAATTATTATATAGATCTA
21059106 TTAGTAGGATGTTATAATTTGAATTGAATTATTATATAGATC
1 TTAGTAGGATGTTATAATTTGAATTGAATTATTATATAGATC
21059148 GAGAATTAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.36, C:0.02, G:0.16, T:0.45
Consensus pattern (44 bp):
TTAGTAGGATGTTATAATTTGAATTGAATTATTATATAGATCTA
Found at i:21068938 original size:47 final size:48
Alignment explanation
Indices: 21068869--21069182 Score: 265
Period size: 46 Copynumber: 6.6 Consensus size: 48
21068859 TTTGTGTGCT
* * * *
21068869 AGTGTAAGA-CATGTCTGAGACATGGCATCGGCTTTGAGACGAGAGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCTTCGAGATGAGAGCC
** *
21068916 AGTGTAAGA-CATGTCTGGGACAT-GCATCAACCTCGAGATGTA-AGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCTTCGAGATG-AGAGCC
* * * * *
21068962 AGTGTAAGA-CATGTCTGGGTCAT-GCATTGGCTACGAGAT--GTGTC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCTTCGAGATGAGAGCC
* * *
21069006 AGTATAAGACCATGTCTGGGACATGGCATCGGC-ACGGATATGTGAGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCTTC-GAGA--TGAGAGCC
* * * * *
21069056 AGTGTAAGACCATGTCTGGGACATGGCGTCGGCCTCGATGACGATAGTC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCTTCGA-GATGAGAGCC
* *
21069105 AGTGTAAGACCATGTCTGGGACATGGCATC-GATT--TGATGGATGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCTTCGAGAT-GA-GAGCC
* *
21069152 AGTGTAAAACCATGTCTGGGACATGACATCG
1 AGTGTAAGACCATGTCTGGGACATGGCATCG
21069183 ACATTCTACC
Statistics
Matches: 216, Mismatches: 37, Indels: 27
0.77 0.13 0.10
Matches are distributed among these distances:
44 10 0.05
45 17 0.08
46 60 0.28
47 54 0.25
48 3 0.01
49 34 0.16
50 36 0.17
51 2 0.01
ACGTcount: A:0.27, C:0.19, G:0.31, T:0.24
Consensus pattern (48 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGGCTTCGAGATGAGAGCC
Found at i:21069183 original size:47 final size:48
Alignment explanation
Indices: 21068869--21069184 Score: 246
Period size: 47 Copynumber: 6.7 Consensus size: 48
21068859 TTTGTGTGCT
* * * *
21068869 AGTGTAAGA-CATGTCTGAGACATGGCATCGGCTTTGA-GACGA-GAGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGAC-TCGATGA-GATGAGCC
* *
21068916 AGTGTAAGA-CATGTCTGGGACAT-GCATCAACCTCGA-GATG-TAAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGA-CTCGATGA-GATGAGCC
* * * * * *
21068962 AGTGTAAGA-CATGTCTGGGTCAT-GCATTGGCT--ACGAGATGTGTC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGACTCGATGAGATGAGCC
* * * *
21069006 AGTATAAGACCATGTCTGGGACATGGCATCGGCACGGATATGTGA-GAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGACTC-G--ATGAGATGAGCC
* * *
21069056 AGTGTAAGACCATGTCTGGGACATGGCGTCGGCCTCGATGACGAT-AGTC
1 AGTGTAAGACCATGTCTGGGACATGGCATC-GACTCGATGA-GATGAGCC
* *
21069105 AGTGTAAGACCATGTCTGGGACATGGCATCGATTTGATG-GATGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGACTCGATGAGATGAGCC
* *
21069152 AGTGTAAAACCATGTCTGGGACATGACATCGAC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGAC
21069185 ATTCTACCCC
Statistics
Matches: 218, Mismatches: 36, Indels: 30
0.77 0.13 0.11
Matches are distributed among these distances:
43 2 0.01
44 13 0.06
45 15 0.07
46 50 0.23
47 56 0.26
48 9 0.04
49 34 0.16
50 32 0.15
51 7 0.03
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.23
Consensus pattern (48 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGACTCGATGAGATGAGCC
Found at i:21075768 original size:43 final size:43
Alignment explanation
Indices: 21075677--21075903 Score: 285
Period size: 43 Copynumber: 5.2 Consensus size: 43
21075667 GGTAACGACT
*
21075677 TTTAGCGGCGTTTGTGGGGAAAGCGCTCCGCTAAAAGTCATGGCC
1 TTTAGCGGCGTTTGTGGGAAAAGCG--CCGCTAAAAGTCATGGCC
* * * *
21075722 TTTAGCGGTGTTTATGGGGAAAGCGCCACTAAAAGTCATGGCC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAAGTCATGGCC
** * * * *
21075765 TTTAGCATCATTTGTGGGAAAAACGCCCCTAAAAGTTATGGCC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAAGTCATGGCC
* *
21075808 TTTAGTGGCGTTTGTGGGAAAAGCGCCGCTAAAAGTCATGACC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAAGTCATGGCC
* *
21075851 TTTAGCGGCGTTTGTGCGAAAAGCGCCGCTAAAAGTCAT-GAC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAAGTCATGGCC
21075893 TTTGAGCGGCG
1 TTT-AGCGGCG
21075904 CTTTTGTTAC
Statistics
Matches: 157, Mismatches: 24, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
42 4 0.03
43 130 0.83
45 23 0.15
ACGTcount: A:0.25, C:0.20, G:0.30, T:0.26
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAAGTCATGGCC
Found at i:21076010 original size:31 final size:31
Alignment explanation
Indices: 21075975--21076033 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
21075965 AATCCTTCCT
21075975 GCATTAAATCCAACCAAAAACAACAAATATA
1 GCATTAAATCCAACCAAAAACAACAAATATA
* * *
21076006 GCATTGAATCCAATCAAATACAACAAAT
1 GCATTAAATCCAACCAAAAACAACAAAT
21076034 GTAACATAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.54, C:0.22, G:0.05, T:0.19
Consensus pattern (31 bp):
GCATTAAATCCAACCAAAAACAACAAATATA
Found at i:21076762 original size:13 final size:14
Alignment explanation
Indices: 21076736--21076764 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
21076726 ACTAACGACG
21076736 AATTAAACCATTAT
1 AATTAAACCATTAT
21076750 AATTAAA-CATTAT
1 AATTAAACCATTAT
21076763 AA
1 AA
21076765 ATATTTATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.34
Consensus pattern (14 bp):
AATTAAACCATTAT
Found at i:21081829 original size:9 final size:9
Alignment explanation
Indices: 21081815--21081911 Score: 67
Period size: 9 Copynumber: 11.0 Consensus size: 9
21081805 TAAGTATAAT
21081815 TAAGTTATG
1 TAAGTTATG
21081824 TAAGTTATG
1 TAAGTTATG
* * *
21081833 ATATGATATA
1 -TAAGTTATG
*
21081843 T-ATTTATG
1 TAAGTTATG
21081851 T-A-TTATG
1 TAAGTTATG
*
21081858 TATGTTATG
1 TAAGTTATG
*
21081867 TAAATTATG
1 TAAGTTATG
*
21081876 TAAGTTATC
1 TAAGTTATG
21081885 TGAA-TTATG
1 T-AAGTTATG
*
21081894 TAAATTATG
1 TAAGTTATG
*
21081903 TAAGATATG
1 TAAGTTATG
21081912 ATATATATTT
Statistics
Matches: 68, Mismatches: 15, Indels: 10
0.73 0.16 0.11
Matches are distributed among these distances:
7 6 0.09
8 7 0.10
9 47 0.69
10 8 0.12
ACGTcount: A:0.36, C:0.01, G:0.16, T:0.46
Consensus pattern (9 bp):
TAAGTTATG
Found at i:21082285 original size:13 final size:14
Alignment explanation
Indices: 21082254--21082285 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
21082244 TTAAATTAAA
21082254 TTAAAATAAAATAT
1 TTAAAATAAAATAT
21082268 TTAAAATAAAAT-T
1 TTAAAATAAAATAT
21082281 TTAAA
1 TTAAA
21082286 TACAATTTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 6 0.33
14 12 0.67
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
TTAAAATAAAATAT
Found at i:21082305 original size:105 final size:105
Alignment explanation
Indices: 21082178--21082852 Score: 1019
Period size: 105 Copynumber: 6.4 Consensus size: 105
21082168 CAATATTTAA
* *
21082178 AAATGCAATTTAATTTAATTAGGTAATTTAAAAATAAAATAAAAGTAGACAAAATATTTTTTGTG
1 AAATACAATTTAATTTAATTAGGTAATTTAAAAATAAAATAAAAGTAGACAAAATATTTTTCGTG
* *
21082243 ATTAAATTAAATTAAAATAAAATATTTAAAATAAAATTTT
66 ATTAAATTAAAATAAAATAAAATATTTAAAATAAAAATTT
* *
21082283 AAATACAATTTACTTTAATTAGGTAATTTAAAAATACAATAAAAGTAGACAAAATATTTTTCATG
1 AAATACAATTTAATTTAATTAGGTAATTTAAAAATAAAATAAAAGTAGACAAAATATTTTTC--G
* *
21082348 ATTAAATTAAATTAAAATAAAATAAAATATTTAAAATAAAACTTT
64 --T-GATTAAATTAAAATAAAATAAAATATTTAAAATAAAAATTT
21082393 AAATACAATTTAATTTAATTAGGTAATTTAAAAATAAAATAAAAGTAGACAAAATATTTTTCGTG
1 AAATACAATTTAATTTAATTAGGTAATTTAAAAATAAAATAAAAGTAGACAAAATATTTTTCGTG
* * **
21082458 ATTAAAATAAAATACAATAAAATATTTAAAATAAATCTTT
66 ATTAAATTAAAATAAAATAAAATATTTAAAATAAAAATTT
21082498 AAATACAATTTAATTTAATTAGGTAATTTAAAAATAAAATAAAAGTAGACAAAATATTTTTCGTG
1 AAATACAATTTAATTTAATTAGGTAATTTAAAAATAAAATAAAAGTAGACAAAATATTTTTCGTG
*
21082563 ATTAAAATAAAATAAAATAAAATATTTAAAATAAAAATTT
66 ATTAAATTAAAATAAAATAAAATATTTAAAATAAAAATTT
*
21082603 AAATACAATTTAATTTAATTAGGTAATTTAAAAATAAAATAAAAGTAGACAAAACATTTTTCGTG
1 AAATACAATTTAATTTAATTAGGTAATTTAAAAATAAAATAAAAGTAGACAAAATATTTTTCGTG
*
21082668 -----A-T----TAAAATAAAATATTTAAAATAAAACTTT
66 ATTAAATTAAAATAAAATAAAATATTTAAAATAAAAATTT
* * *
21082698 AAATACAATTTAATTTAATTAAGTTATTTTAAAAATAAAATAAAAGTAGACAAAAAATTTTTCGT
1 AAATACAATTTAATTTAATT-AGGTAATTTAAAAATAAAATAAAAGTAGACAAAATATTTTTCGT
21082763 GATTAAATTAAAATAAAATAAAATAACATATTCAAAATAAAAATTT
65 GATTAAATTAAAATAAAATAAAAT---AT-TT-AAAATAAAAATTT
21082809 AAATACAATTTAATTTAATTAGGTAATTTAAAAATAAAATAAAA
1 AAATACAATTTAATTTAATTAGGTAATTTAAAAATAAAATAAAA
21082853 TATTTAAAAT
Statistics
Matches: 525, Mismatches: 24, Indels: 37
0.90 0.04 0.06
Matches are distributed among these distances:
95 47 0.09
96 42 0.08
99 1 0.00
100 1 0.00
101 1 0.00
102 1 0.00
105 261 0.50
106 12 0.02
107 1 0.00
108 1 0.00
109 3 0.01
110 122 0.23
111 32 0.06
ACGTcount: A:0.55, C:0.04, G:0.05, T:0.35
Consensus pattern (105 bp):
AAATACAATTTAATTTAATTAGGTAATTTAAAAATAAAATAAAAGTAGACAAAATATTTTTCGTG
ATTAAATTAAAATAAAATAAAATATTTAAAATAAAAATTT
Found at i:21082554 original size:215 final size:212
Alignment explanation
Indices: 21082178--21082852 Score: 1061
Period size: 215 Copynumber: 3.2 Consensus size: 212
21082168 CAATATTTAA
* *
21082178 AAATGCAATTTAATTTAATTAGGTAATTTAAAAATAAAATAAAAGTAGACAAAATATTTTTTGTG
1 AAATACAATTTAATTTAATTAGGTAATTTAAAAATAAAATAAAAGTAGACAAAATATTTTTCGTG
* *
21082243 ATTAAATTAAATTAAAATAAAATATTTAAAATAAAAT-TTTAAATACAATTTACTTTAATTAGGT
66 ATTAAA-TAAAAT-AAATAAAATATTTAAAAT-AAATCTTTAAATACAATTTAATTTAATTAGGT
* *
21082307 AATTTAAAAATACAATAAAAGTAGACAAAATATTTTTCATGATTAAATTAAATTAAAATAAAATA
128 AATTTAAAAATAAAATAAAAGTAGACAAAATATTTTTCGTGATTAAATTAAA-TAAAATAAAATA
*
21082372 AAATATTTAAAATAAAACTTT
192 AAATATTTAAAATAAAAATTT
21082393 AAATACAATTTAATTTAATTAGGTAATTTAAAAATAAAATAAAAGTAGACAAAATATTTTTCGTG
1 AAATACAATTTAATTTAATTAGGTAATTTAAAAATAAAATAAAAGTAGACAAAATATTTTTCGTG
21082458 ATTAAAATAAAATACAATAAAATATTTAAAATAAATCTTTAAATACAATTTAATTTAATTAGGTA
66 ATT-AAATAAAATA-AATAAAATATTTAAAATAAATCTTTAAATACAATTTAATTTAATTAGGTA
21082523 ATTTAAAAATAAAATAAAAGTAGACAAAATATTTTTCGTGATT--A--AAATAAAATAAAATAAA
129 ATTTAAAAATAAAATAAAAGTAGACAAAATATTTTTCGTGATTAAATTAAATAAAATAAAATAAA
21082584 ATATTTAAAATAAAAATTT
194 ATATTTAAAATAAAAATTT
*
21082603 AAATACAATTTAATTTAATTAGGTAATTTAAAAATAAAATAAAAGTAGACAAAACATTTTTCGTG
1 AAATACAATTTAATTTAATTAGGTAATTTAAAAATAAAATAAAAGTAGACAAAATATTTTTCGTG
* * *
21082668 A-T---T---A-AAATAAAATATTTAAAATAAAACTTTAAATACAATTTAATTTAATTAAGTTAT
66 ATTAAATAAAATAAATAAAATATTTAAAATAAATCTTTAAATACAATTTAATTTAATT-AGGTAA
* *
21082725 TTTAAAAATAAAATAAAAGTAGACAAAAAATTTTTCGTGATTAAATTAAAATAAAATAAAATAAC
130 TTTAAAAATAAAATAAAAGTAGACAAAATATTTTTCGTGATTAAATT-AAATAAAATAAAATAAA
*
21082790 ATATTCAAAATAAAAATTT
194 ATATTTAAAATAAAAATTT
21082809 AAATACAATTTAATTTAATTAGGTAATTTAAAAATAAAATAAAA
1 AAATACAATTTAATTTAATTAGGTAATTTAAAAATAAAATAAAA
21082853 TATTTAAAAT
Statistics
Matches: 437, Mismatches: 14, Indels: 27
0.91 0.03 0.06
Matches are distributed among these distances:
200 44 0.10
201 46 0.11
202 1 0.00
203 1 0.00
205 1 0.00
206 78 0.18
209 1 0.00
210 97 0.22
211 3 0.01
213 1 0.00
214 5 0.01
215 156 0.36
216 3 0.01
ACGTcount: A:0.55, C:0.04, G:0.05, T:0.35
Consensus pattern (212 bp):
AAATACAATTTAATTTAATTAGGTAATTTAAAAATAAAATAAAAGTAGACAAAATATTTTTCGTG
ATTAAATAAAATAAATAAAATATTTAAAATAAATCTTTAAATACAATTTAATTTAATTAGGTAAT
TTAAAAATAAAATAAAAGTAGACAAAATATTTTTCGTGATTAAATTAAATAAAATAAAATAAAAT
ATTTAAAATAAAAATTT
Found at i:21082594 original size:14 final size:13
Alignment explanation
Indices: 21082564--21082605 Score: 54
Period size: 14 Copynumber: 3.4 Consensus size: 13
21082554 TTTTTCGTGA
21082564 TTAAAAT-AAAA-
1 TTAAAATAAAAAT
21082575 -TAAAATAAAATAT
1 TTAAAATAAAA-AT
21082588 TTAAAATAAAAAT
1 TTAAAATAAAAAT
21082601 TTAAA
1 TTAAA
21082606 TACAATTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
10 6 0.22
11 3 0.11
12 1 0.04
13 7 0.26
14 10 0.37
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
TTAAAATAAAAAT
Found at i:21082775 original size:96 final size:95
Alignment explanation
Indices: 21082575--21082852 Score: 376
Period size: 95 Copynumber: 2.8 Consensus size: 95
21082565 TAAAATAAAA
21082575 TAAAATAAAATATTTAAAATAAAAATTTAAATACAATTTAATTTAATTAGGTAATTTAAAAATAA
1 TAAAATAAAATATTTAAAATAAAAATTTAAATACAATTTAATTTAATTAGGTAATTTAAAAATAA
*
21082640 AATAAAAGTAGACAAAACATTTTTCGTGAT
66 AATAAAAGTAGACAAAAAATTTTTCGTGAT
* * *
21082670 TAAAATAAAATATTTAAAATAAAACTTTAAATACAATTTAATTTAATTAAGTTATTTTAAAAATA
1 TAAAATAAAATATTTAAAATAAAAATTTAAATACAATTTAATTTAATT-AGGTAATTTAAAAATA
21082735 AAATAAAAGTAGACAAAAAATTTTTCGTGATTAAATT
65 AAATAAAAGTAGACAAAAAATTTTTCGTG-----A-T
21082772 AAAATAAAATAAAATAACATATTCAAAATAAAAATTTAAATACAATTTAATTTAATTAGGTAATT
1 ----TAAAATAAAAT---AT-TT-AAAATAAAAATTTAAATACAATTTAATTTAATTAGGTAATT
21082837 TAAAAATAAAATAAAA
57 TAAAAATAAAATAAAA
21082853 TATTTAAAAT
Statistics
Matches: 160, Mismatches: 7, Indels: 17
0.87 0.04 0.09
Matches are distributed among these distances:
95 47 0.29
96 42 0.26
101 1 0.01
102 1 0.01
106 11 0.07
109 2 0.01
110 24 0.15
111 32 0.20
ACGTcount: A:0.57, C:0.04, G:0.05, T:0.35
Consensus pattern (95 bp):
TAAAATAAAATATTTAAAATAAAAATTTAAATACAATTTAATTTAATTAGGTAATTTAAAAATAA
AATAAAAGTAGACAAAAAATTTTTCGTGAT
Found at i:21085751 original size:19 final size:21
Alignment explanation
Indices: 21085705--21085755 Score: 61
Period size: 19 Copynumber: 2.4 Consensus size: 21
21085695 GGGGTTGAAA
*
21085705 CAAATAAAAATAATAATAATTG
1 CAAAT-AAAATAATAAAAATTG
21085727 CGAAATAAAAT-ATAAAAATT-
1 C-AAATAAAATAATAAAAATTG
21085747 CAAATAAAA
1 CAAATAAAA
21085756 GTAAATTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 8 0.30
20 1 0.04
21 8 0.30
22 6 0.22
23 4 0.15
ACGTcount: A:0.67, C:0.06, G:0.04, T:0.24
Consensus pattern (21 bp):
CAAATAAAATAATAAAAATTG
Found at i:21100451 original size:16 final size:17
Alignment explanation
Indices: 21100432--21100466 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
21100422 ATTATTTAAT
21100432 ATATAAATT-AAAAACA
1 ATATAAATTAAAAAACA
21100448 ATATAAATTAAAAAACA
1 ATATAAATTAAAAAACA
21100465 AT
1 AT
21100467 TATATACCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.26
Consensus pattern (17 bp):
ATATAAATTAAAAAACA
Found at i:21100452 original size:18 final size:19
Alignment explanation
Indices: 21100429--21100472 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 19
21100419 AAAATTATTT
21100429 AATATATAAATT-AAAAAC
1 AATATATAAATTAAAAAAC
21100447 -A-ATATAAATTAAAAAAC
1 AATATATAAATTAAAAAAC
21100464 AATTATATA
1 AA-TATATA
21100473 CCCAAAAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
16 9 0.41
17 7 0.32
18 1 0.05
20 5 0.23
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.30
Consensus pattern (19 bp):
AATATATAAATTAAAAAAC
Found at i:21100539 original size:28 final size:29
Alignment explanation
Indices: 21100489--21100546 Score: 75
Period size: 28 Copynumber: 2.0 Consensus size: 29
21100479 AAACTTTAAA
* *
21100489 TTTATTTTAAATAATAGTATTTTAATTTT
1 TTTATTTTAAATAATAATATTTTAAATTT
21100518 TTTA-TTTAAATAAATAAT-TTTTAAATTT
1 TTTATTTTAAAT-AATAATATTTTAAATTT
21100546 T
1 T
21100547 AACTAATATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 17 0.65
29 9 0.35
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (29 bp):
TTTATTTTAAATAATAATATTTTAAATTT
Found at i:21100754 original size:8 final size:7
Alignment explanation
Indices: 21100739--21100791 Score: 52
Period size: 8 Copynumber: 7.0 Consensus size: 7
21100729 CACTAATTAT
21100739 CCTAAAC
1 CCTAAAC
21100746 CCATAAAC
1 CC-TAAAC
21100754 CCATAAACC
1 CC-TAAA-C
*
21100763 CCTAAAT
1 CCTAAAC
21100770 CCTAAAC
1 CCTAAAC
*
21100777 CCTTAATC
1 CC-TAAAC
21100785 CCTAAAC
1 CCTAAAC
21100792 TTTAAACCAT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
7 14 0.36
8 22 0.56
9 3 0.08
ACGTcount: A:0.42, C:0.40, G:0.00, T:0.19
Consensus pattern (7 bp):
CCTAAAC
Found at i:21100777 original size:15 final size:15
Alignment explanation
Indices: 21100737--21100791 Score: 58
Period size: 15 Copynumber: 3.6 Consensus size: 15
21100727 AACACTAATT
*
21100737 ATCCTAAACCCATAA
1 ATCCTAAACCCCTAA
*
21100752 ACCCATAAACCCCTAA
1 ATCC-TAAACCCCTAA
*
21100768 ATCCTAAA-CCCTTA
1 ATCCTAAACCCCTAA
21100782 ATCCCTAAAC
1 AT-CCTAAAC
21100792 TTTAAACCAT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
14 7 0.21
15 13 0.39
16 13 0.39
ACGTcount: A:0.42, C:0.38, G:0.00, T:0.20
Consensus pattern (15 bp):
ATCCTAAACCCCTAA
Found at i:21100835 original size:8 final size:8
Alignment explanation
Indices: 21100822--21100854 Score: 59
Period size: 8 Copynumber: 4.2 Consensus size: 8
21100812 ACTATGTCCA
21100822 CTTAACCC
1 CTTAACCC
21100830 CTTAACCC
1 CTTAACCC
21100838 CTTAA-CC
1 CTTAACCC
21100845 CTTAACCC
1 CTTAACCC
21100853 CT
1 CT
21100855 AGACCCTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 7 0.29
8 17 0.71
ACGTcount: A:0.24, C:0.48, G:0.00, T:0.27
Consensus pattern (8 bp):
CTTAACCC
Found at i:21100848 original size:7 final size:7
Alignment explanation
Indices: 21100822--21100881 Score: 57
Period size: 7 Copynumber: 8.1 Consensus size: 7
21100812 ACTATGTCCA
21100822 CTTAACCC
1 CTTAA-CC
21100830 CTTAACCC
1 CTTAA-CC
21100838 CTTAACC
1 CTTAACC
21100845 CTTAACC
1 CTTAACC
*
21100852 CCTAGACC
1 CTTA-ACC
*
21100860 CTCAACC
1 CTTAACC
**
21100867 CTTAAAT
1 CTTAACC
21100874 CTTAACC
1 CTTAACC
21100881 C
1 C
21100882 ATAAACCATA
Statistics
Matches: 43, Mismatches: 8, Indels: 3
0.80 0.15 0.06
Matches are distributed among these distances:
7 25 0.58
8 18 0.42
ACGTcount: A:0.28, C:0.45, G:0.02, T:0.25
Consensus pattern (7 bp):
CTTAACC
Found at i:21100848 original size:15 final size:15
Alignment explanation
Indices: 21100822--21100881 Score: 61
Period size: 15 Copynumber: 4.0 Consensus size: 15
21100812 ACTATGTCCA
21100822 CTTAACCCCTTAACCC
1 CTTAA-CCCTTAACCC
21100838 CTTAACCCTTAACCC
1 CTTAACCCTTAACCC
*
21100853 C-TAGACCCTCAA-CC
1 CTTA-ACCCTTAACCC
**
21100867 CTTAAATCTTAACCC
1 CTTAACCCTTAACCC
21100882 ATAAACCATA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
14 10 0.27
15 22 0.59
16 5 0.14
ACGTcount: A:0.28, C:0.45, G:0.02, T:0.25
Consensus pattern (15 bp):
CTTAACCCTTAACCC
Found at i:21100890 original size:7 final size:7
Alignment explanation
Indices: 21100880--21101105 Score: 96
Period size: 7 Copynumber: 30.9 Consensus size: 7
21100870 AAATCTTAAC
21100880 CCATAAA
1 CCATAAA
21100887 CCATAAA
1 CCATAAA
**
21100894 CCCCAAA
1 CCATAAA
*
21100901 TCCCTAAA
1 -CCATAAA
*
21100909 CC-TCAA
1 CCATAAA
*
21100915 CCATTGAA
1 CCA-TAAA
21100923 CCATAAA
1 CCATAAA
*
21100930 CCATAAT
1 CCATAAA
*
21100937 CCCTAAA
1 CCATAAA
* *
21100944 TTCATAAT
1 -CCATAAA
21100952 CCATAAA
1 CCATAAA
*
21100959 CCTTAAA
1 CCATAAA
** *
21100966 ATATTAA
1 CCATAAA
*
21100973 CTCTTAAA
1 C-CATAAA
21100981 CCATAAA
1 CCATAAA
*
21100988 CCCCTAAA
1 -CCATAAA
*
21100996 CCTTAAA
1 CCATAAA
*
21101003 CCCTAAA
1 CCATAAA
*
21101010 GCCATAAT
1 -CCATAAA
*
21101018 CCCTAAA
1 CCATAAA
21101025 CCCATGCATAA
1 -CCAT--A-AA
*
21101036 TCTATAAA
1 -CCATAAA
*
21101044 CCTTAAA
1 CCATAAA
**
21101051 ATATAAA
1 CCATAAA
21101058 CCATAAA
1 CCATAAA
21101065 CTC-TAAA
1 C-CATAAA
*
21101072 CCATATA
1 CCATAAA
*
21101079 CCCTAAA
1 CCATAAA
21101086 CCATAAA
1 CCATAAA
21101093 CCATAAA
1 CCATAAA
*
21101100 CTATAA
1 CCATAA
21101106 TGATAATTAA
Statistics
Matches: 160, Mismatches: 46, Indels: 26
0.69 0.20 0.11
Matches are distributed among these distances:
6 6 0.04
7 110 0.69
8 37 0.23
9 1 0.01
10 1 0.01
11 5 0.03
ACGTcount: A:0.46, C:0.30, G:0.01, T:0.23
Consensus pattern (7 bp):
CCATAAA
Found at i:21100965 original size:22 final size:22
Alignment explanation
Indices: 21100881--21101105 Score: 63
Period size: 22 Copynumber: 10.5 Consensus size: 22
21100871 AATCTTAACC
* *
21100881 CATAAACCATAAACCCCAAATC
1 CATAAACCATAAACCCTAAATT
* * * * *
21100903 CCTAAACC-TCAACCATTGAA-C
1 CATAAACCATAAACC-CTAAATT
*
21100924 CATAAACCATAATCCCTAAATT
1 CATAAACCATAAACCCTAAATT
* * *
21100946 CATAATCCATAAACCTTAAAAT
1 CATAAACCATAAACCCTAAATT
* * * **
21100968 -ATTAACTCTTAAACCATAAACC
1 CATAAAC-CATAAACCCTAAATT
* * **
21100990 CCTAAACCTTAAACCCTAAAGC
1 CATAAACCATAAACCCTAAATT
* * *
21101012 CATAATCCCTAAACCC---ATG
1 CATAAACCATAAACCCTAAATT
* * * *
21101031 CATAATCTATAAACCTTAAAAT
1 CATAAACCATAAACCCTAAATT
* *
21101053 -ATAAACCATAAACTCTAAA-C
1 CATAAACCATAAACCCTAAATT
* * * *
21101073 CATATACCCTAAACCATAAA-C
1 CATAAACCATAAACCCTAAATT
*
21101094 CATAAACTATAA
1 CATAAACCATAA
21101106 TGATAATTAA
Statistics
Matches: 147, Mismatches: 47, Indels: 19
0.69 0.22 0.09
Matches are distributed among these distances:
19 14 0.10
21 60 0.41
22 69 0.47
23 4 0.03
ACGTcount: A:0.47, C:0.29, G:0.01, T:0.23
Consensus pattern (22 bp):
CATAAACCATAAACCCTAAATT
Found at i:21101323 original size:14 final size:14
Alignment explanation
Indices: 21101304--21101330 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
21101294 TACGTGTCAT
21101304 TAGTTTAGGGTTTA
1 TAGTTTAGGGTTTA
21101318 TAGTTTAGGGTTT
1 TAGTTTAGGGTTT
21101331 GAGATTTAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.19, C:0.00, G:0.30, T:0.52
Consensus pattern (14 bp):
TAGTTTAGGGTTTA
Found at i:21102697 original size:21 final size:19
Alignment explanation
Indices: 21102667--21102709 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
21102657 ACTCCTGCAA
21102667 TTTTTGAAAAAATTCAAAGT
1 TTTTTGAAAAAATT-AAAGT
*
21102687 TTTTTGAAAAAAATTAGAGT
1 TTTTTG-AAAAAATTAAAGT
21102707 TTT
1 TTT
21102710 CGATTTAGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.42, C:0.02, G:0.12, T:0.44
Consensus pattern (19 bp):
TTTTTGAAAAAATTAAAGT
Found at i:21104929 original size:46 final size:46
Alignment explanation
Indices: 21104876--21105149 Score: 207
Period size: 46 Copynumber: 5.8 Consensus size: 46
21104866 TATTTGGGCA
21104876 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * *
21104922 TCCGAACTCGTTGAGTTGAGT-TGAGTTCGAGTTCATGAGATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTT-ATG-GATGCAA--A--CG
* * *
21104974 TCCGAGCTCGTTGAGTTGAGTCCGAATTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * * * *
21105020 TTCGAACTCGTTGAGTTGAGTCTGAG-T---TTGTGAAATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATG-GATGCAA--A--CG
* * *
21105067 TCCGAACTCGTTGAGTTGAGTTCGAGTTCACTTATGAATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* ** ** *
21105113 CCCGAGTTCGTTGAGTTGAGTTTGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
21105150 GCGGGTTACA
Statistics
Matches: 178, Mismatches: 33, Indels: 34
0.73 0.13 0.14
Matches are distributed among these distances:
42 4 0.02
43 4 0.02
45 8 0.04
46 79 0.44
47 27 0.15
48 9 0.05
50 11 0.06
51 7 0.04
52 24 0.13
53 5 0.03
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.31
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:21105085 original size:98 final size:93
Alignment explanation
Indices: 21104872--21105140 Score: 369
Period size: 93 Copynumber: 2.8 Consensus size: 93
21104862 CGGATATTTG
*
21104872 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAG
*
21104937 TTGAGTTGAGTTCGAGTTCATGAGATGTAACTA
66 TTGAGTTGAG-T----TTCATGAAATGTAACTA
* * *
21104970 GGCATCCGAGCTCGTTGAGTTGAGTCCGAATTCACTTATGGATGCGAACGTTCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAG
*
21105035 TTGAGTCTGAGTTT-GTGAAATGTAACTA
66 TTGAGT-TGAGTTTCATGAAATGTAACTA
* * * **
21105063 GGCATCCGAACTCGTTGAGTTGAGTTCGAGTTCACTTATGAATGCGAACGCCCGAGTTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAG
21105128 TTGAGTTTGAGTT
66 TTGAG-TTGAGTT
21105141 CGCTTATGGG
Statistics
Matches: 155, Mismatches: 14, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
93 80 0.52
94 3 0.02
98 68 0.44
99 4 0.03
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.31
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAG
TTGAGTTGAGTTTCATGAAATGTAACTA
Found at i:21110938 original size:46 final size:46
Alignment explanation
Indices: 21110887--21111157 Score: 201
Period size: 46 Copynumber: 5.7 Consensus size: 46
21110877 TTGGGCATCC
*
21110887 GAACTCGTTGAGTTGAGTACGAGTTCACTTATGGATGCGAACGTCT
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCT
* * * * *
21110933 GAACTCGTTGAGTTGAGT-TGAGTCCGAGTTCGTGAGATG-TAACTAGGCATCT
1 GAACTCGTTGAGTTGAGTCCGAGTTC-ACTT-ATG-GATGCGAAC---G--TCT
* *
21110985 GAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACAT-T
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCT
* * * * * * * *
21111030 CGAACTCGTTGAGTTGAGTCCGAGTTC-GTGAAATGTA-ACTAGGCATCA
1 -GAACTCGTTGAGTTGAGTCCGAGTTCACT--TATGGATGCGA-ACGTCT
* * *
21111078 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGAATGCGAACGCCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCT
* * *
21111124 GAGCTCGTTGAGTTGAGTCCAAGTTCGCTTATGG
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
21111158 CCGGGTTACA
Statistics
Matches: 175, Mismatches: 33, Indels: 34
0.72 0.14 0.14
Matches are distributed among these distances:
45 7 0.04
46 85 0.49
47 40 0.23
48 5 0.03
50 5 0.03
51 5 0.03
52 23 0.13
53 5 0.03
ACGTcount: A:0.23, C:0.18, G:0.29, T:0.30
Consensus pattern (46 bp):
GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCT
Found at i:21111006 original size:47 final size:47
Alignment explanation
Indices: 21110944--21111103 Score: 186
Period size: 47 Copynumber: 3.4 Consensus size: 47
21110934 AACTCGTTGA
*
21110944 GTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCATCTGAGCTC
1 GTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCATCTGAACTC
* * * *
21110991 GTTGAGTTGAGTCCGAGTTCACTTATGGATG---CGA-ACAT-TCGAACTC
1 GTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCATCT-GAACTC
* *
21111037 GTTGAGTTGAGTCCGAGTTCGTGAAATGTAACTAGGCATCAGAACTC
1 GTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCATCTGAACTC
21111084 GTTGAGTTGAGTCCGAGTTC
1 GTTGAGTTGAGTCCGAGTTC
21111104 ACTTATGAAT
Statistics
Matches: 93, Mismatches: 11, Indels: 18
0.76 0.09 0.15
Matches are distributed among these distances:
43 3 0.03
45 3 0.03
46 30 0.32
47 51 0.55
48 2 0.02
50 4 0.04
ACGTcount: A:0.23, C:0.17, G:0.29, T:0.30
Consensus pattern (47 bp):
GTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCATCTGAACTC
Found at i:21111093 original size:98 final size:92
Alignment explanation
Indices: 21110880--21111150 Score: 371
Period size: 93 Copynumber: 2.9 Consensus size: 92
21110870 TGGATATTTG
* * *
21110880 GGCATCCGAACTCGTTGAGTTGAGTACGAGTTCACTTATGGATGCGAACGTCTGAACTCGTTGAG
1 GGCATCAGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACCTC-GAACTC-----G
*
21110945 TTGAGTTGAGTCCGAGTTCGTGAGATGTAACTA
60 TTGAGTTGAGTCCGAGTTCGTGAAATGTAACTA
* * *
21110978 GGCATCTGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACATTCGAACTCGTTGAG
1 GGCATCAGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAC-CTCGAACTCGTTGAG
21111043 TTGAGTCCGAGTTCGTGAAATGTAACTA
65 TTGAGTCCGAGTTCGTGAAATGTAACTA
* * *
21111071 GGCATCAGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGAATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCAGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAC-CTCGAACTCGTTGAG
*
21111136 TTGAGTCCAAGTTCG
65 TTGAGTCCGAGTTCG
21111151 CTTATGGCCG
Statistics
Matches: 159, Mismatches: 13, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
93 105 0.66
98 52 0.33
99 2 0.01
ACGTcount: A:0.23, C:0.19, G:0.29, T:0.29
Consensus pattern (92 bp):
GGCATCAGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACCTCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAAATGTAACTA
Found at i:21116720 original size:21 final size:21
Alignment explanation
Indices: 21116694--21116739 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
21116684 TTTTCATAAT
*
21116694 GTAAGTTTTGGACTGAATTGA
1 GTAAGTGTTGGACTGAATTGA
21116715 GTAAGTGTTGGACTGAATTGA
1 GTAAGTGTTGGACTGAATTGA
21116736 GTAA
1 GTAA
21116740 TGTGATTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.30, C:0.04, G:0.30, T:0.35
Consensus pattern (21 bp):
GTAAGTGTTGGACTGAATTGA
Found at i:21117115 original size:43 final size:43
Alignment explanation
Indices: 21117034--21117115 Score: 114
Period size: 42 Copynumber: 1.9 Consensus size: 43
21117024 GGTTATTTGA
21117034 GATTACGTGTAAGACCATATCTGGGATATGGCATCGATATGAG
1 GATTACGTGTAAGACCATATCTGGGATATGGCATCGATATGAG
* *
21117077 GATT-CGTGTAAGACCGTAGT-TGGGCTATTGGCATCGATA
1 GATTACGTGTAAGACCATA-TCTGGGATA-TGGCATCGATA
21117116 CGAGATCCCA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
42 19 0.54
43 16 0.46
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.29
Consensus pattern (43 bp):
GATTACGTGTAAGACCATATCTGGGATATGGCATCGATATGAG
Found at i:21117130 original size:43 final size:42
Alignment explanation
Indices: 21117041--21117151 Score: 109
Period size: 43 Copynumber: 2.6 Consensus size: 42
21117031 TGAGATTACG
* * * *
21117041 TGTAAGACCATATCTGGGATATGGCATCGATATGAGGATTCG
1 TGTAAGACCGTATCTGGGATATGGCATCGATACGAGGATCCA
*
21117083 TGTAAGACCGTAGT-TGGGCTATTGGCATCGATACGA-GATCCCA
1 TGTAAGACCGTA-TCTGGGATA-TGGCATCGATACGAGGAT-CCA
* * *
21117126 TGTAAGATCGTATCTAGCATATGGCA
1 TGTAAGACCGTATCTGGGATATGGCA
21117152 CTGGTGTGGT
Statistics
Matches: 56, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
42 26 0.46
43 30 0.54
ACGTcount: A:0.28, C:0.17, G:0.27, T:0.28
Consensus pattern (42 bp):
TGTAAGACCGTATCTGGGATATGGCATCGATACGAGGATCCA
Found at i:21122552 original size:20 final size:23
Alignment explanation
Indices: 21122521--21122565 Score: 69
Period size: 21 Copynumber: 2.1 Consensus size: 23
21122511 TTGCTTGTAC
21122521 TTAAGTACATTTT-GTT-GCATT
1 TTAAGTACATTTTAGTTAGCATT
21122542 TTAAG-ACATTTTAGTTAGCATT
1 TTAAGTACATTTTAGTTAGCATT
21122564 TT
1 TT
21122566 TAATATTGCA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 7 0.32
21 8 0.36
22 7 0.32
ACGTcount: A:0.27, C:0.09, G:0.13, T:0.51
Consensus pattern (23 bp):
TTAAGTACATTTTAGTTAGCATT
Found at i:21126561 original size:43 final size:43
Alignment explanation
Indices: 21126500--21126585 Score: 138
Period size: 43 Copynumber: 2.0 Consensus size: 43
21126490 TATGTGATTG
*
21126500 ATATTGAAATGGAAAAGAT-GAGAAATGAATATGAGATGAGAAA
1 ATATTGAAATGGAAAAGATAG-GAAATGAATATGACATGAGAAA
*
21126543 ATATTGAAATGGAAAAGATAGGAAATGATTATGACATGAGAAA
1 ATATTGAAATGGAAAAGATAGGAAATGAATATGACATGAGAAA
21126586 TGAAATATGA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
43 39 0.98
44 1 0.03
ACGTcount: A:0.52, C:0.01, G:0.24, T:0.22
Consensus pattern (43 bp):
ATATTGAAATGGAAAAGATAGGAAATGAATATGACATGAGAAA
Found at i:21129895 original size:23 final size:25
Alignment explanation
Indices: 21129869--21129915 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
21129859 TATCATTCAT
*
21129869 TTCATTATAT-CA-ATATTTTATGC
1 TTCATCATATCCATATATTTTATGC
*
21129892 TTCATCATTTCCATATATTTTATG
1 TTCATCATATCCATATATTTTATG
21129916 TATATTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 8 0.40
24 2 0.10
25 10 0.50
ACGTcount: A:0.28, C:0.15, G:0.04, T:0.53
Consensus pattern (25 bp):
TTCATCATATCCATATATTTTATGC
Found at i:21130236 original size:46 final size:46
Alignment explanation
Indices: 21130176--21130439 Score: 323
Period size: 46 Copynumber: 5.9 Consensus size: 46
21130166 TTTGACGTGA
* * * * * * *
21130176 TGCCATAGTGTCTTTGAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAAGT
** * *
21130222 TGCCATGGTATCTTTCAACCATGGTCTTATTC-TTTCATGTCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAAGT
* *
21130267 TGCCATGGTATCTTTCAACCATGGTCTTACACATCTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAAGT
21130313 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAAGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAAGT
*
21130359 TGCCATGGTATCTTTCAACCATGGTCTT--ACA---C--A-CAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAAGT
21130397 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCA
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCA
21130440 GAGAGCACAC
Statistics
Matches: 194, Mismatches: 14, Indels: 20
0.85 0.06 0.09
Matches are distributed among these distances:
38 32 0.16
39 1 0.01
40 3 0.02
41 1 0.01
43 1 0.01
44 7 0.04
45 38 0.20
46 111 0.57
ACGTcount: A:0.22, C:0.24, G:0.15, T:0.38
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAAGT
Found at i:21130291 original size:91 final size:88
Alignment explanation
Indices: 21130176--21130439 Score: 331
Period size: 91 Copynumber: 3.0 Consensus size: 88
21130166 TTTGACGTGA
* * * * *
21130176 TGCCATAGTGTCTTTGAACTATGGTCTTACTCATTTTCTGTCATGTTGCCATGGTATCTTTCAAC
1 TGCCATGGTATCTTTCAACCATGGTCTTAC-CA--TTCT-TCAGGTTGCCATGGTATCTTTCAAC
** * *
21130241 CATGGTCTTATTC-TTTCATGTCACGT
62 CATGGTCTTACACATTTCATATCAAGT
21130267 TGCCATGGTATCTTTCAACCATGGTCTTACACATCTCATATCAGGTTGCCATGGTATCTTTCAAC
1 TGCCATGGTATCTTTCAACCATGGTCTTAC-CAT-TC-T-TCAGGTTGCCATGGTATCTTTCAAC
21130332 CATGGTCTTACACATTTCATATCAAGT
62 CATGGTCTTACACATTTCATATCAAGT
*
21130359 TGCCATGGTATCTTTCAACCATGGTCTTA-CA--C-ACAGGTTGCCATGGTATCTTTCAACCATG
1 TGCCATGGTATCTTTCAACCATGGTCTTACCATTCTTCAGGTTGCCATGGTATCTTTCAACCATG
21130420 GTCTTACACATTTCATATCA
66 GTCTTACACATTTCATATCA
21130440 GAGAGCACAC
Statistics
Matches: 158, Mismatches: 12, Indels: 13
0.86 0.07 0.07
Matches are distributed among these distances:
84 48 0.30
87 1 0.01
89 1 0.01
90 4 0.03
91 64 0.41
92 40 0.25
ACGTcount: A:0.22, C:0.24, G:0.15, T:0.38
Consensus pattern (88 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACCATTCTTCAGGTTGCCATGGTATCTTTCAACCATG
GTCTTACACATTTCATATCAAGT
Found at i:21130408 original size:38 final size:38
Alignment explanation
Indices: 21130357--21130429 Score: 146
Period size: 38 Copynumber: 1.9 Consensus size: 38
21130347 TTCATATCAA
21130357 GTTGCCATGGTATCTTTCAACCATGGTCTTACACACAG
1 GTTGCCATGGTATCTTTCAACCATGGTCTTACACACAG
21130395 GTTGCCATGGTATCTTTCAACCATGGTCTTACACA
1 GTTGCCATGGTATCTTTCAACCATGGTCTTACACA
21130430 TTTCATATCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.23, C:0.26, G:0.18, T:0.33
Consensus pattern (38 bp):
GTTGCCATGGTATCTTTCAACCATGGTCTTACACACAG
Found at i:21132583 original size:11 final size:11
Alignment explanation
Indices: 21132567--21132614 Score: 51
Period size: 11 Copynumber: 4.2 Consensus size: 11
21132557 CTTTATATAC
21132567 TAATAAAATAA
1 TAATAAAATAA
21132578 TAATAAAATATA
1 TAATAAAATA-A
* * *
21132590 TTATTAAAGTAT
1 -TAATAAAATAA
21132602 TAATAAAATAA
1 TAATAAAATAA
21132613 TA
1 TA
21132615 TTTATCTAAT
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
11 20 0.69
12 1 0.03
13 8 0.28
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.35
Consensus pattern (11 bp):
TAATAAAATAA
Found at i:21132597 original size:24 final size:24
Alignment explanation
Indices: 21132561--21132616 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
21132551 TTCTTTCTTT
*
21132561 ATATACTAATAAAATAATAATAAA
1 ATATATTAATAAAATAATAATAAA
* * *
21132585 ATATATTATTAAAGTATTAATAAA
1 ATATATTAATAAAATAATAATAAA
21132609 ATAATATT
1 AT-ATATT
21132617 TATCTAATTA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
24 22 0.81
25 5 0.19
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (24 bp):
ATATATTAATAAAATAATAATAAA
Found at i:21133269 original size:13 final size:13
Alignment explanation
Indices: 21133251--21133278 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
21133241 GTCATCAAAA
21133251 ACAACATGTATAG
1 ACAACATGTATAG
21133264 ACAACATGTATAG
1 ACAACATGTATAG
21133277 AC
1 AC
21133279 TCTTCTACTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.46, C:0.18, G:0.14, T:0.21
Consensus pattern (13 bp):
ACAACATGTATAG
Found at i:21139666 original size:16 final size:16
Alignment explanation
Indices: 21139642--21139676 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
21139632 AAATTAATTT
*
21139642 TTTTTAAATTATAAAA
1 TTTTCAAATTATAAAA
*
21139658 TTTTCAAATTATAGAA
1 TTTTCAAATTATAAAA
21139674 TTT
1 TTT
21139677 AAAAATTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (16 bp):
TTTTCAAATTATAAAA
Found at i:21143073 original size:35 final size:35
Alignment explanation
Indices: 21143029--21143195 Score: 201
Period size: 35 Copynumber: 4.6 Consensus size: 35
21143019 TCCTCATTGA
** *
21143029 AATACCATACCTACATTTTTCAACTCGGTATGGGA-
1 AATACCATACCTACATTTCACAACTCAGTAT-GGAT
* **
21143064 AATGCCATACCTACATTTCTTAACTCAGTATGGATTTGAT
1 AATACCATACCTACATTTCACAACTCAGTAT-G----GAT
*
21143104 AATACCATACCTACATTTCACAGCTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
21143139 AATACCATACCTACATTTCACAACTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
*
21143174 GATACCATACCTACATTTCACA
1 AATACCATACCTACATTTCACA
21143196 CTTTGCCATG
Statistics
Matches: 117, Mismatches: 10, Indels: 10
0.85 0.07 0.07
Matches are distributed among these distances:
35 87 0.74
39 3 0.03
40 27 0.23
ACGTcount: A:0.34, C:0.25, G:0.11, T:0.31
Consensus pattern (35 bp):
AATACCATACCTACATTTCACAACTCAGTATGGAT
Found at i:21143112 original size:75 final size:73
Alignment explanation
Indices: 21143024--21143195 Score: 226
Period size: 75 Copynumber: 2.4 Consensus size: 73
21143014 GGTTTTCCTC
** * * **
21143024 ATTGAAATACCATACCTACATTTTTCAACTCGGTATGGGA-AATGCCATACCTACATTTCTTAAC
1 ATTGAAATACCATACCTACATTTCACAACTCAGTAT-GGATAATACCATACCTACATTTCACAAC
21143088 TCAGTATGG
65 TCAGTATGG
*
21143097 ATTTGATAATACCATACCTACATTTCACAGCTCAGTATGGATAATACCATACCTACATTTCACAA
1 A-TTGA-AATACCATACCTACATTTCACAACTCAGTATGGATAATACCATACCTACATTTCACAA
21143162 CTCAGTATGG
64 CTCAGTATGG
21143172 A-TG--ATACCATACCTACATTTCACA
1 ATTGAAATACCATACCTACATTTCACA
21143196 CTTTGCCATG
Statistics
Matches: 89, Mismatches: 7, Indels: 9
0.85 0.07 0.09
Matches are distributed among these distances:
70 21 0.24
73 3 0.03
74 7 0.08
75 58 0.65
ACGTcount: A:0.34, C:0.24, G:0.11, T:0.31
Consensus pattern (73 bp):
ATTGAAATACCATACCTACATTTCACAACTCAGTATGGATAATACCATACCTACATTTCACAACT
CAGTATGG
Found at i:21150558 original size:35 final size:35
Alignment explanation
Indices: 21150514--21150680 Score: 201
Period size: 35 Copynumber: 4.6 Consensus size: 35
21150504 TCCTCATTGA
** *
21150514 AATACCATACCTACATTTTTCAACTCGGTATGGGA-
1 AATACCATACCTACATTTCACAACTCAGTAT-GGAT
* **
21150549 AATGCCATACCTACATTTCTTAACTCAGTATGGATTTGAT
1 AATACCATACCTACATTTCACAACTCAGTAT-G----GAT
*
21150589 AATACCATACCTACATTTCACAGCTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
21150624 AATACCATACCTACATTTCACAACTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
*
21150659 GATACCATACCTACATTTCACA
1 AATACCATACCTACATTTCACA
21150681 CTTTGCCATG
Statistics
Matches: 117, Mismatches: 10, Indels: 10
0.85 0.07 0.07
Matches are distributed among these distances:
35 87 0.74
39 3 0.03
40 27 0.23
ACGTcount: A:0.34, C:0.25, G:0.11, T:0.31
Consensus pattern (35 bp):
AATACCATACCTACATTTCACAACTCAGTATGGAT
Found at i:21150597 original size:75 final size:73
Alignment explanation
Indices: 21150509--21150680 Score: 226
Period size: 75 Copynumber: 2.4 Consensus size: 73
21150499 GGTTTTCCTC
** * * **
21150509 ATTGAAATACCATACCTACATTTTTCAACTCGGTATGGGA-AATGCCATACCTACATTTCTTAAC
1 ATTGAAATACCATACCTACATTTCACAACTCAGTAT-GGATAATACCATACCTACATTTCACAAC
21150573 TCAGTATGG
65 TCAGTATGG
*
21150582 ATTTGATAATACCATACCTACATTTCACAGCTCAGTATGGATAATACCATACCTACATTTCACAA
1 A-TTGA-AATACCATACCTACATTTCACAACTCAGTATGGATAATACCATACCTACATTTCACAA
21150647 CTCAGTATGG
64 CTCAGTATGG
21150657 A-TG--ATACCATACCTACATTTCACA
1 ATTGAAATACCATACCTACATTTCACA
21150681 CTTTGCCATG
Statistics
Matches: 89, Mismatches: 7, Indels: 9
0.85 0.07 0.09
Matches are distributed among these distances:
70 21 0.24
73 3 0.03
74 7 0.08
75 58 0.65
ACGTcount: A:0.34, C:0.24, G:0.11, T:0.31
Consensus pattern (73 bp):
ATTGAAATACCATACCTACATTTCACAACTCAGTATGGATAATACCATACCTACATTTCACAACT
CAGTATGG
Found at i:21157452 original size:27 final size:26
Alignment explanation
Indices: 21157402--21157456 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 26
21157392 ATTGGATATA
* *
21157402 TTTTATAAATTTTTTAATATTTTAATT
1 TTTTACAAATTTTTAAATATTTT-ATT
21157429 TTTTACAAATTTTTAAAT-TATTTATT
1 TTTTACAAATTTTTAAATAT-TTTATT
21157455 TT
1 TT
21157457 GAATTGAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 6 0.24
27 19 0.76
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (26 bp):
TTTTACAAATTTTTAAATATTTTATT
Found at i:21166864 original size:5 final size:6
Alignment explanation
Indices: 21166848--21166872 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
21166838 AAAACACATT
21166848 TAAAAA TAAAAA TAAAAA TAAAAA T
1 TAAAAA TAAAAA TAAAAA TAAAAA T
21166873 CTAATCAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (6 bp):
TAAAAA
Found at i:21172628 original size:22 final size:22
Alignment explanation
Indices: 21172603--21172647 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
21172593 TTTAATAAAA
21172603 AAAATATCTACAAAATATTCCT
1 AAAATATCTACAAAATATTCCT
* *
21172625 AAAATATTTACAGAATATTCCT
1 AAAATATCTACAAAATATTCCT
21172647 A
1 A
21172648 CACTCCCCCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.49, C:0.16, G:0.02, T:0.33
Consensus pattern (22 bp):
AAAATATCTACAAAATATTCCT
Found at i:21177225 original size:22 final size:22
Alignment explanation
Indices: 21177199--21177243 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
21177189 TTTTAATAAA
21177199 AAAATATCTACAAAATATTCCT
1 AAAATATCTACAAAATATTCCT
* *
21177221 AAAATATTTACAGAATATTCCT
1 AAAATATCTACAAAATATTCCT
21177243 A
1 A
21177244 CAAGGTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.49, C:0.16, G:0.02, T:0.33
Consensus pattern (22 bp):
AAAATATCTACAAAATATTCCT
Found at i:21181919 original size:20 final size:24
Alignment explanation
Indices: 21181869--21181926 Score: 107
Period size: 24 Copynumber: 2.4 Consensus size: 24
21181859 AATATAAATT
*
21181869 TTAAATATTTATAAGCAATTAATA
1 TTAATTATTTATAAGCAATTAATA
21181893 TTAATTATTTATAAGCAATTAATA
1 TTAATTATTTATAAGCAATTAATA
21181917 TTAATTATTT
1 TTAATTATTT
21181927 TTAAAATTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.48
Consensus pattern (24 bp):
TTAATTATTTATAAGCAATTAATA
Found at i:21189282 original size:33 final size:33
Alignment explanation
Indices: 21189244--21189308 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
21189234 CATAGCATAA
*
21189244 TTTCATGACATGTTCTTCATTTATTCAATTTAT
1 TTTCATAACATGTTCTTCATTTATTCAATTTAT
21189277 TTTCATAACATGTTCTTCATTTATTCAATTTA
1 TTTCATAACATGTTCTTCATTTATTCAATTTA
21189309 GTCCCTAATA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.26, C:0.15, G:0.05, T:0.54
Consensus pattern (33 bp):
TTTCATAACATGTTCTTCATTTATTCAATTTAT
Found at i:21191394 original size:47 final size:47
Alignment explanation
Indices: 21191285--21191395 Score: 154
Period size: 47 Copynumber: 2.4 Consensus size: 47
21191275 CCGGGATAAG
*
21191285 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACATTATAGTA
1 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTATAGTA
* * *
21191332 CACAAAGTACTTCATCGGAACAAATCCGGAACTTTAACAGTAGTCG-A
1 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTA-TAGTA
21191379 CACATAGTG-TCTCATCG
1 CACATAGTGCT-TCATCG
21191396 ACTCAATGTC
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
46 1 0.02
47 53 0.95
48 2 0.04
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.25
Consensus pattern (47 bp):
CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTATAGTA
Found at i:21192166 original size:4 final size:4
Alignment explanation
Indices: 21192157--21192181 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
21192147 CCCTTTTCTA
21192157 TTTC TTTC TTTC TTTC TTTC TTTC T
1 TTTC TTTC TTTC TTTC TTTC TTTC T
21192182 CACGTTTGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTC
Found at i:21198643 original size:47 final size:47
Alignment explanation
Indices: 21198534--21198644 Score: 154
Period size: 47 Copynumber: 2.4 Consensus size: 47
21198524 CCGGGATAAG
*
21198534 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACATTATAGTA
1 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTATAGTA
* * *
21198581 CACAAAGTACTTCATCGGAACAAATCCGGAACTTTAACAGTAGTCG-A
1 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTA-TAGTA
21198628 CACATAGTG-TCTCATCG
1 CACATAGTGCT-TCATCG
21198645 ACTCAATGTC
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
46 1 0.02
47 53 0.95
48 2 0.04
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.25
Consensus pattern (47 bp):
CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTATAGTA
Found at i:21199424 original size:14 final size:14
Alignment explanation
Indices: 21199401--21199433 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
21199391 AAATTTCCCT
21199401 TTTCTATTTCTTTC
1 TTTCTATTTCTTTC
*
21199415 TTTCTTTTTCTTTC
1 TTTCTATTTCTTTC
21199429 TTTCT
1 TTTCT
21199434 CACGTTTGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTCTATTTCTTTC
Found at i:21201164 original size:21 final size:20
Alignment explanation
Indices: 21201136--21201180 Score: 72
Period size: 21 Copynumber: 2.2 Consensus size: 20
21201126 ATCTAAACAG
21201136 AACTGCTGATGTGGCAAGTT
1 AACTGCTGATGTGGCAAGTT
*
21201156 AACTAGCTGATGTGGCCAGTT
1 AACT-GCTGATGTGGCAAGTT
21201177 AACT
1 AACT
21201181 TGCCACGTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 4 0.17
21 19 0.83
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.29
Consensus pattern (20 bp):
AACTGCTGATGTGGCAAGTT
Found at i:21202440 original size:3 final size:3
Alignment explanation
Indices: 21202434--21202467 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
21202424 CAGCTTTTTT
* *
21202434 TTC TTC TTC TTC CTA TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
21202468 CTGTTAAAGG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.03, C:0.32, G:0.00, T:0.65
Consensus pattern (3 bp):
TTC
Found at i:21202549 original size:21 final size:21
Alignment explanation
Indices: 21202523--21202563 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
21202513 CAACGTGGCA
21202523 AGTTAACTGGCCACATCAGCT
1 AGTTAACTGGCCACATCAGCT
*
21202544 AGTTAACTTGCCACATCAGC
1 AGTTAACTGGCCACATCAGC
21202564 CGTTCTGTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.24
Consensus pattern (21 bp):
AGTTAACTGGCCACATCAGCT
Found at i:21205764 original size:25 final size:25
Alignment explanation
Indices: 21205730--21205780 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
21205720 TTCCTTATAA
**
21205730 ACTTTAAATTAGGAATTCTATTAGG
1 ACTTTAAATTAGGAATTAGATTAGG
21205755 ACTTTAAATTAGGAATTAGATTAGG
1 ACTTTAAATTAGGAATTAGATTAGG
21205780 A
1 A
21205781 TTTTCCTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.39, C:0.06, G:0.18, T:0.37
Consensus pattern (25 bp):
ACTTTAAATTAGGAATTAGATTAGG
Found at i:21205779 original size:12 final size:12
Alignment explanation
Indices: 21205733--21205780 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
21205723 CTTATAAACT
21205733 TTAAATTAGGAA
1 TTAAATTAGGAA
** *
21205745 TTCTATTAGGACT
1 TTAAATTAGGA-A
21205758 TTAAATTAGGAA
1 TTAAATTAGGAA
*
21205770 TTAGATTAGGA
1 TTAAATTAGGA
21205781 TTTTCCTTTG
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
12 19 0.68
13 9 0.32
ACGTcount: A:0.40, C:0.04, G:0.19, T:0.38
Consensus pattern (12 bp):
TTAAATTAGGAA
Found at i:21210406 original size:25 final size:25
Alignment explanation
Indices: 21210372--21210420 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
21210362 CCTTATAAAT
**
21210372 TTTAAATTAGGAATTCTATTAGGAC
1 TTTAAATTAGGAATTAGATTAGGAC
21210397 TTTAAATTAGGAATTAGATTAGGA
1 TTTAAATTAGGAATTAGATTAGGA
21210421 TTTTCCTTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.39, C:0.04, G:0.18, T:0.39
Consensus pattern (25 bp):
TTTAAATTAGGAATTAGATTAGGAC
Found at i:21210419 original size:12 final size:12
Alignment explanation
Indices: 21210373--21210420 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
21210363 CTTATAAATT
21210373 TTAAATTAGGAA
1 TTAAATTAGGAA
** *
21210385 TTCTATTAGGACT
1 TTAAATTAGGA-A
21210398 TTAAATTAGGAA
1 TTAAATTAGGAA
*
21210410 TTAGATTAGGA
1 TTAAATTAGGA
21210421 TTTTCCTTTG
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
12 19 0.68
13 9 0.32
ACGTcount: A:0.40, C:0.04, G:0.19, T:0.38
Consensus pattern (12 bp):
TTAAATTAGGAA
Found at i:21219227 original size:86 final size:85
Alignment explanation
Indices: 21218985--21219227 Score: 290
Period size: 86 Copynumber: 2.8 Consensus size: 85
21218975 AGCCCATGTT
* * * * *
21218985 TTTTCTTTACACTCAATTCGGTACTTGAACTTTCAAAATACATCAAAAGGGCCCTTAAAATTTTT
1 TTTT-TTT-CACTCAATTGGGTACTTGAACTTTCAAAATACATCAAAAAGCCCCTCAAACTTTTT
* *
21219050 CAAAAAAGTAATTAAGCCCCTA
64 CAAAAAAATAACTAAGCCCCTA
* ** * * * * *
21219072 -ATTTCCCATTCAATTGGGTACTTGAACTTTCAAAATGCATCAAAAAGCCTCTCAAACTTCTCCA
1 TTTTTTTCACTCAATTGGGTACTTGAACTTTCAAAATACATCAAAAAGCCCCTCAAACTTTTTCA
*
21219136 CAAAAATCAACTAAGCCCCTA
66 AAAAAAT-AACTAAGCCCCTA
* *
21219157 TTTTTTTCACTCAATTGGGTACTTGAACTTTCAAAACACATAAAAAAGCCCCTCAAACTTTTTCA
1 TTTTTTTCACTCAATTGGGTACTTGAACTTTCAAAATACATCAAAAAGCCCCTCAAACTTTTTCA
21219222 AAAAAA
66 AAAAAA
21219228 GCAATTAAAC
Statistics
Matches: 127, Mismatches: 27, Indels: 5
0.80 0.17 0.03
Matches are distributed among these distances:
84 53 0.42
85 13 0.10
86 61 0.48
ACGTcount: A:0.37, C:0.23, G:0.08, T:0.31
Consensus pattern (85 bp):
TTTTTTTCACTCAATTGGGTACTTGAACTTTCAAAATACATCAAAAAGCCCCTCAAACTTTTTCA
AAAAAATAACTAAGCCCCTA
Found at i:21219452 original size:20 final size:20
Alignment explanation
Indices: 21219429--21219476 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
21219419 AATAAAAGTT
*
21219429 ATAAAAATGA-TTAACTTTTA
1 ATAAAAAT-ATTTAAATTTTA
21219449 ATAAAAATATTTAAATTTTA
1 ATAAAAATATTTAAATTTTA
*
21219469 TTAAAAAT
1 ATAAAAAT
21219477 TAGAAATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 1 0.04
20 24 0.96
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (20 bp):
ATAAAAATATTTAAATTTTA
Found at i:21219514 original size:9 final size:9
Alignment explanation
Indices: 21219502--21219582 Score: 65
Period size: 10 Copynumber: 8.6 Consensus size: 9
21219492 AAAAATTGTA
21219502 AAAATATAT
1 AAAATATAT
21219511 AAAATATAT
1 AAAATATAT
*
21219520 AAAATTTTAT
1 AAAA-TATAT
21219530 AAAA-ATCAT
1 AAAATAT-AT
*
21219539 AAAAAATTAT
1 AAAATA-TAT
*
21219549 AAAACATAT
1 AAAATATAT
*
21219558 AGAAATATAG
1 A-AAATATAT
*
21219568 AAAAAATTAT
1 AAAATA-TAT
21219578 AAAAT
1 AAAAT
21219583 TTTATAAAGT
Statistics
Matches: 58, Mismatches: 8, Indels: 11
0.75 0.10 0.14
Matches are distributed among these distances:
8 1 0.02
9 27 0.47
10 29 0.50
11 1 0.02
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (9 bp):
AAAATATAT
Found at i:21219522 original size:19 final size:18
Alignment explanation
Indices: 21219489--21219572 Score: 71
Period size: 19 Copynumber: 4.4 Consensus size: 18
21219479 GAAATTTTTT
*
21219489 TATAAAAATTGTAAAAATA
1 TATAAAAA-TATAAAAATA
* *
21219508 TATAAAATATATAAAATTT
1 TATAAAA-ATATAAAAATA
21219527 TATAAAAATCATAAAAA-A
1 TATAAAAAT-ATAAAAATA
*
21219545 TTATAAAACATATAGAAATA
1 -TATAAAA-ATATAAAAATA
*
21219565 TAGAAAAA
1 TATAAAAA
21219573 ATTATAAAAT
Statistics
Matches: 53, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
18 3 0.06
19 46 0.87
20 4 0.08
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (18 bp):
TATAAAAATATAAAAATA
Found at i:21219542 original size:38 final size:39
Alignment explanation
Indices: 21219486--21219563 Score: 106
Period size: 38 Copynumber: 2.0 Consensus size: 39
21219476 TTAGAAATTT
** *
21219486 TTTTATAAAAATTGT-AAAAATATATAAAATATATA-AAA
1 TTTTATAAAAATCATAAAAAAT-TATAAAACATATAGAAA
21219524 TTTTATAAAAATCATAAAAAATTATAAAACATATAGAAA
1 TTTTATAAAAATCATAAAAAATTATAAAACATATAGAAA
21219563 T
1 T
21219564 ATAGAAAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
38 25 0.71
39 10 0.29
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.35
Consensus pattern (39 bp):
TTTTATAAAAATCATAAAAAATTATAAAACATATAGAAA
Found at i:21224706 original size:26 final size:26
Alignment explanation
Indices: 21224677--21224904 Score: 213
Period size: 26 Copynumber: 8.8 Consensus size: 26
21224667 CGTAATGTAC
** *
21224677 TTTATTTAATAGGCTTTGAGTCGGTG
1 TTTATTTAGCAGGCTTTGAGCCGGTG
* * ** *
21224703 TTTATTTAGCAAGTTTTGAGCTAGTT
1 TTTATTTAGCAGGCTTTGAGCCGGTG
*
21224729 TTTATTTAGCAGGCTTTGAGCTGGTG
1 TTTATTTAGCAGGCTTTGAGCCGGTG
* *
21224755 TTTATTTAGAAGGCTTTGAGCCGATG
1 TTTATTTAGCAGGCTTTGAGCCGGTG
* *
21224781 ATTATTTAGCAGGCCTTGAGCCGGTG
1 TTTATTTAGCAGGCTTTGAGCCGGTG
* ** * *
21224807 TGTATTTAATAGGCCTTAAGCCGGTG
1 TTTATTTAGCAGGCTTTGAGCCGGTG
* * * **
21224833 TGTATTTAGCAGGCCTTGAGTCAATG
1 TTTATTTAGCAGGCTTTGAGCCGGTG
* *
21224859 TTGATCTAGCAGGCTTTGAGCCGGTG
1 TTTATTTAGCAGGCTTTGAGCCGGTG
* *
21224885 ATTATTTAGTAGGCTTTGAG
1 TTTATTTAGCAGGCTTTGAG
21224905 TTAGTGATTA
Statistics
Matches: 161, Mismatches: 41, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
26 161 1.00
ACGTcount: A:0.21, C:0.13, G:0.28, T:0.39
Consensus pattern (26 bp):
TTTATTTAGCAGGCTTTGAGCCGGTG
Found at i:21235889 original size:46 final size:46
Alignment explanation
Indices: 21235838--21236064 Score: 223
Period size: 46 Copynumber: 5.0 Consensus size: 46
21235828 GACGAGGGCT
21235838 AGTGTAAGACATGTCTGGGACATGCATCAGCCACAGTATGA-GAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCACAG-ATGATGAGCC
* *
21235884 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGAT-AGCC
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCAC-AGATGATGAGCC
* * * * * *
21235930 AGTGTCAGACATGTCTGGGACATGCGTCGGCTAC-GA-GATGTGCT
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCACAGATGATGAGCC
* * * * * *
21235974 AGTGTAAGACATGTCTGGGACATGCGTCAG-CACGGTTACATGTGTC
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCACAGAT-GATGAGCC
* *
21236020 AGTGTAAGACCTGTCTGGGACATGGCATC-GACACAGATGGATGAG
1 AGTGTAAGACATGTCTGGGACAT-GCATCAGCCACAGAT-GATGAG
21236065 AGCTAGTACA
Statistics
Matches: 151, Mismatches: 22, Indels: 15
0.80 0.12 0.08
Matches are distributed among these distances:
43 5 0.03
44 33 0.22
46 98 0.65
47 15 0.10
ACGTcount: A:0.26, C:0.20, G:0.31, T:0.22
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGCATCAGCCACAGATGATGAGCC
Done.