Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008091.1 Hibiscus syriacus cultivar Beakdansim tig00110602_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2471235
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 11
Found at i:1010956 original size:232 final size:237
Alignment explanation
Indices: 1010555--1011025 Score: 880
Period size: 232 Copynumber: 2.0 Consensus size: 237
1010545 TTTTGGTATA
1010555 CAAATATATGGGATACTAGGGTAAATTTCCTAACCCTAATTCATTCTTCCTCTCAACCTAAACCA
1 CAAATATATGGGATACTAGGGTAAATTTCCTAACCCTAATTCATTCTTCCTCTCAACCTAAACCA
1010620 GGTAAACTCTCCCCCCGCCATTTTCCTTATCTCTCCCTTTCTCTCTCACCCTTCCCATTTGTAAC
66 GGTAAACTCTCCCCCCGCCATTTTCC-TA-CTCTCCCTTTCTCTCTCACCCTTCCCATTTGTAAC
1010685 AGAACCCCCAAGCCTCCATGGCTCCCGTCGCCGATTTGCTCTCATAACTCGACCATGACAGCCAC
129 AGAACCCCCAAGCCTCCATGGCTCCCGTCGCCGATTTGCTCTCATAACTCGACCATGACAGCCAC
1010750 CGCGGCTGCCGCCTCTCTTATTTCAACTCACCCCAAAACCAACG
194 CGCGGCTGCCGCCTCTCTTATTTCAACTCACCCCAAAACCAACG
1010794 CAAATATATGGGATACTAGGGT-AATTTCCTAACCCTAATTCATTCTTCCTCTCAACCTAAACCA
1 CAAATATATGGGATACTAGGGTAAATTTCCTAACCCTAATTCATTCTTCCTCTCAACCTAAACCA
1010858 GGTAAACTCT-CCCCCGCCATTTTCC-A-TCTCCCTTTCTCTCTC-CCCTTCCCATTTGTAACAG
66 GGTAAACTCTCCCCCCGCCATTTTCCTACTCTCCCTTTCTCTCTCACCCTTCCCATTTGTAACAG
*
1010919 AACCCCCAAGCCTCCATGGCTCCCGTCGCCGATTTGCTCTCATAACTCGACCATGGCAGCCACCG
131 AACCCCCAAGCCTCCATGGCTCCCGTCGCCGATTTGCTCTCATAACTCGACCATGACAGCCACCG
1010984 CGGCTGCCGCCTCTCTTATTTCAACTCACCCCAAAACCAACG
196 CGGCTGCCGCCTCTCTTATTTCAACTCACCCCAAAACCAACG
1011026 ACCTAAACAC
Statistics
Matches: 231, Mismatches: 1, Indels: 7
0.97 0.00 0.03
Matches are distributed among these distances:
232 125 0.54
233 16 0.07
235 1 0.00
237 15 0.06
238 52 0.23
239 22 0.10
ACGTcount: A:0.23, C:0.38, G:0.12, T:0.27
Consensus pattern (237 bp):
CAAATATATGGGATACTAGGGTAAATTTCCTAACCCTAATTCATTCTTCCTCTCAACCTAAACCA
GGTAAACTCTCCCCCCGCCATTTTCCTACTCTCCCTTTCTCTCTCACCCTTCCCATTTGTAACAG
AACCCCCAAGCCTCCATGGCTCCCGTCGCCGATTTGCTCTCATAACTCGACCATGACAGCCACCG
CGGCTGCCGCCTCTCTTATTTCAACTCACCCCAAAACCAACG
Found at i:1011418 original size:15 final size:16
Alignment explanation
Indices: 1011400--1011438 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
1011390 GGTACTCGGA
1011400 TTTTCTTTTCCT-TTT
1 TTTTCTTTTCCTATTT
* *
1011415 TTTTGTTTTGCTATTT
1 TTTTCTTTTCCTATTT
1011431 TTTTCTTT
1 TTTTCTTT
1011439 GATTACCCGT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.03, C:0.13, G:0.05, T:0.79
Consensus pattern (16 bp):
TTTTCTTTTCCTATTT
Found at i:1012462 original size:41 final size:41
Alignment explanation
Indices: 1012407--1012518 Score: 109
Period size: 42 Copynumber: 2.7 Consensus size: 41
1012397 ATCCTGCCCG
* * * *
1012407 AAGGTCTTATGGATGGCTTGAAGGACTTATCATCC-TGCTCTA
1 AAGG-CTTACGGATGGCCTGAAGGACTTAGCA-CCATGCTCAA
* * *
1012449 AAGGCTTACGGATGACCCGAAGGATTTAAGCACCATGCTCAA
1 AAGGCTTACGGATGGCCTGAAGGACTT-AGCACCATGCTCAA
* *
1012491 AAGACTTACTGATGGCCTGAAGGACTTA
1 AAGGCTTACGGATGGCCTGAAGGACTTA
1012519 CAAATCGTGA
Statistics
Matches: 56, Mismatches: 12, Indels: 5
0.77 0.16 0.07
Matches are distributed among these distances:
41 21 0.38
42 35 0.62
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (41 bp):
AAGGCTTACGGATGGCCTGAAGGACTTAGCACCATGCTCAA
Found at i:1012677 original size:41 final size:41
Alignment explanation
Indices: 1012622--1012733 Score: 116
Period size: 42 Copynumber: 2.7 Consensus size: 41
1012612 ATCCTACCCG
* * * *
1012622 AAGGTCTTATGGATGGTCCGAAGGACTTATCATCCTACTCTA
1 AAGG-CTTATGGATGGCCCGAAGGACTTAGCATCATACTCAA
* * * *
1012664 AAGGCTTACGGATGACCCGAAGGATTTAAGCATCATGCTCAA
1 AAGGCTTATGGATGGCCCGAAGGACTT-AGCATCATACTCAA
* *
1012706 AAGACTTATTGATGGCCCGAAGGACTTA
1 AAGGCTTATGGATGGCCCGAAGGACTTA
1012734 CAAATCGTGA
Statistics
Matches: 56, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
41 20 0.36
42 36 0.64
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (41 bp):
AAGGCTTATGGATGGCCCGAAGGACTTAGCATCATACTCAA
Found at i:1012928 original size:217 final size:215
Alignment explanation
Indices: 1012386--1013156 Score: 1168
Period size: 217 Copynumber: 3.6 Consensus size: 215
1012376 CCTTATTATC
* **
1012386 CTTGTGAAAACATCCTGCCCGAAGGTCTTATGGATGGCTTGAAGGACTTATCATCCTGCTCTAAA
1 CTTGTGAAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCCTGCTCTAAA
* * *
1012451 GGCTTACGGATGACCCGAAGGATTTAAGCACCATGCTCAAAAGACTTACTGATGGCCTGAAGGAC
66 GGCTTACAGATGACCCGAAGGATTTAAGCATCATGCTCAAAAGACTTACTGATGGCCCGAAGGAC
*
1012516 TTACAAATCGTGAAATTTTGAAACTCGCATTCTTTGTTTTCAAAAATTTCATCTTCTTAAAACAT
131 TTACAAATCGTGAAATTTTGAAAATCGCATTCTTTGTTTTCAAAAATTTCATCTTCTTAAAACAT
*
1012581 AATTTTTTCATTTTCAAATT
196 CATTTTTTCATTTTCAAATT
* *
1012601 CTTGTGAAAACATCCTACCCGAAGGTCTTATGGATGGTCCGAAGGACTTATCATCCTACTCTAAA
1 CTTGTGAAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCCTGCTCTAAA
* *
1012666 GGCTTACGGATGACCCGAAGGATTTAAGCATCATGCTCAAAAGACTTATTGATGGCCCGAAGGAC
66 GGCTTACAGATGACCCGAAGGATTTAAGCATCATGCTCAAAAGACTTACTGATGGCCCGAAGGAC
*
1012731 TTACAAATCGTGAAATTTTGAAAATCGCATTCTTTGTTTTCAAACATTTCATCTTCTTAAAACAT
131 TTACAAATCGTGAAATTTTGAAAATCGCATTCTTTGTTTTCAAAAATTTCATCTTCTTAAAACAT
1012796 CATTTTTTTTCATTTTCAAATT
196 CA--TTTTTTCATTTTCAAATT
* * * * *
1012818 CTTGTGAGAACATCCTACCTGAAGGTTTTATGGATGGCCCGAATGACTTATCATCTTGCTCTAAA
1 CTTGTGAAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCCTGCTCTAAA
* *
1012883 GGCTTACAGATGACCCGAAGGATTTAAGCATTATGCTCGAAAGACTTACTGATGGCCCGAAGGAC
66 GGCTTACAGATGACCCGAAGGATTTAAGCATCATGCTCAAAAGACTTACTGATGGCCCGAAGGAC
* ** * * * *
1012948 TTATAAATTATGAAAATTTGAAAATCGCATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACAC
131 TTACAAATCGTGAAATTTTGAAAATCGCATTCTTTGTTTTCAAAAATTTCATCTTCTTAAAACAT
1013013 CA-TTTTTCATTTTCAAATT
196 CATTTTTTCATTTTCAAATT
** *
1013032 AATGTGAAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCTAAA
1 CTTGTGAAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCCTGCTCTAAA
* * * * * * * *
1013097 GACTTACAGATGACCCGAAGGACTT-ATCATCTTGATCTAAAGACTTACAGATGACCCGAA
66 GGCTTACAGATGACCCGAAGGATTTAAGCATCATGCTCAAAAGACTTACTGATGGCCCGAA
1013157 TGATTTAAGC
Statistics
Matches: 509, Mismatches: 45, Indels: 6
0.91 0.08 0.01
Matches are distributed among these distances:
213 28 0.06
214 99 0.19
215 186 0.37
217 196 0.39
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Consensus pattern (215 bp):
CTTGTGAAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCCTGCTCTAAA
GGCTTACAGATGACCCGAAGGATTTAAGCATCATGCTCAAAAGACTTACTGATGGCCCGAAGGAC
TTACAAATCGTGAAATTTTGAAAATCGCATTCTTTGTTTTCAAAAATTTCATCTTCTTAAAACAT
CATTTTTTCATTTTCAAATT
Found at i:1012958 original size:42 final size:42
Alignment explanation
Indices: 1012850--1012959 Score: 111
Period size: 42 Copynumber: 2.6 Consensus size: 42
1012840 AGGTTTTATG
* * * *
1012850 GATGGCCCGAATGACTTAT-CATCT-TGCTCTAAAGGCTTACA
1 GATGGCCCGAAGGACTTATAAAT-TATGCTCGAAAGACTTACA
* *
1012891 GATGACCCGAAGGA-TT-TAAGCATTATGCTCGAAAGACTTACT
1 GATGGCCCGAAGGACTTATAA--ATTATGCTCGAAAGACTTACA
1012933 GATGGCCCGAAGGACTTATAAATTATG
1 GATGGCCCGAAGGACTTATAAATTATG
1012960 AAAATTTGAA
Statistics
Matches: 56, Mismatches: 7, Indels: 11
0.76 0.09 0.15
Matches are distributed among these distances:
39 1 0.02
40 2 0.04
41 13 0.23
42 35 0.62
43 2 0.04
44 3 0.05
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (42 bp):
GATGGCCCGAAGGACTTATAAATTATGCTCGAAAGACTTACA
Found at i:1013101 original size:21 final size:21
Alignment explanation
Indices: 1013076--1013143 Score: 59
Period size: 21 Copynumber: 3.3 Consensus size: 21
1013066 TGGCCCGAAG
1013076 GACTTATCATCTTGCTCTAAA
1 GACTTATCATCTTGCTCTAAA
** * * *
1013097 GACTTA-CA-GATGACCCGAAG
1 GACTTATCATCTTG-CTCTAAA
*
1013117 GACTTATCATCTTGATCTAAA
1 GACTTATCATCTTGCTCTAAA
1013138 GACTTA
1 GACTTA
1013144 CAGATGACCC
Statistics
Matches: 33, Mismatches: 11, Indels: 6
0.66 0.22 0.12
Matches are distributed among these distances:
19 2 0.06
20 12 0.36
21 17 0.52
22 2 0.06
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.31
Consensus pattern (21 bp):
GACTTATCATCTTGCTCTAAA
Found at i:1013197 original size:42 final size:41
Alignment explanation
Indices: 1013064--1013206 Score: 196
Period size: 41 Copynumber: 3.5 Consensus size: 41
1013054 AGGTCTTATG
*
1013064 GATGGCCCGAAGGACTTATCATCTTGCTCTAAAGACTTACA
1 GATGACCCGAAGGACTTATCATCTTGCTCTAAAGACTTACA
*
1013105 GATGACCCGAAGGACTTATCATCTTGATCTAAAGACTTACA
1 GATGACCCGAAGGACTTATCATCTTGCTCTAAAGACTTACA
* * * * * *
1013146 GATGACCCGAATGATTTAAGCATCATGCTCGAAAGACTTACT
1 GATGACCCGAAGGACTT-ATCATCTTGCTCTAAAGACTTACA
*
1013188 GATGGCCCGAAGGACTTAT
1 GATGACCCGAAGGACTTAT
1013207 AAATTGTGAA
Statistics
Matches: 88, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
41 55 0.62
42 33 0.38
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.26
Consensus pattern (41 bp):
GATGACCCGAAGGACTTATCATCTTGCTCTAAAGACTTACA
Found at i:1013225 original size:255 final size:255
Alignment explanation
Indices: 1012850--1013415 Score: 925
Period size: 255 Copynumber: 2.2 Consensus size: 255
1012840 AGGTTTTATG
* * *
1012850 GATGGCCCGAATGACTTATCATCTTGCTCTAAAGGCTTACAGATGACCCGAAGGATTTAAGCATT
1 GATGACCCGAATGACTTATCATCTTGCTCTAAAGACTTACAGATGACCCGAAGGATTTAAGCATC
*
1012915 ATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTATGAAAATTTGAAAATCGCATTC
66 ATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTATGAAAATTTGAAAATCACATTC
1012980 TTCGTTTTCAAAAATTCCATCTTCTTAAAACACCATTTTTCATTTTCAAATTAATGTGAAAACAT
131 TTCGTTTTCAAAAATTCCATCTTCTTAAAACACCATTTTTCATTTTCAAATTAATGTGAAAACAT
*
1013045 CCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCTAAAGACTTACA
196 CCTACCCAAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCTAAAGACTTACA
* * *
1013105 GATGACCCGAAGGACTTATCATCTTGATCTAAAGACTTACAGATGACCCGAATGATTTAAGCATC
1 GATGACCCGAATGACTTATCATCTTGCTCTAAAGACTTACAGATGACCCGAAGGATTTAAGCATC
* *
1013170 ATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTGTGAAATTTTGAAAATCACATTC
66 ATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTATGAAAATTTGAAAATCACATTC
* ** *
1013235 TTTGTTTTCAAAAATTTTATCTTCTTAAAACATCATTTTTCATTTTCAAATTAATGTGAAAACAT
131 TTCGTTTTCAAAAATTCCATCTTCTTAAAACACCATTTTTCATTTTCAAATTAATGTGAAAACAT
* *
1013300 CCTACCCAAAGGTCTTATGGATGGTCTGAAGGACTTATCATCTTGCTCTAAAGACTTACA
196 CCTACCCAAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCTAAAGACTTACA
* * * * * *
1013360 GATGACCCGAATGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGA
1 GATGACCCGAATGACTT-ATCATCTTGCTCTAAAGACTTACAGATGACCCGAAGGA
1013416 CTTACAAATC
Statistics
Matches: 285, Mismatches: 25, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
255 254 0.89
256 31 0.11
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (255 bp):
GATGACCCGAATGACTTATCATCTTGCTCTAAAGACTTACAGATGACCCGAAGGATTTAAGCATC
ATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTATGAAAATTTGAAAATCACATTC
TTCGTTTTCAAAAATTCCATCTTCTTAAAACACCATTTTTCATTTTCAAATTAATGTGAAAACAT
CCTACCCAAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCTAAAGACTTACA
Found at i:1013482 original size:214 final size:214
Alignment explanation
Indices: 1013105--1014169 Score: 1679
Period size: 214 Copynumber: 5.0 Consensus size: 214
1013095 AAGACTTACA
* * * * *
1013105 GATGACCCGAAGGACTTATCATCTTGA-TCTAAAGACTTACAGATGACCCGAATGATTTAAGCAT
1 GATGGCCCGAAGGACTTATCATCCT-ACTCTAAAGGCTTACGGATGACCCGAAGGATTTAAGCAT
* * *
1013169 CATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTGTGAAATTTTGAAAATCACATT
65 CATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACAAATCGTGAAATTTTGAAAATCGCATT
** * *
1013234 CTTTGTTTTCAAAAATTTTATCTTCTTAAAACATCATTTTTCATTTTCAAATTAATGTGAAAACA
130 CTTTGTTTTCAAAAATTCCATCTTCTTAAAACATCATTTTTCATTTTCAAATTCATTTGAAAACA
*
1013299 TCCTACCCAAAGGTCTTATG
195 TCCTACCCGAAGGTCTTATG
* * * * * * *
1013319 GATGGTCTGAAGGACTTATCATCTTGCTCTAAAGACTTACAGATGACCCGAATGATTTAAGCATC
1 GATGGCCCGAAGGACTTATCATCCTACTCTAAAGGCTTACGGATGACCCGAAGGATTTAAGCATC
*
1013384 ATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACAAATCGTGAAATTTTGAAAATCGTATTC
66 ATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACAAATCGTGAAATTTTGAAAATCGCATTC
*
1013449 TTTGTTTTCAAAAATTCCATCTTCTTAAAACATCATTTTTCATTTT-TAATTCATTTGAAAACAT
131 TTTGTTTTCAAAAATTCCATCTTCTTAAAACATCATTTTTCATTTTCAAATTCATTTGAAAACAT
1013513 CCTACCCGAAGGTCTTATG
196 CCTACCCGAAGGTCTTATG
* *
1013532 GATGGCCCGAATGACTTATCATCCTACTCTAAAGGCTTACGGATGACCCGAAAGATTTAAGCATC
1 GATGGCCCGAAGGACTTATCATCCTACTCTAAAGGCTTACGGATGACCCGAAGGATTTAAGCATC
*
1013597 ATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACAAATCGTGAAATTTTGAAAATCGTATTC
66 ATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACAAATCGTGAAATTTTGAAAATCGCATTC
*
1013662 TTTGTTTTCAAAAATTCCATCTTCTTAAAACATCATTTTTCATTTTTAAATTCATTTGAAAACAT
131 TTTGTTTTCAAAAATTCCATCTTCTTAAAACATCATTTTTCATTTTCAAATTCATTTGAAAACAT
1013727 CCTACCCGAAGGTCTTATG
196 CCTACCCGAAGGTCTTATG
1013746 GATGGCCCGAAGGACTTATCATCCTACTCTAAAGGCTTACGGATGACCCGAAGGATTTAAGCATC
1 GATGGCCCGAAGGACTTATCATCCTACTCTAAAGGCTTACGGATGACCCGAAGGATTTAAGCATC
* *
1013811 ATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTGTGAAATTTTGAAAATCGCATTC
66 ATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACAAATCGTGAAATTTTGAAAATCGCATTC
* *
1013876 TTTGTTTTCAAAAATTCCATCTTCTTAAAACATCATTTTTCATTTTTAAATTCATTTGAAAATAT
131 TTTGTTTTCAAAAATTCCATCTTCTTAAAACATCATTTTTCATTTTCAAATTCATTTGAAAACAT
1013941 CCTACCCGAAGGTCTTATG
196 CCTACCCGAAGGTCTTATG
1013960 GATGGCCCGAAGGACTTATCATCCTACTCTAAAGGCTTACGGATGACCCGAAGGATTTAAGCATC
1 GATGGCCCGAAGGACTTATCATCCTACTCTAAAGGCTTACGGATGACCCGAAGGATTTAAGCATC
* * *
1014025 ATGCTCAAAAGACTTACTGATGGCTCGAAAGACTTACAAATCGTGAAATTTTGAAAATCGCATTC
66 ATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACAAATCGTGAAATTTTGAAAATCGCATTC
*
1014090 TTCGTTTTCAAAAA-T---TC--C----AACATCATTTTTTCATTTTCAAATTC-TTGTGAAAAC
131 TTTGTTTTCAAAAATTCCATCTTCTTAAAACATCA-TTTTTCATTTTCAAATTCATT-TGAAAAC
** *
1014144 ATCCTACCTAAAGGTTTTATG
194 ATCCTACCCGAAGGTCTTATG
1014165 GATGG
1 GATGG
1014170 TTTGCTTCAC
Statistics
Matches: 807, Mismatches: 40, Indels: 17
0.93 0.05 0.02
Matches are distributed among these distances:
204 9 0.01
205 46 0.06
208 1 0.00
210 2 0.00
213 202 0.25
214 547 0.68
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.33
Consensus pattern (214 bp):
GATGGCCCGAAGGACTTATCATCCTACTCTAAAGGCTTACGGATGACCCGAAGGATTTAAGCATC
ATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACAAATCGTGAAATTTTGAAAATCGCATTC
TTTGTTTTCAAAAATTCCATCTTCTTAAAACATCATTTTTCATTTTCAAATTCATTTGAAAACAT
CCTACCCGAAGGTCTTATG
Found at i:1013576 original size:41 final size:41
Alignment explanation
Indices: 1013521--1013632 Score: 107
Period size: 42 Copynumber: 2.7 Consensus size: 41
1013511 ATCCTACCCG
* * * * *
1013521 AAGGTCTTATGGATGGCCCGAATGACTTATCATCCTACTCTA
1 AAGG-CTTACGGATGGCCCGAAAGACTTAGCATCATACTCGA
* * *
1013563 AAGGCTTACGGATGACCCGAAAGATTTAAGCATCATGCTCGA
1 AAGGCTTACGGATGGCCCGAAAGACTT-AGCATCATACTCGA
* * *
1013605 AAGACTTACTGATGGCCCGAAGGACTTA
1 AAGGCTTACGGATGGCCCGAAAGACTTA
1013633 CAAATCGTGA
Statistics
Matches: 56, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
41 20 0.36
42 36 0.64
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.25
Consensus pattern (41 bp):
AAGGCTTACGGATGGCCCGAAAGACTTAGCATCATACTCGA
Found at i:1013610 original size:469 final size:470
Alignment explanation
Indices: 1012663--1013628 Score: 1486
Period size: 469 Copynumber: 2.1 Consensus size: 470
1012653 ATCCTACTCT
* * *
1012663 AAAGGCTTACGGATGACCCGAAGGATTTAAGCATCATGCTCAAAAGACTTATTGATGGCCCGAAG
1 AAAGACTTACAGATGACCCGAAGGATTTAAGCATCATGCTCAAAAGACTTACTGATGGCCCGAAG
* *
1012728 GACTTACAAATCGTGAAATTTTGAAAATCGCATTCTTTGTTTTCAAACATTTCATCTTCTTAAAA
66 GACTTACAAATCGTGAAATTTTGAAAATCACATTCTTTGTTTTCAAAAATTTCATCTTCTTAAAA
** * ** *
1012793 CATCATTTTTTTTCATTTTCAAATTCTTGTGAGAACATCCTACCTGAAGGTTTTATGGATGGCCC
131 CATCA--TTTTTTCATTTTCAAATTAATGTGAAAACATCCTACCCAAAGGTCTTATGGATGGCCC
* * *
1012858 GAATGACTTATCATCTTGCTCTAAAGGCTTACAGATGACCCGAAGGATTTAAGCATTATGCTCGA
194 GAAGGACTTATCATCTTGCTCTAAAGACTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGA
* *
1012923 AAGACTTACTGATGGCCCGAAGGACTTATAAATTATGAAAATTTGAAAATCGCATTCTTCGTTTT
259 AAGACTTACTGATGGCCCGAAGGACTTACAAATCATGAAAATTTGAAAATCGCATTCTTCGTTTT
1012988 CAAAAATTCCATCTTCTTAAAACACCATTTTTCATTTTCAAATTAATGTGAAAACATCCTACCCG
324 CAAAAATTCCATCTTCTTAAAACACCATTTTTCATTTTCAAATTAATGTGAAAACATCCTACCCG
* * *
1013053 AAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCTAAAGACTTACAGATGACCCGAAGG
389 AAGGTCTTATGGATGGCCCGAAGGACTTATCATCCTACTCTAAAGACTTACAGATGACCCGAAAG
* * *
1013118 ACTTATCATCTTGATCT
454 ACTTAGCATCATGATCG
* *
1013135 AAAGACTTACAGATGACCCGAATGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAG
1 AAAGACTTACAGATGACCCGAAGGATTTAAGCATCATGCTCAAAAGACTTACTGATGGCCCGAAG
* * *
1013200 GACTTATAAATTGTGAAATTTTGAAAATCACATTCTTTGTTTTCAAAAATTTTATCTTCTTAAAA
66 GACTTACAAATCGTGAAATTTTGAAAATCACATTCTTTGTTTTCAAAAATTTCATCTTCTTAAAA
* *
1013265 CATCA-TTTTTCATTTTCAAATTAATGTGAAAACATCCTACCCAAAGGTCTTATGGATGGTCTGA
131 CATCATTTTTTCATTTTCAAATTAATGTGAAAACATCCTACCCAAAGGTCTTATGGATGGCCCGA
*
1013329 AGGACTTATCATCTTGCTCTAAAGACTTACAGATGACCCGAATGATTTAAGCATCATGCTCGAAA
196 AGGACTTATCATCTTGCTCTAAAGACTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAA
* * * *
1013394 GACTTACTGATGGCCCGAAGGACTTACAAATCGTGAAATTTTGAAAATCGTATTCTTTGTTTTCA
261 GACTTACTGATGGCCCGAAGGACTTACAAATCATGAAAATTTGAAAATCGCATTCTTCGTTTTCA
* * * *
1013459 AAAATTCCATCTTCTTAAAACATCATTTTTCATTTT-TAATTCATTTGAAAACATCCTACCCGAA
326 AAAATTCCATCTTCTTAAAACACCATTTTTCATTTTCAAATTAATGTGAAAACATCCTACCCGAA
* * * *
1013523 GGTCTTATGGATGGCCCGAATGACTTATCATCCTACTCTAAAGGCTTACGGATGACCCGAAAGAT
391 GGTCTTATGGATGGCCCGAAGGACTTATCATCCTACTCTAAAGACTTACAGATGACCCGAAAGAC
*
1013588 TTAAGCATCATGCTCG
456 TT-AGCATCATGATCG
* *
1013604 AAAGACTTACTGATGGCCCGAAGGA
1 AAAGACTTACAGATGACCCGAAGGA
1013629 CTTACAAATC
Statistics
Matches: 447, Mismatches: 46, Indels: 5
0.90 0.09 0.01
Matches are distributed among these distances:
468 85 0.19
469 237 0.53
472 125 0.28
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (470 bp):
AAAGACTTACAGATGACCCGAAGGATTTAAGCATCATGCTCAAAAGACTTACTGATGGCCCGAAG
GACTTACAAATCGTGAAATTTTGAAAATCACATTCTTTGTTTTCAAAAATTTCATCTTCTTAAAA
CATCATTTTTTCATTTTCAAATTAATGTGAAAACATCCTACCCAAAGGTCTTATGGATGGCCCGA
AGGACTTATCATCTTGCTCTAAAGACTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAA
GACTTACTGATGGCCCGAAGGACTTACAAATCATGAAAATTTGAAAATCGCATTCTTCGTTTTCA
AAAATTCCATCTTCTTAAAACACCATTTTTCATTTTCAAATTAATGTGAAAACATCCTACCCGAA
GGTCTTATGGATGGCCCGAAGGACTTATCATCCTACTCTAAAGACTTACAGATGACCCGAAAGAC
TTAGCATCATGATCG
Found at i:1013724 original size:427 final size:426
Alignment explanation
Indices: 1013105--1014170 Score: 1704
Period size: 427 Copynumber: 2.5 Consensus size: 426
1013095 AAGACTTACA
* * * * *
1013105 GATGACCCGAAGGACTTATCATCTTGA-TCTAAAGACTTACAGATGACCCGAATGATTTAAGCAT
1 GATGGCCCGAAGGACTTATCATCCT-ACTCTAAAGGCTTACGGATGACCCGAAAGATTTAAGCAT
* * *
1013169 CATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTGTGAAATTTTGAAAATCACATT
65 CATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACAAATCGTGAAATTTTGAAAATCGCATT
* *
1013234 CTTTGTTTTCAAAAATTTTATCTTCTTAAAACATCATTTTTCATTTTCAAATTAATGTGAAAACA
130 CTTTGTTTTCAAAAA--TTATCTTCTTAAAACATCATTTTTCATTTTCAAATTCATTTGAAAACA
* * *
1013299 TCCTACCCAAAGGTCTTATGGATGGTCTGAAGGACTTATCATCTTGCTCTAAAGACTTACAGATG
193 TCCTACCCAAAGGTCTTATGGATGGTCCGAAGGACTTATCATCCTACTCTAAAGACTTACAGATG
*
1013364 ACCCGAATGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACAAATCGTG
258 ACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACAAATCGTG
*
1013429 AAATTTTGAAAATCGTATTCTTTGTTTTCAAAAATTCCATCTTCTTAAAACATCATTTTTCATTT
323 AAATTTTGAAAATCGCATTCTTTGTTTTCAAAAATTCCATCTTCTTAAAACATCATTTTTCATTT
1013494 TT-AATTCATTTGAAAACATCCTACCCGAAGGTCTTATG
388 TTAAATTCATTTGAAAACATCCTACCCGAAGGTCTTATG
*
1013532 GATGGCCCGAATGACTTATCATCCTACTCTAAAGGCTTACGGATGACCCGAAAGATTTAAGCATC
1 GATGGCCCGAAGGACTTATCATCCTACTCTAAAGGCTTACGGATGACCCGAAAGATTTAAGCATC
*
1013597 ATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACAAATCGTGAAATTTTGAAAATCGTATTC
66 ATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACAAATCGTGAAATTTTGAAAATCGCATTC
*
1013662 TTTGTTTTCAAAAATTCCATCTTCTTAAAACATCATTTTTCATTTTTAAATTCATTTGAAAACAT
131 TTTGTTTTCAAAAATT--ATCTTCTTAAAACATCATTTTTCATTTTCAAATTCATTTGAAAACAT
* * * *
1013727 CCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCCTACTCTAAAGGCTTACGGATGA
194 CCTACCCAAAGGTCTTATGGATGGTCCGAAGGACTTATCATCCTACTCTAAAGACTTACAGATGA
* *
1013792 CCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTGTGA
259 CCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACAAATCGTGA
1013857 AATTTTGAAAATCGCATTCTTTGTTTTCAAAAATTCCATCTTCTTAAAACATCATTTTTCATTTT
324 AATTTTGAAAATCGCATTCTTTGTTTTCAAAAATTCCATCTTCTTAAAACATCATTTTTCATTTT
*
1013922 TAAATTCATTTGAAAATATCCTACCCGAAGGTCTTATG
389 TAAATTCATTTGAAAACATCCTACCCGAAGGTCTTATG
*
1013960 GATGGCCCGAAGGACTTATCATCCTACTCTAAAGGCTTACGGATGACCCGAAGGATTTAAGCATC
1 GATGGCCCGAAGGACTTATCATCCTACTCTAAAGGCTTACGGATGACCCGAAAGATTTAAGCATC
* * *
1014025 ATGCTCAAAAGACTTACTGATGGCTCGAAAGACTTACAAATCGTGAAATTTTGAAAATCGCATTC
66 ATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACAAATCGTGAAATTTTGAAAATCGCATTC
*
1014090 TTCGTTTTCAAAAA-T-TC--C----AACATCATTTTTTCATTTTCAAATTC-TTGTGAAAACAT
131 TTTGTTTTCAAAAATTATCTTCTTAAAACATCA-TTTTTCATTTTCAAATTCATT-TGAAAACAT
* *
1014146 CCTACCTAAAGGTTTTATGGATGGT
194 CCTACCCAAAGGTCTTATGGATGGT
1014171 TTGCTTCACT
Statistics
Matches: 596, Mismatches: 37, Indels: 20
0.91 0.06 0.03
Matches are distributed among these distances:
418 9 0.02
419 47 0.08
422 1 0.00
424 2 0.00
425 2 0.00
426 1 0.00
427 362 0.61
428 172 0.29
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.33
Consensus pattern (426 bp):
GATGGCCCGAAGGACTTATCATCCTACTCTAAAGGCTTACGGATGACCCGAAAGATTTAAGCATC
ATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACAAATCGTGAAATTTTGAAAATCGCATTC
TTTGTTTTCAAAAATTATCTTCTTAAAACATCATTTTTCATTTTCAAATTCATTTGAAAACATCC
TACCCAAAGGTCTTATGGATGGTCCGAAGGACTTATCATCCTACTCTAAAGACTTACAGATGACC
CGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACAAATCGTGAAA
TTTTGAAAATCGCATTCTTTGTTTTCAAAAATTCCATCTTCTTAAAACATCATTTTTCATTTTTA
AATTCATTTGAAAACATCCTACCCGAAGGTCTTATG
Found at i:1013790 original size:41 final size:41
Alignment explanation
Indices: 1013735--1013847 Score: 127
Period size: 42 Copynumber: 2.7 Consensus size: 41
1013725 ATCCTACCCG
* * *
1013735 AAGGTCTTATGGATGGCCCGAAGGACTTATCATCCTACTCTA
1 AAGG-CTTACGGATGGCCCGAAGGACTTATCATCATACTCGA
* * * *
1013777 AAGGCTTACGGATGACCCGAAGGATTTAAGCATCATGCTCGA
1 AAGGCTTACGGATGGCCCGAAGGACTT-ATCATCATACTCGA
* *
1013819 AAGACTTACTGATGGCCCGAAGGACTTAT
1 AAGGCTTACGGATGGCCCGAAGGACTTAT
1013848 AAATTGTGAA
Statistics
Matches: 58, Mismatches: 12, Indels: 3
0.79 0.16 0.04
Matches are distributed among these distances:
41 21 0.36
42 37 0.64
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.25
Consensus pattern (41 bp):
AAGGCTTACGGATGGCCCGAAGGACTTATCATCATACTCGA
Found at i:1014004 original size:41 final size:41
Alignment explanation
Indices: 1013949--1014060 Score: 107
Period size: 42 Copynumber: 2.7 Consensus size: 41
1013939 ATCCTACCCG
* * * *
1013949 AAGGTCTTATGGATGGCCCGAAGGACTTATCATCCTACTCTA
1 AAGG-CTTACGGATGGCCCGAAGGACTTAGCATCATACTCAA
* * *
1013991 AAGGCTTACGGATGACCCGAAGGATTTAAGCATCATGCTCAA
1 AAGGCTTACGGATGGCCCGAAGGACTT-AGCATCATACTCAA
* * * *
1014033 AAGACTTACTGATGGCTCGAAAGACTTA
1 AAGGCTTACGGATGGCCCGAAGGACTTA
1014061 CAAATCGTGA
Statistics
Matches: 56, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
41 21 0.38
42 35 0.62
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.25
Consensus pattern (41 bp):
AAGGCTTACGGATGGCCCGAAGGACTTAGCATCATACTCAA
Found at i:1017045 original size:20 final size:20
Alignment explanation
Indices: 1017017--1017060 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
1017007 TTGAAGGTAG
* *
1017017 TCTTCAATCAACTTGAAACT
1 TCTTAAATCAACATGAAACT
1017037 TCTTAAATCAACATGAAACT
1 TCTTAAATCAACATGAAACT
1017057 TCTT
1 TCTT
1017061 CATTCATCGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.23, G:0.05, T:0.36
Consensus pattern (20 bp):
TCTTAAATCAACATGAAACT
Found at i:1020443 original size:30 final size:32
Alignment explanation
Indices: 1020409--1020473 Score: 98
Period size: 32 Copynumber: 2.1 Consensus size: 32
1020399 GGAGCAGGGT
*
1020409 GCATGAGCTGTTGCT-CG-TGGGAACGGTGAA
1 GCATGAGCTGCTGCTCCGTTGGGAACGGTGAA
*
1020439 GCATGAGTTGCTGCTCCGTTGGGAACGGTGAA
1 GCATGAGCTGCTGCTCCGTTGGGAACGGTGAA
1020471 GCA
1 GCA
1020474 CATGTAACAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 13 0.42
31 2 0.06
32 16 0.52
ACGTcount: A:0.20, C:0.18, G:0.38, T:0.23
Consensus pattern (32 bp):
GCATGAGCTGCTGCTCCGTTGGGAACGGTGAA
Found at i:1029348 original size:26 final size:26
Alignment explanation
Indices: 1029319--1029375 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
1029309 AAGATTAAAA
*
1029319 TTAAAGTTTTAAA-AGTTTGAGGTTTT
1 TTAAAGATTTAAAGA-TTTGAGGTTTT
*
1029345 TTAAAGATTTAAAGATTTTAGGTTTT
1 TTAAAGATTTAAAGATTTGAGGTTTT
1029371 TTAAA
1 TTAAA
1029376 AAATAAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 27 0.96
27 1 0.04
ACGTcount: A:0.35, C:0.00, G:0.16, T:0.49
Consensus pattern (26 bp):
TTAAAGATTTAAAGATTTGAGGTTTT
Found at i:1033791 original size:15 final size:15
Alignment explanation
Indices: 1033771--1033802 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1033761 TATACAGAGA
1033771 TTTTTTCGCAGGGAT
1 TTTTTTCGCAGGGAT
*
1033786 TTTTTTTGCAGGGAT
1 TTTTTTCGCAGGGAT
1033801 TT
1 TT
1033803 CTGCCCATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.12, C:0.09, G:0.25, T:0.53
Consensus pattern (15 bp):
TTTTTTCGCAGGGAT
Found at i:1038769 original size:31 final size:29
Alignment explanation
Indices: 1038731--1038818 Score: 86
Period size: 31 Copynumber: 2.9 Consensus size: 29
1038721 GGTTAATTTT
*
1038731 TAATTTGATTTTTGAACTTTAAATAAAATA
1 TAATTTGATCTTTGAA-TTTAAATAAAATA
* * *
1038761 CTAATTTGATCCTTAAATTTTAGATAAAATA
1 -TAATTTGATCTTTGAA-TTTAAATAAAATA
* *
1038792 TCAATTTGATCTCTGAATTTAACTAAA
1 T-AATTTGATCTTTGAATTTAAATAAA
1038819 GTCTCGCATC
Statistics
Matches: 46, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
30 9 0.20
31 37 0.80
ACGTcount: A:0.41, C:0.09, G:0.07, T:0.43
Consensus pattern (29 bp):
TAATTTGATCTTTGAATTTAAATAAAATA
Found at i:1041602 original size:76 final size:76
Alignment explanation
Indices: 1041476--1041636 Score: 259
Period size: 76 Copynumber: 2.1 Consensus size: 76
1041466 TGTGTCTTCA
* * *
1041476 ACGTGGGTACCAGCTTTGTTATGTTTGGTAGCAAGAAGTTTGCAGCAAAATAAGAAATTCATGGA
1 ACGTGGGGACCAGCTTTGTTATGTTTGATAGCAAGAAGTTTGCAGCAAAATAAGAAAATCATGGA
1041541 AAGAATAATGC
66 AAGAATAATGC
* * * *
1041552 ACGTGGGGACCAGCTTTGTTATGTTTGATAGCATGATGTTTGCAGGAAAATAAGAAAATCATGGG
1 ACGTGGGGACCAGCTTTGTTATGTTTGATAGCAAGAAGTTTGCAGCAAAATAAGAAAATCATGGA
1041617 AAGAATAATGC
66 AAGAATAATGC
1041628 ACGTGGGGA
1 ACGTGGGGA
1041637 TGGGAATGAG
Statistics
Matches: 78, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
76 78 1.00
ACGTcount: A:0.34, C:0.11, G:0.28, T:0.27
Consensus pattern (76 bp):
ACGTGGGGACCAGCTTTGTTATGTTTGATAGCAAGAAGTTTGCAGCAAAATAAGAAAATCATGGA
AAGAATAATGC
Found at i:1045075 original size:20 final size:20
Alignment explanation
Indices: 1045050--1045091 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
1045040 TTCAAGTCAT
1045050 TTTCCGTTAATTTTAAGTGG
1 TTTCCGTTAATTTTAAGTGG
1045070 TTTCCGTTAATTTTAAGTGG
1 TTTCCGTTAATTTTAAGTGG
1045090 TT
1 TT
1045092 ATAATGACGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.19, C:0.10, G:0.19, T:0.52
Consensus pattern (20 bp):
TTTCCGTTAATTTTAAGTGG
Found at i:1049898 original size:29 final size:29
Alignment explanation
Indices: 1049856--1049922 Score: 125
Period size: 29 Copynumber: 2.3 Consensus size: 29
1049846 TATAAAAAAT
*
1049856 AGTGCCTAAACTATTTTTTTATCCATCGA
1 AGTGCCTAAACTATTTTTTTATCCATCAA
1049885 AGTGCCTAAACTATTTTTTTATCCATCAA
1 AGTGCCTAAACTATTTTTTTATCCATCAA
1049914 AGTGCCTAA
1 AGTGCCTAA
1049923 TATTACAAAC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.30, C:0.21, G:0.10, T:0.39
Consensus pattern (29 bp):
AGTGCCTAAACTATTTTTTTATCCATCAA
Found at i:1050372 original size:16 final size:16
Alignment explanation
Indices: 1050351--1050384 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1050341 TTTAGAAAAT
1050351 GAATTTAGAGATTTGA
1 GAATTTAGAGATTTGA
*
1050367 GAATTTAGAGTTTTGA
1 GAATTTAGAGATTTGA
1050383 GA
1 GA
1050385 TTATAGTAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.26, T:0.38
Consensus pattern (16 bp):
GAATTTAGAGATTTGA
Found at i:1053462 original size:24 final size:23
Alignment explanation
Indices: 1053400--1053463 Score: 80
Period size: 24 Copynumber: 2.8 Consensus size: 23
1053390 TCCCCTTGAA
*
1053400 GTGCATCGATGCATCC-TATCGT
1 GTGCATCGATGCATCCTTAACGT
1053422 GT--ATCGATGCATCCCTTAACGT
1 GTGCATCGATGCAT-CCTTAACGT
1053444 GTGCATCGATGCACTCCTTA
1 GTGCATCGATGCA-TCCTTA
1053464 TGCATCGATG
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
20 10 0.28
21 2 0.06
22 9 0.25
24 14 0.39
25 1 0.03
ACGTcount: A:0.20, C:0.28, G:0.20, T:0.31
Consensus pattern (23 bp):
GTGCATCGATGCATCCTTAACGT
Found at i:1055740 original size:16 final size:16
Alignment explanation
Indices: 1055719--1055756 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
1055709 TAATGTGTTA
*
1055719 GGTAATGTTATATTTC
1 GGTAATGTTATATTCC
1055735 GGTAATGTTATATTCC
1 GGTAATGTTATATTCC
1055751 GGTAAT
1 GGTAAT
1055757 CTATTCCCAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.26, C:0.08, G:0.21, T:0.45
Consensus pattern (16 bp):
GGTAATGTTATATTCC
Found at i:1055992 original size:14 final size:15
Alignment explanation
Indices: 1055962--1055994 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
1055952 TATTATTTTT
*
1055962 AATAAACTTATTAAA
1 AATAAACTTAATAAA
1055977 AATAAA-TTAATAAA
1 AATAAACTTAATAAA
1055991 AATA
1 AATA
1055995 GTGAAAAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (15 bp):
AATAAACTTAATAAA
Found at i:1064200 original size:2 final size:2
Alignment explanation
Indices: 1064193--1064267 Score: 136
Period size: 2 Copynumber: 38.5 Consensus size: 2
1064183 TTTAAATTTA
1064193 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1064235 AT AT AT -T AT AT AT AT -T AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1064268 AAGAGAGCAG
Statistics
Matches: 71, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
1 2 0.03
2 69 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1076431 original size:23 final size:23
Alignment explanation
Indices: 1076396--1076443 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
1076386 ATCAAGTACA
*
1076396 ATAATATATTAGGTAGCGCTTAT
1 ATAATATAATAGGTAGCGCTTAT
*
1076419 ATAATGTAATAGGTAGCGCTTAT
1 ATAATATAATAGGTAGCGCTTAT
1076442 AT
1 AT
1076444 TTACCTATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.08, G:0.19, T:0.38
Consensus pattern (23 bp):
ATAATATAATAGGTAGCGCTTAT
Found at i:1077377 original size:179 final size:181
Alignment explanation
Indices: 1077059--1077511 Score: 761
Period size: 179 Copynumber: 2.5 Consensus size: 181
1077049 ACTTTTTTAC
1077059 TACCGGTTTTGTCATTTCGAGATCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGA
1 TACCGGTTTTGTCATTTCGAGATCGATTTTGTCATATTTTTACCTGTT-TATTGTTATGGATCGA
* *
1077124 TACA-TTTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTTTCTTTTAAATTCCAAAAG
65 TACATTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAG
* *
1077188 TGTCGATACTTATAATAAAGTTTCGACACTATCAACATATCCGGTAGCTCTT
130 TGTCGATACTTATAATAAAGTATCGACACTATCAACATATCCGGTAGCGCTT
1077240 TACCGGTTTTGTCATTTCGAGATCGATTTTGTCATATTTTTACCTG-TTATTGTTATGGATCGAT
1 TACCGGTTTTGTCATTTCGAGATCGATTTTGTCATATTTTTACCTGTTTATTGTTATGGATCGAT
1077304 ACATTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTCTC-TTTAAATTCCAAAAGT
66 ACATTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGT
1077368 GTCGATACTTATAATAAAGTATCGACACTATCAACATATCCGGTAGCGCTT
131 GTCGATACTTATAATAAAGTATCGACACTATCAACATATCCGGTAGCGCTT
** * ** *
1077419 TACCTATTTTATCATTTATAGACCGATTTTGTCAT-TTTTTACCTGTTTTATTGTTTATGGATCG
1 TACCGGTTTTGTCATTTCGAGATCGATTTTGTCATATTTTTACCTG-TTTATTG-TTATGGATCG
1077483 ATACATTTTTATAAAGTATCGACACTTTA
64 ATACATTTTTATAAAGTATCGACACTTTA
1077512 ATATAGCTGG
Statistics
Matches: 258, Mismatches: 10, Indels: 8
0.93 0.04 0.03
Matches are distributed among these distances:
178 10 0.04
179 114 0.44
180 49 0.19
181 85 0.33
ACGTcount: A:0.27, C:0.17, G:0.13, T:0.43
Consensus pattern (181 bp):
TACCGGTTTTGTCATTTCGAGATCGATTTTGTCATATTTTTACCTGTTTATTGTTATGGATCGAT
ACATTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGT
GTCGATACTTATAATAAAGTATCGACACTATCAACATATCCGGTAGCGCTT
Found at i:1077850 original size:113 final size:112
Alignment explanation
Indices: 1077381--1077953 Score: 886
Period size: 113 Copynumber: 5.1 Consensus size: 112
1077371 GATACTTATA
* * * *
1077381 ATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTATTTTATCATTTATAGACCGAT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGAT
*
1077446 TTTGTCA-TTTTTTACCTGTTTTATTGTTTATGGATCGATACATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTG-TTATGGATCGATACATTTTT
* * *
1077493 ATAAAGTATCGACACTTT-AATATAGCTGGTGGCGCTTTACCTGTTTTGTCATTTATAGACCGA-
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGAT
*
1077556 TTTATCA-TTTTTTACCTGTTATATTGTTATGGATCGATACA-TTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
* *
1077601 ATAAAGTATCGACACTTTCAATATATTCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGAT
1077666 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
* *
1077713 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACATGTTTTGTCATTTATAGACTGAT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGAT
* *
1077778 TTTGTCATTTTTTTTACATGTTATATTGTTATGGATAGATACATTTTT
66 TTTGTCA-TTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
* *
1077826 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATATACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGAT
* * * * *
1077891 TTTGTCATTTTTTTTACTTGTTATATTGCTAAGGATCAATATATTTTT
66 TTTGTCA-TTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
1077939 ATAAAGTATCGACAC
1 ATAAAGTATCGACAC
1077954 AAACCGACAA
Statistics
Matches: 425, Mismatches: 31, Indels: 9
0.91 0.07 0.02
Matches are distributed among these distances:
108 22 0.05
109 55 0.13
110 30 0.07
111 73 0.17
112 89 0.21
113 156 0.37
ACGTcount: A:0.26, C:0.15, G:0.14, T:0.45
Consensus pattern (112 bp):
ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGAT
TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
Found at i:1084755 original size:18 final size:18
Alignment explanation
Indices: 1084721--1084753 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
1084711 TTATTGTAAT
1084721 TTAATATTATATAATATG
1 TTAATATTATATAATATG
1084739 TTAAT-TT-TATAATAT
1 TTAATATTATATAATAT
1084754 ATATGATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 8 0.53
17 2 0.13
18 5 0.33
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (18 bp):
TTAATATTATATAATATG
Found at i:1086737 original size:149 final size:155
Alignment explanation
Indices: 1086369--1086831 Score: 839
Period size: 149 Copynumber: 3.0 Consensus size: 155
1086359 TTTTCGTCGT
1086369 TAACCGTTATATTATTGGCATGTAACTTCACAGTGCTGATGTGGCAGCCCATCTGCTATGTTTGA
1 TAACCGTTATATTATTGGCATGTAACTTCACAGTGCTGATGTGGCAGCCCATCTGCTATGTTTGA
1086434 GTCATCAATTTAGTCAATCTGTCATGTCATTTGTCACGTTAATCTGTCACCTTAGACTGATATGT
66 GTCATCAATTTAGTCAA-CTGTCATGTCATTTGTCACGTTAATCTGTCACCTTAGACTGA-ATGT
*
1086499 CAGCATCATAGATTGTCATGTTACTAA
129 CACCATCATAGATTGTCATGTTACTAA
1086526 TAACCGTTATATTATTGGCATGTAACTTCACAGTGCTGATGTGGCAGCCCATCTGCTATGTTTGA
1 TAACCGTTATATTATTGGCATGTAACTTCACAGTGCTGATGTGGCAGCCCATCTGCTATGTTTGA
1086591 GTCATCAATTTAGTCAA-TGTCATGTCATTTGTCACGTTAA-CTGTCA-CTTAGA-TG-ATGTCA
66 GTCATCAATTTAGTCAACTGTCATGTCATTTGTCACGTTAATCTGTCACCTTAGACTGAATGTCA
1086651 CCAT-ATAGATTGTCATGTTACTAA
131 CCATCATAGATTGTCATGTTACTAA
1086675 TAACCGTTATATTATTGGCATGTAACTTCACAGTGCTGATGTGGCAGCCCATCTGCTATGTTTGA
1 TAACCGTTATATTATTGGCATGTAACTTCACAGTGCTGATGTGGCAGCCCATCTGCTATGTTTGA
1086740 GTCATCAATTTAGTCAATCTGTCATGTCATTTGTCACGTTAATCTGTCACCTTAGACTGATATGT
66 GTCATCAATTTAGTCAA-CTGTCATGTCATTTGTCACGTTAATCTGTCACCTTAGACTGA-ATGT
1086805 CACCATCATAGATTGTCATGTTACTAA
129 CACCATCATAGATTGTCATGTTACTAA
1086832 CGTGAACTGC
Statistics
Matches: 297, Mismatches: 1, Indels: 16
0.95 0.00 0.05
Matches are distributed among these distances:
149 102 0.34
150 9 0.03
151 23 0.08
152 8 0.03
153 12 0.04
154 8 0.03
155 23 0.08
156 10 0.03
157 102 0.34
ACGTcount: A:0.26, C:0.20, G:0.18, T:0.37
Consensus pattern (155 bp):
TAACCGTTATATTATTGGCATGTAACTTCACAGTGCTGATGTGGCAGCCCATCTGCTATGTTTGA
GTCATCAATTTAGTCAACTGTCATGTCATTTGTCACGTTAATCTGTCACCTTAGACTGAATGTCA
CCATCATAGATTGTCATGTTACTAA
Found at i:1097402 original size:8 final size:8
Alignment explanation
Indices: 1097389--1097423 Score: 52
Period size: 8 Copynumber: 4.2 Consensus size: 8
1097379 TTAAATAATA
1097389 ATTTTTAT
1 ATTTTTAT
1097397 ATTTTTATT
1 ATTTTTA-T
1097406 ATTTTTAT
1 ATTTTTAT
*
1097414 ATATTTAT
1 ATTTTTAT
1097422 AT
1 AT
1097424 AAAAATAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
8 17 0.68
9 8 0.32
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (8 bp):
ATTTTTAT
Found at i:1097409 original size:17 final size:17
Alignment explanation
Indices: 1097389--1097421 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1097379 TTAAATAATA
*
1097389 ATTTTTATATTTTTATT
1 ATTTTTATATATTTATT
1097406 ATTTTTATATATTTAT
1 ATTTTTATATATTTAT
1097422 ATAAAAATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (17 bp):
ATTTTTATATATTTATT
Found at i:1098917 original size:11 final size:11
Alignment explanation
Indices: 1098903--1098928 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1098893 ATATATATAA
1098903 TATATATTATT
1 TATATATTATT
1098914 TATATATTATT
1 TATATATTATT
1098925 TATA
1 TATA
1098929 AATTTCAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TATATATTATT
Found at i:1099413 original size:29 final size:30
Alignment explanation
Indices: 1099363--1099419 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
1099353 GATTTTGAGT
*
1099363 AACGAAATGAAACGTTAGGTACCAAACTGG
1 AACGAAATGAAACGTTACGTACCAAACTGG
* *
1099393 AACGAAAT-AAATGTTACGTACTAAACT
1 AACGAAATGAAACGTTACGTACCAAACT
1099420 AGAAAAAGGG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 16 0.67
30 8 0.33
ACGTcount: A:0.46, C:0.16, G:0.18, T:0.21
Consensus pattern (30 bp):
AACGAAATGAAACGTTACGTACCAAACTGG
Found at i:1102361 original size:3 final size:3
Alignment explanation
Indices: 1102353--1102391 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
1102343 GTTTGATCAA
1102353 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1102392 GTTATTTTTC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1105573 original size:159 final size:157
Alignment explanation
Indices: 1105279--1105645 Score: 470
Period size: 159 Copynumber: 2.3 Consensus size: 157
1105269 CTTCATAATT
* * * **
1105279 GAACCCGATTGCTGTTTCAAATCGCTCTTCTTTGCATCATCGTCAGCATCCACTTTTGATCCATC
1 GAACCGGATTGCTGATCCAAATCGCTCTTC-TTGCATCATTATCAGCA-CCACTTTTGATCCATC
* * * **
1105344 AATTTGATCTCCTCCGTTATCTTTCCCACTAGTGTTTCCTTTCACTTAACCATTCGATTCTTTCC
64 AACTTGATCTCCTCCATTATCTTTCCCACTAGTGTTTCCTATCACTTAACCACCCGATTCTTTCC
*
1105409 AATCCTTTACCAAATTCTTGCCTTCATTC
129 AATCCTTTACCAAATTCTTCCCTTCATTC
*
1105438 GAACCGGATTGCTGATCCAAATCGCTCTTACTTGCATCATTATCAGCACCCCTTTTTGATCCATC
1 GAACCGGATTGCTGATCCAAATCGCTCTT-CTTGCATCATTATCAGCACCAC-TTTTGATCCATC
* **
1105503 AACTTGATCTCCTCCATTATCTTTCCCACTCGTGTTTCCTATCACTTCTCCACCCGATTCTTTCC
64 AACTTGATCTCCTCCATTATCTTTCCCACTAGTGTTTCCTATCACTTAACCACCCGATTCTTTCC
*
1105568 CATCCTTTACCAAATTCTTCCCTTCATTC
129 AATCCTTTACCAAATTCTTCCCTTCATTC
* * * * * * *
1105597 AAACTGGGTTTCTGGTCCACATTG--C-TCTTGCATCATTATCAGCACCACT
1 GAACCGGATTGCTGATCCAAATCGCTCTTCTTGCATCATTATCAGCACCACT
1105646 CTTTCAATAA
Statistics
Matches: 182, Mismatches: 24, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
154 1 0.01
155 21 0.12
156 1 0.01
157 1 0.01
158 3 0.02
159 154 0.85
160 1 0.01
ACGTcount: A:0.20, C:0.32, G:0.10, T:0.38
Consensus pattern (157 bp):
GAACCGGATTGCTGATCCAAATCGCTCTTCTTGCATCATTATCAGCACCACTTTTGATCCATCAA
CTTGATCTCCTCCATTATCTTTCCCACTAGTGTTTCCTATCACTTAACCACCCGATTCTTTCCAA
TCCTTTACCAAATTCTTCCCTTCATTC
Found at i:1106418 original size:16 final size:16
Alignment explanation
Indices: 1106371--1106504 Score: 97
Period size: 16 Copynumber: 8.3 Consensus size: 16
1106361 TTAGCGAAAT
1106371 CGAAATTAACCCGAAC
1 CGAAATTAACCCGAAC
* ** ***
1106387 CAAAAGCAATTTGAAC
1 CGAAATTAACCCGAAC
1106403 CGAAATTAACCCGAAC
1 CGAAATTAACCCGAAC
**
1106419 CGAAAGCAACCCGAAC
1 CGAAATTAACCCGAAC
*
1106435 TGAAATTAACCCGAAC
1 CGAAATTAACCCGAAC
* * *
1106451 CGAATGTTAACACGATC
1 CGAA-ATTAACCCGAAC
** **
1106468 CGAAAGAAACTTGAAC
1 CGAAATTAACCCGAAC
* *
1106484 CGAATTTAACCCGACC
1 CGAAATTAACCCGAAC
1106500 CGAAA
1 CGAAA
1106505 GCAACCGAAC
Statistics
Matches: 83, Mismatches: 34, Indels: 2
0.70 0.29 0.02
Matches are distributed among these distances:
16 70 0.84
17 13 0.16
ACGTcount: A:0.43, C:0.28, G:0.15, T:0.14
Consensus pattern (16 bp):
CGAAATTAACCCGAAC
Found at i:1106452 original size:32 final size:32
Alignment explanation
Indices: 1106371--1106454 Score: 123
Period size: 32 Copynumber: 2.6 Consensus size: 32
1106361 TTAGCGAAAT
* ***
1106371 CGAAATTAACCCGAACCAAAAGCAATTTGAAC
1 CGAAATTAACCCGAACCGAAAGCAACCCGAAC
1106403 CGAAATTAACCCGAACCGAAAGCAACCCGAAC
1 CGAAATTAACCCGAACCGAAAGCAACCCGAAC
*
1106435 TGAAATTAACCCGAACCGAA
1 CGAAATTAACCCGAACCGAA
1106455 TGTTAACACG
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 47 1.00
ACGTcount: A:0.45, C:0.29, G:0.14, T:0.12
Consensus pattern (32 bp):
CGAAATTAACCCGAACCGAAAGCAACCCGAAC
Found at i:1106493 original size:49 final size:48
Alignment explanation
Indices: 1106399--1106504 Score: 122
Period size: 49 Copynumber: 2.2 Consensus size: 48
1106389 AAAGCAATTT
* * *
1106399 GAACCGAAATTAACCCGAACCGAAAGCAACCCGAACTGAAATTAACCC
1 GAACCGAAATTAACACGAACCGAAAGAAACCCGAACCGAAATTAACCC
* * ** *
1106447 GAACCGAATGTTAACACGATCCGAAAGAAACTTGAACCGAATTTAACCC
1 GAACCGAA-ATTAACACGAACCGAAAGAAACCCGAACCGAAATTAACCC
*
1106496 GACCCGAAA
1 GAACCGAAA
1106505 GCAACCGAAC
Statistics
Matches: 47, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
48 8 0.17
49 39 0.83
ACGTcount: A:0.42, C:0.28, G:0.16, T:0.13
Consensus pattern (48 bp):
GAACCGAAATTAACACGAACCGAAAGAAACCCGAACCGAAATTAACCC
Found at i:1106721 original size:19 final size:20
Alignment explanation
Indices: 1106697--1106735 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1106687 ATTATCTTAC
*
1106697 TTTAT-ATAAAAATATTAGA
1 TTTATAATAAAAATAATAGA
1106716 TTTATAATAAAAATAATAGA
1 TTTATAATAAAAATAATAGA
1106736 AAACAACTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.38
Consensus pattern (20 bp):
TTTATAATAAAAATAATAGA
Found at i:1107266 original size:31 final size:31
Alignment explanation
Indices: 1107184--1107276 Score: 80
Period size: 31 Copynumber: 3.0 Consensus size: 31
1107174 ACCTAAACCG
* * *
1107184 AAAAATCAATCGATCCGATATTGACCGACCC
1 AAAAATCAATCGATACGGTATTAACCGACCC
* * * * *
1107215 -TAAATCTAAACAATATGGTATTAACTGACCC
1 AAAAATC-AATCGATACGGTATTAACCGACCC
*
1107246 AAAAATCAATCGATACGGTATTGACCCGACC
1 AAAAATCAATCGATACGGTATT-AACCGACC
1107277 TGATATTGAC
Statistics
Matches: 45, Mismatches: 14, Indels: 5
0.70 0.22 0.08
Matches are distributed among these distances:
30 5 0.11
31 29 0.64
32 11 0.24
ACGTcount: A:0.40, C:0.25, G:0.13, T:0.23
Consensus pattern (31 bp):
AAAAATCAATCGATACGGTATTAACCGACCC
Found at i:1108663 original size:9 final size:10
Alignment explanation
Indices: 1108642--1108674 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
1108632 ATACCCAATA
1108642 AAAAATATAT
1 AAAAATATAT
1108652 AAAAATAT-T
1 AAAAATATAT
1108661 AAAAATTATAT
1 AAAAA-TATAT
1108672 AAA
1 AAA
1108675 TTTTGTTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 6 0.29
10 11 0.52
11 4 0.19
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (10 bp):
AAAAATATAT
Found at i:1118465 original size:24 final size:24
Alignment explanation
Indices: 1118413--1118474 Score: 88
Period size: 24 Copynumber: 2.6 Consensus size: 24
1118403 GTTAGTTTGT
* * *
1118413 GTTCATTCATTTAGGTTCATTTAC
1 GTTCGTTCGTTTATGTTCATTTAC
1118437 GTTCGTTCGTTTATGTTCATTTAC
1 GTTCGTTCGTTTATGTTCATTTAC
*
1118461 TTTCGTTCGTTTAT
1 GTTCGTTCGTTTAT
1118475 ATTCGGTTGT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.15, C:0.16, G:0.15, T:0.55
Consensus pattern (24 bp):
GTTCGTTCGTTTATGTTCATTTAC
Found at i:1122003 original size:41 final size:41
Alignment explanation
Indices: 1121946--1122025 Score: 151
Period size: 41 Copynumber: 2.0 Consensus size: 41
1121936 AATGTCAAGA
*
1121946 TCTTTTCTTCGAGTTGTCTTTGTTCTTCCAAGTACTTAGCT
1 TCTTTTCTTCGAGTTGTATTTGTTCTTCCAAGTACTTAGCT
1121987 TCTTTTCTTCGAGTTGTATTTGTTCTTCCAAGTACTTAG
1 TCTTTTCTTCGAGTTGTATTTGTTCTTCCAAGTACTTAG
1122026 TTTCAGCTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.14, C:0.20, G:0.15, T:0.51
Consensus pattern (41 bp):
TCTTTTCTTCGAGTTGTATTTGTTCTTCCAAGTACTTAGCT
Found at i:1127575 original size:156 final size:156
Alignment explanation
Indices: 1127285--1128004 Score: 1156
Period size: 156 Copynumber: 4.6 Consensus size: 156
1127275 CATATCTCGG
1127285 TTGATTCCCTCACCTTCCTCAGCTCAGCTTCAGAACTTGCAAGCTTTTCACCAAGTGCTTCATTT
1 TTGATTCCCTCACCTTCCTCAGCTCAGCTTCAGAACTTGCAAGCTTTTCACCAAGTGCTTCATTT
** * *
1127350 GCCTGGACTAGCCTTGAATTCGATTCACTC-GAATCCTTTAACTTGCATAGCTCAGCTTCACAAG
66 GCCTGCTCTAGCCTTGAATTCGATTCATTCAG-ATCCTTTAACATGCATAGCTCAGCTTCACAAG
1127414 TGGCAAGCTTCTCGTTAAGTTCTCTAT
130 TGGCAAGCTTCTCGTTAAGTTCTCTAT
* * *
1127441 TTGATTCCCTCACCTTCCTCAGCTCAGCTTTAGAATTTGCAAGCTTTTCGCCAAGTGCTTCATTT
1 TTGATTCCCTCACCTTCCTCAGCTCAGCTTCAGAACTTGCAAGCTTTTCACCAAGTGCTTCATTT
* *
1127506 ACCTGCTCTAGCCTTGAATTCGATTCATTCAGATCCTTTAACATGCATAGCTCAGATTCACAAAG
66 GCCTGCTCTAGCCTTGAATTCGATTCATTCAGATCCTTTAACATGCATAGCTCAGCTTCAC-AAG
*
1127571 -GGCAACCTTCTCGTTAAGTTCTCTAT
130 TGGCAAGCTTCTCGTTAAGTTCTCTAT
* **
1127597 TTGATTCCCTCACCTTCCTCAGCTCAGCTTCAGAATTTGCAAGCTTTTCACCAAGTGCTTCAAAT
1 TTGATTCCCTCACCTTCCTCAGCTCAGCTTCAGAACTTGCAAGCTTTTCACCAAGTGCTTCATTT
* * * * * *
1127662 GTCTGCTCTAGCCTTGAATTTGACTCGTTCAGATCCTTTAACTTGCATAGCTCAGCTTCACAAGA
66 GCCTGCTCTAGCCTTGAATTCGATTCATTCAGATCCTTTAACATGCATAGCTCAGCTTCACAAGT
1127727 GGCAAGCTTCTCGTTAAGTTCTCTAT
131 GGCAAGCTTCTCGTTAAGTTCTCTAT
*
1127753 TTGATTCCCTCACCTTCCTCAGCTCAACTTCAGAACTTGCAAGCTTTTCACCAAGTGCTTCATTT
1 TTGATTCCCTCACCTTCCTCAGCTCAGCTTCAGAACTTGCAAGCTTTTCACCAAGTGCTTCATTT
*
1127818 GCCTGCTCTAGCCTTGAATTCGATTCATTCAGATCCTTTAACATGCATGGCTCAGCTTCACAAGT
66 GCCTGCTCTAGCCTTGAATTCGATTCATTCAGATCCTTTAACATGCATAGCTCAGCTTCACAAGT
* *
1127883 GGCAAGCTTCTCATTAAGCTCTCTAT
131 GGCAAGCTTCTCGTTAAGTTCTCTAT
* *
1127909 TTGATTCCCTCACCTTCCTCAGGTCAGCTTCAGAACTTGCAAGCTTTTCAGCAAGTGCTTCATTT
1 TTGATTCCCTCACCTTCCTCAGCTCAGCTTCAGAACTTGCAAGCTTTTCACCAAGTGCTTCATTT
* * *
1127974 ACCTGCACTAGCCTTGAATTTGATTCATTCA
66 GCCTGCTCTAGCCTTGAATTCGATTCATTCA
1128005 AAGCTTCTGC
Statistics
Matches: 520, Mismatches: 41, Indels: 6
0.92 0.07 0.01
Matches are distributed among these distances:
155 3 0.01
156 513 0.99
157 4 0.01
ACGTcount: A:0.22, C:0.28, G:0.15, T:0.35
Consensus pattern (156 bp):
TTGATTCCCTCACCTTCCTCAGCTCAGCTTCAGAACTTGCAAGCTTTTCACCAAGTGCTTCATTT
GCCTGCTCTAGCCTTGAATTCGATTCATTCAGATCCTTTAACATGCATAGCTCAGCTTCACAAGT
GGCAAGCTTCTCGTTAAGTTCTCTAT
Found at i:1128253 original size:117 final size:117
Alignment explanation
Indices: 1128047--1128298 Score: 405
Period size: 117 Copynumber: 2.2 Consensus size: 117
1128037 CATATCTCAA
* * * *
1128047 CTTCACAAGTAGCAAGTTTCTCATTAAGTTCTCTGTTTGCATGCTCGAGTCGTAAATTGGATTCA
1 CTTCACAAGTAGCAAGCTTCTCATTAAGTTCTCTATTGGCATGCTCAAGTCGTAAATTGGATTCA
*
1128112 GTCAATGCATTTTGGCTTGCCTCCGTCGAATCCCTCAACATCCTCAGGTCAG
66 GTCAATGCATTTTGGCTTGCCTCCGTCGAATCCATCAACATCCTCAGGTCAG
* ** * *
1128164 CTTCACAAGTGGCAAGCTTCTCATTAAGTTCTCTATTGGTGTGCTCAAGTCGTGAATTGGATTCG
1 CTTCACAAGTAGCAAGCTTCTCATTAAGTTCTCTATTGGCATGCTCAAGTCGTAAATTGGATTCA
1128229 GTCAATGCATTTTGGCTTGCCTCCGTCGAATCCATCAACATCCTCAGGTCAG
66 GTCAATGCATTTTGGCTTGCCTCCGTCGAATCCATCAACATCCTCAGGTCAG
*
1128281 CTTCACAAGAAGCAAGCT
1 CTTCACAAGTAGCAAGCT
1128299 GCCTTCTAAG
Statistics
Matches: 123, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
117 123 1.00
ACGTcount: A:0.23, C:0.25, G:0.20, T:0.32
Consensus pattern (117 bp):
CTTCACAAGTAGCAAGCTTCTCATTAAGTTCTCTATTGGCATGCTCAAGTCGTAAATTGGATTCA
GTCAATGCATTTTGGCTTGCCTCCGTCGAATCCATCAACATCCTCAGGTCAG
Found at i:1128367 original size:117 final size:116
Alignment explanation
Indices: 1128047--1128462 Score: 326
Period size: 117 Copynumber: 3.6 Consensus size: 116
1128037 CATATCTCAA
* * * * * * * *
1128047 CTTCACAAGTA-GCAAGTTTCTCATTAAGTTCTCTGTTTG-CATGCTCGAGTCGTAAATTGGATT
1 CTTCACAAG-AGGCAAGCTGCTCATTAAGTTCTCTATTGGTC-TGCTCAAGCCGTGAATTCGATT
1128110 CAGTCAATGCATTTTGGCTTGCCTCCGTCGAATCCCTCAACATCCTCAGGTCAG
64 CAGTCAATGCATTTTGGCTTGCCTCCGTCGAAT-CCTCAACATCCTCAGGTCAG
* * * * * *
1128164 CTTCACAAGTGGCAAGCTTCTCATTAAGTTCTCTATTGGTGTGCTCAAGTCGTGAATTGGATTCG
1 CTTCACAAGAGGCAAGCTGCTCATTAAGTTCTCTATTGGTCTGCTCAAGCCGTGAATTCGATTCA
1128229 GTCAATGCATTTTGGCTTGCCTCCGTCGAATCCATCAACATCCTCAGGTCAG
66 GTCAATGCATTTTGGCTTGCCTCCGTCGAATCC-TCAACATCCTCAGGTCAG
* * * * * * * * *
1128281 CTTCACAAGAAGCAAGCTGC-CTTCTAAGCTT-TTTGTT-TTCTAGTTCTAGCCTTGCATTCGAT
1 CTTCACAAGAGGCAAGCTGCTCAT-TAAG-TTCTCTATTGGTCT-GCTCAAGCCGTGAATTCGAT
* ** * * * ** * *
1128343 TCAGCCAATGCATTTTTTCCTGCCT-TGATCGAACTTCTCGTCTTCCTCAGCTCAG
63 TCAGTCAATGCATTTTGGCTTGCCTCCG-TCGAA-TCCTCAACATCCTCAGGTCAG
* * * * * *
1128398 CTTCACAAGAGGCAAGCTTCTCCTTAAGTGCTCCATT-CTCTTGCTCTAGCC-TCGAATTCGATT
1 CTTCACAAGAGGCAAGCTGCTCATTAAGTTCTCTATTGGTC-TGCTCAAGCCGT-GAATTCGATT
1128461 CA
64 CA
1128463 CCAAATGATT
Statistics
Matches: 244, Mismatches: 43, Indels: 24
0.78 0.14 0.08
Matches are distributed among these distances:
116 9 0.04
117 228 0.93
118 7 0.03
ACGTcount: A:0.21, C:0.27, G:0.18, T:0.34
Consensus pattern (116 bp):
CTTCACAAGAGGCAAGCTGCTCATTAAGTTCTCTATTGGTCTGCTCAAGCCGTGAATTCGATTCA
GTCAATGCATTTTGGCTTGCCTCCGTCGAATCCTCAACATCCTCAGGTCAG
Found at i:1132970 original size:32 final size:32
Alignment explanation
Indices: 1132897--1132970 Score: 78
Period size: 32 Copynumber: 2.3 Consensus size: 32
1132887 GATAAATTCC
* * *
1132897 ATAACAATTTTATAATAATATGATAAAGTTTA
1 ATAACTATTTTATAAAAAAATGATAAAGTTTA
*
1132929 ATAATTATTTTATAAAAAAATTGATAAA-TTTA
1 ATAACTATTTTATAAAAAAA-TGATAAAGTTTA
* *
1132961 GTTACTATTT
1 ATAACTATTT
1132971 GTAACGGTGA
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
32 27 0.79
33 7 0.21
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (32 bp):
ATAACTATTTTATAAAAAAATGATAAAGTTTA
Found at i:1139697 original size:27 final size:28
Alignment explanation
Indices: 1139667--1139723 Score: 89
Period size: 28 Copynumber: 2.1 Consensus size: 28
1139657 ACCTAATTTT
* *
1139667 TTTTA-GTTAAAATAGGTACTTAAAGTA
1 TTTTATGTCAAAATAGGTACTTAAACTA
1139694 TTTTATGTCAAAATAGGTACTTAAACTA
1 TTTTATGTCAAAATAGGTACTTAAACTA
1139722 TT
1 TT
1139724 CAAACCTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
27 5 0.19
28 22 0.81
ACGTcount: A:0.39, C:0.07, G:0.12, T:0.42
Consensus pattern (28 bp):
TTTTATGTCAAAATAGGTACTTAAACTA
Found at i:1140709 original size:25 final size:25
Alignment explanation
Indices: 1140675--1140747 Score: 101
Period size: 26 Copynumber: 2.9 Consensus size: 25
1140665 ATATCAGCTA
*
1140675 CAAACAAAAACGGTTATGGAGGTTT
1 CAAACAAAAACGGTTATGGAGGTTG
* *
1140700 CAAACAAAAACGGTTACGAGGGGTTG
1 CAAACAAAAACGGTTATG-GAGGTTG
*
1140726 CAAACAAAAACAGTTATGGAGG
1 CAAACAAAAACGGTTATGGAGG
1140748 AGAAGAAAAC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
25 20 0.49
26 21 0.51
ACGTcount: A:0.42, C:0.14, G:0.26, T:0.18
Consensus pattern (25 bp):
CAAACAAAAACGGTTATGGAGGTTG
Found at i:1146515 original size:29 final size:29
Alignment explanation
Indices: 1146453--1146543 Score: 96
Period size: 29 Copynumber: 3.2 Consensus size: 29
1146443 TTTTATTTAA
* * *
1146453 CTAAAGTATTTTTTAGTCAAAATAAGTAC
1 CTAAAGTTTTTTTTTGTCAAAATAGGTAC
1146482 CTAAAGTTTTTTTTTGTCAAAATAGGTGA-
1 CTAAAGTTTTTTTTTGTCAAAATAGGT-AC
* * *
1146511 TTAAAG-TATTTTATGTCAAAATAGGTAC
1 CTAAAGTTTTTTTTTGTCAAAATAGGTAC
*
1146539 TTAAA
1 CTAAA
1146544 CTATTCAAAC
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
27 1 0.02
28 23 0.43
29 29 0.54
30 1 0.02
ACGTcount: A:0.38, C:0.08, G:0.13, T:0.41
Consensus pattern (29 bp):
CTAAAGTTTTTTTTTGTCAAAATAGGTAC
Found at i:1146531 original size:28 final size:28
Alignment explanation
Indices: 1146453--1146548 Score: 104
Period size: 28 Copynumber: 3.4 Consensus size: 28
1146443 TTTTATTTAA
*
1146453 CTAAAGTATTTTTTAGTCAAAATAAGTAC
1 CTAAAGTATTTTTT-GTCAAAATAGGTAC
*
1146482 CTAAAGTTTTTTTTTGTCAAAATAGGTGA-
1 CTAAAG-TATTTTTTGTCAAAATAGGT-AC
* *
1146511 TTAAAGTATTTTATGTCAAAATAGGTAC
1 CTAAAGTATTTTTTGTCAAAATAGGTAC
* *
1146539 TTAAACTATT
1 CTAAAGTATT
1146549 CAAACATTTT
Statistics
Matches: 58, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
27 1 0.02
28 27 0.47
29 22 0.38
30 8 0.14
ACGTcount: A:0.38, C:0.08, G:0.12, T:0.42
Consensus pattern (28 bp):
CTAAAGTATTTTTTGTCAAAATAGGTAC
Found at i:1146711 original size:30 final size:28
Alignment explanation
Indices: 1146630--1146713 Score: 78
Period size: 29 Copynumber: 2.9 Consensus size: 28
1146620 AAAACAATTG
* * *
1146630 AATATTTTAAGTATTTATTTTGACCAAAA
1 AATAATTTAAATA-TTATTTTGATCAAAA
* *
1146659 AATACTTTAAATATATGTTTTGATCAAAA
1 AATAATTTAAATAT-TATTTTGATCAAAA
*
1146688 AGATAATTTAGATACTTATTTTGATC
1 A-ATAATTTAAATA-TTATTTTGATC
1146714 GGAAAATACT
Statistics
Matches: 45, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
28 1 0.02
29 24 0.53
30 19 0.42
31 1 0.02
ACGTcount: A:0.40, C:0.07, G:0.08, T:0.44
Consensus pattern (28 bp):
AATAATTTAAATATTATTTTGATCAAAA
Found at i:1148663 original size:20 final size:21
Alignment explanation
Indices: 1148638--1148681 Score: 65
Period size: 20 Copynumber: 2.1 Consensus size: 21
1148628 CGATAAAAAA
1148638 TTATTTAAAA-ATT-ATTATTT
1 TTATTTAAAATATTAATT-TTT
1148658 TTATTTAAAATATTAATTTTT
1 TTATTTAAAATATTAATTTTT
1148679 TTA
1 TTA
1148682 ATATTTTTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 10 0.45
21 9 0.41
22 3 0.14
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
TTATTTAAAATATTAATTTTT
Found at i:1149379 original size:60 final size:60
Alignment explanation
Indices: 1149315--1149465 Score: 164
Period size: 60 Copynumber: 2.5 Consensus size: 60
1149305 TTAAAGGGTC
*
1149315 AATTTAGAATGAGATTCATAGTTTAGGGATAAAATT-CAAT-TGTTAAAATGTTTAA-AGACT
1 AATTTAGAATGAGAATCATAGTTTAGGGATAAAATTACAATAT-TTAAAA-GTTTAAGA-ACT
* * ** * * *
1149375 AATTTAGAATTACAATCATAGTTTAAAGATGAAATTAGAATATTTAAAAGTTTAAGAATT
1 AATTTAGAATGAGAATCATAGTTTAGGGATAAAATTACAATATTTAAAAGTTTAAGAACT
* *
1149435 AATTTAAAATGAGAGTCATAGTTTAGGGATA
1 AATTTAGAATGAGAATCATAGTTTAGGGATA
1149466 TATAATATAA
Statistics
Matches: 73, Mismatches: 15, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
60 62 0.85
61 10 0.14
62 1 0.01
ACGTcount: A:0.44, C:0.04, G:0.16, T:0.36
Consensus pattern (60 bp):
AATTTAGAATGAGAATCATAGTTTAGGGATAAAATTACAATATTTAAAAGTTTAAGAACT
Found at i:1153583 original size:38 final size:38
Alignment explanation
Indices: 1153537--1153616 Score: 110
Period size: 39 Copynumber: 2.1 Consensus size: 38
1153527 AGCTTAATGT
1153537 TAAATTTTTGAA-AG-AGGTACTAAAATGAAACAAAAAC
1 TAAATTTTT-AACAGCAGGTACTAAAATGAAACAAAAAC
* *
1153574 TAAAGTTTTTAACGGCGGGTACTAAAATGAAACAAAAAC
1 TAAA-TTTTTAACAGCAGGTACTAAAATGAAACAAAAAC
1153613 TAAA
1 TAAA
1153617 CTTAGGTATG
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
37 6 0.16
38 6 0.16
39 26 0.68
ACGTcount: A:0.51, C:0.10, G:0.15, T:0.24
Consensus pattern (38 bp):
TAAATTTTTAACAGCAGGTACTAAAATGAAACAAAAAC
Found at i:1159379 original size:14 final size:14
Alignment explanation
Indices: 1159362--1159389 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1159352 TAAAAGAAAT
1159362 TATTTAAATTTAAA
1 TATTTAAATTTAAA
1159376 TATTTAAATTTAAA
1 TATTTAAATTTAAA
1159390 ATAAGTTTCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TATTTAAATTTAAA
Found at i:1166607 original size:2 final size:2
Alignment explanation
Indices: 1166600--1166648 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
1166590 TTGTTAGCAA
1166600 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1166642 AT AT AT A
1 AT AT AT A
1166649 ATAGTGACTA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1168516 original size:13 final size:13
Alignment explanation
Indices: 1168498--1168522 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1168488 AGAGGTAATG
1168498 GGGTTATAGTTTA
1 GGGTTATAGTTTA
1168511 GGGTTATAGTTT
1 GGGTTATAGTTT
1168523 TTTAAGTTAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.00, G:0.32, T:0.48
Consensus pattern (13 bp):
GGGTTATAGTTTA
Found at i:1169110 original size:13 final size:15
Alignment explanation
Indices: 1169094--1169126 Score: 52
Period size: 13 Copynumber: 2.3 Consensus size: 15
1169084 CTTTTTTTTC
1169094 GATATTT-GATTT-A
1 GATATTTGGATTTAA
1169107 GATATTTGGATTTAA
1 GATATTTGGATTTAA
1169122 GATAT
1 GATAT
1169127 GGGTTTTATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 7 0.39
14 5 0.28
15 6 0.33
ACGTcount: A:0.33, C:0.00, G:0.18, T:0.48
Consensus pattern (15 bp):
GATATTTGGATTTAA
Found at i:1170585 original size:44 final size:43
Alignment explanation
Indices: 1170500--1170587 Score: 131
Period size: 44 Copynumber: 2.0 Consensus size: 43
1170490 ACTGCACCTG
* * *
1170500 GATGGTCATATTCGGGTTTTTACTAACCGAGTGGCGCCCGGAT
1 GATGGTCACATTCGGGTTTTTACTAACCGAGTGACACCCGGAT
*
1170543 GATGGTCACATTCGGGTTTTTTACTAACCGAGTGACATCCGGAT
1 GATGGTCACATTCGGG-TTTTTACTAACCGAGTGACACCCGGAT
1170587 G
1 G
1170588 CCCGTATTCG
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
43 15 0.38
44 25 0.62
ACGTcount: A:0.20, C:0.20, G:0.28, T:0.31
Consensus pattern (43 bp):
GATGGTCACATTCGGGTTTTTACTAACCGAGTGACACCCGGAT
Found at i:1171240 original size:14 final size:14
Alignment explanation
Indices: 1171221--1171251 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1171211 AATGAACATA
1171221 AACGAACACAAACG
1 AACGAACACAAACG
*
1171235 AACGAACATAAACG
1 AACGAACACAAACG
1171249 AAC
1 AAC
1171252 ACAAATGAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.58, C:0.26, G:0.13, T:0.03
Consensus pattern (14 bp):
AACGAACACAAACG
Found at i:1171246 original size:24 final size:24
Alignment explanation
Indices: 1171214--1171275 Score: 99
Period size: 24 Copynumber: 2.6 Consensus size: 24
1171204 AATGATAAAT
1171214 GAACATAAACGAACACAAACGAAC
1 GAACATAAACGAACACAAACGAAC
*
1171238 GAACATAAACGAACACAAATGAAC
1 GAACATAAACGAACACAAACGAAC
*
1171262 AAACAT-AACGAACA
1 GAACATAAACGAACA
1171276 ACACAAACAC
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
23 8 0.22
24 28 0.78
ACGTcount: A:0.60, C:0.23, G:0.11, T:0.06
Consensus pattern (24 bp):
GAACATAAACGAACACAAACGAAC
Found at i:1175762 original size:29 final size:29
Alignment explanation
Indices: 1175720--1175776 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
1175710 AATCACTCAG
* *
1175720 GGCCCCCAAATTTTTTATATTTATAATTA
1 GGCCCCCAAATTTTTTACATTCATAATTA
1175749 GGCCTCCC-AATTTTTTACATTCATAATT
1 GGCC-CCCAAATTTTTTACATTCATAATT
1175777 GGGACCCTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 22 0.88
30 3 0.12
ACGTcount: A:0.28, C:0.21, G:0.07, T:0.44
Consensus pattern (29 bp):
GGCCCCCAAATTTTTTACATTCATAATTA
Found at i:1175980 original size:116 final size:112
Alignment explanation
Indices: 1175760--1175992 Score: 290
Period size: 116 Copynumber: 2.0 Consensus size: 112
1175750 GCCTCCCAAT
* * * *
1175760 TTTTTACATTCATAATTGGGACCCTTAATTTTTATAATTTAAAGTTTTAGTTTTAGATCCTCCTT
1 TTTTTACATTCATAATTGGGACCCCTAATTTTTATAATTTAAAATTTTAGTTTTAGACCCTCATT
* * *
1175825 TTTCATTTCTCTTATTAATTTATTCAATTTTGAATTAAATTTAACCA
66 TTTCATTTCTCTTATTAATTCATTCAATTTTGAACTAAATCTAACCA
* * *
1175872 TTTTTATATTTATAATTCGGG-CCCCTAATTTTTATAATTTCATAAAATATTTAGTTTTTGACCC
1 TTTTTACATTCATAATT-GGGACCCCTAATTTTTATAA-TT--TAAAAT-TTTAGTTTTAGACCC
* *
1175936 T-ATTTTTCCATTTCTCTTATTTATTCATTCAATTTTGAACTAAATCTAATCA
61 TCATTTTT-CATTTCTCTTATTAATTCATTCAATTTTGAACTAAATCTAACCA
1175988 TTTTT
1 TTTTT
1175993 TCTCTTTTTT
Statistics
Matches: 103, Mismatches: 12, Indels: 8
0.84 0.10 0.07
Matches are distributed among these distances:
112 30 0.29
113 5 0.05
115 10 0.10
116 58 0.56
ACGTcount: A:0.28, C:0.14, G:0.06, T:0.52
Consensus pattern (112 bp):
TTTTTACATTCATAATTGGGACCCCTAATTTTTATAATTTAAAATTTTAGTTTTAGACCCTCATT
TTTCATTTCTCTTATTAATTCATTCAATTTTGAACTAAATCTAACCA
Found at i:1176772 original size:2 final size:2
Alignment explanation
Indices: 1176765--1176843 Score: 142
Period size: 2 Copynumber: 40.0 Consensus size: 2
1176755 CTTACTTTGA
1176765 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1176807 AT AT AT AT AT AT AT AT AT CT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1176844 GAGCAAATGA
Statistics
Matches: 74, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
1 1 0.01
2 73 0.99
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1177514 original size:18 final size:18
Alignment explanation
Indices: 1177491--1177527 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
1177481 TAGTGTGGAC
1177491 ACCTTCAATAAAATAAGG
1 ACCTTCAATAAAATAAGG
1177509 ACCTTCAATAAAATAAGG
1 ACCTTCAATAAAATAAGG
1177527 A
1 A
1177528 ATTAACCGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.51, C:0.16, G:0.11, T:0.22
Consensus pattern (18 bp):
ACCTTCAATAAAATAAGG
Found at i:1182574 original size:2 final size:2
Alignment explanation
Indices: 1182567--1182627 Score: 99
Period size: 2 Copynumber: 31.5 Consensus size: 2
1182557 AGTGACTTTC
*
1182567 TA TA TA TA TA TA TA TA TA TA -A TA TA TA TA T- TA TA GA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1182607 TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
1182628 GATTTTATGT
Statistics
Matches: 55, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
1 2 0.04
2 53 0.96
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1183239 original size:21 final size:21
Alignment explanation
Indices: 1183214--1183253 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1183204 AAAAAATACA
*
1183214 TAAATTTA-AATATAATTATTT
1 TAAA-TTAGAATAAAATTATTT
1183235 TAAATTAGAATAAAATTAT
1 TAAATTAGAATAAAATTAT
1183254 AAATAATGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (21 bp):
TAAATTAGAATAAAATTATTT
Found at i:1183971 original size:22 final size:20
Alignment explanation
Indices: 1183941--1183980 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
1183931 TTTAACTTTA
1183941 ATTTCTTAATAATATATCATAT
1 ATTTCTTAA-AATA-ATCATAT
*
1183963 ATTTTTTAAAATAATCAT
1 ATTTCTTAAAATAATCAT
1183981 TGATATATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 4 0.24
22 8 0.47
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.50
Consensus pattern (20 bp):
ATTTCTTAAAATAATCATAT
Found at i:1186437 original size:2 final size:2
Alignment explanation
Indices: 1186430--1186475 Score: 56
Period size: 2 Copynumber: 23.0 Consensus size: 2
1186420 GTTTAAAAAG
* * * *
1186430 AT AT AT AT AT AC AT AC AT AC AT AT AT AT AT AT AT AT AT GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1186472 AT AT
1 AT AT
1186476 TCATTTTACA
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (2 bp):
AT
Found at i:1188366 original size:21 final size:21
Alignment explanation
Indices: 1188340--1188379 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1188330 TAAAAATTAT
*
1188340 TTAAAATATTATTATTTTTAC
1 TTAAAATATTAATATTTTTAC
1188361 TTAAAATATTAATATTTTT
1 TTAAAATATTAATATTTTT
1188380 TAATATTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (21 bp):
TTAAAATATTAATATTTTTAC
Found at i:1191752 original size:16 final size:16
Alignment explanation
Indices: 1191731--1191780 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
1191721 AAATAAACTA
1191731 TTTAATATTAAATAAT
1 TTTAATATTAAATAAT
**
1191747 TTTAAT-TTATGTAA-
1 TTTAATATTAAATAAT
1191761 TTTATATATTAAATAAT
1 TTTA-ATATTAAATAAT
1191778 TTT
1 TTT
1191781 TGTTTTAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
14 4 0.15
15 8 0.30
16 12 0.44
17 3 0.11
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (16 bp):
TTTAATATTAAATAAT
Found at i:1192369 original size:35 final size:32
Alignment explanation
Indices: 1192316--1192388 Score: 85
Period size: 35 Copynumber: 2.2 Consensus size: 32
1192306 AAATTTTTTA
* *
1192316 TTATTAAGGTCACTTAATTTGTGTTTTTAGACTAT
1 TTATTAAGGTCACATAATTT-TG-ATTTAGA-TAT
1192351 TTATTAA-GTGCACATAATTTTGATTTAGATAT
1 TTATTAAGGT-CACATAATTTTGATTTAGATAT
1192383 TTATTA
1 TTATTA
1192389 TTCTTGCAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
32 9 0.26
33 6 0.17
34 4 0.11
35 16 0.46
ACGTcount: A:0.30, C:0.07, G:0.12, T:0.51
Consensus pattern (32 bp):
TTATTAAGGTCACATAATTTTGATTTAGATAT
Found at i:1192465 original size:31 final size:32
Alignment explanation
Indices: 1192399--1192465 Score: 84
Period size: 32 Copynumber: 2.1 Consensus size: 32
1192389 TTCTTGCAAT
*
1192399 TTTAGATATTAGAAATTTTATTGAATTTTAAA
1 TTTAGATATTAGAAATTTTATTGAATTGTAAA
* *
1192431 TTTAGATATTA-AAATTATTATT-TATTGTATA
1 TTTAGATATTAGAAATT-TTATTGAATTGTAAA
1192462 TTTA
1 TTTA
1192466 AAATTTTATA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
31 15 0.48
32 16 0.52
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (32 bp):
TTTAGATATTAGAAATTTTATTGAATTGTAAA
Found at i:1192499 original size:17 final size:19
Alignment explanation
Indices: 1192463--1192514 Score: 65
Period size: 17 Copynumber: 2.9 Consensus size: 19
1192453 TATTGTATAT
*
1192463 TTAAAATTTTATATTCTAA
1 TTAATATTTTATATTCTAA
1192482 TTAATATTTTAT-TT-TAA
1 TTAATATTTTATATTCTAA
*
1192499 TTTATATTTTA-ATTCT
1 TTAATATTTTATATTCT
1192515 GGAAAAATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
17 15 0.52
18 3 0.10
19 11 0.38
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.62
Consensus pattern (19 bp):
TTAATATTTTATATTCTAA
Found at i:1194415 original size:16 final size:16
Alignment explanation
Indices: 1194394--1194424 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1194384 TTACCCGACC
*
1194394 TGTTTTCAACTTGACA
1 TGTTTTCAACCTGACA
1194410 TGTTTTCAACCTGAC
1 TGTTTTCAACCTGAC
1194425 TTGTAAATGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.23, G:0.13, T:0.42
Consensus pattern (16 bp):
TGTTTTCAACCTGACA
Found at i:1198250 original size:53 final size:54
Alignment explanation
Indices: 1198192--1198399 Score: 189
Period size: 53 Copynumber: 3.9 Consensus size: 54
1198182 ATATAATATA
1198192 AACAAAGATAGAAGATAAAGATG-CTCAGTTTA-GGTTTAGGGTTAAAGAAGATG
1 AACAAAGATAGAAGATAAAGA-GACTCAGTTTAGGGTTTAGGGTTAAAGAAGATG
* * * * * *
1198245 GACAAAGATATAATATAAAGAGACTTAATTTTA--GTTTGGGGTTAAAGAAGATG
1 AACAAAGATAGAAGATAAAGAGAC-TCAGTTTAGGGTTTAGGGTTAAAGAAGATG
* * * * * *
1198298 AACAAATATAGAAGATAAAGAGACT-AATTTAGGGTTTAAGATTAGAGAAAATG
1 AACAAAGATAGAAGATAAAGAGACTCAGTTTAGGGTTTAGGGTTAAAGAAGATG
* * * *
1198351 AATAGAGATAGAA-AGTGAAGAGGCTCAG-TTAGGGTTTA-GGTTAAAGAAG
1 AACAAAGATAGAAGA-TAAAGAGACTCAGTTTAGGGTTTAGGGTTAAAGAAG
1198400 GTGCACAATG
Statistics
Matches: 124, Mismatches: 25, Indels: 13
0.77 0.15 0.08
Matches are distributed among these distances:
51 5 0.04
52 11 0.09
53 101 0.81
54 7 0.06
ACGTcount: A:0.45, C:0.04, G:0.25, T:0.25
Consensus pattern (54 bp):
AACAAAGATAGAAGATAAAGAGACTCAGTTTAGGGTTTAGGGTTAAAGAAGATG
Found at i:1198372 original size:106 final size:106
Alignment explanation
Indices: 1198166--1198363 Score: 229
Period size: 106 Copynumber: 1.9 Consensus size: 106
1198156 AATATACTCG
* * * * *
1198166 ATTTAAGTTTGGGGTTATATAATATAAACAAAGATAGAAGATAAAGATGCTCAGTTTAGGTTTAG
1 ATTTAAGTTTGGGGTTAAAGAAGATAAACAAAGATAGAAGATAAAGATGCTCAATTTAGGTTTAA
* * * *
1198231 GGTTAAAGAAGATGGACAAAGATATAATATAAAGAGACTTA
66 GATTAAAGAAAATGAACAAAGATAGAATATAAAGAGACTTA
* * *
1198272 ATTTTAGTTTGGGGTTAAAGAAGATGAACAAATATAGAAGATAAAGA-GACT-AATTTAGGGTTT
1 ATTTAAGTTTGGGGTTAAAGAAGATAAACAAAGATAGAAGATAAAGATG-CTCAATTTA-GGTTT
* * *
1198335 AAGATTAGAGAAAATGAATAGAGATAGAA
64 AAGATTAAAGAAAATGAACAAAGATAGAA
1198364 AGTGAAGAGG
Statistics
Matches: 75, Mismatches: 15, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
105 6 0.08
106 69 0.92
ACGTcount: A:0.45, C:0.04, G:0.23, T:0.28
Consensus pattern (106 bp):
ATTTAAGTTTGGGGTTAAAGAAGATAAACAAAGATAGAAGATAAAGATGCTCAATTTAGGTTTAA
GATTAAAGAAAATGAACAAAGATAGAATATAAAGAGACTTA
Found at i:1198768 original size:104 final size:100
Alignment explanation
Indices: 1198615--1198801 Score: 268
Period size: 104 Copynumber: 1.8 Consensus size: 100
1198605 CAAGGGTTGA
* *
1198615 AAATTTTGGTGTTTGATCGAAAAAAAGAATGGGTTTAGGTTTTGTTGTTTGTGAAGATCAAATTA
1 AAATTTTGGTGTTTGATCGAAAAAAAGAATGGGTTTAGGTTTTGGTGTTTGTGAAGATCAAATGA
* *
1198680 GGGTTTTTAGGATGAACAATGATGAACAACAGTTT
66 AGGTTTATAGGATGAACAATGATGAACAACAGTTT
*
1198715 AAATTTTGGGTGTTTGATCGGAAATAATAAGAAAT-GGTTTGGGTTTTGGTGTTTGTGAAGATCA
1 AAATTTT-GGTGTTTGATC-GAAA-AA-AAG-AATGGGTTTAGGTTTTGGTGTTTGTGAAGATCA
*
1198779 AATGAAGGTTTATGGGATGAACA
61 AATGAAGGTTTATAGGATGAACA
1198802 CGGATGAATT
Statistics
Matches: 76, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
100 7 0.09
101 11 0.14
102 4 0.05
103 2 0.03
104 49 0.64
105 3 0.04
ACGTcount: A:0.32, C:0.04, G:0.27, T:0.36
Consensus pattern (100 bp):
AAATTTTGGTGTTTGATCGAAAAAAAGAATGGGTTTAGGTTTTGGTGTTTGTGAAGATCAAATGA
AGGTTTATAGGATGAACAATGATGAACAACAGTTT
Found at i:1199132 original size:2 final size:2
Alignment explanation
Indices: 1199125--1199150 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1199115 CTTTCAATTA
1199125 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1199151 TAATAAATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1199224 original size:26 final size:26
Alignment explanation
Indices: 1199187--1199244 Score: 91
Period size: 26 Copynumber: 2.2 Consensus size: 26
1199177 AATAAATTAA
*
1199187 TATATAATTTATATATACTAATGAAC
1 TATATAATTTATATATACTAATAAAC
1199213 TATATAGA-TTATATATACTAATAAAC
1 TATATA-ATTTATATATACTAATAAAC
1199239 TATATA
1 TATATA
1199245 CTATATAGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
26 29 0.97
27 1 0.03
ACGTcount: A:0.48, C:0.07, G:0.03, T:0.41
Consensus pattern (26 bp):
TATATAATTTATATATACTAATAAAC
Found at i:1199250 original size:33 final size:33
Alignment explanation
Indices: 1199211--1199409 Score: 265
Period size: 33 Copynumber: 6.0 Consensus size: 33
1199201 ATACTAATGA
*
1199211 ACTATATAGATTATATATACTAATAAACTATAT
1 ACTATATAGTTTATATATACTAATAAACTATAT
* * *
1199244 ACTATATAGTTTATATATACTAGTGAACTCTAT
1 ACTATATAGTTTATATATACTAATAAACTATAT
1199277 ACTATATAGTTTATATATACTAATAAACTATAT
1 ACTATATAGTTTATATATACTAATAAACTATAT
* * * *
1199310 AATATATAATTTATATATACTAATAAACAATAA
1 ACTATATAGTTTATATATACTAATAAACTATAT
* * *
1199343 ATTATATAGTTTATATGTACTAATGAACTATAT
1 ACTATATAGTTTATATATACTAATAAACTATAT
* *
1199376 AATATATAGTTTATATATACCAA-AGAACTATAT
1 ACTATATAGTTTATATATACTAATA-AACTATAT
1199409 A
1 A
1199410 GTTTATTAAT
Statistics
Matches: 144, Mismatches: 21, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
33 144 1.00
ACGTcount: A:0.46, C:0.09, G:0.05, T:0.40
Consensus pattern (33 bp):
ACTATATAGTTTATATATACTAATAAACTATAT
Found at i:1199251 original size:26 final size:25
Alignment explanation
Indices: 1199134--1199251 Score: 85
Period size: 26 Copynumber: 4.5 Consensus size: 25
1199124 AATATATATA
* *
1199134 TATATATATATATATATTAATAAAT
1 TATATATATATATATACTAATAAAC
* * * * *
1199159 TA-ATAAATTGTTTATATTAATAAAT
1 TATATATA-TATATATACTAATAAAC
*
1199184 TAATATATAATTTATATATACTAATGAAC
1 T-ATATAT-A--TATATATACTAATAAAC
*
1199213 TATATAGATTATATATACTAATAAAC
1 TATATATA-TATATATACTAATAAAC
1199239 TATATACTATATA
1 TATATA-TATATA
1199252 GTTTATATAT
Statistics
Matches: 75, Mismatches: 12, Indels: 11
0.77 0.12 0.11
Matches are distributed among these distances:
24 4 0.05
25 18 0.24
26 28 0.37
27 5 0.07
28 6 0.08
29 14 0.19
ACGTcount: A:0.49, C:0.04, G:0.03, T:0.44
Consensus pattern (25 bp):
TATATATATATATATACTAATAAAC
Found at i:1199500 original size:30 final size:30
Alignment explanation
Indices: 1199452--1199530 Score: 97
Period size: 34 Copynumber: 2.5 Consensus size: 30
1199442 GCATGTACTT
1199452 TATAGTTTAT-TAATATATATATATTAATAAACCA
1 TATAGTTTATAT-ATATATATATA-T-ATAAA--A
*
1199486 TATAGTTTATATATATATATATATATATAA
1 TATAGTTTATATATATATATATATATAAAA
1199516 TATAGTTTATATATA
1 TATAGTTTATATATA
1199531 GTTCATATAT
Statistics
Matches: 43, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
30 16 0.37
32 4 0.09
33 1 0.02
34 21 0.49
35 1 0.02
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.48
Consensus pattern (30 bp):
TATAGTTTATATATATATATATATATAAAA
Found at i:1199529 original size:11 final size:11
Alignment explanation
Indices: 1199485--1199541 Score: 66
Period size: 11 Copynumber: 5.5 Consensus size: 11
1199475 TTAATAAACC
1199485 ATATAGTTTAT
1 ATATAGTTTAT
*
1199496 ATATA-TATAT
1 ATATAGTTTAT
*
1199506 ATATA-TATA-
1 ATATAGTTTAT
1199515 ATATAGTTTAT
1 ATATAGTTTAT
*
1199526 ATATAGTTCAT
1 ATATAGTTTAT
1199537 ATATA
1 ATATA
1199542 CATTACATAG
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
9 5 0.12
10 16 0.39
11 20 0.49
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (11 bp):
ATATAGTTTAT
Found at i:1199541 original size:2 final size:2
Alignment explanation
Indices: 1199493--1199530 Score: 51
Period size: 2 Copynumber: 19.0 Consensus size: 2
1199483 CCATATAGTT
*
1199493 TA TA TA TA TA TA TA TA TA TA TA -A TA TA GTT TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA
1199531 GTTCATATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
1 1 0.03
2 30 0.94
3 1 0.03
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1209853 original size:20 final size:20
Alignment explanation
Indices: 1209834--1209911 Score: 70
Period size: 19 Copynumber: 3.8 Consensus size: 20
1209824 AGAACCCTAG
*
1209834 GGGGGTATCGATTCCCCT-A
1 GGGGGAATCGATTCCCCTCA
*
1209853 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGATTCCCC-TC--A
*
1209876 GGGGGAATCGGTT-CCCTCA
1 GGGGGAATCGATTCCCCTCA
*
1209895 TGGGGGTATCGATTCCC
1 -GGGGGAATCGATTCCC
1209912 TCTGCACCAA
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
19 16 0.33
20 12 0.24
21 4 0.08
22 3 0.06
23 14 0.29
ACGTcount: A:0.17, C:0.26, G:0.33, T:0.24
Consensus pattern (20 bp):
GGGGGAATCGATTCCCCTCA
Found at i:1209912 original size:20 final size:20
Alignment explanation
Indices: 1209834--1209913 Score: 65
Period size: 20 Copynumber: 3.9 Consensus size: 20
1209824 AGAACCCTAG
*
1209834 GGGGGTATCGATTCCC-C-T
1 GGGGGAATCGATTCCCTCAT
* *
1209852 AGGGGGAATCGGTTCCCCTTCAAA
1 -GGGGGAATCGATT-CCC-TC-AT
*
1209876 GGGGGAATCGGTTCCCTCAT
1 GGGGGAATCGATTCCCTCAT
*
1209896 GGGGGTATCGATTCCCTC
1 GGGGGAATCGATTCCCTC
1209914 TGCACCAAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
19 11 0.22
20 20 0.40
21 2 0.04
22 4 0.08
23 13 0.26
ACGTcount: A:0.16, C:0.26, G:0.33, T:0.25
Consensus pattern (20 bp):
GGGGGAATCGATTCCCTCAT
Found at i:1213757 original size:22 final size:21
Alignment explanation
Indices: 1213715--1213754 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1213705 GAGTTTATTT
*
1213715 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
1213736 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
1213755 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:1222837 original size:23 final size:23
Alignment explanation
Indices: 1222811--1222861 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
1222801 CATGTTCTTG
*
1222811 CCTTTAAGGCACATTTATCTCTC
1 CCTTTAACGCACATTTATCTCTC
** * *
1222834 CCTTTGTCGCACGTTTATCTCTG
1 CCTTTAACGCACATTTATCTCTC
1222857 CCTTT
1 CCTTT
1222862 GTGACACATT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.14, C:0.31, G:0.12, T:0.43
Consensus pattern (23 bp):
CCTTTAACGCACATTTATCTCTC
Found at i:1222862 original size:23 final size:23
Alignment explanation
Indices: 1222819--1222872 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 23
1222809 TGCCTTTAAG
1222819 GCACATTTATCTCTCCCTTTGTC
1 GCACATTTATCTCTCCCTTTGTC
* *
1222842 GCACGTTTATCTCTGCCTTTGT-
1 GCACATTTATCTCTCCCTTTGTC
1222864 GACACATTT
1 G-CACATTT
1222873 TTCTTTGTCT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 1 0.04
23 26 0.96
ACGTcount: A:0.15, C:0.30, G:0.13, T:0.43
Consensus pattern (23 bp):
GCACATTTATCTCTCCCTTTGTC
Found at i:1224211 original size:56 final size:57
Alignment explanation
Indices: 1224115--1224225 Score: 163
Period size: 56 Copynumber: 2.0 Consensus size: 57
1224105 GATGCACACA
* *
1224115 CCATGCATCGATGCACTGGGGATTTTATGAAAACATCGAATGCATTTGATGCATCAG
1 CCATGCATCGATGCACTCGGGATTTTATGAAAACATCGAATGCACTTGATGCATCAG
* *
1224172 CCATGCATCGATGCACTCTGGCTATTT-TG-AAACATCGAATGCACTTGATGCATC
1 CCATGCATCGATGCACTCGGGAT-TTTATGAAAACATCGAATGCACTTGATGCATC
1224226 GTTGCACTCT
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
56 24 0.49
57 22 0.45
58 3 0.06
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.29
Consensus pattern (57 bp):
CCATGCATCGATGCACTCGGGATTTTATGAAAACATCGAATGCACTTGATGCATCAG
Found at i:1229911 original size:21 final size:22
Alignment explanation
Indices: 1229865--1229912 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
1229855 ACACCTAACA
* * *
1229865 GTGCATTGATGCATCCTTGAAT
1 GTGCATTGATACATCCATGAAG
1229887 GTGCATTGATACA-CCATGAAG
1 GTGCATTGATACATCCATGAAG
1229908 GTGCA
1 GTGCA
1229913 CCGATGCACG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 11 0.48
22 12 0.52
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.29
Consensus pattern (22 bp):
GTGCATTGATACATCCATGAAG
Found at i:1230323 original size:21 final size:20
Alignment explanation
Indices: 1230293--1230337 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 20
1230283 TTACAACCAA
*
1230293 TTTCATAAAAAACTTACAAAT
1 TTTCAAAAAAAACTTA-AAAT
*
1230314 TTTCAAAAAAAATTTAAAAT
1 TTTCAAAAAAAACTTAAAAT
1230334 TTTC
1 TTTC
1230338 GAAATTAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (20 bp):
TTTCAAAAAAAACTTAAAAT
Found at i:1240935 original size:5 final size:5
Alignment explanation
Indices: 1240925--1240949 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
1240915 TCTAATGTGA
1240925 ATTTT ATTTT ATTTT ATTTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT
1240950 GTTGACACAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
ATTTT
Found at i:1241485 original size:23 final size:24
Alignment explanation
Indices: 1241432--1241514 Score: 61
Period size: 23 Copynumber: 3.6 Consensus size: 24
1241422 AGTAATCATA
*
1241432 TATATTTTTAATTTTTTGAATAAT
1 TATATTTTTAATTTTTGGAATAAT
* *
1241456 T-TAATTTTT-ATTTTTGGTATTAT
1 TAT-ATTTTTAATTTTTGGAATAAT
1241479 TATA--TTTAAGTTTTT-GAAT-AT
1 TATATTTTTAA-TTTTTGGAATAAT
*
1241500 TTTATATTTTAATTT
1 TATAT-TTTTAATTT
1241515 AAAATATTTT
Statistics
Matches: 47, Mismatches: 5, Indels: 15
0.70 0.07 0.22
Matches are distributed among these distances:
21 8 0.17
22 4 0.09
23 22 0.47
24 13 0.28
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (24 bp):
TATATTTTTAATTTTTGGAATAAT
Found at i:1241532 original size:45 final size:44
Alignment explanation
Indices: 1241437--1241532 Score: 102
Period size: 45 Copynumber: 2.1 Consensus size: 44
1241427 TCATATATAT
* * ****
1241437 TTTTAATTTTTTGAATAATTTAATTTTTATTTTTGGTATTATTA
1 TTTTAAGTTTTTGAATAATTTAATTTTAATTTAAAATATTATTA
* *
1241481 TATTTAAGTTTTTGAATATTTTATATTTTAATTTAAAATATTTTTA
1 T-TTTAAGTTTTTGAATAATTTA-ATTTTAATTTAAAATATTATTA
1241527 TTTTAA
1 TTTTAA
1241533 AAAAATCAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
44 1 0.02
45 24 0.57
46 17 0.40
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (44 bp):
TTTTAAGTTTTTGAATAATTTAATTTTAATTTAAAATATTATTA
Found at i:1241590 original size:27 final size:28
Alignment explanation
Indices: 1241528--1241593 Score: 87
Period size: 28 Copynumber: 2.4 Consensus size: 28
1241518 ATATTTTTAT
*
1241528 TTTAAAAAAATCAAATAAGCCCTTAAAC
1 TTTAAAAAAATCAAATAAGCCCTCAAAC
* **
1241556 TTTAAAAAAATCAATTTGGCCCTCAAAC
1 TTTAAAAAAATCAAATAAGCCCTCAAAC
*
1241584 TTGAAAAAAA
1 TTTAAAAAAA
1241594 CCAACTTAAC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.52, C:0.17, G:0.06, T:0.26
Consensus pattern (28 bp):
TTTAAAAAAATCAAATAAGCCCTCAAAC
Found at i:1251742 original size:19 final size:19
Alignment explanation
Indices: 1251718--1251770 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
1251708 AAAATGTTTA
1251718 AAAGTATCGATACTTATAT
1 AAAGTATCGATACTTATAT
* * *
1251737 AAAGTATCGAAACTTTTGT
1 AAAGTATCGATACTTATAT
1251756 AGAAGTATCGATACT
1 A-AAGTATCGATACT
1251771 CTTGGGCTAG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.40, C:0.11, G:0.15, T:0.34
Consensus pattern (19 bp):
AAAGTATCGATACTTATAT
Found at i:1258793 original size:29 final size:30
Alignment explanation
Indices: 1258698--1258793 Score: 85
Period size: 29 Copynumber: 3.2 Consensus size: 30
1258688 AGAGAAACAT
* *
1258698 AGTTT-AGGAGTGAAATTAGAATGTTCAAA
1 AGTTTAAGGACTGAAATTAGAATATTCAAA
* *
1258727 AGGTTAAGGACT-AATTTA-AA-ATTCAAATCA
1 AGTTTAAGGACTGAAATTAGAATATTC-AA--A
1258757 CAGTTTAAGGA-TGAAATTAGAATATTCAAA
1 -AGTTTAAGGACTGAAATTAGAATATTCAAA
1258787 AGTTTAA
1 AGTTTAA
1258794 AGATCGATTT
Statistics
Matches: 53, Mismatches: 6, Indels: 16
0.71 0.08 0.21
Matches are distributed among these distances:
27 3 0.06
28 4 0.08
29 16 0.30
30 8 0.15
31 14 0.26
32 4 0.08
33 4 0.08
ACGTcount: A:0.45, C:0.06, G:0.18, T:0.31
Consensus pattern (30 bp):
AGTTTAAGGACTGAAATTAGAATATTCAAA
Found at i:1266264 original size:31 final size:31
Alignment explanation
Indices: 1266229--1266294 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
1266219 ACATATTTAC
* *
1266229 TCACTCAACTATCACGTT-AGTTCTATTTTGG
1 TCACTCAACTATCAC-TTCAATTCTATTATGG
*
1266260 TCACTCAATTATCACTTCAATTCTATTATGG
1 TCACTCAACTATCACTTCAATTCTATTATGG
1266291 TCAC
1 TCAC
1266295 CAAACTACTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 2 0.06
31 29 0.94
ACGTcount: A:0.26, C:0.24, G:0.09, T:0.41
Consensus pattern (31 bp):
TCACTCAACTATCACTTCAATTCTATTATGG
Found at i:1269429 original size:19 final size:20
Alignment explanation
Indices: 1269402--1269441 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
1269392 CATTTGATAA
1269402 TACGCTCGAGTCCATA-TGT
1 TACGCTCGAGTCCATAGTGT
*
1269421 TACGTTCGAGTCCATAGTGT
1 TACGCTCGAGTCCATAGTGT
1269441 T
1 T
1269442 GAAGCTCTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.20, C:0.23, G:0.23, T:0.35
Consensus pattern (20 bp):
TACGCTCGAGTCCATAGTGT
Found at i:1270454 original size:37 final size:36
Alignment explanation
Indices: 1270408--1270571 Score: 181
Period size: 38 Copynumber: 4.4 Consensus size: 36
1270398 TAATAATATA
1270408 ATATAGTTTTTGAAAATATTTTTGAAAAACATATAAT
1 ATATAGTTTTTGAAAATATTTTTG-AAAACATATAAT
*
1270445 ATATAGTTTTTAGAAAATGATTTTTTGAAAGCATATAAT
1 ATATAGTTTTT-GAAAAT-A-TTTTTGAAAACATATAAT
*
1270484 ATATAGTTTTTTAAAA-ATCGATTTTGAAAACATATAAT
1 ATATAGTTTTTGAAAATAT---TTTTGAAAACATATAAT
** **
1270522 ATACCGTTTTT-AAAATATTTTTGAAAATGTAT-AT
1 ATATAGTTTTTGAAAATATTTTTGAAAACATATAAT
1270556 AATATAGTTTTTGAAA
1 -ATATAGTTTTTGAAA
1270572 GCGTTCGAAG
Statistics
Matches: 109, Mismatches: 9, Indels: 19
0.80 0.07 0.14
Matches are distributed among these distances:
34 2 0.02
35 22 0.20
36 4 0.04
37 15 0.14
38 37 0.34
39 23 0.21
40 6 0.06
ACGTcount: A:0.43, C:0.04, G:0.10, T:0.44
Consensus pattern (36 bp):
ATATAGTTTTTGAAAATATTTTTGAAAACATATAAT
Found at i:1277466 original size:34 final size:34
Alignment explanation
Indices: 1277421--1277487 Score: 84
Period size: 34 Copynumber: 1.9 Consensus size: 34
1277411 AATTGGAATT
*
1277421 ACAACTTCTCTCGATT-TAACAAGGAGAAAACAATA
1 ACAACTTCTCTC--TTATAAAAAGGAGAAAACAATA
1277456 ACAA-TTCTCTCTTGATAAAAAGGAGAAAACAA
1 ACAACTTCTCTCTT-ATAAAAAGGAGAAAACAA
1277488 CTCTCAAGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
32 2 0.07
34 23 0.79
35 4 0.14
ACGTcount: A:0.48, C:0.18, G:0.12, T:0.22
Consensus pattern (34 bp):
ACAACTTCTCTCTTATAAAAAGGAGAAAACAATA
Found at i:1280737 original size:28 final size:28
Alignment explanation
Indices: 1280701--1280839 Score: 103
Period size: 28 Copynumber: 5.1 Consensus size: 28
1280691 TATTAAAATA
** *
1280701 ATTTT-AAATAATTTAATAAGGTTATTT
1 ATTTTAAAATAATTTAATAAAATAATTT
**
1280728 ATTTTAAAATAATTTTTTAAAATAATTT
1 ATTTTAAAATAATTTAATAAAATAATTT
* *
1280756 ATTATAAAATAATTTATTTTAAAATAATTT
1 ATTTTAAAATAATTTA--ATAAAATAATTT
* * *
1280786 ATTATAAAAT-A-TGAAT----TGATTT
1 ATTTTAAAATAATTTAATAAAATAATTT
*
1280808 ATTTTAAAATAATTTATTTAAAATAATTT
1 ATTTTAAAATAATTTA-ATAAAATAATTT
1280837 ATT
1 ATT
1280840 AGTATGGATT
Statistics
Matches: 88, Mismatches: 14, Indels: 18
0.73 0.12 0.15
Matches are distributed among these distances:
22 14 0.16
23 1 0.01
24 2 0.02
25 1 0.01
26 1 0.01
27 5 0.06
28 33 0.38
29 9 0.10
30 22 0.25
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (28 bp):
ATTTTAAAATAATTTAATAAAATAATTT
Found at i:1280765 original size:15 final size:15
Alignment explanation
Indices: 1280724--1280840 Score: 123
Period size: 15 Copynumber: 7.5 Consensus size: 15
1280714 TAATAAGGTT
*
1280724 ATTTATTTTAAAATA
1 ATTTATTATAAAATA
1280739 ATTT-TT-TAAAATA
1 ATTTATTATAAAATA
1280752 ATTTATTATAAAATA
1 ATTTATTATAAAATA
*
1280767 ATTTATTTTAAAATA
1 ATTTATTATAAAATA
1280782 ATTTATTATAAAATATGAA
1 ATTTATTAT-AAA-AT--A
*
1280801 TTGATTTATTTTAAAATA
1 ---ATTTATTATAAAATA
1280819 ATTTATT-TAAAATA
1 ATTTATTATAAAATA
1280833 ATTTATTA
1 ATTTATTA
1280841 GTATGGATTG
Statistics
Matches: 89, Mismatches: 3, Indels: 20
0.79 0.03 0.18
Matches are distributed among these distances:
13 11 0.12
14 18 0.20
15 40 0.45
16 3 0.03
17 2 0.02
18 1 0.01
19 1 0.01
20 2 0.02
21 3 0.03
22 8 0.09
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (15 bp):
ATTTATTATAAAATA
Found at i:1280857 original size:32 final size:32
Alignment explanation
Indices: 1280819--1281063 Score: 137
Period size: 32 Copynumber: 7.4 Consensus size: 32
1280809 TTTTAAAATA
1280819 ATTTATTTAAAATAATTTATTAGTATGGATTG
1 ATTTATTTAAAATAATTTATTAGTATGGATTG
* *
1280851 ATTTATTTTAAATAATTTATTAGTATGGGTTG
1 ATTTATTTAAAATAATTTATTAGTATGGATTG
** **
1280883 ATTTATTTTAAAAT-ATGGATT-G-ATTTATT-
1 ATTTA-TTTAAAATAATTTATTAGTATGGATTG
* * * * *
1280912 ATTGTAGTTGTATGAATTGATTTATT--T-T-AAATA
1 ATT-TA-TT-TA--AAATAATTTATTAGTATGGATTG
* * *
1280945 ATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTG
1 ATTTATT--TA--AAATAATTTA--TT--AGTATGGATTG
* *
1280985 ATTTATTTTAAATAATTTATTAGTATGGACTG
1 ATTTATTTAAAATAATTTATTAGTATGGATTG
* *
1281017 ATTTATTTTAAATAATTTATTTGTATGGATTG
1 ATTTATTTAAAATAATTTATTAGTATGGATTG
1281049 ATTTATTTTAAAATA
1 ATTTA-TTTAAAATA
1281064 TGGATTGATT
Statistics
Matches: 170, Mismatches: 25, Indels: 35
0.74 0.11 0.15
Matches are distributed among these distances:
29 3 0.02
30 8 0.05
31 5 0.03
32 103 0.61
33 22 0.13
34 9 0.05
36 8 0.05
38 2 0.01
39 1 0.01
40 9 0.05
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (32 bp):
ATTTATTTAAAATAATTTATTAGTATGGATTG
Found at i:1280939 original size:80 final size:80
Alignment explanation
Indices: 1280767--1281157 Score: 488
Period size: 80 Copynumber: 4.8 Consensus size: 80
1280757 TTATAAAATA
* *
1280767 ATTTATTTTAAAATAATTTATTATAAAATATGAATTGATTTATTTTAAAATA---ATTTATTTAA
1 ATTTATTTT-AAATAATTTA-T-T--AGTATGAATTGATTTATTTTAAAATATGGATTGATTT--
*
1280829 AATAATT-TA-TTAGTATGGATTG
59 -ATTATTGTAGTT-GTATGGATTG
**
1280851 ATTTATTTTAAATAATTTATTAGTATGGGTTGATTTATTTTAAAATATGGATTGATTTATTATTG
1 ATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGATTTATTATTG
*
1280916 TAGTTGTATGAATTG
66 TAGTTGTATGGATTG
1280931 ATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
1 ATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGATTTA--TT--
* *
1280996 ATAATTTA-TTAGTATGGACTG
62 AT--TGTAGTT-GTATGGATTG
* *
1281017 ATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTG
1 ATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGATTTATTATTG
1281082 TAGTTGTATGGATTG
66 TAGTTGTATGGATTG
* *
1281097 ATTTATTTTAAATAATTTATTAATATGAATTAATTTATTTTAAAATATGGATTGATTTATT
1 ATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGATTTATT
1281158 TTAAATAATT
Statistics
Matches: 275, Mismatches: 19, Indels: 30
0.85 0.06 0.09
Matches are distributed among these distances:
79 28 0.10
80 137 0.50
81 5 0.02
82 12 0.04
83 10 0.04
84 13 0.05
85 2 0.01
86 68 0.25
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (80 bp):
ATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGATTTATTATTG
TAGTTGTATGGATTG
Found at i:1280966 original size:18 final size:17
Alignment explanation
Indices: 1280919--1280969 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 17
1280909 ATTATTGTAG
1280919 TTGTATGAATTGATTTA
1 TTGTATGAATTGATTTA
* *
1280936 TT-T-T-AAATAATTTA
1 TTGTATGAATTGATTTA
1280950 TTAGTATGAATTGATTTA
1 TT-GTATGAATTGATTTA
1280968 TT
1 TT
1280970 TTAAAATATG
Statistics
Matches: 26, Mismatches: 4, Indels: 7
0.70 0.11 0.19
Matches are distributed among these distances:
14 10 0.38
15 1 0.04
16 2 0.08
17 3 0.12
18 10 0.38
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.55
Consensus pattern (17 bp):
TTGTATGAATTGATTTA
Found at i:1280979 original size:22 final size:22
Alignment explanation
Indices: 1280954--1280996 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
1280944 AATTTATTAG
1280954 TATGAATTGATTTATTTTAAAA
1 TATGAATTGATTTATTTTAAAA
*
1280976 TATGGATTGATTTATTTTAAA
1 TATGAATTGATTTATTTTAAA
1280997 TAATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (22 bp):
TATGAATTGATTTATTTTAAAA
Found at i:1280991 original size:54 final size:54
Alignment explanation
Indices: 1280922--1281172 Score: 249
Period size: 54 Copynumber: 4.6 Consensus size: 54
1280912 ATTGTAGTTG
* *
1280922 TATGAATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAATATGAATTGATTTATTTTAAAA
* * *
1280976 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGACTGATTTATTTT-AAA
1 TATGGATTGATTTATTTTAAATAATTTATTAATATGAATTGATTTATTTTAAAA
* * * ** * * * ***
1281029 TA---ATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTG
1 TATGGATTGATTTATTTTAAATAATTTA--TT--AATATGAATTGATTTA-T-TT-TA-AAA
*
1281088 TATGGATTGATTTATTTTAAATAATTTATTAATATGAATTAATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAATATGAATTGATTTATTTTAAAA
1281142 TATGGATTGATTTATTTTAAATAATTTATTA
1 TATGGATTGATTTATTTTAAATAATTTATTA
1281173 TTGTAGTTGT
Statistics
Matches: 158, Mismatches: 27, Indels: 24
0.76 0.13 0.11
Matches are distributed among these distances:
50 16 0.10
52 2 0.01
53 5 0.03
54 92 0.58
55 3 0.02
56 4 0.03
57 2 0.01
58 14 0.09
59 2 0.01
60 2 0.01
62 16 0.10
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (54 bp):
TATGGATTGATTTATTTTAAATAATTTATTAATATGAATTGATTTATTTTAAAA
Found at i:1281025 original size:166 final size:166
Alignment explanation
Indices: 1280819--1281172 Score: 645
Period size: 166 Copynumber: 2.1 Consensus size: 166
1280809 TTTTAAAATA
* * *
1280819 ATTTATTTAAAATAATTTATTAGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGGTTGA
1 ATTTATTTTAAATAATTTATTAGTATGGACTGATTTATTTTAAATAATTTATTAGTATGGATTGA
1280884 TTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGAATTGATTTATTTTAAATAATTT
66 TTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGAATTGATTTATTTTAAATAATTT
* *
1280949 ATTAGTATGAATTGATTTATTTTAAAATATGGATTG
131 ATTAATATGAATTAATTTATTTTAAAATATGGATTG
*
1280985 ATTTATTTTAAATAATTTATTAGTATGGACTGATTTATTTTAAATAATTTATTTGTATGGATTGA
1 ATTTATTTTAAATAATTTATTAGTATGGACTGATTTATTTTAAATAATTTATTAGTATGGATTGA
*
1281050 TTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTT
66 TTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGAATTGATTTATTTTAAATAATTT
1281115 ATTAATATGAATTAATTTATTTTAAAATATGGATTG
131 ATTAATATGAATTAATTTATTTTAAAATATGGATTG
1281151 ATTTATTTTAAATAATTTATTA
1 ATTTATTTTAAATAATTTATTA
1281173 TTGTAGTTGT
Statistics
Matches: 181, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
166 181 1.00
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (166 bp):
ATTTATTTTAAATAATTTATTAGTATGGACTGATTTATTTTAAATAATTTATTAGTATGGATTGA
TTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGAATTGATTTATTTTAAATAATTT
ATTAATATGAATTAATTTATTTTAAAATATGGATTG
Found at i:1281136 original size:22 final size:22
Alignment explanation
Indices: 1281118--1281162 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
1281108 ATAATTTATT
1281118 AATATGAATTAATTTATTTTAA
1 AATATGAATTAATTTATTTTAA
* *
1281140 AATATGGATTGATTTATTTTAA
1 AATATGAATTAATTTATTTTAA
1281162 A
1 A
1281163 TAATTTATTA
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:0.42, C:0.00, G:0.09, T:0.49
Consensus pattern (22 bp):
AATATGAATTAATTTATTTTAA
Found at i:1285193 original size:22 final size:22
Alignment explanation
Indices: 1285168--1285209 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
1285158 CAATTCATTT
1285168 ATCTT-TTCTTTATCTTGTTTTA
1 ATCTTATT-TTTATCTTGTTTTA
1285190 ATCTTATTTTTATCTTGTTT
1 ATCTTATTTTTATCTTGTTT
1285210 CCAGCACCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.14, C:0.12, G:0.05, T:0.69
Consensus pattern (22 bp):
ATCTTATTTTTATCTTGTTTTA
Found at i:1291832 original size:22 final size:22
Alignment explanation
Indices: 1291807--1291848 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
1291797 CAATTCATTT
1291807 ATCTT-TTCTTTATCTTGTTTTA
1 ATCTTATT-TTTATCTTGTTTTA
1291829 ATCTTATTTTTATCTTGTTT
1 ATCTTATTTTTATCTTGTTT
1291849 CCAGCACCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.14, C:0.12, G:0.05, T:0.69
Consensus pattern (22 bp):
ATCTTATTTTTATCTTGTTTTA
Found at i:1294783 original size:17 final size:17
Alignment explanation
Indices: 1294749--1294787 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
1294739 AATAACCATA
*
1294749 ATAAATTATATGATATT
1 ATAAATTATATGAAATT
* *
1294766 ATAAATTATCTTAAATT
1 ATAAATTATATGAAATT
1294783 ATAAA
1 ATAAA
1294788 ATTGACATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.44
Consensus pattern (17 bp):
ATAAATTATATGAAATT
Done.