Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold247
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: 4737410
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 15 of 29
Found at i:2239722 original size:21 final size:21
Alignment explanation
Indices: 2239698--2239738 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2239688 ATGCAAGTTC
2239698 TTGTTCTTCA-TAGCCAATTCG
1 TTGTT-TTCATTAGCCAATTCG
*
2239719 TTGTTTTCATTAGCTAATTC
1 TTGTTTTCATTAGCCAATTC
2239739 TTTATTACTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.20, C:0.20, G:0.12, T:0.49
Consensus pattern (21 bp):
TTGTTTTCATTAGCCAATTCG
Found at i:2239779 original size:21 final size:21
Alignment explanation
Indices: 2239755--2239801 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
2239745 ACTATCTTGC
2239755 AATTCAATTATCTTCTTTTCT
1 AATTCAATTATCTTCTTTTCT
* *
2239776 AATTCACTTATTTTCTTTTCT
1 AATTCAATTATCTTCTTTTCT
2239797 AATTC
1 AATTC
2239802 TTCTTCTTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.23, C:0.19, G:0.00, T:0.57
Consensus pattern (21 bp):
AATTCAATTATCTTCTTTTCT
Found at i:2239811 original size:21 final size:21
Alignment explanation
Indices: 2239767--2239815 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
2239757 TTCAATTATC
*
2239767 TTCTTTTCTAATTCACTTATT
1 TTCTTTTCTAATTCACTTACT
*
2239788 TTCTTTTCTAATTCTTCTT-CT
1 TTCTTTTCTAATTC-ACTTACT
2239809 TTCTTTT
1 TTCTTTT
2239816 TAAGCACATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 22 0.88
22 3 0.12
ACGTcount: A:0.12, C:0.20, G:0.00, T:0.67
Consensus pattern (21 bp):
TTCTTTTCTAATTCACTTACT
Found at i:2245020 original size:21 final size:21
Alignment explanation
Indices: 2244995--2245043 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
2244985 AAGTTGTATT
*
2244995 TTTCATCCAAAAAATATATCA
1 TTTCATCCAAAAAATACATCA
** *
2245016 TTTCATCCAACCAATGCATCA
1 TTTCATCCAAAAAATACATCA
2245037 TTTCATC
1 TTTCATC
2245044 TAAATACACC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.37, C:0.27, G:0.02, T:0.35
Consensus pattern (21 bp):
TTTCATCCAAAAAATACATCA
Found at i:2245090 original size:28 final size:28
Alignment explanation
Indices: 2245047--2245116 Score: 97
Period size: 28 Copynumber: 2.5 Consensus size: 28
2245037 TTTCATCTAA
2245047 ATACACCTTTTT-ATAAAAGACAATGTCT
1 ATACA-CTTTTTCATAAAAGACAATGTCT
**
2245075 ATACACTTTTTCATAATGGACAATGTCT
1 ATACACTTTTTCATAAAAGACAATGTCT
*
2245103 ATACACCTTTTCAT
1 ATACACTTTTTCAT
2245117 CCAAAGTAGT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
27 6 0.16
28 32 0.84
ACGTcount: A:0.34, C:0.20, G:0.07, T:0.39
Consensus pattern (28 bp):
ATACACTTTTTCATAAAAGACAATGTCT
Found at i:2249565 original size:54 final size:54
Alignment explanation
Indices: 2249467--2249624 Score: 208
Period size: 54 Copynumber: 2.9 Consensus size: 54
2249457 GCAATTAGAA
* * * *
2249467 TTGGAGTGACTTGGTGTCACTTAGTATTGCGATGACACCGAGATGGCGACCGGAT
1 TTGGAGTGACTTGG-GTCACTTAGTATTGTGATGACGCCAAGATGGCGACCAGAT
* * * * * *
2249522 TTGGAGTGGCTCGGGTCATTTAGAATTGTGATGACGCCAAGATGGCAACTAGAT
1 TTGGAGTGACTTGGGTCACTTAGTATTGTGATGACGCCAAGATGGCGACCAGAT
*
2249576 TTAGAGTGACTTGGGTCACTTAGTATTGTGATGACGCCAAGATGGCGAC
1 TTGGAGTGACTTGGGTCACTTAGTATTGTGATGACGCCAAGATGGCGAC
2249625 TAAGGAAGCT
Statistics
Matches: 87, Mismatches: 16, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
54 75 0.86
55 12 0.14
ACGTcount: A:0.24, C:0.16, G:0.32, T:0.28
Consensus pattern (54 bp):
TTGGAGTGACTTGGGTCACTTAGTATTGTGATGACGCCAAGATGGCGACCAGAT
Found at i:2250105 original size:21 final size:20
Alignment explanation
Indices: 2250079--2250134 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
2250069 TTGTATAATT
2250079 TGTATCGATACAAACAGTAAA
1 TGTATCGATACAAA-AGTAAA
* *
2250100 TGTATCGATACATAAGTGAA
1 TGTATCGATACAAAAGTAAA
*
2250120 TGCATCGATACAAAA
1 TGTATCGATACAAAA
2250135 CCACCTTGCA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 18 0.58
21 13 0.42
ACGTcount: A:0.45, C:0.14, G:0.16, T:0.25
Consensus pattern (20 bp):
TGTATCGATACAAAAGTAAA
Found at i:2250224 original size:20 final size:21
Alignment explanation
Indices: 2250179--2250234 Score: 78
Period size: 20 Copynumber: 2.7 Consensus size: 21
2250169 CATAAGTAAA
*
2250179 TGTATCGATACATGATTTCAAT
1 TGTATCGATACAT-TTTTCAAT
*
2250201 TGTATGGATACATTTTTC-AT
1 TGTATCGATACATTTTTCAAT
2250221 TGTATCGATACATT
1 TGTATCGATACATT
2250235 CTGGGTTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
20 15 0.48
21 4 0.13
22 12 0.39
ACGTcount: A:0.29, C:0.12, G:0.14, T:0.45
Consensus pattern (21 bp):
TGTATCGATACATTTTTCAAT
Found at i:2252784 original size:79 final size:79
Alignment explanation
Indices: 2252651--2253123 Score: 476
Period size: 79 Copynumber: 6.0 Consensus size: 79
2252641 TCATTGATAT
* * *
2252651 TTTTATTTCCAAAATAT-GATTTTCTTCA-TCATCGGGGATATTCCAACCCTGTTATTTTCGAAG
1 TTTTATTTCTAAAATATCGA-TTT-TTCACT-ATCAGGGATACTCCAACCCTGTTATTTTCGAAG
* *
2252714 GGATATTCTAACCTCAG
63 GGATACTCCAACCTCAG
* * *
2252731 TTTTATTTCTAAAATAACGATTTTTCACTATCAGGGATACTCCAACCCCGTTATTTTTG-AGGGA
1 TTTTATTTCTAAAATATCGATTTTTCACTATCAGGGATACTCCAACCCTGTTATTTTCGAAGGG-
*
2252795 ATACTCCAA-CTCCG
65 ATACTCCAACCTCAG
* * * **
2252809 ATTTTATTTCTAAAATATCGATTTTTCACCATC-GAGGATATTCCAAACCTGTTATTTTCGAAAA
1 -TTTTATTTCTAAAATATCGATTTTTCACTATCAG-GGATACTCCAACCCTGTTATTTTCGAAGG
*
2252873 GATACTCCAACCACAG
64 GATACTCCAACCTCAG
* * * * * * *
2252889 TTTTTTTTCTAAAACATTGATTTTTCA-TCATCGGGGATACTCCAACCCCGTTATTTTTGAGGGG
1 TTTTATTTCTAAAATATCGATTTTTCACT-ATCAGGGATACTCCAACCCTGTTATTTTCGAAGGG
* *
2252953 ATACTCCAACCCCAA
65 ATACTCCAACCTCAG
* * * * * *
2252968 TTTTATTTCTAAAATATTGATTTTCCACTATAAGGGATACTCCAACTCTGTTATTTTTGAAGAGA
1 TTTTATTTCTAAAATATCGATTTTTCACTATCAGGGATACTCCAACCCTGTTATTTTCGAAGGGA
*
2253033 TACTCCAA-CTCCG
66 TACTCCAACCTCAG
* * * * *
2253046 ATTTTATTTCTAAAACATCGATTTTACACCATTAGGGATACTCCAACCCTGTCATTTTC-AAGGG
1 -TTTTATTTCTAAAATATCGATTTTTCACTATCAGGGATACTCCAACCCTGTTATTTTCGAA-GG
*
2253110 GATACTCTAACCTC
64 GATACTCCAACCTC
2253124 GTTATTTTTA
Statistics
Matches: 326, Mismatches: 54, Indels: 26
0.80 0.13 0.06
Matches are distributed among these distances:
78 13 0.04
79 282 0.87
80 29 0.09
81 2 0.01
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.37
Consensus pattern (79 bp):
TTTTATTTCTAAAATATCGATTTTTCACTATCAGGGATACTCCAACCCTGTTATTTTCGAAGGGA
TACTCCAACCTCAG
Found at i:2252971 original size:158 final size:155
Alignment explanation
Indices: 2252651--2253121 Score: 552
Period size: 158 Copynumber: 3.0 Consensus size: 155
2252641 TCATTGATAT
* * * * *
2252651 TTTTATTTCCAAAATATGATTTTCTTCATCATCGGGGATATTCCAACCCTGTTATTTTCGAAGGG
1 TTTTATTTCTAAAATATGA-TTT-TTCACCATCGAGGATATTCCAAACCTGTTATTTTCGAAGAG
* * * *
2252716 ATATTCTAACCTCAGTTTTATTTCTAAAATAACGATTTTTCACTATCAGGGATACTCCAACCCCG
64 ATACTCCAACC-CAGTTTTATTTCTAAAACATCGATTTTTCAC-ATCAGGGATACTCCAACCCCG
* * *
2252781 TTATTTTTGAGGGAATACTCCAACTCCGA
127 TTATTTTTGAGGGGATACTCCAACCCCAA
*
2252810 TTTTATTTCTAAAATATCGATTTTTCACCATCGAGGATATTCCAAACCTGTTATTTTCGAAAAGA
1 TTTTATTTCTAAAATAT-GATTTTTCACCATCGAGGATATTCCAAACCTGTTATTTTCGAAGAGA
* * *
2252875 TACTCCAACCACAGTTTTTTTTCTAAAACATTGATTTTTCATCATCGGGGATACTCCAACCCCGT
65 TACTCCAACC-CAGTTTTATTTCTAAAACATCGATTTTTCA-CATCAGGGATACTCCAACCCCGT
2252940 TATTTTTGAGGGGATACTCCAACCCCAA
128 TATTTTTGAGGGGATACTCCAACCCCAA
* * * * *
2252968 TTTTATTTCTAAAATATTGATTTTCCACTAT-AAGGGATACTCC-AACTCTGTTATTTTTGAAGA
1 TTTTATTTCTAAAATA-TGATTTTTCACCATCGA-GGATATTCCAAAC-CTGTTATTTTCGAAGA
* *
2253031 GATACTCCAACTCC-GATTTTATTTCTAAAACATCGATTTTACACCATTAGGGATACTCCAACCC
63 GATACTCCAAC-CCAG-TTTTATTTCTAAAACATCGATTTTTCA-CATCAGGGATACTCCAACCC
* * ** *
2253095 TGTCATTTTCAAGGGGATACTCTAACC
125 CGTTATTTTTGAGGGGATACTCCAACC
2253122 TCGTTATTTT
Statistics
Matches: 271, Mismatches: 34, Indels: 15
0.85 0.11 0.05
Matches are distributed among these distances:
157 5 0.02
158 242 0.89
159 22 0.08
160 2 0.01
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.37
Consensus pattern (155 bp):
TTTTATTTCTAAAATATGATTTTTCACCATCGAGGATATTCCAAACCTGTTATTTTCGAAGAGAT
ACTCCAACCCAGTTTTATTTCTAAAACATCGATTTTTCACATCAGGGATACTCCAACCCCGTTAT
TTTTGAGGGGATACTCCAACCCCAA
Found at i:2253116 original size:237 final size:235
Alignment explanation
Indices: 2252649--2253674 Score: 625
Period size: 237 Copynumber: 4.2 Consensus size: 235
2252639 ATTCATTGAT
* * * * * *
2252649 ATTTTTATTTCCAAAATA-TGATTTTCTTCATCATCGGGGATATTCCAACCCTGTTATTTTCGAA
1 ATTTTT-TTTCTAAAACATTGA-TTT-TTCACCATCGGGGATACTCCAACCCCGTTATTTTTGAA
* * * * *
2252713 GGGATATTCTAACCTCAGTTTTATTTCTAAAATAACGATTTTTCACTATCAGGGATACTCCAACC
63 GGGATACTCCAACCCCAATTTTATTTCTAAAATATCGATTTTTCACTAT-AGGGATACTCCAACC
*
2252778 CCGTTATTTTTGAGGGAATACTCCAACTCCGATTTTATTTCTAAAATATCGATTTTTCACCATCG
127 CCGTTATTTTTGAGGGAATACTCCAAC-CCGATTTTATTTCTAAAATATCGATTTTTCACCATTG
* * * * ** *
2252843 AGGATATTCCAAACCTGTTATTTTCGAA-AAGATACTCCAACCAC-
191 GGGATACTCCAACCCTGTCATTTTC-AAGGGGATACTCCAACCTCG
* *
2252887 AGTTTTTTTTCTAAAACATTGATTTTTCATCATCGGGGATACTCCAACCCCGTTATTTTTGAGGG
1 A-TTTTTTTTCTAAAACATTGATTTTTCACCATCGGGGATACTCCAACCCCGTTATTTTTGAAGG
* * * *
2252952 GATACTCCAACCCCAATTTTATTTCTAAAATATTGATTTTCCACTATAAGGGATACTCCAACTCT
65 GATACTCCAACCCCAATTTTATTTCTAAAATATCGATTTTTCACTAT-AGGGATACTCCAACCCC
* * * *
2253017 GTTATTTTTGA-AGAGATACTCCAACTCCGATTTTATTTCTAAAACATCGATTTTACACCATTAG
129 GTTATTTTTGAGGGA-ATACTCCAAC-CCGATTTTATTTCTAAAATATCGATTTTTCACCATTGG
*
2253081 GGATACTCCAACCCTGTCATTTTCAAGGGGATACTCTAACCTCG
192 GGATACTCCAACCCTGTCATTTTCAAGGGGATACTCCAACCTCG
* *** ** *** * ** *** *
2253125 --TTATTTT-TAAGGGGA-T-ACTCTAATC-CCGAT--TTTATTTCTAAAATATCG--ATTTTTC
1 ATTTTTTTTCTAA-AACATTGA-T-TTTTCACC-ATCGGGGA-TACTCCAACCCCGTTATTTTTG
** *
2253180 ACCATCGGGGATACTCCAACTTCGTTATTTTTGAGGGGATACTCTAACCCCGATTTTATTTCTAA
61 A--A---GGGATACTCCAAC--C-CCAATTTT------AT--T-T-----C-----TA-----AA
* * * * * * *
2253245 AGTATCAATTTTTCACCATCGAGAATACTCCAACCCTGTTATTTTTGAGGGAATGCTCTAACCCT
94 A-TATCGATTTTTCACTATAG-GGATACTCCAACCCCGTTATTTTTGAGGGAATACTCCAACCC-
* * * * * *
2253310 GGTTTTATTTCTAAAATTTTGATCTTTCACCATTGGGGATACTCCAACCCTGTTATTTTCGAGGG
156 GATTTTATTTCTAAAATATCGATTTTTCACCATTGGGGATACTCCAACCCTGTCATTTTCAAGGG
* * *
2253375 AATACTCTAATCC-CA
221 GATACTCCAA-CCTCG
** * * * * **
2253390 ATTTAATTTCTAAAATATTAATTTTTCACCATCGGAGATACTCTAACCCTATTATTTTTGAAGGG
1 ATTTTTTTTCTAAAACATTGATTTTTCACCATCGGGGATACTCCAACCCCGTTATTTTTGAAGGG
*
2253455 ATACTCCAA-CCCAATTTTATTT-TCAAAATATCGACTTTTCA-TCATTAGGGATACTCCAACCC
66 ATACTCCAACCCCAATTTTATTTCT-AAAATATCGATTTTTCACT-A-TAGGGATACTCCAACCC
* * * * * *
2253517 CGTTATTTTCGAGGGGATATTCCAACCCCATTTTTATTTCCAAAATATCGATTTTTCACTATTGG
128 CGTTATTTTTGAGGGAATACTCCAACCCGA-TTTTATTTCTAAAATATCGATTTTTCACCATTGG
*
2253582 GGATACTCCAACCCTG-CTATTTTCGAGGGGATACTCCAACCTCG
192 GGATACTCCAACCCTGTC-ATTTTCAAGGGGATACTCCAACCTCG
* * * * *
2253626 ATTTTATTTTC-AAAATATGGACTTTTCACCATTGGGGATACTCTAACCC
1 ATTTT-TTTTCTAAAACATTGATTTTTCACCATCGGGGATACTCCAACCC
2253675 ATTTTATTTC
Statistics
Matches: 603, Mismatches: 121, Indels: 130
0.71 0.14 0.15
Matches are distributed among these distances:
232 7 0.01
233 2 0.00
234 13 0.02
235 14 0.02
236 153 0.25
237 201 0.33
238 13 0.02
239 9 0.01
240 5 0.01
241 1 0.00
242 1 0.00
246 2 0.00
248 1 0.00
249 1 0.00
252 1 0.00
253 1 0.00
254 1 0.00
255 2 0.00
259 2 0.00
261 5 0.01
262 1 0.00
264 6 0.01
265 123 0.20
266 4 0.01
267 12 0.02
268 13 0.02
269 2 0.00
270 7 0.01
ACGTcount: A:0.28, C:0.22, G:0.13, T:0.37
Consensus pattern (235 bp):
ATTTTTTTTCTAAAACATTGATTTTTCACCATCGGGGATACTCCAACCCCGTTATTTTTGAAGGG
ATACTCCAACCCCAATTTTATTTCTAAAATATCGATTTTTCACTATAGGGATACTCCAACCCCGT
TATTTTTGAGGGAATACTCCAACCCGATTTTATTTCTAAAATATCGATTTTTCACCATTGGGGAT
ACTCCAACCCTGTCATTTTCAAGGGGATACTCCAACCTCG
Found at i:2253121 original size:28 final size:28
Alignment explanation
Indices: 2253080--2253147 Score: 93
Period size: 28 Copynumber: 2.4 Consensus size: 28
2253070 TACACCATTA
*
2253080 GGGATACTCCAACC-CTGTCATTTTCAAG
1 GGGATACTCTAACCTC-GTCATTTTCAAG
* *
2253108 GGGATACTCTAACCTCGTTATTTTTAAG
1 GGGATACTCTAACCTCGTCATTTTCAAG
2253136 GGGATACTCTAA
1 GGGATACTCTAA
2253148 TCCCGATTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
28 35 0.97
29 1 0.03
ACGTcount: A:0.26, C:0.22, G:0.19, T:0.32
Consensus pattern (28 bp):
GGGATACTCTAACCTCGTCATTTTCAAG
Found at i:2253190 original size:79 final size:78
Alignment explanation
Indices: 2253107--2253683 Score: 622
Period size: 79 Copynumber: 7.3 Consensus size: 78
2253097 TCATTTTCAA
* *
2253107 GGGGATACTCTAA-CCTCGTTATTTTTAAGGGGATACTCTAATCCCGATTTTATTTCTAAAATAT
1 GGGGATACTCCAACCCT-GTTATTTTTGAGGGGATACTCTAA-CCCGATTTTATTTCTAAAATAT
*
2253171 CGATTTTTCACCATC
64 CGATTTTTCACCATT
* *
2253186 GGGGATACTCCAA-CTTCGTTATTTTTGAGGGGATACTCTAACCCCGATTTTATTTCTAAAGTAT
1 GGGGATACTCCAACCCT-GTTATTTTTGAGGGGATACTCTAA-CCCGATTTTATTTCTAAAATAT
* *
2253250 CAATTTTTCACCATC
64 CGATTTTTCACCATT
* * * * * * *
2253265 GAGAATACTCCAACCCTGTTATTTTTGAGGGAATGCTCTAACCCTGGTTTTATTTCTAAAATTTT
1 GGGGATACTCCAACCCTGTTATTTTTGAGGGGATACTCTAACCC-GATTTTATTTCTAAAATATC
*
2253330 GATCTTTCACCATT
65 GATTTTTCACCATT
* * * * *
2253344 GGGGATACTCCAACCCTGTTATTTTCGAGGGAATACTCTAATCCCAATTTAATTTCTAAAATATT
1 GGGGATACTCCAACCCTGTTATTTTTGAGGGGATACTCTAA-CCCGATTTTATTTCTAAAATATC
* *
2253409 AATTTTTCACCATC
65 GATTTTTCACCATT
* * * * * *
2253423 GGAGATACTCTAACCCTATTATTTTTGAAGGGATACTCCAACCCAATTTTATTT-TCAAAATATC
1 GGGGATACTCCAACCCTGTTATTTTTGAGGGGATACTCTAACCCGATTTTATTTCT-AAAATATC
* *
2253487 GACTTTTCATCATT
65 GATTTTTCACCATT
* * * * * * *
2253501 AGGGATACTCCAACCCCGTTATTTTCGAGGGGATATTCCAACCCCATTTTTATTTCCAAAATATC
1 GGGGATACTCCAACCCTGTTATTTTTGAGGGGATACTCTAACCCGA-TTTTATTTCTAAAATATC
*
2253566 GATTTTTCACTATT
65 GATTTTTCACCATT
* * *
2253580 GGGGATACTCCAACCCTGCTATTTTCGAGGGGATACTCCAACCTCGATTTTATTT-TCAAAATAT
1 GGGGATACTCCAACCCTGTTATTTTTGAGGGGATACTCTAACC-CGATTTTATTTCT-AAAATAT
* *
2253644 GGACTTTTCACCATT
64 CGATTTTTCACCATT
* *
2253659 GGGGATACTCTAACCCATTTTATTT
1 GGGGATACTCCAACCC-TGTTATTT
2253684 CTAAAATATC
Statistics
Matches: 422, Mismatches: 67, Indels: 17
0.83 0.13 0.03
Matches are distributed among these distances:
77 1 0.00
78 69 0.16
79 339 0.80
80 13 0.03
ACGTcount: A:0.27, C:0.22, G:0.14, T:0.38
Consensus pattern (78 bp):
GGGGATACTCCAACCCTGTTATTTTTGAGGGGATACTCTAACCCGATTTTATTTCTAAAATATCG
ATTTTTCACCATT
Found at i:2253210 original size:107 final size:108
Alignment explanation
Indices: 2253001--2253228 Score: 295
Period size: 107 Copynumber: 2.1 Consensus size: 108
2252991 TCCACTATAA
*
2253001 GGGATACTCCAA-CTCTGTTATTTTTGAAGAGATACTCCAACTCCGATTTTATTTCTAAAACATC
1 GGGATACTCTAACCTCTGTTATTTTTGAAGAGATACTCCAACTCCGATTTTATTTCTAAAACATC
*
2253065 GATTTTACACCATTAGGGATACTCCAACCCTGTCATTTTCAAG
66 GATTTTACACCATCAGGGATACTCCAACCCTGTCATTTTCAAG
* * *
2253108 GGGATACTCTAACCTC-GTTATTTTT-AAGGGGATACTCTAA-TCCCGATTTTATTTCTAAAATA
1 GGGATACTCTAACCTCTGTTATTTTTGAA-GAGATACTCCAACT-CCGATTTTATTTCTAAAACA
* * * * **
2253170 TCGATTTTTCACCATCGGGGATACTCCAA-CTTCGTTATTTTTGAG
64 TCGATTTTACACCATCAGGGATACTCCAACCCT-GTCATTTTCAAG
2253215 GGGATACTCTAACC
1 GGGATACTCTAACC
2253229 CCGATTTTAT
Statistics
Matches: 106, Mismatches: 11, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
106 5 0.05
107 98 0.92
108 3 0.03
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.36
Consensus pattern (108 bp):
GGGATACTCTAACCTCTGTTATTTTTGAAGAGATACTCCAACTCCGATTTTATTTCTAAAACATC
GATTTTACACCATCAGGGATACTCCAACCCTGTCATTTTCAAG
Found at i:2253235 original size:186 final size:186
Alignment explanation
Indices: 2252921--2253308 Score: 510
Period size: 186 Copynumber: 2.1 Consensus size: 186
2252911 TTTCATCATC
* * *
2252921 GGGGATACTCCAACCCCGTTATTTTTGAGGGGATACTCCAACCCCAATTTTATTTCTAAAATATT
1 GGGGATACTCTAACCCCGTTATTTTTAAGGGGATACTCCAACCCCAATTTTATTTCTAAAATATC
* *
2252986 GATTTTCCACTATAAGGGATACTCCAACTCTGTTATTTTTGAAGAGATACTCCAACTCCGATTTT
66 GATTTTCCACCATAAGGGATACTCCAACTCTGTTATTTTTGAAGAGATACTCCAACCCCGATTTT
* *
2253051 ATTTCTAAAACATCGATTTTACACCATTAG-GGATACTCCAACCCTGTCATTTTCAA
131 ATTTCTAAAACATCAATTTTACACCA-TAGAGAATACTCCAACCCTGTCATTTTCAA
* * * *
2253107 GGGGATACTCTAACCTCGTTATTTTTAAGGGGATACTCTAATCCCGATTTTATTTCTAAAATATC
1 GGGGATACTCTAACCCCGTTATTTTTAAGGGGATACTCCAACCCCAATTTTATTTCTAAAATATC
* ** * * *
2253172 GATTTTTCACCATCGGGGATACTCCAACT-TCGTTATTTTTGAGGGGATACTCTAACCCCGATTT
66 GATTTTCCACCATAAGGGATACTCCAACTCT-GTTATTTTTGAAGAGATACTCCAACCCCGATTT
** * * * **
2253236 TATTTCTAAAGTATCAATTTTTCACCATCGAGAATACTCCAACCCTGTTATTTTTGA
130 TATTTCTAAAACATCAATTTTACACCATAGAGAATACTCCAACCCTGTCATTTTCAA
* *
2253293 GGGAATGCTCTAACCC
1 GGGGATACTCTAACCC
2253309 TGGTTTTATT
Statistics
Matches: 173, Mismatches: 27, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
185 3 0.02
186 170 0.98
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.36
Consensus pattern (186 bp):
GGGGATACTCTAACCCCGTTATTTTTAAGGGGATACTCCAACCCCAATTTTATTTCTAAAATATC
GATTTTCCACCATAAGGGATACTCCAACTCTGTTATTTTTGAAGAGATACTCCAACCCCGATTTT
ATTTCTAAAACATCAATTTTACACCATAGAGAATACTCCAACCCTGTCATTTTCAA
Found at i:2253401 original size:344 final size:344
Alignment explanation
Indices: 2252763--2253466 Score: 848
Period size: 344 Copynumber: 2.0 Consensus size: 344
2252753 TTTCACTATC
*
2252763 AGGGATACTCCAACCCCGTTATTTTTGAGGGAATACTCCAACTCCGATTTTATTTCTAAAATATC
1 AGGGATACTCCAACCCCGTTATTTTTAAGGGAATACTCCAACTCCGATTTTATTTCTAAAATATC
*
2252828 GATTTTTCACCATCGAGGATATTCCAAACCTGTTATTTTCGAAAAGATACTCCAACCACAGTTTT
66 GATTTTTCACCATCGAGGATACTCCAAACCTGTTATTTTCGAAAAGATACTCCAACCACAGTTTT
* ** * * * *
2252893 TTTTCTAAAACATTGATTTTTCATCATCGGGGATACTCCAACCCCGTTATTTTTGAGGGGATACT
131 ATTTCTAAAACATCAATTTTTCACCATCGAGAATACTCCAACCCCGTTATTTTTGAGGGAATACT
* *
2252958 CCAACCCCAATTTTATTTCTAAAATATTGATTTTCCACTATAAGGGATACTCCAACTCTGTTATT
196 CCAACCCCAATTTTATTTCTAAAATATTGATTTTCCACCATAAGGGATACTCCAACCCTGTTATT
* * * *
2253023 TTTGAAGAGATACTCCAACTCCGATTTTATTTCTAAAACATCGATTTTACACCATTAGG-GATAC
261 TTCGAAGAGATACTCCAACTCCAATTTAATTTCTAAAACATCAATTTTACACCA-TAGGAGATAC
*
2253087 TCCAACCCTGTCA-TTTTCA
325 TCCAACCCTATCATTTTTCA
* * * *
2253106 AGGGGATACTCTAACCTCGTTATTTTTAAGGGGATACTCTAA-TCCCGATTTTATTTCTAAAATA
1 A-GGGATACTCCAACCCCGTTATTTTTAAGGGAATACTCCAACT-CCGATTTTATTTCTAAAATA
* * * *** * *
2253170 TCGATTTTTCACCATCGGGGATACTCC-AACTTCGTTATTTTTGAGGGGATACTCTAACC-CCGA
64 TCGATTTTTCACCATCGAGGATACTCCAAACCT-GTTATTTTCGAAAAGATACTCCAACCACAG-
** *
2253233 TTTTATTTCTAAAGTATCAATTTTTCACCATCGAGAATACTCCAACCCTGTTATTTTTGAGGGAA
127 TTTTATTTCTAAAACATCAATTTTTCACCATCGAGAATACTCCAACCCCGTTATTTTTGAGGGAA
* * *** * **
2253298 TGCTCTAACCCTGGTTTTATTTCTAAAATTTTGATCTTT-CACCATTGGGGATACTCCAACCCTG
192 TACTCCAACCCCAATTTTATTTCTAAAATATTGAT-TTTCCACCATAAGGGATACTCCAACCCTG
* * * * * *
2253362 TTATTTTCG-AGGGAATACTCTAA-TCCCAATTTAATTTCTAAAATATTAATTTTTCACCATCGG
256 TTATTTTCGAAGAG-ATACTCCAACT-CCAATTTAATTTCTAAAACATCAATTTTACACCATAGG
* * *
2253425 AGATACTCTAACCCTATTATTTTTGA
319 AGATACTCCAACCCTATCATTTTTCA
2253451 AGGGATACTCCAACCC
1 AGGGATACTCCAACCC
2253467 AATTTTATTT
Statistics
Matches: 302, Mismatches: 50, Indels: 17
0.82 0.14 0.05
Matches are distributed among these distances:
343 15 0.05
344 278 0.92
345 9 0.03
ACGTcount: A:0.28, C:0.22, G:0.13, T:0.37
Consensus pattern (344 bp):
AGGGATACTCCAACCCCGTTATTTTTAAGGGAATACTCCAACTCCGATTTTATTTCTAAAATATC
GATTTTTCACCATCGAGGATACTCCAAACCTGTTATTTTCGAAAAGATACTCCAACCACAGTTTT
ATTTCTAAAACATCAATTTTTCACCATCGAGAATACTCCAACCCCGTTATTTTTGAGGGAATACT
CCAACCCCAATTTTATTTCTAAAATATTGATTTTCCACCATAAGGGATACTCCAACCCTGTTATT
TTCGAAGAGATACTCCAACTCCAATTTAATTTCTAAAACATCAATTTTACACCATAGGAGATACT
CCAACCCTATCATTTTTCA
Found at i:2253606 original size:236 final size:237
Alignment explanation
Indices: 2253107--2253683 Score: 673
Period size: 236 Copynumber: 2.4 Consensus size: 237
2253097 TCATTTTCAA
* **
2253107 GGGGATACTCTAA-CCTCGTTATTTTTAAGGGGATACTCTAATCCCGATTTTATTTCTAAAATAT
1 GGGGATACTCCAACCCT-GTTATTTTCGAGGGGATACTCTAATCCCGATTTTATTTCTAAAATAT
* * * * * *
2253171 CGATTTTTCACCATCGGGGATACTCCAA-CTTCGTTATTTTTGAGGGGATACTCTAACCCCGATT
65 CGATTTTTCACCATCGGGGATACTCTAACCCT-ATTATTTTTGAAGGGATACTCCAACCCCAATT
* * * * * *
2253235 TTATTTCTAAAGTATCAATTTTTCACCATCGAGAATACTCCAACCCTGTTATTTTTGAGGGAATG
129 TTATTTCTAAAATATCAACTTTTCACCATAGAGAATACTCCAACCCCGTTATTTTCGAGGGAATA
* ** * * *
2253300 CTCTAACCCTGGTTTTATTTCTAAAATTTTGATCTTTCACCATT
194 CTCCAACCCCAGTTTTATTTCCAAAATATCGATCTTTCACCATT
* * * *
2253344 GGGGATACTCCAACCCTGTTATTTTCGAGGGAATACTCTAATCCCAATTTAATTTCTAAAATATT
1 GGGGATACTCCAACCCTGTTATTTTCGAGGGGATACTCTAATCCCGATTTTATTTCTAAAATATC
* *
2253409 AATTTTTCACCATCGGAGATACTCTAACCCTATTATTTTTGAAGGGATACTCCAA-CCCAATTTT
66 GATTTTTCACCATCGGGGATACTCTAACCCTATTATTTTTGAAGGGATACTCCAACCCCAATTTT
* * * *
2253473 ATTT-TCAAAATATCGACTTTTCATCATTAG-GGATACTCCAACCCCGTTATTTTCGAGGGGATA
131 ATTTCT-AAAATATCAACTTTTCACCA-TAGAGAATACTCCAACCCCGTTATTTTCGAGGGAATA
* * * *
2253536 TTCCAACCCCATTTTTATTTCCAAAATATCGATTTTTCACTATT
194 CTCCAACCCCAGTTTTATTTCCAAAATATCGATCTTTCACCATT
* *
2253580 GGGGATACTCCAACCCTGCTATTTTCGAGGGGATACTCCAA-CCTCGATTTTATTT-TCAAAATA
1 GGGGATACTCCAACCCTGTTATTTTCGAGGGGATACTCTAATCC-CGATTTTATTTCT-AAAATA
* * * *
2253643 TGGACTTTTCACCATTGGGGATACTCTAACCCATTTTATTT
64 TCGATTTTTCACCATCGGGGATACTCTAACCC-TATTATTT
2253684 CTAAAATATC
Statistics
Matches: 287, Mismatches: 46, Indels: 14
0.83 0.13 0.04
Matches are distributed among these distances:
235 4 0.01
236 170 0.59
237 108 0.38
238 5 0.02
ACGTcount: A:0.27, C:0.22, G:0.14, T:0.38
Consensus pattern (237 bp):
GGGGATACTCCAACCCTGTTATTTTCGAGGGGATACTCTAATCCCGATTTTATTTCTAAAATATC
GATTTTTCACCATCGGGGATACTCTAACCCTATTATTTTTGAAGGGATACTCCAACCCCAATTTT
ATTTCTAAAATATCAACTTTTCACCATAGAGAATACTCCAACCCCGTTATTTTCGAGGGAATACT
CCAACCCCAGTTTTATTTCCAAAATATCGATCTTTCACCATT
Found at i:2253690 original size:49 final size:51
Alignment explanation
Indices: 2253608--2253718 Score: 147
Period size: 49 Copynumber: 2.2 Consensus size: 51
2253598 CTATTTTCGA
** * *
2253608 GGGGATACTCCAACCTCGATTTTATTTTCAAAATATGGACTTTTCACCATT
1 GGGGATACTCCAACCTCGATTTTATTTTCAAAATATCAAATTTTCACCATC
*
2253659 GGGGATACTCTAACC-C-ATTTTA-TTTCTAAAATATCAAATTTTCACCATC
1 GGGGATACTCCAACCTCGATTTTATTTTC-AAAATATCAAATTTTCACCATC
2253708 GGGGATACTCC
1 GGGGATACTCC
2253719 GACCCTGTTG
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
48 4 0.08
49 34 0.64
50 1 0.02
51 14 0.26
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.35
Consensus pattern (51 bp):
GGGGATACTCCAACCTCGATTTTATTTTCAAAATATCAAATTTTCACCATC
Found at i:2253712 original size:128 final size:129
Alignment explanation
Indices: 2253529--2253767 Score: 313
Period size: 128 Copynumber: 1.9 Consensus size: 129
2253519 TTATTTTCGA
* * * * *
2253529 GGGGATATTCCAACCCCATTTTTATTTCCAAAATATCGATTTTTCACTATTGGGGATACTCCAAC
1 GGGGATACTCCAACCCCATTTTTATTTCCAAAATATCAAATTTTCACCATCGGGGATACTCCAAC
**
2253594 CCTGCTATTTTCGAGGGGATACTCCAACCTCGA-TTTTATTTTCAAAATATGGACTTTTCACCAT
66 CCTGCTATTTTCGAGAAGATACTCCAACC-CGATTTTTA-TTTCAAAATATGGACTTTTCACCAT
2253658 T
129 T
* * *
2253659 GGGGATACTCTAA-CCCA-TTTTATTTCTAAAATATCAAATTTTCACCATCGGGGATACTCCGAC
1 GGGGATACTCCAACCCCATTTTTATTTCCAAAATATCAAATTTTCACCATCGGGGATACTCCAAC
* * * *
2253722 CCTGTTGTTTTCGAGAAGATGCTCCAACCCTATTTTTATTTCAAAA
66 CCTGCTATTTTCGAGAAGATACTCCAACCCGATTTTTATTTCAAAA
2253768 ATATTAATTT
Statistics
Matches: 94, Mismatches: 14, Indels: 5
0.83 0.12 0.04
Matches are distributed among these distances:
127 10 0.11
128 69 0.73
129 4 0.04
130 11 0.12
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.36
Consensus pattern (129 bp):
GGGGATACTCCAACCCCATTTTTATTTCCAAAATATCAAATTTTCACCATCGGGGATACTCCAAC
CCTGCTATTTTCGAGAAGATACTCCAACCCGATTTTTATTTCAAAATATGGACTTTTCACCATT
Found at i:2262239 original size:2 final size:2
Alignment explanation
Indices: 2262232--2262256 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2262222 ATAAATCAAC
2262232 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
2262257 GAGAGAGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2262261 original size:2 final size:2
Alignment explanation
Indices: 2262256--2262282 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2262246 ATATATATAT
2262256 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
2262283 ATGAAGAAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2266165 original size:20 final size:20
Alignment explanation
Indices: 2266135--2266189 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
2266125 AAAAAGACAG
* *
2266135 AATGGATCGATACATTCATA
1 AATGTATCGATACATTCAAA
* *
2266155 CATGTATCGATACATTGAAA
1 AATGTATCGATACATTCAAA
2266175 AATGTATCGATACAT
1 AATGTATCGATACAT
2266190 CTGGGTAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.31
Consensus pattern (20 bp):
AATGTATCGATACATTCAAA
Found at i:2266165 original size:71 final size:71
Alignment explanation
Indices: 2266085--2266221 Score: 247
Period size: 71 Copynumber: 1.9 Consensus size: 71
2266075 TTTTAACTAG
*
2266085 ATGTATCGATACATTGAACAATGTATCGATACATCCGGGTAAAAAGACAGAATGGATCGATACAT
1 ATGTATCGATACATTGAAAAATGTATCGATACATCCGGGTAAAAAGACAGAATGGATCGATACAT
2266150 TCATAC
66 TCATAC
* *
2266156 ATGTATCGATACATTGAAAAATGTATCGATACATCTGGGTAAAAAGACAGAATGTATCGATACAT
1 ATGTATCGATACATTGAAAAATGTATCGATACATCCGGGTAAAAAGACAGAATGGATCGATACAT
2266221 T
66 T
2266222 AAAGAATGTA
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
71 63 1.00
ACGTcount: A:0.40, C:0.15, G:0.18, T:0.27
Consensus pattern (71 bp):
ATGTATCGATACATTGAAAAATGTATCGATACATCCGGGTAAAAAGACAGAATGGATCGATACAT
TCATAC
Found at i:2267346 original size:28 final size:28
Alignment explanation
Indices: 2267129--2267340 Score: 280
Period size: 28 Copynumber: 7.4 Consensus size: 28
2267119 ACTAACTTGT
* * *
2267129 GTGGGCTTTGATAAGAGTTGCCACCGACTTGT
1 GTGGGCTTTGA-AAG-GGTGCCACTGAC-T-C
*
2267161 GTGGGCTTTGAAAGGGTGCCACTGACTT
1 GTGGGCTTTGAAAGGGTGCCACTGACTC
** *
2267189 GTGGGCTTTGAAAGAATGCCATTGACTC
1 GTGGGCTTTGAAAGGGTGCCACTGACTC
2267217 GTGGGCTTTGAAAGGGTGCCACTGACTC
1 GTGGGCTTTGAAAGGGTGCCACTGACTC
*
2267245 ATGGGCTTTGAAAGGGTGCCACTGACTC
1 GTGGGCTTTGAAAGGGTGCCACTGACTC
*
2267273 ATGGGCTTTGAAAGGGTGCCACTGACTC
1 GTGGGCTTTGAAAGGGTGCCACTGACTC
* *
2267301 GTGGGCTTTGAAAGGATGCCACTGACTT
1 GTGGGCTTTGAAAGGGTGCCACTGACTC
*
2267329 GTGAGCTTTGAA
1 GTGGGCTTTGAA
2267341 GAGATGAACG
Statistics
Matches: 166, Mismatches: 14, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
28 141 0.85
29 1 0.01
30 10 0.06
31 3 0.02
32 11 0.07
ACGTcount: A:0.21, C:0.19, G:0.33, T:0.28
Consensus pattern (28 bp):
GTGGGCTTTGAAAGGGTGCCACTGACTC
Found at i:2268591 original size:10 final size:9
Alignment explanation
Indices: 2268578--2268628 Score: 52
Period size: 9 Copynumber: 5.8 Consensus size: 9
2268568 TTTTGCTATT
2268578 TTTTTCTTGG
1 TTTTT-TTGG
*
2268588 TTTTTTTTG
1 TTTTTTTGG
*
2268597 -TTTTTT-A
1 TTTTTTTGG
*
2268604 TTTTTTTGT
1 TTTTTTTGG
2268613 TTTTTTTGG
1 TTTTTTTGG
2268622 TTTTTTT
1 TTTTTTT
2268629 TTTGTGCAAC
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
8 12 0.34
9 18 0.51
10 5 0.14
ACGTcount: A:0.02, C:0.02, G:0.12, T:0.84
Consensus pattern (9 bp):
TTTTTTTGG
Found at i:2268607 original size:15 final size:15
Alignment explanation
Indices: 2268589--2268617 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2268579 TTTTCTTGGT
2268589 TTTTTTTGTTTTTTA
1 TTTTTTTGTTTTTTA
2268604 TTTTTTTGTTTTTT
1 TTTTTTTGTTTTTT
2268618 TTGGTTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.03, C:0.00, G:0.07, T:0.90
Consensus pattern (15 bp):
TTTTTTTGTTTTTTA
Found at i:2268631 original size:24 final size:24
Alignment explanation
Indices: 2268564--2268631 Score: 84
Period size: 24 Copynumber: 2.8 Consensus size: 24
2268554 CCTTTTCTAT
* * *
2268564 TTTTTTTTGCTATTTTTTTCTTGG
1 TTTTTTTTGGTTTTTTTTTTTTGG
*
2268588 TTTTTTTT-GTTTTTTATTTTTTTG
1 TTTTTTTTGGTTTTTT-TTTTTTGG
2268612 TTTTTTTTGGTTTTTTTTTT
1 TTTTTTTTGGTTTTTTTTTT
2268632 GTGCAACGGA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
23 5 0.13
24 26 0.68
25 7 0.18
ACGTcount: A:0.03, C:0.03, G:0.10, T:0.84
Consensus pattern (24 bp):
TTTTTTTTGGTTTTTTTTTTTTGG
Found at i:2277902 original size:20 final size:20
Alignment explanation
Indices: 2277877--2277943 Score: 67
Period size: 20 Copynumber: 3.7 Consensus size: 20
2277867 TTTCAACGAT
2277877 TTGTATCGATACATAAAGTG
1 TTGTATCGATACATAAAGTG
*
2277897 TTGTATTGATAC----A---
1 TTGTATCGATACATAAAGTG
*
2277910 TTGTATTGATACATAAAGTG
1 TTGTATCGATACATAAAGTG
2277930 TTGTATCGATACAT
1 TTGTATCGATACAT
2277944 TGTATCGATA
Statistics
Matches: 38, Mismatches: 2, Indels: 14
0.70 0.04 0.26
Matches are distributed among these distances:
13 12 0.32
16 1 0.03
17 1 0.03
20 24 0.63
ACGTcount: A:0.33, C:0.09, G:0.18, T:0.40
Consensus pattern (20 bp):
TTGTATCGATACATAAAGTG
Found at i:2277915 original size:13 final size:13
Alignment explanation
Indices: 2277897--2277923 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2277887 ACATAAAGTG
2277897 TTGTATTGATACA
1 TTGTATTGATACA
2277910 TTGTATTGATACA
1 TTGTATTGATACA
2277923 T
1 T
2277924 AAAGTGTTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.07, G:0.15, T:0.48
Consensus pattern (13 bp):
TTGTATTGATACA
Found at i:2277921 original size:33 final size:33
Alignment explanation
Indices: 2277877--2277974 Score: 162
Period size: 33 Copynumber: 3.0 Consensus size: 33
2277867 TTTCAACGAT
*
2277877 TTGTATCGATACATAAAGTGTTGTATTGATACA
1 TTGTATCGATACATAAAGTGTTGTATCGATACA
*
2277910 TTGTATTGATACATAAAGTGTTGTATCGATACA
1 TTGTATCGATACATAAAGTGTTGTATCGATACA
*
2277943 TTGTATCGATACAT-AAGTTTTGTATCGATACA
1 TTGTATCGATACATAAAGTGTTGTATCGATACA
2277975 ATTTAAGCTA
Statistics
Matches: 61, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
32 17 0.28
33 44 0.72
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40
Consensus pattern (33 bp):
TTGTATCGATACATAAAGTGTTGTATCGATACA
Found at i:2277948 original size:13 final size:13
Alignment explanation
Indices: 2277930--2277956 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2277920 ACATAAAGTG
2277930 TTGTATCGATACA
1 TTGTATCGATACA
2277943 TTGTATCGATACA
1 TTGTATCGATACA
2277956 T
1 T
2277957 AAGTTTTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:2278051 original size:52 final size:52
Alignment explanation
Indices: 2278016--2278146 Score: 244
Period size: 52 Copynumber: 2.5 Consensus size: 52
2278006 CACTGATCTT
*
2278016 TGTATCGATACATGCAGGCAAATTTTCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTTCCCAGATGTATCGATACACTATAAAA
*
2278068 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTTCCCAGATGTATCGATACACTATAAAA
2278120 TGTATCGATACATGCAGGCAAATTTTC
1 TGTATCGATACATGCAGGCAAATTTTC
2278147 ATATTTCGGG
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 76 1.00
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTTCCCAGATGTATCGATACACTATAAAA
Found at i:2291931 original size:15 final size:15
Alignment explanation
Indices: 2291911--2291947 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
2291901 GTCCTCCACA
2291911 AAAAAAAAACAGAAG
1 AAAAAAAAACAGAAG
2291926 AAAAAAAAACAGAAG
1 AAAAAAAAACAGAAG
2291941 AAAAAAA
1 AAAAAAA
2291948 GAAAAAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.84, C:0.05, G:0.11, T:0.00
Consensus pattern (15 bp):
AAAAAAAAACAGAAG
Found at i:2291944 original size:11 final size:10
Alignment explanation
Indices: 2291927--2291967 Score: 55
Period size: 10 Copynumber: 3.9 Consensus size: 10
2291917 AAACAGAAGA
2291927 AAAAAAAACAG
1 AAAAAAAA-AG
2291938 AAGAAAAAAAG
1 AA-AAAAAAAG
*
2291949 AAAAAAAATG
1 AAAAAAAAAG
2291959 AAAAAAAAA
1 AAAAAAAAA
2291968 AACAACAACA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
10 15 0.56
11 6 0.22
12 6 0.22
ACGTcount: A:0.85, C:0.02, G:0.10, T:0.02
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:2293461 original size:29 final size:30
Alignment explanation
Indices: 2293422--2293541 Score: 95
Period size: 34 Copynumber: 4.0 Consensus size: 30
2293412 TCACCCTTCA
*
2293422 AAAGCCCACAAGTCAGTGGCA-TCTTTTTC
1 AAAGCCCACAACTCAGTGGCACTCTTTTTC
*
2293451 AAAGCCCACAACTCCGTGGCACTCTTTTTCCTTC
1 AAAGCCCACAACTCAGTGGCACTC--TTT--TTC
* * * **
2293485 TAAGTCCACAACTCTGTGGCAC-CCGTTT-
1 AAAGCCCACAACTCAGTGGCACTCTTTTTC
* *
2293513 -AAGCCCACGACTCCGTGGCACTCTTTTTC
1 AAAGCCCACAACTCAGTGGCACTCTTTTTC
2293542 CTTCTAAGTC
Statistics
Matches: 72, Mismatches: 12, Indels: 14
0.73 0.12 0.14
Matches are distributed among these distances:
27 18 0.25
28 4 0.06
29 21 0.29
30 2 0.03
31 1 0.01
32 3 0.04
33 1 0.01
34 22 0.31
ACGTcount: A:0.22, C:0.34, G:0.16, T:0.28
Consensus pattern (30 bp):
AAAGCCCACAACTCAGTGGCACTCTTTTTC
Found at i:2293497 original size:34 final size:34
Alignment explanation
Indices: 2293456--2293640 Score: 206
Period size: 34 Copynumber: 5.7 Consensus size: 34
2293446 TTTTCAAAGC
2293456 CCACAACTCCGTGGCACTCTTTTTCCTTCTAAGT
1 CCACAACTCCGTGGCACTCTTTTTCCTTCTAAGT
* * *
2293490 CCACAACTCTGTGGCAC-C-----CGTT-TAAGC
1 CCACAACTCCGTGGCACTCTTTTTCCTTCTAAGT
*
2293517 CCACGACTCCGTGGCACTCTTTTTCCTTCTAAGT
1 CCACAACTCCGTGGCACTCTTTTTCCTTCTAAGT
* * * *
2293551 CCACAACTTCGTGGCAC-CTTTTTCTTTTTAAGC
1 CCACAACTCCGTGGCACTCTTTTTCCTTCTAAGT
* *
2293584 CCACAACTTCGTGGCACTCTTTCTCCTTCTAAGT
1 CCACAACTCCGTGGCACTCTTTTTCCTTCTAAGT
* *
2293618 CCACAACTCTGTGGCACCCTTTT
1 CCACAACTCCGTGGCACTCTTTT
2293641 ACGTCCACAG
Statistics
Matches: 123, Mismatches: 20, Indels: 16
0.77 0.13 0.10
Matches are distributed among these distances:
27 19 0.15
28 4 0.03
33 34 0.28
34 66 0.54
ACGTcount: A:0.18, C:0.35, G:0.14, T:0.34
Consensus pattern (34 bp):
CCACAACTCCGTGGCACTCTTTTTCCTTCTAAGT
Found at i:2293526 original size:61 final size:61
Alignment explanation
Indices: 2293452--2293671 Score: 282
Period size: 61 Copynumber: 3.5 Consensus size: 61
2293442 ATCTTTTTCA
* *
2293452 AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCTGTGGCACCCGTTT
1 AAGCCCACAACTCCGTGGCACTCTTTCTCCTTCTAAGTCCACAACTCTGTGGCACCCTTTT
* *
2293513 AAGCCCACGACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACT-TCGTGGCACCTTTTTCTT
1 AAGCCCACAACTCCGTGGCACTCTTTCTCCTTCTAAGTCCACAACTCT-GTGGCACC-----C-T
2293577 TTT
59 TTT
*
2293580 AAGCCCACAACTTCGTGGCACTCTTTCTCCTTCTAAGTCCACAACTCTGTGGCACCCTTTT
1 AAGCCCACAACTCCGTGGCACTCTTTCTCCTTCTAAGTCCACAACTCTGTGGCACCCTTTT
* * * *
2293641 ACGTCCACAGCTTCGTGGCA-TCTTTCTCCTT
1 AAGCCCACAACTCCGTGGCACTCTTTCTCCTT
2293672 TTCAAAAGCC
Statistics
Matches: 143, Mismatches: 8, Indels: 17
0.85 0.05 0.10
Matches are distributed among these distances:
60 12 0.08
61 74 0.52
62 1 0.01
66 1 0.01
67 54 0.38
68 1 0.01
ACGTcount: A:0.18, C:0.35, G:0.14, T:0.33
Consensus pattern (61 bp):
AAGCCCACAACTCCGTGGCACTCTTTCTCCTTCTAAGTCCACAACTCTGTGGCACCCTTTT
Found at i:2293695 original size:63 final size:61
Alignment explanation
Indices: 2293456--2293703 Score: 185
Period size: 61 Copynumber: 3.9 Consensus size: 61
2293446 TTTTCAAAGC
* * * * * * * * *
2293456 CCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCTGTGGCACCCGTTTAAGC
1 CCACAACTTCGTGGCACTCTTTCTCCTTCAAAGCCCACAACTCGGTGGCAACCTTTTACGT
* * * * * *
2293517 CCACGACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTTC-GTGGCACCTTTTTCTTTTTA
1 CCACAACTTCGTGGCACTCTTTCTCCTTCAAAGCCCACAAC-TCGGTGGCAAC-----C-TTTTA
* *
2293581 AGC
59 CGT
* * * *
2293584 CCACAACTTCGTGGCACTCTTTCTCCTTCTAAGTCCACAACTCTGTGGCACCCTTTTACGT
1 CCACAACTTCGTGGCACTCTTTCTCCTTCAAAGCCCACAACTCGGTGGCAACCTTTTACGT
* *
2293645 CCACAGCTTCGTGGCA-TCTTTCTCCTTTTCAAAAGCCCACAAGTCGGTGGCAACCTTTT
1 CCACAACTTCGTGGCACTCTTTCTCC--TTC-AAAGCCCACAACTCGGTGGCAACCTTTT
2293704 TCTCAAAGCT
Statistics
Matches: 163, Mismatches: 13, Indels: 20
0.83 0.07 0.10
Matches are distributed among these distances:
60 9 0.06
61 69 0.42
62 6 0.04
63 23 0.14
66 3 0.02
67 53 0.33
ACGTcount: A:0.19, C:0.34, G:0.15, T:0.33
Consensus pattern (61 bp):
CCACAACTTCGTGGCACTCTTTCTCCTTCAAAGCCCACAACTCGGTGGCAACCTTTTACGT
Found at i:2293739 original size:32 final size:32
Alignment explanation
Indices: 2293682--2293970 Score: 440
Period size: 32 Copynumber: 9.0 Consensus size: 32
2293672 TTCAAAAGCC
* *
2293682 CACAAGTCGGTGGCAACCTTTTTCTCAAAGCTCA
1 CACAAGTCGGTGGCAACC--CTTCTCAAAGCCCA
*
2293716 CACAAGTCGGTGGCAACCCTTCTCAAAGCCTA
1 CACAAGTCGGTGGCAACCCTTCTCAAAGCCCA
*
2293748 CACAAGTCGGTGGCAACCCTTCTTAAAGCCCA
1 CACAAGTCGGTGGCAACCCTTCTCAAAGCCCA
2293780 CACAAGTCGGTGGCAACCCTTCTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCTTCTCAAAGCCCA
2293812 CACAAGTCGGTGGCAACCCTTCTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCTTCTCAAAGCCCA
*
2293844 CACAAGTCGGTGGCAACCCTTCTCAAAGTCCA
1 CACAAGTCGGTGGCAACCCTTCTCAAAGCCCA
2293876 CACAAGTCGGTGGCAACCC-TCTCTAAAGCCCA
1 CACAAGTCGGTGGCAACCCTTCTC-AAAGCCCA
* * * *
2293908 CACAAGTTGATGGCAACCATTTTCTAAAGCCCA
1 CACAAGTCGGTGGCAACCCTTCTC-AAAGCCCA
2293941 CACAAGTCGGTGGCAACCCTTCT--AAGCCCA
1 CACAAGTCGGTGGCAACCCTTCTCAAAGCCCA
2293971 ATATTGCTGG
Statistics
Matches: 237, Mismatches: 16, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
30 7 0.03
31 4 0.02
32 177 0.75
33 31 0.13
34 18 0.08
ACGTcount: A:0.28, C:0.34, G:0.18, T:0.19
Consensus pattern (32 bp):
CACAAGTCGGTGGCAACCCTTCTCAAAGCCCA
Found at i:2294072 original size:43 final size:43
Alignment explanation
Indices: 2294009--2294379 Score: 355
Period size: 43 Copynumber: 8.0 Consensus size: 43
2293999 GCATCTTCTT
* * *
2294009 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCAC
*
2294052 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCGTATTGGCATC
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA-C
* * *
2294096 TTCTTTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
1 --C--TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCAC
* *
2294143 CTTTATGTCCAATATCGCTGGCCTTGAATCAGCGTATTGGCACCTTC
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA----C
* * *
2294190 ATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
1 --CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCAC
*
2294235 CTTTAAGTCCAATATCGCTGGCCTTGAATTAGCATATTGGCGCCTTTGTCAC
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATT---G-----G-CAC
*
2294287 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATT---G-----G-CAC
2294339 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGC
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGC
2294380 GTCTTTGTCA
Statistics
Matches: 284, Mismatches: 24, Indels: 40
0.82 0.07 0.11
Matches are distributed among these distances:
43 109 0.38
44 2 0.01
45 2 0.01
46 2 0.01
47 2 0.01
48 37 0.13
49 38 0.13
51 1 0.00
52 91 0.32
ACGTcount: A:0.23, C:0.25, G:0.20, T:0.32
Consensus pattern (43 bp):
CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCAC
Found at i:2294310 original size:52 final size:52
Alignment explanation
Indices: 2294232--2294436 Score: 338
Period size: 52 Copynumber: 3.9 Consensus size: 52
2294222 AGCACATTGG
*
2294232 CACCTTTAAGTCCAATATCGCTGGCCTTGAATTAGCATATTGGCGCCTTTGT
1 CACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGT
2294284 CACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGT
1 CACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGT
* *
2294336 CATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGTCTTTGT
1 CACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGT
* * * * *
2294388 CATCTTTAAGTTCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTT
1 CACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTT
2294437 CATCTTTAAC
Statistics
Matches: 145, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 145 1.00
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.34
Consensus pattern (52 bp):
CACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGT
Found at i:2295291 original size:13 final size:13
Alignment explanation
Indices: 2295273--2295299 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2295263 ACATAAAGTG
2295273 TTGTATCGATACA
1 TTGTATCGATACA
2295286 TTGTATCGATACA
1 TTGTATCGATACA
2295299 T
1 T
2295300 AAGTTTTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:2295314 original size:32 final size:33
Alignment explanation
Indices: 2295253--2295317 Score: 114
Period size: 32 Copynumber: 2.0 Consensus size: 33
2295243 TTTCAATGAT
2295253 TTGTATCGATACATAAAGTGTTGTATCGATACA
1 TTGTATCGATACATAAAGTGTTGTATCGATACA
*
2295286 TTGTATCGATACAT-AAGTTTTGTATCGATACA
1 TTGTATCGATACATAAAGTGTTGTATCGATACA
2295318 ATTTAAGCTA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 17 0.55
33 14 0.45
ACGTcount: A:0.32, C:0.12, G:0.17, T:0.38
Consensus pattern (33 bp):
TTGTATCGATACATAAAGTGTTGTATCGATACA
Found at i:2295397 original size:52 final size:52
Alignment explanation
Indices: 2295359--2295487 Score: 249
Period size: 52 Copynumber: 2.5 Consensus size: 52
2295349 CACTGATCTT
*
2295359 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
2295411 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
2295463 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
2295488 TCATATTTCG
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
52 76 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:2303478 original size:51 final size:51
Alignment explanation
Indices: 2303420--2303598 Score: 191
Period size: 51 Copynumber: 3.7 Consensus size: 51
2303410 TAACTAGATA
* *
2303420 TATCGATACATTGAAAAATGTATCGATACATCCGGGTAAAAAGATAGAATG
1 TATCGATACATTGAAGAATGTATCGATACATCTGGGTAAAAAGATAGAATG
* * * *
2303471 GATCGATACATTGAAGGATGTATCGATACA--T---T-----CATA-CATG
1 TATCGATACATTGAAGAATGTATCGATACATCTGGGTAAAAAGATAGAATG
* * *
2303511 TATCGATACATTGAAGAATGTATTGATACATCTGGGTAAAAAGACAGAACG
1 TATCGATACATTGAAGAATGTATCGATACATCTGGGTAAAAAGATAGAATG
*
2303562 TATCGATACATTGAAGAATGTATCGATATATCTGGGT
1 TATCGATACATTGAAGAATGTATCGATACATCTGGGT
2303599 TCTTTTCCAT
Statistics
Matches: 102, Mismatches: 15, Indels: 22
0.73 0.11 0.16
Matches are distributed among these distances:
40 30 0.29
41 3 0.03
42 1 0.01
45 1 0.01
46 1 0.01
50 2 0.02
51 64 0.63
ACGTcount: A:0.39, C:0.12, G:0.21, T:0.28
Consensus pattern (51 bp):
TATCGATACATTGAAGAATGTATCGATACATCTGGGTAAAAAGATAGAATG
Found at i:2303497 original size:20 final size:20
Alignment explanation
Indices: 2303465--2303541 Score: 93
Period size: 20 Copynumber: 3.9 Consensus size: 20
2303455 GTAAAAAGAT
*
2303465 AGAATGGATCGATACATTGA
1 AGAATGTATCGATACATTGA
* *
2303485 AGGATGTATCGATACATTCA
1 AGAATGTATCGATACATTGA
*
2303505 TA-CATGTATCGATACATTGA
1 -AGAATGTATCGATACATTGA
*
2303525 AGAATGTATTGATACAT
1 AGAATGTATCGATACAT
2303542 CTGGGTAAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
19 1 0.02
20 46 0.96
21 1 0.02
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (20 bp):
AGAATGTATCGATACATTGA
Found at i:2303575 original size:91 final size:91
Alignment explanation
Indices: 2303420--2303589 Score: 277
Period size: 91 Copynumber: 1.9 Consensus size: 91
2303410 TAACTAGATA
* *
2303420 TATCGATACATTGAAAAATGTATCGATACATCCGGGTAAAAAGATAGAATGGATCGATACATTGA
1 TATCGATACATTGAAAAATGTATCGATACATCCGGGTAAAAAGACAGAACGGATCGATACATTGA
*
2303485 AGGATGTATCGATACATTCATACATG
66 AGAATGTATCGATACATTCATACATG
* * * *
2303511 TATCGATACATTGAAGAATGTATTGATACATCTGGGTAAAAAGACAGAACGTATCGATACATTGA
1 TATCGATACATTGAAAAATGTATCGATACATCCGGGTAAAAAGACAGAACGGATCGATACATTGA
2303576 AGAATGTATCGATA
66 AGAATGTATCGATA
2303590 TATCTGGGTT
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
91 72 1.00
ACGTcount: A:0.40, C:0.12, G:0.20, T:0.28
Consensus pattern (91 bp):
TATCGATACATTGAAAAATGTATCGATACATCCGGGTAAAAAGACAGAACGGATCGATACATTGA
AGAATGTATCGATACATTCATACATG
Found at i:2318283 original size:22 final size:22
Alignment explanation
Indices: 2318241--2318283 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
2318231 CCTTCTATAA
*
2318241 TTTATTAGTTAATTATTTTTAG
1 TTTATTAGTTAATTATATTTAG
*
2318263 TTTATTTG-TAATCTATATTTA
1 TTTATTAGTTAAT-TATATTTA
2318284 TATTTATTGG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.28, C:0.02, G:0.07, T:0.63
Consensus pattern (22 bp):
TTTATTAGTTAATTATATTTAG
Found at i:2318348 original size:21 final size:22
Alignment explanation
Indices: 2318319--2318371 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 22
2318309 ATGCAAAGGG
2318319 TTTTCTAATTTATT-TC-TAAGAA
1 TTTT-TAATTT-TTATCATAAGAA
*
2318341 TTTTTAATTTTTATCATAATAA
1 TTTTTAATTTTTATCATAAGAA
2318363 TTTTTAATT
1 TTTTTAATT
2318372 AATTAATTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 2 0.07
21 8 0.29
22 18 0.64
ACGTcount: A:0.32, C:0.06, G:0.02, T:0.60
Consensus pattern (22 bp):
TTTTTAATTTTTATCATAAGAA
Found at i:2318388 original size:24 final size:22
Alignment explanation
Indices: 2318339--2318388 Score: 55
Period size: 24 Copynumber: 2.2 Consensus size: 22
2318329 TATTTCTAAG
* *
2318339 AATTTTTAATTTTTATCATAAT
1 AATTTTTAATTTTAATCATAAA
*
2318361 AATTTTTAATTAATTAATTATAAA
1 AATTTTTAATT--TTAATCATAAA
2318385 AATT
1 AATT
2318389 AATTTTAACT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 11 0.48
24 12 0.52
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (22 bp):
AATTTTTAATTTTAATCATAAA
Found at i:2319877 original size:29 final size:29
Alignment explanation
Indices: 2319839--2319945 Score: 124
Period size: 29 Copynumber: 3.7 Consensus size: 29
2319829 TTAATCTAAG
2319839 GAATTAAAAGTCAACTAAAATACTGAAAA
1 GAATTAAAAGTCAACTAAAATACTGAAAA
* * **
2319868 GAATTAAAAGTTAACTAAAACACAAAAAA
1 GAATTAAAAGTCAACTAAAATACTGAAAA
* * * *
2319897 GAATTAAAAGTCAATTGAAATATTGAAAG
1 GAATTAAAAGTCAACTAAAATACTGAAAA
* *
2319926 GAGTTAAAAGTCAACAAAAA
1 GAATTAAAAGTCAACTAAAA
2319946 CACCAAAACT
Statistics
Matches: 62, Mismatches: 16, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
29 62 1.00
ACGTcount: A:0.59, C:0.08, G:0.12, T:0.21
Consensus pattern (29 bp):
GAATTAAAAGTCAACTAAAATACTGAAAA
Found at i:2319909 original size:58 final size:58
Alignment explanation
Indices: 2319839--2319953 Score: 158
Period size: 58 Copynumber: 2.0 Consensus size: 58
2319829 TTAATCTAAG
* *
2319839 GAATTAAAAGTCAACTAAAATACTGAAAAGAATTAAAAGTTAACTAAAACACAAAAAA
1 GAATTAAAAGTCAACTAAAATACTGAAAAGAATTAAAAGTCAACAAAAACACAAAAAA
* * * * * *
2319897 GAATTAAAAGTCAATTGAAATATTGAAAGGAGTTAAAAGTCAACAAAAACACCAAAA
1 GAATTAAAAGTCAACTAAAATACTGAAAAGAATTAAAAGTCAACAAAAACACAAAAA
2319954 CTTCCATAAT
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
58 49 1.00
ACGTcount: A:0.59, C:0.10, G:0.11, T:0.19
Consensus pattern (58 bp):
GAATTAAAAGTCAACTAAAATACTGAAAAGAATTAAAAGTCAACAAAAACACAAAAAA
Found at i:2322295 original size:76 final size:76
Alignment explanation
Indices: 2322181--2322333 Score: 306
Period size: 76 Copynumber: 2.0 Consensus size: 76
2322171 AAACAAGTAT
2322181 GTCATTAAAATAAACAACAATAAAGTGACCAATGAATTTTTTCAAAACATGGTTCATTAATTGCA
1 GTCATTAAAATAAACAACAATAAAGTGACCAATGAATTTTTTCAAAACATGGTTCATTAATTGCA
2322246 TAAATGTGCTA
66 TAAATGTGCTA
2322257 GTCATTAAAATAAACAACAATAAAGTGACCAATGAATTTTTTCAAAACATGGTTCATTAATTGCA
1 GTCATTAAAATAAACAACAATAAAGTGACCAATGAATTTTTTCAAAACATGGTTCATTAATTGCA
2322322 TAAATGTGCTA
66 TAAATGTGCTA
2322333 G
1 G
2322334 GAGCATTGGA
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 77 1.00
ACGTcount: A:0.43, C:0.13, G:0.12, T:0.31
Consensus pattern (76 bp):
GTCATTAAAATAAACAACAATAAAGTGACCAATGAATTTTTTCAAAACATGGTTCATTAATTGCA
TAAATGTGCTA
Found at i:2322973 original size:19 final size:20
Alignment explanation
Indices: 2322925--2322996 Score: 67
Period size: 20 Copynumber: 3.6 Consensus size: 20
2322915 ACAGCCAGAT
2322925 GTATCGATACATATTGCTTA
1 GTATCGATACATATTGCTTA
** *
2322945 GTATAAATACATGTT-CTTA
1 GTATCGATACATATTGCTTA
* **
2322964 GTATCGATACACATTAAATT-
1 GTATCGATACATATT-GCTTA
2322984 GTATCGATACATA
1 GTATCGATACATA
2322997 AAACTTGTAG
Statistics
Matches: 41, Mismatches: 9, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
19 15 0.37
20 24 0.59
21 2 0.05
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (20 bp):
GTATCGATACATATTGCTTA
Found at i:2323053 original size:61 final size:61
Alignment explanation
Indices: 2322960--2323118 Score: 241
Period size: 61 Copynumber: 2.6 Consensus size: 61
2322950 AATACATGTT
* ** * *
2322960 CTTAGTATCGATACACA-TTAAATTGTATCGATACATAAAACTTG-TAGTAGCTAAAACTCA
1 CTTAGTATCGATACATACTTGGACTGTATCGATACATAAAA-TTGACAGTAGCTAAAACTCA
2323020 CTTAGTATCGATACATACTTGGACTGTATCGATACATAAAATTGACAGTAGCTAAAACTCA
1 CTTAGTATCGATACATACTTGGACTGTATCGATACATAAAATTGACAGTAGCTAAAACTCA
*
2323081 CTTAGTATCGATACATACTTGGACTATATCGATACATA
1 CTTAGTATCGATACATACTTGGACTGTATCGATACATA
2323119 GTGCATTGTA
Statistics
Matches: 91, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
60 19 0.21
61 72 0.79
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.31
Consensus pattern (61 bp):
CTTAGTATCGATACATACTTGGACTGTATCGATACATAAAATTGACAGTAGCTAAAACTCA
Found at i:2323333 original size:10 final size:10
Alignment explanation
Indices: 2323312--2323354 Score: 52
Period size: 10 Copynumber: 4.4 Consensus size: 10
2323302 CCAATAGCTG
2323312 AAGAAA-AAC
1 AAGAAACAAC
*
2323321 AAGAACCAAC
1 AAGAAACAAC
*
2323331 AAGAAACATC
1 AAGAAACAAC
*
2323341 AAGAAACACC
1 AAGAAACAAC
2323351 AAGA
1 AAGA
2323355 TATCCAAGCA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
9 5 0.17
10 24 0.83
ACGTcount: A:0.65, C:0.21, G:0.12, T:0.02
Consensus pattern (10 bp):
AAGAAACAAC
Found at i:2327724 original size:16 final size:17
Alignment explanation
Indices: 2327700--2327735 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
2327690 ATAGACTTTC
*
2327700 AAAGTTTTTAATTGA-A
1 AAAGATTTTAATTGAGA
2327716 AAAGATTTTAATTGAGA
1 AAAGATTTTAATTGAGA
2327733 AAA
1 AAA
2327736 TGTTGATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.50, C:0.00, G:0.14, T:0.36
Consensus pattern (17 bp):
AAAGATTTTAATTGAGA
Found at i:2329615 original size:11 final size:11
Alignment explanation
Indices: 2329596--2329625 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
2329586 AGCCACTCGA
*
2329596 TCACTACCTAG
1 TCACAACCTAG
2329607 TCACAACCTAG
1 TCACAACCTAG
2329618 TCACAACC
1 TCACAACC
2329626 AATAGCTCCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.33, C:0.40, G:0.07, T:0.20
Consensus pattern (11 bp):
TCACAACCTAG
Found at i:2331906 original size:19 final size:20
Alignment explanation
Indices: 2331846--2331937 Score: 107
Period size: 20 Copynumber: 4.7 Consensus size: 20
2331836 ACATCCAGAT
2331846 GTATCGATACATATTACTTA
1 GTATCGATACATATTACTTA
**
2331866 GTATCGATACATATGGCTTA
1 GTATCGATACATATTACTTA
*
2331886 GTATCGATACAT-TTTCTTA
1 GTATCGATACATATTACTTA
* * *
2331905 GTATCGATACACACTGAATT-
1 GTATCGATACATA-TTACTTA
2331925 GTATCGATACATA
1 GTATCGATACATA
2331938 AAACTCGTAG
Statistics
Matches: 61, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
19 16 0.26
20 42 0.69
21 3 0.05
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (20 bp):
GTATCGATACATATTACTTA
Found at i:2331929 original size:39 final size:39
Alignment explanation
Indices: 2331827--2331937 Score: 127
Period size: 39 Copynumber: 2.8 Consensus size: 39
2331817 CCCTAGAAAA
*
2331827 TATCGATACACATCCAGA-TGTATCGATACATATTACTTAG
1 TATCGATACACAT-GA-ATTGTATCGATACATATTACTTAG
* ** *
2331867 TATCGATACATATGGCTTAGTATCGATACAT-TTTCTTAG
1 TATCGATACACATGAATT-GTATCGATACATATTACTTAG
2331906 TATCGATACACACTGAATTGTATCGATACATA
1 TATCGATACACA-TGAATTGTATCGATACATA
2331938 AAACTCGTAG
Statistics
Matches: 59, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
39 31 0.53
40 28 0.47
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (39 bp):
TATCGATACACATGAATTGTATCGATACATATTACTTAG
Found at i:2332021 original size:20 final size:21
Alignment explanation
Indices: 2331974--2332030 Score: 80
Period size: 20 Copynumber: 2.8 Consensus size: 21
2331964 AGTATCGATA
* *
2331974 CATTGTATGGATACATACTTG
1 CATTGTATCGATACATACGTG
*
2331995 TATTGTATCGATACATA-GTG
1 CATTGTATCGATACATACGTG
2332015 CATTGTATCGATACAT
1 CATTGTATCGATACAT
2332031 TGAGCCCAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 17 0.53
21 15 0.47
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.39
Consensus pattern (21 bp):
CATTGTATCGATACATACGTG
Found at i:2335184 original size:29 final size:29
Alignment explanation
Indices: 2335148--2335256 Score: 148
Period size: 29 Copynumber: 3.8 Consensus size: 29
2335138 AAAGCTAAAA
2335148 AATTAAAAGTCAACTAAAACACTTAAAGG
1 AATTAAAAGTCAACTAAAACACTTAAAGG
* ** *
2335177 AATTAAAAGTTAACTAAAACACAAAAATG
1 AATTAAAAGTCAACTAAAACACTTAAAGG
2335206 AATTAAAAGTCAACTAAAACA-TTGAAAGG
1 AATTAAAAGTCAACTAAAACACTT-AAAGG
* *
2335235 AATTAAAAATCAATTAAAACAC
1 AATTAAAAGTCAACTAAAACAC
2335257 CAAAACTTTC
Statistics
Matches: 68, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
29 68 1.00
ACGTcount: A:0.59, C:0.12, G:0.08, T:0.21
Consensus pattern (29 bp):
AATTAAAAGTCAACTAAAACACTTAAAGG
Found at i:2335214 original size:58 final size:58
Alignment explanation
Indices: 2335148--2335261 Score: 176
Period size: 58 Copynumber: 2.0 Consensus size: 58
2335138 AAAGCTAAAA
* *
2335148 AATTAAAAGTCAACTAAAACACTT-AAAGGAATTAAAAGTTAACTAAAACACAAAAATG
1 AATTAAAAGTCAACTAAAACA-TTGAAAGGAATTAAAAATCAACTAAAACACAAAAATG
* *
2335206 AATTAAAAGTCAACTAAAACATTGAAAGGAATTAAAAATCAATTAAAACACCAAAA
1 AATTAAAAGTCAACTAAAACATTGAAAGGAATTAAAAATCAACTAAAACACAAAAA
2335262 CTTTCCTAAT
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
57 2 0.04
58 49 0.96
ACGTcount: A:0.60, C:0.12, G:0.08, T:0.20
Consensus pattern (58 bp):
AATTAAAAGTCAACTAAAACATTGAAAGGAATTAAAAATCAACTAAAACACAAAAATG
Found at i:2336746 original size:25 final size:25
Alignment explanation
Indices: 2336712--2336766 Score: 110
Period size: 25 Copynumber: 2.2 Consensus size: 25
2336702 GATTGCAAAA
2336712 TTTGTAGCTTCAATTACTTTCTAGT
1 TTTGTAGCTTCAATTACTTTCTAGT
2336737 TTTGTAGCTTCAATTACTTTCTAGT
1 TTTGTAGCTTCAATTACTTTCTAGT
2336762 TTTGT
1 TTTGT
2336767 TGTTGCATTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.18, C:0.15, G:0.13, T:0.55
Consensus pattern (25 bp):
TTTGTAGCTTCAATTACTTTCTAGT
Found at i:2337764 original size:17 final size:17
Alignment explanation
Indices: 2337742--2337774 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2337732 TAATTATGTT
2337742 ATGCCACATATCACAAA
1 ATGCCACATATCACAAA
*
2337759 ATGCCACATGTCACAA
1 ATGCCACATATCACAA
2337775 TATAATTTTG
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:0.42, C:0.30, G:0.09, T:0.18
Consensus pattern (17 bp):
ATGCCACATATCACAAA
Found at i:2338517 original size:37 final size:36
Alignment explanation
Indices: 2338458--2338529 Score: 92
Period size: 37 Copynumber: 2.0 Consensus size: 36
2338448 GATATAATAA
* *
2338458 TAAACTAATTATTAAATCAAATTAAT-TAAATATTC
1 TAAACTAATTATGAAATCAAATTAATAAAAATATTC
*
2338493 TAAACATAATTTATGAAATTAAATTAATAAAAATATT
1 TAAAC-TAA-TTATGAAATCAAATTAATAAAAATATT
2338530 ATAATGAGTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
35 5 0.16
36 3 0.10
37 16 0.52
38 7 0.23
ACGTcount: A:0.54, C:0.06, G:0.01, T:0.39
Consensus pattern (36 bp):
TAAACTAATTATGAAATCAAATTAATAAAAATATTC
Found at i:2340968 original size:22 final size:23
Alignment explanation
Indices: 2340942--2341000 Score: 77
Period size: 24 Copynumber: 2.6 Consensus size: 23
2340932 TTTATTTTAG
2340942 TTTTTTATTTTGTT-TTCCATTTC
1 TTTTTTATTTT-TTATTCCATTTC
*
2340965 TTTTTTTATTTTTTATTGCATTT-
1 -TTTTTTATTTTTTATTCCATTTC
2340988 TTTTTTATTTTTT
1 TTTTTTATTTTTT
2341001 CTAGTCATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
22 13 0.39
23 2 0.06
24 18 0.55
ACGTcount: A:0.10, C:0.07, G:0.03, T:0.80
Consensus pattern (23 bp):
TTTTTTATTTTTTATTCCATTTC
Found at i:2341011 original size:21 final size:21
Alignment explanation
Indices: 2340965--2341026 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 21
2340955 TTTCCATTTC
* *
2340965 TTTTTTTATTTTTTATTGCATT
1 TTTTTTTATTTTTTCTAGCA-T
2340987 TTTTTTTATTTTTTCTAGTCAT
1 TTTTTTTATTTTTTCTAG-CAT
* *
2341009 TTTCTTAATTTTATTCTA
1 TTTTTTTATTTT-TTCTA
2341027 CTTTATTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
22 27 0.79
23 7 0.21
ACGTcount: A:0.16, C:0.08, G:0.03, T:0.73
Consensus pattern (21 bp):
TTTTTTTATTTTTTCTAGCAT
Found at i:2341011 original size:22 final size:22
Alignment explanation
Indices: 2340965--2341011 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
2340955 TTTCCATTTC
* *
2340965 TTTTTTTATTTTTTATTGCATT
1 TTTTTTTATTTTTTCTAGCATT
2340987 TTTTTTTATTTTTTCTAGTCATT
1 TTTTTTTATTTTTTCTAG-CATT
2341010 TT
1 TT
2341012 CTTAATTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.13, C:0.06, G:0.04, T:0.77
Consensus pattern (22 bp):
TTTTTTTATTTTTTCTAGCATT
Found at i:2342495 original size:90 final size:92
Alignment explanation
Indices: 2342328--2342515 Score: 272
Period size: 90 Copynumber: 2.0 Consensus size: 92
2342318 AGGTCCTAGA
2342328 TCAAGTCTTGTCTTTTTTTTAACTATTAAATAAATTCATATTTGCAACCAAAAAAAAAAGCAATA
1 TCAAGTCTTGTC-TTTTTTTAACTATTAAATAAATTCATATTT---ACCAAAAAAAAAAGCAATA
* ** *
2342393 TTCCTATGTTAAAATAATCCATGGATTTCTC
62 TCCCTAAATTAAAATAATCCATGAATTTCTC
* *
2342424 TCAAGTCTTGTC-TTTTTTAACTATTAAATAAATTCATGTTT-TCAAAAAAAAAAGCAATATCCC
1 TCAAGTCTTGTCTTTTTTTAACTATTAAATAAATTCATATTTACCAAAAAAAAAAGCAATATCCC
2342487 TAAATTAAAATAATCCATGAATTTCTC
66 TAAATTAAAATAATCCATGAATTTCTC
2342514 TC
1 TC
2342516 GATATATAAA
Statistics
Matches: 86, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
90 46 0.53
94 28 0.33
96 12 0.14
ACGTcount: A:0.39, C:0.16, G:0.06, T:0.38
Consensus pattern (92 bp):
TCAAGTCTTGTCTTTTTTTAACTATTAAATAAATTCATATTTACCAAAAAAAAAAGCAATATCCC
TAAATTAAAATAATCCATGAATTTCTC
Found at i:2345569 original size:2 final size:2
Alignment explanation
Indices: 2345564--2345609 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
2345554 AAAATTGTAG
*
2345564 TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2345606 TA TA
1 TA TA
2345610 GATCCATTAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:2348022 original size:23 final size:25
Alignment explanation
Indices: 2347986--2348032 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 25
2347976 ACTTTTTAAA
* *
2347986 AATAAATATAAATAATTTTTATTTT
1 AATAAATATAAATAAATCTTATTTT
2348011 AATAAA-AT-AATAAATCTTATTT
1 AATAAATATAAATAAATCTTATTT
2348033 ATTATTAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 12 0.60
24 2 0.10
25 6 0.30
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (25 bp):
AATAAATATAAATAAATCTTATTTT
Found at i:2348803 original size:2 final size:2
Alignment explanation
Indices: 2348798--2348846 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
2348788 ATAGATAGCT
2348798 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2348840 AG AG AG A
1 AG AG AG A
2348847 TCGTTCTGTC
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:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2351518 original size:15 final size:16
Alignment explanation
Indices: 2351495--2351534 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
2351485 TGATACATAA
*
2351495 TTTAATTAAAA-AATT
1 TTTAATTAAAAGAAGT
*
2351510 TTTATTTAAAAGAAGT
1 TTTAATTAAAAGAAGT
2351526 TTTAATTAA
1 TTTAATTAA
2351535 CACTTGTCCT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
15 10 0.48
16 11 0.52
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (16 bp):
TTTAATTAAAAGAAGT
Found at i:2352735 original size:11 final size:11
Alignment explanation
Indices: 2352694--2352754 Score: 51
Period size: 10 Copynumber: 6.0 Consensus size: 11
2352684 TATAAATAAA
*
2352694 ATTAATATATT
1 ATTAATATTTT
* *
2352705 A-TCATATGTT
1 ATTAATATTTT
2352715 -TTAATATTTT
1 ATTAATATTTT
*
2352725 ATTAGTA-TTT
1 ATTAATATTTT
2352735 -TTAATATTTT
1 ATTAATATTTT
2352745 ATTAA-ATTTT
1 ATTAATATTTT
2352755 GAGAGATTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
9 5 0.12
10 25 0.62
11 10 0.25
ACGTcount: A:0.34, C:0.02, G:0.03, T:0.61
Consensus pattern (11 bp):
ATTAATATTTT
Found at i:2352747 original size:20 final size:20
Alignment explanation
Indices: 2352695--2352748 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
2352685 ATAAATAAAA
* *
2352695 TTAATATATTATCATATGTT
1 TTAATATTTTATTATATGTT
2352715 TTAATATTTTATTAGTAT-TT
1 TTAATATTTTATTA-TATGTT
2352735 TTAATATTTTATTA
1 TTAATATTTTATTA
2352749 AATTTTGAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 28 0.90
21 3 0.10
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.61
Consensus pattern (20 bp):
TTAATATTTTATTATATGTT
Found at i:2353544 original size:8 final size:8
Alignment explanation
Indices: 2353531--2353555 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
2353521 AATTTTGATA
2353531 TATTTATG
1 TATTTATG
2353539 TATTTATG
1 TATTTATG
2353547 TATTTATG
1 TATTTATG
2353555 T
1 T
2353556 TATAATCATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.12, T:0.64
Consensus pattern (8 bp):
TATTTATG
Found at i:2355135 original size:20 final size:21
Alignment explanation
Indices: 2355086--2355133 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
2355076 GGAAGAAATA
2355086 AATA-AAAGAAAAAAAAAGAG
1 AATAGAAAGAAAAAAAAAGAG
*
2355106 AATGGAAAGAAAAAAAAGAGAG
1 AATAGAAAGAAAAAAAA-AGAG
2355128 AA-AGAA
1 AATAGAA
2355134 GATTTGTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 3 0.12
21 15 0.62
22 6 0.25
ACGTcount: A:0.75, C:0.00, G:0.21, T:0.04
Consensus pattern (21 bp):
AATAGAAAGAAAAAAAAAGAG
Found at i:2356679 original size:24 final size:21
Alignment explanation
Indices: 2356652--2356702 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 21
2356642 TAATTTTTTA
*
2356652 TTATTAAATAATATATATTTAATT
1 TTATTAAA-AATATAT-TTTAA-G
2356676 TTATT-AAAATATATTTTAAG
1 TTATTAAAAATATATTTTAAG
2356696 TTATTAA
1 TTATTAA
2356703 TATATAATGA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 5 0.20
21 6 0.24
22 7 0.28
23 2 0.08
24 5 0.20
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (21 bp):
TTATTAAAAATATATTTTAAG
Found at i:2356699 original size:20 final size:22
Alignment explanation
Indices: 2356652--2356708 Score: 64
Period size: 20 Copynumber: 2.6 Consensus size: 22
2356642 TAATTTTTTA
*
2356652 TTATTAAATAATATATATTTAATT
1 TTATT-AA-AATATATATTTAATG
2356676 TTATTAAAATATAT-TTTAA-G
1 TTATTAAAATATATATTTAATG
*
2356696 TTATTAATATATA
1 TTATTAAAATATA
2356709 ATGATATTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.39
21 5 0.16
22 7 0.23
23 2 0.06
24 5 0.16
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.53
Consensus pattern (22 bp):
TTATTAAAATATATATTTAATG
Found at i:2363988 original size:57 final size:56
Alignment explanation
Indices: 2363927--2364145 Score: 264
Period size: 57 Copynumber: 3.9 Consensus size: 56
2363917 ATAACCAAAT
*
2363927 GCTTGAGAACTCAACCATTTGCAAAGGTCCAAAATTAATATCTTGCCATTGCTAAAA
1 GCTTGAGAACTCAACCATTTGCAAA-GTCCAAAATTATTATCTTGCCATTGCTAAAA
* * * *
2363984 GCTTGAGAACTCGACCATTTGTTAAAGTCCAAAATTATTATCTCGCCATTGCCAAAA
1 GCTTGAGAACTCAACCATTTG-CAAAGTCCAAAATTATTATCTTGCCATTGCTAAAA
* ** * *
2364041 GCTTGA-AAGCTCAACCATTTGCTAAGATCTGAAATTATTTTCTTGCCATT-TTCAAAA
1 GCTTGAGAA-CTCAACCATTTGCAAAG-TCCAAAATTATTATCTTGCCATTGCT-AAAA
*
2364098 GCTTAAGAACTCAACCATTTGCTAAAGTCCAAAATTATTA-CTTGCCAT
1 GCTTGAGAACTCAACCATTTGC-AAAGTCCAAAATTATTATCTTGCCAT
2364146 CACTAAAGGC
Statistics
Matches: 137, Mismatches: 19, Indels: 13
0.81 0.11 0.08
Matches are distributed among these distances:
56 13 0.09
57 116 0.85
58 8 0.06
ACGTcount: A:0.34, C:0.21, G:0.13, T:0.32
Consensus pattern (56 bp):
GCTTGAGAACTCAACCATTTGCAAAGTCCAAAATTATTATCTTGCCATTGCTAAAA
Found at i:2364085 original size:114 final size:114
Alignment explanation
Indices: 2363882--2364145 Score: 336
Period size: 114 Copynumber: 2.3 Consensus size: 114
2363872 ATTATGCCTT
* * * *
2363882 GACCATTTGTTAAATTCCAAAATTACTATCTCGTCATAACCAAATGCTTGAGAACTCAACCATTT
1 GACCATTTGTTAAAGTCCAAAATTATTATCTCGCCATAACCAAAAGCTTGAGAACTCAACCATTT
* *
2363947 GCAAAGGTCCAAAATTAATATCTTGCCATTGCT-AAAAGCTTGAGAACTC
66 GCAAAGATCCAAAATTAATATCTTGCCATT-CTCAAAAGCTTAAGAACTC
**
2363996 GACCATTTGTTAAAGTCCAAAATTATTATCTCGCCATTGCCAAAAGCTTGA-AAGCTCAACCATT
1 GACCATTTGTTAAAGTCCAAAATTATTATCTCGCCATAACCAAAAGCTTGAGAA-CTCAACCATT
* ** * * *
2364060 TGCTAAGATCTGAAATTATTTTCTTGCCATTTTCAAAAGCTTAAGAACTC
65 TGCAAAGATCCAAAATTAATATCTTGCCATTCTCAAAAGCTTAAGAACTC
* * *
2364110 AACCATTTGCTAAAGTCCAAAATTATTA-CTTGCCAT
1 GACCATTTGTTAAAGTCCAAAATTATTATCTCGCCAT
2364146 CACTAAAGGC
Statistics
Matches: 131, Mismatches: 17, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
113 10 0.08
114 121 0.92
ACGTcount: A:0.35, C:0.22, G:0.12, T:0.32
Consensus pattern (114 bp):
GACCATTTGTTAAAGTCCAAAATTATTATCTCGCCATAACCAAAAGCTTGAGAACTCAACCATTT
GCAAAGATCCAAAATTAATATCTTGCCATTCTCAAAAGCTTAAGAACTC
Found at i:2370895 original size:10 final size:11
Alignment explanation
Indices: 2370874--2370916 Score: 54
Period size: 10 Copynumber: 4.0 Consensus size: 11
2370864 CTCTAACATT
2370874 TTTTCATCAAA
1 TTTTCATCAAA
2370885 TTTTC-TCAAA
1 TTTTCATCAAA
*
2370895 TTTTCAT-TAA
1 TTTTCATCAAA
2370905 TTTTACATCAAA
1 TTTT-CATCAAA
2370917 ACATCTCTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
10 16 0.59
11 9 0.33
12 2 0.07
ACGTcount: A:0.35, C:0.16, G:0.00, T:0.49
Consensus pattern (11 bp):
TTTTCATCAAA
Found at i:2372493 original size:17 final size:18
Alignment explanation
Indices: 2372461--2372494 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2372451 TTTATTTTTG
*
2372461 CTTGTCTTTGTGACTTTC
1 CTTGTATTTGTGACTTTC
2372479 CTTGTATTT-TGACTTT
1 CTTGTATTTGTGACTTT
2372495 TGTTTATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.09, C:0.18, G:0.15, T:0.59
Consensus pattern (18 bp):
CTTGTATTTGTGACTTTC
Found at i:2373268 original size:20 final size:19
Alignment explanation
Indices: 2373225--2373278 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 19
2373215 ACATTATGCT
**
2373225 TTGTATCGATACATGTTCA
1 TTGTATCGATACATGCACA
*
2373244 TTGTATCAATACATGCACAA
1 TTGTATCGATACATGCAC-A
2373264 TTGTATCGATACATG
1 TTGTATCGATACATG
2373279 AAACTGGCAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (19 bp):
TTGTATCGATACATGCACA
Found at i:2375243 original size:12 final size:13
Alignment explanation
Indices: 2375214--2375245 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
2375204 AAAAATAATC
2375214 TATTTAAATTTGA
1 TATTTAAATTTGA
2375227 TATTTAAATTT-A
1 TATTTAAATTTGA
2375239 TATTTAA
1 TATTTAA
2375246 TATGTCATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 8 0.42
13 11 0.58
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (13 bp):
TATTTAAATTTGA
Found at i:2376096 original size:27 final size:26
Alignment explanation
Indices: 2376031--2376107 Score: 74
Period size: 27 Copynumber: 3.0 Consensus size: 26
2376021 TATTTTGAAT
*
2376031 ATAAATTTAAAATTTAATTTTA-TTA
1 ATAAATTTAAAATTTAATTATATTTA
*
2376056 AT---TTATATAA-TTAATTAATATTTA
1 ATAAATT-TAAAATTTAATT-ATATTTA
2376080 ATAAATTTAAAATTTAAATTATATTTA
1 ATAAATTTAAAATTT-AATTATATTTA
2376107 A
1 A
2376108 ATTTTTTAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 14
0.71 0.05 0.24
Matches are distributed among these distances:
22 8 0.20
23 6 0.15
24 5 0.12
25 2 0.05
26 4 0.10
27 12 0.29
28 4 0.10
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (26 bp):
ATAAATTTAAAATTTAATTATATTTA
Found at i:2377166 original size:3 final size:3
Alignment explanation
Indices: 2377158--2377195 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
2377148 TTTTCATCAC
2377158 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2377196 ATAACAAATG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2377644 original size:18 final size:19
Alignment explanation
Indices: 2377623--2377658 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
2377613 TTCTTTTGTT
2377623 AATATGTAA-AATTTTTTG
1 AATATGTAACAATTTTTTG
*
2377641 AATATTTAACAATTTTTT
1 AATATGTAACAATTTTTT
2377659 TAAAAGTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.39, C:0.03, G:0.06, T:0.53
Consensus pattern (19 bp):
AATATGTAACAATTTTTTG
Found at i:2378097 original size:18 final size:19
Alignment explanation
Indices: 2378063--2378099 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
2378053 TAAAAAATAA
*
2378063 TTTTTGAAAAATGTAAATT
1 TTTTTAAAAAATGTAAATT
2378082 TTTTTAAAAAAT-TAAATT
1 TTTTTAAAAAATGTAAATT
2378100 GATATTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (19 bp):
TTTTTAAAAAATGTAAATT
Found at i:2378311 original size:22 final size:22
Alignment explanation
Indices: 2378284--2378355 Score: 60
Period size: 22 Copynumber: 3.2 Consensus size: 22
2378274 AAATTAAATT
2378284 TTAAAAATAATATTATTTATTA
1 TTAAAAATAATATTATTTATTA
* *
2378306 TT-AAAATATTAATTATATTAATA
1 TTAAAAATAAT-ATTAT-TTATTA
*
2378329 TTGAAAAAT-AT-TGTAATTATTA
1 TT-AAAAATAATAT-TATTTATTA
2378351 TTAAA
1 TTAAA
2378356 TTAATTTTCA
Statistics
Matches: 40, Mismatches: 5, Indels: 11
0.71 0.09 0.20
Matches are distributed among these distances:
21 10 0.25
22 15 0.38
23 9 0.22
24 1 0.03
25 5 0.12
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (22 bp):
TTAAAAATAATATTATTTATTA
Found at i:2378315 original size:18 final size:17
Alignment explanation
Indices: 2378265--2378326 Score: 54
Period size: 18 Copynumber: 3.6 Consensus size: 17
2378255 ATGTTAAAAT
*
2378265 ATTATATTAAAAT-TAA
1 ATTATATTAAAATATTA
* **
2378281 ATTTTAAAAATAATATTA
1 ATTATATTAA-AATATTA
*
2378299 TTTATTATTAAAATATTA
1 ATTA-TATTAAAATATTA
2378317 ATTATATTAA
1 ATTATATTAA
2378327 TATTGAAAAA
Statistics
Matches: 34, Mismatches: 9, Indels: 5
0.71 0.19 0.10
Matches are distributed among these distances:
16 7 0.21
17 9 0.26
18 14 0.41
19 4 0.12
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
ATTATATTAAAATATTA
Found at i:2378463 original size:23 final size:21
Alignment explanation
Indices: 2378437--2378504 Score: 50
Period size: 23 Copynumber: 3.1 Consensus size: 21
2378427 ATATGATTTT
2378437 ATATCAAAACAGTAATTATATTA
1 ATAT-AAAA-AGTAATTATATTA
* *
2378460 ATATTTAAAA-T-ATTATAATA
1 ATA-TAAAAAGTAATTATATTA
*
2378480 ATTATAAAATAGTATTTATATTA
1 A-TATAAAA-AGTAATTATATTA
2378503 AT
1 AT
2378505 GTAATTATGA
Statistics
Matches: 35, Mismatches: 5, Indels: 11
0.69 0.10 0.22
Matches are distributed among these distances:
20 13 0.37
21 4 0.11
22 3 0.09
23 14 0.40
24 1 0.03
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (21 bp):
ATATAAAAAGTAATTATATTA
Found at i:2378503 original size:43 final size:44
Alignment explanation
Indices: 2378289--2378504 Score: 142
Period size: 43 Copynumber: 4.9 Consensus size: 44
2378279 AAATTTTAAA
* * * *
2378289 AATAATATTAT-TTATTATTAAAATATTAATTATATTAATATTG
1 AATAATATTATATAATTATTAAAATAGTATTTATATTAATATTT
* * * * * *
2378332 AAAAATATTGTAATTATTATTAAATTAAT-TTTCAAATAATAATATTTT
1 AATAATATTAT-ATAATTATTAAAATAGTATTT---ATATTAATA-TTT
* *
2378380 AATAATATTATATAA-TACTAAAA-A-TATTAATATTAAATATTT
1 AATAATATTATATAATTATTAAAATAGTATTTATATT-AATATTT
* * * * * *
2378422 AACTAATATGATTTTA-TATCAAAACAGTAATTATATTAATATTT
1 AA-TAATATTATATAATTATTAAAATAGTATTTATATTAATATTT
2378466 AA-AATATTATAATAATTA-TAAAATAGTATTTATATTAAT
1 AATAATATTAT-ATAATTATTAAAATAGTATTTATATTAAT
2378505 GTAATTATGA
Statistics
Matches: 133, Mismatches: 27, Indels: 26
0.72 0.15 0.14
Matches are distributed among these distances:
42 16 0.12
43 49 0.37
44 15 0.11
45 25 0.19
46 6 0.05
47 11 0.08
48 11 0.08
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (44 bp):
AATAATATTATATAATTATTAAAATAGTATTTATATTAATATTT
Found at i:2378714 original size:23 final size:25
Alignment explanation
Indices: 2378665--2378717 Score: 67
Period size: 22 Copynumber: 2.2 Consensus size: 25
2378655 TATAAATATC
*
2378665 AAAATATTATAAACTATTTATTATT
1 AAAATATTATAAACTATTAATTATT
2378690 AAAATATTA-AAA-TATTAA-TATT
1 AAAATATTATAAACTATTAATTATT
*
2378712 TAAATA
1 AAAATA
2378718 GTAATATTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 9 0.35
23 5 0.19
24 3 0.12
25 9 0.35
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (25 bp):
AAAATATTATAAACTATTAATTATT
Found at i:2378716 original size:22 final size:22
Alignment explanation
Indices: 2378653--2378721 Score: 57
Period size: 22 Copynumber: 3.0 Consensus size: 22
2378643 TAGTCATATC
* * *
2378653 AATATAAATATCAAAATATTATA
1 AATATTAATATTAAAATAGTA-A
* *
2378676 AACTATTTATTATTAAAATATTAA
1 AA-TA-TTAATATTAAAATAGTAA
*
2378700 AATATTAATATTTAAATAGTAA
1 AATATTAATATTAAAATAGTAA
2378722 TATTTGAATA
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
22 15 0.39
23 4 0.11
24 5 0.13
25 14 0.37
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (22 bp):
AATATTAATATTAAAATAGTAA
Found at i:2378726 original size:14 final size:14
Alignment explanation
Indices: 2378692--2378753 Score: 63
Period size: 14 Copynumber: 4.5 Consensus size: 14
2378682 TTATTATTAA
* *
2378692 AATATTAAAATATT
1 AATATTTAAATAAT
*
2378706 AATATTTAAATAGT
1 AATATTTAAATAAT
*
2378720 AATATTTGAATAAT
1 AATATTTAAATAAT
*
2378734 AATGTTT-AATAAT
1 AATATTTAAATAAT
*
2378747 AAAATTT
1 AATATTT
2378754 TATATTAATA
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
13 11 0.27
14 30 0.73
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.44
Consensus pattern (14 bp):
AATATTTAAATAAT
Found at i:2378731 original size:28 final size:26
Alignment explanation
Indices: 2378700--2378764 Score: 67
Period size: 27 Copynumber: 2.4 Consensus size: 26
2378690 AAAATATTAA
* *
2378700 AATATTAATATTTAAATAGTAATATTT
1 AATATTAATATTT-AATAATAAAATTT
* *
2378727 GAATAATAATGTTTAATAATAAAATTT
1 -AATATTAATATTTAATAATAAAATTT
*
2378754 TATATTAATAT
1 AATATTAATAT
2378765 AAAATTTTTA
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
26 8 0.27
27 11 0.37
28 11 0.37
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (26 bp):
AATATTAATATTTAATAATAAAATTT
Found at i:2378781 original size:19 final size:19
Alignment explanation
Indices: 2378740--2378781 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
2378730 TAATAATGTT
* *
2378740 TAATAATAAAATTTTATAT
1 TAATAATAAAATTTTAAAA
2378759 TAAT-ATAAAATTTTTAAAA
1 TAATAATAAAA-TTTTAAAA
2378778 TAAT
1 TAAT
2378782 TATTATTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
TAATAATAAAATTTTAAAA
Found at i:2383405 original size:8 final size:8
Alignment explanation
Indices: 2383392--2383424 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
2383382 CCATTTCATA
2383392 TTTTTTTC
1 TTTTTTTC
2383400 TTTTTTTC
1 TTTTTTTC
2383408 --TTTTTC
1 TTTTTTTC
2383414 TTTTTTTC
1 TTTTTTTC
2383422 TTT
1 TTT
2383425 CTTATTTAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
6 6 0.26
8 17 0.74
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (8 bp):
TTTTTTTC
Found at i:2383413 original size:14 final size:14
Alignment explanation
Indices: 2383394--2383424 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
2383384 ATTTCATATT
2383394 TTTTTCTTTTTTTC
1 TTTTTCTTTTTTTC
2383408 TTTTTCTTTTTTTC
1 TTTTTCTTTTTTTC
2383422 TTT
1 TTT
2383425 CTTATTTAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (14 bp):
TTTTTCTTTTTTTC
Found at i:2388012 original size:60 final size:61
Alignment explanation
Indices: 2387766--2388394 Score: 291
Period size: 61 Copynumber: 10.0 Consensus size: 61
2387756 CGTGGACTTA
* * * *
2387766 GAAAAGAGATGCCACTGAGTTGTGGAC-TT-ACAGGAAAAAGAGATGCCACTGAGTTGTGGACTT
1 GAAAA-AGATGCCACAGAGTTGTGGACTTTGA-AGG-AAAAG-G-TGCCACGGAGTTATGGGCTT
2387829 T
61 T
*
2387830 GAAGGAAAGAGATGCCACAGAGTTGTGGACTTTGAAAAGAAAAAGAGTGCCACGGAGTTATGGGC
1 G-A--AAA-AGATGCCACAGAGTTGTGGACTTTG--AAGGAAAAG-GTGCCACGGAGTTATGGGC
2387895 TTTAAAT
59 -TT---T
** ** * *
2387902 GAAAAAGATGCCATGGAGTTGTGGACTTAAAAGGAGCAAGGTGCCACGGAGTTATGGACTTT
1 GAAAAAGATGCCACAGAGTTGTGGACTTTGAAGGA-AAAGGTGCCACGGAGTTATGGGCTTT
* * * *
2387964 -AAAAGGGTGCCACAGAGTTGTGGGCTTTGAAGGAAAAGGTGCCACGGAGTTGTGGGCTTT
1 GAAAAAGATGCCACAGAGTTGTGGACTTTGAAGGAAAAGGTGCCACGGAGTTATGGGCTTT
* * * * * * *
2388024 GAAGAAAAGATGCCACTGAGTCGTGGACTTTGAA--AAGAGATTGCCACTGAGTTGTGGACTTT
1 G-A-AAAAGATGCCACAGAGTTGTGGACTTTGAAGGAAAAG-GTGCCACGGAGTTATGGGCTTT
* * * * **
2388086 GGAGAACAA-ATGCCACTGAGTCGTGGACTTTG--GGACAAA-ATGCCACTGAGTCGTGGGCTTT
1 -GA-AA-AAGATGCCACAGAGTTGTGGACTTTGAAGGA-AAAGGTGCCACGGAGTTATGGGCTTT
* * * ** * * **
2388147 GAGAAGAGATTGCCACTGAGTTGTGGACTTTGGA-GAAAAAATGCCACTGAGTCATGGATTTT
1 GA-AAAAGA-TGCCACAGAGTTGTGGACTTTGAAGGAAAAGGTGCCACGGAGTTATGGGCTTT
* * * ** * * * *
2388209 GAGAAGAGATGCCACTGAGTCGTGGACTTTG-A-GAAGTGATTGCCACTGAGTTGTGGACTTT
1 GA-AAAAGATGCCACAGAGTTGTGGACTTTGAAGGAAAAG-GTGCCACGGAGTTATGGGCTTT
* ** * * * * ** *
2388270 GGAGAAAAAATGCCACTTAGTTGTGGATTTTG-A-GAAGAGATGCCACTGAGTCGTGGACTTT
1 -GA-AAAAGATGCCACAGAGTTGTGGACTTTGAAGGAAAAGGTGCCACGGAGTTATGGGCTTT
** * * * *
2388331 GAGAAGTGATTGCCACTA-AGTTGTGGACTTTGAA-GAAAAGATGCCACTGAGTCATGGACTTT
1 GA-AAAAGA-TGCCAC-AGAGTTGTGGACTTTGAAGGAAAAGGTGCCACGGAGTTATGGGCTTT
2388393 GA
1 GA
2388395 GAAGAGAGAT
Statistics
Matches: 471, Mismatches: 63, Indels: 64
0.79 0.11 0.11
Matches are distributed among these distances:
59 1 0.00
60 39 0.08
61 152 0.32
62 140 0.30
63 30 0.06
64 1 0.00
65 3 0.01
66 22 0.05
67 27 0.06
68 38 0.08
69 12 0.03
70 2 0.00
71 2 0.00
72 2 0.00
ACGTcount: A:0.30, C:0.14, G:0.31, T:0.25
Consensus pattern (61 bp):
GAAAAAGATGCCACAGAGTTGTGGACTTTGAAGGAAAAGGTGCCACGGAGTTATGGGCTTT
Found at i:2388038 original size:31 final size:31
Alignment explanation
Indices: 2387746--2388394 Score: 536
Period size: 31 Copynumber: 20.7 Consensus size: 31
2387736 TTCGCCGGGC
* * * *
2387746 GCCACAGAGTCGTGGACTTAGAA-AAGAGAT
1 GCCACTGAGTTGTGGACTTTGAAGAAAAGAT
*
2387776 GCCACTGAGTTGTGGACTTACAGGAA-AAAGAGAT
1 GCCACTGAGTTGTGGACTT---TGAAGAAA-AGAT
2387810 GCCACTGAGTTGTGGACTTTGAAGGAAAGAGAT
1 GCCACTGAGTTGTGGACTTTGAA-GAAA-AGAT
*
2387843 GCCACAGAGTTGTGGACTTTGAAAAGAAAAAGAGT
1 GCCACTGAGTTGTGGACTTTG--AAG-AAAAGA-T
* * * *
2387878 GCCACGGAGTTATGGGCTTTAAATGAAAAAGAT
1 GCCACTGAGTTGTGGACTTTGAA-G-AAAAGAT
** * *
2387911 GCCA-TGGAGTTGTGGACTTAAAAGGAGCAAGGT
1 GCCACT-GAGTTGTGGACTTTGAA-GA-AAAGAT
* * * *
2387944 GCCACGGAGTTATGGACTTT--A-AAAGGGT
1 GCCACTGAGTTGTGGACTTTGAAGAAAAGAT
* * *
2387972 GCCACAGAGTTGTGGGCTTTGAAGGAAAAGGT
1 GCCACTGAGTTGTGGACTTTGAA-GAAAAGAT
* *
2388004 GCCACGGAGTTGTGGGCTTTGAAGAAAAGAT
1 GCCACTGAGTTGTGGACTTTGAAGAAAAGAT
* *
2388035 GCCACTGAGTCGTGGACTTTGAA-AAGAGATT
1 GCCACTGAGTTGTGGACTTTGAAGAAAAGA-T
*
2388066 GCCACTGAGTTGTGGACTTTGGAGAACAA-AT
1 GCCACTGAGTTGTGGACTTTGAAGAA-AAGAT
* *
2388097 GCCACTGAGTCGTGGACTTTG-GGACAAA-AT
1 GCCACTGAGTTGTGGACTTTGAAGA-AAAGAT
* * *
2388127 GCCACTGAGTCGTGGGCTTTG-AGAAGAGATT
1 GCCACTGAGTTGTGGACTTTGAAGAAAAGA-T
* *
2388158 GCCACTGAGTTGTGGACTTTGGAGAAAAAAT
1 GCCACTGAGTTGTGGACTTTGAAGAAAAGAT
** * *
2388189 GCCACTGAGTCATGGATTTTG-AGAAGAGAT
1 GCCACTGAGTTGTGGACTTTGAAGAAAAGAT
* **
2388219 GCCACTGAGTCGTGGACTTTG-AGAAGTGATT
1 GCCACTGAGTTGTGGACTTTGAAGAAAAGA-T
* *
2388250 GCCACTGAGTTGTGGACTTTGGAGAAAAAAT
1 GCCACTGAGTTGTGGACTTTGAAGAAAAGAT
* * *
2388281 GCCACTTAGTTGTGGATTTTG-AGAAGAGAT
1 GCCACTGAGTTGTGGACTTTGAAGAAAAGAT
* **
2388311 GCCACTGAGTCGTGGACTTTG-AGAAGTGATT
1 GCCACTGAGTTGTGGACTTTGAAGAAAAGA-T
*
2388342 GCCACTAAGTTGTGGACTTTGAAGAAAAGAT
1 GCCACTGAGTTGTGGACTTTGAAGAAAAGAT
**
2388373 GCCACTGAGTCATGGACTTTGA
1 GCCACTGAGTTGTGGACTTTGA
2388395 GAAGAGAGAT
Statistics
Matches: 519, Mismatches: 71, Indels: 57
0.80 0.11 0.09
Matches are distributed among these distances:
28 21 0.04
29 3 0.01
30 117 0.23
31 195 0.38
32 49 0.09
33 76 0.15
34 35 0.07
35 23 0.04
ACGTcount: A:0.30, C:0.14, G:0.31, T:0.25
Consensus pattern (31 bp):
GCCACTGAGTTGTGGACTTTGAAGAAAAGAT
Found at i:2388398 original size:92 final size:92
Alignment explanation
Indices: 2387746--2388401 Score: 642
Period size: 92 Copynumber: 7.0 Consensus size: 92
2387736 TTCGCCGGGC
* * * *
2387746 GCCACAGAGTCGTGGACTTAGAAAAGAGA-TGCCACTGAGTTGTGGACTTACAGGA-AAAAGAGA
1 GCCACTGAGTCGTGGACTTTGAGAAGAGATTGCCACTGAGTTGTGGACTT--TGGAGAAAA-A-A
*
2387809 TGCCACTGAGTTGTGGACTTTGAAGGAAAGAGAT
62 TGCCACTGAGTCGTGGACTTTG-A-G-AAGAGAT
* * * * * * * **
2387843 GCCACAGAGTTGTGGACTTTGAAAAGAAAAAGAGTGCCACGGAGTTATGGGCTTTAAATGAAAAA
1 GCCACTGAGTCGTGGACTTTG---AG-AAGAGATTGCCACTGAGTTGTGGACTTTGGA-GAAAAA
* ** * *
2387908 GATGCCA-TGGAGTTGTGGACTTAAAAGGAGCAAGGT
61 -ATGCCACT-GAGTCGTGGACTT-TGAGAAG--AGAT
* ** ** * * * **
2387944 GCCACGGAGTTATGGACTTT-A-AA-AGGGTGCCACAGAGTTGTGGGCTTTGAAGGAAAAGGTGC
1 GCCACTGAGTCGTGGACTTTGAGAAGAGATTGCCACTGAGTTGTGGACTTTGGA-GAAAAAATGC
* * * *
2388006 CACGGAGTTGTGGGCTTTGAAGAAAAGAT
65 CACTGAGTCGTGGACTTTG-AGAAGAGAT
* *
2388035 GCCACTGAGTCGTGGACTTTGAAAAGAGATTGCCACTGAGTTGTGGACTTTGGAGAACAAATGCC
1 GCCACTGAGTCGTGGACTTTGAGAAGAGATTGCCACTGAGTTGTGGACTTTGGAGAAAAAATGCC
* *
2388100 ACTGAGTCGTGGACTTTGGGACA-AAAT
66 ACTGAGTCGTGGACTTTGAGA-AGAGAT
*
2388127 GCCACTGAGTCGTGGGCTTTGAGAAGAGATTGCCACTGAGTTGTGGACTTTGGAGAAAAAATGCC
1 GCCACTGAGTCGTGGACTTTGAGAAGAGATTGCCACTGAGTTGTGGACTTTGGAGAAAAAATGCC
* *
2388192 ACTGAGTCATGGATTTTGAGAAGAGAT
66 ACTGAGTCGTGGACTTTGAGAAGAGAT
*
2388219 GCCACTGAGTCGTGGACTTTGAGAAGTGATTGCCACTGAGTTGTGGACTTTGGAGAAAAAATGCC
1 GCCACTGAGTCGTGGACTTTGAGAAGAGATTGCCACTGAGTTGTGGACTTTGGAGAAAAAATGCC
* * *
2388284 ACTTAGTTGTGGATTTTGAGAAGAGAT
66 ACTGAGTCGTGGACTTTGAGAAGAGAT
* * * *
2388311 GCCACTGAGTCGTGGACTTTGAGAAGTGATTGCCACTAAGTTGTGGACTTTGAAGAAAAGATGCC
1 GCCACTGAGTCGTGGACTTTGAGAAGAGATTGCCACTGAGTTGTGGACTTTGGAGAAAAAATGCC
*
2388376 ACTGAGTCATGGACTTTGAGAAGAGA
66 ACTGAGTCGTGGACTTTGAGAAGAGA
2388402 GATTTGAAGA
Statistics
Matches: 476, Mismatches: 65, Indels: 41
0.82 0.11 0.07
Matches are distributed among these distances:
91 21 0.04
92 260 0.55
93 46 0.10
94 52 0.11
95 2 0.00
97 20 0.04
99 2 0.00
100 4 0.01
101 48 0.10
102 21 0.04
ACGTcount: A:0.30, C:0.14, G:0.31, T:0.24
Consensus pattern (92 bp):
GCCACTGAGTCGTGGACTTTGAGAAGAGATTGCCACTGAGTTGTGGACTTTGGAGAAAAAATGCC
ACTGAGTCGTGGACTTTGAGAAGAGAT
Found at i:2389705 original size:13 final size:13
Alignment explanation
Indices: 2389680--2389721 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
2389670 TTTACACTCC
2389680 TTTTTTG-TG-TG
1 TTTTTTGTTGTTG
2389691 TTTTTTGTTGTTG
1 TTTTTTGTTGTTG
*
2389704 TTTTTTTTTGTT-
1 TTTTTTGTTGTTG
2389716 TTTTTT
1 TTTTTT
2389722 CATCATTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
11 7 0.25
12 8 0.29
13 13 0.46
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (13 bp):
TTTTTTGTTGTTG
Found at i:2390673 original size:12 final size:12
Alignment explanation
Indices: 2390656--2390680 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2390646 CTGCCCCGGC
2390656 ATGGTAATCACA
1 ATGGTAATCACA
2390668 ATGGTAATCACA
1 ATGGTAATCACA
2390680 A
1 A
2390681 GAATTCGTCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.16, G:0.16, T:0.24
Consensus pattern (12 bp):
ATGGTAATCACA
Found at i:2392809 original size:172 final size:172
Alignment explanation
Indices: 2392294--2392811 Score: 779
Period size: 172 Copynumber: 3.0 Consensus size: 172
2392284 ACCTTTATTA
* *
2392294 ACCCTTAAAATTGAGTAGGTGAGCTACTTTAACGGGGCCAAGTTAAGTTGCCTTGAATACTTGAC
1 ACCCTTAAAATTGAGTAGGTGAGCTACTTTAATGGGGCCAAGTTAAGTTGCCTTGAGTACTTGAC
* * *
2392359 TTTGGAGATTTTTTGGGAGCATTGTCATAGTTTGGATCCTTTTATTGACCCTAAAGGAAAAGTTG
66 TTTGG-CATTTTTTGGGAGCATTGTCATAGTTTGGATCCTTTTACTGCCCCTAAAGGAAAAGTTG
* * * *
2392424 AATCACTGAAAAAAAAAAGGCCTACCTTATAGCAAGGTAGAAG
130 AATCAGTGAAAAAAAGAAGGCCTACCCTATAGCAAGGTAGAGG
2392467 ACCCTTAAAATTGAGTAGGT-AGCTACTTTAATGGGGCCAAGTTAAGTTGCCTTGAGTACTTGAC
1 ACCCTTAAAATTGAGTAGGTGAGCTACTTTAATGGGGCCAAGTTAAGTTGCCTTGAGTACTTGAC
* * *
2392531 TTTAGCATTTTTTGGGAGCATTGTCATAGTTTGGATCCTTTTACTACCCCTAAAGGAAAAATTGA
66 TTTGGCATTTTTTGGGAGCATTGTCATAGTTTGGATCCTTTTACTGCCCCTAAAGGAAAAGTTGA
2392596 ATCAGTGGAAAAAAAGAAGGCCTACCCTATAGCAAGGTAGAGG
131 ATCAGT-GAAAAAAAGAAGGCCTACCCTATAGCAAGGTAGAGG
* * * * * * *
2392639 ACCCTTGAAATTAAATAGGTGGGCTACTTTAATAGGGCTAAGTTAAGTTTCCTTGAGTACTTGAC
1 ACCCTTAAAATTGAGTAGGTGAGCTACTTTAATGGGGCCAAGTTAAGTTGCCTTGAGTACTTGAC
* * * *
2392704 TTTGGCA-TTTTCGAGAGCATTGTAATAGTTTGGTTCCTTTTACTGCCCCTAAAGGAAAAGTTGA
66 TTTGGCATTTTTTGGGAGCATTGTCATAGTTTGGATCCTTTTACTGCCCCTAAAGGAAAAGTTGA
*
2392768 ATCAGTGTAAAAAAAGAAGGCCTGCCCTATAGCAAGGTAGAGG
131 ATCAGTG-AAAAAAAGAAGGCCTACCCTATAGCAAGGTAGAGG
2392811 A
1 A
2392812 AATATGTATG
Statistics
Matches: 315, Mismatches: 27, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
171 61 0.19
172 188 0.60
173 66 0.21
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (172 bp):
ACCCTTAAAATTGAGTAGGTGAGCTACTTTAATGGGGCCAAGTTAAGTTGCCTTGAGTACTTGAC
TTTGGCATTTTTTGGGAGCATTGTCATAGTTTGGATCCTTTTACTGCCCCTAAAGGAAAAGTTGA
ATCAGTGAAAAAAAGAAGGCCTACCCTATAGCAAGGTAGAGG
Found at i:2398170 original size:11 final size:11
Alignment explanation
Indices: 2398150--2398180 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
2398140 GAAAGTAGAT
*
2398150 AAAATGAATAA
1 AAAATAAATAA
2398161 AAAATAAATAA
1 AAAATAAATAA
2398172 AAAATAAAT
1 AAAATAAAT
2398181 CACCACACAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.19
Consensus pattern (11 bp):
AAAATAAATAA
Found at i:2398671 original size:24 final size:24
Alignment explanation
Indices: 2398635--2398693 Score: 61
Period size: 23 Copynumber: 2.5 Consensus size: 24
2398625 TGAAATAAAC
2398635 TTTTTTCATTTTA-TTTTTTAACTTTT
1 TTTTTTCA-TTTAGTTTTTT--CTTTT
2398661 TTTTTTC-TTTAGTTTTTTCTTTT
1 TTTTTTCATTTAGTTTTTTCTTTT
*
2398684 TTCTTT-ATTT
1 TTTTTTCATTT
2398694 CATGTCAAGC
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
23 13 0.43
24 4 0.13
25 6 0.20
26 7 0.23
ACGTcount: A:0.10, C:0.08, G:0.02, T:0.80
Consensus pattern (24 bp):
TTTTTTCATTTAGTTTTTTCTTTT
Found at i:2403969 original size:33 final size:33
Alignment explanation
Indices: 2403932--2404013 Score: 103
Period size: 33 Copynumber: 2.5 Consensus size: 33
2403922 GCCATTTGAG
* **
2403932 ACAATGTATTGATACAAT-TCTTCATGTATCGAT
1 ACAATGTATCGATACAATGT-GACATGTATCGAT
*
2403965 ACAATGTATCAATACAATGTGACATGTATCGAT
1 ACAATGTATCGATACAATGTGACATGTATCGAT
*
2403998 ACAATATATCGATACA
1 ACAATGTATCGATACA
2404014 TTGGTAGGGT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
33 41 0.98
34 1 0.02
ACGTcount: A:0.39, C:0.16, G:0.12, T:0.33
Consensus pattern (33 bp):
ACAATGTATCGATACAATGTGACATGTATCGAT
Found at i:2403973 original size:13 final size:13
Alignment explanation
Indices: 2403955--2404013 Score: 58
Period size: 13 Copynumber: 5.0 Consensus size: 13
2403945 ACAATTCTTC
2403955 ATGTATCGATACA
1 ATGTATCGATACA
*
2403968 ATGTATCAATACA
1 ATGTATCGATACA
2403981 ATG--T-G--AC-
1 ATGTATCGATACA
2403988 ATGTATCGATACA
1 ATGTATCGATACA
*
2404001 ATATATCGATACA
1 ATGTATCGATACA
2404014 TTGGTAGGGT
Statistics
Matches: 37, Mismatches: 3, Indels: 12
0.71 0.06 0.23
Matches are distributed among these distances:
7 3 0.08
8 2 0.05
9 1 0.03
10 1 0.03
11 1 0.03
12 2 0.05
13 27 0.73
ACGTcount: A:0.41, C:0.15, G:0.14, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2406570 original size:13 final size:13
Alignment explanation
Indices: 2406547--2406612 Score: 87
Period size: 13 Copynumber: 5.1 Consensus size: 13
2406537 ATAGTAACCC
*
2406547 ATGTATTGATACA
1 ATGTATCGATACA
* *
2406560 TTGTATCGATATA
1 ATGTATCGATACA
2406573 ATGTATCGATACA
1 ATGTATCGATACA
* *
2406586 TTGTATCGATATA
1 ATGTATCGATACA
2406599 ATGTATCGATACA
1 ATGTATCGATACA
2406612 A
1 A
2406613 AGAACATTGT
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 44 1.00
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.38
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2406583 original size:26 final size:26
Alignment explanation
Indices: 2406547--2406611 Score: 121
Period size: 26 Copynumber: 2.5 Consensus size: 26
2406537 ATAGTAACCC
*
2406547 ATGTATTGATACATTGTATCGATATA
1 ATGTATCGATACATTGTATCGATATA
2406573 ATGTATCGATACATTGTATCGATATA
1 ATGTATCGATACATTGTATCGATATA
2406599 ATGTATCGATACA
1 ATGTATCGATACA
2406612 AAGAACATTG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.38
Consensus pattern (26 bp):
ATGTATCGATACATTGTATCGATATA
Found at i:2411148 original size:15 final size:15
Alignment explanation
Indices: 2411130--2411164 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
2411120 TGAGTCAACT
2411130 TCATCATTATCATCA
1 TCATCATTATCATCA
*
2411145 TCATCATTATCTTCA
1 TCATCATTATCATCA
2411160 TCATC
1 TCATC
2411165 TTTGATGGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.29, C:0.29, G:0.00, T:0.43
Consensus pattern (15 bp):
TCATCATTATCATCA
Found at i:2412842 original size:20 final size:20
Alignment explanation
Indices: 2412817--2412871 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
2412807 TTGCGAGTTT
**
2412817 CATGTATCAATACAATTGTG
1 CATGTATCAATACAATTGAA
**
2412837 CATGTATTGATACAA-TGAA
1 CATGTATCAATACAATTGAA
2412856 CATGTATCAATACAAT
1 CATGTATCAATACAAT
2412872 GTATCGATAG
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.40, C:0.15, G:0.13, T:0.33
Consensus pattern (20 bp):
CATGTATCAATACAATTGAA
Found at i:2412894 original size:19 final size:19
Alignment explanation
Indices: 2412870--2412999 Score: 143
Period size: 20 Copynumber: 6.7 Consensus size: 19
2412860 TATCAATACA
* *
2412870 ATGTATCGATAGAAAGCTT
1 ATGTATCGATACAAAGCAT
* *
2412889 ATGTATCGATACATACGGAT
1 ATGTATCGATACA-AAGCAT
2412909 ATGTATCGATACAAAGCAT
1 ATGTATCGATACAAAGCAT
* * *
2412928 ATGTATCGATACCTACGGAT
1 ATGTATCGATA-CAAAGCAT
2412948 ATGTATCGATACAAAGCAT
1 ATGTATCGATACAAAGCAT
* *
2412967 ATGTATCGATACATACGGAT
1 ATGTATCGATACA-AAGCAT
*
2412987 ATGTATCAATACA
1 ATGTATCGATACA
2413000 TACAAGGGTT
Statistics
Matches: 93, Mismatches: 15, Indels: 5
0.82 0.13 0.04
Matches are distributed among these distances:
19 45 0.48
20 48 0.52
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (19 bp):
ATGTATCGATACAAAGCAT
Found at i:2412913 original size:20 final size:20
Alignment explanation
Indices: 2412888--2413002 Score: 162
Period size: 20 Copynumber: 5.8 Consensus size: 20
2412878 ATAGAAAGCT
2412888 TATGTATCGATACATACGGA
1 TATGTATCGATACATACGGA
* *
2412908 TATGTATCGATACA-AAGCA
1 TATGTATCGATACATACGGA
*
2412927 TATGTATCGATACCTACGGA
1 TATGTATCGATACATACGGA
* *
2412947 TATGTATCGATACA-AAGCA
1 TATGTATCGATACATACGGA
2412966 TATGTATCGATACATACGGA
1 TATGTATCGATACATACGGA
*
2412986 TATGTATCAATACATAC
1 TATGTATCGATACATAC
2413003 AAGGGTTTTG
Statistics
Matches: 82, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
19 33 0.40
20 49 0.60
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.30
Consensus pattern (20 bp):
TATGTATCGATACATACGGA
Found at i:2412925 original size:39 final size:39
Alignment explanation
Indices: 2412870--2412999 Score: 224
Period size: 39 Copynumber: 3.3 Consensus size: 39
2412860 TATCAATACA
* *
2412870 ATGTATCGATAGAAAGCTTATGTATCGATACATACGGAT
1 ATGTATCGATACAAAGCATATGTATCGATACATACGGAT
*
2412909 ATGTATCGATACAAAGCATATGTATCGATACCTACGGAT
1 ATGTATCGATACAAAGCATATGTATCGATACATACGGAT
2412948 ATGTATCGATACAAAGCATATGTATCGATACATACGGAT
1 ATGTATCGATACAAAGCATATGTATCGATACATACGGAT
*
2412987 ATGTATCAATACA
1 ATGTATCGATACA
2413000 TACAAGGGTT
Statistics
Matches: 86, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 86 1.00
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (39 bp):
ATGTATCGATACAAAGCATATGTATCGATACATACGGAT
Found at i:2414944 original size:31 final size:31
Alignment explanation
Indices: 2414903--2414961 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
2414893 TTTTTTGGAC
*
2414903 AAAAACATTAAATTACCCATAATGTTTTTTT
1 AAAAAAATTAAATTACCCATAATGTTTTTTT
**
2414934 AAAAAAATTAAATTGGCCATAATGTTTT
1 AAAAAAATTAAATTACCCATAATGTTTT
2414962 GGATGGAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.44, C:0.10, G:0.07, T:0.39
Consensus pattern (31 bp):
AAAAAAATTAAATTACCCATAATGTTTTTTT
Found at i:2421178 original size:12 final size:13
Alignment explanation
Indices: 2421161--2421189 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
2421151 ACATCTTAGC
2421161 CAAAAACA-TCAA
1 CAAAAACACTCAA
2421173 CAAAAACACTCAA
1 CAAAAACACTCAA
2421186 CAAA
1 CAAA
2421190 GAATTCATTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.50
13 8 0.50
ACGTcount: A:0.66, C:0.28, G:0.00, T:0.07
Consensus pattern (13 bp):
CAAAAACACTCAA
Done.